From 8eb2a71b290b3581b747e1c3723fb1db2e4e5245 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 18 Jun 2024 23:16:00 -0400 Subject: [PATCH 1/6] Updated Changelog. --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5227e61b..358c4157 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ The format is based on [Keep a Changelog] and this project adheres to [Semantic ## [Unreleased] +## [1.2.0] - 2024-06-18 +- PR #138: Added normalization methods so that Phyx objects can be normalized. +- PR #139: upgraded NPM packages and minor test fixes + ## [1.1.1] - 2023-08-01 - PR #133: Add guards to some usages of `phyloref.internalSpecifiers/phyloref.externalSpecifiers`. - PR #136: Improved GitHub test action, including changing Node versions. @@ -64,7 +68,8 @@ release of this package was based on [commit 14d2c3d5d1] in that repository. - Replaced references to the [phylotree] library with the [newick-js] library. - Made other changes to the initial code as needed to work as an independent NPM package. - [Unreleased]: https://github.com/phyloref/phyx.js/compare/v1.1.1...master + [Unreleased]: https://github.com/phyloref/phyx.js/compare/v1.2.0...master + [1.2.0]: https://github.com/phyloref/phyx.js/compare/v1.1.1...v1.2.0 [1.1.1]: https://github.com/phyloref/phyx.js/compare/v1.1.0...v1.1.1 [1.1.0]: https://github.com/phyloref/phyx.js/compare/v1.0.1...v1.1.0 [1.0.1]: https://github.com/phyloref/phyx.js/compare/v1.0.0...v1.0.1 From 2a36d47de8319239962a74b1180e7a2dcb873e3f Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 18 Jun 2024 23:16:38 -0400 Subject: [PATCH 2/6] Updated version to v1.2.0-alpha1 for test release. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 46963942..8f789aaf 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@phyloref/phyx", - "version": "1.1.1", + "version": "1.2.0-alpha1", "description": "Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files", "keywords": [ "phylogenetics", From 62e0168ddfbbfcc17ca7fda3d345dc700fd511d8 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Tue, 18 Jun 2024 23:18:10 -0400 Subject: [PATCH 3/6] Regenerated documentation. --- .../matchers/TaxonomicUnitMatcher.js.json | 36 +- .../source/wrappers/CitationWrapper.js.json | 28706 +++---- .../source/wrappers/PhylogenyWrapper.js.json | 42297 +++++----- .../source/wrappers/PhylorefWrapper.js.json | 64461 ++++++++-------- docs/ast/source/wrappers/PhyxWrapper.js.json | 36725 +++++---- .../source/wrappers/SpecimenWrapper.js.json | 35384 +++++---- .../wrappers/TaxonConceptWrapper.js.json | 31747 ++++---- .../source/wrappers/TaxonNameWrapper.js.json | 44619 ++++++----- .../wrappers/TaxonomicUnitWrapper.js.json | 30743 ++++---- docs/badge.svg | 4 +- .../CitationWrapper.js~CitationWrapper.html | 108 +- .../PhylogenyWrapper.js~PhylogenyWrapper.html | 131 +- .../PhylorefWrapper.js~PhylorefWrapper.html | 143 +- .../wrappers/PhyxWrapper.js~PhyxWrapper.html | 123 +- .../SpecimenWrapper.js~SpecimenWrapper.html | 122 +- ...ConceptWrapper.js~TaxonConceptWrapper.html | 122 +- .../TaxonNameWrapper.js~TaxonNameWrapper.html | 148 +- ...icUnitWrapper.js~TaxonomicUnitWrapper.html | 120 +- docs/coverage.json | 98 +- .../file/src/wrappers/CitationWrapper.js.html | 18 + .../src/wrappers/PhylogenyWrapper.js.html | 21 +- .../file/src/wrappers/PhylorefWrapper.js.html | 16 + docs/file/src/wrappers/PhyxWrapper.js.html | 26 + .../file/src/wrappers/SpecimenWrapper.js.html | 19 + .../src/wrappers/TaxonConceptWrapper.js.html | 25 +- .../src/wrappers/TaxonNameWrapper.js.html | 19 + .../src/wrappers/TaxonomicUnitWrapper.js.html | 19 + docs/index.json | 2446 +- docs/manual/CHANGELOG.html | 9 +- docs/manual/Introduction.html | 3 +- docs/manual/index.html | 8 +- docs/script/search_index.js | 122 +- docs/source.html | 72 +- docs/test-file/test/jphyloref.js.html | 2 +- docs/test-file/test/scripts/phyx2owl.js.html | 2 +- docs/test-file/test/scripts/resolve.js.html | 6 +- docs/test.html | 60 + 37 files changed, 174533 insertions(+), 144197 deletions(-) diff --git a/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json b/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json index 151d6205..6f3d7491 100644 --- a/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json +++ b/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json @@ -70,9 +70,9 @@ "line": 1, "column": 25 }, - 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"value": "LKT4H13WGRGJJ", + "value": "LXL9JK4849P6M", "start": 12, "end": 25, "loc": { @@ -13785,7 +13785,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H13WGRGJJ", + "value": "LXL9JK4849P6M", "start": 101, "end": 114, "loc": { @@ -13918,7 +13918,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H13WOM817", + "value": "LXL9JK48UIGO0", "start": 128, "end": 141, "loc": { @@ -14154,7 +14154,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H13WOM817", + "value": "LXL9JK48UIGO0", "start": 215, "end": 228, "loc": { @@ -14287,7 +14287,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H13WCAK3M", + "value": "LXL9JK48T1OMI", "start": 242, "end": 255, "loc": { @@ -14523,7 +14523,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H13WCAK3M", + "value": "LXL9JK48T1OMI", "start": 321, "end": 334, "loc": { diff --git a/docs/ast/source/wrappers/CitationWrapper.js.json b/docs/ast/source/wrappers/CitationWrapper.js.json index 7ed31ca4..249461ff 100644 --- a/docs/ast/source/wrappers/CitationWrapper.js.json +++ b/docs/ast/source/wrappers/CitationWrapper.js.json @@ -1,28 +1,28 @@ { "type": "File", "start": 0, - 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We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n ", + "start": 346, + "end": 657, + "loc": { + "start": { + "line": 17, + "column": 2 + }, + "end": { + "line": 23, + "column": 5 + } + } + } + ] + }, + { + "type": "ClassMethod", + "start": 660, + "end": 994, + "loc": { + "start": { + "line": 24, + "column": 2 + }, + "end": { + "line": 33, + "column": 3 + } + }, + "static": true, + "computed": false, + "key": { + "type": "Identifier", + "start": 667, + "end": 676, + "loc": { + "start": { + "line": 24, + "column": 9 + }, + "end": { + "line": 24, + "column": 18 + }, + "identifierName": "normalize" + }, + "name": "normalize" + }, + "kind": "method", + "id": null, + "generator": false, + "expression": false, + "async": false, + "params": [ + { + "type": "Identifier", + "start": 677, + "end": 685, + "loc": { + "start": { + "line": 24, + "column": 19 + }, + "end": { + "line": 24, + "column": 27 + }, + "identifierName": 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We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n ", "start": 346, - "end": 570, + "end": 657, "loc": { "start": { "line": 17, "column": 2 }, "end": { - "line": 22, + "line": 23, + "column": 5 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentBlock", + "value": "*\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n ", + "start": 998, + "end": 1222, + "loc": { + "start": { + "line": 35, + "column": 2 + }, + "end": { + "line": 40, "column": 5 } } @@ -553,15 +1204,15 @@ }, { "type": "ClassMethod", - "start": 573, - "end": 990, + "start": 1225, + "end": 1642, "loc": { "start": { - "line": 23, + "line": 41, "column": 2 }, "end": { - "line": 36, + "line": 54, "column": 3 } }, @@ -569,15 +1220,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 580, - 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"line": 26, + "line": 44, "column": 19 }, "identifierName": "agent" @@ -940,15 +1591,15 @@ }, { "type": "StringLiteral", - "start": 704, - "end": 715, + "start": 1356, + "end": 1367, "loc": { "start": { - "line": 26, + "line": 44, "column": 21 }, "end": { - "line": 26, + "line": 44, "column": 32 } }, @@ -962,58 +1613,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 718, - "end": 910, + "start": 1370, + "end": 1562, "loc": { "start": { - "line": 26, + "line": 44, "column": 35 }, "end": { - "line": 32, + "line": 50, "column": 7 } }, "body": [ { "type": "IfStatement", - "start": 728, - "end": 846, + "start": 1380, + "end": 1498, "loc": { "start": { - "line": 27, + "line": 45, "column": 8 }, "end": { - "line": 29, + "line": 47, "column": 9 } }, "test": { "type": "CallExpression", - "start": 732, - "end": 756, + "start": 1384, + "end": 1408, "loc": { "start": { - "line": 27, + "line": 45, "column": 12 }, "end": { - "line": 27, + "line": 45, "column": 36 } }, "callee": { "type": "Identifier", - "start": 732, - "end": 735, + "start": 1384, + "end": 1387, "loc": { "start": { - "line": 27, + "line": 45, "column": 12 }, "end": { - "line": 27, + "line": 45, "column": 15 }, "identifierName": "has" @@ -1023,15 +1674,15 @@ "arguments": [ { "type": "Identifier", - "start": 736, - "end": 741, + "start": 1388, + "end": 1393, "loc": { "start": { - "line": 27, + "line": 45, "column": 16 }, "end": { - "line": 27, + "line": 45, "column": 21 }, "identifierName": "agent" @@ -1040,15 +1691,15 @@ }, { "type": "StringLiteral", - "start": 743, - "end": 755, + "start": 1395, + "end": 1407, "loc": { "start": { - "line": 27, + "line": 45, "column": 23 }, "end": { - "line": 27, + "line": 45, "column": 35 } }, @@ -1062,73 +1713,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 758, - "end": 846, + "start": 1410, + "end": 1498, "loc": { "start": { - "line": 27, + "line": 45, "column": 38 }, "end": { - "line": 29, + "line": 47, "column": 9 } }, "body": [ { "type": "ReturnStatement", - "start": 770, - "end": 836, + "start": 1422, + "end": 1488, "loc": { "start": { - "line": 28, + "line": 46, "column": 10 }, "end": { - "line": 28, + "line": 46, "column": 76 } }, "argument": { "type": "TemplateLiteral", - "start": 777, - "end": 835, + "start": 1429, + "end": 1487, "loc": { "start": { - "line": 28, + "line": 46, "column": 17 }, "end": { - "line": 28, + "line": 46, "column": 75 } }, "expressions": [ { "type": "MemberExpression", - "start": 780, - "end": 795, + "start": 1432, + "end": 1447, "loc": { "start": { - "line": 28, + "line": 46, "column": 20 }, "end": { - "line": 28, + "line": 46, "column": 35 } }, "object": { "type": "Identifier", - "start": 780, - "end": 785, + "start": 1432, + "end": 1437, "loc": { "start": { - "line": 28, + "line": 46, "column": 20 }, "end": { - "line": 28, + "line": 46, "column": 25 }, "identifierName": "agent" @@ -1137,15 +1788,15 @@ }, "property": { "type": "Identifier", - "start": 786, - "end": 795, + "start": 1438, + "end": 1447, "loc": { "start": { - "line": 28, + "line": 46, "column": 26 }, "end": { - "line": 28, + "line": 46, "column": 35 }, "identifierName": "firstname" @@ -1156,29 +1807,29 @@ }, { "type": "MemberExpression", - "start": 799, - "end": 815, + "start": 1451, + "end": 1467, "loc": { "start": { - "line": 28, + "line": 46, "column": 39 }, "end": { - "line": 28, + "line": 46, "column": 55 } }, "object": { "type": "Identifier", - "start": 799, - "end": 804, + "start": 1451, + "end": 1456, "loc": { "start": { - "line": 28, + "line": 46, "column": 39 }, "end": { - "line": 28, + "line": 46, "column": 44 }, "identifierName": "agent" @@ -1187,15 +1838,15 @@ }, "property": { "type": "Identifier", - "start": 805, - "end": 815, + "start": 1457, + "end": 1467, "loc": { "start": { - "line": 28, + "line": 46, "column": 45 }, "end": { - "line": 28, + "line": 46, "column": 55 }, "identifierName": "middlename" @@ -1206,29 +1857,29 @@ }, { "type": "MemberExpression", - "start": 819, - "end": 833, + "start": 1471, + "end": 1485, "loc": { "start": { - "line": 28, + "line": 46, "column": 59 }, "end": { - "line": 28, + "line": 46, "column": 73 } }, "object": { "type": "Identifier", - "start": 819, - "end": 824, + "start": 1471, + "end": 1476, "loc": { "start": { - "line": 28, + "line": 46, "column": 59 }, "end": { - "line": 28, + "line": 46, "column": 64 }, "identifierName": "agent" @@ -1237,15 +1888,15 @@ }, "property": { "type": "Identifier", - "start": 825, - "end": 833, + "start": 1477, + "end": 1485, "loc": { "start": { - "line": 28, + "line": 46, "column": 65 }, "end": { - "line": 28, + "line": 46, "column": 73 }, "identifierName": "lastname" @@ -1258,15 +1909,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 778, - "end": 778, + "start": 1430, + "end": 1430, "loc": { "start": { - "line": 28, + "line": 46, "column": 18 }, "end": { - "line": 28, + "line": 46, "column": 18 } }, @@ -1278,15 +1929,15 @@ }, { "type": "TemplateElement", - "start": 796, - "end": 797, + "start": 1448, + "end": 1449, "loc": { "start": { - "line": 28, + "line": 46, "column": 36 }, "end": { - "line": 28, + "line": 46, "column": 37 } }, @@ -1298,15 +1949,15 @@ }, { "type": "TemplateElement", - "start": 816, - "end": 817, + "start": 1468, + "end": 1469, "loc": { "start": { - "line": 28, + "line": 46, "column": 56 }, "end": { - "line": 28, + "line": 46, "column": 57 } }, @@ -1318,15 +1969,15 @@ }, { "type": "TemplateElement", - "start": 834, - "end": 834, + "start": 1486, + "end": 1486, "loc": { "start": { - "line": 28, + "line": 46, "column": 74 }, "end": { - "line": 28, + "line": 46, "column": 74 } }, @@ -1346,58 +1997,58 @@ }, { "type": "ReturnStatement", - "start": 856, - "end": 902, + "start": 1508, + "end": 1554, "loc": { "start": { - "line": 31, + "line": 49, "column": 8 }, "end": { - "line": 31, + "line": 49, "column": 54 } }, "argument": { "type": "TemplateLiteral", - "start": 863, - "end": 901, + "start": 1515, + "end": 1553, "loc": { "start": { - "line": 31, + "line": 49, "column": 15 }, "end": { - "line": 31, + "line": 49, "column": 53 } }, "expressions": [ { "type": "MemberExpression", - "start": 866, - "end": 881, + "start": 1518, + "end": 1533, "loc": { "start": { - "line": 31, + "line": 49, "column": 18 }, "end": { - "line": 31, + "line": 49, "column": 33 } }, "object": { "type": "Identifier", - "start": 866, - "end": 871, + "start": 1518, + "end": 1523, "loc": { "start": { - "line": 31, + "line": 49, "column": 18 }, "end": { - "line": 31, + "line": 49, "column": 23 }, "identifierName": "agent" @@ -1406,15 +2057,15 @@ }, "property": { "type": "Identifier", - "start": 872, - "end": 881, + "start": 1524, + "end": 1533, "loc": { "start": { - "line": 31, + "line": 49, "column": 24 }, "end": { - "line": 31, + "line": 49, "column": 33 }, "identifierName": "firstname" @@ -1425,29 +2076,29 @@ }, { "type": "MemberExpression", - "start": 885, - "end": 899, + "start": 1537, + "end": 1551, "loc": { "start": { - "line": 31, + "line": 49, "column": 37 }, "end": { - "line": 31, + "line": 49, "column": 51 } }, "object": { "type": "Identifier", - "start": 885, - "end": 890, + "start": 1537, + "end": 1542, "loc": { "start": { - "line": 31, + "line": 49, "column": 37 }, "end": { - "line": 31, + "line": 49, "column": 42 }, "identifierName": "agent" @@ -1456,15 +2107,15 @@ }, "property": { "type": "Identifier", - "start": 891, - "end": 899, + "start": 1543, + "end": 1551, "loc": { "start": { - "line": 31, + "line": 49, "column": 43 }, "end": { - "line": 31, + "line": 49, "column": 51 }, "identifierName": "lastname" @@ -1477,15 +2128,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 864, - "end": 864, + "start": 1516, + "end": 1516, "loc": { "start": { - "line": 31, + "line": 49, "column": 16 }, "end": { - "line": 31, + "line": 49, "column": 16 } }, @@ -1497,15 +2148,15 @@ }, { "type": "TemplateElement", - "start": 882, - "end": 883, + "start": 1534, + "end": 1535, "loc": { "start": { - "line": 31, + "line": 49, "column": 34 }, "end": { - "line": 31, + "line": 49, "column": 35 } }, @@ -1517,15 +2168,15 @@ }, { "type": "TemplateElement", - "start": 900, - "end": 900, + "start": 1552, + "end": 1552, "loc": { "start": { - "line": 31, + "line": 49, "column": 52 }, "end": { - "line": 31, + "line": 49, "column": 52 } }, @@ -1545,58 +2196,58 @@ }, { "type": "ReturnStatement", - "start": 917, - "end": 944, + "start": 1569, + "end": 1596, "loc": { "start": { - "line": 33, + "line": 51, "column": 6 }, "end": { - "line": 33, + "line": 51, "column": 33 } }, "argument": { "type": "TemplateLiteral", - "start": 924, - "end": 943, + "start": 1576, + "end": 1595, "loc": { "start": { - "line": 33, + "line": 51, "column": 13 }, "end": { - "line": 33, + "line": 51, "column": 32 } }, "expressions": [ { "type": "MemberExpression", - "start": 927, - "end": 941, + "start": 1579, + "end": 1593, "loc": { "start": { - "line": 33, + "line": 51, "column": 16 }, "end": { - "line": 33, + "line": 51, "column": 30 } }, "object": { "type": "Identifier", - "start": 927, - "end": 932, + "start": 1579, + "end": 1584, "loc": { "start": { - "line": 33, + "line": 51, "column": 16 }, "end": { - "line": 33, + "line": 51, "column": 21 }, "identifierName": "agent" @@ -1605,15 +2256,15 @@ }, "property": { "type": "Identifier", - "start": 933, - "end": 941, + "start": 1585, + "end": 1593, "loc": { "start": { - "line": 33, + "line": 51, "column": 22 }, "end": { - "line": 33, + "line": 51, "column": 30 }, "identifierName": "lastname" @@ -1626,15 +2277,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 925, - "end": 925, + "start": 1577, + "end": 1577, "loc": { "start": { - "line": 33, + "line": 51, "column": 14 }, "end": { - "line": 33, + "line": 51, "column": 14 } }, @@ -1646,15 +2297,15 @@ }, { "type": "TemplateElement", - "start": 942, - "end": 942, + "start": 1594, + "end": 1594, "loc": { "start": { - "line": 33, + "line": 51, "column": 31 }, "end": { - "line": 33, + "line": 51, "column": 31 } }, @@ -1674,29 +2325,29 @@ }, { "type": "ReturnStatement", - "start": 955, - "end": 986, + "start": 1607, + "end": 1638, "loc": { "start": { - "line": 35, + "line": 53, "column": 4 }, "end": { - "line": 35, + "line": 53, "column": 35 } }, "argument": { "type": "StringLiteral", - "start": 962, - "end": 985, + "start": 1614, + "end": 1637, "loc": { "start": { - "line": 35, + "line": 53, "column": 11 }, "end": { - "line": 35, + "line": 53, "column": 34 } }, @@ -1715,15 +2366,15 @@ { "type": "CommentBlock", "value": "*\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n ", - "start": 346, - "end": 570, + "start": 998, + "end": 1222, "loc": { "start": { - "line": 17, + "line": 35, "column": 2 }, "end": { - "line": 22, + "line": 40, "column": 5 } } @@ -1733,15 +2384,15 @@ { "type": "CommentBlock", "value": "* Returns a single string with the entire bibliographic citation. ", - "start": 994, - "end": 1064, + "start": 1646, + "end": 1716, "loc": { "start": { - "line": 38, + "line": 56, "column": 2 }, "end": { - "line": 38, + "line": 56, "column": 72 } } @@ -1750,15 +2401,15 @@ }, { "type": "ClassMethod", - "start": 1067, - "end": 4315, + "start": 1719, + "end": 4967, "loc": { "start": { - "line": 39, + "line": 57, "column": 2 }, "end": { - "line": 108, + "line": 126, "column": 3 } }, @@ -1766,15 +2417,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 1067, - "end": 1075, + "start": 1719, + "end": 1727, "loc": { "start": { - "line": 39, + "line": 57, "column": 2 }, "end": { - "line": 39, + "line": 57, "column": 10 }, "identifierName": "toString" @@ -1790,58 +2441,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 1078, - "end": 4315, + "start": 1730, + "end": 4967, "loc": { "start": { - "line": 39, + "line": 57, "column": 13 }, "end": { - "line": 108, + "line": 126, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 1084, - "end": 1147, + "start": 1736, + "end": 1799, "loc": { "start": { - "line": 40, + "line": 58, "column": 4 }, "end": { - "line": 40, + "line": 58, "column": 67 } }, "test": { "type": "LogicalExpression", - "start": 1088, - "end": 1128, + "start": 1740, + "end": 1780, "loc": { "start": { - "line": 40, + "line": 58, "column": 8 }, "end": { - "line": 40, + "line": 58, "column": 48 } }, "left": { "type": "UnaryExpression", - "start": 1088, - "end": 1102, + "start": 1740, + "end": 1754, "loc": { "start": { - "line": 40, + "line": 58, "column": 8 }, "end": { - "line": 40, + "line": 58, "column": 22 } }, @@ -1849,44 +2500,44 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 1089, - "end": 1102, + "start": 1741, + "end": 1754, "loc": { "start": { - "line": 40, + "line": 58, "column": 9 }, "end": { - "line": 40, + "line": 58, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 1089, - "end": 1093, + "start": 1741, + "end": 1745, "loc": { "start": { - "line": 40, + "line": 58, "column": 9 }, "end": { - "line": 40, + "line": 58, "column": 13 } } }, "property": { "type": "Identifier", - "start": 1094, - "end": 1102, + "start": 1746, + "end": 1754, "loc": { "start": { - "line": 40, + "line": 58, "column": 14 }, "end": { - "line": 40, + "line": 58, "column": 22 }, "identifierName": "citation" @@ -1902,29 +2553,29 @@ "operator": "||", "right": { "type": "CallExpression", - "start": 1106, - "end": 1128, + "start": 1758, + "end": 1780, "loc": { "start": { - "line": 40, + "line": 58, "column": 26 }, "end": { - "line": 40, + "line": 58, "column": 48 } }, "callee": { "type": "Identifier", - "start": 1106, - "end": 1113, + "start": 1758, + "end": 1765, "loc": { "start": { - "line": 40, + "line": 58, "column": 26 }, "end": { - "line": 40, + "line": 58, "column": 33 }, "identifierName": "isEmpty" @@ -1934,44 +2585,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1114, - "end": 1127, + "start": 1766, + "end": 1779, "loc": { "start": { - "line": 40, + "line": 58, "column": 34 }, "end": { - "line": 40, + "line": 58, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 1114, - "end": 1118, + "start": 1766, + "end": 1770, "loc": { "start": { - "line": 40, + "line": 58, "column": 34 }, "end": { - "line": 40, + "line": 58, "column": 38 } } }, "property": { "type": "Identifier", - "start": 1119, - "end": 1127, + "start": 1771, + "end": 1779, "loc": { "start": { - "line": 40, + "line": 58, "column": 39 }, "end": { - "line": 40, + "line": 58, "column": 47 }, "identifierName": "citation" @@ -1985,29 +2636,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1130, - "end": 1147, + "start": 1782, + "end": 1799, "loc": { "start": { - "line": 40, + "line": 58, "column": 50 }, "end": { - "line": 40, + "line": 58, "column": 67 } }, "argument": { "type": "Identifier", - "start": 1137, - "end": 1146, + "start": 1789, + "end": 1798, "loc": { "start": { - "line": 40, + "line": 58, "column": 57 }, "end": { - "line": 40, + "line": 58, "column": 66 }, "identifierName": "undefined" @@ -2021,15 +2672,15 @@ { "type": "CommentLine", "value": " If we already have a bibliographic citation, we can just return that.", - "start": 1153, - "end": 1225, + "start": 1805, + "end": 1877, "loc": { "start": { - "line": 42, + "line": 60, "column": 4 }, "end": { - "line": 42, + "line": 60, "column": 76 } } @@ -2038,43 +2689,43 @@ }, { "type": "IfStatement", - "start": 1230, - "end": 1322, + "start": 1882, + "end": 1974, "loc": { "start": { - "line": 43, + "line": 61, "column": 4 }, "end": { - "line": 43, + "line": 61, "column": 96 } }, "test": { "type": "CallExpression", - "start": 1234, - "end": 1277, + "start": 1886, + "end": 1929, "loc": { "start": { - "line": 43, + "line": 61, "column": 8 }, "end": { - "line": 43, + "line": 61, "column": 51 } }, "callee": { "type": "Identifier", - "start": 1234, - "end": 1237, + "start": 1886, + "end": 1889, "loc": { "start": { - "line": 43, + "line": 61, "column": 8 }, "end": { - "line": 43, + "line": 61, "column": 11 }, "identifierName": "has" @@ -2085,44 +2736,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1238, - "end": 1251, + "start": 1890, + "end": 1903, "loc": { "start": { - "line": 43, + "line": 61, "column": 12 }, "end": { - "line": 43, + "line": 61, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1238, - "end": 1242, + "start": 1890, + "end": 1894, "loc": { "start": { - "line": 43, + "line": 61, "column": 12 }, "end": { - "line": 43, + "line": 61, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1243, - "end": 1251, + "start": 1895, + "end": 1903, "loc": { "start": { - "line": 43, + "line": 61, "column": 17 }, "end": { - "line": 43, + "line": 61, "column": 25 }, "identifierName": "citation" @@ -2133,15 +2784,15 @@ }, { "type": "StringLiteral", - "start": 1253, - "end": 1276, + "start": 1905, + "end": 1928, "loc": { "start": { - "line": 43, + "line": 61, "column": 27 }, "end": { - "line": 43, + "line": 61, "column": 50 } }, @@ -2156,72 +2807,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1279, - "end": 1322, + "start": 1931, + "end": 1974, "loc": { "start": { - "line": 43, + "line": 61, "column": 53 }, "end": { - "line": 43, + "line": 61, "column": 96 } }, "argument": { "type": "MemberExpression", - "start": 1286, - "end": 1321, + "start": 1938, + "end": 1973, "loc": { "start": { - "line": 43, + "line": 61, "column": 60 }, "end": { - "line": 43, + "line": 61, "column": 95 } }, "object": { "type": "MemberExpression", - "start": 1286, - "end": 1299, + "start": 1938, + "end": 1951, "loc": { "start": { - "line": 43, + "line": 61, "column": 60 }, "end": { - "line": 43, + "line": 61, "column": 73 } }, "object": { "type": "ThisExpression", - "start": 1286, - "end": 1290, + "start": 1938, + "end": 1942, "loc": { "start": { - "line": 43, + "line": 61, "column": 60 }, "end": { - "line": 43, + "line": 61, "column": 64 } } }, "property": { "type": "Identifier", - "start": 1291, - "end": 1299, + "start": 1943, + "end": 1951, "loc": { "start": { - "line": 43, + "line": 61, "column": 65 }, "end": { - "line": 43, + "line": 61, "column": 73 }, "identifierName": "citation" @@ -2232,15 +2883,15 @@ }, "property": { "type": "Identifier", - "start": 1300, - "end": 1321, + "start": 1952, + "end": 1973, "loc": { "start": { - "line": 43, + "line": 61, "column": 74 }, "end": { - "line": 43, + "line": 61, "column": 95 }, "identifierName": "bibliographicCitation" @@ -2255,15 +2906,15 @@ { "type": "CommentLine", "value": " If we already have a bibliographic citation, we can just return that.", - "start": 1153, - "end": 1225, + "start": 1805, + "end": 1877, "loc": { "start": { - "line": 42, + "line": 60, "column": 4 }, "end": { - "line": 42, + "line": 60, "column": 76 } } @@ -2272,44 +2923,44 @@ }, { "type": "VariableDeclaration", - "start": 1328, - "end": 1406, + "start": 1980, + "end": 2058, "loc": { "start": { - "line": 45, + "line": 63, "column": 4 }, "end": { - "line": 45, + "line": 63, "column": 82 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1332, - "end": 1405, + "start": 1984, + "end": 2057, "loc": { "start": { - "line": 45, + "line": 63, "column": 8 }, "end": { - "line": 45, + "line": 63, "column": 81 } }, "id": { "type": "Identifier", - "start": 1332, - "end": 1339, + "start": 1984, + "end": 1991, "loc": { "start": { - "line": 45, + "line": 63, "column": 8 }, "end": { - "line": 45, + "line": 63, "column": 15 }, "identifierName": "authors" @@ -2318,100 +2969,100 @@ }, "init": { "type": "CallExpression", - "start": 1342, - "end": 1405, + "start": 1994, + "end": 2057, "loc": { "start": { - "line": 45, + "line": 63, "column": 18 }, "end": { - "line": 45, + "line": 63, "column": 81 } }, "callee": { "type": "MemberExpression", - "start": 1342, - "end": 1375, + "start": 1994, + "end": 2027, "loc": { "start": { - "line": 45, + "line": 63, "column": 18 }, "end": { - "line": 45, + "line": 63, "column": 51 } }, "object": { "type": "LogicalExpression", - "start": 1343, - "end": 1370, + "start": 1995, + "end": 2022, "loc": { "start": { - "line": 45, + "line": 63, "column": 19 }, "end": { - "line": 45, + "line": 63, "column": 46 } }, "left": { "type": "MemberExpression", - "start": 1343, - "end": 1364, + "start": 1995, + "end": 2016, "loc": { "start": { - "line": 45, + "line": 63, "column": 19 }, "end": { - "line": 45, + "line": 63, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 1343, - "end": 1356, + "start": 1995, + "end": 2008, "loc": { "start": { - "line": 45, + "line": 63, "column": 19 }, "end": { - "line": 45, + "line": 63, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 1343, - "end": 1347, + "start": 1995, + "end": 1999, "loc": { "start": { - "line": 45, + "line": 63, "column": 19 }, "end": { - "line": 45, + "line": 63, "column": 23 } } }, "property": { "type": "Identifier", - "start": 1348, - "end": 1356, + "start": 2000, + "end": 2008, "loc": { "start": { - "line": 45, + "line": 63, "column": 24 }, "end": { - "line": 45, + "line": 63, "column": 32 }, "identifierName": "citation" @@ -2422,15 +3073,15 @@ }, "property": { "type": "Identifier", - "start": 1357, - "end": 1364, + "start": 2009, + "end": 2016, "loc": { "start": { - "line": 45, + "line": 63, "column": 33 }, "end": { - "line": 45, + "line": 63, "column": 40 }, "identifierName": "authors" @@ -2442,15 +3093,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 1368, - "end": 1370, + "start": 2020, + "end": 2022, "loc": { "start": { - "line": 45, + "line": 63, "column": 44 }, "end": { - "line": 45, + "line": 63, "column": 46 } }, @@ -2458,20 +3109,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 1342 + "parenStart": 1994 } }, "property": { "type": "Identifier", - "start": 1372, - "end": 1375, + "start": 2024, + "end": 2027, "loc": { "start": { - "line": 45, + "line": 63, "column": 48 }, "end": { - "line": 45, + "line": 63, "column": 51 }, "identifierName": "map" @@ -2483,29 +3134,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 1376, - "end": 1404, + "start": 2028, + "end": 2056, "loc": { "start": { - "line": 45, + "line": 63, "column": 52 }, "end": { - "line": 45, + "line": 63, "column": 80 } }, "object": { "type": "Identifier", - "start": 1376, - "end": 1391, + "start": 2028, + "end": 2043, "loc": { "start": { - "line": 45, + "line": 63, "column": 52 }, "end": { - "line": 45, + "line": 63, "column": 67 }, "identifierName": "CitationWrapper" @@ -2514,15 +3165,15 @@ }, "property": { "type": "Identifier", - "start": 1392, - "end": 1404, + "start": 2044, + "end": 2056, "loc": { "start": { - "line": 45, + "line": 63, "column": 68 }, "end": { - "line": 45, + "line": 63, "column": 80 }, "identifierName": "getAgentName" @@ -2539,57 +3190,57 @@ }, { "type": "IfStatement", - "start": 1411, - "end": 1461, + "start": 2063, + "end": 2113, "loc": { "start": { - "line": 46, + "line": 64, "column": 4 }, "end": { - "line": 46, + "line": 64, "column": 54 } }, "test": { "type": "BinaryExpression", - "start": 1415, - "end": 1435, + "start": 2067, + "end": 2087, "loc": { "start": { - "line": 46, + "line": 64, "column": 8 }, "end": { - "line": 46, + "line": 64, "column": 28 } }, "left": { "type": "MemberExpression", - "start": 1415, - "end": 1429, + "start": 2067, + "end": 2081, "loc": { "start": { - "line": 46, + "line": 64, "column": 8 }, "end": { - "line": 46, + "line": 64, "column": 22 } }, "object": { "type": "Identifier", - "start": 1415, - "end": 1422, + "start": 2067, + "end": 2074, "loc": { "start": { - "line": 46, + "line": 64, "column": 8 }, "end": { - "line": 46, + "line": 64, "column": 15 }, "identifierName": "authors" @@ -2598,15 +3249,15 @@ }, "property": { "type": "Identifier", - "start": 1423, - "end": 1429, + "start": 2075, + "end": 2081, "loc": { "start": { - "line": 46, + "line": 64, "column": 16 }, "end": { - "line": 46, + "line": 64, "column": 22 }, "identifierName": "length" @@ -2618,15 +3269,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 1434, - "end": 1435, + "start": 2086, + "end": 2087, "loc": { "start": { - "line": 46, + "line": 64, "column": 27 }, "end": { - "line": 46, + "line": 64, "column": 28 } }, @@ -2639,44 +3290,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 1437, - "end": 1461, + "start": 2089, + "end": 2113, "loc": { "start": { - "line": 46, + "line": 64, "column": 30 }, "end": { - "line": 46, + "line": 64, "column": 54 } }, "expression": { "type": "AssignmentExpression", - "start": 1437, - "end": 1460, + "start": 2089, + "end": 2112, "loc": { "start": { - "line": 46, + "line": 64, "column": 30 }, "end": { - "line": 46, + "line": 64, "column": 53 } }, "operator": "=", "left": { "type": "Identifier", - "start": 1437, - "end": 1444, + "start": 2089, + "end": 2096, "loc": { "start": { - "line": 46, + "line": 64, "column": 30 }, "end": { - "line": 46, + "line": 64, "column": 37 }, "identifierName": "authors" @@ -2685,30 +3336,30 @@ }, "right": { "type": "ArrayExpression", - "start": 1447, - "end": 1460, + "start": 2099, + "end": 2112, "loc": { "start": { - "line": 46, + "line": 64, "column": 40 }, "end": { - "line": 46, + "line": 64, "column": 53 } }, "elements": [ { "type": "StringLiteral", - "start": 1448, - "end": 1459, + "start": 2100, + "end": 2111, "loc": { "start": { - "line": 46, + "line": 64, "column": 41 }, "end": { - "line": 46, + "line": 64, "column": 52 } }, @@ -2726,57 +3377,57 @@ }, { "type": "IfStatement", - "start": 1466, - "end": 1524, + "start": 2118, + "end": 2176, "loc": { "start": { - "line": 47, + "line": 65, "column": 4 }, "end": { - "line": 47, + "line": 65, "column": 62 } }, "test": { "type": "BinaryExpression", - "start": 1470, - "end": 1488, + "start": 2122, + "end": 2140, "loc": { "start": { - "line": 47, + "line": 65, "column": 8 }, "end": { - "line": 47, + "line": 65, "column": 26 } }, "left": { "type": "MemberExpression", - "start": 1470, - "end": 1484, + "start": 2122, + "end": 2136, "loc": { "start": { - "line": 47, + "line": 65, "column": 8 }, "end": { - "line": 47, + "line": 65, "column": 22 } }, "object": { "type": "Identifier", - "start": 1470, - "end": 1477, + "start": 2122, + "end": 2129, "loc": { "start": { - "line": 47, + "line": 65, "column": 8 }, "end": { - "line": 47, + "line": 65, "column": 15 }, "identifierName": "authors" @@ -2785,15 +3436,15 @@ }, "property": { "type": "Identifier", - "start": 1478, - "end": 1484, + "start": 2130, + "end": 2136, "loc": { "start": { - "line": 47, + "line": 65, "column": 16 }, "end": { - "line": 47, + "line": 65, "column": 22 }, "identifierName": "length" @@ -2805,15 +3456,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 1487, - "end": 1488, + "start": 2139, + "end": 2140, "loc": { "start": { - "line": 47, + "line": 65, "column": 25 }, "end": { - "line": 47, + "line": 65, "column": 26 } }, @@ -2826,44 +3477,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 1490, - "end": 1524, + "start": 2142, + "end": 2176, "loc": { "start": { - "line": 47, + "line": 65, "column": 28 }, "end": { - "line": 47, + "line": 65, "column": 62 } }, "expression": { "type": "AssignmentExpression", - "start": 1490, - "end": 1523, + "start": 2142, + "end": 2175, "loc": { "start": { - "line": 47, + "line": 65, "column": 28 }, "end": { - "line": 47, + "line": 65, "column": 61 } }, "operator": "=", "left": { "type": "Identifier", - "start": 1490, - "end": 1497, + "start": 2142, + "end": 2149, "loc": { "start": { - "line": 47, + "line": 65, "column": 28 }, "end": { - "line": 47, + "line": 65, "column": 35 }, "identifierName": "authors" @@ -2872,59 +3523,59 @@ }, "right": { "type": "ArrayExpression", - "start": 1500, - "end": 1523, + "start": 2152, + "end": 2175, "loc": { "start": { - "line": 47, + "line": 65, "column": 38 }, "end": { - "line": 47, + "line": 65, "column": 61 } }, "elements": [ { "type": "TemplateLiteral", - "start": 1501, - "end": 1522, + "start": 2153, + "end": 2174, "loc": { "start": { - "line": 47, + "line": 65, "column": 39 }, "end": { - "line": 47, + "line": 65, "column": 60 } }, "expressions": [ { "type": "MemberExpression", - "start": 1504, - "end": 1514, + "start": 2156, + "end": 2166, "loc": { "start": { - "line": 47, + "line": 65, "column": 42 }, "end": { - "line": 47, + "line": 65, "column": 52 } }, "object": { "type": "Identifier", - "start": 1504, - "end": 1511, + "start": 2156, + "end": 2163, "loc": { "start": { - "line": 47, + "line": 65, "column": 42 }, "end": { - "line": 47, + "line": 65, "column": 49 }, "identifierName": "authors" @@ -2933,15 +3584,15 @@ }, "property": { "type": "NumericLiteral", - "start": 1512, - "end": 1513, + "start": 2164, + "end": 2165, "loc": { "start": { - "line": 47, + "line": 65, "column": 50 }, "end": { - "line": 47, + "line": 65, "column": 51 } }, @@ -2957,15 +3608,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 1502, - "end": 1502, + "start": 2154, + "end": 2154, "loc": { "start": { - "line": 47, + "line": 65, "column": 40 }, "end": { - "line": 47, + "line": 65, "column": 40 } }, @@ -2977,15 +3628,15 @@ }, { "type": "TemplateElement", - "start": 1515, - "end": 1521, + "start": 2167, + "end": 2173, "loc": { "start": { - "line": 47, + "line": 65, "column": 53 }, "end": { - "line": 47, + "line": 65, "column": 59 } }, @@ -3007,15 +3658,15 @@ { "type": "CommentLine", "value": " The title is based on citation.title, but may include citation.section as well.", - "start": 1530, - "end": 1612, + "start": 2182, + "end": 2264, "loc": { "start": { - "line": 49, + "line": 67, "column": 4 }, "end": { - "line": 49, + "line": 67, "column": 86 } } @@ -3024,44 +3675,44 @@ }, { "type": "VariableDeclaration", - "start": 1617, - "end": 1663, + "start": 2269, + "end": 2315, "loc": { "start": { - "line": 50, + "line": 68, "column": 4 }, "end": { - "line": 50, + "line": 68, "column": 50 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1621, - "end": 1662, + "start": 2273, + "end": 2314, "loc": { "start": { - "line": 50, + "line": 68, "column": 8 }, "end": { - "line": 50, + "line": 68, "column": 49 } }, "id": { "type": "Identifier", - "start": 1621, - "end": 1626, + "start": 2273, + "end": 2278, "loc": { "start": { - "line": 50, + "line": 68, "column": 8 }, "end": { - "line": 50, + "line": 68, "column": 13 }, "identifierName": "title" @@ -3071,72 +3722,72 @@ }, "init": { "type": "LogicalExpression", - "start": 1629, - "end": 1662, + "start": 2281, + "end": 2314, "loc": { "start": { - "line": 50, + "line": 68, "column": 16 }, "end": { - "line": 50, + "line": 68, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 1629, - "end": 1648, + "start": 2281, + "end": 2300, "loc": { "start": { - "line": 50, + "line": 68, "column": 16 }, "end": { - "line": 50, + "line": 68, "column": 35 } }, "object": { "type": "MemberExpression", - "start": 1629, - "end": 1642, + "start": 2281, + "end": 2294, "loc": { "start": { - "line": 50, + "line": 68, "column": 16 }, "end": { - "line": 50, + "line": 68, "column": 29 } }, "object": { "type": "ThisExpression", - "start": 1629, - "end": 1633, + "start": 2281, + "end": 2285, "loc": { "start": { - "line": 50, + "line": 68, "column": 16 }, "end": { - "line": 50, + "line": 68, "column": 20 } } }, "property": { "type": "Identifier", - "start": 1634, - "end": 1642, + "start": 2286, + "end": 2294, "loc": { "start": { - "line": 50, + "line": 68, "column": 21 }, "end": { - "line": 50, + "line": 68, "column": 29 }, "identifierName": "citation" @@ -3147,15 +3798,15 @@ }, "property": { "type": "Identifier", - "start": 1643, - "end": 1648, + "start": 2295, + "end": 2300, "loc": { "start": { - "line": 50, + "line": 68, "column": 30 }, "end": { - "line": 50, + "line": 68, "column": 35 }, "identifierName": "title" @@ -3167,15 +3818,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 1652, - "end": 1662, + "start": 2304, + "end": 2314, "loc": { "start": { - "line": 50, + "line": 68, "column": 39 }, "end": { - "line": 50, + "line": 68, "column": 49 } }, @@ -3194,15 +3845,15 @@ { "type": "CommentLine", "value": " The title is based on citation.title, but may include citation.section as well.", - "start": 1530, - "end": 1612, + "start": 2182, + "end": 2264, "loc": { "start": { - "line": 49, + "line": 67, "column": 4 }, "end": { - "line": 49, + "line": 67, "column": 86 } } @@ -3211,43 +3862,43 @@ }, { "type": "IfStatement", - "start": 1668, - "end": 1773, + "start": 2320, + "end": 2425, "loc": { "start": { - "line": 51, + "line": 69, "column": 4 }, "end": { - "line": 51, + "line": 69, "column": 109 } }, "test": { "type": "CallExpression", - "start": 1672, - "end": 1703, + "start": 2324, + "end": 2355, "loc": { "start": { - "line": 51, + "line": 69, "column": 8 }, "end": { - "line": 51, + "line": 69, "column": 39 } }, "callee": { "type": "Identifier", - "start": 1672, - "end": 1675, + "start": 2324, + "end": 2327, "loc": { "start": { - "line": 51, + "line": 69, "column": 8 }, "end": { - "line": 51, + "line": 69, "column": 11 }, "identifierName": "has" @@ -3257,44 +3908,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1676, - "end": 1689, + "start": 2328, + "end": 2341, "loc": { "start": { - "line": 51, + "line": 69, "column": 12 }, "end": { - "line": 51, + "line": 69, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1676, - "end": 1680, + "start": 2328, + "end": 2332, "loc": { "start": { - "line": 51, + "line": 69, "column": 12 }, "end": { - "line": 51, + "line": 69, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1681, - "end": 1689, + "start": 2333, + "end": 2341, "loc": { "start": { - "line": 51, + "line": 69, "column": 17 }, "end": { - "line": 51, + "line": 69, "column": 25 }, "identifierName": "citation" @@ -3305,15 +3956,15 @@ }, { "type": "StringLiteral", - "start": 1691, - "end": 1702, + "start": 2343, + "end": 2354, "loc": { "start": { - "line": 51, + "line": 69, "column": 27 }, "end": { - "line": 51, + "line": 69, "column": 38 } }, @@ -3327,44 +3978,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 1705, - "end": 1773, + "start": 2357, + "end": 2425, "loc": { "start": { - "line": 51, + "line": 69, "column": 41 }, "end": { - "line": 51, + "line": 69, "column": 109 } }, "expression": { "type": "AssignmentExpression", - "start": 1705, - "end": 1772, + "start": 2357, + "end": 2424, "loc": { "start": { - "line": 51, + "line": 69, "column": 41 }, "end": { - "line": 51, + "line": 69, "column": 108 } }, "operator": "=", "left": { "type": "Identifier", - "start": 1705, - "end": 1710, + "start": 2357, + "end": 2362, "loc": { "start": { - "line": 51, + "line": 69, "column": 41 }, "end": { - "line": 51, + "line": 69, "column": 46 }, "identifierName": "title" @@ -3373,30 +4024,30 @@ }, "right": { "type": "TemplateLiteral", - "start": 1713, - "end": 1772, + "start": 2365, + "end": 2424, "loc": { "start": { - "line": 51, + "line": 69, "column": 49 }, "end": { - "line": 51, + "line": 69, "column": 108 } }, "expressions": [ { "type": "Identifier", - "start": 1716, - "end": 1721, + "start": 2368, + "end": 2373, "loc": { "start": { - "line": 51, + "line": 69, "column": 52 }, "end": { - "line": 51, + "line": 69, "column": 57 }, "identifierName": "title" @@ -3405,72 +4056,72 @@ }, { "type": "LogicalExpression", - "start": 1728, - "end": 1770, + "start": 2380, + "end": 2422, "loc": { "start": { - "line": 51, + "line": 69, "column": 64 }, "end": { - "line": 51, + "line": 69, "column": 106 } }, "left": { "type": "MemberExpression", - "start": 1728, - "end": 1751, + "start": 2380, + "end": 2403, "loc": { "start": { - "line": 51, + "line": 69, "column": 64 }, "end": { - "line": 51, + "line": 69, "column": 87 } }, "object": { "type": "MemberExpression", - "start": 1728, - "end": 1741, + "start": 2380, + "end": 2393, "loc": { "start": { - "line": 51, + "line": 69, "column": 64 }, "end": { - "line": 51, + "line": 69, "column": 77 } }, "object": { "type": "ThisExpression", - "start": 1728, - "end": 1732, + "start": 2380, + "end": 2384, "loc": { "start": { - "line": 51, + "line": 69, "column": 64 }, "end": { - "line": 51, + "line": 69, "column": 68 } } }, "property": { "type": "Identifier", - "start": 1733, - "end": 1741, + "start": 2385, + "end": 2393, "loc": { "start": { - "line": 51, + "line": 69, "column": 69 }, "end": { - "line": 51, + "line": 69, "column": 77 }, "identifierName": "citation" @@ -3481,15 +4132,15 @@ }, "property": { "type": "Identifier", - "start": 1742, - "end": 1751, + "start": 2394, + "end": 2403, "loc": { "start": { - "line": 51, + "line": 69, "column": 78 }, "end": { - "line": 51, + "line": 69, "column": 87 }, "identifierName": "booktitle" @@ -3501,15 +4152,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 1755, - "end": 1770, + "start": 2407, + "end": 2422, "loc": { "start": { - "line": 51, + "line": 69, "column": 91 }, "end": { - "line": 51, + "line": 69, "column": 106 } }, @@ -3524,15 +4175,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 1714, - "end": 1714, + "start": 2366, + "end": 2366, "loc": { "start": { - "line": 51, + "line": 69, "column": 50 }, "end": { - "line": 51, + "line": 69, "column": 50 } }, @@ -3544,15 +4195,15 @@ }, { "type": "TemplateElement", - "start": 1722, - "end": 1726, + "start": 2374, + "end": 2378, "loc": { "start": { - "line": 51, + "line": 69, "column": 58 }, "end": { - "line": 51, + "line": 69, "column": 62 } }, @@ -3564,15 +4215,15 @@ }, { "type": "TemplateElement", - "start": 1771, - "end": 1771, + "start": 2423, + "end": 2423, "loc": { "start": { - "line": 51, + "line": 69, "column": 107 }, "end": { - "line": 51, + "line": 69, "column": 107 } }, @@ -3590,44 +4241,44 @@ }, { "type": "VariableDeclaration", - "start": 1778, - "end": 1870, + "start": 2430, + "end": 2522, "loc": { "start": { - "line": 52, + "line": 70, "column": 4 }, "end": { - "line": 52, + "line": 70, "column": 96 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1782, - "end": 1869, + "start": 2434, + "end": 2521, "loc": { "start": { - 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"start": 1803, - "end": 1810, + "start": 2455, + "end": 2462, "loc": { "start": { - "line": 52, + "line": 70, "column": 29 }, "end": { - "line": 52, + "line": 70, "column": 36 }, "identifierName": "authors" @@ -3696,15 +4347,15 @@ }, "property": { "type": "Identifier", - "start": 1811, - "end": 1815, + "start": 2463, + "end": 2467, "loc": { "start": { - "line": 52, + "line": 70, "column": 37 }, "end": { - "line": 52, + "line": 70, "column": 41 }, "identifierName": "join" @@ -3716,15 +4367,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 1816, - "end": 1823, + "start": 2468, + "end": 2475, "loc": { "start": { - "line": 52, + "line": 70, "column": 42 }, "end": { - "line": 52, + "line": 70, "column": 49 } }, @@ -3738,72 +4389,72 @@ }, { "type": "LogicalExpression", - "start": 1829, - "end": 1857, + "start": 2481, + "end": 2509, "loc": { "start": { - "line": 52, + "line": 70, "column": 55 }, "end": { - "line": 52, + "line": 70, "column": 83 } }, "left": { "type": "MemberExpression", - 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"start": 1910, - "end": 1917, + "start": 2562, + "end": 2569, "loc": { "start": { - "line": 55, + "line": 73, "column": 10 }, "end": { - "line": 55, + "line": 73, "column": 17 }, "identifierName": "editors" @@ -4072,100 +4723,100 @@ }, "init": { "type": "CallExpression", - "start": 1920, - "end": 1983, + "start": 2572, + "end": 2635, "loc": { "start": { - "line": 55, + "line": 73, "column": 20 }, "end": { - "line": 55, + "line": 73, "column": 83 } }, "callee": { "type": "MemberExpression", - "start": 1920, - "end": 1953, + "start": 2572, + "end": 2605, "loc": { "start": { - "line": 55, + "line": 73, "column": 20 }, "end": { - "line": 55, + "line": 73, "column": 53 } }, "object": { "type": "LogicalExpression", - "start": 1921, - "end": 1948, + "start": 2573, + "end": 2600, "loc": { "start": { - "line": 55, + "line": 73, "column": 21 }, "end": { - "line": 55, + "line": 73, "column": 48 } }, "left": { "type": "MemberExpression", - "start": 1921, - "end": 1942, + "start": 2573, + "end": 2594, "loc": { "start": { - 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"start": 1970, - "end": 1982, + "start": 2622, + "end": 2634, "loc": { "start": { - "line": 55, + "line": 73, "column": 70 }, "end": { - "line": 55, + "line": 73, "column": 82 }, "identifierName": "getAgentName" @@ -4293,57 +4944,57 @@ }, { "type": "IfStatement", - "start": 1989, - "end": 2063, + "start": 2641, + "end": 2715, "loc": { "start": { - "line": 56, + "line": 74, "column": 4 }, "end": { - "line": 56, + "line": 74, "column": 78 } }, "test": { "type": "BinaryExpression", - "start": 1993, - "end": 2011, + "start": 2645, + "end": 2663, "loc": { "start": { - "line": 56, + "line": 74, "column": 8 }, "end": { - "line": 56, + "line": 74, "column": 26 } }, "left": { "type": "MemberExpression", - "start": 1993, - "end": 2007, + "start": 2645, + "end": 2659, "loc": { "start": { - "line": 56, + "line": 74, "column": 8 }, "end": { - "line": 56, + "line": 74, "column": 22 } }, "object": { "type": "Identifier", - "start": 1993, - "end": 2000, + "start": 2645, + "end": 2652, "loc": { "start": { - "line": 56, + "line": 74, "column": 8 }, "end": { - "line": 56, + "line": 74, "column": 15 }, "identifierName": "editors" @@ -4352,15 +5003,15 @@ }, "property": { "type": "Identifier", - "start": 2001, - "end": 2007, + "start": 2653, + "end": 2659, "loc": { "start": { - "line": 56, + "line": 74, "column": 16 }, "end": { - "line": 56, + "line": 74, "column": 22 }, "identifierName": "length" @@ -4372,15 +5023,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 2010, - "end": 2011, + "start": 2662, + "end": 2663, "loc": { "start": { - "line": 56, + "line": 74, "column": 25 }, "end": { - "line": 56, + "line": 74, "column": 26 } }, @@ -4393,57 +5044,57 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 2013, - "end": 2063, + "start": 2665, + "end": 2715, "loc": { "start": { - "line": 56, + "line": 74, "column": 28 }, "end": { - "line": 56, + "line": 74, "column": 78 } }, "expression": { "type": "CallExpression", - "start": 2013, - "end": 2062, + "start": 2665, + "end": 2714, "loc": { "start": { - 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"start": 2092, - "end": 2120, + "start": 2744, + "end": 2772, "loc": { "start": { - "line": 58, + "line": 76, "column": 27 }, "end": { - "line": 58, + "line": 76, "column": 55 } }, "object": { "type": "MemberExpression", - "start": 2092, - "end": 2105, + "start": 2744, + "end": 2757, "loc": { "start": { - "line": 58, + "line": 76, "column": 27 }, "end": { - "line": 58, + "line": 76, "column": 40 } }, "object": { "type": "ThisExpression", - "start": 2092, - "end": 2096, + "start": 2744, + "end": 2748, "loc": { "start": { - "line": 58, + "line": 76, "column": 27 }, "end": { - "line": 58, + "line": 76, "column": 31 } } }, "property": { "type": "Identifier", - "start": 2097, - "end": 2105, + "start": 2749, + "end": 2757, "loc": { "start": { - "line": 58, + "line": 76, "column": 32 }, "end": { - "line": 58, + "line": 76, "column": 40 }, "identifierName": "citation" @@ -4773,15 +5424,15 @@ }, "property": { "type": "Identifier", - "start": 2106, - "end": 2120, + "start": 2758, + "end": 2772, "loc": { "start": { - "line": 58, + "line": 76, "column": 41 }, "end": { - "line": 58, + "line": 76, "column": 55 }, "identifierName": "series_editors" @@ -4793,15 +5444,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 2124, - "end": 2126, + "start": 2776, + "end": 2778, "loc": { "start": { - "line": 58, + "line": 76, "column": 59 }, "end": { - "line": 58, + "line": 76, "column": 61 } }, @@ -4809,20 +5460,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 2091 + "parenStart": 2743 } }, "property": { "type": "Identifier", - "start": 2128, - "end": 2131, + "start": 2780, + "end": 2783, "loc": { "start": { - "line": 58, + "line": 76, "column": 63 }, "end": { - "line": 58, + "line": 76, "column": 66 }, "identifierName": "map" @@ -4834,29 +5485,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 2132, - "end": 2160, + "start": 2784, + "end": 2812, "loc": { "start": { - "line": 58, + "line": 76, "column": 67 }, "end": { - "line": 58, + "line": 76, "column": 95 } }, "object": { "type": "Identifier", - "start": 2132, - "end": 2147, + "start": 2784, + "end": 2799, "loc": { "start": { - "line": 58, + "line": 76, "column": 67 }, "end": { - "line": 58, + "line": 76, "column": 82 }, "identifierName": "CitationWrapper" @@ -4865,15 +5516,15 @@ }, "property": { "type": "Identifier", - "start": 2148, - "end": 2160, + "start": 2800, + "end": 2812, "loc": { "start": { - "line": 58, + "line": 76, "column": 83 }, "end": { - "line": 58, + "line": 76, "column": 95 }, "identifierName": "getAgentName" @@ -4890,57 +5541,57 @@ }, { "type": "IfStatement", - "start": 2167, - "end": 2260, + "start": 2819, + "end": 2912, "loc": { "start": { - "line": 59, + "line": 77, "column": 4 }, "end": { - "line": 59, + "line": 77, "column": 97 } }, "test": { "type": "BinaryExpression", - "start": 2171, - "end": 2195, + "start": 2823, + "end": 2847, "loc": { "start": { - "line": 59, + "line": 77, "column": 8 }, "end": { - "line": 59, + "line": 77, "column": 32 } }, "left": { "type": "MemberExpression", - "start": 2171, - 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"line": 61, + "line": 79, "column": 26 }, "identifierName": "length" @@ -5299,15 +5950,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 2291, - "end": 2292, + "start": 2943, + "end": 2944, "loc": { "start": { - "line": 61, + "line": 79, "column": 29 }, "end": { - "line": 61, + "line": 79, "column": 30 } }, @@ -5320,44 +5971,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 2294, - "end": 2344, + "start": 2946, + "end": 2996, "loc": { "start": { - "line": 61, + "line": 79, "column": 32 }, "end": { - "line": 61, + "line": 79, "column": 82 } }, "expression": { "type": "AssignmentExpression", - "start": 2294, - "end": 2343, + "start": 2946, + "end": 2995, "loc": { "start": { - "line": 61, + "line": 79, "column": 32 }, "end": { - "line": 61, + "line": 79, "column": 81 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 2294, - "end": 2309, + "start": 2946, + "end": 2961, "loc": { "start": { - "line": 61, + "line": 79, "column": 32 }, "end": { - "line": 61, + "line": 79, "column": 47 }, "identifierName": "authorsAndTitle" @@ -5366,58 +6017,58 @@ }, "right": { "type": "TemplateLiteral", - "start": 2313, - "end": 2343, + "start": 2965, + "end": 2995, "loc": { "start": { - "line": 61, + "line": 79, "column": 51 }, "end": { - "line": 61, + "line": 79, "column": 81 } }, "expressions": [ { "type": "CallExpression", - "start": 2318, - "end": 2340, + "start": 2970, + "end": 2992, "loc": { "start": { - "line": 61, + "line": 79, "column": 56 }, "end": { - "line": 61, + "line": 79, "column": 78 } }, "callee": { "type": "MemberExpression", - "start": 2318, - "end": 2334, + "start": 2970, + "end": 2986, "loc": { "start": { - "line": 61, + "line": 79, "column": 56 }, "end": { - "line": 61, + "line": 79, "column": 72 } }, "object": { "type": "Identifier", - "start": 2318, - "end": 2329, + "start": 2970, + "end": 2981, "loc": { "start": { - "line": 61, + "line": 79, "column": 56 }, "end": { - "line": 61, + "line": 79, "column": 67 }, "identifierName": "editorLists" @@ -5426,15 +6077,15 @@ }, "property": { "type": "Identifier", - "start": 2330, - "end": 2334, + "start": 2982, + "end": 2986, "loc": { "start": { - "line": 61, + "line": 79, "column": 68 }, "end": { - "line": 61, + "line": 79, "column": 72 }, "identifierName": "join" @@ -5446,15 +6097,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 2335, - "end": 2339, + "start": 2987, + "end": 2991, "loc": { "start": { - "line": 61, + "line": 79, "column": 73 }, "end": { - "line": 61, + "line": 79, "column": 77 } }, @@ -5470,15 +6121,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 2314, - "end": 2316, + "start": 2966, + "end": 2968, "loc": { "start": { - "line": 61, + "line": 79, "column": 52 }, "end": { - "line": 61, + "line": 79, "column": 54 } }, @@ -5490,15 +6141,15 @@ }, { "type": "TemplateElement", - "start": 2341, - "end": 2342, + "start": 2993, + "end": 2994, "loc": { "start": { - "line": 61, + "line": 79, "column": 79 }, "end": { - "line": 61, + "line": 79, "column": 80 } }, @@ -5516,43 +6167,43 @@ }, { "type": "IfStatement", - "start": 2350, - "end": 2469, + "start": 3002, + "end": 3121, "loc": { "start": { - "line": 63, + "line": 81, "column": 4 }, "end": { - "line": 65, + "line": 83, "column": 5 } }, "test": { "type": "CallExpression", - "start": 2354, - "end": 2389, + "start": 3006, + "end": 3041, "loc": { "start": { - "line": 63, + "line": 81, "column": 8 }, "end": { - "line": 63, + "line": 81, "column": 43 } }, "callee": { "type": "Identifier", - "start": 2354, - "end": 2357, + "start": 3006, + "end": 3009, "loc": { "start": { - "line": 63, + "line": 81, "column": 8 }, "end": { - "line": 63, + "line": 81, "column": 11 }, "identifierName": "has" @@ -5562,44 +6213,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2358, - "end": 2371, + "start": 3010, + "end": 3023, "loc": { "start": { - "line": 63, + "line": 81, "column": 12 }, "end": { - "line": 63, + "line": 81, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 2358, - "end": 2362, + "start": 3010, + "end": 3014, "loc": { "start": { - "line": 63, + "line": 81, "column": 12 }, "end": { - "line": 63, + "line": 81, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2363, - "end": 2371, + "start": 3015, + "end": 3023, "loc": { "start": { - "line": 63, + "line": 81, "column": 17 }, "end": { - "line": 63, + "line": 81, "column": 25 }, "identifierName": "citation" @@ -5610,15 +6261,15 @@ }, { "type": "StringLiteral", - "start": 2373, - "end": 2388, + "start": 3025, + "end": 3040, "loc": { "start": { - "line": 63, + "line": 81, "column": 27 }, "end": { - "line": 63, + "line": 81, "column": 42 } }, @@ -5632,59 +6283,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 2391, - "end": 2469, + "start": 3043, + "end": 3121, "loc": { "start": { - "line": 63, + "line": 81, "column": 45 }, "end": { - "line": 65, + "line": 83, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2399, - "end": 2463, + "start": 3051, + "end": 3115, "loc": { "start": { - "line": 64, + "line": 82, "column": 6 }, "end": { - "line": 64, + "line": 82, "column": 70 } }, "expression": { "type": "AssignmentExpression", - "start": 2399, - "end": 2462, + "start": 3051, + "end": 3114, "loc": { "start": { - "line": 64, + "line": 82, "column": 6 }, "end": { - "line": 64, + "line": 82, "column": 69 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 2399, - "end": 2414, + "start": 3051, + "end": 3066, "loc": { "start": { - "line": 64, + "line": 82, "column": 6 }, "end": { - "line": 64, + "line": 82, "column": 21 }, "identifierName": "authorsAndTitle" @@ -5693,73 +6344,73 @@ }, "right": { "type": "TemplateLiteral", - "start": 2418, - "end": 2462, + "start": 3070, + "end": 3114, "loc": { "start": { - "line": 64, + "line": 82, "column": 25 }, "end": { - "line": 64, + "line": 82, "column": 69 } }, "expressions": [ { "type": "MemberExpression", - "start": 2432, - "end": 2459, + "start": 3084, + "end": 3111, "loc": { "start": { - "line": 64, + "line": 82, "column": 39 }, "end": { - "line": 64, + "line": 82, "column": 66 } }, "object": { "type": "MemberExpression", - "start": 2432, - "end": 2445, + "start": 3084, + "end": 3097, "loc": { "start": { - "line": 64, + "line": 82, "column": 39 }, "end": { - "line": 64, + "line": 82, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 2432, - "end": 2436, + "start": 3084, + "end": 3088, "loc": { "start": { - "line": 64, + "line": 82, "column": 39 }, "end": { - "line": 64, + "line": 82, "column": 43 } } }, "property": { "type": "Identifier", - "start": 2437, - "end": 2445, + "start": 3089, + "end": 3097, "loc": { "start": { - "line": 64, + "line": 82, "column": 44 }, "end": { - "line": 64, + "line": 82, "column": 52 }, "identifierName": "citation" @@ -5770,15 +6421,15 @@ }, "property": { "type": "Identifier", - "start": 2446, - "end": 2459, + "start": 3098, + "end": 3111, "loc": { "start": { - "line": 64, + "line": 82, "column": 53 }, "end": { - "line": 64, + "line": 82, "column": 66 }, "identifierName": "section_title" @@ -5791,15 +6442,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 2419, - "end": 2430, + "start": 3071, + "end": 3082, "loc": { "start": { - "line": 64, + "line": 82, "column": 26 }, "end": { - "line": 64, + "line": 82, "column": 37 } }, @@ -5811,15 +6462,15 @@ }, { "type": "TemplateElement", - "start": 2460, - "end": 2461, + "start": 3112, + "end": 3113, "loc": { "start": { - "line": 64, + "line": 82, "column": 67 }, "end": { - "line": 64, + "line": 82, "column": 68 } }, @@ -5842,15 +6493,15 @@ { "type": "CommentLine", "value": " Additional info stores details that should be at the end of the figure number,", - "start": 2475, - "end": 2556, + "start": 3127, + "end": 3208, "loc": { "start": { - "line": 67, + "line": 85, "column": 4 }, "end": { - "line": 67, + "line": 85, "column": 85 } } @@ -5858,15 +6509,15 @@ { "type": "CommentLine", "value": " DOIs, URLs, ISBNs and so on.", - "start": 2561, - "end": 2592, + "start": 3213, + "end": 3244, "loc": { "start": { - "line": 68, + "line": 86, "column": 4 }, "end": { - "line": 68, + "line": 86, "column": 35 } } @@ -5875,44 +6526,44 @@ }, { "type": "VariableDeclaration", - "start": 2597, - "end": 2622, + "start": 3249, + "end": 3274, "loc": { "start": { - 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"line": 67, + "line": 85, "column": 4 }, "end": { - "line": 67, + "line": 85, "column": 85 } } @@ -5964,15 +6615,15 @@ { "type": "CommentLine", "value": " DOIs, URLs, ISBNs and so on.", - "start": 2561, - "end": 2592, + "start": 3213, + "end": 3244, "loc": { "start": { - "line": 68, + "line": 86, "column": 4 }, "end": { - "line": 68, + "line": 86, "column": 35 } } @@ -5981,43 +6632,43 @@ }, { "type": "IfStatement", - "start": 2627, - "end": 2710, + "start": 3279, + "end": 3362, "loc": { "start": { - "line": 70, + "line": 88, "column": 4 }, "end": { - "line": 70, + "line": 88, "column": 87 } }, "test": { "type": "CallExpression", - "start": 2631, - "end": 2659, + "start": 3283, + "end": 3311, "loc": { "start": { - "line": 70, + "line": 88, "column": 8 }, "end": { - "line": 70, + "line": 88, "column": 36 } }, "callee": { "type": "Identifier", - "start": 2631, - "end": 2634, + "start": 3283, + "end": 3286, "loc": { "start": { - "line": 70, + "line": 88, "column": 8 }, "end": { - "line": 70, + "line": 88, "column": 11 }, "identifierName": "has" @@ -6027,44 +6678,44 @@ "arguments": [ { "type": "MemberExpression", - 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"start": 2850, - "end": 2867, + "start": 3502, + "end": 3519, "loc": { "start": { - "line": 75, + "line": 93, "column": 18 }, "end": { - "line": 75, + "line": 93, "column": 35 } }, "expressions": [ { "type": "MemberExpression", - "start": 2859, - "end": 2865, + "start": 3511, + "end": 3517, "loc": { "start": { - "line": 75, + "line": 93, "column": 27 }, "end": { - "line": 75, + "line": 93, "column": 33 } }, "object": { "type": "Identifier", - "start": 2859, - "end": 2862, + "start": 3511, + "end": 3514, "loc": { "start": { - "line": 75, + "line": 93, "column": 27 }, "end": { - "line": 75, + "line": 93, "column": 30 }, "identifierName": "doi" @@ -6803,15 +7454,15 @@ }, "property": { "type": "Identifier", - "start": 2863, - "end": 2865, + "start": 3515, + "end": 3517, "loc": { "start": { - "line": 75, + "line": 93, "column": 31 }, "end": { - "line": 75, + "line": 93, "column": 33 }, "identifierName": "id" @@ -6824,15 +7475,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 2851, - 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"line": 77, + "line": 95, "column": 47 } }, "left": { "type": "MemberExpression", - "start": 2909, - "end": 2927, + "start": 3561, + "end": 3579, "loc": { "start": { - "line": 77, + "line": 95, "column": 23 }, "end": { - "line": 77, + "line": 95, "column": 41 } }, "object": { "type": "MemberExpression", - "start": 2909, - "end": 2922, + "start": 3561, + "end": 3574, "loc": { "start": { - "line": 77, + "line": 95, "column": 23 }, "end": { - "line": 77, + "line": 95, "column": 36 } }, "object": { "type": "ThisExpression", - "start": 2909, - "end": 2913, + "start": 3561, + "end": 3565, "loc": { "start": { - "line": 77, + "line": 95, "column": 23 }, "end": { - "line": 77, + "line": 95, "column": 27 } } }, "property": { "type": "Identifier", - "start": 2914, - "end": 2922, + "start": 3566, + "end": 3574, "loc": { "start": { - "line": 77, + "line": 95, "column": 28 }, "end": { - "line": 77, + "line": 95, "column": 36 }, "identifierName": "citation" @@ -7110,15 +7761,15 @@ }, "property": { "type": "Identifier", - "start": 2923, - "end": 2927, + "start": 3575, + "end": 3579, "loc": { "start": { - "line": 77, + "line": 95, "column": 37 }, "end": { - "line": 77, + "line": 95, "column": 41 }, "identifierName": "link" @@ -7130,15 +7781,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 2931, - "end": 2933, + "start": 3583, + "end": 3585, "loc": { "start": { - "line": 77, + "line": 95, "column": 45 }, "end": { - "line": 77, + "line": 95, "column": 47 } }, @@ -7146,20 +7797,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 2908 + "parenStart": 3560 } }, "property": { "type": "Identifier", - "start": 2935, - "end": 2938, + "start": 3587, + "end": 3590, "loc": { "start": { - "line": 77, + "line": 95, "column": 49 }, "end": { - "line": 77, + "line": 95, "column": 52 }, "identifierName": "map" @@ -7171,15 +7822,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 2939, - "end": 2966, + "start": 3591, + "end": 3618, "loc": { "start": { - "line": 77, + "line": 95, "column": 53 }, "end": { - 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We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n ", "start": 346, - "end": 570, + "end": 657, "loc": { "start": { "line": 17, "column": 2 }, "end": { - "line": 22, + "line": 23, "column": 5 } } @@ -11774,15 +12425,15 @@ }, { "type": "ClassMethod", - "start": 573, - "end": 990, + "start": 660, + "end": 994, "loc": { "start": { - "line": 23, + "line": 24, "column": 2 }, "end": { - "line": 36, + "line": 33, "column": 3 } }, @@ -11790,20 +12441,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 580, - "end": 592, + "start": 667, + "end": 676, "loc": { "start": { - "line": 23, + "line": 24, "column": 9 }, "end": { - "line": 23, - "column": 21 + "line": 24, + "column": 18 }, - "identifierName": "getAgentName" + "identifierName": "normalize" }, - "name": "getAgentName" + "name": "normalize" }, "kind": "method", "id": null, @@ -11813,1119 +12464,573 @@ "params": [ { "type": "Identifier", - "start": 593, - "end": 598, + "start": 677, + "end": 685, "loc": { "start": { - 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"loc": { "start": { - "line": 100, + "line": 118, "column": 49 }, "end": { - "line": 100, + "line": 118, "column": 58 }, "identifierName": "publisher" @@ -21878,58 +23180,58 @@ }, { "type": "MemberExpression", - "start": 4080, - "end": 4098, + "start": 4732, + "end": 4750, "loc": { "start": { - "line": 100, + "line": 118, "column": 63 }, "end": { - "line": 100, + "line": 118, "column": 81 } }, "object": { "type": "MemberExpression", - "start": 4080, - "end": 4093, + "start": 4732, + "end": 4745, "loc": { "start": { - "line": 100, + "line": 118, "column": 63 }, "end": { - "line": 100, + "line": 118, "column": 76 } }, "object": { "type": "ThisExpression", - "start": 4080, - "end": 4084, + "start": 4732, + "end": 4736, "loc": { "start": { - "line": 100, + "line": 118, "column": 63 }, "end": { - "line": 100, + "line": 118, "column": 67 } } }, "property": { "type": "Identifier", - "start": 4085, - "end": 4093, + "start": 4737, + "end": 4745, "loc": { "start": { - "line": 100, + "line": 118, "column": 68 }, "end": { - "line": 100, + "line": 118, "column": 76 }, "identifierName": "citation" @@ -21940,15 +23242,15 @@ }, "property": { "type": "Identifier", - "start": 4094, - "end": 4098, + "start": 4746, + "end": 4750, "loc": { "start": { - "line": 100, + "line": 118, "column": 77 }, "end": { - "line": 100, + "line": 118, "column": 81 }, "identifierName": "city" @@ -21959,15 +23261,15 @@ }, { "type": "Identifier", - "start": 4101, - "end": 4115, + "start": 4753, + "end": 4767, "loc": { "start": { - "line": 100, + "line": 118, "column": 84 }, "end": { - "line": 100, + "line": 118, "column": 98 }, "identifierName": "additionalInfo" @@ -21978,15 +23280,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 4031, - "end": 4031, + "start": 4683, + "end": 4683, "loc": { "start": { - "line": 100, + "line": 118, "column": 14 }, "end": { - "line": 100, + "line": 118, "column": 14 } }, @@ -21998,15 +23300,15 @@ }, { "type": "TemplateElement", - "start": 4049, - "end": 4050, + "start": 4701, + "end": 4702, "loc": { "start": { - "line": 100, + "line": 118, "column": 32 }, "end": { - "line": 100, + "line": 118, "column": 33 } }, @@ -22018,15 +23320,15 @@ }, { "type": "TemplateElement", - "start": 4076, - "end": 4078, + "start": 4728, + "end": 4730, "loc": { "start": { - "line": 100, + "line": 118, "column": 59 }, "end": { - "line": 100, + "line": 118, "column": 61 } }, @@ -22038,15 +23340,15 @@ }, { "type": "TemplateElement", - "start": 4099, - "end": 4099, + "start": 4751, + "end": 4751, "loc": { "start": { - "line": 100, + "line": 118, "column": 82 }, "end": { - "line": 100, + "line": 118, "column": 82 } }, @@ -22058,15 +23360,15 @@ }, { "type": "TemplateElement", - "start": 4116, - "end": 4116, + "start": 4768, + "end": 4768, "loc": { "start": { - "line": 100, + "line": 118, "column": 99 }, "end": { - "line": 100, + "line": 118, "column": 99 } }, @@ -22086,43 +23388,43 @@ }, { "type": "IfStatement", - "start": 4130, - "end": 4253, + "start": 4782, + "end": 4905, "loc": { "start": { - "line": 103, + "line": 121, "column": 4 }, "end": { - "line": 105, + "line": 123, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4134, - "end": 4165, + "start": 4786, + "end": 4817, "loc": { "start": { - "line": 103, + "line": 121, "column": 8 }, "end": { - "line": 103, + "line": 121, "column": 39 } }, "callee": { "type": "Identifier", - "start": 4134, - "end": 4137, + "start": 4786, + "end": 4789, "loc": { "start": { - "line": 103, + "line": 121, "column": 8 }, "end": { - "line": 103, + "line": 121, "column": 11 }, "identifierName": "has" @@ -22132,44 +23434,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4138, - "end": 4151, + "start": 4790, + "end": 4803, "loc": { "start": { - "line": 103, + "line": 121, "column": 12 }, "end": { - "line": 103, + "line": 121, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4138, - "end": 4142, + "start": 4790, + "end": 4794, "loc": { "start": { - "line": 103, + "line": 121, "column": 12 }, "end": { - "line": 103, + "line": 121, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4143, - "end": 4151, + "start": 4795, + "end": 4803, "loc": { "start": { - "line": 103, + "line": 121, "column": 17 }, "end": { - "line": 103, + "line": 121, "column": 25 }, "identifierName": "citation" @@ -22180,15 +23482,15 @@ }, { "type": "StringLiteral", - "start": 4153, - "end": 4164, + "start": 4805, + "end": 4816, "loc": { "start": { - "line": 103, + "line": 121, "column": 27 }, "end": { - "line": 103, + "line": 121, "column": 38 } }, @@ -22202,59 +23504,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4167, - "end": 4253, + "start": 4819, + "end": 4905, "loc": { "start": { - "line": 103, + "line": 121, "column": 41 }, "end": { - "line": 105, + "line": 123, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 4175, - "end": 4247, + "start": 4827, + "end": 4899, "loc": { "start": { - "line": 104, + "line": 122, "column": 6 }, "end": { - "line": 104, + "line": 122, "column": 78 } }, "argument": { "type": "TemplateLiteral", - "start": 4182, - "end": 4246, + "start": 4834, + "end": 4898, "loc": { "start": { - "line": 104, + "line": 122, "column": 13 }, "end": { - "line": 104, + "line": 122, "column": 77 } }, "expressions": [ { "type": "Identifier", - "start": 4185, - "end": 4200, + "start": 4837, + "end": 4852, "loc": { "start": { - "line": 104, + "line": 122, "column": 16 }, "end": { - "line": 104, + "line": 122, "column": 31 }, "identifierName": "authorsAndTitle" @@ -22263,58 +23565,58 @@ }, { "type": "MemberExpression", - "start": 4204, - "end": 4227, + "start": 4856, + "end": 4879, "loc": { "start": { - "line": 104, + "line": 122, "column": 35 }, "end": { - "line": 104, + "line": 122, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 4204, - "end": 4217, + "start": 4856, + "end": 4869, "loc": { "start": { - "line": 104, + "line": 122, "column": 35 }, "end": { - "line": 104, + "line": 122, "column": 48 } }, "object": { "type": "ThisExpression", - "start": 4204, - "end": 4208, + "start": 4856, + "end": 4860, "loc": { "start": { - "line": 104, + "line": 122, "column": 35 }, "end": { - "line": 104, + "line": 122, "column": 39 } } }, "property": { "type": "Identifier", - "start": 4209, - "end": 4217, + "start": 4861, + "end": 4869, "loc": { "start": { - "line": 104, + "line": 122, "column": 40 }, "end": { - "line": 104, + "line": 122, "column": 48 }, "identifierName": "citation" @@ -22325,15 +23627,15 @@ }, "property": { "type": "Identifier", - "start": 4218, - "end": 4227, + "start": 4870, + "end": 4879, "loc": { "start": { - "line": 104, + "line": 122, "column": 49 }, "end": { - "line": 104, + "line": 122, "column": 58 }, "identifierName": "publisher" @@ -22344,15 +23646,15 @@ }, { "type": "Identifier", - "start": 4230, - "end": 4244, + "start": 4882, + "end": 4896, "loc": { "start": { - "line": 104, + "line": 122, "column": 61 }, "end": { - "line": 104, + "line": 122, "column": 75 }, "identifierName": "additionalInfo" @@ -22363,15 +23665,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 4183, - "end": 4183, + "start": 4835, + "end": 4835, "loc": { "start": { - "line": 104, + "line": 122, "column": 14 }, "end": { - "line": 104, + "line": 122, "column": 14 } }, @@ -22383,15 +23685,15 @@ }, { "type": "TemplateElement", - "start": 4201, - "end": 4202, + "start": 4853, + "end": 4854, "loc": { "start": { - "line": 104, + "line": 122, "column": 32 }, "end": { - "line": 104, + "line": 122, "column": 33 } }, @@ -22403,15 +23705,15 @@ }, { "type": "TemplateElement", - "start": 4228, - "end": 4228, + "start": 4880, + "end": 4880, "loc": { "start": { - "line": 104, + "line": 122, "column": 59 }, "end": { - "line": 104, + "line": 122, "column": 59 } }, @@ -22423,15 +23725,15 @@ }, { "type": "TemplateElement", - "start": 4245, - "end": 4245, + "start": 4897, + "end": 4897, "loc": { "start": { - "line": 104, + "line": 122, "column": 76 }, "end": { - "line": 104, + "line": 122, "column": 76 } }, @@ -22451,72 +23753,72 @@ }, { "type": "ReturnStatement", - "start": 4259, - "end": 4311, + "start": 4911, + "end": 4963, "loc": { "start": { - "line": 107, + "line": 125, "column": 4 }, "end": { - "line": 107, + "line": 125, "column": 56 } }, "argument": { "type": "CallExpression", - "start": 4266, - "end": 4310, + "start": 4918, + "end": 4962, "loc": { "start": { - "line": 107, + "line": 125, "column": 11 }, "end": { - "line": 107, + "line": 125, "column": 55 } }, "callee": { "type": "MemberExpression", - "start": 4266, - "end": 4308, + "start": 4918, + "end": 4960, "loc": { "start": { - "line": 107, + "line": 125, "column": 11 }, "end": { - "line": 107, + "line": 125, "column": 53 } }, "object": { "type": "TemplateLiteral", - "start": 4266, - "end": 4303, + "start": 4918, + "end": 4955, "loc": { "start": { - "line": 107, + "line": 125, "column": 11 }, "end": { - "line": 107, + "line": 125, "column": 48 } }, "expressions": [ { "type": "Identifier", - "start": 4269, - "end": 4284, + "start": 4921, + "end": 4936, "loc": { "start": { - "line": 107, + "line": 125, "column": 14 }, "end": { - "line": 107, + "line": 125, "column": 29 }, "identifierName": "authorsAndTitle" @@ -22525,15 +23827,15 @@ }, { "type": "Identifier", - "start": 4287, - "end": 4301, + "start": 4939, + "end": 4953, "loc": { "start": { - "line": 107, + "line": 125, "column": 32 }, "end": { - "line": 107, + "line": 125, "column": 46 }, "identifierName": "additionalInfo" @@ -22544,15 +23846,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 4267, - "end": 4267, + "start": 4919, + "end": 4919, "loc": { "start": { - "line": 107, + "line": 125, "column": 12 }, "end": { - "line": 107, + "line": 125, "column": 12 } }, @@ -22564,15 +23866,15 @@ }, { "type": "TemplateElement", - "start": 4285, - "end": 4285, + "start": 4937, + "end": 4937, "loc": { "start": { - "line": 107, + "line": 125, "column": 30 }, "end": { - "line": 107, + "line": 125, "column": 30 } }, @@ -22584,15 +23886,15 @@ }, { "type": "TemplateElement", - "start": 4302, - "end": 4302, + "start": 4954, + "end": 4954, "loc": { "start": { - "line": 107, + "line": 125, "column": 47 }, "end": { - "line": 107, + "line": 125, "column": 47 } }, @@ -22606,15 +23908,15 @@ }, "property": { "type": "Identifier", - "start": 4304, - "end": 4308, + "start": 4956, + "end": 4960, "loc": { "start": { - "line": 107, + "line": 125, "column": 49 }, "end": { - "line": 107, + "line": 125, "column": 53 }, "identifierName": "trim" @@ -22633,15 +23935,15 @@ { "type": "CommentBlock", "value": "* Returns a single string with the entire bibliographic citation. ", - "start": 994, - "end": 1064, + "start": 1646, + "end": 1716, "loc": { "start": { - "line": 38, + "line": 56, "column": 2 }, "end": { - "line": 38, + "line": 56, "column": 72 } } @@ -22680,213 +23982,1344 @@ }, { "type": "CommentBlock", - "value": "*\n * Construct a CitationWrapper.\n ", - "start": 239, - "end": 282, + "value": "*\n * Construct a CitationWrapper.\n ", + "start": 239, + "end": 282, + "loc": { + "start": { + "line": 10, + "column": 2 + }, + "end": { + "line": 12, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return a normalized form of a citation.\n *\n * I'm not really sure how to normalize a citation, but the main thing we can do is delete any key\n * that is equivalent to ''. We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n ", + "start": 346, + "end": 657, + "loc": { + "start": { + "line": 17, + "column": 2 + }, + "end": { + "line": 23, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " As long as citation[key] has a reasonable value, we copy it into the normalized citation.", + "start": 775, + "end": 867, + "loc": { + "start": { + "line": 27, + "column": 6 + }, + "end": { + "line": 27, + "column": 98 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n ", + "start": 998, + "end": 1222, + "loc": { + "start": { + "line": 35, + "column": 2 + }, + "end": { + "line": 40, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "* Returns a single string with the entire bibliographic citation. ", + "start": 1646, + "end": 1716, + "loc": { + "start": { + "line": 56, + "column": 2 + }, + "end": { + "line": 56, + "column": 72 + } + } + }, + { + "type": "CommentLine", + "value": " If we already have a bibliographic citation, we can just return that.", + "start": 1805, + "end": 1877, + "loc": { + "start": { + "line": 60, + "column": 4 + }, + "end": { + "line": 60, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " The title is based on citation.title, but may include citation.section as well.", + "start": 2182, + "end": 2264, + "loc": { + "start": { + "line": 67, + "column": 4 + }, + "end": { + "line": 67, + "column": 86 + } + } + }, + { + "type": "CommentLine", + "value": " Additional info stores details that should be at the end of the figure number,", + "start": 3127, + "end": 3208, + "loc": { + "start": { + "line": 85, + "column": 4 + }, + "end": { + "line": 85, + "column": 85 + } + } + }, + { + "type": "CommentLine", + "value": " DOIs, URLs, ISBNs and so on.", + "start": 3213, + "end": 3244, + "loc": { + "start": { + "line": 86, + "column": 4 + }, + "end": { + "line": 86, + "column": 35 + } + } + }, + { + "type": "CommentLine", + "value": " Add DOIs and URLs.", + "start": 3368, + "end": 3389, + "loc": { + "start": { + "line": 90, + "column": 4 + }, + "end": { + "line": 90, + "column": 25 + } + } + }, + { + "type": "CommentLine", + "value": " A citation for a journal article should be different from others.", + "start": 3788, + "end": 3856, + "loc": { + "start": { + "line": 102, + "column": 4 + }, + "end": { + "line": 102, + "column": 72 + } + } + }, + { + "type": "CommentLine", + "value": " If we are here, this must be a book or a book_section.", + "start": 4448, + "end": 4505, + "loc": { + "start": { + "line": 114, + "column": 4 + }, + "end": { + "line": 114, + "column": 61 + } + } + } + ], + "tokens": [ + { + "type": "CommentBlock", + "value": "*\n * The CitationWrapper wraps a single citation in the Phyx document.\n * Based on 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+ } + }, + { + "type": "CommentBlock", + "value": "*\n * Return a normalized form of a citation.\n *\n * I'm not really sure how to normalize a citation, but the main thing we can do is delete any key\n * that is equivalent to ''. We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n ", + "start": 346, + "end": 657, "loc": { "start": { - "line": 10, + "line": 17, "column": 2 }, "end": { - "line": 12, + "line": 23, "column": 5 } } }, { - "type": "CommentBlock", - "value": "*\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n ", - "start": 346, - "end": 570, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "static", + "start": 660, + "end": 666, "loc": { "start": { - "line": 17, + "line": 24, "column": 2 }, "end": { - "line": 22, - "column": 5 + "line": 24, + "column": 8 } } }, { - "type": "CommentBlock", - "value": "* Returns a single string with the entire bibliographic citation. ", - "start": 994, - "end": 1064, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "normalize", + "start": 667, + "end": 676, "loc": { "start": { - "line": 38, - "column": 2 + "line": 24, + "column": 9 }, "end": { - "line": 38, - "column": 72 + "line": 24, + "column": 18 } } }, { - "type": "CommentLine", - "value": " If we already have a bibliographic citation, we can just return that.", - "start": 1153, - "end": 1225, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 676, + "end": 677, "loc": { "start": { - "line": 42, - "column": 4 + "line": 24, + "column": 18 }, "end": { - "line": 42, - "column": 76 + "line": 24, + "column": 19 } } }, { - "type": "CommentLine", - "value": " The title is based on citation.title, but may include citation.section as well.", - "start": 1530, - "end": 1612, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "citation", + "start": 677, + "end": 685, "loc": { "start": { - "line": 49, - "column": 4 + "line": 24, + "column": 19 }, "end": { - "line": 49, - "column": 86 + "line": 24, + "column": 27 } } }, { - "type": "CommentLine", - "value": " Additional info stores details that should be at the end of the figure number,", - "start": 2475, - "end": 2556, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 685, + "end": 686, "loc": { "start": { - "line": 67, - "column": 4 + "line": 24, + "column": 27 }, "end": { - "line": 67, - "column": 85 + "line": 24, + "column": 28 } } }, { - "type": "CommentLine", - "value": " DOIs, URLs, ISBNs and so on.", - "start": 2561, - "end": 2592, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 687, + "end": 688, "loc": { "start": { - "line": 68, - "column": 4 + "line": 24, + "column": 29 }, "end": { - "line": 68, - "column": 35 + "line": 24, + "column": 30 } } }, { - "type": "CommentLine", - "value": " Add DOIs and URLs.", - "start": 2716, - "end": 2737, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 693, + "end": 698, "loc": { "start": { - "line": 72, + "line": 25, "column": 4 }, "end": { - "line": 72, - "column": 25 + "line": 25, + "column": 9 } } }, { - "type": "CommentLine", - "value": " A citation for a journal article should be different from others.", - "start": 3136, - "end": 3204, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "normalizedCitation", + "start": 699, + "end": 717, "loc": { "start": { - "line": 84, - "column": 4 + "line": 25, + "column": 10 }, "end": { - "line": 84, - "column": 72 + "line": 25, + "column": 28 } } }, { - "type": "CommentLine", - "value": " If we are here, this must be a book or a book_section.", - "start": 3796, - "end": 3853, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 718, + "end": 719, "loc": { "start": { - "line": 96, - "column": 4 + "line": 25, + "column": 29 }, "end": { - "line": 96, - "column": 61 + "line": 25, + "column": 30 } } - } - ], - "tokens": [ + }, { - "type": "CommentBlock", - "value": "*\n * The CitationWrapper wraps a single citation in the Phyx document.\n * Based on BibJSON (http://okfnlabs.org/bibjson/).\n ", - "start": 0, - "end": 128, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 720, + "end": 721, "loc": { "start": { - "line": 1, - "column": 0 + "line": 25, + "column": 31 }, "end": { - "line": 4, - "column": 3 + "line": 25, + "column": 32 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 130, - "end": 136, + "start": 721, + "end": 722, "loc": { "start": { - "line": 6, - "column": 0 + "line": 25, + "column": 32 }, "end": { - "line": 6, - "column": 6 + "line": 25, + "column": 33 } } }, { "type": { - "label": "*", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -22894,20 +25327,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 137, - "end": 138, + "start": 722, + "end": 723, "loc": { "start": { - "line": 6, - "column": 7 + "line": 25, + "column": 33 }, "end": { - "line": 6, - "column": 8 + "line": 25, + "column": 34 } } }, @@ -22923,16 +25355,42 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 139, - "end": 141, + "value": "Object", + "start": 728, + "end": 734, "loc": { "start": { - "line": 6, - "column": 9 + "line": 26, + "column": 4 }, "end": { - "line": 6, + "line": 26, + "column": 10 + } + } + }, + { + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 734, + "end": 735, + "loc": { + "start": { + "line": 26, + "column": 10 + }, + "end": { + "line": 26, "column": 11 } } @@ -22949,17 +25407,119 @@ "postfix": false, "binop": null }, - "value": "LKT4H14LMZCLL", - "start": 142, - "end": 155, + "value": "keys", + "start": 735, + "end": 739, "loc": { "start": { - "line": 6, - "column": 12 + "line": 26, + "column": 11 }, "end": { - "line": 6, + "line": 26, + "column": 15 + } + } + }, + { + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 739, + "end": 740, + "loc": { + "start": { + "line": 26, + "column": 15 + }, + "end": { + "line": 26, + "column": 16 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "citation", + "start": 740, + "end": 748, + "loc": { + "start": { + "line": 26, + "column": 16 + }, + "end": { + "line": 26, + "column": 24 + } + } + }, + { + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 748, + "end": 749, + "loc": { + "start": { + "line": 26, + "column": 24 + }, + "end": { + "line": 26, + "column": 25 + } + } + }, + { + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 749, + "end": 750, + "loc": { + "start": { + "line": 26, "column": 25 + }, + "end": { + "line": 26, + "column": 26 } } }, @@ -22975,23 +25535,73 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 156, - "end": 160, + "value": "forEach", + "start": 750, + "end": 757, "loc": { "start": { - "line": 6, + "line": 26, "column": 26 }, "end": { - "line": 6, - "column": 30 + "line": 26, + "column": 33 } } }, { "type": { - "label": "string", + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 757, + "end": 758, + "loc": { + "start": { + "line": 26, + "column": 33 + }, + "end": { + "line": 26, + "column": 34 + } + } + }, + { + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 758, + "end": 759, + "loc": { + "start": { + "line": 26, + "column": 34 + }, + "end": { + "line": 26, + "column": 35 + } + } + }, + { + "type": { + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -22999,53 +25609,118 @@ "isAssign": false, "prefix": false, "postfix": false, + "binop": null + }, + "value": "key", + "start": 759, + "end": 762, + "loc": { + "start": { + "line": 26, + "column": 35 + }, + "end": { + "line": 26, + "column": 38 + } + } + }, + { + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 762, + "end": 763, + "loc": { + "start": { + "line": 26, + "column": 38 + }, + "end": { + "line": 26, + "column": 39 + } + } + }, + { + "type": { + "label": "=>", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, "binop": null, "updateContext": null }, - "value": "lodash", - "start": 161, - "end": 169, + "start": 764, + "end": 766, "loc": { "start": { - "line": 6, - "column": 31 + "line": 26, + "column": 40 }, "end": { - "line": 6, - "column": 39 + "line": 26, + "column": 42 } } }, { "type": { - "label": ";", + "label": "{", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 169, - "end": 170, + "start": 767, + "end": 768, "loc": { "start": { - "line": 6, - "column": 39 + "line": 26, + "column": 43 }, "end": { - "line": 6, - "column": 40 + "line": 26, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " As long as citation[key] has a reasonable value, we copy it into the normalized citation.", + "start": 775, + "end": 867, + "loc": { + "start": { + "line": 27, + "column": 6 + }, + "end": { + "line": 27, + "column": 98 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "if", + "keyword": "if", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -23056,23 +25731,23 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 172, - "end": 177, + "value": "if", + "start": 874, + "end": 876, "loc": { "start": { - "line": 7, - "column": 0 + "line": 28, + "column": 6 }, "end": { - "line": 7, - "column": 5 + "line": 28, + "column": 8 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -23082,16 +25757,16 @@ "postfix": false, "binop": null }, - "start": 178, - "end": 179, + "start": 877, + "end": 878, "loc": { "start": { - "line": 7, - "column": 6 + "line": 28, + "column": 9 }, "end": { - "line": 7, - "column": 7 + "line": 28, + "column": 10 } } }, @@ -23107,25 +25782,25 @@ "postfix": false, "binop": null }, - "value": "has", - "start": 180, - "end": 183, + "value": "citation", + "start": 878, + "end": 886, "loc": { "start": { - "line": 7, - "column": 8 + "line": 28, + "column": 10 }, "end": { - "line": 7, - "column": 11 + "line": 28, + "column": 18 } } }, { "type": { - "label": ",", + "label": "[", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23134,16 +25809,16 @@ "binop": null, "updateContext": null }, - "start": 183, - "end": 184, + "start": 886, + "end": 887, "loc": { "start": { - "line": 7, - "column": 11 + "line": 28, + "column": 18 }, "end": { - "line": 7, - "column": 12 + "line": 28, + "column": 19 } } }, @@ -23159,23 +25834,23 @@ "postfix": false, "binop": null }, - "value": "isEmpty", - "start": 185, - "end": 192, + "value": "key", + "start": 887, + "end": 890, "loc": { "start": { - "line": 7, - "column": 13 + "line": 28, + "column": 19 }, "end": { - "line": 7, - "column": 20 + "line": 28, + "column": 22 } } }, { "type": { - "label": "}", + "label": "]", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -23183,52 +25858,51 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 193, - "end": 194, + "start": 890, + "end": 891, "loc": { "start": { - "line": 7, - "column": 21 + "line": 28, + "column": 22 }, "end": { - "line": 7, - "column": 22 + "line": 28, + "column": 23 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 195, - "end": 196, + "start": 891, + "end": 892, "loc": { "start": { - "line": 7, + "line": 28, "column": 23 }, "end": { - "line": 7, + "line": 28, "column": 24 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -23237,52 +25911,50 @@ "postfix": false, "binop": null }, - "value": "LKT4H14LMZCLL", - "start": 197, - "end": 210, + "start": 893, + "end": 894, "loc": { "start": { - "line": 7, + "line": 28, "column": 25 }, "end": { - "line": 7, - "column": 38 + "line": 28, + "column": 26 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 210, - "end": 211, + "value": "normalizedCitation", + "start": 903, + "end": 921, "loc": { "start": { - "line": 7, - "column": 38 + "line": 29, + "column": 8 }, "end": { - "line": 7, - "column": 39 + "line": 29, + "column": 26 } } }, { "type": { - "label": "class", - "keyword": "class", - "beforeExpr": false, - "startsExpr": false, + "label": "[", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23291,17 +25963,16 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 213, - "end": 218, + "start": 921, + "end": 922, "loc": { "start": { - "line": 9, - "column": 0 + "line": 29, + "column": 26 }, "end": { - "line": 9, - "column": 5 + "line": 29, + "column": 27 } } }, @@ -23317,58 +25988,70 @@ "postfix": false, "binop": null }, - "value": "CitationWrapper", - "start": 219, - "end": 234, + "value": "key", + "start": 922, + "end": 925, "loc": { "start": { - "line": 9, - "column": 6 + "line": 29, + "column": 27 }, "end": { - "line": 9, - "column": 21 + "line": 29, + "column": 30 } } }, { "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, + "label": "]", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 235, - "end": 236, + "start": 925, + "end": 926, "loc": { "start": { - "line": 9, - "column": 22 + "line": 29, + "column": 30 }, "end": { - "line": 9, - "column": 23 + "line": 29, + "column": 31 } } }, { - "type": "CommentBlock", - "value": "*\n * Construct a CitationWrapper.\n ", - "start": 239, - "end": 282, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 927, + "end": 928, "loc": { "start": { - "line": 10, - "column": 2 + "line": 29, + "column": 32 }, "end": { - "line": 12, - "column": 5 + "line": 29, + "column": 33 } } }, @@ -23384,23 +26067,23 @@ "postfix": false, "binop": null }, - "value": "constructor", - "start": 285, - "end": 296, + "value": "citation", + "start": 929, + "end": 937, "loc": { "start": { - "line": 13, - "column": 2 + "line": 29, + "column": 34 }, "end": { - "line": 13, - "column": 13 + "line": 29, + "column": 42 } } }, { "type": { - "label": "(", + "label": "[", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -23408,18 +26091,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 296, - "end": 297, + "start": 937, + "end": 938, "loc": { "start": { - "line": 13, - "column": 13 + "line": 29, + "column": 42 }, "end": { - "line": 13, - "column": 14 + "line": 29, + "column": 43 } } }, @@ -23435,23 +26119,23 @@ "postfix": false, "binop": null }, - "value": "citation", - "start": 297, - "end": 305, + "value": "key", + "start": 938, + "end": 941, "loc": { "start": { - "line": 13, - "column": 14 + "line": 29, + "column": 43 }, "end": { - "line": 13, - "column": 22 + "line": 29, + "column": 46 } } }, { "type": { - "label": ")", + "label": "]", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -23459,77 +26143,76 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 305, - "end": 306, + "start": 941, + "end": 942, "loc": { "start": { - "line": 13, - "column": 22 + "line": 29, + "column": 46 }, "end": { - "line": 13, - "column": 23 + "line": 29, + "column": 47 } } }, { "type": { - "label": "{", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 307, - "end": 308, + "start": 942, + "end": 943, "loc": { "start": { - "line": 13, - "column": 24 + "line": 29, + "column": 47 }, "end": { - "line": 13, - "column": 25 + "line": 29, + "column": 48 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 313, - "end": 317, + "start": 950, + "end": 951, "loc": { "start": { - "line": 14, - "column": 4 + "line": 30, + "column": 6 }, "end": { - "line": 14, - "column": 8 + "line": 30, + "column": 7 } } }, { "type": { - "label": ".", + "label": "}", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -23537,27 +26220,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 317, - "end": 318, + "start": 956, + "end": 957, "loc": { "start": { - "line": 14, - "column": 8 + "line": 31, + "column": 4 }, "end": { - "line": 14, - "column": 9 + "line": 31, + "column": 5 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23565,44 +26247,70 @@ "postfix": false, "binop": null }, - "value": "citation", - "start": 318, - "end": 326, + "start": 957, + "end": 958, "loc": { "start": { - "line": 14, - "column": 9 + "line": 31, + "column": 5 }, "end": { - "line": 14, - "column": 17 + "line": 31, + "column": 6 } } }, { "type": { - "label": "=", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 327, - "end": 328, + "start": 958, + "end": 959, "loc": { "start": { - "line": 14, - "column": 18 + "line": 31, + "column": 6 }, "end": { - "line": 14, - "column": 19 + "line": 31, + "column": 7 + } + } + }, + { + "type": { + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "return", + "start": 964, + "end": 970, + "loc": { + "start": { + "line": 32, + "column": 4 + }, + "end": { + "line": 32, + "column": 10 } } }, @@ -23618,17 +26326,17 @@ "postfix": false, "binop": null }, - "value": "citation", - "start": 329, - "end": 337, + "value": "normalizedCitation", + "start": 971, + "end": 989, "loc": { "start": { - "line": 14, - "column": 20 + "line": 32, + "column": 11 }, "end": { - "line": 14, - "column": 28 + "line": 32, + "column": 29 } } }, @@ -23645,16 +26353,16 @@ "binop": null, "updateContext": null }, - "start": 337, - "end": 338, + "start": 989, + "end": 990, "loc": { "start": { - "line": 14, - "column": 28 + "line": 32, + "column": 29 }, "end": { - "line": 14, - "column": 29 + "line": 32, + "column": 30 } } }, @@ -23670,15 +26378,15 @@ "postfix": false, "binop": null }, - "start": 341, - "end": 342, + "start": 993, + "end": 994, "loc": { "start": { - "line": 15, + "line": 33, "column": 2 }, "end": { - "line": 15, + "line": 33, "column": 3 } } @@ -23686,15 +26394,15 @@ { "type": "CommentBlock", "value": "*\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n ", - "start": 346, - "end": 570, + "start": 998, + "end": 1222, "loc": { "start": { - "line": 17, + "line": 35, "column": 2 }, "end": { - "line": 22, + "line": 40, "column": 5 } } @@ -23712,15 +26420,15 @@ "binop": null }, "value": "static", - "start": 573, - "end": 579, + "start": 1225, + "end": 1231, "loc": { "start": { - "line": 23, + "line": 41, "column": 2 }, "end": { - "line": 23, + "line": 41, "column": 8 } } @@ -23738,15 +26446,15 @@ "binop": null }, "value": "getAgentName", - "start": 580, - "end": 592, + "start": 1232, + "end": 1244, "loc": { "start": { - "line": 23, + "line": 41, "column": 9 }, "end": { - "line": 23, + "line": 41, "column": 21 } } @@ -23763,15 +26471,15 @@ "postfix": false, "binop": null }, - "start": 592, - "end": 593, + "start": 1244, + "end": 1245, "loc": { "start": { - "line": 23, + "line": 41, "column": 21 }, "end": { - "line": 23, + "line": 41, "column": 22 } } @@ -23789,15 +26497,15 @@ "binop": null }, "value": "agent", - "start": 593, - "end": 598, + "start": 1245, + "end": 1250, "loc": { "start": { - "line": 23, + "line": 41, "column": 22 }, "end": { - "line": 23, + "line": 41, "column": 27 } } @@ -23814,15 +26522,15 @@ "postfix": false, "binop": null }, - "start": 598, - "end": 599, + "start": 1250, + "end": 1251, "loc": { "start": { - "line": 23, + "line": 41, "column": 27 }, "end": { - "line": 23, + "line": 41, "column": 28 } } @@ -23839,15 +26547,15 @@ "postfix": false, "binop": null }, - "start": 600, - "end": 601, + "start": 1252, + "end": 1253, "loc": { "start": { - "line": 23, + "line": 41, "column": 29 }, "end": { - "line": 23, + "line": 41, "column": 30 } } @@ -23867,15 +26575,15 @@ "updateContext": null }, "value": "if", - "start": 606, - "end": 608, + "start": 1258, + "end": 1260, "loc": { "start": { - "line": 24, + "line": 42, "column": 4 }, "end": { - "line": 24, + "line": 42, "column": 6 } } @@ -23892,15 +26600,15 @@ "postfix": false, "binop": null }, - "start": 609, - "end": 610, + "start": 1261, + "end": 1262, "loc": { "start": { - "line": 24, + "line": 42, "column": 7 }, "end": { - "line": 24, + "line": 42, "column": 8 } } @@ -23918,15 +26626,15 @@ "binop": null }, "value": "has", - "start": 610, - "end": 613, + "start": 1262, + "end": 1265, "loc": { "start": { - "line": 24, + "line": 42, "column": 8 }, "end": { - "line": 24, + "line": 42, "column": 11 } } @@ -23943,15 +26651,15 @@ "postfix": false, "binop": null }, - "start": 613, - "end": 614, + "start": 1265, + "end": 1266, "loc": { "start": { - "line": 24, + "line": 42, "column": 11 }, "end": { - "line": 24, + "line": 42, "column": 12 } } @@ -23969,15 +26677,15 @@ "binop": null }, "value": "agent", - "start": 614, - "end": 619, + "start": 1266, + "end": 1271, "loc": { "start": { - "line": 24, + "line": 42, "column": 12 }, "end": { - "line": 24, + "line": 42, "column": 17 } } @@ -23995,15 +26703,15 @@ "binop": null, "updateContext": null }, - "start": 619, - "end": 620, + "start": 1271, + "end": 1272, "loc": { "start": { - "line": 24, + "line": 42, "column": 17 }, "end": { - "line": 24, + "line": 42, "column": 18 } } @@ -24022,15 +26730,15 @@ "updateContext": null }, "value": "name", - "start": 621, - "end": 627, + "start": 1273, + "end": 1279, "loc": { "start": { - "line": 24, + "line": 42, "column": 19 }, "end": { - "line": 24, + "line": 42, "column": 25 } } @@ -24047,15 +26755,15 @@ "postfix": false, "binop": null }, - "start": 627, - "end": 628, + "start": 1279, + "end": 1280, "loc": { "start": { - "line": 24, + "line": 42, "column": 25 }, "end": { - "line": 24, + "line": 42, "column": 26 } } @@ -24072,15 +26780,15 @@ "postfix": false, "binop": null }, - "start": 628, - "end": 629, + "start": 1280, + "end": 1281, "loc": { "start": { - "line": 24, + "line": 42, "column": 26 }, "end": { - "line": 24, + "line": 42, "column": 27 } } @@ -24100,15 +26808,15 @@ "updateContext": null }, "value": "return", - "start": 630, - "end": 636, + "start": 1282, + "end": 1288, "loc": { "start": { - "line": 24, + "line": 42, "column": 28 }, "end": { - "line": 24, + "line": 42, "column": 34 } } @@ -24126,15 +26834,15 @@ "binop": null }, "value": "agent", - "start": 637, - "end": 642, + "start": 1289, + "end": 1294, "loc": { "start": { - "line": 24, + "line": 42, "column": 35 }, "end": { - "line": 24, + "line": 42, "column": 40 } } @@ -24152,15 +26860,15 @@ "binop": null, "updateContext": null }, - "start": 642, - "end": 643, + "start": 1294, + "end": 1295, "loc": { "start": { - "line": 24, + "line": 42, "column": 40 }, "end": { - "line": 24, + "line": 42, "column": 41 } } @@ -24178,15 +26886,15 @@ "binop": null }, "value": "name", - "start": 643, - "end": 647, + "start": 1295, + "end": 1299, "loc": { "start": { - "line": 24, + "line": 42, "column": 41 }, "end": { - "line": 24, + "line": 42, "column": 45 } } @@ -24204,15 +26912,15 @@ "binop": null, "updateContext": null }, - "start": 647, - "end": 648, + "start": 1299, + "end": 1300, "loc": { "start": { - "line": 24, + "line": 42, "column": 45 }, "end": { - "line": 24, + "line": 42, "column": 46 } } @@ -24232,15 +26940,15 @@ "updateContext": null }, "value": "if", - "start": 653, - "end": 655, + "start": 1305, + "end": 1307, "loc": { "start": { - "line": 25, + "line": 43, "column": 4 }, "end": { - "line": 25, + "line": 43, "column": 6 } } @@ -24257,15 +26965,15 @@ "postfix": false, "binop": null }, - "start": 656, - "end": 657, + "start": 1308, + "end": 1309, "loc": { "start": { - "line": 25, + "line": 43, "column": 7 }, "end": { - "line": 25, + "line": 43, "column": 8 } } @@ -24283,15 +26991,15 @@ "binop": null }, "value": "has", - "start": 657, - "end": 660, + "start": 1309, + "end": 1312, "loc": { "start": { - "line": 25, + "line": 43, "column": 8 }, "end": { - "line": 25, + "line": 43, "column": 11 } } @@ -24308,15 +27016,15 @@ "postfix": false, "binop": null }, - "start": 660, - "end": 661, + "start": 1312, + "end": 1313, "loc": { "start": { - "line": 25, + "line": 43, "column": 11 }, "end": { - "line": 25, + "line": 43, "column": 12 } } @@ -24334,15 +27042,15 @@ "binop": null }, "value": "agent", - "start": 661, - "end": 666, + "start": 1313, + "end": 1318, "loc": { "start": { - "line": 25, + "line": 43, "column": 12 }, "end": { - "line": 25, + "line": 43, "column": 17 } } @@ -24360,15 +27068,15 @@ "binop": null, "updateContext": null }, - "start": 666, - "end": 667, + "start": 1318, + "end": 1319, "loc": { "start": { - "line": 25, + "line": 43, "column": 17 }, "end": { - "line": 25, + "line": 43, "column": 18 } } @@ -24387,15 +27095,15 @@ "updateContext": null }, "value": "lastname", - "start": 668, - "end": 678, + "start": 1320, + "end": 1330, "loc": { "start": { - "line": 25, + "line": 43, "column": 19 }, "end": { - "line": 25, + "line": 43, "column": 29 } } @@ -24412,15 +27120,15 @@ "postfix": false, "binop": null }, - "start": 678, - "end": 679, + "start": 1330, + "end": 1331, "loc": { "start": { - "line": 25, + "line": 43, "column": 29 }, "end": { - "line": 25, + "line": 43, "column": 30 } } @@ -24437,15 +27145,15 @@ "postfix": false, "binop": null }, - "start": 679, - "end": 680, + "start": 1331, + "end": 1332, "loc": { "start": { - "line": 25, + "line": 43, "column": 30 }, "end": { - "line": 25, + "line": 43, "column": 31 } } @@ -24462,15 +27170,15 @@ "postfix": false, "binop": null }, - "start": 681, - "end": 682, + "start": 1333, + "end": 1334, "loc": { "start": { - "line": 25, + "line": 43, "column": 32 }, "end": { - "line": 25, + "line": 43, "column": 33 } } @@ -24490,15 +27198,15 @@ "updateContext": null }, "value": "if", - "start": 689, - "end": 691, + "start": 1341, + "end": 1343, "loc": { "start": { - 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"line": 27, + "line": 30, "column": 53 }, "end": { - "line": 27, + "line": 30, "column": 65 }, "identifierName": "UNKNOWN_CODE" @@ -1215,73 +1270,73 @@ ], "body": { "type": "BlockStatement", - "start": 900, - "end": 1521, + "start": 916, + "end": 1537, "loc": { "start": { - "line": 27, + "line": 30, "column": 67 }, "end": { - "line": 39, + "line": 42, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 1444, - "end": 1471, + "start": 1460, + "end": 1487, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - "line": 37, + "line": 40, "column": 31 } }, "expression": { "type": "AssignmentExpression", - "start": 1444, - "end": 1470, + "start": 1460, + "end": 1486, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - "line": 37, + "line": 40, "column": 30 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 1444, - "end": 1458, + "start": 1460, + "end": 1474, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - 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"line": 28, + "line": 31, "column": 4 }, "end": { - "line": 28, + "line": 31, "column": 77 } } @@ -1346,15 +1401,15 @@ { "type": "CommentLine", "value": " Note that this version ONLY uses the `newick` property to determine the", - "start": 984, - "end": 1058, + "start": 1000, + "end": 1074, "loc": { "start": { - "line": 29, + "line": 32, "column": 4 }, "end": { - "line": 29, + "line": 32, "column": 78 } } @@ -1362,15 +1417,15 @@ { "type": "CommentLine", "value": " phylogeny: if other representations are included (such as a node-based", - "start": 1063, - "end": 1136, + "start": 1079, + "end": 1152, "loc": { "start": { - "line": 30, + "line": 33, "column": 4 }, "end": { - "line": 30, + "line": 33, "column": 77 } } @@ -1378,15 +1433,15 @@ { "type": "CommentLine", "value": " format, as used in JSON-LD), they will be ignored and possibly overwritten", - "start": 1141, - "end": 1218, + "start": 1157, + "end": 1234, "loc": { "start": { - "line": 31, + "line": 34, "column": 4 }, "end": { - "line": 31, + "line": 34, "column": 81 } } @@ -1394,15 +1449,15 @@ { "type": "CommentLine", "value": " during export. 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60, "column": 33 }, "end": { - "line": 41, + "line": 60, "column": 39 }, "identifierName": "newick" @@ -1698,59 +2386,59 @@ ], "body": { "type": "BlockStatement", - "start": 1564, - "end": 3375, + "start": 2014, + "end": 3825, "loc": { "start": { - "line": 41, + "line": 60, "column": 41 }, "end": { - "line": 91, + "line": 110, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 2106, - "end": 2142, + "start": 2556, + "end": 2592, "loc": { "start": { - "line": 51, + "line": 70, "column": 4 }, "end": { - "line": 51, + "line": 70, "column": 40 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2112, - "end": 2141, + "start": 2562, + "end": 2591, "loc": { "start": { - "line": 51, + "line": 70, "column": 10 }, "end": { - "line": 51, + "line": 70, "column": 39 } }, "id": { "type": "Identifier", - "start": 2112, - "end": 2125, + "start": 2562, + "end": 2575, "loc": { "start": { - "line": 51, + "line": 70, "column": 10 }, "end": { - "line": 51, + "line": 70, 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37 }, "identifierName": "trim" @@ -1832,15 +2520,15 @@ { "type": "CommentLine", "value": " Given a Newick string, return a list of errors found in parsing this", - "start": 1570, - "end": 1641, + "start": 2020, + "end": 2091, "loc": { "start": { - "line": 42, + "line": 61, "column": 4 }, "end": { - "line": 42, + "line": 61, "column": 75 } } @@ -1848,15 +2536,15 @@ { "type": "CommentLine", "value": " string. 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"start": 2239, - "end": 2252, + "start": 2689, + "end": 2702, "loc": { "start": { - "line": 55, + "line": 74, "column": 32 }, "end": { - "line": 55, + "line": 74, "column": 45 }, "identifierName": "newickTrimmed" @@ -2191,15 +2879,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 2257, - "end": 2261, + "start": 2707, + "end": 2711, "loc": { "start": { - "line": 55, + "line": 74, "column": 50 }, "end": { - "line": 55, + "line": 74, "column": 54 } }, @@ -2215,29 +2903,29 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 2265, - "end": 2288, + "start": 2715, + "end": 2738, "loc": { "start": { - "line": 55, + "line": 74, "column": 58 }, "end": { - "line": 55, + "line": 74, "column": 81 } }, "left": { "type": "Identifier", - "start": 2265, - "end": 2278, + "start": 2715, + "end": 2728, "loc": { "start": { - "line": 55, + "line": 74, "column": 58 }, "end": { - "line": 55, + "line": 74, "column": 71 }, "identifierName": "newickTrimmed" @@ -2247,15 +2935,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 2283, - "end": 2288, + "start": 2733, + "end": 2738, "loc": { "start": { - "line": 55, + "line": 74, "column": 76 }, "end": { - "line": 55, + "line": 74, "column": 81 } }, @@ -2270,74 +2958,74 @@ }, "consequent": { "type": "BlockStatement", - "start": 2290, - "end": 2506, + "start": 2740, + "end": 2956, "loc": { "start": { - "line": 55, + "line": 74, "column": 83 }, "end": { - "line": 61, + "line": 80, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 2368, - "end": 2500, + "start": 2818, + "end": 2950, "loc": { "start": { - "line": 57, + "line": 76, "column": 6 }, "end": { - "line": 60, + "line": 79, "column": 9 } }, "argument": { "type": "ArrayExpression", - "start": 2375, - "end": 2499, + "start": 2825, + "end": 2949, "loc": { "start": { - "line": 57, + "line": 76, "column": 13 }, "end": { - "line": 60, + "line": 79, "column": 8 } }, "elements": [ { "type": "ObjectExpression", - "start": 2376, - "end": 2498, + "start": 2826, + "end": 2948, "loc": { "start": { - "line": 57, + "line": 76, "column": 14 }, "end": { - "line": 60, + "line": 79, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 2386, - "end": 2415, + "start": 2836, + "end": 2865, "loc": { "start": { - "line": 58, + "line": 77, "column": 8 }, "end": { - "line": 58, + "line": 77, "column": 37 } }, @@ -2346,15 +3034,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2386, - "end": 2391, + "start": 2836, + "end": 2841, "loc": { "start": { - "line": 58, + "line": 77, "column": 8 }, "end": { - "line": 58, + "line": 77, "column": 13 }, "identifierName": "title" @@ -2364,15 +3052,15 @@ }, "value": { "type": "StringLiteral", - "start": 2393, - "end": 2415, + "start": 2843, + "end": 2865, "loc": { "start": { - "line": 58, + "line": 77, "column": 15 }, "end": { - "line": 58, + "line": 77, "column": 37 } }, @@ -2386,15 +3074,15 @@ }, { "type": "ObjectProperty", - "start": 2425, - "end": 2489, + "start": 2875, + "end": 2939, "loc": { "start": { - "line": 59, + "line": 78, "column": 8 }, "end": { - "line": 59, + "line": 78, "column": 72 } }, @@ -2403,15 +3091,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2425, - "end": 2432, + "start": 2875, + "end": 2882, "loc": { "start": { - "line": 59, + "line": 78, "column": 8 }, "end": { - "line": 59, + "line": 78, "column": 15 }, "identifierName": "message" @@ -2420,15 +3108,15 @@ }, "value": { "type": "StringLiteral", - "start": 2434, - "end": 2489, + "start": 2884, + "end": 2939, "loc": { "start": { - "line": 59, + "line": 78, "column": 17 }, "end": { - "line": 59, + "line": 78, "column": 72 } }, @@ -2449,15 +3137,15 @@ { "type": "CommentLine", "value": " None of the later errors are relevant here, so bail out now.", - "start": 2298, - "end": 2361, + "start": 2748, + "end": 2811, "loc": { "start": { - "line": 56, + "line": 75, "column": 6 }, "end": { - "line": 56, + "line": 75, "column": 69 } } @@ -2473,15 +3161,15 @@ { "type": "CommentLine", "value": " Look for an empty Newick string.", - "start": 2171, - "end": 2206, + "start": 2621, + "end": 2656, "loc": { "start": { - "line": 54, + "line": 73, "column": 4 }, "end": { - "line": 54, + "line": 73, "column": 39 } } @@ -2491,15 +3179,15 @@ { "type": "CommentLine", "value": " Look for an unbalanced Newick string.", - "start": 2512, - "end": 2552, + "start": 2962, + "end": 3002, "loc": { "start": { - "line": 63, + "line": 82, "column": 4 }, "end": { - "line": 63, + "line": 82, "column": 44 } } @@ -2508,44 +3196,44 @@ }, { "type": "VariableDeclaration", - "start": 2557, - "end": 2577, + "start": 3007, + "end": 3027, "loc": { "start": { - "line": 64, + "line": 83, "column": 4 }, "end": { - "line": 64, + "line": 83, "column": 24 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2561, - "end": 2576, + "start": 3011, + "end": 3026, "loc": { "start": { - "line": 64, + "line": 83, "column": 8 }, "end": { - "line": 64, + "line": 83, "column": 23 } }, "id": { "type": "Identifier", - "start": 2561, - "end": 2572, + "start": 3011, + "end": 3022, "loc": { "start": { - "line": 64, + "line": 83, "column": 8 }, "end": { - "line": 64, + "line": 83, "column": 19 }, "identifierName": "parenLevels" @@ -2555,15 +3243,15 @@ }, "init": { "type": "NumericLiteral", - "start": 2575, - "end": 2576, + "start": 3025, + "end": 3026, "loc": { "start": { - "line": 64, + "line": 83, "column": 22 }, "end": { - "line": 64, + "line": 83, "column": 23 } }, @@ -2581,15 +3269,15 @@ { "type": "CommentLine", "value": " Look for an unbalanced Newick string.", - "start": 2512, - "end": 2552, + "start": 2962, + "end": 3002, "loc": { "start": { - "line": 63, + "line": 82, "column": 4 }, "end": { - "line": 63, + "line": 82, "column": 44 } } @@ -2598,58 +3286,58 @@ }, { "type": "ForStatement", - "start": 2582, - "end": 2747, + "start": 3032, + "end": 3197, "loc": { "start": { - "line": 65, + "line": 84, "column": 4 }, "end": { - "line": 68, + "line": 87, "column": 5 } }, "init": { "type": "VariableDeclaration", - "start": 2587, - "end": 2596, + "start": 3037, + "end": 3046, "loc": { "start": { - "line": 65, + "line": 84, "column": 9 }, "end": { - "line": 65, + "line": 84, "column": 18 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2591, - "end": 2596, + "start": 3041, + "end": 3046, "loc": { "start": { - "line": 65, + "line": 84, "column": 13 }, "end": { - "line": 65, + "line": 84, "column": 18 } }, "id": { "type": "Identifier", - "start": 2591, - "end": 2592, + "start": 3041, + "end": 3042, "loc": { "start": { - "line": 65, + "line": 84, "column": 13 }, "end": { - "line": 65, + "line": 84, "column": 14 }, "identifierName": "x" @@ -2658,15 +3346,15 @@ }, "init": { "type": "NumericLiteral", - "start": 2595, - "end": 2596, + "start": 3045, + "end": 3046, "loc": { "start": { - "line": 65, + "line": 84, "column": 17 }, "end": { - "line": 65, + "line": 84, "column": 18 } }, @@ -2682,29 +3370,29 @@ }, "test": { "type": "BinaryExpression", - "start": 2598, - "end": 2622, + "start": 3048, + "end": 3072, "loc": { "start": { - "line": 65, + "line": 84, "column": 20 }, "end": { - "line": 65, + "line": 84, "column": 44 } }, "left": { "type": "Identifier", - "start": 2598, - "end": 2599, + "start": 3048, + "end": 3049, "loc": { "start": { - "line": 65, + "line": 84, "column": 20 }, "end": { - "line": 65, + "line": 84, "column": 21 }, "identifierName": "x" @@ -2714,29 +3402,29 @@ "operator": "<", "right": { "type": "MemberExpression", - "start": 2602, - "end": 2622, + "start": 3052, + "end": 3072, "loc": { "start": { - "line": 65, + "line": 84, "column": 24 }, "end": { - "line": 65, + "line": 84, "column": 44 } }, "object": { "type": "Identifier", - "start": 2602, - "end": 2615, + "start": 3052, + "end": 3065, "loc": { "start": { - "line": 65, + "line": 84, "column": 24 }, "end": { - "line": 65, + "line": 84, "column": 37 }, "identifierName": "newickTrimmed" @@ -2745,15 +3433,15 @@ }, "property": { "type": "Identifier", - "start": 2616, - "end": 2622, + "start": 3066, + "end": 3072, "loc": { "start": { - "line": 65, + "line": 84, "column": 38 }, "end": { - "line": 65, + "line": 84, "column": 44 }, "identifierName": "length" @@ -2765,30 +3453,30 @@ }, "update": { "type": "AssignmentExpression", - "start": 2624, - "end": 2630, + "start": 3074, + "end": 3080, "loc": { "start": { - "line": 65, + "line": 84, "column": 46 }, "end": { - "line": 65, + "line": 84, "column": 52 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 2624, - "end": 2625, + "start": 3074, + "end": 3075, "loc": { "start": { - "line": 65, + "line": 84, "column": 46 }, "end": { - "line": 65, + "line": 84, "column": 47 }, "identifierName": "x" @@ -2797,15 +3485,15 @@ }, "right": { "type": "NumericLiteral", - "start": 2629, - "end": 2630, + "start": 3079, + "end": 3080, "loc": { "start": { - "line": 65, + "line": 84, "column": 51 }, "end": { - "line": 65, + "line": 84, "column": 52 } }, @@ -2818,72 +3506,72 @@ }, "body": { "type": "BlockStatement", - "start": 2632, - "end": 2747, + "start": 3082, + "end": 3197, "loc": { "start": { - "line": 65, + "line": 84, "column": 54 }, "end": { - "line": 68, + "line": 87, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 2640, - "end": 2687, + "start": 3090, + "end": 3137, "loc": { "start": { - "line": 66, + "line": 85, "column": 6 }, "end": { - "line": 66, + "line": 85, "column": 53 } }, "test": { "type": "BinaryExpression", - "start": 2644, - "end": 2668, + "start": 3094, + "end": 3118, "loc": { "start": { - "line": 66, + "line": 85, "column": 10 }, "end": { - "line": 66, + "line": 85, "column": 34 } }, "left": { "type": "MemberExpression", - "start": 2644, - "end": 2660, + "start": 3094, + "end": 3110, "loc": { "start": { - "line": 66, + "line": 85, "column": 10 }, "end": { - "line": 66, + "line": 85, "column": 26 } }, "object": { "type": "Identifier", - "start": 2644, - "end": 2657, + "start": 3094, + "end": 3107, "loc": { "start": { - "line": 66, + "line": 85, "column": 10 }, "end": { - "line": 66, + "line": 85, "column": 23 }, "identifierName": "newickTrimmed" @@ -2892,15 +3580,15 @@ }, "property": { "type": "Identifier", - "start": 2658, - "end": 2659, + "start": 3108, + "end": 3109, "loc": { "start": { - "line": 66, + "line": 85, "column": 24 }, "end": { - "line": 66, + "line": 85, "column": 25 }, "identifierName": "x" @@ -2912,15 +3600,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 2665, - "end": 2668, + "start": 3115, + "end": 3118, "loc": { "start": { - "line": 66, + "line": 85, "column": 31 }, "end": { - "line": 66, + "line": 85, "column": 34 } }, @@ -2933,44 +3621,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 2670, - "end": 2687, + "start": 3120, + "end": 3137, "loc": { "start": { - "line": 66, + "line": 85, "column": 36 }, "end": { - "line": 66, + "line": 85, "column": 53 } }, "expression": { "type": "AssignmentExpression", - "start": 2670, - "end": 2686, + "start": 3120, + "end": 3136, "loc": { "start": { - "line": 66, + "line": 85, "column": 36 }, "end": { - "line": 66, + "line": 85, "column": 52 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 2670, - "end": 2681, + "start": 3120, + "end": 3131, "loc": { "start": { - "line": 66, + "line": 85, "column": 36 }, "end": { - "line": 66, + "line": 85, "column": 47 }, "identifierName": "parenLevels" @@ -2979,15 +3667,15 @@ }, "right": { "type": "NumericLiteral", - "start": 2685, - "end": 2686, + "start": 3135, + "end": 3136, "loc": { "start": { - "line": 66, + "line": 85, "column": 51 }, "end": { - "line": 66, + "line": 85, "column": 52 } }, @@ -3003,57 +3691,57 @@ }, { "type": "IfStatement", - "start": 2694, - "end": 2741, + "start": 3144, + "end": 3191, "loc": { "start": { - "line": 67, + "line": 86, "column": 6 }, "end": { - "line": 67, + "line": 86, "column": 53 } }, "test": { "type": "BinaryExpression", - "start": 2698, - "end": 2722, + "start": 3148, + "end": 3172, "loc": { "start": { - "line": 67, + "line": 86, "column": 10 }, "end": { - "line": 67, + "line": 86, "column": 34 } }, "left": { "type": "MemberExpression", - "start": 2698, - "end": 2714, + "start": 3148, + "end": 3164, "loc": { "start": { - "line": 67, + "line": 86, "column": 10 }, "end": { - "line": 67, + "line": 86, "column": 26 } }, "object": { "type": "Identifier", - "start": 2698, - "end": 2711, + "start": 3148, + "end": 3161, "loc": { "start": { - "line": 67, + "line": 86, "column": 10 }, "end": { - "line": 67, + "line": 86, "column": 23 }, "identifierName": "newickTrimmed" @@ -3062,15 +3750,15 @@ }, "property": { "type": "Identifier", - "start": 2712, - "end": 2713, + "start": 3162, + "end": 3163, "loc": { "start": { - "line": 67, + "line": 86, "column": 24 }, "end": { - "line": 67, + "line": 86, "column": 25 }, "identifierName": "x" @@ -3082,15 +3770,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 2719, - "end": 2722, + "start": 3169, + "end": 3172, "loc": { "start": { - "line": 67, + "line": 86, "column": 31 }, "end": { - "line": 67, + "line": 86, "column": 34 } }, @@ -3103,44 +3791,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 2724, - "end": 2741, + "start": 3174, + "end": 3191, "loc": { "start": { - "line": 67, + "line": 86, "column": 36 }, "end": { - "line": 67, + "line": 86, "column": 53 } }, "expression": { "type": "AssignmentExpression", - "start": 2724, - "end": 2740, + "start": 3174, + "end": 3190, "loc": { "start": { - "line": 67, + "line": 86, "column": 36 }, "end": { - "line": 67, + "line": 86, "column": 52 } }, "operator": "-=", "left": { "type": "Identifier", - "start": 2724, - "end": 2735, + "start": 3174, + "end": 3185, "loc": { "start": { - "line": 67, + "line": 86, "column": 36 }, "end": { - "line": 67, + "line": 86, "column": 47 }, "identifierName": "parenLevels" @@ -3149,15 +3837,15 @@ }, "right": { "type": "NumericLiteral", - "start": 2739, - "end": 2740, + "start": 3189, + "end": 3190, "loc": { "start": { - "line": 67, + "line": 86, "column": 51 }, "end": { - "line": 67, + "line": 86, "column": 52 } }, @@ -3177,43 +3865,43 @@ }, { "type": "IfStatement", - "start": 2753, - "end": 3044, + "start": 3203, + "end": 3494, "loc": { "start": { - "line": 70, + "line": 89, "column": 4 }, "end": { - "line": 78, + "line": 97, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 2757, - "end": 2774, + "start": 3207, + "end": 3224, "loc": { "start": { - "line": 70, + "line": 89, "column": 8 }, "end": { - "line": 70, + "line": 89, "column": 25 } }, "left": { "type": "Identifier", - "start": 2757, - "end": 2768, + "start": 3207, + "end": 3218, "loc": { "start": { - "line": 70, + "line": 89, "column": 8 }, "end": { - "line": 70, + "line": 89, "column": 19 }, "identifierName": "parenLevels" @@ -3223,15 +3911,15 @@ "operator": "!==", "right": { "type": "NumericLiteral", - "start": 2773, - "end": 2774, + "start": 3223, + "end": 3224, "loc": { "start": { - "line": 70, + "line": 89, "column": 24 }, "end": { - "line": 70, + "line": 89, "column": 25 } }, @@ -3244,72 +3932,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 2776, - "end": 3044, + "start": 3226, + "end": 3494, "loc": { "start": { - "line": 70, + "line": 89, "column": 27 }, "end": { - "line": 78, + "line": 97, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2784, - "end": 3038, + "start": 3234, + "end": 3488, "loc": { "start": { - "line": 71, + "line": 90, "column": 6 }, "end": { - "line": 77, + "line": 96, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 2784, - "end": 3037, + "start": 3234, + "end": 3487, "loc": { "start": { - "line": 71, + "line": 90, "column": 6 }, "end": { - "line": 77, + "line": 96, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 2784, - "end": 2795, + "start": 3234, + "end": 3245, "loc": { "start": { - "line": 71, + "line": 90, "column": 6 }, "end": { - "line": 71, + "line": 90, "column": 17 } }, "object": { "type": "Identifier", - "start": 2784, - "end": 2790, + "start": 3234, + "end": 3240, "loc": { "start": { - "line": 71, + "line": 90, "column": 6 }, "end": { - "line": 71, + "line": 90, "column": 12 }, "identifierName": "errors" @@ -3318,15 +4006,15 @@ }, "property": { "type": "Identifier", - "start": 2791, - "end": 2795, + "start": 3241, + "end": 3245, "loc": { "start": { - "line": 71, + "line": 90, "column": 13 }, "end": { - "line": 71, + "line": 90, "column": 17 }, "identifierName": "push" @@ -3338,30 +4026,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 2796, - "end": 3036, + "start": 3246, + "end": 3486, "loc": { "start": { - "line": 71, + "line": 90, "column": 18 }, "end": { - "line": 77, + "line": 96, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 2806, - "end": 2854, + "start": 3256, + "end": 3304, "loc": { "start": { - "line": 72, + "line": 91, "column": 8 }, "end": { - "line": 72, + "line": 91, "column": 56 } }, @@ -3370,15 +4058,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2806, - "end": 2811, + "start": 3256, + "end": 3261, "loc": { "start": { - "line": 72, + "line": 91, "column": 8 }, "end": { - "line": 72, + "line": 91, "column": 13 }, "identifierName": "title" @@ -3387,15 +4075,15 @@ }, "value": { "type": "StringLiteral", - "start": 2813, - "end": 2854, + "start": 3263, + "end": 3304, "loc": { "start": { - "line": 72, + "line": 91, "column": 15 }, "end": { - "line": 72, + "line": 91, "column": 56 } }, @@ -3408,15 +4096,15 @@ }, { "type": "ObjectProperty", - "start": 2864, - "end": 3027, + "start": 3314, + "end": 3477, "loc": { "start": { - "line": 73, + "line": 92, "column": 8 }, "end": { - "line": 76, + "line": 95, "column": 9 } }, @@ -3425,15 +4113,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2864, - "end": 2871, + "start": 3314, + "end": 3321, "loc": { "start": { - "line": 73, + "line": 92, "column": 8 }, "end": { - "line": 73, + "line": 92, "column": 15 }, "identifierName": "message" @@ -3442,43 +4130,43 @@ }, "value": { "type": "ConditionalExpression", - "start": 2874, - "end": 3017, + "start": 3324, + "end": 3467, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 75, + "line": 94, "column": 63 } }, "test": { "type": "BinaryExpression", - "start": 2874, - "end": 2889, + "start": 3324, + "end": 3339, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 73, + "line": 92, "column": 33 } }, "left": { "type": "Identifier", - "start": 2874, - "end": 2885, + "start": 3324, + "end": 3335, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 73, + "line": 92, "column": 29 }, "identifierName": "parenLevels" @@ -3488,15 +4176,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 2888, - "end": 2889, + "start": 3338, + "end": 3339, "loc": { "start": { - "line": 73, + "line": 92, "column": 32 }, "end": { - "line": 73, + "line": 92, "column": 33 } }, @@ -3509,30 +4197,30 @@ }, "consequent": { "type": "TemplateLiteral", - "start": 2902, - "end": 2953, + "start": 3352, + "end": 3403, "loc": { "start": { - "line": 74, + "line": 93, "column": 12 }, "end": { - "line": 74, + "line": 93, "column": 63 } }, "expressions": [ { "type": "Identifier", - "start": 2914, - "end": 2925, + "start": 3364, + "end": 3375, "loc": { "start": { - "line": 74, + "line": 93, "column": 24 }, "end": { - "line": 74, + "line": 93, "column": 35 }, "identifierName": "parenLevels" @@ -3543,15 +4231,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 2903, - "end": 2912, + "start": 3353, + "end": 3362, "loc": { "start": { - "line": 74, + "line": 93, "column": 13 }, "end": { - "line": 74, + "line": 93, "column": 22 } }, @@ -3563,15 +4251,15 @@ }, { "type": "TemplateElement", - "start": 2926, - "end": 2952, + "start": 3376, + "end": 3402, "loc": { "start": { - "line": 74, + "line": 93, "column": 36 }, "end": { - "line": 74, + "line": 93, "column": 62 } }, @@ -3585,30 +4273,30 @@ }, "alternate": { "type": "TemplateLiteral", - "start": 2966, - "end": 3017, + "start": 3416, + "end": 3467, "loc": { "start": { - "line": 75, + "line": 94, "column": 12 }, "end": { - "line": 75, + "line": 94, "column": 63 } }, "expressions": [ { "type": "UnaryExpression", - "start": 2978, - "end": 2990, + "start": 3428, + "end": 3440, "loc": { "start": { - "line": 75, + "line": 94, "column": 24 }, "end": { - "line": 75, + "line": 94, "column": 36 } }, @@ -3616,15 +4304,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 2979, - "end": 2990, + "start": 3429, + "end": 3440, "loc": { "start": { - "line": 75, + "line": 94, "column": 25 }, "end": { - "line": 75, + "line": 94, "column": 36 }, "identifierName": "parenLevels" @@ -3639,15 +4327,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 2967, - "end": 2976, + "start": 3417, + "end": 3426, "loc": { "start": { - "line": 75, + "line": 94, "column": 13 }, "end": { - "line": 75, + "line": 94, "column": 22 } }, @@ -3659,15 +4347,15 @@ }, { "type": "TemplateElement", - "start": 2991, - "end": 3016, + "start": 3441, + "end": 3466, "loc": { "start": { - "line": 75, + "line": 94, "column": 37 }, "end": { - "line": 75, + "line": 94, "column": 62 } }, @@ -3681,7 +4369,7 @@ }, "extra": { "parenthesized": true, - "parenStart": 2873 + "parenStart": 3323 } } } @@ -3699,15 +4387,15 @@ { "type": "CommentLine", "value": " Finally, try parsing it with newickJs.parse() and see if we get an error.", - "start": 3050, - "end": 3126, + "start": 3500, + "end": 3576, "loc": { "start": { - "line": 80, + "line": 99, "column": 4 }, "end": { - "line": 80, + "line": 99, "column": 80 } } @@ -3716,86 +4404,86 @@ }, { "type": "TryStatement", - "start": 3131, - "end": 3351, + "start": 3581, + "end": 3801, "loc": { "start": { - "line": 81, + "line": 100, "column": 4 }, "end": { - "line": 88, + "line": 107, "column": 5 } }, "block": { "type": "BlockStatement", - "start": 3135, - "end": 3179, + "start": 3585, + "end": 3629, "loc": { "start": { - "line": 81, + "line": 100, "column": 8 }, "end": { - "line": 83, + "line": 102, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3143, - "end": 3173, + "start": 3593, + "end": 3623, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 36 } }, "expression": { "type": "CallExpression", - "start": 3143, - "end": 3172, + "start": 3593, + "end": 3622, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 3143, - "end": 3157, + "start": 3593, + "end": 3607, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 20 } }, "object": { "type": "Identifier", - "start": 3143, - "end": 3151, + "start": 3593, + "end": 3601, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 14 }, "identifierName": "newickJs" @@ -3805,15 +4493,15 @@ }, "property": { "type": "Identifier", - "start": 3152, - "end": 3157, + "start": 3602, + "end": 3607, "loc": { "start": { - "line": 82, + "line": 101, "column": 15 }, "end": { - "line": 82, + "line": 101, "column": 20 }, "identifierName": "parse" @@ -3826,15 +4514,15 @@ "arguments": [ { "type": "Identifier", - "start": 3158, - "end": 3171, + "start": 3608, + "end": 3621, "loc": { "start": { - "line": 82, + "line": 101, "column": 21 }, "end": { - "line": 82, + "line": 101, "column": 34 }, "identifierName": "newickTrimmed" @@ -3852,29 +4540,29 @@ }, "handler": { "type": "CatchClause", - "start": 3180, - "end": 3351, + "start": 3630, + "end": 3801, "loc": { "start": { - "line": 83, + "line": 102, "column": 6 }, "end": { - "line": 88, + "line": 107, "column": 5 } }, "param": { "type": "Identifier", - "start": 3187, - "end": 3189, + "start": 3637, + "end": 3639, "loc": { "start": { - "line": 83, + "line": 102, "column": 13 }, "end": { - "line": 83, + "line": 102, "column": 15 }, "identifierName": "ex" @@ -3883,72 +4571,72 @@ }, "body": { "type": "BlockStatement", - "start": 3191, - "end": 3351, + "start": 3641, + "end": 3801, "loc": { "start": { - "line": 83, + "line": 102, "column": 17 }, "end": { - "line": 88, + "line": 107, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3199, - "end": 3345, + "start": 3649, + "end": 3795, "loc": { "start": { - "line": 84, + "line": 103, "column": 6 }, "end": { - "line": 87, + "line": 106, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 3199, - "end": 3344, + "start": 3649, + "end": 3794, "loc": { "start": { - "line": 84, + "line": 103, "column": 6 }, "end": { - "line": 87, + "line": 106, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 3199, - "end": 3210, + "start": 3649, + "end": 3660, "loc": { "start": { - "line": 84, + "line": 103, "column": 6 }, "end": { - "line": 84, + "line": 103, "column": 17 } }, "object": { "type": "Identifier", - "start": 3199, - "end": 3205, + "start": 3649, + "end": 3655, "loc": { "start": { - "line": 84, + "line": 103, "column": 6 }, "end": { - "line": 84, + "line": 103, "column": 12 }, "identifierName": "errors" @@ -3957,15 +4645,15 @@ }, "property": { "type": "Identifier", - "start": 3206, - "end": 3210, + "start": 3656, + "end": 3660, "loc": { "start": { - "line": 84, + "line": 103, "column": 13 }, "end": { - "line": 84, + "line": 103, "column": 17 }, "identifierName": "push" @@ -3977,30 +4665,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 3211, - "end": 3343, + "start": 3661, + "end": 3793, "loc": { "start": { - "line": 84, + "line": 103, "column": 18 }, "end": { - "line": 87, + "line": 106, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 3221, - "end": 3253, + "start": 3671, + "end": 3703, "loc": { "start": { - "line": 85, + "line": 104, "column": 8 }, "end": { - "line": 85, + "line": 104, "column": 40 } }, @@ -4009,15 +4697,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3221, - "end": 3226, + "start": 3671, + "end": 3676, "loc": { "start": { - "line": 85, + "line": 104, "column": 8 }, "end": { - "line": 85, + "line": 104, "column": 13 }, "identifierName": "title" @@ -4026,15 +4714,15 @@ }, "value": { "type": "StringLiteral", - "start": 3228, - "end": 3253, + "start": 3678, + "end": 3703, "loc": { "start": { - "line": 85, + "line": 104, "column": 15 }, "end": { - "line": 85, + "line": 104, "column": 40 } }, @@ -4047,15 +4735,15 @@ }, { "type": "ObjectProperty", - "start": 3263, - "end": 3334, + "start": 3713, + "end": 3784, "loc": { "start": { - "line": 86, + "line": 105, "column": 8 }, "end": { - "line": 86, + "line": 105, "column": 79 } }, @@ -4064,15 +4752,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3263, - "end": 3270, + "start": 3713, + "end": 3720, "loc": { "start": { - "line": 86, + "line": 105, "column": 8 }, "end": { - "line": 86, + "line": 105, "column": 15 }, "identifierName": "message" @@ -4081,44 +4769,44 @@ }, "value": { "type": "TemplateLiteral", - "start": 3272, - "end": 3334, + "start": 3722, + "end": 3784, "loc": { "start": { - "line": 86, + "line": 105, "column": 17 }, "end": { - "line": 86, + "line": 105, "column": 79 } }, "expressions": [ { "type": "MemberExpression", - "start": 3322, - "end": 3332, + "start": 3772, + "end": 3782, "loc": { "start": { - "line": 86, + "line": 105, "column": 67 }, "end": { - "line": 86, + "line": 105, "column": 77 } }, "object": { "type": "Identifier", - "start": 3322, - "end": 3324, + "start": 3772, + "end": 3774, "loc": { "start": { - "line": 86, + "line": 105, "column": 67 }, "end": { - "line": 86, + "line": 105, "column": 69 }, "identifierName": "ex" @@ -4127,15 +4815,15 @@ }, "property": { "type": "Identifier", - "start": 3325, - "end": 3332, + "start": 3775, + "end": 3782, "loc": { "start": { - "line": 86, + "line": 105, "column": 70 }, "end": { - "line": 86, + "line": 105, "column": 77 }, "identifierName": "message" @@ -4148,15 +4836,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 3273, - "end": 3320, + "start": 3723, + "end": 3770, "loc": { "start": { - "line": 86, + "line": 105, "column": 18 }, "end": { - "line": 86, + "line": 105, "column": 65 } }, @@ -4168,15 +4856,15 @@ }, { "type": "TemplateElement", - "start": 3333, - "end": 3333, + "start": 3783, + "end": 3783, "loc": { "start": { - "line": 86, + "line": 105, "column": 78 }, "end": { - "line": 86, + "line": 105, "column": 78 } }, @@ -4204,15 +4892,15 @@ { "type": "CommentLine", "value": " Finally, try parsing it with newickJs.parse() and see if we get an error.", - "start": 3050, - "end": 3126, + "start": 3500, + "end": 3576, "loc": { "start": { - "line": 80, + "line": 99, "column": 4 }, "end": { - "line": 80, + "line": 99, "column": 80 } } @@ -4221,29 +4909,29 @@ }, { "type": "ReturnStatement", - "start": 3357, - "end": 3371, + "start": 3807, + "end": 3821, "loc": { "start": { - "line": 90, + "line": 109, "column": 4 }, "end": { - "line": 90, + "line": 109, "column": 18 } }, "argument": { "type": "Identifier", - "start": 3364, - "end": 3370, + "start": 3814, + "end": 3820, "loc": { "start": { - "line": 90, + "line": 109, "column": 11 }, "end": { - "line": 90, + "line": 109, "column": 17 }, "identifierName": "errors" @@ -4257,15 +4945,15 @@ }, { "type": "ClassMethod", - "start": 3379, - "end": 4831, + "start": 3829, + "end": 5281, "loc": { "start": { - "line": 93, + "line": 112, "column": 2 }, "end": { - "line": 125, + "line": 144, "column": 3 } }, @@ -4273,15 +4961,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3386, - "end": 3398, + "start": 3836, + "end": 3848, "loc": { "start": { - "line": 93, + "line": 112, "column": 9 }, "end": { - "line": 93, + "line": 112, "column": 21 }, "identifierName": "recurseNodes" @@ -4296,15 +4984,15 @@ "params": [ { "type": "Identifier", - "start": 3399, - "end": 3403, + "start": 3849, + "end": 3853, "loc": { "start": { - "line": 93, + "line": 112, "column": 22 }, "end": { - "line": 93, + "line": 112, "column": 26 }, "identifierName": "node" @@ -4313,15 +5001,15 @@ }, { "type": "Identifier", - "start": 3405, - "end": 3409, + "start": 3855, + "end": 3859, "loc": { "start": { - "line": 93, + "line": 112, "column": 28 }, "end": { - "line": 93, + "line": 112, "column": 32 }, "identifierName": "func" @@ -4330,29 +5018,29 @@ }, { "type": "AssignmentPattern", - "start": 3411, - "end": 3424, + "start": 3861, + "end": 3874, "loc": { "start": { - "line": 93, + "line": 112, "column": 34 }, "end": { - "line": 93, + "line": 112, "column": 47 } }, "left": { "type": "Identifier", - "start": 3411, - "end": 3420, + "start": 3861, + "end": 3870, "loc": { "start": { - "line": 93, + "line": 112, "column": 34 }, "end": { - "line": 93, + "line": 112, "column": 43 }, "identifierName": "nodeCount" @@ -4361,15 +5049,15 @@ }, "right": { "type": "NumericLiteral", - "start": 3423, - "end": 3424, + "start": 3873, + "end": 3874, "loc": { "start": { - "line": 93, + "line": 112, "column": 46 }, "end": { - "line": 93, + "line": 112, "column": 47 } }, @@ -4382,29 +5070,29 @@ }, { "type": "AssignmentPattern", - "start": 3426, - "end": 3449, + "start": 3876, + "end": 3899, "loc": { "start": { - "line": 93, + "line": 112, "column": 49 }, "end": { - "line": 93, + "line": 112, "column": 72 } }, "left": { "type": "Identifier", - "start": 3426, - "end": 3437, + "start": 3876, + "end": 3887, "loc": { "start": { - "line": 93, + "line": 112, "column": 49 }, "end": { - "line": 93, + "line": 112, "column": 60 }, "identifierName": "parentCount" @@ -4413,15 +5101,15 @@ }, "right": { "type": "Identifier", - "start": 3440, - "end": 3449, + "start": 3890, + "end": 3899, "loc": { "start": { - "line": 93, + "line": 112, "column": 63 }, "end": { - "line": 93, + "line": 112, "column": 72 }, "identifierName": "undefined" @@ -4432,58 +5120,58 @@ ], "body": { "type": "BlockStatement", - "start": 3451, - "end": 4831, + "start": 3901, + "end": 5281, "loc": { "start": { - "line": 93, + "line": 112, "column": 74 }, "end": { - "line": 125, + "line": 144, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 4468, - "end": 4503, + "start": 4918, + "end": 4953, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 39 } }, "expression": { "type": "CallExpression", - "start": 4468, - "end": 4502, + "start": 4918, + "end": 4952, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 38 } }, "callee": { "type": "Identifier", - "start": 4468, - "end": 4472, + "start": 4918, + "end": 4922, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 8 }, "identifierName": "func" @@ -4494,15 +5182,15 @@ "arguments": [ { "type": "Identifier", - "start": 4473, - "end": 4477, + "start": 4923, + "end": 4927, "loc": { "start": { - "line": 108, + "line": 127, "column": 9 }, "end": { - "line": 108, + "line": 127, "column": 13 }, "identifierName": "node" @@ -4511,15 +5199,15 @@ }, { "type": "Identifier", - "start": 4479, - "end": 4488, + "start": 4929, + "end": 4938, "loc": { "start": { - "line": 108, + "line": 127, "column": 15 }, "end": { - "line": 108, + "line": 127, "column": 24 }, "identifierName": "nodeCount" @@ -4528,15 +5216,15 @@ }, { "type": "Identifier", - "start": 4490, - "end": 4501, + "start": 4940, + "end": 4951, "loc": { "start": { - "line": 108, + "line": 127, "column": 26 }, "end": { - "line": 108, + "line": 127, "column": 37 }, "identifierName": "parentCount" @@ -4550,15 +5238,15 @@ { "type": "CommentLine", "value": " Recurse through PhyloTree nodes, executing function on each node.", - "start": 3457, - "end": 3525, + "start": 3907, + "end": 3975, "loc": { "start": { - "line": 94, + "line": 113, "column": 4 }, "end": { - "line": 94, + "line": 113, "column": 72 } } @@ -4566,15 +5254,15 @@ { "type": "CommentLine", "value": " - node: The node to recurse from. The function will be called on node", - "start": 3530, - "end": 3603, + "start": 3980, + "end": 4053, "loc": { "start": { - "line": 95, + "line": 114, "column": 4 }, "end": { - "line": 95, + "line": 114, "column": 77 } } @@ -4582,15 +5270,15 @@ { "type": "CommentLine", "value": " *before* being called on its children.", - "start": 3608, - "end": 3658, + "start": 4058, + "end": 4108, "loc": { "start": { - "line": 96, + "line": 115, "column": 4 }, "end": { - "line": 96, + "line": 115, "column": 54 } } @@ -4598,15 +5286,15 @@ { "type": "CommentLine", "value": " - func: The function to call on `node` and all of its children.", - "start": 3663, - "end": 3730, + "start": 4113, + "end": 4180, "loc": { "start": { - "line": 97, + "line": 116, "column": 4 }, "end": { - "line": 97, + "line": 116, "column": 71 } } @@ -4614,15 +5302,15 @@ { "type": "CommentLine", "value": " - nodeCount: `node` will be called with this nodeCount. All of its", - "start": 3735, - "end": 3805, + "start": 4185, + "end": 4255, "loc": { "start": { - "line": 98, + "line": 117, "column": 4 }, "end": { - "line": 98, + "line": 117, "column": 74 } } @@ -4630,15 +5318,15 @@ { "type": "CommentLine", "value": " children will be called with consecutively increasing nodeCounts.", - "start": 3810, - "end": 3887, + "start": 4260, + "end": 4337, "loc": { "start": { - "line": 99, + "line": 118, "column": 4 }, "end": { - "line": 99, + "line": 118, "column": 81 } } @@ -4646,15 +5334,15 @@ { "type": "CommentLine", "value": " - parentCount: The nodeCount associated with the parent of this node", - "start": 3892, - "end": 3964, + "start": 4342, + "end": 4414, "loc": { "start": { - "line": 100, + "line": 119, "column": 4 }, "end": { - "line": 100, + "line": 119, "column": 76 } } @@ -4662,15 +5350,15 @@ { "type": "CommentLine", "value": " within this run of recurseNodes. For instance, immediate children", - "start": 3969, - "end": 4046, + "start": 4419, + "end": 4496, "loc": { "start": { - "line": 101, + "line": 120, "column": 4 }, "end": { - "line": 101, + "line": 120, "column": 81 } } @@ -4678,15 +5366,15 @@ { "type": "CommentLine", "value": " of `node` will have a parentCount of 0. By default, `node` itself", - "start": 4051, - "end": 4128, + "start": 4501, + "end": 4578, "loc": { "start": { - "line": 102, + "line": 121, "column": 4 }, "end": { - "line": 102, + "line": 121, "column": 81 } } @@ -4694,15 +5382,15 @@ { "type": "CommentLine", "value": " will have a parentCount of `undefined`.", - "start": 4133, - "end": 4184, + "start": 4583, + "end": 4634, "loc": { "start": { - "line": 103, + "line": 122, "column": 4 }, "end": { - "line": 103, + "line": 122, "column": 55 } } @@ -4710,15 +5398,15 @@ { "type": "CommentLine", "value": " When the function `func` is called, it is given three arguments:", - "start": 4189, - "end": 4256, + "start": 4639, + "end": 4706, "loc": { "start": { - "line": 104, + "line": 123, "column": 4 }, "end": { - "line": 104, + "line": 123, "column": 71 } } @@ -4726,15 +5414,15 @@ { "type": "CommentLine", "value": " - The current node object (initially: `node`)", - "start": 4261, - "end": 4310, + "start": 4711, + "end": 4760, "loc": { "start": { - "line": 105, + "line": 124, "column": 4 }, "end": { - "line": 105, + "line": 124, "column": 53 } } @@ -4742,15 +5430,15 @@ { "type": "CommentLine", "value": " - The count of the current node object (initially: `nodeCount`)", - "start": 4315, - "end": 4382, + "start": 4765, + "end": 4832, "loc": { "start": { - "line": 106, + "line": 125, "column": 4 }, "end": { - "line": 106, + "line": 125, "column": 71 } } @@ -4758,15 +5446,15 @@ { "type": "CommentLine", "value": " - The parent count of the current node object (initially: `parentCount`)", - "start": 4387, - "end": 4463, + "start": 4837, + "end": 4913, "loc": { "start": { - "line": 107, + "line": 126, "column": 4 }, "end": { - "line": 107, + "line": 126, "column": 80 } } @@ -4775,44 +5463,44 @@ }, { "type": "VariableDeclaration", - "start": 4509, - "end": 4536, + "start": 4959, + "end": 4986, "loc": { "start": { - "line": 110, + "line": 129, "column": 4 }, "end": { - "line": 110, + "line": 129, "column": 31 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4513, - "end": 4535, + "start": 4963, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 8 }, "end": { - "line": 110, + "line": 129, "column": 30 } }, "id": { "type": "Identifier", - "start": 4513, - "end": 4519, + "start": 4963, + "end": 4969, "loc": { "start": { - "line": 110, + "line": 129, "column": 8 }, "end": { - "line": 110, + "line": 129, "column": 14 }, "identifierName": "nextID" @@ -4821,29 +5509,29 @@ }, "init": { "type": "BinaryExpression", - "start": 4522, - "end": 4535, + "start": 4972, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 17 }, "end": { - "line": 110, + "line": 129, "column": 30 } }, "left": { "type": "Identifier", - "start": 4522, - "end": 4531, + "start": 4972, + "end": 4981, "loc": { "start": { - "line": 110, + "line": 129, "column": 17 }, "end": { - "line": 110, + "line": 129, "column": 26 }, "identifierName": "nodeCount" @@ -4853,15 +5541,15 @@ "operator": "+", "right": { "type": "NumericLiteral", - "start": 4534, - "end": 4535, + "start": 4984, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 29 }, "end": { - "line": 110, + "line": 129, "column": 30 } }, @@ -4879,15 +5567,15 @@ { "type": "CommentLine", "value": " Recurse through all children of this node.", - "start": 4542, - "end": 4587, + "start": 4992, + "end": 5037, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 49 } } @@ -4896,43 +5584,43 @@ }, { "type": "IfStatement", - "start": 4592, - "end": 4807, + "start": 5042, + "end": 5257, "loc": { "start": { - "line": 113, + "line": 132, "column": 4 }, "end": { - "line": 122, + "line": 141, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4596, - "end": 4617, + "start": 5046, + "end": 5067, "loc": { "start": { - "line": 113, + "line": 132, "column": 8 }, "end": { - "line": 113, + "line": 132, "column": 29 } }, "callee": { "type": "Identifier", - "start": 4596, - "end": 4599, + "start": 5046, + "end": 5049, "loc": { "start": { - "line": 113, + "line": 132, "column": 8 }, "end": { - "line": 113, + "line": 132, "column": 11 }, "identifierName": "has" @@ -4943,15 +5631,15 @@ "arguments": [ { "type": "Identifier", - "start": 4600, - "end": 4604, + "start": 5050, + "end": 5054, "loc": { "start": { - "line": 113, + "line": 132, "column": 12 }, "end": { - "line": 113, + "line": 132, "column": 16 }, "identifierName": "node" @@ -4960,15 +5648,15 @@ }, { "type": "StringLiteral", - "start": 4606, - "end": 4616, + "start": 5056, + "end": 5066, "loc": { "start": { - "line": 113, + "line": 132, "column": 18 }, "end": { - "line": 113, + "line": 132, "column": 28 } }, @@ -4983,86 +5671,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 4619, - "end": 4807, + "start": 5069, + "end": 5257, "loc": { "start": { - "line": 113, + "line": 132, "column": 31 }, "end": { - "line": 122, + "line": 141, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 4627, - "end": 4801, + "start": 5077, + "end": 5251, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 121, + "line": 140, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 4627, - "end": 4800, + "start": 5077, + "end": 5250, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 121, + "line": 140, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 4627, - "end": 4648, + "start": 5077, + "end": 5098, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 27 } }, "object": { "type": "MemberExpression", - "start": 4627, - "end": 4640, + "start": 5077, + "end": 5090, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 19 } }, "object": { "type": "Identifier", - "start": 4627, - "end": 4631, + "start": 5077, + "end": 5081, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 10 }, "identifierName": "node" @@ -5071,15 +5759,15 @@ }, "property": { "type": "Identifier", - "start": 4632, - "end": 4640, + "start": 5082, + "end": 5090, "loc": { "start": { - "line": 114, + "line": 133, "column": 11 }, "end": { - "line": 114, + "line": 133, "column": 19 }, "identifierName": "children" @@ -5090,15 +5778,15 @@ }, "property": { "type": "Identifier", - "start": 4641, - "end": 4648, + "start": 5091, + "end": 5098, "loc": { "start": { - "line": 114, + "line": 133, "column": 20 }, "end": { - "line": 114, + "line": 133, "column": 27 }, "identifierName": "forEach" @@ -5110,15 +5798,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 4649, - "end": 4799, + "start": 5099, + "end": 5249, "loc": { "start": { - "line": 114, + "line": 133, "column": 28 }, "end": { - "line": 121, + "line": 140, "column": 7 } }, @@ -5129,15 +5817,15 @@ "params": [ { "type": "Identifier", - "start": 4650, - "end": 4655, + "start": 5100, + "end": 5105, "loc": { "start": { - "line": 114, + "line": 133, "column": 29 }, "end": { - "line": 114, + "line": 133, "column": 34 }, "identifierName": "child" @@ -5147,59 +5835,59 @@ ], "body": { "type": "BlockStatement", - "start": 4660, - "end": 4799, + "start": 5110, + "end": 5249, "loc": { "start": { - "line": 114, + "line": 133, "column": 39 }, "end": { - "line": 121, + "line": 140, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 4670, - "end": 4791, + "start": 5120, + "end": 5241, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 4670, - "end": 4790, + "start": 5120, + "end": 5240, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 4670, - "end": 4676, + "start": 5120, + "end": 5126, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 14 }, "identifierName": "nextID" @@ -5208,43 +5896,43 @@ }, "right": { "type": "CallExpression", - "start": 4679, - "end": 4790, + "start": 5129, + "end": 5240, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 120, + "line": 139, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 4679, - "end": 4708, + "start": 5129, + "end": 5158, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 115, + "line": 134, "column": 46 } }, "object": { "type": "Identifier", - "start": 4679, - "end": 4695, + "start": 5129, + "end": 5145, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 115, + "line": 134, "column": 33 }, "identifierName": "PhylogenyWrapper" @@ -5253,15 +5941,15 @@ }, "property": { "type": "Identifier", - "start": 4696, - "end": 4708, + "start": 5146, + "end": 5158, "loc": { "start": { - "line": 115, + "line": 134, "column": 34 }, "end": { - "line": 115, + "line": 134, "column": 46 }, "identifierName": "recurseNodes" @@ -5273,15 +5961,15 @@ "arguments": [ { "type": "Identifier", - "start": 4720, - "end": 4725, + "start": 5170, + "end": 5175, "loc": { "start": { - "line": 116, + "line": 135, "column": 10 }, "end": { - "line": 116, + "line": 135, "column": 15 }, "identifierName": "child" @@ -5290,15 +5978,15 @@ }, { "type": "Identifier", - "start": 4737, - "end": 4741, + "start": 5187, + "end": 5191, "loc": { "start": { - "line": 117, + "line": 136, "column": 10 }, "end": { - "line": 117, + "line": 136, "column": 14 }, "identifierName": "func" @@ -5307,15 +5995,15 @@ }, { "type": "Identifier", - "start": 4753, - "end": 4759, + "start": 5203, + "end": 5209, "loc": { "start": { - "line": 118, + "line": 137, "column": 10 }, "end": { - "line": 118, + "line": 137, "column": 16 }, "identifierName": "nextID" @@ -5324,15 +6012,15 @@ }, { "type": "Identifier", - "start": 4771, - "end": 4780, + "start": 5221, + "end": 5230, "loc": { "start": { - "line": 119, + "line": 138, "column": 10 }, "end": { - "line": 119, + "line": 138, "column": 19 }, "identifierName": "nodeCount" @@ -5358,15 +6046,15 @@ { "type": "CommentLine", "value": " Recurse through all children of this node.", - "start": 4542, - "end": 4587, + "start": 4992, + "end": 5037, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 49 } } @@ -5375,29 +6063,29 @@ }, { "type": "ReturnStatement", - "start": 4813, - "end": 4827, + "start": 5263, + "end": 5277, "loc": { "start": { - "line": 124, + "line": 143, "column": 4 }, "end": { - "line": 124, + "line": 143, "column": 18 } }, "argument": { "type": "Identifier", - "start": 4820, - "end": 4826, + "start": 5270, + "end": 5276, "loc": { "start": { - "line": 124, + "line": 143, "column": 11 }, "end": { - "line": 124, + "line": 143, "column": 17 }, "identifierName": "nextID" @@ -5411,15 +6099,15 @@ }, { "type": "ClassMethod", - "start": 4835, - "end": 5703, + "start": 5285, + "end": 6153, "loc": { "start": { - "line": 127, + "line": 146, "column": 2 }, "end": { - "line": 148, + "line": 167, "column": 3 } }, @@ -5427,15 +6115,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4835, - "end": 4852, + "start": 5285, + "end": 5302, "loc": { "start": { - "line": 127, + "line": 146, "column": 2 }, "end": { - "line": 127, + "line": 146, "column": 19 }, "identifierName": "getTaxonomicUnits" @@ -5450,29 +6138,29 @@ "params": [ { "type": "AssignmentPattern", - "start": 4853, - "end": 4870, + "start": 5303, + "end": 5320, "loc": { "start": { - "line": 127, + "line": 146, "column": 20 }, "end": { - "line": 127, + "line": 146, "column": 37 } }, "left": { "type": "Identifier", - "start": 4853, - "end": 4861, + "start": 5303, + "end": 5311, "loc": { "start": { - "line": 127, + "line": 146, "column": 20 }, "end": { - "line": 127, + "line": 146, "column": 28 }, "identifierName": "nodeType" @@ -5481,15 +6169,15 @@ }, "right": { "type": "StringLiteral", - "start": 4864, - "end": 4870, + "start": 5314, + "end": 5320, "loc": { "start": { - "line": 127, + "line": 146, "column": 31 }, "end": { - "line": 127, + "line": 146, "column": 37 } }, @@ -5503,59 +6191,59 @@ ], "body": { "type": "BlockStatement", - "start": 4872, - "end": 5703, + "start": 5322, + "end": 6153, "loc": { "start": { - "line": 127, + "line": 146, "column": 39 }, "end": { - "line": 148, + "line": 167, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 5459, - "end": 5507, + "start": 5909, + "end": 5957, "loc": { "start": { - "line": 139, + "line": 158, "column": 4 }, "end": { - "line": 139, + "line": 158, "column": 52 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5465, - "end": 5506, + "start": 5915, + "end": 5956, "loc": { "start": { - "line": 139, + "line": 158, "column": 10 }, "end": { - "line": 139, + "line": 158, "column": 51 } }, "id": { "type": "Identifier", - "start": 5465, - "end": 5475, + "start": 5915, + "end": 5925, "loc": { "start": { - "line": 139, + "line": 158, "column": 10 }, "end": { - "line": 139, + "line": 158, "column": 20 }, "identifierName": "nodeLabels" @@ -5565,58 +6253,58 @@ }, "init": { "type": "CallExpression", - "start": 5478, - "end": 5506, + "start": 5928, + "end": 5956, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 5478, - "end": 5496, + "start": 5928, + "end": 5946, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 41 } }, "object": { "type": "ThisExpression", - "start": 5478, - "end": 5482, + "start": 5928, + "end": 5932, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 27 } } }, "property": { "type": "Identifier", - "start": 5483, - "end": 5496, + "start": 5933, + "end": 5946, "loc": { "start": { - "line": 139, + "line": 158, "column": 28 }, "end": { - "line": 139, + "line": 158, "column": 41 }, "identifierName": "getNodeLabels" @@ -5628,15 +6316,15 @@ "arguments": [ { "type": "Identifier", - "start": 5497, - "end": 5505, + "start": 5947, + "end": 5955, "loc": { "start": { - "line": 139, + "line": 158, "column": 42 }, "end": { - "line": 139, + "line": 158, "column": 50 }, "identifierName": "nodeType" @@ -5653,15 +6341,15 @@ { "type": "CommentLine", "value": " Return a list of all taxonomic units in this phylogeny.", - "start": 4878, - "end": 4936, + "start": 5328, + "end": 5386, "loc": { "start": { - "line": 128, + "line": 147, "column": 4 }, "end": { - "line": 128, + "line": 147, "column": 62 } } @@ -5669,15 +6357,15 @@ { "type": "CommentLine", "value": " Node labels will be extracted from:", - "start": 4941, - "end": 4979, + "start": 5391, + "end": 5429, "loc": { "start": { - "line": 129, + "line": 148, "column": 4 }, "end": { - "line": 129, + "line": 148, "column": 42 } } @@ -5685,15 +6373,15 @@ { "type": "CommentLine", "value": " - internal nodes only (if nodeType == 'internal')", - "start": 4984, - "end": 5037, + "start": 5434, + "end": 5487, "loc": { "start": { - "line": 130, + "line": 149, "column": 4 }, "end": { - "line": 130, + "line": 149, "column": 57 } } @@ -5701,15 +6389,15 @@ { "type": "CommentLine", "value": " - terminal nodes only (if nodeType == 'terminal')", - "start": 5042, - "end": 5095, + "start": 5492, + "end": 5545, "loc": { "start": { - "line": 131, + "line": 150, "column": 4 }, "end": { - "line": 131, + "line": 150, "column": 57 } } @@ -5717,15 +6405,15 @@ { "type": "CommentLine", "value": " - both internal and terminal nodes (if nodeType == 'both')", - "start": 5100, - "end": 5162, + "start": 5550, + "end": 5612, "loc": { "start": { - "line": 132, + "line": 151, "column": 4 }, "end": { - "line": 132, + "line": 151, "column": 66 } } @@ -5733,15 +6421,15 @@ { "type": "CommentLine", "value": "", - "start": 5167, - "end": 5169, + "start": 5617, + "end": 5619, "loc": { "start": { - "line": 133, + "line": 152, "column": 4 }, "end": { - "line": 133, + "line": 152, "column": 6 } } @@ -5749,15 +6437,15 @@ { "type": "CommentLine", "value": " See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted", - "start": 5174, - "end": 5249, + "start": 5624, + "end": 5699, "loc": { "start": { - "line": 134, + "line": 153, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 79 } } @@ -5765,15 +6453,15 @@ { "type": "CommentLine", "value": " into node labels, but in brief:", - "start": 5254, - "end": 5288, + "start": 5704, + "end": 5738, "loc": { "start": { - "line": 135, + "line": 154, "column": 4 }, "end": { - "line": 135, + "line": 154, "column": 38 } } @@ -5781,15 +6469,15 @@ { "type": "CommentLine", "value": " 1. We look for taxonomic units in the additionalNodeProperties.", - "start": 5293, - "end": 5360, + "start": 5743, + "end": 5810, "loc": { "start": { - "line": 136, + "line": 155, "column": 4 }, "end": { - "line": 136, + "line": 155, "column": 71 } } @@ -5797,15 +6485,15 @@ { "type": "CommentLine", "value": " 2. If none are found, we attempt to parse the node label as a scientific name.", - "start": 5365, - "end": 5447, + "start": 5815, + "end": 5897, "loc": { "start": { - "line": 137, + "line": 156, "column": 4 }, "end": { - "line": 137, + "line": 156, "column": 86 } } @@ -5813,15 +6501,15 @@ { "type": "CommentLine", "value": "", - "start": 5452, - "end": 5454, + "start": 5902, + "end": 5904, "loc": { "start": { - "line": 138, + "line": 157, "column": 4 }, "end": { - "line": 138, + "line": 157, "column": 6 } } @@ -5830,44 +6518,44 @@ }, { "type": "VariableDeclaration", - "start": 5512, - "end": 5537, + "start": 5962, + "end": 5987, "loc": { "start": { - "line": 140, + "line": 159, "column": 4 }, "end": { - "line": 140, + "line": 159, "column": 29 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5518, - "end": 5536, + "start": 5968, + "end": 5986, "loc": { "start": { - "line": 140, + "line": 159, "column": 10 }, "end": { - "line": 140, + "line": 159, "column": 28 } }, "id": { "type": "Identifier", - "start": 5518, - "end": 5524, + "start": 5968, + "end": 5974, "loc": { "start": { - "line": 140, + "line": 159, "column": 10 }, "end": { - "line": 140, + "line": 159, "column": 16 }, "identifierName": "tunits" @@ -5876,29 +6564,29 @@ }, "init": { "type": "NewExpression", - "start": 5527, - "end": 5536, + "start": 5977, + "end": 5986, "loc": { "start": { - "line": 140, + "line": 159, "column": 19 }, "end": { - "line": 140, + "line": 159, "column": 28 } }, "callee": { "type": "Identifier", - "start": 5531, - "end": 5534, + "start": 5981, + "end": 5984, "loc": { "start": { - "line": 140, + "line": 159, "column": 23 }, "end": { - "line": 140, + "line": 159, "column": 26 }, "identifierName": "Set" @@ -5913,57 +6601,57 @@ }, { "type": "ExpressionStatement", - "start": 5543, - "end": 5679, + "start": 5993, + "end": 6129, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 6 } }, "expression": { "type": "CallExpression", - "start": 5543, - "end": 5678, + "start": 5993, + "end": 6128, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 5 } }, "callee": { "type": "MemberExpression", - "start": 5543, - "end": 5561, + "start": 5993, + "end": 6011, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 142, + "line": 161, "column": 22 } }, "object": { "type": "Identifier", - "start": 5543, - "end": 5553, + "start": 5993, + "end": 6003, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 142, + "line": 161, "column": 14 }, "identifierName": "nodeLabels" @@ -5972,15 +6660,15 @@ }, "property": { "type": "Identifier", - "start": 5554, - "end": 5561, + "start": 6004, + "end": 6011, "loc": { "start": { - "line": 142, + "line": 161, "column": 15 }, "end": { - "line": 142, + "line": 161, "column": 22 }, "identifierName": "forEach" @@ -5992,15 +6680,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5569, - "end": 5672, + "start": 6019, + "end": 6122, "loc": { "start": { - "line": 143, + "line": 162, "column": 6 }, "end": { - "line": 144, + "line": 163, "column": 44 } }, @@ -6011,15 +6699,15 @@ "params": [ { "type": "Identifier", - "start": 5569, - "end": 5578, + "start": 6019, + "end": 6028, "loc": { "start": { - "line": 143, + "line": 162, "column": 6 }, "end": { - "line": 143, + "line": 162, "column": 15 }, "identifierName": "nodeLabel" @@ -6029,86 +6717,86 @@ ], "body": { "type": "CallExpression", - "start": 5582, - "end": 5672, + "start": 6032, + "end": 6122, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 144, + "line": 163, "column": 44 } }, "callee": { "type": "MemberExpression", - "start": 5582, - "end": 5644, + "start": 6032, + "end": 6094, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 144, + "line": 163, "column": 16 } }, "object": { "type": "CallExpression", - "start": 5582, - "end": 5627, + "start": 6032, + "end": 6077, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 64 } }, "callee": { "type": "MemberExpression", - "start": 5582, - "end": 5616, + "start": 6032, + "end": 6066, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 53 } }, "object": { "type": "ThisExpression", - "start": 5582, - "end": 5586, + "start": 6032, + "end": 6036, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 23 } } }, "property": { "type": "Identifier", - "start": 5587, - "end": 5616, + "start": 6037, + "end": 6066, "loc": { "start": { - "line": 143, + "line": 162, "column": 24 }, "end": { - "line": 143, + "line": 162, "column": 53 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -6120,15 +6808,15 @@ "arguments": [ { "type": "Identifier", - "start": 5617, - "end": 5626, + "start": 6067, + "end": 6076, "loc": { "start": { - "line": 143, + "line": 162, "column": 54 }, "end": { - "line": 143, + "line": 162, "column": 63 }, "identifierName": "nodeLabel" @@ -6139,15 +6827,15 @@ }, "property": { "type": "Identifier", - "start": 5637, - "end": 5644, + "start": 6087, + "end": 6094, "loc": { "start": { - "line": 144, + "line": 163, "column": 9 }, "end": { - "line": 144, + "line": 163, "column": 16 }, "identifierName": "forEach" @@ -6159,15 +6847,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5645, - "end": 5671, + "start": 6095, + "end": 6121, "loc": { "start": { - "line": 144, + "line": 163, "column": 17 }, "end": { - "line": 144, + "line": 163, "column": 43 } }, @@ -6178,15 +6866,15 @@ "params": [ { "type": "Identifier", - "start": 5645, - "end": 5650, + "start": 6095, + "end": 6100, "loc": { "start": { - "line": 144, + "line": 163, "column": 17 }, "end": { - "line": 144, + "line": 163, "column": 22 }, "identifierName": "tunit" @@ -6196,43 +6884,43 @@ ], "body": { "type": "CallExpression", - "start": 5654, - "end": 5671, + "start": 6104, + "end": 6121, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 43 } }, "callee": { "type": "MemberExpression", - "start": 5654, - "end": 5664, + "start": 6104, + "end": 6114, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 36 } }, "object": { "type": "Identifier", - "start": 5654, - "end": 5660, + "start": 6104, + "end": 6110, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 32 }, "identifierName": "tunits" @@ -6241,15 +6929,15 @@ }, "property": { "type": "Identifier", - "start": 5661, - "end": 5664, + "start": 6111, + "end": 6114, "loc": { "start": { - "line": 144, + "line": 163, "column": 33 }, "end": { - "line": 144, + "line": 163, "column": 36 }, "identifierName": "add" @@ -6261,15 +6949,15 @@ "arguments": [ { "type": "Identifier", - "start": 5665, - "end": 5670, + "start": 6115, + "end": 6120, "loc": { "start": { - "line": 144, + "line": 163, "column": 37 }, "end": { - "line": 144, + "line": 163, "column": 42 }, "identifierName": "tunit" @@ -6287,29 +6975,29 @@ }, { "type": "ReturnStatement", - "start": 5685, - "end": 5699, + "start": 6135, + "end": 6149, "loc": { "start": { - "line": 147, + "line": 166, "column": 4 }, "end": { - "line": 147, + "line": 166, "column": 18 } }, "argument": { "type": "Identifier", - "start": 5692, - "end": 5698, + "start": 6142, + "end": 6148, "loc": { "start": { - "line": 147, + "line": 166, "column": 11 }, "end": { - "line": 147, + "line": 166, "column": 17 }, "identifierName": "tunits" @@ -6323,15 +7011,15 @@ }, { "type": "ClassMethod", - "start": 5707, - "end": 7617, + "start": 6157, + "end": 8067, "loc": { "start": { - "line": 150, + "line": 169, "column": 2 }, "end": { - "line": 199, + "line": 218, "column": 3 } }, @@ -6339,15 +7027,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 5707, - "end": 5720, + "start": 6157, + "end": 6170, "loc": { "start": { - "line": 150, + "line": 169, "column": 2 }, "end": { - "line": 150, + "line": 169, "column": 15 }, "identifierName": "getNodeLabels" @@ -6362,29 +7050,29 @@ "params": [ { "type": "AssignmentPattern", - "start": 5721, - "end": 5738, + "start": 6171, + "end": 6188, "loc": { "start": { - "line": 150, + "line": 169, "column": 16 }, "end": { - "line": 150, + "line": 169, "column": 33 } }, "left": { "type": "Identifier", - "start": 5721, - "end": 5729, + "start": 6171, + "end": 6179, "loc": { "start": { - "line": 150, + "line": 169, "column": 16 }, "end": { - "line": 150, + "line": 169, "column": 24 }, "identifierName": "nodeType" @@ -6393,15 +7081,15 @@ }, "right": { "type": "StringLiteral", - "start": 5732, - "end": 5738, + "start": 6182, + "end": 6188, "loc": { "start": { - "line": 150, + "line": 169, "column": 27 }, "end": { - "line": 150, + "line": 169, "column": 33 } }, @@ -6415,74 +7103,74 @@ ], "body": { "type": "BlockStatement", - "start": 5740, - "end": 7617, + "start": 6190, + "end": 8067, "loc": { "start": { - "line": 150, + "line": 169, "column": 35 }, "end": { - "line": 199, + "line": 218, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 6111, - "end": 6175, + "start": 6561, + "end": 6625, "loc": { "start": { - "line": 159, + "line": 178, "column": 4 }, "end": { - "line": 159, + "line": 178, "column": 68 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6117, - "end": 6174, + "start": 6567, + "end": 6624, "loc": { "start": { - "line": 159, + "line": 178, "column": 10 }, "end": { - "line": 159, + "line": 178, "column": 67 } }, "id": { "type": "ObjectPattern", - "start": 6117, - "end": 6126, + "start": 6567, + "end": 6576, "loc": { "start": { - "line": 159, + "line": 178, "column": 10 }, "end": { - "line": 159, + "line": 178, "column": 19 } }, "properties": [ { "type": "ObjectProperty", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 } }, @@ -6491,15 +7179,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 }, "identifierName": "graph" @@ -6509,15 +7197,15 @@ }, "value": { "type": "Identifier", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 }, "identifierName": "graph" @@ -6534,43 +7222,43 @@ }, "init": { "type": "CallExpression", - "start": 6129, - "end": 6174, + "start": 6579, + "end": 6624, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 6129, - "end": 6143, + "start": 6579, + "end": 6593, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 36 } }, "object": { "type": "Identifier", - "start": 6129, - "end": 6137, + "start": 6579, + "end": 6587, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 30 }, "identifierName": "newickJs" @@ -6579,15 +7267,15 @@ }, "property": { "type": "Identifier", - "start": 6138, - "end": 6143, + "start": 6588, + "end": 6593, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 36 }, "identifierName": "parse" @@ -6599,72 +7287,72 @@ "arguments": [ { "type": "LogicalExpression", - "start": 6144, - "end": 6173, + "start": 6594, + "end": 6623, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 66 } }, "left": { "type": "MemberExpression", - "start": 6144, - "end": 6165, + "start": 6594, + "end": 6615, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 6144, - "end": 6158, + "start": 6594, + "end": 6608, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 51 } }, "object": { "type": "ThisExpression", - "start": 6144, - "end": 6148, + "start": 6594, + "end": 6598, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 41 } } }, "property": { "type": "Identifier", - "start": 6149, - "end": 6158, + "start": 6599, + "end": 6608, "loc": { "start": { - "line": 159, + "line": 178, "column": 42 }, "end": { - "line": 159, + "line": 178, "column": 51 }, "identifierName": "phylogeny" @@ -6675,15 +7363,15 @@ }, "property": { "type": "Identifier", - "start": 6159, - "end": 6165, + "start": 6609, + "end": 6615, "loc": { "start": { - "line": 159, + "line": 178, "column": 52 }, "end": { - "line": 159, + "line": 178, "column": 58 }, "identifierName": "newick" @@ -6695,15 +7383,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 6169, - "end": 6173, + "start": 6619, + "end": 6623, "loc": { "start": { - "line": 159, + "line": 178, "column": 62 }, "end": { - "line": 159, + "line": 178, "column": 66 } }, @@ -6724,15 +7412,15 @@ { "type": "CommentLine", "value": " Return a list of all the node labels in this phylogeny.", - "start": 5746, - "end": 5804, + "start": 6196, + "end": 6254, "loc": { "start": { - "line": 151, + "line": 170, "column": 4 }, "end": { - "line": 151, + "line": 170, "column": 62 } } @@ -6740,15 +7428,15 @@ { "type": "CommentLine", "value": "", - "start": 5809, - "end": 5811, + "start": 6259, + "end": 6261, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 6 } } @@ -6756,15 +7444,15 @@ { "type": "CommentLine", "value": " nodeType can be one of:", - "start": 5816, - "end": 5842, + "start": 6266, + "end": 6292, "loc": { "start": { - "line": 153, + "line": 172, "column": 4 }, "end": { - "line": 153, + "line": 172, "column": 30 } } @@ -6772,15 +7460,15 @@ { "type": "CommentLine", "value": " - 'internal': Return node labels on internal nodes.", - "start": 5847, - "end": 5901, + "start": 6297, + "end": 6351, "loc": { "start": { - "line": 154, + "line": 173, "column": 4 }, "end": { - "line": 154, + "line": 173, "column": 58 } } @@ -6788,15 +7476,15 @@ { "type": "CommentLine", "value": " - 'terminal': Return node labels on terminal nodes.", - "start": 5906, - "end": 5960, + "start": 6356, + "end": 6410, "loc": { "start": { - "line": 155, + "line": 174, "column": 4 }, "end": { - "line": 155, + "line": 174, "column": 58 } } @@ -6804,15 +7492,15 @@ { "type": "CommentLine", "value": " - 'both': Return node labels on both internal and terminal nodes.", - "start": 5965, - "end": 6033, + "start": 6415, + "end": 6483, "loc": { "start": { - "line": 156, + "line": 175, "column": 4 }, "end": { - "line": 156, + "line": 175, "column": 72 } } @@ -6820,15 +7508,15 @@ { "type": "CommentLine", "value": " Parse the phylogeny (will throw an exception if parsing failed).", - "start": 6039, - "end": 6106, + "start": 6489, + "end": 6556, "loc": { "start": { - "line": 158, + "line": 177, "column": 4 }, "end": { - "line": 158, + "line": 177, "column": 71 } } @@ -6837,59 +7525,59 @@ }, { "type": "VariableDeclaration", - "start": 6180, - "end": 6211, + "start": 6630, + "end": 6661, "loc": { "start": { - "line": 160, + "line": 179, "column": 4 }, "end": { - "line": 160, + "line": 179, "column": 35 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6186, - "end": 6210, + "start": 6636, + "end": 6660, "loc": { "start": { - "line": 160, + "line": 179, "column": 10 }, "end": { - "line": 160, + "line": 179, "column": 34 } }, "id": { "type": "ArrayPattern", - "start": 6186, - "end": 6202, + "start": 6636, + "end": 6652, "loc": { "start": { - "line": 160, + "line": 179, "column": 10 }, "end": { - "line": 160, + "line": 179, "column": 26 } }, "elements": [ { "type": "Identifier", - "start": 6187, - "end": 6195, + "start": 6637, + "end": 6645, "loc": { "start": { - "line": 160, + "line": 179, "column": 11 }, "end": { - "line": 160, + "line": 179, "column": 19 }, "identifierName": "vertices" @@ -6898,15 +7586,15 @@ }, { "type": "Identifier", - "start": 6197, - "end": 6201, + "start": 6647, + "end": 6651, "loc": { "start": { - "line": 160, + "line": 179, "column": 21 }, "end": { - "line": 160, + "line": 179, "column": 25 }, "identifierName": "arcs" @@ -6917,15 +7605,15 @@ }, "init": { "type": "Identifier", - "start": 6205, - "end": 6210, + "start": 6655, + "end": 6660, "loc": { "start": { - "line": 160, + "line": 179, "column": 29 }, "end": { - "line": 160, + "line": 179, "column": 34 }, "identifierName": "graph" @@ -6938,43 +7626,43 @@ }, { "type": "IfStatement", - "start": 6217, - "end": 6465, + "start": 6667, + "end": 6915, "loc": { "start": { - "line": 162, + "line": 181, "column": 4 }, "end": { - "line": 171, + "line": 190, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6221, - "end": 6240, + "start": 6671, + "end": 6690, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 27 } }, "left": { "type": "Identifier", - "start": 6221, - "end": 6229, + "start": 6671, + "end": 6679, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 16 }, "identifierName": "nodeType" @@ -6984,15 +7672,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 6234, - "end": 6240, + "start": 6684, + "end": 6690, "loc": { "start": { - "line": 162, + "line": 181, "column": 21 }, "end": { - "line": 162, + "line": 181, "column": 27 } }, @@ -7005,72 +7693,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 6242, - "end": 6465, + "start": 6692, + "end": 6915, "loc": { "start": { - "line": 162, + "line": 181, "column": 29 }, "end": { - "line": 171, + "line": 190, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 6283, - "end": 6459, + "start": 6733, + "end": 6909, "loc": { "start": { - "line": 164, + "line": 183, "column": 6 }, "end": { - "line": 170, + "line": 189, "column": 8 } }, "argument": { "type": "CallExpression", - "start": 6290, - "end": 6458, + "start": 6740, + "end": 6908, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 170, + "line": 189, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 6290, - "end": 6300, + "start": 6740, + "end": 6750, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 164, + "line": 183, "column": 23 } }, "object": { "type": "Identifier", - "start": 6290, - "end": 6295, + "start": 6740, + "end": 6745, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 164, + "line": 183, "column": 18 }, "identifierName": "Array" @@ -7080,15 +7768,15 @@ }, "property": { "type": "Identifier", - "start": 6296, - "end": 6300, + "start": 6746, + "end": 6750, "loc": { "start": { - "line": 164, + "line": 183, "column": 19 }, "end": { - "line": 164, + "line": 183, "column": 23 }, "identifierName": "from" @@ -7101,29 +7789,29 @@ "arguments": [ { "type": "NewExpression", - "start": 6310, - "end": 6450, + "start": 6760, + "end": 6900, "loc": { "start": { - "line": 165, + "line": 184, "column": 8 }, "end": { - "line": 169, + "line": 188, "column": 9 } }, "callee": { "type": "Identifier", - "start": 6314, - "end": 6317, + "start": 6764, + "end": 6767, "loc": { "start": { - "line": 165, + "line": 184, "column": 12 }, "end": { - "line": 165, + "line": 184, "column": 15 }, "identifierName": "Set" @@ -7133,99 +7821,99 @@ "arguments": [ { "type": "CallExpression", - "start": 6329, - "end": 6440, + "start": 6779, + "end": 6890, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 168, + "line": 187, "column": 49 } }, "callee": { "type": "MemberExpression", - "start": 6329, - "end": 6410, + "start": 6779, + "end": 6860, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 168, + "line": 187, "column": 19 } }, "object": { "type": "CallExpression", - "start": 6329, - "end": 6390, + "start": 6779, + "end": 6840, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 167, + "line": 186, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 6329, - "end": 6366, + "start": 6779, + "end": 6816, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 167, + "line": 186, "column": 16 } }, "object": { "type": "CallExpression", - "start": 6329, - "end": 6349, + "start": 6779, + "end": 6799, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 30 } }, "callee": { "type": "MemberExpression", - "start": 6329, - "end": 6339, + "start": 6779, + "end": 6789, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 20 } }, "object": { "type": "Identifier", - "start": 6329, - "end": 6334, + "start": 6779, + "end": 6784, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 15 }, "identifierName": "Array" @@ -7234,15 +7922,15 @@ }, "property": { "type": "Identifier", - "start": 6335, - "end": 6339, + "start": 6785, + "end": 6789, "loc": { "start": { - "line": 166, + "line": 185, "column": 16 }, "end": { - "line": 166, + "line": 185, "column": 20 }, "identifierName": "from" @@ -7254,15 +7942,15 @@ "arguments": [ { "type": "Identifier", - "start": 6340, - "end": 6348, + "start": 6790, + "end": 6798, "loc": { "start": { - "line": 166, + "line": 185, "column": 21 }, "end": { - "line": 166, + "line": 185, "column": 29 }, "identifierName": "vertices" @@ -7273,15 +7961,15 @@ }, "property": { "type": "Identifier", - "start": 6363, - "end": 6366, + "start": 6813, + "end": 6816, "loc": { "start": { - "line": 167, + "line": 186, "column": 13 }, "end": { - "line": 167, + "line": 186, "column": 16 }, "identifierName": "map" @@ -7293,15 +7981,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6367, - "end": 6389, + "start": 6817, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 17 }, "end": { - "line": 167, + "line": 186, "column": 39 } }, @@ -7312,15 +8000,15 @@ "params": [ { "type": "Identifier", - "start": 6367, - "end": 6373, + "start": 6817, + "end": 6823, "loc": { "start": { - "line": 167, + "line": 186, "column": 17 }, "end": { - "line": 167, + "line": 186, "column": 23 }, "identifierName": "vertex" @@ -7330,29 +8018,29 @@ ], "body": { "type": "MemberExpression", - "start": 6377, - "end": 6389, + "start": 6827, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 27 }, "end": { - "line": 167, + "line": 186, "column": 39 } }, "object": { "type": "Identifier", - "start": 6377, - "end": 6383, + "start": 6827, + "end": 6833, "loc": { "start": { - "line": 167, + "line": 186, "column": 27 }, "end": { - "line": 167, + "line": 186, "column": 33 }, "identifierName": "vertex" @@ -7361,15 +8049,15 @@ }, "property": { "type": "Identifier", - "start": 6384, - "end": 6389, + "start": 6834, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 34 }, "end": { - "line": 167, + "line": 186, "column": 39 }, "identifierName": "label" @@ -7383,15 +8071,15 @@ }, "property": { "type": "Identifier", - "start": 6404, - "end": 6410, + "start": 6854, + "end": 6860, "loc": { "start": { - "line": 168, + "line": 187, "column": 13 }, "end": { - "line": 168, + "line": 187, "column": 19 }, "identifierName": "filter" @@ -7403,15 +8091,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6411, - "end": 6439, + "start": 6861, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 20 }, "end": { - "line": 168, + "line": 187, "column": 48 } }, @@ -7422,15 +8110,15 @@ "params": [ { "type": "Identifier", - "start": 6411, - "end": 6416, + "start": 6861, + "end": 6866, "loc": { "start": { - "line": 168, + "line": 187, "column": 20 }, "end": { - "line": 168, + "line": 187, "column": 25 }, "identifierName": "label" @@ -7440,29 +8128,29 @@ ], "body": { "type": "BinaryExpression", - "start": 6420, - "end": 6439, + "start": 6870, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 29 }, "end": { - "line": 168, + "line": 187, "column": 48 } }, "left": { "type": "Identifier", - "start": 6420, - "end": 6425, + "start": 6870, + "end": 6875, "loc": { "start": { - "line": 168, + "line": 187, "column": 29 }, "end": { - "line": 168, + "line": 187, "column": 34 }, "identifierName": "label" @@ -7472,15 +8160,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 6430, - "end": 6439, + "start": 6880, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 39 }, "end": { - "line": 168, + "line": 187, "column": 48 }, "identifierName": "undefined" @@ -7500,15 +8188,15 @@ { "type": "CommentLine", "value": " Return all node labels.", - "start": 6250, - "end": 6276, + "start": 6700, + "end": 6726, "loc": { "start": { - "line": 163, + "line": 182, "column": 6 }, "end": { - "line": 163, + "line": 182, "column": 32 } } @@ -7522,43 +8210,43 @@ }, { "type": "IfStatement", - "start": 6471, - "end": 6782, + "start": 6921, + "end": 7232, "loc": { "start": { - "line": 173, + "line": 192, "column": 4 }, "end": { - "line": 180, + "line": 199, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6475, - "end": 6498, + "start": 6925, + "end": 6948, "loc": { "start": { - "line": 173, + "line": 192, "column": 8 }, "end": { - "line": 173, + "line": 192, "column": 31 } }, "left": { "type": "Identifier", - "start": 6475, - "end": 6483, + "start": 6925, + "end": 6933, "loc": { "start": { - "line": 173, + "line": 192, "column": 8 }, "end": { - "line": 173, + "line": 192, "column": 16 }, "identifierName": "nodeType" @@ -7568,15 +8256,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 6488, - "end": 6498, + "start": 6938, + "end": 6948, "loc": { "start": { - "line": 173, + "line": 192, "column": 21 }, "end": { - "line": 173, + "line": 192, "column": 31 } }, @@ -7589,72 +8277,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 6500, - "end": 6782, + "start": 6950, + "end": 7232, "loc": { "start": { - "line": 173, + "line": 192, "column": 33 }, "end": { - "line": 180, + "line": 199, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 6575, - "end": 6776, + "start": 7025, + "end": 7226, "loc": { "start": { - "line": 175, + "line": 194, "column": 6 }, "end": { - "line": 179, + "line": 198, "column": 9 } }, "argument": { "type": "CallExpression", - "start": 6582, - "end": 6775, + "start": 7032, + "end": 7225, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 179, + "line": 198, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 6582, - "end": 6592, + "start": 7032, + "end": 7042, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 175, + "line": 194, "column": 23 } }, "object": { "type": "Identifier", - "start": 6582, - "end": 6587, + "start": 7032, + "end": 7037, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 175, + "line": 194, "column": 18 }, "identifierName": "Array" @@ -7664,15 +8352,15 @@ }, "property": { "type": "Identifier", - "start": 6588, - "end": 6592, + "start": 7038, + "end": 7042, "loc": { "start": { - "line": 175, + "line": 194, "column": 19 }, "end": { - "line": 175, + "line": 194, "column": 23 }, "identifierName": "from" @@ -7685,29 +8373,29 @@ "arguments": [ { "type": "NewExpression", - "start": 6593, - "end": 6774, + "start": 7043, + "end": 7224, "loc": { "start": { - "line": 175, + "line": 194, "column": 24 }, "end": { - "line": 179, + "line": 198, "column": 7 } }, "callee": { "type": "Identifier", - "start": 6597, - "end": 6600, + "start": 7047, + "end": 7050, "loc": { "start": { - "line": 175, + "line": 194, "column": 28 }, "end": { - "line": 175, + "line": 194, "column": 31 }, "identifierName": "Set" @@ -7717,99 +8405,99 @@ "arguments": [ { "type": "CallExpression", - "start": 6610, - "end": 6766, + "start": 7060, + "end": 7216, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 178, + "line": 197, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 6610, - "end": 6736, + "start": 7060, + "end": 7186, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 178, + "line": 197, "column": 17 } }, "object": { "type": "CallExpression", - "start": 6610, - "end": 6662, + "start": 7060, + "end": 7112, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 177, + "line": 196, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 6610, - "end": 6641, + "start": 7060, + "end": 7091, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 177, + "line": 196, "column": 14 } }, "object": { "type": "CallExpression", - "start": 6610, - "end": 6626, + "start": 7060, + "end": 7076, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 24 } }, "callee": { "type": "MemberExpression", - "start": 6610, - "end": 6620, + "start": 7060, + "end": 7070, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 18 } }, "object": { "type": "Identifier", - "start": 6610, - "end": 6615, + "start": 7060, + "end": 7065, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 13 }, "identifierName": "Array" @@ -7818,15 +8506,15 @@ }, "property": { "type": "Identifier", - "start": 6616, - "end": 6620, + "start": 7066, + "end": 7070, "loc": { "start": { - "line": 176, + "line": 195, "column": 14 }, "end": { - "line": 176, + "line": 195, "column": 18 }, "identifierName": "from" @@ -7838,15 +8526,15 @@ "arguments": [ { "type": "Identifier", - "start": 6621, - "end": 6625, + "start": 7071, + "end": 7075, "loc": { "start": { - "line": 176, + "line": 195, "column": 19 }, "end": { - "line": 176, + "line": 195, "column": 23 }, "identifierName": "arcs" @@ -7857,15 +8545,15 @@ }, "property": { "type": "Identifier", - "start": 6638, - "end": 6641, + "start": 7088, + "end": 7091, "loc": { "start": { - "line": 177, + "line": 196, "column": 11 }, "end": { - "line": 177, + "line": 196, "column": 14 }, "identifierName": "map" @@ -7877,15 +8565,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6642, - "end": 6661, + "start": 7092, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 15 }, "end": { - "line": 177, + "line": 196, "column": 34 } }, @@ -7896,15 +8584,15 @@ "params": [ { "type": "Identifier", - "start": 6642, - "end": 6645, + "start": 7092, + "end": 7095, "loc": { "start": { - "line": 177, + "line": 196, "column": 15 }, "end": { - "line": 177, + "line": 196, "column": 18 }, "identifierName": "arc" @@ -7914,43 +8602,43 @@ ], "body": { "type": "MemberExpression", - "start": 6649, - "end": 6661, + "start": 7099, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 34 } }, "object": { "type": "MemberExpression", - "start": 6649, - "end": 6655, + "start": 7099, + "end": 7105, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 28 } }, "object": { "type": "Identifier", - "start": 6649, - "end": 6652, + "start": 7099, + "end": 7102, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 25 }, "identifierName": "arc" @@ -7959,15 +8647,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6653, - "end": 6654, + "start": 7103, + "end": 7104, "loc": { "start": { - "line": 177, + "line": 196, "column": 26 }, "end": { - "line": 177, + "line": 196, "column": 27 } }, @@ -7981,15 +8669,15 @@ }, "property": { "type": "Identifier", - "start": 6656, - "end": 6661, + "start": 7106, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 29 }, "end": { - "line": 177, + "line": 196, "column": 34 }, "identifierName": "label" @@ -8004,15 +8692,15 @@ { "type": "CommentLine", "value": " Retrieve the label of the parent vertex in this arc.", - "start": 6663, - "end": 6718, + "start": 7113, + "end": 7168, "loc": { "start": { - "line": 177, + "line": 196, "column": 36 }, "end": { - "line": 177, + "line": 196, "column": 91 } } @@ -8021,15 +8709,15 @@ }, "property": { "type": "Identifier", - "start": 6730, - "end": 6736, + "start": 7180, + "end": 7186, "loc": { "start": { - "line": 178, + "line": 197, "column": 11 }, "end": { - "line": 178, + "line": 197, "column": 17 }, "identifierName": "filter" @@ -8039,15 +8727,15 @@ { "type": "CommentLine", "value": " Retrieve the label of the parent vertex in this arc.", - "start": 6663, - "end": 6718, + "start": 7113, + "end": 7168, "loc": { "start": { - "line": 177, + "line": 196, "column": 36 }, "end": { - "line": 177, + "line": 196, "column": 91 } } @@ -8059,15 +8747,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6737, - "end": 6765, + "start": 7187, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 18 }, "end": { - "line": 178, + "line": 197, "column": 46 } }, @@ -8078,15 +8766,15 @@ "params": [ { "type": "Identifier", - "start": 6737, - "end": 6742, + "start": 7187, + "end": 7192, "loc": { "start": { - "line": 178, + "line": 197, "column": 18 }, "end": { - "line": 178, + "line": 197, "column": 23 }, "identifierName": "label" @@ -8096,29 +8784,29 @@ ], "body": { "type": "BinaryExpression", - "start": 6746, - "end": 6765, + "start": 7196, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 27 }, "end": { - "line": 178, + "line": 197, "column": 46 } }, "left": { "type": "Identifier", - "start": 6746, - "end": 6751, + "start": 7196, + "end": 7201, "loc": { "start": { - "line": 178, + "line": 197, "column": 27 }, "end": { - "line": 178, + "line": 197, "column": 32 }, "identifierName": "label" @@ -8128,15 +8816,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 6756, - "end": 6765, + "start": 7206, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 37 }, "end": { - "line": 178, + "line": 197, "column": 46 }, "identifierName": "undefined" @@ -8156,15 +8844,15 @@ { "type": "CommentLine", "value": " Return the internal nodes (those with atleast one child).", - "start": 6508, - "end": 6568, + "start": 6958, + "end": 7018, "loc": { "start": { - "line": 174, + "line": 193, "column": 6 }, "end": { - "line": 174, + "line": 193, "column": 66 } } @@ -8178,43 +8866,43 @@ }, { "type": "IfStatement", - "start": 6788, - "end": 7556, + "start": 7238, + "end": 8006, "loc": { "start": { - "line": 182, + "line": 201, "column": 4 }, "end": { - "line": 196, + "line": 215, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6792, - "end": 6815, + "start": 7242, + "end": 7265, "loc": { "start": { - "line": 182, + "line": 201, "column": 8 }, "end": { - "line": 182, + "line": 201, "column": 31 } }, "left": { "type": "Identifier", - "start": 6792, - "end": 6800, + "start": 7242, + "end": 7250, "loc": { "start": { - "line": 182, + "line": 201, "column": 8 }, "end": { - "line": 182, + "line": 201, "column": 16 }, "identifierName": "nodeType" @@ -8224,15 +8912,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 6805, - "end": 6815, + "start": 7255, + "end": 7265, "loc": { "start": { - "line": 182, + "line": 201, "column": 21 }, "end": { - "line": 182, + "line": 201, "column": 31 } }, @@ -8245,59 +8933,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6817, - "end": 7556, + "start": 7267, + "end": 8006, "loc": { "start": { - "line": 182, + "line": 201, "column": 33 }, "end": { - "line": 196, + "line": 215, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 7366, - "end": 7411, + "start": 7816, + "end": 7861, "loc": { "start": { - "line": 192, + "line": 211, "column": 6 }, "end": { - "line": 192, + "line": 211, "column": 51 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7372, - "end": 7410, + "start": 7822, + "end": 7860, "loc": { "start": { - "line": 192, + "line": 211, "column": 12 }, "end": { - "line": 192, + "line": 211, "column": 50 } }, "id": { "type": "Identifier", - "start": 7372, - "end": 7381, + "start": 7822, + "end": 7831, "loc": { "start": { - "line": 192, + "line": 211, "column": 12 }, "end": { - "line": 192, + "line": 211, "column": 21 }, "identifierName": "allLabels" @@ -8307,58 +8995,58 @@ }, "init": { "type": "CallExpression", - "start": 7384, - "end": 7410, + "start": 7834, + "end": 7860, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 50 } }, "callee": { "type": "MemberExpression", - "start": 7384, - "end": 7402, + "start": 7834, + "end": 7852, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 42 } }, "object": { "type": "ThisExpression", - "start": 7384, - "end": 7388, + "start": 7834, + "end": 7838, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 28 } } }, "property": { "type": "Identifier", - "start": 7389, - "end": 7402, + "start": 7839, + "end": 7852, "loc": { "start": { - "line": 192, + "line": 211, "column": 29 }, "end": { - "line": 192, + "line": 211, "column": 42 }, "identifierName": "getNodeLabels" @@ -8370,15 +9058,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 7403, - "end": 7409, + "start": 7853, + "end": 7859, "loc": { "start": { - "line": 192, + "line": 211, "column": 43 }, "end": { - "line": 192, + "line": 211, "column": 49 } }, @@ -8398,15 +9086,15 @@ { "type": "CommentLine", "value": " Return the terminal nodes. This would require calculating the children", - "start": 6825, - "end": 6898, + "start": 7275, + "end": 7348, "loc": { "start": { - "line": 183, + "line": 202, "column": 6 }, "end": { - "line": 183, + "line": 202, "column": 79 } } @@ -8414,15 +9102,15 @@ { "type": "CommentLine", "value": " of every vertex in the graph and then identifying vertices without any", - "start": 6905, - "end": 6978, + "start": 7355, + "end": 7428, "loc": { "start": { - "line": 184, + "line": 203, "column": 6 }, "end": { - "line": 184, + "line": 203, "column": 79 } } @@ -8430,15 +9118,15 @@ { "type": "CommentLine", "value": " children.", - "start": 6985, - "end": 6997, + "start": 7435, + "end": 7447, "loc": { "start": { - "line": 185, + "line": 204, "column": 6 }, "end": { - "line": 185, + "line": 204, "column": 18 } } @@ -8446,15 +9134,15 @@ { "type": "CommentLine", "value": "", - "start": 7004, - "end": 7006, + "start": 7454, + "end": 7456, "loc": { "start": { - "line": 186, + "line": 205, "column": 6 }, "end": { - "line": 186, + "line": 205, "column": 8 } } @@ -8462,15 +9150,15 @@ { "type": "CommentLine", "value": " A quicker and dirtier way to do this is by removing internal labels", - "start": 7013, - "end": 7083, + "start": 7463, + "end": 7533, "loc": { "start": { - "line": 187, + "line": 206, "column": 6 }, "end": { - "line": 187, + "line": 206, "column": 76 } } @@ -8478,15 +9166,15 @@ { "type": "CommentLine", "value": " from the list of all node labels. This will report an incorrect result", - "start": 7090, - "end": 7163, + "start": 7540, + "end": 7613, "loc": { "start": { - "line": 188, + "line": 207, "column": 6 }, "end": { - "line": 188, + "line": 207, "column": 79 } } @@ -8494,15 +9182,15 @@ { "type": "CommentLine", "value": " if an internal node has the same label as a terminal node, but at that", - "start": 7170, - "end": 7243, + "start": 7620, + "end": 7693, "loc": { "start": { - "line": 189, + "line": 208, "column": 6 }, "end": { - "line": 189, + "line": 208, "column": 79 } } @@ -8510,15 +9198,15 @@ { "type": "CommentLine", "value": " point a lot of other assumptions are going to fail, too, so this is", - "start": 7250, - "end": 7320, + "start": 7700, + "end": 7770, "loc": { "start": { - "line": 190, + "line": 209, "column": 6 }, "end": { - "line": 190, + "line": 209, "column": 76 } } @@ -8526,15 +9214,15 @@ { "type": "CommentLine", "value": " probably good enough for now.", - "start": 7327, - "end": 7359, + "start": 7777, + "end": 7809, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 38 } } @@ -8543,44 +9231,44 @@ }, { "type": "VariableDeclaration", - "start": 7418, - "end": 7481, + "start": 7868, + "end": 7931, "loc": { "start": { - "line": 193, + "line": 212, "column": 6 }, "end": { - "line": 193, + "line": 212, "column": 69 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7424, - "end": 7480, + "start": 7874, + "end": 7930, "loc": { "start": { - "line": 193, + "line": 212, "column": 12 }, "end": { - "line": 193, + "line": 212, "column": 68 } }, "id": { "type": "Identifier", - "start": 7424, - "end": 7438, + "start": 7874, + "end": 7888, "loc": { "start": { - "line": 193, + "line": 212, "column": 12 }, "end": { - "line": 193, + "line": 212, "column": 26 }, "identifierName": "internalLabels" @@ -8589,29 +9277,29 @@ }, "init": { "type": "NewExpression", - "start": 7441, - "end": 7480, + "start": 7891, + "end": 7930, "loc": { "start": { - "line": 193, + "line": 212, "column": 29 }, "end": { - "line": 193, + "line": 212, "column": 68 } }, "callee": { "type": "Identifier", - "start": 7445, - "end": 7448, + "start": 7895, + "end": 7898, "loc": { "start": { - "line": 193, + "line": 212, "column": 33 }, "end": { - "line": 193, + "line": 212, "column": 36 }, "identifierName": "Set" @@ -8621,58 +9309,58 @@ "arguments": [ { "type": "CallExpression", - "start": 7449, - "end": 7479, + "start": 7899, + "end": 7929, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 7449, - "end": 7467, + "start": 7899, + "end": 7917, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 55 } }, "object": { "type": "ThisExpression", - "start": 7449, - "end": 7453, + "start": 7899, + "end": 7903, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 41 } } }, "property": { "type": "Identifier", - "start": 7454, - "end": 7467, + "start": 7904, + "end": 7917, "loc": { "start": { - "line": 193, + "line": 212, "column": 42 }, "end": { - "line": 193, + "line": 212, "column": 55 }, "identifierName": "getNodeLabels" @@ -8684,15 +9372,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 7468, - "end": 7478, + "start": 7918, + "end": 7928, "loc": { "start": { - "line": 193, + "line": 212, "column": 56 }, "end": { - "line": 193, + "line": 212, "column": 66 } }, @@ -8712,57 +9400,57 @@ }, { "type": "ReturnStatement", - "start": 7489, - "end": 7550, + "start": 7939, + "end": 8000, "loc": { "start": { - "line": 195, + "line": 214, "column": 6 }, "end": { - "line": 195, + "line": 214, "column": 67 } }, "argument": { "type": "CallExpression", - "start": 7496, - "end": 7549, + "start": 7946, + "end": 7999, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 66 } }, "callee": { "type": "MemberExpression", - "start": 7496, - "end": 7512, + "start": 7946, + "end": 7962, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 29 } }, "object": { "type": "Identifier", - "start": 7496, - "end": 7505, + "start": 7946, + "end": 7955, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 22 }, "identifierName": "allLabels" @@ -8771,15 +9459,15 @@ }, "property": { "type": "Identifier", - "start": 7506, - "end": 7512, + "start": 7956, + "end": 7962, "loc": { "start": { - "line": 195, + "line": 214, "column": 23 }, "end": { - "line": 195, + "line": 214, "column": 29 }, "identifierName": "filter" @@ -8791,15 +9479,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 7513, - "end": 7548, + "start": 7963, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 65 } }, @@ -8810,15 +9498,15 @@ "params": [ { "type": "Identifier", - "start": 7513, - "end": 7518, + "start": 7963, + "end": 7968, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 35 }, "identifierName": "label" @@ -8828,15 +9516,15 @@ ], "body": { "type": "UnaryExpression", - "start": 7522, - "end": 7548, + "start": 7972, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 39 }, "end": { - "line": 195, + "line": 214, "column": 65 } }, @@ -8844,43 +9532,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 7523, - "end": 7548, + "start": 7973, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 7523, - "end": 7541, + "start": 7973, + "end": 7991, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 58 } }, "object": { "type": "Identifier", - "start": 7523, - "end": 7537, + "start": 7973, + "end": 7987, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 54 }, "identifierName": "internalLabels" @@ -8889,15 +9577,15 @@ }, "property": { "type": "Identifier", - "start": 7538, - "end": 7541, + "start": 7988, + "end": 7991, "loc": { "start": { - "line": 195, + "line": 214, "column": 55 }, "end": { - "line": 195, + "line": 214, "column": 58 }, "identifierName": "has" @@ -8909,15 +9597,15 @@ "arguments": [ { "type": "Identifier", - "start": 7542, - "end": 7547, + "start": 7992, + "end": 7997, "loc": { "start": { - "line": 195, + "line": 214, "column": 59 }, "end": { - "line": 195, + "line": 214, "column": 64 }, "identifierName": "label" @@ -8941,43 +9629,43 @@ }, { "type": "ThrowStatement", - "start": 7562, - "end": 7613, + "start": 8012, + "end": 8063, "loc": { "start": { - "line": 198, + "line": 217, "column": 4 }, "end": { - "line": 198, + "line": 217, "column": 55 } }, "argument": { "type": "NewExpression", - "start": 7568, - "end": 7612, + "start": 8018, + "end": 8062, "loc": { "start": { - "line": 198, + "line": 217, "column": 10 }, "end": { - "line": 198, + "line": 217, "column": 54 } }, "callee": { "type": "Identifier", - "start": 7572, - "end": 7577, + "start": 8022, + "end": 8027, "loc": { "start": { - "line": 198, + "line": 217, "column": 14 }, "end": { - "line": 198, + "line": 217, "column": 19 }, "identifierName": "Error" @@ -8987,30 +9675,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 7578, - "end": 7611, + "start": 8028, + "end": 8061, "loc": { "start": { - "line": 198, + "line": 217, "column": 20 }, "end": { - "line": 198, + "line": 217, "column": 53 } }, "expressions": [ { "type": "Identifier", - "start": 7600, - "end": 7608, + "start": 8050, + "end": 8058, "loc": { "start": { - "line": 198, + "line": 217, "column": 42 }, "end": { - "line": 198, + "line": 217, "column": 50 }, "identifierName": "nodeType" @@ -9021,15 +9709,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 7579, - "end": 7598, + "start": 8029, + "end": 8048, "loc": { "start": { - "line": 198, + "line": 217, "column": 21 }, "end": { - "line": 198, + "line": 217, "column": 40 } }, @@ -9041,15 +9729,15 @@ }, { "type": "TemplateElement", - "start": 7609, - "end": 7610, + "start": 8059, + "end": 8060, "loc": { "start": { - "line": 198, + "line": 217, "column": 51 }, "end": { - "line": 198, + "line": 217, "column": 52 } }, @@ -9072,15 +9760,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", - "start": 7621, - "end": 7998, + "start": 8071, + "end": 8448, "loc": { "start": { - "line": 201, + "line": 220, "column": 2 }, "end": { - "line": 208, + "line": 227, "column": 5 } } @@ -9089,15 +9777,15 @@ }, { "type": "ClassMethod", - "start": 8001, - "end": 9155, + "start": 8451, + "end": 9605, "loc": { "start": { - "line": 209, + "line": 228, "column": 2 }, "end": { - "line": 234, + "line": 253, "column": 3 } }, @@ -9105,15 +9793,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8001, - "end": 8030, + "start": 8451, + "end": 8480, "loc": { "start": { - "line": 209, + "line": 228, "column": 2 }, "end": { - "line": 209, + "line": 228, "column": 31 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -9129,15 +9817,15 @@ "params": [ { "type": "Identifier", - "start": 8031, - "end": 8040, + "start": 8481, + "end": 8490, "loc": { "start": { - "line": 209, + "line": 228, "column": 32 }, "end": { - "line": 209, + "line": 228, "column": 41 }, "identifierName": "nodeLabel" @@ -9147,59 +9835,59 @@ ], "body": { "type": "BlockStatement", - "start": 8042, - "end": 9155, + "start": 8492, + "end": 9605, "loc": { "start": { - "line": 209, + "line": 228, "column": 43 }, "end": { - "line": 234, + "line": 253, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 8091, - "end": 8125, + "start": 8541, + "end": 8575, "loc": { "start": { - "line": 211, + "line": 230, "column": 4 }, "end": { - "line": 211, + "line": 230, "column": 38 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8095, - "end": 8124, + "start": 8545, + "end": 8574, "loc": { "start": { - "line": 211, + "line": 230, "column": 8 }, "end": { - "line": 211, + "line": 230, "column": 37 } }, "id": { "type": "Identifier", - "start": 8095, - "end": 8119, + "start": 8545, + "end": 8569, "loc": { "start": { - "line": 211, + "line": 230, "column": 8 }, "end": { - "line": 211, + "line": 230, "column": 32 }, "identifierName": "additionalNodeProperties" @@ -9209,15 +9897,15 @@ }, "init": { "type": "ObjectExpression", - "start": 8122, - "end": 8124, + "start": 8572, + "end": 8574, "loc": { "start": { - "line": 211, + "line": 230, "column": 35 }, "end": { - "line": 211, + "line": 230, "column": 37 } }, @@ -9231,15 +9919,15 @@ { "type": "CommentLine", "value": " Look up additional node properties.", - "start": 8048, - "end": 8086, + "start": 8498, + "end": 8536, "loc": { "start": { - "line": 210, + "line": 229, "column": 4 }, "end": { - "line": 210, + "line": 229, "column": 42 } } @@ -9248,57 +9936,57 @@ }, { "type": "IfStatement", - "start": 8130, - "end": 8352, + "start": 8580, + "end": 8802, "loc": { "start": { - "line": 212, + "line": 231, "column": 4 }, "end": { - "line": 217, + "line": 236, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 8141, - "end": 8253, + "start": 8591, + "end": 8703, "loc": { "start": { - "line": 213, + "line": 232, "column": 6 }, "end": { - "line": 214, + "line": 233, "column": 64 } }, "left": { "type": "CallExpression", - "start": 8141, - "end": 8188, + "start": 8591, + "end": 8638, "loc": { "start": { - "line": 213, + "line": 232, "column": 6 }, "end": { - "line": 213, + "line": 232, "column": 53 } }, "callee": { "type": "Identifier", - "start": 8141, - "end": 8144, + "start": 8591, + "end": 8594, "loc": { "start": { - "line": 213, + "line": 232, "column": 6 }, "end": { - "line": 213, + "line": 232, "column": 9 }, "identifierName": "has" @@ -9308,44 +9996,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 8145, - "end": 8159, + "start": 8595, + "end": 8609, "loc": { "start": { - "line": 213, + "line": 232, "column": 10 }, "end": { - "line": 213, + "line": 232, "column": 24 } }, "object": { "type": "ThisExpression", - "start": 8145, - "end": 8149, + "start": 8595, + "end": 8599, "loc": { "start": { - "line": 213, + "line": 232, "column": 10 }, "end": { - "line": 213, + "line": 232, "column": 14 } } }, "property": { "type": "Identifier", - "start": 8150, - "end": 8159, + "start": 8600, + "end": 8609, "loc": { "start": { - "line": 213, + "line": 232, "column": 15 }, "end": { - "line": 213, + "line": 232, "column": 24 }, "identifierName": "phylogeny" @@ -9356,15 +10044,15 @@ }, { "type": "StringLiteral", - "start": 8161, - "end": 8187, + "start": 8611, + "end": 8637, "loc": { "start": { - "line": 213, + "line": 232, "column": 26 }, "end": { - "line": 213, + "line": 232, "column": 52 } }, @@ -9379,29 +10067,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 8198, - "end": 8253, + "start": 8648, + "end": 8703, "loc": { "start": { - "line": 214, + "line": 233, "column": 9 }, "end": { - "line": 214, + "line": 233, "column": 64 } }, "callee": { "type": "Identifier", - "start": 8198, - "end": 8201, + "start": 8648, + "end": 8651, "loc": { "start": { - "line": 214, + "line": 233, "column": 9 }, "end": { - "line": 214, + "line": 233, "column": 12 }, "identifierName": "has" @@ -9411,58 +10099,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 8202, - "end": 8241, + "start": 8652, + "end": 8691, "loc": { "start": { - "line": 214, + "line": 233, "column": 13 }, "end": { - "line": 214, + "line": 233, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 8202, - "end": 8216, + "start": 8652, + "end": 8666, "loc": { "start": { - "line": 214, + "line": 233, "column": 13 }, "end": { - "line": 214, + "line": 233, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 8202, - "end": 8206, + "start": 8652, + "end": 8656, "loc": { "start": { - "line": 214, + "line": 233, "column": 13 }, "end": { - "line": 214, + "line": 233, "column": 17 } } }, "property": { "type": "Identifier", - "start": 8207, - "end": 8216, + "start": 8657, + "end": 8666, "loc": { "start": { - "line": 214, + "line": 233, "column": 18 }, "end": { - "line": 214, + "line": 233, "column": 27 }, "identifierName": "phylogeny" @@ -9473,15 +10161,15 @@ }, "property": { "type": "Identifier", - "start": 8217, - "end": 8241, + "start": 8667, + "end": 8691, "loc": { "start": { - "line": 214, + "line": 233, "column": 28 }, "end": { - "line": 214, + "line": 233, "column": 52 }, "identifierName": "additionalNodeProperties" @@ -9492,15 +10180,15 @@ }, { "type": "Identifier", - "start": 8243, - "end": 8252, + "start": 8693, + "end": 8702, "loc": { "start": { - "line": 214, + "line": 233, "column": 54 }, "end": { - "line": 214, + "line": 233, "column": 63 }, "identifierName": "nodeLabel" @@ -9512,59 +10200,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 8260, - "end": 8352, + "start": 8710, + "end": 8802, "loc": { "start": { - "line": 215, + "line": 234, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 8268, - "end": 8346, + "start": 8718, + "end": 8796, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 84 } }, "expression": { "type": "AssignmentExpression", - "start": 8268, - "end": 8345, + "start": 8718, + "end": 8795, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 83 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8268, - "end": 8292, + "start": 8718, + "end": 8742, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 30 }, "identifierName": "additionalNodeProperties" @@ -9573,72 +10261,72 @@ }, "right": { "type": "MemberExpression", - "start": 8295, - "end": 8345, + "start": 8745, + "end": 8795, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 83 } }, "object": { "type": "MemberExpression", - "start": 8295, - "end": 8334, + "start": 8745, + "end": 8784, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 72 } }, "object": { "type": "MemberExpression", - "start": 8295, - "end": 8309, + "start": 8745, + "end": 8759, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 8295, - "end": 8299, + "start": 8745, + "end": 8749, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 37 } } }, "property": { "type": "Identifier", - "start": 8300, - "end": 8309, + "start": 8750, + "end": 8759, "loc": { "start": { - "line": 216, + "line": 235, "column": 38 }, "end": { - "line": 216, + "line": 235, "column": 47 }, "identifierName": "phylogeny" @@ -9649,15 +10337,15 @@ }, "property": { "type": "Identifier", - "start": 8310, - "end": 8334, + "start": 8760, + "end": 8784, "loc": { "start": { - "line": 216, + "line": 235, "column": 48 }, "end": { - "line": 216, + "line": 235, "column": 72 }, "identifierName": "additionalNodeProperties" @@ -9668,15 +10356,15 @@ }, "property": { "type": "Identifier", - "start": 8335, - "end": 8344, + "start": 8785, + "end": 8794, "loc": { "start": { - "line": 216, + "line": 235, "column": 73 }, "end": { - "line": 216, + "line": 235, "column": 82 }, "identifierName": "nodeLabel" @@ -9696,15 +10384,15 @@ { "type": "CommentLine", "value": " If there are explicit taxonomic units in the", - "start": 8358, - "end": 8405, + "start": 8808, + "end": 8855, "loc": { "start": { - "line": 219, + "line": 238, "column": 4 }, "end": { - "line": 219, + "line": 238, "column": 51 } } @@ -9712,15 +10400,15 @@ { "type": "CommentLine", "value": " representsTaxonomicUnits property, we need to use those.", - "start": 8410, - "end": 8469, + "start": 8860, + "end": 8919, "loc": { "start": { - "line": 220, + "line": 239, "column": 4 }, "end": { - "line": 220, + "line": 239, "column": 63 } } @@ -9729,43 +10417,43 @@ }, { "type": "IfStatement", - "start": 8474, - "end": 8608, + "start": 8924, + "end": 9058, "loc": { "start": { - "line": 221, + "line": 240, "column": 4 }, "end": { - "line": 223, + "line": 242, "column": 5 } }, "test": { "type": "CallExpression", - "start": 8478, - "end": 8535, + "start": 8928, + "end": 8985, "loc": { "start": { - "line": 221, + "line": 240, "column": 8 }, "end": { - "line": 221, + "line": 240, "column": 65 } }, "callee": { "type": "Identifier", - "start": 8478, - "end": 8481, + "start": 8928, + "end": 8931, "loc": { "start": { - "line": 221, + "line": 240, "column": 8 }, "end": { - "line": 221, + "line": 240, "column": 11 }, "identifierName": "has" @@ -9776,15 +10464,15 @@ "arguments": [ { "type": "Identifier", - "start": 8482, - "end": 8506, + "start": 8932, + "end": 8956, "loc": { "start": { - "line": 221, + "line": 240, "column": 12 }, "end": { - "line": 221, + "line": 240, "column": 36 }, "identifierName": "additionalNodeProperties" @@ -9793,15 +10481,15 @@ }, { "type": "StringLiteral", - "start": 8508, - "end": 8534, + "start": 8958, + "end": 8984, "loc": { "start": { - "line": 221, + "line": 240, "column": 38 }, "end": { - "line": 221, + "line": 240, "column": 64 } }, @@ -9816,58 +10504,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 8537, - "end": 8608, + "start": 8987, + "end": 9058, "loc": { "start": { - "line": 221, + "line": 240, "column": 67 }, "end": { - "line": 223, + "line": 242, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 8545, - "end": 8602, + "start": 8995, + "end": 9052, "loc": { "start": { - "line": 222, + "line": 241, "column": 6 }, "end": { - "line": 222, + "line": 241, "column": 63 } }, "argument": { "type": "MemberExpression", - "start": 8552, - "end": 8601, + "start": 9002, + "end": 9051, "loc": { "start": { - "line": 222, + "line": 241, "column": 13 }, "end": { - "line": 222, + "line": 241, "column": 62 } }, "object": { "type": "Identifier", - "start": 8552, - "end": 8576, + "start": 9002, + "end": 9026, "loc": { "start": { - "line": 222, + "line": 241, "column": 13 }, "end": { - "line": 222, + "line": 241, "column": 37 }, "identifierName": "additionalNodeProperties" @@ -9876,15 +10564,15 @@ }, "property": { "type": "Identifier", - "start": 8577, - "end": 8601, + "start": 9027, + "end": 9051, "loc": { "start": { - "line": 222, + "line": 241, "column": 38 }, "end": { - "line": 222, + "line": 241, "column": 62 }, "identifierName": "representsTaxonomicUnits" @@ -9903,15 +10591,15 @@ { "type": "CommentLine", "value": " If there are explicit taxonomic units in the", - "start": 8358, - "end": 8405, + "start": 8808, + "end": 8855, "loc": { "start": { - "line": 219, + "line": 238, "column": 4 }, "end": { - "line": 219, + "line": 238, "column": 51 } } @@ -9919,15 +10607,15 @@ { "type": "CommentLine", "value": " representsTaxonomicUnits property, we need to use those.", - "start": 8410, - "end": 8469, + "start": 8860, + "end": 8919, "loc": { "start": { - "line": 220, + "line": 239, "column": 4 }, "end": { - "line": 220, + "line": 239, "column": 63 } } @@ -9937,15 +10625,15 @@ { "type": "CommentLine", "value": " If that doesn't work, we can try to extract scientific names from", - "start": 8614, - "end": 8682, + "start": 9064, + "end": 9132, "loc": { "start": { - "line": 225, + "line": 244, "column": 4 }, "end": { - "line": 225, + "line": 244, "column": 72 } } @@ -9953,15 +10641,15 @@ { "type": "CommentLine", "value": " the node label. Note that taxonomic units will NOT be extracted from", - "start": 8687, - "end": 8758, + "start": 9137, + "end": 9208, "loc": { "start": { - "line": 226, + "line": 245, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 75 } } @@ -9969,15 +10657,15 @@ { "type": "CommentLine", "value": " the label if there is a taxonomic unit present!", - "start": 8763, - "end": 8813, + "start": 9213, + "end": 9263, "loc": { "start": { - "line": 227, + "line": 246, "column": 4 }, "end": { - "line": 227, + "line": 246, "column": 54 } } @@ -9985,15 +10673,15 @@ { "type": "CommentLine", "value": "", - "start": 8818, - "end": 8820, + "start": 9268, + "end": 9270, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 6 } } @@ -10001,15 +10689,15 @@ { "type": "CommentLine", "value": " Note that old-style taxonomic units were lists while new-style taxonomic", - "start": 8825, - "end": 8900, + "start": 9275, + "end": 9350, "loc": { "start": { - "line": 229, + "line": 248, "column": 4 }, "end": { - "line": 229, + "line": 248, "column": 79 } } @@ -10017,15 +10705,15 @@ { "type": "CommentLine", "value": " units are single objects. So we turn it into a single entry list here.", - "start": 8905, - "end": 8978, + "start": 9355, + "end": 9428, "loc": { "start": { - "line": 230, + "line": 249, "column": 4 }, "end": { - "line": 230, + "line": 249, "column": 77 } } @@ -10034,44 +10722,44 @@ }, { "type": "VariableDeclaration", - "start": 8983, - "end": 9069, + "start": 9433, + "end": 9519, "loc": { "start": { - "line": 231, + "line": 250, "column": 4 }, "end": { - "line": 231, + "line": 250, "column": 90 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8989, - "end": 9068, + "start": 9439, + "end": 9518, "loc": { "start": { - "line": 231, + "line": 250, "column": 10 }, "end": { - "line": 231, + "line": 250, "column": 89 } }, "id": { "type": "Identifier", - "start": 8989, - "end": 8994, + "start": 9439, + "end": 9444, "loc": { "start": { - "line": 231, + "line": 250, "column": 10 }, "end": { - "line": 231, + "line": 250, "column": 15 }, "identifierName": "tunit" @@ -10081,43 +10769,43 @@ }, "init": { "type": "CallExpression", - "start": 8997, - "end": 9068, + "start": 9447, + "end": 9518, "loc": { "start": { - "line": 231, + "line": 250, "column": 18 }, "end": { - "line": 231, + "line": 250, "column": 89 } }, "callee": { "type": "MemberExpression", - "start": 8997, - "end": 9027, + "start": 9447, + "end": 9477, "loc": { "start": { - "line": 231, + "line": 250, "column": 18 }, "end": { - "line": 231, + "line": 250, "column": 48 } }, "object": { "type": "Identifier", - "start": 8997, - "end": 9017, + "start": 9447, + "end": 9467, "loc": { "start": { - "line": 231, + "line": 250, "column": 18 }, "end": { - "line": 231, + "line": 250, "column": 38 }, "identifierName": "TaxonomicUnitWrapper" @@ -10126,15 +10814,15 @@ }, "property": { "type": "Identifier", - "start": 9018, - "end": 9027, + "start": 9468, + "end": 9477, "loc": { "start": { - "line": 231, + "line": 250, "column": 39 }, "end": { - "line": 231, + "line": 250, "column": 48 }, "identifierName": "fromLabel" @@ -10146,43 +10834,43 @@ "arguments": [ { "type": "CallExpression", - "start": 9028, - "end": 9044, + "start": 9478, + "end": 9494, "loc": { "start": { - "line": 231, + "line": 250, "column": 49 }, "end": { - "line": 231, + "line": 250, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 9028, - "end": 9042, + "start": 9478, + "end": 9492, "loc": { "start": { - "line": 231, + "line": 250, "column": 49 }, "end": { - "line": 231, + "line": 250, "column": 63 } }, "object": { "type": "Identifier", - "start": 9028, - "end": 9037, + "start": 9478, + "end": 9487, "loc": { "start": { - "line": 231, + "line": 250, "column": 49 }, "end": { - "line": 231, + "line": 250, "column": 58 }, "identifierName": "nodeLabel" @@ -10191,15 +10879,15 @@ }, "property": { "type": "Identifier", - "start": 9038, - "end": 9042, + "start": 9488, + "end": 9492, "loc": { "start": { - "line": 231, + "line": 250, "column": 59 }, "end": { - "line": 231, + "line": 250, "column": 63 }, "identifierName": "trim" @@ -10212,44 +10900,44 @@ }, { "type": "MemberExpression", - "start": 9046, - "end": 9067, + "start": 9496, + "end": 9517, "loc": { "start": { - "line": 231, + "line": 250, "column": 67 }, "end": { - "line": 231, + "line": 250, "column": 88 } }, "object": { "type": "ThisExpression", - "start": 9046, - "end": 9050, + "start": 9496, + "end": 9500, "loc": { "start": { - "line": 231, + "line": 250, "column": 67 }, "end": { - "line": 231, + "line": 250, "column": 71 } } }, "property": { "type": "Identifier", - "start": 9051, - "end": 9067, + "start": 9501, + "end": 9517, "loc": { "start": { - "line": 231, + "line": 250, "column": 72 }, "end": { - "line": 231, + "line": 250, "column": 88 }, "identifierName": "defaultNomenCode" @@ -10268,15 +10956,15 @@ { "type": "CommentLine", "value": " If that doesn't work, we can try to extract scientific names from", - "start": 8614, - "end": 8682, + "start": 9064, + "end": 9132, "loc": { "start": { - "line": 225, + "line": 244, "column": 4 }, "end": { - "line": 225, + "line": 244, "column": 72 } } @@ -10284,15 +10972,15 @@ { "type": "CommentLine", "value": " the node label. Note that taxonomic units will NOT be extracted from", - "start": 8687, - "end": 8758, + "start": 9137, + "end": 9208, "loc": { "start": { - "line": 226, + "line": 245, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 75 } } @@ -10300,15 +10988,15 @@ { "type": "CommentLine", "value": " the label if there is a taxonomic unit present!", - "start": 8763, - "end": 8813, + "start": 9213, + "end": 9263, "loc": { "start": { - "line": 227, + "line": 246, "column": 4 }, "end": { - "line": 227, + "line": 246, "column": 54 } } @@ -10316,15 +11004,15 @@ { "type": "CommentLine", "value": "", - "start": 8818, - "end": 8820, + "start": 9268, + "end": 9270, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 6 } } @@ -10332,15 +11020,15 @@ { "type": "CommentLine", "value": " Note that old-style taxonomic units were lists while new-style taxonomic", - "start": 8825, - "end": 8900, + "start": 9275, + "end": 9350, "loc": { "start": { - "line": 229, + "line": 248, "column": 4 }, "end": { - "line": 229, + "line": 248, "column": 79 } } @@ -10348,15 +11036,15 @@ { "type": "CommentLine", "value": " units are single objects. So we turn it into a single entry list here.", - "start": 8905, - "end": 8978, + "start": 9355, + "end": 9428, "loc": { "start": { - "line": 230, + "line": 249, "column": 4 }, "end": { - "line": 230, + "line": 249, "column": 77 } } @@ -10365,29 +11053,29 @@ }, { "type": "IfStatement", - "start": 9074, - "end": 9100, + "start": 9524, + "end": 9550, "loc": { "start": { - "line": 232, + "line": 251, "column": 4 }, "end": { - "line": 232, + "line": 251, "column": 30 } }, "test": { "type": "Identifier", - "start": 9078, - "end": 9083, + "start": 9528, + "end": 9533, "loc": { "start": { - "line": 232, + "line": 251, "column": 8 }, "end": { - "line": 232, + "line": 251, "column": 13 }, "identifierName": "tunit" @@ -10396,44 +11084,44 @@ }, "consequent": { "type": "ReturnStatement", - "start": 9085, - "end": 9100, + "start": 9535, + "end": 9550, "loc": { "start": { - "line": 232, + "line": 251, "column": 15 }, "end": { - "line": 232, + "line": 251, "column": 30 } }, "argument": { "type": "ArrayExpression", - "start": 9092, - "end": 9099, + "start": 9542, + "end": 9549, "loc": { "start": { - "line": 232, + "line": 251, "column": 22 }, "end": { - "line": 232, + "line": 251, "column": 29 } }, "elements": [ { "type": "Identifier", - "start": 9093, - "end": 9098, + "start": 9543, + "end": 9548, "loc": { "start": { - "line": 232, + "line": 251, "column": 23 }, "end": { - "line": 232, + "line": 251, "column": 28 }, "identifierName": "tunit" @@ -10447,29 +11135,29 @@ }, { "type": "ReturnStatement", - "start": 9105, - "end": 9115, + "start": 9555, + "end": 9565, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 14 } }, "argument": { "type": "ArrayExpression", - "start": 9112, - "end": 9114, + "start": 9562, + "end": 9564, "loc": { "start": { - "line": 233, + "line": 252, "column": 11 }, "end": { - "line": 233, + "line": 252, "column": 13 } }, @@ -10479,15 +11167,15 @@ { "type": "CommentLine", "value": " No TUnit? Return the empty list.", - "start": 9116, - "end": 9151, + "start": 9566, + "end": 9601, "loc": { "start": { - "line": 233, + "line": 252, "column": 15 }, "end": { - "line": 233, + "line": 252, "column": 50 } } @@ -10501,15 +11189,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", - "start": 7621, - "end": 7998, + "start": 8071, + "end": 8448, "loc": { "start": { - "line": 201, + "line": 220, "column": 2 }, "end": { - "line": 208, + "line": 227, "column": 5 } } @@ -10518,15 +11206,15 @@ }, { "type": "ClassMethod", - "start": 9159, - "end": 9756, + "start": 9609, + "end": 10206, "loc": { "start": { - "line": 236, + "line": 255, "column": 2 }, "end": { - "line": 251, + "line": 270, "column": 3 } }, @@ -10534,15 +11222,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9159, - "end": 9190, + "start": 9609, + "end": 9640, "loc": { "start": { - "line": 236, + "line": 255, "column": 2 }, "end": { - "line": 236, + "line": 255, "column": 33 }, "identifierName": "getNodeLabelsMatchedBySpecifier" @@ -10557,15 +11245,15 @@ "params": [ { "type": "Identifier", - "start": 9191, - "end": 9200, + "start": 9641, + "end": 9650, "loc": { "start": { - "line": 236, + "line": 255, "column": 34 }, "end": { - "line": 236, + "line": 255, "column": 43 }, "identifierName": "specifier" @@ -10575,100 +11263,100 @@ ], "body": { "type": "BlockStatement", - "start": 9202, - "end": 9756, + "start": 9652, + "end": 10206, "loc": { "start": { - "line": 236, + "line": 255, "column": 45 }, "end": { - "line": 251, + "line": 270, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 9303, - "end": 9752, + "start": 9753, + "end": 10202, "loc": { "start": { - "line": 240, + "line": 259, "column": 4 }, "end": { - "line": 250, + "line": 269, "column": 7 } }, "argument": { "type": "CallExpression", - "start": 9310, - "end": 9751, + "start": 9760, + "end": 10201, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 250, + "line": 269, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 9310, - "end": 9337, + "start": 9760, + "end": 9787, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 38 } }, "object": { "type": "CallExpression", - "start": 9310, - "end": 9330, + "start": 9760, + "end": 9780, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 31 } }, "callee": { "type": "MemberExpression", - "start": 9310, - "end": 9328, + "start": 9760, + "end": 9778, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 29 } }, "object": { "type": "ThisExpression", - "start": 9310, - "end": 9314, + "start": 9760, + "end": 9764, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 15 } }, @@ -10676,15 +11364,15 @@ }, "property": { "type": "Identifier", - "start": 9315, - "end": 9328, + "start": 9765, + "end": 9778, "loc": { "start": { - "line": 240, + "line": 259, "column": 16 }, "end": { - "line": 240, + "line": 259, "column": 29 }, "identifierName": "getNodeLabels" @@ -10699,15 +11387,15 @@ }, "property": { "type": "Identifier", - "start": 9331, - "end": 9337, + "start": 9781, + "end": 9787, "loc": { "start": { - "line": 240, + "line": 259, "column": 32 }, "end": { - "line": 240, + "line": 259, "column": 38 }, "identifierName": "filter" @@ -10720,15 +11408,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 9338, - "end": 9750, + "start": 9788, + "end": 10200, "loc": { "start": { - "line": 240, + "line": 259, "column": 39 }, "end": { - "line": 250, + "line": 269, "column": 5 } }, @@ -10739,15 +11427,15 @@ "params": [ { "type": "Identifier", - "start": 9339, - "end": 9348, + "start": 9789, + "end": 9798, "loc": { "start": { - "line": 240, + "line": 259, "column": 40 }, "end": { - "line": 240, + "line": 259, "column": 49 }, "identifierName": "nodeLabel" @@ -10757,59 +11445,59 @@ ], "body": { "type": "BlockStatement", - "start": 9353, - "end": 9750, + "start": 9803, + "end": 10200, "loc": { "start": { - "line": 240, + "line": 259, "column": 54 }, "end": { - "line": 250, + "line": 269, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 9457, - "end": 9522, + "start": 9907, + "end": 9972, "loc": { "start": { - "line": 243, + "line": 262, "column": 6 }, "end": { - "line": 243, + "line": 262, "column": 71 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 9463, - "end": 9521, + "start": 9913, + "end": 9971, "loc": { "start": { - "line": 243, + "line": 262, "column": 12 }, "end": { - "line": 243, + "line": 262, "column": 70 } }, "id": { "type": "Identifier", - "start": 9463, - "end": 9473, + "start": 9913, + "end": 9923, "loc": { "start": { - "line": 243, + "line": 262, "column": 12 }, "end": { - "line": 243, + "line": 262, "column": 22 }, "identifierName": "nodeTUnits" @@ -10819,58 +11507,58 @@ }, "init": { "type": "CallExpression", - "start": 9476, - "end": 9521, + "start": 9926, + "end": 9971, "loc": { "start": { - "line": 243, + "line": 262, "column": 25 }, "end": { - "line": 243, + "line": 262, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 9476, - "end": 9510, + "start": 9926, + "end": 9960, "loc": { "start": { - "line": 243, + "line": 262, "column": 25 }, "end": { - "line": 243, + "line": 262, "column": 59 } }, "object": { "type": "ThisExpression", - "start": 9476, - "end": 9480, + "start": 9926, + "end": 9930, "loc": { "start": { - "line": 243, + "line": 262, "column": 25 }, "end": { - "line": 243, + "line": 262, "column": 29 } } }, "property": { "type": "Identifier", - "start": 9481, - "end": 9510, + "start": 9931, + "end": 9960, "loc": { "start": { - "line": 243, + "line": 262, "column": 30 }, "end": { - "line": 243, + "line": 262, "column": 59 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -10882,15 +11570,15 @@ "arguments": [ { "type": "Identifier", - "start": 9511, - "end": 9520, + "start": 9961, + "end": 9970, "loc": { "start": { - "line": 243, + "line": 262, "column": 60 }, "end": { - "line": 243, + "line": 262, "column": 69 }, "identifierName": "nodeLabel" @@ -10907,15 +11595,15 @@ { "type": "CommentLine", "value": " Find all the taxonomic units associated with the specifier and", - "start": 9361, - "end": 9426, + "start": 9811, + "end": 9876, "loc": { "start": { - "line": 241, + "line": 260, "column": 6 }, "end": { - "line": 241, + "line": 260, "column": 71 } } @@ -10923,15 +11611,15 @@ { "type": "CommentLine", "value": " with the node.", - "start": 9433, - "end": 9450, + "start": 9883, + "end": 9900, "loc": { "start": { - "line": 242, + "line": 261, "column": 6 }, "end": { - "line": 242, + "line": 261, "column": 23 } } @@ -10941,15 +11629,15 @@ { "type": "CommentLine", "value": " Attempt pairwise matches between taxonomic units in the specifier", - "start": 9530, - "end": 9598, + "start": 9980, + "end": 10048, "loc": { "start": { - "line": 245, + "line": 264, "column": 6 }, "end": { - "line": 245, + "line": 264, "column": 74 } } @@ -10957,15 +11645,15 @@ { "type": "CommentLine", "value": " and associated with the node.", - "start": 9605, - "end": 9637, + "start": 10055, + "end": 10087, "loc": { "start": { - "line": 246, + "line": 265, "column": 6 }, "end": { - "line": 246, + "line": 265, "column": 38 } } @@ -10974,57 +11662,57 @@ }, { "type": "ReturnStatement", - "start": 9644, - "end": 9744, + "start": 10094, + "end": 10194, "loc": { "start": { - "line": 247, + "line": 266, "column": 6 }, "end": { - "line": 249, + "line": 268, "column": 8 } }, "argument": { "type": "CallExpression", - "start": 9651, - "end": 9743, + "start": 10101, + "end": 10193, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 249, + "line": 268, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 9651, - "end": 9666, + "start": 10101, + "end": 10116, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 247, + "line": 266, "column": 28 } }, "object": { "type": "Identifier", - "start": 9651, - "end": 9661, + "start": 10101, + "end": 10111, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 247, + "line": 266, "column": 23 }, "identifierName": "nodeTUnits" @@ -11034,15 +11722,15 @@ }, "property": { "type": "Identifier", - "start": 9662, - "end": 9666, + "start": 10112, + "end": 10116, "loc": { "start": { - "line": 247, + "line": 266, "column": 24 }, "end": { - "line": 247, + "line": 266, "column": 28 }, "identifierName": "some" @@ -11055,15 +11743,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 9676, - "end": 9735, + "start": 10126, + "end": 10185, "loc": { "start": { - "line": 248, + "line": 267, "column": 8 }, "end": { - "line": 248, + "line": 267, "column": 67 } }, @@ -11074,15 +11762,15 @@ "params": [ { "type": "Identifier", - "start": 9676, - "end": 9681, + "start": 10126, + "end": 10131, "loc": { "start": { - "line": 248, + "line": 267, "column": 8 }, "end": { - "line": 248, + "line": 267, "column": 13 }, "identifierName": "tunit" @@ -11092,43 +11780,43 @@ ], "body": { "type": "MemberExpression", - "start": 9685, - "end": 9735, + "start": 10135, + "end": 10185, "loc": { "start": { - "line": 248, + "line": 267, "column": 17 }, "end": { - "line": 248, + "line": 267, "column": 67 } }, "object": { "type": "NewExpression", - "start": 9685, - "end": 9727, + "start": 10135, + "end": 10177, "loc": { "start": { - "line": 248, + "line": 267, "column": 17 }, "end": { - "line": 248, + "line": 267, "column": 59 } }, "callee": { "type": "Identifier", - "start": 9689, - "end": 9709, + "start": 10139, + "end": 10159, "loc": { "start": { - "line": 248, + "line": 267, "column": 21 }, "end": { - "line": 248, + "line": 267, "column": 41 }, "identifierName": "TaxonomicUnitMatcher" @@ -11138,15 +11826,15 @@ "arguments": [ { "type": "Identifier", - "start": 9710, - "end": 9719, + "start": 10160, + "end": 10169, "loc": { "start": { - "line": 248, + "line": 267, "column": 42 }, "end": { - "line": 248, + "line": 267, "column": 51 }, "identifierName": "specifier" @@ -11155,15 +11843,15 @@ }, { "type": "Identifier", - "start": 9721, - "end": 9726, + "start": 10171, + "end": 10176, "loc": { "start": { - "line": 248, + "line": 267, "column": 53 }, "end": { - "line": 248, + "line": 267, "column": 58 }, "identifierName": "tunit" @@ -11174,15 +11862,15 @@ }, "property": { "type": "Identifier", - "start": 9728, - "end": 9735, + "start": 10178, + "end": 10185, "loc": { "start": { - "line": 248, + "line": 267, "column": 60 }, "end": { - "line": 248, + "line": 267, "column": 67 }, "identifierName": "matched" @@ -11199,15 +11887,15 @@ { "type": "CommentLine", "value": " Attempt pairwise matches between taxonomic units in the specifier", - "start": 9530, - "end": 9598, + "start": 9980, + "end": 10048, "loc": { "start": { - "line": 245, + "line": 264, "column": 6 }, "end": { - "line": 245, + "line": 264, "column": 74 } } @@ -11215,15 +11903,15 @@ { "type": "CommentLine", "value": " and associated with the node.", - "start": 9605, - "end": 9637, + "start": 10055, + "end": 10087, "loc": { "start": { - "line": 246, + "line": 265, "column": 6 }, "end": { - "line": 246, + "line": 265, "column": 38 } } @@ -11241,15 +11929,15 @@ { "type": "CommentLine", "value": " Return a list of node labels matched by a given specifier on", - "start": 9208, - "end": 9271, + "start": 9658, + "end": 9721, "loc": { "start": { - "line": 237, + "line": 256, "column": 4 }, "end": { - "line": 237, + "line": 256, "column": 67 } } @@ -11257,15 +11945,15 @@ { "type": "CommentLine", "value": " a given phylogeny.", - "start": 9276, - "end": 9297, + "start": 9726, + "end": 9747, "loc": { "start": { - "line": 238, + "line": 257, "column": 4 }, "end": { - "line": 238, + "line": 257, "column": 25 } } @@ -11278,15 +11966,15 @@ }, { "type": "ClassMethod", - "start": 9760, - "end": 11006, + "start": 10210, + "end": 11456, "loc": { "start": { - "line": 253, + "line": 272, "column": 2 }, "end": { - "line": 282, + "line": 301, "column": 3 } }, @@ -11294,15 +11982,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9767, - "end": 9782, + "start": 10217, + "end": 10232, "loc": { "start": { - "line": 253, + "line": 272, "column": 9 }, "end": { - "line": 253, + "line": 272, "column": 24 }, "identifierName": "getParsedNewick" @@ -11317,15 +12005,15 @@ "params": [ { "type": "Identifier", - "start": 9783, - "end": 9789, + "start": 10233, + "end": 10239, "loc": { "start": { - "line": 253, + "line": 272, "column": 25 }, "end": { - "line": 253, + "line": 272, "column": 31 }, "identifierName": "newick" @@ -11335,74 +12023,74 @@ ], "body": { "type": "BlockStatement", - 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"line": 259, + "line": 278, "column": 12 }, "end": { - "line": 259, + "line": 278, "column": 17 } }, @@ -11411,15 +12099,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10107, - "end": 10112, + "start": 10557, + "end": 10562, "loc": { "start": { - "line": 259, + "line": 278, "column": 12 }, "end": { - "line": 259, + "line": 278, "column": 17 }, "identifierName": "graph" @@ -11429,15 +12117,15 @@ }, "value": { "type": "Identifier", - "start": 10107, - "end": 10112, + "start": 10557, + "end": 10562, "loc": { "start": { - "line": 259, + "line": 278, "column": 12 }, "end": { - "line": 259, + "line": 278, "column": 17 }, "identifierName": "graph" @@ -11451,15 +12139,15 @@ }, { "type": "ObjectProperty", - "start": 10114, - "end": 10118, + "start": 10564, + "end": 10568, "loc": { "start": { - "line": 259, + "line": 278, "column": 19 }, "end": { - "line": 259, + "line": 278, "column": 23 } }, @@ -11468,15 +12156,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10114, - "end": 10118, + "start": 10564, + "end": 10568, "loc": { "start": { - "line": 259, + "line": 278, "column": 19 }, "end": { - "line": 259, + "line": 278, "column": 23 }, "identifierName": "root" @@ -11485,15 +12173,15 @@ }, "value": { "type": "Identifier", - "start": 10114, - "end": 10118, + "start": 10564, + "end": 10568, "loc": { "start": { - "line": 259, + "line": 278, "column": 19 }, "end": { - "line": 259, + "line": 278, "column": 23 }, "identifierName": "root" @@ -11506,15 +12194,15 @@ }, { "type": "ObjectProperty", - "start": 10120, - "end": 10130, + "start": 10570, + "end": 10580, "loc": { "start": { - "line": 259, + "line": 278, "column": 25 }, "end": { - "line": 259, + "line": 278, "column": 35 } }, @@ -11523,15 +12211,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10120, - "end": 10130, + "start": 10570, + "end": 10580, "loc": { "start": { - "line": 259, + "line": 278, "column": 25 }, "end": { - "line": 259, + "line": 278, "column": 35 }, "identifierName": "rootWeight" @@ -11540,15 +12228,15 @@ }, "value": { "type": "Identifier", - "start": 10120, - "end": 10130, + "start": 10570, + "end": 10580, "loc": { "start": { - "line": 259, + "line": 278, "column": 25 }, "end": { - "line": 259, + "line": 278, "column": 35 }, "identifierName": "rootWeight" @@ -11564,43 +12252,43 @@ }, "init": { "type": "CallExpression", - "start": 10135, - "end": 10157, + "start": 10585, + "end": 10607, "loc": { "start": { - "line": 259, + "line": 278, "column": 40 }, "end": { - "line": 259, + "line": 278, "column": 62 } }, "callee": { "type": "MemberExpression", - "start": 10135, - "end": 10149, + "start": 10585, + "end": 10599, "loc": { "start": { - "line": 259, + "line": 278, "column": 40 }, "end": { - "line": 259, + "line": 278, "column": 54 } }, "object": { "type": "Identifier", - "start": 10135, - "end": 10143, + "start": 10585, + "end": 10593, "loc": { "start": { - "line": 259, + "line": 278, "column": 40 }, "end": { - "line": 259, + "line": 278, "column": 48 }, "identifierName": "newickJs" @@ -11609,15 +12297,15 @@ }, "property": { "type": "Identifier", - "start": 10144, - "end": 10149, + "start": 10594, + "end": 10599, "loc": { "start": { - "line": 259, + "line": 278, "column": 49 }, "end": { - "line": 259, + "line": 278, "column": 54 }, "identifierName": "parse" @@ -11629,15 +12317,15 @@ "arguments": [ { "type": "Identifier", - "start": 10150, - "end": 10156, + "start": 10600, + "end": 10606, "loc": { "start": { - "line": 259, + "line": 278, "column": 55 }, "end": { - "line": 259, + "line": 278, "column": 61 }, "identifierName": "newick" @@ -11654,15 +12342,15 @@ { "type": "CommentLine", "value": " We previously used phylotree.js's Newick parser to parse Newick into a", - "start": 9797, - "end": 9870, + "start": 10247, + "end": 10320, "loc": { "start": { - "line": 254, + "line": 273, "column": 4 }, "end": { - "line": 254, + "line": 273, "column": 77 } } @@ -11670,15 +12358,15 @@ { "type": "CommentLine", "value": " tree-like structure. However, this is difficult to integrate using NPM.", - "start": 9875, - "end": 9949, + "start": 10325, + "end": 10399, "loc": { "start": { - "line": 255, + "line": 274, "column": 4 }, "end": { - "line": 255, + "line": 274, "column": 78 } } @@ -11686,15 +12374,15 @@ { "type": "CommentLine", "value": " This method provides a similar facility using the newick-js library.", - "start": 9954, - "end": 10025, + "start": 10404, + "end": 10475, "loc": { "start": { - "line": 256, + "line": 275, "column": 4 }, "end": { - "line": 256, + "line": 275, "column": 75 } } @@ -11702,15 +12390,15 @@ { "type": "CommentLine", "value": "", - "start": 10030, - "end": 10032, + "start": 10480, + "end": 10482, "loc": { "start": { - "line": 257, + "line": 276, "column": 4 }, "end": { - "line": 257, + "line": 276, "column": 6 } } @@ -11718,15 +12406,15 @@ { "type": "CommentLine", "value": " Throws an exception if the Newick could not be parsed.", - "start": 10037, - "end": 10094, + "start": 10487, + "end": 10544, "loc": { "start": { - "line": 258, + "line": 277, "column": 4 }, "end": { - "line": 258, + "line": 277, "column": 61 } } @@ -11735,44 +12423,44 @@ }, { "type": "VariableDeclaration", - "start": 10163, - "end": 10186, + "start": 10613, + "end": 10636, "loc": { "start": { - "line": 260, + "line": 279, "column": 4 }, "end": { - "line": 260, + "line": 279, "column": 27 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10169, - "end": 10185, + "start": 10619, + "end": 10635, "loc": { "start": { - "line": 260, + "line": 279, "column": 10 }, "end": { - "line": 260, + "line": 279, "column": 26 } }, "id": { "type": "ArrayPattern", - "start": 10169, - "end": 10177, + "start": 10619, + "end": 10627, "loc": { "start": { - "line": 260, + "line": 279, "column": 10 }, "end": { - "line": 260, + "line": 279, "column": 18 } }, @@ -11780,15 +12468,15 @@ null, { "type": "Identifier", - "start": 10172, - "end": 10176, + "start": 10622, + "end": 10626, "loc": { "start": { - "line": 260, + "line": 279, "column": 13 }, "end": { - "line": 260, + "line": 279, "column": 17 }, "identifierName": "arcs" @@ -11799,15 +12487,15 @@ }, "init": { "type": "Identifier", - "start": 10180, - "end": 10185, + "start": 10630, + "end": 10635, "loc": { "start": { - "line": 260, + "line": 279, "column": 21 }, "end": { - "line": 260, + "line": 279, "column": 26 }, "identifierName": "graph" @@ -11821,15 +12509,15 @@ { "type": "CommentLine", "value": " Go through the arcs, assigning 'children' to the appropriate parent node.", - "start": 10192, - "end": 10268, + "start": 10642, + "end": 10718, "loc": { "start": { - "line": 262, + "line": 281, "column": 4 }, "end": { - "line": 262, + "line": 281, "column": 80 } } @@ -11838,57 +12526,57 @@ }, { "type": "ExpressionStatement", - "start": 10273, - "end": 10838, + "start": 10723, + "end": 11288, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 276, + "line": 295, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 10273, - "end": 10837, + "start": 10723, + "end": 11287, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 276, + "line": 295, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 10273, - "end": 10285, + "start": 10723, + "end": 10735, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 16 } }, "object": { "type": "Identifier", - "start": 10273, - "end": 10277, + "start": 10723, + "end": 10727, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 8 }, "identifierName": "arcs" @@ -11898,15 +12586,15 @@ }, "property": { "type": "Identifier", - "start": 10278, - "end": 10285, + "start": 10728, + "end": 10735, "loc": { "start": { - "line": 263, + "line": 282, "column": 9 }, "end": { - "line": 263, + "line": 282, "column": 16 }, "identifierName": "forEach" @@ -11919,15 +12607,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 10286, - "end": 10836, + "start": 10736, + "end": 11286, "loc": { "start": { - "line": 263, + "line": 282, "column": 17 }, "end": { - "line": 276, + "line": 295, "column": 5 } }, @@ -11938,15 +12626,15 @@ "params": [ { "type": "Identifier", - "start": 10287, - "end": 10290, + "start": 10737, + "end": 10740, "loc": { "start": { - "line": 263, + "line": 282, "column": 18 }, "end": { - "line": 263, + "line": 282, "column": 21 }, "identifierName": "arc" @@ -11956,74 +12644,74 @@ ], "body": { "type": "BlockStatement", - "start": 10295, - "end": 10836, + "start": 10745, + "end": 11286, "loc": { "start": { - "line": 263, + "line": 282, "column": 26 }, "end": { - "line": 276, + "line": 295, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 10303, - "end": 10339, + "start": 10753, + "end": 10789, "loc": { "start": { - "line": 264, + "line": 283, "column": 6 }, "end": { - "line": 264, + "line": 283, "column": 42 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10309, - "end": 10338, + "start": 10759, + "end": 10788, "loc": { "start": { - "line": 264, + "line": 283, "column": 12 }, "end": { - "line": 264, + "line": 283, "column": 41 } }, "id": { "type": "ArrayPattern", - "start": 10309, - "end": 10332, + "start": 10759, + "end": 10782, "loc": { "start": { - "line": 264, + "line": 283, "column": 12 }, "end": { - "line": 264, + "line": 283, "column": 35 } }, "elements": [ { "type": "Identifier", - "start": 10310, - "end": 10316, + "start": 10760, + "end": 10766, "loc": { "start": { - "line": 264, + "line": 283, "column": 13 }, "end": { - "line": 264, + "line": 283, "column": 19 }, "identifierName": "parent" @@ -12032,15 +12720,15 @@ }, { "type": "Identifier", - "start": 10318, - "end": 10323, + "start": 10768, + "end": 10773, "loc": { "start": { - "line": 264, + "line": 283, "column": 21 }, "end": { - "line": 264, + "line": 283, "column": 26 }, "identifierName": "child" @@ -12049,15 +12737,15 @@ }, { "type": "Identifier", - "start": 10325, - "end": 10331, + "start": 10775, + "end": 10781, "loc": { "start": { - "line": 264, + "line": 283, "column": 28 }, "end": { - "line": 264, + "line": 283, "column": 34 }, "identifierName": "weight" @@ -12068,15 +12756,15 @@ }, "init": { "type": "Identifier", - "start": 10335, - "end": 10338, + "start": 10785, + "end": 10788, "loc": { "start": { - "line": 264, + "line": 283, "column": 38 }, "end": { - "line": 264, + "line": 283, "column": 41 }, "identifierName": "arc" @@ -12090,15 +12778,15 @@ { "type": "CommentLine", "value": " Add child to parent.children.", - "start": 10347, - "end": 10379, + "start": 10797, + "end": 10829, "loc": { "start": { - "line": 266, + "line": 285, "column": 6 }, "end": { - "line": 266, + "line": 285, "column": 38 } } @@ -12107,29 +12795,29 @@ }, { "type": "IfStatement", - "start": 10386, - "end": 10437, + "start": 10836, + "end": 10887, "loc": { "start": { - "line": 267, + "line": 286, "column": 6 }, "end": { - "line": 267, + "line": 286, "column": 57 } }, "test": { "type": "UnaryExpression", - "start": 10390, - "end": 10414, + "start": 10840, + "end": 10864, "loc": { "start": { - "line": 267, + "line": 286, "column": 10 }, "end": { - "line": 267, + "line": 286, "column": 34 } }, @@ -12137,29 +12825,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10391, - "end": 10414, + "start": 10841, + "end": 10864, "loc": { "start": { - "line": 267, + "line": 286, "column": 11 }, "end": { - "line": 267, + "line": 286, "column": 34 } }, "callee": { "type": "Identifier", - "start": 10391, - "end": 10394, + "start": 10841, + "end": 10844, "loc": { "start": { - "line": 267, + "line": 286, "column": 11 }, "end": { - "line": 267, + "line": 286, "column": 14 }, "identifierName": "has" @@ -12170,15 +12858,15 @@ "arguments": [ { "type": "Identifier", - "start": 10395, - "end": 10401, + "start": 10845, + "end": 10851, "loc": { "start": { - "line": 267, + "line": 286, "column": 15 }, "end": { - "line": 267, + "line": 286, "column": 21 }, "identifierName": "parent" @@ -12187,15 +12875,15 @@ }, { "type": "StringLiteral", - "start": 10403, - "end": 10413, + "start": 10853, + "end": 10863, "loc": { "start": { - "line": 267, + "line": 286, "column": 23 }, "end": { - "line": 267, + "line": 286, "column": 33 } }, @@ -12215,58 +12903,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10416, - "end": 10437, + "start": 10866, + "end": 10887, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 57 } }, "expression": { "type": "AssignmentExpression", - "start": 10416, - "end": 10436, + "start": 10866, + "end": 10886, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 56 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10416, - "end": 10431, + "start": 10866, + "end": 10881, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 51 } }, "object": { "type": "Identifier", - "start": 10416, - "end": 10422, + "start": 10866, + "end": 10872, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 42 }, "identifierName": "parent" @@ -12275,15 +12963,15 @@ }, "property": { "type": "Identifier", - "start": 10423, - "end": 10431, + "start": 10873, + "end": 10881, "loc": { "start": { - "line": 267, + "line": 286, "column": 43 }, "end": { - "line": 267, + "line": 286, "column": 51 }, "identifierName": "children" @@ -12294,15 +12982,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10434, - "end": 10436, + "start": 10884, + "end": 10886, "loc": { "start": { - "line": 267, + "line": 286, "column": 54 }, "end": { - "line": 267, + "line": 286, "column": 56 } }, @@ -12315,15 +13003,15 @@ { "type": "CommentLine", "value": " Add child to parent.children.", - "start": 10347, - "end": 10379, + "start": 10797, + "end": 10829, "loc": { "start": { - "line": 266, + "line": 285, "column": 6 }, "end": { - "line": 266, + "line": 285, "column": 38 } } @@ -12332,71 +13020,71 @@ }, { "type": "ExpressionStatement", - "start": 10444, - "end": 10472, + "start": 10894, + "end": 10922, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 34 } }, "expression": { "type": "CallExpression", - "start": 10444, - "end": 10471, + "start": 10894, + "end": 10921, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 10444, - "end": 10464, + "start": 10894, + "end": 10914, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 26 } }, "object": { "type": "MemberExpression", - "start": 10444, - "end": 10459, + "start": 10894, + "end": 10909, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 21 } }, "object": { "type": "Identifier", - "start": 10444, - "end": 10450, + "start": 10894, + "end": 10900, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 12 }, "identifierName": "parent" @@ -12405,15 +13093,15 @@ }, "property": { "type": "Identifier", - "start": 10451, - "end": 10459, + "start": 10901, + "end": 10909, "loc": { "start": { - "line": 268, + "line": 287, "column": 13 }, "end": { - "line": 268, + "line": 287, "column": 21 }, "identifierName": "children" @@ -12424,15 +13112,15 @@ }, "property": { "type": "Identifier", - "start": 10460, - "end": 10464, + "start": 10910, + "end": 10914, "loc": { "start": { - "line": 268, + "line": 287, "column": 22 }, "end": { - "line": 268, + "line": 287, "column": 26 }, "identifierName": "push" @@ -12444,15 +13132,15 @@ "arguments": [ { "type": "Identifier", - "start": 10465, - "end": 10470, + "start": 10915, + "end": 10920, "loc": { "start": { - "line": 268, + "line": 287, "column": 27 }, "end": { - "line": 268, + "line": 287, "column": 32 }, "identifierName": "child" @@ -12465,15 +13153,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'name' instead of 'label'.", - "start": 10480, - "end": 10527, + "start": 10930, + "end": 10977, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 53 } } @@ -12482,43 +13170,43 @@ }, { "type": "IfStatement", - "start": 10534, - "end": 10591, + "start": 10984, + "end": 11041, "loc": { "start": { - "line": 271, + "line": 290, "column": 6 }, "end": { - "line": 271, + "line": 290, "column": 63 } }, "test": { "type": "CallExpression", - "start": 10538, - "end": 10558, + "start": 10988, + "end": 11008, "loc": { "start": { - "line": 271, + "line": 290, "column": 10 }, "end": { - "line": 271, + "line": 290, "column": 30 } }, "callee": { "type": "Identifier", - "start": 10538, - "end": 10541, + "start": 10988, + "end": 10991, "loc": { "start": { - "line": 271, + "line": 290, "column": 10 }, "end": { - "line": 271, + "line": 290, "column": 13 }, "identifierName": "has" @@ -12529,15 +13217,15 @@ "arguments": [ { "type": "Identifier", - "start": 10542, - "end": 10548, + "start": 10992, + "end": 10998, "loc": { "start": { - "line": 271, + "line": 290, "column": 14 }, "end": { - "line": 271, + "line": 290, "column": 20 }, "identifierName": "parent" @@ -12546,15 +13234,15 @@ }, { "type": "StringLiteral", - "start": 10550, - "end": 10557, + "start": 11000, + "end": 11007, "loc": { "start": { - "line": 271, + "line": 290, "column": 22 }, "end": { - "line": 271, + "line": 290, "column": 29 } }, @@ -12569,73 +13257,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 10560, - "end": 10591, + "start": 11010, + "end": 11041, "loc": { "start": { - "line": 271, + "line": 290, "column": 32 }, "end": { - "line": 271, + "line": 290, "column": 63 } }, "body": [ { "type": "ExpressionStatement", - "start": 10562, - "end": 10589, + "start": 11012, + "end": 11039, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 61 } }, "expression": { "type": "AssignmentExpression", - "start": 10562, - "end": 10588, + "start": 11012, + "end": 11038, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 60 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10562, - "end": 10573, + "start": 11012, + "end": 11023, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 45 } }, "object": { "type": "Identifier", - "start": 10562, - "end": 10568, + "start": 11012, + "end": 11018, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 40 }, "identifierName": "parent" @@ -12644,15 +13332,15 @@ }, "property": { "type": "Identifier", - "start": 10569, - "end": 10573, + "start": 11019, + "end": 11023, "loc": { "start": { - "line": 271, + "line": 290, "column": 41 }, "end": { - "line": 271, + "line": 290, "column": 45 }, "identifierName": "name" @@ -12663,29 +13351,29 @@ }, "right": { "type": "MemberExpression", - "start": 10576, - "end": 10588, + "start": 11026, + "end": 11038, "loc": { "start": { - "line": 271, + "line": 290, "column": 48 }, "end": { - "line": 271, + "line": 290, "column": 60 } }, "object": { "type": "Identifier", - "start": 10576, - "end": 10582, + "start": 11026, + "end": 11032, "loc": { "start": { - "line": 271, + "line": 290, "column": 48 }, "end": { - "line": 271, + "line": 290, "column": 54 }, "identifierName": "parent" @@ -12694,15 +13382,15 @@ }, "property": { "type": "Identifier", - "start": 10583, - "end": 10588, + "start": 11033, + "end": 11038, "loc": { "start": { - "line": 271, + "line": 290, "column": 55 }, "end": { - "line": 271, + "line": 290, "column": 60 }, "identifierName": "label" @@ -12721,15 +13409,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'name' instead of 'label'.", - "start": 10480, - "end": 10527, + "start": 10930, + "end": 10977, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 53 } } @@ -12738,43 +13426,43 @@ }, { "type": "IfStatement", - "start": 10598, - "end": 10652, + "start": 11048, + "end": 11102, "loc": { "start": { - "line": 272, + "line": 291, "column": 6 }, "end": { - "line": 272, + "line": 291, "column": 60 } }, "test": { "type": "CallExpression", - "start": 10602, - "end": 10621, + "start": 11052, + "end": 11071, "loc": { "start": { - "line": 272, + "line": 291, "column": 10 }, "end": { - "line": 272, + "line": 291, "column": 29 } }, "callee": { "type": "Identifier", - "start": 10602, - "end": 10605, + "start": 11052, + "end": 11055, "loc": { "start": { - "line": 272, + "line": 291, "column": 10 }, "end": { - "line": 272, + "line": 291, "column": 13 }, "identifierName": "has" @@ -12784,15 +13472,15 @@ "arguments": [ { "type": "Identifier", - "start": 10606, - "end": 10611, + "start": 11056, + "end": 11061, "loc": { "start": { - "line": 272, + "line": 291, "column": 14 }, "end": { - "line": 272, + "line": 291, "column": 19 }, "identifierName": "child" @@ -12801,15 +13489,15 @@ }, { "type": "StringLiteral", - "start": 10613, - "end": 10620, + "start": 11063, + "end": 11070, "loc": { "start": { - "line": 272, + "line": 291, "column": 21 }, "end": { - "line": 272, + "line": 291, "column": 28 } }, @@ -12823,73 +13511,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 10623, - "end": 10652, + "start": 11073, + "end": 11102, "loc": { "start": { - "line": 272, + "line": 291, "column": 31 }, "end": { - "line": 272, + "line": 291, "column": 60 } }, "body": [ { "type": "ExpressionStatement", - "start": 10625, - "end": 10650, + "start": 11075, + "end": 11100, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 58 } }, "expression": { "type": "AssignmentExpression", - "start": 10625, - "end": 10649, + "start": 11075, + "end": 11099, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 57 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10625, - "end": 10635, + "start": 11075, + "end": 11085, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 43 } }, "object": { "type": "Identifier", - "start": 10625, - "end": 10630, + "start": 11075, + "end": 11080, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 38 }, "identifierName": "child" @@ -12898,15 +13586,15 @@ }, "property": { "type": "Identifier", - "start": 10631, - "end": 10635, + "start": 11081, + "end": 11085, "loc": { "start": { - "line": 272, + "line": 291, "column": 39 }, "end": { - "line": 272, + "line": 291, "column": 43 }, "identifierName": "name" @@ -12917,29 +13605,29 @@ }, "right": { "type": "MemberExpression", - "start": 10638, - "end": 10649, + "start": 11088, + "end": 11099, "loc": { "start": { - "line": 272, + "line": 291, "column": 46 }, "end": { - "line": 272, + "line": 291, "column": 57 } }, "object": { "type": "Identifier", - "start": 10638, - "end": 10643, + "start": 11088, + "end": 11093, "loc": { "start": { - "line": 272, + "line": 291, "column": 46 }, "end": { - "line": 272, + "line": 291, "column": 51 }, "identifierName": "child" @@ -12948,15 +13636,15 @@ }, "property": { "type": "Identifier", - "start": 10644, - "end": 10649, + "start": 11094, + "end": 11099, "loc": { "start": { - "line": 272, + "line": 291, "column": 52 }, "end": { - "line": 272, + "line": 291, "column": 57 }, "identifierName": "label" @@ -12976,15 +13664,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.", - "start": 10660, - "end": 10743, + "start": 11110, + "end": 11193, "loc": { "start": { - "line": 274, + "line": 293, "column": 6 }, "end": { - "line": 274, + "line": 293, "column": 89 } } @@ -12993,43 +13681,43 @@ }, { "type": "IfStatement", - "start": 10750, - "end": 10830, + "start": 11200, + "end": 11280, "loc": { "start": { - "line": 275, + "line": 294, "column": 6 }, "end": { - "line": 275, + "line": 294, "column": 86 } }, "test": { "type": "LogicalExpression", - "start": 10754, - "end": 10803, + "start": 11204, + "end": 11253, "loc": { "start": { - "line": 275, + "line": 294, "column": 10 }, "end": { - "line": 275, + "line": 294, "column": 59 } }, "left": { "type": "UnaryExpression", - "start": 10754, - "end": 10778, + "start": 11204, + "end": 11228, "loc": { "start": { - "line": 275, + "line": 294, "column": 10 }, "end": { - "line": 275, + "line": 294, "column": 34 } }, @@ -13037,29 +13725,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10755, - "end": 10778, + "start": 11205, + "end": 11228, "loc": { "start": { - "line": 275, + "line": 294, "column": 11 }, "end": { - "line": 275, + "line": 294, "column": 34 } }, "callee": { "type": "Identifier", - "start": 10755, - "end": 10758, + "start": 11205, + "end": 11208, "loc": { "start": { - "line": 275, + "line": 294, "column": 11 }, "end": { - "line": 275, + "line": 294, "column": 14 }, "identifierName": "has" @@ -13070,15 +13758,15 @@ "arguments": [ { "type": "Identifier", - "start": 10759, - "end": 10764, + "start": 11209, + "end": 11214, "loc": { "start": { - "line": 275, + "line": 294, "column": 15 }, "end": { - "line": 275, + "line": 294, "column": 20 }, "identifierName": "child" @@ -13087,15 +13775,15 @@ }, { "type": "StringLiteral", - "start": 10766, - "end": 10777, + "start": 11216, + "end": 11227, "loc": { "start": { - "line": 275, + "line": 294, "column": 22 }, "end": { - "line": 275, + "line": 294, "column": 33 } }, @@ -13116,15 +13804,15 @@ "operator": "&&", "right": { "type": "UnaryExpression", - "start": 10782, - "end": 10803, + "start": 11232, + "end": 11253, "loc": { "start": { - "line": 275, + "line": 294, "column": 38 }, "end": { - "line": 275, + "line": 294, "column": 59 } }, @@ -13132,43 +13820,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10783, - "end": 10803, + "start": 11233, + "end": 11253, "loc": { "start": { - "line": 275, + "line": 294, "column": 39 }, "end": { - "line": 275, + "line": 294, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 10783, - "end": 10795, + "start": 11233, + "end": 11245, "loc": { "start": { - "line": 275, + "line": 294, "column": 39 }, "end": { - "line": 275, + "line": 294, "column": 51 } }, "object": { "type": "Identifier", - "start": 10783, - "end": 10789, + "start": 11233, + "end": 11239, "loc": { "start": { - "line": 275, + "line": 294, "column": 39 }, "end": { - "line": 275, + "line": 294, "column": 45 }, "identifierName": "Number" @@ -13177,15 +13865,15 @@ }, "property": { "type": "Identifier", - "start": 10790, - "end": 10795, + "start": 11240, + "end": 11245, "loc": { "start": { - "line": 275, + "line": 294, "column": 46 }, "end": { - "line": 275, + "line": 294, "column": 51 }, "identifierName": "isNaN" @@ -13197,15 +13885,15 @@ "arguments": [ { "type": "Identifier", - "start": 10796, - "end": 10802, + "start": 11246, + "end": 11252, "loc": { "start": { - "line": 275, + "line": 294, "column": 52 }, "end": { - "line": 275, + "line": 294, "column": 58 }, "identifierName": "weight" @@ -13222,58 +13910,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10805, - "end": 10830, + "start": 11255, + "end": 11280, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 86 } }, "expression": { "type": "AssignmentExpression", - "start": 10805, - "end": 10829, + "start": 11255, + "end": 11279, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 85 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10805, - "end": 10820, + "start": 11255, + "end": 11270, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 76 } }, "object": { "type": "Identifier", - "start": 10805, - "end": 10810, + "start": 11255, + "end": 11260, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 66 }, "identifierName": "child" @@ -13282,15 +13970,15 @@ }, "property": { "type": "Identifier", - "start": 10811, - "end": 10820, + "start": 11261, + "end": 11270, "loc": { "start": { - "line": 275, + "line": 294, "column": 67 }, "end": { - "line": 275, + "line": 294, "column": 76 }, "identifierName": "attribute" @@ -13301,15 +13989,15 @@ }, "right": { "type": "Identifier", - "start": 10823, - "end": 10829, + "start": 11273, + "end": 11279, "loc": { "start": { - "line": 275, + "line": 294, "column": 79 }, "end": { - "line": 275, + "line": 294, "column": 85 }, "identifierName": "weight" @@ -13323,15 +14011,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.", - "start": 10660, - "end": 10743, + "start": 11110, + "end": 11193, "loc": { "start": { - "line": 274, + "line": 293, "column": 6 }, "end": { - "line": 274, + "line": 293, "column": 89 } } @@ -13349,15 +14037,15 @@ { "type": "CommentLine", "value": " Go through the arcs, assigning 'children' to the appropriate parent node.", - "start": 10192, - "end": 10268, + "start": 10642, + "end": 10718, "loc": { "start": { - "line": 262, + "line": 281, "column": 4 }, "end": { - "line": 262, + "line": 281, "column": 80 } } @@ -13367,15 +14055,15 @@ { "type": "CommentLine", "value": " Set root 'attribute' to root weight.", - "start": 10844, - "end": 10883, + "start": 11294, + "end": 11333, "loc": { "start": { - "line": 278, + "line": 297, "column": 4 }, "end": { - "line": 278, + "line": 297, "column": 43 } } @@ -13384,43 +14072,43 @@ }, { "type": "IfStatement", - "start": 10888, - "end": 10974, + "start": 11338, + "end": 11424, "loc": { "start": { - "line": 279, + "line": 298, "column": 4 }, "end": { - "line": 279, + "line": 298, "column": 90 } }, "test": { "type": "LogicalExpression", - "start": 10892, - "end": 10944, + "start": 11342, + "end": 11394, "loc": { "start": { - "line": 279, + "line": 298, "column": 8 }, "end": { - "line": 279, + "line": 298, "column": 60 } }, "left": { "type": "UnaryExpression", - "start": 10892, - "end": 10915, + "start": 11342, + "end": 11365, "loc": { "start": { - "line": 279, + "line": 298, "column": 8 }, "end": { - "line": 279, + "line": 298, "column": 31 } }, @@ -13428,29 +14116,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10893, - "end": 10915, + "start": 11343, + "end": 11365, "loc": { "start": { - "line": 279, + "line": 298, "column": 9 }, "end": { - "line": 279, + "line": 298, "column": 31 } }, "callee": { "type": "Identifier", - "start": 10893, - "end": 10896, + "start": 11343, + "end": 11346, "loc": { "start": { - "line": 279, + "line": 298, "column": 9 }, "end": { - "line": 279, + "line": 298, "column": 12 }, "identifierName": "has" @@ -13461,15 +14149,15 @@ "arguments": [ { "type": "Identifier", - "start": 10897, - "end": 10901, + "start": 11347, + "end": 11351, "loc": { "start": { - "line": 279, + "line": 298, "column": 13 }, "end": { - "line": 279, + "line": 298, "column": 17 }, "identifierName": "root" @@ -13478,15 +14166,15 @@ }, { "type": "StringLiteral", - "start": 10903, - "end": 10914, + "start": 11353, + "end": 11364, "loc": { "start": { - "line": 279, + "line": 298, "column": 19 }, "end": { - "line": 279, + "line": 298, "column": 30 } }, @@ -13507,15 +14195,15 @@ "operator": "&&", "right": { "type": "UnaryExpression", - "start": 10919, - "end": 10944, + "start": 11369, + "end": 11394, "loc": { "start": { - "line": 279, + "line": 298, "column": 35 }, "end": { - "line": 279, + "line": 298, "column": 60 } }, @@ -13523,43 +14211,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10920, - "end": 10944, + "start": 11370, + "end": 11394, "loc": { "start": { - "line": 279, + "line": 298, "column": 36 }, "end": { - "line": 279, + "line": 298, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 10920, - "end": 10932, + "start": 11370, + "end": 11382, "loc": { "start": { - "line": 279, + "line": 298, "column": 36 }, "end": { - "line": 279, + "line": 298, "column": 48 } }, "object": { "type": "Identifier", - "start": 10920, - "end": 10926, + "start": 11370, + "end": 11376, "loc": { "start": { - "line": 279, + "line": 298, "column": 36 }, "end": { - "line": 279, + "line": 298, "column": 42 }, "identifierName": "Number" @@ -13568,15 +14256,15 @@ }, "property": { "type": "Identifier", - "start": 10927, - "end": 10932, + "start": 11377, + "end": 11382, "loc": { "start": { - "line": 279, + "line": 298, "column": 43 }, "end": { - "line": 279, + "line": 298, "column": 48 }, "identifierName": "isNaN" @@ -13588,15 +14276,15 @@ "arguments": [ { "type": "Identifier", - "start": 10933, - "end": 10943, + "start": 11383, + "end": 11393, "loc": { "start": { - "line": 279, + "line": 298, "column": 49 }, "end": { - "line": 279, + "line": 298, "column": 59 }, "identifierName": "rootWeight" @@ -13613,58 +14301,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10946, - "end": 10974, + "start": 11396, + "end": 11424, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 90 } }, "expression": { "type": "AssignmentExpression", - "start": 10946, - "end": 10973, + "start": 11396, + "end": 11423, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 89 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10946, - "end": 10960, + "start": 11396, + "end": 11410, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 76 } }, "object": { "type": "Identifier", - "start": 10946, - "end": 10950, + "start": 11396, + "end": 11400, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 66 }, "identifierName": "root" @@ -13673,15 +14361,15 @@ }, "property": { "type": "Identifier", - "start": 10951, - "end": 10960, + "start": 11401, + "end": 11410, "loc": { "start": { - "line": 279, + "line": 298, "column": 67 }, "end": { - "line": 279, + "line": 298, "column": 76 }, "identifierName": "attribute" @@ -13692,15 +14380,15 @@ }, "right": { "type": "Identifier", - "start": 10963, - "end": 10973, + "start": 11413, + "end": 11423, "loc": { "start": { - "line": 279, + "line": 298, "column": 79 }, "end": { - "line": 279, + "line": 298, "column": 89 }, "identifierName": "rootWeight" @@ -13714,15 +14402,15 @@ { "type": "CommentLine", "value": " Set root 'attribute' to root weight.", - "start": 10844, - "end": 10883, + "start": 11294, + "end": 11333, "loc": { "start": { - "line": 278, + "line": 297, "column": 4 }, "end": { - "line": 278, + "line": 297, "column": 43 } } @@ -13731,44 +14419,44 @@ }, { "type": "ReturnStatement", - "start": 10980, - "end": 11002, + "start": 11430, + "end": 11452, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 26 } }, "argument": { "type": "ObjectExpression", - "start": 10987, - "end": 11001, + "start": 11437, + "end": 11451, "loc": { "start": { - "line": 281, + "line": 300, "column": 11 }, "end": { - "line": 281, + "line": 300, "column": 25 } }, "properties": [ { "type": "ObjectProperty", - "start": 10989, - "end": 10999, + "start": 11439, + "end": 11449, "loc": { "start": { - "line": 281, + "line": 300, "column": 13 }, "end": { - "line": 281, + "line": 300, "column": 23 } }, @@ -13777,15 +14465,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10989, - "end": 10993, + "start": 11439, + "end": 11443, "loc": { "start": { - "line": 281, + "line": 300, "column": 13 }, "end": { - "line": 281, + "line": 300, "column": 17 }, "identifierName": "json" @@ -13794,15 +14482,15 @@ }, "value": { "type": "Identifier", - "start": 10995, - "end": 10999, + "start": 11445, + "end": 11449, "loc": { "start": { - "line": 281, + "line": 300, "column": 19 }, "end": { - "line": 281, + "line": 300, "column": 23 }, "identifierName": "root" @@ -13819,15 +14507,15 @@ }, { "type": "ClassMethod", - "start": 11010, - "end": 11966, + "start": 11460, + "end": 12416, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 306, + "line": 325, "column": 3 } }, @@ -13835,15 +14523,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11010, - "end": 11033, + "start": 11460, + "end": 11483, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 284, + "line": 303, "column": 25 }, "identifierName": "getParsedNewickWithIRIs" @@ -13858,15 +14546,15 @@ "params": [ { "type": "Identifier", - "start": 11034, - "end": 11041, + "start": 11484, + "end": 11491, "loc": { "start": { - "line": 284, + "line": 303, "column": 26 }, "end": { - "line": 284, + "line": 303, "column": 33 }, "identifierName": "baseIRI" @@ -13875,29 +14563,29 @@ }, { "type": "AssignmentPattern", - "start": 11043, - "end": 11090, + "start": 11493, + "end": 11540, "loc": { "start": { - "line": 284, + "line": 303, "column": 35 }, "end": { - "line": 284, + "line": 303, "column": 82 } }, "left": { "type": "Identifier", - "start": 11043, - "end": 11055, + "start": 11493, + "end": 11505, "loc": { "start": { - "line": 284, + "line": 303, "column": 35 }, "end": { - "line": 284, + "line": 303, "column": 47 }, "identifierName": "newickParser" @@ -13906,29 +14594,29 @@ }, "right": { "type": "MemberExpression", - "start": 11058, - "end": 11090, + "start": 11508, + "end": 11540, "loc": { "start": { - "line": 284, + "line": 303, "column": 50 }, "end": { - "line": 284, + "line": 303, "column": 82 } }, "object": { "type": "Identifier", - "start": 11058, - "end": 11074, + "start": 11508, + "end": 11524, "loc": { "start": { - "line": 284, + "line": 303, "column": 50 }, "end": { - "line": 284, + "line": 303, "column": 66 }, "identifierName": "PhylogenyWrapper" @@ -13937,15 +14625,15 @@ }, "property": { "type": "Identifier", - "start": 11075, - "end": 11090, + "start": 11525, + "end": 11540, "loc": { "start": { - "line": 284, + "line": 303, "column": 67 }, "end": { - "line": 284, + "line": 303, "column": 82 }, "identifierName": "getParsedNewick" @@ -13958,59 +14646,59 @@ ], "body": { "type": "BlockStatement", - "start": 11092, - "end": 11966, + "start": 11542, + "end": 12416, "loc": { "start": { - "line": 284, + "line": 303, "column": 84 }, "end": { - "line": 306, + "line": 325, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 11550, - "end": 11609, + "start": 12000, + "end": 12059, "loc": { "start": { - "line": 293, + "line": 312, "column": 4 }, "end": { - "line": 293, + "line": 312, "column": 63 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11556, - "end": 11608, + "start": 12006, + "end": 12058, "loc": { "start": { - "line": 293, + "line": 312, "column": 10 }, "end": { - "line": 293, + "line": 312, "column": 62 } }, "id": { "type": "Identifier", - "start": 11556, - "end": 11562, + "start": 12006, + "end": 12012, "loc": { "start": { - "line": 293, + "line": 312, "column": 10 }, "end": { - "line": 293, + "line": 312, "column": 16 }, "identifierName": "parsed" @@ -14020,29 +14708,29 @@ }, "init": { "type": "CallExpression", - "start": 11565, - "end": 11608, + "start": 12015, + "end": 12058, "loc": { "start": { - "line": 293, + "line": 312, "column": 19 }, "end": { - "line": 293, + "line": 312, "column": 62 } }, "callee": { "type": "Identifier", - "start": 11565, - "end": 11577, + "start": 12015, + "end": 12027, "loc": { "start": { - "line": 293, + "line": 312, "column": 19 }, "end": { - "line": 293, + "line": 312, "column": 31 }, "identifierName": "newickParser" @@ -14052,72 +14740,72 @@ "arguments": [ { "type": "LogicalExpression", - "start": 11578, - "end": 11607, + "start": 12028, + "end": 12057, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 61 } }, "left": { "type": "MemberExpression", - "start": 11578, - "end": 11599, + "start": 12028, + "end": 12049, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 53 } }, "object": { "type": "MemberExpression", - "start": 11578, - "end": 11592, + "start": 12028, + "end": 12042, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 46 } }, "object": { "type": "ThisExpression", - "start": 11578, - "end": 11582, + "start": 12028, + "end": 12032, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 36 } } }, "property": { "type": "Identifier", - "start": 11583, - "end": 11592, + "start": 12033, + "end": 12042, "loc": { "start": { - "line": 293, + "line": 312, "column": 37 }, "end": { - "line": 293, + "line": 312, "column": 46 }, "identifierName": "phylogeny" @@ -14128,15 +14816,15 @@ }, "property": { "type": "Identifier", - "start": 11593, - "end": 11599, + "start": 12043, + "end": 12049, "loc": { "start": { - "line": 293, + "line": 312, "column": 47 }, "end": { - "line": 293, + "line": 312, "column": 53 }, "identifierName": "newick" @@ -14148,15 +14836,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 11603, - "end": 11607, + "start": 12053, + "end": 12057, "loc": { "start": { - "line": 293, + "line": 312, "column": 57 }, "end": { - "line": 293, + "line": 312, "column": 61 } }, @@ -14177,15 +14865,15 @@ { "type": "CommentLine", "value": " Return the parsed Newick string, but with EVERY node given an IRI.", - "start": 11098, - "end": 11167, + "start": 11548, + "end": 11617, "loc": { "start": { - "line": 285, + "line": 304, "column": 4 }, "end": { - "line": 285, + "line": 304, "column": 73 } } @@ -14193,15 +14881,15 @@ { "type": "CommentLine", "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 11172, - "end": 11245, + "start": 11622, + "end": 11695, "loc": { "start": { - "line": 286, + "line": 305, "column": 4 }, "end": { - "line": 286, + "line": 305, "column": 77 } } @@ -14209,15 +14897,15 @@ { "type": "CommentLine", "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 11250, - "end": 11325, + "start": 11700, + "end": 11775, "loc": { "start": { - "line": 287, + "line": 306, "column": 4 }, "end": { - "line": 287, + "line": 306, "column": 79 } } @@ -14225,15 +14913,15 @@ { "type": "CommentLine", "value": " the baseIRI.", - "start": 11330, - "end": 11347, + "start": 11780, + "end": 11797, "loc": { "start": { - "line": 288, + "line": 307, "column": 4 }, "end": { - "line": 288, + "line": 307, "column": 21 } } @@ -14241,15 +14929,15 @@ { "type": "CommentLine", "value": " - newickParser: A method for converting a Newick string to a object-based", - "start": 11352, - "end": 11428, + "start": 11802, + "end": 11878, "loc": { "start": { - "line": 289, + "line": 308, "column": 4 }, "end": { - "line": 289, + "line": 308, "column": 80 } } @@ -14257,15 +14945,15 @@ { "type": "CommentLine", "value": " representation. The static method PhylogenyWrapper.getParsedNewick() is", - "start": 11433, - "end": 11509, + "start": 11883, + "end": 11959, "loc": { "start": { - "line": 290, + "line": 309, "column": 4 }, "end": { - "line": 290, + "line": 309, "column": 80 } } @@ -14273,15 +14961,15 @@ { "type": "CommentLine", "value": " used if none is provided.", - "start": 11514, - "end": 11544, + "start": 11964, + "end": 11994, "loc": { "start": { - "line": 291, + "line": 310, "column": 4 }, "end": { - "line": 291, + "line": 310, "column": 34 } } @@ -14290,43 +14978,43 @@ }, { "type": "IfStatement", - "start": 11614, - "end": 11942, + "start": 12064, + "end": 12392, "loc": { "start": { - "line": 294, + "line": 313, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 5 } }, "test": { "type": "CallExpression", - "start": 11618, - "end": 11637, + "start": 12068, + "end": 12087, "loc": { "start": { - "line": 294, + "line": 313, "column": 8 }, "end": { - "line": 294, + "line": 313, "column": 27 } }, "callee": { "type": "Identifier", - "start": 11618, - "end": 11621, + "start": 12068, + "end": 12071, "loc": { "start": { - "line": 294, + "line": 313, "column": 8 }, "end": { - "line": 294, + "line": 313, "column": 11 }, "identifierName": "has" @@ -14336,15 +15024,15 @@ "arguments": [ { "type": "Identifier", - "start": 11622, - "end": 11628, + "start": 12072, + "end": 12078, "loc": { "start": { - "line": 294, + "line": 313, "column": 12 }, "end": { - "line": 294, + "line": 313, "column": 18 }, "identifierName": "parsed" @@ -14353,15 +15041,15 @@ }, { "type": "StringLiteral", - "start": 11630, - "end": 11636, + "start": 12080, + "end": 12086, "loc": { "start": { - "line": 294, + "line": 313, "column": 20 }, "end": { - "line": 294, + "line": 313, "column": 26 } }, @@ -14375,72 +15063,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 11639, - "end": 11942, + "start": 12089, + "end": 12392, "loc": { "start": { - "line": 294, + "line": 313, "column": 29 }, "end": { - "line": 303, + "line": 322, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 11647, - "end": 11936, + "start": 12097, + "end": 12386, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 11647, - "end": 11935, + "start": 12097, + "end": 12385, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 11647, - "end": 11676, + "start": 12097, + "end": 12126, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 295, + "line": 314, "column": 35 } }, "object": { "type": "Identifier", - "start": 11647, - "end": 11663, + "start": 12097, + "end": 12113, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 295, + "line": 314, "column": 22 }, "identifierName": "PhylogenyWrapper" @@ -14449,15 +15137,15 @@ }, "property": { "type": "Identifier", - "start": 11664, - "end": 11676, + "start": 12114, + "end": 12126, "loc": { "start": { - "line": 295, + "line": 314, "column": 23 }, "end": { - "line": 295, + "line": 314, "column": 35 }, "identifierName": "recurseNodes" @@ -14469,29 +15157,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 11677, - "end": 11688, + "start": 12127, + "end": 12138, "loc": { "start": { - "line": 295, + "line": 314, "column": 36 }, "end": { - "line": 295, + "line": 314, "column": 47 } }, "object": { "type": "Identifier", - "start": 11677, - "end": 11683, + "start": 12127, + "end": 12133, "loc": { "start": { - "line": 295, + "line": 314, "column": 36 }, "end": { - "line": 295, + "line": 314, "column": 42 }, "identifierName": "parsed" @@ -14500,15 +15188,15 @@ }, "property": { "type": "Identifier", - "start": 11684, - "end": 11688, + "start": 12134, + "end": 12138, "loc": { "start": { - "line": 295, + "line": 314, "column": 43 }, "end": { - "line": 295, + "line": 314, "column": 47 }, "identifierName": "json" @@ -14519,15 +15207,15 @@ }, { "type": "ArrowFunctionExpression", - "start": 11690, - "end": 11934, + "start": 12140, + "end": 12384, "loc": { "start": { - "line": 295, + "line": 314, "column": 49 }, "end": { - "line": 302, + "line": 321, "column": 7 } }, @@ -14538,15 +15226,15 @@ "params": [ { "type": "Identifier", - "start": 11691, - "end": 11695, + "start": 12141, + "end": 12145, "loc": { "start": { - "line": 295, + "line": 314, "column": 50 }, "end": { - "line": 295, + "line": 314, "column": 54 }, "identifierName": "node" @@ -14555,15 +15243,15 @@ }, { "type": "Identifier", - "start": 11697, - "end": 11706, + "start": 12147, + "end": 12156, "loc": { "start": { - "line": 295, + "line": 314, "column": 56 }, "end": { - "line": 295, + "line": 314, "column": 65 }, "identifierName": "nodeCount" @@ -14573,59 +15261,59 @@ ], "body": { "type": "BlockStatement", - "start": 11711, - "end": 11934, + "start": 12161, + "end": 12384, "loc": { "start": { - "line": 295, + "line": 314, "column": 70 }, "end": { - "line": 302, + "line": 321, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 11775, - "end": 11801, + "start": 12225, + "end": 12251, "loc": { "start": { - "line": 297, + "line": 316, "column": 8 }, "end": { - "line": 297, + "line": 316, "column": 34 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11781, - "end": 11800, + "start": 12231, + "end": 12250, "loc": { "start": { - "line": 297, + "line": 316, "column": 14 }, "end": { - "line": 297, + "line": 316, "column": 33 } }, "id": { "type": "Identifier", - "start": 11781, - "end": 11793, + "start": 12231, + "end": 12243, "loc": { "start": { - "line": 297, + "line": 316, "column": 14 }, "end": { - "line": 297, + "line": 316, "column": 26 }, "identifierName": "nodeAsJSONLD" @@ -14635,15 +15323,15 @@ }, "init": { "type": "Identifier", - "start": 11796, - "end": 11800, + "start": 12246, + "end": 12250, "loc": { "start": { - "line": 297, + "line": 316, "column": 29 }, "end": { - "line": 297, + "line": 316, "column": 33 }, "identifierName": "node" @@ -14658,15 +15346,15 @@ { "type": "CommentLine", "value": " Start with the additional node properties.", - "start": 11721, - "end": 11766, + "start": 12171, + "end": 12216, "loc": { "start": { - "line": 296, + "line": 315, "column": 8 }, "end": { - "line": 296, + "line": 315, "column": 53 } } @@ -14676,15 +15364,15 @@ { "type": "CommentLine", "value": " Set @id and @type.", - "start": 11811, - "end": 11832, + "start": 12261, + "end": 12282, "loc": { "start": { - "line": 299, + "line": 318, "column": 8 }, "end": { - "line": 299, + "line": 318, "column": 29 } } @@ -14693,44 +15381,44 @@ }, { "type": "VariableDeclaration", - "start": 11841, - "end": 11887, + "start": 12291, + "end": 12337, "loc": { "start": { - "line": 300, + "line": 319, "column": 8 }, "end": { - "line": 300, + "line": 319, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11847, - "end": 11886, + "start": 12297, + "end": 12336, "loc": { "start": { - "line": 300, + "line": 319, "column": 14 }, "end": { - "line": 300, + "line": 319, "column": 53 } }, "id": { "type": "Identifier", - "start": 11847, - "end": 11854, + "start": 12297, + "end": 12304, "loc": { "start": { - "line": 300, + "line": 319, "column": 14 }, "end": { - "line": 300, + "line": 319, "column": 21 }, "identifierName": "nodeIRI" @@ -14740,30 +15428,30 @@ }, "init": { "type": "TemplateLiteral", - "start": 11857, - "end": 11886, + "start": 12307, + "end": 12336, "loc": { "start": { - "line": 300, + "line": 319, "column": 24 }, "end": { - "line": 300, + "line": 319, "column": 53 } }, "expressions": [ { "type": "Identifier", - "start": 11860, - "end": 11867, + "start": 12310, + "end": 12317, "loc": { "start": { - "line": 300, + "line": 319, "column": 27 }, "end": { - "line": 300, + "line": 319, "column": 34 }, "identifierName": "baseIRI" @@ -14772,15 +15460,15 @@ }, { "type": "Identifier", - "start": 11875, - "end": 11884, + "start": 12325, + "end": 12334, "loc": { "start": { - "line": 300, + "line": 319, "column": 42 }, "end": { - "line": 300, + "line": 319, "column": 51 }, "identifierName": "nodeCount" @@ -14791,15 +15479,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 11858, - "end": 11858, + "start": 12308, + "end": 12308, "loc": { "start": { - "line": 300, + "line": 319, "column": 25 }, "end": { - "line": 300, + "line": 319, "column": 25 } }, @@ -14811,15 +15499,15 @@ }, { "type": "TemplateElement", - "start": 11868, - "end": 11873, + "start": 12318, + "end": 12323, "loc": { "start": { - "line": 300, + "line": 319, "column": 35 }, "end": { - "line": 300, + "line": 319, "column": 40 } }, @@ -14831,15 +15519,15 @@ }, { "type": "TemplateElement", - "start": 11885, - "end": 11885, + "start": 12335, + "end": 12335, "loc": { "start": { - "line": 300, + "line": 319, "column": 52 }, "end": { - "line": 300, + "line": 319, "column": 52 } }, @@ -14859,15 +15547,15 @@ { "type": "CommentLine", "value": " Set @id and @type.", - "start": 11811, - "end": 11832, + "start": 12261, + "end": 12282, "loc": { "start": { - "line": 299, + "line": 318, "column": 8 }, "end": { - "line": 299, + "line": 318, "column": 29 } } @@ -14876,58 +15564,58 @@ }, { "type": "ExpressionStatement", - "start": 11896, - "end": 11926, + "start": 12346, + "end": 12376, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 11896, - "end": 11925, + "start": 12346, + "end": 12375, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11896, - "end": 11915, + "start": 12346, + "end": 12365, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 27 } }, "object": { "type": "Identifier", - "start": 11896, - "end": 11908, + "start": 12346, + "end": 12358, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 20 }, "identifierName": "nodeAsJSONLD" @@ -14936,15 +15624,15 @@ }, "property": { "type": "StringLiteral", - "start": 11909, - "end": 11914, + "start": 12359, + "end": 12364, "loc": { "start": { - "line": 301, + "line": 320, "column": 21 }, "end": { - "line": 301, + "line": 320, "column": 26 } }, @@ -14958,15 +15646,15 @@ }, "right": { "type": "Identifier", - "start": 11918, - "end": 11925, + "start": 12368, + "end": 12375, "loc": { "start": { - "line": 301, + "line": 320, "column": 30 }, "end": { - "line": 301, + "line": 320, "column": 37 }, "identifierName": "nodeIRI" @@ -14989,29 +15677,29 @@ }, { "type": "ReturnStatement", - "start": 11948, - "end": 11962, + "start": 12398, + "end": 12412, "loc": { "start": { - "line": 305, + "line": 324, "column": 4 }, "end": { - "line": 305, + "line": 324, "column": 18 } }, "argument": { "type": "Identifier", - "start": 11955, - "end": 11961, + "start": 12405, + "end": 12411, "loc": { "start": { - "line": 305, + "line": 324, "column": 11 }, "end": { - "line": 305, + "line": 324, "column": 17 }, "identifierName": "parsed" @@ -15025,15 +15713,15 @@ }, { "type": "ClassMethod", - "start": 11970, - "end": 16576, + "start": 12420, + "end": 17026, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 422, + "line": 441, "column": 3 } }, @@ -15041,15 +15729,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11970, - "end": 11986, + "start": 12420, + "end": 12436, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 308, + "line": 327, "column": 18 }, "identifierName": "getNodesAsJSONLD" @@ -15064,15 +15752,15 @@ "params": [ { "type": "Identifier", - "start": 11987, - "end": 11994, + "start": 12437, + "end": 12444, "loc": { "start": { - "line": 308, + "line": 327, "column": 19 }, "end": { - "line": 308, + "line": 327, "column": 26 }, "identifierName": "baseIRI" @@ -15081,15 +15769,15 @@ }, { "type": "Identifier", - "start": 11996, - "end": 12008, + "start": 12446, + "end": 12458, "loc": { "start": { - "line": 308, + "line": 327, "column": 28 }, "end": { - "line": 308, + "line": 327, "column": 40 }, "identifierName": "newickParser" @@ -15099,59 +15787,59 @@ ], "body": { "type": "BlockStatement", - "start": 12010, - "end": 16576, + "start": 12460, + "end": 17026, "loc": { "start": { - "line": 308, + "line": 327, "column": 42 }, "end": { - "line": 422, + "line": 441, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 12498, - "end": 12515, + "start": 12948, + "end": 12965, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 21 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12504, - "end": 12514, + "start": 12954, + "end": 12964, "loc": { "start": { - "line": 318, + "line": 337, "column": 10 }, "end": { - "line": 318, + "line": 337, "column": 20 } }, "id": { "type": "Identifier", - "start": 12504, - "end": 12509, + "start": 12954, + "end": 12959, "loc": { "start": { - "line": 318, + "line": 337, "column": 10 }, "end": { - "line": 318, + "line": 337, "column": 15 }, "identifierName": "nodes" @@ -15161,15 +15849,15 @@ }, "init": { "type": "ArrayExpression", - "start": 12512, - "end": 12514, + "start": 12962, + "end": 12964, "loc": { "start": { - "line": 318, + "line": 337, "column": 18 }, "end": { - "line": 318, + "line": 337, "column": 20 } }, @@ -15183,15 +15871,15 @@ { "type": "CommentLine", "value": " Returns a list of all nodes in this phylogeny as a series of nodes.", - "start": 12016, - "end": 12086, + "start": 12466, + "end": 12536, "loc": { "start": { - "line": 309, + "line": 328, "column": 4 }, "end": { - "line": 309, + "line": 328, "column": 74 } } @@ -15199,15 +15887,15 @@ { "type": "CommentLine", "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 12091, - "end": 12164, + "start": 12541, + "end": 12614, "loc": { "start": { - "line": 310, + "line": 329, "column": 4 }, "end": { - "line": 310, + "line": 329, "column": 77 } } @@ -15215,15 +15903,15 @@ { "type": "CommentLine", "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 12169, - "end": 12244, + "start": 12619, + "end": 12694, "loc": { "start": { - "line": 311, + "line": 330, "column": 4 }, "end": { - "line": 311, + "line": 330, "column": 79 } } @@ -15231,15 +15919,15 @@ { "type": "CommentLine", "value": " the baseIRI.", - "start": 12249, - "end": 12266, + "start": 12699, + "end": 12716, "loc": { "start": { - "line": 312, + "line": 331, "column": 4 }, "end": { - "line": 312, + "line": 331, "column": 21 } } @@ -15247,15 +15935,15 @@ { "type": "CommentLine", "value": " - newickParser: A method for converting a Newick string to a object-based", - "start": 12271, - "end": 12347, + "start": 12721, + "end": 12797, "loc": { "start": { - "line": 313, + "line": 332, "column": 4 }, "end": { - "line": 313, + "line": 332, "column": 80 } } @@ -15263,15 +15951,15 @@ { "type": "CommentLine", "value": " representation. See PhylogenyWrapper.getParsedNewick() for an example", - "start": 12352, - "end": 12426, + "start": 12802, + "end": 12876, "loc": { "start": { - "line": 314, + "line": 333, "column": 4 }, "end": { - "line": 314, + "line": 333, "column": 78 } } @@ -15279,15 +15967,15 @@ { "type": "CommentLine", "value": " implementation.", - "start": 12431, - "end": 12451, + "start": 12881, + "end": 12901, "loc": { "start": { - "line": 315, + "line": 334, "column": 4 }, "end": { - "line": 315, + "line": 334, "column": 24 } } @@ -15295,15 +15983,15 @@ { "type": "CommentLine", "value": " List of nodes we have identified.", - "start": 12457, - "end": 12493, + "start": 12907, + "end": 12943, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 40 } } @@ -15313,15 +16001,15 @@ { "type": "CommentLine", "value": " We need to track the identifiers we give each node as we go.", - "start": 12521, - "end": 12584, + "start": 12971, + "end": 13034, "loc": { "start": { - "line": 320, + "line": 339, "column": 4 }, "end": { - "line": 320, + "line": 339, "column": 67 } } @@ -15330,44 +16018,44 @@ }, { "type": "VariableDeclaration", - "start": 12589, - "end": 12610, + "start": 13039, + "end": 13060, "loc": { "start": { - "line": 321, + "line": 340, "column": 4 }, "end": { - "line": 321, + "line": 340, "column": 25 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12595, - "end": 12609, + "start": 13045, + "end": 13059, "loc": { "start": { - "line": 321, + "line": 340, "column": 10 }, "end": { - "line": 321, + "line": 340, "column": 24 } }, "id": { "type": "Identifier", - "start": 12595, - "end": 12604, + "start": 13045, + "end": 13054, "loc": { "start": { - "line": 321, + "line": 340, "column": 10 }, "end": { - "line": 321, + "line": 340, "column": 19 }, "identifierName": "nodesById" @@ -15377,15 +16065,15 @@ }, "init": { "type": "ObjectExpression", - "start": 12607, - "end": 12609, + "start": 13057, + "end": 13059, "loc": { "start": { - "line": 321, + "line": 340, "column": 22 }, "end": { - "line": 321, + "line": 340, "column": 24 } }, @@ -15399,15 +16087,15 @@ { "type": "CommentLine", "value": " We need to track the identifiers we give each node as we go.", - "start": 12521, - "end": 12584, + "start": 12971, + "end": 13034, "loc": { "start": { - "line": 320, + "line": 339, "column": 4 }, "end": { - "line": 320, + "line": 339, "column": 67 } } @@ -15416,44 +16104,44 @@ }, { "type": "VariableDeclaration", - "start": 12615, - "end": 12644, + "start": 13065, + "end": 13094, "loc": { "start": { - "line": 322, + "line": 341, "column": 4 }, "end": { - "line": 322, + "line": 341, "column": 33 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12621, - "end": 12643, + "start": 13071, + "end": 13093, "loc": { "start": { - "line": 322, + "line": 341, "column": 10 }, "end": { - "line": 322, + "line": 341, "column": 32 } }, "id": { "type": "Identifier", - "start": 12621, - "end": 12638, + "start": 13071, + "end": 13088, "loc": { "start": { - "line": 322, + "line": 341, "column": 10 }, "end": { - "line": 322, + "line": 341, "column": 27 }, "identifierName": "nodeIdsByParentId" @@ -15462,15 +16150,15 @@ }, "init": { "type": "ObjectExpression", - "start": 12641, - "end": 12643, + "start": 13091, + "end": 13093, "loc": { "start": { - "line": 322, + "line": 341, "column": 30 }, "end": { - "line": 322, + "line": 341, "column": 32 } }, @@ -15483,15 +16171,15 @@ { "type": "CommentLine", "value": " Extract the newick string.", - "start": 12650, - "end": 12679, + "start": 13100, + "end": 13129, "loc": { "start": { - "line": 324, + "line": 343, "column": 4 }, "end": { - "line": 324, + "line": 343, "column": 33 } } @@ -15500,59 +16188,59 @@ }, { "type": "VariableDeclaration", - "start": 12684, - "end": 12736, + "start": 13134, + "end": 13186, "loc": { "start": { - "line": 325, + "line": 344, "column": 4 }, "end": { - "line": 325, + "line": 344, "column": 56 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12690, - "end": 12735, + "start": 13140, + "end": 13185, "loc": { "start": { - "line": 325, + "line": 344, "column": 10 }, "end": { - "line": 325, + "line": 344, "column": 55 } }, "id": { "type": "ObjectPattern", - "start": 12690, - "end": 12718, + "start": 13140, + "end": 13168, "loc": { "start": { - "line": 325, + "line": 344, "column": 10 }, "end": { - "line": 325, + "line": 344, "column": 38 } }, "properties": [ { "type": "ObjectProperty", - "start": 12692, - "end": 12716, + "start": 13142, + "end": 13166, "loc": { "start": { - "line": 325, + "line": 344, "column": 12 }, "end": { - "line": 325, + "line": 344, "column": 36 } }, @@ -15561,15 +16249,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12692, - "end": 12716, + "start": 13142, + "end": 13166, "loc": { "start": { - "line": 325, + "line": 344, "column": 12 }, "end": { - "line": 325, + "line": 344, "column": 36 }, "identifierName": "additionalNodeProperties" @@ -15579,15 +16267,15 @@ }, "value": { "type": "Identifier", - "start": 12692, - "end": 12716, + "start": 13142, + "end": 13166, "loc": { "start": { - "line": 325, + "line": 344, "column": 12 }, "end": { - "line": 325, + "line": 344, "column": 36 }, "identifierName": "additionalNodeProperties" @@ -15604,44 +16292,44 @@ }, "init": { "type": "MemberExpression", - "start": 12721, - "end": 12735, + "start": 13171, + "end": 13185, "loc": { "start": { - "line": 325, + "line": 344, "column": 41 }, "end": { - "line": 325, + "line": 344, "column": 55 } }, "object": { "type": "ThisExpression", - "start": 12721, - "end": 12725, + "start": 13171, + "end": 13175, "loc": { "start": { - "line": 325, + "line": 344, "column": 41 }, "end": { - "line": 325, + "line": 344, "column": 45 } } }, "property": { "type": "Identifier", - "start": 12726, - "end": 12735, + "start": 13176, + "end": 13185, "loc": { "start": { - "line": 325, + "line": 344, "column": 46 }, "end": { - "line": 325, + "line": 344, "column": 55 }, "identifierName": "phylogeny" @@ -15658,15 +16346,15 @@ { "type": "CommentLine", "value": " Extract the newick string.", - "start": 12650, - "end": 12679, + "start": 13100, + "end": 13129, "loc": { "start": { - "line": 324, + "line": 343, "column": 4 }, "end": { - "line": 324, + "line": 343, "column": 33 } } @@ -15676,15 +16364,15 @@ { "type": "CommentLine", "value": " Parse the Newick string; if parseable, recurse through the nodes,", - "start": 12742, - "end": 12810, + "start": 13192, + "end": 13260, "loc": { "start": { - "line": 327, + "line": 346, "column": 4 }, "end": { - "line": 327, + "line": 346, "column": 72 } } @@ -15692,15 +16380,15 @@ { "type": "CommentLine", "value": " added them to the list of JSON-LD nodes as we go.", - "start": 12815, - "end": 12867, + "start": 13265, + "end": 13317, "loc": { "start": { - "line": 328, + "line": 347, "column": 4 }, "end": { - "line": 328, + "line": 347, "column": 56 } } @@ -15709,44 +16397,44 @@ }, { "type": "VariableDeclaration", - "start": 12873, - "end": 12940, + "start": 13323, + "end": 13390, "loc": { "start": { - "line": 330, + "line": 349, "column": 4 }, "end": { - "line": 330, + "line": 349, "column": 71 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12879, - "end": 12939, + "start": 13329, + "end": 13389, "loc": { "start": { - "line": 330, + "line": 349, "column": 10 }, "end": { - "line": 330, + "line": 349, "column": 70 } }, "id": { "type": "Identifier", - "start": 12879, - "end": 12885, + "start": 13329, + "end": 13335, "loc": { "start": { - "line": 330, + "line": 349, "column": 10 }, "end": { - "line": 330, + "line": 349, "column": 16 }, "identifierName": "parsed" @@ -15756,58 +16444,58 @@ }, "init": { "type": "CallExpression", - "start": 12888, - "end": 12939, + "start": 13338, + "end": 13389, "loc": { "start": { - "line": 330, + "line": 349, "column": 19 }, "end": { - "line": 330, + "line": 349, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 12888, - "end": 12916, + "start": 13338, + "end": 13366, "loc": { "start": { - "line": 330, + "line": 349, "column": 19 }, "end": { - "line": 330, + "line": 349, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 12888, - "end": 12892, + "start": 13338, + "end": 13342, "loc": { "start": { - "line": 330, + "line": 349, "column": 19 }, "end": { - "line": 330, + "line": 349, "column": 23 } } }, "property": { "type": "Identifier", - "start": 12893, - "end": 12916, + "start": 13343, + "end": 13366, "loc": { "start": { - "line": 330, + "line": 349, "column": 24 }, "end": { - "line": 330, + "line": 349, "column": 47 }, "identifierName": "getParsedNewickWithIRIs" @@ -15819,15 +16507,15 @@ "arguments": [ { "type": "Identifier", - "start": 12917, - "end": 12924, + "start": 13367, + "end": 13374, "loc": { "start": { - "line": 330, + "line": 349, "column": 48 }, "end": { - "line": 330, + "line": 349, "column": 55 }, "identifierName": "baseIRI" @@ -15836,15 +16524,15 @@ }, { "type": "Identifier", - "start": 12926, - "end": 12938, + "start": 13376, + "end": 13388, "loc": { "start": { - "line": 330, + "line": 349, "column": 57 }, "end": { - "line": 330, + "line": 349, "column": 69 }, "identifierName": "newickParser" @@ -15861,15 +16549,15 @@ { "type": "CommentLine", "value": " Parse the Newick string; if parseable, recurse through the nodes,", - "start": 12742, - "end": 12810, + "start": 13192, + "end": 13260, "loc": { "start": { - "line": 327, + "line": 346, "column": 4 }, "end": { - "line": 327, + "line": 346, "column": 72 } } @@ -15877,15 +16565,15 @@ { "type": "CommentLine", "value": " added them to the list of JSON-LD nodes as we go.", - "start": 12815, - "end": 12867, + "start": 13265, + "end": 13317, "loc": { "start": { - "line": 328, + "line": 347, "column": 4 }, "end": { - "line": 328, + "line": 347, "column": 56 } } @@ -15894,43 +16582,43 @@ }, { "type": "IfStatement", - "start": 12945, - "end": 15805, + "start": 13395, + "end": 16255, "loc": { "start": { - "line": 331, + "line": 350, "column": 4 }, "end": { - "line": 400, + "line": 419, "column": 5 } }, "test": { "type": "CallExpression", - "start": 12949, - "end": 12968, + "start": 13399, + "end": 13418, "loc": { "start": { - "line": 331, + "line": 350, "column": 8 }, "end": { - "line": 331, + "line": 350, "column": 27 } }, "callee": { "type": "Identifier", - "start": 12949, - "end": 12952, + "start": 13399, + "end": 13402, "loc": { "start": { - "line": 331, + "line": 350, "column": 8 }, "end": { - "line": 331, + "line": 350, "column": 11 }, "identifierName": "has" @@ -15940,15 +16628,15 @@ "arguments": [ { "type": "Identifier", - "start": 12953, - "end": 12959, + "start": 13403, + "end": 13409, "loc": { "start": { - "line": 331, + "line": 350, "column": 12 }, "end": { - "line": 331, + "line": 350, "column": 18 }, "identifierName": "parsed" @@ -15957,15 +16645,15 @@ }, { "type": "StringLiteral", - "start": 12961, - "end": 12967, + "start": 13411, + "end": 13417, "loc": { "start": { - "line": 331, + "line": 350, "column": 20 }, "end": { - "line": 331, + "line": 350, "column": 26 } }, @@ -15979,72 +16667,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 12970, - "end": 15805, + "start": 13420, + "end": 16255, "loc": { "start": { - "line": 331, + "line": 350, "column": 29 }, "end": { - "line": 400, + "line": 419, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 12978, - "end": 15799, + "start": 13428, + "end": 16249, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 399, + "line": 418, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 12978, - "end": 15798, + "start": 13428, + "end": 16248, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 399, + "line": 418, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 12978, - "end": 13007, + "start": 13428, + "end": 13457, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 332, + "line": 351, "column": 35 } }, "object": { "type": "Identifier", - "start": 12978, - "end": 12994, + "start": 13428, + "end": 13444, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 332, + "line": 351, "column": 22 }, "identifierName": "PhylogenyWrapper" @@ -16053,15 +16741,15 @@ }, "property": { "type": "Identifier", - "start": 12995, - "end": 13007, + "start": 13445, + "end": 13457, "loc": { "start": { - "line": 332, + "line": 351, "column": 23 }, "end": { - "line": 332, + "line": 351, "column": 35 }, "identifierName": "recurseNodes" @@ -16073,29 +16761,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 13008, - "end": 13019, + "start": 13458, + "end": 13469, "loc": { "start": { - "line": 332, + "line": 351, "column": 36 }, "end": { - "line": 332, + "line": 351, "column": 47 } }, "object": { "type": "Identifier", - "start": 13008, - "end": 13014, + "start": 13458, + "end": 13464, "loc": { "start": { - "line": 332, + "line": 351, "column": 36 }, "end": { - "line": 332, + "line": 351, "column": 42 }, "identifierName": "parsed" @@ -16104,15 +16792,15 @@ }, "property": { "type": "Identifier", - "start": 13015, - "end": 13019, + "start": 13465, + "end": 13469, "loc": { "start": { - "line": 332, + "line": 351, "column": 43 }, "end": { - "line": 332, + "line": 351, "column": 47 }, "identifierName": "json" @@ -16123,15 +16811,15 @@ }, { "type": "ArrowFunctionExpression", - "start": 13021, - "end": 15797, + "start": 13471, + "end": 16247, "loc": { "start": { - "line": 332, + "line": 351, "column": 49 }, "end": { - "line": 399, + "line": 418, "column": 7 } }, @@ -16142,15 +16830,15 @@ "params": [ { "type": "Identifier", - "start": 13022, - "end": 13026, + "start": 13472, + "end": 13476, "loc": { "start": { - "line": 332, + "line": 351, "column": 50 }, "end": { - "line": 332, + "line": 351, "column": 54 }, "identifierName": "node" @@ -16159,15 +16847,15 @@ }, { "type": "Identifier", - "start": 13028, - "end": 13037, + "start": 13478, + "end": 13487, "loc": { "start": { - "line": 332, + "line": 351, "column": 56 }, "end": { - "line": 332, + "line": 351, "column": 65 }, "identifierName": "nodeCount" @@ -16176,15 +16864,15 @@ }, { "type": "Identifier", - "start": 13039, - "end": 13050, + "start": 13489, + "end": 13500, "loc": { "start": { - "line": 332, + "line": 351, "column": 67 }, "end": { - "line": 332, + "line": 351, "column": 78 }, "identifierName": "parentCount" @@ -16194,59 +16882,59 @@ ], "body": { "type": "BlockStatement", - "start": 13055, - "end": 15797, + "start": 13505, + "end": 16247, "loc": { "start": { - "line": 332, + "line": 351, "column": 83 }, "end": { - "line": 399, + "line": 418, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 13119, - "end": 13143, + "start": 13569, + "end": 13593, "loc": { "start": { - "line": 334, + "line": 353, "column": 8 }, "end": { - "line": 334, + "line": 353, "column": 32 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13125, - "end": 13142, + "start": 13575, + "end": 13592, "loc": { "start": { - "line": 334, + "line": 353, "column": 14 }, "end": { - "line": 334, + "line": 353, "column": 31 } }, "id": { "type": "Identifier", - "start": 13125, - "end": 13137, + "start": 13575, + "end": 13587, "loc": { "start": { - "line": 334, + "line": 353, "column": 14 }, "end": { - "line": 334, + "line": 353, "column": 26 }, "identifierName": "nodeAsJSONLD" @@ -16256,15 +16944,15 @@ }, "init": { "type": "ObjectExpression", - "start": 13140, - "end": 13142, + "start": 13590, + "end": 13592, "loc": { "start": { - "line": 334, + "line": 353, "column": 29 }, "end": { - "line": 334, + "line": 353, "column": 31 } }, @@ -16278,15 +16966,15 @@ { "type": "CommentLine", "value": " Start with the additional node properties.", - "start": 13065, - "end": 13110, + "start": 13515, + "end": 13560, "loc": { "start": { - "line": 333, + "line": 352, "column": 8 }, "end": { - "line": 333, + "line": 352, "column": 53 } } @@ -16296,15 +16984,15 @@ { "type": "CommentLine", "value": " Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!", - "start": 13153, - "end": 13232, + "start": 13603, + "end": 13682, "loc": { "start": { - "line": 336, + "line": 355, "column": 8 }, "end": { - "line": 336, + "line": 355, "column": 87 } } @@ -16313,44 +17001,44 @@ }, { "type": "VariableDeclaration", - "start": 13241, - "end": 13269, + "start": 13691, + "end": 13719, "loc": { "start": { - "line": 337, + "line": 356, "column": 8 }, "end": { - "line": 337, + "line": 356, "column": 36 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13247, - "end": 13268, + "start": 13697, + "end": 13718, "loc": { "start": { - "line": 337, + "line": 356, "column": 14 }, "end": { - "line": 337, + "line": 356, "column": 35 } }, "id": { "type": "Identifier", - "start": 13247, - "end": 13254, + "start": 13697, + "end": 13704, "loc": { "start": { - "line": 337, + "line": 356, "column": 14 }, "end": { - "line": 337, + "line": 356, "column": 21 }, "identifierName": "nodeIRI" @@ -16360,29 +17048,29 @@ }, "init": { "type": "MemberExpression", - "start": 13257, - "end": 13268, + "start": 13707, + "end": 13718, "loc": { "start": { - "line": 337, + "line": 356, "column": 24 }, "end": { - "line": 337, + "line": 356, "column": 35 } }, "object": { "type": "Identifier", - "start": 13257, - "end": 13261, + "start": 13707, + "end": 13711, "loc": { "start": { - "line": 337, + "line": 356, "column": 24 }, "end": { - "line": 337, + "line": 356, "column": 28 }, "identifierName": "node" @@ -16391,15 +17079,15 @@ }, "property": { "type": "StringLiteral", - "start": 13262, - "end": 13267, + "start": 13712, + "end": 13717, "loc": { "start": { - "line": 337, + "line": 356, "column": 29 }, "end": { - "line": 337, + "line": 356, "column": 34 } }, @@ -16419,15 +17107,15 @@ { "type": "CommentLine", "value": " Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!", - "start": 13153, - "end": 13232, + "start": 13603, + "end": 13682, "loc": { "start": { - "line": 336, + "line": 355, "column": 8 }, "end": { - "line": 336, + "line": 355, "column": 87 } } @@ -16436,58 +17124,58 @@ }, { "type": "ExpressionStatement", - "start": 13278, - "end": 13308, + "start": 13728, + "end": 13758, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 13278, - "end": 13307, + "start": 13728, + "end": 13757, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13278, - "end": 13297, + "start": 13728, + "end": 13747, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 27 } }, "object": { "type": "Identifier", - "start": 13278, - "end": 13290, + "start": 13728, + "end": 13740, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 20 }, "identifierName": "nodeAsJSONLD" @@ -16496,15 +17184,15 @@ }, "property": { "type": "StringLiteral", - "start": 13291, - "end": 13296, + "start": 13741, + "end": 13746, "loc": { "start": { - "line": 338, + "line": 357, "column": 21 }, "end": { - "line": 338, + "line": 357, "column": 26 } }, @@ -16518,15 +17206,15 @@ }, "right": { "type": "Identifier", - "start": 13300, - "end": 13307, + "start": 13750, + "end": 13757, "loc": { "start": { - "line": 338, + "line": 357, "column": 30 }, "end": { - "line": 338, + "line": 357, "column": 37 }, "identifierName": "nodeIRI" @@ -16538,15 +17226,15 @@ { "type": "CommentLine", "value": " Since we may need to add multiple classes into the rdf:type, we need", - "start": 13318, - "end": 13389, + "start": 13768, + "end": 13839, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 79 } } @@ -16554,15 +17242,15 @@ { "type": "CommentLine", "value": " to make @type an array. However, the JSON-LD library we use in JPhyloRef", - "start": 13398, - "end": 13473, + "start": 13848, + "end": 13923, "loc": { "start": { - "line": 341, + "line": 360, "column": 8 }, "end": { - "line": 341, + "line": 360, "column": 83 } } @@ -16570,15 +17258,15 @@ { "type": "CommentLine", "value": " can't support @type being an array (despite that being in the standard,", - "start": 13482, - "end": 13556, + "start": 13932, + "end": 14006, "loc": { "start": { - "line": 342, + "line": 361, "column": 8 }, "end": { - "line": 342, + "line": 361, "column": 82 } } @@ -16586,15 +17274,15 @@ { "type": "CommentLine", "value": " see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),", - "start": 13565, - "end": 13659, + "start": 14015, + "end": 14109, "loc": { "start": { - "line": 343, + "line": 362, "column": 8 }, "end": { - "line": 343, + "line": 362, "column": 102 } } @@ -16602,15 +17290,15 @@ { "type": "CommentLine", "value": " so we fall back to using rdf:type instead.", - "start": 13668, - "end": 13713, + "start": 14118, + "end": 14163, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 53 } } @@ -16619,58 +17307,58 @@ }, { "type": "ExpressionStatement", - "start": 13722, - "end": 13788, + "start": 14172, + "end": 14238, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 74 } }, "expression": { "type": "AssignmentExpression", - "start": 13722, - "end": 13787, + "start": 14172, + "end": 14237, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 73 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13722, - "end": 13753, + "start": 14172, + "end": 14203, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 39 } }, "object": { "type": "Identifier", - "start": 13722, - "end": 13734, + "start": 14172, + "end": 14184, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 20 }, "identifierName": "nodeAsJSONLD" @@ -16680,29 +17368,29 @@ }, "property": { "type": "MemberExpression", - "start": 13735, - "end": 13752, + "start": 14185, + "end": 14202, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 38 } }, "object": { "type": "Identifier", - "start": 13735, - "end": 13743, + "start": 14185, + "end": 14193, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 29 }, "identifierName": "owlterms" @@ -16711,15 +17399,15 @@ }, "property": { "type": "Identifier", - "start": 13744, - "end": 13752, + "start": 14194, + "end": 14202, "loc": { "start": { - "line": 345, + "line": 364, "column": 30 }, "end": { - "line": 345, + "line": 364, "column": 38 }, "identifierName": "RDF_TYPE" @@ -16733,45 +17421,45 @@ }, "right": { "type": "ArrayExpression", - "start": 13756, - "end": 13787, + "start": 14206, + "end": 14237, "loc": { "start": { - "line": 345, + "line": 364, "column": 42 }, "end": { - "line": 345, + "line": 364, "column": 73 } }, "elements": [ { "type": "ObjectExpression", - "start": 13757, - "end": 13786, + "start": 14207, + "end": 14236, "loc": { "start": { - "line": 345, + "line": 364, "column": 43 }, "end": { - "line": 345, + "line": 364, "column": 72 } }, "properties": [ { "type": "ObjectProperty", - "start": 13759, - "end": 13784, + "start": 14209, + "end": 14234, "loc": { "start": { - "line": 345, + "line": 364, "column": 45 }, "end": { - "line": 345, + "line": 364, "column": 70 } }, @@ -16780,15 +17468,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 13759, - "end": 13764, + "start": 14209, + "end": 14214, "loc": { "start": { - "line": 345, + "line": 364, "column": 45 }, "end": { - "line": 345, + "line": 364, "column": 50 } }, @@ -16800,29 +17488,29 @@ }, "value": { "type": "MemberExpression", - "start": 13766, - "end": 13784, + "start": 14216, + "end": 14234, "loc": { "start": { - "line": 345, + "line": 364, "column": 52 }, "end": { - "line": 345, + "line": 364, "column": 70 } }, "object": { "type": "Identifier", - "start": 13766, - "end": 13774, + "start": 14216, + "end": 14224, "loc": { "start": { - "line": 345, + "line": 364, "column": 52 }, "end": { - "line": 345, + "line": 364, "column": 60 }, "identifierName": "owlterms" @@ -16831,15 +17519,15 @@ }, "property": { "type": "Identifier", - "start": 13775, - "end": 13784, + "start": 14225, + "end": 14234, "loc": { "start": { - "line": 345, + "line": 364, "column": 61 }, "end": { - "line": 345, + "line": 364, "column": 70 }, "identifierName": "CDAO_NODE" @@ -16859,15 +17547,15 @@ { "type": "CommentLine", "value": " Since we may need to add multiple classes into the rdf:type, we need", - "start": 13318, - "end": 13389, + "start": 13768, + "end": 13839, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 79 } } @@ -16875,15 +17563,15 @@ { "type": "CommentLine", "value": " to make @type an array. However, the JSON-LD library we use in JPhyloRef", - "start": 13398, - "end": 13473, + "start": 13848, + "end": 13923, "loc": { "start": { - "line": 341, + "line": 360, "column": 8 }, "end": { - "line": 341, + "line": 360, "column": 83 } } @@ -16891,15 +17579,15 @@ { "type": "CommentLine", "value": " can't support @type being an array (despite that being in the standard,", - "start": 13482, - "end": 13556, + "start": 13932, + "end": 14006, "loc": { "start": { - "line": 342, + "line": 361, "column": 8 }, "end": { - "line": 342, + "line": 361, "column": 82 } } @@ -16907,15 +17595,15 @@ { "type": "CommentLine", "value": " see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),", - "start": 13565, - "end": 13659, + "start": 14015, + "end": 14109, "loc": { "start": { - "line": 343, + "line": 362, "column": 8 }, "end": { - "line": 343, + "line": 362, "column": 102 } } @@ -16923,15 +17611,15 @@ { "type": "CommentLine", "value": " so we fall back to using rdf:type instead.", - "start": 13668, - "end": 13713, + "start": 14118, + "end": 14163, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 53 } } @@ -16941,15 +17629,15 @@ { "type": "CommentLine", "value": " Add labels, additional node properties and taxonomic units.", - "start": 13798, - "end": 13860, + "start": 14248, + "end": 14310, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 70 } } @@ -16958,57 +17646,57 @@ }, { "type": "IfStatement", - "start": 13869, - "end": 15104, + "start": 14319, + "end": 15554, "loc": { "start": { - "line": 348, + "line": 367, "column": 8 }, "end": { - "line": 379, + "line": 398, "column": 9 } }, "test": { "type": "LogicalExpression", - "start": 13873, - "end": 13910, + "start": 14323, + "end": 14360, "loc": { "start": { - "line": 348, + "line": 367, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 49 } }, "left": { "type": "CallExpression", - "start": 13873, - "end": 13890, + "start": 14323, + "end": 14340, "loc": { "start": { - "line": 348, + "line": 367, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 29 } }, "callee": { "type": "Identifier", - "start": 13873, - "end": 13876, + "start": 14323, + "end": 14326, "loc": { "start": { - "line": 348, + "line": 367, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 15 }, "identifierName": "has" @@ -17019,15 +17707,15 @@ "arguments": [ { "type": "Identifier", - "start": 13877, - "end": 13881, + "start": 14327, + "end": 14331, "loc": { "start": { - "line": 348, + "line": 367, "column": 16 }, "end": { - "line": 348, + "line": 367, "column": 20 }, "identifierName": "node" @@ -17036,15 +17724,15 @@ }, { "type": "StringLiteral", - "start": 13883, - "end": 13889, + "start": 14333, + "end": 14339, "loc": { "start": { - "line": 348, + "line": 367, "column": 22 }, "end": { - "line": 348, + "line": 367, "column": 28 } }, @@ -17060,43 +17748,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 13894, - "end": 13910, + "start": 14344, + "end": 14360, "loc": { "start": { - "line": 348, + "line": 367, "column": 33 }, "end": { - "line": 348, + "line": 367, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 13894, - "end": 13903, + "start": 14344, + "end": 14353, "loc": { "start": { - "line": 348, + "line": 367, "column": 33 }, "end": { - "line": 348, + "line": 367, "column": 42 } }, "object": { "type": "Identifier", - "start": 13894, - "end": 13898, + "start": 14344, + "end": 14348, "loc": { "start": { - "line": 348, + "line": 367, "column": 33 }, "end": { - "line": 348, + "line": 367, "column": 37 }, "identifierName": "node" @@ -17105,15 +17793,15 @@ }, "property": { "type": "Identifier", - "start": 13899, - "end": 13903, + "start": 14349, + "end": 14353, "loc": { "start": { - "line": 348, + "line": 367, "column": 38 }, "end": { - "line": 348, + "line": 367, "column": 42 }, "identifierName": "name" @@ -17125,15 +17813,15 @@ "operator": "!==", "right": { "type": "StringLiteral", - "start": 13908, - "end": 13910, + "start": 14358, + "end": 14360, "loc": { "start": { - "line": 348, + "line": 367, "column": 47 }, "end": { - "line": 348, + "line": 367, "column": 49 } }, @@ -17148,73 +17836,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 13912, - "end": 15104, + "start": 14362, + "end": 15554, "loc": { "start": { - "line": 348, + "line": 367, "column": 51 }, "end": { - "line": 379, + "line": 398, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 13953, - "end": 13987, + "start": 14403, + "end": 14437, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 13953, - "end": 13986, + "start": 14403, + "end": 14436, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13953, - "end": 13972, + "start": 14403, + "end": 14422, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 29 } }, "object": { "type": "Identifier", - "start": 13953, - "end": 13965, + "start": 14403, + "end": 14415, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -17224,15 +17912,15 @@ }, "property": { "type": "Identifier", - "start": 13966, - "end": 13972, + "start": 14416, + "end": 14422, "loc": { "start": { - "line": 350, + "line": 369, "column": 23 }, "end": { - "line": 350, + "line": 369, "column": 29 }, "identifierName": "labels" @@ -17244,44 +17932,44 @@ }, "right": { "type": "ArrayExpression", - "start": 13975, - "end": 13986, + "start": 14425, + "end": 14436, "loc": { "start": { - "line": 350, + "line": 369, "column": 32 }, "end": { - "line": 350, + "line": 369, "column": 43 } }, "elements": [ { "type": "MemberExpression", - "start": 13976, - "end": 13985, + "start": 14426, + "end": 14435, "loc": { "start": { - "line": 350, + "line": 369, "column": 33 }, "end": { - "line": 350, + "line": 369, "column": 42 } }, "object": { "type": "Identifier", - "start": 13976, - "end": 13980, + "start": 14426, + "end": 14430, "loc": { "start": { - "line": 350, + "line": 369, "column": 33 }, "end": { - "line": 350, + "line": 369, "column": 37 }, "identifierName": "node" @@ -17290,15 +17978,15 @@ }, "property": { "type": "Identifier", - "start": 13981, - "end": 13985, + "start": 14431, + "end": 14435, "loc": { "start": { - "line": 350, + "line": 369, "column": 38 }, "end": { - "line": 350, + "line": 369, "column": 42 }, "identifierName": "name" @@ -17315,15 +18003,15 @@ { "type": "CommentLine", "value": " Add node label.", - "start": 13924, - "end": 13942, + "start": 14374, + "end": 14392, "loc": { "start": { - "line": 349, + "line": 368, "column": 10 }, "end": { - "line": 349, + "line": 368, "column": 28 } } @@ -17333,15 +18021,15 @@ { "type": "CommentLine", "value": " Add additional node properties, if any.", - "start": 13999, - "end": 14041, + "start": 14449, + "end": 14491, "loc": { "start": { - "line": 352, + "line": 371, "column": 10 }, "end": { - "line": 352, + "line": 371, "column": 52 } } @@ -17350,43 +18038,43 @@ }, { "type": "IfStatement", - "start": 14052, - "end": 14311, + "start": 14502, + "end": 14761, "loc": { "start": { - "line": 353, + "line": 372, "column": 10 }, "end": { - "line": 357, + "line": 376, "column": 11 } }, "test": { "type": "LogicalExpression", - "start": 14056, - "end": 14124, + "start": 14506, + "end": 14574, "loc": { "start": { - "line": 353, + "line": 372, "column": 14 }, "end": { - "line": 353, + "line": 372, "column": 82 } }, "left": { "type": "Identifier", - "start": 14056, - "end": 14080, + "start": 14506, + "end": 14530, "loc": { "start": { - "line": 353, + "line": 372, "column": 14 }, "end": { - "line": 353, + "line": 372, "column": 38 }, "identifierName": "additionalNodeProperties" @@ -17397,29 +18085,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 14084, - "end": 14124, + "start": 14534, + "end": 14574, "loc": { "start": { - "line": 353, + "line": 372, "column": 42 }, "end": { - "line": 353, + "line": 372, "column": 82 } }, "callee": { "type": "Identifier", - "start": 14084, - "end": 14087, + "start": 14534, + "end": 14537, "loc": { "start": { - "line": 353, + "line": 372, "column": 42 }, "end": { - "line": 353, + "line": 372, "column": 45 }, "identifierName": "has" @@ -17429,15 +18117,15 @@ "arguments": [ { "type": "Identifier", - "start": 14088, - "end": 14112, + "start": 14538, + "end": 14562, "loc": { "start": { - "line": 353, + "line": 372, "column": 46 }, "end": { - "line": 353, + "line": 372, "column": 70 }, "identifierName": "additionalNodeProperties" @@ -17446,29 +18134,29 @@ }, { "type": "MemberExpression", - "start": 14114, - "end": 14123, + "start": 14564, + "end": 14573, "loc": { "start": { - "line": 353, + "line": 372, "column": 72 }, "end": { - "line": 353, + "line": 372, "column": 81 } }, "object": { "type": "Identifier", - "start": 14114, - "end": 14118, + "start": 14564, + "end": 14568, "loc": { "start": { - "line": 353, + "line": 372, "column": 72 }, "end": { - "line": 353, + "line": 372, "column": 76 }, "identifierName": "node" @@ -17477,15 +18165,15 @@ }, "property": { "type": "Identifier", - "start": 14119, - "end": 14123, + "start": 14569, + "end": 14573, "loc": { "start": { - "line": 353, + "line": 372, "column": 77 }, "end": { - "line": 353, + "line": 372, "column": 81 }, "identifierName": "name" @@ -17500,100 +18188,100 @@ }, "consequent": { "type": "BlockStatement", - "start": 14126, - "end": 14311, + "start": 14576, + "end": 14761, "loc": { "start": { - "line": 353, + "line": 372, "column": 84 }, "end": { - "line": 357, + "line": 376, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 14140, - "end": 14299, + "start": 14590, + "end": 14749, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 356, + "line": 375, "column": 15 } }, "expression": { "type": "CallExpression", - "start": 14140, - "end": 14298, + "start": 14590, + "end": 14748, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 356, + "line": 375, "column": 14 } }, "callee": { "type": "MemberExpression", - "start": 14140, - "end": 14196, + "start": 14590, + "end": 14646, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 68 } }, "object": { "type": "CallExpression", - "start": 14140, - "end": 14188, + "start": 14590, + "end": 14638, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 14140, - "end": 14151, + "start": 14590, + "end": 14601, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 23 } }, "object": { "type": "Identifier", - "start": 14140, - "end": 14146, + "start": 14590, + "end": 14596, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 18 }, "identifierName": "Object" @@ -17602,15 +18290,15 @@ }, "property": { "type": "Identifier", - "start": 14147, - "end": 14151, + "start": 14597, + "end": 14601, "loc": { "start": { - "line": 354, + "line": 373, "column": 19 }, "end": { - "line": 354, + "line": 373, "column": 23 }, "identifierName": "keys" @@ -17622,29 +18310,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 14152, - "end": 14187, + "start": 14602, + "end": 14637, "loc": { "start": { - "line": 354, + "line": 373, "column": 24 }, "end": { - "line": 354, + "line": 373, "column": 59 } }, "object": { "type": "Identifier", - "start": 14152, - "end": 14176, + "start": 14602, + "end": 14626, "loc": { "start": { - "line": 354, + "line": 373, "column": 24 }, "end": { - "line": 354, + "line": 373, "column": 48 }, "identifierName": "additionalNodeProperties" @@ -17653,29 +18341,29 @@ }, "property": { "type": "MemberExpression", - "start": 14177, - "end": 14186, + "start": 14627, + "end": 14636, "loc": { "start": { - "line": 354, + "line": 373, "column": 49 }, "end": { - "line": 354, + "line": 373, "column": 58 } }, "object": { "type": "Identifier", - "start": 14177, - "end": 14181, + "start": 14627, + "end": 14631, "loc": { "start": { - "line": 354, + "line": 373, "column": 49 }, "end": { - "line": 354, + "line": 373, "column": 53 }, "identifierName": "node" @@ -17684,15 +18372,15 @@ }, "property": { "type": "Identifier", - "start": 14182, - "end": 14186, + "start": 14632, + "end": 14636, "loc": { "start": { - "line": 354, + "line": 373, "column": 54 }, "end": { - "line": 354, + "line": 373, "column": 58 }, "identifierName": "name" @@ -17707,15 +18395,15 @@ }, "property": { "type": "Identifier", - "start": 14189, - "end": 14196, + "start": 14639, + "end": 14646, "loc": { "start": { - "line": 354, + "line": 373, "column": 61 }, "end": { - "line": 354, + "line": 373, "column": 68 }, "identifierName": "forEach" @@ -17727,15 +18415,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 14197, - "end": 14297, + "start": 14647, + "end": 14747, "loc": { "start": { - "line": 354, + "line": 373, "column": 69 }, "end": { - "line": 356, + "line": 375, "column": 13 } }, @@ -17746,15 +18434,15 @@ "params": [ { "type": "Identifier", - "start": 14198, - "end": 14201, + "start": 14648, + "end": 14651, "loc": { "start": { - "line": 354, + "line": 373, "column": 70 }, "end": { - "line": 354, + "line": 373, "column": 73 }, "identifierName": "key" @@ -17764,73 +18452,73 @@ ], "body": { "type": "BlockStatement", - "start": 14206, - "end": 14297, + "start": 14656, + "end": 14747, "loc": { "start": { - "line": 354, + "line": 373, "column": 78 }, "end": { - "line": 356, + "line": 375, "column": 13 } }, "body": [ { "type": "ExpressionStatement", - "start": 14222, - "end": 14283, + "start": 14672, + "end": 14733, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 75 } }, "expression": { "type": "AssignmentExpression", - "start": 14222, - "end": 14282, + "start": 14672, + "end": 14732, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 74 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 14222, - "end": 14239, + "start": 14672, + "end": 14689, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 31 } }, "object": { "type": "Identifier", - "start": 14222, - "end": 14234, + "start": 14672, + "end": 14684, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 26 }, "identifierName": "nodeAsJSONLD" @@ -17839,15 +18527,15 @@ }, "property": { "type": "Identifier", - "start": 14235, - "end": 14238, + "start": 14685, + "end": 14688, "loc": { "start": { - "line": 355, + "line": 374, "column": 27 }, "end": { - "line": 355, + "line": 374, "column": 30 }, "identifierName": "key" @@ -17858,43 +18546,43 @@ }, "right": { "type": "MemberExpression", - "start": 14242, - "end": 14282, + "start": 14692, + "end": 14732, "loc": { "start": { - "line": 355, + "line": 374, "column": 34 }, "end": { - "line": 355, + "line": 374, "column": 74 } }, "object": { "type": "MemberExpression", - "start": 14242, - "end": 14277, + "start": 14692, + "end": 14727, "loc": { "start": { - "line": 355, + "line": 374, "column": 34 }, "end": { - "line": 355, + "line": 374, "column": 69 } }, "object": { "type": "Identifier", - "start": 14242, - "end": 14266, + "start": 14692, + "end": 14716, "loc": { "start": { - "line": 355, + "line": 374, "column": 34 }, "end": { - "line": 355, + "line": 374, "column": 58 }, "identifierName": "additionalNodeProperties" @@ -17903,29 +18591,29 @@ }, "property": { "type": "MemberExpression", - "start": 14267, - "end": 14276, + "start": 14717, + "end": 14726, "loc": { "start": { - "line": 355, + "line": 374, "column": 59 }, "end": { - "line": 355, + "line": 374, "column": 68 } }, "object": { "type": "Identifier", - "start": 14267, - "end": 14271, + "start": 14717, + "end": 14721, "loc": { "start": { - "line": 355, + "line": 374, "column": 59 }, "end": { - "line": 355, + "line": 374, "column": 63 }, "identifierName": "node" @@ -17934,15 +18622,15 @@ }, "property": { "type": "Identifier", - "start": 14272, - "end": 14276, + "start": 14722, + "end": 14726, "loc": { "start": { - "line": 355, + "line": 374, "column": 64 }, "end": { - "line": 355, + "line": 374, "column": 68 }, "identifierName": "name" @@ -17955,15 +18643,15 @@ }, "property": { "type": "Identifier", - "start": 14278, - "end": 14281, + "start": 14728, + "end": 14731, "loc": { "start": { - "line": 355, + "line": 374, "column": 70 }, "end": { - "line": 355, + "line": 374, "column": 73 }, "identifierName": "key" @@ -17990,15 +18678,15 @@ { "type": "CommentLine", "value": " Add additional node properties, if any.", - "start": 13999, - "end": 14041, + "start": 14449, + "end": 14491, "loc": { "start": { - "line": 352, + "line": 371, "column": 10 }, "end": { - "line": 352, + "line": 371, "column": 52 } } @@ -18008,15 +18696,15 @@ { "type": "CommentLine", "value": " Add taxonomic units into the metadata.", - "start": 14323, - "end": 14364, + "start": 14773, + "end": 14814, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 51 } } @@ -18025,58 +18713,58 @@ }, { "type": "ExpressionStatement", - "start": 14375, - "end": 14461, + "start": 14825, + "end": 14911, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 96 } }, "expression": { "type": "AssignmentExpression", - "start": 14375, - "end": 14460, + "start": 14825, + "end": 14910, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 95 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 14375, - "end": 14412, + "start": 14825, + "end": 14862, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 47 } }, "object": { "type": "Identifier", - "start": 14375, - "end": 14387, + "start": 14825, + "end": 14837, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -18086,15 +18774,15 @@ }, "property": { "type": "Identifier", - "start": 14388, - "end": 14412, + "start": 14838, + "end": 14862, "loc": { "start": { - "line": 360, + "line": 379, "column": 23 }, "end": { - "line": 360, + "line": 379, "column": 47 }, "identifierName": "representsTaxonomicUnits" @@ -18106,58 +18794,58 @@ }, "right": { "type": "CallExpression", - "start": 14415, - "end": 14460, + "start": 14865, + "end": 14910, "loc": { "start": { - "line": 360, + "line": 379, "column": 50 }, "end": { - "line": 360, + "line": 379, "column": 95 } }, "callee": { "type": "MemberExpression", - "start": 14415, - "end": 14449, + "start": 14865, + "end": 14899, "loc": { "start": { - "line": 360, + "line": 379, "column": 50 }, "end": { - "line": 360, + "line": 379, "column": 84 } }, "object": { "type": "ThisExpression", - "start": 14415, - "end": 14419, + "start": 14865, + "end": 14869, "loc": { "start": { - "line": 360, + "line": 379, "column": 50 }, "end": { - "line": 360, + "line": 379, "column": 54 } } }, "property": { "type": "Identifier", - "start": 14420, - "end": 14449, + "start": 14870, + "end": 14899, "loc": { "start": { - "line": 360, + "line": 379, "column": 55 }, "end": { - "line": 360, + "line": 379, "column": 84 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -18169,29 +18857,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 14450, - "end": 14459, + "start": 14900, + "end": 14909, "loc": { "start": { - "line": 360, + "line": 379, "column": 85 }, "end": { - "line": 360, + "line": 379, "column": 94 } }, "object": { "type": "Identifier", - "start": 14450, - "end": 14454, + "start": 14900, + "end": 14904, "loc": { "start": { - "line": 360, + "line": 379, "column": 85 }, "end": { - "line": 360, + "line": 379, "column": 89 }, "identifierName": "node" @@ -18200,15 +18888,15 @@ }, "property": { "type": "Identifier", - "start": 14455, - "end": 14459, + "start": 14905, + "end": 14909, "loc": { "start": { - "line": 360, + "line": 379, "column": 90 }, "end": { - "line": 360, + "line": 379, "column": 94 }, "identifierName": "name" @@ -18225,15 +18913,15 @@ { "type": "CommentLine", "value": " Add taxonomic units into the metadata.", - "start": 14323, - "end": 14364, + "start": 14773, + "end": 14814, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 51 } } @@ -18243,15 +18931,15 @@ { "type": "CommentLine", "value": " Add it into the @type so we can reason over it.", - "start": 14473, - "end": 14523, + "start": 14923, + "end": 14973, "loc": { "start": { - "line": 362, + "line": 381, "column": 10 }, "end": { - "line": 362, + "line": 381, "column": 60 } } @@ -18260,71 +18948,71 @@ }, { "type": "ExpressionStatement", - "start": 14534, - "end": 15094, + "start": 14984, + "end": 15544, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 378, + "line": 397, "column": 13 } }, "expression": { "type": "CallExpression", - "start": 14534, - "end": 15093, + "start": 14984, + "end": 15543, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 378, + "line": 397, "column": 12 } }, "callee": { "type": "MemberExpression", - "start": 14534, - "end": 14579, + "start": 14984, + "end": 15029, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 363, + "line": 382, "column": 55 } }, "object": { "type": "MemberExpression", - "start": 14534, - "end": 14571, + "start": 14984, + "end": 15021, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 363, + "line": 382, "column": 47 } }, "object": { "type": "Identifier", - "start": 14534, - "end": 14546, + "start": 14984, + "end": 14996, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 363, + "line": 382, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -18334,15 +19022,15 @@ }, "property": { "type": "Identifier", - "start": 14547, - "end": 14571, + "start": 14997, + "end": 15021, "loc": { "start": { - "line": 363, + "line": 382, "column": 23 }, "end": { - "line": 363, + "line": 382, "column": 47 }, "identifierName": "representsTaxonomicUnits" @@ -18354,15 +19042,15 @@ }, "property": { "type": "Identifier", - "start": 14572, - "end": 14579, + "start": 15022, + "end": 15029, "loc": { "start": { - "line": 363, + "line": 382, "column": 48 }, "end": { - "line": 363, + "line": 382, "column": 55 }, "identifierName": "forEach" @@ -18375,15 +19063,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 14580, - "end": 15092, + "start": 15030, + "end": 15542, "loc": { "start": { - "line": 363, + "line": 382, "column": 56 }, "end": { - "line": 378, + "line": 397, "column": 11 } }, @@ -18394,15 +19082,15 @@ "params": [ { "type": "Identifier", - "start": 14581, - "end": 14583, + "start": 15031, + "end": 15033, "loc": { "start": { - "line": 363, + "line": 382, "column": 57 }, "end": { - "line": 363, + "line": 382, "column": 59 }, "identifierName": "tu" @@ -18412,59 +19100,59 @@ ], "body": { "type": "BlockStatement", - "start": 14588, - "end": 15092, + "start": 15038, + "end": 15542, "loc": { "start": { - "line": 363, + "line": 382, "column": 64 }, "end": { - "line": 378, + "line": 397, "column": 11 } }, "body": [ { "type": "VariableDeclaration", - "start": 14602, - "end": 14652, + "start": 15052, + "end": 15102, "loc": { "start": { - "line": 364, + "line": 383, "column": 12 }, "end": { - "line": 364, + "line": 383, "column": 62 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 14608, - "end": 14651, + "start": 15058, + "end": 15101, "loc": { "start": { - "line": 364, + "line": 383, "column": 18 }, "end": { - "line": 364, + "line": 383, "column": 61 } }, "id": { "type": "Identifier", - "start": 14608, - "end": 14620, + "start": 15058, + "end": 15070, "loc": { "start": { - "line": 364, + "line": 383, "column": 18 }, "end": { - "line": 364, + "line": 383, "column": 30 }, "identifierName": "wrappedTUnit" @@ -18473,29 +19161,29 @@ }, "init": { "type": "NewExpression", - "start": 14623, - "end": 14651, + "start": 15073, + "end": 15101, "loc": { "start": { - "line": 364, + "line": 383, "column": 33 }, "end": { - "line": 364, + "line": 383, "column": 61 } }, "callee": { "type": "Identifier", - "start": 14627, - "end": 14647, + "start": 15077, + "end": 15097, "loc": { "start": { - "line": 364, + "line": 383, "column": 37 }, "end": { - "line": 364, + "line": 383, "column": 57 }, "identifierName": "TaxonomicUnitWrapper" @@ -18505,15 +19193,15 @@ "arguments": [ { "type": "Identifier", - "start": 14648, - "end": 14650, + "start": 15098, + "end": 15100, "loc": { "start": { - "line": 364, + "line": 383, "column": 58 }, "end": { - "line": 364, + "line": 383, "column": 60 }, "identifierName": "tu" @@ -18528,29 +19216,29 @@ }, { "type": "IfStatement", - "start": 14666, - "end": 15080, + "start": 15116, + "end": 15530, "loc": { "start": { - "line": 366, + "line": 385, "column": 12 }, "end": { - "line": 377, + "line": 396, "column": 13 } }, "test": { "type": "Identifier", - "start": 14670, - "end": 14682, + "start": 15120, + "end": 15132, "loc": { "start": { - "line": 366, + "line": 385, "column": 16 }, "end": { - "line": 366, + "line": 385, "column": 28 }, "identifierName": "wrappedTUnit" @@ -18559,59 +19247,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 14684, - "end": 15080, + "start": 15134, + "end": 15530, "loc": { "start": { - "line": 366, + "line": 385, "column": 30 }, "end": { - "line": 377, + "line": 396, "column": 13 } }, "body": [ { "type": "VariableDeclaration", - "start": 14700, - "end": 14748, + "start": 15150, + "end": 15198, "loc": { "start": { - "line": 367, + "line": 386, "column": 14 }, "end": { - "line": 367, + "line": 386, "column": 62 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 14706, - "end": 14747, + "start": 15156, + "end": 15197, "loc": { "start": { - "line": 367, + "line": 386, "column": 20 }, "end": { - "line": 367, + "line": 386, "column": 61 } }, "id": { "type": "Identifier", - "start": 14706, - "end": 14716, + "start": 15156, + "end": 15166, "loc": { "start": { - "line": 367, + "line": 386, "column": 20 }, "end": { - "line": 367, + "line": 386, "column": 30 }, "identifierName": "equivClass" @@ -18620,29 +19308,29 @@ }, "init": { "type": "MemberExpression", - "start": 14719, - "end": 14747, + "start": 15169, + "end": 15197, "loc": { "start": { - "line": 367, + "line": 386, "column": 33 }, "end": { - "line": 367, + "line": 386, "column": 61 } }, "object": { "type": "Identifier", - "start": 14719, - "end": 14731, + "start": 15169, + "end": 15181, "loc": { "start": { - "line": 367, + "line": 386, "column": 33 }, "end": { - "line": 367, + "line": 386, "column": 45 }, "identifierName": "wrappedTUnit" @@ -18651,15 +19339,15 @@ }, "property": { "type": "Identifier", - "start": 14732, - "end": 14747, + "start": 15182, + "end": 15197, "loc": { "start": { - "line": 367, + "line": 386, "column": 46 }, "end": { - "line": 367, + "line": 386, "column": 61 }, "identifierName": "asOWLEquivClass" @@ -18674,29 +19362,29 @@ }, { "type": "IfStatement", - "start": 14763, - "end": 15066, + "start": 15213, + "end": 15516, "loc": { "start": { - "line": 368, + "line": 387, "column": 14 }, "end": { - "line": 376, + "line": 395, "column": 15 } }, "test": { "type": "Identifier", - "start": 14767, - "end": 14777, + "start": 15217, + "end": 15227, "loc": { "start": { - "line": 368, + "line": 387, "column": 18 }, "end": { - "line": 368, + "line": 387, "column": 28 }, "identifierName": "equivClass" @@ -18705,86 +19393,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 14779, - "end": 15066, + "start": 15229, + "end": 15516, "loc": { "start": { - "line": 368, + "line": 387, "column": 30 }, "end": { - "line": 376, + "line": 395, "column": 15 } }, "body": [ { "type": "ExpressionStatement", - "start": 14797, - "end": 15050, + "start": 15247, + "end": 15500, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 375, + "line": 394, "column": 18 } }, "expression": { "type": "CallExpression", - "start": 14797, - "end": 15049, + "start": 15247, + "end": 15499, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 375, + "line": 394, "column": 17 } }, "callee": { "type": "MemberExpression", - "start": 14797, - "end": 14833, + "start": 15247, + "end": 15283, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 369, + "line": 388, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 14797, - "end": 14828, + "start": 15247, + "end": 15278, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 369, + "line": 388, "column": 47 } }, "object": { "type": "Identifier", - "start": 14797, - "end": 14809, + "start": 15247, + "end": 15259, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 369, + "line": 388, "column": 28 }, "identifierName": "nodeAsJSONLD" @@ -18793,29 +19481,29 @@ }, "property": { "type": "MemberExpression", - "start": 14810, - "end": 14827, + "start": 15260, + "end": 15277, "loc": { "start": { - "line": 369, + "line": 388, "column": 29 }, "end": { - "line": 369, + "line": 388, "column": 46 } }, "object": { "type": "Identifier", - "start": 14810, - "end": 14818, + "start": 15260, + "end": 15268, "loc": { "start": { - "line": 369, + "line": 388, "column": 29 }, "end": { - "line": 369, + "line": 388, "column": 37 }, "identifierName": "owlterms" @@ -18824,15 +19512,15 @@ }, "property": { "type": "Identifier", - "start": 14819, - "end": 14827, + "start": 15269, + "end": 15277, "loc": { "start": { - "line": 369, + "line": 388, "column": 38 }, "end": { - "line": 369, + "line": 388, "column": 46 }, "identifierName": "RDF_TYPE" @@ -18845,15 +19533,15 @@ }, "property": { "type": "Identifier", - "start": 14829, - "end": 14833, + "start": 15279, + "end": 15283, "loc": { "start": { - "line": 369, + "line": 388, "column": 48 }, "end": { - "line": 369, + "line": 388, "column": 52 }, "identifierName": "push" @@ -18865,30 +19553,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 14853, - "end": 15031, + "start": 15303, + "end": 15481, "loc": { "start": { - "line": 370, + "line": 389, "column": 18 }, "end": { - "line": 374, + "line": 393, "column": 19 } }, "properties": [ { "type": "ObjectProperty", - "start": 14875, - "end": 14901, + "start": 15325, + "end": 15351, "loc": { "start": { - "line": 371, + "line": 390, "column": 20 }, "end": { - "line": 371, + "line": 390, "column": 46 } }, @@ -18897,15 +19585,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14875, - "end": 14882, + "start": 15325, + "end": 15332, "loc": { "start": { - "line": 371, + "line": 390, "column": 20 }, "end": { - "line": 371, + "line": 390, "column": 27 } }, @@ -18917,15 +19605,15 @@ }, "value": { "type": "StringLiteral", - "start": 14884, - "end": 14901, + "start": 15334, + "end": 15351, "loc": { "start": { - "line": 371, + "line": 390, "column": 29 }, "end": { - "line": 371, + "line": 390, "column": 46 } }, @@ -18938,15 +19626,15 @@ }, { "type": "ObjectProperty", - "start": 14923, - "end": 14962, + "start": 15373, + "end": 15412, "loc": { "start": { - "line": 372, + "line": 391, "column": 20 }, "end": { - "line": 372, + "line": 391, "column": 59 } }, @@ -18955,15 +19643,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14923, - "end": 14933, + "start": 15373, + "end": 15383, "loc": { "start": { - "line": 372, + "line": 391, "column": 20 }, "end": { - "line": 372, + "line": 391, "column": 30 }, "identifierName": "onProperty" @@ -18972,29 +19660,29 @@ }, "value": { "type": "MemberExpression", - "start": 14935, - "end": 14962, + "start": 15385, + "end": 15412, "loc": { "start": { - "line": 372, + "line": 391, "column": 32 }, "end": { - "line": 372, + "line": 391, "column": 59 } }, "object": { "type": "Identifier", - "start": 14935, - "end": 14943, + "start": 15385, + "end": 15393, "loc": { "start": { - "line": 372, + "line": 391, "column": 32 }, "end": { - "line": 372, + "line": 391, "column": 40 }, "identifierName": "owlterms" @@ -19003,15 +19691,15 @@ }, "property": { "type": "Identifier", - "start": 14944, - "end": 14962, + "start": 15394, + "end": 15412, "loc": { "start": { - "line": 372, + "line": 391, "column": 41 }, "end": { - "line": 372, + "line": 391, "column": 59 }, "identifierName": "CDAO_REPRESENTS_TU" @@ -19023,15 +19711,15 @@ }, { "type": "ObjectProperty", - "start": 14984, - "end": 15010, + "start": 15434, + "end": 15460, "loc": { "start": { - "line": 373, + "line": 392, "column": 20 }, "end": { - "line": 373, + "line": 392, "column": 46 } }, @@ -19040,15 +19728,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14984, - "end": 14998, + "start": 15434, + "end": 15448, "loc": { "start": { - "line": 373, + "line": 392, "column": 20 }, "end": { - "line": 373, + "line": 392, "column": 34 }, "identifierName": "someValuesFrom" @@ -19057,15 +19745,15 @@ }, "value": { "type": "Identifier", - "start": 15000, - "end": 15010, + "start": 15450, + "end": 15460, "loc": { "start": { - "line": 373, + "line": 392, "column": 36 }, "end": { - "line": 373, + "line": 392, "column": 46 }, "identifierName": "equivClass" @@ -19099,15 +19787,15 @@ { "type": "CommentLine", "value": " Add it into the @type so we can reason over it.", - "start": 14473, - "end": 14523, + "start": 14923, + "end": 14973, "loc": { "start": { - "line": 362, + "line": 381, "column": 10 }, "end": { - "line": 362, + "line": 381, "column": 60 } } @@ -19123,15 +19811,15 @@ { "type": "CommentLine", "value": " Add labels, additional node properties and taxonomic units.", - "start": 13798, - "end": 13860, + "start": 14248, + "end": 14310, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 70 } } @@ -19141,15 +19829,15 @@ { "type": "CommentLine", "value": " Add references to parents and siblings.", - "start": 15114, - "end": 15156, + "start": 15564, + "end": 15606, "loc": { "start": { - "line": 381, + "line": 400, "column": 8 }, "end": { - "line": 381, + "line": 400, "column": 50 } } @@ -19158,43 +19846,43 @@ }, { "type": "IfStatement", - "start": 15165, - "end": 15532, + "start": 15615, + "end": 15982, "loc": { "start": { - "line": 382, + "line": 401, "column": 8 }, "end": { - "line": 391, + "line": 410, "column": 9 } }, "test": { "type": "BinaryExpression", - "start": 15169, - "end": 15194, + "start": 15619, + "end": 15644, "loc": { "start": { - "line": 382, + "line": 401, "column": 12 }, "end": { - "line": 382, + "line": 401, "column": 37 } }, "left": { "type": "Identifier", - "start": 15169, - "end": 15180, + "start": 15619, + "end": 15630, "loc": { "start": { - "line": 382, + "line": 401, "column": 12 }, "end": { - "line": 382, + "line": 401, "column": 23 }, "identifierName": "parentCount" @@ -19205,15 +19893,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 15185, - "end": 15194, + "start": 15635, + "end": 15644, "loc": { "start": { - "line": 382, + "line": 401, "column": 28 }, "end": { - "line": 382, + "line": 401, "column": 37 }, "identifierName": "undefined" @@ -19224,59 +19912,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 15196, - "end": 15532, + "start": 15646, + "end": 15982, "loc": { "start": { - "line": 382, + "line": 401, "column": 39 }, "end": { - "line": 391, + "line": 410, "column": 9 } }, "body": [ { "type": "VariableDeclaration", - "start": 15208, - "end": 15258, + "start": 15658, + "end": 15708, "loc": { "start": { - "line": 383, + "line": 402, "column": 10 }, "end": { - "line": 383, + "line": 402, "column": 60 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15214, - "end": 15257, + "start": 15664, + "end": 15707, "loc": { "start": { - "line": 383, + "line": 402, "column": 16 }, "end": { - "line": 383, + "line": 402, "column": 59 } }, "id": { "type": "Identifier", - "start": 15214, - "end": 15223, + "start": 15664, + "end": 15673, "loc": { "start": { - "line": 383, + "line": 402, "column": 16 }, "end": { - "line": 383, + "line": 402, "column": 25 }, "identifierName": "parentIRI" @@ -19285,30 +19973,30 @@ }, "init": { "type": "TemplateLiteral", - "start": 15226, - "end": 15257, + "start": 15676, + "end": 15707, "loc": { "start": { - "line": 383, + "line": 402, "column": 28 }, "end": { - "line": 383, + "line": 402, "column": 59 } }, "expressions": [ { "type": "Identifier", - "start": 15229, - "end": 15236, + "start": 15679, + "end": 15686, "loc": { "start": { - "line": 383, + "line": 402, "column": 31 }, "end": { - "line": 383, + "line": 402, "column": 38 }, "identifierName": "baseIRI" @@ -19317,15 +20005,15 @@ }, { "type": "Identifier", - "start": 15244, - "end": 15255, + "start": 15694, + "end": 15705, "loc": { "start": { - "line": 383, + "line": 402, "column": 46 }, "end": { - "line": 383, + "line": 402, "column": 57 }, "identifierName": "parentCount" @@ -19336,15 +20024,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 15227, - "end": 15227, + "start": 15677, + "end": 15677, "loc": { "start": { - "line": 383, + "line": 402, "column": 29 }, "end": { - "line": 383, + "line": 402, "column": 29 } }, @@ -19356,15 +20044,15 @@ }, { "type": "TemplateElement", - "start": 15237, - "end": 15242, + "start": 15687, + "end": 15692, "loc": { "start": { - "line": 383, + "line": 402, "column": 39 }, "end": { - "line": 383, + "line": 402, "column": 44 } }, @@ -19376,15 +20064,15 @@ }, { "type": "TemplateElement", - "start": 15256, - "end": 15256, + "start": 15706, + "end": 15706, "loc": { "start": { - "line": 383, + "line": 402, "column": 58 }, "end": { - "line": 383, + "line": 402, "column": 58 } }, @@ -19402,58 +20090,58 @@ }, { "type": "ExpressionStatement", - "start": 15269, - "end": 15301, + "start": 15719, + "end": 15751, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 15269, - "end": 15300, + "start": 15719, + "end": 15750, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 15269, - "end": 15288, + "start": 15719, + "end": 15738, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 29 } }, "object": { "type": "Identifier", - "start": 15269, - "end": 15281, + "start": 15719, + "end": 15731, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -19462,15 +20150,15 @@ }, "property": { "type": "Identifier", - "start": 15282, - "end": 15288, + "start": 15732, + "end": 15738, "loc": { "start": { - "line": 384, + "line": 403, "column": 23 }, "end": { - "line": 384, + "line": 403, "column": 29 }, "identifierName": "parent" @@ -19481,15 +20169,15 @@ }, "right": { "type": "Identifier", - "start": 15291, - "end": 15300, + "start": 15741, + "end": 15750, "loc": { "start": { - "line": 384, + "line": 403, "column": 32 }, "end": { - "line": 384, + "line": 403, "column": 41 }, "identifierName": "parentIRI" @@ -19501,15 +20189,15 @@ { "type": "CommentLine", "value": " Update list of nodes by parent IDs.", - "start": 15313, - "end": 15351, + "start": 15763, + "end": 15801, "loc": { "start": { - "line": 386, + "line": 405, "column": 10 }, "end": { - "line": 386, + "line": 405, "column": 48 } } @@ -19518,29 +20206,29 @@ }, { "type": "IfStatement", - "start": 15362, - "end": 15469, + "start": 15812, + "end": 15919, "loc": { "start": { - "line": 387, + "line": 406, "column": 10 }, "end": { - "line": 389, + "line": 408, "column": 11 } }, "test": { "type": "UnaryExpression", - "start": 15366, - "end": 15400, + "start": 15816, + "end": 15850, "loc": { "start": { - "line": 387, + "line": 406, "column": 14 }, "end": { - "line": 387, + "line": 406, "column": 48 } }, @@ -19548,29 +20236,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 15367, - "end": 15400, + "start": 15817, + "end": 15850, "loc": { "start": { - "line": 387, + "line": 406, "column": 15 }, "end": { - "line": 387, + "line": 406, "column": 48 } }, "callee": { "type": "Identifier", - "start": 15367, - "end": 15370, + "start": 15817, + "end": 15820, "loc": { "start": { - "line": 387, + "line": 406, "column": 15 }, "end": { - "line": 387, + "line": 406, "column": 18 }, "identifierName": "has" @@ -19581,15 +20269,15 @@ "arguments": [ { "type": "Identifier", - "start": 15371, - "end": 15388, + "start": 15821, + "end": 15838, "loc": { "start": { - "line": 387, + "line": 406, "column": 19 }, "end": { - "line": 387, + "line": 406, "column": 36 }, "identifierName": "nodeIdsByParentId" @@ -19598,15 +20286,15 @@ }, { "type": "Identifier", - "start": 15390, - "end": 15399, + "start": 15840, + "end": 15849, "loc": { "start": { - "line": 387, + "line": 406, "column": 38 }, "end": { - "line": 387, + "line": 406, "column": 47 }, "identifierName": "parentIRI" @@ -19623,73 +20311,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 15402, - "end": 15469, + "start": 15852, + "end": 15919, "loc": { "start": { - "line": 387, + "line": 406, "column": 50 }, "end": { - "line": 389, + "line": 408, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 15416, - "end": 15457, + "start": 15866, + "end": 15907, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 53 } }, "expression": { "type": "AssignmentExpression", - "start": 15416, - "end": 15456, + "start": 15866, + "end": 15906, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 52 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 15416, - "end": 15444, + "start": 15866, + "end": 15894, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 40 } }, "object": { "type": "Identifier", - "start": 15416, - "end": 15433, + "start": 15866, + "end": 15883, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 29 }, "identifierName": "nodeIdsByParentId" @@ -19698,15 +20386,15 @@ }, "property": { "type": "Identifier", - "start": 15434, - "end": 15443, + "start": 15884, + "end": 15893, "loc": { "start": { - "line": 388, + "line": 407, "column": 30 }, "end": { - "line": 388, + "line": 407, "column": 39 }, "identifierName": "parentIRI" @@ -19717,29 +20405,29 @@ }, "right": { "type": "NewExpression", - "start": 15447, - "end": 15456, + "start": 15897, + "end": 15906, "loc": { "start": { - "line": 388, + "line": 407, "column": 43 }, "end": { - "line": 388, + "line": 407, "column": 52 } }, "callee": { "type": "Identifier", - "start": 15451, - "end": 15454, + "start": 15901, + "end": 15904, "loc": { "start": { - "line": 388, + "line": 407, "column": 47 }, "end": { - "line": 388, + "line": 407, "column": 50 }, "identifierName": "Set" @@ -19758,15 +20446,15 @@ { "type": "CommentLine", "value": " Update list of nodes by parent IDs.", - "start": 15313, - "end": 15351, + "start": 15763, + "end": 15801, "loc": { "start": { - "line": 386, + "line": 405, "column": 10 }, "end": { - "line": 386, + "line": 405, "column": 48 } } @@ -19775,71 +20463,71 @@ }, { "type": "ExpressionStatement", - "start": 15480, - "end": 15522, + "start": 15930, + "end": 15972, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 52 } }, "expression": { "type": "CallExpression", - "start": 15480, - "end": 15521, + "start": 15930, + "end": 15971, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 15480, - "end": 15512, + "start": 15930, + "end": 15962, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 42 } }, "object": { "type": "MemberExpression", - "start": 15480, - "end": 15508, + "start": 15930, + "end": 15958, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 38 } }, "object": { "type": "Identifier", - "start": 15480, - "end": 15497, + "start": 15930, + "end": 15947, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 27 }, "identifierName": "nodeIdsByParentId" @@ -19848,15 +20536,15 @@ }, "property": { "type": "Identifier", - "start": 15498, - "end": 15507, + "start": 15948, + "end": 15957, "loc": { "start": { - "line": 390, + "line": 409, "column": 28 }, "end": { - "line": 390, + "line": 409, "column": 37 }, "identifierName": "parentIRI" @@ -19867,15 +20555,15 @@ }, "property": { "type": "Identifier", - "start": 15509, - "end": 15512, + "start": 15959, + "end": 15962, "loc": { "start": { - "line": 390, + "line": 409, "column": 39 }, "end": { - "line": 390, + "line": 409, "column": 42 }, "identifierName": "add" @@ -19887,15 +20575,15 @@ "arguments": [ { "type": "Identifier", - "start": 15513, - "end": 15520, + "start": 15963, + "end": 15970, "loc": { "start": { - "line": 390, + "line": 409, "column": 43 }, "end": { - "line": 390, + "line": 409, "column": 50 }, "identifierName": "nodeIRI" @@ -19914,15 +20602,15 @@ { "type": "CommentLine", "value": " Add references to parents and siblings.", - "start": 15114, - "end": 15156, + "start": 15564, + "end": 15606, "loc": { "start": { - "line": 381, + "line": 400, "column": 8 }, "end": { - "line": 381, + "line": 400, "column": 50 } } @@ -19932,15 +20620,15 @@ { "type": "CommentLine", "value": " Add nodeAsJSONLD to list", - "start": 15542, - "end": 15569, + "start": 15992, + "end": 16019, "loc": { "start": { - "line": 393, + "line": 412, "column": 8 }, "end": { - "line": 393, + "line": 412, "column": 35 } } @@ -19949,43 +20637,43 @@ }, { "type": "IfStatement", - "start": 15578, - "end": 15712, + "start": 16028, + "end": 16162, "loc": { "start": { - "line": 394, + "line": 413, "column": 8 }, "end": { - "line": 396, + "line": 415, "column": 9 } }, "test": { "type": "CallExpression", - "start": 15582, - "end": 15605, + "start": 16032, + "end": 16055, "loc": { "start": { - "line": 394, + "line": 413, "column": 12 }, "end": { - "line": 394, + "line": 413, "column": 35 } }, "callee": { "type": "Identifier", - "start": 15582, - "end": 15585, + "start": 16032, + "end": 16035, "loc": { "start": { - "line": 394, + "line": 413, "column": 12 }, "end": { - "line": 394, + "line": 413, "column": 15 }, "identifierName": "has" @@ -19996,15 +20684,15 @@ "arguments": [ { "type": "Identifier", - "start": 15586, - "end": 15595, + "start": 16036, + "end": 16045, "loc": { "start": { - "line": 394, + "line": 413, "column": 16 }, "end": { - "line": 394, + "line": 413, "column": 25 }, "identifierName": "nodesById" @@ -20013,15 +20701,15 @@ }, { "type": "Identifier", - "start": 15597, - "end": 15604, + "start": 16047, + "end": 16054, "loc": { "start": { - "line": 394, + "line": 413, "column": 27 }, "end": { - "line": 394, + "line": 413, "column": 34 }, "identifierName": "nodeIRI" @@ -20033,58 +20721,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 15607, - "end": 15712, + "start": 16057, + "end": 16162, "loc": { "start": { - "line": 394, + "line": 413, "column": 37 }, "end": { - "line": 396, + "line": 415, "column": 9 } }, "body": [ { "type": "ThrowStatement", - "start": 15619, - "end": 15702, + "start": 16069, + "end": 16152, "loc": { "start": { - "line": 395, + "line": 414, "column": 10 }, "end": { - "line": 395, + "line": 414, "column": 93 } }, "argument": { "type": "NewExpression", - "start": 15625, - "end": 15701, + "start": 16075, + "end": 16151, "loc": { "start": { - "line": 395, + "line": 414, "column": 16 }, "end": { - "line": 395, + "line": 414, "column": 92 } }, "callee": { "type": "Identifier", - "start": 15629, - "end": 15634, + "start": 16079, + "end": 16084, "loc": { "start": { - "line": 395, + "line": 414, "column": 20 }, "end": { - "line": 395, + "line": 414, "column": 25 }, "identifierName": "Error" @@ -20094,30 +20782,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 15635, - "end": 15700, + "start": 16085, + "end": 16150, "loc": { "start": { - "line": 395, + "line": 414, "column": 26 }, "end": { - "line": 395, + "line": 414, "column": 91 } }, "expressions": [ { "type": "Identifier", - "start": 15690, - "end": 15697, + "start": 16140, + "end": 16147, "loc": { "start": { - "line": 395, + "line": 414, "column": 81 }, "end": { - "line": 395, + "line": 414, "column": 88 }, "identifierName": "nodeIRI" @@ -20128,15 +20816,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 15636, - "end": 15688, + "start": 16086, + "end": 16138, "loc": { "start": { - "line": 395, + "line": 414, "column": 27 }, "end": { - "line": 395, + "line": 414, "column": 79 } }, @@ -20148,15 +20836,15 @@ }, { "type": "TemplateElement", - "start": 15698, - "end": 15699, + "start": 16148, + "end": 16149, "loc": { "start": { - "line": 395, + "line": 414, "column": 89 }, "end": { - "line": 395, + "line": 414, "column": 90 } }, @@ -20179,15 +20867,15 @@ { "type": "CommentLine", "value": " Add nodeAsJSONLD to list", - "start": 15542, - "end": 15569, + "start": 15992, + "end": 16019, "loc": { "start": { - "line": 393, + "line": 412, "column": 8 }, "end": { - "line": 393, + "line": 412, "column": 35 } } @@ -20196,58 +20884,58 @@ }, { "type": "ExpressionStatement", - "start": 15721, - "end": 15755, + "start": 16171, + "end": 16205, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 15721, - "end": 15754, + "start": 16171, + "end": 16204, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 15721, - "end": 15739, + "start": 16171, + "end": 16189, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 26 } }, "object": { "type": "Identifier", - "start": 15721, - "end": 15730, + "start": 16171, + "end": 16180, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 17 }, "identifierName": "nodesById" @@ -20256,15 +20944,15 @@ }, "property": { "type": "Identifier", - "start": 15731, - "end": 15738, + "start": 16181, + "end": 16188, "loc": { "start": { - "line": 397, + "line": 416, "column": 18 }, "end": { - "line": 397, + "line": 416, "column": 25 }, "identifierName": "nodeIRI" @@ -20275,15 +20963,15 @@ }, "right": { "type": "Identifier", - "start": 15742, - "end": 15754, + "start": 16192, + "end": 16204, "loc": { "start": { - "line": 397, + "line": 416, "column": 29 }, "end": { - "line": 397, + "line": 416, "column": 41 }, "identifierName": "nodeAsJSONLD" @@ -20294,57 +20982,57 @@ }, { "type": "ExpressionStatement", - "start": 15764, - "end": 15789, + "start": 16214, + "end": 16239, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 33 } }, "expression": { "type": "CallExpression", - "start": 15764, - "end": 15788, + "start": 16214, + "end": 16238, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 32 } }, "callee": { "type": "MemberExpression", - "start": 15764, - "end": 15774, + "start": 16214, + "end": 16224, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 18 } }, "object": { "type": "Identifier", - "start": 15764, - "end": 15769, + "start": 16214, + "end": 16219, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 13 }, "identifierName": "nodes" @@ -20353,15 +21041,15 @@ }, "property": { "type": "Identifier", - "start": 15770, - "end": 15774, + "start": 16220, + "end": 16224, "loc": { "start": { - "line": 398, + "line": 417, "column": 14 }, "end": { - "line": 398, + "line": 417, "column": 18 }, "identifierName": "push" @@ -20373,15 +21061,15 @@ "arguments": [ { "type": "Identifier", - "start": 15775, - "end": 15787, + "start": 16225, + "end": 16237, "loc": { "start": { - "line": 398, + "line": 417, "column": 19 }, "end": { - "line": 398, + "line": 417, "column": 31 }, "identifierName": "nodeAsJSONLD" @@ -20407,15 +21095,15 @@ { "type": "CommentLine", "value": " Go through nodes again and set children and sibling relationships.", - "start": 15811, - "end": 15880, + "start": 16261, + "end": 16330, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 73 } } @@ -20424,85 +21112,85 @@ }, { "type": "ExpressionStatement", - "start": 15885, - "end": 16553, + "start": 16335, + "end": 17003, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 419, + "line": 438, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 15885, - "end": 16552, + "start": 16335, + "end": 17002, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 419, + "line": 438, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 15885, - "end": 15923, + "start": 16335, + "end": 16373, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 42 } }, "object": { "type": "CallExpression", - "start": 15885, - "end": 15915, + "start": 16335, + "end": 16365, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 34 } }, "callee": { "type": "MemberExpression", - "start": 15885, - "end": 15896, + "start": 16335, + "end": 16346, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 15 } }, "object": { "type": "Identifier", - "start": 15885, - "end": 15891, + "start": 16335, + "end": 16341, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 10 }, "identifierName": "Object" @@ -20512,15 +21200,15 @@ }, "property": { "type": "Identifier", - "start": 15892, - "end": 15896, + "start": 16342, + "end": 16346, "loc": { "start": { - "line": 403, + "line": 422, "column": 11 }, "end": { - "line": 403, + "line": 422, "column": 15 }, "identifierName": "keys" @@ -20533,15 +21221,15 @@ "arguments": [ { "type": "Identifier", - "start": 15897, - "end": 15914, + "start": 16347, + "end": 16364, "loc": { "start": { - "line": 403, + "line": 422, "column": 16 }, "end": { - "line": 403, + "line": 422, "column": 33 }, "identifierName": "nodeIdsByParentId" @@ -20553,15 +21241,15 @@ }, "property": { "type": "Identifier", - "start": 15916, - "end": 15923, + "start": 16366, + "end": 16373, "loc": { "start": { - "line": 403, + "line": 422, "column": 35 }, "end": { - "line": 403, + "line": 422, "column": 42 }, "identifierName": "forEach" @@ -20574,15 +21262,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 15924, - "end": 16551, + "start": 16374, + "end": 17001, "loc": { "start": { - "line": 403, + "line": 422, "column": 43 }, "end": { - "line": 419, + "line": 438, "column": 5 } }, @@ -20593,15 +21281,15 @@ "params": [ { "type": "Identifier", - "start": 15925, - "end": 15933, + "start": 16375, + "end": 16383, "loc": { "start": { - "line": 403, + "line": 422, "column": 44 }, "end": { - "line": 403, + "line": 422, "column": 52 }, "identifierName": "parentId" @@ -20611,59 +21299,59 @@ ], "body": { "type": "BlockStatement", - "start": 15938, - "end": 16551, + "start": 16388, + "end": 17001, "loc": { "start": { - "line": 403, + "line": 422, "column": 57 }, "end": { - "line": 419, + "line": 438, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 15995, - "end": 16055, + "start": 16445, + "end": 16505, "loc": { "start": { - "line": 405, + "line": 424, "column": 6 }, "end": { - "line": 405, + "line": 424, "column": 66 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16001, - "end": 16054, + "start": 16451, + "end": 16504, "loc": { "start": { - "line": 405, + "line": 424, "column": 12 }, "end": { - "line": 405, + "line": 424, "column": 65 } }, "id": { "type": "Identifier", - "start": 16001, - "end": 16012, + "start": 16451, + "end": 16462, "loc": { "start": { - "line": 405, + "line": 424, "column": 12 }, "end": { - "line": 405, + "line": 424, "column": 23 }, "identifierName": "childrenIDs" @@ -20673,43 +21361,43 @@ }, "init": { "type": "CallExpression", - "start": 16015, - "end": 16054, + "start": 16465, + "end": 16504, "loc": { "start": { - "line": 405, + "line": 424, "column": 26 }, "end": { - "line": 405, + "line": 424, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 16015, - "end": 16025, + "start": 16465, + "end": 16475, "loc": { "start": { - "line": 405, + "line": 424, "column": 26 }, "end": { - "line": 405, + "line": 424, "column": 36 } }, "object": { "type": "Identifier", - "start": 16015, - "end": 16020, + "start": 16465, + "end": 16470, "loc": { "start": { - "line": 405, + "line": 424, "column": 26 }, "end": { - "line": 405, + "line": 424, "column": 31 }, "identifierName": "Array" @@ -20718,15 +21406,15 @@ }, "property": { "type": "Identifier", - "start": 16021, - "end": 16025, + "start": 16471, + "end": 16475, "loc": { "start": { - "line": 405, + "line": 424, "column": 32 }, "end": { - "line": 405, + "line": 424, "column": 36 }, "identifierName": "from" @@ -20738,29 +21426,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 16026, - "end": 16053, + "start": 16476, + "end": 16503, "loc": { "start": { - "line": 405, + "line": 424, "column": 37 }, "end": { - "line": 405, + "line": 424, "column": 64 } }, "object": { "type": "Identifier", - "start": 16026, - "end": 16043, + "start": 16476, + "end": 16493, "loc": { "start": { - "line": 405, + "line": 424, "column": 37 }, "end": { - "line": 405, + "line": 424, "column": 54 }, "identifierName": "nodeIdsByParentId" @@ -20769,15 +21457,15 @@ }, "property": { "type": "Identifier", - "start": 16044, - "end": 16052, + "start": 16494, + "end": 16502, "loc": { "start": { - "line": 405, + "line": 424, "column": 55 }, "end": { - "line": 405, + "line": 424, "column": 63 }, "identifierName": "parentId" @@ -20796,15 +21484,15 @@ { "type": "CommentLine", "value": " What are the children of this parentId?", - "start": 15946, - "end": 15988, + "start": 16396, + "end": 16438, "loc": { "start": { - "line": 404, + "line": 423, "column": 6 }, "end": { - "line": 404, + "line": 423, "column": 48 } } @@ -20813,44 +21501,44 @@ }, { "type": "VariableDeclaration", - "start": 16062, - "end": 16126, + "start": 16512, + "end": 16576, "loc": { "start": { - "line": 406, + "line": 425, "column": 6 }, "end": { - "line": 406, + "line": 425, "column": 70 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16068, - "end": 16125, + "start": 16518, + "end": 16575, "loc": { "start": { - "line": 406, + "line": 425, "column": 12 }, "end": { - "line": 406, + "line": 425, "column": 69 } }, "id": { "type": "Identifier", - "start": 16068, - "end": 16076, + "start": 16518, + "end": 16526, "loc": { "start": { - "line": 406, + "line": 425, "column": 12 }, "end": { - "line": 406, + "line": 425, "column": 20 }, "identifierName": "children" @@ -20859,43 +21547,43 @@ }, "init": { "type": "CallExpression", - "start": 16079, - "end": 16125, + "start": 16529, + "end": 16575, "loc": { "start": { - "line": 406, + "line": 425, "column": 23 }, "end": { - "line": 406, + "line": 425, "column": 69 } }, "callee": { "type": "MemberExpression", - "start": 16079, - "end": 16094, + "start": 16529, + "end": 16544, "loc": { "start": { - "line": 406, + "line": 425, "column": 23 }, "end": { - "line": 406, + "line": 425, "column": 38 } }, "object": { "type": "Identifier", - "start": 16079, - "end": 16090, + "start": 16529, + "end": 16540, "loc": { "start": { - "line": 406, + "line": 425, "column": 23 }, "end": { - "line": 406, + "line": 425, "column": 34 }, "identifierName": "childrenIDs" @@ -20904,15 +21592,15 @@ }, "property": { "type": "Identifier", - "start": 16091, - "end": 16094, + "start": 16541, + "end": 16544, "loc": { "start": { - "line": 406, + "line": 425, "column": 35 }, "end": { - "line": 406, + "line": 425, "column": 38 }, "identifierName": "map" @@ -20924,15 +21612,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 16095, - "end": 16124, + "start": 16545, + "end": 16574, "loc": { "start": { - "line": 406, + "line": 425, "column": 39 }, "end": { - "line": 406, + "line": 425, "column": 68 } }, @@ -20943,15 +21631,15 @@ "params": [ { "type": "Identifier", - "start": 16095, - "end": 16102, + "start": 16545, + "end": 16552, "loc": { "start": { - "line": 406, + "line": 425, "column": 39 }, "end": { - "line": 406, + "line": 425, "column": 46 }, "identifierName": "childId" @@ -20961,29 +21649,29 @@ ], "body": { "type": "MemberExpression", - "start": 16106, - "end": 16124, + "start": 16556, + "end": 16574, "loc": { "start": { - "line": 406, + "line": 425, "column": 50 }, "end": { - "line": 406, + "line": 425, "column": 68 } }, "object": { "type": "Identifier", - "start": 16106, - "end": 16115, + "start": 16556, + "end": 16565, "loc": { "start": { - "line": 406, + "line": 425, "column": 50 }, "end": { - "line": 406, + "line": 425, "column": 59 }, "identifierName": "nodesById" @@ -20992,15 +21680,15 @@ }, "property": { "type": "Identifier", - "start": 16116, - "end": 16123, + "start": 16566, + "end": 16573, "loc": { "start": { - "line": 406, + "line": 425, "column": 60 }, "end": { - "line": 406, + "line": 425, "column": 67 }, "identifierName": "childId" @@ -21019,15 +21707,15 @@ { "type": "CommentLine", "value": " Is this the root node?", - "start": 16134, - "end": 16159, + "start": 16584, + "end": 16609, "loc": { "start": { - "line": 408, + "line": 427, "column": 6 }, "end": { - "line": 408, + "line": 427, "column": 31 } } @@ -21036,43 +21724,43 @@ }, { "type": "IfStatement", - "start": 16166, - "end": 16288, + "start": 16616, + "end": 16738, "loc": { "start": { - "line": 409, + "line": 428, "column": 6 }, "end": { - "line": 412, + "line": 431, "column": 7 } }, "test": { "type": "CallExpression", - "start": 16170, - "end": 16194, + "start": 16620, + "end": 16644, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 34 } }, "callee": { "type": "Identifier", - "start": 16170, - "end": 16173, + "start": 16620, + "end": 16623, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 13 }, "identifierName": "has" @@ -21083,15 +21771,15 @@ "arguments": [ { "type": "Identifier", - "start": 16174, - "end": 16183, + "start": 16624, + "end": 16633, "loc": { "start": { - "line": 409, + "line": 428, "column": 14 }, "end": { - "line": 409, + "line": 428, "column": 23 }, "identifierName": "nodesById" @@ -21100,15 +21788,15 @@ }, { "type": "Identifier", - "start": 16185, - "end": 16193, + "start": 16635, + "end": 16643, "loc": { "start": { - "line": 409, + "line": 428, "column": 25 }, "end": { - "line": 409, + "line": 428, "column": 33 }, "identifierName": "parentId" @@ -21120,59 +21808,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 16196, - "end": 16288, + "start": 16646, + "end": 16738, "loc": { "start": { - "line": 409, + "line": 428, "column": 36 }, "end": { - "line": 412, + "line": 431, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 16206, - "end": 16241, + "start": 16656, + "end": 16691, "loc": { "start": { - "line": 410, + "line": 429, "column": 8 }, "end": { - "line": 410, + "line": 429, "column": 43 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16212, - "end": 16240, + "start": 16662, + "end": 16690, "loc": { "start": { - "line": 410, + "line": 429, "column": 14 }, "end": { - "line": 410, + "line": 429, "column": 42 } }, "id": { "type": "Identifier", - "start": 16212, - "end": 16218, + "start": 16662, + "end": 16668, "loc": { "start": { - "line": 410, + "line": 429, "column": 14 }, "end": { - "line": 410, + "line": 429, "column": 20 }, "identifierName": "parent" @@ -21181,29 +21869,29 @@ }, "init": { "type": "MemberExpression", - "start": 16221, - "end": 16240, + "start": 16671, + "end": 16690, "loc": { "start": { - "line": 410, + "line": 429, "column": 23 }, "end": { - "line": 410, + "line": 429, "column": 42 } }, "object": { "type": "Identifier", - "start": 16221, - "end": 16230, + "start": 16671, + "end": 16680, "loc": { "start": { - "line": 410, + "line": 429, "column": 23 }, "end": { - "line": 410, + "line": 429, "column": 32 }, "identifierName": "nodesById" @@ -21212,15 +21900,15 @@ }, "property": { "type": "Identifier", - "start": 16231, - "end": 16239, + "start": 16681, + "end": 16689, "loc": { "start": { - "line": 410, + "line": 429, "column": 33 }, "end": { - "line": 410, + "line": 429, "column": 41 }, "identifierName": "parentId" @@ -21235,58 +21923,58 @@ }, { "type": "ExpressionStatement", - "start": 16250, - "end": 16280, + "start": 16700, + "end": 16730, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 16250, - "end": 16279, + "start": 16700, + "end": 16729, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 16250, - "end": 16265, + "start": 16700, + "end": 16715, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 23 } }, "object": { "type": "Identifier", - "start": 16250, - "end": 16256, + "start": 16700, + "end": 16706, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 14 }, "identifierName": "parent" @@ -21295,15 +21983,15 @@ }, "property": { "type": "Identifier", - "start": 16257, - "end": 16265, + "start": 16707, + "end": 16715, "loc": { "start": { - "line": 411, + "line": 430, "column": 15 }, "end": { - "line": 411, + "line": 430, "column": 23 }, "identifierName": "children" @@ -21314,15 +22002,15 @@ }, "right": { "type": "Identifier", - "start": 16268, - "end": 16279, + "start": 16718, + "end": 16729, "loc": { "start": { - "line": 411, + "line": 430, "column": 26 }, "end": { - "line": 411, + "line": 430, "column": 37 }, "identifierName": "childrenIDs" @@ -21339,15 +22027,15 @@ { "type": "CommentLine", "value": " Is this the root node?", - "start": 16134, - "end": 16159, + "start": 16584, + "end": 16609, "loc": { "start": { - "line": 408, + "line": 427, "column": 6 }, "end": { - "line": 408, + "line": 427, "column": 31 } } @@ -21356,57 +22044,57 @@ }, { "type": "ExpressionStatement", - "start": 16296, - "end": 16545, + "start": 16746, + "end": 16995, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 418, + "line": 437, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 16296, - "end": 16544, + "start": 16746, + "end": 16994, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 418, + "line": 437, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 16296, - "end": 16312, + "start": 16746, + "end": 16762, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 414, + "line": 433, "column": 22 } }, "object": { "type": "Identifier", - "start": 16296, - "end": 16304, + "start": 16746, + "end": 16754, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 414, + "line": 433, "column": 14 }, "identifierName": "children" @@ -21415,15 +22103,15 @@ }, "property": { "type": "Identifier", - "start": 16305, - "end": 16312, + "start": 16755, + "end": 16762, "loc": { "start": { - "line": 414, + "line": 433, "column": 15 }, "end": { - "line": 414, + "line": 433, "column": 22 }, "identifierName": "forEach" @@ -21435,15 +22123,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 16313, - "end": 16543, + "start": 16763, + "end": 16993, "loc": { "start": { - "line": 414, + "line": 433, "column": 23 }, "end": { - "line": 418, + "line": 437, "column": 7 } }, @@ -21454,15 +22142,15 @@ "params": [ { "type": "Identifier", - "start": 16314, - "end": 16319, + "start": 16764, + "end": 16769, "loc": { "start": { - "line": 414, + "line": 433, "column": 24 }, "end": { - "line": 414, + "line": 433, "column": 29 }, "identifierName": "child" @@ -21472,59 +22160,59 @@ ], "body": { "type": "BlockStatement", - "start": 16324, - "end": 16543, + "start": 16774, + "end": 16993, "loc": { "start": { - "line": 414, + "line": 433, "column": 34 }, "end": { - "line": 418, + "line": 437, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 16334, - "end": 16362, + "start": 16784, + "end": 16812, "loc": { "start": { - "line": 415, + "line": 434, "column": 8 }, "end": { - "line": 415, + "line": 434, "column": 36 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16340, - "end": 16361, + "start": 16790, + "end": 16811, "loc": { "start": { - "line": 415, + "line": 434, "column": 14 }, "end": { - "line": 415, + "line": 434, "column": 35 } }, "id": { "type": "Identifier", - "start": 16340, - "end": 16353, + "start": 16790, + "end": 16803, "loc": { "start": { - "line": 415, + "line": 434, "column": 14 }, "end": { - "line": 415, + "line": 434, "column": 27 }, "identifierName": "childToModify" @@ -21533,15 +22221,15 @@ }, "init": { "type": "Identifier", - "start": 16356, - "end": 16361, + "start": 16806, + "end": 16811, "loc": { "start": { - "line": 415, + "line": 434, "column": 30 }, "end": { - "line": 415, + "line": 434, "column": 35 }, "identifierName": "child" @@ -21555,15 +22243,15 @@ { "type": "CommentLine", "value": " Add all other sibling to node.siblings, but don't add this node itself!", - "start": 16371, - "end": 16445, + "start": 16821, + "end": 16895, "loc": { "start": { - "line": 416, + "line": 435, "column": 8 }, "end": { - "line": 416, + "line": 435, "column": 82 } } @@ -21572,58 +22260,58 @@ }, { "type": "ExpressionStatement", - "start": 16454, - "end": 16535, + "start": 16904, + "end": 16985, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 89 } }, "expression": { "type": "AssignmentExpression", - "start": 16454, - "end": 16534, + "start": 16904, + "end": 16984, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 88 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 16454, - "end": 16476, + "start": 16904, + "end": 16926, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 30 } }, "object": { "type": "Identifier", - "start": 16454, - "end": 16467, + "start": 16904, + "end": 16917, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 21 }, "identifierName": "childToModify" @@ -21633,15 +22321,15 @@ }, "property": { "type": "Identifier", - "start": 16468, - "end": 16476, + "start": 16918, + "end": 16926, "loc": { "start": { - "line": 417, + "line": 436, "column": 22 }, "end": { - "line": 417, + "line": 436, "column": 30 }, "identifierName": "siblings" @@ -21653,43 +22341,43 @@ }, "right": { "type": "CallExpression", - "start": 16479, - "end": 16534, + "start": 16929, + "end": 16984, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 88 } }, "callee": { "type": "MemberExpression", - "start": 16479, - "end": 16497, + "start": 16929, + "end": 16947, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 51 } }, "object": { "type": "Identifier", - "start": 16479, - "end": 16490, + "start": 16929, + "end": 16940, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 44 }, "identifierName": "childrenIDs" @@ -21698,15 +22386,15 @@ }, "property": { "type": "Identifier", - "start": 16491, - "end": 16497, + "start": 16941, + "end": 16947, "loc": { "start": { - "line": 417, + "line": 436, "column": 45 }, "end": { - "line": 417, + "line": 436, "column": 51 }, "identifierName": "filter" @@ -21718,15 +22406,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 16498, - "end": 16533, + "start": 16948, + "end": 16983, "loc": { "start": { - "line": 417, + "line": 436, "column": 52 }, "end": { - "line": 417, + "line": 436, "column": 87 } }, @@ -21737,15 +22425,15 @@ "params": [ { "type": "Identifier", - "start": 16498, - "end": 16505, + "start": 16948, + "end": 16955, "loc": { "start": { - "line": 417, + "line": 436, "column": 52 }, "end": { - "line": 417, + "line": 436, "column": 59 }, "identifierName": "childId" @@ -21755,29 +22443,29 @@ ], "body": { "type": "BinaryExpression", - "start": 16509, - "end": 16533, + "start": 16959, + "end": 16983, "loc": { "start": { - "line": 417, + "line": 436, "column": 63 }, "end": { - "line": 417, + "line": 436, "column": 87 } }, "left": { "type": "Identifier", - "start": 16509, - "end": 16516, + "start": 16959, + "end": 16966, "loc": { "start": { - "line": 417, + "line": 436, "column": 63 }, "end": { - "line": 417, + "line": 436, "column": 70 }, "identifierName": "childId" @@ -21787,29 +22475,29 @@ "operator": "!==", "right": { "type": "MemberExpression", - "start": 16521, - "end": 16533, + "start": 16971, + "end": 16983, "loc": { "start": { - "line": 417, + "line": 436, "column": 75 }, "end": { - "line": 417, + "line": 436, "column": 87 } }, "object": { "type": "Identifier", - "start": 16521, - "end": 16526, + "start": 16971, + "end": 16976, "loc": { "start": { - "line": 417, + "line": 436, "column": 75 }, "end": { - "line": 417, + "line": 436, "column": 80 }, "identifierName": "child" @@ -21818,15 +22506,15 @@ }, "property": { "type": "StringLiteral", - "start": 16527, - "end": 16532, + "start": 16977, + "end": 16982, "loc": { "start": { - "line": 417, + "line": 436, "column": 81 }, "end": { - "line": 417, + "line": 436, "column": 86 } }, @@ -21848,15 +22536,15 @@ { "type": "CommentLine", "value": " Add all other sibling to node.siblings, but don't add this node itself!", - "start": 16371, - "end": 16445, + "start": 16821, + "end": 16895, "loc": { "start": { - "line": 416, + "line": 435, "column": 8 }, "end": { - "line": 416, + "line": 435, "column": 82 } } @@ -21881,15 +22569,15 @@ { "type": "CommentLine", "value": " Go through nodes again and set children and sibling relationships.", - "start": 15811, - "end": 15880, + "start": 16261, + "end": 16330, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 73 } } @@ -21898,29 +22586,29 @@ }, { "type": "ReturnStatement", - "start": 16559, - "end": 16572, + "start": 17009, + "end": 17022, "loc": { "start": { - "line": 421, + "line": 440, "column": 4 }, "end": { - "line": 421, + "line": 440, "column": 17 } }, "argument": { "type": "Identifier", - "start": 16566, - "end": 16571, + "start": 17016, + "end": 17021, "loc": { "start": { - "line": 421, + "line": 440, "column": 11 }, "end": { - "line": 421, + "line": 440, "column": 16 }, "identifierName": "nodes" @@ -21934,15 +22622,15 @@ }, { "type": "ClassMethod", - "start": 16580, - "end": 18102, + "start": 17030, + "end": 18552, "loc": { "start": { - "line": 424, + "line": 443, "column": 2 }, "end": { - "line": 460, + "line": 479, "column": 3 } }, @@ -21950,15 +22638,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 16580, - "end": 16588, + "start": 17030, + "end": 17038, "loc": { "start": { - "line": 424, + "line": 443, "column": 2 }, "end": { - "line": 424, + "line": 443, "column": 10 }, "identifierName": "asJSONLD" @@ -21973,15 +22661,15 @@ "params": [ { "type": "Identifier", - "start": 16589, - "end": 16600, + "start": 17039, + "end": 17050, "loc": { "start": { - "line": 424, + "line": 443, "column": 11 }, "end": { - "line": 424, + "line": 443, "column": 22 }, "identifierName": "fallbackIRI" @@ -21990,15 +22678,15 @@ }, { "type": "Identifier", - "start": 16602, - "end": 16614, + "start": 17052, + "end": 17064, "loc": { "start": { - "line": 424, + "line": 443, "column": 24 }, "end": { - "line": 424, + "line": 443, "column": 36 }, "identifierName": "newickParser" @@ -22008,59 +22696,59 @@ ], "body": { "type": "BlockStatement", - "start": 16616, - "end": 18102, + "start": 17066, + "end": 18552, "loc": { "start": { - "line": 424, + "line": 443, "column": 38 }, "end": { - "line": 460, + "line": 479, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 17041, - "end": 17110, + "start": 17491, + "end": 17560, "loc": { "start": { - "line": 433, + "line": 452, "column": 4 }, "end": { - "line": 433, + "line": 452, "column": 73 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 17047, - "end": 17109, + "start": 17497, + "end": 17559, "loc": { "start": { - "line": 433, + "line": 452, "column": 10 }, "end": { - "line": 433, + "line": 452, "column": 72 } }, "id": { "type": "Identifier", - "start": 17047, - "end": 17064, + "start": 17497, + "end": 17514, "loc": { "start": { - "line": 433, + "line": 452, "column": 10 }, "end": { - "line": 433, + "line": 452, "column": 27 }, "identifierName": "phylogenyAsJSONLD" @@ -22070,43 +22758,43 @@ }, "init": { "type": "CallExpression", - "start": 17067, - "end": 17109, + "start": 17517, + "end": 17559, "loc": { "start": { - "line": 433, + "line": 452, "column": 30 }, "end": { - "line": 433, + "line": 452, "column": 72 } }, "callee": { "type": "MemberExpression", - "start": 17067, - "end": 17077, + "start": 17517, + "end": 17527, "loc": { "start": { - "line": 433, + "line": 452, "column": 30 }, "end": { - "line": 433, + "line": 452, "column": 40 } }, "object": { "type": "Identifier", - "start": 17067, - "end": 17071, + "start": 17517, + "end": 17521, "loc": { "start": { - "line": 433, + "line": 452, "column": 30 }, "end": { - "line": 433, + "line": 452, "column": 34 }, "identifierName": "JSON" @@ -22115,15 +22803,15 @@ }, "property": { "type": "Identifier", - "start": 17072, - "end": 17077, + "start": 17522, + "end": 17527, "loc": { "start": { - "line": 433, + "line": 452, "column": 35 }, "end": { - "line": 433, + "line": 452, "column": 40 }, "identifierName": "parse" @@ -22135,43 +22823,43 @@ "arguments": [ { "type": "CallExpression", - "start": 17078, - "end": 17108, + "start": 17528, + "end": 17558, "loc": { "start": { - "line": 433, + "line": 452, "column": 41 }, "end": { - "line": 433, + "line": 452, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 17078, - "end": 17092, + "start": 17528, + "end": 17542, "loc": { "start": { - "line": 433, + "line": 452, "column": 41 }, "end": { - "line": 433, + "line": 452, "column": 55 } }, "object": { "type": "Identifier", - "start": 17078, - "end": 17082, + "start": 17528, + "end": 17532, "loc": { "start": { - "line": 433, + "line": 452, "column": 41 }, "end": { - "line": 433, + "line": 452, "column": 45 }, "identifierName": "JSON" @@ -22180,15 +22868,15 @@ }, "property": { "type": "Identifier", - "start": 17083, - "end": 17092, + "start": 17533, + "end": 17542, "loc": { "start": { - "line": 433, + "line": 452, "column": 46 }, "end": { - "line": 433, + "line": 452, "column": 55 }, "identifierName": "stringify" @@ -22200,44 +22888,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 17093, - "end": 17107, + "start": 17543, + "end": 17557, "loc": { "start": { - "line": 433, + "line": 452, "column": 56 }, "end": { - "line": 433, + "line": 452, "column": 70 } }, "object": { "type": "ThisExpression", - "start": 17093, - "end": 17097, + "start": 17543, + "end": 17547, "loc": { "start": { - "line": 433, + "line": 452, "column": 56 }, "end": { - "line": 433, + "line": 452, "column": 60 } } }, "property": { "type": "Identifier", - "start": 17098, - "end": 17107, + "start": 17548, + "end": 17557, "loc": { "start": { - "line": 433, + "line": 452, "column": 61 }, "end": { - "line": 433, + "line": 452, "column": 70 }, "identifierName": "phylogeny" @@ -22258,15 +22946,15 @@ { "type": "CommentLine", "value": " Export this phylogeny as JSON-LD.", - "start": 16622, - "end": 16658, + "start": 17072, + "end": 17108, "loc": { "start": { - "line": 425, + "line": 444, "column": 4 }, "end": { - "line": 425, + "line": 444, "column": 40 } } @@ -22274,15 +22962,15 @@ { "type": "CommentLine", "value": " - fallbackIRI: The fallback IRI to use for this phylogeny if it does not", - "start": 16663, - "end": 16738, + "start": 17113, + "end": 17188, "loc": { "start": { - "line": 426, + "line": 445, "column": 4 }, "end": { - "line": 426, + "line": 445, "column": 79 } } @@ -22290,15 +22978,15 @@ { "type": "CommentLine", "value": " already have an '@id' set.", - "start": 16743, - "end": 16774, + "start": 17193, + "end": 17224, "loc": { "start": { - "line": 427, + "line": 446, "column": 4 }, "end": { - "line": 427, + "line": 446, "column": 35 } } @@ -22306,15 +22994,15 @@ { "type": "CommentLine", "value": " - newickParser: A function that parses a Newick string and returns a", - "start": 16779, - "end": 16850, + "start": 17229, + "end": 17300, "loc": { "start": { - "line": 428, + "line": 447, "column": 4 }, "end": { - "line": 428, + "line": 447, "column": 75 } } @@ -22322,15 +23010,15 @@ { "type": "CommentLine", "value": " an object based representation of this phylogeny. If not set, the", - "start": 16855, - "end": 16925, + "start": 17305, + "end": 17375, "loc": { "start": { - "line": 429, + "line": 448, "column": 4 }, "end": { - "line": 429, + "line": 448, "column": 74 } } @@ -22338,15 +23026,15 @@ { "type": "CommentLine", "value": " static method PhylogenyWrapper.getParsedNewick will be used instead.", - "start": 16930, - "end": 17003, + "start": 17380, + "end": 17453, "loc": { "start": { - "line": 430, + "line": 449, "column": 4 }, "end": { - "line": 430, + "line": 449, "column": 77 } } @@ -22354,15 +23042,15 @@ { "type": "CommentLine", "value": " Create a copy to export.", - "start": 17009, - "end": 17036, + "start": 17459, + "end": 17486, "loc": { "start": { - "line": 432, + "line": 451, "column": 4 }, "end": { - "line": 432, + "line": 451, "column": 31 } } @@ -22372,15 +23060,15 @@ { "type": "CommentLine", "value": " Set name and class for phylogeny. If no '@id' is set, use the provided", - "start": 17116, - "end": 17189, + "start": 17566, + "end": 17639, "loc": { "start": { - "line": 435, + "line": 454, "column": 4 }, "end": { - "line": 435, + "line": 454, "column": 77 } } @@ -22388,15 +23076,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 17194, - "end": 17209, + "start": 17644, + "end": 17659, "loc": { "start": { - "line": 436, + "line": 455, "column": 4 }, "end": { - "line": 436, + "line": 455, "column": 19 } } @@ -22405,29 +23093,29 @@ }, { "type": "IfStatement", - "start": 17214, - "end": 17289, + "start": 17664, + "end": 17739, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 79 } }, "test": { "type": "UnaryExpression", - "start": 17218, - "end": 17248, + "start": 17668, + "end": 17698, "loc": { "start": { - "line": 437, + "line": 456, "column": 8 }, "end": { - "line": 437, + "line": 456, "column": 38 } }, @@ -22435,29 +23123,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 17219, - "end": 17248, + "start": 17669, + "end": 17698, "loc": { "start": { - "line": 437, + "line": 456, "column": 9 }, "end": { - "line": 437, + "line": 456, "column": 38 } }, "callee": { "type": "Identifier", - "start": 17219, - "end": 17222, + "start": 17669, + "end": 17672, "loc": { "start": { - "line": 437, + "line": 456, "column": 9 }, "end": { - "line": 437, + "line": 456, "column": 12 }, "identifierName": "has" @@ -22468,15 +23156,15 @@ "arguments": [ { "type": "Identifier", - "start": 17223, - "end": 17240, + "start": 17673, + "end": 17690, "loc": { "start": { - "line": 437, + "line": 456, "column": 13 }, "end": { - "line": 437, + "line": 456, "column": 30 }, "identifierName": "phylogenyAsJSONLD" @@ -22485,15 +23173,15 @@ }, { "type": "StringLiteral", - "start": 17242, - "end": 17247, + "start": 17692, + "end": 17697, "loc": { "start": { - "line": 437, + "line": 456, "column": 32 }, "end": { - "line": 437, + "line": 456, "column": 37 } }, @@ -22513,58 +23201,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 17250, - "end": 17289, + "start": 17700, + "end": 17739, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 79 } }, "expression": { "type": "AssignmentExpression", - "start": 17250, - "end": 17288, + "start": 17700, + "end": 17738, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 78 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17250, - "end": 17274, + "start": 17700, + "end": 17724, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 64 } }, "object": { "type": "Identifier", - "start": 17250, - "end": 17267, + "start": 17700, + "end": 17717, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 57 }, "identifierName": "phylogenyAsJSONLD" @@ -22573,15 +23261,15 @@ }, "property": { "type": "StringLiteral", - "start": 17268, - "end": 17273, + "start": 17718, + "end": 17723, "loc": { "start": { - "line": 437, + "line": 456, "column": 58 }, "end": { - "line": 437, + "line": 456, "column": 63 } }, @@ -22595,15 +23283,15 @@ }, "right": { "type": "Identifier", - "start": 17277, - "end": 17288, + "start": 17727, + "end": 17738, "loc": { "start": { - "line": 437, + "line": 456, "column": 67 }, "end": { - "line": 437, + "line": 456, "column": 78 }, "identifierName": "fallbackIRI" @@ -22617,15 +23305,15 @@ { "type": "CommentLine", "value": " Set name and class for phylogeny. If no '@id' is set, use the provided", - "start": 17116, - "end": 17189, + "start": 17566, + "end": 17639, "loc": { "start": { - "line": 435, + "line": 454, "column": 4 }, "end": { - "line": 435, + "line": 454, "column": 77 } } @@ -22633,15 +23321,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 17194, - "end": 17209, + "start": 17644, + "end": 17659, "loc": { "start": { - "line": 436, + "line": 455, "column": 4 }, "end": { - "line": 436, + "line": 455, "column": 19 } } @@ -22650,58 +23338,58 @@ }, { "type": "ExpressionStatement", - "start": 17294, - "end": 17361, + "start": 17744, + "end": 17811, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 17294, - "end": 17360, + "start": 17744, + "end": 17810, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17294, - "end": 17320, + "start": 17744, + "end": 17770, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 30 } }, "object": { "type": "Identifier", - "start": 17294, - "end": 17311, + "start": 17744, + "end": 17761, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 21 }, "identifierName": "phylogenyAsJSONLD" @@ -22710,15 +23398,15 @@ }, "property": { "type": "StringLiteral", - "start": 17312, - "end": 17319, + "start": 17762, + "end": 17769, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 29 } }, @@ -22732,15 +23420,15 @@ }, "right": { "type": "StringLiteral", - "start": 17323, - "end": 17360, + "start": 17773, + "end": 17810, "loc": { "start": { - "line": 438, + "line": 457, "column": 33 }, "end": { - "line": 438, + "line": 457, "column": 70 } }, @@ -22755,15 +23443,15 @@ { "type": "CommentLine", "value": " Translate nodes into JSON-LD objects.", - "start": 17367, - "end": 17407, + "start": 17817, + "end": 17857, "loc": { "start": { - "line": 440, + "line": 459, "column": 4 }, "end": { - "line": 440, + "line": 459, "column": 44 } } @@ -22772,58 +23460,58 @@ }, { "type": "ExpressionStatement", - "start": 17412, - "end": 17500, + "start": 17862, + "end": 17950, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 92 } }, "expression": { "type": "AssignmentExpression", - "start": 17412, - "end": 17499, + "start": 17862, + "end": 17949, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 91 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17412, - "end": 17435, + "start": 17862, + "end": 17885, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 27 } }, "object": { "type": "Identifier", - "start": 17412, - "end": 17429, + "start": 17862, + "end": 17879, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 21 }, "identifierName": "phylogenyAsJSONLD" @@ -22833,15 +23521,15 @@ }, "property": { "type": "Identifier", - "start": 17430, - "end": 17435, + "start": 17880, + "end": 17885, "loc": { "start": { - "line": 441, + "line": 460, "column": 22 }, "end": { - "line": 441, + "line": 460, "column": 27 }, "identifierName": "nodes" @@ -22853,58 +23541,58 @@ }, "right": { "type": "CallExpression", - "start": 17438, - "end": 17499, + "start": 17888, + "end": 17949, "loc": { "start": { - "line": 441, + "line": 460, "column": 30 }, "end": { - "line": 441, + "line": 460, "column": 91 } }, "callee": { "type": "MemberExpression", - "start": 17438, - "end": 17459, + "start": 17888, + "end": 17909, "loc": { "start": { - "line": 441, + "line": 460, "column": 30 }, "end": { - "line": 441, + "line": 460, "column": 51 } }, "object": { "type": "ThisExpression", - "start": 17438, - "end": 17442, + "start": 17888, + "end": 17892, "loc": { "start": { - "line": 441, + "line": 460, "column": 30 }, "end": { - "line": 441, + "line": 460, "column": 34 } } }, "property": { "type": "Identifier", - "start": 17443, - "end": 17459, + "start": 17893, + "end": 17909, "loc": { "start": { - "line": 441, + "line": 460, "column": 35 }, "end": { - "line": 441, + "line": 460, "column": 51 }, "identifierName": "getNodesAsJSONLD" @@ -22916,29 +23604,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 17460, - "end": 17484, + "start": 17910, + "end": 17934, "loc": { "start": { - "line": 441, + "line": 460, "column": 52 }, "end": { - "line": 441, + "line": 460, "column": 76 } }, "object": { "type": "Identifier", - "start": 17460, - "end": 17477, + "start": 17910, + "end": 17927, "loc": { "start": { - "line": 441, + "line": 460, "column": 52 }, "end": { - "line": 441, + "line": 460, "column": 69 }, "identifierName": "phylogenyAsJSONLD" @@ -22947,15 +23635,15 @@ }, "property": { "type": "StringLiteral", - "start": 17478, - "end": 17483, + "start": 17928, + "end": 17933, "loc": { "start": { - "line": 441, + "line": 460, "column": 70 }, "end": { - "line": 441, + "line": 460, "column": 75 } }, @@ -22969,15 +23657,15 @@ }, { "type": "Identifier", - "start": 17486, - "end": 17498, + "start": 17936, + "end": 17948, "loc": { "start": { - "line": 441, + "line": 460, "column": 78 }, "end": { - "line": 441, + "line": 460, "column": 90 }, "identifierName": "newickParser" @@ -22992,15 +23680,15 @@ { "type": "CommentLine", "value": " Translate nodes into JSON-LD objects.", - "start": 17367, - "end": 17407, + "start": 17817, + "end": 17857, "loc": { "start": { - "line": 440, + "line": 459, "column": 4 }, "end": { - "line": 440, + "line": 459, "column": 44 } } @@ -23009,71 +23697,71 @@ }, { "type": "IfStatement", - "start": 17505, - "end": 17760, + "start": 17955, + "end": 18210, "loc": { "start": { - "line": 442, + "line": 461, "column": 4 }, "end": { - "line": 448, + "line": 467, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 17509, - "end": 17543, + "start": 17959, + "end": 17993, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 42 } }, "left": { "type": "MemberExpression", - "start": 17509, - "end": 17539, + "start": 17959, + "end": 17989, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 38 } }, "object": { "type": "MemberExpression", - "start": 17509, - "end": 17532, + "start": 17959, + "end": 17982, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 31 } }, "object": { "type": "Identifier", - "start": 17509, - "end": 17526, + "start": 17959, + "end": 17976, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 25 }, "identifierName": "phylogenyAsJSONLD" @@ -23082,15 +23770,15 @@ }, "property": { "type": "Identifier", - "start": 17527, - "end": 17532, + "start": 17977, + "end": 17982, "loc": { "start": { - "line": 442, + "line": 461, "column": 26 }, "end": { - "line": 442, + "line": 461, "column": 31 }, "identifierName": "nodes" @@ -23101,15 +23789,15 @@ }, "property": { "type": "Identifier", - "start": 17533, - "end": 17539, + "start": 17983, + "end": 17989, "loc": { "start": { - "line": 442, + "line": 461, "column": 32 }, "end": { - "line": 442, + "line": 461, "column": 38 }, "identifierName": "length" @@ -23121,15 +23809,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 17542, - "end": 17543, + "start": 17992, + "end": 17993, "loc": { "start": { - "line": 442, + "line": 461, "column": 41 }, "end": { - "line": 442, + "line": 461, "column": 42 } }, @@ -23142,73 +23830,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 17545, - "end": 17760, + "start": 17995, + "end": 18210, "loc": { "start": { - "line": 442, + "line": 461, "column": 44 }, "end": { - "line": 448, + "line": 467, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 17662, - "end": 17754, + "start": 18112, + "end": 18204, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 17662, - "end": 17753, + "start": 18112, + "end": 18203, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17662, - "end": 17691, + "start": 18112, + "end": 18141, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 445, + "line": 464, "column": 35 } }, "object": { "type": "Identifier", - "start": 17662, - "end": 17679, + "start": 18112, + "end": 18129, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 445, + "line": 464, "column": 23 }, "identifierName": "phylogenyAsJSONLD" @@ -23218,15 +23906,15 @@ }, "property": { "type": "Identifier", - "start": 17680, - "end": 17691, + "start": 18130, + "end": 18141, "loc": { "start": { - "line": 445, + "line": 464, "column": 24 }, "end": { - "line": 445, + "line": 464, "column": 35 }, "identifierName": "hasRootNode" @@ -23238,30 +23926,30 @@ }, "right": { "type": "ObjectExpression", - "start": 17694, - "end": 17753, + "start": 18144, + "end": 18203, "loc": { "start": { - "line": 445, + "line": 464, "column": 38 }, "end": { - "line": 447, + "line": 466, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 17704, - "end": 17744, + "start": 18154, + "end": 18194, "loc": { "start": { - "line": 446, + "line": 465, "column": 8 }, "end": { - "line": 446, + "line": 465, "column": 48 } }, @@ -23270,15 +23958,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 17704, - "end": 17709, + "start": 18154, + "end": 18159, "loc": { "start": { - "line": 446, + "line": 465, "column": 8 }, "end": { - "line": 446, + "line": 465, "column": 13 } }, @@ -23290,57 +23978,57 @@ }, "value": { "type": "MemberExpression", - "start": 17711, - "end": 17744, + "start": 18161, + "end": 18194, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 48 } }, "object": { "type": "MemberExpression", - "start": 17711, - "end": 17737, + "start": 18161, + "end": 18187, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 41 } }, "object": { "type": "MemberExpression", - "start": 17711, - "end": 17734, + "start": 18161, + "end": 18184, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 38 } }, "object": { "type": "Identifier", - "start": 17711, - "end": 17728, + "start": 18161, + "end": 18178, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 32 }, "identifierName": "phylogenyAsJSONLD" @@ -23349,15 +24037,15 @@ }, "property": { "type": "Identifier", - "start": 17729, - "end": 17734, + "start": 18179, + "end": 18184, "loc": { "start": { - "line": 446, + "line": 465, "column": 33 }, "end": { - "line": 446, + "line": 465, "column": 38 }, "identifierName": "nodes" @@ -23368,15 +24056,15 @@ }, "property": { "type": "NumericLiteral", - "start": 17735, - "end": 17736, + "start": 18185, + "end": 18186, "loc": { "start": { - "line": 446, + "line": 465, "column": 39 }, "end": { - "line": 446, + "line": 465, "column": 40 } }, @@ -23390,15 +24078,15 @@ }, "property": { "type": "StringLiteral", - "start": 17738, - "end": 17743, + "start": 18188, + "end": 18193, "loc": { "start": { - "line": 446, + "line": 465, "column": 42 }, "end": { - "line": 446, + "line": 465, "column": 47 } }, @@ -23419,15 +24107,15 @@ { "type": "CommentLine", "value": " We don't have a better way to identify the root node, so we just", - "start": 17553, - "end": 17620, + "start": 18003, + "end": 18070, "loc": { "start": { - "line": 443, + "line": 462, "column": 6 }, "end": { - "line": 443, + "line": 462, "column": 73 } } @@ -23435,15 +24123,15 @@ { "type": "CommentLine", "value": " default to the first one.", - "start": 17627, - "end": 17655, + "start": 18077, + "end": 18105, "loc": { "start": { - "line": 444, + "line": 463, "column": 6 }, "end": { - "line": 444, + "line": 463, "column": 34 } } @@ -23459,15 +24147,15 @@ { "type": "CommentLine", "value": " Add a bibliographicCitation to the source if it is a Citation.", - "start": 17766, - "end": 17831, + "start": 18216, + "end": 18281, "loc": { "start": { - "line": 450, + "line": 469, "column": 4 }, "end": { - "line": 450, + "line": 469, "column": 69 } } @@ -23476,43 +24164,43 @@ }, { "type": "IfStatement", - "start": 17836, - "end": 18067, + "start": 18286, + "end": 18517, "loc": { "start": { - "line": 451, + "line": 470, "column": 4 }, "end": { - "line": 457, + "line": 476, "column": 5 } }, "test": { "type": "CallExpression", - "start": 17840, - "end": 17872, + "start": 18290, + "end": 18322, "loc": { "start": { - "line": 451, + "line": 470, "column": 8 }, "end": { - "line": 451, + "line": 470, "column": 40 } }, "callee": { "type": "Identifier", - "start": 17840, - "end": 17843, + "start": 18290, + "end": 18293, "loc": { "start": { - "line": 451, + "line": 470, "column": 8 }, "end": { - "line": 451, + "line": 470, "column": 11 }, "identifierName": "has" @@ -23523,15 +24211,15 @@ "arguments": [ { "type": "Identifier", - "start": 17844, - "end": 17861, + "start": 18294, + "end": 18311, "loc": { "start": { - "line": 451, + "line": 470, "column": 12 }, "end": { - "line": 451, + "line": 470, "column": 29 }, "identifierName": "phylogenyAsJSONLD" @@ -23540,15 +24228,15 @@ }, { "type": "StringLiteral", - "start": 17863, - "end": 17871, + "start": 18313, + "end": 18321, "loc": { "start": { - "line": 451, + "line": 470, "column": 31 }, "end": { - "line": 451, + "line": 470, "column": 39 } }, @@ -23563,59 +24251,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 17874, - "end": 18067, + "start": 18324, + "end": 18517, "loc": { "start": { - "line": 451, + "line": 470, "column": 42 }, "end": { - "line": 457, + "line": 476, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 17882, - "end": 17922, + "start": 18332, + "end": 18372, "loc": { "start": { - "line": 452, + "line": 471, "column": 6 }, "end": { - "line": 452, + "line": 471, "column": 46 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 17888, - "end": 17921, + "start": 18338, + "end": 18371, "loc": { "start": { - "line": 452, + "line": 471, "column": 12 }, "end": { - "line": 452, + "line": 471, "column": 45 } }, "id": { "type": "Identifier", - "start": 17888, - "end": 17894, + "start": 18338, + "end": 18344, "loc": { "start": { - "line": 452, + "line": 471, "column": 12 }, "end": { - "line": 452, + "line": 471, "column": 18 }, "identifierName": "source" @@ -23624,29 +24312,29 @@ }, "init": { "type": "MemberExpression", - "start": 17897, - "end": 17921, + "start": 18347, + "end": 18371, "loc": { "start": { - "line": 452, + "line": 471, "column": 21 }, "end": { - "line": 452, + "line": 471, "column": 45 } }, "object": { "type": "Identifier", - "start": 17897, - "end": 17914, + "start": 18347, + "end": 18364, "loc": { "start": { - "line": 452, + "line": 471, "column": 21 }, "end": { - "line": 452, + "line": 471, "column": 38 }, "identifierName": "phylogenyAsJSONLD" @@ -23655,15 +24343,15 @@ }, "property": { "type": "Identifier", - "start": 17915, - "end": 17921, + "start": 18365, + "end": 18371, "loc": { "start": { - "line": 452, + "line": 471, "column": 39 }, "end": { - "line": 452, + "line": 471, "column": 45 }, "identifierName": "source" @@ -23678,29 +24366,29 @@ }, { "type": "IfStatement", - "start": 17930, - "end": 18061, + "start": 18380, + "end": 18511, "loc": { "start": { - "line": 454, + "line": 473, "column": 6 }, "end": { - "line": 456, + "line": 475, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 17934, - "end": 17971, + "start": 18384, + "end": 18421, "loc": { "start": { - "line": 454, + "line": 473, "column": 10 }, "end": { - "line": 454, + "line": 473, "column": 47 } }, @@ -23708,29 +24396,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 17935, - "end": 17971, + "start": 18385, + "end": 18421, "loc": { "start": { - "line": 454, + "line": 473, "column": 11 }, "end": { - "line": 454, + "line": 473, "column": 47 } }, "callee": { "type": "Identifier", - "start": 17935, - "end": 17938, + "start": 18385, + "end": 18388, "loc": { "start": { - "line": 454, + "line": 473, "column": 11 }, "end": { - "line": 454, + "line": 473, "column": 14 }, "identifierName": "has" @@ -23740,15 +24428,15 @@ "arguments": [ { "type": "Identifier", - "start": 17939, - "end": 17945, + "start": 18389, + "end": 18395, "loc": { "start": { - "line": 454, + "line": 473, "column": 15 }, "end": { - "line": 454, + "line": 473, "column": 21 }, "identifierName": "source" @@ -23757,15 +24445,15 @@ }, { "type": "StringLiteral", - "start": 17947, - "end": 17970, + "start": 18397, + "end": 18420, "loc": { "start": { - "line": 454, + "line": 473, "column": 23 }, "end": { - "line": 454, + "line": 473, "column": 46 } }, @@ -23783,73 +24471,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 17973, - "end": 18061, + "start": 18423, + "end": 18511, "loc": { "start": { - "line": 454, + "line": 473, "column": 49 }, "end": { - "line": 456, + "line": 475, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 17983, - "end": 18053, + "start": 18433, + "end": 18503, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 78 } }, "expression": { "type": "AssignmentExpression", - "start": 17983, - "end": 18052, + "start": 18433, + "end": 18502, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 77 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17983, - "end": 18011, + "start": 18433, + "end": 18461, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 36 } }, "object": { "type": "Identifier", - "start": 17983, - "end": 17989, + "start": 18433, + "end": 18439, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 14 }, "identifierName": "source" @@ -23858,15 +24546,15 @@ }, "property": { "type": "Identifier", - "start": 17990, - "end": 18011, + "start": 18440, + "end": 18461, "loc": { "start": { - "line": 455, + "line": 474, "column": 15 }, "end": { - "line": 455, + "line": 474, "column": 36 }, "identifierName": "bibliographicCitation" @@ -23877,57 +24565,57 @@ }, "right": { "type": "CallExpression", - "start": 18014, - "end": 18052, + "start": 18464, + "end": 18502, "loc": { "start": { - "line": 455, + "line": 474, "column": 39 }, "end": { - "line": 455, + "line": 474, "column": 77 } }, "callee": { "type": "MemberExpression", - "start": 18014, - "end": 18050, + "start": 18464, + "end": 18500, "loc": { "start": { - "line": 455, + "line": 474, "column": 39 }, "end": { - "line": 455, + "line": 474, "column": 75 } }, "object": { "type": "NewExpression", - "start": 18014, - "end": 18041, + "start": 18464, + "end": 18491, "loc": { "start": { - "line": 455, + "line": 474, "column": 39 }, "end": { - "line": 455, + "line": 474, "column": 66 } }, "callee": { "type": "Identifier", - "start": 18018, - "end": 18033, + "start": 18468, + "end": 18483, "loc": { "start": { - "line": 455, + "line": 474, "column": 43 }, "end": { - "line": 455, + "line": 474, "column": 58 }, "identifierName": "CitationWrapper" @@ -23937,15 +24625,15 @@ "arguments": [ { "type": "Identifier", - "start": 18034, - "end": 18040, + "start": 18484, + "end": 18490, "loc": { "start": { - "line": 455, + "line": 474, "column": 59 }, "end": { - "line": 455, + "line": 474, "column": 65 }, "identifierName": "source" @@ -23956,15 +24644,15 @@ }, "property": { "type": "Identifier", - "start": 18042, - "end": 18050, + "start": 18492, + "end": 18500, "loc": { "start": { - "line": 455, + "line": 474, "column": 67 }, "end": { - "line": 455, + "line": 474, "column": 75 }, "identifierName": "toString" @@ -23990,15 +24678,15 @@ { "type": "CommentLine", "value": " Add a bibliographicCitation to the source if it is a Citation.", - "start": 17766, - "end": 17831, + "start": 18216, + "end": 18281, "loc": { "start": { - "line": 450, + "line": 469, "column": 4 }, "end": { - "line": 450, + "line": 469, "column": 69 } } @@ -24007,29 +24695,29 @@ }, { "type": "ReturnStatement", - "start": 18073, - "end": 18098, + "start": 18523, + "end": 18548, "loc": { "start": { - "line": 459, + "line": 478, "column": 4 }, "end": { - "line": 459, + "line": 478, "column": 29 } }, "argument": { "type": "Identifier", - "start": 18080, - "end": 18097, + "start": 18530, + "end": 18547, "loc": { "start": { - "line": 459, + "line": 478, "column": 11 }, "end": { - "line": 459, + "line": 478, "column": 28 }, "identifierName": "phylogenyAsJSONLD" @@ -24049,15 +24737,15 @@ }, { "type": "ExportNamedDeclaration", - "start": 18106, - "end": 18135, + "start": 18556, + "end": 18585, "loc": { "start": { - "line": 463, + "line": 482, "column": 0 }, "end": { - "line": 463, + "line": 482, "column": 29 } }, @@ -24065,29 +24753,29 @@ "specifiers": [ { "type": "ExportSpecifier", - "start": 18115, - "end": 18131, + "start": 18565, + "end": 18581, "loc": { "start": { - "line": 463, + "line": 482, "column": 9 }, "end": { - "line": 463, + "line": 482, "column": 25 } }, "local": { "type": "Identifier", - "start": 18115, - "end": 18131, + "start": 18565, + "end": 18581, "loc": { "start": { - "line": 463, + "line": 482, "column": 9 }, "end": { - "line": 463, + "line": 482, "column": 25 }, "identifierName": "PhylogenyWrapper" @@ -24096,15 +24784,15 @@ }, "exported": { "type": "Identifier", - "start": 18115, - "end": 18131, + "start": 18565, + "end": 18581, "loc": { "start": { - "line": 463, + "line": 482, "column": 9 }, "end": { - "line": 463, + "line": 482, "column": 25 }, "identifierName": "PhylogenyWrapper" @@ -24117,43 +24805,43 @@ }, { "type": "ExportNamedDeclaration", - "start": 18106, - "end": 18135, + "start": 18556, + "end": 18585, "loc": { "start": { - "line": 463, + "line": 482, "column": 0 }, "end": { - "line": 463, + "line": 482, "column": 29 } }, "declaration": { "type": "ClassDeclaration", - "start": 571, - "end": 18104, + "start": 587, + "end": 18554, "loc": { "start": { - "line": 21, + "line": 24, "column": 0 }, "end": { - "line": 461, + "line": 480, "column": 1 } }, "id": { "type": "Identifier", - "start": 577, - "end": 593, + "start": 593, + "end": 609, "loc": { "start": { - "line": 21, + "line": 24, "column": 6 }, "end": { - "line": 21, + "line": 24, "column": 22 }, "identifierName": "PhylogenyWrapper" @@ -24163,30 +24851,30 @@ "superClass": null, "body": { "type": "ClassBody", - "start": 594, - "end": 18104, + "start": 610, + "end": 18554, "loc": { "start": { - "line": 21, + "line": 24, "column": 23 }, "end": { - "line": 461, + "line": 480, "column": 1 } }, "body": [ { "type": "ClassMethod", - "start": 835, - "end": 1521, + "start": 851, + "end": 1537, "loc": { "start": { - "line": 27, + "line": 30, "column": 2 }, "end": { - "line": 39, + "line": 42, "column": 3 } }, @@ -24194,15 +24882,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 835, - "end": 846, + "start": 851, + "end": 862, "loc": { "start": { - "line": 27, + "line": 30, "column": 2 }, "end": { - "line": 27, + "line": 30, "column": 13 }, "identifierName": "constructor" @@ -24218,15 +24906,15 @@ "params": [ { "type": "Identifier", - "start": 847, - "end": 856, + "start": 863, + "end": 872, "loc": { "start": { - "line": 27, + "line": 30, "column": 14 }, "end": { - "line": 27, + "line": 30, "column": 23 }, "identifierName": "phylogeny" @@ -24235,29 +24923,29 @@ }, { "type": "AssignmentPattern", - "start": 858, - "end": 898, + "start": 874, + "end": 914, "loc": { "start": { - "line": 27, + "line": 30, "column": 25 }, "end": { - "line": 27, + "line": 30, "column": 65 } }, "left": { "type": "Identifier", - "start": 858, - "end": 874, + "start": 874, + "end": 890, "loc": { "start": { - "line": 27, + "line": 30, "column": 25 }, "end": { - "line": 27, + "line": 30, "column": 41 }, "identifierName": "defaultNomenCode" @@ -24266,29 +24954,29 @@ }, "right": { "type": "MemberExpression", - "start": 877, - "end": 898, + "start": 893, + "end": 914, "loc": { "start": { - "line": 27, + "line": 30, "column": 44 }, "end": { - "line": 27, + "line": 30, "column": 65 } }, "object": { "type": "Identifier", - "start": 877, - "end": 885, + "start": 893, + "end": 901, "loc": { "start": { - "line": 27, + "line": 30, "column": 44 }, "end": { - "line": 27, + "line": 30, "column": 52 }, "identifierName": "owlterms" @@ -24297,15 +24985,15 @@ }, "property": { "type": "Identifier", - "start": 886, - "end": 898, + "start": 902, + "end": 914, "loc": { "start": { - "line": 27, + "line": 30, "column": 53 }, "end": { - "line": 27, + "line": 30, "column": 65 }, "identifierName": "UNKNOWN_CODE" @@ -24318,73 +25006,73 @@ ], "body": { "type": "BlockStatement", - "start": 900, - "end": 1521, + "start": 916, + "end": 1537, "loc": { "start": { - "line": 27, + "line": 30, "column": 67 }, "end": { - "line": 39, + "line": 42, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 1444, - "end": 1471, + "start": 1460, + "end": 1487, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - "line": 37, + "line": 40, "column": 31 } }, "expression": { "type": "AssignmentExpression", - "start": 1444, - "end": 1470, + "start": 1460, + "end": 1486, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - "line": 37, + "line": 40, "column": 30 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 1444, - "end": 1458, + "start": 1460, + "end": 1474, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - "line": 37, + "line": 40, "column": 18 } }, "object": { "type": "ThisExpression", - "start": 1444, - "end": 1448, + "start": 1460, + "end": 1464, "loc": { "start": { - "line": 37, + "line": 40, "column": 4 }, "end": { - "line": 37, + "line": 40, "column": 8 } }, @@ -24392,15 +25080,15 @@ }, "property": { "type": "Identifier", - "start": 1449, - "end": 1458, + "start": 1465, + "end": 1474, "loc": { "start": { - "line": 37, + "line": 40, "column": 9 }, "end": { - "line": 37, + "line": 40, "column": 18 }, "identifierName": "phylogeny" @@ -24412,15 +25100,15 @@ }, "right": { "type": "Identifier", - "start": 1461, - "end": 1470, + "start": 1477, + "end": 1486, "loc": { "start": { - "line": 37, + "line": 40, "column": 21 }, "end": { - "line": 37, + "line": 40, "column": 30 }, "identifierName": "phylogeny" @@ -24433,15 +25121,15 @@ { "type": "CommentLine", "value": " Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.", - "start": 906, - "end": 979, + "start": 922, + "end": 995, "loc": { "start": { - "line": 28, + "line": 31, "column": 4 }, "end": { - "line": 28, + "line": 31, "column": 77 } } @@ -24449,15 +25137,15 @@ { "type": "CommentLine", "value": " Note that this version ONLY uses the `newick` property to determine the", - "start": 984, - "end": 1058, + "start": 1000, + "end": 1074, "loc": { "start": { - "line": 29, + "line": 32, "column": 4 }, "end": { - "line": 29, + "line": 32, "column": 78 } } @@ -24465,15 +25153,15 @@ { "type": "CommentLine", "value": " phylogeny: if other representations are included (such as a node-based", - "start": 1063, - "end": 1136, + "start": 1079, + "end": 1152, "loc": { "start": { - "line": 30, + "line": 33, "column": 4 }, "end": { - "line": 30, + "line": 33, "column": 77 } } @@ -24481,15 +25169,15 @@ { "type": "CommentLine", "value": " format, as used in JSON-LD), they will be ignored and possibly overwritten", - 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The errors are returned as a list of objects, each of which", + "start": 2096, + "end": 2166, + "loc": { + "start": { + "line": 62, + "column": 4 + }, + "end": { + "line": 62, + "column": 74 + } + } + }, + { + "type": "CommentLine", + "value": " has two properties:", + "start": 2171, + "end": 2193, + "loc": { + "start": { + "line": 63, + "column": 4 + }, + "end": { + "line": 63, + "column": 26 + } + } + }, + { + "type": "CommentLine", + "value": " - title: A short title of the error, distinct for each type of error.", + "start": 2198, + "end": 2271, + "loc": { + "start": { + "line": 64, + "column": 4 + }, + "end": { + "line": 64, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " - message: A longer description of the error, which might include", + "start": 2276, + "end": 2345, + "loc": { + "start": { + "line": 65, + "column": 4 + }, + "end": { + "line": 65, + "column": 73 + } + } + }, + { + "type": "CommentLine", + "value": " information specific to a particular error.", + "start": 2350, + "end": 2399, + "loc": { + "start": { + "line": 66, + "column": 4 + }, + "end": { + "line": 66, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": "", + "start": 2404, + "end": 2406, + "loc": { + "start": { + "line": 67, + "column": 4 + }, + "end": { + "line": 67, + "column": 6 + } + } + }, + { + "type": "CommentLine", + "value": " We try to order errors from most helpful ('Unbalanced parentheses in", + "start": 2411, + "end": 2482, + "loc": { + "start": { + "line": 68, + "column": 4 + }, + "end": { + "line": 68, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " Newick string') to least helpful ('Error parsing phylogeny').", + "start": 2487, + "end": 2551, + "loc": { + "start": { + "line": 69, + "column": 4 + }, + "end": { + "line": 69, + "column": 68 + } + } + } + ] + }, + { + "type": "VariableDeclaration", + "start": 2597, + "end": 2615, + "loc": { + "start": { + "line": 71, + "column": 4 + }, + "end": { + "line": 71, + "column": 22 + } + }, + "declarations": [ + { + "type": "VariableDeclarator", + "start": 2603, + "end": 2614, + "loc": { + "start": { + "line": 71, + "column": 10 + }, + "end": { + "line": 71, + "column": 21 + } + }, + "id": { + "type": "Identifier", + "start": 2603, + "end": 2609, + "loc": { + "start": { + "line": 71, + "column": 10 + }, + "end": { + "line": 71, + "column": 16 + }, + "identifierName": "errors" + }, + "name": "errors" + }, + "init": { + "type": "ArrayExpression", + "start": 2612, + "end": 2614, + "loc": { + "start": { + "line": 71, + "column": 19 + }, + "end": { + "line": 71, + "column": 21 + } + }, + "elements": [] + } + } + ], + "kind": "const", + "trailingComments": [ + { + "type": "CommentLine", + "value": " Look for an empty Newick string.", + "start": 2621, + "end": 2656, + "loc": { + "start": { + "line": 73, + "column": 4 + }, + "end": { + "line": 73, + "column": 39 + } + } + } + ] + }, + { + "type": "IfStatement", + "start": 2661, + "end": 2956, + "loc": { + "start": { + "line": 74, + "column": 4 + }, + "end": { + "line": 80, + "column": 5 + } + }, + "test": { + "type": "LogicalExpression", + "start": 2665, + "end": 2738, + "loc": { + "start": { + "line": 74, + "column": 8 + }, + "end": { + "line": 74, + "column": 81 + } + }, + "left": { + "type": "LogicalExpression", + "start": 2665, + "end": 2711, + "loc": { + "start": { + "line": 74, + "column": 8 + }, + "end": { + "line": 74, + "column": 54 + } + }, + "left": { + "type": "BinaryExpression", + "start": 2665, + "end": 2685, + "loc": { + "start": { + "line": 74, + "column": 8 + }, + "end": { + "line": 74, + "column": 28 + } + }, + "left": { + "type": "Identifier", + "start": 2665, + "end": 2678, + "loc": { + "start": { + "line": 74, + "column": 8 + }, + "end": { + "line": 74, + "column": 21 + }, "identifierName": "newickTrimmed" }, "name": "newickTrimmed", @@ -25239,15 +26560,15 @@ "operator": "===", "right": { "type": "StringLiteral", - 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"line": 65, + "line": 84, "column": 51 }, "end": { - "line": 65, + "line": 84, "column": 52 } }, @@ -25921,72 +27242,72 @@ }, "body": { "type": "BlockStatement", - "start": 2632, - "end": 2747, + "start": 3082, + "end": 3197, "loc": { "start": { - "line": 65, + "line": 84, "column": 54 }, "end": { - "line": 68, + "line": 87, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 2640, - "end": 2687, + "start": 3090, + "end": 3137, "loc": { "start": { - "line": 66, + "line": 85, "column": 6 }, "end": { - "line": 66, + "line": 85, "column": 53 } }, "test": { "type": "BinaryExpression", - "start": 2644, - "end": 2668, + "start": 3094, + "end": 3118, "loc": { "start": { - "line": 66, + "line": 85, "column": 10 }, "end": { - "line": 66, + "line": 85, "column": 34 } }, "left": { "type": "MemberExpression", - "start": 2644, - "end": 2660, + "start": 3094, + "end": 3110, "loc": { "start": { - "line": 66, + "line": 85, "column": 10 }, "end": { - "line": 66, + "line": 85, "column": 26 } }, "object": { "type": "Identifier", - 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"start": 2784, - "end": 2790, + "start": 3234, + "end": 3240, "loc": { "start": { - "line": 71, + "line": 90, "column": 6 }, "end": { - "line": 71, + "line": 90, "column": 12 }, "identifierName": "errors" @@ -26421,15 +27742,15 @@ }, "property": { "type": "Identifier", - "start": 2791, - "end": 2795, + "start": 3241, + "end": 3245, "loc": { "start": { - "line": 71, + "line": 90, "column": 13 }, "end": { - "line": 71, + "line": 90, "column": 17 }, "identifierName": "push" @@ -26441,30 +27762,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 2796, - "end": 3036, + "start": 3246, + "end": 3486, "loc": { "start": { - "line": 71, + "line": 90, "column": 18 }, "end": { - "line": 77, + "line": 96, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 2806, - "end": 2854, + "start": 3256, + "end": 3304, "loc": { "start": { - "line": 72, + "line": 91, "column": 8 }, "end": { - "line": 72, + "line": 91, "column": 56 } }, @@ -26473,15 +27794,15 @@ "computed": false, "key": { "type": "Identifier", - 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"start": 3322, - "end": 3332, + "start": 3772, + "end": 3782, "loc": { "start": { - "line": 86, + "line": 105, "column": 67 }, "end": { - "line": 86, + "line": 105, "column": 77 } }, "object": { "type": "Identifier", - "start": 3322, - "end": 3324, + "start": 3772, + "end": 3774, "loc": { "start": { - "line": 86, + "line": 105, "column": 67 }, "end": { - "line": 86, + "line": 105, "column": 69 }, "identifierName": "ex" @@ -27230,15 +28551,15 @@ }, "property": { "type": "Identifier", - "start": 3325, - "end": 3332, + "start": 3775, + "end": 3782, "loc": { "start": { - "line": 86, + "line": 105, "column": 70 }, "end": { - "line": 86, + "line": 105, "column": 77 }, "identifierName": "message" @@ -27251,15 +28572,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 3273, - "end": 3320, + "start": 3723, + "end": 3770, "loc": { "start": { - "line": 86, + "line": 105, "column": 18 }, "end": { - "line": 86, + "line": 105, "column": 65 } }, @@ -27271,15 +28592,15 @@ }, { "type": "TemplateElement", - 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"line": 93, + "line": 112, "column": 49 }, "end": { - "line": 93, + "line": 112, "column": 60 }, "identifierName": "parentCount" @@ -27516,15 +28837,15 @@ }, "right": { "type": "Identifier", - "start": 3440, - "end": 3449, + "start": 3890, + "end": 3899, "loc": { "start": { - "line": 93, + "line": 112, "column": 63 }, "end": { - "line": 93, + "line": 112, "column": 72 }, "identifierName": "undefined" @@ -27535,58 +28856,58 @@ ], "body": { "type": "BlockStatement", - "start": 3451, - "end": 4831, + "start": 3901, + "end": 5281, "loc": { "start": { - "line": 93, + "line": 112, "column": 74 }, "end": { - "line": 125, + "line": 144, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 4468, - "end": 4503, + "start": 4918, + "end": 4953, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 39 } }, "expression": { "type": "CallExpression", - "start": 4468, - "end": 4502, + "start": 4918, + "end": 4952, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 38 } }, "callee": { "type": "Identifier", - "start": 4468, - "end": 4472, + "start": 4918, + "end": 4922, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 8 }, "identifierName": "func" @@ -27597,15 +28918,15 @@ "arguments": [ { "type": "Identifier", - "start": 4473, - "end": 4477, + "start": 4923, + "end": 4927, "loc": { "start": { - "line": 108, + "line": 127, "column": 9 }, "end": { - "line": 108, + "line": 127, "column": 13 }, "identifierName": "node" @@ -27614,15 +28935,15 @@ }, { "type": "Identifier", - "start": 4479, - "end": 4488, + "start": 4929, + "end": 4938, "loc": { "start": { - "line": 108, + "line": 127, "column": 15 }, "end": { - "line": 108, + "line": 127, "column": 24 }, "identifierName": "nodeCount" @@ -27631,15 +28952,15 @@ }, { "type": "Identifier", - "start": 4490, - "end": 4501, + "start": 4940, + "end": 4951, "loc": { "start": { - "line": 108, + "line": 127, "column": 26 }, "end": { - "line": 108, + "line": 127, "column": 37 }, "identifierName": "parentCount" @@ -27653,15 +28974,15 @@ { "type": "CommentLine", "value": " Recurse through PhyloTree nodes, executing function on each node.", - "start": 3457, - "end": 3525, + "start": 3907, + "end": 3975, "loc": { "start": { - "line": 94, + "line": 113, "column": 4 }, "end": { - "line": 94, + "line": 113, "column": 72 } } @@ -27669,15 +28990,15 @@ { "type": "CommentLine", "value": " - node: The node to recurse from. The function will be called on node", - "start": 3530, - "end": 3603, + "start": 3980, + "end": 4053, "loc": { "start": { - "line": 95, + "line": 114, "column": 4 }, "end": { - "line": 95, + "line": 114, "column": 77 } } @@ -27685,15 +29006,15 @@ { "type": "CommentLine", "value": " *before* being called on its children.", - "start": 3608, - "end": 3658, + "start": 4058, + "end": 4108, "loc": { "start": { - "line": 96, + "line": 115, "column": 4 }, "end": { - "line": 96, + "line": 115, "column": 54 } } @@ -27701,15 +29022,15 @@ { "type": "CommentLine", "value": " - func: The function to call on `node` and all of its children.", - "start": 3663, - "end": 3730, + "start": 4113, + "end": 4180, "loc": { "start": { - "line": 97, + "line": 116, "column": 4 }, "end": { - "line": 97, + "line": 116, "column": 71 } } @@ -27717,15 +29038,15 @@ { "type": "CommentLine", "value": " - nodeCount: `node` will be called with this nodeCount. All of its", - "start": 3735, - "end": 3805, + "start": 4185, + "end": 4255, "loc": { "start": { - "line": 98, + "line": 117, "column": 4 }, "end": { - "line": 98, + "line": 117, "column": 74 } } @@ -27733,15 +29054,15 @@ { "type": "CommentLine", "value": " children will be called with consecutively increasing nodeCounts.", - "start": 3810, - "end": 3887, + "start": 4260, + "end": 4337, "loc": { "start": { - "line": 99, + "line": 118, "column": 4 }, "end": { - "line": 99, + "line": 118, "column": 81 } } @@ -27749,15 +29070,15 @@ { "type": "CommentLine", "value": " - parentCount: The nodeCount associated with the parent of this node", - "start": 3892, - "end": 3964, + "start": 4342, + "end": 4414, "loc": { "start": { - "line": 100, + "line": 119, "column": 4 }, "end": { - "line": 100, + "line": 119, "column": 76 } } @@ -27765,15 +29086,15 @@ { "type": "CommentLine", "value": " within this run of recurseNodes. For instance, immediate children", - "start": 3969, - "end": 4046, + "start": 4419, + "end": 4496, "loc": { "start": { - "line": 101, + "line": 120, "column": 4 }, "end": { - "line": 101, + "line": 120, "column": 81 } } @@ -27781,15 +29102,15 @@ { "type": "CommentLine", "value": " of `node` will have a parentCount of 0. By default, `node` itself", - "start": 4051, - "end": 4128, + "start": 4501, + "end": 4578, "loc": { "start": { - "line": 102, + "line": 121, "column": 4 }, "end": { - "line": 102, + "line": 121, "column": 81 } } @@ -27797,15 +29118,15 @@ { "type": "CommentLine", "value": " will have a parentCount of `undefined`.", - "start": 4133, - "end": 4184, + "start": 4583, + "end": 4634, "loc": { "start": { - "line": 103, + "line": 122, "column": 4 }, "end": { - "line": 103, + "line": 122, "column": 55 } } @@ -27813,15 +29134,15 @@ { "type": "CommentLine", "value": " When the function `func` is called, it is given three arguments:", - "start": 4189, - "end": 4256, + "start": 4639, + "end": 4706, "loc": { "start": { - "line": 104, + "line": 123, "column": 4 }, "end": { - "line": 104, + "line": 123, "column": 71 } } @@ -27829,15 +29150,15 @@ { "type": "CommentLine", "value": " - The current node object (initially: `node`)", - "start": 4261, - "end": 4310, + "start": 4711, + "end": 4760, "loc": { "start": { - "line": 105, + "line": 124, "column": 4 }, "end": { - "line": 105, + "line": 124, "column": 53 } } @@ -27845,15 +29166,15 @@ { "type": "CommentLine", "value": " - The count of the current node object (initially: `nodeCount`)", - "start": 4315, - "end": 4382, + "start": 4765, + "end": 4832, "loc": { "start": { - "line": 106, + "line": 125, "column": 4 }, "end": { - "line": 106, + "line": 125, "column": 71 } } @@ -27861,15 +29182,15 @@ { "type": "CommentLine", "value": " - The parent count of the current node object (initially: `parentCount`)", - "start": 4387, - "end": 4463, + "start": 4837, + "end": 4913, "loc": { "start": { - "line": 107, + "line": 126, "column": 4 }, "end": { - "line": 107, + "line": 126, "column": 80 } } @@ -27878,44 +29199,44 @@ }, { "type": "VariableDeclaration", - "start": 4509, - "end": 4536, + "start": 4959, + "end": 4986, "loc": { "start": { - "line": 110, + "line": 129, "column": 4 }, "end": { - "line": 110, + "line": 129, "column": 31 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4513, - "end": 4535, + "start": 4963, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 8 }, "end": { - "line": 110, + "line": 129, "column": 30 } }, "id": { "type": "Identifier", - "start": 4513, - "end": 4519, + "start": 4963, + "end": 4969, "loc": { "start": { - "line": 110, + "line": 129, "column": 8 }, "end": { - "line": 110, + "line": 129, "column": 14 }, "identifierName": "nextID" @@ -27924,29 +29245,29 @@ }, "init": { "type": "BinaryExpression", - "start": 4522, - "end": 4535, + "start": 4972, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 17 }, "end": { - "line": 110, + "line": 129, "column": 30 } }, "left": { "type": "Identifier", - "start": 4522, - "end": 4531, + "start": 4972, + "end": 4981, "loc": { "start": { - "line": 110, + "line": 129, "column": 17 }, "end": { - "line": 110, + "line": 129, "column": 26 }, "identifierName": "nodeCount" @@ -27956,15 +29277,15 @@ "operator": "+", "right": { "type": "NumericLiteral", - "start": 4534, - "end": 4535, + "start": 4984, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 29 }, "end": { - "line": 110, + "line": 129, "column": 30 } }, @@ -27982,15 +29303,15 @@ { "type": "CommentLine", "value": " Recurse through all children of this node.", - "start": 4542, - "end": 4587, + "start": 4992, + "end": 5037, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 49 } } @@ -27999,43 +29320,43 @@ }, { "type": "IfStatement", - "start": 4592, - "end": 4807, + "start": 5042, + "end": 5257, "loc": { "start": { - "line": 113, + "line": 132, "column": 4 }, "end": { - "line": 122, + "line": 141, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4596, - "end": 4617, + "start": 5046, + "end": 5067, "loc": { "start": { - "line": 113, + "line": 132, "column": 8 }, "end": { - "line": 113, + "line": 132, "column": 29 } }, "callee": { "type": "Identifier", - "start": 4596, - "end": 4599, + "start": 5046, + "end": 5049, "loc": { "start": { - "line": 113, + "line": 132, "column": 8 }, "end": { - "line": 113, + "line": 132, "column": 11 }, "identifierName": "has" @@ -28046,15 +29367,15 @@ "arguments": [ { "type": "Identifier", - "start": 4600, - "end": 4604, + "start": 5050, + "end": 5054, "loc": { "start": { - "line": 113, + "line": 132, "column": 12 }, "end": { - "line": 113, + "line": 132, "column": 16 }, "identifierName": "node" @@ -28063,15 +29384,15 @@ }, { "type": "StringLiteral", - "start": 4606, - "end": 4616, + "start": 5056, + "end": 5066, "loc": { "start": { - "line": 113, + "line": 132, "column": 18 }, "end": { - "line": 113, + "line": 132, "column": 28 } }, @@ -28086,86 +29407,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 4619, - "end": 4807, + "start": 5069, + "end": 5257, "loc": { "start": { - "line": 113, + "line": 132, "column": 31 }, "end": { - "line": 122, + "line": 141, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 4627, - "end": 4801, + "start": 5077, + "end": 5251, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 121, + "line": 140, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 4627, - "end": 4800, + "start": 5077, + "end": 5250, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 121, + "line": 140, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 4627, - "end": 4648, + "start": 5077, + "end": 5098, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 27 } }, "object": { "type": "MemberExpression", - "start": 4627, - "end": 4640, + "start": 5077, + "end": 5090, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 19 } }, "object": { "type": "Identifier", - "start": 4627, - "end": 4631, + "start": 5077, + "end": 5081, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 10 }, "identifierName": "node" @@ -28174,15 +29495,15 @@ }, "property": { "type": "Identifier", - "start": 4632, - "end": 4640, + "start": 5082, + "end": 5090, "loc": { "start": { - "line": 114, + "line": 133, "column": 11 }, "end": { - "line": 114, + "line": 133, "column": 19 }, "identifierName": "children" @@ -28193,15 +29514,15 @@ }, "property": { "type": "Identifier", - "start": 4641, - "end": 4648, + "start": 5091, + "end": 5098, "loc": { "start": { - "line": 114, + "line": 133, "column": 20 }, "end": { - "line": 114, + "line": 133, "column": 27 }, "identifierName": "forEach" @@ -28213,15 +29534,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 4649, - "end": 4799, + "start": 5099, + "end": 5249, "loc": { "start": { - "line": 114, + "line": 133, "column": 28 }, "end": { - "line": 121, + "line": 140, "column": 7 } }, @@ -28232,15 +29553,15 @@ "params": [ { "type": "Identifier", - "start": 4650, - "end": 4655, + "start": 5100, + "end": 5105, "loc": { "start": { - "line": 114, + "line": 133, "column": 29 }, "end": { - "line": 114, + "line": 133, "column": 34 }, "identifierName": "child" @@ -28250,59 +29571,59 @@ ], "body": { "type": "BlockStatement", - "start": 4660, - "end": 4799, + "start": 5110, + "end": 5249, "loc": { "start": { - "line": 114, + "line": 133, "column": 39 }, "end": { - "line": 121, + "line": 140, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 4670, - "end": 4791, + "start": 5120, + "end": 5241, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 4670, - "end": 4790, + "start": 5120, + "end": 5240, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 4670, - "end": 4676, + "start": 5120, + "end": 5126, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 14 }, "identifierName": "nextID" @@ -28311,43 +29632,43 @@ }, "right": { "type": "CallExpression", - "start": 4679, - "end": 4790, + "start": 5129, + "end": 5240, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 120, + "line": 139, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 4679, - "end": 4708, + "start": 5129, + "end": 5158, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 115, + "line": 134, "column": 46 } }, "object": { "type": "Identifier", - "start": 4679, - "end": 4695, + "start": 5129, + "end": 5145, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 115, + "line": 134, "column": 33 }, "identifierName": "PhylogenyWrapper" @@ -28356,15 +29677,15 @@ }, "property": { "type": "Identifier", - "start": 4696, - "end": 4708, + "start": 5146, + "end": 5158, "loc": { "start": { - "line": 115, + "line": 134, "column": 34 }, "end": { - "line": 115, + "line": 134, "column": 46 }, "identifierName": "recurseNodes" @@ -28376,15 +29697,15 @@ "arguments": [ { "type": "Identifier", - "start": 4720, - "end": 4725, + "start": 5170, + "end": 5175, "loc": { "start": { - "line": 116, + "line": 135, "column": 10 }, "end": { - "line": 116, + "line": 135, "column": 15 }, "identifierName": "child" @@ -28393,15 +29714,15 @@ }, { "type": "Identifier", - "start": 4737, - "end": 4741, + "start": 5187, + "end": 5191, "loc": { "start": { - "line": 117, + "line": 136, "column": 10 }, "end": { - "line": 117, + "line": 136, "column": 14 }, "identifierName": "func" @@ -28410,15 +29731,15 @@ }, { "type": "Identifier", - "start": 4753, - "end": 4759, + "start": 5203, + "end": 5209, "loc": { "start": { - "line": 118, + "line": 137, "column": 10 }, "end": { - "line": 118, + "line": 137, "column": 16 }, "identifierName": "nextID" @@ -28427,15 +29748,15 @@ }, { "type": "Identifier", - "start": 4771, - "end": 4780, + "start": 5221, + "end": 5230, "loc": { "start": { - "line": 119, + "line": 138, "column": 10 }, "end": { - "line": 119, + "line": 138, "column": 19 }, "identifierName": "nodeCount" @@ -28461,15 +29782,15 @@ { "type": "CommentLine", "value": " Recurse through all children of this node.", - "start": 4542, - "end": 4587, + "start": 4992, + "end": 5037, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 49 } } @@ -28478,29 +29799,29 @@ }, { "type": "ReturnStatement", - "start": 4813, - "end": 4827, + "start": 5263, + "end": 5277, "loc": { "start": { - "line": 124, + "line": 143, "column": 4 }, "end": { - "line": 124, + "line": 143, "column": 18 } }, "argument": { "type": "Identifier", - "start": 4820, - "end": 4826, + "start": 5270, + "end": 5276, "loc": { "start": { - "line": 124, + "line": 143, "column": 11 }, "end": { - "line": 124, + "line": 143, "column": 17 }, "identifierName": "nextID" @@ -28514,15 +29835,15 @@ }, { "type": "ClassMethod", - "start": 4835, - "end": 5703, + "start": 5285, + "end": 6153, "loc": { "start": { - "line": 127, + "line": 146, "column": 2 }, "end": { - "line": 148, + "line": 167, "column": 3 } }, @@ -28530,15 +29851,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4835, - "end": 4852, + "start": 5285, + "end": 5302, "loc": { "start": { - "line": 127, + "line": 146, "column": 2 }, "end": { - "line": 127, + "line": 146, "column": 19 }, "identifierName": "getTaxonomicUnits" @@ -28553,29 +29874,29 @@ "params": [ { "type": "AssignmentPattern", - "start": 4853, - "end": 4870, + "start": 5303, + "end": 5320, "loc": { "start": { - "line": 127, + "line": 146, "column": 20 }, "end": { - "line": 127, + "line": 146, "column": 37 } }, "left": { "type": "Identifier", - "start": 4853, - "end": 4861, + "start": 5303, + "end": 5311, "loc": { "start": { - "line": 127, + "line": 146, "column": 20 }, "end": { - "line": 127, + "line": 146, "column": 28 }, "identifierName": "nodeType" @@ -28584,15 +29905,15 @@ }, "right": { "type": "StringLiteral", - "start": 4864, - "end": 4870, + "start": 5314, + "end": 5320, "loc": { "start": { - "line": 127, + "line": 146, "column": 31 }, "end": { - "line": 127, + "line": 146, "column": 37 } }, @@ -28606,59 +29927,59 @@ ], "body": { "type": "BlockStatement", - "start": 4872, - "end": 5703, + "start": 5322, + "end": 6153, "loc": { "start": { - "line": 127, + "line": 146, "column": 39 }, "end": { - "line": 148, + "line": 167, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 5459, - "end": 5507, + "start": 5909, + "end": 5957, "loc": { "start": { - "line": 139, + "line": 158, "column": 4 }, "end": { - "line": 139, + "line": 158, "column": 52 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5465, - "end": 5506, + "start": 5915, + "end": 5956, "loc": { "start": { - "line": 139, + "line": 158, "column": 10 }, "end": { - "line": 139, + "line": 158, "column": 51 } }, "id": { "type": "Identifier", - "start": 5465, - "end": 5475, + "start": 5915, + "end": 5925, "loc": { "start": { - "line": 139, + "line": 158, "column": 10 }, "end": { - "line": 139, + "line": 158, "column": 20 }, "identifierName": "nodeLabels" @@ -28668,58 +29989,58 @@ }, "init": { "type": "CallExpression", - "start": 5478, - "end": 5506, + "start": 5928, + "end": 5956, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 5478, - "end": 5496, + "start": 5928, + "end": 5946, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 41 } }, "object": { "type": "ThisExpression", - "start": 5478, - "end": 5482, + "start": 5928, + "end": 5932, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 27 } } }, "property": { "type": "Identifier", - "start": 5483, - "end": 5496, + "start": 5933, + "end": 5946, "loc": { "start": { - "line": 139, + "line": 158, "column": 28 }, "end": { - "line": 139, + "line": 158, "column": 41 }, "identifierName": "getNodeLabels" @@ -28731,15 +30052,15 @@ "arguments": [ { "type": "Identifier", - "start": 5497, - "end": 5505, + "start": 5947, + "end": 5955, "loc": { "start": { - "line": 139, + "line": 158, "column": 42 }, "end": { - "line": 139, + "line": 158, "column": 50 }, "identifierName": "nodeType" @@ -28756,15 +30077,15 @@ { "type": "CommentLine", "value": " Return a list of all taxonomic units in this phylogeny.", - "start": 4878, - "end": 4936, + "start": 5328, + "end": 5386, "loc": { "start": { - "line": 128, + "line": 147, "column": 4 }, "end": { - "line": 128, + "line": 147, "column": 62 } } @@ -28772,15 +30093,15 @@ { "type": "CommentLine", "value": " Node labels will be extracted from:", - "start": 4941, - "end": 4979, + "start": 5391, + "end": 5429, "loc": { "start": { - "line": 129, + "line": 148, "column": 4 }, "end": { - "line": 129, + "line": 148, "column": 42 } } @@ -28788,15 +30109,15 @@ { "type": "CommentLine", "value": " - internal nodes only (if nodeType == 'internal')", - "start": 4984, - "end": 5037, + "start": 5434, + "end": 5487, "loc": { "start": { - "line": 130, + "line": 149, "column": 4 }, "end": { - "line": 130, + "line": 149, "column": 57 } } @@ -28804,15 +30125,15 @@ { "type": "CommentLine", "value": " - terminal nodes only (if nodeType == 'terminal')", - "start": 5042, - "end": 5095, + "start": 5492, + "end": 5545, "loc": { "start": { - "line": 131, + "line": 150, "column": 4 }, "end": { - "line": 131, + "line": 150, "column": 57 } } @@ -28820,15 +30141,15 @@ { "type": "CommentLine", "value": " - both internal and terminal nodes (if nodeType == 'both')", - "start": 5100, - "end": 5162, + "start": 5550, + "end": 5612, "loc": { "start": { - "line": 132, + "line": 151, "column": 4 }, "end": { - "line": 132, + "line": 151, "column": 66 } } @@ -28836,15 +30157,15 @@ { "type": "CommentLine", "value": "", - "start": 5167, - "end": 5169, + "start": 5617, + "end": 5619, "loc": { "start": { - "line": 133, + "line": 152, "column": 4 }, "end": { - "line": 133, + "line": 152, "column": 6 } } @@ -28852,15 +30173,15 @@ { "type": "CommentLine", "value": " See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted", - "start": 5174, - "end": 5249, + "start": 5624, + "end": 5699, "loc": { "start": { - "line": 134, + "line": 153, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 79 } } @@ -28868,15 +30189,15 @@ { "type": "CommentLine", "value": " into node labels, but in brief:", - "start": 5254, - "end": 5288, + "start": 5704, + "end": 5738, "loc": { "start": { - "line": 135, + "line": 154, "column": 4 }, "end": { - "line": 135, + "line": 154, "column": 38 } } @@ -28884,15 +30205,15 @@ { "type": "CommentLine", "value": " 1. We look for taxonomic units in the additionalNodeProperties.", - "start": 5293, - "end": 5360, + "start": 5743, + "end": 5810, "loc": { "start": { - "line": 136, + "line": 155, "column": 4 }, "end": { - "line": 136, + "line": 155, "column": 71 } } @@ -28900,15 +30221,15 @@ { "type": "CommentLine", "value": " 2. If none are found, we attempt to parse the node label as a scientific name.", - "start": 5365, - "end": 5447, + "start": 5815, + "end": 5897, "loc": { "start": { - "line": 137, + "line": 156, "column": 4 }, "end": { - "line": 137, + "line": 156, "column": 86 } } @@ -28916,15 +30237,15 @@ { "type": "CommentLine", "value": "", - "start": 5452, - "end": 5454, + "start": 5902, + "end": 5904, "loc": { "start": { - "line": 138, + "line": 157, "column": 4 }, "end": { - "line": 138, + "line": 157, "column": 6 } } @@ -28933,44 +30254,44 @@ }, { "type": "VariableDeclaration", - "start": 5512, - "end": 5537, + "start": 5962, + "end": 5987, "loc": { "start": { - "line": 140, + "line": 159, "column": 4 }, "end": { - "line": 140, + "line": 159, "column": 29 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5518, - "end": 5536, + "start": 5968, + "end": 5986, "loc": { "start": { - "line": 140, + "line": 159, "column": 10 }, "end": { - "line": 140, + "line": 159, "column": 28 } }, "id": { "type": "Identifier", - "start": 5518, - "end": 5524, + "start": 5968, + "end": 5974, "loc": { "start": { - "line": 140, + "line": 159, "column": 10 }, "end": { - "line": 140, + "line": 159, "column": 16 }, "identifierName": "tunits" @@ -28979,29 +30300,29 @@ }, "init": { "type": "NewExpression", - "start": 5527, - "end": 5536, + "start": 5977, + "end": 5986, "loc": { "start": { - "line": 140, + "line": 159, "column": 19 }, "end": { - "line": 140, + "line": 159, "column": 28 } }, "callee": { "type": "Identifier", - "start": 5531, - "end": 5534, + "start": 5981, + "end": 5984, "loc": { "start": { - "line": 140, + "line": 159, "column": 23 }, "end": { - "line": 140, + "line": 159, "column": 26 }, "identifierName": "Set" @@ -29016,57 +30337,57 @@ }, { "type": "ExpressionStatement", - "start": 5543, - "end": 5679, + "start": 5993, + "end": 6129, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 6 } }, "expression": { "type": "CallExpression", - "start": 5543, - "end": 5678, + "start": 5993, + "end": 6128, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 5 } }, "callee": { "type": "MemberExpression", - "start": 5543, - "end": 5561, + "start": 5993, + "end": 6011, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 142, + "line": 161, "column": 22 } }, "object": { "type": "Identifier", - "start": 5543, - "end": 5553, + "start": 5993, + "end": 6003, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 142, + "line": 161, "column": 14 }, "identifierName": "nodeLabels" @@ -29075,15 +30396,15 @@ }, "property": { "type": "Identifier", - "start": 5554, - "end": 5561, + "start": 6004, + "end": 6011, "loc": { "start": { - "line": 142, + "line": 161, "column": 15 }, "end": { - "line": 142, + "line": 161, "column": 22 }, "identifierName": "forEach" @@ -29095,15 +30416,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5569, - "end": 5672, + "start": 6019, + "end": 6122, "loc": { "start": { - "line": 143, + "line": 162, "column": 6 }, "end": { - "line": 144, + "line": 163, "column": 44 } }, @@ -29114,15 +30435,15 @@ "params": [ { "type": "Identifier", - "start": 5569, - "end": 5578, + "start": 6019, + "end": 6028, "loc": { "start": { - "line": 143, + "line": 162, "column": 6 }, "end": { - "line": 143, + "line": 162, "column": 15 }, "identifierName": "nodeLabel" @@ -29132,86 +30453,86 @@ ], "body": { "type": "CallExpression", - "start": 5582, - "end": 5672, + "start": 6032, + "end": 6122, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 144, + "line": 163, "column": 44 } }, "callee": { "type": "MemberExpression", - "start": 5582, - "end": 5644, + "start": 6032, + "end": 6094, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 144, + "line": 163, "column": 16 } }, "object": { "type": "CallExpression", - "start": 5582, - "end": 5627, + "start": 6032, + "end": 6077, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 64 } }, "callee": { "type": "MemberExpression", - "start": 5582, - "end": 5616, + "start": 6032, + "end": 6066, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 53 } }, "object": { "type": "ThisExpression", - "start": 5582, - "end": 5586, + "start": 6032, + "end": 6036, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 23 } } }, "property": { "type": "Identifier", - "start": 5587, - "end": 5616, + "start": 6037, + "end": 6066, "loc": { "start": { - "line": 143, + "line": 162, "column": 24 }, "end": { - "line": 143, + "line": 162, "column": 53 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -29223,15 +30544,15 @@ "arguments": [ { "type": "Identifier", - "start": 5617, - "end": 5626, + "start": 6067, + "end": 6076, "loc": { "start": { - "line": 143, + "line": 162, "column": 54 }, "end": { - "line": 143, + "line": 162, "column": 63 }, "identifierName": "nodeLabel" @@ -29242,15 +30563,15 @@ }, "property": { "type": "Identifier", - "start": 5637, - "end": 5644, + "start": 6087, + "end": 6094, "loc": { "start": { - "line": 144, + "line": 163, "column": 9 }, "end": { - "line": 144, + "line": 163, "column": 16 }, "identifierName": "forEach" @@ -29262,15 +30583,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5645, - "end": 5671, + "start": 6095, + "end": 6121, "loc": { "start": { - "line": 144, + "line": 163, "column": 17 }, "end": { - "line": 144, + "line": 163, "column": 43 } }, @@ -29281,15 +30602,15 @@ "params": [ { "type": "Identifier", - "start": 5645, - "end": 5650, + "start": 6095, + "end": 6100, "loc": { "start": { - "line": 144, + "line": 163, "column": 17 }, "end": { - "line": 144, + "line": 163, "column": 22 }, "identifierName": "tunit" @@ -29299,43 +30620,43 @@ ], "body": { "type": "CallExpression", - "start": 5654, - "end": 5671, + "start": 6104, + "end": 6121, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 43 } }, "callee": { "type": "MemberExpression", - "start": 5654, - "end": 5664, + "start": 6104, + "end": 6114, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 36 } }, "object": { "type": "Identifier", - "start": 5654, - "end": 5660, + "start": 6104, + "end": 6110, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 32 }, "identifierName": "tunits" @@ -29344,15 +30665,15 @@ }, "property": { "type": "Identifier", - "start": 5661, - "end": 5664, + "start": 6111, + "end": 6114, "loc": { "start": { - "line": 144, + "line": 163, "column": 33 }, "end": { - "line": 144, + "line": 163, "column": 36 }, "identifierName": "add" @@ -29364,15 +30685,15 @@ "arguments": [ { "type": "Identifier", - "start": 5665, - "end": 5670, + "start": 6115, + "end": 6120, "loc": { "start": { - "line": 144, + "line": 163, "column": 37 }, "end": { - "line": 144, + "line": 163, "column": 42 }, "identifierName": "tunit" @@ -29390,29 +30711,29 @@ }, { "type": "ReturnStatement", - "start": 5685, - "end": 5699, + "start": 6135, + "end": 6149, "loc": { "start": { - "line": 147, + "line": 166, "column": 4 }, "end": { - "line": 147, + "line": 166, "column": 18 } }, "argument": { "type": "Identifier", - "start": 5692, - "end": 5698, + "start": 6142, + "end": 6148, "loc": { "start": { - "line": 147, + "line": 166, "column": 11 }, "end": { - "line": 147, + "line": 166, "column": 17 }, "identifierName": "tunits" @@ -29426,15 +30747,15 @@ }, { "type": "ClassMethod", - "start": 5707, - "end": 7617, + "start": 6157, + "end": 8067, "loc": { "start": { - "line": 150, + "line": 169, "column": 2 }, "end": { - "line": 199, + "line": 218, "column": 3 } }, @@ -29442,15 +30763,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 5707, - "end": 5720, + "start": 6157, + "end": 6170, "loc": { "start": { - "line": 150, + "line": 169, "column": 2 }, "end": { - "line": 150, + "line": 169, "column": 15 }, "identifierName": "getNodeLabels" @@ -29465,29 +30786,29 @@ "params": [ { "type": "AssignmentPattern", - "start": 5721, - "end": 5738, + "start": 6171, + "end": 6188, "loc": { "start": { - "line": 150, + "line": 169, "column": 16 }, "end": { - "line": 150, + "line": 169, "column": 33 } }, "left": { "type": "Identifier", - "start": 5721, - "end": 5729, + "start": 6171, + "end": 6179, "loc": { "start": { - "line": 150, + "line": 169, "column": 16 }, "end": { - "line": 150, + "line": 169, "column": 24 }, "identifierName": "nodeType" @@ -29496,15 +30817,15 @@ }, "right": { "type": "StringLiteral", - "start": 5732, - "end": 5738, + "start": 6182, + "end": 6188, "loc": { "start": { - "line": 150, + "line": 169, "column": 27 }, "end": { - "line": 150, + "line": 169, "column": 33 } }, @@ -29518,74 +30839,74 @@ ], "body": { "type": "BlockStatement", - "start": 5740, - "end": 7617, + "start": 6190, + "end": 8067, "loc": { "start": { - "line": 150, + "line": 169, "column": 35 }, "end": { - "line": 199, + "line": 218, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 6111, - "end": 6175, + "start": 6561, + "end": 6625, "loc": { "start": { - "line": 159, + "line": 178, "column": 4 }, "end": { - "line": 159, + "line": 178, "column": 68 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6117, - "end": 6174, + "start": 6567, + "end": 6624, "loc": { "start": { - "line": 159, + "line": 178, "column": 10 }, "end": { - "line": 159, + "line": 178, "column": 67 } }, "id": { "type": "ObjectPattern", - "start": 6117, - "end": 6126, + "start": 6567, + "end": 6576, "loc": { "start": { - "line": 159, + "line": 178, "column": 10 }, "end": { - "line": 159, + "line": 178, "column": 19 } }, "properties": [ { "type": "ObjectProperty", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 } }, @@ -29594,15 +30915,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 }, "identifierName": "graph" @@ -29612,15 +30933,15 @@ }, "value": { "type": "Identifier", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 }, "identifierName": "graph" @@ -29637,43 +30958,43 @@ }, "init": { "type": "CallExpression", - "start": 6129, - "end": 6174, + "start": 6579, + "end": 6624, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 6129, - "end": 6143, + "start": 6579, + "end": 6593, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 36 } }, "object": { "type": "Identifier", - "start": 6129, - "end": 6137, + "start": 6579, + "end": 6587, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 30 }, "identifierName": "newickJs" @@ -29682,15 +31003,15 @@ }, "property": { "type": "Identifier", - "start": 6138, - "end": 6143, + "start": 6588, + "end": 6593, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 36 }, "identifierName": "parse" @@ -29702,72 +31023,72 @@ "arguments": [ { "type": "LogicalExpression", - "start": 6144, - "end": 6173, + "start": 6594, + "end": 6623, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 66 } }, "left": { "type": "MemberExpression", - "start": 6144, - "end": 6165, + "start": 6594, + "end": 6615, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 6144, - "end": 6158, + "start": 6594, + "end": 6608, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 51 } }, "object": { "type": "ThisExpression", - "start": 6144, - "end": 6148, + "start": 6594, + "end": 6598, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 41 } } }, "property": { "type": "Identifier", - "start": 6149, - "end": 6158, + "start": 6599, + "end": 6608, "loc": { "start": { - "line": 159, + "line": 178, "column": 42 }, "end": { - "line": 159, + "line": 178, "column": 51 }, "identifierName": "phylogeny" @@ -29778,15 +31099,15 @@ }, "property": { "type": "Identifier", - "start": 6159, - "end": 6165, + "start": 6609, + "end": 6615, "loc": { "start": { - "line": 159, + "line": 178, "column": 52 }, "end": { - "line": 159, + "line": 178, "column": 58 }, "identifierName": "newick" @@ -29798,15 +31119,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 6169, - "end": 6173, + "start": 6619, + "end": 6623, "loc": { "start": { - "line": 159, + "line": 178, "column": 62 }, "end": { - "line": 159, + "line": 178, "column": 66 } }, @@ -29827,15 +31148,15 @@ { "type": "CommentLine", "value": " Return a list of all the node labels in this phylogeny.", - "start": 5746, - "end": 5804, + "start": 6196, + "end": 6254, "loc": { "start": { - "line": 151, + "line": 170, "column": 4 }, "end": { - "line": 151, + "line": 170, "column": 62 } } @@ -29843,15 +31164,15 @@ { "type": "CommentLine", "value": "", - "start": 5809, - "end": 5811, + "start": 6259, + "end": 6261, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 6 } } @@ -29859,15 +31180,15 @@ { "type": "CommentLine", "value": " nodeType can be one of:", - "start": 5816, - "end": 5842, + "start": 6266, + "end": 6292, "loc": { "start": { - "line": 153, + "line": 172, "column": 4 }, "end": { - "line": 153, + "line": 172, "column": 30 } } @@ -29875,15 +31196,15 @@ { "type": "CommentLine", "value": " - 'internal': Return node labels on internal nodes.", - "start": 5847, - "end": 5901, + "start": 6297, + "end": 6351, "loc": { "start": { - "line": 154, + "line": 173, "column": 4 }, "end": { - "line": 154, + "line": 173, "column": 58 } } @@ -29891,15 +31212,15 @@ { "type": "CommentLine", "value": " - 'terminal': Return node labels on terminal nodes.", - "start": 5906, - "end": 5960, + "start": 6356, + "end": 6410, "loc": { "start": { - "line": 155, + "line": 174, "column": 4 }, "end": { - "line": 155, + "line": 174, "column": 58 } } @@ -29907,15 +31228,15 @@ { "type": "CommentLine", "value": " - 'both': Return node labels on both internal and terminal nodes.", - "start": 5965, - "end": 6033, + "start": 6415, + "end": 6483, "loc": { "start": { - "line": 156, + "line": 175, "column": 4 }, "end": { - "line": 156, + "line": 175, "column": 72 } } @@ -29923,15 +31244,15 @@ { "type": "CommentLine", "value": " Parse the phylogeny (will throw an exception if parsing failed).", - "start": 6039, - "end": 6106, + "start": 6489, + "end": 6556, "loc": { "start": { - "line": 158, + "line": 177, "column": 4 }, "end": { - "line": 158, + "line": 177, "column": 71 } } @@ -29940,59 +31261,59 @@ }, { "type": "VariableDeclaration", - "start": 6180, - "end": 6211, + "start": 6630, + "end": 6661, "loc": { "start": { - "line": 160, + "line": 179, "column": 4 }, "end": { - "line": 160, + "line": 179, "column": 35 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6186, - "end": 6210, + "start": 6636, + "end": 6660, "loc": { "start": { - "line": 160, + "line": 179, "column": 10 }, "end": { - "line": 160, + "line": 179, "column": 34 } }, "id": { "type": "ArrayPattern", - "start": 6186, - "end": 6202, + "start": 6636, + "end": 6652, "loc": { "start": { - "line": 160, + "line": 179, "column": 10 }, "end": { - "line": 160, + "line": 179, "column": 26 } }, "elements": [ { "type": "Identifier", - "start": 6187, - "end": 6195, + "start": 6637, + "end": 6645, "loc": { "start": { - "line": 160, + "line": 179, "column": 11 }, "end": { - "line": 160, + "line": 179, "column": 19 }, "identifierName": "vertices" @@ -30001,15 +31322,15 @@ }, { "type": "Identifier", - "start": 6197, - "end": 6201, + "start": 6647, + "end": 6651, "loc": { "start": { - "line": 160, + "line": 179, "column": 21 }, "end": { - "line": 160, + "line": 179, "column": 25 }, "identifierName": "arcs" @@ -30020,15 +31341,15 @@ }, "init": { "type": "Identifier", - "start": 6205, - "end": 6210, + "start": 6655, + "end": 6660, "loc": { "start": { - "line": 160, + "line": 179, "column": 29 }, "end": { - "line": 160, + "line": 179, "column": 34 }, "identifierName": "graph" @@ -30041,43 +31362,43 @@ }, { "type": "IfStatement", - "start": 6217, - "end": 6465, + "start": 6667, + "end": 6915, "loc": { "start": { - "line": 162, + "line": 181, "column": 4 }, "end": { - "line": 171, + "line": 190, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6221, - "end": 6240, + "start": 6671, + "end": 6690, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 27 } }, "left": { "type": "Identifier", - "start": 6221, - "end": 6229, + "start": 6671, + "end": 6679, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 16 }, "identifierName": "nodeType" @@ -30087,15 +31408,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 6234, - "end": 6240, + "start": 6684, + "end": 6690, "loc": { "start": { - "line": 162, + "line": 181, "column": 21 }, "end": { - "line": 162, + "line": 181, "column": 27 } }, @@ -30108,72 +31429,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 6242, - "end": 6465, + "start": 6692, + "end": 6915, "loc": { "start": { - "line": 162, + "line": 181, "column": 29 }, "end": { - "line": 171, + "line": 190, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 6283, - "end": 6459, + "start": 6733, + "end": 6909, "loc": { "start": { - "line": 164, + "line": 183, "column": 6 }, "end": { - "line": 170, + "line": 189, "column": 8 } }, "argument": { "type": "CallExpression", - "start": 6290, - "end": 6458, + "start": 6740, + "end": 6908, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 170, + "line": 189, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 6290, - "end": 6300, + "start": 6740, + "end": 6750, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 164, + "line": 183, "column": 23 } }, "object": { "type": "Identifier", - "start": 6290, - "end": 6295, + "start": 6740, + "end": 6745, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 164, + "line": 183, "column": 18 }, "identifierName": "Array" @@ -30183,15 +31504,15 @@ }, "property": { "type": "Identifier", - "start": 6296, - "end": 6300, + "start": 6746, + "end": 6750, "loc": { "start": { - "line": 164, + "line": 183, "column": 19 }, "end": { - "line": 164, + "line": 183, "column": 23 }, "identifierName": "from" @@ -30204,29 +31525,29 @@ "arguments": [ { "type": "NewExpression", - "start": 6310, - "end": 6450, + "start": 6760, + "end": 6900, "loc": { "start": { - "line": 165, + "line": 184, "column": 8 }, "end": { - "line": 169, + "line": 188, "column": 9 } }, "callee": { "type": "Identifier", - "start": 6314, - "end": 6317, + "start": 6764, + "end": 6767, "loc": { "start": { - "line": 165, + "line": 184, "column": 12 }, "end": { - "line": 165, + "line": 184, "column": 15 }, "identifierName": "Set" @@ -30236,99 +31557,99 @@ "arguments": [ { "type": "CallExpression", - "start": 6329, - "end": 6440, + "start": 6779, + "end": 6890, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 168, + "line": 187, "column": 49 } }, "callee": { "type": "MemberExpression", - "start": 6329, - "end": 6410, + "start": 6779, + "end": 6860, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 168, + "line": 187, "column": 19 } }, "object": { "type": "CallExpression", - "start": 6329, - "end": 6390, + "start": 6779, + "end": 6840, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 167, + "line": 186, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 6329, - "end": 6366, + "start": 6779, + "end": 6816, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 167, + "line": 186, "column": 16 } }, "object": { "type": "CallExpression", - "start": 6329, - "end": 6349, + "start": 6779, + "end": 6799, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 30 } }, "callee": { "type": "MemberExpression", - "start": 6329, - "end": 6339, + "start": 6779, + "end": 6789, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 20 } }, "object": { "type": "Identifier", - "start": 6329, - "end": 6334, + "start": 6779, + "end": 6784, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 15 }, "identifierName": "Array" @@ -30337,15 +31658,15 @@ }, "property": { "type": "Identifier", - "start": 6335, - "end": 6339, + "start": 6785, + "end": 6789, "loc": { "start": { - "line": 166, + "line": 185, "column": 16 }, "end": { - "line": 166, + "line": 185, "column": 20 }, "identifierName": "from" @@ -30357,15 +31678,15 @@ "arguments": [ { "type": "Identifier", - "start": 6340, - "end": 6348, + "start": 6790, + "end": 6798, "loc": { "start": { - "line": 166, + "line": 185, "column": 21 }, "end": { - "line": 166, + "line": 185, "column": 29 }, "identifierName": "vertices" @@ -30376,15 +31697,15 @@ }, "property": { "type": "Identifier", - "start": 6363, - "end": 6366, + "start": 6813, + "end": 6816, "loc": { "start": { - "line": 167, + "line": 186, "column": 13 }, "end": { - "line": 167, + "line": 186, "column": 16 }, "identifierName": "map" @@ -30396,15 +31717,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6367, - "end": 6389, + "start": 6817, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 17 }, "end": { - "line": 167, + "line": 186, "column": 39 } }, @@ -30415,15 +31736,15 @@ "params": [ { "type": "Identifier", - "start": 6367, - "end": 6373, + "start": 6817, + "end": 6823, "loc": { "start": { - "line": 167, + "line": 186, "column": 17 }, "end": { - "line": 167, + "line": 186, "column": 23 }, "identifierName": "vertex" @@ -30433,29 +31754,29 @@ ], "body": { "type": "MemberExpression", - "start": 6377, - "end": 6389, + "start": 6827, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 27 }, "end": { - "line": 167, + "line": 186, "column": 39 } }, "object": { "type": "Identifier", - "start": 6377, - "end": 6383, + "start": 6827, + "end": 6833, "loc": { "start": { - "line": 167, + "line": 186, "column": 27 }, "end": { - "line": 167, + "line": 186, "column": 33 }, "identifierName": "vertex" @@ -30464,15 +31785,15 @@ }, "property": { "type": "Identifier", - "start": 6384, - "end": 6389, + "start": 6834, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 34 }, "end": { - "line": 167, + "line": 186, "column": 39 }, "identifierName": "label" @@ -30486,15 +31807,15 @@ }, "property": { "type": "Identifier", - "start": 6404, - "end": 6410, + "start": 6854, + "end": 6860, "loc": { "start": { - "line": 168, + "line": 187, "column": 13 }, "end": { - "line": 168, + "line": 187, "column": 19 }, "identifierName": "filter" @@ -30506,15 +31827,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6411, - "end": 6439, + "start": 6861, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 20 }, "end": { - "line": 168, + "line": 187, "column": 48 } }, @@ -30525,15 +31846,15 @@ "params": [ { "type": "Identifier", - "start": 6411, - "end": 6416, + "start": 6861, + "end": 6866, "loc": { "start": { - "line": 168, + "line": 187, "column": 20 }, "end": { - "line": 168, + "line": 187, "column": 25 }, "identifierName": "label" @@ -30543,29 +31864,29 @@ ], "body": { "type": "BinaryExpression", - "start": 6420, - "end": 6439, + "start": 6870, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 29 }, "end": { - "line": 168, + "line": 187, "column": 48 } }, "left": { "type": "Identifier", - "start": 6420, - "end": 6425, + "start": 6870, + "end": 6875, "loc": { "start": { - "line": 168, + "line": 187, "column": 29 }, "end": { - "line": 168, + "line": 187, "column": 34 }, "identifierName": "label" @@ -30575,15 +31896,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 6430, - "end": 6439, + "start": 6880, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 39 }, "end": { - "line": 168, + "line": 187, "column": 48 }, "identifierName": "undefined" @@ -30603,15 +31924,15 @@ { "type": "CommentLine", "value": " Return all node labels.", - "start": 6250, - "end": 6276, + "start": 6700, + "end": 6726, "loc": { "start": { - "line": 163, + "line": 182, "column": 6 }, "end": { - "line": 163, + "line": 182, "column": 32 } } @@ -30625,43 +31946,43 @@ }, { "type": "IfStatement", - "start": 6471, - "end": 6782, + "start": 6921, + "end": 7232, "loc": { "start": { - "line": 173, + "line": 192, "column": 4 }, "end": { - "line": 180, + "line": 199, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6475, - "end": 6498, + "start": 6925, + "end": 6948, "loc": { "start": { - "line": 173, + "line": 192, "column": 8 }, "end": { - "line": 173, + "line": 192, "column": 31 } }, "left": { "type": "Identifier", - "start": 6475, - "end": 6483, + "start": 6925, + "end": 6933, "loc": { "start": { - "line": 173, + "line": 192, "column": 8 }, "end": { - "line": 173, + "line": 192, "column": 16 }, "identifierName": "nodeType" @@ -30671,15 +31992,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 6488, - "end": 6498, + "start": 6938, + "end": 6948, "loc": { "start": { - "line": 173, + "line": 192, "column": 21 }, "end": { - "line": 173, + "line": 192, "column": 31 } }, @@ -30692,72 +32013,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 6500, - "end": 6782, + "start": 6950, + "end": 7232, "loc": { "start": { - "line": 173, + "line": 192, "column": 33 }, "end": { - "line": 180, + "line": 199, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 6575, - "end": 6776, + "start": 7025, + "end": 7226, "loc": { "start": { - "line": 175, + "line": 194, "column": 6 }, "end": { - "line": 179, + "line": 198, "column": 9 } }, "argument": { "type": "CallExpression", - "start": 6582, - "end": 6775, + "start": 7032, + "end": 7225, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 179, + "line": 198, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 6582, - "end": 6592, + "start": 7032, + "end": 7042, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 175, + "line": 194, "column": 23 } }, "object": { "type": "Identifier", - "start": 6582, - "end": 6587, + "start": 7032, + "end": 7037, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 175, + "line": 194, "column": 18 }, "identifierName": "Array" @@ -30767,15 +32088,15 @@ }, "property": { "type": "Identifier", - "start": 6588, - "end": 6592, + "start": 7038, + "end": 7042, "loc": { "start": { - "line": 175, + "line": 194, "column": 19 }, "end": { - "line": 175, + "line": 194, "column": 23 }, "identifierName": "from" @@ -30788,29 +32109,29 @@ "arguments": [ { "type": "NewExpression", - "start": 6593, - "end": 6774, + "start": 7043, + "end": 7224, "loc": { "start": { - "line": 175, + "line": 194, "column": 24 }, "end": { - "line": 179, + "line": 198, "column": 7 } }, "callee": { "type": "Identifier", - "start": 6597, - "end": 6600, + "start": 7047, + "end": 7050, "loc": { "start": { - "line": 175, + "line": 194, "column": 28 }, "end": { - "line": 175, + "line": 194, "column": 31 }, "identifierName": "Set" @@ -30820,99 +32141,99 @@ "arguments": [ { "type": "CallExpression", - "start": 6610, - "end": 6766, + "start": 7060, + "end": 7216, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 178, + "line": 197, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 6610, - "end": 6736, + "start": 7060, + "end": 7186, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 178, + "line": 197, "column": 17 } }, "object": { "type": "CallExpression", - "start": 6610, - "end": 6662, + "start": 7060, + "end": 7112, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 177, + "line": 196, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 6610, - "end": 6641, + "start": 7060, + "end": 7091, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 177, + "line": 196, "column": 14 } }, "object": { "type": "CallExpression", - "start": 6610, - "end": 6626, + "start": 7060, + "end": 7076, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 24 } }, "callee": { "type": "MemberExpression", - "start": 6610, - "end": 6620, + "start": 7060, + "end": 7070, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 18 } }, "object": { "type": "Identifier", - "start": 6610, - "end": 6615, + "start": 7060, + "end": 7065, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 13 }, "identifierName": "Array" @@ -30921,15 +32242,15 @@ }, "property": { "type": "Identifier", - "start": 6616, - "end": 6620, + "start": 7066, + "end": 7070, "loc": { "start": { - "line": 176, + "line": 195, "column": 14 }, "end": { - "line": 176, + "line": 195, "column": 18 }, "identifierName": "from" @@ -30941,15 +32262,15 @@ "arguments": [ { "type": "Identifier", - "start": 6621, - "end": 6625, + "start": 7071, + "end": 7075, "loc": { "start": { - "line": 176, + "line": 195, "column": 19 }, "end": { - "line": 176, + "line": 195, "column": 23 }, "identifierName": "arcs" @@ -30960,15 +32281,15 @@ }, "property": { "type": "Identifier", - "start": 6638, - "end": 6641, + "start": 7088, + "end": 7091, "loc": { "start": { - "line": 177, + "line": 196, "column": 11 }, "end": { - "line": 177, + "line": 196, "column": 14 }, "identifierName": "map" @@ -30980,15 +32301,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6642, - "end": 6661, + "start": 7092, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 15 }, "end": { - "line": 177, + "line": 196, "column": 34 } }, @@ -30999,15 +32320,15 @@ "params": [ { "type": "Identifier", - "start": 6642, - "end": 6645, + "start": 7092, + "end": 7095, "loc": { "start": { - "line": 177, + "line": 196, "column": 15 }, "end": { - "line": 177, + "line": 196, "column": 18 }, "identifierName": "arc" @@ -31017,43 +32338,43 @@ ], "body": { "type": "MemberExpression", - "start": 6649, - "end": 6661, + "start": 7099, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 34 } }, "object": { "type": "MemberExpression", - "start": 6649, - "end": 6655, + "start": 7099, + "end": 7105, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 28 } }, "object": { "type": "Identifier", - "start": 6649, - "end": 6652, + "start": 7099, + "end": 7102, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 25 }, "identifierName": "arc" @@ -31062,15 +32383,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6653, - "end": 6654, + "start": 7103, + "end": 7104, "loc": { "start": { - "line": 177, + "line": 196, "column": 26 }, "end": { - "line": 177, + "line": 196, "column": 27 } }, @@ -31084,15 +32405,15 @@ }, "property": { "type": "Identifier", - "start": 6656, - "end": 6661, + "start": 7106, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 29 }, "end": { - "line": 177, + "line": 196, "column": 34 }, "identifierName": "label" @@ -31107,15 +32428,15 @@ { "type": "CommentLine", "value": " Retrieve the label of the parent vertex in this arc.", - "start": 6663, - "end": 6718, + "start": 7113, + "end": 7168, "loc": { "start": { - "line": 177, + "line": 196, "column": 36 }, "end": { - "line": 177, + "line": 196, "column": 91 } } @@ -31124,15 +32445,15 @@ }, "property": { "type": "Identifier", - "start": 6730, - "end": 6736, + "start": 7180, + "end": 7186, "loc": { "start": { - "line": 178, + "line": 197, "column": 11 }, "end": { - "line": 178, + "line": 197, "column": 17 }, "identifierName": "filter" @@ -31142,15 +32463,15 @@ { "type": "CommentLine", "value": " Retrieve the label of the parent vertex in this arc.", - "start": 6663, - "end": 6718, + "start": 7113, + "end": 7168, "loc": { "start": { - "line": 177, + "line": 196, "column": 36 }, "end": { - "line": 177, + "line": 196, "column": 91 } } @@ -31162,15 +32483,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6737, - "end": 6765, + "start": 7187, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 18 }, "end": { - "line": 178, + "line": 197, "column": 46 } }, @@ -31181,15 +32502,15 @@ "params": [ { "type": "Identifier", - "start": 6737, - "end": 6742, + "start": 7187, + "end": 7192, "loc": { "start": { - "line": 178, + "line": 197, "column": 18 }, "end": { - "line": 178, + "line": 197, "column": 23 }, "identifierName": "label" @@ -31199,29 +32520,29 @@ ], "body": { "type": "BinaryExpression", - "start": 6746, - "end": 6765, + "start": 7196, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 27 }, "end": { - "line": 178, + "line": 197, "column": 46 } }, "left": { "type": "Identifier", - "start": 6746, - "end": 6751, + "start": 7196, + "end": 7201, "loc": { "start": { - "line": 178, + "line": 197, "column": 27 }, "end": { - "line": 178, + "line": 197, "column": 32 }, "identifierName": "label" @@ -31231,15 +32552,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 6756, - "end": 6765, + "start": 7206, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 37 }, "end": { - "line": 178, + "line": 197, "column": 46 }, "identifierName": "undefined" @@ -31259,15 +32580,15 @@ { "type": "CommentLine", "value": " Return the internal nodes (those with atleast one child).", - "start": 6508, - "end": 6568, + "start": 6958, + "end": 7018, "loc": { "start": { - "line": 174, + "line": 193, "column": 6 }, "end": { - "line": 174, + "line": 193, "column": 66 } } @@ -31281,43 +32602,43 @@ }, { "type": "IfStatement", - "start": 6788, - "end": 7556, + "start": 7238, + "end": 8006, "loc": { "start": { - "line": 182, + "line": 201, "column": 4 }, "end": { - "line": 196, + "line": 215, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6792, - "end": 6815, + "start": 7242, + "end": 7265, "loc": { "start": { - "line": 182, + "line": 201, "column": 8 }, "end": { - "line": 182, + "line": 201, "column": 31 } }, "left": { "type": "Identifier", - "start": 6792, - "end": 6800, + "start": 7242, + "end": 7250, "loc": { "start": { - "line": 182, + "line": 201, "column": 8 }, "end": { - "line": 182, + "line": 201, "column": 16 }, "identifierName": "nodeType" @@ -31327,15 +32648,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 6805, - "end": 6815, + "start": 7255, + "end": 7265, "loc": { "start": { - "line": 182, + "line": 201, "column": 21 }, "end": { - "line": 182, + "line": 201, "column": 31 } }, @@ -31348,59 +32669,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6817, - "end": 7556, + "start": 7267, + "end": 8006, "loc": { "start": { - "line": 182, + "line": 201, "column": 33 }, "end": { - "line": 196, + "line": 215, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 7366, - "end": 7411, + "start": 7816, + "end": 7861, "loc": { "start": { - "line": 192, + "line": 211, "column": 6 }, "end": { - "line": 192, + "line": 211, "column": 51 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7372, - "end": 7410, + "start": 7822, + "end": 7860, "loc": { "start": { - "line": 192, + "line": 211, "column": 12 }, "end": { - "line": 192, + "line": 211, "column": 50 } }, "id": { "type": "Identifier", - "start": 7372, - "end": 7381, + "start": 7822, + "end": 7831, "loc": { "start": { - "line": 192, + "line": 211, "column": 12 }, "end": { - "line": 192, + "line": 211, "column": 21 }, "identifierName": "allLabels" @@ -31410,58 +32731,58 @@ }, "init": { "type": "CallExpression", - "start": 7384, - "end": 7410, + "start": 7834, + "end": 7860, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 50 } }, "callee": { "type": "MemberExpression", - "start": 7384, - "end": 7402, + "start": 7834, + "end": 7852, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 42 } }, "object": { "type": "ThisExpression", - "start": 7384, - "end": 7388, + "start": 7834, + "end": 7838, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 28 } } }, "property": { "type": "Identifier", - "start": 7389, - "end": 7402, + "start": 7839, + "end": 7852, "loc": { "start": { - "line": 192, + "line": 211, "column": 29 }, "end": { - "line": 192, + "line": 211, "column": 42 }, "identifierName": "getNodeLabels" @@ -31473,15 +32794,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 7403, - "end": 7409, + "start": 7853, + "end": 7859, "loc": { "start": { - "line": 192, + "line": 211, "column": 43 }, "end": { - "line": 192, + "line": 211, "column": 49 } }, @@ -31501,15 +32822,15 @@ { "type": "CommentLine", "value": " Return the terminal nodes. This would require calculating the children", - "start": 6825, - "end": 6898, + "start": 7275, + "end": 7348, "loc": { "start": { - "line": 183, + "line": 202, "column": 6 }, "end": { - "line": 183, + "line": 202, "column": 79 } } @@ -31517,15 +32838,15 @@ { "type": "CommentLine", "value": " of every vertex in the graph and then identifying vertices without any", - "start": 6905, - "end": 6978, + "start": 7355, + "end": 7428, "loc": { "start": { - "line": 184, + "line": 203, "column": 6 }, "end": { - "line": 184, + "line": 203, "column": 79 } } @@ -31533,15 +32854,15 @@ { "type": "CommentLine", "value": " children.", - "start": 6985, - "end": 6997, + "start": 7435, + "end": 7447, "loc": { "start": { - "line": 185, + "line": 204, "column": 6 }, "end": { - "line": 185, + "line": 204, "column": 18 } } @@ -31549,15 +32870,15 @@ { "type": "CommentLine", "value": "", - "start": 7004, - "end": 7006, + "start": 7454, + "end": 7456, "loc": { "start": { - "line": 186, + "line": 205, "column": 6 }, "end": { - "line": 186, + "line": 205, "column": 8 } } @@ -31565,15 +32886,15 @@ { "type": "CommentLine", "value": " A quicker and dirtier way to do this is by removing internal labels", - "start": 7013, - "end": 7083, + "start": 7463, + "end": 7533, "loc": { "start": { - "line": 187, + "line": 206, "column": 6 }, "end": { - "line": 187, + "line": 206, "column": 76 } } @@ -31581,15 +32902,15 @@ { "type": "CommentLine", "value": " from the list of all node labels. This will report an incorrect result", - "start": 7090, - "end": 7163, + "start": 7540, + "end": 7613, "loc": { "start": { - "line": 188, + "line": 207, "column": 6 }, "end": { - "line": 188, + "line": 207, "column": 79 } } @@ -31597,15 +32918,15 @@ { "type": "CommentLine", "value": " if an internal node has the same label as a terminal node, but at that", - "start": 7170, - "end": 7243, + "start": 7620, + "end": 7693, "loc": { "start": { - "line": 189, + "line": 208, "column": 6 }, "end": { - "line": 189, + "line": 208, "column": 79 } } @@ -31613,15 +32934,15 @@ { "type": "CommentLine", "value": " point a lot of other assumptions are going to fail, too, so this is", - "start": 7250, - "end": 7320, + "start": 7700, + "end": 7770, "loc": { "start": { - "line": 190, + "line": 209, "column": 6 }, "end": { - "line": 190, + "line": 209, "column": 76 } } @@ -31629,15 +32950,15 @@ { "type": "CommentLine", "value": " probably good enough for now.", - "start": 7327, - "end": 7359, + "start": 7777, + "end": 7809, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 38 } } @@ -31646,44 +32967,44 @@ }, { "type": "VariableDeclaration", - "start": 7418, - "end": 7481, + "start": 7868, + "end": 7931, "loc": { "start": { - "line": 193, + "line": 212, "column": 6 }, "end": { - "line": 193, + "line": 212, "column": 69 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7424, - "end": 7480, + "start": 7874, + "end": 7930, "loc": { "start": { - "line": 193, + "line": 212, "column": 12 }, "end": { - "line": 193, + "line": 212, "column": 68 } }, "id": { "type": "Identifier", - "start": 7424, - "end": 7438, + "start": 7874, + "end": 7888, "loc": { "start": { - "line": 193, + "line": 212, "column": 12 }, "end": { - "line": 193, + "line": 212, "column": 26 }, "identifierName": "internalLabels" @@ -31692,29 +33013,29 @@ }, "init": { "type": "NewExpression", - "start": 7441, - "end": 7480, + "start": 7891, + "end": 7930, "loc": { "start": { - "line": 193, + "line": 212, "column": 29 }, "end": { - "line": 193, + "line": 212, "column": 68 } }, "callee": { "type": "Identifier", - "start": 7445, - "end": 7448, + "start": 7895, + "end": 7898, "loc": { "start": { - "line": 193, + "line": 212, "column": 33 }, "end": { - "line": 193, + "line": 212, "column": 36 }, "identifierName": "Set" @@ -31724,58 +33045,58 @@ "arguments": [ { "type": "CallExpression", - "start": 7449, - "end": 7479, + "start": 7899, + "end": 7929, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 7449, - "end": 7467, + "start": 7899, + "end": 7917, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 55 } }, "object": { "type": "ThisExpression", - "start": 7449, - "end": 7453, + "start": 7899, + "end": 7903, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 41 } } }, "property": { "type": "Identifier", - "start": 7454, - "end": 7467, + "start": 7904, + "end": 7917, "loc": { "start": { - "line": 193, + "line": 212, "column": 42 }, "end": { - "line": 193, + "line": 212, "column": 55 }, "identifierName": "getNodeLabels" @@ -31787,15 +33108,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 7468, - "end": 7478, + "start": 7918, + "end": 7928, "loc": { "start": { - "line": 193, + "line": 212, "column": 56 }, "end": { - "line": 193, + "line": 212, "column": 66 } }, @@ -31815,57 +33136,57 @@ }, { "type": "ReturnStatement", - "start": 7489, - "end": 7550, + "start": 7939, + "end": 8000, "loc": { "start": { - "line": 195, + "line": 214, "column": 6 }, "end": { - "line": 195, + "line": 214, "column": 67 } }, "argument": { "type": "CallExpression", - "start": 7496, - "end": 7549, + "start": 7946, + "end": 7999, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 66 } }, "callee": { "type": "MemberExpression", - "start": 7496, - "end": 7512, + "start": 7946, + "end": 7962, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 29 } }, "object": { "type": "Identifier", - "start": 7496, - "end": 7505, + "start": 7946, + "end": 7955, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 22 }, "identifierName": "allLabels" @@ -31874,15 +33195,15 @@ }, "property": { "type": "Identifier", - "start": 7506, - "end": 7512, + "start": 7956, + "end": 7962, "loc": { "start": { - "line": 195, + "line": 214, "column": 23 }, "end": { - "line": 195, + "line": 214, "column": 29 }, "identifierName": "filter" @@ -31894,15 +33215,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 7513, - "end": 7548, + "start": 7963, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 65 } }, @@ -31913,15 +33234,15 @@ "params": [ { "type": "Identifier", - "start": 7513, - "end": 7518, + "start": 7963, + "end": 7968, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 35 }, "identifierName": "label" @@ -31931,15 +33252,15 @@ ], "body": { "type": "UnaryExpression", - "start": 7522, - "end": 7548, + "start": 7972, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 39 }, "end": { - "line": 195, + "line": 214, "column": 65 } }, @@ -31947,43 +33268,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 7523, - "end": 7548, + "start": 7973, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 7523, - "end": 7541, + "start": 7973, + "end": 7991, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 58 } }, "object": { "type": "Identifier", - "start": 7523, - "end": 7537, + "start": 7973, + "end": 7987, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 54 }, "identifierName": "internalLabels" @@ -31992,15 +33313,15 @@ }, "property": { "type": "Identifier", - "start": 7538, - "end": 7541, + "start": 7988, + "end": 7991, "loc": { "start": { - "line": 195, + "line": 214, "column": 55 }, "end": { - "line": 195, + "line": 214, "column": 58 }, "identifierName": "has" @@ -32012,15 +33333,15 @@ "arguments": [ { "type": "Identifier", - "start": 7542, - "end": 7547, + "start": 7992, + "end": 7997, "loc": { "start": { - "line": 195, + "line": 214, "column": 59 }, "end": { - "line": 195, + "line": 214, "column": 64 }, "identifierName": "label" @@ -32044,43 +33365,43 @@ }, { "type": "ThrowStatement", - "start": 7562, - "end": 7613, + "start": 8012, + "end": 8063, "loc": { "start": { - "line": 198, + "line": 217, "column": 4 }, "end": { - "line": 198, + "line": 217, "column": 55 } }, "argument": { "type": "NewExpression", - "start": 7568, - "end": 7612, + "start": 8018, + "end": 8062, "loc": { "start": { - "line": 198, + "line": 217, "column": 10 }, "end": { - "line": 198, + "line": 217, "column": 54 } }, "callee": { "type": "Identifier", - "start": 7572, - "end": 7577, + "start": 8022, + "end": 8027, "loc": { "start": { - "line": 198, + "line": 217, "column": 14 }, "end": { - "line": 198, + "line": 217, "column": 19 }, "identifierName": "Error" @@ -32090,30 +33411,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 7578, - "end": 7611, + "start": 8028, + "end": 8061, "loc": { "start": { - "line": 198, + "line": 217, "column": 20 }, "end": { - "line": 198, + "line": 217, "column": 53 } }, "expressions": [ { "type": "Identifier", - "start": 7600, - "end": 7608, + "start": 8050, + "end": 8058, "loc": { "start": { - "line": 198, + "line": 217, "column": 42 }, "end": { - "line": 198, + "line": 217, "column": 50 }, "identifierName": "nodeType" @@ -32124,15 +33445,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 7579, - "end": 7598, + "start": 8029, + "end": 8048, "loc": { "start": { - "line": 198, + "line": 217, "column": 21 }, "end": { - "line": 198, + "line": 217, "column": 40 } }, @@ -32144,15 +33465,15 @@ }, { "type": "TemplateElement", - "start": 7609, - "end": 7610, + "start": 8059, + "end": 8060, "loc": { "start": { - "line": 198, + "line": 217, "column": 51 }, "end": { - "line": 198, + "line": 217, "column": 52 } }, @@ -32175,15 +33496,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", - "start": 7621, - "end": 7998, + "start": 8071, + "end": 8448, "loc": { "start": { - "line": 201, + "line": 220, "column": 2 }, "end": { - "line": 208, + "line": 227, "column": 5 } } @@ -32192,15 +33513,15 @@ }, { "type": "ClassMethod", - "start": 8001, - "end": 9155, + "start": 8451, + "end": 9605, "loc": { "start": { - "line": 209, + "line": 228, "column": 2 }, "end": { - "line": 234, + "line": 253, "column": 3 } }, @@ -32208,15 +33529,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8001, - "end": 8030, + "start": 8451, + "end": 8480, "loc": { "start": { - "line": 209, + "line": 228, "column": 2 }, "end": { - "line": 209, + "line": 228, "column": 31 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -32232,15 +33553,15 @@ "params": [ { "type": "Identifier", - "start": 8031, - "end": 8040, + "start": 8481, + "end": 8490, "loc": { "start": { - "line": 209, + "line": 228, "column": 32 }, "end": { - "line": 209, + "line": 228, "column": 41 }, "identifierName": "nodeLabel" @@ -32250,59 +33571,59 @@ ], "body": { "type": "BlockStatement", - "start": 8042, - "end": 9155, + "start": 8492, + "end": 9605, "loc": { "start": { - "line": 209, + "line": 228, "column": 43 }, "end": { - "line": 234, + "line": 253, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 8091, - "end": 8125, + "start": 8541, + "end": 8575, "loc": { "start": { - "line": 211, + "line": 230, "column": 4 }, "end": { - "line": 211, + "line": 230, "column": 38 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8095, - "end": 8124, + "start": 8545, + "end": 8574, "loc": { "start": { - "line": 211, + "line": 230, "column": 8 }, "end": { - "line": 211, + "line": 230, "column": 37 } }, "id": { "type": "Identifier", - "start": 8095, - "end": 8119, + "start": 8545, + "end": 8569, "loc": { "start": { - "line": 211, + "line": 230, "column": 8 }, "end": { - "line": 211, + "line": 230, "column": 32 }, "identifierName": "additionalNodeProperties" @@ -32312,15 +33633,15 @@ }, "init": { "type": "ObjectExpression", - "start": 8122, - "end": 8124, + "start": 8572, + "end": 8574, "loc": { "start": { - "line": 211, + "line": 230, "column": 35 }, "end": { - "line": 211, + "line": 230, "column": 37 } }, @@ -32334,15 +33655,15 @@ { "type": "CommentLine", "value": " Look up additional node properties.", - "start": 8048, - "end": 8086, + "start": 8498, + "end": 8536, "loc": { "start": { - "line": 210, + "line": 229, "column": 4 }, "end": { - "line": 210, + "line": 229, "column": 42 } } @@ -32351,57 +33672,57 @@ }, { "type": "IfStatement", - "start": 8130, - "end": 8352, + "start": 8580, + "end": 8802, "loc": { "start": { - "line": 212, + "line": 231, "column": 4 }, "end": { - "line": 217, + "line": 236, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 8141, - "end": 8253, + "start": 8591, + "end": 8703, "loc": { "start": { - "line": 213, + "line": 232, "column": 6 }, "end": { - "line": 214, + "line": 233, "column": 64 } }, "left": { "type": "CallExpression", - "start": 8141, - "end": 8188, + "start": 8591, + "end": 8638, "loc": { "start": { - "line": 213, + "line": 232, "column": 6 }, "end": { - "line": 213, + "line": 232, "column": 53 } }, "callee": { "type": "Identifier", - "start": 8141, - "end": 8144, + "start": 8591, + "end": 8594, "loc": { "start": { - "line": 213, + "line": 232, "column": 6 }, "end": { - "line": 213, + "line": 232, "column": 9 }, "identifierName": "has" @@ -32411,44 +33732,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 8145, - "end": 8159, + "start": 8595, + "end": 8609, "loc": { "start": { - "line": 213, + "line": 232, "column": 10 }, "end": { - "line": 213, + "line": 232, "column": 24 } }, "object": { "type": "ThisExpression", - "start": 8145, - "end": 8149, + "start": 8595, + "end": 8599, "loc": { "start": { - "line": 213, + "line": 232, "column": 10 }, "end": { - "line": 213, + "line": 232, "column": 14 } } }, "property": { "type": "Identifier", - "start": 8150, - "end": 8159, + "start": 8600, + "end": 8609, "loc": { "start": { - "line": 213, + "line": 232, "column": 15 }, "end": { - "line": 213, + "line": 232, "column": 24 }, "identifierName": "phylogeny" @@ -32459,15 +33780,15 @@ }, { "type": "StringLiteral", - "start": 8161, - "end": 8187, + "start": 8611, + "end": 8637, "loc": { "start": { - "line": 213, + "line": 232, "column": 26 }, "end": { - "line": 213, + "line": 232, "column": 52 } }, @@ -32482,29 +33803,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 8198, - "end": 8253, + "start": 8648, + "end": 8703, "loc": { "start": { - "line": 214, + "line": 233, "column": 9 }, "end": { - "line": 214, + "line": 233, "column": 64 } }, "callee": { "type": "Identifier", - "start": 8198, - "end": 8201, + "start": 8648, + "end": 8651, "loc": { "start": { - "line": 214, + "line": 233, "column": 9 }, "end": { - "line": 214, + "line": 233, "column": 12 }, "identifierName": "has" @@ -32514,58 +33835,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 8202, - "end": 8241, + "start": 8652, + "end": 8691, "loc": { "start": { - "line": 214, + "line": 233, "column": 13 }, "end": { - "line": 214, + "line": 233, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 8202, - "end": 8216, + "start": 8652, + "end": 8666, "loc": { "start": { - "line": 214, + "line": 233, "column": 13 }, "end": { - "line": 214, + "line": 233, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 8202, - "end": 8206, + "start": 8652, + "end": 8656, "loc": { "start": { - "line": 214, + "line": 233, "column": 13 }, "end": { - "line": 214, + "line": 233, "column": 17 } } }, "property": { "type": "Identifier", - "start": 8207, - "end": 8216, + "start": 8657, + "end": 8666, "loc": { "start": { - "line": 214, + "line": 233, "column": 18 }, "end": { - "line": 214, + "line": 233, "column": 27 }, "identifierName": "phylogeny" @@ -32576,15 +33897,15 @@ }, "property": { "type": "Identifier", - "start": 8217, - "end": 8241, + "start": 8667, + "end": 8691, "loc": { "start": { - "line": 214, + "line": 233, "column": 28 }, "end": { - "line": 214, + "line": 233, "column": 52 }, "identifierName": "additionalNodeProperties" @@ -32595,15 +33916,15 @@ }, { "type": "Identifier", - "start": 8243, - "end": 8252, + "start": 8693, + "end": 8702, "loc": { "start": { - "line": 214, + "line": 233, "column": 54 }, "end": { - "line": 214, + "line": 233, "column": 63 }, "identifierName": "nodeLabel" @@ -32615,59 +33936,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 8260, - "end": 8352, + "start": 8710, + "end": 8802, "loc": { "start": { - "line": 215, + "line": 234, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 8268, - "end": 8346, + "start": 8718, + "end": 8796, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 84 } }, "expression": { "type": "AssignmentExpression", - "start": 8268, - "end": 8345, + "start": 8718, + "end": 8795, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 83 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8268, - "end": 8292, + "start": 8718, + "end": 8742, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 30 }, "identifierName": "additionalNodeProperties" @@ -32676,72 +33997,72 @@ }, "right": { "type": "MemberExpression", - "start": 8295, - "end": 8345, + "start": 8745, + "end": 8795, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 83 } }, "object": { "type": "MemberExpression", - "start": 8295, - "end": 8334, + "start": 8745, + "end": 8784, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 72 } }, "object": { "type": "MemberExpression", - "start": 8295, - "end": 8309, + "start": 8745, + "end": 8759, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 8295, - "end": 8299, + "start": 8745, + "end": 8749, "loc": { "start": { - "line": 216, + "line": 235, "column": 33 }, "end": { - "line": 216, + "line": 235, "column": 37 } } }, "property": { "type": "Identifier", - "start": 8300, - "end": 8309, + "start": 8750, + "end": 8759, "loc": { "start": { - "line": 216, + "line": 235, "column": 38 }, "end": { - "line": 216, + "line": 235, "column": 47 }, "identifierName": "phylogeny" @@ -32752,15 +34073,15 @@ }, "property": { "type": "Identifier", - "start": 8310, - "end": 8334, + "start": 8760, + "end": 8784, "loc": { "start": { - "line": 216, + "line": 235, "column": 48 }, "end": { - "line": 216, + "line": 235, "column": 72 }, "identifierName": "additionalNodeProperties" @@ -32771,15 +34092,15 @@ }, "property": { "type": "Identifier", - "start": 8335, - "end": 8344, + "start": 8785, + "end": 8794, "loc": { "start": { - "line": 216, + "line": 235, "column": 73 }, "end": { - "line": 216, + "line": 235, "column": 82 }, "identifierName": "nodeLabel" @@ -32799,15 +34120,15 @@ { "type": "CommentLine", "value": " If there are explicit taxonomic units in the", - "start": 8358, - "end": 8405, + "start": 8808, + "end": 8855, "loc": { "start": { - "line": 219, + "line": 238, "column": 4 }, "end": { - "line": 219, + "line": 238, "column": 51 } } @@ -32815,15 +34136,15 @@ { "type": "CommentLine", "value": " representsTaxonomicUnits property, we need to use those.", - "start": 8410, - "end": 8469, + "start": 8860, + "end": 8919, "loc": { "start": { - "line": 220, + "line": 239, "column": 4 }, "end": { - "line": 220, + "line": 239, "column": 63 } } @@ -32832,43 +34153,43 @@ }, { "type": "IfStatement", - "start": 8474, - "end": 8608, + "start": 8924, + "end": 9058, "loc": { "start": { - "line": 221, + "line": 240, "column": 4 }, "end": { - "line": 223, + "line": 242, "column": 5 } }, "test": { "type": "CallExpression", - "start": 8478, - "end": 8535, + "start": 8928, + "end": 8985, "loc": { "start": { - "line": 221, + "line": 240, "column": 8 }, "end": { - "line": 221, + "line": 240, "column": 65 } }, "callee": { "type": "Identifier", - "start": 8478, - "end": 8481, + "start": 8928, + "end": 8931, "loc": { "start": { - "line": 221, + "line": 240, "column": 8 }, "end": { - "line": 221, + "line": 240, "column": 11 }, "identifierName": "has" @@ -32879,15 +34200,15 @@ "arguments": [ { "type": "Identifier", - "start": 8482, - "end": 8506, + "start": 8932, + "end": 8956, "loc": { "start": { - "line": 221, + "line": 240, "column": 12 }, "end": { - "line": 221, + "line": 240, "column": 36 }, "identifierName": "additionalNodeProperties" @@ -32896,15 +34217,15 @@ }, { "type": "StringLiteral", - "start": 8508, - "end": 8534, + "start": 8958, + "end": 8984, "loc": { "start": { - "line": 221, + "line": 240, "column": 38 }, "end": { - "line": 221, + "line": 240, "column": 64 } }, @@ -32919,58 +34240,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 8537, - "end": 8608, + "start": 8987, + "end": 9058, "loc": { "start": { - "line": 221, + "line": 240, "column": 67 }, "end": { - "line": 223, + "line": 242, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 8545, - "end": 8602, + "start": 8995, + "end": 9052, "loc": { "start": { - "line": 222, + "line": 241, "column": 6 }, "end": { - "line": 222, + "line": 241, "column": 63 } }, "argument": { "type": "MemberExpression", - "start": 8552, - "end": 8601, + "start": 9002, + "end": 9051, "loc": { "start": { - "line": 222, + "line": 241, "column": 13 }, "end": { - "line": 222, + "line": 241, "column": 62 } }, "object": { "type": "Identifier", - "start": 8552, - "end": 8576, + "start": 9002, + "end": 9026, "loc": { "start": { - "line": 222, + "line": 241, "column": 13 }, "end": { - "line": 222, + "line": 241, "column": 37 }, "identifierName": "additionalNodeProperties" @@ -32979,15 +34300,15 @@ }, "property": { "type": "Identifier", - "start": 8577, - "end": 8601, + "start": 9027, + "end": 9051, "loc": { "start": { - "line": 222, + "line": 241, "column": 38 }, "end": { - "line": 222, + "line": 241, "column": 62 }, "identifierName": "representsTaxonomicUnits" @@ -33006,15 +34327,15 @@ { "type": "CommentLine", "value": " If there are explicit taxonomic units in the", - "start": 8358, - "end": 8405, + "start": 8808, + "end": 8855, "loc": { "start": { - "line": 219, + "line": 238, "column": 4 }, "end": { - "line": 219, + "line": 238, "column": 51 } } @@ -33022,15 +34343,15 @@ { "type": "CommentLine", "value": " representsTaxonomicUnits property, we need to use those.", - "start": 8410, - "end": 8469, + "start": 8860, + "end": 8919, "loc": { "start": { - "line": 220, + "line": 239, "column": 4 }, "end": { - "line": 220, + "line": 239, "column": 63 } } @@ -33040,15 +34361,15 @@ { "type": "CommentLine", "value": " If that doesn't work, we can try to extract scientific names from", - "start": 8614, - "end": 8682, + "start": 9064, + "end": 9132, "loc": { "start": { - "line": 225, + "line": 244, "column": 4 }, "end": { - "line": 225, + "line": 244, "column": 72 } } @@ -33056,15 +34377,15 @@ { "type": "CommentLine", "value": " the node label. Note that taxonomic units will NOT be extracted from", - "start": 8687, - "end": 8758, + "start": 9137, + "end": 9208, "loc": { "start": { - "line": 226, + "line": 245, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 75 } } @@ -33072,15 +34393,15 @@ { "type": "CommentLine", "value": " the label if there is a taxonomic unit present!", - "start": 8763, - "end": 8813, + "start": 9213, + "end": 9263, "loc": { "start": { - "line": 227, + "line": 246, "column": 4 }, "end": { - "line": 227, + "line": 246, "column": 54 } } @@ -33088,15 +34409,15 @@ { "type": "CommentLine", "value": "", - "start": 8818, - "end": 8820, + "start": 9268, + "end": 9270, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 6 } } @@ -33104,15 +34425,15 @@ { "type": "CommentLine", "value": " Note that old-style taxonomic units were lists while new-style taxonomic", - "start": 8825, - "end": 8900, + "start": 9275, + "end": 9350, "loc": { "start": { - "line": 229, + "line": 248, "column": 4 }, "end": { - "line": 229, + "line": 248, "column": 79 } } @@ -33120,15 +34441,15 @@ { "type": "CommentLine", "value": " units are single objects. So we turn it into a single entry list here.", - "start": 8905, - "end": 8978, + "start": 9355, + "end": 9428, "loc": { "start": { - "line": 230, + "line": 249, "column": 4 }, "end": { - "line": 230, + "line": 249, "column": 77 } } @@ -33137,44 +34458,44 @@ }, { "type": "VariableDeclaration", - "start": 8983, - "end": 9069, + "start": 9433, + "end": 9519, "loc": { "start": { - "line": 231, + "line": 250, "column": 4 }, "end": { - "line": 231, + "line": 250, "column": 90 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8989, - "end": 9068, + "start": 9439, + "end": 9518, "loc": { "start": { - "line": 231, + "line": 250, "column": 10 }, "end": { - "line": 231, + "line": 250, "column": 89 } }, "id": { "type": "Identifier", - "start": 8989, - "end": 8994, + "start": 9439, + "end": 9444, "loc": { "start": { - "line": 231, + "line": 250, "column": 10 }, "end": { - "line": 231, + "line": 250, "column": 15 }, "identifierName": "tunit" @@ -33184,43 +34505,43 @@ }, "init": { "type": "CallExpression", - "start": 8997, - "end": 9068, + "start": 9447, + "end": 9518, "loc": { "start": { - "line": 231, + "line": 250, "column": 18 }, "end": { - "line": 231, + "line": 250, "column": 89 } }, "callee": { "type": "MemberExpression", - "start": 8997, - "end": 9027, + "start": 9447, + "end": 9477, "loc": { "start": { - "line": 231, + "line": 250, "column": 18 }, "end": { - "line": 231, + "line": 250, "column": 48 } }, "object": { "type": "Identifier", - "start": 8997, - "end": 9017, + "start": 9447, + "end": 9467, "loc": { "start": { - "line": 231, + "line": 250, "column": 18 }, "end": { - "line": 231, + "line": 250, "column": 38 }, "identifierName": "TaxonomicUnitWrapper" @@ -33229,15 +34550,15 @@ }, "property": { "type": "Identifier", - "start": 9018, - "end": 9027, + "start": 9468, + "end": 9477, "loc": { "start": { - "line": 231, + "line": 250, "column": 39 }, "end": { - "line": 231, + "line": 250, "column": 48 }, "identifierName": "fromLabel" @@ -33249,43 +34570,43 @@ "arguments": [ { "type": "CallExpression", - "start": 9028, - "end": 9044, + "start": 9478, + "end": 9494, "loc": { "start": { - "line": 231, + "line": 250, "column": 49 }, "end": { - "line": 231, + "line": 250, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 9028, - "end": 9042, + "start": 9478, + "end": 9492, "loc": { "start": { - "line": 231, + "line": 250, "column": 49 }, "end": { - "line": 231, + "line": 250, "column": 63 } }, "object": { "type": "Identifier", - "start": 9028, - "end": 9037, + "start": 9478, + "end": 9487, "loc": { "start": { - "line": 231, + "line": 250, "column": 49 }, "end": { - "line": 231, + "line": 250, "column": 58 }, "identifierName": "nodeLabel" @@ -33294,15 +34615,15 @@ }, "property": { "type": "Identifier", - "start": 9038, - "end": 9042, + "start": 9488, + "end": 9492, "loc": { "start": { - "line": 231, + "line": 250, "column": 59 }, "end": { - "line": 231, + "line": 250, "column": 63 }, "identifierName": "trim" @@ -33315,44 +34636,44 @@ }, { "type": "MemberExpression", - "start": 9046, - "end": 9067, + "start": 9496, + "end": 9517, "loc": { "start": { - "line": 231, + "line": 250, "column": 67 }, "end": { - "line": 231, + "line": 250, "column": 88 } }, "object": { "type": "ThisExpression", - "start": 9046, - "end": 9050, + "start": 9496, + "end": 9500, "loc": { "start": { - "line": 231, + "line": 250, "column": 67 }, "end": { - "line": 231, + "line": 250, "column": 71 } } }, "property": { "type": "Identifier", - "start": 9051, - "end": 9067, + "start": 9501, + "end": 9517, "loc": { "start": { - "line": 231, + "line": 250, "column": 72 }, "end": { - "line": 231, + "line": 250, "column": 88 }, "identifierName": "defaultNomenCode" @@ -33371,15 +34692,15 @@ { "type": "CommentLine", "value": " If that doesn't work, we can try to extract scientific names from", - "start": 8614, - "end": 8682, + "start": 9064, + "end": 9132, "loc": { "start": { - "line": 225, + "line": 244, "column": 4 }, "end": { - "line": 225, + "line": 244, "column": 72 } } @@ -33387,15 +34708,15 @@ { "type": "CommentLine", "value": " the node label. Note that taxonomic units will NOT be extracted from", - "start": 8687, - "end": 8758, + "start": 9137, + "end": 9208, "loc": { "start": { - "line": 226, + "line": 245, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 75 } } @@ -33403,15 +34724,15 @@ { "type": "CommentLine", "value": " the label if there is a taxonomic unit present!", - "start": 8763, - "end": 8813, + "start": 9213, + "end": 9263, "loc": { "start": { - "line": 227, + "line": 246, "column": 4 }, "end": { - "line": 227, + "line": 246, "column": 54 } } @@ -33419,15 +34740,15 @@ { "type": "CommentLine", "value": "", - "start": 8818, - "end": 8820, + "start": 9268, + "end": 9270, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 6 } } @@ -33435,15 +34756,15 @@ { "type": "CommentLine", "value": " Note that old-style taxonomic units were lists while new-style taxonomic", - "start": 8825, - "end": 8900, + "start": 9275, + "end": 9350, "loc": { "start": { - "line": 229, + "line": 248, "column": 4 }, "end": { - "line": 229, + "line": 248, "column": 79 } } @@ -33451,15 +34772,15 @@ { "type": "CommentLine", "value": " units are single objects. So we turn it into a single entry list here.", - "start": 8905, - "end": 8978, + "start": 9355, + "end": 9428, "loc": { "start": { - "line": 230, + "line": 249, "column": 4 }, "end": { - "line": 230, + "line": 249, "column": 77 } } @@ -33468,29 +34789,29 @@ }, { "type": "IfStatement", - "start": 9074, - "end": 9100, + "start": 9524, + "end": 9550, "loc": { "start": { - "line": 232, + "line": 251, "column": 4 }, "end": { - "line": 232, + "line": 251, "column": 30 } }, "test": { "type": "Identifier", - "start": 9078, - "end": 9083, + "start": 9528, + "end": 9533, "loc": { "start": { - "line": 232, + "line": 251, "column": 8 }, "end": { - "line": 232, + "line": 251, "column": 13 }, "identifierName": "tunit" @@ -33499,44 +34820,44 @@ }, "consequent": { "type": "ReturnStatement", - "start": 9085, - "end": 9100, + "start": 9535, + "end": 9550, "loc": { "start": { - "line": 232, + "line": 251, "column": 15 }, "end": { - "line": 232, + "line": 251, "column": 30 } }, "argument": { "type": "ArrayExpression", - "start": 9092, - "end": 9099, + "start": 9542, + "end": 9549, "loc": { "start": { - "line": 232, + "line": 251, "column": 22 }, "end": { - "line": 232, + "line": 251, "column": 29 } }, "elements": [ { "type": "Identifier", - "start": 9093, - "end": 9098, + "start": 9543, + "end": 9548, "loc": { "start": { - "line": 232, + "line": 251, "column": 23 }, "end": { - "line": 232, + "line": 251, "column": 28 }, "identifierName": "tunit" @@ -33550,29 +34871,29 @@ }, { "type": "ReturnStatement", - "start": 9105, - "end": 9115, + "start": 9555, + "end": 9565, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 14 } }, "argument": { "type": "ArrayExpression", - "start": 9112, - "end": 9114, + "start": 9562, + "end": 9564, "loc": { "start": { - "line": 233, + "line": 252, "column": 11 }, "end": { - "line": 233, + "line": 252, "column": 13 } }, @@ -33582,15 +34903,15 @@ { "type": "CommentLine", "value": " No TUnit? Return the empty list.", - "start": 9116, - "end": 9151, + "start": 9566, + "end": 9601, "loc": { "start": { - "line": 233, + "line": 252, "column": 15 }, "end": { - "line": 233, + "line": 252, "column": 50 } } @@ -33604,15 +34925,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", - "start": 7621, - "end": 7998, + "start": 8071, + "end": 8448, "loc": { "start": { - "line": 201, + "line": 220, "column": 2 }, "end": { - "line": 208, + "line": 227, "column": 5 } } @@ -33621,15 +34942,15 @@ }, { "type": "ClassMethod", - "start": 9159, - "end": 9756, + "start": 9609, + "end": 10206, "loc": { "start": { - "line": 236, + "line": 255, "column": 2 }, "end": { - "line": 251, + "line": 270, "column": 3 } }, @@ -33637,15 +34958,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9159, - "end": 9190, + "start": 9609, + "end": 9640, "loc": { "start": { - "line": 236, + "line": 255, "column": 2 }, "end": { - "line": 236, + "line": 255, "column": 33 }, "identifierName": "getNodeLabelsMatchedBySpecifier" @@ -33660,15 +34981,15 @@ "params": [ { "type": "Identifier", - "start": 9191, - "end": 9200, + "start": 9641, + "end": 9650, "loc": { "start": { - "line": 236, + "line": 255, "column": 34 }, "end": { - "line": 236, + "line": 255, "column": 43 }, "identifierName": "specifier" @@ -33678,100 +34999,100 @@ ], "body": { "type": "BlockStatement", - "start": 9202, - "end": 9756, + "start": 9652, + "end": 10206, "loc": { "start": { - "line": 236, + "line": 255, "column": 45 }, "end": { - "line": 251, + "line": 270, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 9303, - "end": 9752, + "start": 9753, + "end": 10202, "loc": { "start": { - "line": 240, + "line": 259, "column": 4 }, "end": { - "line": 250, + "line": 269, "column": 7 } }, "argument": { "type": "CallExpression", - "start": 9310, - "end": 9751, + "start": 9760, + "end": 10201, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 250, + "line": 269, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 9310, - "end": 9337, + "start": 9760, + "end": 9787, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 38 } }, "object": { "type": "CallExpression", - "start": 9310, - "end": 9330, + "start": 9760, + "end": 9780, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 31 } }, "callee": { "type": "MemberExpression", - "start": 9310, - "end": 9328, + "start": 9760, + "end": 9778, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 29 } }, "object": { "type": "ThisExpression", - "start": 9310, - "end": 9314, + "start": 9760, + "end": 9764, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 15 } }, @@ -33779,15 +35100,15 @@ }, "property": { "type": "Identifier", - "start": 9315, - "end": 9328, + "start": 9765, + "end": 9778, "loc": { "start": { - "line": 240, + "line": 259, "column": 16 }, "end": { - "line": 240, + "line": 259, "column": 29 }, "identifierName": "getNodeLabels" @@ -33802,15 +35123,15 @@ }, "property": { "type": "Identifier", - "start": 9331, - "end": 9337, + "start": 9781, + "end": 9787, "loc": { "start": { - "line": 240, + "line": 259, "column": 32 }, "end": { - "line": 240, + "line": 259, "column": 38 }, "identifierName": "filter" @@ -33823,15 +35144,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 9338, - "end": 9750, + "start": 9788, + "end": 10200, "loc": { "start": { - "line": 240, + "line": 259, "column": 39 }, "end": { - "line": 250, + "line": 269, "column": 5 } }, @@ -33842,15 +35163,15 @@ "params": [ { "type": "Identifier", - "start": 9339, - "end": 9348, + "start": 9789, + "end": 9798, "loc": { "start": { - "line": 240, + "line": 259, "column": 40 }, "end": { - "line": 240, + "line": 259, "column": 49 }, "identifierName": "nodeLabel" @@ -33860,59 +35181,59 @@ ], "body": { "type": "BlockStatement", - "start": 9353, - "end": 9750, + "start": 9803, + "end": 10200, "loc": { "start": { - "line": 240, + "line": 259, "column": 54 }, "end": { - "line": 250, + "line": 269, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 9457, - "end": 9522, + "start": 9907, + "end": 9972, "loc": { "start": { - "line": 243, + "line": 262, "column": 6 }, "end": { - "line": 243, + "line": 262, "column": 71 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 9463, - "end": 9521, + "start": 9913, + "end": 9971, "loc": { "start": { - "line": 243, + "line": 262, "column": 12 }, "end": { - "line": 243, + "line": 262, "column": 70 } }, "id": { "type": "Identifier", - "start": 9463, - "end": 9473, + "start": 9913, + "end": 9923, "loc": { "start": { - "line": 243, + "line": 262, "column": 12 }, "end": { - "line": 243, + "line": 262, "column": 22 }, "identifierName": "nodeTUnits" @@ -33922,58 +35243,58 @@ }, "init": { "type": "CallExpression", - "start": 9476, - "end": 9521, + "start": 9926, + "end": 9971, "loc": { "start": { - "line": 243, + "line": 262, "column": 25 }, "end": { - "line": 243, + "line": 262, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 9476, - "end": 9510, + "start": 9926, + "end": 9960, "loc": { "start": { - "line": 243, + "line": 262, "column": 25 }, "end": { - "line": 243, + "line": 262, "column": 59 } }, "object": { "type": "ThisExpression", - "start": 9476, - "end": 9480, + "start": 9926, + "end": 9930, "loc": { "start": { - "line": 243, + "line": 262, "column": 25 }, "end": { - "line": 243, + "line": 262, "column": 29 } } }, "property": { "type": "Identifier", - "start": 9481, - "end": 9510, + "start": 9931, + "end": 9960, "loc": { "start": { - "line": 243, + "line": 262, "column": 30 }, "end": { - "line": 243, + "line": 262, "column": 59 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -33985,15 +35306,15 @@ "arguments": [ { "type": "Identifier", - "start": 9511, - "end": 9520, + "start": 9961, + "end": 9970, "loc": { "start": { - "line": 243, + "line": 262, "column": 60 }, "end": { - "line": 243, + "line": 262, "column": 69 }, "identifierName": "nodeLabel" @@ -34010,15 +35331,15 @@ { "type": "CommentLine", "value": " Find all the taxonomic units associated with the specifier and", - "start": 9361, - "end": 9426, + "start": 9811, + "end": 9876, "loc": { "start": { - "line": 241, + "line": 260, "column": 6 }, "end": { - "line": 241, + "line": 260, "column": 71 } } @@ -34026,15 +35347,15 @@ { "type": "CommentLine", "value": " with the node.", - "start": 9433, - "end": 9450, + "start": 9883, + "end": 9900, "loc": { "start": { - "line": 242, + "line": 261, "column": 6 }, "end": { - "line": 242, + "line": 261, "column": 23 } } @@ -34044,15 +35365,15 @@ { "type": "CommentLine", "value": " Attempt pairwise matches between taxonomic units in the specifier", - "start": 9530, - "end": 9598, + "start": 9980, + "end": 10048, "loc": { "start": { - "line": 245, + "line": 264, "column": 6 }, "end": { - "line": 245, + "line": 264, "column": 74 } } @@ -34060,15 +35381,15 @@ { "type": "CommentLine", "value": " and associated with the node.", - "start": 9605, - "end": 9637, + "start": 10055, + "end": 10087, "loc": { "start": { - "line": 246, + "line": 265, "column": 6 }, "end": { - "line": 246, + "line": 265, "column": 38 } } @@ -34077,57 +35398,57 @@ }, { "type": "ReturnStatement", - "start": 9644, - "end": 9744, + "start": 10094, + "end": 10194, "loc": { "start": { - "line": 247, + "line": 266, "column": 6 }, "end": { - "line": 249, + "line": 268, "column": 8 } }, "argument": { "type": "CallExpression", - "start": 9651, - "end": 9743, + "start": 10101, + "end": 10193, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 249, + "line": 268, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 9651, - "end": 9666, + "start": 10101, + "end": 10116, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 247, + "line": 266, "column": 28 } }, "object": { "type": "Identifier", - "start": 9651, - "end": 9661, + "start": 10101, + "end": 10111, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 247, + "line": 266, "column": 23 }, "identifierName": "nodeTUnits" @@ -34137,15 +35458,15 @@ }, "property": { "type": "Identifier", - "start": 9662, - "end": 9666, + "start": 10112, + "end": 10116, "loc": { "start": { - "line": 247, + "line": 266, "column": 24 }, "end": { - "line": 247, + "line": 266, "column": 28 }, "identifierName": "some" @@ -34158,15 +35479,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 9676, - "end": 9735, + "start": 10126, + "end": 10185, "loc": { "start": { - "line": 248, + "line": 267, "column": 8 }, "end": { - "line": 248, + "line": 267, "column": 67 } }, @@ -34177,15 +35498,15 @@ "params": [ { "type": "Identifier", - "start": 9676, - "end": 9681, + "start": 10126, + "end": 10131, "loc": { "start": { - "line": 248, + "line": 267, "column": 8 }, "end": { - "line": 248, + "line": 267, "column": 13 }, "identifierName": "tunit" @@ -34195,43 +35516,43 @@ ], "body": { "type": "MemberExpression", - "start": 9685, - "end": 9735, + "start": 10135, + "end": 10185, "loc": { "start": { - "line": 248, + "line": 267, "column": 17 }, "end": { - "line": 248, + "line": 267, "column": 67 } }, "object": { "type": "NewExpression", - "start": 9685, - "end": 9727, + "start": 10135, + "end": 10177, "loc": { "start": { - "line": 248, + "line": 267, "column": 17 }, "end": { - "line": 248, + "line": 267, "column": 59 } }, "callee": { "type": "Identifier", - "start": 9689, - "end": 9709, + "start": 10139, + "end": 10159, "loc": { "start": { - "line": 248, + "line": 267, "column": 21 }, "end": { - "line": 248, + "line": 267, "column": 41 }, "identifierName": "TaxonomicUnitMatcher" @@ -34241,15 +35562,15 @@ "arguments": [ { "type": "Identifier", - "start": 9710, - "end": 9719, + "start": 10160, + "end": 10169, "loc": { "start": { - "line": 248, + "line": 267, "column": 42 }, "end": { - "line": 248, + "line": 267, "column": 51 }, "identifierName": "specifier" @@ -34258,15 +35579,15 @@ }, { "type": "Identifier", - "start": 9721, - "end": 9726, + "start": 10171, + "end": 10176, "loc": { "start": { - "line": 248, + "line": 267, "column": 53 }, "end": { - "line": 248, + "line": 267, "column": 58 }, "identifierName": "tunit" @@ -34277,15 +35598,15 @@ }, "property": { "type": "Identifier", - "start": 9728, - "end": 9735, + "start": 10178, + "end": 10185, "loc": { "start": { - "line": 248, + "line": 267, "column": 60 }, "end": { - "line": 248, + "line": 267, "column": 67 }, "identifierName": "matched" @@ -34302,15 +35623,15 @@ { "type": "CommentLine", "value": " Attempt pairwise matches between taxonomic units in the specifier", - "start": 9530, - "end": 9598, + "start": 9980, + "end": 10048, "loc": { "start": { - "line": 245, + "line": 264, "column": 6 }, "end": { - "line": 245, + "line": 264, "column": 74 } } @@ -34318,15 +35639,15 @@ { "type": "CommentLine", "value": " and associated with the node.", - "start": 9605, - "end": 9637, + "start": 10055, + "end": 10087, "loc": { "start": { - "line": 246, + "line": 265, "column": 6 }, "end": { - "line": 246, + "line": 265, "column": 38 } } @@ -34344,15 +35665,15 @@ { "type": "CommentLine", "value": " Return a list of node labels matched by a given specifier on", - "start": 9208, - "end": 9271, + "start": 9658, + "end": 9721, "loc": { "start": { - "line": 237, + "line": 256, "column": 4 }, "end": { - "line": 237, + "line": 256, "column": 67 } } @@ -34360,15 +35681,15 @@ { "type": "CommentLine", "value": " a given phylogeny.", - 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"line": 259, + "line": 278, "column": 12 }, "end": { - "line": 259, + "line": 278, "column": 17 } }, @@ -34514,15 +35835,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10107, - "end": 10112, + "start": 10557, + "end": 10562, "loc": { "start": { - "line": 259, + "line": 278, "column": 12 }, "end": { - "line": 259, + "line": 278, "column": 17 }, "identifierName": "graph" @@ -34532,15 +35853,15 @@ }, "value": { "type": "Identifier", - "start": 10107, - "end": 10112, + "start": 10557, + "end": 10562, "loc": { "start": { - "line": 259, + "line": 278, "column": 12 }, "end": { - "line": 259, + "line": 278, "column": 17 }, "identifierName": "graph" @@ -34554,15 +35875,15 @@ }, { "type": "ObjectProperty", - "start": 10114, - "end": 10118, + "start": 10564, + "end": 10568, "loc": { "start": { - "line": 259, + "line": 278, "column": 19 }, "end": { - "line": 259, + "line": 278, "column": 23 } }, @@ -34571,15 +35892,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10114, - "end": 10118, + "start": 10564, + "end": 10568, "loc": { "start": { - "line": 259, + "line": 278, "column": 19 }, "end": { - "line": 259, + "line": 278, "column": 23 }, "identifierName": "root" @@ -34588,15 +35909,15 @@ }, "value": { "type": "Identifier", - "start": 10114, - "end": 10118, + "start": 10564, + "end": 10568, "loc": { "start": { - "line": 259, + "line": 278, "column": 19 }, "end": { - "line": 259, + "line": 278, "column": 23 }, "identifierName": "root" @@ -34609,15 +35930,15 @@ }, { "type": "ObjectProperty", - "start": 10120, - "end": 10130, + "start": 10570, + "end": 10580, "loc": { "start": { - "line": 259, + "line": 278, "column": 25 }, "end": { - "line": 259, + "line": 278, "column": 35 } }, @@ -34626,15 +35947,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10120, - "end": 10130, + "start": 10570, + "end": 10580, "loc": { "start": { - "line": 259, + "line": 278, "column": 25 }, "end": { - "line": 259, + "line": 278, "column": 35 }, "identifierName": "rootWeight" @@ -34643,15 +35964,15 @@ }, "value": { "type": "Identifier", - "start": 10120, - "end": 10130, + "start": 10570, + "end": 10580, "loc": { "start": { - "line": 259, + "line": 278, "column": 25 }, "end": { - "line": 259, + "line": 278, "column": 35 }, "identifierName": "rootWeight" @@ -34667,43 +35988,43 @@ }, "init": { "type": "CallExpression", - "start": 10135, - "end": 10157, + "start": 10585, + "end": 10607, "loc": { "start": { - "line": 259, + "line": 278, "column": 40 }, "end": { - "line": 259, + "line": 278, "column": 62 } }, "callee": { "type": "MemberExpression", - "start": 10135, - "end": 10149, + "start": 10585, + "end": 10599, "loc": { "start": { - "line": 259, + "line": 278, "column": 40 }, "end": { - "line": 259, + "line": 278, "column": 54 } }, "object": { "type": "Identifier", - "start": 10135, - "end": 10143, + "start": 10585, + "end": 10593, "loc": { "start": { - "line": 259, + "line": 278, "column": 40 }, "end": { - "line": 259, + "line": 278, "column": 48 }, "identifierName": "newickJs" @@ -34712,15 +36033,15 @@ }, "property": { "type": "Identifier", - "start": 10144, - "end": 10149, + "start": 10594, + "end": 10599, "loc": { "start": { - "line": 259, + "line": 278, "column": 49 }, "end": { - "line": 259, + "line": 278, "column": 54 }, "identifierName": "parse" @@ -34732,15 +36053,15 @@ "arguments": [ { "type": "Identifier", - "start": 10150, - "end": 10156, + "start": 10600, + "end": 10606, "loc": { "start": { - "line": 259, + "line": 278, "column": 55 }, "end": { - "line": 259, + "line": 278, "column": 61 }, "identifierName": "newick" @@ -34757,15 +36078,15 @@ { "type": "CommentLine", "value": " We previously used phylotree.js's Newick parser to parse Newick into a", - "start": 9797, - "end": 9870, + "start": 10247, + "end": 10320, "loc": { "start": { - "line": 254, + "line": 273, "column": 4 }, "end": { - "line": 254, + "line": 273, "column": 77 } } @@ -34773,15 +36094,15 @@ { "type": "CommentLine", "value": " tree-like structure. However, this is difficult to integrate using NPM.", - "start": 9875, - "end": 9949, + "start": 10325, + "end": 10399, "loc": { "start": { - "line": 255, + "line": 274, "column": 4 }, "end": { - "line": 255, + "line": 274, "column": 78 } } @@ -34789,15 +36110,15 @@ { "type": "CommentLine", "value": " This method provides a similar facility using the newick-js library.", - "start": 9954, - "end": 10025, + "start": 10404, + "end": 10475, "loc": { "start": { - "line": 256, + "line": 275, "column": 4 }, "end": { - "line": 256, + "line": 275, "column": 75 } } @@ -34805,15 +36126,15 @@ { "type": "CommentLine", "value": "", - "start": 10030, - "end": 10032, + "start": 10480, + "end": 10482, "loc": { "start": { - "line": 257, + "line": 276, "column": 4 }, "end": { - "line": 257, + "line": 276, "column": 6 } } @@ -34821,15 +36142,15 @@ { "type": "CommentLine", "value": " Throws an exception if the Newick could not be parsed.", - "start": 10037, - "end": 10094, + "start": 10487, + "end": 10544, "loc": { "start": { - "line": 258, + "line": 277, "column": 4 }, "end": { - "line": 258, + "line": 277, "column": 61 } } @@ -34838,44 +36159,44 @@ }, { "type": "VariableDeclaration", - "start": 10163, - "end": 10186, + "start": 10613, + "end": 10636, "loc": { "start": { - "line": 260, + "line": 279, "column": 4 }, "end": { - "line": 260, + "line": 279, "column": 27 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10169, - "end": 10185, + "start": 10619, + "end": 10635, "loc": { "start": { - "line": 260, + "line": 279, "column": 10 }, "end": { - "line": 260, + "line": 279, "column": 26 } }, "id": { "type": "ArrayPattern", - "start": 10169, - "end": 10177, + "start": 10619, + "end": 10627, "loc": { "start": { - "line": 260, + "line": 279, "column": 10 }, "end": { - "line": 260, + "line": 279, "column": 18 } }, @@ -34883,15 +36204,15 @@ null, { "type": "Identifier", - "start": 10172, - "end": 10176, + "start": 10622, + "end": 10626, "loc": { "start": { - "line": 260, + "line": 279, "column": 13 }, "end": { - "line": 260, + "line": 279, "column": 17 }, "identifierName": "arcs" @@ -34902,15 +36223,15 @@ }, "init": { "type": "Identifier", - "start": 10180, - "end": 10185, + "start": 10630, + "end": 10635, "loc": { "start": { - "line": 260, + "line": 279, "column": 21 }, "end": { - "line": 260, + "line": 279, "column": 26 }, "identifierName": "graph" @@ -34924,15 +36245,15 @@ { "type": "CommentLine", "value": " Go through the arcs, assigning 'children' to the appropriate parent node.", - "start": 10192, - "end": 10268, + "start": 10642, + "end": 10718, "loc": { "start": { - "line": 262, + "line": 281, "column": 4 }, "end": { - "line": 262, + "line": 281, "column": 80 } } @@ -34941,57 +36262,57 @@ }, { "type": "ExpressionStatement", - "start": 10273, - "end": 10838, + "start": 10723, + "end": 11288, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 276, + "line": 295, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 10273, - "end": 10837, + "start": 10723, + "end": 11287, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 276, + "line": 295, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 10273, - "end": 10285, + "start": 10723, + "end": 10735, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 16 } }, "object": { "type": "Identifier", - "start": 10273, - "end": 10277, + "start": 10723, + "end": 10727, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 8 }, "identifierName": "arcs" @@ -35001,15 +36322,15 @@ }, "property": { "type": "Identifier", - "start": 10278, - "end": 10285, + "start": 10728, + "end": 10735, "loc": { "start": { - "line": 263, + "line": 282, "column": 9 }, "end": { - "line": 263, + "line": 282, "column": 16 }, "identifierName": "forEach" @@ -35022,15 +36343,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 10286, - "end": 10836, + "start": 10736, + "end": 11286, "loc": { "start": { - "line": 263, + "line": 282, "column": 17 }, "end": { - "line": 276, + "line": 295, "column": 5 } }, @@ -35041,15 +36362,15 @@ "params": [ { "type": "Identifier", - "start": 10287, - "end": 10290, + "start": 10737, + "end": 10740, "loc": { "start": { - "line": 263, + "line": 282, "column": 18 }, "end": { - "line": 263, + "line": 282, "column": 21 }, "identifierName": "arc" @@ -35059,74 +36380,74 @@ ], "body": { "type": "BlockStatement", - "start": 10295, - "end": 10836, + "start": 10745, + "end": 11286, "loc": { "start": { - "line": 263, + "line": 282, "column": 26 }, "end": { - "line": 276, + "line": 295, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 10303, - "end": 10339, + "start": 10753, + "end": 10789, "loc": { "start": { - "line": 264, + "line": 283, "column": 6 }, "end": { - "line": 264, + "line": 283, "column": 42 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10309, - "end": 10338, + "start": 10759, + "end": 10788, "loc": { "start": { - "line": 264, + "line": 283, "column": 12 }, "end": { - "line": 264, + "line": 283, "column": 41 } }, "id": { "type": "ArrayPattern", - "start": 10309, - "end": 10332, + "start": 10759, + "end": 10782, "loc": { "start": { - "line": 264, + "line": 283, "column": 12 }, "end": { - "line": 264, + "line": 283, "column": 35 } }, "elements": [ { "type": "Identifier", - "start": 10310, - "end": 10316, + "start": 10760, + "end": 10766, "loc": { "start": { - "line": 264, + "line": 283, "column": 13 }, "end": { - "line": 264, + "line": 283, "column": 19 }, "identifierName": "parent" @@ -35135,15 +36456,15 @@ }, { "type": "Identifier", - "start": 10318, - "end": 10323, + "start": 10768, + "end": 10773, "loc": { "start": { - "line": 264, + "line": 283, "column": 21 }, "end": { - "line": 264, + "line": 283, "column": 26 }, "identifierName": "child" @@ -35152,15 +36473,15 @@ }, { "type": "Identifier", - "start": 10325, - "end": 10331, + "start": 10775, + "end": 10781, "loc": { "start": { - "line": 264, + "line": 283, "column": 28 }, "end": { - "line": 264, + "line": 283, "column": 34 }, "identifierName": "weight" @@ -35171,15 +36492,15 @@ }, "init": { "type": "Identifier", - "start": 10335, - "end": 10338, + "start": 10785, + "end": 10788, "loc": { "start": { - "line": 264, + "line": 283, "column": 38 }, "end": { - "line": 264, + "line": 283, "column": 41 }, "identifierName": "arc" @@ -35193,15 +36514,15 @@ { "type": "CommentLine", "value": " Add child to parent.children.", - "start": 10347, - "end": 10379, + "start": 10797, + "end": 10829, "loc": { "start": { - "line": 266, + "line": 285, "column": 6 }, "end": { - "line": 266, + "line": 285, "column": 38 } } @@ -35210,29 +36531,29 @@ }, { "type": "IfStatement", - "start": 10386, - "end": 10437, + "start": 10836, + "end": 10887, "loc": { "start": { - "line": 267, + "line": 286, "column": 6 }, "end": { - "line": 267, + "line": 286, "column": 57 } }, "test": { "type": "UnaryExpression", - "start": 10390, - "end": 10414, + "start": 10840, + "end": 10864, "loc": { "start": { - "line": 267, + "line": 286, "column": 10 }, "end": { - "line": 267, + "line": 286, "column": 34 } }, @@ -35240,29 +36561,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10391, - "end": 10414, + "start": 10841, + "end": 10864, "loc": { "start": { - "line": 267, + "line": 286, "column": 11 }, "end": { - "line": 267, + "line": 286, "column": 34 } }, "callee": { "type": "Identifier", - "start": 10391, - "end": 10394, + "start": 10841, + "end": 10844, "loc": { "start": { - "line": 267, + "line": 286, "column": 11 }, "end": { - "line": 267, + "line": 286, "column": 14 }, "identifierName": "has" @@ -35273,15 +36594,15 @@ "arguments": [ { "type": "Identifier", - "start": 10395, - "end": 10401, + "start": 10845, + "end": 10851, "loc": { "start": { - "line": 267, + "line": 286, "column": 15 }, "end": { - "line": 267, + "line": 286, "column": 21 }, "identifierName": "parent" @@ -35290,15 +36611,15 @@ }, { "type": "StringLiteral", - "start": 10403, - "end": 10413, + "start": 10853, + "end": 10863, "loc": { "start": { - "line": 267, + "line": 286, "column": 23 }, "end": { - "line": 267, + "line": 286, "column": 33 } }, @@ -35318,58 +36639,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10416, - "end": 10437, + "start": 10866, + "end": 10887, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 57 } }, "expression": { "type": "AssignmentExpression", - "start": 10416, - "end": 10436, + "start": 10866, + "end": 10886, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 56 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10416, - "end": 10431, + "start": 10866, + "end": 10881, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 51 } }, "object": { "type": "Identifier", - "start": 10416, - "end": 10422, + "start": 10866, + "end": 10872, "loc": { "start": { - "line": 267, + "line": 286, "column": 36 }, "end": { - "line": 267, + "line": 286, "column": 42 }, "identifierName": "parent" @@ -35378,15 +36699,15 @@ }, "property": { "type": "Identifier", - "start": 10423, - "end": 10431, + "start": 10873, + "end": 10881, "loc": { "start": { - "line": 267, + "line": 286, "column": 43 }, "end": { - "line": 267, + "line": 286, "column": 51 }, "identifierName": "children" @@ -35397,15 +36718,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10434, - "end": 10436, + "start": 10884, + "end": 10886, "loc": { "start": { - "line": 267, + "line": 286, "column": 54 }, "end": { - "line": 267, + "line": 286, "column": 56 } }, @@ -35418,15 +36739,15 @@ { "type": "CommentLine", "value": " Add child to parent.children.", - "start": 10347, - "end": 10379, + "start": 10797, + "end": 10829, "loc": { "start": { - "line": 266, + "line": 285, "column": 6 }, "end": { - "line": 266, + "line": 285, "column": 38 } } @@ -35435,71 +36756,71 @@ }, { "type": "ExpressionStatement", - "start": 10444, - "end": 10472, + "start": 10894, + "end": 10922, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 34 } }, "expression": { "type": "CallExpression", - "start": 10444, - "end": 10471, + "start": 10894, + "end": 10921, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 10444, - "end": 10464, + "start": 10894, + "end": 10914, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 26 } }, "object": { "type": "MemberExpression", - "start": 10444, - "end": 10459, + "start": 10894, + "end": 10909, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 21 } }, "object": { "type": "Identifier", - "start": 10444, - "end": 10450, + "start": 10894, + "end": 10900, "loc": { "start": { - "line": 268, + "line": 287, "column": 6 }, "end": { - "line": 268, + "line": 287, "column": 12 }, "identifierName": "parent" @@ -35508,15 +36829,15 @@ }, "property": { "type": "Identifier", - "start": 10451, - "end": 10459, + "start": 10901, + "end": 10909, "loc": { "start": { - "line": 268, + "line": 287, "column": 13 }, "end": { - "line": 268, + "line": 287, "column": 21 }, "identifierName": "children" @@ -35527,15 +36848,15 @@ }, "property": { "type": "Identifier", - "start": 10460, - "end": 10464, + "start": 10910, + "end": 10914, "loc": { "start": { - "line": 268, + "line": 287, "column": 22 }, "end": { - "line": 268, + "line": 287, "column": 26 }, "identifierName": "push" @@ -35547,15 +36868,15 @@ "arguments": [ { "type": "Identifier", - "start": 10465, - "end": 10470, + "start": 10915, + "end": 10920, "loc": { "start": { - "line": 268, + "line": 287, "column": 27 }, "end": { - "line": 268, + "line": 287, "column": 32 }, "identifierName": "child" @@ -35568,15 +36889,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'name' instead of 'label'.", - "start": 10480, - "end": 10527, + "start": 10930, + "end": 10977, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 53 } } @@ -35585,43 +36906,43 @@ }, { "type": "IfStatement", - "start": 10534, - "end": 10591, + "start": 10984, + "end": 11041, "loc": { "start": { - "line": 271, + "line": 290, "column": 6 }, "end": { - "line": 271, + "line": 290, "column": 63 } }, "test": { "type": "CallExpression", - "start": 10538, - "end": 10558, + "start": 10988, + "end": 11008, "loc": { "start": { - "line": 271, + "line": 290, "column": 10 }, "end": { - "line": 271, + "line": 290, "column": 30 } }, "callee": { "type": "Identifier", - "start": 10538, - "end": 10541, + "start": 10988, + "end": 10991, "loc": { "start": { - "line": 271, + "line": 290, "column": 10 }, "end": { - "line": 271, + "line": 290, "column": 13 }, "identifierName": "has" @@ -35632,15 +36953,15 @@ "arguments": [ { "type": "Identifier", - "start": 10542, - "end": 10548, + "start": 10992, + "end": 10998, "loc": { "start": { - "line": 271, + "line": 290, "column": 14 }, "end": { - "line": 271, + "line": 290, "column": 20 }, "identifierName": "parent" @@ -35649,15 +36970,15 @@ }, { "type": "StringLiteral", - "start": 10550, - "end": 10557, + "start": 11000, + "end": 11007, "loc": { "start": { - "line": 271, + "line": 290, "column": 22 }, "end": { - "line": 271, + "line": 290, "column": 29 } }, @@ -35672,73 +36993,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 10560, - "end": 10591, + "start": 11010, + "end": 11041, "loc": { "start": { - "line": 271, + "line": 290, "column": 32 }, "end": { - "line": 271, + "line": 290, "column": 63 } }, "body": [ { "type": "ExpressionStatement", - "start": 10562, - "end": 10589, + "start": 11012, + "end": 11039, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 61 } }, "expression": { "type": "AssignmentExpression", - "start": 10562, - "end": 10588, + "start": 11012, + "end": 11038, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 60 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10562, - "end": 10573, + "start": 11012, + "end": 11023, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 45 } }, "object": { "type": "Identifier", - "start": 10562, - "end": 10568, + "start": 11012, + "end": 11018, "loc": { "start": { - "line": 271, + "line": 290, "column": 34 }, "end": { - "line": 271, + "line": 290, "column": 40 }, "identifierName": "parent" @@ -35747,15 +37068,15 @@ }, "property": { "type": "Identifier", - "start": 10569, - "end": 10573, + "start": 11019, + "end": 11023, "loc": { "start": { - "line": 271, + "line": 290, "column": 41 }, "end": { - "line": 271, + "line": 290, "column": 45 }, "identifierName": "name" @@ -35766,29 +37087,29 @@ }, "right": { "type": "MemberExpression", - "start": 10576, - "end": 10588, + "start": 11026, + "end": 11038, "loc": { "start": { - "line": 271, + "line": 290, "column": 48 }, "end": { - "line": 271, + "line": 290, "column": 60 } }, "object": { "type": "Identifier", - "start": 10576, - "end": 10582, + "start": 11026, + "end": 11032, "loc": { "start": { - "line": 271, + "line": 290, "column": 48 }, "end": { - "line": 271, + "line": 290, "column": 54 }, "identifierName": "parent" @@ -35797,15 +37118,15 @@ }, "property": { "type": "Identifier", - "start": 10583, - "end": 10588, + "start": 11033, + "end": 11038, "loc": { "start": { - "line": 271, + "line": 290, "column": 55 }, "end": { - "line": 271, + "line": 290, "column": 60 }, "identifierName": "label" @@ -35824,15 +37145,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'name' instead of 'label'.", - "start": 10480, - "end": 10527, + "start": 10930, + "end": 10977, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 53 } } @@ -35841,43 +37162,43 @@ }, { "type": "IfStatement", - "start": 10598, - "end": 10652, + "start": 11048, + "end": 11102, "loc": { "start": { - "line": 272, + "line": 291, "column": 6 }, "end": { - "line": 272, + "line": 291, "column": 60 } }, "test": { "type": "CallExpression", - "start": 10602, - "end": 10621, + "start": 11052, + "end": 11071, "loc": { "start": { - "line": 272, + "line": 291, "column": 10 }, "end": { - "line": 272, + "line": 291, "column": 29 } }, "callee": { "type": "Identifier", - "start": 10602, - "end": 10605, + "start": 11052, + "end": 11055, "loc": { "start": { - "line": 272, + "line": 291, "column": 10 }, "end": { - "line": 272, + "line": 291, "column": 13 }, "identifierName": "has" @@ -35887,15 +37208,15 @@ "arguments": [ { "type": "Identifier", - "start": 10606, - "end": 10611, + "start": 11056, + "end": 11061, "loc": { "start": { - "line": 272, + "line": 291, "column": 14 }, "end": { - "line": 272, + "line": 291, "column": 19 }, "identifierName": "child" @@ -35904,15 +37225,15 @@ }, { "type": "StringLiteral", - "start": 10613, - "end": 10620, + "start": 11063, + "end": 11070, "loc": { "start": { - "line": 272, + "line": 291, "column": 21 }, "end": { - "line": 272, + "line": 291, "column": 28 } }, @@ -35926,73 +37247,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 10623, - "end": 10652, + "start": 11073, + "end": 11102, "loc": { "start": { - "line": 272, + "line": 291, "column": 31 }, "end": { - "line": 272, + "line": 291, "column": 60 } }, "body": [ { "type": "ExpressionStatement", - "start": 10625, - "end": 10650, + "start": 11075, + "end": 11100, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 58 } }, "expression": { "type": "AssignmentExpression", - "start": 10625, - "end": 10649, + "start": 11075, + "end": 11099, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 57 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10625, - "end": 10635, + "start": 11075, + "end": 11085, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 43 } }, "object": { "type": "Identifier", - "start": 10625, - "end": 10630, + "start": 11075, + "end": 11080, "loc": { "start": { - "line": 272, + "line": 291, "column": 33 }, "end": { - "line": 272, + "line": 291, "column": 38 }, "identifierName": "child" @@ -36001,15 +37322,15 @@ }, "property": { "type": "Identifier", - "start": 10631, - "end": 10635, + "start": 11081, + "end": 11085, "loc": { "start": { - "line": 272, + "line": 291, "column": 39 }, "end": { - "line": 272, + "line": 291, "column": 43 }, "identifierName": "name" @@ -36020,29 +37341,29 @@ }, "right": { "type": "MemberExpression", - "start": 10638, - "end": 10649, + "start": 11088, + "end": 11099, "loc": { "start": { - "line": 272, + "line": 291, "column": 46 }, "end": { - "line": 272, + "line": 291, "column": 57 } }, "object": { "type": "Identifier", - "start": 10638, - "end": 10643, + "start": 11088, + "end": 11093, "loc": { "start": { - "line": 272, + "line": 291, "column": 46 }, "end": { - "line": 272, + "line": 291, "column": 51 }, "identifierName": "child" @@ -36051,15 +37372,15 @@ }, "property": { "type": "Identifier", - "start": 10644, - "end": 10649, + "start": 11094, + "end": 11099, "loc": { "start": { - "line": 272, + "line": 291, "column": 52 }, "end": { - "line": 272, + "line": 291, "column": 57 }, "identifierName": "label" @@ -36079,15 +37400,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.", - "start": 10660, - "end": 10743, + "start": 11110, + "end": 11193, "loc": { "start": { - "line": 274, + "line": 293, "column": 6 }, "end": { - "line": 274, + "line": 293, "column": 89 } } @@ -36096,43 +37417,43 @@ }, { "type": "IfStatement", - "start": 10750, - "end": 10830, + "start": 11200, + "end": 11280, "loc": { "start": { - "line": 275, + "line": 294, "column": 6 }, "end": { - "line": 275, + "line": 294, "column": 86 } }, "test": { "type": "LogicalExpression", - "start": 10754, - "end": 10803, + "start": 11204, + "end": 11253, "loc": { "start": { - "line": 275, + "line": 294, "column": 10 }, "end": { - "line": 275, + "line": 294, "column": 59 } }, "left": { "type": "UnaryExpression", - "start": 10754, - "end": 10778, + "start": 11204, + "end": 11228, "loc": { "start": { - "line": 275, + "line": 294, "column": 10 }, "end": { - "line": 275, + "line": 294, "column": 34 } }, @@ -36140,29 +37461,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10755, - "end": 10778, + "start": 11205, + "end": 11228, "loc": { "start": { - "line": 275, + "line": 294, "column": 11 }, "end": { - "line": 275, + "line": 294, "column": 34 } }, "callee": { "type": "Identifier", - "start": 10755, - "end": 10758, + "start": 11205, + "end": 11208, "loc": { "start": { - "line": 275, + "line": 294, "column": 11 }, "end": { - "line": 275, + "line": 294, "column": 14 }, "identifierName": "has" @@ -36173,15 +37494,15 @@ "arguments": [ { "type": "Identifier", - "start": 10759, - "end": 10764, + "start": 11209, + "end": 11214, "loc": { "start": { - "line": 275, + "line": 294, "column": 15 }, "end": { - "line": 275, + "line": 294, "column": 20 }, "identifierName": "child" @@ -36190,15 +37511,15 @@ }, { "type": "StringLiteral", - "start": 10766, - "end": 10777, + "start": 11216, + "end": 11227, "loc": { "start": { - "line": 275, + "line": 294, "column": 22 }, "end": { - "line": 275, + "line": 294, "column": 33 } }, @@ -36219,15 +37540,15 @@ "operator": "&&", "right": { "type": "UnaryExpression", - "start": 10782, - "end": 10803, + "start": 11232, + "end": 11253, "loc": { "start": { - "line": 275, + "line": 294, "column": 38 }, "end": { - "line": 275, + "line": 294, "column": 59 } }, @@ -36235,43 +37556,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10783, - "end": 10803, + "start": 11233, + "end": 11253, "loc": { "start": { - "line": 275, + "line": 294, "column": 39 }, "end": { - "line": 275, + "line": 294, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 10783, - "end": 10795, + "start": 11233, + "end": 11245, "loc": { "start": { - "line": 275, + "line": 294, "column": 39 }, "end": { - "line": 275, + "line": 294, "column": 51 } }, "object": { "type": "Identifier", - "start": 10783, - "end": 10789, + "start": 11233, + "end": 11239, "loc": { "start": { - "line": 275, + "line": 294, "column": 39 }, "end": { - "line": 275, + "line": 294, "column": 45 }, "identifierName": "Number" @@ -36280,15 +37601,15 @@ }, "property": { "type": "Identifier", - "start": 10790, - "end": 10795, + "start": 11240, + "end": 11245, "loc": { "start": { - "line": 275, + "line": 294, "column": 46 }, "end": { - "line": 275, + "line": 294, "column": 51 }, "identifierName": "isNaN" @@ -36300,15 +37621,15 @@ "arguments": [ { "type": "Identifier", - "start": 10796, - "end": 10802, + "start": 11246, + "end": 11252, "loc": { "start": { - "line": 275, + "line": 294, "column": 52 }, "end": { - "line": 275, + "line": 294, "column": 58 }, "identifierName": "weight" @@ -36325,58 +37646,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10805, - "end": 10830, + "start": 11255, + "end": 11280, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 86 } }, "expression": { "type": "AssignmentExpression", - "start": 10805, - "end": 10829, + "start": 11255, + "end": 11279, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 85 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10805, - "end": 10820, + "start": 11255, + "end": 11270, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 76 } }, "object": { "type": "Identifier", - "start": 10805, - "end": 10810, + "start": 11255, + "end": 11260, "loc": { "start": { - "line": 275, + "line": 294, "column": 61 }, "end": { - "line": 275, + "line": 294, "column": 66 }, "identifierName": "child" @@ -36385,15 +37706,15 @@ }, "property": { "type": "Identifier", - "start": 10811, - "end": 10820, + "start": 11261, + "end": 11270, "loc": { "start": { - "line": 275, + "line": 294, "column": 67 }, "end": { - "line": 275, + "line": 294, "column": 76 }, "identifierName": "attribute" @@ -36404,15 +37725,15 @@ }, "right": { "type": "Identifier", - "start": 10823, - "end": 10829, + "start": 11273, + "end": 11279, "loc": { "start": { - "line": 275, + "line": 294, "column": 79 }, "end": { - "line": 275, + "line": 294, "column": 85 }, "identifierName": "weight" @@ -36426,15 +37747,15 @@ { "type": "CommentLine", "value": " Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.", - "start": 10660, - "end": 10743, + "start": 11110, + "end": 11193, "loc": { "start": { - "line": 274, + "line": 293, "column": 6 }, "end": { - "line": 274, + "line": 293, "column": 89 } } @@ -36452,15 +37773,15 @@ { "type": "CommentLine", "value": " Go through the arcs, assigning 'children' to the appropriate parent node.", - "start": 10192, - "end": 10268, + "start": 10642, + "end": 10718, "loc": { "start": { - "line": 262, + "line": 281, "column": 4 }, "end": { - "line": 262, + "line": 281, "column": 80 } } @@ -36470,15 +37791,15 @@ { "type": "CommentLine", "value": " Set root 'attribute' to root weight.", - "start": 10844, - "end": 10883, + "start": 11294, + "end": 11333, "loc": { "start": { - "line": 278, + "line": 297, "column": 4 }, "end": { - "line": 278, + "line": 297, "column": 43 } } @@ -36487,43 +37808,43 @@ }, { "type": "IfStatement", - "start": 10888, - "end": 10974, + "start": 11338, + "end": 11424, "loc": { "start": { - "line": 279, + "line": 298, "column": 4 }, "end": { - "line": 279, + "line": 298, "column": 90 } }, "test": { "type": "LogicalExpression", - "start": 10892, - "end": 10944, + "start": 11342, + "end": 11394, "loc": { "start": { - "line": 279, + "line": 298, "column": 8 }, "end": { - "line": 279, + "line": 298, "column": 60 } }, "left": { "type": "UnaryExpression", - "start": 10892, - "end": 10915, + "start": 11342, + "end": 11365, "loc": { "start": { - "line": 279, + "line": 298, "column": 8 }, "end": { - "line": 279, + "line": 298, "column": 31 } }, @@ -36531,29 +37852,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10893, - "end": 10915, + "start": 11343, + "end": 11365, "loc": { "start": { - "line": 279, + "line": 298, "column": 9 }, "end": { - "line": 279, + "line": 298, "column": 31 } }, "callee": { "type": "Identifier", - "start": 10893, - "end": 10896, + "start": 11343, + "end": 11346, "loc": { "start": { - "line": 279, + "line": 298, "column": 9 }, "end": { - "line": 279, + "line": 298, "column": 12 }, "identifierName": "has" @@ -36564,15 +37885,15 @@ "arguments": [ { "type": "Identifier", - "start": 10897, - "end": 10901, + "start": 11347, + "end": 11351, "loc": { "start": { - "line": 279, + "line": 298, "column": 13 }, "end": { - "line": 279, + "line": 298, "column": 17 }, "identifierName": "root" @@ -36581,15 +37902,15 @@ }, { "type": "StringLiteral", - "start": 10903, - "end": 10914, + "start": 11353, + "end": 11364, "loc": { "start": { - "line": 279, + "line": 298, "column": 19 }, "end": { - "line": 279, + "line": 298, "column": 30 } }, @@ -36610,15 +37931,15 @@ "operator": "&&", "right": { "type": "UnaryExpression", - "start": 10919, - "end": 10944, + "start": 11369, + "end": 11394, "loc": { "start": { - "line": 279, + "line": 298, "column": 35 }, "end": { - "line": 279, + "line": 298, "column": 60 } }, @@ -36626,43 +37947,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10920, - "end": 10944, + "start": 11370, + "end": 11394, "loc": { "start": { - "line": 279, + "line": 298, "column": 36 }, "end": { - "line": 279, + "line": 298, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 10920, - "end": 10932, + "start": 11370, + "end": 11382, "loc": { "start": { - "line": 279, + "line": 298, "column": 36 }, "end": { - "line": 279, + "line": 298, "column": 48 } }, "object": { "type": "Identifier", - "start": 10920, - "end": 10926, + "start": 11370, + "end": 11376, "loc": { "start": { - "line": 279, + "line": 298, "column": 36 }, "end": { - "line": 279, + "line": 298, "column": 42 }, "identifierName": "Number" @@ -36671,15 +37992,15 @@ }, "property": { "type": "Identifier", - "start": 10927, - "end": 10932, + "start": 11377, + "end": 11382, "loc": { "start": { - "line": 279, + "line": 298, "column": 43 }, "end": { - "line": 279, + "line": 298, "column": 48 }, "identifierName": "isNaN" @@ -36691,15 +38012,15 @@ "arguments": [ { "type": "Identifier", - "start": 10933, - "end": 10943, + "start": 11383, + "end": 11393, "loc": { "start": { - "line": 279, + "line": 298, "column": 49 }, "end": { - "line": 279, + "line": 298, "column": 59 }, "identifierName": "rootWeight" @@ -36716,58 +38037,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10946, - "end": 10974, + "start": 11396, + "end": 11424, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 90 } }, "expression": { "type": "AssignmentExpression", - "start": 10946, - "end": 10973, + "start": 11396, + "end": 11423, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 89 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10946, - "end": 10960, + "start": 11396, + "end": 11410, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 76 } }, "object": { "type": "Identifier", - "start": 10946, - "end": 10950, + "start": 11396, + "end": 11400, "loc": { "start": { - "line": 279, + "line": 298, "column": 62 }, "end": { - "line": 279, + "line": 298, "column": 66 }, "identifierName": "root" @@ -36776,15 +38097,15 @@ }, "property": { "type": "Identifier", - "start": 10951, - "end": 10960, + "start": 11401, + "end": 11410, "loc": { "start": { - "line": 279, + "line": 298, "column": 67 }, "end": { - "line": 279, + "line": 298, "column": 76 }, "identifierName": "attribute" @@ -36795,15 +38116,15 @@ }, "right": { "type": "Identifier", - "start": 10963, - "end": 10973, + "start": 11413, + "end": 11423, "loc": { "start": { - "line": 279, + "line": 298, "column": 79 }, "end": { - "line": 279, + "line": 298, "column": 89 }, "identifierName": "rootWeight" @@ -36817,15 +38138,15 @@ { "type": "CommentLine", "value": " Set root 'attribute' to root weight.", - "start": 10844, - "end": 10883, + "start": 11294, + "end": 11333, "loc": { "start": { - "line": 278, + "line": 297, "column": 4 }, "end": { - "line": 278, + "line": 297, "column": 43 } } @@ -36834,44 +38155,44 @@ }, { "type": "ReturnStatement", - "start": 10980, - "end": 11002, + "start": 11430, + "end": 11452, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 26 } }, "argument": { "type": "ObjectExpression", - "start": 10987, - "end": 11001, + "start": 11437, + "end": 11451, "loc": { "start": { - "line": 281, + "line": 300, "column": 11 }, "end": { - "line": 281, + "line": 300, "column": 25 } }, "properties": [ { "type": "ObjectProperty", - "start": 10989, - "end": 10999, + "start": 11439, + "end": 11449, "loc": { "start": { - "line": 281, + "line": 300, "column": 13 }, "end": { - "line": 281, + "line": 300, "column": 23 } }, @@ -36880,15 +38201,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10989, - "end": 10993, + "start": 11439, + "end": 11443, "loc": { "start": { - "line": 281, + "line": 300, "column": 13 }, "end": { - "line": 281, + "line": 300, "column": 17 }, "identifierName": "json" @@ -36897,15 +38218,15 @@ }, "value": { "type": "Identifier", - "start": 10995, - "end": 10999, + "start": 11445, + "end": 11449, "loc": { "start": { - "line": 281, + "line": 300, "column": 19 }, "end": { - "line": 281, + "line": 300, "column": 23 }, "identifierName": "root" @@ -36922,15 +38243,15 @@ }, { "type": "ClassMethod", - "start": 11010, - "end": 11966, + "start": 11460, + "end": 12416, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 306, + "line": 325, "column": 3 } }, @@ -36938,15 +38259,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11010, - "end": 11033, + "start": 11460, + "end": 11483, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 284, + "line": 303, "column": 25 }, "identifierName": "getParsedNewickWithIRIs" @@ -36961,15 +38282,15 @@ "params": [ { "type": "Identifier", - "start": 11034, - "end": 11041, + "start": 11484, + "end": 11491, "loc": { "start": { - "line": 284, + "line": 303, "column": 26 }, "end": { - "line": 284, + "line": 303, "column": 33 }, "identifierName": "baseIRI" @@ -36978,29 +38299,29 @@ }, { "type": "AssignmentPattern", - "start": 11043, - "end": 11090, + "start": 11493, + "end": 11540, "loc": { "start": { - "line": 284, + "line": 303, "column": 35 }, "end": { - "line": 284, + "line": 303, "column": 82 } }, "left": { "type": "Identifier", - "start": 11043, - "end": 11055, + "start": 11493, + "end": 11505, "loc": { "start": { - "line": 284, + "line": 303, "column": 35 }, "end": { - "line": 284, + "line": 303, "column": 47 }, "identifierName": "newickParser" @@ -37009,29 +38330,29 @@ }, "right": { "type": "MemberExpression", - "start": 11058, - "end": 11090, + "start": 11508, + "end": 11540, "loc": { "start": { - "line": 284, + "line": 303, "column": 50 }, "end": { - "line": 284, + "line": 303, "column": 82 } }, "object": { "type": "Identifier", - "start": 11058, - "end": 11074, + "start": 11508, + "end": 11524, "loc": { "start": { - "line": 284, + "line": 303, "column": 50 }, "end": { - "line": 284, + "line": 303, "column": 66 }, "identifierName": "PhylogenyWrapper" @@ -37040,15 +38361,15 @@ }, "property": { "type": "Identifier", - "start": 11075, - "end": 11090, + "start": 11525, + "end": 11540, "loc": { "start": { - "line": 284, + "line": 303, "column": 67 }, "end": { - "line": 284, + "line": 303, "column": 82 }, "identifierName": "getParsedNewick" @@ -37061,59 +38382,59 @@ ], "body": { "type": "BlockStatement", - "start": 11092, - "end": 11966, + "start": 11542, + "end": 12416, "loc": { "start": { - "line": 284, + "line": 303, "column": 84 }, "end": { - "line": 306, + "line": 325, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 11550, - "end": 11609, + "start": 12000, + "end": 12059, "loc": { "start": { - "line": 293, + "line": 312, "column": 4 }, "end": { - "line": 293, + "line": 312, "column": 63 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11556, - "end": 11608, + "start": 12006, + "end": 12058, "loc": { "start": { - "line": 293, + "line": 312, "column": 10 }, "end": { - "line": 293, + "line": 312, "column": 62 } }, "id": { "type": "Identifier", - "start": 11556, - "end": 11562, + "start": 12006, + "end": 12012, "loc": { "start": { - "line": 293, + "line": 312, "column": 10 }, "end": { - "line": 293, + "line": 312, "column": 16 }, "identifierName": "parsed" @@ -37123,29 +38444,29 @@ }, "init": { "type": "CallExpression", - "start": 11565, - "end": 11608, + "start": 12015, + "end": 12058, "loc": { "start": { - "line": 293, + "line": 312, "column": 19 }, "end": { - "line": 293, + "line": 312, "column": 62 } }, "callee": { "type": "Identifier", - "start": 11565, - "end": 11577, + "start": 12015, + "end": 12027, "loc": { "start": { - "line": 293, + "line": 312, "column": 19 }, "end": { - "line": 293, + "line": 312, "column": 31 }, "identifierName": "newickParser" @@ -37155,72 +38476,72 @@ "arguments": [ { "type": "LogicalExpression", - "start": 11578, - "end": 11607, + "start": 12028, + "end": 12057, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 61 } }, "left": { "type": "MemberExpression", - "start": 11578, - "end": 11599, + "start": 12028, + "end": 12049, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 53 } }, "object": { "type": "MemberExpression", - "start": 11578, - "end": 11592, + "start": 12028, + "end": 12042, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 46 } }, "object": { "type": "ThisExpression", - "start": 11578, - "end": 11582, + "start": 12028, + "end": 12032, "loc": { "start": { - "line": 293, + "line": 312, "column": 32 }, "end": { - "line": 293, + "line": 312, "column": 36 } } }, "property": { "type": "Identifier", - "start": 11583, - "end": 11592, + "start": 12033, + "end": 12042, "loc": { "start": { - "line": 293, + "line": 312, "column": 37 }, "end": { - "line": 293, + "line": 312, "column": 46 }, "identifierName": "phylogeny" @@ -37231,15 +38552,15 @@ }, "property": { "type": "Identifier", - "start": 11593, - "end": 11599, + "start": 12043, + "end": 12049, "loc": { "start": { - "line": 293, + "line": 312, "column": 47 }, "end": { - "line": 293, + "line": 312, "column": 53 }, "identifierName": "newick" @@ -37251,15 +38572,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 11603, - "end": 11607, + "start": 12053, + "end": 12057, "loc": { "start": { - "line": 293, + "line": 312, "column": 57 }, "end": { - "line": 293, + "line": 312, "column": 61 } }, @@ -37280,15 +38601,15 @@ { "type": "CommentLine", "value": " Return the parsed Newick string, but with EVERY node given an IRI.", - "start": 11098, - "end": 11167, + "start": 11548, + "end": 11617, "loc": { "start": { - "line": 285, + "line": 304, "column": 4 }, "end": { - "line": 285, + "line": 304, "column": 73 } } @@ -37296,15 +38617,15 @@ { "type": "CommentLine", "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 11172, - "end": 11245, + "start": 11622, + "end": 11695, "loc": { "start": { - "line": 286, + "line": 305, "column": 4 }, "end": { - "line": 286, + "line": 305, "column": 77 } } @@ -37312,15 +38633,15 @@ { "type": "CommentLine", "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 11250, - "end": 11325, + "start": 11700, + "end": 11775, "loc": { "start": { - "line": 287, + "line": 306, "column": 4 }, "end": { - "line": 287, + "line": 306, "column": 79 } } @@ -37328,15 +38649,15 @@ { "type": "CommentLine", "value": " the baseIRI.", - "start": 11330, - "end": 11347, + "start": 11780, + "end": 11797, "loc": { "start": { - "line": 288, + "line": 307, "column": 4 }, "end": { - "line": 288, + "line": 307, "column": 21 } } @@ -37344,15 +38665,15 @@ { "type": "CommentLine", "value": " - newickParser: A method for converting a Newick string to a object-based", - "start": 11352, - "end": 11428, + "start": 11802, + "end": 11878, "loc": { "start": { - "line": 289, + "line": 308, "column": 4 }, "end": { - "line": 289, + "line": 308, "column": 80 } } @@ -37360,15 +38681,15 @@ { "type": "CommentLine", "value": " representation. The static method PhylogenyWrapper.getParsedNewick() is", - "start": 11433, - "end": 11509, + "start": 11883, + "end": 11959, "loc": { "start": { - "line": 290, + "line": 309, "column": 4 }, "end": { - "line": 290, + "line": 309, "column": 80 } } @@ -37376,15 +38697,15 @@ { "type": "CommentLine", "value": " used if none is provided.", - "start": 11514, - "end": 11544, + "start": 11964, + "end": 11994, "loc": { "start": { - "line": 291, + "line": 310, "column": 4 }, "end": { - "line": 291, + "line": 310, "column": 34 } } @@ -37393,43 +38714,43 @@ }, { "type": "IfStatement", - "start": 11614, - "end": 11942, + "start": 12064, + "end": 12392, "loc": { "start": { - "line": 294, + "line": 313, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 5 } }, "test": { "type": "CallExpression", - "start": 11618, - "end": 11637, + "start": 12068, + "end": 12087, "loc": { "start": { - "line": 294, + "line": 313, "column": 8 }, "end": { - "line": 294, + "line": 313, "column": 27 } }, "callee": { "type": "Identifier", - "start": 11618, - "end": 11621, + "start": 12068, + "end": 12071, "loc": { "start": { - "line": 294, + "line": 313, "column": 8 }, "end": { - "line": 294, + "line": 313, "column": 11 }, "identifierName": "has" @@ -37439,15 +38760,15 @@ "arguments": [ { "type": "Identifier", - "start": 11622, - "end": 11628, + "start": 12072, + "end": 12078, "loc": { "start": { - "line": 294, + "line": 313, "column": 12 }, "end": { - "line": 294, + "line": 313, "column": 18 }, "identifierName": "parsed" @@ -37456,15 +38777,15 @@ }, { "type": "StringLiteral", - "start": 11630, - "end": 11636, + "start": 12080, + "end": 12086, "loc": { "start": { - "line": 294, + "line": 313, "column": 20 }, "end": { - "line": 294, + "line": 313, "column": 26 } }, @@ -37478,72 +38799,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 11639, - "end": 11942, + "start": 12089, + "end": 12392, "loc": { "start": { - "line": 294, + "line": 313, "column": 29 }, "end": { - "line": 303, + "line": 322, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 11647, - "end": 11936, + "start": 12097, + "end": 12386, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 11647, - "end": 11935, + "start": 12097, + "end": 12385, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 11647, - "end": 11676, + "start": 12097, + "end": 12126, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 295, + "line": 314, "column": 35 } }, "object": { "type": "Identifier", - "start": 11647, - "end": 11663, + "start": 12097, + "end": 12113, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 295, + "line": 314, "column": 22 }, "identifierName": "PhylogenyWrapper" @@ -37552,15 +38873,15 @@ }, "property": { "type": "Identifier", - "start": 11664, - "end": 11676, + "start": 12114, + "end": 12126, "loc": { "start": { - "line": 295, + "line": 314, "column": 23 }, "end": { - "line": 295, + "line": 314, "column": 35 }, "identifierName": "recurseNodes" @@ -37572,29 +38893,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 11677, - "end": 11688, + "start": 12127, + "end": 12138, "loc": { "start": { - "line": 295, + "line": 314, "column": 36 }, "end": { - "line": 295, + "line": 314, "column": 47 } }, "object": { "type": "Identifier", - "start": 11677, - "end": 11683, + "start": 12127, + "end": 12133, "loc": { "start": { - "line": 295, + "line": 314, "column": 36 }, "end": { - "line": 295, + "line": 314, "column": 42 }, "identifierName": "parsed" @@ -37603,15 +38924,15 @@ }, "property": { "type": "Identifier", - "start": 11684, - "end": 11688, + "start": 12134, + "end": 12138, "loc": { "start": { - "line": 295, + "line": 314, "column": 43 }, "end": { - "line": 295, + "line": 314, "column": 47 }, "identifierName": "json" @@ -37622,15 +38943,15 @@ }, { "type": "ArrowFunctionExpression", - "start": 11690, - "end": 11934, + "start": 12140, + "end": 12384, "loc": { "start": { - "line": 295, + "line": 314, "column": 49 }, "end": { - "line": 302, + "line": 321, "column": 7 } }, @@ -37641,15 +38962,15 @@ "params": [ { "type": "Identifier", - "start": 11691, - "end": 11695, + "start": 12141, + "end": 12145, "loc": { "start": { - "line": 295, + "line": 314, "column": 50 }, "end": { - "line": 295, + "line": 314, "column": 54 }, "identifierName": "node" @@ -37658,15 +38979,15 @@ }, { "type": "Identifier", - "start": 11697, - "end": 11706, + "start": 12147, + "end": 12156, "loc": { "start": { - "line": 295, + "line": 314, "column": 56 }, "end": { - "line": 295, + "line": 314, "column": 65 }, "identifierName": "nodeCount" @@ -37676,59 +38997,59 @@ ], "body": { "type": "BlockStatement", - "start": 11711, - "end": 11934, + "start": 12161, + "end": 12384, "loc": { "start": { - "line": 295, + "line": 314, "column": 70 }, "end": { - "line": 302, + "line": 321, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 11775, - "end": 11801, + "start": 12225, + "end": 12251, "loc": { "start": { - "line": 297, + "line": 316, "column": 8 }, "end": { - "line": 297, + "line": 316, "column": 34 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11781, - "end": 11800, + "start": 12231, + "end": 12250, "loc": { "start": { - "line": 297, + "line": 316, "column": 14 }, "end": { - "line": 297, + "line": 316, "column": 33 } }, "id": { "type": "Identifier", - "start": 11781, - "end": 11793, + "start": 12231, + "end": 12243, "loc": { "start": { - "line": 297, + "line": 316, "column": 14 }, "end": { - "line": 297, + "line": 316, "column": 26 }, "identifierName": "nodeAsJSONLD" @@ -37738,15 +39059,15 @@ }, "init": { "type": "Identifier", - "start": 11796, - "end": 11800, + "start": 12246, + "end": 12250, "loc": { "start": { - "line": 297, + "line": 316, "column": 29 }, "end": { - "line": 297, + "line": 316, "column": 33 }, "identifierName": "node" @@ -37761,15 +39082,15 @@ { "type": "CommentLine", "value": " Start with the additional node properties.", - "start": 11721, - "end": 11766, + "start": 12171, + "end": 12216, "loc": { "start": { - "line": 296, + "line": 315, "column": 8 }, "end": { - "line": 296, + "line": 315, "column": 53 } } @@ -37779,15 +39100,15 @@ { "type": "CommentLine", "value": " Set @id and @type.", - "start": 11811, - "end": 11832, + "start": 12261, + "end": 12282, "loc": { "start": { - "line": 299, + "line": 318, "column": 8 }, "end": { - "line": 299, + "line": 318, "column": 29 } } @@ -37796,44 +39117,44 @@ }, { "type": "VariableDeclaration", - "start": 11841, - "end": 11887, + "start": 12291, + "end": 12337, "loc": { "start": { - "line": 300, + "line": 319, "column": 8 }, "end": { - "line": 300, + "line": 319, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11847, - "end": 11886, + "start": 12297, + "end": 12336, "loc": { "start": { - "line": 300, + "line": 319, "column": 14 }, "end": { - "line": 300, + "line": 319, "column": 53 } }, "id": { "type": "Identifier", - "start": 11847, - "end": 11854, + "start": 12297, + "end": 12304, "loc": { "start": { - "line": 300, + "line": 319, "column": 14 }, "end": { - "line": 300, + "line": 319, "column": 21 }, "identifierName": "nodeIRI" @@ -37843,30 +39164,30 @@ }, "init": { "type": "TemplateLiteral", - "start": 11857, - "end": 11886, + "start": 12307, + "end": 12336, "loc": { "start": { - "line": 300, + "line": 319, "column": 24 }, "end": { - "line": 300, + "line": 319, "column": 53 } }, "expressions": [ { "type": "Identifier", - "start": 11860, - "end": 11867, + "start": 12310, + "end": 12317, "loc": { "start": { - "line": 300, + "line": 319, "column": 27 }, "end": { - "line": 300, + "line": 319, "column": 34 }, "identifierName": "baseIRI" @@ -37875,15 +39196,15 @@ }, { "type": "Identifier", - "start": 11875, - "end": 11884, + "start": 12325, + "end": 12334, "loc": { "start": { - "line": 300, + "line": 319, "column": 42 }, "end": { - "line": 300, + "line": 319, "column": 51 }, "identifierName": "nodeCount" @@ -37894,15 +39215,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 11858, - "end": 11858, + "start": 12308, + "end": 12308, "loc": { "start": { - "line": 300, + "line": 319, "column": 25 }, "end": { - "line": 300, + "line": 319, "column": 25 } }, @@ -37914,15 +39235,15 @@ }, { "type": "TemplateElement", - "start": 11868, - "end": 11873, + "start": 12318, + "end": 12323, "loc": { "start": { - "line": 300, + "line": 319, "column": 35 }, "end": { - "line": 300, + "line": 319, "column": 40 } }, @@ -37934,15 +39255,15 @@ }, { "type": "TemplateElement", - "start": 11885, - "end": 11885, + "start": 12335, + "end": 12335, "loc": { "start": { - "line": 300, + "line": 319, "column": 52 }, "end": { - "line": 300, + "line": 319, "column": 52 } }, @@ -37962,15 +39283,15 @@ { "type": "CommentLine", "value": " Set @id and @type.", - "start": 11811, - "end": 11832, + "start": 12261, + "end": 12282, "loc": { "start": { - "line": 299, + "line": 318, "column": 8 }, "end": { - "line": 299, + "line": 318, "column": 29 } } @@ -37979,58 +39300,58 @@ }, { "type": "ExpressionStatement", - "start": 11896, - "end": 11926, + "start": 12346, + "end": 12376, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 11896, - "end": 11925, + "start": 12346, + "end": 12375, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11896, - "end": 11915, + "start": 12346, + "end": 12365, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 27 } }, "object": { "type": "Identifier", - "start": 11896, - "end": 11908, + "start": 12346, + "end": 12358, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 20 }, "identifierName": "nodeAsJSONLD" @@ -38039,15 +39360,15 @@ }, "property": { "type": "StringLiteral", - "start": 11909, - "end": 11914, + "start": 12359, + "end": 12364, "loc": { "start": { - "line": 301, + "line": 320, "column": 21 }, "end": { - "line": 301, + "line": 320, "column": 26 } }, @@ -38061,15 +39382,15 @@ }, "right": { "type": "Identifier", - "start": 11918, - "end": 11925, + "start": 12368, + "end": 12375, "loc": { "start": { - "line": 301, + "line": 320, "column": 30 }, "end": { - "line": 301, + "line": 320, "column": 37 }, "identifierName": "nodeIRI" @@ -38092,29 +39413,29 @@ }, { "type": "ReturnStatement", - "start": 11948, - "end": 11962, + "start": 12398, + "end": 12412, "loc": { "start": { - "line": 305, + "line": 324, "column": 4 }, "end": { - "line": 305, + "line": 324, "column": 18 } }, "argument": { "type": "Identifier", - "start": 11955, - "end": 11961, + "start": 12405, + "end": 12411, "loc": { "start": { - "line": 305, + "line": 324, "column": 11 }, "end": { - "line": 305, + "line": 324, "column": 17 }, "identifierName": "parsed" @@ -38128,15 +39449,15 @@ }, { "type": "ClassMethod", - "start": 11970, - "end": 16576, + "start": 12420, + "end": 17026, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 422, + "line": 441, "column": 3 } }, @@ -38144,15 +39465,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11970, - "end": 11986, + "start": 12420, + "end": 12436, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 308, + "line": 327, "column": 18 }, "identifierName": "getNodesAsJSONLD" @@ -38167,15 +39488,15 @@ "params": [ { "type": "Identifier", - "start": 11987, - "end": 11994, + "start": 12437, + "end": 12444, "loc": { "start": { - "line": 308, + "line": 327, "column": 19 }, "end": { - "line": 308, + "line": 327, "column": 26 }, "identifierName": "baseIRI" @@ -38184,15 +39505,15 @@ }, { "type": "Identifier", - "start": 11996, - "end": 12008, + "start": 12446, + "end": 12458, "loc": { "start": { - "line": 308, + "line": 327, "column": 28 }, "end": { - "line": 308, + "line": 327, "column": 40 }, "identifierName": "newickParser" @@ -38202,59 +39523,59 @@ ], "body": { "type": "BlockStatement", - "start": 12010, - "end": 16576, + "start": 12460, + "end": 17026, "loc": { "start": { - "line": 308, + "line": 327, "column": 42 }, "end": { - "line": 422, + "line": 441, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 12498, - "end": 12515, + "start": 12948, + "end": 12965, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 21 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12504, - "end": 12514, + "start": 12954, + "end": 12964, "loc": { "start": { - "line": 318, + "line": 337, "column": 10 }, "end": { - "line": 318, + "line": 337, "column": 20 } }, "id": { "type": "Identifier", - "start": 12504, - "end": 12509, + "start": 12954, + "end": 12959, "loc": { "start": { - "line": 318, + "line": 337, "column": 10 }, "end": { - "line": 318, + "line": 337, "column": 15 }, "identifierName": "nodes" @@ -38264,15 +39585,15 @@ }, "init": { "type": "ArrayExpression", - "start": 12512, - "end": 12514, + "start": 12962, + "end": 12964, "loc": { "start": { - "line": 318, + "line": 337, "column": 18 }, "end": { - "line": 318, + "line": 337, "column": 20 } }, @@ -38286,15 +39607,15 @@ { "type": "CommentLine", "value": " Returns a list of all nodes in this phylogeny as a series of nodes.", - "start": 12016, - "end": 12086, + "start": 12466, + "end": 12536, "loc": { "start": { - "line": 309, + "line": 328, "column": 4 }, "end": { - "line": 309, + "line": 328, "column": 74 } } @@ -38302,15 +39623,15 @@ { "type": "CommentLine", "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 12091, - "end": 12164, + "start": 12541, + "end": 12614, "loc": { "start": { - "line": 310, + "line": 329, "column": 4 }, "end": { - "line": 310, + "line": 329, "column": 77 } } @@ -38318,15 +39639,15 @@ { "type": "CommentLine", "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 12169, - "end": 12244, + "start": 12619, + "end": 12694, "loc": { "start": { - "line": 311, + "line": 330, "column": 4 }, "end": { - "line": 311, + "line": 330, "column": 79 } } @@ -38334,15 +39655,15 @@ { "type": "CommentLine", "value": " the baseIRI.", - "start": 12249, - "end": 12266, + "start": 12699, + "end": 12716, "loc": { "start": { - "line": 312, + "line": 331, "column": 4 }, "end": { - "line": 312, + "line": 331, "column": 21 } } @@ -38350,15 +39671,15 @@ { "type": "CommentLine", "value": " - newickParser: A method for converting a Newick string to a object-based", - "start": 12271, - "end": 12347, + "start": 12721, + "end": 12797, "loc": { "start": { - "line": 313, + "line": 332, "column": 4 }, "end": { - "line": 313, + "line": 332, "column": 80 } } @@ -38366,15 +39687,15 @@ { "type": "CommentLine", "value": " representation. See PhylogenyWrapper.getParsedNewick() for an example", - "start": 12352, - "end": 12426, + "start": 12802, + "end": 12876, "loc": { "start": { - "line": 314, + "line": 333, "column": 4 }, "end": { - "line": 314, + "line": 333, "column": 78 } } @@ -38382,15 +39703,15 @@ { "type": "CommentLine", "value": " implementation.", - "start": 12431, - "end": 12451, + "start": 12881, + "end": 12901, "loc": { "start": { - "line": 315, + "line": 334, "column": 4 }, "end": { - "line": 315, + "line": 334, "column": 24 } } @@ -38398,15 +39719,15 @@ { "type": "CommentLine", "value": " List of nodes we have identified.", - "start": 12457, - "end": 12493, + "start": 12907, + "end": 12943, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 40 } } @@ -38416,15 +39737,15 @@ { "type": "CommentLine", "value": " We need to track the identifiers we give each node as we go.", - "start": 12521, - "end": 12584, + "start": 12971, + "end": 13034, "loc": { "start": { - "line": 320, + "line": 339, "column": 4 }, "end": { - "line": 320, + "line": 339, "column": 67 } } @@ -38433,44 +39754,44 @@ }, { "type": "VariableDeclaration", - "start": 12589, - "end": 12610, + "start": 13039, + "end": 13060, "loc": { "start": { - "line": 321, + "line": 340, "column": 4 }, "end": { - "line": 321, + "line": 340, "column": 25 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12595, - "end": 12609, + "start": 13045, + "end": 13059, "loc": { "start": { - "line": 321, + "line": 340, "column": 10 }, "end": { - "line": 321, + "line": 340, "column": 24 } }, "id": { "type": "Identifier", - "start": 12595, - "end": 12604, + "start": 13045, + "end": 13054, "loc": { "start": { - "line": 321, + "line": 340, "column": 10 }, "end": { - "line": 321, + "line": 340, "column": 19 }, "identifierName": "nodesById" @@ -38480,15 +39801,15 @@ }, "init": { "type": "ObjectExpression", - "start": 12607, - "end": 12609, + "start": 13057, + "end": 13059, "loc": { "start": { - "line": 321, + "line": 340, "column": 22 }, "end": { - "line": 321, + "line": 340, "column": 24 } }, @@ -38502,15 +39823,15 @@ { "type": "CommentLine", "value": " We need to track the identifiers we give each node as we go.", - "start": 12521, - "end": 12584, + "start": 12971, + "end": 13034, "loc": { "start": { - "line": 320, + "line": 339, "column": 4 }, "end": { - "line": 320, + "line": 339, "column": 67 } } @@ -38519,44 +39840,44 @@ }, { "type": "VariableDeclaration", - "start": 12615, - "end": 12644, + "start": 13065, + "end": 13094, "loc": { "start": { - "line": 322, + "line": 341, "column": 4 }, "end": { - "line": 322, + "line": 341, "column": 33 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12621, - "end": 12643, + "start": 13071, + "end": 13093, "loc": { "start": { - "line": 322, + "line": 341, "column": 10 }, "end": { - "line": 322, + "line": 341, "column": 32 } }, "id": { "type": "Identifier", - "start": 12621, - "end": 12638, + "start": 13071, + "end": 13088, "loc": { "start": { - "line": 322, + "line": 341, "column": 10 }, "end": { - "line": 322, + "line": 341, "column": 27 }, "identifierName": "nodeIdsByParentId" @@ -38565,15 +39886,15 @@ }, "init": { "type": "ObjectExpression", - "start": 12641, - "end": 12643, + "start": 13091, + "end": 13093, "loc": { "start": { - "line": 322, + "line": 341, "column": 30 }, "end": { - "line": 322, + "line": 341, "column": 32 } }, @@ -38586,15 +39907,15 @@ { "type": "CommentLine", "value": " Extract the newick string.", - "start": 12650, - "end": 12679, + "start": 13100, + "end": 13129, "loc": { "start": { - "line": 324, + "line": 343, "column": 4 }, "end": { - "line": 324, + "line": 343, "column": 33 } } @@ -38603,59 +39924,59 @@ }, { "type": "VariableDeclaration", - "start": 12684, - "end": 12736, + "start": 13134, + "end": 13186, "loc": { "start": { - "line": 325, + "line": 344, "column": 4 }, "end": { - "line": 325, + "line": 344, "column": 56 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12690, - "end": 12735, + "start": 13140, + "end": 13185, "loc": { "start": { - "line": 325, + "line": 344, "column": 10 }, "end": { - "line": 325, + "line": 344, "column": 55 } }, "id": { "type": "ObjectPattern", - "start": 12690, - "end": 12718, + "start": 13140, + "end": 13168, "loc": { "start": { - "line": 325, + "line": 344, "column": 10 }, "end": { - "line": 325, + "line": 344, "column": 38 } }, "properties": [ { "type": "ObjectProperty", - "start": 12692, - "end": 12716, + "start": 13142, + "end": 13166, "loc": { "start": { - "line": 325, + "line": 344, "column": 12 }, "end": { - "line": 325, + "line": 344, "column": 36 } }, @@ -38664,15 +39985,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12692, - "end": 12716, + "start": 13142, + "end": 13166, "loc": { "start": { - "line": 325, + "line": 344, "column": 12 }, "end": { - "line": 325, + "line": 344, "column": 36 }, "identifierName": "additionalNodeProperties" @@ -38682,15 +40003,15 @@ }, "value": { "type": "Identifier", - "start": 12692, - "end": 12716, + "start": 13142, + "end": 13166, "loc": { "start": { - "line": 325, + "line": 344, "column": 12 }, "end": { - "line": 325, + "line": 344, "column": 36 }, "identifierName": "additionalNodeProperties" @@ -38707,44 +40028,44 @@ }, "init": { "type": "MemberExpression", - "start": 12721, - "end": 12735, + "start": 13171, + "end": 13185, "loc": { "start": { - "line": 325, + "line": 344, "column": 41 }, "end": { - "line": 325, + "line": 344, "column": 55 } }, "object": { "type": "ThisExpression", - "start": 12721, - "end": 12725, + "start": 13171, + "end": 13175, "loc": { "start": { - "line": 325, + "line": 344, "column": 41 }, "end": { - "line": 325, + "line": 344, "column": 45 } } }, "property": { "type": "Identifier", - "start": 12726, - "end": 12735, + "start": 13176, + "end": 13185, "loc": { "start": { - "line": 325, + "line": 344, "column": 46 }, "end": { - "line": 325, + "line": 344, "column": 55 }, "identifierName": "phylogeny" @@ -38761,15 +40082,15 @@ { "type": "CommentLine", "value": " Extract the newick string.", - "start": 12650, - "end": 12679, + "start": 13100, + "end": 13129, "loc": { "start": { - "line": 324, + "line": 343, "column": 4 }, "end": { - "line": 324, + "line": 343, "column": 33 } } @@ -38779,15 +40100,15 @@ { "type": "CommentLine", "value": " Parse the Newick string; if parseable, recurse through the nodes,", - "start": 12742, - "end": 12810, + "start": 13192, + "end": 13260, "loc": { "start": { - "line": 327, + "line": 346, "column": 4 }, "end": { - "line": 327, + "line": 346, "column": 72 } } @@ -38795,15 +40116,15 @@ { "type": "CommentLine", "value": " added them to the list of JSON-LD nodes as we go.", - "start": 12815, - "end": 12867, + "start": 13265, + "end": 13317, "loc": { "start": { - "line": 328, + "line": 347, "column": 4 }, "end": { - "line": 328, + "line": 347, "column": 56 } } @@ -38812,44 +40133,44 @@ }, { "type": "VariableDeclaration", - "start": 12873, - "end": 12940, + "start": 13323, + "end": 13390, "loc": { "start": { - "line": 330, + "line": 349, "column": 4 }, "end": { - "line": 330, + "line": 349, "column": 71 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12879, - "end": 12939, + "start": 13329, + "end": 13389, "loc": { "start": { - "line": 330, + "line": 349, "column": 10 }, "end": { - "line": 330, + "line": 349, "column": 70 } }, "id": { "type": "Identifier", - "start": 12879, - "end": 12885, + "start": 13329, + "end": 13335, "loc": { "start": { - "line": 330, + "line": 349, "column": 10 }, "end": { - "line": 330, + "line": 349, "column": 16 }, "identifierName": "parsed" @@ -38859,58 +40180,58 @@ }, "init": { "type": "CallExpression", - "start": 12888, - "end": 12939, + "start": 13338, + "end": 13389, "loc": { "start": { - "line": 330, + "line": 349, "column": 19 }, "end": { - "line": 330, + "line": 349, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 12888, - "end": 12916, + "start": 13338, + "end": 13366, "loc": { "start": { - "line": 330, + "line": 349, "column": 19 }, "end": { - "line": 330, + "line": 349, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 12888, - "end": 12892, + "start": 13338, + "end": 13342, "loc": { "start": { - "line": 330, + "line": 349, "column": 19 }, "end": { - "line": 330, + "line": 349, "column": 23 } } }, "property": { "type": "Identifier", - "start": 12893, - "end": 12916, + "start": 13343, + "end": 13366, "loc": { "start": { - "line": 330, + "line": 349, "column": 24 }, "end": { - "line": 330, + "line": 349, "column": 47 }, "identifierName": "getParsedNewickWithIRIs" @@ -38922,15 +40243,15 @@ "arguments": [ { "type": "Identifier", - "start": 12917, - "end": 12924, + "start": 13367, + "end": 13374, "loc": { "start": { - "line": 330, + "line": 349, "column": 48 }, "end": { - "line": 330, + "line": 349, "column": 55 }, "identifierName": "baseIRI" @@ -38939,15 +40260,15 @@ }, { "type": "Identifier", - "start": 12926, - "end": 12938, + "start": 13376, + "end": 13388, "loc": { "start": { - "line": 330, + "line": 349, "column": 57 }, "end": { - "line": 330, + "line": 349, "column": 69 }, "identifierName": "newickParser" @@ -38964,15 +40285,15 @@ { "type": "CommentLine", "value": " Parse the Newick string; if parseable, recurse through the nodes,", - "start": 12742, - "end": 12810, + "start": 13192, + "end": 13260, "loc": { "start": { - "line": 327, + "line": 346, "column": 4 }, "end": { - "line": 327, + "line": 346, "column": 72 } } @@ -38980,15 +40301,15 @@ { "type": "CommentLine", "value": " added them to the list of JSON-LD nodes as we go.", - "start": 12815, - "end": 12867, + "start": 13265, + "end": 13317, "loc": { "start": { - "line": 328, + "line": 347, "column": 4 }, "end": { - "line": 328, + "line": 347, "column": 56 } } @@ -38997,43 +40318,43 @@ }, { "type": "IfStatement", - "start": 12945, - "end": 15805, + "start": 13395, + "end": 16255, "loc": { "start": { - "line": 331, + "line": 350, "column": 4 }, "end": { - "line": 400, + "line": 419, "column": 5 } }, "test": { "type": "CallExpression", - "start": 12949, - "end": 12968, + "start": 13399, + "end": 13418, "loc": { "start": { - "line": 331, + "line": 350, "column": 8 }, "end": { - "line": 331, + "line": 350, "column": 27 } }, "callee": { "type": "Identifier", - "start": 12949, - "end": 12952, + "start": 13399, + "end": 13402, "loc": { "start": { - "line": 331, + "line": 350, "column": 8 }, "end": { - "line": 331, + "line": 350, "column": 11 }, "identifierName": "has" @@ -39043,15 +40364,15 @@ "arguments": [ { "type": "Identifier", - "start": 12953, - "end": 12959, + "start": 13403, + "end": 13409, "loc": { "start": { - "line": 331, + "line": 350, "column": 12 }, "end": { - "line": 331, + "line": 350, "column": 18 }, "identifierName": "parsed" @@ -39060,15 +40381,15 @@ }, { "type": "StringLiteral", - "start": 12961, - "end": 12967, + "start": 13411, + "end": 13417, "loc": { "start": { - "line": 331, + "line": 350, "column": 20 }, "end": { - "line": 331, + "line": 350, "column": 26 } }, @@ -39082,72 +40403,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 12970, - "end": 15805, + "start": 13420, + "end": 16255, "loc": { "start": { - "line": 331, + "line": 350, "column": 29 }, "end": { - "line": 400, + "line": 419, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 12978, - "end": 15799, + "start": 13428, + "end": 16249, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 399, + "line": 418, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 12978, - "end": 15798, + "start": 13428, + "end": 16248, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 399, + "line": 418, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 12978, - "end": 13007, + "start": 13428, + "end": 13457, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 332, + "line": 351, "column": 35 } }, "object": { "type": "Identifier", - "start": 12978, - "end": 12994, + "start": 13428, + "end": 13444, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 332, + "line": 351, "column": 22 }, "identifierName": "PhylogenyWrapper" @@ -39156,15 +40477,15 @@ }, "property": { "type": "Identifier", - "start": 12995, - "end": 13007, + "start": 13445, + "end": 13457, "loc": { "start": { - "line": 332, + "line": 351, "column": 23 }, "end": { - "line": 332, + "line": 351, "column": 35 }, "identifierName": "recurseNodes" @@ -39176,29 +40497,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 13008, - "end": 13019, + "start": 13458, + "end": 13469, "loc": { "start": { - "line": 332, + "line": 351, "column": 36 }, "end": { - "line": 332, + "line": 351, "column": 47 } }, "object": { "type": "Identifier", - "start": 13008, - "end": 13014, + "start": 13458, + "end": 13464, "loc": { "start": { - "line": 332, + "line": 351, "column": 36 }, "end": { - "line": 332, + "line": 351, "column": 42 }, "identifierName": "parsed" @@ -39207,15 +40528,15 @@ }, "property": { "type": "Identifier", - "start": 13015, - "end": 13019, + "start": 13465, + "end": 13469, "loc": { "start": { - "line": 332, + "line": 351, "column": 43 }, "end": { - "line": 332, + "line": 351, "column": 47 }, "identifierName": "json" @@ -39226,15 +40547,15 @@ }, { "type": "ArrowFunctionExpression", - "start": 13021, - "end": 15797, + "start": 13471, + "end": 16247, "loc": { "start": { - "line": 332, + "line": 351, "column": 49 }, "end": { - "line": 399, + "line": 418, "column": 7 } }, @@ -39245,15 +40566,15 @@ "params": [ { "type": "Identifier", - "start": 13022, - "end": 13026, + "start": 13472, + "end": 13476, "loc": { "start": { - "line": 332, + "line": 351, "column": 50 }, "end": { - "line": 332, + "line": 351, "column": 54 }, "identifierName": "node" @@ -39262,15 +40583,15 @@ }, { "type": "Identifier", - "start": 13028, - "end": 13037, + "start": 13478, + "end": 13487, "loc": { "start": { - "line": 332, + "line": 351, "column": 56 }, "end": { - "line": 332, + "line": 351, "column": 65 }, "identifierName": "nodeCount" @@ -39279,15 +40600,15 @@ }, { "type": "Identifier", - "start": 13039, - "end": 13050, + "start": 13489, + "end": 13500, "loc": { "start": { - "line": 332, + "line": 351, "column": 67 }, "end": { - "line": 332, + "line": 351, "column": 78 }, "identifierName": "parentCount" @@ -39297,59 +40618,59 @@ ], "body": { "type": "BlockStatement", - "start": 13055, - "end": 15797, + "start": 13505, + "end": 16247, "loc": { "start": { - "line": 332, + "line": 351, "column": 83 }, "end": { - "line": 399, + "line": 418, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 13119, - "end": 13143, + "start": 13569, + "end": 13593, "loc": { "start": { - "line": 334, + "line": 353, "column": 8 }, "end": { - "line": 334, + "line": 353, "column": 32 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13125, - "end": 13142, + "start": 13575, + "end": 13592, "loc": { "start": { - "line": 334, + "line": 353, "column": 14 }, "end": { - "line": 334, + "line": 353, "column": 31 } }, "id": { "type": "Identifier", - "start": 13125, - "end": 13137, + "start": 13575, + "end": 13587, "loc": { "start": { - "line": 334, + "line": 353, "column": 14 }, "end": { - "line": 334, + "line": 353, "column": 26 }, "identifierName": "nodeAsJSONLD" @@ -39359,15 +40680,15 @@ }, "init": { "type": "ObjectExpression", - "start": 13140, - "end": 13142, + "start": 13590, + "end": 13592, "loc": { "start": { - "line": 334, + "line": 353, "column": 29 }, "end": { - "line": 334, + "line": 353, "column": 31 } }, @@ -39381,15 +40702,15 @@ { "type": "CommentLine", "value": " Start with the additional node properties.", - "start": 13065, - "end": 13110, + "start": 13515, + "end": 13560, "loc": { "start": { - "line": 333, + "line": 352, "column": 8 }, "end": { - "line": 333, + "line": 352, "column": 53 } } @@ -39399,15 +40720,15 @@ { "type": "CommentLine", "value": " Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!", - "start": 13153, - "end": 13232, + "start": 13603, + "end": 13682, "loc": { "start": { - "line": 336, + "line": 355, "column": 8 }, "end": { - "line": 336, + "line": 355, "column": 87 } } @@ -39416,44 +40737,44 @@ }, { "type": "VariableDeclaration", - "start": 13241, - "end": 13269, + "start": 13691, + "end": 13719, "loc": { "start": { - "line": 337, + "line": 356, "column": 8 }, "end": { - "line": 337, + "line": 356, "column": 36 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13247, - "end": 13268, + "start": 13697, + "end": 13718, "loc": { "start": { - "line": 337, + "line": 356, "column": 14 }, "end": { - "line": 337, + "line": 356, "column": 35 } }, "id": { "type": "Identifier", - "start": 13247, - "end": 13254, + "start": 13697, + "end": 13704, "loc": { "start": { - "line": 337, + "line": 356, "column": 14 }, "end": { - "line": 337, + "line": 356, "column": 21 }, "identifierName": "nodeIRI" @@ -39463,29 +40784,29 @@ }, "init": { "type": "MemberExpression", - "start": 13257, - "end": 13268, + "start": 13707, + "end": 13718, "loc": { "start": { - "line": 337, + "line": 356, "column": 24 }, "end": { - "line": 337, + "line": 356, "column": 35 } }, "object": { "type": "Identifier", - "start": 13257, - "end": 13261, + "start": 13707, + "end": 13711, "loc": { "start": { - "line": 337, + "line": 356, "column": 24 }, "end": { - "line": 337, + "line": 356, "column": 28 }, "identifierName": "node" @@ -39494,15 +40815,15 @@ }, "property": { "type": "StringLiteral", - "start": 13262, - "end": 13267, + "start": 13712, + "end": 13717, "loc": { "start": { - "line": 337, + "line": 356, "column": 29 }, "end": { - "line": 337, + "line": 356, "column": 34 } }, @@ -39522,15 +40843,15 @@ { "type": "CommentLine", "value": " Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!", - "start": 13153, - "end": 13232, + "start": 13603, + "end": 13682, "loc": { "start": { - "line": 336, + "line": 355, "column": 8 }, "end": { - "line": 336, + "line": 355, "column": 87 } } @@ -39539,58 +40860,58 @@ }, { "type": "ExpressionStatement", - "start": 13278, - "end": 13308, + "start": 13728, + "end": 13758, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 13278, - "end": 13307, + "start": 13728, + "end": 13757, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13278, - "end": 13297, + "start": 13728, + "end": 13747, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 27 } }, "object": { "type": "Identifier", - "start": 13278, - "end": 13290, + "start": 13728, + "end": 13740, "loc": { "start": { - "line": 338, + "line": 357, "column": 8 }, "end": { - "line": 338, + "line": 357, "column": 20 }, "identifierName": "nodeAsJSONLD" @@ -39599,15 +40920,15 @@ }, "property": { "type": "StringLiteral", - "start": 13291, - "end": 13296, + "start": 13741, + "end": 13746, "loc": { "start": { - "line": 338, + "line": 357, "column": 21 }, "end": { - "line": 338, + "line": 357, "column": 26 } }, @@ -39621,15 +40942,15 @@ }, "right": { "type": "Identifier", - "start": 13300, - "end": 13307, + "start": 13750, + "end": 13757, "loc": { "start": { - "line": 338, + "line": 357, "column": 30 }, "end": { - "line": 338, + "line": 357, "column": 37 }, "identifierName": "nodeIRI" @@ -39641,15 +40962,15 @@ { "type": "CommentLine", "value": " Since we may need to add multiple classes into the rdf:type, we need", - "start": 13318, - "end": 13389, + "start": 13768, + "end": 13839, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 79 } } @@ -39657,15 +40978,15 @@ { "type": "CommentLine", "value": " to make @type an array. However, the JSON-LD library we use in JPhyloRef", - "start": 13398, - "end": 13473, + "start": 13848, + "end": 13923, "loc": { "start": { - "line": 341, + "line": 360, "column": 8 }, "end": { - "line": 341, + "line": 360, "column": 83 } } @@ -39673,15 +40994,15 @@ { "type": "CommentLine", "value": " can't support @type being an array (despite that being in the standard,", - "start": 13482, - "end": 13556, + "start": 13932, + "end": 14006, "loc": { "start": { - "line": 342, + "line": 361, "column": 8 }, "end": { - "line": 342, + "line": 361, "column": 82 } } @@ -39689,15 +41010,15 @@ { "type": "CommentLine", "value": " see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),", - "start": 13565, - "end": 13659, + "start": 14015, + "end": 14109, "loc": { "start": { - "line": 343, + "line": 362, "column": 8 }, "end": { - "line": 343, + "line": 362, "column": 102 } } @@ -39705,15 +41026,15 @@ { "type": "CommentLine", "value": " so we fall back to using rdf:type instead.", - "start": 13668, - "end": 13713, + "start": 14118, + "end": 14163, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 53 } } @@ -39722,58 +41043,58 @@ }, { "type": "ExpressionStatement", - "start": 13722, - "end": 13788, + "start": 14172, + "end": 14238, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 74 } }, "expression": { "type": "AssignmentExpression", - "start": 13722, - "end": 13787, + "start": 14172, + "end": 14237, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 73 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13722, - "end": 13753, + "start": 14172, + "end": 14203, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 39 } }, "object": { "type": "Identifier", - "start": 13722, - "end": 13734, + "start": 14172, + "end": 14184, "loc": { "start": { - "line": 345, + "line": 364, "column": 8 }, "end": { - "line": 345, + "line": 364, "column": 20 }, "identifierName": "nodeAsJSONLD" @@ -39783,29 +41104,29 @@ }, "property": { "type": "MemberExpression", - "start": 13735, - "end": 13752, + "start": 14185, + "end": 14202, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 38 } }, "object": { "type": "Identifier", - "start": 13735, - "end": 13743, + "start": 14185, + "end": 14193, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 29 }, "identifierName": "owlterms" @@ -39814,15 +41135,15 @@ }, "property": { "type": "Identifier", - "start": 13744, - "end": 13752, + "start": 14194, + "end": 14202, "loc": { "start": { - "line": 345, + "line": 364, "column": 30 }, "end": { - "line": 345, + "line": 364, "column": 38 }, "identifierName": "RDF_TYPE" @@ -39836,45 +41157,45 @@ }, "right": { "type": "ArrayExpression", - "start": 13756, - "end": 13787, + "start": 14206, + "end": 14237, "loc": { "start": { - "line": 345, + "line": 364, "column": 42 }, "end": { - "line": 345, + "line": 364, "column": 73 } }, "elements": [ { "type": "ObjectExpression", - "start": 13757, - "end": 13786, + "start": 14207, + "end": 14236, "loc": { "start": { - "line": 345, + "line": 364, "column": 43 }, "end": { - "line": 345, + "line": 364, "column": 72 } }, "properties": [ { "type": "ObjectProperty", - "start": 13759, - "end": 13784, + "start": 14209, + "end": 14234, "loc": { "start": { - "line": 345, + "line": 364, "column": 45 }, "end": { - "line": 345, + "line": 364, "column": 70 } }, @@ -39883,15 +41204,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 13759, - "end": 13764, + "start": 14209, + "end": 14214, "loc": { "start": { - "line": 345, + "line": 364, "column": 45 }, "end": { - "line": 345, + "line": 364, "column": 50 } }, @@ -39903,29 +41224,29 @@ }, "value": { "type": "MemberExpression", - "start": 13766, - "end": 13784, + "start": 14216, + "end": 14234, "loc": { "start": { - "line": 345, + "line": 364, "column": 52 }, "end": { - "line": 345, + "line": 364, "column": 70 } }, "object": { "type": "Identifier", - "start": 13766, - "end": 13774, + "start": 14216, + "end": 14224, "loc": { "start": { - "line": 345, + "line": 364, "column": 52 }, "end": { - "line": 345, + "line": 364, "column": 60 }, "identifierName": "owlterms" @@ -39934,15 +41255,15 @@ }, "property": { "type": "Identifier", - "start": 13775, - "end": 13784, + "start": 14225, + "end": 14234, "loc": { "start": { - "line": 345, + "line": 364, "column": 61 }, "end": { - "line": 345, + "line": 364, "column": 70 }, "identifierName": "CDAO_NODE" @@ -39962,15 +41283,15 @@ { "type": "CommentLine", "value": " Since we may need to add multiple classes into the rdf:type, we need", - "start": 13318, - "end": 13389, + "start": 13768, + "end": 13839, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 79 } } @@ -39978,15 +41299,15 @@ { "type": "CommentLine", "value": " to make @type an array. However, the JSON-LD library we use in JPhyloRef", - "start": 13398, - "end": 13473, + "start": 13848, + "end": 13923, "loc": { "start": { - "line": 341, + "line": 360, "column": 8 }, "end": { - "line": 341, + "line": 360, "column": 83 } } @@ -39994,15 +41315,15 @@ { "type": "CommentLine", "value": " can't support @type being an array (despite that being in the standard,", - "start": 13482, - "end": 13556, + "start": 13932, + "end": 14006, "loc": { "start": { - "line": 342, + "line": 361, "column": 8 }, "end": { - "line": 342, + "line": 361, "column": 82 } } @@ -40010,15 +41331,15 @@ { "type": "CommentLine", "value": " see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),", - "start": 13565, - "end": 13659, + "start": 14015, + "end": 14109, "loc": { "start": { - "line": 343, + "line": 362, "column": 8 }, "end": { - "line": 343, + "line": 362, "column": 102 } } @@ -40026,15 +41347,15 @@ { "type": "CommentLine", "value": " so we fall back to using rdf:type instead.", - "start": 13668, - "end": 13713, + "start": 14118, + "end": 14163, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 53 } } @@ -40044,15 +41365,15 @@ { "type": "CommentLine", "value": " Add labels, additional node properties and taxonomic units.", - "start": 13798, - "end": 13860, + "start": 14248, + "end": 14310, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 70 } } @@ -40061,57 +41382,57 @@ }, { "type": "IfStatement", - "start": 13869, - "end": 15104, + "start": 14319, + "end": 15554, "loc": { "start": { - "line": 348, + "line": 367, "column": 8 }, "end": { - "line": 379, + "line": 398, "column": 9 } }, "test": { "type": "LogicalExpression", - "start": 13873, - "end": 13910, + "start": 14323, + "end": 14360, "loc": { "start": { - "line": 348, + "line": 367, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 49 } }, "left": { "type": "CallExpression", - "start": 13873, - "end": 13890, + "start": 14323, + "end": 14340, "loc": { "start": { - "line": 348, + "line": 367, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 29 } }, "callee": { "type": "Identifier", - "start": 13873, - "end": 13876, + "start": 14323, + "end": 14326, "loc": { "start": { - "line": 348, + "line": 367, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 15 }, "identifierName": "has" @@ -40122,15 +41443,15 @@ "arguments": [ { "type": "Identifier", - "start": 13877, - "end": 13881, + "start": 14327, + "end": 14331, "loc": { "start": { - "line": 348, + "line": 367, "column": 16 }, "end": { - "line": 348, + "line": 367, "column": 20 }, "identifierName": "node" @@ -40139,15 +41460,15 @@ }, { "type": "StringLiteral", - "start": 13883, - "end": 13889, + "start": 14333, + "end": 14339, "loc": { "start": { - "line": 348, + "line": 367, "column": 22 }, "end": { - "line": 348, + "line": 367, "column": 28 } }, @@ -40163,43 +41484,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 13894, - "end": 13910, + "start": 14344, + "end": 14360, "loc": { "start": { - "line": 348, + "line": 367, "column": 33 }, "end": { - "line": 348, + "line": 367, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 13894, - "end": 13903, + "start": 14344, + "end": 14353, "loc": { "start": { - "line": 348, + "line": 367, "column": 33 }, "end": { - "line": 348, + "line": 367, "column": 42 } }, "object": { "type": "Identifier", - "start": 13894, - "end": 13898, + "start": 14344, + "end": 14348, "loc": { "start": { - "line": 348, + "line": 367, "column": 33 }, "end": { - "line": 348, + "line": 367, "column": 37 }, "identifierName": "node" @@ -40208,15 +41529,15 @@ }, "property": { "type": "Identifier", - "start": 13899, - "end": 13903, + "start": 14349, + "end": 14353, "loc": { "start": { - "line": 348, + "line": 367, "column": 38 }, "end": { - "line": 348, + "line": 367, "column": 42 }, "identifierName": "name" @@ -40228,15 +41549,15 @@ "operator": "!==", "right": { "type": "StringLiteral", - "start": 13908, - "end": 13910, + "start": 14358, + "end": 14360, "loc": { "start": { - "line": 348, + "line": 367, "column": 47 }, "end": { - "line": 348, + "line": 367, "column": 49 } }, @@ -40251,73 +41572,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 13912, - "end": 15104, + "start": 14362, + "end": 15554, "loc": { "start": { - "line": 348, + "line": 367, "column": 51 }, "end": { - "line": 379, + "line": 398, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 13953, - "end": 13987, + "start": 14403, + "end": 14437, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 13953, - "end": 13986, + "start": 14403, + "end": 14436, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13953, - "end": 13972, + "start": 14403, + "end": 14422, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 29 } }, "object": { "type": "Identifier", - "start": 13953, - "end": 13965, + "start": 14403, + "end": 14415, "loc": { "start": { - "line": 350, + "line": 369, "column": 10 }, "end": { - "line": 350, + "line": 369, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -40327,15 +41648,15 @@ }, "property": { "type": "Identifier", - "start": 13966, - "end": 13972, + "start": 14416, + "end": 14422, "loc": { "start": { - "line": 350, + "line": 369, "column": 23 }, "end": { - "line": 350, + "line": 369, "column": 29 }, "identifierName": "labels" @@ -40347,44 +41668,44 @@ }, "right": { "type": "ArrayExpression", - "start": 13975, - "end": 13986, + "start": 14425, + "end": 14436, "loc": { "start": { - "line": 350, + "line": 369, "column": 32 }, "end": { - "line": 350, + "line": 369, "column": 43 } }, "elements": [ { "type": "MemberExpression", - "start": 13976, - "end": 13985, + "start": 14426, + "end": 14435, "loc": { "start": { - "line": 350, + "line": 369, "column": 33 }, "end": { - "line": 350, + "line": 369, "column": 42 } }, "object": { "type": "Identifier", - "start": 13976, - "end": 13980, + "start": 14426, + "end": 14430, "loc": { "start": { - "line": 350, + "line": 369, "column": 33 }, "end": { - "line": 350, + "line": 369, "column": 37 }, "identifierName": "node" @@ -40393,15 +41714,15 @@ }, "property": { "type": "Identifier", - "start": 13981, - "end": 13985, + "start": 14431, + "end": 14435, "loc": { "start": { - "line": 350, + "line": 369, "column": 38 }, "end": { - "line": 350, + "line": 369, "column": 42 }, "identifierName": "name" @@ -40418,15 +41739,15 @@ { "type": "CommentLine", "value": " Add node label.", - "start": 13924, - "end": 13942, + "start": 14374, + "end": 14392, "loc": { "start": { - "line": 349, + "line": 368, "column": 10 }, "end": { - "line": 349, + "line": 368, "column": 28 } } @@ -40436,15 +41757,15 @@ { "type": "CommentLine", "value": " Add additional node properties, if any.", - "start": 13999, - "end": 14041, + "start": 14449, + "end": 14491, "loc": { "start": { - "line": 352, + "line": 371, "column": 10 }, "end": { - "line": 352, + "line": 371, "column": 52 } } @@ -40453,43 +41774,43 @@ }, { "type": "IfStatement", - "start": 14052, - "end": 14311, + "start": 14502, + "end": 14761, "loc": { "start": { - "line": 353, + "line": 372, "column": 10 }, "end": { - "line": 357, + "line": 376, "column": 11 } }, "test": { "type": "LogicalExpression", - "start": 14056, - "end": 14124, + "start": 14506, + "end": 14574, "loc": { "start": { - "line": 353, + "line": 372, "column": 14 }, "end": { - "line": 353, + "line": 372, "column": 82 } }, "left": { "type": "Identifier", - "start": 14056, - "end": 14080, + "start": 14506, + "end": 14530, "loc": { "start": { - "line": 353, + "line": 372, "column": 14 }, "end": { - "line": 353, + "line": 372, "column": 38 }, "identifierName": "additionalNodeProperties" @@ -40500,29 +41821,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 14084, - "end": 14124, + "start": 14534, + "end": 14574, "loc": { "start": { - "line": 353, + "line": 372, "column": 42 }, "end": { - "line": 353, + "line": 372, "column": 82 } }, "callee": { "type": "Identifier", - "start": 14084, - "end": 14087, + "start": 14534, + "end": 14537, "loc": { "start": { - "line": 353, + "line": 372, "column": 42 }, "end": { - "line": 353, + "line": 372, "column": 45 }, "identifierName": "has" @@ -40532,15 +41853,15 @@ "arguments": [ { "type": "Identifier", - "start": 14088, - "end": 14112, + "start": 14538, + "end": 14562, "loc": { "start": { - "line": 353, + "line": 372, "column": 46 }, "end": { - "line": 353, + "line": 372, "column": 70 }, "identifierName": "additionalNodeProperties" @@ -40549,29 +41870,29 @@ }, { "type": "MemberExpression", - "start": 14114, - "end": 14123, + "start": 14564, + "end": 14573, "loc": { "start": { - "line": 353, + "line": 372, "column": 72 }, "end": { - "line": 353, + "line": 372, "column": 81 } }, "object": { "type": "Identifier", - "start": 14114, - "end": 14118, + "start": 14564, + "end": 14568, "loc": { "start": { - "line": 353, + "line": 372, "column": 72 }, "end": { - "line": 353, + "line": 372, "column": 76 }, "identifierName": "node" @@ -40580,15 +41901,15 @@ }, "property": { "type": "Identifier", - "start": 14119, - "end": 14123, + "start": 14569, + "end": 14573, "loc": { "start": { - "line": 353, + "line": 372, "column": 77 }, "end": { - "line": 353, + "line": 372, "column": 81 }, "identifierName": "name" @@ -40603,100 +41924,100 @@ }, "consequent": { "type": "BlockStatement", - "start": 14126, - "end": 14311, + "start": 14576, + "end": 14761, "loc": { "start": { - "line": 353, + "line": 372, "column": 84 }, "end": { - "line": 357, + "line": 376, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 14140, - "end": 14299, + "start": 14590, + "end": 14749, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 356, + "line": 375, "column": 15 } }, "expression": { "type": "CallExpression", - "start": 14140, - "end": 14298, + "start": 14590, + "end": 14748, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 356, + "line": 375, "column": 14 } }, "callee": { "type": "MemberExpression", - "start": 14140, - "end": 14196, + "start": 14590, + "end": 14646, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 68 } }, "object": { "type": "CallExpression", - "start": 14140, - "end": 14188, + "start": 14590, + "end": 14638, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 14140, - "end": 14151, + "start": 14590, + "end": 14601, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 23 } }, "object": { "type": "Identifier", - "start": 14140, - "end": 14146, + "start": 14590, + "end": 14596, "loc": { "start": { - "line": 354, + "line": 373, "column": 12 }, "end": { - "line": 354, + "line": 373, "column": 18 }, "identifierName": "Object" @@ -40705,15 +42026,15 @@ }, "property": { "type": "Identifier", - "start": 14147, - "end": 14151, + "start": 14597, + "end": 14601, "loc": { "start": { - "line": 354, + "line": 373, "column": 19 }, "end": { - "line": 354, + "line": 373, "column": 23 }, "identifierName": "keys" @@ -40725,29 +42046,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 14152, - "end": 14187, + "start": 14602, + "end": 14637, "loc": { "start": { - "line": 354, + "line": 373, "column": 24 }, "end": { - "line": 354, + "line": 373, "column": 59 } }, "object": { "type": "Identifier", - "start": 14152, - "end": 14176, + "start": 14602, + "end": 14626, "loc": { "start": { - "line": 354, + "line": 373, "column": 24 }, "end": { - "line": 354, + "line": 373, "column": 48 }, "identifierName": "additionalNodeProperties" @@ -40756,29 +42077,29 @@ }, "property": { "type": "MemberExpression", - "start": 14177, - "end": 14186, + "start": 14627, + "end": 14636, "loc": { "start": { - "line": 354, + "line": 373, "column": 49 }, "end": { - "line": 354, + "line": 373, "column": 58 } }, "object": { "type": "Identifier", - "start": 14177, - "end": 14181, + "start": 14627, + "end": 14631, "loc": { "start": { - "line": 354, + "line": 373, "column": 49 }, "end": { - "line": 354, + "line": 373, "column": 53 }, "identifierName": "node" @@ -40787,15 +42108,15 @@ }, "property": { "type": "Identifier", - "start": 14182, - "end": 14186, + "start": 14632, + "end": 14636, "loc": { "start": { - "line": 354, + "line": 373, "column": 54 }, "end": { - "line": 354, + "line": 373, "column": 58 }, "identifierName": "name" @@ -40810,15 +42131,15 @@ }, "property": { "type": "Identifier", - "start": 14189, - "end": 14196, + "start": 14639, + "end": 14646, "loc": { "start": { - "line": 354, + "line": 373, "column": 61 }, "end": { - "line": 354, + "line": 373, "column": 68 }, "identifierName": "forEach" @@ -40830,15 +42151,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 14197, - "end": 14297, + "start": 14647, + "end": 14747, "loc": { "start": { - "line": 354, + "line": 373, "column": 69 }, "end": { - "line": 356, + "line": 375, "column": 13 } }, @@ -40849,15 +42170,15 @@ "params": [ { "type": "Identifier", - "start": 14198, - "end": 14201, + "start": 14648, + "end": 14651, "loc": { "start": { - "line": 354, + "line": 373, "column": 70 }, "end": { - "line": 354, + "line": 373, "column": 73 }, "identifierName": "key" @@ -40867,73 +42188,73 @@ ], "body": { "type": "BlockStatement", - "start": 14206, - "end": 14297, + "start": 14656, + "end": 14747, "loc": { "start": { - "line": 354, + "line": 373, "column": 78 }, "end": { - "line": 356, + "line": 375, "column": 13 } }, "body": [ { "type": "ExpressionStatement", - "start": 14222, - "end": 14283, + "start": 14672, + "end": 14733, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 75 } }, "expression": { "type": "AssignmentExpression", - "start": 14222, - "end": 14282, + "start": 14672, + "end": 14732, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 74 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 14222, - "end": 14239, + "start": 14672, + "end": 14689, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 31 } }, "object": { "type": "Identifier", - "start": 14222, - "end": 14234, + "start": 14672, + "end": 14684, "loc": { "start": { - "line": 355, + "line": 374, "column": 14 }, "end": { - "line": 355, + "line": 374, "column": 26 }, "identifierName": "nodeAsJSONLD" @@ -40942,15 +42263,15 @@ }, "property": { "type": "Identifier", - "start": 14235, - "end": 14238, + "start": 14685, + "end": 14688, "loc": { "start": { - "line": 355, + "line": 374, "column": 27 }, "end": { - "line": 355, + "line": 374, "column": 30 }, "identifierName": "key" @@ -40961,43 +42282,43 @@ }, "right": { "type": "MemberExpression", - "start": 14242, - "end": 14282, + "start": 14692, + "end": 14732, "loc": { "start": { - "line": 355, + "line": 374, "column": 34 }, "end": { - "line": 355, + "line": 374, "column": 74 } }, "object": { "type": "MemberExpression", - "start": 14242, - "end": 14277, + "start": 14692, + "end": 14727, "loc": { "start": { - "line": 355, + "line": 374, "column": 34 }, "end": { - "line": 355, + "line": 374, "column": 69 } }, "object": { "type": "Identifier", - "start": 14242, - "end": 14266, + "start": 14692, + "end": 14716, "loc": { "start": { - "line": 355, + "line": 374, "column": 34 }, "end": { - "line": 355, + "line": 374, "column": 58 }, "identifierName": "additionalNodeProperties" @@ -41006,29 +42327,29 @@ }, "property": { "type": "MemberExpression", - "start": 14267, - "end": 14276, + "start": 14717, + "end": 14726, "loc": { "start": { - "line": 355, + "line": 374, "column": 59 }, "end": { - "line": 355, + "line": 374, "column": 68 } }, "object": { "type": "Identifier", - "start": 14267, - "end": 14271, + "start": 14717, + "end": 14721, "loc": { "start": { - "line": 355, + "line": 374, "column": 59 }, "end": { - "line": 355, + "line": 374, "column": 63 }, "identifierName": "node" @@ -41037,15 +42358,15 @@ }, "property": { "type": "Identifier", - "start": 14272, - "end": 14276, + "start": 14722, + "end": 14726, "loc": { "start": { - "line": 355, + "line": 374, "column": 64 }, "end": { - "line": 355, + "line": 374, "column": 68 }, "identifierName": "name" @@ -41058,15 +42379,15 @@ }, "property": { "type": "Identifier", - "start": 14278, - "end": 14281, + "start": 14728, + "end": 14731, "loc": { "start": { - "line": 355, + "line": 374, "column": 70 }, "end": { - "line": 355, + "line": 374, "column": 73 }, "identifierName": "key" @@ -41093,15 +42414,15 @@ { "type": "CommentLine", "value": " Add additional node properties, if any.", - "start": 13999, - "end": 14041, + "start": 14449, + "end": 14491, "loc": { "start": { - "line": 352, + "line": 371, "column": 10 }, "end": { - "line": 352, + "line": 371, "column": 52 } } @@ -41111,15 +42432,15 @@ { "type": "CommentLine", "value": " Add taxonomic units into the metadata.", - "start": 14323, - "end": 14364, + "start": 14773, + "end": 14814, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 51 } } @@ -41128,58 +42449,58 @@ }, { "type": "ExpressionStatement", - "start": 14375, - "end": 14461, + "start": 14825, + "end": 14911, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 96 } }, "expression": { "type": "AssignmentExpression", - "start": 14375, - "end": 14460, + "start": 14825, + "end": 14910, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 95 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 14375, - "end": 14412, + "start": 14825, + "end": 14862, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 47 } }, "object": { "type": "Identifier", - "start": 14375, - "end": 14387, + "start": 14825, + "end": 14837, "loc": { "start": { - "line": 360, + "line": 379, "column": 10 }, "end": { - "line": 360, + "line": 379, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -41189,15 +42510,15 @@ }, "property": { "type": "Identifier", - "start": 14388, - "end": 14412, + "start": 14838, + "end": 14862, "loc": { "start": { - "line": 360, + "line": 379, "column": 23 }, "end": { - "line": 360, + "line": 379, "column": 47 }, "identifierName": "representsTaxonomicUnits" @@ -41209,58 +42530,58 @@ }, "right": { "type": "CallExpression", - "start": 14415, - "end": 14460, + "start": 14865, + "end": 14910, "loc": { "start": { - "line": 360, + "line": 379, "column": 50 }, "end": { - "line": 360, + "line": 379, "column": 95 } }, "callee": { "type": "MemberExpression", - "start": 14415, - "end": 14449, + "start": 14865, + "end": 14899, "loc": { "start": { - "line": 360, + "line": 379, "column": 50 }, "end": { - "line": 360, + "line": 379, "column": 84 } }, "object": { "type": "ThisExpression", - "start": 14415, - "end": 14419, + "start": 14865, + "end": 14869, "loc": { "start": { - "line": 360, + "line": 379, "column": 50 }, "end": { - "line": 360, + "line": 379, "column": 54 } } }, "property": { "type": "Identifier", - "start": 14420, - "end": 14449, + "start": 14870, + "end": 14899, "loc": { "start": { - "line": 360, + "line": 379, "column": 55 }, "end": { - "line": 360, + "line": 379, "column": 84 }, "identifierName": "getTaxonomicUnitsForNodeLabel" @@ -41272,29 +42593,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 14450, - "end": 14459, + "start": 14900, + "end": 14909, "loc": { "start": { - "line": 360, + "line": 379, "column": 85 }, "end": { - "line": 360, + "line": 379, "column": 94 } }, "object": { "type": "Identifier", - "start": 14450, - "end": 14454, + "start": 14900, + "end": 14904, "loc": { "start": { - "line": 360, + "line": 379, "column": 85 }, "end": { - "line": 360, + "line": 379, "column": 89 }, "identifierName": "node" @@ -41303,15 +42624,15 @@ }, "property": { "type": "Identifier", - "start": 14455, - "end": 14459, + "start": 14905, + "end": 14909, "loc": { "start": { - "line": 360, + "line": 379, "column": 90 }, "end": { - "line": 360, + "line": 379, "column": 94 }, "identifierName": "name" @@ -41328,15 +42649,15 @@ { "type": "CommentLine", "value": " Add taxonomic units into the metadata.", - "start": 14323, - "end": 14364, + "start": 14773, + "end": 14814, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 51 } } @@ -41346,15 +42667,15 @@ { "type": "CommentLine", "value": " Add it into the @type so we can reason over it.", - "start": 14473, - "end": 14523, + "start": 14923, + "end": 14973, "loc": { "start": { - "line": 362, + "line": 381, "column": 10 }, "end": { - "line": 362, + "line": 381, "column": 60 } } @@ -41363,71 +42684,71 @@ }, { "type": "ExpressionStatement", - "start": 14534, - "end": 15094, + "start": 14984, + "end": 15544, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 378, + "line": 397, "column": 13 } }, "expression": { "type": "CallExpression", - "start": 14534, - "end": 15093, + "start": 14984, + "end": 15543, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 378, + "line": 397, "column": 12 } }, "callee": { "type": "MemberExpression", - "start": 14534, - "end": 14579, + "start": 14984, + "end": 15029, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 363, + "line": 382, "column": 55 } }, "object": { "type": "MemberExpression", - "start": 14534, - "end": 14571, + "start": 14984, + "end": 15021, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 363, + "line": 382, "column": 47 } }, "object": { "type": "Identifier", - "start": 14534, - "end": 14546, + "start": 14984, + "end": 14996, "loc": { "start": { - "line": 363, + "line": 382, "column": 10 }, "end": { - "line": 363, + "line": 382, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -41437,15 +42758,15 @@ }, "property": { "type": "Identifier", - "start": 14547, - "end": 14571, + "start": 14997, + "end": 15021, "loc": { "start": { - "line": 363, + "line": 382, "column": 23 }, "end": { - "line": 363, + "line": 382, "column": 47 }, "identifierName": "representsTaxonomicUnits" @@ -41457,15 +42778,15 @@ }, "property": { "type": "Identifier", - "start": 14572, - "end": 14579, + "start": 15022, + "end": 15029, "loc": { "start": { - "line": 363, + "line": 382, "column": 48 }, "end": { - "line": 363, + "line": 382, "column": 55 }, "identifierName": "forEach" @@ -41478,15 +42799,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 14580, - "end": 15092, + "start": 15030, + "end": 15542, "loc": { "start": { - "line": 363, + "line": 382, "column": 56 }, "end": { - "line": 378, + "line": 397, "column": 11 } }, @@ -41497,15 +42818,15 @@ "params": [ { "type": "Identifier", - "start": 14581, - "end": 14583, + "start": 15031, + "end": 15033, "loc": { "start": { - "line": 363, + "line": 382, "column": 57 }, "end": { - "line": 363, + "line": 382, "column": 59 }, "identifierName": "tu" @@ -41515,59 +42836,59 @@ ], "body": { "type": "BlockStatement", - "start": 14588, - "end": 15092, + "start": 15038, + "end": 15542, "loc": { "start": { - "line": 363, + "line": 382, "column": 64 }, "end": { - "line": 378, + "line": 397, "column": 11 } }, "body": [ { "type": "VariableDeclaration", - "start": 14602, - "end": 14652, + "start": 15052, + "end": 15102, "loc": { "start": { - "line": 364, + "line": 383, "column": 12 }, "end": { - "line": 364, + "line": 383, "column": 62 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 14608, - "end": 14651, + "start": 15058, + "end": 15101, "loc": { "start": { - "line": 364, + "line": 383, "column": 18 }, "end": { - "line": 364, + "line": 383, "column": 61 } }, "id": { "type": "Identifier", - "start": 14608, - "end": 14620, + "start": 15058, + "end": 15070, "loc": { "start": { - "line": 364, + "line": 383, "column": 18 }, "end": { - "line": 364, + "line": 383, "column": 30 }, "identifierName": "wrappedTUnit" @@ -41576,29 +42897,29 @@ }, "init": { "type": "NewExpression", - "start": 14623, - "end": 14651, + "start": 15073, + "end": 15101, "loc": { "start": { - "line": 364, + "line": 383, "column": 33 }, "end": { - "line": 364, + "line": 383, "column": 61 } }, "callee": { "type": "Identifier", - "start": 14627, - "end": 14647, + "start": 15077, + "end": 15097, "loc": { "start": { - "line": 364, + "line": 383, "column": 37 }, "end": { - "line": 364, + "line": 383, "column": 57 }, "identifierName": "TaxonomicUnitWrapper" @@ -41608,15 +42929,15 @@ "arguments": [ { "type": "Identifier", - "start": 14648, - "end": 14650, + "start": 15098, + "end": 15100, "loc": { "start": { - "line": 364, + "line": 383, "column": 58 }, "end": { - "line": 364, + "line": 383, "column": 60 }, "identifierName": "tu" @@ -41631,29 +42952,29 @@ }, { "type": "IfStatement", - "start": 14666, - "end": 15080, + "start": 15116, + "end": 15530, "loc": { "start": { - "line": 366, + "line": 385, "column": 12 }, "end": { - "line": 377, + "line": 396, "column": 13 } }, "test": { "type": "Identifier", - "start": 14670, - "end": 14682, + "start": 15120, + "end": 15132, "loc": { "start": { - "line": 366, + "line": 385, "column": 16 }, "end": { - "line": 366, + "line": 385, "column": 28 }, "identifierName": "wrappedTUnit" @@ -41662,59 +42983,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 14684, - "end": 15080, + "start": 15134, + "end": 15530, "loc": { "start": { - "line": 366, + "line": 385, "column": 30 }, "end": { - "line": 377, + "line": 396, "column": 13 } }, "body": [ { "type": "VariableDeclaration", - "start": 14700, - "end": 14748, + "start": 15150, + "end": 15198, "loc": { "start": { - "line": 367, + "line": 386, "column": 14 }, "end": { - "line": 367, + "line": 386, "column": 62 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 14706, - "end": 14747, + "start": 15156, + "end": 15197, "loc": { "start": { - "line": 367, + "line": 386, "column": 20 }, "end": { - "line": 367, + "line": 386, "column": 61 } }, "id": { "type": "Identifier", - "start": 14706, - "end": 14716, + "start": 15156, + "end": 15166, "loc": { "start": { - "line": 367, + "line": 386, "column": 20 }, "end": { - "line": 367, + "line": 386, "column": 30 }, "identifierName": "equivClass" @@ -41723,29 +43044,29 @@ }, "init": { "type": "MemberExpression", - "start": 14719, - "end": 14747, + "start": 15169, + "end": 15197, "loc": { "start": { - "line": 367, + "line": 386, "column": 33 }, "end": { - "line": 367, + "line": 386, "column": 61 } }, "object": { "type": "Identifier", - "start": 14719, - "end": 14731, + "start": 15169, + "end": 15181, "loc": { "start": { - "line": 367, + "line": 386, "column": 33 }, "end": { - "line": 367, + "line": 386, "column": 45 }, "identifierName": "wrappedTUnit" @@ -41754,15 +43075,15 @@ }, "property": { "type": "Identifier", - "start": 14732, - "end": 14747, + "start": 15182, + "end": 15197, "loc": { "start": { - "line": 367, + "line": 386, "column": 46 }, "end": { - "line": 367, + "line": 386, "column": 61 }, "identifierName": "asOWLEquivClass" @@ -41777,29 +43098,29 @@ }, { "type": "IfStatement", - "start": 14763, - "end": 15066, + "start": 15213, + "end": 15516, "loc": { "start": { - "line": 368, + "line": 387, "column": 14 }, "end": { - "line": 376, + "line": 395, "column": 15 } }, "test": { "type": "Identifier", - "start": 14767, - "end": 14777, + "start": 15217, + "end": 15227, "loc": { "start": { - "line": 368, + "line": 387, "column": 18 }, "end": { - "line": 368, + "line": 387, "column": 28 }, "identifierName": "equivClass" @@ -41808,86 +43129,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 14779, - "end": 15066, + "start": 15229, + "end": 15516, "loc": { "start": { - "line": 368, + "line": 387, "column": 30 }, "end": { - "line": 376, + "line": 395, "column": 15 } }, "body": [ { "type": "ExpressionStatement", - "start": 14797, - "end": 15050, + "start": 15247, + "end": 15500, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 375, + "line": 394, "column": 18 } }, "expression": { "type": "CallExpression", - "start": 14797, - "end": 15049, + "start": 15247, + "end": 15499, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 375, + "line": 394, "column": 17 } }, "callee": { "type": "MemberExpression", - "start": 14797, - "end": 14833, + "start": 15247, + "end": 15283, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 369, + "line": 388, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 14797, - "end": 14828, + "start": 15247, + "end": 15278, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 369, + "line": 388, "column": 47 } }, "object": { "type": "Identifier", - "start": 14797, - "end": 14809, + "start": 15247, + "end": 15259, "loc": { "start": { - "line": 369, + "line": 388, "column": 16 }, "end": { - "line": 369, + "line": 388, "column": 28 }, "identifierName": "nodeAsJSONLD" @@ -41896,29 +43217,29 @@ }, "property": { "type": "MemberExpression", - "start": 14810, - "end": 14827, + "start": 15260, + "end": 15277, "loc": { "start": { - "line": 369, + "line": 388, "column": 29 }, "end": { - "line": 369, + "line": 388, "column": 46 } }, "object": { "type": "Identifier", - "start": 14810, - "end": 14818, + "start": 15260, + "end": 15268, "loc": { "start": { - "line": 369, + "line": 388, "column": 29 }, "end": { - "line": 369, + "line": 388, "column": 37 }, "identifierName": "owlterms" @@ -41927,15 +43248,15 @@ }, "property": { "type": "Identifier", - "start": 14819, - "end": 14827, + "start": 15269, + "end": 15277, "loc": { "start": { - "line": 369, + "line": 388, "column": 38 }, "end": { - "line": 369, + "line": 388, "column": 46 }, "identifierName": "RDF_TYPE" @@ -41948,15 +43269,15 @@ }, "property": { "type": "Identifier", - "start": 14829, - "end": 14833, + "start": 15279, + "end": 15283, "loc": { "start": { - "line": 369, + "line": 388, "column": 48 }, "end": { - "line": 369, + "line": 388, "column": 52 }, "identifierName": "push" @@ -41968,30 +43289,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 14853, - "end": 15031, + "start": 15303, + "end": 15481, "loc": { "start": { - "line": 370, + "line": 389, "column": 18 }, "end": { - "line": 374, + "line": 393, "column": 19 } }, "properties": [ { "type": "ObjectProperty", - "start": 14875, - "end": 14901, + "start": 15325, + "end": 15351, "loc": { "start": { - "line": 371, + "line": 390, "column": 20 }, "end": { - "line": 371, + "line": 390, "column": 46 } }, @@ -42000,15 +43321,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14875, - "end": 14882, + "start": 15325, + "end": 15332, "loc": { "start": { - "line": 371, + "line": 390, "column": 20 }, "end": { - "line": 371, + "line": 390, "column": 27 } }, @@ -42020,15 +43341,15 @@ }, "value": { "type": "StringLiteral", - "start": 14884, - "end": 14901, + "start": 15334, + "end": 15351, "loc": { "start": { - "line": 371, + "line": 390, "column": 29 }, "end": { - "line": 371, + "line": 390, "column": 46 } }, @@ -42041,15 +43362,15 @@ }, { "type": "ObjectProperty", - "start": 14923, - "end": 14962, + "start": 15373, + "end": 15412, "loc": { "start": { - "line": 372, + "line": 391, "column": 20 }, "end": { - "line": 372, + "line": 391, "column": 59 } }, @@ -42058,15 +43379,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14923, - "end": 14933, + "start": 15373, + "end": 15383, "loc": { "start": { - "line": 372, + "line": 391, "column": 20 }, "end": { - "line": 372, + "line": 391, "column": 30 }, "identifierName": "onProperty" @@ -42075,29 +43396,29 @@ }, "value": { "type": "MemberExpression", - "start": 14935, - "end": 14962, + "start": 15385, + "end": 15412, "loc": { "start": { - "line": 372, + "line": 391, "column": 32 }, "end": { - "line": 372, + "line": 391, "column": 59 } }, "object": { "type": "Identifier", - "start": 14935, - "end": 14943, + "start": 15385, + "end": 15393, "loc": { "start": { - "line": 372, + "line": 391, "column": 32 }, "end": { - "line": 372, + "line": 391, "column": 40 }, "identifierName": "owlterms" @@ -42106,15 +43427,15 @@ }, "property": { "type": "Identifier", - "start": 14944, - "end": 14962, + "start": 15394, + "end": 15412, "loc": { "start": { - "line": 372, + "line": 391, "column": 41 }, "end": { - "line": 372, + "line": 391, "column": 59 }, "identifierName": "CDAO_REPRESENTS_TU" @@ -42126,15 +43447,15 @@ }, { "type": "ObjectProperty", - "start": 14984, - "end": 15010, + "start": 15434, + "end": 15460, "loc": { "start": { - "line": 373, + "line": 392, "column": 20 }, "end": { - "line": 373, + "line": 392, "column": 46 } }, @@ -42143,15 +43464,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14984, - "end": 14998, + "start": 15434, + "end": 15448, "loc": { "start": { - "line": 373, + "line": 392, "column": 20 }, "end": { - "line": 373, + "line": 392, "column": 34 }, "identifierName": "someValuesFrom" @@ -42160,15 +43481,15 @@ }, "value": { "type": "Identifier", - "start": 15000, - "end": 15010, + "start": 15450, + "end": 15460, "loc": { "start": { - "line": 373, + "line": 392, "column": 36 }, "end": { - "line": 373, + "line": 392, "column": 46 }, "identifierName": "equivClass" @@ -42202,15 +43523,15 @@ { "type": "CommentLine", "value": " Add it into the @type so we can reason over it.", - "start": 14473, - "end": 14523, + "start": 14923, + "end": 14973, "loc": { "start": { - "line": 362, + "line": 381, "column": 10 }, "end": { - "line": 362, + "line": 381, "column": 60 } } @@ -42226,15 +43547,15 @@ { "type": "CommentLine", "value": " Add labels, additional node properties and taxonomic units.", - "start": 13798, - "end": 13860, + "start": 14248, + "end": 14310, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 70 } } @@ -42244,15 +43565,15 @@ { "type": "CommentLine", "value": " Add references to parents and siblings.", - "start": 15114, - "end": 15156, + "start": 15564, + "end": 15606, "loc": { "start": { - "line": 381, + "line": 400, "column": 8 }, "end": { - "line": 381, + "line": 400, "column": 50 } } @@ -42261,43 +43582,43 @@ }, { "type": "IfStatement", - "start": 15165, - "end": 15532, + "start": 15615, + "end": 15982, "loc": { "start": { - "line": 382, + "line": 401, "column": 8 }, "end": { - "line": 391, + "line": 410, "column": 9 } }, "test": { "type": "BinaryExpression", - "start": 15169, - "end": 15194, + "start": 15619, + "end": 15644, "loc": { "start": { - "line": 382, + "line": 401, "column": 12 }, "end": { - "line": 382, + "line": 401, "column": 37 } }, "left": { "type": "Identifier", - "start": 15169, - "end": 15180, + "start": 15619, + "end": 15630, "loc": { "start": { - "line": 382, + "line": 401, "column": 12 }, "end": { - "line": 382, + "line": 401, "column": 23 }, "identifierName": "parentCount" @@ -42308,15 +43629,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 15185, - "end": 15194, + "start": 15635, + "end": 15644, "loc": { "start": { - "line": 382, + "line": 401, "column": 28 }, "end": { - "line": 382, + "line": 401, "column": 37 }, "identifierName": "undefined" @@ -42327,59 +43648,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 15196, - "end": 15532, + "start": 15646, + "end": 15982, "loc": { "start": { - "line": 382, + "line": 401, "column": 39 }, "end": { - "line": 391, + "line": 410, "column": 9 } }, "body": [ { "type": "VariableDeclaration", - "start": 15208, - "end": 15258, + "start": 15658, + "end": 15708, "loc": { "start": { - "line": 383, + "line": 402, "column": 10 }, "end": { - "line": 383, + "line": 402, "column": 60 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15214, - "end": 15257, + "start": 15664, + "end": 15707, "loc": { "start": { - "line": 383, + "line": 402, "column": 16 }, "end": { - "line": 383, + "line": 402, "column": 59 } }, "id": { "type": "Identifier", - "start": 15214, - "end": 15223, + "start": 15664, + "end": 15673, "loc": { "start": { - "line": 383, + "line": 402, "column": 16 }, "end": { - "line": 383, + "line": 402, "column": 25 }, "identifierName": "parentIRI" @@ -42388,30 +43709,30 @@ }, "init": { "type": "TemplateLiteral", - "start": 15226, - "end": 15257, + "start": 15676, + "end": 15707, "loc": { "start": { - "line": 383, + "line": 402, "column": 28 }, "end": { - "line": 383, + "line": 402, "column": 59 } }, "expressions": [ { "type": "Identifier", - "start": 15229, - "end": 15236, + "start": 15679, + "end": 15686, "loc": { "start": { - "line": 383, + "line": 402, "column": 31 }, "end": { - "line": 383, + "line": 402, "column": 38 }, "identifierName": "baseIRI" @@ -42420,15 +43741,15 @@ }, { "type": "Identifier", - "start": 15244, - "end": 15255, + "start": 15694, + "end": 15705, "loc": { "start": { - "line": 383, + "line": 402, "column": 46 }, "end": { - "line": 383, + "line": 402, "column": 57 }, "identifierName": "parentCount" @@ -42439,15 +43760,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 15227, - "end": 15227, + "start": 15677, + "end": 15677, "loc": { "start": { - "line": 383, + "line": 402, "column": 29 }, "end": { - "line": 383, + "line": 402, "column": 29 } }, @@ -42459,15 +43780,15 @@ }, { "type": "TemplateElement", - "start": 15237, - "end": 15242, + "start": 15687, + "end": 15692, "loc": { "start": { - "line": 383, + "line": 402, "column": 39 }, "end": { - "line": 383, + "line": 402, "column": 44 } }, @@ -42479,15 +43800,15 @@ }, { "type": "TemplateElement", - "start": 15256, - "end": 15256, + "start": 15706, + "end": 15706, "loc": { "start": { - "line": 383, + "line": 402, "column": 58 }, "end": { - "line": 383, + "line": 402, "column": 58 } }, @@ -42505,58 +43826,58 @@ }, { "type": "ExpressionStatement", - "start": 15269, - "end": 15301, + "start": 15719, + "end": 15751, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 15269, - "end": 15300, + "start": 15719, + "end": 15750, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 15269, - "end": 15288, + "start": 15719, + "end": 15738, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 29 } }, "object": { "type": "Identifier", - "start": 15269, - "end": 15281, + "start": 15719, + "end": 15731, "loc": { "start": { - "line": 384, + "line": 403, "column": 10 }, "end": { - "line": 384, + "line": 403, "column": 22 }, "identifierName": "nodeAsJSONLD" @@ -42565,15 +43886,15 @@ }, "property": { "type": "Identifier", - "start": 15282, - "end": 15288, + "start": 15732, + "end": 15738, "loc": { "start": { - "line": 384, + "line": 403, "column": 23 }, "end": { - "line": 384, + "line": 403, "column": 29 }, "identifierName": "parent" @@ -42584,15 +43905,15 @@ }, "right": { "type": "Identifier", - "start": 15291, - "end": 15300, + "start": 15741, + "end": 15750, "loc": { "start": { - "line": 384, + "line": 403, "column": 32 }, "end": { - "line": 384, + "line": 403, "column": 41 }, "identifierName": "parentIRI" @@ -42604,15 +43925,15 @@ { "type": "CommentLine", "value": " Update list of nodes by parent IDs.", - "start": 15313, - "end": 15351, + "start": 15763, + "end": 15801, "loc": { "start": { - "line": 386, + "line": 405, "column": 10 }, "end": { - "line": 386, + "line": 405, "column": 48 } } @@ -42621,29 +43942,29 @@ }, { "type": "IfStatement", - "start": 15362, - "end": 15469, + "start": 15812, + "end": 15919, "loc": { "start": { - "line": 387, + "line": 406, "column": 10 }, "end": { - "line": 389, + "line": 408, "column": 11 } }, "test": { "type": "UnaryExpression", - "start": 15366, - "end": 15400, + "start": 15816, + "end": 15850, "loc": { "start": { - "line": 387, + "line": 406, "column": 14 }, "end": { - "line": 387, + "line": 406, "column": 48 } }, @@ -42651,29 +43972,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 15367, - "end": 15400, + "start": 15817, + "end": 15850, "loc": { "start": { - "line": 387, + "line": 406, "column": 15 }, "end": { - "line": 387, + "line": 406, "column": 48 } }, "callee": { "type": "Identifier", - "start": 15367, - "end": 15370, + "start": 15817, + "end": 15820, "loc": { "start": { - "line": 387, + "line": 406, "column": 15 }, "end": { - "line": 387, + "line": 406, "column": 18 }, "identifierName": "has" @@ -42684,15 +44005,15 @@ "arguments": [ { "type": "Identifier", - "start": 15371, - "end": 15388, + "start": 15821, + "end": 15838, "loc": { "start": { - "line": 387, + "line": 406, "column": 19 }, "end": { - "line": 387, + "line": 406, "column": 36 }, "identifierName": "nodeIdsByParentId" @@ -42701,15 +44022,15 @@ }, { "type": "Identifier", - "start": 15390, - "end": 15399, + "start": 15840, + "end": 15849, "loc": { "start": { - "line": 387, + "line": 406, "column": 38 }, "end": { - "line": 387, + "line": 406, "column": 47 }, "identifierName": "parentIRI" @@ -42726,73 +44047,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 15402, - "end": 15469, + "start": 15852, + "end": 15919, "loc": { "start": { - "line": 387, + "line": 406, "column": 50 }, "end": { - "line": 389, + "line": 408, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 15416, - "end": 15457, + "start": 15866, + "end": 15907, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 53 } }, "expression": { "type": "AssignmentExpression", - "start": 15416, - "end": 15456, + "start": 15866, + "end": 15906, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 52 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 15416, - "end": 15444, + "start": 15866, + "end": 15894, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 40 } }, "object": { "type": "Identifier", - "start": 15416, - "end": 15433, + "start": 15866, + "end": 15883, "loc": { "start": { - "line": 388, + "line": 407, "column": 12 }, "end": { - "line": 388, + "line": 407, "column": 29 }, "identifierName": "nodeIdsByParentId" @@ -42801,15 +44122,15 @@ }, "property": { "type": "Identifier", - "start": 15434, - "end": 15443, + "start": 15884, + "end": 15893, "loc": { "start": { - "line": 388, + "line": 407, "column": 30 }, "end": { - "line": 388, + "line": 407, "column": 39 }, "identifierName": "parentIRI" @@ -42820,29 +44141,29 @@ }, "right": { "type": "NewExpression", - "start": 15447, - "end": 15456, + "start": 15897, + "end": 15906, "loc": { "start": { - "line": 388, + "line": 407, "column": 43 }, "end": { - "line": 388, + "line": 407, "column": 52 } }, "callee": { "type": "Identifier", - "start": 15451, - "end": 15454, + "start": 15901, + "end": 15904, "loc": { "start": { - "line": 388, + "line": 407, "column": 47 }, "end": { - "line": 388, + "line": 407, "column": 50 }, "identifierName": "Set" @@ -42861,15 +44182,15 @@ { "type": "CommentLine", "value": " Update list of nodes by parent IDs.", - "start": 15313, - "end": 15351, + "start": 15763, + "end": 15801, "loc": { "start": { - "line": 386, + "line": 405, "column": 10 }, "end": { - "line": 386, + "line": 405, "column": 48 } } @@ -42878,71 +44199,71 @@ }, { "type": "ExpressionStatement", - "start": 15480, - "end": 15522, + "start": 15930, + "end": 15972, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 52 } }, "expression": { "type": "CallExpression", - "start": 15480, - "end": 15521, + "start": 15930, + "end": 15971, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 15480, - "end": 15512, + "start": 15930, + "end": 15962, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 42 } }, "object": { "type": "MemberExpression", - "start": 15480, - "end": 15508, + "start": 15930, + "end": 15958, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 38 } }, "object": { "type": "Identifier", - "start": 15480, - "end": 15497, + "start": 15930, + "end": 15947, "loc": { "start": { - "line": 390, + "line": 409, "column": 10 }, "end": { - "line": 390, + "line": 409, "column": 27 }, "identifierName": "nodeIdsByParentId" @@ -42951,15 +44272,15 @@ }, "property": { "type": "Identifier", - "start": 15498, - "end": 15507, + "start": 15948, + "end": 15957, "loc": { "start": { - "line": 390, + "line": 409, "column": 28 }, "end": { - "line": 390, + "line": 409, "column": 37 }, "identifierName": "parentIRI" @@ -42970,15 +44291,15 @@ }, "property": { "type": "Identifier", - "start": 15509, - "end": 15512, + "start": 15959, + "end": 15962, "loc": { "start": { - "line": 390, + "line": 409, "column": 39 }, "end": { - "line": 390, + "line": 409, "column": 42 }, "identifierName": "add" @@ -42990,15 +44311,15 @@ "arguments": [ { "type": "Identifier", - "start": 15513, - "end": 15520, + "start": 15963, + "end": 15970, "loc": { "start": { - "line": 390, + "line": 409, "column": 43 }, "end": { - "line": 390, + "line": 409, "column": 50 }, "identifierName": "nodeIRI" @@ -43017,15 +44338,15 @@ { "type": "CommentLine", "value": " Add references to parents and siblings.", - "start": 15114, - "end": 15156, + "start": 15564, + "end": 15606, "loc": { "start": { - "line": 381, + "line": 400, "column": 8 }, "end": { - "line": 381, + "line": 400, "column": 50 } } @@ -43035,15 +44356,15 @@ { "type": "CommentLine", "value": " Add nodeAsJSONLD to list", - "start": 15542, - "end": 15569, + "start": 15992, + "end": 16019, "loc": { "start": { - "line": 393, + "line": 412, "column": 8 }, "end": { - "line": 393, + "line": 412, "column": 35 } } @@ -43052,43 +44373,43 @@ }, { "type": "IfStatement", - "start": 15578, - "end": 15712, + "start": 16028, + "end": 16162, "loc": { "start": { - "line": 394, + "line": 413, "column": 8 }, "end": { - "line": 396, + "line": 415, "column": 9 } }, "test": { "type": "CallExpression", - "start": 15582, - "end": 15605, + "start": 16032, + "end": 16055, "loc": { "start": { - "line": 394, + "line": 413, "column": 12 }, "end": { - "line": 394, + "line": 413, "column": 35 } }, "callee": { "type": "Identifier", - "start": 15582, - "end": 15585, + "start": 16032, + "end": 16035, "loc": { "start": { - "line": 394, + "line": 413, "column": 12 }, "end": { - "line": 394, + "line": 413, "column": 15 }, "identifierName": "has" @@ -43099,15 +44420,15 @@ "arguments": [ { "type": "Identifier", - "start": 15586, - "end": 15595, + "start": 16036, + "end": 16045, "loc": { "start": { - "line": 394, + "line": 413, "column": 16 }, "end": { - "line": 394, + "line": 413, "column": 25 }, "identifierName": "nodesById" @@ -43116,15 +44437,15 @@ }, { "type": "Identifier", - "start": 15597, - "end": 15604, + "start": 16047, + "end": 16054, "loc": { "start": { - "line": 394, + "line": 413, "column": 27 }, "end": { - "line": 394, + "line": 413, "column": 34 }, "identifierName": "nodeIRI" @@ -43136,58 +44457,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 15607, - "end": 15712, + "start": 16057, + "end": 16162, "loc": { "start": { - "line": 394, + "line": 413, "column": 37 }, "end": { - "line": 396, + "line": 415, "column": 9 } }, "body": [ { "type": "ThrowStatement", - "start": 15619, - "end": 15702, + "start": 16069, + "end": 16152, "loc": { "start": { - "line": 395, + "line": 414, "column": 10 }, "end": { - "line": 395, + "line": 414, "column": 93 } }, "argument": { "type": "NewExpression", - "start": 15625, - "end": 15701, + "start": 16075, + "end": 16151, "loc": { "start": { - "line": 395, + "line": 414, "column": 16 }, "end": { - "line": 395, + "line": 414, "column": 92 } }, "callee": { "type": "Identifier", - "start": 15629, - "end": 15634, + "start": 16079, + "end": 16084, "loc": { "start": { - "line": 395, + "line": 414, "column": 20 }, "end": { - "line": 395, + "line": 414, "column": 25 }, "identifierName": "Error" @@ -43197,30 +44518,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 15635, - "end": 15700, + "start": 16085, + "end": 16150, "loc": { "start": { - "line": 395, + "line": 414, "column": 26 }, "end": { - "line": 395, + "line": 414, "column": 91 } }, "expressions": [ { "type": "Identifier", - "start": 15690, - "end": 15697, + "start": 16140, + "end": 16147, "loc": { "start": { - "line": 395, + "line": 414, "column": 81 }, "end": { - "line": 395, + "line": 414, "column": 88 }, "identifierName": "nodeIRI" @@ -43231,15 +44552,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 15636, - "end": 15688, + "start": 16086, + "end": 16138, "loc": { "start": { - "line": 395, + "line": 414, "column": 27 }, "end": { - "line": 395, + "line": 414, "column": 79 } }, @@ -43251,15 +44572,15 @@ }, { "type": "TemplateElement", - "start": 15698, - "end": 15699, + "start": 16148, + "end": 16149, "loc": { "start": { - "line": 395, + "line": 414, "column": 89 }, "end": { - "line": 395, + "line": 414, "column": 90 } }, @@ -43282,15 +44603,15 @@ { "type": "CommentLine", "value": " Add nodeAsJSONLD to list", - "start": 15542, - "end": 15569, + "start": 15992, + "end": 16019, "loc": { "start": { - "line": 393, + "line": 412, "column": 8 }, "end": { - "line": 393, + "line": 412, "column": 35 } } @@ -43299,58 +44620,58 @@ }, { "type": "ExpressionStatement", - "start": 15721, - "end": 15755, + "start": 16171, + "end": 16205, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 15721, - "end": 15754, + "start": 16171, + "end": 16204, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 15721, - "end": 15739, + "start": 16171, + "end": 16189, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 26 } }, "object": { "type": "Identifier", - "start": 15721, - "end": 15730, + "start": 16171, + "end": 16180, "loc": { "start": { - "line": 397, + "line": 416, "column": 8 }, "end": { - "line": 397, + "line": 416, "column": 17 }, "identifierName": "nodesById" @@ -43359,15 +44680,15 @@ }, "property": { "type": "Identifier", - "start": 15731, - "end": 15738, + "start": 16181, + "end": 16188, "loc": { "start": { - "line": 397, + "line": 416, "column": 18 }, "end": { - "line": 397, + "line": 416, "column": 25 }, "identifierName": "nodeIRI" @@ -43378,15 +44699,15 @@ }, "right": { "type": "Identifier", - "start": 15742, - "end": 15754, + "start": 16192, + "end": 16204, "loc": { "start": { - "line": 397, + "line": 416, "column": 29 }, "end": { - "line": 397, + "line": 416, "column": 41 }, "identifierName": "nodeAsJSONLD" @@ -43397,57 +44718,57 @@ }, { "type": "ExpressionStatement", - "start": 15764, - "end": 15789, + "start": 16214, + "end": 16239, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 33 } }, "expression": { "type": "CallExpression", - "start": 15764, - "end": 15788, + "start": 16214, + "end": 16238, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 32 } }, "callee": { "type": "MemberExpression", - "start": 15764, - "end": 15774, + "start": 16214, + "end": 16224, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 18 } }, "object": { "type": "Identifier", - "start": 15764, - "end": 15769, + "start": 16214, + "end": 16219, "loc": { "start": { - "line": 398, + "line": 417, "column": 8 }, "end": { - "line": 398, + "line": 417, "column": 13 }, "identifierName": "nodes" @@ -43456,15 +44777,15 @@ }, "property": { "type": "Identifier", - "start": 15770, - "end": 15774, + "start": 16220, + "end": 16224, "loc": { "start": { - "line": 398, + "line": 417, "column": 14 }, "end": { - "line": 398, + "line": 417, "column": 18 }, "identifierName": "push" @@ -43476,15 +44797,15 @@ "arguments": [ { "type": "Identifier", - "start": 15775, - "end": 15787, + "start": 16225, + "end": 16237, "loc": { "start": { - "line": 398, + "line": 417, "column": 19 }, "end": { - "line": 398, + "line": 417, "column": 31 }, "identifierName": "nodeAsJSONLD" @@ -43510,15 +44831,15 @@ { "type": "CommentLine", "value": " Go through nodes again and set children and sibling relationships.", - "start": 15811, - "end": 15880, + "start": 16261, + "end": 16330, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 73 } } @@ -43527,85 +44848,85 @@ }, { "type": "ExpressionStatement", - "start": 15885, - "end": 16553, + "start": 16335, + "end": 17003, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 419, + "line": 438, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 15885, - "end": 16552, + "start": 16335, + "end": 17002, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 419, + "line": 438, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 15885, - "end": 15923, + "start": 16335, + "end": 16373, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 42 } }, "object": { "type": "CallExpression", - "start": 15885, - "end": 15915, + "start": 16335, + "end": 16365, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 34 } }, "callee": { "type": "MemberExpression", - "start": 15885, - "end": 15896, + "start": 16335, + "end": 16346, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 15 } }, "object": { "type": "Identifier", - "start": 15885, - "end": 15891, + "start": 16335, + "end": 16341, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 10 }, "identifierName": "Object" @@ -43615,15 +44936,15 @@ }, "property": { "type": "Identifier", - "start": 15892, - "end": 15896, + "start": 16342, + "end": 16346, "loc": { "start": { - "line": 403, + "line": 422, "column": 11 }, "end": { - "line": 403, + "line": 422, "column": 15 }, "identifierName": "keys" @@ -43636,15 +44957,15 @@ "arguments": [ { "type": "Identifier", - "start": 15897, - "end": 15914, + "start": 16347, + "end": 16364, "loc": { "start": { - "line": 403, + "line": 422, "column": 16 }, "end": { - "line": 403, + "line": 422, "column": 33 }, "identifierName": "nodeIdsByParentId" @@ -43656,15 +44977,15 @@ }, "property": { "type": "Identifier", - "start": 15916, - "end": 15923, + "start": 16366, + "end": 16373, "loc": { "start": { - "line": 403, + "line": 422, "column": 35 }, "end": { - "line": 403, + "line": 422, "column": 42 }, "identifierName": "forEach" @@ -43677,15 +44998,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 15924, - "end": 16551, + "start": 16374, + "end": 17001, "loc": { "start": { - "line": 403, + "line": 422, "column": 43 }, "end": { - "line": 419, + "line": 438, "column": 5 } }, @@ -43696,15 +45017,15 @@ "params": [ { "type": "Identifier", - "start": 15925, - "end": 15933, + "start": 16375, + "end": 16383, "loc": { "start": { - "line": 403, + "line": 422, "column": 44 }, "end": { - "line": 403, + "line": 422, "column": 52 }, "identifierName": "parentId" @@ -43714,59 +45035,59 @@ ], "body": { "type": "BlockStatement", - "start": 15938, - "end": 16551, + "start": 16388, + "end": 17001, "loc": { "start": { - "line": 403, + "line": 422, "column": 57 }, "end": { - "line": 419, + "line": 438, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 15995, - "end": 16055, + "start": 16445, + "end": 16505, "loc": { "start": { - "line": 405, + "line": 424, "column": 6 }, "end": { - "line": 405, + "line": 424, "column": 66 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16001, - "end": 16054, + "start": 16451, + "end": 16504, "loc": { "start": { - "line": 405, + "line": 424, "column": 12 }, "end": { - "line": 405, + "line": 424, "column": 65 } }, "id": { "type": "Identifier", - "start": 16001, - "end": 16012, + "start": 16451, + "end": 16462, "loc": { "start": { - "line": 405, + "line": 424, "column": 12 }, "end": { - "line": 405, + "line": 424, "column": 23 }, "identifierName": "childrenIDs" @@ -43776,43 +45097,43 @@ }, "init": { "type": "CallExpression", - "start": 16015, - "end": 16054, + "start": 16465, + "end": 16504, "loc": { "start": { - "line": 405, + "line": 424, "column": 26 }, "end": { - "line": 405, + "line": 424, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 16015, - "end": 16025, + "start": 16465, + "end": 16475, "loc": { "start": { - "line": 405, + "line": 424, "column": 26 }, "end": { - "line": 405, + "line": 424, "column": 36 } }, "object": { "type": "Identifier", - "start": 16015, - "end": 16020, + "start": 16465, + "end": 16470, "loc": { "start": { - "line": 405, + "line": 424, "column": 26 }, "end": { - "line": 405, + "line": 424, "column": 31 }, "identifierName": "Array" @@ -43821,15 +45142,15 @@ }, "property": { "type": "Identifier", - "start": 16021, - "end": 16025, + "start": 16471, + "end": 16475, "loc": { "start": { - "line": 405, + "line": 424, "column": 32 }, "end": { - "line": 405, + "line": 424, "column": 36 }, "identifierName": "from" @@ -43841,29 +45162,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 16026, - "end": 16053, + "start": 16476, + "end": 16503, "loc": { "start": { - "line": 405, + "line": 424, "column": 37 }, "end": { - "line": 405, + "line": 424, "column": 64 } }, "object": { "type": "Identifier", - "start": 16026, - "end": 16043, + "start": 16476, + "end": 16493, "loc": { "start": { - "line": 405, + "line": 424, "column": 37 }, "end": { - "line": 405, + "line": 424, "column": 54 }, "identifierName": "nodeIdsByParentId" @@ -43872,15 +45193,15 @@ }, "property": { "type": "Identifier", - "start": 16044, - "end": 16052, + "start": 16494, + "end": 16502, "loc": { "start": { - "line": 405, + "line": 424, "column": 55 }, "end": { - "line": 405, + "line": 424, "column": 63 }, "identifierName": "parentId" @@ -43899,15 +45220,15 @@ { "type": "CommentLine", "value": " What are the children of this parentId?", - "start": 15946, - "end": 15988, + "start": 16396, + "end": 16438, "loc": { "start": { - "line": 404, + "line": 423, "column": 6 }, "end": { - "line": 404, + "line": 423, "column": 48 } } @@ -43916,44 +45237,44 @@ }, { "type": "VariableDeclaration", - "start": 16062, - "end": 16126, + "start": 16512, + "end": 16576, "loc": { "start": { - "line": 406, + "line": 425, "column": 6 }, "end": { - "line": 406, + "line": 425, "column": 70 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16068, - "end": 16125, + "start": 16518, + "end": 16575, "loc": { "start": { - "line": 406, + "line": 425, "column": 12 }, "end": { - "line": 406, + "line": 425, "column": 69 } }, "id": { "type": "Identifier", - "start": 16068, - "end": 16076, + "start": 16518, + "end": 16526, "loc": { "start": { - "line": 406, + "line": 425, "column": 12 }, "end": { - "line": 406, + "line": 425, "column": 20 }, "identifierName": "children" @@ -43962,43 +45283,43 @@ }, "init": { "type": "CallExpression", - "start": 16079, - "end": 16125, + "start": 16529, + "end": 16575, "loc": { "start": { - "line": 406, + "line": 425, "column": 23 }, "end": { - "line": 406, + "line": 425, "column": 69 } }, "callee": { "type": "MemberExpression", - "start": 16079, - "end": 16094, + "start": 16529, + "end": 16544, "loc": { "start": { - "line": 406, + "line": 425, "column": 23 }, "end": { - "line": 406, + "line": 425, "column": 38 } }, "object": { "type": "Identifier", - "start": 16079, - "end": 16090, + "start": 16529, + "end": 16540, "loc": { "start": { - "line": 406, + "line": 425, "column": 23 }, "end": { - "line": 406, + "line": 425, "column": 34 }, "identifierName": "childrenIDs" @@ -44007,15 +45328,15 @@ }, "property": { "type": "Identifier", - "start": 16091, - "end": 16094, + "start": 16541, + "end": 16544, "loc": { "start": { - "line": 406, + "line": 425, "column": 35 }, "end": { - "line": 406, + "line": 425, "column": 38 }, "identifierName": "map" @@ -44027,15 +45348,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 16095, - "end": 16124, + "start": 16545, + "end": 16574, "loc": { "start": { - "line": 406, + "line": 425, "column": 39 }, "end": { - "line": 406, + "line": 425, "column": 68 } }, @@ -44046,15 +45367,15 @@ "params": [ { "type": "Identifier", - "start": 16095, - "end": 16102, + "start": 16545, + "end": 16552, "loc": { "start": { - "line": 406, + "line": 425, "column": 39 }, "end": { - "line": 406, + "line": 425, "column": 46 }, "identifierName": "childId" @@ -44064,29 +45385,29 @@ ], "body": { "type": "MemberExpression", - "start": 16106, - "end": 16124, + "start": 16556, + "end": 16574, "loc": { "start": { - "line": 406, + "line": 425, "column": 50 }, "end": { - "line": 406, + "line": 425, "column": 68 } }, "object": { "type": "Identifier", - "start": 16106, - "end": 16115, + "start": 16556, + "end": 16565, "loc": { "start": { - "line": 406, + "line": 425, "column": 50 }, "end": { - "line": 406, + "line": 425, "column": 59 }, "identifierName": "nodesById" @@ -44095,15 +45416,15 @@ }, "property": { "type": "Identifier", - "start": 16116, - "end": 16123, + "start": 16566, + "end": 16573, "loc": { "start": { - "line": 406, + "line": 425, "column": 60 }, "end": { - "line": 406, + "line": 425, "column": 67 }, "identifierName": "childId" @@ -44122,15 +45443,15 @@ { "type": "CommentLine", "value": " Is this the root node?", - "start": 16134, - "end": 16159, + "start": 16584, + "end": 16609, "loc": { "start": { - "line": 408, + "line": 427, "column": 6 }, "end": { - "line": 408, + "line": 427, "column": 31 } } @@ -44139,43 +45460,43 @@ }, { "type": "IfStatement", - "start": 16166, - "end": 16288, + "start": 16616, + "end": 16738, "loc": { "start": { - "line": 409, + "line": 428, "column": 6 }, "end": { - "line": 412, + "line": 431, "column": 7 } }, "test": { "type": "CallExpression", - "start": 16170, - "end": 16194, + "start": 16620, + "end": 16644, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 34 } }, "callee": { "type": "Identifier", - "start": 16170, - "end": 16173, + "start": 16620, + "end": 16623, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 13 }, "identifierName": "has" @@ -44186,15 +45507,15 @@ "arguments": [ { "type": "Identifier", - "start": 16174, - "end": 16183, + "start": 16624, + "end": 16633, "loc": { "start": { - "line": 409, + "line": 428, "column": 14 }, "end": { - "line": 409, + "line": 428, "column": 23 }, "identifierName": "nodesById" @@ -44203,15 +45524,15 @@ }, { "type": "Identifier", - "start": 16185, - "end": 16193, + "start": 16635, + "end": 16643, "loc": { "start": { - "line": 409, + "line": 428, "column": 25 }, "end": { - "line": 409, + "line": 428, "column": 33 }, "identifierName": "parentId" @@ -44223,59 +45544,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 16196, - "end": 16288, + "start": 16646, + "end": 16738, "loc": { "start": { - "line": 409, + "line": 428, "column": 36 }, "end": { - "line": 412, + "line": 431, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 16206, - "end": 16241, + "start": 16656, + "end": 16691, "loc": { "start": { - "line": 410, + "line": 429, "column": 8 }, "end": { - "line": 410, + "line": 429, "column": 43 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16212, - "end": 16240, + "start": 16662, + "end": 16690, "loc": { "start": { - "line": 410, + "line": 429, "column": 14 }, "end": { - "line": 410, + "line": 429, "column": 42 } }, "id": { "type": "Identifier", - "start": 16212, - "end": 16218, + "start": 16662, + "end": 16668, "loc": { "start": { - "line": 410, + "line": 429, "column": 14 }, "end": { - "line": 410, + "line": 429, "column": 20 }, "identifierName": "parent" @@ -44284,29 +45605,29 @@ }, "init": { "type": "MemberExpression", - "start": 16221, - "end": 16240, + "start": 16671, + "end": 16690, "loc": { "start": { - "line": 410, + "line": 429, "column": 23 }, "end": { - "line": 410, + "line": 429, "column": 42 } }, "object": { "type": "Identifier", - "start": 16221, - "end": 16230, + "start": 16671, + "end": 16680, "loc": { "start": { - "line": 410, + "line": 429, "column": 23 }, "end": { - "line": 410, + "line": 429, "column": 32 }, "identifierName": "nodesById" @@ -44315,15 +45636,15 @@ }, "property": { "type": "Identifier", - "start": 16231, - "end": 16239, + "start": 16681, + "end": 16689, "loc": { "start": { - "line": 410, + "line": 429, "column": 33 }, "end": { - "line": 410, + "line": 429, "column": 41 }, "identifierName": "parentId" @@ -44338,58 +45659,58 @@ }, { "type": "ExpressionStatement", - "start": 16250, - "end": 16280, + "start": 16700, + "end": 16730, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 16250, - "end": 16279, + "start": 16700, + "end": 16729, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 16250, - "end": 16265, + "start": 16700, + "end": 16715, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 23 } }, "object": { "type": "Identifier", - "start": 16250, - "end": 16256, + "start": 16700, + "end": 16706, "loc": { "start": { - "line": 411, + "line": 430, "column": 8 }, "end": { - "line": 411, + "line": 430, "column": 14 }, "identifierName": "parent" @@ -44398,15 +45719,15 @@ }, "property": { "type": "Identifier", - "start": 16257, - "end": 16265, + "start": 16707, + "end": 16715, "loc": { "start": { - "line": 411, + "line": 430, "column": 15 }, "end": { - "line": 411, + "line": 430, "column": 23 }, "identifierName": "children" @@ -44417,15 +45738,15 @@ }, "right": { "type": "Identifier", - "start": 16268, - "end": 16279, + "start": 16718, + "end": 16729, "loc": { "start": { - "line": 411, + "line": 430, "column": 26 }, "end": { - "line": 411, + "line": 430, "column": 37 }, "identifierName": "childrenIDs" @@ -44442,15 +45763,15 @@ { "type": "CommentLine", "value": " Is this the root node?", - "start": 16134, - "end": 16159, + "start": 16584, + "end": 16609, "loc": { "start": { - "line": 408, + "line": 427, "column": 6 }, "end": { - "line": 408, + "line": 427, "column": 31 } } @@ -44459,57 +45780,57 @@ }, { "type": "ExpressionStatement", - "start": 16296, - "end": 16545, + "start": 16746, + "end": 16995, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 418, + "line": 437, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 16296, - "end": 16544, + "start": 16746, + "end": 16994, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 418, + "line": 437, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 16296, - "end": 16312, + "start": 16746, + "end": 16762, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 414, + "line": 433, "column": 22 } }, "object": { "type": "Identifier", - "start": 16296, - "end": 16304, + "start": 16746, + "end": 16754, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 414, + "line": 433, "column": 14 }, "identifierName": "children" @@ -44518,15 +45839,15 @@ }, "property": { "type": "Identifier", - "start": 16305, - "end": 16312, + "start": 16755, + "end": 16762, "loc": { "start": { - "line": 414, + "line": 433, "column": 15 }, "end": { - "line": 414, + "line": 433, "column": 22 }, "identifierName": "forEach" @@ -44538,15 +45859,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 16313, - "end": 16543, + "start": 16763, + "end": 16993, "loc": { "start": { - "line": 414, + "line": 433, "column": 23 }, "end": { - "line": 418, + "line": 437, "column": 7 } }, @@ -44557,15 +45878,15 @@ "params": [ { "type": "Identifier", - "start": 16314, - "end": 16319, + "start": 16764, + "end": 16769, "loc": { "start": { - "line": 414, + "line": 433, "column": 24 }, "end": { - "line": 414, + "line": 433, "column": 29 }, "identifierName": "child" @@ -44575,59 +45896,59 @@ ], "body": { "type": "BlockStatement", - "start": 16324, - "end": 16543, + "start": 16774, + "end": 16993, "loc": { "start": { - "line": 414, + "line": 433, "column": 34 }, "end": { - "line": 418, + "line": 437, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 16334, - "end": 16362, + "start": 16784, + "end": 16812, "loc": { "start": { - "line": 415, + "line": 434, "column": 8 }, "end": { - "line": 415, + "line": 434, "column": 36 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16340, - "end": 16361, + "start": 16790, + "end": 16811, "loc": { "start": { - "line": 415, + "line": 434, "column": 14 }, "end": { - "line": 415, + "line": 434, "column": 35 } }, "id": { "type": "Identifier", - "start": 16340, - "end": 16353, + "start": 16790, + "end": 16803, "loc": { "start": { - "line": 415, + "line": 434, "column": 14 }, "end": { - "line": 415, + "line": 434, "column": 27 }, "identifierName": "childToModify" @@ -44636,15 +45957,15 @@ }, "init": { "type": "Identifier", - "start": 16356, - "end": 16361, + "start": 16806, + "end": 16811, "loc": { "start": { - "line": 415, + "line": 434, "column": 30 }, "end": { - "line": 415, + "line": 434, "column": 35 }, "identifierName": "child" @@ -44658,15 +45979,15 @@ { "type": "CommentLine", "value": " Add all other sibling to node.siblings, but don't add this node itself!", - "start": 16371, - "end": 16445, + "start": 16821, + "end": 16895, "loc": { "start": { - "line": 416, + "line": 435, "column": 8 }, "end": { - "line": 416, + "line": 435, "column": 82 } } @@ -44675,58 +45996,58 @@ }, { "type": "ExpressionStatement", - "start": 16454, - "end": 16535, + "start": 16904, + "end": 16985, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 89 } }, "expression": { "type": "AssignmentExpression", - "start": 16454, - "end": 16534, + "start": 16904, + "end": 16984, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 88 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 16454, - "end": 16476, + "start": 16904, + "end": 16926, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 30 } }, "object": { "type": "Identifier", - "start": 16454, - "end": 16467, + "start": 16904, + "end": 16917, "loc": { "start": { - "line": 417, + "line": 436, "column": 8 }, "end": { - "line": 417, + "line": 436, "column": 21 }, "identifierName": "childToModify" @@ -44736,15 +46057,15 @@ }, "property": { "type": "Identifier", - "start": 16468, - "end": 16476, + "start": 16918, + "end": 16926, "loc": { "start": { - "line": 417, + "line": 436, "column": 22 }, "end": { - "line": 417, + "line": 436, "column": 30 }, "identifierName": "siblings" @@ -44756,43 +46077,43 @@ }, "right": { "type": "CallExpression", - "start": 16479, - "end": 16534, + "start": 16929, + "end": 16984, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 88 } }, "callee": { "type": "MemberExpression", - "start": 16479, - "end": 16497, + "start": 16929, + "end": 16947, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 51 } }, "object": { "type": "Identifier", - "start": 16479, - "end": 16490, + "start": 16929, + "end": 16940, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 44 }, "identifierName": "childrenIDs" @@ -44801,15 +46122,15 @@ }, "property": { "type": "Identifier", - "start": 16491, - "end": 16497, + "start": 16941, + "end": 16947, "loc": { "start": { - "line": 417, + "line": 436, "column": 45 }, "end": { - "line": 417, + "line": 436, "column": 51 }, "identifierName": "filter" @@ -44821,15 +46142,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 16498, - "end": 16533, + "start": 16948, + "end": 16983, "loc": { "start": { - "line": 417, + "line": 436, "column": 52 }, "end": { - "line": 417, + "line": 436, "column": 87 } }, @@ -44840,15 +46161,15 @@ "params": [ { "type": "Identifier", - "start": 16498, - "end": 16505, + "start": 16948, + "end": 16955, "loc": { "start": { - "line": 417, + "line": 436, "column": 52 }, "end": { - "line": 417, + "line": 436, "column": 59 }, "identifierName": "childId" @@ -44858,29 +46179,29 @@ ], "body": { "type": "BinaryExpression", - "start": 16509, - "end": 16533, + "start": 16959, + "end": 16983, "loc": { "start": { - "line": 417, + "line": 436, "column": 63 }, "end": { - "line": 417, + "line": 436, "column": 87 } }, "left": { "type": "Identifier", - "start": 16509, - "end": 16516, + "start": 16959, + "end": 16966, "loc": { "start": { - "line": 417, + "line": 436, "column": 63 }, "end": { - "line": 417, + "line": 436, "column": 70 }, "identifierName": "childId" @@ -44890,29 +46211,29 @@ "operator": "!==", "right": { "type": "MemberExpression", - "start": 16521, - "end": 16533, + "start": 16971, + "end": 16983, "loc": { "start": { - "line": 417, + "line": 436, "column": 75 }, "end": { - "line": 417, + "line": 436, "column": 87 } }, "object": { "type": "Identifier", - "start": 16521, - "end": 16526, + "start": 16971, + "end": 16976, "loc": { "start": { - "line": 417, + "line": 436, "column": 75 }, "end": { - "line": 417, + "line": 436, "column": 80 }, "identifierName": "child" @@ -44921,15 +46242,15 @@ }, "property": { "type": "StringLiteral", - "start": 16527, - "end": 16532, + "start": 16977, + "end": 16982, "loc": { "start": { - "line": 417, + "line": 436, "column": 81 }, "end": { - "line": 417, + "line": 436, "column": 86 } }, @@ -44951,15 +46272,15 @@ { "type": "CommentLine", "value": " Add all other sibling to node.siblings, but don't add this node itself!", - "start": 16371, - "end": 16445, + "start": 16821, + "end": 16895, "loc": { "start": { - "line": 416, + "line": 435, "column": 8 }, "end": { - "line": 416, + "line": 435, "column": 82 } } @@ -44984,15 +46305,15 @@ { "type": "CommentLine", "value": " Go through nodes again and set children and sibling relationships.", - "start": 15811, - "end": 15880, + "start": 16261, + "end": 16330, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 73 } } @@ -45001,29 +46322,29 @@ }, { "type": "ReturnStatement", - "start": 16559, - "end": 16572, + "start": 17009, + "end": 17022, "loc": { "start": { - "line": 421, + "line": 440, "column": 4 }, "end": { - "line": 421, + "line": 440, "column": 17 } }, "argument": { "type": "Identifier", - "start": 16566, - "end": 16571, + "start": 17016, + "end": 17021, "loc": { "start": { - "line": 421, + "line": 440, "column": 11 }, "end": { - "line": 421, + "line": 440, "column": 16 }, "identifierName": "nodes" @@ -45037,15 +46358,15 @@ }, { "type": "ClassMethod", - "start": 16580, - "end": 18102, + "start": 17030, + "end": 18552, "loc": { "start": { - "line": 424, + "line": 443, "column": 2 }, "end": { - "line": 460, + "line": 479, "column": 3 } }, @@ -45053,15 +46374,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 16580, - "end": 16588, + "start": 17030, + "end": 17038, "loc": { "start": { - "line": 424, + "line": 443, "column": 2 }, "end": { - "line": 424, + "line": 443, "column": 10 }, "identifierName": "asJSONLD" @@ -45076,15 +46397,15 @@ "params": [ { "type": "Identifier", - "start": 16589, - "end": 16600, + "start": 17039, + "end": 17050, "loc": { "start": { - "line": 424, + "line": 443, "column": 11 }, "end": { - "line": 424, + "line": 443, "column": 22 }, "identifierName": "fallbackIRI" @@ -45093,15 +46414,15 @@ }, { "type": "Identifier", - "start": 16602, - "end": 16614, + "start": 17052, + "end": 17064, "loc": { "start": { - "line": 424, + "line": 443, "column": 24 }, "end": { - "line": 424, + "line": 443, "column": 36 }, "identifierName": "newickParser" @@ -45111,59 +46432,59 @@ ], "body": { "type": "BlockStatement", - "start": 16616, - "end": 18102, + "start": 17066, + "end": 18552, "loc": { "start": { - "line": 424, + "line": 443, "column": 38 }, "end": { - "line": 460, + "line": 479, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 17041, - "end": 17110, + "start": 17491, + "end": 17560, "loc": { "start": { - "line": 433, + "line": 452, "column": 4 }, "end": { - "line": 433, + "line": 452, "column": 73 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 17047, - "end": 17109, + "start": 17497, + "end": 17559, "loc": { "start": { - "line": 433, + "line": 452, "column": 10 }, "end": { - "line": 433, + "line": 452, "column": 72 } }, "id": { "type": "Identifier", - "start": 17047, - "end": 17064, + "start": 17497, + "end": 17514, "loc": { "start": { - "line": 433, + "line": 452, "column": 10 }, "end": { - "line": 433, + "line": 452, "column": 27 }, "identifierName": "phylogenyAsJSONLD" @@ -45173,43 +46494,43 @@ }, "init": { "type": "CallExpression", - "start": 17067, - "end": 17109, + "start": 17517, + "end": 17559, "loc": { "start": { - "line": 433, + "line": 452, "column": 30 }, "end": { - "line": 433, + "line": 452, "column": 72 } }, "callee": { "type": "MemberExpression", - "start": 17067, - "end": 17077, + "start": 17517, + "end": 17527, "loc": { "start": { - "line": 433, + "line": 452, "column": 30 }, "end": { - "line": 433, + "line": 452, "column": 40 } }, "object": { "type": "Identifier", - "start": 17067, - "end": 17071, + "start": 17517, + "end": 17521, "loc": { "start": { - "line": 433, + "line": 452, "column": 30 }, "end": { - "line": 433, + "line": 452, "column": 34 }, "identifierName": "JSON" @@ -45218,15 +46539,15 @@ }, "property": { "type": "Identifier", - "start": 17072, - "end": 17077, + "start": 17522, + "end": 17527, "loc": { "start": { - "line": 433, + "line": 452, "column": 35 }, "end": { - "line": 433, + "line": 452, "column": 40 }, "identifierName": "parse" @@ -45238,43 +46559,43 @@ "arguments": [ { "type": "CallExpression", - "start": 17078, - "end": 17108, + "start": 17528, + "end": 17558, "loc": { "start": { - "line": 433, + "line": 452, "column": 41 }, "end": { - "line": 433, + "line": 452, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 17078, - "end": 17092, + "start": 17528, + "end": 17542, "loc": { "start": { - "line": 433, + "line": 452, "column": 41 }, "end": { - "line": 433, + "line": 452, "column": 55 } }, "object": { "type": "Identifier", - "start": 17078, - "end": 17082, + "start": 17528, + "end": 17532, "loc": { "start": { - "line": 433, + "line": 452, "column": 41 }, "end": { - "line": 433, + "line": 452, "column": 45 }, "identifierName": "JSON" @@ -45283,15 +46604,15 @@ }, "property": { "type": "Identifier", - "start": 17083, - "end": 17092, + "start": 17533, + "end": 17542, "loc": { "start": { - "line": 433, + "line": 452, "column": 46 }, "end": { - "line": 433, + "line": 452, "column": 55 }, "identifierName": "stringify" @@ -45303,44 +46624,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 17093, - "end": 17107, + "start": 17543, + "end": 17557, "loc": { "start": { - "line": 433, + "line": 452, "column": 56 }, "end": { - "line": 433, + "line": 452, "column": 70 } }, "object": { "type": "ThisExpression", - "start": 17093, - "end": 17097, + "start": 17543, + "end": 17547, "loc": { "start": { - "line": 433, + "line": 452, "column": 56 }, "end": { - "line": 433, + "line": 452, "column": 60 } } }, "property": { "type": "Identifier", - "start": 17098, - "end": 17107, + "start": 17548, + "end": 17557, "loc": { "start": { - "line": 433, + "line": 452, "column": 61 }, "end": { - "line": 433, + "line": 452, "column": 70 }, "identifierName": "phylogeny" @@ -45361,15 +46682,15 @@ { "type": "CommentLine", "value": " Export this phylogeny as JSON-LD.", - "start": 16622, - "end": 16658, + "start": 17072, + "end": 17108, "loc": { "start": { - "line": 425, + "line": 444, "column": 4 }, "end": { - "line": 425, + "line": 444, "column": 40 } } @@ -45377,15 +46698,15 @@ { "type": "CommentLine", "value": " - fallbackIRI: The fallback IRI to use for this phylogeny if it does not", - "start": 16663, - "end": 16738, + "start": 17113, + "end": 17188, "loc": { "start": { - "line": 426, + "line": 445, "column": 4 }, "end": { - "line": 426, + "line": 445, "column": 79 } } @@ -45393,15 +46714,15 @@ { "type": "CommentLine", "value": " already have an '@id' set.", - "start": 16743, - "end": 16774, + "start": 17193, + "end": 17224, "loc": { "start": { - "line": 427, + "line": 446, "column": 4 }, "end": { - "line": 427, + "line": 446, "column": 35 } } @@ -45409,15 +46730,15 @@ { "type": "CommentLine", "value": " - newickParser: A function that parses a Newick string and returns a", - "start": 16779, - "end": 16850, + "start": 17229, + "end": 17300, "loc": { "start": { - "line": 428, + "line": 447, "column": 4 }, "end": { - "line": 428, + "line": 447, "column": 75 } } @@ -45425,15 +46746,15 @@ { "type": "CommentLine", "value": " an object based representation of this phylogeny. If not set, the", - "start": 16855, - "end": 16925, + "start": 17305, + "end": 17375, "loc": { "start": { - "line": 429, + "line": 448, "column": 4 }, "end": { - "line": 429, + "line": 448, "column": 74 } } @@ -45441,15 +46762,15 @@ { "type": "CommentLine", "value": " static method PhylogenyWrapper.getParsedNewick will be used instead.", - "start": 16930, - "end": 17003, + "start": 17380, + "end": 17453, "loc": { "start": { - "line": 430, + "line": 449, "column": 4 }, "end": { - "line": 430, + "line": 449, "column": 77 } } @@ -45457,15 +46778,15 @@ { "type": "CommentLine", "value": " Create a copy to export.", - "start": 17009, - "end": 17036, + "start": 17459, + "end": 17486, "loc": { "start": { - "line": 432, + "line": 451, "column": 4 }, "end": { - "line": 432, + "line": 451, "column": 31 } } @@ -45475,15 +46796,15 @@ { "type": "CommentLine", "value": " Set name and class for phylogeny. If no '@id' is set, use the provided", - "start": 17116, - "end": 17189, + "start": 17566, + "end": 17639, "loc": { "start": { - "line": 435, + "line": 454, "column": 4 }, "end": { - "line": 435, + "line": 454, "column": 77 } } @@ -45491,15 +46812,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 17194, - "end": 17209, + "start": 17644, + "end": 17659, "loc": { "start": { - "line": 436, + "line": 455, "column": 4 }, "end": { - "line": 436, + "line": 455, "column": 19 } } @@ -45508,29 +46829,29 @@ }, { "type": "IfStatement", - "start": 17214, - "end": 17289, + "start": 17664, + "end": 17739, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 79 } }, "test": { "type": "UnaryExpression", - "start": 17218, - "end": 17248, + "start": 17668, + "end": 17698, "loc": { "start": { - "line": 437, + "line": 456, "column": 8 }, "end": { - "line": 437, + "line": 456, "column": 38 } }, @@ -45538,29 +46859,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 17219, - "end": 17248, + "start": 17669, + "end": 17698, "loc": { "start": { - "line": 437, + "line": 456, "column": 9 }, "end": { - "line": 437, + "line": 456, "column": 38 } }, "callee": { "type": "Identifier", - "start": 17219, - "end": 17222, + "start": 17669, + "end": 17672, "loc": { "start": { - "line": 437, + "line": 456, "column": 9 }, "end": { - "line": 437, + "line": 456, "column": 12 }, "identifierName": "has" @@ -45571,15 +46892,15 @@ "arguments": [ { "type": "Identifier", - "start": 17223, - "end": 17240, + "start": 17673, + "end": 17690, "loc": { "start": { - "line": 437, + "line": 456, "column": 13 }, "end": { - "line": 437, + "line": 456, "column": 30 }, "identifierName": "phylogenyAsJSONLD" @@ -45588,15 +46909,15 @@ }, { "type": "StringLiteral", - "start": 17242, - "end": 17247, + "start": 17692, + "end": 17697, "loc": { "start": { - "line": 437, + "line": 456, "column": 32 }, "end": { - "line": 437, + "line": 456, "column": 37 } }, @@ -45616,58 +46937,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 17250, - "end": 17289, + "start": 17700, + "end": 17739, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 79 } }, "expression": { "type": "AssignmentExpression", - "start": 17250, - "end": 17288, + "start": 17700, + "end": 17738, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 78 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17250, - "end": 17274, + "start": 17700, + "end": 17724, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 64 } }, "object": { "type": "Identifier", - "start": 17250, - "end": 17267, + "start": 17700, + "end": 17717, "loc": { "start": { - "line": 437, + "line": 456, "column": 40 }, "end": { - "line": 437, + "line": 456, "column": 57 }, "identifierName": "phylogenyAsJSONLD" @@ -45676,15 +46997,15 @@ }, "property": { "type": "StringLiteral", - "start": 17268, - "end": 17273, + "start": 17718, + "end": 17723, "loc": { "start": { - "line": 437, + "line": 456, "column": 58 }, "end": { - "line": 437, + "line": 456, "column": 63 } }, @@ -45698,15 +47019,15 @@ }, "right": { "type": "Identifier", - "start": 17277, - "end": 17288, + "start": 17727, + "end": 17738, "loc": { "start": { - "line": 437, + "line": 456, "column": 67 }, "end": { - "line": 437, + "line": 456, "column": 78 }, "identifierName": "fallbackIRI" @@ -45720,15 +47041,15 @@ { "type": "CommentLine", "value": " Set name and class for phylogeny. If no '@id' is set, use the provided", - "start": 17116, - "end": 17189, + "start": 17566, + "end": 17639, "loc": { "start": { - "line": 435, + "line": 454, "column": 4 }, "end": { - "line": 435, + "line": 454, "column": 77 } } @@ -45736,15 +47057,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 17194, - "end": 17209, + "start": 17644, + "end": 17659, "loc": { "start": { - "line": 436, + "line": 455, "column": 4 }, "end": { - "line": 436, + "line": 455, "column": 19 } } @@ -45753,58 +47074,58 @@ }, { "type": "ExpressionStatement", - "start": 17294, - "end": 17361, + "start": 17744, + "end": 17811, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 17294, - "end": 17360, + "start": 17744, + "end": 17810, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17294, - "end": 17320, + "start": 17744, + "end": 17770, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 30 } }, "object": { "type": "Identifier", - "start": 17294, - "end": 17311, + "start": 17744, + "end": 17761, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 21 }, "identifierName": "phylogenyAsJSONLD" @@ -45813,15 +47134,15 @@ }, "property": { "type": "StringLiteral", - "start": 17312, - "end": 17319, + "start": 17762, + "end": 17769, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 29 } }, @@ -45835,15 +47156,15 @@ }, "right": { "type": "StringLiteral", - "start": 17323, - "end": 17360, + "start": 17773, + "end": 17810, "loc": { "start": { - "line": 438, + "line": 457, "column": 33 }, "end": { - "line": 438, + "line": 457, "column": 70 } }, @@ -45858,15 +47179,15 @@ { "type": "CommentLine", "value": " Translate nodes into JSON-LD objects.", - "start": 17367, - "end": 17407, + "start": 17817, + "end": 17857, "loc": { "start": { - "line": 440, + "line": 459, "column": 4 }, "end": { - "line": 440, + "line": 459, "column": 44 } } @@ -45875,58 +47196,58 @@ }, { "type": "ExpressionStatement", - "start": 17412, - "end": 17500, + "start": 17862, + "end": 17950, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 92 } }, "expression": { "type": "AssignmentExpression", - "start": 17412, - "end": 17499, + "start": 17862, + "end": 17949, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 91 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17412, - "end": 17435, + "start": 17862, + "end": 17885, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 27 } }, "object": { "type": "Identifier", - "start": 17412, - "end": 17429, + "start": 17862, + "end": 17879, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 21 }, "identifierName": "phylogenyAsJSONLD" @@ -45936,15 +47257,15 @@ }, "property": { "type": "Identifier", - "start": 17430, - "end": 17435, + "start": 17880, + "end": 17885, "loc": { "start": { - "line": 441, + "line": 460, "column": 22 }, "end": { - "line": 441, + "line": 460, "column": 27 }, "identifierName": "nodes" @@ -45956,58 +47277,58 @@ }, "right": { "type": "CallExpression", - "start": 17438, - "end": 17499, + "start": 17888, + "end": 17949, "loc": { "start": { - "line": 441, + "line": 460, "column": 30 }, "end": { - "line": 441, + "line": 460, "column": 91 } }, "callee": { "type": "MemberExpression", - "start": 17438, - "end": 17459, + "start": 17888, + "end": 17909, "loc": { "start": { - "line": 441, + "line": 460, "column": 30 }, "end": { - "line": 441, + "line": 460, "column": 51 } }, "object": { "type": "ThisExpression", - "start": 17438, - "end": 17442, + "start": 17888, + "end": 17892, "loc": { "start": { - "line": 441, + "line": 460, "column": 30 }, "end": { - "line": 441, + "line": 460, "column": 34 } } }, "property": { "type": "Identifier", - "start": 17443, - "end": 17459, + "start": 17893, + "end": 17909, "loc": { "start": { - "line": 441, + "line": 460, "column": 35 }, "end": { - "line": 441, + "line": 460, "column": 51 }, "identifierName": "getNodesAsJSONLD" @@ -46019,29 +47340,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 17460, - "end": 17484, + "start": 17910, + "end": 17934, "loc": { "start": { - "line": 441, + "line": 460, "column": 52 }, "end": { - "line": 441, + "line": 460, "column": 76 } }, "object": { "type": "Identifier", - "start": 17460, - "end": 17477, + "start": 17910, + "end": 17927, "loc": { "start": { - "line": 441, + "line": 460, "column": 52 }, "end": { - "line": 441, + "line": 460, "column": 69 }, "identifierName": "phylogenyAsJSONLD" @@ -46050,15 +47371,15 @@ }, "property": { "type": "StringLiteral", - "start": 17478, - "end": 17483, + "start": 17928, + "end": 17933, "loc": { "start": { - "line": 441, + "line": 460, "column": 70 }, "end": { - "line": 441, + "line": 460, "column": 75 } }, @@ -46072,15 +47393,15 @@ }, { "type": "Identifier", - "start": 17486, - "end": 17498, + "start": 17936, + "end": 17948, "loc": { "start": { - "line": 441, + "line": 460, "column": 78 }, "end": { - "line": 441, + "line": 460, "column": 90 }, "identifierName": "newickParser" @@ -46095,15 +47416,15 @@ { "type": "CommentLine", "value": " Translate nodes into JSON-LD objects.", - "start": 17367, - "end": 17407, + "start": 17817, + "end": 17857, "loc": { "start": { - "line": 440, + "line": 459, "column": 4 }, "end": { - "line": 440, + "line": 459, "column": 44 } } @@ -46112,71 +47433,71 @@ }, { "type": "IfStatement", - "start": 17505, - "end": 17760, + "start": 17955, + "end": 18210, "loc": { "start": { - "line": 442, + "line": 461, "column": 4 }, "end": { - "line": 448, + "line": 467, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 17509, - "end": 17543, + "start": 17959, + "end": 17993, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 42 } }, "left": { "type": "MemberExpression", - "start": 17509, - "end": 17539, + "start": 17959, + "end": 17989, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 38 } }, "object": { "type": "MemberExpression", - "start": 17509, - "end": 17532, + "start": 17959, + "end": 17982, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 31 } }, "object": { "type": "Identifier", - "start": 17509, - "end": 17526, + "start": 17959, + "end": 17976, "loc": { "start": { - "line": 442, + "line": 461, "column": 8 }, "end": { - "line": 442, + "line": 461, "column": 25 }, "identifierName": "phylogenyAsJSONLD" @@ -46185,15 +47506,15 @@ }, "property": { "type": "Identifier", - "start": 17527, - "end": 17532, + "start": 17977, + "end": 17982, "loc": { "start": { - "line": 442, + "line": 461, "column": 26 }, "end": { - "line": 442, + "line": 461, "column": 31 }, "identifierName": "nodes" @@ -46204,15 +47525,15 @@ }, "property": { "type": "Identifier", - "start": 17533, - "end": 17539, + "start": 17983, + "end": 17989, "loc": { "start": { - "line": 442, + "line": 461, "column": 32 }, "end": { - "line": 442, + "line": 461, "column": 38 }, "identifierName": "length" @@ -46224,15 +47545,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 17542, - "end": 17543, + "start": 17992, + "end": 17993, "loc": { "start": { - "line": 442, + "line": 461, "column": 41 }, "end": { - "line": 442, + "line": 461, "column": 42 } }, @@ -46245,73 +47566,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 17545, - "end": 17760, + "start": 17995, + "end": 18210, "loc": { "start": { - "line": 442, + "line": 461, "column": 44 }, "end": { - "line": 448, + "line": 467, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 17662, - "end": 17754, + "start": 18112, + "end": 18204, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 17662, - "end": 17753, + "start": 18112, + "end": 18203, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17662, - "end": 17691, + "start": 18112, + "end": 18141, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 445, + "line": 464, "column": 35 } }, "object": { "type": "Identifier", - "start": 17662, - "end": 17679, + "start": 18112, + "end": 18129, "loc": { "start": { - "line": 445, + "line": 464, "column": 6 }, "end": { - "line": 445, + "line": 464, "column": 23 }, "identifierName": "phylogenyAsJSONLD" @@ -46321,15 +47642,15 @@ }, "property": { "type": "Identifier", - "start": 17680, - "end": 17691, + "start": 18130, + "end": 18141, "loc": { "start": { - "line": 445, + "line": 464, "column": 24 }, "end": { - "line": 445, + "line": 464, "column": 35 }, "identifierName": "hasRootNode" @@ -46341,30 +47662,30 @@ }, "right": { "type": "ObjectExpression", - "start": 17694, - "end": 17753, + "start": 18144, + "end": 18203, "loc": { "start": { - "line": 445, + "line": 464, "column": 38 }, "end": { - "line": 447, + "line": 466, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 17704, - "end": 17744, + "start": 18154, + "end": 18194, "loc": { "start": { - "line": 446, + "line": 465, "column": 8 }, "end": { - "line": 446, + "line": 465, "column": 48 } }, @@ -46373,15 +47694,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 17704, - "end": 17709, + "start": 18154, + "end": 18159, "loc": { "start": { - "line": 446, + "line": 465, "column": 8 }, "end": { - "line": 446, + "line": 465, "column": 13 } }, @@ -46393,57 +47714,57 @@ }, "value": { "type": "MemberExpression", - "start": 17711, - "end": 17744, + "start": 18161, + "end": 18194, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 48 } }, "object": { "type": "MemberExpression", - "start": 17711, - "end": 17737, + "start": 18161, + "end": 18187, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 41 } }, "object": { "type": "MemberExpression", - "start": 17711, - "end": 17734, + "start": 18161, + "end": 18184, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 38 } }, "object": { "type": "Identifier", - "start": 17711, - "end": 17728, + "start": 18161, + "end": 18178, "loc": { "start": { - "line": 446, + "line": 465, "column": 15 }, "end": { - "line": 446, + "line": 465, "column": 32 }, "identifierName": "phylogenyAsJSONLD" @@ -46452,15 +47773,15 @@ }, "property": { "type": "Identifier", - "start": 17729, - "end": 17734, + "start": 18179, + "end": 18184, "loc": { "start": { - "line": 446, + "line": 465, "column": 33 }, "end": { - "line": 446, + "line": 465, "column": 38 }, "identifierName": "nodes" @@ -46471,15 +47792,15 @@ }, "property": { "type": "NumericLiteral", - "start": 17735, - "end": 17736, + "start": 18185, + "end": 18186, "loc": { "start": { - "line": 446, + "line": 465, "column": 39 }, "end": { - "line": 446, + "line": 465, "column": 40 } }, @@ -46493,15 +47814,15 @@ }, "property": { "type": "StringLiteral", - "start": 17738, - "end": 17743, + "start": 18188, + "end": 18193, "loc": { "start": { - "line": 446, + "line": 465, "column": 42 }, "end": { - "line": 446, + "line": 465, "column": 47 } }, @@ -46522,15 +47843,15 @@ { "type": "CommentLine", "value": " We don't have a better way to identify the root node, so we just", - "start": 17553, - "end": 17620, + "start": 18003, + "end": 18070, "loc": { "start": { - "line": 443, + "line": 462, "column": 6 }, "end": { - "line": 443, + "line": 462, "column": 73 } } @@ -46538,15 +47859,15 @@ { "type": "CommentLine", "value": " default to the first one.", - "start": 17627, - "end": 17655, + "start": 18077, + "end": 18105, "loc": { "start": { - "line": 444, + "line": 463, "column": 6 }, "end": { - "line": 444, + "line": 463, "column": 34 } } @@ -46562,15 +47883,15 @@ { "type": "CommentLine", "value": " Add a bibliographicCitation to the source if it is a Citation.", - "start": 17766, - "end": 17831, + "start": 18216, + "end": 18281, "loc": { "start": { - "line": 450, + "line": 469, "column": 4 }, "end": { - "line": 450, + "line": 469, "column": 69 } } @@ -46579,43 +47900,43 @@ }, { "type": "IfStatement", - "start": 17836, - "end": 18067, + "start": 18286, + "end": 18517, "loc": { "start": { - "line": 451, + "line": 470, "column": 4 }, "end": { - "line": 457, + "line": 476, "column": 5 } }, "test": { "type": "CallExpression", - "start": 17840, - "end": 17872, + "start": 18290, + "end": 18322, "loc": { "start": { - "line": 451, + "line": 470, "column": 8 }, "end": { - "line": 451, + "line": 470, "column": 40 } }, "callee": { "type": "Identifier", - "start": 17840, - "end": 17843, + "start": 18290, + "end": 18293, "loc": { "start": { - "line": 451, + "line": 470, "column": 8 }, "end": { - "line": 451, + "line": 470, "column": 11 }, "identifierName": "has" @@ -46626,15 +47947,15 @@ "arguments": [ { "type": "Identifier", - "start": 17844, - "end": 17861, + "start": 18294, + "end": 18311, "loc": { "start": { - "line": 451, + "line": 470, "column": 12 }, "end": { - "line": 451, + "line": 470, "column": 29 }, "identifierName": "phylogenyAsJSONLD" @@ -46643,15 +47964,15 @@ }, { "type": "StringLiteral", - "start": 17863, - "end": 17871, + "start": 18313, + "end": 18321, "loc": { "start": { - "line": 451, + "line": 470, "column": 31 }, "end": { - "line": 451, + "line": 470, "column": 39 } }, @@ -46666,59 +47987,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 17874, - "end": 18067, + "start": 18324, + "end": 18517, "loc": { "start": { - "line": 451, + "line": 470, "column": 42 }, "end": { - "line": 457, + "line": 476, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 17882, - "end": 17922, + "start": 18332, + "end": 18372, "loc": { "start": { - "line": 452, + "line": 471, "column": 6 }, "end": { - "line": 452, + "line": 471, "column": 46 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 17888, - "end": 17921, + "start": 18338, + "end": 18371, "loc": { "start": { - "line": 452, + "line": 471, "column": 12 }, "end": { - "line": 452, + "line": 471, "column": 45 } }, "id": { "type": "Identifier", - "start": 17888, - "end": 17894, + "start": 18338, + "end": 18344, "loc": { "start": { - "line": 452, + "line": 471, "column": 12 }, "end": { - "line": 452, + "line": 471, "column": 18 }, "identifierName": "source" @@ -46727,29 +48048,29 @@ }, "init": { "type": "MemberExpression", - "start": 17897, - "end": 17921, + "start": 18347, + "end": 18371, "loc": { "start": { - "line": 452, + "line": 471, "column": 21 }, "end": { - "line": 452, + "line": 471, "column": 45 } }, "object": { "type": "Identifier", - "start": 17897, - "end": 17914, + "start": 18347, + "end": 18364, "loc": { "start": { - "line": 452, + "line": 471, "column": 21 }, "end": { - "line": 452, + "line": 471, "column": 38 }, "identifierName": "phylogenyAsJSONLD" @@ -46758,15 +48079,15 @@ }, "property": { "type": "Identifier", - "start": 17915, - "end": 17921, + "start": 18365, + "end": 18371, "loc": { "start": { - "line": 452, + "line": 471, "column": 39 }, "end": { - "line": 452, + "line": 471, "column": 45 }, "identifierName": "source" @@ -46781,29 +48102,29 @@ }, { "type": "IfStatement", - "start": 17930, - "end": 18061, + "start": 18380, + "end": 18511, "loc": { "start": { - "line": 454, + "line": 473, "column": 6 }, "end": { - "line": 456, + "line": 475, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 17934, - "end": 17971, + "start": 18384, + "end": 18421, "loc": { "start": { - "line": 454, + "line": 473, "column": 10 }, "end": { - "line": 454, + "line": 473, "column": 47 } }, @@ -46811,29 +48132,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 17935, - "end": 17971, + "start": 18385, + "end": 18421, "loc": { "start": { - "line": 454, + "line": 473, "column": 11 }, "end": { - "line": 454, + "line": 473, "column": 47 } }, "callee": { "type": "Identifier", - "start": 17935, - "end": 17938, + "start": 18385, + "end": 18388, "loc": { "start": { - "line": 454, + "line": 473, "column": 11 }, "end": { - "line": 454, + "line": 473, "column": 14 }, "identifierName": "has" @@ -46843,15 +48164,15 @@ "arguments": [ { "type": "Identifier", - "start": 17939, - "end": 17945, + "start": 18389, + "end": 18395, "loc": { "start": { - "line": 454, + "line": 473, "column": 15 }, "end": { - "line": 454, + "line": 473, "column": 21 }, "identifierName": "source" @@ -46860,15 +48181,15 @@ }, { "type": "StringLiteral", - "start": 17947, - "end": 17970, + "start": 18397, + "end": 18420, "loc": { "start": { - "line": 454, + "line": 473, "column": 23 }, "end": { - "line": 454, + "line": 473, "column": 46 } }, @@ -46886,73 +48207,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 17973, - "end": 18061, + "start": 18423, + "end": 18511, "loc": { "start": { - "line": 454, + "line": 473, "column": 49 }, "end": { - "line": 456, + "line": 475, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 17983, - "end": 18053, + "start": 18433, + "end": 18503, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 78 } }, "expression": { "type": "AssignmentExpression", - "start": 17983, - "end": 18052, + "start": 18433, + "end": 18502, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 77 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17983, - "end": 18011, + "start": 18433, + "end": 18461, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 36 } }, "object": { "type": "Identifier", - "start": 17983, - "end": 17989, + "start": 18433, + "end": 18439, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 14 }, "identifierName": "source" @@ -46961,15 +48282,15 @@ }, "property": { "type": "Identifier", - "start": 17990, - "end": 18011, + "start": 18440, + "end": 18461, "loc": { "start": { - "line": 455, + "line": 474, "column": 15 }, "end": { - "line": 455, + "line": 474, "column": 36 }, "identifierName": "bibliographicCitation" @@ -46980,57 +48301,57 @@ }, "right": { "type": "CallExpression", - "start": 18014, - "end": 18052, + "start": 18464, + "end": 18502, "loc": { "start": { - "line": 455, + "line": 474, "column": 39 }, "end": { - "line": 455, + "line": 474, "column": 77 } }, "callee": { "type": "MemberExpression", - "start": 18014, - "end": 18050, + "start": 18464, + "end": 18500, "loc": { "start": { - "line": 455, + "line": 474, "column": 39 }, "end": { - "line": 455, + "line": 474, "column": 75 } }, "object": { "type": "NewExpression", - "start": 18014, - "end": 18041, + "start": 18464, + "end": 18491, "loc": { "start": { - "line": 455, + "line": 474, "column": 39 }, "end": { - "line": 455, + "line": 474, "column": 66 } }, "callee": { "type": "Identifier", - "start": 18018, - "end": 18033, + "start": 18468, + "end": 18483, "loc": { "start": { - "line": 455, + "line": 474, "column": 43 }, "end": { - "line": 455, + "line": 474, "column": 58 }, "identifierName": "CitationWrapper" @@ -47040,15 +48361,15 @@ "arguments": [ { "type": "Identifier", - "start": 18034, - "end": 18040, + "start": 18484, + "end": 18490, "loc": { "start": { - "line": 455, + "line": 474, "column": 59 }, "end": { - "line": 455, + "line": 474, "column": 65 }, "identifierName": "source" @@ -47059,15 +48380,15 @@ }, "property": { "type": "Identifier", - "start": 18042, - "end": 18050, + "start": 18492, + "end": 18500, "loc": { "start": { - "line": 455, + "line": 474, "column": 67 }, "end": { - "line": 455, + "line": 474, "column": 75 }, "identifierName": "toString" @@ -47093,15 +48414,15 @@ { "type": "CommentLine", "value": " Add a bibliographicCitation to the source if it is a Citation.", - "start": 17766, - "end": 17831, + "start": 18216, + "end": 18281, "loc": { "start": { - "line": 450, + "line": 469, "column": 4 }, "end": { - "line": 450, + "line": 469, "column": 69 } } @@ -47110,29 +48431,29 @@ }, { "type": "ReturnStatement", - "start": 18073, - "end": 18098, + "start": 18523, + "end": 18548, "loc": { "start": { - "line": 459, + "line": 478, "column": 4 }, "end": { - "line": 459, + "line": 478, "column": 29 } }, "argument": { "type": "Identifier", - "start": 18080, - "end": 18097, + "start": 18530, + "end": 18547, "loc": { "start": { - "line": 459, + "line": 478, "column": 11 }, "end": { - "line": 459, + "line": 478, "column": 28 }, "identifierName": "phylogenyAsJSONLD" @@ -47177,15 +48498,15 @@ { "type": "CommentBlock", "value": "* Used to parse Newick strings. ", - "start": 103, - "end": 139, + "start": 119, + "end": 155, "loc": { "start": { - "line": 8, + "line": 11, "column": 0 }, "end": { - "line": 8, + "line": 11, "column": 36 } } @@ -47193,15 +48514,15 @@ { "type": "CommentBlock", "value": "* OWL terms to be used here. ", - "start": 175, - "end": 208, + "start": 191, + "end": 224, "loc": { "start": { - "line": 11, + "line": 14, "column": 0 }, "end": { - "line": 11, + "line": 14, "column": 33 } } @@ -47209,15 +48530,15 @@ { "type": "CommentLine", "value": " Wraps a Phylogeny in a PHYX file and provides access to node, node labels", - "start": 598, - "end": 674, + "start": 614, + "end": 690, "loc": { "start": { - "line": 22, + "line": 25, "column": 2 }, "end": { - "line": 22, + "line": 25, "column": 78 } } @@ -47225,15 +48546,15 @@ { "type": "CommentLine", "value": " and other information. Remember that a Phylogeny also has the", - "start": 677, - "end": 741, + "start": 693, + "end": 757, "loc": { "start": { - "line": 23, + "line": 26, "column": 2 }, "end": { - "line": 23, + "line": 26, "column": 66 } } @@ -47241,15 +48562,15 @@ { "type": "CommentLine", "value": " additionalNodeProperties object which provides additional properties for", - "start": 744, - "end": 819, + "start": 760, + "end": 835, "loc": { "start": { - "line": 24, + "line": 27, "column": 2 }, "end": { - "line": 24, + "line": 27, "column": 77 } } @@ -47257,15 +48578,15 @@ { "type": "CommentLine", "value": " nodes.", - "start": 822, - "end": 831, + "start": 838, + "end": 847, "loc": { "start": { - "line": 25, + "line": 28, "column": 2 }, "end": { - "line": 25, + "line": 28, "column": 11 } } @@ -47273,15 +48594,15 @@ { "type": "CommentLine", "value": " Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.", - "start": 906, - "end": 979, + "start": 922, + "end": 995, "loc": { "start": { - "line": 28, + "line": 31, "column": 4 }, "end": { - "line": 28, + "line": 31, "column": 77 } } @@ -47289,15 +48610,15 @@ { "type": "CommentLine", "value": " Note that this version ONLY uses the `newick` property to determine the", - "start": 984, - "end": 1058, + "start": 1000, + "end": 1074, "loc": { "start": { - "line": 29, + "line": 32, "column": 4 }, "end": { - "line": 29, + "line": 32, "column": 78 } } @@ -47305,15 +48626,15 @@ { "type": "CommentLine", "value": " phylogeny: if other representations are included (such as a node-based", - "start": 1063, - "end": 1136, + "start": 1079, + "end": 1152, "loc": { "start": { - "line": 30, + "line": 33, "column": 4 }, "end": { - "line": 30, + "line": 33, "column": 77 } } @@ -47321,15 +48642,15 @@ { "type": "CommentLine", "value": " format, as used in JSON-LD), they will be ignored and possibly overwritten", - "start": 1141, - "end": 1218, + "start": 1157, + "end": 1234, "loc": { "start": { - "line": 31, + "line": 34, "column": 4 }, "end": { - "line": 31, + "line": 34, "column": 81 } } @@ -47337,15 +48658,15 @@ { "type": "CommentLine", "value": " during export. So, to update the phylogeny, please only update the newick", - "start": 1223, - "end": 1299, + "start": 1239, + "end": 1315, "loc": { "start": { - "line": 32, + "line": 35, "column": 4 }, "end": { - "line": 32, + "line": 35, "column": 80 } } @@ -47353,15 +48674,15 @@ { "type": "CommentLine", "value": " string!", - "start": 1304, - "end": 1314, + "start": 1320, + "end": 1330, "loc": { "start": { - "line": 33, + "line": 36, "column": 4 }, "end": { - "line": 33, + "line": 36, "column": 14 } } @@ -47369,2274 +48690,3067 @@ { "type": "CommentLine", "value": "", - "start": 1319, - "end": 1321, + "start": 1335, + "end": 1337, + "loc": { + "start": { + "line": 37, + "column": 4 + }, + "end": { + "line": 37, + "column": 6 + } + } + }, + { + "type": "CommentLine", + "value": " This ensures that we don't need to reconcile between different", + "start": 1342, + "end": 1407, + "loc": { + "start": { + "line": 38, + "column": 4 + }, + "end": { + "line": 38, + "column": 69 + } + } + }, + { + "type": "CommentLine", + "value": " possible representations of a phylogeny.", + "start": 1412, + "end": 1455, + "loc": { + "start": { + "line": 39, + "column": 4 + }, + "end": { + "line": 39, + "column": 47 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return a normalized form of the phylogeny.\n ", + "start": 1541, + "end": 1598, + "loc": { + "start": { + "line": 44, + "column": 2 + }, + "end": { + "line": 46, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " We could normalize the Newick string, but that doesn't seem very nice.", + "start": 1690, + "end": 1763, + "loc": { + "start": { + "line": 50, + "column": 4 + }, + "end": { + "line": 50, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " Normalize the source if there is one.", + "start": 1769, + "end": 1809, + "loc": { + "start": { + "line": 52, + "column": 4 + }, + "end": { + "line": 52, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " Given a Newick string, return a list of errors found in parsing this", + "start": 2020, + "end": 2091, + "loc": { + "start": { + "line": 61, + "column": 4 + }, + "end": { + "line": 61, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " string. The errors are returned as a list of objects, each of which", + "start": 2096, + "end": 2166, + "loc": { + "start": { + "line": 62, + "column": 4 + }, + "end": { + "line": 62, + "column": 74 + } + } + }, + { + "type": "CommentLine", + "value": " has two properties:", + "start": 2171, + "end": 2193, + "loc": { + "start": { + "line": 63, + "column": 4 + }, + "end": { + "line": 63, + "column": 26 + } + } + }, + { + "type": "CommentLine", + "value": " - title: A short title of the error, distinct for each type of error.", + "start": 2198, + "end": 2271, + "loc": { + "start": { + "line": 64, + "column": 4 + }, + "end": { + "line": 64, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " - message: A longer description of the error, which might include", + "start": 2276, + "end": 2345, + "loc": { + "start": { + "line": 65, + "column": 4 + }, + "end": { + "line": 65, + "column": 73 + } + } + }, + { + "type": "CommentLine", + "value": " information specific to a particular error.", + "start": 2350, + "end": 2399, + "loc": { + "start": { + "line": 66, + "column": 4 + }, + "end": { + "line": 66, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": "", + "start": 2404, + "end": 2406, + "loc": { + "start": { + "line": 67, + "column": 4 + }, + "end": { + "line": 67, + "column": 6 + } + } + }, + { + "type": "CommentLine", + "value": " We try to order errors from most helpful ('Unbalanced parentheses in", + "start": 2411, + "end": 2482, + "loc": { + "start": { + "line": 68, + "column": 4 + }, + "end": { + "line": 68, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " Newick string') to least helpful ('Error parsing phylogeny').", + "start": 2487, + "end": 2551, + "loc": { + "start": { + "line": 69, + "column": 4 + }, + "end": { + "line": 69, + "column": 68 + } + } + }, + { + "type": "CommentLine", + "value": " Look for an empty Newick string.", + "start": 2621, + "end": 2656, + "loc": { + "start": { + "line": 73, + "column": 4 + }, + "end": { + "line": 73, + "column": 39 + } + } + }, + { + "type": "CommentLine", + "value": " None of the later errors are relevant here, so bail out now.", + "start": 2748, + "end": 2811, + "loc": { + "start": { + "line": 75, + "column": 6 + }, + "end": { + "line": 75, + "column": 69 + } + } + }, + { + "type": "CommentLine", + "value": " Look for an unbalanced Newick string.", + "start": 2962, + "end": 3002, + "loc": { + "start": { + "line": 82, + "column": 4 + }, + "end": { + "line": 82, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " Finally, try parsing it with newickJs.parse() and see if we get an error.", + "start": 3500, + "end": 3576, + "loc": { + "start": { + "line": 99, + "column": 4 + }, + "end": { + "line": 99, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " Recurse through PhyloTree nodes, executing function on each node.", + "start": 3907, + "end": 3975, + "loc": { + "start": { + "line": 113, + "column": 4 + }, + "end": { + "line": 113, + "column": 72 + } + } + }, + { + "type": "CommentLine", + "value": " - node: The node to recurse from. The function will be called on node", + "start": 3980, + "end": 4053, + "loc": { + "start": { + "line": 114, + "column": 4 + }, + "end": { + "line": 114, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " *before* being called on its children.", + "start": 4058, + "end": 4108, + "loc": { + "start": { + "line": 115, + "column": 4 + }, + "end": { + "line": 115, + "column": 54 + } + } + }, + { + "type": "CommentLine", + "value": " - func: The function to call on `node` and all of its children.", + "start": 4113, + "end": 4180, + "loc": { + "start": { + "line": 116, + "column": 4 + }, + "end": { + "line": 116, + "column": 71 + } + } + }, + { + "type": "CommentLine", + "value": " - nodeCount: `node` will be called with this nodeCount. All of its", + "start": 4185, + "end": 4255, + "loc": { + "start": { + "line": 117, + "column": 4 + }, + "end": { + "line": 117, + "column": 74 + } + } + }, + { + "type": "CommentLine", + "value": " children will be called with consecutively increasing nodeCounts.", + "start": 4260, + "end": 4337, + "loc": { + "start": { + "line": 118, + "column": 4 + }, + "end": { + "line": 118, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " - parentCount: The nodeCount associated with the parent of this node", + "start": 4342, + "end": 4414, + "loc": { + "start": { + "line": 119, + "column": 4 + }, + "end": { + "line": 119, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " within this run of recurseNodes. For instance, immediate children", + "start": 4419, + "end": 4496, + "loc": { + "start": { + "line": 120, + "column": 4 + }, + "end": { + "line": 120, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " of `node` will have a parentCount of 0. By default, `node` itself", + "start": 4501, + "end": 4578, + "loc": { + "start": { + "line": 121, + "column": 4 + }, + "end": { + "line": 121, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " will have a parentCount of `undefined`.", + "start": 4583, + "end": 4634, + "loc": { + "start": { + "line": 122, + "column": 4 + }, + "end": { + "line": 122, + "column": 55 + } + } + }, + { + "type": "CommentLine", + "value": " When the function `func` is called, it is given three arguments:", + "start": 4639, + "end": 4706, + "loc": { + "start": { + "line": 123, + "column": 4 + }, + "end": { + "line": 123, + "column": 71 + } + } + }, + { + "type": "CommentLine", + "value": " - The current node object (initially: `node`)", + "start": 4711, + "end": 4760, "loc": { "start": { - "line": 34, + "line": 124, "column": 4 }, "end": { - "line": 34, - "column": 6 + "line": 124, + "column": 53 } } }, { "type": "CommentLine", - "value": " This ensures that we don't need to reconcile between different", - "start": 1326, - "end": 1391, + "value": " - The count of the current node object (initially: `nodeCount`)", + "start": 4765, + "end": 4832, "loc": { "start": { - "line": 35, + "line": 125, "column": 4 }, "end": { - "line": 35, - "column": 69 + "line": 125, + "column": 71 } } }, { "type": "CommentLine", - "value": " possible representations of a phylogeny.", - "start": 1396, - "end": 1439, + "value": " - The parent count of the current node object (initially: `parentCount`)", + "start": 4837, + "end": 4913, "loc": { "start": { - "line": 36, + "line": 126, "column": 4 }, "end": { - "line": 36, - "column": 47 + "line": 126, + "column": 80 } } }, { "type": "CommentLine", - "value": " Given a Newick string, return a list of errors found in parsing this", - "start": 1570, - "end": 1641, + "value": " Recurse through all children of this node.", + "start": 4992, + "end": 5037, "loc": { "start": { - "line": 42, + "line": 131, "column": 4 }, "end": { - "line": 42, - "column": 75 + "line": 131, + "column": 49 } } }, { "type": "CommentLine", - "value": " string. The errors are returned as a list of objects, each of which", - "start": 1646, - "end": 1716, + "value": " Return a list of all taxonomic units in this phylogeny.", + "start": 5328, + "end": 5386, "loc": { "start": { - "line": 43, + "line": 147, "column": 4 }, "end": { - "line": 43, - "column": 74 + "line": 147, + "column": 62 } } }, { "type": "CommentLine", - "value": " has two properties:", - "start": 1721, - "end": 1743, + "value": " Node labels will be extracted from:", + "start": 5391, + "end": 5429, "loc": { "start": { - "line": 44, + "line": 148, "column": 4 }, "end": { - "line": 44, - "column": 26 + "line": 148, + "column": 42 } } }, { "type": "CommentLine", - "value": " - title: A short title of the error, distinct for each type of error.", - "start": 1748, - "end": 1821, + "value": " - internal nodes only (if nodeType == 'internal')", + "start": 5434, + "end": 5487, "loc": { "start": { - "line": 45, + "line": 149, "column": 4 }, "end": { - "line": 45, - "column": 77 + "line": 149, + "column": 57 } } }, { "type": "CommentLine", - "value": " - message: A longer description of the error, which might include", - "start": 1826, - "end": 1895, + "value": " - terminal nodes only (if nodeType == 'terminal')", + "start": 5492, + "end": 5545, "loc": { "start": { - "line": 46, + "line": 150, "column": 4 }, "end": { - "line": 46, - "column": 73 + "line": 150, + "column": 57 } } }, { "type": "CommentLine", - "value": " information specific to a particular error.", - "start": 1900, - "end": 1949, + "value": " - both internal and terminal nodes (if nodeType == 'both')", + "start": 5550, + "end": 5612, "loc": { "start": { - "line": 47, + "line": 151, "column": 4 }, "end": { - "line": 47, - "column": 53 + "line": 151, + "column": 66 } } }, { "type": "CommentLine", "value": "", - "start": 1954, - "end": 1956, + "start": 5617, + "end": 5619, "loc": { "start": { - "line": 48, + "line": 152, "column": 4 }, "end": { - "line": 48, + "line": 152, "column": 6 } } }, { "type": "CommentLine", - "value": " We try to order errors from most helpful ('Unbalanced parentheses in", - "start": 1961, - "end": 2032, + "value": " See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted", + "start": 5624, + "end": 5699, "loc": { "start": { - "line": 49, + "line": 153, "column": 4 }, "end": { - "line": 49, - "column": 75 + "line": 153, + "column": 79 } } }, { "type": "CommentLine", - "value": " Newick string') to least helpful ('Error parsing phylogeny').", - "start": 2037, - "end": 2101, + "value": " into node labels, but in brief:", + "start": 5704, + "end": 5738, "loc": { "start": { - "line": 50, + "line": 154, "column": 4 }, "end": { - "line": 50, - "column": 68 + "line": 154, + "column": 38 } } }, { "type": "CommentLine", - "value": " Look for an empty Newick string.", - "start": 2171, - "end": 2206, + "value": " 1. We look for taxonomic units in the additionalNodeProperties.", + "start": 5743, + "end": 5810, "loc": { "start": { - "line": 54, + "line": 155, "column": 4 }, "end": { - "line": 54, - "column": 39 + "line": 155, + "column": 71 } } }, { "type": "CommentLine", - "value": " None of the later errors are relevant here, so bail out now.", - "start": 2298, - "end": 2361, + "value": " 2. If none are found, we attempt to parse the node label as a scientific name.", + "start": 5815, + "end": 5897, "loc": { "start": { - "line": 56, - "column": 6 + "line": 156, + "column": 4 }, "end": { - "line": 56, - "column": 69 + "line": 156, + "column": 86 } } }, { "type": "CommentLine", - "value": " Look for an unbalanced Newick string.", - "start": 2512, - "end": 2552, + "value": "", + "start": 5902, + "end": 5904, "loc": { "start": { - "line": 63, + "line": 157, "column": 4 }, "end": { - "line": 63, - "column": 44 + "line": 157, + "column": 6 } } }, { "type": "CommentLine", - "value": " Finally, try parsing it with newickJs.parse() and see if we get an error.", - "start": 3050, - "end": 3126, + "value": " Return a list of all the node labels in this phylogeny.", + "start": 6196, + "end": 6254, "loc": { "start": { - "line": 80, + "line": 170, "column": 4 }, "end": { - "line": 80, - "column": 80 + "line": 170, + "column": 62 } } }, { "type": "CommentLine", - "value": " Recurse through PhyloTree nodes, executing function on each node.", - "start": 3457, - "end": 3525, + "value": "", + "start": 6259, + "end": 6261, "loc": { "start": { - "line": 94, + "line": 171, "column": 4 }, "end": { - "line": 94, - "column": 72 + "line": 171, + "column": 6 } } }, { "type": "CommentLine", - "value": " - node: The node to recurse from. 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All of its", - "start": 3735, - "end": 3805, + "value": " - 'both': Return node labels on both internal and terminal nodes.", + "start": 6415, + "end": 6483, "loc": { "start": { - "line": 98, + "line": 175, "column": 4 }, "end": { - "line": 98, - "column": 74 + "line": 175, + "column": 72 } } }, { "type": "CommentLine", - "value": " children will be called with consecutively increasing nodeCounts.", - "start": 3810, - "end": 3887, + "value": " Parse the phylogeny (will throw an exception if parsing failed).", + "start": 6489, + "end": 6556, "loc": { "start": { - "line": 99, + "line": 177, "column": 4 }, "end": { - "line": 99, - "column": 81 + "line": 177, + "column": 71 } } }, { "type": "CommentLine", - "value": " - parentCount: The nodeCount associated with the parent of this node", - "start": 3892, - "end": 3964, + "value": " Return all node labels.", + "start": 6700, + "end": 6726, "loc": { "start": { - "line": 100, - "column": 4 + "line": 182, + "column": 6 }, "end": { - "line": 100, - "column": 76 + "line": 182, + "column": 32 } } }, { "type": "CommentLine", - "value": " within this run of recurseNodes. For instance, immediate children", - "start": 3969, - "end": 4046, + "value": " Return the internal nodes (those with atleast one child).", + "start": 6958, + "end": 7018, "loc": { "start": { - "line": 101, - "column": 4 + "line": 193, + "column": 6 }, "end": { - "line": 101, - "column": 81 + "line": 193, + "column": 66 } } }, { "type": "CommentLine", - "value": " of `node` will have a parentCount of 0. By default, `node` itself", - "start": 4051, - "end": 4128, + "value": " Retrieve the label of the parent vertex in this arc.", + "start": 7113, + "end": 7168, "loc": { "start": { - "line": 102, - "column": 4 + "line": 196, + "column": 36 }, "end": { - "line": 102, - "column": 81 + "line": 196, + "column": 91 } } }, { "type": "CommentLine", - "value": " will have a parentCount of `undefined`.", - "start": 4133, - "end": 4184, + "value": " Return the terminal nodes. This would require calculating the children", + "start": 7275, + "end": 7348, "loc": { "start": { - "line": 103, - "column": 4 + "line": 202, + "column": 6 }, "end": { - "line": 103, - "column": 55 + "line": 202, + "column": 79 } } }, { "type": "CommentLine", - "value": " When the function `func` is called, it is given three arguments:", - "start": 4189, - "end": 4256, + "value": " of every vertex in the graph and then identifying vertices without any", + "start": 7355, + "end": 7428, "loc": { "start": { - "line": 104, - "column": 4 + "line": 203, + "column": 6 }, "end": { - "line": 104, - "column": 71 + "line": 203, + "column": 79 } } }, { "type": "CommentLine", - "value": " - The current node object (initially: `node`)", - "start": 4261, - "end": 4310, + "value": " children.", + "start": 7435, + "end": 7447, "loc": { "start": { - "line": 105, - "column": 4 + "line": 204, + "column": 6 }, "end": { - "line": 105, - "column": 53 + "line": 204, + "column": 18 } } }, { "type": "CommentLine", - "value": " - The count of the current node object (initially: `nodeCount`)", - "start": 4315, - "end": 4382, + "value": "", + "start": 7454, + "end": 7456, "loc": { "start": { - "line": 106, - "column": 4 + "line": 205, + "column": 6 }, "end": { - "line": 106, - "column": 71 + "line": 205, + "column": 8 } } }, { "type": "CommentLine", - "value": " - The parent count of the current node object (initially: `parentCount`)", - "start": 4387, - "end": 4463, + "value": " A quicker and dirtier way to do this is by removing internal labels", + "start": 7463, + "end": 7533, "loc": { "start": { - "line": 107, - "column": 4 + "line": 206, + "column": 6 }, "end": { - "line": 107, - "column": 80 + "line": 206, + "column": 76 } } }, { "type": "CommentLine", - "value": " Recurse through all children of this node.", - "start": 4542, - "end": 4587, + "value": " from the list of all node labels. This will report an incorrect result", + "start": 7540, + "end": 7613, "loc": { "start": { - "line": 112, - "column": 4 + "line": 207, + "column": 6 }, "end": { - "line": 112, - "column": 49 + "line": 207, + "column": 79 } } }, { "type": "CommentLine", - "value": " Return a list of all taxonomic units in this phylogeny.", - "start": 4878, - "end": 4936, + "value": " if an internal node has the same label as a terminal node, but at that", + "start": 7620, + "end": 7693, "loc": { "start": { - "line": 128, - "column": 4 + "line": 208, + "column": 6 }, "end": { - "line": 128, - "column": 62 + "line": 208, + "column": 79 } } }, { "type": "CommentLine", - "value": " Node labels will be extracted from:", - "start": 4941, - "end": 4979, + "value": " point a lot of other assumptions are going to fail, too, so this is", + "start": 7700, + "end": 7770, "loc": { "start": { - "line": 129, - "column": 4 + "line": 209, + "column": 6 }, "end": { - "line": 129, - "column": 42 + "line": 209, + "column": 76 } } }, { "type": "CommentLine", - "value": " - internal nodes only (if nodeType == 'internal')", - "start": 4984, - "end": 5037, + "value": " probably good enough for now.", + "start": 7777, + "end": 7809, "loc": { "start": { - "line": 130, - "column": 4 + "line": 210, + "column": 6 }, "end": { - "line": 130, - "column": 57 + "line": 210, + "column": 38 } } }, { - "type": "CommentLine", - "value": " - terminal nodes only (if nodeType == 'terminal')", - "start": 5042, - "end": 5095, + "type": "CommentBlock", + "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", + "start": 8071, + "end": 8448, "loc": { "start": { - "line": 131, - "column": 4 + "line": 220, + "column": 2 }, "end": { - "line": 131, - "column": 57 + "line": 227, + "column": 5 } } }, { "type": "CommentLine", - "value": " - both internal and terminal nodes (if nodeType == 'both')", - "start": 5100, - "end": 5162, + "value": " Look up additional node properties.", + "start": 8498, + "end": 8536, "loc": { "start": { - "line": 132, + "line": 229, "column": 4 }, "end": { - "line": 132, - "column": 66 + "line": 229, + "column": 42 } } }, { "type": "CommentLine", - "value": "", - "start": 5167, - "end": 5169, + "value": " If there are explicit taxonomic units in the", + "start": 8808, + "end": 8855, "loc": { "start": { - "line": 133, + "line": 238, "column": 4 }, "end": { - "line": 133, - "column": 6 + "line": 238, + "column": 51 } } }, { "type": "CommentLine", - "value": " See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted", - "start": 5174, - "end": 5249, + "value": " representsTaxonomicUnits property, we need to use those.", + "start": 8860, + "end": 8919, "loc": { "start": { - "line": 134, + "line": 239, "column": 4 }, "end": { - "line": 134, - "column": 79 + "line": 239, + "column": 63 } } }, { "type": "CommentLine", - "value": " into node labels, but in brief:", - "start": 5254, - "end": 5288, + "value": " If that doesn't work, we can try to extract scientific names from", + "start": 9064, + "end": 9132, "loc": { "start": { - "line": 135, + "line": 244, "column": 4 }, "end": { - "line": 135, - "column": 38 + "line": 244, + "column": 72 } } }, { "type": "CommentLine", - "value": " 1. We look for taxonomic units in the additionalNodeProperties.", - "start": 5293, - "end": 5360, + "value": " the node label. Note that taxonomic units will NOT be extracted from", + "start": 9137, + "end": 9208, "loc": { "start": { - "line": 136, + "line": 245, "column": 4 }, "end": { - "line": 136, - "column": 71 + "line": 245, + "column": 75 } } }, { "type": "CommentLine", - "value": " 2. If none are found, we attempt to parse the node label as a scientific name.", - "start": 5365, - "end": 5447, + "value": " the label if there is a taxonomic unit present!", + "start": 9213, + "end": 9263, "loc": { "start": { - "line": 137, + "line": 246, "column": 4 }, "end": { - "line": 137, - "column": 86 + "line": 246, + "column": 54 } } }, { "type": "CommentLine", "value": "", - "start": 5452, - "end": 5454, + "start": 9268, + "end": 9270, "loc": { "start": { - "line": 138, + "line": 247, "column": 4 }, "end": { - "line": 138, + "line": 247, "column": 6 } } }, { "type": "CommentLine", - "value": " Return a list of all the node labels in this phylogeny.", - "start": 5746, - "end": 5804, + "value": " Note that old-style taxonomic units were lists while new-style taxonomic", + "start": 9275, + "end": 9350, "loc": { "start": { - "line": 151, + "line": 248, "column": 4 }, "end": { - "line": 151, - "column": 62 + "line": 248, + "column": 79 } } }, { "type": "CommentLine", - "value": "", - "start": 5809, - "end": 5811, + "value": " units are single objects. So we turn it into a single entry list here.", + "start": 9355, + "end": 9428, "loc": { "start": { - "line": 152, + "line": 249, "column": 4 }, "end": { - "line": 152, - "column": 6 + "line": 249, + "column": 77 } } }, { "type": "CommentLine", - "value": " nodeType can be one of:", - "start": 5816, - "end": 5842, + "value": " No TUnit? Return the empty list.", + "start": 9566, + "end": 9601, "loc": { "start": { - "line": 153, - "column": 4 + "line": 252, + "column": 15 }, "end": { - "line": 153, - "column": 30 + "line": 252, + "column": 50 } } }, { "type": "CommentLine", - "value": " - 'internal': Return node labels on internal nodes.", - "start": 5847, - "end": 5901, + "value": " Return a list of node labels matched by a given specifier on", + "start": 9658, + "end": 9721, "loc": { "start": { - "line": 154, + "line": 256, "column": 4 }, "end": { - "line": 154, - "column": 58 + "line": 256, + "column": 67 } } }, { "type": "CommentLine", - "value": " - 'terminal': Return node labels on terminal nodes.", - "start": 5906, - "end": 5960, + "value": " a given phylogeny.", + "start": 9726, + "end": 9747, "loc": { "start": { - "line": 155, + "line": 257, "column": 4 }, "end": { - "line": 155, - "column": 58 + "line": 257, + "column": 25 } } }, { "type": "CommentLine", - "value": " - 'both': Return node labels on both internal and terminal nodes.", - "start": 5965, - "end": 6033, + "value": " Find all the taxonomic units associated with the specifier and", + "start": 9811, + "end": 9876, "loc": { "start": { - "line": 156, - "column": 4 + "line": 260, + "column": 6 }, "end": { - "line": 156, - "column": 72 + "line": 260, + "column": 71 } } }, { "type": "CommentLine", - "value": " Parse the phylogeny (will throw an exception if parsing failed).", - "start": 6039, - "end": 6106, + "value": " with the node.", + "start": 9883, + "end": 9900, "loc": { "start": { - "line": 158, - "column": 4 + "line": 261, + "column": 6 }, "end": { - "line": 158, - "column": 71 + "line": 261, + "column": 23 } } }, { "type": "CommentLine", - "value": " Return all node labels.", - "start": 6250, - "end": 6276, + "value": " Attempt pairwise matches between taxonomic units in the specifier", + "start": 9980, + "end": 10048, "loc": { "start": { - "line": 163, + "line": 264, "column": 6 }, "end": { - "line": 163, - "column": 32 + "line": 264, + "column": 74 } } }, { "type": "CommentLine", - "value": " Return the internal nodes (those with atleast one child).", - "start": 6508, - "end": 6568, + "value": " and associated with the node.", + "start": 10055, + "end": 10087, "loc": { "start": { - "line": 174, + "line": 265, "column": 6 }, "end": { - "line": 174, - "column": 66 + "line": 265, + "column": 38 } } }, { "type": "CommentLine", - "value": " Retrieve the label of the parent vertex in this arc.", - "start": 6663, - "end": 6718, + "value": " We previously used phylotree.js's Newick parser to parse Newick into a", + "start": 10247, + "end": 10320, "loc": { "start": { - "line": 177, - "column": 36 + "line": 273, + "column": 4 }, "end": { - "line": 177, - "column": 91 + "line": 273, + "column": 77 } } }, { "type": "CommentLine", - "value": " Return the terminal nodes. This would require calculating the children", - "start": 6825, - "end": 6898, + "value": " tree-like structure. However, this is difficult to integrate using NPM.", + "start": 10325, + "end": 10399, "loc": { "start": { - "line": 183, - "column": 6 + "line": 274, + "column": 4 }, "end": { - "line": 183, - "column": 79 + "line": 274, + "column": 78 } } }, { "type": "CommentLine", - "value": " of every vertex in the graph and then identifying vertices without any", - "start": 6905, - "end": 6978, + "value": " This method provides a similar facility using the newick-js library.", + "start": 10404, + "end": 10475, "loc": { "start": { - "line": 184, - "column": 6 + "line": 275, + "column": 4 }, "end": { - "line": 184, - "column": 79 + "line": 275, + "column": 75 } } }, { "type": "CommentLine", - "value": " children.", - "start": 6985, - "end": 6997, + "value": "", + "start": 10480, + "end": 10482, "loc": { "start": { - "line": 185, + "line": 276, + "column": 4 + }, + "end": { + "line": 276, "column": 6 + } + } + }, + { + "type": "CommentLine", + "value": " Throws an exception if the Newick could not be parsed.", + "start": 10487, + "end": 10544, + "loc": { + "start": { + "line": 277, + "column": 4 }, "end": { - "line": 185, - "column": 18 + "line": 277, + "column": 61 } } }, { "type": "CommentLine", - "value": "", - "start": 7004, - "end": 7006, + "value": " Go through the arcs, assigning 'children' to the appropriate parent node.", + "start": 10642, + "end": 10718, "loc": { "start": { - "line": 186, - "column": 6 + "line": 281, + "column": 4 }, "end": { - "line": 186, - "column": 8 + "line": 281, + "column": 80 } } }, { "type": "CommentLine", - "value": " A quicker and dirtier way to do this is by removing internal labels", - "start": 7013, - "end": 7083, + "value": " Add child to parent.children.", + "start": 10797, + "end": 10829, "loc": { "start": { - "line": 187, + "line": 285, "column": 6 }, "end": { - "line": 187, - "column": 76 + "line": 285, + "column": 38 } } }, { "type": "CommentLine", - "value": " from the list of all node labels. This will report an incorrect result", - "start": 7090, - "end": 7163, + "value": " Phylotree.js uses 'name' instead of 'label'.", + "start": 10930, + "end": 10977, "loc": { "start": { - "line": 188, + "line": 289, "column": 6 }, "end": { - "line": 188, - "column": 79 + "line": 289, + "column": 53 } } }, { "type": "CommentLine", - "value": " if an internal node has the same label as a terminal node, but at that", - "start": 7170, - "end": 7243, + "value": " Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.", + "start": 11110, + "end": 11193, "loc": { "start": { - "line": 189, + "line": 293, "column": 6 }, "end": { - "line": 189, - "column": 79 + "line": 293, + "column": 89 } } }, { "type": "CommentLine", - "value": " point a lot of other assumptions are going to fail, too, so this is", - "start": 7250, - "end": 7320, + "value": " Set root 'attribute' to root weight.", + "start": 11294, + "end": 11333, "loc": { "start": { - "line": 190, - "column": 6 + "line": 297, + "column": 4 }, "end": { - "line": 190, - "column": 76 + "line": 297, + "column": 43 } } }, { "type": "CommentLine", - "value": " probably good enough for now.", - "start": 7327, - "end": 7359, + "value": " Return the parsed Newick string, but with EVERY node given an IRI.", + "start": 11548, + "end": 11617, "loc": { "start": { - "line": 191, - "column": 6 + "line": 304, + "column": 4 }, "end": { - "line": 191, - "column": 38 + "line": 304, + "column": 73 } } }, { - "type": "CommentBlock", - "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", - "start": 7621, - "end": 7998, + "type": "CommentLine", + "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", + "start": 11622, + "end": 11695, "loc": { "start": { - "line": 201, - "column": 2 + "line": 305, + "column": 4 }, "end": { - "line": 208, - "column": 5 + "line": 305, + "column": 77 } } }, { "type": "CommentLine", - "value": " Look up additional node properties.", - "start": 8048, - "end": 8086, + "value": " Node IDs are generated by concatenating `_node${number}` to the end of", + "start": 11700, + "end": 11775, "loc": { "start": { - "line": 210, + "line": 306, "column": 4 }, "end": { - "line": 210, - "column": 42 + "line": 306, + "column": 79 } } }, { "type": "CommentLine", - "value": " If there are explicit taxonomic units in the", - "start": 8358, - "end": 8405, + "value": " the baseIRI.", + "start": 11780, + "end": 11797, "loc": { "start": { - "line": 219, + "line": 307, "column": 4 }, "end": { - "line": 219, - "column": 51 + "line": 307, + "column": 21 } } }, { "type": "CommentLine", - "value": " representsTaxonomicUnits property, we need to use those.", - "start": 8410, - "end": 8469, + "value": " - newickParser: A method for converting a Newick string to a object-based", + "start": 11802, + "end": 11878, "loc": { "start": { - "line": 220, + "line": 308, "column": 4 }, "end": { - "line": 220, - "column": 63 + "line": 308, + "column": 80 } } }, { "type": "CommentLine", - "value": " If that doesn't work, we can try to extract scientific names from", - "start": 8614, - "end": 8682, + "value": " representation. The static method PhylogenyWrapper.getParsedNewick() is", + "start": 11883, + "end": 11959, "loc": { "start": { - "line": 225, + "line": 309, "column": 4 }, "end": { - "line": 225, - "column": 72 + "line": 309, + "column": 80 } } }, { "type": "CommentLine", - "value": " the node label. Note that taxonomic units will NOT be extracted from", - "start": 8687, - "end": 8758, + "value": " used if none is provided.", + "start": 11964, + "end": 11994, "loc": { "start": { - "line": 226, + "line": 310, "column": 4 }, "end": { - "line": 226, - "column": 75 + "line": 310, + "column": 34 } } }, { "type": "CommentLine", - "value": " the label if there is a taxonomic unit present!", - "start": 8763, - "end": 8813, + "value": " Start with the additional node properties.", + "start": 12171, + "end": 12216, "loc": { "start": { - "line": 227, - "column": 4 + "line": 315, + "column": 8 }, "end": { - "line": 227, - "column": 54 + "line": 315, + "column": 53 } } }, { "type": "CommentLine", - "value": "", - "start": 8818, - "end": 8820, + "value": " Set @id and @type.", + "start": 12261, + "end": 12282, "loc": { "start": { - "line": 228, - "column": 4 + "line": 318, + "column": 8 }, "end": { - "line": 228, - "column": 6 + "line": 318, + "column": 29 } } }, { "type": "CommentLine", - "value": " Note that old-style taxonomic units were lists while new-style taxonomic", - "start": 8825, - "end": 8900, + "value": " Returns a list of all nodes in this phylogeny as a series of nodes.", + "start": 12466, + "end": 12536, "loc": { "start": { - "line": 229, + "line": 328, "column": 4 }, "end": { - "line": 229, - "column": 79 + "line": 328, + "column": 74 } } }, { "type": "CommentLine", - "value": " units are single objects. So we turn it into a single entry list here.", - "start": 8905, - "end": 8978, + "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", + "start": 12541, + "end": 12614, "loc": { "start": { - "line": 230, + "line": 329, "column": 4 }, "end": { - "line": 230, + "line": 329, "column": 77 } } }, { "type": "CommentLine", - "value": " No TUnit? Return the empty list.", - "start": 9116, - "end": 9151, + "value": " Node IDs are generated by concatenating `_node${number}` to the end of", + "start": 12619, + "end": 12694, "loc": { "start": { - "line": 233, - "column": 15 + "line": 330, + "column": 4 }, "end": { - "line": 233, - "column": 50 + "line": 330, + "column": 79 } } }, { "type": "CommentLine", - "value": " Return a list of node labels matched by a given specifier on", - "start": 9208, - "end": 9271, + "value": " the baseIRI.", + "start": 12699, + "end": 12716, "loc": { "start": { - "line": 237, + "line": 331, "column": 4 }, "end": { - "line": 237, - "column": 67 + "line": 331, + "column": 21 } } }, { "type": "CommentLine", - "value": " a given phylogeny.", - "start": 9276, - "end": 9297, + "value": " - newickParser: A method for converting a Newick string to a object-based", + "start": 12721, + "end": 12797, "loc": { "start": { - "line": 238, + "line": 332, "column": 4 }, "end": { - "line": 238, - "column": 25 + "line": 332, + "column": 80 } } }, { "type": "CommentLine", - "value": " Find all the taxonomic units associated with the specifier and", - "start": 9361, - "end": 9426, + "value": " representation. See PhylogenyWrapper.getParsedNewick() for an example", + "start": 12802, + "end": 12876, "loc": { "start": { - "line": 241, - "column": 6 + "line": 333, + "column": 4 }, "end": { - "line": 241, - "column": 71 + "line": 333, + "column": 78 } } }, { "type": "CommentLine", - "value": " with the node.", - "start": 9433, - "end": 9450, + "value": " implementation.", + "start": 12881, + "end": 12901, "loc": { "start": { - "line": 242, - "column": 6 + "line": 334, + "column": 4 }, "end": { - "line": 242, - "column": 23 + "line": 334, + "column": 24 } } }, { "type": "CommentLine", - "value": " Attempt pairwise matches between taxonomic units in the specifier", - "start": 9530, - "end": 9598, + "value": " List of nodes we have identified.", + "start": 12907, + "end": 12943, "loc": { "start": { - "line": 245, - "column": 6 + "line": 336, + "column": 4 }, "end": { - "line": 245, - "column": 74 + "line": 336, + "column": 40 } } }, { "type": "CommentLine", - "value": " and associated with the node.", - "start": 9605, - "end": 9637, + "value": " We need to track the identifiers we give each node as we go.", + "start": 12971, + "end": 13034, "loc": { "start": { - "line": 246, - "column": 6 + "line": 339, + "column": 4 }, "end": { - "line": 246, - "column": 38 + "line": 339, + "column": 67 } } }, { "type": "CommentLine", - "value": " We previously used phylotree.js's Newick parser to parse Newick into a", - "start": 9797, - "end": 9870, + "value": " Extract the newick string.", + "start": 13100, + "end": 13129, "loc": { "start": { - "line": 254, + "line": 343, "column": 4 }, "end": { - "line": 254, - "column": 77 + "line": 343, + "column": 33 } } }, { "type": "CommentLine", - "value": " tree-like structure. However, this is difficult to integrate using NPM.", - "start": 9875, - "end": 9949, + "value": " Parse the Newick string; if parseable, recurse through the nodes,", + "start": 13192, + "end": 13260, "loc": { "start": { - "line": 255, + "line": 346, "column": 4 }, "end": { - "line": 255, - "column": 78 + "line": 346, + "column": 72 } } }, { "type": "CommentLine", - "value": " This method provides a similar facility using the newick-js library.", - "start": 9954, - "end": 10025, + "value": " added them to the list of JSON-LD nodes as we go.", + "start": 13265, + "end": 13317, "loc": { "start": { - "line": 256, + "line": 347, "column": 4 }, "end": { - "line": 256, - "column": 75 + "line": 347, + "column": 56 } } }, { "type": "CommentLine", - "value": "", - "start": 10030, - "end": 10032, + "value": " Start with the additional node properties.", + "start": 13515, + "end": 13560, "loc": { "start": { - "line": 257, - "column": 4 + "line": 352, + "column": 8 }, "end": { - "line": 257, - "column": 6 + "line": 352, + "column": 53 } } }, { "type": "CommentLine", - "value": " Throws an exception if the Newick could not be parsed.", - "start": 10037, - "end": 10094, + "value": " Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!", + "start": 13603, + "end": 13682, "loc": { "start": { - "line": 258, - "column": 4 + "line": 355, + "column": 8 }, "end": { - "line": 258, - "column": 61 + "line": 355, + "column": 87 } } }, { "type": "CommentLine", - "value": " Go through the arcs, assigning 'children' to the appropriate parent node.", - "start": 10192, - "end": 10268, + "value": " Since we may need to add multiple classes into the rdf:type, we need", + "start": 13768, + "end": 13839, "loc": { "start": { - "line": 262, - "column": 4 + "line": 359, + "column": 8 }, "end": { - "line": 262, - "column": 80 + "line": 359, + "column": 79 } } }, { "type": "CommentLine", - "value": " Add child to parent.children.", - "start": 10347, - "end": 10379, + "value": " to make @type an array. However, the JSON-LD library we use in JPhyloRef", + "start": 13848, + "end": 13923, "loc": { "start": { - "line": 266, - "column": 6 + "line": 360, + "column": 8 }, "end": { - "line": 266, - "column": 38 + "line": 360, + "column": 83 } } }, { "type": "CommentLine", - "value": " Phylotree.js uses 'name' instead of 'label'.", - "start": 10480, - "end": 10527, + "value": " can't support @type being an array (despite that being in the standard,", + "start": 13932, + "end": 14006, "loc": { "start": { - "line": 270, - "column": 6 + "line": 361, + "column": 8 }, "end": { - "line": 270, - "column": 53 + "line": 361, + "column": 82 } } }, { "type": "CommentLine", - "value": " Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.", - "start": 10660, - "end": 10743, + "value": " see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),", + "start": 14015, + "end": 14109, "loc": { "start": { - "line": 274, - "column": 6 + "line": 362, + "column": 8 }, "end": { - "line": 274, - "column": 89 + "line": 362, + "column": 102 } } }, { "type": "CommentLine", - "value": " Set root 'attribute' to root weight.", - "start": 10844, - "end": 10883, + "value": " so we fall back to using rdf:type instead.", + "start": 14118, + "end": 14163, "loc": { "start": { - "line": 278, - "column": 4 + "line": 363, + "column": 8 }, "end": { - "line": 278, - "column": 43 + "line": 363, + "column": 53 } } }, { "type": "CommentLine", - "value": " Return the parsed Newick string, but with EVERY node given an IRI.", - "start": 11098, - "end": 11167, + "value": " Add labels, additional node properties and taxonomic units.", + "start": 14248, + "end": 14310, "loc": { "start": { - "line": 285, - "column": 4 + "line": 366, + "column": 8 }, "end": { - "line": 285, - "column": 73 + "line": 366, + "column": 70 } } }, { "type": "CommentLine", - "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 11172, - "end": 11245, + "value": " Add node label.", + "start": 14374, + "end": 14392, "loc": { "start": { - "line": 286, - "column": 4 + "line": 368, + "column": 10 }, "end": { - "line": 286, - "column": 77 + "line": 368, + "column": 28 } } }, { "type": "CommentLine", - "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 11250, - "end": 11325, + "value": " Add additional node properties, if any.", + "start": 14449, + "end": 14491, "loc": { "start": { - "line": 287, - "column": 4 + "line": 371, + "column": 10 }, "end": { - "line": 287, - "column": 79 + "line": 371, + "column": 52 } } }, { "type": "CommentLine", - "value": " the baseIRI.", - "start": 11330, - "end": 11347, + "value": " Add taxonomic units into the metadata.", + "start": 14773, + "end": 14814, "loc": { "start": { - "line": 288, - "column": 4 + "line": 378, + "column": 10 }, "end": { - "line": 288, - "column": 21 + "line": 378, + "column": 51 } } }, { "type": "CommentLine", - "value": " - newickParser: A method for converting a Newick string to a object-based", - "start": 11352, - "end": 11428, + "value": " Add it into the @type so we can reason over it.", + "start": 14923, + "end": 14973, "loc": { "start": { - "line": 289, - "column": 4 + "line": 381, + "column": 10 }, "end": { - "line": 289, - "column": 80 + "line": 381, + "column": 60 } } }, { "type": "CommentLine", - "value": " representation. The static method PhylogenyWrapper.getParsedNewick() is", - "start": 11433, - "end": 11509, + "value": " Add references to parents and siblings.", + "start": 15564, + "end": 15606, "loc": { "start": { - "line": 290, - "column": 4 + "line": 400, + "column": 8 }, "end": { - "line": 290, - "column": 80 + "line": 400, + "column": 50 } } }, { "type": "CommentLine", - "value": " used if none is provided.", - "start": 11514, - "end": 11544, + "value": " Update list of nodes by parent IDs.", + "start": 15763, + "end": 15801, "loc": { "start": { - "line": 291, - "column": 4 + "line": 405, + "column": 10 }, "end": { - "line": 291, - "column": 34 + "line": 405, + "column": 48 } } }, { "type": "CommentLine", - "value": " Start with the additional node properties.", - "start": 11721, - "end": 11766, + "value": " Add nodeAsJSONLD to list", + "start": 15992, + "end": 16019, "loc": { "start": { - "line": 296, + "line": 412, "column": 8 }, "end": { - "line": 296, - "column": 53 + "line": 412, + "column": 35 } } }, { "type": "CommentLine", - "value": " Set @id and @type.", - "start": 11811, - "end": 11832, + "value": " Go through nodes again and set children and sibling relationships.", + "start": 16261, + "end": 16330, "loc": { "start": { - "line": 299, - "column": 8 + "line": 421, + "column": 4 }, "end": { - "line": 299, - "column": 29 + "line": 421, + "column": 73 } } }, { "type": "CommentLine", - "value": " Returns a list of all nodes in this phylogeny as a series of nodes.", - "start": 12016, - "end": 12086, + "value": " What are the children of this parentId?", + "start": 16396, + "end": 16438, "loc": { "start": { - "line": 309, - "column": 4 + "line": 423, + "column": 6 }, "end": { - "line": 309, - "column": 74 + "line": 423, + "column": 48 } } }, { "type": "CommentLine", - "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 12091, - "end": 12164, + "value": " Is this the root node?", + "start": 16584, + "end": 16609, "loc": { "start": { - "line": 310, - "column": 4 + "line": 427, + "column": 6 }, "end": { - "line": 310, - "column": 77 + "line": 427, + "column": 31 } } }, { "type": "CommentLine", - "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 12169, - "end": 12244, + "value": " Add all other sibling to node.siblings, but don't add this node itself!", + "start": 16821, + "end": 16895, "loc": { "start": { - "line": 311, - "column": 4 + "line": 435, + "column": 8 }, "end": { - "line": 311, - "column": 79 + "line": 435, + "column": 82 } } }, { "type": "CommentLine", - "value": " the baseIRI.", - "start": 12249, - "end": 12266, + "value": " Export this phylogeny as JSON-LD.", + "start": 17072, + "end": 17108, "loc": { "start": { - "line": 312, + "line": 444, "column": 4 }, "end": { - "line": 312, - "column": 21 + "line": 444, + "column": 40 } } }, { "type": "CommentLine", - "value": " - newickParser: A method for converting a Newick string to a object-based", - "start": 12271, - "end": 12347, + "value": " - fallbackIRI: The fallback IRI to use for this phylogeny if it does not", + "start": 17113, + "end": 17188, "loc": { "start": { - "line": 313, + "line": 445, "column": 4 }, "end": { - "line": 313, - "column": 80 + "line": 445, + "column": 79 } } }, { "type": "CommentLine", - "value": " representation. See PhylogenyWrapper.getParsedNewick() for an example", - "start": 12352, - "end": 12426, + "value": " already have an '@id' set.", + "start": 17193, + "end": 17224, "loc": { "start": { - "line": 314, + "line": 446, "column": 4 }, "end": { - "line": 314, - "column": 78 + "line": 446, + "column": 35 } } }, { "type": "CommentLine", - "value": " implementation.", - "start": 12431, - "end": 12451, + "value": " - newickParser: A function that parses a Newick string and returns a", + "start": 17229, + "end": 17300, "loc": { "start": { - "line": 315, + "line": 447, "column": 4 }, "end": { - "line": 315, - "column": 24 + "line": 447, + "column": 75 } } }, { "type": "CommentLine", - "value": " List of nodes we have identified.", - "start": 12457, - "end": 12493, + "value": " an object based representation of this phylogeny. If not set, the", + "start": 17305, + "end": 17375, "loc": { "start": { - "line": 317, + "line": 448, "column": 4 }, "end": { - "line": 317, - "column": 40 + "line": 448, + "column": 74 } } }, { "type": "CommentLine", - "value": " We need to track the identifiers we give each node as we go.", - "start": 12521, - "end": 12584, + "value": " static method PhylogenyWrapper.getParsedNewick will be used instead.", + "start": 17380, + "end": 17453, "loc": { "start": { - "line": 320, + "line": 449, "column": 4 }, "end": { - "line": 320, - "column": 67 + "line": 449, + "column": 77 } } }, { "type": "CommentLine", - "value": " Extract the newick string.", - "start": 12650, - "end": 12679, + "value": " Create a copy to export.", + "start": 17459, + "end": 17486, "loc": { "start": { - "line": 324, + "line": 451, "column": 4 }, "end": { - "line": 324, - "column": 33 + "line": 451, + "column": 31 } } }, { "type": "CommentLine", - "value": " Parse the Newick string; if parseable, recurse through the nodes,", - "start": 12742, - "end": 12810, + "value": " Set name and class for phylogeny. If no '@id' is set, use the provided", + "start": 17566, + "end": 17639, "loc": { "start": { - "line": 327, + "line": 454, "column": 4 }, "end": { - "line": 327, - "column": 72 + "line": 454, + "column": 77 } } }, { "type": "CommentLine", - "value": " added them to the list of JSON-LD nodes as we go.", - "start": 12815, - "end": 12867, + "value": " fallbackIRI.", + "start": 17644, + "end": 17659, "loc": { "start": { - "line": 328, + "line": 455, "column": 4 }, "end": { - "line": 328, - "column": 56 + "line": 455, + "column": 19 } } }, { "type": "CommentLine", - "value": " Start with the additional node properties.", - "start": 13065, - "end": 13110, + "value": " Translate nodes into JSON-LD objects.", + "start": 17817, + "end": 17857, "loc": { "start": { - "line": 333, - "column": 8 + "line": 459, + "column": 4 }, "end": { - "line": 333, - "column": 53 + "line": 459, + "column": 44 } } }, { "type": "CommentLine", - "value": " Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!", - "start": 13153, - "end": 13232, + "value": " We don't have a better way to identify the root node, so we just", + "start": 18003, + "end": 18070, "loc": { "start": { - "line": 336, - "column": 8 + "line": 462, + "column": 6 }, "end": { - "line": 336, - "column": 87 + "line": 462, + "column": 73 } } }, { "type": "CommentLine", - "value": " Since we may need to add multiple classes into the rdf:type, we need", - "start": 13318, - "end": 13389, + "value": " default to the first one.", + "start": 18077, + "end": 18105, "loc": { "start": { - "line": 340, - "column": 8 + "line": 463, + "column": 6 }, "end": { - "line": 340, - "column": 79 + "line": 463, + "column": 34 } } }, { "type": "CommentLine", - "value": " to make @type an array. However, the JSON-LD library we use in JPhyloRef", - "start": 13398, - "end": 13473, + "value": " Add a bibliographicCitation to the source if it is a Citation.", + "start": 18216, + "end": 18281, "loc": { "start": { - "line": 341, - "column": 8 + "line": 469, + "column": 4 }, "end": { - "line": 341, - "column": 83 + "line": 469, + "column": 69 + } + } + } + ], + "tokens": [ + { + "type": "CommentBlock", + "value": "*\n * PhylogenyWrapper\n ", + "start": 0, + "end": 27, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 3, + "column": 3 } } }, { - "type": "CommentLine", - "value": " can't support @type being an array (despite that being in the standard,", - "start": 13482, - "end": 13556, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 29, + "end": 35, "loc": { "start": { - 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", + "start": 119, + "end": 155, "loc": { "start": { - "line": 427, - "column": 4 + "line": 11, + "column": 0 }, "end": { - "line": 427, - "column": 35 + "line": 11, + "column": 36 } } }, { - "type": "CommentLine", - "value": " - newickParser: A function that parses a Newick string and returns a", - "start": 16779, - "end": 16850, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 156, + "end": 162, "loc": { "start": { - "line": 428, - "column": 4 + "line": 12, + "column": 0 }, "end": { - "line": 428, - "column": 75 + "line": 12, + "column": 6 } } }, { - "type": "CommentLine", - "value": " an object based representation of this phylogeny. If not set, the", - "start": 16855, - "end": 16925, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "newickJs", + "start": 163, + "end": 171, "loc": { "start": { - "line": 429, - "column": 4 + "line": 12, + "column": 7 }, "end": { - "line": 429, - "column": 74 + "line": 12, + "column": 15 } } }, { - "type": "CommentLine", - "value": " static method PhylogenyWrapper.getParsedNewick will be used instead.", - "start": 16930, - "end": 17003, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 172, + "end": 176, "loc": { "start": { - "line": 430, - "column": 4 + "line": 12, + "column": 16 }, "end": { - "line": 430, - "column": 77 + "line": 12, + "column": 20 } } }, { - "type": "CommentLine", - "value": " Create a copy to export.", - "start": 17009, - "end": 17036, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "newick-js", + "start": 177, + "end": 188, "loc": { "start": { - "line": 432, - "column": 4 + "line": 12, + "column": 21 }, "end": { - "line": 432, - "column": 31 + "line": 12, + "column": 32 } } }, { - "type": "CommentLine", - "value": " Set name and class for phylogeny. If no '@id' is set, use the provided", - "start": 17116, - "end": 17189, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 188, + "end": 189, "loc": { "start": { - "line": 435, - "column": 4 + "line": 12, + "column": 32 }, "end": { - "line": 435, - "column": 77 + "line": 12, + "column": 33 } } }, { - "type": "CommentLine", - "value": " fallbackIRI.", - "start": 17194, - "end": 17209, + "type": "CommentBlock", + "value": "* OWL terms to be used here. ", + "start": 191, + "end": 224, "loc": { "start": { - "line": 436, - "column": 4 + "line": 14, + "column": 0 }, "end": { - "line": 436, - "column": 19 + "line": 14, + "column": 33 } } }, { - "type": "CommentLine", - "value": " Translate nodes into JSON-LD objects.", - "start": 17367, - "end": 17407, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 225, + "end": 231, "loc": { "start": { - "line": 440, - "column": 4 + "line": 15, + "column": 0 }, "end": { - "line": 440, - "column": 44 + "line": 15, + "column": 6 } } }, { - "type": "CommentLine", - "value": " We don't have a better way to identify the root node, so we just", - "start": 17553, - "end": 17620, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 232, + "end": 240, "loc": { "start": { - 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"line": 450, - "column": 4 + "line": 15, + "column": 21 }, "end": { - "line": 450, - "column": 69 + "line": 15, + "column": 40 } } - } - ], - "tokens": [ + }, { - "type": "CommentBlock", - "value": "*\n * PhylogenyWrapper\n ", - "start": 0, - "end": 27, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 265, + "end": 266, "loc": { "start": { - "line": 1, - "column": 0 + "line": 15, + "column": 40 }, "end": { - "line": 3, - "column": 3 + "line": 15, + "column": 41 } } }, @@ -49655,15 +51769,15 @@ "updateContext": null }, "value": "import", - "start": 29, - "end": 35, + "start": 268, + "end": 274, "loc": { "start": { - "line": 5, + "line": 17, "column": 0 }, "end": { - "line": 5, + "line": 17, "column": 6 } } @@ -49682,15 +51796,15 @@ "updateContext": null }, "value": "*", - "start": 36, - "end": 37, + "start": 275, + "end": 276, "loc": { "start": { - 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", - "start": 103, - "end": 139, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 374, + "end": 380, "loc": { "start": { - "line": 8, + "line": 19, "column": 0 }, "end": { - "line": 8, - "column": 36 + "line": 19, + "column": 6 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 381, + "end": 382, + "loc": { + "start": { + "line": 19, + "column": 7 + }, + "end": { + "line": 19, + "column": 8 + } + } + }, + { + "type": { + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -50036,20 +52188,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 140, - "end": 146, + "value": "as", + "start": 383, + "end": 385, "loc": { "start": { - "line": 9, - "column": 0 + "line": 19, + "column": 9 }, "end": { - "line": 9, - "column": 6 + "line": 19, + "column": 11 } } }, @@ -50065,17 +52216,17 @@ "postfix": false, "binop": null }, - "value": "newickJs", - "start": 147, - "end": 155, + "value": "LXL9JK5M475GC", + "start": 386, + "end": 399, "loc": { "start": { - "line": 9, - "column": 7 + "line": 19, + "column": 12 }, "end": { - "line": 9, - "column": 15 + "line": 19, + "column": 25 } } }, @@ -50092,16 +52243,16 @@ "binop": null }, "value": "from", - "start": 156, - "end": 160, + "start": 400, + "end": 404, "loc": { "start": { - "line": 9, - "column": 16 + "line": 19, + "column": 26 }, "end": { - "line": 9, - "column": 20 + "line": 19, + "column": 30 } } }, @@ -50118,17 +52269,17 @@ "binop": null, "updateContext": null }, - "value": "newick-js", - "start": 161, - "end": 172, + "value": "../matchers/TaxonomicUnitMatcher", + "start": 405, + "end": 439, "loc": { "start": { - "line": 9, - "column": 21 + "line": 19, + "column": 31 }, "end": { - "line": 9, - "column": 32 + "line": 19, + "column": 65 } } }, @@ -50145,32 +52296,199 @@ "binop": null, "updateContext": null }, - "start": 172, - "end": 173, + "start": 439, + "end": 440, "loc": { "start": { - "line": 9, - "column": 32 + "line": 19, + "column": 65 }, "end": { - "line": 9, - "column": 33 + "line": 19, + "column": 66 } } }, { - "type": "CommentBlock", - "value": "* OWL terms to be used here. ", - "start": 175, - "end": 208, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 442, + "end": 447, "loc": { "start": { - "line": 11, + "line": 20, "column": 0 }, "end": { - "line": 11, + "line": 20, + "column": 5 + } + } + }, + { + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 448, + "end": 449, + "loc": { + "start": { + "line": 20, + "column": 6 + }, + "end": { + "line": 20, + "column": 7 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "TaxonomicUnitMatcher", + "start": 450, + "end": 470, + "loc": { + "start": { + "line": 20, + "column": 8 + }, + "end": { + "line": 20, + "column": 28 + } + } + }, + { + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 471, + "end": 472, + "loc": { + "start": { + "line": 20, + "column": 29 + }, + "end": { + "line": 20, + "column": 30 + } + } + }, + { + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 473, + "end": 474, + "loc": { + "start": { + "line": 20, + "column": 31 + }, + "end": { + "line": 20, + "column": 32 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK5M475GC", + "start": 475, + "end": 488, + "loc": { + "start": { + "line": 20, "column": 33 + }, + "end": { + "line": 20, + "column": 46 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 488, + "end": 489, + "loc": { + "start": { + "line": 20, + "column": 46 + }, + "end": { + "line": 20, + "column": 47 } } }, @@ -50189,19 +52507,72 @@ "updateContext": null }, "value": "import", - "start": 209, - "end": 215, + "start": 490, + "end": 496, "loc": { "start": { - "line": 12, + "line": 21, "column": 0 }, "end": { - "line": 12, + "line": 21, "column": 6 } } }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 497, + "end": 498, + "loc": { + "start": { + "line": 21, + "column": 7 + }, + "end": { + "line": 21, + "column": 8 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 499, + "end": 501, + "loc": { + "start": { + "line": 21, + "column": 9 + }, + "end": { + "line": 21, + "column": 11 + } + } + }, { "type": { "label": "name", @@ -50214,17 +52585,17 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 216, - "end": 224, + "value": "LXL9JK5MUANAE", + "start": 502, + "end": 515, "loc": { "start": { - "line": 12, - "column": 7 + "line": 21, + "column": 12 }, "end": { - "line": 12, - "column": 15 + "line": 21, + "column": 25 } } }, @@ -50241,16 +52612,16 @@ "binop": null }, "value": "from", - "start": 225, - "end": 229, + "start": 516, + "end": 520, "loc": { "start": { - "line": 12, - "column": 16 + "line": 21, + "column": 26 }, "end": { - "line": 12, - "column": 20 + "line": 21, + "column": 30 } } }, @@ -50267,17 +52638,17 @@ "binop": null, "updateContext": null }, - "value": "../utils/owlterms", - "start": 230, - "end": 249, + "value": "./CitationWrapper", + "start": 521, + "end": 540, "loc": { "start": { - "line": 12, - "column": 21 + "line": 21, + "column": 31 }, "end": { - "line": 12, - "column": 40 + "line": 21, + "column": 50 } } }, @@ -50294,25 +52665,25 @@ "binop": null, "updateContext": null }, - "start": 249, - "end": 250, + "start": 540, + "end": 541, "loc": { "start": { - "line": 12, - "column": 40 + "line": 21, + "column": 50 }, "end": { - "line": 12, - "column": 41 + "line": 21, + "column": 51 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "const", + "keyword": "const", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50321,44 +52692,42 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 252, - "end": 258, + "value": "const", + "start": 543, + "end": 548, "loc": { "start": { - "line": 14, + "line": 22, "column": 0 }, "end": { - "line": 14, - "column": 6 + "line": 22, + "column": 5 } } }, { "type": { - "label": "*", + "label": "{", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 259, - "end": 260, + "start": 549, + "end": 550, "loc": { "start": { - "line": 14, - "column": 7 + "line": 22, + "column": 6 }, "end": { - "line": 14, - "column": 8 + "line": 22, + "column": 7 } } }, @@ -50374,25 +52743,25 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 261, - "end": 263, + "value": "CitationWrapper", + "start": 551, + "end": 566, "loc": { "start": { - "line": 14, - "column": 9 + "line": 22, + "column": 8 }, "end": { - "line": 14, - "column": 11 + "line": 22, + "column": 23 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50400,49 +52769,49 @@ "postfix": false, "binop": null }, - "value": "LKT4H156R282A", - "start": 264, - "end": 277, + "start": 567, + "end": 568, "loc": { "start": { - "line": 14, - "column": 12 + "line": 22, + "column": 24 }, "end": { - "line": 14, + "line": 22, "column": 25 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "from", - "start": 278, - "end": 282, + "value": "=", + "start": 569, + "end": 570, "loc": { "start": { - "line": 14, + "line": 22, "column": 26 }, "end": { - "line": 14, - "column": 30 + "line": 22, + "column": 27 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -50450,20 +52819,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "./TaxonomicUnitWrapper", - "start": 283, - "end": 307, + "value": "LXL9JK5MUANAE", + "start": 571, + "end": 584, "loc": { "start": { - "line": 14, - "column": 31 + "line": 22, + "column": 28 }, "end": { - "line": 14, - "column": 55 + "line": 22, + "column": 41 } } }, @@ -50480,23 +52848,23 @@ "binop": null, "updateContext": null }, - "start": 307, - "end": 308, + "start": 584, + "end": 585, "loc": { "start": { - "line": 14, - "column": 55 + "line": 22, + "column": 41 }, "end": { - "line": 14, - "column": 56 + "line": 22, + "column": 42 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "class", + "keyword": "class", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -50507,24 +52875,24 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 310, - "end": 315, + "value": "class", + "start": 587, + "end": 592, "loc": { "start": { - "line": 15, + "line": 24, "column": 0 }, "end": { - "line": 15, + "line": 24, "column": 5 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -50533,23 +52901,24 @@ "postfix": false, "binop": null }, - "start": 316, - "end": 317, + "value": "PhylogenyWrapper", + "start": 593, + "end": 609, "loc": { "start": { - "line": 15, + "line": 24, "column": 6 }, "end": { - "line": 15, - "column": 7 + "line": 24, + "column": 22 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -50558,25 +52927,88 @@ "postfix": false, "binop": null }, - "value": "TaxonomicUnitWrapper", - "start": 318, - "end": 338, + "start": 610, + "end": 611, "loc": { "start": { - "line": 15, - "column": 8 + "line": 24, + "column": 23 }, "end": { - "line": 15, - "column": 28 + "line": 24, + "column": 24 + } + } + }, + { + "type": "CommentLine", + "value": " Wraps a Phylogeny in a PHYX file and provides access to node, node labels", + "start": 614, + "end": 690, + "loc": { + "start": { + "line": 25, + "column": 2 + }, + "end": { + "line": 25, + "column": 78 + } + } + }, + { + "type": "CommentLine", + "value": " and other information. Remember that a Phylogeny also has the", + "start": 693, + "end": 757, + "loc": { + "start": { + "line": 26, + "column": 2 + }, + "end": { + "line": 26, + "column": 66 + } + } + }, + { + "type": "CommentLine", + "value": " additionalNodeProperties object which provides additional properties for", + "start": 760, + "end": 835, + "loc": { + "start": { + "line": 27, + "column": 2 + }, + "end": { + "line": 27, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " nodes.", + "start": 838, + "end": 847, + "loc": { + "start": { + "line": 28, + "column": 2 + }, + "end": { + "line": 28, + "column": 11 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50584,43 +53016,42 @@ "postfix": false, "binop": null }, - "start": 339, - "end": 340, + "value": "constructor", + "start": 851, + "end": 862, "loc": { "start": { - "line": 15, - "column": 29 + "line": 30, + "column": 2 }, "end": { - "line": 15, - "column": 30 + "line": 30, + "column": 13 } } }, { "type": { - "label": "=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 341, - "end": 342, + "start": 862, + "end": 863, "loc": { "start": { - "line": 15, - "column": 31 + "line": 30, + "column": 13 }, "end": { - "line": 15, - "column": 32 + "line": 30, + "column": 14 } } }, @@ -50636,23 +53067,23 @@ "postfix": false, "binop": null }, - "value": "LKT4H156R282A", - "start": 343, - "end": 356, + "value": "phylogeny", + "start": 863, + "end": 872, "loc": { "start": { - "line": 15, - "column": 33 + "line": 30, + "column": 14 }, "end": { - "line": 15, - "column": 46 + "line": 30, + "column": 23 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -50663,23 +53094,22 @@ "binop": null, "updateContext": null }, - "start": 356, - "end": 357, + "start": 872, + "end": 873, "loc": { "start": { - "line": 15, - "column": 46 + "line": 30, + "column": 23 }, "end": { - "line": 15, - "column": 47 + "line": 30, + "column": 24 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -50687,47 +53117,46 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 358, - "end": 364, + "value": "defaultNomenCode", + "start": 874, + "end": 890, "loc": { "start": { - "line": 16, - "column": 0 + "line": 30, + "column": 25 }, "end": { - "line": 16, - "column": 6 + "line": 30, + "column": 41 } } }, { "type": { - "label": "*", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 365, - "end": 366, + "value": "=", + "start": 891, + "end": 892, "loc": { "start": { - "line": 16, - "column": 7 + "line": 30, + "column": 42 }, "end": { - "line": 16, - "column": 8 + "line": 30, + "column": 43 } } }, @@ -50743,43 +53172,43 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 367, - "end": 369, + "value": "owlterms", + "start": 893, + "end": 901, "loc": { "start": { - "line": 16, - "column": 9 + "line": 30, + "column": 44 }, "end": { - "line": 16, - "column": 11 + "line": 30, + "column": 52 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H15648XGU", - "start": 370, - "end": 383, + "start": 901, + "end": 902, "loc": { "start": { - "line": 16, - "column": 12 + "line": 30, + "column": 52 }, "end": { - "line": 16, - "column": 25 + "line": 30, + "column": 53 } } }, @@ -50795,157 +53224,273 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 384, - "end": 388, + "value": "UNKNOWN_CODE", + "start": 902, + "end": 914, "loc": { "start": { - "line": 16, - "column": 26 + "line": 30, + "column": 53 }, "end": { - "line": 16, - "column": 30 + "line": 30, + "column": 65 } } }, { "type": { - "label": "string", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "../matchers/TaxonomicUnitMatcher", - "start": 389, - "end": 423, + "start": 914, + "end": 915, "loc": { "start": { - "line": 16, - "column": 31 + "line": 30, + "column": 65 }, "end": { - "line": 16, - "column": 65 + "line": 30, + "column": 66 } } }, { "type": { - "label": ";", + "label": "{", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 423, - "end": 424, + "start": 916, + "end": 917, "loc": { "start": { - "line": 16, - "column": 65 + "line": 30, + "column": 67 }, "end": { - "line": 16, - "column": 66 + "line": 30, + "column": 68 } } }, { - "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "const", - "start": 426, - "end": 431, + "type": "CommentLine", + "value": " Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.", + "start": 922, + "end": 995, "loc": { "start": { - "line": 17, - "column": 0 + "line": 31, + "column": 4 }, "end": { - "line": 17, - "column": 5 + "line": 31, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " Note that this version ONLY uses the `newick` property to determine the", + "start": 1000, + "end": 1074, + "loc": { + "start": { + "line": 32, + "column": 4 + }, + "end": { + "line": 32, + "column": 78 + } + } + }, + { + "type": "CommentLine", + "value": " phylogeny: if other representations are included (such as a node-based", + "start": 1079, + "end": 1152, + "loc": { + "start": { + "line": 33, + "column": 4 + }, + "end": { + "line": 33, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " format, as used in JSON-LD), they will be ignored and possibly overwritten", + "start": 1157, + "end": 1234, + "loc": { + "start": { + "line": 34, + "column": 4 + }, + "end": { + "line": 34, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " during export. So, to update the phylogeny, please only update the newick", + "start": 1239, + "end": 1315, + "loc": { + "start": { + "line": 35, + "column": 4 + }, + "end": { + "line": 35, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " string!", + "start": 1320, + "end": 1330, + "loc": { + "start": { + "line": 36, + "column": 4 + }, + "end": { + "line": 36, + "column": 14 + } + } + }, + { + "type": "CommentLine", + "value": "", + "start": 1335, + "end": 1337, + "loc": { + "start": { + "line": 37, + "column": 4 + }, + "end": { + "line": 37, + "column": 6 + } + } + }, + { + "type": "CommentLine", + "value": " This ensures that we don't need to reconcile between different", + "start": 1342, + "end": 1407, + "loc": { + "start": { + "line": 38, + "column": 4 + }, + "end": { + "line": 38, + "column": 69 + } + } + }, + { + "type": "CommentLine", + "value": " possible representations of a phylogeny.", + "start": 1412, + "end": 1455, + "loc": { + "start": { + "line": 39, + "column": 4 + }, + "end": { + "line": 39, + "column": 47 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "this", + "keyword": "this", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 432, - "end": 433, + "value": "this", + "start": 1460, + "end": 1464, "loc": { "start": { - "line": 17, - "column": 6 + "line": 40, + "column": 4 }, "end": { - "line": 17, - "column": 7 + "line": 40, + "column": 8 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "TaxonomicUnitMatcher", - "start": 434, - "end": 454, + "start": 1464, + "end": 1465, "loc": { "start": { - "line": 17, + "line": 40, "column": 8 }, "end": { - "line": 17, - "column": 28 + "line": 40, + "column": 9 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50953,16 +53498,17 @@ "postfix": false, "binop": null }, - "start": 455, - "end": 456, + "value": "phylogeny", + "start": 1465, + "end": 1474, "loc": { "start": { - "line": 17, - "column": 29 + "line": 40, + "column": 9 }, "end": { - "line": 17, - "column": 30 + "line": 40, + "column": 18 } } }, @@ -50980,16 +53526,16 @@ "updateContext": null }, "value": "=", - "start": 457, - "end": 458, + "start": 1475, + "end": 1476, "loc": { "start": { - "line": 17, - "column": 31 + "line": 40, + "column": 19 }, "end": { - "line": 17, - "column": 32 + "line": 40, + "column": 20 } } }, @@ -51005,17 +53551,17 @@ "postfix": false, "binop": null }, - "value": "LKT4H15648XGU", - "start": 459, - "end": 472, + "value": "phylogeny", + "start": 1477, + "end": 1486, "loc": { "start": { - "line": 17, - "column": 33 + "line": 40, + "column": 21 }, "end": { - "line": 17, - "column": 46 + "line": 40, + "column": 30 } } }, @@ -51032,23 +53578,23 @@ "binop": null, "updateContext": null }, - "start": 472, - "end": 473, + "start": 1486, + "end": 1487, "loc": { "start": { - "line": 17, - "column": 46 + "line": 40, + "column": 30 }, "end": { - "line": 17, - "column": 47 + "line": 40, + "column": 31 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "this", + "keyword": "this", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -51059,44 +53605,43 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 474, - "end": 480, + "value": "this", + "start": 1492, + "end": 1496, "loc": { "start": { - "line": 18, - "column": 0 + "line": 41, + "column": 4 }, "end": { - "line": 18, - "column": 6 + "line": 41, + "column": 8 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 481, - "end": 482, + "start": 1496, + "end": 1497, "loc": { "start": { - "line": 18, - "column": 7 + "line": 41, + "column": 8 }, "end": { - "line": 18, - "column": 8 + "line": 41, + "column": 9 } } }, @@ -51112,43 +53657,44 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 483, - "end": 485, + "value": "defaultNomenCode", + "start": 1497, + "end": 1513, "loc": { "start": { - "line": 18, + "line": 41, "column": 9 }, "end": { - "line": 18, - "column": 11 + "line": 41, + "column": 25 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H1568V71R", - "start": 486, - "end": 499, + "value": "=", + "start": 1514, + "end": 1515, "loc": { "start": { - "line": 18, - "column": 12 + "line": 41, + "column": 26 }, "end": { - "line": 18, - "column": 25 + "line": 41, + "column": 27 } } }, @@ -51164,25 +53710,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 500, - "end": 504, + "value": "defaultNomenCode", + "start": 1516, + "end": 1532, "loc": { "start": { - "line": 18, - "column": 26 + "line": 41, + "column": 28 }, "end": { - "line": 18, - "column": 30 + "line": 41, + "column": 44 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -51191,78 +53737,64 @@ "binop": null, "updateContext": null }, - "value": "./CitationWrapper", - "start": 505, - "end": 524, + "start": 1532, + "end": 1533, "loc": { "start": { - "line": 18, - "column": 31 + "line": 41, + "column": 44 }, "end": { - "line": 18, - "column": 50 + "line": 41, + "column": 45 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 524, - "end": 525, + "start": 1536, + "end": 1537, "loc": { "start": { - "line": 18, - "column": 50 + "line": 42, + "column": 2 }, "end": { - "line": 18, - "column": 51 + "line": 42, + "column": 3 } } }, { - "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "const", - "start": 527, - "end": 532, + "type": "CommentBlock", + "value": "*\n * Return a normalized form of the phylogeny.\n ", + "start": 1541, + "end": 1598, "loc": { "start": { - "line": 19, - "column": 0 + "line": 44, + "column": 2 }, "end": { - "line": 19, + "line": 46, "column": 5 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -51271,16 +53803,17 @@ "postfix": false, "binop": null }, - "start": 533, - "end": 534, + "value": "static", + "start": 1601, + "end": 1607, "loc": { "start": { - "line": 19, - "column": 6 + "line": 47, + "column": 2 }, "end": { - "line": 19, - "column": 7 + "line": 47, + "column": 8 } } }, @@ -51296,25 +53829,25 @@ "postfix": false, "binop": null }, - "value": "CitationWrapper", - "start": 535, - "end": 550, + "value": "normalize", + "start": 1608, + "end": 1617, "loc": { "start": { - "line": 19, - "column": 8 + "line": 47, + "column": 9 }, "end": { - "line": 19, - "column": 23 + "line": 47, + "column": 18 } } }, { "type": { - "label": "}", - "beforeExpr": false, - "startsExpr": false, + "label": "(", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -51322,51 +53855,50 @@ "postfix": false, "binop": null }, - "start": 551, - "end": 552, + "start": 1617, + "end": 1618, "loc": { "start": { - "line": 19, - "column": 24 + "line": 47, + "column": 18 }, "end": { - "line": 19, - "column": 25 + "line": 47, + "column": 19 } } }, { "type": { - "label": "=", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 553, - "end": 554, + "value": "phylogeny", + "start": 1618, + "end": 1627, "loc": { "start": { - "line": 19, - "column": 26 + "line": 47, + "column": 19 }, "end": { - "line": 19, - "column": 27 + "line": 47, + "column": 28 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -51374,50 +53906,48 @@ "postfix": false, "binop": null }, - "value": "LKT4H1568V71R", - "start": 555, - "end": 568, + "start": 1627, + "end": 1628, "loc": { "start": { - "line": 19, + "line": 47, "column": 28 }, "end": { - "line": 19, - "column": 41 + "line": 47, + "column": 29 } } }, { "type": { - "label": ";", + "label": "{", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 568, - "end": 569, + "start": 1629, + "end": 1630, "loc": { "start": { - "line": 19, - "column": 41 + "line": 47, + "column": 30 }, "end": { - "line": 19, - "column": 42 + "line": 47, + "column": 31 } } }, { "type": { - "label": "class", - "keyword": "class", + "label": "const", + "keyword": "const", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -51428,17 +53958,17 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 571, - "end": 576, + "value": "const", + "start": 1635, + "end": 1640, "loc": { "start": { - "line": 21, - "column": 0 + "line": 48, + "column": 4 }, "end": { - "line": 21, - "column": 5 + "line": 48, + "column": 9 } } }, @@ -51454,113 +53984,77 @@ "postfix": false, "binop": null }, - "value": "PhylogenyWrapper", - "start": 577, - "end": 593, + "value": "normalizedPhylogeny", + "start": 1641, + "end": 1660, "loc": { "start": { - "line": 21, - "column": 6 + "line": 48, + "column": 10 }, "end": { - "line": 21, - "column": 22 + "line": 48, + "column": 29 } } }, { "type": { - "label": "{", + "label": "=", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 594, - "end": 595, - "loc": { - "start": { - "line": 21, - "column": 23 - }, - "end": { - "line": 21, - "column": 24 - } - } - }, - { - "type": "CommentLine", - "value": " Wraps a Phylogeny in a PHYX file and provides access to node, node labels", - "start": 598, - "end": 674, - "loc": { - "start": { - "line": 22, - "column": 2 - }, - "end": { - "line": 22, - "column": 78 - } - } - }, - { - "type": "CommentLine", - "value": " and other information. Remember that a Phylogeny also has the", - "start": 677, - "end": 741, - "loc": { - "start": { - "line": 23, - "column": 2 - }, - "end": { - "line": 23, - "column": 66 - } - } - }, - { - "type": "CommentLine", - "value": " additionalNodeProperties object which provides additional properties for", - "start": 744, - "end": 819, + "value": "=", + "start": 1661, + "end": 1662, "loc": { "start": { - "line": 24, - "column": 2 + "line": 48, + "column": 30 }, "end": { - "line": 24, - "column": 77 + "line": 48, + "column": 31 } } }, { - "type": "CommentLine", - "value": " nodes.", - "start": 822, - "end": 831, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "cloneDeep", + "start": 1663, + "end": 1672, "loc": { "start": { - "line": 25, - "column": 2 + "line": 48, + "column": 32 }, "end": { - "line": 25, - "column": 11 + "line": 48, + "column": 41 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -51569,24 +54063,23 @@ "postfix": false, "binop": null }, - "value": "constructor", - "start": 835, - "end": 846, + "start": 1672, + "end": 1673, "loc": { "start": { - "line": 27, - "column": 2 + "line": 48, + "column": 41 }, "end": { - "line": 27, - "column": 13 + "line": 48, + "column": 42 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -51595,24 +54088,25 @@ "postfix": false, "binop": null }, - "start": 846, - "end": 847, + "value": "phylogeny", + "start": 1673, + "end": 1682, "loc": { "start": { - "line": 27, - "column": 13 + "line": 48, + "column": 42 }, "end": { - "line": 27, - "column": 14 + "line": 48, + "column": 51 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -51620,23 +54114,22 @@ "postfix": false, "binop": null }, - "value": "phylogeny", - "start": 847, - "end": 856, + "start": 1682, + "end": 1683, "loc": { "start": { - "line": 27, - "column": 14 + "line": 48, + "column": 51 }, "end": { - "line": 27, - "column": 23 + "line": 48, + "column": 52 } } }, { "type": { - "label": ",", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -51647,75 +54140,107 @@ "binop": null, "updateContext": null }, - "start": 856, - "end": 857, + "start": 1683, + "end": 1684, "loc": { "start": { - "line": 27, - "column": 23 + "line": 48, + "column": 52 }, "end": { - "line": 27, - "column": 24 + "line": 48, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": " We could normalize the Newick string, but that doesn't seem very nice.", + "start": 1690, + "end": 1763, + "loc": { + "start": { + "line": 50, + "column": 4 + }, + "end": { + "line": 50, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " Normalize the source if there is one.", + "start": 1769, + "end": 1809, + "loc": { + "start": { + "line": 52, + "column": 4 + }, + "end": { + "line": 52, + "column": 44 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "defaultNomenCode", - "start": 858, - "end": 874, + "value": "if", + "start": 1814, + "end": 1816, "loc": { "start": { - "line": 27, - "column": 25 + "line": 53, + "column": 4 }, "end": { - "line": 27, - "column": 41 + "line": 53, + "column": 6 } } }, { "type": { - "label": "=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 875, - "end": 876, + "start": 1817, + "end": 1818, "loc": { "start": { - "line": 27, - "column": 42 + "line": 53, + "column": 7 }, "end": { - "line": 27, - "column": 43 + "line": 53, + "column": 8 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -51723,45 +54248,48 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "owlterms", - "start": 877, - "end": 885, + "value": "source", + "start": 1818, + "end": 1826, "loc": { "start": { - "line": 27, - "column": 44 + "line": 53, + "column": 8 }, "end": { - "line": 27, - "column": 52 + "line": 53, + "column": 16 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "in", + "keyword": "in", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 7, "updateContext": null }, - "start": 885, - "end": 886, + "value": "in", + "start": 1827, + "end": 1829, "loc": { "start": { - "line": 27, - "column": 52 + "line": 53, + "column": 17 }, "end": { - "line": 27, - "column": 53 + "line": 53, + "column": 19 } } }, @@ -51777,17 +54305,17 @@ "postfix": false, "binop": null }, - "value": "UNKNOWN_CODE", - "start": 886, - "end": 898, + "value": "phylogeny", + "start": 1830, + "end": 1839, "loc": { "start": { - "line": 27, - "column": 53 + "line": 53, + "column": 20 }, "end": { - "line": 27, - "column": 65 + "line": 53, + "column": 29 } } }, @@ -51803,16 +54331,16 @@ "postfix": false, "binop": null }, - "start": 898, - "end": 899, + "start": 1839, + "end": 1840, "loc": { "start": { - "line": 27, - "column": 65 + "line": 53, + "column": 29 }, "end": { - "line": 27, - "column": 66 + "line": 53, + "column": 30 } } }, @@ -51828,167 +54356,230 @@ "postfix": false, "binop": null }, - "start": 900, - "end": 901, - "loc": { - "start": { - "line": 27, - "column": 67 - }, - "end": { - "line": 27, - "column": 68 - } - } - }, - { - "type": "CommentLine", - "value": " Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.", - "start": 906, - "end": 979, + "start": 1841, + "end": 1842, "loc": { "start": { - "line": 28, - "column": 4 + "line": 53, + "column": 31 }, "end": { - "line": 28, - "column": 77 + "line": 53, + "column": 32 } } }, { - "type": "CommentLine", - "value": " Note that this version ONLY uses the `newick` property to determine the", - "start": 984, - "end": 1058, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "normalizedPhylogeny", + "start": 1849, + "end": 1868, "loc": { "start": { - "line": 29, - "column": 4 + "line": 54, + "column": 6 }, "end": { - "line": 29, - "column": 78 + "line": 54, + "column": 25 } } }, { - "type": "CommentLine", - "value": " phylogeny: if other representations are included (such as a node-based", - "start": 1063, - "end": 1136, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1868, + "end": 1869, "loc": { "start": { - "line": 30, - "column": 4 + "line": 54, + "column": 25 }, "end": { - "line": 30, - "column": 77 + "line": 54, + "column": 26 } } }, { - "type": "CommentLine", - "value": " format, as used in JSON-LD), they will be ignored and possibly overwritten", - "start": 1141, - "end": 1218, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "source", + "start": 1869, + "end": 1875, "loc": { "start": { - "line": 31, - "column": 4 + "line": 54, + "column": 26 }, "end": { - "line": 31, - "column": 81 + "line": 54, + "column": 32 } } }, { - "type": "CommentLine", - "value": " during export. So, to update the phylogeny, please only update the newick", - "start": 1223, - "end": 1299, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 1876, + "end": 1877, "loc": { "start": { - "line": 32, - "column": 4 + "line": 54, + "column": 33 }, "end": { - "line": 32, - "column": 80 + "line": 54, + "column": 34 } } }, { - "type": "CommentLine", - "value": " string!", - "start": 1304, - "end": 1314, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "CitationWrapper", + "start": 1878, + "end": 1893, "loc": { "start": { - "line": 33, - "column": 4 + "line": 54, + "column": 35 }, "end": { - "line": 33, - "column": 14 + "line": 54, + "column": 50 } } }, { - "type": "CommentLine", - "value": "", - "start": 1319, - "end": 1321, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1893, + "end": 1894, "loc": { "start": { - "line": 34, - "column": 4 + "line": 54, + "column": 50 }, "end": { - "line": 34, - "column": 6 + "line": 54, + "column": 51 } } }, { - "type": "CommentLine", - "value": " This ensures that we don't need to reconcile between different", - "start": 1326, - "end": 1391, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "normalize", + "start": 1894, + "end": 1903, "loc": { "start": { - "line": 35, - "column": 4 + "line": 54, + "column": 51 }, "end": { - "line": 35, - "column": 69 + "line": 54, + "column": 60 } } }, { - "type": "CommentLine", - "value": " possible representations of a phylogeny.", - "start": 1396, - "end": 1439, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1903, + "end": 1904, "loc": { "start": { - "line": 36, - "column": 4 + "line": 54, + "column": 60 }, "end": { - "line": 36, - "column": 47 + "line": 54, + "column": 61 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -51996,20 +54587,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 1444, - "end": 1448, + "value": "phylogeny", + "start": 1904, + "end": 1913, "loc": { "start": { - "line": 37, - "column": 4 + "line": 54, + "column": 61 }, "end": { - "line": 37, - "column": 8 + "line": 54, + "column": 70 } } }, @@ -52026,16 +54616,16 @@ "binop": null, "updateContext": null }, - "start": 1448, - "end": 1449, + "start": 1913, + "end": 1914, "loc": { "start": { - "line": 37, - "column": 8 + "line": 54, + "column": 70 }, "end": { - "line": 37, - "column": 9 + "line": 54, + "column": 71 } } }, @@ -52051,51 +54641,51 @@ "postfix": false, "binop": null }, - "value": "phylogeny", - "start": 1449, - "end": 1458, + "value": "source", + "start": 1914, + "end": 1920, "loc": { "start": { - "line": 37, - "column": 9 + "line": 54, + "column": 71 }, "end": { - "line": 37, - "column": 18 + "line": 54, + "column": 77 } } }, { "type": { - "label": "=", + "label": "||", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 1, "updateContext": null }, - "value": "=", - "start": 1459, - "end": 1460, + "value": "||", + "start": 1921, + "end": 1923, "loc": { "start": { - "line": 37, - "column": 19 + "line": 54, + "column": 78 }, "end": { - "line": 37, - "column": 20 + "line": 54, + "column": 80 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -52104,78 +54694,73 @@ "postfix": false, "binop": null }, - "value": "phylogeny", - "start": 1461, - "end": 1470, + "start": 1924, + "end": 1925, "loc": { "start": { - "line": 37, - "column": 21 + "line": 54, + "column": 81 }, "end": { - "line": 37, - "column": 30 + "line": 54, + "column": 82 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 1470, - "end": 1471, + "start": 1925, + "end": 1926, "loc": { "start": { - "line": 37, - "column": 30 + "line": 54, + "column": 82 }, "end": { - "line": 37, - "column": 31 + "line": 54, + "column": 83 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 1476, - "end": 1480, + "start": 1926, + "end": 1927, "loc": { "start": { - "line": 38, - "column": 4 + "line": 54, + "column": 83 }, "end": { - "line": 38, - "column": 8 + "line": 54, + "column": 84 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -52185,24 +54770,24 @@ "binop": null, "updateContext": null }, - "start": 1480, - "end": 1481, + "start": 1927, + "end": 1928, "loc": { "start": { - "line": 38, - "column": 8 + "line": 54, + "column": 84 }, "end": { - "line": 38, - "column": 9 + "line": 54, + "column": 85 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -52210,44 +54795,44 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 1481, - "end": 1497, + "start": 1933, + "end": 1934, "loc": { "start": { - "line": 38, - "column": 9 + "line": 55, + "column": 4 }, "end": { - "line": 38, - "column": 25 + "line": 55, + "column": 5 } } }, { "type": { - "label": "=", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 1498, - "end": 1499, + "value": "return", + "start": 1940, + "end": 1946, "loc": { "start": { - "line": 38, - "column": 26 + "line": 57, + "column": 4 }, "end": { - "line": 38, - "column": 27 + "line": 57, + "column": 10 } } }, @@ -52263,17 +54848,17 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 1500, - "end": 1516, + "value": "normalizedPhylogeny", + "start": 1947, + "end": 1966, "loc": { "start": { - "line": 38, - "column": 28 + "line": 57, + "column": 11 }, "end": { - "line": 38, - "column": 44 + "line": 57, + "column": 30 } } }, @@ -52290,16 +54875,16 @@ "binop": null, "updateContext": null }, - "start": 1516, - "end": 1517, + "start": 1966, + "end": 1967, "loc": { "start": { - "line": 38, - "column": 44 + "line": 57, + "column": 30 }, "end": { - "line": 38, - "column": 45 + "line": 57, + "column": 31 } } }, @@ -52315,15 +54900,15 @@ "postfix": false, "binop": null }, - "start": 1520, - "end": 1521, + "start": 1970, + "end": 1971, "loc": { "start": { - "line": 39, + "line": 58, "column": 2 }, "end": { - "line": 39, + "line": 58, "column": 3 } } @@ -52341,15 +54926,15 @@ "binop": null }, "value": "static", - "start": 1525, - "end": 1531, + "start": 1975, + "end": 1981, "loc": { "start": { - "line": 41, + "line": 60, "column": 2 }, "end": { - "line": 41, + "line": 60, "column": 8 } } @@ -52367,15 +54952,15 @@ "binop": null }, "value": "getErrorsInNewickString", - "start": 1532, - "end": 1555, + "start": 1982, + "end": 2005, "loc": { "start": { - "line": 41, + "line": 60, "column": 9 }, "end": { - "line": 41, + "line": 60, "column": 32 } } @@ -52392,15 +54977,15 @@ "postfix": false, "binop": null }, - "start": 1555, - "end": 1556, + "start": 2005, + "end": 2006, "loc": { "start": { - "line": 41, + "line": 60, "column": 32 }, "end": { - "line": 41, + "line": 60, "column": 33 } } @@ -52418,15 +55003,15 @@ "binop": null }, "value": "newick", - "start": 1556, - "end": 1562, + "start": 2006, + "end": 2012, "loc": { "start": { - "line": 41, + "line": 60, "column": 33 }, "end": { - "line": 41, + "line": 60, "column": 39 } } @@ -52443,15 +55028,15 @@ "postfix": false, "binop": null }, - "start": 1562, - "end": 1563, + "start": 2012, + "end": 2013, "loc": { "start": { - "line": 41, + "line": 60, "column": 39 }, "end": { - "line": 41, + "line": 60, "column": 40 } } @@ -52468,15 +55053,15 @@ "postfix": false, "binop": null }, - "start": 1564, - "end": 1565, + "start": 2014, + "end": 2015, "loc": { "start": { - "line": 41, + "line": 60, "column": 41 }, "end": { - "line": 41, + "line": 60, "column": 42 } } @@ -52484,15 +55069,15 @@ { "type": "CommentLine", "value": " Given a Newick string, return a list of errors found in parsing this", - "start": 1570, - "end": 1641, + "start": 2020, + "end": 2091, "loc": { "start": { - "line": 42, + "line": 61, "column": 4 }, "end": { - "line": 42, + "line": 61, "column": 75 } } @@ -52500,15 +55085,15 @@ { "type": "CommentLine", "value": " string. The errors are returned as a list of objects, each of which", - "start": 1646, - "end": 1716, + "start": 2096, + "end": 2166, "loc": { "start": { - "line": 43, + "line": 62, "column": 4 }, "end": { - "line": 43, + "line": 62, "column": 74 } } @@ -52516,15 +55101,15 @@ { "type": "CommentLine", "value": " has two properties:", - "start": 1721, - "end": 1743, + "start": 2171, + "end": 2193, "loc": { "start": { - "line": 44, + "line": 63, "column": 4 }, "end": { - "line": 44, + "line": 63, "column": 26 } } @@ -52532,15 +55117,15 @@ { "type": "CommentLine", "value": " - title: A short title of the error, distinct for each type of error.", - "start": 1748, - "end": 1821, + "start": 2198, + "end": 2271, "loc": { "start": { - "line": 45, + "line": 64, "column": 4 }, "end": { - "line": 45, + "line": 64, "column": 77 } } @@ -52548,15 +55133,15 @@ { "type": "CommentLine", "value": " - message: A longer description of the error, which might include", - "start": 1826, - "end": 1895, + "start": 2276, + "end": 2345, "loc": { "start": { - "line": 46, + "line": 65, "column": 4 }, "end": { - "line": 46, + "line": 65, "column": 73 } } @@ -52564,15 +55149,15 @@ { "type": "CommentLine", "value": " information specific to a particular error.", - "start": 1900, - "end": 1949, + "start": 2350, + "end": 2399, "loc": { "start": { - "line": 47, + "line": 66, "column": 4 }, "end": { - "line": 47, + "line": 66, "column": 53 } } @@ -52580,15 +55165,15 @@ { "type": "CommentLine", "value": "", - "start": 1954, - "end": 1956, + "start": 2404, + "end": 2406, "loc": { "start": { - "line": 48, + "line": 67, "column": 4 }, "end": { - "line": 48, + "line": 67, "column": 6 } } @@ -52596,15 +55181,15 @@ { "type": "CommentLine", "value": " We try to order errors from most helpful ('Unbalanced parentheses in", - "start": 1961, - "end": 2032, + "start": 2411, + "end": 2482, "loc": { "start": { - "line": 49, + "line": 68, "column": 4 }, "end": { - "line": 49, + "line": 68, "column": 75 } } @@ -52612,15 +55197,15 @@ { "type": "CommentLine", "value": " Newick string') to least helpful ('Error parsing phylogeny').", - "start": 2037, - "end": 2101, + "start": 2487, + "end": 2551, "loc": { "start": { - "line": 50, + "line": 69, "column": 4 }, "end": { - "line": 50, + "line": 69, "column": 68 } } @@ -52640,15 +55225,15 @@ "updateContext": null }, "value": "const", - "start": 2106, - "end": 2111, + "start": 2556, + "end": 2561, "loc": { "start": { - "line": 51, + "line": 70, "column": 4 }, "end": { - "line": 51, + "line": 70, "column": 9 } } @@ -52666,15 +55251,15 @@ "binop": null }, "value": "newickTrimmed", - "start": 2112, - "end": 2125, + "start": 2562, + "end": 2575, "loc": { "start": { - "line": 51, + "line": 70, "column": 10 }, "end": { - "line": 51, + "line": 70, "column": 23 } } @@ -52693,15 +55278,15 @@ "updateContext": null }, "value": "=", - "start": 2126, - "end": 2127, + "start": 2576, + "end": 2577, "loc": { "start": { - "line": 51, + "line": 70, "column": 24 }, "end": { - "line": 51, + "line": 70, "column": 25 } } @@ -52719,15 +55304,15 @@ "binop": null }, "value": "newick", - "start": 2128, - "end": 2134, + "start": 2578, + "end": 2584, "loc": { "start": { - "line": 51, + "line": 70, "column": 26 }, "end": { - "line": 51, + "line": 70, "column": 32 } } @@ -52745,15 +55330,15 @@ "binop": null, "updateContext": null }, - "start": 2134, - "end": 2135, + "start": 2584, + "end": 2585, "loc": { "start": { - "line": 51, + "line": 70, "column": 32 }, "end": { - "line": 51, + "line": 70, "column": 33 } } @@ -52771,15 +55356,15 @@ "binop": null }, "value": "trim", - "start": 2135, - "end": 2139, + "start": 2585, + "end": 2589, "loc": { "start": { - "line": 51, + "line": 70, "column": 33 }, "end": { - "line": 51, + "line": 70, "column": 37 } } @@ -52796,15 +55381,15 @@ "postfix": false, "binop": null }, - "start": 2139, - "end": 2140, + "start": 2589, + "end": 2590, "loc": { "start": { - "line": 51, + "line": 70, "column": 37 }, "end": { - "line": 51, + "line": 70, "column": 38 } } @@ -52821,15 +55406,15 @@ "postfix": false, "binop": null }, - "start": 2140, - "end": 2141, + "start": 2590, + "end": 2591, "loc": { "start": { - "line": 51, + "line": 70, "column": 38 }, "end": { - "line": 51, + "line": 70, "column": 39 } } @@ -52847,15 +55432,15 @@ "binop": null, "updateContext": null }, - "start": 2141, - "end": 2142, + "start": 2591, + "end": 2592, "loc": { "start": { - "line": 51, + "line": 70, "column": 39 }, "end": { - "line": 51, + "line": 70, "column": 40 } } @@ -52875,15 +55460,15 @@ "updateContext": null }, "value": "const", - "start": 2147, - "end": 2152, + "start": 2597, + "end": 2602, "loc": { "start": { - "line": 52, + "line": 71, "column": 4 }, "end": { - "line": 52, + "line": 71, "column": 9 } } @@ -52901,15 +55486,15 @@ "binop": null }, "value": "errors", - "start": 2153, - "end": 2159, + "start": 2603, + "end": 2609, "loc": { "start": { - "line": 52, + "line": 71, "column": 10 }, "end": { - "line": 52, + "line": 71, "column": 16 } } @@ -52928,15 +55513,15 @@ "updateContext": null }, "value": "=", - "start": 2160, - "end": 2161, + "start": 2610, + "end": 2611, "loc": { "start": { - "line": 52, + "line": 71, "column": 17 }, "end": { - "line": 52, + "line": 71, "column": 18 } } @@ -52954,15 +55539,15 @@ "binop": null, "updateContext": null }, - "start": 2162, - "end": 2163, + "start": 2612, + "end": 2613, "loc": { "start": { - "line": 52, + "line": 71, "column": 19 }, "end": { - "line": 52, + "line": 71, "column": 20 } } @@ -52980,15 +55565,15 @@ "binop": null, "updateContext": null }, - "start": 2163, - "end": 2164, + "start": 2613, + "end": 2614, "loc": { "start": { - "line": 52, + "line": 71, "column": 20 }, "end": { - "line": 52, + "line": 71, "column": 21 } } @@ -53006,15 +55591,15 @@ "binop": null, "updateContext": null }, - "start": 2164, - "end": 2165, + "start": 2614, + "end": 2615, "loc": { "start": { - "line": 52, + "line": 71, "column": 21 }, "end": { - "line": 52, + "line": 71, "column": 22 } } @@ -53022,15 +55607,15 @@ { "type": "CommentLine", "value": " Look for an empty Newick string.", - "start": 2171, - "end": 2206, + "start": 2621, + "end": 2656, "loc": { "start": { - "line": 54, + "line": 73, "column": 4 }, "end": { - "line": 54, + "line": 73, "column": 39 } } @@ -53050,15 +55635,15 @@ "updateContext": null }, "value": "if", - "start": 2211, - "end": 2213, + "start": 2661, + "end": 2663, "loc": { "start": { - "line": 55, + "line": 74, "column": 4 }, "end": { - "line": 55, + "line": 74, "column": 6 } } @@ -53075,15 +55660,15 @@ "postfix": false, "binop": null }, - "start": 2214, - "end": 2215, + "start": 2664, + "end": 2665, "loc": { "start": { - "line": 55, + "line": 74, "column": 7 }, "end": { - "line": 55, + "line": 74, "column": 8 } } @@ -53101,15 +55686,15 @@ "binop": null }, "value": "newickTrimmed", - "start": 2215, - "end": 2228, + "start": 2665, + "end": 2678, "loc": { "start": { - "line": 55, + "line": 74, "column": 8 }, "end": { - "line": 55, + "line": 74, "column": 21 } } @@ -53128,15 +55713,15 @@ "updateContext": null }, "value": "===", - "start": 2229, - "end": 2232, + "start": 2679, + "end": 2682, "loc": { "start": { - "line": 55, + "line": 74, "column": 22 }, "end": { - "line": 55, + "line": 74, "column": 25 } } @@ -53155,15 +55740,15 @@ "updateContext": null }, "value": "", - "start": 2233, - "end": 2235, + "start": 2683, + "end": 2685, "loc": { "start": { - "line": 55, + "line": 74, "column": 26 }, "end": { - "line": 55, + "line": 74, "column": 28 } } @@ -53182,15 +55767,15 @@ "updateContext": null }, "value": "||", - "start": 2236, - "end": 2238, + "start": 2686, + "end": 2688, "loc": { "start": { - "line": 55, + "line": 74, "column": 29 }, "end": { - "line": 55, + "line": 74, "column": 31 } } @@ -53208,15 +55793,15 @@ "binop": null }, "value": "newickTrimmed", - "start": 2239, - "end": 2252, + "start": 2689, + "end": 2702, "loc": { "start": { - "line": 55, + "line": 74, "column": 32 }, "end": { - "line": 55, + "line": 74, "column": 45 } } @@ -53235,15 +55820,15 @@ "updateContext": null }, "value": "===", - "start": 2253, - "end": 2256, + "start": 2703, + "end": 2706, "loc": { "start": { - "line": 55, + "line": 74, "column": 46 }, "end": { - "line": 55, + "line": 74, "column": 49 } } @@ -53262,15 +55847,15 @@ "updateContext": null }, "value": "()", - "start": 2257, - "end": 2261, + "start": 2707, + "end": 2711, "loc": { "start": { - "line": 55, + "line": 74, "column": 50 }, "end": { - "line": 55, + "line": 74, "column": 54 } } @@ -53289,15 +55874,15 @@ "updateContext": null }, "value": "||", - "start": 2262, - "end": 2264, + "start": 2712, + "end": 2714, "loc": { "start": { - "line": 55, + "line": 74, "column": 55 }, "end": { - "line": 55, + "line": 74, "column": 57 } } @@ -53315,15 +55900,15 @@ "binop": null }, "value": "newickTrimmed", - "start": 2265, - "end": 2278, + "start": 2715, + "end": 2728, "loc": { "start": { - "line": 55, + "line": 74, "column": 58 }, "end": { - "line": 55, + "line": 74, "column": 71 } } @@ -53342,15 +55927,15 @@ "updateContext": null }, "value": "===", - "start": 2279, - "end": 2282, + "start": 2729, + "end": 2732, "loc": { "start": { - "line": 55, + "line": 74, "column": 72 }, "end": { - "line": 55, + "line": 74, "column": 75 } } @@ -53369,15 +55954,15 @@ "updateContext": null }, "value": "();", - "start": 2283, - "end": 2288, + "start": 2733, + "end": 2738, "loc": { "start": { - "line": 55, + "line": 74, "column": 76 }, "end": { - "line": 55, + "line": 74, "column": 81 } } @@ -53394,15 +55979,15 @@ "postfix": false, "binop": null }, - "start": 2288, - "end": 2289, + "start": 2738, + "end": 2739, "loc": { "start": { - "line": 55, + "line": 74, "column": 81 }, "end": { - "line": 55, + "line": 74, "column": 82 } } @@ -53419,15 +56004,15 @@ "postfix": false, "binop": null }, - "start": 2290, - "end": 2291, + "start": 2740, + "end": 2741, "loc": { "start": { - "line": 55, + "line": 74, "column": 83 }, "end": { - "line": 55, + "line": 74, "column": 84 } } @@ -53435,15 +56020,15 @@ { "type": "CommentLine", "value": " None of the later errors are relevant here, so bail out now.", - "start": 2298, - "end": 2361, + "start": 2748, + "end": 2811, "loc": { "start": { - "line": 56, + "line": 75, "column": 6 }, "end": { - "line": 56, + "line": 75, "column": 69 } } @@ -53463,15 +56048,15 @@ "updateContext": null }, "value": "return", - "start": 2368, - "end": 2374, + "start": 2818, + "end": 2824, "loc": { "start": { - "line": 57, + "line": 76, "column": 6 }, "end": { - "line": 57, + "line": 76, "column": 12 } } @@ -53489,15 +56074,15 @@ "binop": null, "updateContext": null }, - "start": 2375, - "end": 2376, + "start": 2825, + "end": 2826, "loc": { "start": { - "line": 57, + "line": 76, "column": 13 }, "end": { - "line": 57, + "line": 76, "column": 14 } } @@ -53514,15 +56099,15 @@ "postfix": false, "binop": null }, - "start": 2376, - "end": 2377, + "start": 2826, + "end": 2827, "loc": { "start": { - "line": 57, + "line": 76, "column": 14 }, "end": { - "line": 57, + "line": 76, "column": 15 } } @@ -53540,15 +56125,15 @@ "binop": null }, "value": "title", - "start": 2386, - "end": 2391, + "start": 2836, + "end": 2841, "loc": { "start": { - "line": 58, + "line": 77, "column": 8 }, "end": { - "line": 58, + "line": 77, "column": 13 } } @@ -53566,15 +56151,15 @@ "binop": null, "updateContext": null }, - "start": 2391, - "end": 2392, + "start": 2841, + "end": 2842, "loc": { "start": { - "line": 58, + "line": 77, "column": 13 }, "end": { - "line": 58, + "line": 77, "column": 14 } } @@ -53593,15 +56178,15 @@ "updateContext": null }, "value": "No phylogeny entered", - "start": 2393, - "end": 2415, + "start": 2843, + "end": 2865, "loc": { "start": { - "line": 58, + "line": 77, "column": 15 }, "end": { - "line": 58, + "line": 77, "column": 37 } } @@ -53619,15 +56204,15 @@ "binop": null, "updateContext": null }, - "start": 2415, - "end": 2416, + "start": 2865, + "end": 2866, "loc": { "start": { - "line": 58, + "line": 77, "column": 37 }, "end": { - "line": 58, + "line": 77, "column": 38 } } @@ -53645,15 +56230,15 @@ "binop": null }, "value": "message", - "start": 2425, - "end": 2432, + "start": 2875, + "end": 2882, "loc": { "start": { - "line": 59, + "line": 78, "column": 8 }, "end": { - "line": 59, + "line": 78, "column": 15 } } @@ -53671,15 +56256,15 @@ "binop": null, "updateContext": null }, - "start": 2432, - "end": 2433, + "start": 2882, + "end": 2883, "loc": { "start": { - "line": 59, + "line": 78, "column": 15 }, "end": { - "line": 59, + "line": 78, "column": 16 } } @@ -53698,15 +56283,15 @@ "updateContext": null }, "value": "Click on \"Edit as Newick\" to enter a phylogeny below.", - "start": 2434, - "end": 2489, + "start": 2884, + "end": 2939, "loc": { "start": { - "line": 59, + "line": 78, "column": 17 }, "end": { - "line": 59, + "line": 78, "column": 72 } } @@ -53724,15 +56309,15 @@ "binop": null, "updateContext": null }, - "start": 2489, - "end": 2490, + "start": 2939, + "end": 2940, "loc": { "start": { - "line": 59, + "line": 78, "column": 72 }, "end": { - "line": 59, + "line": 78, "column": 73 } } @@ -53749,15 +56334,15 @@ "postfix": false, "binop": null }, - "start": 2497, - "end": 2498, + "start": 2947, + "end": 2948, "loc": { "start": { - "line": 60, + "line": 79, "column": 6 }, "end": { - "line": 60, + "line": 79, "column": 7 } } @@ -53775,15 +56360,15 @@ "binop": null, "updateContext": null }, - "start": 2498, - "end": 2499, + "start": 2948, + "end": 2949, "loc": { "start": { - "line": 60, + "line": 79, "column": 7 }, "end": { - "line": 60, + "line": 79, "column": 8 } } @@ -53801,15 +56386,15 @@ "binop": null, "updateContext": null }, - "start": 2499, - "end": 2500, + "start": 2949, + "end": 2950, "loc": { "start": { - "line": 60, + "line": 79, "column": 8 }, "end": { - "line": 60, + "line": 79, "column": 9 } } @@ -53826,15 +56411,15 @@ "postfix": false, "binop": null }, - "start": 2505, - "end": 2506, + "start": 2955, + "end": 2956, "loc": { "start": { - "line": 61, + "line": 80, "column": 4 }, "end": { - "line": 61, + "line": 80, "column": 5 } } @@ -53842,15 +56427,15 @@ { "type": "CommentLine", "value": " Look for an unbalanced Newick string.", - "start": 2512, - "end": 2552, + "start": 2962, + "end": 3002, "loc": { "start": { - "line": 63, + "line": 82, "column": 4 }, "end": { - "line": 63, + "line": 82, "column": 44 } } @@ -53870,15 +56455,15 @@ "updateContext": null }, "value": "let", - "start": 2557, - "end": 2560, + "start": 3007, + "end": 3010, "loc": { "start": { - "line": 64, + "line": 83, "column": 4 }, "end": { - "line": 64, + "line": 83, "column": 7 } } @@ -53896,15 +56481,15 @@ "binop": null }, "value": "parenLevels", - "start": 2561, - "end": 2572, + "start": 3011, + "end": 3022, "loc": { "start": { - "line": 64, + "line": 83, "column": 8 }, "end": { - "line": 64, + "line": 83, "column": 19 } } @@ -53923,15 +56508,15 @@ "updateContext": null }, "value": "=", - "start": 2573, - "end": 2574, + "start": 3023, + "end": 3024, "loc": { "start": { - "line": 64, + "line": 83, "column": 20 }, "end": { - "line": 64, + "line": 83, "column": 21 } } @@ -53950,15 +56535,15 @@ "updateContext": null }, "value": 0, - "start": 2575, - "end": 2576, + "start": 3025, + "end": 3026, "loc": { "start": { - "line": 64, + "line": 83, "column": 22 }, "end": { - "line": 64, + "line": 83, "column": 23 } } @@ -53976,15 +56561,15 @@ "binop": null, "updateContext": null }, - "start": 2576, - "end": 2577, + "start": 3026, + "end": 3027, "loc": { "start": { - "line": 64, + "line": 83, "column": 23 }, "end": { - "line": 64, + "line": 83, "column": 24 } } @@ -54004,15 +56589,15 @@ "updateContext": null }, "value": "for", - "start": 2582, - "end": 2585, + "start": 3032, + "end": 3035, "loc": { "start": { - "line": 65, + "line": 84, "column": 4 }, "end": { - "line": 65, + "line": 84, "column": 7 } } @@ -54029,15 +56614,15 @@ "postfix": false, "binop": null }, - "start": 2586, - "end": 2587, + "start": 3036, + "end": 3037, "loc": { "start": { - "line": 65, + "line": 84, "column": 8 }, "end": { - "line": 65, + "line": 84, "column": 9 } } @@ -54057,15 +56642,15 @@ "updateContext": null }, "value": "let", - "start": 2587, - "end": 2590, + "start": 3037, + "end": 3040, "loc": { "start": { - "line": 65, + "line": 84, "column": 9 }, "end": { - "line": 65, + "line": 84, "column": 12 } } @@ -54083,15 +56668,15 @@ "binop": null }, "value": "x", - "start": 2591, - "end": 2592, + "start": 3041, + "end": 3042, "loc": { "start": { - "line": 65, + "line": 84, "column": 13 }, "end": { - "line": 65, + "line": 84, "column": 14 } } @@ -54110,15 +56695,15 @@ "updateContext": null }, "value": "=", - "start": 2593, - "end": 2594, + "start": 3043, + "end": 3044, "loc": { "start": { - "line": 65, + "line": 84, "column": 15 }, "end": { - "line": 65, + "line": 84, "column": 16 } } @@ -54137,15 +56722,15 @@ "updateContext": null }, "value": 0, - "start": 2595, - "end": 2596, + "start": 3045, + "end": 3046, "loc": { "start": { - "line": 65, + "line": 84, "column": 17 }, "end": { - "line": 65, + "line": 84, "column": 18 } } @@ -54163,15 +56748,15 @@ "binop": null, "updateContext": null }, - "start": 2596, - "end": 2597, + "start": 3046, + "end": 3047, "loc": { "start": { - "line": 65, + "line": 84, "column": 18 }, "end": { - "line": 65, + "line": 84, "column": 19 } } @@ -54189,15 +56774,15 @@ "binop": null }, "value": "x", - "start": 2598, - "end": 2599, + "start": 3048, + "end": 3049, "loc": { "start": { - "line": 65, + "line": 84, "column": 20 }, "end": { - "line": 65, + "line": 84, "column": 21 } } @@ -54216,15 +56801,15 @@ "updateContext": null }, "value": "<", - "start": 2600, - "end": 2601, + "start": 3050, + "end": 3051, "loc": { "start": { - "line": 65, + "line": 84, "column": 22 }, "end": { - 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"line": 93, + "line": 112, "column": 63 }, "end": { - "line": 93, + "line": 112, "column": 72 } } @@ -57866,15 +60451,15 @@ "postfix": false, "binop": null }, - "start": 3449, - "end": 3450, + "start": 3899, + "end": 3900, "loc": { "start": { - "line": 93, + "line": 112, "column": 72 }, "end": { - "line": 93, + "line": 112, "column": 73 } } @@ -57891,15 +60476,15 @@ "postfix": false, "binop": null }, - "start": 3451, - "end": 3452, + "start": 3901, + "end": 3902, "loc": { "start": { - "line": 93, + "line": 112, "column": 74 }, "end": { - "line": 93, + "line": 112, "column": 75 } } @@ -57907,15 +60492,15 @@ { "type": "CommentLine", "value": " Recurse through PhyloTree nodes, executing function on each node.", - "start": 3457, - "end": 3525, + "start": 3907, + "end": 3975, "loc": { "start": { - "line": 94, + "line": 113, "column": 4 }, "end": { - "line": 94, + "line": 113, "column": 72 } } @@ -57923,15 +60508,15 @@ { "type": "CommentLine", "value": " - node: The node to recurse from. The function will be called on node", - "start": 3530, - "end": 3603, + "start": 3980, + "end": 4053, "loc": { "start": { - "line": 95, + "line": 114, "column": 4 }, "end": { - "line": 95, + "line": 114, "column": 77 } } @@ -57939,15 +60524,15 @@ { "type": "CommentLine", "value": " *before* being called on its children.", - "start": 3608, - "end": 3658, + "start": 4058, + "end": 4108, "loc": { "start": { - "line": 96, + "line": 115, "column": 4 }, "end": { - "line": 96, + "line": 115, "column": 54 } } @@ -57955,15 +60540,15 @@ { "type": "CommentLine", "value": " - func: The function to call on `node` and all of its children.", - "start": 3663, - "end": 3730, + "start": 4113, + "end": 4180, "loc": { "start": { - "line": 97, + "line": 116, "column": 4 }, "end": { - "line": 97, + "line": 116, "column": 71 } } @@ -57971,15 +60556,15 @@ { "type": "CommentLine", "value": " - nodeCount: `node` will be called with this nodeCount. All of its", - "start": 3735, - "end": 3805, + "start": 4185, + "end": 4255, "loc": { "start": { - "line": 98, + "line": 117, "column": 4 }, "end": { - "line": 98, + "line": 117, "column": 74 } } @@ -57987,15 +60572,15 @@ { "type": "CommentLine", "value": " children will be called with consecutively increasing nodeCounts.", - "start": 3810, - "end": 3887, + "start": 4260, + "end": 4337, "loc": { "start": { - "line": 99, + "line": 118, "column": 4 }, "end": { - "line": 99, + "line": 118, "column": 81 } } @@ -58003,15 +60588,15 @@ { "type": "CommentLine", "value": " - parentCount: The nodeCount associated with the parent of this node", - "start": 3892, - "end": 3964, + "start": 4342, + "end": 4414, "loc": { "start": { - "line": 100, + "line": 119, "column": 4 }, "end": { - "line": 100, + "line": 119, "column": 76 } } @@ -58019,15 +60604,15 @@ { "type": "CommentLine", "value": " within this run of recurseNodes. For instance, immediate children", - "start": 3969, - "end": 4046, + "start": 4419, + "end": 4496, "loc": { "start": { - "line": 101, + "line": 120, "column": 4 }, "end": { - "line": 101, + "line": 120, "column": 81 } } @@ -58035,15 +60620,15 @@ { "type": "CommentLine", "value": " of `node` will have a parentCount of 0. By default, `node` itself", - "start": 4051, - "end": 4128, + "start": 4501, + "end": 4578, "loc": { "start": { - "line": 102, + "line": 121, "column": 4 }, "end": { - "line": 102, + "line": 121, "column": 81 } } @@ -58051,15 +60636,15 @@ { "type": "CommentLine", "value": " will have a parentCount of `undefined`.", - "start": 4133, - "end": 4184, + "start": 4583, + "end": 4634, "loc": { "start": { - "line": 103, + "line": 122, "column": 4 }, "end": { - "line": 103, + "line": 122, "column": 55 } } @@ -58067,15 +60652,15 @@ { "type": "CommentLine", "value": " When the function `func` is called, it is given three arguments:", - "start": 4189, - "end": 4256, + "start": 4639, + "end": 4706, "loc": { "start": { - "line": 104, + "line": 123, "column": 4 }, "end": { - "line": 104, + "line": 123, "column": 71 } } @@ -58083,15 +60668,15 @@ { "type": "CommentLine", "value": " - The current node object (initially: `node`)", - "start": 4261, - "end": 4310, + "start": 4711, + "end": 4760, "loc": { "start": { - "line": 105, + "line": 124, "column": 4 }, "end": { - "line": 105, + "line": 124, "column": 53 } } @@ -58099,15 +60684,15 @@ { "type": "CommentLine", "value": " - The count of the current node object (initially: `nodeCount`)", - "start": 4315, - "end": 4382, + "start": 4765, + "end": 4832, "loc": { "start": { - "line": 106, + "line": 125, "column": 4 }, "end": { - "line": 106, + "line": 125, "column": 71 } } @@ -58115,15 +60700,15 @@ { "type": "CommentLine", "value": " - The parent count of the current node object (initially: `parentCount`)", - "start": 4387, - "end": 4463, + "start": 4837, + "end": 4913, "loc": { "start": { - "line": 107, + "line": 126, "column": 4 }, "end": { - "line": 107, + "line": 126, "column": 80 } } @@ -58141,15 +60726,15 @@ "binop": null }, "value": "func", - "start": 4468, - "end": 4472, + "start": 4918, + "end": 4922, "loc": { "start": { - "line": 108, + "line": 127, "column": 4 }, "end": { - "line": 108, + "line": 127, "column": 8 } } @@ -58166,15 +60751,15 @@ "postfix": false, "binop": null }, - "start": 4472, - "end": 4473, + "start": 4922, + "end": 4923, "loc": { "start": { - "line": 108, + "line": 127, "column": 8 }, "end": { - "line": 108, + "line": 127, "column": 9 } } @@ -58192,15 +60777,15 @@ "binop": null }, "value": "node", - "start": 4473, - "end": 4477, + "start": 4923, + "end": 4927, "loc": { "start": { - "line": 108, + "line": 127, "column": 9 }, "end": { - "line": 108, + "line": 127, "column": 13 } } @@ -58218,15 +60803,15 @@ "binop": null, "updateContext": null }, - "start": 4477, - "end": 4478, + "start": 4927, + "end": 4928, "loc": { "start": { - "line": 108, + "line": 127, "column": 13 }, "end": { - "line": 108, + "line": 127, "column": 14 } } @@ -58244,15 +60829,15 @@ "binop": null }, "value": "nodeCount", - "start": 4479, - "end": 4488, + "start": 4929, + "end": 4938, "loc": { "start": { - "line": 108, + "line": 127, "column": 15 }, "end": { - "line": 108, + "line": 127, "column": 24 } } @@ -58270,15 +60855,15 @@ "binop": null, "updateContext": null }, - "start": 4488, - "end": 4489, + "start": 4938, + "end": 4939, "loc": { "start": { - "line": 108, + "line": 127, "column": 24 }, "end": { - "line": 108, + "line": 127, "column": 25 } } @@ -58296,15 +60881,15 @@ "binop": null }, "value": "parentCount", - "start": 4490, - "end": 4501, + "start": 4940, + "end": 4951, "loc": { "start": { - "line": 108, + "line": 127, "column": 26 }, "end": { - "line": 108, + "line": 127, "column": 37 } } @@ -58321,15 +60906,15 @@ "postfix": false, "binop": null }, - "start": 4501, - "end": 4502, + "start": 4951, + "end": 4952, "loc": { "start": { - "line": 108, + "line": 127, "column": 37 }, "end": { - "line": 108, + "line": 127, "column": 38 } } @@ -58347,15 +60932,15 @@ "binop": null, "updateContext": null }, - "start": 4502, - "end": 4503, + "start": 4952, + "end": 4953, "loc": { "start": { - "line": 108, + "line": 127, "column": 38 }, "end": { - "line": 108, + "line": 127, "column": 39 } } @@ -58375,15 +60960,15 @@ "updateContext": null }, "value": "let", - "start": 4509, - 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"line": 110, + "line": 129, "column": 27 }, "end": { - "line": 110, + "line": 129, "column": 28 } } @@ -58508,15 +61093,15 @@ "updateContext": null }, "value": 1, - "start": 4534, - "end": 4535, + "start": 4984, + "end": 4985, "loc": { "start": { - "line": 110, + "line": 129, "column": 29 }, "end": { - "line": 110, + "line": 129, "column": 30 } } @@ -58534,15 +61119,15 @@ "binop": null, "updateContext": null }, - "start": 4535, - "end": 4536, + "start": 4985, + "end": 4986, "loc": { "start": { - "line": 110, + "line": 129, "column": 30 }, "end": { - "line": 110, + "line": 129, "column": 31 } } @@ -58550,15 +61135,15 @@ { "type": "CommentLine", "value": " Recurse through all children of this node.", - "start": 4542, - "end": 4587, + "start": 4992, + "end": 5037, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 49 } } @@ -58578,15 +61163,15 @@ "updateContext": null }, "value": "if", - "start": 4592, - "end": 4594, + "start": 5042, + "end": 5044, "loc": { "start": { - "line": 113, + "line": 132, "column": 4 }, "end": { - "line": 113, + "line": 132, "column": 6 } } @@ -58603,15 +61188,15 @@ "postfix": false, "binop": null }, - "start": 4595, - "end": 4596, + "start": 5045, + "end": 5046, "loc": { "start": { - "line": 113, + "line": 132, "column": 7 }, "end": { - "line": 113, + "line": 132, "column": 8 } } @@ -58629,15 +61214,15 @@ "binop": null }, "value": "has", - "start": 4596, - "end": 4599, + "start": 5046, + "end": 5049, "loc": { "start": { - "line": 113, + "line": 132, "column": 8 }, "end": { - "line": 113, + "line": 132, "column": 11 } } @@ -58654,15 +61239,15 @@ "postfix": false, "binop": null }, - "start": 4599, - "end": 4600, + "start": 5049, + "end": 5050, "loc": { "start": { - "line": 113, + "line": 132, "column": 11 }, "end": { - "line": 113, + "line": 132, "column": 12 } } @@ -58680,15 +61265,15 @@ "binop": null }, "value": "node", - "start": 4600, - "end": 4604, + "start": 5050, + "end": 5054, "loc": { "start": { - "line": 113, + "line": 132, "column": 12 }, "end": { - "line": 113, + "line": 132, "column": 16 } } @@ -58706,15 +61291,15 @@ "binop": null, "updateContext": null }, - "start": 4604, - "end": 4605, + "start": 5054, + "end": 5055, "loc": { "start": { - "line": 113, + "line": 132, "column": 16 }, "end": { - "line": 113, + "line": 132, "column": 17 } } @@ -58733,15 +61318,15 @@ "updateContext": null }, "value": "children", - "start": 4606, - "end": 4616, + "start": 5056, + "end": 5066, "loc": { "start": { - "line": 113, + "line": 132, "column": 18 }, "end": { - "line": 113, + "line": 132, "column": 28 } } @@ -58758,15 +61343,15 @@ "postfix": false, "binop": null }, - "start": 4616, - "end": 4617, + "start": 5066, + "end": 5067, "loc": { "start": { - "line": 113, + "line": 132, "column": 28 }, "end": { - "line": 113, + "line": 132, "column": 29 } } @@ -58783,15 +61368,15 @@ "postfix": false, "binop": null }, - "start": 4617, - "end": 4618, + "start": 5067, + "end": 5068, "loc": { "start": { - "line": 113, + "line": 132, "column": 29 }, "end": { - "line": 113, + "line": 132, "column": 30 } } @@ -58808,15 +61393,15 @@ "postfix": false, "binop": null }, - "start": 4619, - "end": 4620, + "start": 5069, + "end": 5070, "loc": { "start": { - "line": 113, + "line": 132, "column": 31 }, "end": { - "line": 113, + "line": 132, "column": 32 } } @@ -58834,15 +61419,15 @@ "binop": null }, "value": "node", - "start": 4627, - "end": 4631, + "start": 5077, + "end": 5081, "loc": { "start": { - "line": 114, + "line": 133, "column": 6 }, "end": { - "line": 114, + "line": 133, "column": 10 } } @@ -58860,15 +61445,15 @@ "binop": null, "updateContext": null }, - "start": 4631, - "end": 4632, + "start": 5081, + "end": 5082, "loc": { "start": { - "line": 114, + "line": 133, "column": 10 }, "end": { - "line": 114, + "line": 133, "column": 11 } } @@ -58886,15 +61471,15 @@ "binop": null }, "value": "children", - "start": 4632, - "end": 4640, + "start": 5082, + "end": 5090, "loc": { "start": { - "line": 114, + "line": 133, "column": 11 }, "end": { - "line": 114, + "line": 133, "column": 19 } } @@ -58912,15 +61497,15 @@ "binop": null, "updateContext": null }, - "start": 4640, - "end": 4641, + "start": 5090, + "end": 5091, "loc": { "start": { - "line": 114, + "line": 133, "column": 19 }, "end": { - "line": 114, + "line": 133, "column": 20 } } @@ -58938,15 +61523,15 @@ "binop": null }, "value": "forEach", - "start": 4641, - "end": 4648, + "start": 5091, + "end": 5098, "loc": { "start": { - "line": 114, + "line": 133, "column": 20 }, "end": { - "line": 114, + "line": 133, "column": 27 } } @@ -58963,15 +61548,15 @@ "postfix": false, "binop": null }, - "start": 4648, - "end": 4649, + "start": 5098, + "end": 5099, "loc": { "start": { - "line": 114, + "line": 133, "column": 27 }, "end": { - "line": 114, + "line": 133, "column": 28 } } @@ -58988,15 +61573,15 @@ "postfix": false, "binop": null }, - "start": 4649, - "end": 4650, + "start": 5099, + "end": 5100, "loc": { "start": { - "line": 114, + "line": 133, "column": 28 }, "end": { - "line": 114, + "line": 133, "column": 29 } } @@ -59014,15 +61599,15 @@ "binop": null }, "value": "child", - "start": 4650, - "end": 4655, + "start": 5100, + "end": 5105, "loc": { "start": { - "line": 114, + "line": 133, "column": 29 }, "end": { - "line": 114, + "line": 133, "column": 34 } } @@ -59039,15 +61624,15 @@ "postfix": false, "binop": null }, - "start": 4655, - "end": 4656, + "start": 5105, + "end": 5106, "loc": { "start": { - "line": 114, + "line": 133, "column": 34 }, "end": { - "line": 114, + "line": 133, "column": 35 } } @@ -59065,15 +61650,15 @@ "binop": null, "updateContext": null }, - "start": 4657, - "end": 4659, + "start": 5107, + "end": 5109, "loc": { "start": { - "line": 114, + "line": 133, "column": 36 }, "end": { - "line": 114, + "line": 133, "column": 38 } } @@ -59090,15 +61675,15 @@ "postfix": false, "binop": null }, - "start": 4660, - "end": 4661, + "start": 5110, + "end": 5111, "loc": { "start": { - "line": 114, + "line": 133, "column": 39 }, "end": { - "line": 114, + "line": 133, "column": 40 } } @@ -59116,15 +61701,15 @@ "binop": null }, "value": "nextID", - "start": 4670, - "end": 4676, + "start": 5120, + "end": 5126, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 14 } } @@ -59143,15 +61728,15 @@ "updateContext": null }, "value": "=", - "start": 4677, - "end": 4678, + "start": 5127, + "end": 5128, "loc": { "start": { - "line": 115, + "line": 134, "column": 15 }, "end": { - "line": 115, + "line": 134, "column": 16 } } @@ -59169,15 +61754,15 @@ "binop": null }, "value": "PhylogenyWrapper", - "start": 4679, - "end": 4695, + "start": 5129, + "end": 5145, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 115, + "line": 134, "column": 33 } } @@ -59195,15 +61780,15 @@ "binop": null, "updateContext": null }, - "start": 4695, - "end": 4696, + "start": 5145, + "end": 5146, "loc": { "start": { - "line": 115, + "line": 134, "column": 33 }, "end": { - "line": 115, + "line": 134, "column": 34 } } @@ -59221,15 +61806,15 @@ "binop": null }, "value": "recurseNodes", - "start": 4696, - "end": 4708, + "start": 5146, + "end": 5158, "loc": { "start": { - "line": 115, + "line": 134, "column": 34 }, "end": { - "line": 115, + "line": 134, "column": 46 } } @@ -59246,15 +61831,15 @@ "postfix": false, "binop": null }, - "start": 4708, - "end": 4709, + "start": 5158, + "end": 5159, "loc": { "start": { - "line": 115, + "line": 134, "column": 46 }, "end": { - "line": 115, + "line": 134, "column": 47 } } @@ -59272,15 +61857,15 @@ "binop": null }, "value": "child", - "start": 4720, - "end": 4725, + "start": 5170, + "end": 5175, "loc": { "start": { - "line": 116, + "line": 135, "column": 10 }, "end": { - "line": 116, + "line": 135, "column": 15 } } @@ -59298,15 +61883,15 @@ "binop": null, "updateContext": null }, - "start": 4725, - "end": 4726, + "start": 5175, + "end": 5176, "loc": { "start": { - "line": 116, + "line": 135, "column": 15 }, "end": { - "line": 116, + "line": 135, "column": 16 } } @@ -59324,15 +61909,15 @@ "binop": null }, "value": "func", - "start": 4737, - "end": 4741, + "start": 5187, + "end": 5191, "loc": { "start": { - "line": 117, + "line": 136, "column": 10 }, "end": { - "line": 117, + "line": 136, "column": 14 } } @@ -59350,15 +61935,15 @@ "binop": null, "updateContext": null }, - "start": 4741, - "end": 4742, + "start": 5191, + "end": 5192, "loc": { "start": { - "line": 117, + "line": 136, "column": 14 }, "end": { - "line": 117, + "line": 136, "column": 15 } } @@ -59376,15 +61961,15 @@ "binop": null }, "value": "nextID", - "start": 4753, - "end": 4759, + "start": 5203, + "end": 5209, "loc": { "start": { - "line": 118, + "line": 137, "column": 10 }, "end": { - "line": 118, + "line": 137, "column": 16 } } @@ -59402,15 +61987,15 @@ "binop": null, "updateContext": null }, - "start": 4759, - "end": 4760, + "start": 5209, + "end": 5210, "loc": { "start": { - "line": 118, + "line": 137, "column": 16 }, "end": { - "line": 118, + "line": 137, "column": 17 } } @@ -59428,15 +62013,15 @@ "binop": null }, "value": "nodeCount", - "start": 4771, - "end": 4780, + "start": 5221, + "end": 5230, "loc": { "start": { - "line": 119, + "line": 138, "column": 10 }, "end": { - "line": 119, + "line": 138, "column": 19 } } @@ -59453,15 +62038,15 @@ "postfix": false, "binop": null }, - "start": 4789, - "end": 4790, + "start": 5239, + "end": 5240, "loc": { "start": { - "line": 120, + "line": 139, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 9 } } @@ -59479,15 +62064,15 @@ "binop": null, "updateContext": null }, - "start": 4790, - "end": 4791, + "start": 5240, + "end": 5241, "loc": { "start": { - "line": 120, + "line": 139, "column": 9 }, "end": { - "line": 120, + "line": 139, "column": 10 } } @@ -59504,15 +62089,15 @@ "postfix": false, "binop": null }, - "start": 4798, - "end": 4799, + "start": 5248, + "end": 5249, "loc": { "start": { - "line": 121, + "line": 140, "column": 6 }, "end": { - "line": 121, + "line": 140, "column": 7 } } @@ -59529,15 +62114,15 @@ "postfix": false, "binop": null }, - "start": 4799, - "end": 4800, + "start": 5249, + "end": 5250, "loc": { "start": { - "line": 121, + "line": 140, "column": 7 }, "end": { - "line": 121, + "line": 140, "column": 8 } } @@ -59555,15 +62140,15 @@ "binop": null, "updateContext": null }, - "start": 4800, - "end": 4801, + "start": 5250, + "end": 5251, "loc": { "start": { - "line": 121, + "line": 140, "column": 8 }, "end": { - "line": 121, + "line": 140, "column": 9 } } @@ -59580,15 +62165,15 @@ "postfix": false, "binop": null }, - "start": 4806, - "end": 4807, + "start": 5256, + "end": 5257, "loc": { "start": { - "line": 122, + "line": 141, "column": 4 }, "end": { - "line": 122, + "line": 141, "column": 5 } } @@ -59608,15 +62193,15 @@ "updateContext": null }, "value": "return", - "start": 4813, - "end": 4819, + "start": 5263, + "end": 5269, "loc": { "start": { - "line": 124, + "line": 143, "column": 4 }, "end": { - "line": 124, + "line": 143, "column": 10 } } @@ -59634,15 +62219,15 @@ "binop": null }, "value": "nextID", - "start": 4820, - "end": 4826, + "start": 5270, + "end": 5276, "loc": { "start": { - "line": 124, + "line": 143, "column": 11 }, "end": { - "line": 124, + "line": 143, "column": 17 } } @@ -59660,15 +62245,15 @@ "binop": null, "updateContext": null }, - "start": 4826, - "end": 4827, + "start": 5276, + "end": 5277, "loc": { "start": { - "line": 124, + "line": 143, "column": 17 }, "end": { - "line": 124, + "line": 143, "column": 18 } } @@ -59685,15 +62270,15 @@ "postfix": false, "binop": null }, - "start": 4830, - "end": 4831, + "start": 5280, + "end": 5281, "loc": { "start": { - "line": 125, + "line": 144, "column": 2 }, "end": { - "line": 125, + "line": 144, "column": 3 } } @@ -59711,15 +62296,15 @@ "binop": null }, "value": "getTaxonomicUnits", - "start": 4835, - "end": 4852, + "start": 5285, + "end": 5302, "loc": { "start": { - "line": 127, + "line": 146, "column": 2 }, "end": { - "line": 127, + "line": 146, "column": 19 } } @@ -59736,15 +62321,15 @@ "postfix": false, "binop": null }, - "start": 4852, - "end": 4853, + "start": 5302, + "end": 5303, "loc": { "start": { - "line": 127, + "line": 146, "column": 19 }, "end": { - "line": 127, + "line": 146, "column": 20 } } @@ -59762,15 +62347,15 @@ "binop": null }, "value": "nodeType", - "start": 4853, - "end": 4861, + "start": 5303, + "end": 5311, "loc": { "start": { - "line": 127, + "line": 146, "column": 20 }, "end": { - "line": 127, + "line": 146, "column": 28 } } @@ -59789,15 +62374,15 @@ "updateContext": null }, "value": "=", - "start": 4862, - "end": 4863, + "start": 5312, + "end": 5313, "loc": { "start": { - "line": 127, + "line": 146, "column": 29 }, "end": { - "line": 127, + "line": 146, "column": 30 } } @@ -59816,15 +62401,15 @@ "updateContext": null }, "value": "both", - "start": 4864, - "end": 4870, + "start": 5314, + "end": 5320, "loc": { "start": { - "line": 127, + "line": 146, "column": 31 }, "end": { - "line": 127, + "line": 146, "column": 37 } } @@ -59841,15 +62426,15 @@ "postfix": false, "binop": null }, - "start": 4870, - "end": 4871, + "start": 5320, + "end": 5321, "loc": { "start": { - "line": 127, + "line": 146, "column": 37 }, "end": { - "line": 127, + "line": 146, "column": 38 } } @@ -59866,15 +62451,15 @@ "postfix": false, "binop": null }, - "start": 4872, - "end": 4873, + "start": 5322, + "end": 5323, "loc": { "start": { - "line": 127, + "line": 146, "column": 39 }, "end": { - "line": 127, + "line": 146, "column": 40 } } @@ -59882,15 +62467,15 @@ { "type": "CommentLine", "value": " Return a list of all taxonomic units in this phylogeny.", - "start": 4878, - "end": 4936, + "start": 5328, + "end": 5386, "loc": { "start": { - "line": 128, + "line": 147, "column": 4 }, "end": { - "line": 128, + "line": 147, "column": 62 } } @@ -59898,15 +62483,15 @@ { "type": "CommentLine", "value": " Node labels will be extracted from:", - "start": 4941, - "end": 4979, + "start": 5391, + "end": 5429, "loc": { "start": { - "line": 129, + "line": 148, "column": 4 }, "end": { - "line": 129, + "line": 148, "column": 42 } } @@ -59914,15 +62499,15 @@ { "type": "CommentLine", "value": " - internal nodes only (if nodeType == 'internal')", - "start": 4984, - "end": 5037, + "start": 5434, + "end": 5487, "loc": { "start": { - "line": 130, + "line": 149, "column": 4 }, "end": { - "line": 130, + "line": 149, "column": 57 } } @@ -59930,15 +62515,15 @@ { "type": "CommentLine", "value": " - terminal nodes only (if nodeType == 'terminal')", - "start": 5042, - "end": 5095, + "start": 5492, + "end": 5545, "loc": { "start": { - "line": 131, + "line": 150, "column": 4 }, "end": { - "line": 131, + "line": 150, "column": 57 } } @@ -59946,15 +62531,15 @@ { "type": "CommentLine", "value": " - both internal and terminal nodes (if nodeType == 'both')", - "start": 5100, - "end": 5162, + "start": 5550, + "end": 5612, "loc": { "start": { - "line": 132, + "line": 151, "column": 4 }, "end": { - "line": 132, + "line": 151, "column": 66 } } @@ -59962,15 +62547,15 @@ { "type": "CommentLine", "value": "", - "start": 5167, - "end": 5169, + "start": 5617, + "end": 5619, "loc": { "start": { - "line": 133, + "line": 152, "column": 4 }, "end": { - "line": 133, + "line": 152, "column": 6 } } @@ -59978,15 +62563,15 @@ { "type": "CommentLine", "value": " See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted", - "start": 5174, - "end": 5249, + "start": 5624, + "end": 5699, "loc": { "start": { - "line": 134, + "line": 153, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 79 } } @@ -59994,15 +62579,15 @@ { "type": "CommentLine", "value": " into node labels, but in brief:", - "start": 5254, - "end": 5288, + "start": 5704, + "end": 5738, "loc": { "start": { - "line": 135, + "line": 154, "column": 4 }, "end": { - "line": 135, + "line": 154, "column": 38 } } @@ -60010,15 +62595,15 @@ { "type": "CommentLine", "value": " 1. We look for taxonomic units in the additionalNodeProperties.", - "start": 5293, - "end": 5360, + "start": 5743, + "end": 5810, "loc": { "start": { - "line": 136, + "line": 155, "column": 4 }, "end": { - "line": 136, + "line": 155, "column": 71 } } @@ -60026,15 +62611,15 @@ { "type": "CommentLine", "value": " 2. If none are found, we attempt to parse the node label as a scientific name.", - "start": 5365, - "end": 5447, + "start": 5815, + "end": 5897, "loc": { "start": { - "line": 137, + "line": 156, "column": 4 }, "end": { - "line": 137, + "line": 156, "column": 86 } } @@ -60042,15 +62627,15 @@ { "type": "CommentLine", "value": "", - "start": 5452, - "end": 5454, + "start": 5902, + "end": 5904, "loc": { "start": { - "line": 138, + "line": 157, "column": 4 }, "end": { - "line": 138, + "line": 157, "column": 6 } } @@ -60070,15 +62655,15 @@ "updateContext": null }, "value": "const", - "start": 5459, - "end": 5464, + "start": 5909, + "end": 5914, "loc": { "start": { - "line": 139, + "line": 158, "column": 4 }, "end": { - "line": 139, + "line": 158, "column": 9 } } @@ -60096,15 +62681,15 @@ "binop": null }, "value": "nodeLabels", - "start": 5465, - "end": 5475, + "start": 5915, + "end": 5925, "loc": { "start": { - "line": 139, + "line": 158, "column": 10 }, "end": { - "line": 139, + "line": 158, "column": 20 } } @@ -60123,15 +62708,15 @@ "updateContext": null }, "value": "=", - "start": 5476, - "end": 5477, + "start": 5926, + "end": 5927, "loc": { "start": { - "line": 139, + "line": 158, "column": 21 }, "end": { - "line": 139, + "line": 158, "column": 22 } } @@ -60151,15 +62736,15 @@ "updateContext": null }, "value": "this", - "start": 5478, - "end": 5482, + "start": 5928, + "end": 5932, "loc": { "start": { - "line": 139, + "line": 158, "column": 23 }, "end": { - "line": 139, + "line": 158, "column": 27 } } @@ -60177,15 +62762,15 @@ "binop": null, "updateContext": null }, - "start": 5482, - "end": 5483, + "start": 5932, + "end": 5933, "loc": { "start": { - "line": 139, + "line": 158, "column": 27 }, "end": { - "line": 139, + "line": 158, "column": 28 } } @@ -60203,15 +62788,15 @@ "binop": null }, "value": "getNodeLabels", - "start": 5483, - "end": 5496, + "start": 5933, + "end": 5946, "loc": { "start": { - "line": 139, + "line": 158, "column": 28 }, "end": { - "line": 139, + "line": 158, "column": 41 } } @@ -60228,15 +62813,15 @@ "postfix": false, "binop": null }, - "start": 5496, - "end": 5497, + "start": 5946, + "end": 5947, "loc": { "start": { - "line": 139, + "line": 158, "column": 41 }, "end": { - "line": 139, + "line": 158, "column": 42 } } @@ -60254,15 +62839,15 @@ "binop": null }, "value": "nodeType", - "start": 5497, - "end": 5505, + "start": 5947, + "end": 5955, "loc": { "start": { - "line": 139, + "line": 158, "column": 42 }, "end": { - "line": 139, + "line": 158, "column": 50 } } @@ -60279,15 +62864,15 @@ "postfix": false, "binop": null }, - "start": 5505, - "end": 5506, + "start": 5955, + "end": 5956, "loc": { "start": { - "line": 139, + "line": 158, "column": 50 }, "end": { - "line": 139, + "line": 158, "column": 51 } } @@ -60305,15 +62890,15 @@ "binop": null, "updateContext": null }, - "start": 5506, - "end": 5507, + "start": 5956, + "end": 5957, "loc": { "start": { - "line": 139, + "line": 158, "column": 51 }, "end": { - "line": 139, + "line": 158, "column": 52 } } @@ -60333,15 +62918,15 @@ "updateContext": null }, "value": "const", - "start": 5512, - "end": 5517, + "start": 5962, + "end": 5967, "loc": { "start": { - "line": 140, + "line": 159, "column": 4 }, "end": { - "line": 140, + "line": 159, "column": 9 } } @@ -60359,15 +62944,15 @@ "binop": null }, "value": "tunits", - "start": 5518, - "end": 5524, + "start": 5968, + "end": 5974, "loc": { "start": { - "line": 140, + "line": 159, "column": 10 }, "end": { - "line": 140, + "line": 159, "column": 16 } } @@ -60386,15 +62971,15 @@ "updateContext": null }, "value": "=", - "start": 5525, - "end": 5526, + "start": 5975, + "end": 5976, "loc": { "start": { - "line": 140, + "line": 159, "column": 17 }, "end": { - "line": 140, + "line": 159, "column": 18 } } @@ -60414,15 +62999,15 @@ "updateContext": null }, "value": "new", - "start": 5527, - "end": 5530, + "start": 5977, + "end": 5980, "loc": { "start": { - "line": 140, + "line": 159, "column": 19 }, "end": { - "line": 140, + "line": 159, "column": 22 } } @@ -60440,15 +63025,15 @@ "binop": null }, "value": "Set", - "start": 5531, - "end": 5534, + "start": 5981, + "end": 5984, "loc": { "start": { - "line": 140, + "line": 159, "column": 23 }, "end": { - "line": 140, + "line": 159, "column": 26 } } @@ -60465,15 +63050,15 @@ "postfix": false, "binop": null }, - "start": 5534, - "end": 5535, + "start": 5984, + "end": 5985, "loc": { "start": { - "line": 140, + "line": 159, "column": 26 }, "end": { - "line": 140, + "line": 159, "column": 27 } } @@ -60490,15 +63075,15 @@ "postfix": false, "binop": null }, - "start": 5535, - "end": 5536, + "start": 5985, + "end": 5986, "loc": { "start": { - "line": 140, + "line": 159, "column": 27 }, "end": { - "line": 140, + "line": 159, "column": 28 } } @@ -60516,15 +63101,15 @@ "binop": null, "updateContext": null }, - "start": 5536, - "end": 5537, + "start": 5986, + "end": 5987, "loc": { "start": { - "line": 140, + "line": 159, "column": 28 }, "end": { - "line": 140, + "line": 159, "column": 29 } } @@ -60542,15 +63127,15 @@ "binop": null }, "value": "nodeLabels", - "start": 5543, - "end": 5553, + "start": 5993, + "end": 6003, "loc": { "start": { - "line": 142, + "line": 161, "column": 4 }, "end": { - "line": 142, + "line": 161, "column": 14 } } @@ -60568,15 +63153,15 @@ "binop": null, "updateContext": null }, - "start": 5553, - "end": 5554, + "start": 6003, + "end": 6004, "loc": { "start": { - "line": 142, + "line": 161, "column": 14 }, "end": { - "line": 142, + "line": 161, "column": 15 } } @@ -60594,15 +63179,15 @@ "binop": null }, "value": "forEach", - "start": 5554, - "end": 5561, + "start": 6004, + "end": 6011, "loc": { "start": { - "line": 142, + "line": 161, "column": 15 }, "end": { - "line": 142, + "line": 161, "column": 22 } } @@ -60619,15 +63204,15 @@ "postfix": false, "binop": null }, - "start": 5561, - "end": 5562, + "start": 6011, + "end": 6012, "loc": { "start": { - "line": 142, + "line": 161, "column": 22 }, "end": { - "line": 142, + "line": 161, "column": 23 } } @@ -60645,15 +63230,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5569, - "end": 5578, + "start": 6019, + "end": 6028, "loc": { "start": { - "line": 143, + "line": 162, "column": 6 }, "end": { - "line": 143, + "line": 162, "column": 15 } } @@ -60671,15 +63256,15 @@ "binop": null, "updateContext": null }, - "start": 5579, - "end": 5581, + "start": 6029, + "end": 6031, "loc": { "start": { - "line": 143, + "line": 162, "column": 16 }, "end": { - "line": 143, + "line": 162, "column": 18 } } @@ -60699,15 +63284,15 @@ "updateContext": null }, "value": "this", - "start": 5582, - "end": 5586, + "start": 6032, + "end": 6036, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 23 } } @@ -60725,15 +63310,15 @@ "binop": null, "updateContext": null }, - "start": 5586, - "end": 5587, + "start": 6036, + "end": 6037, "loc": { "start": { - "line": 143, + "line": 162, "column": 23 }, "end": { - "line": 143, + "line": 162, "column": 24 } } @@ -60751,15 +63336,15 @@ "binop": null }, "value": "getTaxonomicUnitsForNodeLabel", - "start": 5587, - "end": 5616, + "start": 6037, + "end": 6066, "loc": { "start": { - "line": 143, + "line": 162, "column": 24 }, "end": { - "line": 143, + "line": 162, "column": 53 } } @@ -60776,15 +63361,15 @@ "postfix": false, "binop": null }, - "start": 5616, - "end": 5617, + "start": 6066, + "end": 6067, "loc": { "start": { - "line": 143, + "line": 162, "column": 53 }, "end": { - "line": 143, + "line": 162, "column": 54 } } @@ -60802,15 +63387,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5617, - "end": 5626, + "start": 6067, + "end": 6076, "loc": { "start": { - "line": 143, + "line": 162, "column": 54 }, "end": { - "line": 143, + "line": 162, "column": 63 } } @@ -60827,15 +63412,15 @@ "postfix": false, "binop": null }, - "start": 5626, - "end": 5627, + "start": 6076, + "end": 6077, "loc": { "start": { - "line": 143, + "line": 162, "column": 63 }, "end": { - "line": 143, + "line": 162, "column": 64 } } @@ -60853,15 +63438,15 @@ "binop": null, "updateContext": null }, - "start": 5636, - "end": 5637, + "start": 6086, + "end": 6087, "loc": { "start": { - "line": 144, + "line": 163, "column": 8 }, "end": { - "line": 144, + "line": 163, "column": 9 } } @@ -60879,15 +63464,15 @@ "binop": null }, "value": "forEach", - "start": 5637, - "end": 5644, + "start": 6087, + "end": 6094, "loc": { "start": { - "line": 144, + "line": 163, "column": 9 }, "end": { - "line": 144, + "line": 163, "column": 16 } } @@ -60904,15 +63489,15 @@ "postfix": false, "binop": null }, - "start": 5644, - "end": 5645, + "start": 6094, + "end": 6095, "loc": { "start": { - "line": 144, + "line": 163, "column": 16 }, "end": { - "line": 144, + "line": 163, "column": 17 } } @@ -60930,15 +63515,15 @@ "binop": null }, "value": "tunit", - "start": 5645, - "end": 5650, + "start": 6095, + "end": 6100, "loc": { "start": { - "line": 144, + "line": 163, "column": 17 }, "end": { - "line": 144, + "line": 163, "column": 22 } } @@ -60956,15 +63541,15 @@ "binop": null, "updateContext": null }, - "start": 5651, - "end": 5653, + "start": 6101, + "end": 6103, "loc": { "start": { - "line": 144, + "line": 163, "column": 23 }, "end": { - "line": 144, + "line": 163, "column": 25 } } @@ -60982,15 +63567,15 @@ "binop": null }, "value": "tunits", - "start": 5654, - "end": 5660, + "start": 6104, + "end": 6110, "loc": { "start": { - "line": 144, + "line": 163, "column": 26 }, "end": { - "line": 144, + "line": 163, "column": 32 } } @@ -61008,15 +63593,15 @@ "binop": null, "updateContext": null }, - "start": 5660, - "end": 5661, + "start": 6110, + "end": 6111, "loc": { "start": { - "line": 144, + "line": 163, "column": 32 }, "end": { - "line": 144, + "line": 163, "column": 33 } } @@ -61034,15 +63619,15 @@ "binop": null }, "value": "add", - "start": 5661, - "end": 5664, + "start": 6111, + "end": 6114, "loc": { "start": { - "line": 144, + "line": 163, "column": 33 }, "end": { - "line": 144, + "line": 163, "column": 36 } } @@ -61059,15 +63644,15 @@ "postfix": false, "binop": null }, - "start": 5664, - "end": 5665, + "start": 6114, + "end": 6115, "loc": { "start": { - "line": 144, + "line": 163, "column": 36 }, "end": { - "line": 144, + "line": 163, "column": 37 } } @@ -61085,15 +63670,15 @@ "binop": null }, "value": "tunit", - "start": 5665, - "end": 5670, + "start": 6115, + "end": 6120, "loc": { "start": { - "line": 144, + "line": 163, "column": 37 }, "end": { - "line": 144, + "line": 163, "column": 42 } } @@ -61110,15 +63695,15 @@ "postfix": false, "binop": null }, - "start": 5670, - "end": 5671, + "start": 6120, + "end": 6121, "loc": { "start": { - "line": 144, + "line": 163, "column": 42 }, "end": { - "line": 144, + "line": 163, "column": 43 } } @@ -61135,15 +63720,15 @@ "postfix": false, "binop": null }, - "start": 5671, - "end": 5672, + "start": 6121, + "end": 6122, "loc": { "start": { - "line": 144, + "line": 163, "column": 43 }, "end": { - "line": 144, + "line": 163, "column": 44 } } @@ -61160,15 +63745,15 @@ "postfix": false, "binop": null }, - "start": 5677, - "end": 5678, + "start": 6127, + "end": 6128, "loc": { "start": { - "line": 145, + "line": 164, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 5 } } @@ -61186,15 +63771,15 @@ "binop": null, "updateContext": null }, - "start": 5678, - "end": 5679, + "start": 6128, + "end": 6129, "loc": { "start": { - "line": 145, + "line": 164, "column": 5 }, "end": { - "line": 145, + "line": 164, "column": 6 } } @@ -61214,15 +63799,15 @@ "updateContext": null }, "value": "return", - "start": 5685, - "end": 5691, + "start": 6135, + "end": 6141, "loc": { "start": { - "line": 147, + "line": 166, "column": 4 }, "end": { - "line": 147, + "line": 166, "column": 10 } } @@ -61240,15 +63825,15 @@ "binop": null }, "value": "tunits", - "start": 5692, - "end": 5698, + "start": 6142, + "end": 6148, "loc": { "start": { - "line": 147, + "line": 166, "column": 11 }, "end": { - "line": 147, + "line": 166, "column": 17 } } @@ -61266,15 +63851,15 @@ "binop": null, "updateContext": null }, - "start": 5698, - "end": 5699, + "start": 6148, + "end": 6149, "loc": { "start": { - "line": 147, + "line": 166, "column": 17 }, "end": { - "line": 147, + "line": 166, "column": 18 } } @@ -61291,15 +63876,15 @@ "postfix": false, "binop": null }, - "start": 5702, - "end": 5703, + "start": 6152, + "end": 6153, "loc": { "start": { - "line": 148, + "line": 167, "column": 2 }, "end": { - "line": 148, + "line": 167, "column": 3 } } @@ -61317,15 +63902,15 @@ "binop": null }, "value": "getNodeLabels", - "start": 5707, - "end": 5720, + "start": 6157, + "end": 6170, "loc": { "start": { - "line": 150, + "line": 169, "column": 2 }, "end": { - "line": 150, + "line": 169, "column": 15 } } @@ -61342,15 +63927,15 @@ "postfix": false, "binop": null }, - "start": 5720, - "end": 5721, + "start": 6170, + "end": 6171, "loc": { "start": { - "line": 150, + "line": 169, "column": 15 }, "end": { - "line": 150, + "line": 169, "column": 16 } } @@ -61368,15 +63953,15 @@ "binop": null }, "value": "nodeType", - "start": 5721, - "end": 5729, + "start": 6171, + "end": 6179, "loc": { "start": { - "line": 150, + "line": 169, "column": 16 }, "end": { - "line": 150, + "line": 169, "column": 24 } } @@ -61395,15 +63980,15 @@ "updateContext": null }, "value": "=", - "start": 5730, - "end": 5731, + "start": 6180, + "end": 6181, "loc": { "start": { - "line": 150, + "line": 169, "column": 25 }, "end": { - "line": 150, + "line": 169, "column": 26 } } @@ -61422,15 +64007,15 @@ "updateContext": null }, "value": "both", - "start": 5732, - "end": 5738, + "start": 6182, + "end": 6188, "loc": { "start": { - "line": 150, + "line": 169, "column": 27 }, "end": { - "line": 150, + "line": 169, "column": 33 } } @@ -61447,15 +64032,15 @@ "postfix": false, "binop": null }, - "start": 5738, - "end": 5739, + "start": 6188, + "end": 6189, "loc": { "start": { - "line": 150, + "line": 169, "column": 33 }, "end": { - "line": 150, + "line": 169, "column": 34 } } @@ -61472,15 +64057,15 @@ "postfix": false, "binop": null }, - "start": 5740, - "end": 5741, + "start": 6190, + "end": 6191, "loc": { "start": { - "line": 150, + "line": 169, "column": 35 }, "end": { - "line": 150, + "line": 169, "column": 36 } } @@ -61488,15 +64073,15 @@ { "type": "CommentLine", "value": " Return a list of all the node labels in this phylogeny.", - "start": 5746, - "end": 5804, + "start": 6196, + "end": 6254, "loc": { "start": { - "line": 151, + "line": 170, "column": 4 }, "end": { - "line": 151, + "line": 170, "column": 62 } } @@ -61504,15 +64089,15 @@ { "type": "CommentLine", "value": "", - "start": 5809, - "end": 5811, + "start": 6259, + "end": 6261, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 6 } } @@ -61520,15 +64105,15 @@ { "type": "CommentLine", "value": " nodeType can be one of:", - "start": 5816, - "end": 5842, + "start": 6266, + "end": 6292, "loc": { "start": { - "line": 153, + "line": 172, "column": 4 }, "end": { - "line": 153, + "line": 172, "column": 30 } } @@ -61536,15 +64121,15 @@ { "type": "CommentLine", "value": " - 'internal': Return node labels on internal nodes.", - "start": 5847, - "end": 5901, + "start": 6297, + "end": 6351, "loc": { "start": { - "line": 154, + "line": 173, "column": 4 }, "end": { - "line": 154, + "line": 173, "column": 58 } } @@ -61552,15 +64137,15 @@ { "type": "CommentLine", "value": " - 'terminal': Return node labels on terminal nodes.", - "start": 5906, - 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"line": 159, + "line": 178, "column": 9 } } @@ -61637,15 +64222,15 @@ "postfix": false, "binop": null }, - "start": 6117, - "end": 6118, + "start": 6567, + "end": 6568, "loc": { "start": { - "line": 159, + "line": 178, "column": 10 }, "end": { - "line": 159, + "line": 178, "column": 11 } } @@ -61663,15 +64248,15 @@ "binop": null }, "value": "graph", - "start": 6119, - "end": 6124, + "start": 6569, + "end": 6574, "loc": { "start": { - "line": 159, + "line": 178, "column": 12 }, "end": { - "line": 159, + "line": 178, "column": 17 } } @@ -61688,15 +64273,15 @@ "postfix": false, "binop": null }, - "start": 6125, - "end": 6126, + "start": 6575, + "end": 6576, "loc": { "start": { - "line": 159, + "line": 178, "column": 18 }, "end": { - "line": 159, + "line": 178, "column": 19 } } @@ -61715,15 +64300,15 @@ "updateContext": null }, "value": "=", - "start": 6127, - "end": 6128, + "start": 6577, + "end": 6578, "loc": { "start": { - "line": 159, + "line": 178, "column": 20 }, "end": { - "line": 159, + "line": 178, "column": 21 } } @@ -61741,15 +64326,15 @@ "binop": null }, "value": "newickJs", - "start": 6129, - "end": 6137, + "start": 6579, + "end": 6587, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 30 } } @@ -61767,15 +64352,15 @@ "binop": null, "updateContext": null }, - "start": 6137, - "end": 6138, + "start": 6587, + "end": 6588, "loc": { "start": { - "line": 159, + "line": 178, "column": 30 }, "end": { - "line": 159, + "line": 178, "column": 31 } } @@ -61793,15 +64378,15 @@ "binop": null }, "value": "parse", - "start": 6138, - "end": 6143, + "start": 6588, + "end": 6593, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 36 } } @@ -61818,15 +64403,15 @@ "postfix": false, "binop": null }, - "start": 6143, - "end": 6144, + "start": 6593, + "end": 6594, "loc": { "start": { - "line": 159, + "line": 178, "column": 36 }, "end": { - "line": 159, + "line": 178, "column": 37 } } @@ -61846,15 +64431,15 @@ "updateContext": null }, "value": "this", - "start": 6144, - "end": 6148, + "start": 6594, + "end": 6598, "loc": { "start": { - "line": 159, + "line": 178, "column": 37 }, "end": { - "line": 159, + "line": 178, "column": 41 } } @@ -61872,15 +64457,15 @@ "binop": null, "updateContext": null }, - "start": 6148, - "end": 6149, + "start": 6598, + "end": 6599, "loc": { "start": { - "line": 159, + "line": 178, "column": 41 }, "end": { - "line": 159, + "line": 178, "column": 42 } } @@ -61898,15 +64483,15 @@ "binop": null }, "value": "phylogeny", - "start": 6149, - "end": 6158, + "start": 6599, + "end": 6608, "loc": { "start": { - "line": 159, + "line": 178, "column": 42 }, "end": { - "line": 159, + "line": 178, "column": 51 } } @@ -61924,15 +64509,15 @@ "binop": null, "updateContext": null }, - "start": 6158, - "end": 6159, + "start": 6608, + "end": 6609, "loc": { "start": { - "line": 159, + "line": 178, "column": 51 }, "end": { - "line": 159, + "line": 178, "column": 52 } } @@ -61950,15 +64535,15 @@ "binop": null }, "value": "newick", - "start": 6159, - "end": 6165, + "start": 6609, + "end": 6615, "loc": { "start": { - "line": 159, + "line": 178, "column": 52 }, "end": { - "line": 159, + "line": 178, "column": 58 } } @@ -61977,15 +64562,15 @@ "updateContext": null }, "value": "||", - "start": 6166, - "end": 6168, + "start": 6616, + "end": 6618, "loc": { "start": { - "line": 159, + "line": 178, "column": 59 }, "end": { - "line": 159, + "line": 178, "column": 61 } } @@ -62004,15 +64589,15 @@ "updateContext": null }, "value": "()", - "start": 6169, - "end": 6173, + "start": 6619, + "end": 6623, "loc": { "start": { - "line": 159, + "line": 178, "column": 62 }, "end": { - "line": 159, + "line": 178, "column": 66 } } @@ -62029,15 +64614,15 @@ "postfix": false, "binop": null }, - "start": 6173, - "end": 6174, + "start": 6623, + "end": 6624, "loc": { "start": { - "line": 159, + "line": 178, "column": 66 }, "end": { - "line": 159, + "line": 178, "column": 67 } } @@ -62055,15 +64640,15 @@ "binop": null, "updateContext": null }, - "start": 6174, - "end": 6175, + "start": 6624, + "end": 6625, "loc": { "start": { - "line": 159, + "line": 178, "column": 67 }, "end": { - "line": 159, + "line": 178, "column": 68 } } @@ -62083,15 +64668,15 @@ "updateContext": null }, "value": "const", - "start": 6180, - "end": 6185, + "start": 6630, + "end": 6635, "loc": { "start": { - "line": 160, + "line": 179, "column": 4 }, "end": { - "line": 160, + "line": 179, "column": 9 } } @@ -62109,15 +64694,15 @@ "binop": null, "updateContext": null }, - "start": 6186, - "end": 6187, + "start": 6636, + "end": 6637, "loc": { "start": { - "line": 160, + "line": 179, "column": 10 }, "end": { - "line": 160, + "line": 179, "column": 11 } } @@ -62135,15 +64720,15 @@ "binop": null }, "value": "vertices", - "start": 6187, - "end": 6195, + "start": 6637, + "end": 6645, "loc": { "start": { - "line": 160, + "line": 179, "column": 11 }, "end": { - "line": 160, + "line": 179, "column": 19 } } @@ -62161,15 +64746,15 @@ "binop": null, "updateContext": null }, - "start": 6195, - "end": 6196, + "start": 6645, + "end": 6646, "loc": { "start": { - "line": 160, + "line": 179, "column": 19 }, "end": { - "line": 160, + "line": 179, "column": 20 } } @@ -62187,15 +64772,15 @@ "binop": null }, "value": "arcs", - "start": 6197, - "end": 6201, + "start": 6647, + "end": 6651, "loc": { "start": { - "line": 160, + "line": 179, "column": 21 }, "end": { - "line": 160, + "line": 179, "column": 25 } } @@ -62213,15 +64798,15 @@ "binop": null, "updateContext": null }, - "start": 6201, - "end": 6202, + "start": 6651, + "end": 6652, "loc": { "start": { - "line": 160, + "line": 179, "column": 25 }, "end": { - "line": 160, + "line": 179, "column": 26 } } @@ -62240,15 +64825,15 @@ "updateContext": null }, "value": "=", - "start": 6203, - "end": 6204, + "start": 6653, + "end": 6654, "loc": { "start": { - "line": 160, + "line": 179, "column": 27 }, "end": { - "line": 160, + "line": 179, "column": 28 } } @@ -62266,15 +64851,15 @@ "binop": null }, "value": "graph", - "start": 6205, - "end": 6210, + "start": 6655, + "end": 6660, "loc": { "start": { - "line": 160, + "line": 179, "column": 29 }, "end": { - "line": 160, + "line": 179, "column": 34 } } @@ -62292,15 +64877,15 @@ "binop": null, "updateContext": null }, - "start": 6210, - "end": 6211, + "start": 6660, + "end": 6661, "loc": { "start": { - "line": 160, + "line": 179, "column": 34 }, "end": { - "line": 160, + "line": 179, "column": 35 } } @@ -62320,15 +64905,15 @@ "updateContext": null }, "value": "if", - "start": 6217, - "end": 6219, + "start": 6667, + "end": 6669, "loc": { "start": { - "line": 162, + "line": 181, "column": 4 }, "end": { - "line": 162, + "line": 181, "column": 6 } } @@ -62345,15 +64930,15 @@ "postfix": false, "binop": null }, - "start": 6220, - "end": 6221, + "start": 6670, + "end": 6671, "loc": { "start": { - "line": 162, + "line": 181, "column": 7 }, "end": { - "line": 162, + "line": 181, "column": 8 } } @@ -62371,15 +64956,15 @@ "binop": null }, "value": "nodeType", - "start": 6221, - "end": 6229, + "start": 6671, + "end": 6679, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 16 } } @@ -62398,15 +64983,15 @@ "updateContext": null }, "value": "===", - "start": 6230, - "end": 6233, + "start": 6680, + "end": 6683, "loc": { "start": { - "line": 162, + "line": 181, "column": 17 }, "end": { - "line": 162, + "line": 181, "column": 20 } } @@ -62425,15 +65010,15 @@ "updateContext": null }, "value": "both", - "start": 6234, - "end": 6240, + "start": 6684, + "end": 6690, "loc": { "start": { - "line": 162, + "line": 181, "column": 21 }, "end": { - "line": 162, + "line": 181, "column": 27 } } @@ -62450,15 +65035,15 @@ "postfix": false, "binop": null }, - "start": 6240, - "end": 6241, + "start": 6690, + "end": 6691, "loc": { "start": { - "line": 162, + "line": 181, "column": 27 }, "end": { - "line": 162, + "line": 181, "column": 28 } } @@ -62475,15 +65060,15 @@ "postfix": false, "binop": null }, - "start": 6242, - "end": 6243, + "start": 6692, + "end": 6693, "loc": { "start": { - "line": 162, + "line": 181, "column": 29 }, "end": { - "line": 162, + "line": 181, "column": 30 } } @@ -62491,15 +65076,15 @@ { "type": "CommentLine", "value": " Return all node labels.", - "start": 6250, - "end": 6276, + "start": 6700, + "end": 6726, "loc": { "start": { - "line": 163, + "line": 182, "column": 6 }, "end": { - "line": 163, + "line": 182, "column": 32 } } @@ -62519,15 +65104,15 @@ "updateContext": null }, "value": "return", - "start": 6283, - "end": 6289, + "start": 6733, + "end": 6739, "loc": { "start": { - "line": 164, + "line": 183, "column": 6 }, "end": { - "line": 164, + "line": 183, "column": 12 } } @@ -62545,15 +65130,15 @@ "binop": null }, "value": "Array", - "start": 6290, - "end": 6295, + "start": 6740, + "end": 6745, "loc": { "start": { - "line": 164, + "line": 183, "column": 13 }, "end": { - "line": 164, + "line": 183, "column": 18 } } @@ -62571,15 +65156,15 @@ "binop": null, "updateContext": null }, - "start": 6295, - "end": 6296, + "start": 6745, + "end": 6746, "loc": { "start": { - "line": 164, + "line": 183, "column": 18 }, "end": { - "line": 164, + "line": 183, "column": 19 } } @@ -62597,15 +65182,15 @@ "binop": null }, "value": "from", - "start": 6296, - "end": 6300, + "start": 6746, + "end": 6750, "loc": { "start": { - "line": 164, + "line": 183, "column": 19 }, "end": { - "line": 164, + "line": 183, "column": 23 } } @@ -62622,15 +65207,15 @@ "postfix": false, "binop": null }, - "start": 6300, - "end": 6301, + "start": 6750, + "end": 6751, "loc": { "start": { - "line": 164, + "line": 183, "column": 23 }, "end": { - "line": 164, + "line": 183, "column": 24 } } @@ -62650,15 +65235,15 @@ "updateContext": null }, "value": "new", - "start": 6310, - "end": 6313, + "start": 6760, + "end": 6763, "loc": { "start": { - "line": 165, + "line": 184, "column": 8 }, "end": { - "line": 165, + "line": 184, "column": 11 } } @@ -62676,15 +65261,15 @@ "binop": null }, "value": "Set", - "start": 6314, - "end": 6317, + "start": 6764, + "end": 6767, "loc": { "start": { - "line": 165, + "line": 184, "column": 12 }, "end": { - "line": 165, + "line": 184, "column": 15 } } @@ -62701,15 +65286,15 @@ "postfix": false, "binop": null }, - "start": 6317, - "end": 6318, + "start": 6767, + "end": 6768, "loc": { "start": { - "line": 165, + "line": 184, "column": 15 }, "end": { - "line": 165, + "line": 184, "column": 16 } } @@ -62727,15 +65312,15 @@ "binop": null }, "value": "Array", - "start": 6329, - "end": 6334, + "start": 6779, + "end": 6784, "loc": { "start": { - "line": 166, + "line": 185, "column": 10 }, "end": { - "line": 166, + "line": 185, "column": 15 } } @@ -62753,15 +65338,15 @@ "binop": null, "updateContext": null }, - "start": 6334, - "end": 6335, + "start": 6784, + "end": 6785, "loc": { "start": { - "line": 166, + "line": 185, "column": 15 }, "end": { - "line": 166, + "line": 185, "column": 16 } } @@ -62779,15 +65364,15 @@ "binop": null }, "value": "from", - "start": 6335, - "end": 6339, + "start": 6785, + "end": 6789, "loc": { "start": { - "line": 166, + "line": 185, "column": 16 }, "end": { - "line": 166, + "line": 185, "column": 20 } } @@ -62804,15 +65389,15 @@ "postfix": false, "binop": null }, - "start": 6339, - "end": 6340, + "start": 6789, + "end": 6790, "loc": { "start": { - "line": 166, + "line": 185, "column": 20 }, "end": { - "line": 166, + "line": 185, "column": 21 } } @@ -62830,15 +65415,15 @@ "binop": null }, "value": "vertices", - "start": 6340, - "end": 6348, + "start": 6790, + "end": 6798, "loc": { "start": { - "line": 166, + "line": 185, "column": 21 }, "end": { - "line": 166, + "line": 185, "column": 29 } } @@ -62855,15 +65440,15 @@ "postfix": false, "binop": null }, - "start": 6348, - "end": 6349, + "start": 6798, + "end": 6799, "loc": { "start": { - "line": 166, + "line": 185, "column": 29 }, "end": { - "line": 166, + "line": 185, "column": 30 } } @@ -62881,15 +65466,15 @@ "binop": null, "updateContext": null }, - "start": 6362, - "end": 6363, + "start": 6812, + "end": 6813, "loc": { "start": { - "line": 167, + "line": 186, "column": 12 }, "end": { - "line": 167, + "line": 186, "column": 13 } } @@ -62907,15 +65492,15 @@ "binop": null }, "value": "map", - "start": 6363, - "end": 6366, + "start": 6813, + "end": 6816, "loc": { "start": { - "line": 167, + "line": 186, "column": 13 }, "end": { - "line": 167, + "line": 186, "column": 16 } } @@ -62932,15 +65517,15 @@ "postfix": false, "binop": null }, - "start": 6366, - "end": 6367, + "start": 6816, + "end": 6817, "loc": { "start": { - "line": 167, + "line": 186, "column": 16 }, "end": { - "line": 167, + "line": 186, "column": 17 } } @@ -62958,15 +65543,15 @@ "binop": null }, "value": "vertex", - "start": 6367, - "end": 6373, + "start": 6817, + "end": 6823, "loc": { "start": { - "line": 167, + "line": 186, "column": 17 }, "end": { - "line": 167, + "line": 186, "column": 23 } } @@ -62984,15 +65569,15 @@ "binop": null, "updateContext": null }, - "start": 6374, - "end": 6376, + "start": 6824, + "end": 6826, "loc": { "start": { - "line": 167, + "line": 186, "column": 24 }, "end": { - "line": 167, + "line": 186, "column": 26 } } @@ -63010,15 +65595,15 @@ "binop": null }, "value": "vertex", - "start": 6377, - "end": 6383, + "start": 6827, + "end": 6833, "loc": { "start": { - "line": 167, + "line": 186, "column": 27 }, "end": { - "line": 167, + "line": 186, "column": 33 } } @@ -63036,15 +65621,15 @@ "binop": null, "updateContext": null }, - "start": 6383, - "end": 6384, + "start": 6833, + "end": 6834, "loc": { "start": { - "line": 167, + "line": 186, "column": 33 }, "end": { - "line": 167, + "line": 186, "column": 34 } } @@ -63062,15 +65647,15 @@ "binop": null }, "value": "label", - "start": 6384, - "end": 6389, + "start": 6834, + "end": 6839, "loc": { "start": { - "line": 167, + "line": 186, "column": 34 }, "end": { - "line": 167, + "line": 186, "column": 39 } } @@ -63087,15 +65672,15 @@ "postfix": false, "binop": null }, - "start": 6389, - "end": 6390, + "start": 6839, + "end": 6840, "loc": { "start": { - "line": 167, + "line": 186, "column": 39 }, "end": { - "line": 167, + "line": 186, "column": 40 } } @@ -63113,15 +65698,15 @@ "binop": null, "updateContext": null }, - "start": 6403, - "end": 6404, + "start": 6853, + "end": 6854, "loc": { "start": { - "line": 168, + "line": 187, "column": 12 }, "end": { - "line": 168, + "line": 187, "column": 13 } } @@ -63139,15 +65724,15 @@ "binop": null }, "value": "filter", - "start": 6404, - "end": 6410, + "start": 6854, + "end": 6860, "loc": { "start": { - "line": 168, + "line": 187, "column": 13 }, "end": { - "line": 168, + "line": 187, "column": 19 } } @@ -63164,15 +65749,15 @@ "postfix": false, "binop": null }, - "start": 6410, - "end": 6411, + "start": 6860, + "end": 6861, "loc": { "start": { - "line": 168, + "line": 187, "column": 19 }, "end": { - "line": 168, + "line": 187, "column": 20 } } @@ -63190,15 +65775,15 @@ "binop": null }, "value": "label", - "start": 6411, - "end": 6416, + "start": 6861, + "end": 6866, "loc": { "start": { - "line": 168, + "line": 187, "column": 20 }, "end": { - "line": 168, + "line": 187, "column": 25 } } @@ -63216,15 +65801,15 @@ "binop": null, "updateContext": null }, - "start": 6417, - "end": 6419, + "start": 6867, + "end": 6869, "loc": { "start": { - "line": 168, + "line": 187, "column": 26 }, "end": { - "line": 168, + "line": 187, "column": 28 } } @@ -63242,15 +65827,15 @@ "binop": null }, "value": "label", - "start": 6420, - "end": 6425, + "start": 6870, + "end": 6875, "loc": { "start": { - "line": 168, + "line": 187, "column": 29 }, "end": { - "line": 168, + "line": 187, "column": 34 } } @@ -63269,15 +65854,15 @@ "updateContext": null }, "value": "!==", - "start": 6426, - "end": 6429, + "start": 6876, + "end": 6879, "loc": { "start": { - "line": 168, + "line": 187, "column": 35 }, "end": { - "line": 168, + "line": 187, "column": 38 } } @@ -63295,15 +65880,15 @@ "binop": null }, "value": "undefined", - "start": 6430, - "end": 6439, + "start": 6880, + "end": 6889, "loc": { "start": { - "line": 168, + "line": 187, "column": 39 }, "end": { - "line": 168, + "line": 187, "column": 48 } } @@ -63320,15 +65905,15 @@ "postfix": false, "binop": null }, - "start": 6439, - "end": 6440, + "start": 6889, + "end": 6890, "loc": { "start": { - "line": 168, + "line": 187, "column": 48 }, "end": { - "line": 168, + "line": 187, "column": 49 } } @@ -63345,15 +65930,15 @@ "postfix": false, "binop": null }, - "start": 6449, - "end": 6450, + "start": 6899, + "end": 6900, "loc": { "start": { - "line": 169, + "line": 188, "column": 8 }, "end": { - "line": 169, + "line": 188, "column": 9 } } @@ -63370,15 +65955,15 @@ "postfix": false, "binop": null }, - "start": 6457, - "end": 6458, + "start": 6907, + "end": 6908, "loc": { "start": { - "line": 170, + "line": 189, "column": 6 }, "end": { - "line": 170, + "line": 189, "column": 7 } } @@ -63396,15 +65981,15 @@ "binop": null, "updateContext": null }, - "start": 6458, - "end": 6459, + "start": 6908, + "end": 6909, "loc": { "start": { - "line": 170, + "line": 189, "column": 7 }, "end": { - "line": 170, + "line": 189, "column": 8 } } @@ -63421,15 +66006,15 @@ "postfix": false, "binop": null }, - "start": 6464, - "end": 6465, + "start": 6914, + "end": 6915, "loc": { "start": { - "line": 171, + "line": 190, "column": 4 }, "end": { - "line": 171, + "line": 190, "column": 5 } } @@ -63449,15 +66034,15 @@ "updateContext": null }, "value": "if", - "start": 6471, - "end": 6473, + "start": 6921, + "end": 6923, "loc": { "start": { - "line": 173, + "line": 192, "column": 4 }, "end": { - "line": 173, + "line": 192, "column": 6 } } @@ -63474,15 +66059,15 @@ "postfix": false, "binop": null }, - "start": 6474, - "end": 6475, + "start": 6924, + "end": 6925, "loc": { "start": { - "line": 173, + "line": 192, "column": 7 }, "end": { - "line": 173, + "line": 192, "column": 8 } } @@ -63500,15 +66085,15 @@ "binop": null }, "value": "nodeType", - "start": 6475, - "end": 6483, + "start": 6925, + "end": 6933, "loc": { "start": { - "line": 173, + "line": 192, "column": 8 }, "end": { - "line": 173, + "line": 192, "column": 16 } } @@ -63527,15 +66112,15 @@ "updateContext": null }, "value": "===", - "start": 6484, - "end": 6487, + "start": 6934, + "end": 6937, "loc": { "start": { - "line": 173, + "line": 192, "column": 17 }, "end": { - "line": 173, + "line": 192, "column": 20 } } @@ -63554,15 +66139,15 @@ "updateContext": null }, "value": "internal", - "start": 6488, - "end": 6498, + "start": 6938, + "end": 6948, "loc": { "start": { - "line": 173, + "line": 192, "column": 21 }, "end": { - "line": 173, + "line": 192, "column": 31 } } @@ -63579,15 +66164,15 @@ "postfix": false, "binop": null }, - "start": 6498, - "end": 6499, + "start": 6948, + "end": 6949, "loc": { "start": { - "line": 173, + "line": 192, "column": 31 }, "end": { - "line": 173, + "line": 192, "column": 32 } } @@ -63604,15 +66189,15 @@ "postfix": false, "binop": null }, - "start": 6500, - "end": 6501, + "start": 6950, + "end": 6951, "loc": { "start": { - "line": 173, + "line": 192, "column": 33 }, "end": { - "line": 173, + "line": 192, "column": 34 } } @@ -63620,15 +66205,15 @@ { "type": "CommentLine", "value": " Return the internal nodes (those with atleast one child).", - "start": 6508, - "end": 6568, + "start": 6958, + "end": 7018, "loc": { "start": { - "line": 174, + "line": 193, "column": 6 }, "end": { - "line": 174, + "line": 193, "column": 66 } } @@ -63648,15 +66233,15 @@ "updateContext": null }, "value": "return", - "start": 6575, - "end": 6581, + "start": 7025, + "end": 7031, "loc": { "start": { - "line": 175, + "line": 194, "column": 6 }, "end": { - "line": 175, + "line": 194, "column": 12 } } @@ -63674,15 +66259,15 @@ "binop": null }, "value": "Array", - "start": 6582, - "end": 6587, + "start": 7032, + "end": 7037, "loc": { "start": { - "line": 175, + "line": 194, "column": 13 }, "end": { - "line": 175, + "line": 194, "column": 18 } } @@ -63700,15 +66285,15 @@ "binop": null, "updateContext": null }, - "start": 6587, - "end": 6588, + "start": 7037, + "end": 7038, "loc": { "start": { - "line": 175, + "line": 194, "column": 18 }, "end": { - "line": 175, + "line": 194, "column": 19 } } @@ -63726,15 +66311,15 @@ "binop": null }, "value": "from", - "start": 6588, - "end": 6592, + "start": 7038, + "end": 7042, "loc": { "start": { - "line": 175, + "line": 194, "column": 19 }, "end": { - "line": 175, + "line": 194, "column": 23 } } @@ -63751,15 +66336,15 @@ "postfix": false, "binop": null }, - "start": 6592, - "end": 6593, + "start": 7042, + "end": 7043, "loc": { "start": { - "line": 175, + "line": 194, "column": 23 }, "end": { - "line": 175, + "line": 194, "column": 24 } } @@ -63779,15 +66364,15 @@ "updateContext": null }, "value": "new", - "start": 6593, - "end": 6596, + "start": 7043, + "end": 7046, "loc": { "start": { - "line": 175, + "line": 194, "column": 24 }, "end": { - "line": 175, + "line": 194, "column": 27 } } @@ -63805,15 +66390,15 @@ "binop": null }, "value": "Set", - "start": 6597, - "end": 6600, + "start": 7047, + "end": 7050, "loc": { "start": { - "line": 175, + "line": 194, "column": 28 }, "end": { - "line": 175, + "line": 194, "column": 31 } } @@ -63830,15 +66415,15 @@ "postfix": false, "binop": null }, - "start": 6600, - "end": 6601, + "start": 7050, + "end": 7051, "loc": { "start": { - "line": 175, + "line": 194, "column": 31 }, "end": { - "line": 175, + "line": 194, "column": 32 } } @@ -63856,15 +66441,15 @@ "binop": null }, "value": "Array", - "start": 6610, - "end": 6615, + "start": 7060, + "end": 7065, "loc": { "start": { - "line": 176, + "line": 195, "column": 8 }, "end": { - "line": 176, + "line": 195, "column": 13 } } @@ -63882,15 +66467,15 @@ "binop": null, "updateContext": null }, - "start": 6615, - "end": 6616, + "start": 7065, + "end": 7066, "loc": { "start": { - "line": 176, + "line": 195, "column": 13 }, "end": { - "line": 176, + "line": 195, "column": 14 } } @@ -63908,15 +66493,15 @@ "binop": null }, "value": "from", - "start": 6616, - "end": 6620, + "start": 7066, + "end": 7070, "loc": { "start": { - "line": 176, + "line": 195, "column": 14 }, "end": { - "line": 176, + "line": 195, "column": 18 } } @@ -63933,15 +66518,15 @@ "postfix": false, "binop": null }, - "start": 6620, - "end": 6621, + "start": 7070, + "end": 7071, "loc": { "start": { - "line": 176, + "line": 195, "column": 18 }, "end": { - "line": 176, + "line": 195, "column": 19 } } @@ -63959,15 +66544,15 @@ "binop": null }, "value": "arcs", - "start": 6621, - "end": 6625, + "start": 7071, + "end": 7075, "loc": { "start": { - "line": 176, + "line": 195, "column": 19 }, "end": { - "line": 176, + "line": 195, "column": 23 } } @@ -63984,15 +66569,15 @@ "postfix": false, "binop": null }, - "start": 6625, - "end": 6626, + "start": 7075, + "end": 7076, "loc": { "start": { - "line": 176, + "line": 195, "column": 23 }, "end": { - "line": 176, + "line": 195, "column": 24 } } @@ -64010,15 +66595,15 @@ "binop": null, "updateContext": null }, - "start": 6637, - "end": 6638, + "start": 7087, + "end": 7088, "loc": { "start": { - "line": 177, + "line": 196, "column": 10 }, "end": { - "line": 177, + "line": 196, "column": 11 } } @@ -64036,15 +66621,15 @@ "binop": null }, "value": "map", - "start": 6638, - "end": 6641, + "start": 7088, + "end": 7091, "loc": { "start": { - "line": 177, + "line": 196, "column": 11 }, "end": { - "line": 177, + "line": 196, "column": 14 } } @@ -64061,15 +66646,15 @@ "postfix": false, "binop": null }, - "start": 6641, - "end": 6642, + "start": 7091, + "end": 7092, "loc": { "start": { - "line": 177, + "line": 196, "column": 14 }, "end": { - "line": 177, + "line": 196, "column": 15 } } @@ -64087,15 +66672,15 @@ "binop": null }, "value": "arc", - "start": 6642, - "end": 6645, + "start": 7092, + "end": 7095, "loc": { "start": { - "line": 177, + "line": 196, "column": 15 }, "end": { - "line": 177, + "line": 196, "column": 18 } } @@ -64113,15 +66698,15 @@ "binop": null, "updateContext": null }, - "start": 6646, - "end": 6648, + "start": 7096, + "end": 7098, "loc": { "start": { - "line": 177, + "line": 196, "column": 19 }, "end": { - "line": 177, + "line": 196, "column": 21 } } @@ -64139,15 +66724,15 @@ "binop": null }, "value": "arc", - "start": 6649, - "end": 6652, + "start": 7099, + "end": 7102, "loc": { "start": { - "line": 177, + "line": 196, "column": 22 }, "end": { - "line": 177, + "line": 196, "column": 25 } } @@ -64165,15 +66750,15 @@ "binop": null, "updateContext": null }, - "start": 6652, - "end": 6653, + "start": 7102, + "end": 7103, "loc": { "start": { - "line": 177, + "line": 196, "column": 25 }, "end": { - "line": 177, + "line": 196, "column": 26 } } @@ -64192,15 +66777,15 @@ "updateContext": null }, "value": 0, - "start": 6653, - "end": 6654, + "start": 7103, + "end": 7104, "loc": { "start": { - "line": 177, + "line": 196, "column": 26 }, "end": { - "line": 177, + "line": 196, "column": 27 } } @@ -64218,15 +66803,15 @@ "binop": null, "updateContext": null }, - "start": 6654, - "end": 6655, + "start": 7104, + "end": 7105, "loc": { "start": { - "line": 177, + "line": 196, "column": 27 }, "end": { - "line": 177, + "line": 196, "column": 28 } } @@ -64244,15 +66829,15 @@ "binop": null, "updateContext": null }, - "start": 6655, - "end": 6656, + "start": 7105, + "end": 7106, "loc": { "start": { - "line": 177, + "line": 196, "column": 28 }, "end": { - "line": 177, + "line": 196, "column": 29 } } @@ -64270,15 +66855,15 @@ "binop": null }, "value": "label", - "start": 6656, - "end": 6661, + "start": 7106, + "end": 7111, "loc": { "start": { - "line": 177, + "line": 196, "column": 29 }, "end": { - "line": 177, + "line": 196, "column": 34 } } @@ -64295,15 +66880,15 @@ "postfix": false, "binop": null }, - "start": 6661, - "end": 6662, + "start": 7111, + "end": 7112, "loc": { "start": { - "line": 177, + "line": 196, "column": 34 }, "end": { - "line": 177, + "line": 196, "column": 35 } } @@ -64311,15 +66896,15 @@ { "type": "CommentLine", "value": " Retrieve the label of the parent vertex in this arc.", - "start": 6663, - "end": 6718, + "start": 7113, + "end": 7168, "loc": { "start": { - "line": 177, + "line": 196, "column": 36 }, "end": { - "line": 177, + "line": 196, "column": 91 } } @@ -64337,15 +66922,15 @@ "binop": null, "updateContext": null }, - "start": 6729, - "end": 6730, + "start": 7179, + "end": 7180, "loc": { "start": { - "line": 178, + "line": 197, "column": 10 }, "end": { - "line": 178, + "line": 197, "column": 11 } } @@ -64363,15 +66948,15 @@ "binop": null }, "value": "filter", - "start": 6730, - "end": 6736, + "start": 7180, + "end": 7186, "loc": { "start": { - "line": 178, + "line": 197, "column": 11 }, "end": { - "line": 178, + "line": 197, "column": 17 } } @@ -64388,15 +66973,15 @@ "postfix": false, "binop": null }, - "start": 6736, - "end": 6737, + "start": 7186, + "end": 7187, "loc": { "start": { - "line": 178, + "line": 197, "column": 17 }, "end": { - "line": 178, + "line": 197, "column": 18 } } @@ -64414,15 +66999,15 @@ "binop": null }, "value": "label", - "start": 6737, - "end": 6742, + "start": 7187, + "end": 7192, "loc": { "start": { - "line": 178, + "line": 197, "column": 18 }, "end": { - "line": 178, + "line": 197, "column": 23 } } @@ -64440,15 +67025,15 @@ "binop": null, "updateContext": null }, - "start": 6743, - "end": 6745, + "start": 7193, + "end": 7195, "loc": { "start": { - "line": 178, + "line": 197, "column": 24 }, "end": { - "line": 178, + "line": 197, "column": 26 } } @@ -64466,15 +67051,15 @@ "binop": null }, "value": "label", - "start": 6746, - "end": 6751, + "start": 7196, + "end": 7201, "loc": { "start": { - "line": 178, + "line": 197, "column": 27 }, "end": { - "line": 178, + "line": 197, "column": 32 } } @@ -64493,15 +67078,15 @@ "updateContext": null }, "value": "!==", - "start": 6752, - "end": 6755, + "start": 7202, + "end": 7205, "loc": { "start": { - "line": 178, + "line": 197, "column": 33 }, "end": { - "line": 178, + "line": 197, "column": 36 } } @@ -64519,15 +67104,15 @@ "binop": null }, "value": "undefined", - "start": 6756, - "end": 6765, + "start": 7206, + "end": 7215, "loc": { "start": { - "line": 178, + "line": 197, "column": 37 }, "end": { - "line": 178, + "line": 197, "column": 46 } } @@ -64544,15 +67129,15 @@ "postfix": false, "binop": null }, - "start": 6765, - "end": 6766, + "start": 7215, + "end": 7216, "loc": { "start": { - "line": 178, + "line": 197, "column": 46 }, "end": { - "line": 178, + "line": 197, "column": 47 } } @@ -64569,15 +67154,15 @@ "postfix": false, "binop": null }, - "start": 6773, - "end": 6774, + "start": 7223, + "end": 7224, "loc": { "start": { - "line": 179, + "line": 198, "column": 6 }, "end": { - "line": 179, + "line": 198, "column": 7 } } @@ -64594,15 +67179,15 @@ "postfix": false, "binop": null }, - "start": 6774, - "end": 6775, + "start": 7224, + "end": 7225, "loc": { "start": { - "line": 179, + "line": 198, "column": 7 }, "end": { - "line": 179, + "line": 198, "column": 8 } } @@ -64620,15 +67205,15 @@ "binop": null, "updateContext": null }, - "start": 6775, - "end": 6776, + "start": 7225, + "end": 7226, "loc": { "start": { - "line": 179, + "line": 198, "column": 8 }, "end": { - "line": 179, + "line": 198, "column": 9 } } @@ -64645,15 +67230,15 @@ "postfix": false, "binop": null }, - "start": 6781, - "end": 6782, + "start": 7231, + "end": 7232, "loc": { "start": { - "line": 180, + "line": 199, "column": 4 }, "end": { - "line": 180, + "line": 199, "column": 5 } } @@ -64673,15 +67258,15 @@ "updateContext": null }, "value": "if", - "start": 6788, - "end": 6790, + "start": 7238, + "end": 7240, "loc": { "start": { - "line": 182, + "line": 201, "column": 4 }, "end": { - "line": 182, + "line": 201, "column": 6 } } @@ -64698,15 +67283,15 @@ "postfix": false, "binop": null }, - "start": 6791, - "end": 6792, + "start": 7241, + "end": 7242, "loc": { "start": { - "line": 182, + "line": 201, "column": 7 }, "end": { - "line": 182, + "line": 201, "column": 8 } } @@ -64724,15 +67309,15 @@ "binop": null }, "value": "nodeType", - "start": 6792, - "end": 6800, + "start": 7242, + "end": 7250, "loc": { "start": { - "line": 182, + "line": 201, "column": 8 }, "end": { - "line": 182, + "line": 201, "column": 16 } } @@ -64751,15 +67336,15 @@ "updateContext": null }, "value": "===", - "start": 6801, - "end": 6804, + "start": 7251, + "end": 7254, "loc": { "start": { - "line": 182, + "line": 201, "column": 17 }, "end": { - "line": 182, + "line": 201, "column": 20 } } @@ -64778,15 +67363,15 @@ "updateContext": null }, "value": "terminal", - "start": 6805, - "end": 6815, + "start": 7255, + "end": 7265, "loc": { "start": { - "line": 182, + "line": 201, "column": 21 }, "end": { - "line": 182, + "line": 201, "column": 31 } } @@ -64803,15 +67388,15 @@ "postfix": false, "binop": null }, - "start": 6815, - "end": 6816, + "start": 7265, + "end": 7266, "loc": { "start": { - "line": 182, + "line": 201, "column": 31 }, "end": { - "line": 182, + "line": 201, "column": 32 } } @@ -64828,15 +67413,15 @@ "postfix": false, "binop": null }, - "start": 6817, - "end": 6818, + "start": 7267, + "end": 7268, "loc": { "start": { - "line": 182, + "line": 201, "column": 33 }, "end": { - "line": 182, + "line": 201, "column": 34 } } @@ -64844,15 +67429,15 @@ { "type": "CommentLine", "value": " Return the terminal nodes. This would require calculating the children", - "start": 6825, - "end": 6898, + "start": 7275, + "end": 7348, "loc": { "start": { - "line": 183, + "line": 202, "column": 6 }, "end": { - "line": 183, + "line": 202, "column": 79 } } @@ -64860,15 +67445,15 @@ { "type": "CommentLine", "value": " of every vertex in the graph and then identifying vertices without any", - "start": 6905, - "end": 6978, + "start": 7355, + "end": 7428, "loc": { "start": { - "line": 184, + "line": 203, "column": 6 }, "end": { - "line": 184, + "line": 203, "column": 79 } } @@ -64876,15 +67461,15 @@ { "type": "CommentLine", "value": " children.", - "start": 6985, - "end": 6997, + "start": 7435, + "end": 7447, "loc": { "start": { - "line": 185, + "line": 204, "column": 6 }, "end": { - "line": 185, + "line": 204, "column": 18 } } @@ -64892,15 +67477,15 @@ { "type": "CommentLine", "value": "", - "start": 7004, - "end": 7006, + "start": 7454, + "end": 7456, "loc": { "start": { - "line": 186, + "line": 205, "column": 6 }, "end": { - "line": 186, + "line": 205, "column": 8 } } @@ -64908,15 +67493,15 @@ { "type": "CommentLine", "value": " A quicker and dirtier way to do this is by removing internal labels", - "start": 7013, - "end": 7083, + "start": 7463, + "end": 7533, "loc": { "start": { - "line": 187, + "line": 206, "column": 6 }, "end": { - "line": 187, + "line": 206, "column": 76 } } @@ -64924,15 +67509,15 @@ { "type": "CommentLine", "value": " from the list of all node labels. This will report an incorrect result", - "start": 7090, - "end": 7163, + "start": 7540, + "end": 7613, "loc": { "start": { - "line": 188, + "line": 207, "column": 6 }, "end": { - "line": 188, + "line": 207, "column": 79 } } @@ -64940,15 +67525,15 @@ { "type": "CommentLine", "value": " if an internal node has the same label as a terminal node, but at that", - "start": 7170, - "end": 7243, + "start": 7620, + "end": 7693, "loc": { "start": { - "line": 189, + "line": 208, "column": 6 }, "end": { - "line": 189, + "line": 208, "column": 79 } } @@ -64956,15 +67541,15 @@ { "type": "CommentLine", "value": " point a lot of other assumptions are going to fail, too, so this is", - "start": 7250, - "end": 7320, + "start": 7700, + "end": 7770, "loc": { "start": { - "line": 190, + "line": 209, "column": 6 }, "end": { - "line": 190, + "line": 209, "column": 76 } } @@ -64972,15 +67557,15 @@ { "type": "CommentLine", "value": " probably good enough for now.", - "start": 7327, - "end": 7359, + "start": 7777, + "end": 7809, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 38 } } @@ -65000,15 +67585,15 @@ "updateContext": null }, "value": "const", - "start": 7366, - "end": 7371, + "start": 7816, + "end": 7821, "loc": { "start": { - "line": 192, + "line": 211, "column": 6 }, "end": { - "line": 192, + "line": 211, "column": 11 } } @@ -65026,15 +67611,15 @@ "binop": null }, "value": "allLabels", - "start": 7372, - "end": 7381, + "start": 7822, + "end": 7831, "loc": { "start": { - "line": 192, + "line": 211, "column": 12 }, "end": { - "line": 192, + "line": 211, "column": 21 } } @@ -65053,15 +67638,15 @@ "updateContext": null }, "value": "=", - "start": 7382, - "end": 7383, + "start": 7832, + "end": 7833, "loc": { "start": { - "line": 192, + "line": 211, "column": 22 }, "end": { - "line": 192, + "line": 211, "column": 23 } } @@ -65081,15 +67666,15 @@ "updateContext": null }, "value": "this", - "start": 7384, - "end": 7388, + "start": 7834, + "end": 7838, "loc": { "start": { - "line": 192, + "line": 211, "column": 24 }, "end": { - "line": 192, + "line": 211, "column": 28 } } @@ -65107,15 +67692,15 @@ "binop": null, "updateContext": null }, - "start": 7388, - "end": 7389, + "start": 7838, + "end": 7839, "loc": { "start": { - "line": 192, + "line": 211, "column": 28 }, "end": { - "line": 192, + "line": 211, "column": 29 } } @@ -65133,15 +67718,15 @@ "binop": null }, "value": "getNodeLabels", - "start": 7389, - "end": 7402, + "start": 7839, + "end": 7852, "loc": { "start": { - "line": 192, + "line": 211, "column": 29 }, "end": { - "line": 192, + "line": 211, "column": 42 } } @@ -65158,15 +67743,15 @@ "postfix": false, "binop": null }, - "start": 7402, - "end": 7403, + "start": 7852, + "end": 7853, "loc": { "start": { - "line": 192, + "line": 211, "column": 42 }, "end": { - "line": 192, + "line": 211, "column": 43 } } @@ -65185,15 +67770,15 @@ "updateContext": null }, "value": "both", - "start": 7403, - "end": 7409, + "start": 7853, + "end": 7859, "loc": { "start": { - "line": 192, + "line": 211, "column": 43 }, "end": { - "line": 192, + "line": 211, "column": 49 } } @@ -65210,15 +67795,15 @@ "postfix": false, "binop": null }, - "start": 7409, - "end": 7410, + "start": 7859, + "end": 7860, "loc": { "start": { - "line": 192, + "line": 211, "column": 49 }, "end": { - "line": 192, + "line": 211, "column": 50 } } @@ -65236,15 +67821,15 @@ "binop": null, "updateContext": null }, - "start": 7410, - "end": 7411, + "start": 7860, + "end": 7861, "loc": { "start": { - "line": 192, + "line": 211, "column": 50 }, "end": { - "line": 192, + "line": 211, "column": 51 } } @@ -65264,15 +67849,15 @@ "updateContext": null }, "value": "const", - "start": 7418, - "end": 7423, + "start": 7868, + "end": 7873, "loc": { "start": { - "line": 193, + "line": 212, "column": 6 }, "end": { - "line": 193, + "line": 212, "column": 11 } } @@ -65290,15 +67875,15 @@ "binop": null }, "value": "internalLabels", - "start": 7424, - "end": 7438, + "start": 7874, + "end": 7888, "loc": { "start": { - "line": 193, + "line": 212, "column": 12 }, "end": { - "line": 193, + "line": 212, "column": 26 } } @@ -65317,15 +67902,15 @@ "updateContext": null }, "value": "=", - "start": 7439, - "end": 7440, + "start": 7889, + "end": 7890, "loc": { "start": { - "line": 193, + "line": 212, "column": 27 }, "end": { - "line": 193, + "line": 212, "column": 28 } } @@ -65345,15 +67930,15 @@ "updateContext": null }, "value": "new", - "start": 7441, - "end": 7444, + "start": 7891, + "end": 7894, "loc": { "start": { - "line": 193, + "line": 212, "column": 29 }, "end": { - "line": 193, + "line": 212, "column": 32 } } @@ -65371,15 +67956,15 @@ "binop": null }, "value": "Set", - "start": 7445, - "end": 7448, + "start": 7895, + "end": 7898, "loc": { "start": { - "line": 193, + "line": 212, "column": 33 }, "end": { - "line": 193, + "line": 212, "column": 36 } } @@ -65396,15 +67981,15 @@ "postfix": false, "binop": null }, - "start": 7448, - "end": 7449, + "start": 7898, + "end": 7899, "loc": { "start": { - "line": 193, + "line": 212, "column": 36 }, "end": { - "line": 193, + "line": 212, "column": 37 } } @@ -65424,15 +68009,15 @@ "updateContext": null }, "value": "this", - "start": 7449, - "end": 7453, + "start": 7899, + "end": 7903, "loc": { "start": { - "line": 193, + "line": 212, "column": 37 }, "end": { - "line": 193, + "line": 212, "column": 41 } } @@ -65450,15 +68035,15 @@ "binop": null, "updateContext": null }, - "start": 7453, - "end": 7454, + "start": 7903, + "end": 7904, "loc": { "start": { - "line": 193, + "line": 212, "column": 41 }, "end": { - "line": 193, + "line": 212, "column": 42 } } @@ -65476,15 +68061,15 @@ "binop": null }, "value": "getNodeLabels", - "start": 7454, - "end": 7467, + "start": 7904, + "end": 7917, "loc": { "start": { - "line": 193, + "line": 212, "column": 42 }, "end": { - "line": 193, + "line": 212, "column": 55 } } @@ -65501,15 +68086,15 @@ "postfix": false, "binop": null }, - "start": 7467, - "end": 7468, + "start": 7917, + "end": 7918, "loc": { "start": { - "line": 193, + "line": 212, "column": 55 }, "end": { - "line": 193, + "line": 212, "column": 56 } } @@ -65528,15 +68113,15 @@ "updateContext": null }, "value": "internal", - "start": 7468, - "end": 7478, + "start": 7918, + "end": 7928, "loc": { "start": { - "line": 193, + "line": 212, "column": 56 }, "end": { - "line": 193, + "line": 212, "column": 66 } } @@ -65553,15 +68138,15 @@ "postfix": false, "binop": null }, - "start": 7478, - "end": 7479, + "start": 7928, + "end": 7929, "loc": { "start": { - "line": 193, + "line": 212, "column": 66 }, "end": { - "line": 193, + "line": 212, "column": 67 } } @@ -65578,15 +68163,15 @@ "postfix": false, "binop": null }, - "start": 7479, - "end": 7480, + "start": 7929, + "end": 7930, "loc": { "start": { - "line": 193, + "line": 212, "column": 67 }, "end": { - "line": 193, + "line": 212, "column": 68 } } @@ -65604,15 +68189,15 @@ "binop": null, "updateContext": null }, - "start": 7480, - "end": 7481, + "start": 7930, + "end": 7931, "loc": { "start": { - "line": 193, + "line": 212, "column": 68 }, "end": { - "line": 193, + "line": 212, "column": 69 } } @@ -65632,15 +68217,15 @@ "updateContext": null }, "value": "return", - "start": 7489, - "end": 7495, + "start": 7939, + "end": 7945, "loc": { "start": { - "line": 195, + "line": 214, "column": 6 }, "end": { - "line": 195, + "line": 214, "column": 12 } } @@ -65658,15 +68243,15 @@ "binop": null }, "value": "allLabels", - "start": 7496, - "end": 7505, + "start": 7946, + "end": 7955, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 22 } } @@ -65684,15 +68269,15 @@ "binop": null, "updateContext": null }, - "start": 7505, - "end": 7506, + "start": 7955, + "end": 7956, "loc": { "start": { - "line": 195, + "line": 214, "column": 22 }, "end": { - "line": 195, + "line": 214, "column": 23 } } @@ -65710,15 +68295,15 @@ "binop": null }, "value": "filter", - "start": 7506, - "end": 7512, + "start": 7956, + "end": 7962, "loc": { "start": { - "line": 195, + "line": 214, "column": 23 }, "end": { - "line": 195, + "line": 214, "column": 29 } } @@ -65735,15 +68320,15 @@ "postfix": false, "binop": null }, - "start": 7512, - "end": 7513, + "start": 7962, + "end": 7963, "loc": { "start": { - "line": 195, + "line": 214, "column": 29 }, "end": { - "line": 195, + "line": 214, "column": 30 } } @@ -65761,15 +68346,15 @@ "binop": null }, "value": "label", - "start": 7513, - "end": 7518, + "start": 7963, + "end": 7968, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 35 } } @@ -65787,15 +68372,15 @@ "binop": null, "updateContext": null }, - "start": 7519, - "end": 7521, + "start": 7969, + "end": 7971, "loc": { "start": { - "line": 195, + "line": 214, "column": 36 }, "end": { - "line": 195, + "line": 214, "column": 38 } } @@ -65814,15 +68399,15 @@ "updateContext": null }, "value": "!", - "start": 7522, - "end": 7523, + "start": 7972, + "end": 7973, "loc": { "start": { - "line": 195, + "line": 214, "column": 39 }, "end": { - "line": 195, + "line": 214, "column": 40 } } @@ -65840,15 +68425,15 @@ "binop": null }, "value": "internalLabels", - "start": 7523, - "end": 7537, + "start": 7973, + "end": 7987, "loc": { "start": { - "line": 195, + "line": 214, "column": 40 }, "end": { - "line": 195, + "line": 214, "column": 54 } } @@ -65866,15 +68451,15 @@ "binop": null, "updateContext": null }, - "start": 7537, - "end": 7538, + "start": 7987, + "end": 7988, "loc": { "start": { - "line": 195, + "line": 214, "column": 54 }, "end": { - "line": 195, + "line": 214, "column": 55 } } @@ -65892,15 +68477,15 @@ "binop": null }, "value": "has", - "start": 7538, - "end": 7541, + "start": 7988, + "end": 7991, "loc": { "start": { - "line": 195, + "line": 214, "column": 55 }, "end": { - "line": 195, + "line": 214, "column": 58 } } @@ -65917,15 +68502,15 @@ "postfix": false, "binop": null }, - "start": 7541, - "end": 7542, + "start": 7991, + "end": 7992, "loc": { "start": { - "line": 195, + "line": 214, "column": 58 }, "end": { - "line": 195, + "line": 214, "column": 59 } } @@ -65943,15 +68528,15 @@ "binop": null }, "value": "label", - "start": 7542, - "end": 7547, + "start": 7992, + "end": 7997, "loc": { "start": { - "line": 195, + "line": 214, "column": 59 }, "end": { - "line": 195, + "line": 214, "column": 64 } } @@ -65968,15 +68553,15 @@ "postfix": false, "binop": null }, - "start": 7547, - "end": 7548, + "start": 7997, + "end": 7998, "loc": { "start": { - "line": 195, + "line": 214, "column": 64 }, "end": { - "line": 195, + "line": 214, "column": 65 } } @@ -65993,15 +68578,15 @@ "postfix": false, "binop": null }, - "start": 7548, - "end": 7549, + "start": 7998, + "end": 7999, "loc": { "start": { - "line": 195, + "line": 214, "column": 65 }, "end": { - "line": 195, + "line": 214, "column": 66 } } @@ -66019,15 +68604,15 @@ "binop": null, "updateContext": null }, - "start": 7549, - "end": 7550, + "start": 7999, + "end": 8000, "loc": { "start": { - "line": 195, + "line": 214, "column": 66 }, "end": { - "line": 195, + "line": 214, "column": 67 } } @@ -66044,15 +68629,15 @@ "postfix": false, "binop": null }, - "start": 7555, - "end": 7556, + "start": 8005, + "end": 8006, "loc": { "start": { - "line": 196, + "line": 215, "column": 4 }, "end": { - "line": 196, + "line": 215, "column": 5 } } @@ -66072,15 +68657,15 @@ "updateContext": null }, "value": "throw", - "start": 7562, - "end": 7567, + "start": 8012, + "end": 8017, "loc": { "start": { - "line": 198, + "line": 217, "column": 4 }, "end": { - "line": 198, + "line": 217, "column": 9 } } @@ -66100,15 +68685,15 @@ "updateContext": null }, "value": "new", - "start": 7568, - "end": 7571, + "start": 8018, + "end": 8021, "loc": { "start": { - "line": 198, + "line": 217, "column": 10 }, "end": { - "line": 198, + "line": 217, "column": 13 } } @@ -66126,15 +68711,15 @@ "binop": null }, "value": "Error", - "start": 7572, - "end": 7577, + "start": 8022, + "end": 8027, "loc": { "start": { - "line": 198, + "line": 217, "column": 14 }, "end": { - "line": 198, + "line": 217, "column": 19 } } @@ -66151,15 +68736,15 @@ "postfix": false, "binop": null }, - "start": 7577, - "end": 7578, + "start": 8027, + "end": 8028, "loc": { "start": { - "line": 198, + "line": 217, "column": 19 }, "end": { - "line": 198, + "line": 217, "column": 20 } } @@ -66176,15 +68761,15 @@ "postfix": false, "binop": null }, - "start": 7578, - "end": 7579, + "start": 8028, + "end": 8029, "loc": { "start": { - "line": 198, + "line": 217, "column": 20 }, "end": { - "line": 198, + "line": 217, "column": 21 } } @@ -66203,15 +68788,15 @@ "updateContext": null }, "value": "Unknown nodeType: '", - "start": 7579, - "end": 7598, + "start": 8029, + "end": 8048, "loc": { "start": { - "line": 198, + "line": 217, "column": 21 }, "end": { - "line": 198, + "line": 217, "column": 40 } } @@ -66228,15 +68813,15 @@ "postfix": false, "binop": null }, - "start": 7598, - "end": 7600, + "start": 8048, + "end": 8050, "loc": { "start": { - "line": 198, + "line": 217, "column": 40 }, "end": { - "line": 198, + "line": 217, "column": 42 } } @@ -66254,15 +68839,15 @@ "binop": null }, "value": "nodeType", - "start": 7600, - "end": 7608, + "start": 8050, + "end": 8058, "loc": { "start": { - "line": 198, + "line": 217, "column": 42 }, "end": { - "line": 198, + "line": 217, "column": 50 } } @@ -66279,15 +68864,15 @@ "postfix": false, "binop": null }, - "start": 7608, - "end": 7609, + "start": 8058, + "end": 8059, "loc": { "start": { - "line": 198, + "line": 217, "column": 50 }, "end": { - "line": 198, + "line": 217, "column": 51 } } @@ -66306,15 +68891,15 @@ "updateContext": null }, "value": "'", - "start": 7609, - "end": 7610, + "start": 8059, + "end": 8060, "loc": { "start": { - "line": 198, + "line": 217, "column": 51 }, "end": { - "line": 198, + "line": 217, "column": 52 } } @@ -66331,15 +68916,15 @@ "postfix": false, "binop": null }, - "start": 7610, - "end": 7611, + "start": 8060, + "end": 8061, "loc": { "start": { - "line": 198, + "line": 217, "column": 52 }, "end": { - "line": 198, + "line": 217, "column": 53 } } @@ -66356,15 +68941,15 @@ "postfix": false, "binop": null }, - "start": 7611, - "end": 7612, + "start": 8061, + "end": 8062, "loc": { "start": { - "line": 198, + "line": 217, "column": 53 }, "end": { - "line": 198, + "line": 217, "column": 54 } } @@ -66382,15 +68967,15 @@ "binop": null, "updateContext": null }, - "start": 7612, - "end": 7613, + "start": 8062, + "end": 8063, "loc": { "start": { - "line": 198, + "line": 217, "column": 54 }, "end": { - "line": 198, + "line": 217, "column": 55 } } @@ -66407,15 +68992,15 @@ "postfix": false, "binop": null }, - "start": 7616, - "end": 7617, + "start": 8066, + "end": 8067, "loc": { "start": { - "line": 199, + "line": 218, "column": 2 }, "end": { - "line": 199, + "line": 218, "column": 3 } } @@ -66423,15 +69008,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n ", - "start": 7621, - "end": 7998, + "start": 8071, + "end": 8448, "loc": { "start": { - "line": 201, + "line": 220, "column": 2 }, "end": { - "line": 208, + "line": 227, "column": 5 } } @@ -66449,15 +69034,15 @@ "binop": null }, "value": "getTaxonomicUnitsForNodeLabel", - "start": 8001, - "end": 8030, + "start": 8451, + "end": 8480, "loc": { "start": { - "line": 209, + "line": 228, "column": 2 }, "end": { - "line": 209, + "line": 228, "column": 31 } } @@ -66474,15 +69059,15 @@ "postfix": false, "binop": null }, - "start": 8030, - "end": 8031, + "start": 8480, + "end": 8481, "loc": { "start": { - "line": 209, + "line": 228, "column": 31 }, "end": { - "line": 209, + "line": 228, "column": 32 } } @@ -66500,15 +69085,15 @@ "binop": null }, "value": "nodeLabel", - "start": 8031, - "end": 8040, + "start": 8481, + "end": 8490, "loc": { "start": { - "line": 209, + "line": 228, "column": 32 }, "end": { - "line": 209, + "line": 228, "column": 41 } } @@ -66525,15 +69110,15 @@ "postfix": false, "binop": null }, - "start": 8040, - "end": 8041, + "start": 8490, + "end": 8491, "loc": { "start": { - "line": 209, + "line": 228, "column": 41 }, "end": { - "line": 209, + "line": 228, "column": 42 } } @@ -66550,15 +69135,15 @@ "postfix": false, "binop": null }, - "start": 8042, - "end": 8043, + "start": 8492, + "end": 8493, "loc": { "start": { - "line": 209, + "line": 228, "column": 43 }, "end": { - "line": 209, + "line": 228, "column": 44 } } @@ -66566,15 +69151,15 @@ { "type": "CommentLine", "value": " Look up additional node properties.", - "start": 8048, - "end": 8086, + "start": 8498, + "end": 8536, "loc": { "start": { - "line": 210, + "line": 229, "column": 4 }, "end": { - "line": 210, + "line": 229, "column": 42 } } @@ -66594,15 +69179,15 @@ "updateContext": null }, "value": "let", - "start": 8091, - "end": 8094, + "start": 8541, + "end": 8544, "loc": { "start": { - "line": 211, + "line": 230, "column": 4 }, "end": { - "line": 211, + "line": 230, "column": 7 } } @@ -66620,15 +69205,15 @@ "binop": null }, "value": "additionalNodeProperties", - "start": 8095, - "end": 8119, + "start": 8545, + "end": 8569, "loc": { "start": { - "line": 211, + "line": 230, "column": 8 }, "end": { - "line": 211, + "line": 230, "column": 32 } } @@ -66647,15 +69232,15 @@ "updateContext": null }, "value": "=", - "start": 8120, - "end": 8121, + "start": 8570, + "end": 8571, "loc": { "start": { - "line": 211, + "line": 230, "column": 33 }, "end": { - "line": 211, + "line": 230, "column": 34 } } @@ -66672,15 +69257,15 @@ "postfix": false, "binop": null }, - "start": 8122, - "end": 8123, + "start": 8572, + "end": 8573, "loc": { "start": { - "line": 211, + "line": 230, "column": 35 }, "end": { - "line": 211, + "line": 230, "column": 36 } } @@ -66697,15 +69282,15 @@ "postfix": false, "binop": null }, - "start": 8123, - "end": 8124, + "start": 8573, + "end": 8574, "loc": { "start": { - "line": 211, + "line": 230, "column": 36 }, "end": { - 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"start": 8144, - "end": 8145, + "start": 8594, + "end": 8595, "loc": { "start": { - "line": 213, + "line": 232, "column": 9 }, "end": { - "line": 213, + "line": 232, "column": 10 } } @@ -66855,15 +69440,15 @@ "updateContext": null }, "value": "this", - "start": 8145, - "end": 8149, + "start": 8595, + "end": 8599, "loc": { "start": { - "line": 213, + "line": 232, "column": 10 }, "end": { - "line": 213, + "line": 232, "column": 14 } } @@ -66881,15 +69466,15 @@ "binop": null, "updateContext": null }, - "start": 8149, - "end": 8150, + "start": 8599, + "end": 8600, "loc": { "start": { - "line": 213, + "line": 232, "column": 14 }, "end": { - "line": 213, + "line": 232, "column": 15 } } @@ -66907,15 +69492,15 @@ "binop": null }, "value": "phylogeny", - "start": 8150, - "end": 8159, + "start": 8600, + "end": 8609, "loc": { "start": { - "line": 213, + "line": 232, "column": 15 }, "end": { - "line": 213, + "line": 232, "column": 24 } } @@ -66933,15 +69518,15 @@ "binop": null, "updateContext": null }, - 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"line": 232, + "line": 251, "column": 7 }, "end": { - "line": 232, + "line": 251, "column": 8 } } @@ -68727,15 +71312,15 @@ "binop": null }, "value": "tunit", - "start": 9078, - "end": 9083, + "start": 9528, + "end": 9533, "loc": { "start": { - "line": 232, + "line": 251, "column": 8 }, "end": { - "line": 232, + "line": 251, "column": 13 } } @@ -68752,15 +71337,15 @@ "postfix": false, "binop": null }, - "start": 9083, - "end": 9084, + "start": 9533, + "end": 9534, "loc": { "start": { - "line": 232, + "line": 251, "column": 13 }, "end": { - "line": 232, + "line": 251, "column": 14 } } @@ -68780,15 +71365,15 @@ "updateContext": null }, "value": "return", - "start": 9085, - "end": 9091, + "start": 9535, + "end": 9541, "loc": { "start": { - "line": 232, + "line": 251, "column": 15 }, "end": { - "line": 232, + "line": 251, "column": 21 } } @@ -68806,15 +71391,15 @@ "binop": null, "updateContext": null }, - "start": 9092, - "end": 9093, + "start": 9542, + "end": 9543, "loc": { "start": { - "line": 232, + "line": 251, "column": 22 }, "end": { - "line": 232, + "line": 251, "column": 23 } } @@ -68832,15 +71417,15 @@ "binop": null }, "value": "tunit", - "start": 9093, - "end": 9098, + "start": 9543, + "end": 9548, "loc": { "start": { - "line": 232, + "line": 251, "column": 23 }, "end": { - "line": 232, + "line": 251, "column": 28 } } @@ -68858,15 +71443,15 @@ "binop": null, "updateContext": null }, - "start": 9098, - "end": 9099, + "start": 9548, + "end": 9549, "loc": { "start": { - "line": 232, + "line": 251, "column": 28 }, "end": { - "line": 232, + "line": 251, "column": 29 } } @@ -68884,15 +71469,15 @@ "binop": null, "updateContext": null }, - "start": 9099, - "end": 9100, + "start": 9549, + "end": 9550, "loc": { "start": { - "line": 232, + "line": 251, "column": 29 }, "end": { - "line": 232, + "line": 251, "column": 30 } } @@ -68912,15 +71497,15 @@ "updateContext": null }, "value": "return", - "start": 9105, - "end": 9111, + "start": 9555, + "end": 9561, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 10 } } @@ -68938,15 +71523,15 @@ "binop": null, "updateContext": null }, - "start": 9112, - "end": 9113, + "start": 9562, + "end": 9563, "loc": { "start": { - "line": 233, + "line": 252, "column": 11 }, "end": { - "line": 233, + "line": 252, "column": 12 } } @@ -68964,15 +71549,15 @@ "binop": null, "updateContext": null }, - "start": 9113, - "end": 9114, + "start": 9563, + "end": 9564, "loc": { "start": { - "line": 233, + "line": 252, "column": 12 }, "end": { - "line": 233, + "line": 252, "column": 13 } } @@ -68990,15 +71575,15 @@ "binop": null, "updateContext": null }, - "start": 9114, - "end": 9115, + "start": 9564, + "end": 9565, "loc": { "start": { - "line": 233, + "line": 252, "column": 13 }, "end": { - "line": 233, + "line": 252, "column": 14 } } @@ -69006,15 +71591,15 @@ { "type": "CommentLine", "value": " No TUnit? Return the empty list.", - "start": 9116, - "end": 9151, + "start": 9566, + "end": 9601, "loc": { "start": { - "line": 233, + "line": 252, "column": 15 }, "end": { - "line": 233, + "line": 252, "column": 50 } } @@ -69031,15 +71616,15 @@ "postfix": false, "binop": null }, - "start": 9154, - "end": 9155, + "start": 9604, + "end": 9605, "loc": { "start": { - "line": 234, + "line": 253, "column": 2 }, "end": { - "line": 234, + "line": 253, "column": 3 } } @@ -69057,15 +71642,15 @@ "binop": null }, "value": "getNodeLabelsMatchedBySpecifier", - "start": 9159, - "end": 9190, + "start": 9609, + "end": 9640, "loc": { "start": { - "line": 236, + "line": 255, "column": 2 }, "end": { - "line": 236, + "line": 255, "column": 33 } } @@ -69082,15 +71667,15 @@ "postfix": false, "binop": null }, - "start": 9190, - "end": 9191, + "start": 9640, + "end": 9641, "loc": { "start": { - "line": 236, + "line": 255, "column": 33 }, "end": { - "line": 236, + "line": 255, "column": 34 } } @@ -69108,15 +71693,15 @@ "binop": null }, "value": "specifier", - "start": 9191, - "end": 9200, + "start": 9641, + "end": 9650, "loc": { "start": { - "line": 236, + "line": 255, "column": 34 }, "end": { - "line": 236, + "line": 255, "column": 43 } } @@ -69133,15 +71718,15 @@ "postfix": false, "binop": null }, - "start": 9200, - "end": 9201, + "start": 9650, + "end": 9651, "loc": { "start": { - "line": 236, + "line": 255, "column": 43 }, "end": { - "line": 236, + "line": 255, "column": 44 } } @@ -69158,15 +71743,15 @@ "postfix": false, "binop": null }, - "start": 9202, - "end": 9203, + "start": 9652, + "end": 9653, "loc": { "start": { - "line": 236, + "line": 255, "column": 45 }, "end": { - "line": 236, + "line": 255, "column": 46 } } @@ -69174,15 +71759,15 @@ { "type": "CommentLine", "value": " Return a list of node labels matched by a given specifier on", - "start": 9208, - "end": 9271, + "start": 9658, + "end": 9721, "loc": { "start": { - "line": 237, + "line": 256, "column": 4 }, "end": { - "line": 237, + "line": 256, "column": 67 } } @@ -69190,15 +71775,15 @@ { "type": "CommentLine", "value": " a given phylogeny.", - "start": 9276, - "end": 9297, + "start": 9726, + "end": 9747, "loc": { "start": { - "line": 238, + "line": 257, "column": 4 }, "end": { - "line": 238, + "line": 257, "column": 25 } } @@ -69218,15 +71803,15 @@ "updateContext": null }, "value": "return", - "start": 9303, - "end": 9309, + "start": 9753, + "end": 9759, "loc": { "start": { - "line": 240, + "line": 259, "column": 4 }, "end": { - "line": 240, + "line": 259, "column": 10 } } @@ -69246,15 +71831,15 @@ "updateContext": null }, "value": "this", - "start": 9310, - "end": 9314, + "start": 9760, + "end": 9764, "loc": { "start": { - "line": 240, + "line": 259, "column": 11 }, "end": { - "line": 240, + "line": 259, "column": 15 } } @@ -69272,15 +71857,15 @@ "binop": null, "updateContext": null }, - "start": 9314, - "end": 9315, + "start": 9764, + "end": 9765, "loc": { "start": { - "line": 240, + "line": 259, "column": 15 }, "end": { - "line": 240, + "line": 259, "column": 16 } } @@ -69298,15 +71883,15 @@ "binop": null }, "value": "getNodeLabels", - 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"end": 9337, + "start": 9781, + "end": 9787, "loc": { "start": { - "line": 240, + "line": 259, "column": 32 }, "end": { - "line": 240, + "line": 259, "column": 38 } } @@ -69425,15 +72010,15 @@ "postfix": false, "binop": null }, - "start": 9337, - "end": 9338, + "start": 9787, + "end": 9788, "loc": { "start": { - "line": 240, + "line": 259, "column": 38 }, "end": { - "line": 240, + "line": 259, "column": 39 } } @@ -69450,15 +72035,15 @@ "postfix": false, "binop": null }, - "start": 9338, - "end": 9339, + "start": 9788, + "end": 9789, "loc": { "start": { - "line": 240, + "line": 259, "column": 39 }, "end": { - "line": 240, + "line": 259, "column": 40 } } @@ -69476,15 +72061,15 @@ "binop": null }, "value": "nodeLabel", - "start": 9339, - "end": 9348, + "start": 9789, + "end": 9798, "loc": { "start": { - "line": 240, + "line": 259, "column": 40 }, "end": { - "line": 240, + "line": 259, "column": 49 } } @@ -69501,15 +72086,15 @@ "postfix": false, "binop": null }, - "start": 9348, - "end": 9349, + "start": 9798, + "end": 9799, "loc": { "start": { - "line": 240, + "line": 259, "column": 49 }, "end": { - "line": 240, + "line": 259, "column": 50 } } @@ -69527,15 +72112,15 @@ "binop": null, "updateContext": null }, - "start": 9350, - "end": 9352, + "start": 9800, + "end": 9802, "loc": { "start": { - "line": 240, + "line": 259, "column": 51 }, "end": { - "line": 240, + "line": 259, "column": 53 } } @@ -69552,15 +72137,15 @@ "postfix": false, "binop": null }, - "start": 9353, - "end": 9354, + "start": 9803, + "end": 9804, "loc": { "start": { - "line": 240, + "line": 259, "column": 54 }, "end": { - "line": 240, + "line": 259, "column": 55 } } @@ -69568,15 +72153,15 @@ { "type": "CommentLine", "value": " Find all the taxonomic units associated with the specifier and", - "start": 9361, - "end": 9426, + "start": 9811, + "end": 9876, "loc": { "start": { - "line": 241, + "line": 260, "column": 6 }, "end": { - "line": 241, + "line": 260, "column": 71 } } @@ -69584,15 +72169,15 @@ { "type": "CommentLine", "value": " with the node.", - "start": 9433, - "end": 9450, + "start": 9883, + "end": 9900, "loc": { "start": { - "line": 242, + "line": 261, "column": 6 }, "end": { - "line": 242, + "line": 261, "column": 23 } } @@ -69612,15 +72197,15 @@ "updateContext": null }, "value": "const", - "start": 9457, - "end": 9462, + "start": 9907, + "end": 9912, "loc": { "start": { - "line": 243, + "line": 262, "column": 6 }, "end": { - "line": 243, + "line": 262, "column": 11 } } @@ -69638,15 +72223,15 @@ "binop": null }, "value": "nodeTUnits", - "start": 9463, - "end": 9473, + "start": 9913, + "end": 9923, "loc": { "start": { - "line": 243, + "line": 262, "column": 12 }, "end": { - "line": 243, + "line": 262, "column": 22 } } @@ -69665,15 +72250,15 @@ "updateContext": null }, "value": "=", - "start": 9474, - "end": 9475, + "start": 9924, + "end": 9925, "loc": { "start": { - "line": 243, + "line": 262, "column": 23 }, "end": { - "line": 243, + "line": 262, "column": 24 } } @@ -69693,15 +72278,15 @@ "updateContext": null }, "value": "this", - "start": 9476, - 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"start": 9511, - "end": 9520, + "start": 9961, + "end": 9970, "loc": { "start": { - "line": 243, + "line": 262, "column": 60 }, "end": { - "line": 243, + "line": 262, "column": 69 } } @@ -69821,15 +72406,15 @@ "postfix": false, "binop": null }, - "start": 9520, - "end": 9521, + "start": 9970, + "end": 9971, "loc": { "start": { - "line": 243, + "line": 262, "column": 69 }, "end": { - "line": 243, + "line": 262, "column": 70 } } @@ -69847,15 +72432,15 @@ "binop": null, "updateContext": null }, - "start": 9521, - "end": 9522, + "start": 9971, + "end": 9972, "loc": { "start": { - "line": 243, + "line": 262, "column": 70 }, "end": { - "line": 243, + "line": 262, "column": 71 } } @@ -69863,15 +72448,15 @@ { "type": "CommentLine", "value": " Attempt pairwise matches between taxonomic units in the specifier", - "start": 9530, - "end": 9598, + "start": 9980, + "end": 10048, "loc": { "start": { - "line": 245, + "line": 264, "column": 6 }, "end": { - "line": 245, + "line": 264, "column": 74 } } @@ -69879,15 +72464,15 @@ { "type": "CommentLine", "value": " and associated with the node.", - "start": 9605, - "end": 9637, + "start": 10055, + "end": 10087, "loc": { "start": { - "line": 246, + "line": 265, "column": 6 }, "end": { - "line": 246, + "line": 265, "column": 38 } } @@ -69907,15 +72492,15 @@ "updateContext": null }, "value": "return", - "start": 9644, - "end": 9650, + "start": 10094, + "end": 10100, "loc": { "start": { - "line": 247, + "line": 266, "column": 6 }, "end": { - "line": 247, + "line": 266, "column": 12 } } @@ -69933,15 +72518,15 @@ "binop": null }, "value": "nodeTUnits", - "start": 9651, - "end": 9661, + "start": 10101, + "end": 10111, "loc": { "start": { - "line": 247, + "line": 266, "column": 13 }, "end": { - "line": 247, + "line": 266, "column": 23 } } @@ -69959,15 +72544,15 @@ "binop": null, "updateContext": null }, - "start": 9661, - "end": 9662, + "start": 10111, + "end": 10112, "loc": { "start": { - "line": 247, + "line": 266, "column": 23 }, "end": { - "line": 247, + "line": 266, "column": 24 } } @@ -69985,15 +72570,15 @@ "binop": null }, "value": "some", - "start": 9662, - "end": 9666, + "start": 10112, + "end": 10116, "loc": { "start": { - "line": 247, + "line": 266, "column": 24 }, "end": { - "line": 247, + "line": 266, "column": 28 } } @@ -70010,15 +72595,15 @@ "postfix": false, "binop": null }, - "start": 9666, - "end": 9667, + "start": 10116, + "end": 10117, "loc": { "start": { - "line": 247, + "line": 266, "column": 28 }, "end": { - "line": 247, + "line": 266, "column": 29 } } @@ -70036,15 +72621,15 @@ "binop": null }, "value": "tunit", - "start": 9676, - "end": 9681, + "start": 10126, + "end": 10131, "loc": { "start": { - "line": 248, + "line": 267, "column": 8 }, "end": { - "line": 248, + "line": 267, "column": 13 } } @@ -70062,15 +72647,15 @@ "binop": null, "updateContext": null }, - "start": 9682, - "end": 9684, + "start": 10132, + "end": 10134, "loc": { "start": { - "line": 248, + "line": 267, "column": 14 }, "end": { - "line": 248, + "line": 267, "column": 16 } } @@ -70090,15 +72675,15 @@ "updateContext": null }, "value": "new", - "start": 9685, - "end": 9688, + "start": 10135, + "end": 10138, "loc": { "start": { - "line": 248, + "line": 267, "column": 17 }, "end": { - "line": 248, + "line": 267, "column": 20 } } @@ -70116,15 +72701,15 @@ "binop": null }, "value": "TaxonomicUnitMatcher", - "start": 9689, - "end": 9709, + "start": 10139, + "end": 10159, "loc": { "start": { - "line": 248, + "line": 267, "column": 21 }, "end": { - "line": 248, + "line": 267, "column": 41 } } @@ -70141,15 +72726,15 @@ "postfix": false, "binop": null }, - "start": 9709, - "end": 9710, + "start": 10159, + "end": 10160, "loc": { "start": { - "line": 248, + "line": 267, "column": 41 }, "end": { - "line": 248, + "line": 267, "column": 42 } } @@ -70167,15 +72752,15 @@ "binop": null }, "value": "specifier", - "start": 9710, - "end": 9719, + "start": 10160, + "end": 10169, "loc": { "start": { - "line": 248, + "line": 267, "column": 42 }, "end": { - "line": 248, + "line": 267, "column": 51 } } @@ -70193,15 +72778,15 @@ "binop": null, "updateContext": null }, - "start": 9719, - "end": 9720, + "start": 10169, + "end": 10170, "loc": { "start": { - "line": 248, + "line": 267, "column": 51 }, "end": { - "line": 248, + "line": 267, "column": 52 } } @@ -70219,15 +72804,15 @@ "binop": null }, "value": "tunit", - "start": 9721, - "end": 9726, + "start": 10171, + "end": 10176, "loc": { "start": { - "line": 248, + "line": 267, "column": 53 }, "end": { - "line": 248, + "line": 267, "column": 58 } } @@ -70244,15 +72829,15 @@ "postfix": false, "binop": null }, - "start": 9726, - "end": 9727, + "start": 10176, + "end": 10177, "loc": { "start": { - "line": 248, + "line": 267, "column": 58 }, "end": { - "line": 248, + "line": 267, "column": 59 } } @@ -70270,15 +72855,15 @@ "binop": null, "updateContext": null }, - "start": 9727, - "end": 9728, + "start": 10177, + "end": 10178, "loc": { "start": { - "line": 248, + "line": 267, "column": 59 }, "end": { - "line": 248, + "line": 267, "column": 60 } } @@ -70296,15 +72881,15 @@ "binop": null }, "value": "matched", - 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The static method PhylogenyWrapper.getParsedNewick() is", - "start": 11433, - "end": 11509, + "start": 11883, + "end": 11959, "loc": { "start": { - "line": 290, + "line": 309, "column": 4 }, "end": { - "line": 290, + "line": 309, "column": 80 } } @@ -75494,15 +78079,15 @@ { "type": "CommentLine", "value": " used if none is provided.", - "start": 11514, - "end": 11544, + "start": 11964, + "end": 11994, "loc": { "start": { - "line": 291, + "line": 310, "column": 4 }, "end": { - "line": 291, + "line": 310, "column": 34 } } @@ -75522,15 +78107,15 @@ "updateContext": null }, "value": "const", - "start": 11550, - "end": 11555, + "start": 12000, + "end": 12005, "loc": { "start": { - "line": 293, + "line": 312, "column": 4 }, "end": { - "line": 293, + "line": 312, "column": 9 } } @@ -75548,15 +78133,15 @@ "binop": null }, "value": "parsed", - "start": 11556, - "end": 11562, + "start": 12006, + "end": 12012, "loc": { "start": { - "line": 293, + "line": 312, "column": 10 }, "end": { - "line": 293, + "line": 312, "column": 16 } } @@ -75575,15 +78160,15 @@ "updateContext": null }, "value": "=", - 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"start": 11695, - "end": 11696, + "start": 12145, + "end": 12146, "loc": { "start": { - "line": 295, + "line": 314, "column": 54 }, "end": { - "line": 295, + "line": 314, "column": 55 } } @@ -76431,15 +79016,15 @@ "binop": null }, "value": "nodeCount", - "start": 11697, - "end": 11706, + "start": 12147, + "end": 12156, "loc": { "start": { - "line": 295, + "line": 314, "column": 56 }, "end": { - "line": 295, + "line": 314, "column": 65 } } @@ -76456,15 +79041,15 @@ "postfix": false, "binop": null }, - "start": 11706, - "end": 11707, + "start": 12156, + "end": 12157, "loc": { "start": { - "line": 295, + "line": 314, "column": 65 }, "end": { - "line": 295, + "line": 314, "column": 66 } } @@ -76482,15 +79067,15 @@ "binop": null, "updateContext": null }, - "start": 11708, - "end": 11710, + "start": 12158, + "end": 12160, "loc": { "start": { - "line": 295, + "line": 314, "column": 67 }, "end": { - "line": 295, + "line": 314, "column": 69 } } @@ -76507,15 +79092,15 @@ "postfix": false, "binop": null }, - 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"start": 11868, - "end": 11873, + "start": 12318, + "end": 12323, "loc": { "start": { - "line": 300, + "line": 319, "column": 35 }, "end": { - "line": 300, + "line": 319, "column": 40 } } @@ -76933,15 +79518,15 @@ "postfix": false, "binop": null }, - "start": 11873, - "end": 11875, + "start": 12323, + "end": 12325, "loc": { "start": { - "line": 300, + "line": 319, "column": 40 }, "end": { - "line": 300, + "line": 319, "column": 42 } } @@ -76959,15 +79544,15 @@ "binop": null }, "value": "nodeCount", - "start": 11875, - "end": 11884, + "start": 12325, + "end": 12334, "loc": { "start": { - "line": 300, + "line": 319, "column": 42 }, "end": { - "line": 300, + "line": 319, "column": 51 } } @@ -76984,15 +79569,15 @@ "postfix": false, "binop": null }, - "start": 11884, - "end": 11885, + "start": 12334, + "end": 12335, "loc": { "start": { - "line": 300, + "line": 319, "column": 51 }, "end": { - "line": 300, + "line": 319, "column": 52 } } @@ -77011,15 +79596,15 @@ "updateContext": null }, "value": "", - "start": 11885, - "end": 11885, + "start": 12335, + "end": 12335, "loc": { "start": { - "line": 300, + "line": 319, "column": 52 }, "end": { - "line": 300, + "line": 319, "column": 52 } } @@ -77036,15 +79621,15 @@ "postfix": false, "binop": null }, - "start": 11885, - "end": 11886, + "start": 12335, + "end": 12336, "loc": { "start": { - "line": 300, + "line": 319, "column": 52 }, "end": { - "line": 300, + "line": 319, "column": 53 } } @@ -77062,15 +79647,15 @@ "binop": null, "updateContext": null }, - "start": 11886, - "end": 11887, + "start": 12336, + "end": 12337, "loc": { "start": { - "line": 300, + "line": 319, "column": 53 }, "end": { - "line": 300, + "line": 319, "column": 54 } } @@ -77088,15 +79673,15 @@ "binop": null }, "value": "nodeAsJSONLD", - "start": 11896, - "end": 11908, + "start": 12346, + "end": 12358, "loc": { "start": { - "line": 301, + "line": 320, "column": 8 }, "end": { - "line": 301, + "line": 320, "column": 20 } } @@ -77114,15 +79699,15 @@ "binop": null, "updateContext": null }, - "start": 11908, - "end": 11909, + "start": 12358, + "end": 12359, "loc": { "start": { - "line": 301, + "line": 320, "column": 20 }, "end": { - "line": 301, + "line": 320, "column": 21 } } @@ -77141,15 +79726,15 @@ "updateContext": null }, "value": "@id", - "start": 11909, - "end": 11914, + "start": 12359, + "end": 12364, "loc": { "start": { - "line": 301, + "line": 320, "column": 21 }, "end": { - "line": 301, + "line": 320, "column": 26 } } @@ -77167,15 +79752,15 @@ "binop": null, "updateContext": null }, - "start": 11914, - "end": 11915, + "start": 12364, + "end": 12365, "loc": { "start": { - "line": 301, + "line": 320, "column": 26 }, "end": { - "line": 301, + "line": 320, "column": 27 } } @@ -77194,15 +79779,15 @@ "updateContext": null }, "value": "=", - "start": 11916, - "end": 11917, + "start": 12366, + "end": 12367, "loc": { "start": { - "line": 301, + "line": 320, "column": 28 }, "end": { - "line": 301, + "line": 320, "column": 29 } } @@ -77220,15 +79805,15 @@ "binop": null }, "value": "nodeIRI", - "start": 11918, - "end": 11925, + "start": 12368, + "end": 12375, "loc": { "start": { - "line": 301, + "line": 320, "column": 30 }, "end": { - "line": 301, + "line": 320, "column": 37 } } @@ -77246,15 +79831,15 @@ "binop": null, "updateContext": null }, - "start": 11925, - "end": 11926, + "start": 12375, + "end": 12376, "loc": { "start": { - "line": 301, + "line": 320, "column": 37 }, "end": { - "line": 301, + "line": 320, "column": 38 } } @@ -77271,15 +79856,15 @@ "postfix": false, "binop": null }, - "start": 11933, - "end": 11934, + "start": 12383, + "end": 12384, "loc": { "start": { - "line": 302, + "line": 321, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 7 } } @@ -77296,15 +79881,15 @@ "postfix": false, "binop": null }, - "start": 11934, - "end": 11935, + "start": 12384, + "end": 12385, "loc": { "start": { - "line": 302, + "line": 321, "column": 7 }, "end": { - "line": 302, + "line": 321, "column": 8 } } @@ -77322,15 +79907,15 @@ "binop": null, "updateContext": null }, - "start": 11935, - "end": 11936, + "start": 12385, + "end": 12386, "loc": { "start": { - "line": 302, + "line": 321, "column": 8 }, "end": { - "line": 302, + "line": 321, "column": 9 } } @@ -77347,15 +79932,15 @@ "postfix": false, "binop": null }, - "start": 11941, - "end": 11942, + "start": 12391, + "end": 12392, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 5 } } @@ -77375,15 +79960,15 @@ "updateContext": null }, "value": "return", - "start": 11948, - "end": 11954, + "start": 12398, + "end": 12404, "loc": { "start": { - "line": 305, + "line": 324, "column": 4 }, "end": { - "line": 305, + "line": 324, "column": 10 } } @@ -77401,15 +79986,15 @@ "binop": null }, "value": "parsed", - "start": 11955, - "end": 11961, + "start": 12405, + "end": 12411, "loc": { "start": { - "line": 305, + "line": 324, "column": 11 }, "end": { - "line": 305, + "line": 324, "column": 17 } } @@ -77427,15 +80012,15 @@ "binop": null, "updateContext": null }, - "start": 11961, - "end": 11962, + "start": 12411, + "end": 12412, "loc": { "start": { - "line": 305, + "line": 324, "column": 17 }, "end": { - "line": 305, + "line": 324, "column": 18 } } @@ -77452,15 +80037,15 @@ "postfix": false, "binop": null }, - "start": 11965, - "end": 11966, + "start": 12415, + "end": 12416, "loc": { "start": { - "line": 306, + "line": 325, "column": 2 }, "end": { - "line": 306, + "line": 325, "column": 3 } } @@ -77478,15 +80063,15 @@ "binop": null }, "value": "getNodesAsJSONLD", - "start": 11970, - "end": 11986, + "start": 12420, + "end": 12436, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 308, + "line": 327, "column": 18 } } @@ -77503,15 +80088,15 @@ "postfix": false, "binop": null }, - "start": 11986, - "end": 11987, + "start": 12436, + "end": 12437, "loc": { "start": { - "line": 308, + "line": 327, "column": 18 }, "end": { - "line": 308, + "line": 327, "column": 19 } } @@ -77529,15 +80114,15 @@ "binop": null }, "value": "baseIRI", - "start": 11987, - "end": 11994, + "start": 12437, + "end": 12444, "loc": { "start": { - "line": 308, + "line": 327, "column": 19 }, "end": { - "line": 308, + "line": 327, "column": 26 } } @@ -77555,15 +80140,15 @@ "binop": null, "updateContext": null }, - "start": 11994, - "end": 11995, + "start": 12444, + "end": 12445, "loc": { "start": { - "line": 308, + "line": 327, "column": 26 }, "end": { - "line": 308, + "line": 327, "column": 27 } } @@ -77581,15 +80166,15 @@ "binop": null }, "value": "newickParser", - "start": 11996, - "end": 12008, + "start": 12446, + "end": 12458, "loc": { "start": { - "line": 308, + "line": 327, "column": 28 }, "end": { - "line": 308, + "line": 327, "column": 40 } } @@ -77606,15 +80191,15 @@ "postfix": false, "binop": null }, - "start": 12008, - "end": 12009, + "start": 12458, + "end": 12459, "loc": { "start": { - "line": 308, + "line": 327, "column": 40 }, "end": { - "line": 308, + "line": 327, "column": 41 } } @@ -77631,15 +80216,15 @@ "postfix": false, "binop": null }, - "start": 12010, - "end": 12011, + "start": 12460, + "end": 12461, "loc": { "start": { - "line": 308, + "line": 327, "column": 42 }, "end": { - "line": 308, + "line": 327, "column": 43 } } @@ -77647,15 +80232,15 @@ { "type": "CommentLine", "value": " Returns a list of all nodes in this phylogeny as a series of nodes.", - "start": 12016, - "end": 12086, + "start": 12466, + "end": 12536, "loc": { "start": { - "line": 309, + "line": 328, "column": 4 }, "end": { - "line": 309, + "line": 328, "column": 74 } } @@ -77663,15 +80248,15 @@ { "type": "CommentLine", "value": " - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').", - "start": 12091, - "end": 12164, + "start": 12541, + "end": 12614, "loc": { "start": { - "line": 310, + "line": 329, "column": 4 }, "end": { - "line": 310, + "line": 329, "column": 77 } } @@ -77679,15 +80264,15 @@ { "type": "CommentLine", "value": " Node IDs are generated by concatenating `_node${number}` to the end of", - "start": 12169, - "end": 12244, + "start": 12619, + "end": 12694, "loc": { "start": { - 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See PhylogenyWrapper.getParsedNewick() for an example", - "start": 12352, - "end": 12426, + "start": 12802, + "end": 12876, "loc": { "start": { - "line": 314, + "line": 333, "column": 4 }, "end": { - "line": 314, + "line": 333, "column": 78 } } @@ -77743,15 +80328,15 @@ { "type": "CommentLine", "value": " implementation.", - "start": 12431, - "end": 12451, + "start": 12881, + "end": 12901, "loc": { "start": { - "line": 315, + "line": 334, "column": 4 }, "end": { - "line": 315, + "line": 334, "column": 24 } } @@ -77759,15 +80344,15 @@ { "type": "CommentLine", "value": " List of nodes we have identified.", - "start": 12457, - "end": 12493, + "start": 12907, + "end": 12943, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 40 } } @@ -77787,15 +80372,15 @@ "updateContext": null }, "value": "const", - "start": 12498, - "end": 12503, + "start": 12948, + "end": 12953, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - 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However, the JSON-LD library we use in JPhyloRef", - "start": 13398, - "end": 13473, + "start": 13848, + "end": 13923, "loc": { "start": { - "line": 341, + "line": 360, "column": 8 }, "end": { - "line": 341, + "line": 360, "column": 83 } } @@ -80177,15 +82762,15 @@ { "type": "CommentLine", "value": " can't support @type being an array (despite that being in the standard,", - "start": 13482, - "end": 13556, + "start": 13932, + "end": 14006, "loc": { "start": { - "line": 342, + "line": 361, "column": 8 }, "end": { - "line": 342, + "line": 361, "column": 82 } } @@ -80193,15 +82778,15 @@ { "type": "CommentLine", "value": " see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),", - "start": 13565, - "end": 13659, + "start": 14015, + "end": 14109, "loc": { "start": { - "line": 343, + "line": 362, "column": 8 }, "end": { - "line": 343, + "line": 362, "column": 102 } } @@ -80209,15 +82794,15 @@ { "type": "CommentLine", "value": " so we fall back to using rdf:type instead.", - 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"start": 16296, - "end": 16304, + "start": 16746, + "end": 16754, "loc": { "start": { - "line": 414, + "line": 433, "column": 6 }, "end": { - "line": 414, + "line": 433, "column": 14 } } @@ -89455,15 +92040,15 @@ "binop": null, "updateContext": null }, - "start": 16304, - "end": 16305, + "start": 16754, + "end": 16755, "loc": { "start": { - "line": 414, + "line": 433, "column": 14 }, "end": { - "line": 414, + "line": 433, "column": 15 } } @@ -89481,15 +92066,15 @@ "binop": null }, "value": "forEach", - "start": 16305, - "end": 16312, + "start": 16755, + "end": 16762, "loc": { "start": { - "line": 414, + "line": 433, "column": 15 }, "end": { - "line": 414, + "line": 433, "column": 22 } } @@ -89506,15 +92091,15 @@ "postfix": false, "binop": null }, - "start": 16312, - "end": 16313, + "start": 16762, + "end": 16763, "loc": { "start": { - "line": 414, + "line": 433, "column": 22 }, "end": { - "line": 414, + "line": 433, "column": 23 } } @@ -89531,15 +92116,15 @@ "postfix": false, "binop": null }, - 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"start": 16467, - "end": 16468, + "start": 16917, + "end": 16918, "loc": { "start": { - "line": 417, + "line": 436, "column": 21 }, "end": { - "line": 417, + "line": 436, "column": 22 } } @@ -89860,15 +92445,15 @@ "binop": null }, "value": "siblings", - "start": 16468, - "end": 16476, + "start": 16918, + "end": 16926, "loc": { "start": { - "line": 417, + "line": 436, "column": 22 }, "end": { - "line": 417, + "line": 436, "column": 30 } } @@ -89887,15 +92472,15 @@ "updateContext": null }, "value": "=", - "start": 16477, - "end": 16478, + "start": 16927, + "end": 16928, "loc": { "start": { - "line": 417, + "line": 436, "column": 31 }, "end": { - "line": 417, + "line": 436, "column": 32 } } @@ -89913,15 +92498,15 @@ "binop": null }, "value": "childrenIDs", - "start": 16479, - "end": 16490, + "start": 16929, + "end": 16940, "loc": { "start": { - "line": 417, + "line": 436, "column": 33 }, "end": { - "line": 417, + "line": 436, "column": 44 } } @@ -89939,15 +92524,15 @@ "binop": null, "updateContext": null }, - 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"Identifier", + "start": 1635, + "end": 1643, + "loc": { + "start": { + "line": 51, + "column": 45 + }, + "end": { + "line": 51, + "column": 53 + }, + "identifierName": "phyloref" + }, + "name": "phyloref" + }, + "property": { + "type": "Identifier", + "start": 1644, + "end": 1662, + "loc": { + "start": { + "line": 51, + "column": 54 + }, + "end": { + "line": 51, + "column": 72 + }, + "identifierName": "externalSpecifiers" + }, + "name": "externalSpecifiers" + }, + "computed": false + }, + "operator": "||", + "right": { + "type": "ArrayExpression", + "start": 1666, + "end": 1668, + "loc": { + "start": { + "line": 51, + "column": 76 + }, + "end": { + "line": 51, + "column": 78 + } + }, + "elements": [] + }, + "extra": { + "parenthesized": true, + "parenStart": 1634 + } + }, + "property": { + "type": "Identifier", + "start": 1677, + "end": 1680, + "loc": { + "start": { + "line": 52, + "column": 7 + }, + "end": { + "line": 52, + "column": 10 + }, + "identifierName": "map" + }, + "name": "map" + }, + "computed": false + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 1681, + "end": 1711, + "loc": { + "start": { + "line": 52, + "column": 11 + }, + "end": { + "line": 52, + "column": 41 + } + }, + "object": { + "type": "Identifier", + "start": 1681, + "end": 1701, + "loc": { + "start": { + "line": 52, + "column": 11 + }, + "end": { + "line": 52, + "column": 31 + }, + "identifierName": "TaxonomicUnitWrapper" + }, + "name": "TaxonomicUnitWrapper" + }, + "property": { + "type": "Identifier", + "start": 1702, + "end": 1711, + "loc": { + "start": { + "line": 52, + "column": 32 + }, + "end": { + "line": 52, + "column": 41 + }, + "identifierName": "normalize" + }, + "name": "normalize" + }, + "computed": false + } + ] + } + } + }, + { + "type": "ReturnStatement", + "start": 1719, + "end": 1745, + "loc": { + "start": { + "line": 54, + "column": 4 + }, + "end": { + "line": 54, + "column": 30 + } + }, + "argument": { + "type": "Identifier", + "start": 1726, + "end": 1744, + "loc": { + "start": { + "line": 54, + "column": 11 + }, + "end": { + "line": 54, + "column": 29 + }, + "identifierName": "normalizedPhyloref" + }, + "name": "normalizedPhyloref" + } + } + ], + "directives": [], + "trailingComments": null + }, + "leadingComments": [ + { + "type": "CommentBlock", + "value": "*\n * Normalize a phyloreference.\n *\n * @param phyloref\n ", + "start": 1313, + "end": 1381, + "loc": { + "start": { "line": 41, + "column": 2 + }, + "end": { + "line": 45, + "column": 5 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentBlock", + "value": "* Return the external specifiers of this phyloref (if any). ", + "start": 1753, + "end": 1817, + "loc": { + "start": { + "line": 57, + "column": 2 + }, + "end": { + "line": 57, "column": 66 } } @@ -2241,15 +3021,15 @@ }, { "type": "ClassMethod", - "start": 1380, - "end": 1695, + "start": 1820, + "end": 2135, "loc": { "start": { - "line": 42, + "line": 58, "column": 2 }, "end": { - "line": 50, + "line": 66, "column": 3 } }, @@ -2257,15 +3037,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 1384, - "end": 1402, + "start": 1824, + "end": 1842, "loc": { "start": { - "line": 42, + "line": 58, "column": 6 }, "end": { - "line": 42, + "line": 58, "column": 24 }, "identifierName": "externalSpecifiers" @@ -2280,44 +3060,44 @@ "params": [], "body": { "type": "BlockStatement", - "start": 1405, - "end": 1695, + "start": 1845, + "end": 2135, "loc": { "start": { - "line": 42, + "line": 58, "column": 27 }, "end": { - "line": 50, + "line": 66, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 1411, - "end": 1645, + "start": 1851, + "end": 2085, "loc": { "start": { - "line": 43, + "line": 59, "column": 4 }, "end": { - "line": 47, + "line": 63, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 1415, - "end": 1456, + "start": 1855, + "end": 1896, "loc": { "start": { - "line": 43, + "line": 59, "column": 8 }, "end": { - "line": 43, + "line": 59, "column": 49 } }, @@ -2325,29 +3105,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 1416, - "end": 1456, + "start": 1856, + "end": 1896, "loc": { "start": { - "line": 43, + "line": 59, "column": 9 }, "end": { - "line": 43, + "line": 59, "column": 49 } }, "callee": { "type": "Identifier", - "start": 1416, - "end": 1419, + "start": 1856, + "end": 1859, "loc": { "start": { - "line": 43, + "line": 59, "column": 9 }, "end": { - "line": 43, + "line": 59, "column": 12 }, "identifierName": "has" @@ -2357,44 +3137,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1420, - "end": 1433, + "start": 1860, + "end": 1873, "loc": { "start": { - "line": 43, + "line": 59, "column": 13 }, "end": { - "line": 43, + "line": 59, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 1420, - "end": 1424, + "start": 1860, + "end": 1864, "loc": { "start": { - "line": 43, + "line": 59, "column": 13 }, "end": { - "line": 43, + "line": 59, "column": 17 } } }, "property": { "type": "Identifier", - "start": 1425, - "end": 1433, + "start": 1865, + "end": 1873, "loc": { "start": { - "line": 43, + "line": 59, "column": 18 }, "end": { - "line": 43, + "line": 59, "column": 26 }, "identifierName": "phyloref" @@ -2405,15 +3185,15 @@ }, { "type": "StringLiteral", - "start": 1435, - "end": 1455, + "start": 1875, + "end": 1895, "loc": { "start": { - "line": 43, + "line": 59, "column": 28 }, "end": { - "line": 43, + "line": 59, "column": 48 } }, @@ -2431,87 +3211,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 1458, - "end": 1645, + "start": 1898, + "end": 2085, "loc": { "start": { - "line": 43, + "line": 59, "column": 51 }, "end": { - "line": 47, + "line": 63, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 1601, - "end": 1639, + "start": 2041, + "end": 2079, "loc": { "start": { - "line": 46, + "line": 62, "column": 6 }, "end": { - "line": 46, + "line": 62, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 1601, - "end": 1638, + "start": 2041, + "end": 2078, "loc": { "start": { - "line": 46, + "line": 62, "column": 6 }, "end": { - "line": 46, + "line": 62, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 1601, - "end": 1633, + "start": 2041, + "end": 2073, "loc": { "start": { - "line": 46, + "line": 62, "column": 6 }, "end": { - "line": 46, + "line": 62, "column": 38 } }, "object": { "type": "MemberExpression", - "start": 1601, - "end": 1614, + "start": 2041, + "end": 2054, "loc": { "start": { - "line": 46, + "line": 62, "column": 6 }, "end": { - "line": 46, + "line": 62, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 1601, - "end": 1605, + "start": 2041, + "end": 2045, "loc": { "start": { - "line": 46, + "line": 62, "column": 6 }, "end": { - "line": 46, + "line": 62, "column": 10 } }, @@ -2519,15 +3299,15 @@ }, "property": { "type": "Identifier", - "start": 1606, - "end": 1614, + "start": 2046, + "end": 2054, "loc": { "start": { - "line": 46, + "line": 62, "column": 11 }, "end": { - "line": 46, + "line": 62, "column": 19 }, "identifierName": "phyloref" @@ -2539,15 +3319,15 @@ }, "property": { "type": "Identifier", - "start": 1615, - "end": 1633, + "start": 2055, + "end": 2073, "loc": { "start": { - "line": 46, + "line": 62, "column": 20 }, "end": { - "line": 46, + "line": 62, "column": 38 }, "identifierName": "externalSpecifiers" @@ -2559,15 +3339,15 @@ }, "right": { "type": "ArrayExpression", - "start": 1636, - "end": 1638, + "start": 2076, + "end": 2078, "loc": { "start": { - "line": 46, + "line": 62, "column": 41 }, "end": { - "line": 46, + "line": 62, "column": 43 } }, @@ -2579,15 +3359,15 @@ { "type": "CommentLine", "value": " If there isn't one, create an empty list so that the caller can do", - "start": 1466, - "end": 1535, + "start": 1906, + "end": 1975, "loc": { "start": { - "line": 44, + "line": 60, "column": 6 }, "end": { - "line": 44, + "line": 60, "column": 75 } } @@ -2595,15 +3375,15 @@ { "type": "CommentLine", "value": " `wrappedPhyloref.externalSpecifiers.push({...})`.", - "start": 1542, - "end": 1594, + "start": 1982, + "end": 2034, "loc": { "start": { - "line": 45, + "line": 61, "column": 6 }, "end": { - "line": 45, + "line": 61, "column": 58 } } @@ -2617,72 +3397,72 @@ }, { "type": "ReturnStatement", - "start": 1651, - "end": 1691, + "start": 2091, + "end": 2131, "loc": { "start": { - "line": 49, + "line": 65, "column": 4 }, "end": { - "line": 49, + "line": 65, "column": 44 } }, "argument": { "type": "MemberExpression", - "start": 1658, - "end": 1690, + "start": 2098, + "end": 2130, "loc": { "start": { - "line": 49, + "line": 65, "column": 11 }, "end": { - "line": 49, + "line": 65, "column": 43 } }, "object": { "type": "MemberExpression", - "start": 1658, - "end": 1671, + "start": 2098, + "end": 2111, "loc": { "start": { - "line": 49, + "line": 65, "column": 11 }, "end": { - "line": 49, + "line": 65, "column": 24 } }, "object": { "type": "ThisExpression", - "start": 1658, - "end": 1662, + "start": 2098, + "end": 2102, "loc": { "start": { - "line": 49, + "line": 65, "column": 11 }, "end": { - "line": 49, + "line": 65, "column": 15 } } }, "property": { "type": "Identifier", - "start": 1663, - "end": 1671, + "start": 2103, + "end": 2111, "loc": { "start": { - "line": 49, + "line": 65, "column": 16 }, "end": { - "line": 49, + "line": 65, "column": 24 }, "identifierName": "phyloref" @@ -2693,15 +3473,15 @@ }, "property": { "type": "Identifier", - "start": 1672, - "end": 1690, + "start": 2112, + "end": 2130, "loc": { "start": { - "line": 49, + "line": 65, "column": 25 }, "end": { - "line": 49, + "line": 65, "column": 43 }, "identifierName": "externalSpecifiers" @@ -2718,15 +3498,15 @@ { "type": "CommentBlock", "value": "* Return the external specifiers of this phyloref (if any). ", - "start": 1313, - "end": 1377, + "start": 1753, + "end": 1817, "loc": { "start": { - "line": 41, + "line": 57, "column": 2 }, "end": { - "line": 41, + "line": 57, "column": 66 } } @@ -2735,15 +3515,15 @@ }, { "type": "ClassMethod", - "start": 1699, - "end": 2021, + "start": 2139, + "end": 2461, "loc": { "start": { - "line": 52, + "line": 68, "column": 2 }, "end": { - "line": 59, + "line": 75, "column": 3 } }, @@ -2751,15 +3531,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 1703, - "end": 1708, + "start": 2143, + "end": 2148, "loc": { "start": { - "line": 52, + "line": 68, "column": 6 }, "end": { - "line": 52, + "line": 68, "column": 11 }, "identifierName": "label" @@ -2774,58 +3554,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 1711, - "end": 2021, + "start": 2151, + "end": 2461, "loc": { "start": { - "line": 52, + "line": 68, "column": 14 }, "end": { - "line": 59, + "line": 75, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 1764, - "end": 1824, + "start": 2204, + "end": 2264, "loc": { "start": { - "line": 54, + "line": 70, "column": 4 }, "end": { - "line": 54, + "line": 70, "column": 64 } }, "test": { "type": "CallExpression", - "start": 1768, - "end": 1795, + "start": 2208, + "end": 2235, "loc": { "start": { - "line": 54, + "line": 70, "column": 8 }, "end": { - "line": 54, + "line": 70, "column": 35 } }, "callee": { "type": "Identifier", - "start": 1768, - "end": 1771, + "start": 2208, + "end": 2211, "loc": { "start": { - "line": 54, + "line": 70, "column": 8 }, "end": { - "line": 54, + "line": 70, "column": 11 }, "identifierName": "has" @@ -2836,44 +3616,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1772, - "end": 1785, + "start": 2212, + "end": 2225, "loc": { "start": { - "line": 54, + "line": 70, "column": 12 }, "end": { - "line": 54, + "line": 70, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1772, - "end": 1776, + "start": 2212, + "end": 2216, "loc": { "start": { - "line": 54, + "line": 70, "column": 12 }, "end": { - "line": 54, + "line": 70, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1777, - "end": 1785, + "start": 2217, + "end": 2225, "loc": { "start": { - "line": 54, + "line": 70, "column": 17 }, "end": { - "line": 54, + "line": 70, "column": 25 }, "identifierName": "phyloref" @@ -2884,15 +3664,15 @@ }, { "type": "StringLiteral", - "start": 1787, - "end": 1794, + "start": 2227, + "end": 2234, "loc": { "start": { - "line": 54, + "line": 70, "column": 27 }, "end": { - "line": 54, + "line": 70, "column": 34 } }, @@ -2907,72 +3687,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1797, - "end": 1824, + "start": 2237, + "end": 2264, "loc": { "start": { - "line": 54, + "line": 70, "column": 37 }, "end": { - "line": 54, + "line": 70, "column": 64 } }, "argument": { "type": "MemberExpression", - "start": 1804, - "end": 1823, + "start": 2244, + "end": 2263, "loc": { "start": { - "line": 54, + "line": 70, "column": 44 }, "end": { - "line": 54, + "line": 70, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 1804, - "end": 1817, + "start": 2244, + "end": 2257, "loc": { "start": { - "line": 54, + "line": 70, "column": 44 }, "end": { - "line": 54, + "line": 70, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 1804, - "end": 1808, + "start": 2244, + "end": 2248, "loc": { "start": { - "line": 54, + "line": 70, "column": 44 }, "end": { - "line": 54, + "line": 70, "column": 48 } } }, "property": { "type": "Identifier", - "start": 1809, - "end": 1817, + "start": 2249, + "end": 2257, "loc": { "start": { - "line": 54, + "line": 70, "column": 49 }, "end": { - "line": 54, + "line": 70, "column": 57 }, "identifierName": "phyloref" @@ -2983,15 +3763,15 @@ }, "property": { "type": "Identifier", - "start": 1818, - "end": 1823, + "start": 2258, + "end": 2263, "loc": { "start": { - "line": 54, + "line": 70, "column": 58 }, "end": { - "line": 54, + "line": 70, "column": 63 }, "identifierName": "label" @@ -3006,15 +3786,15 @@ { "type": "CommentLine", "value": " Return a label for this phyloreference.", - "start": 1717, - "end": 1759, + "start": 2157, + "end": 2199, "loc": { "start": { - "line": 53, + "line": 69, "column": 4 }, "end": { - "line": 53, + "line": 69, "column": 46 } } @@ -3023,57 +3803,57 @@ }, { "type": "IfStatement", - "start": 1829, - "end": 1929, + "start": 2269, + "end": 2369, "loc": { "start": { - "line": 55, + "line": 71, "column": 4 }, "end": { - "line": 55, + "line": 71, "column": 104 } }, "test": { "type": "LogicalExpression", - "start": 1833, - "end": 1896, + "start": 2273, + "end": 2336, "loc": { "start": { - "line": 55, + "line": 71, "column": 8 }, "end": { - "line": 55, + "line": 71, "column": 71 } }, "left": { "type": "CallExpression", - "start": 1833, - "end": 1861, + "start": 2273, + "end": 2301, "loc": { "start": { - "line": 55, + "line": 71, "column": 8 }, "end": { - "line": 55, + "line": 71, "column": 36 } }, "callee": { "type": "Identifier", - "start": 1833, - "end": 1836, + "start": 2273, + "end": 2276, "loc": { "start": { - "line": 55, + "line": 71, "column": 8 }, "end": { - "line": 55, + "line": 71, "column": 11 }, "identifierName": "has" @@ -3083,44 +3863,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1837, - "end": 1850, + "start": 2277, + "end": 2290, "loc": { "start": { - "line": 55, + "line": 71, "column": 12 }, "end": { - "line": 55, + "line": 71, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1837, - "end": 1841, + "start": 2277, + "end": 2281, "loc": { "start": { - "line": 55, + "line": 71, "column": 12 }, "end": { - "line": 55, + "line": 71, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1842, - "end": 1850, + "start": 2282, + "end": 2290, "loc": { "start": { - "line": 55, + "line": 71, "column": 17 }, "end": { - "line": 55, + "line": 71, "column": 25 }, "identifierName": "phyloref" @@ -3131,15 +3911,15 @@ }, { "type": "StringLiteral", - "start": 1852, - "end": 1860, + "start": 2292, + "end": 2300, "loc": { "start": { - "line": 55, + "line": 71, "column": 27 }, "end": { - "line": 55, + "line": 71, "column": 35 } }, @@ -3154,86 +3934,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 1865, - "end": 1896, + "start": 2305, + "end": 2336, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 71 } }, "left": { "type": "MemberExpression", - "start": 1865, - "end": 1892, + "start": 2305, + "end": 2332, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 67 } }, "object": { "type": "MemberExpression", - "start": 1865, - "end": 1885, + "start": 2305, + "end": 2325, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 1865, - "end": 1878, + "start": 2305, + "end": 2318, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 53 } }, "object": { "type": "ThisExpression", - "start": 1865, - "end": 1869, + "start": 2305, + "end": 2309, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 44 } } }, "property": { "type": "Identifier", - "start": 1870, - "end": 1878, + "start": 2310, + "end": 2318, "loc": { "start": { - "line": 55, + "line": 71, "column": 45 }, "end": { - "line": 55, + "line": 71, "column": 53 }, "identifierName": "phyloref" @@ -3244,15 +4024,15 @@ }, "property": { "type": "Identifier", - "start": 1879, - "end": 1885, + "start": 2319, + "end": 2325, "loc": { "start": { - "line": 55, + "line": 71, "column": 54 }, "end": { - "line": 55, + "line": 71, "column": 60 }, "identifierName": "labels" @@ -3263,15 +4043,15 @@ }, "property": { "type": "Identifier", - "start": 1886, - "end": 1892, + "start": 2326, + "end": 2332, "loc": { "start": { - "line": 55, + "line": 71, "column": 61 }, "end": { - "line": 55, + "line": 71, "column": 67 }, "identifierName": "length" @@ -3283,15 +4063,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 1895, - "end": 1896, + "start": 2335, + "end": 2336, "loc": { "start": { - "line": 55, + "line": 71, "column": 70 }, "end": { - "line": 55, + "line": 71, "column": 71 } }, @@ -3305,86 +4085,86 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1898, - "end": 1929, + "start": 2338, + "end": 2369, "loc": { "start": { - "line": 55, + "line": 71, "column": 73 }, "end": { - "line": 55, + "line": 71, "column": 104 } }, "argument": { "type": "MemberExpression", - "start": 1905, - "end": 1928, + "start": 2345, + "end": 2368, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 103 } }, "object": { "type": "MemberExpression", - "start": 1905, - "end": 1925, + "start": 2345, + "end": 2365, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 100 } }, "object": { "type": "MemberExpression", - "start": 1905, - "end": 1918, + "start": 2345, + "end": 2358, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 93 } }, "object": { "type": "ThisExpression", - "start": 1905, - "end": 1909, + "start": 2345, + "end": 2349, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 84 } } }, "property": { "type": "Identifier", - "start": 1910, - "end": 1918, + "start": 2350, + "end": 2358, "loc": { "start": { - "line": 55, + "line": 71, "column": 85 }, "end": { - "line": 55, + "line": 71, "column": 93 }, "identifierName": "phyloref" @@ -3395,15 +4175,15 @@ }, "property": { "type": "Identifier", - "start": 1919, - "end": 1925, + "start": 2359, + "end": 2365, "loc": { "start": { - "line": 55, + "line": 71, "column": 94 }, "end": { - "line": 55, + "line": 71, "column": 100 }, "identifierName": "labels" @@ -3414,15 +4194,15 @@ }, "property": { "type": "NumericLiteral", - "start": 1926, - "end": 1927, + "start": 2366, + "end": 2367, "loc": { "start": { - "line": 55, + "line": 71, "column": 101 }, "end": { - "line": 55, + "line": 71, "column": 102 } }, @@ -3439,43 +4219,43 @@ }, { "type": "IfStatement", - "start": 1934, - "end": 1994, + "start": 2374, + "end": 2434, "loc": { "start": { - "line": 56, + "line": 72, "column": 4 }, "end": { - "line": 56, + "line": 72, "column": 64 } }, "test": { "type": "CallExpression", - "start": 1938, - "end": 1965, + "start": 2378, + "end": 2405, "loc": { "start": { - "line": 56, + "line": 72, "column": 8 }, "end": { - "line": 56, + "line": 72, "column": 35 } }, "callee": { "type": "Identifier", - "start": 1938, - "end": 1941, + "start": 2378, + "end": 2381, "loc": { "start": { - "line": 56, + "line": 72, "column": 8 }, "end": { - "line": 56, + "line": 72, "column": 11 }, "identifierName": "has" @@ -3485,44 +4265,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1942, - "end": 1955, + "start": 2382, + "end": 2395, "loc": { "start": { - "line": 56, + "line": 72, "column": 12 }, "end": { - "line": 56, + "line": 72, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1942, - "end": 1946, + "start": 2382, + "end": 2386, "loc": { "start": { - "line": 56, + "line": 72, "column": 12 }, "end": { - "line": 56, + "line": 72, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1947, - "end": 1955, + "start": 2387, + "end": 2395, "loc": { "start": { - "line": 56, + "line": 72, "column": 17 }, "end": { - "line": 56, + "line": 72, "column": 25 }, "identifierName": "phyloref" @@ -3533,15 +4313,15 @@ }, { "type": "StringLiteral", - "start": 1957, - "end": 1964, + "start": 2397, + "end": 2404, "loc": { "start": { - "line": 56, + "line": 72, "column": 27 }, "end": { - "line": 56, + "line": 72, "column": 34 } }, @@ -3555,72 +4335,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1967, - "end": 1994, + "start": 2407, + "end": 2434, "loc": { "start": { - "line": 56, + "line": 72, "column": 37 }, "end": { - "line": 56, + "line": 72, "column": 64 } }, "argument": { "type": "MemberExpression", - "start": 1974, - "end": 1993, + "start": 2414, + "end": 2433, "loc": { "start": { - "line": 56, + "line": 72, "column": 44 }, "end": { - "line": 56, + "line": 72, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 1974, - "end": 1987, + "start": 2414, + "end": 2427, "loc": { "start": { - "line": 56, + "line": 72, "column": 44 }, "end": { - "line": 56, + "line": 72, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 1974, - "end": 1978, + "start": 2414, + "end": 2418, "loc": { "start": { - "line": 56, + "line": 72, "column": 44 }, "end": { - "line": 56, + "line": 72, "column": 48 } } }, "property": { "type": "Identifier", - "start": 1979, - "end": 1987, + "start": 2419, + "end": 2427, "loc": { "start": { - "line": 56, + "line": 72, "column": 49 }, "end": { - "line": 56, + "line": 72, "column": 57 }, "identifierName": "phyloref" @@ -3631,15 +4411,15 @@ }, "property": { "type": "Identifier", - "start": 1988, - "end": 1993, + "start": 2428, + "end": 2433, "loc": { "start": { - "line": 56, + "line": 72, "column": 58 }, "end": { - "line": 56, + "line": 72, "column": 63 }, "identifierName": "title" @@ -3653,29 +4433,29 @@ }, { "type": "ReturnStatement", - "start": 2000, - "end": 2017, + "start": 2440, + "end": 2457, "loc": { "start": { - "line": 58, + "line": 74, "column": 4 }, "end": { - "line": 58, + "line": 74, "column": 21 } }, "argument": { "type": "Identifier", - "start": 2007, - "end": 2016, + "start": 2447, + "end": 2456, "loc": { "start": { - "line": 58, + "line": 74, "column": 11 }, "end": { - "line": 58, + "line": 74, "column": 20 }, "identifierName": "undefined" @@ -3689,15 +4469,15 @@ }, { "type": "ClassMethod", - "start": 2025, - "end": 2280, + "start": 2465, + "end": 2720, "loc": { "start": { - "line": 61, + "line": 77, "column": 2 }, "end": { - "line": 69, + "line": 85, "column": 3 } }, @@ -3705,15 +4485,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2029, - "end": 2034, + "start": 2469, + "end": 2474, "loc": { "start": { - "line": 61, + "line": 77, "column": 6 }, "end": { - "line": 61, + "line": 77, "column": 11 }, "identifierName": "label" @@ -3728,15 +4508,15 @@ "params": [ { "type": "Identifier", - "start": 2035, - "end": 2043, + "start": 2475, + "end": 2483, "loc": { "start": { - "line": 61, + "line": 77, "column": 12 }, "end": { - "line": 61, + "line": 77, "column": 20 }, "identifierName": "newLabel" @@ -3746,58 +4526,58 @@ ], "body": { "type": "BlockStatement", - "start": 2045, - "end": 2280, + "start": 2485, + "end": 2720, "loc": { "start": { - "line": 61, + "line": 77, "column": 22 }, "end": { - "line": 69, + "line": 85, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 2095, - "end": 2276, + "start": 2535, + "end": 2716, "loc": { "start": { - "line": 63, + "line": 79, "column": 4 }, "end": { - "line": 68, + "line": 84, "column": 5 } }, "test": { "type": "CallExpression", - "start": 2099, - "end": 2126, + "start": 2539, + "end": 2566, "loc": { "start": { - "line": 63, + "line": 79, "column": 8 }, "end": { - "line": 63, + "line": 79, "column": 35 } }, "callee": { "type": "Identifier", - "start": 2099, - "end": 2102, + "start": 2539, + "end": 2542, "loc": { "start": { - "line": 63, + "line": 79, "column": 8 }, "end": { - "line": 63, + "line": 79, "column": 11 }, "identifierName": "has" @@ -3808,44 +4588,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2103, - "end": 2116, + "start": 2543, + "end": 2556, "loc": { "start": { - "line": 63, + "line": 79, "column": 12 }, "end": { - "line": 63, + "line": 79, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 2103, - "end": 2107, + "start": 2543, + "end": 2547, "loc": { "start": { - "line": 63, + "line": 79, "column": 12 }, "end": { - "line": 63, + "line": 79, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2108, - "end": 2116, + "start": 2548, + "end": 2556, "loc": { "start": { - "line": 63, + "line": 79, "column": 17 }, "end": { - "line": 63, + "line": 79, "column": 25 }, "identifierName": "phyloref" @@ -3856,15 +4636,15 @@ }, { "type": "StringLiteral", - "start": 2118, - "end": 2125, + "start": 2558, + "end": 2565, "loc": { "start": { - "line": 63, + "line": 79, "column": 27 }, "end": { - "line": 63, + "line": 79, "column": 34 } }, @@ -3879,102 +4659,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 2128, - "end": 2173, + "start": 2568, + "end": 2613, "loc": { "start": { - "line": 63, + "line": 79, "column": 37 }, "end": { - "line": 65, + "line": 81, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2136, - "end": 2167, + "start": 2576, + "end": 2607, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 37 } }, "expression": { "type": "AssignmentExpression", - "start": 2136, - "end": 2166, + "start": 2576, + "end": 2606, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 36 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 2136, - "end": 2155, + "start": 2576, + "end": 2595, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 2136, - "end": 2149, + "start": 2576, + "end": 2589, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 2136, - "end": 2140, + "start": 2576, + "end": 2580, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 10 } } }, "property": { "type": "Identifier", - "start": 2141, - "end": 2149, + "start": 2581, + "end": 2589, "loc": { "start": { - "line": 64, + "line": 80, "column": 11 }, "end": { - "line": 64, + "line": 80, "column": 19 }, "identifierName": "phyloref" @@ -3985,15 +4765,15 @@ }, "property": { "type": "Identifier", - "start": 2150, - "end": 2155, + "start": 2590, + "end": 2595, "loc": { "start": { - "line": 64, + "line": 80, "column": 20 }, "end": { - "line": 64, + "line": 80, "column": 25 }, "identifierName": "label" @@ -4004,15 +4784,15 @@ }, "right": { "type": "Identifier", - "start": 2158, - "end": 2166, + "start": 2598, + "end": 2606, "loc": { "start": { - "line": 64, + "line": 80, "column": 28 }, "end": { - "line": 64, + "line": 80, "column": 36 }, "identifierName": "newLabel" @@ -4026,87 +4806,87 @@ }, "alternate": { "type": "BlockStatement", - "start": 2179, - "end": 2276, + "start": 2619, + "end": 2716, "loc": { "start": { - "line": 65, + "line": 81, "column": 11 }, "end": { - "line": 68, + "line": 84, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2239, - "end": 2270, + "start": 2679, + "end": 2710, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 37 } }, "expression": { "type": "AssignmentExpression", - "start": 2239, - "end": 2269, + "start": 2679, + "end": 2709, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 36 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 2239, - "end": 2258, + "start": 2679, + "end": 2698, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 2239, - "end": 2252, + "start": 2679, + "end": 2692, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 2239, - "end": 2243, + "start": 2679, + "end": 2683, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 10 } }, @@ -4114,15 +4894,15 @@ }, "property": { "type": "Identifier", - "start": 2244, - "end": 2252, + "start": 2684, + "end": 2692, "loc": { "start": { - "line": 67, + "line": 83, "column": 11 }, "end": { - "line": 67, + "line": 83, "column": 19 }, "identifierName": "phyloref" @@ -4134,15 +4914,15 @@ }, "property": { "type": "Identifier", - "start": 2253, - "end": 2258, + "start": 2693, + "end": 2698, "loc": { "start": { - "line": 67, + "line": 83, "column": 20 }, "end": { - "line": 67, + "line": 83, "column": 25 }, "identifierName": "label" @@ -4154,15 +4934,15 @@ }, "right": { "type": "Identifier", - "start": 2261, - "end": 2269, + "start": 2701, + "end": 2709, "loc": { "start": { - "line": 67, + "line": 83, "column": 28 }, "end": { - "line": 67, + "line": 83, "column": 36 }, "identifierName": "newLabel" @@ -4175,15 +4955,15 @@ { "type": "CommentLine", "value": " Vue.set(this.phyloref, 'label', newLabel);", - "start": 2187, - "end": 2232, + "start": 2627, + "end": 2672, "loc": { "start": { - "line": 66, + "line": 82, "column": 6 }, "end": { - "line": 66, + "line": 82, "column": 51 } } @@ -4197,15 +4977,15 @@ { "type": "CommentLine", "value": " Set a label for this phyloreference.", - "start": 2051, - "end": 2090, + "start": 2491, + "end": 2530, "loc": { "start": { - "line": 62, + "line": 78, "column": 4 }, "end": { - "line": 62, + "line": 78, "column": 43 } } @@ -4220,15 +5000,15 @@ { "type": "CommentBlock", "value": "* Return all the specifiers of this phyloref (if any). ", - "start": 2284, - "end": 2343, + "start": 2724, + "end": 2783, "loc": { "start": { - "line": 71, + "line": 87, "column": 2 }, "end": { - "line": 71, + "line": 87, "column": 61 } } @@ -4237,15 +5017,15 @@ }, { "type": "ClassMethod", - "start": 2346, - "end": 2675, + "start": 2786, + "end": 3115, "loc": { "start": { - "line": 72, + "line": 88, "column": 2 }, "end": { - "line": 79, + "line": 95, "column": 3 } }, @@ -4253,15 +5033,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2350, - "end": 2360, + "start": 2790, + "end": 2800, "loc": { "start": { - "line": 72, + "line": 88, "column": 6 }, "end": { - "line": 72, + "line": 88, "column": 16 }, "identifierName": "specifiers" @@ -4276,59 +5056,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 2363, - "end": 2675, + "start": 2803, + "end": 3115, "loc": { "start": { - "line": 72, + "line": 88, "column": 19 }, "end": { - "line": 79, + "line": 95, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 2546, - "end": 2587, + "start": 2986, + "end": 3027, "loc": { "start": { - "line": 76, + "line": 92, "column": 4 }, "end": { - "line": 76, + "line": 92, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2550, - "end": 2586, + "start": 2990, + "end": 3026, "loc": { "start": { - "line": 76, + "line": 92, "column": 8 }, "end": { - "line": 76, + "line": 92, "column": 44 } }, "id": { "type": "Identifier", - "start": 2550, - "end": 2560, + "start": 2990, + "end": 3000, "loc": { "start": { - "line": 76, + "line": 92, "column": 8 }, "end": { - "line": 76, + "line": 92, "column": 18 }, "identifierName": "specifiers" @@ -4338,44 +5118,44 @@ }, "init": { "type": "MemberExpression", - "start": 2563, - "end": 2586, + "start": 3003, + "end": 3026, "loc": { "start": { - "line": 76, + "line": 92, "column": 21 }, "end": { - "line": 76, + "line": 92, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 2563, - "end": 2567, + "start": 3003, + "end": 3007, "loc": { "start": { - "line": 76, + "line": 92, "column": 21 }, "end": { - "line": 76, + "line": 92, "column": 25 } } }, "property": { "type": "Identifier", - "start": 2568, - "end": 2586, + "start": 3008, + "end": 3026, "loc": { "start": { - "line": 76, + "line": 92, "column": 26 }, "end": { - "line": 76, + "line": 92, "column": 44 }, "identifierName": "internalSpecifiers" @@ -4392,15 +5172,15 @@ { "type": "CommentLine", "value": " Returns a list of all specifiers by combining the internal and external", - "start": 2369, - "end": 2443, + "start": 2809, + "end": 2883, "loc": { "start": { - "line": 73, + "line": 89, "column": 4 }, "end": { - "line": 73, + "line": 89, "column": 78 } } @@ -4408,15 +5188,15 @@ { "type": "CommentLine", "value": " specifiers into a single list, with internal specifiers before", - "start": 2448, - "end": 2513, + "start": 2888, + "end": 2953, "loc": { "start": { - "line": 74, + "line": 90, "column": 4 }, "end": { - "line": 74, + "line": 90, "column": 69 } } @@ -4424,15 +5204,15 @@ { "type": "CommentLine", "value": " external specifiers.", - "start": 2518, - "end": 2541, + "start": 2958, + "end": 2981, "loc": { "start": { - "line": 75, + "line": 91, "column": 4 }, "end": { - "line": 75, + "line": 91, "column": 27 } } @@ -4441,44 +5221,44 @@ }, { "type": "ExpressionStatement", - "start": 2592, - "end": 2648, + "start": 3032, + "end": 3088, "loc": { "start": { - "line": 77, + "line": 93, "column": 4 }, "end": { - "line": 77, + "line": 93, "column": 60 } }, "expression": { "type": "AssignmentExpression", - "start": 2592, - "end": 2647, + "start": 3032, + "end": 3087, "loc": { "start": { - "line": 77, + "line": 93, "column": 4 }, "end": { - "line": 77, + "line": 93, "column": 59 } }, "operator": "=", "left": { "type": "Identifier", - "start": 2592, - "end": 2602, + "start": 3032, + "end": 3042, "loc": { "start": { - "line": 77, + "line": 93, "column": 4 }, "end": { - "line": 77, + "line": 93, "column": 14 }, "identifierName": "specifiers" @@ -4487,43 +5267,43 @@ }, "right": { "type": "CallExpression", - "start": 2605, - "end": 2647, + "start": 3045, + "end": 3087, "loc": { "start": { - "line": 77, + "line": 93, "column": 17 }, "end": { - "line": 77, + "line": 93, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 2605, - "end": 2622, + "start": 3045, + "end": 3062, "loc": { "start": { - "line": 77, + "line": 93, "column": 17 }, "end": { - "line": 77, + "line": 93, "column": 34 } }, "object": { "type": "Identifier", - "start": 2605, - "end": 2615, + "start": 3045, + "end": 3055, "loc": { "start": { - "line": 77, + "line": 93, "column": 17 }, "end": { - "line": 77, + "line": 93, "column": 27 }, "identifierName": "specifiers" @@ -4532,15 +5312,15 @@ }, "property": { "type": "Identifier", - "start": 2616, - "end": 2622, + "start": 3056, + "end": 3062, "loc": { "start": { - "line": 77, + "line": 93, "column": 28 }, "end": { - "line": 77, + "line": 93, "column": 34 }, "identifierName": "concat" @@ -4552,44 +5332,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2623, - "end": 2646, + "start": 3063, + "end": 3086, "loc": { "start": { - "line": 77, + "line": 93, "column": 35 }, "end": { - "line": 77, + "line": 93, "column": 58 } }, "object": { "type": "ThisExpression", - "start": 2623, - "end": 2627, + "start": 3063, + "end": 3067, "loc": { "start": { - "line": 77, + "line": 93, "column": 35 }, "end": { - "line": 77, + "line": 93, "column": 39 } } }, "property": { "type": "Identifier", - "start": 2628, - "end": 2646, + "start": 3068, + "end": 3086, "loc": { "start": { - "line": 77, + "line": 93, "column": 40 }, "end": { - "line": 77, + "line": 93, "column": 58 }, "identifierName": "externalSpecifiers" @@ -4604,29 +5384,29 @@ }, { "type": "ReturnStatement", - "start": 2653, - "end": 2671, + "start": 3093, + "end": 3111, "loc": { "start": { - "line": 78, + "line": 94, "column": 4 }, "end": { - "line": 78, + "line": 94, "column": 22 } }, "argument": { "type": "Identifier", - "start": 2660, - "end": 2670, + "start": 3100, + "end": 3110, "loc": { "start": { - "line": 78, + "line": 94, "column": 11 }, "end": { - "line": 78, + "line": 94, "column": 21 }, "identifierName": "specifiers" @@ -4641,15 +5421,15 @@ { "type": "CommentBlock", "value": "* Return all the specifiers of this phyloref (if any). ", - "start": 2284, - "end": 2343, + "start": 2724, + "end": 2783, "loc": { "start": { - "line": 71, + "line": 87, "column": 2 }, "end": { - "line": 71, + "line": 87, "column": 61 } } @@ -4658,15 +5438,15 @@ }, { "type": "ClassMethod", - "start": 2679, - "end": 2998, + "start": 3119, + "end": 3438, "loc": { "start": { - "line": 81, + "line": 97, "column": 2 }, "end": { - "line": 88, + "line": 104, "column": 3 } }, @@ -4674,15 +5454,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2679, - "end": 2695, + "start": 3119, + "end": 3135, "loc": { "start": { - "line": 81, + "line": 97, "column": 2 }, "end": { - "line": 81, + "line": 97, "column": 18 }, "identifierName": "getSpecifierType" @@ -4697,15 +5477,15 @@ "params": [ { "type": "Identifier", - "start": 2696, - "end": 2705, + "start": 3136, + "end": 3145, "loc": { "start": { - "line": 81, + "line": 97, "column": 19 }, "end": { - "line": 81, + "line": 97, "column": 28 }, "identifierName": "specifier" @@ -4715,86 +5495,86 @@ ], "body": { "type": "BlockStatement", - "start": 2707, - "end": 2998, + "start": 3147, + "end": 3438, "loc": { "start": { - "line": 81, + "line": 97, "column": 30 }, "end": { - "line": 88, + "line": 104, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 2831, - "end": 2898, + "start": 3271, + "end": 3338, "loc": { "start": { - "line": 85, + "line": 101, "column": 4 }, "end": { - "line": 85, + "line": 101, "column": 71 } }, "test": { "type": "CallExpression", - "start": 2835, - "end": 2878, + "start": 3275, + "end": 3318, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 2835, - "end": 2867, + "start": 3275, + "end": 3307, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 2835, - "end": 2858, + "start": 3275, + "end": 3298, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 2835, - "end": 2839, + "start": 3275, + "end": 3279, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 12 } }, @@ -4802,15 +5582,15 @@ }, "property": { "type": "Identifier", - "start": 2840, - "end": 2858, + "start": 3280, + "end": 3298, "loc": { "start": { - "line": 85, + "line": 101, "column": 13 }, "end": { - "line": 85, + "line": 101, "column": 31 }, "identifierName": "internalSpecifiers" @@ -4822,15 +5602,15 @@ }, "property": { "type": "Identifier", - "start": 2859, - "end": 2867, + "start": 3299, + "end": 3307, "loc": { "start": { - "line": 85, + "line": 101, "column": 32 }, "end": { - "line": 85, + "line": 101, "column": 40 }, "identifierName": "includes" @@ -4843,15 +5623,15 @@ "arguments": [ { "type": "Identifier", - "start": 2868, - "end": 2877, + "start": 3308, + "end": 3317, "loc": { "start": { - "line": 85, + "line": 101, "column": 41 }, "end": { - "line": 85, + "line": 101, "column": 50 }, "identifierName": "specifier" @@ -4863,29 +5643,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 2880, - "end": 2898, + "start": 3320, + "end": 3338, "loc": { "start": { - "line": 85, + "line": 101, "column": 53 }, "end": { - "line": 85, + "line": 101, "column": 71 } }, "argument": { "type": "StringLiteral", - "start": 2887, - "end": 2897, + "start": 3327, + "end": 3337, "loc": { "start": { - "line": 85, + "line": 101, "column": 60 }, "end": { - "line": 85, + "line": 101, "column": 70 } }, @@ -4901,15 +5681,15 @@ { "type": "CommentLine", "value": " For a given specifier, return a string indicating whether it is", - "start": 2713, - "end": 2779, + "start": 3153, + "end": 3219, "loc": { "start": { - "line": 82, + "line": 98, "column": 4 }, "end": { - "line": 82, + "line": 98, "column": 70 } } @@ -4917,15 +5697,15 @@ { "type": "CommentLine", "value": " an 'Internal' or 'External' specifier.", - "start": 2784, - "end": 2825, + "start": 3224, + "end": 3265, "loc": { "start": { - "line": 83, + "line": 99, "column": 4 }, "end": { - "line": 83, + "line": 99, "column": 45 } } @@ -4934,86 +5714,86 @@ }, { "type": "IfStatement", - "start": 2903, - "end": 2970, + "start": 3343, + "end": 3410, "loc": { "start": { - "line": 86, + "line": 102, "column": 4 }, "end": { - "line": 86, + "line": 102, "column": 71 } }, "test": { "type": "CallExpression", - "start": 2907, - "end": 2950, + "start": 3347, + "end": 3390, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 2907, - "end": 2939, + "start": 3347, + "end": 3379, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 2907, - "end": 2930, + "start": 3347, + "end": 3370, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 2907, - "end": 2911, + "start": 3347, + "end": 3351, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 12 } } }, "property": { "type": "Identifier", - "start": 2912, - "end": 2930, + "start": 3352, + "end": 3370, "loc": { "start": { - "line": 86, + "line": 102, "column": 13 }, "end": { - "line": 86, + "line": 102, "column": 31 }, "identifierName": "externalSpecifiers" @@ -5024,15 +5804,15 @@ }, "property": { "type": "Identifier", - "start": 2931, - "end": 2939, + "start": 3371, + "end": 3379, "loc": { "start": { - "line": 86, + "line": 102, "column": 32 }, "end": { - "line": 86, + "line": 102, "column": 40 }, "identifierName": "includes" @@ -5044,15 +5824,15 @@ "arguments": [ { "type": "Identifier", - "start": 2940, - "end": 2949, + "start": 3380, + "end": 3389, "loc": { "start": { - "line": 86, + "line": 102, "column": 41 }, "end": { - "line": 86, + "line": 102, "column": 50 }, "identifierName": "specifier" @@ -5063,29 +5843,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 2952, - "end": 2970, + "start": 3392, + "end": 3410, "loc": { "start": { - "line": 86, + "line": 102, "column": 53 }, "end": { - "line": 86, + "line": 102, "column": 71 } }, "argument": { "type": "StringLiteral", - "start": 2959, - "end": 2969, + "start": 3399, + "end": 3409, "loc": { "start": { - "line": 86, + "line": 102, "column": 60 }, "end": { - "line": 86, + "line": 102, "column": 70 } }, @@ -5100,29 +5880,29 @@ }, { "type": "ReturnStatement", - "start": 2975, - "end": 2994, + "start": 3415, + "end": 3434, "loc": { "start": { - "line": 87, + "line": 103, "column": 4 }, "end": { - "line": 87, + "line": 103, "column": 23 } }, "argument": { "type": "StringLiteral", - "start": 2982, - "end": 2993, + "start": 3422, + "end": 3433, "loc": { "start": { - "line": 87, + "line": 103, "column": 11 }, "end": { - "line": 87, + "line": 103, "column": 22 } }, @@ -5139,15 +5919,15 @@ }, { "type": "ClassMethod", - "start": 3002, - "end": 4345, + "start": 3442, + "end": 4785, "loc": { "start": { - "line": 90, + "line": 106, "column": 2 }, "end": { - "line": 119, + "line": 135, "column": 3 } }, @@ -5155,15 +5935,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3002, - "end": 3018, + "start": 3442, + "end": 3458, "loc": { "start": { - "line": 90, + "line": 106, "column": 2 }, "end": { - "line": 90, + "line": 106, "column": 18 }, "identifierName": "setSpecifierType" @@ -5178,15 +5958,15 @@ "params": [ { "type": "Identifier", - "start": 3019, - "end": 3028, + "start": 3459, + "end": 3468, "loc": { "start": { - "line": 90, + "line": 106, "column": 19 }, "end": { - "line": 90, + "line": 106, "column": 28 }, "identifierName": "specifier" @@ -5195,15 +5975,15 @@ }, { "type": "Identifier", - "start": 3030, - "end": 3043, + "start": 3470, + "end": 3483, "loc": { "start": { - "line": 90, + "line": 106, "column": 30 }, "end": { - "line": 90, + "line": 106, "column": 43 }, "identifierName": "specifierType" @@ -5213,59 +5993,59 @@ ], "body": { "type": "BlockStatement", - "start": 3045, - "end": 4345, + "start": 3485, + "end": 4785, "loc": { "start": { - "line": 90, + "line": 106, "column": 45 }, "end": { - "line": 119, + "line": 135, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 3240, - "end": 3250, + "start": 3680, + "end": 3690, "loc": { "start": { - "line": 95, + "line": 111, "column": 4 }, "end": { - "line": 95, + "line": 111, "column": 14 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 3244, - "end": 3249, + "start": 3684, + "end": 3689, "loc": { "start": { - "line": 95, + "line": 111, "column": 8 }, "end": { - "line": 95, + "line": 111, "column": 13 } }, "id": { "type": "Identifier", - "start": 3244, - "end": 3249, + "start": 3684, + "end": 3689, "loc": { "start": { - "line": 95, + "line": 111, "column": 8 }, "end": { - "line": 95, + "line": 111, "column": 13 }, "identifierName": "index" @@ -5282,15 +6062,15 @@ { "type": "CommentLine", "value": " Change the type of a given specifier. To do this, we first need", - "start": 3051, - "end": 3117, + "start": 3491, + "end": 3557, "loc": { "start": { - "line": 91, + "line": 107, "column": 4 }, "end": { - "line": 91, + "line": 107, "column": 70 } } @@ -5298,15 +6078,15 @@ { "type": "CommentLine", "value": " to determine if it was originally an internal or external", - "start": 3122, - "end": 3182, + "start": 3562, + "end": 3622, "loc": { "start": { - "line": 92, + "line": 108, "column": 4 }, "end": { - "line": 92, + "line": 108, "column": 64 } } @@ -5314,15 +6094,15 @@ { "type": "CommentLine", "value": " specifier, then move it into the other list.", - "start": 3187, - "end": 3234, + "start": 3627, + "end": 3674, "loc": { "start": { - "line": 93, + "line": 109, "column": 4 }, "end": { - "line": 93, + "line": 109, "column": 51 } } @@ -5331,43 +6111,43 @@ }, { "type": "IfStatement", - "start": 3255, - "end": 4341, + "start": 3695, + "end": 4781, "loc": { "start": { - "line": 96, + "line": 112, "column": 4 }, "end": { - "line": 118, + "line": 134, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 3259, - "end": 3287, + "start": 3699, + "end": 3727, "loc": { "start": { - "line": 96, + "line": 112, "column": 8 }, "end": { - "line": 96, + "line": 112, "column": 36 } }, "left": { "type": "Identifier", - "start": 3259, - "end": 3272, + "start": 3699, + "end": 3712, "loc": { "start": { - "line": 96, + "line": 112, "column": 8 }, "end": { - "line": 96, + "line": 112, "column": 21 }, "identifierName": "specifierType" @@ -5377,15 +6157,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 3277, - "end": 3287, + "start": 3717, + "end": 3727, "loc": { "start": { - "line": 96, + "line": 112, "column": 26 }, "end": { - "line": 96, + "line": 112, "column": 36 } }, @@ -5398,59 +6178,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 3289, - "end": 3751, + "start": 3729, + "end": 4191, "loc": { "start": { - "line": 96, + "line": 112, "column": 38 }, "end": { - "line": 106, + "line": 122, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3420, - "end": 3471, + "start": 3860, + "end": 3911, "loc": { "start": { - "line": 99, + "line": 115, "column": 6 }, "end": { - "line": 99, + "line": 115, "column": 57 } }, "expression": { "type": "AssignmentExpression", - "start": 3420, - "end": 3470, + "start": 3860, + "end": 3910, "loc": { "start": { - "line": 99, + "line": 115, "column": 6 }, "end": { - "line": 99, + "line": 115, "column": 56 } }, "operator": "=", "left": { "type": "Identifier", - "start": 3420, - "end": 3425, + "start": 3860, + "end": 3865, "loc": { "start": { - "line": 99, + "line": 115, "column": 6 }, "end": { - "line": 99, + "line": 115, "column": 11 }, "identifierName": "index" @@ -5460,72 +6240,72 @@ }, "right": { "type": "CallExpression", - "start": 3428, - "end": 3470, + "start": 3868, + "end": 3910, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 56 } }, "callee": { "type": "MemberExpression", - "start": 3428, - "end": 3459, + "start": 3868, + "end": 3899, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 45 } }, "object": { "type": "MemberExpression", - "start": 3428, - "end": 3451, + "start": 3868, + "end": 3891, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 3428, - "end": 3432, + "start": 3868, + "end": 3872, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 18 } } }, "property": { "type": "Identifier", - "start": 3433, - "end": 3451, + "start": 3873, + "end": 3891, "loc": { "start": { - "line": 99, + "line": 115, "column": 19 }, "end": { - "line": 99, + "line": 115, "column": 37 }, "identifierName": "externalSpecifiers" @@ -5536,15 +6316,15 @@ }, "property": { "type": "Identifier", - "start": 3452, - "end": 3459, + "start": 3892, + "end": 3899, "loc": { "start": { - "line": 99, + "line": 115, "column": 38 }, "end": { - "line": 99, + "line": 115, "column": 45 }, "identifierName": "indexOf" @@ -5556,15 +6336,15 @@ "arguments": [ { "type": "Identifier", - "start": 3460, - "end": 3469, + "start": 3900, + "end": 3909, "loc": { "start": { - "line": 99, + "line": 115, "column": 46 }, "end": { - "line": 99, + "line": 115, "column": 55 }, "identifierName": "specifier" @@ -5579,15 +6359,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'Internal', we might need to delete it from the", - "start": 3297, - "end": 3369, + "start": 3737, + "end": 3809, "loc": { "start": { - "line": 97, + "line": 113, "column": 6 }, "end": { - "line": 97, + "line": 113, "column": 78 } } @@ -5595,15 +6375,15 @@ { "type": "CommentLine", "value": " list of external specifiers first.", - "start": 3376, - "end": 3413, + "start": 3816, + "end": 3853, "loc": { "start": { - "line": 98, + "line": 114, "column": 6 }, "end": { - "line": 98, + "line": 114, "column": 43 } } @@ -5612,43 +6392,43 @@ }, { "type": "IfStatement", - "start": 3478, - "end": 3537, + "start": 3918, + "end": 3977, "loc": { "start": { - "line": 100, + "line": 116, "column": 6 }, "end": { - "line": 100, + "line": 116, "column": 65 } }, "test": { "type": "BinaryExpression", - "start": 3482, - "end": 3494, + "start": 3922, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 10 }, "end": { - "line": 100, + "line": 116, "column": 22 } }, "left": { "type": "Identifier", - "start": 3482, - "end": 3487, + "start": 3922, + "end": 3927, "loc": { "start": { - "line": 100, + "line": 116, "column": 10 }, "end": { - "line": 100, + "line": 116, "column": 15 }, "identifierName": "index" @@ -5658,15 +6438,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 3492, - "end": 3494, + "start": 3932, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 20 }, "end": { - "line": 100, + "line": 116, "column": 22 } }, @@ -5674,15 +6454,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 3493, - "end": 3494, + "start": 3933, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 21 }, "end": { - "line": 100, + "line": 116, "column": 22 } }, @@ -5699,86 +6479,86 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 3496, - "end": 3537, + "start": 3936, + "end": 3977, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 65 } }, "expression": { "type": "CallExpression", - "start": 3496, - "end": 3536, + "start": 3936, + "end": 3976, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 64 } }, "callee": { "type": "MemberExpression", - "start": 3496, - "end": 3526, + "start": 3936, + "end": 3966, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 3496, - "end": 3519, + "start": 3936, + "end": 3959, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 3496, - "end": 3500, + "start": 3936, + "end": 3940, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 28 } } }, "property": { "type": "Identifier", - "start": 3501, - "end": 3519, + "start": 3941, + "end": 3959, "loc": { "start": { - "line": 100, + "line": 116, "column": 29 }, "end": { - "line": 100, + "line": 116, "column": 47 }, "identifierName": "externalSpecifiers" @@ -5789,15 +6569,15 @@ }, "property": { "type": "Identifier", - "start": 3520, - "end": 3526, + "start": 3960, + "end": 3966, "loc": { "start": { - "line": 100, + "line": 116, "column": 48 }, "end": { - "line": 100, + "line": 116, "column": 54 }, "identifierName": "splice" @@ -5809,15 +6589,15 @@ "arguments": [ { "type": "Identifier", - "start": 3527, - "end": 3532, + "start": 3967, + "end": 3972, "loc": { "start": { - "line": 100, + "line": 116, "column": 55 }, "end": { - "line": 100, + "line": 116, "column": 60 }, "identifierName": "index" @@ -5826,15 +6606,15 @@ }, { "type": "NumericLiteral", - "start": 3534, - "end": 3535, + "start": 3974, + "end": 3975, "loc": { "start": { - "line": 100, + "line": 116, "column": 62 }, "end": { - "line": 100, + "line": 116, "column": 63 } }, @@ -5853,15 +6633,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 3545, - "end": 3618, + "start": 3985, + "end": 4058, "loc": { "start": { - "line": 102, + "line": 118, "column": 6 }, "end": { - "line": 102, + "line": 118, "column": 79 } } @@ -5870,29 +6650,29 @@ }, { "type": "IfStatement", - "start": 3625, - "end": 3745, + "start": 4065, + "end": 4185, "loc": { "start": { - "line": 103, + "line": 119, "column": 6 }, "end": { - "line": 105, + "line": 121, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 3629, - "end": 3673, + "start": 4069, + "end": 4113, "loc": { "start": { - "line": 103, + "line": 119, "column": 10 }, "end": { - "line": 103, + "line": 119, "column": 54 } }, @@ -5900,57 +6680,57 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 3630, - "end": 3673, + "start": 4070, + "end": 4113, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 54 } }, "callee": { "type": "MemberExpression", - "start": 3630, - "end": 3662, + "start": 4070, + "end": 4102, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 43 } }, "object": { "type": "MemberExpression", - "start": 3630, - "end": 3653, + "start": 4070, + "end": 4093, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 34 } }, "object": { "type": "ThisExpression", - "start": 3630, - "end": 3634, + "start": 4070, + "end": 4074, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 15 } }, @@ -5958,15 +6738,15 @@ }, "property": { "type": "Identifier", - "start": 3635, - "end": 3653, + "start": 4075, + "end": 4093, "loc": { "start": { - "line": 103, + "line": 119, "column": 16 }, "end": { - "line": 103, + "line": 119, "column": 34 }, "identifierName": "internalSpecifiers" @@ -5978,15 +6758,15 @@ }, "property": { "type": "Identifier", - "start": 3654, - "end": 3662, + "start": 4094, + "end": 4102, "loc": { "start": { - "line": 103, + "line": 119, "column": 35 }, "end": { - "line": 103, + "line": 119, "column": 43 }, "identifierName": "includes" @@ -5999,15 +6779,15 @@ "arguments": [ { "type": "Identifier", - "start": 3663, - "end": 3672, + "start": 4103, + "end": 4112, "loc": { "start": { - "line": 103, + "line": 119, "column": 44 }, "end": { - "line": 103, + "line": 119, "column": 53 }, "identifierName": "specifier" @@ -6024,115 +6804,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 3675, - "end": 3745, + "start": 4115, + "end": 4185, "loc": { "start": { - "line": 103, + "line": 119, "column": 56 }, "end": { - "line": 105, + "line": 121, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 3685, - "end": 3737, + "start": 4125, + "end": 4177, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 60 } }, "expression": { "type": "CallExpression", - "start": 3685, - "end": 3736, + "start": 4125, + "end": 4176, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 3685, - "end": 3725, + "start": 4125, + "end": 4165, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 48 } }, "object": { "type": "MemberExpression", - "start": 3685, - "end": 3717, + "start": 4125, + "end": 4157, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 3685, - "end": 3698, + "start": 4125, + "end": 4138, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 21 } }, "object": { "type": "ThisExpression", - "start": 3685, - "end": 3689, + "start": 4125, + "end": 4129, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 12 } } }, "property": { "type": "Identifier", - "start": 3690, - "end": 3698, + "start": 4130, + "end": 4138, "loc": { "start": { - "line": 104, + "line": 120, "column": 13 }, "end": { - "line": 104, + "line": 120, "column": 21 }, "identifierName": "phyloref" @@ -6143,15 +6923,15 @@ }, "property": { "type": "Identifier", - "start": 3699, - "end": 3717, + "start": 4139, + "end": 4157, "loc": { "start": { - "line": 104, + "line": 120, "column": 22 }, "end": { - "line": 104, + "line": 120, "column": 40 }, "identifierName": "internalSpecifiers" @@ -6162,15 +6942,15 @@ }, "property": { "type": "Identifier", - "start": 3718, - "end": 3725, + "start": 4158, + "end": 4165, "loc": { "start": { - "line": 104, + "line": 120, "column": 41 }, "end": { - "line": 104, + "line": 120, "column": 48 }, "identifierName": "unshift" @@ -6182,15 +6962,15 @@ "arguments": [ { "type": "Identifier", - "start": 3726, - "end": 3735, + "start": 4166, + "end": 4175, "loc": { "start": { - "line": 104, + "line": 120, "column": 49 }, "end": { - "line": 104, + "line": 120, "column": 58 }, "identifierName": "specifier" @@ -6208,15 +6988,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 3545, - "end": 3618, + "start": 3985, + "end": 4058, "loc": { "start": { - "line": 102, + "line": 118, "column": 6 }, "end": { - "line": 102, + "line": 118, "column": 79 } } @@ -6228,43 +7008,43 @@ }, "alternate": { "type": "IfStatement", - "start": 3757, - "end": 4341, + "start": 4197, + "end": 4781, "loc": { "start": { - "line": 106, + "line": 122, "column": 11 }, "end": { - "line": 118, + "line": 134, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 3761, - "end": 3789, + "start": 4201, + "end": 4229, "loc": { "start": { - "line": 106, + "line": 122, "column": 15 }, "end": { - "line": 106, + "line": 122, "column": 43 } }, "left": { "type": "Identifier", - "start": 3761, - "end": 3774, + "start": 4201, + "end": 4214, "loc": { "start": { - "line": 106, + "line": 122, "column": 15 }, "end": { - "line": 106, + "line": 122, "column": 28 }, "identifierName": "specifierType" @@ -6274,15 +7054,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 3779, - "end": 3789, + "start": 4219, + "end": 4229, "loc": { "start": { - "line": 106, + "line": 122, "column": 33 }, "end": { - "line": 106, + "line": 122, "column": 43 } }, @@ -6295,59 +7075,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 3791, - "end": 4280, + "start": 4231, + "end": 4720, "loc": { "start": { - "line": 106, + "line": 122, "column": 45 }, "end": { - "line": 116, + "line": 132, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3922, - "end": 3982, + "start": 4362, + "end": 4422, "loc": { "start": { - "line": 109, + "line": 125, "column": 6 }, "end": { - "line": 109, + "line": 125, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 3922, - "end": 3981, + "start": 4362, + "end": 4421, "loc": { "start": { - "line": 109, + "line": 125, "column": 6 }, "end": { - "line": 109, + "line": 125, "column": 65 } }, "operator": "=", "left": { "type": "Identifier", - "start": 3922, - "end": 3927, + "start": 4362, + "end": 4367, "loc": { "start": { - "line": 109, + "line": 125, "column": 6 }, "end": { - "line": 109, + "line": 125, "column": 11 }, "identifierName": "index" @@ -6357,86 +7137,86 @@ }, "right": { "type": "CallExpression", - "start": 3930, - "end": 3981, + "start": 4370, + "end": 4421, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 3930, - "end": 3970, + "start": 4370, + "end": 4410, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 3930, - "end": 3962, + "start": 4370, + "end": 4402, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 46 } }, "object": { "type": "MemberExpression", - "start": 3930, - "end": 3943, + "start": 4370, + "end": 4383, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 3930, - "end": 3934, + "start": 4370, + "end": 4374, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 18 } } }, "property": { "type": "Identifier", - "start": 3935, - "end": 3943, + "start": 4375, + "end": 4383, "loc": { "start": { - "line": 109, + "line": 125, "column": 19 }, "end": { - "line": 109, + "line": 125, "column": 27 }, "identifierName": "phyloref" @@ -6447,15 +7227,15 @@ }, "property": { "type": "Identifier", - "start": 3944, - "end": 3962, + "start": 4384, + "end": 4402, "loc": { "start": { - "line": 109, + "line": 125, "column": 28 }, "end": { - "line": 109, + "line": 125, "column": 46 }, "identifierName": "internalSpecifiers" @@ -6466,15 +7246,15 @@ }, "property": { "type": "Identifier", - "start": 3963, - "end": 3970, + "start": 4403, + "end": 4410, "loc": { "start": { - "line": 109, + "line": 125, "column": 47 }, "end": { - "line": 109, + "line": 125, "column": 54 }, "identifierName": "indexOf" @@ -6486,15 +7266,15 @@ "arguments": [ { "type": "Identifier", - "start": 3971, - "end": 3980, + "start": 4411, + "end": 4420, "loc": { "start": { - "line": 109, + "line": 125, "column": 55 }, "end": { - "line": 109, + "line": 125, "column": 64 }, "identifierName": "specifier" @@ -6509,15 +7289,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'External', we might need to delete it from the", - "start": 3799, - "end": 3871, + "start": 4239, + "end": 4311, "loc": { "start": { - "line": 107, + "line": 123, "column": 6 }, "end": { - "line": 107, + "line": 123, "column": 78 } } @@ -6525,15 +7305,15 @@ { "type": "CommentLine", "value": " list of internal specifiers first.", - "start": 3878, - "end": 3915, + "start": 4318, + "end": 4355, "loc": { "start": { - "line": 108, + "line": 124, "column": 6 }, "end": { - "line": 108, + "line": 124, "column": 43 } } @@ -6542,43 +7322,43 @@ }, { "type": "IfStatement", - "start": 3989, - "end": 4057, + "start": 4429, + "end": 4497, "loc": { "start": { - "line": 110, + "line": 126, "column": 6 }, "end": { - "line": 110, + "line": 126, "column": 74 } }, "test": { "type": "BinaryExpression", - "start": 3993, - "end": 4005, + "start": 4433, + "end": 4445, "loc": { "start": { - "line": 110, + "line": 126, "column": 10 }, "end": { - "line": 110, + "line": 126, "column": 22 } }, "left": { "type": "Identifier", - "start": 3993, - "end": 3998, + "start": 4433, + "end": 4438, "loc": { "start": { - "line": 110, + "line": 126, "column": 10 }, "end": { - "line": 110, + "line": 126, "column": 15 }, "identifierName": "index" @@ -6588,15 +7368,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 4003, - "end": 4005, + "start": 4443, + "end": 4445, "loc": { "start": { - "line": 110, + "line": 126, "column": 20 }, "end": { - "line": 110, + "line": 126, "column": 22 } }, @@ -6604,15 +7384,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 4004, - "end": 4005, + "start": 4444, + "end": 4445, "loc": { "start": { - "line": 110, + "line": 126, "column": 21 }, "end": { - "line": 110, + "line": 126, "column": 22 } }, @@ -6629,100 +7409,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 4007, - "end": 4057, + "start": 4447, + "end": 4497, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 74 } }, "expression": { "type": "CallExpression", - "start": 4007, - "end": 4056, + "start": 4447, + "end": 4496, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 4007, - "end": 4046, + "start": 4447, + "end": 4486, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 4007, - "end": 4039, + "start": 4447, + "end": 4479, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 56 } }, "object": { "type": "MemberExpression", - "start": 4007, - "end": 4020, + "start": 4447, + "end": 4460, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 4007, - "end": 4011, + "start": 4447, + "end": 4451, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 28 } } }, "property": { "type": "Identifier", - "start": 4012, - "end": 4020, + "start": 4452, + "end": 4460, "loc": { "start": { - "line": 110, + "line": 126, "column": 29 }, "end": { - "line": 110, + "line": 126, "column": 37 }, "identifierName": "phyloref" @@ -6733,15 +7513,15 @@ }, "property": { "type": "Identifier", - "start": 4021, - "end": 4039, + "start": 4461, + "end": 4479, "loc": { "start": { - "line": 110, + "line": 126, "column": 38 }, "end": { - "line": 110, + "line": 126, "column": 56 }, "identifierName": "internalSpecifiers" @@ -6752,15 +7532,15 @@ }, "property": { "type": "Identifier", - "start": 4040, - "end": 4046, + "start": 4480, + "end": 4486, "loc": { "start": { - "line": 110, + "line": 126, "column": 57 }, "end": { - "line": 110, + "line": 126, "column": 63 }, "identifierName": "splice" @@ -6772,15 +7552,15 @@ "arguments": [ { "type": "Identifier", - "start": 4047, - "end": 4052, + "start": 4487, + "end": 4492, "loc": { "start": { - "line": 110, + "line": 126, "column": 64 }, "end": { - "line": 110, + "line": 126, "column": 69 }, "identifierName": "index" @@ -6789,15 +7569,15 @@ }, { "type": "NumericLiteral", - "start": 4054, - "end": 4055, + "start": 4494, + "end": 4495, "loc": { "start": { - "line": 110, + "line": 126, "column": 71 }, "end": { - "line": 110, + "line": 126, "column": 72 } }, @@ -6816,15 +7596,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 4065, - "end": 4138, + "start": 4505, + "end": 4578, "loc": { "start": { - "line": 112, + "line": 128, "column": 6 }, "end": { - "line": 112, + "line": 128, "column": 79 } } @@ -6833,29 +7613,29 @@ }, { "type": "IfStatement", - "start": 4145, - "end": 4274, + "start": 4585, + "end": 4714, "loc": { "start": { - "line": 113, + "line": 129, "column": 6 }, "end": { - "line": 115, + "line": 131, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 4149, - "end": 4202, + "start": 4589, + "end": 4642, "loc": { "start": { - "line": 113, + "line": 129, "column": 10 }, "end": { - "line": 113, + "line": 129, "column": 63 } }, @@ -6863,71 +7643,71 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 4150, - "end": 4202, + "start": 4590, + "end": 4642, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 4150, - "end": 4191, + "start": 4590, + "end": 4631, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 4150, - "end": 4182, + "start": 4590, + "end": 4622, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 43 } }, "object": { "type": "MemberExpression", - "start": 4150, - "end": 4163, + "start": 4590, + "end": 4603, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 24 } }, "object": { "type": "ThisExpression", - "start": 4150, - "end": 4154, + "start": 4590, + "end": 4594, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 15 } }, @@ -6935,15 +7715,15 @@ }, "property": { "type": "Identifier", - "start": 4155, - "end": 4163, + "start": 4595, + "end": 4603, "loc": { "start": { - "line": 113, + "line": 129, "column": 16 }, "end": { - "line": 113, + "line": 129, "column": 24 }, "identifierName": "phyloref" @@ -6955,15 +7735,15 @@ }, "property": { "type": "Identifier", - "start": 4164, - "end": 4182, + "start": 4604, + "end": 4622, "loc": { "start": { - "line": 113, + "line": 129, "column": 25 }, "end": { - "line": 113, + "line": 129, "column": 43 }, "identifierName": "externalSpecifiers" @@ -6975,15 +7755,15 @@ }, "property": { "type": "Identifier", - "start": 4183, - "end": 4191, + "start": 4623, + "end": 4631, "loc": { "start": { - "line": 113, + "line": 129, "column": 44 }, "end": { - "line": 113, + "line": 129, "column": 52 }, "identifierName": "includes" @@ -6996,15 +7776,15 @@ "arguments": [ { "type": "Identifier", - "start": 4192, - "end": 4201, + "start": 4632, + "end": 4641, "loc": { "start": { - "line": 113, + "line": 129, "column": 53 }, "end": { - "line": 113, + "line": 129, "column": 62 }, "identifierName": "specifier" @@ -7021,115 +7801,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 4204, - "end": 4274, + "start": 4644, + "end": 4714, "loc": { "start": { - "line": 113, + "line": 129, "column": 65 }, "end": { - "line": 115, + "line": 131, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 4214, - "end": 4266, + "start": 4654, + "end": 4706, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 60 } }, "expression": { "type": "CallExpression", - "start": 4214, - "end": 4265, + "start": 4654, + "end": 4705, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 4214, - "end": 4254, + "start": 4654, + "end": 4694, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 48 } }, "object": { "type": "MemberExpression", - "start": 4214, - "end": 4246, + "start": 4654, + "end": 4686, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 4214, - "end": 4227, + "start": 4654, + "end": 4667, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 21 } }, "object": { "type": "ThisExpression", - "start": 4214, - "end": 4218, + "start": 4654, + "end": 4658, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 12 } } }, "property": { "type": "Identifier", - "start": 4219, - "end": 4227, + "start": 4659, + "end": 4667, "loc": { "start": { - "line": 114, + "line": 130, "column": 13 }, "end": { - "line": 114, + "line": 130, "column": 21 }, "identifierName": "phyloref" @@ -7140,15 +7920,15 @@ }, "property": { "type": "Identifier", - "start": 4228, - "end": 4246, + "start": 4668, + "end": 4686, "loc": { "start": { - "line": 114, + "line": 130, "column": 22 }, "end": { - "line": 114, + "line": 130, "column": 40 }, "identifierName": "externalSpecifiers" @@ -7159,15 +7939,15 @@ }, "property": { "type": "Identifier", - "start": 4247, - "end": 4254, + "start": 4687, + "end": 4694, "loc": { "start": { - "line": 114, + "line": 130, "column": 41 }, "end": { - "line": 114, + "line": 130, "column": 48 }, "identifierName": "unshift" @@ -7179,15 +7959,15 @@ "arguments": [ { "type": "Identifier", - "start": 4255, - "end": 4264, + "start": 4695, + "end": 4704, "loc": { "start": { - "line": 114, + "line": 130, "column": 49 }, "end": { - "line": 114, + "line": 130, "column": 58 }, "identifierName": "specifier" @@ -7205,15 +7985,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 4065, - "end": 4138, + "start": 4505, + "end": 4578, "loc": { "start": { - "line": 112, + "line": 128, "column": 6 }, "end": { - "line": 112, + "line": 128, "column": 79 } } @@ -7225,15 +8005,15 @@ }, "alternate": { "type": "BlockStatement", - "start": 4286, - "end": 4341, + "start": 4726, + "end": 4781, "loc": { "start": { - "line": 116, + "line": 132, "column": 11 }, "end": { - "line": 118, + "line": 134, "column": 5 } }, @@ -7244,15 +8024,15 @@ { "type": "CommentLine", "value": " Neither internal nor external? Ignore.", - "start": 4294, - "end": 4335, + "start": 4734, + "end": 4775, "loc": { "start": { - "line": 117, + "line": 133, "column": 6 }, "end": { - "line": 117, + "line": 133, "column": 47 } } @@ -7267,15 +8047,15 @@ }, { "type": "ClassMethod", - "start": 4349, - "end": 5102, + "start": 4789, + "end": 5542, "loc": { "start": { - "line": 121, + "line": 137, "column": 2 }, "end": { - "line": 135, + "line": 151, "column": 3 } }, @@ -7283,15 +8063,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4349, - "end": 4364, + "start": 4789, + "end": 4804, "loc": { "start": { - "line": 121, + "line": 137, "column": 2 }, "end": { - "line": 121, + "line": 137, "column": 17 }, "identifierName": "deleteSpecifier" @@ -7306,15 +8086,15 @@ "params": [ { "type": "Identifier", - "start": 4365, - "end": 4374, + "start": 4805, + "end": 4814, "loc": { "start": { - "line": 121, + "line": 137, "column": 18 }, "end": { - "line": 121, + "line": 137, "column": 27 }, "identifierName": "specifier" @@ -7324,72 +8104,72 @@ ], "body": { "type": "BlockStatement", - "start": 4376, - "end": 5102, + "start": 4816, + "end": 5542, "loc": { "start": { - "line": 121, + "line": 137, "column": 29 }, "end": { - "line": 135, + "line": 151, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4596, - "end": 4844, + "start": 5036, + "end": 5284, "loc": { "start": { - "line": 126, + "line": 142, "column": 4 }, "end": { - "line": 129, + "line": 145, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 4600, - "end": 4687, + "start": 5040, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 95 } }, "left": { "type": "CallExpression", - "start": 4600, - "end": 4640, + "start": 5040, + "end": 5080, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 48 } }, "callee": { "type": "Identifier", - "start": 4600, - "end": 4603, + "start": 5040, + "end": 5043, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 11 }, "identifierName": "has" @@ -7400,44 +8180,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4604, - "end": 4617, + "start": 5044, + "end": 5057, "loc": { "start": { - "line": 126, + "line": 142, "column": 12 }, "end": { - "line": 126, + "line": 142, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4604, - "end": 4608, + "start": 5044, + "end": 5048, "loc": { "start": { - "line": 126, + "line": 142, "column": 12 }, "end": { - "line": 126, + "line": 142, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4609, - "end": 4617, + "start": 5049, + "end": 5057, "loc": { "start": { - "line": 126, + "line": 142, "column": 17 }, "end": { - "line": 126, + "line": 142, "column": 25 }, "identifierName": "phyloref" @@ -7448,15 +8228,15 @@ }, { "type": "StringLiteral", - "start": 4619, - "end": 4639, + "start": 5059, + "end": 5079, "loc": { "start": { - "line": 126, + "line": 142, "column": 27 }, "end": { - "line": 126, + "line": 142, "column": 47 } }, @@ -7472,86 +8252,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 4644, - "end": 4687, + "start": 5084, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 95 } }, "left": { "type": "MemberExpression", - "start": 4644, - "end": 4683, + "start": 5084, + "end": 5123, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 91 } }, "object": { "type": "MemberExpression", - "start": 4644, - "end": 4676, + "start": 5084, + "end": 5116, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 84 } }, "object": { "type": "MemberExpression", - "start": 4644, - "end": 4657, + "start": 5084, + "end": 5097, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 4644, - "end": 4648, + "start": 5084, + "end": 5088, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 56 } } }, "property": { "type": "Identifier", - "start": 4649, - "end": 4657, + "start": 5089, + "end": 5097, "loc": { "start": { - "line": 126, + "line": 142, "column": 57 }, "end": { - "line": 126, + "line": 142, "column": 65 }, "identifierName": "phyloref" @@ -7562,15 +8342,15 @@ }, "property": { "type": "Identifier", - "start": 4658, - "end": 4676, + "start": 5098, + "end": 5116, "loc": { "start": { - "line": 126, + "line": 142, "column": 66 }, "end": { - "line": 126, + "line": 142, "column": 84 }, "identifierName": "internalSpecifiers" @@ -7581,15 +8361,15 @@ }, "property": { "type": "Identifier", - "start": 4677, - "end": 4683, + "start": 5117, + "end": 5123, "loc": { "start": { - "line": 126, + "line": 142, "column": 85 }, "end": { - "line": 126, + "line": 142, "column": 91 }, "identifierName": "length" @@ -7601,15 +8381,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 4686, - "end": 4687, + "start": 5126, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 94 }, "end": { - "line": 126, + "line": 142, "column": 95 } }, @@ -7624,59 +8404,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4689, - "end": 4844, + "start": 5129, + "end": 5284, "loc": { "start": { - "line": 126, + "line": 142, "column": 97 }, "end": { - "line": 129, + "line": 145, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 4697, - "end": 4763, + "start": 5137, + "end": 5203, "loc": { "start": { - "line": 127, + "line": 143, "column": 6 }, "end": { - "line": 127, + "line": 143, "column": 72 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4703, - "end": 4762, + "start": 5143, + "end": 5202, "loc": { "start": { - "line": 127, + "line": 143, "column": 12 }, "end": { - "line": 127, + "line": 143, "column": 71 } }, "id": { "type": "Identifier", - "start": 4703, - "end": 4708, + "start": 5143, + "end": 5148, "loc": { "start": { - "line": 127, + "line": 143, "column": 12 }, "end": { - "line": 127, + "line": 143, "column": 17 }, "identifierName": "index" @@ -7685,86 +8465,86 @@ }, "init": { "type": "CallExpression", - "start": 4711, - "end": 4762, + "start": 5151, + "end": 5202, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 4711, - "end": 4751, + "start": 5151, + "end": 5191, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 4711, - "end": 4743, + "start": 5151, + "end": 5183, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 4711, - "end": 4724, + "start": 5151, + "end": 5164, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 4711, - "end": 4715, + "start": 5151, + "end": 5155, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 24 } } }, "property": { "type": "Identifier", - "start": 4716, - "end": 4724, + "start": 5156, + "end": 5164, "loc": { "start": { - "line": 127, + "line": 143, "column": 25 }, "end": { - "line": 127, + "line": 143, "column": 33 }, "identifierName": "phyloref" @@ -7775,15 +8555,15 @@ }, "property": { "type": "Identifier", - "start": 4725, - "end": 4743, + "start": 5165, + "end": 5183, "loc": { "start": { - "line": 127, + "line": 143, "column": 34 }, "end": { - "line": 127, + "line": 143, "column": 52 }, "identifierName": "internalSpecifiers" @@ -7794,15 +8574,15 @@ }, "property": { "type": "Identifier", - "start": 4744, - "end": 4751, + "start": 5184, + "end": 5191, "loc": { "start": { - "line": 127, + "line": 143, "column": 53 }, "end": { - "line": 127, + "line": 143, "column": 60 }, "identifierName": "indexOf" @@ -7814,15 +8594,15 @@ "arguments": [ { "type": "Identifier", - "start": 4752, - "end": 4761, + "start": 5192, + "end": 5201, "loc": { "start": { - "line": 127, + "line": 143, "column": 61 }, "end": { - "line": 127, + "line": 143, "column": 70 }, "identifierName": "specifier" @@ -7837,43 +8617,43 @@ }, { "type": "IfStatement", - "start": 4770, - "end": 4838, + "start": 5210, + "end": 5278, "loc": { "start": { - "line": 128, + "line": 144, "column": 6 }, "end": { - "line": 128, + "line": 144, "column": 74 } }, "test": { "type": "BinaryExpression", - "start": 4774, - "end": 4786, + "start": 5214, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 10 }, "end": { - "line": 128, + "line": 144, "column": 22 } }, "left": { "type": "Identifier", - "start": 4774, - "end": 4779, + "start": 5214, + "end": 5219, "loc": { "start": { - "line": 128, + "line": 144, "column": 10 }, "end": { - "line": 128, + "line": 144, "column": 15 }, "identifierName": "index" @@ -7883,15 +8663,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 4784, - "end": 4786, + "start": 5224, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 20 }, "end": { - "line": 128, + "line": 144, "column": 22 } }, @@ -7899,15 +8679,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 4785, - "end": 4786, + "start": 5225, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 21 }, "end": { - "line": 128, + "line": 144, "column": 22 } }, @@ -7924,100 +8704,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 4788, - "end": 4838, + "start": 5228, + "end": 5278, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 74 } }, "expression": { "type": "CallExpression", - "start": 4788, - "end": 4837, + "start": 5228, + "end": 5277, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 4788, - "end": 4827, + "start": 5228, + "end": 5267, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 4788, - "end": 4820, + "start": 5228, + "end": 5260, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 56 } }, "object": { "type": "MemberExpression", - "start": 4788, - "end": 4801, + "start": 5228, + "end": 5241, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 4788, - "end": 4792, + "start": 5228, + "end": 5232, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 28 } } }, "property": { "type": "Identifier", - "start": 4793, - "end": 4801, + "start": 5233, + "end": 5241, "loc": { "start": { - "line": 128, + "line": 144, "column": 29 }, "end": { - "line": 128, + "line": 144, "column": 37 }, "identifierName": "phyloref" @@ -8028,15 +8808,15 @@ }, "property": { "type": "Identifier", - "start": 4802, - "end": 4820, + "start": 5242, + "end": 5260, "loc": { "start": { - "line": 128, + "line": 144, "column": 38 }, "end": { - "line": 128, + "line": 144, "column": 56 }, "identifierName": "internalSpecifiers" @@ -8047,15 +8827,15 @@ }, "property": { "type": "Identifier", - "start": 4821, - "end": 4827, + "start": 5261, + "end": 5267, "loc": { "start": { - "line": 128, + "line": 144, "column": 57 }, "end": { - "line": 128, + "line": 144, "column": 63 }, "identifierName": "splice" @@ -8067,15 +8847,15 @@ "arguments": [ { "type": "Identifier", - "start": 4828, - "end": 4833, + "start": 5268, + "end": 5273, "loc": { "start": { - "line": 128, + "line": 144, "column": 64 }, "end": { - "line": 128, + "line": 144, "column": 69 }, "identifierName": "index" @@ -8084,15 +8864,15 @@ }, { "type": "NumericLiteral", - "start": 4835, - "end": 4836, + "start": 5275, + "end": 5276, "loc": { "start": { - "line": 128, + "line": 144, "column": 71 }, "end": { - "line": 128, + "line": 144, "column": 72 } }, @@ -8115,15 +8895,15 @@ { "type": "CommentLine", "value": " Since the user interface combines specifiers into a single list,", - "start": 4382, - "end": 4449, + "start": 4822, + "end": 4889, "loc": { "start": { - "line": 122, + "line": 138, "column": 4 }, "end": { - "line": 122, + "line": 138, "column": 71 } } @@ -8131,15 +8911,15 @@ { "type": "CommentLine", "value": " it doesn't remember if the specifier to be deleted is internal", - "start": 4454, - "end": 4519, + "start": 4894, + "end": 4959, "loc": { "start": { - "line": 123, + "line": 139, "column": 4 }, "end": { - "line": 123, + "line": 139, "column": 69 } } @@ -8147,15 +8927,15 @@ { "type": "CommentLine", "value": " or external. We delete the intended specifier from both arrays.", - "start": 4524, - "end": 4590, + "start": 4964, + "end": 5030, "loc": { "start": { - "line": 124, + "line": 140, "column": 4 }, "end": { - "line": 124, + "line": 140, "column": 70 } } @@ -8164,57 +8944,57 @@ }, { "type": "IfStatement", - "start": 4850, - "end": 5098, + "start": 5290, + "end": 5538, "loc": { "start": { - "line": 131, + "line": 147, "column": 4 }, "end": { - "line": 134, + "line": 150, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 4854, - "end": 4941, + "start": 5294, + "end": 5381, "loc": { "start": { - "line": 131, + "line": 147, "column": 8 }, "end": { - "line": 131, + "line": 147, "column": 95 } }, "left": { "type": "CallExpression", - "start": 4854, - "end": 4894, + "start": 5294, + "end": 5334, "loc": { "start": { - "line": 131, + "line": 147, "column": 8 }, "end": { - "line": 131, + "line": 147, "column": 48 } }, "callee": { "type": "Identifier", - "start": 4854, - "end": 4857, + "start": 5294, + "end": 5297, "loc": { "start": { - "line": 131, + "line": 147, "column": 8 }, "end": { - "line": 131, + "line": 147, "column": 11 }, "identifierName": "has" @@ -8224,44 +9004,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4858, - "end": 4871, + "start": 5298, + "end": 5311, "loc": { "start": { - "line": 131, + "line": 147, "column": 12 }, "end": { - "line": 131, + "line": 147, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4858, - "end": 4862, + "start": 5298, + "end": 5302, "loc": { "start": { - "line": 131, + "line": 147, "column": 12 }, "end": { - "line": 131, + "line": 147, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4863, - "end": 4871, + "start": 5303, + "end": 5311, "loc": { "start": { - "line": 131, + "line": 147, "column": 17 }, "end": { - "line": 131, + "line": 147, "column": 25 }, "identifierName": "phyloref" @@ -8272,15 +9052,15 @@ }, { "type": "StringLiteral", - "start": 4873, - "end": 4893, + "start": 5313, + "end": 5333, "loc": { "start": { - "line": 131, + "line": 147, "column": 27 }, "end": { - "line": 131, + "line": 147, "column": 47 } }, @@ -8295,86 +9075,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 4898, - "end": 4941, + "start": 5338, + "end": 5381, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 95 } }, "left": { "type": "MemberExpression", - "start": 4898, - "end": 4937, + "start": 5338, + "end": 5377, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 91 } }, "object": { "type": "MemberExpression", - "start": 4898, - "end": 4930, + "start": 5338, + "end": 5370, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 84 } }, "object": { "type": "MemberExpression", - "start": 4898, - "end": 4911, + "start": 5338, + "end": 5351, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 4898, - "end": 4902, + "start": 5338, + "end": 5342, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 56 } } }, "property": { "type": "Identifier", - "start": 4903, - "end": 4911, + "start": 5343, + "end": 5351, "loc": { "start": { - "line": 131, + "line": 147, "column": 57 }, "end": { - "line": 131, + "line": 147, "column": 65 }, "identifierName": "phyloref" @@ -8385,15 +9165,15 @@ }, "property": { "type": "Identifier", - "start": 4912, - "end": 4930, + "start": 5352, + "end": 5370, "loc": { "start": { - "line": 131, + "line": 147, "column": 66 }, "end": { - "line": 131, + "line": 147, "column": 84 }, "identifierName": "externalSpecifiers" @@ -8404,15 +9184,15 @@ }, "property": { "type": "Identifier", - "start": 4931, - "end": 4937, + "start": 5371, + "end": 5377, "loc": { "start": { - "line": 131, + "line": 147, "column": 85 }, "end": { - "line": 131, + "line": 147, "column": 91 }, "identifierName": "length" @@ -8424,15 +9204,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 4940, - "end": 4941, + "start": 5380, + "end": 5381, "loc": { "start": { - "line": 131, + "line": 147, "column": 94 }, "end": { - "line": 131, + "line": 147, "column": 95 } }, @@ -8446,59 +9226,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4943, - "end": 5098, + "start": 5383, + "end": 5538, "loc": { "start": { - "line": 131, + "line": 147, "column": 97 }, "end": { - "line": 134, + "line": 150, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 4951, - "end": 5017, + "start": 5391, + "end": 5457, "loc": { "start": { - "line": 132, + "line": 148, "column": 6 }, "end": { - "line": 132, + "line": 148, "column": 72 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4957, - "end": 5016, + "start": 5397, + "end": 5456, "loc": { "start": { - "line": 132, + "line": 148, "column": 12 }, "end": { - "line": 132, + "line": 148, "column": 71 } }, "id": { "type": "Identifier", - "start": 4957, - "end": 4962, + "start": 5397, + "end": 5402, "loc": { "start": { - "line": 132, + "line": 148, "column": 12 }, "end": { - "line": 132, + "line": 148, "column": 17 }, "identifierName": "index" @@ -8507,86 +9287,86 @@ }, "init": { "type": "CallExpression", - "start": 4965, - "end": 5016, + "start": 5405, + "end": 5456, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 4965, - "end": 5005, + "start": 5405, + "end": 5445, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 4965, - "end": 4997, + "start": 5405, + "end": 5437, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 4965, - "end": 4978, + "start": 5405, + "end": 5418, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 4965, - "end": 4969, + "start": 5405, + "end": 5409, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 24 } } }, "property": { "type": "Identifier", - "start": 4970, - "end": 4978, + "start": 5410, + "end": 5418, "loc": { "start": { - "line": 132, + "line": 148, "column": 25 }, "end": { - "line": 132, + "line": 148, "column": 33 }, "identifierName": "phyloref" @@ -8597,15 +9377,15 @@ }, "property": { "type": "Identifier", - "start": 4979, - "end": 4997, + "start": 5419, + "end": 5437, "loc": { "start": { - "line": 132, + "line": 148, "column": 34 }, "end": { - "line": 132, + "line": 148, "column": 52 }, "identifierName": "externalSpecifiers" @@ -8616,15 +9396,15 @@ }, "property": { "type": "Identifier", - "start": 4998, - "end": 5005, + "start": 5438, + "end": 5445, "loc": { "start": { - "line": 132, + "line": 148, "column": 53 }, "end": { - "line": 132, + "line": 148, "column": 60 }, "identifierName": "indexOf" @@ -8636,15 +9416,15 @@ "arguments": [ { "type": "Identifier", - "start": 5006, - "end": 5015, + "start": 5446, + "end": 5455, "loc": { "start": { - "line": 132, + "line": 148, "column": 61 }, "end": { - "line": 132, + "line": 148, "column": 70 }, "identifierName": "specifier" @@ -8659,43 +9439,43 @@ }, { "type": "IfStatement", - "start": 5024, - "end": 5092, + "start": 5464, + "end": 5532, "loc": { "start": { - "line": 133, + "line": 149, "column": 6 }, "end": { - "line": 133, + "line": 149, "column": 74 } }, "test": { "type": "BinaryExpression", - "start": 5028, - "end": 5040, + "start": 5468, + "end": 5480, "loc": { "start": { - "line": 133, + "line": 149, "column": 10 }, "end": { - "line": 133, + "line": 149, "column": 22 } }, "left": { "type": "Identifier", - "start": 5028, - "end": 5033, + "start": 5468, + "end": 5473, "loc": { "start": { - "line": 133, + "line": 149, "column": 10 }, "end": { - "line": 133, + "line": 149, "column": 15 }, "identifierName": "index" @@ -8705,15 +9485,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 5038, - "end": 5040, + "start": 5478, + "end": 5480, "loc": { "start": { - "line": 133, + "line": 149, "column": 20 }, "end": { - "line": 133, + "line": 149, "column": 22 } }, @@ -8721,15 +9501,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 5039, - "end": 5040, + "start": 5479, + "end": 5480, "loc": { "start": { - "line": 133, + "line": 149, "column": 21 }, "end": { - "line": 133, + "line": 149, "column": 22 } }, @@ -8746,100 +9526,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 5042, - "end": 5092, + "start": 5482, + "end": 5532, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 74 } }, "expression": { "type": "CallExpression", - "start": 5042, - "end": 5091, + "start": 5482, + "end": 5531, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 5042, - "end": 5081, + "start": 5482, + "end": 5521, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 5042, - "end": 5074, + "start": 5482, + "end": 5514, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 56 } }, "object": { "type": "MemberExpression", - "start": 5042, - "end": 5055, + "start": 5482, + "end": 5495, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 5042, - "end": 5046, + "start": 5482, + "end": 5486, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 28 } } }, "property": { "type": "Identifier", - "start": 5047, - "end": 5055, + "start": 5487, + "end": 5495, "loc": { "start": { - "line": 133, + "line": 149, "column": 29 }, "end": { - "line": 133, + "line": 149, "column": 37 }, "identifierName": "phyloref" @@ -8850,15 +9630,15 @@ }, "property": { "type": "Identifier", - "start": 5056, - "end": 5074, + "start": 5496, + "end": 5514, "loc": { "start": { - "line": 133, + "line": 149, "column": 38 }, "end": { - "line": 133, + "line": 149, "column": 56 }, "identifierName": "externalSpecifiers" @@ -8869,15 +9649,15 @@ }, "property": { "type": "Identifier", - "start": 5075, - "end": 5081, + "start": 5515, + "end": 5521, "loc": { "start": { - "line": 133, + "line": 149, "column": 57 }, "end": { - "line": 133, + "line": 149, "column": 63 }, "identifierName": "splice" @@ -8889,15 +9669,15 @@ "arguments": [ { "type": "Identifier", - "start": 5082, - "end": 5087, + "start": 5522, + "end": 5527, "loc": { "start": { - "line": 133, + "line": 149, "column": 64 }, "end": { - "line": 133, + "line": 149, "column": 69 }, "identifierName": "index" @@ -8906,15 +9686,15 @@ }, { "type": "NumericLiteral", - "start": 5089, - "end": 5090, + "start": 5529, + "end": 5530, "loc": { "start": { - "line": 133, + "line": 149, "column": 71 }, "end": { - "line": 133, + "line": 149, "column": 72 } }, @@ -8940,15 +9720,15 @@ }, { "type": "ClassMethod", - "start": 5106, - "end": 6565, + "start": 5546, + "end": 7005, "loc": { "start": { - "line": 137, + "line": 153, "column": 2 }, "end": { - "line": 175, + "line": 191, "column": 3 } }, @@ -8956,15 +9736,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 5106, - "end": 5127, + "start": 5546, + "end": 5567, "loc": { "start": { - "line": 137, + "line": 153, "column": 2 }, "end": { - "line": 137, + "line": 153, "column": 23 }, "identifierName": "getExpectedNodeLabels" @@ -8979,15 +9759,15 @@ "params": [ { "type": "Identifier", - "start": 5128, - "end": 5137, + "start": 5568, + "end": 5577, "loc": { "start": { - "line": 137, + "line": 153, "column": 24 }, "end": { - "line": 137, + "line": 153, "column": 33 }, "identifierName": "phylogeny" @@ -8997,59 +9777,59 @@ ], "body": { "type": "BlockStatement", - "start": 5139, - "end": 6565, + "start": 5579, + "end": 7005, "loc": { "start": { - "line": 137, + "line": 153, "column": 35 }, "end": { - "line": 175, + "line": 191, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 5535, - "end": 5568, + "start": 5975, + "end": 6008, "loc": { "start": { - "line": 145, + "line": 161, "column": 4 }, "end": { - "line": 145, + "line": 161, "column": 37 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5541, - "end": 5567, + "start": 5981, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 10 }, "end": { - "line": 145, + "line": 161, "column": 36 } }, "id": { "type": "Identifier", - "start": 5541, - "end": 5554, + "start": 5981, + "end": 5994, "loc": { "start": { - "line": 145, + "line": 161, "column": 10 }, "end": { - "line": 145, + "line": 161, "column": 23 }, "identifierName": "phylorefLabel" @@ -9059,44 +9839,44 @@ }, "init": { "type": "MemberExpression", - "start": 5557, - "end": 5567, + "start": 5997, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 26 }, "end": { - "line": 145, + "line": 161, "column": 36 } }, "object": { "type": "ThisExpression", - "start": 5557, - "end": 5561, + "start": 5997, + "end": 6001, "loc": { "start": { - "line": 145, + "line": 161, "column": 26 }, "end": { - "line": 145, + "line": 161, "column": 30 } } }, "property": { "type": "Identifier", - "start": 5562, - "end": 5567, + "start": 6002, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 31 }, "end": { - "line": 145, + "line": 161, "column": 36 }, "identifierName": "label" @@ -9113,15 +9893,15 @@ { "type": "CommentLine", "value": " Given a phylogeny, determine which node labels we expect this phyloref to", - "start": 5145, - "end": 5221, + "start": 5585, + "end": 5661, "loc": { "start": { - "line": 138, + "line": 154, "column": 4 }, "end": { - "line": 138, + "line": 154, "column": 80 } } @@ -9129,15 +9909,15 @@ { "type": "CommentLine", "value": " resolve to. To do this, we:", - "start": 5226, - "end": 5256, + "start": 5666, + "end": 5696, "loc": { "start": { - "line": 139, + "line": 155, "column": 4 }, "end": { - "line": 139, + "line": 155, "column": 34 } } @@ -9145,15 +9925,15 @@ { "type": "CommentLine", "value": " 1. Find all node labels that are case-sensitively identical", - "start": 5261, - "end": 5324, + "start": 5701, + "end": 5764, "loc": { "start": { - "line": 140, + "line": 156, "column": 4 }, "end": { - "line": 140, + "line": 156, "column": 67 } } @@ -9161,15 +9941,15 @@ { "type": "CommentLine", "value": " to the phyloreference.", - "start": 5329, - "end": 5358, + "start": 5769, + "end": 5798, "loc": { "start": { - "line": 141, + "line": 157, "column": 4 }, "end": { - "line": 141, + "line": 157, "column": 33 } } @@ -9177,15 +9957,15 @@ { "type": "CommentLine", "value": " 2. Find all node labels that have additionalNodeProperties with", - "start": 5363, - "end": 5430, + "start": 5803, + "end": 5870, "loc": { "start": { - "line": 142, + "line": 158, "column": 4 }, "end": { - "line": 142, + "line": 158, "column": 71 } } @@ -9193,15 +9973,15 @@ { "type": "CommentLine", "value": " expectedPhyloreferenceNamed case-sensitively identical to", - "start": 5435, - "end": 5499, + "start": 5875, + "end": 5939, "loc": { "start": { - "line": 143, + "line": 159, "column": 4 }, "end": { - "line": 143, + "line": 159, "column": 68 } } @@ -9209,15 +9989,15 @@ { "type": "CommentLine", "value": " the phyloreference.", - "start": 5504, - "end": 5530, + "start": 5944, + "end": 5970, "loc": { "start": { - "line": 144, + "line": 160, "column": 4 }, "end": { - "line": 144, + "line": 160, "column": 30 } } @@ -9226,44 +10006,44 @@ }, { "type": "VariableDeclaration", - "start": 5573, - "end": 5602, + "start": 6013, + "end": 6042, "loc": { "start": { - "line": 146, + "line": 162, "column": 4 }, "end": { - "line": 146, + "line": 162, "column": 33 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5579, - "end": 5601, + "start": 6019, + "end": 6041, "loc": { "start": { - "line": 146, + "line": 162, "column": 10 }, "end": { - "line": 146, + "line": 162, "column": 32 } }, "id": { "type": "Identifier", - "start": 5579, - "end": 5589, + "start": 6019, + "end": 6029, "loc": { "start": { - "line": 146, + "line": 162, "column": 10 }, "end": { - "line": 146, + "line": 162, "column": 20 }, "identifierName": "nodeLabels" @@ -9272,29 +10052,29 @@ }, "init": { "type": "NewExpression", - "start": 5592, - "end": 5601, + "start": 6032, + "end": 6041, "loc": { "start": { - "line": 146, + "line": 162, "column": 23 }, "end": { - "line": 146, + "line": 162, "column": 32 } }, "callee": { "type": "Identifier", - "start": 5596, - "end": 5599, + "start": 6036, + "end": 6039, "loc": { "start": { - "line": 146, + "line": 162, "column": 27 }, "end": { - "line": 146, + "line": 162, "column": 30 }, "identifierName": "Set" @@ -9309,99 +10089,99 @@ }, { "type": "ExpressionStatement", - "start": 5608, - "end": 6469, + "start": 6048, + "end": 6909, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 171, + "line": 187, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 5608, - "end": 6468, + "start": 6048, + "end": 6908, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 171, + "line": 187, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 5608, - "end": 5704, + "start": 6048, + "end": 6144, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 29 } }, "object": { "type": "CallExpression", - "start": 5608, - "end": 5696, + "start": 6048, + "end": 6136, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 21 } }, "callee": { "type": "MemberExpression", - "start": 5608, - "end": 5694, + "start": 6048, + "end": 6134, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 19 } }, "object": { "type": "NewExpression", - "start": 5608, - "end": 5680, + "start": 6048, + "end": 6120, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 5 } }, "callee": { "type": "Identifier", - "start": 5612, - "end": 5628, + "start": 6052, + "end": 6068, "loc": { "start": { - "line": 148, + "line": 164, "column": 8 }, "end": { - "line": 148, + "line": 164, "column": 24 }, "identifierName": "PhylogenyWrapper" @@ -9411,15 +10191,15 @@ "arguments": [ { "type": "Identifier", - "start": 5636, - "end": 5645, + "start": 6076, + "end": 6085, "loc": { "start": { - "line": 149, + "line": 165, "column": 6 }, "end": { - "line": 149, + "line": 165, "column": 15 }, "identifierName": "phylogeny" @@ -9428,44 +10208,44 @@ }, { "type": "MemberExpression", - "start": 5653, - "end": 5674, + "start": 6093, + "end": 6114, "loc": { "start": { - "line": 150, + "line": 166, "column": 6 }, "end": { - "line": 150, + "line": 166, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 5653, - "end": 5657, + "start": 6093, + "end": 6097, "loc": { "start": { - "line": 150, + "line": 166, "column": 6 }, "end": { - "line": 150, + "line": 166, "column": 10 } } }, "property": { "type": "Identifier", - "start": 5658, - "end": 5674, + "start": 6098, + "end": 6114, "loc": { "start": { - "line": 150, + "line": 166, "column": 11 }, "end": { - "line": 150, + "line": 166, "column": 27 }, "identifierName": "defaultNomenCode" @@ -9478,15 +10258,15 @@ }, "property": { "type": "Identifier", - "start": 5681, - "end": 5694, + "start": 6121, + "end": 6134, "loc": { "start": { - "line": 151, + "line": 167, "column": 6 }, "end": { - "line": 151, + "line": 167, "column": 19 }, "identifierName": "getNodeLabels" @@ -9499,15 +10279,15 @@ }, "property": { "type": "Identifier", - "start": 5697, - "end": 5704, + "start": 6137, + "end": 6144, "loc": { "start": { - "line": 151, + "line": 167, "column": 22 }, "end": { - "line": 151, + "line": 167, "column": 29 }, "identifierName": "forEach" @@ -9519,15 +10299,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5705, - "end": 6467, + "start": 6145, + "end": 6907, "loc": { "start": { - "line": 151, + "line": 167, "column": 30 }, "end": { - "line": 171, + "line": 187, "column": 5 } }, @@ -9538,15 +10318,15 @@ "params": [ { "type": "Identifier", - "start": 5706, - "end": 5715, + "start": 6146, + "end": 6155, "loc": { "start": { - "line": 151, + "line": 167, "column": 31 }, "end": { - "line": 151, + "line": 167, "column": 40 }, "identifierName": "nodeLabel" @@ -9556,58 +10336,58 @@ ], "body": { "type": "BlockStatement", - "start": 5720, - "end": 6467, + "start": 6160, + "end": 6907, "loc": { "start": { - "line": 151, + "line": 167, "column": 45 }, "end": { - "line": 171, + "line": 187, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 5794, - "end": 6461, + "start": 6234, + "end": 6901, "loc": { "start": { - "line": 153, + "line": 169, "column": 6 }, "end": { - "line": 170, + "line": 186, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 5798, - "end": 5825, + "start": 6238, + "end": 6265, "loc": { "start": { - "line": 153, + "line": 169, "column": 10 }, "end": { - "line": 153, + "line": 169, "column": 37 } }, "left": { "type": "Identifier", - "start": 5798, - "end": 5807, + "start": 6238, + "end": 6247, "loc": { "start": { - "line": 153, + "line": 169, "column": 10 }, "end": { - "line": 153, + "line": 169, "column": 19 }, "identifierName": "nodeLabel" @@ -9618,15 +10398,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 5812, - "end": 5825, + "start": 6252, + "end": 6265, "loc": { "start": { - "line": 153, + "line": 169, "column": 24 }, "end": { - "line": 153, + "line": 169, "column": 37 }, "identifierName": "phylorefLabel" @@ -9637,72 +10417,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 5827, - "end": 5871, + "start": 6267, + "end": 6311, "loc": { "start": { - "line": 153, + "line": 169, "column": 39 }, "end": { - "line": 155, + "line": 171, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 5837, - "end": 5863, + "start": 6277, + "end": 6303, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 34 } }, "expression": { "type": "CallExpression", - "start": 5837, - "end": 5862, + "start": 6277, + "end": 6302, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 5837, - "end": 5851, + "start": 6277, + "end": 6291, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 22 } }, "object": { "type": "Identifier", - "start": 5837, - "end": 5847, + "start": 6277, + "end": 6287, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 18 }, "identifierName": "nodeLabels" @@ -9711,15 +10491,15 @@ }, "property": { "type": "Identifier", - "start": 5848, - "end": 5851, + "start": 6288, + "end": 6291, "loc": { "start": { - "line": 154, + "line": 170, "column": 19 }, "end": { - "line": 154, + "line": 170, "column": 22 }, "identifierName": "add" @@ -9731,15 +10511,15 @@ "arguments": [ { "type": "Identifier", - "start": 5852, - "end": 5861, + "start": 6292, + "end": 6301, "loc": { "start": { - "line": 154, + "line": 170, "column": 23 }, "end": { - "line": 154, + "line": 170, "column": 32 }, "identifierName": "nodeLabel" @@ -9754,71 +10534,71 @@ }, "alternate": { "type": "IfStatement", - "start": 5877, - "end": 6461, + "start": 6317, + "end": 6901, "loc": { "start": { - "line": 155, + "line": 171, "column": 13 }, "end": { - "line": 170, + "line": 186, "column": 7 } }, "test": { "type": "LogicalExpression", - "start": 5890, - "end": 6087, + "start": 6330, + "end": 6527, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 158, + "line": 174, "column": 92 } }, "left": { "type": "LogicalExpression", - "start": 5890, - "end": 5994, + "start": 6330, + "end": 6434, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 157, + "line": 173, "column": 61 } }, "left": { "type": "CallExpression", - "start": 5890, - "end": 5932, + "start": 6330, + "end": 6372, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 156, + "line": 172, "column": 50 } }, "callee": { "type": "Identifier", - "start": 5890, - "end": 5893, + "start": 6330, + "end": 6333, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 156, + "line": 172, "column": 11 }, "identifierName": "has" @@ -9828,15 +10608,15 @@ "arguments": [ { "type": "Identifier", - "start": 5894, - "end": 5903, + "start": 6334, + "end": 6343, "loc": { "start": { - "line": 156, + "line": 172, "column": 12 }, "end": { - "line": 156, + "line": 172, "column": 21 }, "identifierName": "phylogeny" @@ -9845,15 +10625,15 @@ }, { "type": "StringLiteral", - "start": 5905, - "end": 5931, + "start": 6345, + "end": 6371, "loc": { "start": { - "line": 156, + "line": 172, "column": 23 }, "end": { - "line": 156, + "line": 172, "column": 49 } }, @@ -9868,29 +10648,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 5944, - "end": 5994, + "start": 6384, + "end": 6434, "loc": { "start": { - "line": 157, + "line": 173, "column": 11 }, "end": { - "line": 157, + "line": 173, "column": 61 } }, "callee": { "type": "Identifier", - "start": 5944, - "end": 5947, + "start": 6384, + "end": 6387, "loc": { "start": { - "line": 157, + "line": 173, "column": 11 }, "end": { - "line": 157, + "line": 173, "column": 14 }, "identifierName": "has" @@ -9900,29 +10680,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 5948, - "end": 5982, + "start": 6388, + "end": 6422, "loc": { "start": { - "line": 157, + "line": 173, "column": 15 }, "end": { - "line": 157, + "line": 173, "column": 49 } }, "object": { "type": "Identifier", - "start": 5948, - "end": 5957, + "start": 6388, + "end": 6397, "loc": { "start": { - "line": 157, + "line": 173, "column": 15 }, "end": { - "line": 157, + "line": 173, "column": 24 }, "identifierName": "phylogeny" @@ -9931,15 +10711,15 @@ }, "property": { "type": "Identifier", - "start": 5958, - "end": 5982, + "start": 6398, + "end": 6422, "loc": { "start": { - "line": 157, + "line": 173, "column": 25 }, "end": { - "line": 157, + "line": 173, "column": 49 }, "identifierName": "additionalNodeProperties" @@ -9950,15 +10730,15 @@ }, { "type": "Identifier", - "start": 5984, - "end": 5993, + "start": 6424, + "end": 6433, "loc": { "start": { - "line": 157, + "line": 173, "column": 51 }, "end": { - "line": 157, + "line": 173, "column": 60 }, "identifierName": "nodeLabel" @@ -9971,29 +10751,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 6006, - "end": 6087, + "start": 6446, + "end": 6527, "loc": { "start": { - "line": 158, + "line": 174, "column": 11 }, "end": { - "line": 158, + "line": 174, "column": 92 } }, "callee": { "type": "Identifier", - "start": 6006, - "end": 6009, + "start": 6446, + "end": 6449, "loc": { "start": { - "line": 158, + "line": 174, "column": 11 }, "end": { - "line": 158, + "line": 174, "column": 14 }, "identifierName": "has" @@ -10003,43 +10783,43 @@ "arguments": [ { "type": "MemberExpression", - "start": 6010, - "end": 6055, + "start": 6450, + "end": 6495, "loc": { "start": { - "line": 158, + "line": 174, "column": 15 }, "end": { - "line": 158, + "line": 174, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 6010, - "end": 6044, + "start": 6450, + "end": 6484, "loc": { "start": { - "line": 158, + "line": 174, "column": 15 }, "end": { - "line": 158, + "line": 174, "column": 49 } }, "object": { "type": "Identifier", - "start": 6010, - "end": 6019, + "start": 6450, + "end": 6459, "loc": { "start": { - "line": 158, + "line": 174, "column": 15 }, "end": { - "line": 158, + "line": 174, "column": 24 }, "identifierName": "phylogeny" @@ -10048,15 +10828,15 @@ }, "property": { "type": "Identifier", - "start": 6020, - "end": 6044, + "start": 6460, + "end": 6484, "loc": { "start": { - "line": 158, + "line": 174, "column": 25 }, "end": { - "line": 158, + "line": 174, "column": 49 }, "identifierName": "additionalNodeProperties" @@ -10067,15 +10847,15 @@ }, "property": { "type": "Identifier", - "start": 6045, - "end": 6054, + "start": 6485, + "end": 6494, "loc": { "start": { - "line": 158, + "line": 174, "column": 50 }, "end": { - "line": 158, + "line": 174, "column": 59 }, "identifierName": "nodeLabel" @@ -10086,15 +10866,15 @@ }, { "type": "StringLiteral", - "start": 6057, - "end": 6086, + "start": 6497, + "end": 6526, "loc": { "start": { - "line": 158, + "line": 174, "column": 62 }, "end": { - "line": 158, + "line": 174, "column": 91 } }, @@ -10109,59 +10889,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6096, - "end": 6461, + "start": 6536, + "end": 6901, "loc": { "start": { - "line": 159, + "line": 175, "column": 8 }, "end": { - "line": 170, + "line": 186, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 6226, - "end": 6348, + "start": 6666, + "end": 6788, "loc": { "start": { - "line": 163, + "line": 179, "column": 8 }, "end": { - "line": 165, + "line": 181, "column": 39 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6232, - "end": 6347, + "start": 6672, + "end": 6787, "loc": { "start": { - "line": 163, + "line": 179, "column": 14 }, "end": { - "line": 165, + "line": 181, "column": 38 } }, "id": { "type": "Identifier", - "start": 6232, - "end": 6249, + "start": 6672, + "end": 6689, "loc": { "start": { - "line": 163, + "line": 179, "column": 14 }, "end": { - "line": 163, + "line": 179, "column": 31 }, "identifierName": "expectedPhylorefs" @@ -10171,57 +10951,57 @@ }, "init": { "type": "MemberExpression", - "start": 6252, - "end": 6347, + "start": 6692, + "end": 6787, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 165, + "line": 181, "column": 38 } }, "object": { "type": "MemberExpression", - "start": 6252, - "end": 6308, + "start": 6692, + "end": 6748, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 164, + "line": 180, "column": 46 } }, "object": { "type": "MemberExpression", - "start": 6252, - "end": 6297, + "start": 6692, + "end": 6737, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 164, + "line": 180, "column": 35 } }, "object": { "type": "Identifier", - "start": 6252, - "end": 6261, + "start": 6692, + "end": 6701, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 163, + "line": 179, "column": 43 }, "identifierName": "phylogeny" @@ -10230,15 +11010,15 @@ }, "property": { "type": "Identifier", - "start": 6273, - "end": 6297, + "start": 6713, + "end": 6737, "loc": { "start": { - "line": 164, + "line": 180, "column": 11 }, "end": { - "line": 164, + "line": 180, "column": 35 }, "identifierName": "additionalNodeProperties" @@ -10249,15 +11029,15 @@ }, "property": { "type": "Identifier", - "start": 6298, - "end": 6307, + "start": 6738, + "end": 6747, "loc": { "start": { - "line": 164, + "line": 180, "column": 36 }, "end": { - "line": 164, + "line": 180, "column": 45 }, "identifierName": "nodeLabel" @@ -10268,15 +11048,15 @@ }, "property": { "type": "Identifier", - "start": 6320, - "end": 6347, + "start": 6760, + "end": 6787, "loc": { "start": { - "line": 165, + "line": 181, "column": 11 }, "end": { - "line": 165, + "line": 181, "column": 38 }, "identifierName": "expectedPhyloreferenceNamed" @@ -10293,15 +11073,15 @@ { "type": "CommentLine", "value": " Does this node label have an expectedPhyloreferenceNamed that", - "start": 6106, - "end": 6170, + "start": 6546, + "end": 6610, "loc": { "start": { - "line": 160, + "line": 176, "column": 8 }, "end": { - "line": 160, + "line": 176, "column": 72 } } @@ -10309,15 +11089,15 @@ { "type": "CommentLine", "value": " includes this phyloreference name?", - "start": 6179, - "end": 6216, + "start": 6619, + "end": 6656, "loc": { "start": { - "line": 161, + "line": 177, "column": 8 }, "end": { - "line": 161, + "line": 177, "column": 45 } } @@ -10326,57 +11106,57 @@ }, { "type": "IfStatement", - "start": 6358, - "end": 6453, + "start": 6798, + "end": 6893, "loc": { "start": { - "line": 167, + "line": 183, "column": 8 }, "end": { - "line": 169, + "line": 185, "column": 9 } }, "test": { "type": "CallExpression", - "start": 6362, - "end": 6403, + "start": 6802, + "end": 6843, "loc": { "start": { - "line": 167, + "line": 183, "column": 12 }, "end": { - "line": 167, + "line": 183, "column": 53 } }, "callee": { "type": "MemberExpression", - "start": 6362, - "end": 6388, + "start": 6802, + "end": 6828, "loc": { "start": { - "line": 167, + "line": 183, "column": 12 }, "end": { - "line": 167, + "line": 183, "column": 38 } }, "object": { "type": "Identifier", - "start": 6362, - "end": 6379, + "start": 6802, + "end": 6819, "loc": { "start": { - "line": 167, + "line": 183, "column": 12 }, "end": { - "line": 167, + "line": 183, "column": 29 }, "identifierName": "expectedPhylorefs" @@ -10385,15 +11165,15 @@ }, "property": { "type": "Identifier", - "start": 6380, - "end": 6388, + "start": 6820, + "end": 6828, "loc": { "start": { - "line": 167, + "line": 183, "column": 30 }, "end": { - "line": 167, + "line": 183, "column": 38 }, "identifierName": "includes" @@ -10405,15 +11185,15 @@ "arguments": [ { "type": "Identifier", - "start": 6389, - "end": 6402, + "start": 6829, + "end": 6842, "loc": { "start": { - "line": 167, + "line": 183, "column": 39 }, "end": { - "line": 167, + "line": 183, "column": 52 }, "identifierName": "phylorefLabel" @@ -10424,72 +11204,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 6405, - "end": 6453, + "start": 6845, + "end": 6893, "loc": { "start": { - "line": 167, + "line": 183, "column": 55 }, "end": { - "line": 169, + "line": 185, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 6417, - "end": 6443, + "start": 6857, + "end": 6883, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 36 } }, "expression": { "type": "CallExpression", - "start": 6417, - "end": 6442, + "start": 6857, + "end": 6882, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 6417, - "end": 6431, + "start": 6857, + "end": 6871, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 24 } }, "object": { "type": "Identifier", - "start": 6417, - "end": 6427, + "start": 6857, + "end": 6867, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 20 }, "identifierName": "nodeLabels" @@ -10498,15 +11278,15 @@ }, "property": { "type": "Identifier", - "start": 6428, - "end": 6431, + "start": 6868, + "end": 6871, "loc": { "start": { - "line": 168, + "line": 184, "column": 21 }, "end": { - "line": 168, + "line": 184, "column": 24 }, "identifierName": "add" @@ -10518,15 +11298,15 @@ "arguments": [ { "type": "Identifier", - "start": 6432, - "end": 6441, + "start": 6872, + "end": 6881, "loc": { "start": { - "line": 168, + "line": 184, "column": 25 }, "end": { - "line": 168, + "line": 184, "column": 34 }, "identifierName": "nodeLabel" @@ -10550,15 +11330,15 @@ { "type": "CommentLine", "value": " Is this node label identical to the phyloreference name?", - "start": 5728, - "end": 5787, + "start": 6168, + "end": 6227, "loc": { "start": { - "line": 152, + "line": 168, "column": 6 }, "end": { - "line": 152, + "line": 168, "column": 65 } } @@ -10575,15 +11355,15 @@ { "type": "CommentLine", "value": " Return node labels sorted alphabetically.", - "start": 6475, - "end": 6519, + "start": 6915, + "end": 6959, "loc": { "start": { - "line": 173, + "line": 189, "column": 4 }, "end": { - "line": 173, + "line": 189, "column": 48 } } @@ -10592,85 +11372,85 @@ }, { "type": "ReturnStatement", - "start": 6524, - "end": 6561, + "start": 6964, + "end": 7001, "loc": { "start": { - "line": 174, + "line": 190, "column": 4 }, "end": { - "line": 174, + "line": 190, "column": 41 } }, "argument": { "type": "CallExpression", - "start": 6531, - "end": 6560, + "start": 6971, + "end": 7000, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 6531, - "end": 6558, + "start": 6971, + "end": 6998, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 38 } }, "object": { "type": "CallExpression", - "start": 6531, - "end": 6553, + "start": 6971, + "end": 6993, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 6531, - "end": 6541, + "start": 6971, + "end": 6981, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 21 } }, "object": { "type": "Identifier", - "start": 6531, - "end": 6536, + "start": 6971, + "end": 6976, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 16 }, "identifierName": "Array" @@ -10680,15 +11460,15 @@ }, "property": { "type": "Identifier", - "start": 6537, - "end": 6541, + "start": 6977, + "end": 6981, "loc": { "start": { - "line": 174, + "line": 190, "column": 17 }, "end": { - "line": 174, + "line": 190, "column": 21 }, "identifierName": "from" @@ -10701,15 +11481,15 @@ "arguments": [ { "type": "Identifier", - "start": 6542, - "end": 6552, + "start": 6982, + "end": 6992, "loc": { "start": { - "line": 174, + "line": 190, "column": 22 }, "end": { - "line": 174, + "line": 190, "column": 32 }, "identifierName": "nodeLabels" @@ -10721,15 +11501,15 @@ }, "property": { "type": "Identifier", - "start": 6554, - "end": 6558, + "start": 6994, + "end": 6998, "loc": { "start": { - "line": 174, + "line": 190, "column": 34 }, "end": { - "line": 174, + "line": 190, "column": 38 }, "identifierName": "sort" @@ -10746,15 +11526,15 @@ { "type": "CommentLine", "value": " Return node labels sorted alphabetically.", - "start": 6475, - "end": 6519, + "start": 6915, + "end": 6959, "loc": { "start": { - "line": 173, + "line": 189, "column": 4 }, "end": { - "line": 173, + "line": 189, "column": 48 } } @@ -10767,15 +11547,15 @@ }, { "type": "ClassMethod", - "start": 6569, - "end": 6921, + "start": 7009, + "end": 7361, "loc": { "start": { - "line": 177, + "line": 193, "column": 2 }, "end": { - "line": 187, + "line": 203, "column": 3 } }, @@ -10783,15 +11563,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6576, - "end": 6600, + "start": 7016, + "end": 7040, "loc": { "start": { - "line": 177, + "line": 193, "column": 9 }, "end": { - "line": 177, + "line": 193, "column": 33 }, "identifierName": "getStatusCURIEsInEnglish" @@ -10806,59 +11586,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6603, - "end": 6921, + "start": 7043, + "end": 7361, "loc": { "start": { - "line": 177, + "line": 193, "column": 36 }, "end": { - "line": 187, + "line": 203, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 6670, - "end": 6917, + "start": 7110, + "end": 7357, "loc": { "start": { - "line": 179, + "line": 195, "column": 4 }, "end": { - "line": 186, + "line": 202, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 6677, - "end": 6916, + "start": 7117, + "end": 7356, "loc": { "start": { - "line": 179, + "line": 195, "column": 11 }, "end": { - "line": 186, + "line": 202, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 6685, - "end": 6705, + "start": 7125, + "end": 7145, "loc": { "start": { - "line": 180, + "line": 196, "column": 6 }, "end": { - "line": 180, + "line": 196, "column": 26 } }, @@ -10867,15 +11647,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6685, - "end": 6696, + "start": 7125, + "end": 7136, "loc": { "start": { - "line": 180, + "line": 196, "column": 6 }, "end": { - "line": 180, + "line": 196, "column": 17 } }, @@ -10888,15 +11668,15 @@ }, "value": { "type": "StringLiteral", - "start": 6698, - "end": 6705, + "start": 7138, + "end": 7145, "loc": { "start": { - "line": 180, + "line": 196, "column": 19 }, "end": { - "line": 180, + "line": 196, "column": 26 } }, @@ -10910,15 +11690,15 @@ }, { "type": "ObjectProperty", - "start": 6713, - 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"start": 6753, - "end": 6771, + "start": 7193, + "end": 7211, "loc": { "start": { - "line": 182, + "line": 198, "column": 6 }, "end": { - "line": 182, + "line": 198, "column": 24 } }, @@ -11005,15 +11785,15 @@ }, "value": { "type": "StringLiteral", - "start": 6773, - "end": 6787, + "start": 7213, + "end": 7227, "loc": { "start": { - "line": 182, + "line": 198, "column": 26 }, "end": { - "line": 182, + "line": 198, "column": 40 } }, @@ -11026,15 +11806,15 @@ }, { "type": "ObjectProperty", - "start": 6795, - "end": 6820, + "start": 7235, + "end": 7260, "loc": { "start": { - "line": 183, + "line": 199, "column": 6 }, "end": { - "line": 183, + "line": 199, "column": 31 } }, @@ -11043,15 +11823,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6795, - "end": 6810, + "start": 7235, + "end": 7250, "loc": { "start": { - "line": 183, + "line": 199, "column": 6 }, "end": { - "line": 183, + "line": 199, "column": 21 } }, @@ -11063,15 +11843,15 @@ }, "value": { "type": "StringLiteral", - "start": 6812, - "end": 6820, + "start": 7252, + "end": 7260, "loc": { "start": { - "line": 183, + "line": 199, "column": 23 }, "end": { - "line": 183, + "line": 199, "column": 31 } }, @@ -11084,15 +11864,15 @@ }, { "type": "ObjectProperty", - "start": 6828, - "end": 6856, + "start": 7268, + "end": 7296, "loc": { "start": { - "line": 184, + "line": 200, "column": 6 }, "end": { - "line": 184, + "line": 200, "column": 34 } }, @@ -11101,15 +11881,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6828, - "end": 6843, + "start": 7268, + "end": 7283, "loc": { "start": { - "line": 184, + "line": 200, "column": 6 }, "end": { - "line": 184, + "line": 200, "column": 21 } }, @@ -11121,15 +11901,15 @@ }, "value": { "type": "StringLiteral", - "start": 6845, - "end": 6856, + "start": 7285, + "end": 7296, "loc": { "start": { - "line": 184, + "line": 200, "column": 23 }, "end": { - "line": 184, + "line": 200, "column": 34 } }, @@ -11142,15 +11922,15 @@ }, { "type": "ObjectProperty", - "start": 6864, - "end": 6909, + "start": 7304, + "end": 7349, "loc": { "start": { - "line": 185, + "line": 201, "column": 6 }, "end": { - "line": 185, + "line": 201, "column": 51 } }, @@ -11159,15 +11939,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6864, - "end": 6896, + "start": 7304, + "end": 7336, "loc": { "start": { - "line": 185, + "line": 201, "column": 6 }, "end": { - "line": 185, + "line": 201, "column": 38 } }, @@ -11179,15 +11959,15 @@ }, "value": { "type": "StringLiteral", - "start": 6898, - "end": 6909, + "start": 7338, + "end": 7349, "loc": { "start": { - "line": 185, + "line": 201, "column": 40 }, "end": { - "line": 185, + "line": 201, "column": 51 } }, @@ -11205,15 +11985,15 @@ { "type": "CommentLine", "value": " Return dictionary of all phyloref statuses in English", - "start": 6609, - "end": 6665, + "start": 7049, + "end": 7105, "loc": { "start": { - "line": 178, + "line": 194, "column": 4 }, "end": { - "line": 178, + "line": 194, "column": 60 } } @@ -11226,15 +12006,15 @@ }, { "type": "ClassMethod", - "start": 6925, - "end": 8625, + "start": 7365, + "end": 9065, "loc": { "start": { - "line": 189, + "line": 205, "column": 2 }, "end": { - "line": 230, + "line": 246, "column": 3 } }, @@ -11242,15 +12022,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6925, - "end": 6941, + "start": 7365, + "end": 7381, "loc": { "start": { - "line": 189, + "line": 205, "column": 2 }, "end": { - "line": 189, + "line": 205, "column": 18 }, "identifierName": "getCurrentStatus" @@ -11265,86 +12045,86 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6944, - "end": 8625, + "start": 7384, + "end": 9065, "loc": { "start": { - "line": 189, + "line": 205, "column": 21 }, "end": { - "line": 230, + "line": 246, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 7233, - "end": 8406, + "start": 7673, + "end": 8846, "loc": { "start": { - "line": 196, + "line": 212, "column": 4 }, "end": { - "line": 223, + "line": 239, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 7244, - "end": 7409, + "start": 7684, + "end": 7849, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 199, + "line": 215, "column": 58 } }, "left": { "type": "LogicalExpression", - "start": 7244, - "end": 7350, + "start": 7684, + "end": 7790, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 198, + "line": 214, "column": 62 } }, "left": { "type": "CallExpression", - "start": 7244, - "end": 7287, + "start": 7684, + "end": 7727, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 197, + "line": 213, "column": 49 } }, "callee": { "type": "Identifier", - "start": 7244, - "end": 7247, + "start": 7684, + "end": 7687, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 197, + "line": 213, "column": 9 }, "identifierName": "has" @@ -11355,44 +12135,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7248, - "end": 7261, + "start": 7688, + "end": 7701, "loc": { "start": { - "line": 197, + "line": 213, "column": 10 }, "end": { - "line": 197, + "line": 213, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 7248, - "end": 7252, + "start": 7688, + "end": 7692, "loc": { "start": { - "line": 197, + "line": 213, "column": 10 }, "end": { - "line": 197, + "line": 213, "column": 14 } } }, "property": { "type": "Identifier", - "start": 7253, - "end": 7261, + "start": 7693, + "end": 7701, "loc": { "start": { - "line": 197, + "line": 213, "column": 15 }, "end": { - "line": 197, + "line": 213, "column": 23 }, "identifierName": "phyloref" @@ -11403,15 +12183,15 @@ }, { "type": "StringLiteral", - "start": 7263, - "end": 7286, + "start": 7703, + "end": 7726, "loc": { "start": { - "line": 197, + "line": 213, "column": 25 }, "end": { - "line": 197, + "line": 213, "column": 48 } }, @@ -11427,43 +12207,43 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 7297, - "end": 7350, + "start": 7737, + "end": 7790, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 62 } }, "callee": { "type": "MemberExpression", - "start": 7297, - "end": 7310, + "start": 7737, + "end": 7750, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 22 } }, "object": { "type": "Identifier", - "start": 7297, - "end": 7302, + "start": 7737, + "end": 7742, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 14 }, "identifierName": "Array" @@ -11472,15 +12252,15 @@ }, "property": { "type": "Identifier", - "start": 7303, - "end": 7310, + "start": 7743, + "end": 7750, "loc": { "start": { - "line": 198, + "line": 214, "column": 15 }, "end": { - "line": 198, + "line": 214, "column": 22 }, "identifierName": "isArray" @@ -11492,58 +12272,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 7311, - "end": 7349, + "start": 7751, + "end": 7789, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 61 } }, "object": { "type": "MemberExpression", - "start": 7311, - "end": 7324, + "start": 7751, + "end": 7764, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 36 } }, "object": { "type": "ThisExpression", - "start": 7311, - "end": 7315, + "start": 7751, + "end": 7755, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 27 } } }, "property": { "type": "Identifier", - "start": 7316, - "end": 7324, + "start": 7756, + "end": 7764, "loc": { "start": { - "line": 198, + "line": 214, "column": 28 }, "end": { - "line": 198, + "line": 214, "column": 36 }, "identifierName": "phyloref" @@ -11554,15 +12334,15 @@ }, "property": { "type": "StringLiteral", - "start": 7325, - "end": 7348, + "start": 7765, + "end": 7788, "loc": { "start": { - "line": 198, + "line": 214, "column": 37 }, "end": { - "line": 198, + "line": 214, "column": 60 } }, @@ -11581,86 +12361,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 7360, - "end": 7409, + "start": 7800, + "end": 7849, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 58 } }, "left": { "type": "MemberExpression", - "start": 7360, - "end": 7405, + "start": 7800, + "end": 7845, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 7360, - "end": 7398, + "start": 7800, + "end": 7838, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 47 } }, "object": { "type": "MemberExpression", - "start": 7360, - "end": 7373, + "start": 7800, + "end": 7813, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 7360, - "end": 7364, + "start": 7800, + "end": 7804, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 13 } } }, "property": { "type": "Identifier", - "start": 7365, - "end": 7373, + "start": 7805, + "end": 7813, "loc": { "start": { - "line": 199, + "line": 215, "column": 14 }, "end": { - "line": 199, + "line": 215, "column": 22 }, "identifierName": "phyloref" @@ -11671,15 +12451,15 @@ }, "property": { "type": "StringLiteral", - "start": 7374, - "end": 7397, + "start": 7814, + "end": 7837, "loc": { "start": { - "line": 199, + "line": 215, "column": 23 }, "end": { - "line": 199, + "line": 215, "column": 46 } }, @@ -11693,15 +12473,15 @@ }, "property": { "type": "Identifier", - "start": 7399, - "end": 7405, + "start": 7839, + "end": 7845, "loc": { "start": { - "line": 199, + "line": 215, "column": 48 }, "end": { - "line": 199, + "line": 215, "column": 54 }, "identifierName": "length" @@ -11713,15 +12493,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 7408, - "end": 7409, + "start": 7848, + "end": 7849, "loc": { "start": { - "line": 199, + "line": 215, "column": 57 }, "end": { - "line": 199, + "line": 215, "column": 58 } }, @@ -11736,59 +12516,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7416, - "end": 8406, + "start": 7856, + "end": 8846, "loc": { "start": { - "line": 200, + "line": 216, "column": 6 }, "end": { - "line": 223, + "line": 239, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 7568, - "end": 7683, + "start": 8008, + "end": 8123, "loc": { "start": { - "line": 203, + "line": 219, "column": 6 }, "end": { - "line": 203, + "line": 219, "column": 121 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7574, - "end": 7682, + "start": 8014, + "end": 8122, "loc": { "start": { - "line": 203, + "line": 219, "column": 12 }, "end": { - "line": 203, + "line": 219, "column": 120 } }, "id": { "type": "Identifier", - "start": 7574, - "end": 7590, + "start": 8014, + "end": 8030, "loc": { "start": { - "line": 203, + "line": 219, "column": 12 }, "end": { - "line": 203, + "line": 219, "column": 28 }, "identifierName": "lastStatusInTime" @@ -11798,72 +12578,72 @@ }, "init": { "type": "MemberExpression", - "start": 7593, - "end": 7682, + "start": 8033, + "end": 8122, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 120 } }, "object": { "type": "MemberExpression", - "start": 7593, - "end": 7631, + "start": 8033, + "end": 8071, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 69 } }, "object": { "type": "MemberExpression", - "start": 7593, - "end": 7606, + "start": 8033, + "end": 8046, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 7593, - "end": 7597, + "start": 8033, + "end": 8037, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 35 } } }, "property": { "type": "Identifier", - "start": 7598, - "end": 7606, + "start": 8038, + "end": 8046, "loc": { "start": { - "line": 203, + "line": 219, "column": 36 }, "end": { - "line": 203, + "line": 219, "column": 44 }, "identifierName": "phyloref" @@ -11874,15 +12654,15 @@ }, "property": { "type": "StringLiteral", - "start": 7607, - "end": 7630, + "start": 8047, + "end": 8070, "loc": { "start": { - "line": 203, + "line": 219, "column": 45 }, "end": { - "line": 203, + "line": 219, "column": 68 } }, @@ -11896,86 +12676,86 @@ }, "property": { "type": "BinaryExpression", - "start": 7632, - "end": 7681, + "start": 8072, + "end": 8121, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 119 } }, "left": { "type": "MemberExpression", - "start": 7632, - "end": 7677, + "start": 8072, + "end": 8117, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 115 } }, "object": { "type": "MemberExpression", - "start": 7632, - "end": 7670, + "start": 8072, + "end": 8110, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 108 } }, "object": { "type": "MemberExpression", - "start": 7632, - "end": 7645, + "start": 8072, + "end": 8085, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 83 } }, "object": { "type": "ThisExpression", - "start": 7632, - "end": 7636, + "start": 8072, + "end": 8076, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 74 } } }, "property": { "type": "Identifier", - "start": 7637, - "end": 7645, + "start": 8077, + "end": 8085, "loc": { "start": { - "line": 203, + "line": 219, "column": 75 }, "end": { - "line": 203, + "line": 219, "column": 83 }, "identifierName": "phyloref" @@ -11986,15 +12766,15 @@ }, "property": { "type": "StringLiteral", - "start": 7646, - "end": 7669, + "start": 8086, + "end": 8109, "loc": { "start": { - "line": 203, + "line": 219, "column": 84 }, "end": { - "line": 203, + "line": 219, "column": 107 } }, @@ -12008,15 +12788,15 @@ }, "property": { "type": "Identifier", - "start": 7671, - "end": 7677, + "start": 8111, + "end": 8117, "loc": { "start": { - "line": 203, + "line": 219, "column": 109 }, "end": { - "line": 203, + "line": 219, "column": 115 }, "identifierName": "length" @@ -12028,15 +12808,15 @@ "operator": "-", "right": { "type": "NumericLiteral", - "start": 7680, - "end": 7681, + "start": 8120, + "end": 8121, "loc": { "start": { - "line": 203, + "line": 219, "column": 118 }, "end": { - "line": 203, + "line": 219, "column": 119 } }, @@ -12057,15 +12837,15 @@ { "type": "CommentLine", "value": " If we have any pso:holdsStatusInTime entries, pick the first one and", - "start": 7424, - "end": 7495, + "start": 7864, + "end": 7935, "loc": { "start": { - "line": 201, + "line": 217, "column": 6 }, "end": { - "line": 201, + "line": 217, "column": 77 } } @@ -12073,15 +12853,15 @@ { "type": "CommentLine", "value": " extract the CURIE and time interval information from it.", - "start": 7502, - "end": 7561, + "start": 7942, + "end": 8001, "loc": { "start": { - "line": 202, + "line": 218, "column": 6 }, "end": { - "line": 202, + "line": 218, "column": 65 } } @@ -12090,44 +12870,44 @@ }, { "type": "VariableDeclaration", - "start": 7690, - "end": 7752, + "start": 8130, + "end": 8192, "loc": { "start": { - "line": 204, + "line": 220, "column": 6 }, "end": { - "line": 204, + "line": 220, "column": 68 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7696, - "end": 7751, + "start": 8136, + "end": 8191, "loc": { "start": { - "line": 204, + "line": 220, "column": 12 }, "end": { - "line": 204, + "line": 220, "column": 67 } }, "id": { "type": "Identifier", - "start": 7696, - "end": 7707, + "start": 8136, + "end": 8147, "loc": { "start": { - "line": 204, + "line": 220, "column": 12 }, "end": { - "line": 204, + "line": 220, "column": 23 }, "identifierName": "statusCURIE" @@ -12136,43 +12916,43 @@ }, "init": { "type": "MemberExpression", - "start": 7710, - "end": 7751, + "start": 8150, + "end": 8191, "loc": { "start": { - "line": 204, + "line": 220, "column": 26 }, "end": { - "line": 204, + "line": 220, "column": 67 } }, "object": { "type": "MemberExpression", - "start": 7710, - "end": 7744, + "start": 8150, + "end": 8184, "loc": { "start": { - "line": 204, + "line": 220, "column": 26 }, "end": { - "line": 204, + "line": 220, "column": 60 } }, "object": { "type": "Identifier", - "start": 7710, - "end": 7726, + "start": 8150, + "end": 8166, "loc": { "start": { - "line": 204, + "line": 220, "column": 26 }, "end": { - "line": 204, + "line": 220, "column": 42 }, "identifierName": "lastStatusInTime" @@ -12181,15 +12961,15 @@ }, "property": { "type": "StringLiteral", - "start": 7727, - "end": 7743, + "start": 8167, + "end": 8183, "loc": { "start": { - "line": 204, + "line": 220, "column": 43 }, "end": { - "line": 204, + "line": 220, "column": 59 } }, @@ -12203,15 +12983,15 @@ }, "property": { "type": "StringLiteral", - "start": 7745, - "end": 7750, + "start": 8185, + "end": 8190, "loc": { "start": { - "line": 204, + "line": 220, "column": 61 }, "end": { - "line": 204, + "line": 220, "column": 66 } }, @@ -12230,15 +13010,15 @@ { "type": "CommentLine", "value": " Look for time interval information", - "start": 7760, - "end": 7797, + "start": 8200, + "end": 8237, "loc": { "start": { - "line": 206, + "line": 222, "column": 6 }, "end": { - "line": 206, + "line": 222, "column": 43 } } @@ -12247,44 +13027,44 @@ }, { "type": "VariableDeclaration", - "start": 7804, - "end": 7822, + "start": 8244, + "end": 8262, "loc": { "start": { - "line": 207, + "line": 223, "column": 6 }, "end": { - "line": 207, + "line": 223, "column": 24 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7808, - "end": 7821, + "start": 8248, + "end": 8261, "loc": { "start": { - "line": 207, + "line": 223, "column": 10 }, "end": { - "line": 207, + "line": 223, "column": 23 } }, "id": { "type": "Identifier", - "start": 7808, - "end": 7821, + "start": 8248, + "end": 8261, "loc": { "start": { - "line": 207, + "line": 223, "column": 10 }, "end": { - "line": 207, + "line": 223, "column": 23 }, "identifierName": "intervalStart" @@ -12301,15 +13081,15 @@ { "type": "CommentLine", "value": " Look for time interval information", - "start": 7760, - "end": 7797, + "start": 8200, + "end": 8237, "loc": { "start": { - "line": 206, + "line": 222, "column": 6 }, "end": { - "line": 206, + "line": 222, "column": 43 } } @@ -12318,44 +13098,44 @@ }, { "type": "VariableDeclaration", - "start": 7829, - "end": 7845, + "start": 8269, + "end": 8285, "loc": { "start": { - "line": 208, + "line": 224, "column": 6 }, "end": { - "line": 208, + "line": 224, "column": 22 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7833, - "end": 7844, + "start": 8273, + "end": 8284, "loc": { "start": { - "line": 208, + "line": 224, "column": 10 }, "end": { - "line": 208, + "line": 224, "column": 21 } }, "id": { "type": "Identifier", - "start": 7833, - "end": 7844, + "start": 8273, + "end": 8284, "loc": { "start": { - "line": 208, + "line": 224, "column": 10 }, "end": { - "line": 208, + "line": 224, "column": 21 }, "identifierName": "intervalEnd" @@ -12369,43 +13149,43 @@ }, { "type": "IfStatement", - "start": 7853, - "end": 8198, + "start": 8293, + "end": 8638, "loc": { "start": { - "line": 210, + "line": 226, "column": 6 }, "end": { - "line": 214, + "line": 230, "column": 7 } }, "test": { "type": "CallExpression", - "start": 7857, - "end": 7892, + "start": 8297, + "end": 8332, "loc": { "start": { - "line": 210, + "line": 226, "column": 10 }, "end": { - "line": 210, + "line": 226, "column": 45 } }, "callee": { "type": "Identifier", - "start": 7857, - "end": 7860, + "start": 8297, + "end": 8300, "loc": { "start": { - "line": 210, + "line": 226, "column": 10 }, "end": { - "line": 210, + "line": 226, "column": 13 }, "identifierName": "has" @@ -12415,15 +13195,15 @@ "arguments": [ { "type": "Identifier", - "start": 7861, - "end": 7877, + "start": 8301, + "end": 8317, "loc": { "start": { - "line": 210, + "line": 226, "column": 14 }, "end": { - "line": 210, + "line": 226, "column": 30 }, "identifierName": "lastStatusInTime" @@ -12432,15 +13212,15 @@ }, { "type": "StringLiteral", - "start": 7879, - "end": 7891, + "start": 8319, + "end": 8331, "loc": { "start": { - "line": 210, + "line": 226, "column": 32 }, "end": { - "line": 210, + "line": 226, "column": 44 } }, @@ -12454,59 +13234,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7894, - "end": 8198, + "start": 8334, + "end": 8638, "loc": { "start": { - "line": 210, + "line": 226, "column": 47 }, "end": { - "line": 214, + "line": 230, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 7904, - "end": 7950, + "start": 8344, + "end": 8390, "loc": { "start": { - "line": 211, + "line": 227, "column": 8 }, "end": { - "line": 211, + "line": 227, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7910, - "end": 7949, + "start": 8350, + "end": 8389, "loc": { "start": { - "line": 211, + "line": 227, "column": 14 }, "end": { - "line": 211, + "line": 227, "column": 53 } }, "id": { "type": "Identifier", - "start": 7910, - "end": 7916, + "start": 8350, + "end": 8356, "loc": { "start": { - "line": 211, + "line": 227, "column": 14 }, "end": { - "line": 211, + "line": 227, "column": 20 }, "identifierName": "atTime" @@ -12515,29 +13295,29 @@ }, "init": { "type": "MemberExpression", - "start": 7919, - "end": 7949, + "start": 8359, + "end": 8389, "loc": { "start": { - "line": 211, + "line": 227, "column": 23 }, "end": { - "line": 211, + "line": 227, "column": 53 } }, "object": { "type": "Identifier", - "start": 7919, - "end": 7935, + "start": 8359, + "end": 8375, "loc": { "start": { - "line": 211, + "line": 227, "column": 23 }, "end": { - "line": 211, + "line": 227, "column": 39 }, "identifierName": "lastStatusInTime" @@ -12546,15 +13326,15 @@ }, "property": { "type": "StringLiteral", - "start": 7936, - "end": 7948, + "start": 8376, + "end": 8388, "loc": { "start": { - "line": 211, + "line": 227, "column": 40 }, "end": { - "line": 211, + "line": 227, "column": 52 } }, @@ -12572,43 +13352,43 @@ }, { "type": "IfStatement", - "start": 7959, - "end": 8073, + "start": 8399, + "end": 8513, "loc": { "start": { - "line": 212, + "line": 228, "column": 8 }, "end": { - "line": 212, + "line": 228, "column": 122 } }, "test": { "type": "CallExpression", - "start": 7963, - "end": 8011, + "start": 8403, + "end": 8451, "loc": { "start": { - "line": 212, + "line": 228, "column": 12 }, "end": { - "line": 212, + "line": 228, "column": 60 } }, "callee": { "type": "Identifier", - "start": 7963, - "end": 7966, + "start": 8403, + "end": 8406, "loc": { "start": { - "line": 212, + "line": 228, "column": 12 }, "end": { - "line": 212, + "line": 228, "column": 15 }, "identifierName": "has" @@ -12618,15 +13398,15 @@ "arguments": [ { "type": "Identifier", - "start": 7967, - "end": 7973, + "start": 8407, + "end": 8413, "loc": { "start": { - "line": 212, + "line": 228, "column": 16 }, "end": { - "line": 212, + "line": 228, "column": 22 }, "identifierName": "atTime" @@ -12635,15 +13415,15 @@ }, { "type": "StringLiteral", - "start": 7975, - "end": 8010, + "start": 8415, + "end": 8450, "loc": { "start": { - "line": 212, + "line": 228, "column": 24 }, "end": { - "line": 212, + "line": 228, "column": 59 } }, @@ -12657,44 +13437,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 8013, - "end": 8073, + "start": 8453, + "end": 8513, "loc": { "start": { - "line": 212, + "line": 228, "column": 62 }, "end": { - "line": 212, + "line": 228, "column": 122 } }, "expression": { "type": "AssignmentExpression", - "start": 8013, - "end": 8072, + "start": 8453, + "end": 8512, "loc": { "start": { - "line": 212, + "line": 228, "column": 62 }, "end": { - "line": 212, + "line": 228, "column": 121 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8013, - "end": 8026, + "start": 8453, + "end": 8466, "loc": { "start": { - "line": 212, + "line": 228, "column": 62 }, "end": { - "line": 212, + "line": 228, "column": 75 }, "identifierName": "intervalStart" @@ -12703,29 +13483,29 @@ }, "right": { "type": "MemberExpression", - "start": 8029, - "end": 8072, + "start": 8469, + "end": 8512, "loc": { "start": { - "line": 212, + "line": 228, "column": 78 }, "end": { - "line": 212, + "line": 228, "column": 121 } }, "object": { "type": "Identifier", - "start": 8029, - "end": 8035, + "start": 8469, + "end": 8475, "loc": { "start": { - "line": 212, + "line": 228, "column": 78 }, "end": { - "line": 212, + "line": 228, "column": 84 }, "identifierName": "atTime" @@ -12734,15 +13514,15 @@ }, "property": { "type": "StringLiteral", - "start": 8036, - "end": 8071, + "start": 8476, + "end": 8511, "loc": { "start": { - "line": 212, + "line": 228, "column": 85 }, "end": { - "line": 212, + "line": 228, "column": 120 } }, @@ -12760,43 +13540,43 @@ }, { "type": "IfStatement", - "start": 8082, - "end": 8190, + "start": 8522, + "end": 8630, "loc": { "start": { - "line": 213, + "line": 229, "column": 8 }, "end": { - "line": 213, + "line": 229, "column": 116 } }, "test": { "type": "CallExpression", - "start": 8086, - "end": 8132, + "start": 8526, + "end": 8572, "loc": { "start": { - "line": 213, + "line": 229, "column": 12 }, "end": { - "line": 213, + "line": 229, "column": 58 } }, "callee": { "type": "Identifier", - "start": 8086, - "end": 8089, + "start": 8526, + "end": 8529, "loc": { "start": { - "line": 213, + "line": 229, "column": 12 }, "end": { - "line": 213, + "line": 229, "column": 15 }, "identifierName": "has" @@ -12806,15 +13586,15 @@ "arguments": [ { "type": "Identifier", - "start": 8090, - "end": 8096, + "start": 8530, + "end": 8536, "loc": { "start": { - "line": 213, + "line": 229, "column": 16 }, "end": { - "line": 213, + "line": 229, "column": 22 }, "identifierName": "atTime" @@ -12823,15 +13603,15 @@ }, { "type": "StringLiteral", - "start": 8098, - "end": 8131, + "start": 8538, + "end": 8571, "loc": { "start": { - "line": 213, + "line": 229, "column": 24 }, "end": { - "line": 213, + "line": 229, "column": 57 } }, @@ -12845,44 +13625,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 8134, - "end": 8190, + "start": 8574, + "end": 8630, "loc": { "start": { - "line": 213, + "line": 229, "column": 60 }, "end": { - "line": 213, + "line": 229, "column": 116 } }, "expression": { "type": "AssignmentExpression", - "start": 8134, - "end": 8189, + "start": 8574, + "end": 8629, "loc": { "start": { - "line": 213, + "line": 229, "column": 60 }, "end": { - "line": 213, + "line": 229, "column": 115 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8134, - "end": 8145, + "start": 8574, + "end": 8585, "loc": { "start": { - "line": 213, + "line": 229, "column": 60 }, "end": { - "line": 213, + "line": 229, "column": 71 }, "identifierName": "intervalEnd" @@ -12891,29 +13671,29 @@ }, "right": { "type": "MemberExpression", - "start": 8148, - "end": 8189, + "start": 8588, + "end": 8629, "loc": { "start": { - "line": 213, + "line": 229, "column": 74 }, "end": { - "line": 213, + "line": 229, "column": 115 } }, "object": { "type": "Identifier", - "start": 8148, - "end": 8154, + "start": 8588, + "end": 8594, "loc": { "start": { - "line": 213, + "line": 229, "column": 74 }, "end": { - "line": 213, + "line": 229, "column": 80 }, "identifierName": "atTime" @@ -12922,15 +13702,15 @@ }, "property": { "type": "StringLiteral", - "start": 8155, - "end": 8188, + "start": 8595, + "end": 8628, "loc": { "start": { - "line": 213, + "line": 229, "column": 81 }, "end": { - "line": 213, + "line": 229, "column": 114 } }, @@ -12955,15 +13735,15 @@ { "type": "CommentLine", "value": " Return result object", - "start": 8206, - "end": 8229, + "start": 8646, + "end": 8669, "loc": { "start": { - "line": 216, + "line": 232, "column": 6 }, "end": { - "line": 216, + "line": 232, "column": 29 } } @@ -12972,44 +13752,44 @@ }, { "type": "ReturnStatement", - "start": 8236, - "end": 8400, + "start": 8676, + "end": 8840, "loc": { "start": { - "line": 217, + "line": 233, "column": 6 }, "end": { - "line": 222, + "line": 238, "column": 8 } }, "argument": { "type": "ObjectExpression", - "start": 8243, - "end": 8399, + "start": 8683, + "end": 8839, "loc": { "start": { - "line": 217, + "line": 233, "column": 13 }, "end": { - "line": 222, + "line": 238, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 8253, - "end": 8264, + "start": 8693, + "end": 8704, "loc": { "start": { - "line": 218, + "line": 234, "column": 8 }, "end": { - "line": 218, + "line": 234, "column": 19 } }, @@ -13018,15 +13798,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8253, - "end": 8264, + "start": 8693, + "end": 8704, "loc": { "start": { - "line": 218, + "line": 234, "column": 8 }, "end": { - "line": 218, + "line": 234, "column": 19 }, "identifierName": "statusCURIE" @@ -13036,15 +13816,15 @@ }, "value": { "type": "Identifier", - "start": 8253, - "end": 8264, + "start": 8693, + "end": 8704, "loc": { "start": { - "line": 218, + "line": 234, "column": 8 }, "end": { - "line": 218, + "line": 234, "column": 19 }, "identifierName": "statusCURIE" @@ -13058,15 +13838,15 @@ }, { "type": "ObjectProperty", - "start": 8274, - "end": 8346, + "start": 8714, + "end": 8786, "loc": { "start": { - "line": 219, + "line": 235, "column": 8 }, "end": { - "line": 219, + "line": 235, "column": 80 } }, @@ -13075,15 +13855,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8274, - "end": 8289, + "start": 8714, + "end": 8729, "loc": { "start": { - "line": 219, + "line": 235, "column": 8 }, "end": { - "line": 219, + "line": 235, "column": 23 }, "identifierName": "statusInEnglish" @@ -13092,57 +13872,57 @@ }, "value": { "type": "MemberExpression", - "start": 8291, - "end": 8346, + "start": 8731, + "end": 8786, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 80 } }, "object": { "type": "CallExpression", - "start": 8291, - "end": 8333, + "start": 8731, + "end": 8773, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 8291, - "end": 8331, + "start": 8731, + "end": 8771, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 65 } }, "object": { "type": "Identifier", - "start": 8291, - "end": 8306, + "start": 8731, + "end": 8746, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 40 }, "identifierName": "PhylorefWrapper" @@ -13151,15 +13931,15 @@ }, "property": { "type": "Identifier", - "start": 8307, - "end": 8331, + "start": 8747, + "end": 8771, "loc": { "start": { - "line": 219, + "line": 235, "column": 41 }, "end": { - "line": 219, + "line": 235, "column": 65 }, "identifierName": "getStatusCURIEsInEnglish" @@ -13172,15 +13952,15 @@ }, "property": { "type": "Identifier", - "start": 8334, - "end": 8345, + "start": 8774, + "end": 8785, "loc": { "start": { - "line": 219, + "line": 235, "column": 68 }, "end": { - "line": 219, + "line": 235, "column": 79 }, "identifierName": "statusCURIE" @@ -13192,15 +13972,15 @@ }, { "type": "ObjectProperty", - "start": 8356, - "end": 8369, + "start": 8796, + "end": 8809, "loc": { "start": { - "line": 220, + "line": 236, "column": 8 }, "end": { - "line": 220, + "line": 236, "column": 21 } }, @@ -13209,15 +13989,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8356, - "end": 8369, + "start": 8796, + "end": 8809, "loc": { "start": { - "line": 220, + "line": 236, "column": 8 }, "end": { - "line": 220, + "line": 236, "column": 21 }, "identifierName": "intervalStart" @@ -13226,15 +14006,15 @@ }, "value": { "type": "Identifier", - "start": 8356, - "end": 8369, + "start": 8796, + "end": 8809, "loc": { "start": { - "line": 220, + "line": 236, "column": 8 }, "end": { - "line": 220, + "line": 236, "column": 21 }, "identifierName": "intervalStart" @@ -13247,15 +14027,15 @@ }, { "type": "ObjectProperty", - "start": 8379, - "end": 8390, + "start": 8819, + "end": 8830, "loc": { "start": { - "line": 221, + "line": 237, "column": 8 }, "end": { - "line": 221, + "line": 237, "column": 19 } }, @@ -13264,15 +14044,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8379, - "end": 8390, + "start": 8819, + "end": 8830, "loc": { "start": { - "line": 221, + "line": 237, "column": 8 }, "end": { - "line": 221, + "line": 237, "column": 19 }, "identifierName": "intervalEnd" @@ -13281,15 +14061,15 @@ }, "value": { "type": "Identifier", - "start": 8379, - "end": 8390, + "start": 8819, + "end": 8830, "loc": { "start": { - "line": 221, + "line": 237, "column": 8 }, "end": { - "line": 221, + "line": 237, "column": 19 }, "identifierName": "intervalEnd" @@ -13307,15 +14087,15 @@ { "type": "CommentLine", "value": " Return result object", - "start": 8206, - "end": 8229, + "start": 8646, + "end": 8669, "loc": { "start": { - "line": 216, + "line": 232, "column": 6 }, "end": { - "line": 216, + "line": 232, "column": 29 } } @@ -13331,15 +14111,15 @@ { "type": "CommentLine", "value": " Return a result object that contains:", - "start": 6950, - "end": 6990, + "start": 7390, + "end": 7430, "loc": { "start": { - "line": 190, + "line": 206, "column": 4 }, "end": { - "line": 190, + "line": 206, "column": 44 } } @@ -13347,15 +14127,15 @@ { "type": "CommentLine", "value": " - status: phyloreference status as a short URI (CURIE)", - "start": 6995, - "end": 7053, + "start": 7435, + "end": 7493, "loc": { "start": { - "line": 191, + "line": 207, "column": 4 }, "end": { - "line": 191, + "line": 207, "column": 62 } } @@ -13363,15 +14143,15 @@ { "type": "CommentLine", "value": " - statusInEnglish: an English representation of the phyloref status", - "start": 7058, - "end": 7129, + "start": 7498, + "end": 7569, "loc": { "start": { - "line": 192, + "line": 208, "column": 4 }, "end": { - "line": 192, + "line": 208, "column": 75 } } @@ -13379,15 +14159,15 @@ { "type": "CommentLine", "value": " - intervalStart: the start of the interval", - "start": 7134, - "end": 7180, + "start": 7574, + "end": 7620, "loc": { "start": { - "line": 193, + "line": 209, "column": 4 }, "end": { - "line": 193, + "line": 209, "column": 50 } } @@ -13395,15 +14175,15 @@ { "type": "CommentLine", "value": " - intervalEnd: the end of the interval", - "start": 7185, - "end": 7227, + "start": 7625, + "end": 7667, "loc": { "start": { - "line": 194, + "line": 210, "column": 4 }, "end": { - "line": 194, + "line": 210, "column": 46 } } @@ -13413,15 +14193,15 @@ { "type": "CommentLine", "value": " If we couldn't figure out a status for this phyloref, assume it's a draft.", - "start": 8412, - "end": 8489, + "start": 8852, + "end": 8929, "loc": { "start": { - "line": 225, + "line": 241, "column": 4 }, "end": { - "line": 225, + "line": 241, "column": 81 } } @@ -13430,44 +14210,44 @@ }, { "type": "ReturnStatement", - "start": 8494, - "end": 8621, + "start": 8934, + "end": 9061, "loc": { "start": { - "line": 226, + "line": 242, "column": 4 }, "end": { - "line": 229, + "line": 245, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 8501, - "end": 8620, + "start": 8941, + "end": 9060, "loc": { "start": { - "line": 226, + "line": 242, "column": 11 }, "end": { - "line": 229, + "line": 245, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 8509, - "end": 8533, + "start": 8949, + "end": 8973, "loc": { "start": { - "line": 227, + "line": 243, "column": 6 }, "end": { - "line": 227, + "line": 243, "column": 30 } }, @@ -13476,15 +14256,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8509, - "end": 8520, + "start": 8949, + "end": 8960, "loc": { "start": { - "line": 227, + "line": 243, "column": 6 }, "end": { - "line": 227, + "line": 243, "column": 17 }, "identifierName": "statusCURIE" @@ -13494,15 +14274,15 @@ }, "value": { "type": "StringLiteral", - "start": 8522, - "end": 8533, + "start": 8962, + "end": 8973, "loc": { "start": { - "line": 227, + "line": 243, "column": 19 }, "end": { - "line": 227, + "line": 243, "column": 30 } }, @@ -13516,15 +14296,15 @@ }, { "type": "ObjectProperty", - "start": 8541, - "end": 8613, + "start": 8981, + "end": 9053, "loc": { "start": { - "line": 228, + "line": 244, "column": 6 }, "end": { - "line": 228, + "line": 244, "column": 78 } }, @@ -13533,15 +14313,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8541, - "end": 8556, + "start": 8981, + "end": 8996, "loc": { "start": { - "line": 228, + "line": 244, "column": 6 }, "end": { - "line": 228, + "line": 244, "column": 21 }, "identifierName": "statusInEnglish" @@ -13550,57 +14330,57 @@ }, "value": { "type": "MemberExpression", - "start": 8558, - "end": 8613, + "start": 8998, + "end": 9053, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 78 } }, "object": { "type": "CallExpression", - "start": 8558, - "end": 8600, + "start": 8998, + "end": 9040, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 8558, - "end": 8598, + "start": 8998, + "end": 9038, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 63 } }, "object": { "type": "Identifier", - "start": 8558, - "end": 8573, + "start": 8998, + "end": 9013, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 38 }, "identifierName": "PhylorefWrapper" @@ -13609,15 +14389,15 @@ }, "property": { "type": "Identifier", - "start": 8574, - "end": 8598, + "start": 9014, + "end": 9038, "loc": { "start": { - "line": 228, + "line": 244, "column": 39 }, "end": { - "line": 228, + "line": 244, "column": 63 }, "identifierName": "getStatusCURIEsInEnglish" @@ -13630,15 +14410,15 @@ }, "property": { "type": "StringLiteral", - "start": 8601, - "end": 8612, + "start": 9041, + "end": 9052, "loc": { "start": { - "line": 228, + "line": 244, "column": 66 }, "end": { - "line": 228, + "line": 244, "column": 77 } }, @@ -13658,15 +14438,15 @@ { "type": "CommentLine", "value": " If we couldn't figure out a status for this phyloref, assume it's a draft.", - "start": 8412, - "end": 8489, + "start": 8852, + "end": 8929, "loc": { "start": { - "line": 225, + "line": 241, "column": 4 }, "end": { - "line": 225, + "line": 241, "column": 81 } } @@ -13679,15 +14459,15 @@ }, { "type": "ClassMethod", - "start": 8629, - "end": 9878, + "start": 9069, + "end": 10318, "loc": { "start": { - "line": 232, + "line": 248, "column": 2 }, "end": { - "line": 264, + "line": 280, "column": 3 } }, @@ -13695,15 +14475,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8629, - "end": 8645, + "start": 9069, + "end": 9085, "loc": { "start": { - "line": 232, + "line": 248, "column": 2 }, "end": { - "line": 232, + "line": 248, "column": 18 }, "identifierName": "getStatusChanges" @@ -13718,58 +14498,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8648, - "end": 9878, + "start": 9088, + "end": 10318, "loc": { "start": { - "line": 232, + "line": 248, "column": 21 }, "end": { - "line": 264, + "line": 280, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 8725, - "end": 9817, + "start": 9165, + "end": 10257, "loc": { "start": { - "line": 234, + "line": 250, "column": 4 }, "end": { - "line": 260, + "line": 276, "column": 5 } }, "test": { "type": "CallExpression", - "start": 8729, - "end": 8772, + "start": 9169, + "end": 9212, "loc": { "start": { - "line": 234, + "line": 250, "column": 8 }, "end": { - "line": 234, + "line": 250, "column": 51 } }, "callee": { "type": "Identifier", - "start": 8729, - "end": 8732, + "start": 9169, + "end": 9172, "loc": { "start": { - "line": 234, + "line": 250, "column": 8 }, "end": { - "line": 234, + "line": 250, "column": 11 }, "identifierName": "has" @@ -13780,44 +14560,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 8733, - "end": 8746, + "start": 9173, + "end": 9186, "loc": { "start": { - "line": 234, + "line": 250, "column": 12 }, "end": { - "line": 234, + "line": 250, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 8733, - "end": 8737, + "start": 9173, + "end": 9177, "loc": { "start": { - "line": 234, + "line": 250, "column": 12 }, "end": { - "line": 234, + "line": 250, "column": 16 } } }, "property": { "type": "Identifier", - "start": 8738, - "end": 8746, + "start": 9178, + "end": 9186, "loc": { "start": { - "line": 234, + "line": 250, "column": 17 }, "end": { - "line": 234, + "line": 250, "column": 25 }, "identifierName": "phyloref" @@ -13828,15 +14608,15 @@ }, { "type": "StringLiteral", - "start": 8748, - "end": 8771, + "start": 9188, + "end": 9211, "loc": { "start": { - "line": 234, + "line": 250, "column": 27 }, "end": { - "line": 234, + "line": 250, "column": 50 } }, @@ -13851,115 +14631,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 8774, - "end": 9817, + "start": 9214, + "end": 10257, "loc": { "start": { - "line": 234, + "line": 250, "column": 53 }, "end": { - "line": 260, + "line": 276, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 8782, - "end": 9811, + "start": 9222, + "end": 10251, "loc": { "start": { - "line": 235, + "line": 251, "column": 6 }, "end": { - "line": 259, + "line": 275, "column": 9 } }, "argument": { "type": "CallExpression", - "start": 8789, - "end": 9810, + "start": 9229, + "end": 10250, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 259, + "line": 275, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 8789, - "end": 8831, + "start": 9229, + "end": 9271, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 55 } }, "object": { "type": "MemberExpression", - "start": 8789, - "end": 8827, + "start": 9229, + "end": 9267, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 51 } }, "object": { "type": "MemberExpression", - "start": 8789, - "end": 8802, + "start": 9229, + "end": 9242, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 8789, - "end": 8793, + "start": 9229, + "end": 9233, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 17 } } }, "property": { "type": "Identifier", - "start": 8794, - "end": 8802, + "start": 9234, + "end": 9242, "loc": { "start": { - "line": 235, + "line": 251, "column": 18 }, "end": { - "line": 235, + "line": 251, "column": 26 }, "identifierName": "phyloref" @@ -13970,15 +14750,15 @@ }, "property": { "type": "StringLiteral", - "start": 8803, - "end": 8826, + "start": 9243, + "end": 9266, "loc": { "start": { - "line": 235, + "line": 251, "column": 27 }, "end": { - "line": 235, + "line": 251, "column": 50 } }, @@ -13992,15 +14772,15 @@ }, "property": { "type": "Identifier", - "start": 8828, - "end": 8831, + "start": 9268, + "end": 9271, "loc": { "start": { - "line": 235, + "line": 251, "column": 52 }, "end": { - "line": 235, + "line": 251, "column": 55 }, "identifierName": "map" @@ -14012,15 +14792,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 8832, - "end": 9809, + "start": 9272, + "end": 10249, "loc": { "start": { - "line": 235, + "line": 251, "column": 56 }, "end": { - "line": 259, + "line": 275, "column": 7 } }, @@ -14031,15 +14811,15 @@ "params": [ { "type": "Identifier", - "start": 8833, - "end": 8838, + "start": 9273, + "end": 9278, "loc": { "start": { - "line": 235, + "line": 251, "column": 57 }, "end": { - "line": 235, + "line": 251, "column": 62 }, "identifierName": "entry" @@ -14049,59 +14829,59 @@ ], "body": { "type": "BlockStatement", - "start": 8843, - "end": 9809, + "start": 9283, + "end": 10249, "loc": { "start": { - "line": 235, + "line": 251, "column": 67 }, "end": { - "line": 259, + "line": 275, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 8853, - "end": 8871, + "start": 9293, + "end": 9311, "loc": { "start": { - "line": 236, + "line": 252, "column": 8 }, "end": { - "line": 236, + "line": 252, "column": 26 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8859, - "end": 8870, + "start": 9299, + "end": 9310, "loc": { "start": { - "line": 236, + "line": 252, "column": 14 }, "end": { - "line": 236, + "line": 252, "column": 25 } }, "id": { "type": "Identifier", - "start": 8859, - "end": 8865, + "start": 9299, + "end": 9305, "loc": { "start": { - "line": 236, + "line": 252, "column": 14 }, "end": { - "line": 236, + "line": 252, "column": 20 }, "identifierName": "result" @@ -14110,15 +14890,15 @@ }, "init": { "type": "ObjectExpression", - "start": 8868, - "end": 8870, + "start": 9308, + "end": 9310, "loc": { "start": { - "line": 236, + "line": 252, "column": 23 }, "end": { - "line": 236, + "line": 252, "column": 25 } }, @@ -14131,15 +14911,15 @@ { "type": "CommentLine", "value": " Create a statusCURIE convenience field.", - "start": 8881, - "end": 8923, + "start": 9321, + "end": 9363, "loc": { "start": { - "line": 238, + "line": 254, "column": 8 }, "end": { - "line": 238, + "line": 254, "column": 50 } } @@ -14148,43 +14928,43 @@ }, { "type": "IfStatement", - "start": 8932, - "end": 9139, + "start": 9372, + "end": 9579, "loc": { "start": { - "line": 239, + "line": 255, "column": 8 }, "end": { - "line": 242, + "line": 258, "column": 9 } }, "test": { "type": "CallExpression", - "start": 8936, - "end": 8964, + "start": 9376, + "end": 9404, "loc": { "start": { - "line": 239, + "line": 255, "column": 12 }, "end": { - "line": 239, + "line": 255, "column": 40 } }, "callee": { "type": "Identifier", - "start": 8936, - "end": 8939, + "start": 9376, + "end": 9379, "loc": { "start": { - "line": 239, + "line": 255, "column": 12 }, "end": { - "line": 239, + "line": 255, "column": 15 }, "identifierName": "has" @@ -14195,15 +14975,15 @@ "arguments": [ { "type": "Identifier", - "start": 8940, - "end": 8945, + "start": 9380, + "end": 9385, "loc": { "start": { - "line": 239, + "line": 255, "column": 16 }, "end": { - "line": 239, + "line": 255, "column": 21 }, "identifierName": "entry" @@ -14212,15 +14992,15 @@ }, { "type": "StringLiteral", - "start": 8947, - "end": 8963, + "start": 9387, + "end": 9403, "loc": { "start": { - "line": 239, + "line": 255, "column": 23 }, "end": { - "line": 239, + "line": 255, "column": 39 } }, @@ -14235,73 +15015,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 8966, - "end": 9139, + "start": 9406, + "end": 9579, "loc": { "start": { - "line": 239, + "line": 255, "column": 42 }, "end": { - "line": 242, + "line": 258, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 8978, - "end": 9030, + "start": 9418, + "end": 9470, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 62 } }, "expression": { "type": "AssignmentExpression", - "start": 8978, - "end": 9029, + "start": 9418, + "end": 9469, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 61 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 8978, - "end": 8996, + "start": 9418, + "end": 9436, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 28 } }, "object": { "type": "Identifier", - "start": 8978, - "end": 8984, + "start": 9418, + "end": 9424, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 16 }, "identifierName": "result" @@ -14310,15 +15090,15 @@ }, "property": { "type": "Identifier", - "start": 8985, - "end": 8996, + "start": 9425, + "end": 9436, "loc": { "start": { - "line": 240, + "line": 256, "column": 17 }, "end": { - "line": 240, + "line": 256, "column": 28 }, "identifierName": "statusCURIE" @@ -14329,43 +15109,43 @@ }, "right": { "type": "MemberExpression", - "start": 8999, - "end": 9029, + "start": 9439, + "end": 9469, "loc": { "start": { - "line": 240, + "line": 256, "column": 31 }, "end": { - "line": 240, + "line": 256, "column": 61 } }, "object": { "type": "MemberExpression", - "start": 8999, - "end": 9022, + "start": 9439, + "end": 9462, "loc": { "start": { - "line": 240, + "line": 256, "column": 31 }, "end": { - "line": 240, + "line": 256, "column": 54 } }, "object": { "type": "Identifier", - "start": 8999, - "end": 9004, + "start": 9439, + "end": 9444, "loc": { "start": { - "line": 240, + "line": 256, "column": 31 }, "end": { - "line": 240, + "line": 256, "column": 36 }, "identifierName": "entry" @@ -14374,15 +15154,15 @@ }, "property": { "type": "StringLiteral", - "start": 9005, - "end": 9021, + "start": 9445, + "end": 9461, "loc": { "start": { - "line": 240, + "line": 256, "column": 37 }, "end": { - "line": 240, + "line": 256, "column": 53 } }, @@ -14396,15 +15176,15 @@ }, "property": { "type": "StringLiteral", - "start": 9023, - "end": 9028, + "start": 9463, + "end": 9468, "loc": { "start": { - "line": 240, + "line": 256, "column": 55 }, "end": { - "line": 240, + "line": 256, "column": 60 } }, @@ -14420,58 +15200,58 @@ }, { "type": "ExpressionStatement", - "start": 9041, - "end": 9129, + "start": 9481, + "end": 9569, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 98 } }, "expression": { "type": "AssignmentExpression", - "start": 9041, - "end": 9128, + "start": 9481, + "end": 9568, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 97 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9041, - "end": 9063, + "start": 9481, + "end": 9503, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 32 } }, "object": { "type": "Identifier", - "start": 9041, - "end": 9047, + "start": 9481, + "end": 9487, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 16 }, "identifierName": "result" @@ -14480,15 +15260,15 @@ }, "property": { "type": "Identifier", - "start": 9048, - "end": 9063, + "start": 9488, + "end": 9503, "loc": { "start": { - "line": 241, + "line": 257, "column": 17 }, "end": { - "line": 241, + "line": 257, "column": 32 }, "identifierName": "statusInEnglish" @@ -14499,57 +15279,57 @@ }, "right": { "type": "MemberExpression", - "start": 9066, - "end": 9128, + "start": 9506, + "end": 9568, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 97 } }, "object": { "type": "CallExpression", - "start": 9066, - "end": 9108, + "start": 9506, + "end": 9548, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 77 } }, "callee": { "type": "MemberExpression", - "start": 9066, - "end": 9106, + "start": 9506, + "end": 9546, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 75 } }, "object": { "type": "Identifier", - "start": 9066, - "end": 9081, + "start": 9506, + "end": 9521, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 50 }, "identifierName": "PhylorefWrapper" @@ -14558,15 +15338,15 @@ }, "property": { "type": "Identifier", - "start": 9082, - "end": 9106, + "start": 9522, + "end": 9546, "loc": { "start": { - "line": 241, + "line": 257, "column": 51 }, "end": { - "line": 241, + "line": 257, "column": 75 }, "identifierName": "getStatusCURIEsInEnglish" @@ -14579,29 +15359,29 @@ }, "property": { "type": "MemberExpression", - "start": 9109, - "end": 9127, + "start": 9549, + "end": 9567, "loc": { "start": { - "line": 241, + "line": 257, "column": 78 }, "end": { - "line": 241, + "line": 257, "column": 96 } }, "object": { "type": "Identifier", - "start": 9109, - "end": 9115, + "start": 9549, + "end": 9555, "loc": { "start": { - "line": 241, + "line": 257, "column": 78 }, "end": { - "line": 241, + "line": 257, "column": 84 }, "identifierName": "result" @@ -14610,15 +15390,15 @@ }, "property": { "type": "Identifier", - "start": 9116, - "end": 9127, + "start": 9556, + "end": 9567, "loc": { "start": { - "line": 241, + "line": 257, "column": 85 }, "end": { - "line": 241, + "line": 257, "column": 96 }, "identifierName": "statusCURIE" @@ -14640,15 +15420,15 @@ { "type": "CommentLine", "value": " Create a statusCURIE convenience field.", - "start": 8881, - "end": 8923, + "start": 9321, + "end": 9363, "loc": { "start": { - "line": 238, + "line": 254, "column": 8 }, "end": { - "line": 238, + "line": 254, "column": 50 } } @@ -14658,15 +15438,15 @@ { "type": "CommentLine", "value": " Create intervalStart/intervalEnd convenient fields", - "start": 9149, - "end": 9202, + "start": 9589, + "end": 9642, "loc": { "start": { - "line": 244, + "line": 260, "column": 8 }, "end": { - "line": 244, + "line": 260, "column": 61 } } @@ -14675,43 +15455,43 @@ }, { "type": "IfStatement", - "start": 9211, - "end": 9777, + "start": 9651, + "end": 10217, "loc": { "start": { - "line": 245, + "line": 261, "column": 8 }, "end": { - "line": 256, + "line": 272, "column": 9 } }, "test": { "type": "CallExpression", - "start": 9215, - "end": 9239, + "start": 9655, + "end": 9679, "loc": { "start": { - "line": 245, + "line": 261, "column": 12 }, "end": { - "line": 245, + "line": 261, "column": 36 } }, "callee": { "type": "Identifier", - "start": 9215, - "end": 9218, + "start": 9655, + "end": 9658, "loc": { "start": { - "line": 245, + "line": 261, "column": 12 }, "end": { - "line": 245, + "line": 261, "column": 15 }, "identifierName": "has" @@ -14722,15 +15502,15 @@ "arguments": [ { "type": "Identifier", - "start": 9219, - "end": 9224, + "start": 9659, + "end": 9664, "loc": { "start": { - "line": 245, + "line": 261, "column": 16 }, "end": { - "line": 245, + "line": 261, "column": 21 }, "identifierName": "entry" @@ -14739,15 +15519,15 @@ }, { "type": "StringLiteral", - "start": 9226, - "end": 9238, + "start": 9666, + "end": 9678, "loc": { "start": { - "line": 245, + "line": 261, "column": 23 }, "end": { - "line": 245, + "line": 261, "column": 35 } }, @@ -14762,59 +15542,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 9241, - "end": 9777, + "start": 9681, + "end": 10217, "loc": { "start": { - "line": 245, + "line": 261, "column": 38 }, "end": { - "line": 256, + "line": 272, "column": 9 } }, "body": [ { "type": "VariableDeclaration", - "start": 9253, - "end": 9288, + "start": 9693, + "end": 9728, "loc": { "start": { - "line": 246, + "line": 262, "column": 10 }, "end": { - "line": 246, + "line": 262, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 9259, - "end": 9287, + "start": 9699, + "end": 9727, "loc": { "start": { - "line": 246, + "line": 262, "column": 16 }, "end": { - "line": 246, + "line": 262, "column": 44 } }, "id": { "type": "Identifier", - "start": 9259, - "end": 9265, + "start": 9699, + "end": 9705, "loc": { "start": { - "line": 246, + "line": 262, "column": 16 }, "end": { - "line": 246, + "line": 262, "column": 22 }, "identifierName": "atTime" @@ -14823,29 +15603,29 @@ }, "init": { "type": "MemberExpression", - "start": 9268, - "end": 9287, + "start": 9708, + "end": 9727, "loc": { "start": { - "line": 246, + "line": 262, "column": 25 }, "end": { - "line": 246, + "line": 262, "column": 44 } }, "object": { "type": "Identifier", - "start": 9268, - "end": 9273, + "start": 9708, + "end": 9713, "loc": { "start": { - "line": 246, + "line": 262, "column": 25 }, "end": { - "line": 246, + "line": 262, "column": 30 }, "identifierName": "entry" @@ -14854,15 +15634,15 @@ }, "property": { "type": "StringLiteral", - "start": 9274, - "end": 9286, + "start": 9714, + "end": 9726, "loc": { "start": { - "line": 246, + "line": 262, "column": 31 }, "end": { - "line": 246, + "line": 262, "column": 43 } }, @@ -14880,43 +15660,43 @@ }, { "type": "IfStatement", - "start": 9299, - "end": 9532, + "start": 9739, + "end": 9972, "loc": { "start": { - "line": 247, + "line": 263, "column": 10 }, "end": { - "line": 250, + "line": 266, "column": 11 } }, "test": { "type": "CallExpression", - "start": 9303, - "end": 9351, + "start": 9743, + "end": 9791, "loc": { "start": { - "line": 247, + "line": 263, "column": 14 }, "end": { - "line": 247, + "line": 263, "column": 62 } }, "callee": { "type": "Identifier", - "start": 9303, - "end": 9306, + "start": 9743, + "end": 9746, "loc": { "start": { - "line": 247, + "line": 263, "column": 14 }, "end": { - "line": 247, + "line": 263, "column": 17 }, "identifierName": "has" @@ -14926,15 +15706,15 @@ "arguments": [ { "type": "Identifier", - "start": 9307, - "end": 9313, + "start": 9747, + "end": 9753, "loc": { "start": { - "line": 247, + "line": 263, "column": 18 }, "end": { - "line": 247, + "line": 263, "column": 24 }, "identifierName": "atTime" @@ -14943,15 +15723,15 @@ }, { "type": "StringLiteral", - "start": 9315, - "end": 9350, + "start": 9755, + "end": 9790, "loc": { "start": { - "line": 247, + "line": 263, "column": 26 }, "end": { - "line": 247, + "line": 263, "column": 61 } }, @@ -14965,73 +15745,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 9353, - "end": 9532, + "start": 9793, + "end": 9972, "loc": { "start": { - "line": 247, + "line": 263, "column": 64 }, "end": { - "line": 250, + "line": 266, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 9367, - "end": 9434, + "start": 9807, + "end": 9874, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 79 } }, "expression": { "type": "AssignmentExpression", - "start": 9367, - "end": 9433, + "start": 9807, + "end": 9873, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 78 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9367, - "end": 9387, + "start": 9807, + "end": 9827, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 32 } }, "object": { "type": "Identifier", - "start": 9367, - "end": 9373, + "start": 9807, + "end": 9813, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 18 }, "identifierName": "result" @@ -15040,15 +15820,15 @@ }, "property": { "type": "Identifier", - "start": 9374, - "end": 9387, + "start": 9814, + "end": 9827, "loc": { "start": { - "line": 248, + "line": 264, "column": 19 }, "end": { - "line": 248, + "line": 264, "column": 32 }, "identifierName": "intervalStart" @@ -15059,29 +15839,29 @@ }, "right": { "type": "MemberExpression", - "start": 9390, - "end": 9433, + "start": 9830, + "end": 9873, "loc": { "start": { - "line": 248, + "line": 264, "column": 35 }, "end": { - "line": 248, + "line": 264, "column": 78 } }, "object": { "type": "Identifier", - "start": 9390, - "end": 9396, + "start": 9830, + "end": 9836, "loc": { "start": { - "line": 248, + "line": 264, "column": 35 }, "end": { - "line": 248, + "line": 264, "column": 41 }, "identifierName": "atTime" @@ -15090,15 +15870,15 @@ }, "property": { "type": "StringLiteral", - "start": 9397, - "end": 9432, + "start": 9837, + "end": 9872, "loc": { "start": { - "line": 248, + "line": 264, "column": 42 }, "end": { - "line": 248, + "line": 264, "column": 77 } }, @@ -15114,58 +15894,58 @@ }, { "type": "ExpressionStatement", - "start": 9447, - "end": 9520, + "start": 9887, + "end": 9960, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 85 } }, "expression": { "type": "AssignmentExpression", - "start": 9447, - "end": 9519, + "start": 9887, + "end": 9959, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 84 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9447, - "end": 9477, + "start": 9887, + "end": 9917, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 42 } }, "object": { "type": "Identifier", - "start": 9447, - "end": 9453, + "start": 9887, + "end": 9893, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 18 }, "identifierName": "result" @@ -15174,15 +15954,15 @@ }, "property": { "type": "Identifier", - "start": 9454, - "end": 9477, + "start": 9894, + "end": 9917, "loc": { "start": { - "line": 249, + "line": 265, "column": 19 }, "end": { - "line": 249, + "line": 265, "column": 42 }, "identifierName": "intervalStartAsCalendar" @@ -15193,57 +15973,57 @@ }, "right": { "type": "CallExpression", - "start": 9480, - "end": 9519, + "start": 9920, + "end": 9959, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 84 } }, "callee": { "type": "MemberExpression", - "start": 9480, - "end": 9517, + "start": 9920, + "end": 9957, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 82 } }, "object": { "type": "CallExpression", - "start": 9480, - "end": 9508, + "start": 9920, + "end": 9948, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 73 } }, "callee": { "type": "Identifier", - "start": 9480, - "end": 9486, + "start": 9920, + "end": 9926, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 51 }, "identifierName": "moment" @@ -15253,29 +16033,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 9487, - "end": 9507, + "start": 9927, + "end": 9947, "loc": { "start": { - "line": 249, + "line": 265, "column": 52 }, "end": { - "line": 249, + "line": 265, "column": 72 } }, "object": { "type": "Identifier", - "start": 9487, - "end": 9493, + "start": 9927, + "end": 9933, "loc": { "start": { - "line": 249, + "line": 265, "column": 52 }, "end": { - "line": 249, + "line": 265, "column": 58 }, "identifierName": "result" @@ -15284,15 +16064,15 @@ }, "property": { "type": "Identifier", - "start": 9494, - "end": 9507, + "start": 9934, + "end": 9947, "loc": { "start": { - "line": 249, + "line": 265, "column": 59 }, "end": { - "line": 249, + "line": 265, "column": 72 }, "identifierName": "intervalStart" @@ -15305,15 +16085,15 @@ }, "property": { "type": "Identifier", - "start": 9509, - "end": 9517, + "start": 9949, + "end": 9957, "loc": { "start": { - "line": 249, + "line": 265, "column": 74 }, "end": { - "line": 249, + "line": 265, "column": 82 }, "identifierName": "calendar" @@ -15333,43 +16113,43 @@ }, { "type": "IfStatement", - "start": 9544, - "end": 9767, + "start": 9984, + "end": 10207, "loc": { "start": { - "line": 252, + "line": 268, "column": 10 }, "end": { - "line": 255, + "line": 271, "column": 11 } }, "test": { "type": "CallExpression", - "start": 9548, - "end": 9594, + "start": 9988, + "end": 10034, "loc": { "start": { - "line": 252, + "line": 268, "column": 14 }, "end": { - "line": 252, + "line": 268, "column": 60 } }, "callee": { "type": "Identifier", - "start": 9548, - "end": 9551, + "start": 9988, + "end": 9991, "loc": { "start": { - "line": 252, + "line": 268, "column": 14 }, "end": { - "line": 252, + "line": 268, "column": 17 }, "identifierName": "has" @@ -15379,15 +16159,15 @@ "arguments": [ { "type": "Identifier", - "start": 9552, - "end": 9558, + "start": 9992, + "end": 9998, "loc": { "start": { - "line": 252, + "line": 268, "column": 18 }, "end": { - "line": 252, + "line": 268, "column": 24 }, "identifierName": "atTime" @@ -15396,15 +16176,15 @@ }, { "type": "StringLiteral", - "start": 9560, - "end": 9593, + "start": 10000, + "end": 10033, "loc": { "start": { - "line": 252, + "line": 268, "column": 26 }, "end": { - "line": 252, + "line": 268, "column": 59 } }, @@ -15418,73 +16198,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 9596, - "end": 9767, + "start": 10036, + "end": 10207, "loc": { "start": { - "line": 252, + "line": 268, "column": 62 }, "end": { - "line": 255, + "line": 271, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 9610, - "end": 9673, + "start": 10050, + "end": 10113, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 75 } }, "expression": { "type": "AssignmentExpression", - "start": 9610, - "end": 9672, + "start": 10050, + "end": 10112, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 74 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9610, - "end": 9628, + "start": 10050, + "end": 10068, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 30 } }, "object": { "type": "Identifier", - "start": 9610, - "end": 9616, + "start": 10050, + "end": 10056, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 18 }, "identifierName": "result" @@ -15493,15 +16273,15 @@ }, "property": { "type": "Identifier", - "start": 9617, - "end": 9628, + "start": 10057, + "end": 10068, "loc": { "start": { - "line": 253, + "line": 269, "column": 19 }, "end": { - "line": 253, + "line": 269, "column": 30 }, "identifierName": "intervalEnd" @@ -15512,29 +16292,29 @@ }, "right": { "type": "MemberExpression", - "start": 9631, - "end": 9672, + "start": 10071, + "end": 10112, "loc": { "start": { - "line": 253, + "line": 269, "column": 33 }, "end": { - "line": 253, + "line": 269, "column": 74 } }, "object": { "type": "Identifier", - "start": 9631, - "end": 9637, + "start": 10071, + "end": 10077, "loc": { "start": { - "line": 253, + "line": 269, "column": 33 }, "end": { - "line": 253, + "line": 269, "column": 39 }, "identifierName": "atTime" @@ -15543,15 +16323,15 @@ }, "property": { "type": "StringLiteral", - "start": 9638, - "end": 9671, + "start": 10078, + "end": 10111, "loc": { "start": { - "line": 253, + "line": 269, "column": 40 }, "end": { - "line": 253, + "line": 269, "column": 73 } }, @@ -15567,58 +16347,58 @@ }, { "type": "ExpressionStatement", - "start": 9686, - "end": 9755, + "start": 10126, + "end": 10195, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 81 } }, "expression": { "type": "AssignmentExpression", - "start": 9686, - "end": 9754, + "start": 10126, + "end": 10194, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 80 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9686, - "end": 9714, + "start": 10126, + "end": 10154, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 40 } }, "object": { "type": "Identifier", - "start": 9686, - "end": 9692, + "start": 10126, + "end": 10132, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 18 }, "identifierName": "result" @@ -15627,15 +16407,15 @@ }, "property": { "type": "Identifier", - "start": 9693, - "end": 9714, + "start": 10133, + "end": 10154, "loc": { "start": { - "line": 254, + "line": 270, "column": 19 }, "end": { - "line": 254, + "line": 270, "column": 40 }, "identifierName": "intervalEndAsCalendar" @@ -15646,57 +16426,57 @@ }, "right": { "type": "CallExpression", - "start": 9717, - "end": 9754, + "start": 10157, + "end": 10194, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 80 } }, "callee": { "type": "MemberExpression", - "start": 9717, - "end": 9752, + "start": 10157, + "end": 10192, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 78 } }, "object": { "type": "CallExpression", - "start": 9717, - "end": 9743, + "start": 10157, + "end": 10183, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 69 } }, "callee": { "type": "Identifier", - "start": 9717, - "end": 9723, + "start": 10157, + "end": 10163, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 49 }, "identifierName": "moment" @@ -15706,29 +16486,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 9724, - "end": 9742, + "start": 10164, + "end": 10182, "loc": { "start": { - "line": 254, + "line": 270, "column": 50 }, "end": { - "line": 254, + "line": 270, "column": 68 } }, "object": { "type": "Identifier", - "start": 9724, - "end": 9730, + "start": 10164, + "end": 10170, "loc": { "start": { - "line": 254, + "line": 270, "column": 50 }, "end": { - "line": 254, + "line": 270, "column": 56 }, "identifierName": "result" @@ -15737,15 +16517,15 @@ }, "property": { "type": "Identifier", - "start": 9731, - "end": 9742, + "start": 10171, + "end": 10182, "loc": { "start": { - "line": 254, + "line": 270, "column": 57 }, "end": { - "line": 254, + "line": 270, "column": 68 }, "identifierName": "intervalEnd" @@ -15758,15 +16538,15 @@ }, "property": { "type": "Identifier", - "start": 9744, - "end": 9752, + "start": 10184, + "end": 10192, "loc": { "start": { - "line": 254, + "line": 270, "column": 70 }, "end": { - "line": 254, + "line": 270, "column": 78 }, "identifierName": "calendar" @@ -15792,15 +16572,15 @@ { "type": "CommentLine", "value": " Create intervalStart/intervalEnd convenient fields", - "start": 9149, - "end": 9202, + "start": 9589, + "end": 9642, "loc": { "start": { - "line": 244, + "line": 260, "column": 8 }, "end": { - "line": 244, + "line": 260, "column": 61 } } @@ -15809,29 +16589,29 @@ }, { "type": "ReturnStatement", - "start": 9787, - "end": 9801, + "start": 10227, + "end": 10241, "loc": { "start": { - "line": 258, + "line": 274, "column": 8 }, "end": { - "line": 258, + "line": 274, "column": 22 } }, "argument": { "type": "Identifier", - "start": 9794, - "end": 9800, + "start": 10234, + "end": 10240, "loc": { "start": { - "line": 258, + "line": 274, "column": 15 }, "end": { - "line": 258, + "line": 274, "column": 21 }, "identifierName": "result" @@ -15855,15 +16635,15 @@ { "type": "CommentLine", "value": " Return a list of status changes for a particular phyloreference", - "start": 8654, - "end": 8720, + "start": 9094, + "end": 9160, "loc": { "start": { - "line": 233, + "line": 249, "column": 4 }, "end": { - "line": 233, + "line": 249, "column": 70 } } @@ -15873,15 +16653,15 @@ { "type": "CommentLine", "value": " No changes? Return an empty list.", - "start": 9823, - "end": 9859, + "start": 10263, + "end": 10299, "loc": { "start": { - "line": 262, + "line": 278, "column": 4 }, "end": { - "line": 262, + "line": 278, "column": 40 } } @@ -15890,29 +16670,29 @@ }, { "type": "ReturnStatement", - "start": 9864, - "end": 9874, + "start": 10304, + "end": 10314, "loc": { "start": { - "line": 263, + "line": 279, "column": 4 }, "end": { - "line": 263, + "line": 279, "column": 14 } }, "argument": { "type": "ArrayExpression", - "start": 9871, - "end": 9873, + "start": 10311, + "end": 10313, "loc": { "start": { - "line": 263, + "line": 279, "column": 11 }, "end": { - "line": 263, + "line": 279, "column": 13 } }, @@ -15923,15 +16703,15 @@ { "type": "CommentLine", "value": " No changes? Return an empty list.", - "start": 9823, - "end": 9859, + "start": 10263, + "end": 10299, "loc": { "start": { - "line": 262, + "line": 278, "column": 4 }, "end": { - "line": 262, + "line": 278, "column": 40 } } @@ -15944,15 +16724,15 @@ }, { "type": "ClassMethod", - "start": 9882, - "end": 11543, + "start": 10322, + "end": 11983, "loc": { "start": { - "line": 266, + "line": 282, "column": 2 }, "end": { - "line": 308, + "line": 324, "column": 3 } }, @@ -15960,15 +16740,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9882, - "end": 9891, + "start": 10322, + "end": 10331, "loc": { "start": { - "line": 266, + "line": 282, "column": 2 }, "end": { - "line": 266, + "line": 282, "column": 11 }, "identifierName": "setStatus" @@ -15983,15 +16763,15 @@ "params": [ { "type": "Identifier", - "start": 9892, - "end": 9898, + "start": 10332, + "end": 10338, "loc": { "start": { - "line": 266, + "line": 282, "column": 12 }, "end": { - "line": 266, + "line": 282, "column": 18 }, "identifierName": "status" @@ -16001,44 +16781,44 @@ ], "body": { "type": "BlockStatement", - "start": 9900, - "end": 11543, + "start": 10340, + "end": 11983, "loc": { "start": { - "line": 266, + "line": 282, "column": 20 }, "end": { - "line": 308, + "line": 324, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 10006, - "end": 10162, + "start": 10446, + "end": 10602, "loc": { "start": { - "line": 270, + "line": 286, "column": 4 }, "end": { - "line": 272, + "line": 288, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 10010, - "end": 10066, + "start": 10450, + "end": 10506, "loc": { "start": { - "line": 270, + "line": 286, "column": 8 }, "end": { - "line": 270, + "line": 286, "column": 64 } }, @@ -16046,29 +16826,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10011, - "end": 10066, + "start": 10451, + "end": 10506, "loc": { "start": { - "line": 270, + "line": 286, "column": 9 }, "end": { - "line": 270, + "line": 286, "column": 64 } }, "callee": { "type": "Identifier", - "start": 10011, - "end": 10014, + "start": 10451, + "end": 10454, "loc": { "start": { - "line": 270, + "line": 286, "column": 9 }, "end": { - "line": 270, + "line": 286, "column": 12 }, "identifierName": "has" @@ -16079,43 +16859,43 @@ "arguments": [ { "type": "CallExpression", - "start": 10015, - "end": 10057, + "start": 10455, + "end": 10497, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 55 } }, "callee": { "type": "MemberExpression", - "start": 10015, - "end": 10055, + "start": 10455, + "end": 10495, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 53 } }, "object": { "type": "Identifier", - "start": 10015, - "end": 10030, + "start": 10455, + "end": 10470, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 28 }, "identifierName": "PhylorefWrapper" @@ -16124,15 +16904,15 @@ }, "property": { "type": "Identifier", - "start": 10031, - "end": 10055, + "start": 10471, + "end": 10495, "loc": { "start": { - "line": 270, + "line": 286, "column": 29 }, "end": { - "line": 270, + "line": 286, "column": 53 }, "identifierName": "getStatusCURIEsInEnglish" @@ -16145,15 +16925,15 @@ }, { "type": "Identifier", - "start": 10059, - "end": 10065, + "start": 10499, + "end": 10505, "loc": { "start": { - "line": 270, + "line": 286, "column": 57 }, "end": { - "line": 270, + "line": 286, "column": 63 }, "identifierName": "status" @@ -16170,58 +16950,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 10068, - "end": 10162, + "start": 10508, + "end": 10602, "loc": { "start": { - "line": 270, + "line": 286, "column": 66 }, "end": { - "line": 272, + "line": 288, "column": 5 } }, "body": [ { "type": "ThrowStatement", - "start": 10076, - "end": 10156, + "start": 10516, + "end": 10596, "loc": { "start": { - "line": 271, + "line": 287, "column": 6 }, "end": { - "line": 271, + "line": 287, "column": 86 } }, "argument": { "type": "NewExpression", - "start": 10082, - "end": 10155, + "start": 10522, + "end": 10595, "loc": { "start": { - "line": 271, + "line": 287, "column": 12 }, "end": { - "line": 271, + "line": 287, "column": 85 } }, "callee": { "type": "Identifier", - "start": 10086, - "end": 10095, + "start": 10526, + "end": 10535, "loc": { "start": { - "line": 271, + "line": 287, "column": 16 }, "end": { - "line": 271, + "line": 287, "column": 25 }, "identifierName": "TypeError" @@ -16231,30 +17011,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 10096, - "end": 10154, + "start": 10536, + "end": 10594, "loc": { "start": { - "line": 271, + "line": 287, "column": 26 }, "end": { - "line": 271, + "line": 287, "column": 84 } }, "expressions": [ { "type": "Identifier", - "start": 10145, - "end": 10151, + "start": 10585, + "end": 10591, "loc": { "start": { - "line": 271, + "line": 287, "column": 75 }, "end": { - "line": 271, + "line": 287, "column": 81 }, "identifierName": "status" @@ -16265,15 +17045,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 10097, - "end": 10143, + "start": 10537, + "end": 10583, "loc": { "start": { - "line": 271, + "line": 287, "column": 27 }, "end": { - "line": 271, + "line": 287, "column": 73 } }, @@ -16285,15 +17065,15 @@ }, { "type": "TemplateElement", - "start": 10152, - "end": 10153, + "start": 10592, + "end": 10593, "loc": { "start": { - "line": 271, + "line": 287, "column": 82 }, "end": { - "line": 271, + "line": 287, "column": 83 } }, @@ -16317,15 +17097,15 @@ { "type": "CommentLine", "value": " Set the status of a phyloreference", - "start": 9906, - "end": 9943, + "start": 10346, + "end": 10383, "loc": { "start": { - "line": 267, + "line": 283, "column": 4 }, "end": { - "line": 267, + "line": 283, "column": 41 } } @@ -16333,15 +17113,15 @@ { "type": "CommentLine", "value": "", - "start": 9948, - "end": 9950, + "start": 10388, + "end": 10390, "loc": { "start": { - "line": 268, + "line": 284, "column": 4 }, "end": { - "line": 268, + "line": 284, "column": 6 } } @@ -16349,15 +17129,15 @@ { "type": "CommentLine", "value": " Check whether we have a valid status CURIE.", - "start": 9955, - "end": 10001, + "start": 10395, + "end": 10441, "loc": { "start": { - "line": 269, + "line": 285, "column": 4 }, "end": { - "line": 269, + "line": 285, "column": 50 } } @@ -16367,15 +17147,15 @@ { "type": "CommentLine", "value": " See if we can end the previous interval.", - "start": 10168, - "end": 10211, + "start": 10608, + "end": 10651, "loc": { "start": { - "line": 274, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 290, "column": 47 } } @@ -16384,44 +17164,44 @@ }, { "type": "VariableDeclaration", - "start": 10216, - "end": 10271, + "start": 10656, + "end": 10711, "loc": { "start": { - "line": 275, + "line": 291, "column": 4 }, "end": { - "line": 275, + "line": 291, "column": 59 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10222, - "end": 10270, + "start": 10662, + "end": 10710, "loc": { "start": { - "line": 275, + "line": 291, "column": 10 }, "end": { - "line": 275, + "line": 291, "column": 58 } }, "id": { "type": "Identifier", - "start": 10222, - "end": 10233, + "start": 10662, + "end": 10673, "loc": { "start": { - "line": 275, + "line": 291, "column": 10 }, "end": { - "line": 275, + "line": 291, "column": 21 }, "identifierName": "currentTime" @@ -16431,57 +17211,57 @@ }, "init": { "type": "CallExpression", - "start": 10236, - "end": 10270, + "start": 10676, + "end": 10710, "loc": { "start": { - "line": 275, + "line": 291, "column": 24 }, "end": { - "line": 275, + "line": 291, "column": 58 } }, "callee": { "type": "MemberExpression", - "start": 10236, - "end": 10268, + "start": 10676, + "end": 10708, "loc": { "start": { - "line": 275, + "line": 291, "column": 24 }, "end": { - "line": 275, + "line": 291, "column": 56 } }, "object": { "type": "NewExpression", - "start": 10236, - "end": 10256, + "start": 10676, + "end": 10696, "loc": { "start": { - "line": 275, + "line": 291, "column": 24 }, "end": { - "line": 275, + "line": 291, "column": 44 } }, "callee": { "type": "Identifier", - "start": 10240, - "end": 10244, + "start": 10680, + "end": 10684, "loc": { "start": { - "line": 275, + "line": 291, "column": 28 }, "end": { - "line": 275, + "line": 291, "column": 32 }, "identifierName": "Date" @@ -16491,43 +17271,43 @@ "arguments": [ { "type": "CallExpression", - "start": 10245, - "end": 10255, + "start": 10685, + "end": 10695, "loc": { "start": { - "line": 275, + "line": 291, "column": 33 }, "end": { - "line": 275, + "line": 291, "column": 43 } }, "callee": { "type": "MemberExpression", - "start": 10245, - "end": 10253, + "start": 10685, + "end": 10693, "loc": { "start": { - "line": 275, + "line": 291, "column": 33 }, "end": { - "line": 275, + "line": 291, "column": 41 } }, "object": { "type": "Identifier", - "start": 10245, - "end": 10249, + "start": 10685, + "end": 10689, "loc": { "start": { - "line": 275, + "line": 291, "column": 33 }, "end": { - "line": 275, + "line": 291, "column": 37 }, "identifierName": "Date" @@ -16536,15 +17316,15 @@ }, "property": { "type": "Identifier", - "start": 10250, - "end": 10253, + "start": 10690, + "end": 10693, "loc": { "start": { - "line": 275, + "line": 291, "column": 38 }, "end": { - "line": 275, + "line": 291, "column": 41 }, "identifierName": "now" @@ -16559,15 +17339,15 @@ }, "property": { "type": "Identifier", - "start": 10257, - "end": 10268, + "start": 10697, + "end": 10708, "loc": { "start": { - "line": 275, + "line": 291, "column": 45 }, "end": { - "line": 275, + "line": 291, "column": 56 }, "identifierName": "toISOString" @@ -16586,15 +17366,15 @@ { "type": "CommentLine", "value": " See if we can end the previous interval.", - "start": 10168, - "end": 10211, + "start": 10608, + "end": 10651, "loc": { "start": { - "line": 274, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 290, "column": 47 } } @@ -16603,29 +17383,29 @@ }, { "type": "IfStatement", - "start": 10277, - "end": 10447, + "start": 10717, + "end": 10887, "loc": { "start": { - "line": 277, + "line": 293, "column": 4 }, "end": { - "line": 280, + "line": 296, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 10281, - "end": 10325, + "start": 10721, + "end": 10765, "loc": { "start": { - "line": 277, + "line": 293, "column": 8 }, "end": { - "line": 277, + "line": 293, "column": 52 } }, @@ -16633,29 +17413,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10282, - "end": 10325, + "start": 10722, + "end": 10765, "loc": { "start": { - "line": 277, + "line": 293, "column": 9 }, "end": { - "line": 277, + "line": 293, "column": 52 } }, "callee": { "type": "Identifier", - "start": 10282, - "end": 10285, + "start": 10722, + "end": 10725, "loc": { "start": { - "line": 277, + "line": 293, "column": 9 }, "end": { - "line": 277, + "line": 293, "column": 12 }, "identifierName": "has" @@ -16665,44 +17445,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 10286, - "end": 10299, + "start": 10726, + "end": 10739, "loc": { "start": { - "line": 277, + "line": 293, "column": 13 }, "end": { - "line": 277, + "line": 293, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 10286, - "end": 10290, + "start": 10726, + "end": 10730, "loc": { "start": { - "line": 277, + "line": 293, "column": 13 }, "end": { - "line": 277, + "line": 293, "column": 17 } } }, "property": { "type": "Identifier", - "start": 10291, - "end": 10299, + "start": 10731, + "end": 10739, "loc": { "start": { - "line": 277, + "line": 293, "column": 18 }, "end": { - "line": 277, + "line": 293, "column": 26 }, "identifierName": "phyloref" @@ -16713,15 +17493,15 @@ }, { "type": "StringLiteral", - "start": 10301, - "end": 10324, + "start": 10741, + "end": 10764, "loc": { "start": { - "line": 277, + "line": 293, "column": 28 }, "end": { - "line": 277, + "line": 293, "column": 51 } }, @@ -16739,87 +17519,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 10327, - "end": 10447, + "start": 10767, + "end": 10887, "loc": { "start": { - "line": 277, + "line": 293, "column": 54 }, "end": { - "line": 280, + "line": 296, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 10397, - "end": 10441, + "start": 10837, + "end": 10881, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 50 } }, "expression": { "type": "AssignmentExpression", - "start": 10397, - "end": 10440, + "start": 10837, + "end": 10880, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 49 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10397, - "end": 10435, + "start": 10837, + "end": 10875, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 44 } }, "object": { "type": "MemberExpression", - "start": 10397, - "end": 10410, + "start": 10837, + "end": 10850, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 10397, - "end": 10401, + "start": 10837, + "end": 10841, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 10 } }, @@ -16827,15 +17607,15 @@ }, "property": { "type": "Identifier", - "start": 10402, - "end": 10410, + "start": 10842, + "end": 10850, "loc": { "start": { - "line": 279, + "line": 295, "column": 11 }, "end": { - "line": 279, + "line": 295, "column": 19 }, "identifierName": "phyloref" @@ -16847,15 +17627,15 @@ }, "property": { "type": "StringLiteral", - "start": 10411, - "end": 10434, + "start": 10851, + "end": 10874, "loc": { "start": { - "line": 279, + "line": 295, "column": 20 }, "end": { - "line": 279, + "line": 295, "column": 43 } }, @@ -16870,15 +17650,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10438, - "end": 10440, + "start": 10878, + "end": 10880, "loc": { "start": { - "line": 279, + "line": 295, "column": 47 }, "end": { - "line": 279, + "line": 295, "column": 49 } }, @@ -16890,15 +17670,15 @@ { "type": "CommentLine", "value": " Vue.set(this.phyloref, 'pso:holdsStatusInTime', []);", - "start": 10335, - "end": 10390, + "start": 10775, + "end": 10830, "loc": { "start": { - "line": 278, + "line": 294, "column": 6 }, "end": { - "line": 278, + "line": 294, "column": 61 } } @@ -16914,15 +17694,15 @@ { "type": "CommentLine", "value": " Check to see if there's a previous time interval we should end.", - "start": 10453, - "end": 10519, + "start": 10893, + "end": 10959, "loc": { "start": { - "line": 282, + "line": 298, "column": 4 }, "end": { - "line": 282, + "line": 298, "column": 70 } } @@ -16931,71 +17711,71 @@ }, { "type": "IfStatement", - "start": 10524, - "end": 11267, + "start": 10964, + "end": 11707, "loc": { "start": { - "line": 283, + "line": 299, "column": 4 }, "end": { - "line": 298, + "line": 314, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 10535, - "end": 10647, + "start": 10975, + "end": 11087, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 285, + "line": 301, "column": 58 } }, "left": { "type": "CallExpression", - "start": 10535, - "end": 10588, + "start": 10975, + "end": 11028, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 284, + "line": 300, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 10535, - "end": 10548, + "start": 10975, + "end": 10988, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 284, + "line": 300, "column": 19 } }, "object": { "type": "Identifier", - "start": 10535, - "end": 10540, + "start": 10975, + "end": 10980, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 284, + "line": 300, "column": 11 }, "identifierName": "Array" @@ -17005,15 +17785,15 @@ }, "property": { "type": "Identifier", - "start": 10541, - "end": 10548, + "start": 10981, + "end": 10988, "loc": { "start": { - "line": 284, + "line": 300, "column": 12 }, "end": { - "line": 284, + "line": 300, "column": 19 }, "identifierName": "isArray" @@ -17026,58 +17806,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 10549, - "end": 10587, + "start": 10989, + "end": 11027, "loc": { "start": { - "line": 284, + "line": 300, "column": 20 }, "end": { - "line": 284, + "line": 300, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 10549, - "end": 10562, + "start": 10989, + "end": 11002, "loc": { "start": { - "line": 284, + "line": 300, "column": 20 }, "end": { - "line": 284, + "line": 300, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 10549, - "end": 10553, + "start": 10989, + "end": 10993, "loc": { "start": { - "line": 284, + "line": 300, "column": 20 }, "end": { - "line": 284, + "line": 300, "column": 24 } } }, "property": { "type": "Identifier", - "start": 10554, - "end": 10562, + "start": 10994, + "end": 11002, "loc": { "start": { - "line": 284, + "line": 300, "column": 25 }, "end": { - "line": 284, + "line": 300, "column": 33 }, "identifierName": "phyloref" @@ -17088,15 +17868,15 @@ }, "property": { "type": "StringLiteral", - "start": 10563, - "end": 10586, + "start": 11003, + "end": 11026, "loc": { "start": { - "line": 284, + "line": 300, "column": 34 }, "end": { - "line": 284, + "line": 300, "column": 57 } }, @@ -17114,86 +17894,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 10598, - "end": 10647, + "start": 11038, + "end": 11087, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 58 } }, "left": { "type": "MemberExpression", - "start": 10598, - "end": 10643, + "start": 11038, + "end": 11083, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 10598, - "end": 10636, + "start": 11038, + "end": 11076, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 47 } }, "object": { "type": "MemberExpression", - "start": 10598, - "end": 10611, + "start": 11038, + "end": 11051, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 10598, - "end": 10602, + "start": 11038, + "end": 11042, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 13 } } }, "property": { "type": "Identifier", - "start": 10603, - "end": 10611, + "start": 11043, + "end": 11051, "loc": { "start": { - "line": 285, + "line": 301, "column": 14 }, "end": { - "line": 285, + "line": 301, "column": 22 }, "identifierName": "phyloref" @@ -17204,15 +17984,15 @@ }, "property": { "type": "StringLiteral", - "start": 10612, - "end": 10635, + "start": 11052, + "end": 11075, "loc": { "start": { - "line": 285, + "line": 301, "column": 23 }, "end": { - "line": 285, + "line": 301, "column": 46 } }, @@ -17226,15 +18006,15 @@ }, "property": { "type": "Identifier", - "start": 10637, - "end": 10643, + "start": 11077, + "end": 11083, "loc": { "start": { - "line": 285, + "line": 301, "column": 48 }, "end": { - "line": 285, + "line": 301, "column": 54 }, "identifierName": "length" @@ -17246,15 +18026,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 10646, - "end": 10647, + "start": 11086, + "end": 11087, "loc": { "start": { - "line": 285, + "line": 301, "column": 57 }, "end": { - "line": 285, + "line": 301, "column": 58 } }, @@ -17269,59 +18049,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 10654, - "end": 11267, + "start": 11094, + "end": 11707, "loc": { "start": { - "line": 286, + "line": 302, "column": 6 }, "end": { - "line": 298, + "line": 314, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 10662, - "end": 10777, + "start": 11102, + "end": 11217, "loc": { "start": { - "line": 287, + "line": 303, "column": 6 }, "end": { - "line": 287, + "line": 303, "column": 121 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10668, - "end": 10776, + "start": 11108, + "end": 11216, "loc": { "start": { - "line": 287, + "line": 303, "column": 12 }, "end": { - "line": 287, + "line": 303, "column": 120 } }, "id": { "type": "Identifier", - "start": 10668, - "end": 10684, + "start": 11108, + "end": 11124, "loc": { "start": { - "line": 287, + "line": 303, "column": 12 }, "end": { - "line": 287, + "line": 303, "column": 28 }, "identifierName": "lastStatusInTime" @@ -17330,72 +18110,72 @@ }, "init": { "type": "MemberExpression", - "start": 10687, - "end": 10776, + "start": 11127, + "end": 11216, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 120 } }, "object": { "type": "MemberExpression", - "start": 10687, - "end": 10725, + "start": 11127, + "end": 11165, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 69 } }, "object": { "type": "MemberExpression", - "start": 10687, - "end": 10700, + "start": 11127, + "end": 11140, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 10687, - "end": 10691, + "start": 11127, + "end": 11131, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 35 } } }, "property": { "type": "Identifier", - "start": 10692, - "end": 10700, + "start": 11132, + "end": 11140, "loc": { "start": { - "line": 287, + "line": 303, "column": 36 }, "end": { - "line": 287, + "line": 303, "column": 44 }, "identifierName": "phyloref" @@ -17406,15 +18186,15 @@ }, "property": { "type": "StringLiteral", - "start": 10701, - "end": 10724, + "start": 11141, + "end": 11164, "loc": { "start": { - "line": 287, + "line": 303, "column": 45 }, "end": { - "line": 287, + "line": 303, "column": 68 } }, @@ -17428,86 +18208,86 @@ }, "property": { "type": "BinaryExpression", - "start": 10726, - "end": 10775, + "start": 11166, + "end": 11215, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 119 } }, "left": { "type": "MemberExpression", - "start": 10726, - "end": 10771, + "start": 11166, + "end": 11211, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 115 } }, "object": { "type": "MemberExpression", - "start": 10726, - "end": 10764, + "start": 11166, + "end": 11204, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 108 } }, "object": { "type": "MemberExpression", - "start": 10726, - "end": 10739, + "start": 11166, + "end": 11179, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 83 } }, "object": { "type": "ThisExpression", - "start": 10726, - "end": 10730, + "start": 11166, + "end": 11170, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 74 } } }, "property": { "type": "Identifier", - "start": 10731, - "end": 10739, + "start": 11171, + "end": 11179, "loc": { "start": { - "line": 287, + "line": 303, "column": 75 }, "end": { - "line": 287, + "line": 303, "column": 83 }, "identifierName": "phyloref" @@ -17518,15 +18298,15 @@ }, "property": { "type": "StringLiteral", - "start": 10740, - "end": 10763, + "start": 11180, + "end": 11203, "loc": { "start": { - "line": 287, + "line": 303, "column": 84 }, "end": { - "line": 287, + "line": 303, "column": 107 } }, @@ -17540,15 +18320,15 @@ }, "property": { "type": "Identifier", - "start": 10765, - "end": 10771, + "start": 11205, + "end": 11211, "loc": { "start": { - "line": 287, + "line": 303, "column": 109 }, "end": { - "line": 287, + "line": 303, "column": 115 }, "identifierName": "length" @@ -17560,15 +18340,15 @@ "operator": "-", "right": { "type": "NumericLiteral", - "start": 10774, - "end": 10775, + "start": 11214, + "end": 11215, "loc": { "start": { - "line": 287, + "line": 303, "column": 118 }, "end": { - "line": 287, + "line": 303, "column": 119 } }, @@ -17588,15 +18368,15 @@ { "type": "CommentLine", "value": " if (!has(lastStatusInTime, 'tvc:atTime'))", - "start": 10785, - "end": 10829, + "start": 11225, + "end": 11269, "loc": { "start": { - "line": 289, + "line": 305, "column": 6 }, "end": { - "line": 289, + "line": 305, "column": 50 } } @@ -17604,15 +18384,15 @@ { "type": "CommentLine", "value": " Vue.set(lastStatusInTime, 'tvc:atTime', {});", - "start": 10836, - "end": 10884, + "start": 11276, + "end": 11324, "loc": { "start": { - "line": 290, + "line": 306, "column": 6 }, "end": { - "line": 290, + "line": 306, "column": 54 } } @@ -17621,29 +18401,29 @@ }, { "type": "IfStatement", - "start": 10891, - "end": 10987, + "start": 11331, + "end": 11427, "loc": { "start": { - "line": 291, + "line": 307, "column": 6 }, "end": { - "line": 293, + "line": 309, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 10895, - "end": 10931, + "start": 11335, + "end": 11371, "loc": { "start": { - "line": 291, + "line": 307, "column": 10 }, "end": { - "line": 291, + "line": 307, "column": 46 } }, @@ -17651,29 +18431,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10896, - "end": 10931, + "start": 11336, + "end": 11371, "loc": { "start": { - "line": 291, + "line": 307, "column": 11 }, "end": { - "line": 291, + "line": 307, "column": 46 } }, "callee": { "type": "Identifier", - "start": 10896, - "end": 10899, + "start": 11336, + "end": 11339, "loc": { "start": { - "line": 291, + "line": 307, "column": 11 }, "end": { - "line": 291, + "line": 307, "column": 14 }, "identifierName": "has" @@ -17684,15 +18464,15 @@ "arguments": [ { "type": "Identifier", - "start": 10900, - "end": 10916, + "start": 11340, + "end": 11356, "loc": { "start": { - "line": 291, + "line": 307, "column": 15 }, "end": { - "line": 291, + "line": 307, "column": 31 }, "identifierName": "lastStatusInTime" @@ -17701,15 +18481,15 @@ }, { "type": "StringLiteral", - "start": 10918, - "end": 10930, + "start": 11358, + "end": 11370, "loc": { "start": { - "line": 291, + "line": 307, "column": 33 }, "end": { - "line": 291, + "line": 307, "column": 45 } }, @@ -17729,73 +18509,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 10933, - "end": 10987, + "start": 11373, + "end": 11427, "loc": { "start": { - "line": 291, + "line": 307, "column": 48 }, "end": { - "line": 293, + "line": 309, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 10943, - "end": 10979, + "start": 11383, + "end": 11419, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 10943, - "end": 10978, + "start": 11383, + "end": 11418, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10943, - "end": 10973, + "start": 11383, + "end": 11413, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 38 } }, "object": { "type": "Identifier", - "start": 10943, - "end": 10959, + "start": 11383, + "end": 11399, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 24 }, "identifierName": "lastStatusInTime" @@ -17804,15 +18584,15 @@ }, "property": { "type": "StringLiteral", - "start": 10960, - "end": 10972, + "start": 11400, + "end": 11412, "loc": { "start": { - "line": 292, + "line": 308, "column": 25 }, "end": { - "line": 292, + "line": 308, "column": 37 } }, @@ -17826,15 +18606,15 @@ }, "right": { "type": "ObjectExpression", - "start": 10976, - "end": 10978, + "start": 11416, + "end": 11418, "loc": { "start": { - "line": 292, + "line": 308, "column": 41 }, "end": { - "line": 292, + "line": 308, "column": 43 } }, @@ -17850,15 +18630,15 @@ { "type": "CommentLine", "value": " if (!has(lastStatusInTime, 'tvc:atTime'))", - "start": 10785, - "end": 10829, + "start": 11225, + "end": 11269, "loc": { "start": { - "line": 289, + "line": 305, "column": 6 }, "end": { - "line": 289, + "line": 305, "column": 50 } } @@ -17866,15 +18646,15 @@ { "type": "CommentLine", "value": " Vue.set(lastStatusInTime, 'tvc:atTime', {});", - "start": 10836, - "end": 10884, + "start": 11276, + "end": 11324, "loc": { "start": { - "line": 290, + "line": 306, "column": 6 }, "end": { - "line": 290, + "line": 306, "column": 54 } } @@ -17883,29 +18663,29 @@ }, { "type": "IfStatement", - "start": 10994, - "end": 11261, + "start": 11434, + "end": 11701, "loc": { "start": { - "line": 294, + "line": 310, "column": 6 }, "end": { - "line": 297, + "line": 313, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 10998, - "end": 11069, + "start": 11438, + "end": 11509, "loc": { "start": { - "line": 294, + "line": 310, "column": 10 }, "end": { - "line": 294, + "line": 310, "column": 81 } }, @@ -17913,29 +18693,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10999, - "end": 11069, + "start": 11439, + "end": 11509, "loc": { "start": { - "line": 294, + "line": 310, "column": 11 }, "end": { - "line": 294, + "line": 310, "column": 81 } }, "callee": { "type": "Identifier", - "start": 10999, - "end": 11002, + "start": 11439, + "end": 11442, "loc": { "start": { - "line": 294, + "line": 310, "column": 11 }, "end": { - "line": 294, + "line": 310, "column": 14 }, "identifierName": "has" @@ -17945,29 +18725,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 11003, - "end": 11033, + "start": 11443, + "end": 11473, "loc": { "start": { - "line": 294, + "line": 310, "column": 15 }, "end": { - "line": 294, + "line": 310, "column": 45 } }, "object": { "type": "Identifier", - "start": 11003, - "end": 11019, + "start": 11443, + "end": 11459, "loc": { "start": { - "line": 294, + "line": 310, "column": 15 }, "end": { - "line": 294, + "line": 310, "column": 31 }, "identifierName": "lastStatusInTime" @@ -17976,15 +18756,15 @@ }, "property": { "type": "StringLiteral", - "start": 11020, - "end": 11032, + "start": 11460, + "end": 11472, "loc": { "start": { - "line": 294, + "line": 310, "column": 32 }, "end": { - "line": 294, + "line": 310, "column": 44 } }, @@ -17998,15 +18778,15 @@ }, { "type": "StringLiteral", - "start": 11035, - "end": 11068, + "start": 11475, + "end": 11508, "loc": { "start": { - "line": 294, + "line": 310, "column": 47 }, "end": { - "line": 294, + "line": 310, "column": 80 } }, @@ -18024,87 +18804,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 11071, - "end": 11261, + "start": 11511, + "end": 11701, "loc": { "start": { - "line": 294, + "line": 310, "column": 83 }, "end": { - "line": 297, + "line": 313, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 11173, - "end": 11253, + "start": 11613, + "end": 11693, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 88 } }, "expression": { "type": "AssignmentExpression", - "start": 11173, - "end": 11252, + "start": 11613, + "end": 11692, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 87 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11173, - "end": 11238, + "start": 11613, + "end": 11678, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 73 } }, "object": { "type": "MemberExpression", - "start": 11173, - "end": 11203, + "start": 11613, + "end": 11643, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 38 } }, "object": { "type": "Identifier", - "start": 11173, - "end": 11189, + "start": 11613, + "end": 11629, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 24 }, "identifierName": "lastStatusInTime" @@ -18114,15 +18894,15 @@ }, "property": { "type": "StringLiteral", - "start": 11190, - "end": 11202, + "start": 11630, + "end": 11642, "loc": { "start": { - "line": 296, + "line": 312, "column": 25 }, "end": { - "line": 296, + "line": 312, "column": 37 } }, @@ -18137,15 +18917,15 @@ }, "property": { "type": "StringLiteral", - "start": 11204, - "end": 11237, + "start": 11644, + "end": 11677, "loc": { "start": { - "line": 296, + "line": 312, "column": 39 }, "end": { - "line": 296, + "line": 312, "column": 72 } }, @@ -18160,15 +18940,15 @@ }, "right": { "type": "Identifier", - "start": 11241, - "end": 11252, + "start": 11681, + "end": 11692, "loc": { "start": { - "line": 296, + "line": 312, "column": 76 }, "end": { - "line": 296, + "line": 312, "column": 87 }, "identifierName": "currentTime" @@ -18181,15 +18961,15 @@ { "type": "CommentLine", "value": " If the last time entry doesn't already have an interval end date, set it to now.", - "start": 11081, - "end": 11164, + "start": 11521, + "end": 11604, "loc": { "start": { - "line": 295, + "line": 311, "column": 8 }, "end": { - "line": 295, + "line": 311, "column": 91 } } @@ -18210,15 +18990,15 @@ { "type": "CommentLine", "value": " Check to see if there's a previous time interval we should end.", - "start": 10453, - "end": 10519, + "start": 10893, + "end": 10959, "loc": { "start": { - "line": 282, + "line": 298, "column": 4 }, "end": { - "line": 282, + "line": 298, "column": 70 } } @@ -18228,15 +19008,15 @@ { "type": "CommentLine", "value": " Create new entry.", - "start": 11273, - "end": 11293, + "start": 11713, + "end": 11733, "loc": { "start": { - "line": 300, + "line": 316, "column": 4 }, "end": { - "line": 300, + "line": 316, "column": 24 } } @@ -18245,85 +19025,85 @@ }, { "type": "ExpressionStatement", - "start": 11298, - "end": 11539, + "start": 11738, + "end": 11979, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 307, + "line": 323, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 11298, - "end": 11538, + "start": 11738, + "end": 11978, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 307, + "line": 323, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 11298, - "end": 11341, + "start": 11738, + "end": 11781, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 47 } }, "object": { "type": "MemberExpression", - "start": 11298, - "end": 11336, + "start": 11738, + "end": 11776, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 42 } }, "object": { "type": "MemberExpression", - "start": 11298, - "end": 11311, + "start": 11738, + "end": 11751, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 17 } }, "object": { "type": "ThisExpression", - "start": 11298, - "end": 11302, + "start": 11738, + "end": 11742, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 8 } }, @@ -18331,15 +19111,15 @@ }, "property": { "type": "Identifier", - "start": 11303, - "end": 11311, + "start": 11743, + "end": 11751, "loc": { "start": { - "line": 301, + "line": 317, "column": 9 }, "end": { - "line": 301, + "line": 317, "column": 17 }, "identifierName": "phyloref" @@ -18351,15 +19131,15 @@ }, "property": { "type": "StringLiteral", - "start": 11312, - "end": 11335, + "start": 11752, + "end": 11775, "loc": { "start": { - "line": 301, + "line": 317, "column": 18 }, "end": { - "line": 301, + "line": 317, "column": 41 } }, @@ -18374,15 +19154,15 @@ }, "property": { "type": "Identifier", - "start": 11337, - "end": 11341, + "start": 11777, + "end": 11781, "loc": { "start": { - "line": 301, + "line": 317, "column": 43 }, "end": { - "line": 301, + "line": 317, "column": 47 }, "identifierName": "push" @@ -18395,30 +19175,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 11342, - "end": 11537, + "start": 11782, + "end": 11977, "loc": { "start": { - "line": 301, + "line": 317, "column": 48 }, "end": { - "line": 307, + "line": 323, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 11350, - "end": 11398, + "start": 11790, + "end": 11838, "loc": { "start": { - "line": 302, + "line": 318, "column": 6 }, "end": { - "line": 302, + "line": 318, "column": 54 } }, @@ -18427,15 +19207,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11350, - "end": 11357, + "start": 11790, + "end": 11797, "loc": { "start": { - "line": 302, + "line": 318, "column": 6 }, "end": { - "line": 302, + "line": 318, "column": 13 } }, @@ -18447,15 +19227,15 @@ }, "value": { "type": "StringLiteral", - "start": 11359, - "end": 11398, + "start": 11799, + "end": 11838, "loc": { "start": { - "line": 302, + "line": 318, "column": 15 }, "end": { - "line": 302, + "line": 318, "column": 54 } }, @@ -18468,15 +19248,15 @@ }, { "type": "ObjectProperty", - "start": 11406, - "end": 11441, + "start": 11846, + "end": 11881, "loc": { "start": { - "line": 303, + "line": 319, "column": 6 }, "end": { - "line": 303, + "line": 319, "column": 41 } }, @@ -18485,15 +19265,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11406, - "end": 11422, + "start": 11846, + "end": 11862, "loc": { "start": { - "line": 303, + "line": 319, "column": 6 }, "end": { - "line": 303, + "line": 319, "column": 22 } }, @@ -18505,30 +19285,30 @@ }, "value": { "type": "ObjectExpression", - "start": 11424, - "end": 11441, + "start": 11864, + "end": 11881, "loc": { "start": { - "line": 303, + "line": 319, "column": 24 }, "end": { - "line": 303, + "line": 319, "column": 41 } }, "properties": [ { "type": "ObjectProperty", - "start": 11426, - "end": 11439, + "start": 11866, + "end": 11879, "loc": { "start": { - "line": 303, + "line": 319, "column": 26 }, "end": { - "line": 303, + "line": 319, "column": 39 } }, @@ -18537,15 +19317,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11426, - "end": 11431, + "start": 11866, + "end": 11871, "loc": { "start": { - "line": 303, + "line": 319, "column": 26 }, "end": { - "line": 303, + "line": 319, "column": 31 } }, @@ -18557,15 +19337,15 @@ }, "value": { "type": "Identifier", - "start": 11433, - "end": 11439, + "start": 11873, + "end": 11879, "loc": { "start": { - "line": 303, + "line": 319, "column": 33 }, "end": { - "line": 303, + "line": 319, "column": 39 }, "identifierName": "status" @@ -18578,15 +19358,15 @@ }, { "type": "ObjectProperty", - "start": 11449, - "end": 11530, + "start": 11889, + "end": 11970, "loc": { "start": { - "line": 304, + "line": 320, "column": 6 }, "end": { - "line": 306, + "line": 322, "column": 7 } }, @@ -18595,15 +19375,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11449, - "end": 11461, + "start": 11889, + "end": 11901, "loc": { "start": { - "line": 304, + "line": 320, "column": 6 }, "end": { - "line": 304, + "line": 320, "column": 18 } }, @@ -18615,30 +19395,30 @@ }, "value": { "type": "ObjectExpression", - "start": 11463, - "end": 11530, + "start": 11903, + "end": 11970, "loc": { "start": { - "line": 304, + "line": 320, "column": 20 }, "end": { - "line": 306, + "line": 322, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 11473, - "end": 11521, + "start": 11913, + "end": 11961, "loc": { "start": { - "line": 305, + "line": 321, "column": 8 }, "end": { - "line": 305, + "line": 321, "column": 56 } }, @@ -18647,15 +19427,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11473, - "end": 11508, + "start": 11913, + "end": 11948, "loc": { "start": { - "line": 305, + "line": 321, "column": 8 }, "end": { - "line": 305, + "line": 321, "column": 43 } }, @@ -18667,15 +19447,15 @@ }, "value": { "type": "Identifier", - "start": 11510, - "end": 11521, + "start": 11950, + "end": 11961, "loc": { "start": { - "line": 305, + "line": 321, "column": 45 }, "end": { - "line": 305, + "line": 321, "column": 56 }, "identifierName": "currentTime" @@ -18695,15 +19475,15 @@ { "type": "CommentLine", "value": " Create new entry.", - "start": 11273, - "end": 11293, + "start": 11713, + "end": 11733, "loc": { "start": { - "line": 300, + "line": 316, "column": 4 }, "end": { - "line": 300, + "line": 316, "column": 24 } } @@ -18718,15 +19498,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n ", - "start": 11547, - "end": 11925, + "start": 11987, + "end": 12365, "loc": { "start": { - "line": 310, + "line": 326, "column": 2 }, "end": { - "line": 316, + "line": 332, "column": 5 } } @@ -18735,15 +19515,15 @@ }, { "type": "ClassMethod", - "start": 11928, - "end": 12401, + "start": 12368, + "end": 12841, "loc": { "start": { - "line": 317, + "line": 333, "column": 2 }, "end": { - "line": 333, + "line": 349, "column": 3 } }, @@ -18751,15 +19531,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11932, - "end": 11946, + "start": 12372, + "end": 12386, "loc": { "start": { - "line": 317, + "line": 333, "column": 6 }, "end": { - "line": 317, + "line": 333, "column": 20 }, "identifierName": "uniqNomenCodes" @@ -18774,58 +19554,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 11949, - "end": 12401, + "start": 12389, + "end": 12841, "loc": { "start": { - "line": 317, + "line": 333, "column": 23 }, "end": { - "line": 333, + "line": 349, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 11955, - "end": 12397, + "start": 12395, + "end": 12837, "loc": { "start": { - "line": 318, + "line": 334, "column": 4 }, "end": { - "line": 332, + "line": 348, "column": 8 } }, "argument": { "type": "CallExpression", - "start": 11962, - "end": 12396, + "start": 12402, + "end": 12836, "loc": { "start": { - "line": 318, + "line": 334, "column": 11 }, "end": { - "line": 332, + "line": 348, "column": 7 } }, "callee": { "type": "Identifier", - "start": 11962, - "end": 11966, + "start": 12402, + "end": 12406, "loc": { "start": { - "line": 318, + "line": 334, "column": 11 }, "end": { - "line": 318, + "line": 334, "column": 15 }, "identifierName": "uniq" @@ -18835,72 +19615,72 @@ "arguments": [ { "type": "CallExpression", - "start": 11967, - "end": 12395, + "start": 12407, + "end": 12835, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 332, + "line": 348, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 11967, - "end": 11986, + "start": 12407, + "end": 12426, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 35 } }, "object": { "type": "MemberExpression", - "start": 11967, - "end": 11982, + "start": 12407, + "end": 12422, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 11967, - "end": 11971, + "start": 12407, + "end": 12411, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 20 } } }, "property": { "type": "Identifier", - "start": 11972, - "end": 11982, + "start": 12412, + "end": 12422, "loc": { "start": { - "line": 318, + "line": 334, "column": 21 }, "end": { - "line": 318, + "line": 334, "column": 31 }, "identifierName": "specifiers" @@ -18911,15 +19691,15 @@ }, "property": { "type": "Identifier", - "start": 11983, - "end": 11986, + "start": 12423, + "end": 12426, "loc": { "start": { - "line": 318, + "line": 334, "column": 32 }, "end": { - "line": 318, + "line": 334, "column": 35 }, "identifierName": "map" @@ -18931,15 +19711,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 11987, - "end": 12394, + "start": 12427, + "end": 12834, "loc": { "start": { - "line": 318, + "line": 334, "column": 36 }, "end": { - "line": 332, + "line": 348, "column": 5 } }, @@ -18950,15 +19730,15 @@ "params": [ { "type": "Identifier", - "start": 11988, - "end": 11997, + "start": 12428, + "end": 12437, "loc": { "start": { - "line": 318, + "line": 334, "column": 37 }, "end": { - "line": 318, + "line": 334, "column": 46 }, "identifierName": "specifier" @@ -18968,59 +19748,59 @@ ], "body": { "type": "BlockStatement", - "start": 12002, - "end": 12394, + "start": 12442, + "end": 12834, "loc": { "start": { - "line": 318, + "line": 334, "column": 51 }, "end": { - "line": 332, + "line": 348, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 12010, - "end": 12131, + "start": 12450, + "end": 12571, "loc": { "start": { - "line": 319, + "line": 335, "column": 6 }, "end": { - "line": 322, + "line": 338, "column": 21 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12016, - "end": 12130, + "start": 12456, + "end": 12570, "loc": { "start": { - "line": 319, + "line": 335, "column": 12 }, "end": { - "line": 322, + "line": 338, "column": 20 } }, "id": { "type": "Identifier", - "start": 12016, - "end": 12028, + "start": 12456, + "end": 12468, "loc": { "start": { - "line": 319, + "line": 335, "column": 12 }, "end": { - "line": 319, + "line": 335, "column": 24 }, "identifierName": "taxonConcept" @@ -19029,43 +19809,43 @@ }, "init": { "type": "MemberExpression", - "start": 12031, - "end": 12130, + "start": 12471, + "end": 12570, "loc": { "start": { - "line": 319, + "line": 335, "column": 27 }, "end": { - "line": 322, + "line": 338, "column": 20 } }, "object": { "type": "NewExpression", - "start": 12031, - "end": 12117, + "start": 12471, + "end": 12557, "loc": { "start": { - "line": 319, + "line": 335, "column": 27 }, "end": { - "line": 322, + "line": 338, "column": 7 } }, "callee": { "type": "Identifier", - "start": 12035, - "end": 12055, + "start": 12475, + "end": 12495, "loc": { "start": { - "line": 319, + "line": 335, "column": 31 }, "end": { - "line": 319, + "line": 335, "column": 51 }, "identifierName": "TaxonomicUnitWrapper" @@ -19075,15 +19855,15 @@ "arguments": [ { "type": "Identifier", - "start": 12065, - "end": 12074, + "start": 12505, + "end": 12514, "loc": { "start": { - "line": 320, + "line": 336, "column": 8 }, "end": { - "line": 320, + "line": 336, "column": 17 }, "identifierName": "specifier" @@ -19092,44 +19872,44 @@ }, { "type": "MemberExpression", - "start": 12084, - "end": 12109, + "start": 12524, + "end": 12549, "loc": { "start": { - "line": 321, + "line": 337, "column": 8 }, "end": { - "line": 321, + "line": 337, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 12084, - "end": 12088, + "start": 12524, + "end": 12528, "loc": { "start": { - "line": 321, + "line": 337, "column": 8 }, "end": { - "line": 321, + "line": 337, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12089, - "end": 12109, + "start": 12529, + "end": 12549, "loc": { "start": { - "line": 321, + "line": 337, "column": 13 }, "end": { - "line": 321, + "line": 337, "column": 33 }, "identifierName": "phyxDefaultNomenCode" @@ -19142,15 +19922,15 @@ }, "property": { "type": "Identifier", - "start": 12118, - "end": 12130, + "start": 12558, + "end": 12570, "loc": { "start": { - "line": 322, + "line": 338, "column": 8 }, "end": { - "line": 322, + "line": 338, "column": 20 }, "identifierName": "taxonConcept" @@ -19165,29 +19945,29 @@ }, { "type": "IfStatement", - "start": 12138, - "end": 12186, + "start": 12578, + "end": 12626, "loc": { "start": { - "line": 323, + "line": 339, "column": 6 }, "end": { - "line": 323, + "line": 339, "column": 54 } }, "test": { "type": "UnaryExpression", - "start": 12142, - "end": 12155, + "start": 12582, + "end": 12595, "loc": { "start": { - "line": 323, + "line": 339, "column": 10 }, "end": { - "line": 323, + "line": 339, "column": 23 } }, @@ -19195,15 +19975,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 12143, - "end": 12155, + "start": 12583, + "end": 12595, "loc": { "start": { - "line": 323, + "line": 339, "column": 11 }, "end": { - "line": 323, + "line": 339, "column": 23 }, "identifierName": "taxonConcept" @@ -19216,43 +19996,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12157, - "end": 12186, + "start": 12597, + "end": 12626, "loc": { "start": { - "line": 323, + "line": 339, "column": 25 }, "end": { - "line": 323, + "line": 339, "column": 54 } }, "argument": { "type": "MemberExpression", - "start": 12164, - "end": 12185, + "start": 12604, + "end": 12625, "loc": { "start": { - "line": 323, + "line": 339, "column": 32 }, "end": { - "line": 323, + "line": 339, "column": 53 } }, "object": { "type": "Identifier", - "start": 12164, - "end": 12172, + "start": 12604, + "end": 12612, "loc": { "start": { - "line": 323, + "line": 339, "column": 32 }, "end": { - "line": 323, + "line": 339, "column": 40 }, "identifierName": "owlterms" @@ -19261,15 +20041,15 @@ }, "property": { "type": "Identifier", - "start": 12173, - "end": 12185, + "start": 12613, + "end": 12625, "loc": { "start": { - "line": 323, + "line": 339, "column": 41 }, "end": { - "line": 323, + "line": 339, "column": 53 }, "identifierName": "UNKNOWN_CODE" @@ -19283,44 +20063,44 @@ }, { "type": "VariableDeclaration", - "start": 12194, - "end": 12311, + "start": 12634, + "end": 12751, "loc": { "start": { - "line": 325, + "line": 341, "column": 6 }, "end": { - "line": 328, + "line": 344, "column": 18 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12200, - "end": 12310, + "start": 12640, + "end": 12750, "loc": { "start": { - "line": 325, + "line": 341, "column": 12 }, "end": { - "line": 328, + "line": 344, "column": 17 } }, "id": { "type": "Identifier", - "start": 12200, - "end": 12209, + "start": 12640, + "end": 12649, "loc": { "start": { - "line": 325, + "line": 341, "column": 12 }, "end": { - "line": 325, + "line": 341, "column": 21 }, "identifierName": "nomenCode" @@ -19329,43 +20109,43 @@ }, "init": { "type": "MemberExpression", - "start": 12212, - "end": 12310, + "start": 12652, + "end": 12750, "loc": { "start": { - "line": 325, + "line": 341, "column": 24 }, "end": { - "line": 328, + "line": 344, "column": 17 } }, "object": { "type": "NewExpression", - "start": 12212, - "end": 12300, + "start": 12652, + "end": 12740, "loc": { "start": { - "line": 325, + "line": 341, "column": 24 }, "end": { - "line": 328, + "line": 344, "column": 7 } }, "callee": { "type": "Identifier", - "start": 12216, - "end": 12235, + "start": 12656, + "end": 12675, "loc": { "start": { - "line": 325, + "line": 341, "column": 28 }, "end": { - "line": 325, + "line": 341, "column": 47 }, "identifierName": "TaxonConceptWrapper" @@ -19375,15 +20155,15 @@ "arguments": [ { "type": "Identifier", - "start": 12245, - "end": 12257, + "start": 12685, + "end": 12697, "loc": { "start": { - "line": 326, + "line": 342, "column": 8 }, "end": { - "line": 326, + "line": 342, "column": 20 }, "identifierName": "taxonConcept" @@ -19392,44 +20172,44 @@ }, { "type": "MemberExpression", - "start": 12267, - "end": 12292, + "start": 12707, + "end": 12732, "loc": { "start": { - "line": 327, + "line": 343, "column": 8 }, "end": { - "line": 327, + "line": 343, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 12267, - "end": 12271, + "start": 12707, + "end": 12711, "loc": { "start": { - "line": 327, + "line": 343, "column": 8 }, "end": { - "line": 327, + "line": 343, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12272, - "end": 12292, + "start": 12712, + "end": 12732, "loc": { "start": { - "line": 327, + "line": 343, "column": 13 }, "end": { - "line": 327, + "line": 343, "column": 33 }, "identifierName": "phyxDefaultNomenCode" @@ -19442,15 +20222,15 @@ }, "property": { "type": "Identifier", - "start": 12301, - "end": 12310, + "start": 12741, + "end": 12750, "loc": { "start": { - "line": 328, + "line": 344, "column": 8 }, "end": { - "line": 328, + "line": 344, "column": 17 }, "identifierName": "nomenCode" @@ -19465,29 +20245,29 @@ }, { "type": "IfStatement", - "start": 12318, - "end": 12363, + "start": 12758, + "end": 12803, "loc": { "start": { - "line": 329, + "line": 345, "column": 6 }, "end": { - "line": 329, + "line": 345, "column": 51 } }, "test": { "type": "UnaryExpression", - "start": 12322, - "end": 12332, + "start": 12762, + "end": 12772, "loc": { "start": { - "line": 329, + "line": 345, "column": 10 }, "end": { - "line": 329, + "line": 345, "column": 20 } }, @@ -19495,15 +20275,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 12323, - "end": 12332, + "start": 12763, + "end": 12772, "loc": { "start": { - "line": 329, + "line": 345, "column": 11 }, "end": { - "line": 329, + "line": 345, "column": 20 }, "identifierName": "nomenCode" @@ -19516,43 +20296,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12334, - "end": 12363, + "start": 12774, + "end": 12803, "loc": { "start": { - "line": 329, + "line": 345, "column": 22 }, "end": { - "line": 329, + "line": 345, "column": 51 } }, "argument": { "type": "MemberExpression", - "start": 12341, - "end": 12362, + "start": 12781, + "end": 12802, "loc": { "start": { - "line": 329, + "line": 345, "column": 29 }, "end": { - "line": 329, + "line": 345, "column": 50 } }, "object": { "type": "Identifier", - "start": 12341, - "end": 12349, + "start": 12781, + "end": 12789, "loc": { "start": { - "line": 329, + "line": 345, "column": 29 }, "end": { - "line": 329, + "line": 345, "column": 37 }, "identifierName": "owlterms" @@ -19561,15 +20341,15 @@ }, "property": { "type": "Identifier", - "start": 12350, - "end": 12362, + "start": 12790, + "end": 12802, "loc": { "start": { - "line": 329, + "line": 345, "column": 38 }, "end": { - "line": 329, + "line": 345, "column": 50 }, "identifierName": "UNKNOWN_CODE" @@ -19583,29 +20363,29 @@ }, { "type": "ReturnStatement", - "start": 12371, - "end": 12388, + "start": 12811, + "end": 12828, "loc": { "start": { - "line": 331, + "line": 347, "column": 6 }, "end": { - "line": 331, + "line": 347, "column": 23 } }, "argument": { "type": "Identifier", - "start": 12378, - "end": 12387, + "start": 12818, + "end": 12827, "loc": { "start": { - "line": 331, + "line": 347, "column": 13 }, "end": { - "line": 331, + "line": 347, "column": 22 }, "identifierName": "nomenCode" @@ -19630,15 +20410,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n ", - "start": 11547, - "end": 11925, + "start": 11987, + "end": 12365, "loc": { "start": { - "line": 310, + "line": 326, "column": 2 }, "end": { - "line": 316, + "line": 332, "column": 5 } } @@ -19648,15 +20428,15 @@ { "type": "CommentBlock", "value": "*\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n ", - "start": 12405, - "end": 12681, + "start": 12845, + "end": 13121, "loc": { "start": { - "line": 335, + "line": 351, "column": 2 }, "end": { - "line": 340, + "line": 356, "column": 5 } } @@ -19665,15 +20445,15 @@ }, { "type": "ClassMethod", - "start": 12684, - "end": 13419, + "start": 13124, + "end": 13859, "loc": { "start": { - "line": 341, + "line": 357, "column": 2 }, "end": { - "line": 355, + "line": 371, "column": 3 } }, @@ -19681,15 +20461,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12688, - "end": 12704, + "start": 13128, + "end": 13144, "loc": { "start": { - "line": 341, + "line": 357, "column": 6 }, "end": { - "line": 341, + "line": 357, "column": 22 }, "identifierName": "defaultNomenCode" @@ -19704,86 +20484,86 @@ "params": [], "body": { "type": "BlockStatement", - "start": 12707, - "end": 13419, + "start": 13147, + "end": 13859, "loc": { "start": { - "line": 341, + "line": 357, "column": 25 }, "end": { - "line": 355, + "line": 371, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 12780, - "end": 12848, + "start": 13220, + "end": 13288, "loc": { "start": { - "line": 343, + "line": 359, "column": 4 }, "end": { - "line": 343, + "line": 359, "column": 72 } }, "test": { "type": "BinaryExpression", - "start": 12784, - "end": 12816, + "start": 13224, + "end": 13256, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 40 } }, "left": { "type": "MemberExpression", - "start": 12784, - "end": 12810, + "start": 13224, + "end": 13250, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 34 } }, "object": { "type": "MemberExpression", - "start": 12784, - "end": 12803, + "start": 13224, + "end": 13243, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 12784, - "end": 12788, + "start": 13224, + "end": 13228, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 12 } }, @@ -19791,15 +20571,15 @@ }, "property": { "type": "Identifier", - "start": 12789, - "end": 12803, + "start": 13229, + "end": 13243, "loc": { "start": { - "line": 343, + "line": 359, "column": 13 }, "end": { - "line": 343, + "line": 359, "column": 27 }, "identifierName": "uniqNomenCodes" @@ -19811,15 +20591,15 @@ }, "property": { "type": "Identifier", - "start": 12804, - "end": 12810, + "start": 13244, + "end": 13250, "loc": { "start": { - "line": 343, + "line": 359, "column": 28 }, "end": { - "line": 343, + "line": 359, "column": 34 }, "identifierName": "length" @@ -19832,15 +20612,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 12815, - "end": 12816, + "start": 13255, + "end": 13256, "loc": { "start": { - "line": 343, + "line": 359, "column": 39 }, "end": { - "line": 343, + "line": 359, "column": 40 } }, @@ -19854,72 +20634,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12818, - "end": 12848, + "start": 13258, + "end": 13288, "loc": { "start": { - "line": 343, + "line": 359, "column": 42 }, "end": { - "line": 343, + "line": 359, "column": 72 } }, "argument": { "type": "MemberExpression", - "start": 12825, - "end": 12847, + "start": 13265, + "end": 13287, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 71 } }, "object": { "type": "MemberExpression", - "start": 12825, - "end": 12844, + "start": 13265, + "end": 13284, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 68 } }, "object": { "type": "ThisExpression", - "start": 12825, - "end": 12829, + "start": 13265, + "end": 13269, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 53 } } }, "property": { "type": "Identifier", - "start": 12830, - "end": 12844, + "start": 13270, + "end": 13284, "loc": { "start": { - "line": 343, + "line": 359, "column": 54 }, "end": { - "line": 343, + "line": 359, "column": 68 }, "identifierName": "uniqNomenCodes" @@ -19930,15 +20710,15 @@ }, "property": { "type": "NumericLiteral", - "start": 12845, - "end": 12846, + "start": 13285, + "end": 13286, "loc": { "start": { - "line": 343, + "line": 359, "column": 69 }, "end": { - "line": 343, + "line": 359, "column": 70 } }, @@ -19957,15 +20737,15 @@ { "type": "CommentLine", "value": " Check to see if we have a single nomenclatural code to use.", - "start": 12713, - "end": 12775, + "start": 13153, + "end": 13215, "loc": { "start": { - "line": 342, + "line": 358, "column": 4 }, "end": { - "line": 342, + "line": 358, "column": 66 } } @@ -19975,15 +20755,15 @@ { "type": "CommentLine", "value": " If one or more of our specifiers have no nomenclatural code (e.g. if", - "start": 12854, - "end": 12925, + "start": 13294, + "end": 13365, "loc": { "start": { - "line": 345, + "line": 361, "column": 4 }, "end": { - "line": 345, + "line": 361, "column": 75 } } @@ -19991,15 +20771,15 @@ { "type": "CommentLine", "value": " they are specimens), they will show up as owlterms.UNKNOWN_CODE.", - "start": 12930, - "end": 12997, + "start": 13370, + "end": 13437, "loc": { "start": { - "line": 346, + "line": 362, "column": 4 }, "end": { - "line": 346, + "line": 362, "column": 71 } } @@ -20007,15 +20787,15 @@ { "type": "CommentLine", "value": " If we have a single nomenclatural code *apart* from all the", - "start": 13002, - "end": 13064, + "start": 13442, + "end": 13504, "loc": { "start": { - "line": 347, + "line": 363, "column": 4 }, "end": { - "line": 347, + "line": 363, "column": 66 } } @@ -20023,15 +20803,15 @@ { "type": "CommentLine", "value": " owlterms.UNKNOWN_CODEs, then that is still usable as a default", - "start": 13069, - "end": 13134, + "start": 13509, + "end": 13574, "loc": { "start": { - "line": 348, + "line": 364, "column": 4 }, "end": { - "line": 348, + "line": 364, "column": 69 } } @@ -20039,15 +20819,15 @@ { "type": "CommentLine", "value": " nomenclatural code for this phyloreference.", - "start": 13139, - "end": 13185, + "start": 13579, + "end": 13625, "loc": { "start": { - "line": 349, + "line": 365, "column": 4 }, "end": { - "line": 349, + "line": 365, "column": 50 } } @@ -20056,44 +20836,44 @@ }, { "type": "VariableDeclaration", - "start": 13190, - "end": 13297, + "start": 13630, + "end": 13737, "loc": { "start": { - "line": 350, + "line": 366, "column": 4 }, "end": { - "line": 351, + "line": 367, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13196, - "end": 13296, + "start": 13636, + "end": 13736, "loc": { "start": { - "line": 350, + "line": 366, "column": 10 }, "end": { - "line": 351, + "line": 367, "column": 53 } }, "id": { "type": "Identifier", - "start": 13196, - "end": 13220, + "start": 13636, + "end": 13660, "loc": { "start": { - "line": 350, + "line": 366, "column": 10 }, "end": { - "line": 350, + "line": 366, "column": 34 }, "identifierName": "uniqNomenCodesNoUnknowns" @@ -20103,72 +20883,72 @@ }, "init": { "type": "CallExpression", - "start": 13223, - "end": 13296, + "start": 13663, + "end": 13736, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 351, + "line": 367, "column": 53 } }, "callee": { "type": "MemberExpression", - "start": 13223, - "end": 13256, + "start": 13663, + "end": 13696, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 351, + "line": 367, "column": 13 } }, "object": { "type": "MemberExpression", - "start": 13223, - "end": 13242, + "start": 13663, + "end": 13682, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 350, + "line": 366, "column": 56 } }, "object": { "type": "ThisExpression", - "start": 13223, - "end": 13227, + "start": 13663, + "end": 13667, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 350, + "line": 366, "column": 41 } } }, "property": { "type": "Identifier", - "start": 13228, - "end": 13242, + "start": 13668, + "end": 13682, "loc": { "start": { - "line": 350, + "line": 366, "column": 42 }, "end": { - "line": 350, + "line": 366, "column": 56 }, "identifierName": "uniqNomenCodes" @@ -20179,15 +20959,15 @@ }, "property": { "type": "Identifier", - "start": 13250, - "end": 13256, + "start": 13690, + "end": 13696, "loc": { "start": { - "line": 351, + "line": 367, "column": 7 }, "end": { - "line": 351, + "line": 367, "column": 13 }, "identifierName": "filter" @@ -20199,15 +20979,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 13257, - "end": 13295, + "start": 13697, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 14 }, "end": { - "line": 351, + "line": 367, "column": 52 } }, @@ -20218,15 +20998,15 @@ "params": [ { "type": "Identifier", - "start": 13257, - "end": 13261, + "start": 13697, + "end": 13701, "loc": { "start": { - "line": 351, + "line": 367, "column": 14 }, "end": { - "line": 351, + "line": 367, "column": 18 }, "identifierName": "code" @@ -20236,29 +21016,29 @@ ], "body": { "type": "BinaryExpression", - "start": 13265, - "end": 13295, + "start": 13705, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 22 }, "end": { - "line": 351, + "line": 367, "column": 52 } }, "left": { "type": "Identifier", - "start": 13265, - "end": 13269, + "start": 13705, + "end": 13709, "loc": { "start": { - "line": 351, + "line": 367, "column": 22 }, "end": { - "line": 351, + "line": 367, "column": 26 }, "identifierName": "code" @@ -20268,29 +21048,29 @@ "operator": "!==", "right": { "type": "MemberExpression", - "start": 13274, - "end": 13295, + "start": 13714, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 31 }, "end": { - "line": 351, + "line": 367, "column": 52 } }, "object": { "type": "Identifier", - "start": 13274, - "end": 13282, + "start": 13714, + "end": 13722, "loc": { "start": { - "line": 351, + "line": 367, "column": 31 }, "end": { - "line": 351, + "line": 367, "column": 39 }, "identifierName": "owlterms" @@ -20299,15 +21079,15 @@ }, "property": { "type": "Identifier", - "start": 13283, - "end": 13295, + "start": 13723, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 40 }, "end": { - "line": 351, + "line": 367, "column": 52 }, "identifierName": "UNKNOWN_CODE" @@ -20328,15 +21108,15 @@ { "type": "CommentLine", "value": " If one or more of our specifiers have no nomenclatural code (e.g. if", - "start": 12854, - "end": 12925, + "start": 13294, + "end": 13365, "loc": { "start": { - "line": 345, + "line": 361, "column": 4 }, "end": { - "line": 345, + "line": 361, "column": 75 } } @@ -20344,15 +21124,15 @@ { "type": "CommentLine", "value": " they are specimens), they will show up as owlterms.UNKNOWN_CODE.", - "start": 12930, - "end": 12997, + "start": 13370, + "end": 13437, "loc": { "start": { - "line": 346, + "line": 362, "column": 4 }, "end": { - "line": 346, + "line": 362, "column": 71 } } @@ -20360,15 +21140,15 @@ { "type": "CommentLine", "value": " If we have a single nomenclatural code *apart* from all the", - "start": 13002, - "end": 13064, + "start": 13442, + "end": 13504, "loc": { "start": { - "line": 347, + "line": 363, "column": 4 }, "end": { - "line": 347, + "line": 363, "column": 66 } } @@ -20376,15 +21156,15 @@ { "type": "CommentLine", "value": " owlterms.UNKNOWN_CODEs, then that is still usable as a default", - "start": 13069, - "end": 13134, + "start": 13509, + "end": 13574, "loc": { "start": { - "line": 348, + "line": 364, "column": 4 }, "end": { - "line": 348, + "line": 364, "column": 69 } } @@ -20392,15 +21172,15 @@ { "type": "CommentLine", "value": " nomenclatural code for this phyloreference.", - "start": 13139, - "end": 13185, + "start": 13579, + "end": 13625, "loc": { "start": { - "line": 349, + "line": 365, "column": 4 }, "end": { - "line": 349, + "line": 365, "column": 50 } } @@ -20409,57 +21189,57 @@ }, { "type": "IfStatement", - "start": 13302, - "end": 13380, + "start": 13742, + "end": 13820, "loc": { "start": { - "line": 352, + "line": 368, "column": 4 }, "end": { - "line": 352, + "line": 368, "column": 82 } }, "test": { "type": "BinaryExpression", - "start": 13306, - "end": 13343, + "start": 13746, + "end": 13783, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 45 } }, "left": { "type": "MemberExpression", - "start": 13306, - "end": 13337, + "start": 13746, + "end": 13777, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 39 } }, "object": { "type": "Identifier", - "start": 13306, - "end": 13330, + "start": 13746, + "end": 13770, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 32 }, "identifierName": "uniqNomenCodesNoUnknowns" @@ -20468,15 +21248,15 @@ }, "property": { "type": "Identifier", - "start": 13331, - "end": 13337, + "start": 13771, + "end": 13777, "loc": { "start": { - "line": 352, + "line": 368, "column": 33 }, "end": { - "line": 352, + "line": 368, "column": 39 }, "identifierName": "length" @@ -20488,15 +21268,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 13342, - "end": 13343, + "start": 13782, + "end": 13783, "loc": { "start": { - "line": 352, + "line": 368, "column": 44 }, "end": { - "line": 352, + "line": 368, "column": 45 } }, @@ -20509,43 +21289,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 13345, - "end": 13380, + "start": 13785, + "end": 13820, "loc": { "start": { - "line": 352, + "line": 368, "column": 47 }, "end": { - "line": 352, + "line": 368, "column": 82 } }, "argument": { "type": "MemberExpression", - "start": 13352, - "end": 13379, + "start": 13792, + "end": 13819, "loc": { "start": { - "line": 352, + "line": 368, "column": 54 }, "end": { - "line": 352, + "line": 368, "column": 81 } }, "object": { "type": "Identifier", - "start": 13352, - "end": 13376, + "start": 13792, + "end": 13816, "loc": { "start": { - "line": 352, + "line": 368, "column": 54 }, "end": { - "line": 352, + "line": 368, "column": 78 }, "identifierName": "uniqNomenCodesNoUnknowns" @@ -20554,15 +21334,15 @@ }, "property": { "type": "NumericLiteral", - "start": 13377, - "end": 13378, + "start": 13817, + "end": 13818, "loc": { "start": { - "line": 352, + "line": 368, "column": 79 }, "end": { - "line": 352, + "line": 368, "column": 80 } }, @@ -20579,43 +21359,43 @@ }, { "type": "ReturnStatement", - "start": 13386, - "end": 13415, + "start": 13826, + "end": 13855, "loc": { "start": { - "line": 354, + "line": 370, "column": 4 }, "end": { - "line": 354, + "line": 370, "column": 33 } }, "argument": { "type": "MemberExpression", - "start": 13393, - "end": 13414, + "start": 13833, + "end": 13854, "loc": { "start": { - "line": 354, + "line": 370, "column": 11 }, "end": { - "line": 354, + "line": 370, "column": 32 } }, "object": { "type": "Identifier", - "start": 13393, - "end": 13401, + "start": 13833, + "end": 13841, "loc": { "start": { - "line": 354, + "line": 370, "column": 11 }, "end": { - "line": 354, + "line": 370, "column": 19 }, "identifierName": "owlterms" @@ -20624,15 +21404,15 @@ }, "property": { "type": "Identifier", - "start": 13402, - "end": 13414, + "start": 13842, + "end": 13854, "loc": { "start": { - "line": 354, + "line": 370, "column": 20 }, "end": { - "line": 354, + "line": 370, "column": 32 }, "identifierName": "UNKNOWN_CODE" @@ -20650,15 +21430,15 @@ { "type": "CommentBlock", "value": "*\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n ", - "start": 12405, - "end": 12681, + "start": 12845, + "end": 13121, "loc": { "start": { - "line": 335, + "line": 351, "column": 2 }, "end": { - "line": 340, + "line": 356, "column": 5 } } @@ -20668,15 +21448,15 @@ { "type": "CommentBlock", "value": "*\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n ", - "start": 13423, - "end": 14548, + "start": 13863, + "end": 14988, "loc": { "start": { - "line": 357, + "line": 373, "column": 2 }, "end": { - "line": 373, + "line": 389, "column": 5 } } @@ -20685,15 +21465,15 @@ }, { "type": "ClassMethod", - "start": 14551, - "end": 18001, + "start": 14991, + "end": 18441, "loc": { "start": { - "line": 374, + "line": 390, "column": 2 }, "end": { - "line": 454, + "line": 470, "column": 3 } }, @@ -20701,15 +21481,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14551, - "end": 14571, + "start": 14991, + "end": 15011, "loc": { "start": { - "line": 374, + "line": 390, "column": 2 }, "end": { - "line": 374, + "line": 390, "column": 22 }, "identifierName": "createComponentClass" @@ -20725,15 +21505,15 @@ "params": [ { "type": "Identifier", - "start": 14577, - "end": 14583, + "start": 15017, + "end": 15023, "loc": { "start": { - "line": 375, + "line": 391, "column": 4 }, "end": { - "line": 375, + "line": 391, "column": 10 }, "identifierName": "jsonld" @@ -20742,15 +21522,15 @@ }, { "type": "Identifier", - "start": 14589, - "end": 14607, + "start": 15029, + "end": 15047, "loc": { "start": { - "line": 376, + "line": 392, "column": 4 }, "end": { - "line": 376, + "line": 392, "column": 22 }, "identifierName": "internalSpecifiers" @@ -20759,15 +21539,15 @@ }, { "type": "Identifier", - "start": 14613, - "end": 14631, + "start": 15053, + "end": 15071, "loc": { "start": { - "line": 377, + "line": 393, "column": 4 }, "end": { - "line": 377, + "line": 393, "column": 22 }, "identifierName": "externalSpecifiers" @@ -20776,15 +21556,15 @@ }, { "type": "Identifier", - "start": 14637, - "end": 14647, + "start": 15077, + "end": 15087, "loc": { "start": { - "line": 378, + "line": 394, "column": 4 }, "end": { - "line": 378, + "line": 394, "column": 14 }, "identifierName": "equivClass" @@ -20793,29 +21573,29 @@ }, { "type": "AssignmentPattern", - "start": 14653, - "end": 14673, + "start": 15093, + "end": 15113, "loc": { "start": { - "line": 379, + "line": 395, "column": 4 }, "end": { - "line": 379, + "line": 395, "column": 24 } }, "left": { "type": "Identifier", - "start": 14653, - "end": 14666, + "start": 15093, + "end": 15106, "loc": { "start": { - "line": 379, + "line": 395, "column": 4 }, "end": { - "line": 379, + "line": 395, "column": 17 }, "identifierName": "reusePrevious" @@ -20824,15 +21604,15 @@ }, "right": { "type": "BooleanLiteral", - "start": 14669, - "end": 14673, + "start": 15109, + "end": 15113, "loc": { "start": { - "line": 379, + "line": 395, "column": 20 }, "end": { - "line": 379, + "line": 395, "column": 24 } }, @@ -20841,29 +21621,29 @@ }, { "type": "AssignmentPattern", - "start": 14679, - "end": 14702, + "start": 15119, + "end": 15142, "loc": { "start": { - "line": 380, + "line": 396, "column": 4 }, "end": { - "line": 380, + "line": 396, "column": 27 } }, "left": { "type": "Identifier", - "start": 14679, - "end": 14690, + "start": 15119, + "end": 15130, "loc": { "start": { - "line": 380, + "line": 396, "column": 4 }, "end": { - "line": 380, + "line": 396, "column": 15 }, "identifierName": "parentClass" @@ -20872,15 +21652,15 @@ }, "right": { "type": "Identifier", - "start": 14693, - "end": 14702, + "start": 15133, + "end": 15142, "loc": { "start": { - "line": 380, + "line": 396, "column": 18 }, "end": { - "line": 380, + "line": 396, "column": 27 }, "identifierName": "undefined" @@ -20891,72 +21671,72 @@ ], "body": { "type": "BlockStatement", - "start": 14707, - "end": 18001, + "start": 15147, + "end": 18441, "loc": { "start": { - "line": 381, + "line": 397, "column": 4 }, "end": { - "line": 454, + "line": 470, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 14713, - "end": 14831, + "start": 15153, + "end": 15271, "loc": { "start": { - "line": 382, + "line": 398, "column": 4 }, "end": { - "line": 382, + "line": 398, "column": 122 } }, "test": { "type": "BinaryExpression", - "start": 14717, - "end": 14748, + "start": 15157, + "end": 15188, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 14717, - "end": 14742, + "start": 15157, + "end": 15182, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 33 } }, "object": { "type": "Identifier", - "start": 14717, - "end": 14735, + "start": 15157, + "end": 15175, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 26 }, "identifierName": "internalSpecifiers" @@ -20965,15 +21745,15 @@ }, "property": { "type": "Identifier", - "start": 14736, - "end": 14742, + "start": 15176, + "end": 15182, "loc": { "start": { - "line": 382, + "line": 398, "column": 27 }, "end": { - "line": 382, + "line": 398, "column": 33 }, "identifierName": "length" @@ -20985,15 +21765,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 14747, - "end": 14748, + "start": 15187, + "end": 15188, "loc": { "start": { - "line": 382, + "line": 398, "column": 38 }, "end": { - "line": 382, + "line": 398, "column": 39 } }, @@ -21006,43 +21786,43 @@ }, "consequent": { "type": "ThrowStatement", - "start": 14750, - "end": 14831, + "start": 15190, + "end": 15271, "loc": { "start": { - "line": 382, + "line": 398, "column": 41 }, "end": { - "line": 382, + "line": 398, "column": 122 } }, "argument": { "type": "NewExpression", - "start": 14756, - "end": 14830, + "start": 15196, + "end": 15270, "loc": { "start": { - "line": 382, + "line": 398, "column": 47 }, "end": { - "line": 382, + "line": 398, "column": 121 } }, "callee": { "type": "Identifier", - "start": 14760, - "end": 14765, + "start": 15200, + "end": 15205, "loc": { "start": { - "line": 382, + "line": 398, "column": 51 }, "end": { - "line": 382, + "line": 398, "column": 56 }, "identifierName": "Error" @@ -21052,15 +21832,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 14766, - "end": 14829, + "start": 15206, + "end": 15269, "loc": { "start": { - "line": 382, + "line": 398, "column": 57 }, "end": { - "line": 382, + "line": 398, "column": 120 } }, @@ -21077,71 +21857,71 @@ }, { "type": "IfStatement", - "start": 14836, - "end": 15018, + "start": 15276, + "end": 15458, "loc": { "start": { - "line": 383, + "line": 399, "column": 4 }, "end": { - "line": 383, + "line": 399, "column": 186 } }, "test": { "type": "LogicalExpression", - "start": 14840, - "end": 14906, + "start": 15280, + "end": 15346, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 74 } }, "left": { "type": "BinaryExpression", - "start": 14840, - "end": 14871, + "start": 15280, + "end": 15311, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 14840, - "end": 14865, + "start": 15280, + "end": 15305, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 33 } }, "object": { "type": "Identifier", - "start": 14840, - "end": 14858, + "start": 15280, + "end": 15298, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 26 }, "identifierName": "internalSpecifiers" @@ -21150,15 +21930,15 @@ }, "property": { "type": "Identifier", - "start": 14859, - "end": 14865, + "start": 15299, + "end": 15305, "loc": { "start": { - "line": 383, + "line": 399, "column": 27 }, "end": { - "line": 383, + "line": 399, "column": 33 }, "identifierName": "length" @@ -21170,15 +21950,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 14870, - "end": 14871, + "start": 15310, + "end": 15311, "loc": { "start": { - "line": 383, + "line": 399, "column": 38 }, "end": { - "line": 383, + "line": 399, "column": 39 } }, @@ -21192,43 +21972,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 14875, - "end": 14906, + "start": 15315, + "end": 15346, "loc": { "start": { - "line": 383, + "line": 399, "column": 43 }, "end": { - "line": 383, + "line": 399, "column": 74 } }, "left": { "type": "MemberExpression", - "start": 14875, - "end": 14900, + "start": 15315, + "end": 15340, "loc": { "start": { - "line": 383, + "line": 399, "column": 43 }, "end": { - "line": 383, + "line": 399, "column": 68 } }, "object": { "type": "Identifier", - "start": 14875, - "end": 14893, + "start": 15315, + "end": 15333, "loc": { "start": { - "line": 383, + "line": 399, "column": 43 }, "end": { - "line": 383, + "line": 399, "column": 61 }, "identifierName": "externalSpecifiers" @@ -21237,15 +22017,15 @@ }, "property": { "type": "Identifier", - "start": 14894, - "end": 14900, + "start": 15334, + "end": 15340, "loc": { "start": { - "line": 383, + "line": 399, "column": 62 }, "end": { - "line": 383, + "line": 399, "column": 68 }, "identifierName": "length" @@ -21257,15 +22037,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 14905, - "end": 14906, + "start": 15345, + "end": 15346, "loc": { "start": { - "line": 383, + "line": 399, "column": 73 }, "end": { - "line": 383, + "line": 399, "column": 74 } }, @@ -21279,43 +22059,43 @@ }, "consequent": { "type": "ThrowStatement", - "start": 14908, - "end": 15018, + "start": 15348, + "end": 15458, "loc": { "start": { - "line": 383, + "line": 399, "column": 76 }, "end": { - "line": 383, + "line": 399, "column": 186 } }, "argument": { "type": "NewExpression", - "start": 14914, - "end": 15017, + "start": 15354, + "end": 15457, "loc": { "start": { - "line": 383, + "line": 399, "column": 82 }, "end": { - "line": 383, + "line": 399, "column": 185 } }, "callee": { "type": "Identifier", - "start": 14918, - "end": 14923, + "start": 15358, + "end": 15363, "loc": { "start": { - "line": 383, + "line": 399, "column": 86 }, "end": { - "line": 383, + "line": 399, "column": 91 }, "identifierName": "Error" @@ -21325,15 +22105,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 14924, - "end": 15016, + "start": 15364, + "end": 15456, "loc": { "start": { - "line": 383, + "line": 399, "column": 92 }, "end": { - "line": 383, + "line": 399, "column": 184 } }, @@ -21352,15 +22132,15 @@ { "type": "CommentBlock", "value": " Generate a label that represents this component class. ", - "start": 15024, - "end": 15084, + "start": 15464, + "end": 15524, "loc": { "start": { - "line": 385, + "line": 401, "column": 4 }, "end": { - "line": 385, + "line": 401, "column": 64 } } @@ -21368,15 +22148,15 @@ { "type": "CommentLine", "value": " By default, taxonomic unit labels don't include the nomenclatural code.", - "start": 15090, - "end": 15164, + "start": 15530, + "end": 15604, "loc": { "start": { - "line": 387, + "line": 403, "column": 4 }, "end": { - "line": 387, + "line": 403, "column": 78 } } @@ -21384,15 +22164,15 @@ { "type": "CommentLine", "value": " However, we should include that here in order to distinguish between", - "start": 15169, - "end": 15240, + "start": 15609, + "end": 15680, "loc": { "start": { - "line": 388, + "line": 404, "column": 4 }, "end": { - "line": 388, + "line": 404, "column": 75 } } @@ -21400,15 +22180,15 @@ { "type": "CommentLine", "value": " taxonomic names in different taxonomic codes. This method generates that", - "start": 15245, - "end": 15320, + "start": 15685, + "end": 15760, "loc": { "start": { - "line": 389, + "line": 405, "column": 4 }, "end": { - "line": 389, + "line": 405, "column": 79 } } @@ -21416,15 +22196,15 @@ { "type": "CommentLine", "value": " name for a specifier.", - "start": 15325, - "end": 15349, + "start": 15765, + "end": 15789, "loc": { "start": { - "line": 390, + "line": 406, "column": 4 }, "end": { - "line": 390, + "line": 406, "column": 28 } } @@ -21433,44 +22213,44 @@ }, { "type": "VariableDeclaration", - "start": 15354, - "end": 15377, + "start": 15794, + "end": 15817, "loc": { "start": { - "line": 391, + "line": 407, "column": 4 }, "end": { - "line": 391, + "line": 407, "column": 27 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15360, - "end": 15376, + "start": 15800, + "end": 15816, "loc": { "start": { - "line": 391, + "line": 407, "column": 10 }, "end": { - "line": 391, + "line": 407, "column": 26 } }, "id": { "type": "Identifier", - "start": 15360, - "end": 15369, + "start": 15800, + "end": 15809, "loc": { "start": { - "line": 391, + "line": 407, "column": 10 }, "end": { - "line": 391, + "line": 407, "column": 19 }, "identifierName": "outerThis" @@ -21480,15 +22260,15 @@ }, "init": { "type": "ThisExpression", - "start": 15372, - "end": 15376, + "start": 15812, + "end": 15816, "loc": { "start": { - "line": 391, + "line": 407, "column": 22 }, "end": { - "line": 391, + "line": 407, "column": 26 } } @@ -21501,15 +22281,15 @@ { "type": "CommentBlock", "value": " Generate a label that represents this component class. ", - "start": 15024, - "end": 15084, + "start": 15464, + "end": 15524, "loc": { "start": { - "line": 385, + "line": 401, "column": 4 }, "end": { - "line": 385, + "line": 401, "column": 64 } } @@ -21517,15 +22297,15 @@ { "type": "CommentLine", "value": " By default, taxonomic unit labels don't include the nomenclatural code.", - "start": 15090, - "end": 15164, + "start": 15530, + "end": 15604, "loc": { "start": { - "line": 387, + "line": 403, "column": 4 }, "end": { - "line": 387, + "line": 403, "column": 78 } } @@ -21533,15 +22313,15 @@ { "type": "CommentLine", "value": " However, we should include that here in order to distinguish between", - "start": 15169, - "end": 15240, + "start": 15609, + "end": 15680, "loc": { "start": { - "line": 388, + "line": 404, "column": 4 }, "end": { - "line": 388, + "line": 404, "column": 75 } } @@ -21549,15 +22329,15 @@ { "type": "CommentLine", "value": " taxonomic names in different taxonomic codes. This method generates that", - "start": 15245, - "end": 15320, + "start": 15685, + "end": 15760, "loc": { "start": { - "line": 389, + "line": 405, "column": 4 }, "end": { - "line": 389, + "line": 405, "column": 79 } } @@ -21565,15 +22345,15 @@ { "type": "CommentLine", "value": " name for a specifier.", - "start": 15325, - "end": 15349, + "start": 15765, + "end": 15789, "loc": { "start": { - "line": 390, + "line": 406, "column": 4 }, "end": { - "line": 390, + "line": 406, "column": 28 } } @@ -21582,29 +22362,29 @@ }, { "type": "FunctionDeclaration", - "start": 15382, - "end": 15812, + "start": 15822, + "end": 16252, "loc": { "start": { - "line": 392, + "line": 408, "column": 4 }, "end": { - "line": 400, + "line": 416, "column": 5 } }, "id": { "type": "Identifier", - "start": 15391, - "end": 15412, + "start": 15831, + "end": 15852, "loc": { "start": { - "line": 392, + "line": 408, "column": 13 }, "end": { - "line": 392, + "line": 408, "column": 34 }, "identifierName": "generateSpecifierName" @@ -21617,15 +22397,15 @@ "params": [ { "type": "Identifier", - "start": 15413, - "end": 15422, + "start": 15853, + "end": 15862, "loc": { "start": { - "line": 392, + "line": 408, "column": 35 }, "end": { - "line": 392, + "line": 408, "column": 44 }, "identifierName": "specifier" @@ -21635,59 +22415,59 @@ ], "body": { "type": "BlockStatement", - "start": 15424, - "end": 15812, + "start": 15864, + "end": 16252, "loc": { "start": { - "line": 392, + "line": 408, "column": 46 }, "end": { - "line": 400, + "line": 416, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 15432, - "end": 15512, + "start": 15872, + "end": 15952, "loc": { "start": { - "line": 393, + "line": 409, "column": 6 }, "end": { - "line": 393, + "line": 409, "column": 86 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15438, - "end": 15511, + "start": 15878, + "end": 15951, "loc": { "start": { - "line": 393, + "line": 409, "column": 12 }, "end": { - "line": 393, + "line": 409, "column": 85 } }, "id": { "type": "Identifier", - "start": 15438, - "end": 15445, + "start": 15878, + "end": 15885, "loc": { "start": { - "line": 393, + "line": 409, "column": 12 }, "end": { - "line": 393, + "line": 409, "column": 19 }, "identifierName": "wrapped" @@ -21696,29 +22476,29 @@ }, "init": { "type": "NewExpression", - "start": 15448, - "end": 15511, + "start": 15888, + "end": 15951, "loc": { "start": { - "line": 393, + "line": 409, "column": 22 }, "end": { - "line": 393, + "line": 409, "column": 85 } }, "callee": { "type": "Identifier", - "start": 15452, - "end": 15472, + "start": 15892, + "end": 15912, "loc": { "start": { - "line": 393, + "line": 409, "column": 26 }, "end": { - "line": 393, + "line": 409, "column": 46 }, "identifierName": "TaxonomicUnitWrapper" @@ -21728,15 +22508,15 @@ "arguments": [ { "type": "Identifier", - "start": 15473, - "end": 15482, + "start": 15913, + "end": 15922, "loc": { "start": { - "line": 393, + "line": 409, "column": 47 }, "end": { - "line": 393, + "line": 409, "column": 56 }, "identifierName": "specifier" @@ -21745,29 +22525,29 @@ }, { "type": "MemberExpression", - "start": 15484, - "end": 15510, + "start": 15924, + "end": 15950, "loc": { "start": { - "line": 393, + "line": 409, "column": 58 }, "end": { - "line": 393, + "line": 409, "column": 84 } }, "object": { "type": "Identifier", - "start": 15484, - "end": 15493, + "start": 15924, + "end": 15933, "loc": { "start": { - "line": 393, + "line": 409, "column": 58 }, "end": { - "line": 393, + "line": 409, "column": 67 }, "identifierName": "outerThis" @@ -21776,15 +22556,15 @@ }, "property": { "type": "Identifier", - "start": 15494, - "end": 15510, + "start": 15934, + "end": 15950, "loc": { "start": { - "line": 393, + "line": 409, "column": 68 }, "end": { - "line": 393, + "line": 409, "column": 84 }, "identifierName": "defaultNomenCode" @@ -21801,29 +22581,29 @@ }, { "type": "IfStatement", - "start": 15519, - "end": 15550, + "start": 15959, + "end": 15990, "loc": { "start": { - "line": 394, + "line": 410, "column": 6 }, "end": { - "line": 394, + "line": 410, "column": 37 } }, "test": { "type": "UnaryExpression", - "start": 15523, - "end": 15531, + "start": 15963, + "end": 15971, "loc": { "start": { - "line": 394, + "line": 410, "column": 10 }, "end": { - "line": 394, + "line": 410, "column": 18 } }, @@ -21831,15 +22611,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 15524, - "end": 15531, + "start": 15964, + "end": 15971, "loc": { "start": { - "line": 394, + "line": 410, "column": 11 }, "end": { - "line": 394, + "line": 410, "column": 18 }, "identifierName": "wrapped" @@ -21852,29 +22632,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 15533, - "end": 15550, + "start": 15973, + "end": 15990, "loc": { "start": { - "line": 394, + "line": 410, "column": 20 }, "end": { - "line": 394, + "line": 410, "column": 37 } }, "argument": { "type": "StringLiteral", - "start": 15540, - "end": 15549, + "start": 15980, + "end": 15989, "loc": { "start": { - "line": 394, + "line": 410, "column": 27 }, "end": { - "line": 394, + "line": 410, "column": 36 } }, @@ -21889,43 +22669,43 @@ }, { "type": "IfStatement", - "start": 15557, - "end": 15778, + "start": 15997, + "end": 16218, "loc": { "start": { - "line": 395, + "line": 411, "column": 6 }, "end": { - "line": 398, + "line": 414, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 15561, - "end": 15581, + "start": 16001, + "end": 16021, "loc": { "start": { - "line": 395, + "line": 411, "column": 10 }, "end": { - "line": 395, + "line": 411, "column": 30 } }, "object": { "type": "Identifier", - "start": 15561, - "end": 15568, + "start": 16001, + "end": 16008, "loc": { "start": { - "line": 395, + "line": 411, "column": 10 }, "end": { - "line": 395, + "line": 411, "column": 17 }, "identifierName": "wrapped" @@ -21934,15 +22714,15 @@ }, "property": { "type": "Identifier", - "start": 15569, - "end": 15581, + "start": 16009, + "end": 16021, "loc": { "start": { - "line": 395, + "line": 411, "column": 18 }, "end": { - "line": 395, + "line": 411, "column": 30 }, "identifierName": "taxonConcept" @@ -21953,59 +22733,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 15583, - "end": 15778, + "start": 16023, + "end": 16218, "loc": { "start": { - "line": 395, + "line": 411, "column": 32 }, "end": { - "line": 398, + "line": 414, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 15593, - "end": 15681, + "start": 16033, + "end": 16121, "loc": { "start": { - "line": 396, + "line": 412, "column": 8 }, "end": { - "line": 396, + "line": 412, "column": 96 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15599, - "end": 15680, + "start": 16039, + "end": 16120, "loc": { "start": { - "line": 396, + "line": 412, "column": 14 }, "end": { - "line": 396, + "line": 412, "column": 95 } }, "id": { "type": "Identifier", - "start": 15599, - "end": 15615, + "start": 16039, + "end": 16055, "loc": { "start": { - "line": 396, + "line": 412, "column": 14 }, "end": { - "line": 396, + "line": 412, "column": 30 }, "identifierName": "nomenCodeDetails" @@ -22014,43 +22794,43 @@ }, "init": { "type": "MemberExpression", - "start": 15618, - "end": 15680, + "start": 16058, + "end": 16120, "loc": { "start": { - "line": 396, + "line": 412, "column": 33 }, "end": { - "line": 396, + "line": 412, "column": 95 } }, "object": { "type": "NewExpression", - "start": 15618, - "end": 15663, + "start": 16058, + "end": 16103, "loc": { "start": { - "line": 396, + "line": 412, "column": 33 }, "end": { - "line": 396, + "line": 412, "column": 78 } }, "callee": { "type": "Identifier", - "start": 15622, - "end": 15641, + "start": 16062, + "end": 16081, "loc": { "start": { - "line": 396, + "line": 412, "column": 37 }, "end": { - "line": 396, + "line": 412, "column": 56 }, "identifierName": "TaxonConceptWrapper" @@ -22060,29 +22840,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 15642, - "end": 15662, + "start": 16082, + "end": 16102, "loc": { "start": { - "line": 396, + "line": 412, "column": 57 }, "end": { - "line": 396, + "line": 412, "column": 77 } }, "object": { "type": "Identifier", - "start": 15642, - "end": 15649, + "start": 16082, + "end": 16089, "loc": { "start": { - "line": 396, + "line": 412, "column": 57 }, "end": { - "line": 396, + "line": 412, "column": 64 }, "identifierName": "wrapped" @@ -22091,15 +22871,15 @@ }, "property": { "type": "Identifier", - "start": 15650, - "end": 15662, + "start": 16090, + "end": 16102, "loc": { "start": { - "line": 396, + "line": 412, "column": 65 }, "end": { - "line": 396, + "line": 412, "column": 77 }, "identifierName": "taxonConcept" @@ -22112,15 +22892,15 @@ }, "property": { "type": "Identifier", - "start": 15664, - "end": 15680, + "start": 16104, + "end": 16120, "loc": { "start": { - "line": 396, + "line": 412, "column": 79 }, "end": { - "line": 396, + "line": 412, "column": 95 }, "identifierName": "nomenCodeDetails" @@ -22135,29 +22915,29 @@ }, { "type": "IfStatement", - "start": 15690, - "end": 15770, + "start": 16130, + "end": 16210, "loc": { "start": { - "line": 397, + "line": 413, "column": 8 }, "end": { - "line": 397, + "line": 413, "column": 88 } }, "test": { "type": "Identifier", - "start": 15694, - "end": 15710, + "start": 16134, + "end": 16150, "loc": { "start": { - "line": 397, + "line": 413, "column": 12 }, "end": { - "line": 397, + "line": 413, "column": 28 }, "identifierName": "nomenCodeDetails" @@ -22166,58 +22946,58 @@ }, "consequent": { "type": "ReturnStatement", - "start": 15712, - "end": 15770, + "start": 16152, + "end": 16210, "loc": { "start": { - "line": 397, + "line": 413, "column": 30 }, "end": { - "line": 397, + "line": 413, "column": 88 } }, "argument": { "type": "TemplateLiteral", - "start": 15719, - "end": 15769, + "start": 16159, + "end": 16209, "loc": { "start": { - "line": 397, + "line": 413, "column": 37 }, "end": { - "line": 397, + "line": 413, "column": 87 } }, "expressions": [ { "type": "MemberExpression", - "start": 15722, - "end": 15735, + "start": 16162, + "end": 16175, "loc": { "start": { - "line": 397, + "line": 413, "column": 40 }, "end": { - "line": 397, + "line": 413, "column": 53 } }, "object": { "type": "Identifier", - "start": 15722, - "end": 15729, + "start": 16162, + "end": 16169, "loc": { "start": { - "line": 397, + "line": 413, "column": 40 }, "end": { - "line": 397, + "line": 413, "column": 47 }, "identifierName": "wrapped" @@ -22226,15 +23006,15 @@ }, "property": { "type": "Identifier", - "start": 15730, - "end": 15735, + "start": 16170, + "end": 16175, "loc": { "start": { - "line": 397, + "line": 413, "column": 48 }, "end": { - "line": 397, + "line": 413, "column": 53 }, "identifierName": "label" @@ -22245,29 +23025,29 @@ }, { "type": "MemberExpression", - "start": 15740, - "end": 15766, + "start": 16180, + "end": 16206, "loc": { "start": { - "line": 397, + "line": 413, "column": 58 }, "end": { - "line": 397, + "line": 413, "column": 84 } }, "object": { "type": "Identifier", - "start": 15740, - "end": 15756, + "start": 16180, + "end": 16196, "loc": { "start": { - "line": 397, + "line": 413, "column": 58 }, "end": { - "line": 397, + "line": 413, "column": 74 }, "identifierName": "nomenCodeDetails" @@ -22276,15 +23056,15 @@ }, "property": { "type": "Identifier", - "start": 15757, - "end": 15766, + "start": 16197, + "end": 16206, "loc": { "start": { - "line": 397, + "line": 413, "column": 75 }, "end": { - "line": 397, + "line": 413, "column": 84 }, "identifierName": "shortName" @@ -22297,15 +23077,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 15720, - "end": 15720, + "start": 16160, + "end": 16160, "loc": { "start": { - "line": 397, + "line": 413, "column": 38 }, "end": { - "line": 397, + "line": 413, "column": 38 } }, @@ -22317,15 +23097,15 @@ }, { "type": "TemplateElement", - "start": 15736, - "end": 15738, + "start": 16176, + "end": 16178, "loc": { "start": { - "line": 397, + "line": 413, "column": 54 }, "end": { - "line": 397, + "line": 413, "column": 56 } }, @@ -22337,15 +23117,15 @@ }, { "type": "TemplateElement", - "start": 15767, - "end": 15768, + "start": 16207, + "end": 16208, "loc": { "start": { - "line": 397, + "line": 413, "column": 85 }, "end": { - "line": 397, + "line": 413, "column": 86 } }, @@ -22367,43 +23147,43 @@ }, { "type": "ReturnStatement", - "start": 15785, - "end": 15806, + "start": 16225, + "end": 16246, "loc": { "start": { - "line": 399, + "line": 415, "column": 6 }, "end": { - "line": 399, + "line": 415, "column": 27 } }, "argument": { "type": "MemberExpression", - "start": 15792, - "end": 15805, + "start": 16232, + "end": 16245, "loc": { "start": { - "line": 399, + "line": 415, "column": 13 }, "end": { - "line": 399, + "line": 415, "column": 26 } }, "object": { "type": "Identifier", - "start": 15792, - "end": 15799, + "start": 16232, + "end": 16239, "loc": { "start": { - "line": 399, + "line": 415, "column": 13 }, "end": { - "line": 399, + "line": 415, "column": 20 }, "identifierName": "wrapped" @@ -22412,15 +23192,15 @@ }, "property": { "type": "Identifier", - "start": 15800, - "end": 15805, + "start": 16240, + "end": 16245, "loc": { "start": { - "line": 399, + "line": 415, "column": 21 }, "end": { - "line": 399, + "line": 415, "column": 26 }, "identifierName": "label" @@ -22438,15 +23218,15 @@ { "type": "CommentLine", "value": " Start with the internal specifiers, concatenated with '&'.", - "start": 15818, - "end": 15879, + "start": 16258, + "end": 16319, "loc": { "start": { - "line": 402, + "line": 418, "column": 4 }, "end": { - "line": 402, + "line": 418, "column": 65 } } @@ -22455,44 +23235,44 @@ }, { "type": "VariableDeclaration", - "start": 15884, - "end": 16001, + "start": 16324, + "end": 16441, "loc": { "start": { - "line": 403, + "line": 419, "column": 4 }, "end": { - "line": 406, + "line": 422, "column": 19 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15890, - "end": 16000, + "start": 16330, + "end": 16440, "loc": { "start": { - "line": 403, + "line": 419, "column": 10 }, "end": { - "line": 406, + "line": 422, "column": 18 } }, "id": { "type": "Identifier", - "start": 15890, - "end": 15912, + "start": 16330, + "end": 16352, "loc": { "start": { - "line": 403, + "line": 419, "column": 10 }, "end": { - "line": 403, + "line": 419, "column": 32 }, "identifierName": "internalSpecifierLabel" @@ -22502,99 +23282,99 @@ }, "init": { "type": "CallExpression", - "start": 15915, - "end": 16000, + "start": 16355, + "end": 16440, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 406, + "line": 422, "column": 18 } }, "callee": { "type": "MemberExpression", - "start": 15915, - "end": 15993, + "start": 16355, + "end": 16433, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 406, + "line": 422, "column": 11 } }, "object": { "type": "CallExpression", - "start": 15915, - "end": 15981, + "start": 16355, + "end": 16421, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 405, + "line": 421, "column": 13 } }, "callee": { "type": "MemberExpression", - "start": 15915, - "end": 15979, + "start": 16355, + "end": 16419, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 405, + "line": 421, "column": 11 } }, "object": { "type": "CallExpression", - "start": 15915, - "end": 15967, + "start": 16355, + "end": 16407, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 404, + "line": 420, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 15915, - "end": 15944, + "start": 16355, + "end": 16384, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 404, + "line": 420, "column": 10 } }, "object": { "type": "Identifier", - "start": 15915, - "end": 15933, + "start": 16355, + "end": 16373, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 403, + "line": 419, "column": 53 }, "identifierName": "internalSpecifiers" @@ -22603,15 +23383,15 @@ }, "property": { "type": "Identifier", - "start": 15941, - "end": 15944, + "start": 16381, + "end": 16384, "loc": { "start": { - "line": 404, + "line": 420, "column": 7 }, "end": { - "line": 404, + "line": 420, "column": 10 }, "identifierName": "map" @@ -22623,15 +23403,15 @@ "arguments": [ { "type": "Identifier", - "start": 15945, - "end": 15966, + "start": 16385, + "end": 16406, "loc": { "start": { - "line": 404, + "line": 420, "column": 11 }, "end": { - "line": 404, + "line": 420, "column": 32 }, "identifierName": "generateSpecifierName" @@ -22642,15 +23422,15 @@ }, "property": { "type": "Identifier", - "start": 15975, - "end": 15979, + "start": 16415, + "end": 16419, "loc": { "start": { - "line": 405, + "line": 421, "column": 7 }, "end": { - "line": 405, + "line": 421, "column": 11 }, "identifierName": "sort" @@ -22663,15 +23443,15 @@ }, "property": { "type": "Identifier", - "start": 15989, - "end": 15993, + "start": 16429, + "end": 16433, "loc": { "start": { - "line": 406, + "line": 422, "column": 7 }, "end": { - "line": 406, + "line": 422, "column": 11 }, "identifierName": "join" @@ -22683,15 +23463,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 15994, - "end": 15999, + "start": 16434, + "end": 16439, "loc": { "start": { - "line": 406, + "line": 422, "column": 12 }, "end": { - "line": 406, + "line": 422, "column": 17 } }, @@ -22711,15 +23491,15 @@ { "type": "CommentLine", "value": " Start with the internal specifiers, concatenated with '&'.", - "start": 15818, - "end": 15879, + "start": 16258, + "end": 16319, "loc": { "start": { - "line": 402, + "line": 418, "column": 4 }, "end": { - "line": 402, + "line": 418, "column": 65 } } @@ -22728,44 +23508,44 @@ }, { "type": "VariableDeclaration", - "start": 16006, - "end": 16061, + "start": 16446, + "end": 16501, "loc": { "start": { - "line": 407, + "line": 423, "column": 4 }, "end": { - "line": 407, + "line": 423, "column": 59 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16010, - "end": 16060, + "start": 16450, + "end": 16500, "loc": { "start": { - "line": 407, + "line": 423, "column": 8 }, "end": { - "line": 407, + "line": 423, "column": 58 } }, "id": { "type": "Identifier", - "start": 16010, - "end": 16029, + "start": 16450, + "end": 16469, "loc": { "start": { - "line": 407, + "line": 423, "column": 8 }, "end": { - "line": 407, + "line": 423, "column": 27 }, "identifierName": "componentClassLabel" @@ -22774,30 +23554,30 @@ }, "init": { "type": "TemplateLiteral", - "start": 16032, - "end": 16060, + "start": 16472, + "end": 16500, "loc": { "start": { - "line": 407, + "line": 423, "column": 30 }, "end": { - "line": 407, + "line": 423, "column": 58 } }, "expressions": [ { "type": "Identifier", - "start": 16036, - "end": 16058, + "start": 16476, + "end": 16498, "loc": { "start": { - "line": 407, + "line": 423, "column": 34 }, "end": { - "line": 407, + "line": 423, "column": 56 }, "identifierName": "internalSpecifierLabel" @@ -22808,15 +23588,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 16033, - "end": 16034, + "start": 16473, + "end": 16474, "loc": { "start": { - "line": 407, + "line": 423, "column": 31 }, "end": { - "line": 407, + "line": 423, "column": 32 } }, @@ -22828,15 +23608,15 @@ }, { "type": "TemplateElement", - "start": 16059, - "end": 16059, + "start": 16499, + "end": 16499, "loc": { "start": { - "line": 407, + "line": 423, "column": 57 }, "end": { - "line": 407, + "line": 423, "column": 57 } }, @@ -22854,57 +23634,57 @@ }, { "type": "IfStatement", - "start": 16067, - "end": 16411, + "start": 16507, + "end": 16851, "loc": { "start": { - "line": 409, + "line": 425, "column": 4 }, "end": { - "line": 418, + "line": 434, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 16071, - "end": 16102, + "start": 16511, + "end": 16542, "loc": { "start": { - "line": 409, + "line": 425, "column": 8 }, "end": { - "line": 409, + "line": 425, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 16071, - "end": 16096, + "start": 16511, + "end": 16536, "loc": { "start": { - "line": 409, + "line": 425, "column": 8 }, "end": { - "line": 409, + "line": 425, "column": 33 } }, "object": { "type": "Identifier", - "start": 16071, - "end": 16089, + "start": 16511, + "end": 16529, "loc": { "start": { - "line": 409, + "line": 425, "column": 8 }, "end": { - "line": 409, + "line": 425, "column": 26 }, "identifierName": "externalSpecifiers" @@ -22913,15 +23693,15 @@ }, "property": { "type": "Identifier", - "start": 16090, - "end": 16096, + "start": 16530, + "end": 16536, "loc": { "start": { - "line": 409, + "line": 425, "column": 27 }, "end": { - "line": 409, + "line": 425, "column": 33 }, "identifierName": "length" @@ -22933,15 +23713,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 16101, - "end": 16102, + "start": 16541, + "end": 16542, "loc": { "start": { - "line": 409, + "line": 425, "column": 38 }, "end": { - "line": 409, + "line": 425, "column": 39 } }, @@ -22954,59 +23734,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 16104, - "end": 16145, + "start": 16544, + "end": 16585, "loc": { "start": { - "line": 409, + "line": 425, "column": 41 }, "end": { - "line": 411, + "line": 427, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 16112, - "end": 16139, + "start": 16552, + "end": 16579, "loc": { "start": { - "line": 410, + "line": 426, "column": 6 }, "end": { - "line": 410, + "line": 426, "column": 33 } }, "expression": { "type": "AssignmentExpression", - "start": 16112, - "end": 16138, + "start": 16552, + "end": 16578, "loc": { "start": { - "line": 410, + "line": 426, "column": 6 }, "end": { - "line": 410, + "line": 426, "column": 32 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 16112, - "end": 16131, + "start": 16552, + "end": 16571, "loc": { "start": { - "line": 410, + "line": 426, "column": 6 }, "end": { - "line": 410, + "line": 426, "column": 25 }, "identifierName": "componentClassLabel" @@ -23015,15 +23795,15 @@ }, "right": { "type": "StringLiteral", - "start": 16135, - "end": 16138, + "start": 16575, + "end": 16578, "loc": { "start": { - "line": 410, + "line": 426, "column": 29 }, "end": { - "line": 410, + "line": 426, "column": 32 } }, @@ -23040,59 +23820,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 16151, - "end": 16411, + "start": 16591, + "end": 16851, "loc": { "start": { - "line": 411, + "line": 427, "column": 11 }, "end": { - "line": 418, + "line": 434, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 16220, - "end": 16343, + "start": 16660, + "end": 16783, "loc": { "start": { - "line": 413, + "line": 429, "column": 6 }, "end": { - "line": 416, + "line": 432, "column": 21 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16226, - "end": 16342, + "start": 16666, + "end": 16782, "loc": { "start": { - "line": 413, + "line": 429, "column": 12 }, "end": { - "line": 416, + "line": 432, "column": 20 } }, "id": { "type": "Identifier", - "start": 16226, - "end": 16248, + "start": 16666, + "end": 16688, "loc": { "start": { - "line": 413, + "line": 429, "column": 12 }, "end": { - "line": 413, + "line": 429, "column": 34 }, "identifierName": "externalSpecifierLabel" @@ -23102,99 +23882,99 @@ }, "init": { "type": "CallExpression", - "start": 16251, - "end": 16342, + "start": 16691, + "end": 16782, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 416, + "line": 432, "column": 20 } }, "callee": { "type": "MemberExpression", - "start": 16251, - "end": 16335, + "start": 16691, + "end": 16775, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 416, + "line": 432, "column": 13 } }, "object": { "type": "CallExpression", - "start": 16251, - "end": 16321, + "start": 16691, + "end": 16761, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 415, + "line": 431, "column": 15 } }, "callee": { "type": "MemberExpression", - "start": 16251, - "end": 16319, + "start": 16691, + "end": 16759, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 415, + "line": 431, "column": 13 } }, "object": { "type": "CallExpression", - "start": 16251, - "end": 16305, + "start": 16691, + "end": 16745, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 414, + "line": 430, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 16251, - "end": 16282, + "start": 16691, + "end": 16722, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 414, + "line": 430, "column": 12 } }, "object": { "type": "Identifier", - "start": 16251, - "end": 16269, + "start": 16691, + "end": 16709, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 413, + "line": 429, "column": 55 }, "identifierName": "externalSpecifiers" @@ -23203,15 +23983,15 @@ }, "property": { "type": "Identifier", - "start": 16279, - "end": 16282, + "start": 16719, + "end": 16722, "loc": { "start": { - "line": 414, + "line": 430, "column": 9 }, "end": { - "line": 414, + "line": 430, "column": 12 }, "identifierName": "map" @@ -23223,15 +24003,15 @@ "arguments": [ { "type": "Identifier", - "start": 16283, - "end": 16304, + "start": 16723, + "end": 16744, "loc": { "start": { - "line": 414, + "line": 430, "column": 13 }, "end": { - "line": 414, + "line": 430, "column": 34 }, "identifierName": "generateSpecifierName" @@ -23242,15 +24022,15 @@ }, "property": { "type": "Identifier", - "start": 16315, - "end": 16319, + "start": 16755, + "end": 16759, "loc": { "start": { - "line": 415, + "line": 431, "column": 9 }, "end": { - "line": 415, + "line": 431, "column": 13 }, "identifierName": "sort" @@ -23263,15 +24043,15 @@ }, "property": { "type": "Identifier", - "start": 16331, - "end": 16335, + "start": 16771, + "end": 16775, "loc": { "start": { - "line": 416, + "line": 432, "column": 9 }, "end": { - "line": 416, + "line": 432, "column": 13 }, "identifierName": "join" @@ -23283,15 +24063,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 16336, - "end": 16341, + "start": 16776, + "end": 16781, "loc": { "start": { - "line": 416, + "line": 432, "column": 14 }, "end": { - "line": 416, + "line": 432, "column": 19 } }, @@ -23311,15 +24091,15 @@ { "type": "CommentLine", "value": " Add the external specifiers, concatenated with 'V'.", - "start": 16159, - "end": 16213, + "start": 16599, + "end": 16653, "loc": { "start": { - "line": 412, + "line": 428, "column": 6 }, "end": { - "line": 412, + "line": 428, "column": 60 } } @@ -23328,44 +24108,44 @@ }, { "type": "ExpressionStatement", - "start": 16350, - "end": 16405, + "start": 16790, + "end": 16845, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 61 } }, "expression": { "type": "AssignmentExpression", - "start": 16350, - "end": 16404, + "start": 16790, + "end": 16844, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 60 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 16350, - "end": 16369, + "start": 16790, + "end": 16809, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 25 }, "identifierName": "componentClassLabel" @@ -23374,30 +24154,30 @@ }, "right": { "type": "TemplateLiteral", - "start": 16373, - "end": 16404, + "start": 16813, + "end": 16844, "loc": { "start": { - "line": 417, + "line": 433, "column": 29 }, "end": { - "line": 417, + "line": 433, "column": 60 } }, "expressions": [ { "type": "Identifier", - "start": 16379, - "end": 16401, + "start": 16819, + "end": 16841, "loc": { "start": { - "line": 417, + "line": 433, "column": 35 }, "end": { - "line": 417, + "line": 433, "column": 57 }, "identifierName": "externalSpecifierLabel" @@ -23408,15 +24188,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 16374, - "end": 16377, + "start": 16814, + "end": 16817, "loc": { "start": { - "line": 417, + "line": 433, "column": 30 }, "end": { - "line": 417, + "line": 433, "column": 33 } }, @@ -23428,15 +24208,15 @@ }, { "type": "TemplateElement", - "start": 16402, - "end": 16403, + "start": 16842, + "end": 16843, "loc": { "start": { - "line": 417, + "line": 433, "column": 58 }, "end": { - "line": 417, + "line": 433, "column": 59 } }, @@ -23458,15 +24238,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`component class label: ${componentClassLabel}\\n`);", - "start": 16417, - "end": 16492, + "start": 16857, + "end": 16932, "loc": { "start": { - "line": 420, + "line": 436, "column": 4 }, "end": { - "line": 420, + "line": 436, "column": 79 } } @@ -23474,15 +24254,15 @@ { "type": "CommentLine", "value": " TODO We need to replace this with an actual object-based comparison,", - "start": 16498, - "end": 16569, + "start": 16938, + "end": 17009, "loc": { "start": { - "line": 422, + "line": 438, "column": 4 }, "end": { - "line": 422, + "line": 438, "column": 75 } } @@ -23490,15 +24270,15 @@ { "type": "CommentLine", "value": " rather than trusting the labels to tell us everything.", - "start": 16574, - "end": 16631, + "start": 17014, + "end": 17071, "loc": { "start": { - "line": 423, + "line": 439, "column": 4 }, "end": { - "line": 423, + "line": 439, "column": 61 } } @@ -23507,43 +24287,43 @@ }, { "type": "IfStatement", - "start": 16636, - "end": 16890, + "start": 17076, + "end": 17330, "loc": { "start": { - "line": 424, + "line": 440, "column": 4 }, "end": { - "line": 427, + "line": 443, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 16640, - "end": 16711, + "start": 17080, + "end": 17151, "loc": { "start": { - "line": 424, + "line": 440, "column": 8 }, "end": { - "line": 424, + "line": 440, "column": 79 } }, "left": { "type": "Identifier", - "start": 16640, - "end": 16653, + "start": 17080, + "end": 17093, "loc": { "start": { - "line": 424, + "line": 440, "column": 8 }, "end": { - "line": 424, + "line": 440, "column": 21 }, "identifierName": "reusePrevious" @@ -23554,29 +24334,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 16657, - "end": 16711, + "start": 17097, + "end": 17151, "loc": { "start": { - "line": 424, + "line": 440, "column": 25 }, "end": { - "line": 424, + "line": 440, "column": 79 } }, "callee": { "type": "Identifier", - "start": 16657, - "end": 16660, + "start": 17097, + "end": 17100, "loc": { "start": { - "line": 424, + "line": 440, "column": 25 }, "end": { - "line": 424, + "line": 440, "column": 28 }, "identifierName": "has" @@ -23586,44 +24366,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 16661, - "end": 16689, + "start": 17101, + "end": 17129, "loc": { "start": { - "line": 424, + "line": 440, "column": 29 }, "end": { - "line": 424, + "line": 440, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 16661, - "end": 16665, + "start": 17101, + "end": 17105, "loc": { "start": { - "line": 424, + "line": 440, "column": 29 }, "end": { - "line": 424, + "line": 440, "column": 33 } } }, "property": { "type": "Identifier", - "start": 16666, - "end": 16689, + "start": 17106, + "end": 17129, "loc": { "start": { - "line": 424, + "line": 440, "column": 34 }, "end": { - "line": 424, + "line": 440, "column": 57 }, "identifierName": "componentClassesByLabel" @@ -23634,15 +24414,15 @@ }, { "type": "Identifier", - "start": 16691, - "end": 16710, + "start": 17131, + "end": 17150, "loc": { "start": { - "line": 424, + "line": 440, "column": 59 }, "end": { - "line": 424, + "line": 440, "column": 78 }, "identifierName": "componentClassLabel" @@ -23655,59 +24435,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 16713, - "end": 16890, + "start": 17153, + "end": 17330, "loc": { "start": { - "line": 424, + "line": 440, "column": 81 }, "end": { - "line": 427, + "line": 443, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 16809, - "end": 16884, + "start": 17249, + "end": 17324, "loc": { "start": { - "line": 426, + "line": 442, "column": 6 }, "end": { - "line": 426, + "line": 442, "column": 81 } }, "argument": { "type": "ObjectExpression", - "start": 16816, - "end": 16883, + "start": 17256, + "end": 17323, "loc": { "start": { - "line": 426, + "line": 442, "column": 13 }, "end": { - "line": 426, + "line": 442, "column": 80 } }, "properties": [ { "type": "ObjectProperty", - "start": 16818, - "end": 16881, + "start": 17258, + "end": 17321, "loc": { "start": { - "line": 426, + "line": 442, "column": 15 }, "end": { - "line": 426, + "line": 442, "column": 78 } }, @@ -23716,15 +24496,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 16818, - "end": 16823, + "start": 17258, + "end": 17263, "loc": { "start": { - "line": 426, + "line": 442, "column": 15 }, "end": { - "line": 426, + "line": 442, "column": 20 } }, @@ -23737,72 +24517,72 @@ }, "value": { "type": "MemberExpression", - "start": 16825, - "end": 16881, + "start": 17265, + "end": 17321, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 78 } }, "object": { "type": "MemberExpression", - "start": 16825, - "end": 16874, + "start": 17265, + "end": 17314, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 71 } }, "object": { "type": "MemberExpression", - "start": 16825, - "end": 16853, + "start": 17265, + "end": 17293, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 50 } }, "object": { "type": "ThisExpression", - "start": 16825, - "end": 16829, + "start": 17265, + "end": 17269, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 26 } } }, "property": { "type": "Identifier", - "start": 16830, - "end": 16853, + "start": 17270, + "end": 17293, "loc": { "start": { - "line": 426, + "line": 442, "column": 27 }, "end": { - "line": 426, + "line": 442, "column": 50 }, "identifierName": "componentClassesByLabel" @@ -23813,15 +24593,15 @@ }, "property": { "type": "Identifier", - "start": 16854, - "end": 16873, + "start": 17294, + "end": 17313, "loc": { "start": { - "line": 426, + "line": 442, "column": 51 }, "end": { - "line": 426, + "line": 442, "column": 70 }, "identifierName": "componentClassLabel" @@ -23832,15 +24612,15 @@ }, "property": { "type": "StringLiteral", - "start": 16875, - "end": 16880, + "start": 17315, + "end": 17320, "loc": { "start": { - "line": 426, + "line": 442, "column": 72 }, "end": { - "line": 426, + "line": 442, "column": 77 } }, @@ -23861,15 +24641,15 @@ { "type": "CommentLine", "value": " If we see the same label again, return the previously defined component class.", - "start": 16721, - "end": 16802, + "start": 17161, + "end": 17242, "loc": { "start": { - "line": 425, + "line": 441, "column": 6 }, "end": { - "line": 425, + "line": 441, "column": 87 } } @@ -23885,15 +24665,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`component class label: ${componentClassLabel}\\n`);", - "start": 16417, - "end": 16492, + "start": 16857, + "end": 16932, "loc": { "start": { - "line": 420, + "line": 436, "column": 4 }, "end": { - "line": 420, + "line": 436, "column": 79 } } @@ -23901,15 +24681,15 @@ { "type": "CommentLine", "value": " TODO We need to replace this with an actual object-based comparison,", - "start": 16498, - "end": 16569, + "start": 16938, + "end": 17009, "loc": { "start": { - "line": 422, + "line": 438, "column": 4 }, "end": { - "line": 422, + "line": 438, "column": 75 } } @@ -23917,15 +24697,15 @@ { "type": "CommentLine", "value": " rather than trusting the labels to tell us everything.", - "start": 16574, - "end": 16631, + "start": 17014, + "end": 17071, "loc": { "start": { - "line": 423, + "line": 439, "column": 4 }, "end": { - "line": 423, + "line": 439, "column": 61 } } @@ -23935,15 +24715,15 @@ { "type": "CommentLine", "value": " Create a new component class for this set of internal and external specifiers.", - "start": 16896, - "end": 16977, + "start": 17336, + "end": 17417, "loc": { "start": { - "line": 429, + "line": 445, "column": 4 }, "end": { - "line": 429, + "line": 445, "column": 85 } } @@ -23952,58 +24732,58 @@ }, { "type": "ExpressionStatement", - "start": 16982, - "end": 17012, + "start": 17422, + "end": 17452, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 34 } }, "expression": { "type": "AssignmentExpression", - "start": 16982, - "end": 17011, + "start": 17422, + "end": 17451, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 33 } }, "operator": "+=", "left": { "type": "MemberExpression", - "start": 16982, - "end": 17006, + "start": 17422, + "end": 17446, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 16982, - "end": 16986, + "start": 17422, + "end": 17426, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 8 } }, @@ -24011,15 +24791,15 @@ }, "property": { "type": "Identifier", - "start": 16987, - "end": 17006, + "start": 17427, + "end": 17446, "loc": { "start": { - "line": 430, + "line": 446, "column": 9 }, "end": { - "line": 430, + "line": 446, "column": 28 }, "identifierName": "componentClassCount" @@ -24031,15 +24811,15 @@ }, "right": { "type": "NumericLiteral", - "start": 17010, - "end": 17011, + "start": 17450, + "end": 17451, "loc": { "start": { - "line": 430, + "line": 446, "column": 32 }, "end": { - "line": 430, + "line": 446, "column": 33 } }, @@ -24055,15 +24835,15 @@ { "type": "CommentLine", "value": " Create a new component class for this set of internal and external specifiers.", - "start": 16896, - "end": 16977, + "start": 17336, + "end": 17417, "loc": { "start": { - "line": 429, + "line": 445, "column": 4 }, "end": { - "line": 429, + "line": 445, "column": 85 } } @@ -24072,44 +24852,44 @@ }, { "type": "VariableDeclaration", - "start": 17017, - "end": 17043, + "start": 17457, + "end": 17483, "loc": { "start": { - "line": 431, + "line": 447, "column": 4 }, "end": { - "line": 431, + "line": 447, "column": 30 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 17023, - "end": 17042, + "start": 17463, + "end": 17482, "loc": { "start": { - "line": 431, + "line": 447, "column": 10 }, "end": { - "line": 431, + "line": 447, "column": 29 } }, "id": { "type": "Identifier", - "start": 17023, - "end": 17037, + "start": 17463, + "end": 17477, "loc": { "start": { - "line": 431, + "line": 447, "column": 10 }, "end": { - "line": 431, + "line": 447, "column": 24 }, "identifierName": "componentClass" @@ -24118,15 +24898,15 @@ }, "init": { "type": "ObjectExpression", - "start": 17040, - "end": 17042, + "start": 17480, + "end": 17482, "loc": { "start": { - "line": 431, + "line": 447, "column": 27 }, "end": { - "line": 431, + "line": 447, "column": 29 } }, @@ -24138,58 +24918,58 @@ }, { "type": "ExpressionStatement", - "start": 17048, - "end": 17128, + "start": 17488, + "end": 17568, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 84 } }, "expression": { "type": "AssignmentExpression", - "start": 17048, - "end": 17127, + "start": 17488, + "end": 17567, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 83 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17048, - "end": 17069, + "start": 17488, + "end": 17509, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 25 } }, "object": { "type": "Identifier", - "start": 17048, - "end": 17062, + "start": 17488, + "end": 17502, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 18 }, "identifierName": "componentClass" @@ -24198,15 +24978,15 @@ }, "property": { "type": "StringLiteral", - "start": 17063, - "end": 17068, + "start": 17503, + "end": 17508, "loc": { "start": { - "line": 432, + "line": 448, "column": 19 }, "end": { - "line": 432, + "line": 448, "column": 24 } }, @@ -24220,44 +25000,44 @@ }, "right": { "type": "TemplateLiteral", - "start": 17072, - "end": 17127, + "start": 17512, + "end": 17567, "loc": { "start": { - "line": 432, + "line": 448, "column": 28 }, "end": { - "line": 432, + "line": 448, "column": 83 } }, "expressions": [ { "type": "MemberExpression", - "start": 17075, - "end": 17088, + "start": 17515, + "end": 17528, "loc": { "start": { - "line": 432, + "line": 448, "column": 31 }, "end": { - "line": 432, + "line": 448, "column": 44 } }, "object": { "type": "Identifier", - "start": 17075, - "end": 17081, + "start": 17515, + "end": 17521, "loc": { "start": { - "line": 432, + "line": 448, "column": 31 }, "end": { - "line": 432, + "line": 448, "column": 37 }, "identifierName": "jsonld" @@ -24266,15 +25046,15 @@ }, "property": { "type": "StringLiteral", - "start": 17082, - "end": 17087, + "start": 17522, + "end": 17527, "loc": { "start": { - "line": 432, + "line": 448, "column": 38 }, "end": { - "line": 432, + "line": 448, "column": 43 } }, @@ -24288,44 +25068,44 @@ }, { "type": "MemberExpression", - "start": 17101, - "end": 17125, + "start": 17541, + "end": 17565, "loc": { "start": { - "line": 432, + "line": 448, "column": 57 }, "end": { - "line": 432, + "line": 448, "column": 81 } }, "object": { "type": "ThisExpression", - "start": 17101, - "end": 17105, + "start": 17541, + "end": 17545, "loc": { "start": { - "line": 432, + "line": 448, "column": 57 }, "end": { - "line": 432, + "line": 448, "column": 61 } } }, "property": { "type": "Identifier", - "start": 17106, - "end": 17125, + "start": 17546, + "end": 17565, "loc": { "start": { - "line": 432, + "line": 448, "column": 62 }, "end": { - "line": 432, + "line": 448, "column": 81 }, "identifierName": "componentClassCount" @@ -24338,15 +25118,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 17073, - "end": 17073, + "start": 17513, + "end": 17513, "loc": { "start": { - "line": 432, + "line": 448, "column": 29 }, "end": { - "line": 432, + "line": 448, "column": 29 } }, @@ -24358,15 +25138,15 @@ }, { "type": "TemplateElement", - "start": 17089, - "end": 17099, + "start": 17529, + "end": 17539, "loc": { "start": { - "line": 432, + "line": 448, "column": 45 }, "end": { - "line": 432, + "line": 448, "column": 55 } }, @@ -24378,15 +25158,15 @@ }, { "type": "TemplateElement", - "start": 17126, - "end": 17126, + "start": 17566, + "end": 17566, "loc": { "start": { - "line": 432, + "line": 448, "column": 82 }, "end": { - "line": 432, + "line": 448, "column": 82 } }, @@ -24403,15 +25183,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);", - "start": 17133, - "end": 17222, + "start": 17573, + "end": 17662, "loc": { "start": { - "line": 433, + "line": 449, "column": 4 }, "end": { - "line": 433, + "line": 449, "column": 93 } } @@ -24420,58 +25200,58 @@ }, { "type": "ExpressionStatement", - "start": 17228, - "end": 17266, + "start": 17668, + "end": 17706, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 17228, - "end": 17265, + "start": 17668, + "end": 17705, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17228, - "end": 17251, + "start": 17668, + "end": 17691, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 27 } }, "object": { "type": "Identifier", - "start": 17228, - "end": 17242, + "start": 17668, + "end": 17682, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 18 }, "identifierName": "componentClass" @@ -24481,15 +25261,15 @@ }, "property": { "type": "StringLiteral", - "start": 17243, - "end": 17250, + "start": 17683, + "end": 17690, "loc": { "start": { - "line": 435, + "line": 451, "column": 19 }, "end": { - "line": 435, + "line": 451, "column": 26 } }, @@ -24504,15 +25284,15 @@ }, "right": { "type": "StringLiteral", - "start": 17254, - "end": 17265, + "start": 17694, + "end": 17705, "loc": { "start": { - "line": 435, + "line": 451, "column": 30 }, "end": { - "line": 435, + "line": 451, "column": 41 } }, @@ -24528,15 +25308,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);", - "start": 17133, - "end": 17222, + "start": 17573, + "end": 17662, "loc": { "start": { - "line": 433, + "line": 449, "column": 4 }, "end": { - "line": 433, + "line": 449, "column": 93 } } @@ -24545,58 +25325,58 @@ }, { "type": "ExpressionStatement", - "start": 17271, - "end": 17314, + "start": 17711, + "end": 17754, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 47 } }, "expression": { "type": "AssignmentExpression", - "start": 17271, - "end": 17313, + "start": 17711, + "end": 17753, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 46 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17271, - "end": 17291, + "start": 17711, + "end": 17731, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 24 } }, "object": { "type": "Identifier", - "start": 17271, - "end": 17285, + "start": 17711, + "end": 17725, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 18 }, "identifierName": "componentClass" @@ -24605,15 +25385,15 @@ }, "property": { "type": "Identifier", - "start": 17286, - "end": 17291, + "start": 17726, + "end": 17731, "loc": { "start": { - "line": 436, + "line": 452, "column": 19 }, "end": { - "line": 436, + "line": 452, "column": 24 }, "identifierName": "label" @@ -24624,15 +25404,15 @@ }, "right": { "type": "Identifier", - "start": 17294, - "end": 17313, + "start": 17734, + "end": 17753, "loc": { "start": { - "line": 436, + "line": 452, "column": 27 }, "end": { - "line": 436, + "line": 452, "column": 46 }, "identifierName": "componentClassLabel" @@ -24643,58 +25423,58 @@ }, { "type": "ExpressionStatement", - "start": 17319, - "end": 17363, + "start": 17759, + "end": 17803, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 48 } }, "expression": { "type": "AssignmentExpression", - "start": 17319, - "end": 17362, + "start": 17759, + "end": 17802, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 47 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17319, - "end": 17349, + "start": 17759, + "end": 17789, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 34 } }, "object": { "type": "Identifier", - "start": 17319, - "end": 17333, + "start": 17759, + "end": 17773, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 18 }, "identifierName": "componentClass" @@ -24703,15 +25483,15 @@ }, "property": { "type": "Identifier", - "start": 17334, - "end": 17349, + "start": 17774, + "end": 17789, "loc": { "start": { - "line": 437, + "line": 453, "column": 19 }, "end": { - "line": 437, + "line": 453, "column": 34 }, "identifierName": "equivalentClass" @@ -24722,15 +25502,15 @@ }, "right": { "type": "Identifier", - "start": 17352, - "end": 17362, + "start": 17792, + "end": 17802, "loc": { "start": { - "line": 437, + "line": 453, "column": 37 }, "end": { - "line": 437, + "line": 453, "column": 47 }, "identifierName": "equivClass" @@ -24741,57 +25521,57 @@ }, { "type": "IfStatement", - "start": 17368, - "end": 17559, + "start": 17808, + "end": 17999, "loc": { "start": { - "line": 438, + "line": 454, "column": 4 }, "end": { - "line": 439, + "line": 455, "column": 82 } }, "test": { "type": "BinaryExpression", - "start": 17372, - "end": 17401, + "start": 17812, + "end": 17841, "loc": { "start": { - "line": 438, + "line": 454, "column": 8 }, "end": { - "line": 438, + "line": 454, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 17372, - "end": 17397, + "start": 17812, + "end": 17837, "loc": { "start": { - "line": 438, + "line": 454, "column": 8 }, "end": { - "line": 438, + "line": 454, "column": 33 } }, "object": { "type": "Identifier", - "start": 17372, - "end": 17390, + "start": 17812, + "end": 17830, "loc": { "start": { - "line": 438, + "line": 454, "column": 8 }, "end": { - "line": 438, + "line": 454, "column": 26 }, "identifierName": "externalSpecifiers" @@ -24800,15 +25580,15 @@ }, "property": { "type": "Identifier", - "start": 17391, - "end": 17397, + "start": 17831, + "end": 17837, "loc": { "start": { - "line": 438, + "line": 454, "column": 27 }, "end": { - "line": 438, + "line": 454, "column": 33 }, "identifierName": "length" @@ -24820,15 +25600,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 17400, - "end": 17401, + "start": 17840, + "end": 17841, "loc": { "start": { - "line": 438, + "line": 454, "column": 36 }, "end": { - "line": 438, + "line": 454, "column": 37 } }, @@ -24841,58 +25621,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 17403, - "end": 17476, + "start": 17843, + "end": 17916, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 112 } }, "expression": { "type": "AssignmentExpression", - "start": 17403, - "end": 17475, + "start": 17843, + "end": 17915, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 111 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17403, - "end": 17428, + "start": 17843, + "end": 17868, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 64 } }, "object": { "type": "Identifier", - "start": 17403, - "end": 17417, + "start": 17843, + "end": 17857, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 53 }, "identifierName": "componentClass" @@ -24901,15 +25681,15 @@ }, "property": { "type": "Identifier", - "start": 17418, - "end": 17428, + "start": 17858, + "end": 17868, "loc": { "start": { - "line": 438, + "line": 454, "column": 54 }, "end": { - "line": 438, + "line": 454, "column": 64 }, "identifierName": "subClassOf" @@ -24920,30 +25700,30 @@ }, "right": { "type": "ArrayExpression", - "start": 17431, - "end": 17475, + "start": 17871, + "end": 17915, "loc": { "start": { - "line": 438, + "line": 454, "column": 67 }, "end": { - "line": 438, + "line": 454, "column": 111 } }, "elements": [ { "type": "StringLiteral", - "start": 17432, - "end": 17474, + "start": 17872, + "end": 17914, "loc": { "start": { - "line": 438, + "line": 454, "column": 68 }, "end": { - "line": 438, + "line": 454, "column": 110 } }, @@ -24959,58 +25739,58 @@ }, "alternate": { "type": "ExpressionStatement", - "start": 17486, - "end": 17559, + "start": 17926, + "end": 17999, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 82 } }, "expression": { "type": "AssignmentExpression", - "start": 17486, - "end": 17558, + "start": 17926, + "end": 17998, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 81 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17486, - "end": 17511, + "start": 17926, + "end": 17951, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 34 } }, "object": { "type": "Identifier", - "start": 17486, - "end": 17500, + "start": 17926, + "end": 17940, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 23 }, "identifierName": "componentClass" @@ -25019,15 +25799,15 @@ }, "property": { "type": "Identifier", - "start": 17501, - "end": 17511, + "start": 17941, + "end": 17951, "loc": { "start": { - "line": 439, + "line": 455, "column": 24 }, "end": { - "line": 439, + "line": 455, "column": 34 }, "identifierName": "subClassOf" @@ -25038,30 +25818,30 @@ }, "right": { "type": "ArrayExpression", - "start": 17514, - "end": 17558, + "start": 17954, + "end": 17998, "loc": { "start": { - "line": 439, + "line": 455, "column": 37 }, "end": { - "line": 439, + "line": 455, "column": 81 } }, "elements": [ { "type": "StringLiteral", - "start": 17515, - "end": 17557, + "start": 17955, + "end": 17997, "loc": { "start": { - "line": 439, + "line": 455, "column": 38 }, "end": { - "line": 439, + "line": 455, "column": 80 } }, @@ -25078,29 +25858,29 @@ }, { "type": "IfStatement", - "start": 17565, - "end": 17673, + "start": 18005, + "end": 18113, "loc": { "start": { - "line": 441, + "line": 457, "column": 4 }, "end": { - "line": 445, + "line": 461, "column": 5 } }, "test": { "type": "Identifier", - "start": 17569, - "end": 17580, + "start": 18009, + "end": 18020, "loc": { "start": { - "line": 441, + "line": 457, "column": 8 }, "end": { - "line": 441, + "line": 457, "column": 19 }, "identifierName": "parentClass" @@ -25109,86 +25889,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 17582, - "end": 17673, + "start": 18022, + "end": 18113, "loc": { "start": { - "line": 441, + "line": 457, "column": 21 }, "end": { - "line": 445, + "line": 461, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 17590, - "end": 17667, + "start": 18030, + "end": 18107, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 444, + "line": 460, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 17590, - "end": 17666, + "start": 18030, + "end": 18106, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 444, + "line": 460, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 17590, - "end": 17620, + "start": 18030, + "end": 18060, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 17590, - "end": 17615, + "start": 18030, + "end": 18055, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 31 } }, "object": { "type": "Identifier", - "start": 17590, - "end": 17604, + "start": 18030, + "end": 18044, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 20 }, "identifierName": "componentClass" @@ -25197,15 +25977,15 @@ }, "property": { "type": "Identifier", - "start": 17605, - "end": 17615, + "start": 18045, + "end": 18055, "loc": { "start": { - "line": 442, + "line": 458, "column": 21 }, "end": { - "line": 442, + "line": 458, "column": 31 }, "identifierName": "subClassOf" @@ -25216,15 +25996,15 @@ }, "property": { "type": "Identifier", - "start": 17616, - "end": 17620, + "start": 18056, + "end": 18060, "loc": { "start": { - "line": 442, + "line": 458, "column": 32 }, "end": { - "line": 442, + "line": 458, "column": 36 }, "identifierName": "push" @@ -25236,30 +26016,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 17621, - "end": 17665, + "start": 18061, + "end": 18105, "loc": { "start": { - "line": 442, + "line": 458, "column": 37 }, "end": { - "line": 444, + "line": 460, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 17631, - "end": 17656, + "start": 18071, + "end": 18096, "loc": { "start": { - "line": 443, + "line": 459, "column": 8 }, "end": { - "line": 443, + "line": 459, "column": 33 } }, @@ -25268,15 +26048,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 17631, - "end": 17636, + "start": 18071, + "end": 18076, "loc": { "start": { - "line": 443, + "line": 459, "column": 8 }, "end": { - "line": 443, + "line": 459, "column": 13 } }, @@ -25288,29 +26068,29 @@ }, "value": { "type": "MemberExpression", - "start": 17638, - "end": 17656, + "start": 18078, + "end": 18096, "loc": { "start": { - "line": 443, + "line": 459, "column": 15 }, "end": { - "line": 443, + "line": 459, "column": 33 } }, "object": { "type": "Identifier", - "start": 17638, - "end": 17649, + "start": 18078, + "end": 18089, "loc": { "start": { - "line": 443, + "line": 459, "column": 15 }, "end": { - "line": 443, + "line": 459, "column": 26 }, "identifierName": "parentClass" @@ -25319,15 +26099,15 @@ }, "property": { "type": "StringLiteral", - "start": 17650, - "end": 17655, + "start": 18090, + "end": 18095, "loc": { "start": { - "line": 443, + "line": 459, "column": 27 }, "end": { - "line": 443, + "line": 459, "column": 32 } }, @@ -25354,15 +26134,15 @@ { "type": "CommentLine", "value": " Save it in the cache for later usage.", - "start": 17679, - "end": 17719, + "start": 18119, + "end": 18159, "loc": { "start": { - "line": 447, + "line": 463, "column": 4 }, "end": { - "line": 447, + "line": 463, "column": 44 } } @@ -25371,72 +26151,72 @@ }, { "type": "ExpressionStatement", - "start": 17724, - "end": 17791, + "start": 18164, + "end": 18231, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 17724, - "end": 17790, + "start": 18164, + "end": 18230, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17724, - "end": 17773, + "start": 18164, + "end": 18213, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 53 } }, "object": { "type": "MemberExpression", - "start": 17724, - "end": 17752, + "start": 18164, + "end": 18192, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 17724, - "end": 17728, + "start": 18164, + "end": 18168, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 8 } }, @@ -25444,15 +26224,15 @@ }, "property": { "type": "Identifier", - "start": 17729, - "end": 17752, + "start": 18169, + "end": 18192, "loc": { "start": { - "line": 448, + "line": 464, "column": 9 }, "end": { - "line": 448, + "line": 464, "column": 32 }, "identifierName": "componentClassesByLabel" @@ -25464,15 +26244,15 @@ }, "property": { "type": "Identifier", - "start": 17753, - "end": 17772, + "start": 18193, + "end": 18212, "loc": { "start": { - "line": 448, + "line": 464, "column": 33 }, "end": { - "line": 448, + "line": 464, "column": 52 }, "identifierName": "componentClassLabel" @@ -25484,15 +26264,15 @@ }, "right": { "type": "Identifier", - "start": 17776, - "end": 17790, + "start": 18216, + "end": 18230, "loc": { "start": { - "line": 448, + "line": 464, "column": 56 }, "end": { - "line": 448, + "line": 464, "column": 70 }, "identifierName": "componentClass" @@ -25505,15 +26285,15 @@ { "type": "CommentLine", "value": " Save it in the cache for later usage.", - "start": 17679, - "end": 17719, + "start": 18119, + "end": 18159, "loc": { "start": { - "line": 447, + "line": 463, "column": 4 }, "end": { - "line": 447, + "line": 463, "column": 44 } } @@ -25523,15 +26303,15 @@ { "type": "CommentLine", "value": " The first time we create a componentClass, we include it into the logical", - "start": 17797, - "end": 17873, + "start": 18237, + "end": 18313, "loc": { "start": { - "line": 450, + "line": 466, "column": 4 }, "end": { - "line": 450, + "line": 466, "column": 80 } } @@ -25539,15 +26319,15 @@ { "type": "CommentLine", "value": " expression directly. On subsequent calls, we'll only return the `@id`", - "start": 17878, - "end": 17950, + "start": 18318, + "end": 18390, "loc": { "start": { - "line": 451, + "line": 467, "column": 4 }, "end": { - "line": 451, + "line": 467, "column": 76 } } @@ -25555,15 +26335,15 @@ { "type": "CommentLine", "value": " (see above).", - "start": 17955, - "end": 17970, + "start": 18395, + "end": 18410, "loc": { "start": { - "line": 452, + "line": 468, "column": 4 }, "end": { - "line": 452, + "line": 468, "column": 19 } } @@ -25572,29 +26352,29 @@ }, { "type": "ReturnStatement", - "start": 17975, - "end": 17997, + "start": 18415, + "end": 18437, "loc": { "start": { - "line": 453, + "line": 469, "column": 4 }, "end": { - "line": 453, + "line": 469, "column": 26 } }, "argument": { "type": "Identifier", - "start": 17982, - "end": 17996, + "start": 18422, + "end": 18436, "loc": { "start": { - "line": 453, + "line": 469, "column": 11 }, "end": { - "line": 453, + "line": 469, "column": 25 }, "identifierName": "componentClass" @@ -25606,15 +26386,15 @@ { "type": "CommentLine", "value": " The first time we create a componentClass, we include it into the logical", - "start": 17797, - "end": 17873, + "start": 18237, + "end": 18313, "loc": { "start": { - "line": 450, + "line": 466, "column": 4 }, "end": { - "line": 450, + "line": 466, "column": 80 } } @@ -25622,15 +26402,15 @@ { "type": "CommentLine", "value": " expression directly. On subsequent calls, we'll only return the `@id`", - "start": 17878, - "end": 17950, + "start": 18318, + "end": 18390, "loc": { "start": { - "line": 451, + "line": 467, "column": 4 }, "end": { - "line": 451, + "line": 467, "column": 76 } } @@ -25638,15 +26418,15 @@ { "type": "CommentLine", "value": " (see above).", - "start": 17955, - "end": 17970, + "start": 18395, + "end": 18410, "loc": { "start": { - "line": 452, + "line": 468, "column": 4 }, "end": { - "line": 452, + "line": 468, "column": 19 } } @@ -25660,15 +26440,15 @@ { "type": "CommentBlock", "value": "*\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n ", - "start": 13423, - "end": 14548, + "start": 13863, + "end": 14988, "loc": { "start": { - "line": 357, + "line": 373, "column": 2 }, "end": { - "line": 373, + "line": 389, "column": 5 } } @@ -25677,15 +26457,15 @@ }, { "type": "ClassMethod", - "start": 18005, - "end": 18229, + "start": 18445, + "end": 18669, "loc": { "start": { - "line": 456, + "line": 472, "column": 2 }, "end": { - "line": 462, + "line": 478, "column": 3 } }, @@ -25693,15 +26473,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18005, - "end": 18032, + "start": 18445, + "end": 18472, "loc": { "start": { - "line": 456, + "line": 472, "column": 2 }, "end": { - "line": 456, + "line": 472, "column": 29 }, "identifierName": "getIncludesRestrictionForTU" @@ -25716,15 +26496,15 @@ "params": [ { "type": "Identifier", - "start": 18033, - "end": 18035, + "start": 18473, + "end": 18475, "loc": { "start": { - "line": 456, + "line": 472, "column": 30 }, "end": { - "line": 456, + "line": 472, "column": 32 }, "identifierName": "tu" @@ -25734,59 +26514,59 @@ ], "body": { "type": "BlockStatement", - "start": 18037, - "end": 18229, + "start": 18477, + "end": 18669, "loc": { "start": { - "line": 456, + "line": 472, "column": 34 }, "end": { - "line": 462, + "line": 478, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 18043, - "end": 18225, + "start": 18483, + "end": 18665, "loc": { "start": { - "line": 457, + "line": 473, "column": 4 }, "end": { - "line": 461, + "line": 477, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 18050, - "end": 18224, + "start": 18490, + "end": 18664, "loc": { "start": { - "line": 457, + "line": 473, "column": 11 }, "end": { - "line": 461, + "line": 477, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 18058, - "end": 18084, + "start": 18498, + "end": 18524, "loc": { "start": { - "line": 458, + "line": 474, "column": 6 }, "end": { - "line": 458, + "line": 474, "column": 32 } }, @@ -25795,15 +26575,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18058, - "end": 18065, + "start": 18498, + "end": 18505, "loc": { "start": { - "line": 458, + "line": 474, "column": 6 }, "end": { - "line": 458, + "line": 474, "column": 13 } }, @@ -25815,15 +26595,15 @@ }, "value": { "type": "StringLiteral", - "start": 18067, - "end": 18084, + "start": 18507, + "end": 18524, "loc": { "start": { - "line": 458, + "line": 474, "column": 15 }, "end": { - "line": 458, + "line": 474, "column": 32 } }, @@ -25836,15 +26616,15 @@ }, { "type": "ObjectProperty", - "start": 18092, - "end": 18126, + "start": 18532, + "end": 18566, "loc": { "start": { - "line": 459, + "line": 475, "column": 6 }, "end": { - "line": 459, + "line": 475, "column": 40 } }, @@ -25853,15 +26633,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18092, - "end": 18102, + "start": 18532, + "end": 18542, "loc": { "start": { - "line": 459, + "line": 475, "column": 6 }, "end": { - "line": 459, + "line": 475, "column": 16 }, "identifierName": "onProperty" @@ -25870,15 +26650,15 @@ }, "value": { "type": "StringLiteral", - "start": 18104, - "end": 18126, + "start": 18544, + "end": 18566, "loc": { "start": { - "line": 459, + "line": 475, "column": 18 }, "end": { - "line": 459, + "line": 475, "column": 40 } }, @@ -25891,15 +26671,15 @@ }, { "type": "ObjectProperty", - "start": 18134, - "end": 18217, + "start": 18574, + "end": 18657, "loc": { "start": { - "line": 460, + "line": 476, "column": 6 }, "end": { - "line": 460, + "line": 476, "column": 89 } }, @@ -25908,15 +26688,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18134, - "end": 18148, + "start": 18574, + "end": 18588, "loc": { "start": { - "line": 460, + "line": 476, "column": 6 }, "end": { - "line": 460, + "line": 476, "column": 20 }, "identifierName": "someValuesFrom" @@ -25925,43 +26705,43 @@ }, "value": { "type": "MemberExpression", - "start": 18150, - "end": 18217, + "start": 18590, + "end": 18657, "loc": { "start": { - "line": 460, + "line": 476, "column": 22 }, "end": { - "line": 460, + "line": 476, "column": 89 } }, "object": { "type": "NewExpression", - "start": 18150, - "end": 18201, + "start": 18590, + "end": 18641, "loc": { "start": { - "line": 460, + "line": 476, "column": 22 }, "end": { - "line": 460, + "line": 476, "column": 73 } }, "callee": { "type": "Identifier", - "start": 18154, - "end": 18174, + "start": 18594, + "end": 18614, "loc": { "start": { - "line": 460, + "line": 476, "column": 26 }, "end": { - "line": 460, + "line": 476, "column": 46 }, "identifierName": "TaxonomicUnitWrapper" @@ -25971,15 +26751,15 @@ "arguments": [ { "type": "Identifier", - "start": 18175, - "end": 18177, + "start": 18615, + "end": 18617, "loc": { "start": { - "line": 460, + "line": 476, "column": 47 }, "end": { - "line": 460, + "line": 476, "column": 49 }, "identifierName": "tu" @@ -25988,44 +26768,44 @@ }, { "type": "MemberExpression", - "start": 18179, - "end": 18200, + "start": 18619, + "end": 18640, "loc": { "start": { - "line": 460, + "line": 476, "column": 51 }, "end": { - "line": 460, + "line": 476, "column": 72 } }, "object": { "type": "ThisExpression", - "start": 18179, - "end": 18183, + "start": 18619, + "end": 18623, "loc": { "start": { - "line": 460, + "line": 476, "column": 51 }, "end": { - "line": 460, + "line": 476, "column": 55 } } }, "property": { "type": "Identifier", - "start": 18184, - "end": 18200, + "start": 18624, + "end": 18640, "loc": { "start": { - "line": 460, + "line": 476, "column": 56 }, "end": { - "line": 460, + "line": 476, "column": 72 }, "identifierName": "defaultNomenCode" @@ -26038,15 +26818,15 @@ }, "property": { "type": "Identifier", - "start": 18202, - "end": 18217, + "start": 18642, + "end": 18657, "loc": { "start": { - "line": 460, + "line": 476, "column": 74 }, "end": { - "line": 460, + "line": 476, "column": 89 }, "identifierName": "asOWLEquivClass" @@ -26067,15 +26847,15 @@ { "type": "CommentBlock", "value": "*\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n ", - "start": 18233, - "end": 18345, + "start": 18673, + "end": 18785, "loc": { "start": { - "line": 464, + "line": 480, "column": 2 }, "end": { - "line": 467, + "line": 483, "column": 5 } } @@ -26084,15 +26864,15 @@ }, { "type": "ClassMethod", - "start": 18348, - "end": 18860, + "start": 18788, + "end": 19300, "loc": { "start": { - "line": 468, + "line": 484, "column": 2 }, "end": { - "line": 484, + "line": 500, "column": 3 } }, @@ -26100,15 +26880,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18348, - "end": 18374, + "start": 18788, + "end": 18814, "loc": { "start": { - "line": 468, + "line": 484, "column": 2 }, "end": { - "line": 468, + "line": 484, "column": 28 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -26124,15 +26904,15 @@ "params": [ { "type": "Identifier", - "start": 18375, - "end": 18378, + "start": 18815, + "end": 18818, "loc": { "start": { - "line": 468, + "line": 484, "column": 29 }, "end": { - "line": 468, + "line": 484, "column": 32 }, "identifierName": "tu1" @@ -26141,15 +26921,15 @@ }, { "type": "Identifier", - "start": 18380, - "end": 18383, + "start": 18820, + "end": 18823, "loc": { "start": { - "line": 468, + "line": 484, "column": 34 }, "end": { - "line": 468, + "line": 484, "column": 37 }, "identifierName": "tu2" @@ -26159,59 +26939,59 @@ ], "body": { "type": "BlockStatement", - "start": 18385, - "end": 18860, + "start": 18825, + "end": 19300, "loc": { "start": { - "line": 468, + "line": 484, "column": 39 }, "end": { - "line": 484, + "line": 500, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 18391, - "end": 18856, + "start": 18831, + "end": 19296, "loc": { "start": { - "line": 469, + "line": 485, "column": 4 }, "end": { - "line": 483, + "line": 499, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 18398, - "end": 18855, + "start": 18838, + "end": 19295, "loc": { "start": { - "line": 469, + "line": 485, "column": 11 }, "end": { - "line": 483, + "line": 499, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 18406, - "end": 18432, + "start": 18846, + "end": 18872, "loc": { "start": { - "line": 470, + "line": 486, "column": 6 }, "end": { - "line": 470, + "line": 486, "column": 32 } }, @@ -26220,15 +27000,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18406, - "end": 18413, + "start": 18846, + "end": 18853, "loc": { "start": { - "line": 470, + "line": 486, "column": 6 }, "end": { - "line": 470, + "line": 486, "column": 13 } }, @@ -26240,15 +27020,15 @@ }, "value": { "type": "StringLiteral", - "start": 18415, - "end": 18432, + "start": 18855, + "end": 18872, "loc": { "start": { - "line": 470, + "line": 486, "column": 15 }, "end": { - "line": 470, + "line": 486, "column": 32 } }, @@ -26261,15 +27041,15 @@ }, { "type": "ObjectProperty", - "start": 18440, - "end": 18470, + "start": 18880, + "end": 18910, "loc": { "start": { - "line": 471, + "line": 487, "column": 6 }, "end": { - "line": 471, + "line": 487, "column": 36 } }, @@ -26278,15 +27058,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18440, - "end": 18450, + "start": 18880, + "end": 18890, "loc": { "start": { - "line": 471, + "line": 487, "column": 6 }, "end": { - "line": 471, + "line": 487, "column": 16 }, "identifierName": "onProperty" @@ -26295,15 +27075,15 @@ }, "value": { "type": "StringLiteral", - "start": 18452, - "end": 18470, + "start": 18892, + "end": 18910, "loc": { "start": { - "line": 471, + "line": 487, "column": 18 }, "end": { - "line": 471, + "line": 487, "column": 36 } }, @@ -26316,15 +27096,15 @@ }, { "type": "ObjectProperty", - "start": 18496, - "end": 18848, + "start": 18936, + "end": 19288, "loc": { "start": { - "line": 472, + "line": 488, "column": 6 }, "end": { - "line": 482, + "line": 498, "column": 7 } }, @@ -26333,15 +27113,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18496, - "end": 18510, + "start": 18936, + "end": 18950, "loc": { "start": { - "line": 472, + "line": 488, "column": 6 }, "end": { - "line": 472, + "line": 488, "column": 20 }, "identifierName": "someValuesFrom" @@ -26351,30 +27131,30 @@ }, "value": { "type": "ObjectExpression", - "start": 18512, - "end": 18848, + "start": 18952, + "end": 19288, "loc": { "start": { - "line": 472, + "line": 488, "column": 22 }, "end": { - "line": 482, + "line": 498, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 18522, - "end": 18542, + "start": 18962, + "end": 18982, "loc": { "start": { - "line": 473, + "line": 489, "column": 8 }, "end": { - "line": 473, + "line": 489, "column": 28 } }, @@ -26383,15 +27163,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18522, - "end": 18529, + "start": 18962, + "end": 18969, "loc": { "start": { - "line": 473, + "line": 489, "column": 8 }, "end": { - "line": 473, + "line": 489, "column": 15 } }, @@ -26403,15 +27183,15 @@ }, "value": { "type": "StringLiteral", - "start": 18531, - "end": 18542, + "start": 18971, + "end": 18982, "loc": { "start": { - "line": 473, + "line": 489, "column": 17 }, "end": { - "line": 473, + "line": 489, "column": 28 } }, @@ -26424,15 +27204,15 @@ }, { "type": "ObjectProperty", - "start": 18552, - "end": 18839, + "start": 18992, + "end": 19279, "loc": { "start": { - "line": 474, + "line": 490, "column": 8 }, "end": { - "line": 481, + "line": 497, "column": 9 } }, @@ -26441,15 +27221,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18552, - "end": 18566, + "start": 18992, + "end": 19006, "loc": { "start": { - "line": 474, + "line": 490, "column": 8 }, "end": { - "line": 474, + "line": 490, "column": 22 }, "identifierName": "intersectionOf" @@ -26458,45 +27238,45 @@ }, "value": { "type": "ArrayExpression", - "start": 18568, - "end": 18839, + "start": 19008, + "end": 19279, "loc": { "start": { - "line": 474, + "line": 490, "column": 24 }, "end": { - "line": 481, + "line": 497, "column": 9 } }, "elements": [ { "type": "ObjectExpression", - "start": 18580, - "end": 18779, + "start": 19020, + "end": 19219, "loc": { "start": { - "line": 475, + "line": 491, "column": 10 }, "end": { - "line": 479, + "line": 495, "column": 11 } }, "properties": [ { "type": "ObjectProperty", - "start": 18594, - "end": 18620, + "start": 19034, + "end": 19060, "loc": { "start": { - "line": 476, + "line": 492, "column": 12 }, "end": { - "line": 476, + "line": 492, "column": 38 } }, @@ -26505,15 +27285,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18594, - "end": 18601, + "start": 19034, + "end": 19041, "loc": { "start": { - "line": 476, + "line": 492, "column": 12 }, "end": { - "line": 476, + "line": 492, "column": 19 } }, @@ -26525,15 +27305,15 @@ }, "value": { "type": "StringLiteral", - "start": 18603, - "end": 18620, + "start": 19043, + "end": 19060, "loc": { "start": { - "line": 476, + "line": 492, "column": 21 }, "end": { - "line": 476, + "line": 492, "column": 38 } }, @@ -26546,15 +27326,15 @@ }, { "type": "ObjectProperty", - "start": 18634, - "end": 18668, + "start": 19074, + "end": 19108, "loc": { "start": { - "line": 477, + "line": 493, "column": 12 }, "end": { - "line": 477, + "line": 493, "column": 46 } }, @@ -26563,15 +27343,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18634, - "end": 18644, + "start": 19074, + "end": 19084, "loc": { "start": { - "line": 477, + "line": 493, "column": 12 }, "end": { - "line": 477, + "line": 493, "column": 22 }, "identifierName": "onProperty" @@ -26580,15 +27360,15 @@ }, "value": { "type": "StringLiteral", - "start": 18646, - "end": 18668, + "start": 19086, + "end": 19108, "loc": { "start": { - "line": 477, + "line": 493, "column": 24 }, "end": { - "line": 477, + "line": 493, "column": 46 } }, @@ -26601,15 +27381,15 @@ }, { "type": "ObjectProperty", - "start": 18682, - "end": 18766, + "start": 19122, + "end": 19206, "loc": { "start": { - "line": 478, + "line": 494, "column": 12 }, "end": { - "line": 478, + "line": 494, "column": 96 } }, @@ -26618,15 +27398,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18682, - "end": 18696, + "start": 19122, + "end": 19136, "loc": { "start": { - "line": 478, + "line": 494, "column": 12 }, "end": { - "line": 478, + "line": 494, "column": 26 }, "identifierName": "someValuesFrom" @@ -26635,43 +27415,43 @@ }, "value": { "type": "MemberExpression", - "start": 18698, - "end": 18766, + "start": 19138, + "end": 19206, "loc": { "start": { - "line": 478, + "line": 494, "column": 28 }, "end": { - "line": 478, + "line": 494, "column": 96 } }, "object": { "type": "NewExpression", - "start": 18698, - "end": 18750, + "start": 19138, + "end": 19190, "loc": { "start": { - "line": 478, + "line": 494, "column": 28 }, "end": { - "line": 478, + "line": 494, "column": 80 } }, "callee": { "type": "Identifier", - "start": 18702, - "end": 18722, + "start": 19142, + "end": 19162, "loc": { "start": { - "line": 478, + "line": 494, "column": 32 }, "end": { - "line": 478, + "line": 494, "column": 52 }, "identifierName": "TaxonomicUnitWrapper" @@ -26681,15 +27461,15 @@ "arguments": [ { "type": "Identifier", - "start": 18723, - "end": 18726, + "start": 19163, + "end": 19166, "loc": { "start": { - "line": 478, + "line": 494, "column": 53 }, "end": { - "line": 478, + "line": 494, "column": 56 }, "identifierName": "tu1" @@ -26698,44 +27478,44 @@ }, { "type": "MemberExpression", - "start": 18728, - "end": 18749, + "start": 19168, + "end": 19189, "loc": { "start": { - "line": 478, + "line": 494, "column": 58 }, "end": { - "line": 478, + "line": 494, "column": 79 } }, "object": { "type": "ThisExpression", - "start": 18728, - "end": 18732, + "start": 19168, + "end": 19172, "loc": { "start": { - "line": 478, + "line": 494, "column": 58 }, "end": { - "line": 478, + "line": 494, "column": 62 } } }, "property": { "type": "Identifier", - "start": 18733, - "end": 18749, + "start": 19173, + "end": 19189, "loc": { "start": { - "line": 478, + "line": 494, "column": 63 }, "end": { - "line": 478, + "line": 494, "column": 79 }, "identifierName": "defaultNomenCode" @@ -26748,15 +27528,15 @@ }, "property": { "type": "Identifier", - "start": 18751, - "end": 18766, + "start": 19191, + "end": 19206, "loc": { "start": { - "line": 478, + "line": 494, "column": 81 }, "end": { - "line": 478, + "line": 494, "column": 96 }, "identifierName": "asOWLEquivClass" @@ -26770,58 +27550,58 @@ }, { "type": "CallExpression", - "start": 18791, - "end": 18828, + "start": 19231, + "end": 19268, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 18791, - "end": 18823, + "start": 19231, + "end": 19263, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 42 } }, "object": { "type": "ThisExpression", - "start": 18791, - "end": 18795, + "start": 19231, + "end": 19235, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 14 } } }, "property": { "type": "Identifier", - "start": 18796, - "end": 18823, + "start": 19236, + "end": 19263, "loc": { "start": { - "line": 480, + "line": 496, "column": 15 }, "end": { - "line": 480, + "line": 496, "column": 42 }, "identifierName": "getIncludesRestrictionForTU" @@ -26833,15 +27613,15 @@ "arguments": [ { "type": "Identifier", - "start": 18824, - "end": 18827, + "start": 19264, + "end": 19267, "loc": { "start": { - "line": 480, + "line": 496, "column": 43 }, "end": { - "line": 480, + "line": 496, "column": 46 }, "identifierName": "tu2" @@ -26859,15 +27639,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 18472, - "end": 18489, + "start": 18912, + "end": 18929, "loc": { "start": { - "line": 471, + "line": 487, "column": 38 }, "end": { - "line": 471, + "line": 487, "column": 55 } } @@ -26885,15 +27665,15 @@ { "type": "CommentBlock", "value": "*\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n ", - "start": 18233, - "end": 18345, + "start": 18673, + "end": 18785, "loc": { "start": { - "line": 464, + "line": 480, "column": 2 }, "end": { - "line": 467, + "line": 483, "column": 5 } } @@ -26903,15 +27683,15 @@ { "type": "CommentBlock", "value": "\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n ", - "start": 18864, - "end": 20362, + "start": 19304, + "end": 20802, "loc": { "start": { - "line": 486, + "line": 502, "column": 2 }, "end": { - "line": 511, + "line": 527, "column": 5 } } @@ -26920,15 +27700,15 @@ }, { "type": "ClassMethod", - "start": 20365, - "end": 23762, + "start": 20805, + "end": 24202, "loc": { "start": { - "line": 512, + "line": 528, "column": 2 }, "end": { - "line": 596, + "line": 612, "column": 3 } }, @@ -26936,15 +27716,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 20365, - "end": 20399, + "start": 20805, + "end": 20839, "loc": { "start": { - "line": 512, + "line": 528, "column": 2 }, "end": { - "line": 512, + "line": 528, "column": 36 }, "identifierName": "createClassExpressionsForInternals" @@ -26960,15 +27740,15 @@ "params": [ { "type": "Identifier", - "start": 20400, - "end": 20406, + "start": 20840, + "end": 20846, "loc": { "start": { - "line": 512, + "line": 528, "column": 37 }, "end": { - "line": 512, + "line": 528, "column": 43 }, "identifierName": "jsonld" @@ -26977,15 +27757,15 @@ }, { "type": "Identifier", - "start": 20408, - "end": 20426, + "start": 20848, + "end": 20866, "loc": { "start": { - "line": 512, + "line": 528, "column": 45 }, "end": { - "line": 512, + "line": 528, "column": 63 }, "identifierName": "remainingInternals" @@ -26994,15 +27774,15 @@ }, { "type": "Identifier", - "start": 20428, - "end": 20436, + "start": 20868, + "end": 20876, "loc": { "start": { - "line": 512, + "line": 528, "column": 65 }, "end": { - "line": 512, + "line": 528, "column": 73 }, "identifierName": "selected" @@ -27012,72 +27792,72 @@ ], "body": { "type": "BlockStatement", - "start": 20438, - "end": 23762, + "start": 20878, + "end": 24202, "loc": { "start": { - "line": 512, + "line": 528, "column": 75 }, "end": { - "line": 596, + "line": 612, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 20736, - "end": 21206, + "start": 21176, + "end": 21646, "loc": { "start": { - "line": 518, + "line": 534, "column": 4 }, "end": { - "line": 528, + "line": 544, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 20740, - "end": 20761, + "start": 21180, + "end": 21201, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 29 } }, "left": { "type": "MemberExpression", - "start": 20740, - "end": 20755, + "start": 21180, + "end": 21195, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 23 } }, "object": { "type": "Identifier", - "start": 20740, - "end": 20748, + "start": 21180, + "end": 21188, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 16 }, "identifierName": "selected" @@ -27087,15 +27867,15 @@ }, "property": { "type": "Identifier", - "start": 20749, - "end": 20755, + "start": 21189, + "end": 21195, "loc": { "start": { - "line": 518, + "line": 534, "column": 17 }, "end": { - "line": 518, + "line": 534, "column": 23 }, "identifierName": "length" @@ -27108,15 +27888,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 20760, - "end": 20761, + "start": 21200, + "end": 21201, "loc": { "start": { - "line": 518, + "line": 534, "column": 28 }, "end": { - "line": 518, + "line": 534, "column": 29 } }, @@ -27130,72 +27910,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 20763, - "end": 21206, + "start": 21203, + "end": 21646, "loc": { "start": { - "line": 518, + "line": 534, "column": 31 }, "end": { - "line": 528, + "line": 544, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 20771, - "end": 20934, + "start": 21211, + "end": 21374, "loc": { "start": { - "line": 519, + "line": 535, "column": 6 }, "end": { - "line": 523, + "line": 539, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 20775, - "end": 20806, + "start": 21215, + "end": 21246, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 41 } }, "left": { "type": "MemberExpression", - "start": 20775, - "end": 20800, + "start": 21215, + "end": 21240, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 35 } }, "object": { "type": "Identifier", - "start": 20775, - "end": 20793, + "start": 21215, + "end": 21233, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 28 }, "identifierName": "remainingInternals" @@ -27204,15 +27984,15 @@ }, "property": { "type": "Identifier", - "start": 20794, - "end": 20800, + "start": 21234, + "end": 21240, "loc": { "start": { - "line": 519, + "line": 535, "column": 29 }, "end": { - "line": 519, + "line": 535, "column": 35 }, "identifierName": "length" @@ -27224,15 +28004,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 20805, - "end": 20806, + "start": 21245, + "end": 21246, "loc": { "start": { - "line": 519, + "line": 535, "column": 40 }, "end": { - "line": 519, + "line": 535, "column": 41 } }, @@ -27245,102 +28025,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 20808, - "end": 20934, + "start": 21248, + "end": 21374, "loc": { "start": { - "line": 519, + "line": 535, "column": 43 }, "end": { - "line": 523, + "line": 539, "column": 7 } }, "body": [ { "type": "ReturnStatement", - "start": 20818, - "end": 20926, + "start": 21258, + "end": 21366, "loc": { "start": { - "line": 520, + "line": 536, "column": 8 }, "end": { - "line": 522, + "line": 538, "column": 10 } }, "argument": { "type": "ArrayExpression", - "start": 20825, - "end": 20925, + "start": 21265, + "end": 21365, "loc": { "start": { - "line": 520, + "line": 536, "column": 15 }, "end": { - "line": 522, + "line": 538, "column": 9 } }, "elements": [ { "type": "CallExpression", - "start": 20837, - "end": 20914, + "start": 21277, + "end": 21354, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 87 } }, "callee": { "type": "MemberExpression", - "start": 20837, - "end": 20868, + "start": 21277, + "end": 21308, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 41 } }, "object": { "type": "ThisExpression", - "start": 20837, - "end": 20841, + "start": 21277, + "end": 21281, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 14 } } }, "property": { "type": "Identifier", - "start": 20842, - "end": 20868, + "start": 21282, + "end": 21308, "loc": { "start": { - "line": 521, + "line": 537, "column": 15 }, "end": { - "line": 521, + "line": 537, "column": 41 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -27352,29 +28132,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 20869, - "end": 20890, + "start": 21309, + "end": 21330, "loc": { "start": { - "line": 521, + "line": 537, "column": 42 }, "end": { - "line": 521, + "line": 537, "column": 63 } }, "object": { "type": "Identifier", - "start": 20869, - "end": 20887, + "start": 21309, + "end": 21327, "loc": { "start": { - "line": 521, + "line": 537, "column": 42 }, "end": { - "line": 521, + "line": 537, "column": 60 }, "identifierName": "remainingInternals" @@ -27383,15 +28163,15 @@ }, "property": { "type": "NumericLiteral", - "start": 20888, - "end": 20889, + "start": 21328, + "end": 21329, "loc": { "start": { - "line": 521, + "line": 537, "column": 61 }, "end": { - "line": 521, + "line": 537, "column": 62 } }, @@ -27405,29 +28185,29 @@ }, { "type": "MemberExpression", - "start": 20892, - "end": 20913, + "start": 21332, + "end": 21353, "loc": { "start": { - "line": 521, + "line": 537, "column": 65 }, "end": { - "line": 521, + "line": 537, "column": 86 } }, "object": { "type": "Identifier", - "start": 20892, - "end": 20910, + "start": 21332, + "end": 21350, "loc": { "start": { - "line": 521, + "line": 537, "column": 65 }, "end": { - "line": 521, + "line": 537, "column": 83 }, "identifierName": "remainingInternals" @@ -27436,15 +28216,15 @@ }, "property": { "type": "NumericLiteral", - "start": 20911, - "end": 20912, + "start": 21351, + "end": 21352, "loc": { "start": { - "line": 521, + "line": 537, "column": 84 }, "end": { - "line": 521, + "line": 537, "column": 85 } }, @@ -27468,57 +28248,57 @@ }, { "type": "IfStatement", - "start": 20935, - "end": 21200, + "start": 21375, + "end": 21640, "loc": { "start": { - "line": 523, + "line": 539, "column": 8 }, "end": { - "line": 527, + "line": 543, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 20939, - "end": 20970, + "start": 21379, + "end": 21410, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 43 } }, "left": { "type": "MemberExpression", - "start": 20939, - "end": 20964, + "start": 21379, + "end": 21404, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 37 } }, "object": { "type": "Identifier", - "start": 20939, - "end": 20957, + "start": 21379, + "end": 21397, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 30 }, "identifierName": "remainingInternals" @@ -27527,15 +28307,15 @@ }, "property": { "type": "Identifier", - "start": 20958, - "end": 20964, + "start": 21398, + "end": 21404, "loc": { "start": { - "line": 523, + "line": 539, "column": 31 }, "end": { - "line": 523, + "line": 539, "column": 37 }, "identifierName": "length" @@ -27547,15 +28327,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 20969, - "end": 20970, + "start": 21409, + "end": 21410, "loc": { "start": { - "line": 523, + "line": 539, "column": 42 }, "end": { - "line": 523, + "line": 539, "column": 43 } }, @@ -27568,58 +28348,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 20972, - "end": 21066, + "start": 21412, + "end": 21506, "loc": { "start": { - "line": 523, + "line": 539, "column": 45 }, "end": { - "line": 525, + "line": 541, "column": 7 } }, "body": [ { "type": "ThrowStatement", - "start": 20982, - "end": 21058, + "start": 21422, + "end": 21498, "loc": { "start": { - "line": 524, + "line": 540, "column": 8 }, "end": { - "line": 524, + "line": 540, "column": 84 } }, "argument": { "type": "NewExpression", - "start": 20988, - "end": 21057, + "start": 21428, + "end": 21497, "loc": { "start": { - "line": 524, + "line": 540, "column": 14 }, "end": { - "line": 524, + "line": 540, "column": 83 } }, "callee": { "type": "Identifier", - "start": 20992, - "end": 20997, + "start": 21432, + "end": 21437, "loc": { "start": { - "line": 524, + "line": 540, "column": 18 }, "end": { - "line": 524, + "line": 540, "column": 23 }, "identifierName": "Error" @@ -27629,15 +28409,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 20998, - "end": 21056, + "start": 21438, + "end": 21496, "loc": { "start": { - "line": 524, + "line": 540, "column": 24 }, "end": { - "line": 524, + "line": 540, "column": 82 } }, @@ -27655,57 +28435,57 @@ }, "alternate": { "type": "IfStatement", - "start": 21072, - "end": 21200, + "start": 21512, + "end": 21640, "loc": { "start": { - "line": 525, + "line": 541, "column": 13 }, "end": { - "line": 527, + "line": 543, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21076, - "end": 21107, + "start": 21516, + "end": 21547, "loc": { "start": { - "line": 525, + "line": 541, "column": 17 }, "end": { - "line": 525, + "line": 541, "column": 48 } }, "left": { "type": "MemberExpression", - "start": 21076, - "end": 21101, + "start": 21516, + "end": 21541, "loc": { "start": { - "line": 525, + "line": 541, "column": 17 }, "end": { - "line": 525, + "line": 541, "column": 42 } }, "object": { "type": "Identifier", - "start": 21076, - "end": 21094, + "start": 21516, + "end": 21534, "loc": { "start": { - "line": 525, + "line": 541, "column": 17 }, "end": { - "line": 525, + "line": 541, "column": 35 }, "identifierName": "remainingInternals" @@ -27714,15 +28494,15 @@ }, "property": { "type": "Identifier", - "start": 21095, - "end": 21101, + "start": 21535, + "end": 21541, "loc": { "start": { - "line": 525, + "line": 541, "column": 36 }, "end": { - "line": 525, + "line": 541, "column": 42 }, "identifierName": "length" @@ -27734,15 +28514,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 21106, - "end": 21107, + "start": 21546, + "end": 21547, "loc": { "start": { - "line": 525, + "line": 541, "column": 47 }, "end": { - "line": 525, + "line": 541, "column": 48 } }, @@ -27755,58 +28535,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 21109, - "end": 21200, + "start": 21549, + "end": 21640, "loc": { "start": { - "line": 525, + "line": 541, "column": 50 }, "end": { - "line": 527, + "line": 543, "column": 7 } }, "body": [ { "type": "ThrowStatement", - "start": 21119, - "end": 21192, + "start": 21559, + "end": 21632, "loc": { "start": { - "line": 526, + "line": 542, "column": 8 }, "end": { - "line": 526, + "line": 542, "column": 81 } }, "argument": { "type": "NewExpression", - "start": 21125, - "end": 21191, + "start": 21565, + "end": 21631, "loc": { "start": { - "line": 526, + "line": 542, "column": 14 }, "end": { - "line": 526, + "line": 542, "column": 80 } }, "callee": { "type": "Identifier", - "start": 21129, - "end": 21134, + "start": 21569, + "end": 21574, "loc": { "start": { - "line": 526, + "line": 542, "column": 18 }, "end": { - "line": 526, + "line": 542, "column": 23 }, "identifierName": "Error" @@ -27816,15 +28596,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 21135, - "end": 21190, + "start": 21575, + "end": 21630, "loc": { "start": { - "line": 526, + "line": 542, "column": 24 }, "end": { - "line": 526, + "line": 542, "column": 79 } }, @@ -27852,15 +28632,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:", - "start": 20444, - "end": 20512, + "start": 20884, + "end": 20952, "loc": { "start": { - "line": 513, + "line": 529, "column": 4 }, "end": { - "line": 513, + "line": 529, "column": 72 } } @@ -27868,15 +28648,15 @@ { "type": "CommentLine", "value": " ${remainingInternals.length}, selected: ${selected.length}\\n`);", - "start": 20517, - "end": 20583, + "start": 20957, + "end": 21023, "loc": { "start": { - "line": 514, + "line": 530, "column": 4 }, "end": { - "line": 514, + "line": 530, "column": 70 } } @@ -27884,15 +28664,15 @@ { "type": "CommentLine", "value": " Quick special case: if we have two 'remainingInternals' and zero selecteds,", - "start": 20589, - "end": 20667, + "start": 21029, + "end": 21107, "loc": { "start": { - "line": 516, + "line": 532, "column": 4 }, "end": { - "line": 516, + "line": 532, "column": 82 } } @@ -27900,15 +28680,15 @@ { "type": "CommentLine", "value": " we can just return the MRCA for two internal specifiers.", - "start": 20672, - "end": 20731, + "start": 21112, + "end": 21171, "loc": { "start": { - "line": 517, + "line": 533, "column": 4 }, "end": { - "line": 517, + "line": 533, "column": 63 } } @@ -27918,15 +28698,15 @@ { "type": "CommentLine", "value": " Step 1. If we've already selected something, create an expression for it.", - "start": 21212, - "end": 21288, + "start": 21652, + "end": 21728, "loc": { "start": { - "line": 530, + "line": 546, "column": 4 }, "end": { - "line": 530, + "line": 546, "column": 80 } } @@ -27935,44 +28715,44 @@ }, { "type": "VariableDeclaration", - "start": 21293, - "end": 21315, + "start": 21733, + "end": 21755, "loc": { "start": { - "line": 531, + "line": 547, "column": 4 }, "end": { - "line": 531, + "line": 547, "column": 26 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 21299, - "end": 21314, + "start": 21739, + "end": 21754, "loc": { "start": { - "line": 531, + "line": 547, "column": 10 }, "end": { - "line": 531, + "line": 547, "column": 25 } }, "id": { "type": "Identifier", - "start": 21299, - "end": 21309, + "start": 21739, + "end": 21749, "loc": { "start": { - "line": 531, + "line": 547, "column": 10 }, "end": { - "line": 531, + "line": 547, "column": 20 }, "identifierName": "classExprs" @@ -27982,15 +28762,15 @@ }, "init": { "type": "ArrayExpression", - "start": 21312, - "end": 21314, + "start": 21752, + "end": 21754, "loc": { "start": { - "line": 531, + "line": 547, "column": 23 }, "end": { - "line": 531, + "line": 547, "column": 25 } }, @@ -28004,15 +28784,15 @@ { "type": "CommentLine", "value": " Step 1. If we've already selected something, create an expression for it.", - "start": 21212, - "end": 21288, + "start": 21652, + "end": 21728, "loc": { "start": { - "line": 530, + "line": 546, "column": 4 }, "end": { - "line": 530, + "line": 546, "column": 80 } } @@ -28021,57 +28801,57 @@ }, { "type": "IfStatement", - "start": 21320, - "end": 22828, + "start": 21760, + "end": 23268, "loc": { "start": { - "line": 532, + "line": 548, "column": 4 }, "end": { - "line": 576, + "line": 592, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 21324, - "end": 21343, + "start": 21764, + "end": 21783, "loc": { "start": { - "line": 532, + "line": 548, "column": 8 }, "end": { - "line": 532, + "line": 548, "column": 27 } }, "left": { "type": "MemberExpression", - "start": 21324, - "end": 21339, + "start": 21764, + "end": 21779, "loc": { "start": { - "line": 532, + "line": 548, "column": 8 }, "end": { - "line": 532, + "line": 548, "column": 23 } }, "object": { "type": "Identifier", - "start": 21324, - "end": 21332, + "start": 21764, + "end": 21772, "loc": { "start": { - "line": 532, + "line": 548, "column": 8 }, "end": { - "line": 532, + "line": 548, "column": 16 }, "identifierName": "selected" @@ -28080,15 +28860,15 @@ }, "property": { "type": "Identifier", - "start": 21333, - "end": 21339, + "start": 21773, + "end": 21779, "loc": { "start": { - "line": 532, + "line": 548, "column": 17 }, "end": { - "line": 532, + "line": 548, "column": 23 }, "identifierName": "length" @@ -28100,15 +28880,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 21342, - "end": 21343, + "start": 21782, + "end": 21783, "loc": { "start": { - "line": 532, + "line": 548, "column": 26 }, "end": { - "line": 532, + "line": 548, "column": 27 } }, @@ -28121,59 +28901,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 21345, - "end": 22828, + "start": 21785, + "end": 23268, "loc": { "start": { - "line": 532, + "line": 548, "column": 29 }, "end": { - "line": 576, + "line": 592, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 21353, - "end": 21385, + "start": 21793, + "end": 21825, "loc": { "start": { - "line": 533, + "line": 549, "column": 6 }, "end": { - "line": 533, + "line": 549, "column": 38 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 21357, - "end": 21384, + "start": 21797, + "end": 21824, "loc": { "start": { - "line": 533, + "line": 549, "column": 10 }, "end": { - "line": 533, + "line": 549, "column": 37 } }, "id": { "type": "Identifier", - "start": 21357, - "end": 21379, + "start": 21797, + "end": 21819, "loc": { "start": { - "line": 533, + "line": 549, "column": 10 }, "end": { - "line": 533, + "line": 549, "column": 32 }, "identifierName": "remainingInternalsExpr" @@ -28182,15 +28962,15 @@ }, "init": { "type": "ArrayExpression", - "start": 21382, - "end": 21384, + "start": 21822, + "end": 21824, "loc": { "start": { - "line": 533, + "line": 549, "column": 35 }, "end": { - "line": 533, + "line": 549, "column": 37 } }, @@ -28202,57 +28982,57 @@ }, { "type": "IfStatement", - "start": 21392, - "end": 21952, + "start": 21832, + "end": 22392, "loc": { "start": { - "line": 534, + "line": 550, "column": 6 }, "end": { - "line": 548, + "line": 564, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21396, - "end": 21427, + "start": 21836, + "end": 21867, "loc": { "start": { - "line": 534, + "line": 550, "column": 10 }, "end": { - "line": 534, + "line": 550, "column": 41 } }, "left": { "type": "MemberExpression", - "start": 21396, - "end": 21421, + "start": 21836, + "end": 21861, "loc": { "start": { - "line": 534, + "line": 550, "column": 10 }, "end": { - "line": 534, + "line": 550, "column": 35 } }, "object": { "type": "Identifier", - "start": 21396, - "end": 21414, + "start": 21836, + "end": 21854, "loc": { "start": { - "line": 534, + "line": 550, "column": 10 }, "end": { - "line": 534, + "line": 550, "column": 28 }, "identifierName": "remainingInternals" @@ -28261,15 +29041,15 @@ }, "property": { "type": "Identifier", - "start": 21415, - "end": 21421, + "start": 21855, + "end": 21861, "loc": { "start": { - "line": 534, + "line": 550, "column": 29 }, "end": { - "line": 534, + "line": 550, "column": 35 }, "identifierName": "length" @@ -28281,15 +29061,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 21426, - "end": 21427, + "start": 21866, + "end": 21867, "loc": { "start": { - "line": 534, + "line": 550, "column": 40 }, "end": { - "line": 534, + "line": 550, "column": 41 } }, @@ -28302,59 +29082,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 21429, - "end": 21528, + "start": 21869, + "end": 21968, "loc": { "start": { - "line": 534, + "line": 550, "column": 43 }, "end": { - "line": 536, + "line": 552, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 21439, - "end": 21520, + "start": 21879, + "end": 21960, "loc": { "start": { - "line": 535, + "line": 551, "column": 8 }, "end": { - "line": 535, + "line": 551, "column": 89 } }, "expression": { "type": "AssignmentExpression", - "start": 21439, - "end": 21519, + "start": 21879, + "end": 21959, "loc": { "start": { - "line": 535, + "line": 551, "column": 8 }, "end": { - "line": 535, + "line": 551, "column": 88 } }, "operator": "=", "left": { "type": "Identifier", - "start": 21439, - "end": 21461, + "start": 21879, + "end": 21901, "loc": { "start": { - "line": 535, + "line": 551, "column": 8 }, "end": { - "line": 535, + "line": 551, "column": 30 }, "identifierName": "remainingInternalsExpr" @@ -28363,58 +29143,58 @@ }, "right": { "type": "CallExpression", - "start": 21464, - "end": 21519, + "start": 21904, + "end": 21959, "loc": { "start": { - "line": 535, + "line": 551, "column": 33 }, "end": { - "line": 535, + "line": 551, "column": 88 } }, "callee": { "type": "MemberExpression", - "start": 21464, - "end": 21496, + "start": 21904, + "end": 21936, "loc": { "start": { - "line": 535, + "line": 551, "column": 33 }, "end": { - "line": 535, + "line": 551, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 21464, - "end": 21468, + "start": 21904, + "end": 21908, "loc": { "start": { - "line": 535, + "line": 551, "column": 33 }, "end": { - "line": 535, + "line": 551, "column": 37 } } }, "property": { "type": "Identifier", - "start": 21469, - "end": 21496, + "start": 21909, + "end": 21936, "loc": { "start": { - "line": 535, + "line": 551, "column": 38 }, "end": { - "line": 535, + "line": 551, "column": 65 }, "identifierName": "getIncludesRestrictionForTU" @@ -28426,29 +29206,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 21497, - "end": 21518, + "start": 21937, + "end": 21958, "loc": { "start": { - "line": 535, + "line": 551, "column": 66 }, "end": { - "line": 535, + "line": 551, "column": 87 } }, "object": { "type": "Identifier", - "start": 21497, - "end": 21515, + "start": 21937, + "end": 21955, "loc": { "start": { - "line": 535, + "line": 551, "column": 66 }, "end": { - "line": 535, + "line": 551, "column": 84 }, "identifierName": "remainingInternals" @@ -28457,15 +29237,15 @@ }, "property": { "type": "NumericLiteral", - "start": 21516, - "end": 21517, + "start": 21956, + "end": 21957, "loc": { "start": { - "line": 535, + "line": 551, "column": 85 }, "end": { - "line": 535, + "line": 551, "column": 86 } }, @@ -28486,57 +29266,57 @@ }, "alternate": { "type": "IfStatement", - "start": 21534, - "end": 21952, + "start": 21974, + "end": 22392, "loc": { "start": { - "line": 536, + "line": 552, "column": 13 }, "end": { - "line": 548, + "line": 564, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21538, - "end": 21569, + "start": 21978, + "end": 22009, "loc": { "start": { - "line": 536, + "line": 552, "column": 17 }, "end": { - "line": 536, + "line": 552, "column": 48 } }, "left": { "type": "MemberExpression", - "start": 21538, - "end": 21563, + "start": 21978, + "end": 22003, "loc": { "start": { - "line": 536, + "line": 552, "column": 17 }, "end": { - "line": 536, + "line": 552, "column": 42 } }, "object": { "type": "Identifier", - "start": 21538, - "end": 21556, + "start": 21978, + "end": 21996, "loc": { "start": { - "line": 536, + "line": 552, "column": 17 }, "end": { - "line": 536, + "line": 552, "column": 35 }, "identifierName": "remainingInternals" @@ -28545,15 +29325,15 @@ }, "property": { "type": "Identifier", - "start": 21557, - "end": 21563, + "start": 21997, + "end": 22003, "loc": { "start": { - "line": 536, + "line": 552, "column": 36 }, "end": { - "line": 536, + "line": 552, "column": 42 }, "identifierName": "length" @@ -28565,15 +29345,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 21568, - "end": 21569, + "start": 22008, + "end": 22009, "loc": { "start": { - "line": 536, + "line": 552, "column": 47 }, "end": { - "line": 536, + "line": 552, "column": 48 } }, @@ -28586,59 +29366,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 21571, - "end": 21722, + "start": 22011, + "end": 22162, "loc": { "start": { - "line": 536, + "line": 552, "column": 50 }, "end": { - "line": 541, + "line": 557, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 21581, - "end": 21714, + "start": 22021, + "end": 22154, "loc": { "start": { - "line": 537, + "line": 553, "column": 8 }, "end": { - "line": 540, + "line": 556, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 21581, - "end": 21713, + "start": 22021, + "end": 22153, "loc": { "start": { - "line": 537, + "line": 553, "column": 8 }, "end": { - "line": 540, + "line": 556, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 21581, - "end": 21603, + "start": 22021, + "end": 22043, "loc": { "start": { - "line": 537, + "line": 553, "column": 8 }, "end": { - "line": 537, + "line": 553, "column": 30 }, "identifierName": "remainingInternalsExpr" @@ -28647,58 +29427,58 @@ }, "right": { "type": "CallExpression", - "start": 21606, - "end": 21713, + "start": 22046, + "end": 22153, "loc": { "start": { - "line": 537, + "line": 553, "column": 33 }, "end": { - "line": 540, + "line": 556, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 21606, - "end": 21637, + "start": 22046, + "end": 22077, "loc": { "start": { - "line": 537, + "line": 553, "column": 33 }, "end": { - "line": 537, + "line": 553, "column": 64 } }, "object": { "type": "ThisExpression", - "start": 21606, - "end": 21610, + "start": 22046, + "end": 22050, "loc": { "start": { - "line": 537, + "line": 553, "column": 33 }, "end": { - "line": 537, + "line": 553, "column": 37 } } }, "property": { "type": "Identifier", - "start": 21611, - "end": 21637, + "start": 22051, + "end": 22077, "loc": { "start": { - "line": 537, + "line": 553, "column": 38 }, "end": { - "line": 537, + "line": 553, "column": 64 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -28710,29 +29490,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 21649, - "end": 21670, + "start": 22089, + "end": 22110, "loc": { "start": { - "line": 538, + "line": 554, "column": 10 }, "end": { - "line": 538, + "line": 554, "column": 31 } }, "object": { "type": "Identifier", - "start": 21649, - "end": 21667, + "start": 22089, + "end": 22107, "loc": { "start": { - "line": 538, + "line": 554, "column": 10 }, "end": { - "line": 538, + "line": 554, "column": 28 }, "identifierName": "remainingInternals" @@ -28741,15 +29521,15 @@ }, "property": { "type": "NumericLiteral", - "start": 21668, - "end": 21669, + "start": 22108, + "end": 22109, "loc": { "start": { - "line": 538, + "line": 554, "column": 29 }, "end": { - "line": 538, + "line": 554, "column": 30 } }, @@ -28763,29 +29543,29 @@ }, { "type": "MemberExpression", - "start": 21682, - "end": 21703, + "start": 22122, + "end": 22143, "loc": { "start": { - "line": 539, + "line": 555, "column": 10 }, "end": { - "line": 539, + "line": 555, "column": 31 } }, "object": { "type": "Identifier", - "start": 21682, - "end": 21700, + "start": 22122, + "end": 22140, "loc": { "start": { - "line": 539, + "line": 555, "column": 10 }, "end": { - "line": 539, + "line": 555, "column": 28 }, "identifierName": "remainingInternals" @@ -28794,15 +29574,15 @@ }, "property": { "type": "NumericLiteral", - "start": 21701, - "end": 21702, + "start": 22141, + "end": 22142, "loc": { "start": { - "line": 539, + "line": 555, "column": 29 }, "end": { - "line": 539, + "line": 555, "column": 30 } }, @@ -28823,59 +29603,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 21728, - "end": 21952, + "start": 22168, + "end": 22392, "loc": { "start": { - "line": 541, + "line": 557, "column": 13 }, "end": { - "line": 548, + "line": 564, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 21738, - "end": 21944, + "start": 22178, + "end": 22384, "loc": { "start": { - "line": 542, + "line": 558, "column": 8 }, "end": { - "line": 547, + "line": 563, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 21738, - "end": 21943, + "start": 22178, + "end": 22383, "loc": { "start": { - "line": 542, + "line": 558, "column": 8 }, "end": { - "line": 547, + "line": 563, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 21738, - "end": 21760, + "start": 22178, + "end": 22200, "loc": { "start": { - "line": 542, + "line": 558, "column": 8 }, "end": { - "line": 542, + "line": 558, "column": 30 }, "identifierName": "remainingInternalsExpr" @@ -28884,58 +29664,58 @@ }, "right": { "type": "CallExpression", - "start": 21763, - "end": 21943, + "start": 22203, + "end": 22383, "loc": { "start": { - "line": 542, + "line": 558, "column": 33 }, "end": { - "line": 547, + "line": 563, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 21763, - "end": 21788, + "start": 22203, + "end": 22228, "loc": { "start": { - "line": 542, + "line": 558, "column": 33 }, "end": { - "line": 542, + "line": 558, "column": 58 } }, "object": { "type": "ThisExpression", - "start": 21763, - "end": 21767, + "start": 22203, + "end": 22207, "loc": { "start": { - "line": 542, + "line": 558, "column": 33 }, "end": { - "line": 542, + "line": 558, "column": 37 } } }, "property": { "type": "Identifier", - "start": 21768, - "end": 21788, + "start": 22208, + "end": 22228, "loc": { "start": { - "line": 542, + "line": 558, "column": 38 }, "end": { - "line": 542, + "line": 558, "column": 58 }, "identifierName": "createComponentClass" @@ -28947,15 +29727,15 @@ "arguments": [ { "type": "Identifier", - "start": 21800, - "end": 21806, + "start": 22240, + "end": 22246, "loc": { "start": { - "line": 543, + "line": 559, "column": 10 }, "end": { - "line": 543, + "line": 559, "column": 16 }, "identifierName": "jsonld" @@ -28964,15 +29744,15 @@ }, { "type": "Identifier", - "start": 21818, - "end": 21836, + "start": 22258, + "end": 22276, "loc": { "start": { - "line": 544, + "line": 560, "column": 10 }, "end": { - "line": 544, + "line": 560, "column": 28 }, "identifierName": "remainingInternals" @@ -28981,15 +29761,15 @@ }, { "type": "ArrayExpression", - "start": 21848, - "end": 21850, + "start": 22288, + "end": 22290, "loc": { "start": { - "line": 545, + "line": 561, "column": 10 }, "end": { - "line": 545, + "line": 561, "column": 12 } }, @@ -28997,58 +29777,58 @@ }, { "type": "CallExpression", - "start": 21862, - "end": 21933, + "start": 22302, + "end": 22373, "loc": { "start": { - "line": 546, + "line": 562, "column": 10 }, "end": { - "line": 546, + "line": 562, "column": 81 } }, "callee": { "type": "MemberExpression", - "start": 21862, - "end": 21901, + "start": 22302, + "end": 22341, "loc": { "start": { - "line": 546, + "line": 562, "column": 10 }, "end": { - "line": 546, + "line": 562, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 21862, - "end": 21866, + "start": 22302, + "end": 22306, "loc": { "start": { - "line": 546, + "line": 562, "column": 10 }, "end": { - "line": 546, + "line": 562, "column": 14 } } }, "property": { "type": "Identifier", - "start": 21867, - "end": 21901, + "start": 22307, + "end": 22341, "loc": { "start": { - "line": 546, + "line": 562, "column": 15 }, "end": { - "line": 546, + "line": 562, "column": 49 }, "identifierName": "createClassExpressionsForInternals" @@ -29060,15 +29840,15 @@ "arguments": [ { "type": "Identifier", - "start": 21902, - "end": 21908, + "start": 22342, + "end": 22348, "loc": { "start": { - "line": 546, + "line": 562, "column": 50 }, "end": { - "line": 546, + "line": 562, "column": 56 }, "identifierName": "jsonld" @@ -29077,15 +29857,15 @@ }, { "type": "Identifier", - "start": 21910, - "end": 21928, + "start": 22350, + "end": 22368, "loc": { "start": { - "line": 546, + "line": 562, "column": 58 }, "end": { - "line": 546, + "line": 562, "column": 76 }, "identifierName": "remainingInternals" @@ -29094,15 +29874,15 @@ }, { "type": "ArrayExpression", - "start": 21930, - "end": 21932, + "start": 22370, + "end": 22372, "loc": { "start": { - "line": 546, + "line": 562, "column": 78 }, "end": { - "line": 546, + "line": 562, "column": 80 } }, @@ -29121,44 +29901,44 @@ }, { "type": "VariableDeclaration", - "start": 21960, - "end": 21982, + "start": 22400, + "end": 22422, "loc": { "start": { - "line": 550, + "line": 566, "column": 6 }, "end": { - "line": 550, + "line": 566, "column": 28 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 21964, - "end": 21981, + "start": 22404, + "end": 22421, "loc": { "start": { - "line": 550, + "line": 566, "column": 10 }, "end": { - "line": 550, + "line": 566, "column": 27 } }, "id": { "type": "Identifier", - "start": 21964, - "end": 21976, + "start": 22404, + "end": 22416, "loc": { "start": { - "line": 550, + "line": 566, "column": 10 }, "end": { - "line": 550, + "line": 566, "column": 22 }, "identifierName": "selectedExpr" @@ -29167,15 +29947,15 @@ }, "init": { "type": "ArrayExpression", - "start": 21979, - "end": 21981, + "start": 22419, + "end": 22421, "loc": { "start": { - "line": 550, + "line": 566, "column": 25 }, "end": { - "line": 550, + "line": 566, "column": 27 } }, @@ -29187,57 +29967,57 @@ }, { "type": "IfStatement", - "start": 21989, - "end": 22419, + "start": 22429, + "end": 22859, "loc": { "start": { - "line": 551, + "line": 567, "column": 6 }, "end": { - "line": 562, + "line": 578, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21993, - "end": 22014, + "start": 22433, + "end": 22454, "loc": { "start": { - "line": 551, + "line": 567, "column": 10 }, "end": { - "line": 551, + "line": 567, "column": 31 } }, "left": { "type": "MemberExpression", - "start": 21993, - "end": 22008, + "start": 22433, + "end": 22448, "loc": { "start": { - "line": 551, + "line": 567, "column": 10 }, "end": { - "line": 551, + "line": 567, "column": 25 } }, "object": { "type": "Identifier", - "start": 21993, - "end": 22001, + "start": 22433, + "end": 22441, "loc": { "start": { - "line": 551, + "line": 567, "column": 10 }, "end": { - "line": 551, + "line": 567, "column": 18 }, "identifierName": "selected" @@ -29246,15 +30026,15 @@ }, "property": { "type": "Identifier", - "start": 22002, - "end": 22008, + "start": 22442, + "end": 22448, "loc": { "start": { - "line": 551, + "line": 567, "column": 19 }, "end": { - "line": 551, + "line": 567, "column": 25 }, "identifierName": "length" @@ -29266,15 +30046,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 22013, - "end": 22014, + "start": 22453, + "end": 22454, "loc": { "start": { - "line": 551, + "line": 567, "column": 30 }, "end": { - "line": 551, + "line": 567, "column": 31 } }, @@ -29287,59 +30067,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 22016, - "end": 22095, + "start": 22456, + "end": 22535, "loc": { "start": { - "line": 551, + "line": 567, "column": 33 }, "end": { - "line": 553, + "line": 569, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 22026, - "end": 22087, + "start": 22466, + "end": 22527, "loc": { "start": { - "line": 552, + "line": 568, "column": 8 }, "end": { - "line": 552, + "line": 568, "column": 69 } }, "expression": { "type": "AssignmentExpression", - "start": 22026, - "end": 22086, + "start": 22466, + "end": 22526, "loc": { "start": { - "line": 552, + "line": 568, "column": 8 }, "end": { - "line": 552, + "line": 568, "column": 68 } }, "operator": "=", "left": { "type": "Identifier", - "start": 22026, - "end": 22038, + "start": 22466, + "end": 22478, "loc": { "start": { - "line": 552, + "line": 568, "column": 8 }, "end": { - "line": 552, + "line": 568, "column": 20 }, "identifierName": "selectedExpr" @@ -29348,58 +30128,58 @@ }, "right": { "type": "CallExpression", - "start": 22041, - "end": 22086, + "start": 22481, + "end": 22526, "loc": { "start": { - "line": 552, + "line": 568, "column": 23 }, "end": { - "line": 552, + "line": 568, "column": 68 } }, "callee": { "type": "MemberExpression", - "start": 22041, - "end": 22073, + "start": 22481, + "end": 22513, "loc": { "start": { - "line": 552, + "line": 568, "column": 23 }, "end": { - "line": 552, + "line": 568, "column": 55 } }, "object": { "type": "ThisExpression", - "start": 22041, - "end": 22045, + "start": 22481, + "end": 22485, "loc": { "start": { - "line": 552, + "line": 568, "column": 23 }, "end": { - "line": 552, + "line": 568, "column": 27 } } }, "property": { "type": "Identifier", - "start": 22046, - "end": 22073, + "start": 22486, + "end": 22513, "loc": { "start": { - "line": 552, + "line": 568, "column": 28 }, "end": { - "line": 552, + "line": 568, "column": 55 }, "identifierName": "getIncludesRestrictionForTU" @@ -29411,29 +30191,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 22074, - "end": 22085, + "start": 22514, + "end": 22525, "loc": { "start": { - "line": 552, + "line": 568, "column": 56 }, "end": { - "line": 552, + "line": 568, "column": 67 } }, "object": { "type": "Identifier", - "start": 22074, - "end": 22082, + "start": 22514, + "end": 22522, "loc": { "start": { - "line": 552, + "line": 568, "column": 56 }, "end": { - "line": 552, + "line": 568, "column": 64 }, "identifierName": "selected" @@ -29442,15 +30222,15 @@ }, "property": { "type": "NumericLiteral", - "start": 22083, - "end": 22084, + "start": 22523, + "end": 22524, "loc": { "start": { - "line": 552, + "line": 568, "column": 65 }, "end": { - "line": 552, + "line": 568, "column": 66 } }, @@ -29471,57 +30251,57 @@ }, "alternate": { "type": "IfStatement", - "start": 22101, - "end": 22419, + "start": 22541, + "end": 22859, "loc": { "start": { - "line": 553, + "line": 569, "column": 13 }, "end": { - "line": 562, + "line": 578, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 22105, - "end": 22126, + "start": 22545, + "end": 22566, "loc": { "start": { - "line": 553, + "line": 569, "column": 17 }, "end": { - "line": 553, + "line": 569, "column": 38 } }, "left": { "type": "MemberExpression", - "start": 22105, - "end": 22120, + "start": 22545, + "end": 22560, "loc": { "start": { - "line": 553, + "line": 569, "column": 17 }, "end": { - "line": 553, + "line": 569, "column": 32 } }, "object": { "type": "Identifier", - "start": 22105, - "end": 22113, + "start": 22545, + "end": 22553, "loc": { "start": { - "line": 553, + "line": 569, "column": 17 }, "end": { - "line": 553, + "line": 569, "column": 25 }, "identifierName": "selected" @@ -29530,15 +30310,15 @@ }, "property": { "type": "Identifier", - "start": 22114, - "end": 22120, + "start": 22554, + "end": 22560, "loc": { "start": { - "line": 553, + "line": 569, "column": 26 }, "end": { - "line": 553, + "line": 569, "column": 32 }, "identifierName": "length" @@ -29550,15 +30330,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 22125, - "end": 22126, + "start": 22565, + "end": 22566, "loc": { "start": { - "line": 553, + "line": 569, "column": 37 }, "end": { - "line": 553, + "line": 569, "column": 38 } }, @@ -29571,59 +30351,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 22128, - "end": 22219, + "start": 22568, + "end": 22659, "loc": { "start": { - "line": 553, + "line": 569, "column": 40 }, "end": { - "line": 555, + "line": 571, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 22138, - "end": 22211, + "start": 22578, + "end": 22651, "loc": { "start": { - "line": 554, + "line": 570, "column": 8 }, "end": { - "line": 554, + "line": 570, "column": 81 } }, "expression": { "type": "AssignmentExpression", - "start": 22138, - "end": 22210, + "start": 22578, + "end": 22650, "loc": { "start": { - "line": 554, + "line": 570, "column": 8 }, "end": { - "line": 554, + "line": 570, "column": 80 } }, "operator": "=", "left": { "type": "Identifier", - "start": 22138, - "end": 22150, + "start": 22578, + "end": 22590, "loc": { "start": { - "line": 554, + "line": 570, "column": 8 }, "end": { - "line": 554, + "line": 570, "column": 20 }, "identifierName": "selectedExpr" @@ -29632,58 +30412,58 @@ }, "right": { "type": "CallExpression", - "start": 22153, - "end": 22210, + "start": 22593, + "end": 22650, "loc": { "start": { - "line": 554, + "line": 570, "column": 23 }, "end": { - "line": 554, + "line": 570, "column": 80 } }, "callee": { "type": "MemberExpression", - "start": 22153, - "end": 22184, + "start": 22593, + "end": 22624, "loc": { "start": { - "line": 554, + "line": 570, "column": 23 }, "end": { - "line": 554, + "line": 570, "column": 54 } }, "object": { "type": "ThisExpression", - "start": 22153, - "end": 22157, + "start": 22593, + "end": 22597, "loc": { "start": { - "line": 554, + "line": 570, "column": 23 }, "end": { - "line": 554, + "line": 570, "column": 27 } } }, "property": { "type": "Identifier", - "start": 22158, - "end": 22184, + "start": 22598, + "end": 22624, "loc": { "start": { - "line": 554, + "line": 570, "column": 28 }, "end": { - "line": 554, + "line": 570, "column": 54 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -29695,29 +30475,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 22185, - "end": 22196, + "start": 22625, + "end": 22636, "loc": { "start": { - "line": 554, + "line": 570, "column": 55 }, "end": { - "line": 554, + "line": 570, "column": 66 } }, "object": { "type": "Identifier", - "start": 22185, - "end": 22193, + "start": 22625, + "end": 22633, "loc": { "start": { - "line": 554, + "line": 570, "column": 55 }, "end": { - "line": 554, + "line": 570, "column": 63 }, "identifierName": "selected" @@ -29726,15 +30506,15 @@ }, "property": { "type": "NumericLiteral", - "start": 22194, - "end": 22195, + "start": 22634, + "end": 22635, "loc": { "start": { - "line": 554, + "line": 570, "column": 64 }, "end": { - "line": 554, + "line": 570, "column": 65 } }, @@ -29748,29 +30528,29 @@ }, { "type": "MemberExpression", - "start": 22198, - "end": 22209, + "start": 22638, + "end": 22649, "loc": { "start": { - "line": 554, + "line": 570, "column": 68 }, "end": { - "line": 554, + "line": 570, "column": 79 } }, "object": { "type": "Identifier", - "start": 22198, - "end": 22206, + "start": 22638, + "end": 22646, "loc": { "start": { - "line": 554, + "line": 570, "column": 68 }, "end": { - "line": 554, + "line": 570, "column": 76 }, "identifierName": "selected" @@ -29779,15 +30559,15 @@ }, "property": { "type": "NumericLiteral", - "start": 22207, - "end": 22208, + "start": 22647, + "end": 22648, "loc": { "start": { - "line": 554, + "line": 570, "column": 77 }, "end": { - "line": 554, + "line": 570, "column": 78 } }, @@ -29808,59 +30588,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 22225, - "end": 22419, + "start": 22665, + "end": 22859, "loc": { "start": { - "line": 555, + "line": 571, "column": 13 }, "end": { - "line": 562, + "line": 578, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 22235, - "end": 22411, + "start": 22675, + "end": 22851, "loc": { "start": { - "line": 556, + "line": 572, "column": 8 }, "end": { - "line": 561, + "line": 577, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 22235, - "end": 22410, + "start": 22675, + "end": 22850, "loc": { "start": { - "line": 556, + "line": 572, "column": 8 }, "end": { - "line": 561, + "line": 577, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 22235, - "end": 22247, + "start": 22675, + "end": 22687, "loc": { "start": { - "line": 556, + "line": 572, "column": 8 }, "end": { - "line": 556, + "line": 572, "column": 20 }, "identifierName": "selectedExpr" @@ -29869,58 +30649,58 @@ }, "right": { "type": "CallExpression", - "start": 22250, - "end": 22410, + "start": 22690, + "end": 22850, "loc": { "start": { - "line": 556, + "line": 572, "column": 23 }, "end": { - "line": 561, + "line": 577, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 22250, - "end": 22275, + "start": 22690, + "end": 22715, "loc": { "start": { - "line": 556, + "line": 572, "column": 23 }, "end": { - "line": 556, + "line": 572, "column": 48 } }, "object": { "type": "ThisExpression", - "start": 22250, - "end": 22254, + "start": 22690, + "end": 22694, "loc": { "start": { - "line": 556, + "line": 572, "column": 23 }, "end": { - "line": 556, + "line": 572, "column": 27 } } }, "property": { "type": "Identifier", - "start": 22255, - "end": 22275, + "start": 22695, + "end": 22715, "loc": { "start": { - "line": 556, + "line": 572, "column": 28 }, "end": { - "line": 556, + "line": 572, "column": 48 }, "identifierName": "createComponentClass" @@ -29932,15 +30712,15 @@ "arguments": [ { "type": "Identifier", - "start": 22287, - "end": 22293, + "start": 22727, + "end": 22733, "loc": { "start": { - "line": 557, + "line": 573, "column": 10 }, "end": { - "line": 557, + "line": 573, "column": 16 }, "identifierName": "jsonld" @@ -29949,15 +30729,15 @@ }, { "type": "Identifier", - "start": 22305, - "end": 22313, + "start": 22745, + "end": 22753, "loc": { "start": { - "line": 558, + "line": 574, "column": 10 }, "end": { - "line": 558, + "line": 574, "column": 18 }, "identifierName": "selected" @@ -29966,15 +30746,15 @@ }, { "type": "ArrayExpression", - "start": 22325, - "end": 22327, + "start": 22765, + "end": 22767, "loc": { "start": { - "line": 559, + "line": 575, "column": 10 }, "end": { - "line": 559, + "line": 575, "column": 12 } }, @@ -29982,58 +30762,58 @@ }, { "type": "CallExpression", - "start": 22339, - "end": 22400, + "start": 22779, + "end": 22840, "loc": { "start": { - "line": 560, + "line": 576, "column": 10 }, "end": { - "line": 560, + "line": 576, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 22339, - "end": 22378, + "start": 22779, + "end": 22818, "loc": { "start": { - "line": 560, + "line": 576, "column": 10 }, "end": { - "line": 560, + "line": 576, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 22339, - "end": 22343, + "start": 22779, + "end": 22783, "loc": { "start": { - "line": 560, + "line": 576, "column": 10 }, "end": { - "line": 560, + "line": 576, "column": 14 } } }, "property": { "type": "Identifier", - "start": 22344, - "end": 22378, + "start": 22784, + "end": 22818, "loc": { "start": { - "line": 560, + "line": 576, "column": 15 }, "end": { - "line": 560, + "line": 576, "column": 49 }, "identifierName": "createClassExpressionsForInternals" @@ -30045,15 +30825,15 @@ "arguments": [ { "type": "Identifier", - "start": 22379, - "end": 22385, + "start": 22819, + "end": 22825, "loc": { "start": { - "line": 560, + "line": 576, "column": 50 }, "end": { - "line": 560, + "line": 576, "column": 56 }, "identifierName": "jsonld" @@ -30062,15 +30842,15 @@ }, { "type": "Identifier", - "start": 22387, - "end": 22395, + "start": 22827, + "end": 22835, "loc": { "start": { - "line": 560, + "line": 576, "column": 58 }, "end": { - "line": 560, + "line": 576, "column": 66 }, "identifierName": "selected" @@ -30079,15 +30859,15 @@ }, { "type": "ArrayExpression", - "start": 22397, - "end": 22399, + "start": 22837, + "end": 22839, "loc": { "start": { - "line": 560, + "line": 576, "column": 68 }, "end": { - "line": 560, + "line": 576, "column": 70 } }, @@ -30106,57 +30886,57 @@ }, { "type": "ExpressionStatement", - "start": 22427, - "end": 22822, + "start": 22867, + "end": 23262, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 575, + "line": 591, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 22427, - "end": 22821, + "start": 22867, + "end": 23261, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 575, + "line": 591, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 22427, - "end": 22442, + "start": 22867, + "end": 22882, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 564, + "line": 580, "column": 21 } }, "object": { "type": "Identifier", - "start": 22427, - "end": 22437, + "start": 22867, + "end": 22877, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 564, + "line": 580, "column": 16 }, "identifierName": "classExprs" @@ -30165,15 +30945,15 @@ }, "property": { "type": "Identifier", - "start": 22438, - "end": 22442, + "start": 22878, + "end": 22882, "loc": { "start": { - "line": 564, + "line": 580, "column": 17 }, "end": { - "line": 564, + "line": 580, "column": 21 }, "identifierName": "push" @@ -30185,30 +30965,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 22443, - "end": 22820, + "start": 22883, + "end": 23260, "loc": { "start": { - "line": 564, + "line": 580, "column": 22 }, "end": { - "line": 575, + "line": 591, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 22453, - "end": 22479, + "start": 22893, + "end": 22919, "loc": { "start": { - "line": 565, + "line": 581, "column": 8 }, "end": { - "line": 565, + "line": 581, "column": 34 } }, @@ -30217,15 +30997,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 22453, - "end": 22460, + "start": 22893, + "end": 22900, "loc": { "start": { - "line": 565, + "line": 581, "column": 8 }, "end": { - "line": 565, + "line": 581, "column": 15 } }, @@ -30237,15 +31017,15 @@ }, "value": { "type": "StringLiteral", - "start": 22462, - "end": 22479, + "start": 22902, + "end": 22919, "loc": { "start": { - "line": 565, + "line": 581, "column": 17 }, "end": { - "line": 565, + "line": 581, "column": 34 } }, @@ -30258,15 +31038,15 @@ }, { "type": "ObjectProperty", - "start": 22489, - "end": 22519, + "start": 22929, + "end": 22959, "loc": { "start": { - "line": 566, + "line": 582, "column": 8 }, "end": { - "line": 566, + "line": 582, "column": 38 } }, @@ -30275,15 +31055,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22489, - "end": 22499, + "start": 22929, + "end": 22939, "loc": { "start": { - "line": 566, + "line": 582, "column": 8 }, "end": { - "line": 566, + "line": 582, "column": 18 }, "identifierName": "onProperty" @@ -30292,15 +31072,15 @@ }, "value": { "type": "StringLiteral", - "start": 22501, - "end": 22519, + "start": 22941, + "end": 22959, "loc": { "start": { - "line": 566, + "line": 582, "column": 20 }, "end": { - "line": 566, + "line": 582, "column": 38 } }, @@ -30313,15 +31093,15 @@ }, { "type": "ObjectProperty", - "start": 22547, - "end": 22811, + "start": 22987, + "end": 23251, "loc": { "start": { - "line": 567, + "line": 583, "column": 8 }, "end": { - "line": 574, + "line": 590, "column": 9 } }, @@ -30330,15 +31110,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22547, - "end": 22561, + "start": 22987, + "end": 23001, "loc": { "start": { - "line": 567, + "line": 583, "column": 8 }, "end": { - "line": 567, + "line": 583, "column": 22 }, "identifierName": "someValuesFrom" @@ -30348,30 +31128,30 @@ }, "value": { "type": "ObjectExpression", - "start": 22563, - "end": 22811, + "start": 23003, + "end": 23251, "loc": { "start": { - "line": 567, + "line": 583, "column": 24 }, "end": { - "line": 574, + "line": 590, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 22575, - "end": 22595, + "start": 23015, + "end": 23035, "loc": { "start": { - "line": 568, + "line": 584, "column": 10 }, "end": { - "line": 568, + "line": 584, "column": 30 } }, @@ -30380,15 +31160,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 22575, - "end": 22582, + "start": 23015, + "end": 23022, "loc": { "start": { - "line": 568, + "line": 584, "column": 10 }, "end": { - "line": 568, + "line": 584, "column": 17 } }, @@ -30400,15 +31180,15 @@ }, "value": { "type": "StringLiteral", - "start": 22584, - "end": 22595, + "start": 23024, + "end": 23035, "loc": { "start": { - "line": 568, + "line": 584, "column": 19 }, "end": { - "line": 568, + "line": 584, "column": 30 } }, @@ -30421,15 +31201,15 @@ }, { "type": "ObjectProperty", - "start": 22607, - "end": 22800, + "start": 23047, + "end": 23240, "loc": { "start": { - "line": 569, + "line": 585, "column": 10 }, "end": { - "line": 573, + "line": 589, "column": 26 } }, @@ -30438,15 +31218,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22607, - "end": 22621, + "start": 23047, + "end": 23061, "loc": { "start": { - "line": 569, + "line": 585, "column": 10 }, "end": { - "line": 569, + "line": 585, "column": 24 }, "identifierName": "intersectionOf" @@ -30455,45 +31235,45 @@ }, "value": { "type": "ArrayExpression", - "start": 22623, - "end": 22800, + "start": 23063, + "end": 23240, "loc": { "start": { - "line": 569, + "line": 585, "column": 26 }, "end": { - "line": 573, + "line": 589, "column": 26 } }, "elements": [ { "type": "ObjectExpression", - "start": 22624, - "end": 22785, + "start": 23064, + "end": 23225, "loc": { "start": { - "line": 569, + "line": 585, "column": 27 }, "end": { - "line": 573, + "line": 589, "column": 11 } }, "properties": [ { "type": "ObjectProperty", - "start": 22638, - "end": 22664, + "start": 23078, + "end": 23104, "loc": { "start": { - "line": 570, + "line": 586, "column": 12 }, "end": { - "line": 570, + "line": 586, "column": 38 } }, @@ -30502,15 +31282,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 22638, - "end": 22645, + "start": 23078, + "end": 23085, "loc": { "start": { - "line": 570, + "line": 586, "column": 12 }, "end": { - "line": 570, + "line": 586, "column": 19 } }, @@ -30522,15 +31302,15 @@ }, "value": { "type": "StringLiteral", - "start": 22647, - "end": 22664, + "start": 23087, + "end": 23104, "loc": { "start": { - "line": 570, + "line": 586, "column": 21 }, "end": { - "line": 570, + "line": 586, "column": 38 } }, @@ -30543,15 +31323,15 @@ }, { "type": "ObjectProperty", - "start": 22678, - "end": 22720, + "start": 23118, + "end": 23160, "loc": { "start": { - "line": 571, + "line": 587, "column": 12 }, "end": { - "line": 571, + "line": 587, "column": 54 } }, @@ -30560,15 +31340,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22678, - "end": 22688, + "start": 23118, + "end": 23128, "loc": { "start": { - "line": 571, + "line": 587, "column": 12 }, "end": { - "line": 571, + "line": 587, "column": 22 }, "identifierName": "onProperty" @@ -30577,15 +31357,15 @@ }, "value": { "type": "StringLiteral", - "start": 22690, - "end": 22720, + "start": 23130, + "end": 23160, "loc": { "start": { - "line": 571, + "line": 587, "column": 24 }, "end": { - "line": 571, + "line": 587, "column": 54 } }, @@ -30598,15 +31378,15 @@ }, { "type": "ObjectProperty", - "start": 22734, - "end": 22772, + "start": 23174, + "end": 23212, "loc": { "start": { - "line": 572, + "line": 588, "column": 12 }, "end": { - "line": 572, + "line": 588, "column": 50 } }, @@ -30615,15 +31395,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22734, - "end": 22748, + "start": 23174, + "end": 23188, "loc": { "start": { - "line": 572, + "line": 588, "column": 12 }, "end": { - "line": 572, + "line": 588, "column": 26 }, "identifierName": "someValuesFrom" @@ -30632,15 +31412,15 @@ }, "value": { "type": "Identifier", - "start": 22750, - "end": 22772, + "start": 23190, + "end": 23212, "loc": { "start": { - "line": 572, + "line": 588, "column": 28 }, "end": { - "line": 572, + "line": 588, "column": 50 }, "identifierName": "remainingInternalsExpr" @@ -30652,15 +31432,15 @@ }, { "type": "Identifier", - "start": 22787, - "end": 22799, + "start": 23227, + "end": 23239, "loc": { "start": { - "line": 573, + "line": 589, "column": 13 }, "end": { - "line": 573, + "line": 589, "column": 25 }, "identifierName": "selectedExpr" @@ -30676,15 +31456,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 22521, - "end": 22538, + "start": 22961, + "end": 22978, "loc": { "start": { - "line": 566, + "line": 582, "column": 40 }, "end": { - "line": 566, + "line": 582, "column": 57 } } @@ -30705,15 +31485,15 @@ { "type": "CommentLine", "value": " Step 2. Now select everything from remaining once, and start recursing through", - "start": 22834, - "end": 22915, + "start": 23274, + "end": 23355, "loc": { "start": { - "line": 578, + "line": 594, "column": 4 }, "end": { - "line": 578, + "line": 594, "column": 85 } } @@ -30721,15 +31501,15 @@ { "type": "CommentLine", "value": " every possibility.", - "start": 22920, - "end": 22941, + "start": 23360, + "end": 23381, "loc": { "start": { - "line": 579, + "line": 595, "column": 4 }, "end": { - "line": 579, + "line": 595, "column": 25 } } @@ -30737,15 +31517,15 @@ { "type": "CommentLine", "value": " Note that we only process cases where there are more remainingInternals than", - "start": 22946, - "end": 23025, + "start": 23386, + "end": 23465, "loc": { "start": { - "line": 580, + "line": 596, "column": 4 }, "end": { - "line": 580, + "line": 596, "column": 83 } } @@ -30753,15 +31533,15 @@ { "type": "CommentLine", "value": " selected internals -- when there are fewer, we'll just end up with the inverses", - "start": 23030, - "end": 23112, + "start": 23470, + "end": 23552, "loc": { "start": { - "line": 581, + "line": 597, "column": 4 }, "end": { - "line": 581, + "line": 597, "column": 86 } } @@ -30769,15 +31549,15 @@ { "type": "CommentLine", "value": " of the previous comparisons, which we'll already have covered.", - "start": 23117, - "end": 23182, + "start": 23557, + "end": 23622, "loc": { "start": { - "line": 582, + "line": 598, "column": 4 }, "end": { - "line": 582, + "line": 598, "column": 69 } } @@ -30786,71 +31566,71 @@ }, { "type": "IfStatement", - "start": 23187, - "end": 23734, + "start": 23627, + "end": 24174, "loc": { "start": { - "line": 583, + "line": 599, "column": 4 }, "end": { - "line": 593, + "line": 609, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 23191, - "end": 23268, + "start": 23631, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 85 } }, "left": { "type": "BinaryExpression", - "start": 23191, - "end": 23220, + "start": 23631, + "end": 23660, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 23191, - "end": 23216, + "start": 23631, + "end": 23656, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 33 } }, "object": { "type": "Identifier", - "start": 23191, - "end": 23209, + "start": 23631, + "end": 23649, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 26 }, "identifierName": "remainingInternals" @@ -30860,15 +31640,15 @@ }, "property": { "type": "Identifier", - "start": 23210, - "end": 23216, + "start": 23650, + "end": 23656, "loc": { "start": { - "line": 583, + "line": 599, "column": 27 }, "end": { - "line": 583, + "line": 599, "column": 33 }, "identifierName": "length" @@ -30881,15 +31661,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 23219, - "end": 23220, + "start": 23659, + "end": 23660, "loc": { "start": { - "line": 583, + "line": 599, "column": 36 }, "end": { - "line": 583, + "line": 599, "column": 37 } }, @@ -30904,43 +31684,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 23224, - "end": 23268, + "start": 23664, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 41 }, "end": { - "line": 583, + "line": 599, "column": 85 } }, "left": { "type": "MemberExpression", - "start": 23224, - "end": 23239, + "start": 23664, + "end": 23679, "loc": { "start": { - "line": 583, + "line": 599, "column": 41 }, "end": { - "line": 583, + "line": 599, "column": 56 } }, "object": { "type": "Identifier", - "start": 23224, - "end": 23232, + "start": 23664, + "end": 23672, "loc": { "start": { - "line": 583, + "line": 599, "column": 41 }, "end": { - "line": 583, + "line": 599, "column": 49 }, "identifierName": "selected" @@ -30949,15 +31729,15 @@ }, "property": { "type": "Identifier", - "start": 23233, - "end": 23239, + "start": 23673, + "end": 23679, "loc": { "start": { - "line": 583, + "line": 599, "column": 50 }, "end": { - "line": 583, + "line": 599, "column": 56 }, "identifierName": "length" @@ -30969,29 +31749,29 @@ "operator": "<=", "right": { "type": "MemberExpression", - "start": 23243, - "end": 23268, + "start": 23683, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 60 }, "end": { - "line": 583, + "line": 599, "column": 85 } }, "object": { "type": "Identifier", - "start": 23243, - "end": 23261, + "start": 23683, + "end": 23701, "loc": { "start": { - "line": 583, + "line": 599, "column": 60 }, "end": { - "line": 583, + "line": 599, "column": 78 }, "identifierName": "remainingInternals" @@ -31000,15 +31780,15 @@ }, "property": { "type": "Identifier", - "start": 23262, - "end": 23268, + "start": 23702, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 79 }, "end": { - "line": 583, + "line": 599, "column": 85 }, "identifierName": "length" @@ -31022,128 +31802,128 @@ }, "consequent": { "type": "BlockStatement", - "start": 23270, - "end": 23734, + "start": 23710, + "end": 24174, "loc": { "start": { - "line": 583, + "line": 599, "column": 87 }, "end": { - "line": 593, + "line": 609, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 23278, - "end": 23728, + "start": 23718, + "end": 24168, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 592, + "line": 608, "column": 48 } }, "expression": { "type": "CallExpression", - "start": 23278, - "end": 23727, + "start": 23718, + "end": 24167, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 592, + "line": 608, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 23278, - "end": 23696, + "start": 23718, + "end": 24136, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 592, + "line": 608, "column": 16 } }, "object": { "type": "CallExpression", - "start": 23278, - "end": 23679, + "start": 23718, + "end": 24119, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 591, + "line": 607, "column": 50 } }, "callee": { "type": "MemberExpression", - "start": 23278, - "end": 23644, + "start": 23718, + "end": 24084, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 591, + "line": 607, "column": 15 } }, "object": { "type": "CallExpression", - "start": 23278, - "end": 23628, + "start": 23718, + "end": 24068, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 590, + "line": 606, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 23278, - "end": 23300, + "start": 23718, + "end": 23740, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 584, + "line": 600, "column": 28 } }, "object": { "type": "Identifier", - "start": 23278, - "end": 23296, + "start": 23718, + "end": 23736, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 584, + "line": 600, "column": 24 }, "identifierName": "remainingInternals" @@ -31152,15 +31932,15 @@ }, "property": { "type": "Identifier", - "start": 23297, - "end": 23300, + "start": 23737, + "end": 23740, "loc": { "start": { - "line": 584, + "line": 600, "column": 25 }, "end": { - "line": 584, + "line": 600, "column": 28 }, "identifierName": "map" @@ -31172,15 +31952,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23301, - "end": 23627, + "start": 23741, + "end": 24067, "loc": { "start": { - "line": 584, + "line": 600, "column": 29 }, "end": { - "line": 590, + "line": 606, "column": 7 } }, @@ -31191,15 +31971,15 @@ "params": [ { "type": "Identifier", - "start": 23301, - "end": 23314, + "start": 23741, + "end": 23754, "loc": { "start": { - "line": 584, + "line": 600, "column": 29 }, "end": { - "line": 584, + "line": 600, "column": 42 }, "identifierName": "newlySelected" @@ -31209,58 +31989,58 @@ ], "body": { "type": "CallExpression", - "start": 23318, - "end": 23627, + "start": 23758, + "end": 24067, "loc": { "start": { - "line": 584, + "line": 600, "column": 46 }, "end": { - "line": 590, + "line": 606, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 23318, - "end": 23357, + "start": 23758, + "end": 23797, "loc": { "start": { - "line": 584, + "line": 600, "column": 46 }, "end": { - "line": 584, + "line": 600, "column": 85 } }, "object": { "type": "ThisExpression", - "start": 23318, - "end": 23322, + "start": 23758, + "end": 23762, "loc": { "start": { - "line": 584, + "line": 600, "column": 46 }, "end": { - "line": 584, + "line": 600, "column": 50 } } }, "property": { "type": "Identifier", - "start": 23323, - "end": 23357, + "start": 23763, + "end": 23797, "loc": { "start": { - "line": 584, + "line": 600, "column": 51 }, "end": { - "line": 584, + "line": 600, "column": 85 }, "identifierName": "createClassExpressionsForInternals" @@ -31272,15 +32052,15 @@ "arguments": [ { "type": "Identifier", - "start": 23367, - "end": 23373, + "start": 23807, + "end": 23813, "loc": { "start": { - "line": 585, + "line": 601, "column": 8 }, "end": { - "line": 585, + "line": 601, "column": 14 }, "identifierName": "jsonld" @@ -31289,43 +32069,43 @@ }, { "type": "CallExpression", - "start": 23456, - "end": 23507, + "start": 23896, + "end": 23947, "loc": { "start": { - "line": 587, + "line": 603, "column": 8 }, "end": { - "line": 587, + "line": 603, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 23456, - "end": 23481, + "start": 23896, + "end": 23921, "loc": { "start": { - "line": 587, + "line": 603, "column": 8 }, "end": { - "line": 587, + "line": 603, "column": 33 } }, "object": { "type": "Identifier", - "start": 23456, - "end": 23474, + "start": 23896, + "end": 23914, "loc": { "start": { - "line": 587, + "line": 603, "column": 8 }, "end": { - "line": 587, + "line": 603, "column": 26 }, "identifierName": "remainingInternals" @@ -31335,15 +32115,15 @@ }, "property": { "type": "Identifier", - "start": 23475, - "end": 23481, + "start": 23915, + "end": 23921, "loc": { "start": { - "line": 587, + "line": 603, "column": 27 }, "end": { - "line": 587, + "line": 603, "column": 33 }, "identifierName": "filter" @@ -31356,15 +32136,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23482, - "end": 23506, + "start": 23922, + "end": 23946, "loc": { "start": { - "line": 587, + "line": 603, "column": 34 }, "end": { - "line": 587, + "line": 603, "column": 58 } }, @@ -31375,15 +32155,15 @@ "params": [ { "type": "Identifier", - "start": 23482, - "end": 23483, + "start": 23922, + "end": 23923, "loc": { "start": { - "line": 587, + "line": 603, "column": 34 }, "end": { - "line": 587, + "line": 603, "column": 35 }, "identifierName": "i" @@ -31393,29 +32173,29 @@ ], "body": { "type": "BinaryExpression", - "start": 23487, - "end": 23506, + "start": 23927, + "end": 23946, "loc": { "start": { - "line": 587, + "line": 603, "column": 39 }, "end": { - "line": 587, + "line": 603, "column": 58 } }, "left": { "type": "Identifier", - "start": 23487, - "end": 23488, + "start": 23927, + "end": 23928, "loc": { "start": { - "line": 587, + "line": 603, "column": 39 }, "end": { - "line": 587, + "line": 603, "column": 40 }, "identifierName": "i" @@ -31425,15 +32205,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 23493, - "end": 23506, + "start": 23933, + "end": 23946, "loc": { "start": { - "line": 587, + "line": 603, "column": 45 }, "end": { - "line": 587, + "line": 603, "column": 58 }, "identifierName": "newlySelected" @@ -31447,15 +32227,15 @@ { "type": "CommentLine", "value": " The new remaining is the old remaining minus the selected TU.", - "start": 23383, - "end": 23447, + "start": 23823, + "end": 23887, "loc": { "start": { - "line": 586, + "line": 602, "column": 8 }, "end": { - "line": 586, + "line": 602, "column": 72 } } @@ -31464,43 +32244,43 @@ }, { "type": "CallExpression", - "start": 23587, - "end": 23619, + "start": 24027, + "end": 24059, "loc": { "start": { - "line": 589, + "line": 605, "column": 8 }, "end": { - "line": 589, + "line": 605, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 23587, - "end": 23602, + "start": 24027, + "end": 24042, "loc": { "start": { - "line": 589, + "line": 605, "column": 8 }, "end": { - "line": 589, + "line": 605, "column": 23 } }, "object": { "type": "Identifier", - "start": 23587, - "end": 23595, + "start": 24027, + "end": 24035, "loc": { "start": { - "line": 589, + "line": 605, "column": 8 }, "end": { - "line": 589, + "line": 605, "column": 16 }, "identifierName": "selected" @@ -31510,15 +32290,15 @@ }, "property": { "type": "Identifier", - "start": 23596, - "end": 23602, + "start": 24036, + "end": 24042, "loc": { "start": { - "line": 589, + "line": 605, "column": 17 }, "end": { - "line": 589, + "line": 605, "column": 23 }, "identifierName": "concat" @@ -31531,30 +32311,30 @@ "arguments": [ { "type": "ArrayExpression", - "start": 23603, - "end": 23618, + "start": 24043, + "end": 24058, "loc": { "start": { - "line": 589, + "line": 605, "column": 24 }, "end": { - "line": 589, + "line": 605, "column": 39 } }, "elements": [ { "type": "Identifier", - "start": 23604, - "end": 23617, + "start": 24044, + "end": 24057, "loc": { "start": { - "line": 589, + "line": 605, "column": 25 }, "end": { - "line": 589, + "line": 605, "column": 38 }, "identifierName": "newlySelected" @@ -31568,15 +32348,15 @@ { "type": "CommentLine", "value": " The new selected is the old selected plus the selected TU.", - "start": 23517, - "end": 23578, + "start": 23957, + "end": 24018, "loc": { "start": { - "line": 588, + "line": 604, "column": 8 }, "end": { - "line": 588, + "line": 604, "column": 69 } } @@ -31590,15 +32370,15 @@ }, "property": { "type": "Identifier", - "start": 23638, - "end": 23644, + "start": 24078, + "end": 24084, "loc": { "start": { - "line": 591, + "line": 607, "column": 9 }, "end": { - "line": 591, + "line": 607, "column": 15 }, "identifierName": "reduce" @@ -31610,15 +32390,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23645, - "end": 23674, + "start": 24085, + "end": 24114, "loc": { "start": { - "line": 591, + "line": 607, "column": 16 }, "end": { - "line": 591, + "line": 607, "column": 45 } }, @@ -31629,15 +32409,15 @@ "params": [ { "type": "Identifier", - "start": 23646, - "end": 23649, + "start": 24086, + "end": 24089, "loc": { "start": { - "line": 591, + "line": 607, "column": 17 }, "end": { - "line": 591, + "line": 607, "column": 20 }, "identifierName": "acc" @@ -31646,15 +32426,15 @@ }, { "type": "Identifier", - "start": 23651, - "end": 23654, + "start": 24091, + "end": 24094, "loc": { "start": { - "line": 591, + "line": 607, "column": 22 }, "end": { - "line": 591, + "line": 607, "column": 25 }, "identifierName": "val" @@ -31664,43 +32444,43 @@ ], "body": { "type": "CallExpression", - "start": 23659, - "end": 23674, + "start": 24099, + "end": 24114, "loc": { "start": { - "line": 591, + "line": 607, "column": 30 }, "end": { - "line": 591, + "line": 607, "column": 45 } }, "callee": { "type": "MemberExpression", - "start": 23659, - "end": 23669, + "start": 24099, + "end": 24109, "loc": { "start": { - "line": 591, + "line": 607, "column": 30 }, "end": { - "line": 591, + "line": 607, "column": 40 } }, "object": { "type": "Identifier", - "start": 23659, - "end": 23662, + "start": 24099, + "end": 24102, "loc": { "start": { - "line": 591, + "line": 607, "column": 30 }, "end": { - "line": 591, + "line": 607, "column": 33 }, "identifierName": "acc" @@ -31709,15 +32489,15 @@ }, "property": { "type": "Identifier", - "start": 23663, - "end": 23669, + "start": 24103, + "end": 24109, "loc": { "start": { - "line": 591, + "line": 607, "column": 34 }, "end": { - "line": 591, + "line": 607, "column": 40 }, "identifierName": "concat" @@ -31729,15 +32509,15 @@ "arguments": [ { "type": "Identifier", - "start": 23670, - "end": 23673, + "start": 24110, + "end": 24113, "loc": { "start": { - "line": 591, + "line": 607, "column": 41 }, "end": { - "line": 591, + "line": 607, "column": 44 }, "identifierName": "val" @@ -31749,15 +32529,15 @@ }, { "type": "ArrayExpression", - "start": 23676, - "end": 23678, + "start": 24116, + "end": 24118, "loc": { "start": { - "line": 591, + "line": 607, "column": 47 }, "end": { - "line": 591, + "line": 607, "column": 49 } }, @@ -31767,15 +32547,15 @@ }, "property": { "type": "Identifier", - "start": 23689, - "end": 23696, + "start": 24129, + "end": 24136, "loc": { "start": { - "line": 592, + "line": 608, "column": 9 }, "end": { - "line": 592, + "line": 608, "column": 16 }, "identifierName": "forEach" @@ -31787,15 +32567,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23697, - "end": 23726, + "start": 24137, + "end": 24166, "loc": { "start": { - "line": 592, + "line": 608, "column": 17 }, "end": { - "line": 592, + "line": 608, "column": 46 } }, @@ -31806,15 +32586,15 @@ "params": [ { "type": "Identifier", - "start": 23697, - "end": 23701, + "start": 24137, + "end": 24141, "loc": { "start": { - "line": 592, + "line": 608, "column": 17 }, "end": { - "line": 592, + "line": 608, "column": 21 }, "identifierName": "expr" @@ -31824,43 +32604,43 @@ ], "body": { "type": "CallExpression", - "start": 23705, - "end": 23726, + "start": 24145, + "end": 24166, "loc": { "start": { - "line": 592, + "line": 608, "column": 25 }, "end": { - "line": 592, + "line": 608, "column": 46 } }, "callee": { "type": "MemberExpression", - "start": 23705, - "end": 23720, + "start": 24145, + "end": 24160, "loc": { "start": { - "line": 592, + "line": 608, "column": 25 }, "end": { - "line": 592, + "line": 608, "column": 40 } }, "object": { "type": "Identifier", - "start": 23705, - "end": 23715, + "start": 24145, + "end": 24155, "loc": { "start": { - "line": 592, + "line": 608, "column": 25 }, "end": { - "line": 592, + "line": 608, "column": 35 }, "identifierName": "classExprs" @@ -31869,15 +32649,15 @@ }, "property": { "type": "Identifier", - "start": 23716, - "end": 23720, + "start": 24156, + "end": 24160, "loc": { "start": { - "line": 592, + "line": 608, "column": 36 }, "end": { - "line": 592, + "line": 608, "column": 40 }, "identifierName": "push" @@ -31889,15 +32669,15 @@ "arguments": [ { "type": "Identifier", - "start": 23721, - "end": 23725, + "start": 24161, + "end": 24165, "loc": { "start": { - "line": 592, + "line": 608, "column": 41 }, "end": { - "line": 592, + "line": 608, "column": 45 }, "identifierName": "expr" @@ -31918,15 +32698,15 @@ { "type": "CommentLine", "value": " Step 2. Now select everything from remaining once, and start recursing through", - "start": 22834, - "end": 22915, + "start": 23274, + "end": 23355, "loc": { "start": { - "line": 578, + "line": 594, "column": 4 }, "end": { - "line": 578, + "line": 594, "column": 85 } } @@ -31934,15 +32714,15 @@ { "type": "CommentLine", "value": " every possibility.", - "start": 22920, - "end": 22941, + "start": 23360, + "end": 23381, "loc": { "start": { - "line": 579, + "line": 595, "column": 4 }, "end": { - "line": 579, + "line": 595, "column": 25 } } @@ -31950,15 +32730,15 @@ { "type": "CommentLine", "value": " Note that we only process cases where there are more remainingInternals than", - "start": 22946, - "end": 23025, + "start": 23386, + "end": 23465, "loc": { "start": { - "line": 580, + "line": 596, "column": 4 }, "end": { - "line": 580, + "line": 596, "column": 83 } } @@ -31966,15 +32746,15 @@ { "type": "CommentLine", "value": " selected internals -- when there are fewer, we'll just end up with the inverses", - "start": 23030, - "end": 23112, + "start": 23470, + "end": 23552, "loc": { "start": { - "line": 581, + "line": 597, "column": 4 }, "end": { - "line": 581, + "line": 597, "column": 86 } } @@ -31982,15 +32762,15 @@ { "type": "CommentLine", "value": " of the previous comparisons, which we'll already have covered.", - "start": 23117, - "end": 23182, + "start": 23557, + "end": 23622, "loc": { "start": { - "line": 582, + "line": 598, "column": 4 }, "end": { - "line": 582, + "line": 598, "column": 69 } } @@ -31999,29 +32779,29 @@ }, { "type": "ReturnStatement", - "start": 23740, - "end": 23758, + "start": 24180, + "end": 24198, "loc": { "start": { - "line": 595, + "line": 611, "column": 4 }, "end": { - "line": 595, + "line": 611, "column": 22 } }, "argument": { "type": "Identifier", - "start": 23747, - "end": 23757, + "start": 24187, + "end": 24197, "loc": { "start": { - "line": 595, + "line": 611, "column": 11 }, "end": { - "line": 595, + "line": 611, "column": 21 }, "identifierName": "classExprs" @@ -32037,15 +32817,15 @@ { "type": "CommentBlock", "value": "\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n ", - "start": 18864, - "end": 20362, + "start": 19304, + "end": 20802, "loc": { "start": { - "line": 486, + "line": 502, "column": 2 }, "end": { - "line": 511, + "line": 527, "column": 5 } } @@ -32055,15 +32835,15 @@ { "type": "CommentBlock", "value": "\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n ", - "start": 23766, - "end": 23972, + "start": 24206, + "end": 24412, "loc": { "start": { - "line": 598, + "line": 614, "column": 2 }, "end": { - "line": 606, + "line": 622, "column": 5 } } @@ -32072,15 +32852,15 @@ }, { "type": "ClassMethod", - "start": 23975, - "end": 32363, + "start": 24415, + "end": 32803, "loc": { "start": { - "line": 607, + "line": 623, "column": 2 }, "end": { - "line": 795, + "line": 811, "column": 3 } }, @@ -32088,15 +32868,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 23975, - "end": 23983, + "start": 24415, + "end": 24423, "loc": { "start": { - "line": 607, + "line": 623, "column": 2 }, "end": { - "line": 607, + "line": 623, "column": 10 }, "identifierName": "asJSONLD" @@ -32112,15 +32892,15 @@ "params": [ { "type": "Identifier", - "start": 23984, - "end": 23995, + "start": 24424, + "end": 24435, "loc": { "start": { - "line": 607, + "line": 623, "column": 11 }, "end": { - "line": 607, + "line": 623, "column": 22 }, "identifierName": "fallbackIRI" @@ -32130,59 +32910,59 @@ ], "body": { "type": "BlockStatement", - "start": 23997, - "end": 32363, + "start": 24437, + "end": 32803, "loc": { "start": { - "line": 607, + "line": 623, "column": 24 }, "end": { - "line": 795, + "line": 811, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 24042, - "end": 24092, + "start": 24482, + "end": 24532, "loc": { "start": { - "line": 609, + "line": 625, "column": 4 }, "end": { - "line": 609, + "line": 625, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24048, - "end": 24091, + "start": 24488, + "end": 24531, "loc": { "start": { - "line": 609, + "line": 625, "column": 10 }, "end": { - "line": 609, + "line": 625, "column": 53 } }, "id": { "type": "Identifier", - "start": 24048, - "end": 24064, + "start": 24488, + "end": 24504, "loc": { "start": { - "line": 609, + "line": 625, "column": 10 }, "end": { - "line": 609, + "line": 625, "column": 26 }, "identifierName": "phylorefAsJSONLD" @@ -32192,29 +32972,29 @@ }, "init": { "type": "CallExpression", - "start": 24067, - "end": 24091, + "start": 24507, + "end": 24531, "loc": { "start": { - "line": 609, + "line": 625, "column": 29 }, "end": { - "line": 609, + "line": 625, "column": 53 } }, "callee": { "type": "Identifier", - "start": 24067, - "end": 24076, + "start": 24507, + "end": 24516, "loc": { "start": { - "line": 609, + "line": 625, "column": 29 }, "end": { - "line": 609, + "line": 625, "column": 38 }, "identifierName": "cloneDeep" @@ -32224,44 +33004,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 24077, - "end": 24090, + "start": 24517, + "end": 24530, "loc": { "start": { - "line": 609, + "line": 625, "column": 39 }, "end": { - "line": 609, + "line": 625, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 24077, - "end": 24081, + "start": 24517, + "end": 24521, "loc": { "start": { - "line": 609, + "line": 625, "column": 39 }, "end": { - "line": 609, + "line": 625, "column": 43 } } }, "property": { "type": "Identifier", - "start": 24082, - "end": 24090, + "start": 24522, + "end": 24530, "loc": { "start": { - "line": 609, + "line": 625, "column": 44 }, "end": { - "line": 609, + "line": 625, "column": 52 }, "identifierName": "phyloref" @@ -32280,15 +33060,15 @@ { "type": "CommentLine", "value": " Keep all currently extant data.", - "start": 24003, - "end": 24037, + "start": 24443, + "end": 24477, "loc": { "start": { - "line": 608, + "line": 624, "column": 4 }, "end": { - "line": 608, + "line": 624, "column": 38 } } @@ -32298,15 +33078,15 @@ { "type": "CommentLine", "value": " Set the @id and @type. If we don't already have an '@id', use the", - "start": 24098, - "end": 24166, + "start": 24538, + "end": 24606, "loc": { "start": { - "line": 611, + "line": 627, "column": 4 }, "end": { - "line": 611, + "line": 627, "column": 72 } } @@ -32314,15 +33094,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 24171, - "end": 24186, + "start": 24611, + "end": 24626, "loc": { "start": { - "line": 612, + "line": 628, "column": 4 }, "end": { - "line": 612, + "line": 628, "column": 19 } } @@ -32331,29 +33111,29 @@ }, { "type": "IfStatement", - "start": 24191, - "end": 24264, + "start": 24631, + "end": 24704, "loc": { "start": { - "line": 613, + "line": 629, "column": 4 }, "end": { - "line": 613, + "line": 629, "column": 77 } }, "test": { "type": "UnaryExpression", - "start": 24195, - "end": 24224, + "start": 24635, + "end": 24664, "loc": { "start": { - "line": 613, + "line": 629, "column": 8 }, "end": { - "line": 613, + "line": 629, "column": 37 } }, @@ -32361,29 +33141,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 24196, - "end": 24224, + "start": 24636, + "end": 24664, "loc": { "start": { - "line": 613, + "line": 629, "column": 9 }, "end": { - "line": 613, + "line": 629, "column": 37 } }, "callee": { "type": "Identifier", - "start": 24196, - "end": 24199, + "start": 24636, + "end": 24639, "loc": { "start": { - "line": 613, + "line": 629, "column": 9 }, "end": { - "line": 613, + "line": 629, "column": 12 }, "identifierName": "has" @@ -32394,15 +33174,15 @@ "arguments": [ { "type": "Identifier", - "start": 24200, - "end": 24216, + "start": 24640, + "end": 24656, "loc": { "start": { - "line": 613, + "line": 629, "column": 13 }, "end": { - "line": 613, + "line": 629, "column": 29 }, "identifierName": "phylorefAsJSONLD" @@ -32411,15 +33191,15 @@ }, { "type": "StringLiteral", - "start": 24218, - "end": 24223, + "start": 24658, + "end": 24663, "loc": { "start": { - "line": 613, + "line": 629, "column": 31 }, "end": { - "line": 613, + "line": 629, "column": 36 } }, @@ -32439,58 +33219,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 24226, - "end": 24264, + "start": 24666, + "end": 24704, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 77 } }, "expression": { "type": "AssignmentExpression", - "start": 24226, - "end": 24263, + "start": 24666, + "end": 24703, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 76 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 24226, - "end": 24249, + "start": 24666, + "end": 24689, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 62 } }, "object": { "type": "Identifier", - "start": 24226, - "end": 24242, + "start": 24666, + "end": 24682, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 55 }, "identifierName": "phylorefAsJSONLD" @@ -32499,15 +33279,15 @@ }, "property": { "type": "StringLiteral", - "start": 24243, - "end": 24248, + "start": 24683, + "end": 24688, "loc": { "start": { - "line": 613, + "line": 629, "column": 56 }, "end": { - "line": 613, + "line": 629, "column": 61 } }, @@ -32521,15 +33301,15 @@ }, "right": { "type": "Identifier", - "start": 24252, - "end": 24263, + "start": 24692, + "end": 24703, "loc": { "start": { - "line": 613, + "line": 629, "column": 65 }, "end": { - "line": 613, + "line": 629, "column": 76 }, "identifierName": "fallbackIRI" @@ -32543,15 +33323,15 @@ { "type": "CommentLine", "value": " Set the @id and @type. If we don't already have an '@id', use the", - "start": 24098, - "end": 24166, + "start": 24538, + "end": 24606, "loc": { "start": { - "line": 611, + "line": 627, "column": 4 }, "end": { - "line": 611, + "line": 627, "column": 72 } } @@ -32559,15 +33339,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 24171, - "end": 24186, + "start": 24611, + "end": 24626, "loc": { "start": { - "line": 612, + "line": 628, "column": 4 }, "end": { - "line": 612, + "line": 628, "column": 19 } } @@ -32576,58 +33356,58 @@ }, { "type": "ExpressionStatement", - "start": 24269, - "end": 24309, + "start": 24709, + "end": 24749, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 24269, - "end": 24308, + "start": 24709, + "end": 24748, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 24269, - "end": 24294, + "start": 24709, + "end": 24734, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 29 } }, "object": { "type": "Identifier", - "start": 24269, - "end": 24285, + "start": 24709, + "end": 24725, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 20 }, "identifierName": "phylorefAsJSONLD" @@ -32636,15 +33416,15 @@ }, "property": { "type": "StringLiteral", - "start": 24286, - "end": 24293, + "start": 24726, + "end": 24733, "loc": { "start": { - "line": 614, + "line": 630, "column": 21 }, "end": { - "line": 614, + "line": 630, "column": 28 } }, @@ -32658,15 +33438,15 @@ }, "right": { "type": "StringLiteral", - "start": 24297, - "end": 24308, + "start": 24737, + "end": 24748, "loc": { "start": { - "line": 614, + "line": 630, "column": 32 }, "end": { - "line": 614, + "line": 630, "column": 43 } }, @@ -32681,15 +33461,15 @@ { "type": "CommentLine", "value": " If we don't have a bibliographicCitation but we do have a definition source,", - "start": 24315, - "end": 24394, + "start": 24755, + "end": 24834, "loc": { "start": { - "line": 616, + "line": 632, "column": 4 }, "end": { - "line": 616, + "line": 632, "column": 83 } } @@ -32697,15 +33477,15 @@ { "type": "CommentLine", "value": " then generate a bibliographicCitation for the source.", - "start": 24399, - "end": 24455, + "start": 24839, + "end": 24895, "loc": { "start": { - "line": 617, + "line": 633, "column": 4 }, "end": { - "line": 617, + "line": 633, "column": 60 } } @@ -32714,43 +33494,43 @@ }, { "type": "IfStatement", - "start": 24460, - "end": 24748, + "start": 24900, + "end": 25188, "loc": { "start": { - "line": 618, + "line": 634, "column": 4 }, "end": { - "line": 623, + "line": 639, "column": 5 } }, "test": { "type": "CallExpression", - "start": 24464, - "end": 24505, + "start": 24904, + "end": 24945, "loc": { "start": { - "line": 618, + "line": 634, "column": 8 }, "end": { - "line": 618, + "line": 634, "column": 49 } }, "callee": { "type": "Identifier", - "start": 24464, - "end": 24467, + "start": 24904, + "end": 24907, "loc": { "start": { - "line": 618, + "line": 634, "column": 8 }, "end": { - "line": 618, + "line": 634, "column": 11 }, "identifierName": "has" @@ -32761,15 +33541,15 @@ "arguments": [ { "type": "Identifier", - "start": 24468, - "end": 24484, + "start": 24908, + "end": 24924, "loc": { "start": { - "line": 618, + "line": 634, "column": 12 }, "end": { - "line": 618, + "line": 634, "column": 28 }, "identifierName": "phylorefAsJSONLD" @@ -32778,15 +33558,15 @@ }, { "type": "StringLiteral", - "start": 24486, - "end": 24504, + "start": 24926, + "end": 24944, "loc": { "start": { - "line": 618, + "line": 634, "column": 30 }, "end": { - "line": 618, + "line": 634, "column": 48 } }, @@ -32801,59 +33581,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 24507, - "end": 24748, + "start": 24947, + "end": 25188, "loc": { "start": { - "line": 618, + "line": 634, "column": 51 }, "end": { - "line": 623, + "line": 639, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 24515, - "end": 24574, + "start": 24955, + "end": 25014, "loc": { "start": { - "line": 619, + "line": 635, "column": 6 }, "end": { - "line": 619, + "line": 635, "column": 65 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24521, - "end": 24573, + "start": 24961, + "end": 25013, "loc": { "start": { - "line": 619, + "line": 635, "column": 12 }, "end": { - "line": 619, + "line": 635, "column": 64 } }, "id": { "type": "Identifier", - "start": 24521, - "end": 24537, + "start": 24961, + "end": 24977, "loc": { "start": { - "line": 619, + "line": 635, "column": 12 }, "end": { - "line": 619, + "line": 635, "column": 28 }, "identifierName": "definitionSource" @@ -32862,29 +33642,29 @@ }, "init": { "type": "MemberExpression", - "start": 24540, - "end": 24573, + "start": 24980, + "end": 25013, "loc": { "start": { - "line": 619, + "line": 635, "column": 31 }, "end": { - "line": 619, + "line": 635, "column": 64 } }, "object": { "type": "Identifier", - "start": 24540, - "end": 24556, + "start": 24980, + "end": 24996, "loc": { "start": { - "line": 619, + "line": 635, "column": 31 }, "end": { - "line": 619, + "line": 635, "column": 47 }, "identifierName": "phylorefAsJSONLD" @@ -32893,15 +33673,15 @@ }, "property": { "type": "Identifier", - "start": 24557, - "end": 24573, + "start": 24997, + "end": 25013, "loc": { "start": { - "line": 619, + "line": 635, "column": 48 }, "end": { - "line": 619, + "line": 635, "column": 64 }, "identifierName": "definitionSource" @@ -32916,29 +33696,29 @@ }, { "type": "IfStatement", - "start": 24581, - "end": 24742, + "start": 25021, + "end": 25182, "loc": { "start": { - "line": 620, + "line": 636, "column": 6 }, "end": { - "line": 622, + "line": 638, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 24585, - "end": 24632, + "start": 25025, + "end": 25072, "loc": { "start": { - "line": 620, + "line": 636, "column": 10 }, "end": { - "line": 620, + "line": 636, "column": 57 } }, @@ -32946,29 +33726,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 24586, - "end": 24632, + "start": 25026, + "end": 25072, "loc": { "start": { - "line": 620, + "line": 636, "column": 11 }, "end": { - "line": 620, + "line": 636, "column": 57 } }, "callee": { "type": "Identifier", - "start": 24586, - "end": 24589, + "start": 25026, + "end": 25029, "loc": { "start": { - "line": 620, + "line": 636, "column": 11 }, "end": { - "line": 620, + "line": 636, "column": 14 }, "identifierName": "has" @@ -32978,15 +33758,15 @@ "arguments": [ { "type": "Identifier", - "start": 24590, - "end": 24606, + "start": 25030, + "end": 25046, "loc": { "start": { - "line": 620, + "line": 636, "column": 15 }, "end": { - "line": 620, + "line": 636, "column": 31 }, "identifierName": "definitionSource" @@ -32995,15 +33775,15 @@ }, { "type": "StringLiteral", - "start": 24608, - "end": 24631, + "start": 25048, + "end": 25071, "loc": { "start": { - "line": 620, + "line": 636, "column": 33 }, "end": { - "line": 620, + "line": 636, "column": 56 } }, @@ -33021,73 +33801,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 24634, - "end": 24742, + "start": 25074, + "end": 25182, "loc": { "start": { - "line": 620, + "line": 636, "column": 59 }, "end": { - "line": 622, + "line": 638, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 24644, - "end": 24734, + "start": 25084, + "end": 25174, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 98 } }, "expression": { "type": "AssignmentExpression", - "start": 24644, - "end": 24733, + "start": 25084, + "end": 25173, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 97 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 24644, - "end": 24682, + "start": 25084, + "end": 25122, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 46 } }, "object": { "type": "Identifier", - "start": 24644, - "end": 24660, + "start": 25084, + "end": 25100, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 24 }, "identifierName": "definitionSource" @@ -33096,15 +33876,15 @@ }, "property": { "type": "Identifier", - "start": 24661, - "end": 24682, + "start": 25101, + "end": 25122, "loc": { "start": { - "line": 621, + "line": 637, "column": 25 }, "end": { - "line": 621, + "line": 637, "column": 46 }, "identifierName": "bibliographicCitation" @@ -33115,57 +33895,57 @@ }, "right": { "type": "CallExpression", - "start": 24685, - "end": 24733, + "start": 25125, + "end": 25173, "loc": { "start": { - "line": 621, + "line": 637, "column": 49 }, "end": { - "line": 621, + "line": 637, "column": 97 } }, "callee": { "type": "MemberExpression", - "start": 24685, - "end": 24731, + "start": 25125, + "end": 25171, "loc": { "start": { - "line": 621, + "line": 637, "column": 49 }, "end": { - "line": 621, + "line": 637, "column": 95 } }, "object": { "type": "NewExpression", - "start": 24685, - "end": 24722, + "start": 25125, + "end": 25162, "loc": { "start": { - "line": 621, + "line": 637, "column": 49 }, "end": { - "line": 621, + "line": 637, "column": 86 } }, "callee": { "type": "Identifier", - "start": 24689, - "end": 24704, + "start": 25129, + "end": 25144, "loc": { "start": { - "line": 621, + "line": 637, "column": 53 }, "end": { - "line": 621, + "line": 637, "column": 68 }, "identifierName": "CitationWrapper" @@ -33175,15 +33955,15 @@ "arguments": [ { "type": "Identifier", - "start": 24705, - "end": 24721, + "start": 25145, + "end": 25161, "loc": { "start": { - "line": 621, + "line": 637, "column": 69 }, "end": { - "line": 621, + "line": 637, "column": 85 }, "identifierName": "definitionSource" @@ -33194,15 +33974,15 @@ }, "property": { "type": "Identifier", - "start": 24723, - "end": 24731, + "start": 25163, + "end": 25171, "loc": { "start": { - "line": 621, + "line": 637, "column": 87 }, "end": { - "line": 621, + "line": 637, "column": 95 }, "identifierName": "toString" @@ -33229,15 +34009,15 @@ { "type": "CommentLine", "value": " If we don't have a bibliographicCitation but we do have a definition source,", - "start": 24315, - "end": 24394, + "start": 24755, + "end": 24834, "loc": { "start": { - "line": 616, + "line": 632, "column": 4 }, "end": { - "line": 616, + "line": 632, "column": 83 } } @@ -33245,15 +34025,15 @@ { "type": "CommentLine", "value": " then generate a bibliographicCitation for the source.", - "start": 24399, - "end": 24455, + "start": 24839, + "end": 24895, "loc": { "start": { - "line": 617, + "line": 633, "column": 4 }, "end": { - "line": 617, + "line": 633, "column": 60 } } @@ -33263,15 +34043,15 @@ { "type": "CommentLine", "value": " Construct a class expression for this phyloreference.", - "start": 24754, - "end": 24810, + "start": 25194, + "end": 25250, "loc": { "start": { - "line": 625, + "line": 641, "column": 4 }, "end": { - "line": 625, + "line": 641, "column": 60 } } @@ -33280,44 +34060,44 @@ }, { "type": "VariableDeclaration", - "start": 24815, - "end": 24884, + "start": 25255, + "end": 25324, "loc": { "start": { - "line": 626, + "line": 642, "column": 4 }, "end": { - "line": 626, + "line": 642, "column": 73 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24821, - "end": 24883, + "start": 25261, + "end": 25323, "loc": { "start": { - "line": 626, + "line": 642, "column": 10 }, "end": { - "line": 626, + "line": 642, "column": 72 } }, "id": { "type": "Identifier", - "start": 24821, - "end": 24839, + "start": 25261, + "end": 25279, "loc": { "start": { - "line": 626, + "line": 642, "column": 10 }, "end": { - "line": 626, + "line": 642, "column": 28 }, "identifierName": "internalSpecifiers" @@ -33327,43 +34107,43 @@ }, "init": { "type": "LogicalExpression", - "start": 24842, - "end": 24883, + "start": 25282, + "end": 25323, "loc": { "start": { - "line": 626, + "line": 642, "column": 31 }, "end": { - "line": 626, + "line": 642, "column": 72 } }, "left": { "type": "MemberExpression", - "start": 24842, - "end": 24877, + "start": 25282, + "end": 25317, "loc": { "start": { - "line": 626, + "line": 642, "column": 31 }, "end": { - "line": 626, + "line": 642, "column": 66 } }, "object": { "type": "Identifier", - "start": 24842, - "end": 24858, + "start": 25282, + "end": 25298, "loc": { "start": { - "line": 626, + "line": 642, "column": 31 }, "end": { - "line": 626, + "line": 642, "column": 47 }, "identifierName": "phylorefAsJSONLD" @@ -33372,15 +34152,15 @@ }, "property": { "type": "Identifier", - "start": 24859, - "end": 24877, + "start": 25299, + "end": 25317, "loc": { "start": { - "line": 626, + "line": 642, "column": 48 }, "end": { - "line": 626, + "line": 642, "column": 66 }, "identifierName": "internalSpecifiers" @@ -33392,15 +34172,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 24881, - "end": 24883, + "start": 25321, + "end": 25323, "loc": { "start": { - "line": 626, + "line": 642, "column": 70 }, "end": { - "line": 626, + "line": 642, "column": 72 } }, @@ -33415,15 +34195,15 @@ { "type": "CommentLine", "value": " Construct a class expression for this phyloreference.", - "start": 24754, - "end": 24810, + "start": 25194, + "end": 25250, "loc": { "start": { - "line": 625, + "line": 641, "column": 4 }, "end": { - "line": 625, + "line": 641, "column": 60 } } @@ -33432,44 +34212,44 @@ }, { "type": "VariableDeclaration", - "start": 24889, - "end": 24958, + "start": 25329, + "end": 25398, "loc": { "start": { - "line": 627, + "line": 643, "column": 4 }, "end": { - "line": 627, + "line": 643, "column": 73 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24895, - "end": 24957, + "start": 25335, + "end": 25397, "loc": { "start": { - "line": 627, + "line": 643, "column": 10 }, "end": { - "line": 627, + "line": 643, "column": 72 } }, "id": { "type": "Identifier", - "start": 24895, - "end": 24913, + "start": 25335, + "end": 25353, "loc": { "start": { - "line": 627, + "line": 643, "column": 10 }, "end": { - "line": 627, + "line": 643, "column": 28 }, "identifierName": "externalSpecifiers" @@ -33478,43 +34258,43 @@ }, "init": { "type": "LogicalExpression", - "start": 24916, - "end": 24957, + "start": 25356, + "end": 25397, "loc": { "start": { - "line": 627, + "line": 643, "column": 31 }, "end": { - "line": 627, + "line": 643, "column": 72 } }, "left": { "type": "MemberExpression", - "start": 24916, - "end": 24951, + "start": 25356, + "end": 25391, "loc": { "start": { - "line": 627, + "line": 643, "column": 31 }, "end": { - "line": 627, + "line": 643, "column": 66 } }, "object": { "type": "Identifier", - "start": 24916, - "end": 24932, + "start": 25356, + "end": 25372, "loc": { "start": { - "line": 627, + "line": 643, "column": 31 }, "end": { - "line": 627, + "line": 643, "column": 47 }, "identifierName": "phylorefAsJSONLD" @@ -33523,15 +34303,15 @@ }, "property": { "type": "Identifier", - "start": 24933, - "end": 24951, + "start": 25373, + "end": 25391, "loc": { "start": { - "line": 627, + "line": 643, "column": 48 }, "end": { - "line": 627, + "line": 643, "column": 66 }, "identifierName": "externalSpecifiers" @@ -33543,15 +34323,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 24955, - "end": 24957, + "start": 25395, + "end": 25397, "loc": { "start": { - "line": 627, + "line": 643, "column": 70 }, "end": { - "line": 627, + "line": 643, "column": 72 } }, @@ -33565,15 +34345,15 @@ { "type": "CommentLine", "value": " If it is an apomorphy-based class expression, we should generate a", - "start": 24964, - "end": 25033, + "start": 25404, + "end": 25473, "loc": { "start": { - "line": 629, + "line": 645, "column": 4 }, "end": { - "line": 629, + "line": 645, "column": 73 } } @@ -33581,15 +34361,15 @@ { "type": "CommentLine", "value": " logical expression that describes the apomorphy.", - "start": 25038, - "end": 25089, + "start": 25478, + "end": 25529, "loc": { "start": { - "line": 630, + "line": 646, "column": 4 }, "end": { - "line": 630, + "line": 646, "column": 55 } } @@ -33598,44 +34378,44 @@ }, { "type": "VariableDeclaration", - "start": 25094, - "end": 25145, + "start": 25534, + "end": 25585, "loc": { "start": { - "line": 631, + "line": 647, "column": 4 }, "end": { - "line": 631, + "line": 647, "column": 55 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 25100, - "end": 25144, + "start": 25540, + "end": 25584, "loc": { "start": { - "line": 631, + "line": 647, "column": 10 }, "end": { - "line": 631, + "line": 647, "column": 54 } }, "id": { "type": "Identifier", - "start": 25100, - "end": 25112, + "start": 25540, + "end": 25552, "loc": { "start": { - "line": 631, + "line": 647, "column": 10 }, "end": { - "line": 631, + "line": 647, "column": 22 }, "identifierName": "phylorefType" @@ -33645,29 +34425,29 @@ }, "init": { "type": "MemberExpression", - "start": 25115, - "end": 25144, + "start": 25555, + "end": 25584, "loc": { "start": { - "line": 631, + "line": 647, "column": 25 }, "end": { - "line": 631, + "line": 647, "column": 54 } }, "object": { "type": "Identifier", - "start": 25115, - "end": 25131, + "start": 25555, + "end": 25571, "loc": { "start": { - "line": 631, + "line": 647, "column": 25 }, "end": { - "line": 631, + "line": 647, "column": 41 }, "identifierName": "phylorefAsJSONLD" @@ -33676,15 +34456,15 @@ }, "property": { "type": "Identifier", - "start": 25132, - "end": 25144, + "start": 25572, + "end": 25584, "loc": { "start": { - "line": 631, + "line": 647, "column": 42 }, "end": { - "line": 631, + "line": 647, "column": 54 }, "identifierName": "phylorefType" @@ -33701,15 +34481,15 @@ { "type": "CommentLine", "value": " If it is an apomorphy-based class expression, we should generate a", - "start": 24964, - "end": 25033, + "start": 25404, + "end": 25473, "loc": { "start": { - "line": 629, + "line": 645, "column": 4 }, "end": { - "line": 629, + "line": 645, "column": 73 } } @@ -33717,15 +34497,15 @@ { "type": "CommentLine", "value": " logical expression that describes the apomorphy.", - "start": 25038, - "end": 25089, + "start": 25478, + "end": 25529, "loc": { "start": { - "line": 630, + "line": 646, "column": 4 }, "end": { - "line": 630, + "line": 646, "column": 55 } } @@ -33734,57 +34514,57 @@ }, { "type": "IfStatement", - "start": 25150, - "end": 25776, + "start": 25590, + "end": 26216, "loc": { "start": { - "line": 632, + "line": 648, "column": 4 }, "end": { - "line": 648, + "line": 664, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 25161, - "end": 25281, + "start": 25601, + "end": 25721, "loc": { "start": { - "line": 633, + "line": 649, "column": 6 }, "end": { - "line": 634, + "line": 650, "column": 45 } }, "left": { "type": "LogicalExpression", - "start": 25162, - "end": 25234, + "start": 25602, + "end": 25674, "loc": { "start": { - "line": 633, + "line": 649, "column": 7 }, "end": { - "line": 633, + "line": 649, "column": 79 } }, "left": { "type": "Identifier", - "start": 25162, - "end": 25174, + "start": 25602, + "end": 25614, "loc": { "start": { - "line": 633, + "line": 649, "column": 7 }, "end": { - "line": 633, + "line": 649, "column": 19 }, "identifierName": "phylorefType" @@ -33794,29 +34574,29 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 25178, - "end": 25234, + "start": 25618, + "end": 25674, "loc": { "start": { - "line": 633, + "line": 649, "column": 23 }, "end": { - "line": 633, + "line": 649, "column": 79 } }, "left": { "type": "Identifier", - "start": 25178, - "end": 25190, + "start": 25618, + "end": 25630, "loc": { "start": { - "line": 633, + "line": 649, "column": 23 }, "end": { - "line": 633, + "line": 649, "column": 35 }, "identifierName": "phylorefType" @@ -33826,15 +34606,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 25195, - "end": 25234, + "start": 25635, + "end": 25674, "loc": { "start": { - "line": 633, + "line": 649, "column": 40 }, "end": { - "line": 633, + "line": 649, "column": 79 } }, @@ -33847,35 +34627,35 @@ }, "extra": { "parenthesized": true, - "parenStart": 25161 + "parenStart": 25601 } }, "operator": "||", "right": { "type": "CallExpression", - "start": 25246, - "end": 25280, + "start": 25686, + "end": 25720, "loc": { "start": { - "line": 634, + "line": 650, "column": 10 }, "end": { - "line": 634, + "line": 650, "column": 44 } }, "callee": { "type": "Identifier", - "start": 25246, - "end": 25249, + "start": 25686, + "end": 25689, "loc": { "start": { - "line": 634, + "line": 650, "column": 10 }, "end": { - "line": 634, + "line": 650, "column": 13 }, "identifierName": "has" @@ -33885,15 +34665,15 @@ "arguments": [ { "type": "Identifier", - "start": 25250, - "end": 25266, + "start": 25690, + "end": 25706, "loc": { "start": { - "line": 634, + "line": 650, "column": 14 }, "end": { - "line": 634, + "line": 650, "column": 30 }, "identifierName": "phylorefAsJSONLD" @@ -33902,15 +34682,15 @@ }, { "type": "StringLiteral", - "start": 25268, - "end": 25279, + "start": 25708, + "end": 25719, "loc": { "start": { - "line": 634, + "line": 650, "column": 32 }, "end": { - "line": 634, + "line": 650, "column": 43 } }, @@ -33923,79 +34703,79 @@ ], "extra": { "parenthesized": true, - "parenStart": 25245 + "parenStart": 25685 } } }, "consequent": { "type": "BlockStatement", - "start": 25288, - "end": 25776, + "start": 25728, + "end": 26216, "loc": { "start": { - "line": 635, + "line": 651, "column": 6 }, "end": { - "line": 648, + "line": 664, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 25344, - "end": 25468, + "start": 25784, + "end": 25908, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 640, + "line": 656, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 25344, - "end": 25467, + "start": 25784, + "end": 25907, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 640, + "line": 656, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 25344, - "end": 25371, + "start": 25784, + "end": 25811, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 637, + "line": 653, "column": 33 } }, "object": { "type": "Identifier", - "start": 25344, - "end": 25360, + "start": 25784, + "end": 25800, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 637, + "line": 653, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -34005,15 +34785,15 @@ }, "property": { "type": "Identifier", - "start": 25361, - "end": 25371, + "start": 25801, + "end": 25811, "loc": { "start": { - "line": 637, + "line": 653, "column": 23 }, "end": { - "line": 637, + "line": 653, "column": 33 }, "identifierName": "subClassOf" @@ -34025,30 +34805,30 @@ }, "right": { "type": "ArrayExpression", - "start": 25374, - "end": 25467, + "start": 25814, + "end": 25907, "loc": { "start": { - "line": 637, + "line": 653, "column": 36 }, "end": { - "line": 640, + "line": 656, "column": 7 } }, "elements": [ { "type": "StringLiteral", - "start": 25384, - "end": 25409, + "start": 25824, + "end": 25849, "loc": { "start": { - "line": 638, + "line": 654, "column": 8 }, "end": { - "line": 638, + "line": 654, "column": 33 } }, @@ -34060,15 +34840,15 @@ }, { "type": "StringLiteral", - "start": 25419, - "end": 25458, + "start": 25859, + "end": 25898, "loc": { "start": { - "line": 639, + "line": 655, "column": 8 }, "end": { - "line": 639, + "line": 655, "column": 47 } }, @@ -34086,15 +34866,15 @@ { "type": "CommentLine", "value": " This is an apomorphy-based definition!", - "start": 25296, - "end": 25337, + "start": 25736, + "end": 25777, "loc": { "start": { - "line": 636, + "line": 652, "column": 6 }, "end": { - "line": 636, + "line": 652, "column": 47 } } @@ -34104,15 +34884,15 @@ { "type": "CommentLine", "value": " Someday, we will probably want to turn this apomorphy into a", - "start": 25476, - "end": 25539, + "start": 25916, + "end": 25979, "loc": { "start": { - "line": 642, + "line": 658, "column": 6 }, "end": { - "line": 642, + "line": 658, "column": 69 } } @@ -34120,15 +34900,15 @@ { "type": "CommentLine", "value": " logical expression so that it can be computed alongside other", - "start": 25546, - "end": 25610, + "start": 25986, + "end": 26050, "loc": { "start": { - "line": 643, + "line": 659, "column": 6 }, "end": { - "line": 643, + "line": 659, "column": 70 } } @@ -34136,15 +34916,15 @@ { "type": "CommentLine", "value": " OWL ontologies. This is outside our scope for the moment, so", - "start": 25617, - "end": 25680, + "start": 26057, + "end": 26120, "loc": { "start": { - "line": 644, + "line": 660, "column": 6 }, "end": { - "line": 644, + "line": 660, "column": 69 } } @@ -34152,15 +34932,15 @@ { "type": "CommentLine", "value": " we will simply pass on the phyloreference as-is.", - "start": 25687, - "end": 25738, + "start": 26127, + "end": 26178, "loc": { "start": { - "line": 645, + "line": 661, "column": 6 }, "end": { - "line": 645, + "line": 661, "column": 57 } } @@ -34169,29 +34949,29 @@ }, { "type": "ReturnStatement", - "start": 25746, - "end": 25770, + "start": 26186, + "end": 26210, "loc": { "start": { - "line": 647, + "line": 663, "column": 6 }, "end": { - "line": 647, + "line": 663, "column": 30 } }, "argument": { "type": "Identifier", - "start": 25753, - "end": 25769, + "start": 26193, + "end": 26209, "loc": { "start": { - "line": 647, + "line": 663, "column": 13 }, "end": { - "line": 647, + "line": 663, "column": 29 }, "identifierName": "phylorefAsJSONLD" @@ -34203,15 +34983,15 @@ { "type": "CommentLine", "value": " Someday, we will probably want to turn this apomorphy into a", - "start": 25476, - "end": 25539, + "start": 25916, + "end": 25979, "loc": { "start": { - "line": 642, + "line": 658, "column": 6 }, "end": { - "line": 642, + "line": 658, "column": 69 } } @@ -34219,15 +34999,15 @@ { "type": "CommentLine", "value": " logical expression so that it can be computed alongside other", - "start": 25546, - "end": 25610, + "start": 25986, + "end": 26050, "loc": { "start": { - "line": 643, + "line": 659, "column": 6 }, "end": { - "line": 643, + "line": 659, "column": 70 } } @@ -34235,15 +35015,15 @@ { "type": "CommentLine", "value": " OWL ontologies. This is outside our scope for the moment, so", - "start": 25617, - "end": 25680, + "start": 26057, + "end": 26120, "loc": { "start": { - "line": 644, + "line": 660, "column": 6 }, "end": { - "line": 644, + "line": 660, "column": 69 } } @@ -34251,15 +35031,15 @@ { "type": "CommentLine", "value": " we will simply pass on the phyloreference as-is.", - "start": 25687, - "end": 25738, + "start": 26127, + "end": 26178, "loc": { "start": { - "line": 645, + "line": 661, "column": 6 }, "end": { - "line": 645, + "line": 661, "column": 57 } } @@ -34275,15 +35055,15 @@ { "type": "CommentLine", "value": " We might need to make component classes.", - "start": 25782, - "end": 25825, + "start": 26222, + "end": 26265, "loc": { "start": { - "line": 650, + "line": 666, "column": 4 }, "end": { - "line": 650, + "line": 666, "column": 47 } } @@ -34291,15 +35071,15 @@ { "type": "CommentLine", "value": " So we reset our component class counts and records.", - "start": 25830, - "end": 25884, + "start": 26270, + "end": 26324, "loc": { "start": { - "line": 651, + "line": 667, "column": 4 }, "end": { - "line": 651, + "line": 667, "column": 58 } } @@ -34308,58 +35088,58 @@ }, { "type": "ExpressionStatement", - "start": 25889, - "end": 25918, + "start": 26329, + "end": 26358, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 33 } }, "expression": { "type": "AssignmentExpression", - "start": 25889, - "end": 25917, + "start": 26329, + "end": 26357, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 32 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 25889, - "end": 25913, + "start": 26329, + "end": 26353, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 25889, - "end": 25893, + "start": 26329, + "end": 26333, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 8 } }, @@ -34367,15 +35147,15 @@ }, "property": { "type": "Identifier", - "start": 25894, - "end": 25913, + "start": 26334, + "end": 26353, "loc": { "start": { - "line": 652, + "line": 668, "column": 9 }, "end": { - "line": 652, + "line": 668, "column": 28 }, "identifierName": "componentClassCount" @@ -34387,15 +35167,15 @@ }, "right": { "type": "NumericLiteral", - "start": 25916, - "end": 25917, + "start": 26356, + "end": 26357, "loc": { "start": { - "line": 652, + "line": 668, "column": 31 }, "end": { - "line": 652, + "line": 668, "column": 32 } }, @@ -34411,15 +35191,15 @@ { "type": "CommentLine", "value": " We might need to make component classes.", - "start": 25782, - "end": 25825, + "start": 26222, + "end": 26265, "loc": { "start": { - "line": 650, + "line": 666, "column": 4 }, "end": { - "line": 650, + "line": 666, "column": 47 } } @@ -34427,15 +35207,15 @@ { "type": "CommentLine", "value": " So we reset our component class counts and records.", - "start": 25830, - "end": 25884, + "start": 26270, + "end": 26324, "loc": { "start": { - "line": 651, + "line": 667, "column": 4 }, "end": { - "line": 651, + "line": 667, "column": 58 } } @@ -34444,73 +35224,73 @@ }, { "type": "ExpressionStatement", - "start": 25923, - "end": 25957, + "start": 26363, + "end": 26397, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 25923, - "end": 25956, + "start": 26363, + "end": 26396, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 25923, - "end": 25951, + "start": 26363, + "end": 26391, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 25923, - "end": 25927, + "start": 26363, + "end": 26367, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 8 } } }, "property": { "type": "Identifier", - "start": 25928, - "end": 25951, + "start": 26368, + "end": 26391, "loc": { "start": { - "line": 653, + "line": 669, "column": 9 }, "end": { - "line": 653, + "line": 669, "column": 32 }, "identifierName": "componentClassesByLabel" @@ -34521,15 +35301,15 @@ }, "right": { "type": "ObjectExpression", - "start": 25954, - "end": 25956, + "start": 26394, + "end": 26396, "loc": { "start": { - "line": 653, + "line": 669, "column": 35 }, "end": { - "line": 653, + "line": 669, "column": 37 } }, @@ -34540,15 +35320,15 @@ { "type": "CommentLine", "value": " The type of this phyloreference.", - "start": 25963, - "end": 25998, + "start": 26403, + "end": 26438, "loc": { "start": { - "line": 655, + "line": 671, "column": 4 }, "end": { - "line": 655, + "line": 671, "column": 39 } } @@ -34557,44 +35337,44 @@ }, { "type": "VariableDeclaration", - "start": 26003, - "end": 26030, + "start": 26443, + "end": 26470, "loc": { "start": { - "line": 656, + "line": 672, "column": 4 }, "end": { - "line": 656, + "line": 672, "column": 31 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 26007, - "end": 26029, + "start": 26447, + "end": 26469, "loc": { "start": { - "line": 656, + "line": 672, "column": 8 }, "end": { - "line": 656, + "line": 672, "column": 30 } }, "id": { "type": "Identifier", - "start": 26007, - "end": 26029, + "start": 26447, + "end": 26469, "loc": { "start": { - "line": 656, + "line": 672, "column": 8 }, "end": { - "line": 656, + "line": 672, "column": 30 }, "identifierName": "calculatedPhylorefType" @@ -34611,15 +35391,15 @@ { "type": "CommentLine", "value": " The type of this phyloreference.", - "start": 25963, - "end": 25998, + "start": 26403, + "end": 26438, "loc": { "start": { - "line": 655, + "line": 671, "column": 4 }, "end": { - "line": 655, + "line": 671, "column": 39 } } @@ -34629,15 +35409,15 @@ { "type": "CommentLine", "value": " The list of logical expressions generated for this phyloref.", - "start": 26036, - "end": 26099, + "start": 26476, + "end": 26539, "loc": { "start": { - "line": 658, + "line": 674, "column": 4 }, "end": { - "line": 658, + "line": 674, "column": 67 } } @@ -34646,44 +35426,44 @@ }, { "type": "VariableDeclaration", - "start": 26104, - "end": 26132, + "start": 26544, + "end": 26572, "loc": { "start": { - "line": 659, + "line": 675, "column": 4 }, "end": { - "line": 659, + "line": 675, "column": 32 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 26108, - "end": 26131, + "start": 26548, + "end": 26571, "loc": { "start": { - "line": 659, + "line": 675, "column": 8 }, "end": { - "line": 659, + "line": 675, "column": 31 } }, "id": { "type": "Identifier", - "start": 26108, - "end": 26126, + "start": 26548, + "end": 26566, "loc": { "start": { - "line": 659, + "line": 675, "column": 8 }, "end": { - "line": 659, + "line": 675, "column": 26 }, "identifierName": "logicalExpressions" @@ -34693,15 +35473,15 @@ }, "init": { "type": "ArrayExpression", - "start": 26129, - "end": 26131, + "start": 26569, + "end": 26571, "loc": { "start": { - "line": 659, + "line": 675, "column": 29 }, "end": { - "line": 659, + "line": 675, "column": 31 } }, @@ -34715,15 +35495,15 @@ { "type": "CommentLine", "value": " The list of logical expressions generated for this phyloref.", - "start": 26036, - "end": 26099, + "start": 26476, + "end": 26539, "loc": { "start": { - "line": 658, + "line": 674, "column": 4 }, "end": { - "line": 658, + "line": 674, "column": 67 } } @@ -34732,57 +35512,57 @@ }, { "type": "IfStatement", - "start": 26138, - "end": 28955, + "start": 26578, + "end": 29395, "loc": { "start": { - "line": 661, + "line": 677, "column": 4 }, "end": { - "line": 729, + "line": 745, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 26142, - "end": 26173, + "start": 26582, + "end": 26613, "loc": { "start": { - "line": 661, + "line": 677, "column": 8 }, "end": { - "line": 661, + "line": 677, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 26142, - "end": 26167, + "start": 26582, + "end": 26607, "loc": { "start": { - "line": 661, + "line": 677, "column": 8 }, "end": { - "line": 661, + "line": 677, "column": 33 } }, "object": { "type": "Identifier", - "start": 26142, - "end": 26160, + "start": 26582, + "end": 26600, "loc": { "start": { - "line": 661, + "line": 677, "column": 8 }, "end": { - "line": 661, + "line": 677, "column": 26 }, "identifierName": "internalSpecifiers" @@ -34791,15 +35571,15 @@ }, "property": { "type": "Identifier", - "start": 26161, - "end": 26167, + "start": 26601, + "end": 26607, "loc": { "start": { - "line": 661, + "line": 677, "column": 27 }, "end": { - "line": 661, + "line": 677, "column": 33 }, "identifierName": "length" @@ -34811,15 +35591,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 26172, - "end": 26173, + "start": 26612, + "end": 26613, "loc": { "start": { - "line": 661, + "line": 677, "column": 38 }, "end": { - "line": 661, + "line": 677, "column": 39 } }, @@ -34832,59 +35612,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 26175, - "end": 26415, + "start": 26615, + "end": 26855, "loc": { "start": { - "line": 661, + "line": 677, "column": 41 }, "end": { - "line": 665, + "line": 681, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 26265, - "end": 26325, + "start": 26705, + "end": 26765, "loc": { "start": { - "line": 663, + "line": 679, "column": 6 }, "end": { - "line": 663, + "line": 679, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 26265, - "end": 26324, + "start": 26705, + "end": 26764, "loc": { "start": { - "line": 663, + "line": 679, "column": 6 }, "end": { - "line": 663, + "line": 679, "column": 65 } }, "operator": "=", "left": { "type": "Identifier", - "start": 26265, - "end": 26287, + "start": 26705, + "end": 26727, "loc": { "start": { - "line": 663, + "line": 679, "column": 6 }, "end": { - "line": 663, + "line": 679, "column": 28 }, "identifierName": "calculatedPhylorefType" @@ -34894,15 +35674,15 @@ }, "right": { "type": "StringLiteral", - "start": 26290, - "end": 26324, + "start": 26730, + "end": 26764, "loc": { "start": { - "line": 663, + "line": 679, "column": 31 }, "end": { - "line": 663, + "line": 679, "column": 65 } }, @@ -34918,15 +35698,15 @@ { "type": "CommentLine", "value": " We can't handle phyloreferences without at least one internal specifier.", - "start": 26183, - "end": 26258, + "start": 26623, + "end": 26698, "loc": { "start": { - "line": 662, + "line": 678, "column": 6 }, "end": { - "line": 662, + "line": 678, "column": 81 } } @@ -34935,58 +35715,58 @@ }, { "type": "ExpressionStatement", - "start": 26332, - "end": 26409, + "start": 26772, + "end": 26849, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 83 } }, "expression": { "type": "AssignmentExpression", - "start": 26332, - "end": 26408, + "start": 26772, + "end": 26848, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 82 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 26332, - "end": 26372, + "start": 26772, + "end": 26812, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 46 } }, "object": { "type": "Identifier", - "start": 26332, - "end": 26348, + "start": 26772, + "end": 26788, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -34995,15 +35775,15 @@ }, "property": { "type": "Identifier", - "start": 26349, - "end": 26372, + "start": 26789, + "end": 26812, "loc": { "start": { - "line": 664, + "line": 680, "column": 23 }, "end": { - "line": 664, + "line": 680, "column": 46 }, "identifierName": "malformedPhyloreference" @@ -35014,15 +35794,15 @@ }, "right": { "type": "StringLiteral", - "start": 26375, - "end": 26408, + "start": 26815, + "end": 26848, "loc": { "start": { - "line": 664, + "line": 680, "column": 49 }, "end": { - "line": 664, + "line": 680, "column": 82 } }, @@ -35039,57 +35819,57 @@ }, "alternate": { "type": "IfStatement", - "start": 26421, - "end": 28955, + "start": 26861, + "end": 29395, "loc": { "start": { - "line": 665, + "line": 681, "column": 11 }, "end": { - "line": 729, + "line": 745, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 26425, - "end": 26454, + "start": 26865, + "end": 26894, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 44 } }, "left": { "type": "MemberExpression", - "start": 26425, - "end": 26450, + "start": 26865, + "end": 26890, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 40 } }, "object": { "type": "Identifier", - "start": 26425, - "end": 26443, + "start": 26865, + "end": 26883, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 33 }, "identifierName": "externalSpecifiers" @@ -35098,15 +35878,15 @@ }, "property": { "type": "Identifier", - "start": 26444, - "end": 26450, + "start": 26884, + "end": 26890, "loc": { "start": { - "line": 665, + "line": 681, "column": 34 }, "end": { - "line": 665, + "line": 681, "column": 40 }, "identifierName": "length" @@ -35118,15 +35898,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 26453, - "end": 26454, + "start": 26893, + "end": 26894, "loc": { "start": { - "line": 665, + "line": 681, "column": 43 }, "end": { - "line": 665, + "line": 681, "column": 44 } }, @@ -35139,59 +35919,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 26456, - "end": 28577, + "start": 26896, + "end": 29017, "loc": { "start": { - "line": 665, + "line": 681, "column": 46 }, "end": { - "line": 721, + "line": 737, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 26464, - "end": 26532, + "start": 26904, + "end": 26972, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 74 } }, "expression": { "type": "AssignmentExpression", - "start": 26464, - "end": 26531, + "start": 26904, + "end": 26971, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 73 } }, "operator": "=", "left": { "type": "Identifier", - "start": 26464, - "end": 26486, + "start": 26904, + "end": 26926, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 28 }, "identifierName": "calculatedPhylorefType" @@ -35200,15 +35980,15 @@ }, "right": { "type": "StringLiteral", - "start": 26489, - "end": 26531, + "start": 26929, + "end": 26971, "loc": { "start": { - "line": 666, + "line": 682, "column": 31 }, "end": { - "line": 666, + "line": 682, "column": 73 } }, @@ -35223,15 +36003,15 @@ { "type": "CommentLine", "value": " If the phyloreference has at least one external specifier, we", - "start": 26540, - "end": 26604, + "start": 26980, + "end": 27044, "loc": { "start": { - "line": 668, + "line": 684, "column": 6 }, "end": { - "line": 668, + "line": 684, "column": 70 } } @@ -35239,15 +36019,15 @@ { "type": "CommentLine", "value": " can provide a simplified expression for the internal specifier,", - "start": 26611, - "end": 26677, + "start": 27051, + "end": 27117, "loc": { "start": { - "line": 669, + "line": 685, "column": 6 }, "end": { - "line": 669, + "line": 685, "column": 72 } } @@ -35255,15 +36035,15 @@ { "type": "CommentLine", "value": " in the form:", - "start": 26684, - "end": 26699, + "start": 27124, + "end": 27139, "loc": { "start": { - "line": 670, + "line": 686, "column": 6 }, "end": { - "line": 670, + "line": 686, "column": 21 } } @@ -35271,15 +36051,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal1] and", - "start": 26706, - "end": 26751, + "start": 27146, + "end": 27191, "loc": { "start": { - "line": 671, + "line": 687, "column": 6 }, "end": { - "line": 671, + "line": 687, "column": 51 } } @@ -35287,15 +36067,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal2] and ...", - "start": 26758, - "end": 26807, + "start": 27198, + "end": 27247, "loc": { "start": { - "line": 672, + "line": 688, "column": 6 }, "end": { - "line": 672, + "line": 688, "column": 55 } } @@ -35303,15 +36083,15 @@ { "type": "CommentLine", "value": " phyloref:excludes_TU some [exclusion1] and", - "start": 26814, - "end": 26860, + "start": 27254, + "end": 27300, "loc": { "start": { - "line": 673, + "line": 689, "column": 6 }, "end": { - "line": 673, + "line": 689, "column": 52 } } @@ -35319,15 +36099,15 @@ { "type": "CommentLine", "value": " has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...", - "start": 26867, - "end": 26932, + "start": 27307, + "end": 27372, "loc": { "start": { - "line": 674, + "line": 690, "column": 6 }, "end": { - "line": 674, + "line": 690, "column": 71 } } @@ -35335,15 +36115,15 @@ { "type": "CommentLine", "value": "", - "start": 26939, - "end": 26941, + "start": 27379, + "end": 27381, "loc": { "start": { - "line": 675, + "line": 691, "column": 6 }, "end": { - "line": 675, + "line": 691, "column": 8 } } @@ -35351,15 +36131,15 @@ { "type": "CommentLine", "value": " Since we don't know which of the external specifiers will actually", - "start": 26948, - "end": 27017, + "start": 27388, + "end": 27457, "loc": { "start": { - "line": 676, + "line": 692, "column": 6 }, "end": { - "line": 676, + "line": 692, "column": 75 } } @@ -35367,15 +36147,15 @@ { "type": "CommentLine", "value": " be the one that will be used, we need to generate logical expressions", - "start": 27024, - "end": 27096, + "start": 27464, + "end": 27536, "loc": { "start": { - "line": 677, + "line": 693, "column": 6 }, "end": { - "line": 677, + "line": 693, "column": 78 } } @@ -35383,15 +36163,15 @@ { "type": "CommentLine", "value": " for every possibility.", - "start": 27103, - "end": 27128, + "start": 27543, + "end": 27568, "loc": { "start": { - "line": 678, + "line": 694, "column": 6 }, "end": { - "line": 678, + "line": 694, "column": 31 } } @@ -35400,44 +36180,44 @@ }, { "type": "ExpressionStatement", - "start": 27136, - "end": 28571, + "start": 27576, + "end": 29011, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 720, + "line": 736, "column": 9 } }, "expression": { "type": "AssignmentExpression", - "start": 27136, - "end": 28570, + "start": 27576, + "end": 29010, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 720, + "line": 736, "column": 8 } }, "operator": "=", "left": { "type": "Identifier", - "start": 27136, - "end": 27154, + "start": 27576, + "end": 27594, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 680, + "line": 696, "column": 24 }, "identifierName": "logicalExpressions" @@ -35447,43 +36227,43 @@ }, "right": { "type": "CallExpression", - "start": 27157, - "end": 28570, + "start": 27597, + "end": 29010, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 720, + "line": 736, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 27157, - "end": 27179, + "start": 27597, + "end": 27619, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 680, + "line": 696, "column": 49 } }, "object": { "type": "Identifier", - "start": 27157, - "end": 27175, + "start": 27597, + "end": 27615, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 680, + "line": 696, "column": 45 }, "identifierName": "externalSpecifiers" @@ -35492,15 +36272,15 @@ }, "property": { "type": "Identifier", - "start": 27176, - "end": 27179, + "start": 27616, + "end": 27619, "loc": { "start": { - "line": 680, + "line": 696, "column": 46 }, "end": { - "line": 680, + "line": 696, "column": 49 }, "identifierName": "map" @@ -35512,15 +36292,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27180, - "end": 28569, + "start": 27620, + "end": 29009, "loc": { "start": { - "line": 680, + "line": 696, "column": 50 }, "end": { - "line": 720, + "line": 736, "column": 7 } }, @@ -35531,15 +36311,15 @@ "params": [ { "type": "Identifier", - "start": 27181, - "end": 27197, + "start": 27621, + "end": 27637, "loc": { "start": { - "line": 680, + "line": 696, "column": 51 }, "end": { - "line": 680, + "line": 696, "column": 67 }, "identifierName": "selectedExternal" @@ -35549,59 +36329,59 @@ ], "body": { "type": "BlockStatement", - "start": 27202, - "end": 28569, + "start": 27642, + "end": 29009, "loc": { "start": { - "line": 680, + "line": 696, "column": 72 }, "end": { - "line": 720, + "line": 736, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 27252, - "end": 27365, + "start": 27692, + "end": 27805, "loc": { "start": { - "line": 682, + "line": 698, "column": 8 }, "end": { - "line": 684, + "line": 700, "column": 10 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 27258, - "end": 27364, + "start": 27698, + "end": 27804, "loc": { "start": { - "line": 682, + "line": 698, "column": 14 }, "end": { - "line": 684, + "line": 700, "column": 9 } }, "id": { "type": "Identifier", - "start": 27258, - "end": 27275, + "start": 27698, + "end": 27715, "loc": { "start": { - "line": 682, + "line": 698, "column": 14 }, "end": { - "line": 682, + "line": 698, "column": 31 }, "identifierName": "intersectionExprs" @@ -35611,43 +36391,43 @@ }, "init": { "type": "CallExpression", - "start": 27278, - "end": 27364, + "start": 27718, + "end": 27804, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 684, + "line": 700, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 27278, - "end": 27300, + "start": 27718, + "end": 27740, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 682, + "line": 698, "column": 56 } }, "object": { "type": "Identifier", - "start": 27278, - "end": 27296, + "start": 27718, + "end": 27736, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 682, + "line": 698, "column": 52 }, "identifierName": "internalSpecifiers" @@ -35656,15 +36436,15 @@ }, "property": { "type": "Identifier", - "start": 27297, - "end": 27300, + "start": 27737, + "end": 27740, "loc": { "start": { - "line": 682, + "line": 698, "column": 53 }, "end": { - "line": 682, + "line": 698, "column": 56 }, "identifierName": "map" @@ -35676,15 +36456,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27312, - "end": 27354, + "start": 27752, + "end": 27794, "loc": { "start": { - "line": 683, + "line": 699, "column": 10 }, "end": { - "line": 683, + "line": 699, "column": 52 } }, @@ -35695,15 +36475,15 @@ "params": [ { "type": "Identifier", - "start": 27312, - "end": 27314, + "start": 27752, + "end": 27754, "loc": { "start": { - "line": 683, + "line": 699, "column": 10 }, "end": { - "line": 683, + "line": 699, "column": 12 }, "identifierName": "sp" @@ -35713,58 +36493,58 @@ ], "body": { "type": "CallExpression", - "start": 27318, - "end": 27354, + "start": 27758, + "end": 27794, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 52 } }, "callee": { "type": "MemberExpression", - "start": 27318, - "end": 27350, + "start": 27758, + "end": 27790, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 48 } }, "object": { "type": "ThisExpression", - "start": 27318, - "end": 27322, + "start": 27758, + "end": 27762, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 20 } } }, "property": { "type": "Identifier", - "start": 27323, - "end": 27350, + "start": 27763, + "end": 27790, "loc": { "start": { - "line": 683, + "line": 699, "column": 21 }, "end": { - "line": 683, + "line": 699, "column": 48 }, "identifierName": "getIncludesRestrictionForTU" @@ -35776,15 +36556,15 @@ "arguments": [ { "type": "Identifier", - "start": 27351, - "end": 27353, + "start": 27791, + "end": 27793, "loc": { "start": { - "line": 683, + "line": 699, "column": 49 }, "end": { - "line": 683, + "line": 699, "column": 51 }, "identifierName": "sp" @@ -35804,15 +36584,15 @@ { "type": "CommentLine", "value": " Add the internal specifiers.", - "start": 27212, - "end": 27243, + "start": 27652, + "end": 27683, "loc": { "start": { - "line": 681, + "line": 697, "column": 8 }, "end": { - "line": 681, + "line": 697, "column": 39 } } @@ -35822,15 +36602,15 @@ { "type": "CommentLine", "value": " Add the selected external specifier.", - "start": 27375, - "end": 27414, + "start": 27815, + "end": 27854, "loc": { "start": { - "line": 686, + "line": 702, "column": 8 }, "end": { - "line": 686, + "line": 702, "column": 47 } } @@ -35839,57 +36619,57 @@ }, { "type": "ExpressionStatement", - "start": 27423, - "end": 27688, + "start": 27863, + "end": 28128, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 694, + "line": 710, "column": 11 } }, "expression": { "type": "CallExpression", - "start": 27423, - "end": 27687, + "start": 27863, + "end": 28127, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 694, + "line": 710, "column": 10 } }, "callee": { "type": "MemberExpression", - "start": 27423, - "end": 27445, + "start": 27863, + "end": 27885, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 687, + "line": 703, "column": 30 } }, "object": { "type": "Identifier", - "start": 27423, - "end": 27440, + "start": 27863, + "end": 27880, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 687, + "line": 703, "column": 25 }, "identifierName": "intersectionExprs" @@ -35899,15 +36679,15 @@ }, "property": { "type": "Identifier", - "start": 27441, - "end": 27445, + "start": 27881, + "end": 27885, "loc": { "start": { - "line": 687, + "line": 703, "column": 26 }, "end": { - "line": 687, + "line": 703, "column": 30 }, "identifierName": "push" @@ -35920,30 +36700,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 27446, - "end": 27686, + "start": 27886, + "end": 28126, "loc": { "start": { - "line": 687, + "line": 703, "column": 31 }, "end": { - "line": 694, + "line": 710, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 27458, - "end": 27484, + "start": 27898, + "end": 27924, "loc": { "start": { - "line": 688, + "line": 704, "column": 10 }, "end": { - "line": 688, + "line": 704, "column": 36 } }, @@ -35952,15 +36732,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 27458, - "end": 27465, + "start": 27898, + "end": 27905, "loc": { "start": { - "line": 688, + "line": 704, "column": 10 }, "end": { - "line": 688, + "line": 704, "column": 17 } }, @@ -35972,15 +36752,15 @@ }, "value": { "type": "StringLiteral", - "start": 27467, - "end": 27484, + "start": 27907, + "end": 27924, "loc": { "start": { - "line": 688, + "line": 704, "column": 19 }, "end": { - "line": 688, + "line": 704, "column": 36 } }, @@ -35993,15 +36773,15 @@ }, { "type": "ObjectProperty", - "start": 27496, - "end": 27530, + "start": 27936, + "end": 27970, "loc": { "start": { - "line": 689, + "line": 705, "column": 10 }, "end": { - "line": 689, + "line": 705, "column": 44 } }, @@ -36010,15 +36790,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 27496, - "end": 27506, + "start": 27936, + "end": 27946, "loc": { "start": { - "line": 689, + "line": 705, "column": 10 }, "end": { - "line": 689, + "line": 705, "column": 20 }, "identifierName": "onProperty" @@ -36027,15 +36807,15 @@ }, "value": { "type": "StringLiteral", - "start": 27508, - "end": 27530, + "start": 27948, + "end": 27970, "loc": { "start": { - "line": 689, + "line": 705, "column": 22 }, "end": { - "line": 689, + "line": 705, "column": 44 } }, @@ -36048,15 +36828,15 @@ }, { "type": "ObjectProperty", - "start": 27542, - "end": 27675, + "start": 27982, + "end": 28115, "loc": { "start": { - "line": 690, + "line": 706, "column": 10 }, "end": { - "line": 693, + "line": 709, "column": 27 } }, @@ -36065,15 +36845,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 27542, - "end": 27556, + "start": 27982, + "end": 27996, "loc": { "start": { - "line": 690, + "line": 706, "column": 10 }, "end": { - "line": 690, + "line": 706, "column": 24 }, "identifierName": "someValuesFrom" @@ -36082,43 +36862,43 @@ }, "value": { "type": "MemberExpression", - "start": 27558, - "end": 27675, + "start": 27998, + "end": 28115, "loc": { "start": { - "line": 690, + "line": 706, "column": 26 }, "end": { - "line": 693, + "line": 709, "column": 27 } }, "object": { "type": "NewExpression", - "start": 27558, - "end": 27659, + "start": 27998, + "end": 28099, "loc": { "start": { - "line": 690, + "line": 706, "column": 26 }, "end": { - "line": 693, + "line": 709, "column": 11 } }, "callee": { "type": "Identifier", - "start": 27562, - "end": 27582, + "start": 28002, + "end": 28022, "loc": { "start": { - "line": 690, + "line": 706, "column": 30 }, "end": { - "line": 690, + "line": 706, "column": 50 }, "identifierName": "TaxonomicUnitWrapper" @@ -36128,15 +36908,15 @@ "arguments": [ { "type": "Identifier", - "start": 27596, - "end": 27612, + "start": 28036, + "end": 28052, "loc": { "start": { - "line": 691, + "line": 707, "column": 12 }, "end": { - "line": 691, + "line": 707, "column": 28 }, "identifierName": "selectedExternal" @@ -36145,44 +36925,44 @@ }, { "type": "MemberExpression", - "start": 27626, - "end": 27647, + "start": 28066, + "end": 28087, "loc": { "start": { - "line": 692, + "line": 708, "column": 12 }, "end": { - "line": 692, + "line": 708, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 27626, - "end": 27630, + "start": 28066, + "end": 28070, "loc": { "start": { - "line": 692, + "line": 708, "column": 12 }, "end": { - "line": 692, + "line": 708, "column": 16 } } }, "property": { "type": "Identifier", - "start": 27631, - "end": 27647, + "start": 28071, + "end": 28087, "loc": { "start": { - "line": 692, + "line": 708, "column": 17 }, "end": { - "line": 692, + "line": 708, "column": 33 }, "identifierName": "defaultNomenCode" @@ -36195,15 +36975,15 @@ }, "property": { "type": "Identifier", - "start": 27660, - "end": 27675, + "start": 28100, + "end": 28115, "loc": { "start": { - "line": 693, + "line": 709, "column": 12 }, "end": { - "line": 693, + "line": 709, "column": 27 }, "identifierName": "asOWLEquivClass" @@ -36222,15 +37002,15 @@ { "type": "CommentLine", "value": " Add the selected external specifier.", - "start": 27375, - "end": 27414, + "start": 27815, + "end": 27854, "loc": { "start": { - "line": 686, + "line": 702, "column": 8 }, "end": { - "line": 686, + "line": 702, "column": 47 } } @@ -36240,15 +37020,15 @@ { "type": "CommentLine", "value": " Collect all of the externals that are not selected.", - "start": 27698, - "end": 27752, + "start": 28138, + "end": 28192, "loc": { "start": { - "line": 696, + "line": 712, "column": 8 }, "end": { - "line": 696, + "line": 712, "column": 62 } } @@ -36257,44 +37037,44 @@ }, { "type": "VariableDeclaration", - "start": 27761, - "end": 27845, + "start": 28201, + "end": 28285, "loc": { "start": { - "line": 697, + "line": 713, "column": 8 }, "end": { - "line": 697, + "line": 713, "column": 92 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 27767, - "end": 27844, + "start": 28207, + "end": 28284, "loc": { "start": { - "line": 697, + "line": 713, "column": 14 }, "end": { - "line": 697, + "line": 713, "column": 91 } }, "id": { "type": "Identifier", - "start": 27767, - "end": 27785, + "start": 28207, + "end": 28225, "loc": { "start": { - "line": 697, + "line": 713, "column": 14 }, "end": { - "line": 697, + "line": 713, "column": 32 }, "identifierName": "remainingExternals" @@ -36304,43 +37084,43 @@ }, "init": { "type": "CallExpression", - "start": 27788, - "end": 27844, + "start": 28228, + "end": 28284, "loc": { "start": { - "line": 697, + "line": 713, "column": 35 }, "end": { - "line": 697, + "line": 713, "column": 91 } }, "callee": { "type": "MemberExpression", - "start": 27788, - "end": 27813, + "start": 28228, + "end": 28253, "loc": { "start": { - "line": 697, + "line": 713, "column": 35 }, "end": { - "line": 697, + "line": 713, "column": 60 } }, "object": { "type": "Identifier", - "start": 27788, - "end": 27806, + "start": 28228, + "end": 28246, "loc": { "start": { - "line": 697, + "line": 713, "column": 35 }, "end": { - "line": 697, + "line": 713, "column": 53 }, "identifierName": "externalSpecifiers" @@ -36349,15 +37129,15 @@ }, "property": { "type": "Identifier", - "start": 27807, - "end": 27813, + "start": 28247, + "end": 28253, "loc": { "start": { - "line": 697, + "line": 713, "column": 54 }, "end": { - "line": 697, + "line": 713, "column": 60 }, "identifierName": "filter" @@ -36369,15 +37149,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27814, - "end": 27843, + "start": 28254, + "end": 28283, "loc": { "start": { - "line": 697, + "line": 713, "column": 61 }, "end": { - "line": 697, + "line": 713, "column": 90 } }, @@ -36388,15 +37168,15 @@ "params": [ { "type": "Identifier", - "start": 27814, - "end": 27816, + "start": 28254, + "end": 28256, "loc": { "start": { - "line": 697, + "line": 713, "column": 61 }, "end": { - "line": 697, + "line": 713, "column": 63 }, "identifierName": "ex" @@ -36406,29 +37186,29 @@ ], "body": { "type": "BinaryExpression", - "start": 27820, - "end": 27843, + "start": 28260, + "end": 28283, "loc": { "start": { - "line": 697, + "line": 713, "column": 67 }, "end": { - "line": 697, + "line": 713, "column": 90 } }, "left": { "type": "Identifier", - "start": 27820, - "end": 27822, + "start": 28260, + "end": 28262, "loc": { "start": { - "line": 697, + "line": 713, "column": 67 }, "end": { - "line": 697, + "line": 713, "column": 69 }, "identifierName": "ex" @@ -36438,15 +37218,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 27827, - "end": 27843, + "start": 28267, + "end": 28283, "loc": { "start": { - "line": 697, + "line": 713, "column": 74 }, "end": { - "line": 697, + "line": 713, "column": 90 }, "identifierName": "selectedExternal" @@ -36465,15 +37245,15 @@ { "type": "CommentLine", "value": " Collect all of the externals that are not selected.", - "start": 27698, - "end": 27752, + "start": 28138, + "end": 28192, "loc": { "start": { - "line": 696, + "line": 712, "column": 8 }, "end": { - "line": 696, + "line": 712, "column": 62 } } @@ -36483,15 +37263,15 @@ { "type": "CommentLine", "value": " Add the remaining externals, which we assume will resolve outside of", - "start": 27855, - "end": 27926, + "start": 28295, + "end": 28366, "loc": { "start": { - "line": 699, + "line": 715, "column": 8 }, "end": { - "line": 699, + "line": 715, "column": 79 } } @@ -36499,15 +37279,15 @@ { "type": "CommentLine", "value": " this clade.", - "start": 27935, - "end": 27949, + "start": 28375, + "end": 28389, "loc": { "start": { - "line": 700, + "line": 716, "column": 8 }, "end": { - "line": 700, + "line": 716, "column": 22 } } @@ -36516,57 +37296,57 @@ }, { "type": "ExpressionStatement", - "start": 27958, - "end": 28455, + "start": 28398, + "end": 28895, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 714, + "line": 730, "column": 11 } }, "expression": { "type": "CallExpression", - "start": 27958, - "end": 28454, + "start": 28398, + "end": 28894, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 714, + "line": 730, "column": 10 } }, "callee": { "type": "MemberExpression", - "start": 27958, - "end": 27984, + "start": 28398, + "end": 28424, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 701, + "line": 717, "column": 34 } }, "object": { "type": "Identifier", - "start": 27958, - "end": 27976, + "start": 28398, + "end": 28416, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 701, + "line": 717, "column": 26 }, "identifierName": "remainingExternals" @@ -36576,15 +37356,15 @@ }, "property": { "type": "Identifier", - "start": 27977, - "end": 27984, + "start": 28417, + "end": 28424, "loc": { "start": { - "line": 701, + "line": 717, "column": 27 }, "end": { - "line": 701, + "line": 717, "column": 34 }, "identifierName": "forEach" @@ -36597,15 +37377,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27985, - "end": 28453, + "start": 28425, + "end": 28893, "loc": { "start": { - "line": 701, + "line": 717, "column": 35 }, "end": { - "line": 714, + "line": 730, "column": 9 } }, @@ -36616,15 +37396,15 @@ "params": [ { "type": "Identifier", - "start": 27986, - "end": 27996, + "start": 28426, + "end": 28436, "loc": { "start": { - "line": 701, + "line": 717, "column": 36 }, "end": { - "line": 701, + "line": 717, "column": 46 }, "identifierName": "externalTU" @@ -36634,72 +37414,72 @@ ], "body": { "type": "BlockStatement", - "start": 28001, - "end": 28453, + "start": 28441, + "end": 28893, "loc": { "start": { - "line": 701, + "line": 717, "column": 51 }, "end": { - "line": 714, + "line": 730, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 28013, - "end": 28443, + "start": 28453, + "end": 28883, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 713, + "line": 729, "column": 13 } }, "expression": { "type": "CallExpression", - "start": 28013, - "end": 28442, + "start": 28453, + "end": 28882, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 713, + "line": 729, "column": 12 } }, "callee": { "type": "MemberExpression", - "start": 28013, - "end": 28035, + "start": 28453, + "end": 28475, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 702, + "line": 718, "column": 32 } }, "object": { "type": "Identifier", - "start": 28013, - "end": 28030, + "start": 28453, + "end": 28470, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 702, + "line": 718, "column": 27 }, "identifierName": "intersectionExprs" @@ -36708,15 +37488,15 @@ }, "property": { "type": "Identifier", - "start": 28031, - "end": 28035, + "start": 28471, + "end": 28475, "loc": { "start": { - "line": 702, + "line": 718, "column": 28 }, "end": { - "line": 702, + "line": 718, "column": 32 }, "identifierName": "push" @@ -36728,30 +37508,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 28036, - "end": 28441, + "start": 28476, + "end": 28881, "loc": { "start": { - "line": 702, + "line": 718, "column": 33 }, "end": { - "line": 713, + "line": 729, "column": 11 } }, "properties": [ { "type": "ObjectProperty", - "start": 28050, - "end": 28076, + "start": 28490, + "end": 28516, "loc": { "start": { - "line": 703, + "line": 719, "column": 12 }, "end": { - "line": 703, + "line": 719, "column": 38 } }, @@ -36760,15 +37540,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 28050, - "end": 28057, + "start": 28490, + "end": 28497, "loc": { "start": { - "line": 703, + "line": 719, "column": 12 }, "end": { - "line": 703, + "line": 719, "column": 19 } }, @@ -36780,15 +37560,15 @@ }, "value": { "type": "StringLiteral", - "start": 28059, - "end": 28076, + "start": 28499, + "end": 28516, "loc": { "start": { - "line": 703, + "line": 719, "column": 21 }, "end": { - "line": 703, + "line": 719, "column": 38 } }, @@ -36801,15 +37581,15 @@ }, { "type": "ObjectProperty", - "start": 28090, - "end": 28120, + "start": 28530, + "end": 28560, "loc": { "start": { - "line": 704, + "line": 720, "column": 12 }, "end": { - "line": 704, + "line": 720, "column": 42 } }, @@ -36818,15 +37598,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28090, - "end": 28100, + "start": 28530, + "end": 28540, "loc": { "start": { - "line": 704, + "line": 720, "column": 12 }, "end": { - "line": 704, + "line": 720, "column": 22 }, "identifierName": "onProperty" @@ -36835,15 +37615,15 @@ }, "value": { "type": "StringLiteral", - "start": 28102, - "end": 28120, + "start": 28542, + "end": 28560, "loc": { "start": { - "line": 704, + "line": 720, "column": 24 }, "end": { - "line": 704, + "line": 720, "column": 42 } }, @@ -36856,15 +37636,15 @@ }, { "type": "ObjectProperty", - "start": 28150, - "end": 28428, + "start": 28590, + "end": 28868, "loc": { "start": { - "line": 705, + "line": 721, "column": 12 }, "end": { - "line": 712, + "line": 728, "column": 13 } }, @@ -36873,15 +37653,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28150, - "end": 28164, + "start": 28590, + "end": 28604, "loc": { "start": { - "line": 705, + "line": 721, "column": 12 }, "end": { - "line": 705, + "line": 721, "column": 26 }, "identifierName": "someValuesFrom" @@ -36891,30 +37671,30 @@ }, "value": { "type": "ObjectExpression", - "start": 28166, - "end": 28428, + "start": 28606, + "end": 28868, "loc": { "start": { - "line": 705, + "line": 721, "column": 28 }, "end": { - "line": 712, + "line": 728, "column": 13 } }, "properties": [ { "type": "ObjectProperty", - "start": 28182, - "end": 28208, + "start": 28622, + "end": 28648, "loc": { "start": { - "line": 706, + "line": 722, "column": 14 }, "end": { - "line": 706, + "line": 722, "column": 40 } }, @@ -36923,15 +37703,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 28182, - "end": 28189, + "start": 28622, + "end": 28629, "loc": { "start": { - "line": 706, + "line": 722, "column": 14 }, "end": { - "line": 706, + "line": 722, "column": 21 } }, @@ -36943,15 +37723,15 @@ }, "value": { "type": "StringLiteral", - "start": 28191, - "end": 28208, + "start": 28631, + "end": 28648, "loc": { "start": { - "line": 706, + "line": 722, "column": 23 }, "end": { - "line": 706, + "line": 722, "column": 40 } }, @@ -36964,15 +37744,15 @@ }, { "type": "ObjectProperty", - "start": 28224, - "end": 28258, + "start": 28664, + "end": 28698, "loc": { "start": { - "line": 707, + "line": 723, "column": 14 }, "end": { - "line": 707, + "line": 723, "column": 48 } }, @@ -36981,15 +37761,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28224, - "end": 28234, + "start": 28664, + "end": 28674, "loc": { "start": { - "line": 707, + "line": 723, "column": 14 }, "end": { - "line": 707, + "line": 723, "column": 24 }, "identifierName": "onProperty" @@ -36998,15 +37778,15 @@ }, "value": { "type": "StringLiteral", - "start": 28236, - "end": 28258, + "start": 28676, + "end": 28698, "loc": { "start": { - "line": 707, + "line": 723, "column": 26 }, "end": { - "line": 707, + "line": 723, "column": 48 } }, @@ -37019,15 +37799,15 @@ }, { "type": "ObjectProperty", - "start": 28274, - "end": 28413, + "start": 28714, + "end": 28853, "loc": { "start": { - "line": 708, + "line": 724, "column": 14 }, "end": { - "line": 711, + "line": 727, "column": 31 } }, @@ -37036,15 +37816,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28274, - "end": 28288, + "start": 28714, + "end": 28728, "loc": { "start": { - "line": 708, + "line": 724, "column": 14 }, "end": { - "line": 708, + "line": 724, "column": 28 }, "identifierName": "someValuesFrom" @@ -37053,43 +37833,43 @@ }, "value": { "type": "MemberExpression", - "start": 28290, - "end": 28413, + "start": 28730, + "end": 28853, "loc": { "start": { - "line": 708, + "line": 724, "column": 30 }, "end": { - "line": 711, + "line": 727, "column": 31 } }, "object": { "type": "NewExpression", - "start": 28290, - "end": 28397, + "start": 28730, + "end": 28837, "loc": { "start": { - "line": 708, + "line": 724, "column": 30 }, "end": { - "line": 711, + "line": 727, "column": 15 } }, "callee": { "type": "Identifier", - "start": 28294, - "end": 28314, + "start": 28734, + "end": 28754, "loc": { "start": { - "line": 708, + "line": 724, "column": 34 }, "end": { - "line": 708, + "line": 724, "column": 54 }, "identifierName": "TaxonomicUnitWrapper" @@ -37099,15 +37879,15 @@ "arguments": [ { "type": "Identifier", - "start": 28332, - "end": 28342, + "start": 28772, + "end": 28782, "loc": { "start": { - "line": 709, + "line": 725, "column": 16 }, "end": { - "line": 709, + "line": 725, "column": 26 }, "identifierName": "externalTU" @@ -37116,44 +37896,44 @@ }, { "type": "MemberExpression", - "start": 28360, - "end": 28381, + "start": 28800, + "end": 28821, "loc": { "start": { - "line": 710, + "line": 726, "column": 16 }, "end": { - "line": 710, + "line": 726, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 28360, - "end": 28364, + "start": 28800, + "end": 28804, "loc": { "start": { - "line": 710, + "line": 726, "column": 16 }, "end": { - "line": 710, + "line": 726, "column": 20 } } }, "property": { "type": "Identifier", - "start": 28365, - "end": 28381, + "start": 28805, + "end": 28821, "loc": { "start": { - "line": 710, + "line": 726, "column": 21 }, "end": { - "line": 710, + "line": 726, "column": 37 }, "identifierName": "defaultNomenCode" @@ -37166,15 +37946,15 @@ }, "property": { "type": "Identifier", - "start": 28398, - "end": 28413, + "start": 28838, + "end": 28853, "loc": { "start": { - "line": 711, + "line": 727, "column": 16 }, "end": { - "line": 711, + "line": 727, "column": 31 }, "identifierName": "asOWLEquivClass" @@ -37190,15 +37970,15 @@ { "type": "CommentLine", "value": " has_Ancestor", - "start": 28122, - "end": 28137, + "start": 28562, + "end": 28577, "loc": { "start": { - "line": 704, + "line": 720, "column": 44 }, "end": { - "line": 704, + "line": 720, "column": 59 } } @@ -37221,15 +38001,15 @@ { "type": "CommentLine", "value": " Add the remaining externals, which we assume will resolve outside of", - "start": 27855, - "end": 27926, + "start": 28295, + "end": 28366, "loc": { "start": { - "line": 699, + "line": 715, "column": 8 }, "end": { - "line": 699, + "line": 715, "column": 79 } } @@ -37237,15 +38017,15 @@ { "type": "CommentLine", "value": " this clade.", - "start": 27935, - "end": 27949, + "start": 28375, + "end": 28389, "loc": { "start": { - "line": 700, + "line": 716, "column": 8 }, "end": { - "line": 700, + "line": 716, "column": 22 } } @@ -37254,44 +38034,44 @@ }, { "type": "ReturnStatement", - "start": 28465, - "end": 28561, + "start": 28905, + "end": 29001, "loc": { "start": { - "line": 716, + "line": 732, "column": 8 }, "end": { - "line": 719, + "line": 735, "column": 10 } }, "argument": { "type": "ObjectExpression", - "start": 28472, - "end": 28560, + "start": 28912, + "end": 29000, "loc": { "start": { - "line": 716, + "line": 732, "column": 15 }, "end": { - "line": 719, + "line": 735, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 28484, - "end": 28504, + "start": 28924, + "end": 28944, "loc": { "start": { - "line": 717, + "line": 733, "column": 10 }, "end": { - "line": 717, + "line": 733, "column": 30 } }, @@ -37300,15 +38080,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 28484, - "end": 28491, + "start": 28924, + "end": 28931, "loc": { "start": { - "line": 717, + "line": 733, "column": 10 }, "end": { - "line": 717, + "line": 733, "column": 17 } }, @@ -37320,15 +38100,15 @@ }, "value": { "type": "StringLiteral", - "start": 28493, - "end": 28504, + "start": 28933, + "end": 28944, "loc": { "start": { - "line": 717, + "line": 733, "column": 19 }, "end": { - "line": 717, + "line": 733, "column": 30 } }, @@ -37341,15 +38121,15 @@ }, { "type": "ObjectProperty", - "start": 28516, - "end": 28549, + "start": 28956, + "end": 28989, "loc": { "start": { - "line": 718, + "line": 734, "column": 10 }, "end": { - "line": 718, + "line": 734, "column": 43 } }, @@ -37358,15 +38138,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28516, - "end": 28530, + "start": 28956, + "end": 28970, "loc": { "start": { - "line": 718, + "line": 734, "column": 10 }, "end": { - "line": 718, + "line": 734, "column": 24 }, "identifierName": "intersectionOf" @@ -37375,15 +38155,15 @@ }, "value": { "type": "Identifier", - "start": 28532, - "end": 28549, + "start": 28972, + "end": 28989, "loc": { "start": { - "line": 718, + "line": 734, "column": 26 }, "end": { - "line": 718, + "line": 734, "column": 43 }, "identifierName": "intersectionExprs" @@ -37406,15 +38186,15 @@ { "type": "CommentLine", "value": " If the phyloreference has at least one external specifier, we", - "start": 26540, - "end": 26604, + "start": 26980, + "end": 27044, "loc": { "start": { - "line": 668, + "line": 684, "column": 6 }, "end": { - "line": 668, + "line": 684, "column": 70 } } @@ -37422,15 +38202,15 @@ { "type": "CommentLine", "value": " can provide a simplified expression for the internal specifier,", - "start": 26611, - "end": 26677, + "start": 27051, + "end": 27117, "loc": { "start": { - "line": 669, + "line": 685, "column": 6 }, "end": { - "line": 669, + "line": 685, "column": 72 } } @@ -37438,15 +38218,15 @@ { "type": "CommentLine", "value": " in the form:", - "start": 26684, - "end": 26699, + "start": 27124, + "end": 27139, "loc": { "start": { - "line": 670, + "line": 686, "column": 6 }, "end": { - "line": 670, + "line": 686, "column": 21 } } @@ -37454,15 +38234,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal1] and", - "start": 26706, - "end": 26751, + "start": 27146, + "end": 27191, "loc": { "start": { - "line": 671, + "line": 687, "column": 6 }, "end": { - "line": 671, + "line": 687, "column": 51 } } @@ -37470,15 +38250,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal2] and ...", - "start": 26758, - "end": 26807, + "start": 27198, + "end": 27247, "loc": { "start": { - "line": 672, + "line": 688, "column": 6 }, "end": { - "line": 672, + "line": 688, "column": 55 } } @@ -37486,15 +38266,15 @@ { "type": "CommentLine", "value": " phyloref:excludes_TU some [exclusion1] and", - "start": 26814, - "end": 26860, + "start": 27254, + "end": 27300, "loc": { "start": { - "line": 673, + "line": 689, "column": 6 }, "end": { - "line": 673, + "line": 689, "column": 52 } } @@ -37502,15 +38282,15 @@ { "type": "CommentLine", "value": " has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...", - "start": 26867, - "end": 26932, + "start": 27307, + "end": 27372, "loc": { "start": { - "line": 674, + "line": 690, "column": 6 }, "end": { - "line": 674, + "line": 690, "column": 71 } } @@ -37518,15 +38298,15 @@ { "type": "CommentLine", "value": "", - "start": 26939, - "end": 26941, + "start": 27379, + "end": 27381, "loc": { "start": { - "line": 675, + "line": 691, "column": 6 }, "end": { - "line": 675, + "line": 691, "column": 8 } } @@ -37534,15 +38314,15 @@ { "type": "CommentLine", "value": " Since we don't know which of the external specifiers will actually", - "start": 26948, - "end": 27017, + "start": 27388, + "end": 27457, "loc": { "start": { - "line": 676, + "line": 692, "column": 6 }, "end": { - "line": 676, + "line": 692, "column": 75 } } @@ -37550,15 +38330,15 @@ { "type": "CommentLine", "value": " be the one that will be used, we need to generate logical expressions", - "start": 27024, - "end": 27096, + "start": 27464, + "end": 27536, "loc": { "start": { - "line": 677, + "line": 693, "column": 6 }, "end": { - "line": 677, + "line": 693, "column": 78 } } @@ -37566,15 +38346,15 @@ { "type": "CommentLine", "value": " for every possibility.", - "start": 27103, - "end": 27128, + "start": 27543, + "end": 27568, "loc": { "start": { - "line": 678, + "line": 694, "column": 6 }, "end": { - "line": 678, + "line": 694, "column": 31 } } @@ -37586,59 +38366,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 28583, - "end": 28955, + "start": 29023, + "end": 29395, "loc": { "start": { - "line": 721, + "line": 737, "column": 11 }, "end": { - "line": 729, + "line": 745, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 28591, - "end": 28659, + "start": 29031, + "end": 29099, "loc": { "start": { - "line": 722, + "line": 738, "column": 6 }, "end": { - "line": 722, + "line": 738, "column": 74 } }, "expression": { "type": "AssignmentExpression", - "start": 28591, - "end": 28658, + "start": 29031, + "end": 29098, "loc": { "start": { - "line": 722, + "line": 738, "column": 6 }, "end": { - "line": 722, + "line": 738, "column": 73 } }, "operator": "=", "left": { "type": "Identifier", - "start": 28591, - "end": 28613, + "start": 29031, + "end": 29053, "loc": { "start": { - "line": 722, + "line": 738, "column": 6 }, "end": { - "line": 722, + "line": 738, "column": 28 }, "identifierName": "calculatedPhylorefType" @@ -37647,15 +38427,15 @@ }, "right": { "type": "StringLiteral", - "start": 28616, - "end": 28658, + "start": 29056, + "end": 29098, "loc": { "start": { - "line": 722, + "line": 738, "column": 31 }, "end": { - "line": 722, + "line": 738, "column": 73 } }, @@ -37670,15 +38450,15 @@ { "type": "CommentLine", "value": " We only have internal specifiers. We therefore need to use the algorithm in", - "start": 28667, - "end": 28745, + "start": 29107, + "end": 29185, "loc": { "start": { - "line": 724, + "line": 740, "column": 6 }, "end": { - "line": 724, + "line": 740, "column": 84 } } @@ -37686,15 +38466,15 @@ { "type": "CommentLine", "value": " this.createClassExpressionsForInternals() to create this expression.", - "start": 28752, - "end": 28823, + "start": 29192, + "end": 29263, "loc": { "start": { - "line": 725, + "line": 741, "column": 6 }, "end": { - "line": 725, + "line": 741, "column": 77 } } @@ -37703,44 +38483,44 @@ }, { "type": "ExpressionStatement", - "start": 28830, - "end": 28949, + "start": 29270, + "end": 29389, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 728, + "line": 744, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 28830, - "end": 28948, + "start": 29270, + "end": 29388, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 728, + "line": 744, "column": 7 } }, "operator": "=", "left": { "type": "Identifier", - "start": 28830, - "end": 28848, + "start": 29270, + "end": 29288, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 726, + "line": 742, "column": 24 }, "identifierName": "logicalExpressions" @@ -37750,58 +38530,58 @@ }, "right": { "type": "CallExpression", - "start": 28851, - "end": 28948, + "start": 29291, + "end": 29388, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 728, + "line": 744, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 28851, - "end": 28890, + "start": 29291, + "end": 29330, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 726, + "line": 742, "column": 66 } }, "object": { "type": "ThisExpression", - "start": 28851, - "end": 28855, + "start": 29291, + "end": 29295, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 726, + "line": 742, "column": 31 } } }, "property": { "type": "Identifier", - "start": 28856, - "end": 28890, + "start": 29296, + "end": 29330, "loc": { "start": { - "line": 726, + "line": 742, "column": 32 }, "end": { - "line": 726, + "line": 742, "column": 66 }, "identifierName": "createClassExpressionsForInternals" @@ -37813,15 +38593,15 @@ "arguments": [ { "type": "Identifier", - "start": 28900, - "end": 28916, + "start": 29340, + "end": 29356, "loc": { "start": { - "line": 727, + "line": 743, "column": 8 }, "end": { - "line": 727, + "line": 743, "column": 24 }, "identifierName": "phylorefAsJSONLD" @@ -37830,15 +38610,15 @@ }, { "type": "Identifier", - "start": 28918, - "end": 28936, + "start": 29358, + "end": 29376, "loc": { "start": { - "line": 727, + "line": 743, "column": 26 }, "end": { - "line": 727, + "line": 743, "column": 44 }, "identifierName": "internalSpecifiers" @@ -37847,15 +38627,15 @@ }, { "type": "ArrayExpression", - "start": 28938, - "end": 28940, + "start": 29378, + "end": 29380, "loc": { "start": { - "line": 727, + "line": 743, "column": 46 }, "end": { - "line": 727, + "line": 743, "column": 48 } }, @@ -37869,15 +38649,15 @@ { "type": "CommentLine", "value": " We only have internal specifiers. We therefore need to use the algorithm in", - "start": 28667, - "end": 28745, + "start": 29107, + "end": 29185, "loc": { "start": { - "line": 724, + "line": 740, "column": 6 }, "end": { - "line": 724, + "line": 740, "column": 84 } } @@ -37885,15 +38665,15 @@ { "type": "CommentLine", "value": " this.createClassExpressionsForInternals() to create this expression.", - "start": 28752, - "end": 28823, + "start": 29192, + "end": 29263, "loc": { "start": { - "line": 725, + "line": 741, "column": 6 }, "end": { - "line": 725, + "line": 741, "column": 77 } } @@ -37910,15 +38690,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, we set that as an equivalentClass", - "start": 28961, - "end": 29037, + "start": 29401, + "end": 29477, "loc": { "start": { - "line": 731, + "line": 747, "column": 4 }, "end": { - "line": 731, + "line": 747, "column": 80 } } @@ -37926,15 +38706,15 @@ { "type": "CommentLine", "value": " expression. If we have more than one, we produce multiple component classes", - "start": 29042, - "end": 29120, + "start": 29482, + "end": 29560, "loc": { "start": { - "line": 732, + "line": 748, "column": 4 }, "end": { - "line": 732, + "line": 748, "column": 82 } } @@ -37942,15 +38722,15 @@ { "type": "CommentLine", "value": " to represent it.", - "start": 29125, - "end": 29144, + "start": 29565, + "end": 29584, "loc": { "start": { - "line": 733, + "line": 749, "column": 4 }, "end": { - "line": 733, + "line": 749, "column": 23 } } @@ -37959,57 +38739,57 @@ }, { "type": "IfStatement", - "start": 29149, - "end": 31520, + "start": 29589, + "end": 31960, "loc": { "start": { - "line": 734, + "line": 750, "column": 4 }, "end": { - "line": 776, + "line": 792, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 29153, - "end": 29184, + "start": 29593, + "end": 29624, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 29153, - "end": 29178, + "start": 29593, + "end": 29618, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 33 } }, "object": { "type": "Identifier", - "start": 29153, - "end": 29171, + "start": 29593, + "end": 29611, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 26 }, "identifierName": "logicalExpressions" @@ -38019,15 +38799,15 @@ }, "property": { "type": "Identifier", - "start": 29172, - "end": 29178, + "start": 29612, + "end": 29618, "loc": { "start": { - "line": 734, + "line": 750, "column": 27 }, "end": { - "line": 734, + "line": 750, "column": 33 }, "identifierName": "length" @@ -38040,15 +38820,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 29183, - "end": 29184, + "start": 29623, + "end": 29624, "loc": { "start": { - "line": 734, + "line": 750, "column": 38 }, "end": { - "line": 734, + "line": 750, "column": 39 } }, @@ -38062,44 +38842,44 @@ }, "consequent": { "type": "BlockStatement", - "start": 29186, - "end": 29779, + "start": 29626, + "end": 30219, "loc": { "start": { - "line": 734, + "line": 750, "column": 41 }, "end": { - "line": 744, + "line": 760, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 29391, - "end": 29773, + "start": 29831, + "end": 30213, "loc": { "start": { - "line": 738, + "line": 754, "column": 6 }, "end": { - "line": 743, + "line": 759, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 29395, - "end": 29444, + "start": 29835, + "end": 29884, "loc": { "start": { - "line": 738, + "line": 754, "column": 10 }, "end": { - "line": 738, + "line": 754, "column": 59 } }, @@ -38107,29 +38887,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 29396, - "end": 29444, + "start": 29836, + "end": 29884, "loc": { "start": { - "line": 738, + "line": 754, "column": 11 }, "end": { - "line": 738, + "line": 754, "column": 59 } }, "callee": { "type": "Identifier", - "start": 29396, - "end": 29399, + "start": 29836, + "end": 29839, "loc": { "start": { - "line": 738, + "line": 754, "column": 11 }, "end": { - "line": 738, + "line": 754, "column": 14 }, "identifierName": "has" @@ -38140,15 +38920,15 @@ "arguments": [ { "type": "Identifier", - "start": 29400, - "end": 29416, + "start": 29840, + "end": 29856, "loc": { "start": { - "line": 738, + "line": 754, "column": 15 }, "end": { - "line": 738, + "line": 754, "column": 31 }, "identifierName": "phylorefAsJSONLD" @@ -38157,15 +38937,15 @@ }, { "type": "StringLiteral", - "start": 29418, - "end": 29443, + "start": 29858, + "end": 29883, "loc": { "start": { - "line": 738, + "line": 754, "column": 33 }, "end": { - "line": 738, + "line": 754, "column": 58 } }, @@ -38185,58 +38965,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 29446, - "end": 29773, + "start": 29886, + "end": 30213, "loc": { "start": { - "line": 738, + "line": 754, "column": 61 }, "end": { - "line": 743, + "line": 759, "column": 7 } }, "body": [ { "type": "ThrowStatement", - "start": 29456, - "end": 29765, + "start": 29896, + "end": 30205, "loc": { "start": { - "line": 739, + "line": 755, "column": 8 }, "end": { - "line": 742, + "line": 758, "column": 10 } }, "argument": { "type": "NewExpression", - "start": 29462, - "end": 29764, + "start": 29902, + "end": 30204, "loc": { "start": { - "line": 739, + "line": 755, "column": 14 }, "end": { - "line": 742, + "line": 758, "column": 9 } }, "callee": { "type": "Identifier", - "start": 29466, - "end": 29471, + "start": 29906, + "end": 29911, "loc": { "start": { - "line": 739, + "line": 755, "column": 18 }, "end": { - "line": 739, + "line": 755, "column": 23 }, "identifierName": "Error" @@ -38246,73 +39026,73 @@ "arguments": [ { "type": "BinaryExpression", - "start": 29483, - "end": 29754, + "start": 29923, + "end": 30194, "loc": { "start": { - "line": 740, + "line": 756, "column": 10 }, "end": { - "line": 741, + "line": 757, "column": 131 } }, "left": { "type": "TemplateLiteral", - "start": 29483, - "end": 29622, + "start": 29923, + "end": 30062, "loc": { "start": { - "line": 740, + "line": 756, "column": 10 }, "end": { - "line": 740, + "line": 756, "column": 149 } }, "expressions": [ { "type": "MemberExpression", - "start": 29495, - "end": 29505, + "start": 29935, + "end": 29945, "loc": { "start": { - "line": 740, + "line": 756, "column": 22 }, "end": { - "line": 740, + "line": 756, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 29495, - "end": 29499, + "start": 29935, + "end": 29939, "loc": { "start": { - "line": 740, + "line": 756, "column": 22 }, "end": { - "line": 740, + "line": 756, "column": 26 } } }, "property": { "type": "Identifier", - "start": 29500, - "end": 29505, + "start": 29940, + "end": 29945, "loc": { "start": { - "line": 740, + "line": 756, "column": 27 }, "end": { - "line": 740, + "line": 756, "column": 32 }, "identifierName": "label" @@ -38325,15 +39105,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 29484, - "end": 29493, + "start": 29924, + "end": 29933, "loc": { "start": { - "line": 740, + "line": 756, "column": 11 }, "end": { - "line": 740, + "line": 756, "column": 20 } }, @@ -38345,15 +39125,15 @@ }, { "type": "TemplateElement", - "start": 29506, - "end": 29621, + "start": 29946, + "end": 30061, "loc": { "start": { - "line": 740, + "line": 756, "column": 33 }, "end": { - "line": 740, + "line": 756, "column": 148 } }, @@ -38368,15 +39148,15 @@ "operator": "+", "right": { "type": "StringLiteral", - "start": 29635, - "end": 29754, + "start": 30075, + "end": 30194, "loc": { "start": { - "line": 741, + "line": 757, "column": 12 }, "end": { - "line": 741, + "line": 757, "column": 131 } }, @@ -38398,15 +39178,15 @@ { "type": "CommentLine", "value": " This is fine, as long as there is an explanation in", - "start": 29194, - "end": 29248, + "start": 29634, + "end": 29688, "loc": { "start": { - "line": 735, + "line": 751, "column": 6 }, "end": { - "line": 735, + "line": 751, "column": 60 } } @@ -38414,15 +39194,15 @@ { "type": "CommentLine", "value": " phyloref.malformedPhyloreference explaining why no logical expressions", - "start": 29255, - "end": 29328, + "start": 29695, + "end": 29768, "loc": { "start": { - "line": 736, + "line": 752, "column": 6 }, "end": { - "line": 736, + "line": 752, "column": 79 } } @@ -38430,15 +39210,15 @@ { "type": "CommentLine", "value": " could be generated. Otherwise, throw an error.", - "start": 29335, - "end": 29384, + "start": 29775, + "end": 29824, "loc": { "start": { - "line": 737, + "line": 753, "column": 6 }, "end": { - "line": 737, + "line": 753, "column": 55 } } @@ -38450,57 +39230,57 @@ }, "alternate": { "type": "IfStatement", - "start": 29785, - "end": 31520, + "start": 30225, + "end": 31960, "loc": { "start": { - "line": 744, + "line": 760, "column": 11 }, "end": { - "line": 776, + "line": 792, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 29789, - "end": 29820, + "start": 30229, + "end": 30260, "loc": { "start": { - "line": 744, + "line": 760, "column": 15 }, "end": { - "line": 744, + "line": 760, "column": 46 } }, "left": { "type": "MemberExpression", - "start": 29789, - "end": 29814, + "start": 30229, + "end": 30254, "loc": { "start": { - "line": 744, + "line": 760, "column": 15 }, "end": { - "line": 744, + "line": 760, "column": 40 } }, "object": { "type": "Identifier", - "start": 29789, - "end": 29807, + "start": 30229, + "end": 30247, "loc": { "start": { - "line": 744, + "line": 760, "column": 15 }, "end": { - "line": 744, + "line": 760, "column": 33 }, "identifierName": "logicalExpressions" @@ -38509,15 +39289,15 @@ }, "property": { "type": "Identifier", - "start": 29808, - "end": 29814, + "start": 30248, + "end": 30254, "loc": { "start": { - "line": 744, + "line": 760, "column": 34 }, "end": { - "line": 744, + "line": 760, "column": 40 }, "identifierName": "length" @@ -38529,15 +39309,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 29819, - "end": 29820, + "start": 30259, + "end": 30260, "loc": { "start": { - "line": 744, + "line": 760, "column": 45 }, "end": { - "line": 744, + "line": 760, "column": 46 } }, @@ -38550,73 +39330,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 29822, - "end": 30001, + "start": 30262, + "end": 30441, "loc": { "start": { - "line": 744, + "line": 760, "column": 48 }, "end": { - "line": 748, + "line": 764, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 29938, - "end": 29995, + "start": 30378, + "end": 30435, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 63 } }, "expression": { "type": "AssignmentExpression", - "start": 29938, - "end": 29994, + "start": 30378, + "end": 30434, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 62 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 29938, - "end": 29970, + "start": 30378, + "end": 30410, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 38 } }, "object": { "type": "Identifier", - "start": 29938, - "end": 29954, + "start": 30378, + "end": 30394, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -38626,15 +39406,15 @@ }, "property": { "type": "Identifier", - "start": 29955, - "end": 29970, + "start": 30395, + "end": 30410, "loc": { "start": { - "line": 747, + "line": 763, "column": 23 }, "end": { - "line": 747, + "line": 763, "column": 38 }, "identifierName": "equivalentClass" @@ -38646,29 +39426,29 @@ }, "right": { "type": "MemberExpression", - "start": 29973, - "end": 29994, + "start": 30413, + "end": 30434, "loc": { "start": { - "line": 747, + "line": 763, "column": 41 }, "end": { - "line": 747, + "line": 763, "column": 62 } }, "object": { "type": "Identifier", - "start": 29973, - "end": 29991, + "start": 30413, + "end": 30431, "loc": { "start": { - "line": 747, + "line": 763, "column": 41 }, "end": { - "line": 747, + "line": 763, "column": 59 }, "identifierName": "logicalExpressions" @@ -38677,15 +39457,15 @@ }, "property": { "type": "NumericLiteral", - "start": 29992, - "end": 29993, + "start": 30432, + "end": 30433, "loc": { "start": { - "line": 747, + "line": 763, "column": 60 }, "end": { - "line": 747, + "line": 763, "column": 61 } }, @@ -38703,15 +39483,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, then that is what this phyloref", - "start": 29830, - "end": 29904, + "start": 30270, + "end": 30344, "loc": { "start": { - "line": 745, + "line": 761, "column": 6 }, "end": { - "line": 745, + "line": 761, "column": 80 } } @@ -38719,15 +39499,15 @@ { "type": "CommentLine", "value": " is equivalent to.", - "start": 29911, - "end": 29931, + "start": 30351, + "end": 30371, "loc": { "start": { - "line": 746, + "line": 762, "column": 6 }, "end": { - "line": 746, + "line": 762, "column": 26 } } @@ -38739,73 +39519,73 @@ }, "alternate": { "type": "BlockStatement", - "start": 30007, - "end": 31520, + "start": 30447, + "end": 31960, "loc": { "start": { - "line": 748, + "line": 764, "column": 11 }, "end": { - "line": 776, + "line": 792, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 31113, - "end": 31514, + "start": 31553, + "end": 31954, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 775, + "line": 791, "column": 9 } }, "expression": { "type": "AssignmentExpression", - "start": 31113, - "end": 31513, + "start": 31553, + "end": 31953, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 775, + "line": 791, "column": 8 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 31113, - "end": 31140, + "start": 31553, + "end": 31580, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 766, + "line": 782, "column": 33 } }, "object": { "type": "Identifier", - "start": 31113, - "end": 31129, + "start": 31553, + "end": 31569, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 766, + "line": 782, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -38815,15 +39595,15 @@ }, "property": { "type": "Identifier", - "start": 31130, - "end": 31140, + "start": 31570, + "end": 31580, "loc": { "start": { - "line": 766, + "line": 782, "column": 23 }, "end": { - "line": 766, + "line": 782, "column": 33 }, "identifierName": "subClasses" @@ -38835,43 +39615,43 @@ }, "right": { "type": "CallExpression", - "start": 31143, - "end": 31513, + "start": 31583, + "end": 31953, "loc": { "start": { - "line": 766, + "line": 782, "column": 36 }, "end": { - "line": 775, + "line": 791, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 31143, - "end": 31165, + "start": 31583, + "end": 31605, "loc": { "start": { - "line": 766, + "line": 782, "column": 36 }, "end": { - "line": 766, + "line": 782, "column": 58 } }, "object": { "type": "Identifier", - "start": 31143, - "end": 31161, + "start": 31583, + "end": 31601, "loc": { "start": { - "line": 766, + "line": 782, "column": 36 }, "end": { - "line": 766, + "line": 782, "column": 54 }, "identifierName": "logicalExpressions" @@ -38880,15 +39660,15 @@ }, "property": { "type": "Identifier", - "start": 31162, - "end": 31165, + "start": 31602, + "end": 31605, "loc": { "start": { - "line": 766, + "line": 782, "column": 55 }, "end": { - "line": 766, + "line": 782, "column": 58 }, "identifierName": "map" @@ -38900,15 +39680,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 31166, - "end": 31512, + "start": 31606, + "end": 31952, "loc": { "start": { - "line": 766, + "line": 782, "column": 59 }, "end": { - "line": 775, + "line": 791, "column": 7 } }, @@ -38919,15 +39699,15 @@ "params": [ { "type": "Identifier", - "start": 31166, - "end": 31175, + "start": 31606, + "end": 31615, "loc": { "start": { - "line": 766, + "line": 782, "column": 59 }, "end": { - "line": 766, + "line": 782, "column": 68 }, "identifierName": "classExpr" @@ -38937,58 +39717,58 @@ ], "body": { "type": "CallExpression", - "start": 31179, - "end": 31512, + "start": 31619, + "end": 31952, "loc": { "start": { - "line": 766, + "line": 782, "column": 72 }, "end": { - "line": 775, + "line": 791, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 31179, - "end": 31204, + "start": 31619, + "end": 31644, "loc": { "start": { - "line": 766, + "line": 782, "column": 72 }, "end": { - "line": 766, + "line": 782, "column": 97 } }, "object": { "type": "ThisExpression", - "start": 31179, - "end": 31183, + "start": 31619, + "end": 31623, "loc": { "start": { - "line": 766, + "line": 782, "column": 72 }, "end": { - "line": 766, + "line": 782, "column": 76 } } }, "property": { "type": "Identifier", - "start": 31184, - "end": 31204, + "start": 31624, + "end": 31644, "loc": { "start": { - "line": 766, + "line": 782, "column": 77 }, "end": { - "line": 766, + "line": 782, "column": 97 }, "identifierName": "createComponentClass" @@ -39000,15 +39780,15 @@ "arguments": [ { "type": "Identifier", - "start": 31214, - "end": 31230, + "start": 31654, + "end": 31670, "loc": { "start": { - "line": 767, + "line": 783, "column": 8 }, "end": { - "line": 767, + "line": 783, "column": 24 }, "identifierName": "phylorefAsJSONLD" @@ -39017,15 +39797,15 @@ }, { "type": "Identifier", - "start": 31240, - "end": 31258, + "start": 31680, + "end": 31698, "loc": { "start": { - "line": 768, + "line": 784, "column": 8 }, "end": { - "line": 768, + "line": 784, "column": 26 }, "identifierName": "internalSpecifiers" @@ -39034,15 +39814,15 @@ }, { "type": "Identifier", - "start": 31268, - "end": 31286, + "start": 31708, + "end": 31726, "loc": { "start": { - "line": 769, + "line": 785, "column": 8 }, "end": { - "line": 769, + "line": 785, "column": 26 }, "identifierName": "externalSpecifiers" @@ -39051,15 +39831,15 @@ }, { "type": "Identifier", - "start": 31296, - "end": 31305, + "start": 31736, + "end": 31745, "loc": { "start": { - "line": 770, + "line": 786, "column": 8 }, "end": { - "line": 770, + "line": 786, "column": 17 }, "identifierName": "classExpr" @@ -39068,15 +39848,15 @@ }, { "type": "BooleanLiteral", - "start": 31398, - "end": 31403, + "start": 31838, + "end": 31843, "loc": { "start": { - "line": 772, + "line": 788, "column": 8 }, "end": { - "line": 772, + "line": 788, "column": 13 } }, @@ -39085,15 +39865,15 @@ { "type": "CommentLine", "value": " False in order to turn off caching by internal and external specifiers.", - "start": 31315, - "end": 31389, + "start": 31755, + "end": 31829, "loc": { "start": { - "line": 771, + "line": 787, "column": 8 }, "end": { - "line": 771, + "line": 787, "column": 82 } } @@ -39102,15 +39882,15 @@ }, { "type": "Identifier", - "start": 31488, - "end": 31504, + "start": 31928, + "end": 31944, "loc": { "start": { - "line": 774, + "line": 790, "column": 8 }, "end": { - "line": 774, + "line": 790, "column": 24 }, "identifierName": "phylorefAsJSONLD" @@ -39120,15 +39900,15 @@ { "type": "CommentLine", "value": " Make the new component class a subclass of this phyloreference.", - "start": 31413, - "end": 31479, + "start": 31853, + "end": 31919, "loc": { "start": { - "line": 773, + "line": 789, "column": 8 }, "end": { - "line": 773, + "line": 789, "column": 74 } } @@ -39146,15 +39926,15 @@ { "type": "CommentLine", "value": " If we have multiple logical expressions, the phyloreference can be", - "start": 30015, - "end": 30084, + "start": 30455, + "end": 30524, "loc": { "start": { - "line": 749, + "line": 765, "column": 6 }, "end": { - "line": 749, + "line": 765, "column": 75 } } @@ -39162,15 +39942,15 @@ { "type": "CommentLine", "value": " represented by any of them. We model this by creating subclasses of", - "start": 30091, - "end": 30161, + "start": 30531, + "end": 30601, "loc": { "start": { - "line": 750, + "line": 766, "column": 6 }, "end": { - "line": 750, + "line": 766, "column": 76 } } @@ -39178,15 +39958,15 @@ { "type": "CommentLine", "value": " the phyloreference for each logical expression -- that way, it's clear", - "start": 30168, - "end": 30241, + "start": 30608, + "end": 30681, "loc": { "start": { - "line": 751, + "line": 767, "column": 6 }, "end": { - "line": 751, + "line": 767, "column": 79 } } @@ -39194,15 +39974,15 @@ { "type": "CommentLine", "value": " that these expressions aren't equivalent to each other (which is what", - "start": 30248, - "end": 30320, + "start": 30688, + "end": 30760, "loc": { "start": { - "line": 752, + "line": 768, "column": 6 }, "end": { - "line": 752, + "line": 768, "column": 78 } } @@ -39210,15 +39990,15 @@ { "type": "CommentLine", "value": " caused https://github.com/phyloref/phyx.js/issues/57), but nodes", - "start": 30327, - "end": 30394, + "start": 30767, + "end": 30834, "loc": { "start": { - "line": 753, + "line": 769, "column": 6 }, "end": { - "line": 753, + "line": 769, "column": 73 } } @@ -39226,15 +40006,15 @@ { "type": "CommentLine", "value": " resolved by any of those expressions will also be included in the", - "start": 30401, - "end": 30469, + "start": 30841, + "end": 30909, "loc": { "start": { - "line": 754, + "line": 770, "column": 6 }, "end": { - "line": 754, + "line": 770, "column": 74 } } @@ -39242,15 +40022,15 @@ { "type": "CommentLine", "value": " phyloreference itself.", - "start": 30476, - "end": 30501, + "start": 30916, + "end": 30941, "loc": { "start": { - "line": 755, + "line": 771, "column": 6 }, "end": { - "line": 755, + "line": 771, "column": 31 } } @@ -39258,15 +40038,15 @@ { "type": "CommentLine", "value": "", - "start": 30508, - "end": 30510, + "start": 30948, + "end": 30950, "loc": { "start": { - "line": 756, + "line": 772, "column": 6 }, "end": { - "line": 756, + "line": 772, "column": 8 } } @@ -39274,15 +40054,15 @@ { "type": "CommentLine", "value": " Note that there are two differences from the way in which we usually call", - "start": 30517, - "end": 30593, + "start": 30957, + "end": 31033, "loc": { "start": { - "line": 757, + "line": 773, "column": 6 }, "end": { - "line": 757, + "line": 773, "column": 82 } } @@ -39290,15 +40070,15 @@ { "type": "CommentLine", "value": " this.createComponentClass():", - "start": 30600, - "end": 30631, + "start": 31040, + "end": 31071, "loc": { "start": { - "line": 758, + "line": 774, "column": 6 }, "end": { - "line": 758, + "line": 774, "column": 37 } } @@ -39306,15 +40086,15 @@ { "type": "CommentLine", "value": " 1. Usually, createComponentClass() reuses logical expressions with the", - "start": 30638, - "end": 30712, + "start": 31078, + "end": 31152, "loc": { "start": { - "line": 759, + "line": 775, "column": 6 }, "end": { - "line": 759, + "line": 775, "column": 80 } } @@ -39322,15 +40102,15 @@ { "type": "CommentLine", "value": " same sets of internal and external specifiers. That won't work here,", - "start": 30719, - "end": 30794, + "start": 31159, + "end": 31234, "loc": { "start": { - "line": 760, + "line": 776, "column": 6 }, "end": { - "line": 760, + "line": 776, "column": 81 } } @@ -39338,15 +40118,15 @@ { "type": "CommentLine", "value": " since *all* these logical expressions have the same specifiers. So,", - "start": 30801, - "end": 30875, + "start": 31241, + "end": 31315, "loc": { "start": { - "line": 761, + "line": 777, "column": 6 }, "end": { - "line": 761, + "line": 777, "column": 80 } } @@ -39354,15 +40134,15 @@ { "type": "CommentLine", "value": " we turn off caching.", - "start": 30882, - "end": 30909, + "start": 31322, + "end": 31349, "loc": { "start": { - "line": 762, + "line": 778, "column": 6 }, "end": { - "line": 762, + "line": 778, "column": 33 } } @@ -39370,15 +40150,15 @@ { "type": "CommentLine", "value": " 2. We need to set each of these component classes to be a subclass of", - "start": 30916, - "end": 30989, + "start": 31356, + "end": 31429, "loc": { "start": { - "line": 763, + "line": 779, "column": 6 }, "end": { - "line": 763, + "line": 779, "column": 79 } } @@ -39386,15 +40166,15 @@ { "type": "CommentLine", "value": " this phyloreference so that it can include instances from each of the", - "start": 30996, - "end": 31072, + "start": 31436, + "end": 31512, "loc": { "start": { - "line": 764, + "line": 780, "column": 6 }, "end": { - "line": 764, + "line": 780, "column": 82 } } @@ -39402,15 +40182,15 @@ { "type": "CommentLine", "value": " logical expressions.", - "start": 31079, - "end": 31106, + "start": 31519, + "end": 31546, "loc": { "start": { - "line": 765, + "line": 781, "column": 6 }, "end": { - "line": 765, + "line": 781, "column": 33 } } @@ -39427,15 +40207,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, we set that as an equivalentClass", - "start": 28961, - "end": 29037, + "start": 29401, + "end": 29477, "loc": { "start": { - "line": 731, + "line": 747, "column": 4 }, "end": { - "line": 731, + "line": 747, "column": 80 } } @@ -39443,15 +40223,15 @@ { "type": "CommentLine", "value": " expression. If we have more than one, we produce multiple component classes", - "start": 29042, - "end": 29120, + "start": 29482, + "end": 29560, "loc": { "start": { - "line": 732, + "line": 748, "column": 4 }, "end": { - "line": 732, + "line": 748, "column": 82 } } @@ -39459,15 +40239,15 @@ { "type": "CommentLine", "value": " to represent it.", - "start": 29125, - "end": 29144, + "start": 29565, + "end": 29584, "loc": { "start": { - "line": 733, + "line": 749, "column": 4 }, "end": { - "line": 733, + "line": 749, "column": 23 } } @@ -39477,15 +40257,15 @@ { "type": "CommentLine", "value": " Every phyloreference is a subclass of phyloref:Phyloreference.", - "start": 31526, - "end": 31591, + "start": 31966, + "end": 32031, "loc": { "start": { - "line": 778, + "line": 794, "column": 4 }, "end": { - "line": 778, + "line": 794, "column": 69 } } @@ -39494,29 +40274,29 @@ }, { "type": "IfStatement", - "start": 31596, - "end": 31663, + "start": 32036, + "end": 32103, "loc": { "start": { - "line": 779, + "line": 795, "column": 4 }, "end": { - "line": 779, + "line": 795, "column": 71 } }, "test": { "type": "UnaryExpression", - "start": 31600, - "end": 31628, + "start": 32040, + "end": 32068, "loc": { "start": { - "line": 779, + "line": 795, "column": 8 }, "end": { - "line": 779, + "line": 795, "column": 36 } }, @@ -39524,29 +40304,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 31601, - "end": 31628, + "start": 32041, + "end": 32068, "loc": { "start": { - "line": 779, + "line": 795, "column": 9 }, "end": { - "line": 779, + "line": 795, "column": 36 } }, "object": { "type": "Identifier", - "start": 31601, - "end": 31617, + "start": 32041, + "end": 32057, "loc": { "start": { - "line": 779, + "line": 795, "column": 9 }, "end": { - "line": 779, + "line": 795, "column": 25 }, "identifierName": "phylorefAsJSONLD" @@ -39556,15 +40336,15 @@ }, "property": { "type": "Identifier", - "start": 31618, - "end": 31628, + "start": 32058, + "end": 32068, "loc": { "start": { - "line": 779, + "line": 795, "column": 26 }, "end": { - "line": 779, + "line": 795, "column": 36 }, "identifierName": "subClassOf" @@ -39581,58 +40361,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 31630, - "end": 31663, + "start": 32070, + "end": 32103, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 31630, - "end": 31662, + "start": 32070, + "end": 32102, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 31630, - "end": 31657, + "start": 32070, + "end": 32097, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 65 } }, "object": { "type": "Identifier", - "start": 31630, - "end": 31646, + "start": 32070, + "end": 32086, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 54 }, "identifierName": "phylorefAsJSONLD" @@ -39641,15 +40421,15 @@ }, "property": { "type": "Identifier", - "start": 31647, - "end": 31657, + "start": 32087, + "end": 32097, "loc": { "start": { - "line": 779, + "line": 795, "column": 55 }, "end": { - "line": 779, + "line": 795, "column": 65 }, "identifierName": "subClassOf" @@ -39660,15 +40440,15 @@ }, "right": { "type": "ArrayExpression", - "start": 31660, - "end": 31662, + "start": 32100, + "end": 32102, "loc": { "start": { - "line": 779, + "line": 795, "column": 68 }, "end": { - "line": 779, + "line": 795, "column": 70 } }, @@ -39681,15 +40461,15 @@ { "type": "CommentLine", "value": " Every phyloreference is a subclass of phyloref:Phyloreference.", - "start": 31526, - "end": 31591, + "start": 31966, + "end": 32031, "loc": { "start": { - "line": 778, + "line": 794, "column": 4 }, "end": { - "line": 778, + "line": 794, "column": 69 } } @@ -39698,29 +40478,29 @@ }, { "type": "IfStatement", - "start": 31668, - "end": 31791, + "start": 32108, + "end": 32231, "loc": { "start": { - "line": 780, + "line": 796, "column": 4 }, "end": { - "line": 782, + "line": 798, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 31672, - "end": 31715, + "start": 32112, + "end": 32155, "loc": { "start": { - "line": 780, + "line": 796, "column": 8 }, "end": { - "line": 780, + "line": 796, "column": 51 } }, @@ -39728,43 +40508,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 31673, - "end": 31715, + "start": 32113, + "end": 32155, "loc": { "start": { - "line": 780, + "line": 796, "column": 9 }, "end": { - "line": 780, + "line": 796, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 31673, - "end": 31686, + "start": 32113, + "end": 32126, "loc": { "start": { - "line": 780, + "line": 796, "column": 9 }, "end": { - "line": 780, + "line": 796, "column": 22 } }, "object": { "type": "Identifier", - "start": 31673, - "end": 31678, + "start": 32113, + "end": 32118, "loc": { "start": { - "line": 780, + "line": 796, "column": 9 }, "end": { - "line": 780, + "line": 796, "column": 14 }, "identifierName": "Array" @@ -39773,15 +40553,15 @@ }, "property": { "type": "Identifier", - "start": 31679, - "end": 31686, + "start": 32119, + "end": 32126, "loc": { "start": { - "line": 780, + "line": 796, "column": 15 }, "end": { - "line": 780, + "line": 796, "column": 22 }, "identifierName": "isArray" @@ -39793,29 +40573,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 31687, - "end": 31714, + "start": 32127, + "end": 32154, "loc": { "start": { - "line": 780, + "line": 796, "column": 23 }, "end": { - "line": 780, + "line": 796, "column": 50 } }, "object": { "type": "Identifier", - "start": 31687, - "end": 31703, + "start": 32127, + "end": 32143, "loc": { "start": { - "line": 780, + "line": 796, "column": 23 }, "end": { - "line": 780, + "line": 796, "column": 39 }, "identifierName": "phylorefAsJSONLD" @@ -39824,15 +40604,15 @@ }, "property": { "type": "Identifier", - "start": 31704, - "end": 31714, + "start": 32144, + "end": 32154, "loc": { "start": { - "line": 780, + "line": 796, "column": 40 }, "end": { - "line": 780, + "line": 796, "column": 50 }, "identifierName": "subClassOf" @@ -39849,73 +40629,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 31717, - "end": 31791, + "start": 32157, + "end": 32231, "loc": { "start": { - "line": 780, + "line": 796, "column": 53 }, "end": { - "line": 782, + "line": 798, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 31725, - "end": 31785, + "start": 32165, + "end": 32225, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 31725, - "end": 31784, + "start": 32165, + "end": 32224, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 65 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 31725, - "end": 31752, + "start": 32165, + "end": 32192, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 33 } }, "object": { "type": "Identifier", - "start": 31725, - "end": 31741, + "start": 32165, + "end": 32181, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -39924,15 +40704,15 @@ }, "property": { "type": "Identifier", - "start": 31742, - "end": 31752, + "start": 32182, + "end": 32192, "loc": { "start": { - "line": 781, + "line": 797, "column": 23 }, "end": { - "line": 781, + "line": 797, "column": 33 }, "identifierName": "subClassOf" @@ -39943,44 +40723,44 @@ }, "right": { "type": "ArrayExpression", - "start": 31755, - "end": 31784, + "start": 32195, + "end": 32224, "loc": { "start": { - "line": 781, + "line": 797, "column": 36 }, "end": { - "line": 781, + "line": 797, "column": 65 } }, "elements": [ { "type": "MemberExpression", - "start": 31756, - "end": 31783, + "start": 32196, + "end": 32223, "loc": { "start": { - "line": 781, + "line": 797, "column": 37 }, "end": { - "line": 781, + "line": 797, "column": 64 } }, "object": { "type": "Identifier", - "start": 31756, - "end": 31772, + "start": 32196, + "end": 32212, "loc": { "start": { - "line": 781, + "line": 797, "column": 37 }, "end": { - "line": 781, + "line": 797, "column": 53 }, "identifierName": "phylorefAsJSONLD" @@ -39989,15 +40769,15 @@ }, "property": { "type": "Identifier", - "start": 31773, - "end": 31783, + "start": 32213, + "end": 32223, "loc": { "start": { - "line": 781, + "line": 797, "column": 54 }, "end": { - "line": 781, + "line": 797, "column": 64 }, "identifierName": "subClassOf" @@ -40017,71 +40797,71 @@ }, { "type": "ExpressionStatement", - "start": 31796, - "end": 31856, + "start": 32236, + "end": 32296, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 64 } }, "expression": { "type": "CallExpression", - "start": 31796, - "end": 31855, + "start": 32236, + "end": 32295, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 31796, - "end": 31828, + "start": 32236, + "end": 32268, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 31796, - "end": 31823, + "start": 32236, + "end": 32263, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 31 } }, "object": { "type": "Identifier", - "start": 31796, - "end": 31812, + "start": 32236, + "end": 32252, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 20 }, "identifierName": "phylorefAsJSONLD" @@ -40090,15 +40870,15 @@ }, "property": { "type": "Identifier", - "start": 31813, - "end": 31823, + "start": 32253, + "end": 32263, "loc": { "start": { - "line": 783, + "line": 799, "column": 21 }, "end": { - "line": 783, + "line": 799, "column": 31 }, "identifierName": "subClassOf" @@ -40109,15 +40889,15 @@ }, "property": { "type": "Identifier", - "start": 31824, - "end": 31828, + "start": 32264, + "end": 32268, "loc": { "start": { - "line": 783, + "line": 799, "column": 32 }, "end": { - "line": 783, + "line": 799, "column": 36 }, "identifierName": "push" @@ -40129,15 +40909,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 31829, - "end": 31854, + "start": 32269, + "end": 32294, "loc": { "start": { - "line": 783, + "line": 799, "column": 37 }, "end": { - "line": 783, + "line": 799, "column": 62 } }, @@ -40153,15 +40933,15 @@ { "type": "CommentLine", "value": " If the this Phyloref has a phylorefType that differs from the calculated", - "start": 31862, - "end": 31937, + "start": 32302, + "end": 32377, "loc": { "start": { - "line": 785, + "line": 801, "column": 4 }, "end": { - "line": 785, + "line": 801, "column": 79 } } @@ -40169,15 +40949,15 @@ { "type": "CommentLine", "value": " phyloref type, throw an error.", - 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"line": 53, + "line": 69, "column": 46 } } @@ -42716,57 +44276,57 @@ }, { "type": "IfStatement", - "start": 1829, - "end": 1929, + "start": 2269, + "end": 2369, "loc": { "start": { - "line": 55, + "line": 71, "column": 4 }, "end": { - "line": 55, + "line": 71, "column": 104 } }, "test": { "type": "LogicalExpression", - "start": 1833, - "end": 1896, + "start": 2273, + "end": 2336, "loc": { "start": { - "line": 55, + "line": 71, "column": 8 }, "end": { - "line": 55, + "line": 71, "column": 71 } }, "left": { "type": "CallExpression", - "start": 1833, - "end": 1861, + "start": 2273, + "end": 2301, "loc": { "start": { - "line": 55, + "line": 71, "column": 8 }, "end": { - "line": 55, + "line": 71, "column": 36 } }, "callee": { "type": "Identifier", - "start": 1833, - "end": 1836, + "start": 2273, + "end": 2276, "loc": { "start": { - "line": 55, + "line": 71, "column": 8 }, "end": { - "line": 55, + "line": 71, "column": 11 }, "identifierName": "has" @@ -42776,44 +44336,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1837, - "end": 1850, + "start": 2277, + "end": 2290, "loc": { "start": { - "line": 55, + "line": 71, "column": 12 }, "end": { - "line": 55, + "line": 71, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1837, - "end": 1841, + "start": 2277, + "end": 2281, "loc": { "start": { - "line": 55, + "line": 71, "column": 12 }, "end": { - "line": 55, + "line": 71, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1842, - "end": 1850, + "start": 2282, + "end": 2290, "loc": { "start": { - "line": 55, + "line": 71, "column": 17 }, "end": { - "line": 55, + "line": 71, "column": 25 }, "identifierName": "phyloref" @@ -42824,15 +44384,15 @@ }, { "type": "StringLiteral", - "start": 1852, - "end": 1860, + "start": 2292, + "end": 2300, "loc": { "start": { - "line": 55, + "line": 71, "column": 27 }, "end": { - "line": 55, + "line": 71, "column": 35 } }, @@ -42847,86 +44407,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 1865, - "end": 1896, + "start": 2305, + "end": 2336, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 71 } }, "left": { "type": "MemberExpression", - "start": 1865, - "end": 1892, + "start": 2305, + "end": 2332, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 67 } }, "object": { "type": "MemberExpression", - "start": 1865, - "end": 1885, + "start": 2305, + "end": 2325, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 1865, - "end": 1878, + "start": 2305, + "end": 2318, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 53 } }, "object": { "type": "ThisExpression", - "start": 1865, - "end": 1869, + "start": 2305, + "end": 2309, "loc": { "start": { - "line": 55, + "line": 71, "column": 40 }, "end": { - "line": 55, + "line": 71, "column": 44 } } }, "property": { "type": "Identifier", - "start": 1870, - "end": 1878, + "start": 2310, + "end": 2318, "loc": { "start": { - "line": 55, + "line": 71, "column": 45 }, "end": { - "line": 55, + "line": 71, "column": 53 }, "identifierName": "phyloref" @@ -42937,15 +44497,15 @@ }, "property": { "type": "Identifier", - "start": 1879, - "end": 1885, + "start": 2319, + "end": 2325, "loc": { "start": { - "line": 55, + "line": 71, "column": 54 }, "end": { - "line": 55, + "line": 71, "column": 60 }, "identifierName": "labels" @@ -42956,15 +44516,15 @@ }, "property": { "type": "Identifier", - "start": 1886, - "end": 1892, + "start": 2326, + "end": 2332, "loc": { "start": { - "line": 55, + "line": 71, "column": 61 }, "end": { - "line": 55, + "line": 71, "column": 67 }, "identifierName": "length" @@ -42976,15 +44536,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 1895, - "end": 1896, + "start": 2335, + "end": 2336, "loc": { "start": { - "line": 55, + "line": 71, "column": 70 }, "end": { - "line": 55, + "line": 71, "column": 71 } }, @@ -42998,86 +44558,86 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1898, - "end": 1929, + "start": 2338, + "end": 2369, "loc": { "start": { - "line": 55, + "line": 71, "column": 73 }, "end": { - "line": 55, + "line": 71, "column": 104 } }, "argument": { "type": "MemberExpression", - "start": 1905, - "end": 1928, + "start": 2345, + "end": 2368, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 103 } }, "object": { "type": "MemberExpression", - "start": 1905, - "end": 1925, + "start": 2345, + "end": 2365, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 100 } }, "object": { "type": "MemberExpression", - "start": 1905, - "end": 1918, + "start": 2345, + "end": 2358, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 93 } }, "object": { "type": "ThisExpression", - "start": 1905, - "end": 1909, + "start": 2345, + "end": 2349, "loc": { "start": { - "line": 55, + "line": 71, "column": 80 }, "end": { - "line": 55, + "line": 71, "column": 84 } } }, "property": { "type": "Identifier", - "start": 1910, - "end": 1918, + "start": 2350, + "end": 2358, "loc": { "start": { - "line": 55, + "line": 71, "column": 85 }, "end": { - "line": 55, + "line": 71, "column": 93 }, "identifierName": "phyloref" @@ -43088,15 +44648,15 @@ }, "property": { "type": "Identifier", - "start": 1919, - "end": 1925, + "start": 2359, + "end": 2365, "loc": { "start": { - "line": 55, + "line": 71, "column": 94 }, "end": { - "line": 55, + "line": 71, "column": 100 }, "identifierName": "labels" @@ -43107,15 +44667,15 @@ }, "property": { "type": "NumericLiteral", - "start": 1926, - "end": 1927, + "start": 2366, + "end": 2367, "loc": { "start": { - "line": 55, + "line": 71, "column": 101 }, "end": { - "line": 55, + "line": 71, "column": 102 } }, @@ -43132,43 +44692,43 @@ }, { "type": "IfStatement", - "start": 1934, - "end": 1994, + "start": 2374, + "end": 2434, "loc": { "start": { - "line": 56, + "line": 72, "column": 4 }, "end": { - "line": 56, + "line": 72, "column": 64 } }, "test": { "type": "CallExpression", - "start": 1938, - "end": 1965, + "start": 2378, + "end": 2405, "loc": { "start": { - "line": 56, + "line": 72, "column": 8 }, "end": { - "line": 56, + "line": 72, "column": 35 } }, "callee": { "type": "Identifier", - "start": 1938, - "end": 1941, + "start": 2378, + "end": 2381, "loc": { "start": { - "line": 56, + "line": 72, "column": 8 }, "end": { - "line": 56, + "line": 72, "column": 11 }, "identifierName": "has" @@ -43178,44 +44738,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 1942, - "end": 1955, + "start": 2382, + "end": 2395, "loc": { "start": { - "line": 56, + "line": 72, "column": 12 }, "end": { - "line": 56, + "line": 72, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 1942, - "end": 1946, + "start": 2382, + "end": 2386, "loc": { "start": { - "line": 56, + "line": 72, "column": 12 }, "end": { - "line": 56, + "line": 72, "column": 16 } } }, "property": { "type": "Identifier", - "start": 1947, - "end": 1955, + "start": 2387, + "end": 2395, "loc": { "start": { - "line": 56, + "line": 72, "column": 17 }, "end": { - "line": 56, + "line": 72, "column": 25 }, "identifierName": "phyloref" @@ -43226,15 +44786,15 @@ }, { "type": "StringLiteral", - "start": 1957, - "end": 1964, + "start": 2397, + "end": 2404, "loc": { "start": { - "line": 56, + "line": 72, "column": 27 }, "end": { - "line": 56, + "line": 72, "column": 34 } }, @@ -43248,72 +44808,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 1967, - "end": 1994, + "start": 2407, + "end": 2434, "loc": { "start": { - "line": 56, + "line": 72, "column": 37 }, "end": { - "line": 56, + "line": 72, "column": 64 } }, "argument": { "type": "MemberExpression", - "start": 1974, - "end": 1993, + "start": 2414, + "end": 2433, "loc": { "start": { - "line": 56, + "line": 72, "column": 44 }, "end": { - "line": 56, + "line": 72, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 1974, - "end": 1987, + "start": 2414, + "end": 2427, "loc": { "start": { - "line": 56, + "line": 72, "column": 44 }, "end": { - "line": 56, + "line": 72, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 1974, - "end": 1978, + "start": 2414, + "end": 2418, "loc": { "start": { - "line": 56, + "line": 72, "column": 44 }, "end": { - "line": 56, + "line": 72, "column": 48 } } }, "property": { "type": "Identifier", - "start": 1979, - "end": 1987, + "start": 2419, + "end": 2427, "loc": { "start": { - "line": 56, + "line": 72, "column": 49 }, "end": { - "line": 56, + "line": 72, "column": 57 }, "identifierName": "phyloref" @@ -43324,15 +44884,15 @@ }, "property": { "type": "Identifier", - "start": 1988, - "end": 1993, + "start": 2428, + "end": 2433, "loc": { "start": { - "line": 56, + "line": 72, "column": 58 }, "end": { - "line": 56, + "line": 72, "column": 63 }, "identifierName": "title" @@ -43346,29 +44906,29 @@ }, { "type": "ReturnStatement", - "start": 2000, - "end": 2017, + "start": 2440, + "end": 2457, "loc": { "start": { - "line": 58, + "line": 74, "column": 4 }, "end": { - "line": 58, + "line": 74, "column": 21 } }, "argument": { "type": "Identifier", - "start": 2007, - "end": 2016, + "start": 2447, + "end": 2456, "loc": { "start": { - "line": 58, + "line": 74, "column": 11 }, "end": { - "line": 58, + "line": 74, "column": 20 }, "identifierName": "undefined" @@ -43382,15 +44942,15 @@ }, { "type": "ClassMethod", - "start": 2025, - "end": 2280, + "start": 2465, + "end": 2720, "loc": { "start": { - "line": 61, + "line": 77, "column": 2 }, "end": { - "line": 69, + "line": 85, "column": 3 } }, @@ -43398,15 +44958,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2029, - "end": 2034, + "start": 2469, + "end": 2474, "loc": { "start": { - "line": 61, + "line": 77, "column": 6 }, "end": { - "line": 61, + "line": 77, "column": 11 }, "identifierName": "label" @@ -43421,15 +44981,15 @@ "params": [ { "type": "Identifier", - "start": 2035, - "end": 2043, + "start": 2475, + "end": 2483, "loc": { "start": { - "line": 61, + "line": 77, "column": 12 }, "end": { - "line": 61, + "line": 77, "column": 20 }, "identifierName": "newLabel" @@ -43439,58 +44999,58 @@ ], "body": { "type": "BlockStatement", - "start": 2045, - "end": 2280, + "start": 2485, + "end": 2720, "loc": { "start": { - "line": 61, + "line": 77, "column": 22 }, "end": { - "line": 69, + "line": 85, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 2095, - "end": 2276, + "start": 2535, + "end": 2716, "loc": { "start": { - "line": 63, + "line": 79, "column": 4 }, "end": { - "line": 68, + "line": 84, "column": 5 } }, "test": { "type": "CallExpression", - "start": 2099, - "end": 2126, + "start": 2539, + "end": 2566, "loc": { "start": { - "line": 63, + "line": 79, "column": 8 }, "end": { - "line": 63, + "line": 79, "column": 35 } }, "callee": { "type": "Identifier", - "start": 2099, - "end": 2102, + "start": 2539, + "end": 2542, "loc": { "start": { - "line": 63, + "line": 79, "column": 8 }, "end": { - "line": 63, + "line": 79, "column": 11 }, "identifierName": "has" @@ -43501,44 +45061,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2103, - "end": 2116, + "start": 2543, + "end": 2556, "loc": { "start": { - "line": 63, + "line": 79, "column": 12 }, "end": { - "line": 63, + "line": 79, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 2103, - "end": 2107, + "start": 2543, + "end": 2547, "loc": { "start": { - "line": 63, + "line": 79, "column": 12 }, "end": { - "line": 63, + "line": 79, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2108, - "end": 2116, + "start": 2548, + "end": 2556, "loc": { "start": { - "line": 63, + "line": 79, "column": 17 }, "end": { - "line": 63, + "line": 79, "column": 25 }, "identifierName": "phyloref" @@ -43549,15 +45109,15 @@ }, { "type": "StringLiteral", - "start": 2118, - "end": 2125, + "start": 2558, + "end": 2565, "loc": { "start": { - "line": 63, + "line": 79, "column": 27 }, "end": { - "line": 63, + "line": 79, "column": 34 } }, @@ -43572,102 +45132,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 2128, - "end": 2173, + "start": 2568, + "end": 2613, "loc": { "start": { - "line": 63, + "line": 79, "column": 37 }, "end": { - "line": 65, + "line": 81, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2136, - "end": 2167, + "start": 2576, + "end": 2607, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 37 } }, "expression": { "type": "AssignmentExpression", - "start": 2136, - "end": 2166, + "start": 2576, + "end": 2606, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 36 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 2136, - "end": 2155, + "start": 2576, + "end": 2595, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 2136, - "end": 2149, + "start": 2576, + "end": 2589, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 2136, - "end": 2140, + "start": 2576, + "end": 2580, "loc": { "start": { - "line": 64, + "line": 80, "column": 6 }, "end": { - "line": 64, + "line": 80, "column": 10 } } }, "property": { "type": "Identifier", - "start": 2141, - "end": 2149, + "start": 2581, + "end": 2589, "loc": { "start": { - "line": 64, + "line": 80, "column": 11 }, "end": { - "line": 64, + "line": 80, "column": 19 }, "identifierName": "phyloref" @@ -43678,15 +45238,15 @@ }, "property": { "type": "Identifier", - "start": 2150, - "end": 2155, + "start": 2590, + "end": 2595, "loc": { "start": { - "line": 64, + "line": 80, "column": 20 }, "end": { - "line": 64, + "line": 80, "column": 25 }, "identifierName": "label" @@ -43697,15 +45257,15 @@ }, "right": { "type": "Identifier", - "start": 2158, - "end": 2166, + "start": 2598, + "end": 2606, "loc": { "start": { - "line": 64, + "line": 80, "column": 28 }, "end": { - "line": 64, + "line": 80, "column": 36 }, "identifierName": "newLabel" @@ -43719,87 +45279,87 @@ }, "alternate": { "type": "BlockStatement", - "start": 2179, - "end": 2276, + "start": 2619, + "end": 2716, "loc": { "start": { - "line": 65, + "line": 81, "column": 11 }, "end": { - "line": 68, + "line": 84, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2239, - "end": 2270, + "start": 2679, + "end": 2710, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 37 } }, "expression": { "type": "AssignmentExpression", - "start": 2239, - "end": 2269, + "start": 2679, + "end": 2709, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 36 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 2239, - "end": 2258, + "start": 2679, + "end": 2698, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 2239, - "end": 2252, + "start": 2679, + "end": 2692, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 2239, - "end": 2243, + "start": 2679, + "end": 2683, "loc": { "start": { - "line": 67, + "line": 83, "column": 6 }, "end": { - "line": 67, + "line": 83, "column": 10 } }, @@ -43807,15 +45367,15 @@ }, "property": { "type": "Identifier", - "start": 2244, - "end": 2252, + "start": 2684, + "end": 2692, "loc": { "start": { - "line": 67, + "line": 83, "column": 11 }, "end": { - "line": 67, + "line": 83, "column": 19 }, "identifierName": "phyloref" @@ -43827,15 +45387,15 @@ }, "property": { "type": "Identifier", - "start": 2253, - "end": 2258, + "start": 2693, + "end": 2698, "loc": { "start": { - "line": 67, + "line": 83, "column": 20 }, "end": { - "line": 67, + "line": 83, "column": 25 }, "identifierName": "label" @@ -43847,15 +45407,15 @@ }, "right": { "type": "Identifier", - "start": 2261, - "end": 2269, + "start": 2701, + "end": 2709, "loc": { "start": { - "line": 67, + "line": 83, "column": 28 }, "end": { - "line": 67, + "line": 83, "column": 36 }, "identifierName": "newLabel" @@ -43868,15 +45428,15 @@ { "type": "CommentLine", "value": " Vue.set(this.phyloref, 'label', newLabel);", - "start": 2187, - "end": 2232, + "start": 2627, + "end": 2672, "loc": { "start": { - "line": 66, + "line": 82, "column": 6 }, "end": { - "line": 66, + "line": 82, "column": 51 } } @@ -43890,15 +45450,15 @@ { "type": "CommentLine", "value": " Set a label for this phyloreference.", - "start": 2051, - "end": 2090, + "start": 2491, + "end": 2530, "loc": { "start": { - "line": 62, + "line": 78, "column": 4 }, "end": { - "line": 62, + "line": 78, "column": 43 } } @@ -43913,15 +45473,15 @@ { "type": "CommentBlock", "value": "* Return all the specifiers of this phyloref (if any). ", - "start": 2284, - "end": 2343, + "start": 2724, + "end": 2783, "loc": { "start": { - "line": 71, + "line": 87, "column": 2 }, "end": { - "line": 71, + "line": 87, "column": 61 } } @@ -43930,15 +45490,15 @@ }, { "type": "ClassMethod", - "start": 2346, - "end": 2675, + "start": 2786, + "end": 3115, "loc": { "start": { - "line": 72, + "line": 88, "column": 2 }, "end": { - "line": 79, + "line": 95, "column": 3 } }, @@ -43946,15 +45506,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2350, - "end": 2360, + "start": 2790, + "end": 2800, "loc": { "start": { - "line": 72, + "line": 88, "column": 6 }, "end": { - "line": 72, + "line": 88, "column": 16 }, "identifierName": "specifiers" @@ -43969,59 +45529,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 2363, - "end": 2675, + "start": 2803, + "end": 3115, "loc": { "start": { - "line": 72, + "line": 88, "column": 19 }, "end": { - "line": 79, + "line": 95, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 2546, - "end": 2587, + "start": 2986, + "end": 3027, "loc": { "start": { - "line": 76, + "line": 92, "column": 4 }, "end": { - "line": 76, + "line": 92, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2550, - "end": 2586, + "start": 2990, + "end": 3026, "loc": { "start": { - "line": 76, + "line": 92, "column": 8 }, "end": { - "line": 76, + "line": 92, "column": 44 } }, "id": { "type": "Identifier", - "start": 2550, - "end": 2560, + "start": 2990, + "end": 3000, "loc": { "start": { - "line": 76, + "line": 92, "column": 8 }, "end": { - "line": 76, + "line": 92, "column": 18 }, "identifierName": "specifiers" @@ -44031,44 +45591,44 @@ }, "init": { "type": "MemberExpression", - "start": 2563, - "end": 2586, + "start": 3003, + "end": 3026, "loc": { "start": { - "line": 76, + "line": 92, "column": 21 }, "end": { - "line": 76, + "line": 92, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 2563, - "end": 2567, + "start": 3003, + "end": 3007, "loc": { "start": { - "line": 76, + "line": 92, "column": 21 }, "end": { - "line": 76, + "line": 92, "column": 25 } } }, "property": { "type": "Identifier", - "start": 2568, - "end": 2586, + "start": 3008, + "end": 3026, "loc": { "start": { - "line": 76, + "line": 92, "column": 26 }, "end": { - "line": 76, + "line": 92, "column": 44 }, "identifierName": "internalSpecifiers" @@ -44085,15 +45645,15 @@ { "type": "CommentLine", "value": " Returns a list of all specifiers by combining the internal and external", - "start": 2369, - "end": 2443, + "start": 2809, + "end": 2883, "loc": { "start": { - "line": 73, + "line": 89, "column": 4 }, "end": { - "line": 73, + "line": 89, "column": 78 } } @@ -44101,15 +45661,15 @@ { "type": "CommentLine", "value": " specifiers into a single list, with internal specifiers before", - "start": 2448, - "end": 2513, + "start": 2888, + "end": 2953, "loc": { "start": { - "line": 74, + "line": 90, "column": 4 }, "end": { - "line": 74, + "line": 90, "column": 69 } } @@ -44117,15 +45677,15 @@ { "type": "CommentLine", "value": " external specifiers.", - "start": 2518, - "end": 2541, + "start": 2958, + "end": 2981, "loc": { "start": { - "line": 75, + "line": 91, "column": 4 }, "end": { - "line": 75, + "line": 91, "column": 27 } } @@ -44134,44 +45694,44 @@ }, { "type": "ExpressionStatement", - "start": 2592, - "end": 2648, + "start": 3032, + "end": 3088, "loc": { "start": { - "line": 77, + "line": 93, "column": 4 }, "end": { - "line": 77, + "line": 93, "column": 60 } }, "expression": { "type": "AssignmentExpression", - "start": 2592, - "end": 2647, + "start": 3032, + "end": 3087, "loc": { "start": { - "line": 77, + "line": 93, "column": 4 }, "end": { - "line": 77, + "line": 93, "column": 59 } }, "operator": "=", "left": { "type": "Identifier", - "start": 2592, - "end": 2602, + "start": 3032, + "end": 3042, "loc": { "start": { - "line": 77, + "line": 93, "column": 4 }, "end": { - "line": 77, + "line": 93, "column": 14 }, "identifierName": "specifiers" @@ -44180,43 +45740,43 @@ }, "right": { "type": "CallExpression", - "start": 2605, - "end": 2647, + "start": 3045, + "end": 3087, "loc": { "start": { - "line": 77, + "line": 93, "column": 17 }, "end": { - "line": 77, + "line": 93, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 2605, - "end": 2622, + "start": 3045, + "end": 3062, "loc": { "start": { - "line": 77, + "line": 93, "column": 17 }, "end": { - "line": 77, + "line": 93, "column": 34 } }, "object": { "type": "Identifier", - "start": 2605, - "end": 2615, + "start": 3045, + "end": 3055, "loc": { "start": { - "line": 77, + "line": 93, "column": 17 }, "end": { - "line": 77, + "line": 93, "column": 27 }, "identifierName": "specifiers" @@ -44225,15 +45785,15 @@ }, "property": { "type": "Identifier", - "start": 2616, - "end": 2622, + "start": 3056, + "end": 3062, "loc": { "start": { - "line": 77, + "line": 93, "column": 28 }, "end": { - "line": 77, + "line": 93, "column": 34 }, "identifierName": "concat" @@ -44245,44 +45805,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2623, - "end": 2646, + "start": 3063, + "end": 3086, "loc": { "start": { - "line": 77, + "line": 93, "column": 35 }, "end": { - "line": 77, + "line": 93, "column": 58 } }, "object": { "type": "ThisExpression", - "start": 2623, - "end": 2627, + "start": 3063, + "end": 3067, "loc": { "start": { - "line": 77, + "line": 93, "column": 35 }, "end": { - "line": 77, + "line": 93, "column": 39 } } }, "property": { "type": "Identifier", - "start": 2628, - "end": 2646, + "start": 3068, + "end": 3086, "loc": { "start": { - "line": 77, + "line": 93, "column": 40 }, "end": { - "line": 77, + "line": 93, "column": 58 }, "identifierName": "externalSpecifiers" @@ -44297,29 +45857,29 @@ }, { "type": "ReturnStatement", - "start": 2653, - "end": 2671, + "start": 3093, + "end": 3111, "loc": { "start": { - "line": 78, + "line": 94, "column": 4 }, "end": { - "line": 78, + "line": 94, "column": 22 } }, "argument": { "type": "Identifier", - "start": 2660, - "end": 2670, + "start": 3100, + "end": 3110, "loc": { "start": { - "line": 78, + "line": 94, "column": 11 }, "end": { - "line": 78, + "line": 94, "column": 21 }, "identifierName": "specifiers" @@ -44334,15 +45894,15 @@ { "type": "CommentBlock", "value": "* Return all the specifiers of this phyloref (if any). ", - "start": 2284, - "end": 2343, + "start": 2724, + "end": 2783, "loc": { "start": { - "line": 71, + "line": 87, "column": 2 }, "end": { - "line": 71, + "line": 87, "column": 61 } } @@ -44351,15 +45911,15 @@ }, { "type": "ClassMethod", - "start": 2679, - "end": 2998, + "start": 3119, + "end": 3438, "loc": { "start": { - "line": 81, + "line": 97, "column": 2 }, "end": { - "line": 88, + "line": 104, "column": 3 } }, @@ -44367,15 +45927,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2679, - "end": 2695, + "start": 3119, + "end": 3135, "loc": { "start": { - "line": 81, + "line": 97, "column": 2 }, "end": { - "line": 81, + "line": 97, "column": 18 }, "identifierName": "getSpecifierType" @@ -44390,15 +45950,15 @@ "params": [ { "type": "Identifier", - "start": 2696, - "end": 2705, + "start": 3136, + "end": 3145, "loc": { "start": { - "line": 81, + "line": 97, "column": 19 }, "end": { - "line": 81, + "line": 97, "column": 28 }, "identifierName": "specifier" @@ -44408,86 +45968,86 @@ ], "body": { "type": "BlockStatement", - "start": 2707, - "end": 2998, + "start": 3147, + "end": 3438, "loc": { "start": { - "line": 81, + "line": 97, "column": 30 }, "end": { - "line": 88, + "line": 104, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 2831, - "end": 2898, + "start": 3271, + "end": 3338, "loc": { "start": { - "line": 85, + "line": 101, "column": 4 }, "end": { - "line": 85, + "line": 101, "column": 71 } }, "test": { "type": "CallExpression", - "start": 2835, - "end": 2878, + "start": 3275, + "end": 3318, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 2835, - "end": 2867, + "start": 3275, + "end": 3307, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 2835, - "end": 2858, + "start": 3275, + "end": 3298, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 2835, - "end": 2839, + "start": 3275, + "end": 3279, "loc": { "start": { - "line": 85, + "line": 101, "column": 8 }, "end": { - "line": 85, + "line": 101, "column": 12 } }, @@ -44495,15 +46055,15 @@ }, "property": { "type": "Identifier", - "start": 2840, - "end": 2858, + "start": 3280, + "end": 3298, "loc": { "start": { - "line": 85, + "line": 101, "column": 13 }, "end": { - "line": 85, + "line": 101, "column": 31 }, "identifierName": "internalSpecifiers" @@ -44515,15 +46075,15 @@ }, "property": { "type": "Identifier", - "start": 2859, - "end": 2867, + "start": 3299, + "end": 3307, "loc": { "start": { - "line": 85, + "line": 101, "column": 32 }, "end": { - "line": 85, + "line": 101, "column": 40 }, "identifierName": "includes" @@ -44536,15 +46096,15 @@ "arguments": [ { "type": "Identifier", - "start": 2868, - "end": 2877, + "start": 3308, + "end": 3317, "loc": { "start": { - "line": 85, + "line": 101, "column": 41 }, "end": { - "line": 85, + "line": 101, "column": 50 }, "identifierName": "specifier" @@ -44556,29 +46116,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 2880, - "end": 2898, + "start": 3320, + "end": 3338, "loc": { "start": { - "line": 85, + "line": 101, "column": 53 }, "end": { - "line": 85, + "line": 101, "column": 71 } }, "argument": { "type": "StringLiteral", - "start": 2887, - "end": 2897, + "start": 3327, + "end": 3337, "loc": { "start": { - "line": 85, + "line": 101, "column": 60 }, "end": { - "line": 85, + "line": 101, "column": 70 } }, @@ -44594,15 +46154,15 @@ { "type": "CommentLine", "value": " For a given specifier, return a string indicating whether it is", - "start": 2713, - "end": 2779, + "start": 3153, + "end": 3219, "loc": { "start": { - "line": 82, + "line": 98, "column": 4 }, "end": { - "line": 82, + "line": 98, "column": 70 } } @@ -44610,15 +46170,15 @@ { "type": "CommentLine", "value": " an 'Internal' or 'External' specifier.", - "start": 2784, - "end": 2825, + "start": 3224, + "end": 3265, "loc": { "start": { - "line": 83, + "line": 99, "column": 4 }, "end": { - "line": 83, + "line": 99, "column": 45 } } @@ -44627,86 +46187,86 @@ }, { "type": "IfStatement", - "start": 2903, - "end": 2970, + "start": 3343, + "end": 3410, "loc": { "start": { - "line": 86, + "line": 102, "column": 4 }, "end": { - "line": 86, + "line": 102, "column": 71 } }, "test": { "type": "CallExpression", - "start": 2907, - "end": 2950, + "start": 3347, + "end": 3390, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 2907, - "end": 2939, + "start": 3347, + "end": 3379, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 2907, - "end": 2930, + "start": 3347, + "end": 3370, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 2907, - "end": 2911, + "start": 3347, + "end": 3351, "loc": { "start": { - "line": 86, + "line": 102, "column": 8 }, "end": { - "line": 86, + "line": 102, "column": 12 } } }, "property": { "type": "Identifier", - "start": 2912, - "end": 2930, + "start": 3352, + "end": 3370, "loc": { "start": { - "line": 86, + "line": 102, "column": 13 }, "end": { - "line": 86, + "line": 102, "column": 31 }, "identifierName": "externalSpecifiers" @@ -44717,15 +46277,15 @@ }, "property": { "type": "Identifier", - "start": 2931, - "end": 2939, + "start": 3371, + "end": 3379, "loc": { "start": { - "line": 86, + "line": 102, "column": 32 }, "end": { - "line": 86, + "line": 102, "column": 40 }, "identifierName": "includes" @@ -44737,15 +46297,15 @@ "arguments": [ { "type": "Identifier", - "start": 2940, - "end": 2949, + "start": 3380, + "end": 3389, "loc": { "start": { - "line": 86, + "line": 102, "column": 41 }, "end": { - "line": 86, + "line": 102, "column": 50 }, "identifierName": "specifier" @@ -44756,29 +46316,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 2952, - "end": 2970, + "start": 3392, + "end": 3410, "loc": { "start": { - "line": 86, + "line": 102, "column": 53 }, "end": { - "line": 86, + "line": 102, "column": 71 } }, "argument": { "type": "StringLiteral", - "start": 2959, - "end": 2969, + "start": 3399, + "end": 3409, "loc": { "start": { - "line": 86, + "line": 102, "column": 60 }, "end": { - "line": 86, + "line": 102, "column": 70 } }, @@ -44793,29 +46353,29 @@ }, { "type": "ReturnStatement", - "start": 2975, - "end": 2994, + "start": 3415, + "end": 3434, "loc": { "start": { - "line": 87, + "line": 103, "column": 4 }, "end": { - "line": 87, + "line": 103, "column": 23 } }, "argument": { "type": "StringLiteral", - "start": 2982, - "end": 2993, + "start": 3422, + "end": 3433, "loc": { "start": { - "line": 87, + "line": 103, "column": 11 }, "end": { - "line": 87, + "line": 103, "column": 22 } }, @@ -44832,15 +46392,15 @@ }, { "type": "ClassMethod", - "start": 3002, - "end": 4345, + "start": 3442, + "end": 4785, "loc": { "start": { - "line": 90, + "line": 106, "column": 2 }, "end": { - "line": 119, + "line": 135, "column": 3 } }, @@ -44848,15 +46408,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3002, - "end": 3018, + "start": 3442, + "end": 3458, "loc": { "start": { - "line": 90, + "line": 106, "column": 2 }, "end": { - "line": 90, + "line": 106, "column": 18 }, "identifierName": "setSpecifierType" @@ -44871,15 +46431,15 @@ "params": [ { "type": "Identifier", - "start": 3019, - "end": 3028, + "start": 3459, + "end": 3468, "loc": { "start": { - "line": 90, + "line": 106, "column": 19 }, "end": { - "line": 90, + "line": 106, "column": 28 }, "identifierName": "specifier" @@ -44888,15 +46448,15 @@ }, { "type": "Identifier", - "start": 3030, - "end": 3043, + "start": 3470, + "end": 3483, "loc": { "start": { - "line": 90, + "line": 106, "column": 30 }, "end": { - "line": 90, + "line": 106, "column": 43 }, "identifierName": "specifierType" @@ -44906,59 +46466,59 @@ ], "body": { "type": "BlockStatement", - "start": 3045, - "end": 4345, + "start": 3485, + "end": 4785, "loc": { "start": { - "line": 90, + "line": 106, "column": 45 }, "end": { - "line": 119, + "line": 135, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 3240, - "end": 3250, + "start": 3680, + "end": 3690, "loc": { "start": { - "line": 95, + "line": 111, "column": 4 }, "end": { - "line": 95, + "line": 111, "column": 14 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 3244, - "end": 3249, + "start": 3684, + "end": 3689, "loc": { "start": { - "line": 95, + "line": 111, "column": 8 }, "end": { - "line": 95, + "line": 111, "column": 13 } }, "id": { "type": "Identifier", - "start": 3244, - "end": 3249, + "start": 3684, + "end": 3689, "loc": { "start": { - "line": 95, + "line": 111, "column": 8 }, "end": { - "line": 95, + "line": 111, "column": 13 }, "identifierName": "index" @@ -44975,15 +46535,15 @@ { "type": "CommentLine", "value": " Change the type of a given specifier. To do this, we first need", - "start": 3051, - "end": 3117, + "start": 3491, + "end": 3557, "loc": { "start": { - "line": 91, + "line": 107, "column": 4 }, "end": { - "line": 91, + "line": 107, "column": 70 } } @@ -44991,15 +46551,15 @@ { "type": "CommentLine", "value": " to determine if it was originally an internal or external", - "start": 3122, - "end": 3182, + "start": 3562, + "end": 3622, "loc": { "start": { - "line": 92, + "line": 108, "column": 4 }, "end": { - "line": 92, + "line": 108, "column": 64 } } @@ -45007,15 +46567,15 @@ { "type": "CommentLine", "value": " specifier, then move it into the other list.", - "start": 3187, - "end": 3234, + "start": 3627, + "end": 3674, "loc": { "start": { - "line": 93, + "line": 109, "column": 4 }, "end": { - "line": 93, + "line": 109, "column": 51 } } @@ -45024,43 +46584,43 @@ }, { "type": "IfStatement", - "start": 3255, - "end": 4341, + "start": 3695, + "end": 4781, "loc": { "start": { - "line": 96, + "line": 112, "column": 4 }, "end": { - "line": 118, + "line": 134, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 3259, - "end": 3287, + "start": 3699, + "end": 3727, "loc": { "start": { - "line": 96, + "line": 112, "column": 8 }, "end": { - "line": 96, + "line": 112, "column": 36 } }, "left": { "type": "Identifier", - "start": 3259, - "end": 3272, + "start": 3699, + "end": 3712, "loc": { "start": { - "line": 96, + "line": 112, "column": 8 }, "end": { - "line": 96, + "line": 112, "column": 21 }, "identifierName": "specifierType" @@ -45070,15 +46630,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 3277, - "end": 3287, + "start": 3717, + "end": 3727, "loc": { "start": { - "line": 96, + "line": 112, "column": 26 }, "end": { - "line": 96, + "line": 112, "column": 36 } }, @@ -45091,59 +46651,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 3289, - "end": 3751, + "start": 3729, + "end": 4191, "loc": { "start": { - "line": 96, + "line": 112, "column": 38 }, "end": { - "line": 106, + "line": 122, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3420, - "end": 3471, + "start": 3860, + "end": 3911, "loc": { "start": { - "line": 99, + "line": 115, "column": 6 }, "end": { - "line": 99, + "line": 115, "column": 57 } }, "expression": { "type": "AssignmentExpression", - "start": 3420, - "end": 3470, + "start": 3860, + "end": 3910, "loc": { "start": { - "line": 99, + "line": 115, "column": 6 }, "end": { - "line": 99, + "line": 115, "column": 56 } }, "operator": "=", "left": { "type": "Identifier", - "start": 3420, - "end": 3425, + "start": 3860, + "end": 3865, "loc": { "start": { - "line": 99, + "line": 115, "column": 6 }, "end": { - "line": 99, + "line": 115, "column": 11 }, "identifierName": "index" @@ -45153,72 +46713,72 @@ }, "right": { "type": "CallExpression", - "start": 3428, - "end": 3470, + "start": 3868, + "end": 3910, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 56 } }, "callee": { "type": "MemberExpression", - "start": 3428, - "end": 3459, + "start": 3868, + "end": 3899, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 45 } }, "object": { "type": "MemberExpression", - "start": 3428, - "end": 3451, + "start": 3868, + "end": 3891, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 3428, - "end": 3432, + "start": 3868, + "end": 3872, "loc": { "start": { - "line": 99, + "line": 115, "column": 14 }, "end": { - "line": 99, + "line": 115, "column": 18 } } }, "property": { "type": "Identifier", - "start": 3433, - "end": 3451, + "start": 3873, + "end": 3891, "loc": { "start": { - "line": 99, + "line": 115, "column": 19 }, "end": { - "line": 99, + "line": 115, "column": 37 }, "identifierName": "externalSpecifiers" @@ -45229,15 +46789,15 @@ }, "property": { "type": "Identifier", - "start": 3452, - "end": 3459, + "start": 3892, + "end": 3899, "loc": { "start": { - "line": 99, + "line": 115, "column": 38 }, "end": { - "line": 99, + "line": 115, "column": 45 }, "identifierName": "indexOf" @@ -45249,15 +46809,15 @@ "arguments": [ { "type": "Identifier", - "start": 3460, - "end": 3469, + "start": 3900, + "end": 3909, "loc": { "start": { - "line": 99, + "line": 115, "column": 46 }, "end": { - "line": 99, + "line": 115, "column": 55 }, "identifierName": "specifier" @@ -45272,15 +46832,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'Internal', we might need to delete it from the", - "start": 3297, - "end": 3369, + "start": 3737, + "end": 3809, "loc": { "start": { - "line": 97, + "line": 113, "column": 6 }, "end": { - "line": 97, + "line": 113, "column": 78 } } @@ -45288,15 +46848,15 @@ { "type": "CommentLine", "value": " list of external specifiers first.", - "start": 3376, - "end": 3413, + "start": 3816, + "end": 3853, "loc": { "start": { - "line": 98, + "line": 114, "column": 6 }, "end": { - "line": 98, + "line": 114, "column": 43 } } @@ -45305,43 +46865,43 @@ }, { "type": "IfStatement", - "start": 3478, - "end": 3537, + "start": 3918, + "end": 3977, "loc": { "start": { - "line": 100, + "line": 116, "column": 6 }, "end": { - "line": 100, + "line": 116, "column": 65 } }, "test": { "type": "BinaryExpression", - "start": 3482, - "end": 3494, + "start": 3922, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 10 }, "end": { - "line": 100, + "line": 116, "column": 22 } }, "left": { "type": "Identifier", - "start": 3482, - "end": 3487, + "start": 3922, + "end": 3927, "loc": { "start": { - "line": 100, + "line": 116, "column": 10 }, "end": { - "line": 100, + "line": 116, "column": 15 }, "identifierName": "index" @@ -45351,15 +46911,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 3492, - "end": 3494, + "start": 3932, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 20 }, "end": { - "line": 100, + "line": 116, "column": 22 } }, @@ -45367,15 +46927,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 3493, - "end": 3494, + "start": 3933, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 21 }, "end": { - "line": 100, + "line": 116, "column": 22 } }, @@ -45392,86 +46952,86 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 3496, - "end": 3537, + "start": 3936, + "end": 3977, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 65 } }, "expression": { "type": "CallExpression", - "start": 3496, - "end": 3536, + "start": 3936, + "end": 3976, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 64 } }, "callee": { "type": "MemberExpression", - "start": 3496, - "end": 3526, + "start": 3936, + "end": 3966, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 3496, - "end": 3519, + "start": 3936, + "end": 3959, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 3496, - "end": 3500, + "start": 3936, + "end": 3940, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 28 } } }, "property": { "type": "Identifier", - "start": 3501, - "end": 3519, + "start": 3941, + "end": 3959, "loc": { "start": { - "line": 100, + "line": 116, "column": 29 }, "end": { - "line": 100, + "line": 116, "column": 47 }, "identifierName": "externalSpecifiers" @@ -45482,15 +47042,15 @@ }, "property": { "type": "Identifier", - "start": 3520, - "end": 3526, + "start": 3960, + "end": 3966, "loc": { "start": { - "line": 100, + "line": 116, "column": 48 }, "end": { - "line": 100, + "line": 116, "column": 54 }, "identifierName": "splice" @@ -45502,15 +47062,15 @@ "arguments": [ { "type": "Identifier", - "start": 3527, - "end": 3532, + "start": 3967, + "end": 3972, "loc": { "start": { - "line": 100, + "line": 116, "column": 55 }, "end": { - "line": 100, + "line": 116, "column": 60 }, "identifierName": "index" @@ -45519,15 +47079,15 @@ }, { "type": "NumericLiteral", - "start": 3534, - "end": 3535, + "start": 3974, + "end": 3975, "loc": { "start": { - "line": 100, + "line": 116, "column": 62 }, "end": { - "line": 100, + "line": 116, "column": 63 } }, @@ -45546,15 +47106,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 3545, - "end": 3618, + "start": 3985, + "end": 4058, "loc": { "start": { - "line": 102, + "line": 118, "column": 6 }, "end": { - "line": 102, + "line": 118, "column": 79 } } @@ -45563,29 +47123,29 @@ }, { "type": "IfStatement", - "start": 3625, - "end": 3745, + "start": 4065, + "end": 4185, "loc": { "start": { - "line": 103, + "line": 119, "column": 6 }, "end": { - "line": 105, + "line": 121, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 3629, - "end": 3673, + "start": 4069, + "end": 4113, "loc": { "start": { - "line": 103, + "line": 119, "column": 10 }, "end": { - "line": 103, + "line": 119, "column": 54 } }, @@ -45593,57 +47153,57 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 3630, - "end": 3673, + "start": 4070, + "end": 4113, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 54 } }, "callee": { "type": "MemberExpression", - "start": 3630, - "end": 3662, + "start": 4070, + "end": 4102, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 43 } }, "object": { "type": "MemberExpression", - "start": 3630, - "end": 3653, + "start": 4070, + "end": 4093, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 34 } }, "object": { "type": "ThisExpression", - "start": 3630, - "end": 3634, + "start": 4070, + "end": 4074, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 15 } }, @@ -45651,15 +47211,15 @@ }, "property": { "type": "Identifier", - "start": 3635, - "end": 3653, + "start": 4075, + "end": 4093, "loc": { "start": { - "line": 103, + "line": 119, "column": 16 }, "end": { - "line": 103, + "line": 119, "column": 34 }, "identifierName": "internalSpecifiers" @@ -45671,15 +47231,15 @@ }, "property": { "type": "Identifier", - "start": 3654, - "end": 3662, + "start": 4094, + "end": 4102, "loc": { "start": { - "line": 103, + "line": 119, "column": 35 }, "end": { - "line": 103, + "line": 119, "column": 43 }, "identifierName": "includes" @@ -45692,15 +47252,15 @@ "arguments": [ { "type": "Identifier", - "start": 3663, - "end": 3672, + "start": 4103, + "end": 4112, "loc": { "start": { - "line": 103, + "line": 119, "column": 44 }, "end": { - "line": 103, + "line": 119, "column": 53 }, "identifierName": "specifier" @@ -45717,115 +47277,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 3675, - "end": 3745, + "start": 4115, + "end": 4185, "loc": { "start": { - "line": 103, + "line": 119, "column": 56 }, "end": { - "line": 105, + "line": 121, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 3685, - "end": 3737, + "start": 4125, + "end": 4177, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 60 } }, "expression": { "type": "CallExpression", - "start": 3685, - "end": 3736, + "start": 4125, + "end": 4176, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 3685, - "end": 3725, + "start": 4125, + "end": 4165, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 48 } }, "object": { "type": "MemberExpression", - "start": 3685, - "end": 3717, + "start": 4125, + "end": 4157, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 3685, - "end": 3698, + "start": 4125, + "end": 4138, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 21 } }, "object": { "type": "ThisExpression", - "start": 3685, - "end": 3689, + "start": 4125, + "end": 4129, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 12 } } }, "property": { "type": "Identifier", - "start": 3690, - "end": 3698, + "start": 4130, + "end": 4138, "loc": { "start": { - "line": 104, + "line": 120, "column": 13 }, "end": { - "line": 104, + "line": 120, "column": 21 }, "identifierName": "phyloref" @@ -45836,15 +47396,15 @@ }, "property": { "type": "Identifier", - "start": 3699, - "end": 3717, + "start": 4139, + "end": 4157, "loc": { "start": { - "line": 104, + "line": 120, "column": 22 }, "end": { - "line": 104, + "line": 120, "column": 40 }, "identifierName": "internalSpecifiers" @@ -45855,15 +47415,15 @@ }, "property": { "type": "Identifier", - "start": 3718, - "end": 3725, + "start": 4158, + "end": 4165, "loc": { "start": { - "line": 104, + "line": 120, "column": 41 }, "end": { - "line": 104, + "line": 120, "column": 48 }, "identifierName": "unshift" @@ -45875,15 +47435,15 @@ "arguments": [ { "type": "Identifier", - "start": 3726, - "end": 3735, + "start": 4166, + "end": 4175, "loc": { "start": { - "line": 104, + "line": 120, "column": 49 }, "end": { - "line": 104, + "line": 120, "column": 58 }, "identifierName": "specifier" @@ -45901,15 +47461,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 3545, - "end": 3618, + "start": 3985, + "end": 4058, "loc": { "start": { - "line": 102, + "line": 118, "column": 6 }, "end": { - "line": 102, + "line": 118, "column": 79 } } @@ -45921,43 +47481,43 @@ }, "alternate": { "type": "IfStatement", - "start": 3757, - "end": 4341, + "start": 4197, + "end": 4781, "loc": { "start": { - "line": 106, + "line": 122, "column": 11 }, "end": { - "line": 118, + "line": 134, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 3761, - "end": 3789, + "start": 4201, + "end": 4229, "loc": { "start": { - "line": 106, + "line": 122, "column": 15 }, "end": { - "line": 106, + "line": 122, "column": 43 } }, "left": { "type": "Identifier", - "start": 3761, - "end": 3774, + "start": 4201, + "end": 4214, "loc": { "start": { - "line": 106, + "line": 122, "column": 15 }, "end": { - "line": 106, + "line": 122, "column": 28 }, "identifierName": "specifierType" @@ -45967,15 +47527,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 3779, - "end": 3789, + "start": 4219, + "end": 4229, "loc": { "start": { - "line": 106, + "line": 122, "column": 33 }, "end": { - "line": 106, + "line": 122, "column": 43 } }, @@ -45988,59 +47548,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 3791, - "end": 4280, + "start": 4231, + "end": 4720, "loc": { "start": { - "line": 106, + "line": 122, "column": 45 }, "end": { - "line": 116, + "line": 132, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3922, - "end": 3982, + "start": 4362, + "end": 4422, "loc": { "start": { - "line": 109, + "line": 125, "column": 6 }, "end": { - "line": 109, + "line": 125, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 3922, - "end": 3981, + "start": 4362, + "end": 4421, "loc": { "start": { - "line": 109, + "line": 125, "column": 6 }, "end": { - "line": 109, + "line": 125, "column": 65 } }, "operator": "=", "left": { "type": "Identifier", - "start": 3922, - "end": 3927, + "start": 4362, + "end": 4367, "loc": { "start": { - "line": 109, + "line": 125, "column": 6 }, "end": { - "line": 109, + "line": 125, "column": 11 }, "identifierName": "index" @@ -46050,86 +47610,86 @@ }, "right": { "type": "CallExpression", - "start": 3930, - "end": 3981, + "start": 4370, + "end": 4421, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 3930, - "end": 3970, + "start": 4370, + "end": 4410, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 3930, - "end": 3962, + "start": 4370, + "end": 4402, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 46 } }, "object": { "type": "MemberExpression", - "start": 3930, - "end": 3943, + "start": 4370, + "end": 4383, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 3930, - "end": 3934, + "start": 4370, + "end": 4374, "loc": { "start": { - "line": 109, + "line": 125, "column": 14 }, "end": { - "line": 109, + "line": 125, "column": 18 } } }, "property": { "type": "Identifier", - "start": 3935, - "end": 3943, + "start": 4375, + "end": 4383, "loc": { "start": { - "line": 109, + "line": 125, "column": 19 }, "end": { - "line": 109, + "line": 125, "column": 27 }, "identifierName": "phyloref" @@ -46140,15 +47700,15 @@ }, "property": { "type": "Identifier", - "start": 3944, - "end": 3962, + "start": 4384, + "end": 4402, "loc": { "start": { - "line": 109, + "line": 125, "column": 28 }, "end": { - "line": 109, + "line": 125, "column": 46 }, "identifierName": "internalSpecifiers" @@ -46159,15 +47719,15 @@ }, "property": { "type": "Identifier", - "start": 3963, - "end": 3970, + "start": 4403, + "end": 4410, "loc": { "start": { - "line": 109, + "line": 125, "column": 47 }, "end": { - "line": 109, + "line": 125, "column": 54 }, "identifierName": "indexOf" @@ -46179,15 +47739,15 @@ "arguments": [ { "type": "Identifier", - "start": 3971, - "end": 3980, + "start": 4411, + "end": 4420, "loc": { "start": { - "line": 109, + "line": 125, "column": 55 }, "end": { - "line": 109, + "line": 125, "column": 64 }, "identifierName": "specifier" @@ -46202,15 +47762,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'External', we might need to delete it from the", - "start": 3799, - "end": 3871, + "start": 4239, + "end": 4311, "loc": { "start": { - "line": 107, + "line": 123, "column": 6 }, "end": { - "line": 107, + "line": 123, "column": 78 } } @@ -46218,15 +47778,15 @@ { "type": "CommentLine", "value": " list of internal specifiers first.", - "start": 3878, - "end": 3915, + "start": 4318, + "end": 4355, "loc": { "start": { - "line": 108, + "line": 124, "column": 6 }, "end": { - "line": 108, + "line": 124, "column": 43 } } @@ -46235,43 +47795,43 @@ }, { "type": "IfStatement", - "start": 3989, - "end": 4057, + "start": 4429, + "end": 4497, "loc": { "start": { - "line": 110, + "line": 126, "column": 6 }, "end": { - "line": 110, + "line": 126, "column": 74 } }, "test": { "type": "BinaryExpression", - "start": 3993, - "end": 4005, + "start": 4433, + "end": 4445, "loc": { "start": { - "line": 110, + "line": 126, "column": 10 }, "end": { - "line": 110, + "line": 126, "column": 22 } }, "left": { "type": "Identifier", - "start": 3993, - "end": 3998, + "start": 4433, + "end": 4438, "loc": { "start": { - "line": 110, + "line": 126, "column": 10 }, "end": { - "line": 110, + "line": 126, "column": 15 }, "identifierName": "index" @@ -46281,15 +47841,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 4003, - "end": 4005, + "start": 4443, + "end": 4445, "loc": { "start": { - "line": 110, + "line": 126, "column": 20 }, "end": { - "line": 110, + "line": 126, "column": 22 } }, @@ -46297,15 +47857,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 4004, - "end": 4005, + "start": 4444, + "end": 4445, "loc": { "start": { - "line": 110, + "line": 126, "column": 21 }, "end": { - "line": 110, + "line": 126, "column": 22 } }, @@ -46322,100 +47882,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 4007, - "end": 4057, + "start": 4447, + "end": 4497, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 74 } }, "expression": { "type": "CallExpression", - "start": 4007, - "end": 4056, + "start": 4447, + "end": 4496, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 4007, - "end": 4046, + "start": 4447, + "end": 4486, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 4007, - "end": 4039, + "start": 4447, + "end": 4479, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 56 } }, "object": { "type": "MemberExpression", - "start": 4007, - "end": 4020, + "start": 4447, + "end": 4460, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 4007, - "end": 4011, + "start": 4447, + "end": 4451, "loc": { "start": { - "line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 28 } } }, "property": { "type": "Identifier", - "start": 4012, - "end": 4020, + "start": 4452, + "end": 4460, "loc": { "start": { - "line": 110, + "line": 126, "column": 29 }, "end": { - "line": 110, + "line": 126, "column": 37 }, "identifierName": "phyloref" @@ -46426,15 +47986,15 @@ }, "property": { "type": "Identifier", - "start": 4021, - "end": 4039, + "start": 4461, + "end": 4479, "loc": { "start": { - "line": 110, + "line": 126, "column": 38 }, "end": { - "line": 110, + "line": 126, "column": 56 }, "identifierName": "internalSpecifiers" @@ -46445,15 +48005,15 @@ }, "property": { "type": "Identifier", - "start": 4040, - "end": 4046, + "start": 4480, + "end": 4486, "loc": { "start": { - "line": 110, + "line": 126, "column": 57 }, "end": { - "line": 110, + "line": 126, "column": 63 }, "identifierName": "splice" @@ -46465,15 +48025,15 @@ "arguments": [ { "type": "Identifier", - "start": 4047, - "end": 4052, + "start": 4487, + "end": 4492, "loc": { "start": { - "line": 110, + "line": 126, "column": 64 }, "end": { - "line": 110, + "line": 126, "column": 69 }, "identifierName": "index" @@ -46482,15 +48042,15 @@ }, { "type": "NumericLiteral", - "start": 4054, - "end": 4055, + "start": 4494, + "end": 4495, "loc": { "start": { - "line": 110, + "line": 126, "column": 71 }, "end": { - "line": 110, + "line": 126, "column": 72 } }, @@ -46509,15 +48069,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 4065, - "end": 4138, + "start": 4505, + "end": 4578, "loc": { "start": { - "line": 112, + "line": 128, "column": 6 }, "end": { - "line": 112, + "line": 128, "column": 79 } } @@ -46526,29 +48086,29 @@ }, { "type": "IfStatement", - "start": 4145, - "end": 4274, + "start": 4585, + "end": 4714, "loc": { "start": { - "line": 113, + "line": 129, "column": 6 }, "end": { - "line": 115, + "line": 131, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 4149, - "end": 4202, + "start": 4589, + "end": 4642, "loc": { "start": { - "line": 113, + "line": 129, "column": 10 }, "end": { - "line": 113, + "line": 129, "column": 63 } }, @@ -46556,71 +48116,71 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 4150, - "end": 4202, + "start": 4590, + "end": 4642, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 4150, - "end": 4191, + "start": 4590, + "end": 4631, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 4150, - "end": 4182, + "start": 4590, + "end": 4622, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 43 } }, "object": { "type": "MemberExpression", - "start": 4150, - "end": 4163, + "start": 4590, + "end": 4603, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 24 } }, "object": { "type": "ThisExpression", - "start": 4150, - "end": 4154, + "start": 4590, + "end": 4594, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 15 } }, @@ -46628,15 +48188,15 @@ }, "property": { "type": "Identifier", - "start": 4155, - "end": 4163, + "start": 4595, + "end": 4603, "loc": { "start": { - "line": 113, + "line": 129, "column": 16 }, "end": { - "line": 113, + "line": 129, "column": 24 }, "identifierName": "phyloref" @@ -46648,15 +48208,15 @@ }, "property": { "type": "Identifier", - "start": 4164, - "end": 4182, + "start": 4604, + "end": 4622, "loc": { "start": { - "line": 113, + "line": 129, "column": 25 }, "end": { - "line": 113, + "line": 129, "column": 43 }, "identifierName": "externalSpecifiers" @@ -46668,15 +48228,15 @@ }, "property": { "type": "Identifier", - "start": 4183, - "end": 4191, + "start": 4623, + "end": 4631, "loc": { "start": { - "line": 113, + "line": 129, "column": 44 }, "end": { - "line": 113, + "line": 129, "column": 52 }, "identifierName": "includes" @@ -46689,15 +48249,15 @@ "arguments": [ { "type": "Identifier", - "start": 4192, - "end": 4201, + "start": 4632, + "end": 4641, "loc": { "start": { - "line": 113, + "line": 129, "column": 53 }, "end": { - "line": 113, + "line": 129, "column": 62 }, "identifierName": "specifier" @@ -46714,115 +48274,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 4204, - "end": 4274, + "start": 4644, + "end": 4714, "loc": { "start": { - "line": 113, + "line": 129, "column": 65 }, "end": { - "line": 115, + "line": 131, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 4214, - "end": 4266, + "start": 4654, + "end": 4706, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 60 } }, "expression": { "type": "CallExpression", - "start": 4214, - "end": 4265, + "start": 4654, + "end": 4705, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 4214, - "end": 4254, + "start": 4654, + "end": 4694, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 48 } }, "object": { "type": "MemberExpression", - "start": 4214, - "end": 4246, + "start": 4654, + "end": 4686, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 40 } }, "object": { "type": "MemberExpression", - "start": 4214, - "end": 4227, + "start": 4654, + "end": 4667, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 21 } }, "object": { "type": "ThisExpression", - "start": 4214, - "end": 4218, + "start": 4654, + "end": 4658, "loc": { "start": { - "line": 114, + "line": 130, "column": 8 }, "end": { - "line": 114, + "line": 130, "column": 12 } } }, "property": { "type": "Identifier", - "start": 4219, - "end": 4227, + "start": 4659, + "end": 4667, "loc": { "start": { - "line": 114, + "line": 130, "column": 13 }, "end": { - "line": 114, + "line": 130, "column": 21 }, "identifierName": "phyloref" @@ -46833,15 +48393,15 @@ }, "property": { "type": "Identifier", - "start": 4228, - "end": 4246, + "start": 4668, + "end": 4686, "loc": { "start": { - "line": 114, + "line": 130, "column": 22 }, "end": { - "line": 114, + "line": 130, "column": 40 }, "identifierName": "externalSpecifiers" @@ -46852,15 +48412,15 @@ }, "property": { "type": "Identifier", - "start": 4247, - "end": 4254, + "start": 4687, + "end": 4694, "loc": { "start": { - "line": 114, + "line": 130, "column": 41 }, "end": { - "line": 114, + "line": 130, "column": 48 }, "identifierName": "unshift" @@ -46872,15 +48432,15 @@ "arguments": [ { "type": "Identifier", - "start": 4255, - "end": 4264, + "start": 4695, + "end": 4704, "loc": { "start": { - "line": 114, + "line": 130, "column": 49 }, "end": { - "line": 114, + "line": 130, "column": 58 }, "identifierName": "specifier" @@ -46898,15 +48458,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 4065, - "end": 4138, + "start": 4505, + "end": 4578, "loc": { "start": { - "line": 112, + "line": 128, "column": 6 }, "end": { - "line": 112, + "line": 128, "column": 79 } } @@ -46918,15 +48478,15 @@ }, "alternate": { "type": "BlockStatement", - "start": 4286, - "end": 4341, + "start": 4726, + "end": 4781, "loc": { "start": { - "line": 116, + "line": 132, "column": 11 }, "end": { - "line": 118, + "line": 134, "column": 5 } }, @@ -46937,15 +48497,15 @@ { "type": "CommentLine", "value": " Neither internal nor external? Ignore.", - "start": 4294, - "end": 4335, + "start": 4734, + "end": 4775, "loc": { "start": { - "line": 117, + "line": 133, "column": 6 }, "end": { - "line": 117, + "line": 133, "column": 47 } } @@ -46960,15 +48520,15 @@ }, { "type": "ClassMethod", - "start": 4349, - "end": 5102, + "start": 4789, + "end": 5542, "loc": { "start": { - "line": 121, + "line": 137, "column": 2 }, "end": { - "line": 135, + "line": 151, "column": 3 } }, @@ -46976,15 +48536,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4349, - "end": 4364, + "start": 4789, + "end": 4804, "loc": { "start": { - "line": 121, + "line": 137, "column": 2 }, "end": { - "line": 121, + "line": 137, "column": 17 }, "identifierName": "deleteSpecifier" @@ -46999,15 +48559,15 @@ "params": [ { "type": "Identifier", - "start": 4365, - "end": 4374, + "start": 4805, + "end": 4814, "loc": { "start": { - "line": 121, + "line": 137, "column": 18 }, "end": { - "line": 121, + "line": 137, "column": 27 }, "identifierName": "specifier" @@ -47017,72 +48577,72 @@ ], "body": { "type": "BlockStatement", - "start": 4376, - "end": 5102, + "start": 4816, + "end": 5542, "loc": { "start": { - "line": 121, + "line": 137, "column": 29 }, "end": { - "line": 135, + "line": 151, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4596, - "end": 4844, + "start": 5036, + "end": 5284, "loc": { "start": { - "line": 126, + "line": 142, "column": 4 }, "end": { - "line": 129, + "line": 145, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 4600, - "end": 4687, + "start": 5040, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 95 } }, "left": { "type": "CallExpression", - "start": 4600, - "end": 4640, + "start": 5040, + "end": 5080, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 48 } }, "callee": { "type": "Identifier", - "start": 4600, - "end": 4603, + "start": 5040, + "end": 5043, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 11 }, "identifierName": "has" @@ -47093,44 +48653,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4604, - "end": 4617, + "start": 5044, + "end": 5057, "loc": { "start": { - "line": 126, + "line": 142, "column": 12 }, "end": { - "line": 126, + "line": 142, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4604, - "end": 4608, + "start": 5044, + "end": 5048, "loc": { "start": { - "line": 126, + "line": 142, "column": 12 }, "end": { - "line": 126, + "line": 142, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4609, - "end": 4617, + "start": 5049, + "end": 5057, "loc": { "start": { - "line": 126, + "line": 142, "column": 17 }, "end": { - "line": 126, + "line": 142, "column": 25 }, "identifierName": "phyloref" @@ -47141,15 +48701,15 @@ }, { "type": "StringLiteral", - "start": 4619, - "end": 4639, + "start": 5059, + "end": 5079, "loc": { "start": { - "line": 126, + "line": 142, "column": 27 }, "end": { - "line": 126, + "line": 142, "column": 47 } }, @@ -47165,86 +48725,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 4644, - "end": 4687, + "start": 5084, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 95 } }, "left": { "type": "MemberExpression", - "start": 4644, - "end": 4683, + "start": 5084, + "end": 5123, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 91 } }, "object": { "type": "MemberExpression", - "start": 4644, - "end": 4676, + "start": 5084, + "end": 5116, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 84 } }, "object": { "type": "MemberExpression", - "start": 4644, - "end": 4657, + "start": 5084, + "end": 5097, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 4644, - "end": 4648, + "start": 5084, + "end": 5088, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 56 } } }, "property": { "type": "Identifier", - "start": 4649, - "end": 4657, + "start": 5089, + "end": 5097, "loc": { "start": { - "line": 126, + "line": 142, "column": 57 }, "end": { - "line": 126, + "line": 142, "column": 65 }, "identifierName": "phyloref" @@ -47255,15 +48815,15 @@ }, "property": { "type": "Identifier", - "start": 4658, - "end": 4676, + "start": 5098, + "end": 5116, "loc": { "start": { - "line": 126, + "line": 142, "column": 66 }, "end": { - "line": 126, + "line": 142, "column": 84 }, "identifierName": "internalSpecifiers" @@ -47274,15 +48834,15 @@ }, "property": { "type": "Identifier", - "start": 4677, - "end": 4683, + "start": 5117, + "end": 5123, "loc": { "start": { - "line": 126, + "line": 142, "column": 85 }, "end": { - "line": 126, + "line": 142, "column": 91 }, "identifierName": "length" @@ -47294,15 +48854,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 4686, - "end": 4687, + "start": 5126, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 94 }, "end": { - "line": 126, + "line": 142, "column": 95 } }, @@ -47317,59 +48877,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4689, - "end": 4844, + "start": 5129, + "end": 5284, "loc": { "start": { - "line": 126, + "line": 142, "column": 97 }, "end": { - "line": 129, + "line": 145, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 4697, - "end": 4763, + "start": 5137, + "end": 5203, "loc": { "start": { - "line": 127, + "line": 143, "column": 6 }, "end": { - "line": 127, + "line": 143, "column": 72 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4703, - "end": 4762, + "start": 5143, + "end": 5202, "loc": { "start": { - "line": 127, + "line": 143, "column": 12 }, "end": { - "line": 127, + "line": 143, "column": 71 } }, "id": { "type": "Identifier", - "start": 4703, - "end": 4708, + "start": 5143, + "end": 5148, "loc": { "start": { - "line": 127, + "line": 143, "column": 12 }, "end": { - "line": 127, + "line": 143, "column": 17 }, "identifierName": "index" @@ -47378,86 +48938,86 @@ }, "init": { "type": "CallExpression", - "start": 4711, - "end": 4762, + "start": 5151, + "end": 5202, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 4711, - "end": 4751, + "start": 5151, + "end": 5191, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 4711, - "end": 4743, + "start": 5151, + "end": 5183, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 4711, - "end": 4724, + "start": 5151, + "end": 5164, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 4711, - "end": 4715, + "start": 5151, + "end": 5155, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 24 } } }, "property": { "type": "Identifier", - "start": 4716, - "end": 4724, + "start": 5156, + "end": 5164, "loc": { "start": { - "line": 127, + "line": 143, "column": 25 }, "end": { - "line": 127, + "line": 143, "column": 33 }, "identifierName": "phyloref" @@ -47468,15 +49028,15 @@ }, "property": { "type": "Identifier", - "start": 4725, - "end": 4743, + "start": 5165, + "end": 5183, "loc": { "start": { - "line": 127, + "line": 143, "column": 34 }, "end": { - "line": 127, + "line": 143, "column": 52 }, "identifierName": "internalSpecifiers" @@ -47487,15 +49047,15 @@ }, "property": { "type": "Identifier", - "start": 4744, - "end": 4751, + "start": 5184, + "end": 5191, "loc": { "start": { - "line": 127, + "line": 143, "column": 53 }, "end": { - "line": 127, + "line": 143, "column": 60 }, "identifierName": "indexOf" @@ -47507,15 +49067,15 @@ "arguments": [ { "type": "Identifier", - "start": 4752, - "end": 4761, + "start": 5192, + "end": 5201, "loc": { "start": { - "line": 127, + "line": 143, "column": 61 }, "end": { - "line": 127, + "line": 143, "column": 70 }, "identifierName": "specifier" @@ -47530,43 +49090,43 @@ }, { "type": "IfStatement", - "start": 4770, - "end": 4838, + "start": 5210, + "end": 5278, "loc": { "start": { - "line": 128, + "line": 144, "column": 6 }, "end": { - "line": 128, + "line": 144, "column": 74 } }, "test": { "type": "BinaryExpression", - "start": 4774, - "end": 4786, + "start": 5214, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 10 }, "end": { - "line": 128, + "line": 144, "column": 22 } }, "left": { "type": "Identifier", - "start": 4774, - "end": 4779, + "start": 5214, + "end": 5219, "loc": { "start": { - "line": 128, + "line": 144, "column": 10 }, "end": { - "line": 128, + "line": 144, "column": 15 }, "identifierName": "index" @@ -47576,15 +49136,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 4784, - "end": 4786, + "start": 5224, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 20 }, "end": { - "line": 128, + "line": 144, "column": 22 } }, @@ -47592,15 +49152,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 4785, - "end": 4786, + "start": 5225, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 21 }, "end": { - "line": 128, + "line": 144, "column": 22 } }, @@ -47617,100 +49177,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 4788, - "end": 4838, + "start": 5228, + "end": 5278, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 74 } }, "expression": { "type": "CallExpression", - "start": 4788, - "end": 4837, + "start": 5228, + "end": 5277, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 4788, - "end": 4827, + "start": 5228, + "end": 5267, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 4788, - "end": 4820, + "start": 5228, + "end": 5260, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 56 } }, "object": { "type": "MemberExpression", - "start": 4788, - "end": 4801, + "start": 5228, + "end": 5241, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 4788, - "end": 4792, + "start": 5228, + "end": 5232, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 28 } } }, "property": { "type": "Identifier", - "start": 4793, - "end": 4801, + "start": 5233, + "end": 5241, "loc": { "start": { - "line": 128, + "line": 144, "column": 29 }, "end": { - "line": 128, + "line": 144, "column": 37 }, "identifierName": "phyloref" @@ -47721,15 +49281,15 @@ }, "property": { "type": "Identifier", - "start": 4802, - "end": 4820, + "start": 5242, + "end": 5260, "loc": { "start": { - "line": 128, + "line": 144, "column": 38 }, "end": { - "line": 128, + "line": 144, "column": 56 }, "identifierName": "internalSpecifiers" @@ -47740,15 +49300,15 @@ }, "property": { "type": "Identifier", - "start": 4821, - "end": 4827, + "start": 5261, + "end": 5267, "loc": { "start": { - "line": 128, + "line": 144, "column": 57 }, "end": { - "line": 128, + "line": 144, "column": 63 }, "identifierName": "splice" @@ -47760,15 +49320,15 @@ "arguments": [ { "type": "Identifier", - "start": 4828, - "end": 4833, + "start": 5268, + "end": 5273, "loc": { "start": { - "line": 128, + "line": 144, "column": 64 }, "end": { - "line": 128, + "line": 144, "column": 69 }, "identifierName": "index" @@ -47777,15 +49337,15 @@ }, { "type": "NumericLiteral", - "start": 4835, - "end": 4836, + "start": 5275, + "end": 5276, "loc": { "start": { - "line": 128, + "line": 144, "column": 71 }, "end": { - "line": 128, + "line": 144, "column": 72 } }, @@ -47808,15 +49368,15 @@ { "type": "CommentLine", "value": " Since the user interface combines specifiers into a single list,", - "start": 4382, - "end": 4449, + "start": 4822, + "end": 4889, "loc": { "start": { - "line": 122, + "line": 138, "column": 4 }, "end": { - "line": 122, + "line": 138, "column": 71 } } @@ -47824,15 +49384,15 @@ { "type": "CommentLine", "value": " it doesn't remember if the specifier to be deleted is internal", - "start": 4454, - "end": 4519, + "start": 4894, + "end": 4959, "loc": { "start": { - "line": 123, + "line": 139, "column": 4 }, "end": { - "line": 123, + "line": 139, "column": 69 } } @@ -47840,15 +49400,15 @@ { "type": "CommentLine", "value": " or external. We delete the intended specifier from both arrays.", - "start": 4524, - "end": 4590, + "start": 4964, + "end": 5030, "loc": { "start": { - "line": 124, + "line": 140, "column": 4 }, "end": { - "line": 124, + "line": 140, "column": 70 } } @@ -47857,57 +49417,57 @@ }, { "type": "IfStatement", - "start": 4850, - "end": 5098, + "start": 5290, + "end": 5538, "loc": { "start": { - "line": 131, + "line": 147, "column": 4 }, "end": { - "line": 134, + "line": 150, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 4854, - "end": 4941, + "start": 5294, + "end": 5381, "loc": { "start": { - "line": 131, + "line": 147, "column": 8 }, "end": { - "line": 131, + "line": 147, "column": 95 } }, "left": { "type": "CallExpression", - "start": 4854, - "end": 4894, + "start": 5294, + "end": 5334, "loc": { "start": { - "line": 131, + "line": 147, "column": 8 }, "end": { - "line": 131, + "line": 147, "column": 48 } }, "callee": { "type": "Identifier", - "start": 4854, - "end": 4857, + "start": 5294, + "end": 5297, "loc": { "start": { - "line": 131, + "line": 147, "column": 8 }, "end": { - "line": 131, + "line": 147, "column": 11 }, "identifierName": "has" @@ -47917,44 +49477,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4858, - "end": 4871, + "start": 5298, + "end": 5311, "loc": { "start": { - "line": 131, + "line": 147, "column": 12 }, "end": { - "line": 131, + "line": 147, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4858, - "end": 4862, + "start": 5298, + "end": 5302, "loc": { "start": { - "line": 131, + "line": 147, "column": 12 }, "end": { - "line": 131, + "line": 147, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4863, - "end": 4871, + "start": 5303, + "end": 5311, "loc": { "start": { - "line": 131, + "line": 147, "column": 17 }, "end": { - "line": 131, + "line": 147, "column": 25 }, "identifierName": "phyloref" @@ -47965,15 +49525,15 @@ }, { "type": "StringLiteral", - "start": 4873, - "end": 4893, + "start": 5313, + "end": 5333, "loc": { "start": { - "line": 131, + "line": 147, "column": 27 }, "end": { - "line": 131, + "line": 147, "column": 47 } }, @@ -47988,86 +49548,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 4898, - "end": 4941, + "start": 5338, + "end": 5381, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 95 } }, "left": { "type": "MemberExpression", - "start": 4898, - "end": 4937, + "start": 5338, + "end": 5377, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 91 } }, "object": { "type": "MemberExpression", - "start": 4898, - "end": 4930, + "start": 5338, + "end": 5370, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 84 } }, "object": { "type": "MemberExpression", - "start": 4898, - "end": 4911, + "start": 5338, + "end": 5351, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 4898, - "end": 4902, + "start": 5338, + "end": 5342, "loc": { "start": { - "line": 131, + "line": 147, "column": 52 }, "end": { - "line": 131, + "line": 147, "column": 56 } } }, "property": { "type": "Identifier", - "start": 4903, - "end": 4911, + "start": 5343, + "end": 5351, "loc": { "start": { - "line": 131, + "line": 147, "column": 57 }, "end": { - "line": 131, + "line": 147, "column": 65 }, "identifierName": "phyloref" @@ -48078,15 +49638,15 @@ }, "property": { "type": "Identifier", - "start": 4912, - "end": 4930, + "start": 5352, + "end": 5370, "loc": { "start": { - "line": 131, + "line": 147, "column": 66 }, "end": { - "line": 131, + "line": 147, "column": 84 }, "identifierName": "externalSpecifiers" @@ -48097,15 +49657,15 @@ }, "property": { "type": "Identifier", - "start": 4931, - "end": 4937, + "start": 5371, + "end": 5377, "loc": { "start": { - "line": 131, + "line": 147, "column": 85 }, "end": { - "line": 131, + "line": 147, "column": 91 }, "identifierName": "length" @@ -48117,15 +49677,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 4940, - "end": 4941, + "start": 5380, + "end": 5381, "loc": { "start": { - "line": 131, + "line": 147, "column": 94 }, "end": { - "line": 131, + "line": 147, "column": 95 } }, @@ -48139,59 +49699,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4943, - "end": 5098, + "start": 5383, + "end": 5538, "loc": { "start": { - "line": 131, + "line": 147, "column": 97 }, "end": { - "line": 134, + "line": 150, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 4951, - "end": 5017, + "start": 5391, + "end": 5457, "loc": { "start": { - "line": 132, + "line": 148, "column": 6 }, "end": { - "line": 132, + "line": 148, "column": 72 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4957, - "end": 5016, + "start": 5397, + "end": 5456, "loc": { "start": { - "line": 132, + "line": 148, "column": 12 }, "end": { - "line": 132, + "line": 148, "column": 71 } }, "id": { "type": "Identifier", - "start": 4957, - "end": 4962, + "start": 5397, + "end": 5402, "loc": { "start": { - "line": 132, + "line": 148, "column": 12 }, "end": { - "line": 132, + "line": 148, "column": 17 }, "identifierName": "index" @@ -48200,86 +49760,86 @@ }, "init": { "type": "CallExpression", - "start": 4965, - "end": 5016, + "start": 5405, + "end": 5456, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 4965, - "end": 5005, + "start": 5405, + "end": 5445, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 4965, - "end": 4997, + "start": 5405, + "end": 5437, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 52 } }, "object": { "type": "MemberExpression", - "start": 4965, - "end": 4978, + "start": 5405, + "end": 5418, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 4965, - "end": 4969, + "start": 5405, + "end": 5409, "loc": { "start": { - "line": 132, + "line": 148, "column": 20 }, "end": { - "line": 132, + "line": 148, "column": 24 } } }, "property": { "type": "Identifier", - "start": 4970, - "end": 4978, + "start": 5410, + "end": 5418, "loc": { "start": { - "line": 132, + "line": 148, "column": 25 }, "end": { - "line": 132, + "line": 148, "column": 33 }, "identifierName": "phyloref" @@ -48290,15 +49850,15 @@ }, "property": { "type": "Identifier", - "start": 4979, - "end": 4997, + "start": 5419, + "end": 5437, "loc": { "start": { - "line": 132, + "line": 148, "column": 34 }, "end": { - "line": 132, + "line": 148, "column": 52 }, "identifierName": "externalSpecifiers" @@ -48309,15 +49869,15 @@ }, "property": { "type": "Identifier", - "start": 4998, - "end": 5005, + "start": 5438, + "end": 5445, "loc": { "start": { - "line": 132, + "line": 148, "column": 53 }, "end": { - "line": 132, + "line": 148, "column": 60 }, "identifierName": "indexOf" @@ -48329,15 +49889,15 @@ "arguments": [ { "type": "Identifier", - "start": 5006, - "end": 5015, + "start": 5446, + "end": 5455, "loc": { "start": { - "line": 132, + "line": 148, "column": 61 }, "end": { - "line": 132, + "line": 148, "column": 70 }, "identifierName": "specifier" @@ -48352,43 +49912,43 @@ }, { "type": "IfStatement", - "start": 5024, - "end": 5092, + "start": 5464, + "end": 5532, "loc": { "start": { - "line": 133, + "line": 149, "column": 6 }, "end": { - "line": 133, + "line": 149, "column": 74 } }, "test": { "type": "BinaryExpression", - "start": 5028, - "end": 5040, + "start": 5468, + "end": 5480, "loc": { "start": { - "line": 133, + "line": 149, "column": 10 }, "end": { - "line": 133, + "line": 149, "column": 22 } }, "left": { "type": "Identifier", - "start": 5028, - "end": 5033, + "start": 5468, + "end": 5473, "loc": { "start": { - "line": 133, + "line": 149, "column": 10 }, "end": { - "line": 133, + "line": 149, "column": 15 }, "identifierName": "index" @@ -48398,15 +49958,15 @@ "operator": "!==", "right": { "type": "UnaryExpression", - "start": 5038, - "end": 5040, + "start": 5478, + "end": 5480, "loc": { "start": { - "line": 133, + "line": 149, "column": 20 }, "end": { - "line": 133, + "line": 149, "column": 22 } }, @@ -48414,15 +49974,15 @@ "prefix": true, "argument": { "type": "NumericLiteral", - "start": 5039, - "end": 5040, + "start": 5479, + "end": 5480, "loc": { "start": { - "line": 133, + "line": 149, "column": 21 }, "end": { - "line": 133, + "line": 149, "column": 22 } }, @@ -48439,100 +49999,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 5042, - "end": 5092, + "start": 5482, + "end": 5532, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 74 } }, "expression": { "type": "CallExpression", - "start": 5042, - "end": 5091, + "start": 5482, + "end": 5531, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 5042, - "end": 5081, + "start": 5482, + "end": 5521, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 63 } }, "object": { "type": "MemberExpression", - "start": 5042, - "end": 5074, + "start": 5482, + "end": 5514, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 56 } }, "object": { "type": "MemberExpression", - "start": 5042, - "end": 5055, + "start": 5482, + "end": 5495, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 5042, - "end": 5046, + "start": 5482, + "end": 5486, "loc": { "start": { - "line": 133, + "line": 149, "column": 24 }, "end": { - "line": 133, + "line": 149, "column": 28 } } }, "property": { "type": "Identifier", - "start": 5047, - "end": 5055, + "start": 5487, + "end": 5495, "loc": { "start": { - "line": 133, + "line": 149, "column": 29 }, "end": { - "line": 133, + "line": 149, "column": 37 }, "identifierName": "phyloref" @@ -48543,15 +50103,15 @@ }, "property": { "type": "Identifier", - "start": 5056, - "end": 5074, + "start": 5496, + "end": 5514, "loc": { "start": { - "line": 133, + "line": 149, "column": 38 }, "end": { - "line": 133, + "line": 149, "column": 56 }, "identifierName": "externalSpecifiers" @@ -48562,15 +50122,15 @@ }, "property": { "type": "Identifier", - "start": 5075, - "end": 5081, + "start": 5515, + "end": 5521, "loc": { "start": { - "line": 133, + "line": 149, "column": 57 }, "end": { - "line": 133, + "line": 149, "column": 63 }, "identifierName": "splice" @@ -48582,15 +50142,15 @@ "arguments": [ { "type": "Identifier", - "start": 5082, - "end": 5087, + "start": 5522, + "end": 5527, "loc": { "start": { - "line": 133, + "line": 149, "column": 64 }, "end": { - "line": 133, + "line": 149, "column": 69 }, "identifierName": "index" @@ -48599,15 +50159,15 @@ }, { "type": "NumericLiteral", - "start": 5089, - "end": 5090, + "start": 5529, + "end": 5530, "loc": { "start": { - "line": 133, + "line": 149, "column": 71 }, "end": { - "line": 133, + "line": 149, "column": 72 } }, @@ -48633,15 +50193,15 @@ }, { "type": "ClassMethod", - "start": 5106, - "end": 6565, + "start": 5546, + "end": 7005, "loc": { "start": { - "line": 137, + "line": 153, "column": 2 }, "end": { - "line": 175, + "line": 191, "column": 3 } }, @@ -48649,15 +50209,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 5106, - "end": 5127, + "start": 5546, + "end": 5567, "loc": { "start": { - "line": 137, + "line": 153, "column": 2 }, "end": { - "line": 137, + "line": 153, "column": 23 }, "identifierName": "getExpectedNodeLabels" @@ -48672,15 +50232,15 @@ "params": [ { "type": "Identifier", - "start": 5128, - "end": 5137, + "start": 5568, + "end": 5577, "loc": { "start": { - "line": 137, + "line": 153, "column": 24 }, "end": { - "line": 137, + "line": 153, "column": 33 }, "identifierName": "phylogeny" @@ -48690,59 +50250,59 @@ ], "body": { "type": "BlockStatement", - "start": 5139, - "end": 6565, + "start": 5579, + "end": 7005, "loc": { "start": { - "line": 137, + "line": 153, "column": 35 }, "end": { - "line": 175, + "line": 191, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 5535, - "end": 5568, + "start": 5975, + "end": 6008, "loc": { "start": { - "line": 145, + "line": 161, "column": 4 }, "end": { - "line": 145, + "line": 161, "column": 37 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5541, - "end": 5567, + "start": 5981, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 10 }, "end": { - "line": 145, + "line": 161, "column": 36 } }, "id": { "type": "Identifier", - "start": 5541, - "end": 5554, + "start": 5981, + "end": 5994, "loc": { "start": { - "line": 145, + "line": 161, "column": 10 }, "end": { - "line": 145, + "line": 161, "column": 23 }, "identifierName": "phylorefLabel" @@ -48752,44 +50312,44 @@ }, "init": { "type": "MemberExpression", - "start": 5557, - "end": 5567, + "start": 5997, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 26 }, "end": { - "line": 145, + "line": 161, "column": 36 } }, "object": { "type": "ThisExpression", - "start": 5557, - "end": 5561, + "start": 5997, + "end": 6001, "loc": { "start": { - "line": 145, + "line": 161, "column": 26 }, "end": { - "line": 145, + "line": 161, "column": 30 } } }, "property": { "type": "Identifier", - "start": 5562, - "end": 5567, + "start": 6002, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 31 }, "end": { - "line": 145, + "line": 161, "column": 36 }, "identifierName": "label" @@ -48806,15 +50366,15 @@ { "type": "CommentLine", "value": " Given a phylogeny, determine which node labels we expect this phyloref to", - "start": 5145, - "end": 5221, + "start": 5585, + "end": 5661, "loc": { "start": { - "line": 138, + "line": 154, "column": 4 }, "end": { - "line": 138, + "line": 154, "column": 80 } } @@ -48822,15 +50382,15 @@ { "type": "CommentLine", "value": " resolve to. To do this, we:", - "start": 5226, - "end": 5256, + "start": 5666, + "end": 5696, "loc": { "start": { - "line": 139, + "line": 155, "column": 4 }, "end": { - "line": 139, + "line": 155, "column": 34 } } @@ -48838,15 +50398,15 @@ { "type": "CommentLine", "value": " 1. Find all node labels that are case-sensitively identical", - "start": 5261, - "end": 5324, + "start": 5701, + "end": 5764, "loc": { "start": { - "line": 140, + "line": 156, "column": 4 }, "end": { - "line": 140, + "line": 156, "column": 67 } } @@ -48854,15 +50414,15 @@ { "type": "CommentLine", "value": " to the phyloreference.", - "start": 5329, - "end": 5358, + "start": 5769, + "end": 5798, "loc": { "start": { - "line": 141, + "line": 157, "column": 4 }, "end": { - "line": 141, + "line": 157, "column": 33 } } @@ -48870,15 +50430,15 @@ { "type": "CommentLine", "value": " 2. Find all node labels that have additionalNodeProperties with", - "start": 5363, - "end": 5430, + "start": 5803, + "end": 5870, "loc": { "start": { - "line": 142, + "line": 158, "column": 4 }, "end": { - "line": 142, + "line": 158, "column": 71 } } @@ -48886,15 +50446,15 @@ { "type": "CommentLine", "value": " expectedPhyloreferenceNamed case-sensitively identical to", - "start": 5435, - "end": 5499, + "start": 5875, + "end": 5939, "loc": { "start": { - "line": 143, + "line": 159, "column": 4 }, "end": { - "line": 143, + "line": 159, "column": 68 } } @@ -48902,15 +50462,15 @@ { "type": "CommentLine", "value": " the phyloreference.", - "start": 5504, - "end": 5530, + "start": 5944, + "end": 5970, "loc": { "start": { - "line": 144, + "line": 160, "column": 4 }, "end": { - "line": 144, + "line": 160, "column": 30 } } @@ -48919,44 +50479,44 @@ }, { "type": "VariableDeclaration", - "start": 5573, - "end": 5602, + "start": 6013, + "end": 6042, "loc": { "start": { - "line": 146, + "line": 162, "column": 4 }, "end": { - "line": 146, + "line": 162, "column": 33 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5579, - "end": 5601, + "start": 6019, + "end": 6041, "loc": { "start": { - "line": 146, + "line": 162, "column": 10 }, "end": { - "line": 146, + "line": 162, "column": 32 } }, "id": { "type": "Identifier", - "start": 5579, - "end": 5589, + "start": 6019, + "end": 6029, "loc": { "start": { - "line": 146, + "line": 162, "column": 10 }, "end": { - "line": 146, + "line": 162, "column": 20 }, "identifierName": "nodeLabels" @@ -48965,29 +50525,29 @@ }, "init": { "type": "NewExpression", - "start": 5592, - "end": 5601, + "start": 6032, + "end": 6041, "loc": { "start": { - "line": 146, + "line": 162, "column": 23 }, "end": { - "line": 146, + "line": 162, "column": 32 } }, "callee": { "type": "Identifier", - "start": 5596, - "end": 5599, + "start": 6036, + "end": 6039, "loc": { "start": { - "line": 146, + "line": 162, "column": 27 }, "end": { - "line": 146, + "line": 162, "column": 30 }, "identifierName": "Set" @@ -49002,99 +50562,99 @@ }, { "type": "ExpressionStatement", - "start": 5608, - "end": 6469, + "start": 6048, + "end": 6909, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 171, + "line": 187, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 5608, - "end": 6468, + "start": 6048, + "end": 6908, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 171, + "line": 187, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 5608, - "end": 5704, + "start": 6048, + "end": 6144, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 29 } }, "object": { "type": "CallExpression", - "start": 5608, - "end": 5696, + "start": 6048, + "end": 6136, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 21 } }, "callee": { "type": "MemberExpression", - "start": 5608, - "end": 5694, + "start": 6048, + "end": 6134, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 19 } }, "object": { "type": "NewExpression", - "start": 5608, - "end": 5680, + "start": 6048, + "end": 6120, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 5 } }, "callee": { "type": "Identifier", - "start": 5612, - "end": 5628, + "start": 6052, + "end": 6068, "loc": { "start": { - "line": 148, + "line": 164, "column": 8 }, "end": { - "line": 148, + "line": 164, "column": 24 }, "identifierName": "PhylogenyWrapper" @@ -49104,15 +50664,15 @@ "arguments": [ { "type": "Identifier", - "start": 5636, - "end": 5645, + "start": 6076, + "end": 6085, "loc": { "start": { - "line": 149, + "line": 165, "column": 6 }, "end": { - "line": 149, + "line": 165, "column": 15 }, "identifierName": "phylogeny" @@ -49121,44 +50681,44 @@ }, { "type": "MemberExpression", - "start": 5653, - "end": 5674, + "start": 6093, + "end": 6114, "loc": { "start": { - "line": 150, + "line": 166, "column": 6 }, "end": { - "line": 150, + "line": 166, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 5653, - "end": 5657, + "start": 6093, + "end": 6097, "loc": { "start": { - "line": 150, + "line": 166, "column": 6 }, "end": { - "line": 150, + "line": 166, "column": 10 } } }, "property": { "type": "Identifier", - "start": 5658, - "end": 5674, + "start": 6098, + "end": 6114, "loc": { "start": { - "line": 150, + "line": 166, "column": 11 }, "end": { - "line": 150, + "line": 166, "column": 27 }, "identifierName": "defaultNomenCode" @@ -49171,15 +50731,15 @@ }, "property": { "type": "Identifier", - "start": 5681, - "end": 5694, + "start": 6121, + "end": 6134, "loc": { "start": { - "line": 151, + "line": 167, "column": 6 }, "end": { - "line": 151, + "line": 167, "column": 19 }, "identifierName": "getNodeLabels" @@ -49192,15 +50752,15 @@ }, "property": { "type": "Identifier", - "start": 5697, - "end": 5704, + "start": 6137, + "end": 6144, "loc": { "start": { - "line": 151, + "line": 167, "column": 22 }, "end": { - "line": 151, + "line": 167, "column": 29 }, "identifierName": "forEach" @@ -49212,15 +50772,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5705, - "end": 6467, + "start": 6145, + "end": 6907, "loc": { "start": { - "line": 151, + "line": 167, "column": 30 }, "end": { - "line": 171, + "line": 187, "column": 5 } }, @@ -49231,15 +50791,15 @@ "params": [ { "type": "Identifier", - "start": 5706, - "end": 5715, + "start": 6146, + "end": 6155, "loc": { "start": { - "line": 151, + "line": 167, "column": 31 }, "end": { - "line": 151, + "line": 167, "column": 40 }, "identifierName": "nodeLabel" @@ -49249,58 +50809,58 @@ ], "body": { "type": "BlockStatement", - "start": 5720, - "end": 6467, + "start": 6160, + "end": 6907, "loc": { "start": { - "line": 151, + "line": 167, "column": 45 }, "end": { - "line": 171, + "line": 187, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 5794, - "end": 6461, + "start": 6234, + "end": 6901, "loc": { "start": { - "line": 153, + "line": 169, "column": 6 }, "end": { - "line": 170, + "line": 186, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 5798, - "end": 5825, + "start": 6238, + "end": 6265, "loc": { "start": { - "line": 153, + "line": 169, "column": 10 }, "end": { - "line": 153, + "line": 169, "column": 37 } }, "left": { "type": "Identifier", - "start": 5798, - "end": 5807, + "start": 6238, + "end": 6247, "loc": { "start": { - "line": 153, + "line": 169, "column": 10 }, "end": { - "line": 153, + "line": 169, "column": 19 }, "identifierName": "nodeLabel" @@ -49311,15 +50871,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 5812, - "end": 5825, + "start": 6252, + "end": 6265, "loc": { "start": { - "line": 153, + "line": 169, "column": 24 }, "end": { - "line": 153, + "line": 169, "column": 37 }, "identifierName": "phylorefLabel" @@ -49330,72 +50890,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 5827, - "end": 5871, + "start": 6267, + "end": 6311, "loc": { "start": { - "line": 153, + "line": 169, "column": 39 }, "end": { - "line": 155, + "line": 171, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 5837, - "end": 5863, + "start": 6277, + "end": 6303, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 34 } }, "expression": { "type": "CallExpression", - "start": 5837, - "end": 5862, + "start": 6277, + "end": 6302, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 5837, - "end": 5851, + "start": 6277, + "end": 6291, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 22 } }, "object": { "type": "Identifier", - "start": 5837, - "end": 5847, + "start": 6277, + "end": 6287, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 18 }, "identifierName": "nodeLabels" @@ -49404,15 +50964,15 @@ }, "property": { "type": "Identifier", - "start": 5848, - "end": 5851, + "start": 6288, + "end": 6291, "loc": { "start": { - "line": 154, + "line": 170, "column": 19 }, "end": { - "line": 154, + "line": 170, "column": 22 }, "identifierName": "add" @@ -49424,15 +50984,15 @@ "arguments": [ { "type": "Identifier", - "start": 5852, - "end": 5861, + "start": 6292, + "end": 6301, "loc": { "start": { - "line": 154, + "line": 170, "column": 23 }, "end": { - "line": 154, + "line": 170, "column": 32 }, "identifierName": "nodeLabel" @@ -49447,71 +51007,71 @@ }, "alternate": { "type": "IfStatement", - "start": 5877, - "end": 6461, + "start": 6317, + "end": 6901, "loc": { "start": { - "line": 155, + "line": 171, "column": 13 }, "end": { - "line": 170, + "line": 186, "column": 7 } }, "test": { "type": "LogicalExpression", - "start": 5890, - "end": 6087, + "start": 6330, + "end": 6527, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 158, + "line": 174, "column": 92 } }, "left": { "type": "LogicalExpression", - "start": 5890, - "end": 5994, + "start": 6330, + "end": 6434, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 157, + "line": 173, "column": 61 } }, "left": { "type": "CallExpression", - "start": 5890, - "end": 5932, + "start": 6330, + "end": 6372, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 156, + "line": 172, "column": 50 } }, "callee": { "type": "Identifier", - "start": 5890, - "end": 5893, + "start": 6330, + "end": 6333, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 156, + "line": 172, "column": 11 }, "identifierName": "has" @@ -49521,15 +51081,15 @@ "arguments": [ { "type": "Identifier", - "start": 5894, - "end": 5903, + "start": 6334, + "end": 6343, "loc": { "start": { - "line": 156, + "line": 172, "column": 12 }, "end": { - "line": 156, + "line": 172, "column": 21 }, "identifierName": "phylogeny" @@ -49538,15 +51098,15 @@ }, { "type": "StringLiteral", - "start": 5905, - "end": 5931, + "start": 6345, + "end": 6371, "loc": { "start": { - "line": 156, + "line": 172, "column": 23 }, "end": { - "line": 156, + "line": 172, "column": 49 } }, @@ -49561,29 +51121,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 5944, - "end": 5994, + "start": 6384, + "end": 6434, "loc": { "start": { - "line": 157, + "line": 173, "column": 11 }, "end": { - "line": 157, + "line": 173, "column": 61 } }, "callee": { "type": "Identifier", - "start": 5944, - "end": 5947, + "start": 6384, + "end": 6387, "loc": { "start": { - "line": 157, + "line": 173, "column": 11 }, "end": { - "line": 157, + "line": 173, "column": 14 }, "identifierName": "has" @@ -49593,29 +51153,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 5948, - "end": 5982, + "start": 6388, + "end": 6422, "loc": { "start": { - "line": 157, + "line": 173, "column": 15 }, "end": { - "line": 157, + "line": 173, "column": 49 } }, "object": { "type": "Identifier", - "start": 5948, - "end": 5957, + "start": 6388, + "end": 6397, "loc": { "start": { - "line": 157, + "line": 173, "column": 15 }, "end": { - "line": 157, + "line": 173, "column": 24 }, "identifierName": "phylogeny" @@ -49624,15 +51184,15 @@ }, "property": { "type": "Identifier", - "start": 5958, - "end": 5982, + "start": 6398, + "end": 6422, "loc": { "start": { - "line": 157, + "line": 173, "column": 25 }, "end": { - "line": 157, + "line": 173, "column": 49 }, "identifierName": "additionalNodeProperties" @@ -49643,15 +51203,15 @@ }, { "type": "Identifier", - "start": 5984, - "end": 5993, + "start": 6424, + "end": 6433, "loc": { "start": { - "line": 157, + "line": 173, "column": 51 }, "end": { - "line": 157, + "line": 173, "column": 60 }, "identifierName": "nodeLabel" @@ -49664,29 +51224,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 6006, - "end": 6087, + "start": 6446, + "end": 6527, "loc": { "start": { - "line": 158, + "line": 174, "column": 11 }, "end": { - "line": 158, + "line": 174, "column": 92 } }, "callee": { "type": "Identifier", - "start": 6006, - "end": 6009, + "start": 6446, + "end": 6449, "loc": { "start": { - "line": 158, + "line": 174, "column": 11 }, "end": { - "line": 158, + "line": 174, "column": 14 }, "identifierName": "has" @@ -49696,43 +51256,43 @@ "arguments": [ { "type": "MemberExpression", - "start": 6010, - "end": 6055, + "start": 6450, + "end": 6495, "loc": { "start": { - "line": 158, + "line": 174, "column": 15 }, "end": { - "line": 158, + "line": 174, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 6010, - "end": 6044, + "start": 6450, + "end": 6484, "loc": { "start": { - "line": 158, + "line": 174, "column": 15 }, "end": { - "line": 158, + "line": 174, "column": 49 } }, "object": { "type": "Identifier", - "start": 6010, - "end": 6019, + "start": 6450, + "end": 6459, "loc": { "start": { - "line": 158, + "line": 174, "column": 15 }, "end": { - "line": 158, + "line": 174, "column": 24 }, "identifierName": "phylogeny" @@ -49741,15 +51301,15 @@ }, "property": { "type": "Identifier", - "start": 6020, - "end": 6044, + "start": 6460, + "end": 6484, "loc": { "start": { - "line": 158, + "line": 174, "column": 25 }, "end": { - "line": 158, + "line": 174, "column": 49 }, "identifierName": "additionalNodeProperties" @@ -49760,15 +51320,15 @@ }, "property": { "type": "Identifier", - "start": 6045, - "end": 6054, + "start": 6485, + "end": 6494, "loc": { "start": { - "line": 158, + "line": 174, "column": 50 }, "end": { - "line": 158, + "line": 174, "column": 59 }, "identifierName": "nodeLabel" @@ -49779,15 +51339,15 @@ }, { "type": "StringLiteral", - "start": 6057, - "end": 6086, + "start": 6497, + "end": 6526, "loc": { "start": { - "line": 158, + "line": 174, "column": 62 }, "end": { - "line": 158, + "line": 174, "column": 91 } }, @@ -49802,59 +51362,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6096, - "end": 6461, + "start": 6536, + "end": 6901, "loc": { "start": { - "line": 159, + "line": 175, "column": 8 }, "end": { - "line": 170, + "line": 186, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 6226, - "end": 6348, + "start": 6666, + "end": 6788, "loc": { "start": { - "line": 163, + "line": 179, "column": 8 }, "end": { - "line": 165, + "line": 181, "column": 39 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6232, - "end": 6347, + "start": 6672, + "end": 6787, "loc": { "start": { - "line": 163, + "line": 179, "column": 14 }, "end": { - "line": 165, + "line": 181, "column": 38 } }, "id": { "type": "Identifier", - "start": 6232, - "end": 6249, + "start": 6672, + "end": 6689, "loc": { "start": { - "line": 163, + "line": 179, "column": 14 }, "end": { - "line": 163, + "line": 179, "column": 31 }, "identifierName": "expectedPhylorefs" @@ -49864,57 +51424,57 @@ }, "init": { "type": "MemberExpression", - "start": 6252, - "end": 6347, + "start": 6692, + "end": 6787, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 165, + "line": 181, "column": 38 } }, "object": { "type": "MemberExpression", - "start": 6252, - "end": 6308, + "start": 6692, + "end": 6748, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 164, + "line": 180, "column": 46 } }, "object": { "type": "MemberExpression", - "start": 6252, - "end": 6297, + "start": 6692, + "end": 6737, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 164, + "line": 180, "column": 35 } }, "object": { "type": "Identifier", - "start": 6252, - "end": 6261, + "start": 6692, + "end": 6701, "loc": { "start": { - "line": 163, + "line": 179, "column": 34 }, "end": { - "line": 163, + "line": 179, "column": 43 }, "identifierName": "phylogeny" @@ -49923,15 +51483,15 @@ }, "property": { "type": "Identifier", - "start": 6273, - "end": 6297, + "start": 6713, + "end": 6737, "loc": { "start": { - "line": 164, + "line": 180, "column": 11 }, "end": { - "line": 164, + "line": 180, "column": 35 }, "identifierName": "additionalNodeProperties" @@ -49942,15 +51502,15 @@ }, "property": { "type": "Identifier", - "start": 6298, - "end": 6307, + "start": 6738, + "end": 6747, "loc": { "start": { - "line": 164, + "line": 180, "column": 36 }, "end": { - "line": 164, + "line": 180, "column": 45 }, "identifierName": "nodeLabel" @@ -49961,15 +51521,15 @@ }, "property": { "type": "Identifier", - "start": 6320, - "end": 6347, + "start": 6760, + "end": 6787, "loc": { "start": { - "line": 165, + "line": 181, "column": 11 }, "end": { - "line": 165, + "line": 181, "column": 38 }, "identifierName": "expectedPhyloreferenceNamed" @@ -49986,15 +51546,15 @@ { "type": "CommentLine", "value": " Does this node label have an expectedPhyloreferenceNamed that", - "start": 6106, - "end": 6170, + "start": 6546, + "end": 6610, "loc": { "start": { - "line": 160, + "line": 176, "column": 8 }, "end": { - "line": 160, + "line": 176, "column": 72 } } @@ -50002,15 +51562,15 @@ { "type": "CommentLine", "value": " includes this phyloreference name?", - "start": 6179, - "end": 6216, + "start": 6619, + "end": 6656, "loc": { "start": { - "line": 161, + "line": 177, "column": 8 }, "end": { - "line": 161, + "line": 177, "column": 45 } } @@ -50019,57 +51579,57 @@ }, { "type": "IfStatement", - "start": 6358, - "end": 6453, + "start": 6798, + "end": 6893, "loc": { "start": { - "line": 167, + "line": 183, "column": 8 }, "end": { - "line": 169, + "line": 185, "column": 9 } }, "test": { "type": "CallExpression", - "start": 6362, - "end": 6403, + "start": 6802, + "end": 6843, "loc": { "start": { - "line": 167, + "line": 183, "column": 12 }, "end": { - "line": 167, + "line": 183, "column": 53 } }, "callee": { "type": "MemberExpression", - "start": 6362, - "end": 6388, + "start": 6802, + "end": 6828, "loc": { "start": { - "line": 167, + "line": 183, "column": 12 }, "end": { - "line": 167, + "line": 183, "column": 38 } }, "object": { "type": "Identifier", - "start": 6362, - "end": 6379, + "start": 6802, + "end": 6819, "loc": { "start": { - "line": 167, + "line": 183, "column": 12 }, "end": { - "line": 167, + "line": 183, "column": 29 }, "identifierName": "expectedPhylorefs" @@ -50078,15 +51638,15 @@ }, "property": { "type": "Identifier", - "start": 6380, - "end": 6388, + "start": 6820, + "end": 6828, "loc": { "start": { - "line": 167, + "line": 183, "column": 30 }, "end": { - "line": 167, + "line": 183, "column": 38 }, "identifierName": "includes" @@ -50098,15 +51658,15 @@ "arguments": [ { "type": "Identifier", - "start": 6389, - "end": 6402, + "start": 6829, + "end": 6842, "loc": { "start": { - "line": 167, + "line": 183, "column": 39 }, "end": { - "line": 167, + "line": 183, "column": 52 }, "identifierName": "phylorefLabel" @@ -50117,72 +51677,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 6405, - "end": 6453, + "start": 6845, + "end": 6893, "loc": { "start": { - "line": 167, + "line": 183, "column": 55 }, "end": { - "line": 169, + "line": 185, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 6417, - "end": 6443, + "start": 6857, + "end": 6883, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 36 } }, "expression": { "type": "CallExpression", - "start": 6417, - "end": 6442, + "start": 6857, + "end": 6882, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 6417, - "end": 6431, + "start": 6857, + "end": 6871, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 24 } }, "object": { "type": "Identifier", - "start": 6417, - "end": 6427, + "start": 6857, + "end": 6867, "loc": { "start": { - "line": 168, + "line": 184, "column": 10 }, "end": { - "line": 168, + "line": 184, "column": 20 }, "identifierName": "nodeLabels" @@ -50191,15 +51751,15 @@ }, "property": { "type": "Identifier", - "start": 6428, - "end": 6431, + "start": 6868, + "end": 6871, "loc": { "start": { - "line": 168, + "line": 184, "column": 21 }, "end": { - "line": 168, + "line": 184, "column": 24 }, "identifierName": "add" @@ -50211,15 +51771,15 @@ "arguments": [ { "type": "Identifier", - "start": 6432, - "end": 6441, + "start": 6872, + "end": 6881, "loc": { "start": { - "line": 168, + "line": 184, "column": 25 }, "end": { - "line": 168, + "line": 184, "column": 34 }, "identifierName": "nodeLabel" @@ -50243,15 +51803,15 @@ { "type": "CommentLine", "value": " Is this node label identical to the phyloreference name?", - "start": 5728, - "end": 5787, + "start": 6168, + "end": 6227, "loc": { "start": { - "line": 152, + "line": 168, "column": 6 }, "end": { - "line": 152, + "line": 168, "column": 65 } } @@ -50268,15 +51828,15 @@ { "type": "CommentLine", "value": " Return node labels sorted alphabetically.", - "start": 6475, - "end": 6519, + "start": 6915, + "end": 6959, "loc": { "start": { - "line": 173, + "line": 189, "column": 4 }, "end": { - "line": 173, + "line": 189, "column": 48 } } @@ -50285,85 +51845,85 @@ }, { "type": "ReturnStatement", - "start": 6524, - "end": 6561, + "start": 6964, + "end": 7001, "loc": { "start": { - "line": 174, + "line": 190, "column": 4 }, "end": { - "line": 174, + "line": 190, "column": 41 } }, "argument": { "type": "CallExpression", - "start": 6531, - "end": 6560, + "start": 6971, + "end": 7000, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 6531, - "end": 6558, + "start": 6971, + "end": 6998, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 38 } }, "object": { "type": "CallExpression", - "start": 6531, - "end": 6553, + "start": 6971, + "end": 6993, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 6531, - "end": 6541, + "start": 6971, + "end": 6981, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 21 } }, "object": { "type": "Identifier", - "start": 6531, - "end": 6536, + "start": 6971, + "end": 6976, "loc": { "start": { - "line": 174, + "line": 190, "column": 11 }, "end": { - "line": 174, + "line": 190, "column": 16 }, "identifierName": "Array" @@ -50373,15 +51933,15 @@ }, "property": { "type": "Identifier", - "start": 6537, - "end": 6541, + "start": 6977, + "end": 6981, "loc": { "start": { - "line": 174, + "line": 190, "column": 17 }, "end": { - "line": 174, + "line": 190, "column": 21 }, "identifierName": "from" @@ -50394,15 +51954,15 @@ "arguments": [ { "type": "Identifier", - "start": 6542, - "end": 6552, + "start": 6982, + "end": 6992, "loc": { "start": { - "line": 174, + "line": 190, "column": 22 }, "end": { - "line": 174, + "line": 190, "column": 32 }, "identifierName": "nodeLabels" @@ -50414,15 +51974,15 @@ }, "property": { "type": "Identifier", - "start": 6554, - "end": 6558, + "start": 6994, + "end": 6998, "loc": { "start": { - "line": 174, + "line": 190, "column": 34 }, "end": { - "line": 174, + "line": 190, "column": 38 }, "identifierName": "sort" @@ -50439,15 +51999,15 @@ { "type": "CommentLine", "value": " Return node labels sorted alphabetically.", - "start": 6475, - "end": 6519, + "start": 6915, + "end": 6959, "loc": { "start": { - "line": 173, + "line": 189, "column": 4 }, "end": { - "line": 173, + "line": 189, "column": 48 } } @@ -50460,15 +52020,15 @@ }, { "type": "ClassMethod", - "start": 6569, - "end": 6921, + "start": 7009, + "end": 7361, "loc": { "start": { - "line": 177, + "line": 193, "column": 2 }, "end": { - "line": 187, + "line": 203, "column": 3 } }, @@ -50476,15 +52036,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6576, - "end": 6600, + "start": 7016, + "end": 7040, "loc": { "start": { - "line": 177, + "line": 193, "column": 9 }, "end": { - "line": 177, + "line": 193, "column": 33 }, "identifierName": "getStatusCURIEsInEnglish" @@ -50499,59 +52059,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6603, - "end": 6921, + "start": 7043, + "end": 7361, "loc": { "start": { - "line": 177, + "line": 193, "column": 36 }, "end": { - "line": 187, + "line": 203, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 6670, - "end": 6917, + "start": 7110, + "end": 7357, "loc": { "start": { - "line": 179, + "line": 195, "column": 4 }, "end": { - "line": 186, + "line": 202, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 6677, - "end": 6916, + "start": 7117, + "end": 7356, "loc": { "start": { - "line": 179, + "line": 195, "column": 11 }, "end": { - "line": 186, + "line": 202, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 6685, - "end": 6705, + "start": 7125, + "end": 7145, "loc": { "start": { - "line": 180, + "line": 196, "column": 6 }, "end": { - "line": 180, + "line": 196, "column": 26 } }, @@ -50560,15 +52120,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6685, - "end": 6696, + "start": 7125, + "end": 7136, "loc": { "start": { - "line": 180, + "line": 196, "column": 6 }, "end": { - "line": 180, + "line": 196, "column": 17 } }, @@ -50581,15 +52141,15 @@ }, "value": { "type": "StringLiteral", - "start": 6698, - "end": 6705, + "start": 7138, + "end": 7145, "loc": { "start": { - "line": 180, + "line": 196, "column": 19 }, "end": { - "line": 180, + "line": 196, "column": 26 } }, @@ -50603,15 +52163,15 @@ }, { "type": "ObjectProperty", - "start": 6713, - "end": 6745, + "start": 7153, + "end": 7185, "loc": { "start": { - "line": 181, + "line": 197, "column": 6 }, "end": { - "line": 181, + "line": 197, "column": 38 } }, @@ -50620,15 +52180,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6713, - "end": 6730, + "start": 7153, + "end": 7170, "loc": { "start": { - "line": 181, + "line": 197, "column": 6 }, "end": { - "line": 181, + "line": 197, "column": 23 } }, @@ -50640,15 +52200,15 @@ }, "value": { "type": "StringLiteral", - "start": 6732, - "end": 6745, + "start": 7172, + "end": 7185, "loc": { "start": { - "line": 181, + "line": 197, "column": 25 }, "end": { - "line": 181, + "line": 197, "column": 38 } }, @@ -50661,15 +52221,15 @@ }, { "type": "ObjectProperty", - "start": 6753, - "end": 6787, + "start": 7193, + "end": 7227, "loc": { "start": { - "line": 182, + "line": 198, "column": 6 }, "end": { - "line": 182, + "line": 198, "column": 40 } }, @@ -50678,15 +52238,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6753, - "end": 6771, + "start": 7193, + "end": 7211, "loc": { "start": { - "line": 182, + "line": 198, "column": 6 }, "end": { - "line": 182, + "line": 198, "column": 24 } }, @@ -50698,15 +52258,15 @@ }, "value": { "type": "StringLiteral", - "start": 6773, - "end": 6787, + "start": 7213, + "end": 7227, "loc": { "start": { - "line": 182, + "line": 198, "column": 26 }, "end": { - "line": 182, + "line": 198, "column": 40 } }, @@ -50719,15 +52279,15 @@ }, { "type": "ObjectProperty", - "start": 6795, - "end": 6820, + "start": 7235, + "end": 7260, "loc": { "start": { - "line": 183, + "line": 199, "column": 6 }, "end": { - "line": 183, + "line": 199, "column": 31 } }, @@ -50736,15 +52296,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6795, - "end": 6810, + "start": 7235, + "end": 7250, "loc": { "start": { - "line": 183, + "line": 199, "column": 6 }, "end": { - "line": 183, + "line": 199, "column": 21 } }, @@ -50756,15 +52316,15 @@ }, "value": { "type": "StringLiteral", - "start": 6812, - "end": 6820, + "start": 7252, + "end": 7260, "loc": { "start": { - "line": 183, + "line": 199, "column": 23 }, "end": { - "line": 183, + "line": 199, "column": 31 } }, @@ -50777,15 +52337,15 @@ }, { "type": "ObjectProperty", - "start": 6828, - "end": 6856, + "start": 7268, + "end": 7296, "loc": { "start": { - "line": 184, + "line": 200, "column": 6 }, "end": { - "line": 184, + "line": 200, "column": 34 } }, @@ -50794,15 +52354,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6828, - "end": 6843, + "start": 7268, + "end": 7283, "loc": { "start": { - "line": 184, + "line": 200, "column": 6 }, "end": { - "line": 184, + "line": 200, "column": 21 } }, @@ -50814,15 +52374,15 @@ }, "value": { "type": "StringLiteral", - "start": 6845, - "end": 6856, + "start": 7285, + "end": 7296, "loc": { "start": { - "line": 184, + "line": 200, "column": 23 }, "end": { - "line": 184, + "line": 200, "column": 34 } }, @@ -50835,15 +52395,15 @@ }, { "type": "ObjectProperty", - "start": 6864, - "end": 6909, + "start": 7304, + "end": 7349, "loc": { "start": { - "line": 185, + "line": 201, "column": 6 }, "end": { - "line": 185, + "line": 201, "column": 51 } }, @@ -50852,15 +52412,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6864, - "end": 6896, + "start": 7304, + "end": 7336, "loc": { "start": { - "line": 185, + "line": 201, "column": 6 }, "end": { - "line": 185, + "line": 201, "column": 38 } }, @@ -50872,15 +52432,15 @@ }, "value": { "type": "StringLiteral", - "start": 6898, - "end": 6909, + "start": 7338, + "end": 7349, "loc": { "start": { - "line": 185, + "line": 201, "column": 40 }, "end": { - "line": 185, + "line": 201, "column": 51 } }, @@ -50898,15 +52458,15 @@ { "type": "CommentLine", "value": " Return dictionary of all phyloref statuses in English", - "start": 6609, - "end": 6665, + "start": 7049, + "end": 7105, "loc": { "start": { - "line": 178, + "line": 194, "column": 4 }, "end": { - "line": 178, + "line": 194, "column": 60 } } @@ -50919,15 +52479,15 @@ }, { "type": "ClassMethod", - "start": 6925, - "end": 8625, + "start": 7365, + "end": 9065, "loc": { "start": { - "line": 189, + "line": 205, "column": 2 }, "end": { - "line": 230, + "line": 246, "column": 3 } }, @@ -50935,15 +52495,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6925, - "end": 6941, + "start": 7365, + "end": 7381, "loc": { "start": { - "line": 189, + "line": 205, "column": 2 }, "end": { - "line": 189, + "line": 205, "column": 18 }, "identifierName": "getCurrentStatus" @@ -50958,86 +52518,86 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6944, - "end": 8625, + "start": 7384, + "end": 9065, "loc": { "start": { - "line": 189, + "line": 205, "column": 21 }, "end": { - "line": 230, + "line": 246, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 7233, - "end": 8406, + "start": 7673, + "end": 8846, "loc": { "start": { - "line": 196, + "line": 212, "column": 4 }, "end": { - "line": 223, + "line": 239, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 7244, - "end": 7409, + "start": 7684, + "end": 7849, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 199, + "line": 215, "column": 58 } }, "left": { "type": "LogicalExpression", - "start": 7244, - "end": 7350, + "start": 7684, + "end": 7790, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 198, + "line": 214, "column": 62 } }, "left": { "type": "CallExpression", - "start": 7244, - "end": 7287, + "start": 7684, + "end": 7727, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 197, + "line": 213, "column": 49 } }, "callee": { "type": "Identifier", - "start": 7244, - "end": 7247, + "start": 7684, + "end": 7687, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 197, + "line": 213, "column": 9 }, "identifierName": "has" @@ -51048,44 +52608,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7248, - "end": 7261, + "start": 7688, + "end": 7701, "loc": { "start": { - "line": 197, + "line": 213, "column": 10 }, "end": { - "line": 197, + "line": 213, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 7248, - "end": 7252, + "start": 7688, + "end": 7692, "loc": { "start": { - "line": 197, + "line": 213, "column": 10 }, "end": { - "line": 197, + "line": 213, "column": 14 } } }, "property": { "type": "Identifier", - "start": 7253, - "end": 7261, + "start": 7693, + "end": 7701, "loc": { "start": { - "line": 197, + "line": 213, "column": 15 }, "end": { - "line": 197, + "line": 213, "column": 23 }, "identifierName": "phyloref" @@ -51096,15 +52656,15 @@ }, { "type": "StringLiteral", - "start": 7263, - "end": 7286, + "start": 7703, + "end": 7726, "loc": { "start": { - "line": 197, + "line": 213, "column": 25 }, "end": { - "line": 197, + "line": 213, "column": 48 } }, @@ -51120,43 +52680,43 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 7297, - "end": 7350, + "start": 7737, + "end": 7790, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 62 } }, "callee": { "type": "MemberExpression", - "start": 7297, - "end": 7310, + "start": 7737, + "end": 7750, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 22 } }, "object": { "type": "Identifier", - "start": 7297, - "end": 7302, + "start": 7737, + "end": 7742, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 14 }, "identifierName": "Array" @@ -51165,15 +52725,15 @@ }, "property": { "type": "Identifier", - "start": 7303, - "end": 7310, + "start": 7743, + "end": 7750, "loc": { "start": { - "line": 198, + "line": 214, "column": 15 }, "end": { - "line": 198, + "line": 214, "column": 22 }, "identifierName": "isArray" @@ -51185,58 +52745,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 7311, - "end": 7349, + "start": 7751, + "end": 7789, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 61 } }, "object": { "type": "MemberExpression", - "start": 7311, - "end": 7324, + "start": 7751, + "end": 7764, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 36 } }, "object": { "type": "ThisExpression", - "start": 7311, - "end": 7315, + "start": 7751, + "end": 7755, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 27 } } }, "property": { "type": "Identifier", - "start": 7316, - "end": 7324, + "start": 7756, + "end": 7764, "loc": { "start": { - "line": 198, + "line": 214, "column": 28 }, "end": { - "line": 198, + "line": 214, "column": 36 }, "identifierName": "phyloref" @@ -51247,15 +52807,15 @@ }, "property": { "type": "StringLiteral", - "start": 7325, - "end": 7348, + "start": 7765, + "end": 7788, "loc": { "start": { - "line": 198, + "line": 214, "column": 37 }, "end": { - "line": 198, + "line": 214, "column": 60 } }, @@ -51274,86 +52834,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 7360, - "end": 7409, + "start": 7800, + "end": 7849, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 58 } }, "left": { "type": "MemberExpression", - "start": 7360, - "end": 7405, + "start": 7800, + "end": 7845, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 7360, - "end": 7398, + "start": 7800, + "end": 7838, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 47 } }, "object": { "type": "MemberExpression", - "start": 7360, - "end": 7373, + "start": 7800, + "end": 7813, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 7360, - "end": 7364, + "start": 7800, + "end": 7804, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 13 } } }, "property": { "type": "Identifier", - "start": 7365, - "end": 7373, + "start": 7805, + "end": 7813, "loc": { "start": { - "line": 199, + "line": 215, "column": 14 }, "end": { - "line": 199, + "line": 215, "column": 22 }, "identifierName": "phyloref" @@ -51364,15 +52924,15 @@ }, "property": { "type": "StringLiteral", - "start": 7374, - "end": 7397, + "start": 7814, + "end": 7837, "loc": { "start": { - "line": 199, + "line": 215, "column": 23 }, "end": { - "line": 199, + "line": 215, "column": 46 } }, @@ -51386,15 +52946,15 @@ }, "property": { "type": "Identifier", - "start": 7399, - "end": 7405, + "start": 7839, + "end": 7845, "loc": { "start": { - "line": 199, + "line": 215, "column": 48 }, "end": { - "line": 199, + "line": 215, "column": 54 }, "identifierName": "length" @@ -51406,15 +52966,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 7408, - "end": 7409, + "start": 7848, + "end": 7849, "loc": { "start": { - "line": 199, + "line": 215, "column": 57 }, "end": { - "line": 199, + "line": 215, "column": 58 } }, @@ -51429,59 +52989,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7416, - "end": 8406, + "start": 7856, + "end": 8846, "loc": { "start": { - "line": 200, + "line": 216, "column": 6 }, "end": { - "line": 223, + "line": 239, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 7568, - "end": 7683, + "start": 8008, + "end": 8123, "loc": { "start": { - "line": 203, + "line": 219, "column": 6 }, "end": { - "line": 203, + "line": 219, "column": 121 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7574, - "end": 7682, + "start": 8014, + "end": 8122, "loc": { "start": { - "line": 203, + "line": 219, "column": 12 }, "end": { - "line": 203, + "line": 219, "column": 120 } }, "id": { "type": "Identifier", - "start": 7574, - "end": 7590, + "start": 8014, + "end": 8030, "loc": { "start": { - "line": 203, + "line": 219, "column": 12 }, "end": { - "line": 203, + "line": 219, "column": 28 }, "identifierName": "lastStatusInTime" @@ -51491,72 +53051,72 @@ }, "init": { "type": "MemberExpression", - "start": 7593, - "end": 7682, + "start": 8033, + "end": 8122, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 120 } }, "object": { "type": "MemberExpression", - "start": 7593, - "end": 7631, + "start": 8033, + "end": 8071, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 69 } }, "object": { "type": "MemberExpression", - "start": 7593, - "end": 7606, + "start": 8033, + "end": 8046, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 7593, - "end": 7597, + "start": 8033, + "end": 8037, "loc": { "start": { - "line": 203, + "line": 219, "column": 31 }, "end": { - "line": 203, + "line": 219, "column": 35 } } }, "property": { "type": "Identifier", - "start": 7598, - "end": 7606, + "start": 8038, + "end": 8046, "loc": { "start": { - "line": 203, + "line": 219, "column": 36 }, "end": { - "line": 203, + "line": 219, "column": 44 }, "identifierName": "phyloref" @@ -51567,15 +53127,15 @@ }, "property": { "type": "StringLiteral", - "start": 7607, - "end": 7630, + "start": 8047, + "end": 8070, "loc": { "start": { - "line": 203, + "line": 219, "column": 45 }, "end": { - "line": 203, + "line": 219, "column": 68 } }, @@ -51589,86 +53149,86 @@ }, "property": { "type": "BinaryExpression", - "start": 7632, - "end": 7681, + "start": 8072, + "end": 8121, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 119 } }, "left": { "type": "MemberExpression", - "start": 7632, - "end": 7677, + "start": 8072, + "end": 8117, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 115 } }, "object": { "type": "MemberExpression", - "start": 7632, - "end": 7670, + "start": 8072, + "end": 8110, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 108 } }, "object": { "type": "MemberExpression", - "start": 7632, - "end": 7645, + "start": 8072, + "end": 8085, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 83 } }, "object": { "type": "ThisExpression", - "start": 7632, - "end": 7636, + "start": 8072, + "end": 8076, "loc": { "start": { - "line": 203, + "line": 219, "column": 70 }, "end": { - "line": 203, + "line": 219, "column": 74 } } }, "property": { "type": "Identifier", - "start": 7637, - "end": 7645, + "start": 8077, + "end": 8085, "loc": { "start": { - "line": 203, + "line": 219, "column": 75 }, "end": { - "line": 203, + "line": 219, "column": 83 }, "identifierName": "phyloref" @@ -51679,15 +53239,15 @@ }, "property": { "type": "StringLiteral", - "start": 7646, - "end": 7669, + "start": 8086, + "end": 8109, "loc": { "start": { - "line": 203, + "line": 219, "column": 84 }, "end": { - "line": 203, + "line": 219, "column": 107 } }, @@ -51701,15 +53261,15 @@ }, "property": { "type": "Identifier", - "start": 7671, - "end": 7677, + "start": 8111, + "end": 8117, "loc": { "start": { - "line": 203, + "line": 219, "column": 109 }, "end": { - "line": 203, + "line": 219, "column": 115 }, "identifierName": "length" @@ -51721,15 +53281,15 @@ "operator": "-", "right": { "type": "NumericLiteral", - "start": 7680, - "end": 7681, + "start": 8120, + "end": 8121, "loc": { "start": { - "line": 203, + "line": 219, "column": 118 }, "end": { - "line": 203, + "line": 219, "column": 119 } }, @@ -51750,15 +53310,15 @@ { "type": "CommentLine", "value": " If we have any pso:holdsStatusInTime entries, pick the first one and", - "start": 7424, - "end": 7495, + "start": 7864, + "end": 7935, "loc": { "start": { - "line": 201, + "line": 217, "column": 6 }, "end": { - "line": 201, + "line": 217, "column": 77 } } @@ -51766,15 +53326,15 @@ { "type": "CommentLine", "value": " extract the CURIE and time interval information from it.", - "start": 7502, - "end": 7561, + "start": 7942, + "end": 8001, "loc": { "start": { - "line": 202, + "line": 218, "column": 6 }, "end": { - "line": 202, + "line": 218, "column": 65 } } @@ -51783,44 +53343,44 @@ }, { "type": "VariableDeclaration", - "start": 7690, - "end": 7752, + "start": 8130, + "end": 8192, "loc": { "start": { - "line": 204, + "line": 220, "column": 6 }, "end": { - "line": 204, + "line": 220, "column": 68 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7696, - "end": 7751, + "start": 8136, + "end": 8191, "loc": { "start": { - "line": 204, + "line": 220, "column": 12 }, "end": { - "line": 204, + "line": 220, "column": 67 } }, "id": { "type": "Identifier", - "start": 7696, - "end": 7707, + "start": 8136, + "end": 8147, "loc": { "start": { - "line": 204, + "line": 220, "column": 12 }, "end": { - "line": 204, + "line": 220, "column": 23 }, "identifierName": "statusCURIE" @@ -51829,43 +53389,43 @@ }, "init": { "type": "MemberExpression", - "start": 7710, - "end": 7751, + "start": 8150, + "end": 8191, "loc": { "start": { - "line": 204, + "line": 220, "column": 26 }, "end": { - "line": 204, + "line": 220, "column": 67 } }, "object": { "type": "MemberExpression", - "start": 7710, - "end": 7744, + "start": 8150, + "end": 8184, "loc": { "start": { - "line": 204, + "line": 220, "column": 26 }, "end": { - "line": 204, + "line": 220, "column": 60 } }, "object": { "type": "Identifier", - "start": 7710, - "end": 7726, + "start": 8150, + "end": 8166, "loc": { "start": { - "line": 204, + "line": 220, "column": 26 }, "end": { - "line": 204, + "line": 220, "column": 42 }, "identifierName": "lastStatusInTime" @@ -51874,15 +53434,15 @@ }, "property": { "type": "StringLiteral", - "start": 7727, - "end": 7743, + "start": 8167, + "end": 8183, "loc": { "start": { - "line": 204, + "line": 220, "column": 43 }, "end": { - "line": 204, + "line": 220, "column": 59 } }, @@ -51896,15 +53456,15 @@ }, "property": { "type": "StringLiteral", - "start": 7745, - "end": 7750, + "start": 8185, + "end": 8190, "loc": { "start": { - "line": 204, + "line": 220, "column": 61 }, "end": { - "line": 204, + "line": 220, "column": 66 } }, @@ -51923,15 +53483,15 @@ { "type": "CommentLine", "value": " Look for time interval information", - "start": 7760, - "end": 7797, + "start": 8200, + "end": 8237, "loc": { "start": { - "line": 206, + "line": 222, "column": 6 }, "end": { - "line": 206, + "line": 222, "column": 43 } } @@ -51940,44 +53500,44 @@ }, { "type": "VariableDeclaration", - "start": 7804, - "end": 7822, + "start": 8244, + "end": 8262, "loc": { "start": { - "line": 207, + "line": 223, "column": 6 }, "end": { - "line": 207, + "line": 223, "column": 24 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7808, - "end": 7821, + "start": 8248, + "end": 8261, "loc": { "start": { - "line": 207, + "line": 223, "column": 10 }, "end": { - "line": 207, + "line": 223, "column": 23 } }, "id": { "type": "Identifier", - "start": 7808, - "end": 7821, + "start": 8248, + "end": 8261, "loc": { "start": { - "line": 207, + "line": 223, "column": 10 }, "end": { - "line": 207, + "line": 223, "column": 23 }, "identifierName": "intervalStart" @@ -51994,15 +53554,15 @@ { "type": "CommentLine", "value": " Look for time interval information", - "start": 7760, - "end": 7797, + "start": 8200, + "end": 8237, "loc": { "start": { - "line": 206, + "line": 222, "column": 6 }, "end": { - "line": 206, + "line": 222, "column": 43 } } @@ -52011,44 +53571,44 @@ }, { "type": "VariableDeclaration", - "start": 7829, - "end": 7845, + "start": 8269, + "end": 8285, "loc": { "start": { - "line": 208, + "line": 224, "column": 6 }, "end": { - "line": 208, + "line": 224, "column": 22 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7833, - "end": 7844, + "start": 8273, + "end": 8284, "loc": { "start": { - "line": 208, + "line": 224, "column": 10 }, "end": { - "line": 208, + "line": 224, "column": 21 } }, "id": { "type": "Identifier", - "start": 7833, - "end": 7844, + "start": 8273, + "end": 8284, "loc": { "start": { - "line": 208, + "line": 224, "column": 10 }, "end": { - "line": 208, + "line": 224, "column": 21 }, "identifierName": "intervalEnd" @@ -52062,43 +53622,43 @@ }, { "type": "IfStatement", - "start": 7853, - "end": 8198, + "start": 8293, + "end": 8638, "loc": { "start": { - "line": 210, + "line": 226, "column": 6 }, "end": { - "line": 214, + "line": 230, "column": 7 } }, "test": { "type": "CallExpression", - "start": 7857, - "end": 7892, + "start": 8297, + "end": 8332, "loc": { "start": { - "line": 210, + "line": 226, "column": 10 }, "end": { - "line": 210, + "line": 226, "column": 45 } }, "callee": { "type": "Identifier", - "start": 7857, - "end": 7860, + "start": 8297, + "end": 8300, "loc": { "start": { - "line": 210, + "line": 226, "column": 10 }, "end": { - "line": 210, + "line": 226, "column": 13 }, "identifierName": "has" @@ -52108,15 +53668,15 @@ "arguments": [ { "type": "Identifier", - "start": 7861, - "end": 7877, + "start": 8301, + "end": 8317, "loc": { "start": { - "line": 210, + "line": 226, "column": 14 }, "end": { - "line": 210, + "line": 226, "column": 30 }, "identifierName": "lastStatusInTime" @@ -52125,15 +53685,15 @@ }, { "type": "StringLiteral", - "start": 7879, - "end": 7891, + "start": 8319, + "end": 8331, "loc": { "start": { - "line": 210, + "line": 226, "column": 32 }, "end": { - "line": 210, + "line": 226, "column": 44 } }, @@ -52147,59 +53707,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7894, - "end": 8198, + "start": 8334, + "end": 8638, "loc": { "start": { - "line": 210, + "line": 226, "column": 47 }, "end": { - "line": 214, + "line": 230, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 7904, - "end": 7950, + "start": 8344, + "end": 8390, "loc": { "start": { - "line": 211, + "line": 227, "column": 8 }, "end": { - "line": 211, + "line": 227, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7910, - "end": 7949, + "start": 8350, + "end": 8389, "loc": { "start": { - "line": 211, + "line": 227, "column": 14 }, "end": { - "line": 211, + "line": 227, "column": 53 } }, "id": { "type": "Identifier", - "start": 7910, - "end": 7916, + "start": 8350, + "end": 8356, "loc": { "start": { - "line": 211, + "line": 227, "column": 14 }, "end": { - "line": 211, + "line": 227, "column": 20 }, "identifierName": "atTime" @@ -52208,29 +53768,29 @@ }, "init": { "type": "MemberExpression", - "start": 7919, - "end": 7949, + "start": 8359, + "end": 8389, "loc": { "start": { - "line": 211, + "line": 227, "column": 23 }, "end": { - "line": 211, + "line": 227, "column": 53 } }, "object": { "type": "Identifier", - "start": 7919, - "end": 7935, + "start": 8359, + "end": 8375, "loc": { "start": { - "line": 211, + "line": 227, "column": 23 }, "end": { - "line": 211, + "line": 227, "column": 39 }, "identifierName": "lastStatusInTime" @@ -52239,15 +53799,15 @@ }, "property": { "type": "StringLiteral", - "start": 7936, - "end": 7948, + "start": 8376, + "end": 8388, "loc": { "start": { - "line": 211, + "line": 227, "column": 40 }, "end": { - "line": 211, + "line": 227, "column": 52 } }, @@ -52265,43 +53825,43 @@ }, { "type": "IfStatement", - "start": 7959, - "end": 8073, + "start": 8399, + "end": 8513, "loc": { "start": { - "line": 212, + "line": 228, "column": 8 }, "end": { - "line": 212, + "line": 228, "column": 122 } }, "test": { "type": "CallExpression", - "start": 7963, - "end": 8011, + "start": 8403, + "end": 8451, "loc": { "start": { - "line": 212, + "line": 228, "column": 12 }, "end": { - "line": 212, + "line": 228, "column": 60 } }, "callee": { "type": "Identifier", - "start": 7963, - "end": 7966, + "start": 8403, + "end": 8406, "loc": { "start": { - "line": 212, + "line": 228, "column": 12 }, "end": { - "line": 212, + "line": 228, "column": 15 }, "identifierName": "has" @@ -52311,15 +53871,15 @@ "arguments": [ { "type": "Identifier", - "start": 7967, - "end": 7973, + "start": 8407, + "end": 8413, "loc": { "start": { - "line": 212, + "line": 228, "column": 16 }, "end": { - "line": 212, + "line": 228, "column": 22 }, "identifierName": "atTime" @@ -52328,15 +53888,15 @@ }, { "type": "StringLiteral", - "start": 7975, - "end": 8010, + "start": 8415, + "end": 8450, "loc": { "start": { - "line": 212, + "line": 228, "column": 24 }, "end": { - "line": 212, + "line": 228, "column": 59 } }, @@ -52350,44 +53910,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 8013, - "end": 8073, + "start": 8453, + "end": 8513, "loc": { "start": { - "line": 212, + "line": 228, "column": 62 }, "end": { - "line": 212, + "line": 228, "column": 122 } }, "expression": { "type": "AssignmentExpression", - "start": 8013, - "end": 8072, + "start": 8453, + "end": 8512, "loc": { "start": { - "line": 212, + "line": 228, "column": 62 }, "end": { - "line": 212, + "line": 228, "column": 121 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8013, - "end": 8026, + "start": 8453, + "end": 8466, "loc": { "start": { - "line": 212, + "line": 228, "column": 62 }, "end": { - "line": 212, + "line": 228, "column": 75 }, "identifierName": "intervalStart" @@ -52396,29 +53956,29 @@ }, "right": { "type": "MemberExpression", - "start": 8029, - "end": 8072, + "start": 8469, + "end": 8512, "loc": { "start": { - "line": 212, + "line": 228, "column": 78 }, "end": { - "line": 212, + "line": 228, "column": 121 } }, "object": { "type": "Identifier", - "start": 8029, - "end": 8035, + "start": 8469, + "end": 8475, "loc": { "start": { - "line": 212, + "line": 228, "column": 78 }, "end": { - "line": 212, + "line": 228, "column": 84 }, "identifierName": "atTime" @@ -52427,15 +53987,15 @@ }, "property": { "type": "StringLiteral", - "start": 8036, - "end": 8071, + "start": 8476, + "end": 8511, "loc": { "start": { - "line": 212, + "line": 228, "column": 85 }, "end": { - "line": 212, + "line": 228, "column": 120 } }, @@ -52453,43 +54013,43 @@ }, { "type": "IfStatement", - "start": 8082, - "end": 8190, + "start": 8522, + "end": 8630, "loc": { "start": { - "line": 213, + "line": 229, "column": 8 }, "end": { - "line": 213, + "line": 229, "column": 116 } }, "test": { "type": "CallExpression", - "start": 8086, - "end": 8132, + "start": 8526, + "end": 8572, "loc": { "start": { - "line": 213, + "line": 229, "column": 12 }, "end": { - "line": 213, + "line": 229, "column": 58 } }, "callee": { "type": "Identifier", - "start": 8086, - "end": 8089, + "start": 8526, + "end": 8529, "loc": { "start": { - "line": 213, + "line": 229, "column": 12 }, "end": { - "line": 213, + "line": 229, "column": 15 }, "identifierName": "has" @@ -52499,15 +54059,15 @@ "arguments": [ { "type": "Identifier", - "start": 8090, - "end": 8096, + "start": 8530, + "end": 8536, "loc": { "start": { - "line": 213, + "line": 229, "column": 16 }, "end": { - "line": 213, + "line": 229, "column": 22 }, "identifierName": "atTime" @@ -52516,15 +54076,15 @@ }, { "type": "StringLiteral", - "start": 8098, - "end": 8131, + "start": 8538, + "end": 8571, "loc": { "start": { - "line": 213, + "line": 229, "column": 24 }, "end": { - "line": 213, + "line": 229, "column": 57 } }, @@ -52538,44 +54098,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 8134, - "end": 8190, + "start": 8574, + "end": 8630, "loc": { "start": { - "line": 213, + "line": 229, "column": 60 }, "end": { - "line": 213, + "line": 229, "column": 116 } }, "expression": { "type": "AssignmentExpression", - "start": 8134, - "end": 8189, + "start": 8574, + "end": 8629, "loc": { "start": { - "line": 213, + "line": 229, "column": 60 }, "end": { - "line": 213, + "line": 229, "column": 115 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8134, - "end": 8145, + "start": 8574, + "end": 8585, "loc": { "start": { - "line": 213, + "line": 229, "column": 60 }, "end": { - "line": 213, + "line": 229, "column": 71 }, "identifierName": "intervalEnd" @@ -52584,29 +54144,29 @@ }, "right": { "type": "MemberExpression", - "start": 8148, - "end": 8189, + "start": 8588, + "end": 8629, "loc": { "start": { - "line": 213, + "line": 229, "column": 74 }, "end": { - "line": 213, + "line": 229, "column": 115 } }, "object": { "type": "Identifier", - "start": 8148, - "end": 8154, + "start": 8588, + "end": 8594, "loc": { "start": { - "line": 213, + "line": 229, "column": 74 }, "end": { - "line": 213, + "line": 229, "column": 80 }, "identifierName": "atTime" @@ -52615,15 +54175,15 @@ }, "property": { "type": "StringLiteral", - "start": 8155, - "end": 8188, + "start": 8595, + "end": 8628, "loc": { "start": { - "line": 213, + "line": 229, "column": 81 }, "end": { - "line": 213, + "line": 229, "column": 114 } }, @@ -52648,15 +54208,15 @@ { "type": "CommentLine", "value": " Return result object", - "start": 8206, - "end": 8229, + "start": 8646, + "end": 8669, "loc": { "start": { - "line": 216, + "line": 232, "column": 6 }, "end": { - "line": 216, + "line": 232, "column": 29 } } @@ -52665,44 +54225,44 @@ }, { "type": "ReturnStatement", - "start": 8236, - "end": 8400, + "start": 8676, + "end": 8840, "loc": { "start": { - "line": 217, + "line": 233, "column": 6 }, "end": { - "line": 222, + "line": 238, "column": 8 } }, "argument": { "type": "ObjectExpression", - "start": 8243, - "end": 8399, + "start": 8683, + "end": 8839, "loc": { "start": { - "line": 217, + "line": 233, "column": 13 }, "end": { - "line": 222, + "line": 238, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 8253, - "end": 8264, + "start": 8693, + "end": 8704, "loc": { "start": { - "line": 218, + "line": 234, "column": 8 }, "end": { - "line": 218, + "line": 234, "column": 19 } }, @@ -52711,15 +54271,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8253, - "end": 8264, + "start": 8693, + "end": 8704, "loc": { "start": { - "line": 218, + "line": 234, "column": 8 }, "end": { - "line": 218, + "line": 234, "column": 19 }, "identifierName": "statusCURIE" @@ -52729,15 +54289,15 @@ }, "value": { "type": "Identifier", - "start": 8253, - "end": 8264, + "start": 8693, + "end": 8704, "loc": { "start": { - "line": 218, + "line": 234, "column": 8 }, "end": { - "line": 218, + "line": 234, "column": 19 }, "identifierName": "statusCURIE" @@ -52751,15 +54311,15 @@ }, { "type": "ObjectProperty", - "start": 8274, - "end": 8346, + "start": 8714, + "end": 8786, "loc": { "start": { - "line": 219, + "line": 235, "column": 8 }, "end": { - "line": 219, + "line": 235, "column": 80 } }, @@ -52768,15 +54328,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8274, - "end": 8289, + "start": 8714, + "end": 8729, "loc": { "start": { - "line": 219, + "line": 235, "column": 8 }, "end": { - "line": 219, + "line": 235, "column": 23 }, "identifierName": "statusInEnglish" @@ -52785,57 +54345,57 @@ }, "value": { "type": "MemberExpression", - "start": 8291, - "end": 8346, + "start": 8731, + "end": 8786, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 80 } }, "object": { "type": "CallExpression", - "start": 8291, - "end": 8333, + "start": 8731, + "end": 8773, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 8291, - "end": 8331, + "start": 8731, + "end": 8771, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 65 } }, "object": { "type": "Identifier", - "start": 8291, - "end": 8306, + "start": 8731, + "end": 8746, "loc": { "start": { - "line": 219, + "line": 235, "column": 25 }, "end": { - "line": 219, + "line": 235, "column": 40 }, "identifierName": "PhylorefWrapper" @@ -52844,15 +54404,15 @@ }, "property": { "type": "Identifier", - "start": 8307, - "end": 8331, + "start": 8747, + "end": 8771, "loc": { "start": { - "line": 219, + "line": 235, "column": 41 }, "end": { - "line": 219, + "line": 235, "column": 65 }, "identifierName": "getStatusCURIEsInEnglish" @@ -52865,15 +54425,15 @@ }, "property": { "type": "Identifier", - "start": 8334, - "end": 8345, + "start": 8774, + "end": 8785, "loc": { "start": { - "line": 219, + "line": 235, "column": 68 }, "end": { - "line": 219, + "line": 235, "column": 79 }, "identifierName": "statusCURIE" @@ -52885,15 +54445,15 @@ }, { "type": "ObjectProperty", - "start": 8356, - "end": 8369, + "start": 8796, + "end": 8809, "loc": { "start": { - "line": 220, + "line": 236, "column": 8 }, "end": { - "line": 220, + "line": 236, "column": 21 } }, @@ -52902,15 +54462,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8356, - "end": 8369, + "start": 8796, + "end": 8809, "loc": { "start": { - "line": 220, + "line": 236, "column": 8 }, "end": { - "line": 220, + "line": 236, "column": 21 }, "identifierName": "intervalStart" @@ -52919,15 +54479,15 @@ }, "value": { "type": "Identifier", - "start": 8356, - "end": 8369, + "start": 8796, + "end": 8809, "loc": { "start": { - "line": 220, + "line": 236, "column": 8 }, "end": { - "line": 220, + "line": 236, "column": 21 }, "identifierName": "intervalStart" @@ -52940,15 +54500,15 @@ }, { "type": "ObjectProperty", - "start": 8379, - "end": 8390, + "start": 8819, + "end": 8830, "loc": { "start": { - "line": 221, + "line": 237, "column": 8 }, "end": { - "line": 221, + "line": 237, "column": 19 } }, @@ -52957,15 +54517,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8379, - "end": 8390, + "start": 8819, + "end": 8830, "loc": { "start": { - "line": 221, + "line": 237, "column": 8 }, "end": { - "line": 221, + "line": 237, "column": 19 }, "identifierName": "intervalEnd" @@ -52974,15 +54534,15 @@ }, "value": { "type": "Identifier", - "start": 8379, - "end": 8390, + "start": 8819, + "end": 8830, "loc": { "start": { - "line": 221, + "line": 237, "column": 8 }, "end": { - "line": 221, + "line": 237, "column": 19 }, "identifierName": "intervalEnd" @@ -53000,15 +54560,15 @@ { "type": "CommentLine", "value": " Return result object", - "start": 8206, - "end": 8229, + "start": 8646, + "end": 8669, "loc": { "start": { - "line": 216, + "line": 232, "column": 6 }, "end": { - "line": 216, + "line": 232, "column": 29 } } @@ -53024,15 +54584,15 @@ { "type": "CommentLine", "value": " Return a result object that contains:", - "start": 6950, - "end": 6990, + "start": 7390, + "end": 7430, "loc": { "start": { - "line": 190, + "line": 206, "column": 4 }, "end": { - "line": 190, + "line": 206, "column": 44 } } @@ -53040,15 +54600,15 @@ { "type": "CommentLine", "value": " - status: phyloreference status as a short URI (CURIE)", - "start": 6995, - "end": 7053, + "start": 7435, + "end": 7493, "loc": { "start": { - "line": 191, + "line": 207, "column": 4 }, "end": { - "line": 191, + "line": 207, "column": 62 } } @@ -53056,15 +54616,15 @@ { "type": "CommentLine", "value": " - statusInEnglish: an English representation of the phyloref status", - "start": 7058, - "end": 7129, + "start": 7498, + "end": 7569, "loc": { "start": { - "line": 192, + "line": 208, "column": 4 }, "end": { - "line": 192, + "line": 208, "column": 75 } } @@ -53072,15 +54632,15 @@ { "type": "CommentLine", "value": " - intervalStart: the start of the interval", - "start": 7134, - "end": 7180, + "start": 7574, + "end": 7620, "loc": { "start": { - "line": 193, + "line": 209, "column": 4 }, "end": { - "line": 193, + "line": 209, "column": 50 } } @@ -53088,15 +54648,15 @@ { "type": "CommentLine", "value": " - intervalEnd: the end of the interval", - "start": 7185, - "end": 7227, + "start": 7625, + "end": 7667, "loc": { "start": { - "line": 194, + "line": 210, "column": 4 }, "end": { - "line": 194, + "line": 210, "column": 46 } } @@ -53106,15 +54666,15 @@ { "type": "CommentLine", "value": " If we couldn't figure out a status for this phyloref, assume it's a draft.", - "start": 8412, - "end": 8489, + "start": 8852, + "end": 8929, "loc": { "start": { - "line": 225, + "line": 241, "column": 4 }, "end": { - "line": 225, + "line": 241, "column": 81 } } @@ -53123,44 +54683,44 @@ }, { "type": "ReturnStatement", - "start": 8494, - "end": 8621, + "start": 8934, + "end": 9061, "loc": { "start": { - "line": 226, + "line": 242, "column": 4 }, "end": { - "line": 229, + "line": 245, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 8501, - "end": 8620, + "start": 8941, + "end": 9060, "loc": { "start": { - "line": 226, + "line": 242, "column": 11 }, "end": { - "line": 229, + "line": 245, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 8509, - "end": 8533, + "start": 8949, + "end": 8973, "loc": { "start": { - "line": 227, + "line": 243, "column": 6 }, "end": { - "line": 227, + "line": 243, "column": 30 } }, @@ -53169,15 +54729,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8509, - "end": 8520, + "start": 8949, + "end": 8960, "loc": { "start": { - "line": 227, + "line": 243, "column": 6 }, "end": { - "line": 227, + "line": 243, "column": 17 }, "identifierName": "statusCURIE" @@ -53187,15 +54747,15 @@ }, "value": { "type": "StringLiteral", - "start": 8522, - "end": 8533, + "start": 8962, + "end": 8973, "loc": { "start": { - "line": 227, + "line": 243, "column": 19 }, "end": { - "line": 227, + "line": 243, "column": 30 } }, @@ -53209,15 +54769,15 @@ }, { "type": "ObjectProperty", - "start": 8541, - "end": 8613, + "start": 8981, + "end": 9053, "loc": { "start": { - "line": 228, + "line": 244, "column": 6 }, "end": { - "line": 228, + "line": 244, "column": 78 } }, @@ -53226,15 +54786,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8541, - "end": 8556, + "start": 8981, + "end": 8996, "loc": { "start": { - "line": 228, + "line": 244, "column": 6 }, "end": { - "line": 228, + "line": 244, "column": 21 }, "identifierName": "statusInEnglish" @@ -53243,57 +54803,57 @@ }, "value": { "type": "MemberExpression", - "start": 8558, - "end": 8613, + "start": 8998, + "end": 9053, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 78 } }, "object": { "type": "CallExpression", - "start": 8558, - "end": 8600, + "start": 8998, + "end": 9040, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 65 } }, "callee": { "type": "MemberExpression", - "start": 8558, - "end": 8598, + "start": 8998, + "end": 9038, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 63 } }, "object": { "type": "Identifier", - "start": 8558, - "end": 8573, + "start": 8998, + "end": 9013, "loc": { "start": { - "line": 228, + "line": 244, "column": 23 }, "end": { - "line": 228, + "line": 244, "column": 38 }, "identifierName": "PhylorefWrapper" @@ -53302,15 +54862,15 @@ }, "property": { "type": "Identifier", - "start": 8574, - "end": 8598, + "start": 9014, + "end": 9038, "loc": { "start": { - "line": 228, + "line": 244, "column": 39 }, "end": { - "line": 228, + "line": 244, "column": 63 }, "identifierName": "getStatusCURIEsInEnglish" @@ -53323,15 +54883,15 @@ }, "property": { "type": "StringLiteral", - "start": 8601, - "end": 8612, + "start": 9041, + "end": 9052, "loc": { "start": { - "line": 228, + "line": 244, "column": 66 }, "end": { - "line": 228, + "line": 244, "column": 77 } }, @@ -53351,15 +54911,15 @@ { "type": "CommentLine", "value": " If we couldn't figure out a status for this phyloref, assume it's a draft.", - "start": 8412, - "end": 8489, + "start": 8852, + "end": 8929, "loc": { "start": { - "line": 225, + "line": 241, "column": 4 }, "end": { - "line": 225, + "line": 241, "column": 81 } } @@ -53372,15 +54932,15 @@ }, { "type": "ClassMethod", - "start": 8629, - "end": 9878, + "start": 9069, + "end": 10318, "loc": { "start": { - "line": 232, + "line": 248, "column": 2 }, "end": { - "line": 264, + "line": 280, "column": 3 } }, @@ -53388,15 +54948,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8629, - "end": 8645, + "start": 9069, + "end": 9085, "loc": { "start": { - "line": 232, + "line": 248, "column": 2 }, "end": { - "line": 232, + "line": 248, "column": 18 }, "identifierName": "getStatusChanges" @@ -53411,58 +54971,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8648, - "end": 9878, + "start": 9088, + "end": 10318, "loc": { "start": { - "line": 232, + "line": 248, "column": 21 }, "end": { - "line": 264, + "line": 280, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 8725, - "end": 9817, + "start": 9165, + "end": 10257, "loc": { "start": { - "line": 234, + "line": 250, "column": 4 }, "end": { - "line": 260, + "line": 276, "column": 5 } }, "test": { "type": "CallExpression", - "start": 8729, - "end": 8772, + "start": 9169, + "end": 9212, "loc": { "start": { - "line": 234, + "line": 250, "column": 8 }, "end": { - "line": 234, + "line": 250, "column": 51 } }, "callee": { "type": "Identifier", - "start": 8729, - "end": 8732, + "start": 9169, + "end": 9172, "loc": { "start": { - "line": 234, + "line": 250, "column": 8 }, "end": { - "line": 234, + "line": 250, "column": 11 }, "identifierName": "has" @@ -53473,44 +55033,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 8733, - "end": 8746, + "start": 9173, + "end": 9186, "loc": { "start": { - "line": 234, + "line": 250, "column": 12 }, "end": { - "line": 234, + "line": 250, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 8733, - "end": 8737, + "start": 9173, + "end": 9177, "loc": { "start": { - "line": 234, + "line": 250, "column": 12 }, "end": { - "line": 234, + "line": 250, "column": 16 } } }, "property": { "type": "Identifier", - "start": 8738, - "end": 8746, + "start": 9178, + "end": 9186, "loc": { "start": { - "line": 234, + "line": 250, "column": 17 }, "end": { - "line": 234, + "line": 250, "column": 25 }, "identifierName": "phyloref" @@ -53521,15 +55081,15 @@ }, { "type": "StringLiteral", - "start": 8748, - "end": 8771, + "start": 9188, + "end": 9211, "loc": { "start": { - "line": 234, + "line": 250, "column": 27 }, "end": { - "line": 234, + "line": 250, "column": 50 } }, @@ -53544,115 +55104,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 8774, - "end": 9817, + "start": 9214, + "end": 10257, "loc": { "start": { - "line": 234, + "line": 250, "column": 53 }, "end": { - "line": 260, + "line": 276, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 8782, - "end": 9811, + "start": 9222, + "end": 10251, "loc": { "start": { - "line": 235, + "line": 251, "column": 6 }, "end": { - "line": 259, + "line": 275, "column": 9 } }, "argument": { "type": "CallExpression", - "start": 8789, - "end": 9810, + "start": 9229, + "end": 10250, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 259, + "line": 275, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 8789, - "end": 8831, + "start": 9229, + "end": 9271, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 55 } }, "object": { "type": "MemberExpression", - "start": 8789, - "end": 8827, + "start": 9229, + "end": 9267, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 51 } }, "object": { "type": "MemberExpression", - "start": 8789, - "end": 8802, + "start": 9229, + "end": 9242, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 8789, - "end": 8793, + "start": 9229, + "end": 9233, "loc": { "start": { - "line": 235, + "line": 251, "column": 13 }, "end": { - "line": 235, + "line": 251, "column": 17 } } }, "property": { "type": "Identifier", - "start": 8794, - "end": 8802, + "start": 9234, + "end": 9242, "loc": { "start": { - "line": 235, + "line": 251, "column": 18 }, "end": { - "line": 235, + "line": 251, "column": 26 }, "identifierName": "phyloref" @@ -53663,15 +55223,15 @@ }, "property": { "type": "StringLiteral", - "start": 8803, - "end": 8826, + "start": 9243, + "end": 9266, "loc": { "start": { - "line": 235, + "line": 251, "column": 27 }, "end": { - "line": 235, + "line": 251, "column": 50 } }, @@ -53685,15 +55245,15 @@ }, "property": { "type": "Identifier", - "start": 8828, - "end": 8831, + "start": 9268, + "end": 9271, "loc": { "start": { - "line": 235, + "line": 251, "column": 52 }, "end": { - "line": 235, + "line": 251, "column": 55 }, "identifierName": "map" @@ -53705,15 +55265,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 8832, - "end": 9809, + "start": 9272, + "end": 10249, "loc": { "start": { - "line": 235, + "line": 251, "column": 56 }, "end": { - "line": 259, + "line": 275, "column": 7 } }, @@ -53724,15 +55284,15 @@ "params": [ { "type": "Identifier", - "start": 8833, - "end": 8838, + "start": 9273, + "end": 9278, "loc": { "start": { - "line": 235, + "line": 251, "column": 57 }, "end": { - "line": 235, + "line": 251, "column": 62 }, "identifierName": "entry" @@ -53742,59 +55302,59 @@ ], "body": { "type": "BlockStatement", - "start": 8843, - "end": 9809, + "start": 9283, + "end": 10249, "loc": { "start": { - "line": 235, + "line": 251, "column": 67 }, "end": { - "line": 259, + "line": 275, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 8853, - "end": 8871, + "start": 9293, + "end": 9311, "loc": { "start": { - "line": 236, + "line": 252, "column": 8 }, "end": { - "line": 236, + "line": 252, "column": 26 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8859, - "end": 8870, + "start": 9299, + "end": 9310, "loc": { "start": { - "line": 236, + "line": 252, "column": 14 }, "end": { - "line": 236, + "line": 252, "column": 25 } }, "id": { "type": "Identifier", - "start": 8859, - "end": 8865, + "start": 9299, + "end": 9305, "loc": { "start": { - "line": 236, + "line": 252, "column": 14 }, "end": { - "line": 236, + "line": 252, "column": 20 }, "identifierName": "result" @@ -53803,15 +55363,15 @@ }, "init": { "type": "ObjectExpression", - "start": 8868, - "end": 8870, + "start": 9308, + "end": 9310, "loc": { "start": { - "line": 236, + "line": 252, "column": 23 }, "end": { - "line": 236, + "line": 252, "column": 25 } }, @@ -53824,15 +55384,15 @@ { "type": "CommentLine", "value": " Create a statusCURIE convenience field.", - "start": 8881, - "end": 8923, + "start": 9321, + "end": 9363, "loc": { "start": { - "line": 238, + "line": 254, "column": 8 }, "end": { - "line": 238, + "line": 254, "column": 50 } } @@ -53841,43 +55401,43 @@ }, { "type": "IfStatement", - "start": 8932, - "end": 9139, + "start": 9372, + "end": 9579, "loc": { "start": { - "line": 239, + "line": 255, "column": 8 }, "end": { - "line": 242, + "line": 258, "column": 9 } }, "test": { "type": "CallExpression", - "start": 8936, - "end": 8964, + "start": 9376, + "end": 9404, "loc": { "start": { - "line": 239, + "line": 255, "column": 12 }, "end": { - "line": 239, + "line": 255, "column": 40 } }, "callee": { "type": "Identifier", - "start": 8936, - "end": 8939, + "start": 9376, + "end": 9379, "loc": { "start": { - "line": 239, + "line": 255, "column": 12 }, "end": { - "line": 239, + "line": 255, "column": 15 }, "identifierName": "has" @@ -53888,15 +55448,15 @@ "arguments": [ { "type": "Identifier", - "start": 8940, - "end": 8945, + "start": 9380, + "end": 9385, "loc": { "start": { - "line": 239, + "line": 255, "column": 16 }, "end": { - "line": 239, + "line": 255, "column": 21 }, "identifierName": "entry" @@ -53905,15 +55465,15 @@ }, { "type": "StringLiteral", - "start": 8947, - "end": 8963, + "start": 9387, + "end": 9403, "loc": { "start": { - "line": 239, + "line": 255, "column": 23 }, "end": { - "line": 239, + "line": 255, "column": 39 } }, @@ -53928,73 +55488,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 8966, - "end": 9139, + "start": 9406, + "end": 9579, "loc": { "start": { - "line": 239, + "line": 255, "column": 42 }, "end": { - "line": 242, + "line": 258, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 8978, - "end": 9030, + "start": 9418, + "end": 9470, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 62 } }, "expression": { "type": "AssignmentExpression", - "start": 8978, - "end": 9029, + "start": 9418, + "end": 9469, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 61 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 8978, - "end": 8996, + "start": 9418, + "end": 9436, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 28 } }, "object": { "type": "Identifier", - "start": 8978, - "end": 8984, + "start": 9418, + "end": 9424, "loc": { "start": { - "line": 240, + "line": 256, "column": 10 }, "end": { - "line": 240, + "line": 256, "column": 16 }, "identifierName": "result" @@ -54003,15 +55563,15 @@ }, "property": { "type": "Identifier", - "start": 8985, - "end": 8996, + "start": 9425, + "end": 9436, "loc": { "start": { - "line": 240, + "line": 256, "column": 17 }, "end": { - "line": 240, + "line": 256, "column": 28 }, "identifierName": "statusCURIE" @@ -54022,43 +55582,43 @@ }, "right": { "type": "MemberExpression", - "start": 8999, - "end": 9029, + "start": 9439, + "end": 9469, "loc": { "start": { - "line": 240, + "line": 256, "column": 31 }, "end": { - "line": 240, + "line": 256, "column": 61 } }, "object": { "type": "MemberExpression", - "start": 8999, - "end": 9022, + "start": 9439, + "end": 9462, "loc": { "start": { - "line": 240, + "line": 256, "column": 31 }, "end": { - "line": 240, + "line": 256, "column": 54 } }, "object": { "type": "Identifier", - "start": 8999, - "end": 9004, + "start": 9439, + "end": 9444, "loc": { "start": { - "line": 240, + "line": 256, "column": 31 }, "end": { - "line": 240, + "line": 256, "column": 36 }, "identifierName": "entry" @@ -54067,15 +55627,15 @@ }, "property": { "type": "StringLiteral", - "start": 9005, - "end": 9021, + "start": 9445, + "end": 9461, "loc": { "start": { - "line": 240, + "line": 256, "column": 37 }, "end": { - "line": 240, + "line": 256, "column": 53 } }, @@ -54089,15 +55649,15 @@ }, "property": { "type": "StringLiteral", - "start": 9023, - "end": 9028, + "start": 9463, + "end": 9468, "loc": { "start": { - "line": 240, + "line": 256, "column": 55 }, "end": { - "line": 240, + "line": 256, "column": 60 } }, @@ -54113,58 +55673,58 @@ }, { "type": "ExpressionStatement", - "start": 9041, - "end": 9129, + "start": 9481, + "end": 9569, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 98 } }, "expression": { "type": "AssignmentExpression", - "start": 9041, - "end": 9128, + "start": 9481, + "end": 9568, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 97 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9041, - "end": 9063, + "start": 9481, + "end": 9503, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 32 } }, "object": { "type": "Identifier", - "start": 9041, - "end": 9047, + "start": 9481, + "end": 9487, "loc": { "start": { - "line": 241, + "line": 257, "column": 10 }, "end": { - "line": 241, + "line": 257, "column": 16 }, "identifierName": "result" @@ -54173,15 +55733,15 @@ }, "property": { "type": "Identifier", - "start": 9048, - "end": 9063, + "start": 9488, + "end": 9503, "loc": { "start": { - "line": 241, + "line": 257, "column": 17 }, "end": { - "line": 241, + "line": 257, "column": 32 }, "identifierName": "statusInEnglish" @@ -54192,57 +55752,57 @@ }, "right": { "type": "MemberExpression", - "start": 9066, - "end": 9128, + "start": 9506, + "end": 9568, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 97 } }, "object": { "type": "CallExpression", - "start": 9066, - "end": 9108, + "start": 9506, + "end": 9548, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 77 } }, "callee": { "type": "MemberExpression", - "start": 9066, - "end": 9106, + "start": 9506, + "end": 9546, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 75 } }, "object": { "type": "Identifier", - "start": 9066, - "end": 9081, + "start": 9506, + "end": 9521, "loc": { "start": { - "line": 241, + "line": 257, "column": 35 }, "end": { - "line": 241, + "line": 257, "column": 50 }, "identifierName": "PhylorefWrapper" @@ -54251,15 +55811,15 @@ }, "property": { "type": "Identifier", - "start": 9082, - "end": 9106, + "start": 9522, + "end": 9546, "loc": { "start": { - "line": 241, + "line": 257, "column": 51 }, "end": { - "line": 241, + "line": 257, "column": 75 }, "identifierName": "getStatusCURIEsInEnglish" @@ -54272,29 +55832,29 @@ }, "property": { "type": "MemberExpression", - "start": 9109, - "end": 9127, + "start": 9549, + "end": 9567, "loc": { "start": { - "line": 241, + "line": 257, "column": 78 }, "end": { - "line": 241, + "line": 257, "column": 96 } }, "object": { "type": "Identifier", - "start": 9109, - "end": 9115, + "start": 9549, + "end": 9555, "loc": { "start": { - "line": 241, + "line": 257, "column": 78 }, "end": { - "line": 241, + "line": 257, "column": 84 }, "identifierName": "result" @@ -54303,15 +55863,15 @@ }, "property": { "type": "Identifier", - "start": 9116, - "end": 9127, + "start": 9556, + "end": 9567, "loc": { "start": { - "line": 241, + "line": 257, "column": 85 }, "end": { - "line": 241, + "line": 257, "column": 96 }, "identifierName": "statusCURIE" @@ -54333,15 +55893,15 @@ { "type": "CommentLine", "value": " Create a statusCURIE convenience field.", - "start": 8881, - "end": 8923, + "start": 9321, + "end": 9363, "loc": { "start": { - "line": 238, + "line": 254, "column": 8 }, "end": { - "line": 238, + "line": 254, "column": 50 } } @@ -54351,15 +55911,15 @@ { "type": "CommentLine", "value": " Create intervalStart/intervalEnd convenient fields", - "start": 9149, - "end": 9202, + "start": 9589, + "end": 9642, "loc": { "start": { - "line": 244, + "line": 260, "column": 8 }, "end": { - "line": 244, + "line": 260, "column": 61 } } @@ -54368,43 +55928,43 @@ }, { "type": "IfStatement", - "start": 9211, - "end": 9777, + "start": 9651, + "end": 10217, "loc": { "start": { - "line": 245, + "line": 261, "column": 8 }, "end": { - "line": 256, + "line": 272, "column": 9 } }, "test": { "type": "CallExpression", - "start": 9215, - "end": 9239, + "start": 9655, + "end": 9679, "loc": { "start": { - "line": 245, + "line": 261, "column": 12 }, "end": { - "line": 245, + "line": 261, "column": 36 } }, "callee": { "type": "Identifier", - "start": 9215, - "end": 9218, + "start": 9655, + "end": 9658, "loc": { "start": { - "line": 245, + "line": 261, "column": 12 }, "end": { - "line": 245, + "line": 261, "column": 15 }, "identifierName": "has" @@ -54415,15 +55975,15 @@ "arguments": [ { "type": "Identifier", - "start": 9219, - "end": 9224, + "start": 9659, + "end": 9664, "loc": { "start": { - "line": 245, + "line": 261, "column": 16 }, "end": { - "line": 245, + "line": 261, "column": 21 }, "identifierName": "entry" @@ -54432,15 +55992,15 @@ }, { "type": "StringLiteral", - "start": 9226, - "end": 9238, + "start": 9666, + "end": 9678, "loc": { "start": { - "line": 245, + "line": 261, "column": 23 }, "end": { - "line": 245, + "line": 261, "column": 35 } }, @@ -54455,59 +56015,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 9241, - "end": 9777, + "start": 9681, + "end": 10217, "loc": { "start": { - "line": 245, + "line": 261, "column": 38 }, "end": { - "line": 256, + "line": 272, "column": 9 } }, "body": [ { "type": "VariableDeclaration", - "start": 9253, - "end": 9288, + "start": 9693, + "end": 9728, "loc": { "start": { - "line": 246, + "line": 262, "column": 10 }, "end": { - "line": 246, + "line": 262, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 9259, - "end": 9287, + "start": 9699, + "end": 9727, "loc": { "start": { - "line": 246, + "line": 262, "column": 16 }, "end": { - "line": 246, + "line": 262, "column": 44 } }, "id": { "type": "Identifier", - "start": 9259, - "end": 9265, + "start": 9699, + "end": 9705, "loc": { "start": { - "line": 246, + "line": 262, "column": 16 }, "end": { - "line": 246, + "line": 262, "column": 22 }, "identifierName": "atTime" @@ -54516,29 +56076,29 @@ }, "init": { "type": "MemberExpression", - "start": 9268, - "end": 9287, + "start": 9708, + "end": 9727, "loc": { "start": { - "line": 246, + "line": 262, "column": 25 }, "end": { - "line": 246, + "line": 262, "column": 44 } }, "object": { "type": "Identifier", - "start": 9268, - "end": 9273, + "start": 9708, + "end": 9713, "loc": { "start": { - "line": 246, + "line": 262, "column": 25 }, "end": { - "line": 246, + "line": 262, "column": 30 }, "identifierName": "entry" @@ -54547,15 +56107,15 @@ }, "property": { "type": "StringLiteral", - "start": 9274, - "end": 9286, + "start": 9714, + "end": 9726, "loc": { "start": { - "line": 246, + "line": 262, "column": 31 }, "end": { - "line": 246, + "line": 262, "column": 43 } }, @@ -54573,43 +56133,43 @@ }, { "type": "IfStatement", - "start": 9299, - "end": 9532, + "start": 9739, + "end": 9972, "loc": { "start": { - "line": 247, + "line": 263, "column": 10 }, "end": { - "line": 250, + "line": 266, "column": 11 } }, "test": { "type": "CallExpression", - "start": 9303, - "end": 9351, + "start": 9743, + "end": 9791, "loc": { "start": { - "line": 247, + "line": 263, "column": 14 }, "end": { - "line": 247, + "line": 263, "column": 62 } }, "callee": { "type": "Identifier", - "start": 9303, - "end": 9306, + "start": 9743, + "end": 9746, "loc": { "start": { - "line": 247, + "line": 263, "column": 14 }, "end": { - "line": 247, + "line": 263, "column": 17 }, "identifierName": "has" @@ -54619,15 +56179,15 @@ "arguments": [ { "type": "Identifier", - "start": 9307, - "end": 9313, + "start": 9747, + "end": 9753, "loc": { "start": { - "line": 247, + "line": 263, "column": 18 }, "end": { - "line": 247, + "line": 263, "column": 24 }, "identifierName": "atTime" @@ -54636,15 +56196,15 @@ }, { "type": "StringLiteral", - "start": 9315, - "end": 9350, + "start": 9755, + "end": 9790, "loc": { "start": { - "line": 247, + "line": 263, "column": 26 }, "end": { - "line": 247, + "line": 263, "column": 61 } }, @@ -54658,73 +56218,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 9353, - "end": 9532, + "start": 9793, + "end": 9972, "loc": { "start": { - "line": 247, + "line": 263, "column": 64 }, "end": { - "line": 250, + "line": 266, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 9367, - "end": 9434, + "start": 9807, + "end": 9874, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 79 } }, "expression": { "type": "AssignmentExpression", - "start": 9367, - "end": 9433, + "start": 9807, + "end": 9873, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 78 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9367, - "end": 9387, + "start": 9807, + "end": 9827, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 32 } }, "object": { "type": "Identifier", - "start": 9367, - "end": 9373, + "start": 9807, + "end": 9813, "loc": { "start": { - "line": 248, + "line": 264, "column": 12 }, "end": { - "line": 248, + "line": 264, "column": 18 }, "identifierName": "result" @@ -54733,15 +56293,15 @@ }, "property": { "type": "Identifier", - "start": 9374, - "end": 9387, + "start": 9814, + "end": 9827, "loc": { "start": { - "line": 248, + "line": 264, "column": 19 }, "end": { - "line": 248, + "line": 264, "column": 32 }, "identifierName": "intervalStart" @@ -54752,29 +56312,29 @@ }, "right": { "type": "MemberExpression", - "start": 9390, - "end": 9433, + "start": 9830, + "end": 9873, "loc": { "start": { - "line": 248, + "line": 264, "column": 35 }, "end": { - "line": 248, + "line": 264, "column": 78 } }, "object": { "type": "Identifier", - "start": 9390, - "end": 9396, + "start": 9830, + "end": 9836, "loc": { "start": { - "line": 248, + "line": 264, "column": 35 }, "end": { - "line": 248, + "line": 264, "column": 41 }, "identifierName": "atTime" @@ -54783,15 +56343,15 @@ }, "property": { "type": "StringLiteral", - "start": 9397, - "end": 9432, + "start": 9837, + "end": 9872, "loc": { "start": { - "line": 248, + "line": 264, "column": 42 }, "end": { - "line": 248, + "line": 264, "column": 77 } }, @@ -54807,58 +56367,58 @@ }, { "type": "ExpressionStatement", - "start": 9447, - "end": 9520, + "start": 9887, + "end": 9960, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 85 } }, "expression": { "type": "AssignmentExpression", - "start": 9447, - "end": 9519, + "start": 9887, + "end": 9959, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 84 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9447, - "end": 9477, + "start": 9887, + "end": 9917, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 42 } }, "object": { "type": "Identifier", - "start": 9447, - "end": 9453, + "start": 9887, + "end": 9893, "loc": { "start": { - "line": 249, + "line": 265, "column": 12 }, "end": { - "line": 249, + "line": 265, "column": 18 }, "identifierName": "result" @@ -54867,15 +56427,15 @@ }, "property": { "type": "Identifier", - "start": 9454, - "end": 9477, + "start": 9894, + "end": 9917, "loc": { "start": { - "line": 249, + "line": 265, "column": 19 }, "end": { - "line": 249, + "line": 265, "column": 42 }, "identifierName": "intervalStartAsCalendar" @@ -54886,57 +56446,57 @@ }, "right": { "type": "CallExpression", - "start": 9480, - "end": 9519, + "start": 9920, + "end": 9959, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 84 } }, "callee": { "type": "MemberExpression", - "start": 9480, - "end": 9517, + "start": 9920, + "end": 9957, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 82 } }, "object": { "type": "CallExpression", - "start": 9480, - "end": 9508, + "start": 9920, + "end": 9948, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 73 } }, "callee": { "type": "Identifier", - "start": 9480, - "end": 9486, + "start": 9920, + "end": 9926, "loc": { "start": { - "line": 249, + "line": 265, "column": 45 }, "end": { - "line": 249, + "line": 265, "column": 51 }, "identifierName": "moment" @@ -54946,29 +56506,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 9487, - "end": 9507, + "start": 9927, + "end": 9947, "loc": { "start": { - "line": 249, + "line": 265, "column": 52 }, "end": { - "line": 249, + "line": 265, "column": 72 } }, "object": { "type": "Identifier", - "start": 9487, - "end": 9493, + "start": 9927, + "end": 9933, "loc": { "start": { - "line": 249, + "line": 265, "column": 52 }, "end": { - "line": 249, + "line": 265, "column": 58 }, "identifierName": "result" @@ -54977,15 +56537,15 @@ }, "property": { "type": "Identifier", - "start": 9494, - "end": 9507, + "start": 9934, + "end": 9947, "loc": { "start": { - "line": 249, + "line": 265, "column": 59 }, "end": { - "line": 249, + "line": 265, "column": 72 }, "identifierName": "intervalStart" @@ -54998,15 +56558,15 @@ }, "property": { "type": "Identifier", - "start": 9509, - "end": 9517, + "start": 9949, + "end": 9957, "loc": { "start": { - "line": 249, + "line": 265, "column": 74 }, "end": { - "line": 249, + "line": 265, "column": 82 }, "identifierName": "calendar" @@ -55026,43 +56586,43 @@ }, { "type": "IfStatement", - "start": 9544, - "end": 9767, + "start": 9984, + "end": 10207, "loc": { "start": { - "line": 252, + "line": 268, "column": 10 }, "end": { - "line": 255, + "line": 271, "column": 11 } }, "test": { "type": "CallExpression", - "start": 9548, - "end": 9594, + "start": 9988, + "end": 10034, "loc": { "start": { - "line": 252, + "line": 268, "column": 14 }, "end": { - "line": 252, + "line": 268, "column": 60 } }, "callee": { "type": "Identifier", - "start": 9548, - "end": 9551, + "start": 9988, + "end": 9991, "loc": { "start": { - "line": 252, + "line": 268, "column": 14 }, "end": { - "line": 252, + "line": 268, "column": 17 }, "identifierName": "has" @@ -55072,15 +56632,15 @@ "arguments": [ { "type": "Identifier", - "start": 9552, - "end": 9558, + "start": 9992, + "end": 9998, "loc": { "start": { - "line": 252, + "line": 268, "column": 18 }, "end": { - "line": 252, + "line": 268, "column": 24 }, "identifierName": "atTime" @@ -55089,15 +56649,15 @@ }, { "type": "StringLiteral", - "start": 9560, - "end": 9593, + "start": 10000, + "end": 10033, "loc": { "start": { - "line": 252, + "line": 268, "column": 26 }, "end": { - "line": 252, + "line": 268, "column": 59 } }, @@ -55111,73 +56671,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 9596, - "end": 9767, + "start": 10036, + "end": 10207, "loc": { "start": { - "line": 252, + "line": 268, "column": 62 }, "end": { - "line": 255, + "line": 271, "column": 11 } }, "body": [ { "type": "ExpressionStatement", - "start": 9610, - "end": 9673, + "start": 10050, + "end": 10113, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 75 } }, "expression": { "type": "AssignmentExpression", - "start": 9610, - "end": 9672, + "start": 10050, + "end": 10112, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 74 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9610, - "end": 9628, + "start": 10050, + "end": 10068, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 30 } }, "object": { "type": "Identifier", - "start": 9610, - "end": 9616, + "start": 10050, + "end": 10056, "loc": { "start": { - "line": 253, + "line": 269, "column": 12 }, "end": { - "line": 253, + "line": 269, "column": 18 }, "identifierName": "result" @@ -55186,15 +56746,15 @@ }, "property": { "type": "Identifier", - "start": 9617, - "end": 9628, + "start": 10057, + "end": 10068, "loc": { "start": { - "line": 253, + "line": 269, "column": 19 }, "end": { - "line": 253, + "line": 269, "column": 30 }, "identifierName": "intervalEnd" @@ -55205,29 +56765,29 @@ }, "right": { "type": "MemberExpression", - "start": 9631, - "end": 9672, + "start": 10071, + "end": 10112, "loc": { "start": { - "line": 253, + "line": 269, "column": 33 }, "end": { - "line": 253, + "line": 269, "column": 74 } }, "object": { "type": "Identifier", - "start": 9631, - "end": 9637, + "start": 10071, + "end": 10077, "loc": { "start": { - "line": 253, + "line": 269, "column": 33 }, "end": { - "line": 253, + "line": 269, "column": 39 }, "identifierName": "atTime" @@ -55236,15 +56796,15 @@ }, "property": { "type": "StringLiteral", - "start": 9638, - "end": 9671, + "start": 10078, + "end": 10111, "loc": { "start": { - "line": 253, + "line": 269, "column": 40 }, "end": { - "line": 253, + "line": 269, "column": 73 } }, @@ -55260,58 +56820,58 @@ }, { "type": "ExpressionStatement", - "start": 9686, - "end": 9755, + "start": 10126, + "end": 10195, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 81 } }, "expression": { "type": "AssignmentExpression", - "start": 9686, - "end": 9754, + "start": 10126, + "end": 10194, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 80 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9686, - "end": 9714, + "start": 10126, + "end": 10154, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 40 } }, "object": { "type": "Identifier", - "start": 9686, - "end": 9692, + "start": 10126, + "end": 10132, "loc": { "start": { - "line": 254, + "line": 270, "column": 12 }, "end": { - "line": 254, + "line": 270, "column": 18 }, "identifierName": "result" @@ -55320,15 +56880,15 @@ }, "property": { "type": "Identifier", - "start": 9693, - "end": 9714, + "start": 10133, + "end": 10154, "loc": { "start": { - "line": 254, + "line": 270, "column": 19 }, "end": { - "line": 254, + "line": 270, "column": 40 }, "identifierName": "intervalEndAsCalendar" @@ -55339,57 +56899,57 @@ }, "right": { "type": "CallExpression", - "start": 9717, - "end": 9754, + "start": 10157, + "end": 10194, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 80 } }, "callee": { "type": "MemberExpression", - "start": 9717, - "end": 9752, + "start": 10157, + "end": 10192, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 78 } }, "object": { "type": "CallExpression", - "start": 9717, - "end": 9743, + "start": 10157, + "end": 10183, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 69 } }, "callee": { "type": "Identifier", - "start": 9717, - "end": 9723, + "start": 10157, + "end": 10163, "loc": { "start": { - "line": 254, + "line": 270, "column": 43 }, "end": { - "line": 254, + "line": 270, "column": 49 }, "identifierName": "moment" @@ -55399,29 +56959,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 9724, - "end": 9742, + "start": 10164, + "end": 10182, "loc": { "start": { - "line": 254, + "line": 270, "column": 50 }, "end": { - "line": 254, + "line": 270, "column": 68 } }, "object": { "type": "Identifier", - "start": 9724, - "end": 9730, + "start": 10164, + "end": 10170, "loc": { "start": { - "line": 254, + "line": 270, "column": 50 }, "end": { - "line": 254, + "line": 270, "column": 56 }, "identifierName": "result" @@ -55430,15 +56990,15 @@ }, "property": { "type": "Identifier", - "start": 9731, - "end": 9742, + "start": 10171, + "end": 10182, "loc": { "start": { - "line": 254, + "line": 270, "column": 57 }, "end": { - "line": 254, + "line": 270, "column": 68 }, "identifierName": "intervalEnd" @@ -55451,15 +57011,15 @@ }, "property": { "type": "Identifier", - "start": 9744, - "end": 9752, + "start": 10184, + "end": 10192, "loc": { "start": { - "line": 254, + "line": 270, "column": 70 }, "end": { - "line": 254, + "line": 270, "column": 78 }, "identifierName": "calendar" @@ -55485,15 +57045,15 @@ { "type": "CommentLine", "value": " Create intervalStart/intervalEnd convenient fields", - "start": 9149, - "end": 9202, + "start": 9589, + "end": 9642, "loc": { "start": { - "line": 244, + "line": 260, "column": 8 }, "end": { - "line": 244, + "line": 260, "column": 61 } } @@ -55502,29 +57062,29 @@ }, { "type": "ReturnStatement", - "start": 9787, - "end": 9801, + "start": 10227, + "end": 10241, "loc": { "start": { - "line": 258, + "line": 274, "column": 8 }, "end": { - "line": 258, + "line": 274, "column": 22 } }, "argument": { "type": "Identifier", - "start": 9794, - "end": 9800, + "start": 10234, + "end": 10240, "loc": { "start": { - "line": 258, + "line": 274, "column": 15 }, "end": { - "line": 258, + "line": 274, "column": 21 }, "identifierName": "result" @@ -55548,15 +57108,15 @@ { "type": "CommentLine", "value": " Return a list of status changes for a particular phyloreference", - "start": 8654, - "end": 8720, + "start": 9094, + "end": 9160, "loc": { "start": { - "line": 233, + "line": 249, "column": 4 }, "end": { - "line": 233, + "line": 249, "column": 70 } } @@ -55566,15 +57126,15 @@ { "type": "CommentLine", "value": " No changes? Return an empty list.", - "start": 9823, - "end": 9859, + "start": 10263, + "end": 10299, "loc": { "start": { - "line": 262, + "line": 278, "column": 4 }, "end": { - "line": 262, + "line": 278, "column": 40 } } @@ -55583,29 +57143,29 @@ }, { "type": "ReturnStatement", - "start": 9864, - "end": 9874, + "start": 10304, + "end": 10314, "loc": { "start": { - "line": 263, + "line": 279, "column": 4 }, "end": { - "line": 263, + "line": 279, "column": 14 } }, "argument": { "type": "ArrayExpression", - "start": 9871, - "end": 9873, + "start": 10311, + "end": 10313, "loc": { "start": { - "line": 263, + "line": 279, "column": 11 }, "end": { - "line": 263, + "line": 279, "column": 13 } }, @@ -55616,15 +57176,15 @@ { "type": "CommentLine", "value": " No changes? Return an empty list.", - "start": 9823, - "end": 9859, + "start": 10263, + "end": 10299, "loc": { "start": { - "line": 262, + "line": 278, "column": 4 }, "end": { - "line": 262, + "line": 278, "column": 40 } } @@ -55637,15 +57197,15 @@ }, { "type": "ClassMethod", - "start": 9882, - "end": 11543, + "start": 10322, + "end": 11983, "loc": { "start": { - "line": 266, + "line": 282, "column": 2 }, "end": { - "line": 308, + "line": 324, "column": 3 } }, @@ -55653,15 +57213,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9882, - "end": 9891, + "start": 10322, + "end": 10331, "loc": { "start": { - "line": 266, + "line": 282, "column": 2 }, "end": { - "line": 266, + "line": 282, "column": 11 }, "identifierName": "setStatus" @@ -55676,15 +57236,15 @@ "params": [ { "type": "Identifier", - "start": 9892, - "end": 9898, + "start": 10332, + "end": 10338, "loc": { "start": { - "line": 266, + "line": 282, "column": 12 }, "end": { - "line": 266, + "line": 282, "column": 18 }, "identifierName": "status" @@ -55694,44 +57254,44 @@ ], "body": { "type": "BlockStatement", - "start": 9900, - "end": 11543, + "start": 10340, + "end": 11983, "loc": { "start": { - "line": 266, + "line": 282, "column": 20 }, "end": { - "line": 308, + "line": 324, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 10006, - "end": 10162, + "start": 10446, + "end": 10602, "loc": { "start": { - "line": 270, + "line": 286, "column": 4 }, "end": { - "line": 272, + "line": 288, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 10010, - "end": 10066, + "start": 10450, + "end": 10506, "loc": { "start": { - "line": 270, + "line": 286, "column": 8 }, "end": { - "line": 270, + "line": 286, "column": 64 } }, @@ -55739,29 +57299,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10011, - "end": 10066, + "start": 10451, + "end": 10506, "loc": { "start": { - "line": 270, + "line": 286, "column": 9 }, "end": { - "line": 270, + "line": 286, "column": 64 } }, "callee": { "type": "Identifier", - "start": 10011, - "end": 10014, + "start": 10451, + "end": 10454, "loc": { "start": { - "line": 270, + "line": 286, "column": 9 }, "end": { - "line": 270, + "line": 286, "column": 12 }, "identifierName": "has" @@ -55772,43 +57332,43 @@ "arguments": [ { "type": "CallExpression", - "start": 10015, - "end": 10057, + "start": 10455, + "end": 10497, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 55 } }, "callee": { "type": "MemberExpression", - "start": 10015, - "end": 10055, + "start": 10455, + "end": 10495, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 53 } }, "object": { "type": "Identifier", - "start": 10015, - "end": 10030, + "start": 10455, + "end": 10470, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 28 }, "identifierName": "PhylorefWrapper" @@ -55817,15 +57377,15 @@ }, "property": { "type": "Identifier", - "start": 10031, - "end": 10055, + "start": 10471, + "end": 10495, "loc": { "start": { - "line": 270, + "line": 286, "column": 29 }, "end": { - "line": 270, + "line": 286, "column": 53 }, "identifierName": "getStatusCURIEsInEnglish" @@ -55838,15 +57398,15 @@ }, { "type": "Identifier", - "start": 10059, - "end": 10065, + "start": 10499, + "end": 10505, "loc": { "start": { - "line": 270, + "line": 286, "column": 57 }, "end": { - "line": 270, + "line": 286, "column": 63 }, "identifierName": "status" @@ -55863,58 +57423,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 10068, - "end": 10162, + "start": 10508, + "end": 10602, "loc": { "start": { - "line": 270, + "line": 286, "column": 66 }, "end": { - "line": 272, + "line": 288, "column": 5 } }, "body": [ { "type": "ThrowStatement", - "start": 10076, - "end": 10156, + "start": 10516, + "end": 10596, "loc": { "start": { - "line": 271, + "line": 287, "column": 6 }, "end": { - "line": 271, + "line": 287, "column": 86 } }, "argument": { "type": "NewExpression", - "start": 10082, - "end": 10155, + "start": 10522, + "end": 10595, "loc": { "start": { - "line": 271, + "line": 287, "column": 12 }, "end": { - "line": 271, + "line": 287, "column": 85 } }, "callee": { "type": "Identifier", - "start": 10086, - "end": 10095, + "start": 10526, + "end": 10535, "loc": { "start": { - "line": 271, + "line": 287, "column": 16 }, "end": { - "line": 271, + "line": 287, "column": 25 }, "identifierName": "TypeError" @@ -55924,30 +57484,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 10096, - "end": 10154, + "start": 10536, + "end": 10594, "loc": { "start": { - "line": 271, + "line": 287, "column": 26 }, "end": { - "line": 271, + "line": 287, "column": 84 } }, "expressions": [ { "type": "Identifier", - "start": 10145, - "end": 10151, + "start": 10585, + "end": 10591, "loc": { "start": { - "line": 271, + "line": 287, "column": 75 }, "end": { - "line": 271, + "line": 287, "column": 81 }, "identifierName": "status" @@ -55958,15 +57518,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 10097, - "end": 10143, + "start": 10537, + "end": 10583, "loc": { "start": { - "line": 271, + "line": 287, "column": 27 }, "end": { - "line": 271, + "line": 287, "column": 73 } }, @@ -55978,15 +57538,15 @@ }, { "type": "TemplateElement", - "start": 10152, - "end": 10153, + "start": 10592, + "end": 10593, "loc": { "start": { - "line": 271, + "line": 287, "column": 82 }, "end": { - "line": 271, + "line": 287, "column": 83 } }, @@ -56010,15 +57570,15 @@ { "type": "CommentLine", "value": " Set the status of a phyloreference", - "start": 9906, - "end": 9943, + "start": 10346, + "end": 10383, "loc": { "start": { - "line": 267, + "line": 283, "column": 4 }, "end": { - "line": 267, + "line": 283, "column": 41 } } @@ -56026,15 +57586,15 @@ { "type": "CommentLine", "value": "", - "start": 9948, - "end": 9950, + "start": 10388, + "end": 10390, "loc": { "start": { - "line": 268, + "line": 284, "column": 4 }, "end": { - "line": 268, + "line": 284, "column": 6 } } @@ -56042,15 +57602,15 @@ { "type": "CommentLine", "value": " Check whether we have a valid status CURIE.", - "start": 9955, - "end": 10001, + "start": 10395, + "end": 10441, "loc": { "start": { - "line": 269, + "line": 285, "column": 4 }, "end": { - "line": 269, + "line": 285, "column": 50 } } @@ -56060,15 +57620,15 @@ { "type": "CommentLine", "value": " See if we can end the previous interval.", - "start": 10168, - "end": 10211, + "start": 10608, + "end": 10651, "loc": { "start": { - "line": 274, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 290, "column": 47 } } @@ -56077,44 +57637,44 @@ }, { "type": "VariableDeclaration", - "start": 10216, - "end": 10271, + "start": 10656, + "end": 10711, "loc": { "start": { - "line": 275, + "line": 291, "column": 4 }, "end": { - "line": 275, + "line": 291, "column": 59 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10222, - "end": 10270, + "start": 10662, + "end": 10710, "loc": { "start": { - "line": 275, + "line": 291, "column": 10 }, "end": { - "line": 275, + "line": 291, "column": 58 } }, "id": { "type": "Identifier", - "start": 10222, - "end": 10233, + "start": 10662, + "end": 10673, "loc": { "start": { - "line": 275, + "line": 291, "column": 10 }, "end": { - "line": 275, + "line": 291, "column": 21 }, "identifierName": "currentTime" @@ -56124,57 +57684,57 @@ }, "init": { "type": "CallExpression", - "start": 10236, - "end": 10270, + "start": 10676, + "end": 10710, "loc": { "start": { - "line": 275, + "line": 291, "column": 24 }, "end": { - "line": 275, + "line": 291, "column": 58 } }, "callee": { "type": "MemberExpression", - "start": 10236, - "end": 10268, + "start": 10676, + "end": 10708, "loc": { "start": { - "line": 275, + "line": 291, "column": 24 }, "end": { - "line": 275, + "line": 291, "column": 56 } }, "object": { "type": "NewExpression", - "start": 10236, - "end": 10256, + "start": 10676, + "end": 10696, "loc": { "start": { - "line": 275, + "line": 291, "column": 24 }, "end": { - "line": 275, + "line": 291, "column": 44 } }, "callee": { "type": "Identifier", - "start": 10240, - "end": 10244, + "start": 10680, + "end": 10684, "loc": { "start": { - "line": 275, + "line": 291, "column": 28 }, "end": { - "line": 275, + "line": 291, "column": 32 }, "identifierName": "Date" @@ -56184,43 +57744,43 @@ "arguments": [ { "type": "CallExpression", - "start": 10245, - "end": 10255, + "start": 10685, + "end": 10695, "loc": { "start": { - "line": 275, + "line": 291, "column": 33 }, "end": { - "line": 275, + "line": 291, "column": 43 } }, "callee": { "type": "MemberExpression", - "start": 10245, - "end": 10253, + "start": 10685, + "end": 10693, "loc": { "start": { - "line": 275, + "line": 291, "column": 33 }, "end": { - "line": 275, + "line": 291, "column": 41 } }, "object": { "type": "Identifier", - "start": 10245, - "end": 10249, + "start": 10685, + "end": 10689, "loc": { "start": { - "line": 275, + "line": 291, "column": 33 }, "end": { - "line": 275, + "line": 291, "column": 37 }, "identifierName": "Date" @@ -56229,15 +57789,15 @@ }, "property": { "type": "Identifier", - "start": 10250, - "end": 10253, + "start": 10690, + "end": 10693, "loc": { "start": { - "line": 275, + "line": 291, "column": 38 }, "end": { - "line": 275, + "line": 291, "column": 41 }, "identifierName": "now" @@ -56252,15 +57812,15 @@ }, "property": { "type": "Identifier", - "start": 10257, - "end": 10268, + "start": 10697, + "end": 10708, "loc": { "start": { - "line": 275, + "line": 291, "column": 45 }, "end": { - "line": 275, + "line": 291, "column": 56 }, "identifierName": "toISOString" @@ -56279,15 +57839,15 @@ { "type": "CommentLine", "value": " See if we can end the previous interval.", - "start": 10168, - "end": 10211, + "start": 10608, + "end": 10651, "loc": { "start": { - "line": 274, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 290, "column": 47 } } @@ -56296,29 +57856,29 @@ }, { "type": "IfStatement", - "start": 10277, - "end": 10447, + "start": 10717, + "end": 10887, "loc": { "start": { - "line": 277, + "line": 293, "column": 4 }, "end": { - "line": 280, + "line": 296, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 10281, - "end": 10325, + "start": 10721, + "end": 10765, "loc": { "start": { - "line": 277, + "line": 293, "column": 8 }, "end": { - "line": 277, + "line": 293, "column": 52 } }, @@ -56326,29 +57886,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10282, - "end": 10325, + "start": 10722, + "end": 10765, "loc": { "start": { - "line": 277, + "line": 293, "column": 9 }, "end": { - "line": 277, + "line": 293, "column": 52 } }, "callee": { "type": "Identifier", - "start": 10282, - "end": 10285, + "start": 10722, + "end": 10725, "loc": { "start": { - "line": 277, + "line": 293, "column": 9 }, "end": { - "line": 277, + "line": 293, "column": 12 }, "identifierName": "has" @@ -56358,44 +57918,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 10286, - "end": 10299, + "start": 10726, + "end": 10739, "loc": { "start": { - "line": 277, + "line": 293, "column": 13 }, "end": { - "line": 277, + "line": 293, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 10286, - "end": 10290, + "start": 10726, + "end": 10730, "loc": { "start": { - "line": 277, + "line": 293, "column": 13 }, "end": { - "line": 277, + "line": 293, "column": 17 } } }, "property": { "type": "Identifier", - "start": 10291, - "end": 10299, + "start": 10731, + "end": 10739, "loc": { "start": { - "line": 277, + "line": 293, "column": 18 }, "end": { - "line": 277, + "line": 293, "column": 26 }, "identifierName": "phyloref" @@ -56406,15 +57966,15 @@ }, { "type": "StringLiteral", - "start": 10301, - "end": 10324, + "start": 10741, + "end": 10764, "loc": { "start": { - "line": 277, + "line": 293, "column": 28 }, "end": { - "line": 277, + "line": 293, "column": 51 } }, @@ -56432,87 +57992,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 10327, - "end": 10447, + "start": 10767, + "end": 10887, "loc": { "start": { - "line": 277, + "line": 293, "column": 54 }, "end": { - "line": 280, + "line": 296, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 10397, - "end": 10441, + "start": 10837, + "end": 10881, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 50 } }, "expression": { "type": "AssignmentExpression", - "start": 10397, - "end": 10440, + "start": 10837, + "end": 10880, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 49 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10397, - "end": 10435, + "start": 10837, + "end": 10875, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 44 } }, "object": { "type": "MemberExpression", - "start": 10397, - "end": 10410, + "start": 10837, + "end": 10850, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 10397, - "end": 10401, + "start": 10837, + "end": 10841, "loc": { "start": { - "line": 279, + "line": 295, "column": 6 }, "end": { - "line": 279, + "line": 295, "column": 10 } }, @@ -56520,15 +58080,15 @@ }, "property": { "type": "Identifier", - "start": 10402, - "end": 10410, + "start": 10842, + "end": 10850, "loc": { "start": { - "line": 279, + "line": 295, "column": 11 }, "end": { - "line": 279, + "line": 295, "column": 19 }, "identifierName": "phyloref" @@ -56540,15 +58100,15 @@ }, "property": { "type": "StringLiteral", - "start": 10411, - "end": 10434, + "start": 10851, + "end": 10874, "loc": { "start": { - "line": 279, + "line": 295, "column": 20 }, "end": { - "line": 279, + "line": 295, "column": 43 } }, @@ -56563,15 +58123,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10438, - "end": 10440, + "start": 10878, + "end": 10880, "loc": { "start": { - "line": 279, + "line": 295, "column": 47 }, "end": { - "line": 279, + "line": 295, "column": 49 } }, @@ -56583,15 +58143,15 @@ { "type": "CommentLine", "value": " Vue.set(this.phyloref, 'pso:holdsStatusInTime', []);", - "start": 10335, - "end": 10390, + "start": 10775, + "end": 10830, "loc": { "start": { - "line": 278, + "line": 294, "column": 6 }, "end": { - "line": 278, + "line": 294, "column": 61 } } @@ -56607,15 +58167,15 @@ { "type": "CommentLine", "value": " Check to see if there's a previous time interval we should end.", - "start": 10453, - "end": 10519, + "start": 10893, + "end": 10959, "loc": { "start": { - "line": 282, + "line": 298, "column": 4 }, "end": { - "line": 282, + "line": 298, "column": 70 } } @@ -56624,71 +58184,71 @@ }, { "type": "IfStatement", - "start": 10524, - "end": 11267, + "start": 10964, + "end": 11707, "loc": { "start": { - "line": 283, + "line": 299, "column": 4 }, "end": { - "line": 298, + "line": 314, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 10535, - "end": 10647, + "start": 10975, + "end": 11087, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 285, + "line": 301, "column": 58 } }, "left": { "type": "CallExpression", - "start": 10535, - "end": 10588, + "start": 10975, + "end": 11028, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 284, + "line": 300, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 10535, - "end": 10548, + "start": 10975, + "end": 10988, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 284, + "line": 300, "column": 19 } }, "object": { "type": "Identifier", - "start": 10535, - "end": 10540, + "start": 10975, + "end": 10980, "loc": { "start": { - "line": 284, + "line": 300, "column": 6 }, "end": { - "line": 284, + "line": 300, "column": 11 }, "identifierName": "Array" @@ -56698,15 +58258,15 @@ }, "property": { "type": "Identifier", - "start": 10541, - "end": 10548, + "start": 10981, + "end": 10988, "loc": { "start": { - "line": 284, + "line": 300, "column": 12 }, "end": { - "line": 284, + "line": 300, "column": 19 }, "identifierName": "isArray" @@ -56719,58 +58279,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 10549, - "end": 10587, + "start": 10989, + "end": 11027, "loc": { "start": { - "line": 284, + "line": 300, "column": 20 }, "end": { - "line": 284, + "line": 300, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 10549, - "end": 10562, + "start": 10989, + "end": 11002, "loc": { "start": { - "line": 284, + "line": 300, "column": 20 }, "end": { - "line": 284, + "line": 300, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 10549, - "end": 10553, + "start": 10989, + "end": 10993, "loc": { "start": { - "line": 284, + "line": 300, "column": 20 }, "end": { - "line": 284, + "line": 300, "column": 24 } } }, "property": { "type": "Identifier", - "start": 10554, - "end": 10562, + "start": 10994, + "end": 11002, "loc": { "start": { - "line": 284, + "line": 300, "column": 25 }, "end": { - "line": 284, + "line": 300, "column": 33 }, "identifierName": "phyloref" @@ -56781,15 +58341,15 @@ }, "property": { "type": "StringLiteral", - "start": 10563, - "end": 10586, + "start": 11003, + "end": 11026, "loc": { "start": { - "line": 284, + "line": 300, "column": 34 }, "end": { - "line": 284, + "line": 300, "column": 57 } }, @@ -56807,86 +58367,86 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 10598, - "end": 10647, + "start": 11038, + "end": 11087, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 58 } }, "left": { "type": "MemberExpression", - "start": 10598, - "end": 10643, + "start": 11038, + "end": 11083, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 54 } }, "object": { "type": "MemberExpression", - "start": 10598, - "end": 10636, + "start": 11038, + "end": 11076, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 47 } }, "object": { "type": "MemberExpression", - "start": 10598, - "end": 10611, + "start": 11038, + "end": 11051, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 10598, - "end": 10602, + "start": 11038, + "end": 11042, "loc": { "start": { - "line": 285, + "line": 301, "column": 9 }, "end": { - "line": 285, + "line": 301, "column": 13 } } }, "property": { "type": "Identifier", - "start": 10603, - "end": 10611, + "start": 11043, + "end": 11051, "loc": { "start": { - "line": 285, + "line": 301, "column": 14 }, "end": { - "line": 285, + "line": 301, "column": 22 }, "identifierName": "phyloref" @@ -56897,15 +58457,15 @@ }, "property": { "type": "StringLiteral", - "start": 10612, - "end": 10635, + "start": 11052, + "end": 11075, "loc": { "start": { - "line": 285, + "line": 301, "column": 23 }, "end": { - "line": 285, + "line": 301, "column": 46 } }, @@ -56919,15 +58479,15 @@ }, "property": { "type": "Identifier", - "start": 10637, - "end": 10643, + "start": 11077, + "end": 11083, "loc": { "start": { - "line": 285, + "line": 301, "column": 48 }, "end": { - "line": 285, + "line": 301, "column": 54 }, "identifierName": "length" @@ -56939,15 +58499,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 10646, - "end": 10647, + "start": 11086, + "end": 11087, "loc": { "start": { - "line": 285, + "line": 301, "column": 57 }, "end": { - "line": 285, + "line": 301, "column": 58 } }, @@ -56962,59 +58522,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 10654, - "end": 11267, + "start": 11094, + "end": 11707, "loc": { "start": { - "line": 286, + "line": 302, "column": 6 }, "end": { - "line": 298, + "line": 314, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 10662, - "end": 10777, + "start": 11102, + "end": 11217, "loc": { "start": { - "line": 287, + "line": 303, "column": 6 }, "end": { - "line": 287, + "line": 303, "column": 121 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10668, - "end": 10776, + "start": 11108, + "end": 11216, "loc": { "start": { - "line": 287, + "line": 303, "column": 12 }, "end": { - "line": 287, + "line": 303, "column": 120 } }, "id": { "type": "Identifier", - "start": 10668, - "end": 10684, + "start": 11108, + "end": 11124, "loc": { "start": { - "line": 287, + "line": 303, "column": 12 }, "end": { - "line": 287, + "line": 303, "column": 28 }, "identifierName": "lastStatusInTime" @@ -57023,72 +58583,72 @@ }, "init": { "type": "MemberExpression", - "start": 10687, - "end": 10776, + "start": 11127, + "end": 11216, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 120 } }, "object": { "type": "MemberExpression", - "start": 10687, - "end": 10725, + "start": 11127, + "end": 11165, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 69 } }, "object": { "type": "MemberExpression", - "start": 10687, - "end": 10700, + "start": 11127, + "end": 11140, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 10687, - "end": 10691, + "start": 11127, + "end": 11131, "loc": { "start": { - "line": 287, + "line": 303, "column": 31 }, "end": { - "line": 287, + "line": 303, "column": 35 } } }, "property": { "type": "Identifier", - "start": 10692, - "end": 10700, + "start": 11132, + "end": 11140, "loc": { "start": { - "line": 287, + "line": 303, "column": 36 }, "end": { - "line": 287, + "line": 303, "column": 44 }, "identifierName": "phyloref" @@ -57099,15 +58659,15 @@ }, "property": { "type": "StringLiteral", - "start": 10701, - "end": 10724, + "start": 11141, + "end": 11164, "loc": { "start": { - "line": 287, + "line": 303, "column": 45 }, "end": { - "line": 287, + "line": 303, "column": 68 } }, @@ -57121,86 +58681,86 @@ }, "property": { "type": "BinaryExpression", - "start": 10726, - "end": 10775, + "start": 11166, + "end": 11215, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 119 } }, "left": { "type": "MemberExpression", - "start": 10726, - "end": 10771, + "start": 11166, + "end": 11211, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 115 } }, "object": { "type": "MemberExpression", - "start": 10726, - "end": 10764, + "start": 11166, + "end": 11204, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 108 } }, "object": { "type": "MemberExpression", - "start": 10726, - "end": 10739, + "start": 11166, + "end": 11179, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 83 } }, "object": { "type": "ThisExpression", - "start": 10726, - "end": 10730, + "start": 11166, + "end": 11170, "loc": { "start": { - "line": 287, + "line": 303, "column": 70 }, "end": { - "line": 287, + "line": 303, "column": 74 } } }, "property": { "type": "Identifier", - "start": 10731, - "end": 10739, + "start": 11171, + "end": 11179, "loc": { "start": { - "line": 287, + "line": 303, "column": 75 }, "end": { - "line": 287, + "line": 303, "column": 83 }, "identifierName": "phyloref" @@ -57211,15 +58771,15 @@ }, "property": { "type": "StringLiteral", - "start": 10740, - "end": 10763, + "start": 11180, + "end": 11203, "loc": { "start": { - "line": 287, + "line": 303, "column": 84 }, "end": { - "line": 287, + "line": 303, "column": 107 } }, @@ -57233,15 +58793,15 @@ }, "property": { "type": "Identifier", - "start": 10765, - "end": 10771, + "start": 11205, + "end": 11211, "loc": { "start": { - "line": 287, + "line": 303, "column": 109 }, "end": { - "line": 287, + "line": 303, "column": 115 }, "identifierName": "length" @@ -57253,15 +58813,15 @@ "operator": "-", "right": { "type": "NumericLiteral", - "start": 10774, - "end": 10775, + "start": 11214, + "end": 11215, "loc": { "start": { - "line": 287, + "line": 303, "column": 118 }, "end": { - "line": 287, + "line": 303, "column": 119 } }, @@ -57281,15 +58841,15 @@ { "type": "CommentLine", "value": " if (!has(lastStatusInTime, 'tvc:atTime'))", - "start": 10785, - "end": 10829, + "start": 11225, + "end": 11269, "loc": { "start": { - "line": 289, + "line": 305, "column": 6 }, "end": { - "line": 289, + "line": 305, "column": 50 } } @@ -57297,15 +58857,15 @@ { "type": "CommentLine", "value": " Vue.set(lastStatusInTime, 'tvc:atTime', {});", - "start": 10836, - "end": 10884, + "start": 11276, + "end": 11324, "loc": { "start": { - "line": 290, + "line": 306, "column": 6 }, "end": { - "line": 290, + "line": 306, "column": 54 } } @@ -57314,29 +58874,29 @@ }, { "type": "IfStatement", - "start": 10891, - "end": 10987, + "start": 11331, + "end": 11427, "loc": { "start": { - "line": 291, + "line": 307, "column": 6 }, "end": { - "line": 293, + "line": 309, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 10895, - "end": 10931, + "start": 11335, + "end": 11371, "loc": { "start": { - "line": 291, + "line": 307, "column": 10 }, "end": { - "line": 291, + "line": 307, "column": 46 } }, @@ -57344,29 +58904,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10896, - "end": 10931, + "start": 11336, + "end": 11371, "loc": { "start": { - "line": 291, + "line": 307, "column": 11 }, "end": { - "line": 291, + "line": 307, "column": 46 } }, "callee": { "type": "Identifier", - "start": 10896, - "end": 10899, + "start": 11336, + "end": 11339, "loc": { "start": { - "line": 291, + "line": 307, "column": 11 }, "end": { - "line": 291, + "line": 307, "column": 14 }, "identifierName": "has" @@ -57377,15 +58937,15 @@ "arguments": [ { "type": "Identifier", - "start": 10900, - "end": 10916, + "start": 11340, + "end": 11356, "loc": { "start": { - "line": 291, + "line": 307, "column": 15 }, "end": { - "line": 291, + "line": 307, "column": 31 }, "identifierName": "lastStatusInTime" @@ -57394,15 +58954,15 @@ }, { "type": "StringLiteral", - "start": 10918, - "end": 10930, + "start": 11358, + "end": 11370, "loc": { "start": { - "line": 291, + "line": 307, "column": 33 }, "end": { - "line": 291, + "line": 307, "column": 45 } }, @@ -57422,73 +58982,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 10933, - "end": 10987, + "start": 11373, + "end": 11427, "loc": { "start": { - "line": 291, + "line": 307, "column": 48 }, "end": { - "line": 293, + "line": 309, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 10943, - "end": 10979, + "start": 11383, + "end": 11419, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 10943, - "end": 10978, + "start": 11383, + "end": 11418, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10943, - "end": 10973, + "start": 11383, + "end": 11413, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 38 } }, "object": { "type": "Identifier", - "start": 10943, - "end": 10959, + "start": 11383, + "end": 11399, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 24 }, "identifierName": "lastStatusInTime" @@ -57497,15 +59057,15 @@ }, "property": { "type": "StringLiteral", - "start": 10960, - "end": 10972, + "start": 11400, + "end": 11412, "loc": { "start": { - "line": 292, + "line": 308, "column": 25 }, "end": { - "line": 292, + "line": 308, "column": 37 } }, @@ -57519,15 +59079,15 @@ }, "right": { "type": "ObjectExpression", - "start": 10976, - "end": 10978, + "start": 11416, + "end": 11418, "loc": { "start": { - "line": 292, + "line": 308, "column": 41 }, "end": { - "line": 292, + "line": 308, "column": 43 } }, @@ -57543,15 +59103,15 @@ { "type": "CommentLine", "value": " if (!has(lastStatusInTime, 'tvc:atTime'))", - "start": 10785, - "end": 10829, + "start": 11225, + "end": 11269, "loc": { "start": { - "line": 289, + "line": 305, "column": 6 }, "end": { - "line": 289, + "line": 305, "column": 50 } } @@ -57559,15 +59119,15 @@ { "type": "CommentLine", "value": " Vue.set(lastStatusInTime, 'tvc:atTime', {});", - "start": 10836, - "end": 10884, + "start": 11276, + "end": 11324, "loc": { "start": { - "line": 290, + "line": 306, "column": 6 }, "end": { - "line": 290, + "line": 306, "column": 54 } } @@ -57576,29 +59136,29 @@ }, { "type": "IfStatement", - "start": 10994, - "end": 11261, + "start": 11434, + "end": 11701, "loc": { "start": { - "line": 294, + "line": 310, "column": 6 }, "end": { - "line": 297, + "line": 313, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 10998, - "end": 11069, + "start": 11438, + "end": 11509, "loc": { "start": { - "line": 294, + "line": 310, "column": 10 }, "end": { - "line": 294, + "line": 310, "column": 81 } }, @@ -57606,29 +59166,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10999, - "end": 11069, + "start": 11439, + "end": 11509, "loc": { "start": { - "line": 294, + "line": 310, "column": 11 }, "end": { - "line": 294, + "line": 310, "column": 81 } }, "callee": { "type": "Identifier", - "start": 10999, - "end": 11002, + "start": 11439, + "end": 11442, "loc": { "start": { - "line": 294, + "line": 310, "column": 11 }, "end": { - "line": 294, + "line": 310, "column": 14 }, "identifierName": "has" @@ -57638,29 +59198,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 11003, - "end": 11033, + "start": 11443, + "end": 11473, "loc": { "start": { - "line": 294, + "line": 310, "column": 15 }, "end": { - "line": 294, + "line": 310, "column": 45 } }, "object": { "type": "Identifier", - "start": 11003, - "end": 11019, + "start": 11443, + "end": 11459, "loc": { "start": { - "line": 294, + "line": 310, "column": 15 }, "end": { - "line": 294, + "line": 310, "column": 31 }, "identifierName": "lastStatusInTime" @@ -57669,15 +59229,15 @@ }, "property": { "type": "StringLiteral", - "start": 11020, - "end": 11032, + "start": 11460, + "end": 11472, "loc": { "start": { - "line": 294, + "line": 310, "column": 32 }, "end": { - "line": 294, + "line": 310, "column": 44 } }, @@ -57691,15 +59251,15 @@ }, { "type": "StringLiteral", - "start": 11035, - "end": 11068, + "start": 11475, + "end": 11508, "loc": { "start": { - "line": 294, + "line": 310, "column": 47 }, "end": { - "line": 294, + "line": 310, "column": 80 } }, @@ -57717,87 +59277,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 11071, - "end": 11261, + "start": 11511, + "end": 11701, "loc": { "start": { - "line": 294, + "line": 310, "column": 83 }, "end": { - "line": 297, + "line": 313, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 11173, - "end": 11253, + "start": 11613, + "end": 11693, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 88 } }, "expression": { "type": "AssignmentExpression", - "start": 11173, - "end": 11252, + "start": 11613, + "end": 11692, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 87 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11173, - "end": 11238, + "start": 11613, + "end": 11678, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 73 } }, "object": { "type": "MemberExpression", - "start": 11173, - "end": 11203, + "start": 11613, + "end": 11643, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 38 } }, "object": { "type": "Identifier", - "start": 11173, - "end": 11189, + "start": 11613, + "end": 11629, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 24 }, "identifierName": "lastStatusInTime" @@ -57807,15 +59367,15 @@ }, "property": { "type": "StringLiteral", - "start": 11190, - "end": 11202, + "start": 11630, + "end": 11642, "loc": { "start": { - "line": 296, + "line": 312, "column": 25 }, "end": { - "line": 296, + "line": 312, "column": 37 } }, @@ -57830,15 +59390,15 @@ }, "property": { "type": "StringLiteral", - "start": 11204, - "end": 11237, + "start": 11644, + "end": 11677, "loc": { "start": { - "line": 296, + "line": 312, "column": 39 }, "end": { - "line": 296, + "line": 312, "column": 72 } }, @@ -57853,15 +59413,15 @@ }, "right": { "type": "Identifier", - "start": 11241, - "end": 11252, + "start": 11681, + "end": 11692, "loc": { "start": { - "line": 296, + "line": 312, "column": 76 }, "end": { - "line": 296, + "line": 312, "column": 87 }, "identifierName": "currentTime" @@ -57874,15 +59434,15 @@ { "type": "CommentLine", "value": " If the last time entry doesn't already have an interval end date, set it to now.", - "start": 11081, - "end": 11164, + "start": 11521, + "end": 11604, "loc": { "start": { - "line": 295, + "line": 311, "column": 8 }, "end": { - "line": 295, + "line": 311, "column": 91 } } @@ -57903,15 +59463,15 @@ { "type": "CommentLine", "value": " Check to see if there's a previous time interval we should end.", - "start": 10453, - "end": 10519, + "start": 10893, + "end": 10959, "loc": { "start": { - "line": 282, + "line": 298, "column": 4 }, "end": { - "line": 282, + "line": 298, "column": 70 } } @@ -57921,15 +59481,15 @@ { "type": "CommentLine", "value": " Create new entry.", - "start": 11273, - "end": 11293, + "start": 11713, + "end": 11733, "loc": { "start": { - "line": 300, + "line": 316, "column": 4 }, "end": { - "line": 300, + "line": 316, "column": 24 } } @@ -57938,85 +59498,85 @@ }, { "type": "ExpressionStatement", - "start": 11298, - "end": 11539, + "start": 11738, + "end": 11979, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 307, + "line": 323, "column": 7 } }, "expression": { "type": "CallExpression", - "start": 11298, - "end": 11538, + "start": 11738, + "end": 11978, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 307, + "line": 323, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 11298, - "end": 11341, + "start": 11738, + "end": 11781, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 47 } }, "object": { "type": "MemberExpression", - "start": 11298, - "end": 11336, + "start": 11738, + "end": 11776, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 42 } }, "object": { "type": "MemberExpression", - "start": 11298, - "end": 11311, + "start": 11738, + "end": 11751, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 17 } }, "object": { "type": "ThisExpression", - "start": 11298, - "end": 11302, + "start": 11738, + "end": 11742, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 8 } }, @@ -58024,15 +59584,15 @@ }, "property": { "type": "Identifier", - "start": 11303, - "end": 11311, + "start": 11743, + "end": 11751, "loc": { "start": { - "line": 301, + "line": 317, "column": 9 }, "end": { - "line": 301, + "line": 317, "column": 17 }, "identifierName": "phyloref" @@ -58044,15 +59604,15 @@ }, "property": { "type": "StringLiteral", - "start": 11312, - "end": 11335, + "start": 11752, + "end": 11775, "loc": { "start": { - "line": 301, + "line": 317, "column": 18 }, "end": { - "line": 301, + "line": 317, "column": 41 } }, @@ -58067,15 +59627,15 @@ }, "property": { "type": "Identifier", - "start": 11337, - "end": 11341, + "start": 11777, + "end": 11781, "loc": { "start": { - "line": 301, + "line": 317, "column": 43 }, "end": { - "line": 301, + "line": 317, "column": 47 }, "identifierName": "push" @@ -58088,30 +59648,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 11342, - "end": 11537, + "start": 11782, + "end": 11977, "loc": { "start": { - "line": 301, + "line": 317, "column": 48 }, "end": { - "line": 307, + "line": 323, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 11350, - "end": 11398, + "start": 11790, + "end": 11838, "loc": { "start": { - "line": 302, + "line": 318, "column": 6 }, "end": { - "line": 302, + "line": 318, "column": 54 } }, @@ -58120,15 +59680,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11350, - "end": 11357, + "start": 11790, + "end": 11797, "loc": { "start": { - "line": 302, + "line": 318, "column": 6 }, "end": { - "line": 302, + "line": 318, "column": 13 } }, @@ -58140,15 +59700,15 @@ }, "value": { "type": "StringLiteral", - "start": 11359, - "end": 11398, + "start": 11799, + "end": 11838, "loc": { "start": { - "line": 302, + "line": 318, "column": 15 }, "end": { - "line": 302, + "line": 318, "column": 54 } }, @@ -58161,15 +59721,15 @@ }, { "type": "ObjectProperty", - "start": 11406, - "end": 11441, + "start": 11846, + "end": 11881, "loc": { "start": { - "line": 303, + "line": 319, "column": 6 }, "end": { - "line": 303, + "line": 319, "column": 41 } }, @@ -58178,15 +59738,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11406, - "end": 11422, + "start": 11846, + "end": 11862, "loc": { "start": { - "line": 303, + "line": 319, "column": 6 }, "end": { - "line": 303, + "line": 319, "column": 22 } }, @@ -58198,30 +59758,30 @@ }, "value": { "type": "ObjectExpression", - "start": 11424, - "end": 11441, + "start": 11864, + "end": 11881, "loc": { "start": { - "line": 303, + "line": 319, "column": 24 }, "end": { - "line": 303, + "line": 319, "column": 41 } }, "properties": [ { "type": "ObjectProperty", - "start": 11426, - "end": 11439, + "start": 11866, + "end": 11879, "loc": { "start": { - "line": 303, + "line": 319, "column": 26 }, "end": { - "line": 303, + "line": 319, "column": 39 } }, @@ -58230,15 +59790,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11426, - "end": 11431, + "start": 11866, + "end": 11871, "loc": { "start": { - "line": 303, + "line": 319, "column": 26 }, "end": { - "line": 303, + "line": 319, "column": 31 } }, @@ -58250,15 +59810,15 @@ }, "value": { "type": "Identifier", - "start": 11433, - "end": 11439, + "start": 11873, + "end": 11879, "loc": { "start": { - "line": 303, + "line": 319, "column": 33 }, "end": { - "line": 303, + "line": 319, "column": 39 }, "identifierName": "status" @@ -58271,15 +59831,15 @@ }, { "type": "ObjectProperty", - "start": 11449, - "end": 11530, + "start": 11889, + "end": 11970, "loc": { "start": { - "line": 304, + "line": 320, "column": 6 }, "end": { - "line": 306, + "line": 322, "column": 7 } }, @@ -58288,15 +59848,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11449, - "end": 11461, + "start": 11889, + "end": 11901, "loc": { "start": { - "line": 304, + "line": 320, "column": 6 }, "end": { - "line": 304, + "line": 320, "column": 18 } }, @@ -58308,30 +59868,30 @@ }, "value": { "type": "ObjectExpression", - "start": 11463, - "end": 11530, + "start": 11903, + "end": 11970, "loc": { "start": { - "line": 304, + "line": 320, "column": 20 }, "end": { - "line": 306, + "line": 322, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 11473, - "end": 11521, + "start": 11913, + "end": 11961, "loc": { "start": { - "line": 305, + "line": 321, "column": 8 }, "end": { - "line": 305, + "line": 321, "column": 56 } }, @@ -58340,15 +59900,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 11473, - "end": 11508, + "start": 11913, + "end": 11948, "loc": { "start": { - "line": 305, + "line": 321, "column": 8 }, "end": { - "line": 305, + "line": 321, "column": 43 } }, @@ -58360,15 +59920,15 @@ }, "value": { "type": "Identifier", - "start": 11510, - "end": 11521, + "start": 11950, + "end": 11961, "loc": { "start": { - "line": 305, + "line": 321, "column": 45 }, "end": { - "line": 305, + "line": 321, "column": 56 }, "identifierName": "currentTime" @@ -58388,15 +59948,15 @@ { "type": "CommentLine", "value": " Create new entry.", - "start": 11273, - "end": 11293, + "start": 11713, + "end": 11733, "loc": { "start": { - "line": 300, + "line": 316, "column": 4 }, "end": { - "line": 300, + "line": 316, "column": 24 } } @@ -58411,15 +59971,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n ", - "start": 11547, - "end": 11925, + "start": 11987, + "end": 12365, "loc": { "start": { - "line": 310, + "line": 326, "column": 2 }, "end": { - "line": 316, + "line": 332, "column": 5 } } @@ -58428,15 +59988,15 @@ }, { "type": "ClassMethod", - "start": 11928, - "end": 12401, + "start": 12368, + "end": 12841, "loc": { "start": { - "line": 317, + "line": 333, "column": 2 }, "end": { - "line": 333, + "line": 349, "column": 3 } }, @@ -58444,15 +60004,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11932, - "end": 11946, + "start": 12372, + "end": 12386, "loc": { "start": { - "line": 317, + "line": 333, "column": 6 }, "end": { - "line": 317, + "line": 333, "column": 20 }, "identifierName": "uniqNomenCodes" @@ -58467,58 +60027,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 11949, - "end": 12401, + "start": 12389, + "end": 12841, "loc": { "start": { - "line": 317, + "line": 333, "column": 23 }, "end": { - "line": 333, + "line": 349, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 11955, - "end": 12397, + "start": 12395, + "end": 12837, "loc": { "start": { - "line": 318, + "line": 334, "column": 4 }, "end": { - "line": 332, + "line": 348, "column": 8 } }, "argument": { "type": "CallExpression", - "start": 11962, - "end": 12396, + "start": 12402, + "end": 12836, "loc": { "start": { - "line": 318, + "line": 334, "column": 11 }, "end": { - "line": 332, + "line": 348, "column": 7 } }, "callee": { "type": "Identifier", - "start": 11962, - "end": 11966, + "start": 12402, + "end": 12406, "loc": { "start": { - "line": 318, + "line": 334, "column": 11 }, "end": { - "line": 318, + "line": 334, "column": 15 }, "identifierName": "uniq" @@ -58528,72 +60088,72 @@ "arguments": [ { "type": "CallExpression", - "start": 11967, - "end": 12395, + "start": 12407, + "end": 12835, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 332, + "line": 348, "column": 6 } }, "callee": { "type": "MemberExpression", - "start": 11967, - "end": 11986, + "start": 12407, + "end": 12426, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 35 } }, "object": { "type": "MemberExpression", - "start": 11967, - "end": 11982, + "start": 12407, + "end": 12422, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 11967, - "end": 11971, + "start": 12407, + "end": 12411, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 20 } } }, "property": { "type": "Identifier", - "start": 11972, - "end": 11982, + "start": 12412, + "end": 12422, "loc": { "start": { - "line": 318, + "line": 334, "column": 21 }, "end": { - "line": 318, + "line": 334, "column": 31 }, "identifierName": "specifiers" @@ -58604,15 +60164,15 @@ }, "property": { "type": "Identifier", - "start": 11983, - "end": 11986, + "start": 12423, + "end": 12426, "loc": { "start": { - "line": 318, + "line": 334, "column": 32 }, "end": { - "line": 318, + "line": 334, "column": 35 }, "identifierName": "map" @@ -58624,15 +60184,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 11987, - "end": 12394, + "start": 12427, + "end": 12834, "loc": { "start": { - "line": 318, + "line": 334, "column": 36 }, "end": { - "line": 332, + "line": 348, "column": 5 } }, @@ -58643,15 +60203,15 @@ "params": [ { "type": "Identifier", - "start": 11988, - "end": 11997, + "start": 12428, + "end": 12437, "loc": { "start": { - "line": 318, + "line": 334, "column": 37 }, "end": { - "line": 318, + "line": 334, "column": 46 }, "identifierName": "specifier" @@ -58661,59 +60221,59 @@ ], "body": { "type": "BlockStatement", - "start": 12002, - "end": 12394, + "start": 12442, + "end": 12834, "loc": { "start": { - "line": 318, + "line": 334, "column": 51 }, "end": { - "line": 332, + "line": 348, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 12010, - "end": 12131, + "start": 12450, + "end": 12571, "loc": { "start": { - "line": 319, + "line": 335, "column": 6 }, "end": { - "line": 322, + "line": 338, "column": 21 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12016, - "end": 12130, + "start": 12456, + "end": 12570, "loc": { "start": { - "line": 319, + "line": 335, "column": 12 }, "end": { - "line": 322, + "line": 338, "column": 20 } }, "id": { "type": "Identifier", - "start": 12016, - "end": 12028, + "start": 12456, + "end": 12468, "loc": { "start": { - "line": 319, + "line": 335, "column": 12 }, "end": { - "line": 319, + "line": 335, "column": 24 }, "identifierName": "taxonConcept" @@ -58722,43 +60282,43 @@ }, "init": { "type": "MemberExpression", - "start": 12031, - "end": 12130, + "start": 12471, + "end": 12570, "loc": { "start": { - "line": 319, + "line": 335, "column": 27 }, "end": { - "line": 322, + "line": 338, "column": 20 } }, "object": { "type": "NewExpression", - "start": 12031, - "end": 12117, + "start": 12471, + "end": 12557, "loc": { "start": { - "line": 319, + "line": 335, "column": 27 }, "end": { - "line": 322, + "line": 338, "column": 7 } }, "callee": { "type": "Identifier", - "start": 12035, - "end": 12055, + "start": 12475, + "end": 12495, "loc": { "start": { - "line": 319, + "line": 335, "column": 31 }, "end": { - "line": 319, + "line": 335, "column": 51 }, "identifierName": "TaxonomicUnitWrapper" @@ -58768,15 +60328,15 @@ "arguments": [ { "type": "Identifier", - "start": 12065, - "end": 12074, + "start": 12505, + "end": 12514, "loc": { "start": { - "line": 320, + "line": 336, "column": 8 }, "end": { - "line": 320, + "line": 336, "column": 17 }, "identifierName": "specifier" @@ -58785,44 +60345,44 @@ }, { "type": "MemberExpression", - "start": 12084, - "end": 12109, + "start": 12524, + "end": 12549, "loc": { "start": { - "line": 321, + "line": 337, "column": 8 }, "end": { - "line": 321, + "line": 337, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 12084, - "end": 12088, + "start": 12524, + "end": 12528, "loc": { "start": { - "line": 321, + "line": 337, "column": 8 }, "end": { - "line": 321, + "line": 337, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12089, - "end": 12109, + "start": 12529, + "end": 12549, "loc": { "start": { - "line": 321, + "line": 337, "column": 13 }, "end": { - "line": 321, + "line": 337, "column": 33 }, "identifierName": "phyxDefaultNomenCode" @@ -58835,15 +60395,15 @@ }, "property": { "type": "Identifier", - "start": 12118, - "end": 12130, + "start": 12558, + "end": 12570, "loc": { "start": { - "line": 322, + "line": 338, "column": 8 }, "end": { - "line": 322, + "line": 338, "column": 20 }, "identifierName": "taxonConcept" @@ -58858,29 +60418,29 @@ }, { "type": "IfStatement", - "start": 12138, - "end": 12186, + "start": 12578, + "end": 12626, "loc": { "start": { - "line": 323, + "line": 339, "column": 6 }, "end": { - "line": 323, + "line": 339, "column": 54 } }, "test": { "type": "UnaryExpression", - "start": 12142, - "end": 12155, + "start": 12582, + "end": 12595, "loc": { "start": { - "line": 323, + "line": 339, "column": 10 }, "end": { - "line": 323, + "line": 339, "column": 23 } }, @@ -58888,15 +60448,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 12143, - "end": 12155, + "start": 12583, + "end": 12595, "loc": { "start": { - "line": 323, + "line": 339, "column": 11 }, "end": { - "line": 323, + "line": 339, "column": 23 }, "identifierName": "taxonConcept" @@ -58909,43 +60469,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12157, - "end": 12186, + "start": 12597, + "end": 12626, "loc": { "start": { - "line": 323, + "line": 339, "column": 25 }, "end": { - "line": 323, + "line": 339, "column": 54 } }, "argument": { "type": "MemberExpression", - "start": 12164, - "end": 12185, + "start": 12604, + "end": 12625, "loc": { "start": { - "line": 323, + "line": 339, "column": 32 }, "end": { - "line": 323, + "line": 339, "column": 53 } }, "object": { "type": "Identifier", - "start": 12164, - "end": 12172, + "start": 12604, + "end": 12612, "loc": { "start": { - "line": 323, + "line": 339, "column": 32 }, "end": { - "line": 323, + "line": 339, "column": 40 }, "identifierName": "owlterms" @@ -58954,15 +60514,15 @@ }, "property": { "type": "Identifier", - "start": 12173, - "end": 12185, + "start": 12613, + "end": 12625, "loc": { "start": { - "line": 323, + "line": 339, "column": 41 }, "end": { - "line": 323, + "line": 339, "column": 53 }, "identifierName": "UNKNOWN_CODE" @@ -58976,44 +60536,44 @@ }, { "type": "VariableDeclaration", - "start": 12194, - "end": 12311, + "start": 12634, + "end": 12751, "loc": { "start": { - "line": 325, + "line": 341, "column": 6 }, "end": { - "line": 328, + "line": 344, "column": 18 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12200, - "end": 12310, + "start": 12640, + "end": 12750, "loc": { "start": { - "line": 325, + "line": 341, "column": 12 }, "end": { - "line": 328, + "line": 344, "column": 17 } }, "id": { "type": "Identifier", - "start": 12200, - "end": 12209, + "start": 12640, + "end": 12649, "loc": { "start": { - "line": 325, + "line": 341, "column": 12 }, "end": { - "line": 325, + "line": 341, "column": 21 }, "identifierName": "nomenCode" @@ -59022,43 +60582,43 @@ }, "init": { "type": "MemberExpression", - "start": 12212, - "end": 12310, + "start": 12652, + "end": 12750, "loc": { "start": { - "line": 325, + "line": 341, "column": 24 }, "end": { - "line": 328, + "line": 344, "column": 17 } }, "object": { "type": "NewExpression", - "start": 12212, - "end": 12300, + "start": 12652, + "end": 12740, "loc": { "start": { - "line": 325, + "line": 341, "column": 24 }, "end": { - "line": 328, + "line": 344, "column": 7 } }, "callee": { "type": "Identifier", - "start": 12216, - "end": 12235, + "start": 12656, + "end": 12675, "loc": { "start": { - "line": 325, + "line": 341, "column": 28 }, "end": { - "line": 325, + "line": 341, "column": 47 }, "identifierName": "TaxonConceptWrapper" @@ -59068,15 +60628,15 @@ "arguments": [ { "type": "Identifier", - "start": 12245, - "end": 12257, + "start": 12685, + "end": 12697, "loc": { "start": { - "line": 326, + "line": 342, "column": 8 }, "end": { - "line": 326, + "line": 342, "column": 20 }, "identifierName": "taxonConcept" @@ -59085,44 +60645,44 @@ }, { "type": "MemberExpression", - "start": 12267, - "end": 12292, + "start": 12707, + "end": 12732, "loc": { "start": { - "line": 327, + "line": 343, "column": 8 }, "end": { - "line": 327, + "line": 343, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 12267, - "end": 12271, + "start": 12707, + "end": 12711, "loc": { "start": { - "line": 327, + "line": 343, "column": 8 }, "end": { - "line": 327, + "line": 343, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12272, - "end": 12292, + "start": 12712, + "end": 12732, "loc": { "start": { - "line": 327, + "line": 343, "column": 13 }, "end": { - "line": 327, + "line": 343, "column": 33 }, "identifierName": "phyxDefaultNomenCode" @@ -59135,15 +60695,15 @@ }, "property": { "type": "Identifier", - "start": 12301, - "end": 12310, + "start": 12741, + "end": 12750, "loc": { "start": { - "line": 328, + "line": 344, "column": 8 }, "end": { - "line": 328, + "line": 344, "column": 17 }, "identifierName": "nomenCode" @@ -59158,29 +60718,29 @@ }, { "type": "IfStatement", - "start": 12318, - "end": 12363, + "start": 12758, + "end": 12803, "loc": { "start": { - "line": 329, + "line": 345, "column": 6 }, "end": { - "line": 329, + "line": 345, "column": 51 } }, "test": { "type": "UnaryExpression", - "start": 12322, - "end": 12332, + "start": 12762, + "end": 12772, "loc": { "start": { - "line": 329, + "line": 345, "column": 10 }, "end": { - "line": 329, + "line": 345, "column": 20 } }, @@ -59188,15 +60748,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 12323, - "end": 12332, + "start": 12763, + "end": 12772, "loc": { "start": { - "line": 329, + "line": 345, "column": 11 }, "end": { - "line": 329, + "line": 345, "column": 20 }, "identifierName": "nomenCode" @@ -59209,43 +60769,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12334, - "end": 12363, + "start": 12774, + "end": 12803, "loc": { "start": { - "line": 329, + "line": 345, "column": 22 }, "end": { - "line": 329, + "line": 345, "column": 51 } }, "argument": { "type": "MemberExpression", - "start": 12341, - "end": 12362, + "start": 12781, + "end": 12802, "loc": { "start": { - "line": 329, + "line": 345, "column": 29 }, "end": { - "line": 329, + "line": 345, "column": 50 } }, "object": { "type": "Identifier", - "start": 12341, - "end": 12349, + "start": 12781, + "end": 12789, "loc": { "start": { - "line": 329, + "line": 345, "column": 29 }, "end": { - "line": 329, + "line": 345, "column": 37 }, "identifierName": "owlterms" @@ -59254,15 +60814,15 @@ }, "property": { "type": "Identifier", - "start": 12350, - "end": 12362, + "start": 12790, + "end": 12802, "loc": { "start": { - "line": 329, + "line": 345, "column": 38 }, "end": { - "line": 329, + "line": 345, "column": 50 }, "identifierName": "UNKNOWN_CODE" @@ -59276,29 +60836,29 @@ }, { "type": "ReturnStatement", - "start": 12371, - "end": 12388, + "start": 12811, + "end": 12828, "loc": { "start": { - "line": 331, + "line": 347, "column": 6 }, "end": { - "line": 331, + "line": 347, "column": 23 } }, "argument": { "type": "Identifier", - "start": 12378, - "end": 12387, + "start": 12818, + "end": 12827, "loc": { "start": { - "line": 331, + "line": 347, "column": 13 }, "end": { - "line": 331, + "line": 347, "column": 22 }, "identifierName": "nomenCode" @@ -59323,15 +60883,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n ", - "start": 11547, - "end": 11925, + "start": 11987, + "end": 12365, "loc": { "start": { - "line": 310, + "line": 326, "column": 2 }, "end": { - "line": 316, + "line": 332, "column": 5 } } @@ -59341,15 +60901,15 @@ { "type": "CommentBlock", "value": "*\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n ", - "start": 12405, - "end": 12681, + "start": 12845, + "end": 13121, "loc": { "start": { - "line": 335, + "line": 351, "column": 2 }, "end": { - "line": 340, + "line": 356, "column": 5 } } @@ -59358,15 +60918,15 @@ }, { "type": "ClassMethod", - "start": 12684, - "end": 13419, + "start": 13124, + "end": 13859, "loc": { "start": { - "line": 341, + "line": 357, "column": 2 }, "end": { - "line": 355, + "line": 371, "column": 3 } }, @@ -59374,15 +60934,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12688, - "end": 12704, + "start": 13128, + "end": 13144, "loc": { "start": { - "line": 341, + "line": 357, "column": 6 }, "end": { - "line": 341, + "line": 357, "column": 22 }, "identifierName": "defaultNomenCode" @@ -59397,86 +60957,86 @@ "params": [], "body": { "type": "BlockStatement", - "start": 12707, - "end": 13419, + "start": 13147, + "end": 13859, "loc": { "start": { - "line": 341, + "line": 357, "column": 25 }, "end": { - "line": 355, + "line": 371, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 12780, - "end": 12848, + "start": 13220, + "end": 13288, "loc": { "start": { - "line": 343, + "line": 359, "column": 4 }, "end": { - "line": 343, + "line": 359, "column": 72 } }, "test": { "type": "BinaryExpression", - "start": 12784, - "end": 12816, + "start": 13224, + "end": 13256, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 40 } }, "left": { "type": "MemberExpression", - "start": 12784, - "end": 12810, + "start": 13224, + "end": 13250, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 34 } }, "object": { "type": "MemberExpression", - "start": 12784, - "end": 12803, + "start": 13224, + "end": 13243, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 12784, - "end": 12788, + "start": 13224, + "end": 13228, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 12 } }, @@ -59484,15 +61044,15 @@ }, "property": { "type": "Identifier", - "start": 12789, - "end": 12803, + "start": 13229, + "end": 13243, "loc": { "start": { - "line": 343, + "line": 359, "column": 13 }, "end": { - "line": 343, + "line": 359, "column": 27 }, "identifierName": "uniqNomenCodes" @@ -59504,15 +61064,15 @@ }, "property": { "type": "Identifier", - "start": 12804, - "end": 12810, + "start": 13244, + "end": 13250, "loc": { "start": { - "line": 343, + "line": 359, "column": 28 }, "end": { - "line": 343, + "line": 359, "column": 34 }, "identifierName": "length" @@ -59525,15 +61085,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 12815, - "end": 12816, + "start": 13255, + "end": 13256, "loc": { "start": { - "line": 343, + "line": 359, "column": 39 }, "end": { - "line": 343, + "line": 359, "column": 40 } }, @@ -59547,72 +61107,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12818, - "end": 12848, + "start": 13258, + "end": 13288, "loc": { "start": { - "line": 343, + "line": 359, "column": 42 }, "end": { - "line": 343, + "line": 359, "column": 72 } }, "argument": { "type": "MemberExpression", - "start": 12825, - "end": 12847, + "start": 13265, + "end": 13287, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 71 } }, "object": { "type": "MemberExpression", - "start": 12825, - "end": 12844, + "start": 13265, + "end": 13284, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 68 } }, "object": { "type": "ThisExpression", - "start": 12825, - "end": 12829, + "start": 13265, + "end": 13269, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 53 } } }, "property": { "type": "Identifier", - "start": 12830, - "end": 12844, + "start": 13270, + "end": 13284, "loc": { "start": { - "line": 343, + "line": 359, "column": 54 }, "end": { - "line": 343, + "line": 359, "column": 68 }, "identifierName": "uniqNomenCodes" @@ -59623,15 +61183,15 @@ }, "property": { "type": "NumericLiteral", - "start": 12845, - "end": 12846, + "start": 13285, + "end": 13286, "loc": { "start": { - "line": 343, + "line": 359, "column": 69 }, "end": { - "line": 343, + "line": 359, "column": 70 } }, @@ -59650,15 +61210,15 @@ { "type": "CommentLine", "value": " Check to see if we have a single nomenclatural code to use.", - "start": 12713, - "end": 12775, + "start": 13153, + "end": 13215, "loc": { "start": { - "line": 342, + "line": 358, "column": 4 }, "end": { - "line": 342, + "line": 358, "column": 66 } } @@ -59668,15 +61228,15 @@ { "type": "CommentLine", "value": " If one or more of our specifiers have no nomenclatural code (e.g. if", - "start": 12854, - "end": 12925, + "start": 13294, + "end": 13365, "loc": { "start": { - "line": 345, + "line": 361, "column": 4 }, "end": { - "line": 345, + "line": 361, "column": 75 } } @@ -59684,15 +61244,15 @@ { "type": "CommentLine", "value": " they are specimens), they will show up as owlterms.UNKNOWN_CODE.", - "start": 12930, - "end": 12997, + "start": 13370, + "end": 13437, "loc": { "start": { - "line": 346, + "line": 362, "column": 4 }, "end": { - "line": 346, + "line": 362, "column": 71 } } @@ -59700,15 +61260,15 @@ { "type": "CommentLine", "value": " If we have a single nomenclatural code *apart* from all the", - "start": 13002, - "end": 13064, + "start": 13442, + "end": 13504, "loc": { "start": { - "line": 347, + "line": 363, "column": 4 }, "end": { - "line": 347, + "line": 363, "column": 66 } } @@ -59716,15 +61276,15 @@ { "type": "CommentLine", "value": " owlterms.UNKNOWN_CODEs, then that is still usable as a default", - "start": 13069, - "end": 13134, + "start": 13509, + "end": 13574, "loc": { "start": { - "line": 348, + "line": 364, "column": 4 }, "end": { - "line": 348, + "line": 364, "column": 69 } } @@ -59732,15 +61292,15 @@ { "type": "CommentLine", "value": " nomenclatural code for this phyloreference.", - "start": 13139, - "end": 13185, + "start": 13579, + "end": 13625, "loc": { "start": { - "line": 349, + "line": 365, "column": 4 }, "end": { - "line": 349, + "line": 365, "column": 50 } } @@ -59749,44 +61309,44 @@ }, { "type": "VariableDeclaration", - "start": 13190, - "end": 13297, + "start": 13630, + "end": 13737, "loc": { "start": { - "line": 350, + "line": 366, "column": 4 }, "end": { - "line": 351, + "line": 367, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13196, - "end": 13296, + "start": 13636, + "end": 13736, "loc": { "start": { - "line": 350, + "line": 366, "column": 10 }, "end": { - "line": 351, + "line": 367, "column": 53 } }, "id": { "type": "Identifier", - "start": 13196, - "end": 13220, + "start": 13636, + "end": 13660, "loc": { "start": { - "line": 350, + "line": 366, "column": 10 }, "end": { - "line": 350, + "line": 366, "column": 34 }, "identifierName": "uniqNomenCodesNoUnknowns" @@ -59796,72 +61356,72 @@ }, "init": { "type": "CallExpression", - "start": 13223, - "end": 13296, + "start": 13663, + "end": 13736, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 351, + "line": 367, "column": 53 } }, "callee": { "type": "MemberExpression", - "start": 13223, - "end": 13256, + "start": 13663, + "end": 13696, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 351, + "line": 367, "column": 13 } }, "object": { "type": "MemberExpression", - "start": 13223, - "end": 13242, + "start": 13663, + "end": 13682, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 350, + "line": 366, "column": 56 } }, "object": { "type": "ThisExpression", - "start": 13223, - "end": 13227, + "start": 13663, + "end": 13667, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 350, + "line": 366, "column": 41 } } }, "property": { "type": "Identifier", - "start": 13228, - "end": 13242, + "start": 13668, + "end": 13682, "loc": { "start": { - "line": 350, + "line": 366, "column": 42 }, "end": { - "line": 350, + "line": 366, "column": 56 }, "identifierName": "uniqNomenCodes" @@ -59872,15 +61432,15 @@ }, "property": { "type": "Identifier", - "start": 13250, - "end": 13256, + "start": 13690, + "end": 13696, "loc": { "start": { - "line": 351, + "line": 367, "column": 7 }, "end": { - "line": 351, + "line": 367, "column": 13 }, "identifierName": "filter" @@ -59892,15 +61452,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 13257, - "end": 13295, + "start": 13697, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 14 }, "end": { - "line": 351, + "line": 367, "column": 52 } }, @@ -59911,15 +61471,15 @@ "params": [ { "type": "Identifier", - "start": 13257, - "end": 13261, + "start": 13697, + "end": 13701, "loc": { "start": { - "line": 351, + "line": 367, "column": 14 }, "end": { - "line": 351, + "line": 367, "column": 18 }, "identifierName": "code" @@ -59929,29 +61489,29 @@ ], "body": { "type": "BinaryExpression", - "start": 13265, - "end": 13295, + "start": 13705, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 22 }, "end": { - "line": 351, + "line": 367, "column": 52 } }, "left": { "type": "Identifier", - "start": 13265, - "end": 13269, + "start": 13705, + "end": 13709, "loc": { "start": { - "line": 351, + "line": 367, "column": 22 }, "end": { - "line": 351, + "line": 367, "column": 26 }, "identifierName": "code" @@ -59961,29 +61521,29 @@ "operator": "!==", "right": { "type": "MemberExpression", - "start": 13274, - "end": 13295, + "start": 13714, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 31 }, "end": { - "line": 351, + "line": 367, "column": 52 } }, "object": { "type": "Identifier", - "start": 13274, - "end": 13282, + "start": 13714, + "end": 13722, "loc": { "start": { - "line": 351, + "line": 367, "column": 31 }, "end": { - "line": 351, + "line": 367, "column": 39 }, "identifierName": "owlterms" @@ -59992,15 +61552,15 @@ }, "property": { "type": "Identifier", - "start": 13283, - "end": 13295, + "start": 13723, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 40 }, "end": { - "line": 351, + "line": 367, "column": 52 }, "identifierName": "UNKNOWN_CODE" @@ -60021,15 +61581,15 @@ { "type": "CommentLine", "value": " If one or more of our specifiers have no nomenclatural code (e.g. if", - "start": 12854, - "end": 12925, + "start": 13294, + "end": 13365, "loc": { "start": { - "line": 345, + "line": 361, "column": 4 }, "end": { - "line": 345, + "line": 361, "column": 75 } } @@ -60037,15 +61597,15 @@ { "type": "CommentLine", "value": " they are specimens), they will show up as owlterms.UNKNOWN_CODE.", - "start": 12930, - "end": 12997, + "start": 13370, + "end": 13437, "loc": { "start": { - "line": 346, + "line": 362, "column": 4 }, "end": { - "line": 346, + "line": 362, "column": 71 } } @@ -60053,15 +61613,15 @@ { "type": "CommentLine", "value": " If we have a single nomenclatural code *apart* from all the", - "start": 13002, - "end": 13064, + "start": 13442, + "end": 13504, "loc": { "start": { - "line": 347, + "line": 363, "column": 4 }, "end": { - "line": 347, + "line": 363, "column": 66 } } @@ -60069,15 +61629,15 @@ { "type": "CommentLine", "value": " owlterms.UNKNOWN_CODEs, then that is still usable as a default", - "start": 13069, - "end": 13134, + "start": 13509, + "end": 13574, "loc": { "start": { - "line": 348, + "line": 364, "column": 4 }, "end": { - "line": 348, + "line": 364, "column": 69 } } @@ -60085,15 +61645,15 @@ { "type": "CommentLine", "value": " nomenclatural code for this phyloreference.", - "start": 13139, - "end": 13185, + "start": 13579, + "end": 13625, "loc": { "start": { - "line": 349, + "line": 365, "column": 4 }, "end": { - "line": 349, + "line": 365, "column": 50 } } @@ -60102,57 +61662,57 @@ }, { "type": "IfStatement", - "start": 13302, - "end": 13380, + "start": 13742, + "end": 13820, "loc": { "start": { - "line": 352, + "line": 368, "column": 4 }, "end": { - "line": 352, + "line": 368, "column": 82 } }, "test": { "type": "BinaryExpression", - "start": 13306, - "end": 13343, + "start": 13746, + "end": 13783, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 45 } }, "left": { "type": "MemberExpression", - "start": 13306, - "end": 13337, + "start": 13746, + "end": 13777, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 39 } }, "object": { "type": "Identifier", - "start": 13306, - "end": 13330, + "start": 13746, + "end": 13770, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 32 }, "identifierName": "uniqNomenCodesNoUnknowns" @@ -60161,15 +61721,15 @@ }, "property": { "type": "Identifier", - "start": 13331, - "end": 13337, + "start": 13771, + "end": 13777, "loc": { "start": { - "line": 352, + "line": 368, "column": 33 }, "end": { - "line": 352, + "line": 368, "column": 39 }, "identifierName": "length" @@ -60181,15 +61741,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 13342, - "end": 13343, + "start": 13782, + "end": 13783, "loc": { "start": { - "line": 352, + "line": 368, "column": 44 }, "end": { - "line": 352, + "line": 368, "column": 45 } }, @@ -60202,43 +61762,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 13345, - "end": 13380, + "start": 13785, + "end": 13820, "loc": { "start": { - "line": 352, + "line": 368, "column": 47 }, "end": { - "line": 352, + "line": 368, "column": 82 } }, "argument": { "type": "MemberExpression", - "start": 13352, - "end": 13379, + "start": 13792, + "end": 13819, "loc": { "start": { - "line": 352, + "line": 368, "column": 54 }, "end": { - "line": 352, + "line": 368, "column": 81 } }, "object": { "type": "Identifier", - "start": 13352, - "end": 13376, + "start": 13792, + "end": 13816, "loc": { "start": { - "line": 352, + "line": 368, "column": 54 }, "end": { - "line": 352, + "line": 368, "column": 78 }, "identifierName": "uniqNomenCodesNoUnknowns" @@ -60247,15 +61807,15 @@ }, "property": { "type": "NumericLiteral", - "start": 13377, - "end": 13378, + "start": 13817, + "end": 13818, "loc": { "start": { - "line": 352, + "line": 368, "column": 79 }, "end": { - "line": 352, + "line": 368, "column": 80 } }, @@ -60272,43 +61832,43 @@ }, { "type": "ReturnStatement", - "start": 13386, - "end": 13415, + "start": 13826, + "end": 13855, "loc": { "start": { - "line": 354, + "line": 370, "column": 4 }, "end": { - "line": 354, + "line": 370, "column": 33 } }, "argument": { "type": "MemberExpression", - "start": 13393, - "end": 13414, + "start": 13833, + "end": 13854, "loc": { "start": { - "line": 354, + "line": 370, "column": 11 }, "end": { - "line": 354, + "line": 370, "column": 32 } }, "object": { "type": "Identifier", - "start": 13393, - "end": 13401, + "start": 13833, + "end": 13841, "loc": { "start": { - "line": 354, + "line": 370, "column": 11 }, "end": { - "line": 354, + "line": 370, "column": 19 }, "identifierName": "owlterms" @@ -60317,15 +61877,15 @@ }, "property": { "type": "Identifier", - "start": 13402, - "end": 13414, + "start": 13842, + "end": 13854, "loc": { "start": { - "line": 354, + "line": 370, "column": 20 }, "end": { - "line": 354, + "line": 370, "column": 32 }, "identifierName": "UNKNOWN_CODE" @@ -60343,15 +61903,15 @@ { "type": "CommentBlock", "value": "*\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n ", - "start": 12405, - "end": 12681, + "start": 12845, + "end": 13121, "loc": { "start": { - "line": 335, + "line": 351, "column": 2 }, "end": { - "line": 340, + "line": 356, "column": 5 } } @@ -60361,15 +61921,15 @@ { "type": "CommentBlock", "value": "*\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n ", - "start": 13423, - "end": 14548, + "start": 13863, + "end": 14988, "loc": { "start": { - "line": 357, + "line": 373, "column": 2 }, "end": { - "line": 373, + "line": 389, "column": 5 } } @@ -60378,15 +61938,15 @@ }, { "type": "ClassMethod", - "start": 14551, - "end": 18001, + "start": 14991, + "end": 18441, "loc": { "start": { - "line": 374, + "line": 390, "column": 2 }, "end": { - "line": 454, + "line": 470, "column": 3 } }, @@ -60394,15 +61954,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14551, - "end": 14571, + "start": 14991, + "end": 15011, "loc": { "start": { - "line": 374, + "line": 390, "column": 2 }, "end": { - "line": 374, + "line": 390, "column": 22 }, "identifierName": "createComponentClass" @@ -60418,15 +61978,15 @@ "params": [ { "type": "Identifier", - "start": 14577, - "end": 14583, + "start": 15017, + "end": 15023, "loc": { "start": { - "line": 375, + "line": 391, "column": 4 }, "end": { - "line": 375, + "line": 391, "column": 10 }, "identifierName": "jsonld" @@ -60435,15 +61995,15 @@ }, { "type": "Identifier", - "start": 14589, - "end": 14607, + "start": 15029, + "end": 15047, "loc": { "start": { - "line": 376, + "line": 392, "column": 4 }, "end": { - "line": 376, + "line": 392, "column": 22 }, "identifierName": "internalSpecifiers" @@ -60452,15 +62012,15 @@ }, { "type": "Identifier", - "start": 14613, - "end": 14631, + "start": 15053, + "end": 15071, "loc": { "start": { - "line": 377, + "line": 393, "column": 4 }, "end": { - "line": 377, + "line": 393, "column": 22 }, "identifierName": "externalSpecifiers" @@ -60469,15 +62029,15 @@ }, { "type": "Identifier", - "start": 14637, - "end": 14647, + "start": 15077, + "end": 15087, "loc": { "start": { - "line": 378, + "line": 394, "column": 4 }, "end": { - "line": 378, + "line": 394, "column": 14 }, "identifierName": "equivClass" @@ -60486,29 +62046,29 @@ }, { "type": "AssignmentPattern", - "start": 14653, - "end": 14673, + "start": 15093, + "end": 15113, "loc": { "start": { - "line": 379, + "line": 395, "column": 4 }, "end": { - "line": 379, + "line": 395, "column": 24 } }, "left": { "type": "Identifier", - "start": 14653, - "end": 14666, + "start": 15093, + "end": 15106, "loc": { "start": { - "line": 379, + "line": 395, "column": 4 }, "end": { - "line": 379, + "line": 395, "column": 17 }, "identifierName": "reusePrevious" @@ -60517,15 +62077,15 @@ }, "right": { "type": "BooleanLiteral", - "start": 14669, - "end": 14673, + "start": 15109, + "end": 15113, "loc": { "start": { - "line": 379, + "line": 395, "column": 20 }, "end": { - "line": 379, + "line": 395, "column": 24 } }, @@ -60534,29 +62094,29 @@ }, { "type": "AssignmentPattern", - "start": 14679, - "end": 14702, + "start": 15119, + "end": 15142, "loc": { "start": { - "line": 380, + "line": 396, "column": 4 }, "end": { - "line": 380, + "line": 396, "column": 27 } }, "left": { "type": "Identifier", - "start": 14679, - "end": 14690, + "start": 15119, + "end": 15130, "loc": { "start": { - "line": 380, + "line": 396, "column": 4 }, "end": { - "line": 380, + "line": 396, "column": 15 }, "identifierName": "parentClass" @@ -60565,15 +62125,15 @@ }, "right": { "type": "Identifier", - "start": 14693, - "end": 14702, + "start": 15133, + "end": 15142, "loc": { "start": { - "line": 380, + "line": 396, "column": 18 }, "end": { - "line": 380, + "line": 396, "column": 27 }, "identifierName": "undefined" @@ -60584,72 +62144,72 @@ ], "body": { "type": "BlockStatement", - "start": 14707, - "end": 18001, + "start": 15147, + "end": 18441, "loc": { "start": { - "line": 381, + "line": 397, "column": 4 }, "end": { - "line": 454, + "line": 470, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 14713, - "end": 14831, + "start": 15153, + "end": 15271, "loc": { "start": { - "line": 382, + "line": 398, "column": 4 }, "end": { - "line": 382, + "line": 398, "column": 122 } }, "test": { "type": "BinaryExpression", - "start": 14717, - "end": 14748, + "start": 15157, + "end": 15188, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 14717, - "end": 14742, + "start": 15157, + "end": 15182, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 33 } }, "object": { "type": "Identifier", - "start": 14717, - "end": 14735, + "start": 15157, + "end": 15175, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 26 }, "identifierName": "internalSpecifiers" @@ -60658,15 +62218,15 @@ }, "property": { "type": "Identifier", - "start": 14736, - "end": 14742, + "start": 15176, + "end": 15182, "loc": { "start": { - "line": 382, + "line": 398, "column": 27 }, "end": { - "line": 382, + "line": 398, "column": 33 }, "identifierName": "length" @@ -60678,15 +62238,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 14747, - "end": 14748, + "start": 15187, + "end": 15188, "loc": { "start": { - "line": 382, + "line": 398, "column": 38 }, "end": { - "line": 382, + "line": 398, "column": 39 } }, @@ -60699,43 +62259,43 @@ }, "consequent": { "type": "ThrowStatement", - "start": 14750, - "end": 14831, + "start": 15190, + "end": 15271, "loc": { "start": { - "line": 382, + "line": 398, "column": 41 }, "end": { - "line": 382, + "line": 398, "column": 122 } }, "argument": { "type": "NewExpression", - "start": 14756, - "end": 14830, + "start": 15196, + "end": 15270, "loc": { "start": { - "line": 382, + "line": 398, "column": 47 }, "end": { - "line": 382, + "line": 398, "column": 121 } }, "callee": { "type": "Identifier", - "start": 14760, - "end": 14765, + "start": 15200, + "end": 15205, "loc": { "start": { - "line": 382, + "line": 398, "column": 51 }, "end": { - "line": 382, + "line": 398, "column": 56 }, "identifierName": "Error" @@ -60745,15 +62305,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 14766, - "end": 14829, + "start": 15206, + "end": 15269, "loc": { "start": { - "line": 382, + "line": 398, "column": 57 }, "end": { - "line": 382, + "line": 398, "column": 120 } }, @@ -60770,71 +62330,71 @@ }, { "type": "IfStatement", - "start": 14836, - "end": 15018, + "start": 15276, + "end": 15458, "loc": { "start": { - "line": 383, + "line": 399, "column": 4 }, "end": { - "line": 383, + "line": 399, "column": 186 } }, "test": { "type": "LogicalExpression", - "start": 14840, - "end": 14906, + "start": 15280, + "end": 15346, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 74 } }, "left": { "type": "BinaryExpression", - "start": 14840, - "end": 14871, + "start": 15280, + "end": 15311, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 14840, - "end": 14865, + "start": 15280, + "end": 15305, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 33 } }, "object": { "type": "Identifier", - "start": 14840, - "end": 14858, + "start": 15280, + "end": 15298, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 26 }, "identifierName": "internalSpecifiers" @@ -60843,15 +62403,15 @@ }, "property": { "type": "Identifier", - "start": 14859, - "end": 14865, + "start": 15299, + "end": 15305, "loc": { "start": { - "line": 383, + "line": 399, "column": 27 }, "end": { - "line": 383, + "line": 399, "column": 33 }, "identifierName": "length" @@ -60863,15 +62423,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 14870, - "end": 14871, + "start": 15310, + "end": 15311, "loc": { "start": { - "line": 383, + "line": 399, "column": 38 }, "end": { - "line": 383, + "line": 399, "column": 39 } }, @@ -60885,43 +62445,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 14875, - "end": 14906, + "start": 15315, + "end": 15346, "loc": { "start": { - "line": 383, + "line": 399, "column": 43 }, "end": { - "line": 383, + "line": 399, "column": 74 } }, "left": { "type": "MemberExpression", - "start": 14875, - "end": 14900, + "start": 15315, + "end": 15340, "loc": { "start": { - "line": 383, + "line": 399, "column": 43 }, "end": { - "line": 383, + "line": 399, "column": 68 } }, "object": { "type": "Identifier", - "start": 14875, - "end": 14893, + "start": 15315, + "end": 15333, "loc": { "start": { - "line": 383, + "line": 399, "column": 43 }, "end": { - "line": 383, + "line": 399, "column": 61 }, "identifierName": "externalSpecifiers" @@ -60930,15 +62490,15 @@ }, "property": { "type": "Identifier", - "start": 14894, - "end": 14900, + "start": 15334, + "end": 15340, "loc": { "start": { - "line": 383, + "line": 399, "column": 62 }, "end": { - "line": 383, + "line": 399, "column": 68 }, "identifierName": "length" @@ -60950,15 +62510,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 14905, - "end": 14906, + "start": 15345, + "end": 15346, "loc": { "start": { - "line": 383, + "line": 399, "column": 73 }, "end": { - "line": 383, + "line": 399, "column": 74 } }, @@ -60972,43 +62532,43 @@ }, "consequent": { "type": "ThrowStatement", - "start": 14908, - "end": 15018, + "start": 15348, + "end": 15458, "loc": { "start": { - "line": 383, + "line": 399, "column": 76 }, "end": { - "line": 383, + "line": 399, "column": 186 } }, "argument": { "type": "NewExpression", - "start": 14914, - "end": 15017, + "start": 15354, + "end": 15457, "loc": { "start": { - "line": 383, + "line": 399, "column": 82 }, "end": { - "line": 383, + "line": 399, "column": 185 } }, "callee": { "type": "Identifier", - "start": 14918, - "end": 14923, + "start": 15358, + "end": 15363, "loc": { "start": { - "line": 383, + "line": 399, "column": 86 }, "end": { - "line": 383, + "line": 399, "column": 91 }, "identifierName": "Error" @@ -61018,15 +62578,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 14924, - "end": 15016, + "start": 15364, + "end": 15456, "loc": { "start": { - "line": 383, + "line": 399, "column": 92 }, "end": { - "line": 383, + "line": 399, "column": 184 } }, @@ -61045,15 +62605,15 @@ { "type": "CommentBlock", "value": " Generate a label that represents this component class. ", - "start": 15024, - "end": 15084, + "start": 15464, + "end": 15524, "loc": { "start": { - "line": 385, + "line": 401, "column": 4 }, "end": { - "line": 385, + "line": 401, "column": 64 } } @@ -61061,15 +62621,15 @@ { "type": "CommentLine", "value": " By default, taxonomic unit labels don't include the nomenclatural code.", - "start": 15090, - "end": 15164, + "start": 15530, + "end": 15604, "loc": { "start": { - "line": 387, + "line": 403, "column": 4 }, "end": { - "line": 387, + "line": 403, "column": 78 } } @@ -61077,15 +62637,15 @@ { "type": "CommentLine", "value": " However, we should include that here in order to distinguish between", - "start": 15169, - "end": 15240, + "start": 15609, + "end": 15680, "loc": { "start": { - "line": 388, + "line": 404, "column": 4 }, "end": { - "line": 388, + "line": 404, "column": 75 } } @@ -61093,15 +62653,15 @@ { "type": "CommentLine", "value": " taxonomic names in different taxonomic codes. This method generates that", - "start": 15245, - "end": 15320, + "start": 15685, + "end": 15760, "loc": { "start": { - "line": 389, + "line": 405, "column": 4 }, "end": { - "line": 389, + "line": 405, "column": 79 } } @@ -61109,15 +62669,15 @@ { "type": "CommentLine", "value": " name for a specifier.", - "start": 15325, - "end": 15349, + "start": 15765, + "end": 15789, "loc": { "start": { - "line": 390, + "line": 406, "column": 4 }, "end": { - "line": 390, + "line": 406, "column": 28 } } @@ -61126,44 +62686,44 @@ }, { "type": "VariableDeclaration", - "start": 15354, - "end": 15377, + "start": 15794, + "end": 15817, "loc": { "start": { - "line": 391, + "line": 407, "column": 4 }, "end": { - "line": 391, + "line": 407, "column": 27 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15360, - "end": 15376, + "start": 15800, + "end": 15816, "loc": { "start": { - "line": 391, + "line": 407, "column": 10 }, "end": { - "line": 391, + "line": 407, "column": 26 } }, "id": { "type": "Identifier", - "start": 15360, - "end": 15369, + "start": 15800, + "end": 15809, "loc": { "start": { - "line": 391, + "line": 407, "column": 10 }, "end": { - "line": 391, + "line": 407, "column": 19 }, "identifierName": "outerThis" @@ -61173,15 +62733,15 @@ }, "init": { "type": "ThisExpression", - "start": 15372, - "end": 15376, + "start": 15812, + "end": 15816, "loc": { "start": { - "line": 391, + "line": 407, "column": 22 }, "end": { - "line": 391, + "line": 407, "column": 26 } } @@ -61194,15 +62754,15 @@ { "type": "CommentBlock", "value": " Generate a label that represents this component class. ", - "start": 15024, - "end": 15084, + "start": 15464, + "end": 15524, "loc": { "start": { - "line": 385, + "line": 401, "column": 4 }, "end": { - "line": 385, + "line": 401, "column": 64 } } @@ -61210,15 +62770,15 @@ { "type": "CommentLine", "value": " By default, taxonomic unit labels don't include the nomenclatural code.", - "start": 15090, - "end": 15164, + "start": 15530, + "end": 15604, "loc": { "start": { - "line": 387, + "line": 403, "column": 4 }, "end": { - "line": 387, + "line": 403, "column": 78 } } @@ -61226,15 +62786,15 @@ { "type": "CommentLine", "value": " However, we should include that here in order to distinguish between", - "start": 15169, - "end": 15240, + "start": 15609, + "end": 15680, "loc": { "start": { - "line": 388, + "line": 404, "column": 4 }, "end": { - "line": 388, + "line": 404, "column": 75 } } @@ -61242,15 +62802,15 @@ { "type": "CommentLine", "value": " taxonomic names in different taxonomic codes. This method generates that", - "start": 15245, - "end": 15320, + "start": 15685, + "end": 15760, "loc": { "start": { - "line": 389, + "line": 405, "column": 4 }, "end": { - "line": 389, + "line": 405, "column": 79 } } @@ -61258,15 +62818,15 @@ { "type": "CommentLine", "value": " name for a specifier.", - "start": 15325, - "end": 15349, + "start": 15765, + "end": 15789, "loc": { "start": { - "line": 390, + "line": 406, "column": 4 }, "end": { - "line": 390, + "line": 406, "column": 28 } } @@ -61275,29 +62835,29 @@ }, { "type": "FunctionDeclaration", - "start": 15382, - "end": 15812, + "start": 15822, + "end": 16252, "loc": { "start": { - "line": 392, + "line": 408, "column": 4 }, "end": { - "line": 400, + "line": 416, "column": 5 } }, "id": { "type": "Identifier", - "start": 15391, - "end": 15412, + "start": 15831, + "end": 15852, "loc": { "start": { - "line": 392, + "line": 408, "column": 13 }, "end": { - "line": 392, + "line": 408, "column": 34 }, "identifierName": "generateSpecifierName" @@ -61310,15 +62870,15 @@ "params": [ { "type": "Identifier", - "start": 15413, - "end": 15422, + "start": 15853, + "end": 15862, "loc": { "start": { - "line": 392, + "line": 408, "column": 35 }, "end": { - "line": 392, + "line": 408, "column": 44 }, "identifierName": "specifier" @@ -61328,59 +62888,59 @@ ], "body": { "type": "BlockStatement", - "start": 15424, - "end": 15812, + "start": 15864, + "end": 16252, "loc": { "start": { - "line": 392, + "line": 408, "column": 46 }, "end": { - "line": 400, + "line": 416, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 15432, - "end": 15512, + "start": 15872, + "end": 15952, "loc": { "start": { - "line": 393, + "line": 409, "column": 6 }, "end": { - "line": 393, + "line": 409, "column": 86 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15438, - "end": 15511, + "start": 15878, + "end": 15951, "loc": { "start": { - "line": 393, + "line": 409, "column": 12 }, "end": { - "line": 393, + "line": 409, "column": 85 } }, "id": { "type": "Identifier", - "start": 15438, - "end": 15445, + "start": 15878, + "end": 15885, "loc": { "start": { - "line": 393, + "line": 409, "column": 12 }, "end": { - "line": 393, + "line": 409, "column": 19 }, "identifierName": "wrapped" @@ -61389,29 +62949,29 @@ }, "init": { "type": "NewExpression", - "start": 15448, - "end": 15511, + "start": 15888, + "end": 15951, "loc": { "start": { - "line": 393, + "line": 409, "column": 22 }, "end": { - "line": 393, + "line": 409, "column": 85 } }, "callee": { "type": "Identifier", - "start": 15452, - "end": 15472, + "start": 15892, + "end": 15912, "loc": { "start": { - "line": 393, + "line": 409, "column": 26 }, "end": { - "line": 393, + "line": 409, "column": 46 }, "identifierName": "TaxonomicUnitWrapper" @@ -61421,15 +62981,15 @@ "arguments": [ { "type": "Identifier", - "start": 15473, - "end": 15482, + "start": 15913, + "end": 15922, "loc": { "start": { - "line": 393, + "line": 409, "column": 47 }, "end": { - "line": 393, + "line": 409, "column": 56 }, "identifierName": "specifier" @@ -61438,29 +62998,29 @@ }, { "type": "MemberExpression", - "start": 15484, - "end": 15510, + "start": 15924, + "end": 15950, "loc": { "start": { - "line": 393, + "line": 409, "column": 58 }, "end": { - "line": 393, + "line": 409, "column": 84 } }, "object": { "type": "Identifier", - "start": 15484, - "end": 15493, + "start": 15924, + "end": 15933, "loc": { "start": { - "line": 393, + "line": 409, "column": 58 }, "end": { - "line": 393, + "line": 409, "column": 67 }, "identifierName": "outerThis" @@ -61469,15 +63029,15 @@ }, "property": { "type": "Identifier", - "start": 15494, - "end": 15510, + "start": 15934, + "end": 15950, "loc": { "start": { - "line": 393, + "line": 409, "column": 68 }, "end": { - "line": 393, + "line": 409, "column": 84 }, "identifierName": "defaultNomenCode" @@ -61494,29 +63054,29 @@ }, { "type": "IfStatement", - "start": 15519, - "end": 15550, + "start": 15959, + "end": 15990, "loc": { "start": { - "line": 394, + "line": 410, "column": 6 }, "end": { - "line": 394, + "line": 410, "column": 37 } }, "test": { "type": "UnaryExpression", - "start": 15523, - "end": 15531, + "start": 15963, + "end": 15971, "loc": { "start": { - "line": 394, + "line": 410, "column": 10 }, "end": { - "line": 394, + "line": 410, "column": 18 } }, @@ -61524,15 +63084,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 15524, - "end": 15531, + "start": 15964, + "end": 15971, "loc": { "start": { - "line": 394, + "line": 410, "column": 11 }, "end": { - "line": 394, + "line": 410, "column": 18 }, "identifierName": "wrapped" @@ -61545,29 +63105,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 15533, - "end": 15550, + "start": 15973, + "end": 15990, "loc": { "start": { - "line": 394, + "line": 410, "column": 20 }, "end": { - "line": 394, + "line": 410, "column": 37 } }, "argument": { "type": "StringLiteral", - "start": 15540, - "end": 15549, + "start": 15980, + "end": 15989, "loc": { "start": { - "line": 394, + "line": 410, "column": 27 }, "end": { - "line": 394, + "line": 410, "column": 36 } }, @@ -61582,43 +63142,43 @@ }, { "type": "IfStatement", - "start": 15557, - "end": 15778, + "start": 15997, + "end": 16218, "loc": { "start": { - "line": 395, + "line": 411, "column": 6 }, "end": { - "line": 398, + "line": 414, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 15561, - "end": 15581, + "start": 16001, + "end": 16021, "loc": { "start": { - "line": 395, + "line": 411, "column": 10 }, "end": { - "line": 395, + "line": 411, "column": 30 } }, "object": { "type": "Identifier", - "start": 15561, - "end": 15568, + "start": 16001, + "end": 16008, "loc": { "start": { - "line": 395, + "line": 411, "column": 10 }, "end": { - "line": 395, + "line": 411, "column": 17 }, "identifierName": "wrapped" @@ -61627,15 +63187,15 @@ }, "property": { "type": "Identifier", - "start": 15569, - "end": 15581, + "start": 16009, + "end": 16021, "loc": { "start": { - "line": 395, + "line": 411, "column": 18 }, "end": { - "line": 395, + "line": 411, "column": 30 }, "identifierName": "taxonConcept" @@ -61646,59 +63206,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 15583, - "end": 15778, + "start": 16023, + "end": 16218, "loc": { "start": { - "line": 395, + "line": 411, "column": 32 }, "end": { - "line": 398, + "line": 414, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 15593, - "end": 15681, + "start": 16033, + "end": 16121, "loc": { "start": { - "line": 396, + "line": 412, "column": 8 }, "end": { - "line": 396, + "line": 412, "column": 96 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15599, - "end": 15680, + "start": 16039, + "end": 16120, "loc": { "start": { - "line": 396, + "line": 412, "column": 14 }, "end": { - "line": 396, + "line": 412, "column": 95 } }, "id": { "type": "Identifier", - "start": 15599, - "end": 15615, + "start": 16039, + "end": 16055, "loc": { "start": { - "line": 396, + "line": 412, "column": 14 }, "end": { - "line": 396, + "line": 412, "column": 30 }, "identifierName": "nomenCodeDetails" @@ -61707,43 +63267,43 @@ }, "init": { "type": "MemberExpression", - "start": 15618, - "end": 15680, + "start": 16058, + "end": 16120, "loc": { "start": { - "line": 396, + "line": 412, "column": 33 }, "end": { - "line": 396, + "line": 412, "column": 95 } }, "object": { "type": "NewExpression", - "start": 15618, - "end": 15663, + "start": 16058, + "end": 16103, "loc": { "start": { - "line": 396, + "line": 412, "column": 33 }, "end": { - "line": 396, + "line": 412, "column": 78 } }, "callee": { "type": "Identifier", - "start": 15622, - "end": 15641, + "start": 16062, + "end": 16081, "loc": { "start": { - "line": 396, + "line": 412, "column": 37 }, "end": { - "line": 396, + "line": 412, "column": 56 }, "identifierName": "TaxonConceptWrapper" @@ -61753,29 +63313,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 15642, - "end": 15662, + "start": 16082, + "end": 16102, "loc": { "start": { - "line": 396, + "line": 412, "column": 57 }, "end": { - "line": 396, + "line": 412, "column": 77 } }, "object": { "type": "Identifier", - "start": 15642, - "end": 15649, + "start": 16082, + "end": 16089, "loc": { "start": { - "line": 396, + "line": 412, "column": 57 }, "end": { - "line": 396, + "line": 412, "column": 64 }, "identifierName": "wrapped" @@ -61784,15 +63344,15 @@ }, "property": { "type": "Identifier", - "start": 15650, - "end": 15662, + "start": 16090, + "end": 16102, "loc": { "start": { - "line": 396, + "line": 412, "column": 65 }, "end": { - "line": 396, + "line": 412, "column": 77 }, "identifierName": "taxonConcept" @@ -61805,15 +63365,15 @@ }, "property": { "type": "Identifier", - "start": 15664, - "end": 15680, + "start": 16104, + "end": 16120, "loc": { "start": { - "line": 396, + "line": 412, "column": 79 }, "end": { - "line": 396, + "line": 412, "column": 95 }, "identifierName": "nomenCodeDetails" @@ -61828,29 +63388,29 @@ }, { "type": "IfStatement", - "start": 15690, - "end": 15770, + "start": 16130, + "end": 16210, "loc": { "start": { - "line": 397, + "line": 413, "column": 8 }, "end": { - "line": 397, + "line": 413, "column": 88 } }, "test": { "type": "Identifier", - "start": 15694, - "end": 15710, + "start": 16134, + "end": 16150, "loc": { "start": { - "line": 397, + "line": 413, "column": 12 }, "end": { - "line": 397, + "line": 413, "column": 28 }, "identifierName": "nomenCodeDetails" @@ -61859,58 +63419,58 @@ }, "consequent": { "type": "ReturnStatement", - "start": 15712, - "end": 15770, + "start": 16152, + "end": 16210, "loc": { "start": { - "line": 397, + "line": 413, "column": 30 }, "end": { - "line": 397, + "line": 413, "column": 88 } }, "argument": { "type": "TemplateLiteral", - "start": 15719, - "end": 15769, + "start": 16159, + "end": 16209, "loc": { "start": { - "line": 397, + "line": 413, "column": 37 }, "end": { - "line": 397, + "line": 413, "column": 87 } }, "expressions": [ { "type": "MemberExpression", - "start": 15722, - "end": 15735, + "start": 16162, + "end": 16175, "loc": { "start": { - "line": 397, + "line": 413, "column": 40 }, "end": { - "line": 397, + "line": 413, "column": 53 } }, "object": { "type": "Identifier", - "start": 15722, - "end": 15729, + "start": 16162, + "end": 16169, "loc": { "start": { - "line": 397, + "line": 413, "column": 40 }, "end": { - "line": 397, + "line": 413, "column": 47 }, "identifierName": "wrapped" @@ -61919,15 +63479,15 @@ }, "property": { "type": "Identifier", - "start": 15730, - "end": 15735, + "start": 16170, + "end": 16175, "loc": { "start": { - "line": 397, + "line": 413, "column": 48 }, "end": { - "line": 397, + "line": 413, "column": 53 }, "identifierName": "label" @@ -61938,29 +63498,29 @@ }, { "type": "MemberExpression", - "start": 15740, - "end": 15766, + "start": 16180, + "end": 16206, "loc": { "start": { - "line": 397, + "line": 413, "column": 58 }, "end": { - "line": 397, + "line": 413, "column": 84 } }, "object": { "type": "Identifier", - "start": 15740, - "end": 15756, + "start": 16180, + "end": 16196, "loc": { "start": { - "line": 397, + "line": 413, "column": 58 }, "end": { - "line": 397, + "line": 413, "column": 74 }, "identifierName": "nomenCodeDetails" @@ -61969,15 +63529,15 @@ }, "property": { "type": "Identifier", - "start": 15757, - "end": 15766, + "start": 16197, + "end": 16206, "loc": { "start": { - "line": 397, + "line": 413, "column": 75 }, "end": { - "line": 397, + "line": 413, "column": 84 }, "identifierName": "shortName" @@ -61990,15 +63550,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 15720, - "end": 15720, + "start": 16160, + "end": 16160, "loc": { "start": { - "line": 397, + "line": 413, "column": 38 }, "end": { - "line": 397, + "line": 413, "column": 38 } }, @@ -62010,15 +63570,15 @@ }, { "type": "TemplateElement", - "start": 15736, - "end": 15738, + "start": 16176, + "end": 16178, "loc": { "start": { - "line": 397, + "line": 413, "column": 54 }, "end": { - "line": 397, + "line": 413, "column": 56 } }, @@ -62030,15 +63590,15 @@ }, { "type": "TemplateElement", - "start": 15767, - "end": 15768, + "start": 16207, + "end": 16208, "loc": { "start": { - "line": 397, + "line": 413, "column": 85 }, "end": { - "line": 397, + "line": 413, "column": 86 } }, @@ -62060,43 +63620,43 @@ }, { "type": "ReturnStatement", - "start": 15785, - "end": 15806, + "start": 16225, + "end": 16246, "loc": { "start": { - "line": 399, + "line": 415, "column": 6 }, "end": { - "line": 399, + "line": 415, "column": 27 } }, "argument": { "type": "MemberExpression", - "start": 15792, - "end": 15805, + "start": 16232, + "end": 16245, "loc": { "start": { - "line": 399, + "line": 415, "column": 13 }, "end": { - "line": 399, + "line": 415, "column": 26 } }, "object": { "type": "Identifier", - "start": 15792, - "end": 15799, + "start": 16232, + "end": 16239, "loc": { "start": { - "line": 399, + "line": 415, "column": 13 }, "end": { - "line": 399, + "line": 415, "column": 20 }, "identifierName": "wrapped" @@ -62105,15 +63665,15 @@ }, "property": { "type": "Identifier", - "start": 15800, - "end": 15805, + "start": 16240, + "end": 16245, "loc": { "start": { - "line": 399, + "line": 415, "column": 21 }, "end": { - "line": 399, + "line": 415, "column": 26 }, "identifierName": "label" @@ -62131,15 +63691,15 @@ { "type": "CommentLine", "value": " Start with the internal specifiers, concatenated with '&'.", - "start": 15818, - "end": 15879, + "start": 16258, + "end": 16319, "loc": { "start": { - "line": 402, + "line": 418, "column": 4 }, "end": { - "line": 402, + "line": 418, "column": 65 } } @@ -62148,44 +63708,44 @@ }, { "type": "VariableDeclaration", - "start": 15884, - "end": 16001, + "start": 16324, + "end": 16441, "loc": { "start": { - "line": 403, + "line": 419, "column": 4 }, "end": { - "line": 406, + "line": 422, "column": 19 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 15890, - "end": 16000, + "start": 16330, + "end": 16440, "loc": { "start": { - "line": 403, + "line": 419, "column": 10 }, "end": { - "line": 406, + "line": 422, "column": 18 } }, "id": { "type": "Identifier", - "start": 15890, - "end": 15912, + "start": 16330, + "end": 16352, "loc": { "start": { - "line": 403, + "line": 419, "column": 10 }, "end": { - "line": 403, + "line": 419, "column": 32 }, "identifierName": "internalSpecifierLabel" @@ -62195,99 +63755,99 @@ }, "init": { "type": "CallExpression", - "start": 15915, - "end": 16000, + "start": 16355, + "end": 16440, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 406, + "line": 422, "column": 18 } }, "callee": { "type": "MemberExpression", - "start": 15915, - "end": 15993, + "start": 16355, + "end": 16433, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 406, + "line": 422, "column": 11 } }, "object": { "type": "CallExpression", - "start": 15915, - "end": 15981, + "start": 16355, + "end": 16421, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 405, + "line": 421, "column": 13 } }, "callee": { "type": "MemberExpression", - "start": 15915, - "end": 15979, + "start": 16355, + "end": 16419, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 405, + "line": 421, "column": 11 } }, "object": { "type": "CallExpression", - "start": 15915, - "end": 15967, + "start": 16355, + "end": 16407, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 404, + "line": 420, "column": 33 } }, "callee": { "type": "MemberExpression", - "start": 15915, - "end": 15944, + "start": 16355, + "end": 16384, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 404, + "line": 420, "column": 10 } }, "object": { "type": "Identifier", - "start": 15915, - "end": 15933, + "start": 16355, + "end": 16373, "loc": { "start": { - "line": 403, + "line": 419, "column": 35 }, "end": { - "line": 403, + "line": 419, "column": 53 }, "identifierName": "internalSpecifiers" @@ -62296,15 +63856,15 @@ }, "property": { "type": "Identifier", - "start": 15941, - "end": 15944, + "start": 16381, + "end": 16384, "loc": { "start": { - "line": 404, + "line": 420, "column": 7 }, "end": { - "line": 404, + "line": 420, "column": 10 }, "identifierName": "map" @@ -62316,15 +63876,15 @@ "arguments": [ { "type": "Identifier", - "start": 15945, - "end": 15966, + "start": 16385, + "end": 16406, "loc": { "start": { - "line": 404, + "line": 420, "column": 11 }, "end": { - "line": 404, + "line": 420, "column": 32 }, "identifierName": "generateSpecifierName" @@ -62335,15 +63895,15 @@ }, "property": { "type": "Identifier", - "start": 15975, - "end": 15979, + "start": 16415, + "end": 16419, "loc": { "start": { - "line": 405, + "line": 421, "column": 7 }, "end": { - "line": 405, + "line": 421, "column": 11 }, "identifierName": "sort" @@ -62356,15 +63916,15 @@ }, "property": { "type": "Identifier", - "start": 15989, - "end": 15993, + "start": 16429, + "end": 16433, "loc": { "start": { - "line": 406, + "line": 422, "column": 7 }, "end": { - "line": 406, + "line": 422, "column": 11 }, "identifierName": "join" @@ -62376,15 +63936,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 15994, - "end": 15999, + "start": 16434, + "end": 16439, "loc": { "start": { - "line": 406, + "line": 422, "column": 12 }, "end": { - "line": 406, + "line": 422, "column": 17 } }, @@ -62404,15 +63964,15 @@ { "type": "CommentLine", "value": " Start with the internal specifiers, concatenated with '&'.", - "start": 15818, - "end": 15879, + "start": 16258, + "end": 16319, "loc": { "start": { - "line": 402, + "line": 418, "column": 4 }, "end": { - "line": 402, + "line": 418, "column": 65 } } @@ -62421,44 +63981,44 @@ }, { "type": "VariableDeclaration", - "start": 16006, - "end": 16061, + "start": 16446, + "end": 16501, "loc": { "start": { - "line": 407, + "line": 423, "column": 4 }, "end": { - "line": 407, + "line": 423, "column": 59 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16010, - "end": 16060, + "start": 16450, + "end": 16500, "loc": { "start": { - "line": 407, + "line": 423, "column": 8 }, "end": { - "line": 407, + "line": 423, "column": 58 } }, "id": { "type": "Identifier", - "start": 16010, - "end": 16029, + "start": 16450, + "end": 16469, "loc": { "start": { - "line": 407, + "line": 423, "column": 8 }, "end": { - "line": 407, + "line": 423, "column": 27 }, "identifierName": "componentClassLabel" @@ -62467,30 +64027,30 @@ }, "init": { "type": "TemplateLiteral", - "start": 16032, - "end": 16060, + "start": 16472, + "end": 16500, "loc": { "start": { - "line": 407, + "line": 423, "column": 30 }, "end": { - "line": 407, + "line": 423, "column": 58 } }, "expressions": [ { "type": "Identifier", - "start": 16036, - "end": 16058, + "start": 16476, + "end": 16498, "loc": { "start": { - "line": 407, + "line": 423, "column": 34 }, "end": { - "line": 407, + "line": 423, "column": 56 }, "identifierName": "internalSpecifierLabel" @@ -62501,15 +64061,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 16033, - "end": 16034, + "start": 16473, + "end": 16474, "loc": { "start": { - "line": 407, + "line": 423, "column": 31 }, "end": { - "line": 407, + "line": 423, "column": 32 } }, @@ -62521,15 +64081,15 @@ }, { "type": "TemplateElement", - "start": 16059, - "end": 16059, + "start": 16499, + "end": 16499, "loc": { "start": { - "line": 407, + "line": 423, "column": 57 }, "end": { - "line": 407, + "line": 423, "column": 57 } }, @@ -62547,57 +64107,57 @@ }, { "type": "IfStatement", - "start": 16067, - "end": 16411, + "start": 16507, + "end": 16851, "loc": { "start": { - "line": 409, + "line": 425, "column": 4 }, "end": { - "line": 418, + "line": 434, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 16071, - "end": 16102, + "start": 16511, + "end": 16542, "loc": { "start": { - "line": 409, + "line": 425, "column": 8 }, "end": { - "line": 409, + "line": 425, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 16071, - "end": 16096, + "start": 16511, + "end": 16536, "loc": { "start": { - "line": 409, + "line": 425, "column": 8 }, "end": { - "line": 409, + "line": 425, "column": 33 } }, "object": { "type": "Identifier", - "start": 16071, - "end": 16089, + "start": 16511, + "end": 16529, "loc": { "start": { - "line": 409, + "line": 425, "column": 8 }, "end": { - "line": 409, + "line": 425, "column": 26 }, "identifierName": "externalSpecifiers" @@ -62606,15 +64166,15 @@ }, "property": { "type": "Identifier", - "start": 16090, - "end": 16096, + "start": 16530, + "end": 16536, "loc": { "start": { - "line": 409, + "line": 425, "column": 27 }, "end": { - "line": 409, + "line": 425, "column": 33 }, "identifierName": "length" @@ -62626,15 +64186,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 16101, - "end": 16102, + "start": 16541, + "end": 16542, "loc": { "start": { - "line": 409, + "line": 425, "column": 38 }, "end": { - "line": 409, + "line": 425, "column": 39 } }, @@ -62647,59 +64207,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 16104, - "end": 16145, + "start": 16544, + "end": 16585, "loc": { "start": { - "line": 409, + "line": 425, "column": 41 }, "end": { - "line": 411, + "line": 427, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 16112, - "end": 16139, + "start": 16552, + "end": 16579, "loc": { "start": { - "line": 410, + "line": 426, "column": 6 }, "end": { - "line": 410, + "line": 426, "column": 33 } }, "expression": { "type": "AssignmentExpression", - "start": 16112, - "end": 16138, + "start": 16552, + "end": 16578, "loc": { "start": { - "line": 410, + "line": 426, "column": 6 }, "end": { - "line": 410, + "line": 426, "column": 32 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 16112, - "end": 16131, + "start": 16552, + "end": 16571, "loc": { "start": { - "line": 410, + "line": 426, "column": 6 }, "end": { - "line": 410, + "line": 426, "column": 25 }, "identifierName": "componentClassLabel" @@ -62708,15 +64268,15 @@ }, "right": { "type": "StringLiteral", - "start": 16135, - "end": 16138, + "start": 16575, + "end": 16578, "loc": { "start": { - "line": 410, + "line": 426, "column": 29 }, "end": { - "line": 410, + "line": 426, "column": 32 } }, @@ -62733,59 +64293,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 16151, - "end": 16411, + "start": 16591, + "end": 16851, "loc": { "start": { - "line": 411, + "line": 427, "column": 11 }, "end": { - "line": 418, + "line": 434, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 16220, - "end": 16343, + "start": 16660, + "end": 16783, "loc": { "start": { - "line": 413, + "line": 429, "column": 6 }, "end": { - "line": 416, + "line": 432, "column": 21 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 16226, - "end": 16342, + "start": 16666, + "end": 16782, "loc": { "start": { - "line": 413, + "line": 429, "column": 12 }, "end": { - "line": 416, + "line": 432, "column": 20 } }, "id": { "type": "Identifier", - "start": 16226, - "end": 16248, + "start": 16666, + "end": 16688, "loc": { "start": { - "line": 413, + "line": 429, "column": 12 }, "end": { - "line": 413, + "line": 429, "column": 34 }, "identifierName": "externalSpecifierLabel" @@ -62795,99 +64355,99 @@ }, "init": { "type": "CallExpression", - "start": 16251, - "end": 16342, + "start": 16691, + "end": 16782, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 416, + "line": 432, "column": 20 } }, "callee": { "type": "MemberExpression", - "start": 16251, - "end": 16335, + "start": 16691, + "end": 16775, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 416, + "line": 432, "column": 13 } }, "object": { "type": "CallExpression", - "start": 16251, - "end": 16321, + "start": 16691, + "end": 16761, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 415, + "line": 431, "column": 15 } }, "callee": { "type": "MemberExpression", - "start": 16251, - "end": 16319, + "start": 16691, + "end": 16759, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 415, + "line": 431, "column": 13 } }, "object": { "type": "CallExpression", - "start": 16251, - "end": 16305, + "start": 16691, + "end": 16745, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 414, + "line": 430, "column": 35 } }, "callee": { "type": "MemberExpression", - "start": 16251, - "end": 16282, + "start": 16691, + "end": 16722, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 414, + "line": 430, "column": 12 } }, "object": { "type": "Identifier", - "start": 16251, - "end": 16269, + "start": 16691, + "end": 16709, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 413, + "line": 429, "column": 55 }, "identifierName": "externalSpecifiers" @@ -62896,15 +64456,15 @@ }, "property": { "type": "Identifier", - "start": 16279, - "end": 16282, + "start": 16719, + "end": 16722, "loc": { "start": { - "line": 414, + "line": 430, "column": 9 }, "end": { - "line": 414, + "line": 430, "column": 12 }, "identifierName": "map" @@ -62916,15 +64476,15 @@ "arguments": [ { "type": "Identifier", - "start": 16283, - "end": 16304, + "start": 16723, + "end": 16744, "loc": { "start": { - "line": 414, + "line": 430, "column": 13 }, "end": { - "line": 414, + "line": 430, "column": 34 }, "identifierName": "generateSpecifierName" @@ -62935,15 +64495,15 @@ }, "property": { "type": "Identifier", - "start": 16315, - "end": 16319, + "start": 16755, + "end": 16759, "loc": { "start": { - "line": 415, + "line": 431, "column": 9 }, "end": { - "line": 415, + "line": 431, "column": 13 }, "identifierName": "sort" @@ -62956,15 +64516,15 @@ }, "property": { "type": "Identifier", - "start": 16331, - "end": 16335, + "start": 16771, + "end": 16775, "loc": { "start": { - "line": 416, + "line": 432, "column": 9 }, "end": { - "line": 416, + "line": 432, "column": 13 }, "identifierName": "join" @@ -62976,15 +64536,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 16336, - "end": 16341, + "start": 16776, + "end": 16781, "loc": { "start": { - "line": 416, + "line": 432, "column": 14 }, "end": { - "line": 416, + "line": 432, "column": 19 } }, @@ -63004,15 +64564,15 @@ { "type": "CommentLine", "value": " Add the external specifiers, concatenated with 'V'.", - "start": 16159, - "end": 16213, + "start": 16599, + "end": 16653, "loc": { "start": { - "line": 412, + "line": 428, "column": 6 }, "end": { - "line": 412, + "line": 428, "column": 60 } } @@ -63021,44 +64581,44 @@ }, { "type": "ExpressionStatement", - "start": 16350, - "end": 16405, + "start": 16790, + "end": 16845, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 61 } }, "expression": { "type": "AssignmentExpression", - "start": 16350, - "end": 16404, + "start": 16790, + "end": 16844, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 60 } }, "operator": "+=", "left": { "type": "Identifier", - "start": 16350, - "end": 16369, + "start": 16790, + "end": 16809, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 25 }, "identifierName": "componentClassLabel" @@ -63067,30 +64627,30 @@ }, "right": { "type": "TemplateLiteral", - "start": 16373, - "end": 16404, + "start": 16813, + "end": 16844, "loc": { "start": { - "line": 417, + "line": 433, "column": 29 }, "end": { - "line": 417, + "line": 433, "column": 60 } }, "expressions": [ { "type": "Identifier", - "start": 16379, - "end": 16401, + "start": 16819, + "end": 16841, "loc": { "start": { - "line": 417, + "line": 433, "column": 35 }, "end": { - "line": 417, + "line": 433, "column": 57 }, "identifierName": "externalSpecifierLabel" @@ -63101,15 +64661,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 16374, - "end": 16377, + "start": 16814, + "end": 16817, "loc": { "start": { - "line": 417, + "line": 433, "column": 30 }, "end": { - "line": 417, + "line": 433, "column": 33 } }, @@ -63121,15 +64681,15 @@ }, { "type": "TemplateElement", - "start": 16402, - "end": 16403, + "start": 16842, + "end": 16843, "loc": { "start": { - "line": 417, + "line": 433, "column": 58 }, "end": { - "line": 417, + "line": 433, "column": 59 } }, @@ -63151,15 +64711,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`component class label: ${componentClassLabel}\\n`);", - "start": 16417, - "end": 16492, + "start": 16857, + "end": 16932, "loc": { "start": { - "line": 420, + "line": 436, "column": 4 }, "end": { - "line": 420, + "line": 436, "column": 79 } } @@ -63167,15 +64727,15 @@ { "type": "CommentLine", "value": " TODO We need to replace this with an actual object-based comparison,", - "start": 16498, - "end": 16569, + "start": 16938, + "end": 17009, "loc": { "start": { - "line": 422, + "line": 438, "column": 4 }, "end": { - "line": 422, + "line": 438, "column": 75 } } @@ -63183,15 +64743,15 @@ { "type": "CommentLine", "value": " rather than trusting the labels to tell us everything.", - "start": 16574, - "end": 16631, + "start": 17014, + "end": 17071, "loc": { "start": { - "line": 423, + "line": 439, "column": 4 }, "end": { - "line": 423, + "line": 439, "column": 61 } } @@ -63200,43 +64760,43 @@ }, { "type": "IfStatement", - "start": 16636, - "end": 16890, + "start": 17076, + "end": 17330, "loc": { "start": { - "line": 424, + "line": 440, "column": 4 }, "end": { - "line": 427, + "line": 443, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 16640, - "end": 16711, + "start": 17080, + "end": 17151, "loc": { "start": { - "line": 424, + "line": 440, "column": 8 }, "end": { - "line": 424, + "line": 440, "column": 79 } }, "left": { "type": "Identifier", - "start": 16640, - "end": 16653, + "start": 17080, + "end": 17093, "loc": { "start": { - "line": 424, + "line": 440, "column": 8 }, "end": { - "line": 424, + "line": 440, "column": 21 }, "identifierName": "reusePrevious" @@ -63247,29 +64807,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 16657, - "end": 16711, + "start": 17097, + "end": 17151, "loc": { "start": { - "line": 424, + "line": 440, "column": 25 }, "end": { - "line": 424, + "line": 440, "column": 79 } }, "callee": { "type": "Identifier", - "start": 16657, - "end": 16660, + "start": 17097, + "end": 17100, "loc": { "start": { - "line": 424, + "line": 440, "column": 25 }, "end": { - "line": 424, + "line": 440, "column": 28 }, "identifierName": "has" @@ -63279,44 +64839,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 16661, - "end": 16689, + "start": 17101, + "end": 17129, "loc": { "start": { - "line": 424, + "line": 440, "column": 29 }, "end": { - "line": 424, + "line": 440, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 16661, - "end": 16665, + "start": 17101, + "end": 17105, "loc": { "start": { - "line": 424, + "line": 440, "column": 29 }, "end": { - "line": 424, + "line": 440, "column": 33 } } }, "property": { "type": "Identifier", - "start": 16666, - "end": 16689, + "start": 17106, + "end": 17129, "loc": { "start": { - "line": 424, + "line": 440, "column": 34 }, "end": { - "line": 424, + "line": 440, "column": 57 }, "identifierName": "componentClassesByLabel" @@ -63327,15 +64887,15 @@ }, { "type": "Identifier", - "start": 16691, - "end": 16710, + "start": 17131, + "end": 17150, "loc": { "start": { - "line": 424, + "line": 440, "column": 59 }, "end": { - "line": 424, + "line": 440, "column": 78 }, "identifierName": "componentClassLabel" @@ -63348,59 +64908,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 16713, - "end": 16890, + "start": 17153, + "end": 17330, "loc": { "start": { - "line": 424, + "line": 440, "column": 81 }, "end": { - "line": 427, + "line": 443, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 16809, - "end": 16884, + "start": 17249, + "end": 17324, "loc": { "start": { - "line": 426, + "line": 442, "column": 6 }, "end": { - "line": 426, + "line": 442, "column": 81 } }, "argument": { "type": "ObjectExpression", - "start": 16816, - "end": 16883, + "start": 17256, + "end": 17323, "loc": { "start": { - "line": 426, + "line": 442, "column": 13 }, "end": { - "line": 426, + "line": 442, "column": 80 } }, "properties": [ { "type": "ObjectProperty", - "start": 16818, - "end": 16881, + "start": 17258, + "end": 17321, "loc": { "start": { - "line": 426, + "line": 442, "column": 15 }, "end": { - "line": 426, + "line": 442, "column": 78 } }, @@ -63409,15 +64969,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 16818, - "end": 16823, + "start": 17258, + "end": 17263, "loc": { "start": { - "line": 426, + "line": 442, "column": 15 }, "end": { - "line": 426, + "line": 442, "column": 20 } }, @@ -63430,72 +64990,72 @@ }, "value": { "type": "MemberExpression", - "start": 16825, - "end": 16881, + "start": 17265, + "end": 17321, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 78 } }, "object": { "type": "MemberExpression", - "start": 16825, - "end": 16874, + "start": 17265, + "end": 17314, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 71 } }, "object": { "type": "MemberExpression", - "start": 16825, - "end": 16853, + "start": 17265, + "end": 17293, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 50 } }, "object": { "type": "ThisExpression", - "start": 16825, - "end": 16829, + "start": 17265, + "end": 17269, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 26 } } }, "property": { "type": "Identifier", - "start": 16830, - "end": 16853, + "start": 17270, + "end": 17293, "loc": { "start": { - "line": 426, + "line": 442, "column": 27 }, "end": { - "line": 426, + "line": 442, "column": 50 }, "identifierName": "componentClassesByLabel" @@ -63506,15 +65066,15 @@ }, "property": { "type": "Identifier", - "start": 16854, - "end": 16873, + "start": 17294, + "end": 17313, "loc": { "start": { - "line": 426, + "line": 442, "column": 51 }, "end": { - "line": 426, + "line": 442, "column": 70 }, "identifierName": "componentClassLabel" @@ -63525,15 +65085,15 @@ }, "property": { "type": "StringLiteral", - "start": 16875, - "end": 16880, + "start": 17315, + "end": 17320, "loc": { "start": { - "line": 426, + "line": 442, "column": 72 }, "end": { - "line": 426, + "line": 442, "column": 77 } }, @@ -63554,15 +65114,15 @@ { "type": "CommentLine", "value": " If we see the same label again, return the previously defined component class.", - "start": 16721, - "end": 16802, + "start": 17161, + "end": 17242, "loc": { "start": { - "line": 425, + "line": 441, "column": 6 }, "end": { - "line": 425, + "line": 441, "column": 87 } } @@ -63578,15 +65138,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`component class label: ${componentClassLabel}\\n`);", - "start": 16417, - "end": 16492, + "start": 16857, + "end": 16932, "loc": { "start": { - "line": 420, + "line": 436, "column": 4 }, "end": { - "line": 420, + "line": 436, "column": 79 } } @@ -63594,15 +65154,15 @@ { "type": "CommentLine", "value": " TODO We need to replace this with an actual object-based comparison,", - "start": 16498, - "end": 16569, + "start": 16938, + "end": 17009, "loc": { "start": { - "line": 422, + "line": 438, "column": 4 }, "end": { - "line": 422, + "line": 438, "column": 75 } } @@ -63610,15 +65170,15 @@ { "type": "CommentLine", "value": " rather than trusting the labels to tell us everything.", - "start": 16574, - "end": 16631, + "start": 17014, + "end": 17071, "loc": { "start": { - "line": 423, + "line": 439, "column": 4 }, "end": { - "line": 423, + "line": 439, "column": 61 } } @@ -63628,15 +65188,15 @@ { "type": "CommentLine", "value": " Create a new component class for this set of internal and external specifiers.", - "start": 16896, - "end": 16977, + "start": 17336, + "end": 17417, "loc": { "start": { - "line": 429, + "line": 445, "column": 4 }, "end": { - "line": 429, + "line": 445, "column": 85 } } @@ -63645,58 +65205,58 @@ }, { "type": "ExpressionStatement", - "start": 16982, - "end": 17012, + "start": 17422, + "end": 17452, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 34 } }, "expression": { "type": "AssignmentExpression", - "start": 16982, - "end": 17011, + "start": 17422, + "end": 17451, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 33 } }, "operator": "+=", "left": { "type": "MemberExpression", - "start": 16982, - "end": 17006, + "start": 17422, + "end": 17446, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 16982, - "end": 16986, + "start": 17422, + "end": 17426, "loc": { "start": { - "line": 430, + "line": 446, "column": 4 }, "end": { - "line": 430, + "line": 446, "column": 8 } }, @@ -63704,15 +65264,15 @@ }, "property": { "type": "Identifier", - "start": 16987, - "end": 17006, + "start": 17427, + "end": 17446, "loc": { "start": { - "line": 430, + "line": 446, "column": 9 }, "end": { - "line": 430, + "line": 446, "column": 28 }, "identifierName": "componentClassCount" @@ -63724,15 +65284,15 @@ }, "right": { "type": "NumericLiteral", - "start": 17010, - "end": 17011, + "start": 17450, + "end": 17451, "loc": { "start": { - "line": 430, + "line": 446, "column": 32 }, "end": { - "line": 430, + "line": 446, "column": 33 } }, @@ -63748,15 +65308,15 @@ { "type": "CommentLine", "value": " Create a new component class for this set of internal and external specifiers.", - "start": 16896, - "end": 16977, + "start": 17336, + "end": 17417, "loc": { "start": { - "line": 429, + "line": 445, "column": 4 }, "end": { - "line": 429, + "line": 445, "column": 85 } } @@ -63765,44 +65325,44 @@ }, { "type": "VariableDeclaration", - "start": 17017, - "end": 17043, + "start": 17457, + "end": 17483, "loc": { "start": { - "line": 431, + "line": 447, "column": 4 }, "end": { - "line": 431, + "line": 447, "column": 30 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 17023, - "end": 17042, + "start": 17463, + "end": 17482, "loc": { "start": { - "line": 431, + "line": 447, "column": 10 }, "end": { - "line": 431, + "line": 447, "column": 29 } }, "id": { "type": "Identifier", - "start": 17023, - "end": 17037, + "start": 17463, + "end": 17477, "loc": { "start": { - "line": 431, + "line": 447, "column": 10 }, "end": { - "line": 431, + "line": 447, "column": 24 }, "identifierName": "componentClass" @@ -63811,15 +65371,15 @@ }, "init": { "type": "ObjectExpression", - "start": 17040, - "end": 17042, + "start": 17480, + "end": 17482, "loc": { "start": { - "line": 431, + "line": 447, "column": 27 }, "end": { - "line": 431, + "line": 447, "column": 29 } }, @@ -63831,58 +65391,58 @@ }, { "type": "ExpressionStatement", - "start": 17048, - "end": 17128, + "start": 17488, + "end": 17568, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 84 } }, "expression": { "type": "AssignmentExpression", - "start": 17048, - "end": 17127, + "start": 17488, + "end": 17567, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 83 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17048, - "end": 17069, + "start": 17488, + "end": 17509, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 25 } }, "object": { "type": "Identifier", - "start": 17048, - "end": 17062, + "start": 17488, + "end": 17502, "loc": { "start": { - "line": 432, + "line": 448, "column": 4 }, "end": { - "line": 432, + "line": 448, "column": 18 }, "identifierName": "componentClass" @@ -63891,15 +65451,15 @@ }, "property": { "type": "StringLiteral", - "start": 17063, - "end": 17068, + "start": 17503, + "end": 17508, "loc": { "start": { - "line": 432, + "line": 448, "column": 19 }, "end": { - "line": 432, + "line": 448, "column": 24 } }, @@ -63913,44 +65473,44 @@ }, "right": { "type": "TemplateLiteral", - "start": 17072, - "end": 17127, + "start": 17512, + "end": 17567, "loc": { "start": { - "line": 432, + "line": 448, "column": 28 }, "end": { - "line": 432, + "line": 448, "column": 83 } }, "expressions": [ { "type": "MemberExpression", - "start": 17075, - "end": 17088, + "start": 17515, + "end": 17528, "loc": { "start": { - "line": 432, + "line": 448, "column": 31 }, "end": { - "line": 432, + "line": 448, "column": 44 } }, "object": { "type": "Identifier", - "start": 17075, - "end": 17081, + "start": 17515, + "end": 17521, "loc": { "start": { - "line": 432, + "line": 448, "column": 31 }, "end": { - "line": 432, + "line": 448, "column": 37 }, "identifierName": "jsonld" @@ -63959,15 +65519,15 @@ }, "property": { "type": "StringLiteral", - "start": 17082, - "end": 17087, + "start": 17522, + "end": 17527, "loc": { "start": { - "line": 432, + "line": 448, "column": 38 }, "end": { - "line": 432, + "line": 448, "column": 43 } }, @@ -63981,44 +65541,44 @@ }, { "type": "MemberExpression", - "start": 17101, - "end": 17125, + "start": 17541, + "end": 17565, "loc": { "start": { - "line": 432, + "line": 448, "column": 57 }, "end": { - "line": 432, + "line": 448, "column": 81 } }, "object": { "type": "ThisExpression", - "start": 17101, - "end": 17105, + "start": 17541, + "end": 17545, "loc": { "start": { - "line": 432, + "line": 448, "column": 57 }, "end": { - "line": 432, + "line": 448, "column": 61 } } }, "property": { "type": "Identifier", - "start": 17106, - "end": 17125, + "start": 17546, + "end": 17565, "loc": { "start": { - "line": 432, + "line": 448, "column": 62 }, "end": { - "line": 432, + "line": 448, "column": 81 }, "identifierName": "componentClassCount" @@ -64031,15 +65591,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 17073, - "end": 17073, + "start": 17513, + "end": 17513, "loc": { "start": { - "line": 432, + "line": 448, "column": 29 }, "end": { - "line": 432, + "line": 448, "column": 29 } }, @@ -64051,15 +65611,15 @@ }, { "type": "TemplateElement", - "start": 17089, - "end": 17099, + "start": 17529, + "end": 17539, "loc": { "start": { - "line": 432, + "line": 448, "column": 45 }, "end": { - "line": 432, + "line": 448, "column": 55 } }, @@ -64071,15 +65631,15 @@ }, { "type": "TemplateElement", - "start": 17126, - "end": 17126, + "start": 17566, + "end": 17566, "loc": { "start": { - "line": 432, + "line": 448, "column": 82 }, "end": { - "line": 432, + "line": 448, "column": 82 } }, @@ -64096,15 +65656,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);", - "start": 17133, - "end": 17222, + "start": 17573, + "end": 17662, "loc": { "start": { - "line": 433, + "line": 449, "column": 4 }, "end": { - "line": 433, + "line": 449, "column": 93 } } @@ -64113,58 +65673,58 @@ }, { "type": "ExpressionStatement", - "start": 17228, - "end": 17266, + "start": 17668, + "end": 17706, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 17228, - "end": 17265, + "start": 17668, + "end": 17705, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17228, - "end": 17251, + "start": 17668, + "end": 17691, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 27 } }, "object": { "type": "Identifier", - "start": 17228, - "end": 17242, + "start": 17668, + "end": 17682, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 18 }, "identifierName": "componentClass" @@ -64174,15 +65734,15 @@ }, "property": { "type": "StringLiteral", - "start": 17243, - "end": 17250, + "start": 17683, + "end": 17690, "loc": { "start": { - "line": 435, + "line": 451, "column": 19 }, "end": { - "line": 435, + "line": 451, "column": 26 } }, @@ -64197,15 +65757,15 @@ }, "right": { "type": "StringLiteral", - "start": 17254, - "end": 17265, + "start": 17694, + "end": 17705, "loc": { "start": { - "line": 435, + "line": 451, "column": 30 }, "end": { - "line": 435, + "line": 451, "column": 41 } }, @@ -64221,15 +65781,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);", - "start": 17133, - "end": 17222, + "start": 17573, + "end": 17662, "loc": { "start": { - "line": 433, + "line": 449, "column": 4 }, "end": { - "line": 433, + "line": 449, "column": 93 } } @@ -64238,58 +65798,58 @@ }, { "type": "ExpressionStatement", - "start": 17271, - "end": 17314, + "start": 17711, + "end": 17754, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 47 } }, "expression": { "type": "AssignmentExpression", - "start": 17271, - "end": 17313, + "start": 17711, + "end": 17753, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 46 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17271, - "end": 17291, + "start": 17711, + "end": 17731, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 24 } }, "object": { "type": "Identifier", - "start": 17271, - "end": 17285, + "start": 17711, + "end": 17725, "loc": { "start": { - "line": 436, + "line": 452, "column": 4 }, "end": { - "line": 436, + "line": 452, "column": 18 }, "identifierName": "componentClass" @@ -64298,15 +65858,15 @@ }, "property": { "type": "Identifier", - "start": 17286, - "end": 17291, + "start": 17726, + "end": 17731, "loc": { "start": { - "line": 436, + "line": 452, "column": 19 }, "end": { - "line": 436, + "line": 452, "column": 24 }, "identifierName": "label" @@ -64317,15 +65877,15 @@ }, "right": { "type": "Identifier", - "start": 17294, - "end": 17313, + "start": 17734, + "end": 17753, "loc": { "start": { - "line": 436, + "line": 452, "column": 27 }, "end": { - "line": 436, + "line": 452, "column": 46 }, "identifierName": "componentClassLabel" @@ -64336,58 +65896,58 @@ }, { "type": "ExpressionStatement", - "start": 17319, - "end": 17363, + "start": 17759, + "end": 17803, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 48 } }, "expression": { "type": "AssignmentExpression", - "start": 17319, - "end": 17362, + "start": 17759, + "end": 17802, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 47 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17319, - "end": 17349, + "start": 17759, + "end": 17789, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 34 } }, "object": { "type": "Identifier", - "start": 17319, - "end": 17333, + "start": 17759, + "end": 17773, "loc": { "start": { - "line": 437, + "line": 453, "column": 4 }, "end": { - "line": 437, + "line": 453, "column": 18 }, "identifierName": "componentClass" @@ -64396,15 +65956,15 @@ }, "property": { "type": "Identifier", - "start": 17334, - "end": 17349, + "start": 17774, + "end": 17789, "loc": { "start": { - "line": 437, + "line": 453, "column": 19 }, "end": { - "line": 437, + "line": 453, "column": 34 }, "identifierName": "equivalentClass" @@ -64415,15 +65975,15 @@ }, "right": { "type": "Identifier", - "start": 17352, - "end": 17362, + "start": 17792, + "end": 17802, "loc": { "start": { - "line": 437, + "line": 453, "column": 37 }, "end": { - "line": 437, + "line": 453, "column": 47 }, "identifierName": "equivClass" @@ -64434,57 +65994,57 @@ }, { "type": "IfStatement", - "start": 17368, - "end": 17559, + "start": 17808, + "end": 17999, "loc": { "start": { - "line": 438, + "line": 454, "column": 4 }, "end": { - "line": 439, + "line": 455, "column": 82 } }, "test": { "type": "BinaryExpression", - "start": 17372, - "end": 17401, + "start": 17812, + "end": 17841, "loc": { "start": { - "line": 438, + "line": 454, "column": 8 }, "end": { - "line": 438, + "line": 454, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 17372, - "end": 17397, + "start": 17812, + "end": 17837, "loc": { "start": { - "line": 438, + "line": 454, "column": 8 }, "end": { - "line": 438, + "line": 454, "column": 33 } }, "object": { "type": "Identifier", - "start": 17372, - "end": 17390, + "start": 17812, + "end": 17830, "loc": { "start": { - "line": 438, + "line": 454, "column": 8 }, "end": { - "line": 438, + "line": 454, "column": 26 }, "identifierName": "externalSpecifiers" @@ -64493,15 +66053,15 @@ }, "property": { "type": "Identifier", - "start": 17391, - "end": 17397, + "start": 17831, + "end": 17837, "loc": { "start": { - "line": 438, + "line": 454, "column": 27 }, "end": { - "line": 438, + "line": 454, "column": 33 }, "identifierName": "length" @@ -64513,15 +66073,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 17400, - "end": 17401, + "start": 17840, + "end": 17841, "loc": { "start": { - "line": 438, + "line": 454, "column": 36 }, "end": { - "line": 438, + "line": 454, "column": 37 } }, @@ -64534,58 +66094,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 17403, - "end": 17476, + "start": 17843, + "end": 17916, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 112 } }, "expression": { "type": "AssignmentExpression", - "start": 17403, - "end": 17475, + "start": 17843, + "end": 17915, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 111 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17403, - "end": 17428, + "start": 17843, + "end": 17868, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 64 } }, "object": { "type": "Identifier", - "start": 17403, - "end": 17417, + "start": 17843, + "end": 17857, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 53 }, "identifierName": "componentClass" @@ -64594,15 +66154,15 @@ }, "property": { "type": "Identifier", - "start": 17418, - "end": 17428, + "start": 17858, + "end": 17868, "loc": { "start": { - "line": 438, + "line": 454, "column": 54 }, "end": { - "line": 438, + "line": 454, "column": 64 }, "identifierName": "subClassOf" @@ -64613,30 +66173,30 @@ }, "right": { "type": "ArrayExpression", - "start": 17431, - "end": 17475, + "start": 17871, + "end": 17915, "loc": { "start": { - "line": 438, + "line": 454, "column": 67 }, "end": { - "line": 438, + "line": 454, "column": 111 } }, "elements": [ { "type": "StringLiteral", - "start": 17432, - "end": 17474, + "start": 17872, + "end": 17914, "loc": { "start": { - "line": 438, + "line": 454, "column": 68 }, "end": { - "line": 438, + "line": 454, "column": 110 } }, @@ -64652,58 +66212,58 @@ }, "alternate": { "type": "ExpressionStatement", - "start": 17486, - "end": 17559, + "start": 17926, + "end": 17999, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 82 } }, "expression": { "type": "AssignmentExpression", - "start": 17486, - "end": 17558, + "start": 17926, + "end": 17998, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 81 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17486, - "end": 17511, + "start": 17926, + "end": 17951, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 34 } }, "object": { "type": "Identifier", - "start": 17486, - "end": 17500, + "start": 17926, + "end": 17940, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 23 }, "identifierName": "componentClass" @@ -64712,15 +66272,15 @@ }, "property": { "type": "Identifier", - "start": 17501, - "end": 17511, + "start": 17941, + "end": 17951, "loc": { "start": { - "line": 439, + "line": 455, "column": 24 }, "end": { - "line": 439, + "line": 455, "column": 34 }, "identifierName": "subClassOf" @@ -64731,30 +66291,30 @@ }, "right": { "type": "ArrayExpression", - "start": 17514, - "end": 17558, + "start": 17954, + "end": 17998, "loc": { "start": { - "line": 439, + "line": 455, "column": 37 }, "end": { - "line": 439, + "line": 455, "column": 81 } }, "elements": [ { "type": "StringLiteral", - "start": 17515, - "end": 17557, + "start": 17955, + "end": 17997, "loc": { "start": { - "line": 439, + "line": 455, "column": 38 }, "end": { - "line": 439, + "line": 455, "column": 80 } }, @@ -64771,29 +66331,29 @@ }, { "type": "IfStatement", - "start": 17565, - "end": 17673, + "start": 18005, + "end": 18113, "loc": { "start": { - "line": 441, + "line": 457, "column": 4 }, "end": { - "line": 445, + "line": 461, "column": 5 } }, "test": { "type": "Identifier", - "start": 17569, - "end": 17580, + "start": 18009, + "end": 18020, "loc": { "start": { - "line": 441, + "line": 457, "column": 8 }, "end": { - "line": 441, + "line": 457, "column": 19 }, "identifierName": "parentClass" @@ -64802,86 +66362,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 17582, - "end": 17673, + "start": 18022, + "end": 18113, "loc": { "start": { - "line": 441, + "line": 457, "column": 21 }, "end": { - "line": 445, + "line": 461, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 17590, - "end": 17667, + "start": 18030, + "end": 18107, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 444, + "line": 460, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 17590, - "end": 17666, + "start": 18030, + "end": 18106, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 444, + "line": 460, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 17590, - "end": 17620, + "start": 18030, + "end": 18060, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 17590, - "end": 17615, + "start": 18030, + "end": 18055, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 31 } }, "object": { "type": "Identifier", - "start": 17590, - "end": 17604, + "start": 18030, + "end": 18044, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 20 }, "identifierName": "componentClass" @@ -64890,15 +66450,15 @@ }, "property": { "type": "Identifier", - "start": 17605, - "end": 17615, + "start": 18045, + "end": 18055, "loc": { "start": { - "line": 442, + "line": 458, "column": 21 }, "end": { - "line": 442, + "line": 458, "column": 31 }, "identifierName": "subClassOf" @@ -64909,15 +66469,15 @@ }, "property": { "type": "Identifier", - "start": 17616, - "end": 17620, + "start": 18056, + "end": 18060, "loc": { "start": { - "line": 442, + "line": 458, "column": 32 }, "end": { - "line": 442, + "line": 458, "column": 36 }, "identifierName": "push" @@ -64929,30 +66489,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 17621, - "end": 17665, + "start": 18061, + "end": 18105, "loc": { "start": { - "line": 442, + "line": 458, "column": 37 }, "end": { - "line": 444, + "line": 460, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 17631, - "end": 17656, + "start": 18071, + "end": 18096, "loc": { "start": { - "line": 443, + "line": 459, "column": 8 }, "end": { - "line": 443, + "line": 459, "column": 33 } }, @@ -64961,15 +66521,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 17631, - "end": 17636, + "start": 18071, + "end": 18076, "loc": { "start": { - "line": 443, + "line": 459, "column": 8 }, "end": { - "line": 443, + "line": 459, "column": 13 } }, @@ -64981,29 +66541,29 @@ }, "value": { "type": "MemberExpression", - "start": 17638, - "end": 17656, + "start": 18078, + "end": 18096, "loc": { "start": { - "line": 443, + "line": 459, "column": 15 }, "end": { - "line": 443, + "line": 459, "column": 33 } }, "object": { "type": "Identifier", - "start": 17638, - "end": 17649, + "start": 18078, + "end": 18089, "loc": { "start": { - "line": 443, + "line": 459, "column": 15 }, "end": { - "line": 443, + "line": 459, "column": 26 }, "identifierName": "parentClass" @@ -65012,15 +66572,15 @@ }, "property": { "type": "StringLiteral", - "start": 17650, - "end": 17655, + "start": 18090, + "end": 18095, "loc": { "start": { - "line": 443, + "line": 459, "column": 27 }, "end": { - "line": 443, + "line": 459, "column": 32 } }, @@ -65047,15 +66607,15 @@ { "type": "CommentLine", "value": " Save it in the cache for later usage.", - "start": 17679, - "end": 17719, + "start": 18119, + "end": 18159, "loc": { "start": { - "line": 447, + "line": 463, "column": 4 }, "end": { - "line": 447, + "line": 463, "column": 44 } } @@ -65064,72 +66624,72 @@ }, { "type": "ExpressionStatement", - "start": 17724, - "end": 17791, + "start": 18164, + "end": 18231, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 17724, - "end": 17790, + "start": 18164, + "end": 18230, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 17724, - "end": 17773, + "start": 18164, + "end": 18213, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 53 } }, "object": { "type": "MemberExpression", - "start": 17724, - "end": 17752, + "start": 18164, + "end": 18192, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 17724, - "end": 17728, + "start": 18164, + "end": 18168, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 8 } }, @@ -65137,15 +66697,15 @@ }, "property": { "type": "Identifier", - "start": 17729, - "end": 17752, + "start": 18169, + "end": 18192, "loc": { "start": { - "line": 448, + "line": 464, "column": 9 }, "end": { - "line": 448, + "line": 464, "column": 32 }, "identifierName": "componentClassesByLabel" @@ -65157,15 +66717,15 @@ }, "property": { "type": "Identifier", - "start": 17753, - "end": 17772, + "start": 18193, + "end": 18212, "loc": { "start": { - "line": 448, + "line": 464, "column": 33 }, "end": { - "line": 448, + "line": 464, "column": 52 }, "identifierName": "componentClassLabel" @@ -65177,15 +66737,15 @@ }, "right": { "type": "Identifier", - "start": 17776, - "end": 17790, + "start": 18216, + "end": 18230, "loc": { "start": { - "line": 448, + "line": 464, "column": 56 }, "end": { - "line": 448, + "line": 464, "column": 70 }, "identifierName": "componentClass" @@ -65198,15 +66758,15 @@ { "type": "CommentLine", "value": " Save it in the cache for later usage.", - "start": 17679, - "end": 17719, + "start": 18119, + "end": 18159, "loc": { "start": { - "line": 447, + "line": 463, "column": 4 }, "end": { - "line": 447, + "line": 463, "column": 44 } } @@ -65216,15 +66776,15 @@ { "type": "CommentLine", "value": " The first time we create a componentClass, we include it into the logical", - "start": 17797, - "end": 17873, + "start": 18237, + "end": 18313, "loc": { "start": { - "line": 450, + "line": 466, "column": 4 }, "end": { - "line": 450, + "line": 466, "column": 80 } } @@ -65232,15 +66792,15 @@ { "type": "CommentLine", "value": " expression directly. On subsequent calls, we'll only return the `@id`", - "start": 17878, - "end": 17950, + "start": 18318, + "end": 18390, "loc": { "start": { - "line": 451, + "line": 467, "column": 4 }, "end": { - "line": 451, + "line": 467, "column": 76 } } @@ -65248,15 +66808,15 @@ { "type": "CommentLine", "value": " (see above).", - "start": 17955, - "end": 17970, + "start": 18395, + "end": 18410, "loc": { "start": { - "line": 452, + "line": 468, "column": 4 }, "end": { - "line": 452, + "line": 468, "column": 19 } } @@ -65265,29 +66825,29 @@ }, { "type": "ReturnStatement", - "start": 17975, - "end": 17997, + "start": 18415, + "end": 18437, "loc": { "start": { - "line": 453, + "line": 469, "column": 4 }, "end": { - "line": 453, + "line": 469, "column": 26 } }, "argument": { "type": "Identifier", - "start": 17982, - "end": 17996, + "start": 18422, + "end": 18436, "loc": { "start": { - "line": 453, + "line": 469, "column": 11 }, "end": { - "line": 453, + "line": 469, "column": 25 }, "identifierName": "componentClass" @@ -65299,15 +66859,15 @@ { "type": "CommentLine", "value": " The first time we create a componentClass, we include it into the logical", - "start": 17797, - "end": 17873, + "start": 18237, + "end": 18313, "loc": { "start": { - "line": 450, + "line": 466, "column": 4 }, "end": { - "line": 450, + "line": 466, "column": 80 } } @@ -65315,15 +66875,15 @@ { "type": "CommentLine", "value": " expression directly. On subsequent calls, we'll only return the `@id`", - "start": 17878, - "end": 17950, + "start": 18318, + "end": 18390, "loc": { "start": { - "line": 451, + "line": 467, "column": 4 }, "end": { - "line": 451, + "line": 467, "column": 76 } } @@ -65331,15 +66891,15 @@ { "type": "CommentLine", "value": " (see above).", - "start": 17955, - "end": 17970, + "start": 18395, + "end": 18410, "loc": { "start": { - "line": 452, + "line": 468, "column": 4 }, "end": { - "line": 452, + "line": 468, "column": 19 } } @@ -65353,15 +66913,15 @@ { "type": "CommentBlock", "value": "*\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n ", - "start": 13423, - "end": 14548, + "start": 13863, + "end": 14988, "loc": { "start": { - "line": 357, + "line": 373, "column": 2 }, "end": { - "line": 373, + "line": 389, "column": 5 } } @@ -65370,15 +66930,15 @@ }, { "type": "ClassMethod", - "start": 18005, - "end": 18229, + "start": 18445, + "end": 18669, "loc": { "start": { - "line": 456, + "line": 472, "column": 2 }, "end": { - "line": 462, + "line": 478, "column": 3 } }, @@ -65386,15 +66946,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18005, - "end": 18032, + "start": 18445, + "end": 18472, "loc": { "start": { - "line": 456, + "line": 472, "column": 2 }, "end": { - "line": 456, + "line": 472, "column": 29 }, "identifierName": "getIncludesRestrictionForTU" @@ -65409,15 +66969,15 @@ "params": [ { "type": "Identifier", - "start": 18033, - "end": 18035, + "start": 18473, + "end": 18475, "loc": { "start": { - "line": 456, + "line": 472, "column": 30 }, "end": { - "line": 456, + "line": 472, "column": 32 }, "identifierName": "tu" @@ -65427,59 +66987,59 @@ ], "body": { "type": "BlockStatement", - "start": 18037, - "end": 18229, + "start": 18477, + "end": 18669, "loc": { "start": { - "line": 456, + "line": 472, "column": 34 }, "end": { - "line": 462, + "line": 478, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 18043, - "end": 18225, + "start": 18483, + "end": 18665, "loc": { "start": { - "line": 457, + "line": 473, "column": 4 }, "end": { - "line": 461, + "line": 477, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 18050, - "end": 18224, + "start": 18490, + "end": 18664, "loc": { "start": { - "line": 457, + "line": 473, "column": 11 }, "end": { - "line": 461, + "line": 477, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 18058, - "end": 18084, + "start": 18498, + "end": 18524, "loc": { "start": { - "line": 458, + "line": 474, "column": 6 }, "end": { - "line": 458, + "line": 474, "column": 32 } }, @@ -65488,15 +67048,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18058, - "end": 18065, + "start": 18498, + "end": 18505, "loc": { "start": { - "line": 458, + "line": 474, "column": 6 }, "end": { - "line": 458, + "line": 474, "column": 13 } }, @@ -65508,15 +67068,15 @@ }, "value": { "type": "StringLiteral", - "start": 18067, - "end": 18084, + "start": 18507, + "end": 18524, "loc": { "start": { - "line": 458, + "line": 474, "column": 15 }, "end": { - "line": 458, + "line": 474, "column": 32 } }, @@ -65529,15 +67089,15 @@ }, { "type": "ObjectProperty", - "start": 18092, - "end": 18126, + "start": 18532, + "end": 18566, "loc": { "start": { - "line": 459, + "line": 475, "column": 6 }, "end": { - "line": 459, + "line": 475, "column": 40 } }, @@ -65546,15 +67106,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18092, - "end": 18102, + "start": 18532, + "end": 18542, "loc": { "start": { - "line": 459, + "line": 475, "column": 6 }, "end": { - "line": 459, + "line": 475, "column": 16 }, "identifierName": "onProperty" @@ -65563,15 +67123,15 @@ }, "value": { "type": "StringLiteral", - "start": 18104, - "end": 18126, + "start": 18544, + "end": 18566, "loc": { "start": { - "line": 459, + "line": 475, "column": 18 }, "end": { - "line": 459, + "line": 475, "column": 40 } }, @@ -65584,15 +67144,15 @@ }, { "type": "ObjectProperty", - "start": 18134, - "end": 18217, + "start": 18574, + "end": 18657, "loc": { "start": { - "line": 460, + "line": 476, "column": 6 }, "end": { - "line": 460, + "line": 476, "column": 89 } }, @@ -65601,15 +67161,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18134, - "end": 18148, + "start": 18574, + "end": 18588, "loc": { "start": { - "line": 460, + "line": 476, "column": 6 }, "end": { - "line": 460, + "line": 476, "column": 20 }, "identifierName": "someValuesFrom" @@ -65618,43 +67178,43 @@ }, "value": { "type": "MemberExpression", - "start": 18150, - "end": 18217, + "start": 18590, + "end": 18657, "loc": { "start": { - "line": 460, + "line": 476, "column": 22 }, "end": { - "line": 460, + "line": 476, "column": 89 } }, "object": { "type": "NewExpression", - "start": 18150, - "end": 18201, + "start": 18590, + "end": 18641, "loc": { "start": { - "line": 460, + "line": 476, "column": 22 }, "end": { - "line": 460, + "line": 476, "column": 73 } }, "callee": { "type": "Identifier", - "start": 18154, - "end": 18174, + "start": 18594, + "end": 18614, "loc": { "start": { - "line": 460, + "line": 476, "column": 26 }, "end": { - "line": 460, + "line": 476, "column": 46 }, "identifierName": "TaxonomicUnitWrapper" @@ -65664,15 +67224,15 @@ "arguments": [ { "type": "Identifier", - "start": 18175, - "end": 18177, + "start": 18615, + "end": 18617, "loc": { "start": { - "line": 460, + "line": 476, "column": 47 }, "end": { - "line": 460, + "line": 476, "column": 49 }, "identifierName": "tu" @@ -65681,44 +67241,44 @@ }, { "type": "MemberExpression", - "start": 18179, - "end": 18200, + "start": 18619, + "end": 18640, "loc": { "start": { - "line": 460, + "line": 476, "column": 51 }, "end": { - "line": 460, + "line": 476, "column": 72 } }, "object": { "type": "ThisExpression", - "start": 18179, - "end": 18183, + "start": 18619, + "end": 18623, "loc": { "start": { - "line": 460, + "line": 476, "column": 51 }, "end": { - "line": 460, + "line": 476, "column": 55 } } }, "property": { "type": "Identifier", - "start": 18184, - "end": 18200, + "start": 18624, + "end": 18640, "loc": { "start": { - "line": 460, + "line": 476, "column": 56 }, "end": { - "line": 460, + "line": 476, "column": 72 }, "identifierName": "defaultNomenCode" @@ -65731,15 +67291,15 @@ }, "property": { "type": "Identifier", - "start": 18202, - "end": 18217, + "start": 18642, + "end": 18657, "loc": { "start": { - "line": 460, + "line": 476, "column": 74 }, "end": { - "line": 460, + "line": 476, "column": 89 }, "identifierName": "asOWLEquivClass" @@ -65760,15 +67320,15 @@ { "type": "CommentBlock", "value": "*\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n ", - "start": 18233, - "end": 18345, + "start": 18673, + "end": 18785, "loc": { "start": { - "line": 464, + "line": 480, "column": 2 }, "end": { - "line": 467, + "line": 483, "column": 5 } } @@ -65777,15 +67337,15 @@ }, { "type": "ClassMethod", - "start": 18348, - "end": 18860, + "start": 18788, + "end": 19300, "loc": { "start": { - "line": 468, + "line": 484, "column": 2 }, "end": { - "line": 484, + "line": 500, "column": 3 } }, @@ -65793,15 +67353,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18348, - "end": 18374, + "start": 18788, + "end": 18814, "loc": { "start": { - "line": 468, + "line": 484, "column": 2 }, "end": { - "line": 468, + "line": 484, "column": 28 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -65817,15 +67377,15 @@ "params": [ { "type": "Identifier", - "start": 18375, - "end": 18378, + "start": 18815, + "end": 18818, "loc": { "start": { - "line": 468, + "line": 484, "column": 29 }, "end": { - "line": 468, + "line": 484, "column": 32 }, "identifierName": "tu1" @@ -65834,15 +67394,15 @@ }, { "type": "Identifier", - "start": 18380, - "end": 18383, + "start": 18820, + "end": 18823, "loc": { "start": { - "line": 468, + "line": 484, "column": 34 }, "end": { - "line": 468, + "line": 484, "column": 37 }, "identifierName": "tu2" @@ -65852,59 +67412,59 @@ ], "body": { "type": "BlockStatement", - "start": 18385, - "end": 18860, + "start": 18825, + "end": 19300, "loc": { "start": { - "line": 468, + "line": 484, "column": 39 }, "end": { - "line": 484, + "line": 500, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 18391, - "end": 18856, + "start": 18831, + "end": 19296, "loc": { "start": { - "line": 469, + "line": 485, "column": 4 }, "end": { - "line": 483, + "line": 499, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 18398, - "end": 18855, + "start": 18838, + "end": 19295, "loc": { "start": { - "line": 469, + "line": 485, "column": 11 }, "end": { - "line": 483, + "line": 499, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 18406, - "end": 18432, + "start": 18846, + "end": 18872, "loc": { "start": { - "line": 470, + "line": 486, "column": 6 }, "end": { - "line": 470, + "line": 486, "column": 32 } }, @@ -65913,15 +67473,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18406, - "end": 18413, + "start": 18846, + "end": 18853, "loc": { "start": { - "line": 470, + "line": 486, "column": 6 }, "end": { - "line": 470, + "line": 486, "column": 13 } }, @@ -65933,15 +67493,15 @@ }, "value": { "type": "StringLiteral", - "start": 18415, - "end": 18432, + "start": 18855, + "end": 18872, "loc": { "start": { - "line": 470, + "line": 486, "column": 15 }, "end": { - "line": 470, + "line": 486, "column": 32 } }, @@ -65954,15 +67514,15 @@ }, { "type": "ObjectProperty", - "start": 18440, - "end": 18470, + "start": 18880, + "end": 18910, "loc": { "start": { - "line": 471, + "line": 487, "column": 6 }, "end": { - "line": 471, + "line": 487, "column": 36 } }, @@ -65971,15 +67531,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18440, - "end": 18450, + "start": 18880, + "end": 18890, "loc": { "start": { - "line": 471, + "line": 487, "column": 6 }, "end": { - "line": 471, + "line": 487, "column": 16 }, "identifierName": "onProperty" @@ -65988,15 +67548,15 @@ }, "value": { "type": "StringLiteral", - "start": 18452, - "end": 18470, + "start": 18892, + "end": 18910, "loc": { "start": { - "line": 471, + "line": 487, "column": 18 }, "end": { - "line": 471, + "line": 487, "column": 36 } }, @@ -66009,15 +67569,15 @@ }, { "type": "ObjectProperty", - "start": 18496, - "end": 18848, + "start": 18936, + "end": 19288, "loc": { "start": { - "line": 472, + "line": 488, "column": 6 }, "end": { - "line": 482, + "line": 498, "column": 7 } }, @@ -66026,15 +67586,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18496, - "end": 18510, + "start": 18936, + "end": 18950, "loc": { "start": { - "line": 472, + "line": 488, "column": 6 }, "end": { - "line": 472, + "line": 488, "column": 20 }, "identifierName": "someValuesFrom" @@ -66044,30 +67604,30 @@ }, "value": { "type": "ObjectExpression", - "start": 18512, - "end": 18848, + "start": 18952, + "end": 19288, "loc": { "start": { - "line": 472, + "line": 488, "column": 22 }, "end": { - "line": 482, + "line": 498, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 18522, - "end": 18542, + "start": 18962, + "end": 18982, "loc": { "start": { - "line": 473, + "line": 489, "column": 8 }, "end": { - "line": 473, + "line": 489, "column": 28 } }, @@ -66076,15 +67636,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18522, - "end": 18529, + "start": 18962, + "end": 18969, "loc": { "start": { - "line": 473, + "line": 489, "column": 8 }, "end": { - "line": 473, + "line": 489, "column": 15 } }, @@ -66096,15 +67656,15 @@ }, "value": { "type": "StringLiteral", - "start": 18531, - "end": 18542, + "start": 18971, + "end": 18982, "loc": { "start": { - "line": 473, + "line": 489, "column": 17 }, "end": { - "line": 473, + "line": 489, "column": 28 } }, @@ -66117,15 +67677,15 @@ }, { "type": "ObjectProperty", - "start": 18552, - "end": 18839, + "start": 18992, + "end": 19279, "loc": { "start": { - "line": 474, + "line": 490, "column": 8 }, "end": { - "line": 481, + "line": 497, "column": 9 } }, @@ -66134,15 +67694,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18552, - "end": 18566, + "start": 18992, + "end": 19006, "loc": { "start": { - "line": 474, + "line": 490, "column": 8 }, "end": { - "line": 474, + "line": 490, "column": 22 }, "identifierName": "intersectionOf" @@ -66151,45 +67711,45 @@ }, "value": { "type": "ArrayExpression", - "start": 18568, - "end": 18839, + "start": 19008, + "end": 19279, "loc": { "start": { - "line": 474, + "line": 490, "column": 24 }, "end": { - "line": 481, + "line": 497, "column": 9 } }, "elements": [ { "type": "ObjectExpression", - "start": 18580, - "end": 18779, + "start": 19020, + "end": 19219, "loc": { "start": { - "line": 475, + "line": 491, "column": 10 }, "end": { - "line": 479, + "line": 495, "column": 11 } }, "properties": [ { "type": "ObjectProperty", - "start": 18594, - "end": 18620, + "start": 19034, + "end": 19060, "loc": { "start": { - "line": 476, + "line": 492, "column": 12 }, "end": { - "line": 476, + "line": 492, "column": 38 } }, @@ -66198,15 +67758,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 18594, - "end": 18601, + "start": 19034, + "end": 19041, "loc": { "start": { - "line": 476, + "line": 492, "column": 12 }, "end": { - "line": 476, + "line": 492, "column": 19 } }, @@ -66218,15 +67778,15 @@ }, "value": { "type": "StringLiteral", - "start": 18603, - "end": 18620, + "start": 19043, + "end": 19060, "loc": { "start": { - "line": 476, + "line": 492, "column": 21 }, "end": { - "line": 476, + "line": 492, "column": 38 } }, @@ -66239,15 +67799,15 @@ }, { "type": "ObjectProperty", - "start": 18634, - "end": 18668, + "start": 19074, + "end": 19108, "loc": { "start": { - "line": 477, + "line": 493, "column": 12 }, "end": { - "line": 477, + "line": 493, "column": 46 } }, @@ -66256,15 +67816,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18634, - "end": 18644, + "start": 19074, + "end": 19084, "loc": { "start": { - "line": 477, + "line": 493, "column": 12 }, "end": { - "line": 477, + "line": 493, "column": 22 }, "identifierName": "onProperty" @@ -66273,15 +67833,15 @@ }, "value": { "type": "StringLiteral", - "start": 18646, - "end": 18668, + "start": 19086, + "end": 19108, "loc": { "start": { - "line": 477, + "line": 493, "column": 24 }, "end": { - "line": 477, + "line": 493, "column": 46 } }, @@ -66294,15 +67854,15 @@ }, { "type": "ObjectProperty", - "start": 18682, - "end": 18766, + "start": 19122, + "end": 19206, "loc": { "start": { - "line": 478, + "line": 494, "column": 12 }, "end": { - "line": 478, + "line": 494, "column": 96 } }, @@ -66311,15 +67871,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 18682, - "end": 18696, + "start": 19122, + "end": 19136, "loc": { "start": { - "line": 478, + "line": 494, "column": 12 }, "end": { - "line": 478, + "line": 494, "column": 26 }, "identifierName": "someValuesFrom" @@ -66328,43 +67888,43 @@ }, "value": { "type": "MemberExpression", - "start": 18698, - "end": 18766, + "start": 19138, + "end": 19206, "loc": { "start": { - "line": 478, + "line": 494, "column": 28 }, "end": { - "line": 478, + "line": 494, "column": 96 } }, "object": { "type": "NewExpression", - "start": 18698, - "end": 18750, + "start": 19138, + "end": 19190, "loc": { "start": { - "line": 478, + "line": 494, "column": 28 }, "end": { - "line": 478, + "line": 494, "column": 80 } }, "callee": { "type": "Identifier", - "start": 18702, - "end": 18722, + "start": 19142, + "end": 19162, "loc": { "start": { - "line": 478, + "line": 494, "column": 32 }, "end": { - "line": 478, + "line": 494, "column": 52 }, "identifierName": "TaxonomicUnitWrapper" @@ -66374,15 +67934,15 @@ "arguments": [ { "type": "Identifier", - "start": 18723, - "end": 18726, + "start": 19163, + "end": 19166, "loc": { "start": { - "line": 478, + "line": 494, "column": 53 }, "end": { - "line": 478, + "line": 494, "column": 56 }, "identifierName": "tu1" @@ -66391,44 +67951,44 @@ }, { "type": "MemberExpression", - "start": 18728, - "end": 18749, + "start": 19168, + "end": 19189, "loc": { "start": { - "line": 478, + "line": 494, "column": 58 }, "end": { - "line": 478, + "line": 494, "column": 79 } }, "object": { "type": "ThisExpression", - "start": 18728, - "end": 18732, + "start": 19168, + "end": 19172, "loc": { "start": { - "line": 478, + "line": 494, "column": 58 }, "end": { - "line": 478, + "line": 494, "column": 62 } } }, "property": { "type": "Identifier", - "start": 18733, - "end": 18749, + "start": 19173, + "end": 19189, "loc": { "start": { - "line": 478, + "line": 494, "column": 63 }, "end": { - "line": 478, + "line": 494, "column": 79 }, "identifierName": "defaultNomenCode" @@ -66441,15 +68001,15 @@ }, "property": { "type": "Identifier", - "start": 18751, - "end": 18766, + "start": 19191, + "end": 19206, "loc": { "start": { - "line": 478, + "line": 494, "column": 81 }, "end": { - "line": 478, + "line": 494, "column": 96 }, "identifierName": "asOWLEquivClass" @@ -66463,58 +68023,58 @@ }, { "type": "CallExpression", - "start": 18791, - "end": 18828, + "start": 19231, + "end": 19268, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 18791, - "end": 18823, + "start": 19231, + "end": 19263, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 42 } }, "object": { "type": "ThisExpression", - "start": 18791, - "end": 18795, + "start": 19231, + "end": 19235, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 14 } } }, "property": { "type": "Identifier", - "start": 18796, - "end": 18823, + "start": 19236, + "end": 19263, "loc": { "start": { - "line": 480, + "line": 496, "column": 15 }, "end": { - "line": 480, + "line": 496, "column": 42 }, "identifierName": "getIncludesRestrictionForTU" @@ -66526,15 +68086,15 @@ "arguments": [ { "type": "Identifier", - "start": 18824, - "end": 18827, + "start": 19264, + "end": 19267, "loc": { "start": { - "line": 480, + "line": 496, "column": 43 }, "end": { - "line": 480, + "line": 496, "column": 46 }, "identifierName": "tu2" @@ -66552,15 +68112,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 18472, - "end": 18489, + "start": 18912, + "end": 18929, "loc": { "start": { - "line": 471, + "line": 487, "column": 38 }, "end": { - "line": 471, + "line": 487, "column": 55 } } @@ -66578,15 +68138,15 @@ { "type": "CommentBlock", "value": "*\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n ", - "start": 18233, - "end": 18345, + "start": 18673, + "end": 18785, "loc": { "start": { - "line": 464, + "line": 480, "column": 2 }, "end": { - "line": 467, + "line": 483, "column": 5 } } @@ -66596,15 +68156,15 @@ { "type": "CommentBlock", "value": "\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n ", - "start": 18864, - "end": 20362, + "start": 19304, + "end": 20802, "loc": { "start": { - "line": 486, + "line": 502, "column": 2 }, "end": { - "line": 511, + "line": 527, "column": 5 } } @@ -66613,15 +68173,15 @@ }, { "type": "ClassMethod", - "start": 20365, - "end": 23762, + "start": 20805, + "end": 24202, "loc": { "start": { - "line": 512, + "line": 528, "column": 2 }, "end": { - "line": 596, + "line": 612, "column": 3 } }, @@ -66629,15 +68189,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 20365, - "end": 20399, + "start": 20805, + "end": 20839, "loc": { "start": { - "line": 512, + "line": 528, "column": 2 }, "end": { - "line": 512, + "line": 528, "column": 36 }, "identifierName": "createClassExpressionsForInternals" @@ -66653,15 +68213,15 @@ "params": [ { "type": "Identifier", - "start": 20400, - "end": 20406, + "start": 20840, + "end": 20846, "loc": { "start": { - "line": 512, + "line": 528, "column": 37 }, "end": { - "line": 512, + "line": 528, "column": 43 }, "identifierName": "jsonld" @@ -66670,15 +68230,15 @@ }, { "type": "Identifier", - "start": 20408, - "end": 20426, + "start": 20848, + "end": 20866, "loc": { "start": { - "line": 512, + "line": 528, "column": 45 }, "end": { - "line": 512, + "line": 528, "column": 63 }, "identifierName": "remainingInternals" @@ -66687,15 +68247,15 @@ }, { "type": "Identifier", - "start": 20428, - "end": 20436, + "start": 20868, + "end": 20876, "loc": { "start": { - "line": 512, + "line": 528, "column": 65 }, "end": { - "line": 512, + "line": 528, "column": 73 }, "identifierName": "selected" @@ -66705,72 +68265,72 @@ ], "body": { "type": "BlockStatement", - "start": 20438, - "end": 23762, + "start": 20878, + "end": 24202, "loc": { "start": { - "line": 512, + "line": 528, "column": 75 }, "end": { - "line": 596, + "line": 612, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 20736, - "end": 21206, + "start": 21176, + "end": 21646, "loc": { "start": { - "line": 518, + "line": 534, "column": 4 }, "end": { - "line": 528, + "line": 544, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 20740, - "end": 20761, + "start": 21180, + "end": 21201, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 29 } }, "left": { "type": "MemberExpression", - "start": 20740, - "end": 20755, + "start": 21180, + "end": 21195, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 23 } }, "object": { "type": "Identifier", - "start": 20740, - "end": 20748, + "start": 21180, + "end": 21188, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 16 }, "identifierName": "selected" @@ -66780,15 +68340,15 @@ }, "property": { "type": "Identifier", - "start": 20749, - "end": 20755, + "start": 21189, + "end": 21195, "loc": { "start": { - "line": 518, + "line": 534, "column": 17 }, "end": { - "line": 518, + "line": 534, "column": 23 }, "identifierName": "length" @@ -66801,15 +68361,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 20760, - "end": 20761, + "start": 21200, + "end": 21201, "loc": { "start": { - "line": 518, + "line": 534, "column": 28 }, "end": { - "line": 518, + "line": 534, "column": 29 } }, @@ -66823,72 +68383,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 20763, - "end": 21206, + "start": 21203, + "end": 21646, "loc": { "start": { - "line": 518, + "line": 534, "column": 31 }, "end": { - "line": 528, + "line": 544, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 20771, - "end": 20934, + "start": 21211, + "end": 21374, "loc": { "start": { - "line": 519, + "line": 535, "column": 6 }, "end": { - "line": 523, + "line": 539, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 20775, - "end": 20806, + "start": 21215, + "end": 21246, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 41 } }, "left": { "type": "MemberExpression", - "start": 20775, - "end": 20800, + "start": 21215, + "end": 21240, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 35 } }, "object": { "type": "Identifier", - "start": 20775, - "end": 20793, + "start": 21215, + "end": 21233, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 28 }, "identifierName": "remainingInternals" @@ -66897,15 +68457,15 @@ }, "property": { "type": "Identifier", - "start": 20794, - "end": 20800, + "start": 21234, + "end": 21240, "loc": { "start": { - "line": 519, + "line": 535, "column": 29 }, "end": { - "line": 519, + "line": 535, "column": 35 }, "identifierName": "length" @@ -66917,15 +68477,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 20805, - "end": 20806, + "start": 21245, + "end": 21246, "loc": { "start": { - "line": 519, + "line": 535, "column": 40 }, "end": { - "line": 519, + "line": 535, "column": 41 } }, @@ -66938,102 +68498,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 20808, - "end": 20934, + "start": 21248, + "end": 21374, "loc": { "start": { - "line": 519, + "line": 535, "column": 43 }, "end": { - "line": 523, + "line": 539, "column": 7 } }, "body": [ { "type": "ReturnStatement", - "start": 20818, - "end": 20926, + "start": 21258, + "end": 21366, "loc": { "start": { - "line": 520, + "line": 536, "column": 8 }, "end": { - "line": 522, + "line": 538, "column": 10 } }, "argument": { "type": "ArrayExpression", - "start": 20825, - "end": 20925, + "start": 21265, + "end": 21365, "loc": { "start": { - "line": 520, + "line": 536, "column": 15 }, "end": { - "line": 522, + "line": 538, "column": 9 } }, "elements": [ { "type": "CallExpression", - "start": 20837, - "end": 20914, + "start": 21277, + "end": 21354, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 87 } }, "callee": { "type": "MemberExpression", - "start": 20837, - "end": 20868, + "start": 21277, + "end": 21308, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 41 } }, "object": { "type": "ThisExpression", - "start": 20837, - "end": 20841, + "start": 21277, + "end": 21281, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 14 } } }, "property": { "type": "Identifier", - "start": 20842, - "end": 20868, + "start": 21282, + "end": 21308, "loc": { "start": { - "line": 521, + "line": 537, "column": 15 }, "end": { - "line": 521, + "line": 537, "column": 41 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -67045,29 +68605,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 20869, - "end": 20890, + "start": 21309, + "end": 21330, "loc": { "start": { - "line": 521, + "line": 537, "column": 42 }, "end": { - "line": 521, + "line": 537, "column": 63 } }, "object": { "type": "Identifier", - "start": 20869, - "end": 20887, + "start": 21309, + "end": 21327, "loc": { "start": { - "line": 521, + "line": 537, "column": 42 }, "end": { - "line": 521, + "line": 537, "column": 60 }, "identifierName": "remainingInternals" @@ -67076,15 +68636,15 @@ }, "property": { "type": "NumericLiteral", - "start": 20888, - "end": 20889, + "start": 21328, + "end": 21329, "loc": { "start": { - "line": 521, + "line": 537, "column": 61 }, "end": { - "line": 521, + "line": 537, "column": 62 } }, @@ -67098,29 +68658,29 @@ }, { "type": "MemberExpression", - "start": 20892, - "end": 20913, + "start": 21332, + "end": 21353, "loc": { "start": { - "line": 521, + "line": 537, "column": 65 }, "end": { - "line": 521, + "line": 537, "column": 86 } }, "object": { "type": "Identifier", - "start": 20892, - "end": 20910, + "start": 21332, + "end": 21350, "loc": { "start": { - "line": 521, + "line": 537, "column": 65 }, "end": { - "line": 521, + "line": 537, "column": 83 }, "identifierName": "remainingInternals" @@ -67129,15 +68689,15 @@ }, "property": { "type": "NumericLiteral", - "start": 20911, - "end": 20912, + "start": 21351, + "end": 21352, "loc": { "start": { - "line": 521, + "line": 537, "column": 84 }, "end": { - "line": 521, + "line": 537, "column": 85 } }, @@ -67161,57 +68721,57 @@ }, { "type": "IfStatement", - "start": 20935, - "end": 21200, + "start": 21375, + "end": 21640, "loc": { "start": { - "line": 523, + "line": 539, "column": 8 }, "end": { - "line": 527, + "line": 543, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 20939, - "end": 20970, + "start": 21379, + "end": 21410, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 43 } }, "left": { "type": "MemberExpression", - "start": 20939, - "end": 20964, + "start": 21379, + "end": 21404, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 37 } }, "object": { "type": "Identifier", - "start": 20939, - "end": 20957, + "start": 21379, + "end": 21397, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 30 }, "identifierName": "remainingInternals" @@ -67220,15 +68780,15 @@ }, "property": { "type": "Identifier", - "start": 20958, - "end": 20964, + "start": 21398, + "end": 21404, "loc": { "start": { - "line": 523, + "line": 539, "column": 31 }, "end": { - "line": 523, + "line": 539, "column": 37 }, "identifierName": "length" @@ -67240,15 +68800,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 20969, - "end": 20970, + "start": 21409, + "end": 21410, "loc": { "start": { - "line": 523, + "line": 539, "column": 42 }, "end": { - "line": 523, + "line": 539, "column": 43 } }, @@ -67261,58 +68821,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 20972, - "end": 21066, + "start": 21412, + "end": 21506, "loc": { "start": { - "line": 523, + "line": 539, "column": 45 }, "end": { - "line": 525, + "line": 541, "column": 7 } }, "body": [ { "type": "ThrowStatement", - "start": 20982, - "end": 21058, + "start": 21422, + "end": 21498, "loc": { "start": { - "line": 524, + "line": 540, "column": 8 }, "end": { - "line": 524, + "line": 540, "column": 84 } }, "argument": { "type": "NewExpression", - "start": 20988, - "end": 21057, + "start": 21428, + "end": 21497, "loc": { "start": { - "line": 524, + "line": 540, "column": 14 }, "end": { - "line": 524, + "line": 540, "column": 83 } }, "callee": { "type": "Identifier", - "start": 20992, - "end": 20997, + "start": 21432, + "end": 21437, "loc": { "start": { - "line": 524, + "line": 540, "column": 18 }, "end": { - "line": 524, + "line": 540, "column": 23 }, "identifierName": "Error" @@ -67322,15 +68882,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 20998, - "end": 21056, + "start": 21438, + "end": 21496, "loc": { "start": { - "line": 524, + "line": 540, "column": 24 }, "end": { - "line": 524, + "line": 540, "column": 82 } }, @@ -67348,57 +68908,57 @@ }, "alternate": { "type": "IfStatement", - "start": 21072, - "end": 21200, + "start": 21512, + "end": 21640, "loc": { "start": { - "line": 525, + "line": 541, "column": 13 }, "end": { - "line": 527, + "line": 543, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21076, - "end": 21107, + "start": 21516, + "end": 21547, "loc": { "start": { - "line": 525, + "line": 541, "column": 17 }, "end": { - "line": 525, + "line": 541, "column": 48 } }, "left": { "type": "MemberExpression", - "start": 21076, - "end": 21101, + "start": 21516, + "end": 21541, "loc": { "start": { - "line": 525, + "line": 541, "column": 17 }, "end": { - "line": 525, + "line": 541, "column": 42 } }, "object": { "type": "Identifier", - "start": 21076, - "end": 21094, + "start": 21516, + "end": 21534, "loc": { "start": { - "line": 525, + "line": 541, "column": 17 }, "end": { - "line": 525, + "line": 541, "column": 35 }, "identifierName": "remainingInternals" @@ -67407,15 +68967,15 @@ }, "property": { "type": "Identifier", - "start": 21095, - "end": 21101, + "start": 21535, + "end": 21541, "loc": { "start": { - "line": 525, + "line": 541, "column": 36 }, "end": { - "line": 525, + "line": 541, "column": 42 }, "identifierName": "length" @@ -67427,15 +68987,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 21106, - "end": 21107, + "start": 21546, + "end": 21547, "loc": { "start": { - "line": 525, + "line": 541, "column": 47 }, "end": { - "line": 525, + "line": 541, "column": 48 } }, @@ -67448,58 +69008,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 21109, - "end": 21200, + "start": 21549, + "end": 21640, "loc": { "start": { - "line": 525, + "line": 541, "column": 50 }, "end": { - "line": 527, + "line": 543, "column": 7 } }, "body": [ { "type": "ThrowStatement", - "start": 21119, - "end": 21192, + "start": 21559, + "end": 21632, "loc": { "start": { - "line": 526, + "line": 542, "column": 8 }, "end": { - "line": 526, + "line": 542, "column": 81 } }, "argument": { "type": "NewExpression", - "start": 21125, - "end": 21191, + "start": 21565, + "end": 21631, "loc": { "start": { - "line": 526, + "line": 542, "column": 14 }, "end": { - "line": 526, + "line": 542, "column": 80 } }, "callee": { "type": "Identifier", - "start": 21129, - "end": 21134, + "start": 21569, + "end": 21574, "loc": { "start": { - "line": 526, + "line": 542, "column": 18 }, "end": { - "line": 526, + "line": 542, "column": 23 }, "identifierName": "Error" @@ -67509,15 +69069,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 21135, - "end": 21190, + "start": 21575, + "end": 21630, "loc": { "start": { - "line": 526, + "line": 542, "column": 24 }, "end": { - "line": 526, + "line": 542, "column": 79 } }, @@ -67545,15 +69105,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:", - "start": 20444, - "end": 20512, + "start": 20884, + "end": 20952, "loc": { "start": { - "line": 513, + "line": 529, "column": 4 }, "end": { - "line": 513, + "line": 529, "column": 72 } } @@ -67561,15 +69121,15 @@ { "type": "CommentLine", "value": " ${remainingInternals.length}, selected: ${selected.length}\\n`);", - "start": 20517, - "end": 20583, + "start": 20957, + "end": 21023, "loc": { "start": { - "line": 514, + "line": 530, "column": 4 }, "end": { - "line": 514, + "line": 530, "column": 70 } } @@ -67577,15 +69137,15 @@ { "type": "CommentLine", "value": " Quick special case: if we have two 'remainingInternals' and zero selecteds,", - "start": 20589, - "end": 20667, + "start": 21029, + "end": 21107, "loc": { "start": { - "line": 516, + "line": 532, "column": 4 }, "end": { - "line": 516, + "line": 532, "column": 82 } } @@ -67593,15 +69153,15 @@ { "type": "CommentLine", "value": " we can just return the MRCA for two internal specifiers.", - "start": 20672, - "end": 20731, + "start": 21112, + "end": 21171, "loc": { "start": { - "line": 517, + "line": 533, "column": 4 }, "end": { - "line": 517, + "line": 533, "column": 63 } } @@ -67611,15 +69171,15 @@ { "type": "CommentLine", "value": " Step 1. If we've already selected something, create an expression for it.", - "start": 21212, - "end": 21288, + "start": 21652, + "end": 21728, "loc": { "start": { - "line": 530, + "line": 546, "column": 4 }, "end": { - "line": 530, + "line": 546, "column": 80 } } @@ -67628,44 +69188,44 @@ }, { "type": "VariableDeclaration", - "start": 21293, - "end": 21315, + "start": 21733, + "end": 21755, "loc": { "start": { - "line": 531, + "line": 547, "column": 4 }, "end": { - "line": 531, + "line": 547, "column": 26 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 21299, - "end": 21314, + "start": 21739, + "end": 21754, "loc": { "start": { - "line": 531, + "line": 547, "column": 10 }, "end": { - "line": 531, + "line": 547, "column": 25 } }, "id": { "type": "Identifier", - "start": 21299, - "end": 21309, + "start": 21739, + "end": 21749, "loc": { "start": { - "line": 531, + "line": 547, "column": 10 }, "end": { - "line": 531, + "line": 547, "column": 20 }, "identifierName": "classExprs" @@ -67675,15 +69235,15 @@ }, "init": { "type": "ArrayExpression", - "start": 21312, - "end": 21314, + "start": 21752, + "end": 21754, "loc": { "start": { - "line": 531, + "line": 547, "column": 23 }, "end": { - "line": 531, + "line": 547, "column": 25 } }, @@ -67697,15 +69257,15 @@ { "type": "CommentLine", "value": " Step 1. If we've already selected something, create an expression for it.", - "start": 21212, - "end": 21288, + "start": 21652, + "end": 21728, "loc": { "start": { - "line": 530, + "line": 546, "column": 4 }, "end": { - "line": 530, + "line": 546, "column": 80 } } @@ -67714,57 +69274,57 @@ }, { "type": "IfStatement", - "start": 21320, - "end": 22828, + "start": 21760, + "end": 23268, "loc": { "start": { - "line": 532, + "line": 548, "column": 4 }, "end": { - "line": 576, + "line": 592, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 21324, - "end": 21343, + "start": 21764, + "end": 21783, "loc": { "start": { - "line": 532, + "line": 548, "column": 8 }, "end": { - "line": 532, + "line": 548, "column": 27 } }, "left": { "type": "MemberExpression", - "start": 21324, - "end": 21339, + "start": 21764, + "end": 21779, "loc": { "start": { - "line": 532, + "line": 548, "column": 8 }, "end": { - "line": 532, + "line": 548, "column": 23 } }, "object": { "type": "Identifier", - "start": 21324, - "end": 21332, + "start": 21764, + "end": 21772, "loc": { "start": { - "line": 532, + "line": 548, "column": 8 }, "end": { - "line": 532, + "line": 548, "column": 16 }, "identifierName": "selected" @@ -67773,15 +69333,15 @@ }, "property": { "type": "Identifier", - "start": 21333, - "end": 21339, + "start": 21773, + "end": 21779, "loc": { "start": { - "line": 532, + "line": 548, "column": 17 }, "end": { - "line": 532, + "line": 548, "column": 23 }, "identifierName": "length" @@ -67793,15 +69353,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 21342, - "end": 21343, + "start": 21782, + "end": 21783, "loc": { "start": { - "line": 532, + "line": 548, "column": 26 }, "end": { - "line": 532, + "line": 548, "column": 27 } }, @@ -67814,59 +69374,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 21345, - "end": 22828, + "start": 21785, + "end": 23268, "loc": { "start": { - "line": 532, + "line": 548, "column": 29 }, "end": { - "line": 576, + "line": 592, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 21353, - "end": 21385, + "start": 21793, + "end": 21825, "loc": { "start": { - "line": 533, + "line": 549, "column": 6 }, "end": { - "line": 533, + "line": 549, "column": 38 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 21357, - "end": 21384, + "start": 21797, + "end": 21824, "loc": { "start": { - "line": 533, + "line": 549, "column": 10 }, "end": { - "line": 533, + "line": 549, "column": 37 } }, "id": { "type": "Identifier", - "start": 21357, - "end": 21379, + "start": 21797, + "end": 21819, "loc": { "start": { - "line": 533, + "line": 549, "column": 10 }, "end": { - "line": 533, + "line": 549, "column": 32 }, "identifierName": "remainingInternalsExpr" @@ -67875,15 +69435,15 @@ }, "init": { "type": "ArrayExpression", - "start": 21382, - "end": 21384, + "start": 21822, + "end": 21824, "loc": { "start": { - "line": 533, + "line": 549, "column": 35 }, "end": { - "line": 533, + "line": 549, "column": 37 } }, @@ -67895,57 +69455,57 @@ }, { "type": "IfStatement", - "start": 21392, - "end": 21952, + "start": 21832, + "end": 22392, "loc": { "start": { - "line": 534, + "line": 550, "column": 6 }, "end": { - "line": 548, + "line": 564, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21396, - "end": 21427, + "start": 21836, + "end": 21867, "loc": { "start": { - "line": 534, + "line": 550, "column": 10 }, "end": { - "line": 534, + "line": 550, "column": 41 } }, "left": { "type": "MemberExpression", - "start": 21396, - "end": 21421, + "start": 21836, + "end": 21861, "loc": { "start": { - "line": 534, + "line": 550, "column": 10 }, "end": { - "line": 534, + "line": 550, "column": 35 } }, "object": { "type": "Identifier", - "start": 21396, - "end": 21414, + "start": 21836, + "end": 21854, "loc": { "start": { - "line": 534, + "line": 550, "column": 10 }, "end": { - "line": 534, + "line": 550, "column": 28 }, "identifierName": "remainingInternals" @@ -67954,15 +69514,15 @@ }, "property": { "type": "Identifier", - "start": 21415, - "end": 21421, + "start": 21855, + "end": 21861, "loc": { "start": { - "line": 534, + "line": 550, "column": 29 }, "end": { - "line": 534, + "line": 550, "column": 35 }, "identifierName": "length" @@ -67974,15 +69534,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 21426, - "end": 21427, + "start": 21866, + "end": 21867, "loc": { "start": { - "line": 534, + "line": 550, "column": 40 }, "end": { - "line": 534, + "line": 550, "column": 41 } }, @@ -67995,59 +69555,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 21429, - "end": 21528, + "start": 21869, + "end": 21968, "loc": { "start": { - "line": 534, + "line": 550, "column": 43 }, "end": { - "line": 536, + "line": 552, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 21439, - "end": 21520, + "start": 21879, + "end": 21960, "loc": { "start": { - "line": 535, + "line": 551, "column": 8 }, "end": { - "line": 535, + "line": 551, "column": 89 } }, "expression": { "type": "AssignmentExpression", - "start": 21439, - "end": 21519, + "start": 21879, + "end": 21959, "loc": { "start": { - "line": 535, + "line": 551, "column": 8 }, "end": { - "line": 535, + "line": 551, "column": 88 } }, "operator": "=", "left": { "type": "Identifier", - "start": 21439, - "end": 21461, + "start": 21879, + "end": 21901, "loc": { "start": { - "line": 535, + "line": 551, "column": 8 }, "end": { - "line": 535, + "line": 551, "column": 30 }, "identifierName": "remainingInternalsExpr" @@ -68056,58 +69616,58 @@ }, "right": { "type": "CallExpression", - "start": 21464, - "end": 21519, + "start": 21904, + "end": 21959, "loc": { "start": { - "line": 535, + "line": 551, "column": 33 }, "end": { - "line": 535, + "line": 551, "column": 88 } }, "callee": { "type": "MemberExpression", - "start": 21464, - "end": 21496, + "start": 21904, + "end": 21936, "loc": { "start": { - "line": 535, + "line": 551, "column": 33 }, "end": { - "line": 535, + "line": 551, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 21464, - "end": 21468, + "start": 21904, + "end": 21908, "loc": { "start": { - "line": 535, + "line": 551, "column": 33 }, "end": { - "line": 535, + "line": 551, "column": 37 } } }, "property": { "type": "Identifier", - "start": 21469, - "end": 21496, + "start": 21909, + "end": 21936, "loc": { "start": { - "line": 535, + "line": 551, "column": 38 }, "end": { - "line": 535, + "line": 551, "column": 65 }, "identifierName": "getIncludesRestrictionForTU" @@ -68119,29 +69679,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 21497, - "end": 21518, + "start": 21937, + "end": 21958, "loc": { "start": { - "line": 535, + "line": 551, "column": 66 }, "end": { - "line": 535, + "line": 551, "column": 87 } }, "object": { "type": "Identifier", - "start": 21497, - "end": 21515, + "start": 21937, + "end": 21955, "loc": { "start": { - "line": 535, + "line": 551, "column": 66 }, "end": { - "line": 535, + "line": 551, "column": 84 }, "identifierName": "remainingInternals" @@ -68150,15 +69710,15 @@ }, "property": { "type": "NumericLiteral", - "start": 21516, - "end": 21517, + "start": 21956, + "end": 21957, "loc": { "start": { - "line": 535, + "line": 551, "column": 85 }, "end": { - "line": 535, + "line": 551, "column": 86 } }, @@ -68179,57 +69739,57 @@ }, "alternate": { "type": "IfStatement", - "start": 21534, - "end": 21952, + "start": 21974, + "end": 22392, "loc": { "start": { - "line": 536, + "line": 552, "column": 13 }, "end": { - "line": 548, + "line": 564, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21538, - "end": 21569, + "start": 21978, + "end": 22009, "loc": { "start": { - "line": 536, + "line": 552, "column": 17 }, "end": { - "line": 536, + "line": 552, "column": 48 } }, "left": { "type": "MemberExpression", - "start": 21538, - "end": 21563, + "start": 21978, + "end": 22003, "loc": { "start": { - "line": 536, + "line": 552, "column": 17 }, "end": { - "line": 536, + "line": 552, "column": 42 } }, "object": { "type": "Identifier", - "start": 21538, - "end": 21556, + "start": 21978, + "end": 21996, "loc": { "start": { - "line": 536, + "line": 552, "column": 17 }, "end": { - "line": 536, + "line": 552, "column": 35 }, "identifierName": "remainingInternals" @@ -68238,15 +69798,15 @@ }, "property": { "type": "Identifier", - "start": 21557, - "end": 21563, + "start": 21997, + "end": 22003, "loc": { "start": { - "line": 536, + "line": 552, "column": 36 }, "end": { - "line": 536, + "line": 552, "column": 42 }, "identifierName": "length" @@ -68258,15 +69818,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 21568, - "end": 21569, + "start": 22008, + "end": 22009, "loc": { "start": { - "line": 536, + "line": 552, "column": 47 }, "end": { - "line": 536, + "line": 552, "column": 48 } }, @@ -68279,59 +69839,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 21571, - "end": 21722, + "start": 22011, + "end": 22162, "loc": { "start": { - "line": 536, + "line": 552, "column": 50 }, "end": { - "line": 541, + "line": 557, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 21581, - "end": 21714, + "start": 22021, + "end": 22154, "loc": { "start": { - "line": 537, + "line": 553, "column": 8 }, "end": { - "line": 540, + "line": 556, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 21581, - "end": 21713, + "start": 22021, + "end": 22153, "loc": { "start": { - "line": 537, + "line": 553, "column": 8 }, "end": { - "line": 540, + "line": 556, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 21581, - "end": 21603, + "start": 22021, + "end": 22043, "loc": { "start": { - "line": 537, + "line": 553, "column": 8 }, "end": { - "line": 537, + "line": 553, "column": 30 }, "identifierName": "remainingInternalsExpr" @@ -68340,58 +69900,58 @@ }, "right": { "type": "CallExpression", - "start": 21606, - "end": 21713, + "start": 22046, + "end": 22153, "loc": { "start": { - "line": 537, + "line": 553, "column": 33 }, "end": { - "line": 540, + "line": 556, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 21606, - "end": 21637, + "start": 22046, + "end": 22077, "loc": { "start": { - "line": 537, + "line": 553, "column": 33 }, "end": { - "line": 537, + "line": 553, "column": 64 } }, "object": { "type": "ThisExpression", - "start": 21606, - "end": 21610, + "start": 22046, + "end": 22050, "loc": { "start": { - "line": 537, + "line": 553, "column": 33 }, "end": { - "line": 537, + "line": 553, "column": 37 } } }, "property": { "type": "Identifier", - "start": 21611, - "end": 21637, + "start": 22051, + "end": 22077, "loc": { "start": { - "line": 537, + "line": 553, "column": 38 }, "end": { - "line": 537, + "line": 553, "column": 64 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -68403,29 +69963,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 21649, - "end": 21670, + "start": 22089, + "end": 22110, "loc": { "start": { - "line": 538, + "line": 554, "column": 10 }, "end": { - "line": 538, + "line": 554, "column": 31 } }, "object": { "type": "Identifier", - "start": 21649, - "end": 21667, + "start": 22089, + "end": 22107, "loc": { "start": { - "line": 538, + "line": 554, "column": 10 }, "end": { - "line": 538, + "line": 554, "column": 28 }, "identifierName": "remainingInternals" @@ -68434,15 +69994,15 @@ }, "property": { "type": "NumericLiteral", - "start": 21668, - "end": 21669, + "start": 22108, + "end": 22109, "loc": { "start": { - "line": 538, + "line": 554, "column": 29 }, "end": { - "line": 538, + "line": 554, "column": 30 } }, @@ -68456,29 +70016,29 @@ }, { "type": "MemberExpression", - "start": 21682, - "end": 21703, + "start": 22122, + "end": 22143, "loc": { "start": { - "line": 539, + "line": 555, "column": 10 }, "end": { - "line": 539, + "line": 555, "column": 31 } }, "object": { "type": "Identifier", - "start": 21682, - "end": 21700, + "start": 22122, + "end": 22140, "loc": { "start": { - "line": 539, + "line": 555, "column": 10 }, "end": { - "line": 539, + "line": 555, "column": 28 }, "identifierName": "remainingInternals" @@ -68487,15 +70047,15 @@ }, "property": { "type": "NumericLiteral", - "start": 21701, - "end": 21702, + "start": 22141, + "end": 22142, "loc": { "start": { - "line": 539, + "line": 555, "column": 29 }, "end": { - "line": 539, + "line": 555, "column": 30 } }, @@ -68516,59 +70076,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 21728, - "end": 21952, + "start": 22168, + "end": 22392, "loc": { "start": { - "line": 541, + "line": 557, "column": 13 }, "end": { - "line": 548, + "line": 564, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 21738, - "end": 21944, + "start": 22178, + "end": 22384, "loc": { "start": { - "line": 542, + "line": 558, "column": 8 }, "end": { - "line": 547, + "line": 563, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 21738, - "end": 21943, + "start": 22178, + "end": 22383, "loc": { "start": { - "line": 542, + "line": 558, "column": 8 }, "end": { - "line": 547, + "line": 563, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 21738, - "end": 21760, + "start": 22178, + "end": 22200, "loc": { "start": { - "line": 542, + "line": 558, "column": 8 }, "end": { - "line": 542, + "line": 558, "column": 30 }, "identifierName": "remainingInternalsExpr" @@ -68577,58 +70137,58 @@ }, "right": { "type": "CallExpression", - "start": 21763, - "end": 21943, + "start": 22203, + "end": 22383, "loc": { "start": { - "line": 542, + "line": 558, "column": 33 }, "end": { - "line": 547, + "line": 563, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 21763, - "end": 21788, + "start": 22203, + "end": 22228, "loc": { "start": { - "line": 542, + "line": 558, "column": 33 }, "end": { - "line": 542, + "line": 558, "column": 58 } }, "object": { "type": "ThisExpression", - "start": 21763, - "end": 21767, + "start": 22203, + "end": 22207, "loc": { "start": { - "line": 542, + "line": 558, "column": 33 }, "end": { - "line": 542, + "line": 558, "column": 37 } } }, "property": { "type": "Identifier", - "start": 21768, - "end": 21788, + "start": 22208, + "end": 22228, "loc": { "start": { - "line": 542, + "line": 558, "column": 38 }, "end": { - "line": 542, + "line": 558, "column": 58 }, "identifierName": "createComponentClass" @@ -68640,15 +70200,15 @@ "arguments": [ { "type": "Identifier", - "start": 21800, - "end": 21806, + "start": 22240, + "end": 22246, "loc": { "start": { - "line": 543, + "line": 559, "column": 10 }, "end": { - "line": 543, + "line": 559, "column": 16 }, "identifierName": "jsonld" @@ -68657,15 +70217,15 @@ }, { "type": "Identifier", - "start": 21818, - "end": 21836, + "start": 22258, + "end": 22276, "loc": { "start": { - "line": 544, + "line": 560, "column": 10 }, "end": { - "line": 544, + "line": 560, "column": 28 }, "identifierName": "remainingInternals" @@ -68674,15 +70234,15 @@ }, { "type": "ArrayExpression", - "start": 21848, - "end": 21850, + "start": 22288, + "end": 22290, "loc": { "start": { - "line": 545, + "line": 561, "column": 10 }, "end": { - "line": 545, + "line": 561, "column": 12 } }, @@ -68690,58 +70250,58 @@ }, { "type": "CallExpression", - "start": 21862, - "end": 21933, + "start": 22302, + "end": 22373, "loc": { "start": { - "line": 546, + "line": 562, "column": 10 }, "end": { - "line": 546, + "line": 562, "column": 81 } }, "callee": { "type": "MemberExpression", - "start": 21862, - "end": 21901, + "start": 22302, + "end": 22341, "loc": { "start": { - "line": 546, + "line": 562, "column": 10 }, "end": { - "line": 546, + "line": 562, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 21862, - "end": 21866, + "start": 22302, + "end": 22306, "loc": { "start": { - "line": 546, + "line": 562, "column": 10 }, "end": { - "line": 546, + "line": 562, "column": 14 } } }, "property": { "type": "Identifier", - "start": 21867, - "end": 21901, + "start": 22307, + "end": 22341, "loc": { "start": { - "line": 546, + "line": 562, "column": 15 }, "end": { - "line": 546, + "line": 562, "column": 49 }, "identifierName": "createClassExpressionsForInternals" @@ -68753,15 +70313,15 @@ "arguments": [ { "type": "Identifier", - "start": 21902, - "end": 21908, + "start": 22342, + "end": 22348, "loc": { "start": { - "line": 546, + "line": 562, "column": 50 }, "end": { - "line": 546, + "line": 562, "column": 56 }, "identifierName": "jsonld" @@ -68770,15 +70330,15 @@ }, { "type": "Identifier", - "start": 21910, - "end": 21928, + "start": 22350, + "end": 22368, "loc": { "start": { - "line": 546, + "line": 562, "column": 58 }, "end": { - "line": 546, + "line": 562, "column": 76 }, "identifierName": "remainingInternals" @@ -68787,15 +70347,15 @@ }, { "type": "ArrayExpression", - "start": 21930, - "end": 21932, + "start": 22370, + "end": 22372, "loc": { "start": { - "line": 546, + "line": 562, "column": 78 }, "end": { - "line": 546, + "line": 562, "column": 80 } }, @@ -68814,44 +70374,44 @@ }, { "type": "VariableDeclaration", - "start": 21960, - "end": 21982, + "start": 22400, + "end": 22422, "loc": { "start": { - "line": 550, + "line": 566, "column": 6 }, "end": { - "line": 550, + "line": 566, "column": 28 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 21964, - "end": 21981, + "start": 22404, + "end": 22421, "loc": { "start": { - "line": 550, + "line": 566, "column": 10 }, "end": { - "line": 550, + "line": 566, "column": 27 } }, "id": { "type": "Identifier", - "start": 21964, - "end": 21976, + "start": 22404, + "end": 22416, "loc": { "start": { - "line": 550, + "line": 566, "column": 10 }, "end": { - "line": 550, + "line": 566, "column": 22 }, "identifierName": "selectedExpr" @@ -68860,15 +70420,15 @@ }, "init": { "type": "ArrayExpression", - "start": 21979, - "end": 21981, + "start": 22419, + "end": 22421, "loc": { "start": { - "line": 550, + "line": 566, "column": 25 }, "end": { - "line": 550, + "line": 566, "column": 27 } }, @@ -68880,57 +70440,57 @@ }, { "type": "IfStatement", - "start": 21989, - "end": 22419, + "start": 22429, + "end": 22859, "loc": { "start": { - "line": 551, + "line": 567, "column": 6 }, "end": { - "line": 562, + "line": 578, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 21993, - "end": 22014, + "start": 22433, + "end": 22454, "loc": { "start": { - "line": 551, + "line": 567, "column": 10 }, "end": { - "line": 551, + "line": 567, "column": 31 } }, "left": { "type": "MemberExpression", - "start": 21993, - "end": 22008, + "start": 22433, + "end": 22448, "loc": { "start": { - "line": 551, + "line": 567, "column": 10 }, "end": { - "line": 551, + "line": 567, "column": 25 } }, "object": { "type": "Identifier", - "start": 21993, - "end": 22001, + "start": 22433, + "end": 22441, "loc": { "start": { - "line": 551, + "line": 567, "column": 10 }, "end": { - "line": 551, + "line": 567, "column": 18 }, "identifierName": "selected" @@ -68939,15 +70499,15 @@ }, "property": { "type": "Identifier", - "start": 22002, - "end": 22008, + "start": 22442, + "end": 22448, "loc": { "start": { - "line": 551, + "line": 567, "column": 19 }, "end": { - "line": 551, + "line": 567, "column": 25 }, "identifierName": "length" @@ -68959,15 +70519,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 22013, - "end": 22014, + "start": 22453, + "end": 22454, "loc": { "start": { - "line": 551, + "line": 567, "column": 30 }, "end": { - "line": 551, + "line": 567, "column": 31 } }, @@ -68980,59 +70540,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 22016, - "end": 22095, + "start": 22456, + "end": 22535, "loc": { "start": { - "line": 551, + "line": 567, "column": 33 }, "end": { - "line": 553, + "line": 569, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 22026, - "end": 22087, + "start": 22466, + "end": 22527, "loc": { "start": { - "line": 552, + "line": 568, "column": 8 }, "end": { - "line": 552, + "line": 568, "column": 69 } }, "expression": { "type": "AssignmentExpression", - "start": 22026, - "end": 22086, + "start": 22466, + "end": 22526, "loc": { "start": { - "line": 552, + "line": 568, "column": 8 }, "end": { - "line": 552, + "line": 568, "column": 68 } }, "operator": "=", "left": { "type": "Identifier", - "start": 22026, - "end": 22038, + "start": 22466, + "end": 22478, "loc": { "start": { - "line": 552, + "line": 568, "column": 8 }, "end": { - "line": 552, + "line": 568, "column": 20 }, "identifierName": "selectedExpr" @@ -69041,58 +70601,58 @@ }, "right": { "type": "CallExpression", - "start": 22041, - "end": 22086, + "start": 22481, + "end": 22526, "loc": { "start": { - "line": 552, + "line": 568, "column": 23 }, "end": { - "line": 552, + "line": 568, "column": 68 } }, "callee": { "type": "MemberExpression", - "start": 22041, - "end": 22073, + "start": 22481, + "end": 22513, "loc": { "start": { - "line": 552, + "line": 568, "column": 23 }, "end": { - "line": 552, + "line": 568, "column": 55 } }, "object": { "type": "ThisExpression", - "start": 22041, - "end": 22045, + "start": 22481, + "end": 22485, "loc": { "start": { - "line": 552, + "line": 568, "column": 23 }, "end": { - "line": 552, + "line": 568, "column": 27 } } }, "property": { "type": "Identifier", - "start": 22046, - "end": 22073, + "start": 22486, + "end": 22513, "loc": { "start": { - "line": 552, + "line": 568, "column": 28 }, "end": { - "line": 552, + "line": 568, "column": 55 }, "identifierName": "getIncludesRestrictionForTU" @@ -69104,29 +70664,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 22074, - "end": 22085, + "start": 22514, + "end": 22525, "loc": { "start": { - "line": 552, + "line": 568, "column": 56 }, "end": { - "line": 552, + "line": 568, "column": 67 } }, "object": { "type": "Identifier", - "start": 22074, - "end": 22082, + "start": 22514, + "end": 22522, "loc": { "start": { - "line": 552, + "line": 568, "column": 56 }, "end": { - "line": 552, + "line": 568, "column": 64 }, "identifierName": "selected" @@ -69135,15 +70695,15 @@ }, "property": { "type": "NumericLiteral", - "start": 22083, - "end": 22084, + "start": 22523, + "end": 22524, "loc": { "start": { - "line": 552, + "line": 568, "column": 65 }, "end": { - "line": 552, + "line": 568, "column": 66 } }, @@ -69164,57 +70724,57 @@ }, "alternate": { "type": "IfStatement", - "start": 22101, - "end": 22419, + "start": 22541, + "end": 22859, "loc": { "start": { - "line": 553, + "line": 569, "column": 13 }, "end": { - "line": 562, + "line": 578, "column": 7 } }, "test": { "type": "BinaryExpression", - "start": 22105, - "end": 22126, + "start": 22545, + "end": 22566, "loc": { "start": { - "line": 553, + "line": 569, "column": 17 }, "end": { - "line": 553, + "line": 569, "column": 38 } }, "left": { "type": "MemberExpression", - "start": 22105, - "end": 22120, + "start": 22545, + "end": 22560, "loc": { "start": { - "line": 553, + "line": 569, "column": 17 }, "end": { - "line": 553, + "line": 569, "column": 32 } }, "object": { "type": "Identifier", - "start": 22105, - "end": 22113, + "start": 22545, + "end": 22553, "loc": { "start": { - "line": 553, + "line": 569, "column": 17 }, "end": { - "line": 553, + "line": 569, "column": 25 }, "identifierName": "selected" @@ -69223,15 +70783,15 @@ }, "property": { "type": "Identifier", - "start": 22114, - "end": 22120, + "start": 22554, + "end": 22560, "loc": { "start": { - "line": 553, + "line": 569, "column": 26 }, "end": { - "line": 553, + "line": 569, "column": 32 }, "identifierName": "length" @@ -69243,15 +70803,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 22125, - "end": 22126, + "start": 22565, + "end": 22566, "loc": { "start": { - "line": 553, + "line": 569, "column": 37 }, "end": { - "line": 553, + "line": 569, "column": 38 } }, @@ -69264,59 +70824,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 22128, - "end": 22219, + "start": 22568, + "end": 22659, "loc": { "start": { - "line": 553, + "line": 569, "column": 40 }, "end": { - "line": 555, + "line": 571, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 22138, - "end": 22211, + "start": 22578, + "end": 22651, "loc": { "start": { - "line": 554, + "line": 570, "column": 8 }, "end": { - "line": 554, + "line": 570, "column": 81 } }, "expression": { "type": "AssignmentExpression", - "start": 22138, - "end": 22210, + "start": 22578, + "end": 22650, "loc": { "start": { - "line": 554, + "line": 570, "column": 8 }, "end": { - "line": 554, + "line": 570, "column": 80 } }, "operator": "=", "left": { "type": "Identifier", - "start": 22138, - "end": 22150, + "start": 22578, + "end": 22590, "loc": { "start": { - "line": 554, + "line": 570, "column": 8 }, "end": { - "line": 554, + "line": 570, "column": 20 }, "identifierName": "selectedExpr" @@ -69325,58 +70885,58 @@ }, "right": { "type": "CallExpression", - "start": 22153, - "end": 22210, + "start": 22593, + "end": 22650, "loc": { "start": { - "line": 554, + "line": 570, "column": 23 }, "end": { - "line": 554, + "line": 570, "column": 80 } }, "callee": { "type": "MemberExpression", - "start": 22153, - "end": 22184, + "start": 22593, + "end": 22624, "loc": { "start": { - "line": 554, + "line": 570, "column": 23 }, "end": { - "line": 554, + "line": 570, "column": 54 } }, "object": { "type": "ThisExpression", - "start": 22153, - "end": 22157, + "start": 22593, + "end": 22597, "loc": { "start": { - "line": 554, + "line": 570, "column": 23 }, "end": { - "line": 554, + "line": 570, "column": 27 } } }, "property": { "type": "Identifier", - "start": 22158, - "end": 22184, + "start": 22598, + "end": 22624, "loc": { "start": { - "line": 554, + "line": 570, "column": 28 }, "end": { - "line": 554, + "line": 570, "column": 54 }, "identifierName": "getMRCARestrictionOfTwoTUs" @@ -69388,29 +70948,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 22185, - "end": 22196, + "start": 22625, + "end": 22636, "loc": { "start": { - "line": 554, + "line": 570, "column": 55 }, "end": { - "line": 554, + "line": 570, "column": 66 } }, "object": { "type": "Identifier", - "start": 22185, - "end": 22193, + "start": 22625, + "end": 22633, "loc": { "start": { - "line": 554, + "line": 570, "column": 55 }, "end": { - "line": 554, + "line": 570, "column": 63 }, "identifierName": "selected" @@ -69419,15 +70979,15 @@ }, "property": { "type": "NumericLiteral", - "start": 22194, - "end": 22195, + "start": 22634, + "end": 22635, "loc": { "start": { - "line": 554, + "line": 570, "column": 64 }, "end": { - "line": 554, + "line": 570, "column": 65 } }, @@ -69441,29 +71001,29 @@ }, { "type": "MemberExpression", - "start": 22198, - "end": 22209, + "start": 22638, + "end": 22649, "loc": { "start": { - "line": 554, + "line": 570, "column": 68 }, "end": { - "line": 554, + "line": 570, "column": 79 } }, "object": { "type": "Identifier", - "start": 22198, - "end": 22206, + "start": 22638, + "end": 22646, "loc": { "start": { - "line": 554, + "line": 570, "column": 68 }, "end": { - "line": 554, + "line": 570, "column": 76 }, "identifierName": "selected" @@ -69472,15 +71032,15 @@ }, "property": { "type": "NumericLiteral", - "start": 22207, - "end": 22208, + "start": 22647, + "end": 22648, "loc": { "start": { - "line": 554, + "line": 570, "column": 77 }, "end": { - "line": 554, + "line": 570, "column": 78 } }, @@ -69501,59 +71061,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 22225, - "end": 22419, + "start": 22665, + "end": 22859, "loc": { "start": { - "line": 555, + "line": 571, "column": 13 }, "end": { - "line": 562, + "line": 578, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 22235, - "end": 22411, + "start": 22675, + "end": 22851, "loc": { "start": { - "line": 556, + "line": 572, "column": 8 }, "end": { - "line": 561, + "line": 577, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 22235, - "end": 22410, + "start": 22675, + "end": 22850, "loc": { "start": { - "line": 556, + "line": 572, "column": 8 }, "end": { - "line": 561, + "line": 577, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 22235, - "end": 22247, + "start": 22675, + "end": 22687, "loc": { "start": { - "line": 556, + "line": 572, "column": 8 }, "end": { - "line": 556, + "line": 572, "column": 20 }, "identifierName": "selectedExpr" @@ -69562,58 +71122,58 @@ }, "right": { "type": "CallExpression", - "start": 22250, - "end": 22410, + "start": 22690, + "end": 22850, "loc": { "start": { - "line": 556, + "line": 572, "column": 23 }, "end": { - "line": 561, + "line": 577, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 22250, - "end": 22275, + "start": 22690, + "end": 22715, "loc": { "start": { - "line": 556, + "line": 572, "column": 23 }, "end": { - "line": 556, + "line": 572, "column": 48 } }, "object": { "type": "ThisExpression", - "start": 22250, - "end": 22254, + "start": 22690, + "end": 22694, "loc": { "start": { - "line": 556, + "line": 572, "column": 23 }, "end": { - "line": 556, + "line": 572, "column": 27 } } }, "property": { "type": "Identifier", - "start": 22255, - "end": 22275, + "start": 22695, + "end": 22715, "loc": { "start": { - "line": 556, + "line": 572, "column": 28 }, "end": { - "line": 556, + "line": 572, "column": 48 }, "identifierName": "createComponentClass" @@ -69625,15 +71185,15 @@ "arguments": [ { "type": "Identifier", - "start": 22287, - "end": 22293, + "start": 22727, + "end": 22733, "loc": { "start": { - "line": 557, + "line": 573, "column": 10 }, "end": { - "line": 557, + "line": 573, "column": 16 }, "identifierName": "jsonld" @@ -69642,15 +71202,15 @@ }, { "type": "Identifier", - "start": 22305, - "end": 22313, + "start": 22745, + "end": 22753, "loc": { "start": { - "line": 558, + "line": 574, "column": 10 }, "end": { - "line": 558, + "line": 574, "column": 18 }, "identifierName": "selected" @@ -69659,15 +71219,15 @@ }, { "type": "ArrayExpression", - "start": 22325, - "end": 22327, + "start": 22765, + "end": 22767, "loc": { "start": { - "line": 559, + "line": 575, "column": 10 }, "end": { - "line": 559, + "line": 575, "column": 12 } }, @@ -69675,58 +71235,58 @@ }, { "type": "CallExpression", - "start": 22339, - "end": 22400, + "start": 22779, + "end": 22840, "loc": { "start": { - "line": 560, + "line": 576, "column": 10 }, "end": { - "line": 560, + "line": 576, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 22339, - "end": 22378, + "start": 22779, + "end": 22818, "loc": { "start": { - "line": 560, + "line": 576, "column": 10 }, "end": { - "line": 560, + "line": 576, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 22339, - "end": 22343, + "start": 22779, + "end": 22783, "loc": { "start": { - "line": 560, + "line": 576, "column": 10 }, "end": { - "line": 560, + "line": 576, "column": 14 } } }, "property": { "type": "Identifier", - "start": 22344, - "end": 22378, + "start": 22784, + "end": 22818, "loc": { "start": { - "line": 560, + "line": 576, "column": 15 }, "end": { - "line": 560, + "line": 576, "column": 49 }, "identifierName": "createClassExpressionsForInternals" @@ -69738,15 +71298,15 @@ "arguments": [ { "type": "Identifier", - "start": 22379, - "end": 22385, + "start": 22819, + "end": 22825, "loc": { "start": { - "line": 560, + "line": 576, "column": 50 }, "end": { - "line": 560, + "line": 576, "column": 56 }, "identifierName": "jsonld" @@ -69755,15 +71315,15 @@ }, { "type": "Identifier", - "start": 22387, - "end": 22395, + "start": 22827, + "end": 22835, "loc": { "start": { - "line": 560, + "line": 576, "column": 58 }, "end": { - "line": 560, + "line": 576, "column": 66 }, "identifierName": "selected" @@ -69772,15 +71332,15 @@ }, { "type": "ArrayExpression", - "start": 22397, - "end": 22399, + "start": 22837, + "end": 22839, "loc": { "start": { - "line": 560, + "line": 576, "column": 68 }, "end": { - "line": 560, + "line": 576, "column": 70 } }, @@ -69799,57 +71359,57 @@ }, { "type": "ExpressionStatement", - "start": 22427, - "end": 22822, + "start": 22867, + "end": 23262, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 575, + "line": 591, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 22427, - "end": 22821, + "start": 22867, + "end": 23261, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 575, + "line": 591, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 22427, - "end": 22442, + "start": 22867, + "end": 22882, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 564, + "line": 580, "column": 21 } }, "object": { "type": "Identifier", - "start": 22427, - "end": 22437, + "start": 22867, + "end": 22877, "loc": { "start": { - "line": 564, + "line": 580, "column": 6 }, "end": { - "line": 564, + "line": 580, "column": 16 }, "identifierName": "classExprs" @@ -69858,15 +71418,15 @@ }, "property": { "type": "Identifier", - "start": 22438, - "end": 22442, + "start": 22878, + "end": 22882, "loc": { "start": { - "line": 564, + "line": 580, "column": 17 }, "end": { - "line": 564, + "line": 580, "column": 21 }, "identifierName": "push" @@ -69878,30 +71438,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 22443, - "end": 22820, + "start": 22883, + "end": 23260, "loc": { "start": { - "line": 564, + "line": 580, "column": 22 }, "end": { - "line": 575, + "line": 591, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 22453, - "end": 22479, + "start": 22893, + "end": 22919, "loc": { "start": { - "line": 565, + "line": 581, "column": 8 }, "end": { - "line": 565, + "line": 581, "column": 34 } }, @@ -69910,15 +71470,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 22453, - "end": 22460, + "start": 22893, + "end": 22900, "loc": { "start": { - "line": 565, + "line": 581, "column": 8 }, "end": { - "line": 565, + "line": 581, "column": 15 } }, @@ -69930,15 +71490,15 @@ }, "value": { "type": "StringLiteral", - "start": 22462, - "end": 22479, + "start": 22902, + "end": 22919, "loc": { "start": { - "line": 565, + "line": 581, "column": 17 }, "end": { - "line": 565, + "line": 581, "column": 34 } }, @@ -69951,15 +71511,15 @@ }, { "type": "ObjectProperty", - "start": 22489, - "end": 22519, + "start": 22929, + "end": 22959, "loc": { "start": { - "line": 566, + "line": 582, "column": 8 }, "end": { - "line": 566, + "line": 582, "column": 38 } }, @@ -69968,15 +71528,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22489, - "end": 22499, + "start": 22929, + "end": 22939, "loc": { "start": { - "line": 566, + "line": 582, "column": 8 }, "end": { - "line": 566, + "line": 582, "column": 18 }, "identifierName": "onProperty" @@ -69985,15 +71545,15 @@ }, "value": { "type": "StringLiteral", - "start": 22501, - "end": 22519, + "start": 22941, + "end": 22959, "loc": { "start": { - "line": 566, + "line": 582, "column": 20 }, "end": { - "line": 566, + "line": 582, "column": 38 } }, @@ -70006,15 +71566,15 @@ }, { "type": "ObjectProperty", - "start": 22547, - "end": 22811, + "start": 22987, + "end": 23251, "loc": { "start": { - "line": 567, + "line": 583, "column": 8 }, "end": { - "line": 574, + "line": 590, "column": 9 } }, @@ -70023,15 +71583,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22547, - "end": 22561, + "start": 22987, + "end": 23001, "loc": { "start": { - "line": 567, + "line": 583, "column": 8 }, "end": { - "line": 567, + "line": 583, "column": 22 }, "identifierName": "someValuesFrom" @@ -70041,30 +71601,30 @@ }, "value": { "type": "ObjectExpression", - "start": 22563, - "end": 22811, + "start": 23003, + "end": 23251, "loc": { "start": { - "line": 567, + "line": 583, "column": 24 }, "end": { - "line": 574, + "line": 590, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 22575, - "end": 22595, + "start": 23015, + "end": 23035, "loc": { "start": { - "line": 568, + "line": 584, "column": 10 }, "end": { - "line": 568, + "line": 584, "column": 30 } }, @@ -70073,15 +71633,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 22575, - "end": 22582, + "start": 23015, + "end": 23022, "loc": { "start": { - "line": 568, + "line": 584, "column": 10 }, "end": { - "line": 568, + "line": 584, "column": 17 } }, @@ -70093,15 +71653,15 @@ }, "value": { "type": "StringLiteral", - "start": 22584, - "end": 22595, + "start": 23024, + "end": 23035, "loc": { "start": { - "line": 568, + "line": 584, "column": 19 }, "end": { - "line": 568, + "line": 584, "column": 30 } }, @@ -70114,15 +71674,15 @@ }, { "type": "ObjectProperty", - "start": 22607, - "end": 22800, + "start": 23047, + "end": 23240, "loc": { "start": { - "line": 569, + "line": 585, "column": 10 }, "end": { - "line": 573, + "line": 589, "column": 26 } }, @@ -70131,15 +71691,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22607, - "end": 22621, + "start": 23047, + "end": 23061, "loc": { "start": { - "line": 569, + "line": 585, "column": 10 }, "end": { - "line": 569, + "line": 585, "column": 24 }, "identifierName": "intersectionOf" @@ -70148,45 +71708,45 @@ }, "value": { "type": "ArrayExpression", - "start": 22623, - "end": 22800, + "start": 23063, + "end": 23240, "loc": { "start": { - "line": 569, + "line": 585, "column": 26 }, "end": { - "line": 573, + "line": 589, "column": 26 } }, "elements": [ { "type": "ObjectExpression", - "start": 22624, - "end": 22785, + "start": 23064, + "end": 23225, "loc": { "start": { - "line": 569, + "line": 585, "column": 27 }, "end": { - "line": 573, + "line": 589, "column": 11 } }, "properties": [ { "type": "ObjectProperty", - "start": 22638, - "end": 22664, + "start": 23078, + "end": 23104, "loc": { "start": { - "line": 570, + "line": 586, "column": 12 }, "end": { - "line": 570, + "line": 586, "column": 38 } }, @@ -70195,15 +71755,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 22638, - "end": 22645, + "start": 23078, + "end": 23085, "loc": { "start": { - "line": 570, + "line": 586, "column": 12 }, "end": { - "line": 570, + "line": 586, "column": 19 } }, @@ -70215,15 +71775,15 @@ }, "value": { "type": "StringLiteral", - "start": 22647, - "end": 22664, + "start": 23087, + "end": 23104, "loc": { "start": { - "line": 570, + "line": 586, "column": 21 }, "end": { - "line": 570, + "line": 586, "column": 38 } }, @@ -70236,15 +71796,15 @@ }, { "type": "ObjectProperty", - "start": 22678, - "end": 22720, + "start": 23118, + "end": 23160, "loc": { "start": { - "line": 571, + "line": 587, "column": 12 }, "end": { - "line": 571, + "line": 587, "column": 54 } }, @@ -70253,15 +71813,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22678, - "end": 22688, + "start": 23118, + "end": 23128, "loc": { "start": { - "line": 571, + "line": 587, "column": 12 }, "end": { - "line": 571, + "line": 587, "column": 22 }, "identifierName": "onProperty" @@ -70270,15 +71830,15 @@ }, "value": { "type": "StringLiteral", - "start": 22690, - "end": 22720, + "start": 23130, + "end": 23160, "loc": { "start": { - "line": 571, + "line": 587, "column": 24 }, "end": { - "line": 571, + "line": 587, "column": 54 } }, @@ -70291,15 +71851,15 @@ }, { "type": "ObjectProperty", - "start": 22734, - "end": 22772, + "start": 23174, + "end": 23212, "loc": { "start": { - "line": 572, + "line": 588, "column": 12 }, "end": { - "line": 572, + "line": 588, "column": 50 } }, @@ -70308,15 +71868,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 22734, - "end": 22748, + "start": 23174, + "end": 23188, "loc": { "start": { - "line": 572, + "line": 588, "column": 12 }, "end": { - "line": 572, + "line": 588, "column": 26 }, "identifierName": "someValuesFrom" @@ -70325,15 +71885,15 @@ }, "value": { "type": "Identifier", - "start": 22750, - "end": 22772, + "start": 23190, + "end": 23212, "loc": { "start": { - "line": 572, + "line": 588, "column": 28 }, "end": { - "line": 572, + "line": 588, "column": 50 }, "identifierName": "remainingInternalsExpr" @@ -70345,15 +71905,15 @@ }, { "type": "Identifier", - "start": 22787, - "end": 22799, + "start": 23227, + "end": 23239, "loc": { "start": { - "line": 573, + "line": 589, "column": 13 }, "end": { - "line": 573, + "line": 589, "column": 25 }, "identifierName": "selectedExpr" @@ -70369,15 +71929,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 22521, - "end": 22538, + "start": 22961, + "end": 22978, "loc": { "start": { - "line": 566, + "line": 582, "column": 40 }, "end": { - "line": 566, + "line": 582, "column": 57 } } @@ -70398,15 +71958,15 @@ { "type": "CommentLine", "value": " Step 2. Now select everything from remaining once, and start recursing through", - "start": 22834, - "end": 22915, + "start": 23274, + "end": 23355, "loc": { "start": { - "line": 578, + "line": 594, "column": 4 }, "end": { - "line": 578, + "line": 594, "column": 85 } } @@ -70414,15 +71974,15 @@ { "type": "CommentLine", "value": " every possibility.", - "start": 22920, - "end": 22941, + "start": 23360, + "end": 23381, "loc": { "start": { - "line": 579, + "line": 595, "column": 4 }, "end": { - "line": 579, + "line": 595, "column": 25 } } @@ -70430,15 +71990,15 @@ { "type": "CommentLine", "value": " Note that we only process cases where there are more remainingInternals than", - "start": 22946, - "end": 23025, + "start": 23386, + "end": 23465, "loc": { "start": { - "line": 580, + "line": 596, "column": 4 }, "end": { - "line": 580, + "line": 596, "column": 83 } } @@ -70446,15 +72006,15 @@ { "type": "CommentLine", "value": " selected internals -- when there are fewer, we'll just end up with the inverses", - "start": 23030, - "end": 23112, + "start": 23470, + "end": 23552, "loc": { "start": { - "line": 581, + "line": 597, "column": 4 }, "end": { - "line": 581, + "line": 597, "column": 86 } } @@ -70462,15 +72022,15 @@ { "type": "CommentLine", "value": " of the previous comparisons, which we'll already have covered.", - "start": 23117, - "end": 23182, + "start": 23557, + "end": 23622, "loc": { "start": { - "line": 582, + "line": 598, "column": 4 }, "end": { - "line": 582, + "line": 598, "column": 69 } } @@ -70479,71 +72039,71 @@ }, { "type": "IfStatement", - "start": 23187, - "end": 23734, + "start": 23627, + "end": 24174, "loc": { "start": { - "line": 583, + "line": 599, "column": 4 }, "end": { - "line": 593, + "line": 609, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 23191, - "end": 23268, + "start": 23631, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 85 } }, "left": { "type": "BinaryExpression", - "start": 23191, - "end": 23220, + "start": 23631, + "end": 23660, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 23191, - "end": 23216, + "start": 23631, + "end": 23656, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 33 } }, "object": { "type": "Identifier", - "start": 23191, - "end": 23209, + "start": 23631, + "end": 23649, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 26 }, "identifierName": "remainingInternals" @@ -70553,15 +72113,15 @@ }, "property": { "type": "Identifier", - "start": 23210, - "end": 23216, + "start": 23650, + "end": 23656, "loc": { "start": { - "line": 583, + "line": 599, "column": 27 }, "end": { - "line": 583, + "line": 599, "column": 33 }, "identifierName": "length" @@ -70574,15 +72134,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 23219, - "end": 23220, + "start": 23659, + "end": 23660, "loc": { "start": { - "line": 583, + "line": 599, "column": 36 }, "end": { - "line": 583, + "line": 599, "column": 37 } }, @@ -70597,43 +72157,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 23224, - "end": 23268, + "start": 23664, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 41 }, "end": { - "line": 583, + "line": 599, "column": 85 } }, "left": { "type": "MemberExpression", - "start": 23224, - "end": 23239, + "start": 23664, + "end": 23679, "loc": { "start": { - "line": 583, + "line": 599, "column": 41 }, "end": { - "line": 583, + "line": 599, "column": 56 } }, "object": { "type": "Identifier", - "start": 23224, - "end": 23232, + "start": 23664, + "end": 23672, "loc": { "start": { - "line": 583, + "line": 599, "column": 41 }, "end": { - "line": 583, + "line": 599, "column": 49 }, "identifierName": "selected" @@ -70642,15 +72202,15 @@ }, "property": { "type": "Identifier", - "start": 23233, - "end": 23239, + "start": 23673, + "end": 23679, "loc": { "start": { - "line": 583, + "line": 599, "column": 50 }, "end": { - "line": 583, + "line": 599, "column": 56 }, "identifierName": "length" @@ -70662,29 +72222,29 @@ "operator": "<=", "right": { "type": "MemberExpression", - "start": 23243, - "end": 23268, + "start": 23683, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 60 }, "end": { - "line": 583, + "line": 599, "column": 85 } }, "object": { "type": "Identifier", - "start": 23243, - "end": 23261, + "start": 23683, + "end": 23701, "loc": { "start": { - "line": 583, + "line": 599, "column": 60 }, "end": { - "line": 583, + "line": 599, "column": 78 }, "identifierName": "remainingInternals" @@ -70693,15 +72253,15 @@ }, "property": { "type": "Identifier", - "start": 23262, - "end": 23268, + "start": 23702, + "end": 23708, "loc": { "start": { - "line": 583, + "line": 599, "column": 79 }, "end": { - "line": 583, + "line": 599, "column": 85 }, "identifierName": "length" @@ -70715,128 +72275,128 @@ }, "consequent": { "type": "BlockStatement", - "start": 23270, - "end": 23734, + "start": 23710, + "end": 24174, "loc": { "start": { - "line": 583, + "line": 599, "column": 87 }, "end": { - "line": 593, + "line": 609, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 23278, - "end": 23728, + "start": 23718, + "end": 24168, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 592, + "line": 608, "column": 48 } }, "expression": { "type": "CallExpression", - "start": 23278, - "end": 23727, + "start": 23718, + "end": 24167, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 592, + "line": 608, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 23278, - "end": 23696, + "start": 23718, + "end": 24136, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 592, + "line": 608, "column": 16 } }, "object": { "type": "CallExpression", - "start": 23278, - "end": 23679, + "start": 23718, + "end": 24119, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 591, + "line": 607, "column": 50 } }, "callee": { "type": "MemberExpression", - "start": 23278, - "end": 23644, + "start": 23718, + "end": 24084, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 591, + "line": 607, "column": 15 } }, "object": { "type": "CallExpression", - "start": 23278, - "end": 23628, + "start": 23718, + "end": 24068, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 590, + "line": 606, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 23278, - "end": 23300, + "start": 23718, + "end": 23740, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 584, + "line": 600, "column": 28 } }, "object": { "type": "Identifier", - "start": 23278, - "end": 23296, + "start": 23718, + "end": 23736, "loc": { "start": { - "line": 584, + "line": 600, "column": 6 }, "end": { - "line": 584, + "line": 600, "column": 24 }, "identifierName": "remainingInternals" @@ -70845,15 +72405,15 @@ }, "property": { "type": "Identifier", - "start": 23297, - "end": 23300, + "start": 23737, + "end": 23740, "loc": { "start": { - "line": 584, + "line": 600, "column": 25 }, "end": { - "line": 584, + "line": 600, "column": 28 }, "identifierName": "map" @@ -70865,15 +72425,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23301, - "end": 23627, + "start": 23741, + "end": 24067, "loc": { "start": { - "line": 584, + "line": 600, "column": 29 }, "end": { - "line": 590, + "line": 606, "column": 7 } }, @@ -70884,15 +72444,15 @@ "params": [ { "type": "Identifier", - "start": 23301, - "end": 23314, + "start": 23741, + "end": 23754, "loc": { "start": { - "line": 584, + "line": 600, "column": 29 }, "end": { - "line": 584, + "line": 600, "column": 42 }, "identifierName": "newlySelected" @@ -70902,58 +72462,58 @@ ], "body": { "type": "CallExpression", - "start": 23318, - "end": 23627, + "start": 23758, + "end": 24067, "loc": { "start": { - "line": 584, + "line": 600, "column": 46 }, "end": { - "line": 590, + "line": 606, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 23318, - "end": 23357, + "start": 23758, + "end": 23797, "loc": { "start": { - "line": 584, + "line": 600, "column": 46 }, "end": { - "line": 584, + "line": 600, "column": 85 } }, "object": { "type": "ThisExpression", - "start": 23318, - "end": 23322, + "start": 23758, + "end": 23762, "loc": { "start": { - "line": 584, + "line": 600, "column": 46 }, "end": { - "line": 584, + "line": 600, "column": 50 } } }, "property": { "type": "Identifier", - "start": 23323, - "end": 23357, + "start": 23763, + "end": 23797, "loc": { "start": { - "line": 584, + "line": 600, "column": 51 }, "end": { - "line": 584, + "line": 600, "column": 85 }, "identifierName": "createClassExpressionsForInternals" @@ -70965,15 +72525,15 @@ "arguments": [ { "type": "Identifier", - "start": 23367, - "end": 23373, + "start": 23807, + "end": 23813, "loc": { "start": { - "line": 585, + "line": 601, "column": 8 }, "end": { - "line": 585, + "line": 601, "column": 14 }, "identifierName": "jsonld" @@ -70982,43 +72542,43 @@ }, { "type": "CallExpression", - "start": 23456, - "end": 23507, + "start": 23896, + "end": 23947, "loc": { "start": { - "line": 587, + "line": 603, "column": 8 }, "end": { - "line": 587, + "line": 603, "column": 59 } }, "callee": { "type": "MemberExpression", - "start": 23456, - "end": 23481, + "start": 23896, + "end": 23921, "loc": { "start": { - "line": 587, + "line": 603, "column": 8 }, "end": { - "line": 587, + "line": 603, "column": 33 } }, "object": { "type": "Identifier", - "start": 23456, - "end": 23474, + "start": 23896, + "end": 23914, "loc": { "start": { - "line": 587, + "line": 603, "column": 8 }, "end": { - "line": 587, + "line": 603, "column": 26 }, "identifierName": "remainingInternals" @@ -71028,15 +72588,15 @@ }, "property": { "type": "Identifier", - "start": 23475, - "end": 23481, + "start": 23915, + "end": 23921, "loc": { "start": { - "line": 587, + "line": 603, "column": 27 }, "end": { - "line": 587, + "line": 603, "column": 33 }, "identifierName": "filter" @@ -71049,15 +72609,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23482, - "end": 23506, + "start": 23922, + "end": 23946, "loc": { "start": { - "line": 587, + "line": 603, "column": 34 }, "end": { - "line": 587, + "line": 603, "column": 58 } }, @@ -71068,15 +72628,15 @@ "params": [ { "type": "Identifier", - "start": 23482, - "end": 23483, + "start": 23922, + "end": 23923, "loc": { "start": { - "line": 587, + "line": 603, "column": 34 }, "end": { - "line": 587, + "line": 603, "column": 35 }, "identifierName": "i" @@ -71086,29 +72646,29 @@ ], "body": { "type": "BinaryExpression", - "start": 23487, - "end": 23506, + "start": 23927, + "end": 23946, "loc": { "start": { - "line": 587, + "line": 603, "column": 39 }, "end": { - "line": 587, + "line": 603, "column": 58 } }, "left": { "type": "Identifier", - "start": 23487, - "end": 23488, + "start": 23927, + "end": 23928, "loc": { "start": { - "line": 587, + "line": 603, "column": 39 }, "end": { - "line": 587, + "line": 603, "column": 40 }, "identifierName": "i" @@ -71118,15 +72678,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 23493, - "end": 23506, + "start": 23933, + "end": 23946, "loc": { "start": { - "line": 587, + "line": 603, "column": 45 }, "end": { - "line": 587, + "line": 603, "column": 58 }, "identifierName": "newlySelected" @@ -71140,15 +72700,15 @@ { "type": "CommentLine", "value": " The new remaining is the old remaining minus the selected TU.", - "start": 23383, - "end": 23447, + "start": 23823, + "end": 23887, "loc": { "start": { - "line": 586, + "line": 602, "column": 8 }, "end": { - "line": 586, + "line": 602, "column": 72 } } @@ -71157,43 +72717,43 @@ }, { "type": "CallExpression", - "start": 23587, - "end": 23619, + "start": 24027, + "end": 24059, "loc": { "start": { - "line": 589, + "line": 605, "column": 8 }, "end": { - "line": 589, + "line": 605, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 23587, - "end": 23602, + "start": 24027, + "end": 24042, "loc": { "start": { - "line": 589, + "line": 605, "column": 8 }, "end": { - "line": 589, + "line": 605, "column": 23 } }, "object": { "type": "Identifier", - "start": 23587, - "end": 23595, + "start": 24027, + "end": 24035, "loc": { "start": { - "line": 589, + "line": 605, "column": 8 }, "end": { - "line": 589, + "line": 605, "column": 16 }, "identifierName": "selected" @@ -71203,15 +72763,15 @@ }, "property": { "type": "Identifier", - "start": 23596, - "end": 23602, + "start": 24036, + "end": 24042, "loc": { "start": { - "line": 589, + "line": 605, "column": 17 }, "end": { - "line": 589, + "line": 605, "column": 23 }, "identifierName": "concat" @@ -71224,30 +72784,30 @@ "arguments": [ { "type": "ArrayExpression", - "start": 23603, - "end": 23618, + "start": 24043, + "end": 24058, "loc": { "start": { - "line": 589, + "line": 605, "column": 24 }, "end": { - "line": 589, + "line": 605, "column": 39 } }, "elements": [ { "type": "Identifier", - "start": 23604, - "end": 23617, + "start": 24044, + "end": 24057, "loc": { "start": { - "line": 589, + "line": 605, "column": 25 }, "end": { - "line": 589, + "line": 605, "column": 38 }, "identifierName": "newlySelected" @@ -71261,15 +72821,15 @@ { "type": "CommentLine", "value": " The new selected is the old selected plus the selected TU.", - "start": 23517, - "end": 23578, + "start": 23957, + "end": 24018, "loc": { "start": { - "line": 588, + "line": 604, "column": 8 }, "end": { - "line": 588, + "line": 604, "column": 69 } } @@ -71283,15 +72843,15 @@ }, "property": { "type": "Identifier", - "start": 23638, - "end": 23644, + "start": 24078, + "end": 24084, "loc": { "start": { - "line": 591, + "line": 607, "column": 9 }, "end": { - "line": 591, + "line": 607, "column": 15 }, "identifierName": "reduce" @@ -71303,15 +72863,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23645, - "end": 23674, + "start": 24085, + "end": 24114, "loc": { "start": { - "line": 591, + "line": 607, "column": 16 }, "end": { - "line": 591, + "line": 607, "column": 45 } }, @@ -71322,15 +72882,15 @@ "params": [ { "type": "Identifier", - "start": 23646, - "end": 23649, + "start": 24086, + "end": 24089, "loc": { "start": { - "line": 591, + "line": 607, "column": 17 }, "end": { - "line": 591, + "line": 607, "column": 20 }, "identifierName": "acc" @@ -71339,15 +72899,15 @@ }, { "type": "Identifier", - "start": 23651, - "end": 23654, + "start": 24091, + "end": 24094, "loc": { "start": { - "line": 591, + "line": 607, "column": 22 }, "end": { - "line": 591, + "line": 607, "column": 25 }, "identifierName": "val" @@ -71357,43 +72917,43 @@ ], "body": { "type": "CallExpression", - "start": 23659, - "end": 23674, + "start": 24099, + "end": 24114, "loc": { "start": { - "line": 591, + "line": 607, "column": 30 }, "end": { - "line": 591, + "line": 607, "column": 45 } }, "callee": { "type": "MemberExpression", - "start": 23659, - "end": 23669, + "start": 24099, + "end": 24109, "loc": { "start": { - "line": 591, + "line": 607, "column": 30 }, "end": { - "line": 591, + "line": 607, "column": 40 } }, "object": { "type": "Identifier", - "start": 23659, - "end": 23662, + "start": 24099, + "end": 24102, "loc": { "start": { - "line": 591, + "line": 607, "column": 30 }, "end": { - "line": 591, + "line": 607, "column": 33 }, "identifierName": "acc" @@ -71402,15 +72962,15 @@ }, "property": { "type": "Identifier", - "start": 23663, - "end": 23669, + "start": 24103, + "end": 24109, "loc": { "start": { - "line": 591, + "line": 607, "column": 34 }, "end": { - "line": 591, + "line": 607, "column": 40 }, "identifierName": "concat" @@ -71422,15 +72982,15 @@ "arguments": [ { "type": "Identifier", - "start": 23670, - "end": 23673, + "start": 24110, + "end": 24113, "loc": { "start": { - "line": 591, + "line": 607, "column": 41 }, "end": { - "line": 591, + "line": 607, "column": 44 }, "identifierName": "val" @@ -71442,15 +73002,15 @@ }, { "type": "ArrayExpression", - "start": 23676, - "end": 23678, + "start": 24116, + "end": 24118, "loc": { "start": { - "line": 591, + "line": 607, "column": 47 }, "end": { - "line": 591, + "line": 607, "column": 49 } }, @@ -71460,15 +73020,15 @@ }, "property": { "type": "Identifier", - "start": 23689, - "end": 23696, + "start": 24129, + "end": 24136, "loc": { "start": { - "line": 592, + "line": 608, "column": 9 }, "end": { - "line": 592, + "line": 608, "column": 16 }, "identifierName": "forEach" @@ -71480,15 +73040,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 23697, - "end": 23726, + "start": 24137, + "end": 24166, "loc": { "start": { - "line": 592, + "line": 608, "column": 17 }, "end": { - "line": 592, + "line": 608, "column": 46 } }, @@ -71499,15 +73059,15 @@ "params": [ { "type": "Identifier", - "start": 23697, - "end": 23701, + "start": 24137, + "end": 24141, "loc": { "start": { - "line": 592, + "line": 608, "column": 17 }, "end": { - "line": 592, + "line": 608, "column": 21 }, "identifierName": "expr" @@ -71517,43 +73077,43 @@ ], "body": { "type": "CallExpression", - "start": 23705, - "end": 23726, + "start": 24145, + "end": 24166, "loc": { "start": { - "line": 592, + "line": 608, "column": 25 }, "end": { - "line": 592, + "line": 608, "column": 46 } }, "callee": { "type": "MemberExpression", - "start": 23705, - "end": 23720, + "start": 24145, + "end": 24160, "loc": { "start": { - "line": 592, + "line": 608, "column": 25 }, "end": { - "line": 592, + "line": 608, "column": 40 } }, "object": { "type": "Identifier", - "start": 23705, - "end": 23715, + "start": 24145, + "end": 24155, "loc": { "start": { - "line": 592, + "line": 608, "column": 25 }, "end": { - "line": 592, + "line": 608, "column": 35 }, "identifierName": "classExprs" @@ -71562,15 +73122,15 @@ }, "property": { "type": "Identifier", - "start": 23716, - "end": 23720, + "start": 24156, + "end": 24160, "loc": { "start": { - "line": 592, + "line": 608, "column": 36 }, "end": { - "line": 592, + "line": 608, "column": 40 }, "identifierName": "push" @@ -71582,15 +73142,15 @@ "arguments": [ { "type": "Identifier", - "start": 23721, - "end": 23725, + "start": 24161, + "end": 24165, "loc": { "start": { - "line": 592, + "line": 608, "column": 41 }, "end": { - "line": 592, + "line": 608, "column": 45 }, "identifierName": "expr" @@ -71611,15 +73171,15 @@ { "type": "CommentLine", "value": " Step 2. Now select everything from remaining once, and start recursing through", - "start": 22834, - "end": 22915, + "start": 23274, + "end": 23355, "loc": { "start": { - "line": 578, + "line": 594, "column": 4 }, "end": { - "line": 578, + "line": 594, "column": 85 } } @@ -71627,15 +73187,15 @@ { "type": "CommentLine", "value": " every possibility.", - "start": 22920, - "end": 22941, + "start": 23360, + "end": 23381, "loc": { "start": { - "line": 579, + "line": 595, "column": 4 }, "end": { - "line": 579, + "line": 595, "column": 25 } } @@ -71643,15 +73203,15 @@ { "type": "CommentLine", "value": " Note that we only process cases where there are more remainingInternals than", - "start": 22946, - "end": 23025, + "start": 23386, + "end": 23465, "loc": { "start": { - "line": 580, + "line": 596, "column": 4 }, "end": { - "line": 580, + "line": 596, "column": 83 } } @@ -71659,15 +73219,15 @@ { "type": "CommentLine", "value": " selected internals -- when there are fewer, we'll just end up with the inverses", - "start": 23030, - "end": 23112, + "start": 23470, + "end": 23552, "loc": { "start": { - "line": 581, + "line": 597, "column": 4 }, "end": { - "line": 581, + "line": 597, "column": 86 } } @@ -71675,15 +73235,15 @@ { "type": "CommentLine", "value": " of the previous comparisons, which we'll already have covered.", - "start": 23117, - "end": 23182, + "start": 23557, + "end": 23622, "loc": { "start": { - "line": 582, + "line": 598, "column": 4 }, "end": { - "line": 582, + "line": 598, "column": 69 } } @@ -71692,29 +73252,29 @@ }, { "type": "ReturnStatement", - "start": 23740, - "end": 23758, + "start": 24180, + "end": 24198, "loc": { "start": { - "line": 595, + "line": 611, "column": 4 }, "end": { - "line": 595, + "line": 611, "column": 22 } }, "argument": { "type": "Identifier", - "start": 23747, - "end": 23757, + "start": 24187, + "end": 24197, "loc": { "start": { - "line": 595, + "line": 611, "column": 11 }, "end": { - "line": 595, + "line": 611, "column": 21 }, "identifierName": "classExprs" @@ -71730,15 +73290,15 @@ { "type": "CommentBlock", "value": "\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n ", - "start": 18864, - "end": 20362, + "start": 19304, + "end": 20802, "loc": { "start": { - "line": 486, + "line": 502, "column": 2 }, "end": { - "line": 511, + "line": 527, "column": 5 } } @@ -71748,15 +73308,15 @@ { "type": "CommentBlock", "value": "\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n ", - "start": 23766, - "end": 23972, + "start": 24206, + "end": 24412, "loc": { "start": { - "line": 598, + "line": 614, "column": 2 }, "end": { - "line": 606, + "line": 622, "column": 5 } } @@ -71765,15 +73325,15 @@ }, { "type": "ClassMethod", - "start": 23975, - "end": 32363, + "start": 24415, + "end": 32803, "loc": { "start": { - "line": 607, + "line": 623, "column": 2 }, "end": { - "line": 795, + "line": 811, "column": 3 } }, @@ -71781,15 +73341,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 23975, - "end": 23983, + "start": 24415, + "end": 24423, "loc": { "start": { - "line": 607, + "line": 623, "column": 2 }, "end": { - "line": 607, + "line": 623, "column": 10 }, "identifierName": "asJSONLD" @@ -71805,15 +73365,15 @@ "params": [ { "type": "Identifier", - "start": 23984, - "end": 23995, + "start": 24424, + "end": 24435, "loc": { "start": { - "line": 607, + "line": 623, "column": 11 }, "end": { - "line": 607, + "line": 623, "column": 22 }, "identifierName": "fallbackIRI" @@ -71823,59 +73383,59 @@ ], "body": { "type": "BlockStatement", - "start": 23997, - "end": 32363, + "start": 24437, + "end": 32803, "loc": { "start": { - "line": 607, + "line": 623, "column": 24 }, "end": { - "line": 795, + "line": 811, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 24042, - "end": 24092, + "start": 24482, + "end": 24532, "loc": { "start": { - "line": 609, + "line": 625, "column": 4 }, "end": { - "line": 609, + "line": 625, "column": 54 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24048, - "end": 24091, + "start": 24488, + "end": 24531, "loc": { "start": { - "line": 609, + "line": 625, "column": 10 }, "end": { - "line": 609, + "line": 625, "column": 53 } }, "id": { "type": "Identifier", - "start": 24048, - "end": 24064, + "start": 24488, + "end": 24504, "loc": { "start": { - "line": 609, + "line": 625, "column": 10 }, "end": { - "line": 609, + "line": 625, "column": 26 }, "identifierName": "phylorefAsJSONLD" @@ -71885,29 +73445,29 @@ }, "init": { "type": "CallExpression", - "start": 24067, - "end": 24091, + "start": 24507, + "end": 24531, "loc": { "start": { - "line": 609, + "line": 625, "column": 29 }, "end": { - "line": 609, + "line": 625, "column": 53 } }, "callee": { "type": "Identifier", - "start": 24067, - "end": 24076, + "start": 24507, + "end": 24516, "loc": { "start": { - "line": 609, + "line": 625, "column": 29 }, "end": { - "line": 609, + "line": 625, "column": 38 }, "identifierName": "cloneDeep" @@ -71917,44 +73477,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 24077, - "end": 24090, + "start": 24517, + "end": 24530, "loc": { "start": { - "line": 609, + "line": 625, "column": 39 }, "end": { - "line": 609, + "line": 625, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 24077, - "end": 24081, + "start": 24517, + "end": 24521, "loc": { "start": { - "line": 609, + "line": 625, "column": 39 }, "end": { - "line": 609, + "line": 625, "column": 43 } } }, "property": { "type": "Identifier", - "start": 24082, - "end": 24090, + "start": 24522, + "end": 24530, "loc": { "start": { - "line": 609, + "line": 625, "column": 44 }, "end": { - "line": 609, + "line": 625, "column": 52 }, "identifierName": "phyloref" @@ -71973,15 +73533,15 @@ { "type": "CommentLine", "value": " Keep all currently extant data.", - "start": 24003, - "end": 24037, + "start": 24443, + "end": 24477, "loc": { "start": { - "line": 608, + "line": 624, "column": 4 }, "end": { - "line": 608, + "line": 624, "column": 38 } } @@ -71991,15 +73551,15 @@ { "type": "CommentLine", "value": " Set the @id and @type. If we don't already have an '@id', use the", - "start": 24098, - "end": 24166, + "start": 24538, + "end": 24606, "loc": { "start": { - "line": 611, + "line": 627, "column": 4 }, "end": { - "line": 611, + "line": 627, "column": 72 } } @@ -72007,15 +73567,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 24171, - "end": 24186, + "start": 24611, + "end": 24626, "loc": { "start": { - "line": 612, + "line": 628, "column": 4 }, "end": { - "line": 612, + "line": 628, "column": 19 } } @@ -72024,29 +73584,29 @@ }, { "type": "IfStatement", - "start": 24191, - "end": 24264, + "start": 24631, + "end": 24704, "loc": { "start": { - "line": 613, + "line": 629, "column": 4 }, "end": { - "line": 613, + "line": 629, "column": 77 } }, "test": { "type": "UnaryExpression", - "start": 24195, - "end": 24224, + "start": 24635, + "end": 24664, "loc": { "start": { - "line": 613, + "line": 629, "column": 8 }, "end": { - "line": 613, + "line": 629, "column": 37 } }, @@ -72054,29 +73614,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 24196, - "end": 24224, + "start": 24636, + "end": 24664, "loc": { "start": { - "line": 613, + "line": 629, "column": 9 }, "end": { - "line": 613, + "line": 629, "column": 37 } }, "callee": { "type": "Identifier", - "start": 24196, - "end": 24199, + "start": 24636, + "end": 24639, "loc": { "start": { - "line": 613, + "line": 629, "column": 9 }, "end": { - "line": 613, + "line": 629, "column": 12 }, "identifierName": "has" @@ -72087,15 +73647,15 @@ "arguments": [ { "type": "Identifier", - "start": 24200, - "end": 24216, + "start": 24640, + "end": 24656, "loc": { "start": { - "line": 613, + "line": 629, "column": 13 }, "end": { - "line": 613, + "line": 629, "column": 29 }, "identifierName": "phylorefAsJSONLD" @@ -72104,15 +73664,15 @@ }, { "type": "StringLiteral", - "start": 24218, - "end": 24223, + "start": 24658, + "end": 24663, "loc": { "start": { - "line": 613, + "line": 629, "column": 31 }, "end": { - "line": 613, + "line": 629, "column": 36 } }, @@ -72132,58 +73692,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 24226, - "end": 24264, + "start": 24666, + "end": 24704, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 77 } }, "expression": { "type": "AssignmentExpression", - "start": 24226, - "end": 24263, + "start": 24666, + "end": 24703, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 76 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 24226, - "end": 24249, + "start": 24666, + "end": 24689, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 62 } }, "object": { "type": "Identifier", - "start": 24226, - "end": 24242, + "start": 24666, + "end": 24682, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 55 }, "identifierName": "phylorefAsJSONLD" @@ -72192,15 +73752,15 @@ }, "property": { "type": "StringLiteral", - "start": 24243, - "end": 24248, + "start": 24683, + "end": 24688, "loc": { "start": { - "line": 613, + "line": 629, "column": 56 }, "end": { - "line": 613, + "line": 629, "column": 61 } }, @@ -72214,15 +73774,15 @@ }, "right": { "type": "Identifier", - "start": 24252, - "end": 24263, + "start": 24692, + "end": 24703, "loc": { "start": { - "line": 613, + "line": 629, "column": 65 }, "end": { - "line": 613, + "line": 629, "column": 76 }, "identifierName": "fallbackIRI" @@ -72236,15 +73796,15 @@ { "type": "CommentLine", "value": " Set the @id and @type. If we don't already have an '@id', use the", - "start": 24098, - "end": 24166, + "start": 24538, + "end": 24606, "loc": { "start": { - "line": 611, + "line": 627, "column": 4 }, "end": { - "line": 611, + "line": 627, "column": 72 } } @@ -72252,15 +73812,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 24171, - "end": 24186, + "start": 24611, + "end": 24626, "loc": { "start": { - "line": 612, + "line": 628, "column": 4 }, "end": { - "line": 612, + "line": 628, "column": 19 } } @@ -72269,58 +73829,58 @@ }, { "type": "ExpressionStatement", - "start": 24269, - "end": 24309, + "start": 24709, + "end": 24749, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 44 } }, "expression": { "type": "AssignmentExpression", - "start": 24269, - "end": 24308, + "start": 24709, + "end": 24748, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 43 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 24269, - "end": 24294, + "start": 24709, + "end": 24734, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 29 } }, "object": { "type": "Identifier", - "start": 24269, - "end": 24285, + "start": 24709, + "end": 24725, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 20 }, "identifierName": "phylorefAsJSONLD" @@ -72329,15 +73889,15 @@ }, "property": { "type": "StringLiteral", - "start": 24286, - "end": 24293, + "start": 24726, + "end": 24733, "loc": { "start": { - "line": 614, + "line": 630, "column": 21 }, "end": { - "line": 614, + "line": 630, "column": 28 } }, @@ -72351,15 +73911,15 @@ }, "right": { "type": "StringLiteral", - "start": 24297, - "end": 24308, + "start": 24737, + "end": 24748, "loc": { "start": { - "line": 614, + "line": 630, "column": 32 }, "end": { - "line": 614, + "line": 630, "column": 43 } }, @@ -72374,15 +73934,15 @@ { "type": "CommentLine", "value": " If we don't have a bibliographicCitation but we do have a definition source,", - "start": 24315, - "end": 24394, + "start": 24755, + "end": 24834, "loc": { "start": { - "line": 616, + "line": 632, "column": 4 }, "end": { - "line": 616, + "line": 632, "column": 83 } } @@ -72390,15 +73950,15 @@ { "type": "CommentLine", "value": " then generate a bibliographicCitation for the source.", - "start": 24399, - "end": 24455, + "start": 24839, + "end": 24895, "loc": { "start": { - "line": 617, + "line": 633, "column": 4 }, "end": { - "line": 617, + "line": 633, "column": 60 } } @@ -72407,43 +73967,43 @@ }, { "type": "IfStatement", - "start": 24460, - "end": 24748, + "start": 24900, + "end": 25188, "loc": { "start": { - "line": 618, + "line": 634, "column": 4 }, "end": { - "line": 623, + "line": 639, "column": 5 } }, "test": { "type": "CallExpression", - "start": 24464, - "end": 24505, + "start": 24904, + "end": 24945, "loc": { "start": { - "line": 618, + "line": 634, "column": 8 }, "end": { - "line": 618, + "line": 634, "column": 49 } }, "callee": { "type": "Identifier", - "start": 24464, - "end": 24467, + "start": 24904, + "end": 24907, "loc": { "start": { - "line": 618, + "line": 634, "column": 8 }, "end": { - "line": 618, + "line": 634, "column": 11 }, "identifierName": "has" @@ -72454,15 +74014,15 @@ "arguments": [ { "type": "Identifier", - "start": 24468, - "end": 24484, + "start": 24908, + "end": 24924, "loc": { "start": { - "line": 618, + "line": 634, "column": 12 }, "end": { - "line": 618, + "line": 634, "column": 28 }, "identifierName": "phylorefAsJSONLD" @@ -72471,15 +74031,15 @@ }, { "type": "StringLiteral", - "start": 24486, - "end": 24504, + "start": 24926, + "end": 24944, "loc": { "start": { - "line": 618, + "line": 634, "column": 30 }, "end": { - "line": 618, + "line": 634, "column": 48 } }, @@ -72494,59 +74054,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 24507, - "end": 24748, + "start": 24947, + "end": 25188, "loc": { "start": { - "line": 618, + "line": 634, "column": 51 }, "end": { - "line": 623, + "line": 639, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 24515, - "end": 24574, + "start": 24955, + "end": 25014, "loc": { "start": { - "line": 619, + "line": 635, "column": 6 }, "end": { - "line": 619, + "line": 635, "column": 65 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24521, - "end": 24573, + "start": 24961, + "end": 25013, "loc": { "start": { - "line": 619, + "line": 635, "column": 12 }, "end": { - "line": 619, + "line": 635, "column": 64 } }, "id": { "type": "Identifier", - "start": 24521, - "end": 24537, + "start": 24961, + "end": 24977, "loc": { "start": { - "line": 619, + "line": 635, "column": 12 }, "end": { - "line": 619, + "line": 635, "column": 28 }, "identifierName": "definitionSource" @@ -72555,29 +74115,29 @@ }, "init": { "type": "MemberExpression", - "start": 24540, - "end": 24573, + "start": 24980, + "end": 25013, "loc": { "start": { - "line": 619, + "line": 635, "column": 31 }, "end": { - "line": 619, + "line": 635, "column": 64 } }, "object": { "type": "Identifier", - "start": 24540, - "end": 24556, + "start": 24980, + "end": 24996, "loc": { "start": { - "line": 619, + "line": 635, "column": 31 }, "end": { - "line": 619, + "line": 635, "column": 47 }, "identifierName": "phylorefAsJSONLD" @@ -72586,15 +74146,15 @@ }, "property": { "type": "Identifier", - "start": 24557, - "end": 24573, + "start": 24997, + "end": 25013, "loc": { "start": { - "line": 619, + "line": 635, "column": 48 }, "end": { - "line": 619, + "line": 635, "column": 64 }, "identifierName": "definitionSource" @@ -72609,29 +74169,29 @@ }, { "type": "IfStatement", - "start": 24581, - "end": 24742, + "start": 25021, + "end": 25182, "loc": { "start": { - "line": 620, + "line": 636, "column": 6 }, "end": { - "line": 622, + "line": 638, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 24585, - "end": 24632, + "start": 25025, + "end": 25072, "loc": { "start": { - "line": 620, + "line": 636, "column": 10 }, "end": { - "line": 620, + "line": 636, "column": 57 } }, @@ -72639,29 +74199,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 24586, - "end": 24632, + "start": 25026, + "end": 25072, "loc": { "start": { - "line": 620, + "line": 636, "column": 11 }, "end": { - "line": 620, + "line": 636, "column": 57 } }, "callee": { "type": "Identifier", - "start": 24586, - "end": 24589, + "start": 25026, + "end": 25029, "loc": { "start": { - "line": 620, + "line": 636, "column": 11 }, "end": { - "line": 620, + "line": 636, "column": 14 }, "identifierName": "has" @@ -72671,15 +74231,15 @@ "arguments": [ { "type": "Identifier", - "start": 24590, - "end": 24606, + "start": 25030, + "end": 25046, "loc": { "start": { - "line": 620, + "line": 636, "column": 15 }, "end": { - "line": 620, + "line": 636, "column": 31 }, "identifierName": "definitionSource" @@ -72688,15 +74248,15 @@ }, { "type": "StringLiteral", - "start": 24608, - "end": 24631, + "start": 25048, + "end": 25071, "loc": { "start": { - "line": 620, + "line": 636, "column": 33 }, "end": { - "line": 620, + "line": 636, "column": 56 } }, @@ -72714,73 +74274,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 24634, - "end": 24742, + "start": 25074, + "end": 25182, "loc": { "start": { - "line": 620, + "line": 636, "column": 59 }, "end": { - "line": 622, + "line": 638, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 24644, - "end": 24734, + "start": 25084, + "end": 25174, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 98 } }, "expression": { "type": "AssignmentExpression", - "start": 24644, - "end": 24733, + "start": 25084, + "end": 25173, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 97 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 24644, - "end": 24682, + "start": 25084, + "end": 25122, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 46 } }, "object": { "type": "Identifier", - "start": 24644, - "end": 24660, + "start": 25084, + "end": 25100, "loc": { "start": { - "line": 621, + "line": 637, "column": 8 }, "end": { - "line": 621, + "line": 637, "column": 24 }, "identifierName": "definitionSource" @@ -72789,15 +74349,15 @@ }, "property": { "type": "Identifier", - "start": 24661, - "end": 24682, + "start": 25101, + "end": 25122, "loc": { "start": { - "line": 621, + "line": 637, "column": 25 }, "end": { - "line": 621, + "line": 637, "column": 46 }, "identifierName": "bibliographicCitation" @@ -72808,57 +74368,57 @@ }, "right": { "type": "CallExpression", - "start": 24685, - "end": 24733, + "start": 25125, + "end": 25173, "loc": { "start": { - "line": 621, + "line": 637, "column": 49 }, "end": { - "line": 621, + "line": 637, "column": 97 } }, "callee": { "type": "MemberExpression", - "start": 24685, - "end": 24731, + "start": 25125, + "end": 25171, "loc": { "start": { - "line": 621, + "line": 637, "column": 49 }, "end": { - "line": 621, + "line": 637, "column": 95 } }, "object": { "type": "NewExpression", - "start": 24685, - "end": 24722, + "start": 25125, + "end": 25162, "loc": { "start": { - "line": 621, + "line": 637, "column": 49 }, "end": { - "line": 621, + "line": 637, "column": 86 } }, "callee": { "type": "Identifier", - "start": 24689, - "end": 24704, + "start": 25129, + "end": 25144, "loc": { "start": { - "line": 621, + "line": 637, "column": 53 }, "end": { - "line": 621, + "line": 637, "column": 68 }, "identifierName": "CitationWrapper" @@ -72868,15 +74428,15 @@ "arguments": [ { "type": "Identifier", - "start": 24705, - "end": 24721, + "start": 25145, + "end": 25161, "loc": { "start": { - "line": 621, + "line": 637, "column": 69 }, "end": { - "line": 621, + "line": 637, "column": 85 }, "identifierName": "definitionSource" @@ -72887,15 +74447,15 @@ }, "property": { "type": "Identifier", - "start": 24723, - "end": 24731, + "start": 25163, + "end": 25171, "loc": { "start": { - "line": 621, + "line": 637, "column": 87 }, "end": { - "line": 621, + "line": 637, "column": 95 }, "identifierName": "toString" @@ -72922,15 +74482,15 @@ { "type": "CommentLine", "value": " If we don't have a bibliographicCitation but we do have a definition source,", - "start": 24315, - "end": 24394, + "start": 24755, + "end": 24834, "loc": { "start": { - "line": 616, + "line": 632, "column": 4 }, "end": { - "line": 616, + "line": 632, "column": 83 } } @@ -72938,15 +74498,15 @@ { "type": "CommentLine", "value": " then generate a bibliographicCitation for the source.", - "start": 24399, - "end": 24455, + "start": 24839, + "end": 24895, "loc": { "start": { - "line": 617, + "line": 633, "column": 4 }, "end": { - "line": 617, + "line": 633, "column": 60 } } @@ -72956,15 +74516,15 @@ { "type": "CommentLine", "value": " Construct a class expression for this phyloreference.", - "start": 24754, - "end": 24810, + "start": 25194, + "end": 25250, "loc": { "start": { - "line": 625, + "line": 641, "column": 4 }, "end": { - "line": 625, + "line": 641, "column": 60 } } @@ -72973,44 +74533,44 @@ }, { "type": "VariableDeclaration", - "start": 24815, - "end": 24884, + "start": 25255, + "end": 25324, "loc": { "start": { - "line": 626, + "line": 642, "column": 4 }, "end": { - "line": 626, + "line": 642, "column": 73 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24821, - "end": 24883, + "start": 25261, + "end": 25323, "loc": { "start": { - "line": 626, + "line": 642, "column": 10 }, "end": { - "line": 626, + "line": 642, "column": 72 } }, "id": { "type": "Identifier", - "start": 24821, - "end": 24839, + "start": 25261, + "end": 25279, "loc": { "start": { - "line": 626, + "line": 642, "column": 10 }, "end": { - "line": 626, + "line": 642, "column": 28 }, "identifierName": "internalSpecifiers" @@ -73020,43 +74580,43 @@ }, "init": { "type": "LogicalExpression", - "start": 24842, - "end": 24883, + "start": 25282, + "end": 25323, "loc": { "start": { - "line": 626, + "line": 642, "column": 31 }, "end": { - "line": 626, + "line": 642, "column": 72 } }, "left": { "type": "MemberExpression", - "start": 24842, - "end": 24877, + "start": 25282, + "end": 25317, "loc": { "start": { - "line": 626, + "line": 642, "column": 31 }, "end": { - "line": 626, + "line": 642, "column": 66 } }, "object": { "type": "Identifier", - "start": 24842, - "end": 24858, + "start": 25282, + "end": 25298, "loc": { "start": { - "line": 626, + "line": 642, "column": 31 }, "end": { - "line": 626, + "line": 642, "column": 47 }, "identifierName": "phylorefAsJSONLD" @@ -73065,15 +74625,15 @@ }, "property": { "type": "Identifier", - "start": 24859, - "end": 24877, + "start": 25299, + "end": 25317, "loc": { "start": { - "line": 626, + "line": 642, "column": 48 }, "end": { - "line": 626, + "line": 642, "column": 66 }, "identifierName": "internalSpecifiers" @@ -73085,15 +74645,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 24881, - "end": 24883, + "start": 25321, + "end": 25323, "loc": { "start": { - "line": 626, + "line": 642, "column": 70 }, "end": { - "line": 626, + "line": 642, "column": 72 } }, @@ -73108,15 +74668,15 @@ { "type": "CommentLine", "value": " Construct a class expression for this phyloreference.", - "start": 24754, - "end": 24810, + "start": 25194, + "end": 25250, "loc": { "start": { - "line": 625, + "line": 641, "column": 4 }, "end": { - "line": 625, + "line": 641, "column": 60 } } @@ -73125,44 +74685,44 @@ }, { "type": "VariableDeclaration", - "start": 24889, - "end": 24958, + "start": 25329, + "end": 25398, "loc": { "start": { - "line": 627, + "line": 643, "column": 4 }, "end": { - "line": 627, + "line": 643, "column": 73 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 24895, - "end": 24957, + "start": 25335, + "end": 25397, "loc": { "start": { - "line": 627, + "line": 643, "column": 10 }, "end": { - "line": 627, + "line": 643, "column": 72 } }, "id": { "type": "Identifier", - "start": 24895, - "end": 24913, + "start": 25335, + "end": 25353, "loc": { "start": { - "line": 627, + "line": 643, "column": 10 }, "end": { - "line": 627, + "line": 643, "column": 28 }, "identifierName": "externalSpecifiers" @@ -73171,43 +74731,43 @@ }, "init": { "type": "LogicalExpression", - "start": 24916, - "end": 24957, + "start": 25356, + "end": 25397, "loc": { "start": { - "line": 627, + "line": 643, "column": 31 }, "end": { - "line": 627, + "line": 643, "column": 72 } }, "left": { "type": "MemberExpression", - "start": 24916, - "end": 24951, + "start": 25356, + "end": 25391, "loc": { "start": { - "line": 627, + "line": 643, "column": 31 }, "end": { - "line": 627, + "line": 643, "column": 66 } }, "object": { "type": "Identifier", - "start": 24916, - "end": 24932, + "start": 25356, + "end": 25372, "loc": { "start": { - "line": 627, + "line": 643, "column": 31 }, "end": { - "line": 627, + "line": 643, "column": 47 }, "identifierName": "phylorefAsJSONLD" @@ -73216,15 +74776,15 @@ }, "property": { "type": "Identifier", - "start": 24933, - "end": 24951, + "start": 25373, + "end": 25391, "loc": { "start": { - "line": 627, + "line": 643, "column": 48 }, "end": { - "line": 627, + "line": 643, "column": 66 }, "identifierName": "externalSpecifiers" @@ -73236,15 +74796,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 24955, - "end": 24957, + "start": 25395, + "end": 25397, "loc": { "start": { - "line": 627, + "line": 643, "column": 70 }, "end": { - "line": 627, + "line": 643, "column": 72 } }, @@ -73258,15 +74818,15 @@ { "type": "CommentLine", "value": " If it is an apomorphy-based class expression, we should generate a", - "start": 24964, - "end": 25033, + "start": 25404, + "end": 25473, "loc": { "start": { - "line": 629, + "line": 645, "column": 4 }, "end": { - "line": 629, + "line": 645, "column": 73 } } @@ -73274,15 +74834,15 @@ { "type": "CommentLine", "value": " logical expression that describes the apomorphy.", - "start": 25038, - "end": 25089, + "start": 25478, + "end": 25529, "loc": { "start": { - "line": 630, + "line": 646, "column": 4 }, "end": { - "line": 630, + "line": 646, "column": 55 } } @@ -73291,44 +74851,44 @@ }, { "type": "VariableDeclaration", - "start": 25094, - "end": 25145, + "start": 25534, + "end": 25585, "loc": { "start": { - "line": 631, + "line": 647, "column": 4 }, "end": { - "line": 631, + "line": 647, "column": 55 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 25100, - "end": 25144, + "start": 25540, + "end": 25584, "loc": { "start": { - "line": 631, + "line": 647, "column": 10 }, "end": { - "line": 631, + "line": 647, "column": 54 } }, "id": { "type": "Identifier", - "start": 25100, - "end": 25112, + "start": 25540, + "end": 25552, "loc": { "start": { - "line": 631, + "line": 647, "column": 10 }, "end": { - "line": 631, + "line": 647, "column": 22 }, "identifierName": "phylorefType" @@ -73338,29 +74898,29 @@ }, "init": { "type": "MemberExpression", - "start": 25115, - "end": 25144, + "start": 25555, + "end": 25584, "loc": { "start": { - "line": 631, + "line": 647, "column": 25 }, "end": { - "line": 631, + "line": 647, "column": 54 } }, "object": { "type": "Identifier", - "start": 25115, - "end": 25131, + "start": 25555, + "end": 25571, "loc": { "start": { - "line": 631, + "line": 647, "column": 25 }, "end": { - "line": 631, + "line": 647, "column": 41 }, "identifierName": "phylorefAsJSONLD" @@ -73369,15 +74929,15 @@ }, "property": { "type": "Identifier", - "start": 25132, - "end": 25144, + "start": 25572, + "end": 25584, "loc": { "start": { - "line": 631, + "line": 647, "column": 42 }, "end": { - "line": 631, + "line": 647, "column": 54 }, "identifierName": "phylorefType" @@ -73394,15 +74954,15 @@ { "type": "CommentLine", "value": " If it is an apomorphy-based class expression, we should generate a", - "start": 24964, - "end": 25033, + "start": 25404, + "end": 25473, "loc": { "start": { - "line": 629, + "line": 645, "column": 4 }, "end": { - "line": 629, + "line": 645, "column": 73 } } @@ -73410,15 +74970,15 @@ { "type": "CommentLine", "value": " logical expression that describes the apomorphy.", - "start": 25038, - "end": 25089, + "start": 25478, + "end": 25529, "loc": { "start": { - "line": 630, + "line": 646, "column": 4 }, "end": { - "line": 630, + "line": 646, "column": 55 } } @@ -73427,57 +74987,57 @@ }, { "type": "IfStatement", - "start": 25150, - "end": 25776, + "start": 25590, + "end": 26216, "loc": { "start": { - "line": 632, + "line": 648, "column": 4 }, "end": { - "line": 648, + "line": 664, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 25161, - "end": 25281, + "start": 25601, + "end": 25721, "loc": { "start": { - "line": 633, + "line": 649, "column": 6 }, "end": { - "line": 634, + "line": 650, "column": 45 } }, "left": { "type": "LogicalExpression", - "start": 25162, - "end": 25234, + "start": 25602, + "end": 25674, "loc": { "start": { - "line": 633, + "line": 649, "column": 7 }, "end": { - "line": 633, + "line": 649, "column": 79 } }, "left": { "type": "Identifier", - "start": 25162, - "end": 25174, + "start": 25602, + "end": 25614, "loc": { "start": { - "line": 633, + "line": 649, "column": 7 }, "end": { - "line": 633, + "line": 649, "column": 19 }, "identifierName": "phylorefType" @@ -73487,29 +75047,29 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 25178, - "end": 25234, + "start": 25618, + "end": 25674, "loc": { "start": { - "line": 633, + "line": 649, "column": 23 }, "end": { - "line": 633, + "line": 649, "column": 79 } }, "left": { "type": "Identifier", - "start": 25178, - "end": 25190, + "start": 25618, + "end": 25630, "loc": { "start": { - "line": 633, + "line": 649, "column": 23 }, "end": { - "line": 633, + "line": 649, "column": 35 }, "identifierName": "phylorefType" @@ -73519,15 +75079,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 25195, - "end": 25234, + "start": 25635, + "end": 25674, "loc": { "start": { - "line": 633, + "line": 649, "column": 40 }, "end": { - "line": 633, + "line": 649, "column": 79 } }, @@ -73540,35 +75100,35 @@ }, "extra": { "parenthesized": true, - "parenStart": 25161 + "parenStart": 25601 } }, "operator": "||", "right": { "type": "CallExpression", - "start": 25246, - "end": 25280, + "start": 25686, + "end": 25720, "loc": { "start": { - "line": 634, + "line": 650, "column": 10 }, "end": { - "line": 634, + "line": 650, "column": 44 } }, "callee": { "type": "Identifier", - "start": 25246, - "end": 25249, + "start": 25686, + "end": 25689, "loc": { "start": { - "line": 634, + "line": 650, "column": 10 }, "end": { - "line": 634, + "line": 650, "column": 13 }, "identifierName": "has" @@ -73578,15 +75138,15 @@ "arguments": [ { "type": "Identifier", - "start": 25250, - "end": 25266, + "start": 25690, + "end": 25706, "loc": { "start": { - "line": 634, + "line": 650, "column": 14 }, "end": { - "line": 634, + "line": 650, "column": 30 }, "identifierName": "phylorefAsJSONLD" @@ -73595,15 +75155,15 @@ }, { "type": "StringLiteral", - "start": 25268, - "end": 25279, + "start": 25708, + "end": 25719, "loc": { "start": { - "line": 634, + "line": 650, "column": 32 }, "end": { - "line": 634, + "line": 650, "column": 43 } }, @@ -73616,79 +75176,79 @@ ], "extra": { "parenthesized": true, - "parenStart": 25245 + "parenStart": 25685 } } }, "consequent": { "type": "BlockStatement", - "start": 25288, - "end": 25776, + "start": 25728, + "end": 26216, "loc": { "start": { - "line": 635, + "line": 651, "column": 6 }, "end": { - "line": 648, + "line": 664, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 25344, - "end": 25468, + "start": 25784, + "end": 25908, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 640, + "line": 656, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 25344, - "end": 25467, + "start": 25784, + "end": 25907, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 640, + "line": 656, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 25344, - "end": 25371, + "start": 25784, + "end": 25811, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 637, + "line": 653, "column": 33 } }, "object": { "type": "Identifier", - "start": 25344, - "end": 25360, + "start": 25784, + "end": 25800, "loc": { "start": { - "line": 637, + "line": 653, "column": 6 }, "end": { - "line": 637, + "line": 653, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -73698,15 +75258,15 @@ }, "property": { "type": "Identifier", - "start": 25361, - "end": 25371, + "start": 25801, + "end": 25811, "loc": { "start": { - "line": 637, + "line": 653, "column": 23 }, "end": { - "line": 637, + "line": 653, "column": 33 }, "identifierName": "subClassOf" @@ -73718,30 +75278,30 @@ }, "right": { "type": "ArrayExpression", - "start": 25374, - "end": 25467, + "start": 25814, + "end": 25907, "loc": { "start": { - "line": 637, + "line": 653, "column": 36 }, "end": { - "line": 640, + "line": 656, "column": 7 } }, "elements": [ { "type": "StringLiteral", - "start": 25384, - "end": 25409, + "start": 25824, + "end": 25849, "loc": { "start": { - "line": 638, + "line": 654, "column": 8 }, "end": { - "line": 638, + "line": 654, "column": 33 } }, @@ -73753,15 +75313,15 @@ }, { "type": "StringLiteral", - "start": 25419, - "end": 25458, + "start": 25859, + "end": 25898, "loc": { "start": { - "line": 639, + "line": 655, "column": 8 }, "end": { - "line": 639, + "line": 655, "column": 47 } }, @@ -73779,15 +75339,15 @@ { "type": "CommentLine", "value": " This is an apomorphy-based definition!", - "start": 25296, - "end": 25337, + "start": 25736, + "end": 25777, "loc": { "start": { - "line": 636, + "line": 652, "column": 6 }, "end": { - "line": 636, + "line": 652, "column": 47 } } @@ -73797,15 +75357,15 @@ { "type": "CommentLine", "value": " Someday, we will probably want to turn this apomorphy into a", - "start": 25476, - "end": 25539, + "start": 25916, + "end": 25979, "loc": { "start": { - "line": 642, + "line": 658, "column": 6 }, "end": { - "line": 642, + "line": 658, "column": 69 } } @@ -73813,15 +75373,15 @@ { "type": "CommentLine", "value": " logical expression so that it can be computed alongside other", - "start": 25546, - "end": 25610, + "start": 25986, + "end": 26050, "loc": { "start": { - "line": 643, + "line": 659, "column": 6 }, "end": { - "line": 643, + "line": 659, "column": 70 } } @@ -73829,15 +75389,15 @@ { "type": "CommentLine", "value": " OWL ontologies. This is outside our scope for the moment, so", - "start": 25617, - "end": 25680, + "start": 26057, + "end": 26120, "loc": { "start": { - "line": 644, + "line": 660, "column": 6 }, "end": { - "line": 644, + "line": 660, "column": 69 } } @@ -73845,15 +75405,15 @@ { "type": "CommentLine", "value": " we will simply pass on the phyloreference as-is.", - "start": 25687, - "end": 25738, + "start": 26127, + "end": 26178, "loc": { "start": { - "line": 645, + "line": 661, "column": 6 }, "end": { - "line": 645, + "line": 661, "column": 57 } } @@ -73862,29 +75422,29 @@ }, { "type": "ReturnStatement", - "start": 25746, - "end": 25770, + "start": 26186, + "end": 26210, "loc": { "start": { - "line": 647, + "line": 663, "column": 6 }, "end": { - "line": 647, + "line": 663, "column": 30 } }, "argument": { "type": "Identifier", - "start": 25753, - "end": 25769, + "start": 26193, + "end": 26209, "loc": { "start": { - "line": 647, + "line": 663, "column": 13 }, "end": { - "line": 647, + "line": 663, "column": 29 }, "identifierName": "phylorefAsJSONLD" @@ -73896,15 +75456,15 @@ { "type": "CommentLine", "value": " Someday, we will probably want to turn this apomorphy into a", - "start": 25476, - "end": 25539, + "start": 25916, + "end": 25979, "loc": { "start": { - "line": 642, + "line": 658, "column": 6 }, "end": { - "line": 642, + "line": 658, "column": 69 } } @@ -73912,15 +75472,15 @@ { "type": "CommentLine", "value": " logical expression so that it can be computed alongside other", - "start": 25546, - "end": 25610, + "start": 25986, + "end": 26050, "loc": { "start": { - "line": 643, + "line": 659, "column": 6 }, "end": { - "line": 643, + "line": 659, "column": 70 } } @@ -73928,15 +75488,15 @@ { "type": "CommentLine", "value": " OWL ontologies. This is outside our scope for the moment, so", - "start": 25617, - "end": 25680, + "start": 26057, + "end": 26120, "loc": { "start": { - "line": 644, + "line": 660, "column": 6 }, "end": { - "line": 644, + "line": 660, "column": 69 } } @@ -73944,15 +75504,15 @@ { "type": "CommentLine", "value": " we will simply pass on the phyloreference as-is.", - "start": 25687, - "end": 25738, + "start": 26127, + "end": 26178, "loc": { "start": { - "line": 645, + "line": 661, "column": 6 }, "end": { - "line": 645, + "line": 661, "column": 57 } } @@ -73968,15 +75528,15 @@ { "type": "CommentLine", "value": " We might need to make component classes.", - "start": 25782, - "end": 25825, + "start": 26222, + "end": 26265, "loc": { "start": { - "line": 650, + "line": 666, "column": 4 }, "end": { - "line": 650, + "line": 666, "column": 47 } } @@ -73984,15 +75544,15 @@ { "type": "CommentLine", "value": " So we reset our component class counts and records.", - "start": 25830, - "end": 25884, + "start": 26270, + "end": 26324, "loc": { "start": { - "line": 651, + "line": 667, "column": 4 }, "end": { - "line": 651, + "line": 667, "column": 58 } } @@ -74001,58 +75561,58 @@ }, { "type": "ExpressionStatement", - "start": 25889, - "end": 25918, + "start": 26329, + "end": 26358, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 33 } }, "expression": { "type": "AssignmentExpression", - "start": 25889, - "end": 25917, + "start": 26329, + "end": 26357, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 32 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 25889, - "end": 25913, + "start": 26329, + "end": 26353, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 25889, - "end": 25893, + "start": 26329, + "end": 26333, "loc": { "start": { - "line": 652, + "line": 668, "column": 4 }, "end": { - "line": 652, + "line": 668, "column": 8 } }, @@ -74060,15 +75620,15 @@ }, "property": { "type": "Identifier", - "start": 25894, - "end": 25913, + "start": 26334, + "end": 26353, "loc": { "start": { - "line": 652, + "line": 668, "column": 9 }, "end": { - "line": 652, + "line": 668, "column": 28 }, "identifierName": "componentClassCount" @@ -74080,15 +75640,15 @@ }, "right": { "type": "NumericLiteral", - "start": 25916, - "end": 25917, + "start": 26356, + "end": 26357, "loc": { "start": { - "line": 652, + "line": 668, "column": 31 }, "end": { - "line": 652, + "line": 668, "column": 32 } }, @@ -74104,15 +75664,15 @@ { "type": "CommentLine", "value": " We might need to make component classes.", - "start": 25782, - "end": 25825, + "start": 26222, + "end": 26265, "loc": { "start": { - "line": 650, + "line": 666, "column": 4 }, "end": { - "line": 650, + "line": 666, "column": 47 } } @@ -74120,15 +75680,15 @@ { "type": "CommentLine", "value": " So we reset our component class counts and records.", - "start": 25830, - "end": 25884, + "start": 26270, + "end": 26324, "loc": { "start": { - "line": 651, + "line": 667, "column": 4 }, "end": { - "line": 651, + "line": 667, "column": 58 } } @@ -74137,73 +75697,73 @@ }, { "type": "ExpressionStatement", - "start": 25923, - "end": 25957, + "start": 26363, + "end": 26397, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 25923, - "end": 25956, + "start": 26363, + "end": 26396, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 25923, - "end": 25951, + "start": 26363, + "end": 26391, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 25923, - "end": 25927, + "start": 26363, + "end": 26367, "loc": { "start": { - "line": 653, + "line": 669, "column": 4 }, "end": { - "line": 653, + "line": 669, "column": 8 } } }, "property": { "type": "Identifier", - "start": 25928, - "end": 25951, + "start": 26368, + "end": 26391, "loc": { "start": { - "line": 653, + "line": 669, "column": 9 }, "end": { - "line": 653, + "line": 669, "column": 32 }, "identifierName": "componentClassesByLabel" @@ -74214,15 +75774,15 @@ }, "right": { "type": "ObjectExpression", - "start": 25954, - "end": 25956, + "start": 26394, + "end": 26396, "loc": { "start": { - "line": 653, + "line": 669, "column": 35 }, "end": { - "line": 653, + "line": 669, "column": 37 } }, @@ -74233,15 +75793,15 @@ { "type": "CommentLine", "value": " The type of this phyloreference.", - "start": 25963, - "end": 25998, + "start": 26403, + "end": 26438, "loc": { "start": { - "line": 655, + "line": 671, "column": 4 }, "end": { - "line": 655, + "line": 671, "column": 39 } } @@ -74250,44 +75810,44 @@ }, { "type": "VariableDeclaration", - "start": 26003, - "end": 26030, + "start": 26443, + "end": 26470, "loc": { "start": { - "line": 656, + "line": 672, "column": 4 }, "end": { - "line": 656, + "line": 672, "column": 31 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 26007, - "end": 26029, + "start": 26447, + "end": 26469, "loc": { "start": { - "line": 656, + "line": 672, "column": 8 }, "end": { - "line": 656, + "line": 672, "column": 30 } }, "id": { "type": "Identifier", - "start": 26007, - "end": 26029, + "start": 26447, + "end": 26469, "loc": { "start": { - "line": 656, + "line": 672, "column": 8 }, "end": { - "line": 656, + "line": 672, "column": 30 }, "identifierName": "calculatedPhylorefType" @@ -74304,15 +75864,15 @@ { "type": "CommentLine", "value": " The type of this phyloreference.", - "start": 25963, - "end": 25998, + "start": 26403, + "end": 26438, "loc": { "start": { - "line": 655, + "line": 671, "column": 4 }, "end": { - "line": 655, + "line": 671, "column": 39 } } @@ -74322,15 +75882,15 @@ { "type": "CommentLine", "value": " The list of logical expressions generated for this phyloref.", - "start": 26036, - "end": 26099, + "start": 26476, + "end": 26539, "loc": { "start": { - "line": 658, + "line": 674, "column": 4 }, "end": { - "line": 658, + "line": 674, "column": 67 } } @@ -74339,44 +75899,44 @@ }, { "type": "VariableDeclaration", - "start": 26104, - "end": 26132, + "start": 26544, + "end": 26572, "loc": { "start": { - "line": 659, + "line": 675, "column": 4 }, "end": { - "line": 659, + "line": 675, "column": 32 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 26108, - "end": 26131, + "start": 26548, + "end": 26571, "loc": { "start": { - "line": 659, + "line": 675, "column": 8 }, "end": { - "line": 659, + "line": 675, "column": 31 } }, "id": { "type": "Identifier", - "start": 26108, - "end": 26126, + "start": 26548, + "end": 26566, "loc": { "start": { - "line": 659, + "line": 675, "column": 8 }, "end": { - "line": 659, + "line": 675, "column": 26 }, "identifierName": "logicalExpressions" @@ -74386,15 +75946,15 @@ }, "init": { "type": "ArrayExpression", - 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"start": 26142, - "end": 26167, + "start": 26582, + "end": 26607, "loc": { "start": { - "line": 661, + "line": 677, "column": 8 }, "end": { - "line": 661, + "line": 677, "column": 33 } }, "object": { "type": "Identifier", - "start": 26142, - "end": 26160, + "start": 26582, + "end": 26600, "loc": { "start": { - "line": 661, + "line": 677, "column": 8 }, "end": { - "line": 661, + "line": 677, "column": 26 }, "identifierName": "internalSpecifiers" @@ -74484,15 +76044,15 @@ }, "property": { "type": "Identifier", - "start": 26161, - "end": 26167, + "start": 26601, + "end": 26607, "loc": { "start": { - "line": 661, + "line": 677, "column": 27 }, "end": { - "line": 661, + "line": 677, "column": 33 }, "identifierName": "length" @@ -74504,15 +76064,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 26172, - "end": 26173, + "start": 26612, + "end": 26613, "loc": { "start": { - "line": 661, + "line": 677, "column": 38 }, "end": { - "line": 661, + "line": 677, "column": 39 } }, @@ -74525,59 +76085,59 @@ }, "consequent": { "type": "BlockStatement", - 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"start": 26290, - "end": 26324, + "start": 26730, + "end": 26764, "loc": { "start": { - "line": 663, + "line": 679, "column": 31 }, "end": { - "line": 663, + "line": 679, "column": 65 } }, @@ -74611,15 +76171,15 @@ { "type": "CommentLine", "value": " We can't handle phyloreferences without at least one internal specifier.", - "start": 26183, - "end": 26258, + "start": 26623, + "end": 26698, "loc": { "start": { - "line": 662, + "line": 678, "column": 6 }, "end": { - "line": 662, + "line": 678, "column": 81 } } @@ -74628,58 +76188,58 @@ }, { "type": "ExpressionStatement", - "start": 26332, - "end": 26409, + "start": 26772, + "end": 26849, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 83 } }, "expression": { "type": "AssignmentExpression", - "start": 26332, - "end": 26408, + "start": 26772, + "end": 26848, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 82 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 26332, - "end": 26372, + "start": 26772, + "end": 26812, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 46 } }, "object": { "type": "Identifier", - "start": 26332, - "end": 26348, + "start": 26772, + "end": 26788, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -74688,15 +76248,15 @@ }, "property": { "type": "Identifier", - "start": 26349, - "end": 26372, + "start": 26789, + "end": 26812, "loc": { "start": { - "line": 664, + "line": 680, "column": 23 }, "end": { - "line": 664, + "line": 680, "column": 46 }, "identifierName": "malformedPhyloreference" @@ -74707,15 +76267,15 @@ }, "right": { "type": "StringLiteral", - "start": 26375, - "end": 26408, + "start": 26815, + "end": 26848, "loc": { "start": { - "line": 664, + "line": 680, "column": 49 }, "end": { - "line": 664, + "line": 680, "column": 82 } }, @@ -74732,57 +76292,57 @@ }, "alternate": { "type": "IfStatement", - "start": 26421, - "end": 28955, + "start": 26861, + "end": 29395, "loc": { "start": { - "line": 665, + "line": 681, "column": 11 }, "end": { - "line": 729, + "line": 745, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 26425, - "end": 26454, + "start": 26865, + "end": 26894, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 44 } }, "left": { "type": "MemberExpression", - "start": 26425, - "end": 26450, + "start": 26865, + "end": 26890, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 40 } }, "object": { "type": "Identifier", - "start": 26425, - "end": 26443, + "start": 26865, + "end": 26883, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 33 }, "identifierName": "externalSpecifiers" @@ -74791,15 +76351,15 @@ }, "property": { "type": "Identifier", - "start": 26444, - "end": 26450, + "start": 26884, + "end": 26890, "loc": { "start": { - "line": 665, + "line": 681, "column": 34 }, "end": { - "line": 665, + "line": 681, "column": 40 }, "identifierName": "length" @@ -74811,15 +76371,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 26453, - "end": 26454, + "start": 26893, + "end": 26894, "loc": { "start": { - "line": 665, + "line": 681, "column": 43 }, "end": { - "line": 665, + "line": 681, "column": 44 } }, @@ -74832,59 +76392,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 26456, - "end": 28577, + "start": 26896, + "end": 29017, "loc": { "start": { - "line": 665, + "line": 681, "column": 46 }, "end": { - "line": 721, + "line": 737, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 26464, - "end": 26532, + "start": 26904, + "end": 26972, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 74 } }, "expression": { "type": "AssignmentExpression", - "start": 26464, - "end": 26531, + "start": 26904, + "end": 26971, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 73 } }, "operator": "=", "left": { "type": "Identifier", - "start": 26464, - "end": 26486, + "start": 26904, + "end": 26926, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 28 }, "identifierName": "calculatedPhylorefType" @@ -74893,15 +76453,15 @@ }, "right": { "type": "StringLiteral", - "start": 26489, - "end": 26531, + "start": 26929, + "end": 26971, "loc": { "start": { - "line": 666, + "line": 682, "column": 31 }, "end": { - "line": 666, + "line": 682, "column": 73 } }, @@ -74916,15 +76476,15 @@ { "type": "CommentLine", "value": " If the phyloreference has at least one external specifier, we", - "start": 26540, - "end": 26604, + "start": 26980, + "end": 27044, "loc": { "start": { - "line": 668, + "line": 684, "column": 6 }, "end": { - "line": 668, + "line": 684, "column": 70 } } @@ -74932,15 +76492,15 @@ { "type": "CommentLine", "value": " can provide a simplified expression for the internal specifier,", - "start": 26611, - "end": 26677, + "start": 27051, + "end": 27117, "loc": { "start": { - "line": 669, + "line": 685, "column": 6 }, "end": { - "line": 669, + "line": 685, "column": 72 } } @@ -74948,15 +76508,15 @@ { "type": "CommentLine", "value": " in the form:", - "start": 26684, - "end": 26699, + "start": 27124, + "end": 27139, "loc": { "start": { - "line": 670, + "line": 686, "column": 6 }, "end": { - "line": 670, + "line": 686, "column": 21 } } @@ -74964,15 +76524,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal1] and", - "start": 26706, - "end": 26751, + "start": 27146, + "end": 27191, "loc": { "start": { - "line": 671, + "line": 687, "column": 6 }, "end": { - "line": 671, + "line": 687, "column": 51 } } @@ -74980,15 +76540,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal2] and ...", - "start": 26758, - "end": 26807, + "start": 27198, + "end": 27247, "loc": { "start": { - "line": 672, + "line": 688, "column": 6 }, "end": { - "line": 672, + "line": 688, "column": 55 } } @@ -74996,15 +76556,15 @@ { "type": "CommentLine", "value": " phyloref:excludes_TU some [exclusion1] and", - "start": 26814, - "end": 26860, + "start": 27254, + "end": 27300, "loc": { "start": { - "line": 673, + "line": 689, "column": 6 }, "end": { - "line": 673, + "line": 689, "column": 52 } } @@ -75012,15 +76572,15 @@ { "type": "CommentLine", "value": " has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...", - "start": 26867, - "end": 26932, + "start": 27307, + "end": 27372, "loc": { "start": { - "line": 674, + "line": 690, "column": 6 }, "end": { - "line": 674, + "line": 690, "column": 71 } } @@ -75028,15 +76588,15 @@ { "type": "CommentLine", "value": "", - "start": 26939, - "end": 26941, + "start": 27379, + "end": 27381, "loc": { "start": { - "line": 675, + "line": 691, "column": 6 }, "end": { - "line": 675, + "line": 691, "column": 8 } } @@ -75044,15 +76604,15 @@ { "type": "CommentLine", "value": " Since we don't know which of the external specifiers will actually", - "start": 26948, - "end": 27017, + "start": 27388, + "end": 27457, "loc": { "start": { - "line": 676, + "line": 692, "column": 6 }, "end": { - "line": 676, + "line": 692, "column": 75 } } @@ -75060,15 +76620,15 @@ { "type": "CommentLine", "value": " be the one that will be used, we need to generate logical expressions", - "start": 27024, - "end": 27096, + "start": 27464, + "end": 27536, "loc": { "start": { - "line": 677, + "line": 693, "column": 6 }, "end": { - "line": 677, + "line": 693, "column": 78 } } @@ -75076,15 +76636,15 @@ { "type": "CommentLine", "value": " for every possibility.", - "start": 27103, - "end": 27128, + "start": 27543, + "end": 27568, "loc": { "start": { - "line": 678, + "line": 694, "column": 6 }, "end": { - "line": 678, + "line": 694, "column": 31 } } @@ -75093,44 +76653,44 @@ }, { "type": "ExpressionStatement", - "start": 27136, - "end": 28571, + "start": 27576, + "end": 29011, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 720, + "line": 736, "column": 9 } }, "expression": { "type": "AssignmentExpression", - "start": 27136, - "end": 28570, + "start": 27576, + "end": 29010, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 720, + "line": 736, "column": 8 } }, "operator": "=", "left": { "type": "Identifier", - "start": 27136, - "end": 27154, + "start": 27576, + "end": 27594, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 680, + "line": 696, "column": 24 }, "identifierName": "logicalExpressions" @@ -75140,43 +76700,43 @@ }, "right": { "type": "CallExpression", - "start": 27157, - "end": 28570, + "start": 27597, + "end": 29010, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 720, + "line": 736, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 27157, - "end": 27179, + "start": 27597, + "end": 27619, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 680, + "line": 696, "column": 49 } }, "object": { "type": "Identifier", - "start": 27157, - "end": 27175, + "start": 27597, + "end": 27615, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 680, + "line": 696, "column": 45 }, "identifierName": "externalSpecifiers" @@ -75185,15 +76745,15 @@ }, "property": { "type": "Identifier", - "start": 27176, - "end": 27179, + "start": 27616, + "end": 27619, "loc": { "start": { - "line": 680, + "line": 696, "column": 46 }, "end": { - "line": 680, + "line": 696, "column": 49 }, "identifierName": "map" @@ -75205,15 +76765,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27180, - "end": 28569, + "start": 27620, + "end": 29009, "loc": { "start": { - "line": 680, + "line": 696, "column": 50 }, "end": { - "line": 720, + "line": 736, "column": 7 } }, @@ -75224,15 +76784,15 @@ "params": [ { "type": "Identifier", - "start": 27181, - "end": 27197, + "start": 27621, + "end": 27637, "loc": { "start": { - "line": 680, + "line": 696, "column": 51 }, "end": { - "line": 680, + "line": 696, "column": 67 }, "identifierName": "selectedExternal" @@ -75242,59 +76802,59 @@ ], "body": { "type": "BlockStatement", - "start": 27202, - "end": 28569, + "start": 27642, + "end": 29009, "loc": { "start": { - "line": 680, + "line": 696, "column": 72 }, "end": { - "line": 720, + "line": 736, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 27252, - "end": 27365, + "start": 27692, + "end": 27805, "loc": { "start": { - "line": 682, + "line": 698, "column": 8 }, "end": { - "line": 684, + "line": 700, "column": 10 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 27258, - "end": 27364, + "start": 27698, + "end": 27804, "loc": { "start": { - "line": 682, + "line": 698, "column": 14 }, "end": { - "line": 684, + "line": 700, "column": 9 } }, "id": { "type": "Identifier", - "start": 27258, - "end": 27275, + "start": 27698, + "end": 27715, "loc": { "start": { - "line": 682, + "line": 698, "column": 14 }, "end": { - "line": 682, + "line": 698, "column": 31 }, "identifierName": "intersectionExprs" @@ -75304,43 +76864,43 @@ }, "init": { "type": "CallExpression", - "start": 27278, - "end": 27364, + "start": 27718, + "end": 27804, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 684, + "line": 700, "column": 9 } }, "callee": { "type": "MemberExpression", - "start": 27278, - "end": 27300, + "start": 27718, + "end": 27740, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 682, + "line": 698, "column": 56 } }, "object": { "type": "Identifier", - "start": 27278, - "end": 27296, + "start": 27718, + "end": 27736, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 682, + "line": 698, "column": 52 }, "identifierName": "internalSpecifiers" @@ -75349,15 +76909,15 @@ }, "property": { "type": "Identifier", - "start": 27297, - "end": 27300, + "start": 27737, + "end": 27740, "loc": { "start": { - "line": 682, + "line": 698, "column": 53 }, "end": { - "line": 682, + "line": 698, "column": 56 }, "identifierName": "map" @@ -75369,15 +76929,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27312, - "end": 27354, + "start": 27752, + "end": 27794, "loc": { "start": { - "line": 683, + "line": 699, "column": 10 }, "end": { - "line": 683, + "line": 699, "column": 52 } }, @@ -75388,15 +76948,15 @@ "params": [ { "type": "Identifier", - "start": 27312, - "end": 27314, + "start": 27752, + "end": 27754, "loc": { "start": { - "line": 683, + "line": 699, "column": 10 }, "end": { - "line": 683, + "line": 699, "column": 12 }, "identifierName": "sp" @@ -75406,58 +76966,58 @@ ], "body": { "type": "CallExpression", - "start": 27318, - "end": 27354, + "start": 27758, + "end": 27794, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 52 } }, "callee": { "type": "MemberExpression", - "start": 27318, - "end": 27350, + "start": 27758, + "end": 27790, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 48 } }, "object": { "type": "ThisExpression", - "start": 27318, - "end": 27322, + "start": 27758, + "end": 27762, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 20 } } }, "property": { "type": "Identifier", - "start": 27323, - "end": 27350, + "start": 27763, + "end": 27790, "loc": { "start": { - "line": 683, + "line": 699, "column": 21 }, "end": { - "line": 683, + "line": 699, "column": 48 }, "identifierName": "getIncludesRestrictionForTU" @@ -75469,15 +77029,15 @@ "arguments": [ { "type": "Identifier", - "start": 27351, - "end": 27353, + "start": 27791, + "end": 27793, "loc": { "start": { - "line": 683, + "line": 699, "column": 49 }, "end": { - "line": 683, + "line": 699, "column": 51 }, "identifierName": "sp" @@ -75497,15 +77057,15 @@ { "type": "CommentLine", "value": " Add the internal specifiers.", - "start": 27212, - "end": 27243, + "start": 27652, + "end": 27683, "loc": { "start": { - "line": 681, + "line": 697, "column": 8 }, "end": { - "line": 681, + "line": 697, "column": 39 } } @@ -75515,15 +77075,15 @@ { "type": "CommentLine", "value": " Add the selected external specifier.", - "start": 27375, - "end": 27414, + "start": 27815, + "end": 27854, "loc": { "start": { - "line": 686, + "line": 702, "column": 8 }, "end": { - "line": 686, + "line": 702, "column": 47 } } @@ -75532,57 +77092,57 @@ }, { "type": "ExpressionStatement", - "start": 27423, - "end": 27688, + "start": 27863, + "end": 28128, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 694, + "line": 710, "column": 11 } }, "expression": { "type": "CallExpression", - "start": 27423, - "end": 27687, + "start": 27863, + "end": 28127, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 694, + "line": 710, "column": 10 } }, "callee": { "type": "MemberExpression", - "start": 27423, - "end": 27445, + "start": 27863, + "end": 27885, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 687, + "line": 703, "column": 30 } }, "object": { "type": "Identifier", - "start": 27423, - "end": 27440, + "start": 27863, + "end": 27880, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 687, + "line": 703, "column": 25 }, "identifierName": "intersectionExprs" @@ -75592,15 +77152,15 @@ }, "property": { "type": "Identifier", - "start": 27441, - "end": 27445, + "start": 27881, + "end": 27885, "loc": { "start": { - "line": 687, + "line": 703, "column": 26 }, "end": { - "line": 687, + "line": 703, "column": 30 }, "identifierName": "push" @@ -75613,30 +77173,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 27446, - "end": 27686, + "start": 27886, + "end": 28126, "loc": { "start": { - "line": 687, + "line": 703, "column": 31 }, "end": { - "line": 694, + "line": 710, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 27458, - "end": 27484, + "start": 27898, + "end": 27924, "loc": { "start": { - "line": 688, + "line": 704, "column": 10 }, "end": { - "line": 688, + "line": 704, "column": 36 } }, @@ -75645,15 +77205,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 27458, - "end": 27465, + "start": 27898, + "end": 27905, "loc": { "start": { - "line": 688, + "line": 704, "column": 10 }, "end": { - "line": 688, + "line": 704, "column": 17 } }, @@ -75665,15 +77225,15 @@ }, "value": { "type": "StringLiteral", - "start": 27467, - "end": 27484, + "start": 27907, + "end": 27924, "loc": { "start": { - "line": 688, + "line": 704, "column": 19 }, "end": { - "line": 688, + "line": 704, "column": 36 } }, @@ -75686,15 +77246,15 @@ }, { "type": "ObjectProperty", - "start": 27496, - "end": 27530, + "start": 27936, + "end": 27970, "loc": { "start": { - "line": 689, + "line": 705, "column": 10 }, "end": { - "line": 689, + "line": 705, "column": 44 } }, @@ -75703,15 +77263,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 27496, - "end": 27506, + "start": 27936, + "end": 27946, "loc": { "start": { - "line": 689, + "line": 705, "column": 10 }, "end": { - "line": 689, + "line": 705, "column": 20 }, "identifierName": "onProperty" @@ -75720,15 +77280,15 @@ }, "value": { "type": "StringLiteral", - "start": 27508, - "end": 27530, + "start": 27948, + "end": 27970, "loc": { "start": { - "line": 689, + "line": 705, "column": 22 }, "end": { - "line": 689, + "line": 705, "column": 44 } }, @@ -75741,15 +77301,15 @@ }, { "type": "ObjectProperty", - "start": 27542, - "end": 27675, + "start": 27982, + "end": 28115, "loc": { "start": { - "line": 690, + "line": 706, "column": 10 }, "end": { - "line": 693, + "line": 709, "column": 27 } }, @@ -75758,15 +77318,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 27542, - "end": 27556, + "start": 27982, + "end": 27996, "loc": { "start": { - "line": 690, + "line": 706, "column": 10 }, "end": { - "line": 690, + "line": 706, "column": 24 }, "identifierName": "someValuesFrom" @@ -75775,43 +77335,43 @@ }, "value": { "type": "MemberExpression", - "start": 27558, - "end": 27675, + "start": 27998, + "end": 28115, "loc": { "start": { - "line": 690, + "line": 706, "column": 26 }, "end": { - "line": 693, + "line": 709, "column": 27 } }, "object": { "type": "NewExpression", - "start": 27558, - "end": 27659, + "start": 27998, + "end": 28099, "loc": { "start": { - "line": 690, + "line": 706, "column": 26 }, "end": { - "line": 693, + "line": 709, "column": 11 } }, "callee": { "type": "Identifier", - "start": 27562, - "end": 27582, + "start": 28002, + "end": 28022, "loc": { "start": { - "line": 690, + "line": 706, "column": 30 }, "end": { - "line": 690, + "line": 706, "column": 50 }, "identifierName": "TaxonomicUnitWrapper" @@ -75821,15 +77381,15 @@ "arguments": [ { "type": "Identifier", - "start": 27596, - "end": 27612, + "start": 28036, + "end": 28052, "loc": { "start": { - "line": 691, + "line": 707, "column": 12 }, "end": { - "line": 691, + "line": 707, "column": 28 }, "identifierName": "selectedExternal" @@ -75838,44 +77398,44 @@ }, { "type": "MemberExpression", - "start": 27626, - "end": 27647, + "start": 28066, + "end": 28087, "loc": { "start": { - "line": 692, + "line": 708, "column": 12 }, "end": { - "line": 692, + "line": 708, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 27626, - "end": 27630, + "start": 28066, + "end": 28070, "loc": { "start": { - "line": 692, + "line": 708, "column": 12 }, "end": { - "line": 692, + "line": 708, "column": 16 } } }, "property": { "type": "Identifier", - "start": 27631, - "end": 27647, + "start": 28071, + "end": 28087, "loc": { "start": { - "line": 692, + "line": 708, "column": 17 }, "end": { - "line": 692, + "line": 708, "column": 33 }, "identifierName": "defaultNomenCode" @@ -75888,15 +77448,15 @@ }, "property": { "type": "Identifier", - "start": 27660, - "end": 27675, + "start": 28100, + "end": 28115, "loc": { "start": { - "line": 693, + "line": 709, "column": 12 }, "end": { - "line": 693, + "line": 709, "column": 27 }, "identifierName": "asOWLEquivClass" @@ -75915,15 +77475,15 @@ { "type": "CommentLine", "value": " Add the selected external specifier.", - "start": 27375, - "end": 27414, + "start": 27815, + "end": 27854, "loc": { "start": { - "line": 686, + "line": 702, "column": 8 }, "end": { - "line": 686, + "line": 702, "column": 47 } } @@ -75933,15 +77493,15 @@ { "type": "CommentLine", "value": " Collect all of the externals that are not selected.", - "start": 27698, - "end": 27752, + "start": 28138, + "end": 28192, "loc": { "start": { - "line": 696, + "line": 712, "column": 8 }, "end": { - "line": 696, + "line": 712, "column": 62 } } @@ -75950,44 +77510,44 @@ }, { "type": "VariableDeclaration", - "start": 27761, - "end": 27845, + "start": 28201, + "end": 28285, "loc": { "start": { - "line": 697, + "line": 713, "column": 8 }, "end": { - "line": 697, + "line": 713, "column": 92 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 27767, - "end": 27844, + "start": 28207, + "end": 28284, "loc": { "start": { - "line": 697, + "line": 713, "column": 14 }, "end": { - "line": 697, + "line": 713, "column": 91 } }, "id": { "type": "Identifier", - "start": 27767, - "end": 27785, + "start": 28207, + "end": 28225, "loc": { "start": { - "line": 697, + "line": 713, "column": 14 }, "end": { - "line": 697, + "line": 713, "column": 32 }, "identifierName": "remainingExternals" @@ -75997,43 +77557,43 @@ }, "init": { "type": "CallExpression", - "start": 27788, - "end": 27844, + "start": 28228, + "end": 28284, "loc": { "start": { - "line": 697, + "line": 713, "column": 35 }, "end": { - "line": 697, + "line": 713, "column": 91 } }, "callee": { "type": "MemberExpression", - "start": 27788, - "end": 27813, + "start": 28228, + "end": 28253, "loc": { "start": { - "line": 697, + "line": 713, "column": 35 }, "end": { - "line": 697, + "line": 713, "column": 60 } }, "object": { "type": "Identifier", - "start": 27788, - "end": 27806, + "start": 28228, + "end": 28246, "loc": { "start": { - "line": 697, + "line": 713, "column": 35 }, "end": { - "line": 697, + "line": 713, "column": 53 }, "identifierName": "externalSpecifiers" @@ -76042,15 +77602,15 @@ }, "property": { "type": "Identifier", - "start": 27807, - "end": 27813, + "start": 28247, + "end": 28253, "loc": { "start": { - "line": 697, + "line": 713, "column": 54 }, "end": { - "line": 697, + "line": 713, "column": 60 }, "identifierName": "filter" @@ -76062,15 +77622,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27814, - "end": 27843, + "start": 28254, + "end": 28283, "loc": { "start": { - "line": 697, + "line": 713, "column": 61 }, "end": { - "line": 697, + "line": 713, "column": 90 } }, @@ -76081,15 +77641,15 @@ "params": [ { "type": "Identifier", - "start": 27814, - "end": 27816, + "start": 28254, + "end": 28256, "loc": { "start": { - "line": 697, + "line": 713, "column": 61 }, "end": { - "line": 697, + "line": 713, "column": 63 }, "identifierName": "ex" @@ -76099,29 +77659,29 @@ ], "body": { "type": "BinaryExpression", - "start": 27820, - "end": 27843, + "start": 28260, + "end": 28283, "loc": { "start": { - "line": 697, + "line": 713, "column": 67 }, "end": { - "line": 697, + "line": 713, "column": 90 } }, "left": { "type": "Identifier", - "start": 27820, - "end": 27822, + "start": 28260, + "end": 28262, "loc": { "start": { - "line": 697, + "line": 713, "column": 67 }, "end": { - "line": 697, + "line": 713, "column": 69 }, "identifierName": "ex" @@ -76131,15 +77691,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 27827, - "end": 27843, + "start": 28267, + "end": 28283, "loc": { "start": { - "line": 697, + "line": 713, "column": 74 }, "end": { - "line": 697, + "line": 713, "column": 90 }, "identifierName": "selectedExternal" @@ -76158,15 +77718,15 @@ { "type": "CommentLine", "value": " Collect all of the externals that are not selected.", - "start": 27698, - "end": 27752, + "start": 28138, + "end": 28192, "loc": { "start": { - "line": 696, + "line": 712, "column": 8 }, "end": { - "line": 696, + "line": 712, "column": 62 } } @@ -76176,15 +77736,15 @@ { "type": "CommentLine", "value": " Add the remaining externals, which we assume will resolve outside of", - "start": 27855, - "end": 27926, + "start": 28295, + "end": 28366, "loc": { "start": { - "line": 699, + "line": 715, "column": 8 }, "end": { - "line": 699, + "line": 715, "column": 79 } } @@ -76192,15 +77752,15 @@ { "type": "CommentLine", "value": " this clade.", - "start": 27935, - "end": 27949, + "start": 28375, + "end": 28389, "loc": { "start": { - "line": 700, + "line": 716, "column": 8 }, "end": { - "line": 700, + "line": 716, "column": 22 } } @@ -76209,57 +77769,57 @@ }, { "type": "ExpressionStatement", - "start": 27958, - "end": 28455, + "start": 28398, + "end": 28895, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 714, + "line": 730, "column": 11 } }, "expression": { "type": "CallExpression", - "start": 27958, - "end": 28454, + "start": 28398, + "end": 28894, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 714, + "line": 730, "column": 10 } }, "callee": { "type": "MemberExpression", - "start": 27958, - "end": 27984, + "start": 28398, + "end": 28424, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 701, + "line": 717, "column": 34 } }, "object": { "type": "Identifier", - "start": 27958, - "end": 27976, + "start": 28398, + "end": 28416, "loc": { "start": { - "line": 701, + "line": 717, "column": 8 }, "end": { - "line": 701, + "line": 717, "column": 26 }, "identifierName": "remainingExternals" @@ -76269,15 +77829,15 @@ }, "property": { "type": "Identifier", - "start": 27977, - "end": 27984, + "start": 28417, + "end": 28424, "loc": { "start": { - "line": 701, + "line": 717, "column": 27 }, "end": { - "line": 701, + "line": 717, "column": 34 }, "identifierName": "forEach" @@ -76290,15 +77850,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 27985, - "end": 28453, + "start": 28425, + "end": 28893, "loc": { "start": { - "line": 701, + "line": 717, "column": 35 }, "end": { - "line": 714, + "line": 730, "column": 9 } }, @@ -76309,15 +77869,15 @@ "params": [ { "type": "Identifier", - "start": 27986, - "end": 27996, + "start": 28426, + "end": 28436, "loc": { "start": { - "line": 701, + "line": 717, "column": 36 }, "end": { - "line": 701, + "line": 717, "column": 46 }, "identifierName": "externalTU" @@ -76327,72 +77887,72 @@ ], "body": { "type": "BlockStatement", - "start": 28001, - "end": 28453, + "start": 28441, + "end": 28893, "loc": { "start": { - "line": 701, + "line": 717, "column": 51 }, "end": { - "line": 714, + "line": 730, "column": 9 } }, "body": [ { "type": "ExpressionStatement", - "start": 28013, - "end": 28443, + "start": 28453, + "end": 28883, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 713, + "line": 729, "column": 13 } }, "expression": { "type": "CallExpression", - "start": 28013, - "end": 28442, + "start": 28453, + "end": 28882, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 713, + "line": 729, "column": 12 } }, "callee": { "type": "MemberExpression", - "start": 28013, - "end": 28035, + "start": 28453, + "end": 28475, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 702, + "line": 718, "column": 32 } }, "object": { "type": "Identifier", - "start": 28013, - "end": 28030, + "start": 28453, + "end": 28470, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 702, + "line": 718, "column": 27 }, "identifierName": "intersectionExprs" @@ -76401,15 +77961,15 @@ }, "property": { "type": "Identifier", - "start": 28031, - "end": 28035, + "start": 28471, + "end": 28475, "loc": { "start": { - "line": 702, + "line": 718, "column": 28 }, "end": { - "line": 702, + "line": 718, "column": 32 }, "identifierName": "push" @@ -76421,30 +77981,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 28036, - "end": 28441, + "start": 28476, + "end": 28881, "loc": { "start": { - "line": 702, + "line": 718, "column": 33 }, "end": { - "line": 713, + "line": 729, "column": 11 } }, "properties": [ { "type": "ObjectProperty", - "start": 28050, - "end": 28076, + "start": 28490, + "end": 28516, "loc": { "start": { - "line": 703, + "line": 719, "column": 12 }, "end": { - "line": 703, + "line": 719, "column": 38 } }, @@ -76453,15 +78013,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 28050, - "end": 28057, + "start": 28490, + "end": 28497, "loc": { "start": { - "line": 703, + "line": 719, "column": 12 }, "end": { - "line": 703, + "line": 719, "column": 19 } }, @@ -76473,15 +78033,15 @@ }, "value": { "type": "StringLiteral", - "start": 28059, - "end": 28076, + "start": 28499, + "end": 28516, "loc": { "start": { - "line": 703, + "line": 719, "column": 21 }, "end": { - "line": 703, + "line": 719, "column": 38 } }, @@ -76494,15 +78054,15 @@ }, { "type": "ObjectProperty", - "start": 28090, - "end": 28120, + "start": 28530, + "end": 28560, "loc": { "start": { - "line": 704, + "line": 720, "column": 12 }, "end": { - "line": 704, + "line": 720, "column": 42 } }, @@ -76511,15 +78071,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28090, - "end": 28100, + "start": 28530, + "end": 28540, "loc": { "start": { - "line": 704, + "line": 720, "column": 12 }, "end": { - "line": 704, + "line": 720, "column": 22 }, "identifierName": "onProperty" @@ -76528,15 +78088,15 @@ }, "value": { "type": "StringLiteral", - "start": 28102, - "end": 28120, + "start": 28542, + "end": 28560, "loc": { "start": { - "line": 704, + "line": 720, "column": 24 }, "end": { - "line": 704, + "line": 720, "column": 42 } }, @@ -76549,15 +78109,15 @@ }, { "type": "ObjectProperty", - "start": 28150, - "end": 28428, + "start": 28590, + "end": 28868, "loc": { "start": { - "line": 705, + "line": 721, "column": 12 }, "end": { - "line": 712, + "line": 728, "column": 13 } }, @@ -76566,15 +78126,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28150, - "end": 28164, + "start": 28590, + "end": 28604, "loc": { "start": { - "line": 705, + "line": 721, "column": 12 }, "end": { - "line": 705, + "line": 721, "column": 26 }, "identifierName": "someValuesFrom" @@ -76584,30 +78144,30 @@ }, "value": { "type": "ObjectExpression", - "start": 28166, - "end": 28428, + "start": 28606, + "end": 28868, "loc": { "start": { - "line": 705, + "line": 721, "column": 28 }, "end": { - "line": 712, + "line": 728, "column": 13 } }, "properties": [ { "type": "ObjectProperty", - "start": 28182, - "end": 28208, + "start": 28622, + "end": 28648, "loc": { "start": { - "line": 706, + "line": 722, "column": 14 }, "end": { - "line": 706, + "line": 722, "column": 40 } }, @@ -76616,15 +78176,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 28182, - "end": 28189, + "start": 28622, + "end": 28629, "loc": { "start": { - "line": 706, + "line": 722, "column": 14 }, "end": { - "line": 706, + "line": 722, "column": 21 } }, @@ -76636,15 +78196,15 @@ }, "value": { "type": "StringLiteral", - "start": 28191, - "end": 28208, + "start": 28631, + "end": 28648, "loc": { "start": { - "line": 706, + "line": 722, "column": 23 }, "end": { - "line": 706, + "line": 722, "column": 40 } }, @@ -76657,15 +78217,15 @@ }, { "type": "ObjectProperty", - "start": 28224, - "end": 28258, + "start": 28664, + "end": 28698, "loc": { "start": { - "line": 707, + "line": 723, "column": 14 }, "end": { - "line": 707, + "line": 723, "column": 48 } }, @@ -76674,15 +78234,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28224, - "end": 28234, + "start": 28664, + "end": 28674, "loc": { "start": { - "line": 707, + "line": 723, "column": 14 }, "end": { - "line": 707, + "line": 723, "column": 24 }, "identifierName": "onProperty" @@ -76691,15 +78251,15 @@ }, "value": { "type": "StringLiteral", - "start": 28236, - "end": 28258, + "start": 28676, + "end": 28698, "loc": { "start": { - "line": 707, + "line": 723, "column": 26 }, "end": { - "line": 707, + "line": 723, "column": 48 } }, @@ -76712,15 +78272,15 @@ }, { "type": "ObjectProperty", - "start": 28274, - "end": 28413, + "start": 28714, + "end": 28853, "loc": { "start": { - "line": 708, + "line": 724, "column": 14 }, "end": { - "line": 711, + "line": 727, "column": 31 } }, @@ -76729,15 +78289,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28274, - "end": 28288, + "start": 28714, + "end": 28728, "loc": { "start": { - "line": 708, + "line": 724, "column": 14 }, "end": { - "line": 708, + "line": 724, "column": 28 }, "identifierName": "someValuesFrom" @@ -76746,43 +78306,43 @@ }, "value": { "type": "MemberExpression", - "start": 28290, - "end": 28413, + "start": 28730, + "end": 28853, "loc": { "start": { - "line": 708, + "line": 724, "column": 30 }, "end": { - "line": 711, + "line": 727, "column": 31 } }, "object": { "type": "NewExpression", - "start": 28290, - "end": 28397, + "start": 28730, + "end": 28837, "loc": { "start": { - "line": 708, + "line": 724, "column": 30 }, "end": { - "line": 711, + "line": 727, "column": 15 } }, "callee": { "type": "Identifier", - "start": 28294, - "end": 28314, + "start": 28734, + "end": 28754, "loc": { "start": { - "line": 708, + "line": 724, "column": 34 }, "end": { - "line": 708, + "line": 724, "column": 54 }, "identifierName": "TaxonomicUnitWrapper" @@ -76792,15 +78352,15 @@ "arguments": [ { "type": "Identifier", - "start": 28332, - "end": 28342, + "start": 28772, + "end": 28782, "loc": { "start": { - "line": 709, + "line": 725, "column": 16 }, "end": { - "line": 709, + "line": 725, "column": 26 }, "identifierName": "externalTU" @@ -76809,44 +78369,44 @@ }, { "type": "MemberExpression", - "start": 28360, - "end": 28381, + "start": 28800, + "end": 28821, "loc": { "start": { - "line": 710, + "line": 726, "column": 16 }, "end": { - "line": 710, + "line": 726, "column": 37 } }, "object": { "type": "ThisExpression", - "start": 28360, - "end": 28364, + "start": 28800, + "end": 28804, "loc": { "start": { - "line": 710, + "line": 726, "column": 16 }, "end": { - "line": 710, + "line": 726, "column": 20 } } }, "property": { "type": "Identifier", - "start": 28365, - "end": 28381, + "start": 28805, + "end": 28821, "loc": { "start": { - "line": 710, + "line": 726, "column": 21 }, "end": { - "line": 710, + "line": 726, "column": 37 }, "identifierName": "defaultNomenCode" @@ -76859,15 +78419,15 @@ }, "property": { "type": "Identifier", - "start": 28398, - "end": 28413, + "start": 28838, + "end": 28853, "loc": { "start": { - "line": 711, + "line": 727, "column": 16 }, "end": { - "line": 711, + "line": 727, "column": 31 }, "identifierName": "asOWLEquivClass" @@ -76883,15 +78443,15 @@ { "type": "CommentLine", "value": " has_Ancestor", - "start": 28122, - "end": 28137, + "start": 28562, + "end": 28577, "loc": { "start": { - "line": 704, + "line": 720, "column": 44 }, "end": { - "line": 704, + "line": 720, "column": 59 } } @@ -76914,15 +78474,15 @@ { "type": "CommentLine", "value": " Add the remaining externals, which we assume will resolve outside of", - "start": 27855, - "end": 27926, + "start": 28295, + "end": 28366, "loc": { "start": { - "line": 699, + "line": 715, "column": 8 }, "end": { - "line": 699, + "line": 715, "column": 79 } } @@ -76930,15 +78490,15 @@ { "type": "CommentLine", "value": " this clade.", - "start": 27935, - "end": 27949, + "start": 28375, + "end": 28389, "loc": { "start": { - "line": 700, + "line": 716, "column": 8 }, "end": { - "line": 700, + "line": 716, "column": 22 } } @@ -76947,44 +78507,44 @@ }, { "type": "ReturnStatement", - "start": 28465, - "end": 28561, + "start": 28905, + "end": 29001, "loc": { "start": { - "line": 716, + "line": 732, "column": 8 }, "end": { - "line": 719, + "line": 735, "column": 10 } }, "argument": { "type": "ObjectExpression", - "start": 28472, - "end": 28560, + "start": 28912, + "end": 29000, "loc": { "start": { - "line": 716, + "line": 732, "column": 15 }, "end": { - "line": 719, + "line": 735, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 28484, - "end": 28504, + "start": 28924, + "end": 28944, "loc": { "start": { - "line": 717, + "line": 733, "column": 10 }, "end": { - "line": 717, + "line": 733, "column": 30 } }, @@ -76993,15 +78553,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 28484, - "end": 28491, + "start": 28924, + "end": 28931, "loc": { "start": { - "line": 717, + "line": 733, "column": 10 }, "end": { - "line": 717, + "line": 733, "column": 17 } }, @@ -77013,15 +78573,15 @@ }, "value": { "type": "StringLiteral", - "start": 28493, - "end": 28504, + "start": 28933, + "end": 28944, "loc": { "start": { - "line": 717, + "line": 733, "column": 19 }, "end": { - "line": 717, + "line": 733, "column": 30 } }, @@ -77034,15 +78594,15 @@ }, { "type": "ObjectProperty", - "start": 28516, - "end": 28549, + "start": 28956, + "end": 28989, "loc": { "start": { - "line": 718, + "line": 734, "column": 10 }, "end": { - "line": 718, + "line": 734, "column": 43 } }, @@ -77051,15 +78611,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 28516, - "end": 28530, + "start": 28956, + "end": 28970, "loc": { "start": { - "line": 718, + "line": 734, "column": 10 }, "end": { - "line": 718, + "line": 734, "column": 24 }, "identifierName": "intersectionOf" @@ -77068,15 +78628,15 @@ }, "value": { "type": "Identifier", - "start": 28532, - "end": 28549, + "start": 28972, + "end": 28989, "loc": { "start": { - "line": 718, + "line": 734, "column": 26 }, "end": { - "line": 718, + "line": 734, "column": 43 }, "identifierName": "intersectionExprs" @@ -77099,15 +78659,15 @@ { "type": "CommentLine", "value": " If the phyloreference has at least one external specifier, we", - "start": 26540, - "end": 26604, + "start": 26980, + "end": 27044, "loc": { "start": { - "line": 668, + "line": 684, "column": 6 }, "end": { - "line": 668, + "line": 684, "column": 70 } } @@ -77115,15 +78675,15 @@ { "type": "CommentLine", "value": " can provide a simplified expression for the internal specifier,", - "start": 26611, - "end": 26677, + "start": 27051, + "end": 27117, "loc": { "start": { - "line": 669, + "line": 685, "column": 6 }, "end": { - "line": 669, + "line": 685, "column": 72 } } @@ -77131,15 +78691,15 @@ { "type": "CommentLine", "value": " in the form:", - "start": 26684, - "end": 26699, + "start": 27124, + "end": 27139, "loc": { "start": { - "line": 670, + "line": 686, "column": 6 }, "end": { - "line": 670, + "line": 686, "column": 21 } } @@ -77147,15 +78707,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal1] and", - "start": 26706, - "end": 26751, + "start": 27146, + "end": 27191, "loc": { "start": { - "line": 671, + "line": 687, "column": 6 }, "end": { - "line": 671, + "line": 687, "column": 51 } } @@ -77163,15 +78723,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal2] and ...", - "start": 26758, - "end": 26807, + "start": 27198, + "end": 27247, "loc": { "start": { - "line": 672, + "line": 688, "column": 6 }, "end": { - "line": 672, + "line": 688, "column": 55 } } @@ -77179,15 +78739,15 @@ { "type": "CommentLine", "value": " phyloref:excludes_TU some [exclusion1] and", - "start": 26814, - "end": 26860, + "start": 27254, + "end": 27300, "loc": { "start": { - "line": 673, + "line": 689, "column": 6 }, "end": { - "line": 673, + "line": 689, "column": 52 } } @@ -77195,15 +78755,15 @@ { "type": "CommentLine", "value": " has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...", - "start": 26867, - "end": 26932, + "start": 27307, + "end": 27372, "loc": { "start": { - "line": 674, + "line": 690, "column": 6 }, "end": { - "line": 674, + "line": 690, "column": 71 } } @@ -77211,15 +78771,15 @@ { "type": "CommentLine", "value": "", - "start": 26939, - "end": 26941, + "start": 27379, + "end": 27381, "loc": { "start": { - "line": 675, + "line": 691, "column": 6 }, "end": { - "line": 675, + "line": 691, "column": 8 } } @@ -77227,15 +78787,15 @@ { "type": "CommentLine", "value": " Since we don't know which of the external specifiers will actually", - "start": 26948, - "end": 27017, + "start": 27388, + "end": 27457, "loc": { "start": { - "line": 676, + "line": 692, "column": 6 }, "end": { - "line": 676, + "line": 692, "column": 75 } } @@ -77243,15 +78803,15 @@ { "type": "CommentLine", "value": " be the one that will be used, we need to generate logical expressions", - "start": 27024, - "end": 27096, + "start": 27464, + "end": 27536, "loc": { "start": { - "line": 677, + "line": 693, "column": 6 }, "end": { - "line": 677, + "line": 693, "column": 78 } } @@ -77259,15 +78819,15 @@ { "type": "CommentLine", "value": " for every possibility.", - "start": 27103, - "end": 27128, + "start": 27543, + "end": 27568, "loc": { "start": { - "line": 678, + "line": 694, "column": 6 }, "end": { - "line": 678, + "line": 694, "column": 31 } } @@ -77279,59 +78839,59 @@ }, "alternate": { "type": "BlockStatement", - "start": 28583, - "end": 28955, + "start": 29023, + "end": 29395, "loc": { "start": { - "line": 721, + "line": 737, "column": 11 }, "end": { - "line": 729, + "line": 745, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 28591, - "end": 28659, + "start": 29031, + "end": 29099, "loc": { "start": { - "line": 722, + "line": 738, "column": 6 }, "end": { - "line": 722, + "line": 738, "column": 74 } }, "expression": { "type": "AssignmentExpression", - "start": 28591, - "end": 28658, + "start": 29031, + "end": 29098, "loc": { "start": { - "line": 722, + "line": 738, "column": 6 }, "end": { - "line": 722, + "line": 738, "column": 73 } }, "operator": "=", "left": { "type": "Identifier", - "start": 28591, - "end": 28613, + "start": 29031, + "end": 29053, "loc": { "start": { - "line": 722, + "line": 738, "column": 6 }, "end": { - "line": 722, + "line": 738, "column": 28 }, "identifierName": "calculatedPhylorefType" @@ -77340,15 +78900,15 @@ }, "right": { "type": "StringLiteral", - "start": 28616, - "end": 28658, + "start": 29056, + "end": 29098, "loc": { "start": { - "line": 722, + "line": 738, "column": 31 }, "end": { - "line": 722, + "line": 738, "column": 73 } }, @@ -77363,15 +78923,15 @@ { "type": "CommentLine", "value": " We only have internal specifiers. We therefore need to use the algorithm in", - "start": 28667, - "end": 28745, + "start": 29107, + "end": 29185, "loc": { "start": { - "line": 724, + "line": 740, "column": 6 }, "end": { - "line": 724, + "line": 740, "column": 84 } } @@ -77379,15 +78939,15 @@ { "type": "CommentLine", "value": " this.createClassExpressionsForInternals() to create this expression.", - "start": 28752, - "end": 28823, + "start": 29192, + "end": 29263, "loc": { "start": { - "line": 725, + "line": 741, "column": 6 }, "end": { - "line": 725, + "line": 741, "column": 77 } } @@ -77396,44 +78956,44 @@ }, { "type": "ExpressionStatement", - "start": 28830, - "end": 28949, + "start": 29270, + "end": 29389, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 728, + "line": 744, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 28830, - "end": 28948, + "start": 29270, + "end": 29388, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 728, + "line": 744, "column": 7 } }, "operator": "=", "left": { "type": "Identifier", - "start": 28830, - "end": 28848, + "start": 29270, + "end": 29288, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 726, + "line": 742, "column": 24 }, "identifierName": "logicalExpressions" @@ -77443,58 +79003,58 @@ }, "right": { "type": "CallExpression", - "start": 28851, - "end": 28948, + "start": 29291, + "end": 29388, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 728, + "line": 744, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 28851, - "end": 28890, + "start": 29291, + "end": 29330, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 726, + "line": 742, "column": 66 } }, "object": { "type": "ThisExpression", - "start": 28851, - "end": 28855, + "start": 29291, + "end": 29295, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 726, + "line": 742, "column": 31 } } }, "property": { "type": "Identifier", - "start": 28856, - "end": 28890, + "start": 29296, + "end": 29330, "loc": { "start": { - "line": 726, + "line": 742, "column": 32 }, "end": { - "line": 726, + "line": 742, "column": 66 }, "identifierName": "createClassExpressionsForInternals" @@ -77506,15 +79066,15 @@ "arguments": [ { "type": "Identifier", - "start": 28900, - "end": 28916, + "start": 29340, + "end": 29356, "loc": { "start": { - "line": 727, + "line": 743, "column": 8 }, "end": { - "line": 727, + "line": 743, "column": 24 }, "identifierName": "phylorefAsJSONLD" @@ -77523,15 +79083,15 @@ }, { "type": "Identifier", - "start": 28918, - "end": 28936, + "start": 29358, + "end": 29376, "loc": { "start": { - "line": 727, + "line": 743, "column": 26 }, "end": { - "line": 727, + "line": 743, "column": 44 }, "identifierName": "internalSpecifiers" @@ -77540,15 +79100,15 @@ }, { "type": "ArrayExpression", - "start": 28938, - "end": 28940, + "start": 29378, + "end": 29380, "loc": { "start": { - "line": 727, + "line": 743, "column": 46 }, "end": { - "line": 727, + "line": 743, "column": 48 } }, @@ -77562,15 +79122,15 @@ { "type": "CommentLine", "value": " We only have internal specifiers. We therefore need to use the algorithm in", - "start": 28667, - "end": 28745, + "start": 29107, + "end": 29185, "loc": { "start": { - "line": 724, + "line": 740, "column": 6 }, "end": { - "line": 724, + "line": 740, "column": 84 } } @@ -77578,15 +79138,15 @@ { "type": "CommentLine", "value": " this.createClassExpressionsForInternals() to create this expression.", - "start": 28752, - "end": 28823, + "start": 29192, + "end": 29263, "loc": { "start": { - "line": 725, + "line": 741, "column": 6 }, "end": { - "line": 725, + "line": 741, "column": 77 } } @@ -77603,15 +79163,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, we set that as an equivalentClass", - "start": 28961, - "end": 29037, + "start": 29401, + "end": 29477, "loc": { "start": { - "line": 731, + "line": 747, "column": 4 }, "end": { - "line": 731, + "line": 747, "column": 80 } } @@ -77619,15 +79179,15 @@ { "type": "CommentLine", "value": " expression. If we have more than one, we produce multiple component classes", - "start": 29042, - "end": 29120, + "start": 29482, + "end": 29560, "loc": { "start": { - "line": 732, + "line": 748, "column": 4 }, "end": { - "line": 732, + "line": 748, "column": 82 } } @@ -77635,15 +79195,15 @@ { "type": "CommentLine", "value": " to represent it.", - "start": 29125, - "end": 29144, + "start": 29565, + "end": 29584, "loc": { "start": { - "line": 733, + "line": 749, "column": 4 }, "end": { - "line": 733, + "line": 749, "column": 23 } } @@ -77652,57 +79212,57 @@ }, { "type": "IfStatement", - "start": 29149, - "end": 31520, + "start": 29589, + "end": 31960, "loc": { "start": { - "line": 734, + "line": 750, "column": 4 }, "end": { - "line": 776, + "line": 792, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 29153, - "end": 29184, + "start": 29593, + "end": 29624, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 39 } }, "left": { "type": "MemberExpression", - "start": 29153, - "end": 29178, + "start": 29593, + "end": 29618, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 33 } }, "object": { "type": "Identifier", - "start": 29153, - "end": 29171, + "start": 29593, + "end": 29611, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 26 }, "identifierName": "logicalExpressions" @@ -77712,15 +79272,15 @@ }, "property": { "type": "Identifier", - "start": 29172, - "end": 29178, + "start": 29612, + "end": 29618, "loc": { "start": { - "line": 734, + "line": 750, "column": 27 }, "end": { - "line": 734, + "line": 750, "column": 33 }, "identifierName": "length" @@ -77733,15 +79293,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 29183, - "end": 29184, + "start": 29623, + "end": 29624, "loc": { "start": { - "line": 734, + "line": 750, "column": 38 }, "end": { - "line": 734, + "line": 750, "column": 39 } }, @@ -77755,44 +79315,44 @@ }, "consequent": { "type": "BlockStatement", - "start": 29186, - "end": 29779, + "start": 29626, + "end": 30219, "loc": { "start": { - "line": 734, + "line": 750, "column": 41 }, "end": { - "line": 744, + "line": 760, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 29391, - "end": 29773, + "start": 29831, + "end": 30213, "loc": { "start": { - "line": 738, + "line": 754, "column": 6 }, "end": { - "line": 743, + "line": 759, "column": 7 } }, "test": { "type": "UnaryExpression", - "start": 29395, - "end": 29444, + "start": 29835, + "end": 29884, "loc": { "start": { - "line": 738, + "line": 754, "column": 10 }, "end": { - "line": 738, + "line": 754, "column": 59 } }, @@ -77800,29 +79360,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 29396, - "end": 29444, + "start": 29836, + "end": 29884, "loc": { "start": { - "line": 738, + "line": 754, "column": 11 }, "end": { - "line": 738, + "line": 754, "column": 59 } }, "callee": { "type": "Identifier", - "start": 29396, - "end": 29399, + "start": 29836, + "end": 29839, "loc": { "start": { - "line": 738, + "line": 754, "column": 11 }, "end": { - "line": 738, + "line": 754, "column": 14 }, "identifierName": "has" @@ -77833,15 +79393,15 @@ "arguments": [ { "type": "Identifier", - "start": 29400, - "end": 29416, + "start": 29840, + "end": 29856, "loc": { "start": { - "line": 738, + "line": 754, "column": 15 }, "end": { - "line": 738, + "line": 754, "column": 31 }, "identifierName": "phylorefAsJSONLD" @@ -77850,15 +79410,15 @@ }, { "type": "StringLiteral", - "start": 29418, - "end": 29443, + "start": 29858, + "end": 29883, "loc": { "start": { - "line": 738, + "line": 754, "column": 33 }, "end": { - "line": 738, + "line": 754, "column": 58 } }, @@ -77878,58 +79438,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 29446, - "end": 29773, + "start": 29886, + "end": 30213, "loc": { "start": { - "line": 738, + "line": 754, "column": 61 }, "end": { - "line": 743, + "line": 759, "column": 7 } }, "body": [ { "type": "ThrowStatement", - "start": 29456, - "end": 29765, + "start": 29896, + "end": 30205, "loc": { "start": { - "line": 739, + "line": 755, "column": 8 }, "end": { - "line": 742, + "line": 758, "column": 10 } }, "argument": { "type": "NewExpression", - "start": 29462, - "end": 29764, + "start": 29902, + "end": 30204, "loc": { "start": { - "line": 739, + "line": 755, "column": 14 }, "end": { - "line": 742, + "line": 758, "column": 9 } }, "callee": { "type": "Identifier", - "start": 29466, - "end": 29471, + "start": 29906, + "end": 29911, "loc": { "start": { - "line": 739, + "line": 755, "column": 18 }, "end": { - "line": 739, + "line": 755, "column": 23 }, "identifierName": "Error" @@ -77939,73 +79499,73 @@ "arguments": [ { "type": "BinaryExpression", - "start": 29483, - "end": 29754, + "start": 29923, + "end": 30194, "loc": { "start": { - "line": 740, + "line": 756, "column": 10 }, "end": { - "line": 741, + "line": 757, "column": 131 } }, "left": { "type": "TemplateLiteral", - "start": 29483, - "end": 29622, + "start": 29923, + "end": 30062, "loc": { "start": { - "line": 740, + "line": 756, "column": 10 }, "end": { - "line": 740, + "line": 756, "column": 149 } }, "expressions": [ { "type": "MemberExpression", - "start": 29495, - "end": 29505, + "start": 29935, + "end": 29945, "loc": { "start": { - "line": 740, + "line": 756, "column": 22 }, "end": { - "line": 740, + "line": 756, "column": 32 } }, "object": { "type": "ThisExpression", - "start": 29495, - "end": 29499, + "start": 29935, + "end": 29939, "loc": { "start": { - "line": 740, + "line": 756, "column": 22 }, "end": { - "line": 740, + "line": 756, "column": 26 } } }, "property": { "type": "Identifier", - "start": 29500, - "end": 29505, + "start": 29940, + "end": 29945, "loc": { "start": { - "line": 740, + "line": 756, "column": 27 }, "end": { - "line": 740, + "line": 756, "column": 32 }, "identifierName": "label" @@ -78018,15 +79578,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 29484, - "end": 29493, + "start": 29924, + "end": 29933, "loc": { "start": { - "line": 740, + "line": 756, "column": 11 }, "end": { - "line": 740, + "line": 756, "column": 20 } }, @@ -78038,15 +79598,15 @@ }, { "type": "TemplateElement", - "start": 29506, - "end": 29621, + "start": 29946, + "end": 30061, "loc": { "start": { - "line": 740, + "line": 756, "column": 33 }, "end": { - "line": 740, + "line": 756, "column": 148 } }, @@ -78061,15 +79621,15 @@ "operator": "+", "right": { "type": "StringLiteral", - "start": 29635, - "end": 29754, + "start": 30075, + "end": 30194, "loc": { "start": { - "line": 741, + "line": 757, "column": 12 }, "end": { - "line": 741, + "line": 757, "column": 131 } }, @@ -78091,15 +79651,15 @@ { "type": "CommentLine", "value": " This is fine, as long as there is an explanation in", - "start": 29194, - "end": 29248, + "start": 29634, + "end": 29688, "loc": { "start": { - "line": 735, + "line": 751, "column": 6 }, "end": { - "line": 735, + "line": 751, "column": 60 } } @@ -78107,15 +79667,15 @@ { "type": "CommentLine", "value": " phyloref.malformedPhyloreference explaining why no logical expressions", - "start": 29255, - "end": 29328, + "start": 29695, + "end": 29768, "loc": { "start": { - "line": 736, + "line": 752, "column": 6 }, "end": { - "line": 736, + "line": 752, "column": 79 } } @@ -78123,15 +79683,15 @@ { "type": "CommentLine", "value": " could be generated. Otherwise, throw an error.", - "start": 29335, - "end": 29384, + "start": 29775, + "end": 29824, "loc": { "start": { - "line": 737, + "line": 753, "column": 6 }, "end": { - "line": 737, + "line": 753, "column": 55 } } @@ -78143,57 +79703,57 @@ }, "alternate": { "type": "IfStatement", - "start": 29785, - "end": 31520, + "start": 30225, + "end": 31960, "loc": { "start": { - "line": 744, + "line": 760, "column": 11 }, "end": { - "line": 776, + "line": 792, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 29789, - "end": 29820, + "start": 30229, + "end": 30260, "loc": { "start": { - "line": 744, + "line": 760, "column": 15 }, "end": { - "line": 744, + "line": 760, "column": 46 } }, "left": { "type": "MemberExpression", - "start": 29789, - "end": 29814, + "start": 30229, + "end": 30254, "loc": { "start": { - "line": 744, + "line": 760, "column": 15 }, "end": { - "line": 744, + "line": 760, "column": 40 } }, "object": { "type": "Identifier", - "start": 29789, - "end": 29807, + "start": 30229, + "end": 30247, "loc": { "start": { - "line": 744, + "line": 760, "column": 15 }, "end": { - "line": 744, + "line": 760, "column": 33 }, "identifierName": "logicalExpressions" @@ -78202,15 +79762,15 @@ }, "property": { "type": "Identifier", - "start": 29808, - "end": 29814, + "start": 30248, + "end": 30254, "loc": { "start": { - "line": 744, + "line": 760, "column": 34 }, "end": { - "line": 744, + "line": 760, "column": 40 }, "identifierName": "length" @@ -78222,15 +79782,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 29819, - "end": 29820, + "start": 30259, + "end": 30260, "loc": { "start": { - "line": 744, + "line": 760, "column": 45 }, "end": { - "line": 744, + "line": 760, "column": 46 } }, @@ -78243,73 +79803,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 29822, - "end": 30001, + "start": 30262, + "end": 30441, "loc": { "start": { - "line": 744, + "line": 760, "column": 48 }, "end": { - "line": 748, + "line": 764, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 29938, - "end": 29995, + "start": 30378, + "end": 30435, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 63 } }, "expression": { "type": "AssignmentExpression", - "start": 29938, - "end": 29994, + "start": 30378, + "end": 30434, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 62 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 29938, - "end": 29970, + "start": 30378, + "end": 30410, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 38 } }, "object": { "type": "Identifier", - "start": 29938, - "end": 29954, + "start": 30378, + "end": 30394, "loc": { "start": { - "line": 747, + "line": 763, "column": 6 }, "end": { - "line": 747, + "line": 763, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -78319,15 +79879,15 @@ }, "property": { "type": "Identifier", - "start": 29955, - "end": 29970, + "start": 30395, + "end": 30410, "loc": { "start": { - "line": 747, + "line": 763, "column": 23 }, "end": { - "line": 747, + "line": 763, "column": 38 }, "identifierName": "equivalentClass" @@ -78339,29 +79899,29 @@ }, "right": { "type": "MemberExpression", - "start": 29973, - "end": 29994, + "start": 30413, + "end": 30434, "loc": { "start": { - "line": 747, + "line": 763, "column": 41 }, "end": { - "line": 747, + "line": 763, "column": 62 } }, "object": { "type": "Identifier", - "start": 29973, - "end": 29991, + "start": 30413, + "end": 30431, "loc": { "start": { - "line": 747, + "line": 763, "column": 41 }, "end": { - "line": 747, + "line": 763, "column": 59 }, "identifierName": "logicalExpressions" @@ -78370,15 +79930,15 @@ }, "property": { "type": "NumericLiteral", - "start": 29992, - "end": 29993, + "start": 30432, + "end": 30433, "loc": { "start": { - "line": 747, + "line": 763, "column": 60 }, "end": { - "line": 747, + "line": 763, "column": 61 } }, @@ -78396,15 +79956,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, then that is what this phyloref", - "start": 29830, - "end": 29904, + "start": 30270, + "end": 30344, "loc": { "start": { - "line": 745, + "line": 761, "column": 6 }, "end": { - "line": 745, + "line": 761, "column": 80 } } @@ -78412,15 +79972,15 @@ { "type": "CommentLine", "value": " is equivalent to.", - "start": 29911, - "end": 29931, + "start": 30351, + "end": 30371, "loc": { "start": { - "line": 746, + "line": 762, "column": 6 }, "end": { - "line": 746, + "line": 762, "column": 26 } } @@ -78432,73 +79992,73 @@ }, "alternate": { "type": "BlockStatement", - "start": 30007, - "end": 31520, + "start": 30447, + "end": 31960, "loc": { "start": { - "line": 748, + "line": 764, "column": 11 }, "end": { - "line": 776, + "line": 792, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 31113, - "end": 31514, + "start": 31553, + "end": 31954, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 775, + "line": 791, "column": 9 } }, "expression": { "type": "AssignmentExpression", - "start": 31113, - "end": 31513, + "start": 31553, + "end": 31953, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 775, + "line": 791, "column": 8 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 31113, - "end": 31140, + "start": 31553, + "end": 31580, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 766, + "line": 782, "column": 33 } }, "object": { "type": "Identifier", - "start": 31113, - "end": 31129, + "start": 31553, + "end": 31569, "loc": { "start": { - "line": 766, + "line": 782, "column": 6 }, "end": { - "line": 766, + "line": 782, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -78508,15 +80068,15 @@ }, "property": { "type": "Identifier", - "start": 31130, - "end": 31140, + "start": 31570, + "end": 31580, "loc": { "start": { - "line": 766, + "line": 782, "column": 23 }, "end": { - "line": 766, + "line": 782, "column": 33 }, "identifierName": "subClasses" @@ -78528,43 +80088,43 @@ }, "right": { "type": "CallExpression", - "start": 31143, - "end": 31513, + "start": 31583, + "end": 31953, "loc": { "start": { - "line": 766, + "line": 782, "column": 36 }, "end": { - "line": 775, + "line": 791, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 31143, - "end": 31165, + "start": 31583, + "end": 31605, "loc": { "start": { - "line": 766, + "line": 782, "column": 36 }, "end": { - "line": 766, + "line": 782, "column": 58 } }, "object": { "type": "Identifier", - "start": 31143, - "end": 31161, + "start": 31583, + "end": 31601, "loc": { "start": { - "line": 766, + "line": 782, "column": 36 }, "end": { - "line": 766, + "line": 782, "column": 54 }, "identifierName": "logicalExpressions" @@ -78573,15 +80133,15 @@ }, "property": { "type": "Identifier", - "start": 31162, - "end": 31165, + "start": 31602, + "end": 31605, "loc": { "start": { - "line": 766, + "line": 782, "column": 55 }, "end": { - "line": 766, + "line": 782, "column": 58 }, "identifierName": "map" @@ -78593,15 +80153,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 31166, - "end": 31512, + "start": 31606, + "end": 31952, "loc": { "start": { - "line": 766, + "line": 782, "column": 59 }, "end": { - "line": 775, + "line": 791, "column": 7 } }, @@ -78612,15 +80172,15 @@ "params": [ { "type": "Identifier", - "start": 31166, - "end": 31175, + "start": 31606, + "end": 31615, "loc": { "start": { - "line": 766, + "line": 782, "column": 59 }, "end": { - "line": 766, + "line": 782, "column": 68 }, "identifierName": "classExpr" @@ -78630,58 +80190,58 @@ ], "body": { "type": "CallExpression", - "start": 31179, - "end": 31512, + "start": 31619, + "end": 31952, "loc": { "start": { - "line": 766, + "line": 782, "column": 72 }, "end": { - "line": 775, + "line": 791, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 31179, - "end": 31204, + "start": 31619, + "end": 31644, "loc": { "start": { - "line": 766, + "line": 782, "column": 72 }, "end": { - "line": 766, + "line": 782, "column": 97 } }, "object": { "type": "ThisExpression", - "start": 31179, - "end": 31183, + "start": 31619, + "end": 31623, "loc": { "start": { - "line": 766, + "line": 782, "column": 72 }, "end": { - "line": 766, + "line": 782, "column": 76 } } }, "property": { "type": "Identifier", - "start": 31184, - "end": 31204, + "start": 31624, + "end": 31644, "loc": { "start": { - "line": 766, + "line": 782, "column": 77 }, "end": { - "line": 766, + "line": 782, "column": 97 }, "identifierName": "createComponentClass" @@ -78693,15 +80253,15 @@ "arguments": [ { "type": "Identifier", - "start": 31214, - "end": 31230, + "start": 31654, + "end": 31670, "loc": { "start": { - "line": 767, + "line": 783, "column": 8 }, "end": { - "line": 767, + "line": 783, "column": 24 }, "identifierName": "phylorefAsJSONLD" @@ -78710,15 +80270,15 @@ }, { "type": "Identifier", - "start": 31240, - "end": 31258, + "start": 31680, + "end": 31698, "loc": { "start": { - "line": 768, + "line": 784, "column": 8 }, "end": { - "line": 768, + "line": 784, "column": 26 }, "identifierName": "internalSpecifiers" @@ -78727,15 +80287,15 @@ }, { "type": "Identifier", - "start": 31268, - "end": 31286, + "start": 31708, + "end": 31726, "loc": { "start": { - "line": 769, + "line": 785, "column": 8 }, "end": { - "line": 769, + "line": 785, "column": 26 }, "identifierName": "externalSpecifiers" @@ -78744,15 +80304,15 @@ }, { "type": "Identifier", - "start": 31296, - "end": 31305, + "start": 31736, + "end": 31745, "loc": { "start": { - "line": 770, + "line": 786, "column": 8 }, "end": { - "line": 770, + "line": 786, "column": 17 }, "identifierName": "classExpr" @@ -78761,15 +80321,15 @@ }, { "type": "BooleanLiteral", - "start": 31398, - "end": 31403, + "start": 31838, + "end": 31843, "loc": { "start": { - "line": 772, + "line": 788, "column": 8 }, "end": { - "line": 772, + "line": 788, "column": 13 } }, @@ -78778,15 +80338,15 @@ { "type": "CommentLine", "value": " False in order to turn off caching by internal and external specifiers.", - "start": 31315, - "end": 31389, + "start": 31755, + "end": 31829, "loc": { "start": { - "line": 771, + "line": 787, "column": 8 }, "end": { - "line": 771, + "line": 787, "column": 82 } } @@ -78795,15 +80355,15 @@ }, { "type": "Identifier", - "start": 31488, - "end": 31504, + "start": 31928, + "end": 31944, "loc": { "start": { - "line": 774, + "line": 790, "column": 8 }, "end": { - "line": 774, + "line": 790, "column": 24 }, "identifierName": "phylorefAsJSONLD" @@ -78813,15 +80373,15 @@ { "type": "CommentLine", "value": " Make the new component class a subclass of this phyloreference.", - "start": 31413, - "end": 31479, + "start": 31853, + "end": 31919, "loc": { "start": { - "line": 773, + "line": 789, "column": 8 }, "end": { - "line": 773, + "line": 789, "column": 74 } } @@ -78839,15 +80399,15 @@ { "type": "CommentLine", "value": " If we have multiple logical expressions, the phyloreference can be", - "start": 30015, - "end": 30084, + "start": 30455, + "end": 30524, "loc": { "start": { - "line": 749, + "line": 765, "column": 6 }, "end": { - "line": 749, + "line": 765, "column": 75 } } @@ -78855,15 +80415,15 @@ { "type": "CommentLine", "value": " represented by any of them. We model this by creating subclasses of", - "start": 30091, - "end": 30161, + "start": 30531, + "end": 30601, "loc": { "start": { - "line": 750, + "line": 766, "column": 6 }, "end": { - "line": 750, + "line": 766, "column": 76 } } @@ -78871,15 +80431,15 @@ { "type": "CommentLine", "value": " the phyloreference for each logical expression -- that way, it's clear", - "start": 30168, - "end": 30241, + "start": 30608, + "end": 30681, "loc": { "start": { - "line": 751, + "line": 767, "column": 6 }, "end": { - "line": 751, + "line": 767, "column": 79 } } @@ -78887,15 +80447,15 @@ { "type": "CommentLine", "value": " that these expressions aren't equivalent to each other (which is what", - "start": 30248, - "end": 30320, + "start": 30688, + "end": 30760, "loc": { "start": { - "line": 752, + "line": 768, "column": 6 }, "end": { - "line": 752, + "line": 768, "column": 78 } } @@ -78903,15 +80463,15 @@ { "type": "CommentLine", "value": " caused https://github.com/phyloref/phyx.js/issues/57), but nodes", - "start": 30327, - "end": 30394, + "start": 30767, + "end": 30834, "loc": { "start": { - "line": 753, + "line": 769, "column": 6 }, "end": { - "line": 753, + "line": 769, "column": 73 } } @@ -78919,15 +80479,15 @@ { "type": "CommentLine", "value": " resolved by any of those expressions will also be included in the", - "start": 30401, - "end": 30469, + "start": 30841, + "end": 30909, "loc": { "start": { - "line": 754, + "line": 770, "column": 6 }, "end": { - "line": 754, + "line": 770, "column": 74 } } @@ -78935,15 +80495,15 @@ { "type": "CommentLine", "value": " phyloreference itself.", - "start": 30476, - "end": 30501, + "start": 30916, + "end": 30941, "loc": { "start": { - "line": 755, + "line": 771, "column": 6 }, "end": { - "line": 755, + "line": 771, "column": 31 } } @@ -78951,15 +80511,15 @@ { "type": "CommentLine", "value": "", - "start": 30508, - "end": 30510, + "start": 30948, + "end": 30950, "loc": { "start": { - "line": 756, + "line": 772, "column": 6 }, "end": { - "line": 756, + "line": 772, "column": 8 } } @@ -78967,15 +80527,15 @@ { "type": "CommentLine", "value": " Note that there are two differences from the way in which we usually call", - "start": 30517, - "end": 30593, + "start": 30957, + "end": 31033, "loc": { "start": { - "line": 757, + "line": 773, "column": 6 }, "end": { - "line": 757, + "line": 773, "column": 82 } } @@ -78983,15 +80543,15 @@ { "type": "CommentLine", "value": " this.createComponentClass():", - "start": 30600, - "end": 30631, + "start": 31040, + "end": 31071, "loc": { "start": { - "line": 758, + "line": 774, "column": 6 }, "end": { - "line": 758, + "line": 774, "column": 37 } } @@ -78999,15 +80559,15 @@ { "type": "CommentLine", "value": " 1. Usually, createComponentClass() reuses logical expressions with the", - "start": 30638, - "end": 30712, + "start": 31078, + "end": 31152, "loc": { "start": { - "line": 759, + "line": 775, "column": 6 }, "end": { - "line": 759, + "line": 775, "column": 80 } } @@ -79015,15 +80575,15 @@ { "type": "CommentLine", "value": " same sets of internal and external specifiers. That won't work here,", - "start": 30719, - "end": 30794, + "start": 31159, + "end": 31234, "loc": { "start": { - "line": 760, + "line": 776, "column": 6 }, "end": { - "line": 760, + "line": 776, "column": 81 } } @@ -79031,15 +80591,15 @@ { "type": "CommentLine", "value": " since *all* these logical expressions have the same specifiers. So,", - "start": 30801, - "end": 30875, + "start": 31241, + "end": 31315, "loc": { "start": { - "line": 761, + "line": 777, "column": 6 }, "end": { - "line": 761, + "line": 777, "column": 80 } } @@ -79047,15 +80607,15 @@ { "type": "CommentLine", "value": " we turn off caching.", - "start": 30882, - "end": 30909, + "start": 31322, + "end": 31349, "loc": { "start": { - "line": 762, + "line": 778, "column": 6 }, "end": { - "line": 762, + "line": 778, "column": 33 } } @@ -79063,15 +80623,15 @@ { "type": "CommentLine", "value": " 2. We need to set each of these component classes to be a subclass of", - "start": 30916, - "end": 30989, + "start": 31356, + "end": 31429, "loc": { "start": { - "line": 763, + "line": 779, "column": 6 }, "end": { - "line": 763, + "line": 779, "column": 79 } } @@ -79079,15 +80639,15 @@ { "type": "CommentLine", "value": " this phyloreference so that it can include instances from each of the", - "start": 30996, - "end": 31072, + "start": 31436, + "end": 31512, "loc": { "start": { - "line": 764, + "line": 780, "column": 6 }, "end": { - "line": 764, + "line": 780, "column": 82 } } @@ -79095,15 +80655,15 @@ { "type": "CommentLine", "value": " logical expressions.", - "start": 31079, - "end": 31106, + "start": 31519, + "end": 31546, "loc": { "start": { - "line": 765, + "line": 781, "column": 6 }, "end": { - "line": 765, + "line": 781, "column": 33 } } @@ -79120,15 +80680,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, we set that as an equivalentClass", - "start": 28961, - "end": 29037, + "start": 29401, + "end": 29477, "loc": { "start": { - "line": 731, + "line": 747, "column": 4 }, "end": { - "line": 731, + "line": 747, "column": 80 } } @@ -79136,15 +80696,15 @@ { "type": "CommentLine", "value": " expression. If we have more than one, we produce multiple component classes", - "start": 29042, - "end": 29120, + "start": 29482, + "end": 29560, "loc": { "start": { - "line": 732, + "line": 748, "column": 4 }, "end": { - "line": 732, + "line": 748, "column": 82 } } @@ -79152,15 +80712,15 @@ { "type": "CommentLine", "value": " to represent it.", - "start": 29125, - "end": 29144, + "start": 29565, + "end": 29584, "loc": { "start": { - "line": 733, + "line": 749, "column": 4 }, "end": { - "line": 733, + "line": 749, "column": 23 } } @@ -79170,15 +80730,15 @@ { "type": "CommentLine", "value": " Every phyloreference is a subclass of phyloref:Phyloreference.", - "start": 31526, - "end": 31591, + "start": 31966, + "end": 32031, "loc": { "start": { - "line": 778, + "line": 794, "column": 4 }, "end": { - "line": 778, + "line": 794, "column": 69 } } @@ -79187,29 +80747,29 @@ }, { "type": "IfStatement", - "start": 31596, - "end": 31663, + "start": 32036, + "end": 32103, "loc": { "start": { - "line": 779, + "line": 795, "column": 4 }, "end": { - "line": 779, + "line": 795, "column": 71 } }, "test": { "type": "UnaryExpression", - "start": 31600, - "end": 31628, + "start": 32040, + "end": 32068, "loc": { "start": { - "line": 779, + "line": 795, "column": 8 }, "end": { - "line": 779, + "line": 795, "column": 36 } }, @@ -79217,29 +80777,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 31601, - "end": 31628, + "start": 32041, + "end": 32068, "loc": { "start": { - "line": 779, + "line": 795, "column": 9 }, "end": { - "line": 779, + "line": 795, "column": 36 } }, "object": { "type": "Identifier", - "start": 31601, - "end": 31617, + "start": 32041, + "end": 32057, "loc": { "start": { - "line": 779, + "line": 795, "column": 9 }, "end": { - "line": 779, + "line": 795, "column": 25 }, "identifierName": "phylorefAsJSONLD" @@ -79249,15 +80809,15 @@ }, "property": { "type": "Identifier", - "start": 31618, - "end": 31628, + "start": 32058, + "end": 32068, "loc": { "start": { - "line": 779, + "line": 795, "column": 26 }, "end": { - "line": 779, + "line": 795, "column": 36 }, "identifierName": "subClassOf" @@ -79274,58 +80834,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 31630, - "end": 31663, + "start": 32070, + "end": 32103, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 31630, - "end": 31662, + "start": 32070, + "end": 32102, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 31630, - "end": 31657, + "start": 32070, + "end": 32097, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 65 } }, "object": { "type": "Identifier", - "start": 31630, - "end": 31646, + "start": 32070, + "end": 32086, "loc": { "start": { - "line": 779, + "line": 795, "column": 38 }, "end": { - "line": 779, + "line": 795, "column": 54 }, "identifierName": "phylorefAsJSONLD" @@ -79334,15 +80894,15 @@ }, "property": { "type": "Identifier", - "start": 31647, - "end": 31657, + "start": 32087, + "end": 32097, "loc": { "start": { - "line": 779, + "line": 795, "column": 55 }, "end": { - "line": 779, + "line": 795, "column": 65 }, "identifierName": "subClassOf" @@ -79353,15 +80913,15 @@ }, "right": { "type": "ArrayExpression", - "start": 31660, - "end": 31662, + "start": 32100, + "end": 32102, "loc": { "start": { - "line": 779, + "line": 795, "column": 68 }, "end": { - "line": 779, + "line": 795, "column": 70 } }, @@ -79374,15 +80934,15 @@ { "type": "CommentLine", "value": " Every phyloreference is a subclass of phyloref:Phyloreference.", - "start": 31526, - "end": 31591, + "start": 31966, + "end": 32031, "loc": { "start": { - "line": 778, + "line": 794, "column": 4 }, "end": { - "line": 778, + "line": 794, "column": 69 } } @@ -79391,29 +80951,29 @@ }, { "type": "IfStatement", - "start": 31668, - "end": 31791, + "start": 32108, + "end": 32231, "loc": { "start": { - "line": 780, + "line": 796, "column": 4 }, "end": { - "line": 782, + "line": 798, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 31672, - "end": 31715, + "start": 32112, + "end": 32155, "loc": { "start": { - "line": 780, + "line": 796, "column": 8 }, "end": { - "line": 780, + "line": 796, "column": 51 } }, @@ -79421,43 +80981,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 31673, - "end": 31715, + "start": 32113, + "end": 32155, "loc": { "start": { - "line": 780, + "line": 796, "column": 9 }, "end": { - "line": 780, + "line": 796, "column": 51 } }, "callee": { "type": "MemberExpression", - "start": 31673, - "end": 31686, + "start": 32113, + "end": 32126, "loc": { "start": { - "line": 780, + "line": 796, "column": 9 }, "end": { - "line": 780, + "line": 796, "column": 22 } }, "object": { "type": "Identifier", - "start": 31673, - "end": 31678, + "start": 32113, + "end": 32118, "loc": { "start": { - "line": 780, + "line": 796, "column": 9 }, "end": { - "line": 780, + "line": 796, "column": 14 }, "identifierName": "Array" @@ -79466,15 +81026,15 @@ }, "property": { "type": "Identifier", - "start": 31679, - "end": 31686, + "start": 32119, + "end": 32126, "loc": { "start": { - "line": 780, + "line": 796, "column": 15 }, "end": { - "line": 780, + "line": 796, "column": 22 }, "identifierName": "isArray" @@ -79486,29 +81046,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 31687, - "end": 31714, + "start": 32127, + "end": 32154, "loc": { "start": { - "line": 780, + "line": 796, "column": 23 }, "end": { - "line": 780, + "line": 796, "column": 50 } }, "object": { "type": "Identifier", - "start": 31687, - "end": 31703, + "start": 32127, + "end": 32143, "loc": { "start": { - "line": 780, + "line": 796, "column": 23 }, "end": { - "line": 780, + "line": 796, "column": 39 }, "identifierName": "phylorefAsJSONLD" @@ -79517,15 +81077,15 @@ }, "property": { "type": "Identifier", - "start": 31704, - "end": 31714, + "start": 32144, + "end": 32154, "loc": { "start": { - "line": 780, + "line": 796, "column": 40 }, "end": { - "line": 780, + "line": 796, "column": 50 }, "identifierName": "subClassOf" @@ -79542,73 +81102,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 31717, - "end": 31791, + "start": 32157, + "end": 32231, "loc": { "start": { - "line": 780, + "line": 796, "column": 53 }, "end": { - "line": 782, + "line": 798, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 31725, - "end": 31785, + "start": 32165, + "end": 32225, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 31725, - "end": 31784, + "start": 32165, + "end": 32224, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 65 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 31725, - "end": 31752, + "start": 32165, + "end": 32192, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 33 } }, "object": { "type": "Identifier", - "start": 31725, - "end": 31741, + "start": 32165, + "end": 32181, "loc": { "start": { - "line": 781, + "line": 797, "column": 6 }, "end": { - "line": 781, + "line": 797, "column": 22 }, "identifierName": "phylorefAsJSONLD" @@ -79617,15 +81177,15 @@ }, "property": { "type": "Identifier", - "start": 31742, - "end": 31752, + "start": 32182, + "end": 32192, "loc": { "start": { - "line": 781, + "line": 797, "column": 23 }, "end": { - "line": 781, + "line": 797, "column": 33 }, "identifierName": "subClassOf" @@ -79636,44 +81196,44 @@ }, "right": { "type": "ArrayExpression", - "start": 31755, - "end": 31784, + "start": 32195, + "end": 32224, "loc": { "start": { - "line": 781, + "line": 797, "column": 36 }, "end": { - "line": 781, + "line": 797, "column": 65 } }, "elements": [ { "type": "MemberExpression", - "start": 31756, - "end": 31783, + "start": 32196, + "end": 32223, "loc": { "start": { - "line": 781, + "line": 797, "column": 37 }, "end": { - "line": 781, + "line": 797, "column": 64 } }, "object": { "type": "Identifier", - "start": 31756, - "end": 31772, + "start": 32196, + "end": 32212, "loc": { "start": { - "line": 781, + "line": 797, "column": 37 }, "end": { - "line": 781, + "line": 797, "column": 53 }, "identifierName": "phylorefAsJSONLD" @@ -79682,15 +81242,15 @@ }, "property": { "type": "Identifier", - "start": 31773, - "end": 31783, + "start": 32213, + "end": 32223, "loc": { "start": { - "line": 781, + "line": 797, "column": 54 }, "end": { - "line": 781, + "line": 797, "column": 64 }, "identifierName": "subClassOf" @@ -79710,71 +81270,71 @@ }, { "type": "ExpressionStatement", - "start": 31796, - "end": 31856, + "start": 32236, + "end": 32296, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 64 } }, "expression": { "type": "CallExpression", - "start": 31796, - "end": 31855, + "start": 32236, + "end": 32295, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 31796, - "end": 31828, + "start": 32236, + "end": 32268, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 31796, - "end": 31823, + "start": 32236, + "end": 32263, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 31 } }, "object": { "type": "Identifier", - "start": 31796, - "end": 31812, + "start": 32236, + "end": 32252, "loc": { "start": { - "line": 783, + "line": 799, "column": 4 }, "end": { - "line": 783, + "line": 799, "column": 20 }, "identifierName": "phylorefAsJSONLD" @@ -79783,15 +81343,15 @@ }, "property": { "type": "Identifier", - "start": 31813, - "end": 31823, + "start": 32253, + "end": 32263, "loc": { "start": { - "line": 783, + "line": 799, "column": 21 }, "end": { - "line": 783, + "line": 799, "column": 31 }, "identifierName": "subClassOf" @@ -79802,15 +81362,15 @@ }, "property": { "type": "Identifier", - "start": 31824, - "end": 31828, + "start": 32264, + "end": 32268, "loc": { "start": { - "line": 783, + "line": 799, "column": 32 }, "end": { - "line": 783, + "line": 799, "column": 36 }, "identifierName": "push" @@ -79822,15 +81382,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 31829, - "end": 31854, + "start": 32269, + "end": 32294, "loc": { "start": { - "line": 783, + "line": 799, "column": 37 }, "end": { - "line": 783, + "line": 799, "column": 62 } }, @@ -79846,15 +81406,15 @@ { "type": "CommentLine", "value": " If the this Phyloref has a phylorefType that differs from the calculated", - "start": 31862, - "end": 31937, + "start": 32302, + "end": 32377, "loc": { "start": { - "line": 785, + "line": 801, "column": 4 }, "end": { - "line": 785, + "line": 801, "column": 79 } } @@ -79862,15 +81422,15 @@ { "type": "CommentLine", "value": " phyloref type, throw an error.", - "start": 31942, - "end": 31975, + "start": 32382, + "end": 32415, "loc": { "start": { - "line": 786, + "line": 802, "column": 4 }, "end": { - "line": 786, + "line": 802, "column": 37 } } @@ -79879,57 +81439,57 @@ }, { "type": "IfStatement", - "start": 31980, - "end": 32267, + "start": 32420, + "end": 32707, "loc": { "start": { - "line": 787, + "line": 803, "column": 4 }, "end": { - "line": 791, + "line": 807, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 31984, - "end": 32081, + "start": 32424, + "end": 32521, "loc": { "start": { - "line": 787, + "line": 803, "column": 8 }, "end": { - "line": 787, + "line": 803, "column": 105 } }, "left": { "type": "CallExpression", - "start": 31984, - "end": 32021, + "start": 32424, + "end": 32461, "loc": { "start": { - "line": 787, + "line": 803, "column": 8 }, "end": { - "line": 787, + "line": 803, "column": 45 } }, "callee": { "type": "Identifier", - "start": 31984, - "end": 31987, + "start": 32424, + "end": 32427, "loc": { "start": { - "line": 787, + "line": 803, "column": 8 }, "end": { - "line": 787, + "line": 803, "column": 11 }, "identifierName": "has" @@ -79940,15 +81500,15 @@ "arguments": [ { "type": "Identifier", - "start": 31988, - "end": 32004, + "start": 32428, + "end": 32444, "loc": { "start": { - "line": 787, + "line": 803, "column": 12 }, "end": { - "line": 787, + "line": 803, "column": 28 }, "identifierName": "phylorefAsJSONLD" @@ -79957,15 +81517,15 @@ }, { "type": "StringLiteral", - "start": 32006, - "end": 32020, + "start": 32446, + "end": 32460, "loc": { "start": { - "line": 787, + "line": 803, "column": 30 }, "end": { - "line": 787, + "line": 803, "column": 44 } }, @@ -79981,43 +81541,43 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 32025, - "end": 32081, + "start": 32465, + "end": 32521, "loc": { "start": { - "line": 787, + "line": 803, "column": 49 }, "end": { - "line": 787, + "line": 803, "column": 105 } }, "left": { "type": "MemberExpression", - "start": 32025, - "end": 32054, + "start": 32465, + "end": 32494, "loc": { "start": { - "line": 787, + "line": 803, "column": 49 }, "end": { - "line": 787, + "line": 803, "column": 78 } }, "object": { "type": "Identifier", - "start": 32025, - "end": 32041, + "start": 32465, + "end": 32481, "loc": { "start": { - "line": 787, + "line": 803, "column": 49 }, "end": { - "line": 787, + "line": 803, "column": 65 }, "identifierName": "phylorefAsJSONLD" @@ -80026,15 +81586,15 @@ }, "property": { "type": "Identifier", - "start": 32042, - "end": 32054, + "start": 32482, + "end": 32494, "loc": { "start": { - "line": 787, + "line": 803, "column": 66 }, "end": { - "line": 787, + "line": 803, "column": 78 }, "identifierName": "phylorefType" @@ -80046,15 +81606,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 32059, - "end": 32081, + "start": 32499, + "end": 32521, "loc": { "start": { - "line": 787, + "line": 803, "column": 83 }, "end": { - "line": 787, + "line": 803, "column": 105 }, "identifierName": "calculatedPhylorefType" @@ -80066,58 +81626,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 32083, - "end": 32267, + "start": 32523, + "end": 32707, "loc": { "start": { - "line": 787, + "line": 803, "column": 107 }, "end": { - "line": 791, + "line": 807, "column": 5 } }, "body": [ { "type": "ThrowStatement", - "start": 32091, - "end": 32261, + "start": 32531, + "end": 32701, "loc": { "start": { - "line": 788, + "line": 804, "column": 6 }, "end": { - "line": 790, + "line": 806, "column": 8 } }, "argument": { "type": "NewExpression", - "start": 32097, - "end": 32260, + "start": 32537, + "end": 32700, "loc": { "start": { - "line": 788, + "line": 804, "column": 12 }, "end": { - "line": 790, + "line": 806, "column": 7 } }, "callee": { "type": "Identifier", - "start": 32101, - "end": 32106, + "start": 32541, + "end": 32546, "loc": { "start": { - "line": 788, + "line": 804, "column": 16 }, "end": { - "line": 788, + "line": 804, "column": 21 }, "identifierName": "Error" @@ -80127,59 +81687,59 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 32116, - "end": 32252, + "start": 32556, + "end": 32692, "loc": { "start": { - "line": 789, + "line": 805, "column": 8 }, "end": { - "line": 789, + "line": 805, "column": 144 } }, "expressions": [ { "type": "MemberExpression", - "start": 32128, - "end": 32138, + "start": 32568, + "end": 32578, "loc": { "start": { - "line": 789, + "line": 805, "column": 20 }, "end": { - "line": 789, + "line": 805, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 32128, - "end": 32132, + "start": 32568, + "end": 32572, "loc": { "start": { - "line": 789, + "line": 805, "column": 20 }, "end": { - "line": 789, + "line": 805, "column": 24 } } }, "property": { "type": "Identifier", - "start": 32133, - "end": 32138, + "start": 32573, + "end": 32578, "loc": { "start": { - "line": 789, + "line": 805, "column": 25 }, "end": { - "line": 789, + "line": 805, "column": 30 }, "identifierName": "label" @@ -80190,29 +81750,29 @@ }, { "type": "MemberExpression", - "start": 32167, - "end": 32196, + "start": 32607, + "end": 32636, "loc": { "start": { - "line": 789, + "line": 805, "column": 59 }, "end": { - "line": 789, + "line": 805, "column": 88 } }, "object": { "type": "Identifier", - "start": 32167, - "end": 32183, + "start": 32607, + "end": 32623, "loc": { "start": { - "line": 789, + "line": 805, "column": 59 }, "end": { - "line": 789, + "line": 805, "column": 75 }, "identifierName": "phylorefAsJSONLD" @@ -80221,15 +81781,15 @@ }, "property": { "type": "Identifier", - "start": 32184, - "end": 32196, + "start": 32624, + "end": 32636, "loc": { "start": { - "line": 789, + "line": 805, "column": 76 }, "end": { - "line": 789, + "line": 805, "column": 88 }, "identifierName": "phylorefType" @@ -80240,15 +81800,15 @@ }, { "type": "Identifier", - "start": 32226, - "end": 32248, + "start": 32666, + "end": 32688, "loc": { "start": { - "line": 789, + "line": 805, "column": 118 }, "end": { - "line": 789, + "line": 805, "column": 140 }, "identifierName": "calculatedPhylorefType" @@ -80259,15 +81819,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 32117, - "end": 32126, + "start": 32557, + "end": 32566, "loc": { "start": { - "line": 789, + "line": 805, "column": 9 }, "end": { - "line": 789, + "line": 805, "column": 18 } }, @@ -80279,15 +81839,15 @@ }, { "type": "TemplateElement", - "start": 32139, - "end": 32165, + "start": 32579, + "end": 32605, "loc": { "start": { - "line": 789, + "line": 805, "column": 31 }, "end": { - "line": 789, + "line": 805, "column": 57 } }, @@ -80299,15 +81859,15 @@ }, { "type": "TemplateElement", - "start": 32197, - "end": 32224, + "start": 32637, + "end": 32664, "loc": { "start": { - "line": 789, + "line": 805, "column": 89 }, "end": { - "line": 789, + "line": 805, "column": 116 } }, @@ -80319,15 +81879,15 @@ }, { "type": "TemplateElement", - "start": 32249, - "end": 32251, + "start": 32689, + "end": 32691, "loc": { "start": { - "line": 789, + "line": 805, "column": 141 }, "end": { - "line": 789, + "line": 805, "column": 143 } }, @@ -80350,15 +81910,15 @@ { "type": "CommentLine", "value": " If the this Phyloref has a phylorefType that differs from the calculated", - "start": 31862, - "end": 31937, + "start": 32302, + "end": 32377, "loc": { "start": { - "line": 785, + "line": 801, "column": 4 }, "end": { - "line": 785, + "line": 801, "column": 79 } } @@ -80366,15 +81926,15 @@ { "type": "CommentLine", "value": " phyloref type, throw an error.", - "start": 31942, - "end": 31975, + "start": 32382, + "end": 32415, "loc": { "start": { - "line": 786, + "line": 802, "column": 4 }, "end": { - "line": 786, + "line": 802, "column": 37 } } @@ -80383,71 +81943,71 @@ }, { "type": "ExpressionStatement", - "start": 32272, - "end": 32329, + "start": 32712, + "end": 32769, "loc": { "start": { - "line": 792, + "line": 808, "column": 4 }, "end": { - "line": 792, + "line": 808, "column": 61 } }, "expression": { "type": "CallExpression", - "start": 32272, - "end": 32328, + "start": 32712, + "end": 32768, "loc": { "start": { - "line": 792, + "line": 808, "column": 4 }, "end": { - "line": 792, + "line": 808, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 32272, - "end": 32304, + "start": 32712, + "end": 32744, "loc": { "start": { - "line": 792, + "line": 808, "column": 4 }, "end": { - "line": 792, + "line": 808, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 32272, - "end": 32299, + "start": 32712, + "end": 32739, "loc": { "start": { - "line": 792, + "line": 808, "column": 4 }, "end": { - "line": 792, + "line": 808, "column": 31 } }, "object": { "type": "Identifier", - "start": 32272, - "end": 32288, + "start": 32712, + "end": 32728, "loc": { "start": { - "line": 792, + "line": 808, "column": 4 }, "end": { - "line": 792, + "line": 808, "column": 20 }, "identifierName": "phylorefAsJSONLD" @@ -80456,15 +82016,15 @@ }, "property": { "type": "Identifier", - "start": 32289, - "end": 32299, + "start": 32729, + "end": 32739, "loc": { "start": { - "line": 792, + "line": 808, "column": 21 }, "end": { - "line": 792, + "line": 808, "column": 31 }, "identifierName": "subClassOf" @@ -80475,15 +82035,15 @@ }, "property": { "type": "Identifier", - "start": 32300, - "end": 32304, + "start": 32740, + "end": 32744, "loc": { "start": { - "line": 792, + "line": 808, "column": 32 }, "end": { - "line": 792, + "line": 808, "column": 36 }, "identifierName": "push" @@ -80495,15 +82055,15 @@ "arguments": [ { "type": "Identifier", - "start": 32305, - "end": 32327, + "start": 32745, + "end": 32767, "loc": { "start": { - "line": 792, + "line": 808, "column": 37 }, "end": { - "line": 792, + "line": 808, "column": 59 }, "identifierName": "calculatedPhylorefType" @@ -80515,29 +82075,29 @@ }, { "type": "ReturnStatement", - "start": 32335, - "end": 32359, + "start": 32775, + "end": 32799, "loc": { "start": { - "line": 794, + "line": 810, "column": 4 }, "end": { - "line": 794, + "line": 810, "column": 28 } }, "argument": { "type": "Identifier", - "start": 32342, - "end": 32358, + "start": 32782, + "end": 32798, "loc": { "start": { - "line": 794, + "line": 810, "column": 11 }, "end": { - "line": 794, + "line": 810, "column": 27 }, "identifierName": "phylorefAsJSONLD" @@ -80552,15 +82112,15 @@ { "type": "CommentBlock", "value": "\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n ", - "start": 23766, - "end": 23972, + "start": 24206, + "end": 24412, "loc": { "start": { - "line": 598, + "line": 614, "column": 2 }, "end": { - "line": 606, + "line": 622, "column": 5 } } @@ -80712,16 +82272,32 @@ }, { "type": "CommentBlock", - "value": "* Return the external specifiers of this phyloref (if any). ", + "value": "*\n * Normalize a phyloreference.\n *\n * @param phyloref\n ", "start": 1313, - "end": 1377, + "end": 1381, "loc": { "start": { "line": 41, "column": 2 }, "end": { - "line": 41, + "line": 45, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the external specifiers of this phyloref (if any). ", + "start": 1753, + "end": 1817, + "loc": { + "start": { + "line": 57, + "column": 2 + }, + "end": { + "line": 57, "column": 66 } } @@ -80729,15 +82305,15 @@ { "type": "CommentLine", "value": " If there isn't one, create an empty list so that the caller can do", - "start": 1466, - "end": 1535, + "start": 1906, + "end": 1975, "loc": { "start": { - "line": 44, + "line": 60, "column": 6 }, "end": { - "line": 44, + "line": 60, "column": 75 } } @@ -80745,15 +82321,15 @@ { "type": "CommentLine", "value": " `wrappedPhyloref.externalSpecifiers.push({...})`.", - "start": 1542, - "end": 1594, + "start": 1982, + "end": 2034, "loc": { "start": { - "line": 45, + "line": 61, "column": 6 }, "end": { - "line": 45, + "line": 61, "column": 58 } } @@ -80761,15 +82337,15 @@ { "type": "CommentLine", "value": " Return a label for this phyloreference.", - "start": 1717, - "end": 1759, + "start": 2157, + "end": 2199, "loc": { "start": { - "line": 53, + "line": 69, "column": 4 }, "end": { - "line": 53, + "line": 69, "column": 46 } } @@ -80777,15 +82353,15 @@ { "type": "CommentLine", "value": " Set a label for this phyloreference.", - "start": 2051, - "end": 2090, + "start": 2491, + "end": 2530, "loc": { "start": { - "line": 62, + "line": 78, "column": 4 }, "end": { - "line": 62, + "line": 78, "column": 43 } } @@ -80793,15 +82369,15 @@ { "type": "CommentLine", "value": " Vue.set(this.phyloref, 'label', newLabel);", - "start": 2187, - "end": 2232, + "start": 2627, + "end": 2672, "loc": { "start": { - "line": 66, + "line": 82, "column": 6 }, "end": { - "line": 66, + "line": 82, "column": 51 } } @@ -80809,15 +82385,15 @@ { "type": "CommentBlock", "value": "* Return all the specifiers of this phyloref (if any). ", - "start": 2284, - "end": 2343, + "start": 2724, + "end": 2783, "loc": { "start": { - "line": 71, + "line": 87, "column": 2 }, "end": { - "line": 71, + "line": 87, "column": 61 } } @@ -80825,15 +82401,15 @@ { "type": "CommentLine", "value": " Returns a list of all specifiers by combining the internal and external", - "start": 2369, - "end": 2443, + "start": 2809, + "end": 2883, "loc": { "start": { - "line": 73, + "line": 89, "column": 4 }, "end": { - "line": 73, + "line": 89, "column": 78 } } @@ -80841,15 +82417,15 @@ { "type": "CommentLine", "value": " specifiers into a single list, with internal specifiers before", - "start": 2448, - "end": 2513, + "start": 2888, + "end": 2953, "loc": { "start": { - "line": 74, + "line": 90, "column": 4 }, "end": { - "line": 74, + "line": 90, "column": 69 } } @@ -80857,15 +82433,15 @@ { "type": "CommentLine", "value": " external specifiers.", - "start": 2518, - "end": 2541, + "start": 2958, + "end": 2981, "loc": { "start": { - "line": 75, + "line": 91, "column": 4 }, "end": { - "line": 75, + "line": 91, "column": 27 } } @@ -80873,15 +82449,15 @@ { "type": "CommentLine", "value": " For a given specifier, return a string indicating whether it is", - "start": 2713, - "end": 2779, + "start": 3153, + "end": 3219, "loc": { "start": { - "line": 82, + "line": 98, "column": 4 }, "end": { - "line": 82, + "line": 98, "column": 70 } } @@ -80889,15 +82465,15 @@ { "type": "CommentLine", "value": " an 'Internal' or 'External' specifier.", - "start": 2784, - "end": 2825, + "start": 3224, + "end": 3265, "loc": { "start": { - "line": 83, + "line": 99, "column": 4 }, "end": { - "line": 83, + "line": 99, "column": 45 } } @@ -80905,15 +82481,15 @@ { "type": "CommentLine", "value": " Change the type of a given specifier. To do this, we first need", - "start": 3051, - "end": 3117, + "start": 3491, + "end": 3557, "loc": { "start": { - "line": 91, + "line": 107, "column": 4 }, "end": { - "line": 91, + "line": 107, "column": 70 } } @@ -80921,15 +82497,15 @@ { "type": "CommentLine", "value": " to determine if it was originally an internal or external", - "start": 3122, - "end": 3182, + "start": 3562, + "end": 3622, "loc": { "start": { - "line": 92, + "line": 108, "column": 4 }, "end": { - "line": 92, + "line": 108, "column": 64 } } @@ -80937,15 +82513,15 @@ { "type": "CommentLine", "value": " specifier, then move it into the other list.", - "start": 3187, - "end": 3234, + "start": 3627, + "end": 3674, "loc": { "start": { - "line": 93, + "line": 109, "column": 4 }, "end": { - "line": 93, + "line": 109, "column": 51 } } @@ -80953,15 +82529,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'Internal', we might need to delete it from the", - "start": 3297, - "end": 3369, + "start": 3737, + "end": 3809, "loc": { "start": { - "line": 97, + "line": 113, "column": 6 }, "end": { - "line": 97, + "line": 113, "column": 78 } } @@ -80969,15 +82545,15 @@ { "type": "CommentLine", "value": " list of external specifiers first.", - "start": 3376, - "end": 3413, + "start": 3816, + "end": 3853, "loc": { "start": { - "line": 98, + "line": 114, "column": 6 }, "end": { - "line": 98, + "line": 114, "column": 43 } } @@ -80985,15 +82561,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 3545, - "end": 3618, + "start": 3985, + "end": 4058, "loc": { "start": { - "line": 102, + "line": 118, "column": 6 }, "end": { - "line": 102, + "line": 118, "column": 79 } } @@ -81001,15 +82577,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'External', we might need to delete it from the", - "start": 3799, - "end": 3871, + "start": 4239, + "end": 4311, "loc": { "start": { - "line": 107, + "line": 123, "column": 6 }, "end": { - "line": 107, + "line": 123, "column": 78 } } @@ -81017,15 +82593,15 @@ { "type": "CommentLine", "value": " list of internal specifiers first.", - "start": 3878, - "end": 3915, + "start": 4318, + "end": 4355, "loc": { "start": { - "line": 108, + "line": 124, "column": 6 }, "end": { - "line": 108, + "line": 124, "column": 43 } } @@ -81033,15 +82609,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 4065, - "end": 4138, + "start": 4505, + "end": 4578, "loc": { "start": { - "line": 112, + "line": 128, "column": 6 }, "end": { - "line": 112, + "line": 128, "column": 79 } } @@ -81049,15 +82625,15 @@ { "type": "CommentLine", "value": " Neither internal nor external? Ignore.", - "start": 4294, - "end": 4335, + "start": 4734, + "end": 4775, "loc": { "start": { - "line": 117, + "line": 133, "column": 6 }, "end": { - "line": 117, + "line": 133, "column": 47 } } @@ -81065,15 +82641,15 @@ { "type": "CommentLine", "value": " Since the user interface combines specifiers into a single list,", - "start": 4382, - "end": 4449, + "start": 4822, + "end": 4889, "loc": { "start": { - "line": 122, + "line": 138, "column": 4 }, "end": { - "line": 122, + "line": 138, "column": 71 } } @@ -81081,15 +82657,15 @@ { "type": "CommentLine", "value": " it doesn't remember if the specifier to be deleted is internal", - "start": 4454, - "end": 4519, + "start": 4894, + "end": 4959, "loc": { "start": { - "line": 123, + "line": 139, "column": 4 }, "end": { - "line": 123, + "line": 139, "column": 69 } } @@ -81097,15 +82673,15 @@ { "type": "CommentLine", "value": " or external. We delete the intended specifier from both arrays.", - "start": 4524, - "end": 4590, + "start": 4964, + "end": 5030, "loc": { "start": { - "line": 124, + "line": 140, "column": 4 }, "end": { - "line": 124, + "line": 140, "column": 70 } } @@ -81113,15 +82689,15 @@ { "type": "CommentLine", "value": " Given a phylogeny, determine which node labels we expect this phyloref to", - "start": 5145, - "end": 5221, + "start": 5585, + "end": 5661, "loc": { "start": { - "line": 138, + "line": 154, "column": 4 }, "end": { - "line": 138, + "line": 154, "column": 80 } } @@ -81129,15 +82705,15 @@ { "type": "CommentLine", "value": " resolve to. To do this, we:", - "start": 5226, - "end": 5256, + "start": 5666, + "end": 5696, "loc": { "start": { - "line": 139, + "line": 155, "column": 4 }, "end": { - "line": 139, + "line": 155, "column": 34 } } @@ -81145,15 +82721,15 @@ { "type": "CommentLine", "value": " 1. Find all node labels that are case-sensitively identical", - "start": 5261, - "end": 5324, + "start": 5701, + "end": 5764, "loc": { "start": { - "line": 140, + "line": 156, "column": 4 }, "end": { - "line": 140, + "line": 156, "column": 67 } } @@ -81161,15 +82737,15 @@ { "type": "CommentLine", "value": " to the phyloreference.", - "start": 5329, - "end": 5358, + "start": 5769, + "end": 5798, "loc": { "start": { - "line": 141, + "line": 157, "column": 4 }, "end": { - "line": 141, + "line": 157, "column": 33 } } @@ -81177,15 +82753,15 @@ { "type": "CommentLine", "value": " 2. Find all node labels that have additionalNodeProperties with", - "start": 5363, - "end": 5430, + "start": 5803, + "end": 5870, "loc": { "start": { - "line": 142, + "line": 158, "column": 4 }, "end": { - "line": 142, + "line": 158, "column": 71 } } @@ -81193,15 +82769,15 @@ { "type": "CommentLine", "value": " expectedPhyloreferenceNamed case-sensitively identical to", - "start": 5435, - "end": 5499, + "start": 5875, + "end": 5939, "loc": { "start": { - "line": 143, + "line": 159, "column": 4 }, "end": { - "line": 143, + "line": 159, "column": 68 } } @@ -81209,15 +82785,15 @@ { "type": "CommentLine", "value": " the phyloreference.", - "start": 5504, - "end": 5530, + "start": 5944, + "end": 5970, "loc": { "start": { - "line": 144, + "line": 160, "column": 4 }, "end": { - "line": 144, + "line": 160, "column": 30 } } @@ -81225,15 +82801,15 @@ { "type": "CommentLine", "value": " Is this node label identical to the phyloreference name?", - "start": 5728, - "end": 5787, + "start": 6168, + "end": 6227, "loc": { "start": { - "line": 152, + "line": 168, "column": 6 }, "end": { - "line": 152, + "line": 168, "column": 65 } } @@ -81241,15 +82817,15 @@ { "type": "CommentLine", "value": " Does this node label have an expectedPhyloreferenceNamed that", - "start": 6106, - "end": 6170, + "start": 6546, + "end": 6610, "loc": { "start": { - "line": 160, + "line": 176, "column": 8 }, "end": { - "line": 160, + "line": 176, "column": 72 } } @@ -81257,15 +82833,15 @@ { "type": "CommentLine", "value": " includes this phyloreference name?", - "start": 6179, - "end": 6216, + "start": 6619, + "end": 6656, "loc": { "start": { - "line": 161, + "line": 177, "column": 8 }, "end": { - "line": 161, + "line": 177, "column": 45 } } @@ -81273,15 +82849,15 @@ { "type": "CommentLine", "value": " Return node labels sorted alphabetically.", - "start": 6475, - "end": 6519, + "start": 6915, + "end": 6959, "loc": { "start": { - "line": 173, + "line": 189, "column": 4 }, "end": { - "line": 173, + "line": 189, "column": 48 } } @@ -81289,15 +82865,15 @@ { "type": "CommentLine", "value": " Return dictionary of all phyloref statuses in English", - "start": 6609, - "end": 6665, + "start": 7049, + "end": 7105, "loc": { "start": { - "line": 178, + "line": 194, "column": 4 }, "end": { - "line": 178, + "line": 194, "column": 60 } } @@ -81305,15 +82881,15 @@ { "type": "CommentLine", "value": " Return a result object that contains:", - "start": 6950, - "end": 6990, + "start": 7390, + "end": 7430, "loc": { "start": { - "line": 190, + "line": 206, "column": 4 }, "end": { - "line": 190, + "line": 206, "column": 44 } } @@ -81321,15 +82897,15 @@ { "type": "CommentLine", "value": " - status: phyloreference status as a short URI (CURIE)", - "start": 6995, - "end": 7053, + "start": 7435, + "end": 7493, "loc": { "start": { - "line": 191, + "line": 207, "column": 4 }, "end": { - "line": 191, + "line": 207, "column": 62 } } @@ -81337,15 +82913,15 @@ { "type": "CommentLine", "value": " - statusInEnglish: an English representation of the phyloref status", - "start": 7058, - "end": 7129, + "start": 7498, + "end": 7569, "loc": { "start": { - "line": 192, + "line": 208, "column": 4 }, "end": { - "line": 192, + "line": 208, "column": 75 } } @@ -81353,15 +82929,15 @@ { "type": "CommentLine", "value": " - intervalStart: the start of the interval", - "start": 7134, - "end": 7180, + "start": 7574, + "end": 7620, "loc": { "start": { - "line": 193, + "line": 209, "column": 4 }, "end": { - "line": 193, + "line": 209, "column": 50 } } @@ -81369,15 +82945,15 @@ { "type": "CommentLine", "value": " - intervalEnd: the end of the interval", - "start": 7185, - "end": 7227, + "start": 7625, + "end": 7667, "loc": { "start": { - "line": 194, + "line": 210, "column": 4 }, "end": { - "line": 194, + "line": 210, "column": 46 } } @@ -81385,15 +82961,15 @@ { "type": "CommentLine", "value": " If we have any pso:holdsStatusInTime entries, pick the first one and", - "start": 7424, - "end": 7495, + "start": 7864, + "end": 7935, "loc": { "start": { - "line": 201, + "line": 217, "column": 6 }, "end": { - "line": 201, + "line": 217, "column": 77 } } @@ -81401,15 +82977,15 @@ { "type": "CommentLine", "value": " extract the CURIE and time interval information from it.", - "start": 7502, - "end": 7561, + "start": 7942, + "end": 8001, "loc": { "start": { - "line": 202, + "line": 218, "column": 6 }, "end": { - "line": 202, + "line": 218, "column": 65 } } @@ -81417,15 +82993,15 @@ { "type": "CommentLine", "value": " Look for time interval information", - "start": 7760, - "end": 7797, + "start": 8200, + "end": 8237, "loc": { "start": { - "line": 206, + "line": 222, "column": 6 }, "end": { - "line": 206, + "line": 222, "column": 43 } } @@ -81433,15 +83009,15 @@ { "type": "CommentLine", "value": " Return result object", - "start": 8206, - "end": 8229, + "start": 8646, + "end": 8669, "loc": { "start": { - "line": 216, + "line": 232, "column": 6 }, "end": { - "line": 216, + "line": 232, "column": 29 } } @@ -81449,15 +83025,15 @@ { "type": "CommentLine", "value": " If we couldn't figure out a status for this phyloref, assume it's a draft.", - "start": 8412, - "end": 8489, + "start": 8852, + "end": 8929, "loc": { "start": { - "line": 225, + "line": 241, "column": 4 }, "end": { - "line": 225, + "line": 241, "column": 81 } } @@ -81465,15 +83041,15 @@ { "type": "CommentLine", "value": " Return a list of status changes for a particular phyloreference", - "start": 8654, - "end": 8720, + "start": 9094, + "end": 9160, "loc": { "start": { - "line": 233, + "line": 249, "column": 4 }, "end": { - "line": 233, + "line": 249, "column": 70 } } @@ -81481,15 +83057,15 @@ { "type": "CommentLine", "value": " Create a statusCURIE convenience field.", - "start": 8881, - "end": 8923, + "start": 9321, + "end": 9363, "loc": { "start": { - "line": 238, + "line": 254, "column": 8 }, "end": { - "line": 238, + "line": 254, "column": 50 } } @@ -81497,15 +83073,15 @@ { "type": "CommentLine", "value": " Create intervalStart/intervalEnd convenient fields", - "start": 9149, - "end": 9202, + "start": 9589, + "end": 9642, "loc": { "start": { - "line": 244, + "line": 260, "column": 8 }, "end": { - "line": 244, + "line": 260, "column": 61 } } @@ -81513,15 +83089,15 @@ { "type": "CommentLine", "value": " No changes? Return an empty list.", - "start": 9823, - "end": 9859, + "start": 10263, + "end": 10299, "loc": { "start": { - "line": 262, + "line": 278, "column": 4 }, "end": { - "line": 262, + "line": 278, "column": 40 } } @@ -81529,15 +83105,15 @@ { "type": "CommentLine", "value": " Set the status of a phyloreference", - "start": 9906, - "end": 9943, + "start": 10346, + "end": 10383, "loc": { "start": { - "line": 267, + "line": 283, "column": 4 }, "end": { - "line": 267, + "line": 283, "column": 41 } } @@ -81545,15 +83121,15 @@ { "type": "CommentLine", "value": "", - "start": 9948, - "end": 9950, + "start": 10388, + "end": 10390, "loc": { "start": { - "line": 268, + "line": 284, "column": 4 }, "end": { - "line": 268, + "line": 284, "column": 6 } } @@ -81561,15 +83137,15 @@ { "type": "CommentLine", "value": " Check whether we have a valid status CURIE.", - "start": 9955, - "end": 10001, + "start": 10395, + "end": 10441, "loc": { "start": { - "line": 269, + "line": 285, "column": 4 }, "end": { - "line": 269, + "line": 285, "column": 50 } } @@ -81577,15 +83153,15 @@ { "type": "CommentLine", "value": " See if we can end the previous interval.", - "start": 10168, - "end": 10211, + "start": 10608, + "end": 10651, "loc": { "start": { - "line": 274, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 290, "column": 47 } } @@ -81593,15 +83169,15 @@ { "type": "CommentLine", "value": " Vue.set(this.phyloref, 'pso:holdsStatusInTime', []);", - "start": 10335, - "end": 10390, + "start": 10775, + "end": 10830, "loc": { "start": { - "line": 278, + "line": 294, "column": 6 }, "end": { - "line": 278, + "line": 294, "column": 61 } } @@ -81609,15 +83185,15 @@ { "type": "CommentLine", "value": " Check to see if there's a previous time interval we should end.", - "start": 10453, - "end": 10519, + "start": 10893, + "end": 10959, "loc": { "start": { - "line": 282, + "line": 298, "column": 4 }, "end": { - "line": 282, + "line": 298, "column": 70 } } @@ -81625,15 +83201,15 @@ { "type": "CommentLine", "value": " if (!has(lastStatusInTime, 'tvc:atTime'))", - "start": 10785, - "end": 10829, + "start": 11225, + "end": 11269, "loc": { "start": { - "line": 289, + "line": 305, "column": 6 }, "end": { - "line": 289, + "line": 305, "column": 50 } } @@ -81641,15 +83217,15 @@ { "type": "CommentLine", "value": " Vue.set(lastStatusInTime, 'tvc:atTime', {});", - "start": 10836, - "end": 10884, + "start": 11276, + "end": 11324, "loc": { "start": { - "line": 290, + "line": 306, "column": 6 }, "end": { - "line": 290, + "line": 306, "column": 54 } } @@ -81657,15 +83233,15 @@ { "type": "CommentLine", "value": " If the last time entry doesn't already have an interval end date, set it to now.", - "start": 11081, - "end": 11164, + "start": 11521, + "end": 11604, "loc": { "start": { - "line": 295, + "line": 311, "column": 8 }, "end": { - "line": 295, + "line": 311, "column": 91 } } @@ -81673,15 +83249,15 @@ { "type": "CommentLine", "value": " Create new entry.", - "start": 11273, - "end": 11293, + "start": 11713, + "end": 11733, "loc": { "start": { - "line": 300, + "line": 316, "column": 4 }, "end": { - "line": 300, + "line": 316, "column": 24 } } @@ -81689,15 +83265,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n ", - "start": 11547, - "end": 11925, + "start": 11987, + "end": 12365, "loc": { "start": { - "line": 310, + "line": 326, "column": 2 }, "end": { - "line": 316, + "line": 332, "column": 5 } } @@ -81705,15 +83281,15 @@ { "type": "CommentBlock", "value": "*\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n ", - "start": 12405, - "end": 12681, + "start": 12845, + "end": 13121, "loc": { "start": { - "line": 335, + "line": 351, "column": 2 }, "end": { - "line": 340, + "line": 356, "column": 5 } } @@ -81721,15 +83297,15 @@ { "type": "CommentLine", "value": " Check to see if we have a single nomenclatural code to use.", - "start": 12713, - "end": 12775, + "start": 13153, + "end": 13215, "loc": { "start": { - "line": 342, + "line": 358, "column": 4 }, "end": { - "line": 342, + "line": 358, "column": 66 } } @@ -81737,15 +83313,15 @@ { "type": "CommentLine", "value": " If one or more of our specifiers have no nomenclatural code (e.g. if", - "start": 12854, - "end": 12925, + "start": 13294, + "end": 13365, "loc": { "start": { - "line": 345, + "line": 361, "column": 4 }, "end": { - "line": 345, + "line": 361, "column": 75 } } @@ -81753,15 +83329,15 @@ { "type": "CommentLine", "value": " they are specimens), they will show up as owlterms.UNKNOWN_CODE.", - "start": 12930, - "end": 12997, + "start": 13370, + "end": 13437, "loc": { "start": { - "line": 346, + "line": 362, "column": 4 }, "end": { - "line": 346, + "line": 362, "column": 71 } } @@ -81769,15 +83345,15 @@ { "type": "CommentLine", "value": " If we have a single nomenclatural code *apart* from all the", - "start": 13002, - "end": 13064, + "start": 13442, + "end": 13504, "loc": { "start": { - "line": 347, + "line": 363, "column": 4 }, "end": { - "line": 347, + "line": 363, "column": 66 } } @@ -81785,15 +83361,15 @@ { "type": "CommentLine", "value": " owlterms.UNKNOWN_CODEs, then that is still usable as a default", - "start": 13069, - "end": 13134, + "start": 13509, + "end": 13574, "loc": { "start": { - "line": 348, + "line": 364, "column": 4 }, "end": { - "line": 348, + "line": 364, "column": 69 } } @@ -81801,15 +83377,15 @@ { "type": "CommentLine", "value": " nomenclatural code for this phyloreference.", - "start": 13139, - "end": 13185, + "start": 13579, + "end": 13625, "loc": { "start": { - "line": 349, + "line": 365, "column": 4 }, "end": { - "line": 349, + "line": 365, "column": 50 } } @@ -81817,15 +83393,15 @@ { "type": "CommentBlock", "value": "*\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n ", - "start": 13423, - "end": 14548, + "start": 13863, + "end": 14988, "loc": { "start": { - "line": 357, + "line": 373, "column": 2 }, "end": { - "line": 373, + "line": 389, "column": 5 } } @@ -81833,15 +83409,15 @@ { "type": "CommentBlock", "value": " Generate a label that represents this component class. ", - "start": 15024, - "end": 15084, + "start": 15464, + "end": 15524, "loc": { "start": { - "line": 385, + "line": 401, "column": 4 }, "end": { - "line": 385, + "line": 401, "column": 64 } } @@ -81849,15 +83425,15 @@ { "type": "CommentLine", "value": " By default, taxonomic unit labels don't include the nomenclatural code.", - "start": 15090, - "end": 15164, + "start": 15530, + "end": 15604, "loc": { "start": { - "line": 387, + "line": 403, "column": 4 }, "end": { - "line": 387, + "line": 403, "column": 78 } } @@ -81865,15 +83441,15 @@ { "type": "CommentLine", "value": " However, we should include that here in order to distinguish between", - "start": 15169, - "end": 15240, + "start": 15609, + "end": 15680, "loc": { "start": { - "line": 388, + "line": 404, "column": 4 }, "end": { - "line": 388, + "line": 404, "column": 75 } } @@ -81881,15 +83457,15 @@ { "type": "CommentLine", "value": " taxonomic names in different taxonomic codes. This method generates that", - "start": 15245, - "end": 15320, + "start": 15685, + "end": 15760, "loc": { "start": { - "line": 389, + "line": 405, "column": 4 }, "end": { - "line": 389, + "line": 405, "column": 79 } } @@ -81897,15 +83473,15 @@ { "type": "CommentLine", "value": " name for a specifier.", - "start": 15325, - "end": 15349, + "start": 15765, + "end": 15789, "loc": { "start": { - "line": 390, + "line": 406, "column": 4 }, "end": { - "line": 390, + "line": 406, "column": 28 } } @@ -81913,15 +83489,15 @@ { "type": "CommentLine", "value": " Start with the internal specifiers, concatenated with '&'.", - "start": 15818, - "end": 15879, + "start": 16258, + "end": 16319, "loc": { "start": { - "line": 402, + "line": 418, "column": 4 }, "end": { - "line": 402, + "line": 418, "column": 65 } } @@ -81929,15 +83505,15 @@ { "type": "CommentLine", "value": " Add the external specifiers, concatenated with 'V'.", - "start": 16159, - "end": 16213, + "start": 16599, + "end": 16653, "loc": { "start": { - "line": 412, + "line": 428, "column": 6 }, "end": { - "line": 412, + "line": 428, "column": 60 } } @@ -81945,15 +83521,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`component class label: ${componentClassLabel}\\n`);", - "start": 16417, - "end": 16492, + "start": 16857, + "end": 16932, "loc": { "start": { - "line": 420, + "line": 436, "column": 4 }, "end": { - "line": 420, + "line": 436, "column": 79 } } @@ -81961,15 +83537,15 @@ { "type": "CommentLine", "value": " TODO We need to replace this with an actual object-based comparison,", - "start": 16498, - "end": 16569, + "start": 16938, + "end": 17009, "loc": { "start": { - "line": 422, + "line": 438, "column": 4 }, "end": { - "line": 422, + "line": 438, "column": 75 } } @@ -81977,15 +83553,15 @@ { "type": "CommentLine", "value": " rather than trusting the labels to tell us everything.", - "start": 16574, - "end": 16631, + "start": 17014, + "end": 17071, "loc": { "start": { - "line": 423, + "line": 439, "column": 4 }, "end": { - "line": 423, + "line": 439, "column": 61 } } @@ -81993,15 +83569,15 @@ { "type": "CommentLine", "value": " If we see the same label again, return the previously defined component class.", - "start": 16721, - "end": 16802, + "start": 17161, + "end": 17242, "loc": { "start": { - "line": 425, + "line": 441, "column": 6 }, "end": { - "line": 425, + "line": 441, "column": 87 } } @@ -82009,15 +83585,15 @@ { "type": "CommentLine", "value": " Create a new component class for this set of internal and external specifiers.", - "start": 16896, - "end": 16977, + "start": 17336, + "end": 17417, "loc": { "start": { - "line": 429, + "line": 445, "column": 4 }, "end": { - "line": 429, + "line": 445, "column": 85 } } @@ -82025,15 +83601,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);", - "start": 17133, - "end": 17222, + "start": 17573, + "end": 17662, "loc": { "start": { - "line": 433, + "line": 449, "column": 4 }, "end": { - "line": 433, + "line": 449, "column": 93 } } @@ -82041,15 +83617,15 @@ { "type": "CommentLine", "value": " Save it in the cache for later usage.", - "start": 17679, - "end": 17719, + "start": 18119, + "end": 18159, "loc": { "start": { - "line": 447, + "line": 463, "column": 4 }, "end": { - "line": 447, + "line": 463, "column": 44 } } @@ -82057,15 +83633,15 @@ { "type": "CommentLine", "value": " The first time we create a componentClass, we include it into the logical", - "start": 17797, - "end": 17873, + "start": 18237, + "end": 18313, "loc": { "start": { - "line": 450, + "line": 466, "column": 4 }, "end": { - "line": 450, + "line": 466, "column": 80 } } @@ -82073,15 +83649,15 @@ { "type": "CommentLine", "value": " expression directly. On subsequent calls, we'll only return the `@id`", - "start": 17878, - "end": 17950, + "start": 18318, + "end": 18390, "loc": { "start": { - "line": 451, + "line": 467, "column": 4 }, "end": { - "line": 451, + "line": 467, "column": 76 } } @@ -82089,15 +83665,15 @@ { "type": "CommentLine", "value": " (see above).", - "start": 17955, - "end": 17970, + "start": 18395, + "end": 18410, "loc": { "start": { - "line": 452, + "line": 468, "column": 4 }, "end": { - "line": 452, + "line": 468, "column": 19 } } @@ -82105,15 +83681,15 @@ { "type": "CommentBlock", "value": "*\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n ", - "start": 18233, - "end": 18345, + "start": 18673, + "end": 18785, "loc": { "start": { - "line": 464, + "line": 480, "column": 2 }, "end": { - "line": 467, + "line": 483, "column": 5 } } @@ -82121,15 +83697,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 18472, - "end": 18489, + "start": 18912, + "end": 18929, "loc": { "start": { - "line": 471, + "line": 487, "column": 38 }, "end": { - "line": 471, + "line": 487, "column": 55 } } @@ -82137,15 +83713,15 @@ { "type": "CommentBlock", "value": "\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n ", - "start": 18864, - "end": 20362, + "start": 19304, + "end": 20802, "loc": { "start": { - "line": 486, + "line": 502, "column": 2 }, "end": { - "line": 511, + "line": 527, "column": 5 } } @@ -82153,15 +83729,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:", - "start": 20444, - "end": 20512, + "start": 20884, + "end": 20952, "loc": { "start": { - "line": 513, + "line": 529, "column": 4 }, "end": { - "line": 513, + "line": 529, "column": 72 } } @@ -82169,15 +83745,15 @@ { "type": "CommentLine", "value": " ${remainingInternals.length}, selected: ${selected.length}\\n`);", - "start": 20517, - "end": 20583, + "start": 20957, + "end": 21023, "loc": { "start": { - "line": 514, + "line": 530, "column": 4 }, "end": { - "line": 514, + "line": 530, "column": 70 } } @@ -82185,15 +83761,15 @@ { "type": "CommentLine", "value": " Quick special case: if we have two 'remainingInternals' and zero selecteds,", - "start": 20589, - "end": 20667, + "start": 21029, + "end": 21107, "loc": { "start": { - "line": 516, + "line": 532, "column": 4 }, "end": { - "line": 516, + "line": 532, "column": 82 } } @@ -82201,15 +83777,15 @@ { "type": "CommentLine", "value": " we can just return the MRCA for two internal specifiers.", - "start": 20672, - "end": 20731, + "start": 21112, + "end": 21171, "loc": { "start": { - "line": 517, + "line": 533, "column": 4 }, "end": { - "line": 517, + "line": 533, "column": 63 } } @@ -82217,15 +83793,15 @@ { "type": "CommentLine", "value": " Step 1. If we've already selected something, create an expression for it.", - "start": 21212, - "end": 21288, + "start": 21652, + "end": 21728, "loc": { "start": { - "line": 530, + "line": 546, "column": 4 }, "end": { - "line": 530, + "line": 546, "column": 80 } } @@ -82233,15 +83809,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 22521, - "end": 22538, + "start": 22961, + "end": 22978, "loc": { "start": { - "line": 566, + "line": 582, "column": 40 }, "end": { - "line": 566, + "line": 582, "column": 57 } } @@ -82249,15 +83825,15 @@ { "type": "CommentLine", "value": " Step 2. Now select everything from remaining once, and start recursing through", - "start": 22834, - "end": 22915, + "start": 23274, + "end": 23355, "loc": { "start": { - "line": 578, + "line": 594, "column": 4 }, "end": { - "line": 578, + "line": 594, "column": 85 } } @@ -82265,15 +83841,15 @@ { "type": "CommentLine", "value": " every possibility.", - "start": 22920, - "end": 22941, + "start": 23360, + "end": 23381, "loc": { "start": { - "line": 579, + "line": 595, "column": 4 }, "end": { - "line": 579, + "line": 595, "column": 25 } } @@ -82281,15 +83857,15 @@ { "type": "CommentLine", "value": " Note that we only process cases where there are more remainingInternals than", - "start": 22946, - "end": 23025, + "start": 23386, + "end": 23465, "loc": { "start": { - "line": 580, + "line": 596, "column": 4 }, "end": { - "line": 580, + "line": 596, "column": 83 } } @@ -82297,15 +83873,15 @@ { "type": "CommentLine", "value": " selected internals -- when there are fewer, we'll just end up with the inverses", - "start": 23030, - "end": 23112, + "start": 23470, + "end": 23552, "loc": { "start": { - "line": 581, + "line": 597, "column": 4 }, "end": { - "line": 581, + "line": 597, "column": 86 } } @@ -82313,15 +83889,15 @@ { "type": "CommentLine", "value": " of the previous comparisons, which we'll already have covered.", - "start": 23117, - "end": 23182, + "start": 23557, + "end": 23622, "loc": { "start": { - "line": 582, + "line": 598, "column": 4 }, "end": { - "line": 582, + "line": 598, "column": 69 } } @@ -82329,15 +83905,15 @@ { "type": "CommentLine", "value": " The new remaining is the old remaining minus the selected TU.", - "start": 23383, - "end": 23447, + "start": 23823, + "end": 23887, "loc": { "start": { - "line": 586, + "line": 602, "column": 8 }, "end": { - "line": 586, + "line": 602, "column": 72 } } @@ -82345,15 +83921,15 @@ { "type": "CommentLine", "value": " The new selected is the old selected plus the selected TU.", - "start": 23517, - "end": 23578, + "start": 23957, + "end": 24018, "loc": { "start": { - "line": 588, + "line": 604, "column": 8 }, "end": { - "line": 588, + "line": 604, "column": 69 } } @@ -82361,15 +83937,15 @@ { "type": "CommentBlock", "value": "\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n ", - "start": 23766, - "end": 23972, + "start": 24206, + "end": 24412, "loc": { "start": { - "line": 598, + "line": 614, "column": 2 }, "end": { - "line": 606, + "line": 622, "column": 5 } } @@ -82377,15 +83953,15 @@ { "type": "CommentLine", "value": " Keep all currently extant data.", - "start": 24003, - "end": 24037, + "start": 24443, + "end": 24477, "loc": { "start": { - "line": 608, + "line": 624, "column": 4 }, "end": { - "line": 608, + "line": 624, "column": 38 } } @@ -82393,15 +83969,15 @@ { "type": "CommentLine", "value": " Set the @id and @type. If we don't already have an '@id', use the", - "start": 24098, - "end": 24166, + "start": 24538, + "end": 24606, "loc": { "start": { - "line": 611, + "line": 627, "column": 4 }, "end": { - "line": 611, + "line": 627, "column": 72 } } @@ -82409,15 +83985,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 24171, - "end": 24186, + "start": 24611, + "end": 24626, "loc": { "start": { - "line": 612, + "line": 628, "column": 4 }, "end": { - "line": 612, + "line": 628, "column": 19 } } @@ -82425,15 +84001,15 @@ { "type": "CommentLine", "value": " If we don't have a bibliographicCitation but we do have a definition source,", - "start": 24315, - "end": 24394, + "start": 24755, + "end": 24834, "loc": { "start": { - "line": 616, + "line": 632, "column": 4 }, "end": { - "line": 616, + "line": 632, "column": 83 } } @@ -82441,15 +84017,15 @@ { "type": "CommentLine", "value": " then generate a bibliographicCitation for the source.", - "start": 24399, - "end": 24455, + "start": 24839, + "end": 24895, "loc": { "start": { - "line": 617, + "line": 633, "column": 4 }, "end": { - "line": 617, + "line": 633, "column": 60 } } @@ -82457,15 +84033,15 @@ { "type": "CommentLine", "value": " Construct a class expression for this phyloreference.", - "start": 24754, - "end": 24810, + "start": 25194, + "end": 25250, "loc": { "start": { - "line": 625, + "line": 641, "column": 4 }, "end": { - "line": 625, + "line": 641, "column": 60 } } @@ -82473,15 +84049,15 @@ { "type": "CommentLine", "value": " If it is an apomorphy-based class expression, we should generate a", - "start": 24964, - "end": 25033, + "start": 25404, + "end": 25473, "loc": { "start": { - "line": 629, + "line": 645, "column": 4 }, "end": { - "line": 629, + "line": 645, "column": 73 } } @@ -82489,15 +84065,15 @@ { "type": "CommentLine", "value": " logical expression that describes the apomorphy.", - "start": 25038, - "end": 25089, + "start": 25478, + "end": 25529, "loc": { "start": { - "line": 630, + "line": 646, "column": 4 }, "end": { - "line": 630, + "line": 646, "column": 55 } } @@ -82505,15 +84081,15 @@ { "type": "CommentLine", "value": " This is an apomorphy-based definition!", - "start": 25296, - "end": 25337, + "start": 25736, + "end": 25777, "loc": { "start": { - "line": 636, + "line": 652, "column": 6 }, "end": { - "line": 636, + "line": 652, "column": 47 } } @@ -82521,15 +84097,15 @@ { "type": "CommentLine", "value": " Someday, we will probably want to turn this apomorphy into a", - "start": 25476, - "end": 25539, + "start": 25916, + "end": 25979, "loc": { "start": { - "line": 642, + "line": 658, "column": 6 }, "end": { - "line": 642, + "line": 658, "column": 69 } } @@ -82537,15 +84113,15 @@ { "type": "CommentLine", "value": " logical expression so that it can be computed alongside other", - "start": 25546, - "end": 25610, + "start": 25986, + "end": 26050, "loc": { "start": { - "line": 643, + "line": 659, "column": 6 }, "end": { - "line": 643, + "line": 659, "column": 70 } } @@ -82553,15 +84129,15 @@ { "type": "CommentLine", "value": " OWL ontologies. This is outside our scope for the moment, so", - "start": 25617, - "end": 25680, + "start": 26057, + "end": 26120, "loc": { "start": { - "line": 644, + "line": 660, "column": 6 }, "end": { - "line": 644, + "line": 660, "column": 69 } } @@ -82569,15 +84145,15 @@ { "type": "CommentLine", "value": " we will simply pass on the phyloreference as-is.", - "start": 25687, - "end": 25738, + "start": 26127, + "end": 26178, "loc": { "start": { - "line": 645, + "line": 661, "column": 6 }, "end": { - "line": 645, + "line": 661, "column": 57 } } @@ -82585,15 +84161,15 @@ { "type": "CommentLine", "value": " We might need to make component classes.", - "start": 25782, - "end": 25825, + "start": 26222, + "end": 26265, "loc": { "start": { - "line": 650, + "line": 666, "column": 4 }, "end": { - "line": 650, + "line": 666, "column": 47 } } @@ -82601,15 +84177,15 @@ { "type": "CommentLine", "value": " So we reset our component class counts and records.", - "start": 25830, - "end": 25884, + "start": 26270, + "end": 26324, "loc": { "start": { - "line": 651, + "line": 667, "column": 4 }, "end": { - "line": 651, + "line": 667, "column": 58 } } @@ -82617,15 +84193,15 @@ { "type": "CommentLine", "value": " The type of this phyloreference.", - "start": 25963, - "end": 25998, + "start": 26403, + "end": 26438, "loc": { "start": { - "line": 655, + "line": 671, "column": 4 }, "end": { - "line": 655, + "line": 671, "column": 39 } } @@ -82633,15 +84209,15 @@ { "type": "CommentLine", "value": " The list of logical expressions generated for this phyloref.", - "start": 26036, - "end": 26099, + "start": 26476, + "end": 26539, "loc": { "start": { - "line": 658, + "line": 674, "column": 4 }, "end": { - "line": 658, + "line": 674, "column": 67 } } @@ -82649,15 +84225,15 @@ { "type": "CommentLine", "value": " We can't handle phyloreferences without at least one internal specifier.", - "start": 26183, - "end": 26258, + "start": 26623, + "end": 26698, "loc": { "start": { - "line": 662, + "line": 678, "column": 6 }, "end": { - "line": 662, + "line": 678, "column": 81 } } @@ -82665,15 +84241,15 @@ { "type": "CommentLine", "value": " If the phyloreference has at least one external specifier, we", - "start": 26540, - "end": 26604, + "start": 26980, + "end": 27044, "loc": { "start": { - "line": 668, + "line": 684, "column": 6 }, "end": { - "line": 668, + "line": 684, "column": 70 } } @@ -82681,15 +84257,15 @@ { "type": "CommentLine", "value": " can provide a simplified expression for the internal specifier,", - "start": 26611, - "end": 26677, + "start": 27051, + "end": 27117, "loc": { "start": { - "line": 669, + "line": 685, "column": 6 }, "end": { - "line": 669, + "line": 685, "column": 72 } } @@ -82697,15 +84273,15 @@ { "type": "CommentLine", "value": " in the form:", - "start": 26684, - "end": 26699, + "start": 27124, + "end": 27139, "loc": { "start": { - "line": 670, + "line": 686, "column": 6 }, "end": { - "line": 670, + "line": 686, "column": 21 } } @@ -82713,15 +84289,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal1] and", - "start": 26706, - "end": 26751, + "start": 27146, + "end": 27191, "loc": { "start": { - "line": 671, + "line": 687, "column": 6 }, "end": { - "line": 671, + "line": 687, "column": 51 } } @@ -82729,15 +84305,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal2] and ...", - "start": 26758, - "end": 26807, + "start": 27198, + "end": 27247, "loc": { "start": { - "line": 672, + "line": 688, "column": 6 }, "end": { - "line": 672, + "line": 688, "column": 55 } } @@ -82745,15 +84321,15 @@ { "type": "CommentLine", "value": " phyloref:excludes_TU some [exclusion1] and", - "start": 26814, - "end": 26860, + "start": 27254, + "end": 27300, "loc": { "start": { - "line": 673, + "line": 689, "column": 6 }, "end": { - "line": 673, + "line": 689, "column": 52 } } @@ -82761,15 +84337,15 @@ { "type": "CommentLine", "value": " has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...", - "start": 26867, - "end": 26932, + "start": 27307, + "end": 27372, "loc": { "start": { - "line": 674, + "line": 690, "column": 6 }, "end": { - "line": 674, + "line": 690, "column": 71 } } @@ -82777,15 +84353,15 @@ { "type": "CommentLine", "value": "", - "start": 26939, - "end": 26941, + "start": 27379, + "end": 27381, "loc": { "start": { - "line": 675, + "line": 691, "column": 6 }, "end": { - "line": 675, + "line": 691, "column": 8 } } @@ -82793,15 +84369,15 @@ { "type": "CommentLine", "value": " Since we don't know which of the external specifiers will actually", - "start": 26948, - "end": 27017, + "start": 27388, + "end": 27457, "loc": { "start": { - "line": 676, + "line": 692, "column": 6 }, "end": { - "line": 676, + "line": 692, "column": 75 } } @@ -82809,15 +84385,15 @@ { "type": "CommentLine", "value": " be the one that will be used, we need to generate logical expressions", - "start": 27024, - "end": 27096, + "start": 27464, + "end": 27536, "loc": { "start": { - "line": 677, + "line": 693, "column": 6 }, "end": { - "line": 677, + "line": 693, "column": 78 } } @@ -82825,15 +84401,15 @@ { "type": "CommentLine", "value": " for every possibility.", - "start": 27103, - "end": 27128, + "start": 27543, + "end": 27568, "loc": { "start": { - "line": 678, + "line": 694, "column": 6 }, "end": { - "line": 678, + "line": 694, "column": 31 } } @@ -82841,15 +84417,15 @@ { "type": "CommentLine", "value": " Add the internal specifiers.", - "start": 27212, - "end": 27243, + "start": 27652, + "end": 27683, "loc": { "start": { - "line": 681, + "line": 697, "column": 8 }, "end": { - "line": 681, + "line": 697, "column": 39 } } @@ -82857,15 +84433,15 @@ { "type": "CommentLine", "value": " Add the selected external specifier.", - "start": 27375, - "end": 27414, + "start": 27815, + "end": 27854, "loc": { "start": { - "line": 686, + "line": 702, "column": 8 }, "end": { - "line": 686, + "line": 702, "column": 47 } } @@ -82873,15 +84449,15 @@ { "type": "CommentLine", "value": " Collect all of the externals that are not selected.", - "start": 27698, - "end": 27752, + "start": 28138, + "end": 28192, "loc": { "start": { - "line": 696, + "line": 712, "column": 8 }, "end": { - "line": 696, + "line": 712, "column": 62 } } @@ -82889,15 +84465,15 @@ { "type": "CommentLine", "value": " Add the remaining externals, which we assume will resolve outside of", - "start": 27855, - "end": 27926, + "start": 28295, + "end": 28366, "loc": { "start": { - "line": 699, + "line": 715, "column": 8 }, "end": { - "line": 699, + "line": 715, "column": 79 } } @@ -82905,15 +84481,15 @@ { "type": "CommentLine", "value": " this clade.", - "start": 27935, - "end": 27949, + "start": 28375, + "end": 28389, "loc": { "start": { - "line": 700, + "line": 716, "column": 8 }, "end": { - "line": 700, + "line": 716, "column": 22 } } @@ -82921,15 +84497,15 @@ { "type": "CommentLine", "value": " has_Ancestor", - "start": 28122, - "end": 28137, + "start": 28562, + "end": 28577, "loc": { "start": { - "line": 704, + "line": 720, "column": 44 }, "end": { - "line": 704, + "line": 720, "column": 59 } } @@ -82937,15 +84513,15 @@ { "type": "CommentLine", "value": " We only have internal specifiers. We therefore need to use the algorithm in", - "start": 28667, - "end": 28745, + "start": 29107, + "end": 29185, "loc": { "start": { - "line": 724, + "line": 740, "column": 6 }, "end": { - "line": 724, + "line": 740, "column": 84 } } @@ -82953,15 +84529,15 @@ { "type": "CommentLine", "value": " this.createClassExpressionsForInternals() to create this expression.", - "start": 28752, - "end": 28823, + "start": 29192, + "end": 29263, "loc": { "start": { - "line": 725, + "line": 741, "column": 6 }, "end": { - "line": 725, + "line": 741, "column": 77 } } @@ -82969,15 +84545,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, we set that as an equivalentClass", - "start": 28961, - "end": 29037, + "start": 29401, + "end": 29477, "loc": { "start": { - "line": 731, + "line": 747, "column": 4 }, "end": { - "line": 731, + "line": 747, "column": 80 } } @@ -82985,15 +84561,15 @@ { "type": "CommentLine", "value": " expression. If we have more than one, we produce multiple component classes", - "start": 29042, - "end": 29120, + "start": 29482, + "end": 29560, "loc": { "start": { - "line": 732, + "line": 748, "column": 4 }, "end": { - "line": 732, + "line": 748, "column": 82 } } @@ -83001,15 +84577,15 @@ { "type": "CommentLine", "value": " to represent it.", - "start": 29125, - "end": 29144, + "start": 29565, + "end": 29584, "loc": { "start": { - "line": 733, + "line": 749, "column": 4 }, "end": { - "line": 733, + "line": 749, "column": 23 } } @@ -83017,15 +84593,15 @@ { "type": "CommentLine", "value": " This is fine, as long as there is an explanation in", - "start": 29194, - "end": 29248, + "start": 29634, + "end": 29688, "loc": { "start": { - "line": 735, + "line": 751, "column": 6 }, "end": { - "line": 735, + "line": 751, "column": 60 } } @@ -83033,15 +84609,15 @@ { "type": "CommentLine", "value": " phyloref.malformedPhyloreference explaining why no logical expressions", - "start": 29255, - "end": 29328, + "start": 29695, + "end": 29768, "loc": { "start": { - "line": 736, + "line": 752, "column": 6 }, "end": { - "line": 736, + "line": 752, "column": 79 } } @@ -83049,15 +84625,15 @@ { "type": "CommentLine", "value": " could be generated. Otherwise, throw an error.", - "start": 29335, - "end": 29384, + "start": 29775, + "end": 29824, "loc": { "start": { - "line": 737, + "line": 753, "column": 6 }, "end": { - "line": 737, + "line": 753, "column": 55 } } @@ -83065,15 +84641,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, then that is what this phyloref", - "start": 29830, - "end": 29904, + "start": 30270, + "end": 30344, "loc": { "start": { - "line": 745, + "line": 761, "column": 6 }, "end": { - "line": 745, + "line": 761, "column": 80 } } @@ -83081,15 +84657,15 @@ { "type": "CommentLine", "value": " is equivalent to.", - "start": 29911, - "end": 29931, + "start": 30351, + "end": 30371, "loc": { "start": { - "line": 746, + "line": 762, "column": 6 }, "end": { - "line": 746, + "line": 762, "column": 26 } } @@ -83097,15 +84673,15 @@ { "type": "CommentLine", "value": " If we have multiple logical expressions, the phyloreference can be", - "start": 30015, - "end": 30084, + "start": 30455, + "end": 30524, "loc": { "start": { - "line": 749, + "line": 765, "column": 6 }, "end": { - "line": 749, + "line": 765, "column": 75 } } @@ -83113,15 +84689,15 @@ { "type": "CommentLine", "value": " represented by any of them. We model this by creating subclasses of", - "start": 30091, - "end": 30161, + "start": 30531, + "end": 30601, "loc": { "start": { - "line": 750, + "line": 766, "column": 6 }, "end": { - "line": 750, + "line": 766, "column": 76 } } @@ -83129,15 +84705,15 @@ { "type": "CommentLine", "value": " the phyloreference for each logical expression -- that way, it's clear", - "start": 30168, - "end": 30241, + "start": 30608, + "end": 30681, "loc": { "start": { - "line": 751, + "line": 767, "column": 6 }, "end": { - "line": 751, + "line": 767, "column": 79 } } @@ -83145,15 +84721,15 @@ { "type": "CommentLine", "value": " that these expressions aren't equivalent to each other (which is what", - "start": 30248, - "end": 30320, + "start": 30688, + "end": 30760, "loc": { "start": { - "line": 752, + "line": 768, "column": 6 }, "end": { - "line": 752, + "line": 768, "column": 78 } } @@ -83161,15 +84737,15 @@ { "type": "CommentLine", "value": " caused https://github.com/phyloref/phyx.js/issues/57), but nodes", - "start": 30327, - "end": 30394, + "start": 30767, + "end": 30834, "loc": { "start": { - "line": 753, + "line": 769, "column": 6 }, "end": { - "line": 753, + "line": 769, "column": 73 } } @@ -83177,15 +84753,15 @@ { "type": "CommentLine", "value": " resolved by any of those expressions will also be included in the", - "start": 30401, - "end": 30469, + "start": 30841, + "end": 30909, "loc": { "start": { - "line": 754, + "line": 770, "column": 6 }, "end": { - "line": 754, + "line": 770, "column": 74 } } @@ -83193,15 +84769,15 @@ { "type": "CommentLine", "value": " phyloreference itself.", - "start": 30476, - "end": 30501, + "start": 30916, + "end": 30941, "loc": { "start": { - "line": 755, + "line": 771, "column": 6 }, "end": { - "line": 755, + "line": 771, "column": 31 } } @@ -83209,15 +84785,15 @@ { "type": "CommentLine", "value": "", - "start": 30508, - "end": 30510, + "start": 30948, + "end": 30950, "loc": { "start": { - "line": 756, + "line": 772, "column": 6 }, "end": { - "line": 756, + "line": 772, "column": 8 } } @@ -83225,15 +84801,15 @@ { "type": "CommentLine", "value": " Note that there are two differences from the way in which we usually call", - "start": 30517, - "end": 30593, + "start": 30957, + "end": 31033, "loc": { "start": { - "line": 757, + "line": 773, "column": 6 }, "end": { - "line": 757, + "line": 773, "column": 82 } } @@ -83241,15 +84817,15 @@ { "type": "CommentLine", "value": " this.createComponentClass():", - "start": 30600, - "end": 30631, + "start": 31040, + "end": 31071, "loc": { "start": { - "line": 758, + "line": 774, "column": 6 }, "end": { - "line": 758, + "line": 774, "column": 37 } } @@ -83257,15 +84833,15 @@ { "type": "CommentLine", "value": " 1. Usually, createComponentClass() reuses logical expressions with the", - "start": 30638, - "end": 30712, + "start": 31078, + "end": 31152, "loc": { "start": { - "line": 759, + "line": 775, "column": 6 }, "end": { - "line": 759, + "line": 775, "column": 80 } } @@ -83273,15 +84849,15 @@ { "type": "CommentLine", "value": " same sets of internal and external specifiers. That won't work here,", - "start": 30719, - "end": 30794, + "start": 31159, + "end": 31234, "loc": { "start": { - "line": 760, + "line": 776, "column": 6 }, "end": { - "line": 760, + "line": 776, "column": 81 } } @@ -83289,15 +84865,15 @@ { "type": "CommentLine", "value": " since *all* these logical expressions have the same specifiers. So,", - "start": 30801, - "end": 30875, + "start": 31241, + "end": 31315, "loc": { "start": { - "line": 761, + "line": 777, "column": 6 }, "end": { - "line": 761, + "line": 777, "column": 80 } } @@ -83305,15 +84881,15 @@ { "type": "CommentLine", "value": " we turn off caching.", - "start": 30882, - "end": 30909, + "start": 31322, + "end": 31349, "loc": { "start": { - "line": 762, + "line": 778, "column": 6 }, "end": { - "line": 762, + "line": 778, "column": 33 } } @@ -83321,15 +84897,15 @@ { "type": "CommentLine", "value": " 2. We need to set each of these component classes to be a subclass of", - "start": 30916, - "end": 30989, + "start": 31356, + "end": 31429, "loc": { "start": { - "line": 763, + "line": 779, "column": 6 }, "end": { - "line": 763, + "line": 779, "column": 79 } } @@ -83337,15 +84913,15 @@ { "type": "CommentLine", "value": " this phyloreference so that it can include instances from each of the", - "start": 30996, - "end": 31072, + "start": 31436, + "end": 31512, "loc": { "start": { - "line": 764, + "line": 780, "column": 6 }, "end": { - "line": 764, + "line": 780, "column": 82 } } @@ -83353,15 +84929,15 @@ { "type": "CommentLine", "value": " logical expressions.", - "start": 31079, - "end": 31106, + "start": 31519, + "end": 31546, "loc": { "start": { - "line": 765, + "line": 781, "column": 6 }, "end": { - "line": 765, + "line": 781, "column": 33 } } @@ -83369,15 +84945,15 @@ { "type": "CommentLine", "value": " False in order to turn off caching by internal and external specifiers.", - "start": 31315, - "end": 31389, + "start": 31755, + "end": 31829, "loc": { "start": { - "line": 771, + "line": 787, "column": 8 }, "end": { - "line": 771, + "line": 787, "column": 82 } } @@ -83385,15 +84961,15 @@ { "type": "CommentLine", "value": " Make the new component class a subclass of this phyloreference.", - "start": 31413, - "end": 31479, + "start": 31853, + "end": 31919, "loc": { "start": { - "line": 773, + "line": 789, "column": 8 }, "end": { - "line": 773, + "line": 789, "column": 74 } } @@ -83401,15 +84977,15 @@ { "type": "CommentLine", "value": " Every phyloreference is a subclass of phyloref:Phyloreference.", - "start": 31526, - "end": 31591, + "start": 31966, + "end": 32031, "loc": { "start": { - "line": 778, + "line": 794, "column": 4 }, "end": { - "line": 778, + "line": 794, "column": 69 } } @@ -83417,15 +84993,15 @@ { "type": "CommentLine", "value": " If the this Phyloref has a phylorefType that differs from the calculated", - "start": 31862, - "end": 31937, + "start": 32302, + "end": 32377, "loc": { "start": { - "line": 785, + "line": 801, "column": 4 }, "end": { - "line": 785, + "line": 801, "column": 79 } } @@ -83433,15 +85009,15 @@ { "type": "CommentLine", "value": " phyloref type, throw an error.", - "start": 31942, - "end": 31975, + "start": 32382, + "end": 32415, "loc": { "start": { - "line": 786, + "line": 802, "column": 4 }, "end": { - "line": 786, + "line": 802, "column": 37 } } @@ -83690,7 +85266,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16F16PXH", + "value": "LXL9JK6ODIPBD", "start": 96, "end": 109, "loc": { @@ -84030,7 +85606,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16F16PXH", + "value": "LXL9JK6ODIPBD", "start": 159, "end": 172, "loc": { @@ -84296,7 +85872,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16F3DI31", + "value": "LXL9JK6OWJB6S", "start": 229, "end": 242, "loc": { @@ -84532,7 +86108,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16F3DI31", + "value": "LXL9JK6OWJB6S", "start": 308, "end": 321, "loc": { @@ -84665,7 +86241,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16FLNCZ4", + "value": "LXL9JK6OL1ASK", "start": 335, "end": 348, "loc": { @@ -84901,7 +86477,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16FLNCZ4", + "value": "LXL9JK6OL1ASK", "start": 412, "end": 425, "loc": { @@ -85034,7 +86610,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16FAQJ7Y", + "value": "LXL9JK6ORWVVE", "start": 439, "end": 452, "loc": { @@ -85270,7 +86846,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16FAQJ7Y", + "value": "LXL9JK6ORWVVE", "start": 510, "end": 523, "loc": { @@ -85403,7 +86979,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16FUW4KM", + "value": "LXL9JK6O9OPUJ", "start": 537, "end": 550, "loc": { @@ -85639,7 +87215,7 @@ "postfix": false, "binop": null }, - "value": "LKT4H16FUW4KM", + "value": "LXL9JK6O9OPUJ", "start": 606, "end": 619, "loc": { @@ -87422,16 +88998,1535 @@ }, { "type": "CommentBlock", - "value": "* Return the external specifiers of this phyloref (if any). 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"end": 1993, + "start": 2428, + "end": 2433, "loc": { "start": { - "line": 56, + "line": 72, "column": 58 }, "end": { - "line": 56, + "line": 72, "column": 63 } } @@ -90300,15 +93395,15 @@ "binop": null, "updateContext": null }, - "start": 1993, - "end": 1994, + "start": 2433, + "end": 2434, "loc": { "start": { - "line": 56, + "line": 72, "column": 63 }, "end": { - "line": 56, + "line": 72, "column": 64 } } @@ -90328,15 +93423,15 @@ "updateContext": null }, "value": "return", - "start": 2000, - "end": 2006, + "start": 2440, + "end": 2446, "loc": { "start": { - "line": 58, + "line": 74, "column": 4 }, "end": { - "line": 58, + "line": 74, "column": 10 } } @@ -90354,15 +93449,15 @@ "binop": null }, "value": "undefined", - "start": 2007, - "end": 2016, + "start": 2447, + "end": 2456, "loc": { "start": { - "line": 58, + "line": 74, "column": 11 }, "end": { - "line": 58, + "line": 74, "column": 20 } } @@ -90380,15 +93475,15 @@ "binop": null, "updateContext": null }, - "start": 2016, - "end": 2017, + "start": 2456, + "end": 2457, "loc": { "start": { - "line": 58, + "line": 74, "column": 20 }, "end": { - "line": 58, + "line": 74, "column": 21 } } @@ -90405,15 +93500,15 @@ "postfix": false, "binop": null }, - "start": 2020, - "end": 2021, + "start": 2460, + "end": 2461, "loc": { "start": { - "line": 59, + "line": 75, "column": 2 }, "end": { - "line": 59, + "line": 75, "column": 3 } } @@ -90431,15 +93526,15 @@ "binop": null }, "value": "set", - "start": 2025, - "end": 2028, + "start": 2465, + "end": 2468, "loc": { "start": { - "line": 61, + "line": 77, "column": 2 }, "end": { - "line": 61, + "line": 77, "column": 5 } } @@ -90457,15 +93552,15 @@ "binop": null }, "value": "label", - "start": 2029, - "end": 2034, + "start": 2469, + "end": 2474, "loc": { "start": { - "line": 61, + "line": 77, "column": 6 }, "end": { - "line": 61, + "line": 77, "column": 11 } } @@ -90482,15 +93577,15 @@ "postfix": false, "binop": null }, - "start": 2034, - "end": 2035, + "start": 2474, + "end": 2475, "loc": { "start": { - "line": 61, + "line": 77, "column": 11 }, "end": { - 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"start": 2243, - "end": 2244, + "start": 2683, + "end": 2684, "loc": { "start": { - "line": 67, + "line": 83, "column": 10 }, "end": { - "line": 67, + "line": 83, "column": 11 } } @@ -91271,15 +94366,15 @@ "binop": null }, "value": "phyloref", - "start": 2244, - "end": 2252, + "start": 2684, + "end": 2692, "loc": { "start": { - "line": 67, + "line": 83, "column": 11 }, "end": { - "line": 67, + "line": 83, "column": 19 } } @@ -91297,15 +94392,15 @@ "binop": null, "updateContext": null }, - "start": 2252, - "end": 2253, + "start": 2692, + "end": 2693, "loc": { "start": { - "line": 67, + "line": 83, "column": 19 }, "end": { - "line": 67, + "line": 83, "column": 20 } } @@ -91323,15 +94418,15 @@ "binop": null }, "value": "label", - "start": 2253, - "end": 2258, + "start": 2693, + "end": 2698, "loc": { "start": { - "line": 67, + "line": 83, "column": 20 }, "end": { - "line": 67, + "line": 83, "column": 25 } } @@ -91350,15 +94445,15 @@ "updateContext": null }, "value": "=", - "start": 2259, - 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", - "start": 2284, - "end": 2343, + "start": 2724, + "end": 2783, "loc": { "start": { - "line": 71, + "line": 87, "column": 2 }, "end": { - "line": 71, + "line": 87, "column": 61 } } @@ -91494,15 +94589,15 @@ "binop": null }, "value": "get", - "start": 2346, - "end": 2349, + "start": 2786, + "end": 2789, "loc": { "start": { - "line": 72, + "line": 88, "column": 2 }, "end": { - "line": 72, + "line": 88, "column": 5 } } @@ -91520,15 +94615,15 @@ "binop": null }, "value": "specifiers", - "start": 2350, - "end": 2360, + "start": 2790, + "end": 2800, "loc": { "start": { - "line": 72, + "line": 88, "column": 6 }, "end": { - "line": 72, + "line": 88, "column": 16 } } @@ -91545,15 +94640,15 @@ "postfix": false, "binop": null }, - "start": 2360, - "end": 2361, + "start": 2800, + "end": 2801, "loc": { "start": { - "line": 72, + "line": 88, "column": 16 }, "end": { - "line": 72, + "line": 88, "column": 17 } } @@ -91570,15 +94665,15 @@ "postfix": false, "binop": null }, - "start": 2361, - "end": 2362, + "start": 2801, + "end": 2802, "loc": { "start": { - "line": 72, + "line": 88, "column": 17 }, "end": { - "line": 72, + "line": 88, "column": 18 } } @@ -91595,15 +94690,15 @@ "postfix": false, "binop": null }, - "start": 2363, - "end": 2364, + "start": 2803, + "end": 2804, "loc": { "start": { - "line": 72, + "line": 88, "column": 19 }, "end": { - "line": 72, + "line": 88, "column": 20 } } @@ -91611,15 +94706,15 @@ { "type": "CommentLine", "value": " Returns a list of all specifiers by combining the internal and external", - "start": 2369, - "end": 2443, + "start": 2809, + "end": 2883, "loc": { "start": { - "line": 73, + "line": 89, "column": 4 }, "end": { - "line": 73, + "line": 89, "column": 78 } } @@ -91627,15 +94722,15 @@ { "type": "CommentLine", "value": " specifiers into a single list, with internal specifiers before", - "start": 2448, - "end": 2513, + "start": 2888, + "end": 2953, "loc": { "start": { - "line": 74, + "line": 90, "column": 4 }, "end": { - "line": 74, + "line": 90, "column": 69 } } @@ -91643,15 +94738,15 @@ { "type": "CommentLine", "value": " external specifiers.", - 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"line": 85, + "line": 101, "column": 53 }, "end": { - "line": 85, + "line": 101, "column": 59 } } @@ -92722,15 +95817,15 @@ "updateContext": null }, "value": "Internal", - "start": 2887, - "end": 2897, + "start": 3327, + "end": 3337, "loc": { "start": { - "line": 85, + "line": 101, "column": 60 }, "end": { - "line": 85, + "line": 101, "column": 70 } } @@ -92748,15 +95843,15 @@ "binop": null, "updateContext": null }, - "start": 2897, - "end": 2898, + "start": 3337, + "end": 3338, "loc": { "start": { - "line": 85, + "line": 101, "column": 70 }, "end": { - "line": 85, + "line": 101, "column": 71 } } @@ -92776,15 +95871,15 @@ "updateContext": null }, "value": "if", - "start": 2903, - "end": 2905, + "start": 3343, + "end": 3345, "loc": { "start": { - "line": 86, + "line": 102, "column": 4 }, "end": { - "line": 86, + "line": 102, "column": 6 } } @@ -92801,15 +95896,15 @@ "postfix": false, "binop": null }, - "start": 2906, - "end": 2907, + "start": 3346, + "end": 3347, "loc": { "start": { - "line": 86, + "line": 102, "column": 7 }, "end": { - 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"line": 86, + "line": 102, "column": 32 } } @@ -92933,15 +96028,15 @@ "binop": null }, "value": "includes", - "start": 2931, - "end": 2939, + "start": 3371, + "end": 3379, "loc": { "start": { - "line": 86, + "line": 102, "column": 32 }, "end": { - "line": 86, + "line": 102, "column": 40 } } @@ -92958,15 +96053,15 @@ "postfix": false, "binop": null }, - "start": 2939, - "end": 2940, + "start": 3379, + "end": 3380, "loc": { "start": { - "line": 86, + "line": 102, "column": 40 }, "end": { - "line": 86, + "line": 102, "column": 41 } } @@ -92984,15 +96079,15 @@ "binop": null }, "value": "specifier", - "start": 2940, - "end": 2949, + "start": 3380, + "end": 3389, "loc": { "start": { - "line": 86, + "line": 102, "column": 41 }, "end": { - "line": 86, + "line": 102, "column": 50 } } @@ -93009,15 +96104,15 @@ "postfix": false, "binop": null }, - "start": 2949, - "end": 2950, + "start": 3389, + "end": 3390, "loc": { "start": { - "line": 86, + "line": 102, "column": 50 }, "end": { - "line": 86, + "line": 102, "column": 51 } } @@ -93034,15 +96129,15 @@ "postfix": false, "binop": null }, - 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"start": 3002, - "end": 3018, + "start": 3442, + "end": 3458, "loc": { "start": { - "line": 90, + "line": 106, "column": 2 }, "end": { - "line": 90, + "line": 106, "column": 18 } } @@ -93272,15 +96367,15 @@ "postfix": false, "binop": null }, - "start": 3018, - "end": 3019, + "start": 3458, + "end": 3459, "loc": { "start": { - "line": 90, + "line": 106, "column": 18 }, "end": { - "line": 90, + "line": 106, "column": 19 } } @@ -93298,15 +96393,15 @@ "binop": null }, "value": "specifier", - "start": 3019, - "end": 3028, + "start": 3459, + "end": 3468, "loc": { "start": { - "line": 90, + "line": 106, "column": 19 }, "end": { - "line": 90, + "line": 106, "column": 28 } } @@ -93324,15 +96419,15 @@ "binop": null, "updateContext": null }, - "start": 3028, - "end": 3029, + "start": 3468, + "end": 3469, "loc": { "start": { - "line": 90, + "line": 106, "column": 28 }, "end": { - "line": 90, + "line": 106, "column": 29 } } @@ -93350,15 +96445,15 @@ "binop": null }, "value": "specifierType", - "start": 3030, - 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To do this, we first need", - "start": 3051, - "end": 3117, + "start": 3491, + "end": 3557, "loc": { "start": { - "line": 91, + "line": 107, "column": 4 }, "end": { - "line": 91, + "line": 107, "column": 70 } } @@ -93432,15 +96527,15 @@ { "type": "CommentLine", "value": " to determine if it was originally an internal or external", - "start": 3122, - "end": 3182, + "start": 3562, + "end": 3622, "loc": { "start": { - "line": 92, + "line": 108, "column": 4 }, "end": { - "line": 92, + "line": 108, "column": 64 } } @@ -93448,15 +96543,15 @@ { "type": "CommentLine", "value": " specifier, then move it into the other list.", - "start": 3187, - "end": 3234, + "start": 3627, + "end": 3674, "loc": { "start": { - "line": 93, + "line": 109, "column": 4 }, "end": { - "line": 93, + "line": 109, "column": 51 } } @@ -93476,15 +96571,15 @@ "updateContext": null }, "value": "let", - "start": 3240, - "end": 3243, + "start": 3680, + "end": 3683, "loc": { "start": { - "line": 95, + "line": 111, "column": 4 }, "end": { - "line": 95, + "line": 111, "column": 7 } } @@ -93502,15 +96597,15 @@ "binop": null }, "value": "index", - "start": 3244, - "end": 3249, + "start": 3684, + "end": 3689, "loc": { "start": { - "line": 95, + "line": 111, "column": 8 }, "end": { - "line": 95, + "line": 111, "column": 13 } } @@ -93528,15 +96623,15 @@ "binop": null, "updateContext": null }, - "start": 3249, - "end": 3250, + "start": 3689, + "end": 3690, "loc": { "start": { - "line": 95, + "line": 111, "column": 13 }, "end": { - "line": 95, + "line": 111, "column": 14 } } @@ -93556,15 +96651,15 @@ "updateContext": null }, "value": "if", - "start": 3255, - "end": 3257, + "start": 3695, + "end": 3697, "loc": { "start": { - "line": 96, + "line": 112, "column": 4 }, "end": { - "line": 96, + "line": 112, "column": 6 } } @@ -93581,15 +96676,15 @@ "postfix": false, "binop": null }, - "start": 3258, - "end": 3259, + "start": 3698, + "end": 3699, "loc": { "start": { - "line": 96, + "line": 112, "column": 7 }, "end": { - "line": 96, + "line": 112, "column": 8 } } @@ -93607,15 +96702,15 @@ "binop": null }, "value": "specifierType", - "start": 3259, - "end": 3272, + "start": 3699, + "end": 3712, "loc": { "start": { - "line": 96, + "line": 112, "column": 8 }, "end": { - "line": 96, + "line": 112, "column": 21 } } @@ -93634,15 +96729,15 @@ "updateContext": null }, "value": "===", - "start": 3273, - "end": 3276, + "start": 3713, + "end": 3716, "loc": { "start": { - "line": 96, + "line": 112, "column": 22 }, "end": { - "line": 96, + "line": 112, "column": 25 } } @@ -93661,15 +96756,15 @@ "updateContext": null }, "value": "Internal", - "start": 3277, - "end": 3287, + "start": 3717, + "end": 3727, "loc": { "start": { - "line": 96, + "line": 112, "column": 26 }, "end": { - "line": 96, + "line": 112, "column": 36 } } @@ -93686,15 +96781,15 @@ "postfix": false, "binop": null }, - "start": 3287, - "end": 3288, + "start": 3727, + "end": 3728, "loc": { "start": { - "line": 96, + "line": 112, "column": 36 }, "end": { - "line": 96, + "line": 112, "column": 37 } } @@ -93711,15 +96806,15 @@ "postfix": false, "binop": null }, - "start": 3289, - 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"start": 3451, - "end": 3452, + "start": 3891, + "end": 3892, "loc": { "start": { - "line": 99, + "line": 115, "column": 37 }, "end": { - "line": 99, + "line": 115, "column": 38 } } @@ -93928,15 +97023,15 @@ "binop": null }, "value": "indexOf", - "start": 3452, - "end": 3459, + "start": 3892, + "end": 3899, "loc": { "start": { - "line": 99, + "line": 115, "column": 38 }, "end": { - "line": 99, + "line": 115, "column": 45 } } @@ -93953,15 +97048,15 @@ "postfix": false, "binop": null }, - "start": 3459, - "end": 3460, + "start": 3899, + "end": 3900, "loc": { "start": { - "line": 99, + "line": 115, "column": 45 }, "end": { - "line": 99, + "line": 115, "column": 46 } } @@ -93979,15 +97074,15 @@ "binop": null }, "value": "specifier", - "start": 3460, - "end": 3469, + "start": 3900, + "end": 3909, "loc": { "start": { - "line": 99, + "line": 115, "column": 46 }, "end": { - "line": 99, + "line": 115, "column": 55 } } @@ -94004,15 +97099,15 @@ "postfix": false, "binop": null }, - "start": 3469, - "end": 3470, + "start": 3909, + "end": 3910, "loc": { "start": { - "line": 99, + "line": 115, "column": 55 }, "end": { - "line": 99, + "line": 115, "column": 56 } } @@ -94030,15 +97125,15 @@ "binop": null, "updateContext": null }, - "start": 3470, - "end": 3471, + "start": 3910, + "end": 3911, "loc": { "start": { - "line": 99, + "line": 115, "column": 56 }, "end": { - "line": 99, + "line": 115, "column": 57 } } @@ -94058,15 +97153,15 @@ "updateContext": null }, "value": "if", - "start": 3478, - "end": 3480, + "start": 3918, + "end": 3920, "loc": { "start": { - "line": 100, + "line": 116, "column": 6 }, "end": { - "line": 100, + "line": 116, "column": 8 } } @@ -94083,15 +97178,15 @@ "postfix": false, "binop": null }, - "start": 3481, - "end": 3482, + "start": 3921, + "end": 3922, "loc": { "start": { - "line": 100, + "line": 116, "column": 9 }, "end": { - "line": 100, + "line": 116, "column": 10 } } @@ -94109,15 +97204,15 @@ "binop": null }, "value": "index", - "start": 3482, - "end": 3487, + "start": 3922, + "end": 3927, "loc": { "start": { - "line": 100, + "line": 116, "column": 10 }, "end": { - "line": 100, + "line": 116, "column": 15 } } @@ -94136,15 +97231,15 @@ "updateContext": null }, "value": "!==", - "start": 3488, - "end": 3491, + "start": 3928, + "end": 3931, "loc": { "start": { - "line": 100, + "line": 116, "column": 16 }, "end": { - "line": 100, + "line": 116, "column": 19 } } @@ -94163,15 +97258,15 @@ "updateContext": null }, "value": "-", - "start": 3492, - "end": 3493, + "start": 3932, + "end": 3933, "loc": { "start": { - "line": 100, + "line": 116, "column": 20 }, "end": { - "line": 100, + "line": 116, "column": 21 } } @@ -94190,15 +97285,15 @@ "updateContext": null }, "value": 1, - "start": 3493, - "end": 3494, + "start": 3933, + "end": 3934, "loc": { "start": { - "line": 100, + "line": 116, "column": 21 }, "end": { - "line": 100, + "line": 116, "column": 22 } } @@ -94215,15 +97310,15 @@ "postfix": false, "binop": null }, - "start": 3494, - "end": 3495, + "start": 3934, + "end": 3935, "loc": { "start": { - "line": 100, + "line": 116, "column": 22 }, "end": { - "line": 100, + "line": 116, "column": 23 } } @@ -94243,15 +97338,15 @@ "updateContext": null }, "value": "this", - "start": 3496, - "end": 3500, + "start": 3936, + "end": 3940, "loc": { "start": { - "line": 100, + "line": 116, "column": 24 }, "end": { - "line": 100, + "line": 116, "column": 28 } } @@ -94269,15 +97364,15 @@ "binop": null, "updateContext": null }, - "start": 3500, - "end": 3501, + "start": 3940, + "end": 3941, "loc": { "start": { - "line": 100, + "line": 116, "column": 28 }, "end": { - "line": 100, + "line": 116, "column": 29 } } @@ -94295,15 +97390,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 3501, - "end": 3519, + "start": 3941, + "end": 3959, "loc": { "start": { - "line": 100, + "line": 116, "column": 29 }, "end": { - "line": 100, + "line": 116, "column": 47 } } @@ -94321,15 +97416,15 @@ "binop": null, "updateContext": null }, - "start": 3519, - "end": 3520, + "start": 3959, + "end": 3960, "loc": { "start": { - "line": 100, + "line": 116, "column": 47 }, "end": { - "line": 100, + "line": 116, "column": 48 } } @@ -94347,15 +97442,15 @@ "binop": null }, "value": "splice", - "start": 3520, - "end": 3526, + "start": 3960, + "end": 3966, "loc": { "start": { - "line": 100, + "line": 116, "column": 48 }, "end": { - "line": 100, + "line": 116, "column": 54 } } @@ -94372,15 +97467,15 @@ "postfix": false, "binop": null }, - "start": 3526, - "end": 3527, + "start": 3966, + "end": 3967, "loc": { "start": { - "line": 100, + "line": 116, "column": 54 }, "end": { - "line": 100, + "line": 116, "column": 55 } } @@ -94398,15 +97493,15 @@ "binop": null }, "value": "index", - "start": 3527, - "end": 3532, + "start": 3967, + "end": 3972, "loc": { "start": { - "line": 100, + "line": 116, "column": 55 }, "end": { - "line": 100, + "line": 116, "column": 60 } } @@ -94424,15 +97519,15 @@ "binop": null, "updateContext": null }, - "start": 3532, - "end": 3533, + "start": 3972, + "end": 3973, "loc": { "start": { - "line": 100, + "line": 116, "column": 60 }, "end": { - "line": 100, + "line": 116, "column": 61 } } @@ -94451,15 +97546,15 @@ "updateContext": null }, "value": 1, - "start": 3534, - "end": 3535, + "start": 3974, + "end": 3975, "loc": { "start": { - "line": 100, + "line": 116, "column": 62 }, "end": { - "line": 100, + "line": 116, "column": 63 } } @@ -94476,15 +97571,15 @@ "postfix": false, "binop": null }, - "start": 3535, - "end": 3536, + "start": 3975, + "end": 3976, "loc": { "start": { - "line": 100, + "line": 116, "column": 63 }, "end": { - "line": 100, + "line": 116, "column": 64 } } @@ -94502,15 +97597,15 @@ "binop": null, "updateContext": null }, - "start": 3536, - "end": 3537, + "start": 3976, + "end": 3977, "loc": { "start": { - "line": 100, + "line": 116, "column": 64 }, "end": { - "line": 100, + "line": 116, "column": 65 } } @@ -94518,15 +97613,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 3545, - "end": 3618, + "start": 3985, + "end": 4058, "loc": { "start": { - "line": 102, + "line": 118, "column": 6 }, "end": { - "line": 102, + "line": 118, "column": 79 } } @@ -94546,15 +97641,15 @@ "updateContext": null }, "value": "if", - "start": 3625, - "end": 3627, + "start": 4065, + "end": 4067, "loc": { "start": { - "line": 103, + "line": 119, "column": 6 }, "end": { - "line": 103, + "line": 119, "column": 8 } } @@ -94571,15 +97666,15 @@ "postfix": false, "binop": null }, - "start": 3628, - "end": 3629, + "start": 4068, + "end": 4069, "loc": { "start": { - "line": 103, + "line": 119, "column": 9 }, "end": { - "line": 103, + "line": 119, "column": 10 } } @@ -94598,15 +97693,15 @@ "updateContext": null }, "value": "!", - "start": 3629, - "end": 3630, + "start": 4069, + "end": 4070, "loc": { "start": { - "line": 103, + "line": 119, "column": 10 }, "end": { - "line": 103, + "line": 119, "column": 11 } } @@ -94626,15 +97721,15 @@ "updateContext": null }, "value": "this", - "start": 3630, - "end": 3634, + "start": 4070, + "end": 4074, "loc": { "start": { - "line": 103, + "line": 119, "column": 11 }, "end": { - "line": 103, + "line": 119, "column": 15 } } @@ -94652,15 +97747,15 @@ "binop": null, "updateContext": null }, - "start": 3634, - "end": 3635, + "start": 4074, + "end": 4075, "loc": { "start": { - "line": 103, + "line": 119, "column": 15 }, "end": { - "line": 103, + "line": 119, "column": 16 } } @@ -94678,15 +97773,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 3635, - "end": 3653, + "start": 4075, + "end": 4093, "loc": { "start": { - "line": 103, + "line": 119, "column": 16 }, "end": { - "line": 103, + "line": 119, "column": 34 } } @@ -94704,15 +97799,15 @@ "binop": null, "updateContext": null }, - "start": 3653, - "end": 3654, + "start": 4093, + "end": 4094, "loc": { "start": { - "line": 103, + "line": 119, "column": 34 }, "end": { - "line": 103, + "line": 119, "column": 35 } } @@ -94730,15 +97825,15 @@ "binop": null }, "value": "includes", - "start": 3654, - "end": 3662, + "start": 4094, + "end": 4102, "loc": { "start": { - "line": 103, + "line": 119, "column": 35 }, "end": { - "line": 103, + "line": 119, "column": 43 } } @@ -94755,15 +97850,15 @@ "postfix": false, "binop": null }, - "start": 3662, - "end": 3663, + "start": 4102, + "end": 4103, "loc": { "start": { - "line": 103, + "line": 119, "column": 43 }, "end": { - "line": 103, + "line": 119, "column": 44 } } @@ -94781,15 +97876,15 @@ "binop": null }, "value": "specifier", - "start": 3663, - "end": 3672, + "start": 4103, + "end": 4112, "loc": { "start": { - "line": 103, + "line": 119, "column": 44 }, "end": { - "line": 103, + "line": 119, "column": 53 } } @@ -94806,15 +97901,15 @@ "postfix": false, "binop": null }, - "start": 3672, - "end": 3673, + "start": 4112, + "end": 4113, "loc": { "start": { - "line": 103, + "line": 119, "column": 53 }, "end": { - "line": 103, + "line": 119, "column": 54 } } @@ -94831,15 +97926,15 @@ "postfix": false, "binop": null }, - "start": 3673, - "end": 3674, + "start": 4113, + "end": 4114, "loc": { "start": { - "line": 103, + "line": 119, "column": 54 }, "end": { - "line": 103, + "line": 119, "column": 55 } } @@ -94856,15 +97951,15 @@ "postfix": false, "binop": null }, - "start": 3675, - "end": 3676, + "start": 4115, + "end": 4116, "loc": { "start": { - "line": 103, + "line": 119, "column": 56 }, "end": { - "line": 103, + "line": 119, "column": 57 } } @@ -94884,15 +97979,15 @@ "updateContext": null }, "value": "this", - "start": 3685, - "end": 3689, + "start": 4125, + "end": 4129, "loc": { "start": { - "line": 104, + "line": 120, "column": 8 }, "end": { - "line": 104, + "line": 120, "column": 12 } } @@ -94910,15 +98005,15 @@ "binop": null, "updateContext": null }, - "start": 3689, - "end": 3690, + "start": 4129, + "end": 4130, "loc": { "start": { - "line": 104, + "line": 120, "column": 12 }, "end": { - "line": 104, + "line": 120, "column": 13 } } @@ -94936,15 +98031,15 @@ "binop": null }, "value": "phyloref", - "start": 3690, - "end": 3698, + "start": 4130, + "end": 4138, "loc": { "start": { - "line": 104, + "line": 120, "column": 13 }, "end": { - "line": 104, + "line": 120, "column": 21 } } @@ -94962,15 +98057,15 @@ "binop": null, "updateContext": null }, - "start": 3698, - "end": 3699, + "start": 4138, + "end": 4139, "loc": { "start": { - "line": 104, + "line": 120, "column": 21 }, "end": { - "line": 104, + "line": 120, "column": 22 } } @@ -94988,15 +98083,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 3699, - "end": 3717, + "start": 4139, + "end": 4157, "loc": { "start": { - "line": 104, + "line": 120, "column": 22 }, "end": { - "line": 104, + "line": 120, "column": 40 } } @@ -95014,15 +98109,15 @@ "binop": null, "updateContext": null }, - "start": 3717, - "end": 3718, + "start": 4157, + "end": 4158, "loc": { "start": { - "line": 104, + "line": 120, "column": 40 }, "end": { - "line": 104, + "line": 120, "column": 41 } } @@ -95040,15 +98135,15 @@ "binop": null }, "value": "unshift", - "start": 3718, - "end": 3725, + "start": 4158, + "end": 4165, "loc": { "start": { - "line": 104, + "line": 120, "column": 41 }, "end": { - "line": 104, + "line": 120, "column": 48 } } @@ -95065,15 +98160,15 @@ "postfix": false, "binop": null }, - "start": 3725, - "end": 3726, + "start": 4165, + "end": 4166, "loc": { "start": { - "line": 104, + "line": 120, "column": 48 }, "end": { - "line": 104, + "line": 120, "column": 49 } } @@ -95091,15 +98186,15 @@ "binop": null }, "value": "specifier", - "start": 3726, - "end": 3735, + "start": 4166, + "end": 4175, "loc": { "start": { - "line": 104, + "line": 120, "column": 49 }, "end": { - "line": 104, + "line": 120, "column": 58 } } @@ -95116,15 +98211,15 @@ "postfix": false, "binop": null }, - "start": 3735, - "end": 3736, + "start": 4175, + "end": 4176, "loc": { "start": { - "line": 104, + "line": 120, "column": 58 }, "end": { - "line": 104, + "line": 120, "column": 59 } } @@ -95142,15 +98237,15 @@ "binop": null, "updateContext": null }, - "start": 3736, - "end": 3737, + "start": 4176, + "end": 4177, "loc": { "start": { - "line": 104, + "line": 120, "column": 59 }, "end": { - "line": 104, + "line": 120, "column": 60 } } @@ -95167,15 +98262,15 @@ "postfix": false, "binop": null }, - "start": 3744, - "end": 3745, + "start": 4184, + "end": 4185, "loc": { "start": { - "line": 105, + "line": 121, "column": 6 }, "end": { - "line": 105, + "line": 121, "column": 7 } } @@ -95192,15 +98287,15 @@ "postfix": false, "binop": null }, - "start": 3750, - "end": 3751, + "start": 4190, + "end": 4191, "loc": { "start": { - "line": 106, + "line": 122, "column": 4 }, "end": { - "line": 106, + "line": 122, "column": 5 } } @@ -95220,15 +98315,15 @@ "updateContext": null }, "value": "else", - "start": 3752, - "end": 3756, + "start": 4192, + "end": 4196, "loc": { "start": { - "line": 106, + "line": 122, "column": 6 }, "end": { - "line": 106, + "line": 122, "column": 10 } } @@ -95248,15 +98343,15 @@ "updateContext": null }, "value": "if", - "start": 3757, - "end": 3759, + "start": 4197, + "end": 4199, "loc": { "start": { - "line": 106, + "line": 122, "column": 11 }, "end": { - "line": 106, + "line": 122, "column": 13 } } @@ -95273,15 +98368,15 @@ "postfix": false, "binop": null }, - "start": 3760, - "end": 3761, + "start": 4200, + "end": 4201, "loc": { "start": { - "line": 106, + "line": 122, "column": 14 }, "end": { - "line": 106, + "line": 122, "column": 15 } } @@ -95299,15 +98394,15 @@ "binop": null }, "value": "specifierType", - "start": 3761, - "end": 3774, + "start": 4201, + "end": 4214, "loc": { "start": { - "line": 106, + "line": 122, "column": 15 }, "end": { - "line": 106, + "line": 122, "column": 28 } } @@ -95326,15 +98421,15 @@ "updateContext": null }, "value": "===", - "start": 3775, - "end": 3778, + "start": 4215, + "end": 4218, "loc": { "start": { - "line": 106, + "line": 122, "column": 29 }, "end": { - "line": 106, + "line": 122, "column": 32 } } @@ -95353,15 +98448,15 @@ "updateContext": null }, "value": "External", - "start": 3779, - "end": 3789, + "start": 4219, + "end": 4229, "loc": { "start": { - "line": 106, + "line": 122, "column": 33 }, "end": { - "line": 106, + "line": 122, "column": 43 } } @@ -95378,15 +98473,15 @@ "postfix": false, "binop": null }, - "start": 3789, - "end": 3790, + "start": 4229, + "end": 4230, "loc": { "start": { - "line": 106, + "line": 122, "column": 43 }, "end": { - "line": 106, + "line": 122, "column": 44 } } @@ -95403,15 +98498,15 @@ "postfix": false, "binop": null }, - "start": 3791, - "end": 3792, + "start": 4231, + "end": 4232, "loc": { "start": { - "line": 106, + "line": 122, "column": 45 }, "end": { - "line": 106, + "line": 122, "column": 46 } } @@ -95419,15 +98514,15 @@ { "type": "CommentLine", "value": " To set a specifier to 'External', we might need to delete it from the", - "start": 3799, - "end": 3871, + "start": 4239, + "end": 4311, "loc": { "start": { - "line": 107, + "line": 123, "column": 6 }, "end": { - "line": 107, + "line": 123, "column": 78 } } @@ -95435,15 +98530,15 @@ { "type": "CommentLine", "value": " list of internal specifiers first.", - "start": 3878, - "end": 3915, + "start": 4318, + "end": 4355, "loc": { "start": { - "line": 108, + "line": 124, "column": 6 }, "end": { - "line": 108, + "line": 124, "column": 43 } } @@ -95461,15 +98556,15 @@ "binop": null }, "value": "index", - 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"line": 110, + "line": 126, "column": 24 }, "end": { - "line": 110, + "line": 126, "column": 28 } } @@ -96013,15 +99108,15 @@ "binop": null, "updateContext": null }, - "start": 4011, - "end": 4012, + "start": 4451, + "end": 4452, "loc": { "start": { - "line": 110, + "line": 126, "column": 28 }, "end": { - "line": 110, + "line": 126, "column": 29 } } @@ -96039,15 +99134,15 @@ "binop": null }, "value": "phyloref", - "start": 4012, - "end": 4020, + "start": 4452, + "end": 4460, "loc": { "start": { - "line": 110, + "line": 126, "column": 29 }, "end": { - "line": 110, + "line": 126, "column": 37 } } @@ -96065,15 +99160,15 @@ "binop": null, "updateContext": null }, - "start": 4020, - "end": 4021, + "start": 4460, + "end": 4461, "loc": { "start": { - "line": 110, + "line": 126, "column": 37 }, "end": { - "line": 110, + "line": 126, "column": 38 } } @@ -96091,15 +99186,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 4021, - "end": 4039, + "start": 4461, + "end": 4479, "loc": { "start": { - "line": 110, + "line": 126, "column": 38 }, "end": { - "line": 110, + "line": 126, "column": 56 } } @@ -96117,15 +99212,15 @@ "binop": null, "updateContext": null }, - "start": 4039, - "end": 4040, + "start": 4479, + "end": 4480, "loc": { "start": { - "line": 110, + "line": 126, "column": 56 }, "end": { - "line": 110, + "line": 126, "column": 57 } } @@ -96143,15 +99238,15 @@ "binop": null }, "value": "splice", - "start": 4040, - "end": 4046, + "start": 4480, + "end": 4486, "loc": { "start": { - "line": 110, + "line": 126, "column": 57 }, "end": { - "line": 110, + "line": 126, "column": 63 } } @@ -96168,15 +99263,15 @@ "postfix": false, "binop": null }, - "start": 4046, - "end": 4047, + "start": 4486, + "end": 4487, "loc": { "start": { - "line": 110, + "line": 126, "column": 63 }, "end": { - "line": 110, + "line": 126, "column": 64 } } @@ -96194,15 +99289,15 @@ "binop": null }, "value": "index", - "start": 4047, - "end": 4052, + "start": 4487, + "end": 4492, "loc": { "start": { - "line": 110, + "line": 126, "column": 64 }, "end": { - "line": 110, + "line": 126, "column": 69 } } @@ -96220,15 +99315,15 @@ "binop": null, "updateContext": null }, - "start": 4052, - "end": 4053, + "start": 4492, + "end": 4493, "loc": { "start": { - "line": 110, + "line": 126, "column": 69 }, "end": { - "line": 110, + "line": 126, "column": 70 } } @@ -96247,15 +99342,15 @@ "updateContext": null }, "value": 1, - "start": 4054, - "end": 4055, + "start": 4494, + "end": 4495, "loc": { "start": { - "line": 110, + "line": 126, "column": 71 }, "end": { - "line": 110, + "line": 126, "column": 72 } } @@ -96272,15 +99367,15 @@ "postfix": false, "binop": null }, - "start": 4055, - "end": 4056, + "start": 4495, + "end": 4496, "loc": { "start": { - "line": 110, + "line": 126, "column": 72 }, "end": { - "line": 110, + "line": 126, "column": 73 } } @@ -96298,15 +99393,15 @@ "binop": null, "updateContext": null }, - "start": 4056, - "end": 4057, + "start": 4496, + "end": 4497, "loc": { "start": { - "line": 110, + "line": 126, "column": 73 }, "end": { - "line": 110, + "line": 126, "column": 74 } } @@ -96314,15 +99409,15 @@ { "type": "CommentLine", "value": " Don't add it to the list of internal specifiers if it's already there.", - "start": 4065, - "end": 4138, + "start": 4505, + "end": 4578, "loc": { "start": { - "line": 112, + "line": 128, "column": 6 }, "end": { - "line": 112, + "line": 128, "column": 79 } } @@ -96342,15 +99437,15 @@ "updateContext": null }, "value": "if", - "start": 4145, - "end": 4147, + "start": 4585, + "end": 4587, "loc": { "start": { - "line": 113, + "line": 129, "column": 6 }, "end": { - "line": 113, + "line": 129, "column": 8 } } @@ -96367,15 +99462,15 @@ "postfix": false, "binop": null }, - "start": 4148, - "end": 4149, + "start": 4588, + "end": 4589, "loc": { "start": { - "line": 113, + "line": 129, "column": 9 }, "end": { - "line": 113, + "line": 129, "column": 10 } } @@ -96394,15 +99489,15 @@ "updateContext": null }, "value": "!", - "start": 4149, - "end": 4150, + "start": 4589, + "end": 4590, "loc": { "start": { - "line": 113, + "line": 129, "column": 10 }, "end": { - "line": 113, + "line": 129, "column": 11 } } @@ -96422,15 +99517,15 @@ "updateContext": null }, "value": "this", - "start": 4150, - "end": 4154, + "start": 4590, + "end": 4594, "loc": { "start": { - "line": 113, + "line": 129, "column": 11 }, "end": { - "line": 113, + "line": 129, "column": 15 } } @@ -96448,15 +99543,15 @@ "binop": null, "updateContext": null }, - "start": 4154, - "end": 4155, + "start": 4594, + "end": 4595, "loc": { "start": { - "line": 113, + "line": 129, "column": 15 }, "end": { - "line": 113, + "line": 129, "column": 16 } } @@ -96474,15 +99569,15 @@ "binop": null }, "value": "phyloref", - "start": 4155, - "end": 4163, + "start": 4595, + "end": 4603, "loc": { "start": { - "line": 113, + "line": 129, "column": 16 }, "end": { - "line": 113, + "line": 129, "column": 24 } } @@ -96500,15 +99595,15 @@ "binop": null, "updateContext": null }, - "start": 4163, - "end": 4164, + "start": 4603, + "end": 4604, "loc": { "start": { - "line": 113, + "line": 129, "column": 24 }, "end": { - "line": 113, + "line": 129, "column": 25 } } @@ -96526,15 +99621,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 4164, - "end": 4182, + "start": 4604, + "end": 4622, "loc": { "start": { - "line": 113, + "line": 129, "column": 25 }, "end": { - "line": 113, + "line": 129, "column": 43 } } @@ -96552,15 +99647,15 @@ "binop": null, "updateContext": null }, - "start": 4182, - "end": 4183, + "start": 4622, + "end": 4623, "loc": { "start": { - "line": 113, + "line": 129, "column": 43 }, "end": { - "line": 113, + "line": 129, "column": 44 } } @@ -96578,15 +99673,15 @@ "binop": null }, "value": "includes", - "start": 4183, - "end": 4191, + "start": 4623, + "end": 4631, "loc": { "start": { - "line": 113, + "line": 129, "column": 44 }, "end": { - "line": 113, + "line": 129, "column": 52 } } @@ -96603,15 +99698,15 @@ "postfix": false, "binop": null }, - "start": 4191, - "end": 4192, + "start": 4631, + "end": 4632, "loc": { "start": { - "line": 113, + "line": 129, "column": 52 }, "end": { - "line": 113, + "line": 129, "column": 53 } } @@ -96629,15 +99724,15 @@ "binop": null }, "value": "specifier", - "start": 4192, - "end": 4201, + "start": 4632, + "end": 4641, "loc": { "start": { - "line": 113, + "line": 129, "column": 53 }, "end": { - "line": 113, + "line": 129, "column": 62 } } @@ -96654,15 +99749,15 @@ "postfix": false, "binop": null }, - "start": 4201, - "end": 4202, + "start": 4641, + "end": 4642, "loc": { "start": { - "line": 113, + "line": 129, "column": 62 }, "end": { - "line": 113, + "line": 129, "column": 63 } } @@ -96679,15 +99774,15 @@ "postfix": false, "binop": null }, - "start": 4202, - "end": 4203, + "start": 4642, + "end": 4643, "loc": { "start": { - "line": 113, + "line": 129, "column": 63 }, "end": { - "line": 113, + "line": 129, "column": 64 } } @@ -96704,15 +99799,15 @@ "postfix": false, "binop": null }, - "start": 4204, - "end": 4205, + "start": 4644, + "end": 4645, "loc": { "start": { - "line": 113, + "line": 129, "column": 65 }, "end": { - 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"line": 114, + "line": 130, "column": 22 } } @@ -96836,15 +99931,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 4228, - "end": 4246, + "start": 4668, + "end": 4686, "loc": { "start": { - "line": 114, + "line": 130, "column": 22 }, "end": { - "line": 114, + "line": 130, "column": 40 } } @@ -96862,15 +99957,15 @@ "binop": null, "updateContext": null }, - "start": 4246, - "end": 4247, + "start": 4686, + "end": 4687, "loc": { "start": { - "line": 114, + "line": 130, "column": 40 }, "end": { - "line": 114, + "line": 130, "column": 41 } } @@ -96888,15 +99983,15 @@ "binop": null }, "value": "unshift", - "start": 4247, - "end": 4254, + "start": 4687, + "end": 4694, "loc": { "start": { - "line": 114, + "line": 130, "column": 41 }, "end": { - "line": 114, + "line": 130, "column": 48 } } @@ -96913,15 +100008,15 @@ "postfix": false, "binop": null }, - "start": 4254, - "end": 4255, + "start": 4694, + "end": 4695, "loc": { "start": { - "line": 114, + "line": 130, "column": 48 }, "end": { - "line": 114, + "line": 130, "column": 49 } } @@ -96939,15 +100034,15 @@ "binop": null }, "value": "specifier", - "start": 4255, - "end": 4264, + "start": 4695, + "end": 4704, "loc": { "start": { - "line": 114, + "line": 130, "column": 49 }, "end": { - "line": 114, + "line": 130, "column": 58 } } @@ -96964,15 +100059,15 @@ "postfix": false, "binop": null }, - "start": 4264, - "end": 4265, + "start": 4704, + "end": 4705, "loc": { "start": { - "line": 114, + "line": 130, "column": 58 }, "end": { - "line": 114, + "line": 130, "column": 59 } } @@ -96990,15 +100085,15 @@ "binop": null, "updateContext": null }, - "start": 4265, - "end": 4266, + "start": 4705, + "end": 4706, "loc": { "start": { - "line": 114, + "line": 130, "column": 59 }, "end": { - "line": 114, + "line": 130, "column": 60 } } @@ -97015,15 +100110,15 @@ "postfix": false, "binop": null }, - "start": 4273, - "end": 4274, + "start": 4713, + "end": 4714, "loc": { "start": { - "line": 115, + "line": 131, "column": 6 }, "end": { - "line": 115, + "line": 131, "column": 7 } } @@ -97040,15 +100135,15 @@ "postfix": false, "binop": null }, - "start": 4279, - "end": 4280, + "start": 4719, + "end": 4720, "loc": { "start": { - "line": 116, + "line": 132, "column": 4 }, "end": { - "line": 116, + "line": 132, "column": 5 } } @@ -97068,15 +100163,15 @@ "updateContext": null }, "value": "else", - "start": 4281, - "end": 4285, + "start": 4721, + "end": 4725, "loc": { "start": { - "line": 116, + "line": 132, "column": 6 }, "end": { - "line": 116, + "line": 132, "column": 10 } } @@ -97093,15 +100188,15 @@ "postfix": false, "binop": null }, - "start": 4286, - "end": 4287, + "start": 4726, + "end": 4727, "loc": { "start": { - "line": 116, + "line": 132, "column": 11 }, "end": { - "line": 116, + "line": 132, "column": 12 } } @@ -97109,15 +100204,15 @@ { "type": "CommentLine", "value": " Neither internal nor external? Ignore.", - "start": 4294, - "end": 4335, + "start": 4734, + "end": 4775, "loc": { "start": { - "line": 117, + "line": 133, "column": 6 }, "end": { - "line": 117, + "line": 133, "column": 47 } } @@ -97134,15 +100229,15 @@ "postfix": false, "binop": null }, - "start": 4340, - "end": 4341, + "start": 4780, + "end": 4781, "loc": { "start": { - "line": 118, + "line": 134, "column": 4 }, "end": { - "line": 118, + "line": 134, "column": 5 } } @@ -97159,15 +100254,15 @@ "postfix": false, "binop": null }, - "start": 4344, - "end": 4345, + "start": 4784, + "end": 4785, "loc": { "start": { - "line": 119, + "line": 135, "column": 2 }, "end": { - "line": 119, + "line": 135, "column": 3 } } @@ -97185,15 +100280,15 @@ "binop": null }, "value": "deleteSpecifier", - "start": 4349, - "end": 4364, + "start": 4789, + "end": 4804, "loc": { "start": { - "line": 121, + "line": 137, "column": 2 }, "end": { - "line": 121, + "line": 137, "column": 17 } } @@ -97210,15 +100305,15 @@ "postfix": false, "binop": null }, - "start": 4364, - "end": 4365, + "start": 4804, + "end": 4805, "loc": { "start": { - "line": 121, + "line": 137, "column": 17 }, "end": { - "line": 121, + "line": 137, "column": 18 } } @@ -97236,15 +100331,15 @@ "binop": null }, "value": "specifier", - "start": 4365, - "end": 4374, + "start": 4805, + "end": 4814, "loc": { "start": { - "line": 121, + "line": 137, "column": 18 }, "end": { - "line": 121, + "line": 137, "column": 27 } } @@ -97261,15 +100356,15 @@ "postfix": false, "binop": null }, - "start": 4374, - "end": 4375, + "start": 4814, + "end": 4815, "loc": { "start": { - "line": 121, + "line": 137, "column": 27 }, "end": { - "line": 121, + "line": 137, "column": 28 } } @@ -97286,15 +100381,15 @@ "postfix": false, "binop": null }, - "start": 4376, - "end": 4377, + "start": 4816, + "end": 4817, "loc": { "start": { - "line": 121, + "line": 137, "column": 29 }, "end": { - "line": 121, + "line": 137, "column": 30 } } @@ -97302,15 +100397,15 @@ { "type": "CommentLine", "value": " Since the user interface combines specifiers into a single list,", - "start": 4382, - "end": 4449, + "start": 4822, + "end": 4889, "loc": { "start": { - "line": 122, + "line": 138, "column": 4 }, "end": { - "line": 122, + "line": 138, "column": 71 } } @@ -97318,15 +100413,15 @@ { "type": "CommentLine", "value": " it doesn't remember if the specifier to be deleted is internal", - "start": 4454, - "end": 4519, + "start": 4894, + "end": 4959, "loc": { "start": { - "line": 123, + "line": 139, "column": 4 }, "end": { - "line": 123, + "line": 139, "column": 69 } } @@ -97334,15 +100429,15 @@ { "type": "CommentLine", "value": " or external. We delete the intended specifier from both arrays.", - "start": 4524, - "end": 4590, + "start": 4964, + "end": 5030, "loc": { "start": { - "line": 124, + "line": 140, "column": 4 }, "end": { - "line": 124, + "line": 140, "column": 70 } } @@ -97362,15 +100457,15 @@ "updateContext": null }, "value": "if", - "start": 4596, - "end": 4598, + "start": 5036, + "end": 5038, "loc": { "start": { - "line": 126, + "line": 142, "column": 4 }, "end": { - "line": 126, + "line": 142, "column": 6 } } @@ -97387,15 +100482,15 @@ "postfix": false, "binop": null }, - "start": 4599, - "end": 4600, + "start": 5039, + "end": 5040, "loc": { "start": { - "line": 126, + "line": 142, "column": 7 }, "end": { - "line": 126, + "line": 142, "column": 8 } } @@ -97413,15 +100508,15 @@ "binop": null }, "value": "has", - "start": 4600, - "end": 4603, + "start": 5040, + "end": 5043, "loc": { "start": { - "line": 126, + "line": 142, "column": 8 }, "end": { - "line": 126, + "line": 142, "column": 11 } } @@ -97438,15 +100533,15 @@ "postfix": false, "binop": null }, - "start": 4603, - "end": 4604, + "start": 5043, + "end": 5044, "loc": { "start": { - "line": 126, + "line": 142, "column": 11 }, "end": { - "line": 126, + "line": 142, "column": 12 } } @@ -97466,15 +100561,15 @@ "updateContext": null }, "value": "this", - "start": 4604, - "end": 4608, + "start": 5044, + "end": 5048, "loc": { "start": { - "line": 126, + "line": 142, "column": 12 }, "end": { - "line": 126, + "line": 142, "column": 16 } } @@ -97492,15 +100587,15 @@ "binop": null, "updateContext": null }, - "start": 4608, - "end": 4609, + "start": 5048, + "end": 5049, "loc": { "start": { - "line": 126, + "line": 142, "column": 16 }, "end": { - "line": 126, + "line": 142, "column": 17 } } @@ -97518,15 +100613,15 @@ "binop": null }, "value": "phyloref", - "start": 4609, - "end": 4617, + "start": 5049, + "end": 5057, "loc": { "start": { - "line": 126, + "line": 142, "column": 17 }, "end": { - "line": 126, + "line": 142, "column": 25 } } @@ -97544,15 +100639,15 @@ "binop": null, "updateContext": null }, - "start": 4617, - "end": 4618, + "start": 5057, + "end": 5058, "loc": { "start": { - "line": 126, + "line": 142, "column": 25 }, "end": { - "line": 126, + "line": 142, "column": 26 } } @@ -97571,15 +100666,15 @@ "updateContext": null }, "value": "internalSpecifiers", - "start": 4619, - "end": 4639, + "start": 5059, + "end": 5079, "loc": { "start": { - "line": 126, + "line": 142, "column": 27 }, "end": { - "line": 126, + "line": 142, "column": 47 } } @@ -97596,15 +100691,15 @@ "postfix": false, "binop": null }, - "start": 4639, - "end": 4640, + "start": 5079, + "end": 5080, "loc": { "start": { - "line": 126, + "line": 142, "column": 47 }, "end": { - "line": 126, + "line": 142, "column": 48 } } @@ -97623,15 +100718,15 @@ "updateContext": null }, "value": "&&", - "start": 4641, - "end": 4643, + "start": 5081, + "end": 5083, "loc": { "start": { - "line": 126, + "line": 142, "column": 49 }, "end": { - "line": 126, + "line": 142, "column": 51 } } @@ -97651,15 +100746,15 @@ "updateContext": null }, "value": "this", - "start": 4644, - "end": 4648, + "start": 5084, + "end": 5088, "loc": { "start": { - "line": 126, + "line": 142, "column": 52 }, "end": { - "line": 126, + "line": 142, "column": 56 } } @@ -97677,15 +100772,15 @@ "binop": null, "updateContext": null }, - "start": 4648, - "end": 4649, + "start": 5088, + "end": 5089, "loc": { "start": { - "line": 126, + "line": 142, "column": 56 }, "end": { - "line": 126, + "line": 142, "column": 57 } } @@ -97703,15 +100798,15 @@ "binop": null }, "value": "phyloref", - "start": 4649, - "end": 4657, + "start": 5089, + "end": 5097, "loc": { "start": { - "line": 126, + "line": 142, "column": 57 }, "end": { - "line": 126, + "line": 142, "column": 65 } } @@ -97729,15 +100824,15 @@ "binop": null, "updateContext": null }, - "start": 4657, - "end": 4658, + "start": 5097, + "end": 5098, "loc": { "start": { - "line": 126, + "line": 142, "column": 65 }, "end": { - "line": 126, + "line": 142, "column": 66 } } @@ -97755,15 +100850,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 4658, - "end": 4676, + "start": 5098, + "end": 5116, "loc": { "start": { - "line": 126, + "line": 142, "column": 66 }, "end": { - "line": 126, + "line": 142, "column": 84 } } @@ -97781,15 +100876,15 @@ "binop": null, "updateContext": null }, - "start": 4676, - "end": 4677, + "start": 5116, + "end": 5117, "loc": { "start": { - "line": 126, + "line": 142, "column": 84 }, "end": { - "line": 126, + "line": 142, "column": 85 } } @@ -97807,15 +100902,15 @@ "binop": null }, "value": "length", - "start": 4677, - "end": 4683, + "start": 5117, + "end": 5123, "loc": { "start": { - "line": 126, + "line": 142, "column": 85 }, "end": { - "line": 126, + "line": 142, "column": 91 } } @@ -97834,15 +100929,15 @@ "updateContext": null }, "value": ">", - "start": 4684, - "end": 4685, + "start": 5124, + "end": 5125, "loc": { "start": { - "line": 126, + "line": 142, "column": 92 }, "end": { - "line": 126, + "line": 142, "column": 93 } } @@ -97861,15 +100956,15 @@ "updateContext": null }, "value": 0, - "start": 4686, - "end": 4687, + "start": 5126, + "end": 5127, "loc": { "start": { - "line": 126, + "line": 142, "column": 94 }, "end": { - "line": 126, + "line": 142, "column": 95 } } @@ -97886,15 +100981,15 @@ "postfix": false, "binop": null }, - "start": 4687, - "end": 4688, + "start": 5127, + "end": 5128, "loc": { "start": { - "line": 126, + "line": 142, "column": 95 }, "end": { - "line": 126, + "line": 142, "column": 96 } } @@ -97911,15 +101006,15 @@ "postfix": false, "binop": null }, - "start": 4689, - "end": 4690, + "start": 5129, + "end": 5130, "loc": { "start": { - "line": 126, + "line": 142, "column": 97 }, "end": { - "line": 126, + "line": 142, "column": 98 } } @@ -97939,15 +101034,15 @@ "updateContext": null }, "value": "const", - "start": 4697, - "end": 4702, + "start": 5137, + "end": 5142, "loc": { "start": { - "line": 127, + "line": 143, "column": 6 }, "end": { - "line": 127, + "line": 143, "column": 11 } } @@ -97965,15 +101060,15 @@ "binop": null }, "value": "index", - "start": 4703, - "end": 4708, + "start": 5143, + "end": 5148, "loc": { "start": { - "line": 127, + "line": 143, "column": 12 }, "end": { - "line": 127, + "line": 143, "column": 17 } } @@ -97992,15 +101087,15 @@ "updateContext": null }, "value": "=", - "start": 4709, - "end": 4710, + "start": 5149, + "end": 5150, "loc": { "start": { - "line": 127, + "line": 143, "column": 18 }, "end": { - "line": 127, + "line": 143, "column": 19 } } @@ -98020,15 +101115,15 @@ "updateContext": null }, "value": "this", - "start": 4711, - "end": 4715, + "start": 5151, + "end": 5155, "loc": { "start": { - "line": 127, + "line": 143, "column": 20 }, "end": { - "line": 127, + "line": 143, "column": 24 } } @@ -98046,15 +101141,15 @@ "binop": null, "updateContext": null }, - "start": 4715, - "end": 4716, + "start": 5155, + "end": 5156, "loc": { "start": { - "line": 127, + "line": 143, "column": 24 }, "end": { - "line": 127, + "line": 143, "column": 25 } } @@ -98072,15 +101167,15 @@ "binop": null }, "value": "phyloref", - "start": 4716, - "end": 4724, + "start": 5156, + "end": 5164, "loc": { "start": { - "line": 127, + "line": 143, "column": 25 }, "end": { - "line": 127, + "line": 143, "column": 33 } } @@ -98098,15 +101193,15 @@ "binop": null, "updateContext": null }, - "start": 4724, - "end": 4725, + "start": 5164, + "end": 5165, "loc": { "start": { - "line": 127, + "line": 143, "column": 33 }, "end": { - "line": 127, + "line": 143, "column": 34 } } @@ -98124,15 +101219,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 4725, - "end": 4743, + "start": 5165, + "end": 5183, "loc": { "start": { - "line": 127, + "line": 143, "column": 34 }, "end": { - "line": 127, + "line": 143, "column": 52 } } @@ -98150,15 +101245,15 @@ "binop": null, "updateContext": null }, - "start": 4743, - "end": 4744, + "start": 5183, + "end": 5184, "loc": { "start": { - "line": 127, + "line": 143, "column": 52 }, "end": { - "line": 127, + "line": 143, "column": 53 } } @@ -98176,15 +101271,15 @@ "binop": null }, "value": "indexOf", - "start": 4744, - "end": 4751, + "start": 5184, + "end": 5191, "loc": { "start": { - "line": 127, + "line": 143, "column": 53 }, "end": { - "line": 127, + "line": 143, "column": 60 } } @@ -98201,15 +101296,15 @@ "postfix": false, "binop": null }, - "start": 4751, - "end": 4752, + "start": 5191, + "end": 5192, "loc": { "start": { - "line": 127, + "line": 143, "column": 60 }, "end": { - "line": 127, + "line": 143, "column": 61 } } @@ -98227,15 +101322,15 @@ "binop": null }, "value": "specifier", - "start": 4752, - "end": 4761, + "start": 5192, + "end": 5201, "loc": { "start": { - "line": 127, + "line": 143, "column": 61 }, "end": { - "line": 127, + "line": 143, "column": 70 } } @@ -98252,15 +101347,15 @@ "postfix": false, "binop": null }, - "start": 4761, - "end": 4762, + "start": 5201, + "end": 5202, "loc": { "start": { - "line": 127, + "line": 143, "column": 70 }, "end": { - "line": 127, + "line": 143, "column": 71 } } @@ -98278,15 +101373,15 @@ "binop": null, "updateContext": null }, - "start": 4762, - "end": 4763, + "start": 5202, + "end": 5203, "loc": { "start": { - "line": 127, + "line": 143, "column": 71 }, "end": { - "line": 127, + "line": 143, "column": 72 } } @@ -98306,15 +101401,15 @@ "updateContext": null }, "value": "if", - "start": 4770, - "end": 4772, + "start": 5210, + "end": 5212, "loc": { "start": { - "line": 128, + "line": 144, "column": 6 }, "end": { - "line": 128, + "line": 144, "column": 8 } } @@ -98331,15 +101426,15 @@ "postfix": false, "binop": null }, - "start": 4773, - "end": 4774, + "start": 5213, + "end": 5214, "loc": { "start": { - "line": 128, + "line": 144, "column": 9 }, "end": { - "line": 128, + "line": 144, "column": 10 } } @@ -98357,15 +101452,15 @@ "binop": null }, "value": "index", - "start": 4774, - "end": 4779, + "start": 5214, + "end": 5219, "loc": { "start": { - "line": 128, + "line": 144, "column": 10 }, "end": { - "line": 128, + "line": 144, "column": 15 } } @@ -98384,15 +101479,15 @@ "updateContext": null }, "value": "!==", - "start": 4780, - "end": 4783, + "start": 5220, + "end": 5223, "loc": { "start": { - "line": 128, + "line": 144, "column": 16 }, "end": { - "line": 128, + "line": 144, "column": 19 } } @@ -98411,15 +101506,15 @@ "updateContext": null }, "value": "-", - "start": 4784, - "end": 4785, + "start": 5224, + "end": 5225, "loc": { "start": { - "line": 128, + "line": 144, "column": 20 }, "end": { - "line": 128, + "line": 144, "column": 21 } } @@ -98438,15 +101533,15 @@ "updateContext": null }, "value": 1, - "start": 4785, - "end": 4786, + "start": 5225, + "end": 5226, "loc": { "start": { - "line": 128, + "line": 144, "column": 21 }, "end": { - "line": 128, + "line": 144, "column": 22 } } @@ -98463,15 +101558,15 @@ "postfix": false, "binop": null }, - "start": 4786, - "end": 4787, + "start": 5226, + "end": 5227, "loc": { "start": { - "line": 128, + "line": 144, "column": 22 }, "end": { - "line": 128, + "line": 144, "column": 23 } } @@ -98491,15 +101586,15 @@ "updateContext": null }, "value": "this", - "start": 4788, - "end": 4792, + "start": 5228, + "end": 5232, "loc": { "start": { - "line": 128, + "line": 144, "column": 24 }, "end": { - "line": 128, + "line": 144, "column": 28 } } @@ -98517,15 +101612,15 @@ "binop": null, "updateContext": null }, - "start": 4792, - "end": 4793, + "start": 5232, + "end": 5233, "loc": { "start": { - "line": 128, + "line": 144, "column": 28 }, "end": { - "line": 128, + "line": 144, "column": 29 } } @@ -98543,15 +101638,15 @@ "binop": null }, "value": "phyloref", - "start": 4793, - "end": 4801, + "start": 5233, + "end": 5241, "loc": { "start": { - "line": 128, + "line": 144, "column": 29 }, "end": { - "line": 128, + "line": 144, "column": 37 } } @@ -98569,15 +101664,15 @@ "binop": null, "updateContext": null }, - "start": 4801, - "end": 4802, + "start": 5241, + "end": 5242, "loc": { "start": { - "line": 128, + "line": 144, "column": 37 }, "end": { - "line": 128, + "line": 144, "column": 38 } } @@ -98595,15 +101690,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 4802, - "end": 4820, + "start": 5242, + "end": 5260, "loc": { "start": { - "line": 128, + "line": 144, "column": 38 }, "end": { - "line": 128, + "line": 144, "column": 56 } } @@ -98621,15 +101716,15 @@ "binop": null, "updateContext": null }, - "start": 4820, - "end": 4821, + "start": 5260, + "end": 5261, "loc": { "start": { - "line": 128, + "line": 144, "column": 56 }, "end": { - "line": 128, + "line": 144, "column": 57 } } @@ -98647,15 +101742,15 @@ "binop": null }, "value": "splice", - "start": 4821, - "end": 4827, + "start": 5261, + "end": 5267, "loc": { "start": { - "line": 128, + "line": 144, "column": 57 }, "end": { - "line": 128, + "line": 144, "column": 63 } } @@ -98672,15 +101767,15 @@ "postfix": false, "binop": null }, - "start": 4827, - "end": 4828, + "start": 5267, + "end": 5268, "loc": { "start": { - "line": 128, + "line": 144, "column": 63 }, "end": { - "line": 128, + "line": 144, "column": 64 } } @@ -98698,15 +101793,15 @@ "binop": null }, "value": "index", - "start": 4828, - 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"line": 145, + "line": 161, "column": 9 } } @@ -100638,15 +103733,15 @@ "binop": null }, "value": "phylorefLabel", - "start": 5541, - "end": 5554, + "start": 5981, + "end": 5994, "loc": { "start": { - "line": 145, + "line": 161, "column": 10 }, "end": { - "line": 145, + "line": 161, "column": 23 } } @@ -100665,15 +103760,15 @@ "updateContext": null }, "value": "=", - "start": 5555, - "end": 5556, + "start": 5995, + "end": 5996, "loc": { "start": { - "line": 145, + "line": 161, "column": 24 }, "end": { - "line": 145, + "line": 161, "column": 25 } } @@ -100693,15 +103788,15 @@ "updateContext": null }, "value": "this", - "start": 5557, - "end": 5561, + "start": 5997, + "end": 6001, "loc": { "start": { - "line": 145, + "line": 161, "column": 26 }, "end": { - "line": 145, + "line": 161, "column": 30 } } @@ -100719,15 +103814,15 @@ "binop": null, "updateContext": null }, - "start": 5561, - "end": 5562, + "start": 6001, + "end": 6002, "loc": { "start": { - "line": 145, + "line": 161, "column": 30 }, "end": { - "line": 145, + "line": 161, "column": 31 } } @@ -100745,15 +103840,15 @@ "binop": null }, "value": "label", - "start": 5562, - "end": 5567, + "start": 6002, + "end": 6007, "loc": { "start": { - "line": 145, + "line": 161, "column": 31 }, "end": { - "line": 145, + "line": 161, "column": 36 } } @@ -100771,15 +103866,15 @@ "binop": null, "updateContext": null }, - "start": 5567, - "end": 5568, + "start": 6007, + "end": 6008, "loc": { "start": { - "line": 145, + "line": 161, "column": 36 }, "end": { - "line": 145, + "line": 161, "column": 37 } } @@ -100799,15 +103894,15 @@ "updateContext": null }, "value": "const", - "start": 5573, - "end": 5578, + "start": 6013, + "end": 6018, "loc": { "start": { - "line": 146, + "line": 162, "column": 4 }, "end": { - "line": 146, + "line": 162, "column": 9 } } @@ -100825,15 +103920,15 @@ "binop": null }, "value": "nodeLabels", - "start": 5579, - "end": 5589, + "start": 6019, + "end": 6029, "loc": { "start": { - "line": 146, + "line": 162, "column": 10 }, "end": { - "line": 146, + "line": 162, "column": 20 } } @@ -100852,15 +103947,15 @@ "updateContext": null }, "value": "=", - "start": 5590, - "end": 5591, + "start": 6030, + "end": 6031, "loc": { "start": { - "line": 146, + "line": 162, "column": 21 }, "end": { - "line": 146, + "line": 162, "column": 22 } } @@ -100880,15 +103975,15 @@ "updateContext": null }, "value": "new", - "start": 5592, - "end": 5595, + "start": 6032, + "end": 6035, "loc": { "start": { - "line": 146, + "line": 162, "column": 23 }, "end": { - "line": 146, + "line": 162, "column": 26 } } @@ -100906,15 +104001,15 @@ "binop": null }, "value": "Set", - "start": 5596, - "end": 5599, + "start": 6036, + "end": 6039, "loc": { "start": { - "line": 146, + "line": 162, "column": 27 }, "end": { - "line": 146, + "line": 162, "column": 30 } } @@ -100931,15 +104026,15 @@ "postfix": false, "binop": null }, - "start": 5599, - "end": 5600, + "start": 6039, + "end": 6040, "loc": { "start": { - "line": 146, + "line": 162, "column": 30 }, "end": { - "line": 146, + "line": 162, "column": 31 } } @@ -100956,15 +104051,15 @@ "postfix": false, "binop": null }, - "start": 5600, - "end": 5601, + "start": 6040, + "end": 6041, "loc": { "start": { - "line": 146, + "line": 162, "column": 31 }, "end": { - "line": 146, + "line": 162, "column": 32 } } @@ -100982,15 +104077,15 @@ "binop": null, "updateContext": null }, - "start": 5601, - "end": 5602, + "start": 6041, + "end": 6042, "loc": { "start": { - "line": 146, + "line": 162, "column": 32 }, "end": { - "line": 146, + "line": 162, "column": 33 } } @@ -101010,15 +104105,15 @@ "updateContext": null }, "value": "new", - "start": 5608, - "end": 5611, + "start": 6048, + "end": 6051, "loc": { "start": { - "line": 148, + "line": 164, "column": 4 }, "end": { - "line": 148, + "line": 164, "column": 7 } } @@ -101036,15 +104131,15 @@ "binop": null }, "value": "PhylogenyWrapper", - "start": 5612, - "end": 5628, + "start": 6052, + "end": 6068, "loc": { "start": { - "line": 148, + "line": 164, "column": 8 }, "end": { - "line": 148, + "line": 164, "column": 24 } } @@ -101061,15 +104156,15 @@ "postfix": false, "binop": null }, - "start": 5628, - "end": 5629, + "start": 6068, + "end": 6069, "loc": { "start": { - "line": 148, + "line": 164, "column": 24 }, "end": { - "line": 148, + "line": 164, "column": 25 } } @@ -101087,15 +104182,15 @@ "binop": null }, "value": "phylogeny", - "start": 5636, - "end": 5645, + "start": 6076, + "end": 6085, "loc": { "start": { - "line": 149, + "line": 165, "column": 6 }, "end": { - "line": 149, + "line": 165, "column": 15 } } @@ -101113,15 +104208,15 @@ "binop": null, "updateContext": null }, - "start": 5645, - "end": 5646, + "start": 6085, + "end": 6086, "loc": { "start": { - "line": 149, + "line": 165, "column": 15 }, "end": { - "line": 149, + "line": 165, "column": 16 } } @@ -101141,15 +104236,15 @@ "updateContext": null }, "value": "this", - "start": 5653, - "end": 5657, + "start": 6093, + "end": 6097, "loc": { "start": { - "line": 150, + "line": 166, "column": 6 }, "end": { - "line": 150, + "line": 166, "column": 10 } } @@ -101167,15 +104262,15 @@ "binop": null, "updateContext": null }, - "start": 5657, - "end": 5658, + "start": 6097, + "end": 6098, "loc": { "start": { - "line": 150, + "line": 166, "column": 10 }, "end": { - "line": 150, + "line": 166, "column": 11 } } @@ -101193,15 +104288,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 5658, - "end": 5674, + "start": 6098, + "end": 6114, "loc": { "start": { - "line": 150, + "line": 166, "column": 11 }, "end": { - "line": 150, + "line": 166, "column": 27 } } @@ -101218,15 +104313,15 @@ "postfix": false, "binop": null }, - "start": 5679, - "end": 5680, + "start": 6119, + "end": 6120, "loc": { "start": { - "line": 151, + "line": 167, "column": 4 }, "end": { - "line": 151, + "line": 167, "column": 5 } } @@ -101244,15 +104339,15 @@ "binop": null, "updateContext": null }, - "start": 5680, - "end": 5681, + "start": 6120, + "end": 6121, "loc": { "start": { - "line": 151, + "line": 167, "column": 5 }, "end": { - "line": 151, + "line": 167, "column": 6 } } @@ -101270,15 +104365,15 @@ "binop": null }, "value": "getNodeLabels", - "start": 5681, - "end": 5694, + "start": 6121, + "end": 6134, "loc": { "start": { - "line": 151, + "line": 167, "column": 6 }, "end": { - "line": 151, + "line": 167, "column": 19 } } @@ -101295,15 +104390,15 @@ "postfix": false, "binop": null }, - "start": 5694, - "end": 5695, + "start": 6134, + "end": 6135, "loc": { "start": { - "line": 151, + "line": 167, "column": 19 }, "end": { - "line": 151, + "line": 167, "column": 20 } } @@ -101320,15 +104415,15 @@ "postfix": false, "binop": null }, - "start": 5695, - "end": 5696, + "start": 6135, + "end": 6136, "loc": { "start": { - "line": 151, + "line": 167, "column": 20 }, "end": { - "line": 151, + "line": 167, "column": 21 } } @@ -101346,15 +104441,15 @@ "binop": null, "updateContext": null }, - "start": 5696, - "end": 5697, + "start": 6136, + "end": 6137, "loc": { "start": { - "line": 151, + "line": 167, "column": 21 }, "end": { - "line": 151, + "line": 167, "column": 22 } } @@ -101372,15 +104467,15 @@ "binop": null }, "value": "forEach", - "start": 5697, - "end": 5704, + "start": 6137, + "end": 6144, "loc": { "start": { - "line": 151, + "line": 167, "column": 22 }, "end": { - "line": 151, + "line": 167, "column": 29 } } @@ -101397,15 +104492,15 @@ "postfix": false, "binop": null }, - "start": 5704, - "end": 5705, + "start": 6144, + "end": 6145, "loc": { "start": { - "line": 151, + "line": 167, "column": 29 }, "end": { - "line": 151, + "line": 167, "column": 30 } } @@ -101422,15 +104517,15 @@ "postfix": false, "binop": null }, - "start": 5705, - "end": 5706, + "start": 6145, + "end": 6146, "loc": { "start": { - "line": 151, + "line": 167, "column": 30 }, "end": { - "line": 151, + "line": 167, "column": 31 } } @@ -101448,15 +104543,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5706, - "end": 5715, + "start": 6146, + "end": 6155, "loc": { "start": { - "line": 151, + "line": 167, "column": 31 }, "end": { - "line": 151, + "line": 167, "column": 40 } } @@ -101473,15 +104568,15 @@ "postfix": false, "binop": null }, - "start": 5715, - "end": 5716, + "start": 6155, + "end": 6156, "loc": { "start": { - "line": 151, + "line": 167, "column": 40 }, "end": { - "line": 151, + "line": 167, "column": 41 } } @@ -101499,15 +104594,15 @@ "binop": null, "updateContext": null }, - "start": 5717, - "end": 5719, + "start": 6157, + "end": 6159, "loc": { "start": { - "line": 151, + "line": 167, "column": 42 }, "end": { - "line": 151, + "line": 167, "column": 44 } } @@ -101524,15 +104619,15 @@ "postfix": false, "binop": null }, - "start": 5720, - "end": 5721, + "start": 6160, + "end": 6161, "loc": { "start": { - "line": 151, + "line": 167, "column": 45 }, "end": { - "line": 151, + "line": 167, "column": 46 } } @@ -101540,15 +104635,15 @@ { "type": "CommentLine", "value": " Is this node label identical to the phyloreference name?", - "start": 5728, - "end": 5787, + "start": 6168, + "end": 6227, "loc": { "start": { - "line": 152, + "line": 168, "column": 6 }, "end": { - "line": 152, + "line": 168, "column": 65 } } @@ -101568,15 +104663,15 @@ "updateContext": null }, "value": "if", - "start": 5794, - "end": 5796, + "start": 6234, + "end": 6236, "loc": { "start": { - "line": 153, + "line": 169, "column": 6 }, "end": { - "line": 153, + "line": 169, "column": 8 } } @@ -101593,15 +104688,15 @@ "postfix": false, "binop": null }, - "start": 5797, - "end": 5798, + "start": 6237, + "end": 6238, "loc": { "start": { - "line": 153, + "line": 169, "column": 9 }, "end": { - "line": 153, + "line": 169, "column": 10 } } @@ -101619,15 +104714,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5798, - "end": 5807, + "start": 6238, + "end": 6247, "loc": { "start": { - "line": 153, + "line": 169, "column": 10 }, "end": { - "line": 153, + "line": 169, "column": 19 } } @@ -101646,15 +104741,15 @@ "updateContext": null }, "value": "===", - "start": 5808, - "end": 5811, + "start": 6248, + "end": 6251, "loc": { "start": { - "line": 153, + "line": 169, "column": 20 }, "end": { - "line": 153, + "line": 169, "column": 23 } } @@ -101672,15 +104767,15 @@ "binop": null }, "value": "phylorefLabel", - "start": 5812, - "end": 5825, + "start": 6252, + "end": 6265, "loc": { "start": { - "line": 153, + "line": 169, "column": 24 }, "end": { - "line": 153, + "line": 169, "column": 37 } } @@ -101697,15 +104792,15 @@ "postfix": false, "binop": null }, - "start": 5825, - "end": 5826, + "start": 6265, + "end": 6266, "loc": { "start": { - "line": 153, + "line": 169, "column": 37 }, "end": { - "line": 153, + "line": 169, "column": 38 } } @@ -101722,15 +104817,15 @@ "postfix": false, "binop": null }, - "start": 5827, - "end": 5828, + "start": 6267, + "end": 6268, "loc": { "start": { - "line": 153, + "line": 169, "column": 39 }, "end": { - "line": 153, + "line": 169, "column": 40 } } @@ -101748,15 +104843,15 @@ "binop": null }, "value": "nodeLabels", - "start": 5837, - "end": 5847, + "start": 6277, + "end": 6287, "loc": { "start": { - "line": 154, + "line": 170, "column": 8 }, "end": { - "line": 154, + "line": 170, "column": 18 } } @@ -101774,15 +104869,15 @@ "binop": null, "updateContext": null }, - "start": 5847, - "end": 5848, + "start": 6287, + "end": 6288, "loc": { "start": { - "line": 154, + "line": 170, "column": 18 }, "end": { - "line": 154, + "line": 170, "column": 19 } } @@ -101800,15 +104895,15 @@ "binop": null }, "value": "add", - "start": 5848, - "end": 5851, + "start": 6288, + "end": 6291, "loc": { "start": { - "line": 154, + "line": 170, "column": 19 }, "end": { - "line": 154, + "line": 170, "column": 22 } } @@ -101825,15 +104920,15 @@ "postfix": false, "binop": null }, - "start": 5851, - "end": 5852, + "start": 6291, + "end": 6292, "loc": { "start": { - "line": 154, + "line": 170, "column": 22 }, "end": { - "line": 154, + "line": 170, "column": 23 } } @@ -101851,15 +104946,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5852, - "end": 5861, + "start": 6292, + "end": 6301, "loc": { "start": { - "line": 154, + "line": 170, "column": 23 }, "end": { - "line": 154, + "line": 170, "column": 32 } } @@ -101876,15 +104971,15 @@ "postfix": false, "binop": null }, - "start": 5861, - "end": 5862, + "start": 6301, + "end": 6302, "loc": { "start": { - "line": 154, + "line": 170, "column": 32 }, "end": { - "line": 154, + "line": 170, "column": 33 } } @@ -101902,15 +104997,15 @@ "binop": null, "updateContext": null }, - "start": 5862, - "end": 5863, + "start": 6302, + "end": 6303, "loc": { "start": { - "line": 154, + "line": 170, "column": 33 }, "end": { - "line": 154, + "line": 170, "column": 34 } } @@ -101927,15 +105022,15 @@ "postfix": false, "binop": null }, - "start": 5870, - "end": 5871, + "start": 6310, + "end": 6311, "loc": { "start": { - "line": 155, + "line": 171, "column": 6 }, "end": { - "line": 155, + "line": 171, "column": 7 } } @@ -101955,15 +105050,15 @@ "updateContext": null }, "value": "else", - "start": 5872, - "end": 5876, + "start": 6312, + "end": 6316, "loc": { "start": { - "line": 155, + "line": 171, "column": 8 }, "end": { - "line": 155, + "line": 171, "column": 12 } } @@ -101983,15 +105078,15 @@ "updateContext": null }, "value": "if", - "start": 5877, - "end": 5879, + "start": 6317, + "end": 6319, "loc": { "start": { - "line": 155, + "line": 171, "column": 13 }, "end": { - "line": 155, + "line": 171, "column": 15 } } @@ -102008,15 +105103,15 @@ "postfix": false, "binop": null }, - "start": 5880, - "end": 5881, + "start": 6320, + "end": 6321, "loc": { "start": { - "line": 155, + "line": 171, "column": 16 }, "end": { - "line": 155, + "line": 171, "column": 17 } } @@ -102034,15 +105129,15 @@ "binop": null }, "value": "has", - "start": 5890, - "end": 5893, + "start": 6330, + "end": 6333, "loc": { "start": { - "line": 156, + "line": 172, "column": 8 }, "end": { - "line": 156, + "line": 172, "column": 11 } } @@ -102059,15 +105154,15 @@ "postfix": false, "binop": null }, - "start": 5893, - "end": 5894, + "start": 6333, + "end": 6334, "loc": { "start": { - "line": 156, + "line": 172, "column": 11 }, "end": { - "line": 156, + "line": 172, "column": 12 } } @@ -102085,15 +105180,15 @@ "binop": null }, "value": "phylogeny", - "start": 5894, - "end": 5903, + "start": 6334, + "end": 6343, "loc": { "start": { - "line": 156, + "line": 172, "column": 12 }, "end": { - "line": 156, + "line": 172, "column": 21 } } @@ -102111,15 +105206,15 @@ "binop": null, "updateContext": null }, - "start": 5903, - "end": 5904, + "start": 6343, + "end": 6344, "loc": { "start": { - "line": 156, + "line": 172, "column": 21 }, "end": { - "line": 156, + "line": 172, "column": 22 } } @@ -102138,15 +105233,15 @@ "updateContext": null }, "value": "additionalNodeProperties", - "start": 5905, - "end": 5931, + "start": 6345, + "end": 6371, "loc": { "start": { - "line": 156, + "line": 172, "column": 23 }, "end": { - "line": 156, + "line": 172, "column": 49 } } @@ -102163,15 +105258,15 @@ "postfix": false, "binop": null }, - "start": 5931, - "end": 5932, + "start": 6371, + "end": 6372, "loc": { "start": { - "line": 156, + "line": 172, "column": 49 }, "end": { - "line": 156, + "line": 172, "column": 50 } } @@ -102190,15 +105285,15 @@ "updateContext": null }, "value": "&&", - "start": 5941, - "end": 5943, + "start": 6381, + "end": 6383, "loc": { "start": { - "line": 157, + "line": 173, "column": 8 }, "end": { - "line": 157, + "line": 173, "column": 10 } } @@ -102216,15 +105311,15 @@ "binop": null }, "value": "has", - "start": 5944, - "end": 5947, + "start": 6384, + "end": 6387, "loc": { "start": { - "line": 157, + "line": 173, "column": 11 }, "end": { - "line": 157, + "line": 173, "column": 14 } } @@ -102241,15 +105336,15 @@ "postfix": false, "binop": null }, - "start": 5947, - "end": 5948, + "start": 6387, + "end": 6388, "loc": { "start": { - "line": 157, + "line": 173, "column": 14 }, "end": { - "line": 157, + "line": 173, "column": 15 } } @@ -102267,15 +105362,15 @@ "binop": null }, "value": "phylogeny", - "start": 5948, - "end": 5957, + "start": 6388, + "end": 6397, "loc": { "start": { - "line": 157, + "line": 173, "column": 15 }, "end": { - "line": 157, + "line": 173, "column": 24 } } @@ -102293,15 +105388,15 @@ "binop": null, "updateContext": null }, - "start": 5957, - "end": 5958, + "start": 6397, + "end": 6398, "loc": { "start": { - "line": 157, + "line": 173, "column": 24 }, "end": { - "line": 157, + "line": 173, "column": 25 } } @@ -102319,15 +105414,15 @@ "binop": null }, "value": "additionalNodeProperties", - "start": 5958, - "end": 5982, + "start": 6398, + "end": 6422, "loc": { "start": { - "line": 157, + "line": 173, "column": 25 }, "end": { - "line": 157, + "line": 173, "column": 49 } } @@ -102345,15 +105440,15 @@ "binop": null, "updateContext": null }, - "start": 5982, - "end": 5983, + "start": 6422, + "end": 6423, "loc": { "start": { - "line": 157, + "line": 173, "column": 49 }, "end": { - "line": 157, + "line": 173, "column": 50 } } @@ -102371,15 +105466,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5984, - "end": 5993, + "start": 6424, + "end": 6433, "loc": { "start": { - "line": 157, + "line": 173, "column": 51 }, "end": { - 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"line": 179, + "line": 195, "column": 11 }, "end": { - "line": 179, + "line": 195, "column": 12 } } @@ -104242,15 +107337,15 @@ "updateContext": null }, "value": "pso:draft", - "start": 6685, - "end": 6696, + "start": 7125, + "end": 7136, "loc": { "start": { - "line": 180, + "line": 196, "column": 6 }, "end": { - "line": 180, + "line": 196, "column": 17 } } @@ -104268,15 +107363,15 @@ "binop": null, "updateContext": null }, - "start": 6696, - "end": 6697, + "start": 7136, + "end": 7137, "loc": { "start": { - "line": 180, + "line": 196, "column": 17 }, "end": { - "line": 180, + "line": 196, "column": 18 } } @@ -104295,15 +107390,15 @@ "updateContext": null }, "value": "Draft", - "start": 6698, - "end": 6705, + "start": 7138, + "end": 7145, "loc": { "start": { - "line": 180, + "line": 196, "column": 19 }, "end": { - "line": 180, + "line": 196, "column": 26 } } @@ -104321,15 +107416,15 @@ "binop": null, "updateContext": null }, - "start": 6705, - "end": 6706, + "start": 7145, + "end": 7146, "loc": { "start": { - "line": 180, + "line": 196, "column": 26 }, "end": { - "line": 180, + "line": 196, "column": 27 } } @@ -104348,15 +107443,15 @@ "updateContext": null }, "value": "pso:final-draft", - "start": 6713, - "end": 6730, + "start": 7153, + "end": 7170, "loc": { "start": { - "line": 181, + "line": 197, "column": 6 }, "end": { - "line": 181, + "line": 197, "column": 23 } } @@ -104374,15 +107469,15 @@ "binop": null, "updateContext": null }, - "start": 6730, - "end": 6731, + "start": 7170, + "end": 7171, "loc": { "start": { - "line": 181, + "line": 197, "column": 23 }, "end": { - "line": 181, + "line": 197, "column": 24 } } @@ -104401,15 +107496,15 @@ "updateContext": null }, "value": "Final draft", - "start": 6732, - "end": 6745, + "start": 7172, + "end": 7185, "loc": { "start": { - "line": 181, + "line": 197, "column": 25 }, "end": { - "line": 181, + "line": 197, "column": 38 } } @@ -104427,15 +107522,15 @@ "binop": null, "updateContext": null }, - "start": 6745, - "end": 6746, + "start": 7185, + "end": 7186, "loc": { "start": { - "line": 181, + "line": 197, "column": 38 }, "end": { - "line": 181, + "line": 197, "column": 39 } } @@ -104454,15 +107549,15 @@ "updateContext": null }, "value": "pso:under-review", - "start": 6753, - "end": 6771, + "start": 7193, + "end": 7211, "loc": { "start": { - "line": 182, + "line": 198, "column": 6 }, "end": { - "line": 182, + "line": 198, "column": 24 } } @@ -104480,15 +107575,15 @@ "binop": null, "updateContext": null }, - "start": 6771, - "end": 6772, + "start": 7211, + "end": 7212, "loc": { "start": { - "line": 182, + "line": 198, "column": 24 }, "end": { - "line": 182, + "line": 198, "column": 25 } } @@ -104507,15 +107602,15 @@ "updateContext": null }, "value": "Under review", - "start": 6773, - "end": 6787, + "start": 7213, + "end": 7227, "loc": { "start": { - "line": 182, + "line": 198, "column": 26 }, "end": { - "line": 182, + "line": 198, "column": 40 } } @@ -104533,15 +107628,15 @@ "binop": null, "updateContext": null }, - "start": 6787, - "end": 6788, + "start": 7227, + "end": 7228, "loc": { "start": { - "line": 182, + "line": 198, "column": 40 }, "end": { - "line": 182, + "line": 198, "column": 41 } } @@ -104560,15 +107655,15 @@ "updateContext": null }, "value": "pso:submitted", - "start": 6795, - "end": 6810, + "start": 7235, + "end": 7250, "loc": { "start": { - "line": 183, + "line": 199, "column": 6 }, "end": { - "line": 183, + "line": 199, "column": 21 } } @@ -104586,15 +107681,15 @@ "binop": null, "updateContext": null }, - "start": 6810, - "end": 6811, + "start": 7250, + "end": 7251, "loc": { "start": { - "line": 183, + "line": 199, "column": 21 }, "end": { - "line": 183, + "line": 199, "column": 22 } } @@ -104613,15 +107708,15 @@ "updateContext": null }, "value": "Tested", - "start": 6812, - "end": 6820, + "start": 7252, + "end": 7260, "loc": { "start": { - "line": 183, + "line": 199, "column": 23 }, "end": { - "line": 183, + "line": 199, "column": 31 } } @@ -104639,15 +107734,15 @@ "binop": null, "updateContext": null }, - "start": 6820, - "end": 6821, + "start": 7260, + "end": 7261, "loc": { "start": { - "line": 183, + "line": 199, "column": 31 }, "end": { - "line": 183, + "line": 199, "column": 32 } } @@ -104666,15 +107761,15 @@ "updateContext": null }, "value": "pso:published", - "start": 6828, - "end": 6843, + "start": 7268, + "end": 7283, "loc": { "start": { - "line": 184, + "line": 200, "column": 6 }, "end": { - "line": 184, + "line": 200, "column": 21 } } @@ -104692,15 +107787,15 @@ "binop": null, "updateContext": null }, - "start": 6843, - "end": 6844, + "start": 7283, + "end": 7284, "loc": { "start": { - "line": 184, + "line": 200, "column": 21 }, "end": { - "line": 184, + "line": 200, "column": 22 } } @@ -104719,15 +107814,15 @@ "updateContext": null }, "value": "Published", - "start": 6845, - "end": 6856, + "start": 7285, + "end": 7296, "loc": { "start": { - "line": 184, + "line": 200, "column": 23 }, "end": { - "line": 184, + "line": 200, "column": 34 } } @@ -104745,15 +107840,15 @@ "binop": null, "updateContext": null }, - "start": 6856, - "end": 6857, + "start": 7296, + "end": 7297, "loc": { "start": { - "line": 184, + "line": 200, "column": 34 }, "end": { - "line": 184, + "line": 200, "column": 35 } } @@ -104772,15 +107867,15 @@ "updateContext": null }, "value": "pso:retracted-from-publication", - "start": 6864, - "end": 6896, + "start": 7304, + "end": 7336, "loc": { "start": { - "line": 185, + "line": 201, "column": 6 }, "end": { - "line": 185, + "line": 201, "column": 38 } } @@ -104798,15 +107893,15 @@ "binop": null, "updateContext": null }, - "start": 6896, - "end": 6897, + "start": 7336, + "end": 7337, "loc": { "start": { - "line": 185, + "line": 201, "column": 38 }, "end": { - "line": 185, + "line": 201, "column": 39 } } @@ -104825,15 +107920,15 @@ "updateContext": null }, "value": "Retracted", - "start": 6898, - "end": 6909, + "start": 7338, + "end": 7349, "loc": { "start": { - "line": 185, + "line": 201, "column": 40 }, "end": { - "line": 185, + "line": 201, "column": 51 } } @@ -104851,15 +107946,15 @@ "binop": null, "updateContext": null }, - "start": 6909, - "end": 6910, + "start": 7349, + "end": 7350, "loc": { "start": { - "line": 185, + "line": 201, "column": 51 }, "end": { - "line": 185, + "line": 201, "column": 52 } } @@ -104876,15 +107971,15 @@ "postfix": false, "binop": null }, - "start": 6915, - "end": 6916, + "start": 7355, + "end": 7356, "loc": { "start": { - "line": 186, + "line": 202, "column": 4 }, "end": { - "line": 186, + "line": 202, "column": 5 } } @@ -104902,15 +107997,15 @@ "binop": null, "updateContext": null }, - "start": 6916, - "end": 6917, + "start": 7356, + "end": 7357, "loc": { "start": { - "line": 186, + "line": 202, "column": 5 }, "end": { - "line": 186, + "line": 202, "column": 6 } } @@ -104927,15 +108022,15 @@ "postfix": false, "binop": null }, - "start": 6920, - "end": 6921, + "start": 7360, + "end": 7361, "loc": { "start": { - "line": 187, + "line": 203, "column": 2 }, "end": { - "line": 187, + "line": 203, "column": 3 } } @@ -104953,15 +108048,15 @@ "binop": null }, "value": "getCurrentStatus", - "start": 6925, - "end": 6941, + "start": 7365, + "end": 7381, "loc": { "start": { - "line": 189, + "line": 205, "column": 2 }, "end": { - "line": 189, + "line": 205, "column": 18 } } @@ -104978,15 +108073,15 @@ "postfix": false, "binop": null }, - "start": 6941, - "end": 6942, + "start": 7381, + "end": 7382, "loc": { "start": { - "line": 189, + "line": 205, "column": 18 }, "end": { - "line": 189, + "line": 205, "column": 19 } } @@ -105003,15 +108098,15 @@ "postfix": false, "binop": null }, - "start": 6942, - "end": 6943, + "start": 7382, + "end": 7383, "loc": { "start": { - "line": 189, + "line": 205, "column": 19 }, "end": { - "line": 189, + "line": 205, "column": 20 } } @@ -105028,15 +108123,15 @@ "postfix": false, "binop": null }, - "start": 6944, - "end": 6945, + "start": 7384, + "end": 7385, "loc": { "start": { - "line": 189, + "line": 205, "column": 21 }, "end": { - "line": 189, + "line": 205, "column": 22 } } @@ -105044,15 +108139,15 @@ { "type": "CommentLine", "value": " Return a result object that contains:", - "start": 6950, - "end": 6990, + "start": 7390, + "end": 7430, "loc": { "start": { - 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intervalEnd: the end of the interval", - "start": 7185, - "end": 7227, + "start": 7625, + "end": 7667, "loc": { "start": { - "line": 194, + "line": 210, "column": 4 }, "end": { - "line": 194, + "line": 210, "column": 46 } } @@ -105136,15 +108231,15 @@ "updateContext": null }, "value": "if", - "start": 7233, - "end": 7235, + "start": 7673, + "end": 7675, "loc": { "start": { - "line": 196, + "line": 212, "column": 4 }, "end": { - "line": 196, + "line": 212, "column": 6 } } @@ -105161,15 +108256,15 @@ "postfix": false, "binop": null }, - "start": 7236, - "end": 7237, + "start": 7676, + "end": 7677, "loc": { "start": { - "line": 196, + "line": 212, "column": 7 }, "end": { - "line": 196, + "line": 212, "column": 8 } } @@ -105187,15 +108282,15 @@ "binop": null }, "value": "has", - "start": 7244, - "end": 7247, + "start": 7684, + "end": 7687, "loc": { "start": { - "line": 197, + "line": 213, "column": 6 }, "end": { - "line": 197, + "line": 213, "column": 9 } } @@ -105212,15 +108307,15 @@ "postfix": false, "binop": null }, - "start": 7247, - "end": 7248, + "start": 7687, + "end": 7688, "loc": { "start": { - "line": 197, + "line": 213, "column": 9 }, "end": { - "line": 197, + "line": 213, "column": 10 } } @@ -105240,15 +108335,15 @@ "updateContext": null }, "value": "this", - "start": 7248, - "end": 7252, + "start": 7688, + "end": 7692, "loc": { "start": { - "line": 197, + "line": 213, "column": 10 }, "end": { - "line": 197, + "line": 213, "column": 14 } } @@ -105266,15 +108361,15 @@ "binop": null, "updateContext": null }, - "start": 7252, - "end": 7253, + "start": 7692, + "end": 7693, "loc": { "start": { - "line": 197, + "line": 213, "column": 14 }, "end": { - "line": 197, + "line": 213, "column": 15 } } @@ -105292,15 +108387,15 @@ "binop": null }, "value": "phyloref", - "start": 7253, - "end": 7261, + "start": 7693, + "end": 7701, "loc": { "start": { - "line": 197, + "line": 213, "column": 15 }, "end": { - "line": 197, + "line": 213, "column": 23 } } @@ -105318,15 +108413,15 @@ "binop": null, "updateContext": null }, - "start": 7261, - "end": 7262, + "start": 7701, + "end": 7702, "loc": { "start": { - "line": 197, + "line": 213, "column": 23 }, "end": { - "line": 197, + "line": 213, "column": 24 } } @@ -105345,15 +108440,15 @@ "updateContext": null }, "value": "pso:holdsStatusInTime", - "start": 7263, - "end": 7286, + "start": 7703, + "end": 7726, "loc": { "start": { - "line": 197, + "line": 213, "column": 25 }, "end": { - "line": 197, + "line": 213, "column": 48 } } @@ -105370,15 +108465,15 @@ "postfix": false, "binop": null }, - "start": 7286, - "end": 7287, + "start": 7726, + "end": 7727, "loc": { "start": { - "line": 197, + "line": 213, "column": 48 }, "end": { - "line": 197, + "line": 213, "column": 49 } } @@ -105397,15 +108492,15 @@ "updateContext": null }, "value": "&&", - "start": 7294, - "end": 7296, + "start": 7734, + "end": 7736, "loc": { "start": { - "line": 198, + "line": 214, "column": 6 }, "end": { - "line": 198, + "line": 214, "column": 8 } } @@ -105423,15 +108518,15 @@ "binop": null }, "value": "Array", - "start": 7297, - "end": 7302, + "start": 7737, + "end": 7742, "loc": { "start": { - "line": 198, + "line": 214, "column": 9 }, "end": { - "line": 198, + "line": 214, "column": 14 } } @@ -105449,15 +108544,15 @@ "binop": null, "updateContext": null }, - "start": 7302, - "end": 7303, + "start": 7742, + "end": 7743, "loc": { "start": { - "line": 198, + "line": 214, "column": 14 }, "end": { - "line": 198, + "line": 214, "column": 15 } } @@ -105475,15 +108570,15 @@ "binop": null }, "value": "isArray", - "start": 7303, - "end": 7310, + "start": 7743, + "end": 7750, "loc": { "start": { - "line": 198, + "line": 214, "column": 15 }, "end": { - "line": 198, + "line": 214, "column": 22 } } @@ -105500,15 +108595,15 @@ "postfix": false, "binop": null }, - "start": 7310, - "end": 7311, + "start": 7750, + "end": 7751, "loc": { "start": { - "line": 198, + "line": 214, "column": 22 }, "end": { - "line": 198, + "line": 214, "column": 23 } } @@ -105528,15 +108623,15 @@ "updateContext": null }, "value": "this", - "start": 7311, - "end": 7315, + "start": 7751, + "end": 7755, "loc": { "start": { - "line": 198, + "line": 214, "column": 23 }, "end": { - "line": 198, + "line": 214, "column": 27 } } @@ -105554,15 +108649,15 @@ "binop": null, "updateContext": null }, - "start": 7315, - "end": 7316, + "start": 7755, + "end": 7756, "loc": { "start": { - "line": 198, + "line": 214, "column": 27 }, "end": { - "line": 198, + "line": 214, "column": 28 } } @@ -105580,15 +108675,15 @@ "binop": null }, "value": "phyloref", - "start": 7316, - "end": 7324, + "start": 7756, + "end": 7764, "loc": { "start": { - "line": 198, + "line": 214, "column": 28 }, "end": { - "line": 198, + "line": 214, "column": 36 } } @@ -105606,15 +108701,15 @@ "binop": null, "updateContext": null }, - "start": 7324, - "end": 7325, + "start": 7764, + "end": 7765, "loc": { "start": { - "line": 198, + "line": 214, "column": 36 }, "end": { - "line": 198, + "line": 214, "column": 37 } } @@ -105633,15 +108728,15 @@ "updateContext": null }, "value": "pso:holdsStatusInTime", - "start": 7325, - "end": 7348, + "start": 7765, + "end": 7788, "loc": { "start": { - "line": 198, + "line": 214, "column": 37 }, "end": { - "line": 198, + "line": 214, "column": 60 } } @@ -105659,15 +108754,15 @@ "binop": null, "updateContext": null }, - "start": 7348, - "end": 7349, + "start": 7788, + "end": 7789, "loc": { "start": { - "line": 198, + "line": 214, "column": 60 }, "end": { - "line": 198, + "line": 214, "column": 61 } } @@ -105684,15 +108779,15 @@ "postfix": false, "binop": null }, - "start": 7349, - "end": 7350, + "start": 7789, + "end": 7790, "loc": { "start": { - "line": 198, + "line": 214, "column": 61 }, "end": { - "line": 198, + "line": 214, "column": 62 } } @@ -105711,15 +108806,15 @@ "updateContext": null }, "value": "&&", - "start": 7357, - "end": 7359, + "start": 7797, + "end": 7799, "loc": { "start": { - "line": 199, + "line": 215, "column": 6 }, "end": { - "line": 199, + "line": 215, "column": 8 } } @@ -105739,15 +108834,15 @@ "updateContext": null }, "value": "this", - "start": 7360, - "end": 7364, + "start": 7800, + "end": 7804, "loc": { "start": { - "line": 199, + "line": 215, "column": 9 }, "end": { - "line": 199, + "line": 215, "column": 13 } } @@ -105765,15 +108860,15 @@ "binop": null, "updateContext": null }, - "start": 7364, - "end": 7365, + "start": 7804, + "end": 7805, "loc": { "start": { - "line": 199, + "line": 215, "column": 13 }, "end": { - "line": 199, + "line": 215, "column": 14 } } @@ -105791,15 +108886,15 @@ "binop": null }, "value": "phyloref", - "start": 7365, - "end": 7373, + "start": 7805, + "end": 7813, "loc": { "start": { - "line": 199, + "line": 215, "column": 14 }, "end": { - "line": 199, + "line": 215, "column": 22 } } @@ -105817,15 +108912,15 @@ "binop": null, "updateContext": null }, - "start": 7373, - "end": 7374, + "start": 7813, + "end": 7814, "loc": { "start": { - "line": 199, + "line": 215, "column": 22 }, "end": { - "line": 199, + "line": 215, "column": 23 } } @@ -105844,15 +108939,15 @@ "updateContext": null }, "value": "pso:holdsStatusInTime", - "start": 7374, - "end": 7397, + "start": 7814, + "end": 7837, "loc": { "start": { - "line": 199, + "line": 215, "column": 23 }, "end": { - "line": 199, + "line": 215, "column": 46 } } @@ -105870,15 +108965,15 @@ "binop": null, "updateContext": null }, - "start": 7397, - "end": 7398, + "start": 7837, + "end": 7838, "loc": { "start": { - "line": 199, + "line": 215, "column": 46 }, "end": { - "line": 199, + "line": 215, "column": 47 } } @@ -105896,15 +108991,15 @@ "binop": null, "updateContext": null }, - "start": 7398, - "end": 7399, + "start": 7838, + "end": 7839, "loc": { "start": { - "line": 199, + "line": 215, "column": 47 }, "end": { - "line": 199, + "line": 215, "column": 48 } } @@ -105922,15 +109017,15 @@ "binop": null }, "value": "length", - "start": 7399, - "end": 7405, + "start": 7839, + "end": 7845, "loc": { "start": { - "line": 199, + "line": 215, "column": 48 }, "end": { - "line": 199, + "line": 215, "column": 54 } } @@ -105949,15 +109044,15 @@ "updateContext": null }, "value": ">", - 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"start": 8624, - "end": 8625, + "start": 9064, + "end": 9065, "loc": { "start": { - "line": 230, + "line": 246, "column": 2 }, "end": { - "line": 230, + "line": 246, "column": 3 } } @@ -109583,15 +112678,15 @@ "binop": null }, "value": "getStatusChanges", - "start": 8629, - "end": 8645, + "start": 9069, + "end": 9085, "loc": { "start": { - "line": 232, + "line": 248, "column": 2 }, "end": { - "line": 232, + "line": 248, "column": 18 } } @@ -109608,15 +112703,15 @@ "postfix": false, "binop": null }, - "start": 8645, - "end": 8646, + "start": 9085, + "end": 9086, "loc": { "start": { - "line": 232, + "line": 248, "column": 18 }, "end": { - "line": 232, + "line": 248, "column": 19 } } @@ -109633,15 +112728,15 @@ "postfix": false, "binop": null }, - "start": 8646, - "end": 8647, + "start": 9086, + "end": 9087, "loc": { "start": { - "line": 232, + "line": 248, "column": 19 }, "end": { - "line": 232, + "line": 248, "column": 20 } } @@ -109658,15 +112753,15 @@ "postfix": false, "binop": null }, - 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Return an empty list.", - "start": 9823, - "end": 9859, + "start": 10263, + "end": 10299, "loc": { "start": { - "line": 262, + "line": 278, "column": 4 }, "end": { - "line": 262, + "line": 278, "column": 40 } } @@ -114085,15 +117180,15 @@ "updateContext": null }, "value": "return", - "start": 9864, - "end": 9870, + "start": 10304, + "end": 10310, "loc": { "start": { - "line": 263, + "line": 279, "column": 4 }, "end": { - "line": 263, + "line": 279, "column": 10 } } @@ -114111,15 +117206,15 @@ "binop": null, "updateContext": null }, - "start": 9871, - "end": 9872, + "start": 10311, + "end": 10312, "loc": { "start": { - "line": 263, + "line": 279, "column": 11 }, "end": { - "line": 263, + "line": 279, "column": 12 } } @@ -114137,15 +117232,15 @@ "binop": null, "updateContext": null }, - "start": 9872, - "end": 9873, + "start": 10312, + "end": 10313, "loc": { "start": { - "line": 263, + "line": 279, "column": 12 }, "end": { - "line": 263, + "line": 279, "column": 13 } } @@ -114163,15 +117258,15 @@ "binop": null, "updateContext": null }, - "start": 9873, - "end": 9874, + "start": 10313, + "end": 10314, "loc": { "start": { - "line": 263, + "line": 279, "column": 13 }, "end": { - "line": 263, + "line": 279, "column": 14 } } @@ -114188,15 +117283,15 @@ "postfix": false, "binop": null }, - "start": 9877, - "end": 9878, + "start": 10317, + "end": 10318, "loc": { "start": { - "line": 264, + "line": 280, "column": 2 }, "end": { - "line": 264, + "line": 280, "column": 3 } } @@ -114214,15 +117309,15 @@ "binop": null }, "value": "setStatus", - "start": 9882, - "end": 9891, + "start": 10322, + "end": 10331, "loc": { "start": { - "line": 266, + "line": 282, "column": 2 }, "end": { - "line": 266, + "line": 282, "column": 11 } } @@ -114239,15 +117334,15 @@ "postfix": false, "binop": null }, - "start": 9891, - "end": 9892, + "start": 10331, + "end": 10332, "loc": { "start": { - "line": 266, + "line": 282, "column": 11 }, "end": { - "line": 266, + "line": 282, "column": 12 } } @@ -114265,15 +117360,15 @@ "binop": null }, "value": "status", - "start": 9892, - "end": 9898, + "start": 10332, + "end": 10338, "loc": { "start": { - "line": 266, + "line": 282, "column": 12 }, "end": { - "line": 266, + "line": 282, "column": 18 } } @@ -114290,15 +117385,15 @@ "postfix": false, "binop": null }, - "start": 9898, - "end": 9899, + "start": 10338, + "end": 10339, "loc": { "start": { - "line": 266, + "line": 282, "column": 18 }, "end": { - "line": 266, + "line": 282, "column": 19 } } @@ -114315,15 +117410,15 @@ "postfix": false, "binop": null }, - "start": 9900, - "end": 9901, + "start": 10340, + "end": 10341, "loc": { "start": { - "line": 266, + "line": 282, "column": 20 }, "end": { - "line": 266, + "line": 282, "column": 21 } } @@ -114331,15 +117426,15 @@ { "type": "CommentLine", "value": " Set the status of a phyloreference", - "start": 9906, - "end": 9943, + "start": 10346, + "end": 10383, "loc": { "start": { - "line": 267, + "line": 283, "column": 4 }, "end": { - "line": 267, + "line": 283, "column": 41 } } @@ -114347,15 +117442,15 @@ { "type": "CommentLine", "value": "", - "start": 9948, - "end": 9950, + "start": 10388, + "end": 10390, "loc": { "start": { - "line": 268, + "line": 284, "column": 4 }, "end": { - "line": 268, + "line": 284, "column": 6 } } @@ -114363,15 +117458,15 @@ { "type": "CommentLine", "value": " Check whether we have a valid status CURIE.", - "start": 9955, - "end": 10001, + "start": 10395, + "end": 10441, "loc": { "start": { - "line": 269, + "line": 285, "column": 4 }, "end": { - "line": 269, + "line": 285, "column": 50 } } @@ -114391,15 +117486,15 @@ "updateContext": null }, "value": "if", - "start": 10006, - "end": 10008, + "start": 10446, + "end": 10448, "loc": { "start": { - "line": 270, + "line": 286, "column": 4 }, "end": { - "line": 270, + "line": 286, "column": 6 } } @@ -114416,15 +117511,15 @@ "postfix": false, "binop": null }, - "start": 10009, - "end": 10010, + "start": 10449, + "end": 10450, "loc": { "start": { - "line": 270, + "line": 286, "column": 7 }, "end": { - "line": 270, + "line": 286, "column": 8 } } @@ -114443,15 +117538,15 @@ "updateContext": null }, "value": "!", - "start": 10010, - "end": 10011, + "start": 10450, + "end": 10451, "loc": { "start": { - "line": 270, + "line": 286, "column": 8 }, "end": { - "line": 270, + "line": 286, "column": 9 } } @@ -114469,15 +117564,15 @@ "binop": null }, "value": "has", - "start": 10011, - "end": 10014, + "start": 10451, + "end": 10454, "loc": { "start": { - "line": 270, + "line": 286, "column": 9 }, "end": { - "line": 270, + "line": 286, "column": 12 } } @@ -114494,15 +117589,15 @@ "postfix": false, "binop": null }, - "start": 10014, - "end": 10015, + "start": 10454, + "end": 10455, "loc": { "start": { - "line": 270, + "line": 286, "column": 12 }, "end": { - "line": 270, + "line": 286, "column": 13 } } @@ -114520,15 +117615,15 @@ "binop": null }, "value": "PhylorefWrapper", - "start": 10015, - "end": 10030, + "start": 10455, + "end": 10470, "loc": { "start": { - "line": 270, + "line": 286, "column": 13 }, "end": { - "line": 270, + "line": 286, "column": 28 } } @@ -114546,15 +117641,15 @@ "binop": null, "updateContext": null }, - "start": 10030, - "end": 10031, + "start": 10470, + "end": 10471, "loc": { "start": { - "line": 270, + "line": 286, "column": 28 }, "end": { - "line": 270, + "line": 286, "column": 29 } } @@ -114572,15 +117667,15 @@ "binop": null }, "value": "getStatusCURIEsInEnglish", - "start": 10031, - "end": 10055, + "start": 10471, + "end": 10495, "loc": { "start": { - "line": 270, + "line": 286, "column": 29 }, "end": { - "line": 270, + "line": 286, "column": 53 } } @@ -114597,15 +117692,15 @@ "postfix": false, "binop": null }, - "start": 10055, - "end": 10056, + "start": 10495, + "end": 10496, "loc": { "start": { - "line": 270, + "line": 286, "column": 53 }, "end": { - "line": 270, + "line": 286, "column": 54 } } @@ -114622,15 +117717,15 @@ "postfix": false, "binop": null }, - "start": 10056, - "end": 10057, + "start": 10496, + "end": 10497, "loc": { "start": { - "line": 270, + "line": 286, "column": 54 }, "end": { - "line": 270, + "line": 286, "column": 55 } } @@ -114648,15 +117743,15 @@ "binop": null, "updateContext": null }, - "start": 10057, - "end": 10058, + "start": 10497, + "end": 10498, "loc": { "start": { - "line": 270, + "line": 286, "column": 55 }, "end": { - "line": 270, + "line": 286, "column": 56 } } @@ -114674,15 +117769,15 @@ "binop": null }, "value": "status", - "start": 10059, - "end": 10065, + "start": 10499, + "end": 10505, "loc": { "start": { - "line": 270, + "line": 286, "column": 57 }, "end": { - "line": 270, + "line": 286, "column": 63 } } @@ -114699,15 +117794,15 @@ "postfix": false, "binop": null }, - "start": 10065, - "end": 10066, + "start": 10505, + "end": 10506, "loc": { "start": { - "line": 270, + "line": 286, "column": 63 }, "end": { - "line": 270, + "line": 286, "column": 64 } } @@ -114724,15 +117819,15 @@ "postfix": false, "binop": null }, - "start": 10066, - "end": 10067, + "start": 10506, + "end": 10507, "loc": { "start": { - "line": 270, + "line": 286, "column": 64 }, "end": { - "line": 270, + "line": 286, "column": 65 } } @@ -114749,15 +117844,15 @@ "postfix": false, "binop": null }, - "start": 10068, - "end": 10069, + "start": 10508, + "end": 10509, "loc": { "start": { - "line": 270, + "line": 286, "column": 66 }, "end": { - "line": 270, + "line": 286, "column": 67 } } @@ -114777,15 +117872,15 @@ "updateContext": null }, "value": "throw", - "start": 10076, - "end": 10081, + "start": 10516, + "end": 10521, "loc": { "start": { - "line": 271, + "line": 287, "column": 6 }, "end": { - "line": 271, + "line": 287, "column": 11 } } @@ -114805,15 +117900,15 @@ "updateContext": null }, "value": "new", - "start": 10082, - "end": 10085, + "start": 10522, + "end": 10525, "loc": { "start": { - "line": 271, + "line": 287, "column": 12 }, "end": { - "line": 271, + "line": 287, "column": 15 } } @@ -114831,15 +117926,15 @@ "binop": null }, "value": "TypeError", - "start": 10086, - "end": 10095, + "start": 10526, + "end": 10535, "loc": { "start": { - "line": 271, + "line": 287, "column": 16 }, "end": { - "line": 271, + "line": 287, "column": 25 } } @@ -114856,15 +117951,15 @@ "postfix": false, "binop": null }, - "start": 10095, - "end": 10096, + "start": 10535, + "end": 10536, "loc": { "start": { - "line": 271, + "line": 287, "column": 25 }, "end": { - "line": 271, + "line": 287, "column": 26 } } @@ -114881,15 +117976,15 @@ "postfix": false, "binop": null }, - "start": 10096, - "end": 10097, + "start": 10536, + "end": 10537, "loc": { "start": { - "line": 271, + "line": 287, "column": 26 }, "end": { - "line": 271, + "line": 287, "column": 27 } } @@ -114908,15 +118003,15 @@ "updateContext": null }, "value": "setStatus() called with invalid status CURIE '", - "start": 10097, - "end": 10143, + "start": 10537, + "end": 10583, "loc": { "start": { - "line": 271, + "line": 287, "column": 27 }, "end": { - "line": 271, + "line": 287, "column": 73 } } @@ -114933,15 +118028,15 @@ "postfix": false, "binop": null }, - "start": 10143, - "end": 10145, + "start": 10583, + "end": 10585, "loc": { "start": { - "line": 271, + "line": 287, "column": 73 }, "end": { - "line": 271, + "line": 287, "column": 75 } } @@ -114959,15 +118054,15 @@ "binop": null }, "value": "status", - "start": 10145, - "end": 10151, + "start": 10585, + "end": 10591, "loc": { "start": { - "line": 271, + "line": 287, "column": 75 }, "end": { - "line": 271, + "line": 287, "column": 81 } } @@ -114984,15 +118079,15 @@ "postfix": false, "binop": null }, - "start": 10151, - "end": 10152, + "start": 10591, + "end": 10592, "loc": { "start": { - "line": 271, + "line": 287, "column": 81 }, "end": { - "line": 271, + "line": 287, "column": 82 } } @@ -115011,15 +118106,15 @@ "updateContext": null }, "value": "'", - "start": 10152, - "end": 10153, + "start": 10592, + "end": 10593, "loc": { "start": { - "line": 271, + "line": 287, "column": 82 }, "end": { - "line": 271, + "line": 287, "column": 83 } } @@ -115036,15 +118131,15 @@ "postfix": false, "binop": null }, - "start": 10153, - "end": 10154, + "start": 10593, + "end": 10594, "loc": { "start": { - "line": 271, + "line": 287, "column": 83 }, "end": { - "line": 271, + "line": 287, "column": 84 } } @@ -115061,15 +118156,15 @@ "postfix": false, "binop": null }, - "start": 10154, - "end": 10155, + "start": 10594, + "end": 10595, "loc": { "start": { - "line": 271, + "line": 287, "column": 84 }, "end": { - "line": 271, + "line": 287, "column": 85 } } @@ -115087,15 +118182,15 @@ "binop": null, "updateContext": null }, - "start": 10155, - "end": 10156, + "start": 10595, + "end": 10596, "loc": { "start": { - "line": 271, + "line": 287, "column": 85 }, "end": { - "line": 271, + "line": 287, "column": 86 } } @@ -115112,15 +118207,15 @@ "postfix": false, "binop": null }, - "start": 10161, - "end": 10162, + "start": 10601, + "end": 10602, "loc": { "start": { - "line": 272, + "line": 288, "column": 4 }, "end": { - "line": 272, + "line": 288, "column": 5 } } @@ -115128,15 +118223,15 @@ { "type": "CommentLine", "value": " See if we can end the previous interval.", - "start": 10168, - "end": 10211, + "start": 10608, + "end": 10651, "loc": { "start": { - "line": 274, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 290, "column": 47 } } @@ -115156,15 +118251,15 @@ "updateContext": null }, "value": "const", - 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"start": 10918, - "end": 10930, + "start": 11358, + "end": 11370, "loc": { "start": { - "line": 291, + "line": 307, "column": 33 }, "end": { - "line": 291, + "line": 307, "column": 45 } } @@ -117761,15 +120856,15 @@ "postfix": false, "binop": null }, - "start": 10930, - "end": 10931, + "start": 11370, + "end": 11371, "loc": { "start": { - "line": 291, + "line": 307, "column": 45 }, "end": { - "line": 291, + "line": 307, "column": 46 } } @@ -117786,15 +120881,15 @@ "postfix": false, "binop": null }, - "start": 10931, - "end": 10932, + "start": 11371, + "end": 11372, "loc": { "start": { - "line": 291, + "line": 307, "column": 46 }, "end": { - "line": 291, + "line": 307, "column": 47 } } @@ -117811,15 +120906,15 @@ "postfix": false, "binop": null }, - "start": 10933, - "end": 10934, + "start": 11373, + "end": 11374, "loc": { "start": { - "line": 291, + "line": 307, "column": 48 }, "end": { - "line": 291, + "line": 307, "column": 49 } } @@ -117837,15 +120932,15 @@ "binop": null }, "value": "lastStatusInTime", - "start": 10943, - "end": 10959, + "start": 11383, + "end": 11399, "loc": { "start": { - "line": 292, + "line": 308, "column": 8 }, "end": { - "line": 292, + "line": 308, "column": 24 } } @@ -117863,15 +120958,15 @@ "binop": null, "updateContext": null }, - "start": 10959, - "end": 10960, + "start": 11399, + "end": 11400, "loc": { "start": { - "line": 292, + "line": 308, "column": 24 }, "end": { - "line": 292, + "line": 308, "column": 25 } } @@ -117890,15 +120985,15 @@ "updateContext": null }, "value": "tvc:atTime", - "start": 10960, - "end": 10972, + "start": 11400, + "end": 11412, "loc": { "start": { - "line": 292, + "line": 308, "column": 25 }, "end": { - "line": 292, + "line": 308, "column": 37 } } @@ -117916,15 +121011,15 @@ "binop": null, "updateContext": null }, - "start": 10972, - "end": 10973, + "start": 11412, + "end": 11413, "loc": { "start": { - "line": 292, + "line": 308, "column": 37 }, "end": { - "line": 292, + "line": 308, "column": 38 } } @@ -117943,15 +121038,15 @@ "updateContext": null }, "value": "=", - 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"start": 10999, - "end": 11002, + "start": 11439, + "end": 11442, "loc": { "start": { - "line": 294, + "line": 310, "column": 11 }, "end": { - "line": 294, + "line": 310, "column": 14 } } @@ -118175,15 +121270,15 @@ "postfix": false, "binop": null }, - "start": 11002, - "end": 11003, + "start": 11442, + "end": 11443, "loc": { "start": { - "line": 294, + "line": 310, "column": 14 }, "end": { - "line": 294, + "line": 310, "column": 15 } } @@ -118201,15 +121296,15 @@ "binop": null }, "value": "lastStatusInTime", - "start": 11003, - "end": 11019, + "start": 11443, + "end": 11459, "loc": { "start": { - "line": 294, + "line": 310, "column": 15 }, "end": { - "line": 294, + "line": 310, "column": 31 } } @@ -118227,15 +121322,15 @@ "binop": null, "updateContext": null }, - "start": 11019, - "end": 11020, + "start": 11459, + "end": 11460, "loc": { "start": { - "line": 294, + "line": 310, "column": 31 }, "end": { - "line": 294, + "line": 310, "column": 32 } } @@ -118254,15 +121349,15 @@ "updateContext": null }, "value": "tvc:atTime", - "start": 11020, - "end": 11032, + "start": 11460, + "end": 11472, "loc": { "start": { - "line": 294, + "line": 310, "column": 32 }, "end": { - "line": 294, + "line": 310, "column": 44 } } @@ -118280,15 +121375,15 @@ "binop": null, "updateContext": null }, - "start": 11032, - "end": 11033, + "start": 11472, + "end": 11473, "loc": { "start": { - "line": 294, + "line": 310, "column": 44 }, "end": { - "line": 294, + "line": 310, "column": 45 } } @@ -118306,15 +121401,15 @@ "binop": null, "updateContext": null }, - "start": 11033, - "end": 11034, + "start": 11473, + "end": 11474, "loc": { "start": { - "line": 294, + "line": 310, "column": 45 }, "end": { - "line": 294, + "line": 310, "column": 46 } } @@ -118333,15 +121428,15 @@ "updateContext": null }, "value": "timeinterval:hasIntervalEndDate", - "start": 11035, - "end": 11068, + "start": 11475, + "end": 11508, "loc": { "start": { - "line": 294, + "line": 310, "column": 47 }, "end": { - "line": 294, + "line": 310, "column": 80 } } @@ -118358,15 +121453,15 @@ "postfix": false, "binop": null }, - "start": 11068, - "end": 11069, + "start": 11508, + "end": 11509, "loc": { "start": { - "line": 294, + "line": 310, "column": 80 }, "end": { - "line": 294, + "line": 310, "column": 81 } } @@ -118383,15 +121478,15 @@ "postfix": false, "binop": null }, - "start": 11069, - "end": 11070, + "start": 11509, + "end": 11510, "loc": { "start": { - "line": 294, + "line": 310, "column": 81 }, "end": { - "line": 294, + "line": 310, "column": 82 } } @@ -118408,15 +121503,15 @@ "postfix": false, "binop": null }, - "start": 11071, - "end": 11072, + "start": 11511, + "end": 11512, "loc": { "start": { - "line": 294, + "line": 310, "column": 83 }, "end": { - "line": 294, + "line": 310, "column": 84 } } @@ -118424,15 +121519,15 @@ { "type": "CommentLine", "value": " If the last time entry doesn't already have an interval end date, set it to now.", - "start": 11081, - "end": 11164, + "start": 11521, + "end": 11604, "loc": { "start": { - "line": 295, + "line": 311, "column": 8 }, "end": { - "line": 295, + "line": 311, "column": 91 } } @@ -118450,15 +121545,15 @@ "binop": null }, "value": "lastStatusInTime", - "start": 11173, - "end": 11189, + "start": 11613, + "end": 11629, "loc": { "start": { - "line": 296, + "line": 312, "column": 8 }, "end": { - "line": 296, + "line": 312, "column": 24 } } @@ -118476,15 +121571,15 @@ "binop": null, "updateContext": null }, - "start": 11189, - "end": 11190, + "start": 11629, + "end": 11630, "loc": { "start": { - "line": 296, + "line": 312, "column": 24 }, "end": { - "line": 296, + "line": 312, "column": 25 } } @@ -118503,15 +121598,15 @@ "updateContext": null }, "value": "tvc:atTime", - "start": 11190, - "end": 11202, + "start": 11630, + "end": 11642, "loc": { "start": { - "line": 296, + "line": 312, "column": 25 }, "end": { - "line": 296, + "line": 312, "column": 37 } } @@ -118529,15 +121624,15 @@ "binop": null, "updateContext": null }, - "start": 11202, - "end": 11203, + "start": 11642, + "end": 11643, "loc": { "start": { - "line": 296, + "line": 312, "column": 37 }, "end": { - "line": 296, + "line": 312, "column": 38 } } @@ -118555,15 +121650,15 @@ "binop": null, "updateContext": null }, - "start": 11203, - "end": 11204, + "start": 11643, + "end": 11644, "loc": { "start": { - "line": 296, + "line": 312, "column": 38 }, "end": { - "line": 296, + "line": 312, "column": 39 } } @@ -118582,15 +121677,15 @@ "updateContext": null }, "value": "timeinterval:hasIntervalEndDate", - "start": 11204, - "end": 11237, + "start": 11644, + "end": 11677, "loc": { "start": { - "line": 296, + "line": 312, "column": 39 }, "end": { - "line": 296, + "line": 312, "column": 72 } } @@ -118608,15 +121703,15 @@ "binop": null, "updateContext": null }, - "start": 11237, - "end": 11238, + "start": 11677, + "end": 11678, "loc": { "start": { - "line": 296, + "line": 312, "column": 72 }, "end": { - "line": 296, + "line": 312, "column": 73 } } @@ -118635,15 +121730,15 @@ "updateContext": null }, "value": "=", - "start": 11239, - "end": 11240, + "start": 11679, + "end": 11680, "loc": { "start": { - "line": 296, + "line": 312, "column": 74 }, "end": { - "line": 296, + "line": 312, "column": 75 } } @@ -118661,15 +121756,15 @@ "binop": null }, "value": "currentTime", - "start": 11241, - "end": 11252, + "start": 11681, + "end": 11692, "loc": { "start": { - "line": 296, + "line": 312, "column": 76 }, "end": { - "line": 296, + "line": 312, "column": 87 } } @@ -118687,15 +121782,15 @@ "binop": null, "updateContext": null }, - "start": 11252, - "end": 11253, + "start": 11692, + "end": 11693, "loc": { "start": { - "line": 296, + "line": 312, "column": 87 }, "end": { - "line": 296, + "line": 312, "column": 88 } } @@ -118712,15 +121807,15 @@ "postfix": false, "binop": null }, - "start": 11260, - "end": 11261, + "start": 11700, + "end": 11701, "loc": { "start": { - "line": 297, + "line": 313, "column": 6 }, "end": { - "line": 297, + "line": 313, "column": 7 } } @@ -118737,15 +121832,15 @@ "postfix": false, "binop": null }, - "start": 11266, - "end": 11267, + "start": 11706, + "end": 11707, "loc": { "start": { - "line": 298, + "line": 314, "column": 4 }, "end": { - "line": 298, + "line": 314, "column": 5 } } @@ -118753,15 +121848,15 @@ { "type": "CommentLine", "value": " Create new entry.", - "start": 11273, - "end": 11293, + "start": 11713, + "end": 11733, "loc": { "start": { - "line": 300, + "line": 316, "column": 4 }, "end": { - "line": 300, + "line": 316, "column": 24 } } @@ -118781,15 +121876,15 @@ "updateContext": null }, "value": "this", - "start": 11298, - "end": 11302, + "start": 11738, + "end": 11742, "loc": { "start": { - "line": 301, + "line": 317, "column": 4 }, "end": { - "line": 301, + "line": 317, "column": 8 } } @@ -118807,15 +121902,15 @@ "binop": null, "updateContext": null }, - "start": 11302, - "end": 11303, + "start": 11742, + "end": 11743, "loc": { "start": { - "line": 301, + "line": 317, "column": 8 }, "end": { - "line": 301, + "line": 317, "column": 9 } } @@ -118833,15 +121928,15 @@ "binop": null }, "value": "phyloref", - "start": 11303, - "end": 11311, + "start": 11743, + "end": 11751, "loc": { "start": { - "line": 301, + "line": 317, "column": 9 }, "end": { - "line": 301, + "line": 317, "column": 17 } } @@ -118859,15 +121954,15 @@ "binop": null, "updateContext": null }, - "start": 11311, - "end": 11312, + "start": 11751, + "end": 11752, "loc": { "start": { - "line": 301, + "line": 317, "column": 17 }, "end": { - "line": 301, + "line": 317, "column": 18 } } @@ -118886,15 +121981,15 @@ "updateContext": null }, "value": "pso:holdsStatusInTime", - "start": 11312, - "end": 11335, + "start": 11752, + "end": 11775, "loc": { "start": { - "line": 301, + "line": 317, "column": 18 }, "end": { - "line": 301, + "line": 317, "column": 41 } } @@ -118912,15 +122007,15 @@ "binop": null, "updateContext": null }, - "start": 11335, - "end": 11336, + "start": 11775, + "end": 11776, "loc": { "start": { - "line": 301, + "line": 317, "column": 41 }, "end": { - "line": 301, + "line": 317, "column": 42 } } @@ -118938,15 +122033,15 @@ "binop": null, "updateContext": null }, - "start": 11336, - "end": 11337, + "start": 11776, + "end": 11777, "loc": { "start": { - "line": 301, + "line": 317, "column": 42 }, "end": { - "line": 301, + "line": 317, "column": 43 } } @@ -118964,15 +122059,15 @@ "binop": null }, "value": "push", - "start": 11337, - "end": 11341, + "start": 11777, + "end": 11781, "loc": { "start": { - "line": 301, + "line": 317, "column": 43 }, "end": { - "line": 301, + "line": 317, "column": 47 } } @@ -118989,15 +122084,15 @@ "postfix": false, "binop": null }, - "start": 11341, - "end": 11342, + "start": 11781, + "end": 11782, "loc": { "start": { - "line": 301, + "line": 317, "column": 47 }, "end": { - "line": 301, + "line": 317, "column": 48 } } @@ -119014,15 +122109,15 @@ "postfix": false, "binop": null }, - "start": 11342, - "end": 11343, + "start": 11782, + "end": 11783, "loc": { "start": { - "line": 301, + "line": 317, "column": 48 }, "end": { - "line": 301, + "line": 317, "column": 49 } } @@ -119041,15 +122136,15 @@ "updateContext": null }, "value": "@type", - "start": 11350, - "end": 11357, + "start": 11790, + "end": 11797, "loc": { "start": { - "line": 302, + "line": 318, "column": 6 }, "end": { - "line": 302, + "line": 318, "column": 13 } } @@ -119067,15 +122162,15 @@ "binop": null, "updateContext": null }, - "start": 11357, - "end": 11358, + "start": 11797, + "end": 11798, "loc": { "start": { - "line": 302, + "line": 318, "column": 13 }, "end": { - "line": 302, + "line": 318, "column": 14 } } @@ -119094,15 +122189,15 @@ "updateContext": null }, "value": "http://purl.org/spar/pso/StatusInTime", - "start": 11359, - "end": 11398, + "start": 11799, + "end": 11838, "loc": { "start": { - "line": 302, + "line": 318, "column": 15 }, "end": { - "line": 302, + "line": 318, "column": 54 } } @@ -119120,15 +122215,15 @@ "binop": null, "updateContext": null }, - "start": 11398, - "end": 11399, + "start": 11838, + "end": 11839, "loc": { "start": { - "line": 302, + "line": 318, "column": 54 }, "end": { - "line": 302, + "line": 318, "column": 55 } } @@ -119147,15 +122242,15 @@ "updateContext": null }, "value": "pso:withStatus", - "start": 11406, - "end": 11422, + "start": 11846, + "end": 11862, "loc": { "start": { - "line": 303, + "line": 319, "column": 6 }, "end": { - "line": 303, + "line": 319, "column": 22 } } @@ -119173,15 +122268,15 @@ "binop": null, "updateContext": null }, - "start": 11422, - "end": 11423, + "start": 11862, + "end": 11863, "loc": { "start": { - "line": 303, + "line": 319, "column": 22 }, "end": { - "line": 303, + "line": 319, "column": 23 } } @@ -119198,15 +122293,15 @@ "postfix": false, "binop": null }, - "start": 11424, - "end": 11425, + "start": 11864, + "end": 11865, "loc": { "start": { - "line": 303, + "line": 319, "column": 24 }, "end": { - "line": 303, + "line": 319, "column": 25 } } @@ -119225,15 +122320,15 @@ "updateContext": null }, "value": "@id", - "start": 11426, - "end": 11431, + "start": 11866, + "end": 11871, "loc": { "start": { - "line": 303, + "line": 319, "column": 26 }, "end": { - "line": 303, + "line": 319, "column": 31 } } @@ -119251,15 +122346,15 @@ "binop": null, "updateContext": null }, - "start": 11431, - "end": 11432, + "start": 11871, + "end": 11872, "loc": { "start": { - "line": 303, + "line": 319, "column": 31 }, "end": { - "line": 303, + "line": 319, "column": 32 } } @@ -119277,15 +122372,15 @@ "binop": null }, "value": "status", - "start": 11433, - "end": 11439, + "start": 11873, + "end": 11879, "loc": { "start": { - "line": 303, + "line": 319, "column": 33 }, "end": { - "line": 303, + "line": 319, "column": 39 } } @@ -119302,15 +122397,15 @@ "postfix": false, "binop": null }, - "start": 11440, - "end": 11441, + "start": 11880, + "end": 11881, "loc": { "start": { - "line": 303, + "line": 319, "column": 40 }, "end": { - "line": 303, + "line": 319, "column": 41 } } @@ -119328,15 +122423,15 @@ "binop": null, "updateContext": null }, - "start": 11441, - "end": 11442, + "start": 11881, + "end": 11882, "loc": { "start": { - "line": 303, + "line": 319, "column": 41 }, "end": { - "line": 303, + "line": 319, "column": 42 } } @@ -119355,15 +122450,15 @@ "updateContext": null }, "value": "tvc:atTime", - "start": 11449, - "end": 11461, + "start": 11889, + "end": 11901, "loc": { "start": { - "line": 304, + "line": 320, "column": 6 }, "end": { - "line": 304, + "line": 320, "column": 18 } } @@ -119381,15 +122476,15 @@ "binop": null, "updateContext": null }, - "start": 11461, - "end": 11462, + "start": 11901, + "end": 11902, "loc": { "start": { - "line": 304, + "line": 320, "column": 18 }, "end": { - "line": 304, + "line": 320, "column": 19 } } @@ -119406,15 +122501,15 @@ "postfix": false, "binop": null }, - "start": 11463, - "end": 11464, + "start": 11903, + "end": 11904, "loc": { "start": { - "line": 304, + "line": 320, "column": 20 }, "end": { - "line": 304, + "line": 320, "column": 21 } } @@ -119433,15 +122528,15 @@ "updateContext": null }, "value": "timeinterval:hasIntervalStartDate", - "start": 11473, - "end": 11508, + "start": 11913, + "end": 11948, "loc": { "start": { - "line": 305, + "line": 321, "column": 8 }, "end": { - "line": 305, + "line": 321, "column": 43 } } @@ -119459,15 +122554,15 @@ "binop": null, "updateContext": null }, - "start": 11508, - "end": 11509, + "start": 11948, + "end": 11949, "loc": { "start": { - "line": 305, + "line": 321, "column": 43 }, "end": { - "line": 305, + "line": 321, "column": 44 } } @@ -119485,15 +122580,15 @@ "binop": null }, "value": "currentTime", - "start": 11510, - "end": 11521, + "start": 11950, + "end": 11961, "loc": { "start": { - "line": 305, + "line": 321, "column": 45 }, "end": { - "line": 305, + "line": 321, "column": 56 } } @@ -119511,15 +122606,15 @@ "binop": null, "updateContext": null }, - "start": 11521, - "end": 11522, + "start": 11961, + "end": 11962, "loc": { "start": { - "line": 305, + "line": 321, "column": 56 }, "end": { - "line": 305, + "line": 321, "column": 57 } } @@ -119536,15 +122631,15 @@ "postfix": false, "binop": null }, - "start": 11529, - "end": 11530, + "start": 11969, + "end": 11970, "loc": { "start": { - "line": 306, + "line": 322, "column": 6 }, "end": { - "line": 306, + "line": 322, "column": 7 } } @@ -119562,15 +122657,15 @@ "binop": null, "updateContext": null }, - "start": 11530, - "end": 11531, + "start": 11970, + "end": 11971, "loc": { "start": { - "line": 306, + "line": 322, "column": 7 }, "end": { - "line": 306, + "line": 322, "column": 8 } } @@ -119587,15 +122682,15 @@ "postfix": false, "binop": null }, - "start": 11536, - "end": 11537, + "start": 11976, + "end": 11977, "loc": { "start": { - "line": 307, + "line": 323, "column": 4 }, "end": { - "line": 307, + "line": 323, "column": 5 } } @@ -119612,15 +122707,15 @@ "postfix": false, "binop": null }, - "start": 11537, - "end": 11538, + "start": 11977, + "end": 11978, "loc": { "start": { - "line": 307, + "line": 323, "column": 5 }, "end": { - "line": 307, + "line": 323, "column": 6 } } @@ -119638,15 +122733,15 @@ "binop": null, "updateContext": null }, - "start": 11538, - "end": 11539, + "start": 11978, + "end": 11979, "loc": { "start": { - "line": 307, + "line": 323, "column": 6 }, "end": { - "line": 307, + "line": 323, "column": 7 } } @@ -119663,15 +122758,15 @@ "postfix": false, "binop": null }, - "start": 11542, - "end": 11543, + "start": 11982, + "end": 11983, "loc": { "start": { - "line": 308, + "line": 324, "column": 2 }, "end": { - "line": 308, + "line": 324, "column": 3 } } @@ -119679,15 +122774,15 @@ { "type": "CommentBlock", "value": "*\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n ", - "start": 11547, - "end": 11925, + "start": 11987, + "end": 12365, "loc": { "start": { - "line": 310, + "line": 326, "column": 2 }, "end": { - "line": 316, + "line": 332, "column": 5 } } @@ -119705,15 +122800,15 @@ "binop": null }, "value": "get", - "start": 11928, - "end": 11931, + "start": 12368, + "end": 12371, "loc": { "start": { - "line": 317, + "line": 333, "column": 2 }, "end": { - "line": 317, + "line": 333, "column": 5 } } @@ -119731,15 +122826,15 @@ "binop": null }, "value": "uniqNomenCodes", - "start": 11932, - "end": 11946, + "start": 12372, + "end": 12386, "loc": { "start": { - "line": 317, + "line": 333, "column": 6 }, "end": { - "line": 317, + "line": 333, "column": 20 } } @@ -119756,15 +122851,15 @@ "postfix": false, "binop": null }, - "start": 11946, - "end": 11947, + "start": 12386, + "end": 12387, "loc": { "start": { - "line": 317, + "line": 333, "column": 20 }, "end": { - "line": 317, + "line": 333, "column": 21 } } @@ -119781,15 +122876,15 @@ "postfix": false, "binop": null }, - "start": 11947, - "end": 11948, + "start": 12387, + "end": 12388, "loc": { "start": { - "line": 317, + "line": 333, "column": 21 }, "end": { - "line": 317, + "line": 333, "column": 22 } } @@ -119806,15 +122901,15 @@ "postfix": false, "binop": null }, - "start": 11949, - "end": 11950, + "start": 12389, + "end": 12390, "loc": { "start": { - "line": 317, + "line": 333, "column": 23 }, "end": { - "line": 317, + "line": 333, "column": 24 } } @@ -119834,15 +122929,15 @@ "updateContext": null }, "value": "return", - "start": 11955, - "end": 11961, + "start": 12395, + "end": 12401, "loc": { "start": { - "line": 318, + "line": 334, "column": 4 }, "end": { - "line": 318, + "line": 334, "column": 10 } } @@ -119860,15 +122955,15 @@ "binop": null }, "value": "uniq", - "start": 11962, - "end": 11966, + "start": 12402, + "end": 12406, "loc": { "start": { - "line": 318, + "line": 334, "column": 11 }, "end": { - "line": 318, + "line": 334, "column": 15 } } @@ -119885,15 +122980,15 @@ "postfix": false, "binop": null }, - "start": 11966, - "end": 11967, + "start": 12406, + "end": 12407, "loc": { "start": { - "line": 318, + "line": 334, "column": 15 }, "end": { - "line": 318, + "line": 334, "column": 16 } } @@ -119913,15 +123008,15 @@ "updateContext": null }, "value": "this", - "start": 11967, - "end": 11971, + "start": 12407, + "end": 12411, "loc": { "start": { - "line": 318, + "line": 334, "column": 16 }, "end": { - "line": 318, + "line": 334, "column": 20 } } @@ -119939,15 +123034,15 @@ "binop": null, "updateContext": null }, - "start": 11971, - "end": 11972, + "start": 12411, + "end": 12412, "loc": { "start": { - "line": 318, + "line": 334, "column": 20 }, "end": { - "line": 318, + "line": 334, "column": 21 } } @@ -119965,15 +123060,15 @@ "binop": null }, "value": "specifiers", - "start": 11972, - "end": 11982, + "start": 12412, + "end": 12422, "loc": { "start": { - "line": 318, + "line": 334, "column": 21 }, "end": { - "line": 318, + "line": 334, "column": 31 } } @@ -119991,15 +123086,15 @@ "binop": null, "updateContext": null }, - "start": 11982, - "end": 11983, + "start": 12422, + "end": 12423, "loc": { "start": { - "line": 318, + "line": 334, "column": 31 }, "end": { - "line": 318, + "line": 334, "column": 32 } } @@ -120017,15 +123112,15 @@ "binop": null }, "value": "map", - "start": 11983, - "end": 11986, + "start": 12423, + "end": 12426, "loc": { "start": { - "line": 318, + "line": 334, "column": 32 }, "end": { - "line": 318, + "line": 334, "column": 35 } } @@ -120042,15 +123137,15 @@ "postfix": false, "binop": null }, - "start": 11986, - "end": 11987, + "start": 12426, + "end": 12427, "loc": { "start": { - "line": 318, + "line": 334, "column": 35 }, "end": { - "line": 318, + "line": 334, "column": 36 } } @@ -120067,15 +123162,15 @@ "postfix": false, "binop": null }, - "start": 11987, - "end": 11988, + "start": 12427, + "end": 12428, "loc": { "start": { - "line": 318, + "line": 334, "column": 36 }, "end": { - "line": 318, + "line": 334, "column": 37 } } @@ -120093,15 +123188,15 @@ "binop": null }, "value": "specifier", - "start": 11988, - "end": 11997, + "start": 12428, + "end": 12437, "loc": { "start": { - "line": 318, + "line": 334, "column": 37 }, "end": { - "line": 318, + "line": 334, "column": 46 } } @@ -120118,15 +123213,15 @@ "postfix": false, "binop": null }, - "start": 11997, - "end": 11998, + "start": 12437, + "end": 12438, "loc": { "start": { - "line": 318, + "line": 334, "column": 46 }, "end": { - "line": 318, + "line": 334, "column": 47 } } @@ -120144,15 +123239,15 @@ "binop": null, "updateContext": null }, - "start": 11999, - "end": 12001, + "start": 12439, + "end": 12441, "loc": { "start": { - "line": 318, + "line": 334, "column": 48 }, "end": { - "line": 318, + "line": 334, "column": 50 } } @@ -120169,15 +123264,15 @@ "postfix": false, "binop": null }, - "start": 12002, - "end": 12003, + "start": 12442, + "end": 12443, "loc": { "start": { - "line": 318, + "line": 334, "column": 51 }, "end": { - "line": 318, + "line": 334, "column": 52 } } @@ -120197,15 +123292,15 @@ "updateContext": null }, "value": "const", - "start": 12010, - "end": 12015, + "start": 12450, + "end": 12455, "loc": { "start": { - "line": 319, + "line": 335, "column": 6 }, "end": { - "line": 319, + "line": 335, "column": 11 } } @@ -120223,15 +123318,15 @@ "binop": null }, "value": "taxonConcept", - "start": 12016, - "end": 12028, + "start": 12456, + "end": 12468, "loc": { "start": { - "line": 319, + "line": 335, "column": 12 }, "end": { - "line": 319, + "line": 335, "column": 24 } } @@ -120250,15 +123345,15 @@ "updateContext": null }, "value": "=", - "start": 12029, - "end": 12030, + "start": 12469, + "end": 12470, "loc": { "start": { - "line": 319, + "line": 335, "column": 25 }, "end": { - "line": 319, + "line": 335, "column": 26 } } @@ -120278,15 +123373,15 @@ "updateContext": null }, "value": "new", - "start": 12031, - "end": 12034, + "start": 12471, + "end": 12474, "loc": { "start": { - "line": 319, + "line": 335, "column": 27 }, "end": { - "line": 319, + "line": 335, "column": 30 } } @@ -120304,15 +123399,15 @@ "binop": null }, "value": "TaxonomicUnitWrapper", - "start": 12035, - "end": 12055, + "start": 12475, + "end": 12495, "loc": { "start": { - "line": 319, + "line": 335, "column": 31 }, "end": { - "line": 319, + "line": 335, "column": 51 } } @@ -120329,15 +123424,15 @@ "postfix": false, "binop": null }, - "start": 12055, - "end": 12056, + "start": 12495, + "end": 12496, "loc": { "start": { - "line": 319, + "line": 335, "column": 51 }, "end": { - "line": 319, + "line": 335, "column": 52 } } @@ -120355,15 +123450,15 @@ "binop": null }, "value": "specifier", - "start": 12065, - "end": 12074, + "start": 12505, + "end": 12514, "loc": { "start": { - "line": 320, + "line": 336, "column": 8 }, "end": { - "line": 320, + "line": 336, "column": 17 } } @@ -120381,15 +123476,15 @@ "binop": null, "updateContext": null }, - "start": 12074, - "end": 12075, + "start": 12514, + "end": 12515, "loc": { "start": { - "line": 320, + "line": 336, "column": 17 }, "end": { - "line": 320, + "line": 336, "column": 18 } } @@ -120409,15 +123504,15 @@ "updateContext": null }, "value": "this", - "start": 12084, - "end": 12088, + "start": 12524, + "end": 12528, "loc": { "start": { - "line": 321, + "line": 337, "column": 8 }, "end": { - "line": 321, + "line": 337, "column": 12 } } @@ -120435,15 +123530,15 @@ "binop": null, "updateContext": null }, - "start": 12088, - "end": 12089, + "start": 12528, + "end": 12529, "loc": { "start": { - "line": 321, + "line": 337, "column": 12 }, "end": { - "line": 321, + "line": 337, "column": 13 } } @@ -120461,15 +123556,15 @@ "binop": null }, "value": "phyxDefaultNomenCode", - "start": 12089, - "end": 12109, + "start": 12529, + "end": 12549, "loc": { "start": { - "line": 321, + "line": 337, "column": 13 }, "end": { - "line": 321, + "line": 337, "column": 33 } } @@ -120486,15 +123581,15 @@ "postfix": false, "binop": null }, - "start": 12116, - "end": 12117, + "start": 12556, + "end": 12557, "loc": { "start": { - "line": 322, + "line": 338, "column": 6 }, "end": { - "line": 322, + "line": 338, "column": 7 } } @@ -120512,15 +123607,15 @@ "binop": null, "updateContext": null }, - "start": 12117, - "end": 12118, + "start": 12557, + "end": 12558, "loc": { "start": { - "line": 322, + "line": 338, "column": 7 }, "end": { - "line": 322, + "line": 338, "column": 8 } } @@ -120538,15 +123633,15 @@ "binop": null }, "value": "taxonConcept", - "start": 12118, - "end": 12130, + "start": 12558, + "end": 12570, "loc": { "start": { - "line": 322, + "line": 338, "column": 8 }, "end": { - "line": 322, + "line": 338, "column": 20 } } @@ -120564,15 +123659,15 @@ "binop": null, "updateContext": null }, - "start": 12130, - "end": 12131, + "start": 12570, + "end": 12571, "loc": { "start": { - "line": 322, + "line": 338, "column": 20 }, "end": { - "line": 322, + "line": 338, "column": 21 } } @@ -120592,15 +123687,15 @@ "updateContext": null }, "value": "if", - "start": 12138, - "end": 12140, + "start": 12578, + "end": 12580, "loc": { "start": { - "line": 323, + "line": 339, "column": 6 }, "end": { - "line": 323, + "line": 339, "column": 8 } } @@ -120617,15 +123712,15 @@ "postfix": false, "binop": null }, - "start": 12141, - "end": 12142, + "start": 12581, + "end": 12582, "loc": { "start": { - "line": 323, + "line": 339, "column": 9 }, "end": { - "line": 323, + "line": 339, "column": 10 } } @@ -120644,15 +123739,15 @@ "updateContext": null }, "value": "!", - "start": 12142, - "end": 12143, + "start": 12582, + "end": 12583, "loc": { "start": { - "line": 323, + "line": 339, "column": 10 }, "end": { - "line": 323, + "line": 339, "column": 11 } } @@ -120670,15 +123765,15 @@ "binop": null }, "value": "taxonConcept", - "start": 12143, - "end": 12155, + "start": 12583, + "end": 12595, "loc": { "start": { - "line": 323, + "line": 339, "column": 11 }, "end": { - "line": 323, + "line": 339, "column": 23 } } @@ -120695,15 +123790,15 @@ "postfix": false, "binop": null }, - "start": 12155, - "end": 12156, + "start": 12595, + "end": 12596, "loc": { "start": { - "line": 323, + "line": 339, "column": 23 }, "end": { - "line": 323, + "line": 339, "column": 24 } } @@ -120723,15 +123818,15 @@ "updateContext": null }, "value": "return", - "start": 12157, - "end": 12163, + "start": 12597, + "end": 12603, "loc": { "start": { - "line": 323, + "line": 339, "column": 25 }, "end": { - "line": 323, + "line": 339, "column": 31 } } @@ -120749,15 +123844,15 @@ "binop": null }, "value": "owlterms", - "start": 12164, - "end": 12172, + "start": 12604, + "end": 12612, "loc": { "start": { - "line": 323, + "line": 339, "column": 32 }, "end": { - "line": 323, + "line": 339, "column": 40 } } @@ -120775,15 +123870,15 @@ "binop": null, "updateContext": null }, - "start": 12172, - "end": 12173, + "start": 12612, + "end": 12613, "loc": { "start": { - "line": 323, + "line": 339, "column": 40 }, "end": { - "line": 323, + "line": 339, "column": 41 } } @@ -120801,15 +123896,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 12173, - "end": 12185, + "start": 12613, + "end": 12625, "loc": { "start": { - "line": 323, + "line": 339, "column": 41 }, "end": { - "line": 323, + "line": 339, "column": 53 } } @@ -120827,15 +123922,15 @@ "binop": null, "updateContext": null }, - "start": 12185, - "end": 12186, + "start": 12625, + "end": 12626, "loc": { "start": { - "line": 323, + "line": 339, "column": 53 }, "end": { - "line": 323, + "line": 339, "column": 54 } } @@ -120855,15 +123950,15 @@ "updateContext": null }, "value": "const", - "start": 12194, - "end": 12199, + "start": 12634, + "end": 12639, "loc": { "start": { - "line": 325, + "line": 341, "column": 6 }, "end": { - "line": 325, + "line": 341, "column": 11 } } @@ -120881,15 +123976,15 @@ "binop": null }, "value": "nomenCode", - "start": 12200, - "end": 12209, + "start": 12640, + "end": 12649, "loc": { "start": { - "line": 325, + "line": 341, "column": 12 }, "end": { - "line": 325, + "line": 341, "column": 21 } } @@ -120908,15 +124003,15 @@ "updateContext": null }, "value": "=", - "start": 12210, - "end": 12211, + "start": 12650, + "end": 12651, "loc": { "start": { - "line": 325, + "line": 341, "column": 22 }, "end": { - "line": 325, + "line": 341, "column": 23 } } @@ -120936,15 +124031,15 @@ "updateContext": null }, "value": "new", - "start": 12212, - "end": 12215, + "start": 12652, + "end": 12655, "loc": { "start": { - "line": 325, + "line": 341, "column": 24 }, "end": { - "line": 325, + "line": 341, "column": 27 } } @@ -120962,15 +124057,15 @@ "binop": null }, "value": "TaxonConceptWrapper", - "start": 12216, - "end": 12235, + "start": 12656, + "end": 12675, "loc": { "start": { - "line": 325, + "line": 341, "column": 28 }, "end": { - "line": 325, + "line": 341, "column": 47 } } @@ -120987,15 +124082,15 @@ "postfix": false, "binop": null }, - "start": 12235, - "end": 12236, + "start": 12675, + "end": 12676, "loc": { "start": { - "line": 325, + "line": 341, "column": 47 }, "end": { - "line": 325, + "line": 341, "column": 48 } } @@ -121013,15 +124108,15 @@ "binop": null }, "value": "taxonConcept", - "start": 12245, - "end": 12257, + "start": 12685, + "end": 12697, "loc": { "start": { - "line": 326, + "line": 342, "column": 8 }, "end": { - "line": 326, + "line": 342, "column": 20 } } @@ -121039,15 +124134,15 @@ "binop": null, "updateContext": null }, - "start": 12257, - "end": 12258, + "start": 12697, + "end": 12698, "loc": { "start": { - "line": 326, + "line": 342, "column": 20 }, "end": { - "line": 326, + "line": 342, "column": 21 } } @@ -121067,15 +124162,15 @@ "updateContext": null }, "value": "this", - "start": 12267, - "end": 12271, + "start": 12707, + "end": 12711, "loc": { "start": { - "line": 327, + "line": 343, "column": 8 }, "end": { - "line": 327, + "line": 343, "column": 12 } } @@ -121093,15 +124188,15 @@ "binop": null, "updateContext": null }, - "start": 12271, - "end": 12272, + "start": 12711, + "end": 12712, "loc": { "start": { - "line": 327, + "line": 343, "column": 12 }, "end": { - "line": 327, + "line": 343, "column": 13 } } @@ -121119,15 +124214,15 @@ "binop": null }, "value": "phyxDefaultNomenCode", - "start": 12272, - "end": 12292, + "start": 12712, + "end": 12732, "loc": { "start": { - "line": 327, + "line": 343, "column": 13 }, "end": { - "line": 327, + "line": 343, "column": 33 } } @@ -121144,15 +124239,15 @@ "postfix": false, "binop": null }, - "start": 12299, - "end": 12300, + "start": 12739, + "end": 12740, "loc": { "start": { - "line": 328, + "line": 344, "column": 6 }, "end": { - "line": 328, + "line": 344, "column": 7 } } @@ -121170,15 +124265,15 @@ "binop": null, "updateContext": null }, - "start": 12300, - "end": 12301, + "start": 12740, + "end": 12741, "loc": { "start": { - "line": 328, + "line": 344, "column": 7 }, "end": { - "line": 328, + "line": 344, "column": 8 } } @@ -121196,15 +124291,15 @@ "binop": null }, "value": "nomenCode", - "start": 12301, - "end": 12310, + "start": 12741, + "end": 12750, "loc": { "start": { - "line": 328, + "line": 344, "column": 8 }, "end": { - "line": 328, + "line": 344, "column": 17 } } @@ -121222,15 +124317,15 @@ "binop": null, "updateContext": null }, - "start": 12310, - "end": 12311, + "start": 12750, + "end": 12751, "loc": { "start": { - "line": 328, + "line": 344, "column": 17 }, "end": { - "line": 328, + "line": 344, "column": 18 } } @@ -121250,15 +124345,15 @@ "updateContext": null }, "value": "if", - "start": 12318, - "end": 12320, + "start": 12758, + "end": 12760, "loc": { "start": { - "line": 329, + "line": 345, "column": 6 }, "end": { - "line": 329, + "line": 345, "column": 8 } } @@ -121275,15 +124370,15 @@ "postfix": false, "binop": null }, - "start": 12321, - "end": 12322, + "start": 12761, + "end": 12762, "loc": { "start": { - "line": 329, + "line": 345, "column": 9 }, "end": { - "line": 329, + "line": 345, "column": 10 } } @@ -121302,15 +124397,15 @@ "updateContext": null }, "value": "!", - "start": 12322, - "end": 12323, + "start": 12762, + "end": 12763, "loc": { "start": { - "line": 329, + "line": 345, "column": 10 }, "end": { - "line": 329, + "line": 345, "column": 11 } } @@ -121328,15 +124423,15 @@ "binop": null }, "value": "nomenCode", - "start": 12323, - "end": 12332, + "start": 12763, + "end": 12772, "loc": { "start": { - "line": 329, + "line": 345, "column": 11 }, "end": { - "line": 329, + "line": 345, "column": 20 } } @@ -121353,15 +124448,15 @@ "postfix": false, "binop": null }, - "start": 12332, - "end": 12333, + "start": 12772, + "end": 12773, "loc": { "start": { - "line": 329, + "line": 345, "column": 20 }, "end": { - "line": 329, + "line": 345, "column": 21 } } @@ -121381,15 +124476,15 @@ "updateContext": null }, "value": "return", - "start": 12334, - "end": 12340, + "start": 12774, + "end": 12780, "loc": { "start": { - "line": 329, + "line": 345, "column": 22 }, "end": { - "line": 329, + "line": 345, "column": 28 } } @@ -121407,15 +124502,15 @@ "binop": null }, "value": "owlterms", - "start": 12341, - "end": 12349, + "start": 12781, + "end": 12789, "loc": { "start": { - "line": 329, + "line": 345, "column": 29 }, "end": { - "line": 329, + "line": 345, "column": 37 } } @@ -121433,15 +124528,15 @@ "binop": null, "updateContext": null }, - "start": 12349, - "end": 12350, + "start": 12789, + "end": 12790, "loc": { "start": { - "line": 329, + "line": 345, "column": 37 }, "end": { - "line": 329, + "line": 345, "column": 38 } } @@ -121459,15 +124554,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 12350, - "end": 12362, + "start": 12790, + "end": 12802, "loc": { "start": { - "line": 329, + "line": 345, "column": 38 }, "end": { - "line": 329, + "line": 345, "column": 50 } } @@ -121485,15 +124580,15 @@ "binop": null, "updateContext": null }, - "start": 12362, - "end": 12363, + "start": 12802, + "end": 12803, "loc": { "start": { - "line": 329, + "line": 345, "column": 50 }, "end": { - "line": 329, + "line": 345, "column": 51 } } @@ -121513,15 +124608,15 @@ "updateContext": null }, "value": "return", - "start": 12371, - "end": 12377, + "start": 12811, + "end": 12817, "loc": { "start": { - "line": 331, + "line": 347, "column": 6 }, "end": { - "line": 331, + "line": 347, "column": 12 } } @@ -121539,15 +124634,15 @@ "binop": null }, "value": "nomenCode", - "start": 12378, - "end": 12387, + "start": 12818, + "end": 12827, "loc": { "start": { - "line": 331, + "line": 347, "column": 13 }, "end": { - "line": 331, + "line": 347, "column": 22 } } @@ -121565,15 +124660,15 @@ "binop": null, "updateContext": null }, - "start": 12387, - "end": 12388, + "start": 12827, + "end": 12828, "loc": { "start": { - "line": 331, + "line": 347, "column": 22 }, "end": { - "line": 331, + "line": 347, "column": 23 } } @@ -121590,15 +124685,15 @@ "postfix": false, "binop": null }, - "start": 12393, - "end": 12394, + "start": 12833, + "end": 12834, "loc": { "start": { - "line": 332, + "line": 348, "column": 4 }, "end": { - "line": 332, + "line": 348, "column": 5 } } @@ -121615,15 +124710,15 @@ "postfix": false, "binop": null }, - "start": 12394, - "end": 12395, + "start": 12834, + "end": 12835, "loc": { "start": { - "line": 332, + "line": 348, "column": 5 }, "end": { - "line": 332, + "line": 348, "column": 6 } } @@ -121640,15 +124735,15 @@ "postfix": false, "binop": null }, - "start": 12395, - "end": 12396, + "start": 12835, + "end": 12836, "loc": { "start": { - "line": 332, + "line": 348, "column": 6 }, "end": { - "line": 332, + "line": 348, "column": 7 } } @@ -121666,15 +124761,15 @@ "binop": null, "updateContext": null }, - "start": 12396, - "end": 12397, + "start": 12836, + "end": 12837, "loc": { "start": { - "line": 332, + "line": 348, "column": 7 }, "end": { - "line": 332, + "line": 348, "column": 8 } } @@ -121691,15 +124786,15 @@ "postfix": false, "binop": null }, - "start": 12400, - "end": 12401, + "start": 12840, + "end": 12841, "loc": { "start": { - "line": 333, + "line": 349, "column": 2 }, "end": { - "line": 333, + "line": 349, "column": 3 } } @@ -121707,15 +124802,15 @@ { "type": "CommentBlock", "value": "*\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n ", - "start": 12405, - "end": 12681, + "start": 12845, + "end": 13121, "loc": { "start": { - "line": 335, + "line": 351, "column": 2 }, "end": { - "line": 340, + "line": 356, "column": 5 } } @@ -121733,15 +124828,15 @@ "binop": null }, "value": "get", - "start": 12684, - "end": 12687, + "start": 13124, + "end": 13127, "loc": { "start": { - "line": 341, + "line": 357, "column": 2 }, "end": { - "line": 341, + "line": 357, "column": 5 } } @@ -121759,15 +124854,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 12688, - "end": 12704, + "start": 13128, + "end": 13144, "loc": { "start": { - "line": 341, + "line": 357, "column": 6 }, "end": { - "line": 341, + "line": 357, "column": 22 } } @@ -121784,15 +124879,15 @@ "postfix": false, "binop": null }, - "start": 12704, - "end": 12705, + "start": 13144, + "end": 13145, "loc": { "start": { - "line": 341, + "line": 357, "column": 22 }, "end": { - "line": 341, + "line": 357, "column": 23 } } @@ -121809,15 +124904,15 @@ "postfix": false, "binop": null }, - "start": 12705, - "end": 12706, + "start": 13145, + "end": 13146, "loc": { "start": { - "line": 341, + "line": 357, "column": 23 }, "end": { - "line": 341, + "line": 357, "column": 24 } } @@ -121834,15 +124929,15 @@ "postfix": false, "binop": null }, - "start": 12707, - "end": 12708, + "start": 13147, + "end": 13148, "loc": { "start": { - "line": 341, + "line": 357, "column": 25 }, "end": { - "line": 341, + "line": 357, "column": 26 } } @@ -121850,15 +124945,15 @@ { "type": "CommentLine", "value": " Check to see if we have a single nomenclatural code to use.", - "start": 12713, - "end": 12775, + "start": 13153, + "end": 13215, "loc": { "start": { - "line": 342, + "line": 358, "column": 4 }, "end": { - "line": 342, + "line": 358, "column": 66 } } @@ -121878,15 +124973,15 @@ "updateContext": null }, "value": "if", - "start": 12780, - "end": 12782, + "start": 13220, + "end": 13222, "loc": { "start": { - "line": 343, + "line": 359, "column": 4 }, "end": { - "line": 343, + "line": 359, "column": 6 } } @@ -121903,15 +124998,15 @@ "postfix": false, "binop": null }, - "start": 12783, - "end": 12784, + "start": 13223, + "end": 13224, "loc": { "start": { - "line": 343, + "line": 359, "column": 7 }, "end": { - "line": 343, + "line": 359, "column": 8 } } @@ -121931,15 +125026,15 @@ "updateContext": null }, "value": "this", - "start": 12784, - "end": 12788, + "start": 13224, + "end": 13228, "loc": { "start": { - "line": 343, + "line": 359, "column": 8 }, "end": { - "line": 343, + "line": 359, "column": 12 } } @@ -121957,15 +125052,15 @@ "binop": null, "updateContext": null }, - "start": 12788, - "end": 12789, + "start": 13228, + "end": 13229, "loc": { "start": { - "line": 343, + "line": 359, "column": 12 }, "end": { - "line": 343, + "line": 359, "column": 13 } } @@ -121983,15 +125078,15 @@ "binop": null }, "value": "uniqNomenCodes", - "start": 12789, - "end": 12803, + "start": 13229, + "end": 13243, "loc": { "start": { - "line": 343, + "line": 359, "column": 13 }, "end": { - "line": 343, + "line": 359, "column": 27 } } @@ -122009,15 +125104,15 @@ "binop": null, "updateContext": null }, - "start": 12803, - "end": 12804, + "start": 13243, + "end": 13244, "loc": { "start": { - "line": 343, + "line": 359, "column": 27 }, "end": { - "line": 343, + "line": 359, "column": 28 } } @@ -122035,15 +125130,15 @@ "binop": null }, "value": "length", - "start": 12804, - "end": 12810, + "start": 13244, + "end": 13250, "loc": { "start": { - "line": 343, + "line": 359, "column": 28 }, "end": { - "line": 343, + "line": 359, "column": 34 } } @@ -122062,15 +125157,15 @@ "updateContext": null }, "value": "===", - "start": 12811, - "end": 12814, + "start": 13251, + "end": 13254, "loc": { "start": { - "line": 343, + "line": 359, "column": 35 }, "end": { - "line": 343, + "line": 359, "column": 38 } } @@ -122089,15 +125184,15 @@ "updateContext": null }, "value": 1, - "start": 12815, - "end": 12816, + "start": 13255, + "end": 13256, "loc": { "start": { - "line": 343, + "line": 359, "column": 39 }, "end": { - "line": 343, + "line": 359, "column": 40 } } @@ -122114,15 +125209,15 @@ "postfix": false, "binop": null }, - "start": 12816, - "end": 12817, + "start": 13256, + "end": 13257, "loc": { "start": { - "line": 343, + "line": 359, "column": 40 }, "end": { - "line": 343, + "line": 359, "column": 41 } } @@ -122142,15 +125237,15 @@ "updateContext": null }, "value": "return", - "start": 12818, - "end": 12824, + "start": 13258, + "end": 13264, "loc": { "start": { - "line": 343, + "line": 359, "column": 42 }, "end": { - "line": 343, + "line": 359, "column": 48 } } @@ -122170,15 +125265,15 @@ "updateContext": null }, "value": "this", - "start": 12825, - "end": 12829, + "start": 13265, + "end": 13269, "loc": { "start": { - "line": 343, + "line": 359, "column": 49 }, "end": { - "line": 343, + "line": 359, "column": 53 } } @@ -122196,15 +125291,15 @@ "binop": null, "updateContext": null }, - "start": 12829, - "end": 12830, + "start": 13269, + "end": 13270, "loc": { "start": { - "line": 343, + "line": 359, "column": 53 }, "end": { - "line": 343, + "line": 359, "column": 54 } } @@ -122222,15 +125317,15 @@ "binop": null }, "value": "uniqNomenCodes", - "start": 12830, - "end": 12844, + "start": 13270, + "end": 13284, "loc": { "start": { - "line": 343, + "line": 359, "column": 54 }, "end": { - "line": 343, + "line": 359, "column": 68 } } @@ -122248,15 +125343,15 @@ "binop": null, "updateContext": null }, - "start": 12844, - "end": 12845, + "start": 13284, + "end": 13285, "loc": { "start": { - "line": 343, + "line": 359, "column": 68 }, "end": { - "line": 343, + "line": 359, "column": 69 } } @@ -122275,15 +125370,15 @@ "updateContext": null }, "value": 0, - "start": 12845, - "end": 12846, + "start": 13285, + "end": 13286, "loc": { "start": { - "line": 343, + "line": 359, "column": 69 }, "end": { - "line": 343, + "line": 359, "column": 70 } } @@ -122301,15 +125396,15 @@ "binop": null, "updateContext": null }, - "start": 12846, - "end": 12847, + "start": 13286, + "end": 13287, "loc": { "start": { - "line": 343, + "line": 359, "column": 70 }, "end": { - "line": 343, + "line": 359, "column": 71 } } @@ -122327,15 +125422,15 @@ "binop": null, "updateContext": null }, - "start": 12847, - "end": 12848, + "start": 13287, + "end": 13288, "loc": { "start": { - "line": 343, + "line": 359, "column": 71 }, "end": { - "line": 343, + "line": 359, "column": 72 } } @@ -122343,15 +125438,15 @@ { "type": "CommentLine", "value": " If one or more of our specifiers have no nomenclatural code (e.g. if", - "start": 12854, - "end": 12925, + "start": 13294, + "end": 13365, "loc": { "start": { - "line": 345, + "line": 361, "column": 4 }, "end": { - "line": 345, + "line": 361, "column": 75 } } @@ -122359,15 +125454,15 @@ { "type": "CommentLine", "value": " they are specimens), they will show up as owlterms.UNKNOWN_CODE.", - "start": 12930, - "end": 12997, + "start": 13370, + "end": 13437, "loc": { "start": { - "line": 346, + "line": 362, "column": 4 }, "end": { - "line": 346, + "line": 362, "column": 71 } } @@ -122375,15 +125470,15 @@ { "type": "CommentLine", "value": " If we have a single nomenclatural code *apart* from all the", - "start": 13002, - "end": 13064, + "start": 13442, + "end": 13504, "loc": { "start": { - "line": 347, + "line": 363, "column": 4 }, "end": { - "line": 347, + "line": 363, "column": 66 } } @@ -122391,15 +125486,15 @@ { "type": "CommentLine", "value": " owlterms.UNKNOWN_CODEs, then that is still usable as a default", - "start": 13069, - "end": 13134, + "start": 13509, + "end": 13574, "loc": { "start": { - "line": 348, + "line": 364, "column": 4 }, "end": { - "line": 348, + "line": 364, "column": 69 } } @@ -122407,15 +125502,15 @@ { "type": "CommentLine", "value": " nomenclatural code for this phyloreference.", - "start": 13139, - "end": 13185, + "start": 13579, + "end": 13625, "loc": { "start": { - "line": 349, + "line": 365, "column": 4 }, "end": { - "line": 349, + "line": 365, "column": 50 } } @@ -122435,15 +125530,15 @@ "updateContext": null }, "value": "const", - "start": 13190, - "end": 13195, + "start": 13630, + "end": 13635, "loc": { "start": { - "line": 350, + "line": 366, "column": 4 }, "end": { - "line": 350, + "line": 366, "column": 9 } } @@ -122461,15 +125556,15 @@ "binop": null }, "value": "uniqNomenCodesNoUnknowns", - "start": 13196, - "end": 13220, + "start": 13636, + "end": 13660, "loc": { "start": { - "line": 350, + "line": 366, "column": 10 }, "end": { - "line": 350, + "line": 366, "column": 34 } } @@ -122488,15 +125583,15 @@ "updateContext": null }, "value": "=", - "start": 13221, - "end": 13222, + "start": 13661, + "end": 13662, "loc": { "start": { - "line": 350, + "line": 366, "column": 35 }, "end": { - "line": 350, + "line": 366, "column": 36 } } @@ -122516,15 +125611,15 @@ "updateContext": null }, "value": "this", - "start": 13223, - "end": 13227, + "start": 13663, + "end": 13667, "loc": { "start": { - "line": 350, + "line": 366, "column": 37 }, "end": { - "line": 350, + "line": 366, "column": 41 } } @@ -122542,15 +125637,15 @@ "binop": null, "updateContext": null }, - "start": 13227, - "end": 13228, + "start": 13667, + "end": 13668, "loc": { "start": { - "line": 350, + "line": 366, "column": 41 }, "end": { - "line": 350, + "line": 366, "column": 42 } } @@ -122568,15 +125663,15 @@ "binop": null }, "value": "uniqNomenCodes", - "start": 13228, - "end": 13242, + "start": 13668, + "end": 13682, "loc": { "start": { - "line": 350, + "line": 366, "column": 42 }, "end": { - "line": 350, + "line": 366, "column": 56 } } @@ -122594,15 +125689,15 @@ "binop": null, "updateContext": null }, - "start": 13249, - "end": 13250, + "start": 13689, + "end": 13690, "loc": { "start": { - "line": 351, + "line": 367, "column": 6 }, "end": { - "line": 351, + "line": 367, "column": 7 } } @@ -122620,15 +125715,15 @@ "binop": null }, "value": "filter", - "start": 13250, - "end": 13256, + "start": 13690, + "end": 13696, "loc": { "start": { - "line": 351, + "line": 367, "column": 7 }, "end": { - "line": 351, + "line": 367, "column": 13 } } @@ -122645,15 +125740,15 @@ "postfix": false, "binop": null }, - "start": 13256, - "end": 13257, + "start": 13696, + "end": 13697, "loc": { "start": { - "line": 351, + "line": 367, "column": 13 }, "end": { - "line": 351, + "line": 367, "column": 14 } } @@ -122671,15 +125766,15 @@ "binop": null }, "value": "code", - "start": 13257, - "end": 13261, + "start": 13697, + "end": 13701, "loc": { "start": { - "line": 351, + "line": 367, "column": 14 }, "end": { - "line": 351, + "line": 367, "column": 18 } } @@ -122697,15 +125792,15 @@ "binop": null, "updateContext": null }, - "start": 13262, - "end": 13264, + "start": 13702, + "end": 13704, "loc": { "start": { - "line": 351, + "line": 367, "column": 19 }, "end": { - "line": 351, + "line": 367, "column": 21 } } @@ -122723,15 +125818,15 @@ "binop": null }, "value": "code", - "start": 13265, - "end": 13269, + "start": 13705, + "end": 13709, "loc": { "start": { - "line": 351, + "line": 367, "column": 22 }, "end": { - "line": 351, + "line": 367, "column": 26 } } @@ -122750,15 +125845,15 @@ "updateContext": null }, "value": "!==", - "start": 13270, - "end": 13273, + "start": 13710, + "end": 13713, "loc": { "start": { - "line": 351, + "line": 367, "column": 27 }, "end": { - "line": 351, + "line": 367, "column": 30 } } @@ -122776,15 +125871,15 @@ "binop": null }, "value": "owlterms", - "start": 13274, - "end": 13282, + "start": 13714, + "end": 13722, "loc": { "start": { - "line": 351, + "line": 367, "column": 31 }, "end": { - "line": 351, + "line": 367, "column": 39 } } @@ -122802,15 +125897,15 @@ "binop": null, "updateContext": null }, - "start": 13282, - "end": 13283, + "start": 13722, + "end": 13723, "loc": { "start": { - "line": 351, + "line": 367, "column": 39 }, "end": { - "line": 351, + "line": 367, "column": 40 } } @@ -122828,15 +125923,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 13283, - "end": 13295, + "start": 13723, + "end": 13735, "loc": { "start": { - "line": 351, + "line": 367, "column": 40 }, "end": { - "line": 351, + "line": 367, "column": 52 } } @@ -122853,15 +125948,15 @@ "postfix": false, "binop": null }, - "start": 13295, - "end": 13296, + "start": 13735, + "end": 13736, "loc": { "start": { - "line": 351, + "line": 367, "column": 52 }, "end": { - "line": 351, + "line": 367, "column": 53 } } @@ -122879,15 +125974,15 @@ "binop": null, "updateContext": null }, - "start": 13296, - "end": 13297, + "start": 13736, + "end": 13737, "loc": { "start": { - "line": 351, + "line": 367, "column": 53 }, "end": { - "line": 351, + "line": 367, "column": 54 } } @@ -122907,15 +126002,15 @@ "updateContext": null }, "value": "if", - "start": 13302, - "end": 13304, + "start": 13742, + "end": 13744, "loc": { "start": { - "line": 352, + "line": 368, "column": 4 }, "end": { - "line": 352, + "line": 368, "column": 6 } } @@ -122932,15 +126027,15 @@ "postfix": false, "binop": null }, - "start": 13305, - "end": 13306, + "start": 13745, + "end": 13746, "loc": { "start": { - "line": 352, + "line": 368, "column": 7 }, "end": { - "line": 352, + "line": 368, "column": 8 } } @@ -122958,15 +126053,15 @@ "binop": null }, "value": "uniqNomenCodesNoUnknowns", - "start": 13306, - "end": 13330, + "start": 13746, + "end": 13770, "loc": { "start": { - "line": 352, + "line": 368, "column": 8 }, "end": { - "line": 352, + "line": 368, "column": 32 } } @@ -122984,15 +126079,15 @@ "binop": null, "updateContext": null }, - "start": 13330, - "end": 13331, + "start": 13770, + "end": 13771, "loc": { "start": { - "line": 352, + "line": 368, "column": 32 }, "end": { - "line": 352, + "line": 368, "column": 33 } } @@ -123010,15 +126105,15 @@ "binop": null }, "value": "length", - "start": 13331, - "end": 13337, + "start": 13771, + "end": 13777, "loc": { "start": { - "line": 352, + "line": 368, "column": 33 }, "end": { - "line": 352, + "line": 368, "column": 39 } } @@ -123037,15 +126132,15 @@ "updateContext": null }, "value": "===", - "start": 13338, - "end": 13341, + "start": 13778, + "end": 13781, "loc": { "start": { - "line": 352, + "line": 368, "column": 40 }, "end": { - "line": 352, + "line": 368, "column": 43 } } @@ -123064,15 +126159,15 @@ "updateContext": null }, "value": 1, - "start": 13342, - "end": 13343, + "start": 13782, + "end": 13783, "loc": { "start": { - "line": 352, + "line": 368, "column": 44 }, "end": { - "line": 352, + "line": 368, "column": 45 } } @@ -123089,15 +126184,15 @@ "postfix": false, "binop": null }, - "start": 13343, - "end": 13344, + "start": 13783, + "end": 13784, "loc": { "start": { - "line": 352, + "line": 368, "column": 45 }, "end": { - "line": 352, + "line": 368, "column": 46 } } @@ -123117,15 +126212,15 @@ "updateContext": null }, "value": "return", - "start": 13345, - "end": 13351, + "start": 13785, + "end": 13791, "loc": { "start": { - "line": 352, + "line": 368, "column": 47 }, "end": { - "line": 352, + "line": 368, "column": 53 } } @@ -123143,15 +126238,15 @@ "binop": null }, "value": "uniqNomenCodesNoUnknowns", - "start": 13352, - "end": 13376, + "start": 13792, + "end": 13816, "loc": { "start": { - "line": 352, + "line": 368, "column": 54 }, "end": { - "line": 352, + "line": 368, "column": 78 } } @@ -123169,15 +126264,15 @@ "binop": null, "updateContext": null }, - "start": 13376, - "end": 13377, + "start": 13816, + "end": 13817, "loc": { "start": { - "line": 352, + "line": 368, "column": 78 }, "end": { - "line": 352, + "line": 368, "column": 79 } } @@ -123196,15 +126291,15 @@ "updateContext": null }, "value": 0, - "start": 13377, - "end": 13378, + "start": 13817, + "end": 13818, "loc": { "start": { - "line": 352, + "line": 368, "column": 79 }, "end": { - "line": 352, + "line": 368, "column": 80 } } @@ -123222,15 +126317,15 @@ "binop": null, "updateContext": null }, - "start": 13378, - "end": 13379, + "start": 13818, + "end": 13819, "loc": { "start": { - "line": 352, + "line": 368, "column": 80 }, "end": { - "line": 352, + "line": 368, "column": 81 } } @@ -123248,15 +126343,15 @@ "binop": null, "updateContext": null }, - "start": 13379, - "end": 13380, + "start": 13819, + "end": 13820, "loc": { "start": { - "line": 352, + "line": 368, "column": 81 }, "end": { - "line": 352, + "line": 368, "column": 82 } } @@ -123276,15 +126371,15 @@ "updateContext": null }, "value": "return", - "start": 13386, - "end": 13392, + "start": 13826, + "end": 13832, "loc": { "start": { - "line": 354, + "line": 370, "column": 4 }, "end": { - "line": 354, + "line": 370, "column": 10 } } @@ -123302,15 +126397,15 @@ "binop": null }, "value": "owlterms", - "start": 13393, - "end": 13401, + "start": 13833, + "end": 13841, "loc": { "start": { - "line": 354, + "line": 370, "column": 11 }, "end": { - "line": 354, + "line": 370, "column": 19 } } @@ -123328,15 +126423,15 @@ "binop": null, "updateContext": null }, - "start": 13401, - "end": 13402, + "start": 13841, + "end": 13842, "loc": { "start": { - "line": 354, + "line": 370, "column": 19 }, "end": { - "line": 354, + "line": 370, "column": 20 } } @@ -123354,15 +126449,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 13402, - "end": 13414, + "start": 13842, + "end": 13854, "loc": { "start": { - "line": 354, + "line": 370, "column": 20 }, "end": { - "line": 354, + "line": 370, "column": 32 } } @@ -123380,15 +126475,15 @@ "binop": null, "updateContext": null }, - "start": 13414, - "end": 13415, + "start": 13854, + "end": 13855, "loc": { "start": { - "line": 354, + "line": 370, "column": 32 }, "end": { - "line": 354, + "line": 370, "column": 33 } } @@ -123405,15 +126500,15 @@ "postfix": false, "binop": null }, - "start": 13418, - "end": 13419, + "start": 13858, + "end": 13859, "loc": { "start": { - "line": 355, + "line": 371, "column": 2 }, "end": { - "line": 355, + "line": 371, "column": 3 } } @@ -123421,15 +126516,15 @@ { "type": "CommentBlock", "value": "*\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n ", - "start": 13423, - "end": 14548, + "start": 13863, + "end": 14988, "loc": { "start": { - "line": 357, + "line": 373, "column": 2 }, "end": { - "line": 373, + "line": 389, "column": 5 } } @@ -123447,15 +126542,15 @@ "binop": null }, "value": "createComponentClass", - "start": 14551, - "end": 14571, + "start": 14991, + "end": 15011, "loc": { "start": { - "line": 374, + "line": 390, "column": 2 }, "end": { - "line": 374, + "line": 390, "column": 22 } } @@ -123472,15 +126567,15 @@ "postfix": false, "binop": null }, - "start": 14571, - "end": 14572, + "start": 15011, + "end": 15012, "loc": { "start": { - "line": 374, + "line": 390, "column": 22 }, "end": { - "line": 374, + "line": 390, "column": 23 } } @@ -123498,15 +126593,15 @@ "binop": null }, "value": "jsonld", - "start": 14577, - "end": 14583, + "start": 15017, + "end": 15023, "loc": { "start": { - "line": 375, + "line": 391, "column": 4 }, "end": { - "line": 375, + "line": 391, "column": 10 } } @@ -123524,15 +126619,15 @@ "binop": null, "updateContext": null }, - "start": 14583, - "end": 14584, + "start": 15023, + "end": 15024, "loc": { "start": { - "line": 375, + "line": 391, "column": 10 }, "end": { - "line": 375, + "line": 391, "column": 11 } } @@ -123550,15 +126645,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 14589, - "end": 14607, + "start": 15029, + "end": 15047, "loc": { "start": { - "line": 376, + "line": 392, "column": 4 }, "end": { - "line": 376, + "line": 392, "column": 22 } } @@ -123576,15 +126671,15 @@ "binop": null, "updateContext": null }, - "start": 14607, - "end": 14608, + "start": 15047, + "end": 15048, "loc": { "start": { - "line": 376, + "line": 392, "column": 22 }, "end": { - "line": 376, + "line": 392, "column": 23 } } @@ -123602,15 +126697,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 14613, - "end": 14631, + "start": 15053, + "end": 15071, "loc": { "start": { - "line": 377, + "line": 393, "column": 4 }, "end": { - "line": 377, + "line": 393, "column": 22 } } @@ -123628,15 +126723,15 @@ "binop": null, "updateContext": null }, - "start": 14631, - "end": 14632, + "start": 15071, + "end": 15072, "loc": { "start": { - "line": 377, + "line": 393, "column": 22 }, "end": { - "line": 377, + "line": 393, "column": 23 } } @@ -123654,15 +126749,15 @@ "binop": null }, "value": "equivClass", - "start": 14637, - "end": 14647, + "start": 15077, + "end": 15087, "loc": { "start": { - "line": 378, + "line": 394, "column": 4 }, "end": { - "line": 378, + "line": 394, "column": 14 } } @@ -123680,15 +126775,15 @@ "binop": null, "updateContext": null }, - "start": 14647, - "end": 14648, + "start": 15087, + "end": 15088, "loc": { "start": { - "line": 378, + "line": 394, "column": 14 }, "end": { - "line": 378, + "line": 394, "column": 15 } } @@ -123706,15 +126801,15 @@ "binop": null }, "value": "reusePrevious", - "start": 14653, - "end": 14666, + "start": 15093, + "end": 15106, "loc": { "start": { - "line": 379, + "line": 395, "column": 4 }, "end": { - "line": 379, + "line": 395, "column": 17 } } @@ -123733,15 +126828,15 @@ "updateContext": null }, "value": "=", - "start": 14667, - "end": 14668, + "start": 15107, + "end": 15108, "loc": { "start": { - "line": 379, + "line": 395, "column": 18 }, "end": { - "line": 379, + "line": 395, "column": 19 } } @@ -123761,15 +126856,15 @@ "updateContext": null }, "value": "true", - "start": 14669, - "end": 14673, + "start": 15109, + "end": 15113, "loc": { "start": { - "line": 379, + "line": 395, "column": 20 }, "end": { - "line": 379, + "line": 395, "column": 24 } } @@ -123787,15 +126882,15 @@ "binop": null, "updateContext": null }, - "start": 14673, - "end": 14674, + "start": 15113, + "end": 15114, "loc": { "start": { - "line": 379, + "line": 395, "column": 24 }, "end": { - "line": 379, + "line": 395, "column": 25 } } @@ -123813,15 +126908,15 @@ "binop": null }, "value": "parentClass", - "start": 14679, - "end": 14690, + "start": 15119, + "end": 15130, "loc": { "start": { - "line": 380, + "line": 396, "column": 4 }, "end": { - "line": 380, + "line": 396, "column": 15 } } @@ -123840,15 +126935,15 @@ "updateContext": null }, "value": "=", - "start": 14691, - "end": 14692, + "start": 15131, + "end": 15132, "loc": { "start": { - "line": 380, + "line": 396, "column": 16 }, "end": { - "line": 380, + "line": 396, "column": 17 } } @@ -123866,15 +126961,15 @@ "binop": null }, "value": "undefined", - "start": 14693, - "end": 14702, + "start": 15133, + "end": 15142, "loc": { "start": { - "line": 380, + "line": 396, "column": 18 }, "end": { - "line": 380, + "line": 396, "column": 27 } } @@ -123891,15 +126986,15 @@ "postfix": false, "binop": null }, - "start": 14705, - "end": 14706, + "start": 15145, + "end": 15146, "loc": { "start": { - "line": 381, + "line": 397, "column": 2 }, "end": { - "line": 381, + "line": 397, "column": 3 } } @@ -123916,15 +127011,15 @@ "postfix": false, "binop": null }, - "start": 14707, - "end": 14708, + "start": 15147, + "end": 15148, "loc": { "start": { - "line": 381, + "line": 397, "column": 4 }, "end": { - "line": 381, + "line": 397, "column": 5 } } @@ -123944,15 +127039,15 @@ "updateContext": null }, "value": "if", - "start": 14713, - "end": 14715, + "start": 15153, + "end": 15155, "loc": { "start": { - "line": 382, + "line": 398, "column": 4 }, "end": { - "line": 382, + "line": 398, "column": 6 } } @@ -123969,15 +127064,15 @@ "postfix": false, "binop": null }, - "start": 14716, - "end": 14717, + "start": 15156, + "end": 15157, "loc": { "start": { - "line": 382, + "line": 398, "column": 7 }, "end": { - "line": 382, + "line": 398, "column": 8 } } @@ -123995,15 +127090,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 14717, - "end": 14735, + "start": 15157, + "end": 15175, "loc": { "start": { - "line": 382, + "line": 398, "column": 8 }, "end": { - "line": 382, + "line": 398, "column": 26 } } @@ -124021,15 +127116,15 @@ "binop": null, "updateContext": null }, - "start": 14735, - "end": 14736, + "start": 15175, + "end": 15176, "loc": { "start": { - "line": 382, + "line": 398, "column": 26 }, "end": { - "line": 382, + "line": 398, "column": 27 } } @@ -124047,15 +127142,15 @@ "binop": null }, "value": "length", - "start": 14736, - "end": 14742, + "start": 15176, + "end": 15182, "loc": { "start": { - "line": 382, + "line": 398, "column": 27 }, "end": { - "line": 382, + "line": 398, "column": 33 } } @@ -124074,15 +127169,15 @@ "updateContext": null }, "value": "===", - "start": 14743, - "end": 14746, + "start": 15183, + "end": 15186, "loc": { "start": { - "line": 382, + "line": 398, "column": 34 }, "end": { - "line": 382, + "line": 398, "column": 37 } } @@ -124101,15 +127196,15 @@ "updateContext": null }, "value": 0, - "start": 14747, - "end": 14748, + "start": 15187, + "end": 15188, "loc": { "start": { - "line": 382, + "line": 398, "column": 38 }, "end": { - "line": 382, + "line": 398, "column": 39 } } @@ -124126,15 +127221,15 @@ "postfix": false, "binop": null }, - "start": 14748, - "end": 14749, + "start": 15188, + "end": 15189, "loc": { "start": { - "line": 382, + "line": 398, "column": 39 }, "end": { - "line": 382, + "line": 398, "column": 40 } } @@ -124154,15 +127249,15 @@ "updateContext": null }, "value": "throw", - "start": 14750, - "end": 14755, + "start": 15190, + "end": 15195, "loc": { "start": { - "line": 382, + "line": 398, "column": 41 }, "end": { - "line": 382, + "line": 398, "column": 46 } } @@ -124182,15 +127277,15 @@ "updateContext": null }, "value": "new", - "start": 14756, - "end": 14759, + "start": 15196, + "end": 15199, "loc": { "start": { - "line": 382, + "line": 398, "column": 47 }, "end": { - "line": 382, + "line": 398, "column": 50 } } @@ -124208,15 +127303,15 @@ "binop": null }, "value": "Error", - "start": 14760, - "end": 14765, + "start": 15200, + "end": 15205, "loc": { "start": { - "line": 382, + "line": 398, "column": 51 }, "end": { - "line": 382, + "line": 398, "column": 56 } } @@ -124233,15 +127328,15 @@ "postfix": false, "binop": null }, - "start": 14765, - "end": 14766, + "start": 15205, + "end": 15206, "loc": { "start": { - "line": 382, + "line": 398, "column": 56 }, "end": { - "line": 382, + "line": 398, "column": 57 } } @@ -124260,15 +127355,15 @@ "updateContext": null }, "value": "Cannot create component class without any internal specifiers", - "start": 14766, - "end": 14829, + "start": 15206, + "end": 15269, "loc": { "start": { - "line": 382, + "line": 398, "column": 57 }, "end": { - "line": 382, + "line": 398, "column": 120 } } @@ -124285,15 +127380,15 @@ "postfix": false, "binop": null }, - "start": 14829, - "end": 14830, + "start": 15269, + "end": 15270, "loc": { "start": { - "line": 382, + "line": 398, "column": 120 }, "end": { - "line": 382, + "line": 398, "column": 121 } } @@ -124311,15 +127406,15 @@ "binop": null, "updateContext": null }, - "start": 14830, - "end": 14831, + "start": 15270, + "end": 15271, "loc": { "start": { - "line": 382, + "line": 398, "column": 121 }, "end": { - "line": 382, + "line": 398, "column": 122 } } @@ -124339,15 +127434,15 @@ "updateContext": null }, "value": "if", - "start": 14836, - "end": 14838, + "start": 15276, + "end": 15278, "loc": { "start": { - "line": 383, + "line": 399, "column": 4 }, "end": { - "line": 383, + "line": 399, "column": 6 } } @@ -124364,15 +127459,15 @@ "postfix": false, "binop": null }, - "start": 14839, - "end": 14840, + "start": 15279, + "end": 15280, "loc": { "start": { - "line": 383, + "line": 399, "column": 7 }, "end": { - "line": 383, + "line": 399, "column": 8 } } @@ -124390,15 +127485,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 14840, - "end": 14858, + "start": 15280, + "end": 15298, "loc": { "start": { - "line": 383, + "line": 399, "column": 8 }, "end": { - "line": 383, + "line": 399, "column": 26 } } @@ -124416,15 +127511,15 @@ "binop": null, "updateContext": null }, - "start": 14858, - "end": 14859, + "start": 15298, + "end": 15299, "loc": { "start": { - "line": 383, + "line": 399, "column": 26 }, "end": { - "line": 383, + "line": 399, "column": 27 } } @@ -124442,15 +127537,15 @@ "binop": null }, "value": "length", - "start": 14859, - "end": 14865, + "start": 15299, + "end": 15305, "loc": { "start": { - "line": 383, + "line": 399, "column": 27 }, "end": { - "line": 383, + "line": 399, "column": 33 } } @@ -124469,15 +127564,15 @@ "updateContext": null }, "value": "===", - 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"start": 16135, - "end": 16138, + "start": 16575, + "end": 16578, "loc": { "start": { - "line": 410, + "line": 426, "column": 29 }, "end": { - "line": 410, + "line": 426, "column": 32 } } @@ -128172,15 +131267,15 @@ "binop": null, "updateContext": null }, - "start": 16138, - "end": 16139, + "start": 16578, + "end": 16579, "loc": { "start": { - "line": 410, + "line": 426, "column": 32 }, "end": { - "line": 410, + "line": 426, "column": 33 } } @@ -128197,15 +131292,15 @@ "postfix": false, "binop": null }, - "start": 16144, - "end": 16145, + "start": 16584, + "end": 16585, "loc": { "start": { - "line": 411, + "line": 427, "column": 4 }, "end": { - "line": 411, + "line": 427, "column": 5 } } @@ -128225,15 +131320,15 @@ "updateContext": null }, "value": "else", - "start": 16146, - "end": 16150, + "start": 16586, + "end": 16590, "loc": { "start": { - "line": 411, + "line": 427, "column": 6 }, "end": { - "line": 411, + "line": 427, "column": 10 } } @@ -128250,15 +131345,15 @@ "postfix": false, "binop": null }, - "start": 16151, - "end": 16152, + "start": 16591, + "end": 16592, "loc": { "start": { - "line": 411, + "line": 427, "column": 11 }, "end": { - "line": 411, + "line": 427, "column": 12 } } @@ -128266,15 +131361,15 @@ { "type": "CommentLine", "value": " Add the external specifiers, concatenated with 'V'.", - "start": 16159, - "end": 16213, + "start": 16599, + "end": 16653, "loc": { "start": { - "line": 412, + "line": 428, "column": 6 }, "end": { - "line": 412, + "line": 428, "column": 60 } } @@ -128294,15 +131389,15 @@ "updateContext": null }, "value": "const", - "start": 16220, - "end": 16225, + "start": 16660, + "end": 16665, "loc": { "start": { - "line": 413, + "line": 429, "column": 6 }, "end": { - "line": 413, + "line": 429, "column": 11 } } @@ -128320,15 +131415,15 @@ "binop": null }, "value": "externalSpecifierLabel", - "start": 16226, - "end": 16248, + "start": 16666, + "end": 16688, "loc": { "start": { - "line": 413, + "line": 429, "column": 12 }, "end": { - "line": 413, + "line": 429, "column": 34 } } @@ -128347,15 +131442,15 @@ "updateContext": null }, "value": "=", - "start": 16249, - "end": 16250, + "start": 16689, + "end": 16690, "loc": { "start": { - "line": 413, + "line": 429, "column": 35 }, "end": { - "line": 413, + "line": 429, "column": 36 } } @@ -128373,15 +131468,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 16251, - "end": 16269, + "start": 16691, + "end": 16709, "loc": { "start": { - "line": 413, + "line": 429, "column": 37 }, "end": { - "line": 413, + "line": 429, "column": 55 } } @@ -128399,15 +131494,15 @@ "binop": null, "updateContext": null }, - "start": 16278, - "end": 16279, + "start": 16718, + "end": 16719, "loc": { "start": { - "line": 414, + "line": 430, "column": 8 }, "end": { - "line": 414, + "line": 430, "column": 9 } } @@ -128425,15 +131520,15 @@ "binop": null }, "value": "map", - "start": 16279, - "end": 16282, + "start": 16719, + "end": 16722, "loc": { "start": { - "line": 414, + "line": 430, "column": 9 }, "end": { - "line": 414, + "line": 430, "column": 12 } } @@ -128450,15 +131545,15 @@ "postfix": false, "binop": null }, - "start": 16282, - "end": 16283, + "start": 16722, + "end": 16723, "loc": { "start": { - "line": 414, + "line": 430, "column": 12 }, "end": { - "line": 414, + "line": 430, "column": 13 } } @@ -128476,15 +131571,15 @@ "binop": null }, "value": "generateSpecifierName", - "start": 16283, - "end": 16304, + "start": 16723, + "end": 16744, "loc": { "start": { - "line": 414, + "line": 430, "column": 13 }, "end": { - "line": 414, + "line": 430, "column": 34 } } @@ -128501,15 +131596,15 @@ "postfix": false, "binop": null }, - "start": 16304, - "end": 16305, + "start": 16744, + "end": 16745, "loc": { "start": { - "line": 414, + "line": 430, "column": 34 }, "end": { - "line": 414, + "line": 430, "column": 35 } } @@ -128527,15 +131622,15 @@ "binop": null, "updateContext": null }, - "start": 16314, - "end": 16315, + "start": 16754, + "end": 16755, "loc": { "start": { - "line": 415, + "line": 431, "column": 8 }, "end": { - "line": 415, + "line": 431, "column": 9 } } @@ -128553,15 +131648,15 @@ "binop": null }, "value": "sort", - "start": 16315, - "end": 16319, + "start": 16755, + "end": 16759, "loc": { "start": { - "line": 415, + "line": 431, "column": 9 }, "end": { - "line": 415, + "line": 431, "column": 13 } } @@ -128578,15 +131673,15 @@ "postfix": false, "binop": null }, - "start": 16319, - "end": 16320, + "start": 16759, + "end": 16760, "loc": { "start": { - "line": 415, + "line": 431, "column": 13 }, "end": { - "line": 415, + "line": 431, "column": 14 } } @@ -128603,15 +131698,15 @@ "postfix": false, "binop": null }, - "start": 16320, - "end": 16321, + "start": 16760, + "end": 16761, "loc": { "start": { - "line": 415, + "line": 431, "column": 14 }, "end": { - "line": 415, + "line": 431, "column": 15 } } @@ -128629,15 +131724,15 @@ "binop": null, "updateContext": null }, - "start": 16330, - "end": 16331, + "start": 16770, + "end": 16771, "loc": { "start": { - "line": 416, + "line": 432, "column": 8 }, "end": { - "line": 416, + "line": 432, "column": 9 } } @@ -128655,15 +131750,15 @@ "binop": null }, "value": "join", - "start": 16331, - "end": 16335, + "start": 16771, + "end": 16775, "loc": { "start": { - "line": 416, + "line": 432, "column": 9 }, "end": { - "line": 416, + "line": 432, "column": 13 } } @@ -128680,15 +131775,15 @@ "postfix": false, "binop": null }, - "start": 16335, - "end": 16336, + "start": 16775, + "end": 16776, "loc": { "start": { - "line": 416, + "line": 432, "column": 13 }, "end": { - "line": 416, + "line": 432, "column": 14 } } @@ -128707,15 +131802,15 @@ "updateContext": null }, "value": " V ", - "start": 16336, - "end": 16341, + "start": 16776, + "end": 16781, "loc": { "start": { - "line": 416, + "line": 432, "column": 14 }, "end": { - "line": 416, + "line": 432, "column": 19 } } @@ -128732,15 +131827,15 @@ "postfix": false, "binop": null }, - "start": 16341, - "end": 16342, + "start": 16781, + "end": 16782, "loc": { "start": { - "line": 416, + "line": 432, "column": 19 }, "end": { - "line": 416, + "line": 432, "column": 20 } } @@ -128758,15 +131853,15 @@ "binop": null, "updateContext": null }, - "start": 16342, - "end": 16343, + "start": 16782, + "end": 16783, "loc": { "start": { - "line": 416, + "line": 432, "column": 20 }, "end": { - "line": 416, + "line": 432, "column": 21 } } @@ -128784,15 +131879,15 @@ "binop": null }, "value": "componentClassLabel", - "start": 16350, - "end": 16369, + "start": 16790, + "end": 16809, "loc": { "start": { - "line": 417, + "line": 433, "column": 6 }, "end": { - "line": 417, + "line": 433, "column": 25 } } @@ -128811,15 +131906,15 @@ "updateContext": null }, "value": "+=", - "start": 16370, - "end": 16372, + "start": 16810, + "end": 16812, "loc": { "start": { - "line": 417, + "line": 433, "column": 26 }, "end": { - "line": 417, + "line": 433, "column": 28 } } @@ -128836,15 +131931,15 @@ "postfix": false, "binop": null }, - "start": 16373, - "end": 16374, + "start": 16813, + "end": 16814, "loc": { "start": { - "line": 417, + "line": 433, "column": 29 }, "end": { - "line": 417, + "line": 433, "column": 30 } } @@ -128863,15 +131958,15 @@ "updateContext": null }, "value": " ~ ", - "start": 16374, - "end": 16377, + "start": 16814, + "end": 16817, "loc": { "start": { - "line": 417, + "line": 433, "column": 30 }, "end": { - "line": 417, + "line": 433, "column": 33 } } @@ -128888,15 +131983,15 @@ "postfix": false, "binop": null }, - "start": 16377, - "end": 16379, + "start": 16817, + "end": 16819, "loc": { "start": { - "line": 417, + "line": 433, "column": 33 }, "end": { - "line": 417, + "line": 433, "column": 35 } } @@ -128914,15 +132009,15 @@ "binop": null }, "value": "externalSpecifierLabel", - "start": 16379, - "end": 16401, + "start": 16819, + "end": 16841, "loc": { "start": { - "line": 417, + "line": 433, "column": 35 }, "end": { - "line": 417, + "line": 433, "column": 57 } } @@ -128939,15 +132034,15 @@ "postfix": false, "binop": null }, - "start": 16401, - "end": 16402, + "start": 16841, + "end": 16842, "loc": { "start": { - "line": 417, + "line": 433, "column": 57 }, "end": { - "line": 417, + "line": 433, "column": 58 } } @@ -128966,15 +132061,15 @@ "updateContext": null }, "value": ")", - "start": 16402, - "end": 16403, + "start": 16842, + "end": 16843, "loc": { "start": { - "line": 417, + "line": 433, "column": 58 }, "end": { - "line": 417, + "line": 433, "column": 59 } } @@ -128991,15 +132086,15 @@ "postfix": false, "binop": null }, - "start": 16403, - "end": 16404, + "start": 16843, + "end": 16844, "loc": { "start": { - "line": 417, + "line": 433, "column": 59 }, "end": { - "line": 417, + "line": 433, "column": 60 } } @@ -129017,15 +132112,15 @@ "binop": null, "updateContext": null }, - "start": 16404, - "end": 16405, + "start": 16844, + "end": 16845, "loc": { "start": { - "line": 417, + "line": 433, "column": 60 }, "end": { - "line": 417, + "line": 433, "column": 61 } } @@ -129042,15 +132137,15 @@ "postfix": false, "binop": null }, - "start": 16410, - "end": 16411, + "start": 16850, + "end": 16851, "loc": { "start": { - "line": 418, + "line": 434, "column": 4 }, "end": { - "line": 418, + "line": 434, "column": 5 } } @@ -129058,15 +132153,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`component class label: ${componentClassLabel}\\n`);", - "start": 16417, - "end": 16492, + "start": 16857, + "end": 16932, "loc": { "start": { - "line": 420, + "line": 436, "column": 4 }, "end": { - "line": 420, + "line": 436, "column": 79 } } @@ -129074,15 +132169,15 @@ { "type": "CommentLine", "value": " TODO We need to replace this with an actual object-based comparison,", - "start": 16498, - "end": 16569, + "start": 16938, + "end": 17009, "loc": { "start": { - "line": 422, + "line": 438, "column": 4 }, "end": { - "line": 422, + "line": 438, "column": 75 } } @@ -129090,15 +132185,15 @@ { "type": "CommentLine", "value": " rather than trusting the labels to tell us everything.", - "start": 16574, - "end": 16631, + "start": 17014, + "end": 17071, "loc": { "start": { - "line": 423, + "line": 439, "column": 4 }, "end": { - "line": 423, + "line": 439, "column": 61 } } @@ -129118,15 +132213,15 @@ "updateContext": null }, "value": "if", - "start": 16636, - "end": 16638, + "start": 17076, + "end": 17078, "loc": { "start": { - "line": 424, + "line": 440, "column": 4 }, "end": { - "line": 424, + "line": 440, "column": 6 } } @@ -129143,15 +132238,15 @@ "postfix": false, "binop": null }, - "start": 16639, - "end": 16640, + "start": 17079, + "end": 17080, "loc": { "start": { - "line": 424, + "line": 440, "column": 7 }, "end": { - "line": 424, + "line": 440, "column": 8 } } @@ -129169,15 +132264,15 @@ "binop": null }, "value": "reusePrevious", - "start": 16640, - "end": 16653, + "start": 17080, + "end": 17093, "loc": { "start": { - "line": 424, + "line": 440, "column": 8 }, "end": { - "line": 424, + "line": 440, "column": 21 } } @@ -129196,15 +132291,15 @@ "updateContext": null }, "value": "&&", - "start": 16654, - "end": 16656, + "start": 17094, + "end": 17096, "loc": { "start": { - "line": 424, + "line": 440, "column": 22 }, "end": { - "line": 424, + "line": 440, "column": 24 } } @@ -129222,15 +132317,15 @@ "binop": null }, "value": "has", - "start": 16657, - "end": 16660, + "start": 17097, + "end": 17100, "loc": { "start": { - "line": 424, + "line": 440, "column": 25 }, "end": { - "line": 424, + "line": 440, "column": 28 } } @@ -129247,15 +132342,15 @@ "postfix": false, "binop": null }, - "start": 16660, - "end": 16661, + "start": 17100, + "end": 17101, "loc": { "start": { - "line": 424, + "line": 440, "column": 28 }, "end": { - "line": 424, + "line": 440, "column": 29 } } @@ -129275,15 +132370,15 @@ "updateContext": null }, "value": "this", - "start": 16661, - "end": 16665, + "start": 17101, + "end": 17105, "loc": { "start": { - "line": 424, + "line": 440, "column": 29 }, "end": { - "line": 424, + "line": 440, "column": 33 } } @@ -129301,15 +132396,15 @@ "binop": null, "updateContext": null }, - "start": 16665, - "end": 16666, + "start": 17105, + "end": 17106, "loc": { "start": { - "line": 424, + "line": 440, "column": 33 }, "end": { - "line": 424, + "line": 440, "column": 34 } } @@ -129327,15 +132422,15 @@ "binop": null }, "value": "componentClassesByLabel", - "start": 16666, - "end": 16689, + "start": 17106, + "end": 17129, "loc": { "start": { - "line": 424, + "line": 440, "column": 34 }, "end": { - "line": 424, + "line": 440, "column": 57 } } @@ -129353,15 +132448,15 @@ "binop": null, "updateContext": null }, - "start": 16689, - "end": 16690, + "start": 17129, + "end": 17130, "loc": { "start": { - "line": 424, + "line": 440, "column": 57 }, "end": { - "line": 424, + "line": 440, "column": 58 } } @@ -129379,15 +132474,15 @@ "binop": null }, "value": "componentClassLabel", - "start": 16691, - "end": 16710, + "start": 17131, + "end": 17150, "loc": { "start": { - "line": 424, + "line": 440, "column": 59 }, "end": { - "line": 424, + "line": 440, "column": 78 } } @@ -129404,15 +132499,15 @@ "postfix": false, "binop": null }, - "start": 16710, - "end": 16711, + "start": 17150, + "end": 17151, "loc": { "start": { - "line": 424, + "line": 440, "column": 78 }, "end": { - "line": 424, + "line": 440, "column": 79 } } @@ -129429,15 +132524,15 @@ "postfix": false, "binop": null }, - "start": 16711, - "end": 16712, + "start": 17151, + "end": 17152, "loc": { "start": { - "line": 424, + "line": 440, "column": 79 }, "end": { - "line": 424, + "line": 440, "column": 80 } } @@ -129454,15 +132549,15 @@ "postfix": false, "binop": null }, - "start": 16713, - "end": 16714, + "start": 17153, + "end": 17154, "loc": { "start": { - "line": 424, + "line": 440, "column": 81 }, "end": { - "line": 424, + "line": 440, "column": 82 } } @@ -129470,15 +132565,15 @@ { "type": "CommentLine", "value": " If we see the same label again, return the previously defined component class.", - "start": 16721, - "end": 16802, + "start": 17161, + "end": 17242, "loc": { "start": { - "line": 425, + "line": 441, "column": 6 }, "end": { - "line": 425, + "line": 441, "column": 87 } } @@ -129498,15 +132593,15 @@ "updateContext": null }, "value": "return", - "start": 16809, - "end": 16815, + "start": 17249, + "end": 17255, "loc": { "start": { - "line": 426, + "line": 442, "column": 6 }, "end": { - "line": 426, + "line": 442, "column": 12 } } @@ -129523,15 +132618,15 @@ "postfix": false, "binop": null }, - "start": 16816, - "end": 16817, + "start": 17256, + "end": 17257, "loc": { "start": { - "line": 426, + "line": 442, "column": 13 }, "end": { - "line": 426, + "line": 442, "column": 14 } } @@ -129550,15 +132645,15 @@ "updateContext": null }, "value": "@id", - "start": 16818, - "end": 16823, + "start": 17258, + "end": 17263, "loc": { "start": { - "line": 426, + "line": 442, "column": 15 }, "end": { - "line": 426, + "line": 442, "column": 20 } } @@ -129576,15 +132671,15 @@ "binop": null, "updateContext": null }, - "start": 16823, - "end": 16824, + "start": 17263, + "end": 17264, "loc": { "start": { - "line": 426, + "line": 442, "column": 20 }, "end": { - "line": 426, + "line": 442, "column": 21 } } @@ -129604,15 +132699,15 @@ "updateContext": null }, "value": "this", - "start": 16825, - "end": 16829, + "start": 17265, + "end": 17269, "loc": { "start": { - "line": 426, + "line": 442, "column": 22 }, "end": { - "line": 426, + "line": 442, "column": 26 } } @@ -129630,15 +132725,15 @@ "binop": null, "updateContext": null }, - "start": 16829, - "end": 16830, + "start": 17269, + "end": 17270, "loc": { "start": { - "line": 426, + "line": 442, "column": 26 }, "end": { - "line": 426, + "line": 442, "column": 27 } } @@ -129656,15 +132751,15 @@ "binop": null }, "value": "componentClassesByLabel", - "start": 16830, - "end": 16853, + "start": 17270, + "end": 17293, "loc": { "start": { - "line": 426, + "line": 442, "column": 27 }, "end": { - "line": 426, + "line": 442, "column": 50 } } @@ -129682,15 +132777,15 @@ "binop": null, "updateContext": null }, - "start": 16853, - "end": 16854, + "start": 17293, + "end": 17294, "loc": { "start": { - "line": 426, + "line": 442, "column": 50 }, "end": { - "line": 426, + "line": 442, "column": 51 } } @@ -129708,15 +132803,15 @@ "binop": null }, "value": "componentClassLabel", - "start": 16854, - "end": 16873, + "start": 17294, + "end": 17313, "loc": { "start": { - "line": 426, + "line": 442, "column": 51 }, "end": { - "line": 426, + "line": 442, "column": 70 } } @@ -129734,15 +132829,15 @@ "binop": null, "updateContext": null }, - "start": 16873, - "end": 16874, + "start": 17313, + "end": 17314, "loc": { "start": { - "line": 426, + "line": 442, "column": 70 }, "end": { - "line": 426, + "line": 442, "column": 71 } } @@ -129760,15 +132855,15 @@ "binop": null, "updateContext": null }, - "start": 16874, - "end": 16875, + "start": 17314, + "end": 17315, "loc": { "start": { - "line": 426, + "line": 442, "column": 71 }, "end": { - "line": 426, + "line": 442, "column": 72 } } @@ -129787,15 +132882,15 @@ "updateContext": null }, "value": "@id", - "start": 16875, - "end": 16880, + "start": 17315, + "end": 17320, "loc": { "start": { - "line": 426, + "line": 442, "column": 72 }, "end": { - "line": 426, + "line": 442, "column": 77 } } @@ -129813,15 +132908,15 @@ "binop": null, "updateContext": null }, - "start": 16880, - "end": 16881, + "start": 17320, + "end": 17321, "loc": { "start": { - "line": 426, + "line": 442, "column": 77 }, "end": { - "line": 426, + "line": 442, "column": 78 } } @@ -129838,15 +132933,15 @@ "postfix": false, "binop": null }, - "start": 16882, - "end": 16883, + "start": 17322, + "end": 17323, "loc": { "start": { - "line": 426, + "line": 442, "column": 79 }, "end": { - "line": 426, + "line": 442, "column": 80 } } @@ -129864,15 +132959,15 @@ "binop": null, "updateContext": null }, - "start": 16883, - "end": 16884, + "start": 17323, + "end": 17324, "loc": { "start": { - "line": 426, + "line": 442, "column": 80 }, "end": { - "line": 426, + "line": 442, "column": 81 } } @@ -129889,15 +132984,15 @@ "postfix": false, "binop": null }, - "start": 16889, - "end": 16890, + "start": 17329, + "end": 17330, "loc": { "start": { - "line": 427, + "line": 443, "column": 4 }, "end": { - "line": 427, + "line": 443, "column": 5 } } @@ -129905,15 +133000,15 @@ { "type": "CommentLine", "value": " Create a new component class for this set of internal and external specifiers.", - "start": 16896, - "end": 16977, + "start": 17336, + "end": 17417, "loc": { "start": { - "line": 429, + "line": 445, "column": 4 }, "end": { - "line": 429, + "line": 445, "column": 85 } } @@ -129933,15 +133028,15 @@ "updateContext": null }, "value": "this", - 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"start": 17075, - "end": 17081, + "start": 17515, + "end": 17521, "loc": { "start": { - "line": 432, + "line": 448, "column": 31 }, "end": { - "line": 432, + "line": 448, "column": 37 } } @@ -130483,15 +133578,15 @@ "binop": null, "updateContext": null }, - "start": 17081, - "end": 17082, + "start": 17521, + "end": 17522, "loc": { "start": { - "line": 432, + "line": 448, "column": 37 }, "end": { - "line": 432, + "line": 448, "column": 38 } } @@ -130510,15 +133605,15 @@ "updateContext": null }, "value": "@id", - "start": 17082, - "end": 17087, + "start": 17522, + "end": 17527, "loc": { "start": { - "line": 432, + "line": 448, "column": 38 }, "end": { - "line": 432, + "line": 448, "column": 43 } } @@ -130536,15 +133631,15 @@ "binop": null, "updateContext": null }, - "start": 17087, - "end": 17088, + "start": 17527, + "end": 17528, "loc": { "start": { - "line": 432, + "line": 448, "column": 43 }, "end": { - "line": 432, + "line": 448, "column": 44 } } @@ -130561,15 +133656,15 @@ "postfix": false, "binop": null }, - "start": 17088, - "end": 17089, + "start": 17528, + "end": 17529, "loc": { "start": { - "line": 432, + "line": 448, "column": 44 }, "end": { - "line": 432, + "line": 448, "column": 45 } } @@ -130588,15 +133683,15 @@ "updateContext": null }, "value": "_component", - "start": 17089, - "end": 17099, + "start": 17529, + "end": 17539, "loc": { "start": { - "line": 432, + "line": 448, "column": 45 }, "end": { - "line": 432, + "line": 448, "column": 55 } } @@ -130613,15 +133708,15 @@ "postfix": false, "binop": null }, - "start": 17099, - "end": 17101, + "start": 17539, + "end": 17541, "loc": { "start": { - "line": 432, + "line": 448, "column": 55 }, "end": { - "line": 432, + "line": 448, "column": 57 } } @@ -130641,15 +133736,15 @@ "updateContext": null }, "value": "this", - "start": 17101, - "end": 17105, + "start": 17541, + "end": 17545, "loc": { "start": { - "line": 432, + "line": 448, "column": 57 }, "end": { - "line": 432, + "line": 448, "column": 61 } } @@ -130667,15 +133762,15 @@ "binop": null, "updateContext": null }, - "start": 17105, - "end": 17106, + "start": 17545, + "end": 17546, "loc": { "start": { - "line": 432, + "line": 448, "column": 61 }, "end": { - "line": 432, + "line": 448, "column": 62 } } @@ -130693,15 +133788,15 @@ "binop": null }, "value": "componentClassCount", - "start": 17106, - "end": 17125, + "start": 17546, + "end": 17565, "loc": { "start": { - "line": 432, + "line": 448, "column": 62 }, "end": { - "line": 432, + "line": 448, "column": 81 } } @@ -130718,15 +133813,15 @@ "postfix": false, "binop": null }, - "start": 17125, - "end": 17126, + "start": 17565, + "end": 17566, "loc": { "start": { - "line": 432, + "line": 448, "column": 81 }, "end": { - "line": 432, + "line": 448, "column": 82 } } @@ -130745,15 +133840,15 @@ "updateContext": null }, "value": "", - "start": 17126, - "end": 17126, + "start": 17566, + "end": 17566, "loc": { "start": { - "line": 432, + "line": 448, "column": 82 }, "end": { - "line": 432, + "line": 448, "column": 82 } } @@ -130770,15 +133865,15 @@ "postfix": false, "binop": null }, - "start": 17126, - "end": 17127, + "start": 17566, + "end": 17567, "loc": { "start": { - "line": 432, + "line": 448, "column": 82 }, "end": { - "line": 432, + "line": 448, "column": 83 } } @@ -130796,15 +133891,15 @@ "binop": null, "updateContext": null }, - "start": 17127, - "end": 17128, + "start": 17567, + "end": 17568, "loc": { "start": { - "line": 432, + "line": 448, "column": 83 }, "end": { - "line": 432, + "line": 448, "column": 84 } } @@ -130812,15 +133907,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);", - "start": 17133, - "end": 17222, + "start": 17573, + "end": 17662, "loc": { "start": { - "line": 433, + "line": 449, "column": 4 }, "end": { - "line": 433, + "line": 449, "column": 93 } } @@ -130838,15 +133933,15 @@ "binop": null }, "value": "componentClass", - "start": 17228, - "end": 17242, + "start": 17668, + "end": 17682, "loc": { "start": { - "line": 435, + "line": 451, "column": 4 }, "end": { - "line": 435, + "line": 451, "column": 18 } } @@ -130864,15 +133959,15 @@ "binop": null, "updateContext": null }, - "start": 17242, - "end": 17243, + "start": 17682, + "end": 17683, "loc": { "start": { - "line": 435, + "line": 451, "column": 18 }, "end": { - "line": 435, + "line": 451, "column": 19 } } @@ -130891,15 +133986,15 @@ "updateContext": null }, "value": "@type", - "start": 17243, - "end": 17250, + "start": 17683, + "end": 17690, "loc": { "start": { - "line": 435, + "line": 451, "column": 19 }, "end": { - "line": 435, + "line": 451, "column": 26 } } @@ -130917,15 +134012,15 @@ "binop": null, "updateContext": null }, - "start": 17250, - "end": 17251, + "start": 17690, + "end": 17691, "loc": { "start": { - "line": 435, + "line": 451, "column": 26 }, "end": { - "line": 435, + "line": 451, "column": 27 } } @@ -130944,15 +134039,15 @@ "updateContext": null }, "value": "=", - "start": 17252, - "end": 17253, + "start": 17692, + "end": 17693, "loc": { "start": { - "line": 435, + "line": 451, "column": 28 }, "end": { - 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"line": 437, + "line": 453, "column": 36 } } @@ -131285,15 +134380,15 @@ "binop": null }, "value": "equivClass", - "start": 17352, - "end": 17362, + "start": 17792, + "end": 17802, "loc": { "start": { - "line": 437, + "line": 453, "column": 37 }, "end": { - "line": 437, + "line": 453, "column": 47 } } @@ -131311,15 +134406,15 @@ "binop": null, "updateContext": null }, - "start": 17362, - "end": 17363, + "start": 17802, + "end": 17803, "loc": { "start": { - "line": 437, + "line": 453, "column": 47 }, "end": { - "line": 437, + "line": 453, "column": 48 } } @@ -131339,15 +134434,15 @@ "updateContext": null }, "value": "if", - "start": 17368, - "end": 17370, + "start": 17808, + "end": 17810, "loc": { "start": { - "line": 438, + "line": 454, "column": 4 }, "end": { - "line": 438, + "line": 454, "column": 6 } } @@ -131364,15 +134459,15 @@ "postfix": false, "binop": null }, - "start": 17371, - "end": 17372, + "start": 17811, + "end": 17812, "loc": { "start": { - "line": 438, + "line": 454, "column": 7 }, "end": { - 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"line": 438, + "line": 454, "column": 35 } } @@ -131496,15 +134591,15 @@ "updateContext": null }, "value": 0, - "start": 17400, - "end": 17401, + "start": 17840, + "end": 17841, "loc": { "start": { - "line": 438, + "line": 454, "column": 36 }, "end": { - "line": 438, + "line": 454, "column": 37 } } @@ -131521,15 +134616,15 @@ "postfix": false, "binop": null }, - "start": 17401, - "end": 17402, + "start": 17841, + "end": 17842, "loc": { "start": { - "line": 438, + "line": 454, "column": 37 }, "end": { - "line": 438, + "line": 454, "column": 38 } } @@ -131547,15 +134642,15 @@ "binop": null }, "value": "componentClass", - "start": 17403, - "end": 17417, + "start": 17843, + "end": 17857, "loc": { "start": { - "line": 438, + "line": 454, "column": 39 }, "end": { - "line": 438, + "line": 454, "column": 53 } } @@ -131573,15 +134668,15 @@ "binop": null, "updateContext": null }, - "start": 17417, - "end": 17418, + "start": 17857, + "end": 17858, "loc": { "start": { - "line": 438, + "line": 454, "column": 53 }, "end": { - "line": 438, + "line": 454, "column": 54 } } @@ -131599,15 +134694,15 @@ "binop": null }, "value": "subClassOf", - "start": 17418, - "end": 17428, + "start": 17858, + "end": 17868, "loc": { "start": { - "line": 438, + "line": 454, "column": 54 }, "end": { - "line": 438, + "line": 454, "column": 64 } } @@ -131626,15 +134721,15 @@ "updateContext": null }, "value": "=", - "start": 17429, - "end": 17430, + "start": 17869, + "end": 17870, "loc": { "start": { - "line": 438, + "line": 454, "column": 65 }, "end": { - "line": 438, + "line": 454, "column": 66 } } @@ -131652,15 +134747,15 @@ "binop": null, "updateContext": null }, - "start": 17431, - "end": 17432, + "start": 17871, + "end": 17872, "loc": { "start": { - "line": 438, + "line": 454, "column": 67 }, "end": { - "line": 438, + "line": 454, "column": 68 } } @@ -131679,15 +134774,15 @@ "updateContext": null }, "value": "phyloref:PhyloreferenceUsingMaximumClade", - "start": 17432, - "end": 17474, + "start": 17872, + "end": 17914, "loc": { "start": { - "line": 438, + "line": 454, "column": 68 }, "end": { - "line": 438, + "line": 454, "column": 110 } } @@ -131705,15 +134800,15 @@ "binop": null, "updateContext": null }, - "start": 17474, - "end": 17475, + "start": 17914, + "end": 17915, "loc": { "start": { - "line": 438, + "line": 454, "column": 110 }, "end": { - "line": 438, + "line": 454, "column": 111 } } @@ -131731,15 +134826,15 @@ "binop": null, "updateContext": null }, - "start": 17475, - "end": 17476, + "start": 17915, + "end": 17916, "loc": { "start": { - "line": 438, + "line": 454, "column": 111 }, "end": { - "line": 438, + "line": 454, "column": 112 } } @@ -131759,15 +134854,15 @@ "updateContext": null }, "value": "else", - "start": 17481, - "end": 17485, + "start": 17921, + "end": 17925, "loc": { "start": { - "line": 439, + "line": 455, "column": 4 }, "end": { - "line": 439, + "line": 455, "column": 8 } } @@ -131785,15 +134880,15 @@ "binop": null }, "value": "componentClass", - "start": 17486, - "end": 17500, + "start": 17926, + "end": 17940, "loc": { "start": { - "line": 439, + "line": 455, "column": 9 }, "end": { - "line": 439, + "line": 455, "column": 23 } } @@ -131811,15 +134906,15 @@ "binop": null, "updateContext": null }, - "start": 17500, - "end": 17501, + "start": 17940, + "end": 17941, "loc": { "start": { - "line": 439, + "line": 455, "column": 23 }, "end": { - "line": 439, + "line": 455, "column": 24 } } @@ -131837,15 +134932,15 @@ "binop": null }, "value": "subClassOf", - "start": 17501, - "end": 17511, + "start": 17941, + "end": 17951, "loc": { "start": { - "line": 439, + "line": 455, "column": 24 }, "end": { - "line": 439, + "line": 455, "column": 34 } } @@ -131864,15 +134959,15 @@ "updateContext": null }, "value": "=", - "start": 17512, - "end": 17513, + "start": 17952, + "end": 17953, "loc": { "start": { - "line": 439, + "line": 455, "column": 35 }, "end": { - "line": 439, + "line": 455, "column": 36 } } @@ -131890,15 +134985,15 @@ "binop": null, "updateContext": null }, - "start": 17514, - "end": 17515, + "start": 17954, + "end": 17955, "loc": { "start": { - "line": 439, + "line": 455, "column": 37 }, "end": { - "line": 439, + "line": 455, "column": 38 } } @@ -131917,15 +135012,15 @@ "updateContext": null }, "value": "phyloref:PhyloreferenceUsingMinimumClade", - "start": 17515, - "end": 17557, + "start": 17955, + "end": 17997, "loc": { "start": { - "line": 439, + "line": 455, "column": 38 }, "end": { - "line": 439, + "line": 455, "column": 80 } } @@ -131943,15 +135038,15 @@ "binop": null, "updateContext": null }, - "start": 17557, - "end": 17558, + "start": 17997, + "end": 17998, "loc": { "start": { - "line": 439, + "line": 455, "column": 80 }, "end": { - "line": 439, + "line": 455, "column": 81 } } @@ -131969,15 +135064,15 @@ "binop": null, "updateContext": null }, - "start": 17558, - "end": 17559, + "start": 17998, + "end": 17999, "loc": { "start": { - "line": 439, + "line": 455, "column": 81 }, "end": { - "line": 439, + "line": 455, "column": 82 } } @@ -131997,15 +135092,15 @@ "updateContext": null }, "value": "if", - "start": 17565, - 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"end": 17583, + "start": 18022, + "end": 18023, "loc": { "start": { - "line": 441, + "line": 457, "column": 21 }, "end": { - "line": 441, + "line": 457, "column": 22 } } @@ -132124,15 +135219,15 @@ "binop": null }, "value": "componentClass", - "start": 17590, - "end": 17604, + "start": 18030, + "end": 18044, "loc": { "start": { - "line": 442, + "line": 458, "column": 6 }, "end": { - "line": 442, + "line": 458, "column": 20 } } @@ -132150,15 +135245,15 @@ "binop": null, "updateContext": null }, - "start": 17604, - "end": 17605, + "start": 18044, + "end": 18045, "loc": { "start": { - "line": 442, + "line": 458, "column": 20 }, "end": { - "line": 442, + "line": 458, "column": 21 } } @@ -132176,15 +135271,15 @@ "binop": null }, "value": "subClassOf", - "start": 17605, - "end": 17615, + "start": 18045, + "end": 18055, "loc": { "start": { - "line": 442, + "line": 458, "column": 21 }, "end": { - "line": 442, + "line": 458, "column": 31 } } @@ -132202,15 +135297,15 @@ "binop": null, "updateContext": null }, - 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"start": 17650, - "end": 17655, + "start": 18090, + "end": 18095, "loc": { "start": { - "line": 443, + "line": 459, "column": 27 }, "end": { - "line": 443, + "line": 459, "column": 32 } } @@ -132436,15 +135531,15 @@ "binop": null, "updateContext": null }, - "start": 17655, - "end": 17656, + "start": 18095, + "end": 18096, "loc": { "start": { - "line": 443, + "line": 459, "column": 32 }, "end": { - "line": 443, + "line": 459, "column": 33 } } @@ -132462,15 +135557,15 @@ "binop": null, "updateContext": null }, - "start": 17656, - "end": 17657, + "start": 18096, + "end": 18097, "loc": { "start": { - "line": 443, + "line": 459, "column": 33 }, "end": { - "line": 443, + "line": 459, "column": 34 } } @@ -132487,15 +135582,15 @@ "postfix": false, "binop": null }, - "start": 17664, - "end": 17665, + "start": 18104, + "end": 18105, "loc": { "start": { - "line": 444, + "line": 460, "column": 6 }, "end": { - "line": 444, + "line": 460, "column": 7 } } @@ -132512,15 +135607,15 @@ "postfix": false, "binop": null }, - "start": 17665, - "end": 17666, + "start": 18105, + "end": 18106, "loc": { "start": { - "line": 444, + "line": 460, "column": 7 }, "end": { - "line": 444, + "line": 460, "column": 8 } } @@ -132538,15 +135633,15 @@ "binop": null, "updateContext": null }, - "start": 17666, - "end": 17667, + "start": 18106, + "end": 18107, "loc": { "start": { - "line": 444, + "line": 460, "column": 8 }, "end": { - "line": 444, + "line": 460, "column": 9 } } @@ -132563,15 +135658,15 @@ "postfix": false, "binop": null }, - "start": 17672, - "end": 17673, + "start": 18112, + "end": 18113, "loc": { "start": { - "line": 445, + "line": 461, "column": 4 }, "end": { - "line": 445, + "line": 461, "column": 5 } } @@ -132579,15 +135674,15 @@ { "type": "CommentLine", "value": " Save it in the cache for later usage.", - "start": 17679, - "end": 17719, + "start": 18119, + "end": 18159, "loc": { "start": { - "line": 447, + "line": 463, "column": 4 }, "end": { - "line": 447, + "line": 463, "column": 44 } } @@ -132607,15 +135702,15 @@ "updateContext": null }, "value": "this", - "start": 17724, - "end": 17728, + "start": 18164, + "end": 18168, "loc": { "start": { - "line": 448, + "line": 464, "column": 4 }, "end": { - "line": 448, + "line": 464, "column": 8 } } @@ -132633,15 +135728,15 @@ "binop": null, "updateContext": null }, - "start": 17728, - "end": 17729, + "start": 18168, + "end": 18169, "loc": { "start": { - "line": 448, + "line": 464, "column": 8 }, "end": { - "line": 448, + "line": 464, "column": 9 } } @@ -132659,15 +135754,15 @@ "binop": null }, "value": "componentClassesByLabel", - "start": 17729, - "end": 17752, + "start": 18169, + "end": 18192, "loc": { "start": { - "line": 448, + "line": 464, "column": 9 }, "end": { - "line": 448, + "line": 464, "column": 32 } } @@ -132685,15 +135780,15 @@ "binop": null, "updateContext": null }, - "start": 17752, - "end": 17753, + "start": 18192, + "end": 18193, "loc": { "start": { - "line": 448, + "line": 464, "column": 32 }, "end": { - "line": 448, + "line": 464, "column": 33 } } @@ -132711,15 +135806,15 @@ "binop": null }, "value": "componentClassLabel", - "start": 17753, - "end": 17772, + "start": 18193, + "end": 18212, "loc": { "start": { - "line": 448, + "line": 464, "column": 33 }, "end": { - "line": 448, + "line": 464, "column": 52 } } @@ -132737,15 +135832,15 @@ "binop": null, "updateContext": null }, - "start": 17772, - "end": 17773, + "start": 18212, + "end": 18213, "loc": { "start": { - "line": 448, + "line": 464, "column": 52 }, "end": { - "line": 448, + "line": 464, "column": 53 } } @@ -132764,15 +135859,15 @@ "updateContext": null }, "value": "=", - "start": 17774, - "end": 17775, + "start": 18214, + "end": 18215, "loc": { "start": { - "line": 448, + "line": 464, "column": 54 }, "end": { - "line": 448, + "line": 464, "column": 55 } } @@ -132790,15 +135885,15 @@ "binop": null }, "value": "componentClass", - "start": 17776, - "end": 17790, + "start": 18216, + "end": 18230, "loc": { "start": { - "line": 448, + "line": 464, "column": 56 }, "end": { - "line": 448, + "line": 464, "column": 70 } } @@ -132816,15 +135911,15 @@ "binop": null, "updateContext": null }, - "start": 17790, - "end": 17791, + "start": 18230, + "end": 18231, "loc": { "start": { - "line": 448, + "line": 464, "column": 70 }, "end": { - "line": 448, + "line": 464, "column": 71 } } @@ -132832,15 +135927,15 @@ { "type": "CommentLine", "value": " The first time we create a componentClass, we include it into the logical", - "start": 17797, - "end": 17873, + "start": 18237, + "end": 18313, "loc": { "start": { - "line": 450, + "line": 466, "column": 4 }, "end": { - "line": 450, + "line": 466, "column": 80 } } @@ -132848,15 +135943,15 @@ { "type": "CommentLine", "value": " expression directly. On subsequent calls, we'll only return the `@id`", - "start": 17878, - "end": 17950, + "start": 18318, + "end": 18390, "loc": { "start": { - "line": 451, + "line": 467, "column": 4 }, "end": { - "line": 451, + "line": 467, "column": 76 } } @@ -132864,15 +135959,15 @@ { "type": "CommentLine", "value": " (see above).", - "start": 17955, - "end": 17970, + "start": 18395, + "end": 18410, "loc": { "start": { - "line": 452, + "line": 468, "column": 4 }, "end": { - "line": 452, + "line": 468, "column": 19 } } @@ -132892,15 +135987,15 @@ "updateContext": null }, "value": "return", - "start": 17975, - "end": 17981, + "start": 18415, + "end": 18421, "loc": { "start": { - "line": 453, + "line": 469, "column": 4 }, "end": { - "line": 453, + "line": 469, "column": 10 } } @@ -132918,15 +136013,15 @@ "binop": null }, "value": "componentClass", - "start": 17982, - "end": 17996, + "start": 18422, + "end": 18436, "loc": { "start": { - "line": 453, + "line": 469, "column": 11 }, "end": { - "line": 453, + "line": 469, "column": 25 } } @@ -132944,15 +136039,15 @@ "binop": null, "updateContext": null }, - "start": 17996, - "end": 17997, + "start": 18436, + "end": 18437, "loc": { "start": { - "line": 453, + "line": 469, "column": 25 }, "end": { - "line": 453, + "line": 469, "column": 26 } } @@ -132969,15 +136064,15 @@ "postfix": false, "binop": null }, - "start": 18000, - "end": 18001, + "start": 18440, + "end": 18441, "loc": { "start": { - "line": 454, + "line": 470, "column": 2 }, "end": { - "line": 454, + "line": 470, "column": 3 } } @@ -132995,15 +136090,15 @@ "binop": null }, "value": "getIncludesRestrictionForTU", - "start": 18005, - "end": 18032, + "start": 18445, + "end": 18472, "loc": { "start": { - "line": 456, + "line": 472, "column": 2 }, "end": { - "line": 456, + "line": 472, "column": 29 } } @@ -133020,15 +136115,15 @@ "postfix": false, "binop": null }, - "start": 18032, - "end": 18033, + "start": 18472, + "end": 18473, "loc": { "start": { - "line": 456, + "line": 472, "column": 29 }, "end": { - "line": 456, + "line": 472, "column": 30 } } @@ -133046,15 +136141,15 @@ "binop": null }, "value": "tu", - "start": 18033, - "end": 18035, + "start": 18473, + "end": 18475, "loc": { "start": { - "line": 456, + "line": 472, "column": 30 }, "end": { - "line": 456, + "line": 472, "column": 32 } } @@ -133071,15 +136166,15 @@ "postfix": false, "binop": null }, - "start": 18035, - "end": 18036, + "start": 18475, + "end": 18476, "loc": { "start": { - "line": 456, + "line": 472, "column": 32 }, "end": { - "line": 456, + "line": 472, "column": 33 } } @@ -133096,15 +136191,15 @@ "postfix": false, "binop": null }, - "start": 18037, - "end": 18038, + "start": 18477, + "end": 18478, "loc": { "start": { - "line": 456, + "line": 472, "column": 34 }, "end": { - "line": 456, + "line": 472, "column": 35 } } @@ -133124,15 +136219,15 @@ "updateContext": null }, "value": "return", - "start": 18043, - "end": 18049, + "start": 18483, + "end": 18489, "loc": { "start": { - "line": 457, + "line": 473, "column": 4 }, "end": { - "line": 457, + "line": 473, "column": 10 } } @@ -133149,15 +136244,15 @@ "postfix": false, "binop": null }, - "start": 18050, - "end": 18051, + "start": 18490, + "end": 18491, "loc": { "start": { - "line": 457, + "line": 473, "column": 11 }, "end": { - "line": 457, + "line": 473, "column": 12 } } @@ -133176,15 +136271,15 @@ "updateContext": null }, "value": "@type", - "start": 18058, - "end": 18065, + "start": 18498, + "end": 18505, "loc": { "start": { - "line": 458, + "line": 474, "column": 6 }, "end": { - "line": 458, + "line": 474, "column": 13 } } @@ -133202,15 +136297,15 @@ "binop": null, "updateContext": null }, - "start": 18065, - "end": 18066, + "start": 18505, + "end": 18506, "loc": { "start": { - "line": 458, + "line": 474, "column": 13 }, "end": { - "line": 458, + "line": 474, "column": 14 } } @@ -133229,15 +136324,15 @@ "updateContext": null }, "value": "owl:Restriction", - "start": 18067, - "end": 18084, + "start": 18507, + "end": 18524, "loc": { "start": { - "line": 458, + "line": 474, "column": 15 }, "end": { - "line": 458, + "line": 474, "column": 32 } } @@ -133255,15 +136350,15 @@ "binop": null, "updateContext": null }, - "start": 18084, - "end": 18085, + "start": 18524, + "end": 18525, "loc": { "start": { - "line": 458, + "line": 474, "column": 32 }, "end": { - "line": 458, + "line": 474, "column": 33 } } @@ -133281,15 +136376,15 @@ "binop": null }, "value": "onProperty", - "start": 18092, - "end": 18102, + "start": 18532, + "end": 18542, "loc": { "start": { - "line": 459, + "line": 475, "column": 6 }, "end": { - "line": 459, + "line": 475, "column": 16 } } @@ -133307,15 +136402,15 @@ "binop": null, "updateContext": null }, - "start": 18102, - "end": 18103, + "start": 18542, + "end": 18543, "loc": { "start": { - "line": 459, + "line": 475, "column": 16 }, "end": { - "line": 459, + "line": 475, "column": 17 } } @@ -133334,15 +136429,15 @@ "updateContext": null }, "value": "phyloref:includes_TU", - "start": 18104, - "end": 18126, + "start": 18544, + "end": 18566, "loc": { "start": { - "line": 459, + "line": 475, "column": 18 }, "end": { - "line": 459, + "line": 475, "column": 40 } } @@ -133360,15 +136455,15 @@ "binop": null, "updateContext": null }, - 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"line": 479, + "line": 495, "column": 12 } } @@ -135219,15 +138314,15 @@ "updateContext": null }, "value": "this", - "start": 18791, - "end": 18795, + "start": 19231, + "end": 19235, "loc": { "start": { - "line": 480, + "line": 496, "column": 10 }, "end": { - "line": 480, + "line": 496, "column": 14 } } @@ -135245,15 +138340,15 @@ "binop": null, "updateContext": null }, - "start": 18795, - "end": 18796, + "start": 19235, + "end": 19236, "loc": { "start": { - "line": 480, + "line": 496, "column": 14 }, "end": { - "line": 480, + "line": 496, "column": 15 } } @@ -135271,15 +138366,15 @@ "binop": null }, "value": "getIncludesRestrictionForTU", - "start": 18796, - "end": 18823, + "start": 19236, + "end": 19263, "loc": { "start": { - "line": 480, + "line": 496, "column": 15 }, "end": { - "line": 480, + "line": 496, "column": 42 } } @@ -135296,15 +138391,15 @@ "postfix": false, "binop": null }, - "start": 18823, - "end": 18824, + "start": 19263, + "end": 19264, "loc": { "start": { - "line": 480, + "line": 496, "column": 42 }, "end": { - "line": 480, + "line": 496, "column": 43 } } @@ -135322,15 +138417,15 @@ "binop": null }, "value": "tu2", - "start": 18824, - "end": 18827, + "start": 19264, + "end": 19267, "loc": { "start": { - "line": 480, + "line": 496, "column": 43 }, "end": { - "line": 480, + "line": 496, "column": 46 } } @@ -135347,15 +138442,15 @@ "postfix": false, "binop": null }, - "start": 18827, - "end": 18828, + "start": 19267, + "end": 19268, "loc": { "start": { - "line": 480, + "line": 496, "column": 46 }, "end": { - "line": 480, + "line": 496, "column": 47 } } @@ -135373,15 +138468,15 @@ "binop": null, "updateContext": null }, - "start": 18828, - "end": 18829, + "start": 19268, + "end": 19269, "loc": { "start": { - "line": 480, + "line": 496, "column": 47 }, "end": { - "line": 480, + "line": 496, "column": 48 } } @@ -135399,15 +138494,15 @@ "binop": null, "updateContext": null }, - "start": 18838, - "end": 18839, + "start": 19278, + "end": 19279, "loc": { "start": { - "line": 481, + "line": 497, "column": 8 }, "end": { - "line": 481, + "line": 497, "column": 9 } } @@ -135425,15 +138520,15 @@ "binop": null, "updateContext": null }, - "start": 18839, - "end": 18840, + "start": 19279, + "end": 19280, "loc": { "start": { - "line": 481, + "line": 497, "column": 9 }, "end": { - "line": 481, + "line": 497, "column": 10 } } @@ -135450,15 +138545,15 @@ "postfix": false, "binop": null }, - "start": 18847, - "end": 18848, + "start": 19287, + "end": 19288, "loc": { "start": { - "line": 482, + "line": 498, "column": 6 }, "end": { - "line": 482, + "line": 498, "column": 7 } } @@ -135476,15 +138571,15 @@ "binop": null, "updateContext": null }, - "start": 18848, - "end": 18849, + "start": 19288, + "end": 19289, "loc": { "start": { - "line": 482, + "line": 498, "column": 7 }, "end": { - "line": 482, + "line": 498, "column": 8 } } @@ -135501,15 +138596,15 @@ "postfix": false, "binop": null }, - "start": 18854, - "end": 18855, + "start": 19294, + "end": 19295, "loc": { "start": { - "line": 483, + "line": 499, "column": 4 }, "end": { - "line": 483, + "line": 499, "column": 5 } } @@ -135527,15 +138622,15 @@ "binop": null, "updateContext": null }, - "start": 18855, - "end": 18856, + "start": 19295, + "end": 19296, "loc": { "start": { - "line": 483, + "line": 499, "column": 5 }, "end": { - "line": 483, + "line": 499, "column": 6 } } @@ -135552,15 +138647,15 @@ "postfix": false, "binop": null }, - "start": 18859, - "end": 18860, + "start": 19299, + "end": 19300, "loc": { "start": { - "line": 484, + "line": 500, "column": 2 }, "end": { - "line": 484, + "line": 500, "column": 3 } } @@ -135568,15 +138663,15 @@ { "type": "CommentBlock", "value": "\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n ", - "start": 18864, - "end": 20362, + "start": 19304, + "end": 20802, "loc": { "start": { - "line": 486, + "line": 502, "column": 2 }, "end": { - "line": 511, + "line": 527, "column": 5 } } @@ -135594,15 +138689,15 @@ "binop": null }, "value": "createClassExpressionsForInternals", - "start": 20365, - "end": 20399, + "start": 20805, + "end": 20839, "loc": { "start": { - "line": 512, + "line": 528, "column": 2 }, "end": { - "line": 512, + "line": 528, "column": 36 } } @@ -135619,15 +138714,15 @@ "postfix": false, "binop": null }, - "start": 20399, - "end": 20400, + "start": 20839, + "end": 20840, "loc": { "start": { - "line": 512, + "line": 528, "column": 36 }, "end": { - "line": 512, + "line": 528, "column": 37 } } @@ -135645,15 +138740,15 @@ "binop": null }, "value": "jsonld", - "start": 20400, - "end": 20406, + "start": 20840, + "end": 20846, "loc": { "start": { - "line": 512, + "line": 528, "column": 37 }, "end": { - "line": 512, + "line": 528, "column": 43 } } @@ -135671,15 +138766,15 @@ "binop": null, "updateContext": null }, - "start": 20406, - "end": 20407, + "start": 20846, + "end": 20847, "loc": { "start": { - "line": 512, + "line": 528, "column": 43 }, "end": { - "line": 512, + "line": 528, "column": 44 } } @@ -135697,15 +138792,15 @@ "binop": null }, "value": "remainingInternals", - "start": 20408, - "end": 20426, + "start": 20848, + "end": 20866, "loc": { "start": { - "line": 512, + "line": 528, "column": 45 }, "end": { - "line": 512, + "line": 528, "column": 63 } } @@ -135723,15 +138818,15 @@ "binop": null, "updateContext": null }, - "start": 20426, - "end": 20427, + "start": 20866, + "end": 20867, "loc": { "start": { - "line": 512, + "line": 528, "column": 63 }, "end": { - "line": 512, + "line": 528, "column": 64 } } @@ -135749,15 +138844,15 @@ "binop": null }, "value": "selected", - "start": 20428, - "end": 20436, + "start": 20868, + "end": 20876, "loc": { "start": { - "line": 512, + "line": 528, "column": 65 }, "end": { - "line": 512, + "line": 528, "column": 73 } } @@ -135774,15 +138869,15 @@ "postfix": false, "binop": null }, - "start": 20436, - "end": 20437, + "start": 20876, + "end": 20877, "loc": { "start": { - "line": 512, + "line": 528, "column": 73 }, "end": { - "line": 512, + "line": 528, "column": 74 } } @@ -135799,15 +138894,15 @@ "postfix": false, "binop": null }, - "start": 20438, - "end": 20439, + "start": 20878, + "end": 20879, "loc": { "start": { - "line": 512, + "line": 528, "column": 75 }, "end": { - "line": 512, + "line": 528, "column": 76 } } @@ -135815,15 +138910,15 @@ { "type": "CommentLine", "value": " process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:", - "start": 20444, - "end": 20512, + "start": 20884, + "end": 20952, "loc": { "start": { - "line": 513, + "line": 529, "column": 4 }, "end": { - "line": 513, + "line": 529, "column": 72 } } @@ -135831,15 +138926,15 @@ { "type": "CommentLine", "value": " ${remainingInternals.length}, selected: ${selected.length}\\n`);", - "start": 20517, - "end": 20583, + "start": 20957, + "end": 21023, "loc": { "start": { - "line": 514, + "line": 530, "column": 4 }, "end": { - "line": 514, + "line": 530, "column": 70 } } @@ -135847,15 +138942,15 @@ { "type": "CommentLine", "value": " Quick special case: if we have two 'remainingInternals' and zero selecteds,", - "start": 20589, - "end": 20667, + "start": 21029, + "end": 21107, "loc": { "start": { - "line": 516, + "line": 532, "column": 4 }, "end": { - "line": 516, + "line": 532, "column": 82 } } @@ -135863,15 +138958,15 @@ { "type": "CommentLine", "value": " we can just return the MRCA for two internal specifiers.", - "start": 20672, - "end": 20731, + "start": 21112, + "end": 21171, "loc": { "start": { - "line": 517, + "line": 533, "column": 4 }, "end": { - "line": 517, + "line": 533, "column": 63 } } @@ -135891,15 +138986,15 @@ "updateContext": null }, "value": "if", - "start": 20736, - "end": 20738, + "start": 21176, + "end": 21178, "loc": { "start": { - "line": 518, + "line": 534, "column": 4 }, "end": { - "line": 518, + "line": 534, "column": 6 } } @@ -135916,15 +139011,15 @@ "postfix": false, "binop": null }, - "start": 20739, - "end": 20740, + "start": 21179, + "end": 21180, "loc": { "start": { - "line": 518, + "line": 534, "column": 7 }, "end": { - "line": 518, + "line": 534, "column": 8 } } @@ -135942,15 +139037,15 @@ "binop": null }, "value": "selected", - "start": 20740, - "end": 20748, + "start": 21180, + "end": 21188, "loc": { "start": { - "line": 518, + "line": 534, "column": 8 }, "end": { - "line": 518, + "line": 534, "column": 16 } } @@ -135968,15 +139063,15 @@ "binop": null, "updateContext": null }, - "start": 20748, - "end": 20749, + "start": 21188, + "end": 21189, "loc": { "start": { - "line": 518, + "line": 534, "column": 16 }, "end": { - "line": 518, + "line": 534, "column": 17 } } @@ -135994,15 +139089,15 @@ "binop": null }, "value": "length", - "start": 20749, - "end": 20755, + "start": 21189, + "end": 21195, "loc": { "start": { - "line": 518, + "line": 534, "column": 17 }, "end": { - "line": 518, + "line": 534, "column": 23 } } @@ -136021,15 +139116,15 @@ "updateContext": null }, "value": "===", - "start": 20756, - "end": 20759, + "start": 21196, + "end": 21199, "loc": { "start": { - "line": 518, + "line": 534, "column": 24 }, "end": { - "line": 518, + "line": 534, "column": 27 } } @@ -136048,15 +139143,15 @@ "updateContext": null }, "value": 0, - "start": 20760, - "end": 20761, + "start": 21200, + "end": 21201, "loc": { "start": { - "line": 518, + "line": 534, "column": 28 }, "end": { - "line": 518, + "line": 534, "column": 29 } } @@ -136073,15 +139168,15 @@ "postfix": false, "binop": null }, - "start": 20761, - "end": 20762, + "start": 21201, + "end": 21202, "loc": { "start": { - "line": 518, + "line": 534, "column": 29 }, "end": { - "line": 518, + "line": 534, "column": 30 } } @@ -136098,15 +139193,15 @@ "postfix": false, "binop": null }, - "start": 20763, - "end": 20764, + "start": 21203, + "end": 21204, "loc": { "start": { - "line": 518, + "line": 534, "column": 31 }, "end": { - "line": 518, + "line": 534, "column": 32 } } @@ -136126,15 +139221,15 @@ "updateContext": null }, "value": "if", - "start": 20771, - "end": 20773, + "start": 21211, + "end": 21213, "loc": { "start": { - "line": 519, + "line": 535, "column": 6 }, "end": { - "line": 519, + "line": 535, "column": 8 } } @@ -136151,15 +139246,15 @@ "postfix": false, "binop": null }, - "start": 20774, - "end": 20775, + "start": 21214, + "end": 21215, "loc": { "start": { - "line": 519, + "line": 535, "column": 9 }, "end": { - "line": 519, + "line": 535, "column": 10 } } @@ -136177,15 +139272,15 @@ "binop": null }, "value": "remainingInternals", - "start": 20775, - "end": 20793, + "start": 21215, + "end": 21233, "loc": { "start": { - "line": 519, + "line": 535, "column": 10 }, "end": { - "line": 519, + "line": 535, "column": 28 } } @@ -136203,15 +139298,15 @@ "binop": null, "updateContext": null }, - "start": 20793, - "end": 20794, + "start": 21233, + "end": 21234, "loc": { "start": { - "line": 519, + "line": 535, "column": 28 }, "end": { - "line": 519, + "line": 535, "column": 29 } } @@ -136229,15 +139324,15 @@ "binop": null }, "value": "length", - "start": 20794, - "end": 20800, + "start": 21234, + "end": 21240, "loc": { "start": { - "line": 519, + "line": 535, "column": 29 }, "end": { - "line": 519, + "line": 535, "column": 35 } } @@ -136256,15 +139351,15 @@ "updateContext": null }, "value": "===", - "start": 20801, - "end": 20804, + "start": 21241, + "end": 21244, "loc": { "start": { - "line": 519, + "line": 535, "column": 36 }, "end": { - "line": 519, + "line": 535, "column": 39 } } @@ -136283,15 +139378,15 @@ "updateContext": null }, "value": 2, - "start": 20805, - "end": 20806, + "start": 21245, + "end": 21246, "loc": { "start": { - "line": 519, + "line": 535, "column": 40 }, "end": { - "line": 519, + "line": 535, "column": 41 } } @@ -136308,15 +139403,15 @@ "postfix": false, "binop": null }, - "start": 20806, - "end": 20807, + "start": 21246, + "end": 21247, "loc": { "start": { - "line": 519, + "line": 535, "column": 41 }, "end": { - "line": 519, + "line": 535, "column": 42 } } @@ -136333,15 +139428,15 @@ "postfix": false, "binop": null }, - "start": 20808, - "end": 20809, + "start": 21248, + "end": 21249, "loc": { "start": { - "line": 519, + "line": 535, "column": 43 }, "end": { - "line": 519, + "line": 535, "column": 44 } } @@ -136361,15 +139456,15 @@ "updateContext": null }, "value": "return", - "start": 20818, - "end": 20824, + "start": 21258, + "end": 21264, "loc": { "start": { - "line": 520, + "line": 536, "column": 8 }, "end": { - "line": 520, + "line": 536, "column": 14 } } @@ -136387,15 +139482,15 @@ "binop": null, "updateContext": null }, - "start": 20825, - "end": 20826, + "start": 21265, + "end": 21266, "loc": { "start": { - "line": 520, + "line": 536, "column": 15 }, "end": { - "line": 520, + "line": 536, "column": 16 } } @@ -136415,15 +139510,15 @@ "updateContext": null }, "value": "this", - "start": 20837, - "end": 20841, + "start": 21277, + "end": 21281, "loc": { "start": { - "line": 521, + "line": 537, "column": 10 }, "end": { - "line": 521, + "line": 537, "column": 14 } } @@ -136441,15 +139536,15 @@ "binop": null, "updateContext": null }, - "start": 20841, - "end": 20842, + "start": 21281, + "end": 21282, "loc": { "start": { - "line": 521, + "line": 537, "column": 14 }, "end": { - "line": 521, + "line": 537, "column": 15 } } @@ -136467,15 +139562,15 @@ "binop": null }, "value": "getMRCARestrictionOfTwoTUs", - "start": 20842, - "end": 20868, + "start": 21282, + "end": 21308, "loc": { "start": { - "line": 521, + "line": 537, "column": 15 }, "end": { - "line": 521, + "line": 537, "column": 41 } } @@ -136492,15 +139587,15 @@ "postfix": false, "binop": null }, - "start": 20868, - "end": 20869, + "start": 21308, + "end": 21309, "loc": { "start": { - "line": 521, + "line": 537, "column": 41 }, "end": { - "line": 521, + "line": 537, "column": 42 } } @@ -136518,15 +139613,15 @@ "binop": null }, "value": "remainingInternals", - "start": 20869, - "end": 20887, + "start": 21309, + "end": 21327, "loc": { "start": { - "line": 521, + "line": 537, "column": 42 }, "end": { - "line": 521, + "line": 537, "column": 60 } } @@ -136544,15 +139639,15 @@ "binop": null, "updateContext": null }, - "start": 20887, - "end": 20888, + "start": 21327, + "end": 21328, "loc": { "start": { - "line": 521, + "line": 537, "column": 60 }, "end": { - "line": 521, + "line": 537, "column": 61 } } @@ -136571,15 +139666,15 @@ "updateContext": null }, "value": 0, - "start": 20888, - "end": 20889, + "start": 21328, + "end": 21329, "loc": { "start": { - "line": 521, + "line": 537, "column": 61 }, "end": { - "line": 521, + "line": 537, "column": 62 } } @@ -136597,15 +139692,15 @@ "binop": null, "updateContext": null }, - "start": 20889, - "end": 20890, + "start": 21329, + "end": 21330, "loc": { "start": { - "line": 521, + "line": 537, "column": 62 }, "end": { - "line": 521, + "line": 537, "column": 63 } } @@ -136623,15 +139718,15 @@ "binop": null, "updateContext": null }, - "start": 20890, - "end": 20891, + "start": 21330, + "end": 21331, "loc": { "start": { - "line": 521, + "line": 537, "column": 63 }, "end": { - "line": 521, + "line": 537, "column": 64 } } @@ -136649,15 +139744,15 @@ "binop": null }, "value": "remainingInternals", - "start": 20892, - "end": 20910, + "start": 21332, + "end": 21350, "loc": { "start": { - "line": 521, + "line": 537, "column": 65 }, "end": { - "line": 521, + "line": 537, "column": 83 } } @@ -136675,15 +139770,15 @@ "binop": null, "updateContext": null }, - "start": 20910, - "end": 20911, + "start": 21350, + "end": 21351, "loc": { "start": { - "line": 521, + "line": 537, "column": 83 }, "end": { - "line": 521, + "line": 537, "column": 84 } } @@ -136702,15 +139797,15 @@ "updateContext": null }, "value": 1, - "start": 20911, - "end": 20912, + "start": 21351, + "end": 21352, "loc": { "start": { - "line": 521, + "line": 537, "column": 84 }, "end": { - "line": 521, + "line": 537, "column": 85 } } @@ -136728,15 +139823,15 @@ "binop": null, "updateContext": null }, - "start": 20912, - "end": 20913, + "start": 21352, + "end": 21353, "loc": { "start": { - "line": 521, + "line": 537, "column": 85 }, "end": { - "line": 521, + "line": 537, "column": 86 } } @@ -136753,15 +139848,15 @@ "postfix": false, "binop": null }, - "start": 20913, - "end": 20914, + "start": 21353, + "end": 21354, "loc": { "start": { - "line": 521, + "line": 537, "column": 86 }, "end": { - "line": 521, + "line": 537, "column": 87 } } @@ -136779,15 +139874,15 @@ "binop": null, "updateContext": null }, - "start": 20914, - "end": 20915, + "start": 21354, + "end": 21355, "loc": { "start": { - "line": 521, + "line": 537, "column": 87 }, "end": { - "line": 521, + "line": 537, "column": 88 } } @@ -136805,15 +139900,15 @@ "binop": null, "updateContext": null }, - "start": 20924, - "end": 20925, + "start": 21364, + "end": 21365, "loc": { "start": { - "line": 522, + "line": 538, "column": 8 }, "end": { - "line": 522, + "line": 538, "column": 9 } } @@ -136831,15 +139926,15 @@ "binop": null, "updateContext": null }, - "start": 20925, - "end": 20926, + "start": 21365, + "end": 21366, "loc": { "start": { - "line": 522, + "line": 538, "column": 9 }, "end": { - "line": 522, + "line": 538, "column": 10 } } @@ -136856,15 +139951,15 @@ "postfix": false, "binop": null }, - "start": 20933, - "end": 20934, + "start": 21373, + "end": 21374, "loc": { "start": { - "line": 523, + "line": 539, "column": 6 }, "end": { - "line": 523, + "line": 539, "column": 7 } } @@ -136884,15 +139979,15 @@ "updateContext": null }, "value": "if", - "start": 20935, - "end": 20937, + "start": 21375, + "end": 21377, "loc": { "start": { - "line": 523, + "line": 539, "column": 8 }, "end": { - "line": 523, + "line": 539, "column": 10 } } @@ -136909,15 +140004,15 @@ "postfix": false, "binop": null }, - "start": 20938, - "end": 20939, + "start": 21378, + "end": 21379, "loc": { "start": { - "line": 523, + "line": 539, "column": 11 }, "end": { - "line": 523, + "line": 539, "column": 12 } } @@ -136935,15 +140030,15 @@ "binop": null }, "value": "remainingInternals", - "start": 20939, - "end": 20957, + "start": 21379, + "end": 21397, "loc": { "start": { - "line": 523, + "line": 539, "column": 12 }, "end": { - "line": 523, + "line": 539, "column": 30 } } @@ -136961,15 +140056,15 @@ "binop": null, "updateContext": null }, - "start": 20957, - "end": 20958, + "start": 21397, + "end": 21398, "loc": { "start": { - "line": 523, + "line": 539, "column": 30 }, "end": { - "line": 523, + "line": 539, "column": 31 } } @@ -136987,15 +140082,15 @@ "binop": null }, "value": "length", - "start": 20958, - "end": 20964, + "start": 21398, + "end": 21404, "loc": { "start": { - "line": 523, + "line": 539, "column": 31 }, "end": { - "line": 523, + "line": 539, "column": 37 } } @@ -137014,15 +140109,15 @@ "updateContext": null }, "value": "===", - "start": 20965, - "end": 20968, + "start": 21405, + "end": 21408, "loc": { "start": { - "line": 523, + "line": 539, "column": 38 }, "end": { - "line": 523, + "line": 539, "column": 41 } } @@ -137041,15 +140136,15 @@ "updateContext": null }, "value": 1, - "start": 20969, - "end": 20970, + "start": 21409, + "end": 21410, "loc": { "start": { - "line": 523, + "line": 539, "column": 42 }, "end": { - 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"start": 22499, - "end": 22500, + "start": 22939, + "end": 22940, "loc": { "start": { - "line": 566, + "line": 582, "column": 18 }, "end": { - "line": 566, + "line": 582, "column": 19 } } @@ -142964,15 +146059,15 @@ "updateContext": null }, "value": "obo:CDAO_0000149", - "start": 22501, - "end": 22519, + "start": 22941, + "end": 22959, "loc": { "start": { - "line": 566, + "line": 582, "column": 20 }, "end": { - "line": 566, + "line": 582, "column": 38 } } @@ -142990,15 +146085,15 @@ "binop": null, "updateContext": null }, - "start": 22519, - "end": 22520, + "start": 22959, + "end": 22960, "loc": { "start": { - "line": 566, + "line": 582, "column": 38 }, "end": { - "line": 566, + "line": 582, "column": 39 } } @@ -143006,15 +146101,15 @@ { "type": "CommentLine", "value": " cdao:has_Child", - "start": 22521, - "end": 22538, + "start": 22961, + "end": 22978, "loc": { "start": { - "line": 566, + "line": 582, "column": 40 }, "end": { - "line": 566, + "line": 582, "column": 57 } } @@ -143032,15 +146127,15 @@ "binop": null }, "value": "someValuesFrom", - 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"start": 22582, - "end": 22583, + "start": 23022, + "end": 23023, "loc": { "start": { - "line": 568, + "line": 584, "column": 17 }, "end": { - "line": 568, + "line": 584, "column": 18 } } @@ -143163,15 +146258,15 @@ "updateContext": null }, "value": "owl:Class", - "start": 22584, - "end": 22595, + "start": 23024, + "end": 23035, "loc": { "start": { - "line": 568, + "line": 584, "column": 19 }, "end": { - "line": 568, + "line": 584, "column": 30 } } @@ -143189,15 +146284,15 @@ "binop": null, "updateContext": null }, - "start": 22595, - "end": 22596, + "start": 23035, + "end": 23036, "loc": { "start": { - "line": 568, + "line": 584, "column": 30 }, "end": { - "line": 568, + "line": 584, "column": 31 } } @@ -143215,15 +146310,15 @@ "binop": null }, "value": "intersectionOf", - "start": 22607, - "end": 22621, + "start": 23047, + "end": 23061, "loc": { "start": { - "line": 569, + "line": 585, "column": 10 }, "end": { - "line": 569, + "line": 585, "column": 24 } } @@ -143241,15 +146336,15 @@ "binop": null, "updateContext": null }, - "start": 22621, - "end": 22622, + "start": 23061, + "end": 23062, "loc": { "start": { - "line": 569, + "line": 585, "column": 24 }, "end": { - "line": 569, + "line": 585, "column": 25 } } @@ -143267,15 +146362,15 @@ "binop": null, "updateContext": null }, - "start": 22623, - "end": 22624, + "start": 23063, + "end": 23064, "loc": { "start": { - "line": 569, + "line": 585, "column": 26 }, "end": { - "line": 569, + "line": 585, "column": 27 } } @@ -143292,15 +146387,15 @@ "postfix": false, "binop": null }, - "start": 22624, - "end": 22625, + "start": 23064, + "end": 23065, "loc": { "start": { - "line": 569, + "line": 585, "column": 27 }, "end": { - "line": 569, + "line": 585, "column": 28 } } @@ -143319,15 +146414,15 @@ "updateContext": null }, "value": "@type", - "start": 22638, - "end": 22645, + "start": 23078, + "end": 23085, "loc": { "start": { - "line": 570, + "line": 586, "column": 12 }, "end": { - "line": 570, + "line": 586, "column": 19 } } @@ -143345,15 +146440,15 @@ "binop": null, "updateContext": null }, - "start": 22645, - "end": 22646, + "start": 23085, + "end": 23086, "loc": { "start": { - "line": 570, + "line": 586, "column": 19 }, "end": { - "line": 570, + "line": 586, "column": 20 } } @@ -143372,15 +146467,15 @@ "updateContext": null }, "value": "owl:Restriction", - "start": 22647, - "end": 22664, + "start": 23087, + "end": 23104, "loc": { "start": { - "line": 570, + "line": 586, "column": 21 }, "end": { - "line": 570, + "line": 586, "column": 38 } } @@ -143398,15 +146493,15 @@ "binop": null, "updateContext": null }, - "start": 22664, - "end": 22665, + "start": 23104, + "end": 23105, "loc": { "start": { - "line": 570, + "line": 586, "column": 38 }, "end": { - "line": 570, + "line": 586, "column": 39 } } @@ -143424,15 +146519,15 @@ "binop": null }, "value": "onProperty", - "start": 22678, - "end": 22688, + "start": 23118, + "end": 23128, "loc": { "start": { - "line": 571, + "line": 587, "column": 12 }, "end": { - "line": 571, + "line": 587, "column": 22 } } @@ -143450,15 +146545,15 @@ "binop": null, "updateContext": null }, - "start": 22688, - "end": 22689, + "start": 23128, + "end": 23129, "loc": { "start": { - "line": 571, + "line": 587, "column": 22 }, "end": { - "line": 571, + "line": 587, "column": 23 } } @@ -143477,15 +146572,15 @@ "updateContext": null }, "value": "phyloref:excludes_lineage_to", - "start": 22690, - "end": 22720, + "start": 23130, + "end": 23160, "loc": { "start": { - "line": 571, + "line": 587, "column": 24 }, "end": { - "line": 571, + "line": 587, "column": 54 } } @@ -143503,15 +146598,15 @@ "binop": null, "updateContext": null }, - "start": 22720, - "end": 22721, + "start": 23160, + "end": 23161, "loc": { "start": { - "line": 571, + "line": 587, "column": 54 }, "end": { - "line": 571, + "line": 587, "column": 55 } } @@ -143529,15 +146624,15 @@ "binop": null }, "value": "someValuesFrom", - "start": 22734, - "end": 22748, + "start": 23174, + "end": 23188, "loc": { "start": { - "line": 572, + "line": 588, "column": 12 }, "end": { - "line": 572, + "line": 588, "column": 26 } } @@ -143555,15 +146650,15 @@ "binop": null, "updateContext": null }, - "start": 22748, - "end": 22749, + "start": 23188, + "end": 23189, "loc": { "start": { - "line": 572, + "line": 588, "column": 26 }, "end": { - "line": 572, + "line": 588, "column": 27 } } @@ -143581,15 +146676,15 @@ "binop": null }, "value": "remainingInternalsExpr", - "start": 22750, - "end": 22772, + "start": 23190, + "end": 23212, "loc": { "start": { - "line": 572, + "line": 588, "column": 28 }, "end": { - "line": 572, + "line": 588, "column": 50 } } @@ -143607,15 +146702,15 @@ "binop": null, "updateContext": null }, - "start": 22772, - "end": 22773, + "start": 23212, + "end": 23213, "loc": { "start": { - "line": 572, + "line": 588, "column": 50 }, "end": { - "line": 572, + "line": 588, "column": 51 } } @@ -143632,15 +146727,15 @@ "postfix": false, "binop": null }, - "start": 22784, - "end": 22785, + "start": 23224, + "end": 23225, "loc": { "start": { - "line": 573, + "line": 589, "column": 10 }, "end": { - "line": 573, + "line": 589, "column": 11 } } @@ -143658,15 +146753,15 @@ "binop": null, "updateContext": null }, - "start": 22785, - "end": 22786, + "start": 23225, + "end": 23226, "loc": { "start": { - "line": 573, + "line": 589, "column": 11 }, "end": { - "line": 573, + "line": 589, "column": 12 } } @@ -143684,15 +146779,15 @@ "binop": null }, "value": "selectedExpr", - "start": 22787, - "end": 22799, + "start": 23227, + "end": 23239, "loc": { "start": { - "line": 573, + "line": 589, "column": 13 }, "end": { - "line": 573, + "line": 589, "column": 25 } } @@ -143710,15 +146805,15 @@ "binop": null, "updateContext": null }, - "start": 22799, - "end": 22800, + "start": 23239, + "end": 23240, "loc": { "start": { - "line": 573, + "line": 589, "column": 25 }, "end": { - "line": 573, + "line": 589, "column": 26 } } @@ -143736,15 +146831,15 @@ "binop": null, "updateContext": null }, - "start": 22800, - "end": 22801, + "start": 23240, + "end": 23241, "loc": { "start": { - "line": 573, + "line": 589, "column": 26 }, "end": { - "line": 573, + "line": 589, "column": 27 } } @@ -143761,15 +146856,15 @@ "postfix": false, "binop": null }, - "start": 22810, - "end": 22811, + "start": 23250, + "end": 23251, "loc": { "start": { - "line": 574, + "line": 590, "column": 8 }, "end": { - "line": 574, + "line": 590, "column": 9 } } @@ -143787,15 +146882,15 @@ "binop": null, "updateContext": null }, - "start": 22811, - "end": 22812, + "start": 23251, + "end": 23252, "loc": { "start": { - "line": 574, + "line": 590, "column": 9 }, "end": { - "line": 574, + "line": 590, "column": 10 } } @@ -143812,15 +146907,15 @@ "postfix": false, "binop": null }, - "start": 22819, - "end": 22820, + "start": 23259, + "end": 23260, "loc": { "start": { - "line": 575, + "line": 591, "column": 6 }, "end": { - "line": 575, + "line": 591, "column": 7 } } @@ -143837,15 +146932,15 @@ "postfix": false, "binop": null }, - "start": 22820, - "end": 22821, + "start": 23260, + "end": 23261, "loc": { "start": { - "line": 575, + "line": 591, "column": 7 }, "end": { - "line": 575, + "line": 591, "column": 8 } } @@ -143863,15 +146958,15 @@ "binop": null, "updateContext": null }, - "start": 22821, - "end": 22822, + "start": 23261, + "end": 23262, "loc": { "start": { - "line": 575, + "line": 591, "column": 8 }, "end": { - "line": 575, + "line": 591, "column": 9 } } @@ -143888,15 +146983,15 @@ "postfix": false, "binop": null }, - "start": 22827, - "end": 22828, + "start": 23267, + "end": 23268, "loc": { "start": { - "line": 576, + "line": 592, "column": 4 }, "end": { - "line": 576, + "line": 592, "column": 5 } } @@ -143904,15 +146999,15 @@ { "type": "CommentLine", "value": " Step 2. Now select everything from remaining once, and start recursing through", - "start": 22834, - "end": 22915, + "start": 23274, + "end": 23355, "loc": { "start": { - "line": 578, + "line": 594, "column": 4 }, "end": { - "line": 578, + "line": 594, "column": 85 } } @@ -143920,15 +147015,15 @@ { "type": "CommentLine", "value": " every possibility.", - "start": 22920, - "end": 22941, + "start": 23360, + "end": 23381, "loc": { "start": { - "line": 579, + "line": 595, "column": 4 }, "end": { - "line": 579, + "line": 595, "column": 25 } } @@ -143936,15 +147031,15 @@ { "type": "CommentLine", "value": " Note that we only process cases where there are more remainingInternals than", - "start": 22946, - "end": 23025, + "start": 23386, + "end": 23465, "loc": { "start": { - "line": 580, + "line": 596, "column": 4 }, "end": { - "line": 580, + "line": 596, "column": 83 } } @@ -143952,15 +147047,15 @@ { "type": "CommentLine", "value": " selected internals -- when there are fewer, we'll just end up with the inverses", - "start": 23030, - "end": 23112, + "start": 23470, + "end": 23552, "loc": { "start": { - "line": 581, + "line": 597, "column": 4 }, "end": { - "line": 581, + "line": 597, "column": 86 } } @@ -143968,15 +147063,15 @@ { "type": "CommentLine", "value": " of the previous comparisons, which we'll already have covered.", - "start": 23117, - "end": 23182, + "start": 23557, + "end": 23622, "loc": { "start": { - "line": 582, + "line": 598, "column": 4 }, "end": { - "line": 582, + "line": 598, "column": 69 } } @@ -143996,15 +147091,15 @@ "updateContext": null }, "value": "if", - "start": 23187, - "end": 23189, + "start": 23627, + "end": 23629, "loc": { "start": { - "line": 583, + "line": 599, "column": 4 }, "end": { - "line": 583, + "line": 599, "column": 6 } } @@ -144021,15 +147116,15 @@ "postfix": false, "binop": null }, - "start": 23190, - "end": 23191, + "start": 23630, + "end": 23631, "loc": { "start": { - "line": 583, + "line": 599, "column": 7 }, "end": { - "line": 583, + "line": 599, "column": 8 } } @@ -144047,15 +147142,15 @@ "binop": null }, "value": "remainingInternals", - "start": 23191, - "end": 23209, + "start": 23631, + "end": 23649, "loc": { "start": { - "line": 583, + "line": 599, "column": 8 }, "end": { - "line": 583, + "line": 599, "column": 26 } } @@ -144073,15 +147168,15 @@ "binop": null, "updateContext": null }, - "start": 23209, - "end": 23210, + "start": 23649, + "end": 23650, "loc": { "start": { - "line": 583, + "line": 599, "column": 26 }, "end": { - "line": 583, + "line": 599, "column": 27 } } @@ -144099,15 +147194,15 @@ "binop": null }, "value": "length", - "start": 23210, - "end": 23216, + "start": 23650, + "end": 23656, "loc": { "start": { - "line": 583, + "line": 599, "column": 27 }, "end": { - "line": 583, + "line": 599, "column": 33 } } @@ -144126,15 +147221,15 @@ "updateContext": null }, "value": ">", - "start": 23217, - "end": 23218, + "start": 23657, + "end": 23658, "loc": { "start": { - "line": 583, + "line": 599, "column": 34 }, "end": { - "line": 583, + "line": 599, "column": 35 } } @@ -144153,15 +147248,15 @@ "updateContext": null }, "value": 1, - 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"start": 23716, - "end": 23720, + "start": 24156, + "end": 24160, "loc": { "start": { - "line": 592, + "line": 608, "column": 36 }, "end": { - "line": 592, + "line": 608, "column": 40 } } @@ -146018,15 +149113,15 @@ "postfix": false, "binop": null }, - "start": 23720, - "end": 23721, + "start": 24160, + "end": 24161, "loc": { "start": { - "line": 592, + "line": 608, "column": 40 }, "end": { - "line": 592, + "line": 608, "column": 41 } } @@ -146044,15 +149139,15 @@ "binop": null }, "value": "expr", - "start": 23721, - "end": 23725, + "start": 24161, + "end": 24165, "loc": { "start": { - "line": 592, + "line": 608, "column": 41 }, "end": { - "line": 592, + "line": 608, "column": 45 } } @@ -146069,15 +149164,15 @@ "postfix": false, "binop": null }, - "start": 23725, - "end": 23726, + "start": 24165, + "end": 24166, "loc": { "start": { - "line": 592, + "line": 608, "column": 45 }, "end": { - "line": 592, + "line": 608, "column": 46 } } @@ -146094,15 +149189,15 @@ "postfix": false, "binop": null }, - "start": 23726, - "end": 23727, + "start": 24166, + "end": 24167, "loc": { "start": { - "line": 592, + "line": 608, "column": 46 }, "end": { - "line": 592, + "line": 608, "column": 47 } } @@ -146120,15 +149215,15 @@ "binop": null, "updateContext": null }, - "start": 23727, - "end": 23728, + "start": 24167, + "end": 24168, "loc": { "start": { - "line": 592, + "line": 608, "column": 47 }, "end": { - "line": 592, + "line": 608, "column": 48 } } @@ -146145,15 +149240,15 @@ "postfix": false, "binop": null }, - "start": 23733, - "end": 23734, + "start": 24173, + "end": 24174, "loc": { "start": { - "line": 593, + "line": 609, "column": 4 }, "end": { - "line": 593, + "line": 609, "column": 5 } } @@ -146173,15 +149268,15 @@ "updateContext": null }, "value": "return", - "start": 23740, - "end": 23746, + "start": 24180, + "end": 24186, "loc": { "start": { - "line": 595, + "line": 611, "column": 4 }, "end": { - "line": 595, + "line": 611, "column": 10 } } @@ -146199,15 +149294,15 @@ "binop": null }, "value": "classExprs", - "start": 23747, - "end": 23757, + "start": 24187, + "end": 24197, "loc": { "start": { - "line": 595, + "line": 611, "column": 11 }, "end": { - "line": 595, + "line": 611, "column": 21 } } @@ -146225,15 +149320,15 @@ "binop": null, "updateContext": null }, - "start": 23757, - "end": 23758, + "start": 24197, + "end": 24198, "loc": { "start": { - "line": 595, + "line": 611, "column": 21 }, "end": { - "line": 595, + "line": 611, "column": 22 } } @@ -146250,15 +149345,15 @@ "postfix": false, "binop": null }, - "start": 23761, - "end": 23762, + "start": 24201, + "end": 24202, "loc": { "start": { - "line": 596, + "line": 612, "column": 2 }, "end": { - "line": 596, + "line": 612, "column": 3 } } @@ -146266,15 +149361,15 @@ { "type": "CommentBlock", "value": "\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n ", - "start": 23766, - "end": 23972, + "start": 24206, + "end": 24412, "loc": { "start": { - "line": 598, + "line": 614, "column": 2 }, "end": { - "line": 606, + "line": 622, "column": 5 } } @@ -146292,15 +149387,15 @@ "binop": null }, "value": "asJSONLD", - "start": 23975, - "end": 23983, + "start": 24415, + "end": 24423, "loc": { "start": { - "line": 607, + "line": 623, "column": 2 }, "end": { - "line": 607, + "line": 623, "column": 10 } } @@ -146317,15 +149412,15 @@ "postfix": false, "binop": null }, - "start": 23983, - "end": 23984, + "start": 24423, + "end": 24424, "loc": { "start": { - "line": 607, + "line": 623, "column": 10 }, "end": { - "line": 607, + "line": 623, "column": 11 } } @@ -146343,15 +149438,15 @@ "binop": null }, "value": "fallbackIRI", - "start": 23984, - "end": 23995, + "start": 24424, + "end": 24435, "loc": { "start": { - "line": 607, + "line": 623, "column": 11 }, "end": { - "line": 607, + "line": 623, "column": 22 } } @@ -146368,15 +149463,15 @@ "postfix": false, "binop": null }, - "start": 23995, - "end": 23996, + "start": 24435, + "end": 24436, "loc": { "start": { - "line": 607, + "line": 623, "column": 22 }, "end": { - "line": 607, + "line": 623, "column": 23 } } @@ -146393,15 +149488,15 @@ "postfix": false, "binop": null }, - "start": 23997, - "end": 23998, + "start": 24437, + "end": 24438, "loc": { "start": { - "line": 607, + "line": 623, "column": 24 }, "end": { - "line": 607, + "line": 623, "column": 25 } } @@ -146409,15 +149504,15 @@ { "type": "CommentLine", "value": " Keep all currently extant data.", - "start": 24003, - "end": 24037, + "start": 24443, + "end": 24477, "loc": { "start": { - "line": 608, + "line": 624, "column": 4 }, "end": { - "line": 608, + "line": 624, "column": 38 } } @@ -146437,15 +149532,15 @@ "updateContext": null }, "value": "const", - "start": 24042, - "end": 24047, + "start": 24482, + "end": 24487, "loc": { "start": { - "line": 609, + "line": 625, "column": 4 }, "end": { - "line": 609, + "line": 625, "column": 9 } } @@ -146463,15 +149558,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 24048, - "end": 24064, + "start": 24488, + "end": 24504, "loc": { "start": { - "line": 609, + "line": 625, "column": 10 }, "end": { - "line": 609, + "line": 625, "column": 26 } } @@ -146490,15 +149585,15 @@ "updateContext": null }, "value": "=", - "start": 24065, - "end": 24066, + "start": 24505, + "end": 24506, "loc": { "start": { - "line": 609, + "line": 625, "column": 27 }, "end": { - "line": 609, + "line": 625, "column": 28 } } @@ -146516,15 +149611,15 @@ "binop": null }, "value": "cloneDeep", - "start": 24067, - "end": 24076, + "start": 24507, + "end": 24516, "loc": { "start": { - "line": 609, + "line": 625, "column": 29 }, "end": { - "line": 609, + "line": 625, "column": 38 } } @@ -146541,15 +149636,15 @@ "postfix": false, "binop": null }, - "start": 24076, - "end": 24077, + "start": 24516, + "end": 24517, "loc": { "start": { - "line": 609, + "line": 625, "column": 38 }, "end": { - "line": 609, + "line": 625, "column": 39 } } @@ -146569,15 +149664,15 @@ "updateContext": null }, "value": "this", - "start": 24077, - "end": 24081, + "start": 24517, + "end": 24521, "loc": { "start": { - "line": 609, + "line": 625, "column": 39 }, "end": { - "line": 609, + "line": 625, "column": 43 } } @@ -146595,15 +149690,15 @@ "binop": null, "updateContext": null }, - "start": 24081, - "end": 24082, + "start": 24521, + "end": 24522, "loc": { "start": { - "line": 609, + "line": 625, "column": 43 }, "end": { - "line": 609, + "line": 625, "column": 44 } } @@ -146621,15 +149716,15 @@ "binop": null }, "value": "phyloref", - "start": 24082, - "end": 24090, + "start": 24522, + "end": 24530, "loc": { "start": { - "line": 609, + "line": 625, "column": 44 }, "end": { - "line": 609, + "line": 625, "column": 52 } } @@ -146646,15 +149741,15 @@ "postfix": false, "binop": null }, - "start": 24090, - "end": 24091, + "start": 24530, + "end": 24531, "loc": { "start": { - "line": 609, + "line": 625, "column": 52 }, "end": { - "line": 609, + "line": 625, "column": 53 } } @@ -146672,15 +149767,15 @@ "binop": null, "updateContext": null }, - "start": 24091, - "end": 24092, + "start": 24531, + "end": 24532, "loc": { "start": { - "line": 609, + "line": 625, "column": 53 }, "end": { - "line": 609, + "line": 625, "column": 54 } } @@ -146688,15 +149783,15 @@ { "type": "CommentLine", "value": " Set the @id and @type. If we don't already have an '@id', use the", - "start": 24098, - "end": 24166, + "start": 24538, + "end": 24606, "loc": { "start": { - "line": 611, + "line": 627, "column": 4 }, "end": { - "line": 611, + "line": 627, "column": 72 } } @@ -146704,15 +149799,15 @@ { "type": "CommentLine", "value": " fallbackIRI.", - "start": 24171, - "end": 24186, + "start": 24611, + "end": 24626, "loc": { "start": { - "line": 612, + "line": 628, "column": 4 }, "end": { - "line": 612, + "line": 628, "column": 19 } } @@ -146732,15 +149827,15 @@ "updateContext": null }, "value": "if", - "start": 24191, - "end": 24193, + "start": 24631, + "end": 24633, "loc": { "start": { - "line": 613, + "line": 629, "column": 4 }, "end": { - "line": 613, + "line": 629, "column": 6 } } @@ -146757,15 +149852,15 @@ "postfix": false, "binop": null }, - "start": 24194, - "end": 24195, + "start": 24634, + "end": 24635, "loc": { "start": { - "line": 613, + "line": 629, "column": 7 }, "end": { - "line": 613, + "line": 629, "column": 8 } } @@ -146784,15 +149879,15 @@ "updateContext": null }, "value": "!", - "start": 24195, - "end": 24196, + "start": 24635, + "end": 24636, "loc": { "start": { - "line": 613, + "line": 629, "column": 8 }, "end": { - "line": 613, + "line": 629, "column": 9 } } @@ -146810,15 +149905,15 @@ "binop": null }, "value": "has", - "start": 24196, - "end": 24199, + "start": 24636, + "end": 24639, "loc": { "start": { - "line": 613, + "line": 629, "column": 9 }, "end": { - "line": 613, + "line": 629, "column": 12 } } @@ -146835,15 +149930,15 @@ "postfix": false, "binop": null }, - "start": 24199, - "end": 24200, + "start": 24639, + "end": 24640, "loc": { "start": { - "line": 613, + "line": 629, "column": 12 }, "end": { - "line": 613, + "line": 629, "column": 13 } } @@ -146861,15 +149956,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 24200, - "end": 24216, + "start": 24640, + "end": 24656, "loc": { "start": { - "line": 613, + "line": 629, "column": 13 }, "end": { - "line": 613, + "line": 629, "column": 29 } } @@ -146887,15 +149982,15 @@ "binop": null, "updateContext": null }, - "start": 24216, - "end": 24217, + "start": 24656, + "end": 24657, "loc": { "start": { - "line": 613, + "line": 629, "column": 29 }, "end": { - "line": 613, + "line": 629, "column": 30 } } @@ -146914,15 +150009,15 @@ "updateContext": null }, "value": "@id", - "start": 24218, - "end": 24223, + "start": 24658, + "end": 24663, "loc": { "start": { - "line": 613, + "line": 629, "column": 31 }, "end": { - "line": 613, + "line": 629, "column": 36 } } @@ -146939,15 +150034,15 @@ "postfix": false, "binop": null }, - "start": 24223, - "end": 24224, + "start": 24663, + "end": 24664, "loc": { "start": { - "line": 613, + "line": 629, "column": 36 }, "end": { - "line": 613, + "line": 629, "column": 37 } } @@ -146964,15 +150059,15 @@ "postfix": false, "binop": null }, - "start": 24224, - "end": 24225, + "start": 24664, + "end": 24665, "loc": { "start": { - "line": 613, + "line": 629, "column": 37 }, "end": { - "line": 613, + "line": 629, "column": 38 } } @@ -146990,15 +150085,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 24226, - "end": 24242, + "start": 24666, + "end": 24682, "loc": { "start": { - "line": 613, + "line": 629, "column": 39 }, "end": { - "line": 613, + "line": 629, "column": 55 } } @@ -147016,15 +150111,15 @@ "binop": null, "updateContext": null }, - "start": 24242, - "end": 24243, + "start": 24682, + "end": 24683, "loc": { "start": { - "line": 613, + "line": 629, "column": 55 }, "end": { - "line": 613, + "line": 629, "column": 56 } } @@ -147043,15 +150138,15 @@ "updateContext": null }, "value": "@id", - "start": 24243, - "end": 24248, + "start": 24683, + "end": 24688, "loc": { "start": { - "line": 613, + "line": 629, "column": 56 }, "end": { - "line": 613, + "line": 629, "column": 61 } } @@ -147069,15 +150164,15 @@ "binop": null, "updateContext": null }, - "start": 24248, - "end": 24249, + "start": 24688, + "end": 24689, "loc": { "start": { - "line": 613, + "line": 629, "column": 61 }, "end": { - "line": 613, + "line": 629, "column": 62 } } @@ -147096,15 +150191,15 @@ "updateContext": null }, "value": "=", - "start": 24250, - "end": 24251, + "start": 24690, + "end": 24691, "loc": { "start": { - "line": 613, + "line": 629, "column": 63 }, "end": { - "line": 613, + "line": 629, "column": 64 } } @@ -147122,15 +150217,15 @@ "binop": null }, "value": "fallbackIRI", - "start": 24252, - "end": 24263, + "start": 24692, + "end": 24703, "loc": { "start": { - "line": 613, + "line": 629, "column": 65 }, "end": { - "line": 613, + "line": 629, "column": 76 } } @@ -147148,15 +150243,15 @@ "binop": null, "updateContext": null }, - "start": 24263, - "end": 24264, + "start": 24703, + "end": 24704, "loc": { "start": { - "line": 613, + "line": 629, "column": 76 }, "end": { - "line": 613, + "line": 629, "column": 77 } } @@ -147174,15 +150269,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 24269, - "end": 24285, + "start": 24709, + "end": 24725, "loc": { "start": { - "line": 614, + "line": 630, "column": 4 }, "end": { - "line": 614, + "line": 630, "column": 20 } } @@ -147200,15 +150295,15 @@ "binop": null, "updateContext": null }, - "start": 24285, - "end": 24286, + "start": 24725, + "end": 24726, "loc": { "start": { - "line": 614, + "line": 630, "column": 20 }, "end": { - "line": 614, + "line": 630, "column": 21 } } @@ -147227,15 +150322,15 @@ "updateContext": null }, "value": "@type", - "start": 24286, - "end": 24293, + "start": 24726, + "end": 24733, "loc": { "start": { - "line": 614, + "line": 630, "column": 21 }, "end": { - "line": 614, + "line": 630, "column": 28 } } @@ -147253,15 +150348,15 @@ "binop": null, "updateContext": null }, - "start": 24293, - "end": 24294, + "start": 24733, + "end": 24734, "loc": { "start": { - "line": 614, + "line": 630, "column": 28 }, "end": { - "line": 614, + "line": 630, "column": 29 } } @@ -147280,15 +150375,15 @@ "updateContext": null }, "value": "=", - "start": 24295, - "end": 24296, + "start": 24735, + "end": 24736, "loc": { "start": { - "line": 614, + "line": 630, "column": 30 }, "end": { - "line": 614, + "line": 630, "column": 31 } } @@ -147307,15 +150402,15 @@ "updateContext": null }, "value": "owl:Class", - "start": 24297, - "end": 24308, + "start": 24737, + "end": 24748, "loc": { "start": { - "line": 614, + "line": 630, "column": 32 }, "end": { - "line": 614, + "line": 630, "column": 43 } } @@ -147333,15 +150428,15 @@ "binop": null, "updateContext": null }, - "start": 24308, - "end": 24309, + "start": 24748, + "end": 24749, "loc": { "start": { - "line": 614, + "line": 630, "column": 43 }, "end": { - "line": 614, + "line": 630, "column": 44 } } @@ -147349,15 +150444,15 @@ { "type": "CommentLine", "value": " If we don't have a bibliographicCitation but we do have a definition source,", - "start": 24315, - "end": 24394, + "start": 24755, + "end": 24834, "loc": { "start": { - "line": 616, + "line": 632, "column": 4 }, "end": { - "line": 616, + "line": 632, "column": 83 } } @@ -147365,15 +150460,15 @@ { "type": "CommentLine", "value": " then generate a bibliographicCitation for the source.", - "start": 24399, - "end": 24455, + "start": 24839, + "end": 24895, "loc": { "start": { - "line": 617, + "line": 633, "column": 4 }, "end": { - "line": 617, + "line": 633, "column": 60 } } @@ -147393,15 +150488,15 @@ "updateContext": null }, "value": "if", - "start": 24460, - "end": 24462, + "start": 24900, + "end": 24902, "loc": { "start": { - "line": 618, + "line": 634, "column": 4 }, "end": { - "line": 618, + "line": 634, "column": 6 } } @@ -147418,15 +150513,15 @@ "postfix": false, "binop": null }, - "start": 24463, - "end": 24464, + "start": 24903, + "end": 24904, "loc": { "start": { - "line": 618, + "line": 634, "column": 7 }, "end": { - "line": 618, + "line": 634, "column": 8 } } @@ -147444,15 +150539,15 @@ "binop": null }, "value": "has", - "start": 24464, - "end": 24467, + "start": 24904, + "end": 24907, "loc": { "start": { - "line": 618, + "line": 634, "column": 8 }, "end": { - "line": 618, + "line": 634, "column": 11 } } @@ -147469,15 +150564,15 @@ "postfix": false, "binop": null }, - "start": 24467, - "end": 24468, + "start": 24907, + "end": 24908, "loc": { "start": { - "line": 618, + "line": 634, "column": 11 }, "end": { - "line": 618, + "line": 634, "column": 12 } } @@ -147495,15 +150590,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 24468, - "end": 24484, + "start": 24908, + "end": 24924, "loc": { "start": { - "line": 618, + "line": 634, "column": 12 }, "end": { - "line": 618, + "line": 634, "column": 28 } } @@ -147521,15 +150616,15 @@ "binop": null, "updateContext": null }, - "start": 24484, - "end": 24485, + "start": 24924, + "end": 24925, "loc": { "start": { - "line": 618, + "line": 634, "column": 28 }, "end": { - "line": 618, + "line": 634, "column": 29 } } @@ -147548,15 +150643,15 @@ "updateContext": null }, "value": "definitionSource", - "start": 24486, - "end": 24504, + "start": 24926, + "end": 24944, "loc": { "start": { - "line": 618, + "line": 634, "column": 30 }, "end": { - "line": 618, + "line": 634, "column": 48 } } @@ -147573,15 +150668,15 @@ "postfix": false, "binop": null }, - "start": 24504, - "end": 24505, + "start": 24944, + "end": 24945, "loc": { "start": { - "line": 618, + "line": 634, "column": 48 }, "end": { - 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This is outside our scope for the moment, so", - "start": 25617, - "end": 25680, + "start": 26057, + "end": 26120, "loc": { "start": { - "line": 644, + "line": 660, "column": 6 }, "end": { - "line": 644, + "line": 660, "column": 69 } } @@ -150154,15 +153249,15 @@ { "type": "CommentLine", "value": " we will simply pass on the phyloreference as-is.", - "start": 25687, - "end": 25738, + "start": 26127, + "end": 26178, "loc": { "start": { - "line": 645, + "line": 661, "column": 6 }, "end": { - "line": 645, + "line": 661, "column": 57 } } @@ -150182,15 +153277,15 @@ "updateContext": null }, "value": "return", - "start": 25746, - "end": 25752, + "start": 26186, + "end": 26192, "loc": { "start": { - "line": 647, + "line": 663, "column": 6 }, "end": { - "line": 647, + "line": 663, "column": 12 } } @@ -150208,15 +153303,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 25753, - "end": 25769, + "start": 26193, + "end": 26209, "loc": { "start": { - "line": 647, + "line": 663, "column": 13 }, "end": { - 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"start": 26108, - "end": 26126, + "start": 26548, + "end": 26566, "loc": { "start": { - "line": 659, + "line": 675, "column": 8 }, "end": { - "line": 659, + "line": 675, "column": 26 } } @@ -150827,15 +153922,15 @@ "updateContext": null }, "value": "=", - "start": 26127, - "end": 26128, + "start": 26567, + "end": 26568, "loc": { "start": { - "line": 659, + "line": 675, "column": 27 }, "end": { - "line": 659, + "line": 675, "column": 28 } } @@ -150853,15 +153948,15 @@ "binop": null, "updateContext": null }, - "start": 26129, - "end": 26130, + "start": 26569, + "end": 26570, "loc": { "start": { - "line": 659, + "line": 675, "column": 29 }, "end": { - "line": 659, + "line": 675, "column": 30 } } @@ -150879,15 +153974,15 @@ "binop": null, "updateContext": null }, - "start": 26130, - "end": 26131, + "start": 26570, + "end": 26571, "loc": { "start": { - "line": 659, + "line": 675, "column": 30 }, "end": { - "line": 659, + "line": 675, "column": 31 } } @@ -150905,15 +154000,15 @@ "binop": null, "updateContext": null }, - "start": 26131, - "end": 26132, + "start": 26571, + "end": 26572, "loc": { "start": { - "line": 659, + "line": 675, "column": 31 }, "end": { - "line": 659, + "line": 675, "column": 32 } } @@ -150933,15 +154028,15 @@ "updateContext": null }, "value": "if", - "start": 26138, - "end": 26140, + "start": 26578, + "end": 26580, "loc": { "start": { - "line": 661, + "line": 677, "column": 4 }, "end": { - "line": 661, + "line": 677, "column": 6 } } @@ -150958,15 +154053,15 @@ "postfix": false, "binop": null }, - "start": 26141, - "end": 26142, + "start": 26581, + "end": 26582, "loc": { "start": { - "line": 661, + "line": 677, "column": 7 }, "end": { - "line": 661, + "line": 677, "column": 8 } } @@ -150984,15 +154079,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 26142, - "end": 26160, + "start": 26582, + "end": 26600, "loc": { "start": { - "line": 661, + "line": 677, "column": 8 }, "end": { - "line": 661, + "line": 677, "column": 26 } } @@ -151010,15 +154105,15 @@ "binop": null, "updateContext": null }, - "start": 26160, - "end": 26161, + "start": 26600, + "end": 26601, "loc": { "start": { - "line": 661, + "line": 677, "column": 26 }, "end": { - "line": 661, + "line": 677, "column": 27 } } @@ -151036,15 +154131,15 @@ "binop": null }, "value": "length", - "start": 26161, - "end": 26167, + "start": 26601, + "end": 26607, "loc": { "start": { - "line": 661, + "line": 677, "column": 27 }, "end": { - "line": 661, + "line": 677, "column": 33 } } @@ -151063,15 +154158,15 @@ "updateContext": null }, "value": "===", - "start": 26168, - "end": 26171, + "start": 26608, + "end": 26611, "loc": { "start": { - "line": 661, + "line": 677, "column": 34 }, "end": { - "line": 661, + "line": 677, "column": 37 } } @@ -151090,15 +154185,15 @@ "updateContext": null }, "value": 0, - "start": 26172, - "end": 26173, + "start": 26612, + "end": 26613, "loc": { "start": { - "line": 661, + "line": 677, "column": 38 }, "end": { - "line": 661, + "line": 677, "column": 39 } } @@ -151115,15 +154210,15 @@ "postfix": false, "binop": null }, - "start": 26173, - "end": 26174, + "start": 26613, + "end": 26614, "loc": { "start": { - "line": 661, + "line": 677, "column": 39 }, "end": { - "line": 661, + "line": 677, "column": 40 } } @@ -151140,15 +154235,15 @@ "postfix": false, "binop": null }, - "start": 26175, - "end": 26176, + "start": 26615, + "end": 26616, "loc": { "start": { - "line": 661, + "line": 677, "column": 41 }, "end": { - "line": 661, + "line": 677, "column": 42 } } @@ -151156,15 +154251,15 @@ { "type": "CommentLine", "value": " We can't handle phyloreferences without at least one internal specifier.", - "start": 26183, - "end": 26258, + "start": 26623, + "end": 26698, "loc": { "start": { - "line": 662, + "line": 678, "column": 6 }, "end": { - "line": 662, + "line": 678, "column": 81 } } @@ -151182,15 +154277,15 @@ "binop": null }, "value": "calculatedPhylorefType", - "start": 26265, - "end": 26287, + "start": 26705, + "end": 26727, "loc": { "start": { - "line": 663, + "line": 679, "column": 6 }, "end": { - "line": 663, + "line": 679, "column": 28 } } @@ -151209,15 +154304,15 @@ "updateContext": null }, "value": "=", - "start": 26288, - "end": 26289, + "start": 26728, + "end": 26729, "loc": { "start": { - "line": 663, + "line": 679, "column": 29 }, "end": { - "line": 663, + "line": 679, "column": 30 } } @@ -151236,15 +154331,15 @@ "updateContext": null }, "value": "phyloref:MalformedPhyloreference", - "start": 26290, - "end": 26324, + "start": 26730, + "end": 26764, "loc": { "start": { - "line": 663, + "line": 679, "column": 31 }, "end": { - "line": 663, + "line": 679, "column": 65 } } @@ -151262,15 +154357,15 @@ "binop": null, "updateContext": null }, - "start": 26324, - "end": 26325, + "start": 26764, + "end": 26765, "loc": { "start": { - "line": 663, + "line": 679, "column": 65 }, "end": { - "line": 663, + "line": 679, "column": 66 } } @@ -151288,15 +154383,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 26332, - "end": 26348, + "start": 26772, + "end": 26788, "loc": { "start": { - "line": 664, + "line": 680, "column": 6 }, "end": { - "line": 664, + "line": 680, "column": 22 } } @@ -151314,15 +154409,15 @@ "binop": null, "updateContext": null }, - "start": 26348, - "end": 26349, + "start": 26788, + "end": 26789, "loc": { "start": { - "line": 664, + "line": 680, "column": 22 }, "end": { - "line": 664, + "line": 680, "column": 23 } } @@ -151340,15 +154435,15 @@ "binop": null }, "value": "malformedPhyloreference", - "start": 26349, - "end": 26372, + "start": 26789, + "end": 26812, "loc": { "start": { - "line": 664, + "line": 680, "column": 23 }, "end": { - "line": 664, + "line": 680, "column": 46 } } @@ -151367,15 +154462,15 @@ "updateContext": null }, "value": "=", - "start": 26373, - "end": 26374, + "start": 26813, + "end": 26814, "loc": { "start": { - "line": 664, + "line": 680, "column": 47 }, "end": { - "line": 664, + "line": 680, "column": 48 } } @@ -151394,15 +154489,15 @@ "updateContext": null }, "value": "No internal specifiers provided", - "start": 26375, - "end": 26408, + "start": 26815, + "end": 26848, "loc": { "start": { - "line": 664, + "line": 680, "column": 49 }, "end": { - "line": 664, + "line": 680, "column": 82 } } @@ -151420,15 +154515,15 @@ "binop": null, "updateContext": null }, - "start": 26408, - "end": 26409, + "start": 26848, + "end": 26849, "loc": { "start": { - "line": 664, + "line": 680, "column": 82 }, "end": { - "line": 664, + "line": 680, "column": 83 } } @@ -151445,15 +154540,15 @@ "postfix": false, "binop": null }, - "start": 26414, - "end": 26415, + "start": 26854, + "end": 26855, "loc": { "start": { - "line": 665, + "line": 681, "column": 4 }, "end": { - "line": 665, + "line": 681, "column": 5 } } @@ -151473,15 +154568,15 @@ "updateContext": null }, "value": "else", - "start": 26416, - "end": 26420, + "start": 26856, + "end": 26860, "loc": { "start": { - "line": 665, + "line": 681, "column": 6 }, "end": { - "line": 665, + "line": 681, "column": 10 } } @@ -151501,15 +154596,15 @@ "updateContext": null }, "value": "if", - "start": 26421, - "end": 26423, + "start": 26861, + "end": 26863, "loc": { "start": { - "line": 665, + "line": 681, "column": 11 }, "end": { - "line": 665, + "line": 681, "column": 13 } } @@ -151526,15 +154621,15 @@ "postfix": false, "binop": null }, - "start": 26424, - "end": 26425, + "start": 26864, + "end": 26865, "loc": { "start": { - "line": 665, + "line": 681, "column": 14 }, "end": { - "line": 665, + "line": 681, "column": 15 } } @@ -151552,15 +154647,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 26425, - "end": 26443, + "start": 26865, + "end": 26883, "loc": { "start": { - "line": 665, + "line": 681, "column": 15 }, "end": { - "line": 665, + "line": 681, "column": 33 } } @@ -151578,15 +154673,15 @@ "binop": null, "updateContext": null }, - "start": 26443, - "end": 26444, + "start": 26883, + "end": 26884, "loc": { "start": { - "line": 665, + "line": 681, "column": 33 }, "end": { - "line": 665, + "line": 681, "column": 34 } } @@ -151604,15 +154699,15 @@ "binop": null }, "value": "length", - "start": 26444, - "end": 26450, + "start": 26884, + "end": 26890, "loc": { "start": { - "line": 665, + "line": 681, "column": 34 }, "end": { - "line": 665, + "line": 681, "column": 40 } } @@ -151631,15 +154726,15 @@ "updateContext": null }, "value": ">", - "start": 26451, - "end": 26452, + "start": 26891, + "end": 26892, "loc": { "start": { - "line": 665, + "line": 681, "column": 41 }, "end": { - "line": 665, + "line": 681, "column": 42 } } @@ -151658,15 +154753,15 @@ "updateContext": null }, "value": 0, - "start": 26453, - "end": 26454, + "start": 26893, + "end": 26894, "loc": { "start": { - "line": 665, + "line": 681, "column": 43 }, "end": { - "line": 665, + "line": 681, "column": 44 } } @@ -151683,15 +154778,15 @@ "postfix": false, "binop": null }, - "start": 26454, - "end": 26455, + "start": 26894, + "end": 26895, "loc": { "start": { - "line": 665, + "line": 681, "column": 44 }, "end": { - "line": 665, + "line": 681, "column": 45 } } @@ -151708,15 +154803,15 @@ "postfix": false, "binop": null }, - "start": 26456, - "end": 26457, + "start": 26896, + "end": 26897, "loc": { "start": { - "line": 665, + "line": 681, "column": 46 }, "end": { - "line": 665, + "line": 681, "column": 47 } } @@ -151734,15 +154829,15 @@ "binop": null }, "value": "calculatedPhylorefType", - "start": 26464, - "end": 26486, + "start": 26904, + "end": 26926, "loc": { "start": { - "line": 666, + "line": 682, "column": 6 }, "end": { - "line": 666, + "line": 682, "column": 28 } } @@ -151761,15 +154856,15 @@ "updateContext": null }, "value": "=", - "start": 26487, - "end": 26488, + "start": 26927, + "end": 26928, "loc": { "start": { - "line": 666, + "line": 682, "column": 29 }, "end": { - "line": 666, + "line": 682, "column": 30 } } @@ -151788,15 +154883,15 @@ "updateContext": null }, "value": "phyloref:PhyloreferenceUsingMaximumClade", - "start": 26489, - "end": 26531, + "start": 26929, + "end": 26971, "loc": { "start": { - "line": 666, + "line": 682, "column": 31 }, "end": { - "line": 666, + "line": 682, "column": 73 } } @@ -151814,15 +154909,15 @@ "binop": null, "updateContext": null }, - "start": 26531, - "end": 26532, + "start": 26971, + "end": 26972, "loc": { "start": { - "line": 666, + "line": 682, "column": 73 }, "end": { - "line": 666, + "line": 682, "column": 74 } } @@ -151830,15 +154925,15 @@ { "type": "CommentLine", "value": " If the phyloreference has at least one external specifier, we", - "start": 26540, - "end": 26604, + "start": 26980, + "end": 27044, "loc": { "start": { - "line": 668, + "line": 684, "column": 6 }, "end": { - "line": 668, + "line": 684, "column": 70 } } @@ -151846,15 +154941,15 @@ { "type": "CommentLine", "value": " can provide a simplified expression for the internal specifier,", - "start": 26611, - "end": 26677, + "start": 27051, + "end": 27117, "loc": { "start": { - "line": 669, + "line": 685, "column": 6 }, "end": { - "line": 669, + "line": 685, "column": 72 } } @@ -151862,15 +154957,15 @@ { "type": "CommentLine", "value": " in the form:", - "start": 26684, - "end": 26699, + "start": 27124, + "end": 27139, "loc": { "start": { - "line": 670, + "line": 686, "column": 6 }, "end": { - "line": 670, + "line": 686, "column": 21 } } @@ -151878,15 +154973,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal1] and", - "start": 26706, - "end": 26751, + "start": 27146, + "end": 27191, "loc": { "start": { - "line": 671, + "line": 687, "column": 6 }, "end": { - "line": 671, + "line": 687, "column": 51 } } @@ -151894,15 +154989,15 @@ { "type": "CommentLine", "value": " phyloref:includes_TU some [internal2] and ...", - "start": 26758, - "end": 26807, + "start": 27198, + "end": 27247, "loc": { "start": { - "line": 672, + "line": 688, "column": 6 }, "end": { - "line": 672, + "line": 688, "column": 55 } } @@ -151910,15 +155005,15 @@ { "type": "CommentLine", "value": " phyloref:excludes_TU some [exclusion1] and", - "start": 26814, - "end": 26860, + "start": 27254, + "end": 27300, "loc": { "start": { - "line": 673, + "line": 689, "column": 6 }, "end": { - "line": 673, + "line": 689, "column": 52 } } @@ -151926,15 +155021,15 @@ { "type": "CommentLine", "value": " has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...", - "start": 26867, - "end": 26932, + "start": 27307, + "end": 27372, "loc": { "start": { - "line": 674, + "line": 690, "column": 6 }, "end": { - "line": 674, + "line": 690, "column": 71 } } @@ -151942,15 +155037,15 @@ { "type": "CommentLine", "value": "", - "start": 26939, - "end": 26941, + "start": 27379, + "end": 27381, "loc": { "start": { - "line": 675, + "line": 691, "column": 6 }, "end": { - "line": 675, + "line": 691, "column": 8 } } @@ -151958,15 +155053,15 @@ { "type": "CommentLine", "value": " Since we don't know which of the external specifiers will actually", - "start": 26948, - "end": 27017, + "start": 27388, + "end": 27457, "loc": { "start": { - "line": 676, + "line": 692, "column": 6 }, "end": { - "line": 676, + "line": 692, "column": 75 } } @@ -151974,15 +155069,15 @@ { "type": "CommentLine", "value": " be the one that will be used, we need to generate logical expressions", - "start": 27024, - "end": 27096, + "start": 27464, + "end": 27536, "loc": { "start": { - "line": 677, + "line": 693, "column": 6 }, "end": { - "line": 677, + "line": 693, "column": 78 } } @@ -151990,15 +155085,15 @@ { "type": "CommentLine", "value": " for every possibility.", - "start": 27103, - "end": 27128, + "start": 27543, + "end": 27568, "loc": { "start": { - "line": 678, + "line": 694, "column": 6 }, "end": { - "line": 678, + "line": 694, "column": 31 } } @@ -152016,15 +155111,15 @@ "binop": null }, "value": "logicalExpressions", - "start": 27136, - "end": 27154, + "start": 27576, + "end": 27594, "loc": { "start": { - "line": 680, + "line": 696, "column": 6 }, "end": { - "line": 680, + "line": 696, "column": 24 } } @@ -152043,15 +155138,15 @@ "updateContext": null }, "value": "=", - "start": 27155, - "end": 27156, + "start": 27595, + "end": 27596, "loc": { "start": { - "line": 680, + "line": 696, "column": 25 }, "end": { - "line": 680, + "line": 696, "column": 26 } } @@ -152069,15 +155164,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 27157, - "end": 27175, + "start": 27597, + "end": 27615, "loc": { "start": { - "line": 680, + "line": 696, "column": 27 }, "end": { - "line": 680, + "line": 696, "column": 45 } } @@ -152095,15 +155190,15 @@ "binop": null, "updateContext": null }, - "start": 27175, - "end": 27176, + "start": 27615, + "end": 27616, "loc": { "start": { - "line": 680, + "line": 696, "column": 45 }, "end": { - "line": 680, + "line": 696, "column": 46 } } @@ -152121,15 +155216,15 @@ "binop": null }, "value": "map", - "start": 27176, - "end": 27179, + "start": 27616, + "end": 27619, "loc": { "start": { - "line": 680, + "line": 696, "column": 46 }, "end": { - "line": 680, + "line": 696, "column": 49 } } @@ -152146,15 +155241,15 @@ "postfix": false, "binop": null }, - "start": 27179, - "end": 27180, + "start": 27619, + "end": 27620, "loc": { "start": { - "line": 680, + "line": 696, "column": 49 }, "end": { - "line": 680, + "line": 696, "column": 50 } } @@ -152171,15 +155266,15 @@ "postfix": false, "binop": null }, - "start": 27180, - "end": 27181, + "start": 27620, + "end": 27621, "loc": { "start": { - "line": 680, + "line": 696, "column": 50 }, "end": { - "line": 680, + "line": 696, "column": 51 } } @@ -152197,15 +155292,15 @@ "binop": null }, "value": "selectedExternal", - "start": 27181, - "end": 27197, + "start": 27621, + "end": 27637, "loc": { "start": { - "line": 680, + "line": 696, "column": 51 }, "end": { - "line": 680, + "line": 696, "column": 67 } } @@ -152222,15 +155317,15 @@ "postfix": false, "binop": null }, - "start": 27197, - "end": 27198, + "start": 27637, + "end": 27638, "loc": { "start": { - "line": 680, + "line": 696, "column": 67 }, "end": { - "line": 680, + "line": 696, "column": 68 } } @@ -152248,15 +155343,15 @@ "binop": null, "updateContext": null }, - "start": 27199, - "end": 27201, + "start": 27639, + "end": 27641, "loc": { "start": { - "line": 680, + "line": 696, "column": 69 }, "end": { - "line": 680, + "line": 696, "column": 71 } } @@ -152273,15 +155368,15 @@ "postfix": false, "binop": null }, - "start": 27202, - "end": 27203, + "start": 27642, + "end": 27643, "loc": { "start": { - "line": 680, + "line": 696, "column": 72 }, "end": { - "line": 680, + "line": 696, "column": 73 } } @@ -152289,15 +155384,15 @@ { "type": "CommentLine", "value": " Add the internal specifiers.", - "start": 27212, - "end": 27243, + "start": 27652, + "end": 27683, "loc": { "start": { - "line": 681, + "line": 697, "column": 8 }, "end": { - "line": 681, + "line": 697, "column": 39 } } @@ -152317,15 +155412,15 @@ "updateContext": null }, "value": "const", - "start": 27252, - "end": 27257, + "start": 27692, + "end": 27697, "loc": { "start": { - "line": 682, + "line": 698, "column": 8 }, "end": { - "line": 682, + "line": 698, "column": 13 } } @@ -152343,15 +155438,15 @@ "binop": null }, "value": "intersectionExprs", - "start": 27258, - "end": 27275, + "start": 27698, + "end": 27715, "loc": { "start": { - "line": 682, + "line": 698, "column": 14 }, "end": { - "line": 682, + "line": 698, "column": 31 } } @@ -152370,15 +155465,15 @@ "updateContext": null }, "value": "=", - "start": 27276, - "end": 27277, + "start": 27716, + "end": 27717, "loc": { "start": { - "line": 682, + "line": 698, "column": 32 }, "end": { - "line": 682, + "line": 698, "column": 33 } } @@ -152396,15 +155491,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 27278, - "end": 27296, + "start": 27718, + "end": 27736, "loc": { "start": { - "line": 682, + "line": 698, "column": 34 }, "end": { - "line": 682, + "line": 698, "column": 52 } } @@ -152422,15 +155517,15 @@ "binop": null, "updateContext": null }, - "start": 27296, - "end": 27297, + "start": 27736, + "end": 27737, "loc": { "start": { - "line": 682, + "line": 698, "column": 52 }, "end": { - "line": 682, + "line": 698, "column": 53 } } @@ -152448,15 +155543,15 @@ "binop": null }, "value": "map", - "start": 27297, - "end": 27300, + "start": 27737, + "end": 27740, "loc": { "start": { - "line": 682, + "line": 698, "column": 53 }, "end": { - "line": 682, + "line": 698, "column": 56 } } @@ -152473,15 +155568,15 @@ "postfix": false, "binop": null }, - "start": 27300, - "end": 27301, + "start": 27740, + "end": 27741, "loc": { "start": { - "line": 682, + "line": 698, "column": 56 }, "end": { - "line": 682, + "line": 698, "column": 57 } } @@ -152499,15 +155594,15 @@ "binop": null }, "value": "sp", - "start": 27312, - "end": 27314, + "start": 27752, + "end": 27754, "loc": { "start": { - "line": 683, + "line": 699, "column": 10 }, "end": { - "line": 683, + "line": 699, "column": 12 } } @@ -152525,15 +155620,15 @@ "binop": null, "updateContext": null }, - "start": 27315, - "end": 27317, + "start": 27755, + "end": 27757, "loc": { "start": { - "line": 683, + "line": 699, "column": 13 }, "end": { - "line": 683, + "line": 699, "column": 15 } } @@ -152553,15 +155648,15 @@ "updateContext": null }, "value": "this", - "start": 27318, - "end": 27322, + "start": 27758, + "end": 27762, "loc": { "start": { - "line": 683, + "line": 699, "column": 16 }, "end": { - "line": 683, + "line": 699, "column": 20 } } @@ -152579,15 +155674,15 @@ "binop": null, "updateContext": null }, - "start": 27322, - "end": 27323, + "start": 27762, + "end": 27763, "loc": { "start": { - "line": 683, + "line": 699, "column": 20 }, "end": { - "line": 683, + "line": 699, "column": 21 } } @@ -152605,15 +155700,15 @@ "binop": null }, "value": "getIncludesRestrictionForTU", - "start": 27323, - "end": 27350, + "start": 27763, + "end": 27790, "loc": { "start": { - "line": 683, + "line": 699, "column": 21 }, "end": { - "line": 683, + "line": 699, "column": 48 } } @@ -152630,15 +155725,15 @@ "postfix": false, "binop": null }, - "start": 27350, - "end": 27351, + "start": 27790, + "end": 27791, "loc": { "start": { - "line": 683, + "line": 699, "column": 48 }, "end": { - "line": 683, + "line": 699, "column": 49 } } @@ -152656,15 +155751,15 @@ "binop": null }, "value": "sp", - "start": 27351, - "end": 27353, + "start": 27791, + "end": 27793, "loc": { "start": { - "line": 683, + "line": 699, "column": 49 }, "end": { - "line": 683, + "line": 699, "column": 51 } } @@ -152681,15 +155776,15 @@ "postfix": false, "binop": null }, - "start": 27353, - "end": 27354, + "start": 27793, + "end": 27794, "loc": { "start": { - "line": 683, + "line": 699, "column": 51 }, "end": { - "line": 683, + "line": 699, "column": 52 } } @@ -152706,15 +155801,15 @@ "postfix": false, "binop": null }, - "start": 27363, - "end": 27364, + "start": 27803, + "end": 27804, "loc": { "start": { - "line": 684, + "line": 700, "column": 8 }, "end": { - "line": 684, + "line": 700, "column": 9 } } @@ -152732,15 +155827,15 @@ "binop": null, "updateContext": null }, - "start": 27364, - "end": 27365, + "start": 27804, + "end": 27805, "loc": { "start": { - "line": 684, + "line": 700, "column": 9 }, "end": { - "line": 684, + "line": 700, "column": 10 } } @@ -152748,15 +155843,15 @@ { "type": "CommentLine", "value": " Add the selected external specifier.", - "start": 27375, - "end": 27414, + "start": 27815, + "end": 27854, "loc": { "start": { - "line": 686, + "line": 702, "column": 8 }, "end": { - "line": 686, + "line": 702, "column": 47 } } @@ -152774,15 +155869,15 @@ "binop": null }, "value": "intersectionExprs", - "start": 27423, - "end": 27440, + "start": 27863, + "end": 27880, "loc": { "start": { - "line": 687, + "line": 703, "column": 8 }, "end": { - "line": 687, + "line": 703, "column": 25 } } @@ -152800,15 +155895,15 @@ "binop": null, "updateContext": null }, - "start": 27440, - "end": 27441, + "start": 27880, + "end": 27881, "loc": { "start": { - 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"line": 694, + "line": 710, "column": 10 }, "end": { - "line": 694, + "line": 710, "column": 11 } } @@ -153545,15 +156640,15 @@ { "type": "CommentLine", "value": " Collect all of the externals that are not selected.", - "start": 27698, - "end": 27752, + "start": 28138, + "end": 28192, "loc": { "start": { - "line": 696, + "line": 712, "column": 8 }, "end": { - "line": 696, + "line": 712, "column": 62 } } @@ -153573,15 +156668,15 @@ "updateContext": null }, "value": "const", - "start": 27761, - "end": 27766, + "start": 28201, + "end": 28206, "loc": { "start": { - "line": 697, + "line": 713, "column": 8 }, "end": { - "line": 697, + "line": 713, "column": 13 } } @@ -153599,15 +156694,15 @@ "binop": null }, "value": "remainingExternals", - "start": 27767, - "end": 27785, + "start": 28207, + "end": 28225, "loc": { "start": { - "line": 697, + "line": 713, "column": 14 }, "end": { - "line": 697, + "line": 713, "column": 32 } } @@ -153626,15 +156721,15 @@ "updateContext": null }, "value": "=", - 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"start": 27977, - "end": 27984, + "start": 28417, + "end": 28424, "loc": { "start": { - "line": 701, + "line": 717, "column": 27 }, "end": { - "line": 701, + "line": 717, "column": 34 } } @@ -154046,15 +157141,15 @@ "postfix": false, "binop": null }, - "start": 27984, - "end": 27985, + "start": 28424, + "end": 28425, "loc": { "start": { - "line": 701, + "line": 717, "column": 34 }, "end": { - "line": 701, + "line": 717, "column": 35 } } @@ -154071,15 +157166,15 @@ "postfix": false, "binop": null }, - "start": 27985, - "end": 27986, + "start": 28425, + "end": 28426, "loc": { "start": { - "line": 701, + "line": 717, "column": 35 }, "end": { - "line": 701, + "line": 717, "column": 36 } } @@ -154097,15 +157192,15 @@ "binop": null }, "value": "externalTU", - "start": 27986, - "end": 27996, + "start": 28426, + "end": 28436, "loc": { "start": { - "line": 701, + "line": 717, "column": 36 }, "end": { - "line": 701, + "line": 717, "column": 46 } } @@ -154122,15 +157217,15 @@ "postfix": false, "binop": null }, - "start": 27996, - "end": 27997, + "start": 28436, + "end": 28437, "loc": { "start": { - "line": 701, + "line": 717, "column": 46 }, "end": { - "line": 701, + "line": 717, "column": 47 } } @@ -154148,15 +157243,15 @@ "binop": null, "updateContext": null }, - "start": 27998, - "end": 28000, + "start": 28438, + "end": 28440, "loc": { "start": { - "line": 701, + "line": 717, "column": 48 }, "end": { - "line": 701, + "line": 717, "column": 50 } } @@ -154173,15 +157268,15 @@ "postfix": false, "binop": null }, - "start": 28001, - "end": 28002, + "start": 28441, + "end": 28442, "loc": { "start": { - "line": 701, + "line": 717, "column": 51 }, "end": { - "line": 701, + "line": 717, "column": 52 } } @@ -154199,15 +157294,15 @@ "binop": null }, "value": "intersectionExprs", - "start": 28013, - "end": 28030, + "start": 28453, + "end": 28470, "loc": { "start": { - "line": 702, + "line": 718, "column": 10 }, "end": { - "line": 702, + "line": 718, "column": 27 } } @@ -154225,15 +157320,15 @@ "binop": null, "updateContext": null }, - "start": 28030, - "end": 28031, + "start": 28470, + "end": 28471, "loc": { "start": { - "line": 702, + "line": 718, "column": 27 }, "end": { - "line": 702, + "line": 718, "column": 28 } } @@ -154251,15 +157346,15 @@ "binop": null }, "value": "push", - "start": 28031, - "end": 28035, + "start": 28471, + "end": 28475, "loc": { "start": { - "line": 702, + "line": 718, "column": 28 }, "end": { - "line": 702, + "line": 718, "column": 32 } } @@ -154276,15 +157371,15 @@ "postfix": false, "binop": null }, - "start": 28035, - "end": 28036, + "start": 28475, + "end": 28476, "loc": { "start": { - "line": 702, + "line": 718, "column": 32 }, "end": { - "line": 702, + "line": 718, "column": 33 } } @@ -154301,15 +157396,15 @@ "postfix": false, "binop": null }, - "start": 28036, - "end": 28037, + "start": 28476, + "end": 28477, "loc": { "start": { - "line": 702, + "line": 718, "column": 33 }, "end": { - "line": 702, + "line": 718, "column": 34 } } @@ -154328,15 +157423,15 @@ "updateContext": null }, "value": "@type", - 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We therefore need to use the algorithm in", - "start": 28667, - "end": 28745, + "start": 29107, + "end": 29185, "loc": { "start": { - "line": 724, + "line": 740, "column": 6 }, "end": { - "line": 724, + "line": 740, "column": 84 } } @@ -155991,15 +159086,15 @@ { "type": "CommentLine", "value": " this.createClassExpressionsForInternals() to create this expression.", - "start": 28752, - "end": 28823, + "start": 29192, + "end": 29263, "loc": { "start": { - "line": 725, + "line": 741, "column": 6 }, "end": { - "line": 725, + "line": 741, "column": 77 } } @@ -156017,15 +159112,15 @@ "binop": null }, "value": "logicalExpressions", - "start": 28830, - "end": 28848, + "start": 29270, + "end": 29288, "loc": { "start": { - "line": 726, + "line": 742, "column": 6 }, "end": { - "line": 726, + "line": 742, "column": 24 } } @@ -156044,15 +159139,15 @@ "updateContext": null }, "value": "=", - "start": 28849, - "end": 28850, + "start": 29289, + "end": 29290, "loc": { "start": { - "line": 726, + "line": 742, "column": 25 }, "end": { - "line": 726, + "line": 742, "column": 26 } } @@ -156072,15 +159167,15 @@ "updateContext": null }, "value": "this", - "start": 28851, - "end": 28855, + "start": 29291, + "end": 29295, "loc": { "start": { - "line": 726, + "line": 742, "column": 27 }, "end": { - "line": 726, + "line": 742, "column": 31 } } @@ -156098,15 +159193,15 @@ "binop": null, "updateContext": null }, - "start": 28855, - "end": 28856, + "start": 29295, + "end": 29296, "loc": { "start": { - "line": 726, + "line": 742, "column": 31 }, "end": { - "line": 726, + "line": 742, "column": 32 } } @@ -156124,15 +159219,15 @@ "binop": null }, "value": "createClassExpressionsForInternals", - "start": 28856, - "end": 28890, + "start": 29296, + "end": 29330, "loc": { "start": { - "line": 726, + "line": 742, "column": 32 }, "end": { - "line": 726, + "line": 742, "column": 66 } } @@ -156149,15 +159244,15 @@ "postfix": false, "binop": null }, - "start": 28890, - "end": 28891, + "start": 29330, + "end": 29331, "loc": { "start": { - "line": 726, + "line": 742, "column": 66 }, "end": { - "line": 726, + "line": 742, "column": 67 } } @@ -156175,15 +159270,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 28900, - "end": 28916, + "start": 29340, + "end": 29356, "loc": { "start": { - "line": 727, + "line": 743, "column": 8 }, "end": { - "line": 727, + "line": 743, "column": 24 } } @@ -156201,15 +159296,15 @@ "binop": null, "updateContext": null }, - "start": 28916, - "end": 28917, + "start": 29356, + "end": 29357, "loc": { "start": { - "line": 727, + "line": 743, "column": 24 }, "end": { - "line": 727, + "line": 743, "column": 25 } } @@ -156227,15 +159322,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 28918, - "end": 28936, + "start": 29358, + "end": 29376, "loc": { "start": { - "line": 727, + "line": 743, "column": 26 }, "end": { - "line": 727, + "line": 743, "column": 44 } } @@ -156253,15 +159348,15 @@ "binop": null, "updateContext": null }, - "start": 28936, - "end": 28937, + "start": 29376, + "end": 29377, "loc": { "start": { - "line": 727, + "line": 743, "column": 44 }, "end": { - "line": 727, + "line": 743, "column": 45 } } @@ -156279,15 +159374,15 @@ "binop": null, "updateContext": null }, - "start": 28938, - "end": 28939, + "start": 29378, + "end": 29379, "loc": { "start": { - "line": 727, + "line": 743, "column": 46 }, "end": { - "line": 727, + "line": 743, "column": 47 } } @@ -156305,15 +159400,15 @@ "binop": null, "updateContext": null }, - "start": 28939, - "end": 28940, + "start": 29379, + "end": 29380, "loc": { "start": { - "line": 727, + "line": 743, "column": 47 }, "end": { - "line": 727, + "line": 743, "column": 48 } } @@ -156330,15 +159425,15 @@ "postfix": false, "binop": null }, - "start": 28947, - "end": 28948, + "start": 29387, + "end": 29388, "loc": { "start": { - "line": 728, + "line": 744, "column": 6 }, "end": { - "line": 728, + "line": 744, "column": 7 } } @@ -156356,15 +159451,15 @@ "binop": null, "updateContext": null }, - "start": 28948, - "end": 28949, + "start": 29388, + "end": 29389, "loc": { "start": { - "line": 728, + "line": 744, "column": 7 }, "end": { - "line": 728, + "line": 744, "column": 8 } } @@ -156381,15 +159476,15 @@ "postfix": false, "binop": null }, - "start": 28954, - "end": 28955, + "start": 29394, + "end": 29395, "loc": { "start": { - "line": 729, + "line": 745, "column": 4 }, "end": { - "line": 729, + "line": 745, "column": 5 } } @@ -156397,15 +159492,15 @@ { "type": "CommentLine", "value": " If we have a single logical expression, we set that as an equivalentClass", - "start": 28961, - "end": 29037, + "start": 29401, + "end": 29477, "loc": { "start": { - "line": 731, + "line": 747, "column": 4 }, "end": { - "line": 731, + "line": 747, "column": 80 } } @@ -156413,15 +159508,15 @@ { "type": "CommentLine", "value": " expression. If we have more than one, we produce multiple component classes", - "start": 29042, - "end": 29120, + "start": 29482, + "end": 29560, "loc": { "start": { - "line": 732, + "line": 748, "column": 4 }, "end": { - "line": 732, + "line": 748, "column": 82 } } @@ -156429,15 +159524,15 @@ { "type": "CommentLine", "value": " to represent it.", - "start": 29125, - "end": 29144, + "start": 29565, + "end": 29584, "loc": { "start": { - "line": 733, + "line": 749, "column": 4 }, "end": { - "line": 733, + "line": 749, "column": 23 } } @@ -156457,15 +159552,15 @@ "updateContext": null }, "value": "if", - "start": 29149, - "end": 29151, + "start": 29589, + "end": 29591, "loc": { "start": { - "line": 734, + "line": 750, "column": 4 }, "end": { - "line": 734, + "line": 750, "column": 6 } } @@ -156482,15 +159577,15 @@ "postfix": false, "binop": null }, - "start": 29152, - "end": 29153, + "start": 29592, + "end": 29593, "loc": { "start": { - "line": 734, + "line": 750, "column": 7 }, "end": { - "line": 734, + "line": 750, "column": 8 } } @@ -156508,15 +159603,15 @@ "binop": null }, "value": "logicalExpressions", - "start": 29153, - "end": 29171, + "start": 29593, + "end": 29611, "loc": { "start": { - "line": 734, + "line": 750, "column": 8 }, "end": { - "line": 734, + "line": 750, "column": 26 } } @@ -156534,15 +159629,15 @@ "binop": null, "updateContext": null }, - "start": 29171, - "end": 29172, + "start": 29611, + "end": 29612, "loc": { "start": { - "line": 734, + "line": 750, "column": 26 }, "end": { - "line": 734, + "line": 750, "column": 27 } } @@ -156560,15 +159655,15 @@ "binop": null }, "value": "length", - "start": 29172, - "end": 29178, + "start": 29612, + "end": 29618, "loc": { "start": { - "line": 734, + "line": 750, "column": 27 }, "end": { - "line": 734, + "line": 750, "column": 33 } } @@ -156587,15 +159682,15 @@ "updateContext": null }, "value": "===", - "start": 29179, - "end": 29182, + "start": 29619, + "end": 29622, "loc": { "start": { - "line": 734, + "line": 750, "column": 34 }, "end": { - "line": 734, + "line": 750, "column": 37 } } @@ -156614,15 +159709,15 @@ "updateContext": null }, "value": 0, - "start": 29183, - "end": 29184, + "start": 29623, + "end": 29624, "loc": { "start": { - "line": 734, + "line": 750, "column": 38 }, "end": { - "line": 734, + "line": 750, "column": 39 } } @@ -156639,15 +159734,15 @@ "postfix": false, "binop": null }, - "start": 29184, - "end": 29185, + "start": 29624, + "end": 29625, "loc": { "start": { - "line": 734, + "line": 750, "column": 39 }, "end": { - "line": 734, + "line": 750, "column": 40 } } @@ -156664,15 +159759,15 @@ "postfix": false, "binop": null }, - "start": 29186, - "end": 29187, + "start": 29626, + "end": 29627, "loc": { "start": { - "line": 734, + "line": 750, "column": 41 }, "end": { - "line": 734, + "line": 750, "column": 42 } } @@ -156680,15 +159775,15 @@ { "type": "CommentLine", "value": " This is fine, as long as there is an explanation in", - "start": 29194, - "end": 29248, + "start": 29634, + "end": 29688, "loc": { "start": { - "line": 735, + "line": 751, "column": 6 }, "end": { - "line": 735, + "line": 751, "column": 60 } } @@ -156696,15 +159791,15 @@ { "type": "CommentLine", "value": " phyloref.malformedPhyloreference explaining why no logical expressions", - "start": 29255, - "end": 29328, + "start": 29695, + "end": 29768, "loc": { "start": { - "line": 736, + "line": 752, "column": 6 }, "end": { - "line": 736, + "line": 752, "column": 79 } } @@ -156712,15 +159807,15 @@ { "type": "CommentLine", "value": " could be generated. Otherwise, throw an error.", - "start": 29335, - "end": 29384, + "start": 29775, + "end": 29824, "loc": { "start": { - "line": 737, + "line": 753, "column": 6 }, "end": { - "line": 737, + "line": 753, "column": 55 } } @@ -156740,15 +159835,15 @@ "updateContext": null }, "value": "if", - "start": 29391, - "end": 29393, + "start": 29831, + "end": 29833, "loc": { "start": { - "line": 738, + "line": 754, "column": 6 }, "end": { - "line": 738, + "line": 754, "column": 8 } } @@ -156765,15 +159860,15 @@ "postfix": false, "binop": null }, - "start": 29394, - "end": 29395, + "start": 29834, + "end": 29835, "loc": { "start": { - "line": 738, + "line": 754, "column": 9 }, "end": { - "line": 738, + "line": 754, "column": 10 } } @@ -156792,15 +159887,15 @@ "updateContext": null }, "value": "!", - "start": 29395, - "end": 29396, + "start": 29835, + "end": 29836, "loc": { "start": { - "line": 738, + "line": 754, "column": 10 }, "end": { - "line": 738, + "line": 754, "column": 11 } } @@ -156818,15 +159913,15 @@ "binop": null }, "value": "has", - 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"start": 29483, - "end": 29484, + "start": 29923, + "end": 29924, "loc": { "start": { - "line": 740, + "line": 756, "column": 10 }, "end": { - "line": 740, + "line": 756, "column": 11 } } @@ -157156,15 +160251,15 @@ "updateContext": null }, "value": "Phyloref ", - "start": 29484, - "end": 29493, + "start": 29924, + "end": 29933, "loc": { "start": { - "line": 740, + "line": 756, "column": 11 }, "end": { - "line": 740, + "line": 756, "column": 20 } } @@ -157181,15 +160276,15 @@ "postfix": false, "binop": null }, - "start": 29493, - "end": 29495, + "start": 29933, + "end": 29935, "loc": { "start": { - "line": 740, + "line": 756, "column": 20 }, "end": { - "line": 740, + "line": 756, "column": 22 } } @@ -157209,15 +160304,15 @@ "updateContext": null }, "value": "this", - "start": 29495, - "end": 29499, + "start": 29935, + "end": 29939, "loc": { "start": { - "line": 740, + "line": 756, "column": 22 }, "end": { - "line": 740, + "line": 756, "column": 26 } } @@ -157235,15 +160330,15 @@ "binop": null, "updateContext": null }, - "start": 29499, - "end": 29500, + "start": 29939, + "end": 29940, "loc": { "start": { - "line": 740, + "line": 756, "column": 26 }, "end": { - "line": 740, + "line": 756, "column": 27 } } @@ -157261,15 +160356,15 @@ "binop": null }, "value": "label", - "start": 29500, - "end": 29505, + "start": 29940, + "end": 29945, "loc": { "start": { - "line": 740, + "line": 756, "column": 27 }, "end": { - "line": 740, + "line": 756, "column": 32 } } @@ -157286,15 +160381,15 @@ "postfix": false, "binop": null }, - "start": 29505, - "end": 29506, + "start": 29945, + "end": 29946, "loc": { "start": { - "line": 740, + "line": 756, "column": 32 }, "end": { - "line": 740, + "line": 756, "column": 33 } } @@ -157313,15 +160408,15 @@ "updateContext": null }, "value": " was generated by Phyx.js with neither logical expressions nor an explanation for the lack of logical expressions. ", - "start": 29506, - "end": 29621, + "start": 29946, + "end": 30061, "loc": { "start": { - "line": 740, + "line": 756, "column": 33 }, "end": { - "line": 740, + "line": 756, "column": 148 } } @@ -157338,15 +160433,15 @@ "postfix": false, "binop": null }, - "start": 29621, - "end": 29622, + "start": 30061, + "end": 30062, "loc": { "start": { - "line": 740, + "line": 756, "column": 148 }, "end": { - "line": 740, + "line": 756, "column": 149 } } @@ -157365,15 +160460,15 @@ "updateContext": null }, "value": "+", - "start": 29633, - "end": 29634, + "start": 30073, + "end": 30074, "loc": { "start": { - "line": 741, + "line": 757, "column": 10 }, "end": { - "line": 741, + "line": 757, "column": 11 } } @@ -157392,15 +160487,15 @@ "updateContext": null }, "value": "This indicates an error in the Phyx.js library. Please report this bug at https://github.com/phyloref/phyx.js/issues.", - "start": 29635, - "end": 29754, + "start": 30075, + "end": 30194, "loc": { "start": { - "line": 741, + "line": 757, "column": 12 }, "end": { - "line": 741, + "line": 757, "column": 131 } } @@ -157417,15 +160512,15 @@ "postfix": false, "binop": null }, - "start": 29763, - "end": 29764, + "start": 30203, + "end": 30204, "loc": { "start": { - "line": 742, + "line": 758, "column": 8 }, "end": { - "line": 742, + "line": 758, "column": 9 } } @@ -157443,15 +160538,15 @@ "binop": null, "updateContext": null }, - "start": 29764, - "end": 29765, + "start": 30204, + "end": 30205, "loc": { "start": { - "line": 742, + "line": 758, "column": 9 }, "end": { - "line": 742, + "line": 758, "column": 10 } } @@ -157468,15 +160563,15 @@ "postfix": false, "binop": null }, - "start": 29772, - "end": 29773, + "start": 30212, + "end": 30213, "loc": { "start": { - "line": 743, + "line": 759, "column": 6 }, "end": { - "line": 743, + "line": 759, "column": 7 } } @@ -157493,15 +160588,15 @@ "postfix": false, "binop": null }, - "start": 29778, - "end": 29779, + "start": 30218, + "end": 30219, "loc": { "start": { - "line": 744, + "line": 760, "column": 4 }, "end": { - "line": 744, + "line": 760, "column": 5 } } @@ -157521,15 +160616,15 @@ "updateContext": null }, "value": "else", - "start": 29780, - "end": 29784, + "start": 30220, + "end": 30224, "loc": { "start": { - "line": 744, + "line": 760, "column": 6 }, "end": { - "line": 744, + "line": 760, "column": 10 } } @@ -157549,15 +160644,15 @@ "updateContext": null }, "value": "if", - "start": 29785, - "end": 29787, + "start": 30225, + "end": 30227, "loc": { "start": { - "line": 744, + "line": 760, "column": 11 }, "end": { - "line": 744, + "line": 760, "column": 13 } } @@ -157574,15 +160669,15 @@ "postfix": false, "binop": null }, - "start": 29788, - "end": 29789, + "start": 30228, + "end": 30229, "loc": { "start": { - "line": 744, + "line": 760, "column": 14 }, "end": { - "line": 744, + "line": 760, "column": 15 } } @@ -157600,15 +160695,15 @@ "binop": null }, "value": "logicalExpressions", - 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We model this by creating subclasses of", - "start": 30091, - "end": 30161, + "start": 30531, + "end": 30601, "loc": { "start": { - "line": 750, + "line": 766, "column": 6 }, "end": { - "line": 750, + "line": 766, "column": 76 } } @@ -158150,15 +161245,15 @@ { "type": "CommentLine", "value": " the phyloreference for each logical expression -- that way, it's clear", - "start": 30168, - "end": 30241, + "start": 30608, + "end": 30681, "loc": { "start": { - "line": 751, + "line": 767, "column": 6 }, "end": { - "line": 751, + "line": 767, "column": 79 } } @@ -158166,15 +161261,15 @@ { "type": "CommentLine", "value": " that these expressions aren't equivalent to each other (which is what", - "start": 30248, - "end": 30320, + "start": 30688, + "end": 30760, "loc": { "start": { - "line": 752, + "line": 768, "column": 6 }, "end": { - "line": 752, + "line": 768, "column": 78 } } @@ -158182,15 +161277,15 @@ { "type": "CommentLine", "value": " caused https://github.com/phyloref/phyx.js/issues/57), but nodes", - "start": 30327, - "end": 30394, + "start": 30767, + "end": 30834, "loc": { "start": { - "line": 753, + "line": 769, "column": 6 }, "end": { - "line": 753, + "line": 769, "column": 73 } } @@ -158198,15 +161293,15 @@ { "type": "CommentLine", "value": " resolved by any of those expressions will also be included in the", - "start": 30401, - "end": 30469, + "start": 30841, + "end": 30909, "loc": { "start": { - "line": 754, + "line": 770, "column": 6 }, "end": { - "line": 754, + "line": 770, "column": 74 } } @@ -158214,15 +161309,15 @@ { "type": "CommentLine", "value": " phyloreference itself.", - "start": 30476, - "end": 30501, + "start": 30916, + "end": 30941, "loc": { "start": { - "line": 755, + "line": 771, "column": 6 }, "end": { - "line": 755, + "line": 771, "column": 31 } } @@ -158230,15 +161325,15 @@ { "type": "CommentLine", "value": "", - "start": 30508, - "end": 30510, + "start": 30948, + "end": 30950, "loc": { "start": { - "line": 756, + "line": 772, "column": 6 }, "end": { - "line": 756, + "line": 772, "column": 8 } } @@ -158246,15 +161341,15 @@ { "type": "CommentLine", "value": " Note that there are two differences from the way in which we usually call", - "start": 30517, - "end": 30593, + "start": 30957, + "end": 31033, "loc": { "start": { - "line": 757, + "line": 773, "column": 6 }, "end": { - "line": 757, + "line": 773, "column": 82 } } @@ -158262,15 +161357,15 @@ { "type": "CommentLine", "value": " this.createComponentClass():", - "start": 30600, - "end": 30631, + "start": 31040, + "end": 31071, "loc": { "start": { - "line": 758, + "line": 774, "column": 6 }, "end": { - "line": 758, + "line": 774, "column": 37 } } @@ -158278,15 +161373,15 @@ { "type": "CommentLine", "value": " 1. Usually, createComponentClass() reuses logical expressions with the", - "start": 30638, - "end": 30712, + "start": 31078, + "end": 31152, "loc": { "start": { - "line": 759, + "line": 775, "column": 6 }, "end": { - "line": 759, + "line": 775, "column": 80 } } @@ -158294,15 +161389,15 @@ { "type": "CommentLine", "value": " same sets of internal and external specifiers. That won't work here,", - "start": 30719, - "end": 30794, + "start": 31159, + "end": 31234, "loc": { "start": { - "line": 760, + "line": 776, "column": 6 }, "end": { - "line": 760, + "line": 776, "column": 81 } } @@ -158310,15 +161405,15 @@ { "type": "CommentLine", "value": " since *all* these logical expressions have the same specifiers. So,", - "start": 30801, - "end": 30875, + "start": 31241, + "end": 31315, "loc": { "start": { - "line": 761, + "line": 777, "column": 6 }, "end": { - "line": 761, + "line": 777, "column": 80 } } @@ -158326,15 +161421,15 @@ { "type": "CommentLine", "value": " we turn off caching.", - "start": 30882, - "end": 30909, + "start": 31322, + "end": 31349, "loc": { "start": { - "line": 762, + "line": 778, "column": 6 }, "end": { - "line": 762, + "line": 778, "column": 33 } } @@ -158342,15 +161437,15 @@ { "type": "CommentLine", "value": " 2. We need to set each of these component classes to be a subclass of", - "start": 30916, - "end": 30989, + "start": 31356, + "end": 31429, "loc": { "start": { - "line": 763, + "line": 779, "column": 6 }, "end": { - "line": 763, + "line": 779, "column": 79 } } @@ -158358,15 +161453,15 @@ { "type": "CommentLine", "value": " this phyloreference so that it can include instances from each of the", - "start": 30996, - "end": 31072, + "start": 31436, + "end": 31512, "loc": { "start": { - "line": 764, + "line": 780, "column": 6 }, "end": { - "line": 764, + "line": 780, "column": 82 } } @@ -158374,15 +161469,15 @@ { "type": "CommentLine", "value": " logical expressions.", - "start": 31079, - "end": 31106, + "start": 31519, + "end": 31546, "loc": { "start": { - "line": 765, + "line": 781, "column": 6 }, "end": { - "line": 765, + "line": 781, "column": 33 } } @@ -158400,15 +161495,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 31113, - "end": 31129, + "start": 31553, + "end": 31569, "loc": { "start": { - 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"line": 766, + "line": 782, "column": 77 }, "end": { - "line": 766, + "line": 782, "column": 97 } } @@ -158739,15 +161834,15 @@ "postfix": false, "binop": null }, - "start": 31204, - "end": 31205, + "start": 31644, + "end": 31645, "loc": { "start": { - "line": 766, + "line": 782, "column": 97 }, "end": { - "line": 766, + "line": 782, "column": 98 } } @@ -158765,15 +161860,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 31214, - "end": 31230, + "start": 31654, + "end": 31670, "loc": { "start": { - "line": 767, + "line": 783, "column": 8 }, "end": { - "line": 767, + "line": 783, "column": 24 } } @@ -158791,15 +161886,15 @@ "binop": null, "updateContext": null }, - "start": 31230, - "end": 31231, + "start": 31670, + "end": 31671, "loc": { "start": { - "line": 767, + "line": 783, "column": 24 }, "end": { - "line": 767, + "line": 783, "column": 25 } } @@ -158817,15 +161912,15 @@ "binop": null }, "value": "internalSpecifiers", - "start": 31240, - "end": 31258, + "start": 31680, + "end": 31698, "loc": { "start": { - "line": 768, + "line": 784, "column": 8 }, "end": { - "line": 768, + "line": 784, "column": 26 } } @@ -158843,15 +161938,15 @@ "binop": null, "updateContext": null }, - "start": 31258, - "end": 31259, + "start": 31698, + "end": 31699, "loc": { "start": { - "line": 768, + "line": 784, "column": 26 }, "end": { - "line": 768, + "line": 784, "column": 27 } } @@ -158869,15 +161964,15 @@ "binop": null }, "value": "externalSpecifiers", - "start": 31268, - "end": 31286, + "start": 31708, + "end": 31726, "loc": { "start": { - "line": 769, + "line": 785, "column": 8 }, "end": { - "line": 769, + "line": 785, "column": 26 } } @@ -158895,15 +161990,15 @@ "binop": null, "updateContext": null }, - "start": 31286, - "end": 31287, + "start": 31726, + "end": 31727, "loc": { "start": { - "line": 769, + "line": 785, "column": 26 }, "end": { - "line": 769, + "line": 785, "column": 27 } } @@ -158921,15 +162016,15 @@ "binop": null }, "value": "classExpr", - "start": 31296, - "end": 31305, + "start": 31736, + "end": 31745, "loc": { "start": { - 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"start": 32042, - "end": 32054, + "start": 32482, + "end": 32494, "loc": { "start": { - "line": 787, + "line": 803, "column": 66 }, "end": { - "line": 787, + "line": 803, "column": 78 } } @@ -160769,15 +163864,15 @@ "updateContext": null }, "value": "!==", - "start": 32055, - "end": 32058, + "start": 32495, + "end": 32498, "loc": { "start": { - "line": 787, + "line": 803, "column": 79 }, "end": { - "line": 787, + "line": 803, "column": 82 } } @@ -160795,15 +163890,15 @@ "binop": null }, "value": "calculatedPhylorefType", - "start": 32059, - "end": 32081, + "start": 32499, + "end": 32521, "loc": { "start": { - "line": 787, + "line": 803, "column": 83 }, "end": { - "line": 787, + "line": 803, "column": 105 } } @@ -160820,15 +163915,15 @@ "postfix": false, "binop": null }, - "start": 32081, - "end": 32082, + "start": 32521, + "end": 32522, "loc": { "start": { - "line": 787, + "line": 803, "column": 105 }, "end": { - "line": 787, + "line": 803, "column": 106 } } @@ -160845,15 +163940,15 @@ "postfix": false, "binop": null }, - "start": 32083, - "end": 32084, + "start": 32523, + "end": 32524, "loc": { "start": { - "line": 787, + "line": 803, "column": 107 }, "end": { - "line": 787, + "line": 803, "column": 108 } } @@ -160873,15 +163968,15 @@ "updateContext": null }, "value": "throw", - "start": 32091, - "end": 32096, + "start": 32531, + "end": 32536, "loc": { "start": { - "line": 788, + "line": 804, "column": 6 }, "end": { - "line": 788, + "line": 804, "column": 11 } } @@ -160901,15 +163996,15 @@ "updateContext": null }, "value": "new", - "start": 32097, - "end": 32100, + "start": 32537, + "end": 32540, "loc": { "start": { - "line": 788, + "line": 804, "column": 12 }, "end": { - "line": 788, + "line": 804, "column": 15 } } @@ -160927,15 +164022,15 @@ "binop": null }, "value": "Error", - "start": 32101, - "end": 32106, + "start": 32541, + "end": 32546, "loc": { "start": { - "line": 788, + "line": 804, "column": 16 }, "end": { - "line": 788, + "line": 804, "column": 21 } } @@ -160952,15 +164047,15 @@ "postfix": false, "binop": null }, - "start": 32106, - "end": 32107, + "start": 32546, + "end": 32547, "loc": { "start": { - "line": 788, + "line": 804, "column": 21 }, "end": { - "line": 788, + "line": 804, "column": 22 } } @@ -160977,15 +164072,15 @@ "postfix": false, "binop": null }, - "start": 32116, - "end": 32117, + "start": 32556, + "end": 32557, "loc": { "start": { - "line": 789, + "line": 805, "column": 8 }, "end": { - "line": 789, + "line": 805, "column": 9 } } @@ -161004,15 +164099,15 @@ "updateContext": null }, "value": "Phyloref ", - "start": 32117, - "end": 32126, + "start": 32557, + "end": 32566, "loc": { "start": { - "line": 789, + "line": 805, "column": 9 }, "end": { - "line": 789, + "line": 805, "column": 18 } } @@ -161029,15 +164124,15 @@ "postfix": false, "binop": null }, - "start": 32126, - "end": 32128, + "start": 32566, + "end": 32568, "loc": { "start": { - "line": 789, + "line": 805, "column": 18 }, "end": { - "line": 789, + "line": 805, "column": 20 } } @@ -161057,15 +164152,15 @@ "updateContext": null }, "value": "this", - "start": 32128, - "end": 32132, + "start": 32568, + "end": 32572, "loc": { "start": { - "line": 789, + "line": 805, "column": 20 }, "end": { - "line": 789, + "line": 805, "column": 24 } } @@ -161083,15 +164178,15 @@ "binop": null, "updateContext": null }, - "start": 32132, - "end": 32133, + "start": 32572, + "end": 32573, "loc": { "start": { - "line": 789, + "line": 805, "column": 24 }, "end": { - "line": 789, + "line": 805, "column": 25 } } @@ -161109,15 +164204,15 @@ "binop": null }, "value": "label", - "start": 32133, - "end": 32138, + "start": 32573, + "end": 32578, "loc": { "start": { - "line": 789, + "line": 805, "column": 25 }, "end": { - "line": 789, + "line": 805, "column": 30 } } @@ -161134,15 +164229,15 @@ "postfix": false, "binop": null }, - "start": 32138, - "end": 32139, + "start": 32578, + "end": 32579, "loc": { "start": { - "line": 789, + "line": 805, "column": 30 }, "end": { - "line": 789, + "line": 805, "column": 31 } } @@ -161161,15 +164256,15 @@ "updateContext": null }, "value": " has phylorefType set to '", - "start": 32139, - "end": 32165, + "start": 32579, + "end": 32605, "loc": { "start": { - "line": 789, + "line": 805, "column": 31 }, "end": { - "line": 789, + "line": 805, "column": 57 } } @@ -161186,15 +164281,15 @@ "postfix": false, "binop": null }, - "start": 32165, - "end": 32167, + "start": 32605, + "end": 32607, "loc": { "start": { - "line": 789, + "line": 805, "column": 57 }, "end": { - "line": 789, + "line": 805, "column": 59 } } @@ -161212,15 +164307,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 32167, - "end": 32183, + "start": 32607, + "end": 32623, "loc": { "start": { - "line": 789, + "line": 805, "column": 59 }, "end": { - "line": 789, + "line": 805, "column": 75 } } @@ -161238,15 +164333,15 @@ "binop": null, "updateContext": null }, - "start": 32183, - "end": 32184, + "start": 32623, + "end": 32624, "loc": { "start": { - "line": 789, + "line": 805, "column": 75 }, "end": { - "line": 789, + "line": 805, "column": 76 } } @@ -161264,15 +164359,15 @@ "binop": null }, "value": "phylorefType", - "start": 32184, - "end": 32196, + "start": 32624, + "end": 32636, "loc": { "start": { - "line": 789, + "line": 805, "column": 76 }, "end": { - "line": 789, + "line": 805, "column": 88 } } @@ -161289,15 +164384,15 @@ "postfix": false, "binop": null }, - "start": 32196, - "end": 32197, + "start": 32636, + "end": 32637, "loc": { "start": { - "line": 789, + "line": 805, "column": 88 }, "end": { - "line": 789, + "line": 805, "column": 89 } } @@ -161316,15 +164411,15 @@ "updateContext": null }, "value": "', but it appears to be a '", - "start": 32197, - "end": 32224, + "start": 32637, + "end": 32664, "loc": { "start": { - "line": 789, + "line": 805, "column": 89 }, "end": { - "line": 789, + "line": 805, "column": 116 } } @@ -161341,15 +164436,15 @@ "postfix": false, "binop": null }, - "start": 32224, - "end": 32226, + "start": 32664, + "end": 32666, "loc": { "start": { - "line": 789, + "line": 805, "column": 116 }, "end": { - "line": 789, + "line": 805, "column": 118 } } @@ -161367,15 +164462,15 @@ "binop": null }, "value": "calculatedPhylorefType", - "start": 32226, - "end": 32248, + "start": 32666, + "end": 32688, "loc": { "start": { - "line": 789, + "line": 805, "column": 118 }, "end": { - "line": 789, + "line": 805, "column": 140 } } @@ -161392,15 +164487,15 @@ "postfix": false, "binop": null }, - "start": 32248, - "end": 32249, + "start": 32688, + "end": 32689, "loc": { "start": { - "line": 789, + "line": 805, "column": 140 }, "end": { - "line": 789, + "line": 805, "column": 141 } } @@ -161419,15 +164514,15 @@ "updateContext": null }, "value": "'.", - "start": 32249, - "end": 32251, + "start": 32689, + "end": 32691, "loc": { "start": { - "line": 789, + "line": 805, "column": 141 }, "end": { - "line": 789, + "line": 805, "column": 143 } } @@ -161444,15 +164539,15 @@ "postfix": false, "binop": null }, - "start": 32251, - "end": 32252, + "start": 32691, + "end": 32692, "loc": { "start": { - "line": 789, + "line": 805, "column": 143 }, "end": { - "line": 789, + "line": 805, "column": 144 } } @@ -161469,15 +164564,15 @@ "postfix": false, "binop": null }, - "start": 32259, - "end": 32260, + "start": 32699, + "end": 32700, "loc": { "start": { - "line": 790, + "line": 806, "column": 6 }, "end": { - "line": 790, + "line": 806, "column": 7 } } @@ -161495,15 +164590,15 @@ "binop": null, "updateContext": null }, - "start": 32260, - "end": 32261, + "start": 32700, + "end": 32701, "loc": { "start": { - "line": 790, + "line": 806, "column": 7 }, "end": { - "line": 790, + "line": 806, "column": 8 } } @@ -161520,15 +164615,15 @@ "postfix": false, "binop": null }, - "start": 32266, - "end": 32267, + "start": 32706, + "end": 32707, "loc": { "start": { - "line": 791, + "line": 807, "column": 4 }, "end": { - "line": 791, + "line": 807, "column": 5 } } @@ -161546,15 +164641,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 32272, - "end": 32288, + "start": 32712, + "end": 32728, "loc": { "start": { - "line": 792, + "line": 808, "column": 4 }, "end": { - "line": 792, + "line": 808, "column": 20 } } @@ -161572,15 +164667,15 @@ "binop": null, "updateContext": null }, - "start": 32288, - "end": 32289, + "start": 32728, + "end": 32729, "loc": { "start": { - "line": 792, + "line": 808, "column": 20 }, "end": { - "line": 792, + "line": 808, "column": 21 } } @@ -161598,15 +164693,15 @@ "binop": null }, "value": "subClassOf", - "start": 32289, - "end": 32299, + "start": 32729, + "end": 32739, "loc": { "start": { - "line": 792, + "line": 808, "column": 21 }, "end": { - "line": 792, + "line": 808, "column": 31 } } @@ -161624,15 +164719,15 @@ "binop": null, "updateContext": null }, - "start": 32299, - "end": 32300, + "start": 32739, + "end": 32740, "loc": { "start": { - "line": 792, + "line": 808, "column": 31 }, "end": { - "line": 792, + "line": 808, "column": 32 } } @@ -161650,15 +164745,15 @@ "binop": null }, "value": "push", - "start": 32300, - "end": 32304, + "start": 32740, + "end": 32744, "loc": { "start": { - "line": 792, + "line": 808, "column": 32 }, "end": { - "line": 792, + "line": 808, "column": 36 } } @@ -161675,15 +164770,15 @@ "postfix": false, "binop": null }, - "start": 32304, - "end": 32305, + "start": 32744, + "end": 32745, "loc": { "start": { - "line": 792, + "line": 808, "column": 36 }, "end": { - "line": 792, + "line": 808, "column": 37 } } @@ -161701,15 +164796,15 @@ "binop": null }, "value": "calculatedPhylorefType", - "start": 32305, - "end": 32327, + "start": 32745, + "end": 32767, "loc": { "start": { - "line": 792, + "line": 808, "column": 37 }, "end": { - "line": 792, + "line": 808, "column": 59 } } @@ -161726,15 +164821,15 @@ "postfix": false, "binop": null }, - "start": 32327, - "end": 32328, + "start": 32767, + "end": 32768, "loc": { "start": { - "line": 792, + "line": 808, "column": 59 }, "end": { - "line": 792, + "line": 808, "column": 60 } } @@ -161752,15 +164847,15 @@ "binop": null, "updateContext": null }, - "start": 32328, - "end": 32329, + "start": 32768, + "end": 32769, "loc": { "start": { - "line": 792, + "line": 808, "column": 60 }, "end": { - "line": 792, + "line": 808, "column": 61 } } @@ -161780,15 +164875,15 @@ "updateContext": null }, "value": "return", - "start": 32335, - "end": 32341, + "start": 32775, + "end": 32781, "loc": { "start": { - "line": 794, + "line": 810, "column": 4 }, "end": { - "line": 794, + "line": 810, "column": 10 } } @@ -161806,15 +164901,15 @@ "binop": null }, "value": "phylorefAsJSONLD", - "start": 32342, - "end": 32358, + "start": 32782, + "end": 32798, "loc": { "start": { - "line": 794, + "line": 810, "column": 11 }, "end": { - "line": 794, + "line": 810, "column": 27 } } @@ -161832,15 +164927,15 @@ "binop": null, "updateContext": null }, - "start": 32358, - "end": 32359, + "start": 32798, + "end": 32799, "loc": { "start": { - "line": 794, + "line": 810, "column": 27 }, "end": { - "line": 794, + "line": 810, "column": 28 } } @@ -161857,15 +164952,15 @@ "postfix": false, "binop": null }, - "start": 32362, - "end": 32363, + "start": 32802, + "end": 32803, "loc": { "start": { - "line": 795, + "line": 811, "column": 2 }, "end": { - "line": 795, + "line": 811, "column": 3 } } @@ -161882,15 +164977,15 @@ "postfix": false, "binop": null }, - "start": 32364, - "end": 32365, + "start": 32804, + "end": 32805, "loc": { "start": { - "line": 796, + "line": 812, "column": 0 }, "end": { - "line": 796, + "line": 812, "column": 1 } } @@ -161910,15 +165005,15 @@ "updateContext": null }, "value": "export", - "start": 32367, - "end": 32373, + "start": 32807, + "end": 32813, "loc": { "start": { - "line": 798, + "line": 814, "column": 0 }, "end": { - "line": 798, + "line": 814, "column": 6 } } @@ -161935,15 +165030,15 @@ "postfix": false, "binop": null }, - "start": 32374, - "end": 32375, + "start": 32814, + "end": 32815, "loc": { "start": { - "line": 798, + "line": 814, "column": 7 }, "end": { - "line": 798, + "line": 814, "column": 8 } } @@ -161961,15 +165056,15 @@ "binop": null }, "value": "PhylorefWrapper", - "start": 32376, - "end": 32391, + "start": 32816, + "end": 32831, "loc": { "start": { - "line": 798, + "line": 814, "column": 9 }, "end": { - "line": 798, + "line": 814, "column": 24 } } @@ -161987,15 +165082,15 @@ "binop": null, "updateContext": null }, - "start": 32391, - "end": 32392, + "start": 32831, + "end": 32832, "loc": { "start": { - "line": 798, + "line": 814, "column": 24 }, "end": { - "line": 798, + "line": 814, "column": 25 } } @@ -162012,15 +165107,15 @@ "postfix": false, "binop": null }, - "start": 32393, - "end": 32394, + "start": 32833, + "end": 32834, "loc": { "start": { - "line": 798, + "line": 814, "column": 26 }, "end": { - "line": 798, + "line": 814, "column": 27 } } @@ -162038,15 +165133,15 @@ "binop": null, "updateContext": null }, - "start": 32394, - "end": 32395, + "start": 32834, + "end": 32835, "loc": { "start": { - "line": 798, + "line": 814, "column": 27 }, "end": { - "line": 798, + "line": 814, "column": 28 } } @@ -162064,15 +165159,15 @@ "binop": null, "updateContext": null }, - "start": 32396, - "end": 32396, + "start": 32836, + "end": 32836, "loc": { "start": { - "line": 799, + "line": 815, "column": 0 }, "end": { - "line": 799, + "line": 815, "column": 0 } } diff --git a/docs/ast/source/wrappers/PhyxWrapper.js.json b/docs/ast/source/wrappers/PhyxWrapper.js.json index 16f9ebea..13fa994e 100644 --- a/docs/ast/source/wrappers/PhyxWrapper.js.json +++ b/docs/ast/source/wrappers/PhyxWrapper.js.json @@ -1,28 +1,28 @@ { "type": "File", "start": 0, - "end": 12994, + "end": 14157, "loc": { "start": { "line": 1, "column": 0 }, "end": { - "line": 289, + "line": 315, "column": 0 } }, "program": { "type": "Program", "start": 0, - "end": 12994, + "end": 14157, "loc": { "start": { "line": 1, "column": 0 }, "end": { - "line": 289, + "line": 315, "column": 0 } }, @@ -226,9 +226,9 @@ "line": 5, "column": 25 }, - "identifierName": "LKT4H17Y6XV4Y" + "identifierName": "LXL9JK83PH1BW" }, - "name": "LKT4H17Y6XV4Y", + "name": "LXL9JK83PH1BW", "leadingComments": null }, "leadingComments": null @@ -497,9 +497,9 @@ "line": 6, "column": 46 }, - "identifierName": "LKT4H17Y6XV4Y" + "identifierName": "LXL9JK83PH1BW" }, - "name": "LKT4H17Y6XV4Y" + "name": "LXL9JK83PH1BW" } } ], @@ -723,9 +723,9 @@ "line": 13, "column": 25 }, - "identifierName": "LKT4H17YSQH4Y" + "identifierName": "LXL9JK836PI9S" }, - "name": "LKT4H17YSQH4Y" + "name": "LXL9JK836PI9S" } } ], @@ -864,9 +864,9 @@ "line": 14, "column": 41 }, - "identifierName": "LKT4H17YSQH4Y" + "identifierName": "LXL9JK836PI9S" }, - "name": "LKT4H17YSQH4Y" + "name": "LXL9JK836PI9S" } } ], @@ -914,9 +914,9 @@ "line": 15, "column": 25 }, - "identifierName": "LKT4H17YPJAMM" + "identifierName": "LXL9JK830DC8M" }, - "name": "LKT4H17YPJAMM" + "name": "LXL9JK830DC8M" } } ], @@ -1055,9 +1055,9 @@ "line": 16, "column": 42 }, - "identifierName": "LKT4H17YPJAMM" + "identifierName": "LXL9JK830DC8M" }, - "name": "LKT4H17YPJAMM" + "name": "LXL9JK830DC8M" } } ], @@ -1105,9 +1105,9 @@ "line": 17, "column": 25 }, - "identifierName": "LKT4H17YNLTNS" + "identifierName": "LXL9JK83OXXQ2" }, - "name": "LKT4H17YNLTNS" + "name": "LXL9JK83OXXQ2" } } ], @@ -1246,9 +1246,9 @@ "line": 18, "column": 41 }, - "identifierName": "LKT4H17YNLTNS" + "identifierName": "LXL9JK83OXXQ2" }, - "name": "LKT4H17YNLTNS" + "name": "LXL9JK83OXXQ2" } } ], @@ -1275,14 +1275,14 @@ { "type": "Identifier", "start": 622, - "end": 12967, + "end": 14130, "loc": { "start": { "line": 24, "column": 0 }, "end": { - "line": 286, + "line": 312, "column": 1 } }, @@ -1308,14 +1308,14 @@ "body": { "type": "ClassBody", "start": 640, - "end": 12967, + "end": 14130, "loc": { "start": { "line": 24, "column": 18 }, "end": { - "line": 286, + "line": 312, "column": 1 } }, @@ -2889,16 +2889,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", + "value": "*\n * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\n * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\n * package will be wrapped and normalized before being returned.\n *\n * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\n * identical ways. But if we implement it at every level, we can implement comparison code in\n * Klados easily.\n *\n * Two Phyx documents should -- upon being normalized -- be comparable with each other with\n * lodash.deepEqual().\n ", "start": 2310, - "end": 3304, + "end": 3009, "loc": { "start": { "line": 58, "column": 2 }, "end": { - "line": 73, + "line": 70, "column": 5 } } @@ -2907,37 +2907,36 @@ }, { "type": "ClassMethod", - "start": 3307, - "end": 11314, + "start": 3012, + "end": 3469, "loc": { "start": { - "line": 74, + "line": 71, "column": 2 }, "end": { - "line": 254, + "line": 82, "column": 3 } }, - "static": false, + "static": true, "computed": false, "key": { "type": "Identifier", - "start": 3307, - "end": 3315, + "start": 3019, + "end": 3028, "loc": { "start": { - "line": 74, - "column": 2 + "line": 71, + "column": 9 }, "end": { - "line": 74, - "column": 10 + "line": 71, + "column": 18 }, - "identifierName": "asJSONLD" + "identifierName": "normalize" }, - "name": "asJSONLD", - "leadingComments": null + "name": "normalize" }, "kind": "method", "id": null, @@ -2946,145 +2945,110 @@ "async": false, "params": [ { - 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"identifierName": "phyloref" @@ -5242,15 +6307,15 @@ }, "property": { "type": "StringLiteral", - "start": 4695, - "end": 4700, + "start": 5858, + "end": 5863, "loc": { "start": { - "line": 107, + "line": 133, "column": 24 }, "end": { - "line": 107, + "line": 133, "column": 29 } }, @@ -5265,15 +6330,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 4705, - "end": 4707, + "start": 5868, + "end": 5870, "loc": { "start": { - "line": 107, + "line": 133, "column": 34 }, "end": { - "line": 107, + "line": 133, "column": 36 } }, @@ -5285,20 +6350,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 4685 + "parenStart": 5848 } }, "property": { "type": "Identifier", - "start": 4709, - "end": 4719, + "start": 5872, + "end": 5882, "loc": { "start": { - "line": 107, + "line": 133, "column": 38 }, "end": { - "line": 107, + "line": 133, "column": 48 }, "identifierName": "startsWith" @@ -5310,15 +6375,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 4720, - "end": 4723, + "start": 5883, + "end": 5886, "loc": { "start": { - "line": 107, + "line": 133, "column": 49 }, "end": { - "line": 107, + "line": 133, "column": 52 } }, @@ -5332,59 +6397,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4726, - "end": 4905, + "start": 5889, + "end": 6068, "loc": { "start": { - "line": 107, + "line": 133, "column": 55 }, "end": { - "line": 111, + "line": 137, "column": 11 } }, "body": [ { "type": "VariableDeclaration", - "start": 4740, - "end": 4785, + "start": 5903, + "end": 5948, "loc": { "start": { - "line": 108, + "line": 134, "column": 12 }, "end": { - "line": 108, + "line": 134, "column": 57 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4746, - "end": 4784, + "start": 5909, + "end": 5947, "loc": { "start": { - "line": 108, + "line": 134, "column": 18 }, "end": { - "line": 108, + "line": 134, "column": 56 } }, "id": { "type": "Identifier", - "start": 4746, - "end": 4762, + "start": 5909, + "end": 5925, "loc": { "start": { - "line": 108, + "line": 134, "column": 18 }, "end": { - "line": 108, + "line": 134, "column": 34 }, "identifierName": "modifiedPhyloref" @@ -5393,29 +6458,29 @@ }, "init": { "type": "CallExpression", - "start": 4765, - "end": 4784, + "start": 5928, + "end": 5947, "loc": { "start": { - "line": 108, + "line": 134, "column": 37 }, "end": { - "line": 108, + "line": 134, "column": 56 } }, "callee": { "type": "Identifier", - "start": 4765, - "end": 4774, + "start": 5928, + "end": 5937, "loc": { "start": { - "line": 108, + "line": 134, "column": 37 }, "end": { - "line": 108, + "line": 134, "column": 46 }, "identifierName": "cloneDeep" @@ -5425,15 +6490,15 @@ "arguments": [ { "type": "Identifier", - "start": 4775, - "end": 4783, + "start": 5938, + "end": 5946, "loc": { "start": { - "line": 108, + "line": 134, "column": 47 }, "end": { - "line": 108, + "line": 134, "column": 55 }, "identifierName": "phyloref" @@ -5448,58 +6513,58 @@ }, { "type": "ExpressionStatement", - "start": 4798, - "end": 4856, + "start": 5961, + "end": 6019, "loc": { "start": { - "line": 109, + "line": 135, "column": 12 }, "end": { - "line": 109, + "line": 135, "column": 70 } }, "expression": { "type": "AssignmentExpression", - "start": 4798, - "end": 4855, + "start": 5961, + "end": 6018, "loc": { "start": { - "line": 109, + "line": 135, "column": 12 }, "end": { - "line": 109, + "line": 135, "column": 69 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 4798, - "end": 4821, + "start": 5961, + "end": 5984, "loc": { "start": { - "line": 109, + "line": 135, "column": 12 }, "end": { - "line": 109, + "line": 135, "column": 35 } }, "object": { "type": "Identifier", - "start": 4798, - "end": 4814, + "start": 5961, + "end": 5977, "loc": { "start": { - "line": 109, + "line": 135, "column": 12 }, "end": { - "line": 109, + "line": 135, "column": 28 }, "identifierName": "modifiedPhyloref" @@ -5508,15 +6573,15 @@ }, "property": { "type": "StringLiteral", - "start": 4815, - "end": 4820, + "start": 5978, + "end": 5983, "loc": { "start": { - "line": 109, + "line": 135, "column": 29 }, "end": { - "line": 109, + "line": 135, "column": 34 } }, @@ -5530,29 +6595,29 @@ }, "right": { "type": "CallExpression", - "start": 4824, - "end": 4855, + "start": 5987, + "end": 6018, "loc": { "start": { - "line": 109, + "line": 135, "column": 38 }, "end": { - "line": 109, + "line": 135, "column": 69 } }, "callee": { "type": "Identifier", - "start": 4824, - "end": 4838, + "start": 5987, + "end": 6001, "loc": { "start": { - "line": 109, + "line": 135, "column": 38 }, "end": { - "line": 109, + "line": 135, "column": 52 }, "identifierName": "makeIDAbsolute" @@ -5562,29 +6627,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 4839, - "end": 4854, + "start": 6002, + "end": 6017, "loc": { "start": { - "line": 109, + "line": 135, "column": 53 }, "end": { - "line": 109, + "line": 135, "column": 68 } }, "object": { "type": "Identifier", - "start": 4839, - "end": 4847, + "start": 6002, + "end": 6010, "loc": { "start": { - "line": 109, + "line": 135, "column": 53 }, "end": { - "line": 109, + "line": 135, "column": 61 }, "identifierName": "phyloref" @@ -5593,15 +6658,15 @@ }, "property": { "type": "StringLiteral", - "start": 4848, - "end": 4853, + "start": 6011, + "end": 6016, "loc": { "start": { - "line": 109, + "line": 135, "column": 62 }, "end": { - "line": 109, + "line": 135, "column": 67 } }, @@ -5619,29 +6684,29 @@ }, { "type": "ReturnStatement", - "start": 4869, - "end": 4893, + "start": 6032, + "end": 6056, "loc": { "start": { - "line": 110, + "line": 136, "column": 12 }, "end": { - "line": 110, + "line": 136, "column": 36 } }, "argument": { "type": "Identifier", - "start": 4876, - "end": 4892, + "start": 6039, + "end": 6055, "loc": { "start": { - "line": 110, + "line": 136, "column": 19 }, "end": { - "line": 110, + "line": 136, "column": 35 }, "identifierName": "modifiedPhyloref" @@ -5656,29 +6721,29 @@ }, { "type": "ReturnStatement", - "start": 4916, - "end": 4932, + "start": 6079, + "end": 6095, "loc": { "start": { - "line": 112, + "line": 138, "column": 10 }, "end": { - "line": 112, + "line": 138, "column": 26 } }, "argument": { "type": "Identifier", - "start": 4923, - "end": 4931, + "start": 6086, + "end": 6094, "loc": { "start": { - "line": 112, + "line": 138, "column": 17 }, "end": { - "line": 112, + "line": 138, "column": 25 }, "identifierName": "phyloref" @@ -5703,15 +6768,15 @@ { "type": "CommentLine", "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", - "start": 4323, - "end": 4394, + "start": 5486, + "end": 5557, "loc": { "start": { - "line": 101, + "line": 127, "column": 6 }, "end": { - "line": 101, + "line": 127, "column": 77 } } @@ -5719,15 +6784,15 @@ { "type": "CommentLine", "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", - "start": 4401, - "end": 4470, + "start": 5564, + "end": 5633, "loc": { "start": { - "line": 102, + "line": 128, "column": 6 }, "end": { - "line": 102, + "line": 128, "column": 75 } } @@ -5735,15 +6800,15 @@ { "type": "CommentLine", "value": " to the relative IRI to make it absolute. This seems to avoid problems", - "start": 4477, - "end": 4549, + "start": 5640, + "end": 5712, "loc": { "start": { - "line": 103, + "line": 129, "column": 6 }, "end": { - "line": 103, + "line": 129, "column": 78 } } @@ -5751,15 +6816,15 @@ { "type": "CommentLine", "value": " with some JSON-LD parsers.", - "start": 4556, - "end": 4585, + "start": 5719, + "end": 5748, "loc": { "start": { - "line": 104, + "line": 130, "column": 6 }, "end": { - "line": 104, + "line": 130, "column": 35 } } @@ -5769,15 +6834,15 @@ { "type": "CommentLine", "value": " Convert phyloreferences into an OWL class restriction", - "start": 4960, - "end": 5016, + "start": 6123, + "end": 6179, "loc": { "start": { - "line": 116, + "line": 142, "column": 6 }, "end": { - "line": 116, + "line": 142, "column": 62 } } @@ -5786,58 +6851,58 @@ }, { "type": "ExpressionStatement", - "start": 5023, - "end": 5220, + "start": 6186, + "end": 6383, "loc": { "start": { - "line": 117, + "line": 143, "column": 6 }, "end": { - "line": 120, + "line": 146, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 5023, - "end": 5219, + "start": 6186, + "end": 6382, "loc": { "start": { - "line": 117, + "line": 143, "column": 6 }, "end": { - "line": 120, + "line": 146, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5023, - "end": 5039, + "start": 6186, + "end": 6202, "loc": { "start": { - "line": 117, + "line": 143, "column": 6 }, "end": { - "line": 117, + "line": 143, "column": 22 } }, "object": { "type": "Identifier", - "start": 5023, - "end": 5029, + "start": 6186, + "end": 6192, "loc": { "start": { - "line": 117, + "line": 143, "column": 6 }, "end": { - "line": 117, + "line": 143, "column": 12 }, "identifierName": "jsonld" @@ -5847,15 +6912,15 @@ }, "property": { "type": "Identifier", - "start": 5030, - "end": 5039, + "start": 6193, + "end": 6202, "loc": { "start": { - "line": 117, + "line": 143, "column": 13 }, "end": { - "line": 117, + "line": 143, "column": 22 }, "identifierName": "phylorefs" @@ -5867,57 +6932,57 @@ }, "right": { "type": "CallExpression", - "start": 5042, - "end": 5219, + "start": 6205, + "end": 6382, "loc": { "start": { - "line": 117, + "line": 143, "column": 25 }, "end": { - "line": 120, + "line": 146, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 5042, - "end": 5062, + "start": 6205, + "end": 6225, "loc": { "start": { - "line": 117, + "line": 143, "column": 25 }, "end": { - "line": 117, + "line": 143, "column": 45 } }, "object": { "type": "MemberExpression", - "start": 5042, - "end": 5058, + "start": 6205, + "end": 6221, "loc": { "start": { - "line": 117, + "line": 143, "column": 25 }, "end": { - "line": 117, + "line": 143, "column": 41 } }, "object": { "type": "Identifier", - "start": 5042, - "end": 5048, + "start": 6205, + "end": 6211, "loc": { "start": { - "line": 117, + "line": 143, "column": 25 }, "end": { - "line": 117, + "line": 143, "column": 31 }, "identifierName": "jsonld" @@ -5926,15 +6991,15 @@ }, "property": { "type": "Identifier", - "start": 5049, - "end": 5058, + "start": 6212, + "end": 6221, "loc": { "start": { - "line": 117, + "line": 143, "column": 32 }, "end": { - "line": 117, + "line": 143, "column": 41 }, "identifierName": "phylorefs" @@ -5945,15 +7010,15 @@ }, "property": { "type": "Identifier", - "start": 5059, - "end": 5062, + "start": 6222, + "end": 6225, "loc": { "start": { - "line": 117, + "line": 143, "column": 42 }, "end": { - "line": 117, + "line": 143, "column": 45 }, "identifierName": "map" @@ -5965,15 +7030,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5072, - "end": 5211, + "start": 6235, + "end": 6374, "loc": { "start": { - "line": 118, + "line": 144, "column": 8 }, "end": { - "line": 119, + "line": 145, "column": 57 } }, @@ -5984,15 +7049,15 @@ "params": [ { "type": "Identifier", - "start": 5073, - "end": 5081, + "start": 6236, + "end": 6244, "loc": { "start": { - "line": 118, + "line": 144, "column": 9 }, "end": { - "line": 118, + "line": 144, "column": 17 }, "identifierName": "phyloref" @@ -6001,15 +7066,15 @@ }, { "type": "Identifier", - "start": 5083, - "end": 5096, + "start": 6246, + "end": 6259, "loc": { "start": { - "line": 118, + "line": 144, "column": 19 }, "end": { - "line": 118, + "line": 144, "column": 32 }, "identifierName": "countPhyloref" @@ -6019,57 +7084,57 @@ ], "body": { "type": "CallExpression", - "start": 5101, - "end": 5211, + "start": 6264, + "end": 6374, "loc": { "start": { - "line": 118, + "line": 144, "column": 37 }, "end": { - "line": 119, + "line": 145, "column": 57 } }, "callee": { "type": "MemberExpression", - "start": 5101, - "end": 5173, + "start": 6264, + "end": 6336, "loc": { "start": { - "line": 118, + "line": 144, "column": 37 }, "end": { - "line": 119, + "line": 145, "column": 19 } }, "object": { "type": "NewExpression", - "start": 5101, - "end": 5153, + "start": 6264, + "end": 6316, "loc": { "start": { - "line": 118, + "line": 144, "column": 37 }, "end": { - "line": 118, + "line": 144, "column": 89 } }, "callee": { "type": "Identifier", - "start": 5105, - "end": 5120, + "start": 6268, + "end": 6283, "loc": { "start": { - "line": 118, + "line": 144, "column": 41 }, "end": { - "line": 118, + "line": 144, "column": 56 }, "identifierName": "PhylorefWrapper" @@ -6079,15 +7144,15 @@ "arguments": [ { "type": "Identifier", - "start": 5121, - "end": 5129, + "start": 6284, + "end": 6292, "loc": { "start": { - "line": 118, + "line": 144, "column": 57 }, "end": { - "line": 118, + "line": 144, "column": 65 }, "identifierName": "phyloref" @@ -6096,44 +7161,44 @@ }, { "type": "MemberExpression", - "start": 5131, - "end": 5152, + "start": 6294, + "end": 6315, "loc": { "start": { - "line": 118, + "line": 144, "column": 67 }, "end": { - "line": 118, + "line": 144, "column": 88 } }, "object": { "type": "ThisExpression", - "start": 5131, - "end": 5135, + "start": 6294, + "end": 6298, "loc": { "start": { - "line": 118, + "line": 144, "column": 67 }, "end": { - "line": 118, + "line": 144, "column": 71 } } }, "property": { "type": "Identifier", - "start": 5136, - "end": 5152, + "start": 6299, + "end": 6315, "loc": { "start": { - "line": 118, + "line": 144, "column": 72 }, "end": { - "line": 118, + "line": 144, "column": 88 }, "identifierName": "defaultNomenCode" @@ -6146,15 +7211,15 @@ }, "property": { "type": "Identifier", - "start": 5165, - "end": 5173, + "start": 6328, + "end": 6336, "loc": { "start": { - "line": 119, + "line": 145, "column": 11 }, "end": { - "line": 119, + "line": 145, "column": 19 }, "identifierName": "asJSONLD" @@ -6166,29 +7231,29 @@ "arguments": [ { "type": "CallExpression", - "start": 5174, - "end": 5210, + "start": 6337, + "end": 6373, "loc": { "start": { - "line": 119, + "line": 145, "column": 20 }, "end": { - "line": 119, + "line": 145, "column": 56 } }, "callee": { "type": "Identifier", - "start": 5174, - "end": 5195, + "start": 6337, + "end": 6358, "loc": { "start": { - "line": 119, + "line": 145, "column": 20 }, "end": { - "line": 119, + "line": 145, "column": 41 }, "identifierName": "getBaseIRIForPhyloref" @@ -6198,15 +7263,15 @@ "arguments": [ { "type": "Identifier", - "start": 5196, - "end": 5209, + "start": 6359, + "end": 6372, "loc": { "start": { - "line": 119, + "line": 145, "column": 42 }, "end": { - "line": 119, + "line": 145, "column": 55 }, "identifierName": "countPhyloref" @@ -6226,15 +7291,15 @@ { "type": "CommentLine", "value": " Convert phyloreferences into an OWL class restriction", - "start": 4960, - "end": 5016, + "start": 6123, + "end": 6179, "loc": { "start": { - "line": 116, + "line": 142, "column": 6 }, "end": { - "line": 116, + "line": 142, "column": 62 } } @@ -6248,43 +7313,43 @@ }, { "type": "IfStatement", - "start": 5232, - "end": 9720, + "start": 6395, + "end": 10883, "loc": { "start": { - "line": 123, + "line": 149, "column": 4 }, "end": { - "line": 222, + "line": 248, "column": 5 } }, "test": { "type": "CallExpression", - "start": 5236, - "end": 5262, + "start": 6399, + "end": 6425, "loc": { "start": { - "line": 123, + "line": 149, "column": 8 }, "end": { - "line": 123, + "line": 149, "column": 34 } }, "callee": { "type": "Identifier", - "start": 5236, - "end": 5239, + "start": 6399, + "end": 6402, "loc": { "start": { - "line": 123, + "line": 149, "column": 8 }, "end": { - "line": 123, + "line": 149, "column": 11 }, "identifierName": "has" @@ -6294,15 +7359,15 @@ "arguments": [ { "type": "Identifier", - "start": 5240, - "end": 5246, + "start": 6403, + "end": 6409, "loc": { "start": { - "line": 123, + "line": 149, "column": 12 }, "end": { - "line": 123, + "line": 149, "column": 18 }, "identifierName": "jsonld" @@ -6311,15 +7376,15 @@ }, { "type": "StringLiteral", - "start": 5248, - "end": 5261, + "start": 6411, + "end": 6424, "loc": { "start": { - "line": 123, + "line": 149, "column": 20 }, "end": { - "line": 123, + "line": 149, "column": 33 } }, @@ -6333,44 +7398,44 @@ }, "consequent": { "type": "BlockStatement", - "start": 5264, - "end": 9720, + "start": 6427, + "end": 10883, "loc": { "start": { - "line": 123, + "line": 149, "column": 36 }, "end": { - "line": 222, + "line": 248, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 5541, - "end": 5913, + "start": 6704, + "end": 7076, "loc": { "start": { - "line": 128, + "line": 154, "column": 6 }, "end": { - "line": 137, + "line": 163, "column": 7 } }, "test": { "type": "Identifier", - "start": 5545, - "end": 5552, + "start": 6708, + "end": 6715, "loc": { "start": { - "line": 128, + "line": 154, "column": 10 }, "end": { - "line": 128, + "line": 154, "column": 17 }, "identifierName": "baseIRI" @@ -6380,73 +7445,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 5554, - "end": 5913, + "start": 6717, + "end": 7076, "loc": { "start": { - "line": 128, + "line": 154, "column": 19 }, "end": { - "line": 137, + "line": 163, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 5564, - "end": 5905, + "start": 6727, + "end": 7068, "loc": { "start": { - "line": 129, + "line": 155, "column": 8 }, "end": { - "line": 136, + "line": 162, "column": 11 } }, "expression": { "type": "AssignmentExpression", - "start": 5564, - "end": 5904, + "start": 6727, + "end": 7067, "loc": { "start": { - "line": 129, + "line": 155, "column": 8 }, "end": { - "line": 136, + "line": 162, "column": 10 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5564, - "end": 5582, + "start": 6727, + "end": 6745, "loc": { "start": { - "line": 129, + "line": 155, "column": 8 }, "end": { - "line": 129, + "line": 155, "column": 26 } }, "object": { "type": "Identifier", - "start": 5564, - "end": 5570, + "start": 6727, + "end": 6733, "loc": { "start": { - "line": 129, + "line": 155, "column": 8 }, "end": { - "line": 129, + "line": 155, "column": 14 }, "identifierName": "jsonld" @@ -6455,15 +7520,15 @@ }, "property": { "type": "Identifier", - "start": 5571, - "end": 5582, + "start": 6734, + "end": 6745, "loc": { "start": { - "line": 129, + "line": 155, "column": 15 }, "end": { - "line": 129, + "line": 155, "column": 26 }, "identifierName": "phylogenies" @@ -6474,57 +7539,57 @@ }, "right": { "type": "CallExpression", - "start": 5585, - "end": 5904, + "start": 6748, + "end": 7067, "loc": { "start": { - "line": 129, + "line": 155, "column": 29 }, "end": { - "line": 136, + "line": 162, "column": 10 } }, "callee": { "type": "MemberExpression", - "start": 5585, - "end": 5607, + "start": 6748, + "end": 6770, "loc": { "start": { - "line": 129, + "line": 155, "column": 29 }, "end": { - "line": 129, + "line": 155, "column": 51 } }, "object": { "type": "MemberExpression", - "start": 5585, - "end": 5603, + "start": 6748, + "end": 6766, "loc": { "start": { - "line": 129, + "line": 155, "column": 29 }, "end": { - "line": 129, + "line": 155, "column": 47 } }, "object": { "type": "Identifier", - "start": 5585, - "end": 5591, + "start": 6748, + "end": 6754, "loc": { "start": { - "line": 129, + "line": 155, "column": 29 }, "end": { - "line": 129, + "line": 155, "column": 35 }, "identifierName": "jsonld" @@ -6533,15 +7598,15 @@ }, "property": { "type": "Identifier", - "start": 5592, - "end": 5603, + "start": 6755, + "end": 6766, "loc": { "start": { - "line": 129, + "line": 155, "column": 36 }, "end": { - "line": 129, + "line": 155, "column": 47 }, "identifierName": "phylogenies" @@ -6552,15 +7617,15 @@ }, "property": { "type": "Identifier", - "start": 5604, - "end": 5607, + "start": 6767, + "end": 6770, "loc": { "start": { - "line": 129, + "line": 155, "column": 48 }, "end": { - "line": 129, + "line": 155, "column": 51 }, "identifierName": "map" @@ -6572,15 +7637,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 5608, - "end": 5903, + "start": 6771, + "end": 7066, "loc": { "start": { - "line": 129, + "line": 155, "column": 52 }, "end": { - "line": 136, + "line": 162, "column": 9 } }, @@ -6591,15 +7656,15 @@ "params": [ { "type": "Identifier", - "start": 5609, - "end": 5618, + "start": 6772, + "end": 6781, "loc": { "start": { - "line": 129, + "line": 155, "column": 53 }, "end": { - "line": 129, + "line": 155, "column": 62 }, "identifierName": "phylogeny" @@ -6609,100 +7674,100 @@ ], "body": { "type": "BlockStatement", - "start": 5623, - "end": 5903, + "start": 6786, + "end": 7066, "loc": { "start": { - "line": 129, + "line": 155, "column": 67 }, "end": { - "line": 136, + "line": 162, "column": 9 } }, "body": [ { "type": "IfStatement", - "start": 5635, - "end": 5865, + "start": 6798, + "end": 7028, "loc": { "start": { - "line": 130, + "line": 156, "column": 10 }, "end": { - "line": 134, + "line": 160, "column": 11 } }, "test": { "type": "CallExpression", - "start": 5639, - "end": 5679, + "start": 6802, + "end": 6842, "loc": { "start": { - "line": 130, + "line": 156, "column": 14 }, "end": { - "line": 130, + "line": 156, "column": 54 } }, "callee": { "type": "MemberExpression", - "start": 5639, - "end": 5674, + "start": 6802, + "end": 6837, "loc": { "start": { - "line": 130, + "line": 156, "column": 14 }, "end": { - "line": 130, + "line": 156, "column": 49 } }, "object": { "type": "LogicalExpression", - "start": 5640, - "end": 5662, + "start": 6803, + "end": 6825, "loc": { "start": { - "line": 130, + "line": 156, "column": 15 }, "end": { - "line": 130, + "line": 156, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 5640, - "end": 5656, + "start": 6803, + "end": 6819, "loc": { "start": { - "line": 130, + "line": 156, "column": 15 }, "end": { - "line": 130, + "line": 156, "column": 31 } }, "object": { "type": "Identifier", - "start": 5640, - "end": 5649, + "start": 6803, + "end": 6812, "loc": { "start": { - "line": 130, + "line": 156, "column": 15 }, "end": { - "line": 130, + "line": 156, "column": 24 }, "identifierName": "phylogeny" @@ -6711,15 +7776,15 @@ }, "property": { "type": "StringLiteral", - "start": 5650, - "end": 5655, + "start": 6813, + "end": 6818, "loc": { "start": { - "line": 130, + "line": 156, "column": 25 }, "end": { - "line": 130, + "line": 156, "column": 30 } }, @@ -6734,15 +7799,15 @@ "operator": "||", "right": { "type": "StringLiteral", - "start": 5660, - "end": 5662, + "start": 6823, + "end": 6825, "loc": { "start": { - "line": 130, + "line": 156, "column": 35 }, "end": { - "line": 130, + "line": 156, "column": 37 } }, @@ -6754,20 +7819,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 5639 + "parenStart": 6802 } }, "property": { "type": "Identifier", - "start": 5664, - "end": 5674, + "start": 6827, + "end": 6837, "loc": { "start": { - "line": 130, + "line": 156, "column": 39 }, "end": { - "line": 130, + "line": 156, "column": 49 }, "identifierName": "startsWith" @@ -6779,15 +7844,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 5675, - "end": 5678, + "start": 6838, + "end": 6841, "loc": { "start": { - "line": 130, + "line": 156, "column": 50 }, "end": { - "line": 130, + "line": 156, "column": 53 } }, @@ -6801,59 +7866,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5681, - "end": 5865, + "start": 6844, + "end": 7028, "loc": { "start": { - "line": 130, + "line": 156, "column": 56 }, "end": { - "line": 134, + "line": 160, "column": 11 } }, "body": [ { "type": "VariableDeclaration", - "start": 5695, - "end": 5742, + "start": 6858, + "end": 6905, "loc": { "start": { - "line": 131, + "line": 157, "column": 12 }, "end": { - "line": 131, + "line": 157, "column": 59 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5701, - "end": 5741, + "start": 6864, + "end": 6904, "loc": { "start": { - "line": 131, + "line": 157, "column": 18 }, "end": { - "line": 131, + "line": 157, "column": 58 } }, "id": { "type": "Identifier", - "start": 5701, - "end": 5718, + "start": 6864, + "end": 6881, "loc": { "start": { - "line": 131, + "line": 157, "column": 18 }, "end": { - "line": 131, + "line": 157, "column": 35 }, "identifierName": "modifiedPhylogeny" @@ -6862,29 +7927,29 @@ }, "init": { "type": "CallExpression", - "start": 5721, - "end": 5741, + "start": 6884, + "end": 6904, "loc": { "start": { - "line": 131, + "line": 157, "column": 38 }, "end": { - "line": 131, + "line": 157, "column": 58 } }, "callee": { "type": "Identifier", - "start": 5721, - "end": 5730, + "start": 6884, + "end": 6893, "loc": { "start": { - "line": 131, + "line": 157, "column": 38 }, "end": { - "line": 131, + "line": 157, "column": 47 }, "identifierName": "cloneDeep" @@ -6894,15 +7959,15 @@ "arguments": [ { "type": "Identifier", - "start": 5731, - "end": 5740, + "start": 6894, + "end": 6903, "loc": { "start": { - "line": 131, + "line": 157, "column": 48 }, "end": { - "line": 131, + "line": 157, "column": 57 }, "identifierName": "phylogeny" @@ -6917,58 +7982,58 @@ }, { "type": "ExpressionStatement", - "start": 5755, - "end": 5815, + "start": 6918, + "end": 6978, "loc": { "start": { - "line": 132, + "line": 158, "column": 12 }, "end": { - "line": 132, + "line": 158, "column": 72 } }, "expression": { "type": "AssignmentExpression", - "start": 5755, - "end": 5814, + "start": 6918, + "end": 6977, "loc": { "start": { - "line": 132, + "line": 158, "column": 12 }, "end": { - "line": 132, + "line": 158, "column": 71 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5755, - "end": 5779, + "start": 6918, + "end": 6942, "loc": { "start": { - "line": 132, + "line": 158, "column": 12 }, "end": { - "line": 132, + "line": 158, "column": 36 } }, "object": { "type": "Identifier", - "start": 5755, - "end": 5772, + "start": 6918, + "end": 6935, "loc": { "start": { - "line": 132, + "line": 158, "column": 12 }, "end": { - "line": 132, + "line": 158, "column": 29 }, "identifierName": "modifiedPhylogeny" @@ -6977,15 +8042,15 @@ }, "property": { "type": "StringLiteral", - "start": 5773, - "end": 5778, + "start": 6936, + "end": 6941, "loc": { "start": { - "line": 132, + "line": 158, "column": 30 }, "end": { - "line": 132, + "line": 158, "column": 35 } }, @@ -6999,29 +8064,29 @@ }, "right": { "type": "CallExpression", - "start": 5782, - "end": 5814, + "start": 6945, + "end": 6977, "loc": { "start": { - "line": 132, + "line": 158, "column": 39 }, "end": { - "line": 132, + "line": 158, "column": 71 } }, "callee": { "type": "Identifier", - "start": 5782, - "end": 5796, + "start": 6945, + "end": 6959, "loc": { "start": { - "line": 132, + "line": 158, "column": 39 }, "end": { - "line": 132, + "line": 158, "column": 53 }, "identifierName": "makeIDAbsolute" @@ -7031,29 +8096,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 5797, - "end": 5813, + "start": 6960, + "end": 6976, "loc": { "start": { - "line": 132, + "line": 158, "column": 54 }, "end": { - "line": 132, + "line": 158, "column": 70 } }, "object": { "type": "Identifier", - "start": 5797, - "end": 5806, + "start": 6960, + "end": 6969, "loc": { "start": { - "line": 132, + "line": 158, "column": 54 }, "end": { - "line": 132, + "line": 158, "column": 63 }, "identifierName": "phylogeny" @@ -7062,15 +8127,15 @@ }, "property": { "type": "StringLiteral", - "start": 5807, - "end": 5812, + "start": 6970, + "end": 6975, "loc": { "start": { - "line": 132, + "line": 158, "column": 64 }, "end": { - "line": 132, + "line": 158, "column": 69 } }, @@ -7088,29 +8153,29 @@ }, { "type": "ReturnStatement", - "start": 5828, - "end": 5853, + "start": 6991, + "end": 7016, "loc": { "start": { - "line": 133, + "line": 159, "column": 12 }, "end": { - "line": 133, + "line": 159, "column": 37 } }, "argument": { "type": "Identifier", - "start": 5835, - "end": 5852, + "start": 6998, + "end": 7015, "loc": { "start": { - "line": 133, + "line": 159, "column": 19 }, "end": { - "line": 133, + "line": 159, "column": 36 }, "identifierName": "modifiedPhylogeny" @@ -7125,29 +8190,29 @@ }, { "type": "ReturnStatement", - "start": 5876, - "end": 5893, + "start": 7039, + "end": 7056, "loc": { "start": { - "line": 135, + "line": 161, "column": 10 }, "end": { - "line": 135, + "line": 161, "column": 27 } }, "argument": { "type": "Identifier", - "start": 5883, - "end": 5892, + "start": 7046, + "end": 7055, "loc": { "start": { - "line": 135, + "line": 161, "column": 17 }, "end": { - "line": 135, + "line": 161, "column": 26 }, "identifierName": "phylogeny" @@ -7172,15 +8237,15 @@ { "type": "CommentLine", "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", - "start": 5272, - "end": 5343, + "start": 6435, + "end": 6506, "loc": { "start": { - "line": 124, + "line": 150, "column": 6 }, "end": { - "line": 124, + "line": 150, "column": 77 } } @@ -7188,15 +8253,15 @@ { "type": "CommentLine", "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", - "start": 5350, - "end": 5419, + "start": 6513, + "end": 6582, "loc": { "start": { - "line": 125, + "line": 151, "column": 6 }, "end": { - "line": 125, + "line": 151, "column": 75 } } @@ -7204,15 +8269,15 @@ { "type": "CommentLine", "value": " to the relative IRI to make it absolute. This seems to avoid problems", - "start": 5426, - "end": 5498, + "start": 6589, + "end": 6661, "loc": { "start": { - "line": 126, + "line": 152, "column": 6 }, "end": { - "line": 126, + "line": 152, "column": 78 } } @@ -7220,15 +8285,15 @@ { "type": "CommentLine", "value": " with some JSON-LD parsers.", - "start": 5505, - "end": 5534, + "start": 6668, + "end": 6697, "loc": { "start": { - "line": 127, + "line": 153, "column": 6 }, "end": { - "line": 127, + "line": 153, "column": 35 } } @@ -7238,15 +8303,15 @@ { "type": "CommentLine", "value": " Add descriptions for individual nodes in each phylogeny.", - "start": 5921, - "end": 5980, + "start": 7084, + "end": 7143, "loc": { "start": { - "line": 139, + "line": 165, "column": 6 }, "end": { - "line": 139, + "line": 165, "column": 65 } } @@ -7255,58 +8320,58 @@ }, { "type": "ExpressionStatement", - "start": 5987, - "end": 6213, + "start": 7150, + "end": 7376, "loc": { "start": { - "line": 140, + "line": 166, "column": 6 }, "end": { - "line": 143, + "line": 169, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 5987, - "end": 6212, + "start": 7150, + "end": 7375, "loc": { "start": { - "line": 140, + "line": 166, "column": 6 }, "end": { - "line": 143, + "line": 169, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5987, - "end": 6005, + "start": 7150, + "end": 7168, "loc": { "start": { - "line": 140, + "line": 166, "column": 6 }, "end": { - "line": 140, + "line": 166, "column": 24 } }, "object": { "type": "Identifier", - "start": 5987, - "end": 5993, + "start": 7150, + "end": 7156, "loc": { "start": { - "line": 140, + "line": 166, "column": 6 }, "end": { - "line": 140, + "line": 166, "column": 12 }, "identifierName": "jsonld" @@ -7316,15 +8381,15 @@ }, "property": { "type": "Identifier", - "start": 5994, - "end": 6005, + "start": 7157, + "end": 7168, "loc": { "start": { - "line": 140, + "line": 166, "column": 13 }, "end": { - "line": 140, + "line": 166, "column": 24 }, "identifierName": "phylogenies" @@ -7336,57 +8401,57 @@ }, "right": { "type": "CallExpression", - "start": 6008, - "end": 6212, + "start": 7171, + "end": 7375, "loc": { "start": { - "line": 140, + "line": 166, "column": 27 }, "end": { - "line": 143, + "line": 169, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 6008, - "end": 6030, + "start": 7171, + "end": 7193, "loc": { "start": { - "line": 140, + "line": 166, "column": 27 }, "end": { - "line": 140, + "line": 166, "column": 49 } }, "object": { "type": "MemberExpression", - "start": 6008, - "end": 6026, + "start": 7171, + "end": 7189, "loc": { "start": { - "line": 140, + "line": 166, "column": 27 }, "end": { - "line": 140, + "line": 166, "column": 45 } }, "object": { "type": "Identifier", - "start": 6008, - "end": 6014, + "start": 7171, + "end": 7177, "loc": { "start": { - "line": 140, + "line": 166, "column": 27 }, "end": { - "line": 140, + "line": 166, "column": 33 }, "identifierName": "jsonld" @@ -7395,15 +8460,15 @@ }, "property": { "type": "Identifier", - "start": 6015, - "end": 6026, + "start": 7178, + "end": 7189, "loc": { "start": { - "line": 140, + "line": 166, "column": 34 }, "end": { - "line": 140, + "line": 166, "column": 45 }, "identifierName": "phylogenies" @@ -7414,15 +8479,15 @@ }, "property": { "type": "Identifier", - "start": 6027, - "end": 6030, + "start": 7190, + "end": 7193, "loc": { "start": { - "line": 140, + "line": 166, "column": 46 }, "end": { - "line": 140, + "line": 166, "column": 49 }, "identifierName": "map" @@ -7434,15 +8499,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6040, - "end": 6204, + "start": 7203, + "end": 7367, "loc": { "start": { - "line": 141, + "line": 167, "column": 8 }, "end": { - "line": 142, + "line": 168, "column": 78 } }, @@ -7453,15 +8518,15 @@ "params": [ { "type": "Identifier", - "start": 6041, - "end": 6050, + "start": 7204, + "end": 7213, "loc": { "start": { - "line": 141, + "line": 167, "column": 9 }, "end": { - "line": 141, + "line": 167, "column": 18 }, "identifierName": "phylogeny" @@ -7470,15 +8535,15 @@ }, { "type": "Identifier", - "start": 6052, - "end": 6066, + "start": 7215, + "end": 7229, "loc": { "start": { - "line": 141, + "line": 167, "column": 20 }, "end": { - "line": 141, + "line": 167, "column": 34 }, "identifierName": "countPhylogeny" @@ -7488,57 +8553,57 @@ ], "body": { "type": "CallExpression", - "start": 6071, - "end": 6204, + "start": 7234, + "end": 7367, "loc": { "start": { - "line": 141, + "line": 167, "column": 39 }, "end": { - "line": 142, + "line": 168, "column": 78 } }, "callee": { "type": "MemberExpression", - "start": 6071, - "end": 6145, + "start": 7234, + "end": 7308, "loc": { "start": { - "line": 141, + "line": 167, "column": 39 }, "end": { - "line": 142, + "line": 168, "column": 19 } }, "object": { "type": "NewExpression", - "start": 6071, - "end": 6125, + "start": 7234, + "end": 7288, "loc": { "start": { - "line": 141, + "line": 167, "column": 39 }, "end": { - "line": 141, + "line": 167, "column": 93 } }, "callee": { "type": "Identifier", - "start": 6075, - "end": 6091, + "start": 7238, + "end": 7254, "loc": { "start": { - "line": 141, + "line": 167, "column": 43 }, "end": { - "line": 141, + "line": 167, "column": 59 }, "identifierName": "PhylogenyWrapper" @@ -7548,15 +8613,15 @@ "arguments": [ { "type": "Identifier", - "start": 6092, - "end": 6101, + "start": 7255, + "end": 7264, "loc": { "start": { - "line": 141, + "line": 167, "column": 60 }, "end": { - "line": 141, + "line": 167, "column": 69 }, "identifierName": "phylogeny" @@ -7565,44 +8630,44 @@ }, { "type": "MemberExpression", - "start": 6103, - "end": 6124, + "start": 7266, + "end": 7287, "loc": { "start": { - "line": 141, + "line": 167, "column": 71 }, "end": { - "line": 141, + "line": 167, "column": 92 } }, "object": { "type": "ThisExpression", - "start": 6103, - "end": 6107, + "start": 7266, + "end": 7270, "loc": { "start": { - "line": 141, + "line": 167, "column": 71 }, "end": { - "line": 141, + "line": 167, "column": 75 } } }, "property": { "type": "Identifier", - "start": 6108, - "end": 6124, + "start": 7271, + "end": 7287, "loc": { "start": { - "line": 141, + "line": 167, "column": 76 }, "end": { - "line": 141, + "line": 167, "column": 92 }, "identifierName": "defaultNomenCode" @@ -7615,15 +8680,15 @@ }, "property": { "type": "Identifier", - "start": 6137, - "end": 6145, + "start": 7300, + "end": 7308, "loc": { "start": { - "line": 142, + "line": 168, "column": 11 }, "end": { - "line": 142, + "line": 168, "column": 19 }, "identifierName": "asJSONLD" @@ -7635,29 +8700,29 @@ "arguments": [ { "type": "CallExpression", - "start": 6146, - "end": 6184, + "start": 7309, + "end": 7347, "loc": { "start": { - "line": 142, + "line": 168, "column": 20 }, "end": { - "line": 142, + "line": 168, "column": 58 } }, "callee": { "type": "Identifier", - "start": 6146, - "end": 6168, + "start": 7309, + "end": 7331, "loc": { "start": { - "line": 142, + "line": 168, "column": 20 }, "end": { - "line": 142, + "line": 168, "column": 42 }, "identifierName": "getBaseIRIForPhylogeny" @@ -7667,15 +8732,15 @@ "arguments": [ { "type": "Identifier", - "start": 6169, - "end": 6183, + "start": 7332, + "end": 7346, "loc": { "start": { - "line": 142, + "line": 168, "column": 43 }, "end": { - "line": 142, + "line": 168, "column": 57 }, "identifierName": "countPhylogeny" @@ -7686,44 +8751,44 @@ }, { "type": "MemberExpression", - "start": 6186, - "end": 6203, + "start": 7349, + "end": 7366, "loc": { "start": { - "line": 142, + "line": 168, "column": 60 }, "end": { - "line": 142, + "line": 168, "column": 77 } }, "object": { "type": "ThisExpression", - "start": 6186, - "end": 6190, + "start": 7349, + "end": 7353, "loc": { "start": { - "line": 142, + "line": 168, "column": 60 }, "end": { - "line": 142, + "line": 168, "column": 64 } } }, "property": { "type": "Identifier", - "start": 6191, - "end": 6203, + "start": 7354, + "end": 7366, "loc": { "start": { - "line": 142, + "line": 168, "column": 65 }, "end": { - "line": 142, + "line": 168, "column": 77 }, "identifierName": "newickParser" @@ -7743,15 +8808,15 @@ { "type": "CommentLine", "value": " Add descriptions for individual nodes in each phylogeny.", - "start": 5921, - "end": 5980, + "start": 7084, + "end": 7143, "loc": { "start": { - "line": 139, + "line": 165, "column": 6 }, "end": { - "line": 139, + "line": 165, "column": 65 } } @@ -7761,15 +8826,15 @@ { "type": "CommentLine", "value": " Go through all the nodes and add information on expected resolution.", - "start": 6221, - "end": 6292, + "start": 7384, + "end": 7455, "loc": { "start": { - "line": 145, + "line": 171, "column": 6 }, "end": { - "line": 145, + "line": 171, "column": 77 } } @@ -7778,71 +8843,71 @@ }, { "type": "ExpressionStatement", - "start": 6299, - "end": 9714, + "start": 7462, + "end": 10877, "loc": { "start": { - "line": 146, + "line": 172, "column": 6 }, "end": { - "line": 221, + "line": 247, "column": 9 } }, "expression": { "type": "CallExpression", - "start": 6299, - "end": 9713, + "start": 7462, + "end": 10876, "loc": { "start": { - "line": 146, + "line": 172, "column": 6 }, "end": { - "line": 221, + "line": 247, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 6299, - "end": 6325, + "start": 7462, + "end": 7488, "loc": { "start": { - "line": 146, + "line": 172, "column": 6 }, "end": { - "line": 146, + "line": 172, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 6299, - "end": 6317, + "start": 7462, + "end": 7480, "loc": { "start": { - "line": 146, + "line": 172, "column": 6 }, "end": { - "line": 146, + "line": 172, "column": 24 } }, "object": { "type": "Identifier", - "start": 6299, - "end": 6305, + "start": 7462, + "end": 7468, "loc": { "start": { - "line": 146, + "line": 172, "column": 6 }, "end": { - "line": 146, + "line": 172, "column": 12 }, "identifierName": "jsonld" @@ -7852,15 +8917,15 @@ }, "property": { "type": "Identifier", - "start": 6306, - "end": 6317, + "start": 7469, + "end": 7480, "loc": { "start": { - "line": 146, + "line": 172, "column": 13 }, "end": { - "line": 146, + "line": 172, "column": 24 }, "identifierName": "phylogenies" @@ -7872,15 +8937,15 @@ }, "property": { "type": "Identifier", - "start": 6318, - "end": 6325, + "start": 7481, + "end": 7488, "loc": { "start": { - "line": 146, + "line": 172, "column": 25 }, "end": { - "line": 146, + "line": 172, "column": 32 }, "identifierName": "forEach" @@ -7893,15 +8958,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6326, - "end": 9712, + "start": 7489, + "end": 10875, "loc": { "start": { - "line": 146, + "line": 172, "column": 33 }, "end": { - "line": 221, + "line": 247, "column": 7 } }, @@ -7912,15 +8977,15 @@ "params": [ { "type": "Identifier", - "start": 6327, - "end": 6336, + "start": 7490, + "end": 7499, "loc": { "start": { - "line": 146, + "line": 172, "column": 34 }, "end": { - "line": 146, + "line": 172, "column": 43 }, "identifierName": "phylogeny" @@ -7930,59 +8995,59 @@ ], "body": { "type": "BlockStatement", - "start": 6341, - "end": 9712, + "start": 7504, + "end": 10875, "loc": { "start": { - "line": 146, + "line": 172, "column": 48 }, "end": { - "line": 221, + "line": 247, "column": 7 } }, "body": [ { "type": "VariableDeclaration", - "start": 6351, - "end": 6388, + "start": 7514, + "end": 7551, "loc": { "start": { - "line": 147, + "line": 173, "column": 8 }, "end": { - "line": 147, + "line": 173, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6357, - "end": 6387, + "start": 7520, + "end": 7550, "loc": { "start": { - "line": 147, + "line": 173, "column": 14 }, "end": { - "line": 147, + "line": 173, "column": 44 } }, "id": { "type": "Identifier", - "start": 6357, - "end": 6368, + "start": 7520, + "end": 7531, "loc": { "start": { - "line": 147, + "line": 173, "column": 14 }, "end": { - "line": 147, + "line": 173, "column": 25 }, "identifierName": "phylogenyId" @@ -7991,29 +9056,29 @@ }, "init": { "type": "MemberExpression", - "start": 6371, - "end": 6387, + "start": 7534, + "end": 7550, "loc": { "start": { - "line": 147, + "line": 173, "column": 28 }, "end": { - "line": 147, + "line": 173, "column": 44 } }, "object": { "type": "Identifier", - "start": 6371, - "end": 6380, + "start": 7534, + "end": 7543, "loc": { "start": { - "line": 147, + "line": 173, "column": 28 }, "end": { - "line": 147, + "line": 173, "column": 37 }, "identifierName": "phylogeny" @@ -8022,15 +9087,15 @@ }, "property": { "type": "StringLiteral", - "start": 6381, - "end": 6386, + "start": 7544, + "end": 7549, "loc": { "start": { - "line": 147, + "line": 173, "column": 38 }, "end": { - "line": 147, + "line": 173, "column": 43 } }, @@ -8048,85 +9113,85 @@ }, { "type": "ExpressionStatement", - "start": 6397, - "end": 9704, + "start": 7560, + "end": 10867, "loc": { "start": { - "line": 148, + "line": 174, "column": 8 }, "end": { - "line": 220, + "line": 246, "column": 11 } }, "expression": { "type": "CallExpression", - "start": 6397, - "end": 9703, + "start": 7560, + "end": 10866, "loc": { "start": { - "line": 148, + "line": 174, "column": 8 }, "end": { - "line": 220, + "line": 246, "column": 10 } }, "callee": { "type": "MemberExpression", - "start": 6397, - "end": 6428, + "start": 7560, + "end": 7591, "loc": { "start": { - "line": 148, + "line": 174, "column": 8 }, "end": { - "line": 148, + "line": 174, "column": 39 } }, "object": { "type": "LogicalExpression", - "start": 6398, - "end": 6419, + "start": 7561, + "end": 7582, "loc": { "start": { - "line": 148, + "line": 174, "column": 9 }, "end": { - "line": 148, + "line": 174, "column": 30 } }, "left": { "type": "MemberExpression", - "start": 6398, - "end": 6413, + "start": 7561, + "end": 7576, "loc": { "start": { - "line": 148, + "line": 174, "column": 9 }, "end": { - "line": 148, + "line": 174, "column": 24 } }, "object": { "type": "Identifier", - "start": 6398, - "end": 6407, + "start": 7561, + "end": 7570, "loc": { "start": { - "line": 148, + "line": 174, "column": 9 }, "end": { - "line": 148, + "line": 174, "column": 18 }, "identifierName": "phylogeny" @@ -8135,15 +9200,15 @@ }, "property": { "type": "Identifier", - "start": 6408, - "end": 6413, + "start": 7571, + "end": 7576, "loc": { "start": { - "line": 148, + "line": 174, "column": 19 }, "end": { - "line": 148, + "line": 174, "column": 24 }, "identifierName": "nodes" @@ -8155,15 +9220,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 6417, - "end": 6419, + "start": 7580, + "end": 7582, "loc": { "start": { - "line": 148, + "line": 174, "column": 28 }, "end": { - "line": 148, + "line": 174, "column": 30 } }, @@ -8171,20 +9236,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 6397 + "parenStart": 7560 } }, "property": { "type": "Identifier", - "start": 6421, - "end": 6428, + "start": 7584, + "end": 7591, "loc": { "start": { - "line": 148, + "line": 174, "column": 32 }, "end": { - "line": 148, + "line": 174, "column": 39 }, "identifierName": "forEach" @@ -8196,15 +9261,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6429, - "end": 9702, + "start": 7592, + "end": 10865, "loc": { "start": { - "line": 148, + "line": 174, "column": 40 }, "end": { - "line": 220, + "line": 246, "column": 9 } }, @@ -8215,15 +9280,15 @@ "params": [ { "type": "Identifier", - "start": 6430, - "end": 6434, + "start": 7593, + "end": 7597, "loc": { "start": { - "line": 148, + "line": 174, "column": 41 }, "end": { - "line": 148, + "line": 174, "column": 45 }, "identifierName": "node" @@ -8233,44 +9298,44 @@ ], "body": { "type": "BlockStatement", - "start": 6439, - "end": 9702, + "start": 7602, + "end": 10865, "loc": { "start": { - "line": 148, + "line": 174, "column": 50 }, "end": { - "line": 220, + "line": 246, "column": 9 } }, "body": [ { "type": "IfStatement", - "start": 6529, - "end": 6554, + "start": 7692, + "end": 7717, "loc": { "start": { - "line": 150, + "line": 176, "column": 10 }, "end": { - "line": 150, + "line": 176, "column": 35 } }, "test": { "type": "UnaryExpression", - "start": 6533, - "end": 6545, + "start": 7696, + "end": 7708, "loc": { "start": { - "line": 150, + "line": 176, "column": 14 }, "end": { - "line": 150, + "line": 176, "column": 26 } }, @@ -8278,29 +9343,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 6534, - "end": 6545, + "start": 7697, + "end": 7708, "loc": { "start": { - "line": 150, + "line": 176, "column": 15 }, "end": { - "line": 150, + "line": 176, "column": 26 } }, "object": { "type": "Identifier", - "start": 6534, - "end": 6538, + "start": 7697, + "end": 7701, "loc": { "start": { - "line": 150, + "line": 176, "column": 15 }, "end": { - "line": 150, + "line": 176, "column": 19 }, "identifierName": "node" @@ -8310,15 +9375,15 @@ }, "property": { "type": "Identifier", - "start": 6539, - "end": 6545, + "start": 7702, + "end": 7708, "loc": { "start": { - "line": 150, + "line": 176, "column": 20 }, "end": { - "line": 150, + "line": 176, "column": 26 }, "identifierName": "labels" @@ -8335,15 +9400,15 @@ }, "consequent": { "type": "ReturnStatement", - "start": 6547, - "end": 6554, + "start": 7710, + "end": 7717, "loc": { "start": { - "line": 150, + "line": 176, "column": 28 }, "end": { - "line": 150, + "line": 176, "column": 35 } }, @@ -8354,15 +9419,15 @@ { "type": "CommentLine", "value": " We can't set expected resolution information on unlabeled nodes.", - "start": 6451, - "end": 6518, + "start": 7614, + "end": 7681, "loc": { "start": { - "line": 149, + "line": 175, "column": 10 }, "end": { - "line": 149, + "line": 175, "column": 77 } } @@ -8371,71 +9436,71 @@ }, { "type": "ExpressionStatement", - "start": 6566, - "end": 9692, + "start": 7729, + "end": 10855, "loc": { "start": { - "line": 152, + "line": 178, "column": 10 }, "end": { - "line": 219, + "line": 245, "column": 13 } }, "expression": { "type": "CallExpression", - "start": 6566, - "end": 9691, + "start": 7729, + "end": 10854, "loc": { "start": { - "line": 152, + "line": 178, "column": 10 }, "end": { - "line": 219, + "line": 245, "column": 12 } }, "callee": { "type": "MemberExpression", - "start": 6566, - "end": 6590, + "start": 7729, + "end": 7753, "loc": { "start": { - "line": 152, + "line": 178, "column": 10 }, "end": { - "line": 152, + "line": 178, "column": 34 } }, "object": { "type": "MemberExpression", - "start": 6566, - "end": 6582, + "start": 7729, + "end": 7745, "loc": { "start": { - "line": 152, + "line": 178, "column": 10 }, "end": { - "line": 152, + "line": 178, "column": 26 } }, "object": { "type": "Identifier", - "start": 6566, - "end": 6572, + "start": 7729, + "end": 7735, "loc": { "start": { - "line": 152, + "line": 178, "column": 10 }, "end": { - "line": 152, + "line": 178, "column": 16 }, "identifierName": "jsonld" @@ -8444,15 +9509,15 @@ }, "property": { "type": "Identifier", - "start": 6573, - "end": 6582, + "start": 7736, + "end": 7745, "loc": { "start": { - "line": 152, + "line": 178, "column": 17 }, "end": { - "line": 152, + "line": 178, "column": 26 }, "identifierName": "phylorefs" @@ -8463,15 +9528,15 @@ }, "property": { "type": "Identifier", - "start": 6583, - "end": 6590, + "start": 7746, + "end": 7753, "loc": { "start": { - "line": 152, + "line": 178, "column": 27 }, "end": { - "line": 152, + "line": 178, "column": 34 }, "identifierName": "forEach" @@ -8483,15 +9548,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6591, - "end": 9690, + "start": 7754, + "end": 10853, "loc": { "start": { - "line": 152, + "line": 178, "column": 35 }, "end": { - "line": 219, + "line": 245, "column": 11 } }, @@ -8502,15 +9567,15 @@ "params": [ { "type": "Identifier", - "start": 6592, - "end": 6600, + "start": 7755, + "end": 7763, "loc": { "start": { - "line": 152, + "line": 178, "column": 36 }, "end": { - "line": 152, + "line": 178, "column": 44 }, "identifierName": "phyloref" @@ -8520,59 +9585,59 @@ ], "body": { "type": "BlockStatement", - "start": 6605, - "end": 9690, + "start": 7768, + "end": 10853, "loc": { "start": { - "line": 152, + "line": 178, "column": 49 }, "end": { - "line": 219, + "line": 245, "column": 11 } }, "body": [ { "type": "VariableDeclaration", - "start": 6619, - "end": 6654, + "start": 7782, + "end": 7817, "loc": { "start": { - "line": 153, + "line": 179, "column": 12 }, "end": { - "line": 153, + "line": 179, "column": 47 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6625, - "end": 6653, + "start": 7788, + "end": 7816, "loc": { "start": { - "line": 153, + "line": 179, "column": 18 }, "end": { - "line": 153, + "line": 179, "column": 46 } }, "id": { "type": "Identifier", - "start": 6625, - "end": 6635, + "start": 7788, + "end": 7798, "loc": { "start": { - "line": 153, + "line": 179, "column": 18 }, "end": { - "line": 153, + "line": 179, "column": 28 }, "identifierName": "phylorefId" @@ -8581,29 +9646,29 @@ }, "init": { "type": "MemberExpression", - "start": 6638, - "end": 6653, + "start": 7801, + "end": 7816, "loc": { "start": { - "line": 153, + "line": 179, "column": 31 }, "end": { - "line": 153, + "line": 179, "column": 46 } }, "object": { "type": "Identifier", - "start": 6638, - "end": 6646, + "start": 7801, + "end": 7809, "loc": { "start": { - "line": 153, + "line": 179, "column": 31 }, "end": { - "line": 153, + "line": 179, "column": 39 }, "identifierName": "phyloref" @@ -8612,15 +9677,15 @@ }, "property": { "type": "StringLiteral", - "start": 6647, - "end": 6652, + "start": 7810, + "end": 7815, "loc": { "start": { - "line": 153, + "line": 179, "column": 40 }, "end": { - "line": 153, + "line": 179, "column": 45 } }, @@ -8639,15 +9704,15 @@ { "type": "CommentLine", "value": " There are two ways in which we determine that a phyloreference", - "start": 6668, - "end": 6733, + "start": 7831, + "end": 7896, "loc": { "start": { - "line": 155, + "line": 181, "column": 12 }, "end": { - "line": 155, + "line": 181, "column": 77 } } @@ -8655,15 +9720,15 @@ { "type": "CommentLine", "value": " is expected to resolve to a node:", - "start": 6746, - "end": 6782, + "start": 7909, + "end": 7945, "loc": { "start": { - "line": 156, + "line": 182, "column": 12 }, "end": { - "line": 156, + "line": 182, "column": 48 } } @@ -8671,15 +9736,15 @@ { "type": "CommentLine", "value": " (1) If nodeLabel is set, then that must be one of the node's labels.", - "start": 6795, - "end": 6867, + "start": 7958, + "end": 8030, "loc": { "start": { - "line": 157, + "line": 183, "column": 12 }, "end": { - "line": 157, + "line": 183, "column": 84 } } @@ -8687,15 +9752,15 @@ { "type": "CommentLine", "value": " (2) If nodeLabel is not set, then one of the node's label should be", - "start": 6880, - "end": 6951, + "start": 8043, + "end": 8114, "loc": { "start": { - "line": 158, + "line": 184, "column": 12 }, "end": { - "line": 158, + "line": 184, "column": 83 } } @@ -8703,15 +9768,15 @@ { "type": "CommentLine", "value": " identical to the phyloreference's label.", - "start": 6964, - "end": 7012, + "start": 8127, + "end": 8175, "loc": { "start": { - "line": 159, + "line": 185, "column": 12 }, "end": { - "line": 159, + "line": 185, "column": 60 } } @@ -8719,15 +9784,15 @@ { "type": "CommentLine", "value": "", - "start": 7025, - "end": 7027, + "start": 8188, + "end": 8190, "loc": { "start": { - "line": 160, + "line": 186, "column": 12 }, "end": { - "line": 160, + "line": 186, "column": 14 } } @@ -8735,15 +9800,15 @@ { "type": "CommentLine", "value": " We set flagNodeExpectsPhyloref in all cases where we should note", - "start": 7040, - "end": 7107, + "start": 8203, + "end": 8270, "loc": { "start": { - "line": 161, + "line": 187, "column": 12 }, "end": { - "line": 161, + "line": 187, "column": 79 } } @@ -8751,15 +9816,15 @@ { "type": "CommentLine", "value": " that this node expects to resolve to this phyloreference.", - "start": 7120, - "end": 7180, + "start": 8283, + "end": 8343, "loc": { "start": { - "line": 162, + "line": 188, "column": 12 }, "end": { - "line": 162, + "line": 188, "column": 72 } } @@ -8768,44 +9833,44 @@ }, { "type": "VariableDeclaration", - "start": 7193, - "end": 7229, + "start": 8356, + "end": 8392, "loc": { "start": { - "line": 163, + "line": 189, "column": 12 }, "end": { - "line": 163, + "line": 189, "column": 48 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7197, - "end": 7228, + "start": 8360, + "end": 8391, "loc": { "start": { - "line": 163, + "line": 189, "column": 16 }, "end": { - "line": 163, + "line": 189, "column": 47 } }, "id": { "type": "Identifier", - "start": 7197, - "end": 7220, + "start": 8360, + "end": 8383, "loc": { "start": { - "line": 163, + "line": 189, "column": 16 }, "end": { - "line": 163, + "line": 189, "column": 39 }, "identifierName": "flagNodeExpectsPhyloref" @@ -8815,15 +9880,15 @@ }, "init": { "type": "BooleanLiteral", - "start": 7223, - "end": 7228, + "start": 8386, + "end": 8391, "loc": { "start": { - "line": 163, + "line": 189, "column": 42 }, "end": { - "line": 163, + "line": 189, "column": 47 } }, @@ -8837,15 +9902,15 @@ { "type": "CommentLine", "value": " There are two ways in which we determine that a phyloreference", - "start": 6668, - "end": 6733, + "start": 7831, + "end": 7896, "loc": { "start": { - "line": 155, + "line": 181, "column": 12 }, "end": { - "line": 155, + "line": 181, "column": 77 } } @@ -8853,15 +9918,15 @@ { "type": "CommentLine", "value": " is expected to resolve to a node:", - "start": 6746, - "end": 6782, + "start": 7909, + "end": 7945, "loc": { "start": { - "line": 156, + "line": 182, "column": 12 }, "end": { - "line": 156, + "line": 182, "column": 48 } } @@ -8869,15 +9934,15 @@ { "type": "CommentLine", "value": " (1) If nodeLabel is set, then that must be one of the node's labels.", - "start": 6795, - "end": 6867, + "start": 7958, + "end": 8030, "loc": { "start": { - "line": 157, + "line": 183, "column": 12 }, "end": { - "line": 157, + "line": 183, "column": 84 } } @@ -8885,15 +9950,15 @@ { "type": "CommentLine", "value": " (2) If nodeLabel is not set, then one of the node's label should be", - "start": 6880, - "end": 6951, + "start": 8043, + "end": 8114, "loc": { "start": { - "line": 158, + "line": 184, "column": 12 }, "end": { - "line": 158, + "line": 184, "column": 83 } } @@ -8901,15 +9966,15 @@ { "type": "CommentLine", "value": " identical to the phyloreference's label.", - "start": 6964, - "end": 7012, + "start": 8127, + "end": 8175, "loc": { "start": { - "line": 159, + "line": 185, "column": 12 }, "end": { - "line": 159, + "line": 185, "column": 60 } } @@ -8917,15 +9982,15 @@ { "type": "CommentLine", "value": "", - "start": 7025, - "end": 7027, + "start": 8188, + "end": 8190, "loc": { "start": { - "line": 160, + "line": 186, "column": 12 }, "end": { - "line": 160, + "line": 186, "column": 14 } } @@ -8933,15 +9998,15 @@ { "type": "CommentLine", "value": " We set flagNodeExpectsPhyloref in all cases where we should note", - "start": 7040, - "end": 7107, + "start": 8203, + "end": 8270, "loc": { "start": { - "line": 161, + "line": 187, "column": 12 }, "end": { - "line": 161, + "line": 187, "column": 79 } } @@ -8949,15 +10014,15 @@ { "type": "CommentLine", "value": " that this node expects to resolve to this phyloreference.", - "start": 7120, - "end": 7180, + "start": 8283, + "end": 8343, "loc": { "start": { - "line": 162, + "line": 188, "column": 12 }, "end": { - "line": 162, + "line": 188, "column": 72 } } @@ -8967,15 +10032,15 @@ { "type": "CommentLine", "value": " console.log(`Testing expected resolution of '${phylorefId}' on `", - "start": 7243, - "end": 7310, + "start": 8406, + "end": 8473, "loc": { "start": { - "line": 165, + "line": 191, "column": 12 }, "end": { - "line": 165, + "line": 191, "column": 79 } } @@ -8983,15 +10048,15 @@ { "type": "CommentLine", "value": " + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);", - "start": 7323, - "end": 7382, + "start": 8486, + "end": 8545, "loc": { "start": { - "line": 166, + "line": 192, "column": 12 }, "end": { - "line": 166, + "line": 192, "column": 71 } } @@ -9000,57 +10065,57 @@ }, { "type": "IfStatement", - "start": 7396, - "end": 8695, + "start": 8559, + "end": 9858, "loc": { "start": { - "line": 168, + "line": 194, "column": 12 }, "end": { - "line": 193, + "line": 219, "column": 13 } }, "test": { "type": "LogicalExpression", - "start": 7415, - "end": 7773, + "start": 8578, + "end": 8936, "loc": { "start": { - "line": 169, + "line": 195, "column": 14 }, "end": { - "line": 176, + "line": 202, "column": 15 } }, "left": { "type": "CallExpression", - "start": 7415, - "end": 7450, + "start": 8578, + "end": 8613, "loc": { "start": { - "line": 169, + "line": 195, "column": 14 }, "end": { - "line": 169, + "line": 195, "column": 49 } }, "callee": { "type": "Identifier", - "start": 7415, - "end": 7418, + "start": 8578, + "end": 8581, "loc": { "start": { - "line": 169, + "line": 195, "column": 14 }, "end": { - "line": 169, + "line": 195, "column": 17 }, "identifierName": "has" @@ -9061,15 +10126,15 @@ "arguments": [ { "type": "Identifier", - "start": 7419, - "end": 7427, + "start": 8582, + "end": 8590, "loc": { "start": { - "line": 169, + "line": 195, "column": 18 }, "end": { - "line": 169, + "line": 195, "column": 26 }, "identifierName": "phyloref" @@ -9078,15 +10143,15 @@ }, { "type": "StringLiteral", - "start": 7429, - "end": 7449, + "start": 8592, + "end": 8612, "loc": { "start": { - "line": 169, + "line": 195, "column": 28 }, "end": { - "line": 169, + "line": 195, "column": 48 } }, @@ -9102,43 +10167,43 @@ "operator": "&&", "right": { "type": "LogicalExpression", - "start": 7562, - "end": 7757, + "start": 8725, + "end": 8920, "loc": { "start": { - "line": 172, + "line": 198, "column": 16 }, "end": { - "line": 175, + "line": 201, "column": 80 } }, "left": { "type": "CallExpression", - "start": 7562, - "end": 7607, + "start": 8725, + "end": 8770, "loc": { "start": { - "line": 172, + "line": 198, "column": 16 }, "end": { - "line": 172, + "line": 198, "column": 61 } }, "callee": { "type": "Identifier", - "start": 7562, - "end": 7565, + "start": 8725, + "end": 8728, "loc": { "start": { - "line": 172, + "line": 198, "column": 16 }, "end": { - "line": 172, + "line": 198, "column": 19 }, "identifierName": "has" @@ -9149,29 +10214,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 7566, - "end": 7593, + "start": 8729, + "end": 8756, "loc": { "start": { - "line": 172, + "line": 198, "column": 20 }, "end": { - "line": 172, + "line": 198, "column": 47 } }, "object": { "type": "Identifier", - "start": 7566, - "end": 7574, + "start": 8729, + "end": 8737, "loc": { "start": { - "line": 172, + "line": 198, "column": 20 }, "end": { - "line": 172, + "line": 198, "column": 28 }, "identifierName": "phyloref" @@ -9180,15 +10245,15 @@ }, "property": { "type": "Identifier", - "start": 7575, - "end": 7593, + "start": 8738, + "end": 8756, "loc": { "start": { - "line": 172, + "line": 198, "column": 29 }, "end": { - "line": 172, + "line": 198, "column": 47 }, "identifierName": "expectedResolution" @@ -9199,15 +10264,15 @@ }, { "type": "Identifier", - "start": 7595, - "end": 7606, + "start": 8758, + "end": 8769, "loc": { "start": { - "line": 172, + "line": 198, "column": 49 }, "end": { - "line": 172, + "line": 198, "column": 60 }, "identifierName": "phylogenyId" @@ -9220,15 +10285,15 @@ { "type": "CommentLine", "value": " Or they might have used a relative phylogeny ID.", - "start": 7625, - "end": 7676, + "start": 8788, + "end": 8839, "loc": { "start": { - "line": 174, + "line": 200, "column": 16 }, "end": { - "line": 174, + "line": 200, "column": 67 } } @@ -9238,29 +10303,29 @@ "operator": "||", "right": { "type": "CallExpression", - "start": 7696, - "end": 7757, + "start": 8859, + "end": 8920, "loc": { "start": { - "line": 175, + "line": 201, "column": 19 }, "end": { - "line": 175, + "line": 201, "column": 80 } }, "callee": { "type": "Identifier", - "start": 7696, - "end": 7699, + "start": 8859, + "end": 8862, "loc": { "start": { - "line": 175, + "line": 201, "column": 19 }, "end": { - "line": 175, + "line": 201, "column": 22 }, "identifierName": "has" @@ -9271,29 +10336,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 7700, - "end": 7727, + "start": 8863, + "end": 8890, "loc": { "start": { - "line": 175, + "line": 201, "column": 23 }, "end": { - "line": 175, + "line": 201, "column": 50 } }, "object": { "type": "Identifier", - "start": 7700, - "end": 7708, + "start": 8863, + "end": 8871, "loc": { "start": { - "line": 175, + "line": 201, "column": 23 }, "end": { - "line": 175, + "line": 201, "column": 31 }, "identifierName": "phyloref" @@ -9302,15 +10367,15 @@ }, "property": { "type": "Identifier", - "start": 7709, - "end": 7727, + "start": 8872, + "end": 8890, "loc": { "start": { - "line": 175, + "line": 201, "column": 32 }, "end": { - "line": 175, + "line": 201, "column": 50 }, "identifierName": "expectedResolution" @@ -9321,29 +10386,29 @@ }, { "type": "CallExpression", - "start": 7729, - "end": 7756, + "start": 8892, + "end": 8919, "loc": { "start": { - "line": 175, + "line": 201, "column": 52 }, "end": { - "line": 175, + "line": 201, "column": 79 } }, "callee": { "type": "Identifier", - "start": 7729, - "end": 7743, + "start": 8892, + "end": 8906, "loc": { "start": { - "line": 175, + "line": 201, "column": 52 }, "end": { - "line": 175, + "line": 201, "column": 66 }, "identifierName": "makeIDRelative" @@ -9353,15 +10418,15 @@ "arguments": [ { "type": "Identifier", - "start": 7744, - "end": 7755, + "start": 8907, + "end": 8918, "loc": { "start": { - "line": 175, + "line": 201, "column": 67 }, "end": { - "line": 175, + "line": 201, "column": 78 }, "identifierName": "phylogenyId" @@ -9375,15 +10440,15 @@ { "type": "CommentLine", "value": " Or they might have used a relative phylogeny ID.", - "start": 7625, - "end": 7676, + "start": 8788, + "end": 8839, "loc": { "start": { - "line": 174, + "line": 200, "column": 16 }, "end": { - "line": 174, + "line": 200, "column": 67 } } @@ -9394,15 +10459,15 @@ { "type": "CommentLine", "value": " The user might have used the absolute phylogeny ID here.", - "start": 7486, - "end": 7545, + "start": 8649, + "end": 8708, "loc": { "start": { - "line": 171, + "line": 197, "column": 16 }, "end": { - "line": 171, + "line": 197, "column": 75 } } @@ -9410,66 +10475,66 @@ ], "extra": { "parenthesized": true, - "parenStart": 7468 + "parenStart": 8631 } }, "leadingComments": null }, "consequent": { "type": "BlockStatement", - "start": 7788, - "end": 8419, + "start": 8951, + "end": 9582, "loc": { "start": { - "line": 177, + "line": 203, "column": 14 }, "end": { - "line": 189, + "line": 215, "column": 13 } }, "body": [ { "type": "VariableDeclaration", - "start": 8048, - "end": 8266, + "start": 9211, + "end": 9429, "loc": { "start": { - "line": 182, + "line": 208, "column": 14 }, "end": { - "line": 184, + "line": 210, "column": 85 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8054, - "end": 8265, + "start": 9217, + "end": 9428, "loc": { "start": { - "line": 182, + "line": 208, "column": 20 }, "end": { - "line": 184, + "line": 210, "column": 84 } }, "id": { "type": "Identifier", - "start": 8054, - "end": 8063, + "start": 9217, + "end": 9226, "loc": { "start": { - "line": 182, + "line": 208, "column": 20 }, "end": { - "line": 182, + "line": 208, "column": 29 }, "identifierName": "nodeLabel" @@ -9479,43 +10544,43 @@ }, "init": { "type": "ConditionalExpression", - "start": 8066, - "end": 8265, + "start": 9229, + "end": 9428, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 184, + "line": 210, "column": 84 } }, "test": { "type": "CallExpression", - "start": 8066, - "end": 8111, + "start": 9229, + "end": 9274, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 182, + "line": 208, "column": 77 } }, "callee": { "type": "Identifier", - "start": 8066, - "end": 8069, + "start": 9229, + "end": 9232, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 182, + "line": 208, "column": 35 }, "identifierName": "has" @@ -9525,29 +10590,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 8070, - "end": 8097, + "start": 9233, + "end": 9260, "loc": { "start": { - "line": 182, + "line": 208, "column": 36 }, "end": { - "line": 182, + "line": 208, "column": 63 } }, "object": { "type": "Identifier", - "start": 8070, - "end": 8078, + "start": 9233, + "end": 9241, "loc": { "start": { - "line": 182, + "line": 208, "column": 36 }, "end": { - "line": 182, + "line": 208, "column": 44 }, "identifierName": "phyloref" @@ -9556,15 +10621,15 @@ }, "property": { "type": "Identifier", - "start": 8079, - "end": 8097, + "start": 9242, + "end": 9260, "loc": { "start": { - "line": 182, + "line": 208, "column": 45 }, "end": { - "line": 182, + "line": 208, "column": 63 }, "identifierName": "expectedResolution" @@ -9575,15 +10640,15 @@ }, { "type": "Identifier", - "start": 8099, - "end": 8110, + "start": 9262, + "end": 9273, "loc": { "start": { - "line": 182, + "line": 208, "column": 65 }, "end": { - "line": 182, + "line": 208, "column": 76 }, "identifierName": "phylogenyId" @@ -9594,57 +10659,57 @@ }, "consequent": { "type": "MemberExpression", - "start": 8130, - "end": 8180, + "start": 9293, + "end": 9343, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 68 } }, "object": { "type": "MemberExpression", - "start": 8130, - "end": 8170, + "start": 9293, + "end": 9333, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 8130, - "end": 8157, + "start": 9293, + "end": 9320, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 45 } }, "object": { "type": "Identifier", - "start": 8130, - "end": 8138, + "start": 9293, + "end": 9301, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 26 }, "identifierName": "phyloref" @@ -9653,15 +10718,15 @@ }, "property": { "type": "Identifier", - "start": 8139, - "end": 8157, + "start": 9302, + "end": 9320, "loc": { "start": { - "line": 183, + "line": 209, "column": 27 }, "end": { - "line": 183, + "line": 209, "column": 45 }, "identifierName": "expectedResolution" @@ -9672,15 +10737,15 @@ }, "property": { "type": "Identifier", - "start": 8158, - "end": 8169, + "start": 9321, + "end": 9332, "loc": { "start": { - "line": 183, + "line": 209, "column": 46 }, "end": { - "line": 183, + "line": 209, "column": 57 }, "identifierName": "phylogenyId" @@ -9691,15 +10756,15 @@ }, "property": { "type": "Identifier", - "start": 8171, - "end": 8180, + "start": 9334, + "end": 9343, "loc": { "start": { - "line": 183, + "line": 209, "column": 59 }, "end": { - "line": 183, + "line": 209, "column": 68 }, "identifierName": "nodeLabel" @@ -9710,57 +10775,57 @@ }, "alternate": { "type": "MemberExpression", - "start": 8199, - "end": 8265, + "start": 9362, + "end": 9428, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 84 } }, "object": { "type": "MemberExpression", - "start": 8199, - "end": 8255, + "start": 9362, + "end": 9418, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 74 } }, "object": { "type": "MemberExpression", - "start": 8199, - "end": 8226, + "start": 9362, + "end": 9389, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 45 } }, "object": { "type": "Identifier", - "start": 8199, - "end": 8207, + "start": 9362, + "end": 9370, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 26 }, "identifierName": "phyloref" @@ -9769,15 +10834,15 @@ }, "property": { "type": "Identifier", - "start": 8208, - "end": 8226, + "start": 9371, + "end": 9389, "loc": { "start": { - "line": 184, + "line": 210, "column": 27 }, "end": { - "line": 184, + "line": 210, "column": 45 }, "identifierName": "expectedResolution" @@ -9788,29 +10853,29 @@ }, "property": { "type": "CallExpression", - "start": 8227, - "end": 8254, + "start": 9390, + "end": 9417, "loc": { "start": { - "line": 184, + "line": 210, "column": 46 }, "end": { - "line": 184, + "line": 210, "column": 73 } }, "callee": { "type": "Identifier", - "start": 8227, - "end": 8241, + "start": 9390, + "end": 9404, "loc": { "start": { - "line": 184, + "line": 210, "column": 46 }, "end": { - "line": 184, + "line": 210, "column": 60 }, "identifierName": "makeIDRelative" @@ -9820,15 +10885,15 @@ "arguments": [ { "type": "Identifier", - "start": 8242, - "end": 8253, + "start": 9405, + "end": 9416, "loc": { "start": { - "line": 184, + "line": 210, "column": 61 }, "end": { - "line": 184, + "line": 210, "column": 72 }, "identifierName": "phylogenyId" @@ -9841,15 +10906,15 @@ }, "property": { "type": "Identifier", - "start": 8256, - "end": 8265, + "start": 9419, + "end": 9428, "loc": { "start": { - "line": 184, + "line": 210, "column": 75 }, "end": { - "line": 184, + "line": 210, "column": 84 }, "identifierName": "nodeLabel" @@ -9867,15 +10932,15 @@ { "type": "CommentLine", "value": " Expected resolution information set! The node label mentioned in that", - "start": 7804, - "end": 7876, + "start": 8967, + "end": 9039, "loc": { "start": { - "line": 178, + "line": 204, "column": 14 }, "end": { - "line": 178, + "line": 204, "column": 86 } } @@ -9883,15 +10948,15 @@ { "type": "CommentLine", "value": " information must be identical to one of the labels of this phylogeny node.", - "start": 7891, - "end": 7968, + "start": 9054, + "end": 9131, "loc": { "start": { - "line": 179, + "line": 205, "column": 14 }, "end": { - "line": 179, + "line": 205, "column": 91 } } @@ -9899,15 +10964,15 @@ { "type": "CommentLine", "value": " Figure out which phylogenyId was matched here.", - "start": 7984, - "end": 8033, + "start": 9147, + "end": 9196, "loc": { "start": { - "line": 181, + "line": 207, "column": 14 }, "end": { - "line": 181, + "line": 207, "column": 63 } } @@ -9916,43 +10981,43 @@ }, { "type": "IfStatement", - "start": 8282, - "end": 8405, + "start": 9445, + "end": 9568, "loc": { "start": { - "line": 186, + "line": 212, "column": 14 }, "end": { - "line": 188, + "line": 214, "column": 15 } }, "test": { "type": "LogicalExpression", - "start": 8286, - "end": 8338, + "start": 9449, + "end": 9501, "loc": { "start": { - "line": 186, + "line": 212, "column": 18 }, "end": { - "line": 186, + "line": 212, "column": 70 } }, "left": { "type": "Identifier", - "start": 8286, - "end": 8295, + "start": 9449, + "end": 9458, "loc": { "start": { - "line": 186, + "line": 212, "column": 18 }, "end": { - "line": 186, + "line": 212, "column": 27 }, "identifierName": "nodeLabel" @@ -9962,71 +11027,71 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 8299, - "end": 8338, + "start": 9462, + "end": 9501, "loc": { "start": { - "line": 186, + "line": 212, "column": 31 }, "end": { - "line": 186, + "line": 212, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 8299, - "end": 8327, + "start": 9462, + "end": 9490, "loc": { "start": { - "line": 186, + "line": 212, "column": 31 }, "end": { - "line": 186, + "line": 212, "column": 59 } }, "object": { "type": "LogicalExpression", - "start": 8300, - "end": 8317, + "start": 9463, + "end": 9480, "loc": { "start": { - "line": 186, + "line": 212, "column": 32 }, "end": { - "line": 186, + "line": 212, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 8300, - "end": 8311, + "start": 9463, + "end": 9474, "loc": { "start": { - "line": 186, + "line": 212, "column": 32 }, "end": { - "line": 186, + "line": 212, "column": 43 } }, "object": { "type": "Identifier", - "start": 8300, - "end": 8304, + "start": 9463, + "end": 9467, "loc": { "start": { - "line": 186, + "line": 212, "column": 32 }, "end": { - "line": 186, + "line": 212, "column": 36 }, "identifierName": "node" @@ -10035,15 +11100,15 @@ }, "property": { "type": "Identifier", - "start": 8305, - "end": 8311, + "start": 9468, + "end": 9474, "loc": { "start": { - "line": 186, + "line": 212, "column": 37 }, "end": { - "line": 186, + "line": 212, "column": 43 }, "identifierName": "labels" @@ -10055,15 +11120,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 8315, - "end": 8317, + "start": 9478, + "end": 9480, "loc": { "start": { - "line": 186, + "line": 212, "column": 47 }, "end": { - "line": 186, + "line": 212, "column": 49 } }, @@ -10071,20 +11136,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 8299 + "parenStart": 9462 } }, "property": { "type": "Identifier", - "start": 8319, - "end": 8327, + "start": 9482, + "end": 9490, "loc": { "start": { - "line": 186, + "line": 212, "column": 51 }, "end": { - "line": 186, + "line": 212, "column": 59 }, "identifierName": "includes" @@ -10096,15 +11161,15 @@ "arguments": [ { "type": "Identifier", - "start": 8328, - "end": 8337, + "start": 9491, + "end": 9500, "loc": { "start": { - "line": 186, + "line": 212, "column": 60 }, "end": { - "line": 186, + "line": 212, "column": 69 }, "identifierName": "nodeLabel" @@ -10116,59 +11181,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 8340, - "end": 8405, + "start": 9503, + "end": 9568, "loc": { "start": { - "line": 186, + "line": 212, "column": 72 }, "end": { - "line": 188, + "line": 214, "column": 15 } }, "body": [ { "type": "ExpressionStatement", - "start": 8358, - "end": 8389, + "start": 9521, + "end": 9552, "loc": { "start": { - "line": 187, + "line": 213, "column": 16 }, "end": { - "line": 187, + "line": 213, "column": 47 } }, "expression": { "type": "AssignmentExpression", - "start": 8358, - "end": 8388, + "start": 9521, + "end": 9551, "loc": { "start": { - "line": 187, + "line": 213, "column": 16 }, "end": { - "line": 187, + "line": 213, "column": 46 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8358, - "end": 8381, + "start": 9521, + "end": 9544, "loc": { "start": { - "line": 187, + "line": 213, "column": 16 }, "end": { - "line": 187, + "line": 213, "column": 39 }, "identifierName": "flagNodeExpectsPhyloref" @@ -10177,15 +11242,15 @@ }, "right": { "type": "BooleanLiteral", - "start": 8384, - "end": 8388, + "start": 9547, + "end": 9551, "loc": { "start": { - "line": 187, + "line": 213, "column": 42 }, "end": { - "line": 187, + "line": 213, "column": 46 } }, @@ -10203,85 +11268,85 @@ }, "alternate": { "type": "IfStatement", - "start": 8425, - "end": 8695, + "start": 9588, + "end": 9858, "loc": { "start": { - "line": 189, + "line": 215, "column": 19 }, "end": { - "line": 193, + "line": 219, "column": 13 } }, "test": { "type": "CallExpression", - "start": 8429, - "end": 8473, + "start": 9592, + "end": 9636, "loc": { "start": { - "line": 189, + "line": 215, "column": 23 }, "end": { - "line": 189, + "line": 215, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 8429, - "end": 8457, + "start": 9592, + "end": 9620, "loc": { "start": { - "line": 189, + "line": 215, "column": 23 }, "end": { - "line": 189, + "line": 215, "column": 51 } }, "object": { "type": "LogicalExpression", - "start": 8430, - "end": 8447, + "start": 9593, + "end": 9610, "loc": { "start": { - "line": 189, + "line": 215, "column": 24 }, "end": { - "line": 189, + "line": 215, "column": 41 } }, "left": { "type": "MemberExpression", - "start": 8430, - "end": 8441, + "start": 9593, + "end": 9604, "loc": { "start": { - "line": 189, + "line": 215, "column": 24 }, "end": { - "line": 189, + "line": 215, "column": 35 } }, "object": { "type": "Identifier", - "start": 8430, - "end": 8434, + "start": 9593, + "end": 9597, "loc": { "start": { - "line": 189, + "line": 215, "column": 24 }, "end": { - "line": 189, + "line": 215, "column": 28 }, "identifierName": "node" @@ -10290,15 +11355,15 @@ }, "property": { "type": "Identifier", - "start": 8435, - "end": 8441, + "start": 9598, + "end": 9604, "loc": { "start": { - "line": 189, + "line": 215, "column": 29 }, "end": { - "line": 189, + "line": 215, "column": 35 }, "identifierName": "labels" @@ -10310,15 +11375,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 8445, - "end": 8447, + "start": 9608, + "end": 9610, "loc": { "start": { - "line": 189, + "line": 215, "column": 39 }, "end": { - "line": 189, + "line": 215, "column": 41 } }, @@ -10326,20 +11391,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 8429 + "parenStart": 9592 } }, "property": { "type": "Identifier", - "start": 8449, - "end": 8457, + "start": 9612, + "end": 9620, "loc": { "start": { - "line": 189, + "line": 215, "column": 43 }, "end": { - "line": 189, + "line": 215, "column": 51 }, "identifierName": "includes" @@ -10351,29 +11416,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 8458, - "end": 8472, + "start": 9621, + "end": 9635, "loc": { "start": { - "line": 189, + "line": 215, "column": 52 }, "end": { - "line": 189, + "line": 215, "column": 66 } }, "object": { "type": "Identifier", - "start": 8458, - "end": 8466, + "start": 9621, + "end": 9629, "loc": { "start": { - "line": 189, + "line": 215, "column": 52 }, "end": { - "line": 189, + "line": 215, "column": 60 }, "identifierName": "phyloref" @@ -10382,15 +11447,15 @@ }, "property": { "type": "Identifier", - "start": 8467, - "end": 8472, + "start": 9630, + "end": 9635, "loc": { "start": { - "line": 189, + "line": 215, "column": 61 }, "end": { - "line": 189, + "line": 215, "column": 66 }, "identifierName": "label" @@ -10403,59 +11468,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 8475, - "end": 8695, + "start": 9638, + "end": 9858, "loc": { "start": { - "line": 189, + "line": 215, "column": 69 }, "end": { - "line": 193, + "line": 219, "column": 13 } }, "body": [ { "type": "ExpressionStatement", - "start": 8650, - "end": 8681, + "start": 9813, + "end": 9844, "loc": { "start": { - "line": 192, + "line": 218, "column": 14 }, "end": { - "line": 192, + "line": 218, "column": 45 } }, "expression": { "type": "AssignmentExpression", - "start": 8650, - "end": 8680, + "start": 9813, + "end": 9843, "loc": { "start": { - "line": 192, + "line": 218, "column": 14 }, "end": { - "line": 192, + "line": 218, "column": 44 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8650, - "end": 8673, + "start": 9813, + "end": 9836, "loc": { "start": { - "line": 192, + "line": 218, "column": 14 }, "end": { - "line": 192, + "line": 218, "column": 37 }, "identifierName": "flagNodeExpectsPhyloref" @@ -10465,15 +11530,15 @@ }, "right": { "type": "BooleanLiteral", - "start": 8676, - "end": 8680, + "start": 9839, + "end": 9843, "loc": { "start": { - "line": 192, + "line": 218, "column": 40 }, "end": { - "line": 192, + "line": 218, "column": 44 } }, @@ -10485,15 +11550,15 @@ { "type": "CommentLine", "value": " No expected resolution information, so we just check whether", - "start": 8491, - "end": 8554, + "start": 9654, + "end": 9717, "loc": { "start": { - "line": 190, + "line": 216, "column": 14 }, "end": { - "line": 190, + "line": 216, "column": 77 } } @@ -10501,15 +11566,15 @@ { "type": "CommentLine", "value": " the phyloref label is one of the labels on this phylogeny node.", - "start": 8569, - "end": 8635, + "start": 9732, + "end": 9798, "loc": { "start": { - "line": 191, + "line": 217, "column": 14 }, "end": { - "line": 191, + "line": 217, "column": 80 } } @@ -10525,15 +11590,15 @@ { "type": "CommentLine", "value": " console.log(`Testing expected resolution of '${phylorefId}' on `", - "start": 7243, - "end": 7310, + "start": 8406, + "end": 8473, "loc": { "start": { - "line": 165, + "line": 191, "column": 12 }, "end": { - "line": 165, + "line": 191, "column": 79 } } @@ -10541,15 +11606,15 @@ { "type": "CommentLine", "value": " + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);", - "start": 7323, - "end": 7382, + "start": 8486, + "end": 8545, "loc": { "start": { - "line": 166, + "line": 192, "column": 12 }, "end": { - "line": 166, + "line": 192, "column": 71 } } @@ -10558,29 +11623,29 @@ }, { "type": "IfStatement", - "start": 8709, - "end": 9678, + "start": 9872, + "end": 10841, "loc": { "start": { - "line": 195, + "line": 221, "column": 12 }, "end": { - "line": 218, + "line": 244, "column": 13 } }, "test": { "type": "Identifier", - "start": 8713, - "end": 8736, + "start": 9876, + "end": 9899, "loc": { "start": { - "line": 195, + "line": 221, "column": 16 }, "end": { - "line": 195, + "line": 221, "column": 39 }, "identifierName": "flagNodeExpectsPhyloref" @@ -10589,86 +11654,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 8738, - "end": 9678, + "start": 9901, + "end": 10841, "loc": { "start": { - "line": 195, + "line": 221, "column": 41 }, "end": { - "line": 218, + "line": 244, "column": 13 } }, "body": [ { "type": "ExpressionStatement", - "start": 9009, - "end": 9664, + "start": 10172, + "end": 10827, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 217, + "line": 243, "column": 17 } }, "expression": { "type": "CallExpression", - "start": 9009, - "end": 9663, + "start": 10172, + "end": 10826, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 217, + "line": 243, "column": 16 } }, "callee": { "type": "MemberExpression", - "start": 9009, - "end": 9037, + "start": 10172, + "end": 10200, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 201, + "line": 227, "column": 42 } }, "object": { "type": "MemberExpression", - "start": 9009, - "end": 9032, + "start": 10172, + "end": 10195, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 201, + "line": 227, "column": 37 } }, "object": { "type": "Identifier", - "start": 9009, - "end": 9013, + "start": 10172, + "end": 10176, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 201, + "line": 227, "column": 18 }, "identifierName": "node" @@ -10678,29 +11743,29 @@ }, "property": { "type": "MemberExpression", - "start": 9014, - "end": 9031, + "start": 10177, + "end": 10194, "loc": { "start": { - "line": 201, + "line": 227, "column": 19 }, "end": { - "line": 201, + "line": 227, "column": 36 } }, "object": { "type": "Identifier", - "start": 9014, - "end": 9022, + "start": 10177, + "end": 10185, "loc": { "start": { - "line": 201, + "line": 227, "column": 19 }, "end": { - "line": 201, + "line": 227, "column": 27 }, "identifierName": "owlterms" @@ -10709,15 +11774,15 @@ }, "property": { "type": "Identifier", - "start": 9023, - "end": 9031, + "start": 10186, + "end": 10194, "loc": { "start": { - "line": 201, + "line": 227, "column": 28 }, "end": { - "line": 201, + "line": 227, "column": 36 }, "identifierName": "RDF_TYPE" @@ -10731,15 +11796,15 @@ }, "property": { "type": "Identifier", - "start": 9033, - "end": 9037, + "start": 10196, + "end": 10200, "loc": { "start": { - "line": 201, + "line": 227, "column": 38 }, "end": { - "line": 201, + "line": 227, "column": 42 }, "identifierName": "push" @@ -10752,30 +11817,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 9038, - "end": 9662, + "start": 10201, + "end": 10825, "loc": { "start": { - "line": 201, + "line": 227, "column": 43 }, "end": { - "line": 217, + "line": 243, "column": 15 } }, "properties": [ { "type": "ObjectProperty", - "start": 9056, - "end": 9089, + "start": 10219, + "end": 10252, "loc": { "start": { - "line": 202, + "line": 228, "column": 16 }, "end": { - "line": 202, + "line": 228, "column": 49 } }, @@ -10784,15 +11849,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9056, - "end": 9063, + "start": 10219, + "end": 10226, "loc": { "start": { - "line": 202, + "line": 228, "column": 16 }, "end": { - "line": 202, + "line": 228, "column": 23 } }, @@ -10804,29 +11869,29 @@ }, "value": { "type": "MemberExpression", - "start": 9065, - "end": 9089, + "start": 10228, + "end": 10252, "loc": { "start": { - "line": 202, + "line": 228, "column": 25 }, "end": { - "line": 202, + "line": 228, "column": 49 } }, "object": { "type": "Identifier", - "start": 9065, - "end": 9073, + "start": 10228, + "end": 10236, "loc": { "start": { - "line": 202, + "line": 228, "column": 25 }, "end": { - "line": 202, + "line": 228, "column": 33 }, "identifierName": "owlterms" @@ -10835,15 +11900,15 @@ }, "property": { "type": "Identifier", - "start": 9074, - "end": 9089, + "start": 10237, + "end": 10252, "loc": { "start": { - "line": 202, + "line": 228, "column": 34 }, "end": { - "line": 202, + "line": 228, "column": 49 }, "identifierName": "OWL_RESTRICTION" @@ -10855,15 +11920,15 @@ }, { "type": "ObjectProperty", - "start": 9107, - "end": 9154, + "start": 10270, + "end": 10317, "loc": { "start": { - "line": 203, + "line": 229, "column": 16 }, "end": { - "line": 203, + "line": 229, "column": 63 } }, @@ -10872,15 +11937,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9107, - "end": 9117, + "start": 10270, + "end": 10280, "loc": { "start": { - "line": 203, + "line": 229, "column": 16 }, "end": { - "line": 203, + "line": 229, "column": 26 }, "identifierName": "onProperty" @@ -10889,29 +11954,29 @@ }, "value": { "type": "MemberExpression", - "start": 9119, - "end": 9154, + "start": 10282, + "end": 10317, "loc": { "start": { - "line": 203, + "line": 229, "column": 28 }, "end": { - "line": 203, + "line": 229, "column": 63 } }, "object": { "type": "Identifier", - "start": 9119, - "end": 9127, + "start": 10282, + "end": 10290, "loc": { "start": { - "line": 203, + "line": 229, "column": 28 }, "end": { - "line": 203, + "line": 229, "column": 36 }, "identifierName": "owlterms" @@ -10920,15 +11985,15 @@ }, "property": { "type": "Identifier", - "start": 9128, - "end": 9154, + "start": 10291, + "end": 10317, "loc": { "start": { - "line": 203, + "line": 229, "column": 37 }, "end": { - "line": 203, + "line": 229, "column": 63 }, "identifierName": "OBI_IS_SPECIFIED_OUTPUT_OF" @@ -10940,15 +12005,15 @@ }, { "type": "ObjectProperty", - "start": 9172, - "end": 9645, + "start": 10335, + "end": 10808, "loc": { "start": { - "line": 204, + "line": 230, "column": 16 }, "end": { - "line": 216, + "line": 242, "column": 17 } }, @@ -10957,15 +12022,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9172, - "end": 9186, + "start": 10335, + "end": 10349, "loc": { "start": { - "line": 204, + "line": 230, "column": 16 }, "end": { - "line": 204, + "line": 230, "column": 30 }, "identifierName": "someValuesFrom" @@ -10974,30 +12039,30 @@ }, "value": { "type": "ObjectExpression", - "start": 9188, - "end": 9645, + "start": 10351, + "end": 10808, "loc": { "start": { - "line": 204, + "line": 230, "column": 32 }, "end": { - "line": 216, + "line": 242, "column": 17 } }, "properties": [ { "type": "ObjectProperty", - "start": 9208, - "end": 9235, + "start": 10371, + "end": 10398, "loc": { "start": { - "line": 205, + "line": 231, "column": 18 }, "end": { - "line": 205, + "line": 231, "column": 45 } }, @@ -11006,15 +12071,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9208, - "end": 9215, + "start": 10371, + "end": 10378, "loc": { "start": { - "line": 205, + "line": 231, "column": 18 }, "end": { - "line": 205, + "line": 231, "column": 25 } }, @@ -11026,29 +12091,29 @@ }, "value": { "type": "MemberExpression", - "start": 9217, - "end": 9235, + "start": 10380, + "end": 10398, "loc": { "start": { - "line": 205, + "line": 231, "column": 27 }, "end": { - "line": 205, + "line": 231, "column": 45 } }, "object": { "type": "Identifier", - "start": 9217, - "end": 9225, + "start": 10380, + "end": 10388, "loc": { "start": { - "line": 205, + "line": 231, "column": 27 }, "end": { - "line": 205, + "line": 231, "column": 35 }, "identifierName": "owlterms" @@ -11057,15 +12122,15 @@ }, "property": { "type": "Identifier", - "start": 9226, - "end": 9235, + "start": 10389, + "end": 10398, "loc": { "start": { - "line": 205, + "line": 231, "column": 36 }, "end": { - "line": 205, + "line": 231, "column": 45 }, "identifierName": "OWL_CLASS" @@ -11077,15 +12142,15 @@ }, { "type": "ObjectProperty", - "start": 9255, - "end": 9626, + "start": 10418, + "end": 10789, "loc": { "start": { - "line": 206, + "line": 232, "column": 18 }, "end": { - "line": 215, + "line": 241, "column": 19 } }, @@ -11094,15 +12159,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9255, - "end": 9269, + "start": 10418, + "end": 10432, "loc": { "start": { - "line": 206, + "line": 232, "column": 18 }, "end": { - "line": 206, + "line": 232, "column": 32 }, "identifierName": "intersectionOf" @@ -11111,45 +12176,45 @@ }, "value": { "type": "ArrayExpression", - "start": 9271, - "end": 9626, + "start": 10434, + "end": 10789, "loc": { "start": { - "line": 206, + "line": 232, "column": 34 }, "end": { - "line": 215, + "line": 241, "column": 19 } }, "elements": [ { "type": "ObjectExpression", - "start": 9293, - "end": 9327, + "start": 10456, + "end": 10490, "loc": { "start": { - "line": 207, + "line": 233, "column": 20 }, "end": { - "line": 207, + "line": 233, "column": 54 } }, "properties": [ { "type": "ObjectProperty", - "start": 9295, - "end": 9325, + "start": 10458, + "end": 10488, "loc": { "start": { - "line": 207, + "line": 233, "column": 22 }, "end": { - "line": 207, + "line": 233, "column": 52 } }, @@ -11158,15 +12223,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9295, - "end": 9300, + "start": 10458, + "end": 10463, "loc": { "start": { - "line": 207, + "line": 233, "column": 22 }, "end": { - "line": 207, + "line": 233, "column": 27 } }, @@ -11178,29 +12243,29 @@ }, "value": { "type": "MemberExpression", - "start": 9302, - "end": 9325, + "start": 10465, + "end": 10488, "loc": { "start": { - "line": 207, + "line": 233, "column": 29 }, "end": { - "line": 207, + "line": 233, "column": 52 } }, "object": { "type": "Identifier", - "start": 9302, - "end": 9310, + "start": 10465, + "end": 10473, "loc": { "start": { - "line": 207, + "line": 233, "column": 29 }, "end": { - "line": 207, + "line": 233, "column": 37 }, "identifierName": "owlterms" @@ -11209,15 +12274,15 @@ }, "property": { "type": "Identifier", - "start": 9311, - "end": 9325, + "start": 10474, + "end": 10488, "loc": { "start": { - "line": 207, + "line": 233, "column": 38 }, "end": { - "line": 207, + "line": 233, "column": 52 }, "identifierName": "OBI_PREDICTION" @@ -11231,30 +12296,30 @@ }, { "type": "ObjectExpression", - "start": 9349, - "end": 9605, + "start": 10512, + "end": 10768, "loc": { "start": { - "line": 208, + "line": 234, "column": 20 }, "end": { - "line": 214, + "line": 240, "column": 21 } }, "properties": [ { "type": "ObjectProperty", - "start": 9373, - "end": 9406, + "start": 10536, + "end": 10569, "loc": { "start": { - "line": 209, + "line": 235, "column": 22 }, "end": { - "line": 209, + "line": 235, "column": 55 } }, @@ -11263,15 +12328,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9373, - "end": 9380, + "start": 10536, + "end": 10543, "loc": { "start": { - "line": 209, + "line": 235, "column": 22 }, "end": { - "line": 209, + "line": 235, "column": 29 } }, @@ -11283,29 +12348,29 @@ }, "value": { "type": "MemberExpression", - "start": 9382, - "end": 9406, + "start": 10545, + "end": 10569, "loc": { "start": { - "line": 209, + "line": 235, "column": 31 }, "end": { - "line": 209, + "line": 235, "column": 55 } }, "object": { "type": "Identifier", - "start": 9382, - "end": 9390, + "start": 10545, + "end": 10553, "loc": { "start": { - "line": 209, + "line": 235, "column": 31 }, "end": { - "line": 209, + "line": 235, "column": 39 }, "identifierName": "owlterms" @@ -11314,15 +12379,15 @@ }, "property": { "type": "Identifier", - "start": 9391, - "end": 9406, + "start": 10554, + "end": 10569, "loc": { "start": { - "line": 209, + "line": 235, "column": 40 }, "end": { - "line": 209, + "line": 235, "column": 55 }, "identifierName": "OWL_RESTRICTION" @@ -11334,15 +12399,15 @@ }, { "type": "ObjectProperty", - "start": 9430, - "end": 9474, + "start": 10593, + "end": 10637, "loc": { "start": { - "line": 210, + "line": 236, "column": 22 }, "end": { - "line": 210, + "line": 236, "column": 66 } }, @@ -11351,15 +12416,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9430, - "end": 9440, + "start": 10593, + "end": 10603, "loc": { "start": { - "line": 210, + "line": 236, "column": 22 }, "end": { - "line": 210, + "line": 236, "column": 32 }, "identifierName": "onProperty" @@ -11368,29 +12433,29 @@ }, "value": { "type": "MemberExpression", - "start": 9442, - "end": 9474, + "start": 10605, + "end": 10637, "loc": { "start": { - "line": 210, + "line": 236, "column": 34 }, "end": { - "line": 210, + "line": 236, "column": 66 } }, "object": { "type": "Identifier", - "start": 9442, - "end": 9450, + "start": 10605, + "end": 10613, "loc": { "start": { - "line": 210, + "line": 236, "column": 34 }, "end": { - "line": 210, + "line": 236, "column": 42 }, "identifierName": "owlterms" @@ -11399,15 +12464,15 @@ }, "property": { "type": "Identifier", - "start": 9451, - "end": 9474, + "start": 10614, + "end": 10637, "loc": { "start": { - "line": 210, + "line": 236, "column": 43 }, "end": { - "line": 210, + "line": 236, "column": 66 }, "identifierName": "OBI_HAS_SPECIFIED_INPUT" @@ -11419,15 +12484,15 @@ }, { "type": "ObjectProperty", - "start": 9498, - "end": 9582, + "start": 10661, + "end": 10745, "loc": { "start": { - "line": 211, + "line": 237, "column": 22 }, "end": { - "line": 213, + "line": 239, "column": 23 } }, @@ -11436,15 +12501,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9498, - "end": 9512, + "start": 10661, + "end": 10675, "loc": { "start": { - "line": 211, + "line": 237, "column": 22 }, "end": { - "line": 211, + "line": 237, "column": 36 }, "identifierName": "someValuesFrom" @@ -11453,30 +12518,30 @@ }, "value": { "type": "ObjectExpression", - "start": 9514, - "end": 9582, + "start": 10677, + "end": 10745, "loc": { "start": { - "line": 211, + "line": 237, "column": 38 }, "end": { - "line": 213, + "line": 239, "column": 23 } }, "properties": [ { "type": "ObjectProperty", - "start": 9540, - "end": 9557, + "start": 10703, + "end": 10720, "loc": { "start": { - "line": 212, + "line": 238, "column": 24 }, "end": { - "line": 212, + "line": 238, "column": 41 } }, @@ -11485,15 +12550,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9540, - "end": 9545, + "start": 10703, + "end": 10708, "loc": { "start": { - "line": 212, + "line": 238, "column": 24 }, "end": { - "line": 212, + "line": 238, "column": 29 } }, @@ -11505,15 +12570,15 @@ }, "value": { "type": "Identifier", - "start": 9547, - "end": 9557, + "start": 10710, + "end": 10720, "loc": { "start": { - "line": 212, + "line": 238, "column": 31 }, "end": { - "line": 212, + "line": 238, "column": 41 }, "identifierName": "phylorefId" @@ -11541,15 +12606,15 @@ { "type": "CommentLine", "value": " Modify this phylogeny node's type to include that it is a type", - "start": 8754, - "end": 8819, + "start": 9917, + "end": 9982, "loc": { "start": { - "line": 196, + "line": 222, "column": 14 }, "end": { - "line": 196, + "line": 222, "column": 79 } } @@ -11557,15 +12622,15 @@ { "type": "CommentLine", "value": " of:", - "start": 8834, - "end": 8840, + "start": 9997, + "end": 10003, "loc": { "start": { - "line": 197, + "line": 223, "column": 14 }, "end": { - "line": 197, + "line": 223, "column": 20 } } @@ -11573,15 +12638,15 @@ { "type": "CommentLine", "value": " obi:is_specified_output_of some (", - "start": 8855, - "end": 8892, + "start": 10018, + "end": 10055, "loc": { "start": { - "line": 198, + "line": 224, "column": 14 }, "end": { - "line": 198, + "line": 224, "column": 51 } } @@ -11589,15 +12654,15 @@ { "type": "CommentLine", "value": " obi:Prediction and obi:has_specified_output some #phyloref_id", - "start": 8907, - "end": 8974, + "start": 10070, + "end": 10137, "loc": { "start": { - "line": 199, + "line": 225, "column": 14 }, "end": { - "line": 199, + "line": 225, "column": 81 } } @@ -11605,15 +12670,15 @@ { "type": "CommentLine", "value": " )", - "start": 8989, - "end": 8994, + "start": 10152, + "end": 10157, "loc": { "start": { - "line": 200, + "line": 226, "column": 14 }, "end": { - "line": 200, + "line": 226, "column": 19 } } @@ -11650,15 +12715,15 @@ { "type": "CommentLine", "value": " Go through all the nodes and add information on expected resolution.", - "start": 6221, - "end": 6292, + "start": 7384, + "end": 7455, "loc": { "start": { - "line": 145, + "line": 171, "column": 6 }, "end": { - "line": 145, + "line": 171, "column": 77 } } @@ -11674,15 +12739,15 @@ { "type": "CommentLine", "value": " Earlier, we used to generate a list of taxonomic matches here (stored in", - "start": 9726, - "end": 9801, + "start": 10889, + "end": 10964, "loc": { "start": { - "line": 224, + "line": 250, "column": 4 }, "end": { - "line": 224, + "line": 250, "column": 79 } } @@ -11690,15 +12755,15 @@ { "type": "CommentLine", "value": " jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic", - "start": 9806, - "end": 9879, + "start": 10969, + "end": 11042, "loc": { "start": { - "line": 225, + "line": 251, "column": 4 }, "end": { - "line": 225, + "line": 251, "column": 77 } } @@ -11706,15 +12771,15 @@ { "type": "CommentLine", "value": " units in phyloref specifiers were related to taxonomic units in phylogeny", - "start": 9884, - "end": 9960, + "start": 11047, + "end": 11123, "loc": { "start": { - "line": 226, + "line": 252, "column": 4 }, "end": { - "line": 226, + "line": 252, "column": 80 } } @@ -11722,15 +12787,15 @@ { "type": "CommentLine", "value": " nodes. This is no longer necessary, since phyloref specifiers are now logical", - "start": 9965, - "end": 10045, + "start": 11128, + "end": 11208, "loc": { "start": { - "line": 227, + "line": 253, "column": 4 }, "end": { - "line": 227, + "line": 253, "column": 84 } } @@ -11738,15 +12803,15 @@ { "type": "CommentLine", "value": " expressions that directly evaluate to phylogeny nodes. However, if in the", - "start": 10050, - "end": 10126, + "start": 11213, + "end": 11289, "loc": { "start": { - "line": 228, + "line": 254, "column": 4 }, "end": { - "line": 228, + "line": 254, "column": 80 } } @@ -11754,15 +12819,15 @@ { "type": "CommentLine", "value": " future we decide that we need to perform more advanced TU matching, this", - "start": 10131, - "end": 10206, + "start": 11294, + "end": 11369, "loc": { "start": { - "line": 229, + "line": 255, "column": 4 }, "end": { - "line": 229, + "line": 255, "column": 79 } } @@ -11770,15 +12835,15 @@ { "type": "CommentLine", "value": " would be the place to implement that.", - "start": 10211, - "end": 10251, + "start": 11374, + "end": 11414, "loc": { "start": { - "line": 230, + "line": 256, "column": 4 }, "end": { - "line": 230, + "line": 256, "column": 44 } } @@ -11786,15 +12851,15 @@ { "type": "CommentLine", "value": " If there is a top-level source, generate a bibliographicCitation for it.", - "start": 10257, - "end": 10332, + "start": 11420, + "end": 11495, "loc": { "start": { - "line": 232, + "line": 258, "column": 4 }, "end": { - "line": 232, + "line": 258, "column": 79 } } @@ -11803,43 +12868,43 @@ }, { "type": "IfStatement", - "start": 10337, - "end": 10462, + "start": 11500, + "end": 11625, "loc": { "start": { - "line": 233, + "line": 259, "column": 4 }, "end": { - "line": 235, + "line": 261, "column": 5 } }, "test": { "type": "CallExpression", - "start": 10341, - "end": 10362, + "start": 11504, + "end": 11525, "loc": { "start": { - "line": 233, + "line": 259, "column": 8 }, "end": { - "line": 233, + "line": 259, "column": 29 } }, "callee": { "type": "Identifier", - "start": 10341, - "end": 10344, + "start": 11504, + "end": 11507, "loc": { "start": { - "line": 233, + "line": 259, "column": 8 }, "end": { - "line": 233, + "line": 259, "column": 11 }, "identifierName": "has" @@ -11850,15 +12915,15 @@ "arguments": [ { "type": "Identifier", - "start": 10345, - "end": 10351, + "start": 11508, + "end": 11514, "loc": { "start": { - "line": 233, + "line": 259, "column": 12 }, "end": { - "line": 233, + "line": 259, "column": 18 }, "identifierName": "jsonld" @@ -11867,15 +12932,15 @@ }, { "type": "StringLiteral", - "start": 10353, - "end": 10361, + "start": 11516, + "end": 11524, "loc": { "start": { - "line": 233, + "line": 259, "column": 20 }, "end": { - "line": 233, + "line": 259, "column": 28 } }, @@ -11890,87 +12955,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 10364, - "end": 10462, + "start": 11527, + "end": 11625, "loc": { "start": { - "line": 233, + "line": 259, "column": 31 }, "end": { - "line": 235, + "line": 261, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 10372, - "end": 10456, + "start": 11535, + "end": 11619, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - "line": 234, + "line": 260, "column": 90 } }, "expression": { "type": "AssignmentExpression", - "start": 10372, - "end": 10455, + "start": 11535, + "end": 11618, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - "line": 234, + "line": 260, "column": 89 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10372, - "end": 10407, + "start": 11535, + "end": 11570, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - "line": 234, + "line": 260, "column": 41 } }, "object": { "type": "MemberExpression", - "start": 10372, - "end": 10385, + "start": 11535, + "end": 11548, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - "line": 234, + "line": 260, "column": 19 } }, "object": { "type": "Identifier", - "start": 10372, - "end": 10378, + "start": 11535, + "end": 11541, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - "line": 234, + "line": 260, "column": 12 }, "identifierName": "jsonld" @@ -11979,15 +13044,15 @@ }, "property": { "type": "Identifier", - "start": 10379, - "end": 10385, + "start": 11542, + "end": 11548, "loc": { "start": { - "line": 234, + "line": 260, "column": 13 }, "end": { - "line": 234, + "line": 260, "column": 19 }, "identifierName": "source" @@ -11998,15 +13063,15 @@ }, "property": { "type": "Identifier", - "start": 10386, - "end": 10407, + "start": 11549, + "end": 11570, "loc": { "start": { - "line": 234, + "line": 260, "column": 20 }, "end": { - "line": 234, + "line": 260, "column": 41 }, "identifierName": "bibliographicCitation" @@ -12017,57 +13082,57 @@ }, "right": { "type": "CallExpression", - "start": 10410, - "end": 10455, + "start": 11573, + "end": 11618, "loc": { "start": { - "line": 234, + "line": 260, "column": 44 }, "end": { - "line": 234, + "line": 260, "column": 89 } }, "callee": { "type": "MemberExpression", - "start": 10410, - "end": 10453, + "start": 11573, + "end": 11616, "loc": { "start": { - "line": 234, + "line": 260, "column": 44 }, "end": { - "line": 234, + "line": 260, "column": 87 } }, "object": { "type": "NewExpression", - "start": 10410, - "end": 10444, + "start": 11573, + "end": 11607, "loc": { "start": { - "line": 234, + "line": 260, "column": 44 }, "end": { - "line": 234, + "line": 260, "column": 78 } }, "callee": { "type": "Identifier", - "start": 10414, - "end": 10429, + "start": 11577, + "end": 11592, "loc": { "start": { - "line": 234, + "line": 260, "column": 48 }, "end": { - "line": 234, + "line": 260, "column": 63 }, "identifierName": "CitationWrapper" @@ -12077,29 +13142,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 10430, - "end": 10443, + "start": 11593, + "end": 11606, "loc": { "start": { - "line": 234, + "line": 260, "column": 64 }, "end": { - "line": 234, + "line": 260, "column": 77 } }, "object": { "type": "Identifier", - "start": 10430, - "end": 10436, + "start": 11593, + "end": 11599, "loc": { "start": { - "line": 234, + "line": 260, "column": 64 }, "end": { - "line": 234, + "line": 260, "column": 70 }, "identifierName": "jsonld" @@ -12108,15 +13173,15 @@ }, "property": { "type": "Identifier", - "start": 10437, - "end": 10443, + "start": 11600, + "end": 11606, "loc": { "start": { - "line": 234, + "line": 260, "column": 71 }, "end": { - "line": 234, + "line": 260, "column": 77 }, "identifierName": "source" @@ -12129,15 +13194,15 @@ }, "property": { "type": "Identifier", - "start": 10445, - "end": 10453, + "start": 11608, + "end": 11616, "loc": { "start": { - "line": 234, + "line": 260, "column": 79 }, "end": { - "line": 234, + "line": 260, "column": 87 }, "identifierName": "toString" @@ -12159,15 +13224,15 @@ { "type": "CommentLine", "value": " Earlier, we used to generate a list of taxonomic matches here (stored in", - "start": 9726, - "end": 9801, + "start": 10889, + "end": 10964, "loc": { "start": { - "line": 224, + "line": 250, "column": 4 }, "end": { - "line": 224, + "line": 250, "column": 79 } } @@ -12175,15 +13240,15 @@ { "type": "CommentLine", "value": " jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic", - "start": 9806, - "end": 9879, + "start": 10969, + "end": 11042, "loc": { "start": { - "line": 225, + "line": 251, "column": 4 }, "end": { - "line": 225, + "line": 251, "column": 77 } } @@ -12191,15 +13256,15 @@ { "type": "CommentLine", "value": " units in phyloref specifiers were related to taxonomic units in phylogeny", - "start": 9884, - "end": 9960, + "start": 11047, + "end": 11123, "loc": { "start": { - "line": 226, + "line": 252, "column": 4 }, "end": { - "line": 226, + "line": 252, "column": 80 } } @@ -12207,15 +13272,15 @@ { "type": "CommentLine", "value": " nodes. This is no longer necessary, since phyloref specifiers are now logical", - "start": 9965, - "end": 10045, + "start": 11128, + "end": 11208, "loc": { "start": { - "line": 227, + "line": 253, "column": 4 }, "end": { - "line": 227, + "line": 253, "column": 84 } } @@ -12223,15 +13288,15 @@ { "type": "CommentLine", "value": " expressions that directly evaluate to phylogeny nodes. However, if in the", - "start": 10050, - "end": 10126, + "start": 11213, + "end": 11289, "loc": { "start": { - "line": 228, + "line": 254, "column": 4 }, "end": { - "line": 228, + "line": 254, "column": 80 } } @@ -12239,15 +13304,15 @@ { "type": "CommentLine", "value": " future we decide that we need to perform more advanced TU matching, this", - "start": 10131, - "end": 10206, + "start": 11294, + "end": 11369, "loc": { "start": { - "line": 229, + "line": 255, "column": 4 }, "end": { - "line": 229, + "line": 255, "column": 79 } } @@ -12255,15 +13320,15 @@ { "type": "CommentLine", "value": " would be the place to implement that.", - "start": 10211, - "end": 10251, + "start": 11374, + "end": 11414, "loc": { "start": { - "line": 230, + "line": 256, "column": 4 }, "end": { - "line": 230, + "line": 256, "column": 44 } } @@ -12271,15 +13336,15 @@ { "type": "CommentLine", "value": " If there is a top-level source, generate a bibliographicCitation for it.", - "start": 10257, - "end": 10332, + "start": 11420, + "end": 11495, "loc": { "start": { - "line": 232, + "line": 258, "column": 4 }, "end": { - "line": 232, + "line": 258, "column": 79 } } @@ -12289,15 +13354,15 @@ { "type": "CommentLine", "value": " Set up the top-level object '@type'. If one is present, we add our terms to that.", - "start": 10468, - "end": 10552, + "start": 11631, + "end": 11715, "loc": { "start": { - "line": 237, + "line": 263, "column": 4 }, "end": { - "line": 237, + "line": 263, "column": 88 } } @@ -12306,29 +13371,29 @@ }, { "type": "IfStatement", - "start": 10557, - "end": 10605, + "start": 11720, + "end": 11768, "loc": { "start": { - "line": 238, + "line": 264, "column": 4 }, "end": { - "line": 238, + "line": 264, "column": 52 } }, "test": { "type": "UnaryExpression", - "start": 10561, - "end": 10582, + "start": 11724, + "end": 11745, "loc": { "start": { - "line": 238, + "line": 264, "column": 8 }, "end": { - "line": 238, + "line": 264, "column": 29 } }, @@ -12336,29 +13401,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10562, - "end": 10582, + "start": 11725, + "end": 11745, "loc": { "start": { - "line": 238, + "line": 264, "column": 9 }, "end": { - "line": 238, + "line": 264, "column": 29 } }, "callee": { "type": "Identifier", - "start": 10562, - "end": 10565, + "start": 11725, + "end": 11728, "loc": { "start": { - "line": 238, + "line": 264, "column": 9 }, "end": { - "line": 238, + "line": 264, "column": 12 }, "identifierName": "has" @@ -12369,15 +13434,15 @@ "arguments": [ { "type": "Identifier", - "start": 10566, - "end": 10572, + "start": 11729, + "end": 11735, "loc": { "start": { - "line": 238, + "line": 264, "column": 13 }, "end": { - "line": 238, + "line": 264, "column": 19 }, "identifierName": "jsonld" @@ -12386,15 +13451,15 @@ }, { "type": "StringLiteral", - "start": 10574, - "end": 10581, + "start": 11737, + "end": 11744, "loc": { "start": { - "line": 238, + "line": 264, "column": 21 }, "end": { - "line": 238, + "line": 264, "column": 28 } }, @@ -12414,58 +13479,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10584, - "end": 10605, + "start": 11747, + "end": 11768, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 52 } }, "expression": { "type": "AssignmentExpression", - "start": 10584, - "end": 10604, + "start": 11747, + "end": 11767, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 51 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10584, - "end": 10599, + "start": 11747, + "end": 11762, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 46 } }, "object": { "type": "Identifier", - "start": 10584, - "end": 10590, + "start": 11747, + "end": 11753, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 37 }, "identifierName": "jsonld" @@ -12474,15 +13539,15 @@ }, "property": { "type": "StringLiteral", - "start": 10591, - "end": 10598, + "start": 11754, + "end": 11761, "loc": { "start": { - "line": 238, + "line": 264, "column": 38 }, "end": { - "line": 238, + "line": 264, "column": 45 } }, @@ -12496,15 +13561,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10602, - "end": 10604, + "start": 11765, + "end": 11767, "loc": { "start": { - "line": 238, + "line": 264, "column": 49 }, "end": { - "line": 238, + "line": 264, "column": 51 } }, @@ -12517,15 +13582,15 @@ { "type": "CommentLine", "value": " Set up the top-level object '@type'. If one is present, we add our terms to that.", - "start": 10468, - "end": 10552, + "start": 11631, + "end": 11715, "loc": { "start": { - "line": 237, + "line": 263, "column": 4 }, "end": { - "line": 237, + "line": 263, "column": 88 } } @@ -12534,29 +13599,29 @@ }, { "type": "IfStatement", - "start": 10610, - "end": 10683, + "start": 11773, + "end": 11846, "loc": { "start": { - "line": 239, + "line": 265, "column": 4 }, "end": { - "line": 239, + "line": 265, "column": 77 } }, "test": { "type": "UnaryExpression", - "start": 10614, - "end": 10645, + "start": 11777, + "end": 11808, "loc": { "start": { - "line": 239, + "line": 265, "column": 8 }, "end": { - "line": 239, + "line": 265, "column": 39 } }, @@ -12564,43 +13629,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10615, - "end": 10645, + "start": 11778, + "end": 11808, "loc": { "start": { - "line": 239, + "line": 265, "column": 9 }, "end": { - "line": 239, + "line": 265, "column": 39 } }, "callee": { "type": "MemberExpression", - "start": 10615, - "end": 10628, + "start": 11778, + "end": 11791, "loc": { "start": { - "line": 239, + "line": 265, "column": 9 }, "end": { - "line": 239, + "line": 265, "column": 22 } }, "object": { "type": "Identifier", - "start": 10615, - "end": 10620, + "start": 11778, + "end": 11783, "loc": { "start": { - "line": 239, + "line": 265, "column": 9 }, "end": { - "line": 239, + "line": 265, "column": 14 }, "identifierName": "Array" @@ -12609,15 +13674,15 @@ }, "property": { "type": "Identifier", - "start": 10621, - "end": 10628, + "start": 11784, + "end": 11791, "loc": { "start": { - "line": 239, + "line": 265, "column": 15 }, "end": { - "line": 239, + "line": 265, "column": 22 }, "identifierName": "isArray" @@ -12629,29 +13694,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 10629, - "end": 10644, + "start": 11792, + "end": 11807, "loc": { "start": { - "line": 239, + "line": 265, "column": 23 }, "end": { - "line": 239, + "line": 265, "column": 38 } }, "object": { "type": "Identifier", - "start": 10629, - "end": 10635, + "start": 11792, + "end": 11798, "loc": { "start": { - "line": 239, + "line": 265, "column": 23 }, "end": { - "line": 239, + "line": 265, "column": 29 }, "identifierName": "jsonld" @@ -12660,15 +13725,15 @@ }, "property": { "type": "StringLiteral", - "start": 10636, - "end": 10643, + "start": 11799, + "end": 11806, "loc": { "start": { - "line": 239, + "line": 265, "column": 30 }, "end": { - "line": 239, + "line": 265, "column": 37 } }, @@ -12688,58 +13753,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10647, - "end": 10683, + "start": 11810, + "end": 11846, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 77 } }, "expression": { "type": "AssignmentExpression", - "start": 10647, - "end": 10682, + "start": 11810, + "end": 11845, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 76 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10647, - "end": 10662, + "start": 11810, + "end": 11825, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 56 } }, "object": { "type": "Identifier", - "start": 10647, - "end": 10653, + "start": 11810, + "end": 11816, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 47 }, "identifierName": "jsonld" @@ -12748,15 +13813,15 @@ }, "property": { "type": "StringLiteral", - "start": 10654, - "end": 10661, + "start": 11817, + "end": 11824, "loc": { "start": { - "line": 239, + "line": 265, "column": 48 }, "end": { - "line": 239, + "line": 265, "column": 55 } }, @@ -12770,44 +13835,44 @@ }, "right": { "type": "ArrayExpression", - "start": 10665, - "end": 10682, + "start": 11828, + "end": 11845, "loc": { "start": { - "line": 239, + "line": 265, "column": 59 }, "end": { - "line": 239, + "line": 265, "column": 76 } }, "elements": [ { "type": "MemberExpression", - "start": 10666, - "end": 10681, + "start": 11829, + "end": 11844, "loc": { "start": { - "line": 239, + "line": 265, "column": 60 }, "end": { - "line": 239, + "line": 265, "column": 75 } }, "object": { "type": "Identifier", - "start": 10666, - "end": 10672, + "start": 11829, + "end": 11835, "loc": { "start": { - "line": 239, + "line": 265, "column": 60 }, "end": { - "line": 239, + "line": 265, "column": 66 }, "identifierName": "jsonld" @@ -12816,15 +13881,15 @@ }, "property": { "type": "StringLiteral", - "start": 10673, - "end": 10680, + "start": 11836, + "end": 11843, "loc": { "start": { - "line": 239, + "line": 265, "column": 67 }, "end": { - "line": 239, + "line": 265, "column": 74 } }, @@ -12844,71 +13909,71 @@ }, { "type": "ExpressionStatement", - "start": 10688, - "end": 10725, + "start": 11851, + "end": 11888, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 41 } }, "expression": { "type": "CallExpression", - "start": 10688, - "end": 10724, + "start": 11851, + "end": 11887, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 10688, - "end": 10708, + "start": 11851, + "end": 11871, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 24 } }, "object": { "type": "MemberExpression", - "start": 10688, - "end": 10703, + "start": 11851, + "end": 11866, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 19 } }, "object": { "type": "Identifier", - "start": 10688, - "end": 10694, + "start": 11851, + "end": 11857, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 10 }, "identifierName": "jsonld" @@ -12917,15 +13982,15 @@ }, "property": { "type": "StringLiteral", - "start": 10695, - "end": 10702, + "start": 11858, + "end": 11865, "loc": { "start": { - "line": 240, + "line": 266, "column": 11 }, "end": { - "line": 240, + "line": 266, "column": 18 } }, @@ -12939,15 +14004,15 @@ }, "property": { "type": "Identifier", - "start": 10704, - "end": 10708, + "start": 11867, + "end": 11871, "loc": { "start": { - "line": 240, + "line": 266, "column": 20 }, "end": { - "line": 240, + "line": 266, "column": 24 }, "identifierName": "push" @@ -12959,15 +14024,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 10709, - "end": 10723, + "start": 11872, + "end": 11886, "loc": { "start": { - "line": 240, + "line": 266, "column": 25 }, "end": { - "line": 240, + "line": 266, "column": 39 } }, @@ -12983,15 +14048,15 @@ { "type": "CommentLine", "value": " Set up the ontology imports. If one is present, we add our imports to that.", - "start": 10731, - "end": 10809, + "start": 11894, + "end": 11972, "loc": { "start": { - "line": 242, + "line": 268, "column": 4 }, "end": { - "line": 242, + "line": 268, "column": 82 } } @@ -13000,29 +14065,29 @@ }, { "type": "IfStatement", - "start": 10814, - "end": 10874, + "start": 11977, + "end": 12037, "loc": { "start": { - "line": 243, + "line": 269, "column": 4 }, "end": { - "line": 243, + "line": 269, "column": 64 } }, "test": { "type": "UnaryExpression", - "start": 10818, - "end": 10845, + "start": 11981, + "end": 12008, "loc": { "start": { - "line": 243, + "line": 269, "column": 8 }, "end": { - "line": 243, + "line": 269, "column": 35 } }, @@ -13030,29 +14095,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10819, - "end": 10845, + "start": 11982, + "end": 12008, "loc": { "start": { - "line": 243, + "line": 269, "column": 9 }, "end": { - "line": 243, + "line": 269, "column": 35 } }, "callee": { "type": "Identifier", - "start": 10819, - "end": 10822, + "start": 11982, + "end": 11985, "loc": { "start": { - "line": 243, + "line": 269, "column": 9 }, "end": { - "line": 243, + "line": 269, "column": 12 }, "identifierName": "has" @@ -13063,15 +14128,15 @@ "arguments": [ { "type": "Identifier", - "start": 10823, - "end": 10829, + "start": 11986, + "end": 11992, "loc": { "start": { - "line": 243, + "line": 269, "column": 13 }, "end": { - "line": 243, + "line": 269, "column": 19 }, "identifierName": "jsonld" @@ -13080,15 +14145,15 @@ }, { "type": "StringLiteral", - "start": 10831, - "end": 10844, + "start": 11994, + "end": 12007, "loc": { "start": { - "line": 243, + "line": 269, "column": 21 }, "end": { - "line": 243, + "line": 269, "column": 34 } }, @@ -13108,58 +14173,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10847, - "end": 10874, + "start": 12010, + "end": 12037, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 64 } }, "expression": { "type": "AssignmentExpression", - "start": 10847, - "end": 10873, + "start": 12010, + "end": 12036, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 63 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10847, - "end": 10868, + "start": 12010, + "end": 12031, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 58 } }, "object": { "type": "Identifier", - "start": 10847, - "end": 10853, + "start": 12010, + "end": 12016, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 43 }, "identifierName": "jsonld" @@ -13168,15 +14233,15 @@ }, "property": { "type": "StringLiteral", - "start": 10854, - "end": 10867, + "start": 12017, + "end": 12030, "loc": { "start": { - "line": 243, + "line": 269, "column": 44 }, "end": { - "line": 243, + "line": 269, "column": 57 } }, @@ -13190,15 +14255,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10871, - "end": 10873, + "start": 12034, + "end": 12036, "loc": { "start": { - "line": 243, + "line": 269, "column": 61 }, "end": { - "line": 243, + "line": 269, "column": 63 } }, @@ -13211,15 +14276,15 @@ { "type": "CommentLine", "value": " Set up the ontology imports. If one is present, we add our imports to that.", - "start": 10731, - "end": 10809, + "start": 11894, + "end": 11972, "loc": { "start": { - "line": 242, + "line": 268, "column": 4 }, "end": { - "line": 242, + "line": 268, "column": 82 } } @@ -13228,29 +14293,29 @@ }, { "type": "IfStatement", - "start": 10879, - "end": 10970, + "start": 12042, + "end": 12133, "loc": { "start": { - "line": 244, + "line": 270, "column": 4 }, "end": { - "line": 244, + "line": 270, "column": 95 } }, "test": { "type": "UnaryExpression", - "start": 10883, - "end": 10920, + "start": 12046, + "end": 12083, "loc": { "start": { - "line": 244, + "line": 270, "column": 8 }, "end": { - "line": 244, + "line": 270, "column": 45 } }, @@ -13258,43 +14323,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10884, - "end": 10920, + "start": 12047, + "end": 12083, "loc": { "start": { - "line": 244, + "line": 270, "column": 9 }, "end": { - "line": 244, + "line": 270, "column": 45 } }, "callee": { "type": "MemberExpression", - "start": 10884, - "end": 10897, + "start": 12047, + "end": 12060, "loc": { "start": { - "line": 244, + "line": 270, "column": 9 }, "end": { - "line": 244, + "line": 270, "column": 22 } }, "object": { "type": "Identifier", - "start": 10884, - "end": 10889, + "start": 12047, + "end": 12052, "loc": { "start": { - "line": 244, + "line": 270, "column": 9 }, "end": { - "line": 244, + "line": 270, "column": 14 }, "identifierName": "Array" @@ -13303,15 +14368,15 @@ }, "property": { "type": "Identifier", - "start": 10890, - "end": 10897, + "start": 12053, + "end": 12060, "loc": { "start": { - "line": 244, + "line": 270, "column": 15 }, "end": { - "line": 244, + "line": 270, "column": 22 }, "identifierName": "isArray" @@ -13323,29 +14388,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 10898, - "end": 10919, + "start": 12061, + "end": 12082, "loc": { "start": { - "line": 244, + "line": 270, "column": 23 }, "end": { - "line": 244, + "line": 270, "column": 44 } }, "object": { "type": "Identifier", - "start": 10898, - "end": 10904, + "start": 12061, + "end": 12067, "loc": { "start": { - "line": 244, + "line": 270, "column": 23 }, "end": { - "line": 244, + "line": 270, "column": 29 }, "identifierName": "jsonld" @@ -13354,15 +14419,15 @@ }, "property": { "type": "StringLiteral", - "start": 10905, - "end": 10918, + "start": 12068, + "end": 12081, "loc": { "start": { - "line": 244, + "line": 270, "column": 30 }, "end": { - "line": 244, + "line": 270, "column": 43 } }, @@ -13382,58 +14447,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10922, - "end": 10970, + "start": 12085, + "end": 12133, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 95 } }, "expression": { "type": "AssignmentExpression", - "start": 10922, - "end": 10969, + "start": 12085, + "end": 12132, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 94 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10922, - "end": 10943, + "start": 12085, + "end": 12106, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 68 } }, "object": { "type": "Identifier", - "start": 10922, - "end": 10928, + "start": 12085, + "end": 12091, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 53 }, "identifierName": "jsonld" @@ -13442,15 +14507,15 @@ }, "property": { "type": "StringLiteral", - "start": 10929, - "end": 10942, + "start": 12092, + "end": 12105, "loc": { "start": { - "line": 244, + "line": 270, "column": 54 }, "end": { - "line": 244, + "line": 270, "column": 67 } }, @@ -13464,44 +14529,44 @@ }, "right": { "type": "ArrayExpression", - "start": 10946, - "end": 10969, + "start": 12109, + "end": 12132, "loc": { "start": { - "line": 244, + "line": 270, "column": 71 }, "end": { - "line": 244, + "line": 270, "column": 94 } }, "elements": [ { "type": "MemberExpression", - "start": 10947, - "end": 10968, + "start": 12110, + "end": 12131, "loc": { "start": { - "line": 244, + "line": 270, "column": 72 }, "end": { - "line": 244, + "line": 270, "column": 93 } }, "object": { "type": "Identifier", - "start": 10947, - "end": 10953, + "start": 12110, + "end": 12116, "loc": { "start": { - "line": 244, + "line": 270, "column": 72 }, "end": { - "line": 244, + "line": 270, "column": 78 }, "identifierName": "jsonld" @@ -13510,15 +14575,15 @@ }, "property": { "type": "StringLiteral", - "start": 10954, - "end": 10967, + "start": 12117, + "end": 12130, "loc": { "start": { - "line": 244, + "line": 270, "column": 79 }, "end": { - "line": 244, + "line": 270, "column": 92 } }, @@ -13538,71 +14603,71 @@ }, { "type": "ExpressionStatement", - "start": 10975, - "end": 11058, + "start": 12138, + "end": 12221, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 87 } }, "expression": { "type": "CallExpression", - "start": 10975, - "end": 11057, + "start": 12138, + "end": 12220, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 86 } }, "callee": { "type": "MemberExpression", - "start": 10975, - "end": 11001, + "start": 12138, + "end": 12164, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 30 } }, "object": { "type": "MemberExpression", - "start": 10975, - "end": 10996, + "start": 12138, + "end": 12159, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 25 } }, "object": { "type": "Identifier", - "start": 10975, - "end": 10981, + "start": 12138, + "end": 12144, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 10 }, "identifierName": "jsonld" @@ -13611,15 +14676,15 @@ }, "property": { "type": "StringLiteral", - "start": 10982, - "end": 10995, + "start": 12145, + "end": 12158, "loc": { "start": { - "line": 245, + "line": 271, "column": 11 }, "end": { - "line": 245, + "line": 271, "column": 24 } }, @@ -13633,15 +14698,15 @@ }, "property": { "type": "Identifier", - "start": 10997, - "end": 11001, + "start": 12160, + "end": 12164, "loc": { "start": { - "line": 245, + "line": 271, "column": 26 }, "end": { - "line": 245, + "line": 271, "column": 30 }, "identifierName": "push" @@ -13653,15 +14718,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 11002, - "end": 11056, + "start": 12165, + "end": 12219, "loc": { "start": { - "line": 245, + "line": 271, "column": 31 }, "end": { - "line": 245, + "line": 271, "column": 85 } }, @@ -13676,71 +14741,71 @@ }, { "type": "ExpressionStatement", - "start": 11063, - "end": 11142, + "start": 12226, + "end": 12305, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 83 } }, "expression": { "type": "CallExpression", - "start": 11063, - "end": 11141, + "start": 12226, + "end": 12304, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 82 } }, "callee": { "type": "MemberExpression", - "start": 11063, - "end": 11089, + "start": 12226, + "end": 12252, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 30 } }, "object": { "type": "MemberExpression", - "start": 11063, - "end": 11084, + "start": 12226, + "end": 12247, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 25 } }, "object": { "type": "Identifier", - "start": 11063, - "end": 11069, + "start": 12226, + "end": 12232, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 10 }, "identifierName": "jsonld" @@ -13749,15 +14814,15 @@ }, "property": { "type": "StringLiteral", - "start": 11070, - "end": 11083, + "start": 12233, + "end": 12246, "loc": { "start": { - "line": 246, + "line": 272, "column": 11 }, "end": { - "line": 246, + "line": 272, "column": 24 } }, @@ -13771,15 +14836,15 @@ }, "property": { "type": "Identifier", - "start": 11085, - "end": 11089, + "start": 12248, + "end": 12252, "loc": { "start": { - "line": 246, + "line": 272, "column": 26 }, "end": { - "line": 246, + "line": 272, "column": 30 }, "identifierName": "push" @@ -13791,15 +14856,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 11090, - "end": 11140, + "start": 12253, + "end": 12303, "loc": { "start": { - "line": 246, + "line": 272, "column": 31 }, "end": { - "line": 246, + "line": 272, "column": 81 } }, @@ -13815,15 +14880,15 @@ { "type": "CommentLine", "value": " If the '@context' is missing, add it here.", - "start": 11148, - "end": 11193, + "start": 12311, + "end": 12356, "loc": { "start": { - "line": 248, + "line": 274, "column": 4 }, "end": { - "line": 248, + "line": 274, "column": 49 } } @@ -13832,29 +14897,29 @@ }, { "type": "IfStatement", - "start": 11198, - "end": 11290, + "start": 12361, + "end": 12453, "loc": { "start": { - "line": 249, + "line": 275, "column": 4 }, "end": { - "line": 251, + "line": 277, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 11202, - "end": 11226, + "start": 12365, + "end": 12389, "loc": { "start": { - "line": 249, + "line": 275, "column": 8 }, "end": { - "line": 249, + "line": 275, "column": 32 } }, @@ -13862,29 +14927,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 11203, - "end": 11226, + "start": 12366, + "end": 12389, "loc": { "start": { - "line": 249, + "line": 275, "column": 9 }, "end": { - "line": 249, + "line": 275, "column": 32 } }, "callee": { "type": "Identifier", - "start": 11203, - "end": 11206, + "start": 12366, + "end": 12369, "loc": { "start": { - "line": 249, + "line": 275, "column": 9 }, "end": { - "line": 249, + "line": 275, "column": 12 }, "identifierName": "has" @@ -13895,15 +14960,15 @@ "arguments": [ { "type": "Identifier", - "start": 11207, - "end": 11213, + "start": 12370, + "end": 12376, "loc": { "start": { - "line": 249, + "line": 275, "column": 13 }, "end": { - "line": 249, + "line": 275, "column": 19 }, "identifierName": "jsonld" @@ -13912,15 +14977,15 @@ }, { "type": "StringLiteral", - "start": 11215, - "end": 11225, + "start": 12378, + "end": 12388, "loc": { "start": { - "line": 249, + "line": 275, "column": 21 }, "end": { - "line": 249, + "line": 275, "column": 31 } }, @@ -13940,73 +15005,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 11228, - "end": 11290, + "start": 12391, + "end": 12453, "loc": { "start": { - "line": 249, + "line": 275, "column": 34 }, "end": { - "line": 251, + "line": 277, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 11236, - "end": 11284, + "start": 12399, + "end": 12447, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 54 } }, "expression": { "type": "AssignmentExpression", - "start": 11236, - "end": 11283, + "start": 12399, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 53 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11236, - "end": 11254, + "start": 12399, + "end": 12417, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 24 } }, "object": { "type": "Identifier", - "start": 11236, - "end": 11242, + "start": 12399, + "end": 12405, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 12 }, "identifierName": "jsonld" @@ -14015,15 +15080,15 @@ }, "property": { "type": "StringLiteral", - "start": 11243, - "end": 11253, + "start": 12406, + "end": 12416, "loc": { "start": { - "line": 250, + "line": 276, "column": 13 }, "end": { - "line": 250, + "line": 276, "column": 23 } }, @@ -14037,29 +15102,29 @@ }, "right": { "type": "MemberExpression", - "start": 11257, - "end": 11283, + "start": 12420, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 27 }, "end": { - "line": 250, + "line": 276, "column": 53 } }, "object": { "type": "Identifier", - "start": 11257, - "end": 11265, + "start": 12420, + "end": 12428, "loc": { "start": { - "line": 250, + "line": 276, "column": 27 }, "end": { - "line": 250, + "line": 276, "column": 35 }, "identifierName": "owlterms" @@ -14068,15 +15133,15 @@ }, "property": { "type": "Identifier", - "start": 11266, - "end": 11283, + "start": 12429, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 36 }, "end": { - "line": 250, + "line": 276, "column": 53 }, "identifierName": "PHYX_CONTEXT_JSON" @@ -14095,15 +15160,15 @@ { "type": "CommentLine", "value": " If the '@context' is missing, add it here.", - "start": 11148, - "end": 11193, + "start": 12311, + "end": 12356, "loc": { "start": { - "line": 248, + "line": 274, "column": 4 }, "end": { - "line": 248, + "line": 274, "column": 49 } } @@ -14112,29 +15177,29 @@ }, { "type": "ReturnStatement", - "start": 11296, - "end": 11310, + "start": 12459, + "end": 12473, "loc": { "start": { - "line": 253, + "line": 279, "column": 4 }, "end": { - "line": 253, + "line": 279, "column": 18 } }, "argument": { "type": "Identifier", - "start": 11303, - "end": 11309, + "start": 12466, + "end": 12472, "loc": { "start": { - "line": 253, + "line": 279, "column": 11 }, "end": { - "line": 253, + "line": 279, "column": 17 }, "identifierName": "jsonld" @@ -14150,15 +15215,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", - "start": 2310, - "end": 3304, + "start": 3473, + "end": 4467, "loc": { "start": { - "line": 58, + "line": 84, "column": 2 }, "end": { - "line": 73, + "line": 99, "column": 5 } } @@ -14168,15 +15233,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", - "start": 11318, - "end": 12359, + "start": 12481, + "end": 13522, "loc": { "start": { - "line": 256, + "line": 282, "column": 2 }, "end": { - "line": 271, + "line": 297, "column": 5 } } @@ -14185,15 +15250,15 @@ }, { "type": "ClassMethod", - "start": 12362, - "end": 12965, + "start": 13525, + "end": 14128, "loc": { "start": { - "line": 272, + "line": 298, "column": 2 }, "end": { - "line": 285, + "line": 311, "column": 3 } }, @@ -14201,15 +15266,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12362, - "end": 12367, + "start": 13525, + "end": 13530, "loc": { "start": { - "line": 272, + "line": 298, "column": 2 }, "end": { - "line": 272, + "line": 298, "column": 7 }, "identifierName": "toRDF" @@ -14225,29 +15290,29 @@ "params": [ { "type": "AssignmentPattern", - "start": 12368, - "end": 12380, + "start": 13531, + "end": 13543, "loc": { "start": { - "line": 272, + "line": 298, "column": 8 }, "end": { - "line": 272, + "line": 298, "column": 20 } }, "left": { "type": "Identifier", - "start": 12368, - "end": 12375, + "start": 13531, + "end": 13538, "loc": { "start": { - "line": 272, + "line": 298, "column": 8 }, "end": { - "line": 272, + "line": 298, "column": 15 }, "identifierName": "baseIRI" @@ -14256,15 +15321,15 @@ }, "right": { "type": "StringLiteral", - "start": 12378, - "end": 12380, + "start": 13541, + "end": 13543, "loc": { "start": { - "line": 272, + "line": 298, "column": 18 }, "end": { - "line": 272, + "line": 298, "column": 20 } }, @@ -14277,29 +15342,29 @@ }, { "type": "AssignmentPattern", - "start": 12382, - "end": 12402, + "start": 13545, + "end": 13565, "loc": { "start": { - "line": 272, + "line": 298, "column": 22 }, "end": { - "line": 272, + "line": 298, "column": 42 } }, "left": { "type": "Identifier", - "start": 12382, - "end": 12390, + "start": 13545, + "end": 13553, "loc": { "start": { - "line": 272, + "line": 298, "column": 22 }, "end": { - "line": 272, + "line": 298, "column": 30 }, "identifierName": "filePath" @@ -14308,15 +15373,15 @@ }, "right": { "type": "Identifier", - "start": 12393, - "end": 12402, + "start": 13556, + "end": 13565, "loc": { "start": { - "line": 272, + "line": 298, "column": 33 }, "end": { - "line": 272, + "line": 298, "column": 42 }, "identifierName": "undefined" @@ -14327,59 +15392,59 @@ ], "body": { "type": "BlockStatement", - "start": 12404, - "end": 12965, + "start": 13567, + "end": 14128, "loc": { "start": { - "line": 272, + "line": 298, "column": 44 }, "end": { - "line": 285, + "line": 311, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 12410, - "end": 12451, + "start": 13573, + "end": 13614, "loc": { "start": { - "line": 273, + "line": 299, "column": 4 }, "end": { - "line": 273, + "line": 299, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12416, - "end": 12450, + "start": 13579, + "end": 13613, "loc": { "start": { - "line": 273, + "line": 299, "column": 10 }, "end": { - "line": 273, + "line": 299, "column": 44 } }, "id": { "type": "Identifier", - "start": 12416, - "end": 12425, + "start": 13579, + "end": 13588, "loc": { "start": { - "line": 273, + "line": 299, "column": 10 }, "end": { - "line": 273, + "line": 299, "column": 19 }, "identifierName": "owlJSONLD" @@ -14388,58 +15453,58 @@ }, "init": { "type": "CallExpression", - "start": 12428, - "end": 12450, + "start": 13591, + "end": 13613, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 44 } }, "callee": { "type": "MemberExpression", - "start": 12428, - "end": 12441, + "start": 13591, + "end": 13604, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 12428, - "end": 12432, + "start": 13591, + "end": 13595, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 26 } } }, "property": { "type": "Identifier", - "start": 12433, - "end": 12441, + "start": 13596, + "end": 13604, "loc": { "start": { - "line": 273, + "line": 299, "column": 27 }, "end": { - "line": 273, + "line": 299, "column": 35 }, "identifierName": "asJSONLD" @@ -14451,15 +15516,15 @@ "arguments": [ { "type": "Identifier", - "start": 12442, - "end": 12449, + "start": 13605, + "end": 13612, "loc": { "start": { - "line": 273, + "line": 299, "column": 36 }, "end": { - "line": 273, + "line": 299, "column": 43 }, "identifierName": "baseIRI" @@ -14475,15 +15540,15 @@ { "type": "CommentLine", "value": " For the purposes of testing, we are sometimes given a relative path to `@context`,", - "start": 12457, - "end": 12542, + "start": 13620, + "end": 13705, "loc": { "start": { - "line": 275, + "line": 301, "column": 4 }, "end": { - "line": 275, + "line": 301, "column": 89 } } @@ -14491,15 +15556,15 @@ { "type": "CommentLine", "value": " but the JSONLD package does not support this. Instead, we'll import the contents", - "start": 12547, - "end": 12630, + "start": 13710, + "end": 13793, "loc": { "start": { - "line": 276, + "line": 302, "column": 4 }, "end": { - "line": 276, + "line": 302, "column": 87 } } @@ -14507,15 +15572,15 @@ { "type": "CommentLine", "value": " of the relative path on the fly.", - "start": 12635, - "end": 12670, + "start": 13798, + "end": 13833, "loc": { "start": { - "line": 277, + "line": 303, "column": 4 }, "end": { - "line": 277, + "line": 303, "column": 39 } } @@ -14524,57 +15589,57 @@ }, { "type": "IfStatement", - "start": 12675, - "end": 12889, + "start": 13838, + "end": 14052, "loc": { "start": { - "line": 278, + "line": 304, "column": 4 }, "end": { - "line": 282, + "line": 308, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 12679, - "end": 12758, + "start": 13842, + "end": 13921, "loc": { "start": { - "line": 278, + "line": 304, "column": 8 }, "end": { - "line": 278, + "line": 304, "column": 87 } }, "left": { "type": "LogicalExpression", - "start": 12679, - "end": 12717, + "start": 13842, + "end": 13880, "loc": { "start": { - "line": 278, + "line": 304, "column": 8 }, "end": { - "line": 278, + "line": 304, "column": 46 } }, "left": { "type": "Identifier", - "start": 12679, - "end": 12687, + "start": 13842, + "end": 13850, "loc": { "start": { - "line": 278, + "line": 304, "column": 8 }, "end": { - "line": 278, + "line": 304, "column": 16 }, "identifierName": "filePath" @@ -14585,29 +15650,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 12691, - "end": 12717, + "start": 13854, + "end": 13880, "loc": { "start": { - "line": 278, + "line": 304, "column": 20 }, "end": { - "line": 278, + "line": 304, "column": 46 } }, "callee": { "type": "Identifier", - "start": 12691, - "end": 12694, + "start": 13854, + "end": 13857, "loc": { "start": { - "line": 278, + "line": 304, "column": 20 }, "end": { - "line": 278, + "line": 304, "column": 23 }, "identifierName": "has" @@ -14617,15 +15682,15 @@ "arguments": [ { "type": "Identifier", - "start": 12695, - "end": 12704, + "start": 13858, + "end": 13867, "loc": { "start": { - "line": 278, + "line": 304, "column": 24 }, "end": { - "line": 278, + "line": 304, "column": 33 }, "identifierName": "owlJSONLD" @@ -14634,15 +15699,15 @@ }, { "type": "StringLiteral", - "start": 12706, - "end": 12716, + "start": 13869, + "end": 13879, "loc": { "start": { - "line": 278, + "line": 304, "column": 35 }, "end": { - "line": 278, + "line": 304, "column": 45 } }, @@ -14659,57 +15724,57 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 12721, - "end": 12758, + "start": 13884, + "end": 13921, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 87 } }, "callee": { "type": "MemberExpression", - "start": 12721, - "end": 12753, + "start": 13884, + "end": 13916, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 12721, - "end": 12742, + "start": 13884, + "end": 13905, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 71 } }, "object": { "type": "Identifier", - "start": 12721, - "end": 12730, + "start": 13884, + "end": 13893, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 59 }, "identifierName": "owlJSONLD" @@ -14718,15 +15783,15 @@ }, "property": { "type": "StringLiteral", - "start": 12731, - "end": 12741, + "start": 13894, + "end": 13904, "loc": { "start": { - "line": 278, + "line": 304, "column": 60 }, "end": { - "line": 278, + "line": 304, "column": 70 } }, @@ -14740,15 +15805,15 @@ }, "property": { "type": "Identifier", - "start": 12743, - "end": 12753, + "start": 13906, + "end": 13916, "loc": { "start": { - "line": 278, + "line": 304, "column": 72 }, "end": { - "line": 278, + "line": 304, "column": 82 }, "identifierName": "startsWith" @@ -14760,15 +15825,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 12754, - "end": 12757, + "start": 13917, + "end": 13920, "loc": { "start": { - "line": 278, + "line": 304, "column": 83 }, "end": { - "line": 278, + "line": 304, "column": 86 } }, @@ -14784,73 +15849,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 12760, - "end": 12889, + "start": 13923, + "end": 14052, "loc": { "start": { - "line": 278, + "line": 304, "column": 89 }, "end": { - "line": 282, + "line": 308, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 12768, - "end": 12883, + "start": 13931, + "end": 14046, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 281, + "line": 307, "column": 9 } }, "expression": { "type": "AssignmentExpression", - "start": 12768, - "end": 12882, + "start": 13931, + "end": 14045, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 281, + "line": 307, "column": 8 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 12768, - "end": 12789, + "start": 13931, + "end": 13952, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 279, + "line": 305, "column": 27 } }, "object": { "type": "Identifier", - "start": 12768, - "end": 12777, + "start": 13931, + "end": 13940, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 279, + "line": 305, "column": 15 }, "identifierName": "owlJSONLD" @@ -14859,15 +15924,15 @@ }, "property": { "type": "StringLiteral", - "start": 12778, - "end": 12788, + "start": 13941, + "end": 13951, "loc": { "start": { - "line": 279, + "line": 305, "column": 16 }, "end": { - "line": 279, + "line": 305, "column": 26 } }, @@ -14881,43 +15946,43 @@ }, "right": { "type": "CallExpression", - "start": 12792, - "end": 12882, + "start": 13955, + "end": 14045, "loc": { "start": { - "line": 279, + "line": 305, "column": 30 }, "end": { - "line": 281, + "line": 307, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 12792, - "end": 12802, + "start": 13955, + "end": 13965, "loc": { "start": { - "line": 279, + "line": 305, "column": 30 }, "end": { - "line": 279, + "line": 305, "column": 40 } }, "object": { "type": "Identifier", - "start": 12792, - "end": 12796, + "start": 13955, + "end": 13959, "loc": { "start": { - "line": 279, + "line": 305, "column": 30 }, "end": { - "line": 279, + "line": 305, "column": 34 }, "identifierName": "JSON" @@ -14926,15 +15991,15 @@ }, "property": { "type": "Identifier", - "start": 12797, - "end": 12802, + "start": 13960, + "end": 13965, "loc": { "start": { - "line": 279, + "line": 305, "column": 35 }, "end": { - "line": 279, + "line": 305, "column": 40 }, "identifierName": "parse" @@ -14946,43 +16011,43 @@ "arguments": [ { "type": "CallExpression", - "start": 12803, - "end": 12881, + "start": 13966, + "end": 14044, "loc": { "start": { - "line": 279, + "line": 305, "column": 41 }, "end": { - "line": 281, + "line": 307, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 12803, - "end": 12818, + "start": 13966, + "end": 13981, "loc": { "start": { - "line": 279, + "line": 305, "column": 41 }, "end": { - "line": 279, + "line": 305, "column": 56 } }, "object": { "type": "Identifier", - "start": 12803, - "end": 12805, + "start": 13966, + "end": 13968, "loc": { "start": { - "line": 279, + "line": 305, "column": 41 }, "end": { - "line": 279, + "line": 305, "column": 43 }, "identifierName": "fs" @@ -14991,15 +16056,15 @@ }, "property": { "type": "Identifier", - "start": 12806, - "end": 12818, + "start": 13969, + "end": 13981, "loc": { "start": { - "line": 279, + "line": 305, "column": 44 }, "end": { - "line": 279, + "line": 305, "column": 56 }, "identifierName": "readFileSync" @@ -15011,43 +16076,43 @@ "arguments": [ { "type": "CallExpression", - "start": 12828, - "end": 12873, + "start": 13991, + "end": 14036, "loc": { "start": { - "line": 280, + "line": 306, "column": 8 }, "end": { - "line": 280, + "line": 306, "column": 53 } }, "callee": { "type": "MemberExpression", - "start": 12828, - "end": 12840, + "start": 13991, + "end": 14003, "loc": { "start": { - "line": 280, + "line": 306, "column": 8 }, "end": { - "line": 280, + "line": 306, "column": 20 } }, "object": { "type": "Identifier", - "start": 12828, - "end": 12832, + "start": 13991, + "end": 13995, "loc": { "start": { - "line": 280, + "line": 306, "column": 8 }, "end": { - "line": 280, + "line": 306, "column": 12 }, "identifierName": "path" @@ -15056,15 +16121,15 @@ }, "property": { "type": "Identifier", - "start": 12833, - "end": 12840, + "start": 13996, + "end": 14003, "loc": { "start": { - "line": 280, + "line": 306, "column": 13 }, "end": { - "line": 280, + "line": 306, "column": 20 }, "identifierName": "resolve" @@ -15076,15 +16141,15 @@ "arguments": [ { "type": "Identifier", - "start": 12841, - "end": 12849, + "start": 14004, + "end": 14012, "loc": { "start": { - "line": 280, + "line": 306, "column": 21 }, "end": { - "line": 280, + "line": 306, "column": 29 }, "identifierName": "filePath" @@ -15093,29 +16158,29 @@ }, { "type": "MemberExpression", - "start": 12851, - "end": 12872, + "start": 14014, + "end": 14035, "loc": { "start": { - "line": 280, + "line": 306, "column": 31 }, "end": { - "line": 280, + "line": 306, "column": 52 } }, "object": { "type": "Identifier", - "start": 12851, - "end": 12860, + "start": 14014, + "end": 14023, "loc": { "start": { - "line": 280, + "line": 306, "column": 31 }, "end": { - "line": 280, + "line": 306, "column": 40 }, "identifierName": "owlJSONLD" @@ -15124,15 +16189,15 @@ }, "property": { "type": "StringLiteral", - "start": 12861, - "end": 12871, + "start": 14024, + "end": 14034, "loc": { "start": { - "line": 280, + "line": 306, "column": 41 }, "end": { - "line": 280, + "line": 306, "column": 51 } }, @@ -15160,15 +16225,15 @@ { "type": "CommentLine", "value": " For the purposes of testing, we are sometimes given a relative path to `@context`,", - "start": 12457, - "end": 12542, + "start": 13620, + "end": 13705, "loc": { "start": { - "line": 275, + "line": 301, "column": 4 }, "end": { - "line": 275, + "line": 301, "column": 89 } } @@ -15176,15 +16241,15 @@ { "type": "CommentLine", "value": " but the JSONLD package does not support this. Instead, we'll import the contents", - "start": 12547, - "end": 12630, + "start": 13710, + "end": 13793, "loc": { "start": { - "line": 276, + "line": 302, "column": 4 }, "end": { - "line": 276, + "line": 302, "column": 87 } } @@ -15192,15 +16257,15 @@ { "type": "CommentLine", "value": " of the relative path on the fly.", - "start": 12635, - "end": 12670, + "start": 13798, + "end": 13833, "loc": { "start": { - "line": 277, + "line": 303, "column": 4 }, "end": { - "line": 277, + "line": 303, "column": 39 } } @@ -15209,57 +16274,57 @@ }, { "type": "ReturnStatement", - "start": 12895, - "end": 12961, + "start": 14058, + "end": 14124, "loc": { "start": { - "line": 284, + "line": 310, "column": 4 }, "end": { - "line": 284, + "line": 310, "column": 70 } }, "argument": { "type": "CallExpression", - "start": 12902, - "end": 12960, + "start": 14065, + "end": 14123, "loc": { "start": { - "line": 284, + "line": 310, "column": 11 }, "end": { - "line": 284, + "line": 310, "column": 69 } }, "callee": { "type": "MemberExpression", - "start": 12902, - "end": 12914, + "start": 14065, + "end": 14077, "loc": { "start": { - "line": 284, + "line": 310, "column": 11 }, "end": { - "line": 284, + "line": 310, "column": 23 } }, "object": { "type": "Identifier", - "start": 12902, - "end": 12908, + "start": 14065, + "end": 14071, "loc": { "start": { - "line": 284, + "line": 310, "column": 11 }, "end": { - "line": 284, + "line": 310, "column": 17 }, "identifierName": "JSONLD" @@ -15268,15 +16333,15 @@ }, "property": { "type": "Identifier", - "start": 12909, - "end": 12914, + "start": 14072, + "end": 14077, "loc": { "start": { - "line": 284, + "line": 310, "column": 18 }, "end": { - "line": 284, + "line": 310, "column": 23 }, "identifierName": "toRDF" @@ -15288,15 +16353,15 @@ "arguments": [ { "type": "Identifier", - "start": 12915, - "end": 12924, + "start": 14078, + "end": 14087, "loc": { "start": { - "line": 284, + "line": 310, "column": 24 }, "end": { - "line": 284, + "line": 310, "column": 33 }, "identifierName": "owlJSONLD" @@ -15305,30 +16370,30 @@ }, { "type": "ObjectExpression", - "start": 12926, - "end": 12959, + "start": 14089, + "end": 14122, "loc": { "start": { - "line": 284, + "line": 310, "column": 35 }, "end": { - "line": 284, + "line": 310, "column": 68 } }, "properties": [ { "type": "ObjectProperty", - "start": 12928, - "end": 12957, + "start": 14091, + "end": 14120, "loc": { "start": { - "line": 284, + "line": 310, "column": 37 }, "end": { - "line": 284, + "line": 310, "column": 66 } }, @@ -15337,15 +16402,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12928, - "end": 12934, + "start": 14091, + "end": 14097, "loc": { "start": { - "line": 284, + "line": 310, "column": 37 }, "end": { - "line": 284, + "line": 310, "column": 43 }, "identifierName": "format" @@ -15354,15 +16419,15 @@ }, "value": { "type": "StringLiteral", - "start": 12936, - "end": 12957, + "start": 14099, + "end": 14120, "loc": { "start": { - "line": 284, + "line": 310, "column": 45 }, "end": { - "line": 284, + "line": 310, "column": 66 } }, @@ -15385,15 +16450,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", - "start": 11318, - "end": 12359, + "start": 12481, + "end": 13522, "loc": { "start": { - "line": 256, + "line": 282, "column": 2 }, "end": { - "line": 271, + "line": 297, "column": 5 } } @@ -15408,15 +16473,15 @@ }, { "type": "ExportNamedDeclaration", - "start": 12969, - "end": 12993, + "start": 14132, + "end": 14156, "loc": { "start": { - "line": 288, + "line": 314, "column": 0 }, "end": { - "line": 288, + "line": 314, "column": 24 } }, @@ -15424,29 +16489,29 @@ "specifiers": [ { "type": "ExportSpecifier", - "start": 12978, - "end": 12989, + "start": 14141, + "end": 14152, "loc": { "start": { - "line": 288, + "line": 314, "column": 9 }, "end": { - "line": 288, + "line": 314, "column": 20 } }, "local": { "type": "Identifier", - "start": 12978, - "end": 12989, + "start": 14141, + "end": 14152, "loc": { "start": { - "line": 288, + "line": 314, "column": 9 }, "end": { - "line": 288, + "line": 314, "column": 20 }, "identifierName": "PhyxWrapper" @@ -15455,15 +16520,15 @@ }, "exported": { "type": "Identifier", - "start": 12978, - "end": 12989, + "start": 14141, + "end": 14152, "loc": { "start": { - "line": 288, + "line": 314, "column": 9 }, "end": { - "line": 288, + "line": 314, "column": 20 }, "identifierName": "PhyxWrapper" @@ -15476,29 +16541,29 @@ }, { "type": "ExportNamedDeclaration", - "start": 12969, - "end": 12993, + "start": 14132, + "end": 14156, "loc": { "start": { - "line": 288, + "line": 314, "column": 0 }, "end": { - "line": 288, + "line": 314, "column": 24 } }, "declaration": { "type": "ClassDeclaration", "start": 622, - "end": 12967, + "end": 14130, "loc": { "start": { "line": 24, "column": 0 }, "end": { - "line": 286, + "line": 312, "column": 1 } }, @@ -15524,14 +16589,14 @@ "body": { "type": "ClassBody", "start": 640, - "end": 12967, + "end": 14130, "loc": { "start": { "line": 24, "column": 18 }, "end": { - "line": 286, + "line": 312, "column": 1 } }, @@ -17105,16 +18170,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", + "value": "*\n * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\n * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\n * package will be wrapped and normalized before being returned.\n *\n * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\n * identical ways. But if we implement it at every level, we can implement comparison code in\n * Klados easily.\n *\n * Two Phyx documents should -- upon being normalized -- be comparable with each other with\n * lodash.deepEqual().\n ", "start": 2310, - "end": 3304, + "end": 3009, "loc": { "start": { "line": 58, "column": 2 }, "end": { - "line": 73, + "line": 70, "column": 5 } } @@ -17123,37 +18188,36 @@ }, { "type": "ClassMethod", - "start": 3307, - "end": 11314, + "start": 3012, + "end": 3469, "loc": { "start": { - "line": 74, + "line": 71, "column": 2 }, "end": { - "line": 254, + "line": 82, "column": 3 } }, - "static": false, + "static": true, "computed": false, "key": { "type": "Identifier", - "start": 3307, - "end": 3315, + "start": 3019, + "end": 3028, "loc": { "start": { - "line": 74, - "column": 2 + "line": 71, + "column": 9 }, "end": { - "line": 74, - "column": 10 + "line": 71, + "column": 18 }, - "identifierName": "asJSONLD" + "identifierName": "normalize" }, - "name": "asJSONLD", - "leadingComments": null + "name": "normalize" }, "kind": "method", "id": null, @@ -17162,145 +18226,110 @@ "async": false, "params": [ { - "type": "AssignmentPattern", - "start": 3316, - "end": 3328, + "type": "Identifier", + "start": 3029, + "end": 3041, "loc": { "start": { - "line": 74, - "column": 11 + "line": 71, + "column": 19 }, "end": { - "line": 74, - "column": 23 - } - }, - "left": { - "type": "Identifier", - "start": 3316, - "end": 3323, - "loc": { - "start": { - "line": 74, - "column": 11 - }, - "end": { - "line": 74, - "column": 18 - }, - "identifierName": "baseIRI" + "line": 71, + "column": 31 }, - "name": "baseIRI" + "identifierName": "phyxDocument" }, - "right": { - "type": "StringLiteral", - "start": 3326, - "end": 3328, - "loc": { - "start": { - "line": 74, - "column": 21 - }, - "end": { - "line": 74, - "column": 23 - } - }, - "extra": { - "rawValue": "", - "raw": "''" - }, - "value": "" - } + "name": "phyxDocument" } ], "body": { "type": "BlockStatement", - "start": 3330, - "end": 11314, + "start": 3043, + "end": 3469, "loc": { "start": { - "line": 74, - "column": 25 + "line": 71, + "column": 33 }, "end": { - 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"start": 5664, - "end": 5674, + "start": 5872, + "end": 5882, "loc": { "start": { - "line": 130, - "column": 39 + "line": 133, + "column": 38 }, "end": { - "line": 130, - "column": 49 + "line": 133, + "column": 48 }, "identifierName": "startsWith" }, @@ -20995,16 +21656,16 @@ "arguments": [ { "type": "StringLiteral", - "start": 5675, - "end": 5678, + "start": 5883, + "end": 5886, "loc": { "start": { - "line": 130, - "column": 50 + "line": 133, + "column": 49 }, "end": { - "line": 130, - "column": 53 + "line": 133, + "column": 52 } }, "extra": { @@ -21017,91 +21678,91 @@ }, "consequent": { "type": "BlockStatement", - "start": 5681, - "end": 5865, + "start": 5889, + "end": 6068, "loc": { "start": { - "line": 130, - "column": 56 + "line": 133, + "column": 55 }, "end": { - "line": 134, + "line": 137, "column": 11 } }, "body": [ { "type": "VariableDeclaration", - "start": 5695, - "end": 5742, + "start": 5903, + "end": 5948, "loc": { "start": { - "line": 131, + "line": 134, "column": 12 }, "end": { - 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"end": 5730, + "start": 5928, + "end": 5937, "loc": { "start": { - "line": 131, - "column": 38 + "line": 134, + "column": 37 }, "end": { - "line": 131, - "column": 47 + "line": 134, + "column": 46 }, "identifierName": "cloneDeep" }, @@ -21110,20 +21771,20 @@ "arguments": [ { "type": "Identifier", - "start": 5731, - "end": 5740, + "start": 5938, + "end": 5946, "loc": { "start": { - "line": 131, - "column": 48 + "line": 134, + "column": 47 }, "end": { - "line": 131, - "column": 57 + "line": 134, + "column": 55 }, - "identifierName": "phylogeny" + "identifierName": "phyloref" }, - "name": "phylogeny" + "name": "phyloref" } ] } @@ -21133,76 +21794,76 @@ }, { "type": "ExpressionStatement", - "start": 5755, - "end": 5815, + "start": 5961, + "end": 6019, "loc": { "start": { - "line": 132, + "line": 135, "column": 12 }, "end": { - "line": 132, - "column": 72 + "line": 135, + "column": 70 } }, "expression": { "type": "AssignmentExpression", - "start": 5755, - "end": 5814, + "start": 5961, + "end": 6018, "loc": { "start": { - "line": 132, + "line": 135, "column": 12 }, "end": { - "line": 132, - "column": 71 + "line": 135, + "column": 69 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5755, - "end": 5779, + "start": 5961, + "end": 5984, "loc": { "start": { - "line": 132, + "line": 135, "column": 12 }, "end": { - "line": 132, - "column": 36 + "line": 135, + "column": 35 } }, "object": { "type": "Identifier", - "start": 5755, - "end": 5772, + "start": 5961, + "end": 5977, "loc": { "start": { - "line": 132, + "line": 135, "column": 12 }, "end": { - "line": 132, - "column": 29 + "line": 135, + "column": 28 }, - "identifierName": "modifiedPhylogeny" + "identifierName": "modifiedPhyloref" }, - "name": "modifiedPhylogeny" + "name": "modifiedPhyloref" }, "property": { "type": "StringLiteral", - "start": 5773, - "end": 5778, + "start": 5978, + "end": 5983, "loc": { "start": { - "line": 132, - "column": 30 + "line": 135, + "column": 29 }, "end": { - "line": 132, - "column": 35 + "line": 135, + "column": 34 } }, "extra": { @@ -21215,30 +21876,30 @@ }, "right": { "type": "CallExpression", - "start": 5782, - "end": 5814, + "start": 5987, + "end": 6018, "loc": { "start": { - "line": 132, - "column": 39 + "line": 135, + "column": 38 }, "end": { - "line": 132, - "column": 71 + "line": 135, + "column": 69 } }, "callee": { "type": "Identifier", - "start": 5782, - "end": 5796, + "start": 5987, + "end": 6001, "loc": { "start": { - "line": 132, - "column": 39 + "line": 135, + "column": 38 }, "end": { - "line": 132, - "column": 53 + "line": 135, + "column": 52 }, "identifierName": "makeIDAbsolute" }, @@ -21247,47 +21908,47 @@ "arguments": [ { "type": "MemberExpression", - "start": 5797, - "end": 5813, + "start": 6002, + "end": 6017, "loc": { "start": { - "line": 132, - "column": 54 + "line": 135, + "column": 53 }, "end": { - "line": 132, - "column": 70 + "line": 135, + "column": 68 } }, "object": { "type": "Identifier", - "start": 5797, - "end": 5806, + "start": 6002, + "end": 6010, "loc": { "start": { - "line": 132, - "column": 54 + "line": 135, + "column": 53 }, "end": { - "line": 132, - "column": 63 + "line": 135, + "column": 61 }, - "identifierName": "phylogeny" + "identifierName": "phyloref" }, - "name": "phylogeny" + "name": "phyloref" }, "property": { "type": "StringLiteral", - "start": 5807, - "end": 5812, + "start": 6011, + "end": 6016, "loc": { "start": { - "line": 132, - "column": 64 + "line": 135, + "column": 62 }, "end": { - "line": 132, - "column": 69 + "line": 135, + "column": 67 } }, "extra": { @@ -21304,34 +21965,34 @@ }, { "type": "ReturnStatement", - "start": 5828, - "end": 5853, + "start": 6032, + "end": 6056, "loc": { "start": { - "line": 133, + "line": 136, "column": 12 }, "end": { - "line": 133, - "column": 37 + "line": 136, + "column": 36 } }, "argument": { "type": "Identifier", - "start": 5835, - "end": 5852, + "start": 6039, + "end": 6055, "loc": { "start": { - "line": 133, + "line": 136, "column": 19 }, "end": { - "line": 133, - "column": 36 + "line": 136, + "column": 35 }, - "identifierName": "modifiedPhylogeny" + "identifierName": "modifiedPhyloref" }, - "name": "modifiedPhylogeny" + "name": "modifiedPhyloref" } } ], @@ -21341,34 +22002,34 @@ }, { "type": "ReturnStatement", - "start": 5876, - "end": 5893, + "start": 6079, + "end": 6095, "loc": { "start": { - "line": 135, + "line": 138, "column": 10 }, "end": { - "line": 135, - "column": 27 + "line": 138, + "column": 26 } }, "argument": { "type": "Identifier", - "start": 5883, - "end": 5892, + "start": 6086, + "end": 6094, "loc": { "start": { - "line": 135, + "line": 138, "column": 17 }, "end": { - "line": 135, - "column": 26 + "line": 138, + "column": 25 }, - "identifierName": "phylogeny" + "identifierName": "phyloref" }, - "name": "phylogeny" + "name": "phyloref" } } ], @@ -21388,15 +22049,15 @@ { "type": "CommentLine", "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", - "start": 5272, - "end": 5343, + "start": 5486, + "end": 5557, "loc": { "start": { - "line": 124, + "line": 127, "column": 6 }, "end": { - "line": 124, + "line": 127, "column": 77 } } @@ -21404,15 +22065,15 @@ { "type": "CommentLine", "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", - "start": 5350, - "end": 5419, + "start": 5564, + "end": 5633, "loc": { "start": { - "line": 125, + "line": 128, "column": 6 }, "end": { - "line": 125, + "line": 128, "column": 75 } } @@ -21420,15 +22081,15 @@ { "type": "CommentLine", "value": " to the relative IRI to make it absolute. This seems to avoid problems", - "start": 5426, - "end": 5498, + "start": 5640, + "end": 5712, "loc": { "start": { - "line": 126, + "line": 129, "column": 6 }, "end": { - "line": 126, + "line": 129, "column": 78 } } @@ -21436,15 +22097,15 @@ { "type": "CommentLine", "value": " with some JSON-LD parsers.", - "start": 5505, - "end": 5534, + "start": 5719, + "end": 5748, "loc": { "start": { - "line": 127, + "line": 130, "column": 6 }, "end": { - "line": 127, + "line": 130, "column": 35 } } @@ -21453,17 +22114,17 @@ "trailingComments": [ { "type": "CommentLine", - "value": " Add descriptions for individual nodes in each phylogeny.", - "start": 5921, - "end": 5980, + "value": " Convert phyloreferences into an OWL class restriction", + "start": 6123, + "end": 6179, "loc": { "start": { - "line": 139, + "line": 142, "column": 6 }, "end": { - "line": 139, - "column": 65 + "line": 142, + "column": 62 } } } @@ -21471,58 +22132,58 @@ }, { "type": "ExpressionStatement", - "start": 5987, - "end": 6213, + "start": 6186, + "end": 6383, "loc": { "start": { - "line": 140, + "line": 143, "column": 6 }, "end": { - "line": 143, + "line": 146, "column": 8 } }, "expression": { "type": "AssignmentExpression", - "start": 5987, - "end": 6212, + "start": 6186, + "end": 6382, "loc": { "start": { - "line": 140, + "line": 143, "column": 6 }, "end": { - "line": 143, + "line": 146, "column": 7 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5987, - "end": 6005, + "start": 6186, + "end": 6202, "loc": { "start": { - "line": 140, + "line": 143, "column": 6 }, "end": { - "line": 140, - "column": 24 + "line": 143, + "column": 22 } }, "object": { "type": "Identifier", - "start": 5987, - "end": 5993, + "start": 6186, + "end": 6192, "loc": { "start": { - "line": 140, + "line": 143, "column": 6 }, "end": { - "line": 140, + "line": 143, "column": 12 }, "identifierName": "jsonld" @@ -21532,78 +22193,78 @@ }, "property": { "type": "Identifier", - "start": 5994, - "end": 6005, + "start": 6193, + "end": 6202, "loc": { "start": { - "line": 140, + "line": 143, "column": 13 }, "end": { - "line": 140, - "column": 24 + "line": 143, + "column": 22 }, - "identifierName": "phylogenies" + "identifierName": "phylorefs" }, - "name": "phylogenies" + "name": "phylorefs" }, "computed": false, "leadingComments": null }, "right": { "type": "CallExpression", - "start": 6008, - "end": 6212, + "start": 6205, + "end": 6382, "loc": { "start": { - "line": 140, - "column": 27 + "line": 143, + "column": 25 }, "end": { - "line": 143, + "line": 146, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 6008, - "end": 6030, + "start": 6205, + "end": 6225, "loc": { "start": { - "line": 140, - "column": 27 + "line": 143, + "column": 25 }, "end": { - "line": 140, - "column": 49 + "line": 143, + "column": 45 } }, "object": { "type": "MemberExpression", - "start": 6008, - "end": 6026, + "start": 6205, + "end": 6221, "loc": { "start": { - "line": 140, - "column": 27 + "line": 143, + "column": 25 }, "end": { - "line": 140, - "column": 45 + "line": 143, + "column": 41 } }, "object": { "type": "Identifier", - "start": 6008, - "end": 6014, + "start": 6205, + "end": 6211, "loc": { "start": { - "line": 140, - "column": 27 + "line": 143, + "column": 25 }, "end": { - "line": 140, - "column": 33 + "line": 143, + "column": 31 }, "identifierName": "jsonld" }, @@ -21611,35 +22272,35 @@ }, "property": { "type": "Identifier", - "start": 6015, - "end": 6026, + "start": 6212, + "end": 6221, "loc": { "start": { - "line": 140, - "column": 34 + "line": 143, + "column": 32 }, "end": { - "line": 140, - "column": 45 + "line": 143, + "column": 41 }, - "identifierName": "phylogenies" + "identifierName": "phylorefs" }, - "name": "phylogenies" + "name": "phylorefs" }, "computed": false }, "property": { "type": "Identifier", - "start": 6027, - "end": 6030, + "start": 6222, + "end": 6225, "loc": { "start": { - "line": 140, - "column": 46 + "line": 143, + "column": 42 }, "end": { - "line": 140, - "column": 49 + "line": 143, + "column": 45 }, "identifierName": "map" }, @@ -21650,16 +22311,16 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6040, - "end": 6204, + "start": 6235, + "end": 6374, "loc": { "start": { - "line": 141, + "line": 144, "column": 8 }, "end": { - "line": 142, - "column": 78 + "line": 145, + "column": 57 } }, "id": null, @@ -21669,157 +22330,157 @@ "params": [ { "type": "Identifier", - "start": 6041, - "end": 6050, + "start": 6236, + "end": 6244, "loc": { "start": { - "line": 141, + "line": 144, "column": 9 }, "end": { - "line": 141, - "column": 18 + "line": 144, + "column": 17 }, - "identifierName": "phylogeny" + "identifierName": "phyloref" }, - "name": "phylogeny" + "name": "phyloref" }, { "type": "Identifier", - "start": 6052, - "end": 6066, + "start": 6246, + "end": 6259, "loc": { "start": { - "line": 141, - "column": 20 + "line": 144, + "column": 19 }, "end": { - "line": 141, - "column": 34 + "line": 144, + "column": 32 }, - "identifierName": "countPhylogeny" + "identifierName": "countPhyloref" }, - "name": "countPhylogeny" + "name": "countPhyloref" } ], "body": { "type": "CallExpression", - "start": 6071, - "end": 6204, + "start": 6264, + "end": 6374, "loc": { "start": { - "line": 141, - "column": 39 + "line": 144, + "column": 37 }, "end": { - "line": 142, - "column": 78 + "line": 145, + "column": 57 } }, "callee": { "type": "MemberExpression", - "start": 6071, - "end": 6145, + "start": 6264, + "end": 6336, "loc": { "start": { - "line": 141, - "column": 39 + "line": 144, + "column": 37 }, "end": { - "line": 142, + "line": 145, "column": 19 } }, "object": { "type": "NewExpression", - "start": 6071, - "end": 6125, + "start": 6264, + "end": 6316, "loc": { "start": { - "line": 141, - "column": 39 + "line": 144, + "column": 37 }, "end": { - "line": 141, - "column": 93 + "line": 144, + "column": 89 } }, "callee": { "type": "Identifier", - "start": 6075, - "end": 6091, + "start": 6268, + "end": 6283, "loc": { "start": { - "line": 141, - "column": 43 + "line": 144, + "column": 41 }, "end": { - "line": 141, - "column": 59 + "line": 144, + "column": 56 }, - "identifierName": "PhylogenyWrapper" + "identifierName": "PhylorefWrapper" }, - 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"loc": { + "start": { + "line": 195, + "column": 14 + }, + "end": { + "line": 202, + "column": 15 + } + }, + "left": { + "type": "CallExpression", + "start": 8578, + "end": 8613, + "loc": { + "start": { + "line": 195, + "column": 14 + }, + "end": { + "line": 195, + "column": 49 + } + }, + "callee": { + "type": "Identifier", + "start": 8578, + "end": 8581, + "loc": { + "start": { + "line": 195, + "column": 14 + }, + "end": { + "line": 195, + "column": 17 + }, + "identifierName": "has" + }, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "Identifier", + "start": 8582, + "end": 8590, + "loc": { + "start": { + "line": 195, + "column": 18 + }, + "end": { + "line": 195, + "column": 26 + }, + "identifierName": "phyloref" + }, + "name": "phyloref" + }, + { + "type": "StringLiteral", + "start": 8592, + "end": 8612, + "loc": { + "start": { + "line": 195, + "column": 28 + }, + "end": { + "line": 195, + "column": 48 + } + }, + "extra": { + "rawValue": "expectedResolution", + "raw": "'expectedResolution'" + }, + "value": "expectedResolution" + } + ], + "leadingComments": null + }, + "operator": "&&", + "right": { + "type": "LogicalExpression", + "start": 8725, + "end": 8920, + "loc": { + "start": { + "line": 198, + "column": 16 + }, + "end": { + "line": 201, + "column": 80 + } + }, + "left": { + "type": "CallExpression", + "start": 8725, + "end": 8770, + "loc": { + "start": { + "line": 198, + "column": 16 + }, + "end": { + "line": 198, + "column": 61 + } + }, + "callee": { + "type": "Identifier", + "start": 8725, + "end": 8728, + "loc": { + "start": { + "line": 198, + "column": 16 + }, + "end": { + "line": 198, + "column": 19 + }, + "identifierName": "has" + }, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 8729, + "end": 8756, + "loc": { + "start": { + "line": 198, + "column": 20 + }, + "end": { + "line": 198, + "column": 47 + } + }, + "object": { + "type": "Identifier", + "start": 8729, + "end": 8737, + "loc": { + "start": { + "line": 198, + "column": 20 + }, + "end": { + "line": 198, + "column": 28 + }, + "identifierName": "phyloref" + }, + "name": "phyloref" + }, + "property": { + "type": "Identifier", + "start": 8738, + "end": 8756, + "loc": { + "start": { + "line": 198, + "column": 29 + }, + "end": { + "line": 198, + "column": 47 + }, + "identifierName": "expectedResolution" + }, + "name": "expectedResolution" + }, + "computed": false + }, + { + "type": "Identifier", + "start": 8758, + "end": 8769, + "loc": { + "start": { + "line": 198, + "column": 49 + }, + "end": { + "line": 198, + "column": 60 + }, + "identifierName": "phylogenyId" + }, + "name": "phylogenyId" + } + ], + "leadingComments": null, + "trailingComments": [ + { + "type": "CommentLine", + "value": " Or they might have used a relative phylogeny ID.", + "start": 8788, + "end": 8839, + "loc": { + "start": { + "line": 200, + "column": 16 + }, + "end": { + "line": 200, + "column": 67 + } + } + } + ] + }, + "operator": "||", + "right": { + "type": "CallExpression", + "start": 8859, + "end": 8920, + "loc": { + "start": { + "line": 201, + "column": 19 + }, + "end": { + "line": 201, + "column": 80 + } + }, + "callee": { + "type": "Identifier", + "start": 8859, + "end": 8862, + "loc": { + "start": { + "line": 201, + "column": 19 + }, + "end": { + "line": 201, + "column": 22 + }, + "identifierName": "has" + }, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 8863, + "end": 8890, + "loc": { + "start": { + "line": 201, + "column": 23 + }, + "end": { + "line": 201, + "column": 50 + } + }, + "object": { + "type": "Identifier", + "start": 8863, + "end": 8871, + "loc": { + "start": { + "line": 201, + "column": 23 + }, + "end": { + "line": 201, + "column": 31 + }, + "identifierName": "phyloref" + }, + "name": "phyloref" + }, + "property": { + "type": "Identifier", + "start": 8872, + "end": 8890, + "loc": { + "start": { + "line": 201, + "column": 32 + }, + "end": { + "line": 201, + "column": 50 + }, + "identifierName": "expectedResolution" + }, + "name": "expectedResolution" + }, + "computed": false + }, + { + "type": "CallExpression", + "start": 8892, + "end": 8919, + "loc": { + "start": { + "line": 201, + "column": 52 + }, + "end": { + "line": 201, + "column": 79 + } + }, "callee": { "type": "Identifier", - "start": 7729, - "end": 7743, + "start": 8892, + "end": 8906, "loc": { "start": { - "line": 175, + "line": 201, "column": 52 }, "end": { - "line": 175, + "line": 201, "column": 66 }, "identifierName": "makeIDRelative" @@ -23569,15 +25699,15 @@ "arguments": [ { "type": "Identifier", - "start": 7744, - "end": 7755, + "start": 8907, + "end": 8918, "loc": { "start": { - "line": 175, + "line": 201, "column": 67 }, "end": { - "line": 175, + "line": 201, "column": 78 }, "identifierName": "phylogenyId" @@ -23591,15 +25721,15 @@ { "type": "CommentLine", "value": " Or they might have used a relative phylogeny ID.", - "start": 7625, - "end": 7676, + "start": 8788, + "end": 8839, "loc": { "start": { - "line": 174, + "line": 200, "column": 16 }, "end": { - "line": 174, + "line": 200, "column": 67 } } @@ -23610,15 +25740,15 @@ { "type": "CommentLine", "value": " The user might have used the absolute phylogeny ID here.", - "start": 7486, - "end": 7545, + "start": 8649, + "end": 8708, "loc": { "start": { - "line": 171, + "line": 197, "column": 16 }, "end": { - "line": 171, + "line": 197, "column": 75 } } @@ -23626,66 +25756,66 @@ ], "extra": { "parenthesized": true, - "parenStart": 7468 + "parenStart": 8631 } }, "leadingComments": null }, "consequent": { "type": "BlockStatement", - "start": 7788, - "end": 8419, + "start": 8951, + "end": 9582, "loc": { "start": { - "line": 177, + "line": 203, "column": 14 }, "end": { - "line": 189, + "line": 215, "column": 13 } }, "body": [ { "type": "VariableDeclaration", - "start": 8048, - "end": 8266, + "start": 9211, + "end": 9429, "loc": { "start": { - "line": 182, + "line": 208, "column": 14 }, "end": { - "line": 184, + "line": 210, "column": 85 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 8054, - "end": 8265, + "start": 9217, + "end": 9428, "loc": { "start": { - "line": 182, + "line": 208, "column": 20 }, "end": { - "line": 184, + "line": 210, "column": 84 } }, "id": { "type": "Identifier", - "start": 8054, - "end": 8063, + "start": 9217, + "end": 9226, "loc": { "start": { - "line": 182, + "line": 208, "column": 20 }, "end": { - "line": 182, + "line": 208, "column": 29 }, "identifierName": "nodeLabel" @@ -23695,43 +25825,43 @@ }, "init": { "type": "ConditionalExpression", - "start": 8066, - "end": 8265, + "start": 9229, + "end": 9428, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 184, + "line": 210, "column": 84 } }, "test": { "type": "CallExpression", - "start": 8066, - "end": 8111, + "start": 9229, + "end": 9274, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 182, + "line": 208, "column": 77 } }, "callee": { "type": "Identifier", - "start": 8066, - "end": 8069, + "start": 9229, + "end": 9232, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 182, + "line": 208, "column": 35 }, "identifierName": "has" @@ -23741,29 +25871,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 8070, - "end": 8097, + "start": 9233, + "end": 9260, "loc": { "start": { - "line": 182, + "line": 208, "column": 36 }, "end": { - "line": 182, + "line": 208, "column": 63 } }, "object": { "type": "Identifier", - "start": 8070, - "end": 8078, + "start": 9233, + "end": 9241, "loc": { "start": { - "line": 182, + "line": 208, "column": 36 }, "end": { - "line": 182, + "line": 208, "column": 44 }, "identifierName": "phyloref" @@ -23772,15 +25902,15 @@ }, "property": { "type": "Identifier", - "start": 8079, - "end": 8097, + "start": 9242, + "end": 9260, "loc": { "start": { - "line": 182, + "line": 208, "column": 45 }, "end": { - "line": 182, + "line": 208, "column": 63 }, "identifierName": "expectedResolution" @@ -23791,15 +25921,15 @@ }, { "type": "Identifier", - "start": 8099, - "end": 8110, + "start": 9262, + "end": 9273, "loc": { "start": { - "line": 182, + "line": 208, "column": 65 }, "end": { - "line": 182, + "line": 208, "column": 76 }, "identifierName": "phylogenyId" @@ -23810,57 +25940,57 @@ }, "consequent": { "type": "MemberExpression", - "start": 8130, - "end": 8180, + "start": 9293, + "end": 9343, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 68 } }, "object": { "type": "MemberExpression", - "start": 8130, - "end": 8170, + "start": 9293, + "end": 9333, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 58 } }, "object": { "type": "MemberExpression", - "start": 8130, - "end": 8157, + "start": 9293, + "end": 9320, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 45 } }, "object": { "type": "Identifier", - "start": 8130, - "end": 8138, + "start": 9293, + "end": 9301, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 26 }, "identifierName": "phyloref" @@ -23869,15 +25999,15 @@ }, "property": { "type": "Identifier", - "start": 8139, - "end": 8157, + "start": 9302, + "end": 9320, "loc": { "start": { - "line": 183, + "line": 209, "column": 27 }, "end": { - "line": 183, + "line": 209, "column": 45 }, "identifierName": "expectedResolution" @@ -23888,15 +26018,15 @@ }, "property": { "type": "Identifier", - "start": 8158, - "end": 8169, + "start": 9321, + "end": 9332, "loc": { "start": { - "line": 183, + "line": 209, "column": 46 }, "end": { - "line": 183, + "line": 209, "column": 57 }, "identifierName": "phylogenyId" @@ -23907,15 +26037,15 @@ }, "property": { "type": "Identifier", - "start": 8171, - "end": 8180, + "start": 9334, + "end": 9343, "loc": { "start": { - "line": 183, + "line": 209, "column": 59 }, "end": { - "line": 183, + "line": 209, "column": 68 }, "identifierName": "nodeLabel" @@ -23926,57 +26056,57 @@ }, "alternate": { "type": "MemberExpression", - "start": 8199, - "end": 8265, + "start": 9362, + "end": 9428, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 84 } }, "object": { "type": "MemberExpression", - "start": 8199, - "end": 8255, + "start": 9362, + "end": 9418, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 74 } }, "object": { "type": "MemberExpression", - "start": 8199, - "end": 8226, + "start": 9362, + "end": 9389, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 45 } }, "object": { "type": "Identifier", - "start": 8199, - "end": 8207, + "start": 9362, + "end": 9370, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 26 }, "identifierName": "phyloref" @@ -23985,15 +26115,15 @@ }, "property": { "type": "Identifier", - "start": 8208, - "end": 8226, + "start": 9371, + "end": 9389, "loc": { "start": { - "line": 184, + "line": 210, "column": 27 }, "end": { - "line": 184, + "line": 210, "column": 45 }, "identifierName": "expectedResolution" @@ -24004,29 +26134,29 @@ }, "property": { "type": "CallExpression", - "start": 8227, - "end": 8254, + "start": 9390, + "end": 9417, "loc": { "start": { - "line": 184, + "line": 210, "column": 46 }, "end": { - "line": 184, + "line": 210, "column": 73 } }, "callee": { "type": "Identifier", - "start": 8227, - "end": 8241, + "start": 9390, + "end": 9404, "loc": { "start": { - "line": 184, + "line": 210, "column": 46 }, "end": { - "line": 184, + "line": 210, "column": 60 }, "identifierName": "makeIDRelative" @@ -24036,15 +26166,15 @@ "arguments": [ { "type": "Identifier", - "start": 8242, - "end": 8253, + "start": 9405, + "end": 9416, "loc": { "start": { - "line": 184, + "line": 210, "column": 61 }, "end": { - "line": 184, + "line": 210, "column": 72 }, "identifierName": "phylogenyId" @@ -24057,15 +26187,15 @@ }, "property": { "type": "Identifier", - "start": 8256, - "end": 8265, + "start": 9419, + "end": 9428, "loc": { "start": { - "line": 184, + "line": 210, "column": 75 }, "end": { - "line": 184, + "line": 210, "column": 84 }, "identifierName": "nodeLabel" @@ -24083,15 +26213,15 @@ { "type": "CommentLine", "value": " Expected resolution information set! The node label mentioned in that", - "start": 7804, - "end": 7876, + "start": 8967, + "end": 9039, "loc": { "start": { - "line": 178, + "line": 204, "column": 14 }, "end": { - "line": 178, + "line": 204, "column": 86 } } @@ -24099,15 +26229,15 @@ { "type": "CommentLine", "value": " information must be identical to one of the labels of this phylogeny node.", - "start": 7891, - "end": 7968, + "start": 9054, + "end": 9131, "loc": { "start": { - "line": 179, + "line": 205, "column": 14 }, "end": { - "line": 179, + "line": 205, "column": 91 } } @@ -24115,15 +26245,15 @@ { "type": "CommentLine", "value": " Figure out which phylogenyId was matched here.", - "start": 7984, - "end": 8033, + "start": 9147, + "end": 9196, "loc": { "start": { - "line": 181, + "line": 207, "column": 14 }, "end": { - "line": 181, + "line": 207, "column": 63 } } @@ -24132,43 +26262,43 @@ }, { "type": "IfStatement", - "start": 8282, - "end": 8405, + "start": 9445, + "end": 9568, "loc": { "start": { - "line": 186, + "line": 212, "column": 14 }, "end": { - "line": 188, + "line": 214, "column": 15 } }, "test": { "type": "LogicalExpression", - "start": 8286, - "end": 8338, + "start": 9449, + "end": 9501, "loc": { "start": { - "line": 186, + "line": 212, "column": 18 }, "end": { - "line": 186, + "line": 212, "column": 70 } }, "left": { "type": "Identifier", - "start": 8286, - "end": 8295, + "start": 9449, + "end": 9458, "loc": { "start": { - "line": 186, + "line": 212, "column": 18 }, "end": { - "line": 186, + "line": 212, "column": 27 }, "identifierName": "nodeLabel" @@ -24178,71 +26308,71 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 8299, - "end": 8338, + "start": 9462, + "end": 9501, "loc": { "start": { - "line": 186, + "line": 212, "column": 31 }, "end": { - "line": 186, + "line": 212, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 8299, - "end": 8327, + "start": 9462, + "end": 9490, "loc": { "start": { - "line": 186, + "line": 212, "column": 31 }, "end": { - "line": 186, + "line": 212, "column": 59 } }, "object": { "type": "LogicalExpression", - "start": 8300, - "end": 8317, + "start": 9463, + "end": 9480, "loc": { "start": { - "line": 186, + "line": 212, "column": 32 }, "end": { - "line": 186, + "line": 212, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 8300, - "end": 8311, + "start": 9463, + "end": 9474, "loc": { "start": { - "line": 186, + "line": 212, "column": 32 }, "end": { - "line": 186, + "line": 212, "column": 43 } }, "object": { "type": "Identifier", - "start": 8300, - "end": 8304, + "start": 9463, + "end": 9467, "loc": { "start": { - "line": 186, + "line": 212, "column": 32 }, "end": { - "line": 186, + "line": 212, "column": 36 }, "identifierName": "node" @@ -24251,15 +26381,15 @@ }, "property": { "type": "Identifier", - "start": 8305, - "end": 8311, + "start": 9468, + "end": 9474, "loc": { "start": { - "line": 186, + "line": 212, "column": 37 }, "end": { - "line": 186, + "line": 212, "column": 43 }, "identifierName": "labels" @@ -24271,15 +26401,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 8315, - "end": 8317, + "start": 9478, + "end": 9480, "loc": { "start": { - "line": 186, + "line": 212, "column": 47 }, "end": { - "line": 186, + "line": 212, "column": 49 } }, @@ -24287,20 +26417,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 8299 + "parenStart": 9462 } }, "property": { "type": "Identifier", - "start": 8319, - "end": 8327, + "start": 9482, + "end": 9490, "loc": { "start": { - "line": 186, + "line": 212, "column": 51 }, "end": { - "line": 186, + "line": 212, "column": 59 }, "identifierName": "includes" @@ -24312,15 +26442,15 @@ "arguments": [ { "type": "Identifier", - "start": 8328, - "end": 8337, + "start": 9491, + "end": 9500, "loc": { "start": { - "line": 186, + "line": 212, "column": 60 }, "end": { - "line": 186, + "line": 212, "column": 69 }, "identifierName": "nodeLabel" @@ -24332,59 +26462,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 8340, - "end": 8405, + "start": 9503, + "end": 9568, "loc": { "start": { - "line": 186, + "line": 212, "column": 72 }, "end": { - "line": 188, + "line": 214, "column": 15 } }, "body": [ { "type": "ExpressionStatement", - "start": 8358, - "end": 8389, + "start": 9521, + "end": 9552, "loc": { "start": { - "line": 187, + "line": 213, "column": 16 }, "end": { - "line": 187, + "line": 213, "column": 47 } }, "expression": { "type": "AssignmentExpression", - "start": 8358, - "end": 8388, + "start": 9521, + "end": 9551, "loc": { "start": { - "line": 187, + "line": 213, "column": 16 }, "end": { - "line": 187, + "line": 213, "column": 46 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8358, - "end": 8381, + "start": 9521, + "end": 9544, "loc": { "start": { - "line": 187, + "line": 213, "column": 16 }, "end": { - "line": 187, + "line": 213, "column": 39 }, "identifierName": "flagNodeExpectsPhyloref" @@ -24393,15 +26523,15 @@ }, "right": { "type": "BooleanLiteral", - "start": 8384, - "end": 8388, + "start": 9547, + "end": 9551, "loc": { "start": { - "line": 187, + "line": 213, "column": 42 }, "end": { - "line": 187, + "line": 213, "column": 46 } }, @@ -24419,85 +26549,85 @@ }, "alternate": { "type": "IfStatement", - "start": 8425, - "end": 8695, + "start": 9588, + "end": 9858, "loc": { "start": { - "line": 189, + "line": 215, "column": 19 }, "end": { - "line": 193, + "line": 219, "column": 13 } }, "test": { "type": "CallExpression", - "start": 8429, - "end": 8473, + "start": 9592, + "end": 9636, "loc": { "start": { - "line": 189, + "line": 215, "column": 23 }, "end": { - "line": 189, + "line": 215, "column": 67 } }, "callee": { "type": "MemberExpression", - "start": 8429, - "end": 8457, + "start": 9592, + "end": 9620, "loc": { "start": { - "line": 189, + "line": 215, "column": 23 }, "end": { - "line": 189, + "line": 215, "column": 51 } }, "object": { "type": "LogicalExpression", - "start": 8430, - "end": 8447, + "start": 9593, + "end": 9610, "loc": { "start": { - "line": 189, + "line": 215, "column": 24 }, "end": { - "line": 189, + "line": 215, "column": 41 } }, "left": { "type": "MemberExpression", - "start": 8430, - "end": 8441, + "start": 9593, + "end": 9604, "loc": { "start": { - "line": 189, + "line": 215, "column": 24 }, "end": { - "line": 189, + "line": 215, "column": 35 } }, "object": { "type": "Identifier", - "start": 8430, - "end": 8434, + "start": 9593, + "end": 9597, "loc": { "start": { - "line": 189, + "line": 215, "column": 24 }, "end": { - "line": 189, + "line": 215, "column": 28 }, "identifierName": "node" @@ -24506,15 +26636,15 @@ }, "property": { "type": "Identifier", - "start": 8435, - "end": 8441, + "start": 9598, + "end": 9604, "loc": { "start": { - "line": 189, + "line": 215, "column": 29 }, "end": { - "line": 189, + "line": 215, "column": 35 }, "identifierName": "labels" @@ -24526,15 +26656,15 @@ "operator": "||", "right": { "type": "ArrayExpression", - "start": 8445, - "end": 8447, + "start": 9608, + "end": 9610, "loc": { "start": { - "line": 189, + "line": 215, "column": 39 }, "end": { - "line": 189, + "line": 215, "column": 41 } }, @@ -24542,20 +26672,20 @@ }, "extra": { "parenthesized": true, - "parenStart": 8429 + "parenStart": 9592 } }, "property": { "type": "Identifier", - "start": 8449, - "end": 8457, + "start": 9612, + "end": 9620, "loc": { "start": { - "line": 189, + "line": 215, "column": 43 }, "end": { - "line": 189, + "line": 215, "column": 51 }, "identifierName": "includes" @@ -24567,29 +26697,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 8458, - "end": 8472, + "start": 9621, + "end": 9635, "loc": { "start": { - "line": 189, + "line": 215, "column": 52 }, "end": { - "line": 189, + "line": 215, "column": 66 } }, "object": { "type": "Identifier", - "start": 8458, - "end": 8466, + "start": 9621, + "end": 9629, "loc": { "start": { - "line": 189, + "line": 215, "column": 52 }, "end": { - "line": 189, + "line": 215, "column": 60 }, "identifierName": "phyloref" @@ -24598,15 +26728,15 @@ }, "property": { "type": "Identifier", - "start": 8467, - "end": 8472, + "start": 9630, + "end": 9635, "loc": { "start": { - "line": 189, + "line": 215, "column": 61 }, "end": { - "line": 189, + "line": 215, "column": 66 }, "identifierName": "label" @@ -24619,59 +26749,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 8475, - "end": 8695, + "start": 9638, + "end": 9858, "loc": { "start": { - "line": 189, + "line": 215, "column": 69 }, "end": { - "line": 193, + "line": 219, "column": 13 } }, "body": [ { "type": "ExpressionStatement", - "start": 8650, - "end": 8681, + "start": 9813, + "end": 9844, "loc": { "start": { - "line": 192, + "line": 218, "column": 14 }, "end": { - "line": 192, + "line": 218, "column": 45 } }, "expression": { "type": "AssignmentExpression", - "start": 8650, - "end": 8680, + "start": 9813, + "end": 9843, "loc": { "start": { - "line": 192, + "line": 218, "column": 14 }, "end": { - "line": 192, + "line": 218, "column": 44 } }, "operator": "=", "left": { "type": "Identifier", - "start": 8650, - "end": 8673, + "start": 9813, + "end": 9836, "loc": { "start": { - "line": 192, + "line": 218, "column": 14 }, "end": { - "line": 192, + "line": 218, "column": 37 }, "identifierName": "flagNodeExpectsPhyloref" @@ -24681,15 +26811,15 @@ }, "right": { "type": "BooleanLiteral", - "start": 8676, - "end": 8680, + "start": 9839, + "end": 9843, "loc": { "start": { - "line": 192, + "line": 218, "column": 40 }, "end": { - "line": 192, + "line": 218, "column": 44 } }, @@ -24701,15 +26831,15 @@ { "type": "CommentLine", "value": " No expected resolution information, so we just check whether", - "start": 8491, - "end": 8554, + "start": 9654, + "end": 9717, "loc": { "start": { - "line": 190, + "line": 216, "column": 14 }, "end": { - "line": 190, + "line": 216, "column": 77 } } @@ -24717,15 +26847,15 @@ { "type": "CommentLine", "value": " the phyloref label is one of the labels on this phylogeny node.", - "start": 8569, - "end": 8635, + "start": 9732, + "end": 9798, "loc": { "start": { - "line": 191, + "line": 217, "column": 14 }, "end": { - "line": 191, + "line": 217, "column": 80 } } @@ -24741,15 +26871,15 @@ { "type": "CommentLine", "value": " console.log(`Testing expected resolution of '${phylorefId}' on `", - "start": 7243, - "end": 7310, + "start": 8406, + "end": 8473, "loc": { "start": { - "line": 165, + "line": 191, "column": 12 }, "end": { - "line": 165, + "line": 191, "column": 79 } } @@ -24757,15 +26887,15 @@ { "type": "CommentLine", "value": " + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);", - "start": 7323, - "end": 7382, + "start": 8486, + "end": 8545, "loc": { "start": { - "line": 166, + "line": 192, "column": 12 }, "end": { - "line": 166, + "line": 192, "column": 71 } } @@ -24774,29 +26904,29 @@ }, { "type": "IfStatement", - "start": 8709, - "end": 9678, + "start": 9872, + "end": 10841, "loc": { "start": { - "line": 195, + "line": 221, "column": 12 }, "end": { - "line": 218, + "line": 244, "column": 13 } }, "test": { "type": "Identifier", - "start": 8713, - "end": 8736, + "start": 9876, + "end": 9899, "loc": { "start": { - "line": 195, + "line": 221, "column": 16 }, "end": { - "line": 195, + "line": 221, "column": 39 }, "identifierName": "flagNodeExpectsPhyloref" @@ -24805,86 +26935,86 @@ }, "consequent": { "type": "BlockStatement", - "start": 8738, - "end": 9678, + "start": 9901, + "end": 10841, "loc": { "start": { - "line": 195, + "line": 221, "column": 41 }, "end": { - "line": 218, + "line": 244, "column": 13 } }, "body": [ { "type": "ExpressionStatement", - "start": 9009, - "end": 9664, + "start": 10172, + "end": 10827, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 217, + "line": 243, "column": 17 } }, "expression": { "type": "CallExpression", - "start": 9009, - "end": 9663, + "start": 10172, + "end": 10826, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 217, + "line": 243, "column": 16 } }, "callee": { "type": "MemberExpression", - "start": 9009, - "end": 9037, + "start": 10172, + "end": 10200, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 201, + "line": 227, "column": 42 } }, "object": { "type": "MemberExpression", - "start": 9009, - "end": 9032, + "start": 10172, + "end": 10195, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 201, + "line": 227, "column": 37 } }, "object": { "type": "Identifier", - "start": 9009, - "end": 9013, + "start": 10172, + "end": 10176, "loc": { "start": { - "line": 201, + "line": 227, "column": 14 }, "end": { - "line": 201, + "line": 227, "column": 18 }, "identifierName": "node" @@ -24894,29 +27024,29 @@ }, "property": { "type": "MemberExpression", - "start": 9014, - "end": 9031, + "start": 10177, + "end": 10194, "loc": { "start": { - "line": 201, + "line": 227, "column": 19 }, "end": { - "line": 201, + "line": 227, "column": 36 } }, "object": { "type": "Identifier", - "start": 9014, - "end": 9022, + "start": 10177, + "end": 10185, "loc": { "start": { - "line": 201, + "line": 227, "column": 19 }, "end": { - "line": 201, + "line": 227, "column": 27 }, "identifierName": "owlterms" @@ -24925,15 +27055,15 @@ }, "property": { "type": "Identifier", - "start": 9023, - "end": 9031, + "start": 10186, + "end": 10194, "loc": { "start": { - "line": 201, + "line": 227, "column": 28 }, "end": { - "line": 201, + "line": 227, "column": 36 }, "identifierName": "RDF_TYPE" @@ -24947,15 +27077,15 @@ }, "property": { "type": "Identifier", - "start": 9033, - "end": 9037, + "start": 10196, + "end": 10200, "loc": { "start": { - "line": 201, + "line": 227, "column": 38 }, "end": { - "line": 201, + "line": 227, "column": 42 }, "identifierName": "push" @@ -24968,30 +27098,30 @@ "arguments": [ { "type": "ObjectExpression", - "start": 9038, - "end": 9662, + "start": 10201, + "end": 10825, "loc": { "start": { - "line": 201, + "line": 227, "column": 43 }, "end": { - "line": 217, + "line": 243, "column": 15 } }, "properties": [ { "type": "ObjectProperty", - "start": 9056, - "end": 9089, + "start": 10219, + "end": 10252, "loc": { "start": { - "line": 202, + "line": 228, "column": 16 }, "end": { - "line": 202, + "line": 228, "column": 49 } }, @@ -25000,15 +27130,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9056, - "end": 9063, + "start": 10219, + "end": 10226, "loc": { "start": { - "line": 202, + "line": 228, "column": 16 }, "end": { - "line": 202, + "line": 228, "column": 23 } }, @@ -25020,29 +27150,29 @@ }, "value": { "type": "MemberExpression", - "start": 9065, - "end": 9089, + "start": 10228, + "end": 10252, "loc": { "start": { - "line": 202, + "line": 228, "column": 25 }, "end": { - "line": 202, + "line": 228, "column": 49 } }, "object": { "type": "Identifier", - "start": 9065, - "end": 9073, + "start": 10228, + "end": 10236, "loc": { "start": { - "line": 202, + "line": 228, "column": 25 }, "end": { - "line": 202, + "line": 228, "column": 33 }, "identifierName": "owlterms" @@ -25051,15 +27181,15 @@ }, "property": { "type": "Identifier", - "start": 9074, - "end": 9089, + "start": 10237, + "end": 10252, "loc": { "start": { - "line": 202, + "line": 228, "column": 34 }, "end": { - "line": 202, + "line": 228, "column": 49 }, "identifierName": "OWL_RESTRICTION" @@ -25071,15 +27201,15 @@ }, { "type": "ObjectProperty", - "start": 9107, - "end": 9154, + "start": 10270, + "end": 10317, "loc": { "start": { - "line": 203, + "line": 229, "column": 16 }, "end": { - "line": 203, + "line": 229, "column": 63 } }, @@ -25088,15 +27218,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9107, - "end": 9117, + "start": 10270, + "end": 10280, "loc": { "start": { - "line": 203, + "line": 229, "column": 16 }, "end": { - "line": 203, + "line": 229, "column": 26 }, "identifierName": "onProperty" @@ -25105,29 +27235,29 @@ }, "value": { "type": "MemberExpression", - "start": 9119, - "end": 9154, + "start": 10282, + "end": 10317, "loc": { "start": { - "line": 203, + "line": 229, "column": 28 }, "end": { - "line": 203, + "line": 229, "column": 63 } }, "object": { "type": "Identifier", - "start": 9119, - "end": 9127, + "start": 10282, + "end": 10290, "loc": { "start": { - "line": 203, + "line": 229, "column": 28 }, "end": { - "line": 203, + "line": 229, "column": 36 }, "identifierName": "owlterms" @@ -25136,15 +27266,15 @@ }, "property": { "type": "Identifier", - "start": 9128, - "end": 9154, + "start": 10291, + "end": 10317, "loc": { "start": { - "line": 203, + "line": 229, "column": 37 }, "end": { - "line": 203, + "line": 229, "column": 63 }, "identifierName": "OBI_IS_SPECIFIED_OUTPUT_OF" @@ -25156,15 +27286,15 @@ }, { "type": "ObjectProperty", - "start": 9172, - "end": 9645, + "start": 10335, + "end": 10808, "loc": { "start": { - "line": 204, + "line": 230, "column": 16 }, "end": { - "line": 216, + "line": 242, "column": 17 } }, @@ -25173,15 +27303,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9172, - "end": 9186, + "start": 10335, + "end": 10349, "loc": { "start": { - "line": 204, + "line": 230, "column": 16 }, "end": { - "line": 204, + "line": 230, "column": 30 }, "identifierName": "someValuesFrom" @@ -25190,30 +27320,30 @@ }, "value": { "type": "ObjectExpression", - "start": 9188, - "end": 9645, + "start": 10351, + "end": 10808, "loc": { "start": { - "line": 204, + "line": 230, "column": 32 }, "end": { - "line": 216, + "line": 242, "column": 17 } }, "properties": [ { "type": "ObjectProperty", - "start": 9208, - "end": 9235, + "start": 10371, + "end": 10398, "loc": { "start": { - "line": 205, + "line": 231, "column": 18 }, "end": { - "line": 205, + "line": 231, "column": 45 } }, @@ -25222,15 +27352,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9208, - "end": 9215, + "start": 10371, + "end": 10378, "loc": { "start": { - "line": 205, + "line": 231, "column": 18 }, "end": { - "line": 205, + "line": 231, "column": 25 } }, @@ -25242,29 +27372,29 @@ }, "value": { "type": "MemberExpression", - "start": 9217, - "end": 9235, + "start": 10380, + "end": 10398, "loc": { "start": { - "line": 205, + "line": 231, "column": 27 }, "end": { - "line": 205, + "line": 231, "column": 45 } }, "object": { "type": "Identifier", - "start": 9217, - "end": 9225, + "start": 10380, + "end": 10388, "loc": { "start": { - "line": 205, + "line": 231, "column": 27 }, "end": { - "line": 205, + "line": 231, "column": 35 }, "identifierName": "owlterms" @@ -25273,15 +27403,15 @@ }, "property": { "type": "Identifier", - "start": 9226, - "end": 9235, + "start": 10389, + "end": 10398, "loc": { "start": { - "line": 205, + "line": 231, "column": 36 }, "end": { - "line": 205, + "line": 231, "column": 45 }, "identifierName": "OWL_CLASS" @@ -25293,15 +27423,15 @@ }, { "type": "ObjectProperty", - "start": 9255, - "end": 9626, + "start": 10418, + "end": 10789, "loc": { "start": { - "line": 206, + "line": 232, "column": 18 }, "end": { - "line": 215, + "line": 241, "column": 19 } }, @@ -25310,15 +27440,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9255, - "end": 9269, + "start": 10418, + "end": 10432, "loc": { "start": { - "line": 206, + "line": 232, "column": 18 }, "end": { - "line": 206, + "line": 232, "column": 32 }, "identifierName": "intersectionOf" @@ -25327,45 +27457,45 @@ }, "value": { "type": "ArrayExpression", - "start": 9271, - "end": 9626, + "start": 10434, + "end": 10789, "loc": { "start": { - "line": 206, + "line": 232, "column": 34 }, "end": { - "line": 215, + "line": 241, "column": 19 } }, "elements": [ { "type": "ObjectExpression", - "start": 9293, - "end": 9327, + "start": 10456, + "end": 10490, "loc": { "start": { - "line": 207, + "line": 233, "column": 20 }, "end": { - "line": 207, + "line": 233, "column": 54 } }, "properties": [ { "type": "ObjectProperty", - "start": 9295, - "end": 9325, + "start": 10458, + "end": 10488, "loc": { "start": { - "line": 207, + "line": 233, "column": 22 }, "end": { - "line": 207, + "line": 233, "column": 52 } }, @@ -25374,15 +27504,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9295, - "end": 9300, + "start": 10458, + "end": 10463, "loc": { "start": { - "line": 207, + "line": 233, "column": 22 }, "end": { - "line": 207, + "line": 233, "column": 27 } }, @@ -25394,29 +27524,29 @@ }, "value": { "type": "MemberExpression", - "start": 9302, - "end": 9325, + "start": 10465, + "end": 10488, "loc": { "start": { - "line": 207, + "line": 233, "column": 29 }, "end": { - "line": 207, + "line": 233, "column": 52 } }, "object": { "type": "Identifier", - "start": 9302, - "end": 9310, + "start": 10465, + "end": 10473, "loc": { "start": { - "line": 207, + "line": 233, "column": 29 }, "end": { - "line": 207, + "line": 233, "column": 37 }, "identifierName": "owlterms" @@ -25425,15 +27555,15 @@ }, "property": { "type": "Identifier", - "start": 9311, - "end": 9325, + "start": 10474, + "end": 10488, "loc": { "start": { - "line": 207, + "line": 233, "column": 38 }, "end": { - "line": 207, + "line": 233, "column": 52 }, "identifierName": "OBI_PREDICTION" @@ -25447,30 +27577,30 @@ }, { "type": "ObjectExpression", - "start": 9349, - "end": 9605, + "start": 10512, + "end": 10768, "loc": { "start": { - "line": 208, + "line": 234, "column": 20 }, "end": { - "line": 214, + "line": 240, "column": 21 } }, "properties": [ { "type": "ObjectProperty", - "start": 9373, - "end": 9406, + "start": 10536, + "end": 10569, "loc": { "start": { - "line": 209, + "line": 235, "column": 22 }, "end": { - "line": 209, + "line": 235, "column": 55 } }, @@ -25479,15 +27609,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9373, - "end": 9380, + "start": 10536, + "end": 10543, "loc": { "start": { - "line": 209, + "line": 235, "column": 22 }, "end": { - "line": 209, + "line": 235, "column": 29 } }, @@ -25499,29 +27629,29 @@ }, "value": { "type": "MemberExpression", - "start": 9382, - "end": 9406, + "start": 10545, + "end": 10569, "loc": { "start": { - "line": 209, + "line": 235, "column": 31 }, "end": { - "line": 209, + "line": 235, "column": 55 } }, "object": { "type": "Identifier", - "start": 9382, - "end": 9390, + "start": 10545, + "end": 10553, "loc": { "start": { - "line": 209, + "line": 235, "column": 31 }, "end": { - "line": 209, + "line": 235, "column": 39 }, "identifierName": "owlterms" @@ -25530,15 +27660,15 @@ }, "property": { "type": "Identifier", - "start": 9391, - "end": 9406, + "start": 10554, + "end": 10569, "loc": { "start": { - "line": 209, + "line": 235, "column": 40 }, "end": { - "line": 209, + "line": 235, "column": 55 }, "identifierName": "OWL_RESTRICTION" @@ -25550,15 +27680,15 @@ }, { "type": "ObjectProperty", - "start": 9430, - "end": 9474, + "start": 10593, + "end": 10637, "loc": { "start": { - "line": 210, + "line": 236, "column": 22 }, "end": { - "line": 210, + "line": 236, "column": 66 } }, @@ -25567,15 +27697,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9430, - "end": 9440, + "start": 10593, + "end": 10603, "loc": { "start": { - "line": 210, + "line": 236, "column": 22 }, "end": { - "line": 210, + "line": 236, "column": 32 }, "identifierName": "onProperty" @@ -25584,29 +27714,29 @@ }, "value": { "type": "MemberExpression", - "start": 9442, - "end": 9474, + "start": 10605, + "end": 10637, "loc": { "start": { - "line": 210, + "line": 236, "column": 34 }, "end": { - "line": 210, + "line": 236, "column": 66 } }, "object": { "type": "Identifier", - "start": 9442, - "end": 9450, + "start": 10605, + "end": 10613, "loc": { "start": { - "line": 210, + "line": 236, "column": 34 }, "end": { - "line": 210, + "line": 236, "column": 42 }, "identifierName": "owlterms" @@ -25615,15 +27745,15 @@ }, "property": { "type": "Identifier", - "start": 9451, - "end": 9474, + "start": 10614, + "end": 10637, "loc": { "start": { - "line": 210, + "line": 236, "column": 43 }, "end": { - "line": 210, + "line": 236, "column": 66 }, "identifierName": "OBI_HAS_SPECIFIED_INPUT" @@ -25635,15 +27765,15 @@ }, { "type": "ObjectProperty", - "start": 9498, - "end": 9582, + "start": 10661, + "end": 10745, "loc": { "start": { - "line": 211, + "line": 237, "column": 22 }, "end": { - "line": 213, + "line": 239, "column": 23 } }, @@ -25652,15 +27782,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9498, - "end": 9512, + "start": 10661, + "end": 10675, "loc": { "start": { - "line": 211, + "line": 237, "column": 22 }, "end": { - "line": 211, + "line": 237, "column": 36 }, "identifierName": "someValuesFrom" @@ -25669,30 +27799,30 @@ }, "value": { "type": "ObjectExpression", - "start": 9514, - "end": 9582, + "start": 10677, + "end": 10745, "loc": { "start": { - "line": 211, + "line": 237, "column": 38 }, "end": { - "line": 213, + "line": 239, "column": 23 } }, "properties": [ { "type": "ObjectProperty", - "start": 9540, - "end": 9557, + "start": 10703, + "end": 10720, "loc": { "start": { - "line": 212, + "line": 238, "column": 24 }, "end": { - "line": 212, + "line": 238, "column": 41 } }, @@ -25701,15 +27831,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 9540, - "end": 9545, + "start": 10703, + "end": 10708, "loc": { "start": { - "line": 212, + "line": 238, "column": 24 }, "end": { - "line": 212, + "line": 238, "column": 29 } }, @@ -25721,15 +27851,15 @@ }, "value": { "type": "Identifier", - "start": 9547, - "end": 9557, + "start": 10710, + "end": 10720, "loc": { "start": { - "line": 212, + "line": 238, "column": 31 }, "end": { - "line": 212, + "line": 238, "column": 41 }, "identifierName": "phylorefId" @@ -25757,15 +27887,15 @@ { "type": "CommentLine", "value": " Modify this phylogeny node's type to include that it is a type", - "start": 8754, - "end": 8819, + "start": 9917, + "end": 9982, "loc": { "start": { - "line": 196, + "line": 222, "column": 14 }, "end": { - "line": 196, + "line": 222, "column": 79 } } @@ -25773,15 +27903,15 @@ { "type": "CommentLine", "value": " of:", - "start": 8834, - "end": 8840, + "start": 9997, + "end": 10003, "loc": { "start": { - "line": 197, + "line": 223, "column": 14 }, "end": { - "line": 197, + "line": 223, "column": 20 } } @@ -25789,15 +27919,15 @@ { "type": "CommentLine", "value": " obi:is_specified_output_of some (", - "start": 8855, - "end": 8892, + "start": 10018, + "end": 10055, "loc": { "start": { - "line": 198, + "line": 224, "column": 14 }, "end": { - "line": 198, + "line": 224, "column": 51 } } @@ -25805,15 +27935,15 @@ { "type": "CommentLine", "value": " obi:Prediction and obi:has_specified_output some #phyloref_id", - "start": 8907, - "end": 8974, + "start": 10070, + "end": 10137, "loc": { "start": { - "line": 199, + "line": 225, "column": 14 }, "end": { - "line": 199, + "line": 225, "column": 81 } } @@ -25821,15 +27951,15 @@ { "type": "CommentLine", "value": " )", - "start": 8989, - "end": 8994, + "start": 10152, + "end": 10157, "loc": { "start": { - "line": 200, + "line": 226, "column": 14 }, "end": { - "line": 200, + "line": 226, "column": 19 } } @@ -25866,15 +27996,15 @@ { "type": "CommentLine", "value": " Go through all the nodes and add information on expected resolution.", - 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However, if in the", - "start": 10050, - "end": 10126, + "start": 11213, + "end": 11289, "loc": { "start": { - "line": 228, + "line": 254, "column": 4 }, "end": { - "line": 228, + "line": 254, "column": 80 } } @@ -25970,15 +28100,15 @@ { "type": "CommentLine", "value": " future we decide that we need to perform more advanced TU matching, this", - "start": 10131, - "end": 10206, + "start": 11294, + "end": 11369, "loc": { "start": { - "line": 229, + "line": 255, "column": 4 }, "end": { - "line": 229, + "line": 255, "column": 79 } } @@ -25986,15 +28116,15 @@ { "type": "CommentLine", "value": " would be the place to implement that.", - "start": 10211, - "end": 10251, + "start": 11374, + "end": 11414, "loc": { "start": { - "line": 230, + "line": 256, "column": 4 }, "end": { - "line": 230, + "line": 256, "column": 44 } } @@ -26002,15 +28132,15 @@ { "type": "CommentLine", "value": " If there is a top-level source, generate a bibliographicCitation for it.", - "start": 10257, - "end": 10332, + "start": 11420, + "end": 11495, "loc": { "start": { - 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"line": 233, + "line": 259, "column": 18 }, "identifierName": "jsonld" @@ -26083,15 +28213,15 @@ }, { "type": "StringLiteral", - "start": 10353, - "end": 10361, + "start": 11516, + "end": 11524, "loc": { "start": { - "line": 233, + "line": 259, "column": 20 }, "end": { - "line": 233, + "line": 259, "column": 28 } }, @@ -26106,87 +28236,87 @@ }, "consequent": { "type": "BlockStatement", - "start": 10364, - "end": 10462, + "start": 11527, + "end": 11625, "loc": { "start": { - "line": 233, + "line": 259, "column": 31 }, "end": { - "line": 235, + "line": 261, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 10372, - "end": 10456, + "start": 11535, + "end": 11619, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - "line": 234, + "line": 260, "column": 90 } }, "expression": { "type": "AssignmentExpression", - "start": 10372, - "end": 10455, + "start": 11535, + "end": 11618, "loc": { "start": { - "line": 234, + "line": 260, "column": 6 }, "end": { - 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"line": 234, + "line": 260, "column": 48 }, "end": { - "line": 234, + "line": 260, "column": 63 }, "identifierName": "CitationWrapper" @@ -26293,29 +28423,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 10430, - "end": 10443, + "start": 11593, + "end": 11606, "loc": { "start": { - "line": 234, + "line": 260, "column": 64 }, "end": { - "line": 234, + "line": 260, "column": 77 } }, "object": { "type": "Identifier", - "start": 10430, - "end": 10436, + "start": 11593, + "end": 11599, "loc": { "start": { - "line": 234, + "line": 260, "column": 64 }, "end": { - "line": 234, + "line": 260, "column": 70 }, "identifierName": "jsonld" @@ -26324,15 +28454,15 @@ }, "property": { "type": "Identifier", - "start": 10437, - "end": 10443, + "start": 11600, + "end": 11606, "loc": { "start": { - "line": 234, + "line": 260, "column": 71 }, "end": { - "line": 234, + "line": 260, "column": 77 }, "identifierName": "source" @@ -26345,15 +28475,15 @@ }, "property": { "type": "Identifier", - "start": 10445, - "end": 10453, + "start": 11608, + "end": 11616, "loc": { "start": { - "line": 234, + "line": 260, "column": 79 }, "end": { - "line": 234, + "line": 260, "column": 87 }, "identifierName": "toString" @@ -26375,15 +28505,15 @@ { "type": "CommentLine", "value": " Earlier, we used to generate a list of taxonomic matches here (stored in", - "start": 9726, - "end": 9801, + "start": 10889, + "end": 10964, "loc": { "start": { - "line": 224, + "line": 250, "column": 4 }, "end": { - "line": 224, + "line": 250, "column": 79 } } @@ -26391,15 +28521,15 @@ { "type": "CommentLine", "value": " jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic", - "start": 9806, - "end": 9879, + "start": 10969, + "end": 11042, "loc": { "start": { - "line": 225, + "line": 251, "column": 4 }, "end": { - "line": 225, + "line": 251, "column": 77 } } @@ -26407,15 +28537,15 @@ { "type": "CommentLine", "value": " units in phyloref specifiers were related to taxonomic units in phylogeny", - "start": 9884, - "end": 9960, + "start": 11047, + "end": 11123, "loc": { "start": { - "line": 226, + "line": 252, "column": 4 }, "end": { - "line": 226, + "line": 252, "column": 80 } } @@ -26423,15 +28553,15 @@ { "type": "CommentLine", "value": " nodes. This is no longer necessary, since phyloref specifiers are now logical", - "start": 9965, - "end": 10045, + "start": 11128, + "end": 11208, "loc": { "start": { - "line": 227, + "line": 253, "column": 4 }, "end": { - "line": 227, + "line": 253, "column": 84 } } @@ -26439,15 +28569,15 @@ { "type": "CommentLine", "value": " expressions that directly evaluate to phylogeny nodes. However, if in the", - "start": 10050, - "end": 10126, + "start": 11213, + "end": 11289, "loc": { "start": { - "line": 228, + "line": 254, "column": 4 }, "end": { - "line": 228, + "line": 254, "column": 80 } } @@ -26455,15 +28585,15 @@ { "type": "CommentLine", "value": " future we decide that we need to perform more advanced TU matching, this", - "start": 10131, - "end": 10206, + "start": 11294, + "end": 11369, "loc": { "start": { - "line": 229, + "line": 255, "column": 4 }, "end": { - "line": 229, + "line": 255, "column": 79 } } @@ -26471,15 +28601,15 @@ { "type": "CommentLine", "value": " would be the place to implement that.", - "start": 10211, - "end": 10251, + "start": 11374, + "end": 11414, "loc": { "start": { - "line": 230, + "line": 256, "column": 4 }, "end": { - "line": 230, + "line": 256, "column": 44 } } @@ -26487,15 +28617,15 @@ { "type": "CommentLine", "value": " If there is a top-level source, generate a bibliographicCitation for it.", - "start": 10257, - "end": 10332, + "start": 11420, + "end": 11495, "loc": { "start": { - "line": 232, + "line": 258, "column": 4 }, "end": { - "line": 232, + "line": 258, "column": 79 } } @@ -26505,15 +28635,15 @@ { "type": "CommentLine", "value": " Set up the top-level object '@type'. If one is present, we add our terms to that.", - "start": 10468, - "end": 10552, + "start": 11631, + "end": 11715, "loc": { "start": { - "line": 237, + "line": 263, "column": 4 }, "end": { - "line": 237, + "line": 263, "column": 88 } } @@ -26522,29 +28652,29 @@ }, { "type": "IfStatement", - "start": 10557, - "end": 10605, + "start": 11720, + "end": 11768, "loc": { "start": { - "line": 238, + "line": 264, "column": 4 }, "end": { - "line": 238, + "line": 264, "column": 52 } }, "test": { "type": "UnaryExpression", - "start": 10561, - "end": 10582, + "start": 11724, + "end": 11745, "loc": { "start": { - "line": 238, + "line": 264, "column": 8 }, "end": { - "line": 238, + "line": 264, "column": 29 } }, @@ -26552,29 +28682,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10562, - "end": 10582, + "start": 11725, + "end": 11745, "loc": { "start": { - "line": 238, + "line": 264, "column": 9 }, "end": { - "line": 238, + "line": 264, "column": 29 } }, "callee": { "type": "Identifier", - "start": 10562, - "end": 10565, + "start": 11725, + "end": 11728, "loc": { "start": { - "line": 238, + "line": 264, "column": 9 }, "end": { - "line": 238, + "line": 264, "column": 12 }, "identifierName": "has" @@ -26585,15 +28715,15 @@ "arguments": [ { "type": "Identifier", - "start": 10566, - "end": 10572, + "start": 11729, + "end": 11735, "loc": { "start": { - "line": 238, + "line": 264, "column": 13 }, "end": { - "line": 238, + "line": 264, "column": 19 }, "identifierName": "jsonld" @@ -26602,15 +28732,15 @@ }, { "type": "StringLiteral", - "start": 10574, - "end": 10581, + "start": 11737, + "end": 11744, "loc": { "start": { - "line": 238, + "line": 264, "column": 21 }, "end": { - "line": 238, + "line": 264, "column": 28 } }, @@ -26630,58 +28760,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10584, - "end": 10605, + "start": 11747, + "end": 11768, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 52 } }, "expression": { "type": "AssignmentExpression", - "start": 10584, - "end": 10604, + "start": 11747, + "end": 11767, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 51 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10584, - "end": 10599, + "start": 11747, + "end": 11762, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 46 } }, "object": { "type": "Identifier", - "start": 10584, - "end": 10590, + "start": 11747, + "end": 11753, "loc": { "start": { - "line": 238, + "line": 264, "column": 31 }, "end": { - "line": 238, + "line": 264, "column": 37 }, "identifierName": "jsonld" @@ -26690,15 +28820,15 @@ }, "property": { "type": "StringLiteral", - "start": 10591, - "end": 10598, + "start": 11754, + "end": 11761, "loc": { "start": { - "line": 238, + "line": 264, "column": 38 }, "end": { - "line": 238, + "line": 264, "column": 45 } }, @@ -26712,15 +28842,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10602, - "end": 10604, + "start": 11765, + "end": 11767, "loc": { "start": { - "line": 238, + "line": 264, "column": 49 }, "end": { - "line": 238, + "line": 264, "column": 51 } }, @@ -26733,15 +28863,15 @@ { "type": "CommentLine", "value": " Set up the top-level object '@type'. If one is present, we add our terms to that.", - "start": 10468, - "end": 10552, + "start": 11631, + "end": 11715, "loc": { "start": { - "line": 237, + "line": 263, "column": 4 }, "end": { - "line": 237, + "line": 263, "column": 88 } } @@ -26750,29 +28880,29 @@ }, { "type": "IfStatement", - "start": 10610, - "end": 10683, + "start": 11773, + "end": 11846, "loc": { "start": { - "line": 239, + "line": 265, "column": 4 }, "end": { - "line": 239, + "line": 265, "column": 77 } }, "test": { "type": "UnaryExpression", - "start": 10614, - "end": 10645, + "start": 11777, + "end": 11808, "loc": { "start": { - "line": 239, + "line": 265, "column": 8 }, "end": { - "line": 239, + "line": 265, "column": 39 } }, @@ -26780,43 +28910,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10615, - "end": 10645, + "start": 11778, + "end": 11808, "loc": { "start": { - "line": 239, + "line": 265, "column": 9 }, "end": { - "line": 239, + "line": 265, "column": 39 } }, "callee": { "type": "MemberExpression", - 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"start": 10629, - "end": 10635, + "start": 11792, + "end": 11798, "loc": { "start": { - "line": 239, + "line": 265, "column": 23 }, "end": { - "line": 239, + "line": 265, "column": 29 }, "identifierName": "jsonld" @@ -26876,15 +29006,15 @@ }, "property": { "type": "StringLiteral", - "start": 10636, - "end": 10643, + "start": 11799, + "end": 11806, "loc": { "start": { - "line": 239, + "line": 265, "column": 30 }, "end": { - "line": 239, + "line": 265, "column": 37 } }, @@ -26904,58 +29034,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10647, - "end": 10683, + "start": 11810, + "end": 11846, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 77 } }, "expression": { "type": "AssignmentExpression", - "start": 10647, - "end": 10682, + "start": 11810, + "end": 11845, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 76 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10647, - "end": 10662, + "start": 11810, + "end": 11825, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 56 } }, "object": { "type": "Identifier", - "start": 10647, - "end": 10653, + "start": 11810, + "end": 11816, "loc": { "start": { - "line": 239, + "line": 265, "column": 41 }, "end": { - "line": 239, + "line": 265, "column": 47 }, "identifierName": "jsonld" @@ -26964,15 +29094,15 @@ }, "property": { "type": "StringLiteral", - "start": 10654, - "end": 10661, + "start": 11817, + "end": 11824, "loc": { "start": { - "line": 239, + "line": 265, "column": 48 }, "end": { - "line": 239, + "line": 265, "column": 55 } }, @@ -26986,44 +29116,44 @@ }, "right": { "type": "ArrayExpression", - "start": 10665, - "end": 10682, + "start": 11828, + "end": 11845, "loc": { "start": { - "line": 239, + "line": 265, "column": 59 }, "end": { - "line": 239, + "line": 265, "column": 76 } }, "elements": [ { "type": "MemberExpression", - "start": 10666, - "end": 10681, + "start": 11829, + "end": 11844, "loc": { "start": { - "line": 239, + "line": 265, "column": 60 }, "end": { - "line": 239, + "line": 265, "column": 75 } }, "object": { "type": "Identifier", - "start": 10666, - "end": 10672, + "start": 11829, + "end": 11835, "loc": { "start": { - "line": 239, + "line": 265, "column": 60 }, "end": { - "line": 239, + "line": 265, "column": 66 }, "identifierName": "jsonld" @@ -27032,15 +29162,15 @@ }, "property": { "type": "StringLiteral", - "start": 10673, - "end": 10680, + "start": 11836, + "end": 11843, "loc": { "start": { - "line": 239, + "line": 265, "column": 67 }, "end": { - "line": 239, + "line": 265, "column": 74 } }, @@ -27060,71 +29190,71 @@ }, { "type": "ExpressionStatement", - "start": 10688, - "end": 10725, + "start": 11851, + "end": 11888, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 41 } }, "expression": { "type": "CallExpression", - "start": 10688, - "end": 10724, + "start": 11851, + "end": 11887, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 40 } }, "callee": { "type": "MemberExpression", - "start": 10688, - "end": 10708, + "start": 11851, + "end": 11871, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 24 } }, "object": { "type": "MemberExpression", - "start": 10688, - "end": 10703, + "start": 11851, + "end": 11866, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 19 } }, "object": { "type": "Identifier", - "start": 10688, - "end": 10694, + "start": 11851, + "end": 11857, "loc": { "start": { - "line": 240, + "line": 266, "column": 4 }, "end": { - "line": 240, + "line": 266, "column": 10 }, "identifierName": "jsonld" @@ -27133,15 +29263,15 @@ }, "property": { "type": "StringLiteral", - "start": 10695, - "end": 10702, + "start": 11858, + "end": 11865, "loc": { "start": { - "line": 240, + "line": 266, "column": 11 }, "end": { - "line": 240, + "line": 266, "column": 18 } }, @@ -27155,15 +29285,15 @@ }, "property": { "type": "Identifier", - "start": 10704, - "end": 10708, + "start": 11867, + "end": 11871, "loc": { "start": { - "line": 240, + "line": 266, "column": 20 }, "end": { - "line": 240, + "line": 266, "column": 24 }, "identifierName": "push" @@ -27175,15 +29305,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 10709, - "end": 10723, + "start": 11872, + "end": 11886, "loc": { "start": { - "line": 240, + "line": 266, "column": 25 }, "end": { - "line": 240, + "line": 266, "column": 39 } }, @@ -27199,15 +29329,15 @@ { "type": "CommentLine", "value": " Set up the ontology imports. If one is present, we add our imports to that.", - "start": 10731, - "end": 10809, + "start": 11894, + "end": 11972, "loc": { "start": { - "line": 242, + "line": 268, "column": 4 }, "end": { - "line": 242, + "line": 268, "column": 82 } } @@ -27216,29 +29346,29 @@ }, { "type": "IfStatement", - "start": 10814, - "end": 10874, + "start": 11977, + "end": 12037, "loc": { "start": { - "line": 243, + "line": 269, "column": 4 }, "end": { - "line": 243, + "line": 269, "column": 64 } }, "test": { "type": "UnaryExpression", - "start": 10818, - "end": 10845, + "start": 11981, + "end": 12008, "loc": { "start": { - "line": 243, + "line": 269, "column": 8 }, "end": { - "line": 243, + "line": 269, "column": 35 } }, @@ -27246,29 +29376,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10819, - "end": 10845, + "start": 11982, + "end": 12008, "loc": { "start": { - "line": 243, + "line": 269, "column": 9 }, "end": { - "line": 243, + "line": 269, "column": 35 } }, "callee": { "type": "Identifier", - "start": 10819, - "end": 10822, + "start": 11982, + "end": 11985, "loc": { "start": { - "line": 243, + "line": 269, "column": 9 }, "end": { - "line": 243, + "line": 269, "column": 12 }, "identifierName": "has" @@ -27279,15 +29409,15 @@ "arguments": [ { "type": "Identifier", - "start": 10823, - "end": 10829, + "start": 11986, + "end": 11992, "loc": { "start": { - "line": 243, + "line": 269, "column": 13 }, "end": { - "line": 243, + "line": 269, "column": 19 }, "identifierName": "jsonld" @@ -27296,15 +29426,15 @@ }, { "type": "StringLiteral", - "start": 10831, - "end": 10844, + "start": 11994, + "end": 12007, "loc": { "start": { - "line": 243, + "line": 269, "column": 21 }, "end": { - "line": 243, + "line": 269, "column": 34 } }, @@ -27324,58 +29454,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10847, - "end": 10874, + "start": 12010, + "end": 12037, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 64 } }, "expression": { "type": "AssignmentExpression", - "start": 10847, - "end": 10873, + "start": 12010, + "end": 12036, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 63 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10847, - "end": 10868, + "start": 12010, + "end": 12031, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 58 } }, "object": { "type": "Identifier", - "start": 10847, - "end": 10853, + "start": 12010, + "end": 12016, "loc": { "start": { - "line": 243, + "line": 269, "column": 37 }, "end": { - "line": 243, + "line": 269, "column": 43 }, "identifierName": "jsonld" @@ -27384,15 +29514,15 @@ }, "property": { "type": "StringLiteral", - "start": 10854, - "end": 10867, + "start": 12017, + "end": 12030, "loc": { "start": { - "line": 243, + "line": 269, "column": 44 }, "end": { - "line": 243, + "line": 269, "column": 57 } }, @@ -27406,15 +29536,15 @@ }, "right": { "type": "ArrayExpression", - "start": 10871, - "end": 10873, + "start": 12034, + "end": 12036, "loc": { "start": { - "line": 243, + "line": 269, "column": 61 }, "end": { - "line": 243, + "line": 269, "column": 63 } }, @@ -27427,15 +29557,15 @@ { "type": "CommentLine", "value": " Set up the ontology imports. If one is present, we add our imports to that.", - "start": 10731, - "end": 10809, + "start": 11894, + "end": 11972, "loc": { "start": { - "line": 242, + "line": 268, "column": 4 }, "end": { - "line": 242, + "line": 268, "column": 82 } } @@ -27444,29 +29574,29 @@ }, { "type": "IfStatement", - "start": 10879, - "end": 10970, + "start": 12042, + "end": 12133, "loc": { "start": { - "line": 244, + "line": 270, "column": 4 }, "end": { - "line": 244, + "line": 270, "column": 95 } }, "test": { "type": "UnaryExpression", - "start": 10883, - "end": 10920, + "start": 12046, + "end": 12083, "loc": { "start": { - "line": 244, + "line": 270, "column": 8 }, "end": { - "line": 244, + "line": 270, "column": 45 } }, @@ -27474,43 +29604,43 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 10884, - "end": 10920, + "start": 12047, + "end": 12083, "loc": { "start": { - "line": 244, + "line": 270, "column": 9 }, "end": { - "line": 244, + "line": 270, "column": 45 } }, "callee": { "type": "MemberExpression", - "start": 10884, - "end": 10897, + "start": 12047, + "end": 12060, "loc": { "start": { - "line": 244, + "line": 270, "column": 9 }, "end": { - "line": 244, + "line": 270, "column": 22 } }, "object": { "type": "Identifier", - "start": 10884, - "end": 10889, + "start": 12047, + "end": 12052, "loc": { "start": { - "line": 244, + "line": 270, "column": 9 }, "end": { - "line": 244, + "line": 270, "column": 14 }, "identifierName": "Array" @@ -27519,15 +29649,15 @@ }, "property": { "type": "Identifier", - "start": 10890, - "end": 10897, + "start": 12053, + "end": 12060, "loc": { "start": { - "line": 244, + "line": 270, "column": 15 }, "end": { - "line": 244, + "line": 270, "column": 22 }, "identifierName": "isArray" @@ -27539,29 +29669,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 10898, - "end": 10919, + "start": 12061, + "end": 12082, "loc": { "start": { - "line": 244, + "line": 270, "column": 23 }, "end": { - "line": 244, + "line": 270, "column": 44 } }, "object": { "type": "Identifier", - "start": 10898, - "end": 10904, + "start": 12061, + "end": 12067, "loc": { "start": { - "line": 244, + "line": 270, "column": 23 }, "end": { - "line": 244, + "line": 270, "column": 29 }, "identifierName": "jsonld" @@ -27570,15 +29700,15 @@ }, "property": { "type": "StringLiteral", - "start": 10905, - "end": 10918, + "start": 12068, + "end": 12081, "loc": { "start": { - "line": 244, + "line": 270, "column": 30 }, "end": { - "line": 244, + "line": 270, "column": 43 } }, @@ -27598,58 +29728,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 10922, - "end": 10970, + "start": 12085, + "end": 12133, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 95 } }, "expression": { "type": "AssignmentExpression", - "start": 10922, - "end": 10969, + "start": 12085, + "end": 12132, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 94 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10922, - "end": 10943, + "start": 12085, + "end": 12106, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 68 } }, "object": { "type": "Identifier", - "start": 10922, - "end": 10928, + "start": 12085, + "end": 12091, "loc": { "start": { - "line": 244, + "line": 270, "column": 47 }, "end": { - "line": 244, + "line": 270, "column": 53 }, "identifierName": "jsonld" @@ -27658,15 +29788,15 @@ }, "property": { "type": "StringLiteral", - "start": 10929, - "end": 10942, + "start": 12092, + "end": 12105, "loc": { "start": { - "line": 244, + "line": 270, "column": 54 }, "end": { - "line": 244, + "line": 270, "column": 67 } }, @@ -27680,44 +29810,44 @@ }, "right": { "type": "ArrayExpression", - "start": 10946, - "end": 10969, + "start": 12109, + "end": 12132, "loc": { "start": { - "line": 244, + "line": 270, "column": 71 }, "end": { - "line": 244, + "line": 270, "column": 94 } }, "elements": [ { "type": "MemberExpression", - "start": 10947, - "end": 10968, + "start": 12110, + "end": 12131, "loc": { "start": { - "line": 244, + "line": 270, "column": 72 }, "end": { - "line": 244, + "line": 270, "column": 93 } }, "object": { "type": "Identifier", - "start": 10947, - "end": 10953, + "start": 12110, + "end": 12116, "loc": { "start": { - "line": 244, + "line": 270, "column": 72 }, "end": { - "line": 244, + "line": 270, "column": 78 }, "identifierName": "jsonld" @@ -27726,15 +29856,15 @@ }, "property": { "type": "StringLiteral", - "start": 10954, - "end": 10967, + "start": 12117, + "end": 12130, "loc": { "start": { - "line": 244, + "line": 270, "column": 79 }, "end": { - "line": 244, + "line": 270, "column": 92 } }, @@ -27754,71 +29884,71 @@ }, { "type": "ExpressionStatement", - "start": 10975, - "end": 11058, + "start": 12138, + "end": 12221, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 87 } }, "expression": { "type": "CallExpression", - "start": 10975, - "end": 11057, + "start": 12138, + "end": 12220, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 86 } }, "callee": { "type": "MemberExpression", - "start": 10975, - "end": 11001, + "start": 12138, + "end": 12164, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 30 } }, "object": { "type": "MemberExpression", - "start": 10975, - "end": 10996, + "start": 12138, + "end": 12159, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 25 } }, "object": { "type": "Identifier", - "start": 10975, - "end": 10981, + "start": 12138, + "end": 12144, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 10 }, "identifierName": "jsonld" @@ -27827,15 +29957,15 @@ }, "property": { "type": "StringLiteral", - "start": 10982, - "end": 10995, + "start": 12145, + "end": 12158, "loc": { "start": { - "line": 245, + "line": 271, "column": 11 }, "end": { - "line": 245, + "line": 271, "column": 24 } }, @@ -27849,15 +29979,15 @@ }, "property": { "type": "Identifier", - "start": 10997, - "end": 11001, + "start": 12160, + "end": 12164, "loc": { "start": { - "line": 245, + "line": 271, "column": 26 }, "end": { - "line": 245, + "line": 271, "column": 30 }, "identifierName": "push" @@ -27869,15 +29999,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 11002, - "end": 11056, + "start": 12165, + "end": 12219, "loc": { "start": { - "line": 245, + "line": 271, "column": 31 }, "end": { - "line": 245, + "line": 271, "column": 85 } }, @@ -27892,71 +30022,71 @@ }, { "type": "ExpressionStatement", - "start": 11063, - "end": 11142, + "start": 12226, + "end": 12305, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 83 } }, "expression": { "type": "CallExpression", - "start": 11063, - "end": 11141, + "start": 12226, + "end": 12304, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 82 } }, "callee": { "type": "MemberExpression", - "start": 11063, - "end": 11089, + "start": 12226, + "end": 12252, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 30 } }, "object": { "type": "MemberExpression", - "start": 11063, - "end": 11084, + "start": 12226, + "end": 12247, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 25 } }, "object": { "type": "Identifier", - "start": 11063, - "end": 11069, + "start": 12226, + "end": 12232, "loc": { "start": { - "line": 246, + "line": 272, "column": 4 }, "end": { - "line": 246, + "line": 272, "column": 10 }, "identifierName": "jsonld" @@ -27965,15 +30095,15 @@ }, "property": { "type": "StringLiteral", - "start": 11070, - "end": 11083, + "start": 12233, + "end": 12246, "loc": { "start": { - "line": 246, + "line": 272, "column": 11 }, "end": { - "line": 246, + "line": 272, "column": 24 } }, @@ -27987,15 +30117,15 @@ }, "property": { "type": "Identifier", - "start": 11085, - "end": 11089, + "start": 12248, + "end": 12252, "loc": { "start": { - "line": 246, + "line": 272, "column": 26 }, "end": { - "line": 246, + "line": 272, "column": 30 }, "identifierName": "push" @@ -28007,15 +30137,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 11090, - "end": 11140, + "start": 12253, + "end": 12303, "loc": { "start": { - "line": 246, + "line": 272, "column": 31 }, "end": { - "line": 246, + "line": 272, "column": 81 } }, @@ -28031,15 +30161,15 @@ { "type": "CommentLine", "value": " If the '@context' is missing, add it here.", - "start": 11148, - "end": 11193, + "start": 12311, + "end": 12356, "loc": { "start": { - "line": 248, + "line": 274, "column": 4 }, "end": { - "line": 248, + "line": 274, "column": 49 } } @@ -28048,29 +30178,29 @@ }, { "type": "IfStatement", - "start": 11198, - "end": 11290, + "start": 12361, + "end": 12453, "loc": { "start": { - "line": 249, + "line": 275, "column": 4 }, "end": { - "line": 251, + "line": 277, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 11202, - "end": 11226, + "start": 12365, + "end": 12389, "loc": { "start": { - "line": 249, + "line": 275, "column": 8 }, "end": { - "line": 249, + "line": 275, "column": 32 } }, @@ -28078,29 +30208,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 11203, - "end": 11226, + "start": 12366, + "end": 12389, "loc": { "start": { - "line": 249, + "line": 275, "column": 9 }, "end": { - "line": 249, + "line": 275, "column": 32 } }, "callee": { "type": "Identifier", - "start": 11203, - "end": 11206, + "start": 12366, + "end": 12369, "loc": { "start": { - "line": 249, + "line": 275, "column": 9 }, "end": { - "line": 249, + "line": 275, "column": 12 }, "identifierName": "has" @@ -28111,15 +30241,15 @@ "arguments": [ { "type": "Identifier", - "start": 11207, - "end": 11213, + "start": 12370, + "end": 12376, "loc": { "start": { - "line": 249, + "line": 275, "column": 13 }, "end": { - "line": 249, + "line": 275, "column": 19 }, "identifierName": "jsonld" @@ -28128,15 +30258,15 @@ }, { "type": "StringLiteral", - "start": 11215, - "end": 11225, + "start": 12378, + "end": 12388, "loc": { "start": { - "line": 249, + "line": 275, "column": 21 }, "end": { - "line": 249, + "line": 275, "column": 31 } }, @@ -28156,73 +30286,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 11228, - "end": 11290, + "start": 12391, + "end": 12453, "loc": { "start": { - "line": 249, + "line": 275, "column": 34 }, "end": { - "line": 251, + "line": 277, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 11236, - "end": 11284, + "start": 12399, + "end": 12447, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 54 } }, "expression": { "type": "AssignmentExpression", - "start": 11236, - "end": 11283, + "start": 12399, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 53 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11236, - "end": 11254, + "start": 12399, + "end": 12417, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 24 } }, "object": { "type": "Identifier", - "start": 11236, - "end": 11242, + "start": 12399, + "end": 12405, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 12 }, "identifierName": "jsonld" @@ -28231,15 +30361,15 @@ }, "property": { "type": "StringLiteral", - "start": 11243, - "end": 11253, + "start": 12406, + "end": 12416, "loc": { "start": { - "line": 250, + "line": 276, "column": 13 }, "end": { - "line": 250, + "line": 276, "column": 23 } }, @@ -28253,29 +30383,29 @@ }, "right": { "type": "MemberExpression", - "start": 11257, - "end": 11283, + "start": 12420, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 27 }, "end": { - "line": 250, + "line": 276, "column": 53 } }, "object": { "type": "Identifier", - "start": 11257, - "end": 11265, + "start": 12420, + "end": 12428, "loc": { "start": { - "line": 250, + "line": 276, "column": 27 }, "end": { - "line": 250, + "line": 276, "column": 35 }, "identifierName": "owlterms" @@ -28284,15 +30414,15 @@ }, "property": { "type": "Identifier", - "start": 11266, - "end": 11283, + "start": 12429, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 36 }, "end": { - "line": 250, + "line": 276, "column": 53 }, "identifierName": "PHYX_CONTEXT_JSON" @@ -28311,15 +30441,15 @@ { "type": "CommentLine", "value": " If the '@context' is missing, add it here.", - "start": 11148, - "end": 11193, + "start": 12311, + "end": 12356, "loc": { "start": { - "line": 248, + "line": 274, "column": 4 }, "end": { - "line": 248, + "line": 274, "column": 49 } } @@ -28328,29 +30458,29 @@ }, { "type": "ReturnStatement", - "start": 11296, - "end": 11310, + "start": 12459, + "end": 12473, "loc": { "start": { - "line": 253, + "line": 279, "column": 4 }, "end": { - "line": 253, + "line": 279, "column": 18 } }, "argument": { "type": "Identifier", - "start": 11303, - "end": 11309, + "start": 12466, + "end": 12472, "loc": { "start": { - "line": 253, + "line": 279, "column": 11 }, "end": { - "line": 253, + "line": 279, "column": 17 }, "identifierName": "jsonld" @@ -28366,15 +30496,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", - "start": 2310, - "end": 3304, + "start": 3473, + "end": 4467, "loc": { "start": { - "line": 58, + "line": 84, "column": 2 }, "end": { - "line": 73, + "line": 99, "column": 5 } } @@ -28384,15 +30514,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", - "start": 11318, - "end": 12359, + "start": 12481, + "end": 13522, "loc": { "start": { - "line": 256, + "line": 282, "column": 2 }, "end": { - "line": 271, + "line": 297, "column": 5 } } @@ -28401,15 +30531,15 @@ }, { "type": "ClassMethod", - "start": 12362, - "end": 12965, + "start": 13525, + "end": 14128, "loc": { "start": { - "line": 272, + "line": 298, "column": 2 }, "end": { - "line": 285, + "line": 311, "column": 3 } }, @@ -28417,15 +30547,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12362, - "end": 12367, + "start": 13525, + "end": 13530, "loc": { "start": { - "line": 272, + "line": 298, "column": 2 }, "end": { - "line": 272, + "line": 298, "column": 7 }, "identifierName": "toRDF" @@ -28441,29 +30571,29 @@ "params": [ { "type": "AssignmentPattern", - "start": 12368, - "end": 12380, + "start": 13531, + "end": 13543, "loc": { "start": { - "line": 272, + "line": 298, "column": 8 }, "end": { - "line": 272, + "line": 298, "column": 20 } }, "left": { "type": "Identifier", - "start": 12368, - "end": 12375, + "start": 13531, + "end": 13538, "loc": { "start": { - "line": 272, + "line": 298, "column": 8 }, "end": { - "line": 272, + "line": 298, "column": 15 }, "identifierName": "baseIRI" @@ -28472,15 +30602,15 @@ }, "right": { "type": "StringLiteral", - "start": 12378, - "end": 12380, + "start": 13541, + "end": 13543, "loc": { "start": { - "line": 272, + "line": 298, "column": 18 }, "end": { - "line": 272, + "line": 298, "column": 20 } }, @@ -28493,29 +30623,29 @@ }, { "type": "AssignmentPattern", - "start": 12382, - "end": 12402, + "start": 13545, + "end": 13565, "loc": { "start": { - "line": 272, + "line": 298, "column": 22 }, "end": { - "line": 272, + "line": 298, "column": 42 } }, "left": { "type": "Identifier", - "start": 12382, - "end": 12390, + "start": 13545, + "end": 13553, "loc": { "start": { - "line": 272, + "line": 298, "column": 22 }, "end": { - "line": 272, + "line": 298, "column": 30 }, "identifierName": "filePath" @@ -28524,15 +30654,15 @@ }, "right": { "type": "Identifier", - "start": 12393, - "end": 12402, + "start": 13556, + "end": 13565, "loc": { "start": { - "line": 272, + "line": 298, "column": 33 }, "end": { - "line": 272, + "line": 298, "column": 42 }, "identifierName": "undefined" @@ -28543,59 +30673,59 @@ ], "body": { "type": "BlockStatement", - "start": 12404, - "end": 12965, + "start": 13567, + "end": 14128, "loc": { "start": { - "line": 272, + "line": 298, "column": 44 }, "end": { - "line": 285, + "line": 311, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 12410, - "end": 12451, + "start": 13573, + "end": 13614, "loc": { "start": { - "line": 273, + "line": 299, "column": 4 }, "end": { - "line": 273, + "line": 299, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12416, - "end": 12450, + "start": 13579, + "end": 13613, "loc": { "start": { - "line": 273, + "line": 299, "column": 10 }, "end": { - "line": 273, + "line": 299, "column": 44 } }, "id": { "type": "Identifier", - "start": 12416, - "end": 12425, + "start": 13579, + "end": 13588, "loc": { "start": { - "line": 273, + "line": 299, "column": 10 }, "end": { - "line": 273, + "line": 299, "column": 19 }, "identifierName": "owlJSONLD" @@ -28604,58 +30734,58 @@ }, "init": { "type": "CallExpression", - "start": 12428, - "end": 12450, + "start": 13591, + "end": 13613, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 44 } }, "callee": { "type": "MemberExpression", - "start": 12428, - "end": 12441, + "start": 13591, + "end": 13604, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 12428, - "end": 12432, + "start": 13591, + "end": 13595, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 26 } } }, "property": { "type": "Identifier", - "start": 12433, - "end": 12441, + "start": 13596, + "end": 13604, "loc": { "start": { - "line": 273, + "line": 299, "column": 27 }, "end": { - "line": 273, + "line": 299, "column": 35 }, "identifierName": "asJSONLD" @@ -28667,15 +30797,15 @@ "arguments": [ { "type": "Identifier", - "start": 12442, - "end": 12449, + "start": 13605, + "end": 13612, "loc": { "start": { - "line": 273, + "line": 299, "column": 36 }, "end": { - "line": 273, + "line": 299, "column": 43 }, "identifierName": "baseIRI" @@ -28691,15 +30821,15 @@ { "type": "CommentLine", "value": " For the purposes of testing, we are sometimes given a relative path to `@context`,", - "start": 12457, - "end": 12542, + "start": 13620, + "end": 13705, "loc": { "start": { - "line": 275, + "line": 301, "column": 4 }, "end": { - "line": 275, + "line": 301, "column": 89 } } @@ -28707,15 +30837,15 @@ { "type": "CommentLine", "value": " but the JSONLD package does not support this. Instead, we'll import the contents", - "start": 12547, - "end": 12630, + "start": 13710, + "end": 13793, "loc": { "start": { - "line": 276, + "line": 302, "column": 4 }, "end": { - "line": 276, + "line": 302, "column": 87 } } @@ -28723,15 +30853,15 @@ { "type": "CommentLine", "value": " of the relative path on the fly.", - "start": 12635, - "end": 12670, + "start": 13798, + "end": 13833, "loc": { "start": { - "line": 277, + "line": 303, "column": 4 }, "end": { - "line": 277, + "line": 303, "column": 39 } } @@ -28740,57 +30870,57 @@ }, { "type": "IfStatement", - "start": 12675, - "end": 12889, + "start": 13838, + "end": 14052, "loc": { "start": { - "line": 278, + "line": 304, "column": 4 }, "end": { - "line": 282, + "line": 308, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 12679, - "end": 12758, + "start": 13842, + "end": 13921, "loc": { "start": { - "line": 278, + "line": 304, "column": 8 }, "end": { - "line": 278, + "line": 304, "column": 87 } }, "left": { "type": "LogicalExpression", - "start": 12679, - "end": 12717, + "start": 13842, + "end": 13880, "loc": { "start": { - "line": 278, + "line": 304, "column": 8 }, "end": { - "line": 278, + "line": 304, "column": 46 } }, "left": { "type": "Identifier", - "start": 12679, - "end": 12687, + "start": 13842, + "end": 13850, "loc": { "start": { - "line": 278, + "line": 304, "column": 8 }, "end": { - "line": 278, + "line": 304, "column": 16 }, "identifierName": "filePath" @@ -28801,29 +30931,29 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 12691, - "end": 12717, + "start": 13854, + "end": 13880, "loc": { "start": { - "line": 278, + "line": 304, "column": 20 }, "end": { - "line": 278, + "line": 304, "column": 46 } }, "callee": { "type": "Identifier", - "start": 12691, - "end": 12694, + "start": 13854, + "end": 13857, "loc": { "start": { - "line": 278, + "line": 304, "column": 20 }, "end": { - "line": 278, + "line": 304, "column": 23 }, "identifierName": "has" @@ -28833,15 +30963,15 @@ "arguments": [ { "type": "Identifier", - "start": 12695, - "end": 12704, + "start": 13858, + "end": 13867, "loc": { "start": { - "line": 278, + "line": 304, "column": 24 }, "end": { - "line": 278, + "line": 304, "column": 33 }, "identifierName": "owlJSONLD" @@ -28850,15 +30980,15 @@ }, { "type": "StringLiteral", - "start": 12706, - "end": 12716, + "start": 13869, + "end": 13879, "loc": { "start": { - "line": 278, + "line": 304, "column": 35 }, "end": { - "line": 278, + "line": 304, "column": 45 } }, @@ -28875,57 +31005,57 @@ "operator": "&&", "right": { "type": "CallExpression", - "start": 12721, - "end": 12758, + "start": 13884, + "end": 13921, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 87 } }, "callee": { "type": "MemberExpression", - "start": 12721, - "end": 12753, + "start": 13884, + "end": 13916, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 12721, - "end": 12742, + "start": 13884, + "end": 13905, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 71 } }, "object": { "type": "Identifier", - "start": 12721, - "end": 12730, + "start": 13884, + "end": 13893, "loc": { "start": { - "line": 278, + "line": 304, "column": 50 }, "end": { - "line": 278, + "line": 304, "column": 59 }, "identifierName": "owlJSONLD" @@ -28934,15 +31064,15 @@ }, "property": { "type": "StringLiteral", - "start": 12731, - "end": 12741, + "start": 13894, + "end": 13904, "loc": { "start": { - "line": 278, + "line": 304, "column": 60 }, "end": { - "line": 278, + "line": 304, "column": 70 } }, @@ -28956,15 +31086,15 @@ }, "property": { "type": "Identifier", - "start": 12743, - "end": 12753, + "start": 13906, + "end": 13916, "loc": { "start": { - "line": 278, + "line": 304, "column": 72 }, "end": { - "line": 278, + "line": 304, "column": 82 }, "identifierName": "startsWith" @@ -28976,15 +31106,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 12754, - "end": 12757, + "start": 13917, + "end": 13920, "loc": { "start": { - "line": 278, + "line": 304, "column": 83 }, "end": { - "line": 278, + "line": 304, "column": 86 } }, @@ -29000,73 +31130,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 12760, - "end": 12889, + "start": 13923, + "end": 14052, "loc": { "start": { - "line": 278, + "line": 304, "column": 89 }, "end": { - "line": 282, + "line": 308, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 12768, - "end": 12883, + "start": 13931, + "end": 14046, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 281, + "line": 307, "column": 9 } }, "expression": { "type": "AssignmentExpression", - "start": 12768, - "end": 12882, + "start": 13931, + "end": 14045, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 281, + "line": 307, "column": 8 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 12768, - "end": 12789, + "start": 13931, + "end": 13952, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 279, + "line": 305, "column": 27 } }, "object": { "type": "Identifier", - "start": 12768, - "end": 12777, + "start": 13931, + "end": 13940, "loc": { "start": { - "line": 279, + "line": 305, "column": 6 }, "end": { - "line": 279, + "line": 305, "column": 15 }, "identifierName": "owlJSONLD" @@ -29075,15 +31205,15 @@ }, "property": { "type": "StringLiteral", - "start": 12778, - "end": 12788, + "start": 13941, + "end": 13951, "loc": { "start": { - "line": 279, + "line": 305, "column": 16 }, "end": { - "line": 279, + "line": 305, "column": 26 } }, @@ -29097,43 +31227,43 @@ }, "right": { "type": "CallExpression", - "start": 12792, - "end": 12882, + "start": 13955, + "end": 14045, "loc": { "start": { - "line": 279, + "line": 305, "column": 30 }, "end": { - "line": 281, + "line": 307, "column": 8 } }, "callee": { "type": "MemberExpression", - "start": 12792, - "end": 12802, + "start": 13955, + "end": 13965, "loc": { "start": { - "line": 279, + "line": 305, "column": 30 }, "end": { - "line": 279, + "line": 305, "column": 40 } }, "object": { "type": "Identifier", - "start": 12792, - "end": 12796, + "start": 13955, + "end": 13959, "loc": { "start": { - "line": 279, + "line": 305, "column": 30 }, "end": { - "line": 279, + "line": 305, "column": 34 }, "identifierName": "JSON" @@ -29142,15 +31272,15 @@ }, "property": { "type": "Identifier", - "start": 12797, - "end": 12802, + "start": 13960, + "end": 13965, "loc": { "start": { - "line": 279, + "line": 305, "column": 35 }, "end": { - "line": 279, + "line": 305, "column": 40 }, "identifierName": "parse" @@ -29162,43 +31292,43 @@ "arguments": [ { "type": "CallExpression", - "start": 12803, - "end": 12881, + "start": 13966, + "end": 14044, "loc": { "start": { - "line": 279, + "line": 305, "column": 41 }, "end": { - "line": 281, + "line": 307, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 12803, - "end": 12818, + "start": 13966, + "end": 13981, "loc": { "start": { - "line": 279, + "line": 305, "column": 41 }, "end": { - "line": 279, + "line": 305, "column": 56 } }, "object": { "type": "Identifier", - "start": 12803, - "end": 12805, + "start": 13966, + "end": 13968, "loc": { "start": { - "line": 279, + "line": 305, "column": 41 }, "end": { - "line": 279, + "line": 305, "column": 43 }, "identifierName": "fs" @@ -29207,15 +31337,15 @@ }, "property": { "type": "Identifier", - "start": 12806, - "end": 12818, + "start": 13969, + "end": 13981, "loc": { "start": { - "line": 279, + "line": 305, "column": 44 }, "end": { - "line": 279, + "line": 305, "column": 56 }, "identifierName": "readFileSync" @@ -29227,43 +31357,43 @@ "arguments": [ { "type": "CallExpression", - "start": 12828, - "end": 12873, + "start": 13991, + "end": 14036, "loc": { "start": { - "line": 280, + "line": 306, "column": 8 }, "end": { - "line": 280, + "line": 306, "column": 53 } }, "callee": { "type": "MemberExpression", - "start": 12828, - "end": 12840, + "start": 13991, + "end": 14003, "loc": { "start": { - "line": 280, + "line": 306, "column": 8 }, "end": { - "line": 280, + "line": 306, "column": 20 } }, "object": { "type": "Identifier", - "start": 12828, - "end": 12832, + "start": 13991, + "end": 13995, "loc": { "start": { - "line": 280, + "line": 306, "column": 8 }, "end": { - "line": 280, + "line": 306, "column": 12 }, "identifierName": "path" @@ -29272,15 +31402,15 @@ }, "property": { "type": "Identifier", - "start": 12833, - "end": 12840, + "start": 13996, + "end": 14003, "loc": { "start": { - "line": 280, + "line": 306, "column": 13 }, "end": { - "line": 280, + "line": 306, "column": 20 }, "identifierName": "resolve" @@ -29292,15 +31422,15 @@ "arguments": [ { "type": "Identifier", - "start": 12841, - "end": 12849, + "start": 14004, + "end": 14012, "loc": { "start": { - "line": 280, + "line": 306, "column": 21 }, "end": { - "line": 280, + "line": 306, "column": 29 }, "identifierName": "filePath" @@ -29309,29 +31439,29 @@ }, { "type": "MemberExpression", - "start": 12851, - "end": 12872, + "start": 14014, + "end": 14035, "loc": { "start": { - "line": 280, + "line": 306, "column": 31 }, "end": { - "line": 280, + "line": 306, "column": 52 } }, "object": { "type": "Identifier", - "start": 12851, - "end": 12860, + "start": 14014, + "end": 14023, "loc": { "start": { - "line": 280, + "line": 306, "column": 31 }, "end": { - "line": 280, + "line": 306, "column": 40 }, "identifierName": "owlJSONLD" @@ -29340,15 +31470,15 @@ }, "property": { "type": "StringLiteral", - "start": 12861, - "end": 12871, + "start": 14024, + "end": 14034, "loc": { "start": { - "line": 280, + "line": 306, "column": 41 }, "end": { - "line": 280, + "line": 306, "column": 51 } }, @@ -29376,15 +31506,15 @@ { "type": "CommentLine", "value": " For the purposes of testing, we are sometimes given a relative path to `@context`,", - "start": 12457, - "end": 12542, + "start": 13620, + "end": 13705, "loc": { "start": { - "line": 275, + "line": 301, "column": 4 }, "end": { - "line": 275, + "line": 301, "column": 89 } } @@ -29392,15 +31522,15 @@ { "type": "CommentLine", "value": " but the JSONLD package does not support this. Instead, we'll import the contents", - "start": 12547, - "end": 12630, + "start": 13710, + "end": 13793, "loc": { "start": { - "line": 276, + "line": 302, "column": 4 }, "end": { - "line": 276, + "line": 302, "column": 87 } } @@ -29408,15 +31538,15 @@ { "type": "CommentLine", "value": " of the relative path on the fly.", - "start": 12635, - "end": 12670, + "start": 13798, + "end": 13833, "loc": { "start": { - "line": 277, + "line": 303, "column": 4 }, "end": { - "line": 277, + "line": 303, "column": 39 } } @@ -29425,57 +31555,57 @@ }, { "type": "ReturnStatement", - "start": 12895, - "end": 12961, + "start": 14058, + "end": 14124, "loc": { "start": { - "line": 284, + "line": 310, "column": 4 }, "end": { - "line": 284, + "line": 310, "column": 70 } }, "argument": { "type": "CallExpression", - "start": 12902, - "end": 12960, + "start": 14065, + "end": 14123, "loc": { "start": { - "line": 284, + "line": 310, "column": 11 }, "end": { - "line": 284, + "line": 310, "column": 69 } }, "callee": { "type": "MemberExpression", - "start": 12902, - "end": 12914, + "start": 14065, + "end": 14077, "loc": { "start": { - "line": 284, + "line": 310, "column": 11 }, "end": { - "line": 284, + "line": 310, "column": 23 } }, "object": { "type": "Identifier", - "start": 12902, - "end": 12908, + "start": 14065, + "end": 14071, "loc": { "start": { - "line": 284, + "line": 310, "column": 11 }, "end": { - "line": 284, + "line": 310, "column": 17 }, "identifierName": "JSONLD" @@ -29484,15 +31614,15 @@ }, "property": { "type": "Identifier", - "start": 12909, - "end": 12914, + "start": 14072, + "end": 14077, "loc": { "start": { - "line": 284, + "line": 310, "column": 18 }, "end": { - "line": 284, + "line": 310, "column": 23 }, "identifierName": "toRDF" @@ -29504,15 +31634,15 @@ "arguments": [ { "type": "Identifier", - "start": 12915, - "end": 12924, + "start": 14078, + "end": 14087, "loc": { "start": { - "line": 284, + "line": 310, "column": 24 }, "end": { - "line": 284, + "line": 310, "column": 33 }, "identifierName": "owlJSONLD" @@ -29521,30 +31651,30 @@ }, { "type": "ObjectExpression", - "start": 12926, - "end": 12959, + "start": 14089, + "end": 14122, "loc": { "start": { - "line": 284, + "line": 310, "column": 35 }, "end": { - "line": 284, + "line": 310, "column": 68 } }, "properties": [ { "type": "ObjectProperty", - "start": 12928, - "end": 12957, + "start": 14091, + "end": 14120, "loc": { "start": { - "line": 284, + "line": 310, "column": 37 }, "end": { - "line": 284, + "line": 310, "column": 66 } }, @@ -29553,15 +31683,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12928, - "end": 12934, + "start": 14091, + "end": 14097, "loc": { "start": { - "line": 284, + "line": 310, "column": 37 }, "end": { - "line": 284, + "line": 310, "column": 43 }, "identifierName": "format" @@ -29570,15 +31700,15 @@ }, "value": { "type": "StringLiteral", - "start": 12936, - "end": 12957, + "start": 14099, + "end": 14120, "loc": { "start": { - "line": 284, + "line": 310, "column": 45 }, "end": { - "line": 284, + "line": 310, "column": 66 } }, @@ -29601,15 +31731,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", - "start": 11318, - "end": 12359, + "start": 12481, + "end": 13522, "loc": { "start": { - "line": 256, + "line": 282, "column": 2 }, "end": { - "line": 271, + "line": 297, "column": 5 } } @@ -29639,14 +31769,1354 @@ "__PseudoExport__": false, "trailingComments": [] }, - "specifiers": null, - "source": null, - "leadingComments": null + "specifiers": null, + "source": null, + "leadingComments": null + } + ], + "directives": [] + }, + "comments": [ + { + "type": "CommentBlock", + "value": "* Helper methods from lodash. ", + "start": 47, + "end": 81, + "loc": { + "start": { + "line": 4, + "column": 0 + }, + "end": { + "line": 4, + "column": 34 + } + } + }, + { + "type": "CommentBlock", + "value": "* For NQuads export. ", + "start": 173, + "end": 198, + "loc": { + "start": { + "line": 8, + "column": 0 + }, + "end": { + "line": 8, + "column": 25 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The PhyxWrapper wraps an entire Phyx document.\n ", + "start": 563, + "end": 620, + "loc": { + "start": { + "line": 20, + "column": 0 + }, + "end": { + "line": 22, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n ", + "start": 644, + "end": 1292, + "loc": { + "start": { + "line": 25, + "column": 2 + }, + "end": { + "line": 35, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": "", + "start": 1368, + "end": 1370, + "loc": { + "start": { + "line": 37, + "column": 4 + }, + "end": { + "line": 37, + "column": 6 + } + } + }, + { + "type": "CommentLine", + "value": " Determine a 'default nomenclatural code' for this Phyx file. There are", + "start": 1438, + "end": 1511, + "loc": { + "start": { + "line": 42, + "column": 2 + }, + "end": { + "line": 42, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " two ways to do this:", + "start": 1514, + "end": 1537, + "loc": { + "start": { + "line": 43, + "column": 2 + }, + "end": { + "line": 43, + "column": 25 + } + } + }, + { + "type": "CommentLine", + "value": " 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.", + "start": 1540, + "end": 1622, + "loc": { + "start": { + "line": 44, + "column": 2 + }, + "end": { + "line": 44, + "column": 84 + } + } + }, + { + "type": "CommentLine", + "value": " 2. Otherwise, we check to see if every phyloref in this file has the same", + "start": 1625, + "end": 1702, + "loc": { + "start": { + "line": 45, + "column": 2 + }, + "end": { + "line": 45, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " nomenclatural code. If so, we can use that code. If not, i.e. if any of", + "start": 1705, + "end": 1783, + "loc": { + "start": { + "line": 46, + "column": 2 + }, + "end": { + "line": 46, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " the phylorefs are missing a nomenclatural code or include a specifier,", + "start": 1786, + "end": 1863, + "loc": { + "start": { + "line": 47, + "column": 2 + }, + "end": { + "line": 47, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " we default to owlterms.UNKNOWN_CODE.", + "start": 1866, + "end": 1909, + "loc": { + "start": { + "line": 48, + "column": 2 + }, + "end": { + "line": 48, + "column": 45 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\n * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\n * package will be wrapped and normalized before being returned.\n *\n * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\n * identical ways. But if we implement it at every level, we can implement comparison code in\n * Klados easily.\n *\n * Two Phyx documents should -- upon being normalized -- be comparable with each other with\n * lodash.deepEqual().\n ", + "start": 2310, + "end": 3009, + "loc": { + "start": { + "line": 58, + "column": 2 + }, + "end": { + "line": 70, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", + "start": 3473, + "end": 4467, + "loc": { + "start": { + "line": 84, + "column": 2 + }, + "end": { + "line": 99, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Some helper methods for generating base IRIs for phylorefs and phylogenies.", + "start": 4541, + "end": 4619, + "loc": { + "start": { + "line": 103, + "column": 4 + }, + "end": { + "line": 103, + "column": 82 + } + } + }, + { + "type": "CommentLine", + "value": " Given a relative ID (e.g. '#phylo1') make it absolute (`${baseIRI}phylo1`).", + "start": 4909, + "end": 4987, + "loc": { + "start": { + "line": 114, + "column": 4 + }, + "end": { + "line": 114, + "column": 82 + } + } + }, + { + "type": "CommentLine", + "value": " Remove the initial '#'.", + "start": 5129, + "end": 5155, + "loc": { + "start": { + "line": 116, + "column": 98 + }, + "end": { + "line": 116, + "column": 124 + } + } + }, + { + "type": "CommentLine", + "value": " Given an absolute ID (`${baseIRI}phylo1`) make it relative (e.g. '#phylo1').", + "start": 5193, + "end": 5272, + "loc": { + "start": { + "line": 120, + "column": 4 + }, + "end": { + "line": 120, + "column": 83 + } + } + }, + { + "type": "CommentLine", + "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", + "start": 5486, + "end": 5557, + "loc": { + "start": { + "line": 127, + "column": 6 + }, + "end": { + "line": 127, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", + "start": 5564, + "end": 5633, + "loc": { + "start": { + "line": 128, + "column": 6 + }, + "end": { + "line": 128, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " to the relative IRI to make it absolute. This seems to avoid problems", + "start": 5640, + "end": 5712, + "loc": { + "start": { + "line": 129, + "column": 6 + }, + "end": { + "line": 129, + "column": 78 + } + } + }, + { + "type": "CommentLine", + "value": " with some JSON-LD parsers.", + "start": 5719, + "end": 5748, + "loc": { + "start": { + "line": 130, + "column": 6 + }, + "end": { + "line": 130, + "column": 35 + } + } + }, + { + "type": "CommentLine", + "value": " Convert phyloreferences into an OWL class restriction", + "start": 6123, + "end": 6179, + "loc": { + "start": { + "line": 142, + "column": 6 + }, + "end": { + "line": 142, + "column": 62 + } + } + }, + { + "type": "CommentLine", + "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", + "start": 6435, + "end": 6506, + "loc": { + "start": { + "line": 150, + "column": 6 + }, + "end": { + "line": 150, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", + "start": 6513, + "end": 6582, + "loc": { + "start": { + "line": 151, + "column": 6 + }, + "end": { + "line": 151, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " to the relative IRI to make it absolute. This seems to avoid problems", + "start": 6589, + "end": 6661, + "loc": { + "start": { + "line": 152, + "column": 6 + }, + "end": { + "line": 152, + "column": 78 + } + } + }, + { + "type": "CommentLine", + "value": " with some JSON-LD parsers.", + "start": 6668, + "end": 6697, + "loc": { + "start": { + "line": 153, + "column": 6 + }, + "end": { + "line": 153, + "column": 35 + } + } + }, + { + "type": "CommentLine", + "value": " Add descriptions for individual nodes in each phylogeny.", + "start": 7084, + "end": 7143, + "loc": { + "start": { + "line": 165, + "column": 6 + }, + "end": { + "line": 165, + "column": 65 + } + } + }, + { + "type": "CommentLine", + "value": " Go through all the nodes and add information on expected resolution.", + "start": 7384, + "end": 7455, + "loc": { + "start": { + "line": 171, + "column": 6 + }, + "end": { + "line": 171, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " We can't set expected resolution information on unlabeled nodes.", + "start": 7614, + "end": 7681, + "loc": { + "start": { + "line": 175, + "column": 10 + }, + "end": { + "line": 175, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " There are two ways in which we determine that a phyloreference", + "start": 7831, + "end": 7896, + "loc": { + "start": { + "line": 181, + "column": 12 + }, + "end": { + "line": 181, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " is expected to resolve to a node:", + "start": 7909, + "end": 7945, + "loc": { + "start": { + "line": 182, + "column": 12 + }, + "end": { + "line": 182, + "column": 48 + } + } + }, + { + "type": "CommentLine", + "value": " (1) If nodeLabel is set, then that must be one of the node's labels.", + "start": 7958, + "end": 8030, + "loc": { + "start": { + "line": 183, + "column": 12 + }, + "end": { + "line": 183, + "column": 84 + } + } + }, + { + "type": "CommentLine", + "value": " (2) If nodeLabel is not set, then one of the node's label should be", + "start": 8043, + "end": 8114, + "loc": { + "start": { + "line": 184, + "column": 12 + }, + "end": { + "line": 184, + "column": 83 + } + } + }, + { + "type": "CommentLine", + "value": " identical to the phyloreference's label.", + "start": 8127, + "end": 8175, + "loc": { + "start": { + "line": 185, + "column": 12 + }, + "end": { + "line": 185, + "column": 60 + } + } + }, + { + "type": "CommentLine", + "value": "", + "start": 8188, + "end": 8190, + "loc": { + "start": { + "line": 186, + "column": 12 + }, + "end": { + "line": 186, + "column": 14 + } + } + }, + { + "type": "CommentLine", + "value": " We set flagNodeExpectsPhyloref in all cases where we should note", + "start": 8203, + "end": 8270, + "loc": { + "start": { + "line": 187, + "column": 12 + }, + "end": { + "line": 187, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " that this node expects to resolve to this phyloreference.", + "start": 8283, + "end": 8343, + "loc": { + "start": { + "line": 188, + "column": 12 + }, + "end": { + "line": 188, + "column": 72 + } + } + }, + { + "type": "CommentLine", + "value": " console.log(`Testing expected resolution of '${phylorefId}' on `", + "start": 8406, + "end": 8473, + "loc": { + "start": { + "line": 191, + "column": 12 + }, + "end": { + "line": 191, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);", + "start": 8486, + "end": 8545, + "loc": { + "start": { + "line": 192, + "column": 12 + }, + "end": { + "line": 192, + "column": 71 + } + } + }, + { + "type": "CommentLine", + "value": " The user might have used the absolute phylogeny ID here.", + "start": 8649, + "end": 8708, + "loc": { + "start": { + "line": 197, + "column": 16 + }, + "end": { + "line": 197, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " Or they might have used a relative phylogeny ID.", + "start": 8788, + "end": 8839, + "loc": { + "start": { + "line": 200, + "column": 16 + }, + "end": { + "line": 200, + "column": 67 + } + } + }, + { + "type": "CommentLine", + "value": " Expected resolution information set! The node label mentioned in that", + "start": 8967, + "end": 9039, + "loc": { + "start": { + "line": 204, + "column": 14 + }, + "end": { + "line": 204, + "column": 86 + } + } + }, + { + "type": "CommentLine", + "value": " information must be identical to one of the labels of this phylogeny node.", + "start": 9054, + "end": 9131, + "loc": { + "start": { + "line": 205, + "column": 14 + }, + "end": { + "line": 205, + "column": 91 + } + } + }, + { + "type": "CommentLine", + "value": " Figure out which phylogenyId was matched here.", + "start": 9147, + "end": 9196, + "loc": { + "start": { + "line": 207, + "column": 14 + }, + "end": { + "line": 207, + "column": 63 + } + } + }, + { + "type": "CommentLine", + "value": " No expected resolution information, so we just check whether", + "start": 9654, + "end": 9717, + "loc": { + "start": { + "line": 216, + "column": 14 + }, + "end": { + "line": 216, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " the phyloref label is one of the labels on this phylogeny node.", + "start": 9732, + "end": 9798, + "loc": { + "start": { + "line": 217, + "column": 14 + }, + "end": { + "line": 217, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " Modify this phylogeny node's type to include that it is a type", + "start": 9917, + "end": 9982, + "loc": { + "start": { + "line": 222, + "column": 14 + }, + "end": { + "line": 222, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " of:", + "start": 9997, + "end": 10003, + "loc": { + "start": { + "line": 223, + "column": 14 + }, + "end": { + "line": 223, + "column": 20 + } + } + }, + { + "type": "CommentLine", + "value": " obi:is_specified_output_of some (", + "start": 10018, + "end": 10055, + "loc": { + "start": { + "line": 224, + "column": 14 + }, + "end": { + "line": 224, + "column": 51 + } + } + }, + { + "type": "CommentLine", + "value": " obi:Prediction and obi:has_specified_output some #phyloref_id", + "start": 10070, + "end": 10137, + "loc": { + "start": { + "line": 225, + "column": 14 + }, + "end": { + "line": 225, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " )", + "start": 10152, + "end": 10157, + "loc": { + "start": { + "line": 226, + "column": 14 + }, + "end": { + "line": 226, + "column": 19 + } + } + }, + { + "type": "CommentLine", + "value": " Earlier, we used to generate a list of taxonomic matches here (stored in", + "start": 10889, + "end": 10964, + "loc": { + "start": { + "line": 250, + "column": 4 + }, + "end": { + "line": 250, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic", + "start": 10969, + "end": 11042, + "loc": { + "start": { + "line": 251, + "column": 4 + }, + "end": { + "line": 251, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " units in phyloref specifiers were related to taxonomic units in phylogeny", + "start": 11047, + "end": 11123, + "loc": { + "start": { + "line": 252, + "column": 4 + }, + "end": { + "line": 252, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " nodes. This is no longer necessary, since phyloref specifiers are now logical", + "start": 11128, + "end": 11208, + "loc": { + "start": { + "line": 253, + "column": 4 + }, + "end": { + "line": 253, + "column": 84 + } + } + }, + { + "type": "CommentLine", + "value": " expressions that directly evaluate to phylogeny nodes. However, if in the", + "start": 11213, + "end": 11289, + "loc": { + "start": { + "line": 254, + "column": 4 + }, + "end": { + "line": 254, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " future we decide that we need to perform more advanced TU matching, this", + "start": 11294, + "end": 11369, + "loc": { + "start": { + "line": 255, + "column": 4 + }, + "end": { + "line": 255, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " would be the place to implement that.", + "start": 11374, + "end": 11414, + "loc": { + "start": { + "line": 256, + "column": 4 + }, + "end": { + "line": 256, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " If there is a top-level source, generate a bibliographicCitation for it.", + "start": 11420, + "end": 11495, + "loc": { + "start": { + "line": 258, + "column": 4 + }, + "end": { + "line": 258, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " Set up the top-level object '@type'. If one is present, we add our terms to that.", + "start": 11631, + "end": 11715, + "loc": { + "start": { + "line": 263, + "column": 4 + }, + "end": { + "line": 263, + "column": 88 + } + } + }, + { + "type": "CommentLine", + "value": " Set up the ontology imports. If one is present, we add our imports to that.", + "start": 11894, + "end": 11972, + "loc": { + "start": { + "line": 268, + "column": 4 + }, + "end": { + "line": 268, + "column": 82 + } + } + }, + { + "type": "CommentLine", + "value": " If the '@context' is missing, add it here.", + "start": 12311, + "end": 12356, + "loc": { + "start": { + "line": 274, + "column": 4 + }, + "end": { + "line": 274, + "column": 49 + } } - ], - "directives": [] - }, - "comments": [ + }, + { + "type": "CommentBlock", + "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", + "start": 12481, + "end": 13522, + "loc": { + "start": { + "line": 282, + "column": 2 + }, + "end": { + "line": 297, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " For the purposes of testing, we are sometimes given a relative path to `@context`,", + "start": 13620, + "end": 13705, + "loc": { + "start": { + "line": 301, + "column": 4 + }, + "end": { + "line": 301, + "column": 89 + } + } + }, + { + "type": "CommentLine", + "value": " but the JSONLD package does not support this. Instead, we'll import the contents", + "start": 13710, + "end": 13793, + "loc": { + "start": { + "line": 302, + "column": 4 + }, + "end": { + "line": 302, + "column": 87 + } + } + }, + { + "type": "CommentLine", + "value": " of the relative path on the fly.", + "start": 13798, + "end": 13833, + "loc": { + "start": { + "line": 303, + "column": 4 + }, + "end": { + "line": 303, + "column": 39 + } + } + } + ], + "tokens": [ + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 0, + "end": 6, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 6 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "fs", + "start": 7, + "end": 9, + "loc": { + "start": { + "line": 1, + "column": 7 + }, + "end": { + "line": 1, + "column": 9 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 10, + "end": 14, + "loc": { + "start": { + "line": 1, + "column": 10 + }, + "end": { + "line": 1, + "column": 14 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "fs", + "start": 15, + "end": 19, + "loc": { + "start": { + "line": 1, + "column": 15 + }, + "end": { + "line": 1, + "column": 19 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 19, + "end": 20, + "loc": { + "start": { + "line": 1, + "column": 19 + }, + "end": { + "line": 1, + "column": 20 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 21, + "end": 27, + "loc": { + "start": { + "line": 2, + "column": 0 + }, + "end": { + "line": 2, + "column": 6 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "path", + "start": 28, + "end": 32, + "loc": { + "start": { + "line": 2, + "column": 7 + }, + "end": { + "line": 2, + "column": 11 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 33, + "end": 37, + "loc": { + "start": { + "line": 2, + "column": 12 + }, + "end": { + "line": 2, + "column": 16 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "path", + "start": 38, + "end": 44, + "loc": { + "start": { + "line": 2, + "column": 17 + }, + "end": { + "line": 2, + "column": 23 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 44, + "end": 45, + "loc": { + "start": { + "line": 2, + "column": 23 + }, + "end": { + "line": 2, + "column": 24 + } + } + }, { "type": "CommentBlock", "value": "* Helper methods from lodash. ", @@ -29654,1063 +33124,1899 @@ "end": 81, "loc": { "start": { - "line": 4, - "column": 0 + "line": 4, + "column": 0 + }, + "end": { + "line": 4, + "column": 34 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 82, + "end": 88, + "loc": { + "start": { + "line": 5, + "column": 0 + }, + "end": { + "line": 5, + "column": 6 + } + } + }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 89, + "end": 90, + "loc": { + "start": { + "line": 5, + "column": 7 + }, + "end": { + "line": 5, + "column": 8 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 91, + "end": 93, + "loc": { + "start": { + "line": 5, + "column": 9 + }, + "end": { + "line": 5, + "column": 11 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK83PH1BW", + "start": 94, + "end": 107, + "loc": { + "start": { + "line": 5, + "column": 12 + }, + "end": { + "line": 5, + "column": 25 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 108, + "end": 112, + "loc": { + "start": { + "line": 5, + "column": 26 + }, + "end": { + "line": 5, + "column": 30 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "lodash", + "start": 113, + "end": 121, + "loc": { + "start": { + "line": 5, + "column": 31 + }, + "end": { + "line": 5, + "column": 39 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 121, + "end": 122, + "loc": { + "start": { + "line": 5, + "column": 39 }, "end": { - "line": 4, - "column": 34 + "line": 5, + "column": 40 } } }, { - "type": "CommentBlock", - "value": "* For NQuads export. ", - "start": 173, - "end": 198, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 124, + "end": 129, "loc": { "start": { - "line": 8, + "line": 6, "column": 0 }, "end": { - "line": 8, - "column": 25 + "line": 6, + "column": 5 } } }, { - "type": "CommentBlock", - "value": "*\n * The PhyxWrapper wraps an entire Phyx document.\n ", - "start": 563, - "end": 620, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 130, + "end": 131, "loc": { "start": { - "line": 20, - "column": 0 + "line": 6, + "column": 6 }, "end": { - "line": 22, - "column": 3 + "line": 6, + "column": 7 } } }, { - "type": "CommentBlock", - "value": "*\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n ", - "start": 644, - "end": 1292, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "has", + "start": 132, + "end": 135, "loc": { "start": { - "line": 25, - "column": 2 + "line": 6, + "column": 8 }, "end": { - "line": 35, - "column": 5 + "line": 6, + "column": 11 } } }, { - "type": "CommentLine", - "value": "", - "start": 1368, - "end": 1370, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 135, + "end": 136, "loc": { "start": { - "line": 37, - "column": 4 + "line": 6, + "column": 11 }, "end": { - "line": 37, - "column": 6 + "line": 6, + "column": 12 } } }, { - "type": "CommentLine", - "value": " Determine a 'default nomenclatural code' for this Phyx file. There are", - "start": 1438, - "end": 1511, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "cloneDeep", + "start": 137, + "end": 146, "loc": { "start": { - "line": 42, - "column": 2 + "line": 6, + "column": 13 }, "end": { - "line": 42, - "column": 75 + "line": 6, + "column": 22 } } }, { - "type": "CommentLine", - "value": " two ways to do this:", - "start": 1514, - "end": 1537, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 146, + "end": 147, "loc": { "start": { - "line": 43, - "column": 2 + "line": 6, + "column": 22 }, "end": { - "line": 43, - "column": 25 + "line": 6, + "column": 23 } } }, { - "type": "CommentLine", - "value": " 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.", - "start": 1540, - "end": 1622, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "uniq", + "start": 148, + "end": 152, "loc": { "start": { - "line": 44, - "column": 2 + "line": 6, + "column": 24 }, "end": { - "line": 44, - "column": 84 + "line": 6, + "column": 28 } } }, { - "type": "CommentLine", - "value": " 2. Otherwise, we check to see if every phyloref in this file has the same", - "start": 1625, - "end": 1702, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 153, + "end": 154, "loc": { "start": { - "line": 45, - "column": 2 + "line": 6, + "column": 29 }, "end": { - "line": 45, - "column": 79 + "line": 6, + "column": 30 } } }, { - "type": "CommentLine", - "value": " nomenclatural code. If so, we can use that code. If not, i.e. if any of", - "start": 1705, - "end": 1783, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 155, + "end": 156, "loc": { "start": { - "line": 46, - "column": 2 + "line": 6, + "column": 31 }, "end": { - "line": 46, - "column": 80 + "line": 6, + "column": 32 } } }, { - "type": "CommentLine", - "value": " the phylorefs are missing a nomenclatural code or include a specifier,", - "start": 1786, - "end": 1863, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK83PH1BW", + "start": 157, + "end": 170, "loc": { "start": { - "line": 47, - "column": 2 + "line": 6, + "column": 33 }, "end": { - "line": 47, - "column": 79 + "line": 6, + "column": 46 } } }, { - "type": "CommentLine", - "value": " we default to owlterms.UNKNOWN_CODE.", - "start": 1866, - "end": 1909, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 170, + "end": 171, "loc": { "start": { - "line": 48, - "column": 2 + "line": 6, + "column": 46 }, "end": { - "line": 48, - "column": 45 + "line": 6, + "column": 47 } } }, { "type": "CommentBlock", - "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", - "start": 2310, - "end": 3304, + "value": "* For NQuads export. ", + "start": 173, + "end": 198, "loc": { "start": { - "line": 58, - "column": 2 + "line": 8, + "column": 0 }, "end": { - "line": 73, - "column": 5 + "line": 8, + "column": 25 } } }, { - "type": "CommentLine", - "value": " Some helper methods for generating base IRIs for phylorefs and phylogenies.", - "start": 3378, - "end": 3456, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 199, + "end": 205, "loc": { "start": { - "line": 77, - "column": 4 + "line": 9, + "column": 0 }, "end": { - "line": 77, - "column": 82 + "line": 9, + "column": 6 } } }, { - "type": "CommentLine", - "value": " Given a relative ID (e.g. '#phylo1') make it absolute (`${baseIRI}phylo1`).", - "start": 3746, - "end": 3824, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "JSONLD", + "start": 206, + "end": 212, "loc": { "start": { - "line": 88, - "column": 4 + "line": 9, + "column": 7 }, "end": { - "line": 88, - "column": 82 + "line": 9, + "column": 13 } } }, { - "type": "CommentLine", - "value": " Remove the initial '#'.", - "start": 3966, - "end": 3992, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 213, + "end": 217, "loc": { "start": { - "line": 90, - "column": 98 + "line": 9, + "column": 14 }, "end": { - "line": 90, - "column": 124 + "line": 9, + "column": 18 } } }, { - "type": "CommentLine", - "value": " Given an absolute ID (`${baseIRI}phylo1`) make it relative (e.g. '#phylo1').", - "start": 4030, - "end": 4109, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "jsonld", + "start": 218, + "end": 226, "loc": { "start": { - "line": 94, - "column": 4 + "line": 9, + "column": 19 }, "end": { - "line": 94, - "column": 83 + "line": 9, + "column": 27 } } }, { - "type": "CommentLine", - "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", - "start": 4323, - "end": 4394, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 226, + "end": 227, "loc": { "start": { - "line": 101, - "column": 6 + "line": 9, + "column": 27 }, "end": { - "line": 101, - "column": 77 + "line": 9, + "column": 28 } } }, { - "type": "CommentLine", - "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", - "start": 4401, - "end": 4470, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 229, + "end": 235, "loc": { "start": { - "line": 102, + "line": 11, + "column": 0 + }, + "end": { + "line": 11, "column": 6 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 236, + "end": 244, + "loc": { + "start": { + "line": 11, + "column": 7 }, "end": { - "line": 102, - "column": 75 + "line": 11, + "column": 15 } } }, { - "type": "CommentLine", - "value": " to the relative IRI to make it absolute. This seems to avoid problems", - "start": 4477, - "end": 4549, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 245, + "end": 249, "loc": { "start": { - "line": 103, - "column": 6 + "line": 11, + "column": 16 }, "end": { - "line": 103, - "column": 78 + "line": 11, + "column": 20 } } }, { - "type": "CommentLine", - "value": " with some JSON-LD parsers.", - "start": 4556, - "end": 4585, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/owlterms", + "start": 250, + "end": 269, "loc": { "start": { - "line": 104, - "column": 6 + "line": 11, + "column": 21 }, "end": { - "line": 104, - "column": 35 + "line": 11, + "column": 40 } } }, { - "type": "CommentLine", - "value": " Convert phyloreferences into an OWL class restriction", - "start": 4960, - "end": 5016, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 269, + "end": 270, "loc": { "start": { - "line": 116, - "column": 6 + "line": 11, + "column": 40 }, "end": { - "line": 116, - "column": 62 + "line": 11, + "column": 41 } } }, { - "type": "CommentLine", - "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", - "start": 5272, - "end": 5343, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 272, + "end": 278, "loc": { "start": { - "line": 124, - "column": 6 + "line": 13, + "column": 0 }, "end": { - "line": 124, - "column": 77 + "line": 13, + "column": 6 } } }, { - "type": "CommentLine", - "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", - "start": 5350, - "end": 5419, + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 279, + "end": 280, "loc": { "start": { - "line": 125, - "column": 6 + "line": 13, + "column": 7 }, "end": { - "line": 125, - "column": 75 + "line": 13, + "column": 8 } } }, { - "type": "CommentLine", - "value": " to the relative IRI to make it absolute. This seems to avoid problems", - "start": 5426, - "end": 5498, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 281, + "end": 283, "loc": { "start": { - "line": 126, - "column": 6 + "line": 13, + "column": 9 }, "end": { - "line": 126, - "column": 78 + "line": 13, + "column": 11 } } }, { - "type": "CommentLine", - "value": " with some JSON-LD parsers.", - "start": 5505, - "end": 5534, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK836PI9S", + "start": 284, + "end": 297, "loc": { "start": { - "line": 127, - "column": 6 + "line": 13, + "column": 12 }, "end": { - "line": 127, - "column": 35 + "line": 13, + "column": 25 } } }, { - "type": "CommentLine", - "value": " Add descriptions for individual nodes in each phylogeny.", - "start": 5921, - "end": 5980, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 298, + "end": 302, "loc": { "start": { - "line": 139, - "column": 6 + "line": 13, + "column": 26 }, "end": { - "line": 139, - "column": 65 + "line": 13, + "column": 30 } } }, { - "type": "CommentLine", - "value": " Go through all the nodes and add information on expected resolution.", - "start": 6221, - "end": 6292, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "./PhylorefWrapper", + "start": 303, + "end": 322, "loc": { "start": { - "line": 145, - "column": 6 + "line": 13, + "column": 31 }, "end": { - "line": 145, - "column": 77 + "line": 13, + "column": 50 } } }, { - "type": "CommentLine", - "value": " We can't set expected resolution information on unlabeled nodes.", - "start": 6451, - "end": 6518, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 322, + "end": 323, "loc": { "start": { - "line": 149, - "column": 10 + "line": 13, + "column": 50 }, "end": { - "line": 149, - "column": 77 + "line": 13, + "column": 51 } } }, { - "type": "CommentLine", - "value": " There are two ways in which we determine that a phyloreference", - "start": 6668, - "end": 6733, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 325, + "end": 330, "loc": { "start": { - "line": 155, - "column": 12 + "line": 14, + "column": 0 }, "end": { - "line": 155, - "column": 77 + "line": 14, + "column": 5 } } }, { - "type": "CommentLine", - "value": " is expected to resolve to a node:", - "start": 6746, - "end": 6782, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 331, + "end": 332, "loc": { "start": { - "line": 156, - "column": 12 + "line": 14, + "column": 6 }, "end": { - "line": 156, - "column": 48 + "line": 14, + "column": 7 } } }, { - "type": "CommentLine", - "value": " (1) If nodeLabel is set, then that must be one of the node's labels.", - "start": 6795, - "end": 6867, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "PhylorefWrapper", + "start": 333, + "end": 348, "loc": { "start": { - "line": 157, - "column": 12 + "line": 14, + "column": 8 }, "end": { - "line": 157, - "column": 84 + "line": 14, + "column": 23 } } }, { - "type": "CommentLine", - "value": " (2) If nodeLabel is not set, then one of the node's label should be", - "start": 6880, - "end": 6951, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 349, + "end": 350, "loc": { "start": { - "line": 158, - "column": 12 + "line": 14, + "column": 24 }, "end": { - "line": 158, - "column": 83 + "line": 14, + "column": 25 } } }, { - "type": "CommentLine", - "value": " identical to the phyloreference's label.", - "start": 6964, - "end": 7012, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 351, + "end": 352, "loc": { "start": { - "line": 159, - "column": 12 + "line": 14, + "column": 26 }, "end": { - "line": 159, - "column": 60 + "line": 14, + "column": 27 } } }, { - "type": "CommentLine", - "value": "", - "start": 7025, - "end": 7027, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK836PI9S", + "start": 353, + "end": 366, "loc": { "start": { - "line": 160, - "column": 12 + "line": 14, + "column": 28 }, "end": { - "line": 160, - "column": 14 + "line": 14, + "column": 41 } } }, { - "type": "CommentLine", - "value": " We set flagNodeExpectsPhyloref in all cases where we should note", - "start": 7040, - "end": 7107, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 366, + "end": 367, "loc": { "start": { - "line": 161, - "column": 12 + "line": 14, + "column": 41 }, "end": { - "line": 161, - "column": 79 + "line": 14, + "column": 42 } } }, { - "type": "CommentLine", - "value": " that this node expects to resolve to this phyloreference.", - "start": 7120, - "end": 7180, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 368, + "end": 374, "loc": { "start": { - "line": 162, - "column": 12 + "line": 15, + "column": 0 }, "end": { - "line": 162, - "column": 72 + "line": 15, + "column": 6 } } }, { - "type": "CommentLine", - "value": " console.log(`Testing expected resolution of '${phylorefId}' on `", - "start": 7243, - "end": 7310, + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 375, + "end": 376, "loc": { "start": { - "line": 165, - "column": 12 + "line": 15, + "column": 7 }, "end": { - "line": 165, - "column": 79 + "line": 15, + "column": 8 } } }, { - "type": "CommentLine", - "value": " + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);", - "start": 7323, - "end": 7382, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 377, + "end": 379, "loc": { "start": { - "line": 166, - "column": 12 + "line": 15, + "column": 9 }, "end": { - "line": 166, - "column": 71 + "line": 15, + "column": 11 } } }, { - "type": "CommentLine", - "value": " The user might have used the absolute phylogeny ID here.", - "start": 7486, - "end": 7545, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK830DC8M", + "start": 380, + "end": 393, "loc": { "start": { - "line": 171, - "column": 16 + "line": 15, + "column": 12 }, "end": { - "line": 171, - "column": 75 + "line": 15, + "column": 25 } } }, { - "type": "CommentLine", - "value": " Or they might have used a relative phylogeny ID.", - "start": 7625, - "end": 7676, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 394, + "end": 398, "loc": { "start": { - "line": 174, - "column": 16 + "line": 15, + "column": 26 }, "end": { - "line": 174, - "column": 67 + "line": 15, + "column": 30 } } }, { - "type": "CommentLine", - "value": " Expected resolution information set! The node label mentioned in that", - "start": 7804, - "end": 7876, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "./PhylogenyWrapper", + "start": 399, + "end": 419, "loc": { "start": { - "line": 178, - "column": 14 + "line": 15, + "column": 31 }, "end": { - "line": 178, - "column": 86 + "line": 15, + "column": 51 } } }, { - "type": "CommentLine", - "value": " information must be identical to one of the labels of this phylogeny node.", - "start": 7891, - "end": 7968, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 419, + "end": 420, "loc": { "start": { - "line": 179, - "column": 14 + "line": 15, + "column": 51 }, "end": { - "line": 179, - "column": 91 + "line": 15, + "column": 52 } } }, { - "type": "CommentLine", - "value": " Figure out which phylogenyId was matched here.", - "start": 7984, - "end": 8033, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 422, + "end": 427, "loc": { "start": { - "line": 181, - "column": 14 + "line": 16, + "column": 0 }, "end": { - "line": 181, - "column": 63 + "line": 16, + "column": 5 } } }, { - "type": "CommentLine", - "value": " No expected resolution information, so we just check whether", - "start": 8491, - "end": 8554, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 428, + "end": 429, "loc": { "start": { - "line": 190, - "column": 14 + "line": 16, + "column": 6 }, "end": { - "line": 190, - "column": 77 + "line": 16, + "column": 7 } } }, { - "type": "CommentLine", - "value": " the phyloref label is one of the labels on this phylogeny node.", - "start": 8569, - "end": 8635, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "PhylogenyWrapper", + "start": 430, + "end": 446, "loc": { "start": { - "line": 191, - "column": 14 + "line": 16, + "column": 8 }, "end": { - "line": 191, - "column": 80 + "line": 16, + "column": 24 } } }, { - "type": "CommentLine", - "value": " Modify this phylogeny node's type to include that it is a type", - "start": 8754, - "end": 8819, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 447, + "end": 448, "loc": { "start": { - "line": 196, - "column": 14 + "line": 16, + "column": 25 }, "end": { - "line": 196, - "column": 79 + "line": 16, + "column": 26 } } }, { - "type": "CommentLine", - "value": " of:", - "start": 8834, - "end": 8840, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 449, + "end": 450, "loc": { "start": { - "line": 197, - "column": 14 + "line": 16, + "column": 27 }, "end": { - "line": 197, - "column": 20 + "line": 16, + "column": 28 } } }, { - "type": "CommentLine", - "value": " obi:is_specified_output_of some (", - "start": 8855, - "end": 8892, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK830DC8M", + "start": 451, + "end": 464, "loc": { "start": { - "line": 198, - "column": 14 + "line": 16, + "column": 29 }, "end": { - "line": 198, - "column": 51 + "line": 16, + "column": 42 } } }, { - "type": "CommentLine", - "value": " obi:Prediction and obi:has_specified_output some #phyloref_id", - "start": 8907, - "end": 8974, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 464, + "end": 465, "loc": { "start": { - "line": 199, - "column": 14 + "line": 16, + "column": 42 }, "end": { - "line": 199, - "column": 81 + "line": 16, + "column": 43 } } }, { - "type": "CommentLine", - "value": " )", - "start": 8989, - "end": 8994, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 466, + "end": 472, "loc": { "start": { - "line": 200, - "column": 14 + "line": 17, + "column": 0 }, "end": { - "line": 200, - "column": 19 + "line": 17, + "column": 6 } } }, { - "type": "CommentLine", - "value": " Earlier, we used to generate a list of taxonomic matches here (stored in", - "start": 9726, - "end": 9801, + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 473, + "end": 474, "loc": { "start": { - "line": 224, - "column": 4 + "line": 17, + "column": 7 }, "end": { - "line": 224, - "column": 79 + "line": 17, + "column": 8 } } }, { - "type": "CommentLine", - "value": " jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic", - "start": 9806, - "end": 9879, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 475, + "end": 477, "loc": { "start": { - "line": 225, - "column": 4 + "line": 17, + "column": 9 }, "end": { - "line": 225, - "column": 77 + "line": 17, + "column": 11 } } }, { - "type": "CommentLine", - "value": " units in phyloref specifiers were related to taxonomic units in phylogeny", - "start": 9884, - "end": 9960, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK83OXXQ2", + "start": 478, + "end": 491, "loc": { "start": { - "line": 226, - "column": 4 + "line": 17, + "column": 12 }, "end": { - "line": 226, - "column": 80 + "line": 17, + "column": 25 } } }, { - "type": "CommentLine", - "value": " nodes. This is no longer necessary, since phyloref specifiers are now logical", - "start": 9965, - "end": 10045, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 492, + "end": 496, "loc": { "start": { - "line": 227, - "column": 4 + "line": 17, + "column": 26 }, "end": { - "line": 227, - "column": 84 + "line": 17, + "column": 30 } } }, { - "type": "CommentLine", - "value": " expressions that directly evaluate to phylogeny nodes. However, if in the", - "start": 10050, - "end": 10126, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "./CitationWrapper", + "start": 497, + "end": 516, "loc": { "start": { - "line": 228, - "column": 4 + "line": 17, + "column": 31 }, "end": { - "line": 228, - "column": 80 + "line": 17, + "column": 50 } } }, { - "type": "CommentLine", - "value": " future we decide that we need to perform more advanced TU matching, this", - "start": 10131, - "end": 10206, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 516, + "end": 517, "loc": { "start": { - "line": 229, - "column": 4 + "line": 17, + "column": 50 }, "end": { - "line": 229, - "column": 79 + "line": 17, + "column": 51 } } }, { - "type": "CommentLine", - "value": " would be the place to implement that.", - "start": 10211, - "end": 10251, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 519, + "end": 524, "loc": { "start": { - "line": 230, - "column": 4 + "line": 18, + "column": 0 }, "end": { - "line": 230, - "column": 44 + "line": 18, + "column": 5 } } }, { - "type": "CommentLine", - "value": " If there is a top-level source, generate a bibliographicCitation for it.", - "start": 10257, - "end": 10332, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 525, + "end": 526, "loc": { "start": { - "line": 232, - "column": 4 + "line": 18, + "column": 6 }, "end": { - "line": 232, - "column": 79 + "line": 18, + "column": 7 } } }, { - "type": "CommentLine", - "value": " Set up the top-level object '@type'. If one is present, we add our terms to that.", - "start": 10468, - "end": 10552, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "CitationWrapper", + "start": 527, + "end": 542, "loc": { "start": { - "line": 237, - "column": 4 + "line": 18, + "column": 8 }, "end": { - "line": 237, - "column": 88 + "line": 18, + "column": 23 } } }, { - "type": "CommentLine", - "value": " Set up the ontology imports. If one is present, we add our imports to that.", - "start": 10731, - "end": 10809, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 543, + "end": 544, "loc": { "start": { - "line": 242, - "column": 4 + "line": 18, + "column": 24 }, "end": { - "line": 242, - "column": 82 + "line": 18, + "column": 25 } } }, { - "type": "CommentLine", - "value": " If the '@context' is missing, add it here.", - "start": 11148, - "end": 11193, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 545, + "end": 546, "loc": { "start": { - "line": 248, - "column": 4 + "line": 18, + "column": 26 }, "end": { - "line": 248, - "column": 49 + "line": 18, + "column": 27 } } }, { - "type": "CommentBlock", - "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", - "start": 11318, - "end": 12359, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK83OXXQ2", + "start": 547, + "end": 560, "loc": { "start": { - "line": 256, - "column": 2 + "line": 18, + "column": 28 }, "end": { - "line": 271, - "column": 5 + "line": 18, + "column": 41 } } }, { - "type": "CommentLine", - "value": " For the purposes of testing, we are sometimes given a relative path to `@context`,", - "start": 12457, - "end": 12542, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 560, + "end": 561, "loc": { "start": { - "line": 275, - "column": 4 + "line": 18, + "column": 41 }, "end": { - "line": 275, - "column": 89 + "line": 18, + "column": 42 } } }, { - "type": "CommentLine", - "value": " but the JSONLD package does not support this. Instead, we'll import the contents", - "start": 12547, - "end": 12630, + "type": "CommentBlock", + "value": "*\n * The PhyxWrapper wraps an entire Phyx document.\n ", + "start": 563, + "end": 620, "loc": { "start": { - "line": 276, - "column": 4 + "line": 20, + "column": 0 }, "end": { - "line": 276, - "column": 87 + "line": 22, + "column": 3 } } }, - { - "type": "CommentLine", - "value": " of the relative path on the fly.", - "start": 12635, - "end": 12670, - "loc": { - "start": { - "line": 277, - "column": 4 - }, - "end": { - "line": 277, - "column": 39 - } - } - } - ], - "tokens": [ { "type": { - "label": "import", - "keyword": "import", + "label": "class", + "keyword": "class", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -30719,17 +35025,17 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 0, - "end": 6, + "value": "class", + "start": 622, + "end": 627, "loc": { "start": { - "line": 1, + "line": 24, "column": 0 }, "end": { - "line": 1, - "column": 6 + "line": 24, + "column": 5 } } }, @@ -30745,24 +35051,24 @@ "postfix": false, "binop": null }, - "value": "fs", - "start": 7, - "end": 9, + "value": "PhyxWrapper", + "start": 628, + "end": 639, "loc": { "start": { - "line": 1, - "column": 7 + "line": 24, + "column": 6 }, "end": { - "line": 1, - "column": 9 + "line": 24, + "column": 17 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -30771,23 +35077,38 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 10, - "end": 14, + "start": 640, + "end": 641, "loc": { "start": { - "line": 1, - "column": 10 + "line": 24, + "column": 18 }, "end": { - "line": 1, - "column": 14 + "line": 24, + "column": 19 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n ", + "start": 644, + "end": 1292, + "loc": { + "start": { + "line": 25, + "column": 2 + }, + "end": { + "line": 35, + "column": 5 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -30795,53 +35116,50 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "fs", - "start": 15, - "end": 19, + "value": "constructor", + "start": 1295, + "end": 1306, "loc": { "start": { - "line": 1, - "column": 15 + "line": 36, + "column": 2 }, "end": { - "line": 1, - "column": 19 + "line": 36, + "column": 13 } } }, { "type": { - "label": ";", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 19, - "end": 20, + "start": 1306, + "end": 1307, "loc": { "start": { - "line": 1, - "column": 19 + "line": 36, + "column": 13 }, "end": { - "line": 1, - "column": 20 + "line": 36, + "column": 14 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -30849,46 +35167,45 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 21, - "end": 27, + "value": "phyx", + "start": 1307, + "end": 1311, "loc": { "start": { - "line": 2, - "column": 0 + "line": 36, + "column": 14 }, "end": { - "line": 2, - "column": 6 + "line": 36, + "column": 18 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "path", - "start": 28, - "end": 32, + "start": 1311, + "end": 1312, "loc": { "start": { - "line": 2, - "column": 7 + "line": 36, + "column": 18 }, "end": { - "line": 2, - "column": 11 + "line": 36, + "column": 19 } } }, @@ -30904,93 +35221,102 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 33, - "end": 37, + "value": "newickParser", + "start": 1313, + "end": 1325, "loc": { "start": { - "line": 2, - "column": 12 + "line": 36, + "column": 20 }, "end": { - "line": 2, - "column": 16 + "line": 36, + "column": 32 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "path", - "start": 38, - "end": 44, + "value": "=", + "start": 1326, + "end": 1327, "loc": { "start": { - "line": 2, - "column": 17 + "line": 36, + "column": 33 }, "end": { - "line": 2, - "column": 23 + "line": 36, + "column": 34 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 44, - "end": 45, + "value": "PhylogenyWrapper", + "start": 1328, + "end": 1344, "loc": { "start": { - "line": 2, - "column": 23 + "line": 36, + "column": 35 }, "end": { - "line": 2, - "column": 24 + "line": 36, + "column": 51 } } }, { - "type": "CommentBlock", - "value": "* Helper methods from lodash. ", - "start": 47, - "end": 81, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1344, + "end": 1345, "loc": { "start": { - "line": 4, - "column": 0 + "line": 36, + "column": 51 }, "end": { - "line": 4, - "column": 34 + "line": 36, + "column": 52 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -30998,54 +35324,51 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 82, - "end": 88, + "value": "getParsedNewick", + "start": 1345, + "end": 1360, "loc": { "start": { - "line": 5, - "column": 0 + "line": 36, + "column": 52 }, "end": { - "line": 5, - "column": 6 + "line": 36, + "column": 67 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 89, - "end": 90, + "start": 1360, + "end": 1361, "loc": { "start": { - "line": 5, - "column": 7 + "line": 36, + "column": 67 }, "end": { - "line": 5, - "column": 8 + "line": 36, + "column": 68 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -31054,23 +35377,39 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 91, - "end": 93, + "start": 1362, + "end": 1363, "loc": { "start": { - "line": 5, - "column": 9 + "line": 36, + "column": 69 }, "end": { - "line": 5, - "column": 11 + "line": 36, + "column": 70 + } + } + }, + { + "type": "CommentLine", + "value": "", + "start": 1368, + "end": 1370, + "loc": { + "start": { + "line": 37, + "column": 4 + }, + "end": { + "line": 37, + "column": 6 } } }, { "type": { - "label": "name", + "label": "this", + "keyword": "this", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -31078,51 +35417,52 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H17Y6XV4Y", - "start": 94, - "end": 107, + "value": "this", + "start": 1375, + "end": 1379, "loc": { "start": { - "line": 5, - "column": 12 + "line": 38, + "column": 4 }, "end": { - "line": 5, - "column": 25 + "line": 38, + "column": 8 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "from", - "start": 108, - "end": 112, + "start": 1379, + "end": 1380, "loc": { "start": { - "line": 5, - "column": 26 + "line": 38, + "column": 8 }, "end": { - "line": 5, - "column": 30 + "line": 38, + "column": 9 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -31130,105 +35470,105 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "lodash", - "start": 113, - "end": 121, + "value": "phyx", + "start": 1380, + "end": 1384, "loc": { "start": { - "line": 5, - "column": 31 + "line": 38, + "column": 9 }, "end": { - "line": 5, - "column": 39 + "line": 38, + "column": 13 } } }, { "type": { - "label": ";", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 121, - "end": 122, + "value": "=", + "start": 1385, + "end": 1386, "loc": { "start": { - "line": 5, - "column": 39 + "line": 38, + "column": 14 }, "end": { - "line": 5, - "column": 40 + "line": 38, + "column": 15 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 124, - "end": 129, + "value": "phyx", + "start": 1387, + "end": 1391, "loc": { "start": { - "line": 6, - "column": 0 + "line": 38, + "column": 16 }, "end": { - "line": 6, - "column": 5 + "line": 38, + "column": 20 } } }, { "type": { - "label": "{", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 130, - "end": 131, + "start": 1391, + "end": 1392, "loc": { "start": { - "line": 6, - "column": 6 + "line": 38, + "column": 20 }, "end": { - "line": 6, - "column": 7 + "line": 38, + "column": 21 } } }, { "type": { - "label": "name", + "label": "this", + "keyword": "this", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -31236,26 +35576,27 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "has", - "start": 132, - "end": 135, + "value": "this", + "start": 1397, + "end": 1401, "loc": { "start": { - "line": 6, - "column": 8 + "line": 39, + "column": 4 }, "end": { - "line": 6, - "column": 11 + "line": 39, + "column": 8 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -31265,16 +35606,16 @@ "binop": null, "updateContext": null }, - "start": 135, - "end": 136, + "start": 1401, + "end": 1402, "loc": { "start": { - "line": 6, - "column": 11 + "line": 39, + "column": 8 }, "end": { - "line": 6, - "column": 12 + "line": 39, + "column": 9 } } }, @@ -31290,42 +35631,43 @@ "postfix": false, "binop": null }, - "value": "cloneDeep", - "start": 137, - "end": 146, + "value": "newickParser", + "start": 1402, + "end": 1414, "loc": { "start": { - "line": 6, - "column": 13 + "line": 39, + "column": 9 }, "end": { - "line": 6, - "column": 22 + "line": 39, + "column": 21 } } }, { "type": { - "label": ",", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 146, - "end": 147, + "value": "=", + "start": 1415, + "end": 1416, "loc": { "start": { - "line": 6, + "line": 39, "column": 22 }, "end": { - "line": 6, + "line": 39, "column": 23 } } @@ -31342,223 +35684,186 @@ "postfix": false, "binop": null }, - "value": "uniq", - "start": 148, - "end": 152, + "value": "newickParser", + "start": 1417, + "end": 1429, "loc": { "start": { - "line": 6, + "line": 39, "column": 24 }, "end": { - "line": 6, - "column": 28 + "line": 39, + "column": 36 } } }, { "type": { - "label": "}", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 153, - "end": 154, + "start": 1429, + "end": 1430, "loc": { "start": { - "line": 6, - "column": 29 + "line": 39, + "column": 36 }, "end": { - "line": 6, - "column": 30 + "line": 39, + "column": 37 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 155, - "end": 156, + "start": 1433, + "end": 1434, "loc": { "start": { - "line": 6, - "column": 31 + "line": 40, + "column": 2 }, "end": { - "line": 6, - "column": 32 + "line": 40, + "column": 3 } } }, { - "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "value": "LKT4H17Y6XV4Y", - "start": 157, - "end": 170, + "type": "CommentLine", + "value": " Determine a 'default nomenclatural code' for this Phyx file. There are", + "start": 1438, + "end": 1511, "loc": { "start": { - "line": 6, - "column": 33 + "line": 42, + "column": 2 }, "end": { - "line": 6, - "column": 46 + "line": 42, + "column": 75 } } }, { - "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 170, - "end": 171, + "type": "CommentLine", + "value": " two ways to do this:", + "start": 1514, + "end": 1537, "loc": { "start": { - "line": 6, - "column": 46 + "line": 43, + "column": 2 }, "end": { - "line": 6, - "column": 47 + "line": 43, + "column": 25 } } }, { - "type": "CommentBlock", - "value": "* For NQuads export. ", - "start": 173, - "end": 198, + "type": "CommentLine", + "value": " 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.", + "start": 1540, + "end": 1622, "loc": { "start": { - "line": 8, - "column": 0 + "line": 44, + "column": 2 }, "end": { - "line": 8, - "column": 25 + "line": 44, + "column": 84 } } }, { - "type": { - "label": "import", - "keyword": "import", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "import", - "start": 199, - "end": 205, + "type": "CommentLine", + "value": " 2. Otherwise, we check to see if every phyloref in this file has the same", + "start": 1625, + "end": 1702, "loc": { "start": { - "line": 9, - "column": 0 + "line": 45, + "column": 2 }, "end": { - "line": 9, - "column": 6 + "line": 45, + "column": 79 } } }, { - "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "value": "JSONLD", - "start": 206, - "end": 212, + "type": "CommentLine", + "value": " nomenclatural code. If so, we can use that code. If not, i.e. if any of", + "start": 1705, + "end": 1783, "loc": { "start": { - "line": 9, - "column": 7 + "line": 46, + "column": 2 }, "end": { - "line": 9, - "column": 13 + "line": 46, + "column": 80 } } }, { - "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "value": "from", - "start": 213, - "end": 217, + "type": "CommentLine", + "value": " the phylorefs are missing a nomenclatural code or include a specifier,", + "start": 1786, + "end": 1863, "loc": { "start": { - "line": 9, - "column": 14 + "line": 47, + "column": 2 }, "end": { - "line": 9, - "column": 18 + "line": 47, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " we default to owlterms.UNKNOWN_CODE.", + "start": 1866, + "end": 1909, + "loc": { + "start": { + "line": 48, + "column": 2 + }, + "end": { + "line": 48, + "column": 45 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -31566,82 +35871,78 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "jsonld", - "start": 218, - "end": 226, + "value": "get", + "start": 1912, + "end": 1915, "loc": { "start": { - "line": 9, - "column": 19 + "line": 49, + "column": 2 }, "end": { - "line": 9, - "column": 27 + "line": 49, + "column": 5 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 226, - "end": 227, + "value": "defaultNomenCode", + "start": 1916, + "end": 1932, "loc": { "start": { - "line": 9, - "column": 27 + "line": 49, + "column": 6 }, "end": { - "line": 9, - "column": 28 + "line": 49, + "column": 22 } } }, { "type": { - "label": "import", - "keyword": "import", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 229, - "end": 235, + "start": 1932, + "end": 1933, "loc": { "start": { - "line": 11, - "column": 0 + "line": 49, + "column": 22 }, "end": { - "line": 11, - "column": 6 + "line": 49, + "column": 23 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -31649,24 +35950,23 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 236, - "end": 244, + "start": 1933, + "end": 1934, "loc": { "start": { - "line": 11, - "column": 7 + "line": 49, + "column": 23 }, "end": { - "line": 11, - "column": 15 + "line": 49, + "column": 24 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -31675,25 +35975,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 245, - "end": 249, + "start": 1935, + "end": 1936, "loc": { "start": { - "line": 11, - "column": 16 + "line": 49, + "column": 25 }, "end": { - "line": 11, - "column": 20 + "line": 49, + "column": 26 } } }, { "type": { - "label": "string", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -31702,50 +36002,48 @@ "binop": null, "updateContext": null }, - "value": "../utils/owlterms", - "start": 250, - "end": 269, + "value": "if", + "start": 1941, + "end": 1943, "loc": { "start": { - "line": 11, - "column": 21 + "line": 50, + "column": 4 }, "end": { - "line": 11, - "column": 40 + "line": 50, + "column": 6 } } }, { "type": { - "label": ";", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 269, - "end": 270, + "start": 1944, + "end": 1945, "loc": { "start": { - "line": 11, - "column": 40 + "line": 50, + "column": 7 }, "end": { - "line": 11, - "column": 41 + "line": 50, + "column": 8 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -31753,53 +36051,51 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 272, - "end": 278, + "value": "has", + "start": 1945, + "end": 1948, "loc": { "start": { - "line": 13, - "column": 0 + "line": 50, + "column": 8 }, "end": { - "line": 13, - "column": 6 + "line": 50, + "column": 11 } } }, { "type": { - "label": "*", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 279, - "end": 280, + "start": 1948, + "end": 1949, "loc": { "start": { - "line": 13, - "column": 7 + "line": 50, + "column": 11 }, "end": { - "line": 13, - "column": 8 + "line": 50, + "column": 12 } } }, { "type": { - "label": "name", + "label": "this", + "keyword": "this", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -31807,45 +36103,46 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "as", - "start": 281, - "end": 283, + "value": "this", + "start": 1949, + "end": 1953, "loc": { "start": { - "line": 13, - "column": 9 + "line": 50, + "column": 12 }, "end": { - "line": 13, - "column": 11 + "line": 50, + "column": 16 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H17YSQH4Y", - "start": 284, - "end": 297, + "start": 1953, + "end": 1954, "loc": { "start": { - "line": 13, - "column": 12 + "line": 50, + "column": 16 }, "end": { - "line": 13, - "column": 25 + "line": 50, + "column": 17 } } }, @@ -31861,25 +36158,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 298, - "end": 302, + "value": "phyx", + "start": 1954, + "end": 1958, "loc": { "start": { - "line": 13, - "column": 26 + "line": 50, + "column": 17 }, "end": { - "line": 13, - "column": 30 + "line": 50, + "column": 21 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -31888,25 +36185,24 @@ "binop": null, "updateContext": null }, - "value": "./PhylorefWrapper", - "start": 303, - "end": 322, + "start": 1958, + "end": 1959, "loc": { "start": { - "line": 13, - "column": 31 + "line": 50, + "column": 21 }, "end": { - "line": 13, - "column": 50 + "line": 50, + "column": 22 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "string", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -31915,23 +36211,23 @@ "binop": null, "updateContext": null }, - "start": 322, - "end": 323, + "value": "defaultNomenclaturalCodeIRI", + "start": 1960, + "end": 1989, "loc": { "start": { - "line": 13, - "column": 50 + "line": 50, + "column": 23 }, "end": { - "line": 13, - "column": 51 + "line": 50, + "column": 52 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -31939,28 +36235,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 325, - "end": 330, + "start": 1989, + "end": 1990, "loc": { "start": { - "line": 14, - "column": 0 + "line": 50, + "column": 52 }, "end": { - "line": 14, - "column": 5 + "line": 50, + "column": 53 } } }, { "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, + "label": ")", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -31968,94 +36262,98 @@ "postfix": false, "binop": null }, - "start": 331, - "end": 332, + "start": 1990, + "end": 1991, "loc": { "start": { - "line": 14, - "column": 6 + "line": 50, + "column": 53 }, "end": { - "line": 14, - "column": 7 + "line": 50, + "column": 54 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "PhylorefWrapper", - "start": 333, - "end": 348, + "value": "return", + "start": 1992, + "end": 1998, "loc": { "start": { - "line": 14, - "column": 8 + "line": 50, + "column": 55 }, "end": { - "line": 14, - "column": 23 + "line": 50, + "column": 61 } } }, { "type": { - "label": "}", + "label": "this", + "keyword": "this", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 349, - "end": 350, + "value": "this", + "start": 1999, + "end": 2003, "loc": { "start": { - "line": 14, - "column": 24 + "line": 50, + "column": 62 }, "end": { - "line": 14, - "column": 25 + "line": 50, + "column": 66 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 351, - "end": 352, + "start": 2003, + "end": 2004, "loc": { "start": { - "line": 14, - "column": 26 + "line": 50, + "column": 66 }, "end": { - "line": 14, - "column": 27 + "line": 50, + "column": 67 } } }, @@ -32071,24 +36369,24 @@ "postfix": false, "binop": null }, - "value": "LKT4H17YSQH4Y", - "start": 353, - "end": 366, + "value": "phyx", + "start": 2004, + "end": 2008, "loc": { "start": { - "line": 14, - "column": 28 + "line": 50, + "column": 67 }, "end": { - "line": 14, - "column": 41 + "line": 50, + "column": 71 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -32098,23 +36396,22 @@ "binop": null, "updateContext": null }, - "start": 366, - "end": 367, + "start": 2008, + "end": 2009, "loc": { "start": { - "line": 14, - "column": 41 + "line": 50, + "column": 71 }, "end": { - "line": 14, - "column": 42 + "line": 50, + "column": 72 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -32122,26 +36419,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 368, - "end": 374, + "value": "defaultNomenclaturalCodeIRI", + "start": 2009, + "end": 2036, "loc": { "start": { - "line": 15, - "column": 0 + "line": 50, + "column": 72 }, "end": { - "line": 15, - "column": 6 + "line": 50, + "column": 99 } } }, { "type": { - "label": "*", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -32149,46 +36445,47 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 375, - "end": 376, + "start": 2036, + "end": 2037, "loc": { "start": { - "line": 15, - "column": 7 + "line": 50, + "column": 99 }, "end": { - "line": 15, - "column": 8 + "line": 50, + "column": 100 } } }, { "type": { - "label": "name", + "label": "const", + "keyword": "const", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "as", - "start": 377, - "end": 379, + "value": "const", + "start": 2042, + "end": 2047, "loc": { "start": { - "line": 15, - "column": 9 + "line": 51, + "column": 4 }, "end": { - "line": 15, - "column": 11 + "line": 51, + "column": 9 } } }, @@ -32204,78 +36501,78 @@ "postfix": false, "binop": null }, - "value": "LKT4H17YPJAMM", - "start": 380, - "end": 393, + "value": "nomenCodes", + "start": 2048, + "end": 2058, "loc": { "start": { - "line": 15, - "column": 12 + "line": 51, + "column": 10 }, "end": { - "line": 15, - "column": 25 + "line": 51, + "column": 20 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "from", - "start": 394, - "end": 398, + "value": "=", + "start": 2059, + "end": 2060, "loc": { "start": { - "line": 15, - "column": 26 + "line": 51, + "column": 21 }, "end": { - "line": 15, - "column": 30 + "line": 51, + "column": 22 } } }, { "type": { - "label": "string", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "./PhylogenyWrapper", - "start": 399, - "end": 419, + "start": 2061, + "end": 2062, "loc": { "start": { - "line": 15, - "column": 31 + "line": 51, + "column": 23 }, "end": { - "line": 15, - "column": 51 + "line": 51, + "column": 24 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "this", + "keyword": "this", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -32284,23 +36581,23 @@ "binop": null, "updateContext": null }, - "start": 419, - "end": 420, + "value": "this", + "start": 2062, + "end": 2066, "loc": { "start": { - "line": 15, - "column": 51 + "line": 51, + "column": 24 }, "end": { - "line": 15, - "column": 52 + "line": 51, + "column": 28 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -32311,24 +36608,23 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 422, - "end": 427, + "start": 2066, + "end": 2067, "loc": { "start": { - "line": 16, - "column": 0 + "line": 51, + "column": 28 }, "end": { - "line": 16, - "column": 5 + "line": 51, + "column": 29 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -32337,50 +36633,51 @@ "postfix": false, "binop": null }, - "start": 428, - "end": 429, + "value": "phyx", + "start": 2067, + "end": 2071, "loc": { "start": { - "line": 16, - "column": 6 + "line": 51, + "column": 29 }, "end": { - "line": 16, - "column": 7 + "line": 51, + "column": 33 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "PhylogenyWrapper", - "start": 430, - "end": 446, + "start": 2071, + "end": 2072, "loc": { "start": { - "line": 16, - "column": 8 + "line": 51, + "column": 33 }, "end": { - "line": 16, - "column": 24 + "line": 51, + "column": 34 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -32388,76 +36685,77 @@ "postfix": false, "binop": null }, - "start": 447, - "end": 448, + "value": "phylorefs", + "start": 2072, + "end": 2081, "loc": { "start": { - "line": 16, - "column": 25 + "line": 51, + "column": 34 }, "end": { - "line": 16, - "column": 26 + "line": 51, + "column": 43 } } }, { "type": { - "label": "=", + "label": "||", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 1, "updateContext": null }, - "value": "=", - "start": 449, - "end": 450, + "value": "||", + "start": 2082, + "end": 2084, "loc": { "start": { - "line": 16, - "column": 27 + "line": 51, + "column": 44 }, "end": { - "line": 16, - "column": 28 + "line": 51, + "column": 46 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "[", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H17YPJAMM", - "start": 451, - "end": 464, + "start": 2085, + "end": 2086, "loc": { "start": { - "line": 16, - "column": 29 + "line": 51, + "column": 47 }, "end": { - "line": 16, - "column": 42 + "line": 51, + "column": 48 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": "]", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -32467,71 +36765,67 @@ "binop": null, "updateContext": null }, - "start": 464, - "end": 465, + "start": 2086, + "end": 2087, "loc": { "start": { - "line": 16, - "column": 42 + "line": 51, + "column": 48 }, "end": { - "line": 16, - "column": 43 + "line": 51, + "column": 49 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 466, - "end": 472, + "start": 2087, + "end": 2088, "loc": { "start": { - "line": 17, - "column": 0 + "line": 51, + "column": 49 }, "end": { - "line": 17, - "column": 6 + "line": 51, + "column": 50 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 473, - "end": 474, + "start": 2095, + "end": 2096, "loc": { "start": { - "line": 17, - "column": 7 + "line": 52, + "column": 6 }, "end": { - "line": 17, - "column": 8 + "line": 52, + "column": 7 } } }, @@ -32547,24 +36841,24 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 475, - "end": 477, + "value": "map", + "start": 2096, + "end": 2099, "loc": { "start": { - "line": 17, - "column": 9 + "line": 52, + "column": 7 }, "end": { - "line": 17, - "column": 11 + "line": 52, + "column": 10 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -32573,17 +36867,16 @@ "postfix": false, "binop": null }, - "value": "LKT4H17YNLTNS", - "start": 478, - "end": 491, + "start": 2099, + "end": 2100, "loc": { "start": { - "line": 17, - "column": 12 + "line": 52, + "column": 10 }, "end": { - "line": 17, - "column": 25 + "line": 52, + "column": 11 } } }, @@ -32599,25 +36892,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 492, - "end": 496, + "value": "phyloref", + "start": 2100, + "end": 2108, "loc": { "start": { - "line": 17, - "column": 26 + "line": 52, + "column": 11 }, "end": { - "line": 17, - "column": 30 + "line": 52, + "column": 19 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": "=>", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -32626,25 +36919,25 @@ "binop": null, "updateContext": null }, - "value": "./CitationWrapper", - "start": 497, - "end": 516, + "start": 2109, + "end": 2111, "loc": { "start": { - "line": 17, - "column": 31 + "line": 52, + "column": 20 }, "end": { - "line": 17, - "column": 50 + "line": 52, + "column": 22 } } }, { "type": { - "label": ";", + "label": "new", + "keyword": "new", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -32653,50 +36946,49 @@ "binop": null, "updateContext": null }, - "start": 516, - "end": 517, + "value": "new", + "start": 2112, + "end": 2115, "loc": { "start": { - "line": 17, - "column": 50 + "line": 52, + "column": 23 }, "end": { - "line": 17, - "column": 51 + "line": 52, + "column": 26 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 519, - "end": 524, + "value": "PhylorefWrapper", + "start": 2116, + "end": 2131, "loc": { "start": { - "line": 18, - "column": 0 + "line": 52, + "column": 27 }, "end": { - "line": 18, - "column": 5 + "line": 52, + "column": 42 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -32706,16 +36998,16 @@ "postfix": false, "binop": null }, - "start": 525, - "end": 526, + "start": 2131, + "end": 2132, "loc": { "start": { - "line": 18, - "column": 6 + "line": 52, + "column": 42 }, "end": { - "line": 18, - "column": 7 + "line": 52, + "column": 43 } } }, @@ -32731,23 +37023,23 @@ "postfix": false, "binop": null }, - "value": "CitationWrapper", - "start": 527, - "end": 542, + "value": "phyloref", + "start": 2132, + "end": 2140, "loc": { "start": { - "line": 18, - "column": 8 + "line": 52, + "column": 43 }, "end": { - "line": 18, - "column": 23 + "line": 52, + "column": 51 } } }, { "type": { - "label": "}", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -32757,43 +37049,42 @@ "postfix": false, "binop": null }, - "start": 543, - "end": 544, + "start": 2140, + "end": 2141, "loc": { "start": { - "line": 18, - "column": 24 + "line": 52, + "column": 51 }, "end": { - "line": 18, - "column": 25 + "line": 52, + "column": 52 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 545, - "end": 546, + "start": 2141, + "end": 2142, "loc": { "start": { - "line": 18, - "column": 26 + "line": 52, + "column": 52 }, "end": { - "line": 18, - "column": 27 + "line": 52, + "column": 53 } } }, @@ -32809,66 +37100,75 @@ "postfix": false, "binop": null }, - "value": "LKT4H17YNLTNS", - "start": 547, - "end": 560, + "value": "defaultNomenCode", + "start": 2142, + "end": 2158, "loc": { "start": { - "line": 18, - "column": 28 + "line": 52, + "column": 53 }, "end": { - "line": 18, - "column": 41 + "line": 52, + "column": 69 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 560, - "end": 561, + "start": 2158, + "end": 2159, "loc": { "start": { - "line": 18, - "column": 41 + "line": 52, + "column": 69 }, "end": { - "line": 18, - "column": 42 + "line": 52, + "column": 70 } } }, { - "type": "CommentBlock", - "value": "*\n * The PhyxWrapper wraps an entire Phyx document.\n ", - "start": 563, - "end": 620, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2159, + "end": 2160, "loc": { "start": { - "line": 20, - "column": 0 + "line": 52, + "column": 70 }, "end": { - "line": 22, - "column": 3 + "line": 52, + "column": 71 } } }, { "type": { - "label": "class", - "keyword": "class", + "label": "const", + "keyword": "const", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -32879,17 +37179,17 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 622, - "end": 627, + "value": "const", + "start": 2165, + "end": 2170, "loc": { "start": { - "line": 24, - "column": 0 + "line": 53, + "column": 4 }, "end": { - "line": 24, - "column": 5 + "line": 53, + "column": 9 } } }, @@ -32905,65 +37205,77 @@ "postfix": false, "binop": null }, - "value": "PhyxWrapper", - "start": 628, - "end": 639, + "value": "uniqNomenCodes", + "start": 2171, + "end": 2185, "loc": { "start": { - "line": 24, - "column": 6 + "line": 53, + "column": 10 }, "end": { - "line": 24, - "column": 17 + "line": 53, + "column": 24 } } }, { "type": { - "label": "{", + "label": "=", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 640, - "end": 641, + "value": "=", + "start": 2186, + "end": 2187, "loc": { "start": { - "line": 24, - "column": 18 + "line": 53, + "column": 25 }, "end": { - "line": 24, - "column": 19 + "line": 53, + "column": 26 } } }, { - "type": "CommentBlock", - "value": "*\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n ", - "start": 644, - "end": 1292, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "uniq", + "start": 2188, + "end": 2192, "loc": { "start": { - "line": 25, - "column": 2 + "line": 53, + "column": 27 }, "end": { - "line": 35, - "column": 5 + "line": 53, + "column": 31 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -32972,24 +37284,23 @@ "postfix": false, "binop": null }, - "value": "constructor", - "start": 1295, - "end": 1306, + "start": 2192, + "end": 2193, "loc": { "start": { - "line": 36, - "column": 2 + "line": 53, + "column": 31 }, "end": { - "line": 36, - "column": 13 + "line": 53, + "column": 32 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -32998,24 +37309,25 @@ "postfix": false, "binop": null }, - "start": 1306, - "end": 1307, + "value": "nomenCodes", + "start": 2193, + "end": 2203, "loc": { "start": { - "line": 36, - "column": 13 + "line": 53, + "column": 32 }, "end": { - "line": 36, - "column": 14 + "line": 53, + "column": 42 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -33023,23 +37335,22 @@ "postfix": false, "binop": null }, - "value": "phyx", - "start": 1307, - "end": 1311, + "start": 2203, + "end": 2204, "loc": { "start": { - "line": 36, - "column": 14 + "line": 53, + "column": 42 }, "end": { - "line": 36, - "column": 18 + "line": 53, + "column": 43 } } }, { "type": { - "label": ",", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -33050,69 +37361,69 @@ "binop": null, "updateContext": null }, - "start": 1311, - "end": 1312, + "start": 2204, + "end": 2205, "loc": { "start": { - "line": 36, - "column": 18 + "line": 53, + "column": 43 }, "end": { - "line": 36, - "column": 19 + "line": 53, + "column": 44 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "newickParser", - "start": 1313, - "end": 1325, + "value": "if", + "start": 2210, + "end": 2212, "loc": { "start": { - "line": 36, - "column": 20 + "line": 54, + "column": 4 }, "end": { - "line": 36, - "column": 32 + "line": 54, + "column": 6 } } }, { "type": { - "label": "=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 1326, - "end": 1327, + "start": 2213, + "end": 2214, "loc": { "start": { - "line": 36, - "column": 33 + "line": 54, + "column": 7 }, "end": { - "line": 36, - "column": 34 + "line": 54, + "column": 8 } } }, @@ -33128,17 +37439,17 @@ "postfix": false, "binop": null }, - "value": "PhylogenyWrapper", - "start": 1328, - "end": 1344, + "value": "uniqNomenCodes", + "start": 2214, + "end": 2228, "loc": { "start": { - "line": 36, - "column": 35 + "line": 54, + "column": 8 }, "end": { - "line": 36, - "column": 51 + "line": 54, + "column": 22 } } }, @@ -33155,16 +37466,16 @@ "binop": null, "updateContext": null }, - "start": 1344, - "end": 1345, + "start": 2228, + "end": 2229, "loc": { "start": { - "line": 36, - "column": 51 + "line": 54, + "column": 22 }, "end": { - "line": 36, - "column": 52 + "line": 54, + "column": 23 } } }, @@ -33180,118 +37491,104 @@ "postfix": false, "binop": null }, - "value": "getParsedNewick", - "start": 1345, - "end": 1360, + "value": "length", + "start": 2229, + "end": 2235, "loc": { "start": { - "line": 36, - "column": 52 + "line": 54, + "column": 23 }, "end": { - "line": 36, - "column": 67 + "line": 54, + "column": 29 } } }, { "type": { - "label": ")", - "beforeExpr": false, + "label": "==/!=", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": 6, + "updateContext": null }, - "start": 1360, - "end": 1361, + "value": "===", + "start": 2236, + "end": 2239, "loc": { "start": { - "line": 36, - "column": 67 + "line": 54, + "column": 30 }, "end": { - "line": 36, - "column": 68 + "line": 54, + "column": 33 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "num", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1362, - "end": 1363, - "loc": { - "start": { - "line": 36, - "column": 69 - }, - "end": { - "line": 36, - "column": 70 - } - } - }, - { - "type": "CommentLine", - "value": "", - "start": 1368, - "end": 1370, + "value": 1, + "start": 2240, + "end": 2241, "loc": { "start": { - "line": 37, - "column": 4 + "line": 54, + "column": 34 }, "end": { - "line": 37, - "column": 6 + "line": 54, + "column": 35 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 1375, - "end": 1379, + "start": 2241, + "end": 2242, "loc": { "start": { - "line": 38, - "column": 4 + "line": 54, + "column": 35 }, "end": { - "line": 38, - "column": 8 + "line": 54, + "column": 36 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "return", + "keyword": "return", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -33301,16 +37598,17 @@ "binop": null, "updateContext": null }, - "start": 1379, - "end": 1380, + "value": "return", + "start": 2243, + "end": 2249, "loc": { "start": { - "line": 38, - "column": 8 + "line": 54, + "column": 37 }, "end": { - "line": 38, - "column": 9 + "line": 54, + "column": 43 } } }, @@ -33326,50 +37624,49 @@ "postfix": false, "binop": null }, - "value": "phyx", - "start": 1380, - "end": 1384, + "value": "uniqNomenCodes", + "start": 2250, + "end": 2264, "loc": { "start": { - "line": 38, - "column": 9 + "line": 54, + "column": 44 }, "end": { - "line": 38, - "column": 13 + "line": 54, + "column": 58 } } }, { "type": { - "label": "=", + "label": "[", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 1385, - "end": 1386, + "start": 2264, + "end": 2265, "loc": { "start": { - "line": 38, - "column": 14 + "line": 54, + "column": 58 }, "end": { - "line": 38, - "column": 15 + "line": 54, + "column": 59 } } }, { "type": { - "label": "name", + "label": "num", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -33377,26 +37674,27 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "phyx", - "start": 1387, - "end": 1391, + "value": 0, + "start": 2265, + "end": 2266, "loc": { "start": { - "line": 38, - "column": 16 + "line": 54, + "column": 59 }, "end": { - "line": 38, - "column": 20 + "line": 54, + "column": 60 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": "]", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -33406,25 +37704,24 @@ "binop": null, "updateContext": null }, - "start": 1391, - "end": 1392, + "start": 2266, + "end": 2267, "loc": { "start": { - "line": 38, - "column": 20 + "line": 54, + "column": 60 }, "end": { - "line": 38, - "column": 21 + "line": 54, + "column": 61 } } }, { "type": { - "label": "this", - "keyword": "this", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -33433,24 +37730,24 @@ "binop": null, "updateContext": null }, - "value": "this", - "start": 1397, - "end": 1401, + "start": 2267, + "end": 2268, "loc": { "start": { - "line": 39, - "column": 4 + "line": 54, + "column": 61 }, "end": { - "line": 39, - "column": 8 + "line": 54, + "column": 62 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "return", + "keyword": "return", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -33460,16 +37757,17 @@ "binop": null, "updateContext": null }, - "start": 1401, - "end": 1402, + "value": "return", + "start": 2273, + "end": 2279, "loc": { "start": { - "line": 39, - "column": 8 + "line": 55, + "column": 4 }, "end": { - "line": 39, - "column": 9 + "line": 55, + "column": 10 } } }, @@ -33485,44 +37783,43 @@ "postfix": false, "binop": null }, - "value": "newickParser", - "start": 1402, - "end": 1414, + "value": "owlterms", + "start": 2280, + "end": 2288, "loc": { "start": { - "line": 39, - "column": 9 + "line": 55, + "column": 11 }, "end": { - "line": 39, - "column": 21 + "line": 55, + "column": 19 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 1415, - "end": 1416, + "start": 2288, + "end": 2289, "loc": { "start": { - "line": 39, - "column": 22 + "line": 55, + "column": 19 }, "end": { - "line": 39, - "column": 23 + "line": 55, + "column": 20 } } }, @@ -33538,17 +37835,17 @@ "postfix": false, "binop": null }, - "value": "newickParser", - "start": 1417, - "end": 1429, + "value": "UNKNOWN_CODE", + "start": 2289, + "end": 2301, "loc": { "start": { - "line": 39, - "column": 24 + "line": 55, + "column": 20 }, "end": { - "line": 39, - "column": 36 + "line": 55, + "column": 32 } } }, @@ -33565,16 +37862,16 @@ "binop": null, "updateContext": null }, - "start": 1429, - "end": 1430, + "start": 2301, + "end": 2302, "loc": { "start": { - "line": 39, - "column": 36 + "line": 55, + "column": 32 }, "end": { - "line": 39, - "column": 37 + "line": 55, + "column": 33 } } }, @@ -33590,128 +37887,58 @@ "postfix": false, "binop": null }, - "start": 1433, - "end": 1434, + "start": 2305, + "end": 2306, "loc": { "start": { - "line": 40, + "line": 56, "column": 2 }, "end": { - "line": 40, + "line": 56, "column": 3 } } }, { - "type": "CommentLine", - "value": " Determine a 'default nomenclatural code' for this Phyx file. There are", - "start": 1438, - "end": 1511, - "loc": { - "start": { - "line": 42, - "column": 2 - }, - "end": { - "line": 42, - "column": 75 - } - } - }, - { - "type": "CommentLine", - "value": " two ways to do this:", - "start": 1514, - "end": 1537, - "loc": { - "start": { - "line": 43, - "column": 2 - }, - "end": { - "line": 43, - "column": 25 - } - } - }, - { - "type": "CommentLine", - "value": " 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.", - "start": 1540, - "end": 1622, - "loc": { - "start": { - "line": 44, - "column": 2 - }, - "end": { - "line": 44, - "column": 84 - } - } - }, - { - "type": "CommentLine", - "value": " 2. Otherwise, we check to see if every phyloref in this file has the same", - "start": 1625, - "end": 1702, - "loc": { - "start": { - "line": 45, - "column": 2 - }, - "end": { - "line": 45, - "column": 79 - } - } - }, - { - "type": "CommentLine", - "value": " nomenclatural code. If so, we can use that code. If not, i.e. if any of", - "start": 1705, - "end": 1783, - "loc": { - "start": { - "line": 46, - "column": 2 - }, - "end": { - "line": 46, - "column": 80 - } - } - }, - { - "type": "CommentLine", - "value": " the phylorefs are missing a nomenclatural code or include a specifier,", - "start": 1786, - "end": 1863, + "type": "CommentBlock", + "value": "*\n * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\n * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\n * package will be wrapped and normalized before being returned.\n *\n * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\n * identical ways. But if we implement it at every level, we can implement comparison code in\n * Klados easily.\n *\n * Two Phyx documents should -- upon being normalized -- be comparable with each other with\n * lodash.deepEqual().\n ", + "start": 2310, + "end": 3009, "loc": { "start": { - "line": 47, + "line": 58, "column": 2 }, "end": { - "line": 47, - "column": 79 + "line": 70, + "column": 5 } } }, { - "type": "CommentLine", - "value": " we default to owlterms.UNKNOWN_CODE.", - "start": 1866, - "end": 1909, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "static", + "start": 3012, + "end": 3018, "loc": { "start": { - "line": 48, + "line": 71, "column": 2 }, "end": { - "line": 48, - "column": 45 + "line": 71, + "column": 8 } } }, @@ -33727,24 +37954,24 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 1912, - "end": 1915, + "value": "normalize", + "start": 3019, + "end": 3028, "loc": { "start": { - "line": 49, - "column": 2 + "line": 71, + "column": 9 }, "end": { - "line": 49, - "column": 5 + "line": 71, + "column": 18 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -33753,24 +37980,23 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 1916, - "end": 1932, + "start": 3028, + "end": 3029, "loc": { "start": { - "line": 49, - "column": 6 + "line": 71, + "column": 18 }, "end": { - "line": 49, - "column": 22 + "line": 71, + "column": 19 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -33779,16 +38005,17 @@ "postfix": false, "binop": null }, - "start": 1932, - "end": 1933, + "value": "phyxDocument", + "start": 3029, + "end": 3041, "loc": { "start": { - "line": 49, - "column": 22 + "line": 71, + "column": 19 }, "end": { - "line": 49, - "column": 23 + "line": 71, + "column": 31 } } }, @@ -33804,16 +38031,16 @@ "postfix": false, "binop": null }, - "start": 1933, - "end": 1934, + "start": 3041, + "end": 3042, "loc": { "start": { - "line": 49, - "column": 23 + "line": 71, + "column": 31 }, "end": { - "line": 49, - "column": 24 + "line": 71, + "column": 32 } } }, @@ -33829,23 +38056,23 @@ "postfix": false, "binop": null }, - "start": 1935, - "end": 1936, + "start": 3043, + "end": 3044, "loc": { "start": { - "line": 49, - "column": 25 + "line": 71, + "column": 33 }, "end": { - "line": 49, - "column": 26 + "line": 71, + "column": 34 } } }, { "type": { - "label": "if", - "keyword": "if", + "label": "const", + "keyword": "const", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -33856,24 +38083,24 @@ "binop": null, "updateContext": null }, - "value": "if", - "start": 1941, - "end": 1943, + "value": "const", + "start": 3049, + "end": 3054, "loc": { "start": { - "line": 50, + "line": 72, "column": 4 }, "end": { - "line": 50, - "column": 6 + "line": 72, + "column": 9 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -33882,49 +38109,51 @@ "postfix": false, "binop": null }, - "start": 1944, - "end": 1945, + "value": "normalizedDocument", + "start": 3055, + "end": 3073, "loc": { "start": { - "line": 50, - "column": 7 + "line": 72, + "column": 10 }, "end": { - "line": 50, - "column": 8 + "line": 72, + "column": 28 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "has", - "start": 1945, - "end": 1948, + "value": "=", + "start": 3074, + "end": 3075, "loc": { "start": { - "line": 50, - "column": 8 + "line": 72, + "column": 29 }, "end": { - "line": 50, - "column": 11 + "line": 72, + "column": 30 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -33933,78 +38162,76 @@ "postfix": false, "binop": null }, - "start": 1948, - "end": 1949, + "value": "cloneDeep", + "start": 3076, + "end": 3085, "loc": { "start": { - "line": 50, - "column": 11 + "line": 72, + "column": 31 }, "end": { - "line": 50, - "column": 12 + "line": 72, + "column": 40 } } }, { "type": { - "label": "this", - "keyword": "this", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 1949, - "end": 1953, + "start": 3085, + "end": 3086, "loc": { "start": { - "line": 50, - "column": 12 + "line": 72, + "column": 40 }, "end": { - "line": 50, - "column": 16 + "line": 72, + "column": 41 } } }, { "type": { - "label": ".", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 1953, - "end": 1954, + "value": "phyxDocument", + "start": 3086, + "end": 3098, "loc": { "start": { - "line": 50, - "column": 16 + "line": 72, + "column": 41 }, "end": { - "line": 50, - "column": 17 + "line": 72, + "column": 53 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -34012,23 +38239,22 @@ "postfix": false, "binop": null }, - "value": "phyx", - "start": 1954, - "end": 1958, + "start": 3098, + "end": 3099, "loc": { "start": { - "line": 50, - "column": 17 + "line": 72, + "column": 53 }, "end": { - "line": 50, - "column": 21 + "line": 72, + "column": 54 } } }, { "type": { - "label": ",", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -34039,22 +38265,22 @@ "binop": null, "updateContext": null }, - "start": 1958, - "end": 1959, + "start": 3099, + "end": 3100, "loc": { "start": { - "line": 50, - "column": 21 + "line": 72, + "column": 54 }, "end": { - "line": 50, - "column": 22 + "line": 72, + "column": 55 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -34062,26 +38288,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "defaultNomenclaturalCodeIRI", - "start": 1960, - "end": 1989, + "value": "normalizedDocument", + "start": 3106, + "end": 3124, "loc": { "start": { - "line": 50, - "column": 23 + "line": 74, + "column": 4 }, "end": { - "line": 50, - "column": 52 + "line": 74, + "column": 22 } } }, { "type": { - "label": ")", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -34089,26 +38314,27 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1989, - "end": 1990, + "start": 3124, + "end": 3125, "loc": { "start": { - "line": 50, - "column": 52 + "line": 74, + "column": 22 }, "end": { - "line": 50, - "column": 53 + "line": 74, + "column": 23 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -34116,98 +38342,69 @@ "postfix": false, "binop": null }, - "start": 1990, - "end": 1991, + "value": "phylorefs", + "start": 3125, + "end": 3134, "loc": { "start": { - "line": 50, - "column": 53 + "line": 74, + "column": 23 }, "end": { - "line": 50, - "column": 54 + "line": 74, + "column": 32 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "return", - "start": 1992, - "end": 1998, + "value": "=", + "start": 3135, + "end": 3136, "loc": { "start": { - "line": 50, - "column": 55 + "line": 74, + "column": 33 }, "end": { - "line": 50, - "column": 61 + "line": 74, + "column": 34 } } }, { "type": { - "label": "this", - "keyword": "this", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "this", - "start": 1999, - "end": 2003, - "loc": { - "start": { - "line": 50, - "column": 62 - }, - "end": { - "line": 50, - "column": 66 - } - } - }, - { - "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2003, - "end": 2004, + "start": 3137, + "end": 3138, "loc": { "start": { - "line": 50, - "column": 66 + "line": 74, + "column": 35 }, "end": { - "line": 50, - "column": 67 + "line": 74, + "column": 36 } } }, @@ -34222,18 +38419,18 @@ "prefix": false, "postfix": false, "binop": null - }, - "value": "phyx", - "start": 2004, - "end": 2008, + }, + "value": "phyxDocument", + "start": 3138, + "end": 3150, "loc": { "start": { - "line": 50, - "column": 67 + "line": 74, + "column": 36 }, "end": { - "line": 50, - "column": 71 + "line": 74, + "column": 48 } } }, @@ -34250,16 +38447,16 @@ "binop": null, "updateContext": null }, - "start": 2008, - "end": 2009, + "start": 3150, + "end": 3151, "loc": { "start": { - "line": 50, - "column": 71 + "line": 74, + "column": 48 }, "end": { - "line": 50, - "column": 72 + "line": 74, + "column": 49 } } }, @@ -34275,23 +38472,23 @@ "postfix": false, "binop": null }, - "value": "defaultNomenclaturalCodeIRI", - "start": 2009, - "end": 2036, + "value": "phylorefs", + "start": 3151, + "end": 3160, "loc": { "start": { - "line": 50, - "column": 72 + "line": 74, + "column": 49 }, "end": { - "line": 50, - "column": 99 + "line": 74, + "column": 58 } } }, { "type": { - "label": ";", + "label": "||", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -34299,28 +38496,28 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 1, "updateContext": null }, - "start": 2036, - "end": 2037, + "value": "||", + "start": 3161, + "end": 3163, "loc": { "start": { - "line": 50, - "column": 99 + "line": 74, + "column": 59 }, "end": { - "line": 50, - "column": 100 + "line": 74, + "column": 61 } } }, { "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, - "startsExpr": false, + "label": "[", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -34329,102 +38526,99 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 2042, - "end": 2047, + "start": 3164, + "end": 3165, "loc": { "start": { - "line": 51, - "column": 4 + "line": 74, + "column": 62 }, "end": { - "line": 51, - "column": 9 + "line": 74, + "column": 63 } } }, { "type": { - "label": "name", + "label": "]", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "nomenCodes", - "start": 2048, - "end": 2058, + "start": 3165, + "end": 3166, "loc": { "start": { - "line": 51, - "column": 10 + "line": 74, + "column": 63 }, "end": { - "line": 51, - "column": 20 + "line": 74, + "column": 64 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 2059, - "end": 2060, + "start": 3166, + "end": 3167, "loc": { "start": { - "line": 51, - "column": 21 + "line": 74, + "column": 64 }, "end": { - "line": 51, - "column": 22 + "line": 74, + "column": 65 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": ".", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2061, - "end": 2062, + "start": 3167, + "end": 3168, "loc": { "start": { - "line": 51, - "column": 23 + "line": 74, + "column": 65 }, "end": { - "line": 51, - "column": 24 + "line": 74, + "column": 66 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -34432,46 +38626,44 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 2062, - "end": 2066, + "value": "map", + "start": 3168, + "end": 3171, "loc": { "start": { - "line": 51, - "column": 24 + "line": 74, + "column": 66 }, "end": { - "line": 51, - "column": 28 + "line": 74, + "column": 69 } } }, { "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, + "label": "(", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2066, - "end": 2067, + "start": 3171, + "end": 3172, "loc": { "start": { - "line": 51, - "column": 28 + "line": 74, + "column": 69 }, "end": { - "line": 51, - "column": 29 + "line": 74, + "column": 70 } } }, @@ -34487,17 +38679,17 @@ "postfix": false, "binop": null }, - "value": "phyx", - "start": 2067, - "end": 2071, + "value": "PhylorefWrapper", + "start": 3172, + "end": 3187, "loc": { "start": { - "line": 51, - "column": 29 + "line": 74, + "column": 70 }, "end": { - "line": 51, - "column": 33 + "line": 74, + "column": 85 } } }, @@ -34514,16 +38706,16 @@ "binop": null, "updateContext": null }, - "start": 2071, - "end": 2072, + "start": 3187, + "end": 3188, "loc": { "start": { - "line": 51, - "column": 33 + "line": 74, + "column": 85 }, "end": { - "line": 51, - "column": 34 + "line": 74, + "column": 86 } } }, @@ -34539,52 +38731,50 @@ "postfix": false, "binop": null }, - "value": "phylorefs", - "start": 2072, - "end": 2081, + "value": "normalize", + "start": 3188, + "end": 3197, "loc": { "start": { - "line": 51, - "column": 34 + "line": 74, + "column": 86 }, "end": { - "line": 51, - "column": 43 + "line": 74, + "column": 95 } } }, { "type": { - "label": "||", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 1, - "updateContext": null + "binop": null }, - "value": "||", - "start": 2082, - "end": 2084, + "start": 3197, + "end": 3198, "loc": { "start": { - "line": 51, - "column": 44 + "line": 74, + "column": 95 }, "end": { - "line": 51, - "column": 46 + "line": 74, + "column": 96 } } }, { "type": { - "label": "[", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -34593,48 +38783,48 @@ "binop": null, "updateContext": null }, - "start": 2085, - "end": 2086, + "start": 3198, + "end": 3199, "loc": { "start": { - "line": 51, - "column": 47 + "line": 74, + "column": 96 }, "end": { - "line": 51, - "column": 48 + "line": 74, + "column": 97 } } }, { "type": { - "label": "]", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2086, - "end": 2087, + "value": "normalizedDocument", + "start": 3204, + "end": 3222, "loc": { "start": { - "line": 51, - "column": 48 + "line": 75, + "column": 4 }, "end": { - "line": 51, - "column": 49 + "line": 75, + "column": 22 } } }, { "type": { - "label": ")", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -34642,70 +38832,72 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2087, - "end": 2088, + "start": 3222, + "end": 3223, "loc": { "start": { - "line": 51, - "column": 49 + "line": 75, + "column": 22 }, "end": { - "line": 51, - "column": 50 + "line": 75, + "column": 23 } } }, { "type": { - "label": ".", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2095, - "end": 2096, + "value": "phylogenies", + "start": 3223, + "end": 3234, "loc": { "start": { - "line": 52, - "column": 6 + "line": 75, + "column": 23 }, "end": { - "line": 52, - "column": 7 + "line": 75, + "column": 34 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "map", - "start": 2096, - "end": 2099, + "value": "=", + "start": 3235, + "end": 3236, "loc": { "start": { - "line": 52, - "column": 7 + "line": 75, + "column": 35 }, "end": { - "line": 52, - "column": 10 + "line": 75, + "column": 36 } } }, @@ -34721,16 +38913,16 @@ "postfix": false, "binop": null }, - "start": 2099, - "end": 2100, + "start": 3237, + "end": 3238, "loc": { "start": { - "line": 52, - "column": 10 + "line": 75, + "column": 37 }, "end": { - "line": 52, - "column": 11 + "line": 75, + "column": 38 } } }, @@ -34746,24 +38938,24 @@ "postfix": false, "binop": null }, - "value": "phyloref", - "start": 2100, - "end": 2108, + "value": "phyxDocument", + "start": 3238, + "end": 3250, "loc": { "start": { - "line": 52, - "column": 11 + "line": 75, + "column": 38 }, "end": { - "line": 52, - "column": 19 + "line": 75, + "column": 50 } } }, { "type": { - "label": "=>", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -34773,76 +38965,75 @@ "binop": null, "updateContext": null }, - "start": 2109, - "end": 2111, + "start": 3250, + "end": 3251, "loc": { "start": { - "line": 52, - "column": 20 + "line": 75, + "column": 50 }, "end": { - "line": 52, - "column": 22 + "line": 75, + "column": 51 } } }, { "type": { - "label": "new", - "keyword": "new", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "new", - "start": 2112, - "end": 2115, + "value": "phylogenies", + "start": 3251, + "end": 3262, "loc": { "start": { - "line": 52, - "column": 23 + "line": 75, + "column": 51 }, "end": { - "line": 52, - "column": 26 + "line": 75, + "column": 62 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "||", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": 1, + "updateContext": null }, - "value": "PhylorefWrapper", - "start": 2116, - "end": 2131, + "value": "||", + "start": 3263, + "end": 3265, "loc": { "start": { - "line": 52, - "column": 27 + "line": 75, + "column": 63 }, "end": { - "line": 52, - "column": 42 + "line": 75, + "column": 65 } } }, { "type": { - "label": "(", + "label": "[", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -34850,44 +39041,45 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2131, - "end": 2132, + "start": 3266, + "end": 3267, "loc": { "start": { - "line": 52, - "column": 42 + "line": 75, + "column": 66 }, "end": { - "line": 52, - "column": 43 + "line": 75, + "column": 67 } } }, { "type": { - "label": "name", + "label": "]", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "phyloref", - "start": 2132, - "end": 2140, + "start": 3267, + "end": 3268, "loc": { "start": { - "line": 52, - "column": 43 + "line": 75, + "column": 67 }, "end": { - "line": 52, - "column": 51 + "line": 75, + "column": 68 } } }, @@ -34903,16 +39095,16 @@ "postfix": false, "binop": null }, - "start": 2140, - "end": 2141, + "start": 3268, + "end": 3269, "loc": { "start": { - "line": 52, - "column": 51 + "line": 75, + "column": 68 }, "end": { - "line": 52, - "column": 52 + "line": 75, + "column": 69 } } }, @@ -34929,16 +39121,16 @@ "binop": null, "updateContext": null }, - "start": 2141, - "end": 2142, + "start": 3276, + "end": 3277, "loc": { "start": { - "line": 52, - "column": 52 + "line": 76, + "column": 6 }, "end": { - "line": 52, - "column": 53 + "line": 76, + "column": 7 } } }, @@ -34954,25 +39146,25 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 2142, - "end": 2158, + "value": "map", + "start": 3277, + "end": 3280, "loc": { "start": { - "line": 52, - "column": 53 + "line": 76, + "column": 7 }, "end": { - "line": 52, - "column": 69 + "line": 76, + "column": 10 } } }, { "type": { - "label": ")", - "beforeExpr": false, - "startsExpr": false, + "label": "(", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -34980,49 +39172,48 @@ "postfix": false, "binop": null }, - "start": 2158, - "end": 2159, + "start": 3280, + "end": 3281, "loc": { "start": { - "line": 52, - "column": 69 + "line": 76, + "column": 10 }, "end": { - "line": 52, - "column": 70 + "line": 76, + "column": 11 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2159, - "end": 2160, + "value": "PhylogenyWrapper", + "start": 3281, + "end": 3297, "loc": { "start": { - "line": 52, - "column": 70 + "line": 76, + "column": 11 }, "end": { - "line": 52, - "column": 71 + "line": 76, + "column": 27 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -35033,17 +39224,16 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 2165, - "end": 2170, + "start": 3297, + "end": 3298, "loc": { "start": { - "line": 53, - "column": 4 + "line": 76, + "column": 27 }, "end": { - "line": 53, - "column": 9 + "line": 76, + "column": 28 } } }, @@ -35059,70 +39249,96 @@ "postfix": false, "binop": null }, - "value": "uniqNomenCodes", - "start": 2171, - "end": 2185, + "value": "normalize", + "start": 3298, + "end": 3307, "loc": { "start": { - "line": 53, - "column": 10 + "line": 76, + "column": 28 }, "end": { - "line": 53, - "column": 24 + "line": 76, + "column": 37 } } }, { "type": { - "label": "=", + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 3307, + "end": 3308, + "loc": { + "start": { + "line": 76, + "column": 37 + }, + "end": { + "line": 76, + "column": 38 + } + } + }, + { + "type": { + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 2186, - "end": 2187, + "start": 3308, + "end": 3309, "loc": { "start": { - "line": 53, - "column": 25 + "line": 76, + "column": 38 }, "end": { - "line": 53, - "column": 26 + "line": 76, + "column": 39 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "uniq", - "start": 2188, - "end": 2192, + "value": "if", + "start": 3314, + "end": 3316, "loc": { "start": { - "line": 53, - "column": 27 + "line": 77, + "column": 4 }, "end": { - "line": 53, - "column": 31 + "line": 77, + "column": 6 } } }, @@ -35138,22 +39354,22 @@ "postfix": false, "binop": null }, - "start": 2192, - "end": 2193, + "start": 3317, + "end": 3318, "loc": { "start": { - "line": 53, - "column": 31 + "line": 77, + "column": 7 }, "end": { - "line": 53, - "column": 32 + "line": 77, + "column": 8 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -35161,77 +39377,80 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "nomenCodes", - "start": 2193, - "end": 2203, + "value": "source", + "start": 3318, + "end": 3326, "loc": { "start": { - "line": 53, - "column": 32 + "line": 77, + "column": 8 }, "end": { - "line": 53, - "column": 42 + "line": 77, + "column": 16 } } }, { "type": { - "label": ")", - "beforeExpr": false, + "label": "in", + "keyword": "in", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": 7, + "updateContext": null }, - "start": 2203, - "end": 2204, + "value": "in", + "start": 3327, + "end": 3329, "loc": { "start": { - "line": 53, - "column": 42 + "line": 77, + "column": 17 }, "end": { - "line": 53, - "column": 43 + "line": 77, + "column": 19 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2204, - "end": 2205, + "value": "phyxDocument", + "start": 3330, + "end": 3342, "loc": { "start": { - "line": 53, - "column": 43 + "line": 77, + "column": 20 }, "end": { - "line": 53, - "column": 44 + "line": 77, + "column": 32 } } }, { "type": { - "label": "if", - "keyword": "if", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -35239,26 +39458,24 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "if", - "start": 2210, - "end": 2212, + "start": 3342, + "end": 3343, "loc": { "start": { - "line": 54, - "column": 4 + "line": 77, + "column": 32 }, "end": { - "line": 54, - "column": 6 + "line": 77, + "column": 33 } } }, { "type": { - "label": "(", + "label": "{", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -35268,16 +39485,16 @@ "postfix": false, "binop": null }, - "start": 2213, - "end": 2214, + "start": 3344, + "end": 3345, "loc": { "start": { - "line": 54, - "column": 7 + "line": 77, + "column": 34 }, "end": { - "line": 54, - "column": 8 + "line": 77, + "column": 35 } } }, @@ -35293,17 +39510,17 @@ "postfix": false, "binop": null }, - "value": "uniqNomenCodes", - "start": 2214, - "end": 2228, + "value": "normalizedDocument", + "start": 3352, + "end": 3370, "loc": { "start": { - "line": 54, - "column": 8 + "line": 78, + "column": 6 }, "end": { - "line": 54, - "column": 22 + "line": 78, + "column": 24 } } }, @@ -35320,16 +39537,16 @@ "binop": null, "updateContext": null }, - "start": 2228, - "end": 2229, + "start": 3370, + "end": 3371, "loc": { "start": { - "line": 54, - "column": 22 + "line": 78, + "column": 24 }, "end": { - "line": 54, - "column": 23 + "line": 78, + "column": 25 } } }, @@ -35345,50 +39562,50 @@ "postfix": false, "binop": null }, - "value": "length", - "start": 2229, - "end": 2235, + "value": "source", + "start": 3371, + "end": 3377, "loc": { "start": { - "line": 54, - "column": 23 + "line": 78, + "column": 25 }, "end": { - "line": 54, - "column": 29 + "line": 78, + "column": 31 } } }, { "type": { - "label": "==/!=", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": 6, + "binop": null, "updateContext": null }, - "value": "===", - "start": 2236, - "end": 2239, + "value": "=", + "start": 3378, + "end": 3379, "loc": { "start": { - "line": 54, - "column": 30 + "line": 78, + "column": 32 }, "end": { - "line": 54, + "line": 78, "column": 33 } } }, { "type": { - "label": "num", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -35396,26 +39613,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": 1, - "start": 2240, - "end": 2241, + "value": "CitationWrapper", + "start": 3380, + "end": 3395, "loc": { "start": { - "line": 54, + "line": 78, "column": 34 }, "end": { - "line": 54, - "column": 35 + "line": 78, + "column": 49 } } }, { "type": { - "label": ")", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -35423,53 +39639,52 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2241, - "end": 2242, + "start": 3395, + "end": 3396, "loc": { "start": { - "line": 54, - "column": 35 + "line": 78, + "column": 49 }, "end": { - "line": 54, - "column": 36 + "line": 78, + "column": 50 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "return", - "start": 2243, - "end": 2249, + "value": "normalize", + "start": 3396, + "end": 3405, "loc": { "start": { - "line": 54, - "column": 37 + "line": 78, + "column": 50 }, "end": { - "line": 54, - "column": 43 + "line": 78, + "column": 59 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -35478,51 +39693,50 @@ "postfix": false, "binop": null }, - "value": "uniqNomenCodes", - "start": 2250, - "end": 2264, + "start": 3405, + "end": 3406, "loc": { "start": { - "line": 54, - "column": 44 + "line": 78, + "column": 59 }, "end": { - "line": 54, - "column": 58 + "line": 78, + "column": 60 } } }, { "type": { - "label": "[", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2264, - "end": 2265, + "value": "phyxDocument", + "start": 3406, + "end": 3418, "loc": { "start": { - "line": 54, - "column": 58 + "line": 78, + "column": 60 }, "end": { - "line": 54, - "column": 59 + "line": 78, + "column": 72 } } }, { "type": { - "label": "num", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -35531,76 +39745,73 @@ "binop": null, "updateContext": null }, - "value": 0, - "start": 2265, - "end": 2266, + "start": 3418, + "end": 3419, "loc": { "start": { - "line": 54, - "column": 59 + "line": 78, + "column": 72 }, "end": { - "line": 54, - "column": 60 + "line": 78, + "column": 73 } } }, { "type": { - "label": "]", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2266, - "end": 2267, + "value": "source", + "start": 3419, + "end": 3425, "loc": { "start": { - "line": 54, - "column": 60 + "line": 78, + "column": 73 }, "end": { - "line": 54, - "column": 61 + "line": 78, + "column": 79 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2267, - "end": 2268, + "start": 3425, + "end": 3426, "loc": { "start": { - "line": 54, - "column": 61 + "line": 78, + "column": 79 }, "end": { - "line": 54, - "column": 62 + "line": 78, + "column": 80 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -35611,25 +39822,24 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2273, - "end": 2279, + "start": 3426, + "end": 3427, "loc": { "start": { - "line": 55, - "column": 4 + "line": 78, + "column": 80 }, "end": { - "line": 55, - "column": 10 + "line": 78, + "column": 81 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -35637,24 +39847,24 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 2280, - "end": 2288, + "start": 3432, + "end": 3433, "loc": { "start": { - "line": 55, - "column": 11 + "line": 79, + "column": 4 }, "end": { - "line": 55, - "column": 19 + "line": 79, + "column": 5 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "return", + "keyword": "return", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -35664,16 +39874,17 @@ "binop": null, "updateContext": null }, - "start": 2288, - "end": 2289, + "value": "return", + "start": 3439, + "end": 3445, "loc": { "start": { - "line": 55, - "column": 19 + "line": 81, + "column": 4 }, "end": { - "line": 55, - "column": 20 + "line": 81, + "column": 10 } } }, @@ -35689,17 +39900,17 @@ "postfix": false, "binop": null }, - "value": "UNKNOWN_CODE", - "start": 2289, - "end": 2301, + "value": "normalizedDocument", + "start": 3446, + "end": 3464, "loc": { "start": { - "line": 55, - "column": 20 + "line": 81, + "column": 11 }, "end": { - "line": 55, - "column": 32 + "line": 81, + "column": 29 } } }, @@ -35716,16 +39927,16 @@ "binop": null, "updateContext": null }, - "start": 2301, - "end": 2302, + "start": 3464, + "end": 3465, "loc": { "start": { - "line": 55, - "column": 32 + "line": 81, + "column": 29 }, "end": { - "line": 55, - "column": 33 + "line": 81, + "column": 30 } } }, @@ -35741,15 +39952,15 @@ "postfix": false, "binop": null }, - "start": 2305, - "end": 2306, + "start": 3468, + "end": 3469, "loc": { "start": { - "line": 56, + "line": 82, "column": 2 }, "end": { - "line": 56, + "line": 82, "column": 3 } } @@ -35757,15 +39968,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n ", - "start": 2310, - "end": 3304, + "start": 3473, + "end": 4467, "loc": { "start": { - "line": 58, + "line": 84, "column": 2 }, "end": { - "line": 73, + "line": 99, "column": 5 } } @@ -35783,15 +39994,15 @@ "binop": null }, "value": "asJSONLD", - "start": 3307, - "end": 3315, + "start": 4470, + "end": 4478, "loc": { "start": { - "line": 74, + "line": 100, "column": 2 }, "end": { - "line": 74, + "line": 100, "column": 10 } } @@ -35808,15 +40019,15 @@ "postfix": false, "binop": null }, - "start": 3315, - "end": 3316, + "start": 4478, + "end": 4479, "loc": { "start": { - "line": 74, + "line": 100, "column": 10 }, "end": { - "line": 74, + "line": 100, "column": 11 } } @@ -35834,15 +40045,15 @@ "binop": null }, "value": "baseIRI", - "start": 3316, - "end": 3323, + "start": 4479, + "end": 4486, "loc": { "start": { - "line": 74, + "line": 100, "column": 11 }, "end": { - "line": 74, + "line": 100, "column": 18 } } @@ -35861,15 +40072,15 @@ "updateContext": null }, "value": "=", - "start": 3324, - "end": 3325, + "start": 4487, + "end": 4488, "loc": { "start": { - "line": 74, + "line": 100, "column": 19 }, "end": { - "line": 74, + "line": 100, "column": 20 } } @@ -35888,15 +40099,15 @@ "updateContext": null }, "value": "", - "start": 3326, - "end": 3328, + "start": 4489, + "end": 4491, "loc": { "start": { - "line": 74, + "line": 100, "column": 21 }, "end": { - "line": 74, + "line": 100, "column": 23 } } @@ -35913,15 +40124,15 @@ "postfix": false, "binop": null }, - "start": 3328, - "end": 3329, + "start": 4491, + "end": 4492, "loc": { "start": { - "line": 74, + "line": 100, "column": 23 }, "end": { - "line": 74, + "line": 100, "column": 24 } } @@ -35938,15 +40149,15 @@ "postfix": false, "binop": null }, - "start": 3330, - "end": 3331, + "start": 4493, + "end": 4494, "loc": { "start": { - "line": 74, + "line": 100, "column": 25 }, "end": { - "line": 74, + "line": 100, "column": 26 } } @@ -35966,15 +40177,15 @@ "updateContext": null }, "value": "const", - "start": 3336, - "end": 3341, + "start": 4499, + "end": 4504, "loc": { "start": { - "line": 75, + "line": 101, "column": 4 }, "end": { - "line": 75, + "line": 101, "column": 9 } } @@ -35992,15 +40203,15 @@ "binop": null }, "value": "jsonld", - "start": 3342, - "end": 3348, + "start": 4505, + "end": 4511, "loc": { "start": { - "line": 75, + "line": 101, "column": 10 }, "end": { - "line": 75, + "line": 101, "column": 16 } } @@ -36019,15 +40230,15 @@ "updateContext": null }, "value": "=", - "start": 3349, - "end": 3350, + "start": 4512, + "end": 4513, "loc": { "start": { - "line": 75, + "line": 101, "column": 17 }, "end": { - "line": 75, + "line": 101, "column": 18 } } @@ -36045,15 +40256,15 @@ "binop": null }, "value": "cloneDeep", - "start": 3351, - "end": 3360, + "start": 4514, + "end": 4523, "loc": { "start": { - "line": 75, + "line": 101, "column": 19 }, "end": { - "line": 75, + "line": 101, "column": 28 } } @@ -36070,15 +40281,15 @@ "postfix": false, "binop": null }, - "start": 3360, - "end": 3361, + "start": 4523, + "end": 4524, "loc": { "start": { - "line": 75, + "line": 101, "column": 28 }, "end": { - "line": 75, + "line": 101, "column": 29 } } @@ -36098,15 +40309,15 @@ "updateContext": null }, "value": "this", - "start": 3361, - "end": 3365, + "start": 4524, + "end": 4528, "loc": { "start": { - "line": 75, + "line": 101, "column": 29 }, "end": { - "line": 75, + "line": 101, "column": 33 } } @@ -36124,15 +40335,15 @@ "binop": null, "updateContext": null }, - "start": 3365, - "end": 3366, + "start": 4528, + "end": 4529, "loc": { "start": { - "line": 75, + "line": 101, "column": 33 }, "end": { - "line": 75, + "line": 101, "column": 34 } } @@ -36150,15 +40361,15 @@ "binop": null }, "value": "phyx", - "start": 3366, - "end": 3370, + "start": 4529, + "end": 4533, "loc": { "start": { - "line": 75, + "line": 101, "column": 34 }, "end": { - "line": 75, + "line": 101, "column": 38 } } @@ -36175,15 +40386,15 @@ "postfix": false, "binop": null }, - "start": 3370, - "end": 3371, + "start": 4533, + "end": 4534, "loc": { "start": { - "line": 75, + "line": 101, "column": 38 }, "end": { - "line": 75, + "line": 101, "column": 39 } } @@ -36201,15 +40412,15 @@ "binop": null, "updateContext": null }, - "start": 3371, - "end": 3372, + "start": 4534, + "end": 4535, "loc": { "start": { - "line": 75, + "line": 101, "column": 39 }, "end": { - "line": 75, + "line": 101, "column": 40 } } @@ -36217,15 +40428,15 @@ { "type": "CommentLine", "value": " Some helper methods for generating base IRIs for phylorefs and phylogenies.", - "start": 3378, - "end": 3456, + "start": 4541, + "end": 4619, "loc": { "start": { - "line": 77, + "line": 103, "column": 4 }, "end": { - "line": 77, + "line": 103, "column": 82 } } @@ -36244,15 +40455,15 @@ "binop": null }, "value": "function", - "start": 3461, - "end": 3469, + "start": 4624, + "end": 4632, "loc": { "start": { - "line": 78, + "line": 104, "column": 4 }, "end": { - "line": 78, + "line": 104, "column": 12 } } @@ -36270,15 +40481,15 @@ "binop": null }, "value": "getBaseIRIForPhyloref", - "start": 3470, - "end": 3491, + "start": 4633, + "end": 4654, "loc": { "start": { - "line": 78, + "line": 104, "column": 13 }, "end": { - "line": 78, + "line": 104, "column": 34 } } @@ -36295,15 +40506,15 @@ "postfix": false, "binop": null }, - "start": 3491, - "end": 3492, + "start": 4654, + "end": 4655, "loc": { "start": { - "line": 78, + "line": 104, "column": 34 }, "end": { - "line": 78, + "line": 104, "column": 35 } } @@ -36321,15 +40532,15 @@ "binop": null }, "value": "index", - "start": 3492, - "end": 3497, + "start": 4655, + "end": 4660, "loc": { "start": { - "line": 78, + "line": 104, "column": 35 }, "end": { - "line": 78, + "line": 104, "column": 40 } } @@ -36346,15 +40557,15 @@ "postfix": false, "binop": null }, - "start": 3497, - "end": 3498, + "start": 4660, + "end": 4661, "loc": { "start": { - "line": 78, + "line": 104, "column": 40 }, "end": { - "line": 78, + "line": 104, "column": 41 } } @@ -36371,15 +40582,15 @@ "postfix": false, "binop": null }, - "start": 3499, - "end": 3500, + "start": 4662, + "end": 4663, "loc": { "start": { - "line": 78, + "line": 104, "column": 42 }, "end": { - "line": 78, + "line": 104, "column": 43 } } @@ -36399,15 +40610,15 @@ "updateContext": null }, "value": "if", - "start": 3507, - "end": 3509, + "start": 4670, + "end": 4672, "loc": { "start": { - "line": 79, + "line": 105, "column": 6 }, "end": { - "line": 79, + "line": 105, "column": 8 } } @@ -36424,15 +40635,15 @@ "postfix": false, "binop": null }, - "start": 3510, - "end": 3511, + "start": 4673, + "end": 4674, "loc": { "start": { - "line": 79, + "line": 105, "column": 9 }, "end": { - "line": 79, + "line": 105, "column": 10 } } @@ -36450,15 +40661,15 @@ "binop": null }, "value": "baseIRI", - "start": 3511, - "end": 3518, + "start": 4674, + "end": 4681, "loc": { "start": { - "line": 79, + "line": 105, "column": 10 }, "end": { - "line": 79, + "line": 105, "column": 17 } } @@ -36475,15 +40686,15 @@ "postfix": false, "binop": null }, - "start": 3518, - "end": 3519, + "start": 4681, + "end": 4682, "loc": { "start": { - "line": 79, + "line": 105, "column": 17 }, "end": { - "line": 79, + "line": 105, "column": 18 } } @@ -36503,15 +40714,15 @@ "updateContext": null }, "value": "return", - "start": 3520, - "end": 3526, + "start": 4683, + "end": 4689, "loc": { "start": { - "line": 79, + "line": 105, "column": 19 }, "end": { - "line": 79, + "line": 105, "column": 25 } } @@ -36528,15 +40739,15 @@ "postfix": false, "binop": null }, - "start": 3527, - "end": 3528, + "start": 4690, + "end": 4691, "loc": { "start": { - "line": 79, + "line": 105, "column": 26 }, "end": { - "line": 79, + "line": 105, "column": 27 } } @@ -36555,15 +40766,15 @@ "updateContext": null }, "value": "", - "start": 3528, - "end": 3528, + "start": 4691, + "end": 4691, "loc": { "start": { - "line": 79, + "line": 105, "column": 27 }, "end": { - "line": 79, + "line": 105, "column": 27 } } @@ -36580,15 +40791,15 @@ "postfix": false, "binop": null }, - "start": 3528, - "end": 3530, + "start": 4691, + "end": 4693, "loc": { "start": { - "line": 79, + "line": 105, "column": 27 }, "end": { - "line": 79, + "line": 105, "column": 29 } } @@ -36606,15 +40817,15 @@ "binop": null }, "value": "baseIRI", - "start": 3530, - "end": 3537, + "start": 4693, + "end": 4700, "loc": { "start": { - "line": 79, + "line": 105, "column": 29 }, "end": { - "line": 79, + "line": 105, "column": 36 } } @@ -36631,15 +40842,15 @@ "postfix": false, "binop": null }, - "start": 3537, - "end": 3538, + "start": 4700, + "end": 4701, "loc": { "start": { - "line": 79, + "line": 105, "column": 36 }, "end": { - "line": 79, + "line": 105, "column": 37 } } @@ -36658,15 +40869,15 @@ "updateContext": null }, "value": "phyloref", - "start": 3538, - "end": 3546, + "start": 4701, + "end": 4709, "loc": { "start": { - "line": 79, + "line": 105, "column": 37 }, "end": { - "line": 79, + "line": 105, "column": 45 } } @@ -36683,15 +40894,15 @@ "postfix": false, "binop": null }, - "start": 3546, - "end": 3548, + "start": 4709, + "end": 4711, "loc": { "start": { - "line": 79, + "line": 105, "column": 45 }, "end": { - "line": 79, + "line": 105, "column": 47 } } @@ -36709,15 +40920,15 @@ "binop": null }, "value": "index", - "start": 3548, - "end": 3553, + "start": 4711, + "end": 4716, "loc": { "start": { - "line": 79, + "line": 105, "column": 47 }, "end": { - "line": 79, + "line": 105, "column": 52 } } @@ -36734,15 +40945,15 @@ "postfix": false, "binop": null }, - "start": 3553, - "end": 3554, + "start": 4716, + "end": 4717, "loc": { "start": { - "line": 79, + "line": 105, "column": 52 }, "end": { - "line": 79, + "line": 105, "column": 53 } } @@ -36761,15 +40972,15 @@ "updateContext": null }, "value": "", - "start": 3554, - "end": 3554, + "start": 4717, + "end": 4717, "loc": { "start": { - "line": 79, + "line": 105, "column": 53 }, "end": { - "line": 79, + "line": 105, "column": 53 } } @@ -36786,15 +40997,15 @@ "postfix": false, "binop": null }, - "start": 3554, - "end": 3555, + "start": 4717, + "end": 4718, "loc": { "start": { - "line": 79, + "line": 105, "column": 53 }, "end": { - "line": 79, + "line": 105, "column": 54 } } @@ -36812,15 +41023,15 @@ "binop": null, "updateContext": null }, - "start": 3555, - "end": 3556, + "start": 4718, + "end": 4719, "loc": { "start": { - "line": 79, + "line": 105, "column": 54 }, "end": { - "line": 79, + "line": 105, "column": 55 } } @@ -36840,15 +41051,15 @@ "updateContext": null }, "value": "return", - "start": 3563, - "end": 3569, + "start": 4726, + "end": 4732, "loc": { "start": { - "line": 80, + "line": 106, "column": 6 }, "end": { - "line": 80, + "line": 106, "column": 12 } } @@ -36865,15 +41076,15 @@ "postfix": false, "binop": null }, - "start": 3570, - "end": 3571, + "start": 4733, + "end": 4734, "loc": { "start": { - "line": 80, + "line": 106, "column": 13 }, "end": { - "line": 80, + "line": 106, "column": 14 } } @@ -36892,15 +41103,15 @@ "updateContext": null }, "value": "#phyloref", - "start": 3571, - "end": 3580, + "start": 4734, + "end": 4743, "loc": { "start": { - "line": 80, + "line": 106, "column": 14 }, "end": { - 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"line": 100, + "line": 126, "column": 32 }, "end": { - "line": 100, + "line": 126, "column": 33 } } @@ -40147,15 +44358,15 @@ "postfix": false, "binop": null }, - "start": 4315, - "end": 4316, + "start": 5478, + "end": 5479, "loc": { "start": { - "line": 100, + "line": 126, "column": 34 }, "end": { - "line": 100, + "line": 126, "column": 35 } } @@ -40163,15 +44374,15 @@ { "type": "CommentLine", "value": " We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").", - "start": 4323, - "end": 4394, + "start": 5486, + "end": 5557, "loc": { "start": { - "line": 101, + "line": 127, "column": 6 }, "end": { - "line": 101, + "line": 127, "column": 77 } } @@ -40179,15 +44390,15 @@ { "type": "CommentLine", "value": " If the baseIRI is set to '', that's fine. But if not, we'll add it", - "start": 4401, - "end": 4470, + "start": 5564, + "end": 5633, "loc": { "start": { - "line": 102, + "line": 128, "column": 6 }, "end": { - "line": 102, + "line": 128, "column": 75 } } @@ -40195,15 +44406,15 @@ { "type": "CommentLine", "value": " to the relative IRI to make it absolute. 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But if not, we'll add it", - "start": 5350, - "end": 5419, + "start": 6513, + "end": 6582, "loc": { "start": { - "line": 125, + "line": 151, "column": 6 }, "end": { - "line": 125, + "line": 151, "column": 75 } } @@ -43254,15 +47465,15 @@ { "type": "CommentLine", "value": " to the relative IRI to make it absolute. 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"end": 6327, + "start": 7489, + "end": 7490, "loc": { "start": { - "line": 146, + "line": 172, "column": 33 }, "end": { - "line": 146, + "line": 172, "column": 34 } } @@ -46310,15 +50521,15 @@ "binop": null }, "value": "phylogeny", - "start": 6327, - "end": 6336, + "start": 7490, + "end": 7499, "loc": { "start": { - "line": 146, + "line": 172, "column": 34 }, "end": { - "line": 146, + "line": 172, "column": 43 } } @@ -46335,15 +50546,15 @@ "postfix": false, "binop": null }, - "start": 6336, - "end": 6337, + "start": 7499, + "end": 7500, "loc": { "start": { - "line": 146, + "line": 172, "column": 43 }, "end": { - "line": 146, + "line": 172, "column": 44 } } @@ -46361,15 +50572,15 @@ "binop": null, "updateContext": null }, - "start": 6338, - "end": 6340, + "start": 7501, + "end": 7503, "loc": { "start": { - "line": 146, + "line": 172, "column": 45 }, "end": { - "line": 146, + "line": 172, "column": 47 } } @@ -46386,15 +50597,15 @@ "postfix": false, "binop": null }, - "start": 6341, - "end": 6342, + "start": 7504, + "end": 7505, "loc": { "start": { - "line": 146, + "line": 172, "column": 48 }, "end": { - "line": 146, + "line": 172, "column": 49 } } @@ -46414,15 +50625,15 @@ "updateContext": null }, "value": "const", - "start": 6351, - "end": 6356, + "start": 7514, + "end": 7519, "loc": { "start": { - "line": 147, + "line": 173, "column": 8 }, "end": { - "line": 147, + "line": 173, "column": 13 } } @@ -46440,15 +50651,15 @@ "binop": null }, "value": "phylogenyId", - "start": 6357, - "end": 6368, + "start": 7520, + "end": 7531, "loc": { "start": { - "line": 147, + "line": 173, "column": 14 }, "end": { - "line": 147, + "line": 173, "column": 25 } } @@ -46467,15 +50678,15 @@ "updateContext": null }, "value": "=", - "start": 6369, - "end": 6370, + "start": 7532, + "end": 7533, "loc": { "start": { - "line": 147, + "line": 173, "column": 26 }, "end": { - "line": 147, + "line": 173, "column": 27 } } @@ -46493,15 +50704,15 @@ "binop": null }, "value": "phylogeny", - "start": 6371, - "end": 6380, + "start": 7534, + "end": 7543, "loc": { "start": { - "line": 147, + "line": 173, "column": 28 }, "end": { - "line": 147, + "line": 173, "column": 37 } } @@ -46519,15 +50730,15 @@ "binop": null, "updateContext": null }, - "start": 6380, - "end": 6381, + "start": 7543, + "end": 7544, "loc": { "start": { - "line": 147, + "line": 173, "column": 37 }, "end": { - "line": 147, + "line": 173, "column": 38 } } @@ -46546,15 +50757,15 @@ "updateContext": null }, "value": "@id", - "start": 6381, - "end": 6386, + "start": 7544, + "end": 7549, "loc": { "start": { - "line": 147, + "line": 173, "column": 38 }, "end": { - "line": 147, + "line": 173, "column": 43 } } @@ -46572,15 +50783,15 @@ "binop": null, "updateContext": null }, - "start": 6386, - "end": 6387, + "start": 7549, + "end": 7550, "loc": { "start": { - "line": 147, + "line": 173, "column": 43 }, "end": { - "line": 147, + "line": 173, "column": 44 } } @@ -46598,15 +50809,15 @@ "binop": null, "updateContext": null }, - "start": 6387, - "end": 6388, + "start": 7550, + "end": 7551, "loc": { "start": { - "line": 147, + "line": 173, "column": 44 }, "end": { - "line": 147, + "line": 173, "column": 45 } } @@ -46623,15 +50834,15 @@ "postfix": false, "binop": null }, - "start": 6397, - "end": 6398, + "start": 7560, + "end": 7561, "loc": { "start": { - "line": 148, + "line": 174, "column": 8 }, "end": { - "line": 148, + "line": 174, "column": 9 } } @@ -46649,15 +50860,15 @@ "binop": null }, "value": "phylogeny", - "start": 6398, - "end": 6407, + "start": 7561, + "end": 7570, "loc": { "start": { - "line": 148, + "line": 174, "column": 9 }, "end": { - "line": 148, + "line": 174, "column": 18 } } @@ -46675,15 +50886,15 @@ "binop": null, "updateContext": null }, - "start": 6407, - "end": 6408, + "start": 7570, + "end": 7571, "loc": { "start": { - "line": 148, + "line": 174, "column": 18 }, "end": { - "line": 148, + "line": 174, "column": 19 } } @@ -46701,15 +50912,15 @@ "binop": null }, "value": "nodes", - "start": 6408, - "end": 6413, + "start": 7571, + "end": 7576, "loc": { "start": { - "line": 148, + "line": 174, "column": 19 }, "end": { - 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"start": 6451, - "end": 6518, + "start": 7614, + "end": 7681, "loc": { "start": { - "line": 149, + "line": 175, "column": 10 }, "end": { - "line": 149, + "line": 175, "column": 77 } } @@ -47053,15 +51264,15 @@ "updateContext": null }, "value": "if", - "start": 6529, - "end": 6531, + "start": 7692, + "end": 7694, "loc": { "start": { - "line": 150, + "line": 176, "column": 10 }, "end": { - "line": 150, + "line": 176, "column": 12 } } @@ -47078,15 +51289,15 @@ "postfix": false, "binop": null }, - "start": 6532, - "end": 6533, + "start": 7695, + "end": 7696, "loc": { "start": { - "line": 150, + "line": 176, "column": 13 }, "end": { - "line": 150, + "line": 176, "column": 14 } } @@ -47105,15 +51316,15 @@ "updateContext": null }, "value": "!", - "start": 6533, - "end": 6534, + "start": 7696, + "end": 7697, "loc": { "start": { - "line": 150, + "line": 176, "column": 14 }, "end": { - "line": 150, + "line": 176, "column": 15 } } @@ -47131,15 +51342,15 @@ "binop": null }, "value": "node", - "start": 6534, - "end": 6538, + "start": 7697, + "end": 7701, "loc": { "start": { - "line": 150, + "line": 176, "column": 15 }, "end": { - "line": 150, + "line": 176, "column": 19 } } @@ -47157,15 +51368,15 @@ "binop": null, "updateContext": null }, - "start": 6538, - "end": 6539, + "start": 7701, + "end": 7702, "loc": { "start": { - "line": 150, + "line": 176, "column": 19 }, "end": { - "line": 150, + "line": 176, "column": 20 } } @@ -47183,15 +51394,15 @@ "binop": null }, "value": "labels", - "start": 6539, - "end": 6545, + "start": 7702, + "end": 7708, "loc": { "start": { - "line": 150, + "line": 176, "column": 20 }, "end": { - "line": 150, + "line": 176, "column": 26 } } @@ -47208,15 +51419,15 @@ "postfix": false, "binop": null }, - "start": 6545, - "end": 6546, + "start": 7708, + "end": 7709, "loc": { "start": { - "line": 150, + "line": 176, "column": 26 }, "end": { - "line": 150, + "line": 176, "column": 27 } } @@ -47236,15 +51447,15 @@ "updateContext": null }, "value": "return", - "start": 6547, - 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"end": 6582, + "start": 7736, + "end": 7745, "loc": { "start": { - "line": 152, + "line": 178, "column": 17 }, "end": { - "line": 152, + "line": 178, "column": 26 } } @@ -47366,15 +51577,15 @@ "binop": null, "updateContext": null }, - "start": 6582, - "end": 6583, + "start": 7745, + "end": 7746, "loc": { "start": { - "line": 152, + "line": 178, "column": 26 }, "end": { - "line": 152, + "line": 178, "column": 27 } } @@ -47392,15 +51603,15 @@ "binop": null }, "value": "forEach", - "start": 6583, - "end": 6590, + "start": 7746, + "end": 7753, "loc": { "start": { - "line": 152, + "line": 178, "column": 27 }, "end": { - "line": 152, + "line": 178, "column": 34 } } @@ -47417,15 +51628,15 @@ "postfix": false, "binop": null }, - "start": 6590, - "end": 6591, + "start": 7753, + "end": 7754, "loc": { "start": { - "line": 152, + "line": 178, "column": 34 }, "end": { - "line": 152, + "line": 178, "column": 35 } } @@ -47442,15 +51653,15 @@ "postfix": false, "binop": null }, - "start": 6591, - "end": 6592, + "start": 7754, + "end": 7755, "loc": { "start": { - "line": 152, + "line": 178, "column": 35 }, "end": { - "line": 152, + "line": 178, "column": 36 } } @@ -47468,15 +51679,15 @@ "binop": null }, "value": "phyloref", - "start": 6592, - "end": 6600, + "start": 7755, + "end": 7763, "loc": { "start": { - "line": 152, + "line": 178, "column": 36 }, "end": { - "line": 152, + "line": 178, "column": 44 } } @@ -47493,15 +51704,15 @@ "postfix": false, "binop": null }, - "start": 6600, - "end": 6601, + "start": 7763, + "end": 7764, "loc": { "start": { - "line": 152, + "line": 178, "column": 44 }, "end": { - "line": 152, + "line": 178, "column": 45 } } @@ -47519,15 +51730,15 @@ "binop": null, "updateContext": null }, - "start": 6602, - "end": 6604, + "start": 7765, + "end": 7767, "loc": { "start": { - "line": 152, + "line": 178, "column": 46 }, "end": { - "line": 152, + "line": 178, "column": 48 } } @@ -47544,15 +51755,15 @@ "postfix": false, "binop": null }, - "start": 6605, - "end": 6606, + "start": 7768, + "end": 7769, "loc": { "start": { - "line": 152, + "line": 178, "column": 49 }, "end": { - "line": 152, + "line": 178, "column": 50 } } @@ -47572,15 +51783,15 @@ "updateContext": null }, "value": "const", - "start": 6619, - "end": 6624, + "start": 7782, + "end": 7787, "loc": { "start": { - "line": 153, + "line": 179, "column": 12 }, "end": { - "line": 153, + "line": 179, "column": 17 } } @@ -47598,15 +51809,15 @@ "binop": null }, "value": "phylorefId", - "start": 6625, - "end": 6635, + "start": 7788, + "end": 7798, "loc": { "start": { - "line": 153, + "line": 179, "column": 18 }, "end": { - "line": 153, + "line": 179, "column": 28 } } @@ -47625,15 +51836,15 @@ "updateContext": null }, "value": "=", - "start": 6636, - "end": 6637, + "start": 7799, + "end": 7800, "loc": { "start": { - "line": 153, + "line": 179, "column": 29 }, "end": { - "line": 153, + "line": 179, "column": 30 } } @@ -47651,15 +51862,15 @@ "binop": null }, "value": "phyloref", - "start": 6638, - "end": 6646, + "start": 7801, + "end": 7809, "loc": { "start": { - "line": 153, + "line": 179, "column": 31 }, "end": { - "line": 153, + "line": 179, "column": 39 } } @@ -47677,15 +51888,15 @@ "binop": null, "updateContext": null }, - "start": 6646, - "end": 6647, + "start": 7809, + "end": 7810, "loc": { "start": { - "line": 153, + "line": 179, "column": 39 }, "end": { - "line": 153, + "line": 179, "column": 40 } } @@ -47704,15 +51915,15 @@ "updateContext": null }, "value": "@id", - "start": 6647, - "end": 6652, + "start": 7810, + "end": 7815, "loc": { "start": { - "line": 153, + "line": 179, "column": 40 }, "end": { - "line": 153, + "line": 179, "column": 45 } } @@ -47730,15 +51941,15 @@ "binop": null, "updateContext": null }, - "start": 6652, - "end": 6653, + "start": 7815, + "end": 7816, "loc": { "start": { - "line": 153, + "line": 179, "column": 45 }, "end": { - "line": 153, + "line": 179, "column": 46 } } @@ -47756,15 +51967,15 @@ "binop": null, "updateContext": null }, - "start": 6653, - "end": 6654, + "start": 7816, + "end": 7817, "loc": { "start": { - "line": 153, + "line": 179, "column": 46 }, "end": { - "line": 153, + "line": 179, "column": 47 } } @@ -47772,15 +51983,15 @@ { "type": "CommentLine", "value": " There are two ways in which we determine that a phyloreference", - "start": 6668, - "end": 6733, + "start": 7831, + "end": 7896, "loc": { "start": { - "line": 155, + "line": 181, "column": 12 }, "end": { - "line": 155, + "line": 181, "column": 77 } } @@ -47788,15 +51999,15 @@ { "type": "CommentLine", "value": " is expected to resolve to a node:", - "start": 6746, - "end": 6782, + "start": 7909, + "end": 7945, "loc": { "start": { - "line": 156, + "line": 182, "column": 12 }, "end": { - "line": 156, + "line": 182, "column": 48 } } @@ -47804,15 +52015,15 @@ { "type": "CommentLine", "value": " (1) If nodeLabel is set, then that must be one of the node's labels.", - "start": 6795, - "end": 6867, + "start": 7958, + "end": 8030, "loc": { "start": { - "line": 157, + "line": 183, "column": 12 }, "end": { - "line": 157, + "line": 183, "column": 84 } } @@ -47820,15 +52031,15 @@ { "type": "CommentLine", "value": " (2) If nodeLabel is not set, then one of the node's label should be", - "start": 6880, - "end": 6951, + "start": 8043, + "end": 8114, "loc": { "start": { - "line": 158, + "line": 184, "column": 12 }, "end": { - "line": 158, + "line": 184, "column": 83 } } @@ -47836,15 +52047,15 @@ { "type": "CommentLine", "value": " identical to the phyloreference's label.", - "start": 6964, - "end": 7012, + "start": 8127, + "end": 8175, "loc": { "start": { - "line": 159, + "line": 185, "column": 12 }, "end": { - "line": 159, + "line": 185, "column": 60 } } @@ -47852,15 +52063,15 @@ { "type": "CommentLine", "value": "", - "start": 7025, - "end": 7027, + "start": 8188, + "end": 8190, "loc": { "start": { - "line": 160, + "line": 186, "column": 12 }, "end": { - "line": 160, + "line": 186, "column": 14 } } @@ -47868,15 +52079,15 @@ { "type": "CommentLine", "value": " We set flagNodeExpectsPhyloref in all cases where we should note", - "start": 7040, - "end": 7107, + "start": 8203, + "end": 8270, "loc": { "start": { - "line": 161, + "line": 187, "column": 12 }, "end": { - "line": 161, + "line": 187, "column": 79 } } @@ -47884,15 +52095,15 @@ { "type": "CommentLine", "value": " that this node expects to resolve to this phyloreference.", - "start": 7120, - "end": 7180, + "start": 8283, + "end": 8343, "loc": { "start": { - "line": 162, + "line": 188, "column": 12 }, "end": { - "line": 162, + "line": 188, "column": 72 } } @@ -47912,15 +52123,15 @@ "updateContext": null }, "value": "let", - "start": 7193, - "end": 7196, + "start": 8356, + "end": 8359, "loc": { "start": { - "line": 163, + "line": 189, "column": 12 }, "end": { - "line": 163, + "line": 189, "column": 15 } } @@ -47938,15 +52149,15 @@ "binop": null }, "value": "flagNodeExpectsPhyloref", - "start": 7197, - "end": 7220, + "start": 8360, + "end": 8383, "loc": { "start": { - "line": 163, + "line": 189, "column": 16 }, "end": { - "line": 163, + "line": 189, "column": 39 } } @@ -47965,15 +52176,15 @@ "updateContext": null }, "value": "=", - "start": 7221, - "end": 7222, + "start": 8384, + "end": 8385, "loc": { "start": { - "line": 163, + "line": 189, "column": 40 }, "end": { - "line": 163, + "line": 189, "column": 41 } } @@ -47993,15 +52204,15 @@ "updateContext": null }, "value": "false", - "start": 7223, - "end": 7228, + "start": 8386, + "end": 8391, "loc": { "start": { - "line": 163, + "line": 189, "column": 42 }, "end": { - "line": 163, + "line": 189, "column": 47 } } @@ -48019,15 +52230,15 @@ "binop": null, "updateContext": null }, - "start": 7228, - "end": 7229, + "start": 8391, + "end": 8392, "loc": { "start": { - "line": 163, + "line": 189, "column": 47 }, "end": { - "line": 163, + "line": 189, "column": 48 } } @@ -48035,15 +52246,15 @@ { "type": "CommentLine", "value": " console.log(`Testing expected resolution of '${phylorefId}' on `", - "start": 7243, - "end": 7310, + "start": 8406, + "end": 8473, "loc": { "start": { - "line": 165, + "line": 191, "column": 12 }, "end": { - "line": 165, + "line": 191, "column": 79 } } @@ -48051,15 +52262,15 @@ { "type": "CommentLine", "value": " + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);", - "start": 7323, - "end": 7382, + "start": 8486, + "end": 8545, "loc": { "start": { - "line": 166, + "line": 192, "column": 12 }, "end": { - "line": 166, + "line": 192, "column": 71 } } @@ -48079,15 +52290,15 @@ "updateContext": null }, "value": "if", - "start": 7396, - "end": 7398, + "start": 8559, + "end": 8561, "loc": { "start": { - "line": 168, + "line": 194, "column": 12 }, "end": { - "line": 168, + "line": 194, "column": 14 } } @@ -48104,15 +52315,15 @@ "postfix": false, "binop": null }, - "start": 7399, - "end": 7400, + "start": 8562, + "end": 8563, "loc": { "start": { - "line": 168, + "line": 194, "column": 15 }, "end": { - "line": 168, + "line": 194, "column": 16 } } @@ -48130,15 +52341,15 @@ "binop": null }, "value": "has", - "start": 7415, - "end": 7418, + "start": 8578, + "end": 8581, "loc": { "start": { - "line": 169, + "line": 195, "column": 14 }, "end": { - "line": 169, + "line": 195, "column": 17 } } @@ -48155,15 +52366,15 @@ "postfix": false, "binop": null }, - "start": 7418, - "end": 7419, + "start": 8581, + "end": 8582, "loc": { "start": { - "line": 169, + "line": 195, "column": 17 }, "end": { - "line": 169, + "line": 195, "column": 18 } } @@ -48181,15 +52392,15 @@ "binop": null }, "value": "phyloref", - "start": 7419, - "end": 7427, + "start": 8582, + "end": 8590, "loc": { "start": { - "line": 169, + "line": 195, "column": 18 }, "end": { - "line": 169, + "line": 195, "column": 26 } } @@ -48207,15 +52418,15 @@ "binop": null, "updateContext": null }, - "start": 7427, - "end": 7428, + "start": 8590, + "end": 8591, "loc": { "start": { - "line": 169, + "line": 195, "column": 26 }, "end": { - "line": 169, + "line": 195, "column": 27 } } @@ -48234,15 +52445,15 @@ "updateContext": null }, "value": "expectedResolution", - "start": 7429, - "end": 7449, + "start": 8592, + "end": 8612, "loc": { "start": { - "line": 169, + "line": 195, "column": 28 }, "end": { - "line": 169, + "line": 195, "column": 48 } } @@ -48259,15 +52470,15 @@ "postfix": false, "binop": null }, - "start": 7449, - "end": 7450, + "start": 8612, + "end": 8613, "loc": { "start": { - "line": 169, + "line": 195, "column": 48 }, "end": { - "line": 169, + "line": 195, "column": 49 } } @@ -48286,15 +52497,15 @@ "updateContext": null }, "value": "&&", - "start": 7465, - "end": 7467, + "start": 8628, + "end": 8630, "loc": { "start": { - "line": 170, + "line": 196, "column": 14 }, "end": { - "line": 170, + "line": 196, "column": 16 } } @@ -48311,15 +52522,15 @@ "postfix": false, "binop": null }, - "start": 7468, - "end": 7469, + "start": 8631, + "end": 8632, "loc": { "start": { - "line": 170, + "line": 196, "column": 17 }, "end": { - "line": 170, + "line": 196, "column": 18 } } @@ -48327,15 +52538,15 @@ { "type": "CommentLine", "value": " The user might have used the absolute phylogeny ID here.", - "start": 7486, - "end": 7545, + "start": 8649, + "end": 8708, "loc": { "start": { - "line": 171, + "line": 197, "column": 16 }, "end": { - "line": 171, + "line": 197, "column": 75 } } @@ -48353,15 +52564,15 @@ "binop": null }, "value": "has", - "start": 7562, - "end": 7565, + "start": 8725, + "end": 8728, "loc": { "start": { - "line": 172, + "line": 198, "column": 16 }, "end": { - "line": 172, + "line": 198, "column": 19 } } @@ -48378,15 +52589,15 @@ "postfix": false, "binop": null }, - "start": 7565, - "end": 7566, + "start": 8728, + "end": 8729, "loc": { "start": { - "line": 172, + "line": 198, "column": 19 }, "end": { - "line": 172, + "line": 198, "column": 20 } } @@ -48404,15 +52615,15 @@ "binop": null }, "value": "phyloref", - "start": 7566, - "end": 7574, + "start": 8729, + "end": 8737, "loc": { "start": { - "line": 172, + "line": 198, "column": 20 }, "end": { - "line": 172, + "line": 198, "column": 28 } } @@ -48430,15 +52641,15 @@ "binop": null, "updateContext": null }, - "start": 7574, - "end": 7575, + "start": 8737, + "end": 8738, "loc": { "start": { - "line": 172, + "line": 198, "column": 28 }, "end": { - "line": 172, + "line": 198, "column": 29 } } @@ -48456,15 +52667,15 @@ "binop": null }, "value": "expectedResolution", - "start": 7575, - "end": 7593, + "start": 8738, + "end": 8756, "loc": { "start": { - "line": 172, + "line": 198, "column": 29 }, "end": { - "line": 172, + "line": 198, "column": 47 } } @@ -48482,15 +52693,15 @@ "binop": null, "updateContext": null }, - "start": 7593, - "end": 7594, + "start": 8756, + "end": 8757, "loc": { "start": { - "line": 172, + "line": 198, "column": 47 }, "end": { - "line": 172, + "line": 198, "column": 48 } } @@ -48508,15 +52719,15 @@ "binop": null }, "value": "phylogenyId", - "start": 7595, - "end": 7606, + "start": 8758, + "end": 8769, "loc": { "start": { - "line": 172, + "line": 198, "column": 49 }, "end": { - "line": 172, + "line": 198, "column": 60 } } @@ -48533,15 +52744,15 @@ "postfix": false, "binop": null }, - "start": 7606, - "end": 7607, + "start": 8769, + "end": 8770, "loc": { "start": { - "line": 172, + "line": 198, "column": 60 }, "end": { - "line": 172, + "line": 198, "column": 61 } } @@ -48549,15 +52760,15 @@ { "type": "CommentLine", "value": " Or they might have used a relative phylogeny ID.", - "start": 7625, - "end": 7676, + "start": 8788, + "end": 8839, "loc": { "start": { - "line": 174, + "line": 200, "column": 16 }, "end": { - "line": 174, + "line": 200, "column": 67 } } @@ -48576,15 +52787,15 @@ "updateContext": null }, "value": "||", - "start": 7693, - "end": 7695, + "start": 8856, + "end": 8858, "loc": { "start": { - "line": 175, + "line": 201, "column": 16 }, "end": { - "line": 175, + "line": 201, "column": 18 } } @@ -48602,15 +52813,15 @@ "binop": null }, "value": "has", - "start": 7696, - "end": 7699, + "start": 8859, + "end": 8862, "loc": { "start": { - "line": 175, + "line": 201, "column": 19 }, "end": { - "line": 175, + "line": 201, "column": 22 } } @@ -48627,15 +52838,15 @@ "postfix": false, "binop": null }, - "start": 7699, - "end": 7700, + "start": 8862, + "end": 8863, "loc": { "start": { - "line": 175, + "line": 201, "column": 22 }, "end": { - "line": 175, + "line": 201, "column": 23 } } @@ -48653,15 +52864,15 @@ "binop": null }, "value": "phyloref", - "start": 7700, - "end": 7708, + "start": 8863, + "end": 8871, "loc": { "start": { - "line": 175, + "line": 201, "column": 23 }, "end": { - "line": 175, + "line": 201, "column": 31 } } @@ -48679,15 +52890,15 @@ "binop": null, "updateContext": null }, - "start": 7708, - "end": 7709, + "start": 8871, + "end": 8872, "loc": { "start": { - "line": 175, + "line": 201, "column": 31 }, "end": { - "line": 175, + "line": 201, "column": 32 } } @@ -48705,15 +52916,15 @@ "binop": null }, "value": "expectedResolution", - "start": 7709, - "end": 7727, + "start": 8872, + "end": 8890, "loc": { "start": { - "line": 175, + "line": 201, "column": 32 }, "end": { - "line": 175, + "line": 201, "column": 50 } } @@ -48731,15 +52942,15 @@ "binop": null, "updateContext": null }, - "start": 7727, - "end": 7728, + "start": 8890, + "end": 8891, "loc": { "start": { - "line": 175, + "line": 201, "column": 50 }, "end": { - "line": 175, + "line": 201, "column": 51 } } @@ -48757,15 +52968,15 @@ "binop": null }, "value": "makeIDRelative", - "start": 7729, - "end": 7743, + "start": 8892, + "end": 8906, "loc": { "start": { - "line": 175, + "line": 201, "column": 52 }, "end": { - "line": 175, + "line": 201, "column": 66 } } @@ -48782,15 +52993,15 @@ "postfix": false, "binop": null }, - "start": 7743, - "end": 7744, + "start": 8906, + "end": 8907, "loc": { "start": { - "line": 175, + "line": 201, "column": 66 }, "end": { - "line": 175, + "line": 201, "column": 67 } } @@ -48808,15 +53019,15 @@ "binop": null }, "value": "phylogenyId", - "start": 7744, - "end": 7755, + "start": 8907, + "end": 8918, "loc": { "start": { - "line": 175, + "line": 201, "column": 67 }, "end": { - "line": 175, + "line": 201, "column": 78 } } @@ -48833,15 +53044,15 @@ "postfix": false, "binop": null }, - "start": 7755, - "end": 7756, + "start": 8918, + "end": 8919, "loc": { "start": { - "line": 175, + "line": 201, "column": 78 }, "end": { - "line": 175, + "line": 201, "column": 79 } } @@ -48858,15 +53069,15 @@ "postfix": false, "binop": null }, - "start": 7756, - "end": 7757, + "start": 8919, + "end": 8920, "loc": { "start": { - "line": 175, + "line": 201, "column": 79 }, "end": { - "line": 175, + "line": 201, "column": 80 } } @@ -48883,15 +53094,15 @@ "postfix": false, "binop": null }, - "start": 7772, - "end": 7773, + "start": 8935, + "end": 8936, "loc": { "start": { - "line": 176, + "line": 202, "column": 14 }, "end": { - "line": 176, + "line": 202, "column": 15 } } @@ -48908,15 +53119,15 @@ "postfix": false, "binop": null }, - "start": 7786, - "end": 7787, + "start": 8949, + "end": 8950, "loc": { "start": { - "line": 177, + "line": 203, "column": 12 }, "end": { - "line": 177, + "line": 203, "column": 13 } } @@ -48933,15 +53144,15 @@ "postfix": false, "binop": null }, - "start": 7788, - "end": 7789, + "start": 8951, + "end": 8952, "loc": { "start": { - "line": 177, + "line": 203, "column": 14 }, "end": { - "line": 177, + "line": 203, "column": 15 } } @@ -48949,15 +53160,15 @@ { "type": "CommentLine", "value": " Expected resolution information set! The node label mentioned in that", - "start": 7804, - "end": 7876, + "start": 8967, + "end": 9039, "loc": { "start": { - "line": 178, + "line": 204, "column": 14 }, "end": { - "line": 178, + "line": 204, "column": 86 } } @@ -48965,15 +53176,15 @@ { "type": "CommentLine", "value": " information must be identical to one of the labels of this phylogeny node.", - "start": 7891, - "end": 7968, + "start": 9054, + "end": 9131, "loc": { "start": { - "line": 179, + "line": 205, "column": 14 }, "end": { - "line": 179, + "line": 205, "column": 91 } } @@ -48981,15 +53192,15 @@ { "type": "CommentLine", "value": " Figure out which phylogenyId was matched here.", - "start": 7984, - "end": 8033, + "start": 9147, + "end": 9196, "loc": { "start": { - "line": 181, + "line": 207, "column": 14 }, "end": { - "line": 181, + "line": 207, "column": 63 } } @@ -49009,15 +53220,15 @@ "updateContext": null }, "value": "const", - "start": 8048, - "end": 8053, + "start": 9211, + "end": 9216, "loc": { "start": { - "line": 182, + "line": 208, "column": 14 }, "end": { - "line": 182, + "line": 208, "column": 19 } } @@ -49035,15 +53246,15 @@ "binop": null }, "value": "nodeLabel", - "start": 8054, - "end": 8063, + "start": 9217, + "end": 9226, "loc": { "start": { - "line": 182, + "line": 208, "column": 20 }, "end": { - "line": 182, + "line": 208, "column": 29 } } @@ -49062,15 +53273,15 @@ "updateContext": null }, "value": "=", - "start": 8064, - "end": 8065, + "start": 9227, + "end": 9228, "loc": { "start": { - "line": 182, + "line": 208, "column": 30 }, "end": { - "line": 182, + "line": 208, "column": 31 } } @@ -49088,15 +53299,15 @@ "binop": null }, "value": "has", - "start": 8066, - "end": 8069, + "start": 9229, + "end": 9232, "loc": { "start": { - "line": 182, + "line": 208, "column": 32 }, "end": { - "line": 182, + "line": 208, "column": 35 } } @@ -49113,15 +53324,15 @@ "postfix": false, "binop": null }, - "start": 8069, - "end": 8070, + "start": 9232, + "end": 9233, "loc": { "start": { - "line": 182, + "line": 208, "column": 35 }, "end": { - "line": 182, + "line": 208, "column": 36 } } @@ -49139,15 +53350,15 @@ "binop": null }, "value": "phyloref", - "start": 8070, - "end": 8078, + "start": 9233, + "end": 9241, "loc": { "start": { - "line": 182, + "line": 208, "column": 36 }, "end": { - "line": 182, + "line": 208, "column": 44 } } @@ -49165,15 +53376,15 @@ "binop": null, "updateContext": null }, - "start": 8078, - "end": 8079, + "start": 9241, + "end": 9242, "loc": { "start": { - "line": 182, + "line": 208, "column": 44 }, "end": { - "line": 182, + "line": 208, "column": 45 } } @@ -49191,15 +53402,15 @@ "binop": null }, "value": "expectedResolution", - "start": 8079, - "end": 8097, + "start": 9242, + "end": 9260, "loc": { "start": { - "line": 182, + "line": 208, "column": 45 }, "end": { - "line": 182, + "line": 208, "column": 63 } } @@ -49217,15 +53428,15 @@ "binop": null, "updateContext": null }, - "start": 8097, - "end": 8098, + "start": 9260, + "end": 9261, "loc": { "start": { - "line": 182, + "line": 208, "column": 63 }, "end": { - "line": 182, + "line": 208, "column": 64 } } @@ -49243,15 +53454,15 @@ "binop": null }, "value": "phylogenyId", - "start": 8099, - "end": 8110, + "start": 9262, + "end": 9273, "loc": { "start": { - "line": 182, + "line": 208, "column": 65 }, "end": { - "line": 182, + "line": 208, "column": 76 } } @@ -49268,15 +53479,15 @@ "postfix": false, "binop": null }, - "start": 8110, - "end": 8111, + "start": 9273, + "end": 9274, "loc": { "start": { - "line": 182, + "line": 208, "column": 76 }, "end": { - "line": 182, + "line": 208, "column": 77 } } @@ -49294,15 +53505,15 @@ "binop": null, "updateContext": null }, - "start": 8128, - "end": 8129, + "start": 9291, + "end": 9292, "loc": { "start": { - "line": 183, + "line": 209, "column": 16 }, "end": { - "line": 183, + "line": 209, "column": 17 } } @@ -49320,15 +53531,15 @@ "binop": null }, "value": "phyloref", - "start": 8130, - "end": 8138, + "start": 9293, + "end": 9301, "loc": { "start": { - "line": 183, + "line": 209, "column": 18 }, "end": { - "line": 183, + "line": 209, "column": 26 } } @@ -49346,15 +53557,15 @@ "binop": null, "updateContext": null }, - "start": 8138, - "end": 8139, + "start": 9301, + "end": 9302, "loc": { "start": { - "line": 183, + "line": 209, "column": 26 }, "end": { - "line": 183, + "line": 209, "column": 27 } } @@ -49372,15 +53583,15 @@ "binop": null }, "value": "expectedResolution", - "start": 8139, - "end": 8157, + "start": 9302, + "end": 9320, "loc": { "start": { - "line": 183, + "line": 209, "column": 27 }, "end": { - "line": 183, + "line": 209, "column": 45 } } @@ -49398,15 +53609,15 @@ "binop": null, "updateContext": null }, - "start": 8157, - "end": 8158, + "start": 9320, + "end": 9321, "loc": { "start": { - "line": 183, + "line": 209, "column": 45 }, "end": { - "line": 183, + "line": 209, "column": 46 } } @@ -49424,15 +53635,15 @@ "binop": null }, "value": "phylogenyId", - "start": 8158, - "end": 8169, + "start": 9321, + "end": 9332, "loc": { "start": { - "line": 183, + "line": 209, "column": 46 }, "end": { - "line": 183, + "line": 209, "column": 57 } } @@ -49450,15 +53661,15 @@ "binop": null, "updateContext": null }, - 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"start": 8199, - "end": 8207, + "start": 9362, + "end": 9370, "loc": { "start": { - "line": 184, + "line": 210, "column": 18 }, "end": { - "line": 184, + "line": 210, "column": 26 } } @@ -49580,15 +53791,15 @@ "binop": null, "updateContext": null }, - "start": 8207, - "end": 8208, + "start": 9370, + "end": 9371, "loc": { "start": { - "line": 184, + "line": 210, "column": 26 }, "end": { - "line": 184, + "line": 210, "column": 27 } } @@ -49606,15 +53817,15 @@ "binop": null }, "value": "expectedResolution", - "start": 8208, - "end": 8226, + "start": 9371, + "end": 9389, "loc": { "start": { - "line": 184, + "line": 210, "column": 27 }, "end": { - "line": 184, + "line": 210, "column": 45 } } @@ -49632,15 +53843,15 @@ "binop": null, "updateContext": null }, - "start": 8226, - "end": 8227, + "start": 9389, + "end": 9390, "loc": { "start": { - "line": 184, + "line": 210, "column": 45 }, "end": { - "line": 184, + "line": 210, "column": 46 } } @@ -49658,15 +53869,15 @@ "binop": null }, "value": "makeIDRelative", - 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If one is present, we add our terms to that.", - "start": 10468, - "end": 10552, + "start": 11631, + "end": 11715, "loc": { "start": { - "line": 237, + "line": 263, "column": 4 }, "end": { - "line": 237, + "line": 263, "column": 88 } } @@ -54468,15 +58679,15 @@ "updateContext": null }, "value": "if", - "start": 10557, - "end": 10559, + "start": 11720, + "end": 11722, "loc": { "start": { - "line": 238, + "line": 264, "column": 4 }, "end": { - "line": 238, + "line": 264, "column": 6 } } @@ -54493,15 +58704,15 @@ "postfix": false, "binop": null }, - "start": 10560, - "end": 10561, + "start": 11723, + "end": 11724, "loc": { "start": { - "line": 238, + "line": 264, "column": 7 }, "end": { - "line": 238, + "line": 264, "column": 8 } } @@ -54520,15 +58731,15 @@ "updateContext": null }, "value": "!", - "start": 10561, - "end": 10562, + "start": 11724, + "end": 11725, "loc": { "start": { - "line": 238, + "line": 264, "column": 8 }, "end": { - "line": 238, + "line": 264, "column": 9 } } @@ -54546,15 +58757,15 @@ "binop": null }, "value": "has", - 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"start": 10954, - "end": 10967, + "start": 12117, + "end": 12130, "loc": { "start": { - "line": 244, + "line": 270, "column": 79 }, "end": { - "line": 244, + "line": 270, "column": 92 } } @@ -56910,15 +61121,15 @@ "binop": null, "updateContext": null }, - "start": 10967, - "end": 10968, + "start": 12130, + "end": 12131, "loc": { "start": { - "line": 244, + "line": 270, "column": 92 }, "end": { - "line": 244, + "line": 270, "column": 93 } } @@ -56936,15 +61147,15 @@ "binop": null, "updateContext": null }, - "start": 10968, - "end": 10969, + "start": 12131, + "end": 12132, "loc": { "start": { - "line": 244, + "line": 270, "column": 93 }, "end": { - "line": 244, + "line": 270, "column": 94 } } @@ -56962,15 +61173,15 @@ "binop": null, "updateContext": null }, - "start": 10969, - "end": 10970, + "start": 12132, + "end": 12133, "loc": { "start": { - "line": 244, + "line": 270, "column": 94 }, "end": { - "line": 244, + "line": 270, "column": 95 } } @@ -56988,15 +61199,15 @@ "binop": null }, "value": "jsonld", - "start": 10975, - "end": 10981, + "start": 12138, + "end": 12144, "loc": { "start": { - "line": 245, + "line": 271, "column": 4 }, "end": { - "line": 245, + "line": 271, "column": 10 } } @@ -57014,15 +61225,15 @@ "binop": null, "updateContext": null }, - "start": 10981, - "end": 10982, + "start": 12144, + "end": 12145, "loc": { "start": { - "line": 245, + "line": 271, "column": 10 }, "end": { - "line": 245, + "line": 271, "column": 11 } } @@ -57041,15 +61252,15 @@ "updateContext": null }, "value": "owl:imports", - "start": 10982, - "end": 10995, + "start": 12145, + "end": 12158, "loc": { "start": { - "line": 245, + "line": 271, "column": 11 }, "end": { - "line": 245, + "line": 271, "column": 24 } } @@ -57067,15 +61278,15 @@ "binop": null, "updateContext": null }, - "start": 10995, - "end": 10996, + "start": 12158, + "end": 12159, "loc": { "start": { - "line": 245, + "line": 271, "column": 24 }, "end": { - "line": 245, + "line": 271, "column": 25 } } @@ -57093,15 +61304,15 @@ "binop": null, "updateContext": null }, - "start": 10996, - "end": 10997, + "start": 12159, + "end": 12160, "loc": { "start": { - "line": 245, + "line": 271, "column": 25 }, "end": { - "line": 245, + "line": 271, "column": 26 } } @@ -57119,15 +61330,15 @@ "binop": null }, "value": "push", - "start": 10997, - "end": 11001, + "start": 12160, + "end": 12164, "loc": { "start": { - "line": 245, + "line": 271, "column": 26 }, "end": { - "line": 245, + "line": 271, "column": 30 } } @@ -57144,15 +61355,15 @@ "postfix": false, "binop": null }, - "start": 11001, - "end": 11002, + "start": 12164, + "end": 12165, "loc": { "start": { - "line": 245, + "line": 271, "column": 30 }, "end": { - "line": 245, + "line": 271, "column": 31 } } @@ -57171,15 +61382,15 @@ "updateContext": null }, "value": "http://ontology.phyloref.org/2018-12-14/phyloref.owl", - "start": 11002, - "end": 11056, + "start": 12165, + "end": 12219, "loc": { "start": { - "line": 245, + "line": 271, "column": 31 }, "end": { - "line": 245, + "line": 271, "column": 85 } } @@ -57196,15 +61407,15 @@ "postfix": false, "binop": null }, - 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"start": 11089, - "end": 11090, + "start": 12252, + "end": 12253, "loc": { "start": { - "line": 246, + "line": 272, "column": 30 }, "end": { - "line": 246, + "line": 272, "column": 31 } } @@ -57431,15 +61642,15 @@ "updateContext": null }, "value": "http://ontology.phyloref.org/2018-12-14/tcan.owl", - "start": 11090, - "end": 11140, + "start": 12253, + "end": 12303, "loc": { "start": { - "line": 246, + "line": 272, "column": 31 }, "end": { - "line": 246, + "line": 272, "column": 81 } } @@ -57456,15 +61667,15 @@ "postfix": false, "binop": null }, - "start": 11140, - "end": 11141, + "start": 12303, + "end": 12304, "loc": { "start": { - "line": 246, + "line": 272, "column": 81 }, "end": { - "line": 246, + "line": 272, "column": 82 } } @@ -57482,15 +61693,15 @@ "binop": null, "updateContext": null }, - "start": 11141, - "end": 11142, + "start": 12304, + "end": 12305, "loc": { "start": { - "line": 246, + "line": 272, "column": 82 }, "end": { - "line": 246, + "line": 272, "column": 83 } } @@ -57498,15 +61709,15 @@ { "type": "CommentLine", "value": " If the '@context' is missing, add it here.", - 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"start": 11215, - "end": 11225, + "start": 12378, + "end": 12388, "loc": { "start": { - "line": 249, + "line": 275, "column": 21 }, "end": { - "line": 249, + "line": 275, "column": 31 } } @@ -57733,15 +61944,15 @@ "postfix": false, "binop": null }, - "start": 11225, - "end": 11226, + "start": 12388, + "end": 12389, "loc": { "start": { - "line": 249, + "line": 275, "column": 31 }, "end": { - "line": 249, + "line": 275, "column": 32 } } @@ -57758,15 +61969,15 @@ "postfix": false, "binop": null }, - "start": 11226, - "end": 11227, + "start": 12389, + "end": 12390, "loc": { "start": { - "line": 249, + "line": 275, "column": 32 }, "end": { - "line": 249, + "line": 275, "column": 33 } } @@ -57783,15 +61994,15 @@ "postfix": false, "binop": null }, - "start": 11228, - "end": 11229, + "start": 12391, + "end": 12392, "loc": { "start": { - "line": 249, + "line": 275, "column": 34 }, "end": { - "line": 249, + "line": 275, "column": 35 } } @@ -57809,15 +62020,15 @@ "binop": null }, "value": "jsonld", - "start": 11236, - "end": 11242, + "start": 12399, + "end": 12405, "loc": { "start": { - "line": 250, + "line": 276, "column": 6 }, "end": { - "line": 250, + "line": 276, "column": 12 } } @@ -57835,15 +62046,15 @@ "binop": null, "updateContext": null }, - "start": 11242, - "end": 11243, + "start": 12405, + "end": 12406, "loc": { "start": { - "line": 250, + "line": 276, "column": 12 }, "end": { - "line": 250, + "line": 276, "column": 13 } } @@ -57862,15 +62073,15 @@ "updateContext": null }, "value": "@context", - "start": 11243, - "end": 11253, + "start": 12406, + "end": 12416, "loc": { "start": { - "line": 250, + "line": 276, "column": 13 }, "end": { - "line": 250, + "line": 276, "column": 23 } } @@ -57888,15 +62099,15 @@ "binop": null, "updateContext": null }, - "start": 11253, - "end": 11254, + "start": 12416, + "end": 12417, "loc": { "start": { - "line": 250, + "line": 276, "column": 23 }, "end": { - "line": 250, + "line": 276, "column": 24 } } @@ -57915,15 +62126,15 @@ "updateContext": null }, "value": "=", - "start": 11255, - "end": 11256, + "start": 12418, + "end": 12419, "loc": { "start": { - "line": 250, + "line": 276, "column": 25 }, "end": { - "line": 250, + "line": 276, "column": 26 } } @@ -57941,15 +62152,15 @@ "binop": null }, "value": "owlterms", - "start": 11257, - "end": 11265, + "start": 12420, + "end": 12428, "loc": { "start": { - "line": 250, + "line": 276, "column": 27 }, "end": { - "line": 250, + "line": 276, "column": 35 } } @@ -57967,15 +62178,15 @@ "binop": null, "updateContext": null }, - "start": 11265, - "end": 11266, + "start": 12428, + "end": 12429, "loc": { "start": { - "line": 250, + "line": 276, "column": 35 }, "end": { - "line": 250, + "line": 276, "column": 36 } } @@ -57993,15 +62204,15 @@ "binop": null }, "value": "PHYX_CONTEXT_JSON", - "start": 11266, - "end": 11283, + "start": 12429, + "end": 12446, "loc": { "start": { - "line": 250, + "line": 276, "column": 36 }, "end": { - "line": 250, + "line": 276, "column": 53 } } @@ -58019,15 +62230,15 @@ "binop": null, "updateContext": null }, - "start": 11283, - "end": 11284, + "start": 12446, + "end": 12447, "loc": { "start": { - "line": 250, + "line": 276, "column": 53 }, "end": { - "line": 250, + "line": 276, "column": 54 } } @@ -58044,15 +62255,15 @@ "postfix": false, "binop": null }, - "start": 11289, - "end": 11290, + "start": 12452, + "end": 12453, "loc": { "start": { - "line": 251, + "line": 277, "column": 4 }, "end": { - "line": 251, + "line": 277, "column": 5 } } @@ -58072,15 +62283,15 @@ "updateContext": null }, "value": "return", - "start": 11296, - "end": 11302, + "start": 12459, + "end": 12465, "loc": { "start": { - "line": 253, + "line": 279, "column": 4 }, "end": { - "line": 253, + "line": 279, "column": 10 } } @@ -58098,15 +62309,15 @@ "binop": null }, "value": "jsonld", - "start": 11303, - "end": 11309, + "start": 12466, + "end": 12472, "loc": { "start": { - "line": 253, + "line": 279, "column": 11 }, "end": { - "line": 253, + "line": 279, "column": 17 } } @@ -58124,15 +62335,15 @@ "binop": null, "updateContext": null }, - "start": 11309, - "end": 11310, + "start": 12472, + "end": 12473, "loc": { "start": { - "line": 253, + "line": 279, "column": 17 }, "end": { - "line": 253, + "line": 279, "column": 18 } } @@ -58149,15 +62360,15 @@ "postfix": false, "binop": null }, - "start": 11313, - "end": 11314, + "start": 12476, + "end": 12477, "loc": { "start": { - "line": 254, + "line": 280, "column": 2 }, "end": { - "line": 254, + "line": 280, "column": 3 } } @@ -58165,15 +62376,15 @@ { "type": "CommentBlock", "value": "*\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n ", - "start": 11318, - "end": 12359, + "start": 12481, + "end": 13522, "loc": { "start": { - "line": 256, + "line": 282, "column": 2 }, "end": { - "line": 271, + "line": 297, "column": 5 } } @@ -58191,15 +62402,15 @@ "binop": null }, "value": "toRDF", - "start": 12362, - "end": 12367, + "start": 13525, + "end": 13530, "loc": { "start": { - "line": 272, + "line": 298, "column": 2 }, "end": { - "line": 272, + "line": 298, "column": 7 } } @@ -58216,15 +62427,15 @@ "postfix": false, "binop": null }, - "start": 12367, - "end": 12368, + "start": 13530, + "end": 13531, "loc": { "start": { - "line": 272, + "line": 298, "column": 7 }, "end": { - "line": 272, + "line": 298, "column": 8 } } @@ -58242,15 +62453,15 @@ "binop": null }, "value": "baseIRI", - "start": 12368, - "end": 12375, + "start": 13531, + "end": 13538, "loc": { "start": { - "line": 272, + "line": 298, "column": 8 }, "end": { - "line": 272, + "line": 298, "column": 15 } } @@ -58269,15 +62480,15 @@ "updateContext": null }, "value": "=", - "start": 12376, - "end": 12377, + "start": 13539, + "end": 13540, "loc": { "start": { - "line": 272, + "line": 298, "column": 16 }, "end": { - "line": 272, + "line": 298, "column": 17 } } @@ -58296,15 +62507,15 @@ "updateContext": null }, "value": "", - "start": 12378, - "end": 12380, + "start": 13541, + "end": 13543, "loc": { "start": { - "line": 272, + "line": 298, "column": 18 }, "end": { - "line": 272, + "line": 298, "column": 20 } } @@ -58322,15 +62533,15 @@ "binop": null, "updateContext": null }, - "start": 12380, - "end": 12381, + "start": 13543, + "end": 13544, "loc": { "start": { - "line": 272, + "line": 298, "column": 20 }, "end": { - "line": 272, + "line": 298, "column": 21 } } @@ -58348,15 +62559,15 @@ "binop": null }, "value": "filePath", - "start": 12382, - "end": 12390, + "start": 13545, + "end": 13553, "loc": { "start": { - "line": 272, + "line": 298, "column": 22 }, "end": { - "line": 272, + "line": 298, "column": 30 } } @@ -58375,15 +62586,15 @@ "updateContext": null }, "value": "=", - "start": 12391, - "end": 12392, + "start": 13554, + "end": 13555, "loc": { "start": { - "line": 272, + "line": 298, "column": 31 }, "end": { - "line": 272, + "line": 298, "column": 32 } } @@ -58401,15 +62612,15 @@ "binop": null }, "value": "undefined", - "start": 12393, - "end": 12402, + "start": 13556, + "end": 13565, "loc": { "start": { - "line": 272, + "line": 298, "column": 33 }, "end": { - "line": 272, + "line": 298, "column": 42 } } @@ -58426,15 +62637,15 @@ "postfix": false, "binop": null }, - 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"start": 12426, - "end": 12427, + "start": 13589, + "end": 13590, "loc": { "start": { - "line": 273, + "line": 299, "column": 20 }, "end": { - "line": 273, + "line": 299, "column": 21 } } @@ -58560,15 +62771,15 @@ "updateContext": null }, "value": "this", - "start": 12428, - "end": 12432, + "start": 13591, + "end": 13595, "loc": { "start": { - "line": 273, + "line": 299, "column": 22 }, "end": { - "line": 273, + "line": 299, "column": 26 } } @@ -58586,15 +62797,15 @@ "binop": null, "updateContext": null }, - "start": 12432, - "end": 12433, + "start": 13595, + "end": 13596, "loc": { "start": { - "line": 273, + "line": 299, "column": 26 }, "end": { - "line": 273, + "line": 299, "column": 27 } } @@ -58612,15 +62823,15 @@ "binop": null }, "value": "asJSONLD", - "start": 12433, - "end": 12441, + "start": 13596, + "end": 13604, "loc": { "start": { - "line": 273, + "line": 299, "column": 27 }, "end": { - "line": 273, + "line": 299, "column": 35 } } @@ -58637,15 +62848,15 @@ "postfix": false, "binop": null }, - 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"start": 12928, - "end": 12934, + "start": 14091, + "end": 14097, "loc": { "start": { - "line": 284, + "line": 310, "column": 37 }, "end": { - "line": 284, + "line": 310, "column": 43 } } @@ -60318,15 +64529,15 @@ "binop": null, "updateContext": null }, - "start": 12934, - "end": 12935, + "start": 14097, + "end": 14098, "loc": { "start": { - "line": 284, + "line": 310, "column": 43 }, "end": { - "line": 284, + "line": 310, "column": 44 } } @@ -60345,15 +64556,15 @@ "updateContext": null }, "value": "application/n-quads", - "start": 12936, - "end": 12957, + "start": 14099, + "end": 14120, "loc": { "start": { - "line": 284, + "line": 310, "column": 45 }, "end": { - "line": 284, + "line": 310, "column": 66 } } @@ -60370,15 +64581,15 @@ "postfix": false, "binop": null }, - "start": 12958, - "end": 12959, + "start": 14121, + "end": 14122, "loc": { "start": { - "line": 284, + "line": 310, "column": 67 }, "end": { - "line": 284, + "line": 310, "column": 68 } } @@ -60395,15 +64606,15 @@ "postfix": false, "binop": null }, - "start": 12959, - "end": 12960, + "start": 14122, + "end": 14123, "loc": { "start": { - "line": 284, + "line": 310, "column": 68 }, "end": { - "line": 284, + "line": 310, "column": 69 } } @@ -60421,15 +64632,15 @@ "binop": null, "updateContext": null }, - "start": 12960, - "end": 12961, + "start": 14123, + "end": 14124, "loc": { "start": { - "line": 284, + "line": 310, "column": 69 }, "end": { - "line": 284, + "line": 310, "column": 70 } } @@ -60446,15 +64657,15 @@ "postfix": false, "binop": null }, - "start": 12964, - "end": 12965, + "start": 14127, + "end": 14128, "loc": { "start": { - "line": 285, + "line": 311, "column": 2 }, "end": { - "line": 285, + "line": 311, "column": 3 } } @@ -60471,15 +64682,15 @@ "postfix": false, "binop": null }, - "start": 12966, - "end": 12967, + "start": 14129, + "end": 14130, "loc": { "start": { - "line": 286, + "line": 312, "column": 0 }, "end": { - "line": 286, + "line": 312, "column": 1 } } @@ -60499,15 +64710,15 @@ "updateContext": null }, "value": "export", - "start": 12969, - "end": 12975, + "start": 14132, + "end": 14138, "loc": { "start": { - "line": 288, + "line": 314, "column": 0 }, "end": { - "line": 288, + "line": 314, "column": 6 } } @@ -60524,15 +64735,15 @@ "postfix": false, "binop": null }, - "start": 12976, - "end": 12977, + "start": 14139, + "end": 14140, "loc": { "start": { - "line": 288, + "line": 314, "column": 7 }, "end": { - "line": 288, + "line": 314, "column": 8 } } @@ -60550,15 +64761,15 @@ "binop": null }, "value": "PhyxWrapper", - "start": 12978, - "end": 12989, + "start": 14141, + "end": 14152, "loc": { "start": { - "line": 288, + "line": 314, "column": 9 }, "end": { - "line": 288, + "line": 314, "column": 20 } } @@ -60576,15 +64787,15 @@ "binop": null, "updateContext": null }, - "start": 12989, - "end": 12990, + "start": 14152, + "end": 14153, "loc": { "start": { - "line": 288, + "line": 314, "column": 20 }, "end": { - "line": 288, + "line": 314, "column": 21 } } @@ -60601,15 +64812,15 @@ "postfix": false, "binop": null }, - "start": 12991, - "end": 12992, + "start": 14154, + "end": 14155, "loc": { "start": { - "line": 288, + "line": 314, "column": 22 }, "end": { - "line": 288, + "line": 314, "column": 23 } } @@ -60627,15 +64838,15 @@ "binop": null, "updateContext": null }, - "start": 12992, - "end": 12993, + "start": 14155, + "end": 14156, "loc": { "start": { - "line": 288, + "line": 314, "column": 23 }, "end": { - "line": 288, + "line": 314, "column": 24 } } @@ -60653,15 +64864,15 @@ "binop": null, "updateContext": null }, - "start": 12994, - "end": 12994, + "start": 14157, + "end": 14157, "loc": { "start": { - "line": 289, + "line": 315, "column": 0 }, "end": { - "line": 289, + "line": 315, "column": 0 } } diff --git a/docs/ast/source/wrappers/SpecimenWrapper.js.json b/docs/ast/source/wrappers/SpecimenWrapper.js.json index de080a08..5b102473 100644 --- a/docs/ast/source/wrappers/SpecimenWrapper.js.json +++ b/docs/ast/source/wrappers/SpecimenWrapper.js.json @@ -1,28 +1,28 @@ { "type": "File", "start": 0, - "end": 8232, + "end": 8867, "loc": { "start": { "line": 1, "column": 0 }, "end": { - "line": 224, + "line": 243, "column": 0 } }, "program": { "type": "Program", "start": 0, - "end": 8232, + "end": 8867, "loc": { "start": { "line": 1, "column": 0 }, "end": { - "line": 224, + "line": 243, "column": 0 } }, @@ -70,9 +70,9 @@ "line": 1, "column": 25 }, - "identifierName": "LKT4H18NKRQE3" + "identifierName": "LXL9JK8J7MTDE" }, - "name": "LKT4H18NKRQE3" + "name": "LXL9JK8J7MTDE" } } ], @@ -211,9 +211,9 @@ "line": 2, "column": 29 }, - "identifierName": "LKT4H18NKRQE3" + "identifierName": "LXL9JK8J7MTDE" }, - "name": "LKT4H18NKRQE3" + "name": "LXL9JK8J7MTDE" } } ], @@ -261,9 +261,9 @@ "line": 3, "column": 25 }, - "identifierName": "LKT4H18N3GRL0" + "identifierName": "LXL9JK8JTNLQE" }, - "name": "LKT4H18N3GRL0" + "name": "LXL9JK8JTNLQE" } } ], @@ -402,9 +402,9 @@ "line": 4, "column": 45 }, - "identifierName": "LKT4H18N3GRL0" + "identifierName": "LXL9JK8JTNLQE" }, - "name": "LKT4H18N3GRL0" + "name": "LXL9JK8JTNLQE" } } ], @@ -521,9 +521,9 @@ "line": 6, "column": 25 }, - "identifierName": "LKT4H18N9PCKE" + "identifierName": "LXL9JK8JDZPL7" }, - "name": "LKT4H18N9PCKE" + "name": "LXL9JK8JDZPL7" } } ], @@ -662,9 +662,9 @@ "line": 7, "column": 42 }, - "identifierName": "LKT4H18N9PCKE" + "identifierName": "LXL9JK8JDZPL7" }, - "name": "LKT4H18N9PCKE" + "name": "LXL9JK8JDZPL7" } } ], @@ -691,14 +691,14 @@ { "type": "Identifier", "start": 1089, - "end": 8201, + "end": 8836, "loc": { "start": { "line": 24, "column": 0 }, "end": { - "line": 221, + "line": 240, "column": 1 } }, @@ -724,14 +724,14 @@ "body": { "type": "ClassBody", "start": 1111, - "end": 8201, + "end": 8836, "loc": { "start": { "line": 24, "column": 22 }, "end": { - "line": 221, + "line": 240, "column": 1 } }, @@ -1090,16 +1090,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", + "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", "start": 1351, - "end": 1632, + "end": 1449, "loc": { "start": { "line": 35, "column": 2 }, "end": { - "line": 40, + "line": 38, "column": 5 } } @@ -1108,15 +1108,15 @@ }, { "type": "ClassMethod", - "start": 1635, - "end": 3470, + "start": 1452, + "end": 1982, "loc": { "start": { - "line": 41, + "line": 39, "column": 2 }, "end": { - "line": 88, + "line": 52, "column": 3 } }, @@ -1124,20 +1124,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 1642, - "end": 1658, + "start": 1459, + "end": 1468, "loc": { "start": { - "line": 41, + "line": 39, "column": 9 }, "end": { - "line": 41, - "column": 25 + "line": 39, + "column": 18 }, - "identifierName": "fromOccurrenceID" + "identifierName": "normalize" }, - "name": "fromOccurrenceID" + "name": "normalize" }, "kind": "method", "id": null, @@ -1147,506 +1147,210 @@ "params": [ { "type": "Identifier", - "start": 1659, - "end": 1671, - "loc": { - "start": { - "line": 41, - "column": 26 - }, - "end": { - "line": 41, - "column": 38 - }, - "identifierName": "occurrenceID" - }, - "name": "occurrenceID" - }, - { - "type": "AssignmentPattern", - "start": 1673, - "end": 1708, + "start": 1469, + "end": 1477, "loc": { "start": { - "line": 41, - "column": 40 + "line": 39, + "column": 19 }, "end": { - "line": 41, - "column": 75 - } - }, - "left": { - "type": "Identifier", - "start": 1673, - "end": 1686, - "loc": { - "start": { - "line": 41, - "column": 40 - }, - "end": { - "line": 41, - "column": 53 - }, - "identifierName": "basisOfRecord" + "line": 39, + "column": 27 }, - "name": "basisOfRecord" + "identifierName": "specimen" }, - "right": { - "type": "StringLiteral", - "start": 1689, - "end": 1708, - "loc": { - "start": { - "line": 41, - "column": 56 - }, - "end": { - "line": 41, - "column": 75 - } - }, - "extra": { - "rawValue": "PreservedSpecimen", - "raw": "'PreservedSpecimen'" - }, - "value": "PreservedSpecimen" - } + "name": "specimen" } ], "body": { "type": "BlockStatement", - "start": 1710, - "end": 3470, + "start": 1479, + "end": 1982, "loc": { "start": { - "line": 41, - "column": 77 + "line": 39, + "column": 29 }, "end": { - "line": 88, + "line": 52, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 1782, - "end": 1809, + "start": 1485, + "end": 1531, "loc": { "start": { - "line": 43, + "line": 40, "column": 4 }, "end": { - "line": 43, - "column": 31 + "line": 40, + "column": 50 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1786, - "end": 1808, + "start": 1491, + "end": 1530, "loc": { "start": { - "line": 43, - "column": 8 + "line": 40, + "column": 10 }, "end": { - "line": 43, - "column": 30 + "line": 40, + "column": 49 } }, "id": { "type": "Identifier", - "start": 1786, - "end": 1793, + "start": 1491, + "end": 1498, "loc": { "start": { - "line": 43, - "column": 8 + "line": 40, + "column": 10 }, "end": { - "line": 43, - "column": 15 + "line": 40, + "column": 17 }, - "identifierName": "occurID" + "identifierName": "wrapped" }, - "name": "occurID", - "leadingComments": null + "name": "wrapped" }, "init": { - "type": "Identifier", - "start": 1796, - "end": 1808, - "loc": { - "start": { - "line": 43, - "column": 18 - }, - "end": { - "line": 43, - "column": 30 - }, - "identifierName": "occurrenceID" - }, - "name": "occurrenceID" - }, - "leadingComments": null - } - ], - "kind": "let", - "leadingComments": [ - { - "type": "CommentLine", - "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 1716, - "end": 1777, - "loc": { - "start": { - "line": 42, - "column": 4 - }, - "end": { - "line": 42, - "column": 65 - } - } - } - ] - }, - { - "type": "IfStatement", - "start": 1814, - "end": 1883, - "loc": { - "start": { - "line": 44, - "column": 4 - }, - "end": { - "line": 44, - "column": 73 - } - }, - "test": { - "type": "CallExpression", - "start": 1818, - "end": 1852, - "loc": { - "start": { - "line": 44, - "column": 8 - }, - "end": { - "line": 44, - "column": 42 - } - }, - "callee": { - "type": "MemberExpression", - "start": 1818, - "end": 1836, - "loc": { - "start": { - "line": 44, - "column": 8 - }, - "end": { - "line": 44, - "column": 26 - } - }, - "object": { - "type": "Identifier", - "start": 1818, - "end": 1825, - "loc": { - "start": { - "line": 44, - "column": 8 - }, - "end": { - "line": 44, - "column": 15 - }, - "identifierName": "occurID" - }, - "name": "occurID" - }, - "property": { - "type": "Identifier", - "start": 1826, - "end": 1836, - "loc": { - "start": { - "line": 44, - "column": 16 - }, - "end": { - "line": 44, - "column": 26 - }, - "identifierName": "startsWith" - }, - "name": "startsWith" - }, - "computed": false - }, - "arguments": [ - { - "type": "StringLiteral", - "start": 1837, - "end": 1851, - "loc": { - "start": { - "line": 44, - "column": 27 - }, - "end": { - "line": 44, - "column": 41 - } - }, - "extra": { - "rawValue": "urn:catalog:", - "raw": "'urn:catalog:'" - }, - "value": "urn:catalog:" - } - ] - }, - "consequent": { - "type": "ExpressionStatement", - "start": 1854, - "end": 1883, - "loc": { - "start": { - "line": 44, - "column": 44 - }, - "end": { - "line": 44, - "column": 73 - } - }, - "expression": { - "type": "AssignmentExpression", - "start": 1854, - "end": 1882, - "loc": { - "start": { - "line": 44, - "column": 44 - }, - "end": { - "line": 44, - "column": 72 - } - }, - "operator": "=", - "left": { - "type": "Identifier", - "start": 1854, - "end": 1861, - "loc": { - "start": { - "line": 44, - "column": 44 - }, - "end": { - "line": 44, - "column": 51 - }, - "identifierName": "occurID" - }, - "name": "occurID" - }, - "right": { - "type": "CallExpression", - "start": 1864, - "end": 1882, + "type": "NewExpression", + "start": 1501, + "end": 1530, "loc": { "start": { - "line": 44, - "column": 54 + "line": 40, + "column": 20 }, "end": { - "line": 44, - "column": 72 + "line": 40, + "column": 49 } }, "callee": { - "type": "MemberExpression", - "start": 1864, - "end": 1878, + "type": "Identifier", + "start": 1505, + "end": 1520, "loc": { "start": { - "line": 44, - "column": 54 + "line": 40, + "column": 24 }, "end": { - "line": 44, - "column": 68 - } - }, - "object": { - "type": "Identifier", - "start": 1864, - "end": 1871, - "loc": { - "start": { - "line": 44, - "column": 54 - }, - "end": { - "line": 44, - "column": 61 - }, - "identifierName": "occurID" - }, - "name": "occurID" - }, - "property": { - "type": "Identifier", - "start": 1872, - "end": 1878, - "loc": { - "start": { - "line": 44, - "column": 62 - }, - "end": { - "line": 44, - "column": 68 - }, - "identifierName": "substr" + "line": 40, + "column": 39 }, - "name": "substr" + "identifierName": "SpecimenWrapper" }, - "computed": false + "name": "SpecimenWrapper" }, "arguments": [ { - "type": "NumericLiteral", - "start": 1879, - "end": 1881, + "type": "Identifier", + "start": 1521, + "end": 1529, "loc": { "start": { - "line": 44, - "column": 69 + "line": 40, + "column": 40 }, "end": { - "line": 44, - "column": 71 - } - }, - "extra": { - "rawValue": 12, - "raw": "12" + "line": 40, + "column": 48 + }, + "identifierName": "specimen" }, - "value": 12 + "name": "specimen" } ] } - }, - "trailingComments": null - }, - "alternate": null, - "trailingComments": [ - { - "type": "CommentLine", - "value": " Prepare the specimen.", - "start": 1889, - "end": 1913, - "loc": { - "start": { - "line": 46, - "column": 4 - }, - "end": { - "line": 46, - "column": 28 - } - } } - ] + ], + "kind": "const" }, { "type": "VariableDeclaration", - "start": 1918, - "end": 2060, + "start": 1536, + "end": 1875, "loc": { "start": { - "line": 47, + "line": 41, "column": 4 }, "end": { - "line": 51, + "line": 49, "column": 6 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1924, - "end": 2059, + "start": 1542, + "end": 1874, "loc": { "start": { - "line": 47, + "line": 41, "column": 10 }, "end": { - "line": 51, + "line": 49, "column": 5 } }, "id": { "type": "Identifier", - "start": 1924, - "end": 1932, + "start": 1542, + "end": 1560, "loc": { "start": { - "line": 47, + "line": 41, "column": 10 }, "end": { - "line": 47, - "column": 18 + "line": 41, + "column": 28 }, - "identifierName": "specimen" + "identifierName": "normalizedSpecimen" }, - "name": "specimen", - "leadingComments": null + "name": "normalizedSpecimen" }, "init": { "type": "ObjectExpression", - "start": 1935, - "end": 2059, + "start": 1563, + "end": 1874, "loc": { "start": { - "line": 47, - "column": 21 + "line": 41, + "column": 31 }, "end": { - "line": 51, + "line": 49, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 1943, - "end": 1981, + "start": 1571, + "end": 1609, "loc": { "start": { - "line": 48, + "line": 42, "column": 6 }, "end": { - "line": 48, + "line": 42, "column": 44 } }, @@ -1655,15 +1359,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 1943, - "end": 1950, + "start": 1571, + "end": 1578, "loc": { "start": { - "line": 48, + "line": 42, "column": 6 }, "end": { - "line": 48, + "line": 42, "column": 13 } }, @@ -1675,29 +1379,29 @@ }, "value": { "type": "MemberExpression", - "start": 1952, - "end": 1981, + "start": 1580, + "end": 1609, "loc": { "start": { - "line": 48, + "line": 42, "column": 15 }, "end": { - "line": 48, + "line": 42, "column": 44 } }, "object": { "type": "Identifier", - "start": 1952, - "end": 1967, + "start": 1580, + "end": 1595, "loc": { "start": { - "line": 48, + "line": 42, "column": 15 }, "end": { - "line": 48, + "line": 42, "column": 30 }, "identifierName": "SpecimenWrapper" @@ -1706,15 +1410,15 @@ }, "property": { "type": "Identifier", - "start": 1968, - "end": 1981, + "start": 1596, + "end": 1609, "loc": { "start": { - "line": 48, + "line": 42, "column": 31 }, "end": { - "line": 48, + "line": 42, "column": 44 }, "identifierName": "TYPE_SPECIMEN" @@ -1726,16 +1430,101 @@ }, { "type": "ObjectProperty", - "start": 1989, - "end": 2023, + "start": 1617, + "end": 1637, "loc": { "start": { - "line": 49, + "line": 43, "column": 6 }, "end": { - "line": 49, - "column": 40 + "line": 43, + "column": 26 + } + }, + "method": false, + "shorthand": false, + "computed": false, + "key": { + "type": "Identifier", + "start": 1617, + "end": 1622, + "loc": { + "start": { + "line": 43, + "column": 6 + }, + "end": { + "line": 43, + "column": 11 + }, + "identifierName": "label" + }, + "name": "label" + }, + "value": { + "type": "MemberExpression", + "start": 1624, + "end": 1637, + "loc": { + "start": { + "line": 43, + "column": 13 + }, + "end": { + "line": 43, + "column": 26 + } + }, + "object": { + "type": "Identifier", + "start": 1624, + "end": 1631, + "loc": { + "start": { + "line": 43, + "column": 13 + }, + "end": { + "line": 43, + "column": 20 + }, + "identifierName": "wrapped" + }, + "name": "wrapped" + }, + "property": { + "type": "Identifier", + "start": 1632, + "end": 1637, + "loc": { + "start": { + "line": 43, + "column": 21 + }, + "end": { + "line": 43, + "column": 26 + }, + "identifierName": "label" + }, + "name": "label" + }, + "computed": false + } + }, + { + "type": "ObjectProperty", + "start": 1645, + "end": 1687, + "loc": { + "start": { + "line": 44, + "column": 6 + }, + "end": { + "line": 44, + "column": 48 } }, "method": false, @@ -1743,15 +1532,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 1989, - "end": 2008, + "start": 1645, + "end": 1664, "loc": { "start": { - "line": 49, + "line": 44, "column": 6 }, "end": { - "line": 49, + "line": 44, "column": 25 } }, @@ -1762,35 +1551,68 @@ "value": "dwc:basisOfRecord" }, "value": { - "type": "Identifier", - "start": 2010, - "end": 2023, + "type": "MemberExpression", + "start": 1666, + "end": 1687, "loc": { "start": { - "line": 49, + "line": 44, "column": 27 }, "end": { - "line": 49, - "column": 40 + "line": 44, + "column": 48 + } + }, + "object": { + "type": "Identifier", + "start": 1666, + "end": 1673, + "loc": { + "start": { + "line": 44, + "column": 27 + }, + "end": { + "line": 44, + "column": 34 + }, + "identifierName": "wrapped" }, - "identifierName": "basisOfRecord" + "name": "wrapped" }, - "name": "basisOfRecord" + "property": { + "type": "Identifier", + "start": 1674, + "end": 1687, + "loc": { + "start": { + "line": 44, + "column": 35 + }, + "end": { + "line": 44, + "column": 48 + }, + "identifierName": "basisOfRecord" + }, + "name": "basisOfRecord" + }, + "computed": false } }, { "type": "ObjectProperty", - "start": 2031, - "end": 2052, + "start": 1695, + "end": 1729, "loc": { "start": { - "line": 50, + "line": 45, "column": 6 }, "end": { - "line": 50, - "column": 27 + "line": 45, + "column": 40 } }, "method": false, @@ -1798,15 +1620,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2031, - "end": 2043, + "start": 1695, + "end": 1707, "loc": { "start": { - "line": 50, + "line": 45, "column": 6 }, "end": { - "line": 50, + "line": 45, "column": 18 }, "identifierName": "occurrenceID" @@ -1814,692 +1636,802 @@ "name": "occurrenceID" }, "value": { - "type": "Identifier", - "start": 2045, - "end": 2052, + "type": "MemberExpression", + "start": 1709, + "end": 1729, "loc": { "start": { - "line": 50, + "line": 45, "column": 20 }, "end": { - "line": 50, - "column": 27 + "line": 45, + "column": 40 + } + }, + "object": { + "type": "Identifier", + "start": 1709, + "end": 1716, + "loc": { + "start": { + "line": 45, + "column": 20 + }, + "end": { + "line": 45, + "column": 27 + }, + "identifierName": "wrapped" }, - "identifierName": "occurID" + "name": "wrapped" }, - "name": "occurID" + "property": { + "type": "Identifier", + "start": 1717, + "end": 1729, + "loc": { + "start": { + "line": 45, + "column": 28 + }, + "end": { + "line": 45, + "column": 40 + }, + "identifierName": "occurrenceID" + }, + "name": "occurrenceID" + }, + "computed": false } - } - ] - }, - "leadingComments": null - } - ], - "kind": "const", - "leadingComments": [ - { - "type": "CommentLine", - "value": " Prepare the specimen.", - "start": 1889, - "end": 1913, - "loc": { - "start": { - "line": 46, - "column": 4 - }, - "end": { - "line": 46, - "column": 28 - } - } - } - ], - "trailingComments": [ - { - "type": "CommentLine", - "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2066, - "end": 2139, - "loc": { - "start": { - "line": 53, - "column": 4 - }, - "end": { - "line": 53, - "column": 77 - } - } - }, - { - "type": "CommentLine", - "value": " URL instead. 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The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", + "start": 1986, + "end": 2267, + "loc": { + "start": { + "line": 54, + "column": 2 + }, + "end": { + "line": 59, + "column": 5 + } + } + } + ] + }, + { + "type": "ClassMethod", + "start": 2270, + "end": 4105, + "loc": { + "start": { + "line": 60, + "column": 2 + }, + "end": { + "line": 107, + "column": 3 + } + }, + "static": true, + "computed": false, + "key": { + "type": "Identifier", + "start": 2277, + "end": 2293, + "loc": { + "start": { + "line": 60, + "column": 9 + }, + "end": { + "line": 60, + "column": 25 + }, + "identifierName": "fromOccurrenceID" + }, + "name": "fromOccurrenceID" + }, + "kind": "method", + "id": null, + "generator": false, + "expression": false, + "async": false, + "params": [ + { + "type": "Identifier", + "start": 2294, + "end": 2306, + "loc": { + "start": { + "line": 60, + "column": 26 + }, + "end": { + "line": 60, + "column": 38 + }, + "identifierName": "occurrenceID" + }, + "name": "occurrenceID" + }, + { + "type": "AssignmentPattern", + "start": 2308, + "end": 2343, + "loc": { + "start": { + "line": 60, + "column": 40 + }, + "end": { + "line": 60, + "column": 75 + } + }, + "left": { + "type": "Identifier", + "start": 2308, + "end": 2321, + "loc": { + "start": { + "line": 60, + "column": 40 + }, + "end": { + "line": 60, + "column": 53 + }, + "identifierName": "basisOfRecord" + }, + "name": "basisOfRecord" + }, + "right": { + "type": "StringLiteral", + "start": 2324, + "end": 2343, + "loc": { + "start": { + "line": 60, + "column": 56 + }, + "end": { + "line": 60, + "column": 75 + } + }, + "extra": { + "rawValue": "PreservedSpecimen", + "raw": "'PreservedSpecimen'" + }, + "value": "PreservedSpecimen" + } + } + ], + "body": { + "type": "BlockStatement", + "start": 2345, + "end": 4105, + "loc": { + "start": { + "line": 60, + "column": 77 + }, + "end": { + "line": 107, + "column": 3 + } + }, + "body": [ + { + "type": "VariableDeclaration", + "start": 2417, + "end": 2444, + "loc": { + "start": { + "line": 62, + "column": 4 + }, + "end": { + "line": 62, + "column": 31 + } + }, + "declarations": [ + { + "type": "VariableDeclarator", + "start": 2421, + "end": 2443, + "loc": { + "start": { + "line": 62, + "column": 8 + }, + "end": { + "line": 62, + "column": 30 + } + }, + "id": { + "type": "Identifier", + "start": 2421, + "end": 2428, "loc": { "start": { - 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} - ] + ] + } }, { "type": "ReturnStatement", - "start": 4603, - "end": 4620, + "start": 4085, + "end": 4101, "loc": { "start": { - "line": 119, + "line": 106, "column": 4 }, "end": { - "line": 119, - "column": 21 + "line": 106, + "column": 20 } }, "argument": { "type": "Identifier", - "start": 4610, - "end": 4619, + "start": 4092, + "end": 4100, "loc": { "start": { - "line": 119, + "line": 106, "column": 11 }, "end": { - "line": 119, - "column": 20 + "line": 106, + "column": 19 }, - "identifierName": "undefined" + "identifierName": "specimen" }, - "name": "undefined" + "name": "specimen" } } ], @@ -6117,16 +5401,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Get the institutionCode if present.\n ", - "start": 4044, - "end": 4094, + "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", + "start": 1986, + "end": 2267, "loc": { "start": { - "line": 106, + "line": 54, "column": 2 }, "end": { - "line": 108, + "line": 59, "column": 5 } } @@ -6135,16 +5419,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Get the collectionCode if present.\n ", - "start": 4628, - "end": 4677, + "value": "*\n * Get the catalogNumber if present.\n ", + "start": 4109, + "end": 4157, "loc": { "start": { - "line": 122, + "line": 109, "column": 2 }, "end": { - "line": 124, + "line": 111, "column": 5 } } @@ -6153,15 +5437,15 @@ }, { "type": "ClassMethod", - "start": 4680, - "end": 5201, + "start": 4160, + "end": 4675, "loc": { "start": { - "line": 125, + "line": 112, "column": 2 }, "end": { - "line": 136, + "line": 123, "column": 3 } }, @@ -6169,20 +5453,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 4684, - "end": 4698, + "start": 4164, + "end": 4177, "loc": { "start": { - "line": 125, + "line": 112, "column": 6 }, "end": { - "line": 125, - "column": 20 + "line": 112, + "column": 19 }, - "identifierName": "collectionCode" + "identifierName": "catalogNumber" }, - "name": "collectionCode" + "name": "catalogNumber" }, "kind": "get", "id": null, @@ -6192,58 +5476,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4701, - "end": 5201, + "start": 4180, + "end": 4675, "loc": { "start": { - "line": 125, - "column": 23 + "line": 112, + "column": 22 }, "end": { - "line": 136, + "line": 123, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4775, - "end": 4853, + "start": 4253, + "end": 4329, "loc": { "start": { - "line": 127, + "line": 114, "column": 4 }, "end": { - "line": 127, - "column": 82 + "line": 114, + "column": 80 } }, "test": { "type": "CallExpression", - "start": 4779, - "end": 4815, + "start": 4257, + "end": 4292, "loc": { "start": { - "line": 127, + "line": 114, "column": 8 }, "end": { - "line": 127, - "column": 44 + "line": 114, + "column": 43 } }, "callee": { "type": "Identifier", - "start": 4779, - "end": 4782, + "start": 4257, + "end": 4260, "loc": { "start": { - "line": 127, + "line": 114, "column": 8 }, "end": { - "line": 127, + "line": 114, "column": 11 }, "identifierName": "has" @@ -6254,44 +5538,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4783, - "end": 4796, + "start": 4261, + "end": 4274, "loc": { "start": { - "line": 127, + "line": 114, "column": 12 }, "end": { - "line": 127, + "line": 114, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4783, - "end": 4787, + "start": 4261, + "end": 4265, "loc": { "start": { - "line": 127, + "line": 114, "column": 12 }, "end": { - "line": 127, + "line": 114, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4788, - "end": 4796, + "start": 4266, + "end": 4274, "loc": { "start": { - "line": 127, + "line": 114, "column": 17 }, "end": { - "line": 127, + "line": 114, "column": 25 }, "identifierName": "specimen" @@ -6302,96 +5586,96 @@ }, { "type": "StringLiteral", - "start": 4798, - "end": 4814, + "start": 4276, + "end": 4291, "loc": { "start": { - "line": 127, + "line": 114, "column": 27 }, "end": { - "line": 127, - "column": 43 + "line": 114, + "column": 42 } }, "extra": { - "rawValue": "collectionCode", - "raw": "'collectionCode'" + "rawValue": "catalogNumber", + "raw": "'catalogNumber'" }, - "value": "collectionCode" + "value": "catalogNumber" } ], "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 4817, - "end": 4853, + "start": 4294, + "end": 4329, "loc": { "start": { - "line": 127, - "column": 46 + "line": 114, + "column": 45 }, "end": { - "line": 127, - "column": 82 + "line": 114, + "column": 80 } }, "argument": { "type": "MemberExpression", - "start": 4824, - "end": 4852, + "start": 4301, + "end": 4328, "loc": { "start": { - "line": 127, - "column": 53 + "line": 114, + "column": 52 }, "end": { - "line": 127, - "column": 81 + "line": 114, + "column": 79 } }, "object": { "type": "MemberExpression", - "start": 4824, - "end": 4837, + "start": 4301, + "end": 4314, "loc": { "start": { - "line": 127, - "column": 53 + "line": 114, + "column": 52 }, "end": { - "line": 127, - "column": 66 + "line": 114, + "column": 65 } }, "object": { "type": "ThisExpression", - "start": 4824, - "end": 4828, + "start": 4301, + "end": 4305, "loc": { "start": { - "line": 127, - "column": 53 + "line": 114, + "column": 52 }, "end": { - "line": 127, - "column": 57 + "line": 114, + "column": 56 } } }, "property": { "type": "Identifier", - "start": 4829, - "end": 4837, + "start": 4306, + "end": 4314, "loc": { "start": { - "line": 127, - "column": 58 + "line": 114, + "column": 57 }, "end": { - "line": 127, - "column": 66 + "line": 114, + "column": 65 }, "identifierName": "specimen" }, @@ -6401,20 +5685,20 @@ }, "property": { "type": "Identifier", - "start": 4838, - "end": 4852, + "start": 4315, + "end": 4328, "loc": { "start": { - "line": 127, - "column": 67 + "line": 114, + "column": 66 }, "end": { - "line": 127, - "column": 81 + "line": 114, + "column": 79 }, - "identifierName": "collectionCode" + "identifierName": "catalogNumber" }, - "name": "collectionCode" + "name": "catalogNumber" }, "computed": false }, @@ -6424,17 +5708,17 @@ "leadingComments": [ { "type": "CommentLine", - "value": " Get the collection code from the specimen object if present.", - "start": 4707, - "end": 4770, + "value": " Get the catalog number from the specimen object if present.", + "start": 4186, + "end": 4248, "loc": { "start": { - "line": 126, + "line": 113, "column": 4 }, "end": { - "line": 126, - "column": 67 + "line": 113, + "column": 66 } } } @@ -6442,33 +5726,33 @@ "trailingComments": [ { "type": "CommentLine", - "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4859, - "end": 4931, + "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", + "start": 4335, + "end": 4406, "loc": { "start": { - "line": 129, + "line": 116, "column": 4 }, "end": { - "line": 129, - "column": 76 + "line": 116, + "column": 75 } } }, { "type": "CommentLine", - "value": " occurrenceID from there.", - "start": 4936, - "end": 4963, + "value": " catalogNumber from there.", + "start": 4411, + "end": 4439, "loc": { "start": { - "line": 130, + "line": 117, "column": 4 }, "end": { - "line": 130, - "column": 31 + "line": 117, + "column": 32 } } } @@ -6476,43 +5760,43 @@ }, { "type": "IfStatement", - "start": 4968, - "end": 5175, + "start": 4444, + "end": 4649, "loc": { "start": { - "line": 131, + "line": 118, "column": 4 }, "end": { - "line": 134, + "line": 121, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4972, - "end": 5006, + "start": 4448, + "end": 4482, "loc": { "start": { - "line": 131, + "line": 118, "column": 8 }, "end": { - "line": 131, + "line": 118, "column": 42 } }, "callee": { "type": "Identifier", - "start": 4972, - "end": 4975, + "start": 4448, + "end": 4451, "loc": { "start": { - "line": 131, + "line": 118, "column": 8 }, "end": { - "line": 131, + "line": 118, "column": 11 }, "identifierName": "has" @@ -6523,44 +5807,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4976, - "end": 4989, + "start": 4452, + "end": 4465, "loc": { "start": { - "line": 131, + "line": 118, "column": 12 }, "end": { - "line": 131, + "line": 118, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4976, - "end": 4980, + "start": 4452, + "end": 4456, "loc": { "start": { - "line": 131, + "line": 118, "column": 12 }, "end": { - "line": 131, + "line": 118, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4981, - "end": 4989, + "start": 4457, + "end": 4465, "loc": { "start": { - "line": 131, + "line": 118, "column": 17 }, "end": { - "line": 131, + "line": 118, "column": 25 }, "identifierName": "specimen" @@ -6571,15 +5855,15 @@ }, { "type": "StringLiteral", - "start": 4991, - "end": 5005, + "start": 4467, + "end": 4481, "loc": { "start": { - "line": 131, + "line": 118, "column": 27 }, "end": { - "line": 131, + "line": 118, "column": 41 } }, @@ -6594,59 +5878,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5008, - "end": 5175, + "start": 4484, + "end": 4649, "loc": { "start": { - "line": 131, + "line": 118, "column": 44 }, "end": { - "line": 134, + "line": 121, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 5016, - "end": 5094, + "start": 4492, + "end": 4570, "loc": { "start": { - "line": 132, + "line": 119, "column": 6 }, "end": { - "line": 132, + "line": 119, "column": 84 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5022, - "end": 5093, + "start": 4498, + "end": 4569, "loc": { "start": { - "line": 132, + "line": 119, "column": 12 }, "end": { - "line": 132, + "line": 119, "column": 83 } }, "id": { "type": "Identifier", - "start": 5022, - "end": 5030, + "start": 4498, + "end": 4506, "loc": { "start": { - "line": 132, + "line": 119, "column": 12 }, "end": { - "line": 132, + "line": 119, "column": 20 }, "identifierName": "specimen" @@ -6655,43 +5939,43 @@ }, "init": { "type": "CallExpression", - "start": 5033, - "end": 5093, + "start": 4509, + "end": 4569, "loc": { "start": { - "line": 132, + "line": 119, "column": 23 }, "end": { - "line": 132, + "line": 119, "column": 83 } }, "callee": { "type": "MemberExpression", - "start": 5033, - "end": 5065, + "start": 4509, + "end": 4541, "loc": { "start": { - "line": 132, + "line": 119, "column": 23 }, "end": { - "line": 132, + "line": 119, "column": 55 } }, "object": { "type": "Identifier", - "start": 5033, - "end": 5048, + "start": 4509, + "end": 4524, "loc": { "start": { - "line": 132, + "line": 119, "column": 23 }, "end": { - "line": 132, + "line": 119, "column": 38 }, "identifierName": "SpecimenWrapper" @@ -6700,15 +5984,15 @@ }, "property": { "type": "Identifier", - "start": 5049, - "end": 5065, + "start": 4525, + "end": 4541, "loc": { "start": { - "line": 132, + "line": 119, "column": 39 }, "end": { - "line": 132, + "line": 119, "column": 55 }, "identifierName": "fromOccurrenceID" @@ -6720,58 +6004,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 5066, - "end": 5092, + "start": 4542, + "end": 4568, "loc": { "start": { - "line": 132, + "line": 119, "column": 56 }, "end": { - "line": 132, + "line": 119, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 5066, - "end": 5079, + "start": 4542, + "end": 4555, "loc": { "start": { - "line": 132, + "line": 119, "column": 56 }, "end": { - "line": 132, + "line": 119, "column": 69 } }, "object": { "type": "ThisExpression", - "start": 5066, - "end": 5070, + "start": 4542, + "end": 4546, "loc": { "start": { - "line": 132, + "line": 119, "column": 56 }, "end": { - "line": 132, + "line": 119, "column": 60 } } }, "property": { "type": "Identifier", - "start": 5071, - "end": 5079, + "start": 4547, + "end": 4555, "loc": { "start": { - "line": 132, + "line": 119, "column": 61 }, "end": { - "line": 132, + "line": 119, "column": 69 }, "identifierName": "specimen" @@ -6782,15 +6066,15 @@ }, "property": { "type": "Identifier", - "start": 5080, - "end": 5092, + "start": 4556, + "end": 4568, "loc": { "start": { - "line": 132, + "line": 119, "column": 70 }, "end": { - "line": 132, + "line": 119, "column": 82 }, "identifierName": "occurrenceID" @@ -6807,43 +6091,43 @@ }, { "type": "IfStatement", - "start": 5101, - "end": 5169, + "start": 4577, + "end": 4643, "loc": { "start": { - "line": 133, + "line": 120, "column": 6 }, "end": { - "line": 133, - "column": 74 + "line": 120, + "column": 72 } }, "test": { "type": "CallExpression", - "start": 5105, - "end": 5136, + "start": 4581, + "end": 4611, "loc": { "start": { - "line": 133, + "line": 120, "column": 10 }, "end": { - "line": 133, - "column": 41 + "line": 120, + "column": 40 } }, "callee": { "type": "Identifier", - "start": 5105, - "end": 5108, + "start": 4581, + "end": 4584, "loc": { "start": { - "line": 133, + "line": 120, "column": 10 }, "end": { - "line": 133, + "line": 120, "column": 13 }, "identifierName": "has" @@ -6853,15 +6137,15 @@ "arguments": [ { "type": "Identifier", - "start": 5109, - "end": 5117, + "start": 4585, + "end": 4593, "loc": { "start": { - "line": 133, + "line": 120, "column": 14 }, "end": { - "line": 133, + "line": 120, "column": 22 }, "identifierName": "specimen" @@ -6870,66 +6154,66 @@ }, { "type": "StringLiteral", - "start": 5119, - "end": 5135, + "start": 4595, + "end": 4610, "loc": { "start": { - "line": 133, + "line": 120, "column": 24 }, "end": { - "line": 133, - "column": 40 + "line": 120, + "column": 39 } }, "extra": { - "rawValue": "collectionCode", - "raw": "'collectionCode'" + "rawValue": "catalogNumber", + "raw": "'catalogNumber'" }, - "value": "collectionCode" + "value": "catalogNumber" } ] }, "consequent": { "type": "ReturnStatement", - "start": 5138, - "end": 5169, + "start": 4613, + "end": 4643, "loc": { "start": { - "line": 133, - "column": 43 + "line": 120, + "column": 42 }, "end": { - "line": 133, - "column": 74 + "line": 120, + "column": 72 } }, "argument": { "type": "MemberExpression", - "start": 5145, - "end": 5168, + "start": 4620, + "end": 4642, "loc": { "start": { - "line": 133, - "column": 50 + "line": 120, + "column": 49 }, "end": { - "line": 133, - "column": 73 + "line": 120, + "column": 71 } }, "object": { "type": "Identifier", - "start": 5145, - "end": 5153, + "start": 4620, + "end": 4628, "loc": { "start": { - "line": 133, - "column": 50 + "line": 120, + "column": 49 }, "end": { - "line": 133, - "column": 58 + "line": 120, + "column": 57 }, "identifierName": "specimen" }, @@ -6937,20 +6221,20 @@ }, "property": { "type": "Identifier", - "start": 5154, - "end": 5168, + "start": 4629, + "end": 4642, "loc": { "start": { - "line": 133, - "column": 59 + "line": 120, + "column": 58 }, "end": { - "line": 133, - "column": 73 + "line": 120, + "column": 71 }, - "identifierName": "collectionCode" + "identifierName": "catalogNumber" }, - "name": "collectionCode" + "name": "catalogNumber" }, "computed": false } @@ -6964,33 +6248,33 @@ "leadingComments": [ { "type": "CommentLine", - "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4859, - "end": 4931, + "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", + "start": 4335, + "end": 4406, "loc": { "start": { - "line": 129, + "line": 116, "column": 4 }, "end": { - "line": 129, - "column": 76 + "line": 116, + "column": 75 } } }, { "type": "CommentLine", - "value": " occurrenceID from there.", - "start": 4936, - "end": 4963, + "value": " catalogNumber from there.", + "start": 4411, + "end": 4439, "loc": { "start": { - "line": 130, + "line": 117, "column": 4 }, "end": { - "line": 130, - "column": 31 + "line": 117, + "column": 32 } } } @@ -6998,29 +6282,29 @@ }, { "type": "ReturnStatement", - "start": 5180, - "end": 5197, + "start": 4654, + "end": 4671, "loc": { "start": { - "line": 135, + "line": 122, "column": 4 }, "end": { - "line": 135, + "line": 122, "column": 21 } }, "argument": { "type": "Identifier", - "start": 5187, - "end": 5196, + "start": 4661, + "end": 4670, "loc": { "start": { - "line": 135, + "line": 122, "column": 11 }, "end": { - "line": 135, + "line": 122, "column": 20 }, "identifierName": "undefined" @@ -7035,16 +6319,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Get the collectionCode if present.\n ", - "start": 4628, - "end": 4677, + "value": "*\n * Get the catalogNumber if present.\n ", + "start": 4109, + "end": 4157, "loc": { "start": { - "line": 122, + "line": 109, "column": 2 }, "end": { - "line": 124, + "line": 111, "column": 5 } } @@ -7053,16 +6337,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5205, - "end": 5464, + "value": "*\n * Get the institutionCode if present.\n ", + "start": 4679, + "end": 4729, "loc": { "start": { - "line": 138, + "line": 125, "column": 2 }, "end": { - "line": 143, + "line": 127, "column": 5 } } @@ -7071,15 +6355,15 @@ }, { "type": "ClassMethod", - "start": 5467, - "end": 6507, + "start": 4732, + "end": 5259, "loc": { "start": { - "line": 144, + "line": 128, "column": 2 }, "end": { - "line": 166, + "line": 139, "column": 3 } }, @@ -7087,20 +6371,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 5471, - "end": 5483, + "start": 4736, + "end": 4751, "loc": { "start": { - "line": 144, + "line": 128, "column": 6 }, "end": { - "line": 144, - "column": 18 + "line": 128, + "column": 21 }, - "identifierName": "occurrenceID" + "identifierName": "institutionCode" }, - "name": "occurrenceID" + "name": "institutionCode" }, "kind": "get", "id": null, @@ -7110,499 +6394,249 @@ "params": [], "body": { "type": "BlockStatement", - "start": 5486, - "end": 6507, + "start": 4754, + "end": 5259, "loc": { "start": { - "line": 144, - "column": 21 + "line": 128, + "column": 24 }, "end": { - "line": 166, + "line": 139, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 5537, - "end": 5676, + "start": 4829, + "end": 4909, "loc": { "start": { - "line": 146, + "line": 130, "column": 4 }, "end": { - "line": 148, - "column": 5 + "line": 130, + "column": 84 } }, "test": { - "type": "LogicalExpression", - "start": 5541, - "end": 5619, + "type": "CallExpression", + "start": 4833, + "end": 4870, "loc": { "start": { - "line": 146, + "line": 130, "column": 8 }, "end": { - "line": 146, - "column": 86 + "line": 130, + "column": 45 } }, - "left": { - "type": "CallExpression", - "start": 5541, - "end": 5575, + "callee": { + "type": "Identifier", + "start": 4833, + "end": 4836, "loc": { "start": { - "line": 146, + "line": 130, "column": 8 }, "end": { - "line": 146, - "column": 42 - } + "line": 130, + "column": 11 + }, + "identifierName": "has" }, - "callee": { - "type": "Identifier", - "start": 5541, - "end": 5544, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 4837, + "end": 4850, "loc": { "start": { - "line": 146, - "column": 8 + "line": 130, + "column": 12 }, "end": { - "line": 146, - "column": 11 - }, - "identifierName": "has" + "line": 130, + "column": 25 + } }, - "name": "has", - "leadingComments": null - }, - "arguments": [ - { - "type": "MemberExpression", - "start": 5545, - "end": 5558, + "object": { + "type": "ThisExpression", + "start": 4837, + "end": 4841, "loc": { "start": { - "line": 146, + "line": 130, "column": 12 }, "end": { - "line": 146, - "column": 25 - } - }, - "object": { - "type": "ThisExpression", - "start": 5545, - "end": 5549, - "loc": { - "start": { - "line": 146, - "column": 12 - }, - "end": { - 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"start": 6605, - "end": 6644, + "start": 5414, + "end": 5450, "loc": { "start": { - "line": 172, + "line": 146, "column": 8 }, "end": { - "line": 172, - "column": 47 + "line": 146, + "column": 44 } }, "callee": { "type": "Identifier", - "start": 6605, - "end": 6608, + "start": 5414, + "end": 5417, "loc": { "start": { - "line": 172, + "line": 146, "column": 8 }, "end": { - "line": 172, + "line": 146, "column": 11 }, "identifierName": "has" }, - "name": "has" + "name": "has", + "leadingComments": null }, "arguments": [ { "type": "MemberExpression", - "start": 6609, - "end": 6622, + "start": 5418, + "end": 5431, "loc": { "start": { - "line": 172, + "line": 146, "column": 12 }, "end": { - "line": 172, + "line": 146, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 6609, - "end": 6613, + "start": 5418, + "end": 5422, "loc": { "start": { - "line": 172, + "line": 146, "column": 12 }, "end": { - "line": 172, + "line": 146, "column": 16 } } }, "property": { "type": "Identifier", - "start": 6614, - "end": 6622, + "start": 5423, + "end": 5431, "loc": { "start": { - "line": 172, + "line": 146, "column": 17 }, "end": { - "line": 172, + "line": 146, "column": 25 }, "identifierName": "specimen" @@ -9867,95 +7422,96 @@ }, { "type": "StringLiteral", - "start": 6624, - "end": 6643, + "start": 5433, + "end": 5449, "loc": { "start": { - "line": 172, + "line": 146, "column": 27 }, "end": { - "line": 172, - "column": 46 + "line": 146, + "column": 43 } }, "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "rawValue": "collectionCode", + "raw": "'collectionCode'" }, - "value": "dwc:basisOfRecord" + "value": "collectionCode" } - ] + ], + "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 6646, - "end": 6688, + "start": 5452, + "end": 5488, "loc": { "start": { - "line": 172, - "column": 49 + "line": 146, + "column": 46 }, "end": { - "line": 172, - "column": 91 + "line": 146, + "column": 82 } }, "argument": { "type": "MemberExpression", - "start": 6653, - "end": 6687, + "start": 5459, + "end": 5487, "loc": { "start": { - "line": 172, - "column": 56 + "line": 146, + "column": 53 }, "end": { - "line": 172, - "column": 90 + "line": 146, + "column": 81 } }, "object": { "type": "MemberExpression", - "start": 6653, - "end": 6666, + "start": 5459, + "end": 5472, "loc": { "start": { - "line": 172, - "column": 56 + "line": 146, + "column": 53 }, "end": { - "line": 172, - "column": 69 + "line": 146, + "column": 66 } }, "object": { "type": "ThisExpression", - "start": 6653, - "end": 6657, + "start": 5459, + "end": 5463, "loc": { "start": { - "line": 172, - "column": 56 + "line": 146, + "column": 53 }, "end": { - "line": 172, - "column": 60 + "line": 146, + "column": 57 } } }, "property": { "type": "Identifier", - "start": 6658, - "end": 6666, + "start": 5464, + "end": 5472, "loc": { "start": { - "line": 172, - "column": 61 + "line": 146, + "column": 58 }, "end": { - "line": 172, - "column": 69 + "line": 146, + "column": 66 }, "identifierName": "specimen" }, @@ -9964,488 +7520,167 @@ "computed": false }, "property": { - "type": "StringLiteral", - "start": 6667, - "end": 6686, + "type": "Identifier", + "start": 5473, + "end": 5487, "loc": { "start": { - "line": 172, - "column": 70 + "line": 146, + "column": 67 }, "end": { - "line": 172, - "column": 89 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "line": 146, + "column": 81 + }, + "identifierName": "collectionCode" }, - "value": "dwc:basisOfRecord" - }, - "computed": true - } - }, - "alternate": null - }, - { - "type": "ReturnStatement", - "start": 6693, - "end": 6710, - "loc": { - "start": { - "line": 173, - "column": 4 - }, - "end": { - "line": 173, - "column": 21 - } - }, - "argument": { - "type": "Identifier", - "start": 6700, - "end": 6709, - "loc": { - "start": { - "line": 173, - "column": 11 - }, - "end": { - "line": 173, - "column": 20 + "name": "collectionCode" }, - "identifierName": "undefined" - }, - "name": "undefined" - } - } - ], - "directives": [], - "trailingComments": null - }, - "leadingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 6511, - "end": 6572, - "loc": { - "start": { - "line": 168, - "column": 2 - }, - "end": { - "line": 170, - "column": 5 - } - } - } - ], - "trailingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 6718, - "end": 6833, - "loc": { - "start": { - "line": 176, - "column": 2 - }, - "end": { - "line": 179, - "column": 5 - } - } - } - ] - }, - { - "type": "ClassMethod", - "start": 6836, - "end": 6910, - "loc": { - "start": { - "line": 180, - "column": 2 - }, - "end": { - "line": 182, - "column": 3 - } - }, - "static": false, - "computed": false, - "key": { - "type": "Identifier", - "start": 6840, - "end": 6853, - "loc": { - "start": { - "line": 180, - "column": 6 - }, - "end": { - "line": 180, - "column": 19 - }, - "identifierName": "basisOfRecord" - }, - "name": "basisOfRecord" - }, - "kind": "set", - "id": null, - "generator": false, - "expression": false, - "async": false, - "params": [ - { - "type": "Identifier", - "start": 6854, - "end": 6857, - "loc": { - "start": { - "line": 180, - "column": 20 - }, - "end": { - "line": 180, - "column": 23 - }, - "identifierName": "bor" - }, - "name": "bor" - } - ], - "body": { - "type": "BlockStatement", - "start": 6859, - "end": 6910, - "loc": { - "start": { - "line": 180, - "column": 25 - }, - "end": { - "line": 182, - "column": 3 - } - }, - "body": [ - { - "type": "ExpressionStatement", - "start": 6865, - "end": 6906, - "loc": { - "start": { - "line": 181, - "column": 4 + "computed": false }, - "end": { - "line": 181, - "column": 45 - } + "trailingComments": null }, - "expression": { - "type": "AssignmentExpression", - "start": 6865, - "end": 6905, - "loc": { - "start": { - "line": 181, - "column": 4 - }, - "end": { - "line": 181, - "column": 44 - } - }, - "operator": "=", - "left": { - "type": "MemberExpression", - "start": 6865, - "end": 6899, + "alternate": null, + "leadingComments": [ + { + "type": "CommentLine", + "value": " Get the collection code from the specimen object if present.", + "start": 5342, + "end": 5405, "loc": { "start": { - "line": 181, + "line": 145, "column": 4 }, "end": { - "line": 181, - "column": 38 + "line": 145, + "column": 67 } - }, - "object": { - "type": "MemberExpression", - "start": 6865, - "end": 6878, - "loc": { - "start": { - "line": 181, - "column": 4 - }, - "end": { - "line": 181, - "column": 17 - } - }, - "object": { - "type": "ThisExpression", - "start": 6865, - "end": 6869, - "loc": { - "start": { - "line": 181, - "column": 4 - }, - "end": { - "line": 181, - "column": 8 - } - } - }, - "property": { - "type": "Identifier", - "start": 6870, - "end": 6878, - "loc": { - "start": { - "line": 181, - "column": 9 - }, - "end": { - "line": 181, - "column": 17 - }, - "identifierName": "specimen" - }, - "name": "specimen" - }, - "computed": false - }, - "property": { - "type": "StringLiteral", - "start": 6879, - "end": 6898, - "loc": { - "start": { - "line": 181, - "column": 18 - }, - "end": { - "line": 181, - "column": 37 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + } + } + ], + "trailingComments": [ + { + "type": "CommentLine", + "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", + "start": 5494, + "end": 5566, + "loc": { + "start": { + "line": 148, + "column": 4 }, - "value": "dwc:basisOfRecord" - }, - "computed": true + "end": { + "line": 148, + "column": 76 + } + } }, - "right": { - "type": "Identifier", - "start": 6902, - "end": 6905, + { + "type": "CommentLine", + "value": " occurrenceID from there.", + "start": 5571, + "end": 5598, "loc": { "start": { - "line": 181, - "column": 41 + "line": 149, + "column": 4 }, "end": { - "line": 181, - "column": 44 - }, - "identifierName": "bor" - }, - "name": "bor" + "line": 149, + "column": 31 + } + } } - } - } - ], - "directives": [], - "trailingComments": null - }, - "leadingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 6718, - "end": 6833, - "loc": { - "start": { - "line": 176, - "column": 2 - }, - "end": { - "line": 179, - "column": 5 - } - } - } - ], - "trailingComments": [ - { - "type": "CommentBlock", - "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 6914, - "end": 6999, - "loc": { - "start": { - "line": 184, - "column": 2 - }, - "end": { - "line": 184, - "column": 87 - } - } - } - ] - }, - { - "type": "ClassMethod", - "start": 7002, - "end": 7173, - "loc": { - "start": { - "line": 185, - "column": 2 - }, - "end": { - "line": 189, - "column": 3 - } - }, - "static": false, - "computed": false, - "key": { - "type": "Identifier", - "start": 7006, - "end": 7018, - "loc": { - "start": { - "line": 185, - "column": 6 - }, - "end": { - "line": 185, - "column": 18 - }, - "identifierName": "taxonConcept" - }, - "name": "taxonConcept" - }, - "kind": "get", - "id": null, - "generator": false, - "expression": false, - "async": false, - "params": [], - "body": { - "type": "BlockStatement", - "start": 7021, - "end": 7173, - "loc": { - "start": { - "line": 185, - "column": 21 + ] }, - "end": { - "line": 189, - "column": 3 - } - }, - "body": [ { "type": "IfStatement", - "start": 7027, - "end": 7083, + "start": 5603, + "end": 5810, "loc": { "start": { - "line": 186, + "line": 150, "column": 4 }, "end": { - "line": 186, - "column": 60 + "line": 153, + "column": 5 } }, "test": { "type": "CallExpression", - "start": 7031, - "end": 7060, + "start": 5607, + "end": 5641, "loc": { "start": { - "line": 186, + "line": 150, "column": 8 }, "end": { - "line": 186, - "column": 37 + "line": 150, + "column": 42 } }, "callee": { "type": "Identifier", - "start": 7031, - "end": 7034, + "start": 5607, + "end": 5610, "loc": { "start": { - "line": 186, + "line": 150, "column": 8 }, "end": { - "line": 186, + "line": 150, "column": 11 }, "identifierName": "has" }, - "name": "has" + "name": "has", + "leadingComments": null }, "arguments": [ { "type": "MemberExpression", - "start": 7035, - "end": 7048, + "start": 5611, + "end": 5624, "loc": { "start": { - "line": 186, + "line": 150, "column": 12 }, "end": { - "line": 186, + "line": 150, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 7035, - "end": 7039, + "start": 5611, + "end": 5615, "loc": { "start": { - 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}, - "argument": { - "type": "MemberExpression", - "start": 7069, - "end": 7082, - "loc": { - "start": { - "line": 186, - "column": 46 - }, - "end": { - "line": 186, - "column": 59 - } - }, - "object": { - "type": "ThisExpression", - "start": 7069, - "end": 7073, - "loc": { - "start": { - "line": 186, - "column": 46 - }, - "end": { - "line": 186, - "column": 50 - } - } - }, - "property": { - "type": "Identifier", - "start": 7074, - "end": 7082, - "loc": { - "start": { - "line": 186, - "column": 51 - }, - "end": { - "line": 186, - "column": 59 - }, - "identifierName": "specimen" - }, - "name": "specimen" - }, - "computed": false - } - }, - "alternate": null - }, - { - "type": "IfStatement", - "start": 7088, - "end": 7147, - "loc": { - "start": { - "line": 187, - "column": 4 - }, - "end": { - "line": 187, - "column": 63 - } - }, - "test": { - "type": "CallExpression", - "start": 7092, - "end": 7124, + "type": "BlockStatement", + "start": 5643, + "end": 5810, "loc": { "start": { - "line": 187, - 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Hmm.", + "start": 8610, + "end": 8657, + "loc": { + "start": { + "line": 231, + "column": 4 + }, + "end": { + "line": 231, + "column": 51 + } + } + }, + { + "type": "CommentLine", + "value": " Return as an OWL restriction.", + "start": 8663, + "end": 8695, + "loc": { + "start": { + "line": 233, + "column": 4 + }, + "end": { + "line": 233, + "column": 36 + } } } ] @@ -12158,15 +13278,15 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. 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", - "start": 1242, - "end": 1287, + "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", + "start": 1351, + "end": 1449, "loc": { "start": { - "line": 30, + "line": 35, "column": 2 }, "end": { - "line": 30, - "column": 47 + "line": 38, + "column": 5 } } } @@ -12664,15 +14904,15 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1351, - "end": 1632, + "start": 1986, + "end": 2267, "loc": { "start": { - "line": 35, + "line": 54, "column": 2 }, "end": { - "line": 40, + "line": 59, "column": 5 } } @@ -12681,15 +14921,15 @@ }, { "type": "ClassMethod", - "start": 1635, - "end": 3470, + "start": 2270, + "end": 4105, "loc": { "start": { - "line": 41, + "line": 60, "column": 2 }, "end": { - "line": 88, + "line": 107, "column": 3 } }, @@ -12697,15 +14937,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 1642, - "end": 1658, + "start": 2277, + "end": 2293, "loc": { "start": { - "line": 41, + "line": 60, "column": 9 }, "end": { - "line": 41, + "line": 60, "column": 25 }, "identifierName": "fromOccurrenceID" @@ -12720,15 +14960,15 @@ "params": [ { "type": "Identifier", - "start": 1659, - "end": 1671, + "start": 2294, + "end": 2306, "loc": { "start": { - "line": 41, + "line": 60, "column": 26 }, "end": { - "line": 41, + "line": 60, "column": 38 }, "identifierName": "occurrenceID" @@ -12737,29 +14977,29 @@ }, { "type": "AssignmentPattern", - "start": 1673, - "end": 1708, + "start": 2308, + "end": 2343, "loc": { "start": { - "line": 41, + "line": 60, "column": 40 }, "end": { - "line": 41, + "line": 60, "column": 75 } }, "left": { "type": "Identifier", - "start": 1673, - "end": 1686, + "start": 2308, + "end": 2321, "loc": { "start": { - "line": 41, + "line": 60, "column": 40 }, "end": { - "line": 41, + "line": 60, "column": 53 }, "identifierName": "basisOfRecord" @@ -12768,15 +15008,15 @@ }, "right": { "type": "StringLiteral", - "start": 1689, - "end": 1708, + "start": 2324, + "end": 2343, "loc": { "start": { - "line": 41, + "line": 60, "column": 56 }, "end": { - "line": 41, + "line": 60, "column": 75 } }, @@ -12790,59 +15030,59 @@ ], "body": { "type": "BlockStatement", - "start": 1710, - "end": 3470, + "start": 2345, + "end": 4105, "loc": { "start": { - "line": 41, + "line": 60, "column": 77 }, "end": { - "line": 88, + "line": 107, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 1782, - "end": 1809, + "start": 2417, + "end": 2444, "loc": { "start": { - "line": 43, + "line": 62, "column": 4 }, "end": { - "line": 43, + "line": 62, "column": 31 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1786, - "end": 1808, + "start": 2421, + "end": 2443, "loc": { "start": { - "line": 43, + "line": 62, "column": 8 }, "end": { - "line": 43, + "line": 62, "column": 30 } }, "id": { "type": "Identifier", - "start": 1786, - "end": 1793, + "start": 2421, + "end": 2428, "loc": { "start": { - "line": 43, + "line": 62, "column": 8 }, "end": { - "line": 43, + "line": 62, "column": 15 }, "identifierName": "occurID" @@ -12852,15 +15092,15 @@ }, "init": { "type": "Identifier", - "start": 1796, - "end": 1808, + "start": 2431, + "end": 2443, "loc": { "start": { - "line": 43, + "line": 62, "column": 18 }, "end": { - "line": 43, + "line": 62, "column": 30 }, "identifierName": "occurrenceID" @@ -12875,15 +15115,15 @@ { "type": "CommentLine", "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 1716, - "end": 1777, + "start": 2351, + "end": 2412, "loc": { "start": { - "line": 42, + "line": 61, "column": 4 }, "end": { - "line": 42, + "line": 61, "column": 65 } } @@ -12892,57 +15132,57 @@ }, { "type": "IfStatement", - "start": 1814, - "end": 1883, + "start": 2449, + "end": 2518, "loc": { "start": { - "line": 44, + "line": 63, "column": 4 }, "end": { - "line": 44, + "line": 63, "column": 73 } }, "test": { "type": "CallExpression", - "start": 1818, - "end": 1852, + "start": 2453, + "end": 2487, "loc": { "start": { - "line": 44, + "line": 63, "column": 8 }, "end": { - "line": 44, + "line": 63, "column": 42 } }, "callee": { "type": "MemberExpression", - "start": 1818, - "end": 1836, + "start": 2453, + "end": 2471, "loc": { "start": { - "line": 44, + "line": 63, "column": 8 }, "end": { - "line": 44, + "line": 63, "column": 26 } }, "object": { "type": "Identifier", - "start": 1818, - "end": 1825, + "start": 2453, + "end": 2460, "loc": { "start": { - "line": 44, + "line": 63, "column": 8 }, "end": { - "line": 44, + "line": 63, "column": 15 }, "identifierName": "occurID" @@ -12951,15 +15191,15 @@ }, "property": { "type": "Identifier", - "start": 1826, - "end": 1836, + "start": 2461, + "end": 2471, "loc": { "start": { - "line": 44, + "line": 63, "column": 16 }, "end": { - "line": 44, + "line": 63, "column": 26 }, "identifierName": "startsWith" @@ -12971,15 +15211,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 1837, - "end": 1851, + "start": 2472, + "end": 2486, "loc": { "start": { - "line": 44, + "line": 63, "column": 27 }, "end": { - "line": 44, + "line": 63, "column": 41 } }, @@ -12993,44 +15233,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 1854, - "end": 1883, + "start": 2489, + "end": 2518, "loc": { "start": { - "line": 44, + "line": 63, "column": 44 }, "end": { - "line": 44, + "line": 63, "column": 73 } }, "expression": { "type": "AssignmentExpression", - "start": 1854, - "end": 1882, + "start": 2489, + "end": 2517, "loc": { "start": { - "line": 44, + "line": 63, "column": 44 }, "end": { - "line": 44, + "line": 63, "column": 72 } }, "operator": "=", "left": { "type": "Identifier", - "start": 1854, - "end": 1861, + "start": 2489, + "end": 2496, "loc": { "start": { - "line": 44, + "line": 63, "column": 44 }, "end": { - "line": 44, + "line": 63, "column": 51 }, "identifierName": "occurID" @@ -13039,43 +15279,43 @@ }, "right": { "type": "CallExpression", - "start": 1864, - "end": 1882, + "start": 2499, + "end": 2517, "loc": { "start": { - "line": 44, + "line": 63, "column": 54 }, "end": { - "line": 44, + "line": 63, "column": 72 } }, "callee": { "type": "MemberExpression", - "start": 1864, - "end": 1878, + "start": 2499, + "end": 2513, "loc": { "start": { - "line": 44, + "line": 63, "column": 54 }, "end": { - "line": 44, + "line": 63, "column": 68 } }, "object": { "type": "Identifier", - "start": 1864, - "end": 1871, + "start": 2499, + "end": 2506, "loc": { "start": { - "line": 44, + "line": 63, "column": 54 }, "end": { - "line": 44, + "line": 63, "column": 61 }, "identifierName": "occurID" @@ -13084,15 +15324,15 @@ }, "property": { "type": "Identifier", - "start": 1872, - "end": 1878, + "start": 2507, + "end": 2513, "loc": { "start": { - "line": 44, + "line": 63, "column": 62 }, "end": { - "line": 44, + "line": 63, "column": 68 }, "identifierName": "substr" @@ -13104,15 +15344,15 @@ "arguments": [ { "type": "NumericLiteral", - "start": 1879, - "end": 1881, + "start": 2514, + "end": 2516, "loc": { "start": { - "line": 44, + "line": 63, "column": 69 }, "end": { - "line": 44, + "line": 63, "column": 71 } }, @@ -13132,15 +15372,15 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 1889, - "end": 1913, + "start": 2524, + "end": 2548, "loc": { "start": { - "line": 46, + "line": 65, "column": 4 }, "end": { - "line": 46, + "line": 65, "column": 28 } } @@ -13149,44 +15389,44 @@ }, { "type": "VariableDeclaration", - "start": 1918, - "end": 2060, + "start": 2553, + "end": 2695, "loc": { "start": { - "line": 47, + "line": 66, "column": 4 }, "end": { - "line": 51, + "line": 70, "column": 6 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 1924, - "end": 2059, + "start": 2559, + "end": 2694, "loc": { "start": { - "line": 47, + "line": 66, "column": 10 }, "end": { - "line": 51, + "line": 70, "column": 5 } }, "id": { "type": "Identifier", - "start": 1924, - "end": 1932, + "start": 2559, + "end": 2567, "loc": { "start": { - "line": 47, + "line": 66, "column": 10 }, "end": { - "line": 47, + "line": 66, "column": 18 }, "identifierName": "specimen" @@ -13196,30 +15436,30 @@ }, "init": { "type": "ObjectExpression", - "start": 1935, - "end": 2059, + "start": 2570, + "end": 2694, "loc": { "start": { - "line": 47, + "line": 66, "column": 21 }, "end": { - "line": 51, + "line": 70, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 1943, - "end": 1981, + "start": 2578, + "end": 2616, "loc": { "start": { - "line": 48, + "line": 67, "column": 6 }, "end": { - "line": 48, + "line": 67, "column": 44 } }, @@ -13228,15 +15468,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 1943, - "end": 1950, + "start": 2578, + "end": 2585, "loc": { "start": { - "line": 48, + "line": 67, "column": 6 }, "end": { - "line": 48, + "line": 67, "column": 13 } }, @@ -13248,29 +15488,29 @@ }, "value": { "type": "MemberExpression", - "start": 1952, - "end": 1981, + "start": 2587, + "end": 2616, "loc": { "start": { - "line": 48, + "line": 67, "column": 15 }, "end": { - "line": 48, + "line": 67, "column": 44 } }, "object": { "type": "Identifier", - "start": 1952, - "end": 1967, + "start": 2587, + "end": 2602, "loc": { "start": { - "line": 48, + "line": 67, "column": 15 }, "end": { - "line": 48, + "line": 67, "column": 30 }, "identifierName": "SpecimenWrapper" @@ -13279,15 +15519,15 @@ }, "property": { "type": "Identifier", - "start": 1968, - "end": 1981, + "start": 2603, + "end": 2616, "loc": { "start": { - "line": 48, + "line": 67, "column": 31 }, "end": { - "line": 48, + "line": 67, "column": 44 }, "identifierName": "TYPE_SPECIMEN" @@ -13299,15 +15539,15 @@ }, { "type": "ObjectProperty", - "start": 1989, - "end": 2023, + "start": 2624, + "end": 2658, "loc": { "start": { - "line": 49, + "line": 68, "column": 6 }, "end": { - "line": 49, + "line": 68, "column": 40 } }, @@ -13316,15 +15556,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 1989, - "end": 2008, + "start": 2624, + "end": 2643, "loc": { "start": { - "line": 49, + "line": 68, "column": 6 }, "end": { - "line": 49, + "line": 68, "column": 25 } }, @@ -13336,15 +15576,15 @@ }, "value": { "type": "Identifier", - "start": 2010, - "end": 2023, + "start": 2645, + "end": 2658, "loc": { "start": { - "line": 49, + "line": 68, "column": 27 }, "end": { - "line": 49, + "line": 68, "column": 40 }, "identifierName": "basisOfRecord" @@ -13354,15 +15594,15 @@ }, { "type": "ObjectProperty", - "start": 2031, - "end": 2052, + "start": 2666, + "end": 2687, "loc": { "start": { - "line": 50, + "line": 69, "column": 6 }, "end": { - "line": 50, + "line": 69, "column": 27 } }, @@ -13371,15 +15611,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 2031, - "end": 2043, + "start": 2666, + "end": 2678, "loc": { "start": { - "line": 50, + "line": 69, "column": 6 }, "end": { - "line": 50, + "line": 69, "column": 18 }, "identifierName": "occurrenceID" @@ -13388,15 +15628,15 @@ }, "value": { "type": "Identifier", - "start": 2045, - "end": 2052, + "start": 2680, + "end": 2687, "loc": { "start": { - "line": 50, + "line": 69, "column": 20 }, "end": { - "line": 50, + "line": 69, "column": 27 }, "identifierName": "occurID" @@ -13414,15 +15654,15 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 1889, - "end": 1913, + "start": 2524, + "end": 2548, "loc": { "start": { - "line": 46, + "line": 65, "column": 4 }, "end": { - "line": 46, + "line": 65, "column": 28 } } @@ -13432,15 +15672,15 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2066, - "end": 2139, + "start": 2701, + "end": 2774, "loc": { "start": { - "line": 53, + "line": 72, "column": 4 }, "end": { - "line": 53, + "line": 72, "column": 77 } } @@ -13448,15 +15688,15 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2144, - "end": 2199, + "start": 2779, + "end": 2834, "loc": { "start": { - "line": 54, + "line": 73, "column": 4 }, "end": { - "line": 54, + "line": 73, "column": 59 } } @@ -13465,44 +15705,44 @@ }, { "type": "VariableDeclaration", - "start": 2204, - "end": 2336, + "start": 2839, + "end": 2971, "loc": { "start": { - "line": 55, + "line": 74, "column": 4 }, "end": { - "line": 62, + "line": 81, "column": 6 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2210, - "end": 2335, + "start": 2845, + "end": 2970, "loc": { "start": { - "line": 55, + "line": 74, "column": 10 }, "end": { - "line": 62, + "line": 81, "column": 5 } }, "id": { "type": "Identifier", - "start": 2210, - "end": 2226, + "start": 2845, + "end": 2861, "loc": { "start": { - "line": 55, + "line": 74, "column": 10 }, "end": { - "line": 55, + "line": 74, "column": 26 }, "identifierName": "URL_URN_PREFIXES" @@ -13512,30 +15752,30 @@ }, "init": { "type": "ArrayExpression", - "start": 2229, - "end": 2335, + "start": 2864, + "end": 2970, "loc": { "start": { - "line": 55, + "line": 74, "column": 29 }, "end": { - "line": 62, + "line": 81, "column": 5 } }, "elements": [ { "type": "StringLiteral", - "start": 2237, - "end": 2246, + "start": 2872, + "end": 2881, "loc": { "start": { - "line": 56, + "line": 75, "column": 6 }, "end": { - "line": 56, + "line": 75, "column": 15 } }, @@ -13547,15 +15787,15 @@ }, { "type": "StringLiteral", - "start": 2254, - "end": 2264, + "start": 2889, + "end": 2899, "loc": { "start": { - "line": 57, + "line": 76, "column": 6 }, "end": { - "line": 57, + "line": 76, "column": 16 } }, @@ -13567,15 +15807,15 @@ }, { "type": "StringLiteral", - "start": 2272, - "end": 2280, + "start": 2907, + "end": 2915, "loc": { "start": { - "line": 58, + "line": 77, "column": 6 }, "end": { - "line": 58, + "line": 77, "column": 14 } }, @@ -13587,15 +15827,15 @@ }, { "type": "StringLiteral", - "start": 2288, - "end": 2297, + "start": 2923, + "end": 2932, "loc": { "start": { - "line": 59, + "line": 78, "column": 6 }, "end": { - "line": 59, + "line": 78, "column": 15 } }, @@ -13607,15 +15847,15 @@ }, { "type": "StringLiteral", - "start": 2305, - "end": 2314, + "start": 2940, + "end": 2949, "loc": { "start": { - "line": 60, + "line": 79, "column": 6 }, "end": { - "line": 60, + "line": 79, "column": 15 } }, @@ -13627,15 +15867,15 @@ }, { "type": "StringLiteral", - "start": 2322, - "end": 2328, + "start": 2957, + "end": 2963, "loc": { "start": { - "line": 61, + "line": 80, "column": 6 }, "end": { - "line": 61, + "line": 80, "column": 12 } }, @@ -13655,15 +15895,15 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2066, - "end": 2139, + "start": 2701, + "end": 2774, "loc": { "start": { - "line": 53, + "line": 72, "column": 4 }, "end": { - "line": 53, + "line": 72, "column": 77 } } @@ -13671,15 +15911,15 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2144, - "end": 2199, + "start": 2779, + "end": 2834, "loc": { "start": { - "line": 54, + "line": 73, "column": 4 }, "end": { - "line": 54, + "line": 73, "column": 59 } } @@ -13688,85 +15928,85 @@ }, { "type": "IfStatement", - "start": 2341, - "end": 2463, + "start": 2976, + "end": 3098, "loc": { "start": { - "line": 63, + "line": 82, "column": 4 }, "end": { - "line": 65, + "line": 84, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 2345, - "end": 2431, + "start": 2980, + "end": 3066, "loc": { "start": { - "line": 63, + "line": 82, "column": 8 }, "end": { - "line": 63, + "line": 82, "column": 94 } }, "left": { "type": "MemberExpression", - "start": 2345, - "end": 2427, + "start": 2980, + "end": 3062, "loc": { "start": { - "line": 63, + "line": 82, "column": 8 }, "end": { - "line": 63, + "line": 82, "column": 90 } }, "object": { "type": "CallExpression", - "start": 2345, - "end": 2420, + "start": 2980, + "end": 3055, "loc": { "start": { - "line": 63, + "line": 82, "column": 8 }, "end": { - "line": 63, + "line": 82, "column": 83 } }, "callee": { "type": "MemberExpression", - "start": 2345, - "end": 2368, + "start": 2980, + "end": 3003, "loc": { "start": { - "line": 63, + "line": 82, "column": 8 }, "end": { - "line": 63, + "line": 82, "column": 31 } }, "object": { "type": "Identifier", - "start": 2345, - "end": 2361, + "start": 2980, + "end": 2996, "loc": { "start": { - "line": 63, + "line": 82, "column": 8 }, "end": { - "line": 63, + "line": 82, "column": 24 }, "identifierName": "URL_URN_PREFIXES" @@ -13775,15 +16015,15 @@ }, "property": { "type": "Identifier", - "start": 2362, - "end": 2368, + "start": 2997, + "end": 3003, "loc": { "start": { - "line": 63, + "line": 82, "column": 25 }, "end": { - "line": 63, + "line": 82, "column": 31 }, "identifierName": "filter" @@ -13795,15 +16035,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 2369, - "end": 2419, + "start": 3004, + "end": 3054, "loc": { "start": { - "line": 63, + "line": 82, "column": 32 }, "end": { - "line": 63, + "line": 82, "column": 82 } }, @@ -13814,15 +16054,15 @@ "params": [ { "type": "Identifier", - "start": 2369, - "end": 2375, + "start": 3004, + "end": 3010, "loc": { "start": { - "line": 63, + "line": 82, "column": 32 }, "end": { - "line": 63, + "line": 82, "column": 38 }, "identifierName": "prefix" @@ -13832,71 +16072,71 @@ ], "body": { "type": "CallExpression", - "start": 2379, - "end": 2419, + "start": 3014, + "end": 3054, "loc": { "start": { - "line": 63, + "line": 82, "column": 42 }, "end": { - "line": 63, + "line": 82, "column": 82 } }, "callee": { "type": "MemberExpression", - "start": 2379, - "end": 2411, + "start": 3014, + "end": 3046, "loc": { "start": { - "line": 63, + "line": 82, "column": 42 }, "end": { - "line": 63, + "line": 82, "column": 74 } }, "object": { "type": "CallExpression", - "start": 2379, - "end": 2400, + "start": 3014, + "end": 3035, "loc": { "start": { - "line": 63, + "line": 82, "column": 42 }, "end": { - "line": 63, + "line": 82, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 2379, - "end": 2398, + "start": 3014, + "end": 3033, "loc": { "start": { - "line": 63, + "line": 82, "column": 42 }, "end": { - "line": 63, + "line": 82, "column": 61 } }, "object": { "type": "Identifier", - "start": 2379, - "end": 2386, + "start": 3014, + "end": 3021, "loc": { "start": { - "line": 63, + "line": 82, "column": 42 }, "end": { - "line": 63, + "line": 82, "column": 49 }, "identifierName": "occurID" @@ -13905,15 +16145,15 @@ }, "property": { "type": "Identifier", - "start": 2387, - "end": 2398, + "start": 3022, + "end": 3033, "loc": { "start": { - "line": 63, + "line": 82, "column": 50 }, "end": { - "line": 63, + "line": 82, "column": 61 }, "identifierName": "toLowerCase" @@ -13926,15 +16166,15 @@ }, "property": { "type": "Identifier", - "start": 2401, - "end": 2411, + "start": 3036, + "end": 3046, "loc": { "start": { - "line": 63, + "line": 82, "column": 64 }, "end": { - "line": 63, + "line": 82, "column": 74 }, "identifierName": "startsWith" @@ -13946,15 +16186,15 @@ "arguments": [ { "type": "Identifier", - "start": 2412, - "end": 2418, + "start": 3047, + "end": 3053, "loc": { "start": { - "line": 63, + "line": 82, "column": 75 }, "end": { - "line": 63, + "line": 82, "column": 81 }, "identifierName": "prefix" @@ -13968,15 +16208,15 @@ }, "property": { "type": "Identifier", - "start": 2421, - "end": 2427, + "start": 3056, + "end": 3062, "loc": { "start": { - "line": 63, + "line": 82, "column": 84 }, "end": { - "line": 63, + "line": 82, "column": 90 }, "identifierName": "length" @@ -13988,15 +16228,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 2430, - "end": 2431, + "start": 3065, + "end": 3066, "loc": { "start": { - "line": 63, + "line": 82, "column": 93 }, "end": { - "line": 63, + "line": 82, "column": 94 } }, @@ -14009,44 +16249,44 @@ }, "consequent": { "type": "BlockStatement", - "start": 2433, - "end": 2463, + "start": 3068, + "end": 3098, "loc": { "start": { - "line": 63, + "line": 82, "column": 96 }, "end": { - "line": 65, + "line": 84, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 2441, - "end": 2457, + "start": 3076, + "end": 3092, "loc": { "start": { - "line": 64, + "line": 83, "column": 6 }, "end": { - "line": 64, + "line": 83, "column": 22 } }, "argument": { "type": "Identifier", - "start": 2448, - "end": 2456, + "start": 3083, + "end": 3091, "loc": { "start": { - "line": 64, + "line": 83, "column": 13 }, "end": { - "line": 64, + "line": 83, "column": 21 }, "identifierName": "specimen" @@ -14063,15 +16303,15 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 2469, - "end": 2538, + "start": 3104, + "end": 3173, "loc": { "start": { - "line": 67, + "line": 86, "column": 4 }, "end": { - "line": 67, + "line": 86, "column": 73 } } @@ -14080,57 +16320,57 @@ }, { "type": "IfStatement", - "start": 2543, - "end": 2703, + "start": 3178, + "end": 3338, "loc": { "start": { - "line": 68, + "line": 87, "column": 4 }, "end": { - "line": 70, + "line": 89, "column": 5 } }, "test": { "type": "CallExpression", - "start": 2547, - "end": 2613, + "start": 3182, + "end": 3248, "loc": { "start": { - "line": 68, + "line": 87, "column": 8 }, "end": { - "line": 68, + "line": 87, "column": 74 } }, "callee": { "type": "MemberExpression", - "start": 2547, - "end": 2567, + "start": 3182, + "end": 3202, "loc": { "start": { - "line": 68, + "line": 87, "column": 8 }, "end": { - "line": 68, + "line": 87, "column": 28 } }, "object": { "type": "Identifier", - "start": 2547, - "end": 2563, + "start": 3182, + "end": 3198, "loc": { "start": { - "line": 68, + "line": 87, "column": 8 }, "end": { - "line": 68, + "line": 87, "column": 24 }, "identifierName": "PhyxCacheManager" @@ -14140,15 +16380,15 @@ }, "property": { "type": "Identifier", - "start": 2564, - "end": 2567, + "start": 3199, + "end": 3202, "loc": { "start": { - "line": 68, + "line": 87, "column": 25 }, "end": { - "line": 68, + "line": 87, "column": 28 }, "identifierName": "has" @@ -14161,15 +16401,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 2568, - "end": 2603, + "start": 3203, + "end": 3238, "loc": { "start": { - "line": 68, + "line": 87, "column": 29 }, "end": { - "line": 68, + "line": 87, "column": 64 } }, @@ -14181,15 +16421,15 @@ }, { "type": "Identifier", - "start": 2605, - "end": 2612, + "start": 3240, + "end": 3247, "loc": { "start": { - "line": 68, + "line": 87, "column": 66 }, "end": { - "line": 68, + "line": 87, "column": 73 }, "identifierName": "occurID" @@ -14201,72 +16441,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 2615, - "end": 2703, + "start": 3250, + "end": 3338, "loc": { "start": { - "line": 68, + "line": 87, "column": 76 }, "end": { - "line": 70, + "line": 89, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 2623, - "end": 2697, + "start": 3258, + "end": 3332, "loc": { "start": { - "line": 69, + "line": 88, "column": 6 }, "end": { - "line": 69, + "line": 88, "column": 80 } }, "argument": { "type": "CallExpression", - "start": 2630, - "end": 2696, + "start": 3265, + "end": 3331, "loc": { "start": { - "line": 69, + "line": 88, "column": 13 }, "end": { - "line": 69, + "line": 88, "column": 79 } }, "callee": { "type": "MemberExpression", - "start": 2630, - "end": 2650, + "start": 3265, + "end": 3285, "loc": { "start": { - "line": 69, + "line": 88, "column": 13 }, "end": { - "line": 69, + "line": 88, "column": 33 } }, "object": { "type": "Identifier", - "start": 2630, - "end": 2646, + "start": 3265, + "end": 3281, "loc": { "start": { - "line": 69, + "line": 88, "column": 13 }, "end": { - "line": 69, + "line": 88, "column": 29 }, "identifierName": "PhyxCacheManager" @@ -14275,15 +16515,15 @@ }, "property": { "type": "Identifier", - "start": 2647, - "end": 2650, + "start": 3282, + "end": 3285, "loc": { "start": { - "line": 69, + "line": 88, "column": 30 }, "end": { - "line": 69, + "line": 88, "column": 33 }, "identifierName": "get" @@ -14295,15 +16535,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 2651, - "end": 2686, + "start": 3286, + "end": 3321, "loc": { "start": { - "line": 69, + "line": 88, "column": 34 }, "end": { - "line": 69, + "line": 88, "column": 69 } }, @@ -14315,15 +16555,15 @@ }, { "type": "Identifier", - "start": 2688, - "end": 2695, + "start": 3323, + "end": 3330, "loc": { "start": { - "line": 69, + "line": 88, "column": 71 }, "end": { - "line": 69, + "line": 88, "column": 78 }, "identifierName": "occurID" @@ -14342,15 +16582,15 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 2469, - "end": 2538, + "start": 3104, + "end": 3173, "loc": { "start": { - "line": 67, + "line": 86, "column": 4 }, "end": { - "line": 67, + "line": 86, "column": 73 } } @@ -14360,15 +16600,15 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 2709, - "end": 2794, + "start": 3344, + "end": 3429, "loc": { "start": { - "line": 72, + "line": 91, "column": 4 }, "end": { - "line": 72, + "line": 91, "column": 89 } } @@ -14377,44 +16617,44 @@ }, { "type": "VariableDeclaration", - "start": 2799, - "end": 2832, + "start": 3434, + "end": 3467, "loc": { "start": { - "line": 73, + "line": 92, "column": 4 }, "end": { - "line": 73, + "line": 92, "column": 37 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 2805, - "end": 2831, + "start": 3440, + "end": 3466, "loc": { "start": { - "line": 73, + "line": 92, "column": 10 }, "end": { - "line": 73, + "line": 92, "column": 36 } }, "id": { "type": "Identifier", - "start": 2805, - "end": 2810, + "start": 3440, + "end": 3445, "loc": { "start": { - "line": 73, + "line": 92, "column": 10 }, "end": { - "line": 73, + "line": 92, "column": 15 }, "identifierName": "comps" @@ -14424,43 +16664,43 @@ }, "init": { "type": "CallExpression", - "start": 2813, - "end": 2831, + "start": 3448, + "end": 3466, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 73, + "line": 92, "column": 36 } }, "callee": { "type": "MemberExpression", - "start": 2813, - "end": 2826, + "start": 3448, + "end": 3461, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 73, + "line": 92, "column": 31 } }, "object": { "type": "Identifier", - "start": 2813, - "end": 2820, + "start": 3448, + "end": 3455, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 73, + "line": 92, "column": 25 }, "identifierName": "occurID" @@ -14469,15 +16709,15 @@ }, "property": { "type": "Identifier", - "start": 2821, - "end": 2826, + "start": 3456, + "end": 3461, "loc": { "start": { - "line": 73, + "line": 92, "column": 26 }, "end": { - "line": 73, + "line": 92, "column": 31 }, "identifierName": "split" @@ -14489,15 +16729,15 @@ "arguments": [ { "type": "RegExpLiteral", - "start": 2827, - "end": 2830, + "start": 3462, + "end": 3465, "loc": { "start": { - "line": 73, + "line": 92, "column": 32 }, "end": { - "line": 73, + "line": 92, "column": 35 } }, @@ -14517,15 +16757,15 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 2709, - "end": 2794, + "start": 3344, + "end": 3429, "loc": { "start": { - "line": 72, + "line": 91, "column": 4 }, "end": { - "line": 72, + "line": 91, "column": 89 } } @@ -14534,57 +16774,57 @@ }, { "type": "IfStatement", - "start": 2837, - "end": 3362, + "start": 3472, + "end": 3997, "loc": { "start": { - "line": 74, + "line": 93, "column": 4 }, "end": { - "line": 84, + "line": 103, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 2841, - "end": 2859, + "start": 3476, + "end": 3494, "loc": { "start": { - "line": 74, + "line": 93, "column": 8 }, "end": { - "line": 74, + "line": 93, "column": 26 } }, "left": { "type": "MemberExpression", - "start": 2841, - "end": 2853, + "start": 3476, + "end": 3488, "loc": { "start": { - "line": 74, + "line": 93, "column": 8 }, "end": { - "line": 74, + "line": 93, "column": 20 } }, "object": { "type": "Identifier", - "start": 2841, - "end": 2846, + "start": 3476, + "end": 3481, "loc": { "start": { - "line": 74, + "line": 93, "column": 8 }, "end": { - "line": 74, + "line": 93, "column": 13 }, "identifierName": "comps" @@ -14593,15 +16833,15 @@ }, "property": { "type": "Identifier", - "start": 2847, - "end": 2853, + "start": 3482, + "end": 3488, "loc": { "start": { - "line": 74, + "line": 93, "column": 14 }, "end": { - "line": 74, + "line": 93, "column": 20 }, "identifierName": "length" @@ -14613,15 +16853,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 2858, - "end": 2859, + "start": 3493, + "end": 3494, "loc": { "start": { - "line": 74, + "line": 93, "column": 25 }, "end": { - "line": 74, + "line": 93, "column": 26 } }, @@ -14634,88 +16874,88 @@ }, "consequent": { "type": "BlockStatement", - "start": 2861, - "end": 3001, + "start": 3496, + "end": 3636, "loc": { "start": { - "line": 74, + "line": 93, "column": 28 }, "end": { - "line": 78, + "line": 97, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 2962, - "end": 2995, + "start": 3597, + "end": 3630, "loc": { "start": { - "line": 77, + "line": 96, "column": 6 }, "end": { - "line": 77, + "line": 96, "column": 39 } }, "expression": { "type": "AssignmentExpression", - "start": 2962, - "end": 2994, + "start": 3597, + "end": 3629, "loc": { "start": { - "line": 77, + "line": 96, "column": 6 }, "end": { - "line": 77, + "line": 96, "column": 38 } }, "operator": "=", "left": { "type": "ArrayPattern", - "start": 2962, - "end": 2986, + "start": 3597, + "end": 3621, "loc": { "start": { - "line": 77, + "line": 96, "column": 6 }, "end": { - "line": 77, + "line": 96, "column": 30 } }, "elements": [ { "type": "MemberExpression", - "start": 2963, - "end": 2985, + "start": 3598, + "end": 3620, "loc": { "start": { - "line": 77, + "line": 96, "column": 7 }, "end": { - "line": 77, + "line": 96, "column": 29 } }, "object": { "type": "Identifier", - "start": 2963, - "end": 2971, + "start": 3598, + "end": 3606, "loc": { "start": { - "line": 77, + "line": 96, "column": 7 }, "end": { - "line": 77, + "line": 96, "column": 15 }, "identifierName": "specimen" @@ -14725,15 +16965,15 @@ }, "property": { "type": "Identifier", - "start": 2972, - "end": 2985, + "start": 3607, + "end": 3620, "loc": { "start": { - "line": 77, + "line": 96, "column": 16 }, "end": { - "line": 77, + "line": 96, "column": 29 }, "identifierName": "catalogNumber" @@ -14748,15 +16988,15 @@ }, "right": { "type": "Identifier", - "start": 2989, - "end": 2994, + "start": 3624, + "end": 3629, "loc": { "start": { - "line": 77, + "line": 96, "column": 33 }, "end": { - "line": 77, + "line": 96, "column": 38 }, "identifierName": "comps" @@ -14769,15 +17009,15 @@ { "type": "CommentLine", "value": " specimen.institutionCode = undefined;", - "start": 2869, - "end": 2909, + "start": 3504, + "end": 3544, "loc": { "start": { - "line": 75, + "line": 94, "column": 6 }, "end": { - "line": 75, + "line": 94, "column": 46 } } @@ -14785,15 +17025,15 @@ { "type": "CommentLine", "value": " specimen.collectionCode = undefined;", - "start": 2916, - "end": 2955, + "start": 3551, + "end": 3590, "loc": { "start": { - "line": 76, + "line": 95, "column": 6 }, "end": { - "line": 76, + "line": 95, "column": 45 } } @@ -14805,57 +17045,57 @@ }, "alternate": { "type": "IfStatement", - "start": 3007, - "end": 3362, + "start": 3642, + "end": 3997, "loc": { "start": { - "line": 78, + "line": 97, "column": 11 }, "end": { - "line": 84, + "line": 103, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 3011, - "end": 3029, + "start": 3646, + "end": 3664, "loc": { "start": { - "line": 78, + "line": 97, "column": 15 }, "end": { - "line": 78, + "line": 97, "column": 33 } }, "left": { "type": "MemberExpression", - "start": 3011, - "end": 3023, + "start": 3646, + "end": 3658, "loc": { "start": { - "line": 78, + "line": 97, "column": 15 }, "end": { - "line": 78, + "line": 97, "column": 27 } }, "object": { "type": "Identifier", - "start": 3011, - "end": 3016, + "start": 3646, + "end": 3651, "loc": { "start": { - "line": 78, + "line": 97, "column": 15 }, "end": { - "line": 78, + "line": 97, "column": 20 }, "identifierName": "comps" @@ -14864,15 +17104,15 @@ }, "property": { "type": "Identifier", - "start": 3017, - "end": 3023, + "start": 3652, + "end": 3658, "loc": { "start": { - "line": 78, + "line": 97, "column": 21 }, "end": { - "line": 78, + "line": 97, "column": 27 }, "identifierName": "length" @@ -14884,15 +17124,15 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 3028, - "end": 3029, + "start": 3663, + "end": 3664, "loc": { "start": { - "line": 78, + "line": 97, "column": 32 }, "end": { - "line": 78, + "line": 97, "column": 33 } }, @@ -14905,88 +17145,88 @@ }, "consequent": { "type": "BlockStatement", - "start": 3031, - "end": 3104, + "start": 3666, + "end": 3739, "loc": { "start": { - "line": 78, + "line": 97, "column": 35 }, "end": { - "line": 80, + "line": 99, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 3039, - "end": 3098, + "start": 3674, + "end": 3733, "loc": { "start": { - "line": 79, + "line": 98, "column": 6 }, "end": { - "line": 79, + "line": 98, "column": 65 } }, "expression": { "type": "AssignmentExpression", - "start": 3039, - "end": 3097, + "start": 3674, + "end": 3732, "loc": { "start": { - "line": 79, + "line": 98, "column": 6 }, "end": { - "line": 79, + "line": 98, "column": 64 } }, "operator": "=", "left": { "type": "ArrayPattern", - "start": 3039, - "end": 3089, + "start": 3674, + "end": 3724, "loc": { "start": { - "line": 79, + "line": 98, "column": 6 }, "end": { - "line": 79, + "line": 98, "column": 56 } }, "elements": [ { "type": "MemberExpression", - "start": 3040, - "end": 3064, + "start": 3675, + "end": 3699, "loc": { "start": { - "line": 79, + "line": 98, "column": 7 }, "end": { - "line": 79, + "line": 98, "column": 31 } }, "object": { "type": "Identifier", - "start": 3040, - "end": 3048, + "start": 3675, + "end": 3683, "loc": { "start": { - "line": 79, + "line": 98, "column": 7 }, "end": { - "line": 79, + "line": 98, "column": 15 }, "identifierName": "specimen" @@ -14995,15 +17235,15 @@ }, "property": { "type": "Identifier", - "start": 3049, - "end": 3064, + "start": 3684, + "end": 3699, "loc": { "start": { - "line": 79, + "line": 98, "column": 16 }, "end": { - "line": 79, + "line": 98, "column": 31 }, "identifierName": "institutionCode" @@ -15014,29 +17254,29 @@ }, { "type": "MemberExpression", - "start": 3066, - "end": 3088, + "start": 3701, + "end": 3723, "loc": { "start": { - "line": 79, + "line": 98, "column": 33 }, "end": { - "line": 79, + "line": 98, "column": 55 } }, "object": { "type": "Identifier", - "start": 3066, - "end": 3074, + "start": 3701, + "end": 3709, "loc": { "start": { - "line": 79, + "line": 98, "column": 33 }, "end": { - "line": 79, + "line": 98, "column": 41 }, "identifierName": "specimen" @@ -15045,15 +17285,15 @@ }, "property": { "type": "Identifier", - "start": 3075, - "end": 3088, + "start": 3710, + "end": 3723, "loc": { "start": { - "line": 79, + "line": 98, "column": 42 }, "end": { - "line": 79, + "line": 98, "column": 55 }, "identifierName": "catalogNumber" @@ -15066,15 +17306,15 @@ }, "right": { "type": "Identifier", - "start": 3092, - "end": 3097, + "start": 3727, + "end": 3732, "loc": { "start": { - "line": 79, + "line": 98, "column": 59 }, "end": { - "line": 79, + "line": 98, "column": 64 }, "identifierName": "comps" @@ -15088,57 +17328,57 @@ }, "alternate": { "type": "IfStatement", - "start": 3110, - "end": 3362, + "start": 3745, + "end": 3997, "loc": { "start": { - "line": 80, + "line": 99, "column": 11 }, "end": { - "line": 84, + "line": 103, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 3114, - "end": 3131, + "start": 3749, + "end": 3766, "loc": { "start": { - "line": 80, + "line": 99, "column": 15 }, "end": { - "line": 80, + "line": 99, "column": 32 } }, "left": { "type": "MemberExpression", - "start": 3114, - "end": 3126, + "start": 3749, + "end": 3761, "loc": { "start": { - "line": 80, + "line": 99, "column": 15 }, "end": { - "line": 80, + "line": 99, "column": 27 } }, "object": { "type": "Identifier", - "start": 3114, - "end": 3119, + "start": 3749, + "end": 3754, "loc": { "start": { - "line": 80, + "line": 99, "column": 15 }, "end": { - "line": 80, + "line": 99, "column": 20 }, "identifierName": "comps" @@ -15147,15 +17387,15 @@ }, "property": { "type": "Identifier", - "start": 3120, - "end": 3126, + "start": 3755, + "end": 3761, "loc": { "start": { - "line": 80, + "line": 99, "column": 21 }, "end": { - "line": 80, + "line": 99, "column": 27 }, "identifierName": "length" @@ -15167,15 +17407,15 @@ "operator": ">=", "right": { "type": "NumericLiteral", - "start": 3130, - "end": 3131, + "start": 3765, + "end": 3766, "loc": { "start": { - "line": 80, + "line": 99, "column": 31 }, "end": { - "line": 80, + "line": 99, "column": 32 } }, @@ -15188,59 +17428,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 3133, - "end": 3362, + "start": 3768, + "end": 3997, "loc": { "start": { - "line": 80, + "line": 99, "column": 34 }, "end": { - "line": 84, + "line": 103, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 3141, - "end": 3167, + "start": 3776, + "end": 3802, "loc": { "start": { - "line": 81, + "line": 100, "column": 6 }, "end": { - "line": 81, + "line": 100, "column": 32 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 3145, - "end": 3166, + "start": 3780, + "end": 3801, "loc": { "start": { - "line": 81, + "line": 100, "column": 10 }, "end": { - "line": 81, + "line": 100, "column": 31 } }, "id": { "type": "Identifier", - "start": 3145, - "end": 3161, + "start": 3780, + "end": 3796, "loc": { "start": { - "line": 81, + "line": 100, "column": 10 }, "end": { - "line": 81, + "line": 100, "column": 26 }, "identifierName": "catalogNumValues" @@ -15249,15 +17489,15 @@ }, "init": { "type": "ArrayExpression", - "start": 3164, - "end": 3166, + "start": 3799, + "end": 3801, "loc": { "start": { - "line": 81, + "line": 100, "column": 29 }, "end": { - "line": 81, + "line": 100, "column": 31 } }, @@ -15270,15 +17510,15 @@ { "type": "CommentLine", "value": " Store all split catalog number values.", - "start": 3168, - "end": 3209, + "start": 3803, + "end": 3844, "loc": { "start": { - "line": 81, + "line": 100, "column": 33 }, "end": { - "line": 81, + "line": 100, "column": 74 } } @@ -15287,73 +17527,73 @@ }, { "type": "ExpressionStatement", - "start": 3216, - "end": 3297, + "start": 3851, + "end": 3932, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 87 } }, "expression": { "type": "AssignmentExpression", - "start": 3216, - "end": 3296, + "start": 3851, + "end": 3931, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 86 } }, "operator": "=", "left": { "type": "ArrayPattern", - "start": 3216, - "end": 3288, + "start": 3851, + "end": 3923, "loc": { "start": { - "line": 82, + "line": 101, "column": 6 }, "end": { - "line": 82, + "line": 101, "column": 78 } }, "elements": [ { "type": "MemberExpression", - "start": 3217, - "end": 3241, + "start": 3852, + "end": 3876, "loc": { "start": { - "line": 82, + "line": 101, "column": 7 }, "end": { - "line": 82, + "line": 101, "column": 31 } }, "object": { "type": "Identifier", - "start": 3217, - "end": 3225, + "start": 3852, + "end": 3860, "loc": { "start": { - "line": 82, + "line": 101, "column": 7 }, "end": { - "line": 82, + "line": 101, "column": 15 }, "identifierName": "specimen" @@ -15363,15 +17603,15 @@ }, "property": { "type": "Identifier", - "start": 3226, - "end": 3241, + "start": 3861, + "end": 3876, "loc": { "start": { - "line": 82, + "line": 101, "column": 16 }, "end": { - "line": 82, + "line": 101, "column": 31 }, "identifierName": "institutionCode" @@ -15383,29 +17623,29 @@ }, { "type": "MemberExpression", - "start": 3243, - "end": 3266, + "start": 3878, + "end": 3901, "loc": { "start": { - "line": 82, + "line": 101, "column": 33 }, "end": { - "line": 82, + "line": 101, "column": 56 } }, "object": { "type": "Identifier", - "start": 3243, - "end": 3251, + "start": 3878, + "end": 3886, "loc": { "start": { - "line": 82, + "line": 101, "column": 33 }, "end": { - "line": 82, + "line": 101, "column": 41 }, "identifierName": "specimen" @@ -15414,15 +17654,15 @@ }, "property": { "type": "Identifier", - "start": 3252, - "end": 3266, + "start": 3887, + "end": 3901, "loc": { "start": { - "line": 82, + "line": 101, "column": 42 }, "end": { - "line": 82, + "line": 101, "column": 56 }, "identifierName": "collectionCode" @@ -15433,29 +17673,29 @@ }, { "type": "RestElement", - "start": 3268, - "end": 3287, + "start": 3903, + "end": 3922, "loc": { "start": { - "line": 82, + "line": 101, "column": 58 }, "end": { - "line": 82, + "line": 101, "column": 77 } }, "argument": { "type": "Identifier", - "start": 3271, - "end": 3287, + "start": 3906, + "end": 3922, "loc": { "start": { - "line": 82, + "line": 101, "column": 61 }, "end": { - "line": 82, + "line": 101, "column": 77 }, "identifierName": "catalogNumValues" @@ -15468,15 +17708,15 @@ }, "right": { "type": "Identifier", - "start": 3291, - "end": 3296, + "start": 3926, + "end": 3931, "loc": { "start": { - "line": 82, + "line": 101, "column": 81 }, "end": { - "line": 82, + "line": 101, "column": 86 }, "identifierName": "comps" @@ -15489,15 +17729,15 @@ { "type": "CommentLine", "value": " Store all split catalog number values.", - "start": 3168, - "end": 3209, + "start": 3803, + "end": 3844, "loc": { "start": { - "line": 81, + "line": 100, "column": 33 }, "end": { - "line": 81, + "line": 100, "column": 74 } } @@ -15506,58 +17746,58 @@ }, { "type": "ExpressionStatement", - "start": 3304, - "end": 3356, + "start": 3939, + "end": 3991, "loc": { "start": { - "line": 83, + "line": 102, "column": 6 }, "end": { - "line": 83, + "line": 102, "column": 58 } }, "expression": { "type": "AssignmentExpression", - "start": 3304, - "end": 3355, + "start": 3939, + "end": 3990, "loc": { "start": { - "line": 83, + "line": 102, "column": 6 }, "end": { - "line": 83, + "line": 102, "column": 57 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 3304, - "end": 3326, + "start": 3939, + "end": 3961, "loc": { "start": { - "line": 83, + "line": 102, "column": 6 }, "end": { - "line": 83, + "line": 102, "column": 28 } }, "object": { "type": "Identifier", - "start": 3304, - "end": 3312, + "start": 3939, + "end": 3947, "loc": { "start": { - "line": 83, + "line": 102, "column": 6 }, "end": { - "line": 83, + "line": 102, "column": 14 }, "identifierName": "specimen" @@ -15566,15 +17806,15 @@ }, "property": { "type": "Identifier", - "start": 3313, - "end": 3326, + "start": 3948, + "end": 3961, "loc": { "start": { - "line": 83, + "line": 102, "column": 15 }, "end": { - "line": 83, + "line": 102, "column": 28 }, "identifierName": "catalogNumber" @@ -15585,43 +17825,43 @@ }, "right": { "type": "CallExpression", - "start": 3329, - "end": 3355, + "start": 3964, + "end": 3990, "loc": { "start": { - "line": 83, + "line": 102, "column": 31 }, "end": { - "line": 83, + "line": 102, "column": 57 } }, "callee": { "type": "MemberExpression", - "start": 3329, - "end": 3350, + "start": 3964, + "end": 3985, "loc": { "start": { - "line": 83, + "line": 102, "column": 31 }, "end": { - "line": 83, + "line": 102, "column": 52 } }, "object": { "type": "Identifier", - "start": 3329, - "end": 3345, + "start": 3964, + "end": 3980, "loc": { "start": { - "line": 83, + "line": 102, "column": 31 }, "end": { - "line": 83, + "line": 102, "column": 47 }, "identifierName": "catalogNumValues" @@ -15630,15 +17870,15 @@ }, "property": { "type": "Identifier", - "start": 3346, - "end": 3350, + "start": 3981, + "end": 3985, "loc": { "start": { - "line": 83, + "line": 102, "column": 48 }, "end": { - "line": 83, + "line": 102, "column": 52 }, "identifierName": "join" @@ -15650,15 +17890,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 3351, - "end": 3354, + "start": 3986, + "end": 3989, "loc": { "start": { - "line": 83, + "line": 102, "column": 53 }, "end": { - "line": 83, + "line": 102, "column": 56 } }, @@ -15681,57 +17921,57 @@ }, { "type": "ExpressionStatement", - "start": 3368, - "end": 3445, + "start": 4003, + "end": 4080, "loc": { "start": { - "line": 86, + "line": 105, "column": 4 }, "end": { - "line": 86, + "line": 105, "column": 81 } }, "expression": { "type": "CallExpression", - "start": 3368, - "end": 3444, + "start": 4003, + "end": 4079, "loc": { "start": { - "line": 86, + "line": 105, "column": 4 }, "end": { - "line": 86, + "line": 105, "column": 80 } }, "callee": { "type": "MemberExpression", - "start": 3368, - "end": 3388, + "start": 4003, + "end": 4023, "loc": { "start": { - "line": 86, + "line": 105, "column": 4 }, "end": { - "line": 86, + "line": 105, "column": 24 } }, "object": { "type": "Identifier", - "start": 3368, - "end": 3384, + "start": 4003, + "end": 4019, "loc": { "start": { - "line": 86, + "line": 105, "column": 4 }, "end": { - "line": 86, + "line": 105, "column": 20 }, "identifierName": "PhyxCacheManager" @@ -15740,15 +17980,15 @@ }, "property": { "type": "Identifier", - "start": 3385, - "end": 3388, + "start": 4020, + "end": 4023, "loc": { "start": { - "line": 86, + "line": 105, "column": 21 }, "end": { - "line": 86, + "line": 105, "column": 24 }, "identifierName": "put" @@ -15760,15 +18000,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 3389, - "end": 3424, + "start": 4024, + "end": 4059, "loc": { "start": { - "line": 86, + "line": 105, "column": 25 }, "end": { - "line": 86, + "line": 105, "column": 60 } }, @@ -15780,15 +18020,15 @@ }, { "type": "Identifier", - "start": 3426, - "end": 3433, + "start": 4061, + "end": 4068, "loc": { "start": { - "line": 86, + "line": 105, "column": 62 }, "end": { - "line": 86, + "line": 105, "column": 69 }, "identifierName": "occurID" @@ -15797,15 +18037,15 @@ }, { "type": "Identifier", - "start": 3435, - "end": 3443, + "start": 4070, + "end": 4078, "loc": { "start": { - "line": 86, + "line": 105, "column": 71 }, "end": { - "line": 86, + "line": 105, "column": 79 }, "identifierName": "specimen" @@ -15817,29 +18057,29 @@ }, { "type": "ReturnStatement", - "start": 3450, - "end": 3466, + "start": 4085, + "end": 4101, "loc": { "start": { - "line": 87, + "line": 106, "column": 4 }, "end": { - "line": 87, + "line": 106, "column": 20 } }, "argument": { "type": "Identifier", - "start": 3457, - "end": 3465, + "start": 4092, + "end": 4100, "loc": { "start": { - "line": 87, + "line": 106, "column": 11 }, "end": { - "line": 87, + "line": 106, "column": 19 }, "identifierName": "specimen" @@ -15855,15 +18095,15 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1351, - "end": 1632, + "start": 1986, + "end": 2267, "loc": { "start": { - "line": 35, + "line": 54, "column": 2 }, "end": { - "line": 40, + "line": 59, "column": 5 } } @@ -15873,15 +18113,15 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 3474, - "end": 3522, + "start": 4109, + "end": 4157, "loc": { "start": { - "line": 90, + "line": 109, "column": 2 }, "end": { - "line": 92, + "line": 111, "column": 5 } } @@ -15890,15 +18130,15 @@ }, { "type": "ClassMethod", - "start": 3525, - "end": 4040, + "start": 4160, + "end": 4675, "loc": { "start": { - "line": 93, + "line": 112, "column": 2 }, "end": { - "line": 104, + "line": 123, "column": 3 } }, @@ -15906,15 +18146,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3529, - "end": 3542, + "start": 4164, + "end": 4177, "loc": { "start": { - "line": 93, + "line": 112, "column": 6 }, "end": { - "line": 93, + "line": 112, "column": 19 }, "identifierName": "catalogNumber" @@ -15929,58 +18169,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3545, - "end": 4040, + "start": 4180, + "end": 4675, "loc": { "start": { - "line": 93, + "line": 112, "column": 22 }, "end": { - "line": 104, + "line": 123, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 3618, - "end": 3694, + "start": 4253, + "end": 4329, "loc": { "start": { - "line": 95, + "line": 114, "column": 4 }, "end": { - "line": 95, + "line": 114, "column": 80 } }, "test": { "type": "CallExpression", - "start": 3622, - "end": 3657, + "start": 4257, + "end": 4292, "loc": { "start": { - "line": 95, + "line": 114, "column": 8 }, "end": { - "line": 95, + "line": 114, "column": 43 } }, "callee": { "type": "Identifier", - "start": 3622, - "end": 3625, + "start": 4257, + "end": 4260, "loc": { "start": { - "line": 95, + "line": 114, "column": 8 }, "end": { - "line": 95, + "line": 114, "column": 11 }, "identifierName": "has" @@ -15991,44 +18231,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3626, - "end": 3639, + "start": 4261, + "end": 4274, "loc": { "start": { - "line": 95, + "line": 114, "column": 12 }, "end": { - "line": 95, + "line": 114, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 3626, - "end": 3630, + "start": 4261, + "end": 4265, "loc": { "start": { - "line": 95, + "line": 114, "column": 12 }, "end": { - "line": 95, + "line": 114, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3631, - "end": 3639, + "start": 4266, + "end": 4274, "loc": { "start": { - "line": 95, + "line": 114, "column": 17 }, "end": { - "line": 95, + "line": 114, "column": 25 }, "identifierName": "specimen" @@ -16039,15 +18279,15 @@ }, { "type": "StringLiteral", - "start": 3641, - "end": 3656, + "start": 4276, + "end": 4291, "loc": { "start": { - "line": 95, + "line": 114, "column": 27 }, "end": { - "line": 95, + "line": 114, "column": 42 } }, @@ -16062,72 +18302,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3659, - "end": 3694, + "start": 4294, + "end": 4329, "loc": { "start": { - "line": 95, + "line": 114, "column": 45 }, "end": { - "line": 95, + "line": 114, "column": 80 } }, "argument": { "type": "MemberExpression", - "start": 3666, - "end": 3693, + "start": 4301, + "end": 4328, "loc": { "start": { - "line": 95, + "line": 114, "column": 52 }, "end": { - "line": 95, + "line": 114, "column": 79 } }, "object": { "type": "MemberExpression", - "start": 3666, - "end": 3679, + "start": 4301, + "end": 4314, "loc": { "start": { - "line": 95, + "line": 114, "column": 52 }, "end": { - "line": 95, + "line": 114, "column": 65 } }, "object": { "type": "ThisExpression", - "start": 3666, - "end": 3670, + "start": 4301, + "end": 4305, "loc": { "start": { - "line": 95, + "line": 114, "column": 52 }, "end": { - "line": 95, + "line": 114, "column": 56 } } }, "property": { "type": "Identifier", - "start": 3671, - "end": 3679, + "start": 4306, + "end": 4314, "loc": { "start": { - "line": 95, + "line": 114, "column": 57 }, "end": { - "line": 95, + "line": 114, "column": 65 }, "identifierName": "specimen" @@ -16138,15 +18378,15 @@ }, "property": { "type": "Identifier", - "start": 3680, - "end": 3693, + "start": 4315, + "end": 4328, "loc": { "start": { - "line": 95, + "line": 114, "column": 66 }, "end": { - "line": 95, + "line": 114, "column": 79 }, "identifierName": "catalogNumber" @@ -16162,15 +18402,15 @@ { "type": "CommentLine", "value": " Get the catalog number from the specimen object if present.", - "start": 3551, - "end": 3613, + "start": 4186, + "end": 4248, "loc": { "start": { - "line": 94, + "line": 113, "column": 4 }, "end": { - "line": 94, + "line": 113, "column": 66 } } @@ -16180,15 +18420,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 3700, - "end": 3771, + "start": 4335, + "end": 4406, "loc": { "start": { - "line": 97, + "line": 116, "column": 4 }, "end": { - "line": 97, + "line": 116, "column": 75 } } @@ -16196,15 +18436,15 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 3776, - "end": 3804, + "start": 4411, + "end": 4439, "loc": { "start": { - "line": 98, + "line": 117, "column": 4 }, "end": { - "line": 98, + "line": 117, "column": 32 } } @@ -16213,43 +18453,43 @@ }, { "type": "IfStatement", - "start": 3809, - "end": 4014, + "start": 4444, + "end": 4649, "loc": { "start": { - "line": 99, + "line": 118, "column": 4 }, "end": { - "line": 102, + "line": 121, "column": 5 } }, "test": { "type": "CallExpression", - "start": 3813, - "end": 3847, + "start": 4448, + "end": 4482, "loc": { "start": { - "line": 99, + "line": 118, "column": 8 }, "end": { - "line": 99, + "line": 118, "column": 42 } }, "callee": { "type": "Identifier", - "start": 3813, - "end": 3816, + "start": 4448, + "end": 4451, "loc": { "start": { - "line": 99, + "line": 118, "column": 8 }, "end": { - "line": 99, + "line": 118, "column": 11 }, "identifierName": "has" @@ -16260,44 +18500,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3817, - "end": 3830, + "start": 4452, + "end": 4465, "loc": { "start": { - "line": 99, + "line": 118, "column": 12 }, "end": { - "line": 99, + "line": 118, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 3817, - "end": 3821, + "start": 4452, + "end": 4456, "loc": { "start": { - "line": 99, + "line": 118, "column": 12 }, "end": { - "line": 99, + "line": 118, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3822, - "end": 3830, + "start": 4457, + "end": 4465, "loc": { "start": { - "line": 99, + "line": 118, "column": 17 }, "end": { - "line": 99, + "line": 118, "column": 25 }, "identifierName": "specimen" @@ -16308,15 +18548,15 @@ }, { "type": "StringLiteral", - "start": 3832, - "end": 3846, + "start": 4467, + "end": 4481, "loc": { "start": { - "line": 99, + "line": 118, "column": 27 }, "end": { - "line": 99, + "line": 118, "column": 41 } }, @@ -16331,59 +18571,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 3849, - "end": 4014, + "start": 4484, + "end": 4649, "loc": { "start": { - "line": 99, + "line": 118, "column": 44 }, "end": { - "line": 102, + "line": 121, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 3857, - "end": 3935, + "start": 4492, + "end": 4570, "loc": { "start": { - "line": 100, + "line": 119, "column": 6 }, "end": { - "line": 100, + "line": 119, "column": 84 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 3863, - "end": 3934, + "start": 4498, + "end": 4569, "loc": { "start": { - "line": 100, + "line": 119, "column": 12 }, "end": { - "line": 100, + "line": 119, "column": 83 } }, "id": { "type": "Identifier", - "start": 3863, - "end": 3871, + "start": 4498, + "end": 4506, "loc": { "start": { - "line": 100, + "line": 119, "column": 12 }, "end": { - "line": 100, + "line": 119, "column": 20 }, "identifierName": "specimen" @@ -16392,43 +18632,43 @@ }, "init": { "type": "CallExpression", - "start": 3874, - "end": 3934, + "start": 4509, + "end": 4569, "loc": { "start": { - "line": 100, + "line": 119, "column": 23 }, "end": { - "line": 100, + "line": 119, "column": 83 } }, "callee": { "type": "MemberExpression", - "start": 3874, - "end": 3906, + "start": 4509, + "end": 4541, "loc": { "start": { - "line": 100, + "line": 119, "column": 23 }, "end": { - "line": 100, + "line": 119, "column": 55 } }, "object": { "type": "Identifier", - "start": 3874, - "end": 3889, + "start": 4509, + "end": 4524, "loc": { "start": { - "line": 100, + "line": 119, "column": 23 }, "end": { - "line": 100, + "line": 119, "column": 38 }, "identifierName": "SpecimenWrapper" @@ -16437,15 +18677,15 @@ }, "property": { "type": "Identifier", - "start": 3890, - "end": 3906, + "start": 4525, + "end": 4541, "loc": { "start": { - "line": 100, + "line": 119, "column": 39 }, "end": { - "line": 100, + "line": 119, "column": 55 }, "identifierName": "fromOccurrenceID" @@ -16457,58 +18697,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 3907, - "end": 3933, + "start": 4542, + "end": 4568, "loc": { "start": { - "line": 100, + "line": 119, "column": 56 }, "end": { - "line": 100, + "line": 119, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 3907, - "end": 3920, + "start": 4542, + "end": 4555, "loc": { "start": { - "line": 100, + "line": 119, "column": 56 }, "end": { - "line": 100, + "line": 119, "column": 69 } }, "object": { "type": "ThisExpression", - "start": 3907, - "end": 3911, + "start": 4542, + "end": 4546, "loc": { "start": { - "line": 100, + "line": 119, "column": 56 }, "end": { - "line": 100, + "line": 119, "column": 60 } } }, "property": { "type": "Identifier", - "start": 3912, - "end": 3920, + "start": 4547, + "end": 4555, "loc": { "start": { - "line": 100, + "line": 119, "column": 61 }, "end": { - "line": 100, + "line": 119, "column": 69 }, "identifierName": "specimen" @@ -16519,15 +18759,15 @@ }, "property": { "type": "Identifier", - "start": 3921, - "end": 3933, + "start": 4556, + "end": 4568, "loc": { "start": { - "line": 100, + "line": 119, "column": 70 }, "end": { - "line": 100, + "line": 119, "column": 82 }, "identifierName": "occurrenceID" @@ -16544,43 +18784,43 @@ }, { "type": "IfStatement", - "start": 3942, - "end": 4008, + "start": 4577, + "end": 4643, "loc": { "start": { - "line": 101, + "line": 120, "column": 6 }, "end": { - "line": 101, + "line": 120, "column": 72 } }, "test": { "type": "CallExpression", - "start": 3946, - "end": 3976, + "start": 4581, + "end": 4611, "loc": { "start": { - "line": 101, + "line": 120, "column": 10 }, "end": { - "line": 101, + "line": 120, "column": 40 } }, "callee": { "type": "Identifier", - "start": 3946, - "end": 3949, + "start": 4581, + "end": 4584, "loc": { "start": { - "line": 101, + "line": 120, "column": 10 }, "end": { - "line": 101, + "line": 120, "column": 13 }, "identifierName": "has" @@ -16590,15 +18830,15 @@ "arguments": [ { "type": "Identifier", - "start": 3950, - "end": 3958, + "start": 4585, + "end": 4593, "loc": { "start": { - "line": 101, + "line": 120, "column": 14 }, "end": { - "line": 101, + "line": 120, "column": 22 }, "identifierName": "specimen" @@ -16607,15 +18847,15 @@ }, { "type": "StringLiteral", - "start": 3960, - "end": 3975, + "start": 4595, + "end": 4610, "loc": { "start": { - "line": 101, + "line": 120, "column": 24 }, "end": { - "line": 101, + "line": 120, "column": 39 } }, @@ -16629,43 +18869,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3978, - "end": 4008, + "start": 4613, + "end": 4643, "loc": { "start": { - "line": 101, + "line": 120, "column": 42 }, "end": { - "line": 101, + "line": 120, "column": 72 } }, "argument": { "type": "MemberExpression", - "start": 3985, - "end": 4007, + "start": 4620, + "end": 4642, "loc": { "start": { - "line": 101, + "line": 120, "column": 49 }, "end": { - "line": 101, + "line": 120, "column": 71 } }, "object": { "type": "Identifier", - "start": 3985, - "end": 3993, + "start": 4620, + "end": 4628, "loc": { "start": { - "line": 101, + "line": 120, "column": 49 }, "end": { - "line": 101, + "line": 120, "column": 57 }, "identifierName": "specimen" @@ -16674,15 +18914,15 @@ }, "property": { "type": "Identifier", - "start": 3994, - "end": 4007, + "start": 4629, + "end": 4642, "loc": { "start": { - "line": 101, + "line": 120, "column": 58 }, "end": { - "line": 101, + "line": 120, "column": 71 }, "identifierName": "catalogNumber" @@ -16702,15 +18942,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 3700, - "end": 3771, + "start": 4335, + "end": 4406, "loc": { "start": { - "line": 97, + "line": 116, "column": 4 }, "end": { - "line": 97, + "line": 116, "column": 75 } } @@ -16718,15 +18958,15 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 3776, - "end": 3804, + "start": 4411, + "end": 4439, "loc": { "start": { - "line": 98, + "line": 117, "column": 4 }, "end": { - "line": 98, + "line": 117, "column": 32 } } @@ -16735,29 +18975,29 @@ }, { "type": "ReturnStatement", - "start": 4019, - "end": 4036, + "start": 4654, + "end": 4671, "loc": { "start": { - "line": 103, + "line": 122, "column": 4 }, "end": { - "line": 103, + "line": 122, "column": 21 } }, "argument": { "type": "Identifier", - "start": 4026, - "end": 4035, + "start": 4661, + "end": 4670, "loc": { "start": { - "line": 103, + "line": 122, "column": 11 }, "end": { - "line": 103, + "line": 122, "column": 20 }, "identifierName": "undefined" @@ -16773,15 +19013,15 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 3474, - "end": 3522, + "start": 4109, + "end": 4157, "loc": { "start": { - "line": 90, + "line": 109, "column": 2 }, "end": { - "line": 92, + "line": 111, "column": 5 } } @@ -16791,15 +19031,15 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4044, - "end": 4094, + "start": 4679, + "end": 4729, "loc": { "start": { - "line": 106, + "line": 125, "column": 2 }, "end": { - "line": 108, + "line": 127, "column": 5 } } @@ -16808,15 +19048,15 @@ }, { "type": "ClassMethod", - "start": 4097, - "end": 4624, + "start": 4732, + "end": 5259, "loc": { "start": { - "line": 109, + "line": 128, "column": 2 }, "end": { - "line": 120, + "line": 139, "column": 3 } }, @@ -16824,15 +19064,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4101, - "end": 4116, + "start": 4736, + "end": 4751, "loc": { "start": { - "line": 109, + "line": 128, "column": 6 }, "end": { - "line": 109, + "line": 128, "column": 21 }, "identifierName": "institutionCode" @@ -16847,58 +19087,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4119, - "end": 4624, + "start": 4754, + "end": 5259, "loc": { "start": { - "line": 109, + "line": 128, "column": 24 }, "end": { - "line": 120, + "line": 139, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4194, - "end": 4274, + "start": 4829, + "end": 4909, "loc": { "start": { - "line": 111, + "line": 130, "column": 4 }, "end": { - "line": 111, + "line": 130, "column": 84 } }, "test": { "type": "CallExpression", - "start": 4198, - "end": 4235, + "start": 4833, + "end": 4870, "loc": { "start": { - "line": 111, + "line": 130, "column": 8 }, "end": { - "line": 111, + "line": 130, "column": 45 } }, "callee": { "type": "Identifier", - "start": 4198, - "end": 4201, + "start": 4833, + "end": 4836, "loc": { "start": { - "line": 111, + "line": 130, "column": 8 }, "end": { - "line": 111, + "line": 130, "column": 11 }, "identifierName": "has" @@ -16909,44 +19149,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4202, - "end": 4215, + "start": 4837, + "end": 4850, "loc": { "start": { - "line": 111, + "line": 130, "column": 12 }, "end": { - "line": 111, + "line": 130, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4202, - "end": 4206, + "start": 4837, + "end": 4841, "loc": { "start": { - "line": 111, + "line": 130, "column": 12 }, "end": { - "line": 111, + "line": 130, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4207, - "end": 4215, + "start": 4842, + "end": 4850, "loc": { "start": { - "line": 111, + "line": 130, "column": 17 }, "end": { - "line": 111, + "line": 130, "column": 25 }, "identifierName": "specimen" @@ -16957,15 +19197,15 @@ }, { "type": "StringLiteral", - "start": 4217, - "end": 4234, + "start": 4852, + "end": 4869, "loc": { "start": { - "line": 111, + "line": 130, "column": 27 }, "end": { - "line": 111, + "line": 130, "column": 44 } }, @@ -16980,72 +19220,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4237, - "end": 4274, + "start": 4872, + "end": 4909, "loc": { "start": { - "line": 111, + "line": 130, "column": 47 }, "end": { - "line": 111, + "line": 130, "column": 84 } }, "argument": { "type": "MemberExpression", - "start": 4244, - "end": 4273, + "start": 4879, + "end": 4908, "loc": { "start": { - "line": 111, + "line": 130, "column": 54 }, "end": { - "line": 111, + "line": 130, "column": 83 } }, "object": { "type": "MemberExpression", - "start": 4244, - "end": 4257, + "start": 4879, + "end": 4892, "loc": { "start": { - "line": 111, + "line": 130, "column": 54 }, "end": { - "line": 111, + "line": 130, "column": 67 } }, "object": { "type": "ThisExpression", - "start": 4244, - "end": 4248, + "start": 4879, + "end": 4883, "loc": { "start": { - "line": 111, + "line": 130, "column": 54 }, "end": { - "line": 111, + "line": 130, "column": 58 } } }, "property": { "type": "Identifier", - "start": 4249, - "end": 4257, + "start": 4884, + "end": 4892, "loc": { "start": { - "line": 111, + "line": 130, "column": 59 }, "end": { - "line": 111, + "line": 130, "column": 67 }, "identifierName": "specimen" @@ -17056,15 +19296,15 @@ }, "property": { "type": "Identifier", - "start": 4258, - "end": 4273, + "start": 4893, + "end": 4908, "loc": { "start": { - "line": 111, + "line": 130, "column": 68 }, "end": { - "line": 111, + "line": 130, "column": 83 }, "identifierName": "institutionCode" @@ -17080,15 +19320,15 @@ { "type": "CommentLine", "value": " Get the institution code from the specimen object if present.", - "start": 4125, - "end": 4189, + "start": 4760, + "end": 4824, "loc": { "start": { - "line": 110, + "line": 129, "column": 4 }, "end": { - "line": 110, + "line": 129, "column": 68 } } @@ -17098,15 +19338,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4280, - "end": 4352, + "start": 4915, + "end": 4987, "loc": { "start": { - "line": 113, + "line": 132, "column": 4 }, "end": { - "line": 113, + "line": 132, "column": 76 } } @@ -17114,15 +19354,15 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4357, - "end": 4384, + "start": 4992, + "end": 5019, "loc": { "start": { - "line": 114, + "line": 133, "column": 4 }, "end": { - "line": 114, + "line": 133, "column": 31 } } @@ -17131,43 +19371,43 @@ }, { "type": "IfStatement", - "start": 4389, - "end": 4598, + "start": 5024, + "end": 5233, "loc": { "start": { - "line": 115, + "line": 134, "column": 4 }, "end": { - "line": 118, + "line": 137, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4393, - "end": 4427, + "start": 5028, + "end": 5062, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 42 } }, "callee": { "type": "Identifier", - "start": 4393, - "end": 4396, + "start": 5028, + "end": 5031, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 11 }, "identifierName": "has" @@ -17178,44 +19418,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4397, - "end": 4410, + "start": 5032, + "end": 5045, "loc": { "start": { - "line": 115, + "line": 134, "column": 12 }, "end": { - "line": 115, + "line": 134, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4397, - "end": 4401, + "start": 5032, + "end": 5036, "loc": { "start": { - "line": 115, + "line": 134, "column": 12 }, "end": { - "line": 115, + "line": 134, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4402, - "end": 4410, + "start": 5037, + "end": 5045, "loc": { "start": { - "line": 115, + "line": 134, "column": 17 }, "end": { - "line": 115, + "line": 134, "column": 25 }, "identifierName": "specimen" @@ -17226,15 +19466,15 @@ }, { "type": "StringLiteral", - "start": 4412, - "end": 4426, + "start": 5047, + "end": 5061, "loc": { "start": { - "line": 115, + "line": 134, "column": 27 }, "end": { - "line": 115, + "line": 134, "column": 41 } }, @@ -17249,59 +19489,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 4429, - "end": 4598, + "start": 5064, + "end": 5233, "loc": { "start": { - "line": 115, + "line": 134, "column": 44 }, "end": { - "line": 118, + "line": 137, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 4437, - "end": 4515, + "start": 5072, + "end": 5150, "loc": { "start": { - "line": 116, + "line": 135, "column": 6 }, "end": { - "line": 116, + "line": 135, "column": 84 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4443, - "end": 4514, + "start": 5078, + "end": 5149, "loc": { "start": { - "line": 116, + "line": 135, "column": 12 }, "end": { - "line": 116, + "line": 135, "column": 83 } }, "id": { "type": "Identifier", - "start": 4443, - "end": 4451, + "start": 5078, + "end": 5086, "loc": { "start": { - "line": 116, + "line": 135, "column": 12 }, "end": { - "line": 116, + "line": 135, "column": 20 }, "identifierName": "specimen" @@ -17310,43 +19550,43 @@ }, "init": { "type": "CallExpression", - "start": 4454, - "end": 4514, + "start": 5089, + "end": 5149, "loc": { "start": { - "line": 116, + "line": 135, "column": 23 }, "end": { - "line": 116, + "line": 135, "column": 83 } }, "callee": { "type": "MemberExpression", - "start": 4454, - "end": 4486, + "start": 5089, + "end": 5121, "loc": { "start": { - "line": 116, + "line": 135, "column": 23 }, "end": { - "line": 116, + "line": 135, "column": 55 } }, "object": { "type": "Identifier", - "start": 4454, - "end": 4469, + "start": 5089, + "end": 5104, "loc": { "start": { - "line": 116, + "line": 135, "column": 23 }, "end": { - "line": 116, + "line": 135, "column": 38 }, "identifierName": "SpecimenWrapper" @@ -17355,15 +19595,15 @@ }, "property": { "type": "Identifier", - "start": 4470, - "end": 4486, + "start": 5105, + "end": 5121, "loc": { "start": { - "line": 116, + "line": 135, "column": 39 }, "end": { - "line": 116, + "line": 135, "column": 55 }, "identifierName": "fromOccurrenceID" @@ -17375,58 +19615,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 4487, - "end": 4513, + "start": 5122, + "end": 5148, "loc": { "start": { - "line": 116, + "line": 135, "column": 56 }, "end": { - "line": 116, + "line": 135, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 4487, - "end": 4500, + "start": 5122, + "end": 5135, "loc": { "start": { - "line": 116, + "line": 135, "column": 56 }, "end": { - "line": 116, + "line": 135, "column": 69 } }, "object": { "type": "ThisExpression", - "start": 4487, - "end": 4491, + "start": 5122, + "end": 5126, "loc": { "start": { - "line": 116, + "line": 135, "column": 56 }, "end": { - "line": 116, + "line": 135, "column": 60 } } }, "property": { "type": "Identifier", - "start": 4492, - "end": 4500, + "start": 5127, + "end": 5135, "loc": { "start": { - "line": 116, + "line": 135, "column": 61 }, "end": { - "line": 116, + "line": 135, "column": 69 }, "identifierName": "specimen" @@ -17437,15 +19677,15 @@ }, "property": { "type": "Identifier", - "start": 4501, - "end": 4513, + "start": 5136, + "end": 5148, "loc": { "start": { - "line": 116, + "line": 135, "column": 70 }, "end": { - "line": 116, + "line": 135, "column": 82 }, "identifierName": "occurrenceID" @@ -17462,43 +19702,43 @@ }, { "type": "IfStatement", - "start": 4522, - "end": 4592, + "start": 5157, + "end": 5227, "loc": { "start": { - "line": 117, + "line": 136, "column": 6 }, "end": { - "line": 117, + "line": 136, "column": 76 } }, "test": { "type": "CallExpression", - "start": 4526, - "end": 4558, + "start": 5161, + "end": 5193, "loc": { "start": { - "line": 117, + "line": 136, "column": 10 }, "end": { - "line": 117, + "line": 136, "column": 42 } }, "callee": { "type": "Identifier", - "start": 4526, - "end": 4529, + "start": 5161, + "end": 5164, "loc": { "start": { - "line": 117, + "line": 136, "column": 10 }, "end": { - "line": 117, + "line": 136, "column": 13 }, "identifierName": "has" @@ -17508,15 +19748,15 @@ "arguments": [ { "type": "Identifier", - "start": 4530, - "end": 4538, + "start": 5165, + "end": 5173, "loc": { "start": { - "line": 117, + "line": 136, "column": 14 }, "end": { - "line": 117, + "line": 136, "column": 22 }, "identifierName": "specimen" @@ -17525,15 +19765,15 @@ }, { "type": "StringLiteral", - "start": 4540, - "end": 4557, + "start": 5175, + "end": 5192, "loc": { "start": { - "line": 117, + "line": 136, "column": 24 }, "end": { - "line": 117, + "line": 136, "column": 41 } }, @@ -17547,43 +19787,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4560, - "end": 4592, + "start": 5195, + "end": 5227, "loc": { "start": { - "line": 117, + "line": 136, "column": 44 }, "end": { - "line": 117, + "line": 136, "column": 76 } }, "argument": { "type": "MemberExpression", - "start": 4567, - "end": 4591, + "start": 5202, + "end": 5226, "loc": { "start": { - "line": 117, + "line": 136, "column": 51 }, "end": { - "line": 117, + "line": 136, "column": 75 } }, "object": { "type": "Identifier", - "start": 4567, - "end": 4575, + "start": 5202, + "end": 5210, "loc": { "start": { - "line": 117, + "line": 136, "column": 51 }, "end": { - "line": 117, + "line": 136, "column": 59 }, "identifierName": "specimen" @@ -17592,15 +19832,15 @@ }, "property": { "type": "Identifier", - "start": 4576, - "end": 4591, + "start": 5211, + "end": 5226, "loc": { "start": { - "line": 117, + "line": 136, "column": 60 }, "end": { - "line": 117, + "line": 136, "column": 75 }, "identifierName": "institutionCode" @@ -17620,15 +19860,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4280, - "end": 4352, + "start": 4915, + "end": 4987, "loc": { "start": { - "line": 113, + "line": 132, "column": 4 }, "end": { - "line": 113, + "line": 132, "column": 76 } } @@ -17636,15 +19876,15 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4357, - "end": 4384, + "start": 4992, + "end": 5019, "loc": { "start": { - "line": 114, + "line": 133, "column": 4 }, "end": { - "line": 114, + "line": 133, "column": 31 } } @@ -17653,29 +19893,29 @@ }, { "type": "ReturnStatement", - "start": 4603, - "end": 4620, + "start": 5238, + "end": 5255, "loc": { "start": { - "line": 119, + "line": 138, "column": 4 }, "end": { - "line": 119, + "line": 138, "column": 21 } }, "argument": { "type": "Identifier", - "start": 4610, - "end": 4619, + "start": 5245, + "end": 5254, "loc": { "start": { - "line": 119, + "line": 138, "column": 11 }, "end": { - "line": 119, + "line": 138, "column": 20 }, "identifierName": "undefined" @@ -17691,15 +19931,15 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4044, - "end": 4094, + "start": 4679, + "end": 4729, "loc": { "start": { - "line": 106, + "line": 125, "column": 2 }, "end": { - "line": 108, + "line": 127, "column": 5 } } @@ -17709,15 +19949,15 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 4628, - "end": 4677, + "start": 5263, + "end": 5312, "loc": { "start": { - "line": 122, + "line": 141, "column": 2 }, "end": { - "line": 124, + "line": 143, "column": 5 } } @@ -17726,15 +19966,15 @@ }, { "type": "ClassMethod", - "start": 4680, - "end": 5201, + "start": 5315, + "end": 5836, "loc": { "start": { - "line": 125, + "line": 144, "column": 2 }, "end": { - "line": 136, + "line": 155, "column": 3 } }, @@ -17742,15 +19982,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4684, - "end": 4698, + "start": 5319, + "end": 5333, "loc": { "start": { - "line": 125, + "line": 144, "column": 6 }, "end": { - "line": 125, + "line": 144, "column": 20 }, "identifierName": "collectionCode" @@ -17765,58 +20005,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4701, - "end": 5201, + "start": 5336, + "end": 5836, "loc": { "start": { - "line": 125, + "line": 144, "column": 23 }, "end": { - "line": 136, + "line": 155, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4775, - "end": 4853, + "start": 5410, + "end": 5488, "loc": { "start": { - "line": 127, + "line": 146, "column": 4 }, "end": { - "line": 127, + "line": 146, "column": 82 } }, "test": { "type": "CallExpression", - "start": 4779, - "end": 4815, + "start": 5414, + "end": 5450, "loc": { "start": { - "line": 127, + "line": 146, "column": 8 }, "end": { - "line": 127, + "line": 146, "column": 44 } }, "callee": { "type": "Identifier", - "start": 4779, - "end": 4782, + "start": 5414, + "end": 5417, "loc": { "start": { - "line": 127, + "line": 146, "column": 8 }, "end": { - "line": 127, + "line": 146, "column": 11 }, "identifierName": "has" @@ -17827,44 +20067,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4783, - "end": 4796, + "start": 5418, + "end": 5431, "loc": { "start": { - "line": 127, + "line": 146, "column": 12 }, "end": { - "line": 127, + "line": 146, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4783, - "end": 4787, + "start": 5418, + "end": 5422, "loc": { "start": { - "line": 127, + "line": 146, "column": 12 }, "end": { - "line": 127, + "line": 146, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4788, - "end": 4796, + "start": 5423, + "end": 5431, "loc": { "start": { - "line": 127, + "line": 146, "column": 17 }, "end": { - "line": 127, + "line": 146, "column": 25 }, "identifierName": "specimen" @@ -17875,15 +20115,15 @@ }, { "type": "StringLiteral", - "start": 4798, - "end": 4814, + "start": 5433, + "end": 5449, "loc": { "start": { - "line": 127, + "line": 146, "column": 27 }, "end": { - "line": 127, + "line": 146, "column": 43 } }, @@ -17898,72 +20138,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4817, - "end": 4853, + "start": 5452, + "end": 5488, "loc": { "start": { - "line": 127, + "line": 146, "column": 46 }, "end": { - "line": 127, + "line": 146, "column": 82 } }, "argument": { "type": "MemberExpression", - "start": 4824, - "end": 4852, + "start": 5459, + "end": 5487, "loc": { "start": { - "line": 127, + "line": 146, "column": 53 }, "end": { - "line": 127, + "line": 146, "column": 81 } }, "object": { "type": "MemberExpression", - "start": 4824, - "end": 4837, + "start": 5459, + "end": 5472, "loc": { "start": { - "line": 127, + "line": 146, "column": 53 }, "end": { - "line": 127, + "line": 146, "column": 66 } }, "object": { "type": "ThisExpression", - "start": 4824, - "end": 4828, + "start": 5459, + "end": 5463, "loc": { "start": { - "line": 127, + "line": 146, "column": 53 }, "end": { - "line": 127, + "line": 146, "column": 57 } } }, "property": { "type": "Identifier", - "start": 4829, - "end": 4837, + "start": 5464, + "end": 5472, "loc": { "start": { - "line": 127, + "line": 146, "column": 58 }, "end": { - "line": 127, + "line": 146, "column": 66 }, "identifierName": "specimen" @@ -17974,15 +20214,15 @@ }, "property": { "type": "Identifier", - "start": 4838, - "end": 4852, + "start": 5473, + "end": 5487, "loc": { "start": { - "line": 127, + "line": 146, "column": 67 }, "end": { - "line": 127, + "line": 146, "column": 81 }, "identifierName": "collectionCode" @@ -17998,15 +20238,15 @@ { "type": "CommentLine", "value": " Get the collection code from the specimen object if present.", - "start": 4707, - "end": 4770, + "start": 5342, + "end": 5405, "loc": { "start": { - "line": 126, + "line": 145, "column": 4 }, "end": { - "line": 126, + "line": 145, "column": 67 } } @@ -18016,15 +20256,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4859, - "end": 4931, + "start": 5494, + "end": 5566, "loc": { "start": { - "line": 129, + "line": 148, "column": 4 }, "end": { - "line": 129, + "line": 148, "column": 76 } } @@ -18032,15 +20272,15 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4936, - "end": 4963, + "start": 5571, + "end": 5598, "loc": { "start": { - "line": 130, + "line": 149, "column": 4 }, "end": { - "line": 130, + "line": 149, "column": 31 } } @@ -18049,43 +20289,43 @@ }, { "type": "IfStatement", - "start": 4968, - "end": 5175, + "start": 5603, + "end": 5810, "loc": { "start": { - "line": 131, + "line": 150, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4972, - "end": 5006, + "start": 5607, + "end": 5641, "loc": { "start": { - "line": 131, + "line": 150, "column": 8 }, "end": { - "line": 131, + "line": 150, "column": 42 } }, "callee": { "type": "Identifier", - "start": 4972, - "end": 4975, + "start": 5607, + "end": 5610, "loc": { "start": { - "line": 131, + "line": 150, "column": 8 }, "end": { - "line": 131, + "line": 150, "column": 11 }, "identifierName": "has" @@ -18096,44 +20336,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 4976, - "end": 4989, + "start": 5611, + "end": 5624, "loc": { "start": { - "line": 131, + "line": 150, "column": 12 }, "end": { - "line": 131, + "line": 150, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 4976, - "end": 4980, + "start": 5611, + "end": 5615, "loc": { "start": { - "line": 131, + "line": 150, "column": 12 }, "end": { - "line": 131, + "line": 150, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4981, - "end": 4989, + "start": 5616, + "end": 5624, "loc": { "start": { - "line": 131, + "line": 150, "column": 17 }, "end": { - "line": 131, + "line": 150, "column": 25 }, "identifierName": "specimen" @@ -18144,15 +20384,15 @@ }, { "type": "StringLiteral", - "start": 4991, - "end": 5005, + "start": 5626, + "end": 5640, "loc": { "start": { - "line": 131, + "line": 150, "column": 27 }, "end": { - "line": 131, + "line": 150, "column": 41 } }, @@ -18167,59 +20407,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5008, - "end": 5175, + "start": 5643, + "end": 5810, "loc": { "start": { - "line": 131, + "line": 150, "column": 44 }, "end": { - "line": 134, + "line": 153, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 5016, - "end": 5094, + "start": 5651, + "end": 5729, "loc": { "start": { - "line": 132, + "line": 151, "column": 6 }, "end": { - "line": 132, + "line": 151, "column": 84 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5022, - "end": 5093, + "start": 5657, + "end": 5728, "loc": { "start": { - "line": 132, + "line": 151, "column": 12 }, "end": { - "line": 132, + "line": 151, "column": 83 } }, "id": { "type": "Identifier", - "start": 5022, - "end": 5030, + "start": 5657, + "end": 5665, "loc": { "start": { - "line": 132, + "line": 151, "column": 12 }, "end": { - "line": 132, + "line": 151, "column": 20 }, "identifierName": "specimen" @@ -18228,43 +20468,43 @@ }, "init": { "type": "CallExpression", - "start": 5033, - "end": 5093, + "start": 5668, + "end": 5728, "loc": { "start": { - "line": 132, + "line": 151, "column": 23 }, "end": { - "line": 132, + "line": 151, "column": 83 } }, "callee": { "type": "MemberExpression", - "start": 5033, - "end": 5065, + "start": 5668, + "end": 5700, "loc": { "start": { - "line": 132, + "line": 151, "column": 23 }, "end": { - "line": 132, + "line": 151, "column": 55 } }, "object": { "type": "Identifier", - "start": 5033, - "end": 5048, + "start": 5668, + "end": 5683, "loc": { "start": { - "line": 132, + "line": 151, "column": 23 }, "end": { - "line": 132, + "line": 151, "column": 38 }, "identifierName": "SpecimenWrapper" @@ -18273,15 +20513,15 @@ }, "property": { "type": "Identifier", - "start": 5049, - "end": 5065, + "start": 5684, + "end": 5700, "loc": { "start": { - "line": 132, + "line": 151, "column": 39 }, "end": { - "line": 132, + "line": 151, "column": 55 }, "identifierName": "fromOccurrenceID" @@ -18293,58 +20533,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 5066, - "end": 5092, + "start": 5701, + "end": 5727, "loc": { "start": { - "line": 132, + "line": 151, "column": 56 }, "end": { - "line": 132, + "line": 151, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 5066, - "end": 5079, + "start": 5701, + "end": 5714, "loc": { "start": { - "line": 132, + "line": 151, "column": 56 }, "end": { - "line": 132, + "line": 151, "column": 69 } }, "object": { "type": "ThisExpression", - "start": 5066, - "end": 5070, + "start": 5701, + "end": 5705, "loc": { "start": { - "line": 132, + "line": 151, "column": 56 }, "end": { - "line": 132, + "line": 151, "column": 60 } } }, "property": { "type": "Identifier", - "start": 5071, - "end": 5079, + "start": 5706, + "end": 5714, "loc": { "start": { - "line": 132, + "line": 151, "column": 61 }, "end": { - "line": 132, + "line": 151, "column": 69 }, "identifierName": "specimen" @@ -18355,15 +20595,15 @@ }, "property": { "type": "Identifier", - "start": 5080, - "end": 5092, + "start": 5715, + "end": 5727, "loc": { "start": { - "line": 132, + "line": 151, "column": 70 }, "end": { - "line": 132, + "line": 151, "column": 82 }, "identifierName": "occurrenceID" @@ -18380,43 +20620,43 @@ }, { "type": "IfStatement", - "start": 5101, - "end": 5169, + "start": 5736, + "end": 5804, "loc": { "start": { - "line": 133, + "line": 152, "column": 6 }, "end": { - "line": 133, + "line": 152, "column": 74 } }, "test": { "type": "CallExpression", - "start": 5105, - "end": 5136, + "start": 5740, + "end": 5771, "loc": { "start": { - "line": 133, + "line": 152, "column": 10 }, "end": { - "line": 133, + "line": 152, "column": 41 } }, "callee": { "type": "Identifier", - "start": 5105, - "end": 5108, + "start": 5740, + "end": 5743, "loc": { "start": { - "line": 133, + "line": 152, "column": 10 }, "end": { - "line": 133, + "line": 152, "column": 13 }, "identifierName": "has" @@ -18426,15 +20666,15 @@ "arguments": [ { "type": "Identifier", - "start": 5109, - "end": 5117, + "start": 5744, + "end": 5752, "loc": { "start": { - "line": 133, + "line": 152, "column": 14 }, "end": { - "line": 133, + "line": 152, "column": 22 }, "identifierName": "specimen" @@ -18443,15 +20683,15 @@ }, { "type": "StringLiteral", - "start": 5119, - "end": 5135, + "start": 5754, + "end": 5770, "loc": { "start": { - "line": 133, + "line": 152, "column": 24 }, "end": { - "line": 133, + "line": 152, "column": 40 } }, @@ -18465,43 +20705,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5138, - "end": 5169, + "start": 5773, + "end": 5804, "loc": { "start": { - "line": 133, + "line": 152, "column": 43 }, "end": { - "line": 133, + "line": 152, "column": 74 } }, "argument": { "type": "MemberExpression", - "start": 5145, - "end": 5168, + "start": 5780, + "end": 5803, "loc": { "start": { - "line": 133, + "line": 152, "column": 50 }, "end": { - "line": 133, + "line": 152, "column": 73 } }, "object": { "type": "Identifier", - "start": 5145, - "end": 5153, + "start": 5780, + "end": 5788, "loc": { "start": { - "line": 133, + "line": 152, "column": 50 }, "end": { - "line": 133, + "line": 152, "column": 58 }, "identifierName": "specimen" @@ -18510,15 +20750,15 @@ }, "property": { "type": "Identifier", - "start": 5154, - "end": 5168, + "start": 5789, + "end": 5803, "loc": { "start": { - "line": 133, + "line": 152, "column": 59 }, "end": { - "line": 133, + "line": 152, "column": 73 }, "identifierName": "collectionCode" @@ -18538,15 +20778,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4859, - "end": 4931, + "start": 5494, + "end": 5566, "loc": { "start": { - "line": 129, + "line": 148, "column": 4 }, "end": { - "line": 129, + "line": 148, "column": 76 } } @@ -18554,15 +20794,15 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4936, - "end": 4963, + "start": 5571, + "end": 5598, "loc": { "start": { - "line": 130, + "line": 149, "column": 4 }, "end": { - "line": 130, + "line": 149, "column": 31 } } @@ -18571,29 +20811,29 @@ }, { "type": "ReturnStatement", - "start": 5180, - "end": 5197, + "start": 5815, + "end": 5832, "loc": { "start": { - "line": 135, + "line": 154, "column": 4 }, "end": { - "line": 135, + "line": 154, "column": 21 } }, "argument": { "type": "Identifier", - "start": 5187, - "end": 5196, + "start": 5822, + "end": 5831, "loc": { "start": { - "line": 135, + "line": 154, "column": 11 }, "end": { - "line": 135, + "line": 154, "column": 20 }, "identifierName": "undefined" @@ -18609,15 +20849,15 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 4628, - "end": 4677, + "start": 5263, + "end": 5312, "loc": { "start": { - "line": 122, + "line": 141, "column": 2 }, "end": { - "line": 124, + "line": 143, "column": 5 } } @@ -18627,15 +20867,15 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5205, - "end": 5464, + "start": 5840, + "end": 6099, "loc": { "start": { - "line": 138, + "line": 157, "column": 2 }, "end": { - "line": 143, + "line": 162, "column": 5 } } @@ -18644,15 +20884,15 @@ }, { "type": "ClassMethod", - "start": 5467, - "end": 6507, + "start": 6102, + "end": 7142, "loc": { "start": { - "line": 144, + "line": 163, "column": 2 }, "end": { - "line": 166, + "line": 185, "column": 3 } }, @@ -18660,15 +20900,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 5471, - "end": 5483, + "start": 6106, + "end": 6118, "loc": { "start": { - "line": 144, + "line": 163, "column": 6 }, "end": { - "line": 144, + "line": 163, "column": 18 }, "identifierName": "occurrenceID" @@ -18683,72 +20923,72 @@ "params": [], "body": { "type": "BlockStatement", - "start": 5486, - "end": 6507, + "start": 6121, + "end": 7142, "loc": { "start": { - "line": 144, + "line": 163, "column": 21 }, "end": { - "line": 166, + "line": 185, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 5537, - "end": 5676, + "start": 6172, + "end": 6311, "loc": { "start": { - "line": 146, + "line": 165, "column": 4 }, "end": { - "line": 148, + "line": 167, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 5541, - "end": 5619, + "start": 6176, + "end": 6254, "loc": { "start": { - "line": 146, + "line": 165, "column": 8 }, "end": { - "line": 146, + "line": 165, "column": 86 } }, "left": { "type": "CallExpression", - "start": 5541, - "end": 5575, + "start": 6176, + "end": 6210, "loc": { "start": { - "line": 146, + "line": 165, "column": 8 }, "end": { - "line": 146, + "line": 165, "column": 42 } }, "callee": { "type": "Identifier", - "start": 5541, - "end": 5544, + "start": 6176, + "end": 6179, "loc": { "start": { - "line": 146, + "line": 165, "column": 8 }, "end": { - "line": 146, + "line": 165, "column": 11 }, "identifierName": "has" @@ -18759,44 +20999,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 5545, - "end": 5558, + "start": 6180, + "end": 6193, "loc": { "start": { - "line": 146, + "line": 165, "column": 12 }, "end": { - "line": 146, + "line": 165, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 5545, - "end": 5549, + "start": 6180, + "end": 6184, "loc": { "start": { - "line": 146, + "line": 165, "column": 12 }, "end": { - "line": 146, + "line": 165, "column": 16 } } }, "property": { "type": "Identifier", - "start": 5550, - "end": 5558, + "start": 6185, + "end": 6193, "loc": { "start": { - "line": 146, + "line": 165, "column": 17 }, "end": { - "line": 146, + "line": 165, "column": 25 }, "identifierName": "specimen" @@ -18807,15 +21047,15 @@ }, { "type": "StringLiteral", - "start": 5560, - "end": 5574, + "start": 6195, + "end": 6209, "loc": { "start": { - "line": 146, + "line": 165, "column": 27 }, "end": { - "line": 146, + "line": 165, "column": 41 } }, @@ -18831,100 +21071,100 @@ "operator": "&&", "right": { "type": "BinaryExpression", - "start": 5579, - "end": 5619, + "start": 6214, + "end": 6254, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 86 } }, "left": { "type": "CallExpression", - "start": 5579, - "end": 5612, + "start": 6214, + "end": 6247, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 79 } }, "callee": { "type": "MemberExpression", - "start": 5579, - "end": 5610, + "start": 6214, + "end": 6245, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 77 } }, "object": { "type": "MemberExpression", - "start": 5579, - "end": 5605, + "start": 6214, + "end": 6240, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 72 } }, "object": { "type": "MemberExpression", - "start": 5579, - "end": 5592, + "start": 6214, + "end": 6227, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 59 } }, "object": { "type": "ThisExpression", - "start": 5579, - "end": 5583, + "start": 6214, + "end": 6218, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 50 } } }, "property": { "type": "Identifier", - "start": 5584, - "end": 5592, + "start": 6219, + "end": 6227, "loc": { "start": { - "line": 146, + "line": 165, "column": 51 }, "end": { - "line": 146, + "line": 165, "column": 59 }, "identifierName": "specimen" @@ -18935,15 +21175,15 @@ }, "property": { "type": "Identifier", - "start": 5593, - "end": 5605, + "start": 6228, + "end": 6240, "loc": { "start": { - "line": 146, + "line": 165, "column": 60 }, "end": { - "line": 146, + "line": 165, "column": 72 }, "identifierName": "occurrenceID" @@ -18954,15 +21194,15 @@ }, "property": { "type": "Identifier", - "start": 5606, - "end": 5610, + "start": 6241, + "end": 6245, "loc": { "start": { - "line": 146, + "line": 165, "column": 73 }, "end": { - "line": 146, + "line": 165, "column": 77 }, "identifierName": "trim" @@ -18976,15 +21216,15 @@ "operator": "!==", "right": { "type": "StringLiteral", - "start": 5617, - "end": 5619, + "start": 6252, + "end": 6254, "loc": { "start": { - "line": 146, + "line": 165, "column": 84 }, "end": { - "line": 146, + "line": 165, "column": 86 } }, @@ -18999,115 +21239,115 @@ }, "consequent": { "type": "BlockStatement", - "start": 5621, - "end": 5676, + "start": 6256, + "end": 6311, "loc": { "start": { - "line": 146, + "line": 165, "column": 88 }, "end": { - "line": 148, + "line": 167, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 5629, - "end": 5670, + "start": 6264, + "end": 6305, "loc": { "start": { - "line": 147, + "line": 166, "column": 6 }, "end": { - "line": 147, + "line": 166, "column": 47 } }, "argument": { "type": "CallExpression", - "start": 5636, - "end": 5669, + "start": 6271, + "end": 6304, "loc": { "start": { - "line": 147, + "line": 166, "column": 13 }, "end": { - "line": 147, + "line": 166, "column": 46 } }, "callee": { "type": "MemberExpression", - "start": 5636, - "end": 5667, + "start": 6271, + "end": 6302, "loc": { "start": { - "line": 147, + "line": 166, "column": 13 }, "end": { - "line": 147, + "line": 166, "column": 44 } }, "object": { "type": "MemberExpression", - "start": 5636, - "end": 5662, + "start": 6271, + "end": 6297, "loc": { "start": { - "line": 147, + "line": 166, "column": 13 }, "end": { - "line": 147, + "line": 166, "column": 39 } }, "object": { "type": "MemberExpression", - "start": 5636, - "end": 5649, + "start": 6271, + "end": 6284, "loc": { "start": { - "line": 147, + "line": 166, "column": 13 }, "end": { - "line": 147, + "line": 166, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 5636, - "end": 5640, + "start": 6271, + "end": 6275, "loc": { "start": { - "line": 147, + "line": 166, "column": 13 }, "end": { - "line": 147, + "line": 166, "column": 17 } } }, "property": { "type": "Identifier", - "start": 5641, - "end": 5649, + "start": 6276, + "end": 6284, "loc": { "start": { - "line": 147, + "line": 166, "column": 18 }, "end": { - "line": 147, + "line": 166, "column": 26 }, "identifierName": "specimen" @@ -19118,15 +21358,15 @@ }, "property": { "type": "Identifier", - "start": 5650, - "end": 5662, + "start": 6285, + "end": 6297, "loc": { "start": { - "line": 147, + "line": 166, "column": 27 }, "end": { - "line": 147, + "line": 166, "column": 39 }, "identifierName": "occurrenceID" @@ -19137,15 +21377,15 @@ }, "property": { "type": "Identifier", - "start": 5663, - "end": 5667, + "start": 6298, + "end": 6302, "loc": { "start": { - "line": 147, + "line": 166, "column": 40 }, "end": { - "line": 147, + "line": 166, "column": 44 }, "identifierName": "trim" @@ -19166,15 +21406,15 @@ { "type": "CommentLine", "value": " Return the occurrenceID if it exists.", - "start": 5492, - "end": 5532, + "start": 6127, + "end": 6167, "loc": { "start": { - "line": 145, + "line": 164, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 44 } } @@ -19184,15 +21424,15 @@ { "type": "CommentLine", "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 5682, - "end": 5759, + "start": 6317, + "end": 6394, "loc": { "start": { - "line": 150, + "line": 169, "column": 4 }, "end": { - "line": 150, + "line": 169, "column": 81 } } @@ -19201,43 +21441,43 @@ }, { "type": "IfStatement", - "start": 5764, - "end": 6425, + "start": 6399, + "end": 7060, "loc": { "start": { - "line": 151, + "line": 170, "column": 4 }, "end": { - "line": 162, + "line": 181, "column": 5 } }, "test": { "type": "CallExpression", - "start": 5768, - "end": 5803, + "start": 6403, + "end": 6438, "loc": { "start": { - "line": 151, + "line": 170, "column": 8 }, "end": { - "line": 151, + "line": 170, "column": 43 } }, "callee": { "type": "Identifier", - "start": 5768, - "end": 5771, + "start": 6403, + "end": 6406, "loc": { "start": { - "line": 151, + "line": 170, "column": 8 }, "end": { - "line": 151, + "line": 170, "column": 11 }, "identifierName": "has" @@ -19248,44 +21488,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 5772, - "end": 5785, + "start": 6407, + "end": 6420, "loc": { "start": { - "line": 151, + "line": 170, "column": 12 }, "end": { - "line": 151, + "line": 170, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 5772, - "end": 5776, + "start": 6407, + "end": 6411, "loc": { "start": { - "line": 151, + "line": 170, "column": 12 }, "end": { - "line": 151, + "line": 170, "column": 16 } } }, "property": { "type": "Identifier", - "start": 5777, - "end": 5785, + "start": 6412, + "end": 6420, "loc": { "start": { - "line": 151, + "line": 170, "column": 17 }, "end": { - "line": 151, + "line": 170, "column": 25 }, "identifierName": "specimen" @@ -19296,15 +21536,15 @@ }, { "type": "StringLiteral", - "start": 5787, - "end": 5802, + "start": 6422, + "end": 6437, "loc": { "start": { - "line": 151, + "line": 170, "column": 27 }, "end": { - "line": 151, + "line": 170, "column": 42 } }, @@ -19319,58 +21559,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 5805, - "end": 6425, + "start": 6440, + "end": 7060, "loc": { "start": { - "line": 151, + "line": 170, "column": 45 }, "end": { - 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"start": 5821, - "end": 5825, + "start": 6456, + "end": 6460, "loc": { "start": { - "line": 152, + "line": 171, "column": 14 }, "end": { - "line": 152, + "line": 171, "column": 18 } } }, "property": { "type": "Identifier", - "start": 5826, - "end": 5834, + "start": 6461, + "end": 6469, "loc": { "start": { - "line": 152, + "line": 171, "column": 19 }, "end": { - "line": 152, + "line": 171, "column": 27 }, "identifierName": "specimen" @@ -19428,15 +21668,15 @@ }, { "type": "StringLiteral", - "start": 5836, - "end": 5853, + "start": 6471, + "end": 6488, "loc": { "start": { - "line": 152, + "line": 171, "column": 29 }, "end": { - "line": 152, + "line": 171, "column": 46 } }, @@ -19450,58 +21690,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 5856, - "end": 6185, + "start": 6491, + "end": 6820, "loc": { "start": { - "line": 152, + "line": 171, "column": 49 }, "end": { - "line": 157, + "line": 176, "column": 7 } }, "body": [ { "type": "IfStatement", - "start": 5866, - "end": 6068, + "start": 6501, + "end": 6703, "loc": { "start": { - "line": 153, + "line": 172, "column": 8 }, "end": { - "line": 155, + "line": 174, "column": 9 } }, "test": { "type": "CallExpression", - "start": 5870, - "end": 5906, + "start": 6505, + "end": 6541, "loc": { "start": { - "line": 153, + "line": 172, "column": 12 }, "end": { - "line": 153, + "line": 172, "column": 48 } }, "callee": { "type": "Identifier", - "start": 5870, - "end": 5873, + "start": 6505, + "end": 6508, "loc": { "start": { - "line": 153, + "line": 172, "column": 12 }, "end": { - "line": 153, + "line": 172, "column": 15 }, "identifierName": "has" @@ -19511,44 +21751,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 5874, - "end": 5887, + "start": 6509, + "end": 6522, "loc": { "start": { - "line": 153, + "line": 172, "column": 16 }, "end": { - "line": 153, + "line": 172, "column": 29 } }, "object": { "type": "ThisExpression", - "start": 5874, - "end": 5878, + "start": 6509, + "end": 6513, "loc": { "start": { - "line": 153, + "line": 172, "column": 16 }, "end": { - "line": 153, + "line": 172, "column": 20 } } }, "property": { "type": "Identifier", - "start": 5879, - "end": 5887, + "start": 6514, + "end": 6522, "loc": { "start": { - "line": 153, + "line": 172, "column": 21 }, "end": { - "line": 153, + "line": 172, "column": 29 }, "identifierName": "specimen" @@ -19559,15 +21799,15 @@ }, { "type": "StringLiteral", - "start": 5889, - "end": 5905, + "start": 6524, + "end": 6540, "loc": { "start": { - "line": 153, + "line": 172, "column": 31 }, "end": { - "line": 153, + "line": 172, "column": 47 } }, @@ -19581,130 +21821,130 @@ }, "consequent": { "type": "BlockStatement", - "start": 5908, - "end": 6068, + "start": 6543, + "end": 6703, "loc": { "start": { - "line": 153, + "line": 172, "column": 50 }, "end": { - "line": 155, + "line": 174, "column": 9 } }, "body": [ { "type": "ReturnStatement", - "start": 5920, - "end": 6058, + "start": 6555, + "end": 6693, "loc": { "start": { - "line": 154, + "line": 173, "column": 10 }, "end": { - "line": 154, + "line": 173, "column": 148 } }, "argument": { "type": "TemplateLiteral", - 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"line": 154, + "line": 173, "column": 45 } }, "object": { "type": "ThisExpression", - "start": 5942, - "end": 5946, + "start": 6577, + "end": 6581, "loc": { "start": { - "line": 154, + "line": 173, "column": 32 }, "end": { - "line": 154, + "line": 173, "column": 36 } } }, "property": { "type": "Identifier", - "start": 5947, - "end": 5955, + "start": 6582, + "end": 6590, "loc": { "start": { - "line": 154, + "line": 173, "column": 37 }, "end": { - "line": 154, + "line": 173, "column": 45 }, "identifierName": "specimen" @@ -19715,15 +21955,15 @@ }, "property": { "type": "Identifier", - "start": 5956, - "end": 5971, + "start": 6591, + "end": 6606, "loc": { "start": { - "line": 154, + "line": 173, "column": 46 }, "end": { - "line": 154, + "line": 173, "column": 61 }, "identifierName": "institutionCode" @@ -19734,15 +21974,15 @@ }, "property": { "type": "Identifier", - "start": 5972, - "end": 5976, + "start": 6607, + "end": 6611, "loc": { "start": { - "line": 154, + "line": 173, "column": 62 }, "end": { - "line": 154, + "line": 173, "column": 66 }, "identifierName": "trim" @@ -19755,86 +21995,86 @@ }, { "type": "CallExpression", - "start": 5982, - "end": 6017, + "start": 6617, + "end": 6652, "loc": { "start": { - "line": 154, + "line": 173, "column": 72 }, "end": { - "line": 154, + "line": 173, "column": 107 } }, "callee": { "type": "MemberExpression", - "start": 5982, - "end": 6015, + "start": 6617, + "end": 6650, "loc": { "start": { - "line": 154, + "line": 173, "column": 72 }, "end": { - "line": 154, + "line": 173, "column": 105 } }, "object": { "type": "MemberExpression", - "start": 5982, - "end": 6010, + "start": 6617, + "end": 6645, "loc": { "start": { - "line": 154, + "line": 173, "column": 72 }, "end": { - "line": 154, + "line": 173, "column": 100 } }, "object": { "type": "MemberExpression", - "start": 5982, - "end": 5995, + "start": 6617, + "end": 6630, "loc": { "start": { - "line": 154, + "line": 173, "column": 72 }, "end": { - "line": 154, + "line": 173, "column": 85 } }, "object": { "type": "ThisExpression", - "start": 5982, - "end": 5986, + "start": 6617, + "end": 6621, "loc": { "start": { - "line": 154, + "line": 173, "column": 72 }, "end": { - "line": 154, + "line": 173, "column": 76 } } }, "property": { "type": "Identifier", - "start": 5987, - "end": 5995, + "start": 6622, + "end": 6630, "loc": { "start": { - "line": 154, + "line": 173, "column": 77 }, "end": { - "line": 154, + "line": 173, "column": 85 }, "identifierName": "specimen" @@ -19845,15 +22085,15 @@ }, "property": { "type": "Identifier", - "start": 5996, - "end": 6010, + "start": 6631, + "end": 6645, "loc": { "start": { - "line": 154, + "line": 173, "column": 86 }, "end": { - "line": 154, + "line": 173, "column": 100 }, "identifierName": "collectionCode" @@ -19864,15 +22104,15 @@ }, "property": { "type": "Identifier", - "start": 6011, - "end": 6015, + "start": 6646, + "end": 6650, "loc": { "start": { - "line": 154, + "line": 173, "column": 101 }, "end": { - "line": 154, + "line": 173, "column": 105 }, "identifierName": "trim" @@ -19885,86 +22125,86 @@ }, { "type": "CallExpression", - "start": 6021, - "end": 6055, + "start": 6656, + "end": 6690, "loc": { "start": { - "line": 154, + "line": 173, "column": 111 }, "end": { - "line": 154, + "line": 173, "column": 145 } }, "callee": { "type": "MemberExpression", - "start": 6021, - "end": 6053, + "start": 6656, + "end": 6688, "loc": { "start": { - "line": 154, + "line": 173, "column": 111 }, "end": { - "line": 154, + "line": 173, "column": 143 } }, "object": { "type": "MemberExpression", - "start": 6021, - "end": 6048, + "start": 6656, + "end": 6683, "loc": { "start": { - "line": 154, + "line": 173, "column": 111 }, "end": { - "line": 154, + "line": 173, "column": 138 } }, "object": { "type": "MemberExpression", - "start": 6021, - "end": 6034, + "start": 6656, + "end": 6669, "loc": { "start": { - "line": 154, + "line": 173, "column": 111 }, "end": { - "line": 154, + "line": 173, "column": 124 } }, "object": { "type": "ThisExpression", - "start": 6021, - "end": 6025, + "start": 6656, + "end": 6660, "loc": { "start": { - "line": 154, + "line": 173, "column": 111 }, "end": { - "line": 154, + "line": 173, "column": 115 } } }, "property": { "type": "Identifier", - "start": 6026, - "end": 6034, + "start": 6661, + "end": 6669, "loc": { "start": { - "line": 154, + "line": 173, "column": 116 }, "end": { - "line": 154, + "line": 173, "column": 124 }, "identifierName": "specimen" @@ -19975,15 +22215,15 @@ }, "property": { "type": "Identifier", - "start": 6035, - "end": 6048, + "start": 6670, + "end": 6683, "loc": { "start": { - "line": 154, + "line": 173, "column": 125 }, "end": { - "line": 154, + "line": 173, "column": 138 }, "identifierName": "catalogNumber" @@ -19994,15 +22234,15 @@ }, "property": { "type": "Identifier", - "start": 6049, - "end": 6053, + "start": 6684, + "end": 6688, "loc": { "start": { - "line": 154, + "line": 173, "column": 139 }, "end": { - "line": 154, + "line": 173, "column": 143 }, "identifierName": "trim" @@ -20017,15 +22257,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 5928, - "end": 5940, + "start": 6563, + "end": 6575, "loc": { "start": { - "line": 154, + "line": 173, "column": 18 }, "end": { - "line": 154, + "line": 173, "column": 30 } }, @@ -20037,15 +22277,15 @@ }, { "type": "TemplateElement", - "start": 5979, - "end": 5980, + "start": 6614, + "end": 6615, "loc": { "start": { - "line": 154, + "line": 173, "column": 69 }, "end": { - "line": 154, + "line": 173, "column": 70 } }, @@ -20057,15 +22297,15 @@ }, { "type": "TemplateElement", - "start": 6018, - "end": 6019, + "start": 6653, + "end": 6654, "loc": { "start": { - "line": 154, + "line": 173, "column": 108 }, "end": { - "line": 154, + "line": 173, "column": 109 } }, @@ -20077,15 +22317,15 @@ }, { "type": "TemplateElement", - "start": 6056, - "end": 6056, + "start": 6691, + "end": 6691, "loc": { "start": { - "line": 154, + "line": 173, "column": 146 }, "end": { - "line": 154, + "line": 173, "column": 146 } }, @@ -20105,115 +22345,115 @@ }, { "type": "ReturnStatement", - "start": 6077, - "end": 6177, + "start": 6712, + "end": 6812, "loc": { "start": { - "line": 156, + "line": 175, "column": 8 }, "end": { - "line": 156, + "line": 175, "column": 108 } }, "argument": { "type": "TemplateLiteral", - "start": 6084, - "end": 6176, + "start": 6719, + "end": 6811, "loc": { "start": { - "line": 156, + "line": 175, "column": 15 }, "end": { - "line": 156, + "line": 175, "column": 107 } }, "expressions": [ { "type": "CallExpression", - "start": 6099, - "end": 6135, + "start": 6734, + "end": 6770, "loc": { "start": { - "line": 156, + "line": 175, "column": 30 }, "end": { - "line": 156, + "line": 175, "column": 66 } }, "callee": { "type": "MemberExpression", - "start": 6099, - "end": 6133, + "start": 6734, + "end": 6768, "loc": { "start": { - "line": 156, + "line": 175, "column": 30 }, "end": { - "line": 156, + "line": 175, "column": 64 } }, "object": { "type": "MemberExpression", - "start": 6099, - "end": 6128, + "start": 6734, + "end": 6763, "loc": { "start": { - "line": 156, + "line": 175, "column": 30 }, "end": { - "line": 156, + "line": 175, "column": 59 } }, "object": { "type": "MemberExpression", - "start": 6099, - "end": 6112, + "start": 6734, + "end": 6747, "loc": { "start": { - "line": 156, + "line": 175, "column": 30 }, "end": { - "line": 156, + "line": 175, "column": 43 } }, "object": { "type": "ThisExpression", - "start": 6099, - "end": 6103, + "start": 6734, + "end": 6738, "loc": { "start": { - "line": 156, + "line": 175, "column": 30 }, "end": { - "line": 156, + "line": 175, "column": 34 } } }, "property": { "type": "Identifier", - "start": 6104, - "end": 6112, + "start": 6739, + "end": 6747, "loc": { "start": { - "line": 156, + "line": 175, "column": 35 }, "end": { - "line": 156, + "line": 175, "column": 43 }, "identifierName": "specimen" @@ -20224,15 +22464,15 @@ }, "property": { "type": "Identifier", - "start": 6113, - "end": 6128, + "start": 6748, + "end": 6763, "loc": { "start": { - "line": 156, + "line": 175, "column": 44 }, "end": { - "line": 156, + "line": 175, "column": 59 }, "identifierName": "institutionCode" @@ -20243,15 +22483,15 @@ }, "property": { "type": "Identifier", - "start": 6129, - "end": 6133, + "start": 6764, + "end": 6768, "loc": { "start": { - "line": 156, + "line": 175, "column": 60 }, "end": { - "line": 156, + "line": 175, "column": 64 }, "identifierName": "trim" @@ -20264,86 +22504,86 @@ }, { "type": "CallExpression", - "start": 6140, - "end": 6174, + "start": 6775, + "end": 6809, "loc": { "start": { - "line": 156, + "line": 175, "column": 71 }, "end": { - "line": 156, + "line": 175, "column": 105 } }, "callee": { "type": "MemberExpression", - "start": 6140, - "end": 6172, + "start": 6775, + "end": 6807, "loc": { "start": { - "line": 156, + "line": 175, "column": 71 }, "end": { - "line": 156, + "line": 175, "column": 103 } }, "object": { "type": "MemberExpression", - "start": 6140, - "end": 6167, + "start": 6775, + "end": 6802, "loc": { "start": { - "line": 156, + "line": 175, "column": 71 }, "end": { - "line": 156, + "line": 175, "column": 98 } }, "object": { "type": "MemberExpression", - "start": 6140, - "end": 6153, + "start": 6775, + "end": 6788, "loc": { "start": { - "line": 156, + "line": 175, "column": 71 }, "end": { - "line": 156, + "line": 175, "column": 84 } }, "object": { "type": "ThisExpression", - "start": 6140, - "end": 6144, + "start": 6775, + "end": 6779, "loc": { "start": { - "line": 156, + "line": 175, "column": 71 }, "end": { - "line": 156, + "line": 175, "column": 75 } } }, "property": { "type": "Identifier", - "start": 6145, - "end": 6153, + "start": 6780, + "end": 6788, "loc": { "start": { - "line": 156, + "line": 175, "column": 76 }, "end": { - "line": 156, + "line": 175, "column": 84 }, "identifierName": "specimen" @@ -20354,15 +22594,15 @@ }, "property": { "type": "Identifier", - "start": 6154, - "end": 6167, + "start": 6789, + "end": 6802, "loc": { "start": { - "line": 156, + "line": 175, "column": 85 }, "end": { - "line": 156, + "line": 175, "column": 98 }, "identifierName": "catalogNumber" @@ -20373,15 +22613,15 @@ }, "property": { "type": "Identifier", - "start": 6168, - "end": 6172, + "start": 6803, + "end": 6807, "loc": { "start": { - "line": 156, + "line": 175, "column": 99 }, "end": { - "line": 156, + "line": 175, "column": 103 }, "identifierName": "trim" @@ -20396,15 +22636,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6085, - "end": 6097, + "start": 6720, + "end": 6732, "loc": { "start": { - "line": 156, + "line": 175, "column": 16 }, "end": { - "line": 156, + "line": 175, "column": 28 } }, @@ -20416,15 +22656,15 @@ }, { "type": "TemplateElement", - "start": 6136, - "end": 6138, + "start": 6771, + "end": 6773, "loc": { "start": { - "line": 156, + "line": 175, "column": 67 }, "end": { - "line": 156, + "line": 175, "column": 69 } }, @@ -20436,15 +22676,15 @@ }, { "type": "TemplateElement", - "start": 6175, - "end": 6175, + "start": 6810, + "end": 6810, "loc": { "start": { - "line": 156, + "line": 175, "column": 106 }, "end": { - "line": 156, + "line": 175, "column": 106 } }, @@ -20464,43 +22704,43 @@ }, { "type": "IfStatement", - "start": 6192, - "end": 6351, + "start": 6827, + "end": 6986, "loc": { "start": { - "line": 158, + "line": 177, "column": 6 }, "end": { - "line": 160, + "line": 179, "column": 7 } }, "test": { "type": "CallExpression", - "start": 6196, - "end": 6232, + "start": 6831, + "end": 6867, "loc": { "start": { - "line": 158, + "line": 177, "column": 10 }, "end": { - "line": 158, + "line": 177, "column": 46 } }, "callee": { "type": "Identifier", - "start": 6196, - "end": 6199, + "start": 6831, + "end": 6834, "loc": { "start": { - "line": 158, + "line": 177, "column": 10 }, "end": { - "line": 158, + "line": 177, "column": 13 }, "identifierName": "has" @@ -20510,44 +22750,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 6200, - "end": 6213, + "start": 6835, + "end": 6848, "loc": { "start": { - "line": 158, + "line": 177, "column": 14 }, "end": { - "line": 158, + "line": 177, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 6200, - "end": 6204, + "start": 6835, + "end": 6839, "loc": { "start": { - "line": 158, + "line": 177, "column": 14 }, "end": { - "line": 158, + "line": 177, "column": 18 } } }, "property": { "type": "Identifier", - "start": 6205, - "end": 6213, + "start": 6840, + "end": 6848, "loc": { "start": { - "line": 158, + "line": 177, "column": 19 }, "end": { - "line": 158, + "line": 177, "column": 27 }, "identifierName": "specimen" @@ -20558,15 +22798,15 @@ }, { "type": "StringLiteral", - "start": 6215, - "end": 6231, + "start": 6850, + "end": 6866, "loc": { "start": { - "line": 158, + "line": 177, "column": 29 }, "end": { - "line": 158, + "line": 177, "column": 45 } }, @@ -20580,130 +22820,130 @@ }, "consequent": { "type": "BlockStatement", - "start": 6234, - "end": 6351, + "start": 6869, + "end": 6986, "loc": { "start": { - "line": 158, + "line": 177, "column": 48 }, "end": { - "line": 160, + "line": 179, "column": 7 } }, "body": [ { "type": "ReturnStatement", - "start": 6244, - "end": 6343, + "start": 6879, + "end": 6978, "loc": { "start": { - "line": 159, + "line": 178, "column": 8 }, "end": { - "line": 159, + "line": 178, "column": 107 } }, "argument": { "type": "TemplateLiteral", - "start": 6251, - "end": 6342, + "start": 6886, + "end": 6977, "loc": { "start": { - "line": 159, + "line": 178, "column": 15 }, "end": { - "line": 159, + "line": 178, "column": 106 } }, "expressions": [ { "type": "CallExpression", - "start": 6267, - "end": 6302, + "start": 6902, + "end": 6937, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 66 } }, "callee": { "type": "MemberExpression", - "start": 6267, - "end": 6300, + "start": 6902, + "end": 6935, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 64 } }, "object": { "type": "MemberExpression", - "start": 6267, - "end": 6295, + "start": 6902, + "end": 6930, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 59 } }, "object": { "type": "MemberExpression", - "start": 6267, - "end": 6280, + "start": 6902, + "end": 6915, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 6267, - "end": 6271, + "start": 6902, + "end": 6906, "loc": { "start": { - "line": 159, + "line": 178, "column": 31 }, "end": { - "line": 159, + "line": 178, "column": 35 } } }, "property": { "type": "Identifier", - "start": 6272, - "end": 6280, + "start": 6907, + "end": 6915, "loc": { "start": { - "line": 159, + "line": 178, "column": 36 }, "end": { - "line": 159, + "line": 178, "column": 44 }, "identifierName": "specimen" @@ -20714,15 +22954,15 @@ }, "property": { "type": "Identifier", - "start": 6281, - "end": 6295, + "start": 6916, + "end": 6930, "loc": { "start": { - "line": 159, + "line": 178, "column": 45 }, "end": { - "line": 159, + "line": 178, "column": 59 }, "identifierName": "collectionCode" @@ -20733,15 +22973,15 @@ }, "property": { "type": "Identifier", - "start": 6296, - "end": 6300, + "start": 6931, + "end": 6935, "loc": { "start": { - "line": 159, + "line": 178, "column": 60 }, "end": { - "line": 159, + "line": 178, "column": 64 }, "identifierName": "trim" @@ -20754,86 +22994,86 @@ }, { "type": "CallExpression", - "start": 6306, - "end": 6340, + "start": 6941, + "end": 6975, "loc": { "start": { - "line": 159, + "line": 178, "column": 70 }, "end": { - "line": 159, + "line": 178, "column": 104 } }, "callee": { "type": "MemberExpression", - "start": 6306, - "end": 6338, + "start": 6941, + "end": 6973, "loc": { "start": { - "line": 159, + "line": 178, "column": 70 }, "end": { - "line": 159, + "line": 178, "column": 102 } }, "object": { "type": "MemberExpression", - "start": 6306, - "end": 6333, + "start": 6941, + "end": 6968, "loc": { "start": { - "line": 159, + "line": 178, "column": 70 }, "end": { - "line": 159, + "line": 178, "column": 97 } }, "object": { "type": "MemberExpression", - "start": 6306, - "end": 6319, + "start": 6941, + "end": 6954, "loc": { "start": { - "line": 159, + "line": 178, "column": 70 }, "end": { - "line": 159, + "line": 178, "column": 83 } }, "object": { "type": "ThisExpression", - "start": 6306, - "end": 6310, + "start": 6941, + "end": 6945, "loc": { "start": { - "line": 159, + "line": 178, "column": 70 }, "end": { - "line": 159, + "line": 178, "column": 74 } } }, "property": { "type": "Identifier", - "start": 6311, - "end": 6319, + "start": 6946, + "end": 6954, "loc": { "start": { - "line": 159, + "line": 178, "column": 75 }, "end": { - "line": 159, + "line": 178, "column": 83 }, "identifierName": "specimen" @@ -20844,15 +23084,15 @@ }, "property": { "type": "Identifier", - "start": 6320, - "end": 6333, + "start": 6955, + "end": 6968, "loc": { "start": { - "line": 159, + "line": 178, "column": 84 }, "end": { - "line": 159, + "line": 178, "column": 97 }, "identifierName": "catalogNumber" @@ -20863,15 +23103,15 @@ }, "property": { "type": "Identifier", - "start": 6334, - "end": 6338, + "start": 6969, + "end": 6973, "loc": { "start": { - "line": 159, + "line": 178, "column": 98 }, "end": { - "line": 159, + "line": 178, "column": 102 }, "identifierName": "trim" @@ -20886,15 +23126,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6252, - "end": 6265, + "start": 6887, + "end": 6900, "loc": { "start": { - "line": 159, + "line": 178, "column": 16 }, "end": { - "line": 159, + "line": 178, "column": 29 } }, @@ -20906,15 +23146,15 @@ }, { "type": "TemplateElement", - "start": 6303, - "end": 6304, + "start": 6938, + "end": 6939, "loc": { "start": { - "line": 159, + "line": 178, "column": 67 }, "end": { - "line": 159, + "line": 178, "column": 68 } }, @@ -20926,15 +23166,15 @@ }, { "type": "TemplateElement", - "start": 6341, - "end": 6341, + "start": 6976, + "end": 6976, "loc": { "start": { - "line": 159, + "line": 178, "column": 105 }, "end": { - "line": 159, + "line": 178, "column": 105 } }, @@ -20954,115 +23194,115 @@ }, { "type": "ReturnStatement", - "start": 6358, - "end": 6419, + "start": 6993, + "end": 7054, "loc": { "start": { - "line": 161, + "line": 180, "column": 6 }, "end": { - "line": 161, + "line": 180, "column": 67 } }, "argument": { "type": "TemplateLiteral", - "start": 6365, - "end": 6418, + "start": 7000, + "end": 7053, "loc": { "start": { - "line": 161, + "line": 180, "column": 13 }, "end": { - "line": 161, + "line": 180, "column": 66 } }, "expressions": [ { "type": "CallExpression", - "start": 6382, - "end": 6416, + "start": 7017, + "end": 7051, "loc": { "start": { - "line": 161, + "line": 180, "column": 30 }, "end": { - "line": 161, + "line": 180, "column": 64 } }, "callee": { "type": "MemberExpression", - "start": 6382, - "end": 6414, + "start": 7017, + "end": 7049, "loc": { "start": { - "line": 161, + "line": 180, "column": 30 }, "end": { - "line": 161, + "line": 180, "column": 62 } }, "object": { "type": "MemberExpression", - "start": 6382, - "end": 6409, + "start": 7017, + "end": 7044, "loc": { "start": { - "line": 161, + "line": 180, "column": 30 }, "end": { - "line": 161, + "line": 180, "column": 57 } }, "object": { "type": "MemberExpression", - "start": 6382, - "end": 6395, + "start": 7017, + "end": 7030, "loc": { "start": { - "line": 161, + "line": 180, "column": 30 }, "end": { - "line": 161, + "line": 180, "column": 43 } }, "object": { "type": "ThisExpression", - "start": 6382, - "end": 6386, + "start": 7017, + "end": 7021, "loc": { "start": { - "line": 161, + "line": 180, "column": 30 }, "end": { - "line": 161, + "line": 180, "column": 34 } } }, "property": { "type": "Identifier", - "start": 6387, - "end": 6395, + "start": 7022, + "end": 7030, "loc": { "start": { - "line": 161, + "line": 180, "column": 35 }, "end": { - "line": 161, + "line": 180, "column": 43 }, "identifierName": "specimen" @@ -21073,15 +23313,15 @@ }, "property": { "type": "Identifier", - "start": 6396, - "end": 6409, + "start": 7031, + "end": 7044, "loc": { "start": { - "line": 161, + "line": 180, "column": 44 }, "end": { - "line": 161, + "line": 180, "column": 57 }, "identifierName": "catalogNumber" @@ -21092,15 +23332,15 @@ }, "property": { "type": "Identifier", - "start": 6410, - "end": 6414, + "start": 7045, + "end": 7049, "loc": { "start": { - "line": 161, + "line": 180, "column": 58 }, "end": { - "line": 161, + "line": 180, "column": 62 }, "identifierName": "trim" @@ -21115,15 +23355,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6366, - "end": 6380, + "start": 7001, + "end": 7015, "loc": { "start": { - "line": 161, + "line": 180, "column": 14 }, "end": { - "line": 161, + "line": 180, "column": 28 } }, @@ -21135,15 +23375,15 @@ }, { "type": "TemplateElement", - "start": 6417, - "end": 6417, + "start": 7052, + "end": 7052, "loc": { "start": { - "line": 161, + "line": 180, "column": 65 }, "end": { - "line": 161, + "line": 180, "column": 65 } }, @@ -21165,15 +23405,15 @@ { "type": "CommentLine", "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 5682, - "end": 5759, + "start": 6317, + "end": 6394, "loc": { "start": { - "line": 150, + "line": 169, "column": 4 }, "end": { - "line": 150, + "line": 169, "column": 81 } } @@ -21183,15 +23423,15 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 6431, - "end": 6481, + "start": 7066, + "end": 7116, "loc": { "start": { - "line": 164, + "line": 183, "column": 4 }, "end": { - "line": 164, + "line": 183, "column": 54 } } @@ -21200,29 +23440,29 @@ }, { "type": "ReturnStatement", - "start": 6486, - "end": 6503, + "start": 7121, + "end": 7138, "loc": { "start": { - "line": 165, + "line": 184, "column": 4 }, "end": { - "line": 165, + "line": 184, "column": 21 } }, "argument": { "type": "Identifier", - "start": 6493, - "end": 6502, + "start": 7128, + "end": 7137, "loc": { "start": { - "line": 165, + "line": 184, "column": 11 }, "end": { - "line": 165, + "line": 184, "column": 20 }, "identifierName": "undefined" @@ -21234,15 +23474,15 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 6431, - "end": 6481, + "start": 7066, + "end": 7116, "loc": { "start": { - "line": 164, + "line": 183, "column": 4 }, "end": { - "line": 164, + "line": 183, "column": 54 } } @@ -21257,15 +23497,15 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5205, - "end": 5464, + "start": 5840, + "end": 6099, "loc": { "start": { - "line": 138, + "line": 157, "column": 2 }, "end": { - "line": 143, + "line": 162, "column": 5 } } @@ -21275,15 +23515,15 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 6511, - "end": 6572, + "start": 7146, + "end": 7207, "loc": { "start": { - "line": 168, + "line": 187, "column": 2 }, "end": { - "line": 170, + "line": 189, "column": 5 } } @@ -21292,15 +23532,15 @@ }, { "type": "ClassMethod", - "start": 6575, - "end": 6714, + "start": 7210, + "end": 7349, "loc": { "start": { - "line": 171, + "line": 190, "column": 2 }, "end": { - "line": 174, + "line": 193, "column": 3 } }, @@ -21308,15 +23548,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6579, - "end": 6592, + "start": 7214, + "end": 7227, "loc": { "start": { - "line": 171, + "line": 190, "column": 6 }, "end": { - "line": 171, + "line": 190, "column": 19 }, "identifierName": "basisOfRecord" @@ -21331,58 +23571,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6595, - "end": 6714, + "start": 7230, + "end": 7349, "loc": { "start": { - "line": 171, + "line": 190, "column": 22 }, "end": { - "line": 174, + "line": 193, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 6601, - "end": 6688, + "start": 7236, + "end": 7323, "loc": { "start": { - "line": 172, + "line": 191, "column": 4 }, "end": { - "line": 172, + "line": 191, "column": 91 } }, "test": { "type": "CallExpression", - "start": 6605, - "end": 6644, + "start": 7240, + "end": 7279, "loc": { "start": { - "line": 172, + "line": 191, "column": 8 }, "end": { - "line": 172, + "line": 191, "column": 47 } }, "callee": { "type": "Identifier", - "start": 6605, - "end": 6608, + "start": 7240, + "end": 7243, "loc": { "start": { - "line": 172, + "line": 191, "column": 8 }, "end": { - "line": 172, + "line": 191, "column": 11 }, "identifierName": "has" @@ -21392,44 +23632,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 6609, - "end": 6622, + "start": 7244, + "end": 7257, "loc": { "start": { - "line": 172, + "line": 191, "column": 12 }, "end": { - "line": 172, + "line": 191, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 6609, - "end": 6613, + "start": 7244, + "end": 7248, "loc": { "start": { - "line": 172, + "line": 191, "column": 12 }, "end": { - "line": 172, + "line": 191, "column": 16 } } }, "property": { "type": "Identifier", - "start": 6614, - "end": 6622, + "start": 7249, + "end": 7257, "loc": { "start": { - "line": 172, + "line": 191, "column": 17 }, "end": { - "line": 172, + "line": 191, "column": 25 }, "identifierName": "specimen" @@ -21440,15 +23680,15 @@ }, { "type": "StringLiteral", - "start": 6624, - "end": 6643, + "start": 7259, + "end": 7278, "loc": { "start": { - "line": 172, + "line": 191, "column": 27 }, "end": { - "line": 172, + "line": 191, "column": 46 } }, @@ -21462,72 +23702,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 6646, - "end": 6688, + "start": 7281, + "end": 7323, "loc": { "start": { - "line": 172, + "line": 191, "column": 49 }, "end": { - "line": 172, + "line": 191, "column": 91 } }, "argument": { "type": "MemberExpression", - "start": 6653, - "end": 6687, + "start": 7288, + "end": 7322, "loc": { "start": { - "line": 172, + "line": 191, "column": 56 }, "end": { - "line": 172, + "line": 191, "column": 90 } }, "object": { "type": "MemberExpression", - "start": 6653, - "end": 6666, + "start": 7288, + "end": 7301, "loc": { "start": { - "line": 172, + "line": 191, "column": 56 }, "end": { - "line": 172, + "line": 191, "column": 69 } }, "object": { "type": "ThisExpression", - "start": 6653, - "end": 6657, + "start": 7288, + "end": 7292, "loc": { "start": { - "line": 172, + "line": 191, "column": 56 }, "end": { - "line": 172, + "line": 191, "column": 60 } } }, "property": { "type": "Identifier", - "start": 6658, - "end": 6666, + "start": 7293, + "end": 7301, "loc": { "start": { - "line": 172, + "line": 191, "column": 61 }, "end": { - "line": 172, + "line": 191, "column": 69 }, "identifierName": "specimen" @@ -21538,15 +23778,15 @@ }, "property": { "type": "StringLiteral", - "start": 6667, - "end": 6686, + "start": 7302, + "end": 7321, "loc": { "start": { - "line": 172, + "line": 191, "column": 70 }, "end": { - "line": 172, + "line": 191, "column": 89 } }, @@ -21563,29 +23803,29 @@ }, { "type": "ReturnStatement", - "start": 6693, - "end": 6710, + "start": 7328, + "end": 7345, "loc": { "start": { - "line": 173, + "line": 192, "column": 4 }, "end": { - "line": 173, + "line": 192, "column": 21 } }, "argument": { "type": "Identifier", - "start": 6700, - "end": 6709, + "start": 7335, + "end": 7344, "loc": { "start": { - "line": 173, + "line": 192, "column": 11 }, "end": { - "line": 173, + "line": 192, "column": 20 }, "identifierName": "undefined" @@ -21601,15 +23841,15 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 6511, - "end": 6572, + "start": 7146, + "end": 7207, "loc": { "start": { - "line": 168, + "line": 187, "column": 2 }, "end": { - "line": 170, + "line": 189, "column": 5 } } @@ -21619,15 +23859,15 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 6718, - "end": 6833, + "start": 7353, + "end": 7468, "loc": { "start": { - "line": 176, + "line": 195, "column": 2 }, "end": { - "line": 179, + "line": 198, "column": 5 } } @@ -21636,15 +23876,15 @@ }, { "type": "ClassMethod", - "start": 6836, - "end": 6910, + "start": 7471, + "end": 7545, "loc": { "start": { - "line": 180, + "line": 199, "column": 2 }, "end": { - "line": 182, + "line": 201, "column": 3 } }, @@ -21652,15 +23892,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6840, - "end": 6853, + "start": 7475, + "end": 7488, "loc": { "start": { - "line": 180, + "line": 199, "column": 6 }, "end": { - "line": 180, + "line": 199, "column": 19 }, "identifierName": "basisOfRecord" @@ -21675,15 +23915,15 @@ "params": [ { "type": "Identifier", - "start": 6854, - "end": 6857, + "start": 7489, + "end": 7492, "loc": { "start": { - "line": 180, + "line": 199, "column": 20 }, "end": { - "line": 180, + "line": 199, "column": 23 }, "identifierName": "bor" @@ -21693,102 +23933,102 @@ ], "body": { "type": "BlockStatement", - "start": 6859, - "end": 6910, + "start": 7494, + "end": 7545, "loc": { "start": { - "line": 180, + "line": 199, "column": 25 }, "end": { - "line": 182, + "line": 201, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 6865, - "end": 6906, + "start": 7500, + "end": 7541, "loc": { "start": { - "line": 181, + "line": 200, "column": 4 }, "end": { - "line": 181, + "line": 200, "column": 45 } }, "expression": { "type": "AssignmentExpression", - "start": 6865, - "end": 6905, + "start": 7500, + "end": 7540, "loc": { "start": { - "line": 181, + "line": 200, "column": 4 }, "end": { - "line": 181, + "line": 200, "column": 44 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 6865, - "end": 6899, + "start": 7500, + "end": 7534, "loc": { "start": { - "line": 181, + "line": 200, "column": 4 }, "end": { - "line": 181, + "line": 200, "column": 38 } }, "object": { "type": "MemberExpression", - "start": 6865, - "end": 6878, + "start": 7500, + "end": 7513, "loc": { "start": { - "line": 181, + "line": 200, "column": 4 }, "end": { - "line": 181, + "line": 200, "column": 17 } }, "object": { "type": "ThisExpression", - "start": 6865, - "end": 6869, + "start": 7500, + "end": 7504, "loc": { "start": { - "line": 181, + "line": 200, "column": 4 }, "end": { - "line": 181, + "line": 200, "column": 8 } } }, "property": { "type": "Identifier", - "start": 6870, - "end": 6878, + "start": 7505, + "end": 7513, "loc": { "start": { - "line": 181, + "line": 200, "column": 9 }, "end": { - "line": 181, + "line": 200, "column": 17 }, "identifierName": "specimen" @@ -21799,15 +24039,15 @@ }, "property": { "type": "StringLiteral", - "start": 6879, - "end": 6898, + "start": 7514, + "end": 7533, "loc": { "start": { - "line": 181, + "line": 200, "column": 18 }, "end": { - "line": 181, + "line": 200, "column": 37 } }, @@ -21821,15 +24061,15 @@ }, "right": { "type": "Identifier", - "start": 6902, - "end": 6905, + "start": 7537, + "end": 7540, "loc": { "start": { - "line": 181, + "line": 200, "column": 41 }, "end": { - "line": 181, + "line": 200, "column": 44 }, "identifierName": "bor" @@ -21846,15 +24086,15 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 6718, - "end": 6833, + "start": 7353, + "end": 7468, "loc": { "start": { - "line": 176, + "line": 195, "column": 2 }, "end": { - "line": 179, + "line": 198, "column": 5 } } @@ -21864,15 +24104,15 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 6914, - "end": 6999, + "start": 7549, + "end": 7634, "loc": { "start": { - "line": 184, + "line": 203, "column": 2 }, "end": { - "line": 184, + "line": 203, "column": 87 } } @@ -21881,15 +24121,15 @@ }, { "type": "ClassMethod", - "start": 7002, - "end": 7173, + "start": 7637, + "end": 7808, "loc": { "start": { - "line": 185, + "line": 204, "column": 2 }, "end": { - "line": 189, + "line": 208, "column": 3 } }, @@ -21897,15 +24137,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7006, - "end": 7018, + "start": 7641, + "end": 7653, "loc": { "start": { - "line": 185, + "line": 204, "column": 6 }, "end": { - "line": 185, + "line": 204, "column": 18 }, "identifierName": "taxonConcept" @@ -21920,58 +24160,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7021, - "end": 7173, + "start": 7656, + "end": 7808, "loc": { "start": { - "line": 185, + "line": 204, "column": 21 }, "end": { - "line": 189, + "line": 208, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 7027, - "end": 7083, + "start": 7662, + "end": 7718, "loc": { "start": { - "line": 186, + "line": 205, "column": 4 }, "end": { - "line": 186, + "line": 205, "column": 60 } }, "test": { "type": "CallExpression", - "start": 7031, - "end": 7060, + "start": 7666, + "end": 7695, "loc": { "start": { - "line": 186, + "line": 205, "column": 8 }, "end": { - "line": 186, + "line": 205, "column": 37 } }, "callee": { "type": "Identifier", - "start": 7031, - "end": 7034, + "start": 7666, + "end": 7669, "loc": { "start": { - "line": 186, + "line": 205, "column": 8 }, "end": { - "line": 186, + "line": 205, "column": 11 }, "identifierName": "has" @@ -21981,44 +24221,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7035, - "end": 7048, + "start": 7670, + "end": 7683, "loc": { "start": { - "line": 186, + "line": 205, "column": 12 }, "end": { - "line": 186, + "line": 205, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 7035, - "end": 7039, + "start": 7670, + "end": 7674, "loc": { "start": { - "line": 186, + "line": 205, "column": 12 }, "end": { - "line": 186, + "line": 205, "column": 16 } } }, "property": { "type": "Identifier", - "start": 7040, - "end": 7048, + "start": 7675, + "end": 7683, "loc": { "start": { - "line": 186, + "line": 205, "column": 17 }, "end": { - "line": 186, + "line": 205, "column": 25 }, "identifierName": "specimen" @@ -22029,15 +24269,15 @@ }, { "type": "StringLiteral", - "start": 7050, - "end": 7059, + "start": 7685, + "end": 7694, "loc": { "start": { - "line": 186, + "line": 205, "column": 27 }, "end": { - "line": 186, + "line": 205, "column": 36 } }, @@ -22051,58 +24291,58 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7062, - "end": 7083, + "start": 7697, + "end": 7718, "loc": { "start": { - "line": 186, + "line": 205, "column": 39 }, "end": { - "line": 186, + "line": 205, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 7069, - "end": 7082, + "start": 7704, + "end": 7717, "loc": { "start": { - "line": 186, + "line": 205, "column": 46 }, "end": { - "line": 186, + "line": 205, "column": 59 } }, "object": { "type": "ThisExpression", - "start": 7069, - "end": 7073, + "start": 7704, + "end": 7708, "loc": { "start": { - "line": 186, + "line": 205, "column": 46 }, "end": { - "line": 186, + "line": 205, "column": 50 } } }, "property": { "type": "Identifier", - "start": 7074, - "end": 7082, + "start": 7709, + "end": 7717, "loc": { "start": { - "line": 186, + "line": 205, "column": 51 }, "end": { - "line": 186, + "line": 205, "column": 59 }, "identifierName": "specimen" @@ -22116,43 +24356,43 @@ }, { "type": "IfStatement", - "start": 7088, - "end": 7147, + "start": 7723, + "end": 7782, "loc": { "start": { - "line": 187, + "line": 206, "column": 4 }, "end": { - "line": 187, + "line": 206, "column": 63 } }, "test": { "type": "CallExpression", - "start": 7092, - "end": 7124, + "start": 7727, + "end": 7759, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 40 } }, "callee": { "type": "Identifier", - "start": 7092, - "end": 7095, + "start": 7727, + "end": 7730, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 11 }, "identifierName": "has" @@ -22162,44 +24402,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7096, - "end": 7109, + "start": 7731, + "end": 7744, "loc": { "start": { - "line": 187, + "line": 206, "column": 12 }, "end": { - "line": 187, + "line": 206, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 7096, - "end": 7100, + "start": 7731, + "end": 7735, "loc": { "start": { - "line": 187, + "line": 206, "column": 12 }, "end": { - "line": 187, + "line": 206, "column": 16 } } }, "property": { "type": "Identifier", - "start": 7101, - "end": 7109, + "start": 7736, + "end": 7744, "loc": { "start": { - "line": 187, + "line": 206, "column": 17 }, "end": { - "line": 187, + "line": 206, "column": 25 }, "identifierName": "specimen" @@ -22210,15 +24450,15 @@ }, { "type": "StringLiteral", - "start": 7111, - "end": 7123, + "start": 7746, + "end": 7758, "loc": { "start": { - "line": 187, + "line": 206, "column": 27 }, "end": { - "line": 187, + "line": 206, "column": 39 } }, @@ -22232,58 +24472,58 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7126, - "end": 7147, + "start": 7761, + "end": 7782, "loc": { "start": { - "line": 187, + "line": 206, "column": 42 }, "end": { - "line": 187, + "line": 206, "column": 63 } }, "argument": { "type": "MemberExpression", - "start": 7133, - "end": 7146, + "start": 7768, + "end": 7781, "loc": { "start": { - "line": 187, + "line": 206, "column": 49 }, "end": { - "line": 187, + "line": 206, "column": 62 } }, "object": { "type": "ThisExpression", - "start": 7133, - "end": 7137, + "start": 7768, + "end": 7772, "loc": { "start": { - "line": 187, + "line": 206, "column": 49 }, "end": { - "line": 187, + "line": 206, "column": 53 } } }, "property": { "type": "Identifier", - "start": 7138, - "end": 7146, + "start": 7773, + "end": 7781, "loc": { "start": { - "line": 187, + "line": 206, "column": 54 }, "end": { - "line": 187, + "line": 206, "column": 62 }, "identifierName": "specimen" @@ -22297,29 +24537,29 @@ }, { "type": "ReturnStatement", - "start": 7152, - "end": 7169, + "start": 7787, + "end": 7804, "loc": { "start": { - "line": 188, + "line": 207, "column": 4 }, "end": { - "line": 188, + "line": 207, "column": 21 } }, "argument": { "type": "Identifier", - "start": 7159, - "end": 7168, + "start": 7794, + "end": 7803, "loc": { "start": { - "line": 188, + "line": 207, "column": 11 }, "end": { - "line": 188, + "line": 207, "column": 20 }, "identifierName": "undefined" @@ -22335,15 +24575,15 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 6914, - "end": 6999, + "start": 7549, + "end": 7634, "loc": { "start": { - "line": 184, + "line": 203, "column": 2 }, "end": { - "line": 184, + "line": 203, "column": 87 } } @@ -22353,15 +24593,15 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7177, - "end": 7217, + "start": 7812, + "end": 7852, "loc": { "start": { - "line": 191, + "line": 210, "column": 2 }, "end": { - "line": 191, + "line": 210, "column": 42 } } @@ -22370,15 +24610,15 @@ }, { "type": "ClassMethod", - "start": 7220, - "end": 7702, + "start": 7855, + "end": 8337, "loc": { "start": { - "line": 192, + "line": 211, "column": 2 }, "end": { - "line": 204, + "line": 223, "column": 3 } }, @@ -22386,15 +24626,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7224, - "end": 7229, + "start": 7859, + "end": 7864, "loc": { "start": { - "line": 192, + "line": 211, "column": 6 }, "end": { - "line": 192, + "line": 211, "column": 11 }, "identifierName": "label" @@ -22409,44 +24649,44 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7232, - "end": 7702, + "start": 7867, + "end": 8337, "loc": { "start": { - "line": 192, + "line": 211, "column": 14 }, "end": { - "line": 204, + "line": 223, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 7295, - "end": 7336, + "start": 7930, + "end": 7971, "loc": { "start": { - "line": 194, + "line": 213, "column": 4 }, "end": { - "line": 194, + "line": 213, "column": 45 } }, "test": { "type": "UnaryExpression", - "start": 7299, - "end": 7317, + "start": 7934, + "end": 7952, "loc": { "start": { - "line": 194, + "line": 213, "column": 8 }, "end": { - "line": 194, + "line": 213, "column": 26 } }, @@ -22454,29 +24694,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 7300, - "end": 7317, + "start": 7935, + "end": 7952, "loc": { "start": { - "line": 194, + "line": 213, "column": 9 }, "end": { - "line": 194, + "line": 213, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 7300, - "end": 7304, + "start": 7935, + "end": 7939, "loc": { "start": { - "line": 194, + "line": 213, "column": 9 }, "end": { - "line": 194, + "line": 213, "column": 13 } }, @@ -22484,15 +24724,15 @@ }, "property": { "type": "Identifier", - "start": 7305, - "end": 7317, + "start": 7940, + "end": 7952, "loc": { "start": { - "line": 194, + "line": 213, "column": 14 }, "end": { - "line": 194, + "line": 213, "column": 26 }, "identifierName": "occurrenceID" @@ -22509,29 +24749,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7319, - "end": 7336, + "start": 7954, + "end": 7971, "loc": { "start": { - "line": 194, + "line": 213, "column": 28 }, "end": { - "line": 194, + "line": 213, "column": 45 } }, "argument": { "type": "Identifier", - "start": 7326, - "end": 7335, + "start": 7961, + "end": 7970, "loc": { "start": { - "line": 194, + "line": 213, "column": 35 }, "end": { - "line": 194, + "line": 213, "column": 44 }, "identifierName": "undefined" @@ -22545,15 +24785,15 @@ { "type": "CommentLine", "value": " We can't return anything without an occurrenceID.", - "start": 7238, - "end": 7290, + "start": 7873, + "end": 7925, "loc": { "start": { - "line": 193, + "line": 212, "column": 4 }, "end": { - "line": 193, + "line": 212, "column": 56 } } @@ -22563,15 +24803,15 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7342, - "end": 7419, + "start": 7977, + "end": 8054, "loc": { "start": { - "line": 196, + "line": 215, "column": 4 }, "end": { - "line": 196, + "line": 215, "column": 81 } } @@ -22579,15 +24819,15 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 7424, - "end": 7465, + "start": 8059, + "end": 8100, "loc": { "start": { - "line": 197, + "line": 216, "column": 4 }, "end": { - "line": 197, + "line": 216, "column": 45 } } @@ -22596,43 +24836,43 @@ }, { "type": "IfStatement", - "start": 7470, - "end": 7612, + "start": 8105, + "end": 8247, "loc": { "start": { - "line": 198, + "line": 217, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 7474, - "end": 7491, + "start": 8109, + "end": 8126, "loc": { "start": { - "line": 198, + "line": 217, "column": 8 }, "end": { - "line": 198, + "line": 217, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 7474, - "end": 7478, + "start": 8109, + "end": 8113, "loc": { "start": { - "line": 198, + "line": 217, "column": 8 }, "end": { - "line": 198, + "line": 217, "column": 12 } }, @@ -22640,15 +24880,15 @@ }, "property": { "type": "Identifier", - "start": 7479, - "end": 7491, + "start": 8114, + "end": 8126, "loc": { "start": { - "line": 198, + "line": 217, "column": 13 }, "end": { - "line": 198, + "line": 217, "column": 25 }, "identifierName": "taxonConcept" @@ -22660,88 +24900,88 @@ }, "consequent": { "type": "BlockStatement", - "start": 7493, - "end": 7612, + "start": 8128, + "end": 8247, "loc": { "start": { - "line": 198, + "line": 217, "column": 27 }, "end": { - "line": 200, + "line": 219, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 7501, - "end": 7606, + "start": 8136, + "end": 8241, "loc": { "start": { - "line": 199, + "line": 218, "column": 6 }, "end": { - "line": 199, + "line": 218, "column": 111 } }, "argument": { "type": "TemplateLiteral", - "start": 7508, - "end": 7605, + "start": 8143, + "end": 8240, "loc": { "start": { - "line": 199, + "line": 218, "column": 13 }, "end": { - "line": 199, + "line": 218, "column": 110 } }, "expressions": [ { "type": "MemberExpression", - "start": 7520, - "end": 7537, + "start": 8155, + "end": 8172, "loc": { "start": { - "line": 199, + "line": 218, "column": 25 }, "end": { - "line": 199, + "line": 218, "column": 42 } }, "object": { "type": "ThisExpression", - "start": 7520, - "end": 7524, + "start": 8155, + "end": 8159, "loc": { "start": { - "line": 199, + "line": 218, "column": 25 }, "end": { - "line": 199, + "line": 218, "column": 29 } } }, "property": { "type": "Identifier", - "start": 7525, - "end": 7537, + "start": 8160, + "end": 8172, "loc": { "start": { - "line": 199, + "line": 218, "column": 30 }, "end": { - "line": 199, + "line": 218, "column": 42 }, "identifierName": "occurrenceID" @@ -22752,43 +24992,43 @@ }, { "type": "MemberExpression", - "start": 7555, - "end": 7603, + "start": 8190, + "end": 8238, "loc": { "start": { - "line": 199, + "line": 218, "column": 60 }, "end": { - "line": 199, + "line": 218, "column": 108 } }, "object": { "type": "NewExpression", - "start": 7555, - "end": 7597, + "start": 8190, + "end": 8232, "loc": { "start": { - "line": 199, + "line": 218, "column": 60 }, "end": { - "line": 199, + "line": 218, "column": 102 } }, "callee": { "type": "Identifier", - "start": 7559, - "end": 7578, + "start": 8194, + "end": 8213, "loc": { "start": { - "line": 199, + "line": 218, "column": 64 }, "end": { - "line": 199, + "line": 218, "column": 83 }, "identifierName": "TaxonConceptWrapper" @@ -22798,44 +25038,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7579, - "end": 7596, + "start": 8214, + "end": 8231, "loc": { "start": { - "line": 199, + "line": 218, "column": 84 }, "end": { - "line": 199, + "line": 218, "column": 101 } }, "object": { "type": "ThisExpression", - "start": 7579, - "end": 7583, + "start": 8214, + "end": 8218, "loc": { "start": { - "line": 199, + "line": 218, "column": 84 }, "end": { - "line": 199, + "line": 218, "column": 88 } } }, "property": { "type": "Identifier", - "start": 7584, - "end": 7596, + "start": 8219, + "end": 8231, "loc": { "start": { - "line": 199, + "line": 218, "column": 89 }, "end": { - "line": 199, + "line": 218, "column": 101 }, "identifierName": "taxonConcept" @@ -22848,15 +25088,15 @@ }, "property": { "type": "Identifier", - "start": 7598, - "end": 7603, + "start": 8233, + "end": 8238, "loc": { "start": { - "line": 199, + "line": 218, "column": 103 }, "end": { - "line": 199, + "line": 218, "column": 108 }, "identifierName": "label" @@ -22869,15 +25109,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 7509, - "end": 7518, + "start": 8144, + "end": 8153, "loc": { "start": { - "line": 199, + "line": 218, "column": 14 }, "end": { - "line": 199, + "line": 218, "column": 23 } }, @@ -22889,15 +25129,15 @@ }, { "type": "TemplateElement", - "start": 7538, - "end": 7553, + "start": 8173, + "end": 8188, "loc": { "start": { - "line": 199, + "line": 218, "column": 43 }, "end": { - "line": 199, + "line": 218, "column": 58 } }, @@ -22909,15 +25149,15 @@ }, { "type": "TemplateElement", - "start": 7604, - "end": 7604, + "start": 8239, + "end": 8239, "loc": { "start": { - "line": 199, + "line": 218, "column": 109 }, "end": { - "line": 199, + "line": 218, "column": 109 } }, @@ -22939,15 +25179,15 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7342, - "end": 7419, + "start": 7977, + "end": 8054, "loc": { "start": { - "line": 196, + "line": 215, "column": 4 }, "end": { - "line": 196, + "line": 215, "column": 81 } } @@ -22955,15 +25195,15 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 7424, - "end": 7465, + "start": 8059, + "end": 8100, "loc": { "start": { - "line": 197, + "line": 216, "column": 4 }, "end": { - "line": 197, + "line": 216, "column": 45 } } @@ -22973,15 +25213,15 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 7618, - "end": 7654, + "start": 8253, + "end": 8289, "loc": { "start": { - "line": 202, + "line": 221, "column": 4 }, "end": { - "line": 202, + "line": 221, "column": 40 } } @@ -22990,73 +25230,73 @@ }, { "type": "ReturnStatement", - "start": 7659, - "end": 7698, + "start": 8294, + "end": 8333, "loc": { "start": { - "line": 203, + "line": 222, "column": 4 }, "end": { - "line": 203, + "line": 222, "column": 43 } }, "argument": { "type": "TemplateLiteral", - "start": 7666, - "end": 7697, + "start": 8301, + "end": 8332, "loc": { "start": { - "line": 203, + "line": 222, "column": 11 }, "end": { - "line": 203, + "line": 222, "column": 42 } }, "expressions": [ { "type": "MemberExpression", - "start": 7678, - "end": 7695, + "start": 8313, + "end": 8330, "loc": { "start": { - "line": 203, + "line": 222, "column": 23 }, "end": { - "line": 203, + "line": 222, "column": 40 } }, "object": { "type": "ThisExpression", - "start": 7678, - "end": 7682, + "start": 8313, + "end": 8317, "loc": { "start": { - "line": 203, + "line": 222, "column": 23 }, "end": { - "line": 203, + "line": 222, "column": 27 } } }, "property": { "type": "Identifier", - "start": 7683, - "end": 7695, + "start": 8318, + "end": 8330, "loc": { "start": { - "line": 203, + "line": 222, "column": 28 }, "end": { - "line": 203, + "line": 222, "column": 40 }, "identifierName": "occurrenceID" @@ -23069,15 +25309,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 7667, - "end": 7676, + "start": 8302, + "end": 8311, "loc": { "start": { - "line": 203, + "line": 222, "column": 12 }, "end": { - "line": 203, + "line": 222, "column": 21 } }, @@ -23090,15 +25330,15 @@ }, { "type": "TemplateElement", - "start": 7696, - "end": 7696, + "start": 8331, + "end": 8331, "loc": { "start": { - "line": 203, + "line": 222, "column": 41 }, "end": { - "line": 203, + "line": 222, "column": 41 } }, @@ -23115,15 +25355,15 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 7618, - "end": 7654, + "start": 8253, + "end": 8289, "loc": { "start": { - "line": 202, + "line": 221, "column": 4 }, "end": { - "line": 202, + "line": 221, "column": 40 } } @@ -23138,15 +25378,15 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7177, - "end": 7217, + "start": 7812, + "end": 7852, "loc": { "start": { - "line": 191, + "line": 210, "column": 2 }, "end": { - "line": 191, + "line": 210, "column": 42 } } @@ -23156,15 +25396,15 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 7706, - "end": 7767, + "start": 8341, + "end": 8402, "loc": { "start": { - "line": 206, + "line": 225, "column": 2 }, "end": { - "line": 206, + "line": 225, "column": 63 } } @@ -23173,15 +25413,15 @@ }, { "type": "ClassMethod", - "start": 7770, - "end": 8199, + "start": 8405, + "end": 8834, "loc": { "start": { - "line": 207, + "line": 226, "column": 2 }, "end": { - "line": 220, + "line": 239, "column": 3 } }, @@ -23189,15 +25429,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7774, - "end": 7789, + "start": 8409, + "end": 8424, "loc": { "start": { - "line": 207, + "line": 226, "column": 6 }, "end": { - "line": 207, + "line": 226, "column": 21 }, "identifierName": "asOWLEquivClass" @@ -23212,44 +25452,44 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7792, - "end": 8199, + "start": 8427, + "end": 8834, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 220, + "line": 239, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 7852, - "end": 7893, + "start": 8487, + "end": 8528, "loc": { "start": { - "line": 209, + "line": 228, "column": 4 }, "end": { - "line": 209, + "line": 228, "column": 45 } }, "test": { "type": "UnaryExpression", - "start": 7856, - "end": 7874, + "start": 8491, + "end": 8509, "loc": { "start": { - "line": 209, + "line": 228, "column": 8 }, "end": { - "line": 209, + "line": 228, "column": 26 } }, @@ -23257,29 +25497,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 7857, - "end": 7874, + "start": 8492, + "end": 8509, "loc": { "start": { - "line": 209, + "line": 228, "column": 9 }, "end": { - "line": 209, + "line": 228, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 7857, - "end": 7861, + "start": 8492, + "end": 8496, "loc": { "start": { - "line": 209, + "line": 228, "column": 9 }, "end": { - "line": 209, + "line": 228, "column": 13 } }, @@ -23287,15 +25527,15 @@ }, "property": { "type": "Identifier", - "start": 7862, - "end": 7874, + "start": 8497, + "end": 8509, "loc": { "start": { - "line": 209, + "line": 228, "column": 14 }, "end": { - "line": 209, + "line": 228, "column": 26 }, "identifierName": "occurrenceID" @@ -23312,29 +25552,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7876, - "end": 7893, + "start": 8511, + "end": 8528, "loc": { "start": { - "line": 209, + "line": 228, "column": 28 }, "end": { - "line": 209, + "line": 228, "column": 45 } }, "argument": { "type": "Identifier", - "start": 7883, - "end": 7892, + "start": 8518, + "end": 8527, "loc": { "start": { - "line": 209, + "line": 228, "column": 35 }, "end": { - "line": 209, + "line": 228, "column": 44 }, "identifierName": "undefined" @@ -23348,15 +25588,15 @@ { "type": "CommentLine", "value": " We can't do anything without an occurrence ID!", - "start": 7798, - "end": 7847, + "start": 8433, + "end": 8482, "loc": { "start": { - "line": 208, + "line": 227, "column": 4 }, "end": { - "line": 208, + "line": 227, "column": 53 } } @@ -23366,15 +25606,15 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 7899, - "end": 7970, + "start": 8534, + "end": 8605, "loc": { "start": { - "line": 211, + "line": 230, "column": 4 }, "end": { - "line": 211, + "line": 230, "column": 75 } } @@ -23382,15 +25622,15 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 7975, - "end": 8022, + "start": 8610, + "end": 8657, "loc": { "start": { - "line": 212, + "line": 231, "column": 4 }, "end": { - "line": 212, + "line": 231, "column": 51 } } @@ -23398,15 +25638,15 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8028, - "end": 8060, + "start": 8663, + "end": 8695, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 36 } } @@ -23415,44 +25655,44 @@ }, { "type": "ReturnStatement", - "start": 8065, - "end": 8195, + "start": 8700, + "end": 8830, "loc": { "start": { - "line": 215, + "line": 234, "column": 4 }, "end": { - "line": 219, + "line": 238, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 8072, - "end": 8194, + "start": 8707, + "end": 8829, "loc": { "start": { - "line": 215, + "line": 234, "column": 11 }, "end": { - "line": 219, + "line": 238, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 8080, - "end": 8106, + "start": 8715, + "end": 8741, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 32 } }, @@ -23461,15 +25701,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 8080, - "end": 8087, + "start": 8715, + "end": 8722, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 13 } }, @@ -23482,15 +25722,15 @@ }, "value": { "type": "StringLiteral", - "start": 8089, - "end": 8106, + "start": 8724, + "end": 8741, "loc": { "start": { - "line": 216, + "line": 235, "column": 15 }, "end": { - "line": 216, + "line": 235, "column": 32 } }, @@ -23504,15 +25744,15 @@ }, { "type": "ObjectProperty", - "start": 8114, - "end": 8152, + "start": 8749, + "end": 8787, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 44 } }, @@ -23521,15 +25761,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8114, - "end": 8124, + "start": 8749, + "end": 8759, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 16 }, "identifierName": "onProperty" @@ -23538,29 +25778,29 @@ }, "value": { "type": "MemberExpression", - "start": 8126, - "end": 8152, + "start": 8761, + "end": 8787, "loc": { "start": { - "line": 217, + "line": 236, "column": 18 }, "end": { - "line": 217, + "line": 236, "column": 44 } }, "object": { "type": "Identifier", - "start": 8126, - "end": 8134, + "start": 8761, + "end": 8769, "loc": { "start": { - "line": 217, + "line": 236, "column": 18 }, "end": { - "line": 217, + "line": 236, "column": 26 }, "identifierName": "owlterms" @@ -23569,15 +25809,15 @@ }, "property": { "type": "Identifier", - "start": 8135, - "end": 8152, + "start": 8770, + "end": 8787, "loc": { "start": { - "line": 217, + "line": 236, "column": 27 }, "end": { - "line": 217, + "line": 236, "column": 44 }, "identifierName": "DWC_OCCURRENCE_ID" @@ -23589,15 +25829,15 @@ }, { "type": "ObjectProperty", - "start": 8160, - "end": 8187, + "start": 8795, + "end": 8822, "loc": { "start": { - "line": 218, + "line": 237, "column": 6 }, "end": { - "line": 218, + "line": 237, "column": 33 } }, @@ -23606,15 +25846,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8160, - "end": 8168, + "start": 8795, + "end": 8803, "loc": { "start": { - "line": 218, + "line": 237, "column": 6 }, "end": { - "line": 218, + "line": 237, "column": 14 }, "identifierName": "hasValue" @@ -23623,44 +25863,44 @@ }, "value": { "type": "MemberExpression", - "start": 8170, - "end": 8187, + "start": 8805, + "end": 8822, "loc": { "start": { - "line": 218, + "line": 237, "column": 16 }, "end": { - "line": 218, + "line": 237, "column": 33 } }, "object": { "type": "ThisExpression", - "start": 8170, - "end": 8174, + "start": 8805, + "end": 8809, "loc": { "start": { - "line": 218, + "line": 237, "column": 16 }, "end": { - "line": 218, + "line": 237, "column": 20 } } }, "property": { "type": "Identifier", - "start": 8175, - "end": 8187, + "start": 8810, + "end": 8822, "loc": { "start": { - "line": 218, + "line": 237, "column": 21 }, "end": { - "line": 218, + "line": 237, "column": 33 }, "identifierName": "occurrenceID" @@ -23677,15 +25917,15 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 7899, - "end": 7970, + "start": 8534, + "end": 8605, "loc": { "start": { - "line": 211, + "line": 230, "column": 4 }, "end": { - "line": 211, + "line": 230, "column": 75 } } @@ -23693,15 +25933,15 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 7975, - "end": 8022, + "start": 8610, + "end": 8657, "loc": { "start": { - "line": 212, + "line": 231, "column": 4 }, "end": { - "line": 212, + "line": 231, "column": 51 } } @@ -23709,15 +25949,15 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8028, - "end": 8060, + "start": 8663, + "end": 8695, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 36 } } @@ -23731,15 +25971,15 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 7706, - "end": 7767, + "start": 8341, + "end": 8402, "loc": { "start": { - "line": 206, + "line": 225, "column": 2 }, "end": { - "line": 206, + "line": 225, "column": 63 } } @@ -23769,692 +26009,2788 @@ "__PseudoExport__": false, "trailingComments": [] }, - "specifiers": null, - "source": null, - "leadingComments": null + "specifiers": null, + "source": null, + "leadingComments": null + } + ], + "directives": [] + }, + "comments": [ + { + "type": "CommentBlock", + "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", + "start": 325, + "end": 1088, + "loc": { + "start": { + "line": 9, + "column": 0 + }, + "end": { + "line": 23, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "* The '@type' of specimens in JSON-LD document. ", + "start": 1115, + "end": 1167, + "loc": { + "start": { + "line": 25, + "column": 2 + }, + "end": { + "line": 25, + "column": 54 + } + } + }, + { + "type": "CommentBlock", + "value": "* Construct a wrapper around a specimen. ", + "start": 1242, + "end": 1287, + "loc": { + "start": { + "line": 30, + "column": 2 + }, + "end": { + "line": 30, + "column": 47 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", + "start": 1351, + "end": 1449, + "loc": { + "start": { + "line": 35, + "column": 2 + }, + "end": { + "line": 38, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", + "start": 1986, + "end": 2267, + "loc": { + "start": { + "line": 54, + "column": 2 + }, + "end": { + "line": 59, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Copy the occurrence ID so we can truncate it if necessary.", + "start": 2351, + "end": 2412, + "loc": { + "start": { + "line": 61, + "column": 4 + }, + "end": { + "line": 61, + "column": 65 + } + } + }, + { + "type": "CommentLine", + "value": " Prepare the specimen.", + "start": 2524, + "end": 2548, + "loc": { + "start": { + "line": 65, + "column": 4 + }, + "end": { + "line": 65, + "column": 28 + } + } + }, + { + "type": "CommentLine", + "value": " Look for certain prefixes that suggest that we've been passed a URN or", + "start": 2701, + "end": 2774, + "loc": { + "start": { + "line": 72, + "column": 4 + }, + "end": { + "line": 72, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " URL instead. If so, don't do any further processing!", + "start": 2779, + "end": 2834, + "loc": { + "start": { + "line": 73, + "column": 4 + }, + "end": { + "line": 73, + "column": 59 + } + } + }, + { + "type": "CommentLine", + "value": " Parsing an occurrence ID takes some time, so we should memoize it.", + "start": 3104, + "end": 3173, + "loc": { + "start": { + "line": 86, + "column": 4 + }, + "end": { + "line": 86, + "column": 73 + } + } + }, + { + "type": "CommentLine", + "value": " Split the occurrence ID into components, and store them in the appropriate fields.", + "start": 3344, + "end": 3429, + "loc": { + "start": { + "line": 91, + "column": 4 + }, + "end": { + "line": 91, + "column": 89 + } + } + }, + { + "type": "CommentLine", + "value": " specimen.institutionCode = undefined;", + "start": 3504, + "end": 3544, + "loc": { + "start": { + "line": 94, + "column": 6 + }, + "end": { + "line": 94, + "column": 46 + } + } + }, + { + "type": "CommentLine", + "value": " specimen.collectionCode = undefined;", + "start": 3551, + "end": 3590, + "loc": { + "start": { + "line": 95, + "column": 6 + }, + "end": { + "line": 95, + "column": 45 + } + } + }, + { + "type": "CommentLine", + "value": " Store all split catalog number values.", + "start": 3803, + "end": 3844, + "loc": { + "start": { + "line": 100, + "column": 33 + }, + "end": { + "line": 100, + "column": 74 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Get the catalogNumber if present.\n ", + "start": 4109, + "end": 4157, + "loc": { + "start": { + "line": 109, + "column": 2 + }, + "end": { + "line": 111, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Get the catalog number from the specimen object if present.", + "start": 4186, + "end": 4248, + "loc": { + "start": { + "line": 113, + "column": 4 + }, + "end": { + "line": 113, + "column": 66 + } + } + }, + { + "type": "CommentLine", + "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", + "start": 4335, + "end": 4406, + "loc": { + "start": { + "line": 116, + "column": 4 + }, + "end": { + "line": 116, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " catalogNumber from there.", + "start": 4411, + "end": 4439, + "loc": { + "start": { + "line": 117, + "column": 4 + }, + "end": { + "line": 117, + "column": 32 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Get the institutionCode if present.\n ", + "start": 4679, + "end": 4729, + "loc": { + "start": { + "line": 125, + "column": 2 + }, + "end": { + "line": 127, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Get the institution code from the specimen object if present.", + "start": 4760, + "end": 4824, + "loc": { + "start": { + "line": 129, + "column": 4 + }, + "end": { + "line": 129, + "column": 68 + } + } + }, + { + "type": "CommentLine", + "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", + "start": 4915, + "end": 4987, + "loc": { + "start": { + "line": 132, + "column": 4 + }, + "end": { + "line": 132, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " occurrenceID from there.", + "start": 4992, + "end": 5019, + "loc": { + "start": { + "line": 133, + "column": 4 + }, + "end": { + "line": 133, + "column": 31 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Get the collectionCode if present.\n ", + "start": 5263, + "end": 5312, + "loc": { + "start": { + "line": 141, + "column": 2 + }, + "end": { + "line": 143, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Get the collection code from the specimen object if present.", + "start": 5342, + "end": 5405, + "loc": { + "start": { + "line": 145, + "column": 4 + }, + "end": { + "line": 145, + "column": 67 + } + } + }, + { + "type": "CommentLine", + "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", + "start": 5494, + "end": 5566, + "loc": { + "start": { + "line": 148, + "column": 4 + }, + "end": { + "line": 148, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " occurrenceID from there.", + "start": 5571, + "end": 5598, + "loc": { + "start": { + "line": 149, + "column": 4 + }, + "end": { + "line": 149, + "column": 31 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", + "start": 5840, + "end": 6099, + "loc": { + "start": { + "line": 157, + "column": 2 + }, + "end": { + "line": 162, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Return the occurrenceID if it exists.", + "start": 6127, + "end": 6167, + "loc": { + "start": { + "line": 164, + "column": 4 + }, + "end": { + "line": 164, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " Otherwise, we could try to construct the occurrenceID from its components.", + "start": 6317, + "end": 6394, + "loc": { + "start": { + "line": 169, + "column": 4 + }, + "end": { + "line": 169, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " None of our specimen identifier schemes worked.", + "start": 7066, + "end": 7116, + "loc": { + "start": { + "line": 183, + "column": 4 + }, + "end": { + "line": 183, + "column": 54 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the basis of record, if one is present.\n ", + "start": 7146, + "end": 7207, + "loc": { + "start": { + "line": 187, + "column": 2 + }, + "end": { + "line": 189, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", + "start": 7353, + "end": 7468, + "loc": { + "start": { + "line": 195, + "column": 2 + }, + "end": { + "line": 198, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", + "start": 7549, + "end": 7634, + "loc": { + "start": { + "line": 203, + "column": 2 + }, + "end": { + "line": 203, + "column": 87 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return a label for this specimen. ", + "start": 7812, + "end": 7852, + "loc": { + "start": { + "line": 210, + "column": 2 + }, + "end": { + "line": 210, + "column": 42 + } + } + }, + { + "type": "CommentLine", + "value": " We can't return anything without an occurrenceID.", + "start": 7873, + "end": 7925, + "loc": { + "start": { + "line": 212, + "column": 4 + }, + "end": { + "line": 212, + "column": 56 + } + } + }, + { + "type": "CommentLine", + "value": " Note that specimens may be identified to a taxon concept. If so, we should", + "start": 7977, + "end": 8054, + "loc": { + "start": { + "line": 215, + "column": 4 + }, + "end": { + "line": 215, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " include that information in the label.", + "start": 8059, + "end": 8100, + "loc": { + "start": { + "line": 216, + "column": 4 + }, + "end": { + "line": 216, + "column": 45 + } + } + }, + { + "type": "CommentLine", + "value": " Return a label for this specimen.", + "start": 8253, + "end": 8289, + "loc": { + "start": { + "line": 221, + "column": 4 + }, + "end": { + "line": 221, + "column": 40 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return this specimen as an equivalentClass expression. ", + "start": 8341, + "end": 8402, + "loc": { + "start": { + "line": 225, + "column": 2 + }, + "end": { + "line": 225, + "column": 63 + } + } + }, + { + "type": "CommentLine", + "value": " We can't do anything without an occurrence ID!", + "start": 8433, + "end": 8482, + "loc": { + "start": { + "line": 227, + "column": 4 + }, + "end": { + "line": 227, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": " TODO: Should we also match by this.taxonConcept is one is available?", + "start": 8534, + "end": 8605, + "loc": { + "start": { + "line": 230, + "column": 4 + }, + "end": { + "line": 230, + "column": 75 + } + } + }, + { + "type": "CommentLine", + "value": " Technically no, but it might be useful. Hmm.", + "start": 8610, + "end": 8657, + "loc": { + "start": { + "line": 231, + "column": 4 + }, + "end": { + "line": 231, + "column": 51 + } + } + }, + { + "type": "CommentLine", + "value": " Return as an OWL restriction.", + "start": 8663, + "end": 8695, + "loc": { + "start": { + "line": 233, + "column": 4 + }, + "end": { + "line": 233, + "column": 36 + } + } + } + ], + "tokens": [ + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 0, + "end": 6, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 6 + } + } + }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, 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"rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 26, + "end": 30, + "loc": { + "start": { + "line": 1, + "column": 26 + }, + "end": { + "line": 1, + "column": 30 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "lodash", + "start": 31, + "end": 39, + "loc": { + "start": { + "line": 1, + "column": 31 + }, + "end": { + "line": 1, + "column": 39 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 39, + "end": 40, + "loc": { + "start": { + "line": 1, + "column": 39 + }, + "end": { + "line": 1, + "column": 40 + } + } + }, + { + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 42, + "end": 47, + "loc": { + "start": { + "line": 2, + "column": 0 + }, + "end": { + "line": 2, + "column": 5 + } + } + }, + { + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 48, + "end": 49, + "loc": { + "start": { + "line": 2, + "column": 6 + }, + "end": { + "line": 2, + "column": 7 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + 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193, + "end": 197, + "loc": { + "start": { + "line": 5, + "column": 16 + }, + "end": { + "line": 5, + "column": 20 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/owlterms", + "start": 198, + "end": 217, + "loc": { + "start": { + "line": 5, + "column": 21 + }, + "end": { + "line": 5, + "column": 40 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 217, + "end": 218, + "loc": { + "start": { + "line": 5, + "column": 40 + }, + "end": { + "line": 5, + "column": 41 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 219, + "end": 225, + "loc": { + "start": { + "line": 6, + "column": 0 + }, + "end": { + "line": 6, + "column": 6 + } + } + }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 226, + "end": 227, + "loc": { + "start": { + "line": 6, + "column": 7 + }, + "end": { + "line": 6, + "column": 8 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 228, + "end": 230, + "loc": { + "start": { + "line": 6, + "column": 9 + }, + "end": { + "line": 6, + "column": 11 + } } - ], - "directives": [] - }, - "comments": [ + }, { - "type": "CommentBlock", - "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", - "start": 325, - "end": 1088, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK8JDZPL7", + "start": 231, + "end": 244, "loc": { "start": { - "line": 9, - "column": 0 + "line": 6, + "column": 12 }, "end": { - "line": 23, - "column": 3 + "line": 6, + "column": 25 } } }, { - "type": "CommentBlock", - "value": "* The '@type' of specimens in JSON-LD document. ", - "start": 1115, - "end": 1167, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 245, + "end": 249, "loc": { "start": { - "line": 25, - "column": 2 + "line": 6, + "column": 26 }, "end": { - "line": 25, - "column": 54 + "line": 6, + "column": 30 } } }, { - "type": "CommentBlock", - "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/PhyxCacheManager", + "start": 250, + "end": 277, "loc": { "start": { - "line": 30, - "column": 2 + "line": 6, + "column": 31 }, "end": { - "line": 30, - "column": 47 + "line": 6, + "column": 58 } } }, { - "type": "CommentBlock", - "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1351, - "end": 1632, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 277, + "end": 278, "loc": { "start": { - "line": 35, - "column": 2 + "line": 6, + "column": 58 }, "end": { - "line": 40, + "line": 6, + "column": 59 + } + } + }, + { + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 280, + "end": 285, + "loc": { + "start": { + "line": 7, + "column": 0 + }, + "end": { + "line": 7, "column": 5 } } }, { - "type": "CommentLine", - "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 1716, - "end": 1777, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 286, + "end": 287, "loc": { "start": { - "line": 42, - "column": 4 + "line": 7, + "column": 6 }, "end": { - "line": 42, - "column": 65 + "line": 7, + "column": 7 } } }, { - "type": "CommentLine", - "value": " Prepare the specimen.", - "start": 1889, - "end": 1913, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "PhyxCacheManager", + "start": 288, + "end": 304, "loc": { "start": { - "line": 46, - "column": 4 + "line": 7, + "column": 8 }, "end": { - "line": 46, - "column": 28 + "line": 7, + "column": 24 } } }, { - "type": "CommentLine", - "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2066, - "end": 2139, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 305, + "end": 306, "loc": { "start": { - "line": 53, - "column": 4 + "line": 7, + "column": 25 }, "end": { - "line": 53, - "column": 77 + "line": 7, + "column": 26 } } }, { - "type": "CommentLine", - "value": " URL instead. If so, don't do any further processing!", - "start": 2144, - "end": 2199, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 307, + "end": 308, "loc": { "start": { - "line": 54, - "column": 4 + "line": 7, + "column": 27 }, "end": { - "line": 54, - "column": 59 + "line": 7, + "column": 28 } } }, { - "type": "CommentLine", - "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 2469, - "end": 2538, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK8JDZPL7", + "start": 309, + "end": 322, "loc": { "start": { - "line": 67, - "column": 4 + "line": 7, + "column": 29 }, "end": { - "line": 67, - "column": 73 + "line": 7, + "column": 42 } } }, { - "type": "CommentLine", - "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 2709, - "end": 2794, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 322, + "end": 323, "loc": { "start": { - "line": 72, - "column": 4 + "line": 7, + "column": 42 }, "end": { - "line": 72, - "column": 89 + "line": 7, + "column": 43 } } }, { - "type": "CommentLine", - "value": " specimen.institutionCode = undefined;", - "start": 2869, - "end": 2909, + "type": "CommentBlock", + "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", + "start": 325, + "end": 1088, "loc": { "start": { - "line": 75, - "column": 6 + "line": 9, + "column": 0 }, "end": { - "line": 75, - "column": 46 + "line": 23, + "column": 3 } } }, { - "type": "CommentLine", - "value": " specimen.collectionCode = undefined;", - "start": 2916, - "end": 2955, + "type": { + "label": "class", + "keyword": "class", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "class", + "start": 1089, + "end": 1094, "loc": { "start": { - "line": 76, + "line": 24, + "column": 0 + }, + "end": { + "line": 24, + "column": 5 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "SpecimenWrapper", + "start": 1095, + "end": 1110, + "loc": { + "start": { + "line": 24, "column": 6 }, "end": { - "line": 76, - "column": 45 + "line": 24, + "column": 21 } } }, { - "type": "CommentLine", - "value": " Store all split catalog number values.", - "start": 3168, - "end": 3209, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1111, + "end": 1112, "loc": { "start": { - "line": 81, - "column": 33 + "line": 24, + "column": 22 }, "end": { - "line": 81, - "column": 74 + "line": 24, + "column": 23 } } }, { "type": "CommentBlock", - "value": "*\n * Get the catalogNumber if present.\n ", - "start": 3474, - "end": 3522, + "value": "* The '@type' of specimens in JSON-LD document. ", + "start": 1115, + "end": 1167, "loc": { "start": { - "line": 90, + "line": 25, "column": 2 }, "end": { - "line": 92, - "column": 5 + "line": 25, + "column": 54 } } }, { - "type": "CommentLine", - "value": " Get the catalog number from the specimen object if present.", - "start": 3551, - "end": 3613, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "static", + "start": 1170, + "end": 1176, "loc": { "start": { - "line": 94, - "column": 4 + "line": 26, + "column": 2 }, "end": { - "line": 94, - "column": 66 + "line": 26, + "column": 8 } } }, { - "type": "CommentLine", - "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 3700, - "end": 3771, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "get", + "start": 1177, + "end": 1180, "loc": { "start": { - "line": 97, - "column": 4 + "line": 26, + "column": 9 }, "end": { - "line": 97, - "column": 75 + "line": 26, + "column": 12 } } }, { - "type": "CommentLine", - "value": " catalogNumber from there.", - "start": 3776, - "end": 3804, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "TYPE_SPECIMEN", + "start": 1181, + "end": 1194, "loc": { "start": { - "line": 98, - "column": 4 + "line": 26, + "column": 13 }, "end": { - "line": 98, - "column": 32 + "line": 26, + "column": 26 } } }, { - "type": "CommentBlock", - "value": "*\n * Get the institutionCode if present.\n ", - "start": 4044, - "end": 4094, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1194, + "end": 1195, + "loc": { + "start": { + "line": 26, + "column": 26 + }, + "end": { + "line": 26, + "column": 27 + } + } + }, + { + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1195, + "end": 1196, + "loc": { + "start": { + "line": 26, + "column": 27 + }, + "end": { + "line": 26, + "column": 28 + } + } + }, + { + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1197, + "end": 1198, "loc": { "start": { - "line": 106, - "column": 2 + "line": 26, + "column": 29 }, "end": { - "line": 108, - "column": 5 + "line": 26, + "column": 30 } } }, { - "type": "CommentLine", - "value": " Get the institution code from the specimen object if present.", - "start": 4125, - "end": 4189, + "type": { + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "return", + "start": 1203, + "end": 1209, "loc": { "start": { - "line": 110, + "line": 27, "column": 4 }, "end": { - "line": 110, - "column": 68 + "line": 27, + "column": 10 } } }, { - "type": "CommentLine", - "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4280, - "end": 4352, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 1210, + "end": 1218, "loc": { "start": { - "line": 113, - "column": 4 + "line": 27, + "column": 11 }, "end": { - "line": 113, - "column": 76 + "line": 27, + "column": 19 } } }, { - "type": "CommentLine", - "value": " occurrenceID from there.", - "start": 4357, - "end": 4384, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1218, + "end": 1219, "loc": { "start": { - "line": 114, - "column": 4 + "line": 27, + "column": 19 }, "end": { - "line": 114, - "column": 31 + "line": 27, + "column": 20 } } }, { - "type": "CommentBlock", - "value": "*\n * Get the collectionCode if present.\n ", - "start": 4628, - "end": 4677, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "DWC_OCCURRENCE", + "start": 1219, + "end": 1233, "loc": { "start": { - "line": 122, - "column": 2 + "line": 27, + "column": 20 }, "end": { - "line": 124, - "column": 5 + "line": 27, + "column": 34 } } }, { - "type": "CommentLine", - "value": " Get the collection code from the specimen object if present.", - "start": 4707, - "end": 4770, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1233, + "end": 1234, "loc": { "start": { - "line": 126, - "column": 4 + "line": 27, + "column": 34 }, "end": { - "line": 126, - "column": 67 + "line": 27, + "column": 35 } } }, { - "type": "CommentLine", - "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4859, - "end": 4931, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1237, + "end": 1238, "loc": { "start": { - "line": 129, - "column": 4 + "line": 28, + "column": 2 }, "end": { - "line": 129, - "column": 76 + "line": 28, + "column": 3 } } }, { - "type": "CommentLine", - "value": " occurrenceID from there.", - "start": 4936, - "end": 4963, + "type": "CommentBlock", + "value": "* Construct a wrapper around a specimen. ", + "start": 1242, + "end": 1287, "loc": { "start": { - "line": 130, - "column": 4 + "line": 30, + "column": 2 }, "end": { - "line": 130, - "column": 31 + "line": 30, + "column": 47 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5205, - "end": 5464, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "constructor", + "start": 1290, + "end": 1301, "loc": { "start": { - "line": 138, + "line": 31, "column": 2 }, "end": { - "line": 143, - "column": 5 + "line": 31, + "column": 13 } } }, { - "type": "CommentLine", - "value": " Return the occurrenceID if it exists.", - "start": 5492, - "end": 5532, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1301, + "end": 1302, "loc": { "start": { - "line": 145, - "column": 4 + "line": 31, + "column": 13 }, "end": { - "line": 145, - "column": 44 + "line": 31, + "column": 14 } } }, { - "type": "CommentLine", - "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 5682, - "end": 5759, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "specimen", + "start": 1302, + "end": 1310, "loc": { "start": { - "line": 150, - "column": 4 + "line": 31, + "column": 14 }, "end": { - "line": 150, - "column": 81 + "line": 31, + "column": 22 } } }, { - "type": "CommentLine", - "value": " None of our specimen identifier schemes worked.", - "start": 6431, - "end": 6481, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1310, + "end": 1311, "loc": { "start": { - "line": 164, - "column": 4 + "line": 31, + "column": 22 }, "end": { - "line": 164, - "column": 54 + "line": 31, + "column": 23 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 6511, - "end": 6572, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1312, + "end": 1313, "loc": { "start": { - "line": 168, - "column": 2 + "line": 31, + "column": 24 }, "end": { - "line": 170, - "column": 5 + "line": 31, + "column": 25 } } }, { - "type": "CommentBlock", - "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 6718, - "end": 6833, + "type": { + "label": "this", + "keyword": "this", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "this", + "start": 1318, + "end": 1322, "loc": { "start": { - "line": 176, - "column": 2 + "line": 32, + "column": 4 }, "end": { - "line": 179, - "column": 5 + "line": 32, + "column": 8 } } }, { - "type": "CommentBlock", - "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 6914, - "end": 6999, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1322, + "end": 1323, "loc": { "start": { - "line": 184, - "column": 2 + "line": 32, + "column": 8 }, "end": { - "line": 184, - "column": 87 + "line": 32, + "column": 9 } } }, { - "type": "CommentBlock", - "value": "* Return a label for this specimen. ", - "start": 7177, - "end": 7217, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "specimen", + "start": 1323, + "end": 1331, "loc": { "start": { - "line": 191, - "column": 2 + "line": 32, + "column": 9 }, "end": { - "line": 191, - "column": 42 + "line": 32, + "column": 17 } } }, { - "type": "CommentLine", - "value": " We can't return anything without an occurrenceID.", - "start": 7238, - "end": 7290, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 1332, + "end": 1333, "loc": { "start": { - "line": 193, - "column": 4 + "line": 32, + "column": 18 }, "end": { - "line": 193, - "column": 56 + "line": 32, + "column": 19 } } }, { - "type": "CommentLine", - "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7342, - "end": 7419, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "specimen", + "start": 1334, + "end": 1342, "loc": { "start": { - "line": 196, - "column": 4 + "line": 32, + "column": 20 }, "end": { - "line": 196, - "column": 81 + "line": 32, + "column": 28 } } }, { - "type": "CommentLine", - "value": " include that information in the label.", - "start": 7424, - "end": 7465, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1342, + "end": 1343, "loc": { "start": { - "line": 197, - "column": 4 + "line": 32, + "column": 28 }, "end": { - "line": 197, - "column": 45 + "line": 32, + "column": 29 } } }, { - "type": "CommentLine", - "value": " Return a label for this specimen.", - "start": 7618, - "end": 7654, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1346, + "end": 1347, "loc": { "start": { - "line": 202, - "column": 4 + "line": 33, + "column": 2 }, "end": { - "line": 202, - "column": 40 + "line": 33, + "column": 3 } } }, { "type": "CommentBlock", - "value": "* Return this specimen as an equivalentClass expression. ", - "start": 7706, - "end": 7767, + "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", + "start": 1351, + "end": 1449, "loc": { "start": { - "line": 206, + "line": 35, "column": 2 }, "end": { - "line": 206, - "column": 63 + "line": 38, + "column": 5 } } }, { - "type": "CommentLine", - "value": " We can't do anything without an occurrence ID!", - "start": 7798, - "end": 7847, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "static", + "start": 1452, + "end": 1458, "loc": { "start": { - "line": 208, - "column": 4 + "line": 39, + "column": 2 }, "end": { - "line": 208, - "column": 53 + "line": 39, + "column": 8 } } }, { - "type": "CommentLine", - "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 7899, - "end": 7970, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "normalize", + "start": 1459, + "end": 1468, "loc": { "start": { - "line": 211, - "column": 4 + "line": 39, + "column": 9 }, "end": { - "line": 211, - "column": 75 + "line": 39, + "column": 18 } } }, { - "type": "CommentLine", - "value": " Technically no, but it might be useful. Hmm.", - "start": 7975, - "end": 8022, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1468, + "end": 1469, "loc": { "start": { - "line": 212, - "column": 4 + "line": 39, + "column": 18 }, "end": { - "line": 212, - "column": 51 + "line": 39, + "column": 19 } } }, - { - "type": "CommentLine", - "value": " Return as an OWL restriction.", - "start": 8028, - "end": 8060, - "loc": { - "start": { - "line": 214, - "column": 4 - }, - "end": { - "line": 214, - "column": 36 - } - } - } - ], - "tokens": [ { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -24462,54 +28798,51 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 0, - "end": 6, + "value": "specimen", + "start": 1469, + "end": 1477, "loc": { "start": { - "line": 1, - "column": 0 + "line": 39, + "column": 19 }, "end": { - "line": 1, - "column": 6 + "line": 39, + "column": 27 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 7, - "end": 8, + "start": 1477, + "end": 1478, "loc": { "start": { - "line": 1, - "column": 7 + "line": 39, + "column": 27 }, "end": { - "line": 1, - "column": 8 + "line": 39, + "column": 28 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24518,43 +28851,44 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 9, - "end": 11, + "start": 1479, + "end": 1480, "loc": { "start": { - "line": 1, - "column": 9 + "line": 39, + "column": 29 }, "end": { - "line": 1, - "column": 11 + "line": 39, + "column": 30 } } }, { "type": { - "label": "name", + "label": "const", + "keyword": "const", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H18NKRQE3", - "start": 12, - "end": 25, + "value": "const", + "start": 1485, + "end": 1490, "loc": { "start": { - "line": 1, - "column": 12 + "line": 40, + "column": 4 }, "end": { - "line": 1, - "column": 25 + "line": 40, + "column": 9 } } }, @@ -24570,52 +28904,53 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 26, - "end": 30, + "value": "wrapped", + "start": 1491, + "end": 1498, "loc": { "start": { - "line": 1, - "column": 26 + "line": 40, + "column": 10 }, "end": { - "line": 1, - "column": 30 + "line": 40, + "column": 17 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "lodash", - "start": 31, - "end": 39, + "value": "=", + "start": 1499, + "end": 1500, "loc": { "start": { - "line": 1, - "column": 31 + "line": 40, + "column": 18 }, "end": { - "line": 1, - "column": 39 + "line": 40, + "column": 19 } } }, { "type": { - "label": ";", + "label": "new", + "keyword": "new", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -24624,50 +28959,49 @@ "binop": null, "updateContext": null }, - "start": 39, - "end": 40, + "value": "new", + "start": 1501, + "end": 1504, "loc": { "start": { - "line": 1, - "column": 39 + "line": 40, + "column": 20 }, "end": { - "line": 1, - "column": 40 + "line": 40, + "column": 23 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 42, - "end": 47, + "value": "SpecimenWrapper", + "start": 1505, + "end": 1520, "loc": { "start": { - "line": 2, - "column": 0 + "line": 40, + "column": 24 }, "end": { - "line": 2, - "column": 5 + "line": 40, + "column": 39 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -24677,16 +29011,16 @@ "postfix": false, "binop": null }, - "start": 48, - "end": 49, + "start": 1520, + "end": 1521, "loc": { "start": { - "line": 2, - "column": 6 + "line": 40, + "column": 39 }, "end": { - "line": 2, - "column": 7 + "line": 40, + "column": 40 } } }, @@ -24702,23 +29036,23 @@ "postfix": false, "binop": null }, - "value": "has", - "start": 50, - "end": 53, + "value": "specimen", + "start": 1521, + "end": 1529, "loc": { "start": { - "line": 2, - "column": 8 + "line": 40, + "column": 40 }, "end": { - "line": 2, - "column": 11 + "line": 40, + "column": 48 } } }, { "type": { - "label": "}", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -24728,43 +29062,70 @@ "postfix": false, "binop": null }, - "start": 54, - "end": 55, + "start": 1529, + "end": 1530, "loc": { "start": { - "line": 2, - "column": 12 + "line": 40, + "column": 48 }, "end": { - "line": 2, - "column": 13 + "line": 40, + "column": 49 } } }, { "type": { - "label": "=", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 56, - "end": 57, + "start": 1530, + "end": 1531, "loc": { "start": { - "line": 2, - "column": 14 + "line": 40, + "column": 49 }, "end": { - "line": 2, - "column": 15 + "line": 40, + "column": 50 + } + } + }, + { + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 1536, + "end": 1541, + "loc": { + "start": { + "line": 41, + "column": 4 + }, + "end": { + "line": 41, + "column": 9 } } }, @@ -24780,50 +29141,75 @@ "postfix": false, "binop": null }, - "value": "LKT4H18NKRQE3", - "start": 58, - "end": 71, + "value": "normalizedSpecimen", + "start": 1542, + "end": 1560, "loc": { "start": { - "line": 2, - "column": 16 + "line": 41, + "column": 10 }, "end": { - "line": 2, - "column": 29 + "line": 41, + "column": 28 } } }, { "type": { - "label": ";", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 71, - "end": 72, + "value": "=", + "start": 1561, + "end": 1562, "loc": { "start": { - "line": 2, + "line": 41, "column": 29 }, "end": { - "line": 2, + "line": 41, "column": 30 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1563, + "end": 1564, + "loc": { + "start": { + "line": 41, + "column": 31 + }, + "end": { + "line": 41, + "column": 32 + } + } + }, + { + "type": { + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -24834,23 +29220,23 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 73, - "end": 79, + "value": "@type", + "start": 1571, + "end": 1578, "loc": { "start": { - "line": 3, - "column": 0 + "line": 42, + "column": 6 }, "end": { - "line": 3, - "column": 6 + "line": 42, + "column": 13 } } }, { "type": { - "label": "*", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -24858,20 +29244,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 80, - "end": 81, + "start": 1578, + "end": 1579, "loc": { "start": { - "line": 3, - "column": 7 + "line": 42, + "column": 13 }, "end": { - "line": 3, - "column": 8 + "line": 42, + "column": 14 } } }, @@ -24887,43 +29272,43 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 82, - "end": 84, + "value": "SpecimenWrapper", + "start": 1580, + "end": 1595, "loc": { "start": { - "line": 3, - "column": 9 + "line": 42, + "column": 15 }, "end": { - "line": 3, - "column": 11 + "line": 42, + "column": 30 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H18N3GRL0", - "start": 85, - "end": 98, + "start": 1595, + "end": 1596, "loc": { "start": { - "line": 3, - "column": 12 + "line": 42, + "column": 30 }, "end": { - "line": 3, - "column": 25 + "line": 42, + "column": 31 } } }, @@ -24939,25 +29324,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 99, - "end": 103, + "value": "TYPE_SPECIMEN", + "start": 1596, + "end": 1609, "loc": { "start": { - "line": 3, - "column": 26 + "line": 42, + "column": 31 }, "end": { - "line": 3, - "column": 30 + "line": 42, + "column": 44 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -24966,51 +29351,49 @@ "binop": null, "updateContext": null }, - "value": "./TaxonConceptWrapper", - "start": 104, - "end": 127, + "start": 1609, + "end": 1610, "loc": { "start": { - "line": 3, - "column": 31 + "line": 42, + "column": 44 }, "end": { - "line": 3, - "column": 54 + "line": 42, + "column": 45 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 127, - "end": 128, + "value": "label", + "start": 1617, + "end": 1622, "loc": { "start": { - "line": 3, - "column": 54 + "line": 43, + "column": 6 }, "end": { - "line": 3, - "column": 55 + "line": 43, + "column": 11 } } }, { "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -25020,24 +29403,23 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 130, - "end": 135, + "start": 1622, + "end": 1623, "loc": { "start": { - "line": 4, - "column": 0 + "line": 43, + "column": 11 }, "end": { - "line": 4, - "column": 5 + "line": 43, + "column": 12 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -25046,50 +29428,51 @@ "postfix": false, "binop": null }, - "start": 136, - "end": 137, + "value": "wrapped", + "start": 1624, + "end": 1631, "loc": { "start": { - "line": 4, - "column": 6 + "line": 43, + "column": 13 }, "end": { - "line": 4, - "column": 7 + "line": 43, + "column": 20 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "TaxonConceptWrapper", - "start": 138, - "end": 157, + "start": 1631, + "end": 1632, "loc": { "start": { - "line": 4, - "column": 8 + "line": 43, + "column": 20 }, "end": { - "line": 4, - "column": 27 + "line": 43, + "column": 21 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -25097,49 +29480,49 @@ "postfix": false, "binop": null }, - "start": 158, - "end": 159, + "value": "label", + "start": 1632, + "end": 1637, "loc": { "start": { - "line": 4, - "column": 28 + "line": 43, + "column": 21 }, "end": { - "line": 4, - "column": 29 + "line": 43, + "column": 26 } } }, { "type": { - "label": "=", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 160, - "end": 161, + "start": 1637, + "end": 1638, "loc": { "start": { - "line": 4, - "column": 30 + "line": 43, + "column": 26 }, "end": { - "line": 4, - "column": 31 + "line": 43, + "column": 27 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -25147,25 +29530,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H18N3GRL0", - "start": 162, - "end": 175, + "value": "dwc:basisOfRecord", + "start": 1645, + "end": 1664, "loc": { "start": { - "line": 4, - "column": 32 + "line": 44, + "column": 6 }, "end": { - "line": 4, - "column": 45 + "line": 44, + "column": 25 } } }, { "type": { - "label": ";", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -25176,23 +29560,22 @@ "binop": null, "updateContext": null }, - "start": 175, - "end": 176, + "start": 1664, + "end": 1665, "loc": { "start": { - "line": 4, - "column": 45 + "line": 44, + "column": 25 }, "end": { - "line": 4, - "column": 46 + "line": 44, + "column": 26 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -25200,20 +29583,45 @@ "isAssign": false, "prefix": false, "postfix": false, + "binop": null + }, + "value": "wrapped", + "start": 1666, + "end": 1673, + "loc": { + "start": { + "line": 44, + "column": 27 + }, + "end": { + "line": 44, + "column": 34 + } + } + }, + { + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, "binop": null, "updateContext": null }, - "value": "import", - "start": 177, - "end": 183, + "start": 1673, + "end": 1674, "loc": { "start": { - "line": 5, - "column": 0 + "line": 44, + "column": 34 }, "end": { - "line": 5, - "column": 6 + "line": 44, + "column": 35 } } }, @@ -25229,49 +29637,49 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 184, - "end": 192, + "value": "basisOfRecord", + "start": 1674, + "end": 1687, "loc": { "start": { - "line": 5, - "column": 7 + "line": 44, + "column": 35 }, "end": { - "line": 5, - "column": 15 + "line": 44, + "column": 48 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "from", - "start": 193, - "end": 197, + "start": 1687, + "end": 1688, "loc": { "start": { - "line": 5, - "column": 16 + "line": 44, + "column": 48 }, "end": { - "line": 5, - "column": 20 + "line": 44, + "column": 49 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -25279,26 +29687,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "../utils/owlterms", - "start": 198, - "end": 217, + "value": "occurrenceID", + "start": 1695, + "end": 1707, "loc": { "start": { - "line": 5, - "column": 21 + "line": 45, + "column": 6 }, "end": { - "line": 5, - "column": 40 + "line": 45, + "column": 18 } } }, { "type": { - "label": ";", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -25309,23 +29716,22 @@ "binop": null, "updateContext": null }, - "start": 217, - "end": 218, + "start": 1707, + "end": 1708, "loc": { "start": { - "line": 5, - "column": 40 + "line": 45, + "column": 18 }, "end": { - "line": 5, - "column": 41 + "line": 45, + "column": 19 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -25333,47 +29739,45 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 219, - "end": 225, + "value": "wrapped", + "start": 1709, + "end": 1716, "loc": { "start": { - "line": 6, - "column": 0 + "line": 45, + "column": 20 }, "end": { - "line": 6, - "column": 6 + "line": 45, + "column": 27 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 226, - "end": 227, + "start": 1716, + "end": 1717, "loc": { "start": { - "line": 6, - "column": 7 + "line": 45, + "column": 27 }, "end": { - "line": 6, - "column": 8 + "line": 45, + "column": 28 } } }, @@ -25389,43 +29793,43 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 228, - "end": 230, + "value": "occurrenceID", + "start": 1717, + "end": 1729, "loc": { "start": { - "line": 6, - "column": 9 + "line": 45, + "column": 28 }, "end": { - "line": 6, - "column": 11 + "line": 45, + "column": 40 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H18N9PCKE", - "start": 231, - "end": 244, + "start": 1729, + "end": 1730, "loc": { "start": { - "line": 6, - "column": 12 + "line": 45, + "column": 40 }, "end": { - "line": 6, - "column": 25 + "line": 45, + "column": 41 } } }, @@ -25441,25 +29845,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 245, - "end": 249, + "value": "catalogNumber", + "start": 1737, + "end": 1750, "loc": { "start": { - "line": 6, - "column": 26 + "line": 46, + "column": 6 }, "end": { - "line": 6, - "column": 30 + "line": 46, + "column": 19 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -25468,50 +29872,48 @@ "binop": null, "updateContext": null }, - "value": "../utils/PhyxCacheManager", - "start": 250, - "end": 277, + "start": 1750, + "end": 1751, "loc": { "start": { - "line": 6, - "column": 31 + "line": 46, + "column": 19 }, "end": { - "line": 6, - "column": 58 + "line": 46, + "column": 20 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 277, - "end": 278, + "value": "wrapped", + "start": 1752, + "end": 1759, "loc": { "start": { - "line": 6, - "column": 58 + "line": 46, + "column": 21 }, "end": { - "line": 6, - "column": 59 + "line": 46, + "column": 28 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -25522,24 +29924,23 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 280, - "end": 285, + "start": 1759, + "end": 1760, "loc": { "start": { - "line": 7, - "column": 0 + "line": 46, + "column": 28 }, "end": { - "line": 7, - "column": 5 + "line": 46, + "column": 29 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -25548,50 +29949,51 @@ "postfix": false, "binop": null }, - "start": 286, - "end": 287, + "value": "catalogNumber", + "start": 1760, + "end": 1773, "loc": { "start": { - "line": 7, - "column": 6 + "line": 46, + "column": 29 }, "end": { - "line": 7, - "column": 7 + "line": 46, + "column": 42 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "PhyxCacheManager", - "start": 288, - "end": 304, + "start": 1773, + "end": 1774, "loc": { "start": { - "line": 7, - "column": 8 + "line": 46, + "column": 42 }, "end": { - "line": 7, - "column": 24 + "line": 46, + "column": 43 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -25599,43 +30001,43 @@ "postfix": false, "binop": null }, - "start": 305, - "end": 306, + "value": "institutionCode", + "start": 1781, + "end": 1796, "loc": { "start": { - "line": 7, - "column": 25 + "line": 47, + "column": 6 }, "end": { - "line": 7, - "column": 26 + "line": 47, + "column": 21 } } }, { "type": { - "label": "=", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 307, - "end": 308, + "start": 1796, + "end": 1797, "loc": { "start": { - "line": 7, - "column": 27 + "line": 47, + "column": 21 }, "end": { - "line": 7, - "column": 28 + "line": 47, + "column": 22 } } }, @@ -25651,24 +30053,24 @@ "postfix": false, "binop": null }, - "value": "LKT4H18N9PCKE", - "start": 309, - "end": 322, + "value": "wrapped", + "start": 1798, + "end": 1805, "loc": { "start": { - "line": 7, - "column": 29 + "line": 47, + "column": 23 }, "end": { - "line": 7, - "column": 42 + "line": 47, + "column": 30 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -25678,40 +30080,49 @@ "binop": null, "updateContext": null }, - "start": 322, - "end": 323, + "start": 1805, + "end": 1806, "loc": { "start": { - "line": 7, - "column": 42 + "line": 47, + "column": 30 }, "end": { - "line": 7, - "column": 43 + "line": 47, + "column": 31 } } }, { - "type": "CommentBlock", - "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", - "start": 325, - "end": 1088, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "institutionCode", + "start": 1806, + "end": 1821, "loc": { "start": { - "line": 9, - "column": 0 + "line": 47, + "column": 31 }, "end": { - "line": 23, - "column": 3 + "line": 47, + "column": 46 } } }, { "type": { - "label": "class", - "keyword": "class", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -25721,17 +30132,16 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 1089, - "end": 1094, + "start": 1821, + "end": 1822, "loc": { "start": { - "line": 24, - "column": 0 + "line": 47, + "column": 46 }, "end": { - "line": 24, - "column": 5 + "line": 47, + "column": 47 } } }, @@ -25747,58 +30157,43 @@ "postfix": false, "binop": null }, - "value": "SpecimenWrapper", - "start": 1095, - "end": 1110, + "value": "collectionCode", + "start": 1829, + "end": 1843, "loc": { "start": { - "line": 24, + "line": 48, "column": 6 }, "end": { - "line": 24, - "column": 21 + "line": 48, + "column": 20 } } }, { "type": { - "label": "{", + "label": ":", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1111, - "end": 1112, - "loc": { - "start": { - "line": 24, - "column": 22 - }, - "end": { - "line": 24, - "column": 23 - } - } - }, - { - "type": "CommentBlock", - "value": "* The '@type' of specimens in JSON-LD document. ", - "start": 1115, - "end": 1167, + "start": 1843, + "end": 1844, "loc": { "start": { - "line": 25, - "column": 2 + "line": 48, + "column": 20 }, "end": { - "line": 25, - "column": 54 + "line": 48, + "column": 21 } } }, @@ -25814,43 +30209,43 @@ "postfix": false, "binop": null }, - "value": "static", - "start": 1170, - "end": 1176, + "value": "wrapped", + "start": 1845, + "end": 1852, "loc": { "start": { - "line": 26, - "column": 2 + "line": 48, + "column": 22 }, "end": { - "line": 26, - "column": 8 + "line": 48, + "column": 29 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "get", - "start": 1177, - "end": 1180, + "start": 1852, + "end": 1853, "loc": { "start": { - "line": 26, - "column": 9 + "line": 48, + "column": 29 }, "end": { - "line": 26, - "column": 12 + "line": 48, + "column": 30 } } }, @@ -25866,48 +30261,49 @@ "postfix": false, "binop": null }, - "value": "TYPE_SPECIMEN", - "start": 1181, - "end": 1194, + "value": "collectionCode", + "start": 1853, + "end": 1867, "loc": { "start": { - "line": 26, - "column": 13 + "line": 48, + "column": 30 }, "end": { - "line": 26, - "column": 26 + "line": 48, + "column": 44 } } }, { "type": { - "label": "(", + "label": ",", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1194, - "end": 1195, + "start": 1867, + "end": 1868, "loc": { "start": { - "line": 26, - "column": 26 + "line": 48, + "column": 44 }, "end": { - "line": 26, - "column": 27 + "line": 48, + "column": 45 } } }, { "type": { - "label": ")", + "label": "}", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -25917,49 +30313,50 @@ "postfix": false, "binop": null }, - "start": 1195, - "end": 1196, + "start": 1873, + "end": 1874, "loc": { "start": { - "line": 26, - "column": 27 + "line": 49, + "column": 4 }, "end": { - "line": 26, - "column": 28 + "line": 49, + "column": 5 } } }, { "type": { - "label": "{", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1197, - "end": 1198, + "start": 1874, + "end": 1875, "loc": { "start": { - "line": 26, - "column": 29 + "line": 49, + "column": 5 }, "end": { - "line": 26, - "column": 30 + "line": 49, + "column": 6 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, + "label": "if", + "keyword": "if", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -25969,24 +30366,24 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 1203, - "end": 1209, + "value": "if", + "start": 1880, + "end": 1882, "loc": { "start": { - "line": 27, + "line": 50, "column": 4 }, "end": { - "line": 27, - "column": 10 + "line": 50, + "column": 6 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -25995,43 +30392,71 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 1210, - "end": 1218, + "start": 1883, + "end": 1884, "loc": { "start": { - "line": 27, - "column": 11 + "line": 50, + "column": 7 }, "end": { - "line": 27, - "column": 19 + "line": 50, + "column": 8 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "@id", + "start": 1884, + "end": 1889, + "loc": { + "start": { + "line": 50, + "column": 8 + }, + "end": { + "line": 50, + "column": 13 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "in", + "keyword": "in", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 7, "updateContext": null }, - "start": 1218, - "end": 1219, + "value": "in", + "start": 1890, + "end": 1892, "loc": { "start": { - "line": 27, - "column": 19 + "line": 50, + "column": 14 }, "end": { - "line": 27, - "column": 20 + "line": 50, + "column": 16 } } }, @@ -26047,51 +30472,50 @@ "postfix": false, "binop": null }, - "value": "DWC_OCCURRENCE", - "start": 1219, - "end": 1233, + "value": "specimen", + "start": 1893, + "end": 1901, "loc": { "start": { - "line": 27, - "column": 20 + "line": 50, + "column": 17 }, "end": { - "line": 27, - "column": 34 + "line": 50, + "column": 25 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 1233, - "end": 1234, + "start": 1901, + "end": 1902, "loc": { "start": { - "line": 27, - "column": 34 + "line": 50, + "column": 25 }, "end": { - "line": 27, - "column": 35 + "line": 50, + "column": 26 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -26099,38 +30523,49 @@ "postfix": false, "binop": null }, - "start": 1237, - "end": 1238, + "value": "normalizedSpecimen", + "start": 1903, + "end": 1921, "loc": { "start": { - "line": 28, - "column": 2 + "line": 50, + "column": 27 }, "end": { - "line": 28, - "column": 3 + "line": 50, + "column": 45 } } }, { - "type": "CommentBlock", - "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "type": { + "label": "[", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1921, + "end": 1922, "loc": { "start": { - "line": 30, - "column": 2 + "line": 50, + "column": 45 }, "end": { - "line": 30, - "column": 47 + "line": 50, + "column": 46 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -26138,78 +30573,81 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "constructor", - "start": 1290, - "end": 1301, + "value": "@id", + "start": 1922, + "end": 1927, "loc": { "start": { - "line": 31, - "column": 2 + "line": 50, + "column": 46 }, "end": { - "line": 31, - "column": 13 + "line": 50, + "column": 51 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": "]", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1301, - "end": 1302, + "start": 1927, + "end": 1928, "loc": { "start": { - "line": 31, - "column": 13 + "line": 50, + "column": 51 }, "end": { - "line": 31, - "column": 14 + "line": 50, + "column": 52 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "specimen", - "start": 1302, - "end": 1310, + "value": "=", + "start": 1929, + "end": 1930, "loc": { "start": { - "line": 31, - "column": 14 + "line": 50, + "column": 53 }, "end": { - "line": 31, - "column": 22 + "line": 50, + "column": 54 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -26217,22 +30655,23 @@ "postfix": false, "binop": null }, - "start": 1310, - "end": 1311, + "value": "specimen", + "start": 1931, + "end": 1939, "loc": { "start": { - "line": 31, - "column": 22 + "line": 50, + "column": 55 }, "end": { - "line": 31, - "column": 23 + "line": 50, + "column": 63 } } }, { "type": { - "label": "{", + "label": "[", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -26240,25 +30679,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1312, - "end": 1313, + "start": 1939, + "end": 1940, "loc": { "start": { - "line": 31, - "column": 24 + "line": 50, + "column": 63 }, "end": { - "line": 31, - "column": 25 + "line": 50, + "column": 64 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -26269,23 +30708,23 @@ "binop": null, "updateContext": null }, - "value": "this", - "start": 1318, - "end": 1322, + "value": "@id", + "start": 1940, + "end": 1945, "loc": { "start": { - "line": 32, - "column": 4 + "line": 50, + "column": 64 }, "end": { - "line": 32, - "column": 8 + "line": 50, + "column": 69 } } }, { "type": { - "label": ".", + "label": "]", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -26296,69 +30735,70 @@ "binop": null, "updateContext": null }, - "start": 1322, - "end": 1323, + "start": 1945, + "end": 1946, "loc": { "start": { - "line": 32, - "column": 8 + "line": 50, + "column": 69 }, "end": { - "line": 32, - "column": 9 + "line": 50, + "column": 70 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "specimen", - "start": 1323, - "end": 1331, + "start": 1946, + "end": 1947, "loc": { "start": { - "line": 32, - "column": 9 + "line": 50, + "column": 70 }, "end": { - "line": 32, - "column": 17 + "line": 50, + "column": 71 } } }, { "type": { - "label": "=", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 1332, - "end": 1333, + "value": "return", + "start": 1952, + "end": 1958, "loc": { "start": { - "line": 32, - "column": 18 + "line": 51, + "column": 4 }, "end": { - "line": 32, - "column": 19 + "line": 51, + "column": 10 } } }, @@ -26374,17 +30814,17 @@ "postfix": false, "binop": null }, - "value": "specimen", - "start": 1334, - "end": 1342, + "value": "normalizedSpecimen", + "start": 1959, + "end": 1977, "loc": { "start": { - "line": 32, - "column": 20 + "line": 51, + "column": 11 }, "end": { - "line": 32, - "column": 28 + "line": 51, + "column": 29 } } }, @@ -26401,16 +30841,16 @@ "binop": null, "updateContext": null }, - "start": 1342, - "end": 1343, + "start": 1977, + "end": 1978, "loc": { "start": { - "line": 32, - "column": 28 + "line": 51, + "column": 29 }, "end": { - "line": 32, - "column": 29 + "line": 51, + "column": 30 } } }, @@ -26426,15 +30866,15 @@ "postfix": false, "binop": null }, - "start": 1346, - "end": 1347, + "start": 1981, + "end": 1982, "loc": { "start": { - "line": 33, + "line": 52, "column": 2 }, "end": { - "line": 33, + "line": 52, "column": 3 } } @@ -26442,15 +30882,15 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1351, - "end": 1632, + "start": 1986, + "end": 2267, "loc": { "start": { - "line": 35, + "line": 54, "column": 2 }, "end": { - "line": 40, + "line": 59, "column": 5 } } @@ -26468,15 +30908,15 @@ "binop": null }, "value": "static", - "start": 1635, - "end": 1641, + "start": 2270, + "end": 2276, "loc": { "start": { - "line": 41, + "line": 60, "column": 2 }, "end": { - "line": 41, + "line": 60, "column": 8 } } @@ -26494,15 +30934,15 @@ "binop": null }, "value": "fromOccurrenceID", - "start": 1642, - "end": 1658, + "start": 2277, + "end": 2293, "loc": { "start": { - "line": 41, + "line": 60, "column": 9 }, "end": { - "line": 41, + "line": 60, "column": 25 } } @@ -26519,15 +30959,15 @@ "postfix": false, "binop": null }, - "start": 1658, - "end": 1659, + "start": 2293, + "end": 2294, "loc": { "start": { - "line": 41, + "line": 60, "column": 25 }, "end": { - "line": 41, + "line": 60, "column": 26 } } @@ -26545,15 +30985,15 @@ "binop": null }, "value": "occurrenceID", - "start": 1659, - "end": 1671, + "start": 2294, + "end": 2306, "loc": { "start": { - "line": 41, + "line": 60, "column": 26 }, "end": { - "line": 41, + "line": 60, "column": 38 } } @@ -26571,15 +31011,15 @@ "binop": null, "updateContext": null }, - "start": 1671, - "end": 1672, + "start": 2306, + "end": 2307, "loc": { "start": { - "line": 41, + "line": 60, "column": 38 }, "end": { - "line": 41, + "line": 60, "column": 39 } } @@ -26597,15 +31037,15 @@ "binop": null }, "value": "basisOfRecord", - "start": 1673, - "end": 1686, + "start": 2308, + "end": 2321, "loc": { "start": { - "line": 41, + "line": 60, "column": 40 }, "end": { - "line": 41, + "line": 60, "column": 53 } } @@ -26624,15 +31064,15 @@ "updateContext": null }, "value": "=", - "start": 1687, - "end": 1688, + "start": 2322, + "end": 2323, "loc": { "start": { - "line": 41, + "line": 60, "column": 54 }, "end": { - "line": 41, + "line": 60, "column": 55 } } @@ -26651,15 +31091,15 @@ "updateContext": null }, "value": "PreservedSpecimen", - "start": 1689, - "end": 1708, + "start": 2324, + "end": 2343, "loc": { "start": { - "line": 41, + "line": 60, "column": 56 }, "end": { - "line": 41, + "line": 60, "column": 75 } } @@ -26676,15 +31116,15 @@ "postfix": false, "binop": null }, - "start": 1708, - "end": 1709, + "start": 2343, + "end": 2344, "loc": { "start": { - "line": 41, + "line": 60, "column": 75 }, "end": { - "line": 41, + "line": 60, "column": 76 } } @@ -26701,15 +31141,15 @@ "postfix": false, "binop": null }, - "start": 1710, - "end": 1711, + "start": 2345, + "end": 2346, "loc": { "start": { - "line": 41, + "line": 60, "column": 77 }, "end": { - "line": 41, + "line": 60, "column": 78 } } @@ -26717,15 +31157,15 @@ { "type": "CommentLine", "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 1716, - "end": 1777, + "start": 2351, + "end": 2412, "loc": { "start": { - "line": 42, + "line": 61, "column": 4 }, "end": { - "line": 42, + "line": 61, "column": 65 } } @@ -26745,15 +31185,15 @@ "updateContext": null }, "value": "let", - "start": 1782, - "end": 1785, + "start": 2417, + "end": 2420, "loc": { "start": { - "line": 43, + "line": 62, "column": 4 }, "end": { - "line": 43, + "line": 62, "column": 7 } } @@ -26771,15 +31211,15 @@ "binop": null }, "value": "occurID", - "start": 1786, - "end": 1793, + "start": 2421, + "end": 2428, "loc": { "start": { - "line": 43, + "line": 62, "column": 8 }, "end": { - "line": 43, + "line": 62, "column": 15 } } @@ -26798,15 +31238,15 @@ "updateContext": null }, "value": "=", - "start": 1794, - "end": 1795, + "start": 2429, + "end": 2430, "loc": { "start": { - "line": 43, + "line": 62, "column": 16 }, "end": { - "line": 43, + "line": 62, "column": 17 } } @@ -26824,15 +31264,15 @@ "binop": null }, "value": "occurrenceID", - "start": 1796, - "end": 1808, + "start": 2431, + "end": 2443, "loc": { "start": { - "line": 43, + "line": 62, "column": 18 }, "end": { - "line": 43, + "line": 62, "column": 30 } } @@ -26850,15 +31290,15 @@ "binop": null, "updateContext": null }, - "start": 1808, - "end": 1809, + "start": 2443, + "end": 2444, "loc": { "start": { - "line": 43, + "line": 62, "column": 30 }, "end": { - "line": 43, + "line": 62, "column": 31 } } @@ -26878,15 +31318,15 @@ "updateContext": null }, "value": "if", - "start": 1814, - "end": 1816, + "start": 2449, + "end": 2451, "loc": { "start": { - "line": 44, + "line": 63, "column": 4 }, "end": { - "line": 44, + "line": 63, "column": 6 } } @@ -26903,15 +31343,15 @@ "postfix": false, "binop": null }, - "start": 1817, - "end": 1818, + "start": 2452, + "end": 2453, "loc": { "start": { - "line": 44, + "line": 63, "column": 7 }, "end": { - "line": 44, + "line": 63, "column": 8 } } @@ -26929,15 +31369,15 @@ "binop": null }, "value": "occurID", - "start": 1818, - "end": 1825, + "start": 2453, + "end": 2460, "loc": { "start": { - "line": 44, + "line": 63, "column": 8 }, "end": { - "line": 44, + "line": 63, "column": 15 } } @@ -26955,15 +31395,15 @@ "binop": null, "updateContext": null }, - "start": 1825, - "end": 1826, + "start": 2460, + "end": 2461, "loc": { "start": { - "line": 44, + "line": 63, "column": 15 }, "end": { - "line": 44, + "line": 63, "column": 16 } } @@ -26981,15 +31421,15 @@ "binop": null }, "value": "startsWith", - "start": 1826, - "end": 1836, + "start": 2461, + "end": 2471, "loc": { "start": { - "line": 44, + "line": 63, "column": 16 }, "end": { - "line": 44, + "line": 63, "column": 26 } } @@ -27006,15 +31446,15 @@ "postfix": false, "binop": null }, - "start": 1836, - "end": 1837, + "start": 2471, + "end": 2472, "loc": { "start": { - "line": 44, + "line": 63, "column": 26 }, "end": { - "line": 44, + "line": 63, "column": 27 } } @@ -27033,15 +31473,15 @@ "updateContext": null }, "value": "urn:catalog:", - "start": 1837, - "end": 1851, + "start": 2472, + "end": 2486, "loc": { "start": { - "line": 44, + "line": 63, "column": 27 }, "end": { - "line": 44, + "line": 63, "column": 41 } } @@ -27058,15 +31498,15 @@ "postfix": false, "binop": null }, - "start": 1851, - "end": 1852, + "start": 2486, + "end": 2487, "loc": { "start": { - "line": 44, + "line": 63, "column": 41 }, "end": { - "line": 44, + "line": 63, "column": 42 } } @@ -27083,15 +31523,15 @@ "postfix": false, "binop": null }, - "start": 1852, - "end": 1853, + "start": 2487, + "end": 2488, "loc": { "start": { - "line": 44, + "line": 63, "column": 42 }, "end": { - "line": 44, + "line": 63, "column": 43 } } @@ -27109,15 +31549,15 @@ "binop": null }, "value": "occurID", - "start": 1854, - "end": 1861, + "start": 2489, + "end": 2496, "loc": { "start": { - "line": 44, + "line": 63, "column": 44 }, "end": { - "line": 44, + "line": 63, "column": 51 } } @@ -27136,15 +31576,15 @@ "updateContext": null }, "value": "=", - "start": 1862, - "end": 1863, + "start": 2497, + "end": 2498, "loc": { "start": { - "line": 44, + "line": 63, "column": 52 }, "end": { - "line": 44, + "line": 63, "column": 53 } } @@ -27162,15 +31602,15 @@ "binop": null }, "value": "occurID", - "start": 1864, - "end": 1871, + "start": 2499, + "end": 2506, "loc": { "start": { - "line": 44, + "line": 63, "column": 54 }, "end": { - "line": 44, + "line": 63, "column": 61 } } @@ -27188,15 +31628,15 @@ "binop": null, "updateContext": null }, - "start": 1871, - "end": 1872, + "start": 2506, + "end": 2507, "loc": { "start": { - "line": 44, + "line": 63, "column": 61 }, "end": { - "line": 44, + "line": 63, "column": 62 } } @@ -27214,15 +31654,15 @@ "binop": null }, "value": "substr", - "start": 1872, - "end": 1878, + "start": 2507, + "end": 2513, "loc": { "start": { - "line": 44, + "line": 63, "column": 62 }, "end": { - "line": 44, + "line": 63, "column": 68 } } @@ -27239,15 +31679,15 @@ "postfix": false, "binop": null }, - "start": 1878, - "end": 1879, + "start": 2513, + "end": 2514, "loc": { "start": { - "line": 44, + "line": 63, "column": 68 }, "end": { - "line": 44, + "line": 63, "column": 69 } } @@ -27266,15 +31706,15 @@ "updateContext": null }, "value": 12, - "start": 1879, - "end": 1881, + "start": 2514, + "end": 2516, "loc": { "start": { - "line": 44, + "line": 63, "column": 69 }, "end": { - "line": 44, + "line": 63, "column": 71 } } @@ -27291,15 +31731,15 @@ "postfix": false, "binop": null }, - "start": 1881, - "end": 1882, + "start": 2516, + "end": 2517, "loc": { "start": { - "line": 44, + "line": 63, "column": 71 }, "end": { - "line": 44, + "line": 63, "column": 72 } } @@ -27317,15 +31757,15 @@ "binop": null, "updateContext": null }, - "start": 1882, - "end": 1883, + "start": 2517, + "end": 2518, "loc": { "start": { - "line": 44, + "line": 63, "column": 72 }, "end": { - "line": 44, + "line": 63, "column": 73 } } @@ -27333,15 +31773,15 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 1889, - "end": 1913, + "start": 2524, + "end": 2548, "loc": { "start": { - "line": 46, + "line": 65, "column": 4 }, "end": { - "line": 46, + "line": 65, "column": 28 } } @@ -27361,15 +31801,15 @@ "updateContext": null }, "value": "const", - "start": 1918, - "end": 1923, + "start": 2553, + "end": 2558, "loc": { "start": { - "line": 47, + "line": 66, "column": 4 }, "end": { - "line": 47, + "line": 66, "column": 9 } } @@ -27387,15 +31827,15 @@ "binop": null }, "value": "specimen", - "start": 1924, - "end": 1932, + "start": 2559, + "end": 2567, "loc": { "start": { - "line": 47, + "line": 66, "column": 10 }, "end": { - "line": 47, + "line": 66, "column": 18 } } @@ -27414,15 +31854,15 @@ "updateContext": null }, "value": "=", - "start": 1933, - "end": 1934, + "start": 2568, + "end": 2569, "loc": { "start": { - "line": 47, + "line": 66, "column": 19 }, "end": { - "line": 47, + "line": 66, "column": 20 } } @@ -27439,15 +31879,15 @@ "postfix": false, "binop": null }, - "start": 1935, - "end": 1936, + "start": 2570, + "end": 2571, "loc": { "start": { - "line": 47, + "line": 66, "column": 21 }, "end": { - "line": 47, + "line": 66, "column": 22 } } @@ -27466,15 +31906,15 @@ "updateContext": null }, "value": "@type", - "start": 1943, - "end": 1950, + "start": 2578, + "end": 2585, "loc": { "start": { - "line": 48, + "line": 67, "column": 6 }, "end": { - "line": 48, + "line": 67, "column": 13 } } @@ -27492,15 +31932,15 @@ "binop": null, "updateContext": null }, - "start": 1950, - "end": 1951, + "start": 2585, + "end": 2586, "loc": { "start": { - "line": 48, + "line": 67, "column": 13 }, "end": { - "line": 48, + "line": 67, "column": 14 } } @@ -27518,15 +31958,15 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 1952, - "end": 1967, + "start": 2587, + "end": 2602, "loc": { "start": { - "line": 48, + "line": 67, "column": 15 }, "end": { - "line": 48, + "line": 67, "column": 30 } } @@ -27544,15 +31984,15 @@ "binop": null, "updateContext": null }, - "start": 1967, - "end": 1968, + "start": 2602, + "end": 2603, "loc": { "start": { - "line": 48, + "line": 67, "column": 30 }, "end": { - "line": 48, + "line": 67, "column": 31 } } @@ -27570,15 +32010,15 @@ "binop": null }, "value": "TYPE_SPECIMEN", - "start": 1968, - "end": 1981, + "start": 2603, + "end": 2616, "loc": { "start": { - "line": 48, + "line": 67, "column": 31 }, "end": { - "line": 48, + "line": 67, "column": 44 } } @@ -27596,15 +32036,15 @@ "binop": null, "updateContext": null }, - "start": 1981, - "end": 1982, + "start": 2616, + "end": 2617, "loc": { "start": { - "line": 48, + "line": 67, "column": 44 }, "end": { - "line": 48, + "line": 67, "column": 45 } } @@ -27623,15 +32063,15 @@ "updateContext": null }, "value": "dwc:basisOfRecord", - "start": 1989, - "end": 2008, + "start": 2624, + "end": 2643, "loc": { "start": { - "line": 49, + "line": 68, "column": 6 }, "end": { - "line": 49, + "line": 68, "column": 25 } } @@ -27649,15 +32089,15 @@ "binop": null, "updateContext": null }, - "start": 2008, - "end": 2009, + "start": 2643, + "end": 2644, "loc": { "start": { - "line": 49, + "line": 68, "column": 25 }, "end": { - "line": 49, + "line": 68, "column": 26 } } @@ -27675,15 +32115,15 @@ "binop": null }, "value": "basisOfRecord", - "start": 2010, - "end": 2023, + "start": 2645, + "end": 2658, "loc": { "start": { - "line": 49, + "line": 68, "column": 27 }, "end": { - "line": 49, + "line": 68, "column": 40 } } @@ -27701,15 +32141,15 @@ "binop": null, "updateContext": null }, - "start": 2023, - "end": 2024, + "start": 2658, + "end": 2659, "loc": { "start": { - "line": 49, + "line": 68, "column": 40 }, "end": { - "line": 49, + "line": 68, "column": 41 } } @@ -27727,15 +32167,15 @@ "binop": null }, "value": "occurrenceID", - "start": 2031, - "end": 2043, + "start": 2666, + "end": 2678, "loc": { "start": { - "line": 50, + "line": 69, "column": 6 }, "end": { - "line": 50, + "line": 69, "column": 18 } } @@ -27753,15 +32193,15 @@ "binop": null, "updateContext": null }, - "start": 2043, - "end": 2044, + "start": 2678, + "end": 2679, "loc": { "start": { - "line": 50, + "line": 69, "column": 18 }, "end": { - "line": 50, + "line": 69, "column": 19 } } @@ -27779,15 +32219,15 @@ "binop": null }, "value": "occurID", - "start": 2045, - "end": 2052, + "start": 2680, + "end": 2687, "loc": { "start": { - "line": 50, + "line": 69, "column": 20 }, "end": { - "line": 50, + "line": 69, "column": 27 } } @@ -27805,15 +32245,15 @@ "binop": null, "updateContext": null }, - "start": 2052, - "end": 2053, + "start": 2687, + "end": 2688, "loc": { "start": { - "line": 50, + "line": 69, "column": 27 }, "end": { - "line": 50, + "line": 69, "column": 28 } } @@ -27830,15 +32270,15 @@ "postfix": false, "binop": null }, - "start": 2058, - "end": 2059, + "start": 2693, + "end": 2694, "loc": { "start": { - "line": 51, + "line": 70, "column": 4 }, "end": { - "line": 51, + "line": 70, "column": 5 } } @@ -27856,15 +32296,15 @@ "binop": null, "updateContext": null }, - "start": 2059, - "end": 2060, + "start": 2694, + "end": 2695, "loc": { "start": { - "line": 51, + "line": 70, "column": 5 }, "end": { - "line": 51, + "line": 70, "column": 6 } } @@ -27872,15 +32312,15 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2066, - "end": 2139, + "start": 2701, + "end": 2774, "loc": { "start": { - "line": 53, + "line": 72, "column": 4 }, "end": { - "line": 53, + "line": 72, "column": 77 } } @@ -27888,15 +32328,15 @@ { "type": "CommentLine", "value": " URL instead. 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"line": 63, + "line": 82, "column": 64 }, "end": { - "line": 63, + "line": 82, "column": 74 } } @@ -28778,15 +33218,15 @@ "postfix": false, "binop": null }, - "start": 2411, - "end": 2412, + "start": 3046, + "end": 3047, "loc": { "start": { - "line": 63, + "line": 82, "column": 74 }, "end": { - "line": 63, + "line": 82, "column": 75 } } @@ -28804,15 +33244,15 @@ "binop": null }, "value": "prefix", - "start": 2412, - "end": 2418, + "start": 3047, + "end": 3053, "loc": { "start": { - "line": 63, + "line": 82, "column": 75 }, "end": { - "line": 63, + "line": 82, "column": 81 } } @@ -28829,15 +33269,15 @@ "postfix": false, "binop": null }, - "start": 2418, - "end": 2419, + "start": 3053, + "end": 3054, "loc": { "start": { - "line": 63, + "line": 82, "column": 81 }, "end": { - "line": 63, + "line": 82, "column": 82 } } @@ -28854,15 +33294,15 @@ "postfix": false, "binop": null }, - "start": 2419, - "end": 2420, + "start": 3054, + "end": 3055, "loc": { "start": { - "line": 63, + "line": 82, "column": 82 }, "end": { - 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"line": 116, + "line": 135, "column": 82 }, "end": { - "line": 116, + "line": 135, "column": 83 } } @@ -35821,15 +40261,15 @@ "binop": null, "updateContext": null }, - "start": 4514, - "end": 4515, + "start": 5149, + "end": 5150, "loc": { "start": { - "line": 116, + "line": 135, "column": 83 }, "end": { - "line": 116, + "line": 135, "column": 84 } } @@ -35849,15 +40289,15 @@ "updateContext": null }, "value": "if", - "start": 4522, - "end": 4524, + "start": 5157, + "end": 5159, "loc": { "start": { - "line": 117, + "line": 136, "column": 6 }, "end": { - "line": 117, + "line": 136, "column": 8 } } @@ -35874,15 +40314,15 @@ "postfix": false, "binop": null }, - "start": 4525, - "end": 4526, + "start": 5160, + "end": 5161, "loc": { "start": { - "line": 117, + "line": 136, "column": 9 }, "end": { - "line": 117, + "line": 136, "column": 10 } } @@ -35900,15 +40340,15 @@ "binop": null }, "value": "has", - "start": 4526, - "end": 4529, + "start": 5161, + "end": 5164, "loc": { "start": { - "line": 117, + "line": 136, "column": 10 }, "end": { - 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"line": 117, + "line": 136, "column": 59 } } @@ -36134,15 +40574,15 @@ "binop": null, "updateContext": null }, - "start": 4575, - "end": 4576, + "start": 5210, + "end": 5211, "loc": { "start": { - "line": 117, + "line": 136, "column": 59 }, "end": { - "line": 117, + "line": 136, "column": 60 } } @@ -36160,15 +40600,15 @@ "binop": null }, "value": "institutionCode", - "start": 4576, - "end": 4591, + "start": 5211, + "end": 5226, "loc": { "start": { - "line": 117, + "line": 136, "column": 60 }, "end": { - "line": 117, + "line": 136, "column": 75 } } @@ -36186,15 +40626,15 @@ "binop": null, "updateContext": null }, - "start": 4591, - "end": 4592, + "start": 5226, + "end": 5227, "loc": { "start": { - "line": 117, + "line": 136, "column": 75 }, "end": { - "line": 117, + "line": 136, "column": 76 } } @@ -36211,15 +40651,15 @@ "postfix": false, "binop": null }, - "start": 4597, - "end": 4598, + "start": 5232, + "end": 5233, "loc": { "start": { - "line": 118, + "line": 137, "column": 4 }, "end": { - 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"line": 125, + "line": 144, "column": 21 } } @@ -36434,15 +40874,15 @@ "postfix": false, "binop": null }, - "start": 4699, - "end": 4700, + "start": 5334, + "end": 5335, "loc": { "start": { - "line": 125, + "line": 144, "column": 21 }, "end": { - "line": 125, + "line": 144, "column": 22 } } @@ -36459,15 +40899,15 @@ "postfix": false, "binop": null }, - "start": 4701, - "end": 4702, + "start": 5336, + "end": 5337, "loc": { "start": { - "line": 125, + "line": 144, "column": 23 }, "end": { - "line": 125, + "line": 144, "column": 24 } } @@ -36475,15 +40915,15 @@ { "type": "CommentLine", "value": " Get the collection code from the specimen object if present.", - "start": 4707, - "end": 4770, + "start": 5342, + "end": 5405, "loc": { "start": { - "line": 126, + "line": 145, "column": 4 }, "end": { - "line": 126, + "line": 145, "column": 67 } } @@ -36503,15 +40943,15 @@ "updateContext": null }, "value": "if", - "start": 4775, - "end": 4777, + "start": 5410, + "end": 5412, "loc": { "start": { - "line": 127, + "line": 146, "column": 4 }, "end": { - "line": 127, + "line": 146, "column": 6 } } @@ -36528,15 +40968,15 @@ "postfix": false, "binop": null }, - "start": 4778, - "end": 4779, + "start": 5413, + "end": 5414, "loc": { "start": { - "line": 127, + "line": 146, "column": 7 }, "end": { - "line": 127, + "line": 146, "column": 8 } } @@ -36554,15 +40994,15 @@ "binop": null }, "value": "has", - "start": 4779, - "end": 4782, + "start": 5414, + "end": 5417, "loc": { "start": { - "line": 127, + "line": 146, "column": 8 }, "end": { - "line": 127, + "line": 146, "column": 11 } } @@ -36579,15 +41019,15 @@ "postfix": false, "binop": null }, - "start": 4782, - "end": 4783, + "start": 5417, + "end": 5418, "loc": { "start": { - "line": 127, + "line": 146, "column": 11 }, "end": { - "line": 127, + "line": 146, "column": 12 } } @@ -36607,15 +41047,15 @@ "updateContext": null }, "value": "this", - "start": 4783, - "end": 4787, + "start": 5418, + "end": 5422, "loc": { "start": { - "line": 127, + "line": 146, "column": 12 }, "end": { - 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"line": 127, + "line": 146, "column": 43 } } @@ -36737,15 +41177,15 @@ "postfix": false, "binop": null }, - "start": 4814, - "end": 4815, + "start": 5449, + "end": 5450, "loc": { "start": { - "line": 127, + "line": 146, "column": 43 }, "end": { - "line": 127, + "line": 146, "column": 44 } } @@ -36762,15 +41202,15 @@ "postfix": false, "binop": null }, - "start": 4815, - "end": 4816, + "start": 5450, + "end": 5451, "loc": { "start": { - "line": 127, + "line": 146, "column": 44 }, "end": { - "line": 127, + "line": 146, "column": 45 } } @@ -36790,15 +41230,15 @@ "updateContext": null }, "value": "return", - "start": 4817, - "end": 4823, + "start": 5452, + "end": 5458, "loc": { "start": { - "line": 127, + "line": 146, "column": 46 }, "end": { - "line": 127, + "line": 146, "column": 52 } } @@ -36818,15 +41258,15 @@ "updateContext": null }, "value": "this", - "start": 4824, - "end": 4828, + "start": 5459, + "end": 5463, "loc": { "start": { - "line": 127, + "line": 146, "column": 53 }, "end": { - "line": 127, + "line": 146, "column": 57 } } @@ -36844,15 +41284,15 @@ "binop": null, "updateContext": null }, - "start": 4828, - "end": 4829, + "start": 5463, + "end": 5464, "loc": { "start": { - "line": 127, + "line": 146, "column": 57 }, "end": { - "line": 127, + "line": 146, "column": 58 } } @@ -36870,15 +41310,15 @@ "binop": null }, "value": "specimen", - "start": 4829, - "end": 4837, + "start": 5464, + "end": 5472, "loc": { "start": { - "line": 127, + "line": 146, "column": 58 }, "end": { - "line": 127, + "line": 146, "column": 66 } } @@ -36896,15 +41336,15 @@ "binop": null, "updateContext": null }, - "start": 4837, - "end": 4838, + "start": 5472, + "end": 5473, "loc": { "start": { - "line": 127, + "line": 146, "column": 66 }, "end": { - "line": 127, + "line": 146, "column": 67 } } @@ -36922,15 +41362,15 @@ "binop": null }, "value": "collectionCode", - "start": 4838, - "end": 4852, + "start": 5473, + "end": 5487, "loc": { "start": { - "line": 127, + "line": 146, "column": 67 }, "end": { - "line": 127, + "line": 146, "column": 81 } } @@ -36948,15 +41388,15 @@ "binop": null, "updateContext": null }, - "start": 4852, - "end": 4853, + "start": 5487, + "end": 5488, "loc": { "start": { - "line": 127, + "line": 146, "column": 81 }, "end": { - "line": 127, + "line": 146, "column": 82 } } @@ -36964,15 +41404,15 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4859, - "end": 4931, + "start": 5494, + "end": 5566, "loc": { "start": { - "line": 129, + "line": 148, "column": 4 }, "end": { - "line": 129, + "line": 148, "column": 76 } } @@ -36980,15 +41420,15 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4936, - "end": 4963, + "start": 5571, + "end": 5598, "loc": { "start": { - "line": 130, + "line": 149, "column": 4 }, "end": { - "line": 130, + "line": 149, "column": 31 } } @@ -37008,15 +41448,15 @@ "updateContext": null }, "value": "if", - "start": 4968, - "end": 4970, + "start": 5603, + "end": 5605, "loc": { "start": { - "line": 131, + "line": 150, "column": 4 }, "end": { - "line": 131, + "line": 150, "column": 6 } } @@ -37033,15 +41473,15 @@ "postfix": false, "binop": null }, - "start": 4971, - "end": 4972, + "start": 5606, + "end": 5607, "loc": { "start": { - "line": 131, + "line": 150, "column": 7 }, "end": { - "line": 131, + "line": 150, "column": 8 } } @@ -37059,15 +41499,15 @@ "binop": null }, "value": "has", - "start": 4972, - "end": 4975, + "start": 5607, + "end": 5610, "loc": { "start": { - "line": 131, + "line": 150, "column": 8 }, "end": { - "line": 131, + "line": 150, "column": 11 } } @@ -37084,15 +41524,15 @@ "postfix": false, "binop": null }, - "start": 4975, - "end": 4976, + "start": 5610, + "end": 5611, "loc": { "start": { - "line": 131, + "line": 150, "column": 11 }, "end": { - "line": 131, + "line": 150, "column": 12 } } @@ -37112,15 +41552,15 @@ "updateContext": null }, "value": "this", - "start": 4976, - "end": 4980, + "start": 5611, + "end": 5615, "loc": { "start": { - "line": 131, + "line": 150, "column": 12 }, "end": { - "line": 131, + "line": 150, "column": 16 } } @@ -37138,15 +41578,15 @@ "binop": null, "updateContext": null }, - "start": 4980, - "end": 4981, + "start": 5615, + "end": 5616, "loc": { "start": { - "line": 131, + "line": 150, "column": 16 }, "end": { - "line": 131, + "line": 150, "column": 17 } } @@ -37164,15 +41604,15 @@ "binop": null }, "value": "specimen", - "start": 4981, - "end": 4989, + "start": 5616, + "end": 5624, "loc": { "start": { - "line": 131, + "line": 150, "column": 17 }, "end": { - "line": 131, + "line": 150, "column": 25 } } @@ -37190,15 +41630,15 @@ "binop": null, "updateContext": null }, - "start": 4989, - "end": 4990, + "start": 5624, + "end": 5625, "loc": { "start": { - "line": 131, + "line": 150, "column": 25 }, "end": { - "line": 131, + "line": 150, "column": 26 } } @@ -37217,15 +41657,15 @@ "updateContext": null }, "value": "occurrenceID", - "start": 4991, - "end": 5005, + "start": 5626, + "end": 5640, "loc": { "start": { - "line": 131, + "line": 150, "column": 27 }, "end": { - "line": 131, + "line": 150, "column": 41 } } @@ -37242,15 +41682,15 @@ "postfix": false, "binop": null }, - "start": 5005, - "end": 5006, + "start": 5640, + "end": 5641, "loc": { "start": { - "line": 131, + "line": 150, "column": 41 }, "end": { - "line": 131, + "line": 150, "column": 42 } } @@ -37267,15 +41707,15 @@ "postfix": false, "binop": null }, - "start": 5006, - "end": 5007, + "start": 5641, + "end": 5642, "loc": { "start": { - "line": 131, + "line": 150, "column": 42 }, "end": { - "line": 131, + "line": 150, "column": 43 } } @@ -37292,15 +41732,15 @@ "postfix": false, "binop": null }, - "start": 5008, - "end": 5009, + "start": 5643, + "end": 5644, "loc": { "start": { - "line": 131, + "line": 150, "column": 44 }, "end": { - "line": 131, + "line": 150, "column": 45 } } @@ -37320,15 +41760,15 @@ "updateContext": null }, "value": "const", - "start": 5016, - "end": 5021, + "start": 5651, + "end": 5656, "loc": { "start": { - "line": 132, + "line": 151, "column": 6 }, "end": { - "line": 132, + "line": 151, "column": 11 } } @@ -37346,15 +41786,15 @@ "binop": null }, "value": "specimen", - "start": 5022, - "end": 5030, + "start": 5657, + "end": 5665, "loc": { "start": { - "line": 132, + "line": 151, "column": 12 }, "end": { - "line": 132, + "line": 151, "column": 20 } } @@ -37373,15 +41813,15 @@ "updateContext": null }, "value": "=", - "start": 5031, - "end": 5032, + "start": 5666, + "end": 5667, "loc": { "start": { - "line": 132, + "line": 151, "column": 21 }, "end": { - "line": 132, + "line": 151, "column": 22 } } @@ -37399,15 +41839,15 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 5033, - "end": 5048, + "start": 5668, + "end": 5683, "loc": { "start": { - "line": 132, + "line": 151, "column": 23 }, "end": { - "line": 132, + "line": 151, "column": 38 } } @@ -37425,15 +41865,15 @@ "binop": null, "updateContext": null }, - "start": 5048, - "end": 5049, + "start": 5683, + "end": 5684, "loc": { "start": { - "line": 132, + "line": 151, "column": 38 }, "end": { - "line": 132, + "line": 151, "column": 39 } } @@ -37451,15 +41891,15 @@ "binop": null }, "value": "fromOccurrenceID", - "start": 5049, - "end": 5065, + "start": 5684, + "end": 5700, "loc": { "start": { - "line": 132, + "line": 151, "column": 39 }, "end": { - "line": 132, + "line": 151, "column": 55 } } @@ -37476,15 +41916,15 @@ "postfix": false, "binop": null }, - "start": 5065, - "end": 5066, + "start": 5700, + "end": 5701, "loc": { "start": { - "line": 132, + "line": 151, "column": 55 }, "end": { - "line": 132, + "line": 151, "column": 56 } } @@ -37504,15 +41944,15 @@ "updateContext": null }, "value": "this", - "start": 5066, - "end": 5070, + "start": 5701, + "end": 5705, "loc": { "start": { - "line": 132, + "line": 151, "column": 56 }, "end": { - "line": 132, + "line": 151, "column": 60 } } @@ -37530,15 +41970,15 @@ "binop": null, "updateContext": null }, - "start": 5070, - "end": 5071, + "start": 5705, + "end": 5706, "loc": { "start": { - "line": 132, + "line": 151, "column": 60 }, "end": { - "line": 132, + "line": 151, "column": 61 } } @@ -37556,15 +41996,15 @@ "binop": null }, "value": "specimen", - "start": 5071, - "end": 5079, + "start": 5706, + "end": 5714, "loc": { "start": { - "line": 132, + "line": 151, "column": 61 }, "end": { - "line": 132, + "line": 151, "column": 69 } } @@ -37582,15 +42022,15 @@ "binop": null, "updateContext": null }, - "start": 5079, - "end": 5080, + "start": 5714, + "end": 5715, "loc": { "start": { - "line": 132, + "line": 151, "column": 69 }, "end": { - "line": 132, + "line": 151, "column": 70 } } @@ -37608,15 +42048,15 @@ "binop": null }, "value": "occurrenceID", - "start": 5080, - "end": 5092, + "start": 5715, + "end": 5727, "loc": { "start": { - "line": 132, + "line": 151, "column": 70 }, "end": { - "line": 132, + "line": 151, "column": 82 } } @@ -37633,15 +42073,15 @@ "postfix": false, "binop": null }, - "start": 5092, - "end": 5093, + "start": 5727, + "end": 5728, "loc": { "start": { - "line": 132, + "line": 151, "column": 82 }, "end": { - "line": 132, + "line": 151, "column": 83 } } @@ -37659,15 +42099,15 @@ "binop": null, "updateContext": null }, - "start": 5093, - "end": 5094, + "start": 5728, + "end": 5729, "loc": { "start": { - "line": 132, + "line": 151, "column": 83 }, "end": { - "line": 132, + "line": 151, "column": 84 } } @@ -37687,15 +42127,15 @@ "updateContext": null }, "value": "if", - "start": 5101, - "end": 5103, + "start": 5736, + "end": 5738, "loc": { "start": { - "line": 133, + "line": 152, "column": 6 }, "end": { - "line": 133, + "line": 152, "column": 8 } } @@ -37712,15 +42152,15 @@ "postfix": false, "binop": null }, - "start": 5104, - "end": 5105, + "start": 5739, + "end": 5740, "loc": { "start": { - "line": 133, + "line": 152, "column": 9 }, "end": { - "line": 133, + "line": 152, "column": 10 } } @@ -37738,15 +42178,15 @@ "binop": null }, "value": "has", - "start": 5105, - "end": 5108, + "start": 5740, + "end": 5743, "loc": { "start": { - "line": 133, + "line": 152, "column": 10 }, "end": { - "line": 133, + "line": 152, "column": 13 } } @@ -37763,15 +42203,15 @@ "postfix": false, "binop": null }, - "start": 5108, - 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"end": 5136, + "start": 5770, + "end": 5771, "loc": { "start": { - "line": 133, + "line": 152, "column": 40 }, "end": { - "line": 133, + "line": 152, "column": 41 } } @@ -37892,15 +42332,15 @@ "postfix": false, "binop": null }, - "start": 5136, - "end": 5137, + "start": 5771, + "end": 5772, "loc": { "start": { - "line": 133, + "line": 152, "column": 41 }, "end": { - "line": 133, + "line": 152, "column": 42 } } @@ -37920,15 +42360,15 @@ "updateContext": null }, "value": "return", - "start": 5138, - "end": 5144, + "start": 5773, + "end": 5779, "loc": { "start": { - "line": 133, + "line": 152, "column": 43 }, "end": { - "line": 133, + "line": 152, "column": 49 } } @@ -37946,15 +42386,15 @@ "binop": null }, "value": "specimen", - "start": 5145, - "end": 5153, + "start": 5780, + "end": 5788, "loc": { "start": { - "line": 133, + "line": 152, "column": 50 }, "end": { - "line": 133, + "line": 152, "column": 58 } } @@ -37972,15 +42412,15 @@ "binop": null, "updateContext": null }, - "start": 5153, - "end": 5154, + "start": 5788, + "end": 5789, "loc": { "start": { - "line": 133, + "line": 152, "column": 58 }, "end": { - "line": 133, + "line": 152, "column": 59 } } @@ -37998,15 +42438,15 @@ "binop": null }, "value": "collectionCode", - "start": 5154, - "end": 5168, + "start": 5789, + "end": 5803, "loc": { "start": { - "line": 133, + "line": 152, "column": 59 }, "end": { - "line": 133, + "line": 152, "column": 73 } } @@ -38024,15 +42464,15 @@ "binop": null, "updateContext": null }, - "start": 5168, - "end": 5169, + "start": 5803, + "end": 5804, "loc": { "start": { - "line": 133, + "line": 152, "column": 73 }, "end": { - "line": 133, + "line": 152, "column": 74 } } @@ -38049,15 +42489,15 @@ "postfix": false, "binop": null }, - "start": 5174, - "end": 5175, + "start": 5809, + "end": 5810, "loc": { "start": { - "line": 134, + "line": 153, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 5 } } @@ -38077,15 +42517,15 @@ "updateContext": null }, "value": "return", - "start": 5180, - "end": 5186, + "start": 5815, + "end": 5821, "loc": { "start": { - "line": 135, + "line": 154, "column": 4 }, "end": { - "line": 135, + "line": 154, "column": 10 } } @@ -38103,15 +42543,15 @@ "binop": null }, "value": "undefined", - "start": 5187, - "end": 5196, + "start": 5822, + "end": 5831, "loc": { "start": { - "line": 135, + "line": 154, "column": 11 }, "end": { - "line": 135, + "line": 154, "column": 20 } } @@ -38129,15 +42569,15 @@ "binop": null, "updateContext": null }, - "start": 5196, - "end": 5197, + "start": 5831, + "end": 5832, "loc": { "start": { - "line": 135, + "line": 154, "column": 20 }, "end": { - "line": 135, + "line": 154, "column": 21 } } @@ -38154,15 +42594,15 @@ "postfix": false, "binop": null }, - "start": 5200, - "end": 5201, + "start": 5835, + "end": 5836, "loc": { "start": { - "line": 136, + "line": 155, "column": 2 }, "end": { - "line": 136, + "line": 155, "column": 3 } } @@ -38170,15 +42610,15 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5205, - "end": 5464, + "start": 5840, + "end": 6099, "loc": { "start": { - "line": 138, + "line": 157, "column": 2 }, "end": { - "line": 143, + "line": 162, "column": 5 } } @@ -38196,15 +42636,15 @@ "binop": null }, "value": "get", - "start": 5467, - "end": 5470, + "start": 6102, + "end": 6105, "loc": { "start": { - "line": 144, + "line": 163, "column": 2 }, "end": { - "line": 144, + "line": 163, "column": 5 } } @@ -38222,15 +42662,15 @@ "binop": null }, "value": "occurrenceID", - "start": 5471, - "end": 5483, + "start": 6106, + "end": 6118, "loc": { "start": { - "line": 144, + "line": 163, "column": 6 }, "end": { - "line": 144, + "line": 163, "column": 18 } } @@ -38247,15 +42687,15 @@ "postfix": false, "binop": null }, - "start": 5483, - "end": 5484, + "start": 6118, + "end": 6119, "loc": { "start": { - "line": 144, + "line": 163, "column": 18 }, "end": { - "line": 144, + "line": 163, "column": 19 } } @@ -38272,15 +42712,15 @@ "postfix": false, "binop": null }, - "start": 5484, - "end": 5485, + "start": 6119, + "end": 6120, "loc": { "start": { - "line": 144, + "line": 163, "column": 19 }, "end": { - "line": 144, + "line": 163, "column": 20 } } @@ -38297,15 +42737,15 @@ "postfix": false, "binop": null }, - "start": 5486, - "end": 5487, + "start": 6121, + "end": 6122, "loc": { "start": { - "line": 144, + "line": 163, "column": 21 }, "end": { - "line": 144, + "line": 163, "column": 22 } } @@ -38313,15 +42753,15 @@ { "type": "CommentLine", "value": " Return the occurrenceID if it exists.", - "start": 5492, - "end": 5532, + "start": 6127, + "end": 6167, "loc": { "start": { - "line": 145, + "line": 164, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 44 } } @@ -38341,15 +42781,15 @@ "updateContext": null }, "value": "if", - "start": 5537, - "end": 5539, + "start": 6172, + "end": 6174, "loc": { "start": { - "line": 146, + "line": 165, "column": 4 }, "end": { - "line": 146, + "line": 165, "column": 6 } } @@ -38366,15 +42806,15 @@ "postfix": false, "binop": null }, - "start": 5540, - "end": 5541, + "start": 6175, + "end": 6176, "loc": { "start": { - "line": 146, + "line": 165, "column": 7 }, "end": { - "line": 146, + "line": 165, "column": 8 } } @@ -38392,15 +42832,15 @@ "binop": null }, "value": "has", - "start": 5541, - "end": 5544, + "start": 6176, + "end": 6179, "loc": { "start": { - "line": 146, + "line": 165, "column": 8 }, "end": { - "line": 146, + "line": 165, "column": 11 } } @@ -38417,15 +42857,15 @@ "postfix": false, "binop": null }, - "start": 5544, - "end": 5545, + "start": 6179, + "end": 6180, "loc": { "start": { - "line": 146, + "line": 165, "column": 11 }, "end": { - "line": 146, + "line": 165, "column": 12 } } @@ -38445,15 +42885,15 @@ "updateContext": null }, "value": "this", - "start": 5545, - "end": 5549, + "start": 6180, + "end": 6184, "loc": { "start": { - "line": 146, + "line": 165, "column": 12 }, "end": { - "line": 146, + "line": 165, "column": 16 } } @@ -38471,15 +42911,15 @@ "binop": null, "updateContext": null }, - "start": 5549, - "end": 5550, + "start": 6184, + "end": 6185, "loc": { "start": { - "line": 146, + "line": 165, "column": 16 }, "end": { - "line": 146, + "line": 165, "column": 17 } } @@ -38497,15 +42937,15 @@ "binop": null }, "value": "specimen", - "start": 5550, - "end": 5558, + "start": 6185, + "end": 6193, "loc": { "start": { - "line": 146, + "line": 165, "column": 17 }, "end": { - "line": 146, + "line": 165, "column": 25 } } @@ -38523,15 +42963,15 @@ "binop": null, "updateContext": null }, - "start": 5558, - "end": 5559, + "start": 6193, + "end": 6194, "loc": { "start": { - "line": 146, + "line": 165, "column": 25 }, "end": { - "line": 146, + "line": 165, "column": 26 } } @@ -38550,15 +42990,15 @@ "updateContext": null }, "value": "occurrenceID", - "start": 5560, - "end": 5574, + "start": 6195, + "end": 6209, "loc": { "start": { - "line": 146, + "line": 165, "column": 27 }, "end": { - "line": 146, + "line": 165, "column": 41 } } @@ -38575,15 +43015,15 @@ "postfix": false, "binop": null }, - "start": 5574, - "end": 5575, + "start": 6209, + "end": 6210, "loc": { "start": { - "line": 146, + "line": 165, "column": 41 }, "end": { - "line": 146, + "line": 165, "column": 42 } } @@ -38602,15 +43042,15 @@ "updateContext": null }, "value": "&&", - "start": 5576, - "end": 5578, + "start": 6211, + "end": 6213, "loc": { "start": { - "line": 146, + "line": 165, "column": 43 }, "end": { - "line": 146, + "line": 165, "column": 45 } } @@ -38630,15 +43070,15 @@ "updateContext": null }, "value": "this", - "start": 5579, - "end": 5583, + "start": 6214, + "end": 6218, "loc": { "start": { - "line": 146, + "line": 165, "column": 46 }, "end": { - "line": 146, + "line": 165, "column": 50 } } @@ -38656,15 +43096,15 @@ "binop": null, "updateContext": null }, - "start": 5583, - "end": 5584, + "start": 6218, + "end": 6219, "loc": { "start": { - "line": 146, + "line": 165, "column": 50 }, "end": { - "line": 146, + "line": 165, "column": 51 } } @@ -38682,15 +43122,15 @@ "binop": null }, "value": "specimen", - "start": 5584, - "end": 5592, + "start": 6219, + "end": 6227, "loc": { "start": { - "line": 146, + "line": 165, "column": 51 }, "end": { - "line": 146, + "line": 165, "column": 59 } } @@ -38708,15 +43148,15 @@ "binop": null, "updateContext": null }, - "start": 5592, - "end": 5593, + "start": 6227, + "end": 6228, "loc": { "start": { - "line": 146, + "line": 165, "column": 59 }, "end": { - "line": 146, + "line": 165, "column": 60 } } @@ -38734,15 +43174,15 @@ "binop": null }, "value": "occurrenceID", - "start": 5593, - "end": 5605, + "start": 6228, + "end": 6240, "loc": { "start": { - "line": 146, + "line": 165, "column": 60 }, "end": { - "line": 146, + "line": 165, "column": 72 } } @@ -38760,15 +43200,15 @@ "binop": null, "updateContext": null }, - "start": 5605, - "end": 5606, + "start": 6240, + "end": 6241, "loc": { "start": { - "line": 146, + "line": 165, "column": 72 }, "end": { - 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", - "start": 7177, - "end": 7217, + "start": 7812, + "end": 7852, "loc": { "start": { - "line": 191, + "line": 210, "column": 2 }, "end": { - "line": 191, + "line": 210, "column": 42 } } @@ -46062,15 +50502,15 @@ "binop": null }, "value": "get", - "start": 7220, - "end": 7223, + "start": 7855, + "end": 7858, "loc": { "start": { - "line": 192, + "line": 211, "column": 2 }, "end": { - "line": 192, + "line": 211, "column": 5 } } @@ -46088,15 +50528,15 @@ "binop": null }, "value": "label", - "start": 7224, - "end": 7229, + "start": 7859, + "end": 7864, "loc": { "start": { - "line": 192, + "line": 211, "column": 6 }, "end": { - "line": 192, + "line": 211, "column": 11 } } @@ -46113,15 +50553,15 @@ "postfix": false, "binop": null }, - "start": 7229, - "end": 7230, + "start": 7864, + "end": 7865, "loc": { "start": { - "line": 192, + "line": 211, "column": 11 }, "end": { - "line": 192, + "line": 211, "column": 12 } } @@ -46138,15 +50578,15 @@ "postfix": false, "binop": null }, - "start": 7230, - "end": 7231, + "start": 7865, + "end": 7866, "loc": { "start": { - "line": 192, + "line": 211, "column": 12 }, "end": { - "line": 192, + "line": 211, "column": 13 } } @@ -46163,15 +50603,15 @@ "postfix": false, "binop": null }, - "start": 7232, - "end": 7233, + "start": 7867, + "end": 7868, "loc": { "start": { - "line": 192, + "line": 211, "column": 14 }, "end": { - "line": 192, + "line": 211, "column": 15 } } @@ -46179,15 +50619,15 @@ { "type": "CommentLine", "value": " We can't return anything without an occurrenceID.", - "start": 7238, - "end": 7290, + "start": 7873, + "end": 7925, "loc": { "start": { - "line": 193, + "line": 212, "column": 4 }, "end": { - "line": 193, + "line": 212, "column": 56 } } @@ -46207,15 +50647,15 @@ "updateContext": null }, "value": "if", - "start": 7295, - "end": 7297, + "start": 7930, + "end": 7932, "loc": { "start": { - "line": 194, + "line": 213, "column": 4 }, "end": { - "line": 194, + "line": 213, "column": 6 } } @@ -46232,15 +50672,15 @@ "postfix": false, "binop": null }, - "start": 7298, - "end": 7299, + "start": 7933, + "end": 7934, "loc": { "start": { - "line": 194, + "line": 213, "column": 7 }, "end": { - "line": 194, + "line": 213, "column": 8 } } @@ -46259,15 +50699,15 @@ "updateContext": null }, "value": "!", - "start": 7299, - "end": 7300, + "start": 7934, + "end": 7935, "loc": { "start": { - "line": 194, + "line": 213, "column": 8 }, "end": { - "line": 194, + "line": 213, "column": 9 } } @@ -46287,15 +50727,15 @@ "updateContext": null }, "value": "this", - "start": 7300, - "end": 7304, + "start": 7935, + "end": 7939, "loc": { "start": { - "line": 194, + "line": 213, "column": 9 }, "end": { - "line": 194, + "line": 213, "column": 13 } } @@ -46313,15 +50753,15 @@ "binop": null, "updateContext": null }, - "start": 7304, - "end": 7305, + "start": 7939, + "end": 7940, "loc": { "start": { - "line": 194, + "line": 213, "column": 13 }, "end": { - "line": 194, + "line": 213, "column": 14 } } @@ -46339,15 +50779,15 @@ "binop": null }, "value": "occurrenceID", - "start": 7305, - "end": 7317, + "start": 7940, + "end": 7952, "loc": { "start": { - "line": 194, + "line": 213, "column": 14 }, "end": { - "line": 194, + "line": 213, "column": 26 } } @@ -46364,15 +50804,15 @@ "postfix": false, "binop": null }, - "start": 7317, - "end": 7318, + "start": 7952, + "end": 7953, "loc": { "start": { - "line": 194, + "line": 213, "column": 26 }, "end": { - "line": 194, + "line": 213, "column": 27 } } @@ -46392,15 +50832,15 @@ "updateContext": null }, "value": "return", - "start": 7319, - "end": 7325, + "start": 7954, + "end": 7960, "loc": { "start": { - "line": 194, + "line": 213, "column": 28 }, "end": { - "line": 194, + "line": 213, "column": 34 } } @@ -46418,15 +50858,15 @@ "binop": null }, "value": "undefined", - "start": 7326, - "end": 7335, + "start": 7961, + "end": 7970, "loc": { "start": { - "line": 194, + "line": 213, "column": 35 }, "end": { - "line": 194, + "line": 213, "column": 44 } } @@ -46444,15 +50884,15 @@ "binop": null, "updateContext": null }, - "start": 7335, - "end": 7336, + "start": 7970, + "end": 7971, "loc": { "start": { - "line": 194, + "line": 213, "column": 44 }, "end": { - "line": 194, + "line": 213, "column": 45 } } @@ -46460,15 +50900,15 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7342, - "end": 7419, + "start": 7977, + "end": 8054, "loc": { "start": { - "line": 196, + "line": 215, "column": 4 }, "end": { - "line": 196, + "line": 215, "column": 81 } } @@ -46476,15 +50916,15 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 7424, - "end": 7465, + "start": 8059, + "end": 8100, "loc": { "start": { - "line": 197, + "line": 216, "column": 4 }, "end": { - "line": 197, + "line": 216, "column": 45 } } @@ -46504,15 +50944,15 @@ "updateContext": null }, "value": "if", - "start": 7470, - "end": 7472, + "start": 8105, + "end": 8107, "loc": { "start": { - "line": 198, + "line": 217, "column": 4 }, "end": { - "line": 198, + "line": 217, "column": 6 } } @@ -46529,15 +50969,15 @@ "postfix": false, "binop": null }, - "start": 7473, - "end": 7474, + "start": 8108, + "end": 8109, "loc": { "start": { - "line": 198, + "line": 217, "column": 7 }, "end": { - "line": 198, + "line": 217, "column": 8 } } @@ -46557,15 +50997,15 @@ "updateContext": null }, "value": "this", - "start": 7474, - "end": 7478, + "start": 8109, + "end": 8113, "loc": { "start": { - "line": 198, + "line": 217, "column": 8 }, "end": { - "line": 198, + "line": 217, "column": 12 } } @@ -46583,15 +51023,15 @@ "binop": null, "updateContext": null }, - "start": 7478, - "end": 7479, + "start": 8113, + "end": 8114, "loc": { "start": { - "line": 198, + "line": 217, "column": 12 }, "end": { - "line": 198, + "line": 217, "column": 13 } } @@ -46609,15 +51049,15 @@ "binop": null }, "value": "taxonConcept", - "start": 7479, - "end": 7491, + "start": 8114, + "end": 8126, "loc": { "start": { - "line": 198, + "line": 217, "column": 13 }, "end": { - "line": 198, + "line": 217, "column": 25 } } @@ -46634,15 +51074,15 @@ "postfix": false, "binop": null }, - "start": 7491, - "end": 7492, + "start": 8126, + "end": 8127, "loc": { "start": { - "line": 198, + "line": 217, "column": 25 }, "end": { - "line": 198, + "line": 217, "column": 26 } } @@ -46659,15 +51099,15 @@ "postfix": false, "binop": null }, - "start": 7493, - "end": 7494, + "start": 8128, + "end": 8129, "loc": { "start": { - "line": 198, + "line": 217, "column": 27 }, "end": { - "line": 198, + "line": 217, "column": 28 } } @@ -46687,15 +51127,15 @@ "updateContext": null }, "value": "return", - "start": 7501, - "end": 7507, + "start": 8136, + "end": 8142, "loc": { "start": { - "line": 199, + "line": 218, "column": 6 }, "end": { - "line": 199, + "line": 218, "column": 12 } } @@ -46712,15 +51152,15 @@ "postfix": false, "binop": null }, - "start": 7508, - "end": 7509, + "start": 8143, + "end": 8144, "loc": { "start": { - "line": 199, + "line": 218, "column": 13 }, "end": { - "line": 199, + "line": 218, "column": 14 } } @@ -46739,15 +51179,15 @@ "updateContext": null }, "value": "Specimen ", - "start": 7509, - "end": 7518, + "start": 8144, + "end": 8153, "loc": { "start": { - "line": 199, + "line": 218, "column": 14 }, "end": { - "line": 199, + "line": 218, "column": 23 } } @@ -46764,15 +51204,15 @@ "postfix": false, "binop": null }, - "start": 7518, - "end": 7520, + "start": 8153, + "end": 8155, "loc": { "start": { - "line": 199, + "line": 218, "column": 23 }, "end": { - "line": 199, + "line": 218, "column": 25 } } @@ -46792,15 +51232,15 @@ "updateContext": null }, "value": "this", - "start": 7520, - "end": 7524, + "start": 8155, + "end": 8159, "loc": { "start": { - "line": 199, + "line": 218, "column": 25 }, "end": { - "line": 199, + "line": 218, "column": 29 } } @@ -46818,15 +51258,15 @@ "binop": null, "updateContext": null }, - "start": 7524, - "end": 7525, + "start": 8159, + "end": 8160, "loc": { "start": { - "line": 199, + "line": 218, "column": 29 }, "end": { - "line": 199, + "line": 218, "column": 30 } } @@ -46844,15 +51284,15 @@ "binop": null }, "value": "occurrenceID", - "start": 7525, - "end": 7537, + "start": 8160, + "end": 8172, "loc": { "start": { - "line": 199, + "line": 218, "column": 30 }, "end": { - "line": 199, + "line": 218, "column": 42 } } @@ -46869,15 +51309,15 @@ "postfix": false, "binop": null }, - "start": 7537, - "end": 7538, + "start": 8172, + "end": 8173, "loc": { "start": { - "line": 199, + "line": 218, "column": 42 }, "end": { - "line": 199, + "line": 218, "column": 43 } } @@ -46896,15 +51336,15 @@ "updateContext": null }, "value": " identified as ", - "start": 7538, - "end": 7553, + "start": 8173, + "end": 8188, "loc": { "start": { - "line": 199, + "line": 218, "column": 43 }, "end": { - "line": 199, + "line": 218, "column": 58 } } @@ -46921,15 +51361,15 @@ "postfix": false, "binop": null }, - "start": 7553, - "end": 7555, + "start": 8188, + "end": 8190, "loc": { "start": { - "line": 199, + "line": 218, "column": 58 }, "end": { - "line": 199, + "line": 218, "column": 60 } } @@ -46949,15 +51389,15 @@ "updateContext": null }, "value": "new", - "start": 7555, - "end": 7558, + "start": 8190, + "end": 8193, "loc": { "start": { - "line": 199, + "line": 218, "column": 60 }, "end": { - "line": 199, + "line": 218, "column": 63 } } @@ -46975,15 +51415,15 @@ "binop": null }, "value": "TaxonConceptWrapper", - "start": 7559, - "end": 7578, + "start": 8194, + "end": 8213, "loc": { "start": { - "line": 199, + "line": 218, "column": 64 }, "end": { - "line": 199, + "line": 218, "column": 83 } } @@ -47000,15 +51440,15 @@ "postfix": false, "binop": null }, - "start": 7578, - "end": 7579, + "start": 8213, + "end": 8214, "loc": { "start": { - "line": 199, + "line": 218, "column": 83 }, "end": { - "line": 199, + "line": 218, "column": 84 } } @@ -47028,15 +51468,15 @@ "updateContext": null }, "value": "this", - "start": 7579, - "end": 7583, + "start": 8214, + "end": 8218, "loc": { "start": { - "line": 199, + "line": 218, "column": 84 }, "end": { - "line": 199, + "line": 218, "column": 88 } } @@ -47054,15 +51494,15 @@ "binop": null, "updateContext": null }, - "start": 7583, - "end": 7584, + "start": 8218, + "end": 8219, "loc": { "start": { - "line": 199, + "line": 218, "column": 88 }, "end": { - "line": 199, + "line": 218, "column": 89 } } @@ -47080,15 +51520,15 @@ "binop": null }, "value": "taxonConcept", - "start": 7584, - "end": 7596, + "start": 8219, + "end": 8231, "loc": { "start": { - "line": 199, + "line": 218, "column": 89 }, "end": { - "line": 199, + "line": 218, "column": 101 } } @@ -47105,15 +51545,15 @@ "postfix": false, "binop": null }, - "start": 7596, - "end": 7597, + "start": 8231, + "end": 8232, "loc": { "start": { - "line": 199, + "line": 218, "column": 101 }, "end": { - "line": 199, + "line": 218, "column": 102 } } @@ -47131,15 +51571,15 @@ "binop": null, "updateContext": null }, - "start": 7597, - "end": 7598, + "start": 8232, + "end": 8233, "loc": { "start": { - "line": 199, + "line": 218, "column": 102 }, "end": { - "line": 199, + "line": 218, "column": 103 } } @@ -47157,15 +51597,15 @@ "binop": null }, "value": "label", - "start": 7598, - "end": 7603, + "start": 8233, + "end": 8238, "loc": { "start": { - "line": 199, + "line": 218, "column": 103 }, "end": { - "line": 199, + "line": 218, "column": 108 } } @@ -47182,15 +51622,15 @@ "postfix": false, "binop": null }, - "start": 7603, - "end": 7604, + "start": 8238, + "end": 8239, "loc": { "start": { - "line": 199, + "line": 218, "column": 108 }, "end": { - "line": 199, + "line": 218, "column": 109 } } @@ -47209,15 +51649,15 @@ "updateContext": null }, "value": "", - "start": 7604, - "end": 7604, + "start": 8239, + "end": 8239, "loc": { "start": { - "line": 199, + "line": 218, "column": 109 }, "end": { - "line": 199, + "line": 218, "column": 109 } } @@ -47234,15 +51674,15 @@ "postfix": false, "binop": null }, - "start": 7604, - "end": 7605, + "start": 8239, + "end": 8240, "loc": { "start": { - "line": 199, + "line": 218, "column": 109 }, "end": { - "line": 199, + "line": 218, "column": 110 } } @@ -47260,15 +51700,15 @@ "binop": null, "updateContext": null }, - "start": 7605, - "end": 7606, + "start": 8240, + "end": 8241, "loc": { "start": { - "line": 199, + "line": 218, "column": 110 }, "end": { - "line": 199, + "line": 218, "column": 111 } } @@ -47285,15 +51725,15 @@ "postfix": false, "binop": null }, - "start": 7611, - "end": 7612, + "start": 8246, + "end": 8247, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 5 } } @@ -47301,15 +51741,15 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 7618, - "end": 7654, + "start": 8253, + "end": 8289, "loc": { "start": { - "line": 202, + "line": 221, "column": 4 }, "end": { - "line": 202, + "line": 221, "column": 40 } } @@ -47329,15 +51769,15 @@ "updateContext": null }, "value": "return", - "start": 7659, - "end": 7665, + "start": 8294, + "end": 8300, "loc": { "start": { - "line": 203, + "line": 222, "column": 4 }, "end": { - "line": 203, + "line": 222, "column": 10 } } @@ -47354,15 +51794,15 @@ "postfix": false, "binop": null }, - "start": 7666, - "end": 7667, + "start": 8301, + "end": 8302, "loc": { "start": { - "line": 203, + "line": 222, "column": 11 }, "end": { - "line": 203, + "line": 222, "column": 12 } } @@ -47381,15 +51821,15 @@ "updateContext": null }, "value": "Specimen ", - "start": 7667, - "end": 7676, + "start": 8302, + "end": 8311, "loc": { "start": { - "line": 203, + "line": 222, "column": 12 }, "end": { - "line": 203, + "line": 222, "column": 21 } } @@ -47406,15 +51846,15 @@ "postfix": false, "binop": null }, - "start": 7676, - "end": 7678, + "start": 8311, + "end": 8313, "loc": { "start": { - "line": 203, + "line": 222, "column": 21 }, "end": { - "line": 203, + "line": 222, "column": 23 } } @@ -47434,15 +51874,15 @@ "updateContext": null }, "value": "this", - "start": 7678, - "end": 7682, + "start": 8313, + "end": 8317, "loc": { "start": { - "line": 203, + "line": 222, "column": 23 }, "end": { - "line": 203, + "line": 222, "column": 27 } } @@ -47460,15 +51900,15 @@ "binop": null, "updateContext": null }, - "start": 7682, - "end": 7683, + "start": 8317, + "end": 8318, "loc": { "start": { - "line": 203, + "line": 222, "column": 27 }, "end": { - "line": 203, + "line": 222, "column": 28 } } @@ -47486,15 +51926,15 @@ "binop": null }, "value": "occurrenceID", - "start": 7683, - "end": 7695, + "start": 8318, + "end": 8330, "loc": { "start": { - "line": 203, + "line": 222, "column": 28 }, "end": { - "line": 203, + "line": 222, "column": 40 } } @@ -47511,15 +51951,15 @@ "postfix": false, "binop": null }, - "start": 7695, - "end": 7696, + "start": 8330, + "end": 8331, "loc": { "start": { - "line": 203, + "line": 222, "column": 40 }, "end": { - "line": 203, + "line": 222, "column": 41 } } @@ -47538,15 +51978,15 @@ "updateContext": null }, "value": "", - "start": 7696, - "end": 7696, + "start": 8331, + "end": 8331, "loc": { "start": { - "line": 203, + "line": 222, "column": 41 }, "end": { - "line": 203, + "line": 222, "column": 41 } } @@ -47563,15 +52003,15 @@ "postfix": false, "binop": null }, - "start": 7696, - "end": 7697, + "start": 8331, + "end": 8332, "loc": { "start": { - "line": 203, + "line": 222, "column": 41 }, "end": { - "line": 203, + "line": 222, "column": 42 } } @@ -47589,15 +52029,15 @@ "binop": null, "updateContext": null }, - "start": 7697, - "end": 7698, + "start": 8332, + "end": 8333, "loc": { "start": { - "line": 203, + "line": 222, "column": 42 }, "end": { - "line": 203, + "line": 222, "column": 43 } } @@ -47614,15 +52054,15 @@ "postfix": false, "binop": null }, - "start": 7701, - "end": 7702, + "start": 8336, + "end": 8337, "loc": { "start": { - "line": 204, + "line": 223, "column": 2 }, "end": { - "line": 204, + "line": 223, "column": 3 } } @@ -47630,15 +52070,15 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 7706, - "end": 7767, + "start": 8341, + "end": 8402, "loc": { "start": { - "line": 206, + "line": 225, "column": 2 }, "end": { - "line": 206, + "line": 225, "column": 63 } } @@ -47656,15 +52096,15 @@ "binop": null }, "value": "get", - "start": 7770, - "end": 7773, + "start": 8405, + "end": 8408, "loc": { "start": { - "line": 207, + "line": 226, "column": 2 }, "end": { - "line": 207, + "line": 226, "column": 5 } } @@ -47682,15 +52122,15 @@ "binop": null }, "value": "asOWLEquivClass", - "start": 7774, - "end": 7789, + "start": 8409, + "end": 8424, "loc": { "start": { - "line": 207, + "line": 226, "column": 6 }, "end": { - "line": 207, + "line": 226, "column": 21 } } @@ -47707,15 +52147,15 @@ "postfix": false, "binop": null }, - "start": 7789, - "end": 7790, + "start": 8424, + "end": 8425, "loc": { "start": { - "line": 207, + "line": 226, "column": 21 }, "end": { - "line": 207, + "line": 226, "column": 22 } } @@ -47732,15 +52172,15 @@ "postfix": false, "binop": null }, - "start": 7790, - "end": 7791, + "start": 8425, + "end": 8426, "loc": { "start": { - "line": 207, + "line": 226, "column": 22 }, "end": { - "line": 207, + "line": 226, "column": 23 } } @@ -47757,15 +52197,15 @@ "postfix": false, "binop": null }, - "start": 7792, - "end": 7793, + "start": 8427, + "end": 8428, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 25 } } @@ -47773,15 +52213,15 @@ { "type": "CommentLine", "value": " We can't do anything without an occurrence ID!", - "start": 7798, - "end": 7847, + "start": 8433, + "end": 8482, "loc": { "start": { - "line": 208, + "line": 227, "column": 4 }, "end": { - "line": 208, + "line": 227, "column": 53 } } @@ -47801,15 +52241,15 @@ "updateContext": null }, "value": "if", - "start": 7852, - "end": 7854, + "start": 8487, + "end": 8489, "loc": { "start": { - "line": 209, + "line": 228, "column": 4 }, "end": { - "line": 209, + "line": 228, "column": 6 } } @@ -47826,15 +52266,15 @@ "postfix": false, "binop": null }, - "start": 7855, - "end": 7856, + "start": 8490, + "end": 8491, "loc": { "start": { - "line": 209, + "line": 228, "column": 7 }, "end": { - "line": 209, + "line": 228, "column": 8 } } @@ -47853,15 +52293,15 @@ "updateContext": null }, "value": "!", - "start": 7856, - "end": 7857, + "start": 8491, + "end": 8492, "loc": { "start": { - "line": 209, + "line": 228, "column": 8 }, "end": { - "line": 209, + "line": 228, "column": 9 } } @@ -47881,15 +52321,15 @@ "updateContext": null }, "value": "this", - "start": 7857, - "end": 7861, + "start": 8492, + "end": 8496, "loc": { "start": { - "line": 209, + "line": 228, "column": 9 }, "end": { - "line": 209, + "line": 228, "column": 13 } } @@ -47907,15 +52347,15 @@ "binop": null, "updateContext": null }, - "start": 7861, - "end": 7862, + "start": 8496, + "end": 8497, "loc": { "start": { - "line": 209, + "line": 228, "column": 13 }, "end": { - "line": 209, + "line": 228, "column": 14 } } @@ -47933,15 +52373,15 @@ "binop": null }, "value": "occurrenceID", - "start": 7862, - "end": 7874, + "start": 8497, + "end": 8509, "loc": { "start": { - "line": 209, + "line": 228, "column": 14 }, "end": { - "line": 209, + "line": 228, "column": 26 } } @@ -47958,15 +52398,15 @@ "postfix": false, "binop": null }, - "start": 7874, - "end": 7875, + "start": 8509, + "end": 8510, "loc": { "start": { - "line": 209, + "line": 228, "column": 26 }, "end": { - "line": 209, + "line": 228, "column": 27 } } @@ -47986,15 +52426,15 @@ "updateContext": null }, "value": "return", - "start": 7876, - "end": 7882, + "start": 8511, + "end": 8517, "loc": { "start": { - "line": 209, + "line": 228, "column": 28 }, "end": { - "line": 209, + "line": 228, "column": 34 } } @@ -48012,15 +52452,15 @@ "binop": null }, "value": "undefined", - "start": 7883, - "end": 7892, + "start": 8518, + "end": 8527, "loc": { "start": { - "line": 209, + "line": 228, "column": 35 }, "end": { - "line": 209, + "line": 228, "column": 44 } } @@ -48038,15 +52478,15 @@ "binop": null, "updateContext": null }, - "start": 7892, - "end": 7893, + "start": 8527, + "end": 8528, "loc": { "start": { - "line": 209, + "line": 228, "column": 44 }, "end": { - "line": 209, + "line": 228, "column": 45 } } @@ -48054,15 +52494,15 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 7899, - "end": 7970, + "start": 8534, + "end": 8605, "loc": { "start": { - "line": 211, + "line": 230, "column": 4 }, "end": { - "line": 211, + "line": 230, "column": 75 } } @@ -48070,15 +52510,15 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 7975, - "end": 8022, + "start": 8610, + "end": 8657, "loc": { "start": { - "line": 212, + "line": 231, "column": 4 }, "end": { - "line": 212, + "line": 231, "column": 51 } } @@ -48086,15 +52526,15 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8028, - "end": 8060, + "start": 8663, + "end": 8695, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 36 } } @@ -48114,15 +52554,15 @@ "updateContext": null }, "value": "return", - "start": 8065, - "end": 8071, + "start": 8700, + "end": 8706, "loc": { "start": { - "line": 215, + "line": 234, "column": 4 }, "end": { - "line": 215, + "line": 234, "column": 10 } } @@ -48139,15 +52579,15 @@ "postfix": false, "binop": null }, - "start": 8072, - "end": 8073, + "start": 8707, + "end": 8708, "loc": { "start": { - "line": 215, + "line": 234, "column": 11 }, "end": { - "line": 215, + "line": 234, "column": 12 } } @@ -48166,15 +52606,15 @@ "updateContext": null }, "value": "@type", - 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"start": 8114, - "end": 8124, + "start": 8749, + "end": 8759, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 16 } } @@ -48297,15 +52737,15 @@ "binop": null, "updateContext": null }, - "start": 8124, - "end": 8125, + "start": 8759, + "end": 8760, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 17 } } @@ -48323,15 +52763,15 @@ "binop": null }, "value": "owlterms", - "start": 8126, - "end": 8134, + "start": 8761, + "end": 8769, "loc": { "start": { - "line": 217, + "line": 236, "column": 18 }, "end": { - "line": 217, + "line": 236, "column": 26 } } @@ -48349,15 +52789,15 @@ "binop": null, "updateContext": null }, - "start": 8134, - "end": 8135, + "start": 8769, + "end": 8770, "loc": { "start": { - "line": 217, + "line": 236, "column": 26 }, "end": { - "line": 217, + "line": 236, "column": 27 } } @@ -48375,15 +52815,15 @@ "binop": null }, "value": "DWC_OCCURRENCE_ID", - "start": 8135, - "end": 8152, + "start": 8770, + "end": 8787, "loc": { "start": { - "line": 217, + "line": 236, "column": 27 }, "end": { - "line": 217, + "line": 236, "column": 44 } } @@ -48401,15 +52841,15 @@ "binop": null, "updateContext": null }, - "start": 8152, - "end": 8153, + "start": 8787, + "end": 8788, "loc": { "start": { - "line": 217, + "line": 236, "column": 44 }, "end": { - "line": 217, + "line": 236, "column": 45 } } @@ -48427,15 +52867,15 @@ "binop": null }, "value": "hasValue", - "start": 8160, - "end": 8168, + "start": 8795, + "end": 8803, "loc": { "start": { - "line": 218, + "line": 237, "column": 6 }, "end": { - "line": 218, + "line": 237, "column": 14 } } @@ -48453,15 +52893,15 @@ "binop": null, "updateContext": null }, - "start": 8168, - "end": 8169, + "start": 8803, + "end": 8804, "loc": { "start": { - "line": 218, + "line": 237, "column": 14 }, "end": { - "line": 218, + "line": 237, "column": 15 } } @@ -48481,15 +52921,15 @@ "updateContext": null }, "value": "this", - "start": 8170, - "end": 8174, + "start": 8805, + "end": 8809, "loc": { "start": { - "line": 218, + "line": 237, "column": 16 }, "end": { - "line": 218, + "line": 237, "column": 20 } } @@ -48507,15 +52947,15 @@ "binop": null, "updateContext": null }, - "start": 8174, - "end": 8175, + "start": 8809, + "end": 8810, "loc": { "start": { - "line": 218, + "line": 237, "column": 20 }, "end": { - "line": 218, + "line": 237, "column": 21 } } @@ -48533,15 +52973,15 @@ "binop": null }, "value": "occurrenceID", - "start": 8175, - "end": 8187, + "start": 8810, + "end": 8822, "loc": { "start": { - "line": 218, + "line": 237, "column": 21 }, "end": { - "line": 218, + "line": 237, "column": 33 } } @@ -48559,15 +52999,15 @@ "binop": null, "updateContext": null }, - "start": 8187, - "end": 8188, + "start": 8822, + "end": 8823, "loc": { "start": { - "line": 218, + "line": 237, "column": 33 }, "end": { - "line": 218, + "line": 237, "column": 34 } } @@ -48584,15 +53024,15 @@ "postfix": false, "binop": null }, - "start": 8193, - "end": 8194, + "start": 8828, + "end": 8829, "loc": { "start": { - "line": 219, + "line": 238, "column": 4 }, "end": { - "line": 219, + "line": 238, "column": 5 } } @@ -48610,15 +53050,15 @@ "binop": null, "updateContext": null }, - "start": 8194, - "end": 8195, + "start": 8829, + "end": 8830, "loc": { "start": { - "line": 219, + "line": 238, "column": 5 }, "end": { - "line": 219, + "line": 238, "column": 6 } } @@ -48635,15 +53075,15 @@ "postfix": false, "binop": null }, - "start": 8198, - "end": 8199, + "start": 8833, + "end": 8834, "loc": { "start": { - "line": 220, + "line": 239, "column": 2 }, "end": { - "line": 220, + "line": 239, "column": 3 } } @@ -48660,15 +53100,15 @@ "postfix": false, "binop": null }, - "start": 8200, - "end": 8201, + "start": 8835, + "end": 8836, "loc": { "start": { - "line": 221, + "line": 240, "column": 0 }, "end": { - "line": 221, + "line": 240, "column": 1 } } @@ -48688,15 +53128,15 @@ "updateContext": null }, "value": "export", - "start": 8203, - "end": 8209, + "start": 8838, + "end": 8844, "loc": { "start": { - "line": 223, + "line": 242, "column": 0 }, "end": { - "line": 223, + "line": 242, "column": 6 } } @@ -48713,15 +53153,15 @@ "postfix": false, "binop": null }, - "start": 8210, - "end": 8211, + "start": 8845, + "end": 8846, "loc": { "start": { - "line": 223, + "line": 242, "column": 7 }, "end": { - "line": 223, + "line": 242, "column": 8 } } @@ -48739,15 +53179,15 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 8212, - "end": 8227, + "start": 8847, + "end": 8862, "loc": { "start": { - "line": 223, + "line": 242, "column": 9 }, "end": { - "line": 223, + "line": 242, "column": 24 } } @@ -48765,15 +53205,15 @@ "binop": null, "updateContext": null }, - "start": 8227, - "end": 8228, + "start": 8862, + "end": 8863, "loc": { "start": { - "line": 223, + "line": 242, "column": 24 }, "end": { - "line": 223, + "line": 242, "column": 25 } } @@ -48790,15 +53230,15 @@ "postfix": false, "binop": null }, - "start": 8229, - "end": 8230, + "start": 8864, + "end": 8865, "loc": { "start": { - "line": 223, + "line": 242, "column": 26 }, "end": { - "line": 223, + "line": 242, "column": 27 } } @@ -48816,15 +53256,15 @@ "binop": null, "updateContext": null }, - "start": 8230, - "end": 8231, + "start": 8865, + "end": 8866, "loc": { "start": { - "line": 223, + "line": 242, "column": 27 }, "end": { - "line": 223, + "line": 242, "column": 28 } } @@ -48842,15 +53282,15 @@ "binop": null, "updateContext": null }, - "start": 8232, - "end": 8232, + "start": 8867, + "end": 8867, "loc": { "start": { - "line": 224, + "line": 243, "column": 0 }, "end": { - "line": 224, + "line": 243, "column": 0 } } diff --git a/docs/ast/source/wrappers/TaxonConceptWrapper.js.json b/docs/ast/source/wrappers/TaxonConceptWrapper.js.json index 76162744..10a9b9c5 100644 --- a/docs/ast/source/wrappers/TaxonConceptWrapper.js.json +++ b/docs/ast/source/wrappers/TaxonConceptWrapper.js.json @@ -1,28 +1,28 @@ { "type": "File", "start": 0, - "end": 6770, + "end": 7306, "loc": { "start": { "line": 1, "column": 0 }, "end": { - "line": 195, + "line": 212, "column": 0 } }, "program": { "type": "Program", "start": 0, - "end": 6770, + "end": 7306, "loc": { "start": { "line": 1, "column": 0 }, "end": { - "line": 195, + "line": 212, "column": 0 } }, @@ -70,9 +70,9 @@ "line": 2, "column": 25 }, - "identifierName": "LKT4H192AHWT0" + "identifierName": "LXL9JK8W7XYSP" }, - "name": "LKT4H192AHWT0", + "name": "LXL9JK8W7XYSP", "leadingComments": null }, "leadingComments": null @@ -231,9 +231,9 @@ "line": 3, "column": 29 }, - "identifierName": "LKT4H192AHWT0" + "identifierName": "LXL9JK8W7XYSP" }, - "name": "LKT4H192AHWT0" + "name": "LXL9JK8W7XYSP" } } ], @@ -406,9 +406,9 @@ "line": 9, "column": 25 }, - "identifierName": "LKT4H192JH5K0" + "identifierName": "LXL9JK8W1GXXG" }, - "name": "LKT4H192JH5K0", + "name": "LXL9JK8W1GXXG", "leadingComments": null }, "leadingComments": null @@ -567,9 +567,9 @@ "line": 10, "column": 42 }, - "identifierName": "LKT4H192JH5K0" + "identifierName": "LXL9JK8W1GXXG" }, - "name": "LKT4H192JH5K0" + "name": "LXL9JK8W1GXXG" } } ], @@ -596,14 +596,14 @@ { "type": "Identifier", "start": 1161, - "end": 6735, + "end": 7271, "loc": { "start": { "line": 27, "column": 0 }, "end": { - "line": 192, + "line": 209, "column": 1 } }, @@ -629,14 +629,14 @@ "body": { "type": "ClassBody", "start": 1187, - "end": 6735, + "end": 7271, "loc": { "start": { "line": 27, "column": 26 }, "end": { - "line": 192, + "line": 209, "column": 1 } }, @@ -1173,16 +1173,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", + "value": "*\n * Normalize the specified taxon concept.\n * @param tc A taxon concept to be normalized.\n ", "start": 1526, - "end": 1607, + "end": 1628, "loc": { "start": { "line": 39, "column": 2 }, "end": { - "line": 41, + "line": 42, "column": 5 } } @@ -1191,62 +1191,80 @@ }, { "type": "ClassMethod", - "start": 1610, - "end": 1988, + "start": 1631, + "end": 2054, "loc": { "start": { - "line": 42, + "line": 43, "column": 2 }, "end": { - "line": 51, + "line": 54, "column": 3 } }, - "static": false, + "static": true, "computed": false, "key": { "type": "Identifier", - "start": 1614, - "end": 1623, + "start": 1638, + "end": 1647, "loc": { "start": { - "line": 42, - "column": 6 + "line": 43, + "column": 9 }, "end": { - "line": 42, - "column": 15 + "line": 43, + "column": 18 }, - "identifierName": "taxonName" + "identifierName": "normalize" }, - "name": "taxonName" + "name": "normalize" }, - "kind": "get", + "kind": "method", "id": null, "generator": false, "expression": false, "async": false, - "params": [], + "params": [ + { + "type": "Identifier", + "start": 1648, + "end": 1650, + "loc": { + "start": { + "line": 43, + "column": 19 + }, + "end": { + "line": 43, + "column": 21 + }, + "identifierName": "tc" + }, + "name": "tc" + } + ], "body": { "type": "BlockStatement", - "start": 1626, - "end": 1988, + "start": 1652, + "end": 2054, "loc": { "start": { - "line": 42, - "column": 18 + "line": 43, + "column": 23 }, "end": { - "line": 51, + "line": 54, "column": 3 } }, "body": [ { - "type": "IfStatement", - "start": 1683, - "end": 1741, + "type": "VariableDeclaration", + "start": 1658, + "end": 1702, "loc": { "start": { "line": 44, @@ -1254,666 +1272,928 @@ }, "end": { "line": 44, - 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] + }, + "alternate": null + }, + { + "type": "ReturnStatement", + "start": 2030, + "end": 2050, + "loc": { + "start": { + "line": 53, + "column": 4 + }, + "end": { + "line": 53, + "column": 24 + } + }, + "argument": { + "type": "Identifier", + "start": 2037, + "end": 2049, + "loc": { + "start": { + "line": 53, + "column": 11 + }, + "end": { + "line": 53, + "column": 23 + }, + "identifierName": "normalizedTC" + }, + "name": "normalizedTC" + } } ], "directives": [], @@ -1922,16 +2202,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", + "value": "*\n * Normalize the specified taxon concept.\n * @param tc A taxon concept to be normalized.\n ", "start": 1526, - "end": 1607, + "end": 1628, "loc": { "start": { "line": 39, "column": 2 }, "end": { - "line": 41, + "line": 42, "column": 5 } } @@ -1940,16 +2220,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", - "start": 1992, - "end": 2126, + "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", + "start": 2058, + "end": 2139, "loc": { "start": { - "line": 53, + "line": 56, "column": 2 }, "end": { - "line": 56, + "line": 58, "column": 5 } } @@ -1958,15 +2238,15 @@ }, { "type": "ClassMethod", - "start": 2129, - "end": 2581, + "start": 2142, + "end": 2520, "loc": { "start": { - "line": 57, + "line": 59, "column": 2 }, "end": { - "line": 66, + "line": 68, "column": 3 } }, @@ -1974,20 +2254,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 2133, - "end": 2145, + "start": 2146, + "end": 2155, "loc": { "start": { - "line": 57, + "line": 59, "column": 6 }, "end": { - "line": 57, - "column": 18 + "line": 59, + "column": 15 }, - "identifierName": "nameComplete" + "identifierName": "taxonName" }, - "name": "nameComplete" + "name": "taxonName" }, "kind": "get", "id": null, @@ -1997,58 +2277,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 2148, - "end": 2581, + "start": 2158, + "end": 2520, "loc": { "start": { - "line": 57, - "column": 21 + "line": 59, + "column": 18 }, "end": { - "line": 66, + "line": 68, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 2205, - "end": 2321, + "start": 2215, + "end": 2273, "loc": { "start": { - "line": 59, + "line": 61, "column": 4 }, "end": { - "line": 59, - "column": 120 + "line": 61, + "column": 62 } }, "test": { "type": "CallExpression", - "start": 2209, - "end": 2235, + "start": 2219, + "end": 2245, "loc": { "start": { - "line": 59, + "line": 61, "column": 8 }, "end": { - "line": 59, + "line": 61, "column": 34 } }, "callee": { "type": "Identifier", - "start": 2209, - "end": 2212, + "start": 2219, + "end": 2222, "loc": { "start": { - "line": 59, + "line": 61, "column": 8 }, "end": { - "line": 59, + "line": 61, "column": 11 }, "identifierName": "has" @@ -2059,44 +2339,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2213, - "end": 2223, + "start": 2223, + "end": 2233, "loc": { "start": { - "line": 59, + "line": 61, "column": 12 }, "end": { - "line": 59, + "line": 61, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 2213, - "end": 2217, + "start": 2223, + "end": 2227, "loc": { "start": { - "line": 59, + "line": 61, "column": 12 }, "end": { - "line": 59, + "line": 61, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2218, - "end": 2223, + "start": 2228, + "end": 2233, "loc": { "start": { - "line": 59, + "line": 61, "column": 17 }, "end": { - "line": 59, + "line": 61, "column": 22 }, "identifierName": "tunit" @@ -2107,15 +2387,15 @@ }, { "type": "StringLiteral", - "start": 2225, - "end": 2234, + "start": 2235, + "end": 2244, "loc": { "start": { - "line": 59, + "line": 61, "column": 24 }, "end": { - "line": 59, + "line": 61, "column": 33 } }, @@ -2130,211 +2410,96 @@ }, "consequent": { "type": "ReturnStatement", - "start": 2237, - "end": 2321, + "start": 2247, + "end": 2273, "loc": { "start": { - "line": 59, + "line": 61, "column": 36 }, "end": { - "line": 59, - "column": 120 + "line": 61, + "column": 62 } }, "argument": { "type": "MemberExpression", - "start": 2244, - "end": 2320, + "start": 2254, + "end": 2272, "loc": { "start": { - "line": 59, + "line": 61, "column": 43 }, "end": { - "line": 59, - "column": 119 + "line": 61, + "column": 61 } }, "object": { - "type": "NewExpression", - "start": 2244, - "end": 2307, + "type": "MemberExpression", + "start": 2254, + "end": 2264, "loc": { "start": { - "line": 59, + "line": 61, "column": 43 }, "end": { - "line": 59, - "column": 106 + "line": 61, + "column": 53 } }, - "callee": { + "object": { + "type": "ThisExpression", + "start": 2254, + "end": 2258, + "loc": { + "start": { + "line": 61, + "column": 43 + }, + "end": { + "line": 61, + "column": 47 + } + } + }, + "property": { "type": "Identifier", - "start": 2248, + "start": 2259, "end": 2264, "loc": { "start": { - "line": 59, - "column": 47 + "line": 61, + "column": 48 }, "end": { - "line": 59, - "column": 63 + "line": 61, + "column": 53 }, - "identifierName": "TaxonNameWrapper" + "identifierName": "tunit" }, - "name": "TaxonNameWrapper" + "name": "tunit" }, - "arguments": [ - { - "type": "MemberExpression", - "start": 2265, - "end": 2283, - "loc": { - "start": { - "line": 59, - "column": 64 - }, - "end": { - "line": 59, - "column": 82 - } - }, - "object": { - "type": "MemberExpression", - "start": 2265, - "end": 2275, - "loc": { - "start": { - "line": 59, - "column": 64 - }, - "end": { - "line": 59, - "column": 74 - } - }, - "object": { - "type": "ThisExpression", - "start": 2265, - "end": 2269, - "loc": { - "start": { - "line": 59, - "column": 64 - }, - "end": { - "line": 59, - "column": 68 - } - } - }, - "property": { - "type": "Identifier", - "start": 2270, - "end": 2275, - "loc": { - "start": { - "line": 59, - "column": 69 - }, - "end": { - "line": 59, - "column": 74 - }, - "identifierName": "tunit" - }, - "name": "tunit" - }, - "computed": false - }, - "property": { - "type": "Identifier", - "start": 2276, - "end": 2283, - "loc": { - "start": { - "line": 59, - "column": 75 - }, - "end": { - "line": 59, - "column": 82 - }, - "identifierName": "hasName" - }, - "name": "hasName" - }, - "computed": false - }, - { - "type": "MemberExpression", - "start": 2285, - "end": 2306, - "loc": { - "start": { - "line": 59, - "column": 84 - }, - "end": { - "line": 59, - "column": 105 - } - }, - "object": { - "type": "ThisExpression", - "start": 2285, - "end": 2289, - "loc": { - "start": { - "line": 59, - "column": 84 - }, - "end": { - "line": 59, - "column": 88 - } - } - }, - "property": { - "type": "Identifier", - "start": 2290, - "end": 2306, - "loc": { - "start": { - "line": 59, - "column": 89 - }, - "end": { - "line": 59, - "column": 105 - }, - "identifierName": "defaultNomenCode" - }, - "name": "defaultNomenCode" - }, - "computed": false - } - ] + "computed": false }, "property": { "type": "Identifier", - "start": 2308, - "end": 2320, + "start": 2265, + "end": 2272, "loc": { "start": { - "line": 59, - "column": 107 + "line": 61, + "column": 54 }, "end": { - "line": 59, - "column": 119 + "line": 61, + "column": 61 }, - "identifierName": "nameComplete" + "identifierName": "hasName" }, - "name": "nameComplete" + "name": "hasName" }, "computed": false }, @@ -2345,15 +2510,15 @@ { "type": "CommentLine", "value": " Do we have any names as taxon name objects?", - "start": 2154, - "end": 2200, + "start": 2164, + "end": 2210, "loc": { "start": { - "line": 58, + "line": 60, "column": 4 }, "end": { - "line": 58, + "line": 60, "column": 50 } } @@ -2363,15 +2528,15 @@ { "type": "CommentLine", "value": " Do we have a nameString with a taxon name as string?", - "start": 2327, - "end": 2382, + "start": 2279, + "end": 2334, "loc": { "start": { - "line": 61, + "line": 63, "column": 4 }, "end": { - "line": 61, + "line": 63, "column": 59 } } @@ -2380,43 +2545,43 @@ }, { "type": "IfStatement", - "start": 2387, - "end": 2522, + "start": 2339, + "end": 2461, "loc": { "start": { - "line": 62, + "line": 64, "column": 4 }, "end": { - "line": 62, - "column": 139 + "line": 64, + "column": 126 } }, "test": { "type": "CallExpression", - "start": 2391, - "end": 2420, + "start": 2343, + "end": 2372, "loc": { "start": { - "line": 62, + "line": 64, "column": 8 }, "end": { - "line": 62, + "line": 64, "column": 37 } }, "callee": { "type": "Identifier", - "start": 2391, - "end": 2394, + "start": 2343, + "end": 2346, "loc": { "start": { - "line": 62, + "line": 64, "column": 8 }, "end": { - "line": 62, + "line": 64, "column": 11 }, "identifierName": "has" @@ -2427,44 +2592,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 2395, - "end": 2405, + "start": 2347, + "end": 2357, "loc": { "start": { - "line": 62, + "line": 64, "column": 12 }, "end": { - "line": 62, + "line": 64, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 2395, - "end": 2399, + "start": 2347, + "end": 2351, "loc": { "start": { - "line": 62, + "line": 64, "column": 12 }, "end": { - "line": 62, + "line": 64, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2400, - "end": 2405, + "start": 2352, + "end": 2357, "loc": { "start": { - "line": 62, + "line": 64, "column": 17 }, "end": { - "line": 62, + "line": 64, "column": 22 }, "identifierName": "tunit" @@ -2475,15 +2640,15 @@ }, { "type": "StringLiteral", - "start": 2407, - "end": 2419, + "start": 2359, + "end": 2371, "loc": { "start": { - "line": 62, + "line": 64, "column": 24 }, "end": { - "line": 62, + "line": 64, "column": 36 } }, @@ -2498,246 +2663,213 @@ }, "consequent": { "type": "ReturnStatement", - "start": 2422, - "end": 2522, + "start": 2374, + "end": 2461, "loc": { "start": { - "line": 62, + "line": 64, "column": 39 }, "end": { - "line": 62, - "column": 139 + "line": 64, + "column": 126 } }, "argument": { - "type": "MemberExpression", - "start": 2429, - "end": 2521, + "type": "CallExpression", + "start": 2381, + "end": 2460, "loc": { "start": { - "line": 62, + "line": 64, "column": 46 }, "end": { - "line": 62, - "column": 138 + "line": 64, + "column": 125 } }, - "object": { - "type": "CallExpression", - "start": 2429, - "end": 2508, + "callee": { + "type": "MemberExpression", + "start": 2381, + "end": 2414, "loc": { "start": { - "line": 62, + "line": 64, "column": 46 }, "end": { - "line": 62, - "column": 125 + "line": 64, + "column": 79 } }, - "callee": { - "type": "MemberExpression", - "start": 2429, - "end": 2462, + "object": { + "type": "Identifier", + "start": 2381, + "end": 2397, "loc": { "start": { - "line": 62, + "line": 64, "column": 46 }, "end": { - "line": 62, - "column": 79 - } - }, - "object": { - "type": "Identifier", - "start": 2429, - "end": 2445, - "loc": { - "start": { - "line": 62, - "column": 46 - }, - "end": { - "line": 62, - "column": 62 - }, - "identifierName": "TaxonNameWrapper" + "line": 64, + "column": 62 }, - "name": "TaxonNameWrapper" + "identifierName": "TaxonNameWrapper" }, - "property": { - "type": "Identifier", - "start": 2446, - "end": 2462, - "loc": { - "start": { - "line": 62, - "column": 63 - }, - "end": { - "line": 62, - "column": 79 - }, - "identifierName": "fromVerbatimName" + "name": "TaxonNameWrapper" + }, + "property": { + "type": "Identifier", + "start": 2398, + "end": 2414, + "loc": { + "start": { + "line": 64, + "column": 63 }, - "name": "fromVerbatimName" + "end": { + "line": 64, + "column": 79 + }, + "identifierName": "fromVerbatimName" }, - "computed": false + "name": "fromVerbatimName" }, - "arguments": [ - { + "computed": false + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 2415, + "end": 2436, + "loc": { + "start": { + "line": 64, + "column": 80 + }, + "end": { + "line": 64, + "column": 101 + } + }, + "object": { "type": "MemberExpression", - "start": 2463, - "end": 2484, + "start": 2415, + "end": 2425, "loc": { "start": { - "line": 62, + "line": 64, "column": 80 }, "end": { - "line": 62, - "column": 101 + "line": 64, + "column": 90 } }, "object": { - "type": "MemberExpression", - "start": 2463, - "end": 2473, + "type": "ThisExpression", + "start": 2415, + "end": 2419, "loc": { "start": { - "line": 62, + "line": 64, "column": 80 }, "end": { - "line": 62, - "column": 90 - } - }, - "object": { - "type": "ThisExpression", - "start": 2463, - "end": 2467, - "loc": { - "start": { - "line": 62, - "column": 80 - }, - "end": { - "line": 62, - "column": 84 - } + "line": 64, + "column": 84 } - }, - "property": { - "type": "Identifier", - "start": 2468, - "end": 2473, - "loc": { - "start": { - "line": 62, - "column": 85 - }, - "end": { - "line": 62, - "column": 90 - }, - "identifierName": "tunit" - }, - "name": "tunit" - }, - "computed": false + } }, "property": { "type": "Identifier", - "start": 2474, - "end": 2484, + "start": 2420, + "end": 2425, "loc": { "start": { - "line": 62, - "column": 91 + "line": 64, + "column": 85 }, "end": { - "line": 62, - "column": 101 + "line": 64, + "column": 90 }, - "identifierName": "nameString" + "identifierName": "tunit" }, - "name": "nameString" + "name": "tunit" }, "computed": false }, - { - "type": "MemberExpression", - "start": 2486, - "end": 2507, + "property": { + "type": "Identifier", + "start": 2426, + "end": 2436, "loc": { "start": { - "line": 62, - "column": 103 + "line": 64, + "column": 91 }, "end": { - "line": 62, - "column": 124 - } - }, - "object": { - "type": "ThisExpression", - "start": 2486, - "end": 2490, - "loc": { - "start": { - "line": 62, - "column": 103 - }, - "end": { - "line": 62, - "column": 107 - } - } + "line": 64, + "column": 101 + }, + "identifierName": "nameString" }, - "property": { - "type": "Identifier", - "start": 2491, - "end": 2507, - "loc": { - "start": { - "line": 62, - "column": 108 - }, - "end": { - "line": 62, - "column": 124 - }, - "identifierName": "defaultNomenCode" - }, - "name": "defaultNomenCode" + "name": "nameString" + }, + "computed": false + }, + { + "type": "MemberExpression", + "start": 2438, + "end": 2459, + "loc": { + "start": { + "line": 64, + "column": 103 }, - "computed": false - } - ] - }, - "property": { - "type": "Identifier", - "start": 2509, - "end": 2521, - "loc": { - "start": { - "line": 62, - "column": 126 + "end": { + "line": 64, + "column": 124 + } }, - "end": { - "line": 62, - "column": 138 + "object": { + "type": "ThisExpression", + "start": 2438, + "end": 2442, + "loc": { + "start": { + "line": 64, + "column": 103 + }, + "end": { + "line": 64, + "column": 107 + } + } }, - "identifierName": "nameComplete" - }, - "name": "nameComplete" - }, - "computed": false + "property": { + "type": "Identifier", + "start": 2443, + "end": 2459, + "loc": { + "start": { + "line": 64, + "column": 108 + }, + "end": { + "line": 64, + "column": 124 + }, + "identifierName": "defaultNomenCode" + }, + "name": "defaultNomenCode" + }, + "computed": false + } + ] }, "trailingComments": null }, @@ -2746,15 +2878,15 @@ { "type": "CommentLine", "value": " Do we have a nameString with a taxon name as string?", - "start": 2327, - "end": 2382, + "start": 2279, + "end": 2334, "loc": { "start": { - "line": 61, + "line": 63, "column": 4 }, "end": { - "line": 61, + "line": 63, "column": 59 } } @@ -2764,15 +2896,15 @@ { "type": "CommentLine", "value": " If not, we have no name!", - "start": 2528, - "end": 2555, + "start": 2467, + "end": 2494, "loc": { "start": { - "line": 64, + "line": 66, "column": 4 }, "end": { - "line": 64, + "line": 66, "column": 31 } } @@ -2781,29 +2913,29 @@ }, { "type": "ReturnStatement", - "start": 2560, - "end": 2577, + "start": 2499, + "end": 2516, "loc": { "start": { - "line": 65, + "line": 67, "column": 4 }, "end": { - "line": 65, + "line": 67, "column": 21 } }, "argument": { "type": "Identifier", - "start": 2567, - "end": 2576, + "start": 2506, + "end": 2515, "loc": { "start": { - "line": 65, + "line": 67, "column": 11 }, "end": { - "line": 65, + "line": 67, "column": 20 }, "identifierName": "undefined" @@ -2815,15 +2947,15 @@ { "type": "CommentLine", "value": " If not, we have no name!", - "start": 2528, - "end": 2555, + "start": 2467, + "end": 2494, "loc": { "start": { - "line": 64, + "line": 66, "column": 4 }, "end": { - "line": 64, + "line": 66, "column": 31 } } @@ -2837,16 +2969,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", - "start": 1992, - "end": 2126, + "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", + "start": 2058, + "end": 2139, "loc": { "start": { - "line": 53, + "line": 56, "column": 2 }, "end": { - "line": 56, + "line": 58, "column": 5 } } @@ -2855,16 +2987,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", - "start": 2585, - "end": 2664, + "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", + "start": 2524, + "end": 2658, "loc": { "start": { - "line": 68, + "line": 70, "column": 2 }, "end": { - "line": 70, + "line": 73, "column": 5 } } @@ -2873,15 +3005,15 @@ }, { "type": "ClassMethod", - "start": 2667, - "end": 2849, + "start": 2661, + "end": 3113, "loc": { "start": { - "line": 71, + "line": 74, "column": 2 }, "end": { - "line": 75, + "line": 83, "column": 3 } }, @@ -2889,20 +3021,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 2671, - "end": 2680, + "start": 2665, + "end": 2677, "loc": { "start": { - "line": 71, + "line": 74, "column": 6 }, "end": { - "line": 71, - "column": 15 + "line": 74, + "column": 18 }, - "identifierName": "nomenCode" + "identifierName": "nameComplete" }, - "name": "nomenCode" + "name": "nameComplete" }, "kind": "get", "id": null, @@ -2912,105 +3044,106 @@ "params": [], "body": { "type": "BlockStatement", - "start": 2683, - "end": 2849, + "start": 2680, + "end": 3113, "loc": { "start": { - "line": 71, - "column": 18 + "line": 74, + "column": 21 }, "end": { - "line": 75, + "line": 83, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 2689, - "end": 2810, + "start": 2737, + "end": 2853, "loc": { "start": { - "line": 72, + "line": 76, "column": 4 }, "end": { - "line": 72, - "column": 125 + "line": 76, + "column": 120 } }, "test": { "type": "CallExpression", - "start": 2693, - "end": 2719, + "start": 2741, + "end": 2767, "loc": { "start": { - "line": 72, + "line": 76, "column": 8 }, "end": { - "line": 72, + "line": 76, "column": 34 } }, "callee": { "type": "Identifier", - "start": 2693, - "end": 2696, + "start": 2741, + "end": 2744, "loc": { "start": { - "line": 72, + "line": 76, "column": 8 }, "end": { - "line": 72, + "line": 76, "column": 11 }, "identifierName": "has" }, - "name": "has" + "name": "has", + "leadingComments": null }, "arguments": [ { "type": "MemberExpression", - "start": 2697, - "end": 2707, + "start": 2745, + "end": 2755, "loc": { "start": { - "line": 72, + "line": 76, "column": 12 }, "end": { - "line": 72, + "line": 76, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 2697, - "end": 2701, + "start": 2745, + "end": 2749, "loc": { "start": { - "line": 72, + "line": 76, "column": 12 }, "end": { - "line": 72, + "line": 76, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2702, - "end": 2707, + "start": 2750, + "end": 2755, "loc": { "start": { - "line": 72, + "line": 76, "column": 17 }, "end": { - "line": 72, + "line": 76, "column": 22 }, "identifierName": "tunit" @@ -3021,15 +3154,15 @@ }, { "type": "StringLiteral", - "start": 2709, - "end": 2718, + "start": 2757, + "end": 2766, "loc": { "start": { - "line": 72, + "line": 76, "column": 24 }, "end": { - "line": 72, + "line": 76, "column": 33 } }, @@ -3039,61 +3172,62 @@ }, "value": "hasName" } - ] + ], + "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 2721, - "end": 2810, + "start": 2769, + "end": 2853, "loc": { "start": { - "line": 72, + "line": 76, "column": 36 }, "end": { - "line": 72, - "column": 125 + "line": 76, + "column": 120 } }, "argument": { "type": "MemberExpression", - "start": 2728, - "end": 2809, + "start": 2776, + "end": 2852, "loc": { "start": { - "line": 72, + "line": 76, "column": 43 }, "end": { - "line": 72, - "column": 124 + "line": 76, + "column": 119 } }, "object": { "type": "NewExpression", - "start": 2728, - "end": 2791, + "start": 2776, + "end": 2839, "loc": { "start": { - "line": 72, + "line": 76, "column": 43 }, "end": { - "line": 72, + "line": 76, "column": 106 } }, "callee": { "type": "Identifier", - "start": 2732, - "end": 2748, + "start": 2780, + "end": 2796, "loc": { "start": { - "line": 72, + "line": 76, "column": 47 }, "end": { - "line": 72, + "line": 76, "column": 63 }, "identifierName": "TaxonNameWrapper" @@ -3103,58 +3237,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 2749, - "end": 2767, + "start": 2797, + "end": 2815, "loc": { "start": { - "line": 72, + "line": 76, "column": 64 }, "end": { - "line": 72, + "line": 76, "column": 82 } }, "object": { "type": "MemberExpression", - "start": 2749, - "end": 2759, + "start": 2797, + "end": 2807, "loc": { "start": { - "line": 72, + "line": 76, "column": 64 }, "end": { - "line": 72, + "line": 76, "column": 74 } }, "object": { "type": "ThisExpression", - "start": 2749, - "end": 2753, + "start": 2797, + "end": 2801, "loc": { "start": { - "line": 72, + "line": 76, "column": 64 }, "end": { - "line": 72, + "line": 76, "column": 68 } } }, "property": { "type": "Identifier", - "start": 2754, - "end": 2759, + "start": 2802, + "end": 2807, "loc": { "start": { - "line": 72, + "line": 76, "column": 69 }, "end": { - "line": 72, + "line": 76, "column": 74 }, "identifierName": "tunit" @@ -3165,15 +3299,15 @@ }, "property": { "type": "Identifier", - "start": 2760, - "end": 2767, + "start": 2808, + "end": 2815, "loc": { "start": { - "line": 72, + "line": 76, "column": 75 }, "end": { - "line": 72, + "line": 76, "column": 82 }, "identifierName": "hasName" @@ -3184,44 +3318,44 @@ }, { "type": "MemberExpression", - "start": 2769, - "end": 2790, + "start": 2817, + "end": 2838, "loc": { "start": { - "line": 72, + "line": 76, "column": 84 }, "end": { - "line": 72, + "line": 76, "column": 105 } }, "object": { "type": "ThisExpression", - "start": 2769, - "end": 2773, + "start": 2817, + "end": 2821, "loc": { "start": { - "line": 72, + "line": 76, "column": 84 }, "end": { - "line": 72, + "line": 76, "column": 88 } } }, "property": { "type": "Identifier", - "start": 2774, - "end": 2790, + "start": 2822, + "end": 2838, "loc": { "start": { - "line": 72, + "line": 76, "column": 89 }, "end": { - "line": 72, + "line": 76, "column": 105 }, "identifierName": "defaultNomenCode" @@ -3234,272 +3368,150 @@ }, "property": { "type": "Identifier", - "start": 2792, - "end": 2809, + "start": 2840, + "end": 2852, "loc": { "start": { - "line": 72, + "line": 76, "column": 107 }, "end": { - "line": 72, - "column": 124 + "line": 76, + "column": 119 }, - "identifierName": "nomenclaturalCode" + "identifierName": "nameComplete" }, - "name": "nomenclaturalCode" + "name": "nameComplete" }, "computed": false - } - }, - "alternate": null - }, - { - "type": "ReturnStatement", - "start": 2816, - "end": 2845, - "loc": { - "start": { - "line": 74, - "column": 4 }, - "end": { - "line": 74, - "column": 33 - } + "trailingComments": null }, - "argument": { - "type": "MemberExpression", - "start": 2823, - "end": 2844, - "loc": { - "start": { - "line": 74, - "column": 11 - }, - "end": { - "line": 74, - "column": 32 - } - }, - "object": { - "type": "Identifier", - "start": 2823, - "end": 2831, + "alternate": null, + "leadingComments": [ + { + "type": "CommentLine", + "value": " Do we have any names as taxon name objects?", + "start": 2686, + "end": 2732, "loc": { "start": { - "line": 74, - "column": 11 + "line": 75, + "column": 4 }, "end": { - "line": 74, - "column": 19 - }, - "identifierName": "owlterms" - }, - "name": "owlterms" - }, - "property": { - "type": "Identifier", - "start": 2832, - "end": 2844, + "line": 75, + "column": 50 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentLine", + "value": " Do we have a nameString with a taxon name as string?", + "start": 2859, + "end": 2914, "loc": { "start": { - "line": 74, - "column": 20 + "line": 78, + "column": 4 }, "end": { - "line": 74, - "column": 32 - }, - "identifierName": "UNKNOWN_CODE" - }, - "name": "UNKNOWN_CODE" - }, - "computed": false - } - } - ], - "directives": [], - "trailingComments": null - }, - "leadingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", - "start": 2585, - "end": 2664, - "loc": { - "start": { - "line": 68, - "column": 2 - }, - "end": { - "line": 70, - "column": 5 - } - } - } - ], - "trailingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", - "start": 2853, - "end": 2933, - "loc": { - "start": { - "line": 77, - "column": 2 - }, - "end": { - "line": 79, - "column": 5 - } - } - } - ] - }, - { - "type": "ClassMethod", - "start": 2936, - "end": 3170, - "loc": { - "start": { - "line": 80, - "column": 2 - }, - "end": { - "line": 84, - "column": 3 - } - }, - "static": false, - "computed": false, - "key": { - "type": "Identifier", - "start": 2940, - "end": 2956, - "loc": { - "start": { - "line": 80, - "column": 6 - }, - "end": { - "line": 80, - "column": 22 - }, - "identifierName": "nomenCodeDetails" - }, - "name": "nomenCodeDetails" - }, - "kind": "get", - "id": null, - "generator": false, - "expression": false, - "async": false, - "params": [], - "body": { - "type": "BlockStatement", - "start": 2959, - "end": 3170, - "loc": { - "start": { - "line": 80, - "column": 25 + "line": 78, + "column": 59 + } + } + } + ] }, - "end": { - "line": 84, - "column": 3 - } - }, - "body": [ { "type": "IfStatement", - "start": 2965, - "end": 3093, + "start": 2919, + "end": 3054, "loc": { "start": { - "line": 81, + "line": 79, "column": 4 }, "end": { - "line": 81, - "column": 132 + "line": 79, + "column": 139 } }, "test": { "type": "CallExpression", - "start": 2969, - "end": 2995, + "start": 2923, + "end": 2952, "loc": { "start": { - "line": 81, + "line": 79, "column": 8 }, "end": { - "line": 81, - "column": 34 + "line": 79, + "column": 37 } }, "callee": { "type": "Identifier", - "start": 2969, - "end": 2972, + "start": 2923, + "end": 2926, "loc": { "start": { - "line": 81, + "line": 79, "column": 8 }, "end": { - "line": 81, + "line": 79, "column": 11 }, "identifierName": "has" }, - "name": "has" - }, + "name": "has", + "leadingComments": null + }, "arguments": [ { "type": "MemberExpression", - "start": 2973, - "end": 2983, + "start": 2927, + "end": 2937, "loc": { "start": { - "line": 81, + "line": 79, "column": 12 }, "end": { - "line": 81, + "line": 79, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 2973, - "end": 2977, + "start": 2927, + "end": 2931, "loc": { "start": { - "line": 81, + "line": 79, "column": 12 }, "end": { - "line": 81, + "line": 79, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2978, - "end": 2983, + "start": 2932, + "end": 2937, "loc": { "start": { - "line": 81, + "line": 79, "column": 17 }, "end": { - "line": 81, + "line": 79, "column": 22 }, "identifierName": "tunit" @@ -3510,141 +3522,175 @@ }, { "type": "StringLiteral", - "start": 2985, - "end": 2994, + "start": 2939, + "end": 2951, "loc": { "start": { - "line": 81, + "line": 79, "column": 24 }, "end": { - "line": 81, - "column": 33 + "line": 79, + "column": 36 } }, "extra": { - "rawValue": "hasName", - "raw": "'hasName'" + "rawValue": "nameString", + "raw": "'nameString'" }, - "value": "hasName" + "value": "nameString" } - ] + ], + "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 2997, - "end": 3093, + "start": 2954, + "end": 3054, "loc": { "start": { - "line": 81, - "column": 36 + "line": 79, + "column": 39 }, "end": { - "line": 81, - "column": 132 + "line": 79, + "column": 139 } }, "argument": { "type": "MemberExpression", - "start": 3004, - "end": 3092, + "start": 2961, + "end": 3053, "loc": { "start": { - "line": 81, - "column": 43 + "line": 79, + "column": 46 }, "end": { - "line": 81, - "column": 131 + "line": 79, + "column": 138 } }, "object": { - "type": "NewExpression", - "start": 3004, - "end": 3067, + "type": "CallExpression", + "start": 2961, + "end": 3040, "loc": { "start": { - "line": 81, - "column": 43 + "line": 79, + "column": 46 }, "end": { - "line": 81, - "column": 106 + "line": 79, + "column": 125 } }, "callee": { - "type": "Identifier", - "start": 3008, - "end": 3024, + "type": "MemberExpression", + "start": 2961, + "end": 2994, "loc": { "start": { - "line": 81, - "column": 47 + "line": 79, + "column": 46 }, "end": { - "line": 81, - "column": 63 + "line": 79, + "column": 79 + } + }, + "object": { + "type": "Identifier", + "start": 2961, + "end": 2977, + "loc": { + "start": { + "line": 79, + "column": 46 + }, + "end": { + "line": 79, + "column": 62 + }, + "identifierName": "TaxonNameWrapper" }, - "identifierName": "TaxonNameWrapper" + "name": "TaxonNameWrapper" }, - "name": "TaxonNameWrapper" + "property": { + "type": "Identifier", + "start": 2978, + "end": 2994, + "loc": { + "start": { + "line": 79, + "column": 63 + }, + "end": { + "line": 79, + "column": 79 + }, + "identifierName": "fromVerbatimName" + }, + "name": "fromVerbatimName" + }, + "computed": false }, "arguments": [ { "type": "MemberExpression", - "start": 3025, - "end": 3043, + "start": 2995, + "end": 3016, "loc": { "start": { - "line": 81, - "column": 64 + "line": 79, + "column": 80 }, "end": { - "line": 81, - "column": 82 + "line": 79, + "column": 101 } }, "object": { "type": "MemberExpression", - "start": 3025, - "end": 3035, + "start": 2995, + "end": 3005, "loc": { "start": { - "line": 81, - "column": 64 + "line": 79, + "column": 80 }, "end": { - "line": 81, - "column": 74 + "line": 79, + "column": 90 } }, "object": { "type": "ThisExpression", - "start": 3025, - "end": 3029, + "start": 2995, + "end": 2999, "loc": { "start": { - "line": 81, - "column": 64 + "line": 79, + "column": 80 }, "end": { - "line": 81, - "column": 68 + "line": 79, + "column": 84 } } }, "property": { "type": "Identifier", - "start": 3030, - "end": 3035, + "start": 3000, + "end": 3005, "loc": { "start": { - "line": 81, - "column": 69 + "line": 79, + "column": 85 }, "end": { - "line": 81, - "column": 74 + "line": 79, + "column": 90 }, "identifierName": "tunit" }, @@ -3654,64 +3700,64 @@ }, "property": { "type": "Identifier", - "start": 3036, - "end": 3043, + "start": 3006, + "end": 3016, "loc": { "start": { - "line": 81, - "column": 75 + "line": 79, + "column": 91 }, "end": { - "line": 81, - "column": 82 + "line": 79, + "column": 101 }, - "identifierName": "hasName" + "identifierName": "nameString" }, - "name": "hasName" + "name": "nameString" }, "computed": false }, { "type": "MemberExpression", - "start": 3045, - "end": 3066, + "start": 3018, + "end": 3039, "loc": { "start": { - "line": 81, - "column": 84 + "line": 79, + "column": 103 }, "end": { - "line": 81, - "column": 105 + "line": 79, + "column": 124 } }, "object": { "type": "ThisExpression", - "start": 3045, - "end": 3049, + "start": 3018, + "end": 3022, "loc": { "start": { - "line": 81, - "column": 84 + "line": 79, + "column": 103 }, "end": { - "line": 81, - "column": 88 + "line": 79, + "column": 107 } } }, "property": { "type": "Identifier", - "start": 3050, - "end": 3066, + "start": 3023, + "end": 3039, "loc": { "start": { - "line": 81, - "column": 89 + "line": 79, + "column": 108 }, "end": { - "line": 81, - "column": 105 + "line": 79, + "column": 124 }, "identifierName": "defaultNomenCode" }, @@ -3723,157 +3769,113 @@ }, "property": { "type": "Identifier", - "start": 3068, - "end": 3092, + "start": 3041, + "end": 3053, "loc": { "start": { - "line": 81, - "column": 107 + "line": 79, + "column": 126 }, "end": { - "line": 81, - "column": 131 + "line": 79, + "column": 138 }, - "identifierName": "nomenclaturalCodeDetails" + "identifierName": "nameComplete" }, - "name": "nomenclaturalCodeDetails" + "name": "nameComplete" }, "computed": false - } + }, + "trailingComments": null }, - "alternate": null + "alternate": null, + "leadingComments": [ + { + "type": "CommentLine", + "value": " Do we have a nameString with a taxon name as string?", + "start": 2859, + "end": 2914, + "loc": { + "start": { + "line": 78, + "column": 4 + }, + "end": { + "line": 78, + "column": 59 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentLine", + "value": " If not, we have no name!", + "start": 3060, + "end": 3087, + "loc": { + "start": { + "line": 81, + "column": 4 + }, + "end": { + "line": 81, + "column": 31 + } + } + } + ] }, { "type": "ReturnStatement", - "start": 3099, - "end": 3166, + "start": 3092, + "end": 3109, "loc": { "start": { - "line": 83, + "line": 82, "column": 4 }, "end": { - "line": 83, - "column": 71 + "line": 82, + "column": 21 } }, "argument": { - "type": "CallExpression", - "start": 3106, - "end": 3165, + "type": "Identifier", + "start": 3099, + "end": 3108, "loc": { "start": { - "line": 83, + "line": 82, "column": 11 }, "end": { - "line": 83, - "column": 70 - } + "line": 82, + "column": 20 + }, + "identifierName": "undefined" }, - "callee": { - "type": "MemberExpression", - "start": 3106, - "end": 3142, + "name": "undefined", + "leadingComments": null + }, + "leadingComments": [ + { + "type": "CommentLine", + "value": " If not, we have no name!", + "start": 3060, + "end": 3087, "loc": { "start": { - "line": 83, - "column": 11 + "line": 81, + "column": 4 }, "end": { - "line": 83, - "column": 47 + "line": 81, + "column": 31 } - }, - "object": { - "type": "Identifier", - "start": 3106, - "end": 3122, - "loc": { - "start": { - "line": 83, - "column": 11 - }, - "end": { - "line": 83, - "column": 27 - }, - "identifierName": "TaxonNameWrapper" - }, - "name": "TaxonNameWrapper" - }, - "property": { - "type": "Identifier", - "start": 3123, - "end": 3142, - "loc": { - "start": { - "line": 83, - "column": 28 - }, - "end": { - "line": 83, - "column": 47 - }, - "identifierName": "getNomenCodeDetails" - }, - "name": "getNomenCodeDetails" - }, - "computed": false - }, - "arguments": [ - { - "type": "MemberExpression", - "start": 3143, - "end": 3164, - "loc": { - "start": { - "line": 83, - "column": 48 - }, - "end": { - "line": 83, - "column": 69 - } - }, - "object": { - "type": "Identifier", - "start": 3143, - "end": 3151, - "loc": { - "start": { - "line": 83, - "column": 48 - }, - "end": { - "line": 83, - "column": 56 - }, - "identifierName": "owlterms" - }, - "name": "owlterms" - }, - "property": { - "type": "Identifier", - "start": 3152, - "end": 3164, - "loc": { - "start": { - "line": 83, - "column": 57 - }, - "end": { - "line": 83, - "column": 69 - }, - "identifierName": "UNKNOWN_CODE" - }, - "name": "UNKNOWN_CODE" - }, - "computed": false } - ] - } + } + ] } ], "directives": [], @@ -3882,16 +3884,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", - "start": 2853, - "end": 2933, + "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", + "start": 2524, + "end": 2658, "loc": { "start": { - "line": 77, + "line": 70, "column": 2 }, "end": { - "line": 79, + "line": 73, "column": 5 } } @@ -3900,16 +3902,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", - "start": 3174, - "end": 3365, + "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", + "start": 3117, + "end": 3196, "loc": { "start": { - "line": 86, + "line": 85, "column": 2 }, "end": { - "line": 91, + "line": 87, "column": 5 } } @@ -3918,15 +3920,15 @@ }, { "type": "ClassMethod", - "start": 3368, - "end": 3704, + "start": 3199, + "end": 3381, "loc": { "start": { - "line": 92, + "line": 88, "column": 2 }, "end": { - "line": 101, + "line": 92, "column": 3 } }, @@ -3934,20 +3936,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 3372, - "end": 3383, + "start": 3203, + "end": 3212, "loc": { "start": { - "line": 92, + "line": 88, "column": 6 }, "end": { - "line": 92, - "column": 17 + "line": 88, + "column": 15 }, - "identifierName": "accordingTo" + "identifierName": "nomenCode" }, - "name": "accordingTo" + "name": "nomenCode" }, "kind": "get", "id": null, @@ -3957,106 +3959,105 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3386, - "end": 3704, + "start": 3215, + "end": 3381, "loc": { "start": { - "line": 92, - "column": 20 + "line": 88, + "column": 18 }, "end": { - "line": 101, + "line": 92, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 3439, - "end": 3504, + "start": 3221, + "end": 3342, "loc": { "start": { - "line": 94, + "line": 89, "column": 4 }, "end": { - "line": 94, - "column": 69 + "line": 89, + "column": 125 } }, "test": { "type": "CallExpression", - "start": 3443, - "end": 3473, + "start": 3225, + "end": 3251, "loc": { "start": { - "line": 94, + "line": 89, "column": 8 }, "end": { - "line": 94, - "column": 38 + "line": 89, + "column": 34 } }, "callee": { "type": "Identifier", - "start": 3443, - "end": 3446, + "start": 3225, + "end": 3228, "loc": { "start": { - "line": 94, + "line": 89, "column": 8 }, "end": { - "line": 94, + "line": 89, "column": 11 }, "identifierName": "has" }, - "name": "has", - "leadingComments": null + "name": "has" }, "arguments": [ { "type": "MemberExpression", - "start": 3447, - "end": 3457, + "start": 3229, + "end": 3239, "loc": { "start": { - "line": 94, + "line": 89, "column": 12 }, "end": { - "line": 94, + "line": 89, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3447, - "end": 3451, + "start": 3229, + "end": 3233, "loc": { "start": { - "line": 94, + "line": 89, "column": 12 }, "end": { - "line": 94, + "line": 89, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3452, - "end": 3457, + "start": 3234, + "end": 3239, "loc": { "start": { - "line": 94, + "line": 89, "column": 17 }, "end": { - "line": 94, + "line": 89, "column": 22 }, "identifierName": "tunit" @@ -4067,465 +4068,303 @@ }, { "type": "StringLiteral", - "start": 3459, - "end": 3472, + "start": 3241, + "end": 3250, "loc": { "start": { - "line": 94, + "line": 89, "column": 24 }, "end": { - "line": 94, - "column": 37 + "line": 89, + "column": 33 } }, "extra": { - "rawValue": "accordingTo", - "raw": "'accordingTo'" + "rawValue": "hasName", + "raw": "'hasName'" }, - 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"value": " If not, we have no accodingTo information!", - "start": 3633, - "end": 3678, - "loc": { - "start": { - "line": 99, - "column": 4 - }, - "end": { - "line": 99, - "column": 49 - } - } - } - ] + "computed": false + } } ], "directives": [], @@ -4534,16 +4373,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", - "start": 3174, - "end": 3365, + "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", + "start": 3117, + "end": 3196, "loc": { "start": { - "line": 86, + "line": 85, "column": 2 }, "end": { - "line": 91, + "line": 87, "column": 5 } } @@ -4552,16 +4391,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", - "start": 3708, - "end": 3940, + "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", + "start": 3385, + "end": 3465, "loc": { "start": { - "line": 103, + "line": 94, "column": 2 }, "end": { - "line": 108, + "line": 96, "column": 5 } } @@ -4570,15 +4409,15 @@ }, { "type": "ClassMethod", - "start": 3943, - "end": 4301, + "start": 3468, + "end": 3702, "loc": { "start": { - "line": 109, + "line": 97, "column": 2 }, "end": { - "line": 118, + "line": 101, "column": 3 } }, @@ -4586,20 +4425,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 3947, - "end": 3964, + "start": 3472, + "end": 3488, "loc": { "start": { - "line": 109, + "line": 97, "column": 6 }, "end": { - "line": 109, - "column": 23 + "line": 97, + "column": 22 }, - "identifierName": "accordingToString" + "identifierName": "nomenCodeDetails" }, - "name": "accordingToString" + "name": "nomenCodeDetails" }, "kind": "get", "id": null, @@ -4609,106 +4448,105 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3967, - "end": 4301, + "start": 3491, + "end": 3702, "loc": { "start": { - "line": 109, - "column": 26 + "line": 97, + "column": 25 }, "end": { - "line": 118, + "line": 101, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4020, - "end": 4101, + "start": 3497, + "end": 3625, "loc": { "start": { - "line": 111, + "line": 98, "column": 4 }, "end": { - "line": 111, - "column": 85 + "line": 98, + "column": 132 } }, "test": { "type": "CallExpression", - "start": 4024, - "end": 4054, + "start": 3501, + "end": 3527, "loc": { "start": { - "line": 111, + "line": 98, "column": 8 }, "end": { - "line": 111, - "column": 38 + "line": 98, + "column": 34 } }, "callee": { "type": "Identifier", - "start": 4024, - "end": 4027, + "start": 3501, + "end": 3504, "loc": { "start": { - "line": 111, + "line": 98, "column": 8 }, "end": { - "line": 111, + "line": 98, "column": 11 }, "identifierName": "has" }, - "name": "has", - "leadingComments": null + "name": "has" }, "arguments": [ { "type": "MemberExpression", - "start": 4028, - "end": 4038, + "start": 3505, + "end": 3515, "loc": { "start": { - "line": 111, + "line": 98, "column": 12 }, "end": { - "line": 111, + "line": 98, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 4028, - "end": 4032, + "start": 3505, + "end": 3509, "loc": { "start": { - "line": 111, + "line": 98, "column": 12 }, "end": { - "line": 111, + "line": 98, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4033, - "end": 4038, + "start": 3510, + "end": 3515, "loc": { "start": { - "line": 111, + "line": 98, "column": 17 }, "end": { - "line": 111, + "line": 98, "column": 22 }, "identifierName": "tunit" @@ -4719,319 +4557,556 @@ }, { "type": "StringLiteral", - "start": 4040, - "end": 4053, + "start": 3517, + "end": 3526, "loc": { "start": { - "line": 111, + "line": 98, "column": 24 }, "end": { - "line": 111, - "column": 37 + "line": 98, + "column": 33 } }, "extra": { - "rawValue": "accordingTo", - "raw": "'accordingTo'" + "rawValue": "hasName", + "raw": "'hasName'" }, - "value": "accordingTo" + "value": "hasName" } - ], - "leadingComments": null + ] }, "consequent": { "type": "ReturnStatement", - "start": 4056, - "end": 4101, + "start": 3529, + "end": 3625, "loc": { "start": { - "line": 111, - "column": 40 + "line": 98, + "column": 36 }, "end": { - "line": 111, - "column": 85 + "line": 98, + "column": 132 } }, "argument": { - "type": "CallExpression", - "start": 4063, - "end": 4100, + "type": "MemberExpression", + "start": 3536, + "end": 3624, "loc": { "start": { - "line": 111, - "column": 47 + "line": 98, + "column": 43 }, "end": { - "line": 111, - "column": 84 + "line": 98, + "column": 131 } }, - "callee": { - "type": "MemberExpression", - "start": 4063, - "end": 4077, + "object": { + "type": "NewExpression", + "start": 3536, + "end": 3599, "loc": { "start": { - "line": 111, - "column": 47 + "line": 98, + "column": 43 }, "end": { - "line": 111, - "column": 61 + "line": 98, + "column": 106 } }, - "object": { + "callee": { "type": "Identifier", - "start": 4063, - 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Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", + "start": 3706, + "end": 3897, + "loc": { + "start": { + "line": 103, + "column": 2 + }, + "end": { + "line": 108, + "column": 5 + } + } + } + ] + }, + { + "type": "ClassMethod", + "start": 3900, + "end": 4238, + "loc": { + "start": { + "line": 109, + "column": 2 + }, + "end": { + "line": 118, + "column": 3 + } + }, + "static": false, + "computed": false, + "key": { + "type": "Identifier", + "start": 3904, + "end": 3915, + "loc": { + "start": { + "line": 109, + "column": 6 + }, + "end": { + "line": 109, + "column": 17 + }, + "identifierName": "accordingTo" + }, + "name": "accordingTo" + }, + "kind": "get", + "id": null, + "generator": false, + "expression": false, + "async": false, + "params": [], + "body": { + "type": "BlockStatement", + "start": 3918, + "end": 4238, + "loc": { + "start": { + "line": 109, + "column": 20 + }, + "end": { + "line": 118, + "column": 3 + } + }, + "body": [ + { + "type": "IfStatement", + "start": 3971, + "end": 4037, + "loc": { + "start": { + "line": 111, + "column": 4 + }, + "end": { + "line": 111, + "column": 70 + } + }, + "test": { + "type": "CallExpression", + "start": 3975, + "end": 4005, + "loc": { + "start": { + "line": 111, + "column": 8 + }, + "end": { + "line": 111, + "column": 38 + } + }, + "callee": { + "type": "Identifier", + "start": 3975, + "end": 3978, + "loc": { + "start": { + "line": 111, + "column": 8 + }, + "end": { + "line": 111, + "column": 11 + }, + "identifierName": "has" + }, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 3979, + "end": 3989, + "loc": { + "start": { + "line": 111, + "column": 12 + }, + "end": { + "line": 111, + "column": 22 + } + }, + "object": { + "type": "ThisExpression", + "start": 3979, + "end": 3983, + "loc": { + "start": { + "line": 111, + "column": 12 + }, + "end": { + "line": 111, + "column": 16 + } + } + }, + "property": { + "type": "Identifier", + "start": 3984, + "end": 3989, + "loc": { + "start": { + "line": 111, + "column": 17 + }, + "end": { + "line": 111, + "column": 22 + }, + "identifierName": "tunit" }, "name": "tunit" }, @@ -5039,119 +5114,119 @@ }, { "type": "StringLiteral", - "start": 4167, - "end": 4186, + "start": 3991, + "end": 4004, "loc": { "start": { - "line": 114, + "line": 111, "column": 24 }, "end": { - "line": 114, - "column": 43 + "line": 111, + "column": 37 } }, "extra": { - "rawValue": "accordingToString", - "raw": "'accordingToString'" + "rawValue": "accordingTo", + "raw": "'accordingTo'" }, - "value": "accordingToString" + "value": "accordingTo" } ], "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 4189, - "end": 4224, + "start": 4007, + "end": 4037, "loc": { "start": { - "line": 114, - "column": 46 + "line": 111, + "column": 40 }, "end": { - "line": 114, - "column": 81 + "line": 111, + "column": 70 } }, "argument": { "type": "MemberExpression", - "start": 4196, - "end": 4223, + "start": 4014, + "end": 4036, "loc": { "start": { - "line": 114, - "column": 53 + "line": 111, + "column": 47 }, "end": { - "line": 114, - "column": 80 + "line": 111, + "column": 69 } }, "object": { "type": "MemberExpression", - "start": 4196, - "end": 4205, + "start": 4014, + "end": 4024, "loc": { "start": { - "line": 114, - "column": 53 + "line": 111, + "column": 47 }, "end": { - "line": 114, - "column": 62 + "line": 111, + "column": 57 } }, "object": { "type": "ThisExpression", - "start": 4196, - "end": 4200, + "start": 4014, + "end": 4018, "loc": { "start": { - "line": 114, - "column": 53 + "line": 111, + "column": 47 }, "end": { - "line": 114, - "column": 57 + "line": 111, + "column": 51 } } }, "property": { "type": "Identifier", - "start": 4201, - "end": 4205, + "start": 4019, + "end": 4024, "loc": { "start": { - "line": 114, - "column": 58 + "line": 111, + "column": 52 }, "end": { - "line": 114, - "column": 62 + "line": 111, + "column": 57 }, - "identifierName": "type" + "identifierName": "tunit" }, - "name": "type" + "name": "tunit" }, "computed": false }, "property": { "type": "Identifier", - "start": 4206, - "end": 4223, + "start": 4025, + "end": 4036, "loc": { "start": { - "line": 114, - "column": 63 + "line": 111, + "column": 58 }, "end": { - "line": 114, - "column": 80 + "line": 111, + "column": 69 }, - "identifierName": "accordingToString" + "identifierName": "accordingTo" }, - "name": "accordingToString" + "name": "accordingTo" }, "computed": false }, @@ -5161,17 +5236,17 @@ "leadingComments": [ { "type": "CommentLine", - "value": " Do we have an accordingToString?", - "start": 4107, - "end": 4142, + "value": " Do we have any accordingTo information?", + "start": 3924, + "end": 3966, "loc": { "start": { - "line": 113, + "line": 110, "column": 4 }, "end": { - "line": 113, - "column": 39 + "line": 110, + "column": 46 } } } @@ -5179,40 +5254,293 @@ "trailingComments": [ { "type": "CommentLine", - "value": " If not, we have no accodingTo information!", - "start": 4230, - "end": 4275, + "value": " Do we have an accordingToString?", + "start": 4043, + "end": 4078, "loc": { "start": { - "line": 116, + "line": 113, "column": 4 }, "end": { - "line": 116, - "column": 49 + "line": 113, + "column": 39 } } } ] }, { - "type": "ReturnStatement", - "start": 4280, - "end": 4297, + "type": "IfStatement", + "start": 4083, + "end": 4161, "loc": { "start": { - "line": 117, + "line": 114, "column": 4 }, "end": { - "line": 117, - "column": 21 + "line": 114, + "column": 82 + } + }, + "test": { + "type": "CallExpression", + "start": 4087, + "end": 4123, + "loc": { + "start": { + "line": 114, + "column": 8 + }, + "end": { + "line": 114, + "column": 44 + } + }, + "callee": { + "type": "Identifier", + "start": 4087, + "end": 4090, + "loc": { + "start": { + "line": 114, + "column": 8 + }, + "end": { + "line": 114, + "column": 11 + }, + "identifierName": "has" + }, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 4091, + "end": 4101, + "loc": { + "start": { + "line": 114, + "column": 12 + }, + "end": { + "line": 114, + "column": 22 + } + }, + "object": { + "type": "ThisExpression", + "start": 4091, + "end": 4095, + "loc": { + "start": { + "line": 114, + "column": 12 + }, + "end": { + "line": 114, + "column": 16 + } + } + }, + "property": { + "type": "Identifier", + "start": 4096, + "end": 4101, + "loc": { + "start": { + "line": 114, + "column": 17 + }, + "end": { + "line": 114, + "column": 22 + }, + "identifierName": "tunit" + }, + "name": "tunit" + }, + "computed": false + }, + { + "type": "StringLiteral", + "start": 4103, + "end": 4122, + "loc": { + "start": { + "line": 114, + "column": 24 + }, + "end": { + "line": 114, + "column": 43 + } + }, + "extra": { + "rawValue": "accordingToString", + "raw": "'accordingToString'" + }, + "value": "accordingToString" + } + ], + "leadingComments": null + }, + "consequent": { + "type": "ReturnStatement", + "start": 4125, + "end": 4161, + "loc": { + "start": { + "line": 114, + "column": 46 + }, + "end": { + "line": 114, + "column": 82 + } + }, + "argument": { + "type": "MemberExpression", + "start": 4132, + "end": 4160, + "loc": { + "start": { + "line": 114, + "column": 53 + }, + "end": { + "line": 114, + "column": 81 + } + }, + "object": { + "type": "MemberExpression", + "start": 4132, + "end": 4142, + "loc": { + "start": { + "line": 114, + "column": 53 + }, + "end": { + "line": 114, + "column": 63 + } + }, + "object": { + "type": "ThisExpression", + "start": 4132, + "end": 4136, + "loc": { + "start": { + "line": 114, + "column": 53 + }, + "end": { + "line": 114, + "column": 57 + } + } + }, + "property": { + "type": "Identifier", + "start": 4137, + "end": 4142, + "loc": { + "start": { + "line": 114, + "column": 58 + }, + "end": { + "line": 114, + "column": 63 + }, + "identifierName": "tunit" + }, + "name": "tunit" + }, + "computed": false + }, + "property": { + "type": "Identifier", + "start": 4143, + "end": 4160, + "loc": { + "start": { + "line": 114, + "column": 64 + }, + "end": { + "line": 114, + "column": 81 + }, + "identifierName": "accordingToString" + }, + "name": "accordingToString" + }, + "computed": false + }, + "trailingComments": null + }, + "alternate": null, + "leadingComments": [ + { + "type": "CommentLine", + "value": " Do we have an accordingToString?", + "start": 4043, + "end": 4078, + "loc": { + "start": { + "line": 113, + "column": 4 + }, + "end": { + "line": 113, + "column": 39 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentLine", + "value": " If not, we have no accodingTo information!", + "start": 4167, + "end": 4212, + "loc": { + "start": { + "line": 116, + "column": 4 + }, + "end": { + "line": 116, + "column": 49 + } + } + } + ] + }, + { + "type": "ReturnStatement", + "start": 4217, + "end": 4234, + "loc": { + "start": { + "line": 117, + "column": 4 + }, + "end": { + "line": 117, + "column": 21 } }, "argument": { "type": "Identifier", - "start": 4287, - "end": 4296, + "start": 4224, + "end": 4233, "loc": { "start": { "line": 117, @@ -5231,8 +5559,8 @@ { "type": "CommentLine", "value": " If not, we have no accodingTo information!", - "start": 4230, - "end": 4275, + "start": 4167, + "end": 4212, "loc": { "start": { "line": 116, @@ -5253,9 +5581,9 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", - "start": 3708, - "end": 3940, + "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", + "start": 3706, + "end": 3897, "loc": { "start": { "line": 103, @@ -5271,16 +5599,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the label of this taxon concept.\n ", - "start": 4305, - "end": 4359, + "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", + "start": 4242, + "end": 4474, "loc": { "start": { "line": 120, "column": 2 }, "end": { - "line": 122, + "line": 125, "column": 5 } } @@ -5289,11 +5617,11 @@ }, { "type": "ClassMethod", - "start": 4362, - "end": 4781, + "start": 4477, + "end": 4837, "loc": { "start": { - "line": 123, + "line": 126, "column": 2 }, "end": { @@ -5305,20 +5633,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 4366, - "end": 4371, + "start": 4481, + "end": 4498, "loc": { "start": { - "line": 123, + "line": 126, "column": 6 }, "end": { - "line": 123, - "column": 11 + "line": 126, + "column": 23 }, - "identifierName": "label" + "identifierName": "accordingToString" }, - "name": "label" + "name": "accordingToString" }, "kind": "get", "id": null, @@ -5328,12 +5656,12 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4374, - "end": 4781, + "start": 4501, + "end": 4837, "loc": { "start": { - "line": 123, - 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"end": 2707, + "start": 2223, + "end": 2233, "loc": { "start": { - "line": 72, + "line": 61, "column": 12 }, "end": { - "line": 72, + "line": 61, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 2697, - "end": 2701, + "start": 2223, + "end": 2227, "loc": { "start": { - "line": 72, + "line": 61, "column": 12 }, "end": { - "line": 72, + "line": 61, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2702, - "end": 2707, + "start": 2228, + "end": 2233, "loc": { "start": { - "line": 72, + "line": 61, "column": 17 }, "end": { - "line": 72, + "line": 61, "column": 22 }, "identifierName": "tunit" @@ -10984,15 +11397,15 @@ }, { "type": "StringLiteral", - "start": 2709, - "end": 2718, + "start": 2235, + "end": 2244, "loc": { "start": { - "line": 72, + "line": 61, "column": 24 }, "end": { - "line": 72, + "line": 61, "column": 33 } }, @@ -11002,467 +11415,231 @@ }, "value": "hasName" } - ] + ], + "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 2721, - "end": 2810, + "start": 2247, + "end": 2273, "loc": { "start": { - "line": 72, + "line": 61, "column": 36 }, "end": { - "line": 72, - "column": 125 + "line": 61, + "column": 62 } }, "argument": { "type": "MemberExpression", - "start": 2728, - "end": 2809, + "start": 2254, + "end": 2272, "loc": { "start": { - "line": 72, + "line": 61, "column": 43 }, "end": { - "line": 72, - "column": 124 + "line": 61, + "column": 61 } }, "object": { - "type": "NewExpression", - "start": 2728, - "end": 2791, + "type": "MemberExpression", + "start": 2254, + "end": 2264, "loc": { "start": { - "line": 72, + "line": 61, "column": 43 }, "end": { - "line": 72, - "column": 106 + "line": 61, + "column": 53 } }, - "callee": { - "type": "Identifier", - "start": 2732, - "end": 2748, + "object": { + "type": "ThisExpression", + "start": 2254, + "end": 2258, "loc": { "start": { - "line": 72, - "column": 47 + "line": 61, + "column": 43 }, "end": { - "line": 72, - "column": 63 - }, - "identifierName": "TaxonNameWrapper" - }, - "name": "TaxonNameWrapper" + "line": 61, + "column": 47 + } + } }, - "arguments": [ - { - "type": "MemberExpression", - "start": 2749, - "end": 2767, - "loc": { - "start": { - "line": 72, - "column": 64 - }, - "end": { - "line": 72, - "column": 82 - } - }, - "object": { - "type": "MemberExpression", - "start": 2749, - "end": 2759, - "loc": { - "start": { - "line": 72, - "column": 64 - }, - "end": { - "line": 72, - "column": 74 - } - }, - "object": { - "type": "ThisExpression", - "start": 2749, - "end": 2753, - "loc": { - "start": { - "line": 72, - "column": 64 - }, - "end": { - "line": 72, - "column": 68 - } - } - }, - "property": { - "type": "Identifier", - "start": 2754, - "end": 2759, - "loc": { - "start": { - "line": 72, - "column": 69 - }, - "end": { - "line": 72, - "column": 74 - }, - "identifierName": "tunit" - }, - "name": "tunit" - }, - "computed": false + "property": { + "type": "Identifier", + "start": 2259, + "end": 2264, + "loc": { + "start": { + "line": 61, + "column": 48 }, - "property": { - "type": "Identifier", - "start": 2760, - "end": 2767, - "loc": { - "start": { - "line": 72, - "column": 75 - }, - "end": { - "line": 72, - "column": 82 - }, - "identifierName": "hasName" - }, - "name": "hasName" + "end": { + "line": 61, + "column": 53 }, - "computed": false + "identifierName": "tunit" }, - { - "type": "MemberExpression", - "start": 2769, - "end": 2790, - "loc": { - "start": { - "line": 72, - "column": 84 - }, - "end": { - "line": 72, - "column": 105 - } - }, - "object": { - "type": "ThisExpression", - "start": 2769, - "end": 2773, - "loc": { - "start": { - "line": 72, - "column": 84 - }, - "end": { - "line": 72, - "column": 88 - } - } - }, - "property": { - "type": "Identifier", - "start": 2774, - "end": 2790, - "loc": { - "start": { - "line": 72, - "column": 89 - }, - "end": { - "line": 72, - "column": 105 - }, - "identifierName": "defaultNomenCode" - }, - "name": "defaultNomenCode" - }, - "computed": false - } - ] + "name": "tunit" + }, + "computed": false }, "property": { "type": "Identifier", - "start": 2792, - "end": 2809, + "start": 2265, + "end": 2272, "loc": { "start": { - "line": 72, - "column": 107 + "line": 61, + "column": 54 }, "end": { - "line": 72, - "column": 124 + "line": 61, + "column": 61 }, - "identifierName": "nomenclaturalCode" + "identifierName": "hasName" }, - "name": "nomenclaturalCode" + "name": "hasName" }, "computed": false - } - }, - "alternate": null - }, - { - "type": "ReturnStatement", - "start": 2816, - "end": 2845, - "loc": { - "start": { - "line": 74, - "column": 4 }, - "end": { - "line": 74, - "column": 33 - } + "trailingComments": null }, - "argument": { - "type": "MemberExpression", - "start": 2823, - "end": 2844, - "loc": { - "start": { - "line": 74, - "column": 11 - }, - "end": { - "line": 74, - "column": 32 - } - }, - "object": { - "type": "Identifier", - "start": 2823, - "end": 2831, + "alternate": null, + "leadingComments": [ + { + "type": "CommentLine", + "value": " Do we have any names as taxon name objects?", + "start": 2164, + "end": 2210, "loc": { "start": { - "line": 74, - "column": 11 + "line": 60, + "column": 4 }, "end": { - "line": 74, - "column": 19 - }, - "identifierName": "owlterms" - }, - "name": "owlterms" - }, - "property": { - "type": "Identifier", - "start": 2832, - "end": 2844, + "line": 60, + "column": 50 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentLine", + "value": " Do we have a nameString with a taxon name as string?", + "start": 2279, + "end": 2334, "loc": { "start": { - "line": 74, - "column": 20 + "line": 63, + "column": 4 }, "end": { - "line": 74, - "column": 32 - }, - "identifierName": "UNKNOWN_CODE" - }, - "name": "UNKNOWN_CODE" - }, - "computed": false - } - } - ], - "directives": [], - "trailingComments": null - }, - "leadingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", - "start": 2585, - "end": 2664, - "loc": { - "start": { - "line": 68, - "column": 2 - }, - "end": { - "line": 70, - "column": 5 - } - } - } - ], - "trailingComments": [ - { - "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", - "start": 2853, - "end": 2933, - "loc": { - "start": { - "line": 77, - "column": 2 - }, - "end": { - "line": 79, - "column": 5 - } - } - } - ] - }, - { - "type": "ClassMethod", - "start": 2936, - "end": 3170, - "loc": { - "start": { - "line": 80, - "column": 2 - }, - "end": { - "line": 84, - "column": 3 - } - }, - "static": false, - "computed": false, - "key": { - "type": "Identifier", - "start": 2940, - "end": 2956, - "loc": { - "start": { - "line": 80, - "column": 6 - }, - "end": { - "line": 80, - "column": 22 - }, - "identifierName": "nomenCodeDetails" - }, - "name": "nomenCodeDetails" - }, - "kind": "get", - "id": null, - "generator": false, - "expression": false, - "async": false, - "params": [], - "body": { - "type": "BlockStatement", - "start": 2959, - "end": 3170, - "loc": { - "start": { - "line": 80, - "column": 25 + "line": 63, + "column": 59 + } + } + } + ] }, - "end": { - "line": 84, - "column": 3 - } - }, - "body": [ { "type": "IfStatement", - "start": 2965, - "end": 3093, + "start": 2339, + "end": 2461, "loc": { "start": { - "line": 81, + "line": 64, "column": 4 }, "end": { - "line": 81, - "column": 132 + "line": 64, + "column": 126 } }, "test": { "type": "CallExpression", - "start": 2969, - "end": 2995, + "start": 2343, + "end": 2372, "loc": { "start": { - "line": 81, + "line": 64, "column": 8 }, "end": { - "line": 81, - "column": 34 + "line": 64, + "column": 37 } }, "callee": { "type": "Identifier", - "start": 2969, - "end": 2972, + "start": 2343, + "end": 2346, "loc": { "start": { - "line": 81, + "line": 64, "column": 8 }, "end": { - "line": 81, + "line": 64, "column": 11 }, "identifierName": "has" }, - "name": "has" + "name": "has", + "leadingComments": null }, "arguments": [ { "type": "MemberExpression", - "start": 2973, - "end": 2983, + "start": 2347, + "end": 2357, "loc": { "start": { - "line": 81, + "line": 64, "column": 12 }, "end": { - "line": 81, + "line": 64, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 2973, - "end": 2977, + "start": 2347, + "end": 2351, "loc": { "start": { - "line": 81, + "line": 64, "column": 12 }, "end": { - "line": 81, + "line": 64, "column": 16 } } }, "property": { "type": "Identifier", - "start": 2978, - "end": 2983, + "start": 2352, + "end": 2357, "loc": { "start": { - "line": 81, + "line": 64, "column": 17 }, "end": { - "line": 81, + "line": 64, "column": 22 }, "identifierName": "tunit" @@ -11473,370 +11650,327 @@ }, { "type": "StringLiteral", - "start": 2985, - "end": 2994, + "start": 2359, + "end": 2371, "loc": { "start": { - "line": 81, + "line": 64, "column": 24 }, "end": { - "line": 81, - "column": 33 + "line": 64, + "column": 36 } }, "extra": { - "rawValue": "hasName", - "raw": "'hasName'" + "rawValue": "nameString", + "raw": "'nameString'" }, - "value": "hasName" + "value": "nameString" } - ] + ], + "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 2997, - "end": 3093, + "start": 2374, + "end": 2461, "loc": { "start": { - "line": 81, - "column": 36 + "line": 64, + "column": 39 }, "end": { - "line": 81, - "column": 132 + "line": 64, + "column": 126 } }, "argument": { - "type": "MemberExpression", - "start": 3004, - "end": 3092, + "type": "CallExpression", + "start": 2381, + "end": 2460, "loc": { "start": { - "line": 81, - "column": 43 + "line": 64, + "column": 46 }, "end": { - "line": 81, - "column": 131 + "line": 64, + "column": 125 } }, - "object": { - "type": "NewExpression", - "start": 3004, - "end": 3067, + "callee": { + "type": "MemberExpression", + "start": 2381, + "end": 2414, "loc": { "start": { - "line": 81, - "column": 43 + "line": 64, + "column": 46 }, "end": { - "line": 81, - "column": 106 + "line": 64, + "column": 79 } }, - "callee": { + "object": { "type": "Identifier", - "start": 3008, - "end": 3024, + "start": 2381, + "end": 2397, "loc": { "start": { - "line": 81, - "column": 47 + "line": 64, + "column": 46 }, "end": { - "line": 81, - "column": 63 + "line": 64, + "column": 62 }, "identifierName": "TaxonNameWrapper" }, "name": "TaxonNameWrapper" }, - "arguments": [ - { - "type": "MemberExpression", - "start": 3025, - "end": 3043, - "loc": { - "start": { - "line": 81, - "column": 64 - }, - "end": { - "line": 81, - "column": 82 - } - }, - "object": { - "type": "MemberExpression", - "start": 3025, - "end": 3035, - "loc": { - "start": { - "line": 81, - "column": 64 - }, - "end": { - "line": 81, - "column": 74 - } - }, - "object": { - "type": "ThisExpression", - "start": 3025, - "end": 3029, - "loc": { - "start": { - "line": 81, - "column": 64 - }, - "end": { - "line": 81, - "column": 68 - } - } - }, - "property": { - "type": "Identifier", - "start": 3030, - "end": 3035, - "loc": { - "start": { - "line": 81, - "column": 69 - }, - "end": { - "line": 81, - "column": 74 - }, - "identifierName": "tunit" - }, - "name": "tunit" - }, - "computed": false + "property": { + "type": "Identifier", + "start": 2398, + "end": 2414, + "loc": { + "start": { + "line": 64, + "column": 63 }, - "property": { - "type": "Identifier", - "start": 3036, - "end": 3043, - "loc": { - "start": { - "line": 81, - "column": 75 - }, - "end": { - "line": 81, - "column": 82 - }, - "identifierName": "hasName" - }, - "name": "hasName" + "end": { + "line": 64, + "column": 79 }, - "computed": false + "identifierName": "fromVerbatimName" }, - { + "name": "fromVerbatimName" + }, + "computed": false + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 2415, + "end": 2436, + "loc": { + "start": { + "line": 64, + "column": 80 + }, + "end": { + "line": 64, + "column": 101 + } + }, + "object": { "type": "MemberExpression", - "start": 3045, - "end": 3066, + "start": 2415, + "end": 2425, "loc": { "start": { - "line": 81, - "column": 84 + "line": 64, + "column": 80 }, "end": { - "line": 81, - "column": 105 + "line": 64, + "column": 90 } }, "object": { "type": "ThisExpression", - "start": 3045, - "end": 3049, + "start": 2415, + "end": 2419, "loc": { "start": { - "line": 81, - "column": 84 + "line": 64, + "column": 80 }, "end": { - "line": 81, - "column": 88 + "line": 64, + "column": 84 } } }, "property": { "type": "Identifier", - "start": 3050, - "end": 3066, + "start": 2420, + "end": 2425, "loc": { "start": { - "line": 81, - "column": 89 + "line": 64, + "column": 85 }, "end": { - "line": 81, - "column": 105 + "line": 64, + "column": 90 }, - "identifierName": "defaultNomenCode" + "identifierName": "tunit" }, - "name": "defaultNomenCode" + "name": "tunit" }, "computed": false - } - ] - }, - "property": { - "type": "Identifier", - "start": 3068, - "end": 3092, - "loc": { - "start": { - "line": 81, - "column": 107 }, - "end": { - "line": 81, - "column": 131 + "property": { + "type": "Identifier", + "start": 2426, + "end": 2436, + "loc": { + "start": { + "line": 64, + "column": 91 + }, + "end": { + "line": 64, + "column": 101 + }, + "identifierName": "nameString" + }, + "name": "nameString" }, - "identifierName": "nomenclaturalCodeDetails" + "computed": false }, - "name": "nomenclaturalCodeDetails" - }, - "computed": false - } + { + "type": "MemberExpression", + "start": 2438, + "end": 2459, + "loc": { + "start": { + "line": 64, + "column": 103 + }, + "end": { + "line": 64, + "column": 124 + } + }, + "object": { + "type": "ThisExpression", + "start": 2438, + "end": 2442, + "loc": { + "start": { + "line": 64, + "column": 103 + }, + "end": { + "line": 64, + "column": 107 + } + } + }, + "property": { + "type": "Identifier", + "start": 2443, + "end": 2459, + "loc": { + "start": { + "line": 64, + "column": 108 + }, + "end": { + "line": 64, + "column": 124 + }, + "identifierName": "defaultNomenCode" + }, + "name": "defaultNomenCode" + }, + "computed": false + } + ] + }, + "trailingComments": null }, - "alternate": null + "alternate": null, + "leadingComments": [ + { + "type": "CommentLine", + "value": " Do we have a nameString with a taxon name as string?", + "start": 2279, + "end": 2334, + "loc": { + "start": { + "line": 63, + "column": 4 + }, + "end": { + "line": 63, + "column": 59 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentLine", + "value": " If not, we have no name!", + "start": 2467, + "end": 2494, + "loc": { + "start": { + "line": 66, + "column": 4 + }, + "end": { + "line": 66, + "column": 31 + } + } + } + ] }, { "type": "ReturnStatement", - "start": 3099, - "end": 3166, + "start": 2499, + "end": 2516, "loc": { "start": { - "line": 83, + "line": 67, "column": 4 }, "end": { - "line": 83, - "column": 71 + "line": 67, + "column": 21 } }, "argument": { - "type": "CallExpression", - "start": 3106, - "end": 3165, + "type": "Identifier", + "start": 2506, + "end": 2515, "loc": { "start": { - "line": 83, + "line": 67, "column": 11 }, "end": { - "line": 83, - "column": 70 - } + "line": 67, + "column": 20 + }, + "identifierName": "undefined" }, - "callee": { - "type": "MemberExpression", - "start": 3106, - "end": 3142, + "name": "undefined", + "leadingComments": null + }, + "leadingComments": [ + { + "type": "CommentLine", + "value": " If not, we have no name!", + "start": 2467, + "end": 2494, "loc": { "start": { - "line": 83, - "column": 11 + "line": 66, + "column": 4 }, "end": { - "line": 83, - "column": 47 + "line": 66, + "column": 31 } - }, - "object": { - "type": "Identifier", - "start": 3106, - "end": 3122, - "loc": { - "start": { - "line": 83, - "column": 11 - }, - "end": { - "line": 83, - "column": 27 - }, - "identifierName": "TaxonNameWrapper" - }, - "name": "TaxonNameWrapper" - }, - "property": { - "type": "Identifier", - "start": 3123, - "end": 3142, - "loc": { - "start": { - "line": 83, - "column": 28 - }, - "end": { - "line": 83, - "column": 47 - }, - "identifierName": "getNomenCodeDetails" - }, - "name": "getNomenCodeDetails" - }, - "computed": false - }, - "arguments": [ - { - "type": "MemberExpression", - "start": 3143, - "end": 3164, - "loc": { - "start": { - "line": 83, - "column": 48 - }, - "end": { - "line": 83, - "column": 69 - } - }, - "object": { - "type": "Identifier", - "start": 3143, - "end": 3151, - "loc": { - "start": { - "line": 83, - "column": 48 - }, - "end": { - "line": 83, - "column": 56 - }, - "identifierName": "owlterms" - }, - "name": "owlterms" - }, - "property": { - "type": "Identifier", - "start": 3152, - "end": 3164, - "loc": { - "start": { - "line": 83, - "column": 57 - }, - "end": { - "line": 83, - "column": 69 - }, - "identifierName": "UNKNOWN_CODE" - }, - "name": "UNKNOWN_CODE" - }, - "computed": false } - ] - } + } + ] } ], "directives": [], @@ -11845,16 +11979,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", - "start": 2853, - "end": 2933, + "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", + "start": 2058, + "end": 2139, "loc": { "start": { - "line": 77, + "line": 56, "column": 2 }, "end": { - "line": 79, + "line": 58, "column": 5 } } @@ -11863,16 +11997,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", - "start": 3174, - "end": 3365, + "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", + "start": 2524, + "end": 2658, "loc": { "start": { - "line": 86, + "line": 70, "column": 2 }, "end": { - "line": 91, + "line": 73, "column": 5 } } @@ -11881,15 +12015,15 @@ }, { "type": "ClassMethod", - "start": 3368, - "end": 3704, + "start": 2661, + "end": 3113, "loc": { "start": { - "line": 92, + "line": 74, "column": 2 }, "end": { - "line": 101, + "line": 83, "column": 3 } }, @@ -11897,20 +12031,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 3372, - "end": 3383, + "start": 2665, + "end": 2677, "loc": { "start": { - "line": 92, + "line": 74, "column": 6 }, "end": { - "line": 92, - "column": 17 + "line": 74, + "column": 18 }, - "identifierName": "accordingTo" + "identifierName": "nameComplete" }, - "name": "accordingTo" + "name": "nameComplete" }, "kind": "get", "id": null, @@ -11920,58 +12054,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3386, - "end": 3704, + "start": 2680, + "end": 3113, "loc": { "start": { - "line": 92, - "column": 20 + "line": 74, + "column": 21 }, "end": { - "line": 101, + "line": 83, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 3439, - "end": 3504, + "start": 2737, + "end": 2853, "loc": { "start": { - "line": 94, + "line": 76, "column": 4 }, "end": { - "line": 94, - "column": 69 + "line": 76, + "column": 120 } }, "test": { "type": "CallExpression", - "start": 3443, - "end": 3473, + "start": 2741, + "end": 2767, "loc": { "start": { - "line": 94, + "line": 76, "column": 8 }, "end": { - "line": 94, - "column": 38 + "line": 76, + "column": 34 } }, "callee": { "type": "Identifier", - "start": 3443, - "end": 3446, + "start": 2741, + "end": 2744, "loc": { "start": { - "line": 94, + "line": 76, "column": 8 }, "end": { - "line": 94, + "line": 76, "column": 11 }, "identifierName": "has" @@ -11982,44 +12116,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3447, - "end": 3457, + "start": 2745, + "end": 2755, "loc": { "start": { - "line": 94, + "line": 76, "column": 12 }, "end": { - "line": 94, + "line": 76, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3447, - "end": 3451, + "start": 2745, + "end": 2749, "loc": { "start": { - "line": 94, + "line": 76, "column": 12 }, "end": { - "line": 94, + "line": 76, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3452, - "end": 3457, + "start": 2750, + "end": 2755, "loc": { "start": { - "line": 94, + "line": 76, "column": 17 }, "end": { - "line": 94, + "line": 76, "column": 22 }, "identifierName": "tunit" @@ -12030,119 +12164,234 @@ }, { "type": "StringLiteral", - "start": 3459, - "end": 3472, + "start": 2757, + "end": 2766, "loc": { "start": { - "line": 94, + "line": 76, "column": 24 }, "end": { - "line": 94, - "column": 37 + "line": 76, + "column": 33 } }, "extra": { - "rawValue": "accordingTo", - "raw": "'accordingTo'" + "rawValue": "hasName", + "raw": "'hasName'" }, - "value": "accordingTo" + "value": "hasName" } ], "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 3475, - "end": 3504, + "start": 2769, + "end": 2853, "loc": { "start": { - "line": 94, - "column": 40 + "line": 76, + "column": 36 }, "end": { - "line": 94, - "column": 69 + "line": 76, + "column": 120 } }, "argument": { "type": "MemberExpression", - "start": 3482, - "end": 3503, + "start": 2776, + "end": 2852, "loc": { "start": { - "line": 94, - "column": 47 + "line": 76, + "column": 43 }, "end": { - "line": 94, - "column": 68 + "line": 76, + "column": 119 } }, "object": { - "type": "MemberExpression", - "start": 3482, - "end": 3491, + "type": "NewExpression", + "start": 2776, + "end": 2839, "loc": { "start": { - "line": 94, - "column": 47 + "line": 76, + "column": 43 }, "end": { - "line": 94, - "column": 56 + "line": 76, + "column": 106 } }, - "object": { - "type": "ThisExpression", - "start": 3482, - "end": 3486, + "callee": { + "type": "Identifier", + "start": 2780, + "end": 2796, "loc": { "start": { - "line": 94, + "line": 76, "column": 47 }, "end": { - "line": 94, - "column": 51 - } - } + "line": 76, + "column": 63 + }, + "identifierName": "TaxonNameWrapper" + }, + "name": "TaxonNameWrapper" }, - "property": { - "type": "Identifier", - "start": 3487, - "end": 3491, - "loc": { - "start": { - "line": 94, - "column": 52 + "arguments": [ + { + "type": "MemberExpression", + "start": 2797, + "end": 2815, + "loc": { + "start": { + "line": 76, + "column": 64 + }, + "end": { + "line": 76, + "column": 82 + } }, - "end": { - "line": 94, - "column": 56 + "object": { + "type": "MemberExpression", + "start": 2797, + "end": 2807, + "loc": { + "start": { + "line": 76, + "column": 64 + }, + "end": { + "line": 76, + "column": 74 + } + }, + "object": { + "type": "ThisExpression", + "start": 2797, + "end": 2801, + "loc": { + "start": { + "line": 76, + "column": 64 + }, + "end": { + "line": 76, + "column": 68 + } + } + }, + "property": { + "type": "Identifier", + "start": 2802, + "end": 2807, + "loc": { + "start": { + "line": 76, + "column": 69 + }, + "end": { + "line": 76, + "column": 74 + }, + "identifierName": "tunit" + }, + "name": "tunit" + }, + "computed": false + }, + "property": { + "type": "Identifier", + "start": 2808, + "end": 2815, + "loc": { + "start": { + "line": 76, + "column": 75 + }, + "end": { + "line": 76, + "column": 82 + }, + "identifierName": "hasName" + }, + "name": "hasName" }, - "identifierName": "type" + "computed": false }, - "name": "type" - }, - "computed": false + { + "type": "MemberExpression", + "start": 2817, + "end": 2838, + "loc": { + "start": { + "line": 76, + "column": 84 + }, + "end": { + "line": 76, + "column": 105 + } + }, + "object": { + "type": "ThisExpression", + "start": 2817, + "end": 2821, + "loc": { + "start": { + "line": 76, + "column": 84 + }, + "end": { + "line": 76, + "column": 88 + } + } + }, + "property": { + "type": "Identifier", + "start": 2822, + "end": 2838, + "loc": { + "start": { + "line": 76, + "column": 89 + }, + "end": { + "line": 76, + "column": 105 + }, + "identifierName": "defaultNomenCode" + }, + "name": "defaultNomenCode" + }, + "computed": false + } + ] }, "property": { "type": "Identifier", - "start": 3492, - "end": 3503, + "start": 2840, + "end": 2852, "loc": { "start": { - "line": 94, - "column": 57 + "line": 76, + "column": 107 }, "end": { - "line": 94, - "column": 68 + "line": 76, + "column": 119 }, - "identifierName": "accordingTo" + "identifierName": "nameComplete" }, - "name": "accordingTo" + "name": "nameComplete" }, "computed": false }, @@ -12152,17 +12401,17 @@ "leadingComments": [ { "type": "CommentLine", - "value": " Do we have any accordingTo information?", - "start": 3392, - "end": 3434, + "value": " Do we have any names as taxon name objects?", + "start": 2686, + "end": 2732, "loc": { "start": { - "line": 93, + "line": 75, "column": 4 }, "end": { - "line": 93, - "column": 46 + "line": 75, + "column": 50 } } } @@ -12170,17 +12419,17 @@ "trailingComments": [ { "type": "CommentLine", - "value": " Do we have an accordingToString?", - "start": 3510, - "end": 3545, + "value": " Do we have a nameString with a taxon name as string?", + "start": 2859, + "end": 2914, "loc": { "start": { - "line": 96, + "line": 78, "column": 4 }, "end": { - "line": 96, - "column": 39 + "line": 78, + "column": 59 } } } @@ -12188,43 +12437,43 @@ }, { "type": "IfStatement", - "start": 3550, - "end": 3627, + "start": 2919, + "end": 3054, "loc": { "start": { - "line": 97, + "line": 79, "column": 4 }, "end": { - "line": 97, - "column": 81 + "line": 79, + "column": 139 } }, "test": { "type": "CallExpression", - "start": 3554, - "end": 3590, + "start": 2923, + "end": 2952, "loc": { "start": { - "line": 97, + "line": 79, "column": 8 }, "end": { - "line": 97, - "column": 44 + "line": 79, + "column": 37 } }, "callee": { "type": "Identifier", - "start": 3554, - "end": 3557, + "start": 2923, + "end": 2926, "loc": { "start": { - "line": 97, + "line": 79, "column": 8 }, "end": { - "line": 97, + "line": 79, "column": 11 }, "identifierName": "has" @@ -12235,44 +12484,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3558, - "end": 3568, + "start": 2927, + "end": 2937, "loc": { "start": { - "line": 97, + "line": 79, "column": 12 }, "end": { - "line": 97, + "line": 79, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3558, - "end": 3562, + "start": 2927, + "end": 2931, "loc": { "start": { - "line": 97, + "line": 79, "column": 12 }, "end": { - "line": 97, + "line": 79, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3563, - "end": 3568, + "start": 2932, + "end": 2937, "loc": { "start": { - "line": 97, + "line": 79, "column": 17 }, "end": { - "line": 97, + "line": 79, "column": 22 }, "identifierName": "tunit" @@ -12283,119 +12532,267 @@ }, { "type": "StringLiteral", - "start": 3570, - "end": 3589, + "start": 2939, + "end": 2951, "loc": { "start": { - "line": 97, + "line": 79, "column": 24 }, "end": { - "line": 97, - "column": 43 + "line": 79, + "column": 36 } }, "extra": { - "rawValue": "accordingToString", - "raw": "'accordingToString'" + "rawValue": "nameString", + "raw": "'nameString'" }, - "value": "accordingToString" + "value": "nameString" } ], "leadingComments": null }, "consequent": { "type": "ReturnStatement", - "start": 3592, - "end": 3627, + "start": 2954, + "end": 3054, "loc": { "start": { - "line": 97, - "column": 46 + "line": 79, + "column": 39 }, "end": { - "line": 97, - "column": 81 + "line": 79, + "column": 139 } }, "argument": { "type": "MemberExpression", - "start": 3599, - "end": 3626, + "start": 2961, + "end": 3053, "loc": { "start": { - "line": 97, - "column": 53 + "line": 79, + "column": 46 }, "end": { - "line": 97, - "column": 80 + "line": 79, + "column": 138 } }, "object": { - "type": "MemberExpression", - "start": 3599, - "end": 3608, + "type": "CallExpression", + "start": 2961, + "end": 3040, "loc": { "start": { - "line": 97, - "column": 53 + "line": 79, + "column": 46 }, "end": { - "line": 97, - "column": 62 + "line": 79, + "column": 125 } }, - "object": { - "type": "ThisExpression", - "start": 3599, - "end": 3603, + "callee": { + "type": "MemberExpression", + "start": 2961, + "end": 2994, "loc": { "start": { - "line": 97, - "column": 53 + "line": 79, + "column": 46 }, "end": { - "line": 97, - "column": 57 + "line": 79, + "column": 79 } - } - }, - "property": { - "type": "Identifier", - "start": 3604, - "end": 3608, - "loc": { - "start": { - "line": 97, - "column": 58 - }, - "end": { - "line": 97, - "column": 62 + }, + "object": { + "type": "Identifier", + "start": 2961, + "end": 2977, + "loc": { + "start": { + "line": 79, + "column": 46 + }, + "end": { + "line": 79, + "column": 62 + }, + "identifierName": "TaxonNameWrapper" }, - "identifierName": "type" + "name": "TaxonNameWrapper" }, - "name": "type" + "property": { + "type": "Identifier", + "start": 2978, + "end": 2994, + "loc": { + "start": { + "line": 79, + "column": 63 + }, + "end": { + "line": 79, + "column": 79 + }, + "identifierName": "fromVerbatimName" + }, + "name": "fromVerbatimName" + }, + "computed": false }, - "computed": false + "arguments": [ + { + "type": "MemberExpression", + "start": 2995, + "end": 3016, + "loc": { + "start": { + "line": 79, + "column": 80 + }, + "end": { + "line": 79, + "column": 101 + } + }, + "object": { + "type": "MemberExpression", + "start": 2995, + "end": 3005, + "loc": { + "start": { + "line": 79, + "column": 80 + }, + "end": { + "line": 79, + "column": 90 + } + }, + "object": { + "type": "ThisExpression", + "start": 2995, + "end": 2999, + "loc": { + "start": { + "line": 79, + "column": 80 + }, + "end": { + "line": 79, + "column": 84 + } + } + }, + "property": { + "type": "Identifier", + "start": 3000, + "end": 3005, + "loc": { + "start": { + "line": 79, + "column": 85 + }, + "end": { + "line": 79, + "column": 90 + }, + "identifierName": "tunit" + }, + "name": "tunit" + }, + "computed": false + }, + "property": { + "type": "Identifier", + "start": 3006, + "end": 3016, + "loc": { + "start": { + "line": 79, + "column": 91 + }, + "end": { + "line": 79, + "column": 101 + }, + "identifierName": "nameString" + }, + "name": "nameString" + }, + "computed": false + }, + { + "type": "MemberExpression", + "start": 3018, + "end": 3039, + "loc": { + "start": { + "line": 79, + "column": 103 + }, + "end": { + "line": 79, + "column": 124 + } + }, + "object": { + "type": "ThisExpression", + "start": 3018, + "end": 3022, + "loc": { + "start": { + "line": 79, + "column": 103 + }, + "end": { + "line": 79, + "column": 107 + } + } + }, + "property": { + "type": "Identifier", + "start": 3023, + "end": 3039, + "loc": { + "start": { + "line": 79, + "column": 108 + }, + "end": { + "line": 79, + "column": 124 + }, + "identifierName": "defaultNomenCode" + }, + "name": "defaultNomenCode" + }, + "computed": false + } + ] }, "property": { "type": "Identifier", - "start": 3609, - "end": 3626, + "start": 3041, + "end": 3053, "loc": { "start": { - "line": 97, - "column": 63 + "line": 79, + "column": 126 }, "end": { - "line": 97, - "column": 80 + "line": 79, + "column": 138 }, - "identifierName": "accordingToString" + "identifierName": "nameComplete" }, - "name": "accordingToString" + "name": "nameComplete" }, "computed": false }, @@ -12405,17 +12802,17 @@ "leadingComments": [ { "type": "CommentLine", - "value": " Do we have an accordingToString?", - "start": 3510, - "end": 3545, + "value": " Do we have a nameString with a taxon name as string?", + "start": 2859, + "end": 2914, "loc": { "start": { - "line": 96, + "line": 78, "column": 4 }, "end": { - "line": 96, - "column": 39 + "line": 78, + "column": 59 } } } @@ -12423,17 +12820,17 @@ "trailingComments": [ { "type": "CommentLine", - "value": " If not, we have no accodingTo information!", - "start": 3633, - "end": 3678, + "value": " If not, we have no name!", + "start": 3060, + "end": 3087, "loc": { "start": { - "line": 99, + "line": 81, "column": 4 }, "end": { - "line": 99, - "column": 49 + "line": 81, + "column": 31 } } } @@ -12441,29 +12838,29 @@ }, { "type": "ReturnStatement", - "start": 3683, - "end": 3700, + "start": 3092, + "end": 3109, "loc": { "start": { - "line": 100, + "line": 82, "column": 4 }, "end": { - "line": 100, + "line": 82, "column": 21 } }, "argument": { "type": "Identifier", - "start": 3690, - "end": 3699, + "start": 3099, + "end": 3108, "loc": { "start": { - "line": 100, + "line": 82, "column": 11 }, "end": { - "line": 100, + "line": 82, "column": 20 }, "identifierName": "undefined" @@ -12474,17 +12871,17 @@ "leadingComments": [ { "type": "CommentLine", - "value": " If not, we have no accodingTo information!", - "start": 3633, - "end": 3678, + "value": " If not, we have no name!", + "start": 3060, + "end": 3087, "loc": { "start": { - "line": 99, + "line": 81, "column": 4 }, "end": { - "line": 99, - "column": 49 + "line": 81, + "column": 31 } } } @@ -12497,16 +12894,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", - "start": 3174, - "end": 3365, + "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", + "start": 2524, + "end": 2658, "loc": { "start": { - "line": 86, + "line": 70, "column": 2 }, "end": { - "line": 91, + "line": 73, "column": 5 } } @@ -12515,16 +12912,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", - "start": 3708, - "end": 3940, + "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", + "start": 3117, + "end": 3196, "loc": { "start": { - "line": 103, + "line": 85, "column": 2 }, "end": { - "line": 108, + "line": 87, "column": 5 } } @@ -12533,15 +12930,15 @@ }, { "type": "ClassMethod", - "start": 3943, - "end": 4301, + "start": 3199, + "end": 3381, "loc": { "start": { - "line": 109, + "line": 88, "column": 2 }, "end": { - "line": 118, + "line": 92, "column": 3 } }, @@ -12549,20 +12946,20 @@ "computed": false, "key": { "type": "Identifier", - "start": 3947, - "end": 3964, + "start": 3203, + "end": 3212, "loc": { "start": { - "line": 109, + "line": 88, "column": 6 }, "end": { - "line": 109, - "column": 23 + "line": 88, + "column": 15 }, - "identifierName": "accordingToString" + "identifierName": "nomenCode" }, - "name": "accordingToString" + "name": "nomenCode" }, "kind": "get", "id": null, @@ -12572,106 +12969,105 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3967, - "end": 4301, + "start": 3215, + "end": 3381, "loc": { "start": { - "line": 109, - "column": 26 + "line": 88, + "column": 18 }, "end": { - "line": 118, + "line": 92, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4020, - "end": 4101, + "start": 3221, + "end": 3342, "loc": { "start": { - "line": 111, + "line": 89, "column": 4 }, "end": { - "line": 111, - "column": 85 + "line": 89, + "column": 125 } }, "test": { "type": "CallExpression", - "start": 4024, - "end": 4054, + "start": 3225, + "end": 3251, "loc": { "start": { - "line": 111, + "line": 89, "column": 8 }, "end": { - "line": 111, - "column": 38 + "line": 89, + "column": 34 } }, "callee": { "type": "Identifier", - "start": 4024, - "end": 4027, + "start": 3225, + "end": 3228, "loc": { "start": { - "line": 111, + "line": 89, "column": 8 }, "end": { - "line": 111, + "line": 89, "column": 11 }, "identifierName": "has" }, - "name": "has", - "leadingComments": null + "name": "has" }, "arguments": [ { "type": "MemberExpression", - "start": 4028, - "end": 4038, + "start": 3229, + "end": 3239, "loc": { "start": { - "line": 111, + "line": 89, "column": 12 }, "end": { - "line": 111, + "line": 89, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 4028, - "end": 4032, + "start": 3229, + "end": 3233, "loc": { "start": { - "line": 111, + "line": 89, "column": 12 }, "end": { - "line": 111, + "line": 89, "column": 16 } } }, "property": { "type": "Identifier", - "start": 4033, - "end": 4038, + "start": 3234, + "end": 3239, "loc": { "start": { - "line": 111, + "line": 89, "column": 17 }, "end": { - "line": 111, + "line": 89, "column": 22 }, "identifierName": "tunit" @@ -12682,532 +13078,303 @@ }, { "type": "StringLiteral", - "start": 4040, - "end": 4053, + "start": 3241, + "end": 3250, "loc": { "start": { - "line": 111, + "line": 89, "column": 24 }, "end": { - "line": 111, - "column": 37 + "line": 89, + "column": 33 } }, "extra": { - "rawValue": "accordingTo", - "raw": "'accordingTo'" + "rawValue": "hasName", + "raw": "'hasName'" }, - 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Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", + "start": 3706, + "end": 3897, + "loc": { + "start": { + "line": 103, + "column": 2 + }, + "end": { + "line": 108, + "column": 5 + } + } + } + ], + "trailingComments": [ + { + "type": "CommentBlock", + "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", + "start": 4242, + "end": 4474, + "loc": { + "start": { + "line": 120, + "column": 2 + }, + "end": { + "line": 125, + "column": 5 + } + } + } + ] + }, + { + "type": "ClassMethod", + "start": 4477, + "end": 4837, + "loc": { + "start": { + "line": 126, + "column": 2 + }, + "end": { + "line": 135, + "column": 3 + } + }, + "static": false, + "computed": false, + "key": { + "type": "Identifier", + "start": 4481, + "end": 4498, + "loc": { + "start": { + "line": 126, + "column": 6 + }, + "end": { + "line": 126, + "column": 23 + }, + "identifierName": "accordingToString" + }, + "name": "accordingToString" + }, + "kind": "get", + "id": null, + "generator": false, + "expression": false, + "async": false, + "params": [], + "body": { + "type": "BlockStatement", + "start": 4501, + "end": 4837, + "loc": { + "start": { + "line": 126, + "column": 26 }, + "end": { + "line": 135, + "column": 3 + } + }, + "body": [ { "type": "IfStatement", - 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"line": 153, - "column": 20 + "line": 128, + "column": 62 }, "end": { - "line": 153, - "column": 28 + "line": 128, + "column": 72 } }, "object": { - "type": "Identifier", - "start": 5508, - "end": 5513, + "type": "ThisExpression", + "start": 4612, + "end": 4616, "loc": { "start": { - "line": 153, - "column": 20 + "line": 128, + "column": 62 }, "end": { - "line": 153, - "column": 25 - }, - "identifierName": "match" - }, - "name": "match" + "line": 128, + "column": 66 + } + } }, "property": { - "type": "NumericLiteral", - "start": 5514, - "end": 5515, + "type": "Identifier", + "start": 4617, + "end": 4622, "loc": { "start": { - "line": 153, - "column": 26 + "line": 128, + "column": 67 }, "end": { - "line": 153, - "column": 27 - } + "line": 128, + "column": 72 + }, + "identifierName": "tunit" }, - "extra": { - "rawValue": 2, - "raw": "2" + "name": "tunit" + }, + "computed": false + }, + "property": { + "type": "Identifier", + "start": 4623, + "end": 4634, + "loc": { + "start": { + "line": 128, + "column": 73 }, - 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If not, we will return undefined.", - "start": 5529, - "end": 5598, + "value": " Do we have any accordingTo information?", + "start": 4507, + "end": 4549, "loc": { "start": { - "line": 156, + "line": 127, "column": 4 }, "end": { - "line": 156, - "column": 73 + "line": 127, + "column": 46 } } } - ] - }, - { - "type": "VariableDeclaration", - "start": 5603, - "end": 5677, - "loc": { - "start": { - "line": 157, - "column": 4 - }, - "end": { - "line": 157, - "column": 78 - } - }, - "declarations": [ - { - "type": "VariableDeclarator", - "start": 5609, - "end": 5676, - "loc": { - "start": { - "line": 157, - "column": 10 - }, - "end": { - "line": 157, - "column": 77 - } - }, - "id": { - "type": "Identifier", - "start": 5609, - "end": 5618, - "loc": { - "start": { - "line": 157, - "column": 10 - }, - "end": { - "line": 157, - "column": 19 - }, - "identifierName": "taxonName" - }, - "name": "taxonName", - "leadingComments": null - }, - "init": { - "type": "CallExpression", - "start": 5621, - "end": 5676, - "loc": { - "start": { - "line": 157, - "column": 22 - }, - "end": { - "line": 157, - "column": 77 - } - }, - "callee": { - "type": "MemberExpression", - "start": 5621, - "end": 5654, - "loc": { - "start": { - "line": 157, - "column": 22 - }, - "end": { - "line": 157, - "column": 55 - } - }, - "object": { - "type": "Identifier", - "start": 5621, - "end": 5637, - "loc": { - "start": { - "line": 157, - "column": 22 - }, - "end": { - "line": 157, - "column": 38 - }, - "identifierName": "TaxonNameWrapper" - }, - "name": "TaxonNameWrapper" - }, - "property": { - "type": "Identifier", - "start": 5638, - "end": 5654, - "loc": { - "start": { - "line": 157, - "column": 39 - }, - "end": { - "line": 157, - "column": 55 - }, - "identifierName": "fromVerbatimName" - }, - "name": "fromVerbatimName" - }, - "computed": false - }, - "arguments": [ - { - "type": "Identifier", - "start": 5655, - "end": 5664, - "loc": { - "start": { - "line": 157, - "column": 56 - }, - "end": { - "line": 157, - "column": 65 - }, - "identifierName": "nodeLabel" - }, - "name": "nodeLabel" - }, - { - "type": "Identifier", - "start": 5666, - "end": 5675, - "loc": { - "start": { - "line": 157, - "column": 67 - }, - "end": { - "line": 157, - "column": 76 - }, - "identifierName": "nomenCode" - }, - "name": "nomenCode" - } - ] - }, - "leadingComments": null - } ], - "kind": "const", - "leadingComments": [ + "trailingComments": [ { "type": "CommentLine", - "value": " Can we parse it as a taxon name? If not, we will return undefined.", - "start": 5529, - "end": 5598, + "value": " Do we have an accordingToString?", + "start": 4642, + "end": 4677, "loc": { "start": { - "line": 156, + "line": 130, "column": 4 }, "end": { - "line": 156, - "column": 73 + "line": 130, + "column": 39 } } } @@ -15069,185 +15001,252 @@ }, { "type": "IfStatement", - "start": 5682, - "end": 5776, + "start": 4682, + "end": 4760, "loc": { "start": { - "line": 158, + "line": 131, "column": 4 }, "end": { - "line": 160, - "column": 5 + "line": 131, + "column": 82 } }, "test": { - "type": "Identifier", - "start": 5686, - "end": 5695, + "type": "CallExpression", + "start": 4686, + "end": 4722, "loc": { "start": { - "line": 158, + "line": 131, "column": 8 }, "end": { - "line": 158, - "column": 17 - }, - "identifierName": "taxonName" + "line": 131, + "column": 44 + } }, - "name": "taxonName" - }, - "consequent": { - "type": "BlockStatement", - "start": 5697, - "end": 5776, - "loc": { - "start": { - "line": 158, - "column": 19 + "callee": { + "type": "Identifier", + "start": 4686, + "end": 4689, + "loc": { + "start": { + "line": 131, + "column": 8 + }, + "end": { + "line": 131, + "column": 11 + }, + "identifierName": "has" }, - "end": { - "line": 160, - "column": 5 - } + "name": "has", + "leadingComments": null }, - "body": [ + "arguments": [ { - "type": "ReturnStatement", - "start": 5705, - "end": 5770, + "type": "MemberExpression", + "start": 4690, + "end": 4700, "loc": { "start": { - "line": 159, - "column": 6 + "line": 131, + "column": 12 }, "end": { - "line": 159, - "column": 71 + "line": 131, + "column": 22 } }, - "argument": { - "type": "CallExpression", - "start": 5712, - "end": 5769, + "object": { + "type": "ThisExpression", + "start": 4690, + "end": 4694, "loc": { "start": { - "line": 159, - "column": 13 + "line": 131, + "column": 12 }, "end": { - "line": 159, - "column": 70 + "line": 131, + "column": 16 } - }, - "callee": { - "type": "MemberExpression", - "start": 5712, - "end": 5745, - "loc": { - "start": { - "line": 159, - "column": 13 - }, - "end": { - "line": 159, - "column": 46 - } - }, - "object": { - "type": "Identifier", - "start": 5712, - "end": 5731, - "loc": { - "start": { - "line": 159, - "column": 13 - }, - "end": { - "line": 159, - "column": 32 - }, - "identifierName": "TaxonConceptWrapper" - }, - "name": "TaxonConceptWrapper" + } + }, + "property": { + "type": "Identifier", + "start": 4695, + "end": 4700, + "loc": { + "start": { + "line": 131, + "column": 17 }, - "property": { - "type": "Identifier", - "start": 5732, - "end": 5745, - "loc": { - "start": { - "line": 159, - "column": 33 - }, - "end": { - "line": 159, - "column": 46 - }, - "identifierName": "wrapTaxonName" - }, - "name": "wrapTaxonName" + "end": { + "line": 131, + "column": 22 }, - "computed": false + "identifierName": "tunit" }, - "arguments": [ - { - "type": "Identifier", - "start": 5746, - "end": 5755, - "loc": { - "start": { - "line": 159, - "column": 47 - }, - "end": { - "line": 159, - "column": 56 - }, - "identifierName": "taxonName" - }, - "name": "taxonName" - }, - { - "type": "Identifier", - "start": 5757, - "end": 5768, - "loc": { - "start": { - "line": 159, - "column": 58 - }, - "end": { - "line": 159, - 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"identifierName": "someValuesFrom" + }, + "name": "someValuesFrom" + }, + "value": { + "type": "MemberExpression", + "start": 7182, + "end": 7257, + "loc": { + "start": { + "line": 206, + "column": 22 + }, + "end": { + "line": 206, + "column": 97 + } + }, + "object": { + "type": "NewExpression", + "start": 7182, + "end": 7241, + "loc": { + "start": { + "line": 206, + "column": 22 + }, + "end": { + "line": 206, + "column": 81 + } + }, + "callee": { + "type": "Identifier", + "start": 7186, + "end": 7202, + "loc": { + "start": { + "line": 206, + "column": 26 + }, + "end": { + "line": 206, + "column": 42 + }, + "identifierName": "TaxonNameWrapper" + }, + "name": "TaxonNameWrapper" + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 7203, + "end": 7217, + "loc": { + "start": { + "line": 206, + "column": 43 + }, + "end": { + "line": 206, + "column": 57 + } + }, + "object": { + "type": "ThisExpression", + "start": 7203, + "end": 7207, + "loc": { + "start": { + "line": 206, + "column": 43 + }, + "end": { + "line": 206, + "column": 47 + } + } + }, + "property": { + "type": "Identifier", + "start": 7208, + "end": 7217, + "loc": { + "start": { + "line": 206, + "column": 48 + }, + "end": { + "line": 206, + "column": 57 + }, + "identifierName": "taxonName" + }, + "name": "taxonName" + }, + "computed": false + }, + { + "type": "MemberExpression", + "start": 7219, + "end": 7240, + "loc": { + "start": { + "line": 206, + "column": 59 + }, + "end": { + "line": 206, + "column": 80 + } + }, + "object": { + "type": "ThisExpression", + "start": 7219, + "end": 7223, + "loc": { + "start": { + "line": 206, + "column": 59 + }, + "end": { + "line": 206, + "column": 63 + } + } + }, + "property": { + "type": "Identifier", + "start": 7224, + "end": 7240, + "loc": { + "start": { + "line": 206, + "column": 64 + }, + "end": { + "line": 206, + "column": 80 + }, + "identifierName": "defaultNomenCode" + }, + "name": "defaultNomenCode" + }, + "computed": false + } + ] + }, + "property": { + "type": "Identifier", + "start": 7242, + "end": 7257, + "loc": { + "start": { + "line": 206, + "column": 82 + }, + "end": { + "line": 206, + "column": 97 + }, + "identifierName": "asOWLEquivClass" + }, + "name": "asOWLEquivClass" + }, + "computed": false + } + } + ] + } + } + ], + "directives": [] + }, + "leadingComments": [ + { + "type": "CommentBlock", + "value": "*\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n ", + "start": 6704, + "end": 6942, + "loc": { + "start": { + "line": 193, + "column": 2 + }, + "end": { + "line": 198, + "column": 5 + } + } + } + ] + } + ] + }, + "leadingComments": [ + { + "type": "CommentBlock", + "value": "*\n * The TaxonConceptWrapper wraps taxon concepts. These are taxonomic units with\n * a type of TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT. They are based on the\n * Taxon Concept ontology at https://github.com/tdwg/ontology/tree/master/ontology/voc.\n *\n * A taxon concept:\n * - SHOULD have a hasName property indicating the name this taxon refers to.\n * - MAY have accordingTo, describedBy or circumscribedBy to indicate how this\n * taxon concept should be circumscribed. If none of these are present,\n * this taxonomic unit will be considered a taxon rather than a taxon concept\n * (i.e. as a nominal taxon concept, as in https://github.com/darwin-sw/dsw/wiki/ClassTaxon).\n * - MAY have nameString and accordingToString properties. We will fall back\n * to these properties if hasName or accordingTo are missing.\n ", + "start": 316, + "end": 1159, + "loc": { + "start": { + "line": 12, + "column": 0 + }, + "end": { + "line": 25, + "column": 3 + } + } + } + ], + "__PseudoExport__": false, + "trailingComments": [] + }, + "specifiers": null, + "source": null, + "leadingComments": null + } + ], + "directives": [] + }, + "comments": [ + { + "type": "CommentBlock", + "value": "* Utility functions. ", + "start": 0, + "end": 25, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 25 + } + } + }, + { + "type": "CommentBlock", + "value": "* List of OWL/RDF terms we use. ", + "start": 100, + "end": 136, + "loc": { + "start": { + "line": 5, + "column": 0 + }, + "end": { + "line": 5, + "column": 36 + } + } + }, + { + "type": "CommentBlock", + "value": "* For parsing scientific names. ", + "start": 180, + "end": 216, + "loc": { + "start": { + "line": 8, + "column": 0 + }, + "end": { + "line": 8, + "column": 36 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The TaxonConceptWrapper wraps taxon concepts. These are taxonomic units with\n * a type of TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT. They are based on the\n * Taxon Concept ontology at https://github.com/tdwg/ontology/tree/master/ontology/voc.\n *\n * A taxon concept:\n * - SHOULD have a hasName property indicating the name this taxon refers to.\n * - MAY have accordingTo, describedBy or circumscribedBy to indicate how this\n * taxon concept should be circumscribed. If none of these are present,\n * this taxonomic unit will be considered a taxon rather than a taxon concept\n * (i.e. as a nominal taxon concept, as in https://github.com/darwin-sw/dsw/wiki/ClassTaxon).\n * - MAY have nameString and accordingToString properties. We will fall back\n * to these properties if hasName or accordingTo are missing.\n ", + "start": 316, + "end": 1159, + "loc": { + "start": { + "line": 12, + "column": 0 + }, + "end": { + "line": 25, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "* The @type of a taxon or taxon concept. ", + "start": 1191, + "end": 1236, + "loc": { + "start": { + "line": 28, + "column": 2 + }, + "end": { + "line": 28, + "column": 47 + } + } + }, + { + "type": "CommentBlock", + "value": "* Create a TaxonConceptWrapper around a taxon concept. ", + "start": 1324, + "end": 1383, + "loc": { + "start": { + "line": 33, + "column": 2 + }, + "end": { + "line": 33, + "column": 61 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Normalize the specified taxon concept.\n * @param tc A taxon concept to be normalized.\n ", + "start": 1526, + "end": 1628, + "loc": { + "start": { + "line": 39, + "column": 2 + }, + "end": { + "line": 42, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", + "start": 2058, + "end": 2139, + "loc": { + "start": { + "line": 56, + "column": 2 + }, + "end": { + "line": 58, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have any names as taxon name objects?", + "start": 2164, + "end": 2210, + "loc": { + "start": { + "line": 60, + "column": 4 + }, + "end": { + "line": 60, + "column": 50 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have a nameString with a taxon name as string?", + "start": 2279, + "end": 2334, + "loc": { + "start": { + "line": 63, + "column": 4 + }, + "end": { + "line": 63, + "column": 59 + } + } + }, + { + "type": "CommentLine", + "value": " If not, we have no name!", + "start": 2467, + "end": 2494, + "loc": { + "start": { + "line": 66, + "column": 4 + }, + "end": { + "line": 66, + "column": 31 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", + "start": 2524, + "end": 2658, + "loc": { + "start": { + "line": 70, + "column": 2 + }, + "end": { + "line": 73, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have any names as taxon name objects?", + "start": 2686, + "end": 2732, + "loc": { + "start": { + "line": 75, + "column": 4 + }, + "end": { + "line": 75, + "column": 50 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have a nameString with a taxon name as string?", + "start": 2859, + "end": 2914, + "loc": { + "start": { + "line": 78, + "column": 4 + }, + "end": { + "line": 78, + "column": 59 + } + } + }, + { + "type": "CommentLine", + "value": " If not, we have no name!", + "start": 3060, + "end": 3087, + "loc": { + "start": { + "line": 81, + "column": 4 + }, + "end": { + "line": 81, + "column": 31 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", + "start": 3117, + "end": 3196, + "loc": { + "start": { + "line": 85, + "column": 2 + }, + "end": { + "line": 87, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", + "start": 3385, + "end": 3465, + "loc": { + "start": { + "line": 94, + "column": 2 + }, + "end": { + "line": 96, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", + "start": 3706, + "end": 3897, + "loc": { + "start": { + "line": 103, + "column": 2 + }, + "end": { + "line": 108, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have any accordingTo information?", + "start": 3924, + "end": 3966, + "loc": { + "start": { + "line": 110, + "column": 4 + }, + "end": { + "line": 110, + "column": 46 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have an accordingToString?", + "start": 4043, + "end": 4078, + "loc": { + "start": { + "line": 113, + "column": 4 + }, + "end": { + "line": 113, + "column": 39 + } + } + }, + { + "type": "CommentLine", + "value": " If not, we have no accodingTo information!", + "start": 4167, + "end": 4212, + "loc": { + "start": { + "line": 116, + "column": 4 + }, + "end": { + "line": 116, + "column": 49 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", + "start": 4242, + "end": 4474, + "loc": { + "start": { + "line": 120, + "column": 2 + }, + "end": { + "line": 125, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have any accordingTo information?", + "start": 4507, + "end": 4549, + "loc": { + "start": { + "line": 127, + "column": 4 + }, + "end": { + "line": 127, + "column": 46 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have an accordingToString?", + "start": 4642, + "end": 4677, + "loc": { + "start": { + "line": 130, + "column": 4 + }, + "end": { + "line": 130, + "column": 39 + } + } + }, + { + "type": "CommentLine", + "value": " If not, we have no accodingTo information!", + "start": 4766, + "end": 4811, + "loc": { + "start": { + "line": 133, + "column": 4 + }, + "end": { + "line": 133, + "column": 49 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the label of this taxon concept.\n ", + "start": 4841, + "end": 4895, + "loc": { + "start": { + "line": 137, + "column": 2 + }, + "end": { + "line": 139, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " If we're wrapping a taxonName, use its label.", + "start": 4916, + "end": 4964, + "loc": { + "start": { + "line": 141, + "column": 4 + }, + "end": { + "line": 141, + "column": 52 + } + } + }, + { + "type": "CommentLine", + "value": " Do we also have accordingTo information?", + "start": 4997, + "end": 5040, + "loc": { + "start": { + "line": 143, + "column": 6 + }, + "end": { + "line": 143, + "column": 49 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Given a node label, attempt to parse it as a scientific name.\n *\n * Note that this is NOT memoized -- you should really be using\n * TaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\n * than calling this directly.\n *\n * @return A taxonomic unit that corresponds to this taxon concept.\n ", + "start": 5321, + "end": 5660, + "loc": { + "start": { + "line": 154, + "column": 2 + }, + "end": { + "line": 162, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Check if this label can be divided into a name and a sensu/sec component.", + "start": 5833, + "end": 5909, + "loc": { + "start": { + "line": 166, + "column": 4 + }, + "end": { + "line": 166, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " Can we parse it as a taxon name? If not, we will return undefined.", + "start": 6065, + "end": 6134, + "loc": { + "start": { + "line": 173, + "column": 4 + }, + "end": { + "line": 173, + "column": 73 + } + } + }, + { + "type": "CommentLine", + "value": " Couldn't parse it at all.", + "start": 6318, + "end": 6346, + "loc": { + "start": { + "line": 179, + "column": 4 + }, + "end": { + "line": 179, + "column": 32 + } + } + }, + { + "type": "CommentBlock", + "value": "* Wrap a taxon name with a particular TaxonName object and an accordingTo (string). ", + "start": 6376, + "end": 6464, + "loc": { + "start": { + "line": 183, + "column": 2 + }, + "end": { + "line": 183, + "column": 90 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n ", + "start": 6704, + "end": 6942, + "loc": { + "start": { + "line": 193, + "column": 2 + }, + "end": { + "line": 198, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Without a taxonomicName, we can't do anything.", + "start": 6973, + "end": 7022, + "loc": { + "start": { + "line": 200, + "column": 4 + }, + "end": { + "line": 200, + "column": 53 + } + } + } + ], + "tokens": [ + { + "type": "CommentBlock", + "value": "* Utility functions. ", + "start": 0, + "end": 25, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 25 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 26, + "end": 32, + "loc": { + "start": { + "line": 2, + "column": 0 + }, + "end": { + "line": 2, + "column": 6 + } + } + }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 33, + "end": 34, + "loc": { + "start": { + "line": 2, + "column": 7 + }, + "end": { + "line": 2, + "column": 8 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + 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", - "start": 1191, - "end": 1236, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1315, + "end": 1316, "loc": { "start": { - "line": 28, - "column": 2 + "line": 30, + "column": 42 }, "end": { - "line": 28, - "column": 47 + "line": 30, + "column": 43 } } }, { - "type": "CommentBlock", - "value": "* Create a TaxonConceptWrapper around a taxon concept. ", - "start": 1324, - "end": 1383, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1319, + "end": 1320, "loc": { "start": { - "line": 33, + "line": 31, "column": 2 }, "end": { - "line": 33, - "column": 61 + "line": 31, + "column": 3 } } }, { "type": "CommentBlock", - "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", - "start": 1526, - "end": 1607, + "value": "* Create a TaxonConceptWrapper around a taxon concept. 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"line": 53, - "column": 2 + "line": 34, + "column": 19 }, "end": { - "line": 56, - "column": 5 + "line": 34, + "column": 20 } } }, { - "type": "CommentLine", - "value": " Do we have any names as taxon name objects?", - "start": 2154, - "end": 2200, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "defaultNomenCode", + "start": 1405, + "end": 1421, "loc": { "start": { - "line": 58, - "column": 4 + "line": 34, + "column": 21 }, "end": { - "line": 58, - "column": 50 + "line": 34, + "column": 37 } } }, { - "type": "CommentLine", - "value": " Do we have a nameString with a taxon name as string?", - "start": 2327, - "end": 2382, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 1422, + "end": 1423, "loc": { "start": { - "line": 61, - "column": 4 + "line": 34, + "column": 38 }, "end": { - "line": 61, - "column": 59 + "line": 34, + "column": 39 } } }, { - "type": "CommentLine", - "value": " If not, we have no name!", - "start": 2528, - "end": 2555, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 1424, + "end": 1432, "loc": { "start": { - "line": 64, - "column": 4 + "line": 34, + "column": 40 }, "end": { - "line": 64, - "column": 31 + "line": 34, + "column": 48 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as a string.\n ", - "start": 2585, - "end": 2664, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1432, + "end": 1433, "loc": { "start": { - "line": 68, - "column": 2 + "line": 34, + "column": 48 }, "end": { - "line": 70, - "column": 5 + "line": 34, + "column": 49 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", - "start": 2853, - "end": 2933, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "UNKNOWN_CODE", + "start": 1433, + "end": 1445, "loc": { "start": { - "line": 77, - "column": 2 + "line": 34, + "column": 49 }, "end": { - "line": 79, - "column": 5 + "line": 34, + "column": 61 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", - "start": 3174, - "end": 3365, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1445, + "end": 1446, "loc": { "start": { - "line": 86, - "column": 2 + "line": 34, + "column": 61 }, "end": { - "line": 91, - "column": 5 + "line": 34, + "column": 62 } } }, { - "type": "CommentLine", - "value": " Do we have any accordingTo information?", - "start": 3392, - "end": 3434, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1447, + "end": 1448, "loc": { "start": { - "line": 93, - "column": 4 + "line": 34, + "column": 63 }, "end": { - "line": 93, - "column": 46 + "line": 34, + "column": 64 } } }, { - "type": "CommentLine", - "value": " Do we have an accordingToString?", - "start": 3510, - "end": 3545, + "type": { + "label": "this", + "keyword": "this", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "this", + "start": 1453, + "end": 1457, "loc": { "start": { - "line": 96, + "line": 35, "column": 4 }, "end": { - "line": 96, - "column": 39 + "line": 35, + "column": 8 } } }, { - "type": "CommentLine", - "value": " If not, we have no accodingTo information!", - "start": 3633, - "end": 3678, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1457, + "end": 1458, "loc": { "start": { - "line": 99, - "column": 4 + "line": 35, + "column": 8 }, "end": { - "line": 99, - "column": 49 + "line": 35, + "column": 9 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", - "start": 3708, - "end": 3940, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "tunit", + "start": 1458, + "end": 1463, "loc": { "start": { - "line": 103, - "column": 2 + "line": 35, + "column": 9 }, "end": { - "line": 108, - "column": 5 + "line": 35, + "column": 14 } } }, { - "type": "CommentLine", - "value": " Do we have any accordingTo information?", - "start": 3973, - "end": 4015, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 1464, + "end": 1465, "loc": { "start": { - "line": 110, - "column": 4 + "line": 35, + "column": 15 }, "end": { - "line": 110, - "column": 46 + "line": 35, + "column": 16 } } }, { - "type": "CommentLine", - "value": " Do we have an accordingToString?", - "start": 4107, - "end": 4142, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "tunit", + "start": 1466, + "end": 1471, "loc": { "start": { - "line": 113, - "column": 4 + "line": 35, + "column": 17 }, "end": { - "line": 113, - "column": 39 + "line": 35, + "column": 22 } } }, { - "type": "CommentLine", - "value": " If not, we have no accodingTo information!", - "start": 4230, - "end": 4275, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1471, + "end": 1472, "loc": { "start": { - "line": 116, - "column": 4 + "line": 35, + "column": 22 }, "end": { - "line": 116, - "column": 49 + "line": 35, + "column": 23 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the label of this taxon concept.\n ", - "start": 4305, - "end": 4359, + "type": { + "label": "this", + "keyword": "this", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "this", + "start": 1477, + "end": 1481, "loc": { "start": { - "line": 120, - "column": 2 + "line": 36, + "column": 4 }, "end": { - "line": 122, - "column": 5 + "line": 36, + "column": 8 } } }, { - "type": "CommentLine", - "value": " If we're wrapping a taxonName, use its label.", - "start": 4380, - "end": 4428, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1481, + "end": 1482, "loc": { "start": { - "line": 124, - "column": 4 + "line": 36, + "column": 8 }, "end": { - "line": 124, - "column": 52 + "line": 36, + "column": 9 } } }, { - "type": "CommentLine", - "value": " Do we also have accordingTo information?", - "start": 4461, - "end": 4504, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "defaultNomenCode", + "start": 1482, + "end": 1498, "loc": { "start": { - "line": 126, - "column": 6 + "line": 36, + "column": 9 }, "end": { - "line": 126, - "column": 49 + "line": 36, + "column": 25 } } }, { - "type": "CommentBlock", - "value": "*\n * Given a node label, attempt to parse it as a scientific name.\n *\n * Note that this is NOT memoized -- you should really be using\n * TaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\n * than calling this directly.\n *\n * @return A taxonomic unit that corresponds to this taxon concept.\n ", - "start": 4785, - "end": 5124, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 1499, + "end": 1500, "loc": { "start": { - "line": 137, - "column": 2 + "line": 36, + "column": 26 }, "end": { - "line": 145, - "column": 5 + "line": 36, + "column": 27 } } }, { - "type": "CommentLine", - "value": " Check if this label can be divided into a name and a sensu/sec component.", - "start": 5297, - "end": 5373, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "defaultNomenCode", + "start": 1501, + "end": 1517, "loc": { "start": { - "line": 149, - "column": 4 + "line": 36, + "column": 28 }, "end": { - "line": 149, - "column": 80 + "line": 36, + "column": 44 } } }, { - "type": "CommentLine", - "value": " Can we parse it as a taxon name? If not, we will return undefined.", - "start": 5529, - "end": 5598, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1517, + "end": 1518, "loc": { "start": { - "line": 156, - "column": 4 + "line": 36, + "column": 44 }, "end": { - "line": 156, - "column": 73 + "line": 36, + "column": 45 } } }, { - "type": "CommentLine", - "value": " Couldn't parse it at all.", - "start": 5782, - "end": 5810, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1521, + "end": 1522, "loc": { "start": { - "line": 162, - "column": 4 + "line": 37, + "column": 2 }, "end": { - "line": 162, - "column": 32 + "line": 37, + "column": 3 } } }, { "type": "CommentBlock", - "value": "* Wrap a taxon name with a particular TaxonName object and an accordingTo (string). ", - "start": 5840, - "end": 5928, + "value": "*\n * Normalize the specified taxon concept.\n * @param tc A taxon concept to be normalized.\n ", + "start": 1526, + "end": 1628, "loc": { "start": { - "line": 166, + "line": 39, "column": 2 }, "end": { - "line": 166, - "column": 90 + "line": 42, + "column": 5 } } }, { - "type": "CommentBlock", - "value": "*\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n ", - "start": 6168, - "end": 6406, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "static", + "start": 1631, + "end": 1637, "loc": { "start": { - "line": 176, + "line": 43, "column": 2 }, "end": { - "line": 181, - "column": 5 + "line": 43, + "column": 8 } } }, { - "type": "CommentLine", - "value": " Without a taxonomicName, we can't do anything.", - "start": 6437, - "end": 6486, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "normalize", + "start": 1638, + "end": 1647, "loc": { "start": { - "line": 183, - "column": 4 + "line": 43, + "column": 9 }, "end": { - "line": 183, - "column": 53 + "line": 43, + "column": 18 } } - } - ], - "tokens": [ + }, { - "type": "CommentBlock", - "value": "* Utility functions. ", - "start": 0, - "end": 25, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1647, + "end": 1648, "loc": { "start": { - "line": 1, - "column": 0 + "line": 43, + "column": 18 }, "end": { - "line": 1, - "column": 25 + "line": 43, + "column": 19 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -17035,54 +21204,51 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 26, - "end": 32, + "value": "tc", + "start": 1648, + "end": 1650, "loc": { "start": { - "line": 2, - "column": 0 + "line": 43, + "column": 19 }, "end": { - "line": 2, - "column": 6 + "line": 43, + "column": 21 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 33, - "end": 34, + "start": 1650, + "end": 1651, "loc": { "start": { - "line": 2, - "column": 7 + "line": 43, + "column": 21 }, "end": { - "line": 2, - "column": 8 + "line": 43, + "column": 22 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -17091,43 +21257,44 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 35, - "end": 37, + "start": 1652, + "end": 1653, "loc": { "start": { - "line": 2, - "column": 9 + "line": 43, + "column": 23 }, "end": { - "line": 2, - "column": 11 + "line": 43, + "column": 24 } } }, { "type": { - "label": "name", + "label": "const", + "keyword": "const", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H192AHWT0", - "start": 38, - "end": 51, + "value": "const", + "start": 1658, + "end": 1663, "loc": { "start": { - "line": 2, - "column": 12 + "line": 44, + "column": 4 }, "end": { - "line": 2, - "column": 25 + "line": 44, + "column": 9 } } }, @@ -17143,52 +21310,53 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 52, - "end": 56, + "value": "wrapped", + "start": 1664, + "end": 1671, "loc": { "start": { - "line": 2, - "column": 26 + "line": 44, + "column": 10 }, "end": { - "line": 2, - "column": 30 + "line": 44, + "column": 17 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": "=", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "lodash", - "start": 57, - "end": 65, + "value": "=", + "start": 1672, + "end": 1673, "loc": { "start": { - "line": 2, - "column": 31 + "line": 44, + "column": 18 }, "end": { - "line": 2, - "column": 39 + "line": 44, + "column": 19 } } }, { "type": { - "label": ";", + "label": "new", + "keyword": "new", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -17197,50 +21365,49 @@ "binop": null, "updateContext": null }, - "start": 65, - "end": 66, + "value": "new", + "start": 1674, + "end": 1677, "loc": { "start": { - "line": 2, - "column": 39 + "line": 44, + "column": 20 }, "end": { - "line": 2, - "column": 40 + "line": 44, + "column": 23 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 68, - "end": 73, + "value": "TaxonConceptWrapper", + "start": 1678, + "end": 1697, "loc": { "start": { - "line": 3, - "column": 0 + "line": 44, + "column": 24 }, "end": { - "line": 3, - "column": 5 + "line": 44, + "column": 43 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -17250,16 +21417,16 @@ "postfix": false, "binop": null }, - "start": 74, - "end": 75, + "start": 1697, + "end": 1698, "loc": { "start": { - "line": 3, - "column": 6 + "line": 44, + "column": 43 }, "end": { - "line": 3, - "column": 7 + "line": 44, + "column": 44 } } }, @@ -17275,23 +21442,23 @@ "postfix": false, "binop": null }, - "value": "has", - "start": 76, - "end": 79, + "value": "tc", + "start": 1698, + "end": 1700, "loc": { "start": { - "line": 3, - "column": 8 + "line": 44, + "column": 44 }, "end": { - "line": 3, - "column": 11 + "line": 44, + "column": 46 } } }, { "type": { - "label": "}", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -17301,43 +21468,70 @@ "postfix": false, "binop": null }, - "start": 80, - "end": 81, + "start": 1700, + "end": 1701, + "loc": { + "start": { + "line": 44, + "column": 46 + }, + "end": { + "line": 44, + "column": 47 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1701, + "end": 1702, "loc": { "start": { - "line": 3, - "column": 12 + "line": 44, + "column": 47 }, "end": { - "line": 3, - "column": 13 + "line": 44, + "column": 48 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": "const", + "keyword": "const", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 82, - "end": 83, + "value": "const", + "start": 1707, + "end": 1712, "loc": { "start": { - "line": 3, - "column": 14 + "line": 45, + "column": 4 }, "end": { - "line": 3, - "column": 15 + "line": 45, + "column": 9 } } }, @@ -17353,66 +21547,75 @@ "postfix": false, "binop": null }, - "value": "LKT4H192AHWT0", - "start": 84, - "end": 97, + "value": "normalizedTC", + "start": 1713, + "end": 1725, "loc": { "start": { - "line": 3, - "column": 16 + "line": 45, + "column": 10 }, "end": { - "line": 3, - "column": 29 + "line": 45, + "column": 22 } } }, { "type": { - "label": ";", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 97, - "end": 98, + "value": "=", + "start": 1726, + "end": 1727, "loc": { "start": { - "line": 3, - "column": 29 + "line": 45, + "column": 23 }, "end": { - "line": 3, - "column": 30 + "line": 45, + "column": 24 } } }, { - "type": "CommentBlock", - "value": "* List of OWL/RDF terms we use. ", - "start": 100, - "end": 136, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1728, + "end": 1729, "loc": { "start": { - "line": 5, - "column": 0 + "line": 45, + "column": 25 }, "end": { - "line": 5, - "column": 36 + "line": 45, + "column": 26 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -17423,43 +21626,43 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 137, - "end": 143, + "value": "@type", + "start": 1736, + "end": 1743, "loc": { "start": { - "line": 6, - "column": 0 + "line": 46, + "column": 6 }, "end": { - "line": 6, - "column": 6 + "line": 46, + "column": 13 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "owlterms", - "start": 144, - "end": 152, + "start": 1743, + "end": 1744, "loc": { "start": { - "line": 6, - "column": 7 + "line": 46, + "column": 13 }, "end": { - "line": 6, - "column": 15 + "line": 46, + "column": 14 } } }, @@ -17475,25 +21678,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 153, - "end": 157, + "value": "TaxonConceptWrapper", + "start": 1745, + "end": 1764, "loc": { "start": { - "line": 6, - "column": 16 + "line": 46, + "column": 15 }, "end": { - "line": 6, - "column": 20 + "line": 46, + "column": 34 } } }, { "type": { - "label": "string", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -17502,68 +21705,50 @@ "binop": null, "updateContext": null }, - "value": "../utils/owlterms", - "start": 158, - "end": 177, + "start": 1764, + "end": 1765, "loc": { "start": { - "line": 6, - "column": 21 + "line": 46, + "column": 34 }, "end": { - "line": 6, - "column": 40 + "line": 46, + "column": 35 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 177, - "end": 178, - "loc": { - "start": { - "line": 6, - "column": 40 - }, - "end": { - "line": 6, - "column": 41 - } - } - }, - { - "type": "CommentBlock", - "value": "* For parsing scientific names. ", - "start": 180, - "end": 216, + "value": "TYPE_TAXON_CONCEPT", + "start": 1765, + "end": 1783, "loc": { "start": { - "line": 8, - "column": 0 + "line": 46, + "column": 35 }, "end": { - "line": 8, - "column": 36 + "line": 46, + "column": 53 } } }, { "type": { - "label": "import", - "keyword": "import", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -17572,70 +21757,68 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 217, - "end": 223, + "start": 1783, + "end": 1784, "loc": { "start": { - "line": 9, - "column": 0 + "line": 46, + "column": 53 }, "end": { - "line": 9, - "column": 6 + "line": 46, + "column": 54 } } }, { "type": { - "label": "*", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 224, - "end": 225, + "value": "label", + "start": 1791, + "end": 1796, "loc": { "start": { - "line": 9, - "column": 7 + "line": 47, + "column": 6 }, "end": { - "line": 9, - "column": 8 + "line": 47, + "column": 11 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "as", - "start": 226, - "end": 228, + "start": 1796, + "end": 1797, "loc": { "start": { - "line": 9, - "column": 9 + "line": 47, + "column": 11 }, "end": { - "line": 9, - "column": 11 + "line": 47, + "column": 12 } } }, @@ -17651,49 +21834,49 @@ "postfix": false, "binop": null }, - "value": "LKT4H192JH5K0", - "start": 229, - "end": 242, + "value": "wrapped", + "start": 1798, + "end": 1805, "loc": { "start": { - "line": 9, - "column": 12 + "line": 47, + "column": 13 }, "end": { - "line": 9, - "column": 25 + "line": 47, + "column": 20 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "from", - "start": 243, - "end": 247, + "start": 1805, + "end": 1806, "loc": { "start": { - "line": 9, - "column": 26 + "line": 47, + "column": 20 }, "end": { - "line": 9, - "column": 30 + "line": 47, + "column": 21 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -17701,26 +21884,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "./TaxonNameWrapper", - "start": 248, - "end": 268, + "value": "label", + "start": 1806, + "end": 1811, "loc": { "start": { - "line": 9, - "column": 31 + "line": 47, + "column": 21 }, "end": { - "line": 9, - "column": 51 + "line": 47, + "column": 26 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -17731,69 +21913,68 @@ "binop": null, "updateContext": null }, - "start": 268, - "end": 269, + "start": 1811, + "end": 1812, "loc": { "start": { - "line": 9, - "column": 51 + "line": 47, + "column": 26 }, "end": { - "line": 9, - "column": 52 + "line": 47, + "column": 27 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 271, - "end": 276, + "value": "hasName", + "start": 1819, + "end": 1826, "loc": { "start": { - "line": 10, - "column": 0 + "line": 48, + "column": 6 }, "end": { - "line": 10, - "column": 5 + "line": 48, + "column": 13 } } }, { "type": { - "label": "{", + "label": ":", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 277, - "end": 278, + "start": 1826, + "end": 1827, "loc": { "start": { - "line": 10, - "column": 6 + "line": 48, + "column": 13 }, "end": { - "line": 10, - "column": 7 + "line": 48, + "column": 14 } } }, @@ -17810,22 +21991,22 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 279, - "end": 295, + "start": 1828, + "end": 1844, "loc": { "start": { - "line": 10, - "column": 8 + "line": 48, + "column": 15 }, "end": { - "line": 10, - "column": 24 + "line": 48, + "column": 31 } } }, { "type": { - "label": "}", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -17833,52 +22014,52 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 296, - "end": 297, + "start": 1844, + "end": 1845, "loc": { "start": { - "line": 10, - "column": 25 + "line": 48, + "column": 31 }, "end": { - "line": 10, - "column": 26 + "line": 48, + "column": 32 } } }, { "type": { - "label": "=", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 298, - "end": 299, + "value": "normalize", + "start": 1845, + "end": 1854, "loc": { "start": { - "line": 10, - "column": 27 + "line": 48, + "column": 32 }, "end": { - "line": 10, - "column": 28 + "line": 48, + "column": 41 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -17887,66 +22068,48 @@ "postfix": false, "binop": null }, - "value": "LKT4H192JH5K0", - "start": 300, - "end": 313, + "start": 1854, + "end": 1855, "loc": { "start": { - "line": 10, - "column": 29 + "line": 48, + "column": 41 }, "end": { - "line": 10, + "line": 48, "column": 42 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 313, - "end": 314, + "value": "wrapped", + "start": 1855, + "end": 1862, "loc": { "start": { - "line": 10, + "line": 48, "column": 42 }, "end": { - "line": 10, - "column": 43 - } - } - }, - { - "type": "CommentBlock", - "value": "*\n * The TaxonConceptWrapper wraps taxon concepts. These are taxonomic units with\n * a type of TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT. They are based on the\n * Taxon Concept ontology at https://github.com/tdwg/ontology/tree/master/ontology/voc.\n *\n * A taxon concept:\n * - SHOULD have a hasName property indicating the name this taxon refers to.\n * - MAY have accordingTo, describedBy or circumscribedBy to indicate how this\n * taxon concept should be circumscribed. If none of these are present,\n * this taxonomic unit will be considered a taxon rather than a taxon concept\n * (i.e. as a nominal taxon concept, as in https://github.com/darwin-sw/dsw/wiki/ClassTaxon).\n * - MAY have nameString and accordingToString properties. We will fall back\n * to these properties if hasName or accordingTo are missing.\n ", - "start": 316, - "end": 1159, - "loc": { - "start": { - "line": 12, - "column": 0 - }, - "end": { - "line": 25, - "column": 3 + "line": 48, + "column": 49 } } }, { "type": { - "label": "class", - "keyword": "class", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -17957,17 +22120,16 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 1161, - "end": 1166, + "start": 1862, + "end": 1863, "loc": { "start": { - "line": 27, - "column": 0 + "line": 48, + "column": 49 }, "end": { - "line": 27, - "column": 5 + "line": 48, + "column": 50 } } }, @@ -17983,25 +22145,25 @@ "postfix": false, "binop": null }, - "value": "TaxonConceptWrapper", - "start": 1167, - "end": 1186, + "value": "taxonName", + "start": 1863, + "end": 1872, "loc": { "start": { - "line": 27, - "column": 6 + "line": 48, + "column": 50 }, "end": { - "line": 27, - "column": 25 + "line": 48, + "column": 59 } } }, { "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, + "label": ")", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -18009,58 +22171,42 @@ "postfix": false, "binop": null }, - "start": 1187, - "end": 1188, - "loc": { - "start": { - "line": 27, - "column": 26 - }, - "end": { - "line": 27, - "column": 27 - } - } - }, - { - "type": "CommentBlock", - "value": "* The @type of a taxon or taxon concept. ", - "start": 1191, - "end": 1236, + "start": 1872, + "end": 1873, "loc": { "start": { - "line": 28, - "column": 2 + "line": 48, + "column": 59 }, "end": { - "line": 28, - "column": 47 + "line": 48, + "column": 60 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 1239, - "end": 1245, + "start": 1873, + "end": 1874, "loc": { "start": { - "line": 29, - "column": 2 + "line": 48, + "column": 60 }, "end": { - "line": 29, - "column": 8 + "line": 48, + "column": 61 } } }, @@ -18076,50 +22222,50 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 1246, - "end": 1249, + "value": "nameString", + "start": 1881, + "end": 1891, "loc": { "start": { - "line": 29, - "column": 9 + "line": 49, + "column": 6 }, "end": { - "line": 29, - "column": 12 + "line": 49, + "column": 16 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "TYPE_TAXON_CONCEPT", - "start": 1250, - "end": 1268, + "start": 1891, + "end": 1892, "loc": { "start": { - "line": 29, - "column": 13 + "line": 49, + "column": 16 }, "end": { - "line": 29, - "column": 31 + "line": 49, + "column": 17 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -18128,22 +22274,23 @@ "postfix": false, "binop": null }, - "start": 1268, - "end": 1269, + "value": "wrapped", + "start": 1893, + "end": 1900, "loc": { "start": { - "line": 29, - "column": 31 + "line": 49, + "column": 18 }, "end": { - "line": 29, - "column": 32 + "line": 49, + "column": 25 } } }, { "type": { - "label": ")", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -18151,25 +22298,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1269, - "end": 1270, + "start": 1900, + "end": 1901, "loc": { "start": { - "line": 29, - "column": 32 + "line": 49, + "column": 25 }, "end": { - "line": 29, - "column": 33 + "line": 49, + "column": 26 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -18178,24 +22326,24 @@ "postfix": false, "binop": null }, - "start": 1271, - "end": 1272, + "value": "taxonName", + "start": 1901, + "end": 1910, "loc": { "start": { - "line": 29, - "column": 34 + "line": 49, + "column": 26 }, "end": { - "line": 29, + "line": 49, "column": 35 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -18205,17 +22353,16 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 1277, - "end": 1283, + "start": 1910, + "end": 1911, "loc": { "start": { - "line": 30, - "column": 4 + "line": 49, + "column": 35 }, "end": { - "line": 30, - "column": 10 + "line": 49, + "column": 36 } } }, @@ -18231,24 +22378,24 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 1284, - "end": 1292, + "value": "nameComplete", + "start": 1911, + "end": 1923, "loc": { "start": { - "line": 30, - "column": 11 + "line": 49, + "column": 36 }, "end": { - "line": 30, - "column": 19 + "line": 49, + "column": 48 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -18258,16 +22405,16 @@ "binop": null, "updateContext": null }, - "start": 1292, - "end": 1293, + "start": 1923, + "end": 1924, "loc": { "start": { - "line": 30, - "column": 19 + "line": 49, + "column": 48 }, "end": { - "line": 30, - "column": 20 + "line": 49, + "column": 49 } } }, @@ -18283,23 +22430,23 @@ "postfix": false, "binop": null }, - "value": "TDWG_VOC_TAXON_CONCEPT", - "start": 1293, - "end": 1315, + "value": "accordingTo", + "start": 1931, + "end": 1942, "loc": { "start": { - "line": 30, - "column": 20 + "line": 50, + "column": 6 }, "end": { - "line": 30, - "column": 42 + "line": 50, + "column": 17 } } }, { "type": { - "label": ";", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -18310,24 +22457,24 @@ "binop": null, "updateContext": null }, - "start": 1315, - "end": 1316, + "start": 1942, + "end": 1943, "loc": { "start": { - "line": 30, - "column": 42 + "line": 50, + "column": 17 }, "end": { - "line": 30, - "column": 43 + "line": 50, + "column": 18 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -18335,32 +22482,43 @@ "postfix": false, "binop": null }, - "start": 1319, - "end": 1320, + "value": "wrapped", + "start": 1944, + "end": 1951, "loc": { "start": { - "line": 31, - "column": 2 + "line": 50, + "column": 19 }, "end": { - "line": 31, - "column": 3 + "line": 50, + "column": 26 } } }, { - "type": "CommentBlock", - "value": "* Create a TaxonConceptWrapper around a taxon concept. ", - "start": 1324, - "end": 1383, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1951, + "end": 1952, "loc": { "start": { - "line": 33, - "column": 2 + "line": 50, + "column": 26 }, "end": { - "line": 33, - "column": 61 + "line": 50, + "column": 27 } } }, @@ -18376,50 +22534,51 @@ "postfix": false, "binop": null }, - "value": "constructor", - "start": 1386, - "end": 1397, + "value": "accordingTo", + "start": 1952, + "end": 1963, "loc": { "start": { - "line": 34, - "column": 2 + "line": 50, + "column": 27 }, "end": { - "line": 34, - "column": 13 + "line": 50, + "column": 38 } } }, { "type": { - "label": "(", + "label": ",", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1397, - "end": 1398, + "start": 1963, + "end": 1964, "loc": { "start": { - "line": 34, - "column": 13 + "line": 50, + "column": 38 }, "end": { - "line": 34, - "column": 14 + "line": 50, + "column": 39 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -18427,23 +22586,22 @@ "postfix": false, "binop": null }, - "value": "tunit", - "start": 1398, - "end": 1403, + "start": 1969, + "end": 1970, "loc": { "start": { - "line": 34, - "column": 14 + "line": 51, + "column": 4 }, "end": { - "line": 34, - "column": 19 + "line": 51, + "column": 5 } } }, { "type": { - "label": ",", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -18454,75 +22612,75 @@ "binop": null, "updateContext": null }, - "start": 1403, - "end": 1404, + "start": 1970, + "end": 1971, "loc": { "start": { - "line": 34, - "column": 19 + "line": 51, + "column": 5 }, "end": { - "line": 34, - "column": 20 + "line": 51, + "column": 6 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "defaultNomenCode", - "start": 1405, - "end": 1421, + "value": "if", + "start": 1976, + "end": 1978, "loc": { "start": { - "line": 34, - "column": 21 + "line": 52, + "column": 4 }, "end": { - "line": 34, - "column": 37 + "line": 52, + "column": 6 } } }, { "type": { - "label": "=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 1422, - "end": 1423, + "start": 1979, + "end": 1980, "loc": { "start": { - "line": 34, - "column": 38 + "line": 52, + "column": 7 }, "end": { - "line": 34, - "column": 39 + "line": 52, + "column": 8 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -18530,45 +22688,48 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "owlterms", - "start": 1424, - "end": 1432, + "value": "@id", + "start": 1980, + "end": 1985, "loc": { "start": { - "line": 34, - "column": 40 + "line": 52, + "column": 8 }, "end": { - "line": 34, - "column": 48 + "line": 52, + "column": 13 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "in", + "keyword": "in", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 7, "updateContext": null }, - "start": 1432, - "end": 1433, + "value": "in", + "start": 1986, + "end": 1988, "loc": { "start": { - "line": 34, - "column": 48 + "line": 52, + "column": 14 }, "end": { - "line": 34, - "column": 49 + "line": 52, + "column": 16 } } }, @@ -18584,17 +22745,17 @@ "postfix": false, "binop": null }, - "value": "UNKNOWN_CODE", - "start": 1433, - "end": 1445, + "value": "tc", + "start": 1989, + "end": 1991, "loc": { "start": { - "line": 34, - "column": 49 + "line": 52, + "column": 17 }, "end": { - "line": 34, - "column": 61 + "line": 52, + "column": 19 } } }, @@ -18610,23 +22771,23 @@ "postfix": false, "binop": null }, - "start": 1445, - "end": 1446, + "start": 1991, + "end": 1992, "loc": { "start": { - "line": 34, - "column": 61 + "line": 52, + "column": 19 }, "end": { - "line": 34, - "column": 62 + "line": 52, + "column": 20 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -18635,24 +22796,24 @@ "postfix": false, "binop": null }, - "start": 1447, - "end": 1448, + "value": "normalizedTC", + "start": 1993, + "end": 2005, "loc": { "start": { - "line": 34, - "column": 63 + "line": 52, + "column": 21 }, "end": { - "line": 34, - "column": 64 + "line": 52, + "column": 33 } } }, { "type": { - "label": "this", - "keyword": "this", - "beforeExpr": false, + "label": "[", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -18662,25 +22823,24 @@ "binop": null, "updateContext": null }, - "value": "this", - "start": 1453, - "end": 1457, + "start": 2005, + "end": 2006, "loc": { "start": { - "line": 35, - "column": 4 + "line": 52, + "column": 33 }, "end": { - "line": 35, - "column": 8 + "line": 52, + "column": 34 } } }, { "type": { - "label": ".", + "label": "string", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -18689,42 +22849,43 @@ "binop": null, "updateContext": null }, - "start": 1457, - "end": 1458, + "value": "@id", + "start": 2006, + "end": 2011, "loc": { "start": { - "line": 35, - "column": 8 + "line": 52, + "column": 34 }, "end": { - "line": 35, - "column": 9 + "line": 52, + "column": 39 } } }, { "type": { - "label": "name", + "label": "]", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "tunit", - "start": 1458, - "end": 1463, + "start": 2011, + "end": 2012, "loc": { "start": { - "line": 35, - "column": 9 + "line": 52, + "column": 39 }, "end": { - "line": 35, - "column": 14 + "line": 52, + "column": 40 } } }, @@ -18742,16 +22903,16 @@ "updateContext": null }, "value": "=", - "start": 1464, - "end": 1465, + "start": 2013, + "end": 2014, "loc": { "start": { - "line": 35, - "column": 15 + "line": 52, + "column": 41 }, "end": { - "line": 35, - "column": 16 + "line": 52, + "column": 42 } } }, @@ -18767,25 +22928,25 @@ "postfix": false, "binop": null }, - "value": "tunit", - "start": 1466, - "end": 1471, + "value": "tc", + "start": 2015, + "end": 2017, "loc": { "start": { - "line": 35, - "column": 17 + "line": 52, + "column": 43 }, "end": { - "line": 35, - "column": 22 + "line": 52, + "column": 45 } } }, { "type": { - "label": ";", + "label": "[", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -18794,23 +22955,22 @@ "binop": null, "updateContext": null }, - "start": 1471, - "end": 1472, + "start": 2017, + "end": 2018, "loc": { "start": { - "line": 35, - "column": 22 + "line": 52, + "column": 45 }, "end": { - "line": 35, - "column": 23 + "line": 52, + "column": 46 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -18821,23 +22981,23 @@ "binop": null, "updateContext": null }, - "value": "this", - "start": 1477, - "end": 1481, + "value": "@id", + "start": 2018, + "end": 2023, "loc": { "start": { - "line": 36, - "column": 4 + "line": 52, + "column": 46 }, "end": { - "line": 36, - "column": 8 + "line": 52, + "column": 51 } } }, { "type": { - "label": ".", + "label": "]", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -18848,69 +23008,70 @@ "binop": null, "updateContext": null }, - "start": 1481, - "end": 1482, + "start": 2023, + "end": 2024, "loc": { "start": { - "line": 36, - "column": 8 + "line": 52, + "column": 51 }, "end": { - "line": 36, - "column": 9 + "line": 52, + "column": 52 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "defaultNomenCode", - "start": 1482, - "end": 1498, + "start": 2024, + "end": 2025, "loc": { "start": { - "line": 36, - "column": 9 + "line": 52, + "column": 52 }, "end": { - "line": 36, - "column": 25 + "line": 52, + "column": 53 } } }, { "type": { - "label": "=", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 1499, - "end": 1500, + "value": "return", + "start": 2030, + "end": 2036, "loc": { "start": { - "line": 36, - "column": 26 + "line": 53, + "column": 4 }, "end": { - "line": 36, - "column": 27 + "line": 53, + "column": 10 } } }, @@ -18926,17 +23087,17 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 1501, - "end": 1517, + "value": "normalizedTC", + "start": 2037, + "end": 2049, "loc": { "start": { - "line": 36, - "column": 28 + "line": 53, + "column": 11 }, "end": { - "line": 36, - "column": 44 + "line": 53, + "column": 23 } } }, @@ -18953,16 +23114,16 @@ "binop": null, "updateContext": null }, - "start": 1517, - "end": 1518, + "start": 2049, + "end": 2050, "loc": { "start": { - "line": 36, - "column": 44 + "line": 53, + "column": 23 }, "end": { - "line": 36, - "column": 45 + "line": 53, + "column": 24 } } }, @@ -18978,15 +23139,15 @@ "postfix": false, "binop": null }, - "start": 1521, - "end": 1522, + "start": 2053, + "end": 2054, "loc": { "start": { - "line": 37, + "line": 54, "column": 2 }, "end": { - "line": 37, + "line": 54, "column": 3 } } @@ -18994,15 +23155,15 @@ { "type": "CommentBlock", "value": "*\n * Return the taxon name of this taxon concept (if any) as an object.\n ", - "start": 1526, - "end": 1607, + "start": 2058, + "end": 2139, "loc": { "start": { - "line": 39, + "line": 56, "column": 2 }, "end": { - "line": 41, + "line": 58, "column": 5 } } @@ -19020,15 +23181,15 @@ "binop": null }, "value": "get", - "start": 1610, - "end": 1613, + "start": 2142, + "end": 2145, "loc": { "start": { - "line": 42, + "line": 59, "column": 2 }, "end": { - "line": 42, + "line": 59, "column": 5 } } @@ -19046,15 +23207,15 @@ "binop": null }, "value": "taxonName", - "start": 1614, - "end": 1623, + "start": 2146, + "end": 2155, "loc": { "start": { - "line": 42, + "line": 59, "column": 6 }, "end": { - "line": 42, + "line": 59, "column": 15 } } @@ -19071,15 +23232,15 @@ "postfix": false, "binop": null }, - "start": 1623, - "end": 1624, + "start": 2155, + "end": 2156, "loc": { "start": { - "line": 42, + "line": 59, "column": 15 }, "end": { - "line": 42, + "line": 59, "column": 16 } } @@ -19096,15 +23257,15 @@ "postfix": false, "binop": null }, - "start": 1624, - "end": 1625, + "start": 2156, + "end": 2157, "loc": { "start": { - "line": 42, + "line": 59, "column": 16 }, "end": { - "line": 42, + "line": 59, "column": 17 } } @@ -19121,15 +23282,15 @@ "postfix": false, "binop": null }, - "start": 1626, - "end": 1627, + "start": 2158, + "end": 2159, "loc": { "start": { - "line": 42, + "line": 59, "column": 18 }, "end": { - "line": 42, + "line": 59, "column": 19 } } @@ -19137,15 +23298,15 @@ { "type": "CommentLine", "value": " Do we have any names as taxon name objects?", - "start": 1632, - "end": 1678, + "start": 2164, + "end": 2210, "loc": { "start": { - "line": 43, + "line": 60, "column": 4 }, "end": { - "line": 43, + "line": 60, "column": 50 } } @@ -19165,15 +23326,15 @@ "updateContext": null }, "value": "if", - "start": 1683, - "end": 1685, + "start": 2215, + "end": 2217, "loc": { "start": { - "line": 44, + "line": 61, "column": 4 }, "end": { - "line": 44, + "line": 61, "column": 6 } } @@ -19190,15 +23351,15 @@ "postfix": false, "binop": null }, - "start": 1686, - "end": 1687, + "start": 2218, + "end": 2219, "loc": { "start": { - "line": 44, + "line": 61, "column": 7 }, "end": { - "line": 44, + "line": 61, "column": 8 } } @@ -19216,15 +23377,15 @@ "binop": null }, "value": "has", - "start": 1687, - "end": 1690, + "start": 2219, + "end": 2222, "loc": { "start": { - "line": 44, + "line": 61, "column": 8 }, "end": { - "line": 44, + "line": 61, "column": 11 } } @@ -19241,15 +23402,15 @@ "postfix": false, "binop": null }, - "start": 1690, - "end": 1691, + "start": 2222, + "end": 2223, "loc": { "start": { - "line": 44, + "line": 61, "column": 11 }, "end": { - "line": 44, + "line": 61, "column": 12 } } @@ -19269,15 +23430,15 @@ "updateContext": null }, "value": "this", - "start": 1691, - "end": 1695, + "start": 2223, + "end": 2227, "loc": { "start": { - "line": 44, + "line": 61, "column": 12 }, "end": { - "line": 44, + "line": 61, "column": 16 } } @@ -19295,15 +23456,15 @@ "binop": null, "updateContext": null }, - "start": 1695, - "end": 1696, + "start": 2227, + "end": 2228, "loc": { "start": { - "line": 44, + "line": 61, "column": 16 }, "end": { - "line": 44, + "line": 61, "column": 17 } } @@ -19321,15 +23482,15 @@ "binop": null }, "value": "tunit", - "start": 1696, - "end": 1701, + "start": 2228, + "end": 2233, "loc": { "start": { - "line": 44, + "line": 61, "column": 17 }, "end": { - "line": 44, + "line": 61, "column": 22 } } @@ -19347,15 +23508,15 @@ "binop": null, "updateContext": null }, - "start": 1701, - "end": 1702, + "start": 2233, + "end": 2234, "loc": { "start": { - "line": 44, + "line": 61, "column": 22 }, "end": { - "line": 44, + "line": 61, "column": 23 } } @@ -19374,15 +23535,15 @@ "updateContext": null }, "value": "hasName", - "start": 1703, - "end": 1712, + "start": 2235, + "end": 2244, "loc": { "start": { - "line": 44, + "line": 61, "column": 24 }, "end": { - "line": 44, + "line": 61, "column": 33 } } @@ -19399,15 +23560,15 @@ "postfix": false, "binop": null }, - "start": 1712, - "end": 1713, + "start": 2244, + "end": 2245, "loc": { "start": { - "line": 44, + "line": 61, "column": 33 }, "end": { - "line": 44, + "line": 61, "column": 34 } } @@ -19424,15 +23585,15 @@ "postfix": false, "binop": null }, - "start": 1713, - "end": 1714, + "start": 2245, + "end": 2246, "loc": { "start": { - "line": 44, + "line": 61, "column": 34 }, "end": { - "line": 44, + "line": 61, "column": 35 } } @@ -19452,15 +23613,15 @@ "updateContext": null }, "value": "return", - "start": 1715, - "end": 1721, + "start": 2247, + "end": 2253, "loc": { "start": { - "line": 44, + "line": 61, "column": 36 }, "end": { - "line": 44, + "line": 61, "column": 42 } } @@ -19480,15 +23641,15 @@ "updateContext": null }, "value": "this", - "start": 1722, - "end": 1726, + "start": 2254, + "end": 2258, "loc": { "start": { - "line": 44, + "line": 61, "column": 43 }, "end": { - "line": 44, + "line": 61, "column": 47 } } @@ -19506,15 +23667,15 @@ "binop": null, "updateContext": null }, - "start": 1726, - "end": 1727, + "start": 2258, + "end": 2259, "loc": { "start": { - "line": 44, + "line": 61, "column": 47 }, "end": { - "line": 44, + "line": 61, "column": 48 } } @@ -19532,15 +23693,15 @@ "binop": null }, "value": "tunit", - "start": 1727, - "end": 1732, + "start": 2259, + "end": 2264, "loc": { "start": { - "line": 44, + "line": 61, "column": 48 }, "end": { - "line": 44, + "line": 61, "column": 53 } } @@ -19558,15 +23719,15 @@ "binop": null, "updateContext": null }, - "start": 1732, - "end": 1733, + "start": 2264, + "end": 2265, "loc": { "start": { - "line": 44, + "line": 61, "column": 53 }, "end": { - "line": 44, + "line": 61, "column": 54 } } @@ -19584,15 +23745,15 @@ "binop": null }, "value": "hasName", - "start": 1733, - "end": 1740, + "start": 2265, + "end": 2272, "loc": { "start": { - "line": 44, + "line": 61, "column": 54 }, "end": { - "line": 44, + "line": 61, "column": 61 } } @@ -19610,15 +23771,15 @@ "binop": null, "updateContext": null }, - "start": 1740, - "end": 1741, + "start": 2272, + "end": 2273, "loc": { "start": { - "line": 44, + "line": 61, "column": 61 }, "end": { - "line": 44, + "line": 61, "column": 62 } } @@ -19626,15 +23787,15 @@ { "type": "CommentLine", "value": " Do we have a nameString with a taxon name as string?", - "start": 1747, - "end": 1802, + "start": 2279, + "end": 2334, "loc": { "start": { - "line": 46, + "line": 63, "column": 4 }, "end": { - "line": 46, + "line": 63, "column": 59 } } @@ -19654,15 +23815,15 @@ "updateContext": null }, "value": "if", - "start": 1807, - "end": 1809, + "start": 2339, + "end": 2341, "loc": { "start": { - "line": 47, + "line": 64, "column": 4 }, "end": { - "line": 47, + "line": 64, "column": 6 } } @@ -19679,15 +23840,15 @@ "postfix": false, "binop": null }, - "start": 1810, - "end": 1811, + "start": 2342, + "end": 2343, "loc": { "start": { - "line": 47, + "line": 64, "column": 7 }, "end": { - "line": 47, + "line": 64, "column": 8 } } @@ -19705,15 +23866,15 @@ "binop": null }, "value": "has", - "start": 1811, - "end": 1814, + "start": 2343, + "end": 2346, "loc": { "start": { - "line": 47, + "line": 64, "column": 8 }, "end": { - "line": 47, + "line": 64, "column": 11 } } @@ -19730,15 +23891,15 @@ "postfix": false, "binop": null }, - "start": 1814, - "end": 1815, + "start": 2346, + "end": 2347, "loc": { "start": { - "line": 47, + "line": 64, "column": 11 }, "end": { - "line": 47, + "line": 64, "column": 12 } } @@ -19758,15 +23919,15 @@ "updateContext": null }, "value": "this", - "start": 1815, - "end": 1819, + "start": 2347, + "end": 2351, "loc": { "start": { - "line": 47, + "line": 64, "column": 12 }, "end": { - "line": 47, + "line": 64, "column": 16 } } @@ -19784,15 +23945,15 @@ "binop": null, "updateContext": null }, - "start": 1819, - "end": 1820, + "start": 2351, + "end": 2352, "loc": { "start": { - "line": 47, + "line": 64, "column": 16 }, "end": { - "line": 47, + "line": 64, "column": 17 } } @@ -19810,15 +23971,15 @@ "binop": null }, "value": "tunit", - "start": 1820, - "end": 1825, + "start": 2352, + "end": 2357, "loc": { "start": { - "line": 47, + "line": 64, "column": 17 }, "end": { - "line": 47, + "line": 64, "column": 22 } } @@ -19836,15 +23997,15 @@ "binop": null, "updateContext": null }, - "start": 1825, - "end": 1826, + "start": 2357, + "end": 2358, "loc": { "start": { - "line": 47, + "line": 64, "column": 22 }, "end": { - "line": 47, + "line": 64, "column": 23 } } @@ -19863,15 +24024,15 @@ "updateContext": null }, "value": "nameString", - "start": 1827, - "end": 1839, + "start": 2359, + "end": 2371, "loc": { "start": { - "line": 47, + "line": 64, "column": 24 }, "end": { - "line": 47, + "line": 64, "column": 36 } } @@ -19888,15 +24049,15 @@ "postfix": false, "binop": null }, - "start": 1839, - "end": 1840, + "start": 2371, + "end": 2372, "loc": { "start": { - "line": 47, + "line": 64, "column": 36 }, "end": { - "line": 47, + "line": 64, "column": 37 } } @@ -19913,15 +24074,15 @@ "postfix": false, "binop": null }, - "start": 1840, - "end": 1841, + "start": 2372, + "end": 2373, "loc": { "start": { - "line": 47, + "line": 64, "column": 37 }, "end": { - "line": 47, + "line": 64, "column": 38 } } @@ -19941,15 +24102,15 @@ "updateContext": null }, "value": "return", - "start": 1842, - "end": 1848, + "start": 2374, + "end": 2380, "loc": { "start": { - "line": 47, + "line": 64, "column": 39 }, "end": { - "line": 47, + "line": 64, "column": 45 } } @@ -19967,15 +24128,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 1849, - "end": 1865, + "start": 2381, + "end": 2397, "loc": { "start": { - "line": 47, + "line": 64, "column": 46 }, "end": { - "line": 47, + "line": 64, "column": 62 } } @@ -19993,15 +24154,15 @@ "binop": null, "updateContext": null }, - "start": 1865, - "end": 1866, + "start": 2397, + "end": 2398, "loc": { "start": { - "line": 47, + "line": 64, "column": 62 }, "end": { - "line": 47, + "line": 64, "column": 63 } } @@ -20019,15 +24180,15 @@ "binop": null }, "value": "fromVerbatimName", - "start": 1866, - "end": 1882, + "start": 2398, + "end": 2414, "loc": { "start": { - "line": 47, + "line": 64, "column": 63 }, "end": { - "line": 47, + "line": 64, "column": 79 } } @@ -20044,15 +24205,15 @@ "postfix": false, "binop": null }, - "start": 1882, - "end": 1883, + "start": 2414, + "end": 2415, "loc": { "start": { - "line": 47, + "line": 64, "column": 79 }, "end": { - "line": 47, + "line": 64, "column": 80 } } @@ -20072,15 +24233,15 @@ "updateContext": null }, "value": "this", - "start": 1883, - "end": 1887, + "start": 2415, + "end": 2419, "loc": { "start": { - "line": 47, + "line": 64, "column": 80 }, "end": { - "line": 47, + "line": 64, "column": 84 } } @@ -20098,15 +24259,15 @@ "binop": null, "updateContext": null }, - "start": 1887, - "end": 1888, + "start": 2419, + "end": 2420, "loc": { "start": { - "line": 47, + "line": 64, "column": 84 }, "end": { - "line": 47, + "line": 64, "column": 85 } } @@ -20124,15 +24285,15 @@ "binop": null }, "value": "tunit", - "start": 1888, - "end": 1893, + "start": 2420, + "end": 2425, "loc": { "start": { - "line": 47, + "line": 64, "column": 85 }, "end": { - "line": 47, + "line": 64, "column": 90 } } @@ -20150,15 +24311,15 @@ "binop": null, "updateContext": null }, - "start": 1893, - "end": 1894, + "start": 2425, + "end": 2426, "loc": { "start": { - "line": 47, + "line": 64, "column": 90 }, "end": { - "line": 47, + "line": 64, "column": 91 } } @@ -20176,15 +24337,15 @@ "binop": null }, "value": "nameString", - "start": 1894, - "end": 1904, + "start": 2426, + "end": 2436, "loc": { "start": { - "line": 47, + "line": 64, "column": 91 }, "end": { - "line": 47, + "line": 64, "column": 101 } } @@ -20202,15 +24363,15 @@ "binop": null, "updateContext": null }, - "start": 1904, - "end": 1905, + "start": 2436, + "end": 2437, "loc": { "start": { - "line": 47, + "line": 64, "column": 101 }, "end": { - "line": 47, + "line": 64, "column": 102 } } @@ -20230,15 +24391,15 @@ "updateContext": null }, "value": "this", - "start": 1906, - "end": 1910, + "start": 2438, + "end": 2442, "loc": { "start": { - "line": 47, + "line": 64, "column": 103 }, "end": { - "line": 47, + "line": 64, "column": 107 } } @@ -20256,15 +24417,15 @@ "binop": null, "updateContext": null }, - "start": 1910, - "end": 1911, + "start": 2442, + "end": 2443, "loc": { "start": { - "line": 47, + "line": 64, "column": 107 }, "end": { - "line": 47, + "line": 64, "column": 108 } } @@ -20282,15 +24443,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 1911, - "end": 1927, + "start": 2443, + "end": 2459, "loc": { "start": { - "line": 47, + "line": 64, "column": 108 }, "end": { - "line": 47, + "line": 64, "column": 124 } } @@ -20307,15 +24468,15 @@ "postfix": false, "binop": null }, - "start": 1927, - "end": 1928, + "start": 2459, + "end": 2460, "loc": { "start": { - "line": 47, + "line": 64, "column": 124 }, "end": { - "line": 47, + "line": 64, "column": 125 } } @@ -20333,15 +24494,15 @@ "binop": null, "updateContext": null }, - "start": 1928, - "end": 1929, + "start": 2460, + "end": 2461, "loc": { "start": { - "line": 47, + "line": 64, "column": 125 }, "end": { - "line": 47, + "line": 64, "column": 126 } } @@ -20349,15 +24510,15 @@ { "type": "CommentLine", "value": " If not, we have no name!", - "start": 1935, - "end": 1962, + "start": 2467, + "end": 2494, "loc": { "start": { - "line": 49, + "line": 66, "column": 4 }, "end": { - "line": 49, + "line": 66, "column": 31 } } @@ -20377,15 +24538,15 @@ "updateContext": null }, "value": "return", - "start": 1967, - "end": 1973, + "start": 2499, + "end": 2505, "loc": { "start": { - "line": 50, + "line": 67, "column": 4 }, "end": { - "line": 50, + "line": 67, "column": 10 } } @@ -20403,15 +24564,15 @@ "binop": null }, "value": "undefined", - "start": 1974, - "end": 1983, + "start": 2506, + "end": 2515, "loc": { "start": { - "line": 50, + "line": 67, "column": 11 }, "end": { - "line": 50, + "line": 67, "column": 20 } } @@ -20429,15 +24590,15 @@ "binop": null, "updateContext": null }, - "start": 1983, - "end": 1984, + "start": 2515, + "end": 2516, "loc": { "start": { - "line": 50, + "line": 67, "column": 20 }, "end": { - "line": 50, + "line": 67, "column": 21 } } @@ -20454,15 +24615,15 @@ "postfix": false, "binop": null }, - "start": 1987, - "end": 1988, + "start": 2519, + "end": 2520, "loc": { "start": { - "line": 51, + "line": 68, "column": 2 }, "end": { - "line": 51, + "line": 68, "column": 3 } } @@ -20470,15 +24631,15 @@ { "type": "CommentBlock", "value": "*\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n ", - "start": 1992, - "end": 2126, + "start": 2524, + "end": 2658, "loc": { "start": { - "line": 53, + "line": 70, "column": 2 }, "end": { - "line": 56, + "line": 73, "column": 5 } } @@ -20496,15 +24657,15 @@ "binop": null }, "value": "get", - "start": 2129, - "end": 2132, + "start": 2661, + "end": 2664, "loc": { "start": { - "line": 57, + "line": 74, "column": 2 }, "end": { - "line": 57, + "line": 74, "column": 5 } } @@ -20522,15 +24683,15 @@ "binop": null }, "value": "nameComplete", - "start": 2133, - "end": 2145, + "start": 2665, + "end": 2677, "loc": { "start": { - "line": 57, + "line": 74, "column": 6 }, "end": { - "line": 57, + "line": 74, "column": 18 } } @@ -20547,15 +24708,15 @@ "postfix": false, "binop": null }, - "start": 2145, - "end": 2146, + "start": 2677, + "end": 2678, "loc": { "start": { - "line": 57, + "line": 74, "column": 18 }, "end": { - "line": 57, + "line": 74, "column": 19 } } @@ -20572,15 +24733,15 @@ "postfix": false, "binop": null }, - "start": 2146, - "end": 2147, + "start": 2678, + "end": 2679, "loc": { "start": { - "line": 57, + "line": 74, "column": 19 }, "end": { - "line": 57, + "line": 74, "column": 20 } } @@ -20597,15 +24758,15 @@ "postfix": false, "binop": null }, - "start": 2148, - "end": 2149, + "start": 2680, + "end": 2681, "loc": { "start": { - "line": 57, + "line": 74, "column": 21 }, "end": { - "line": 57, + "line": 74, "column": 22 } } @@ -20613,15 +24774,15 @@ { "type": "CommentLine", "value": " Do we have any names as taxon name objects?", - "start": 2154, - "end": 2200, + "start": 2686, + "end": 2732, "loc": { "start": { - "line": 58, + "line": 75, "column": 4 }, "end": { - "line": 58, + "line": 75, "column": 50 } } @@ -20641,15 +24802,15 @@ "updateContext": null }, "value": "if", - "start": 2205, - "end": 2207, + "start": 2737, + "end": 2739, "loc": { "start": { - "line": 59, + "line": 76, "column": 4 }, "end": { - "line": 59, + "line": 76, "column": 6 } } @@ -20666,15 +24827,15 @@ "postfix": false, "binop": null }, - "start": 2208, - "end": 2209, + "start": 2740, + "end": 2741, "loc": { "start": { - "line": 59, + "line": 76, "column": 7 }, "end": { - "line": 59, + "line": 76, "column": 8 } } @@ -20692,15 +24853,15 @@ "binop": null }, "value": "has", - "start": 2209, - "end": 2212, + "start": 2741, + "end": 2744, "loc": { "start": { - "line": 59, + "line": 76, "column": 8 }, "end": { - "line": 59, + "line": 76, "column": 11 } } @@ -20717,15 +24878,15 @@ "postfix": false, "binop": null }, - "start": 2212, - "end": 2213, + "start": 2744, + "end": 2745, "loc": { "start": { - "line": 59, + "line": 76, "column": 11 }, "end": { - "line": 59, + "line": 76, "column": 12 } } @@ -20745,15 +24906,15 @@ "updateContext": null }, "value": "this", - "start": 2213, - "end": 2217, + "start": 2745, + "end": 2749, "loc": { "start": { - "line": 59, + "line": 76, "column": 12 }, "end": { - "line": 59, + "line": 76, "column": 16 } } @@ -20771,15 +24932,15 @@ "binop": null, "updateContext": null }, - "start": 2217, - "end": 2218, + "start": 2749, + "end": 2750, "loc": { "start": { - "line": 59, + "line": 76, "column": 16 }, "end": { - "line": 59, + "line": 76, "column": 17 } } @@ -20797,15 +24958,15 @@ "binop": null }, "value": "tunit", - "start": 2218, - "end": 2223, + "start": 2750, + "end": 2755, "loc": { "start": { - "line": 59, + "line": 76, "column": 17 }, "end": { - "line": 59, + "line": 76, "column": 22 } } @@ -20823,15 +24984,15 @@ "binop": null, "updateContext": null }, - "start": 2223, - "end": 2224, + "start": 2755, + "end": 2756, "loc": { "start": { - "line": 59, + "line": 76, "column": 22 }, "end": { - "line": 59, + "line": 76, "column": 23 } } @@ -20850,15 +25011,15 @@ "updateContext": null }, "value": "hasName", - "start": 2225, - "end": 2234, + "start": 2757, + "end": 2766, "loc": { "start": { - "line": 59, + "line": 76, "column": 24 }, "end": { - "line": 59, + "line": 76, "column": 33 } } @@ -20875,15 +25036,15 @@ "postfix": false, "binop": null }, - "start": 2234, - "end": 2235, + "start": 2766, + "end": 2767, "loc": { "start": { - "line": 59, + "line": 76, "column": 33 }, "end": { - "line": 59, + "line": 76, "column": 34 } } @@ -20900,15 +25061,15 @@ "postfix": false, "binop": null }, - "start": 2235, - "end": 2236, + "start": 2767, + "end": 2768, "loc": { "start": { - "line": 59, + "line": 76, "column": 34 }, "end": { - "line": 59, + "line": 76, "column": 35 } } @@ -20928,15 +25089,15 @@ "updateContext": null }, "value": "return", - "start": 2237, - "end": 2243, + "start": 2769, + "end": 2775, "loc": { "start": { - "line": 59, + "line": 76, "column": 36 }, "end": { - "line": 59, + "line": 76, "column": 42 } } @@ -20956,15 +25117,15 @@ "updateContext": null }, "value": "new", - "start": 2244, - "end": 2247, + "start": 2776, + "end": 2779, "loc": { "start": { - "line": 59, + "line": 76, "column": 43 }, "end": { - "line": 59, + "line": 76, "column": 46 } } @@ -20982,15 +25143,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 2248, - "end": 2264, + "start": 2780, + "end": 2796, "loc": { "start": { - "line": 59, + "line": 76, "column": 47 }, "end": { - "line": 59, + "line": 76, "column": 63 } } @@ -21007,15 +25168,15 @@ "postfix": false, "binop": null }, - "start": 2264, - "end": 2265, + "start": 2796, + "end": 2797, "loc": { "start": { - "line": 59, + "line": 76, "column": 63 }, "end": { - "line": 59, + "line": 76, "column": 64 } } @@ -21035,15 +25196,15 @@ "updateContext": null }, "value": "this", - "start": 2265, - "end": 2269, + "start": 2797, + "end": 2801, "loc": { "start": { - "line": 59, + "line": 76, "column": 64 }, "end": { - "line": 59, + "line": 76, "column": 68 } } @@ -21061,15 +25222,15 @@ "binop": null, "updateContext": null }, - "start": 2269, - "end": 2270, + "start": 2801, + "end": 2802, "loc": { "start": { - "line": 59, + "line": 76, "column": 68 }, "end": { - "line": 59, + "line": 76, "column": 69 } } @@ -21087,15 +25248,15 @@ "binop": null }, "value": "tunit", - "start": 2270, - "end": 2275, + "start": 2802, + "end": 2807, "loc": { "start": { - "line": 59, + "line": 76, "column": 69 }, "end": { - "line": 59, + "line": 76, "column": 74 } } @@ -21113,15 +25274,15 @@ "binop": null, "updateContext": null }, - "start": 2275, - "end": 2276, + "start": 2807, + "end": 2808, "loc": { "start": { - "line": 59, + "line": 76, "column": 74 }, "end": { - "line": 59, + "line": 76, "column": 75 } } @@ -21139,15 +25300,15 @@ "binop": null }, "value": "hasName", - "start": 2276, - "end": 2283, + "start": 2808, + "end": 2815, "loc": { "start": { - "line": 59, + "line": 76, "column": 75 }, "end": { - "line": 59, + "line": 76, "column": 82 } } @@ -21165,15 +25326,15 @@ "binop": null, "updateContext": null }, - "start": 2283, - "end": 2284, + "start": 2815, + "end": 2816, "loc": { "start": { - "line": 59, + "line": 76, "column": 82 }, "end": { - "line": 59, + "line": 76, "column": 83 } } @@ -21193,15 +25354,15 @@ "updateContext": null }, "value": "this", - "start": 2285, - "end": 2289, + "start": 2817, + "end": 2821, "loc": { "start": { - "line": 59, + "line": 76, "column": 84 }, "end": { - "line": 59, + "line": 76, "column": 88 } } @@ -21219,15 +25380,15 @@ "binop": null, "updateContext": null }, - "start": 2289, - "end": 2290, + "start": 2821, + "end": 2822, "loc": { "start": { - "line": 59, + "line": 76, "column": 88 }, "end": { - "line": 59, + "line": 76, "column": 89 } } @@ -21245,15 +25406,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 2290, - "end": 2306, + "start": 2822, + "end": 2838, "loc": { "start": { - "line": 59, + "line": 76, "column": 89 }, "end": { - "line": 59, + "line": 76, "column": 105 } } @@ -21270,15 +25431,15 @@ "postfix": false, "binop": null }, - "start": 2306, - "end": 2307, + "start": 2838, + "end": 2839, "loc": { "start": { - "line": 59, + "line": 76, "column": 105 }, "end": { - "line": 59, + "line": 76, "column": 106 } } @@ -21296,15 +25457,15 @@ "binop": null, "updateContext": null }, - "start": 2307, - "end": 2308, + "start": 2839, + "end": 2840, "loc": { "start": { - "line": 59, + "line": 76, "column": 106 }, "end": { - "line": 59, + "line": 76, "column": 107 } } @@ -21322,15 +25483,15 @@ "binop": null }, "value": "nameComplete", - "start": 2308, - "end": 2320, + "start": 2840, + "end": 2852, "loc": { "start": { - "line": 59, + "line": 76, "column": 107 }, "end": { - "line": 59, + "line": 76, "column": 119 } } @@ -21348,15 +25509,15 @@ "binop": null, "updateContext": null }, - "start": 2320, - "end": 2321, + "start": 2852, + "end": 2853, "loc": { "start": { - "line": 59, + "line": 76, "column": 119 }, "end": { - "line": 59, + "line": 76, "column": 120 } } @@ -21364,15 +25525,15 @@ { "type": "CommentLine", "value": " Do we have a nameString with a taxon name as string?", - "start": 2327, - "end": 2382, + "start": 2859, + "end": 2914, "loc": { "start": { - "line": 61, + "line": 78, "column": 4 }, "end": { - "line": 61, + "line": 78, "column": 59 } } @@ -21392,15 +25553,15 @@ "updateContext": null }, "value": "if", - "start": 2387, - "end": 2389, + "start": 2919, + "end": 2921, "loc": { "start": { - "line": 62, + "line": 79, "column": 4 }, "end": { - "line": 62, + "line": 79, "column": 6 } } @@ -21417,15 +25578,15 @@ "postfix": false, "binop": null }, - "start": 2390, - "end": 2391, + "start": 2922, + "end": 2923, "loc": { "start": { - "line": 62, + "line": 79, "column": 7 }, "end": { - "line": 62, + "line": 79, "column": 8 } } @@ -21443,15 +25604,15 @@ "binop": null }, "value": "has", - "start": 2391, - "end": 2394, + "start": 2923, + "end": 2926, "loc": { "start": { - "line": 62, + "line": 79, "column": 8 }, "end": { - "line": 62, + "line": 79, "column": 11 } } @@ -21468,15 +25629,15 @@ "postfix": false, "binop": null }, - "start": 2394, - "end": 2395, + "start": 2926, + "end": 2927, "loc": { "start": { - "line": 62, + "line": 79, "column": 11 }, "end": { - "line": 62, + "line": 79, "column": 12 } } @@ -21496,15 +25657,15 @@ "updateContext": null }, "value": "this", - "start": 2395, - "end": 2399, + "start": 2927, + "end": 2931, "loc": { "start": { - "line": 62, + "line": 79, "column": 12 }, "end": { - "line": 62, + "line": 79, "column": 16 } } @@ -21522,15 +25683,15 @@ "binop": null, "updateContext": null }, - "start": 2399, - "end": 2400, + "start": 2931, + "end": 2932, "loc": { "start": { - "line": 62, + "line": 79, "column": 16 }, "end": { - "line": 62, + "line": 79, "column": 17 } } @@ -21548,15 +25709,15 @@ "binop": null }, "value": "tunit", - "start": 2400, - "end": 2405, + "start": 2932, + "end": 2937, "loc": { "start": { - "line": 62, + "line": 79, "column": 17 }, "end": { - "line": 62, + "line": 79, "column": 22 } } @@ -21574,15 +25735,15 @@ "binop": null, "updateContext": null }, - "start": 2405, - "end": 2406, + "start": 2937, + "end": 2938, "loc": { "start": { - "line": 62, + "line": 79, "column": 22 }, "end": { - "line": 62, + "line": 79, "column": 23 } } @@ -21601,15 +25762,15 @@ "updateContext": null }, "value": "nameString", - "start": 2407, - "end": 2419, + "start": 2939, + "end": 2951, "loc": { "start": { - "line": 62, + "line": 79, "column": 24 }, "end": { - "line": 62, + "line": 79, "column": 36 } } @@ -21626,15 +25787,15 @@ "postfix": false, "binop": null }, - "start": 2419, - "end": 2420, + "start": 2951, + "end": 2952, "loc": { "start": { - "line": 62, + "line": 79, "column": 36 }, "end": { - "line": 62, + "line": 79, "column": 37 } } @@ -21651,15 +25812,15 @@ "postfix": false, "binop": null }, - "start": 2420, - "end": 2421, + "start": 2952, + "end": 2953, "loc": { "start": { - "line": 62, + "line": 79, "column": 37 }, "end": { - "line": 62, + "line": 79, "column": 38 } } @@ -21679,15 +25840,15 @@ "updateContext": null }, "value": "return", - "start": 2422, - "end": 2428, + "start": 2954, + "end": 2960, "loc": { "start": { - "line": 62, + "line": 79, "column": 39 }, "end": { - "line": 62, + "line": 79, "column": 45 } } @@ -21705,15 +25866,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 2429, - "end": 2445, + "start": 2961, + "end": 2977, "loc": { "start": { - "line": 62, + "line": 79, "column": 46 }, "end": { - "line": 62, + "line": 79, "column": 62 } } @@ -21731,15 +25892,15 @@ "binop": null, "updateContext": null }, - "start": 2445, - "end": 2446, + "start": 2977, + "end": 2978, "loc": { "start": { - "line": 62, + "line": 79, "column": 62 }, "end": { - "line": 62, + "line": 79, "column": 63 } } @@ -21757,15 +25918,15 @@ "binop": null }, "value": "fromVerbatimName", - "start": 2446, - "end": 2462, + "start": 2978, + "end": 2994, "loc": { "start": { - "line": 62, + "line": 79, "column": 63 }, "end": { - "line": 62, + "line": 79, "column": 79 } } @@ -21782,15 +25943,15 @@ "postfix": false, "binop": null }, - "start": 2462, - "end": 2463, + "start": 2994, + "end": 2995, "loc": { "start": { - "line": 62, + "line": 79, "column": 79 }, "end": { - "line": 62, + "line": 79, "column": 80 } } @@ -21810,15 +25971,15 @@ "updateContext": null }, "value": "this", - "start": 2463, - "end": 2467, + "start": 2995, + "end": 2999, "loc": { "start": { - "line": 62, + "line": 79, "column": 80 }, "end": { - 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"start": 2507, - "end": 2508, + "start": 3039, + "end": 3040, "loc": { "start": { - "line": 62, + "line": 79, "column": 124 }, "end": { - "line": 62, + "line": 79, "column": 125 } } @@ -22071,15 +26232,15 @@ "binop": null, "updateContext": null }, - "start": 2508, - "end": 2509, + "start": 3040, + "end": 3041, "loc": { "start": { - "line": 62, + "line": 79, "column": 125 }, "end": { - "line": 62, + "line": 79, "column": 126 } } @@ -22097,15 +26258,15 @@ "binop": null }, "value": "nameComplete", - "start": 2509, - "end": 2521, + "start": 3041, + "end": 3053, "loc": { "start": { - "line": 62, + "line": 79, "column": 126 }, "end": { - "line": 62, + "line": 79, "column": 138 } } @@ -22123,15 +26284,15 @@ "binop": null, "updateContext": null }, - "start": 2521, - "end": 2522, + "start": 3053, + "end": 3054, "loc": { "start": { - "line": 62, + "line": 79, "column": 138 }, "end": { - "line": 62, + "line": 79, "column": 139 } } @@ -22139,15 +26300,15 @@ { "type": "CommentLine", "value": " If not, we have no name!", - 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"line": 72, + "line": 89, "column": 7 }, "end": { - "line": 72, + "line": 89, "column": 8 } } @@ -22466,15 +26627,15 @@ "binop": null }, "value": "has", - "start": 2693, - "end": 2696, + "start": 3225, + "end": 3228, "loc": { "start": { - "line": 72, + "line": 89, "column": 8 }, "end": { - "line": 72, + "line": 89, "column": 11 } } @@ -22491,15 +26652,15 @@ "postfix": false, "binop": null }, - "start": 2696, - "end": 2697, + "start": 3228, + "end": 3229, "loc": { "start": { - "line": 72, + "line": 89, "column": 11 }, "end": { - "line": 72, + "line": 89, "column": 12 } } @@ -22519,15 +26680,15 @@ "updateContext": null }, "value": "this", - "start": 2697, - "end": 2701, + "start": 3229, + "end": 3233, "loc": { "start": { - "line": 72, + "line": 89, "column": 12 }, "end": { - "line": 72, + "line": 89, "column": 16 } } @@ -22545,15 +26706,15 @@ "binop": null, "updateContext": null }, - "start": 2701, - "end": 2702, + "start": 3233, + "end": 3234, "loc": { "start": { - "line": 72, + "line": 89, "column": 16 }, "end": { - 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"line": 72, + "line": 89, "column": 74 }, "end": { - "line": 72, + "line": 89, "column": 75 } } @@ -22913,15 +27074,15 @@ "binop": null }, "value": "hasName", - "start": 2760, - "end": 2767, + "start": 3292, + "end": 3299, "loc": { "start": { - "line": 72, + "line": 89, "column": 75 }, "end": { - "line": 72, + "line": 89, "column": 82 } } @@ -22939,15 +27100,15 @@ "binop": null, "updateContext": null }, - "start": 2767, - "end": 2768, + "start": 3299, + "end": 3300, "loc": { "start": { - "line": 72, + "line": 89, "column": 82 }, "end": { - "line": 72, + "line": 89, "column": 83 } } @@ -22967,15 +27128,15 @@ "updateContext": null }, "value": "this", - "start": 2769, - "end": 2773, + "start": 3301, + "end": 3305, "loc": { "start": { - "line": 72, + "line": 89, "column": 84 }, "end": { - "line": 72, + "line": 89, "column": 88 } } @@ -22993,15 +27154,15 @@ "binop": null, "updateContext": null }, - "start": 2773, - "end": 2774, + "start": 3305, + "end": 3306, "loc": { "start": { - "line": 72, + "line": 89, "column": 88 }, "end": { - "line": 72, + "line": 89, "column": 89 } } @@ -23019,15 +27180,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 2774, - "end": 2790, + "start": 3306, + "end": 3322, "loc": { "start": { - "line": 72, + "line": 89, "column": 89 }, "end": { - "line": 72, + "line": 89, "column": 105 } } @@ -23044,15 +27205,15 @@ "postfix": false, "binop": null }, - "start": 2790, - "end": 2791, + "start": 3322, + "end": 3323, "loc": { "start": { - "line": 72, + "line": 89, "column": 105 }, "end": { - "line": 72, + "line": 89, "column": 106 } } @@ -23070,15 +27231,15 @@ "binop": null, "updateContext": null }, - "start": 2791, - "end": 2792, + "start": 3323, + "end": 3324, "loc": { "start": { - "line": 72, + "line": 89, "column": 106 }, "end": { - "line": 72, + "line": 89, "column": 107 } } @@ -23096,15 +27257,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 2792, - "end": 2809, + "start": 3324, + "end": 3341, "loc": { "start": { - "line": 72, + "line": 89, "column": 107 }, "end": { - "line": 72, + "line": 89, "column": 124 } } @@ -23122,15 +27283,15 @@ "binop": null, "updateContext": null }, - "start": 2809, - "end": 2810, + "start": 3341, + "end": 3342, "loc": { "start": { - "line": 72, + "line": 89, "column": 124 }, "end": { - "line": 72, + "line": 89, "column": 125 } } @@ -23150,15 +27311,15 @@ "updateContext": null }, "value": "return", - "start": 2816, - "end": 2822, + "start": 3348, + "end": 3354, "loc": { "start": { - "line": 74, + "line": 91, "column": 4 }, "end": { - "line": 74, + "line": 91, "column": 10 } } @@ -23176,15 +27337,15 @@ "binop": null }, "value": "owlterms", - "start": 2823, - "end": 2831, + "start": 3355, + "end": 3363, "loc": { "start": { - "line": 74, + "line": 91, "column": 11 }, "end": { - "line": 74, + "line": 91, "column": 19 } } @@ -23202,15 +27363,15 @@ "binop": null, "updateContext": null }, - "start": 2831, - "end": 2832, + "start": 3363, + "end": 3364, "loc": { "start": { - "line": 74, + "line": 91, "column": 19 }, "end": { - "line": 74, + "line": 91, "column": 20 } } @@ -23228,15 +27389,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 2832, - "end": 2844, + "start": 3364, + "end": 3376, "loc": { "start": { - "line": 74, + "line": 91, "column": 20 }, "end": { - "line": 74, + "line": 91, "column": 32 } } @@ -23254,15 +27415,15 @@ "binop": null, "updateContext": null }, - "start": 2844, - "end": 2845, + "start": 3376, + "end": 3377, "loc": { "start": { - "line": 74, + "line": 91, "column": 32 }, "end": { - "line": 74, + "line": 91, "column": 33 } } @@ -23279,15 +27440,15 @@ "postfix": false, "binop": null }, - "start": 2848, - "end": 2849, + "start": 3380, + "end": 3381, "loc": { "start": { - "line": 75, + "line": 92, "column": 2 }, "end": { - "line": 75, + "line": 92, "column": 3 } } @@ -23295,15 +27456,15 @@ { "type": "CommentBlock", "value": "*\n * Return the nomenclatural code of this taxon concept as an object.\n ", - "start": 2853, - "end": 2933, + "start": 3385, + "end": 3465, "loc": { "start": { - "line": 77, + "line": 94, "column": 2 }, "end": { - "line": 79, + "line": 96, "column": 5 } } @@ -23321,15 +27482,15 @@ "binop": null }, "value": "get", - "start": 2936, - "end": 2939, + "start": 3468, + "end": 3471, "loc": { "start": { - "line": 80, + "line": 97, "column": 2 }, "end": { - "line": 80, + "line": 97, "column": 5 } } @@ -23347,15 +27508,15 @@ "binop": null }, "value": "nomenCodeDetails", - "start": 2940, - "end": 2956, + "start": 3472, + "end": 3488, "loc": { "start": { - "line": 80, + "line": 97, "column": 6 }, "end": { - "line": 80, + "line": 97, "column": 22 } } @@ -23372,15 +27533,15 @@ "postfix": false, "binop": null }, - "start": 2956, - "end": 2957, + "start": 3488, + "end": 3489, "loc": { "start": { - "line": 80, + "line": 97, "column": 22 }, "end": { - "line": 80, + "line": 97, "column": 23 } } @@ -23397,15 +27558,15 @@ "postfix": false, "binop": null }, - "start": 2957, - "end": 2958, + "start": 3489, + "end": 3490, "loc": { "start": { - "line": 80, + "line": 97, "column": 23 }, "end": { - "line": 80, + "line": 97, "column": 24 } } @@ -23422,15 +27583,15 @@ "postfix": false, "binop": null }, - "start": 2959, - "end": 2960, + "start": 3491, + "end": 3492, "loc": { "start": { - "line": 80, + "line": 97, "column": 25 }, "end": { - "line": 80, + "line": 97, "column": 26 } } @@ -23450,15 +27611,15 @@ "updateContext": null }, "value": "if", - "start": 2965, - "end": 2967, + "start": 3497, + "end": 3499, "loc": { "start": { - "line": 81, + "line": 98, "column": 4 }, "end": { - "line": 81, + "line": 98, "column": 6 } } @@ -23475,15 +27636,15 @@ "postfix": false, "binop": null }, - "start": 2968, - "end": 2969, + "start": 3500, + "end": 3501, "loc": { "start": { - "line": 81, + "line": 98, "column": 7 }, "end": { - "line": 81, + "line": 98, "column": 8 } } @@ -23501,15 +27662,15 @@ "binop": null }, "value": "has", - "start": 2969, - "end": 2972, + "start": 3501, + "end": 3504, "loc": { "start": { - "line": 81, + "line": 98, "column": 8 }, "end": { - "line": 81, + "line": 98, "column": 11 } } @@ -23526,15 +27687,15 @@ "postfix": false, "binop": null }, - "start": 2972, - "end": 2973, + "start": 3504, + "end": 3505, "loc": { "start": { - "line": 81, + "line": 98, "column": 11 }, "end": { - "line": 81, + "line": 98, "column": 12 } } @@ -23554,15 +27715,15 @@ "updateContext": null }, "value": "this", - "start": 2973, - "end": 2977, + "start": 3505, + "end": 3509, "loc": { "start": { - "line": 81, + "line": 98, "column": 12 }, "end": { - "line": 81, + "line": 98, "column": 16 } } @@ -23580,15 +27741,15 @@ "binop": null, "updateContext": null }, - "start": 2977, - "end": 2978, + "start": 3509, + "end": 3510, "loc": { "start": { - "line": 81, + "line": 98, "column": 16 }, "end": { - "line": 81, + "line": 98, "column": 17 } } @@ -23606,15 +27767,15 @@ "binop": null }, "value": "tunit", - "start": 2978, - "end": 2983, + "start": 3510, + "end": 3515, "loc": { "start": { - "line": 81, + "line": 98, "column": 17 }, "end": { - "line": 81, + "line": 98, "column": 22 } } @@ -23632,15 +27793,15 @@ "binop": null, "updateContext": null }, - "start": 2983, - "end": 2984, + "start": 3515, + "end": 3516, "loc": { "start": { - "line": 81, + "line": 98, "column": 22 }, "end": { - "line": 81, + "line": 98, "column": 23 } } @@ -23659,15 +27820,15 @@ "updateContext": null }, "value": "hasName", - "start": 2985, - "end": 2994, + "start": 3517, + "end": 3526, "loc": { "start": { - "line": 81, + "line": 98, "column": 24 }, "end": { - "line": 81, + "line": 98, "column": 33 } } @@ -23684,15 +27845,15 @@ "postfix": false, "binop": null }, - "start": 2994, - "end": 2995, + "start": 3526, + "end": 3527, "loc": { "start": { - "line": 81, + "line": 98, "column": 33 }, "end": { - "line": 81, + "line": 98, "column": 34 } } @@ -23709,15 +27870,15 @@ "postfix": false, "binop": null }, - "start": 2995, - "end": 2996, + "start": 3527, + "end": 3528, "loc": { "start": { - "line": 81, + "line": 98, "column": 34 }, "end": { - "line": 81, + "line": 98, "column": 35 } } @@ -23737,15 +27898,15 @@ "updateContext": null }, "value": "return", - "start": 2997, - "end": 3003, + "start": 3529, + "end": 3535, "loc": { "start": { - "line": 81, + "line": 98, "column": 36 }, "end": { - "line": 81, + "line": 98, "column": 42 } } @@ -23765,15 +27926,15 @@ "updateContext": null }, "value": "new", - "start": 3004, - "end": 3007, + "start": 3536, + "end": 3539, "loc": { "start": { - "line": 81, + "line": 98, "column": 43 }, "end": { - "line": 81, + "line": 98, "column": 46 } } @@ -23791,15 +27952,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 3008, - "end": 3024, + "start": 3540, + "end": 3556, "loc": { "start": { - "line": 81, + "line": 98, "column": 47 }, "end": { - "line": 81, + "line": 98, "column": 63 } } @@ -23816,15 +27977,15 @@ "postfix": false, "binop": null }, - "start": 3024, - "end": 3025, + "start": 3556, + "end": 3557, "loc": { "start": { - "line": 81, + "line": 98, "column": 63 }, "end": { - "line": 81, + "line": 98, "column": 64 } } @@ -23844,15 +28005,15 @@ "updateContext": null }, "value": "this", - "start": 3025, - "end": 3029, + "start": 3557, + "end": 3561, "loc": { "start": { - "line": 81, + "line": 98, "column": 64 }, "end": { - "line": 81, + "line": 98, "column": 68 } } @@ -23870,15 +28031,15 @@ "binop": null, "updateContext": null }, - "start": 3029, - "end": 3030, + "start": 3561, + "end": 3562, "loc": { "start": { - 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"line": 81, + "line": 98, "column": 83 } } @@ -24002,15 +28163,15 @@ "updateContext": null }, "value": "this", - "start": 3045, - "end": 3049, + "start": 3577, + "end": 3581, "loc": { "start": { - "line": 81, + "line": 98, "column": 84 }, "end": { - "line": 81, + "line": 98, "column": 88 } } @@ -24028,15 +28189,15 @@ "binop": null, "updateContext": null }, - "start": 3049, - "end": 3050, + "start": 3581, + "end": 3582, "loc": { "start": { - "line": 81, + "line": 98, "column": 88 }, "end": { - "line": 81, + "line": 98, "column": 89 } } @@ -24054,15 +28215,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 3050, - "end": 3066, + "start": 3582, + "end": 3598, "loc": { "start": { - "line": 81, + "line": 98, "column": 89 }, "end": { - "line": 81, + "line": 98, "column": 105 } } @@ -24079,15 +28240,15 @@ "postfix": false, "binop": null }, - "start": 3066, - "end": 3067, + "start": 3598, + "end": 3599, "loc": { "start": { - "line": 81, + "line": 98, "column": 105 }, "end": { - "line": 81, + "line": 98, "column": 106 } } @@ -24105,15 +28266,15 @@ "binop": null, "updateContext": null }, - "start": 3067, - "end": 3068, + "start": 3599, + "end": 3600, "loc": { "start": { - "line": 81, + "line": 98, "column": 106 }, "end": { - "line": 81, + "line": 98, "column": 107 } } @@ -24131,15 +28292,15 @@ "binop": null }, "value": "nomenclaturalCodeDetails", - "start": 3068, - "end": 3092, + "start": 3600, + "end": 3624, "loc": { "start": { - "line": 81, + "line": 98, "column": 107 }, "end": { - "line": 81, + "line": 98, "column": 131 } } @@ -24157,15 +28318,15 @@ "binop": null, "updateContext": null }, - "start": 3092, - "end": 3093, + "start": 3624, + "end": 3625, "loc": { "start": { - "line": 81, + "line": 98, "column": 131 }, "end": { - "line": 81, + "line": 98, "column": 132 } } @@ -24185,15 +28346,15 @@ "updateContext": null }, "value": "return", - "start": 3099, - "end": 3105, + "start": 3631, + "end": 3637, "loc": { "start": { - "line": 83, + "line": 100, "column": 4 }, "end": { - "line": 83, + "line": 100, "column": 10 } } @@ -24211,15 +28372,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 3106, - "end": 3122, + "start": 3638, + "end": 3654, "loc": { "start": { - "line": 83, + "line": 100, "column": 11 }, "end": { - "line": 83, + "line": 100, "column": 27 } } @@ -24237,15 +28398,15 @@ "binop": null, "updateContext": null }, - "start": 3122, - "end": 3123, + "start": 3654, + "end": 3655, "loc": { "start": { - "line": 83, + "line": 100, "column": 27 }, "end": { - "line": 83, + "line": 100, "column": 28 } } @@ -24263,15 +28424,15 @@ "binop": null }, "value": "getNomenCodeDetails", - "start": 3123, - "end": 3142, + "start": 3655, + "end": 3674, "loc": { "start": { - "line": 83, + "line": 100, "column": 28 }, "end": { - "line": 83, + "line": 100, "column": 47 } } @@ -24288,15 +28449,15 @@ "postfix": false, "binop": null }, - "start": 3142, - "end": 3143, + "start": 3674, + "end": 3675, "loc": { "start": { - "line": 83, + "line": 100, "column": 47 }, "end": { - "line": 83, + "line": 100, "column": 48 } } @@ -24314,15 +28475,15 @@ "binop": null }, "value": "owlterms", - "start": 3143, - "end": 3151, + "start": 3675, + "end": 3683, "loc": { "start": { - "line": 83, + "line": 100, "column": 48 }, "end": { - "line": 83, + "line": 100, "column": 56 } } @@ -24340,15 +28501,15 @@ "binop": null, "updateContext": null }, - "start": 3151, - "end": 3152, + "start": 3683, + "end": 3684, "loc": { "start": { - "line": 83, + "line": 100, "column": 56 }, "end": { - "line": 83, + "line": 100, "column": 57 } } @@ -24366,15 +28527,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 3152, - "end": 3164, + "start": 3684, + "end": 3696, "loc": { "start": { - "line": 83, + "line": 100, "column": 57 }, "end": { - "line": 83, + "line": 100, "column": 69 } } @@ -24391,15 +28552,15 @@ "postfix": false, "binop": null }, - "start": 3164, - "end": 3165, + "start": 3696, + "end": 3697, "loc": { "start": { - "line": 83, + "line": 100, "column": 69 }, "end": { - "line": 83, + "line": 100, "column": 70 } } @@ -24417,15 +28578,15 @@ "binop": null, "updateContext": null }, - "start": 3165, - "end": 3166, + "start": 3697, + "end": 3698, "loc": { "start": { - "line": 83, + "line": 100, "column": 70 }, "end": { - "line": 83, + "line": 100, "column": 71 } } @@ -24442,15 +28603,15 @@ "postfix": false, "binop": null }, - "start": 3169, - "end": 3170, + "start": 3701, + "end": 3702, "loc": { "start": { - "line": 84, + "line": 101, "column": 2 }, "end": { - "line": 84, + "line": 101, "column": 3 } } @@ -24458,15 +28619,15 @@ { "type": "CommentBlock", "value": "*\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n ", - "start": 3174, - "end": 3365, + "start": 3706, + "end": 3897, "loc": { "start": { - "line": 86, + "line": 103, "column": 2 }, "end": { - "line": 91, + "line": 108, "column": 5 } } @@ -24484,15 +28645,15 @@ "binop": null }, "value": "get", - "start": 3368, - "end": 3371, + "start": 3900, + "end": 3903, "loc": { "start": { - "line": 92, + "line": 109, "column": 2 }, "end": { - "line": 92, + "line": 109, "column": 5 } } @@ -24510,15 +28671,15 @@ "binop": null }, "value": "accordingTo", - "start": 3372, - "end": 3383, + "start": 3904, + "end": 3915, "loc": { "start": { - "line": 92, + "line": 109, "column": 6 }, "end": { - "line": 92, + "line": 109, "column": 17 } } @@ -24535,15 +28696,15 @@ "postfix": false, "binop": null }, - "start": 3383, - "end": 3384, + "start": 3915, + "end": 3916, "loc": { "start": { - "line": 92, + "line": 109, "column": 17 }, "end": { - "line": 92, + "line": 109, "column": 18 } } @@ -24560,15 +28721,15 @@ "postfix": false, "binop": null }, - "start": 3384, - "end": 3385, + "start": 3916, + "end": 3917, "loc": { "start": { - "line": 92, + "line": 109, "column": 18 }, "end": { - "line": 92, + "line": 109, "column": 19 } } @@ -24585,15 +28746,15 @@ "postfix": false, "binop": null }, - "start": 3386, - "end": 3387, + "start": 3918, + "end": 3919, "loc": { "start": { - "line": 92, + "line": 109, "column": 20 }, "end": { - "line": 92, + "line": 109, "column": 21 } } @@ -24601,15 +28762,15 @@ { "type": "CommentLine", "value": " Do we have any accordingTo information?", - "start": 3392, - "end": 3434, + "start": 3924, + "end": 3966, "loc": { "start": { - "line": 93, + "line": 110, "column": 4 }, "end": { - "line": 93, + "line": 110, "column": 46 } } @@ -24629,15 +28790,15 @@ "updateContext": null }, "value": "if", - "start": 3439, - "end": 3441, + "start": 3971, + "end": 3973, "loc": { "start": { - "line": 94, + "line": 111, "column": 4 }, "end": { - "line": 94, + "line": 111, "column": 6 } } @@ -24654,15 +28815,15 @@ "postfix": false, "binop": null }, - "start": 3442, - "end": 3443, + "start": 3974, + "end": 3975, "loc": { "start": { - "line": 94, + "line": 111, "column": 7 }, "end": { - "line": 94, + "line": 111, "column": 8 } } @@ -24680,15 +28841,15 @@ "binop": null }, "value": "has", - "start": 3443, - "end": 3446, + "start": 3975, + "end": 3978, "loc": { "start": { - "line": 94, + "line": 111, "column": 8 }, "end": { - "line": 94, + "line": 111, "column": 11 } } @@ -24705,15 +28866,15 @@ "postfix": false, "binop": null }, - "start": 3446, - "end": 3447, + "start": 3978, + "end": 3979, "loc": { "start": { - "line": 94, + "line": 111, "column": 11 }, "end": { - "line": 94, + "line": 111, "column": 12 } } @@ -24733,15 +28894,15 @@ "updateContext": null }, "value": "this", - "start": 3447, - "end": 3451, + "start": 3979, + "end": 3983, "loc": { "start": { - "line": 94, + "line": 111, "column": 12 }, "end": { - "line": 94, + "line": 111, "column": 16 } } @@ -24759,15 +28920,15 @@ "binop": null, "updateContext": null }, - "start": 3451, - "end": 3452, + "start": 3983, + "end": 3984, "loc": { "start": { - "line": 94, + "line": 111, "column": 16 }, "end": { - "line": 94, + "line": 111, "column": 17 } } @@ -24785,15 +28946,15 @@ "binop": null }, "value": "tunit", - "start": 3452, - "end": 3457, + "start": 3984, + "end": 3989, "loc": { "start": { - "line": 94, + "line": 111, "column": 17 }, "end": { - "line": 94, + "line": 111, "column": 22 } } @@ -24811,15 +28972,15 @@ "binop": null, "updateContext": null }, - "start": 3457, - "end": 3458, + "start": 3989, + "end": 3990, "loc": { "start": { - "line": 94, + "line": 111, "column": 22 }, "end": { - "line": 94, + "line": 111, "column": 23 } } @@ -24838,15 +28999,15 @@ "updateContext": null }, "value": "accordingTo", - "start": 3459, - "end": 3472, + "start": 3991, + "end": 4004, "loc": { "start": { - "line": 94, + "line": 111, "column": 24 }, "end": { - "line": 94, + "line": 111, "column": 37 } } @@ -24863,15 +29024,15 @@ "postfix": false, "binop": null }, - "start": 3472, - "end": 3473, + "start": 4004, + "end": 4005, "loc": { "start": { - "line": 94, + "line": 111, "column": 37 }, "end": { - "line": 94, + "line": 111, "column": 38 } } @@ -24888,15 +29049,15 @@ "postfix": false, "binop": null }, - "start": 3473, - "end": 3474, + "start": 4005, + "end": 4006, "loc": { "start": { - "line": 94, + "line": 111, "column": 38 }, "end": { - "line": 94, + "line": 111, "column": 39 } } @@ -24916,15 +29077,15 @@ "updateContext": null }, "value": "return", - "start": 3475, - "end": 3481, + "start": 4007, + "end": 4013, "loc": { "start": { - "line": 94, + "line": 111, "column": 40 }, "end": { - "line": 94, + "line": 111, "column": 46 } } @@ -24944,15 +29105,15 @@ "updateContext": null }, "value": "this", - "start": 3482, - "end": 3486, + "start": 4014, + "end": 4018, "loc": { "start": { - "line": 94, + "line": 111, "column": 47 }, "end": { - "line": 94, + "line": 111, "column": 51 } } @@ -24970,15 +29131,15 @@ "binop": null, "updateContext": null }, - "start": 3486, - "end": 3487, + "start": 4018, + "end": 4019, "loc": { "start": { - "line": 94, + "line": 111, "column": 51 }, "end": { - "line": 94, + "line": 111, "column": 52 } } @@ -24995,17 +29156,17 @@ "postfix": false, "binop": null }, - "value": "type", - "start": 3487, - "end": 3491, + "value": "tunit", + "start": 4019, + "end": 4024, "loc": { "start": { - "line": 94, + "line": 111, "column": 52 }, "end": { - "line": 94, - "column": 56 + "line": 111, + "column": 57 } } }, @@ -25022,16 +29183,16 @@ "binop": null, "updateContext": null }, - "start": 3491, - "end": 3492, + "start": 4024, + "end": 4025, "loc": { "start": { - "line": 94, - "column": 56 + "line": 111, + "column": 57 }, "end": { - "line": 94, - "column": 57 + "line": 111, + "column": 58 } } }, @@ -25048,16 +29209,16 @@ "binop": null }, "value": "accordingTo", - "start": 3492, - "end": 3503, + "start": 4025, + "end": 4036, "loc": { "start": { - "line": 94, - "column": 57 + "line": 111, + "column": 58 }, "end": { - "line": 94, - "column": 68 + "line": 111, + "column": 69 } } }, @@ -25074,31 +29235,31 @@ "binop": null, "updateContext": null }, - "start": 3503, - "end": 3504, + "start": 4036, + "end": 4037, "loc": { "start": { - "line": 94, - "column": 68 + "line": 111, + "column": 69 }, "end": { - "line": 94, - "column": 69 + "line": 111, + "column": 70 } } }, { "type": "CommentLine", "value": " Do we have an accordingToString?", - "start": 3510, - "end": 3545, + "start": 4043, + "end": 4078, "loc": { "start": { - "line": 96, + "line": 113, "column": 4 }, "end": { - "line": 96, + "line": 113, "column": 39 } } @@ -25118,15 +29279,15 @@ "updateContext": null }, "value": "if", - "start": 3550, - "end": 3552, + "start": 4083, + "end": 4085, "loc": { "start": { - "line": 97, + "line": 114, "column": 4 }, "end": { - "line": 97, + "line": 114, "column": 6 } } @@ -25143,15 +29304,15 @@ "postfix": false, "binop": null }, - "start": 3553, - "end": 3554, + "start": 4086, + "end": 4087, "loc": { "start": { - "line": 97, + "line": 114, "column": 7 }, "end": { - "line": 97, + "line": 114, "column": 8 } } @@ -25169,15 +29330,15 @@ "binop": null }, "value": "has", - "start": 3554, - "end": 3557, + "start": 4087, + "end": 4090, "loc": { "start": { - "line": 97, + "line": 114, "column": 8 }, "end": { - "line": 97, + "line": 114, "column": 11 } } @@ -25194,15 +29355,15 @@ "postfix": false, "binop": null }, - "start": 3557, - "end": 3558, + "start": 4090, + "end": 4091, "loc": { "start": { - "line": 97, + "line": 114, "column": 11 }, "end": { - "line": 97, + "line": 114, "column": 12 } } @@ -25222,15 +29383,15 @@ "updateContext": null }, "value": "this", - "start": 3558, - "end": 3562, + "start": 4091, + "end": 4095, "loc": { "start": { - "line": 97, + "line": 114, "column": 12 }, "end": { - "line": 97, + "line": 114, "column": 16 } } @@ -25248,15 +29409,15 @@ "binop": null, "updateContext": null }, - "start": 3562, - "end": 3563, + "start": 4095, + "end": 4096, "loc": { "start": { - "line": 97, + "line": 114, "column": 16 }, "end": { - "line": 97, + "line": 114, "column": 17 } } @@ -25274,15 +29435,15 @@ "binop": null }, "value": "tunit", - "start": 3563, - "end": 3568, + "start": 4096, + "end": 4101, "loc": { "start": { - "line": 97, + "line": 114, "column": 17 }, "end": { - "line": 97, + "line": 114, "column": 22 } } @@ -25300,15 +29461,15 @@ "binop": null, "updateContext": null }, - "start": 3568, - "end": 3569, + "start": 4101, + "end": 4102, "loc": { "start": { - "line": 97, + "line": 114, "column": 22 }, "end": { - "line": 97, + "line": 114, "column": 23 } } @@ -25327,15 +29488,15 @@ "updateContext": null }, "value": "accordingToString", - "start": 3570, - "end": 3589, + "start": 4103, + "end": 4122, "loc": { "start": { - "line": 97, + "line": 114, "column": 24 }, "end": { - "line": 97, + "line": 114, "column": 43 } } @@ -25352,15 +29513,15 @@ "postfix": false, "binop": null }, - "start": 3589, - "end": 3590, + "start": 4122, + "end": 4123, "loc": { "start": { - "line": 97, + "line": 114, "column": 43 }, "end": { - "line": 97, + "line": 114, "column": 44 } } @@ -25377,15 +29538,15 @@ "postfix": false, "binop": null }, - "start": 3590, - "end": 3591, + "start": 4123, + "end": 4124, "loc": { "start": { - "line": 97, + "line": 114, "column": 44 }, "end": { - "line": 97, + "line": 114, "column": 45 } } @@ -25405,15 +29566,15 @@ "updateContext": null }, "value": "return", - "start": 3592, - "end": 3598, + "start": 4125, + "end": 4131, "loc": { "start": { - "line": 97, + "line": 114, "column": 46 }, "end": { - "line": 97, + "line": 114, "column": 52 } } @@ -25433,15 +29594,15 @@ "updateContext": null }, "value": "this", - "start": 3599, - "end": 3603, + "start": 4132, + "end": 4136, "loc": { "start": { - "line": 97, + "line": 114, "column": 53 }, "end": { - "line": 97, + "line": 114, "column": 57 } } @@ -25459,15 +29620,15 @@ "binop": null, "updateContext": null }, - "start": 3603, - "end": 3604, + "start": 4136, + "end": 4137, "loc": { "start": { - "line": 97, + "line": 114, "column": 57 }, "end": { - "line": 97, + "line": 114, "column": 58 } } @@ -25484,17 +29645,17 @@ "postfix": false, "binop": null }, - "value": "type", - "start": 3604, - "end": 3608, + "value": "tunit", + "start": 4137, + "end": 4142, "loc": { "start": { - "line": 97, + "line": 114, "column": 58 }, "end": { - "line": 97, - "column": 62 + "line": 114, + "column": 63 } } }, @@ -25511,16 +29672,16 @@ "binop": null, "updateContext": null }, - "start": 3608, - "end": 3609, + "start": 4142, + "end": 4143, "loc": { "start": { - "line": 97, - "column": 62 + "line": 114, + "column": 63 }, "end": { - "line": 97, - "column": 63 + "line": 114, + "column": 64 } } }, @@ -25537,16 +29698,16 @@ "binop": null }, "value": "accordingToString", - "start": 3609, - "end": 3626, + "start": 4143, + "end": 4160, "loc": { "start": { - "line": 97, - "column": 63 + "line": 114, + "column": 64 }, "end": { - "line": 97, - "column": 80 + "line": 114, + "column": 81 } } }, @@ -25563,31 +29724,31 @@ "binop": null, "updateContext": null }, - "start": 3626, - "end": 3627, + "start": 4160, + "end": 4161, "loc": { "start": { - "line": 97, - "column": 80 + "line": 114, + "column": 81 }, "end": { - "line": 97, - "column": 81 + "line": 114, + "column": 82 } } }, { "type": "CommentLine", "value": " If not, we have no accodingTo information!", - "start": 3633, - "end": 3678, + "start": 4167, + "end": 4212, "loc": { "start": { - "line": 99, + "line": 116, "column": 4 }, "end": { - "line": 99, + "line": 116, "column": 49 } } @@ -25607,15 +29768,15 @@ "updateContext": null }, "value": "return", - "start": 3683, - "end": 3689, + "start": 4217, + "end": 4223, "loc": { "start": { - "line": 100, + "line": 117, "column": 4 }, "end": { - "line": 100, + "line": 117, "column": 10 } } @@ -25633,15 +29794,15 @@ "binop": null }, "value": "undefined", - "start": 3690, - "end": 3699, + "start": 4224, + "end": 4233, "loc": { "start": { - "line": 100, + "line": 117, "column": 11 }, "end": { - "line": 100, + "line": 117, "column": 20 } } @@ -25659,15 +29820,15 @@ "binop": null, "updateContext": null }, - "start": 3699, - "end": 3700, + "start": 4233, + "end": 4234, "loc": { "start": { - "line": 100, + "line": 117, "column": 20 }, "end": { - "line": 100, + "line": 117, "column": 21 } } @@ -25684,15 +29845,15 @@ "postfix": false, "binop": null }, - "start": 3703, - "end": 3704, + "start": 4237, + "end": 4238, "loc": { "start": { - "line": 101, + "line": 118, "column": 2 }, "end": { - "line": 101, + "line": 118, "column": 3 } } @@ -25700,15 +29861,15 @@ { "type": "CommentBlock", "value": "*\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n ", - "start": 3708, - "end": 3940, + "start": 4242, + "end": 4474, "loc": { "start": { - "line": 103, + "line": 120, "column": 2 }, "end": { - "line": 108, + "line": 125, "column": 5 } } @@ -25726,15 +29887,15 @@ "binop": null }, "value": "get", - "start": 3943, - "end": 3946, + "start": 4477, + "end": 4480, "loc": { "start": { - "line": 109, + "line": 126, "column": 2 }, "end": { - "line": 109, + "line": 126, "column": 5 } } @@ -25752,15 +29913,15 @@ "binop": null }, "value": "accordingToString", - "start": 3947, - "end": 3964, + "start": 4481, + "end": 4498, "loc": { "start": { - "line": 109, + "line": 126, "column": 6 }, "end": { - "line": 109, + "line": 126, "column": 23 } } @@ -25777,15 +29938,15 @@ "postfix": false, "binop": null }, - "start": 3964, - "end": 3965, + "start": 4498, + "end": 4499, "loc": { "start": { - "line": 109, + "line": 126, "column": 23 }, "end": { - "line": 109, + "line": 126, "column": 24 } } @@ -25802,15 +29963,15 @@ "postfix": false, "binop": null }, - "start": 3965, - "end": 3966, + "start": 4499, + "end": 4500, "loc": { "start": { - "line": 109, + "line": 126, "column": 24 }, "end": { - "line": 109, + "line": 126, "column": 25 } } @@ -25827,15 +29988,15 @@ "postfix": false, "binop": null }, - "start": 3967, - "end": 3968, + "start": 4501, + "end": 4502, "loc": { "start": { - "line": 109, + "line": 126, "column": 26 }, "end": { - "line": 109, + "line": 126, "column": 27 } } @@ -25843,15 +30004,15 @@ { "type": "CommentLine", "value": " Do we have any accordingTo information?", - "start": 3973, - "end": 4015, + "start": 4507, + "end": 4549, "loc": { "start": { - "line": 110, + "line": 127, "column": 4 }, "end": { - "line": 110, + "line": 127, "column": 46 } } @@ -25871,15 +30032,15 @@ "updateContext": null }, "value": "if", - "start": 4020, - "end": 4022, + "start": 4554, + "end": 4556, "loc": { "start": { - "line": 111, + "line": 128, "column": 4 }, "end": { - "line": 111, + "line": 128, "column": 6 } } @@ -25896,15 +30057,15 @@ "postfix": false, "binop": null }, - "start": 4023, - "end": 4024, + "start": 4557, + "end": 4558, "loc": { "start": { - "line": 111, + "line": 128, "column": 7 }, "end": { - "line": 111, + "line": 128, "column": 8 } } @@ -25922,15 +30083,15 @@ "binop": null }, "value": "has", - "start": 4024, - "end": 4027, + "start": 4558, + "end": 4561, "loc": { "start": { - "line": 111, + "line": 128, "column": 8 }, "end": { - "line": 111, + "line": 128, "column": 11 } } @@ -25947,15 +30108,15 @@ "postfix": false, "binop": null }, - "start": 4027, - "end": 4028, + "start": 4561, + "end": 4562, "loc": { "start": { - "line": 111, + "line": 128, "column": 11 }, "end": { - "line": 111, + "line": 128, "column": 12 } } @@ -25975,15 +30136,15 @@ "updateContext": null }, "value": "this", - "start": 4028, - "end": 4032, + "start": 4562, + "end": 4566, "loc": { "start": { - "line": 111, + "line": 128, "column": 12 }, "end": { - "line": 111, + "line": 128, "column": 16 } } @@ -26001,15 +30162,15 @@ "binop": null, "updateContext": null }, - "start": 4032, - "end": 4033, + "start": 4566, + "end": 4567, "loc": { "start": { - "line": 111, + "line": 128, "column": 16 }, "end": { - "line": 111, + "line": 128, "column": 17 } } @@ -26027,15 +30188,15 @@ "binop": null }, "value": "tunit", - "start": 4033, - "end": 4038, + "start": 4567, + "end": 4572, "loc": { "start": { - "line": 111, + "line": 128, "column": 17 }, "end": { - "line": 111, + "line": 128, "column": 22 } } @@ -26053,15 +30214,15 @@ "binop": null, "updateContext": null }, - "start": 4038, - "end": 4039, + "start": 4572, + "end": 4573, "loc": { "start": { - "line": 111, + "line": 128, "column": 22 }, "end": { - "line": 111, + "line": 128, "column": 23 } } @@ -26080,15 +30241,15 @@ "updateContext": null }, "value": "accordingTo", - "start": 4040, - "end": 4053, + "start": 4574, + "end": 4587, "loc": { "start": { - "line": 111, + "line": 128, "column": 24 }, "end": { - "line": 111, + "line": 128, "column": 37 } } @@ -26105,15 +30266,15 @@ "postfix": false, "binop": null }, - "start": 4053, - "end": 4054, + "start": 4587, + "end": 4588, "loc": { "start": { - "line": 111, + "line": 128, "column": 37 }, "end": { - "line": 111, + "line": 128, "column": 38 } } @@ -26130,15 +30291,15 @@ "postfix": false, "binop": null }, - "start": 4054, - "end": 4055, + "start": 4588, + "end": 4589, "loc": { "start": { - "line": 111, + "line": 128, "column": 38 }, "end": { - "line": 111, + "line": 128, "column": 39 } } @@ -26158,15 +30319,15 @@ "updateContext": null }, "value": "return", - "start": 4056, - "end": 4062, + "start": 4590, + "end": 4596, "loc": { "start": { - "line": 111, + "line": 128, "column": 40 }, "end": { - "line": 111, + "line": 128, "column": 46 } } @@ -26184,15 +30345,15 @@ "binop": null }, "value": "JSON", - "start": 4063, - "end": 4067, + "start": 4597, + "end": 4601, "loc": { "start": { - "line": 111, + "line": 128, "column": 47 }, "end": { - "line": 111, + "line": 128, "column": 51 } } @@ -26210,15 +30371,15 @@ "binop": null, "updateContext": null }, - "start": 4067, - "end": 4068, + "start": 4601, + "end": 4602, "loc": { "start": { - "line": 111, + "line": 128, "column": 51 }, "end": { - "line": 111, + "line": 128, "column": 52 } } @@ -26236,15 +30397,15 @@ "binop": null }, "value": "stringify", - "start": 4068, - "end": 4077, + "start": 4602, + "end": 4611, "loc": { "start": { - "line": 111, + "line": 128, "column": 52 }, "end": { - "line": 111, + "line": 128, "column": 61 } } @@ -26261,15 +30422,15 @@ "postfix": false, "binop": null }, - "start": 4077, - "end": 4078, + "start": 4611, + "end": 4612, "loc": { "start": { - "line": 111, + "line": 128, "column": 61 }, "end": { - "line": 111, + "line": 128, "column": 62 } } @@ -26289,15 +30450,15 @@ "updateContext": null }, "value": "this", - "start": 4078, - "end": 4082, + "start": 4612, + "end": 4616, "loc": { "start": { - "line": 111, + "line": 128, "column": 62 }, "end": { - "line": 111, + "line": 128, "column": 66 } } @@ -26315,15 +30476,15 @@ "binop": null, "updateContext": null }, - "start": 4082, - "end": 4083, + "start": 4616, + "end": 4617, "loc": { "start": { - "line": 111, + "line": 128, "column": 66 }, "end": { - "line": 111, + "line": 128, "column": 67 } } @@ -26340,17 +30501,17 @@ "postfix": false, "binop": null }, - "value": "type", - "start": 4083, - "end": 4087, + "value": "tunit", + "start": 4617, + "end": 4622, "loc": { "start": { - "line": 111, + "line": 128, "column": 67 }, "end": { - "line": 111, - "column": 71 + "line": 128, + "column": 72 } } }, @@ -26367,16 +30528,16 @@ "binop": null, "updateContext": null }, - "start": 4087, - "end": 4088, + "start": 4622, + "end": 4623, "loc": { "start": { - "line": 111, - "column": 71 + "line": 128, + "column": 72 }, "end": { - "line": 111, - "column": 72 + "line": 128, + "column": 73 } } }, @@ -26393,16 +30554,16 @@ "binop": null }, "value": "accordingTo", - "start": 4088, - "end": 4099, + "start": 4623, + "end": 4634, "loc": { "start": { - "line": 111, - "column": 72 + "line": 128, + "column": 73 }, "end": { - "line": 111, - "column": 83 + "line": 128, + "column": 84 } } }, @@ -26418,16 +30579,16 @@ "postfix": false, "binop": null }, - "start": 4099, - "end": 4100, + "start": 4634, + "end": 4635, "loc": { "start": { - "line": 111, - "column": 83 + "line": 128, + "column": 84 }, "end": { - "line": 111, - "column": 84 + "line": 128, + "column": 85 } } }, @@ -26444,31 +30605,31 @@ "binop": null, "updateContext": null }, - "start": 4100, - "end": 4101, + "start": 4635, + "end": 4636, "loc": { "start": { - "line": 111, - "column": 84 + "line": 128, + "column": 85 }, "end": { - "line": 111, - "column": 85 + "line": 128, + "column": 86 } } }, { "type": "CommentLine", "value": " Do we have an accordingToString?", - "start": 4107, - "end": 4142, + "start": 4642, + "end": 4677, "loc": { "start": { - "line": 113, + "line": 130, "column": 4 }, "end": { - "line": 113, + "line": 130, "column": 39 } } @@ -26488,15 +30649,15 @@ "updateContext": null }, "value": "if", - "start": 4147, - "end": 4149, + "start": 4682, + "end": 4684, "loc": { "start": { - "line": 114, + "line": 131, "column": 4 }, "end": { - "line": 114, + "line": 131, "column": 6 } } @@ -26513,15 +30674,15 @@ "postfix": false, "binop": null }, - "start": 4150, - "end": 4151, + "start": 4685, + "end": 4686, "loc": { "start": { - "line": 114, + "line": 131, "column": 7 }, "end": { - "line": 114, + "line": 131, "column": 8 } } @@ -26539,15 +30700,15 @@ "binop": null }, "value": "has", - "start": 4151, - "end": 4154, + "start": 4686, + "end": 4689, "loc": { "start": { - "line": 114, + "line": 131, "column": 8 }, "end": { - "line": 114, + "line": 131, "column": 11 } } @@ -26564,15 +30725,15 @@ "postfix": false, "binop": null }, - "start": 4154, - "end": 4155, + "start": 4689, + "end": 4690, "loc": { "start": { - "line": 114, + "line": 131, "column": 11 }, "end": { - "line": 114, + "line": 131, "column": 12 } } @@ -26592,15 +30753,15 @@ "updateContext": null }, "value": "this", - "start": 4155, - "end": 4159, + "start": 4690, + "end": 4694, "loc": { "start": { - "line": 114, + "line": 131, "column": 12 }, "end": { - "line": 114, + "line": 131, "column": 16 } } @@ -26618,15 +30779,15 @@ "binop": null, "updateContext": null }, - "start": 4159, - "end": 4160, + "start": 4694, + "end": 4695, "loc": { "start": { - "line": 114, + "line": 131, "column": 16 }, "end": { - "line": 114, + "line": 131, "column": 17 } } @@ -26644,15 +30805,15 @@ "binop": null }, "value": "tunit", - "start": 4160, - "end": 4165, + "start": 4695, + "end": 4700, "loc": { "start": { - "line": 114, + "line": 131, "column": 17 }, "end": { - "line": 114, + "line": 131, "column": 22 } } @@ -26670,15 +30831,15 @@ "binop": null, "updateContext": null }, - "start": 4165, - "end": 4166, + "start": 4700, + "end": 4701, "loc": { "start": { - "line": 114, + "line": 131, "column": 22 }, "end": { - "line": 114, + "line": 131, "column": 23 } } @@ -26697,15 +30858,15 @@ "updateContext": null }, "value": "accordingToString", - "start": 4167, - "end": 4186, + "start": 4702, + "end": 4721, "loc": { "start": { - "line": 114, + "line": 131, "column": 24 }, "end": { - "line": 114, + "line": 131, "column": 43 } } @@ -26722,15 +30883,15 @@ "postfix": false, "binop": null }, - "start": 4186, - "end": 4187, + "start": 4721, + "end": 4722, "loc": { "start": { - "line": 114, + "line": 131, "column": 43 }, "end": { - "line": 114, + "line": 131, "column": 44 } } @@ -26747,15 +30908,15 @@ "postfix": false, "binop": null }, - "start": 4187, - "end": 4188, + "start": 4722, + "end": 4723, "loc": { "start": { - "line": 114, + "line": 131, "column": 44 }, "end": { - "line": 114, + "line": 131, "column": 45 } } @@ -26775,15 +30936,15 @@ "updateContext": null }, "value": "return", - "start": 4189, - "end": 4195, + "start": 4724, + "end": 4730, "loc": { "start": { - "line": 114, + "line": 131, "column": 46 }, "end": { - "line": 114, + "line": 131, "column": 52 } } @@ -26803,15 +30964,15 @@ "updateContext": null }, "value": "this", - "start": 4196, - "end": 4200, + "start": 4731, + "end": 4735, "loc": { "start": { - "line": 114, + "line": 131, "column": 53 }, "end": { - "line": 114, + "line": 131, "column": 57 } } @@ -26829,15 +30990,15 @@ "binop": null, "updateContext": null }, - "start": 4200, - "end": 4201, + "start": 4735, + "end": 4736, "loc": { "start": { - "line": 114, + "line": 131, "column": 57 }, "end": { - "line": 114, + "line": 131, "column": 58 } } @@ -26854,17 +31015,17 @@ "postfix": false, "binop": null }, - "value": "type", - "start": 4201, - "end": 4205, + "value": "tunit", + "start": 4736, + "end": 4741, "loc": { "start": { - "line": 114, + "line": 131, "column": 58 }, "end": { - "line": 114, - "column": 62 + "line": 131, + "column": 63 } } }, @@ -26881,16 +31042,16 @@ "binop": null, "updateContext": null }, - "start": 4205, - "end": 4206, + "start": 4741, + "end": 4742, "loc": { "start": { - "line": 114, - "column": 62 + "line": 131, + "column": 63 }, "end": { - "line": 114, - "column": 63 + "line": 131, + "column": 64 } } }, @@ -26907,16 +31068,16 @@ "binop": null }, "value": "accordingToString", - "start": 4206, - "end": 4223, + "start": 4742, + "end": 4759, "loc": { "start": { - "line": 114, - "column": 63 + "line": 131, + "column": 64 }, "end": { - "line": 114, - "column": 80 + "line": 131, + "column": 81 } } }, @@ -26933,31 +31094,31 @@ "binop": null, "updateContext": null }, - "start": 4223, - "end": 4224, + "start": 4759, + "end": 4760, "loc": { "start": { - "line": 114, - "column": 80 + "line": 131, + "column": 81 }, "end": { - "line": 114, - "column": 81 + "line": 131, + "column": 82 } } }, { "type": "CommentLine", "value": " If not, we have no accodingTo information!", - "start": 4230, - "end": 4275, + "start": 4766, + "end": 4811, "loc": { "start": { - "line": 116, + "line": 133, "column": 4 }, "end": { - "line": 116, + "line": 133, "column": 49 } } @@ -26977,15 +31138,15 @@ "updateContext": null }, "value": "return", - "start": 4280, - "end": 4286, + "start": 4816, + "end": 4822, "loc": { "start": { - "line": 117, + "line": 134, "column": 4 }, "end": { - "line": 117, + "line": 134, "column": 10 } } @@ -27003,15 +31164,15 @@ "binop": null }, "value": "undefined", - "start": 4287, - "end": 4296, + "start": 4823, + "end": 4832, "loc": { "start": { - "line": 117, + "line": 134, "column": 11 }, "end": { - "line": 117, + "line": 134, "column": 20 } } @@ -27029,15 +31190,15 @@ "binop": null, "updateContext": null }, - "start": 4296, - "end": 4297, + "start": 4832, + "end": 4833, "loc": { "start": { - "line": 117, + "line": 134, "column": 20 }, "end": { - "line": 117, + "line": 134, "column": 21 } } @@ -27054,15 +31215,15 @@ "postfix": false, "binop": null }, - "start": 4300, - "end": 4301, + "start": 4836, + "end": 4837, "loc": { "start": { - "line": 118, + "line": 135, "column": 2 }, "end": { - "line": 118, + "line": 135, "column": 3 } } @@ -27070,15 +31231,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this taxon concept.\n ", - "start": 4305, - "end": 4359, + "start": 4841, + "end": 4895, "loc": { "start": { - "line": 120, + "line": 137, "column": 2 }, "end": { - "line": 122, + "line": 139, "column": 5 } } @@ -27096,15 +31257,15 @@ "binop": null }, "value": "get", - "start": 4362, - "end": 4365, + "start": 4898, + "end": 4901, "loc": { "start": { - "line": 123, + "line": 140, "column": 2 }, "end": { - "line": 123, + "line": 140, "column": 5 } } @@ -27122,15 +31283,15 @@ "binop": null }, "value": "label", - "start": 4366, - "end": 4371, + "start": 4902, + "end": 4907, "loc": { "start": { - "line": 123, + "line": 140, "column": 6 }, "end": { - "line": 123, + "line": 140, "column": 11 } } @@ -27147,15 +31308,15 @@ "postfix": false, "binop": null }, - "start": 4371, - "end": 4372, + "start": 4907, + "end": 4908, "loc": { "start": { - "line": 123, + "line": 140, "column": 11 }, "end": { - "line": 123, + "line": 140, "column": 12 } } @@ -27172,15 +31333,15 @@ "postfix": false, "binop": null }, - "start": 4372, - "end": 4373, + "start": 4908, + "end": 4909, "loc": { "start": { - "line": 123, + "line": 140, "column": 12 }, "end": { - "line": 123, + "line": 140, "column": 13 } } @@ -27197,15 +31358,15 @@ "postfix": false, "binop": null }, - "start": 4374, - "end": 4375, + "start": 4910, + "end": 4911, "loc": { "start": { - "line": 123, + "line": 140, "column": 14 }, "end": { - "line": 123, + "line": 140, "column": 15 } } @@ -27213,15 +31374,15 @@ { "type": "CommentLine", "value": " If we're wrapping a taxonName, use its label.", - "start": 4380, - "end": 4428, + "start": 4916, + "end": 4964, "loc": { "start": { - "line": 124, + "line": 141, "column": 4 }, "end": { - "line": 124, + "line": 141, "column": 52 } } @@ -27241,15 +31402,15 @@ "updateContext": null }, "value": "if", - "start": 4433, - "end": 4435, + "start": 4969, + "end": 4971, "loc": { "start": { - "line": 125, + "line": 142, "column": 4 }, "end": { - "line": 125, + "line": 142, "column": 6 } } @@ -27266,15 +31427,15 @@ "postfix": false, "binop": null }, - "start": 4436, - "end": 4437, + "start": 4972, + "end": 4973, "loc": { "start": { - "line": 125, + "line": 142, "column": 7 }, "end": { - "line": 125, + "line": 142, "column": 8 } } @@ -27294,15 +31455,15 @@ "updateContext": null }, "value": "this", - "start": 4437, - "end": 4441, + "start": 4973, + "end": 4977, "loc": { "start": { - "line": 125, + "line": 142, "column": 8 }, "end": { - "line": 125, + "line": 142, "column": 12 } } @@ -27320,15 +31481,15 @@ "binop": null, "updateContext": null }, - "start": 4441, - "end": 4442, + "start": 4977, + "end": 4978, "loc": { "start": { - "line": 125, + "line": 142, "column": 12 }, "end": { - "line": 125, + "line": 142, "column": 13 } } @@ -27346,15 +31507,15 @@ "binop": null }, "value": "taxonName", - "start": 4442, - "end": 4451, + "start": 4978, + "end": 4987, "loc": { "start": { - "line": 125, + "line": 142, "column": 13 }, "end": { - "line": 125, + "line": 142, "column": 22 } } @@ -27371,15 +31532,15 @@ "postfix": false, "binop": null }, - "start": 4451, - "end": 4452, + "start": 4987, + "end": 4988, "loc": { "start": { - "line": 125, + "line": 142, "column": 22 }, "end": { - "line": 125, + "line": 142, "column": 23 } } @@ -27396,15 +31557,15 @@ "postfix": false, "binop": null }, - "start": 4453, - "end": 4454, + "start": 4989, + "end": 4990, "loc": { "start": { - "line": 125, + "line": 142, "column": 24 }, "end": { - "line": 125, + "line": 142, "column": 25 } } @@ -27412,15 +31573,15 @@ { "type": "CommentLine", "value": " Do we also have accordingTo information?", - "start": 4461, - "end": 4504, + "start": 4997, + "end": 5040, "loc": { "start": { - "line": 126, + "line": 143, "column": 6 }, "end": { - "line": 126, + "line": 143, "column": 49 } } @@ -27440,15 +31601,15 @@ "updateContext": null }, "value": "if", - "start": 4511, - "end": 4513, + "start": 5047, + "end": 5049, "loc": { "start": { - "line": 127, + "line": 144, "column": 6 }, "end": { - "line": 127, + "line": 144, "column": 8 } } @@ -27465,15 +31626,15 @@ "postfix": false, "binop": null }, - "start": 4514, - "end": 4515, + "start": 5050, + "end": 5051, "loc": { "start": { - "line": 127, + "line": 144, "column": 9 }, "end": { - "line": 127, + "line": 144, "column": 10 } } @@ -27493,15 +31654,15 @@ "updateContext": null }, "value": "this", - "start": 4515, - "end": 4519, + "start": 5051, + "end": 5055, "loc": { "start": { - "line": 127, + "line": 144, "column": 10 }, "end": { - "line": 127, + "line": 144, "column": 14 } } @@ -27519,15 +31680,15 @@ "binop": null, "updateContext": null }, - "start": 4519, - "end": 4520, + "start": 5055, + "end": 5056, "loc": { "start": { - "line": 127, + "line": 144, "column": 14 }, "end": { - "line": 127, + "line": 144, "column": 15 } } @@ -27545,15 +31706,15 @@ "binop": null }, "value": "accordingToString", - "start": 4520, - "end": 4537, + "start": 5056, + "end": 5073, "loc": { "start": { - "line": 127, + "line": 144, "column": 15 }, "end": { - "line": 127, + "line": 144, "column": 32 } } @@ -27570,15 +31731,15 @@ "postfix": false, "binop": null }, - "start": 4537, - "end": 4538, + "start": 5073, + "end": 5074, "loc": { "start": { - "line": 127, + "line": 144, "column": 32 }, "end": { - "line": 127, + "line": 144, "column": 33 } } @@ -27595,15 +31756,15 @@ "postfix": false, "binop": null }, - "start": 4539, - "end": 4540, + "start": 5075, + "end": 5076, "loc": { "start": { - "line": 127, + "line": 144, "column": 34 }, "end": { - "line": 127, + "line": 144, "column": 35 } } @@ -27623,15 +31784,15 @@ "updateContext": null }, "value": "return", - "start": 4549, - "end": 4555, + "start": 5085, + "end": 5091, "loc": { "start": { - "line": 128, + "line": 145, "column": 8 }, "end": { - "line": 128, + "line": 145, "column": 14 } } @@ -27648,15 +31809,15 @@ "postfix": false, "binop": null }, - "start": 4556, - "end": 4557, + "start": 5092, + "end": 5093, "loc": { "start": { - "line": 128, + "line": 145, "column": 15 }, "end": { - "line": 128, + "line": 145, "column": 16 } } @@ -27675,15 +31836,15 @@ "updateContext": null }, "value": "", - "start": 4557, - "end": 4557, + "start": 5093, + "end": 5093, "loc": { "start": { - "line": 128, + "line": 145, "column": 16 }, "end": { - "line": 128, + "line": 145, "column": 16 } } @@ -27700,15 +31861,15 @@ "postfix": false, "binop": null }, - "start": 4557, - "end": 4559, + "start": 5093, + "end": 5095, "loc": { "start": { - "line": 128, + "line": 145, "column": 16 }, "end": { - "line": 128, + "line": 145, "column": 18 } } @@ -27728,15 +31889,15 @@ "updateContext": null }, "value": "new", - "start": 4559, - "end": 4562, + "start": 5095, + "end": 5098, "loc": { "start": { - "line": 128, + "line": 145, "column": 18 }, "end": { - "line": 128, + "line": 145, "column": 21 } } @@ -27754,15 +31915,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 4563, - "end": 4579, + "start": 5099, + "end": 5115, "loc": { "start": { - "line": 128, + "line": 145, "column": 22 }, "end": { - "line": 128, + "line": 145, "column": 38 } } @@ -27779,15 +31940,15 @@ "postfix": false, "binop": null }, - "start": 4579, - "end": 4580, + "start": 5115, + "end": 5116, "loc": { "start": { - "line": 128, + "line": 145, "column": 38 }, "end": { - "line": 128, + "line": 145, "column": 39 } } @@ -27807,15 +31968,15 @@ "updateContext": null }, "value": "this", - "start": 4580, - "end": 4584, + "start": 5116, + "end": 5120, "loc": { "start": { - "line": 128, + "line": 145, "column": 39 }, "end": { - "line": 128, + "line": 145, "column": 43 } } @@ -27833,15 +31994,15 @@ "binop": null, "updateContext": null }, - "start": 4584, - "end": 4585, + "start": 5120, + "end": 5121, "loc": { "start": { - "line": 128, + "line": 145, "column": 43 }, "end": { - "line": 128, + "line": 145, "column": 44 } } @@ -27859,15 +32020,15 @@ "binop": null }, "value": "taxonName", - "start": 4585, - "end": 4594, + "start": 5121, + "end": 5130, "loc": { "start": { - "line": 128, + "line": 145, "column": 44 }, "end": { - "line": 128, + "line": 145, "column": 53 } } @@ -27885,15 +32046,15 @@ "binop": null, "updateContext": null }, - "start": 4594, - "end": 4595, + "start": 5130, + "end": 5131, "loc": { "start": { - "line": 128, + "line": 145, "column": 53 }, "end": { - "line": 128, + "line": 145, "column": 54 } } @@ -27913,15 +32074,15 @@ "updateContext": null }, "value": "this", - "start": 4596, - "end": 4600, + "start": 5132, + "end": 5136, "loc": { "start": { - "line": 128, + "line": 145, "column": 55 }, "end": { - "line": 128, + "line": 145, "column": 59 } } @@ -27939,15 +32100,15 @@ "binop": null, "updateContext": null }, - "start": 4600, - "end": 4601, + "start": 5136, + "end": 5137, "loc": { "start": { - "line": 128, + "line": 145, "column": 59 }, "end": { - "line": 128, + "line": 145, "column": 60 } } @@ -27965,15 +32126,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 4601, - "end": 4617, + "start": 5137, + "end": 5153, "loc": { "start": { - "line": 128, + "line": 145, "column": 60 }, "end": { - "line": 128, + "line": 145, "column": 76 } } @@ -27990,15 +32151,15 @@ "postfix": false, "binop": null }, - "start": 4617, - "end": 4618, + "start": 5153, + "end": 5154, "loc": { "start": { - "line": 128, + "line": 145, "column": 76 }, "end": { - "line": 128, + "line": 145, "column": 77 } } @@ -28016,15 +32177,15 @@ "binop": null, "updateContext": null }, - "start": 4618, - "end": 4619, + "start": 5154, + "end": 5155, "loc": { "start": { - "line": 128, + "line": 145, "column": 77 }, "end": { - "line": 128, + "line": 145, "column": 78 } } @@ -28042,15 +32203,15 @@ "binop": null }, "value": "label", - "start": 4619, - "end": 4624, + "start": 5155, + "end": 5160, "loc": { "start": { - "line": 128, + "line": 145, "column": 78 }, "end": { - "line": 128, + "line": 145, "column": 83 } } @@ -28067,15 +32228,15 @@ "postfix": false, "binop": null }, - "start": 4624, - "end": 4625, + "start": 5160, + "end": 5161, "loc": { "start": { - "line": 128, + "line": 145, "column": 83 }, "end": { - "line": 128, + "line": 145, "column": 84 } } @@ -28094,15 +32255,15 @@ "updateContext": null }, "value": " sensu ", - "start": 4625, - "end": 4632, + "start": 5161, + "end": 5168, "loc": { "start": { - "line": 128, + "line": 145, "column": 84 }, "end": { - "line": 128, + "line": 145, "column": 91 } } @@ -28119,15 +32280,15 @@ "postfix": false, "binop": null }, - "start": 4632, - "end": 4634, + "start": 5168, + "end": 5170, "loc": { "start": { - "line": 128, + "line": 145, "column": 91 }, "end": { - "line": 128, + "line": 145, "column": 93 } } @@ -28147,15 +32308,15 @@ "updateContext": null }, "value": "this", - "start": 4634, - "end": 4638, + "start": 5170, + "end": 5174, "loc": { "start": { - "line": 128, + "line": 145, "column": 93 }, "end": { - "line": 128, + "line": 145, "column": 97 } } @@ -28173,15 +32334,15 @@ "binop": null, "updateContext": null }, - "start": 4638, - "end": 4639, + "start": 5174, + "end": 5175, "loc": { "start": { - "line": 128, + "line": 145, "column": 97 }, "end": { - "line": 128, + "line": 145, "column": 98 } } @@ -28199,15 +32360,15 @@ "binop": null }, "value": "accordingToString", - "start": 4639, - "end": 4656, + "start": 5175, + "end": 5192, "loc": { "start": { - "line": 128, + "line": 145, "column": 98 }, "end": { - "line": 128, + "line": 145, "column": 115 } } @@ -28224,15 +32385,15 @@ "postfix": false, "binop": null }, - "start": 4656, - "end": 4657, + "start": 5192, + "end": 5193, "loc": { "start": { - "line": 128, + "line": 145, "column": 115 }, "end": { - "line": 128, + "line": 145, "column": 116 } } @@ -28251,15 +32412,15 @@ "updateContext": null }, "value": "", - "start": 4657, - "end": 4657, + "start": 5193, + "end": 5193, "loc": { "start": { - "line": 128, + "line": 145, "column": 116 }, "end": { - "line": 128, + "line": 145, "column": 116 } } @@ -28276,15 +32437,15 @@ "postfix": false, "binop": null }, - "start": 4657, - "end": 4658, + "start": 5193, + "end": 5194, "loc": { "start": { - "line": 128, + "line": 145, "column": 116 }, "end": { - "line": 128, + "line": 145, "column": 117 } } @@ -28302,15 +32463,15 @@ "binop": null, "updateContext": null }, - "start": 4658, - "end": 4659, + "start": 5194, + "end": 5195, "loc": { "start": { - "line": 128, + "line": 145, "column": 117 }, "end": { - "line": 128, + "line": 145, "column": 118 } } @@ -28327,15 +32488,15 @@ "postfix": false, "binop": null }, - "start": 4666, - "end": 4667, + "start": 5202, + "end": 5203, "loc": { "start": { - "line": 129, + "line": 146, "column": 6 }, "end": { - "line": 129, + "line": 146, "column": 7 } } @@ -28355,15 +32516,15 @@ "updateContext": null }, "value": "return", - "start": 4675, - "end": 4681, + "start": 5211, + "end": 5217, "loc": { "start": { - "line": 131, + "line": 148, "column": 6 }, "end": { - "line": 131, + "line": 148, "column": 12 } } @@ -28383,15 +32544,15 @@ "updateContext": null }, "value": "new", - "start": 4682, - "end": 4685, + "start": 5218, + "end": 5221, "loc": { "start": { - "line": 131, + "line": 148, "column": 13 }, "end": { - "line": 131, + "line": 148, "column": 16 } } @@ -28409,15 +32570,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 4686, - "end": 4702, + "start": 5222, + "end": 5238, "loc": { "start": { - "line": 131, + "line": 148, "column": 17 }, "end": { - "line": 131, + "line": 148, "column": 33 } } @@ -28434,15 +32595,15 @@ "postfix": false, "binop": null }, - "start": 4702, - "end": 4703, + "start": 5238, + "end": 5239, "loc": { "start": { - "line": 131, + "line": 148, "column": 33 }, "end": { - "line": 131, + "line": 148, "column": 34 } } @@ -28462,15 +32623,15 @@ "updateContext": null }, "value": "this", - "start": 4703, - "end": 4707, + "start": 5239, + "end": 5243, "loc": { "start": { - "line": 131, + "line": 148, "column": 34 }, "end": { - "line": 131, + "line": 148, "column": 38 } } @@ -28488,15 +32649,15 @@ "binop": null, "updateContext": null }, - "start": 4707, - "end": 4708, + "start": 5243, + "end": 5244, "loc": { "start": { - "line": 131, + "line": 148, "column": 38 }, "end": { - "line": 131, + "line": 148, "column": 39 } } @@ -28514,15 +32675,15 @@ "binop": null }, "value": "taxonName", - "start": 4708, - "end": 4717, + "start": 5244, + "end": 5253, "loc": { "start": { - "line": 131, + "line": 148, "column": 39 }, "end": { - "line": 131, + "line": 148, "column": 48 } } @@ -28540,15 +32701,15 @@ "binop": null, "updateContext": null }, - "start": 4717, - "end": 4718, + "start": 5253, + "end": 5254, "loc": { "start": { - "line": 131, + "line": 148, "column": 48 }, "end": { - "line": 131, + "line": 148, "column": 49 } } @@ -28568,15 +32729,15 @@ "updateContext": null }, "value": "this", - "start": 4719, - "end": 4723, + "start": 5255, + "end": 5259, "loc": { "start": { - "line": 131, + "line": 148, "column": 50 }, "end": { - "line": 131, + "line": 148, "column": 54 } } @@ -28594,15 +32755,15 @@ "binop": null, "updateContext": null }, - "start": 4723, - "end": 4724, + "start": 5259, + "end": 5260, "loc": { "start": { - "line": 131, + "line": 148, "column": 54 }, "end": { - "line": 131, + "line": 148, "column": 55 } } @@ -28620,15 +32781,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 4724, - "end": 4740, + "start": 5260, + "end": 5276, "loc": { "start": { - "line": 131, + "line": 148, "column": 55 }, "end": { - "line": 131, + "line": 148, "column": 71 } } @@ -28645,15 +32806,15 @@ "postfix": false, "binop": null }, - "start": 4740, - "end": 4741, + "start": 5276, + "end": 5277, "loc": { "start": { - "line": 131, + "line": 148, "column": 71 }, "end": { - "line": 131, + "line": 148, "column": 72 } } @@ -28671,15 +32832,15 @@ "binop": null, "updateContext": null }, - "start": 4741, - "end": 4742, + "start": 5277, + "end": 5278, "loc": { "start": { - "line": 131, + "line": 148, "column": 72 }, "end": { - "line": 131, + "line": 148, "column": 73 } } @@ -28697,15 +32858,15 @@ "binop": null }, "value": "label", - "start": 4742, - "end": 4747, + "start": 5278, + "end": 5283, "loc": { "start": { - "line": 131, + "line": 148, "column": 73 }, "end": { - "line": 131, + "line": 148, "column": 78 } } @@ -28723,15 +32884,15 @@ "binop": null, "updateContext": null }, - "start": 4747, - "end": 4748, + "start": 5283, + "end": 5284, "loc": { "start": { - "line": 131, + "line": 148, "column": 78 }, "end": { - "line": 131, + "line": 148, "column": 79 } } @@ -28748,15 +32909,15 @@ "postfix": false, "binop": null }, - "start": 4753, - "end": 4754, + "start": 5289, + "end": 5290, "loc": { "start": { - "line": 132, + "line": 149, "column": 4 }, "end": { - "line": 132, + "line": 149, "column": 5 } } @@ -28776,15 +32937,15 @@ "updateContext": null }, "value": "return", - "start": 4760, - "end": 4766, + "start": 5296, + "end": 5302, "loc": { "start": { - "line": 134, + "line": 151, "column": 4 }, "end": { - "line": 134, + "line": 151, "column": 10 } } @@ -28802,15 +32963,15 @@ "binop": null }, "value": "undefined", - "start": 4767, - "end": 4776, + "start": 5303, + "end": 5312, "loc": { "start": { - "line": 134, + "line": 151, "column": 11 }, "end": { - "line": 134, + "line": 151, "column": 20 } } @@ -28828,15 +32989,15 @@ "binop": null, "updateContext": null }, - "start": 4776, - "end": 4777, + "start": 5312, + "end": 5313, "loc": { "start": { - "line": 134, + "line": 151, "column": 20 }, "end": { - "line": 134, + "line": 151, "column": 21 } } @@ -28853,15 +33014,15 @@ "postfix": false, "binop": null }, - "start": 4780, - "end": 4781, + "start": 5316, + "end": 5317, "loc": { "start": { - "line": 135, + "line": 152, "column": 2 }, "end": { - "line": 135, + "line": 152, "column": 3 } } @@ -28869,15 +33030,15 @@ { "type": "CommentBlock", "value": "*\n * Given a node label, attempt to parse it as a scientific name.\n *\n * Note that this is NOT memoized -- you should really be using\n * TaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\n * than calling this directly.\n *\n * @return A taxonomic unit that corresponds to this taxon concept.\n ", - "start": 4785, - "end": 5124, + "start": 5321, + "end": 5660, "loc": { "start": { - "line": 137, + "line": 154, "column": 2 }, "end": { - "line": 145, + "line": 162, "column": 5 } } @@ -28895,15 +33056,15 @@ "binop": null }, "value": "static", - "start": 5127, - "end": 5133, + "start": 5663, + "end": 5669, "loc": { "start": { - "line": 146, + "line": 163, "column": 2 }, "end": { - "line": 146, + "line": 163, "column": 8 } } @@ -28921,15 +33082,15 @@ "binop": null }, "value": "fromLabel", - "start": 5134, - "end": 5143, + "start": 5670, + "end": 5679, "loc": { "start": { - "line": 146, + "line": 163, "column": 9 }, "end": { - "line": 146, + "line": 163, "column": 18 } } @@ -28946,15 +33107,15 @@ "postfix": false, "binop": null }, - "start": 5143, - "end": 5144, + "start": 5679, + "end": 5680, "loc": { "start": { - "line": 146, + "line": 163, "column": 18 }, "end": { - "line": 146, + "line": 163, "column": 19 } } @@ -28972,15 +33133,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5144, - "end": 5153, + "start": 5680, + "end": 5689, "loc": { "start": { - "line": 146, + "line": 163, "column": 19 }, "end": { - "line": 146, + "line": 163, "column": 28 } } @@ -28998,15 +33159,15 @@ "binop": null, "updateContext": null }, - "start": 5153, - "end": 5154, + "start": 5689, + "end": 5690, "loc": { "start": { - "line": 146, + "line": 163, "column": 28 }, "end": { - "line": 146, + "line": 163, "column": 29 } } @@ -29024,15 +33185,15 @@ "binop": null }, "value": "nomenCode", - "start": 5155, - "end": 5164, + "start": 5691, + "end": 5700, "loc": { "start": { - "line": 146, + "line": 163, "column": 30 }, "end": { - "line": 146, + "line": 163, "column": 39 } } @@ -29051,15 +33212,15 @@ "updateContext": null }, "value": "=", - "start": 5165, - "end": 5166, + "start": 5701, + "end": 5702, "loc": { "start": { - "line": 146, + "line": 163, "column": 40 }, "end": { - "line": 146, + "line": 163, "column": 41 } } @@ -29077,15 +33238,15 @@ "binop": null }, "value": "owlterms", - "start": 5167, - "end": 5175, + "start": 5703, + "end": 5711, "loc": { "start": { - "line": 146, + "line": 163, "column": 42 }, "end": { - "line": 146, + "line": 163, "column": 50 } } @@ -29103,15 +33264,15 @@ "binop": null, "updateContext": null }, - "start": 5175, - "end": 5176, + "start": 5711, + "end": 5712, "loc": { "start": { - "line": 146, + "line": 163, "column": 50 }, "end": { - "line": 146, + "line": 163, "column": 51 } } @@ -29129,15 +33290,15 @@ "binop": null }, "value": "UNKNOWN_CODE", - "start": 5176, - "end": 5188, + "start": 5712, + "end": 5724, "loc": { "start": { - "line": 146, + "line": 163, "column": 51 }, "end": { - "line": 146, + "line": 163, "column": 63 } } @@ -29154,15 +33315,15 @@ "postfix": false, "binop": null }, - "start": 5188, - "end": 5189, + "start": 5724, + "end": 5725, "loc": { "start": { - "line": 146, + "line": 163, "column": 63 }, "end": { - "line": 146, + "line": 163, "column": 64 } } @@ -29179,15 +33340,15 @@ "postfix": false, "binop": null }, - "start": 5190, - "end": 5191, + "start": 5726, + "end": 5727, "loc": { "start": { - "line": 146, + "line": 163, "column": 65 }, "end": { - "line": 146, + "line": 163, "column": 66 } } @@ -29207,15 +33368,15 @@ "updateContext": null }, "value": "if", - "start": 5196, - "end": 5198, + "start": 5732, + "end": 5734, "loc": { "start": { - "line": 147, + "line": 164, "column": 4 }, "end": { - "line": 147, + "line": 164, "column": 6 } } @@ -29232,15 +33393,15 @@ "postfix": false, "binop": null }, - "start": 5199, - "end": 5200, + "start": 5735, + "end": 5736, "loc": { "start": { - "line": 147, + "line": 164, "column": 7 }, "end": { - "line": 147, + "line": 164, "column": 8 } } @@ -29258,15 +33419,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5200, - "end": 5209, + "start": 5736, + "end": 5745, "loc": { "start": { - "line": 147, + "line": 164, "column": 8 }, "end": { - "line": 147, + "line": 164, "column": 17 } } @@ -29285,15 +33446,15 @@ "updateContext": null }, "value": "===", - "start": 5210, - "end": 5213, + "start": 5746, + "end": 5749, "loc": { "start": { - "line": 147, + "line": 164, "column": 18 }, "end": { - "line": 147, + "line": 164, "column": 21 } } @@ -29311,15 +33472,15 @@ "binop": null }, "value": "undefined", - "start": 5214, - "end": 5223, + "start": 5750, + "end": 5759, "loc": { "start": { - "line": 147, + "line": 164, "column": 22 }, "end": { - "line": 147, + "line": 164, "column": 31 } } @@ -29338,15 +33499,15 @@ "updateContext": null }, "value": "||", - "start": 5224, - "end": 5226, + "start": 5760, + "end": 5762, "loc": { "start": { - "line": 147, + "line": 164, "column": 32 }, "end": { - "line": 147, + "line": 164, "column": 34 } } @@ -29364,15 +33525,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5227, - "end": 5236, + "start": 5763, + "end": 5772, "loc": { "start": { - "line": 147, + "line": 164, "column": 35 }, "end": { - "line": 147, + "line": 164, "column": 44 } } @@ -29391,15 +33552,15 @@ "updateContext": null }, "value": "===", - "start": 5237, - "end": 5240, + "start": 5773, + "end": 5776, "loc": { "start": { - "line": 147, + "line": 164, "column": 45 }, "end": { - "line": 147, + "line": 164, "column": 48 } } @@ -29419,15 +33580,15 @@ "updateContext": null }, "value": "null", - "start": 5241, - "end": 5245, + "start": 5777, + "end": 5781, "loc": { "start": { - "line": 147, + "line": 164, "column": 49 }, "end": { - "line": 147, + "line": 164, "column": 53 } } @@ -29446,15 +33607,15 @@ "updateContext": null }, "value": "||", - "start": 5246, - "end": 5248, + "start": 5782, + "end": 5784, "loc": { "start": { - "line": 147, + "line": 164, "column": 54 }, "end": { - "line": 147, + "line": 164, "column": 56 } } @@ -29472,15 +33633,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5249, - "end": 5258, + "start": 5785, + "end": 5794, "loc": { "start": { - "line": 147, + "line": 164, "column": 57 }, "end": { - "line": 147, + "line": 164, "column": 66 } } @@ -29498,15 +33659,15 @@ "binop": null, "updateContext": null }, - "start": 5258, - "end": 5259, + "start": 5794, + "end": 5795, "loc": { "start": { - "line": 147, + "line": 164, "column": 66 }, "end": { - "line": 147, + "line": 164, "column": 67 } } @@ -29524,15 +33685,15 @@ "binop": null }, "value": "trim", - "start": 5259, - "end": 5263, + "start": 5795, + "end": 5799, "loc": { "start": { - "line": 147, + "line": 164, "column": 67 }, "end": { - "line": 147, + "line": 164, "column": 71 } } @@ -29549,15 +33710,15 @@ "postfix": false, "binop": null }, - "start": 5263, - "end": 5264, + "start": 5799, + "end": 5800, "loc": { "start": { - "line": 147, + "line": 164, "column": 71 }, "end": { - "line": 147, + "line": 164, "column": 72 } } @@ -29574,15 +33735,15 @@ "postfix": false, "binop": null }, - "start": 5264, - "end": 5265, + "start": 5800, + "end": 5801, "loc": { "start": { - "line": 147, + "line": 164, "column": 72 }, "end": { - "line": 147, + "line": 164, "column": 73 } } @@ -29601,15 +33762,15 @@ "updateContext": null }, "value": "===", - "start": 5266, - "end": 5269, + "start": 5802, + "end": 5805, "loc": { "start": { - "line": 147, + "line": 164, "column": 74 }, "end": { - "line": 147, + "line": 164, "column": 77 } } @@ -29628,15 +33789,15 @@ "updateContext": null }, "value": "", - "start": 5270, - "end": 5272, + "start": 5806, + "end": 5808, "loc": { "start": { - "line": 147, + "line": 164, "column": 78 }, "end": { - "line": 147, + "line": 164, "column": 80 } } @@ -29653,15 +33814,15 @@ "postfix": false, "binop": null }, - "start": 5272, - "end": 5273, + "start": 5808, + "end": 5809, "loc": { "start": { - "line": 147, + "line": 164, "column": 80 }, "end": { - "line": 147, + "line": 164, "column": 81 } } @@ -29681,15 +33842,15 @@ "updateContext": null }, "value": "return", - "start": 5274, - "end": 5280, + "start": 5810, + "end": 5816, "loc": { "start": { - "line": 147, + "line": 164, "column": 82 }, "end": { - "line": 147, + "line": 164, "column": 88 } } @@ -29707,15 +33868,15 @@ "binop": null }, "value": "undefined", - "start": 5281, - "end": 5290, + "start": 5817, + "end": 5826, "loc": { "start": { - "line": 147, + "line": 164, "column": 89 }, "end": { - "line": 147, + "line": 164, "column": 98 } } @@ -29733,15 +33894,15 @@ "binop": null, "updateContext": null }, - "start": 5290, - "end": 5291, + "start": 5826, + "end": 5827, "loc": { "start": { - "line": 147, + "line": 164, "column": 98 }, "end": { - "line": 147, + "line": 164, "column": 99 } } @@ -29749,15 +33910,15 @@ { "type": "CommentLine", "value": " Check if this label can be divided into a name and a sensu/sec component.", - "start": 5297, - "end": 5373, + "start": 5833, + "end": 5909, "loc": { "start": { - "line": 149, + "line": 166, "column": 4 }, "end": { - "line": 149, + "line": 166, "column": 80 } } @@ -29777,15 +33938,15 @@ "updateContext": null }, "value": "const", - "start": 5378, - "end": 5383, + "start": 5914, + "end": 5919, "loc": { "start": { - "line": 150, + "line": 167, "column": 4 }, "end": { - "line": 150, + "line": 167, "column": 9 } } @@ -29803,15 +33964,15 @@ "binop": null }, "value": "match", - "start": 5384, - "end": 5389, + "start": 5920, + "end": 5925, "loc": { "start": { - "line": 150, + "line": 167, "column": 10 }, "end": { - "line": 150, + "line": 167, "column": 15 } } @@ -29830,15 +33991,15 @@ "updateContext": null }, "value": "=", - "start": 5390, - "end": 5391, + "start": 5926, + "end": 5927, "loc": { "start": { - "line": 150, + "line": 167, "column": 16 }, "end": { - "line": 150, + "line": 167, "column": 17 } } @@ -29860,15 +34021,15 @@ "pattern": "^\\s*(.*)\\s+(?:sec|sensu)\\.?\\s+(.*)\\s*$", "flags": "" }, - "start": 5392, - "end": 5432, + "start": 5928, + "end": 5968, "loc": { "start": { - "line": 150, + "line": 167, "column": 18 }, "end": { - "line": 150, + "line": 167, "column": 58 } } @@ -29886,15 +34047,15 @@ "binop": null, "updateContext": null }, - "start": 5432, - "end": 5433, + "start": 5968, + "end": 5969, "loc": { "start": { - "line": 150, + "line": 167, "column": 58 }, "end": { - "line": 150, + "line": 167, "column": 59 } } @@ -29912,15 +34073,15 @@ "binop": null }, "value": "exec", - "start": 5433, - "end": 5437, + "start": 5969, + "end": 5973, "loc": { "start": { - "line": 150, + "line": 167, "column": 59 }, "end": { - "line": 150, + "line": 167, "column": 63 } } @@ -29937,15 +34098,15 @@ "postfix": false, "binop": null }, - "start": 5437, - "end": 5438, + "start": 5973, + "end": 5974, "loc": { "start": { - "line": 150, + "line": 167, "column": 63 }, "end": { - "line": 150, + "line": 167, "column": 64 } } @@ -29963,15 +34124,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5438, - "end": 5447, + "start": 5974, + "end": 5983, "loc": { "start": { - "line": 150, + "line": 167, "column": 64 }, "end": { - "line": 150, + "line": 167, "column": 73 } } @@ -29988,15 +34149,15 @@ "postfix": false, "binop": null }, - "start": 5447, - "end": 5448, + "start": 5983, + "end": 5984, "loc": { "start": { - "line": 150, + "line": 167, "column": 73 }, "end": { - "line": 150, + "line": 167, "column": 74 } } @@ -30014,15 +34175,15 @@ "binop": null, "updateContext": null }, - "start": 5448, - "end": 5449, + "start": 5984, + "end": 5985, "loc": { "start": { - "line": 150, + "line": 167, "column": 74 }, "end": { - "line": 150, + "line": 167, "column": 75 } } @@ -30042,15 +34203,15 @@ "updateContext": null }, "value": "let", - "start": 5454, - "end": 5457, + "start": 5990, + "end": 5993, "loc": { "start": { - "line": 151, + "line": 168, "column": 4 }, "end": { - "line": 151, + "line": 168, "column": 7 } } @@ -30068,15 +34229,15 @@ "binop": null }, "value": "accordingTo", - "start": 5458, - "end": 5469, + "start": 5994, + "end": 6005, "loc": { "start": { - "line": 151, + "line": 168, "column": 8 }, "end": { - "line": 151, + "line": 168, "column": 19 } } @@ -30094,15 +34255,15 @@ "binop": null, "updateContext": null }, - "start": 5469, - "end": 5470, + "start": 6005, + "end": 6006, "loc": { "start": { - "line": 151, + "line": 168, "column": 19 }, "end": { - "line": 151, + "line": 168, "column": 20 } } @@ -30122,15 +34283,15 @@ "updateContext": null }, "value": "if", - "start": 5475, - "end": 5477, + "start": 6011, + "end": 6013, "loc": { "start": { - "line": 152, + "line": 169, "column": 4 }, "end": { - "line": 152, + "line": 169, "column": 6 } } @@ -30147,15 +34308,15 @@ "postfix": false, "binop": null }, - "start": 5478, - "end": 5479, + "start": 6014, + "end": 6015, "loc": { "start": { - "line": 152, + "line": 169, "column": 7 }, "end": { - "line": 152, + "line": 169, "column": 8 } } @@ -30173,15 +34334,15 @@ "binop": null }, "value": "match", - "start": 5479, - "end": 5484, + "start": 6015, + "end": 6020, "loc": { "start": { - "line": 152, + "line": 169, "column": 8 }, "end": { - "line": 152, + "line": 169, "column": 13 } } @@ -30198,15 +34359,15 @@ "postfix": false, "binop": null }, - "start": 5484, - "end": 5485, + "start": 6020, + "end": 6021, "loc": { "start": { - "line": 152, + "line": 169, "column": 13 }, "end": { - "line": 152, + "line": 169, "column": 14 } } @@ -30223,15 +34384,15 @@ "postfix": false, "binop": null }, - "start": 5486, - "end": 5487, + "start": 6022, + "end": 6023, "loc": { "start": { - "line": 152, + "line": 169, "column": 15 }, "end": { - "line": 152, + "line": 169, "column": 16 } } @@ -30249,15 +34410,15 @@ "binop": null }, "value": "accordingTo", - "start": 5494, - "end": 5505, + "start": 6030, + "end": 6041, "loc": { "start": { - "line": 153, + "line": 170, "column": 6 }, "end": { - "line": 153, + "line": 170, "column": 17 } } @@ -30276,15 +34437,15 @@ "updateContext": null }, "value": "=", - "start": 5506, - "end": 5507, + "start": 6042, + "end": 6043, "loc": { "start": { - "line": 153, + "line": 170, "column": 18 }, "end": { - "line": 153, + "line": 170, "column": 19 } } @@ -30302,15 +34463,15 @@ "binop": null }, "value": "match", - "start": 5508, - "end": 5513, + "start": 6044, + "end": 6049, "loc": { "start": { - "line": 153, + "line": 170, "column": 20 }, "end": { - "line": 153, + "line": 170, "column": 25 } } @@ -30328,15 +34489,15 @@ "binop": null, "updateContext": null }, - "start": 5513, - "end": 5514, + "start": 6049, + "end": 6050, "loc": { "start": { - "line": 153, + "line": 170, "column": 25 }, "end": { - "line": 153, + "line": 170, "column": 26 } } @@ -30355,15 +34516,15 @@ "updateContext": null }, "value": 2, - "start": 5514, - "end": 5515, + "start": 6050, + "end": 6051, "loc": { "start": { - "line": 153, + "line": 170, "column": 26 }, "end": { - "line": 153, + "line": 170, "column": 27 } } @@ -30381,15 +34542,15 @@ "binop": null, "updateContext": null }, - "start": 5515, - "end": 5516, + "start": 6051, + "end": 6052, "loc": { "start": { - "line": 153, + "line": 170, "column": 27 }, "end": { - "line": 153, + "line": 170, "column": 28 } } @@ -30407,15 +34568,15 @@ "binop": null, "updateContext": null }, - "start": 5516, - "end": 5517, + "start": 6052, + "end": 6053, "loc": { "start": { - "line": 153, + "line": 170, "column": 28 }, "end": { - "line": 153, + "line": 170, "column": 29 } } @@ -30432,15 +34593,15 @@ "postfix": false, "binop": null }, - "start": 5522, - "end": 5523, + "start": 6058, + "end": 6059, "loc": { "start": { - "line": 154, + "line": 171, "column": 4 }, "end": { - "line": 154, + "line": 171, "column": 5 } } @@ -30448,15 +34609,15 @@ { "type": "CommentLine", "value": " Can we parse it as a taxon name? If not, we will return undefined.", - "start": 5529, - "end": 5598, + "start": 6065, + "end": 6134, "loc": { "start": { - "line": 156, + "line": 173, "column": 4 }, "end": { - "line": 156, + "line": 173, "column": 73 } } @@ -30476,15 +34637,15 @@ "updateContext": null }, "value": "const", - "start": 5603, - "end": 5608, + "start": 6139, + "end": 6144, "loc": { "start": { - "line": 157, + "line": 174, "column": 4 }, "end": { - "line": 157, + "line": 174, "column": 9 } } @@ -30502,15 +34663,15 @@ "binop": null }, "value": "taxonName", - "start": 5609, - "end": 5618, + "start": 6145, + "end": 6154, "loc": { "start": { - "line": 157, + "line": 174, "column": 10 }, "end": { - "line": 157, + "line": 174, "column": 19 } } @@ -30529,15 +34690,15 @@ "updateContext": null }, "value": "=", - "start": 5619, - "end": 5620, + "start": 6155, + "end": 6156, "loc": { "start": { - "line": 157, + "line": 174, "column": 20 }, "end": { - "line": 157, + "line": 174, "column": 21 } } @@ -30555,15 +34716,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 5621, - "end": 5637, + "start": 6157, + "end": 6173, "loc": { "start": { - "line": 157, + "line": 174, "column": 22 }, "end": { - "line": 157, + "line": 174, "column": 38 } } @@ -30581,15 +34742,15 @@ "binop": null, "updateContext": null }, - "start": 5637, - "end": 5638, + "start": 6173, + "end": 6174, "loc": { "start": { - "line": 157, + "line": 174, "column": 38 }, "end": { - "line": 157, + "line": 174, "column": 39 } } @@ -30607,15 +34768,15 @@ "binop": null }, "value": "fromVerbatimName", - "start": 5638, - "end": 5654, + "start": 6174, + "end": 6190, "loc": { "start": { - "line": 157, + "line": 174, "column": 39 }, "end": { - "line": 157, + "line": 174, "column": 55 } } @@ -30632,15 +34793,15 @@ "postfix": false, "binop": null }, - "start": 5654, - "end": 5655, + "start": 6190, + "end": 6191, "loc": { "start": { - "line": 157, + "line": 174, "column": 55 }, "end": { - "line": 157, + "line": 174, "column": 56 } } @@ -30658,15 +34819,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5655, - "end": 5664, + "start": 6191, + "end": 6200, "loc": { "start": { - "line": 157, + "line": 174, "column": 56 }, "end": { - "line": 157, + "line": 174, "column": 65 } } @@ -30684,15 +34845,15 @@ "binop": null, "updateContext": null }, - "start": 5664, - "end": 5665, + "start": 6200, + "end": 6201, "loc": { "start": { - "line": 157, + "line": 174, "column": 65 }, "end": { - "line": 157, + "line": 174, "column": 66 } } @@ -30710,15 +34871,15 @@ "binop": null }, "value": "nomenCode", - "start": 5666, - "end": 5675, + "start": 6202, + "end": 6211, "loc": { "start": { - "line": 157, + "line": 174, "column": 67 }, "end": { - "line": 157, + "line": 174, "column": 76 } } @@ -30735,15 +34896,15 @@ "postfix": false, "binop": null }, - "start": 5675, - "end": 5676, + "start": 6211, + "end": 6212, "loc": { "start": { - "line": 157, + "line": 174, "column": 76 }, "end": { - "line": 157, + "line": 174, "column": 77 } } @@ -30761,15 +34922,15 @@ "binop": null, "updateContext": null }, - "start": 5676, - "end": 5677, + "start": 6212, + "end": 6213, "loc": { "start": { - "line": 157, + "line": 174, "column": 77 }, "end": { - "line": 157, + "line": 174, "column": 78 } } @@ -30789,15 +34950,15 @@ "updateContext": null }, "value": "if", - "start": 5682, - "end": 5684, + "start": 6218, + "end": 6220, "loc": { "start": { - "line": 158, + "line": 175, "column": 4 }, "end": { - "line": 158, + "line": 175, "column": 6 } } @@ -30814,15 +34975,15 @@ "postfix": false, "binop": null }, - "start": 5685, - "end": 5686, + "start": 6221, + "end": 6222, "loc": { "start": { - "line": 158, + "line": 175, "column": 7 }, "end": { - "line": 158, + "line": 175, "column": 8 } } @@ -30840,15 +35001,15 @@ "binop": null }, "value": "taxonName", - "start": 5686, - "end": 5695, + "start": 6222, + "end": 6231, "loc": { "start": { - "line": 158, + "line": 175, "column": 8 }, "end": { - "line": 158, + "line": 175, "column": 17 } } @@ -30865,15 +35026,15 @@ "postfix": false, "binop": null }, - "start": 5695, - "end": 5696, + "start": 6231, + "end": 6232, "loc": { "start": { - "line": 158, + "line": 175, "column": 17 }, "end": { - "line": 158, + "line": 175, "column": 18 } } @@ -30890,15 +35051,15 @@ "postfix": false, "binop": null }, - "start": 5697, - "end": 5698, + "start": 6233, + "end": 6234, "loc": { "start": { - "line": 158, + "line": 175, "column": 19 }, "end": { - "line": 158, + "line": 175, "column": 20 } } @@ -30918,15 +35079,15 @@ "updateContext": null }, "value": "return", - "start": 5705, - "end": 5711, + "start": 6241, + "end": 6247, "loc": { "start": { - "line": 159, + "line": 176, "column": 6 }, "end": { - "line": 159, + "line": 176, "column": 12 } } @@ -30944,15 +35105,15 @@ "binop": null }, "value": "TaxonConceptWrapper", - "start": 5712, - "end": 5731, + "start": 6248, + "end": 6267, "loc": { "start": { - "line": 159, + "line": 176, "column": 13 }, "end": { - "line": 159, + "line": 176, "column": 32 } } @@ -30970,15 +35131,15 @@ "binop": null, "updateContext": null }, - "start": 5731, - "end": 5732, + "start": 6267, + "end": 6268, "loc": { "start": { - "line": 159, + "line": 176, "column": 32 }, "end": { - "line": 159, + "line": 176, "column": 33 } } @@ -30996,15 +35157,15 @@ "binop": null }, "value": "wrapTaxonName", - "start": 5732, - "end": 5745, + "start": 6268, + "end": 6281, "loc": { "start": { - "line": 159, + "line": 176, "column": 33 }, "end": { - "line": 159, + "line": 176, "column": 46 } } @@ -31021,15 +35182,15 @@ "postfix": false, "binop": null }, - "start": 5745, - "end": 5746, + "start": 6281, + "end": 6282, "loc": { "start": { - "line": 159, + "line": 176, "column": 46 }, "end": { - "line": 159, + "line": 176, "column": 47 } } @@ -31047,15 +35208,15 @@ "binop": null }, "value": "taxonName", - "start": 5746, - "end": 5755, + "start": 6282, + "end": 6291, "loc": { "start": { - "line": 159, + "line": 176, "column": 47 }, "end": { - "line": 159, + "line": 176, "column": 56 } } @@ -31073,15 +35234,15 @@ "binop": null, "updateContext": null }, - "start": 5755, - "end": 5756, + "start": 6291, + "end": 6292, "loc": { "start": { - "line": 159, + "line": 176, "column": 56 }, "end": { - "line": 159, + "line": 176, "column": 57 } } @@ -31099,15 +35260,15 @@ "binop": null }, "value": "accordingTo", - "start": 5757, - "end": 5768, + "start": 6293, + "end": 6304, "loc": { "start": { - "line": 159, + "line": 176, "column": 58 }, "end": { - "line": 159, + "line": 176, "column": 69 } } @@ -31124,15 +35285,15 @@ "postfix": false, "binop": null }, - "start": 5768, - "end": 5769, + "start": 6304, + "end": 6305, "loc": { "start": { - "line": 159, + "line": 176, "column": 69 }, "end": { - "line": 159, + "line": 176, "column": 70 } } @@ -31150,15 +35311,15 @@ "binop": null, "updateContext": null }, - "start": 5769, - "end": 5770, + "start": 6305, + "end": 6306, "loc": { "start": { - "line": 159, + "line": 176, "column": 70 }, "end": { - "line": 159, + "line": 176, "column": 71 } } @@ -31175,15 +35336,15 @@ "postfix": false, "binop": null }, - "start": 5775, - "end": 5776, + "start": 6311, + "end": 6312, "loc": { "start": { - "line": 160, + "line": 177, "column": 4 }, "end": { - "line": 160, + "line": 177, "column": 5 } } @@ -31191,15 +35352,15 @@ { "type": "CommentLine", "value": " Couldn't parse it at all.", - "start": 5782, - "end": 5810, + "start": 6318, + "end": 6346, "loc": { "start": { - "line": 162, + "line": 179, "column": 4 }, "end": { - "line": 162, + "line": 179, "column": 32 } } @@ -31219,15 +35380,15 @@ "updateContext": null }, "value": "return", - "start": 5815, - "end": 5821, + "start": 6351, + "end": 6357, "loc": { "start": { - "line": 163, + "line": 180, "column": 4 }, "end": { - "line": 163, + "line": 180, "column": 10 } } @@ -31245,15 +35406,15 @@ "binop": null }, "value": "undefined", - "start": 5822, - "end": 5831, + "start": 6358, + "end": 6367, "loc": { "start": { - "line": 163, + "line": 180, "column": 11 }, "end": { - "line": 163, + "line": 180, "column": 20 } } @@ -31271,15 +35432,15 @@ "binop": null, "updateContext": null }, - "start": 5831, - "end": 5832, + "start": 6367, + "end": 6368, "loc": { "start": { - "line": 163, + "line": 180, "column": 20 }, "end": { - "line": 163, + "line": 180, "column": 21 } } @@ -31296,15 +35457,15 @@ "postfix": false, "binop": null }, - "start": 5835, - "end": 5836, + "start": 6371, + "end": 6372, "loc": { "start": { - "line": 164, + "line": 181, "column": 2 }, "end": { - "line": 164, + "line": 181, "column": 3 } } @@ -31312,15 +35473,15 @@ { "type": "CommentBlock", "value": "* Wrap a taxon name with a particular TaxonName object and an accordingTo (string). ", - "start": 5840, - "end": 5928, + "start": 6376, + "end": 6464, "loc": { "start": { - "line": 166, + "line": 183, "column": 2 }, "end": { - "line": 166, + "line": 183, "column": 90 } } @@ -31338,15 +35499,15 @@ "binop": null }, "value": "static", - "start": 5931, - "end": 5937, + "start": 6467, + "end": 6473, "loc": { "start": { - "line": 167, + "line": 184, "column": 2 }, "end": { - "line": 167, + "line": 184, "column": 8 } } @@ -31364,15 +35525,15 @@ "binop": null }, "value": "wrapTaxonName", - "start": 5938, - "end": 5951, + "start": 6474, + "end": 6487, "loc": { "start": { - "line": 167, + "line": 184, "column": 9 }, "end": { - "line": 167, + "line": 184, "column": 22 } } @@ -31389,15 +35550,15 @@ "postfix": false, "binop": null }, - "start": 5951, - "end": 5952, + "start": 6487, + "end": 6488, "loc": { "start": { - "line": 167, + "line": 184, "column": 22 }, "end": { - "line": 167, + "line": 184, "column": 23 } } @@ -31415,15 +35576,15 @@ "binop": null }, "value": "taxonName", - "start": 5952, - "end": 5961, + "start": 6488, + "end": 6497, "loc": { "start": { - "line": 167, + "line": 184, "column": 23 }, "end": { - "line": 167, + "line": 184, "column": 32 } } @@ -31441,15 +35602,15 @@ "binop": null, "updateContext": null }, - "start": 5961, - "end": 5962, + "start": 6497, + "end": 6498, "loc": { "start": { - "line": 167, + "line": 184, "column": 32 }, "end": { - "line": 167, + "line": 184, "column": 33 } } @@ -31467,15 +35628,15 @@ "binop": null }, "value": "accordingTo", - "start": 5963, - "end": 5974, + "start": 6499, + "end": 6510, "loc": { "start": { - "line": 167, + "line": 184, "column": 34 }, "end": { - "line": 167, + "line": 184, "column": 45 } } @@ -31492,15 +35653,15 @@ "postfix": false, "binop": null }, - "start": 5974, - "end": 5975, + "start": 6510, + "end": 6511, "loc": { "start": { - "line": 167, + "line": 184, "column": 45 }, "end": { - "line": 167, + "line": 184, "column": 46 } } @@ -31517,15 +35678,15 @@ "postfix": false, "binop": null }, - "start": 5976, - "end": 5977, + "start": 6512, + "end": 6513, "loc": { "start": { - "line": 167, + "line": 184, "column": 47 }, "end": { - "line": 167, + "line": 184, "column": 48 } } @@ -31545,15 +35706,15 @@ "updateContext": null }, "value": "const", - "start": 5982, - "end": 5987, + "start": 6518, + "end": 6523, "loc": { "start": { - "line": 168, + "line": 185, "column": 4 }, "end": { - "line": 168, + "line": 185, "column": 9 } } @@ -31571,15 +35732,15 @@ "binop": null }, "value": "result", - "start": 5988, - "end": 5994, + "start": 6524, + "end": 6530, "loc": { "start": { - "line": 168, + "line": 185, "column": 10 }, "end": { - "line": 168, + "line": 185, "column": 16 } } @@ -31598,15 +35759,15 @@ "updateContext": null }, "value": "=", - "start": 5995, - "end": 5996, + "start": 6531, + "end": 6532, "loc": { "start": { - "line": 168, + "line": 185, "column": 17 }, "end": { - "line": 168, + "line": 185, "column": 18 } } @@ -31623,15 +35784,15 @@ "postfix": false, "binop": null }, - "start": 5997, - "end": 5998, + "start": 6533, + "end": 6534, "loc": { "start": { - "line": 168, + "line": 185, "column": 19 }, "end": { - "line": 168, + "line": 185, "column": 20 } } @@ -31650,15 +35811,15 @@ "updateContext": null }, "value": "@type", - "start": 6005, - "end": 6012, + "start": 6541, + "end": 6548, "loc": { "start": { - "line": 169, + "line": 186, "column": 6 }, "end": { - "line": 169, + "line": 186, "column": 13 } } @@ -31676,15 +35837,15 @@ "binop": null, "updateContext": null }, - "start": 6012, - "end": 6013, + "start": 6548, + "end": 6549, "loc": { "start": { - "line": 169, + "line": 186, "column": 13 }, "end": { - "line": 169, + "line": 186, "column": 14 } } @@ -31702,15 +35863,15 @@ "binop": null }, "value": "TaxonConceptWrapper", - "start": 6014, - "end": 6033, + "start": 6550, + "end": 6569, "loc": { "start": { - "line": 169, + "line": 186, "column": 15 }, "end": { - "line": 169, + "line": 186, "column": 34 } } @@ -31728,15 +35889,15 @@ "binop": null, "updateContext": null }, - "start": 6033, - "end": 6034, + "start": 6569, + "end": 6570, "loc": { "start": { - "line": 169, + "line": 186, "column": 34 }, "end": { - "line": 169, + "line": 186, "column": 35 } } @@ -31754,15 +35915,15 @@ "binop": null }, "value": "TYPE_TAXON_CONCEPT", - "start": 6034, - "end": 6052, + "start": 6570, + "end": 6588, "loc": { "start": { - "line": 169, + "line": 186, "column": 35 }, "end": { - "line": 169, + "line": 186, "column": 53 } } @@ -31780,15 +35941,15 @@ "binop": null, "updateContext": null }, - "start": 6052, - "end": 6053, + "start": 6588, + "end": 6589, "loc": { "start": { - "line": 169, + "line": 186, "column": 53 }, "end": { - "line": 169, + "line": 186, "column": 54 } } @@ -31806,15 +35967,15 @@ "binop": null }, "value": "hasName", - "start": 6060, - "end": 6067, + "start": 6596, + "end": 6603, "loc": { "start": { - "line": 170, + "line": 187, "column": 6 }, "end": { - "line": 170, + "line": 187, "column": 13 } } @@ -31832,15 +35993,15 @@ "binop": null, "updateContext": null }, - "start": 6067, - "end": 6068, + "start": 6603, + "end": 6604, "loc": { "start": { - "line": 170, + "line": 187, "column": 13 }, "end": { - "line": 170, + "line": 187, "column": 14 } } @@ -31858,15 +36019,15 @@ "binop": null }, "value": "taxonName", - "start": 6069, - "end": 6078, + "start": 6605, + "end": 6614, "loc": { "start": { - "line": 170, + "line": 187, "column": 15 }, "end": { - "line": 170, + "line": 187, "column": 24 } } @@ -31884,15 +36045,15 @@ "binop": null, "updateContext": null }, - "start": 6078, - "end": 6079, + "start": 6614, + "end": 6615, "loc": { "start": { - "line": 170, + "line": 187, "column": 24 }, "end": { - "line": 170, + "line": 187, "column": 25 } } @@ -31909,15 +36070,15 @@ "postfix": false, "binop": null }, - "start": 6084, - "end": 6085, + "start": 6620, + "end": 6621, "loc": { "start": { - "line": 171, + "line": 188, "column": 4 }, "end": { - "line": 171, + "line": 188, "column": 5 } } @@ -31935,15 +36096,15 @@ "binop": null, "updateContext": null }, - "start": 6085, - "end": 6086, + "start": 6621, + "end": 6622, "loc": { "start": { - "line": 171, + "line": 188, "column": 5 }, "end": { - "line": 171, + "line": 188, "column": 6 } } @@ -31963,15 +36124,15 @@ "updateContext": null }, "value": "if", - "start": 6091, - "end": 6093, + "start": 6627, + "end": 6629, "loc": { "start": { - "line": 172, + "line": 189, "column": 4 }, "end": { - "line": 172, + "line": 189, "column": 6 } } @@ -31988,15 +36149,15 @@ "postfix": false, "binop": null }, - "start": 6094, - "end": 6095, + "start": 6630, + "end": 6631, "loc": { "start": { - "line": 172, + "line": 189, "column": 7 }, "end": { - "line": 172, + "line": 189, "column": 8 } } @@ -32014,15 +36175,15 @@ "binop": null }, "value": "accordingTo", - "start": 6095, - "end": 6106, + "start": 6631, + "end": 6642, "loc": { "start": { - "line": 172, + "line": 189, "column": 8 }, "end": { - "line": 172, + "line": 189, "column": 19 } } @@ -32039,15 +36200,15 @@ "postfix": false, "binop": null }, - "start": 6106, - "end": 6107, + "start": 6642, + "end": 6643, "loc": { "start": { - "line": 172, + "line": 189, "column": 19 }, "end": { - "line": 172, + "line": 189, "column": 20 } } @@ -32065,15 +36226,15 @@ "binop": null }, "value": "result", - "start": 6108, - "end": 6114, + "start": 6644, + "end": 6650, "loc": { "start": { - "line": 172, + "line": 189, "column": 21 }, "end": { - "line": 172, + "line": 189, "column": 27 } } @@ -32091,15 +36252,15 @@ "binop": null, "updateContext": null }, - "start": 6114, - "end": 6115, + "start": 6650, + "end": 6651, "loc": { "start": { - "line": 172, + "line": 189, "column": 27 }, "end": { - "line": 172, + "line": 189, "column": 28 } } @@ -32117,15 +36278,15 @@ "binop": null }, "value": "accordingTo", - "start": 6115, - "end": 6126, + "start": 6651, + "end": 6662, "loc": { "start": { - "line": 172, + "line": 189, "column": 28 }, "end": { - "line": 172, + "line": 189, "column": 39 } } @@ -32144,15 +36305,15 @@ "updateContext": null }, "value": "=", - "start": 6127, - "end": 6128, + "start": 6663, + "end": 6664, "loc": { "start": { - "line": 172, + "line": 189, "column": 40 }, "end": { - "line": 172, + "line": 189, "column": 41 } } @@ -32170,15 +36331,15 @@ "binop": null }, "value": "accordingTo", - "start": 6129, - "end": 6140, + "start": 6665, + "end": 6676, "loc": { "start": { - "line": 172, + "line": 189, "column": 42 }, "end": { - "line": 172, + "line": 189, "column": 53 } } @@ -32196,15 +36357,15 @@ "binop": null, "updateContext": null }, - "start": 6140, - "end": 6141, + "start": 6676, + "end": 6677, "loc": { "start": { - "line": 172, + "line": 189, "column": 53 }, "end": { - "line": 172, + "line": 189, "column": 54 } } @@ -32224,15 +36385,15 @@ "updateContext": null }, "value": "return", - "start": 6146, - "end": 6152, + "start": 6682, + "end": 6688, "loc": { "start": { - "line": 173, + "line": 190, "column": 4 }, "end": { - "line": 173, + "line": 190, "column": 10 } } @@ -32250,15 +36411,15 @@ "binop": null }, "value": "result", - "start": 6153, - "end": 6159, + "start": 6689, + "end": 6695, "loc": { "start": { - "line": 173, + "line": 190, "column": 11 }, "end": { - "line": 173, + "line": 190, "column": 17 } } @@ -32276,15 +36437,15 @@ "binop": null, "updateContext": null }, - "start": 6159, - "end": 6160, + "start": 6695, + "end": 6696, "loc": { "start": { - "line": 173, + "line": 190, "column": 17 }, "end": { - "line": 173, + "line": 190, "column": 18 } } @@ -32301,15 +36462,15 @@ "postfix": false, "binop": null }, - "start": 6163, - "end": 6164, + "start": 6699, + "end": 6700, "loc": { "start": { - "line": 174, + "line": 191, "column": 2 }, "end": { - "line": 174, + "line": 191, "column": 3 } } @@ -32317,15 +36478,15 @@ { "type": "CommentBlock", "value": "*\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n ", - "start": 6168, - "end": 6406, + "start": 6704, + "end": 6942, "loc": { "start": { - "line": 176, + "line": 193, "column": 2 }, "end": { - "line": 181, + "line": 198, "column": 5 } } @@ -32343,15 +36504,15 @@ "binop": null }, "value": "get", - "start": 6409, - "end": 6412, + "start": 6945, + "end": 6948, "loc": { "start": { - "line": 182, + "line": 199, "column": 2 }, "end": { - "line": 182, + "line": 199, "column": 5 } } @@ -32369,15 +36530,15 @@ "binop": null }, "value": "asOWLEquivClass", - "start": 6413, - "end": 6428, + "start": 6949, + "end": 6964, "loc": { "start": { - "line": 182, + "line": 199, "column": 6 }, "end": { - "line": 182, + "line": 199, "column": 21 } } @@ -32394,15 +36555,15 @@ "postfix": false, "binop": null }, - "start": 6428, - "end": 6429, + "start": 6964, + "end": 6965, "loc": { "start": { - "line": 182, + "line": 199, "column": 21 }, "end": { - "line": 182, + "line": 199, "column": 22 } } @@ -32419,15 +36580,15 @@ "postfix": false, "binop": null }, - "start": 6429, - "end": 6430, + "start": 6965, + "end": 6966, "loc": { "start": { - "line": 182, + "line": 199, "column": 22 }, "end": { - "line": 182, + "line": 199, "column": 23 } } @@ -32444,15 +36605,15 @@ "postfix": false, "binop": null }, - "start": 6431, - "end": 6432, + "start": 6967, + "end": 6968, "loc": { "start": { - "line": 182, + "line": 199, "column": 24 }, "end": { - "line": 182, + "line": 199, "column": 25 } } @@ -32460,15 +36621,15 @@ { "type": "CommentLine", "value": " Without a taxonomicName, we can't do anything.", - "start": 6437, - "end": 6486, + "start": 6973, + "end": 7022, "loc": { "start": { - "line": 183, + "line": 200, "column": 4 }, "end": { - "line": 183, + "line": 200, "column": 53 } } @@ -32488,15 +36649,15 @@ "updateContext": null }, "value": "if", - "start": 6491, - "end": 6493, + "start": 7027, + "end": 7029, "loc": { "start": { - "line": 184, + "line": 201, "column": 4 }, "end": { - "line": 184, + "line": 201, "column": 6 } } @@ 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"line": 201, + "line": 220, "column": 74 }, "identifierName": "verbatimName" @@ -7821,29 +8938,29 @@ }, { "type": "IfStatement", - "start": 6803, - "end": 7073, + "start": 7436, + "end": 7706, "loc": { "start": { - "line": 203, + "line": 222, "column": 6 }, "end": { - "line": 211, + "line": 230, "column": 7 } }, "test": { "type": "Identifier", - "start": 6807, - "end": 6814, + "start": 7440, + "end": 7447, "loc": { "start": { - "line": 203, + "line": 222, "column": 10 }, "end": { - "line": 203, + "line": 222, "column": 17 }, "identifierName": "results" @@ -7852,59 +8969,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6816, - "end": 7073, + "start": 7449, + "end": 7706, "loc": { "start": { - "line": 203, + "line": 222, "column": 19 }, "end": { - "line": 211, + "line": 230, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 6826, - "end": 7065, + "start": 7459, + "end": 7698, "loc": { "start": { - "line": 204, + "line": 223, "column": 8 }, "end": { - "line": 210, + "line": 229, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 6826, - "end": 7064, + "start": 7459, + "end": 7697, "loc": { "start": { - "line": 204, + "line": 223, "column": 8 }, "end": { - "line": 210, + "line": 229, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 6826, - "end": 6832, + "start": 7459, + "end": 7465, "loc": { "start": { - "line": 204, + "line": 223, "column": 8 }, "end": { - "line": 204, + "line": 223, "column": 14 }, "identifierName": "txname" @@ -7913,30 +9030,30 @@ }, "right": { "type": "ObjectExpression", - "start": 6835, - "end": 7064, + "start": 7468, + "end": 7697, "loc": { "start": { - "line": 204, + "line": 223, "column": 17 }, "end": { - "line": 210, + "line": 229, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 6847, - "end": 6888, + "start": 7480, + "end": 7521, "loc": { "start": { - "line": 205, + "line": 224, "column": 10 }, "end": { - "line": 205, + "line": 224, "column": 51 } }, @@ -7945,15 +9062,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6847, - "end": 6854, + "start": 7480, + "end": 7487, "loc": { "start": { - "line": 205, + "line": 224, "column": 10 }, "end": { - "line": 205, + "line": 224, "column": 17 } }, @@ -7965,29 +9082,29 @@ }, "value": { "type": "MemberExpression", - "start": 6856, - "end": 6888, + "start": 7489, + "end": 7521, "loc": { "start": { - "line": 205, + "line": 224, "column": 19 }, "end": { - "line": 205, + "line": 224, "column": 51 } }, "object": { "type": "Identifier", - "start": 6856, - "end": 6872, + "start": 7489, + "end": 7505, "loc": { "start": { - "line": 205, + "line": 224, "column": 19 }, "end": { - "line": 205, + "line": 224, "column": 35 }, "identifierName": "TaxonNameWrapper" @@ -7996,15 +9113,15 @@ }, "property": { "type": "Identifier", - "start": 6873, - "end": 6888, + "start": 7506, + "end": 7521, "loc": { "start": { - "line": 205, + "line": 224, "column": 36 }, "end": { - "line": 205, + "line": 224, "column": 51 }, "identifierName": "TYPE_TAXON_NAME" @@ -8016,15 +9133,15 @@ }, { "type": "ObjectProperty", - "start": 6900, - "end": 6919, + "start": 7533, + "end": 7552, "loc": { "start": { - "line": 206, + "line": 225, "column": 10 }, "end": { - "line": 206, + "line": 225, "column": 29 } }, @@ -8033,15 +9150,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6900, - "end": 6905, + "start": 7533, + "end": 7538, "loc": { "start": { - "line": 206, + "line": 225, "column": 10 }, "end": { - "line": 206, + "line": 225, "column": 15 }, "identifierName": "label" @@ -8050,15 +9167,15 @@ }, "value": { "type": "Identifier", - "start": 6907, - "end": 6919, + "start": 7540, + "end": 7552, "loc": { "start": { - "line": 206, + "line": 225, "column": 17 }, "end": { - "line": 206, + "line": 225, "column": 29 }, "identifierName": "verbatimName" @@ -8068,15 +9185,15 @@ }, { "type": "ObjectProperty", - "start": 6931, - "end": 6981, + "start": 7564, + "end": 7614, "loc": { "start": { - "line": 207, + "line": 226, "column": 10 }, "end": { - "line": 207, + "line": 226, "column": 60 } }, @@ -8085,15 +9202,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6931, - "end": 6943, + "start": 7564, + "end": 7576, "loc": { "start": { - "line": 207, + "line": 226, "column": 10 }, "end": { - "line": 207, + "line": 226, "column": 22 }, "identifierName": "nameComplete" @@ -8102,72 +9219,72 @@ }, "value": { "type": "CallExpression", - "start": 6945, - "end": 6981, + "start": 7578, + "end": 7614, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 6945, - "end": 6979, + "start": 7578, + "end": 7612, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 58 } }, "object": { "type": "TemplateLiteral", - "start": 6945, - "end": 6974, + "start": 7578, + "end": 7607, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 53 } }, "expressions": [ { "type": "MemberExpression", - "start": 6948, - "end": 6958, + "start": 7581, + "end": 7591, "loc": { "start": { - "line": 207, + "line": 226, "column": 27 }, "end": { - "line": 207, + "line": 226, "column": 37 } }, "object": { "type": "Identifier", - "start": 6948, - "end": 6955, + "start": 7581, + "end": 7588, "loc": { "start": { - "line": 207, + "line": 226, "column": 27 }, "end": { - "line": 207, + "line": 226, "column": 34 }, "identifierName": "results" @@ -8176,15 +9293,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6956, - "end": 6957, + "start": 7589, + "end": 7590, "loc": { "start": { - "line": 207, + "line": 226, "column": 35 }, "end": { - "line": 207, + "line": 226, "column": 36 } }, @@ -8198,29 +9315,29 @@ }, { "type": "MemberExpression", - "start": 6962, - "end": 6972, + "start": 7595, + "end": 7605, "loc": { "start": { - "line": 207, + "line": 226, "column": 41 }, "end": { - "line": 207, + "line": 226, "column": 51 } }, "object": { "type": "Identifier", - "start": 6962, - "end": 6969, + "start": 7595, + "end": 7602, "loc": { "start": { - "line": 207, + "line": 226, "column": 41 }, "end": { - "line": 207, + "line": 226, "column": 48 }, "identifierName": "results" @@ -8229,15 +9346,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6970, - "end": 6971, + "start": 7603, + "end": 7604, "loc": { "start": { - "line": 207, + "line": 226, "column": 49 }, "end": { - "line": 207, + "line": 226, "column": 50 } }, @@ -8253,15 +9370,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6946, - "end": 6946, + "start": 7579, + "end": 7579, "loc": { "start": { - "line": 207, + "line": 226, "column": 25 }, "end": { - "line": 207, + "line": 226, "column": 25 } }, @@ -8273,15 +9390,15 @@ }, { "type": "TemplateElement", - "start": 6959, - "end": 6960, + "start": 7592, + "end": 7593, "loc": { "start": { - "line": 207, + "line": 226, "column": 38 }, "end": { - "line": 207, + "line": 226, "column": 39 } }, @@ -8293,15 +9410,15 @@ }, { "type": "TemplateElement", - "start": 6973, - "end": 6973, + "start": 7606, + "end": 7606, "loc": { "start": { - "line": 207, + "line": 226, "column": 52 }, "end": { - "line": 207, + "line": 226, "column": 52 } }, @@ -8315,15 +9432,15 @@ }, "property": { "type": "Identifier", - "start": 6975, - "end": 6979, + "start": 7608, + "end": 7612, "loc": { "start": { - "line": 207, + "line": 226, "column": 54 }, "end": { - "line": 207, + "line": 226, "column": 58 }, "identifierName": "trim" @@ -8337,15 +9454,15 @@ }, { "type": "ObjectProperty", - "start": 6993, - "end": 7014, + "start": 7626, + "end": 7647, "loc": { "start": { - "line": 208, + "line": 227, "column": 10 }, "end": { - "line": 208, + "line": 227, "column": 31 } }, @@ -8354,15 +9471,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6993, - "end": 7002, + "start": 7626, + "end": 7635, "loc": { "start": { - "line": 208, + "line": 227, "column": 10 }, "end": { - "line": 208, + "line": 227, "column": 19 }, "identifierName": "genusPart" @@ -8371,29 +9488,29 @@ }, "value": { "type": "MemberExpression", - "start": 7004, - "end": 7014, + "start": 7637, + "end": 7647, "loc": { "start": { - "line": 208, + "line": 227, "column": 21 }, "end": { - "line": 208, + "line": 227, "column": 31 } }, "object": { "type": "Identifier", - "start": 7004, - "end": 7011, + "start": 7637, + "end": 7644, "loc": { "start": { - "line": 208, + "line": 227, "column": 21 }, "end": { - "line": 208, + "line": 227, "column": 28 }, "identifierName": "results" @@ -8402,15 +9519,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7012, - "end": 7013, + "start": 7645, + "end": 7646, "loc": { "start": { - "line": 208, + "line": 227, "column": 29 }, "end": { - "line": 208, + "line": 227, "column": 30 } }, @@ -8425,15 +9542,15 @@ }, { "type": "ObjectProperty", - "start": 7026, - "end": 7053, + "start": 7659, + "end": 7686, "loc": { "start": { - "line": 209, + "line": 228, "column": 10 }, "end": { - "line": 209, + "line": 228, "column": 37 } }, @@ -8442,15 +9559,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7026, - "end": 7041, + "start": 7659, + "end": 7674, "loc": { "start": { - "line": 209, + "line": 228, "column": 10 }, "end": { - "line": 209, + "line": 228, "column": 25 }, "identifierName": "specificEpithet" @@ -8459,29 +9576,29 @@ }, "value": { "type": "MemberExpression", - "start": 7043, - "end": 7053, + "start": 7676, + "end": 7686, "loc": { "start": { - "line": 209, + "line": 228, "column": 27 }, "end": { - "line": 209, + "line": 228, "column": 37 } }, "object": { "type": "Identifier", - "start": 7043, - "end": 7050, + "start": 7676, + "end": 7683, "loc": { "start": { - "line": 209, + "line": 228, "column": 27 }, "end": { - "line": 209, + "line": 228, "column": 34 }, "identifierName": "results" @@ -8490,15 +9607,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7051, - "end": 7052, + "start": 7684, + "end": 7685, "loc": { "start": { - "line": 209, + "line": 228, "column": 35 }, "end": { - "line": 209, + "line": 228, "column": 36 } }, @@ -8529,15 +9646,15 @@ { "type": "CommentLine", "value": " Attempt 2. Look for a binomial name.", - "start": 6660, - "end": 6699, + "start": 7293, + "end": 7332, "loc": { "start": { - "line": 199, + "line": 218, "column": 4 }, "end": { - "line": 199, + "line": 218, "column": 43 } } @@ -8547,15 +9664,15 @@ { "type": "CommentLine", "value": " Attempt 3. Look for a uninomial name.", - "start": 7085, - "end": 7125, + "start": 7718, + "end": 7758, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 44 } } @@ -8564,29 +9681,29 @@ }, { "type": "IfStatement", - "start": 7130, - "end": 7460, + "start": 7763, + "end": 8093, "loc": { "start": { - "line": 215, + "line": 234, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 7134, - "end": 7141, + "start": 7767, + "end": 7774, "loc": { "start": { - "line": 215, + "line": 234, "column": 8 }, "end": { - "line": 215, + "line": 234, "column": 15 } }, @@ -8594,15 +9711,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 7135, - "end": 7141, + "start": 7768, + "end": 7774, "loc": { "start": { - "line": 215, + "line": 234, "column": 9 }, "end": { - "line": 215, + "line": 234, "column": 15 }, "identifierName": "txname" @@ -8617,59 +9734,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7143, - "end": 7460, + "start": 7776, + "end": 8093, "loc": { "start": { - "line": 215, + "line": 234, "column": 17 }, "end": { - "line": 226, + "line": 245, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7184, - "end": 7242, + "start": 7817, + "end": 7875, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 64 } }, "expression": { "type": "AssignmentExpression", - "start": 7184, - "end": 7241, + "start": 7817, + "end": 7874, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 63 } }, "operator": "=", "left": { "type": "Identifier", - "start": 7184, - "end": 7191, + "start": 7817, + "end": 7824, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 13 }, "identifierName": "results" @@ -8679,43 +9796,43 @@ }, "right": { "type": "CallExpression", - "start": 7194, - "end": 7241, + "start": 7827, + "end": 7874, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 7194, - "end": 7227, + "start": 7827, + "end": 7860, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 49 } }, "object": { "type": "RegExpLiteral", - "start": 7194, - "end": 7222, + "start": 7827, + "end": 7855, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 44 } }, @@ -8727,15 +9844,15 @@ }, "property": { "type": "Identifier", - "start": 7223, - "end": 7227, + "start": 7856, + "end": 7860, "loc": { "start": { - "line": 217, + "line": 236, "column": 45 }, "end": { - "line": 217, + "line": 236, "column": 49 }, "identifierName": "exec" @@ -8747,15 +9864,15 @@ "arguments": [ { "type": "Identifier", - "start": 7228, - "end": 7240, + "start": 7861, + "end": 7873, "loc": { "start": { - "line": 217, + "line": 236, "column": 50 }, "end": { - "line": 217, + "line": 236, "column": 62 }, "identifierName": "verbatimName" @@ -8770,15 +9887,15 @@ { "type": "CommentLine", "value": " Is it a uninomial name?", - "start": 7151, - "end": 7177, + "start": 7784, + "end": 7810, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 32 } } @@ -8787,29 +9904,29 @@ }, { "type": "IfStatement", - "start": 7249, - "end": 7454, + "start": 7882, + "end": 8087, "loc": { "start": { - "line": 218, + "line": 237, "column": 6 }, "end": { - "line": 225, + "line": 244, "column": 7 } }, "test": { "type": "Identifier", - "start": 7253, - "end": 7260, + "start": 7886, + "end": 7893, "loc": { "start": { - "line": 218, + "line": 237, "column": 10 }, "end": { - "line": 218, + "line": 237, "column": 17 }, "identifierName": "results" @@ -8818,59 +9935,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7262, - "end": 7454, + "start": 7895, + "end": 8087, "loc": { "start": { - "line": 218, + "line": 237, "column": 19 }, "end": { - "line": 225, + "line": 244, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 7272, - "end": 7446, + "start": 7905, + "end": 8079, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 224, + "line": 243, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 7272, - "end": 7445, + "start": 7905, + "end": 8078, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 224, + "line": 243, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 7272, - "end": 7278, + "start": 7905, + "end": 7911, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 219, + "line": 238, "column": 14 }, "identifierName": "txname" @@ -8879,30 +9996,30 @@ }, "right": { "type": "ObjectExpression", - "start": 7281, - "end": 7445, + "start": 7914, + "end": 8078, "loc": { "start": { - "line": 219, + "line": 238, "column": 17 }, "end": { - "line": 224, + "line": 243, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 7293, - "end": 7334, + "start": 7926, + "end": 7967, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 51 } }, @@ -8911,15 +10028,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 7293, - "end": 7300, + "start": 7926, + "end": 7933, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 17 } }, @@ -8931,29 +10048,29 @@ }, "value": { "type": "MemberExpression", - "start": 7302, - "end": 7334, + "start": 7935, + "end": 7967, "loc": { "start": { - "line": 220, + "line": 239, "column": 19 }, "end": { - "line": 220, + "line": 239, "column": 51 } }, "object": { "type": "Identifier", - "start": 7302, - "end": 7318, + "start": 7935, + "end": 7951, "loc": { "start": { - "line": 220, + "line": 239, "column": 19 }, "end": { - "line": 220, + "line": 239, "column": 35 }, "identifierName": "TaxonNameWrapper" @@ -8962,15 +10079,15 @@ }, "property": { "type": "Identifier", - "start": 7319, - "end": 7334, + "start": 7952, + "end": 7967, "loc": { "start": { - "line": 220, + "line": 239, "column": 36 }, "end": { - "line": 220, + "line": 239, "column": 51 }, "identifierName": "TYPE_TAXON_NAME" @@ -8982,15 +10099,15 @@ }, { "type": "ObjectProperty", - "start": 7346, - "end": 7365, + "start": 7979, + "end": 7998, "loc": { "start": { - "line": 221, + "line": 240, "column": 10 }, "end": { - "line": 221, + "line": 240, "column": 29 } }, @@ -8999,15 +10116,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7346, - "end": 7351, + "start": 7979, + "end": 7984, "loc": { "start": { - "line": 221, + "line": 240, "column": 10 }, "end": { - "line": 221, + "line": 240, "column": 15 }, "identifierName": "label" @@ -9016,15 +10133,15 @@ }, "value": { "type": "Identifier", - "start": 7353, - "end": 7365, + "start": 7986, + "end": 7998, "loc": { "start": { - "line": 221, + "line": 240, "column": 17 }, "end": { - "line": 221, + "line": 240, "column": 29 }, "identifierName": "verbatimName" @@ -9034,15 +10151,15 @@ }, { "type": "ObjectProperty", - "start": 7377, - "end": 7401, + "start": 8010, + "end": 8034, "loc": { "start": { - "line": 222, + "line": 241, "column": 10 }, "end": { - "line": 222, + "line": 241, "column": 34 } }, @@ -9051,15 +10168,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7377, - "end": 7389, + "start": 8010, + "end": 8022, "loc": { "start": { - "line": 222, + "line": 241, "column": 10 }, "end": { - "line": 222, + "line": 241, "column": 22 }, "identifierName": "nameComplete" @@ -9068,29 +10185,29 @@ }, "value": { "type": "MemberExpression", - "start": 7391, - "end": 7401, + "start": 8024, + "end": 8034, "loc": { "start": { - "line": 222, + "line": 241, "column": 24 }, "end": { - "line": 222, + "line": 241, "column": 34 } }, "object": { "type": "Identifier", - "start": 7391, - "end": 7398, + "start": 8024, + "end": 8031, "loc": { "start": { - "line": 222, + "line": 241, "column": 24 }, "end": { - "line": 222, + "line": 241, "column": 31 }, "identifierName": "results" @@ -9099,15 +10216,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7399, - "end": 7400, + "start": 8032, + "end": 8033, "loc": { "start": { - "line": 222, + "line": 241, "column": 32 }, "end": { - "line": 222, + "line": 241, "column": 33 } }, @@ -9122,15 +10239,15 @@ }, { "type": "ObjectProperty", - "start": 7413, - "end": 7434, + "start": 8046, + "end": 8067, "loc": { "start": { - "line": 223, + "line": 242, "column": 10 }, "end": { - "line": 223, + "line": 242, "column": 31 } }, @@ -9139,15 +10256,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7413, - "end": 7422, + "start": 8046, + "end": 8055, "loc": { "start": { - "line": 223, + "line": 242, "column": 10 }, "end": { - "line": 223, + "line": 242, "column": 19 }, "identifierName": "uninomial" @@ -9156,29 +10273,29 @@ }, "value": { "type": "MemberExpression", - "start": 7424, - "end": 7434, + "start": 8057, + "end": 8067, "loc": { "start": { - "line": 223, + "line": 242, "column": 21 }, "end": { - "line": 223, + "line": 242, "column": 31 } }, "object": { "type": "Identifier", - "start": 7424, - "end": 7431, + "start": 8057, + "end": 8064, "loc": { "start": { - "line": 223, + "line": 242, "column": 21 }, "end": { - "line": 223, + "line": 242, "column": 28 }, "identifierName": "results" @@ -9187,15 +10304,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7432, - "end": 7433, + "start": 8065, + "end": 8066, "loc": { "start": { - "line": 223, + "line": 242, "column": 29 }, "end": { - "line": 223, + "line": 242, "column": 30 } }, @@ -9226,15 +10343,15 @@ { "type": "CommentLine", "value": " Attempt 3. Look for a uninomial name.", - "start": 7085, - "end": 7125, + "start": 7718, + "end": 7758, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 44 } } @@ -9244,15 +10361,15 @@ { "type": "CommentLine", "value": " Add a nomenclatural code if possible.", - "start": 7466, - "end": 7506, + "start": 8099, + "end": 8139, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 44 } } @@ -9261,43 +10378,43 @@ }, { "type": "IfStatement", - "start": 7511, - "end": 7587, + "start": 8144, + "end": 8220, "loc": { "start": { - "line": 229, + "line": 248, "column": 4 }, "end": { - "line": 231, + "line": 250, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 7515, - "end": 7534, + "start": 8148, + "end": 8167, "loc": { "start": { - "line": 229, + "line": 248, "column": 8 }, "end": { - "line": 229, + "line": 248, "column": 27 } }, "left": { "type": "Identifier", - "start": 7515, - "end": 7521, + "start": 8148, + "end": 8154, "loc": { "start": { - "line": 229, + "line": 248, "column": 8 }, "end": { - "line": 229, + "line": 248, "column": 14 }, "identifierName": "txname" @@ -9308,15 +10425,15 @@ "operator": "&&", "right": { "type": "Identifier", - "start": 7525, - "end": 7534, + "start": 8158, + "end": 8167, "loc": { "start": { - "line": 229, + "line": 248, "column": 18 }, "end": { - "line": 229, + "line": 248, "column": 27 }, "identifierName": "nomenCode" @@ -9327,73 +10444,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 7536, - "end": 7587, + "start": 8169, + "end": 8220, "loc": { "start": { - "line": 229, + "line": 248, "column": 29 }, "end": { - "line": 231, + "line": 250, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7544, - "end": 7581, + "start": 8177, + "end": 8214, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 43 } }, "expression": { "type": "AssignmentExpression", - "start": 7544, - "end": 7580, + "start": 8177, + "end": 8213, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 42 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7544, - "end": 7568, + "start": 8177, + "end": 8201, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 30 } }, "object": { "type": "Identifier", - "start": 7544, - "end": 7550, + "start": 8177, + "end": 8183, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 12 }, "identifierName": "txname" @@ -9402,15 +10519,15 @@ }, "property": { "type": "Identifier", - "start": 7551, - "end": 7568, + "start": 8184, + "end": 8201, "loc": { "start": { - "line": 230, + "line": 249, "column": 13 }, "end": { - "line": 230, + "line": 249, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -9421,15 +10538,15 @@ }, "right": { "type": "Identifier", - "start": 7571, - "end": 7580, + "start": 8204, + "end": 8213, "loc": { "start": { - "line": 230, + "line": 249, "column": 33 }, "end": { - "line": 230, + "line": 249, "column": 42 }, "identifierName": "nomenCode" @@ -9447,15 +10564,15 @@ { "type": "CommentLine", "value": " Add a nomenclatural code if possible.", - "start": 7466, - "end": 7506, + "start": 8099, + "end": 8139, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 44 } } @@ -9465,15 +10582,15 @@ { "type": "CommentLine", "value": " Store in the cache.", - "start": 7593, - "end": 7615, + "start": 8226, + "end": 8248, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 26 } } @@ -9482,43 +10599,43 @@ }, { "type": "IfStatement", - "start": 7620, - "end": 7751, + "start": 8253, + "end": 8384, "loc": { "start": { - "line": 234, + "line": 253, "column": 4 }, "end": { - "line": 236, + "line": 255, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 7624, - "end": 7644, + "start": 8257, + "end": 8277, "loc": { "start": { - "line": 234, + "line": 253, "column": 8 }, "end": { - "line": 234, + "line": 253, "column": 28 } }, "left": { "type": "Identifier", - "start": 7624, - "end": 7630, + "start": 8257, + "end": 8263, "loc": { "start": { - "line": 234, + "line": 253, "column": 8 }, "end": { - "line": 234, + "line": 253, "column": 14 }, "identifierName": "txname" @@ -9529,15 +10646,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 7635, - "end": 7644, + "start": 8268, + "end": 8277, "loc": { "start": { - "line": 234, + "line": 253, "column": 19 }, "end": { - "line": 234, + "line": 253, "column": 28 }, "identifierName": "undefined" @@ -9548,72 +10665,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 7646, - "end": 7751, + "start": 8279, + "end": 8384, "loc": { "start": { - "line": 234, + "line": 253, "column": 30 }, "end": { - "line": 236, + "line": 255, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7654, - "end": 7745, + "start": 8287, + "end": 8378, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 97 } }, "expression": { "type": "CallExpression", - "start": 7654, - "end": 7744, + "start": 8287, + "end": 8377, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 96 } }, "callee": { "type": "MemberExpression", - "start": 7654, - "end": 7674, + "start": 8287, + "end": 8307, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 26 } }, "object": { "type": "Identifier", - "start": 7654, - "end": 7670, + "start": 8287, + "end": 8303, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 22 }, "identifierName": "PhyxCacheManager" @@ -9622,15 +10739,15 @@ }, "property": { "type": "Identifier", - "start": 7671, - "end": 7674, + "start": 8304, + "end": 8307, "loc": { "start": { - "line": 235, + "line": 254, "column": 23 }, "end": { - "line": 235, + "line": 254, "column": 26 }, "identifierName": "put" @@ -9642,30 +10759,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 7675, - "end": 7721, + "start": 8308, + "end": 8354, "loc": { "start": { - "line": 235, + "line": 254, "column": 27 }, "end": { - "line": 235, + "line": 254, "column": 73 } }, "expressions": [ { "type": "Identifier", - "start": 7710, - "end": 7719, + "start": 8343, + "end": 8352, "loc": { "start": { - "line": 235, + "line": 254, "column": 62 }, "end": { - "line": 235, + "line": 254, "column": 71 }, "identifierName": "nomenCode" @@ -9676,15 +10793,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 7676, - "end": 7708, + "start": 8309, + "end": 8341, "loc": { "start": { - "line": 235, + "line": 254, "column": 28 }, "end": { - "line": 235, + "line": 254, "column": 60 } }, @@ -9696,15 +10813,15 @@ }, { "type": "TemplateElement", - "start": 7720, - "end": 7720, + "start": 8353, + "end": 8353, "loc": { "start": { - "line": 235, + "line": 254, "column": 72 }, "end": { - "line": 235, + "line": 254, "column": 72 } }, @@ -9718,15 +10835,15 @@ }, { "type": "Identifier", - "start": 7723, - "end": 7735, + "start": 8356, + "end": 8368, "loc": { "start": { - "line": 235, + "line": 254, "column": 75 }, "end": { - "line": 235, + "line": 254, "column": 87 }, "identifierName": "verbatimName" @@ -9735,15 +10852,15 @@ }, { "type": "Identifier", - "start": 7737, - "end": 7743, + "start": 8370, + "end": 8376, "loc": { "start": { - "line": 235, + "line": 254, "column": 89 }, "end": { - "line": 235, + "line": 254, "column": 95 }, "identifierName": "txname" @@ -9761,15 +10878,15 @@ { "type": "CommentLine", "value": " Store in the cache.", - "start": 7593, - "end": 7615, + "start": 8226, + "end": 8248, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 26 } } @@ -9778,29 +10895,29 @@ }, { "type": "ReturnStatement", - "start": 7757, - "end": 7771, + "start": 8390, + "end": 8404, "loc": { "start": { - "line": 238, + "line": 257, "column": 4 }, "end": { - "line": 238, + "line": 257, "column": 18 } }, "argument": { "type": "Identifier", - "start": 7764, - "end": 7770, + "start": 8397, + "end": 8403, "loc": { "start": { - "line": 238, + "line": 257, "column": 11 }, "end": { - "line": 238, + "line": 257, "column": 17 }, "identifierName": "txname" @@ -9816,15 +10933,15 @@ { "type": "CommentBlock", "value": "*\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n ", - "start": 5725, - "end": 5799, + "start": 6358, + "end": 6432, "loc": { "start": { - "line": 173, + "line": 192, "column": 2 }, "end": { - "line": 175, + "line": 194, "column": 5 } } @@ -9834,15 +10951,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this scientific name.\n ", - "start": 7779, - "end": 7835, + "start": 8412, + "end": 8468, "loc": { "start": { - "line": 241, + "line": 260, "column": 2 }, "end": { - "line": 243, + "line": 262, "column": 5 } } @@ -9851,15 +10968,15 @@ }, { "type": "ClassMethod", - "start": 7838, - "end": 7906, + "start": 8471, + "end": 8539, "loc": { "start": { - "line": 244, + "line": 263, "column": 2 }, "end": { - "line": 246, + "line": 265, "column": 3 } }, @@ -9867,15 +10984,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7842, - "end": 7847, + "start": 8475, + "end": 8480, "loc": { "start": { - "line": 244, + "line": 263, "column": 6 }, "end": { - "line": 244, + "line": 263, "column": 11 }, "identifierName": "label" @@ -9890,101 +11007,101 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7850, - "end": 7906, + "start": 8483, + "end": 8539, "loc": { "start": { - "line": 244, + "line": 263, "column": 14 }, "end": { - "line": 246, + "line": 265, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 7856, - "end": 7902, + "start": 8489, + "end": 8535, "loc": { "start": { - "line": 245, + "line": 264, "column": 4 }, "end": { - "line": 245, + "line": 264, "column": 50 } }, "argument": { "type": "LogicalExpression", - "start": 7863, - "end": 7901, + "start": 8496, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 7863, - "end": 7880, + "start": 8496, + "end": 8513, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 7863, - "end": 7874, + "start": 8496, + "end": 8507, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 7863, - "end": 7867, + "start": 8496, + "end": 8500, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 15 } } }, "property": { "type": "Identifier", - "start": 7868, - "end": 7874, + "start": 8501, + "end": 8507, "loc": { "start": { - "line": 245, + "line": 264, "column": 16 }, "end": { - "line": 245, + "line": 264, "column": 22 }, "identifierName": "txname" @@ -9995,15 +11112,15 @@ }, "property": { "type": "Identifier", - "start": 7875, - "end": 7880, + "start": 8508, + "end": 8513, "loc": { "start": { - "line": 245, + "line": 264, "column": 23 }, "end": { - "line": 245, + "line": 264, "column": 28 }, "identifierName": "label" @@ -10015,44 +11132,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 7884, - "end": 7901, + "start": 8517, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 32 }, "end": { - "line": 245, + "line": 264, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 7884, - "end": 7888, + "start": 8517, + "end": 8521, "loc": { "start": { - "line": 245, + "line": 264, "column": 32 }, "end": { - "line": 245, + "line": 264, "column": 36 } } }, "property": { "type": "Identifier", - "start": 7889, - "end": 7901, + "start": 8522, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 37 }, "end": { - "line": 245, + "line": 264, "column": 49 }, "identifierName": "nameComplete" @@ -10071,15 +11188,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this scientific name.\n ", - "start": 7779, - "end": 7835, + "start": 8412, + "end": 8468, "loc": { "start": { - "line": 241, + "line": 260, "column": 2 }, "end": { - "line": 243, + "line": 262, "column": 5 } } @@ -10089,15 +11206,15 @@ { "type": "CommentBlock", "value": "*\n * Set the label of this scientific name.\n ", - "start": 7910, - "end": 7963, + "start": 8543, + "end": 8596, "loc": { "start": { - "line": 248, + "line": 267, "column": 2 }, "end": { - "line": 250, + "line": 269, "column": 5 } } @@ -10106,15 +11223,15 @@ }, { "type": "ClassMethod", - "start": 7966, - "end": 8157, + "start": 8599, + "end": 8790, "loc": { "start": { - "line": 251, + "line": 270, "column": 2 }, "end": { - "line": 257, + "line": 276, "column": 3 } }, @@ -10122,15 +11239,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7970, - "end": 7975, + "start": 8603, + "end": 8608, "loc": { "start": { - "line": 251, + "line": 270, "column": 6 }, "end": { - "line": 251, + "line": 270, "column": 11 }, "identifierName": "label" @@ -10145,15 +11262,15 @@ "params": [ { "type": "Identifier", - "start": 7976, - "end": 7979, + "start": 8609, + "end": 8612, "loc": { "start": { - "line": 251, + "line": 270, "column": 12 }, "end": { - "line": 251, + "line": 270, "column": 15 }, "identifierName": "lab" @@ -10163,102 +11280,102 @@ ], "body": { "type": "BlockStatement", - "start": 7981, - "end": 8157, + "start": 8614, + "end": 8790, "loc": { "start": { - "line": 251, + "line": 270, "column": 17 }, "end": { - "line": 257, + "line": 276, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 7987, - "end": 8011, + "start": 8620, + "end": 8644, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 28 } }, "expression": { "type": "AssignmentExpression", - "start": 7987, - "end": 8010, + "start": 8620, + "end": 8643, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 27 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7987, - "end": 8004, + "start": 8620, + "end": 8637, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 21 } }, "object": { "type": "MemberExpression", - "start": 7987, - "end": 7998, + "start": 8620, + "end": 8631, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 7987, - "end": 7991, + "start": 8620, + "end": 8624, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 8 } } }, "property": { "type": "Identifier", - "start": 7992, - "end": 7998, + "start": 8625, + "end": 8631, "loc": { "start": { - "line": 252, + "line": 271, "column": 9 }, "end": { - "line": 252, + "line": 271, "column": 15 }, "identifierName": "txname" @@ -10269,15 +11386,15 @@ }, "property": { "type": "Identifier", - "start": 7999, - "end": 8004, + "start": 8632, + "end": 8637, "loc": { "start": { - "line": 252, + "line": 271, "column": 16 }, "end": { - "line": 252, + "line": 271, "column": 21 }, "identifierName": "label" @@ -10288,15 +11405,15 @@ }, "right": { "type": "Identifier", - "start": 8007, - "end": 8010, + "start": 8640, + "end": 8643, "loc": { "start": { - "line": 252, + "line": 271, "column": 24 }, "end": { - "line": 252, + "line": 271, "column": 27 }, "identifierName": "lab" @@ -10307,29 +11424,29 @@ }, { "type": "IfStatement", - "start": 8016, - "end": 8153, + "start": 8649, + "end": 8786, "loc": { "start": { - "line": 253, + "line": 272, "column": 4 }, "end": { - "line": 256, + "line": 275, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 8020, - "end": 8038, + "start": 8653, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 8 }, "end": { - "line": 253, + "line": 272, "column": 26 } }, @@ -10337,44 +11454,44 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 8021, - "end": 8038, + "start": 8654, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 9 }, "end": { - "line": 253, + "line": 272, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 8021, - "end": 8025, + "start": 8654, + "end": 8658, "loc": { "start": { - "line": 253, + "line": 272, "column": 9 }, "end": { - "line": 253, + "line": 272, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8026, - "end": 8038, + "start": 8659, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 14 }, "end": { - "line": 253, + "line": 272, "column": 26 }, "identifierName": "nameComplete" @@ -10389,73 +11506,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 8040, - "end": 8153, + "start": 8673, + "end": 8786, "loc": { "start": { - "line": 253, + "line": 272, "column": 28 }, "end": { - "line": 256, + "line": 275, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 8123, - "end": 8147, + "start": 8756, + "end": 8780, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 30 } }, "expression": { "type": "AssignmentExpression", - "start": 8123, - "end": 8146, + "start": 8756, + "end": 8779, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 29 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 8123, - "end": 8140, + "start": 8756, + "end": 8773, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 8123, - "end": 8127, + "start": 8756, + "end": 8760, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 10 } }, @@ -10463,15 +11580,15 @@ }, "property": { "type": "Identifier", - "start": 8128, - "end": 8140, + "start": 8761, + "end": 8773, "loc": { "start": { - "line": 255, + "line": 274, "column": 11 }, "end": { - "line": 255, + "line": 274, "column": 23 }, "identifierName": "nameComplete" @@ -10483,15 +11600,15 @@ }, "right": { "type": "Identifier", - "start": 8143, - "end": 8146, + "start": 8776, + "end": 8779, "loc": { "start": { - "line": 255, + "line": 274, "column": 26 }, "end": { - "line": 255, + "line": 274, "column": 29 }, "identifierName": "lab" @@ -10504,15 +11621,15 @@ { "type": "CommentLine", "value": " If we don't have a nameComplete, treat this as the name complete.", - "start": 8048, - "end": 8116, + "start": 8681, + "end": 8749, "loc": { "start": { - "line": 254, + "line": 273, "column": 6 }, "end": { - "line": 254, + "line": 273, "column": 74 } } @@ -10532,15 +11649,15 @@ { "type": "CommentBlock", "value": "*\n * Set the label of this scientific name.\n ", - "start": 7910, - "end": 7963, + "start": 8543, + "end": 8596, "loc": { "start": { - "line": 248, + "line": 267, "column": 2 }, "end": { - "line": 250, + "line": 269, "column": 5 } } @@ -10550,15 +11667,15 @@ { "type": "CommentBlock", "value": "*\n * Return the verbatim name of this taxon name.\n ", - "start": 8161, - "end": 8220, + "start": 8794, + "end": 8853, "loc": { "start": { - "line": 259, + "line": 278, "column": 2 }, "end": { - "line": 261, + "line": 280, "column": 5 } } @@ -10567,15 +11684,15 @@ }, { "type": "ClassMethod", - "start": 8223, - "end": 8277, + "start": 8856, + "end": 8910, "loc": { "start": { - "line": 262, + "line": 281, "column": 2 }, "end": { - "line": 264, + "line": 283, "column": 3 } }, @@ -10583,15 +11700,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8227, - "end": 8239, + "start": 8860, + "end": 8872, "loc": { "start": { - "line": 262, + "line": 281, "column": 6 }, "end": { - "line": 262, + "line": 281, "column": 18 }, "identifierName": "verbatimName" @@ -10606,87 +11723,87 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8242, - "end": 8277, + "start": 8875, + "end": 8910, "loc": { "start": { - "line": 262, + "line": 281, "column": 21 }, "end": { - "line": 264, + "line": 283, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 8248, - "end": 8273, + "start": 8881, + "end": 8906, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 29 } }, "argument": { "type": "MemberExpression", - "start": 8255, - "end": 8272, + "start": 8888, + "end": 8905, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 8255, - "end": 8266, + "start": 8888, + "end": 8899, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 8255, - "end": 8259, + "start": 8888, + "end": 8892, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 15 } } }, "property": { "type": "Identifier", - "start": 8260, - "end": 8266, + "start": 8893, + "end": 8899, "loc": { "start": { - "line": 263, + "line": 282, "column": 16 }, "end": { - "line": 263, + "line": 282, "column": 22 }, "identifierName": "txname" @@ -10697,15 +11814,15 @@ }, "property": { "type": "Identifier", - "start": 8267, - "end": 8272, + "start": 8900, + "end": 8905, "loc": { "start": { - "line": 263, + "line": 282, "column": 23 }, "end": { - "line": 263, + "line": 282, "column": 28 }, "identifierName": "label" @@ -10723,15 +11840,15 @@ { "type": "CommentBlock", "value": "*\n * Return the verbatim name of this taxon name.\n ", - "start": 8161, - "end": 8220, + "start": 8794, + "end": 8853, "loc": { "start": { - "line": 259, + "line": 278, "column": 2 }, "end": { - "line": 261, + "line": 280, "column": 5 } } @@ -10741,15 +11858,15 @@ { "type": "CommentBlock", "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", - "start": 8281, - "end": 8404, + "start": 8914, + "end": 9037, "loc": { "start": { - "line": 266, + "line": 285, "column": 2 }, "end": { - "line": 269, + "line": 288, "column": 5 } } @@ -10758,15 +11875,15 @@ }, { "type": "ClassMethod", - "start": 8407, - "end": 8551, + "start": 9040, + "end": 9184, "loc": { "start": { - "line": 270, + "line": 289, "column": 2 }, "end": { - "line": 275, + "line": 294, "column": 3 } }, @@ -10774,15 +11891,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8411, - "end": 8423, + "start": 9044, + "end": 9056, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 18 }, "identifierName": "nameComplete" @@ -10797,129 +11914,129 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8426, - "end": 8551, + "start": 9059, + "end": 9184, "loc": { "start": { - "line": 270, + "line": 289, "column": 21 }, "end": { - "line": 275, + "line": 294, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 8432, - "end": 8547, + "start": 9065, + "end": 9180, "loc": { "start": { - "line": 271, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 293, "column": 28 } }, "argument": { "type": "LogicalExpression", - "start": 8439, - "end": 8546, + "start": 9072, + "end": 9179, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 274, + "line": 293, "column": 27 } }, "left": { "type": "LogicalExpression", - "start": 8439, - "end": 8518, + "start": 9072, + "end": 9151, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 273, + "line": 292, "column": 26 } }, "left": { "type": "LogicalExpression", - "start": 8439, - "end": 8491, + "start": 9072, + "end": 9124, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 272, + "line": 291, "column": 27 } }, "left": { "type": "MemberExpression", - "start": 8439, - "end": 8463, + "start": 9072, + "end": 9096, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 35 } }, "object": { "type": "MemberExpression", - "start": 8439, - "end": 8450, + "start": 9072, + "end": 9083, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 8439, - "end": 8443, + "start": 9072, + "end": 9076, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 15 } } }, "property": { "type": "Identifier", - "start": 8444, - "end": 8450, + "start": 9077, + "end": 9083, "loc": { "start": { - "line": 271, + "line": 290, "column": 16 }, "end": { - "line": 271, + "line": 290, "column": 22 }, "identifierName": "txname" @@ -10930,15 +12047,15 @@ }, "property": { "type": "Identifier", - "start": 8451, - "end": 8463, + "start": 9084, + "end": 9096, "loc": { "start": { - "line": 271, + "line": 290, "column": 23 }, "end": { - "line": 271, + "line": 290, "column": 35 }, "identifierName": "nameComplete" @@ -10950,44 +12067,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 8473, - "end": 8491, + "start": 9106, + "end": 9124, "loc": { "start": { - "line": 272, + "line": 291, "column": 9 }, "end": { - "line": 272, + "line": 291, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 8473, - "end": 8477, + "start": 9106, + "end": 9110, "loc": { "start": { - "line": 272, + "line": 291, "column": 9 }, "end": { - "line": 272, + "line": 291, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8478, - "end": 8491, + "start": 9111, + "end": 9124, "loc": { "start": { - "line": 272, + "line": 291, "column": 14 }, "end": { - "line": 272, + "line": 291, "column": 27 }, "identifierName": "trinomialName" @@ -11000,44 +12117,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 8501, - "end": 8518, + "start": 9134, + "end": 9151, "loc": { "start": { - "line": 273, + "line": 292, "column": 9 }, "end": { - "line": 273, + "line": 292, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 8501, - "end": 8505, + "start": 9134, + "end": 9138, "loc": { "start": { - "line": 273, + "line": 292, "column": 9 }, "end": { - "line": 273, + "line": 292, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8506, - "end": 8518, + "start": 9139, + "end": 9151, "loc": { "start": { - "line": 273, + "line": 292, "column": 14 }, "end": { - "line": 273, + "line": 292, "column": 26 }, "identifierName": "binomialName" @@ -11050,44 +12167,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 8528, - "end": 8546, + "start": 9161, + "end": 9179, "loc": { "start": { - "line": 274, + "line": 293, "column": 9 }, "end": { - "line": 274, + "line": 293, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 8528, - "end": 8532, + "start": 9161, + "end": 9165, "loc": { "start": { - "line": 274, + "line": 293, "column": 9 }, "end": { - "line": 274, + "line": 293, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8533, - "end": 8546, + "start": 9166, + "end": 9179, "loc": { "start": { - "line": 274, + "line": 293, "column": 14 }, "end": { - "line": 274, + "line": 293, "column": 27 }, "identifierName": "uninomialName" @@ -11106,15 +12223,15 @@ { "type": "CommentBlock", "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", - "start": 8281, - "end": 8404, + "start": 8914, + "end": 9037, "loc": { "start": { - "line": 266, + "line": 285, "column": 2 }, "end": { - "line": 269, + "line": 288, "column": 5 } } @@ -11124,15 +12241,15 @@ { "type": "CommentBlock", "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", - "start": 8555, - "end": 8635, + "start": 9188, + "end": 9268, "loc": { "start": { - "line": 277, + "line": 296, "column": 2 }, "end": { - "line": 279, + "line": 298, "column": 5 } } @@ -11141,15 +12258,15 @@ }, { "type": "ClassMethod", - "start": 8638, - "end": 8749, + "start": 9271, + "end": 9382, "loc": { "start": { - "line": 280, + "line": 299, "column": 2 }, "end": { - "line": 282, + "line": 301, "column": 3 } }, @@ -11157,15 +12274,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8642, - "end": 8654, + "start": 9275, + "end": 9287, "loc": { "start": { - "line": 280, + "line": 299, "column": 6 }, "end": { - "line": 280, + "line": 299, "column": 18 }, "identifierName": "nameComplete" @@ -11180,15 +12297,15 @@ "params": [ { "type": "Identifier", - "start": 8655, - "end": 8659, + "start": 9288, + "end": 9292, "loc": { "start": { - "line": 280, + "line": 299, "column": 19 }, "end": { - "line": 280, + "line": 299, "column": 23 }, "identifierName": "name" @@ -11198,88 +12315,88 @@ ], "body": { "type": "BlockStatement", - "start": 8661, - "end": 8749, + "start": 9294, + "end": 9382, "loc": { "start": { - "line": 280, + "line": 299, "column": 25 }, "end": { - "line": 282, + "line": 301, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 8667, - "end": 8745, + "start": 9300, + "end": 9378, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 82 } }, "expression": { "type": "AssignmentExpression", - "start": 8667, - "end": 8744, + "start": 9300, + "end": 9377, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 81 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 8667, - "end": 8678, + "start": 9300, + "end": 9311, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 8667, - "end": 8671, + "start": 9300, + "end": 9304, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 8 } } }, "property": { "type": "Identifier", - "start": 8672, - "end": 8678, + "start": 9305, + "end": 9311, "loc": { "start": { - "line": 281, + "line": 300, "column": 9 }, "end": { - "line": 281, + "line": 300, "column": 15 }, "identifierName": "txname" @@ -11290,43 +12407,43 @@ }, "right": { "type": "CallExpression", - "start": 8681, - "end": 8744, + "start": 9314, + "end": 9377, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 81 } }, "callee": { "type": "MemberExpression", - "start": 8681, - "end": 8714, + "start": 9314, + "end": 9347, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 51 } }, "object": { "type": "Identifier", - "start": 8681, - "end": 8697, + "start": 9314, + "end": 9330, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 34 }, "identifierName": "TaxonNameWrapper" @@ -11335,15 +12452,15 @@ }, "property": { "type": "Identifier", - "start": 8698, - "end": 8714, + "start": 9331, + "end": 9347, "loc": { "start": { - "line": 281, + "line": 300, "column": 35 }, "end": { - "line": 281, + "line": 300, "column": 51 }, "identifierName": "fromVerbatimName" @@ -11355,15 +12472,15 @@ "arguments": [ { "type": "Identifier", - "start": 8715, - "end": 8719, + "start": 9348, + "end": 9352, "loc": { "start": { - "line": 281, + "line": 300, "column": 52 }, "end": { - "line": 281, + "line": 300, "column": 56 }, "identifierName": "name" @@ -11372,44 +12489,44 @@ }, { "type": "MemberExpression", - "start": 8721, - "end": 8743, + "start": 9354, + "end": 9376, "loc": { "start": { - "line": 281, + "line": 300, "column": 58 }, "end": { - "line": 281, + "line": 300, "column": 80 } }, "object": { "type": "ThisExpression", - "start": 8721, - "end": 8725, + "start": 9354, + "end": 9358, "loc": { "start": { - "line": 281, + "line": 300, "column": 58 }, "end": { - "line": 281, + "line": 300, "column": 62 } } }, "property": { "type": "Identifier", - "start": 8726, - "end": 8743, + "start": 9359, + "end": 9376, "loc": { "start": { - "line": 281, + "line": 300, "column": 63 }, "end": { - "line": 281, + "line": 300, "column": 80 }, "identifierName": "nomenclaturalCode" @@ -11430,15 +12547,15 @@ { "type": "CommentBlock", "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", - "start": 8555, - "end": 8635, + "start": 9188, + "end": 9268, "loc": { "start": { - "line": 277, + "line": 296, "column": 2 }, "end": { - "line": 279, + "line": 298, "column": 5 } } @@ -11448,15 +12565,15 @@ { "type": "CommentBlock", "value": "* Return the uninomial name if there is one. ", - "start": 8753, - "end": 8802, + "start": 9386, + "end": 9435, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 284, + "line": 303, "column": 51 } } @@ -11465,15 +12582,15 @@ }, { "type": "ClassMethod", - "start": 8805, - "end": 9242, + "start": 9438, + "end": 9875, "loc": { "start": { - "line": 285, + "line": 304, "column": 2 }, "end": { - "line": 299, + "line": 318, "column": 3 } }, @@ -11481,15 +12598,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8809, - "end": 8818, + "start": 9442, + "end": 9451, "loc": { "start": { - "line": 285, + "line": 304, "column": 6 }, "end": { - "line": 285, + "line": 304, "column": 15 }, "identifierName": "uninomial" @@ -11504,87 +12621,87 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8821, - "end": 9242, + "start": 9454, + "end": 9875, "loc": { "start": { - "line": 285, + "line": 304, "column": 18 }, "end": { - "line": 299, + "line": 318, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 8827, - "end": 8883, + "start": 9460, + "end": 9516, "loc": { "start": { - "line": 286, + "line": 305, "column": 4 }, "end": { - "line": 286, + "line": 305, "column": 60 } }, "test": { "type": "MemberExpression", - "start": 8831, - "end": 8852, + "start": 9464, + "end": 9485, "loc": { "start": { - "line": 286, + "line": 305, "column": 8 }, "end": { - "line": 286, + "line": 305, "column": 29 } }, "object": { "type": "MemberExpression", - "start": 8831, - "end": 8842, + "start": 9464, + "end": 9475, "loc": { "start": { - "line": 286, + "line": 305, "column": 8 }, "end": { - "line": 286, + "line": 305, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 8831, - "end": 8835, + "start": 9464, + "end": 9468, "loc": { "start": { - "line": 286, + "line": 305, "column": 8 }, "end": { - "line": 286, + "line": 305, "column": 12 } } }, "property": { "type": "Identifier", - "start": 8836, - "end": 8842, + "start": 9469, + "end": 9475, "loc": { "start": { - "line": 286, + "line": 305, "column": 13 }, "end": { - "line": 286, + "line": 305, "column": 19 }, "identifierName": "txname" @@ -11595,15 +12712,15 @@ }, "property": { "type": "Identifier", - "start": 8843, - "end": 8852, + "start": 9476, + "end": 9485, "loc": { "start": { - "line": 286, + "line": 305, "column": 20 }, "end": { - "line": 286, + "line": 305, "column": 29 }, "identifierName": "uninomial" @@ -11614,72 +12731,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 8854, - "end": 8883, + "start": 9487, + "end": 9516, "loc": { "start": { - "line": 286, + "line": 305, "column": 31 }, "end": { - "line": 286, + "line": 305, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 8861, - "end": 8882, + "start": 9494, + "end": 9515, "loc": { "start": { - "line": 286, + "line": 305, "column": 38 }, "end": { - "line": 286, + "line": 305, "column": 59 } }, "object": { "type": "MemberExpression", - "start": 8861, - "end": 8872, + "start": 9494, + "end": 9505, "loc": { "start": { - "line": 286, + "line": 305, "column": 38 }, "end": { - "line": 286, + "line": 305, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 8861, - "end": 8865, + "start": 9494, + "end": 9498, "loc": { "start": { - "line": 286, + "line": 305, "column": 38 }, "end": { - "line": 286, + "line": 305, "column": 42 } } }, "property": { "type": "Identifier", - "start": 8866, - "end": 8872, + "start": 9499, + "end": 9505, "loc": { "start": { - "line": 286, + "line": 305, "column": 43 }, "end": { - "line": 286, + "line": 305, "column": 49 }, "identifierName": "txname" @@ -11690,15 +12807,15 @@ }, "property": { "type": "Identifier", - "start": 8873, - "end": 8882, + "start": 9506, + "end": 9515, "loc": { "start": { - "line": 286, + "line": 305, "column": 50 }, "end": { - "line": 286, + "line": 305, "column": 59 }, "identifierName": "uninomial" @@ -11714,15 +12831,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 8889, - "end": 8966, + "start": 9522, + "end": 9599, "loc": { "start": { - "line": 288, + "line": 307, "column": 4 }, "end": { - "line": 288, + "line": 307, "column": 81 } } @@ -11730,15 +12847,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 8971, - "end": 8982, + "start": 9604, + "end": 9615, "loc": { "start": { - "line": 289, + "line": 308, "column": 4 }, "end": { - "line": 289, + "line": 308, "column": 15 } } @@ -11747,57 +12864,57 @@ }, { "type": "IfStatement", - "start": 8987, - "end": 9215, + "start": 9620, + "end": 9848, "loc": { "start": { - "line": 290, + "line": 309, "column": 4 }, "end": { - "line": 296, + "line": 315, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 8991, - "end": 9015, + "start": 9624, + "end": 9648, "loc": { "start": { - "line": 290, + "line": 309, "column": 8 }, "end": { - "line": 290, + "line": 309, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 8991, - "end": 9002, + "start": 9624, + "end": 9635, "loc": { "start": { - "line": 290, + "line": 309, "column": 8 }, "end": { - "line": 290, + "line": 309, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 8991, - "end": 8995, + "start": 9624, + "end": 9628, "loc": { "start": { - "line": 290, + "line": 309, "column": 8 }, "end": { - "line": 290, + "line": 309, "column": 12 } }, @@ -11805,15 +12922,15 @@ }, "property": { "type": "Identifier", - "start": 8996, - "end": 9002, + "start": 9629, + "end": 9635, "loc": { "start": { - "line": 290, + "line": 309, "column": 13 }, "end": { - "line": 290, + "line": 309, "column": 19 }, "identifierName": "txname" @@ -11825,15 +12942,15 @@ }, "property": { "type": "Identifier", - "start": 9003, - "end": 9015, + "start": 9636, + "end": 9648, "loc": { "start": { - "line": 290, + "line": 309, "column": 20 }, "end": { - "line": 290, + "line": 309, "column": 32 }, "identifierName": "nameComplete" @@ -11845,59 +12962,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 9017, - "end": 9215, + "start": 9650, + "end": 9848, "loc": { "start": { - "line": 290, + "line": 309, "column": 34 }, "end": { - "line": 296, + "line": 315, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 9025, - "end": 9148, + "start": 9658, + "end": 9781, "loc": { "start": { - "line": 291, + "line": 310, "column": 6 }, "end": { - "line": 294, + "line": 313, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 9031, - "end": 9147, + "start": 9664, + "end": 9780, "loc": { "start": { - "line": 291, + "line": 310, "column": 12 }, "end": { - "line": 294, + "line": 313, "column": 7 } }, "id": { "type": "Identifier", - "start": 9031, - "end": 9037, + "start": 9664, + "end": 9670, "loc": { "start": { - "line": 291, + "line": 310, "column": 12 }, "end": { - "line": 291, + "line": 310, "column": 18 }, "identifierName": "txname" @@ -11906,43 +13023,43 @@ }, "init": { "type": "CallExpression", - "start": 9040, - "end": 9147, + "start": 9673, + "end": 9780, "loc": { "start": { - "line": 291, + "line": 310, "column": 21 }, "end": { - "line": 294, + "line": 313, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 9040, - "end": 9073, + "start": 9673, + "end": 9706, "loc": { "start": { - "line": 291, + "line": 310, "column": 21 }, "end": { - "line": 291, + "line": 310, "column": 54 } }, "object": { "type": "Identifier", - "start": 9040, - "end": 9056, + "start": 9673, + "end": 9689, "loc": { "start": { - "line": 291, + "line": 310, "column": 21 }, "end": { - "line": 291, + "line": 310, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -11951,15 +13068,15 @@ }, "property": { "type": "Identifier", - "start": 9057, - "end": 9073, + "start": 9690, + "end": 9706, "loc": { "start": { - "line": 291, + "line": 310, "column": 38 }, "end": { - "line": 291, + "line": 310, "column": 54 }, "identifierName": "fromVerbatimName" @@ -11971,58 +13088,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 9083, - "end": 9107, + "start": 9716, + "end": 9740, "loc": { "start": { - "line": 292, + "line": 311, "column": 8 }, "end": { - "line": 292, + "line": 311, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 9083, - "end": 9094, + "start": 9716, + "end": 9727, "loc": { "start": { - "line": 292, + "line": 311, "column": 8 }, "end": { - "line": 292, + "line": 311, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 9083, - "end": 9087, + "start": 9716, + "end": 9720, "loc": { "start": { - "line": 292, + "line": 311, "column": 8 }, "end": { - "line": 292, + "line": 311, "column": 12 } } }, "property": { "type": "Identifier", - "start": 9088, - "end": 9094, + "start": 9721, + "end": 9727, "loc": { "start": { - "line": 292, + "line": 311, "column": 13 }, "end": { - "line": 292, + "line": 311, "column": 19 }, "identifierName": "txname" @@ -12033,15 +13150,15 @@ }, "property": { "type": "Identifier", - "start": 9095, - "end": 9107, + "start": 9728, + "end": 9740, "loc": { "start": { - "line": 292, + "line": 311, "column": 20 }, "end": { - "line": 292, + "line": 311, "column": 32 }, "identifierName": "nameComplete" @@ -12052,44 +13169,44 @@ }, { "type": "MemberExpression", - "start": 9117, - "end": 9139, + "start": 9750, + "end": 9772, "loc": { "start": { - "line": 293, + "line": 312, "column": 8 }, "end": { - "line": 293, + "line": 312, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 9117, - "end": 9121, + "start": 9750, + "end": 9754, "loc": { "start": { - "line": 293, + "line": 312, "column": 8 }, "end": { - "line": 293, + "line": 312, "column": 12 } } }, "property": { "type": "Identifier", - "start": 9122, - "end": 9139, + "start": 9755, + "end": 9772, "loc": { "start": { - "line": 293, + "line": 312, "column": 13 }, "end": { - "line": 293, + "line": 312, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -12106,43 +13223,43 @@ }, { "type": "IfStatement", - "start": 9155, - "end": 9209, + "start": 9788, + "end": 9842, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 295, + "line": 314, "column": 60 } }, "test": { "type": "CallExpression", - "start": 9159, - "end": 9183, + "start": 9792, + "end": 9816, "loc": { "start": { - "line": 295, + "line": 314, "column": 10 }, "end": { - "line": 295, + "line": 314, "column": 34 } }, "callee": { "type": "Identifier", - "start": 9159, - "end": 9162, + "start": 9792, + "end": 9795, "loc": { "start": { - "line": 295, + "line": 314, "column": 10 }, "end": { - "line": 295, + "line": 314, "column": 13 }, "identifierName": "has" @@ -12152,15 +13269,15 @@ "arguments": [ { "type": "Identifier", - "start": 9163, - "end": 9169, + "start": 9796, + "end": 9802, "loc": { "start": { - "line": 295, + "line": 314, "column": 14 }, "end": { - "line": 295, + "line": 314, "column": 20 }, "identifierName": "txname" @@ -12169,15 +13286,15 @@ }, { "type": "StringLiteral", - "start": 9171, - "end": 9182, + "start": 9804, + "end": 9815, "loc": { "start": { - "line": 295, + "line": 314, "column": 22 }, "end": { - "line": 295, + "line": 314, "column": 33 } }, @@ -12191,43 +13308,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 9185, - "end": 9209, + "start": 9818, + "end": 9842, "loc": { "start": { - "line": 295, + "line": 314, "column": 36 }, "end": { - "line": 295, + "line": 314, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 9192, - "end": 9208, + "start": 9825, + "end": 9841, "loc": { "start": { - "line": 295, + "line": 314, "column": 43 }, "end": { - "line": 295, + "line": 314, "column": 59 } }, "object": { "type": "Identifier", - "start": 9192, - "end": 9198, + "start": 9825, + "end": 9831, "loc": { "start": { - "line": 295, + "line": 314, "column": 43 }, "end": { - "line": 295, + "line": 314, "column": 49 }, "identifierName": "txname" @@ -12236,15 +13353,15 @@ }, "property": { "type": "Identifier", - "start": 9199, - "end": 9208, + "start": 9832, + "end": 9841, "loc": { "start": { - "line": 295, + "line": 314, "column": 50 }, "end": { - "line": 295, + "line": 314, "column": 59 }, "identifierName": "uninomial" @@ -12264,15 +13381,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 8889, - "end": 8966, + "start": 9522, + "end": 9599, "loc": { "start": { - "line": 288, + "line": 307, "column": 4 }, "end": { - "line": 288, + "line": 307, "column": 81 } } @@ -12280,15 +13397,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 8971, - "end": 8982, + "start": 9604, + "end": 9615, "loc": { "start": { - "line": 289, + "line": 308, "column": 4 }, "end": { - "line": 289, + "line": 308, "column": 15 } } @@ -12297,29 +13414,29 @@ }, { "type": "ReturnStatement", - "start": 9221, - "end": 9238, + "start": 9854, + "end": 9871, "loc": { "start": { - "line": 298, + "line": 317, "column": 4 }, "end": { - "line": 298, + "line": 317, "column": 21 } }, "argument": { "type": "Identifier", - "start": 9228, - "end": 9237, + "start": 9861, + "end": 9870, "loc": { "start": { - "line": 298, + "line": 317, "column": 11 }, "end": { - "line": 298, + "line": 317, "column": 20 }, "identifierName": "undefined" @@ -12335,15 +13452,15 @@ { "type": "CommentBlock", "value": "* Return the uninomial name if there is one. ", - "start": 8753, - "end": 8802, + "start": 9386, + "end": 9435, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 284, + "line": 303, "column": 51 } } @@ -12353,15 +13470,15 @@ { "type": "CommentBlock", "value": "* Set the uninomial name. ", - "start": 9246, - "end": 9276, + "start": 9879, + "end": 9909, "loc": { "start": { - "line": 301, + "line": 320, "column": 2 }, "end": { - "line": 301, + "line": 320, "column": 32 } } @@ -12370,15 +13487,15 @@ }, { "type": "ClassMethod", - "start": 9279, - "end": 9381, + "start": 9912, + "end": 10014, "loc": { "start": { - "line": 302, + "line": 321, "column": 2 }, "end": { - "line": 305, + "line": 324, "column": 3 } }, @@ -12386,15 +13503,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9283, - "end": 9292, + "start": 9916, + "end": 9925, "loc": { "start": { - "line": 302, + "line": 321, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 15 }, "identifierName": "uninomial" @@ -12409,15 +13526,15 @@ "params": [ { "type": "Identifier", - "start": 9293, - "end": 9299, + "start": 9926, + "end": 9932, "loc": { "start": { - "line": 302, + "line": 321, "column": 16 }, "end": { - "line": 302, + "line": 321, "column": 22 }, "identifierName": "uninom" @@ -12427,102 +13544,102 @@ ], "body": { "type": "BlockStatement", - "start": 9301, - "end": 9381, + "start": 9934, + "end": 10014, "loc": { "start": { - "line": 302, + "line": 321, "column": 24 }, "end": { - "line": 305, + "line": 324, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 9307, - "end": 9338, + "start": 9940, + "end": 9971, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 35 } }, "expression": { "type": "AssignmentExpression", - "start": 9307, - "end": 9337, + "start": 9940, + "end": 9970, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 34 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9307, - "end": 9328, + "start": 9940, + "end": 9961, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 9307, - "end": 9318, + "start": 9940, + "end": 9951, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9307, - "end": 9311, + "start": 9940, + "end": 9944, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9312, - "end": 9318, + "start": 9945, + "end": 9951, "loc": { "start": { - "line": 303, + "line": 322, "column": 9 }, "end": { - "line": 303, + "line": 322, "column": 15 }, "identifierName": "txname" @@ -12533,15 +13650,15 @@ }, "property": { "type": "Identifier", - "start": 9319, - "end": 9328, + "start": 9952, + "end": 9961, "loc": { "start": { - "line": 303, + "line": 322, "column": 16 }, "end": { - "line": 303, + "line": 322, "column": 25 }, "identifierName": "uninomial" @@ -12552,15 +13669,15 @@ }, "right": { "type": "Identifier", - "start": 9331, - "end": 9337, + "start": 9964, + "end": 9970, "loc": { "start": { - "line": 303, + "line": 322, "column": 28 }, "end": { - "line": 303, + "line": 322, "column": 34 }, "identifierName": "uninom" @@ -12571,87 +13688,87 @@ }, { "type": "ExpressionStatement", - "start": 9343, - "end": 9377, + "start": 9976, + "end": 10010, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 9343, - "end": 9376, + "start": 9976, + "end": 10009, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9343, - "end": 9367, + "start": 9976, + "end": 10000, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 9343, - "end": 9354, + "start": 9976, + "end": 9987, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9343, - "end": 9347, + "start": 9976, + "end": 9980, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9348, - "end": 9354, + "start": 9981, + "end": 9987, "loc": { "start": { - "line": 304, + "line": 323, "column": 9 }, "end": { - "line": 304, + "line": 323, "column": 15 }, "identifierName": "txname" @@ -12662,15 +13779,15 @@ }, "property": { "type": "Identifier", - "start": 9355, - "end": 9367, + "start": 9988, + "end": 10000, "loc": { "start": { - "line": 304, + "line": 323, "column": 16 }, "end": { - "line": 304, + "line": 323, "column": 28 }, "identifierName": "nameComplete" @@ -12681,15 +13798,15 @@ }, "right": { "type": "Identifier", - "start": 9370, - "end": 9376, + "start": 10003, + "end": 10009, "loc": { "start": { - "line": 304, + "line": 323, "column": 31 }, "end": { - "line": 304, + "line": 323, "column": 37 }, "identifierName": "uninom" @@ -12706,15 +13823,15 @@ { "type": "CommentBlock", "value": "* Set the uninomial name. ", - "start": 9246, - "end": 9276, + "start": 9879, + "end": 9909, "loc": { "start": { - "line": 301, + "line": 320, "column": 2 }, "end": { - "line": 301, + "line": 320, "column": 32 } } @@ -12724,15 +13841,15 @@ { "type": "CommentBlock", "value": "* Return the binomial name if available. ", - "start": 9385, - "end": 9430, + "start": 10018, + "end": 10063, "loc": { "start": { - "line": 307, + "line": 326, "column": 2 }, "end": { - "line": 307, + "line": 326, "column": 47 } } @@ -12741,15 +13858,15 @@ }, { "type": "ClassMethod", - "start": 9433, - "end": 9706, + "start": 10066, + "end": 10339, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 313, + "line": 332, "column": 3 } }, @@ -12757,15 +13874,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9437, - "end": 9449, + "start": 10070, + "end": 10082, "loc": { "start": { - "line": 308, + "line": 327, "column": 6 }, "end": { - "line": 308, + "line": 327, "column": 18 }, "identifierName": "binomialName" @@ -12780,86 +13897,86 @@ "params": [], "body": { "type": "BlockStatement", - "start": 9452, - "end": 9706, + "start": 10085, + "end": 10339, "loc": { "start": { - "line": 308, + "line": 327, "column": 21 }, "end": { - "line": 313, + "line": 332, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 9557, - "end": 9646, + "start": 10190, + "end": 10279, "loc": { "start": { - "line": 311, + "line": 330, "column": 4 }, "end": { - "line": 311, + "line": 330, "column": 93 } }, "test": { "type": "LogicalExpression", - "start": 9561, - "end": 9627, + "start": 10194, + "end": 10260, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 74 } }, "left": { "type": "BinaryExpression", - "start": 9561, - "end": 9589, + "start": 10194, + "end": 10222, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 36 } }, "left": { "type": "MemberExpression", - "start": 9561, - "end": 9575, + "start": 10194, + "end": 10208, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 9561, - "end": 9565, + "start": 10194, + "end": 10198, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 12 } }, @@ -12867,15 +13984,15 @@ }, "property": { "type": "Identifier", - "start": 9566, - "end": 9575, + "start": 10199, + "end": 10208, "loc": { "start": { - "line": 311, + "line": 330, "column": 13 }, "end": { - "line": 311, + "line": 330, "column": 22 }, "identifierName": "genusPart" @@ -12888,15 +14005,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 9580, - "end": 9589, + "start": 10213, + "end": 10222, "loc": { "start": { - "line": 311, + "line": 330, "column": 27 }, "end": { - "line": 311, + "line": 330, "column": 36 }, "identifierName": "undefined" @@ -12908,58 +14025,58 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 9593, - "end": 9627, + "start": 10226, + "end": 10260, "loc": { "start": { - "line": 311, + "line": 330, "column": 40 }, "end": { - "line": 311, + "line": 330, "column": 74 } }, "left": { "type": "MemberExpression", - "start": 9593, - "end": 9613, + "start": 10226, + "end": 10246, "loc": { "start": { - "line": 311, + "line": 330, "column": 40 }, "end": { - "line": 311, + "line": 330, "column": 60 } }, "object": { "type": "ThisExpression", - "start": 9593, - "end": 9597, + "start": 10226, + "end": 10230, "loc": { "start": { - "line": 311, + "line": 330, "column": 40 }, "end": { - "line": 311, + "line": 330, "column": 44 } } }, "property": { "type": "Identifier", - "start": 9598, - "end": 9613, + "start": 10231, + "end": 10246, "loc": { "start": { - "line": 311, + "line": 330, "column": 45 }, "end": { - "line": 311, + "line": 330, "column": 60 }, "identifierName": "specificEpithet" @@ -12971,15 +14088,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 9618, - "end": 9627, + "start": 10251, + "end": 10260, "loc": { "start": { - "line": 311, + "line": 330, "column": 65 }, "end": { - "line": 311, + "line": 330, "column": 74 }, "identifierName": "undefined" @@ -12991,29 +14108,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 9629, - "end": 9646, + "start": 10262, + "end": 10279, "loc": { "start": { - "line": 311, + "line": 330, "column": 76 }, "end": { - "line": 311, + "line": 330, "column": 93 } }, "argument": { "type": "Identifier", - "start": 9636, - "end": 9645, + "start": 10269, + "end": 10278, "loc": { "start": { - "line": 311, + "line": 330, "column": 83 }, "end": { - "line": 311, + "line": 330, "column": 92 }, "identifierName": "undefined" @@ -13026,15 +14143,15 @@ { "type": "CommentLine", "value": " Get the binomial name. 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", - "start": 9385, - "end": 9430, + "start": 10018, + "end": 10063, "loc": { "start": { - "line": 307, + "line": 326, "column": 2 }, "end": { - "line": 307, + "line": 326, "column": 47 } } @@ -13273,15 +14390,15 @@ { "type": "CommentBlock", "value": "* Set the binomial name. ", - "start": 9710, - "end": 9739, + "start": 10343, + "end": 10372, "loc": { "start": { - "line": 315, + "line": 334, "column": 2 }, "end": { - "line": 315, + "line": 334, "column": 31 } } @@ -13290,15 +14407,15 @@ }, { "type": "ClassMethod", - "start": 9742, - "end": 9848, + "start": 10375, + "end": 10481, "loc": { "start": { - "line": 316, + "line": 335, "column": 2 }, "end": { - "line": 319, + "line": 338, "column": 3 } }, @@ -13306,15 +14423,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9746, - "end": 9758, + "start": 10379, + "end": 10391, "loc": { "start": { - "line": 316, + "line": 335, "column": 6 }, "end": { - "line": 316, + "line": 335, "column": 18 }, "identifierName": "binomialName" @@ -13329,15 +14446,15 @@ "params": [ { "type": "Identifier", - "start": 9759, - "end": 9764, + "start": 10392, + "end": 10397, "loc": { "start": { - "line": 316, + "line": 335, "column": 19 }, "end": { - "line": 316, + "line": 335, "column": 24 }, "identifierName": "binom" @@ -13347,102 +14464,102 @@ ], "body": { "type": "BlockStatement", - "start": 9766, - "end": 9848, + "start": 10399, + "end": 10481, "loc": { "start": { - "line": 316, + "line": 335, "column": 26 }, "end": { - "line": 319, + "line": 338, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 9772, - "end": 9806, + "start": 10405, + "end": 10439, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 9772, - "end": 9805, + "start": 10405, + "end": 10438, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9772, - "end": 9793, + "start": 10405, + "end": 10426, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 9772, - "end": 9783, + "start": 10405, + "end": 10416, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9772, - "end": 9776, + "start": 10405, + "end": 10409, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9777, - "end": 9783, + "start": 10410, + "end": 10416, "loc": { "start": { - "line": 317, + "line": 336, "column": 9 }, "end": { - "line": 317, + "line": 336, "column": 15 }, "identifierName": "txname" @@ -13453,15 +14570,15 @@ }, "property": { "type": "Identifier", - "start": 9784, - "end": 9793, + "start": 10417, + "end": 10426, "loc": { "start": { - "line": 317, + "line": 336, "column": 16 }, "end": { - "line": 317, + "line": 336, "column": 25 }, "identifierName": "uninomial" @@ -13472,15 +14589,15 @@ }, "right": { "type": "Identifier", - "start": 9796, - "end": 9805, + "start": 10429, + "end": 10438, "loc": { "start": { - "line": 317, + "line": 336, "column": 28 }, "end": { - "line": 317, + "line": 336, "column": 37 }, "identifierName": "undefined" @@ -13491,87 +14608,87 @@ }, { "type": "ExpressionStatement", - "start": 9811, - "end": 9844, + "start": 10444, + "end": 10477, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 37 } }, "expression": { "type": "AssignmentExpression", - "start": 9811, - "end": 9843, + "start": 10444, + "end": 10476, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 36 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9811, - "end": 9835, + "start": 10444, + "end": 10468, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 9811, - "end": 9822, + "start": 10444, + "end": 10455, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9811, - "end": 9815, + "start": 10444, + "end": 10448, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9816, - "end": 9822, + "start": 10449, + "end": 10455, "loc": { "start": { - "line": 318, + "line": 337, "column": 9 }, "end": { - "line": 318, + "line": 337, "column": 15 }, "identifierName": "txname" @@ -13582,15 +14699,15 @@ }, "property": { "type": "Identifier", - "start": 9823, - "end": 9835, + "start": 10456, + "end": 10468, "loc": { "start": { - "line": 318, + "line": 337, "column": 16 }, "end": { - "line": 318, + "line": 337, "column": 28 }, "identifierName": "nameComplete" @@ -13601,15 +14718,15 @@ }, "right": { "type": "Identifier", - "start": 9838, - "end": 9843, + "start": 10471, + "end": 10476, "loc": { "start": { - "line": 318, + "line": 337, "column": 31 }, "end": { - "line": 318, + "line": 337, "column": 36 }, "identifierName": "binom" @@ -13626,15 +14743,15 @@ { "type": "CommentBlock", "value": "* Set the binomial name. ", - "start": 9710, - "end": 9739, + "start": 10343, + "end": 10372, "loc": { "start": { - "line": 315, + "line": 334, "column": 2 }, "end": { - "line": 315, + "line": 334, "column": 31 } } @@ -13644,15 +14761,15 @@ { "type": "CommentBlock", "value": "* Return the trinomial name if available. ", - "start": 9852, - "end": 9898, + "start": 10485, + "end": 10531, "loc": { "start": { - "line": 321, + "line": 340, "column": 2 }, "end": { - "line": 321, + "line": 340, "column": 48 } } @@ -13661,15 +14778,15 @@ }, { "type": "ClassMethod", - "start": 9901, - "end": 10172, + "start": 10534, + "end": 10805, "loc": { "start": { - "line": 322, + "line": 341, "column": 2 }, "end": { - "line": 329, + "line": 348, "column": 3 } }, @@ -13677,15 +14794,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9905, - "end": 9918, + "start": 10538, + "end": 10551, "loc": { "start": { - "line": 322, + "line": 341, "column": 6 }, "end": { - "line": 322, + "line": 341, "column": 19 }, "identifierName": "trinomialName" @@ -13700,115 +14817,115 @@ "params": [], "body": { "type": "BlockStatement", - "start": 9921, - "end": 10172, + "start": 10554, + "end": 10805, "loc": { "start": { - "line": 322, + "line": 341, "column": 22 }, "end": { - "line": 329, + "line": 348, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 9927, - "end": 10083, + "start": 10560, + "end": 10716, "loc": { "start": { - "line": 323, + "line": 342, "column": 4 }, "end": { - "line": 327, + "line": 346, "column": 23 } }, "test": { "type": "LogicalExpression", - "start": 9938, - "end": 10059, + "start": 10571, + "end": 10692, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 326, + "line": 345, "column": 37 } }, "left": { "type": "LogicalExpression", - "start": 9938, - "end": 10021, + "start": 10571, + "end": 10654, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 325, + "line": 344, "column": 43 } }, "left": { "type": "BinaryExpression", - "start": 9938, - "end": 9977, + "start": 10571, + "end": 10610, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 324, + "line": 343, "column": 45 } }, "left": { "type": "MemberExpression", - "start": 9938, - "end": 9963, + "start": 10571, + "end": 10596, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 324, + "line": 343, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 9938, - "end": 9942, + "start": 10571, + "end": 10575, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 324, + "line": 343, "column": 10 } } }, "property": { "type": "Identifier", - "start": 9943, - "end": 9963, + "start": 10576, + "end": 10596, "loc": { "start": { - "line": 324, + "line": 343, "column": 11 }, "end": { - "line": 324, + "line": 343, "column": 31 }, "identifierName": "infraspecificEpithet" @@ -13820,15 +14937,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 9968, - "end": 9977, + "start": 10601, + "end": 10610, "loc": { "start": { - "line": 324, + "line": 343, "column": 36 }, "end": { - "line": 324, + "line": 343, "column": 45 }, "identifierName": "undefined" @@ -13839,58 +14956,58 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 9987, - "end": 10021, + "start": 10620, + "end": 10654, "loc": { "start": { - "line": 325, + "line": 344, "column": 9 }, "end": { - "line": 325, + "line": 344, "column": 43 } }, "left": { "type": "MemberExpression", - "start": 9987, - "end": 10007, + "start": 10620, + "end": 10640, "loc": { "start": { - "line": 325, + "line": 344, "column": 9 }, "end": { - "line": 325, + "line": 344, "column": 29 } }, "object": { "type": "ThisExpression", - "start": 9987, - "end": 9991, + "start": 10620, + "end": 10624, "loc": { "start": { - "line": 325, + "line": 344, "column": 9 }, "end": { - "line": 325, + "line": 344, "column": 13 } } }, "property": { "type": "Identifier", - "start": 9992, - "end": 10007, + "start": 10625, + "end": 10640, "loc": { "start": { - "line": 325, + "line": 344, "column": 14 }, "end": { - "line": 325, + "line": 344, "column": 29 }, "identifierName": "specificEpithet" @@ -13902,15 +15019,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 10012, - "end": 10021, + "start": 10645, + "end": 10654, "loc": { "start": { - "line": 325, + "line": 344, "column": 34 }, "end": { - "line": 325, + "line": 344, "column": 43 }, "identifierName": "undefined" @@ -13922,58 +15039,58 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 10031, - "end": 10059, + "start": 10664, + "end": 10692, "loc": { "start": { - "line": 326, + "line": 345, "column": 9 }, "end": { - "line": 326, + "line": 345, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 10031, - "end": 10045, + "start": 10664, + "end": 10678, "loc": { "start": { - "line": 326, + "line": 345, "column": 9 }, "end": { - "line": 326, + "line": 345, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 10031, - "end": 10035, + "start": 10664, + "end": 10668, "loc": { "start": { - "line": 326, + "line": 345, "column": 9 }, "end": { - "line": 326, + "line": 345, "column": 13 } } }, "property": { "type": "Identifier", - "start": 10036, - "end": 10045, + "start": 10669, + "end": 10678, "loc": { "start": { - "line": 326, + "line": 345, "column": 14 }, "end": { - "line": 326, + "line": 345, "column": 23 }, "identifierName": "genusPart" @@ -13985,15 +15102,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 10050, - "end": 10059, + "start": 10683, + "end": 10692, "loc": { "start": { - "line": 326, + "line": 345, "column": 28 }, "end": { - "line": 326, + "line": 345, "column": 37 }, "identifierName": "undefined" @@ -14004,29 +15121,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 10066, - "end": 10083, + "start": 10699, + "end": 10716, "loc": { "start": { - "line": 327, + "line": 346, "column": 6 }, "end": { - "line": 327, + "line": 346, "column": 23 } }, "argument": { "type": "Identifier", - "start": 10073, - "end": 10082, + "start": 10706, + "end": 10715, "loc": { "start": { - "line": 327, + "line": 346, "column": 13 }, "end": { - "line": 327, + "line": 346, "column": 22 }, "identifierName": "undefined" @@ -14038,73 +15155,73 @@ }, { "type": "ReturnStatement", - "start": 10088, - "end": 10168, + "start": 10721, + "end": 10801, "loc": { "start": { - "line": 328, + "line": 347, "column": 4 }, "end": { - "line": 328, + "line": 347, "column": 84 } }, "argument": { "type": "TemplateLiteral", - "start": 10095, - "end": 10167, + "start": 10728, + "end": 10800, "loc": { "start": { - "line": 328, + "line": 347, "column": 11 }, "end": { - "line": 328, + "line": 347, "column": 83 } }, "expressions": [ { "type": "MemberExpression", - "start": 10098, - "end": 10112, + "start": 10731, + "end": 10745, "loc": { "start": { - "line": 328, + "line": 347, "column": 14 }, "end": { - "line": 328, + "line": 347, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 10098, - "end": 10102, + "start": 10731, + "end": 10735, "loc": { "start": { - "line": 328, + "line": 347, "column": 14 }, "end": { - "line": 328, + "line": 347, "column": 18 } } }, "property": { "type": "Identifier", - "start": 10103, - "end": 10112, + "start": 10736, + "end": 10745, "loc": { "start": { - "line": 328, + "line": 347, "column": 19 }, "end": { - "line": 328, + "line": 347, "column": 28 }, "identifierName": "genusPart" @@ -14115,44 +15232,44 @@ }, { "type": "MemberExpression", - "start": 10116, - "end": 10136, + "start": 10749, + "end": 10769, "loc": { "start": { - "line": 328, + "line": 347, "column": 32 }, "end": { - "line": 328, + "line": 347, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 10116, - "end": 10120, + "start": 10749, + "end": 10753, "loc": { "start": { - "line": 328, + "line": 347, "column": 32 }, "end": { - "line": 328, + "line": 347, "column": 36 } } }, "property": { "type": "Identifier", - "start": 10121, - "end": 10136, + "start": 10754, + "end": 10769, "loc": { "start": { - "line": 328, + "line": 347, "column": 37 }, "end": { - "line": 328, + "line": 347, "column": 52 }, "identifierName": "specificEpithet" @@ -14163,44 +15280,44 @@ }, { "type": "MemberExpression", - "start": 10140, - "end": 10165, + "start": 10773, + "end": 10798, "loc": { "start": { - "line": 328, + "line": 347, "column": 56 }, "end": { - "line": 328, + "line": 347, "column": 81 } }, "object": { "type": "ThisExpression", - "start": 10140, - "end": 10144, + "start": 10773, + "end": 10777, "loc": { "start": { - "line": 328, + "line": 347, "column": 56 }, "end": { - "line": 328, + "line": 347, "column": 60 } } }, "property": { "type": "Identifier", - "start": 10145, - "end": 10165, + "start": 10778, + "end": 10798, "loc": { "start": { - "line": 328, + "line": 347, "column": 61 }, "end": { - "line": 328, + "line": 347, "column": 81 }, "identifierName": "infraspecificEpithet" @@ -14213,15 +15330,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 10096, - "end": 10096, + "start": 10729, + "end": 10729, "loc": { "start": { - "line": 328, + "line": 347, "column": 12 }, "end": { - "line": 328, + "line": 347, "column": 12 } }, @@ -14233,15 +15350,15 @@ }, { "type": "TemplateElement", - "start": 10113, - "end": 10114, + "start": 10746, + "end": 10747, "loc": { "start": { - "line": 328, + "line": 347, "column": 29 }, "end": { - "line": 328, + "line": 347, "column": 30 } }, @@ -14253,15 +15370,15 @@ }, { "type": "TemplateElement", - "start": 10137, - "end": 10138, + "start": 10770, + "end": 10771, "loc": { "start": { - "line": 328, + "line": 347, "column": 53 }, "end": { - "line": 328, + "line": 347, "column": 54 } }, @@ -14273,15 +15390,15 @@ }, { "type": "TemplateElement", - "start": 10166, - "end": 10166, + "start": 10799, + "end": 10799, "loc": { "start": { - "line": 328, + "line": 347, "column": 82 }, "end": { - "line": 328, + "line": 347, "column": 82 } }, @@ -14302,15 +15419,15 @@ { "type": "CommentBlock", "value": "* Return the trinomial name if available. ", - "start": 9852, - "end": 9898, + "start": 10485, + "end": 10531, "loc": { "start": { - "line": 321, + "line": 340, "column": 2 }, "end": { - "line": 321, + "line": 340, "column": 48 } } @@ -14320,15 +15437,15 @@ { "type": "CommentBlock", "value": "* Set the trinomial name. ", - "start": 10176, - "end": 10206, + "start": 10809, + "end": 10839, "loc": { "start": { - "line": 331, + "line": 350, "column": 2 }, "end": { - "line": 331, + "line": 350, "column": 32 } } @@ -14337,15 +15454,15 @@ }, { "type": "ClassMethod", - "start": 10209, - "end": 10318, + "start": 10842, + "end": 10951, "loc": { "start": { - "line": 332, + "line": 351, "column": 2 }, "end": { - "line": 335, + "line": 354, "column": 3 } }, @@ -14353,15 +15470,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10213, - "end": 10226, + "start": 10846, + "end": 10859, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 332, + "line": 351, "column": 19 }, "identifierName": "trinomialName" @@ -14376,15 +15493,15 @@ "params": [ { "type": "Identifier", - "start": 10227, - "end": 10233, + "start": 10860, + "end": 10866, "loc": { "start": { - "line": 332, + "line": 351, "column": 20 }, "end": { - "line": 332, + "line": 351, "column": 26 }, "identifierName": "trinom" @@ -14394,102 +15511,102 @@ ], "body": { "type": "BlockStatement", - "start": 10235, - "end": 10318, + "start": 10868, + "end": 10951, "loc": { "start": { - "line": 332, + "line": 351, "column": 28 }, "end": { - "line": 335, + "line": 354, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 10241, - "end": 10275, + "start": 10874, + "end": 10908, "loc": { "start": { - "line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 10241, - "end": 10274, + "start": 10874, + "end": 10907, "loc": { "start": { - "line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10241, - "end": 10262, + "start": 10874, + "end": 10895, "loc": { "start": { - "line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 10241, - "end": 10252, + "start": 10874, + "end": 10885, "loc": { "start": { - "line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 10241, - "end": 10245, + "start": 10874, + "end": 10878, "loc": { "start": { - "line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 8 } } }, "property": { "type": "Identifier", - "start": 10246, - "end": 10252, + "start": 10879, + "end": 10885, "loc": { "start": { - "line": 333, + "line": 352, "column": 9 }, "end": { - "line": 333, + "line": 352, "column": 15 }, "identifierName": "txname" @@ -14500,15 +15617,15 @@ }, "property": { "type": "Identifier", - "start": 10253, - "end": 10262, + "start": 10886, + "end": 10895, "loc": { "start": { - "line": 333, + "line": 352, "column": 16 }, "end": { - "line": 333, + "line": 352, "column": 25 }, "identifierName": "uninomial" @@ -14519,15 +15636,15 @@ }, "right": { "type": "Identifier", - "start": 10265, - "end": 10274, + "start": 10898, + "end": 10907, "loc": { "start": { - "line": 333, + "line": 352, "column": 28 }, "end": { - "line": 333, + "line": 352, "column": 37 }, "identifierName": "undefined" @@ -14538,87 +15655,87 @@ }, { "type": "ExpressionStatement", - "start": 10280, - "end": 10314, + "start": 10913, + "end": 10947, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 10280, - "end": 10313, + "start": 10913, + "end": 10946, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10280, - "end": 10304, + "start": 10913, + "end": 10937, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 10280, - "end": 10291, + "start": 10913, + "end": 10924, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 10280, - "end": 10284, + "start": 10913, + "end": 10917, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 8 } } }, "property": { "type": "Identifier", - "start": 10285, - "end": 10291, + "start": 10918, + "end": 10924, "loc": { "start": { - "line": 334, + "line": 353, "column": 9 }, "end": { - "line": 334, + "line": 353, "column": 15 }, "identifierName": "txname" @@ -14629,15 +15746,15 @@ }, "property": { "type": "Identifier", - "start": 10292, - "end": 10304, + "start": 10925, + "end": 10937, "loc": { "start": { - "line": 334, + "line": 353, "column": 16 }, "end": { - "line": 334, + "line": 353, "column": 28 }, "identifierName": "nameComplete" @@ -14648,15 +15765,15 @@ }, "right": { "type": "Identifier", - "start": 10307, - "end": 10313, + "start": 10940, + "end": 10946, "loc": { "start": { - "line": 334, + "line": 353, "column": 31 }, "end": { - "line": 334, + "line": 353, "column": 37 }, "identifierName": "trinom" @@ -14673,15 +15790,15 @@ { "type": "CommentBlock", "value": "* Set the trinomial name. ", - "start": 10176, - "end": 10206, + "start": 10809, + "end": 10839, "loc": { "start": { - "line": 331, + "line": 350, "column": 2 }, "end": { - "line": 331, + "line": 350, "column": 32 } } @@ -14691,15 +15808,15 @@ { "type": "CommentBlock", "value": "* Return the genus part of this scientific name if available. ", - "start": 10322, - "end": 10388, + "start": 10955, + "end": 11021, "loc": { "start": { - "line": 337, + "line": 356, "column": 2 }, "end": { - "line": 337, + "line": 356, "column": 68 } } @@ -14708,15 +15825,15 @@ }, { "type": "ClassMethod", - "start": 10391, - "end": 10879, + "start": 11024, + "end": 11512, "loc": { "start": { - "line": 338, + "line": 357, "column": 2 }, "end": { - "line": 353, + "line": 372, "column": 3 } }, @@ -14724,15 +15841,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10395, - "end": 10404, + "start": 11028, + "end": 11037, "loc": { "start": { - "line": 338, + "line": 357, "column": 6 }, "end": { - "line": 338, + "line": 357, "column": 15 }, "identifierName": "genusPart" @@ -14747,58 +15864,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 10407, - "end": 10879, + "start": 11040, + "end": 11512, "loc": { "start": { - "line": 338, + "line": 357, "column": 18 }, "end": { - "line": 353, + "line": 372, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 10456, - "end": 10520, + "start": 11089, + "end": 11153, "loc": { "start": { - "line": 340, + "line": 359, "column": 4 }, "end": { - "line": 340, + "line": 359, "column": 68 } }, "test": { "type": "CallExpression", - "start": 10460, - "end": 10489, + "start": 11093, + "end": 11122, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 37 } }, "callee": { "type": "Identifier", - "start": 10460, - "end": 10463, + "start": 11093, + "end": 11096, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 11 }, "identifierName": "has" @@ -14809,44 +15926,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 10464, - "end": 10475, + "start": 11097, + "end": 11108, "loc": { "start": { - "line": 340, + "line": 359, "column": 12 }, "end": { - "line": 340, + "line": 359, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 10464, - "end": 10468, + "start": 11097, + "end": 11101, "loc": { "start": { - "line": 340, + "line": 359, "column": 12 }, "end": { - "line": 340, + "line": 359, "column": 16 } } }, "property": { "type": "Identifier", - "start": 10469, - "end": 10475, + "start": 11102, + "end": 11108, "loc": { "start": { - "line": 340, + "line": 359, "column": 17 }, "end": { - "line": 340, + "line": 359, "column": 23 }, "identifierName": "txname" @@ -14857,15 +15974,15 @@ }, { "type": "StringLiteral", - "start": 10477, - "end": 10488, + "start": 11110, + "end": 11121, "loc": { "start": { - "line": 340, + "line": 359, "column": 25 }, "end": { - "line": 340, + "line": 359, "column": 36 } }, @@ -14880,72 +15997,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 10491, - "end": 10520, + "start": 11124, + "end": 11153, "loc": { "start": { - "line": 340, + "line": 359, "column": 39 }, "end": { - "line": 340, + "line": 359, "column": 68 } }, "argument": { "type": "MemberExpression", - "start": 10498, - "end": 10519, + "start": 11131, + "end": 11152, "loc": { "start": { - "line": 340, + "line": 359, "column": 46 }, "end": { - "line": 340, + "line": 359, "column": 67 } }, "object": { "type": "MemberExpression", - "start": 10498, - "end": 10509, + "start": 11131, + "end": 11142, "loc": { "start": { - "line": 340, + "line": 359, "column": 46 }, "end": { - "line": 340, + "line": 359, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 10498, - "end": 10502, + "start": 11131, + "end": 11135, "loc": { "start": { - "line": 340, + "line": 359, "column": 46 }, "end": { - "line": 340, + "line": 359, "column": 50 } } }, "property": { "type": "Identifier", - "start": 10503, - "end": 10509, + "start": 11136, + "end": 11142, "loc": { "start": { - "line": 340, + "line": 359, "column": 51 }, "end": { - "line": 340, + "line": 359, "column": 57 }, "identifierName": "txname" @@ -14956,15 +16073,15 @@ }, "property": { "type": "Identifier", - "start": 10510, - "end": 10519, + "start": 11143, + "end": 11152, "loc": { "start": { - "line": 340, + "line": 359, "column": 58 }, "end": { - "line": 340, + "line": 359, "column": 67 }, "identifierName": "genusPart" @@ -14980,15 +16097,15 @@ { "type": "CommentLine", "value": " Try to read the genus if available.", - "start": 10413, - "end": 10451, + "start": 11046, + "end": 11084, "loc": { "start": { - "line": 339, + "line": 358, "column": 4 }, "end": { - "line": 339, + "line": 358, "column": 42 } } @@ -14998,15 +16115,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 10526, - "end": 10603, + "start": 11159, + "end": 11236, "loc": { "start": { - "line": 342, + "line": 361, "column": 4 }, "end": { - "line": 342, + "line": 361, "column": 81 } } @@ -15014,15 +16131,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 10608, - "end": 10619, + "start": 11241, + "end": 11252, "loc": { "start": { - "line": 343, + "line": 362, "column": 4 }, "end": { - "line": 343, + "line": 362, "column": 15 } } @@ -15031,57 +16148,57 @@ }, { "type": "IfStatement", - "start": 10624, - "end": 10852, + "start": 11257, + "end": 11485, "loc": { "start": { - "line": 344, + "line": 363, "column": 4 }, "end": { - "line": 350, + "line": 369, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 10628, - "end": 10652, + "start": 11261, + "end": 11285, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 10628, - "end": 10639, + "start": 11261, + "end": 11272, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 10628, - "end": 10632, + "start": 11261, + "end": 11265, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 12 } }, @@ -15089,15 +16206,15 @@ }, "property": { "type": "Identifier", - "start": 10633, - "end": 10639, + "start": 11266, + "end": 11272, "loc": { "start": { - "line": 344, + "line": 363, "column": 13 }, "end": { - "line": 344, + "line": 363, "column": 19 }, "identifierName": "txname" @@ -15109,15 +16226,15 @@ }, "property": { "type": "Identifier", - "start": 10640, - "end": 10652, + "start": 11273, + "end": 11285, "loc": { "start": { - "line": 344, + "line": 363, "column": 20 }, "end": { - "line": 344, + "line": 363, "column": 32 }, "identifierName": "nameComplete" @@ -15129,59 +16246,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 10654, - "end": 10852, + "start": 11287, + "end": 11485, "loc": { "start": { - "line": 344, + "line": 363, "column": 34 }, "end": { - "line": 350, + "line": 369, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 10662, - "end": 10785, + "start": 11295, + "end": 11418, "loc": { "start": { - "line": 345, + "line": 364, "column": 6 }, "end": { - "line": 348, + "line": 367, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10668, - "end": 10784, + "start": 11301, + "end": 11417, "loc": { "start": { - "line": 345, + "line": 364, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 7 } }, "id": { "type": "Identifier", - "start": 10668, - "end": 10674, + "start": 11301, + "end": 11307, "loc": { "start": { - "line": 345, + "line": 364, "column": 12 }, "end": { - "line": 345, + "line": 364, "column": 18 }, "identifierName": "txname" @@ -15190,43 +16307,43 @@ }, "init": { "type": "CallExpression", - "start": 10677, - "end": 10784, + "start": 11310, + "end": 11417, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 348, + "line": 367, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 10677, - "end": 10710, + "start": 11310, + "end": 11343, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 54 } }, "object": { "type": "Identifier", - "start": 10677, - "end": 10693, + "start": 11310, + "end": 11326, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -15235,15 +16352,15 @@ }, "property": { "type": "Identifier", - "start": 10694, - "end": 10710, + "start": 11327, + "end": 11343, "loc": { "start": { - "line": 345, + "line": 364, "column": 38 }, "end": { - "line": 345, + "line": 364, "column": 54 }, "identifierName": "fromVerbatimName" @@ -15255,58 +16372,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 10720, - "end": 10744, + "start": 11353, + "end": 11377, "loc": { "start": { - "line": 346, + "line": 365, "column": 8 }, "end": { - "line": 346, + "line": 365, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 10720, - "end": 10731, + "start": 11353, + "end": 11364, "loc": { "start": { - "line": 346, + "line": 365, "column": 8 }, "end": { - "line": 346, + "line": 365, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 10720, - "end": 10724, + "start": 11353, + "end": 11357, "loc": { "start": { - "line": 346, + "line": 365, "column": 8 }, "end": { - "line": 346, + "line": 365, "column": 12 } } }, "property": { "type": "Identifier", - "start": 10725, - "end": 10731, + "start": 11358, + "end": 11364, "loc": { "start": { - "line": 346, + "line": 365, "column": 13 }, "end": { - "line": 346, + "line": 365, "column": 19 }, "identifierName": "txname" @@ -15317,15 +16434,15 @@ }, "property": { "type": "Identifier", - "start": 10732, - "end": 10744, + "start": 11365, + "end": 11377, "loc": { "start": { - "line": 346, + "line": 365, "column": 20 }, "end": { - "line": 346, + "line": 365, "column": 32 }, "identifierName": "nameComplete" @@ -15336,44 +16453,44 @@ }, { "type": "MemberExpression", - "start": 10754, - "end": 10776, + "start": 11387, + "end": 11409, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 10754, - "end": 10758, + "start": 11387, + "end": 11391, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 12 } } }, "property": { "type": "Identifier", - "start": 10759, - "end": 10776, + "start": 11392, + "end": 11409, "loc": { "start": { - "line": 347, + "line": 366, "column": 13 }, "end": { - "line": 347, + "line": 366, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -15390,43 +16507,43 @@ }, { "type": "IfStatement", - "start": 10792, - "end": 10846, + "start": 11425, + "end": 11479, "loc": { "start": { - "line": 349, + "line": 368, "column": 6 }, "end": { - "line": 349, + "line": 368, "column": 60 } }, "test": { "type": "CallExpression", - "start": 10796, - "end": 10820, + "start": 11429, + "end": 11453, "loc": { "start": { - "line": 349, + "line": 368, "column": 10 }, "end": { - "line": 349, + "line": 368, "column": 34 } }, "callee": { "type": "Identifier", - "start": 10796, - "end": 10799, + "start": 11429, + "end": 11432, "loc": { "start": { - "line": 349, + "line": 368, "column": 10 }, "end": { - "line": 349, + "line": 368, "column": 13 }, "identifierName": "has" @@ -15436,15 +16553,15 @@ "arguments": [ { "type": "Identifier", - "start": 10800, - "end": 10806, + "start": 11433, + "end": 11439, "loc": { "start": { - "line": 349, + "line": 368, "column": 14 }, "end": { - "line": 349, + "line": 368, "column": 20 }, "identifierName": "txname" @@ -15453,15 +16570,15 @@ }, { "type": "StringLiteral", - "start": 10808, - "end": 10819, + "start": 11441, + "end": 11452, "loc": { "start": { - "line": 349, + "line": 368, "column": 22 }, "end": { - "line": 349, + "line": 368, "column": 33 } }, @@ -15475,43 +16592,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 10822, - "end": 10846, + "start": 11455, + "end": 11479, "loc": { "start": { - "line": 349, + "line": 368, "column": 36 }, "end": { - "line": 349, + "line": 368, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 10829, - "end": 10845, + "start": 11462, + "end": 11478, "loc": { "start": { - "line": 349, + "line": 368, "column": 43 }, "end": { - "line": 349, + "line": 368, "column": 59 } }, "object": { "type": "Identifier", - "start": 10829, - "end": 10835, + "start": 11462, + "end": 11468, "loc": { "start": { - "line": 349, + "line": 368, "column": 43 }, "end": { - "line": 349, + "line": 368, "column": 49 }, "identifierName": "txname" @@ -15520,15 +16637,15 @@ }, "property": { "type": "Identifier", - "start": 10836, - "end": 10845, + "start": 11469, + "end": 11478, "loc": { "start": { - "line": 349, + "line": 368, "column": 50 }, "end": { - "line": 349, + "line": 368, "column": 59 }, "identifierName": "genusPart" @@ -15548,15 +16665,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 10526, - "end": 10603, + "start": 11159, + "end": 11236, "loc": { "start": { - "line": 342, + "line": 361, "column": 4 }, "end": { - "line": 342, + "line": 361, "column": 81 } } @@ -15564,15 +16681,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 10608, - "end": 10619, + "start": 11241, + "end": 11252, "loc": { "start": { - "line": 343, + "line": 362, "column": 4 }, "end": { - "line": 343, + "line": 362, "column": 15 } } @@ -15581,29 +16698,29 @@ }, { "type": "ReturnStatement", - "start": 10858, - "end": 10875, + "start": 11491, + "end": 11508, "loc": { "start": { - "line": 352, + "line": 371, "column": 4 }, "end": { - "line": 352, + "line": 371, "column": 21 } }, "argument": { "type": "Identifier", - "start": 10865, - "end": 10874, + "start": 11498, + "end": 11507, "loc": { "start": { - "line": 352, + "line": 371, "column": 11 }, "end": { - "line": 352, + "line": 371, "column": 20 }, "identifierName": "undefined" @@ -15619,15 +16736,15 @@ { "type": "CommentBlock", "value": "* Return the genus part of this scientific name if available. ", - "start": 10322, - "end": 10388, + "start": 10955, + "end": 11021, "loc": { "start": { - "line": 337, + "line": 356, "column": 2 }, "end": { - "line": 337, + "line": 356, "column": 68 } } @@ -15637,15 +16754,15 @@ { "type": "CommentBlock", "value": "* Set the genus part of this name. ", - "start": 10883, - "end": 10922, + "start": 11516, + "end": 11555, "loc": { "start": { - "line": 355, + "line": 374, "column": 2 }, "end": { - "line": 355, + "line": 374, "column": 41 } } @@ -15654,15 +16771,15 @@ }, { "type": "ClassMethod", - "start": 10925, - "end": 11257, + "start": 11558, + "end": 11890, "loc": { "start": { - "line": 356, + "line": 375, "column": 2 }, "end": { - "line": 365, + "line": 384, "column": 3 } }, @@ -15670,15 +16787,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10929, - "end": 10938, + "start": 11562, + "end": 11571, "loc": { "start": { - "line": 356, + "line": 375, "column": 6 }, "end": { - "line": 356, + "line": 375, "column": 15 }, "identifierName": "genusPart" @@ -15693,15 +16810,15 @@ "params": [ { "type": "Identifier", - "start": 10939, - "end": 10944, + "start": 11572, + "end": 11577, "loc": { "start": { - "line": 356, + "line": 375, "column": 16 }, "end": { - "line": 356, + "line": 375, "column": 21 }, "identifierName": "genus" @@ -15711,102 +16828,102 @@ ], "body": { "type": "BlockStatement", - "start": 10946, - "end": 11257, + "start": 11579, + "end": 11890, "loc": { "start": { - "line": 356, + "line": 375, "column": 23 }, "end": { - "line": 365, + "line": 384, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 10952, - "end": 10982, + "start": 11585, + "end": 11615, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 34 } }, "expression": { "type": "AssignmentExpression", - "start": 10952, - "end": 10981, + "start": 11585, + "end": 11614, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 33 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10952, - "end": 10973, + "start": 11585, + "end": 11606, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 10952, - "end": 10963, + "start": 11585, + "end": 11596, "loc": { "start": { - 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"line": 357, + "line": 376, "column": 28 }, "end": { - "line": 357, + "line": 376, "column": 33 }, "identifierName": "genus" @@ -15855,58 +16972,58 @@ }, { "type": "IfStatement", - "start": 10987, - "end": 11253, + "start": 11620, + "end": 11886, "loc": { "start": { - "line": 358, + "line": 377, "column": 4 }, "end": { - "line": 364, + "line": 383, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 10991, - "end": 11011, + "start": 11624, + "end": 11644, "loc": { "start": { - "line": 358, + "line": 377, "column": 8 }, "end": { - "line": 358, + "line": 377, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 10991, - "end": 10995, + "start": 11624, + "end": 11628, "loc": { "start": { - "line": 358, + "line": 377, "column": 8 }, "end": { - "line": 358, + "line": 377, "column": 12 } } }, "property": { "type": "Identifier", - "start": 10996, - "end": 11011, + "start": 11629, + "end": 11644, "loc": { "start": { - "line": 358, + "line": 377, "column": 13 }, "end": { - "line": 358, + "line": 377, "column": 28 }, "identifierName": "specificEpithet" @@ -15917,73 +17034,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 11013, - "end": 11253, + "start": 11646, + "end": 11886, "loc": { "start": { - "line": 358, + "line": 377, "column": 30 }, "end": { - "line": 364, + "line": 383, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 11021, - "end": 11247, + "start": 11654, + "end": 11880, "loc": { "start": { - "line": 359, + "line": 378, "column": 6 }, "end": { - "line": 363, + "line": 382, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 11025, - "end": 11050, + "start": 11658, + "end": 11683, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 11025, - "end": 11029, + "start": 11658, + "end": 11662, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 14 } } }, "property": { "type": "Identifier", - "start": 11030, - "end": 11050, + "start": 11663, + "end": 11683, "loc": { "start": { - "line": 359, + "line": 378, "column": 15 }, "end": { - "line": 359, + "line": 378, "column": 35 }, "identifierName": "infraspecificEpithet" @@ -15994,102 +17111,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 11052, - "end": 11161, + "start": 11685, + "end": 11794, "loc": { "start": { - "line": 359, + "line": 378, "column": 37 }, "end": { - "line": 361, + "line": 380, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 11062, - "end": 11153, + "start": 11695, + "end": 11786, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 99 } }, "expression": { "type": "AssignmentExpression", - "start": 11062, - "end": 11152, + "start": 11695, + "end": 11785, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 98 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11062, - "end": 11086, + "start": 11695, + "end": 11719, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 11062, - "end": 11073, + "start": 11695, + "end": 11706, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 11062, - "end": 11066, + "start": 11695, + "end": 11699, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 12 } } }, "property": { "type": "Identifier", - "start": 11067, - "end": 11073, + "start": 11700, + "end": 11706, "loc": { "start": { - "line": 360, + "line": 379, "column": 13 }, "end": { - "line": 360, + "line": 379, "column": 19 }, "identifierName": "txname" @@ -16100,15 +17217,15 @@ }, "property": { "type": "Identifier", - "start": 11074, - "end": 11086, + "start": 11707, + "end": 11719, "loc": { "start": { - "line": 360, + "line": 379, "column": 20 }, "end": { - "line": 360, + "line": 379, "column": 32 }, "identifierName": "nameComplete" @@ -16119,30 +17236,30 @@ }, "right": { "type": "TemplateLiteral", - "start": 11089, - "end": 11152, + "start": 11722, + "end": 11785, "loc": { "start": { - "line": 360, + "line": 379, "column": 35 }, "end": { - "line": 360, + "line": 379, "column": 98 } }, "expressions": [ { "type": "Identifier", - "start": 11092, - "end": 11097, + "start": 11725, + "end": 11730, "loc": { "start": { - "line": 360, + "line": 379, "column": 38 }, "end": { - "line": 360, + "line": 379, "column": 43 }, "identifierName": "genus" @@ -16151,44 +17268,44 @@ }, { "type": "MemberExpression", - "start": 11101, - "end": 11121, + "start": 11734, + "end": 11754, "loc": { "start": { - "line": 360, + "line": 379, "column": 47 }, "end": { - "line": 360, + "line": 379, "column": 67 } }, "object": { "type": "ThisExpression", - "start": 11101, - "end": 11105, + "start": 11734, + "end": 11738, "loc": { "start": { - "line": 360, + "line": 379, "column": 47 }, "end": { - "line": 360, + "line": 379, "column": 51 } } }, "property": { "type": "Identifier", - "start": 11106, - "end": 11121, + "start": 11739, + "end": 11754, "loc": { "start": { - "line": 360, + "line": 379, "column": 52 }, "end": { - "line": 360, + "line": 379, "column": 67 }, "identifierName": "specificEpithet" @@ -16199,44 +17316,44 @@ }, { "type": "MemberExpression", - "start": 11125, - "end": 11150, + "start": 11758, + "end": 11783, "loc": { "start": { - "line": 360, + "line": 379, "column": 71 }, "end": { - "line": 360, + "line": 379, "column": 96 } }, "object": { "type": "ThisExpression", - "start": 11125, - "end": 11129, + "start": 11758, + "end": 11762, "loc": { "start": { - "line": 360, + "line": 379, "column": 71 }, "end": { - "line": 360, + "line": 379, "column": 75 } } }, "property": { "type": "Identifier", - "start": 11130, - "end": 11150, + "start": 11763, + "end": 11783, "loc": { "start": { - "line": 360, + "line": 379, "column": 76 }, "end": { - "line": 360, + "line": 379, "column": 96 }, "identifierName": "infraspecificEpithet" @@ -16249,15 +17366,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 11090, - "end": 11090, + "start": 11723, + "end": 11723, "loc": { "start": { - "line": 360, + "line": 379, "column": 36 }, "end": { - "line": 360, + "line": 379, "column": 36 } }, @@ -16269,15 +17386,15 @@ }, { "type": "TemplateElement", - "start": 11098, - "end": 11099, + "start": 11731, + "end": 11732, "loc": { "start": { - "line": 360, + "line": 379, "column": 44 }, "end": { - "line": 360, + "line": 379, "column": 45 } }, @@ -16289,15 +17406,15 @@ }, { "type": "TemplateElement", - "start": 11122, - "end": 11123, + "start": 11755, + "end": 11756, "loc": { "start": { - "line": 360, + "line": 379, "column": 68 }, "end": { - "line": 360, + "line": 379, "column": 69 } }, @@ -16309,15 +17426,15 @@ }, { "type": "TemplateElement", - "start": 11151, - "end": 11151, + "start": 11784, + "end": 11784, "loc": { "start": { - "line": 360, + "line": 379, "column": 97 }, "end": { - 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"start": 11204, - "end": 11238, + "start": 11837, + "end": 11871, "loc": { "start": { - "line": 362, + "line": 381, "column": 35 }, "end": { - "line": 362, + "line": 381, "column": 69 } }, "expressions": [ { "type": "Identifier", - "start": 11207, - "end": 11212, + "start": 11840, + "end": 11845, "loc": { "start": { - "line": 362, + "line": 381, "column": 38 }, "end": { - "line": 362, + "line": 381, "column": 43 }, "identifierName": "genus" @@ -16493,44 +17610,44 @@ }, { "type": "MemberExpression", - "start": 11216, - "end": 11236, + "start": 11849, + "end": 11869, "loc": { "start": { - "line": 362, + "line": 381, "column": 47 }, "end": { - "line": 362, + "line": 381, "column": 67 } }, "object": { "type": "ThisExpression", - "start": 11216, - "end": 11220, + "start": 11849, + "end": 11853, "loc": { "start": { - "line": 362, + "line": 381, "column": 47 }, "end": { - "line": 362, + "line": 381, "column": 51 } } }, "property": { "type": "Identifier", - "start": 11221, - "end": 11236, + "start": 11854, + "end": 11869, "loc": { "start": { - "line": 362, + "line": 381, "column": 52 }, "end": { - "line": 362, + "line": 381, "column": 67 }, "identifierName": "specificEpithet" @@ -16543,15 +17660,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 11205, - "end": 11205, + "start": 11838, + "end": 11838, "loc": { "start": { - "line": 362, + "line": 381, "column": 36 }, "end": { - "line": 362, + "line": 381, "column": 36 } }, @@ -16563,15 +17680,15 @@ }, { "type": "TemplateElement", - "start": 11213, - "end": 11214, + "start": 11846, + "end": 11847, "loc": { "start": { - "line": 362, + "line": 381, "column": 44 }, "end": { - "line": 362, + "line": 381, "column": 45 } }, @@ -16583,15 +17700,15 @@ }, { "type": "TemplateElement", - "start": 11237, - "end": 11237, + "start": 11870, + "end": 11870, "loc": { "start": { - "line": 362, + "line": 381, "column": 68 }, "end": { - "line": 362, + "line": 381, "column": 68 } }, @@ -16622,15 +17739,15 @@ { "type": "CommentBlock", "value": "* Set the genus part of this name. ", - "start": 10883, - "end": 10922, + "start": 11516, + "end": 11555, "loc": { "start": { - "line": 355, + "line": 374, "column": 2 }, "end": { - "line": 355, + "line": 374, "column": 41 } } @@ -16640,15 +17757,15 @@ { "type": "CommentBlock", "value": "* Return the specific epithet of this scientific name if available. ", - "start": 11261, - "end": 11333, + "start": 11894, + "end": 11966, "loc": { "start": { - "line": 367, + "line": 386, "column": 2 }, "end": { - "line": 367, + "line": 386, "column": 74 } } @@ -16657,15 +17774,15 @@ }, { "type": "ClassMethod", - "start": 11336, - "end": 11873, + "start": 11969, + "end": 12506, "loc": { "start": { - "line": 368, + "line": 387, "column": 2 }, "end": { - "line": 383, + "line": 402, "column": 3 } }, @@ -16673,15 +17790,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11340, - "end": 11355, + "start": 11973, + "end": 11988, "loc": { "start": { - "line": 368, + "line": 387, "column": 6 }, "end": { - "line": 368, + "line": 387, "column": 21 }, "identifierName": "specificEpithet" @@ -16696,58 +17813,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 11358, - "end": 11873, + "start": 11991, + "end": 12506, "loc": { "start": { - "line": 368, + "line": 387, "column": 24 }, "end": { - "line": 383, + "line": 402, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 11418, - "end": 11494, + "start": 12051, + "end": 12127, "loc": { "start": { - "line": 370, + "line": 389, "column": 4 }, "end": { - "line": 370, + "line": 389, "column": 80 } }, "test": { "type": "CallExpression", - "start": 11422, - "end": 11457, + "start": 12055, + "end": 12090, "loc": { "start": { - "line": 370, + "line": 389, "column": 8 }, "end": { - "line": 370, + "line": 389, "column": 43 } }, "callee": { "type": "Identifier", - "start": 11422, - "end": 11425, + "start": 12055, + "end": 12058, "loc": { "start": { - "line": 370, + "line": 389, "column": 8 }, "end": { - "line": 370, + "line": 389, "column": 11 }, "identifierName": "has" @@ -16758,44 +17875,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 11426, - "end": 11437, + "start": 12059, + "end": 12070, "loc": { "start": { - "line": 370, + "line": 389, "column": 12 }, "end": { - "line": 370, + "line": 389, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 11426, - "end": 11430, + "start": 12059, + "end": 12063, "loc": { "start": { - "line": 370, + "line": 389, "column": 12 }, "end": { - "line": 370, + "line": 389, "column": 16 } } }, "property": { "type": "Identifier", - "start": 11431, - "end": 11437, + "start": 12064, + "end": 12070, "loc": { "start": { - "line": 370, + "line": 389, "column": 17 }, "end": { - "line": 370, + "line": 389, "column": 23 }, "identifierName": "txname" @@ -16806,15 +17923,15 @@ }, { "type": "StringLiteral", - "start": 11439, - "end": 11456, + "start": 12072, + "end": 12089, "loc": { "start": { - "line": 370, + "line": 389, "column": 25 }, "end": { - "line": 370, + "line": 389, "column": 42 } }, @@ -16829,72 +17946,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 11459, - "end": 11494, + "start": 12092, + "end": 12127, "loc": { "start": { - "line": 370, + "line": 389, "column": 45 }, "end": { - "line": 370, + "line": 389, "column": 80 } }, "argument": { "type": "MemberExpression", - "start": 11466, - "end": 11493, + "start": 12099, + "end": 12126, "loc": { "start": { - "line": 370, + "line": 389, "column": 52 }, "end": { - "line": 370, + "line": 389, "column": 79 } }, "object": { "type": "MemberExpression", - "start": 11466, - "end": 11477, + "start": 12099, + "end": 12110, "loc": { "start": { - "line": 370, + "line": 389, "column": 52 }, "end": { - "line": 370, + "line": 389, "column": 63 } }, "object": { "type": "ThisExpression", - "start": 11466, - "end": 11470, + "start": 12099, + "end": 12103, "loc": { "start": { - "line": 370, + "line": 389, "column": 52 }, "end": { - "line": 370, + "line": 389, "column": 56 } } }, "property": { "type": "Identifier", - "start": 11471, - "end": 11477, + "start": 12104, + "end": 12110, "loc": { "start": { - "line": 370, + "line": 389, "column": 57 }, "end": { - "line": 370, + "line": 389, "column": 63 }, "identifierName": "txname" @@ -16905,15 +18022,15 @@ }, "property": { "type": "Identifier", - "start": 11478, - "end": 11493, + "start": 12111, + "end": 12126, "loc": { "start": { - "line": 370, + "line": 389, "column": 64 }, "end": { - "line": 370, + "line": 389, "column": 79 }, "identifierName": "specificEpithet" @@ -16929,15 +18046,15 @@ { "type": "CommentLine", "value": " Try to read the specific epithet if available.", - "start": 11364, - "end": 11413, + "start": 11997, + "end": 12046, "loc": { "start": { - "line": 369, + "line": 388, "column": 4 }, "end": { - "line": 369, + "line": 388, "column": 53 } } @@ -16947,15 +18064,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 11500, - "end": 11572, + "start": 12133, + "end": 12205, "loc": { "start": { - "line": 372, + "line": 391, "column": 4 }, "end": { - "line": 372, + "line": 391, "column": 76 } } @@ -16963,15 +18080,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 11577, - "end": 11615, + "start": 12210, + "end": 12248, "loc": { "start": { - "line": 373, + "line": 392, "column": 4 }, "end": { - "line": 373, + "line": 392, "column": 42 } } @@ -16980,43 +18097,43 @@ }, { "type": "IfStatement", - "start": 11620, - "end": 11846, + "start": 12253, + "end": 12479, "loc": { "start": { - "line": 374, + "line": 393, "column": 4 }, "end": { - "line": 380, + "line": 399, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 11624, - "end": 11641, + "start": 12257, + "end": 12274, "loc": { "start": { - "line": 374, + "line": 393, "column": 8 }, "end": { - "line": 374, + "line": 393, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 11624, - "end": 11628, + "start": 12257, + "end": 12261, "loc": { "start": { - "line": 374, + "line": 393, "column": 8 }, "end": { - "line": 374, + "line": 393, "column": 12 } }, @@ -17024,15 +18141,15 @@ }, "property": { "type": "Identifier", - "start": 11629, - "end": 11641, + "start": 12262, + "end": 12274, "loc": { "start": { - "line": 374, + "line": 393, "column": 13 }, "end": { - "line": 374, + "line": 393, "column": 25 }, "identifierName": "nameComplete" @@ -17044,59 +18161,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 11643, - "end": 11846, + "start": 12276, + "end": 12479, "loc": { "start": { - "line": 374, + "line": 393, "column": 27 }, "end": { - "line": 380, + "line": 399, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 11651, - "end": 11767, + "start": 12284, + "end": 12400, "loc": { "start": { - "line": 375, + "line": 394, "column": 6 }, "end": { - "line": 378, + "line": 397, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11657, - "end": 11766, + "start": 12290, + "end": 12399, "loc": { "start": { - "line": 375, + "line": 394, "column": 12 }, "end": { - "line": 378, + "line": 397, "column": 7 } }, "id": { "type": "Identifier", - "start": 11657, - "end": 11663, + "start": 12290, + "end": 12296, "loc": { "start": { - "line": 375, + "line": 394, "column": 12 }, "end": { - "line": 375, + "line": 394, "column": 18 }, "identifierName": "txname" @@ -17105,43 +18222,43 @@ }, "init": { "type": "CallExpression", - "start": 11666, - "end": 11766, + "start": 12299, + "end": 12399, "loc": { "start": { - "line": 375, + "line": 394, "column": 21 }, "end": { - "line": 378, + "line": 397, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 11666, - "end": 11699, + "start": 12299, + "end": 12332, "loc": { "start": { - "line": 375, + "line": 394, "column": 21 }, "end": { - "line": 375, + "line": 394, "column": 54 } }, "object": { "type": "Identifier", - "start": 11666, - "end": 11682, + "start": 12299, + "end": 12315, "loc": { "start": { - "line": 375, + "line": 394, "column": 21 }, "end": { - "line": 375, + "line": 394, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -17150,15 +18267,15 @@ }, "property": { "type": "Identifier", - "start": 11683, - "end": 11699, + "start": 12316, + "end": 12332, "loc": { "start": { - "line": 375, + "line": 394, "column": 38 }, "end": { - "line": 375, + "line": 394, "column": 54 }, "identifierName": "fromVerbatimName" @@ -17170,44 +18287,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 11709, - "end": 11726, + "start": 12342, + "end": 12359, "loc": { "start": { - "line": 376, + "line": 395, "column": 8 }, "end": { - "line": 376, + "line": 395, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 11709, - "end": 11713, + "start": 12342, + "end": 12346, "loc": { "start": { - "line": 376, + "line": 395, "column": 8 }, "end": { - "line": 376, + "line": 395, "column": 12 } } }, "property": { "type": "Identifier", - "start": 11714, - "end": 11726, + "start": 12347, + "end": 12359, "loc": { "start": { - "line": 376, + "line": 395, "column": 13 }, "end": { - "line": 376, + "line": 395, "column": 25 }, "identifierName": "nameComplete" @@ -17218,44 +18335,44 @@ }, { "type": "MemberExpression", - "start": 11736, - "end": 11758, + "start": 12369, + "end": 12391, "loc": { "start": { - "line": 377, + "line": 396, "column": 8 }, "end": { - "line": 377, + "line": 396, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 11736, - "end": 11740, + "start": 12369, + "end": 12373, "loc": { "start": { - "line": 377, + "line": 396, "column": 8 }, "end": { - "line": 377, + "line": 396, "column": 12 } } }, "property": { "type": "Identifier", - "start": 11741, - "end": 11758, + "start": 12374, + "end": 12391, "loc": { "start": { - "line": 377, + "line": 396, "column": 13 }, "end": { - "line": 377, + "line": 396, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -17272,43 +18389,43 @@ }, { "type": "IfStatement", - "start": 11774, - "end": 11840, + "start": 12407, + "end": 12473, "loc": { "start": { - "line": 379, + "line": 398, "column": 6 }, "end": { - "line": 379, + "line": 398, "column": 72 } }, "test": { "type": "CallExpression", - "start": 11778, - "end": 11808, + "start": 12411, + "end": 12441, "loc": { "start": { - "line": 379, + "line": 398, "column": 10 }, "end": { - "line": 379, + "line": 398, "column": 40 } }, "callee": { "type": "Identifier", - "start": 11778, - "end": 11781, + "start": 12411, + "end": 12414, "loc": { "start": { - "line": 379, + "line": 398, "column": 10 }, "end": { - "line": 379, + "line": 398, "column": 13 }, "identifierName": "has" @@ -17318,15 +18435,15 @@ "arguments": [ { "type": "Identifier", - "start": 11782, - "end": 11788, + "start": 12415, + "end": 12421, "loc": { "start": { - "line": 379, + "line": 398, "column": 14 }, "end": { - "line": 379, + "line": 398, "column": 20 }, "identifierName": "txname" @@ -17335,15 +18452,15 @@ }, { "type": "StringLiteral", - "start": 11790, - "end": 11807, + "start": 12423, + "end": 12440, "loc": { "start": { - "line": 379, + "line": 398, "column": 22 }, "end": { - "line": 379, + "line": 398, "column": 39 } }, @@ -17357,43 +18474,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 11810, - "end": 11840, + "start": 12443, + "end": 12473, "loc": { "start": { - "line": 379, + "line": 398, "column": 42 }, "end": { - "line": 379, + "line": 398, "column": 72 } }, "argument": { "type": "MemberExpression", - "start": 11817, - "end": 11839, + "start": 12450, + "end": 12472, "loc": { "start": { - "line": 379, + "line": 398, "column": 49 }, "end": { - "line": 379, + "line": 398, "column": 71 } }, "object": { "type": "Identifier", - "start": 11817, - "end": 11823, + "start": 12450, + "end": 12456, "loc": { "start": { - "line": 379, + "line": 398, "column": 49 }, "end": { - "line": 379, + "line": 398, "column": 55 }, "identifierName": "txname" @@ -17402,15 +18519,15 @@ }, "property": { "type": "Identifier", - "start": 11824, - "end": 11839, + "start": 12457, + "end": 12472, "loc": { "start": { - "line": 379, + "line": 398, "column": 56 }, "end": { - "line": 379, + "line": 398, "column": 71 }, "identifierName": "specificEpithet" @@ -17430,15 +18547,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 11500, - "end": 11572, + "start": 12133, + "end": 12205, "loc": { "start": { - "line": 372, + "line": 391, "column": 4 }, "end": { - "line": 372, + "line": 391, "column": 76 } } @@ -17446,15 +18563,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 11577, - "end": 11615, + "start": 12210, + "end": 12248, "loc": { "start": { - "line": 373, + "line": 392, "column": 4 }, "end": { - "line": 373, + "line": 392, "column": 42 } } @@ -17463,29 +18580,29 @@ }, { "type": "ReturnStatement", - "start": 11852, - "end": 11869, + "start": 12485, + "end": 12502, "loc": { "start": { - "line": 382, + "line": 401, "column": 4 }, "end": { - "line": 382, + "line": 401, "column": 21 } }, "argument": { "type": "Identifier", - "start": 11859, - "end": 11868, + "start": 12492, + "end": 12501, "loc": { "start": { - "line": 382, + "line": 401, "column": 11 }, "end": { - "line": 382, + "line": 401, "column": 20 }, "identifierName": "undefined" @@ -17501,15 +18618,15 @@ { "type": "CommentBlock", "value": "* Return the specific epithet of this scientific name if available. ", - "start": 11261, - "end": 11333, + "start": 11894, + "end": 11966, "loc": { "start": { - "line": 367, + "line": 386, "column": 2 }, "end": { - "line": 367, + "line": 386, "column": 74 } } @@ -17519,15 +18636,15 @@ { "type": "CommentBlock", "value": "* Set the specificEpithet part of this name. ", - "start": 11877, - "end": 11926, + "start": 12510, + "end": 12559, "loc": { "start": { - "line": 385, + "line": 404, "column": 2 }, "end": { - "line": 385, + "line": 404, "column": 51 } } @@ -17536,15 +18653,15 @@ }, { "type": "ClassMethod", - "start": 11929, - "end": 12263, + "start": 12562, + "end": 12896, "loc": { "start": { - "line": 386, + "line": 405, "column": 2 }, "end": { - "line": 395, + "line": 414, "column": 3 } }, @@ -17552,15 +18669,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11933, - "end": 11948, + "start": 12566, + "end": 12581, "loc": { "start": { - "line": 386, + "line": 405, "column": 6 }, "end": { - "line": 386, + "line": 405, "column": 21 }, "identifierName": "specificEpithet" @@ -17575,15 +18692,15 @@ "params": [ { "type": "Identifier", - "start": 11949, - "end": 11956, + "start": 12582, + "end": 12589, "loc": { "start": { - "line": 386, + "line": 405, "column": 22 }, "end": { - "line": 386, + "line": 405, "column": 29 }, "identifierName": "epithet" @@ -17593,102 +18710,102 @@ ], "body": { "type": "BlockStatement", - "start": 11958, - "end": 12263, + "start": 12591, + "end": 12896, "loc": { "start": { - "line": 386, + "line": 405, "column": 31 }, "end": { - "line": 395, + "line": 414, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 11964, - "end": 12002, + "start": 12597, + "end": 12635, "loc": { "start": { - "line": 387, + "line": 406, "column": 4 }, "end": { - "line": 387, + "line": 406, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 11964, - "end": 12001, + "start": 12597, + "end": 12634, "loc": { "start": { - "line": 387, + "line": 406, "column": 4 }, "end": { - "line": 387, + "line": 406, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11964, - "end": 11991, + "start": 12597, + "end": 12624, "loc": { "start": { - "line": 387, + "line": 406, "column": 4 }, "end": { - "line": 387, + "line": 406, "column": 31 } }, "object": { "type": "MemberExpression", - "start": 11964, - "end": 11975, + "start": 12597, + "end": 12608, "loc": { "start": { - 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"line": 387, + "line": 406, "column": 34 }, "end": { - "line": 387, + "line": 406, "column": 41 }, "identifierName": "epithet" @@ -17737,58 +18854,58 @@ }, { "type": "IfStatement", - "start": 12007, - "end": 12259, + "start": 12640, + "end": 12892, "loc": { "start": { - "line": 388, + "line": 407, "column": 4 }, "end": { - "line": 394, + "line": 413, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 12011, - "end": 12025, + "start": 12644, + "end": 12658, "loc": { "start": { - "line": 388, + "line": 407, "column": 8 }, "end": { - "line": 388, + "line": 407, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 12011, - "end": 12015, + "start": 12644, + "end": 12648, "loc": { "start": { - "line": 388, + "line": 407, "column": 8 }, "end": { - "line": 388, + "line": 407, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12016, - "end": 12025, + "start": 12649, + "end": 12658, "loc": { "start": { - "line": 388, + "line": 407, "column": 13 }, "end": { - "line": 388, + "line": 407, "column": 22 }, "identifierName": "genusPart" @@ -17799,73 +18916,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 12027, - "end": 12259, + "start": 12660, + "end": 12892, "loc": { "start": { - "line": 388, + "line": 407, "column": 24 }, "end": { - "line": 394, + "line": 413, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 12035, - "end": 12253, + "start": 12668, + "end": 12886, "loc": { "start": { - "line": 389, + "line": 408, "column": 6 }, "end": { - "line": 393, + "line": 412, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 12039, - "end": 12064, + "start": 12672, + "end": 12697, "loc": { "start": { - "line": 389, + "line": 408, "column": 10 }, "end": { - "line": 389, + "line": 408, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 12039, - "end": 12043, + "start": 12672, + "end": 12676, "loc": { "start": { - "line": 389, + "line": 408, "column": 10 }, "end": { - "line": 389, + "line": 408, "column": 14 } } }, "property": { "type": "Identifier", - "start": 12044, - "end": 12064, + "start": 12677, + "end": 12697, "loc": { "start": { - "line": 389, + "line": 408, "column": 15 }, "end": { - "line": 389, + "line": 408, "column": 35 }, "identifierName": "infraspecificEpithet" @@ -17876,102 +18993,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 12066, - "end": 12171, + "start": 12699, + "end": 12804, "loc": { "start": { - "line": 389, + "line": 408, "column": 37 }, "end": { - "line": 391, + "line": 410, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 12076, - "end": 12163, + "start": 12709, + "end": 12796, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 95 } }, "expression": { "type": "AssignmentExpression", - "start": 12076, - "end": 12162, + "start": 12709, + "end": 12795, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 94 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 12076, - "end": 12100, + "start": 12709, + "end": 12733, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 12076, - "end": 12087, + "start": 12709, + "end": 12720, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 12076, - "end": 12080, + "start": 12709, + "end": 12713, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12081, - "end": 12087, + "start": 12714, + "end": 12720, "loc": { "start": { - "line": 390, + "line": 409, "column": 13 }, "end": { - "line": 390, + "line": 409, "column": 19 }, "identifierName": "txname" @@ -17982,15 +19099,15 @@ }, "property": { "type": "Identifier", - "start": 12088, - "end": 12100, + "start": 12721, + "end": 12733, "loc": { "start": { - "line": 390, + "line": 409, "column": 20 }, "end": { - "line": 390, + "line": 409, "column": 32 }, "identifierName": "nameComplete" @@ -18001,59 +19118,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 12103, - "end": 12162, + "start": 12736, + "end": 12795, "loc": { "start": { - "line": 390, + "line": 409, "column": 35 }, "end": { - "line": 390, + "line": 409, "column": 94 } }, "expressions": [ { "type": "MemberExpression", - "start": 12106, - "end": 12120, + "start": 12739, + "end": 12753, "loc": { "start": { - "line": 390, + "line": 409, "column": 38 }, "end": { - "line": 390, + "line": 409, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 12106, - "end": 12110, + "start": 12739, + "end": 12743, "loc": { "start": { - "line": 390, + "line": 409, "column": 38 }, "end": { - "line": 390, + "line": 409, "column": 42 } } }, "property": { "type": "Identifier", - "start": 12111, - "end": 12120, + "start": 12744, + "end": 12753, "loc": { "start": { - "line": 390, + "line": 409, "column": 43 }, "end": { - "line": 390, + "line": 409, "column": 52 }, "identifierName": "genusPart" @@ -18064,15 +19181,15 @@ }, { "type": "Identifier", - "start": 12124, - "end": 12131, + "start": 12757, + "end": 12764, "loc": { "start": { - "line": 390, + "line": 409, "column": 56 }, "end": { - "line": 390, + "line": 409, "column": 63 }, "identifierName": "epithet" @@ -18081,44 +19198,44 @@ }, { "type": "MemberExpression", - "start": 12135, - "end": 12160, + "start": 12768, + "end": 12793, "loc": { "start": { - "line": 390, + "line": 409, "column": 67 }, "end": { - "line": 390, + "line": 409, "column": 92 } }, "object": { "type": "ThisExpression", - "start": 12135, - "end": 12139, + "start": 12768, + "end": 12772, "loc": { "start": { - "line": 390, + "line": 409, "column": 67 }, "end": { - "line": 390, + "line": 409, "column": 71 } } }, "property": { "type": "Identifier", - "start": 12140, - "end": 12160, + "start": 12773, + "end": 12793, "loc": { "start": { - "line": 390, + "line": 409, "column": 72 }, "end": { - "line": 390, + "line": 409, "column": 92 }, "identifierName": "infraspecificEpithet" @@ -18131,15 +19248,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 12104, - "end": 12104, + "start": 12737, + "end": 12737, "loc": { "start": { - "line": 390, + "line": 409, "column": 36 }, "end": { - "line": 390, + "line": 409, "column": 36 } }, @@ -18151,15 +19268,15 @@ }, { "type": "TemplateElement", - "start": 12121, - "end": 12122, + "start": 12754, + "end": 12755, "loc": { "start": { - "line": 390, + "line": 409, "column": 53 }, "end": { - "line": 390, + "line": 409, "column": 54 } }, @@ -18171,15 +19288,15 @@ }, { "type": "TemplateElement", - "start": 12132, - "end": 12133, + "start": 12765, + "end": 12766, "loc": { "start": { - "line": 390, + "line": 409, "column": 64 }, "end": { - "line": 390, + "line": 409, "column": 65 } }, @@ -18191,15 +19308,15 @@ }, { "type": "TemplateElement", - "start": 12161, - "end": 12161, + "start": 12794, + "end": 12794, "loc": { "start": { - "line": 390, + "line": 409, "column": 93 }, "end": { - "line": 390, + "line": 409, "column": 93 } }, @@ -18218,102 +19335,102 @@ }, "alternate": { "type": "BlockStatement", - "start": 12177, - "end": 12253, + "start": 12810, + "end": 12886, "loc": { "start": { - "line": 391, + "line": 410, "column": 13 }, "end": { - "line": 393, + "line": 412, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 12187, - "end": 12245, + "start": 12820, + "end": 12878, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 12187, - "end": 12244, + "start": 12820, + "end": 12877, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 65 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 12187, - "end": 12211, + "start": 12820, + "end": 12844, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 12187, - "end": 12198, + "start": 12820, + "end": 12831, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 12187, - "end": 12191, + "start": 12820, + "end": 12824, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12192, - "end": 12198, + "start": 12825, + "end": 12831, "loc": { "start": { - "line": 392, + "line": 411, "column": 13 }, "end": { - "line": 392, + "line": 411, "column": 19 }, "identifierName": "txname" @@ -18324,15 +19441,15 @@ }, "property": { "type": "Identifier", - "start": 12199, - "end": 12211, + "start": 12832, + "end": 12844, "loc": { "start": { - "line": 392, + "line": 411, "column": 20 }, "end": { - "line": 392, + "line": 411, "column": 32 }, "identifierName": "nameComplete" @@ -18343,59 +19460,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 12214, - "end": 12244, + "start": 12847, + "end": 12877, "loc": { "start": { - "line": 392, + "line": 411, "column": 35 }, "end": { - "line": 392, + "line": 411, "column": 65 } }, "expressions": [ { "type": "MemberExpression", - "start": 12217, - "end": 12231, + "start": 12850, + "end": 12864, "loc": { "start": { - "line": 392, + "line": 411, "column": 38 }, "end": { - "line": 392, + "line": 411, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 12217, - "end": 12221, + "start": 12850, + "end": 12854, "loc": { "start": { - "line": 392, + "line": 411, "column": 38 }, "end": { - "line": 392, + "line": 411, "column": 42 } } }, "property": { "type": "Identifier", - "start": 12222, - "end": 12231, + "start": 12855, + "end": 12864, "loc": { "start": { - "line": 392, + "line": 411, "column": 43 }, "end": { - "line": 392, + "line": 411, "column": 52 }, "identifierName": "genusPart" @@ -18406,15 +19523,15 @@ }, { "type": "Identifier", - "start": 12235, - "end": 12242, + "start": 12868, + "end": 12875, "loc": { "start": { - "line": 392, + "line": 411, "column": 56 }, "end": { - "line": 392, + "line": 411, "column": 63 }, "identifierName": "epithet" @@ -18425,15 +19542,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 12215, - "end": 12215, + "start": 12848, + "end": 12848, "loc": { "start": { - "line": 392, + "line": 411, "column": 36 }, "end": { - "line": 392, + "line": 411, "column": 36 } }, @@ -18445,15 +19562,15 @@ }, { "type": "TemplateElement", - "start": 12232, - "end": 12233, + "start": 12865, + "end": 12866, "loc": { "start": { - "line": 392, + "line": 411, "column": 53 }, "end": { - "line": 392, + "line": 411, "column": 54 } }, @@ -18465,15 +19582,15 @@ }, { "type": "TemplateElement", - "start": 12243, - "end": 12243, + "start": 12876, + "end": 12876, "loc": { "start": { - "line": 392, + "line": 411, "column": 64 }, "end": { - "line": 392, + "line": 411, "column": 64 } }, @@ -18504,15 +19621,15 @@ { "type": "CommentBlock", "value": "* Set the specificEpithet part of this name. ", - "start": 11877, - "end": 11926, + "start": 12510, + "end": 12559, "loc": { "start": { - "line": 385, + "line": 404, "column": 2 }, "end": { - "line": 385, + "line": 404, "column": 51 } } @@ -18522,15 +19639,15 @@ { "type": "CommentBlock", "value": "* Return the infraspecific epithet of this scientific name if available. ", - "start": 12267, - "end": 12344, + "start": 12900, + "end": 12977, "loc": { "start": { - "line": 397, + "line": 416, "column": 2 }, "end": { - "line": 397, + "line": 416, "column": 79 } } @@ -18539,15 +19656,15 @@ }, { "type": "ClassMethod", - "start": 12347, - "end": 12916, + "start": 12980, + "end": 13549, "loc": { "start": { - "line": 398, + "line": 417, "column": 2 }, "end": { - "line": 413, + "line": 432, "column": 3 } }, @@ -18555,15 +19672,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12351, - "end": 12371, + "start": 12984, + "end": 13004, "loc": { "start": { - "line": 398, + "line": 417, "column": 6 }, "end": { - "line": 398, + "line": 417, "column": 26 }, "identifierName": "infraspecificEpithet" @@ -18578,58 +19695,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 12374, - "end": 12916, + "start": 13007, + "end": 13549, "loc": { "start": { - "line": 398, + "line": 417, "column": 29 }, "end": { - "line": 413, + "line": 432, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 12434, - "end": 12520, + "start": 13067, + "end": 13153, "loc": { "start": { - "line": 400, + "line": 419, "column": 4 }, "end": { - "line": 400, + "line": 419, "column": 90 } }, "test": { "type": "CallExpression", - "start": 12438, - "end": 12478, + "start": 13071, + "end": 13111, "loc": { "start": { - "line": 400, + "line": 419, "column": 8 }, "end": { - "line": 400, + "line": 419, "column": 48 } }, "callee": { "type": "Identifier", - "start": 12438, - "end": 12441, + "start": 13071, + "end": 13074, "loc": { "start": { - "line": 400, + "line": 419, "column": 8 }, "end": { - "line": 400, + "line": 419, "column": 11 }, "identifierName": "has" @@ -18640,44 +19757,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 12442, - "end": 12453, + "start": 13075, + "end": 13086, "loc": { "start": { - "line": 400, + "line": 419, "column": 12 }, "end": { - "line": 400, + "line": 419, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 12442, - "end": 12446, + "start": 13075, + "end": 13079, "loc": { "start": { - "line": 400, + "line": 419, "column": 12 }, "end": { - "line": 400, + "line": 419, "column": 16 } } }, "property": { "type": "Identifier", - "start": 12447, - "end": 12453, + "start": 13080, + "end": 13086, "loc": { "start": { - "line": 400, + "line": 419, "column": 17 }, "end": { - "line": 400, + "line": 419, "column": 23 }, "identifierName": "txname" @@ -18688,15 +19805,15 @@ }, { "type": "StringLiteral", - "start": 12455, - "end": 12477, + "start": 13088, + "end": 13110, "loc": { "start": { - "line": 400, + "line": 419, "column": 25 }, "end": { - "line": 400, + "line": 419, "column": 47 } }, @@ -18711,72 +19828,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12480, - "end": 12520, + "start": 13113, + "end": 13153, "loc": { "start": { - "line": 400, + "line": 419, "column": 50 }, "end": { - "line": 400, + "line": 419, "column": 90 } }, "argument": { "type": "MemberExpression", - "start": 12487, - "end": 12519, + "start": 13120, + "end": 13152, "loc": { "start": { - "line": 400, + "line": 419, "column": 57 }, "end": { - "line": 400, + "line": 419, "column": 89 } }, "object": { "type": "MemberExpression", - "start": 12487, - "end": 12498, + "start": 13120, + "end": 13131, "loc": { "start": { - "line": 400, + "line": 419, "column": 57 }, "end": { - "line": 400, + "line": 419, "column": 68 } }, "object": { "type": "ThisExpression", - "start": 12487, - "end": 12491, + "start": 13120, + "end": 13124, "loc": { "start": { - "line": 400, + "line": 419, "column": 57 }, "end": { - "line": 400, + "line": 419, "column": 61 } } }, "property": { "type": "Identifier", - "start": 12492, - "end": 12498, + "start": 13125, + "end": 13131, "loc": { "start": { - "line": 400, + "line": 419, "column": 62 }, "end": { - "line": 400, + "line": 419, "column": 68 }, "identifierName": "txname" @@ -18787,15 +19904,15 @@ }, "property": { "type": "Identifier", - "start": 12499, - "end": 12519, + "start": 13132, + "end": 13152, "loc": { "start": { - "line": 400, + "line": 419, "column": 69 }, "end": { - "line": 400, + "line": 419, "column": 89 }, "identifierName": "infraspecificEpithet" @@ -18811,15 +19928,15 @@ { "type": "CommentLine", "value": " Try to read the specific epithet if available.", - "start": 12380, - "end": 12429, + "start": 13013, + "end": 13062, "loc": { "start": { - "line": 399, + "line": 418, "column": 4 }, "end": { - "line": 399, + "line": 418, "column": 53 } } @@ -18829,15 +19946,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 12526, - "end": 12598, + "start": 13159, + "end": 13231, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 76 } } @@ -18845,15 +19962,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 12603, - "end": 12641, + "start": 13236, + "end": 13274, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 42 } } @@ -18862,57 +19979,57 @@ }, { "type": "IfStatement", - "start": 12646, - "end": 12889, + "start": 13279, + "end": 13522, "loc": { "start": { - "line": 404, + "line": 423, "column": 4 }, "end": { - "line": 410, + "line": 429, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 12650, - "end": 12674, + "start": 13283, + "end": 13307, "loc": { "start": { - "line": 404, + "line": 423, "column": 8 }, "end": { - "line": 404, + "line": 423, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 12650, - "end": 12661, + "start": 13283, + "end": 13294, "loc": { "start": { - "line": 404, + "line": 423, "column": 8 }, "end": { - "line": 404, + "line": 423, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 12650, - "end": 12654, + "start": 13283, + "end": 13287, "loc": { "start": { - "line": 404, + "line": 423, "column": 8 }, "end": { - "line": 404, + "line": 423, "column": 12 } }, @@ -18920,15 +20037,15 @@ }, "property": { "type": "Identifier", - "start": 12655, - "end": 12661, + "start": 13288, + "end": 13294, "loc": { "start": { - "line": 404, + "line": 423, "column": 13 }, "end": { - "line": 404, + "line": 423, "column": 19 }, "identifierName": "txname" @@ -18940,15 +20057,15 @@ }, "property": { "type": "Identifier", - "start": 12662, - 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"line": 405, + "line": 424, "column": 12 }, "end": { - "line": 405, + "line": 424, "column": 18 }, "identifierName": "txname" @@ -19021,43 +20138,43 @@ }, "init": { "type": "CallExpression", - "start": 12699, - "end": 12799, + "start": 13332, + "end": 13432, "loc": { "start": { - "line": 405, + "line": 424, "column": 21 }, "end": { - "line": 408, + "line": 427, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 12699, - "end": 12732, + "start": 13332, + "end": 13365, "loc": { "start": { - "line": 405, + "line": 424, "column": 21 }, "end": { - "line": 405, + "line": 424, "column": 54 } }, "object": { "type": "Identifier", - "start": 12699, - "end": 12715, + "start": 13332, + "end": 13348, "loc": { "start": { - "line": 405, + "line": 424, "column": 21 }, "end": { - "line": 405, + "line": 424, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -19066,15 +20183,15 @@ }, "property": { "type": "Identifier", - "start": 12716, - "end": 12732, + "start": 13349, + "end": 13365, "loc": { "start": { - "line": 405, + "line": 424, "column": 38 }, "end": { - "line": 405, + "line": 424, "column": 54 }, "identifierName": "fromVerbatimName" @@ -19086,44 +20203,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 12742, - "end": 12759, + "start": 13375, + "end": 13392, "loc": { "start": { - "line": 406, + "line": 425, "column": 8 }, "end": { - "line": 406, + "line": 425, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 12742, - "end": 12746, + "start": 13375, + "end": 13379, "loc": { "start": { - "line": 406, + "line": 425, "column": 8 }, "end": { - "line": 406, + "line": 425, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12747, - "end": 12759, + "start": 13380, + "end": 13392, "loc": { "start": { - "line": 406, + "line": 425, "column": 13 }, "end": { - "line": 406, + "line": 425, "column": 25 }, "identifierName": "nameComplete" @@ -19134,44 +20251,44 @@ }, { "type": "MemberExpression", - "start": 12769, - "end": 12791, + "start": 13402, + "end": 13424, "loc": { "start": { - "line": 407, + "line": 426, "column": 8 }, "end": { - "line": 407, + "line": 426, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 12769, - "end": 12773, + "start": 13402, + "end": 13406, "loc": { "start": { - "line": 407, + "line": 426, "column": 8 }, "end": { - "line": 407, + "line": 426, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12774, - "end": 12791, + "start": 13407, + "end": 13424, "loc": { "start": { - "line": 407, + "line": 426, "column": 13 }, "end": { - "line": 407, + "line": 426, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -19188,43 +20305,43 @@ }, { "type": "IfStatement", - "start": 12807, - "end": 12883, + "start": 13440, + "end": 13516, "loc": { "start": { - "line": 409, + "line": 428, "column": 6 }, "end": { - "line": 409, + "line": 428, "column": 82 } }, "test": { "type": "CallExpression", - "start": 12811, - "end": 12846, + "start": 13444, + "end": 13479, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 45 } }, "callee": { "type": "Identifier", - "start": 12811, - "end": 12814, + "start": 13444, + "end": 13447, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 13 }, "identifierName": "has" @@ -19234,15 +20351,15 @@ "arguments": [ { "type": "Identifier", - "start": 12815, - "end": 12821, + "start": 13448, + "end": 13454, "loc": { "start": { - "line": 409, + "line": 428, "column": 14 }, "end": { - "line": 409, + "line": 428, "column": 20 }, "identifierName": "txname" @@ -19251,15 +20368,15 @@ }, { "type": "StringLiteral", - "start": 12823, - "end": 12845, + "start": 13456, + "end": 13478, "loc": { "start": { - "line": 409, + "line": 428, "column": 22 }, "end": { - "line": 409, + "line": 428, "column": 44 } }, @@ -19273,43 +20390,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12848, - "end": 12883, + "start": 13481, + "end": 13516, "loc": { "start": { - "line": 409, + "line": 428, "column": 47 }, "end": { - "line": 409, + "line": 428, "column": 82 } }, "argument": { "type": "MemberExpression", - "start": 12855, - "end": 12882, + "start": 13488, + "end": 13515, "loc": { "start": { - "line": 409, + "line": 428, "column": 54 }, "end": { - "line": 409, + "line": 428, "column": 81 } }, "object": { "type": "Identifier", - "start": 12855, - "end": 12861, + "start": 13488, + "end": 13494, "loc": { "start": { - "line": 409, + "line": 428, "column": 54 }, "end": { - "line": 409, + "line": 428, "column": 60 }, "identifierName": "txname" @@ -19318,15 +20435,15 @@ }, "property": { "type": "Identifier", - "start": 12862, - "end": 12882, + "start": 13495, + "end": 13515, "loc": { "start": { - "line": 409, + "line": 428, "column": 61 }, "end": { - "line": 409, + "line": 428, "column": 81 }, "identifierName": "infraspecificEpithet" @@ -19346,15 +20463,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 12526, - "end": 12598, + "start": 13159, + "end": 13231, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 76 } } @@ -19362,15 +20479,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 12603, - "end": 12641, + "start": 13236, + "end": 13274, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 42 } } @@ -19379,29 +20496,29 @@ }, { "type": "ReturnStatement", - "start": 12895, - "end": 12912, + "start": 13528, + "end": 13545, "loc": { "start": { - "line": 412, + "line": 431, "column": 4 }, "end": { - "line": 412, + "line": 431, "column": 21 } }, "argument": { "type": "Identifier", - "start": 12902, - "end": 12911, + "start": 13535, + "end": 13544, "loc": { "start": { - "line": 412, + "line": 431, "column": 11 }, "end": { - "line": 412, + "line": 431, "column": 20 }, "identifierName": "undefined" @@ -19417,15 +20534,15 @@ { "type": "CommentBlock", "value": "* Return the infraspecific epithet of this scientific name if available. ", - "start": 12267, - "end": 12344, + "start": 12900, + "end": 12977, "loc": { "start": { - "line": 397, + "line": 416, "column": 2 }, "end": { - "line": 397, + "line": 416, "column": 79 } } @@ -19435,15 +20552,15 @@ { "type": "CommentBlock", "value": "* Set the infraspecificEpithet part of this name. ", - "start": 12920, - "end": 12974, + "start": 13553, + "end": 13607, "loc": { "start": { - "line": 415, + "line": 434, "column": 2 }, "end": { - "line": 415, + "line": 434, "column": 56 } } @@ -19452,15 +20569,15 @@ }, { "type": "ClassMethod", - "start": 12977, - "end": 13315, + "start": 13610, + "end": 13948, "loc": { "start": { - "line": 416, + "line": 435, "column": 2 }, "end": { - "line": 425, + "line": 444, "column": 3 } }, @@ -19468,15 +20585,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12981, - "end": 13001, + "start": 13614, + "end": 13634, "loc": { "start": { - "line": 416, + "line": 435, "column": 6 }, "end": { - "line": 416, + "line": 435, "column": 26 }, "identifierName": "infraspecificEpithet" @@ -19491,15 +20608,15 @@ "params": [ { "type": "Identifier", - "start": 13002, - "end": 13009, + "start": 13635, + "end": 13642, "loc": { "start": { - "line": 416, + "line": 435, "column": 27 }, "end": { - "line": 416, + "line": 435, "column": 34 }, "identifierName": "epithet" @@ -19509,102 +20626,102 @@ ], "body": { "type": "BlockStatement", - "start": 13011, - "end": 13315, + "start": 13644, + "end": 13948, "loc": { "start": { - "line": 416, + "line": 435, "column": 36 }, "end": { - "line": 425, + "line": 444, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 13017, - "end": 13060, + "start": 13650, + "end": 13693, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 47 } }, "expression": { "type": "AssignmentExpression", - "start": 13017, - "end": 13059, + "start": 13650, + "end": 13692, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 46 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13017, - "end": 13049, + "start": 13650, + "end": 13682, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 13017, - "end": 13028, + "start": 13650, + "end": 13661, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 13017, - "end": 13021, + "start": 13650, + "end": 13654, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 8 } } }, "property": { "type": "Identifier", - "start": 13022, - "end": 13028, + "start": 13655, + "end": 13661, "loc": { "start": { - "line": 417, + "line": 436, "column": 9 }, "end": { - "line": 417, + "line": 436, "column": 15 }, "identifierName": "txname" @@ -19615,15 +20732,15 @@ }, "property": { "type": "Identifier", - "start": 13029, - "end": 13049, + "start": 13662, + "end": 13682, "loc": { "start": { - "line": 417, + "line": 436, "column": 16 }, "end": { - "line": 417, + "line": 436, "column": 36 }, "identifierName": "infraspecificEpithet" @@ -19634,15 +20751,15 @@ }, "right": { "type": "Identifier", - "start": 13052, - "end": 13059, + "start": 13685, + "end": 13692, "loc": { "start": { - "line": 417, + "line": 436, "column": 39 }, "end": { - "line": 417, + "line": 436, "column": 46 }, "identifierName": "epithet" @@ -19653,58 +20770,58 @@ }, { "type": "IfStatement", - "start": 13065, - "end": 13311, + "start": 13698, + "end": 13944, "loc": { "start": { - "line": 418, + "line": 437, "column": 4 }, "end": { - "line": 424, + "line": 443, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 13069, - "end": 13083, + "start": 13702, + "end": 13716, "loc": { "start": { - "line": 418, + "line": 437, "column": 8 }, "end": { - "line": 418, + "line": 437, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 13069, - "end": 13073, + "start": 13702, + "end": 13706, "loc": { "start": { - "line": 418, + "line": 437, "column": 8 }, "end": { - "line": 418, + "line": 437, "column": 12 } } }, "property": { "type": "Identifier", - "start": 13074, - "end": 13083, + "start": 13707, + "end": 13716, "loc": { "start": { - "line": 418, + "line": 437, "column": 13 }, "end": { - "line": 418, + "line": 437, "column": 22 }, "identifierName": "genusPart" @@ -19715,73 +20832,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 13085, - "end": 13311, + "start": 13718, + "end": 13944, "loc": { "start": { - "line": 418, + "line": 437, "column": 24 }, "end": { - "line": 424, + "line": 443, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 13093, - "end": 13305, + "start": 13726, + "end": 13938, "loc": { "start": { - "line": 419, + "line": 438, "column": 6 }, "end": { - "line": 423, + "line": 442, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 13097, - "end": 13117, + "start": 13730, + "end": 13750, "loc": { "start": { - "line": 419, + "line": 438, "column": 10 }, "end": { - "line": 419, + "line": 438, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 13097, - "end": 13101, + "start": 13730, + "end": 13734, "loc": { "start": { - "line": 419, + "line": 438, "column": 10 }, "end": { - "line": 419, + "line": 438, "column": 14 } } }, "property": { "type": "Identifier", - "start": 13102, - "end": 13117, + "start": 13735, + "end": 13750, "loc": { "start": { - "line": 419, + "line": 438, "column": 15 }, "end": { - "line": 419, + "line": 438, "column": 30 }, "identifierName": "specificEpithet" @@ -19792,102 +20909,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 13119, - "end": 13219, + "start": 13752, + "end": 13852, "loc": { "start": { - "line": 419, + "line": 438, "column": 32 }, "end": { - "line": 421, + "line": 440, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 13129, - "end": 13211, + "start": 13762, + "end": 13844, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 90 } }, "expression": { "type": "AssignmentExpression", - "start": 13129, - "end": 13210, + "start": 13762, + "end": 13843, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 89 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13129, - "end": 13153, + "start": 13762, + "end": 13786, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 13129, - "end": 13140, + "start": 13762, + "end": 13773, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 13129, - "end": 13133, + "start": 13762, + "end": 13766, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 12 } } }, "property": { "type": "Identifier", - "start": 13134, - "end": 13140, + "start": 13767, + "end": 13773, "loc": { "start": { - "line": 420, + "line": 439, "column": 13 }, "end": { - "line": 420, + "line": 439, "column": 19 }, "identifierName": "txname" @@ -19898,15 +21015,15 @@ }, "property": { "type": "Identifier", - "start": 13141, - "end": 13153, + "start": 13774, + "end": 13786, "loc": { "start": { - "line": 420, + "line": 439, "column": 20 }, "end": { - "line": 420, + "line": 439, "column": 32 }, "identifierName": "nameComplete" @@ -19917,59 +21034,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 13156, - "end": 13210, + "start": 13789, + "end": 13843, "loc": { "start": { - "line": 420, + "line": 439, "column": 35 }, "end": { - "line": 420, + "line": 439, "column": 89 } }, "expressions": [ { "type": "MemberExpression", - "start": 13159, - "end": 13173, + "start": 13792, + "end": 13806, "loc": { "start": { - "line": 420, + "line": 439, "column": 38 }, "end": { - "line": 420, + "line": 439, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 13159, - "end": 13163, + "start": 13792, + "end": 13796, "loc": { "start": { - "line": 420, + "line": 439, "column": 38 }, "end": { - "line": 420, + "line": 439, "column": 42 } } }, "property": { "type": "Identifier", - "start": 13164, - "end": 13173, + "start": 13797, + "end": 13806, "loc": { "start": { - "line": 420, + "line": 439, "column": 43 }, "end": { - "line": 420, + "line": 439, "column": 52 }, "identifierName": "genusPart" @@ -19980,44 +21097,44 @@ }, { "type": "MemberExpression", - "start": 13177, - "end": 13197, + "start": 13810, + "end": 13830, "loc": { "start": { - "line": 420, + "line": 439, "column": 56 }, "end": { - "line": 420, + "line": 439, "column": 76 } }, "object": { "type": "ThisExpression", - "start": 13177, - "end": 13181, + "start": 13810, + "end": 13814, "loc": { "start": { - "line": 420, + "line": 439, "column": 56 }, "end": { - "line": 420, + "line": 439, "column": 60 } } }, "property": { "type": "Identifier", - "start": 13182, - "end": 13197, + "start": 13815, + "end": 13830, "loc": { "start": { - "line": 420, + "line": 439, "column": 61 }, "end": { - "line": 420, + "line": 439, "column": 76 }, "identifierName": "specificEpithet" @@ -20028,15 +21145,15 @@ }, { "type": "Identifier", - "start": 13201, - "end": 13208, + "start": 13834, + "end": 13841, "loc": { "start": { - "line": 420, + "line": 439, "column": 80 }, "end": { - "line": 420, + "line": 439, "column": 87 }, "identifierName": "epithet" @@ -20047,15 +21164,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 13157, - "end": 13157, + "start": 13790, + "end": 13790, "loc": { "start": { - "line": 420, + "line": 439, "column": 36 }, "end": { - "line": 420, + "line": 439, "column": 36 } }, @@ -20067,15 +21184,15 @@ }, { "type": "TemplateElement", - "start": 13174, - "end": 13175, + "start": 13807, + "end": 13808, "loc": { "start": { - "line": 420, + "line": 439, "column": 53 }, "end": { - "line": 420, + "line": 439, "column": 54 } }, @@ -20087,15 +21204,15 @@ }, { "type": "TemplateElement", - "start": 13198, - "end": 13199, + "start": 13831, + "end": 13832, "loc": { "start": { - "line": 420, + "line": 439, "column": 77 }, "end": { - "line": 420, + "line": 439, "column": 78 } }, @@ -20107,15 +21224,15 @@ }, { "type": "TemplateElement", - "start": 13209, - "end": 13209, + "start": 13842, + "end": 13842, "loc": { "start": { - "line": 420, + "line": 439, "column": 88 }, "end": { - "line": 420, + "line": 439, "column": 88 } }, @@ -20134,102 +21251,102 @@ }, "alternate": { "type": "BlockStatement", - "start": 13225, - "end": 13305, + "start": 13858, + "end": 13938, "loc": { "start": { - "line": 421, + "line": 440, "column": 13 }, "end": { - "line": 423, + "line": 442, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 13235, - "end": 13297, + "start": 13868, + "end": 13930, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 70 } }, "expression": { "type": "AssignmentExpression", - "start": 13235, - "end": 13296, + "start": 13868, + "end": 13929, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 69 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13235, - "end": 13259, + "start": 13868, + "end": 13892, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 13235, - "end": 13246, + "start": 13868, + "end": 13879, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 13235, - "end": 13239, + "start": 13868, + "end": 13872, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 12 } } }, "property": { "type": "Identifier", - "start": 13240, - "end": 13246, + "start": 13873, + "end": 13879, "loc": { "start": { - "line": 422, + "line": 441, "column": 13 }, "end": { - "line": 422, + "line": 441, "column": 19 }, "identifierName": "txname" @@ -20240,15 +21357,15 @@ }, "property": { "type": "Identifier", - "start": 13247, - "end": 13259, + "start": 13880, + "end": 13892, "loc": { "start": { - "line": 422, + "line": 441, "column": 20 }, "end": { - "line": 422, + "line": 441, "column": 32 }, "identifierName": "nameComplete" @@ -20259,59 +21376,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 13262, - "end": 13296, + "start": 13895, + "end": 13929, "loc": { "start": { - "line": 422, + "line": 441, "column": 35 }, "end": { - "line": 422, + "line": 441, "column": 69 } }, "expressions": [ { "type": "MemberExpression", - "start": 13265, - "end": 13279, + "start": 13898, + "end": 13912, "loc": { "start": { - "line": 422, + "line": 441, "column": 38 }, "end": { - "line": 422, + "line": 441, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 13265, - "end": 13269, + "start": 13898, + "end": 13902, "loc": { "start": { - "line": 422, + "line": 441, "column": 38 }, "end": { - "line": 422, + "line": 441, "column": 42 } } }, "property": { "type": "Identifier", - "start": 13270, - "end": 13279, + "start": 13903, + "end": 13912, "loc": { "start": { - "line": 422, + "line": 441, "column": 43 }, "end": { - "line": 422, + "line": 441, "column": 52 }, "identifierName": "genusPart" @@ -20322,15 +21439,15 @@ }, { "type": "Identifier", - "start": 13287, - "end": 13294, + "start": 13920, + "end": 13927, "loc": { "start": { - "line": 422, + "line": 441, "column": 60 }, "end": { - "line": 422, + "line": 441, "column": 67 }, "identifierName": "epithet" @@ -20341,15 +21458,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 13263, - "end": 13263, + "start": 13896, + "end": 13896, "loc": { "start": { - "line": 422, + "line": 441, "column": 36 }, "end": { - "line": 422, + "line": 441, "column": 36 } }, @@ -20361,15 +21478,15 @@ }, { "type": "TemplateElement", - "start": 13280, - "end": 13285, + "start": 13913, + "end": 13918, "loc": { "start": { - "line": 422, + "line": 441, "column": 53 }, "end": { - "line": 422, + "line": 441, "column": 58 } }, @@ -20381,15 +21498,15 @@ }, { "type": "TemplateElement", - "start": 13295, - "end": 13295, + "start": 13928, + "end": 13928, "loc": { "start": { - "line": 422, + "line": 441, "column": 68 }, "end": { - "line": 422, + "line": 441, "column": 68 } }, @@ -20420,15 +21537,15 @@ { "type": "CommentBlock", "value": "* Set the infraspecificEpithet part of this name. ", - "start": 12920, - "end": 12974, + "start": 13553, + "end": 13607, "loc": { "start": { - "line": 415, + "line": 434, "column": 2 }, "end": { - "line": 415, + "line": 434, "column": 56 } } @@ -20438,15 +21555,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name in an JSON-LD representation.\n ", - "start": 13319, - "end": 13386, + "start": 13952, + "end": 14019, "loc": { "start": { - "line": 427, + "line": 446, "column": 2 }, "end": { - "line": 429, + "line": 448, "column": 5 } } @@ -20455,15 +21572,15 @@ }, { "type": "ClassMethod", - "start": 13389, - "end": 13832, + "start": 14022, + "end": 14465, "loc": { "start": { - "line": 430, + "line": 449, "column": 2 }, "end": { - "line": 442, + "line": 461, "column": 3 } }, @@ -20471,15 +21588,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 13393, - "end": 13401, + "start": 14026, + "end": 14034, "loc": { "start": { - "line": 430, + "line": 449, "column": 6 }, "end": { - "line": 430, + "line": 449, "column": 14 }, "identifierName": "asJSONLD" @@ -20494,59 +21611,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 13404, - "end": 13832, + "start": 14037, + "end": 14465, "loc": { "start": { - "line": 430, + "line": 449, "column": 17 }, "end": { - "line": 442, + "line": 461, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 13410, - "end": 13448, + "start": 14043, + "end": 14081, "loc": { "start": { - "line": 431, + "line": 450, "column": 4 }, "end": { - "line": 431, + "line": 450, "column": 42 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13416, - "end": 13447, + "start": 14049, + "end": 14080, "loc": { "start": { - "line": 431, + "line": 450, "column": 10 }, "end": { - "line": 431, + "line": 450, "column": 41 } }, "id": { "type": "Identifier", - "start": 13416, - "end": 13422, + "start": 14049, + "end": 14055, "loc": { "start": { - "line": 431, + "line": 450, "column": 10 }, "end": { - "line": 431, + "line": 450, "column": 16 }, "identifierName": "jsonld" @@ -20555,29 +21672,29 @@ }, "init": { "type": "CallExpression", - "start": 13425, - "end": 13447, + "start": 14058, + "end": 14080, "loc": { "start": { - "line": 431, + "line": 450, "column": 19 }, "end": { - "line": 431, + "line": 450, "column": 41 } }, "callee": { "type": "Identifier", - "start": 13425, - "end": 13434, + "start": 14058, + "end": 14067, "loc": { "start": { - "line": 431, + "line": 450, "column": 19 }, "end": { - "line": 431, + "line": 450, "column": 28 }, "identifierName": "cloneDeep" @@ -20587,44 +21704,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 13435, - "end": 13446, + "start": 14068, + "end": 14079, "loc": { "start": { - "line": 431, + "line": 450, "column": 29 }, "end": { - "line": 431, + "line": 450, "column": 40 } }, "object": { "type": "ThisExpression", - "start": 13435, - "end": 13439, + "start": 14068, + "end": 14072, "loc": { "start": { - "line": 431, + "line": 450, "column": 29 }, "end": { - "line": 431, + "line": 450, "column": 33 } } }, "property": { "type": "Identifier", - "start": 13440, - "end": 13446, + "start": 14073, + "end": 14079, "loc": { "start": { - "line": 431, + "line": 450, "column": 34 }, "end": { - "line": 431, + "line": 450, "column": 40 }, "identifierName": "txname" @@ -20642,15 +21759,15 @@ { "type": "CommentLine", "value": " Make sure '@type' is an array.", - "start": 13454, - "end": 13487, + "start": 14087, + "end": 14120, "loc": { "start": { - "line": 433, + "line": 452, "column": 4 }, "end": { - "line": 433, + "line": 452, "column": 37 } } @@ -20659,29 +21776,29 @@ }, { "type": "IfStatement", - "start": 13492, - "end": 13540, + "start": 14125, + "end": 14173, "loc": { "start": { - "line": 434, + "line": 453, "column": 4 }, "end": { - "line": 434, + "line": 453, "column": 52 } }, "test": { "type": "UnaryExpression", - "start": 13496, - "end": 13517, + "start": 14129, + "end": 14150, "loc": { "start": { - "line": 434, + "line": 453, "column": 8 }, "end": { - "line": 434, + "line": 453, "column": 29 } }, @@ -20689,29 +21806,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 13497, - "end": 13517, + "start": 14130, + "end": 14150, "loc": { "start": { - "line": 434, + "line": 453, "column": 9 }, "end": { - "line": 434, + "line": 453, "column": 29 } }, "callee": { "type": "Identifier", - "start": 13497, - "end": 13500, + "start": 14130, + "end": 14133, "loc": { "start": { - "line": 434, + "line": 453, "column": 9 }, "end": { - "line": 434, + "line": 453, "column": 12 }, "identifierName": "has" @@ -20722,15 +21839,15 @@ "arguments": [ { "type": "Identifier", - "start": 13501, - "end": 13507, + "start": 14134, + "end": 14140, "loc": { "start": { - "line": 434, + "line": 453, "column": 13 }, "end": { - "line": 434, + "line": 453, "column": 19 }, "identifierName": "jsonld" @@ -20739,15 +21856,15 @@ }, { "type": "StringLiteral", - "start": 13509, - "end": 13516, + "start": 14142, + "end": 14149, "loc": { "start": { - "line": 434, + "line": 453, "column": 21 }, "end": { - "line": 434, + "line": 453, "column": 28 } }, @@ -20767,58 +21884,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 13519, - "end": 13540, + "start": 14152, + "end": 14173, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 52 } }, "expression": { "type": "AssignmentExpression", - "start": 13519, - "end": 13539, + "start": 14152, + "end": 14172, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 51 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13519, - "end": 13534, + "start": 14152, + "end": 14167, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 46 } }, "object": { "type": "Identifier", - "start": 13519, - "end": 13525, + "start": 14152, + "end": 14158, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 37 }, "identifierName": "jsonld" @@ -20827,15 +21944,15 @@ }, "property": { "type": "StringLiteral", - "start": 13526, - "end": 13533, + "start": 14159, + "end": 14166, "loc": { "start": { - "line": 434, + "line": 453, "column": 38 }, "end": { - "line": 434, + "line": 453, "column": 45 } }, @@ -20849,15 +21966,15 @@ }, "right": { "type": "ArrayExpression", - "start": 13537, - "end": 13539, + "start": 14170, + "end": 14172, "loc": { "start": { - "line": 434, + "line": 453, "column": 49 }, "end": { - "line": 434, + "line": 453, "column": 51 } }, @@ -20870,15 +21987,15 @@ { "type": "CommentLine", "value": " Make sure '@type' is an array.", - "start": 13454, - "end": 13487, + "start": 14087, + "end": 14120, "loc": { "start": { - "line": 433, + "line": 452, "column": 4 }, "end": { - "line": 433, + "line": 452, "column": 37 } } @@ -20887,29 +22004,29 @@ }, { "type": "IfStatement", - "start": 13545, - "end": 13612, + "start": 14178, + "end": 14245, "loc": { "start": { - "line": 435, + "line": 454, "column": 4 }, "end": { - "line": 435, + "line": 454, "column": 71 } }, "test": { "type": "UnaryExpression", - "start": 13549, - "end": 13574, + "start": 14182, + "end": 14207, "loc": { "start": { - "line": 435, + "line": 454, "column": 8 }, "end": { - "line": 435, + "line": 454, "column": 33 } }, @@ -20917,29 +22034,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 13550, - "end": 13574, + "start": 14183, + "end": 14207, "loc": { "start": { - "line": 435, + "line": 454, "column": 9 }, "end": { - "line": 435, + "line": 454, "column": 33 } }, "callee": { "type": "Identifier", - "start": 13550, - "end": 13557, + "start": 14183, + "end": 14190, "loc": { "start": { - "line": 435, + "line": 454, "column": 9 }, "end": { - "line": 435, + "line": 454, "column": 16 }, "identifierName": "isArray" @@ -20949,29 +22066,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 13558, - "end": 13573, + "start": 14191, + "end": 14206, "loc": { "start": { - "line": 435, + "line": 454, "column": 17 }, "end": { - "line": 435, + "line": 454, "column": 32 } }, "object": { "type": "Identifier", - "start": 13558, - "end": 13564, + "start": 14191, + "end": 14197, "loc": { "start": { - "line": 435, + "line": 454, "column": 17 }, "end": { - "line": 435, + "line": 454, "column": 23 }, "identifierName": "jsonld" @@ -20980,15 +22097,15 @@ }, "property": { "type": "StringLiteral", - "start": 13565, - "end": 13572, + "start": 14198, + "end": 14205, "loc": { "start": { - "line": 435, + "line": 454, "column": 24 }, "end": { - "line": 435, + "line": 454, "column": 31 } }, @@ -21008,58 +22125,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 13576, - "end": 13612, + "start": 14209, + "end": 14245, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 13576, - "end": 13611, + "start": 14209, + "end": 14244, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13576, - "end": 13591, + "start": 14209, + "end": 14224, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 50 } }, "object": { "type": "Identifier", - "start": 13576, - "end": 13582, + "start": 14209, + "end": 14215, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 41 }, "identifierName": "jsonld" @@ -21068,15 +22185,15 @@ }, "property": { "type": "StringLiteral", - "start": 13583, - "end": 13590, + "start": 14216, + "end": 14223, "loc": { "start": { - "line": 435, + "line": 454, "column": 42 }, "end": { - "line": 435, + "line": 454, "column": 49 } }, @@ -21090,44 +22207,44 @@ }, "right": { "type": "ArrayExpression", - "start": 13594, - "end": 13611, + "start": 14227, + "end": 14244, "loc": { "start": { - "line": 435, + "line": 454, "column": 53 }, "end": { - "line": 435, + "line": 454, "column": 70 } }, "elements": [ { "type": "MemberExpression", - "start": 13595, - "end": 13610, + "start": 14228, + "end": 14243, "loc": { "start": { - "line": 435, + "line": 454, "column": 54 }, "end": { - "line": 435, + "line": 454, "column": 69 } }, "object": { "type": "Identifier", - "start": 13595, - "end": 13601, + "start": 14228, + "end": 14234, "loc": { "start": { - "line": 435, + "line": 454, "column": 54 }, "end": { - "line": 435, + "line": 454, "column": 60 }, "identifierName": "jsonld" @@ -21136,15 +22253,15 @@ }, "property": { "type": "StringLiteral", - "start": 13602, - "end": 13609, + "start": 14235, + "end": 14242, "loc": { "start": { - "line": 435, + "line": 454, "column": 61 }, "end": { - "line": 435, + "line": 454, "column": 68 } }, @@ -21166,15 +22283,15 @@ { "type": "CommentLine", "value": " Make it explicit that the type includes the nomenclaturalCode.", - "start": 13618, - "end": 13683, + "start": 14251, + "end": 14316, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 69 } } @@ -21183,44 +22300,44 @@ }, { "type": "VariableDeclaration", - "start": 13688, - "end": 13729, + "start": 14321, + "end": 14362, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13694, - "end": 13728, + "start": 14327, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 10 }, "end": { - "line": 438, + "line": 457, "column": 44 } }, "id": { "type": "Identifier", - "start": 13694, - "end": 13703, + "start": 14327, + "end": 14336, "loc": { "start": { - "line": 438, + "line": 457, "column": 10 }, "end": { - "line": 438, + "line": 457, "column": 19 }, "identifierName": "nomenCode" @@ -21230,44 +22347,44 @@ }, "init": { "type": "MemberExpression", - "start": 13706, - "end": 13728, + "start": 14339, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 13706, - "end": 13710, + "start": 14339, + "end": 14343, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 26 } } }, "property": { "type": "Identifier", - "start": 13711, - "end": 13728, + "start": 14344, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 27 }, "end": { - "line": 438, + "line": 457, "column": 44 }, "identifierName": "nomenclaturalCode" @@ -21284,15 +22401,15 @@ { "type": "CommentLine", "value": " Make it explicit that the type includes the nomenclaturalCode.", - "start": 13618, - "end": 13683, + "start": 14251, + "end": 14316, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 69 } } @@ -21301,29 +22418,29 @@ }, { "type": "IfStatement", - "start": 13734, - "end": 13808, + "start": 14367, + "end": 14441, "loc": { "start": { - "line": 439, + "line": 458, "column": 4 }, "end": { - "line": 439, + "line": 458, "column": 78 } }, "test": { "type": "UnaryExpression", - "start": 13738, - "end": 13774, + "start": 14371, + "end": 14407, "loc": { "start": { - "line": 439, + "line": 458, "column": 8 }, "end": { - "line": 439, + "line": 458, "column": 44 } }, @@ -21331,57 +22448,57 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 13739, - "end": 13774, + "start": 14372, + "end": 14407, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 44 } }, "callee": { "type": "MemberExpression", - "start": 13739, - "end": 13763, + "start": 14372, + "end": 14396, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 33 } }, "object": { "type": "MemberExpression", - "start": 13739, - "end": 13754, + "start": 14372, + "end": 14387, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 24 } }, "object": { "type": "Identifier", - "start": 13739, - "end": 13745, + "start": 14372, + "end": 14378, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 15 }, "identifierName": "jsonld" @@ -21390,15 +22507,15 @@ }, "property": { "type": "StringLiteral", - "start": 13746, - "end": 13753, + "start": 14379, + "end": 14386, "loc": { "start": { - "line": 439, + "line": 458, "column": 16 }, "end": { - "line": 439, + "line": 458, "column": 23 } }, @@ -21412,15 +22529,15 @@ }, "property": { "type": "Identifier", - "start": 13755, - "end": 13763, + "start": 14388, + "end": 14396, "loc": { "start": { - "line": 439, + "line": 458, "column": 25 }, "end": { - "line": 439, + "line": 458, "column": 33 }, "identifierName": "includes" @@ -21432,15 +22549,15 @@ "arguments": [ { "type": "Identifier", - "start": 13764, - "end": 13773, + "start": 14397, + "end": 14406, "loc": { "start": { - "line": 439, + "line": 458, "column": 34 }, "end": { - "line": 439, + "line": 458, "column": 43 }, "identifierName": "nomenCode" @@ -21455,71 +22572,71 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 13776, - "end": 13808, + "start": 14409, + "end": 14441, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 78 } }, "expression": { "type": "CallExpression", - "start": 13776, - "end": 13807, + "start": 14409, + "end": 14440, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 77 } }, "callee": { "type": "MemberExpression", - "start": 13776, - "end": 13796, + "start": 14409, + "end": 14429, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 66 } }, "object": { "type": "MemberExpression", - "start": 13776, - "end": 13791, + "start": 14409, + "end": 14424, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 61 } }, "object": { "type": "Identifier", - "start": 13776, - "end": 13782, + "start": 14409, + "end": 14415, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 52 }, "identifierName": "jsonld" @@ -21528,15 +22645,15 @@ }, "property": { "type": "StringLiteral", - "start": 13783, - "end": 13790, + "start": 14416, + "end": 14423, "loc": { "start": { - "line": 439, + "line": 458, "column": 53 }, "end": { - "line": 439, + "line": 458, "column": 60 } }, @@ -21550,15 +22667,15 @@ }, "property": { "type": "Identifier", - "start": 13792, - "end": 13796, + "start": 14425, + "end": 14429, "loc": { "start": { - "line": 439, + "line": 458, "column": 62 }, "end": { - "line": 439, + "line": 458, "column": 66 }, "identifierName": "push" @@ -21570,15 +22687,15 @@ "arguments": [ { "type": "Identifier", - "start": 13797, - "end": 13806, + "start": 14430, + "end": 14439, "loc": { "start": { - "line": 439, + "line": 458, "column": 67 }, "end": { - "line": 439, + "line": 458, "column": 76 }, "identifierName": "nomenCode" @@ -21592,29 +22709,29 @@ }, { "type": "ReturnStatement", - "start": 13814, - "end": 13828, + "start": 14447, + "end": 14461, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 18 } }, "argument": { "type": "Identifier", - "start": 13821, - "end": 13827, + "start": 14454, + "end": 14460, "loc": { "start": { - "line": 441, + "line": 460, "column": 11 }, "end": { - "line": 441, + "line": 460, "column": 17 }, "identifierName": "jsonld" @@ -21630,15 +22747,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name in an JSON-LD representation.\n ", - "start": 13319, - "end": 13386, + "start": 13952, + "end": 14019, "loc": { "start": { - "line": 427, + "line": 446, "column": 2 }, "end": { - "line": 429, + "line": 448, "column": 5 } } @@ -21648,15 +22765,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", - "start": 13836, - "end": 13911, + "start": 14469, + "end": 14544, "loc": { "start": { - "line": 444, + "line": 463, "column": 2 }, "end": { - "line": 446, + "line": 465, "column": 5 } } @@ -21665,15 +22782,15 @@ }, { "type": "ClassMethod", - "start": 13914, - "end": 14748, + "start": 14547, + "end": 15381, "loc": { "start": { - "line": 447, + "line": 466, "column": 2 }, "end": { - "line": 476, + "line": 495, "column": 3 } }, @@ -21681,15 +22798,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 13918, - "end": 13933, + "start": 14551, + "end": 14566, "loc": { "start": { - "line": 447, + "line": 466, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 21 }, "identifierName": "asOWLEquivClass" @@ -21704,44 +22821,44 @@ "params": [], "body": { "type": "BlockStatement", - "start": 13936, - "end": 14748, + "start": 14569, + "end": 15381, "loc": { "start": { - "line": 447, + "line": 466, "column": 24 }, "end": { - "line": 476, + "line": 495, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 13990, - "end": 14031, + "start": 14623, + "end": 14664, "loc": { "start": { - "line": 449, + "line": 468, "column": 4 }, "end": { - "line": 449, + "line": 468, "column": 45 } }, "test": { "type": "UnaryExpression", - "start": 13994, - "end": 14012, + "start": 14627, + "end": 14645, "loc": { "start": { - "line": 449, + "line": 468, "column": 8 }, "end": { - "line": 449, + "line": 468, "column": 26 } }, @@ -21749,29 +22866,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 13995, - "end": 14012, + "start": 14628, + "end": 14645, "loc": { "start": { - "line": 449, + "line": 468, "column": 9 }, "end": { - "line": 449, + "line": 468, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 13995, - "end": 13999, + "start": 14628, + "end": 14632, "loc": { "start": { - "line": 449, + "line": 468, "column": 9 }, "end": { - "line": 449, + "line": 468, "column": 13 } }, @@ -21779,15 +22896,15 @@ }, "property": { "type": "Identifier", - "start": 14000, - "end": 14012, + "start": 14633, + "end": 14645, "loc": { "start": { - "line": 449, + "line": 468, "column": 14 }, "end": { - "line": 449, + "line": 468, "column": 26 }, "identifierName": "nameComplete" @@ -21804,29 +22921,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 14014, - "end": 14031, + "start": 14647, + "end": 14664, "loc": { "start": { - "line": 449, + "line": 468, "column": 28 }, "end": { - "line": 449, + "line": 468, "column": 45 } }, "argument": { "type": "Identifier", - "start": 14021, - "end": 14030, + "start": 14654, + "end": 14663, "loc": { "start": { - "line": 449, + "line": 468, "column": 35 }, "end": { - "line": 449, + "line": 468, "column": 44 }, "identifierName": "undefined" @@ -21840,15 +22957,15 @@ { "type": "CommentLine", "value": " No complete name, can't return anything.", - "start": 13942, - "end": 13985, + "start": 14575, + "end": 14618, "loc": { "start": { - "line": 448, + "line": 467, "column": 4 }, "end": { - "line": 448, + "line": 467, "column": 47 } } @@ -21858,15 +22975,15 @@ { "type": "CommentLine", "value": " Do we have a nomenclaturalCode?", - "start": 14037, - "end": 14071, + "start": 14670, + "end": 14704, "loc": { "start": { - "line": 451, + "line": 470, "column": 4 }, "end": { - "line": 451, + "line": 470, "column": 38 } } @@ -21875,29 +22992,29 @@ }, { "type": "IfStatement", - "start": 14076, - "end": 14262, + "start": 14709, + "end": 14895, "loc": { "start": { - "line": 452, + "line": 471, "column": 4 }, "end": { - "line": 458, + "line": 477, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 14080, - "end": 14103, + "start": 14713, + "end": 14736, "loc": { "start": { - "line": 452, + "line": 471, "column": 8 }, "end": { - "line": 452, + "line": 471, "column": 31 } }, @@ -21905,29 +23022,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 14081, - "end": 14103, + "start": 14714, + "end": 14736, "loc": { "start": { - "line": 452, + "line": 471, "column": 9 }, "end": { - "line": 452, + "line": 471, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 14081, - "end": 14085, + "start": 14714, + "end": 14718, "loc": { "start": { - "line": 452, + "line": 471, "column": 9 }, "end": { - "line": 452, + "line": 471, "column": 13 } }, @@ -21935,15 +23052,15 @@ }, "property": { "type": "Identifier", - "start": 14086, - "end": 14103, + "start": 14719, + "end": 14736, "loc": { "start": { - "line": 452, + "line": 471, "column": 14 }, "end": { - "line": 452, + "line": 471, "column": 31 }, "identifierName": "nomenclaturalCode" @@ -21960,59 +23077,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 14105, - "end": 14262, + "start": 14738, + "end": 14895, "loc": { "start": { - "line": 452, + "line": 471, "column": 33 }, "end": { - "line": 458, + "line": 477, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 14113, - "end": 14256, + "start": 14746, + "end": 14889, "loc": { "start": { - "line": 453, + "line": 472, "column": 6 }, "end": { - "line": 457, + "line": 476, "column": 8 } }, "argument": { "type": "ObjectExpression", - "start": 14120, - "end": 14255, + "start": 14753, + "end": 14888, "loc": { "start": { - "line": 453, + "line": 472, "column": 13 }, "end": { - "line": 457, + "line": 476, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 14130, - "end": 14156, + "start": 14763, + "end": 14789, "loc": { "start": { - "line": 454, + "line": 473, "column": 8 }, "end": { - "line": 454, + "line": 473, "column": 34 } }, @@ -22021,15 +23138,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14130, - "end": 14137, + "start": 14763, + "end": 14770, "loc": { "start": { - "line": 454, + "line": 473, "column": 8 }, "end": { - "line": 454, + "line": 473, "column": 15 } }, @@ -22041,15 +23158,15 @@ }, "value": { "type": "StringLiteral", - "start": 14139, - "end": 14156, + "start": 14772, + "end": 14789, "loc": { "start": { - "line": 454, + "line": 473, "column": 17 }, "end": { - "line": 454, + "line": 473, "column": 34 } }, @@ -22062,15 +23179,15 @@ }, { "type": "ObjectProperty", - "start": 14166, - "end": 14209, + "start": 14799, + "end": 14842, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 51 } }, @@ -22079,15 +23196,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14166, - "end": 14176, + "start": 14799, + "end": 14809, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 18 }, "identifierName": "onProperty" @@ -22096,29 +23213,29 @@ }, "value": { "type": "MemberExpression", - "start": 14178, - "end": 14209, + "start": 14811, + "end": 14842, "loc": { "start": { - "line": 455, + "line": 474, "column": 20 }, "end": { - "line": 455, + "line": 474, "column": 51 } }, "object": { "type": "Identifier", - "start": 14178, - "end": 14186, + "start": 14811, + "end": 14819, "loc": { "start": { - "line": 455, + "line": 474, "column": 20 }, "end": { - "line": 455, + "line": 474, "column": 28 }, "identifierName": "owlterms" @@ -22127,15 +23244,15 @@ }, "property": { "type": "Identifier", - "start": 14187, - "end": 14209, + "start": 14820, + "end": 14842, "loc": { "start": { - "line": 455, + "line": 474, "column": 29 }, "end": { - "line": 455, + "line": 474, "column": 51 }, "identifierName": "TDWG_VOC_NAME_COMPLETE" @@ -22147,15 +23264,15 @@ }, { "type": "ObjectProperty", - "start": 14219, - "end": 14246, + "start": 14852, + "end": 14879, "loc": { "start": { - "line": 456, + "line": 475, "column": 8 }, "end": { - "line": 456, + "line": 475, "column": 35 } }, @@ -22164,15 +23281,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14219, - "end": 14227, + "start": 14852, + "end": 14860, "loc": { "start": { - "line": 456, + "line": 475, "column": 8 }, "end": { - "line": 456, + "line": 475, "column": 16 }, "identifierName": "hasValue" @@ -22181,44 +23298,44 @@ }, "value": { "type": "MemberExpression", - "start": 14229, - "end": 14246, + "start": 14862, + "end": 14879, "loc": { "start": { - "line": 456, + "line": 475, "column": 18 }, "end": { - "line": 456, + "line": 475, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 14229, - "end": 14233, + "start": 14862, + "end": 14866, "loc": { "start": { - "line": 456, + "line": 475, "column": 18 }, "end": { - "line": 456, + "line": 475, "column": 22 } } }, "property": { "type": "Identifier", - "start": 14234, - "end": 14246, + "start": 14867, + "end": 14879, "loc": { "start": { - "line": 456, + "line": 475, "column": 23 }, "end": { - "line": 456, + "line": 475, "column": 35 }, "identifierName": "nameComplete" @@ -22240,15 +23357,15 @@ { "type": "CommentLine", "value": " Do we have a nomenclaturalCode?", - "start": 14037, - "end": 14071, + "start": 14670, + "end": 14704, "loc": { "start": { - "line": 451, + "line": 470, "column": 4 }, "end": { - "line": 451, + "line": 470, "column": 38 } } @@ -22258,15 +23375,15 @@ { "type": "CommentLine", "value": " If we do have a nomenclatural code, incorporate that into the logical", - "start": 14268, - "end": 14340, + "start": 14901, + "end": 14973, "loc": { "start": { - "line": 460, + "line": 479, "column": 4 }, "end": { - "line": 460, + "line": 479, "column": 76 } } @@ -22274,15 +23391,15 @@ { "type": "CommentLine", "value": " expression as well.", - "start": 14345, - "end": 14367, + "start": 14978, + "end": 15000, "loc": { "start": { - "line": 461, + "line": 480, "column": 4 }, "end": { - "line": 461, + "line": 480, "column": 26 } } @@ -22291,44 +23408,44 @@ }, { "type": "ReturnStatement", - "start": 14372, - "end": 14744, + "start": 15005, + "end": 15377, "loc": { "start": { - "line": 462, + "line": 481, "column": 4 }, "end": { - "line": 475, + "line": 494, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 14379, - "end": 14743, + "start": 15012, + "end": 15376, "loc": { "start": { - "line": 462, + "line": 481, "column": 11 }, "end": { - "line": 475, + "line": 494, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 14387, - "end": 14407, + "start": 15020, + "end": 15040, "loc": { "start": { - "line": 463, + "line": 482, "column": 6 }, "end": { - "line": 463, + "line": 482, "column": 26 } }, @@ -22337,15 +23454,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14387, - "end": 14394, + "start": 15020, + "end": 15027, "loc": { "start": { - "line": 463, + "line": 482, "column": 6 }, "end": { - "line": 463, + "line": 482, "column": 13 } }, @@ -22358,15 +23475,15 @@ }, "value": { "type": "StringLiteral", - "start": 14396, - "end": 14407, + "start": 15029, + "end": 15040, "loc": { "start": { - "line": 463, + "line": 482, "column": 15 }, "end": { - "line": 463, + "line": 482, "column": 26 } }, @@ -22380,15 +23497,15 @@ }, { "type": "ObjectProperty", - "start": 14415, - "end": 14736, + "start": 15048, + "end": 15369, "loc": { "start": { - "line": 464, + "line": 483, "column": 6 }, "end": { - "line": 474, + "line": 493, "column": 8 } }, @@ -22397,15 +23514,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14415, - "end": 14429, + "start": 15048, + "end": 15062, "loc": { "start": { - "line": 464, + "line": 483, "column": 6 }, "end": { - "line": 464, + "line": 483, "column": 20 }, "identifierName": "intersectionOf" @@ -22414,45 +23531,45 @@ }, "value": { "type": "ArrayExpression", - "start": 14431, - "end": 14736, + "start": 15064, + "end": 15369, "loc": { "start": { - "line": 464, + "line": 483, "column": 22 }, "end": { - "line": 474, + "line": 493, "column": 8 } }, "elements": [ { "type": "ObjectExpression", - "start": 14432, - "end": 14567, + "start": 15065, + "end": 15200, "loc": { "start": { - "line": 464, + "line": 483, "column": 23 }, "end": { - "line": 468, + "line": 487, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 14442, - "end": 14468, + "start": 15075, + "end": 15101, "loc": { "start": { - "line": 465, + "line": 484, "column": 8 }, "end": { - "line": 465, + "line": 484, "column": 34 } }, @@ -22461,15 +23578,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14442, - "end": 14449, + "start": 15075, + "end": 15082, "loc": { "start": { - "line": 465, + "line": 484, "column": 8 }, "end": { - "line": 465, + "line": 484, "column": 15 } }, @@ -22481,15 +23598,15 @@ }, "value": { "type": "StringLiteral", - "start": 14451, - "end": 14468, + "start": 15084, + "end": 15101, "loc": { "start": { - "line": 465, + "line": 484, "column": 17 }, "end": { - "line": 465, + "line": 484, "column": 34 } }, @@ -22502,15 +23619,15 @@ }, { "type": "ObjectProperty", - "start": 14478, - "end": 14521, + "start": 15111, + "end": 15154, "loc": { "start": { - "line": 466, + "line": 485, "column": 8 }, "end": { - "line": 466, + "line": 485, "column": 51 } }, @@ -22519,15 +23636,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14478, - "end": 14488, + "start": 15111, + "end": 15121, "loc": { "start": { - "line": 466, + "line": 485, "column": 8 }, "end": { - "line": 466, + "line": 485, "column": 18 }, "identifierName": "onProperty" @@ -22536,29 +23653,29 @@ }, "value": { "type": "MemberExpression", - "start": 14490, - "end": 14521, + "start": 15123, + "end": 15154, "loc": { "start": { - "line": 466, + "line": 485, "column": 20 }, "end": { - "line": 466, + "line": 485, "column": 51 } }, "object": { "type": "Identifier", - "start": 14490, - "end": 14498, + "start": 15123, + "end": 15131, "loc": { "start": { - "line": 466, + "line": 485, "column": 20 }, "end": { - "line": 466, + "line": 485, "column": 28 }, "identifierName": "owlterms" @@ -22567,15 +23684,15 @@ }, "property": { "type": "Identifier", - "start": 14499, - "end": 14521, + "start": 15132, + "end": 15154, "loc": { "start": { - "line": 466, + "line": 485, "column": 29 }, "end": { - "line": 466, + "line": 485, "column": 51 }, "identifierName": "TDWG_VOC_NAME_COMPLETE" @@ -22587,15 +23704,15 @@ }, { "type": "ObjectProperty", - "start": 14531, - "end": 14558, + "start": 15164, + "end": 15191, "loc": { "start": { - "line": 467, + "line": 486, "column": 8 }, "end": { - "line": 467, + "line": 486, "column": 35 } }, @@ -22604,15 +23721,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14531, - "end": 14539, + "start": 15164, + "end": 15172, "loc": { "start": { - "line": 467, + "line": 486, "column": 8 }, "end": { - "line": 467, + "line": 486, "column": 16 }, "identifierName": "hasValue" @@ -22621,44 +23738,44 @@ }, "value": { "type": "MemberExpression", - "start": 14541, - "end": 14558, + "start": 15174, + "end": 15191, "loc": { "start": { - "line": 467, + "line": 486, "column": 18 }, "end": { - "line": 467, + "line": 486, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 14541, - "end": 14545, + "start": 15174, + "end": 15178, "loc": { "start": { - "line": 467, + "line": 486, "column": 18 }, "end": { - "line": 467, + "line": 486, "column": 22 } } }, "property": { "type": "Identifier", - "start": 14546, - "end": 14558, + "start": 15179, + "end": 15191, "loc": { "start": { - "line": 467, + "line": 486, "column": 23 }, "end": { - "line": 467, + "line": 486, "column": 35 }, "identifierName": "nameComplete" @@ -22672,30 +23789,30 @@ }, { "type": "ObjectExpression", - "start": 14569, - "end": 14735, + "start": 15202, + "end": 15368, "loc": { "start": { - "line": 468, + "line": 487, "column": 9 }, "end": { - "line": 474, + "line": 493, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 14579, - "end": 14605, + "start": 15212, + "end": 15238, "loc": { "start": { - "line": 469, + "line": 488, "column": 8 }, "end": { - "line": 469, + "line": 488, "column": 34 } }, @@ -22704,15 +23821,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14579, - "end": 14586, + "start": 15212, + "end": 15219, "loc": { "start": { - "line": 469, + "line": 488, "column": 8 }, "end": { - "line": 469, + "line": 488, "column": 15 } }, @@ -22724,15 +23841,15 @@ }, "value": { "type": "StringLiteral", - "start": 14588, - "end": 14605, + "start": 15221, + "end": 15238, "loc": { "start": { - "line": 469, + "line": 488, "column": 17 }, "end": { - "line": 469, + "line": 488, "column": 34 } }, @@ -22745,15 +23862,15 @@ }, { "type": "ObjectProperty", - "start": 14615, - "end": 14654, + "start": 15248, + "end": 15287, "loc": { "start": { - "line": 470, + "line": 489, "column": 8 }, "end": { - "line": 470, + "line": 489, "column": 47 } }, @@ -22762,15 +23879,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14615, - "end": 14625, + "start": 15248, + "end": 15258, "loc": { "start": { - "line": 470, + "line": 489, "column": 8 }, "end": { - "line": 470, + "line": 489, "column": 18 }, "identifierName": "onProperty" @@ -22779,29 +23896,29 @@ }, "value": { "type": "MemberExpression", - "start": 14627, - "end": 14654, + "start": 15260, + "end": 15287, "loc": { "start": { - "line": 470, + "line": 489, "column": 20 }, "end": { - "line": 470, + "line": 489, "column": 47 } }, "object": { "type": "Identifier", - "start": 14627, - "end": 14635, + "start": 15260, + "end": 15268, "loc": { "start": { - "line": 470, + "line": 489, "column": 20 }, "end": { - "line": 470, + "line": 489, "column": 28 }, "identifierName": "owlterms" @@ -22810,15 +23927,15 @@ }, "property": { "type": "Identifier", - "start": 14636, - "end": 14654, + "start": 15269, + "end": 15287, "loc": { "start": { - "line": 470, + "line": 489, "column": 29 }, "end": { - "line": 470, + "line": 489, "column": 47 }, "identifierName": "NOMENCLATURAL_CODE" @@ -22830,15 +23947,15 @@ }, { "type": "ObjectProperty", - "start": 14664, - "end": 14726, + "start": 15297, + "end": 15359, "loc": { "start": { - "line": 471, + "line": 490, "column": 8 }, "end": { - "line": 473, + "line": 492, "column": 9 } }, @@ -22847,15 +23964,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14664, - "end": 14672, + "start": 15297, + "end": 15305, "loc": { "start": { - "line": 471, + "line": 490, "column": 8 }, "end": { - "line": 471, + "line": 490, "column": 16 }, "identifierName": "hasValue" @@ -22864,30 +23981,30 @@ }, "value": { "type": "ObjectExpression", - "start": 14674, - "end": 14726, + "start": 15307, + "end": 15359, "loc": { "start": { - "line": 471, + "line": 490, "column": 18 }, "end": { - "line": 473, + "line": 492, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 14686, - "end": 14715, + "start": 15319, + "end": 15348, "loc": { "start": { - "line": 472, + "line": 491, "column": 10 }, "end": { - "line": 472, + "line": 491, "column": 39 } }, @@ -22896,15 +24013,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14686, - "end": 14691, + "start": 15319, + "end": 15324, "loc": { "start": { - "line": 472, + "line": 491, "column": 10 }, "end": { - "line": 472, + "line": 491, "column": 15 } }, @@ -22916,44 +24033,44 @@ }, "value": { "type": "MemberExpression", - "start": 14693, - "end": 14715, + "start": 15326, + "end": 15348, "loc": { "start": { - "line": 472, + "line": 491, "column": 17 }, "end": { - "line": 472, + "line": 491, "column": 39 } }, "object": { "type": "ThisExpression", - "start": 14693, - "end": 14697, + "start": 15326, + "end": 15330, "loc": { "start": { - "line": 472, + "line": 491, "column": 17 }, "end": { - "line": 472, + "line": 491, "column": 21 } } }, "property": { "type": "Identifier", - "start": 14698, - "end": 14715, + "start": 15331, + "end": 15348, "loc": { "start": { - "line": 472, + "line": 491, "column": 22 }, "end": { - "line": 472, + "line": 491, "column": 39 }, "identifierName": "nomenclaturalCode" @@ -22978,15 +24095,15 @@ { "type": "CommentLine", "value": " If we do have a nomenclatural code, incorporate that into the logical", - "start": 14268, - "end": 14340, + "start": 14901, + "end": 14973, "loc": { "start": { - "line": 460, + "line": 479, "column": 4 }, "end": { - "line": 460, + "line": 479, "column": 76 } } @@ -22994,15 +24111,15 @@ { "type": "CommentLine", "value": " expression as well.", - "start": 14345, - "end": 14367, + "start": 14978, + "end": 15000, "loc": { "start": { - "line": 461, + "line": 480, "column": 4 }, "end": { - "line": 461, + "line": 480, "column": 26 } } @@ -23016,15 +24133,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", - "start": 13836, - "end": 13911, + "start": 14469, + "end": 14544, "loc": { "start": { - "line": 444, + "line": 463, "column": 2 }, "end": { - "line": 446, + "line": 465, "column": 5 } } @@ -23039,15 +24156,15 @@ }, { "type": "ExportNamedDeclaration", - "start": 14752, - "end": 14781, + "start": 15385, + "end": 15414, "loc": { "start": { - "line": 479, + "line": 498, "column": 0 }, "end": { - "line": 479, + "line": 498, "column": 29 } }, @@ -23055,29 +24172,29 @@ "specifiers": [ { "type": "ExportSpecifier", - "start": 14761, - "end": 14777, + "start": 15394, + "end": 15410, "loc": { "start": { - "line": 479, + "line": 498, "column": 9 }, "end": { - "line": 479, + "line": 498, "column": 25 } }, "local": { "type": "Identifier", - "start": 14761, - "end": 14777, + "start": 15394, + "end": 15410, "loc": { "start": { - "line": 479, + "line": 498, "column": 9 }, "end": { - "line": 479, + "line": 498, "column": 25 }, "identifierName": "TaxonNameWrapper" @@ -23086,15 +24203,15 @@ }, "exported": { "type": "Identifier", - "start": 14761, - "end": 14777, + "start": 15394, + "end": 15410, "loc": { "start": { - "line": 479, + "line": 498, "column": 9 }, "end": { - "line": 479, + "line": 498, "column": 25 }, "identifierName": "TaxonNameWrapper" @@ -23107,29 +24224,29 @@ }, { "type": "ExportNamedDeclaration", - "start": 14752, - "end": 14781, + "start": 15385, + "end": 15414, "loc": { "start": { - "line": 479, + "line": 498, "column": 0 }, "end": { - "line": 479, + "line": 498, "column": 29 } }, "declaration": { "type": "ClassDeclaration", "start": 1752, - "end": 14750, + "end": 15383, "loc": { "start": { "line": 40, "column": 0 }, "end": { - "line": 477, + "line": 496, "column": 1 } }, @@ -23155,14 +24272,14 @@ "body": { "type": "ClassBody", "start": 1775, - "end": 14750, + "end": 15383, "loc": { "start": { "line": 40, "column": 23 }, "end": { - "line": 477, + "line": 496, "column": 1 } }, @@ -27391,16 +28508,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Returns the nomenclatural code of this taxon name.\n ", + "value": "*\n * Normalize the specified taxon name.\n * @param txname A taxon name to be normalized.\n ", "start": 5112, - 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Look for a trinomial name.", + "start": 6822, + "end": 6862, + "loc": { + "start": { + "line": 203, + "column": 4 + }, + "end": { + "line": 203, + "column": 44 + } + } + } + ] + }, + { + "type": "VariableDeclaration", + "start": 6867, + "end": 6878, + "loc": { + "start": { + "line": 204, + "column": 4 + }, + "end": { + "line": 204, + "column": 15 + } + }, + "declarations": [ + { + "type": "VariableDeclarator", + "start": 6871, + "end": 6877, + "loc": { + "start": { + "line": 204, + "column": 8 + }, + "end": { + "line": 204, + "column": 14 + } + }, + "id": { + "type": "Identifier", + "start": 6871, + "end": 6877, + "loc": { + "start": { + "line": 204, + "column": 8 + }, + "end": { + "line": 204, + "column": 14 + }, + "identifierName": "txname" + }, + "name": "txname", + "leadingComments": null + }, + "init": null, + "leadingComments": null + } + ], + "kind": "let", + "leadingComments": [ + { + "type": "CommentLine", + "value": " Use a regular expression to parse the verbatimName.", + "start": 6762, + "end": 6816, + "loc": { + "start": { + "line": 201, + "column": 4 + }, + "end": { + "line": 201, + "column": 58 + } + } + }, + { + "type": "CommentLine", + "value": " Attempt 1. Look for a trinomial name.", + "start": 6822, + "end": 6862, + "loc": { + "start": { + "line": 203, + "column": 4 + }, + "end": { + "line": 203, + "column": 44 + } + } + } + ] + }, + { + "type": "VariableDeclaration", + "start": 6883, + "end": 6971, + "loc": { + "start": { + "line": 205, + "column": 4 + }, + "end": { + "line": 205, + "column": 92 + } + }, + "declarations": [ + { + "type": "VariableDeclarator", + "start": 6887, + "end": 6970, + "loc": { + "start": { + "line": 205, + "column": 8 + }, + "end": { + "line": 205, + "column": 91 + } + }, + "id": { + "type": "Identifier", + "start": 6887, + "end": 6894, + "loc": { + "start": { + "line": 205, + "column": 8 + }, + "end": { + "line": 205, + "column": 15 + }, + "identifierName": "results" + }, + "name": "results" + }, + "init": { + "type": "CallExpression", + "start": 6897, + "end": 6970, + "loc": { + "start": { + "line": 205, + "column": 18 + }, + "end": { + "line": 205, + "column": 91 + } + }, + "callee": { + "type": "MemberExpression", + "start": 6897, + "end": 6956, + "loc": { + "start": { + "line": 205, + "column": 18 + }, + "end": { + "line": 205, + "column": 77 + } + }, + "object": { + "type": "RegExpLiteral", + "start": 6897, + "end": 6951, + "loc": { + "start": { + "line": 205, + "column": 18 + }, + "end": { + "line": 205, + "column": 72 + } + }, + "extra": { + "raw": "/^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)\\s*([a-z-]+)\\b/" + }, + "pattern": "^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)\\s*([a-z-]+)\\b", + "flags": "" + }, + "property": { + "type": "Identifier", + "start": 6952, + "end": 6956, + "loc": { + "start": { + "line": 205, + "column": 73 + }, + "end": { + "line": 205, + "column": 77 + }, + "identifierName": "exec" + }, + "name": "exec" + }, + "computed": false + }, + "arguments": [ + { + "type": "Identifier", + "start": 6957, + "end": 6969, + "loc": { + "start": { + "line": 205, + "column": 78 + }, + "end": { + "line": 205, + "column": 90 + }, + "identifierName": "verbatimName" + }, + "name": "verbatimName" + } + ] + } + } + ], + "kind": "let" + }, + { + "type": "IfStatement", + "start": 6977, + "end": 7287, + "loc": { + "start": { + "line": 207, + "column": 4 + }, + "end": { + "line": 216, + "column": 5 + } + }, + "test": { + "type": "Identifier", + "start": 6981, + "end": 6988, + "loc": { + "start": { + "line": 207, + "column": 8 + }, + "end": { + "line": 207, + "column": 15 + }, + "identifierName": "results" + }, + "name": "results" + }, + "consequent": { + "type": "BlockStatement", + "start": 6990, + "end": 7287, + "loc": { + "start": { + "line": 207, + "column": 17 + }, + "end": { + "line": 216, + "column": 5 + } + }, + "body": [ + { + "type": "ExpressionStatement", + "start": 6998, + "end": 7281, + "loc": { + "start": { + "line": 208, + "column": 6 + }, + "end": { + "line": 215, + "column": 8 + } + }, + "expression": { + "type": "AssignmentExpression", + "start": 6998, + "end": 7280, + "loc": { + "start": { + "line": 208, + "column": 6 + }, + "end": { + "line": 215, + "column": 7 + } + }, + "operator": "=", + "left": { + "type": "Identifier", + "start": 6998, + "end": 7004, + "loc": { + "start": { + "line": 208, + "column": 6 + }, + "end": { + "line": 208, + "column": 12 + }, + "identifierName": "txname" + }, + "name": "txname" + }, + "right": { + "type": "ObjectExpression", + "start": 7007, + "end": 7280, + "loc": { + "start": { + "line": 208, + "column": 15 + }, + "end": { + "line": 215, + "column": 7 + } + }, + "properties": [ + { + "type": "ObjectProperty", + "start": 7017, + "end": 7058, + "loc": { + "start": { + "line": 209, + "column": 8 + }, + "end": { + "line": 209, + "column": 49 + } + }, + "method": false, + "shorthand": false, + "computed": false, + "key": { + "type": "StringLiteral", + "start": 7017, + "end": 7024, + "loc": { + "start": { + "line": 209, + "column": 8 + }, + "end": { + "line": 209, + "column": 15 + } + }, + "extra": { + "rawValue": "@type", + "raw": "'@type'" + }, + "value": "@type" + }, + "value": { + "type": "MemberExpression", + "start": 7026, + "end": 7058, + "loc": { + "start": { + "line": 209, + "column": 17 + }, + "end": { + "line": 209, + "column": 49 + } + }, + "object": { + "type": "Identifier", + "start": 7026, + "end": 7042, + "loc": { + "start": { + "line": 209, + "column": 17 + }, + "end": { + "line": 209, + "column": 33 + }, + "identifierName": "TaxonNameWrapper" + }, + "name": "TaxonNameWrapper" + }, + "property": { + "type": "Identifier", + "start": 7043, + "end": 7058, + "loc": { + "start": { + "line": 209, + "column": 34 }, "end": { - "line": 192, + "line": 209, + "column": 49 + }, + "identifierName": "TYPE_TAXON_NAME" + }, + "name": "TYPE_TAXON_NAME" + }, + "computed": false + } + }, + { + "type": "ObjectProperty", + "start": 7068, + "end": 7087, + "loc": { + "start": { + "line": 210, + "column": 8 + }, + "end": { + "line": 210, + "column": 27 + } + }, + "method": false, + "shorthand": false, + "computed": false, + "key": { + "type": "Identifier", + "start": 7068, + "end": 7073, + "loc": { + "start": { + "line": 210, + "column": 8 + }, + "end": { + "line": 210, + "column": 13 + }, + "identifierName": "label" + }, + "name": "label" + }, + "value": { + "type": "Identifier", + "start": 7075, + "end": 7087, + "loc": { + "start": { + "line": 210, + "column": 15 + }, + "end": { + "line": 210, + "column": 27 + }, + "identifierName": "verbatimName" + }, + "name": "verbatimName" + } + }, + { + "type": "ObjectProperty", + "start": 7097, + "end": 7161, + "loc": { + "start": { + "line": 211, + "column": 8 + }, + "end": { + "line": 211, + "column": 72 + } + }, + "method": false, + "shorthand": false, + "computed": false, + "key": { + "type": "Identifier", + "start": 7097, + "end": 7109, + "loc": { + "start": { + "line": 211, + "column": 8 + }, + "end": { + "line": 211, + "column": 20 + }, + "identifierName": "nameComplete" + }, + "name": "nameComplete" + }, + "value": { + "type": "CallExpression", + "start": 7111, + "end": 7161, + "loc": { + "start": { + "line": 211, + "column": 22 + }, + "end": { + "line": 211, + "column": 72 + } + }, + "callee": { + "type": "MemberExpression", + "start": 7111, + "end": 7159, + "loc": { + "start": { + "line": 211, + "column": 22 + }, + "end": { + "line": 211, "column": 70 } }, "object": { "type": "TemplateLiteral", - "start": 6478, - "end": 6521, + "start": 7111, + "end": 7154, "loc": { "start": { - "line": 192, + "line": 211, "column": 22 }, "end": { - "line": 192, + "line": 211, "column": 65 } }, "expressions": [ { "type": "MemberExpression", - "start": 6481, - "end": 6491, + "start": 7114, + "end": 7124, "loc": { "start": { - "line": 192, + "line": 211, "column": 25 }, "end": { - "line": 192, + "line": 211, "column": 35 } }, "object": { "type": "Identifier", - "start": 6481, - "end": 6488, + "start": 7114, + "end": 7121, "loc": { "start": { - "line": 192, + "line": 211, "column": 25 }, "end": { - "line": 192, + "line": 211, "column": 32 }, "identifierName": "results" @@ -29508,15 +31742,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6489, - "end": 6490, + "start": 7122, + "end": 7123, "loc": { "start": { - "line": 192, + "line": 211, "column": 33 }, "end": { - "line": 192, + "line": 211, "column": 34 } }, @@ -29530,29 +31764,29 @@ }, { "type": "MemberExpression", - "start": 6495, - "end": 6505, + "start": 7128, + "end": 7138, "loc": { "start": { - "line": 192, + "line": 211, "column": 39 }, "end": { - "line": 192, + "line": 211, "column": 49 } }, "object": { "type": "Identifier", - "start": 6495, - "end": 6502, + "start": 7128, + "end": 7135, "loc": { "start": { - "line": 192, + "line": 211, "column": 39 }, "end": { - "line": 192, + "line": 211, "column": 46 }, "identifierName": "results" @@ -29561,15 +31795,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6503, - "end": 6504, + "start": 7136, + "end": 7137, "loc": { "start": { - "line": 192, + "line": 211, "column": 47 }, "end": { - "line": 192, + "line": 211, "column": 48 } }, @@ -29583,29 +31817,29 @@ }, { "type": "MemberExpression", - "start": 6509, - "end": 6519, + "start": 7142, + "end": 7152, "loc": { "start": { - "line": 192, + "line": 211, "column": 53 }, "end": { - "line": 192, + "line": 211, "column": 63 } }, "object": { "type": "Identifier", - "start": 6509, - "end": 6516, + "start": 7142, + "end": 7149, "loc": { "start": { - "line": 192, + "line": 211, "column": 53 }, "end": { - "line": 192, + "line": 211, "column": 60 }, "identifierName": "results" @@ -29614,15 +31848,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6517, - "end": 6518, + "start": 7150, + "end": 7151, "loc": { "start": { - "line": 192, + "line": 211, "column": 61 }, "end": { - "line": 192, + "line": 211, "column": 62 } }, @@ -29638,15 +31872,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6479, - "end": 6479, + "start": 7112, + "end": 7112, "loc": { "start": { - "line": 192, + "line": 211, "column": 23 }, "end": { - "line": 192, + "line": 211, "column": 23 } }, @@ -29658,15 +31892,15 @@ }, { "type": "TemplateElement", - "start": 6492, - "end": 6493, + "start": 7125, + "end": 7126, "loc": { "start": { - "line": 192, + "line": 211, "column": 36 }, "end": { - "line": 192, + "line": 211, "column": 37 } }, @@ -29678,15 +31912,15 @@ }, { "type": "TemplateElement", - "start": 6506, - "end": 6507, + "start": 7139, + "end": 7140, "loc": { "start": { - "line": 192, + "line": 211, "column": 50 }, "end": { - "line": 192, + "line": 211, "column": 51 } }, @@ -29698,15 +31932,15 @@ }, { "type": "TemplateElement", - "start": 6520, - "end": 6520, + "start": 7153, + "end": 7153, "loc": { "start": { - "line": 192, + "line": 211, "column": 64 }, "end": { - "line": 192, + "line": 211, "column": 64 } }, @@ -29720,15 +31954,15 @@ }, "property": { "type": "Identifier", - "start": 6522, - "end": 6526, + "start": 7155, + "end": 7159, "loc": { "start": { - "line": 192, + "line": 211, "column": 66 }, "end": { - "line": 192, + "line": 211, "column": 70 }, "identifierName": "trim" @@ -29742,15 +31976,15 @@ }, { "type": "ObjectProperty", - "start": 6538, - "end": 6559, + "start": 7171, + "end": 7192, "loc": { "start": { - "line": 193, + "line": 212, "column": 8 }, "end": { - "line": 193, + "line": 212, "column": 29 } }, @@ -29759,15 +31993,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6538, - "end": 6547, + "start": 7171, + "end": 7180, "loc": { "start": { - "line": 193, + "line": 212, "column": 8 }, "end": { - "line": 193, + "line": 212, "column": 17 }, "identifierName": "genusPart" @@ -29776,29 +32010,29 @@ }, "value": { "type": "MemberExpression", - "start": 6549, - "end": 6559, + "start": 7182, + "end": 7192, "loc": { "start": { - "line": 193, + "line": 212, "column": 19 }, "end": { - "line": 193, + "line": 212, "column": 29 } }, "object": { "type": "Identifier", - "start": 6549, - "end": 6556, + "start": 7182, + "end": 7189, "loc": { "start": { - "line": 193, + "line": 212, "column": 19 }, "end": { - "line": 193, + "line": 212, "column": 26 }, "identifierName": "results" @@ -29807,15 +32041,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6557, - "end": 6558, + "start": 7190, + "end": 7191, "loc": { "start": { - "line": 193, + "line": 212, "column": 27 }, "end": { - "line": 193, + "line": 212, "column": 28 } }, @@ -29830,15 +32064,15 @@ }, { "type": "ObjectProperty", - "start": 6569, - "end": 6596, + "start": 7202, + "end": 7229, "loc": { "start": { - "line": 194, + "line": 213, "column": 8 }, "end": { - "line": 194, + "line": 213, "column": 35 } }, @@ -29847,15 +32081,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6569, - "end": 6584, + "start": 7202, + "end": 7217, "loc": { "start": { - "line": 194, + "line": 213, "column": 8 }, "end": { - "line": 194, + "line": 213, "column": 23 }, "identifierName": "specificEpithet" @@ -29864,29 +32098,29 @@ }, "value": { "type": "MemberExpression", - "start": 6586, - "end": 6596, + "start": 7219, + "end": 7229, "loc": { "start": { - "line": 194, + "line": 213, "column": 25 }, "end": { - "line": 194, + "line": 213, "column": 35 } }, "object": { "type": "Identifier", - "start": 6586, - "end": 6593, + "start": 7219, + "end": 7226, "loc": { "start": { - "line": 194, + "line": 213, "column": 25 }, "end": { - "line": 194, + "line": 213, "column": 32 }, "identifierName": "results" @@ -29895,15 +32129,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6594, - "end": 6595, + "start": 7227, + "end": 7228, "loc": { "start": { - "line": 194, + "line": 213, "column": 33 }, "end": { - "line": 194, + "line": 213, "column": 34 } }, @@ -29918,15 +32152,15 @@ }, { "type": "ObjectProperty", - "start": 6606, - "end": 6638, + "start": 7239, + "end": 7271, "loc": { "start": { - "line": 195, + "line": 214, "column": 8 }, "end": { - "line": 195, + "line": 214, "column": 40 } }, @@ -29935,15 +32169,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6606, - "end": 6626, + "start": 7239, + "end": 7259, "loc": { "start": { - "line": 195, + "line": 214, "column": 8 }, "end": { - "line": 195, + "line": 214, "column": 28 }, "identifierName": "infraspecificEpithet" @@ -29952,29 +32186,29 @@ }, "value": { "type": "MemberExpression", - "start": 6628, - "end": 6638, + "start": 7261, + "end": 7271, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 40 } }, "object": { "type": "Identifier", - "start": 6628, - "end": 6635, + "start": 7261, + "end": 7268, "loc": { "start": { - "line": 195, + "line": 214, "column": 30 }, "end": { - "line": 195, + "line": 214, "column": 37 }, "identifierName": "results" @@ -29983,15 +32217,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6636, - "end": 6637, + "start": 7269, + "end": 7270, "loc": { "start": { - "line": 195, + "line": 214, "column": 38 }, "end": { - "line": 195, + "line": 214, "column": 39 } }, @@ -30017,15 +32251,15 @@ { "type": "CommentLine", "value": " Attempt 2. Look for a binomial name.", - "start": 6660, - "end": 6699, + "start": 7293, + "end": 7332, "loc": { "start": { - "line": 199, + "line": 218, "column": 4 }, "end": { - "line": 199, + "line": 218, "column": 43 } } @@ -30034,29 +32268,29 @@ }, { "type": "IfStatement", - "start": 6704, - "end": 7079, + "start": 7337, + "end": 7712, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 212, + "line": 231, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 6708, - "end": 6715, + "start": 7341, + "end": 7348, "loc": { "start": { - "line": 200, + "line": 219, "column": 8 }, "end": { - "line": 200, + "line": 219, "column": 15 } }, @@ -30064,15 +32298,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 6709, - "end": 6715, + "start": 7342, + "end": 7348, "loc": { "start": { - "line": 200, + "line": 219, "column": 9 }, "end": { - "line": 200, + "line": 219, "column": 15 }, "identifierName": "txname" @@ -30087,59 +32321,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6717, - "end": 7079, + "start": 7350, + "end": 7712, "loc": { "start": { - "line": 200, + "line": 219, "column": 17 }, "end": { - "line": 212, + "line": 231, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 6725, - "end": 6795, + "start": 7358, + "end": 7428, "loc": { "start": { - "line": 201, + "line": 220, "column": 6 }, "end": { - "line": 201, + "line": 220, "column": 76 } }, "expression": { "type": "AssignmentExpression", - "start": 6725, - "end": 6794, + "start": 7358, + "end": 7427, "loc": { "start": { - "line": 201, + "line": 220, "column": 6 }, "end": { - "line": 201, + "line": 220, "column": 75 } }, "operator": "=", "left": { "type": "Identifier", - "start": 6725, - "end": 6732, + "start": 7358, + "end": 7365, "loc": { "start": { - "line": 201, + "line": 220, "column": 6 }, "end": { - "line": 201, + "line": 220, "column": 13 }, "identifierName": "results" @@ -30148,43 +32382,43 @@ }, "right": { "type": "CallExpression", - "start": 6735, - "end": 6794, + "start": 7368, + "end": 7427, "loc": { "start": { - "line": 201, + "line": 220, "column": 16 }, "end": { - "line": 201, + "line": 220, "column": 75 } }, "callee": { "type": "MemberExpression", - "start": 6735, - "end": 6780, + "start": 7368, + "end": 7413, "loc": { "start": { - "line": 201, + "line": 220, "column": 16 }, "end": { - "line": 201, + "line": 220, "column": 61 } }, "object": { "type": "RegExpLiteral", - "start": 6735, - "end": 6775, + "start": 7368, + "end": 7408, "loc": { "start": { - "line": 201, + "line": 220, "column": 16 }, "end": { - "line": 201, + "line": 220, "column": 56 } }, @@ -30196,15 +32430,15 @@ }, "property": { "type": "Identifier", - "start": 6776, - "end": 6780, + "start": 7409, + "end": 7413, "loc": { "start": { - "line": 201, + "line": 220, "column": 57 }, "end": { - "line": 201, + "line": 220, "column": 61 }, "identifierName": "exec" @@ -30216,15 +32450,15 @@ "arguments": [ { "type": "Identifier", - "start": 6781, - "end": 6793, + "start": 7414, + "end": 7426, "loc": { "start": { - "line": 201, + "line": 220, "column": 62 }, "end": { - "line": 201, + "line": 220, "column": 74 }, "identifierName": "verbatimName" @@ -30237,29 +32471,29 @@ }, { "type": "IfStatement", - "start": 6803, - "end": 7073, + "start": 7436, + "end": 7706, "loc": { "start": { - "line": 203, + "line": 222, "column": 6 }, "end": { - "line": 211, + "line": 230, "column": 7 } }, "test": { "type": "Identifier", - "start": 6807, - "end": 6814, + "start": 7440, + "end": 7447, "loc": { "start": { - "line": 203, + "line": 222, "column": 10 }, "end": { - "line": 203, + "line": 222, "column": 17 }, "identifierName": "results" @@ -30268,59 +32502,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 6816, - "end": 7073, + "start": 7449, + "end": 7706, "loc": { "start": { - "line": 203, + "line": 222, "column": 19 }, "end": { - "line": 211, + "line": 230, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 6826, - "end": 7065, + "start": 7459, + "end": 7698, "loc": { "start": { - "line": 204, + "line": 223, "column": 8 }, "end": { - "line": 210, + "line": 229, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 6826, - "end": 7064, + "start": 7459, + "end": 7697, "loc": { "start": { - "line": 204, + "line": 223, "column": 8 }, "end": { - "line": 210, + "line": 229, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 6826, - "end": 6832, + "start": 7459, + "end": 7465, "loc": { "start": { - "line": 204, + "line": 223, "column": 8 }, "end": { - "line": 204, + "line": 223, "column": 14 }, "identifierName": "txname" @@ -30329,30 +32563,30 @@ }, "right": { "type": "ObjectExpression", - "start": 6835, - "end": 7064, + "start": 7468, + "end": 7697, "loc": { "start": { - "line": 204, + "line": 223, "column": 17 }, "end": { - "line": 210, + "line": 229, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 6847, - "end": 6888, + "start": 7480, + "end": 7521, "loc": { "start": { - "line": 205, + "line": 224, "column": 10 }, "end": { - "line": 205, + "line": 224, "column": 51 } }, @@ -30361,15 +32595,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 6847, - "end": 6854, + "start": 7480, + "end": 7487, "loc": { "start": { - "line": 205, + "line": 224, "column": 10 }, "end": { - "line": 205, + "line": 224, "column": 17 } }, @@ -30381,29 +32615,29 @@ }, "value": { "type": "MemberExpression", - "start": 6856, - "end": 6888, + "start": 7489, + "end": 7521, "loc": { "start": { - "line": 205, + "line": 224, "column": 19 }, "end": { - "line": 205, + "line": 224, "column": 51 } }, "object": { "type": "Identifier", - "start": 6856, - "end": 6872, + "start": 7489, + "end": 7505, "loc": { "start": { - "line": 205, + "line": 224, "column": 19 }, "end": { - "line": 205, + "line": 224, "column": 35 }, "identifierName": "TaxonNameWrapper" @@ -30412,15 +32646,15 @@ }, "property": { "type": "Identifier", - "start": 6873, - "end": 6888, + "start": 7506, + "end": 7521, "loc": { "start": { - "line": 205, + "line": 224, "column": 36 }, "end": { - "line": 205, + "line": 224, "column": 51 }, "identifierName": "TYPE_TAXON_NAME" @@ -30432,15 +32666,15 @@ }, { "type": "ObjectProperty", - "start": 6900, - "end": 6919, + "start": 7533, + "end": 7552, "loc": { "start": { - "line": 206, + "line": 225, "column": 10 }, "end": { - "line": 206, + "line": 225, "column": 29 } }, @@ -30449,15 +32683,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6900, - "end": 6905, + "start": 7533, + "end": 7538, "loc": { "start": { - "line": 206, + "line": 225, "column": 10 }, "end": { - "line": 206, + "line": 225, "column": 15 }, "identifierName": "label" @@ -30466,15 +32700,15 @@ }, "value": { "type": "Identifier", - "start": 6907, - "end": 6919, + "start": 7540, + "end": 7552, "loc": { "start": { - "line": 206, + "line": 225, "column": 17 }, "end": { - "line": 206, + "line": 225, "column": 29 }, "identifierName": "verbatimName" @@ -30484,15 +32718,15 @@ }, { "type": "ObjectProperty", - "start": 6931, - "end": 6981, + "start": 7564, + "end": 7614, "loc": { "start": { - "line": 207, + "line": 226, "column": 10 }, "end": { - "line": 207, + "line": 226, "column": 60 } }, @@ -30501,15 +32735,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6931, - "end": 6943, + "start": 7564, + "end": 7576, "loc": { "start": { - "line": 207, + "line": 226, "column": 10 }, "end": { - "line": 207, + "line": 226, "column": 22 }, "identifierName": "nameComplete" @@ -30518,72 +32752,72 @@ }, "value": { "type": "CallExpression", - "start": 6945, - "end": 6981, + "start": 7578, + "end": 7614, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 60 } }, "callee": { "type": "MemberExpression", - "start": 6945, - "end": 6979, + "start": 7578, + "end": 7612, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 58 } }, "object": { "type": "TemplateLiteral", - "start": 6945, - "end": 6974, + "start": 7578, + "end": 7607, "loc": { "start": { - "line": 207, + "line": 226, "column": 24 }, "end": { - "line": 207, + "line": 226, "column": 53 } }, "expressions": [ { "type": "MemberExpression", - "start": 6948, - "end": 6958, + "start": 7581, + "end": 7591, "loc": { "start": { - "line": 207, + "line": 226, "column": 27 }, "end": { - "line": 207, + "line": 226, "column": 37 } }, "object": { "type": "Identifier", - "start": 6948, - "end": 6955, + "start": 7581, + "end": 7588, "loc": { "start": { - "line": 207, + "line": 226, "column": 27 }, "end": { - "line": 207, + "line": 226, "column": 34 }, "identifierName": "results" @@ -30592,15 +32826,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6956, - "end": 6957, + "start": 7589, + "end": 7590, "loc": { "start": { - "line": 207, + "line": 226, "column": 35 }, "end": { - "line": 207, + "line": 226, "column": 36 } }, @@ -30614,29 +32848,29 @@ }, { "type": "MemberExpression", - "start": 6962, - "end": 6972, + "start": 7595, + "end": 7605, "loc": { "start": { - "line": 207, + "line": 226, "column": 41 }, "end": { - "line": 207, + "line": 226, "column": 51 } }, "object": { "type": "Identifier", - "start": 6962, - "end": 6969, + "start": 7595, + "end": 7602, "loc": { "start": { - "line": 207, + "line": 226, "column": 41 }, "end": { - "line": 207, + "line": 226, "column": 48 }, "identifierName": "results" @@ -30645,15 +32879,15 @@ }, "property": { "type": "NumericLiteral", - "start": 6970, - "end": 6971, + "start": 7603, + "end": 7604, "loc": { "start": { - "line": 207, + "line": 226, "column": 49 }, "end": { - "line": 207, + "line": 226, "column": 50 } }, @@ -30669,15 +32903,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6946, - "end": 6946, + "start": 7579, + "end": 7579, "loc": { "start": { - "line": 207, + "line": 226, "column": 25 }, "end": { - "line": 207, + "line": 226, "column": 25 } }, @@ -30689,15 +32923,15 @@ }, { "type": "TemplateElement", - "start": 6959, - "end": 6960, + "start": 7592, + "end": 7593, "loc": { "start": { - "line": 207, + "line": 226, "column": 38 }, "end": { - "line": 207, + "line": 226, "column": 39 } }, @@ -30709,15 +32943,15 @@ }, { "type": "TemplateElement", - "start": 6973, - "end": 6973, + "start": 7606, + "end": 7606, "loc": { "start": { - "line": 207, + "line": 226, "column": 52 }, "end": { - "line": 207, + "line": 226, "column": 52 } }, @@ -30731,15 +32965,15 @@ }, "property": { "type": "Identifier", - "start": 6975, - "end": 6979, + "start": 7608, + "end": 7612, "loc": { "start": { - "line": 207, + "line": 226, "column": 54 }, "end": { - "line": 207, + "line": 226, "column": 58 }, "identifierName": "trim" @@ -30753,15 +32987,15 @@ }, { "type": "ObjectProperty", - "start": 6993, - "end": 7014, + "start": 7626, + "end": 7647, "loc": { "start": { - "line": 208, + "line": 227, "column": 10 }, "end": { - "line": 208, + "line": 227, "column": 31 } }, @@ -30770,15 +33004,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6993, - "end": 7002, + "start": 7626, + "end": 7635, "loc": { "start": { - "line": 208, + "line": 227, "column": 10 }, "end": { - "line": 208, + "line": 227, "column": 19 }, "identifierName": "genusPart" @@ -30787,29 +33021,29 @@ }, "value": { "type": "MemberExpression", - "start": 7004, - "end": 7014, + "start": 7637, + "end": 7647, "loc": { "start": { - "line": 208, + "line": 227, "column": 21 }, "end": { - "line": 208, + "line": 227, "column": 31 } }, "object": { "type": "Identifier", - "start": 7004, - "end": 7011, + "start": 7637, + "end": 7644, "loc": { "start": { - "line": 208, + "line": 227, "column": 21 }, "end": { - "line": 208, + "line": 227, "column": 28 }, "identifierName": "results" @@ -30818,15 +33052,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7012, - "end": 7013, + "start": 7645, + "end": 7646, "loc": { "start": { - "line": 208, + "line": 227, "column": 29 }, "end": { - "line": 208, + "line": 227, "column": 30 } }, @@ -30841,15 +33075,15 @@ }, { "type": "ObjectProperty", - "start": 7026, - "end": 7053, + "start": 7659, + "end": 7686, "loc": { "start": { - "line": 209, + "line": 228, "column": 10 }, "end": { - "line": 209, + "line": 228, "column": 37 } }, @@ -30858,15 +33092,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7026, - "end": 7041, + "start": 7659, + "end": 7674, "loc": { "start": { - "line": 209, + "line": 228, "column": 10 }, "end": { - "line": 209, + "line": 228, "column": 25 }, "identifierName": "specificEpithet" @@ -30875,29 +33109,29 @@ }, "value": { "type": "MemberExpression", - "start": 7043, - "end": 7053, + "start": 7676, + "end": 7686, "loc": { "start": { - "line": 209, + "line": 228, "column": 27 }, "end": { - "line": 209, + "line": 228, "column": 37 } }, "object": { "type": "Identifier", - "start": 7043, - "end": 7050, + "start": 7676, + "end": 7683, "loc": { "start": { - "line": 209, + "line": 228, "column": 27 }, "end": { - "line": 209, + "line": 228, "column": 34 }, "identifierName": "results" @@ -30906,15 +33140,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7051, - "end": 7052, + "start": 7684, + "end": 7685, "loc": { "start": { - "line": 209, + "line": 228, "column": 35 }, "end": { - "line": 209, + "line": 228, "column": 36 } }, @@ -30945,15 +33179,15 @@ { "type": "CommentLine", "value": " Attempt 2. Look for a binomial name.", - "start": 6660, - "end": 6699, + "start": 7293, + "end": 7332, "loc": { "start": { - "line": 199, + "line": 218, "column": 4 }, "end": { - "line": 199, + "line": 218, "column": 43 } } @@ -30963,15 +33197,15 @@ { "type": "CommentLine", "value": " Attempt 3. Look for a uninomial name.", - "start": 7085, - "end": 7125, + "start": 7718, + "end": 7758, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 44 } } @@ -30980,29 +33214,29 @@ }, { "type": "IfStatement", - "start": 7130, - "end": 7460, + "start": 7763, + "end": 8093, "loc": { "start": { - "line": 215, + "line": 234, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 7134, - "end": 7141, + "start": 7767, + "end": 7774, "loc": { "start": { - "line": 215, + "line": 234, "column": 8 }, "end": { - "line": 215, + "line": 234, "column": 15 } }, @@ -31010,15 +33244,15 @@ "prefix": true, "argument": { "type": "Identifier", - "start": 7135, - "end": 7141, + "start": 7768, + "end": 7774, "loc": { "start": { - "line": 215, + "line": 234, "column": 9 }, "end": { - "line": 215, + "line": 234, "column": 15 }, "identifierName": "txname" @@ -31033,59 +33267,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7143, - "end": 7460, + "start": 7776, + "end": 8093, "loc": { "start": { - "line": 215, + "line": 234, "column": 17 }, "end": { - "line": 226, + "line": 245, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7184, - "end": 7242, + "start": 7817, + "end": 7875, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 64 } }, "expression": { "type": "AssignmentExpression", - "start": 7184, - "end": 7241, + "start": 7817, + "end": 7874, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 63 } }, "operator": "=", "left": { "type": "Identifier", - "start": 7184, - "end": 7191, + "start": 7817, + "end": 7824, "loc": { "start": { - "line": 217, + "line": 236, "column": 6 }, "end": { - "line": 217, + "line": 236, "column": 13 }, "identifierName": "results" @@ -31095,43 +33329,43 @@ }, "right": { "type": "CallExpression", - "start": 7194, - "end": 7241, + "start": 7827, + "end": 7874, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 7194, - "end": 7227, + "start": 7827, + "end": 7860, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 49 } }, "object": { "type": "RegExpLiteral", - "start": 7194, - "end": 7222, + "start": 7827, + "end": 7855, "loc": { "start": { - "line": 217, + "line": 236, "column": 16 }, "end": { - "line": 217, + "line": 236, "column": 44 } }, @@ -31143,15 +33377,15 @@ }, "property": { "type": "Identifier", - "start": 7223, - "end": 7227, + "start": 7856, + "end": 7860, "loc": { "start": { - "line": 217, + "line": 236, "column": 45 }, "end": { - "line": 217, + "line": 236, "column": 49 }, "identifierName": "exec" @@ -31163,15 +33397,15 @@ "arguments": [ { "type": "Identifier", - "start": 7228, - "end": 7240, + "start": 7861, + "end": 7873, "loc": { "start": { - "line": 217, + "line": 236, "column": 50 }, "end": { - "line": 217, + "line": 236, "column": 62 }, "identifierName": "verbatimName" @@ -31186,15 +33420,15 @@ { "type": "CommentLine", "value": " Is it a uninomial name?", - "start": 7151, - "end": 7177, + "start": 7784, + "end": 7810, "loc": { "start": { - "line": 216, + "line": 235, "column": 6 }, "end": { - "line": 216, + "line": 235, "column": 32 } } @@ -31203,29 +33437,29 @@ }, { "type": "IfStatement", - "start": 7249, - "end": 7454, + "start": 7882, + "end": 8087, "loc": { "start": { - "line": 218, + "line": 237, "column": 6 }, "end": { - "line": 225, + "line": 244, "column": 7 } }, "test": { "type": "Identifier", - "start": 7253, - "end": 7260, + "start": 7886, + "end": 7893, "loc": { "start": { - "line": 218, + "line": 237, "column": 10 }, "end": { - "line": 218, + "line": 237, "column": 17 }, "identifierName": "results" @@ -31234,59 +33468,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 7262, - "end": 7454, + "start": 7895, + "end": 8087, "loc": { "start": { - "line": 218, + "line": 237, "column": 19 }, "end": { - "line": 225, + "line": 244, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 7272, - "end": 7446, + "start": 7905, + "end": 8079, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 224, + "line": 243, "column": 10 } }, "expression": { "type": "AssignmentExpression", - "start": 7272, - "end": 7445, + "start": 7905, + "end": 8078, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 224, + "line": 243, "column": 9 } }, "operator": "=", "left": { "type": "Identifier", - "start": 7272, - "end": 7278, + "start": 7905, + "end": 7911, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 219, + "line": 238, "column": 14 }, "identifierName": "txname" @@ -31295,30 +33529,30 @@ }, "right": { "type": "ObjectExpression", - "start": 7281, - "end": 7445, + "start": 7914, + "end": 8078, "loc": { "start": { - "line": 219, + "line": 238, "column": 17 }, "end": { - "line": 224, + "line": 243, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 7293, - "end": 7334, + "start": 7926, + "end": 7967, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 51 } }, @@ -31327,15 +33561,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 7293, - "end": 7300, + "start": 7926, + "end": 7933, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 17 } }, @@ -31347,29 +33581,29 @@ }, "value": { "type": "MemberExpression", - "start": 7302, - "end": 7334, + "start": 7935, + "end": 7967, "loc": { "start": { - "line": 220, + "line": 239, "column": 19 }, "end": { - "line": 220, + "line": 239, "column": 51 } }, "object": { "type": "Identifier", - "start": 7302, - "end": 7318, + "start": 7935, + "end": 7951, "loc": { "start": { - "line": 220, + "line": 239, "column": 19 }, "end": { - "line": 220, + "line": 239, "column": 35 }, "identifierName": "TaxonNameWrapper" @@ -31378,15 +33612,15 @@ }, "property": { "type": "Identifier", - "start": 7319, - "end": 7334, + "start": 7952, + "end": 7967, "loc": { "start": { - "line": 220, + "line": 239, "column": 36 }, "end": { - "line": 220, + "line": 239, "column": 51 }, "identifierName": "TYPE_TAXON_NAME" @@ -31398,15 +33632,15 @@ }, { "type": "ObjectProperty", - "start": 7346, - "end": 7365, + "start": 7979, + "end": 7998, "loc": { "start": { - "line": 221, + "line": 240, "column": 10 }, "end": { - "line": 221, + "line": 240, "column": 29 } }, @@ -31415,15 +33649,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7346, - "end": 7351, + "start": 7979, + "end": 7984, "loc": { "start": { - "line": 221, + "line": 240, "column": 10 }, "end": { - "line": 221, + "line": 240, "column": 15 }, "identifierName": "label" @@ -31432,15 +33666,15 @@ }, "value": { "type": "Identifier", - "start": 7353, - "end": 7365, + "start": 7986, + "end": 7998, "loc": { "start": { - "line": 221, + "line": 240, "column": 17 }, "end": { - "line": 221, + "line": 240, "column": 29 }, "identifierName": "verbatimName" @@ -31450,15 +33684,15 @@ }, { "type": "ObjectProperty", - "start": 7377, - "end": 7401, + "start": 8010, + "end": 8034, "loc": { "start": { - "line": 222, + "line": 241, "column": 10 }, "end": { - "line": 222, + "line": 241, "column": 34 } }, @@ -31467,15 +33701,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7377, - "end": 7389, + "start": 8010, + "end": 8022, "loc": { "start": { - "line": 222, + "line": 241, "column": 10 }, "end": { - "line": 222, + "line": 241, "column": 22 }, "identifierName": "nameComplete" @@ -31484,29 +33718,29 @@ }, "value": { "type": "MemberExpression", - "start": 7391, - "end": 7401, + "start": 8024, + "end": 8034, "loc": { "start": { - "line": 222, + "line": 241, "column": 24 }, "end": { - "line": 222, + "line": 241, "column": 34 } }, "object": { "type": "Identifier", - "start": 7391, - "end": 7398, + "start": 8024, + "end": 8031, "loc": { "start": { - "line": 222, + "line": 241, "column": 24 }, "end": { - "line": 222, + "line": 241, "column": 31 }, "identifierName": "results" @@ -31515,15 +33749,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7399, - "end": 7400, + "start": 8032, + "end": 8033, "loc": { "start": { - "line": 222, + "line": 241, "column": 32 }, "end": { - "line": 222, + "line": 241, "column": 33 } }, @@ -31538,15 +33772,15 @@ }, { "type": "ObjectProperty", - "start": 7413, - "end": 7434, + "start": 8046, + "end": 8067, "loc": { "start": { - "line": 223, + "line": 242, "column": 10 }, "end": { - "line": 223, + "line": 242, "column": 31 } }, @@ -31555,15 +33789,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7413, - "end": 7422, + "start": 8046, + "end": 8055, "loc": { "start": { - "line": 223, + "line": 242, "column": 10 }, "end": { - "line": 223, + "line": 242, "column": 19 }, "identifierName": "uninomial" @@ -31572,29 +33806,29 @@ }, "value": { "type": "MemberExpression", - "start": 7424, - "end": 7434, + "start": 8057, + "end": 8067, "loc": { "start": { - "line": 223, + "line": 242, "column": 21 }, "end": { - "line": 223, + "line": 242, "column": 31 } }, "object": { "type": "Identifier", - "start": 7424, - "end": 7431, + "start": 8057, + "end": 8064, "loc": { "start": { - "line": 223, + "line": 242, "column": 21 }, "end": { - "line": 223, + "line": 242, "column": 28 }, "identifierName": "results" @@ -31603,15 +33837,15 @@ }, "property": { "type": "NumericLiteral", - "start": 7432, - "end": 7433, + "start": 8065, + "end": 8066, "loc": { "start": { - "line": 223, + "line": 242, "column": 29 }, "end": { - "line": 223, + "line": 242, "column": 30 } }, @@ -31642,15 +33876,15 @@ { "type": "CommentLine", "value": " Attempt 3. Look for a uninomial name.", - "start": 7085, - "end": 7125, + "start": 7718, + "end": 7758, "loc": { "start": { - "line": 214, + "line": 233, "column": 4 }, "end": { - "line": 214, + "line": 233, "column": 44 } } @@ -31660,15 +33894,15 @@ { "type": "CommentLine", "value": " Add a nomenclatural code if possible.", - "start": 7466, - "end": 7506, + "start": 8099, + "end": 8139, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 44 } } @@ -31677,43 +33911,43 @@ }, { "type": "IfStatement", - "start": 7511, - "end": 7587, + "start": 8144, + "end": 8220, "loc": { "start": { - "line": 229, + "line": 248, "column": 4 }, "end": { - "line": 231, + "line": 250, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 7515, - "end": 7534, + "start": 8148, + "end": 8167, "loc": { "start": { - "line": 229, + "line": 248, "column": 8 }, "end": { - "line": 229, + "line": 248, "column": 27 } }, "left": { "type": "Identifier", - "start": 7515, - "end": 7521, + "start": 8148, + "end": 8154, "loc": { "start": { - "line": 229, + "line": 248, "column": 8 }, "end": { - "line": 229, + "line": 248, "column": 14 }, "identifierName": "txname" @@ -31724,15 +33958,15 @@ "operator": "&&", "right": { "type": "Identifier", - "start": 7525, - "end": 7534, + "start": 8158, + "end": 8167, "loc": { "start": { - "line": 229, + "line": 248, "column": 18 }, "end": { - "line": 229, + "line": 248, "column": 27 }, "identifierName": "nomenCode" @@ -31743,73 +33977,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 7536, - "end": 7587, + "start": 8169, + "end": 8220, "loc": { "start": { - "line": 229, + "line": 248, "column": 29 }, "end": { - "line": 231, + "line": 250, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7544, - "end": 7581, + "start": 8177, + "end": 8214, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 43 } }, "expression": { "type": "AssignmentExpression", - "start": 7544, - "end": 7580, + "start": 8177, + "end": 8213, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 42 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7544, - "end": 7568, + "start": 8177, + "end": 8201, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 30 } }, "object": { "type": "Identifier", - "start": 7544, - "end": 7550, + "start": 8177, + "end": 8183, "loc": { "start": { - "line": 230, + "line": 249, "column": 6 }, "end": { - "line": 230, + "line": 249, "column": 12 }, "identifierName": "txname" @@ -31818,15 +34052,15 @@ }, "property": { "type": "Identifier", - "start": 7551, - "end": 7568, + "start": 8184, + "end": 8201, "loc": { "start": { - "line": 230, + "line": 249, "column": 13 }, "end": { - "line": 230, + "line": 249, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -31837,15 +34071,15 @@ }, "right": { "type": "Identifier", - "start": 7571, - "end": 7580, + "start": 8204, + "end": 8213, "loc": { "start": { - "line": 230, + "line": 249, "column": 33 }, "end": { - "line": 230, + "line": 249, "column": 42 }, "identifierName": "nomenCode" @@ -31863,15 +34097,15 @@ { "type": "CommentLine", "value": " Add a nomenclatural code if possible.", - "start": 7466, - "end": 7506, + "start": 8099, + "end": 8139, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 44 } } @@ -31881,15 +34115,15 @@ { "type": "CommentLine", "value": " Store in the cache.", - "start": 7593, - "end": 7615, + "start": 8226, + "end": 8248, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 26 } } @@ -31898,43 +34132,43 @@ }, { "type": "IfStatement", - "start": 7620, - "end": 7751, + "start": 8253, + "end": 8384, "loc": { "start": { - "line": 234, + "line": 253, "column": 4 }, "end": { - "line": 236, + "line": 255, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 7624, - "end": 7644, + "start": 8257, + "end": 8277, "loc": { "start": { - "line": 234, + "line": 253, "column": 8 }, "end": { - "line": 234, + "line": 253, "column": 28 } }, "left": { "type": "Identifier", - "start": 7624, - "end": 7630, + "start": 8257, + "end": 8263, "loc": { "start": { - "line": 234, + "line": 253, "column": 8 }, "end": { - "line": 234, + "line": 253, "column": 14 }, "identifierName": "txname" @@ -31945,15 +34179,15 @@ "operator": "!==", "right": { "type": "Identifier", - "start": 7635, - "end": 7644, + "start": 8268, + "end": 8277, "loc": { "start": { - "line": 234, + "line": 253, "column": 19 }, "end": { - "line": 234, + "line": 253, "column": 28 }, "identifierName": "undefined" @@ -31964,72 +34198,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 7646, - "end": 7751, + "start": 8279, + "end": 8384, "loc": { "start": { - "line": 234, + "line": 253, "column": 30 }, "end": { - "line": 236, + "line": 255, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7654, - "end": 7745, + "start": 8287, + "end": 8378, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 97 } }, "expression": { "type": "CallExpression", - "start": 7654, - "end": 7744, + "start": 8287, + "end": 8377, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 96 } }, "callee": { "type": "MemberExpression", - "start": 7654, - "end": 7674, + "start": 8287, + "end": 8307, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 26 } }, "object": { "type": "Identifier", - "start": 7654, - "end": 7670, + "start": 8287, + "end": 8303, "loc": { "start": { - "line": 235, + "line": 254, "column": 6 }, "end": { - "line": 235, + "line": 254, "column": 22 }, "identifierName": "PhyxCacheManager" @@ -32038,15 +34272,15 @@ }, "property": { "type": "Identifier", - "start": 7671, - "end": 7674, + "start": 8304, + "end": 8307, "loc": { "start": { - "line": 235, + "line": 254, "column": 23 }, "end": { - "line": 235, + "line": 254, "column": 26 }, "identifierName": "put" @@ -32058,30 +34292,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 7675, - "end": 7721, + "start": 8308, + "end": 8354, "loc": { "start": { - "line": 235, + "line": 254, "column": 27 }, "end": { - "line": 235, + "line": 254, "column": 73 } }, "expressions": [ { "type": "Identifier", - "start": 7710, - "end": 7719, + "start": 8343, + "end": 8352, "loc": { "start": { - "line": 235, + "line": 254, "column": 62 }, "end": { - "line": 235, + "line": 254, "column": 71 }, "identifierName": "nomenCode" @@ -32092,15 +34326,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 7676, - "end": 7708, + "start": 8309, + "end": 8341, "loc": { "start": { - "line": 235, + "line": 254, "column": 28 }, "end": { - "line": 235, + "line": 254, "column": 60 } }, @@ -32112,15 +34346,15 @@ }, { "type": "TemplateElement", - "start": 7720, - "end": 7720, + "start": 8353, + "end": 8353, "loc": { "start": { - "line": 235, + "line": 254, "column": 72 }, "end": { - "line": 235, + "line": 254, "column": 72 } }, @@ -32134,15 +34368,15 @@ }, { "type": "Identifier", - "start": 7723, - "end": 7735, + "start": 8356, + "end": 8368, "loc": { "start": { - "line": 235, + "line": 254, "column": 75 }, "end": { - "line": 235, + "line": 254, "column": 87 }, "identifierName": "verbatimName" @@ -32151,15 +34385,15 @@ }, { "type": "Identifier", - "start": 7737, - "end": 7743, + "start": 8370, + "end": 8376, "loc": { "start": { - "line": 235, + "line": 254, "column": 89 }, "end": { - "line": 235, + "line": 254, "column": 95 }, "identifierName": "txname" @@ -32177,15 +34411,15 @@ { "type": "CommentLine", "value": " Store in the cache.", - "start": 7593, - "end": 7615, + "start": 8226, + "end": 8248, "loc": { "start": { - "line": 233, + "line": 252, "column": 4 }, "end": { - "line": 233, + "line": 252, "column": 26 } } @@ -32194,29 +34428,29 @@ }, { "type": "ReturnStatement", - "start": 7757, - "end": 7771, + "start": 8390, + "end": 8404, "loc": { "start": { - "line": 238, + "line": 257, "column": 4 }, "end": { - "line": 238, + "line": 257, "column": 18 } }, "argument": { "type": "Identifier", - "start": 7764, - "end": 7770, + "start": 8397, + "end": 8403, "loc": { "start": { - "line": 238, + "line": 257, "column": 11 }, "end": { - "line": 238, + "line": 257, "column": 17 }, "identifierName": "txname" @@ -32232,15 +34466,15 @@ { "type": "CommentBlock", "value": "*\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n ", - "start": 5725, - "end": 5799, + "start": 6358, + "end": 6432, "loc": { "start": { - "line": 173, + "line": 192, "column": 2 }, "end": { - "line": 175, + "line": 194, "column": 5 } } @@ -32250,15 +34484,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this scientific name.\n ", - "start": 7779, - "end": 7835, + "start": 8412, + "end": 8468, "loc": { "start": { - "line": 241, + "line": 260, "column": 2 }, "end": { - "line": 243, + "line": 262, "column": 5 } } @@ -32267,15 +34501,15 @@ }, { "type": "ClassMethod", - "start": 7838, - "end": 7906, + "start": 8471, + "end": 8539, "loc": { "start": { - "line": 244, + "line": 263, "column": 2 }, "end": { - "line": 246, + "line": 265, "column": 3 } }, @@ -32283,15 +34517,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7842, - "end": 7847, + "start": 8475, + "end": 8480, "loc": { "start": { - "line": 244, + "line": 263, "column": 6 }, "end": { - "line": 244, + "line": 263, "column": 11 }, "identifierName": "label" @@ -32306,101 +34540,101 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7850, - "end": 7906, + "start": 8483, + "end": 8539, "loc": { "start": { - "line": 244, + "line": 263, "column": 14 }, "end": { - "line": 246, + "line": 265, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 7856, - "end": 7902, + "start": 8489, + "end": 8535, "loc": { "start": { - "line": 245, + "line": 264, "column": 4 }, "end": { - "line": 245, + "line": 264, "column": 50 } }, "argument": { "type": "LogicalExpression", - "start": 7863, - "end": 7901, + "start": 8496, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 49 } }, "left": { "type": "MemberExpression", - "start": 7863, - "end": 7880, + "start": 8496, + "end": 8513, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 7863, - "end": 7874, + "start": 8496, + "end": 8507, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 7863, - "end": 7867, + "start": 8496, + "end": 8500, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 15 } } }, "property": { "type": "Identifier", - "start": 7868, - "end": 7874, + "start": 8501, + "end": 8507, "loc": { "start": { - "line": 245, + "line": 264, "column": 16 }, "end": { - "line": 245, + "line": 264, "column": 22 }, "identifierName": "txname" @@ -32411,15 +34645,15 @@ }, "property": { "type": "Identifier", - "start": 7875, - "end": 7880, + "start": 8508, + "end": 8513, "loc": { "start": { - "line": 245, + "line": 264, "column": 23 }, "end": { - "line": 245, + "line": 264, "column": 28 }, "identifierName": "label" @@ -32431,44 +34665,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 7884, - "end": 7901, + "start": 8517, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 32 }, "end": { - "line": 245, + "line": 264, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 7884, - "end": 7888, + "start": 8517, + "end": 8521, "loc": { "start": { - "line": 245, + "line": 264, "column": 32 }, "end": { - "line": 245, + "line": 264, "column": 36 } } }, "property": { "type": "Identifier", - "start": 7889, - "end": 7901, + "start": 8522, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 37 }, "end": { - "line": 245, + "line": 264, "column": 49 }, "identifierName": "nameComplete" @@ -32487,15 +34721,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this scientific name.\n ", - "start": 7779, - "end": 7835, + "start": 8412, + "end": 8468, "loc": { "start": { - "line": 241, + "line": 260, "column": 2 }, "end": { - "line": 243, + "line": 262, "column": 5 } } @@ -32505,15 +34739,15 @@ { "type": "CommentBlock", "value": "*\n * Set the label of this scientific name.\n ", - "start": 7910, - "end": 7963, + "start": 8543, + "end": 8596, "loc": { "start": { - "line": 248, + "line": 267, "column": 2 }, "end": { - "line": 250, + "line": 269, "column": 5 } } @@ -32522,15 +34756,15 @@ }, { "type": "ClassMethod", - "start": 7966, - "end": 8157, + "start": 8599, + "end": 8790, "loc": { "start": { - "line": 251, + "line": 270, "column": 2 }, "end": { - "line": 257, + "line": 276, "column": 3 } }, @@ -32538,15 +34772,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7970, - "end": 7975, + "start": 8603, + "end": 8608, "loc": { "start": { - "line": 251, + "line": 270, "column": 6 }, "end": { - "line": 251, + "line": 270, "column": 11 }, "identifierName": "label" @@ -32561,15 +34795,15 @@ "params": [ { "type": "Identifier", - "start": 7976, - "end": 7979, + "start": 8609, + "end": 8612, "loc": { "start": { - "line": 251, + "line": 270, "column": 12 }, "end": { - "line": 251, + "line": 270, "column": 15 }, "identifierName": "lab" @@ -32579,102 +34813,102 @@ ], "body": { "type": "BlockStatement", - "start": 7981, - "end": 8157, + "start": 8614, + "end": 8790, "loc": { "start": { - "line": 251, + "line": 270, "column": 17 }, "end": { - "line": 257, + "line": 276, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 7987, - "end": 8011, + "start": 8620, + "end": 8644, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 28 } }, "expression": { "type": "AssignmentExpression", - "start": 7987, - "end": 8010, + "start": 8620, + "end": 8643, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 27 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7987, - "end": 8004, + "start": 8620, + "end": 8637, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 21 } }, "object": { "type": "MemberExpression", - "start": 7987, - "end": 7998, + "start": 8620, + "end": 8631, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 7987, - "end": 7991, + "start": 8620, + "end": 8624, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 8 } } }, "property": { "type": "Identifier", - "start": 7992, - "end": 7998, + "start": 8625, + "end": 8631, "loc": { "start": { - "line": 252, + "line": 271, "column": 9 }, "end": { - "line": 252, + "line": 271, "column": 15 }, "identifierName": "txname" @@ -32685,15 +34919,15 @@ }, "property": { "type": "Identifier", - "start": 7999, - "end": 8004, + "start": 8632, + "end": 8637, "loc": { "start": { - "line": 252, + "line": 271, "column": 16 }, "end": { - "line": 252, + "line": 271, "column": 21 }, "identifierName": "label" @@ -32704,15 +34938,15 @@ }, "right": { "type": "Identifier", - "start": 8007, - "end": 8010, + "start": 8640, + "end": 8643, "loc": { "start": { - "line": 252, + "line": 271, "column": 24 }, "end": { - "line": 252, + "line": 271, "column": 27 }, "identifierName": "lab" @@ -32723,29 +34957,29 @@ }, { "type": "IfStatement", - "start": 8016, - "end": 8153, + "start": 8649, + "end": 8786, "loc": { "start": { - "line": 253, + "line": 272, "column": 4 }, "end": { - "line": 256, + "line": 275, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 8020, - "end": 8038, + "start": 8653, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 8 }, "end": { - "line": 253, + "line": 272, "column": 26 } }, @@ -32753,44 +34987,44 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 8021, - "end": 8038, + "start": 8654, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 9 }, "end": { - "line": 253, + "line": 272, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 8021, - "end": 8025, + "start": 8654, + "end": 8658, "loc": { "start": { - "line": 253, + "line": 272, "column": 9 }, "end": { - "line": 253, + "line": 272, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8026, - "end": 8038, + "start": 8659, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 14 }, "end": { - "line": 253, + "line": 272, "column": 26 }, "identifierName": "nameComplete" @@ -32805,73 +35039,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 8040, - "end": 8153, + "start": 8673, + "end": 8786, "loc": { "start": { - "line": 253, + "line": 272, "column": 28 }, "end": { - "line": 256, + "line": 275, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 8123, - "end": 8147, + "start": 8756, + "end": 8780, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 30 } }, "expression": { "type": "AssignmentExpression", - "start": 8123, - "end": 8146, + "start": 8756, + "end": 8779, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 29 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 8123, - "end": 8140, + "start": 8756, + "end": 8773, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 8123, - "end": 8127, + "start": 8756, + "end": 8760, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 10 } }, @@ -32879,15 +35113,15 @@ }, "property": { "type": "Identifier", - "start": 8128, - "end": 8140, + "start": 8761, + "end": 8773, "loc": { "start": { - "line": 255, + "line": 274, "column": 11 }, "end": { - "line": 255, + "line": 274, "column": 23 }, "identifierName": "nameComplete" @@ -32899,15 +35133,15 @@ }, "right": { "type": "Identifier", - "start": 8143, - "end": 8146, + "start": 8776, + "end": 8779, "loc": { "start": { - "line": 255, + "line": 274, "column": 26 }, "end": { - "line": 255, + "line": 274, "column": 29 }, "identifierName": "lab" @@ -32920,15 +35154,15 @@ { "type": "CommentLine", "value": " If we don't have a nameComplete, treat this as the name complete.", - "start": 8048, - "end": 8116, + "start": 8681, + "end": 8749, "loc": { "start": { - "line": 254, + "line": 273, "column": 6 }, "end": { - "line": 254, + "line": 273, "column": 74 } } @@ -32948,15 +35182,15 @@ { "type": "CommentBlock", "value": "*\n * Set the label of this scientific name.\n ", - "start": 7910, - "end": 7963, + "start": 8543, + "end": 8596, "loc": { "start": { - "line": 248, + "line": 267, "column": 2 }, "end": { - "line": 250, + "line": 269, "column": 5 } } @@ -32966,15 +35200,15 @@ { "type": "CommentBlock", "value": "*\n * Return the verbatim name of this taxon name.\n ", - "start": 8161, - "end": 8220, + "start": 8794, + "end": 8853, "loc": { "start": { - "line": 259, + "line": 278, "column": 2 }, "end": { - "line": 261, + "line": 280, "column": 5 } } @@ -32983,15 +35217,15 @@ }, { "type": "ClassMethod", - "start": 8223, - "end": 8277, + "start": 8856, + "end": 8910, "loc": { "start": { - "line": 262, + "line": 281, "column": 2 }, "end": { - "line": 264, + "line": 283, "column": 3 } }, @@ -32999,15 +35233,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8227, - "end": 8239, + "start": 8860, + "end": 8872, "loc": { "start": { - "line": 262, + "line": 281, "column": 6 }, "end": { - "line": 262, + "line": 281, "column": 18 }, "identifierName": "verbatimName" @@ -33022,87 +35256,87 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8242, - "end": 8277, + "start": 8875, + "end": 8910, "loc": { "start": { - "line": 262, + "line": 281, "column": 21 }, "end": { - "line": 264, + "line": 283, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 8248, - "end": 8273, + "start": 8881, + "end": 8906, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 29 } }, "argument": { "type": "MemberExpression", - "start": 8255, - "end": 8272, + "start": 8888, + "end": 8905, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 8255, - "end": 8266, + "start": 8888, + "end": 8899, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 8255, - "end": 8259, + "start": 8888, + "end": 8892, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 15 } } }, "property": { "type": "Identifier", - "start": 8260, - "end": 8266, + "start": 8893, + "end": 8899, "loc": { "start": { - "line": 263, + "line": 282, "column": 16 }, "end": { - "line": 263, + "line": 282, "column": 22 }, "identifierName": "txname" @@ -33113,15 +35347,15 @@ }, "property": { "type": "Identifier", - "start": 8267, - "end": 8272, + "start": 8900, + "end": 8905, "loc": { "start": { - "line": 263, + "line": 282, "column": 23 }, "end": { - "line": 263, + "line": 282, "column": 28 }, "identifierName": "label" @@ -33139,15 +35373,15 @@ { "type": "CommentBlock", "value": "*\n * Return the verbatim name of this taxon name.\n ", - "start": 8161, - "end": 8220, + "start": 8794, + "end": 8853, "loc": { "start": { - "line": 259, + "line": 278, "column": 2 }, "end": { - "line": 261, + "line": 280, "column": 5 } } @@ -33157,15 +35391,15 @@ { "type": "CommentBlock", "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", - "start": 8281, - "end": 8404, + "start": 8914, + "end": 9037, "loc": { "start": { - "line": 266, + "line": 285, "column": 2 }, "end": { - "line": 269, + "line": 288, "column": 5 } } @@ -33174,15 +35408,15 @@ }, { "type": "ClassMethod", - "start": 8407, - "end": 8551, + "start": 9040, + "end": 9184, "loc": { "start": { - "line": 270, + "line": 289, "column": 2 }, "end": { - "line": 275, + "line": 294, "column": 3 } }, @@ -33190,15 +35424,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8411, - "end": 8423, + "start": 9044, + "end": 9056, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 18 }, "identifierName": "nameComplete" @@ -33213,129 +35447,129 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8426, - "end": 8551, + "start": 9059, + "end": 9184, "loc": { "start": { - "line": 270, + "line": 289, "column": 21 }, "end": { - "line": 275, + "line": 294, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 8432, - "end": 8547, + "start": 9065, + "end": 9180, "loc": { "start": { - "line": 271, + "line": 290, "column": 4 }, "end": { - "line": 274, + "line": 293, "column": 28 } }, "argument": { "type": "LogicalExpression", - "start": 8439, - "end": 8546, + "start": 9072, + "end": 9179, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 274, + "line": 293, "column": 27 } }, "left": { "type": "LogicalExpression", - "start": 8439, - "end": 8518, + "start": 9072, + "end": 9151, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 273, + "line": 292, "column": 26 } }, "left": { "type": "LogicalExpression", - "start": 8439, - "end": 8491, + "start": 9072, + "end": 9124, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 272, + "line": 291, "column": 27 } }, "left": { "type": "MemberExpression", - "start": 8439, - "end": 8463, + "start": 9072, + "end": 9096, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 35 } }, "object": { "type": "MemberExpression", - "start": 8439, - "end": 8450, + "start": 9072, + "end": 9083, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 8439, - "end": 8443, + "start": 9072, + "end": 9076, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 15 } } }, "property": { "type": "Identifier", - "start": 8444, - "end": 8450, + "start": 9077, + "end": 9083, "loc": { "start": { - "line": 271, + "line": 290, "column": 16 }, "end": { - "line": 271, + "line": 290, "column": 22 }, "identifierName": "txname" @@ -33346,15 +35580,15 @@ }, "property": { "type": "Identifier", - "start": 8451, - "end": 8463, + "start": 9084, + "end": 9096, "loc": { "start": { - "line": 271, + "line": 290, "column": 23 }, "end": { - "line": 271, + "line": 290, "column": 35 }, "identifierName": "nameComplete" @@ -33366,44 +35600,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 8473, - "end": 8491, + "start": 9106, + "end": 9124, "loc": { "start": { - "line": 272, + "line": 291, "column": 9 }, "end": { - "line": 272, + "line": 291, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 8473, - "end": 8477, + "start": 9106, + "end": 9110, "loc": { "start": { - "line": 272, + "line": 291, "column": 9 }, "end": { - "line": 272, + "line": 291, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8478, - "end": 8491, + "start": 9111, + "end": 9124, "loc": { "start": { - "line": 272, + "line": 291, "column": 14 }, "end": { - "line": 272, + "line": 291, "column": 27 }, "identifierName": "trinomialName" @@ -33416,44 +35650,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 8501, - "end": 8518, + "start": 9134, + "end": 9151, "loc": { "start": { - "line": 273, + "line": 292, "column": 9 }, "end": { - "line": 273, + "line": 292, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 8501, - "end": 8505, + "start": 9134, + "end": 9138, "loc": { "start": { - "line": 273, + "line": 292, "column": 9 }, "end": { - "line": 273, + "line": 292, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8506, - "end": 8518, + "start": 9139, + "end": 9151, "loc": { "start": { - "line": 273, + "line": 292, "column": 14 }, "end": { - "line": 273, + "line": 292, "column": 26 }, "identifierName": "binomialName" @@ -33466,44 +35700,44 @@ "operator": "||", "right": { "type": "MemberExpression", - "start": 8528, - "end": 8546, + "start": 9161, + "end": 9179, "loc": { "start": { - "line": 274, + "line": 293, "column": 9 }, "end": { - "line": 274, + "line": 293, "column": 27 } }, "object": { "type": "ThisExpression", - "start": 8528, - "end": 8532, + "start": 9161, + "end": 9165, "loc": { "start": { - "line": 274, + "line": 293, "column": 9 }, "end": { - "line": 274, + "line": 293, "column": 13 } } }, "property": { "type": "Identifier", - "start": 8533, - "end": 8546, + "start": 9166, + "end": 9179, "loc": { "start": { - "line": 274, + "line": 293, "column": 14 }, "end": { - "line": 274, + "line": 293, "column": 27 }, "identifierName": "uninomialName" @@ -33522,15 +35756,15 @@ { "type": "CommentBlock", "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", - "start": 8281, - "end": 8404, + "start": 8914, + "end": 9037, "loc": { "start": { - "line": 266, + "line": 285, "column": 2 }, "end": { - "line": 269, + "line": 288, "column": 5 } } @@ -33540,15 +35774,15 @@ { "type": "CommentBlock", "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", - "start": 8555, - "end": 8635, + "start": 9188, + "end": 9268, "loc": { "start": { - "line": 277, + "line": 296, "column": 2 }, "end": { - "line": 279, + "line": 298, "column": 5 } } @@ -33557,15 +35791,15 @@ }, { "type": "ClassMethod", - "start": 8638, - "end": 8749, + "start": 9271, + "end": 9382, "loc": { "start": { - "line": 280, + "line": 299, "column": 2 }, "end": { - "line": 282, + "line": 301, "column": 3 } }, @@ -33573,15 +35807,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8642, - "end": 8654, + "start": 9275, + "end": 9287, "loc": { "start": { - "line": 280, + "line": 299, "column": 6 }, "end": { - "line": 280, + "line": 299, "column": 18 }, "identifierName": "nameComplete" @@ -33596,15 +35830,15 @@ "params": [ { "type": "Identifier", - "start": 8655, - "end": 8659, + "start": 9288, + "end": 9292, "loc": { "start": { - "line": 280, + "line": 299, "column": 19 }, "end": { - "line": 280, + "line": 299, "column": 23 }, "identifierName": "name" @@ -33614,88 +35848,88 @@ ], "body": { "type": "BlockStatement", - "start": 8661, - "end": 8749, + "start": 9294, + "end": 9382, "loc": { "start": { - "line": 280, + "line": 299, "column": 25 }, "end": { - "line": 282, + "line": 301, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 8667, - "end": 8745, + "start": 9300, + "end": 9378, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 82 } }, "expression": { "type": "AssignmentExpression", - "start": 8667, - "end": 8744, + "start": 9300, + "end": 9377, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 81 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 8667, - "end": 8678, + "start": 9300, + "end": 9311, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 8667, - "end": 8671, + "start": 9300, + "end": 9304, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 8 } } }, "property": { "type": "Identifier", - "start": 8672, - "end": 8678, + "start": 9305, + "end": 9311, "loc": { "start": { - "line": 281, + "line": 300, "column": 9 }, "end": { - "line": 281, + "line": 300, "column": 15 }, "identifierName": "txname" @@ -33706,43 +35940,43 @@ }, "right": { "type": "CallExpression", - "start": 8681, - "end": 8744, + "start": 9314, + "end": 9377, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 81 } }, "callee": { "type": "MemberExpression", - "start": 8681, - "end": 8714, + "start": 9314, + "end": 9347, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 51 } }, "object": { "type": "Identifier", - "start": 8681, - "end": 8697, + "start": 9314, + "end": 9330, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 34 }, "identifierName": "TaxonNameWrapper" @@ -33751,15 +35985,15 @@ }, "property": { "type": "Identifier", - "start": 8698, - "end": 8714, + "start": 9331, + "end": 9347, "loc": { "start": { - "line": 281, + "line": 300, "column": 35 }, "end": { - "line": 281, + "line": 300, "column": 51 }, "identifierName": "fromVerbatimName" @@ -33771,15 +36005,15 @@ "arguments": [ { "type": "Identifier", - "start": 8715, - "end": 8719, + "start": 9348, + "end": 9352, "loc": { "start": { - "line": 281, + "line": 300, "column": 52 }, "end": { - "line": 281, + "line": 300, "column": 56 }, "identifierName": "name" @@ -33788,44 +36022,44 @@ }, { "type": "MemberExpression", - "start": 8721, - "end": 8743, + "start": 9354, + "end": 9376, "loc": { "start": { - "line": 281, + "line": 300, "column": 58 }, "end": { - "line": 281, + "line": 300, "column": 80 } }, "object": { "type": "ThisExpression", - "start": 8721, - "end": 8725, + "start": 9354, + "end": 9358, "loc": { "start": { - "line": 281, + "line": 300, "column": 58 }, "end": { - "line": 281, + "line": 300, "column": 62 } } }, "property": { "type": "Identifier", - "start": 8726, - "end": 8743, + "start": 9359, + "end": 9376, "loc": { "start": { - "line": 281, + "line": 300, "column": 63 }, "end": { - "line": 281, + "line": 300, "column": 80 }, "identifierName": "nomenclaturalCode" @@ -33846,15 +36080,15 @@ { "type": "CommentBlock", "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", - "start": 8555, - "end": 8635, + "start": 9188, + "end": 9268, "loc": { "start": { - "line": 277, + "line": 296, "column": 2 }, "end": { - "line": 279, + "line": 298, "column": 5 } } @@ -33864,15 +36098,15 @@ { "type": "CommentBlock", "value": "* Return the uninomial name if there is one. ", - "start": 8753, - "end": 8802, + "start": 9386, + "end": 9435, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 284, + "line": 303, "column": 51 } } @@ -33881,15 +36115,15 @@ }, { "type": "ClassMethod", - "start": 8805, - "end": 9242, + "start": 9438, + "end": 9875, "loc": { "start": { - "line": 285, + "line": 304, "column": 2 }, "end": { - "line": 299, + "line": 318, "column": 3 } }, @@ -33897,15 +36131,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 8809, - "end": 8818, + "start": 9442, + "end": 9451, "loc": { "start": { - "line": 285, + "line": 304, "column": 6 }, "end": { - "line": 285, + "line": 304, "column": 15 }, "identifierName": "uninomial" @@ -33920,87 +36154,87 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8821, - "end": 9242, + "start": 9454, + "end": 9875, "loc": { "start": { - "line": 285, + "line": 304, "column": 18 }, "end": { - "line": 299, + "line": 318, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 8827, - "end": 8883, + "start": 9460, + "end": 9516, "loc": { "start": { - "line": 286, + "line": 305, "column": 4 }, "end": { - "line": 286, + "line": 305, "column": 60 } }, "test": { "type": "MemberExpression", - "start": 8831, - "end": 8852, + "start": 9464, + "end": 9485, "loc": { "start": { - "line": 286, + "line": 305, "column": 8 }, "end": { - "line": 286, + "line": 305, "column": 29 } }, "object": { "type": "MemberExpression", - "start": 8831, - "end": 8842, + "start": 9464, + "end": 9475, "loc": { "start": { - "line": 286, + "line": 305, "column": 8 }, "end": { - "line": 286, + "line": 305, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 8831, - "end": 8835, + "start": 9464, + "end": 9468, "loc": { "start": { - "line": 286, + "line": 305, "column": 8 }, "end": { - "line": 286, + "line": 305, "column": 12 } } }, "property": { "type": "Identifier", - "start": 8836, - "end": 8842, + "start": 9469, + "end": 9475, "loc": { "start": { - "line": 286, + "line": 305, "column": 13 }, "end": { - "line": 286, + "line": 305, "column": 19 }, "identifierName": "txname" @@ -34011,15 +36245,15 @@ }, "property": { "type": "Identifier", - "start": 8843, - "end": 8852, + "start": 9476, + "end": 9485, "loc": { "start": { - "line": 286, + "line": 305, "column": 20 }, "end": { - "line": 286, + "line": 305, "column": 29 }, "identifierName": "uninomial" @@ -34030,72 +36264,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 8854, - "end": 8883, + "start": 9487, + "end": 9516, "loc": { "start": { - "line": 286, + "line": 305, "column": 31 }, "end": { - "line": 286, + "line": 305, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 8861, - "end": 8882, + "start": 9494, + "end": 9515, "loc": { "start": { - "line": 286, + "line": 305, "column": 38 }, "end": { - "line": 286, + "line": 305, "column": 59 } }, "object": { "type": "MemberExpression", - "start": 8861, - "end": 8872, + "start": 9494, + "end": 9505, "loc": { "start": { - "line": 286, + "line": 305, "column": 38 }, "end": { - "line": 286, + "line": 305, "column": 49 } }, "object": { "type": "ThisExpression", - "start": 8861, - "end": 8865, + "start": 9494, + "end": 9498, "loc": { "start": { - "line": 286, + "line": 305, "column": 38 }, "end": { - "line": 286, + "line": 305, "column": 42 } } }, "property": { "type": "Identifier", - "start": 8866, - "end": 8872, + "start": 9499, + "end": 9505, "loc": { "start": { - "line": 286, + "line": 305, "column": 43 }, "end": { - "line": 286, + "line": 305, "column": 49 }, "identifierName": "txname" @@ -34106,15 +36340,15 @@ }, "property": { "type": "Identifier", - "start": 8873, - "end": 8882, + "start": 9506, + "end": 9515, "loc": { "start": { - "line": 286, + "line": 305, "column": 50 }, "end": { - "line": 286, + "line": 305, "column": 59 }, "identifierName": "uninomial" @@ -34130,15 +36364,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 8889, - "end": 8966, + "start": 9522, + "end": 9599, "loc": { "start": { - "line": 288, + "line": 307, "column": 4 }, "end": { - "line": 288, + "line": 307, "column": 81 } } @@ -34146,15 +36380,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 8971, - "end": 8982, + "start": 9604, + "end": 9615, "loc": { "start": { - "line": 289, + "line": 308, "column": 4 }, "end": { - "line": 289, + "line": 308, "column": 15 } } @@ -34163,57 +36397,57 @@ }, { "type": "IfStatement", - "start": 8987, - "end": 9215, + "start": 9620, + "end": 9848, "loc": { "start": { - "line": 290, + "line": 309, "column": 4 }, "end": { - "line": 296, + "line": 315, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 8991, - "end": 9015, + "start": 9624, + "end": 9648, "loc": { "start": { - "line": 290, + "line": 309, "column": 8 }, "end": { - "line": 290, + "line": 309, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 8991, - "end": 9002, + "start": 9624, + "end": 9635, "loc": { "start": { - "line": 290, + "line": 309, "column": 8 }, "end": { - "line": 290, + "line": 309, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 8991, - "end": 8995, + "start": 9624, + "end": 9628, "loc": { "start": { - "line": 290, + "line": 309, "column": 8 }, "end": { - "line": 290, + "line": 309, "column": 12 } }, @@ -34221,15 +36455,15 @@ }, "property": { "type": "Identifier", - "start": 8996, - "end": 9002, + "start": 9629, + "end": 9635, "loc": { "start": { - "line": 290, + "line": 309, "column": 13 }, "end": { - "line": 290, + "line": 309, "column": 19 }, "identifierName": "txname" @@ -34241,15 +36475,15 @@ }, "property": { "type": "Identifier", - "start": 9003, - "end": 9015, + "start": 9636, + "end": 9648, "loc": { "start": { - "line": 290, + "line": 309, "column": 20 }, "end": { - "line": 290, + "line": 309, "column": 32 }, "identifierName": "nameComplete" @@ -34261,59 +36495,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 9017, - "end": 9215, + "start": 9650, + "end": 9848, "loc": { "start": { - "line": 290, + "line": 309, "column": 34 }, "end": { - "line": 296, + "line": 315, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 9025, - "end": 9148, + "start": 9658, + "end": 9781, "loc": { "start": { - "line": 291, + "line": 310, "column": 6 }, "end": { - "line": 294, + "line": 313, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 9031, - "end": 9147, + "start": 9664, + "end": 9780, "loc": { "start": { - "line": 291, + "line": 310, "column": 12 }, "end": { - "line": 294, + "line": 313, "column": 7 } }, "id": { "type": "Identifier", - "start": 9031, - "end": 9037, + "start": 9664, + "end": 9670, "loc": { "start": { - "line": 291, + "line": 310, "column": 12 }, "end": { - "line": 291, + "line": 310, "column": 18 }, "identifierName": "txname" @@ -34322,43 +36556,43 @@ }, "init": { "type": "CallExpression", - "start": 9040, - "end": 9147, + "start": 9673, + "end": 9780, "loc": { "start": { - "line": 291, + "line": 310, "column": 21 }, "end": { - "line": 294, + "line": 313, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 9040, - "end": 9073, + "start": 9673, + "end": 9706, "loc": { "start": { - "line": 291, + "line": 310, "column": 21 }, "end": { - "line": 291, + "line": 310, "column": 54 } }, "object": { "type": "Identifier", - "start": 9040, - "end": 9056, + "start": 9673, + "end": 9689, "loc": { "start": { - "line": 291, + "line": 310, "column": 21 }, "end": { - "line": 291, + "line": 310, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -34367,15 +36601,15 @@ }, "property": { "type": "Identifier", - "start": 9057, - "end": 9073, + "start": 9690, + "end": 9706, "loc": { "start": { - "line": 291, + "line": 310, "column": 38 }, "end": { - "line": 291, + "line": 310, "column": 54 }, "identifierName": "fromVerbatimName" @@ -34387,58 +36621,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 9083, - "end": 9107, + "start": 9716, + "end": 9740, "loc": { "start": { - "line": 292, + "line": 311, "column": 8 }, "end": { - "line": 292, + "line": 311, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 9083, - "end": 9094, + "start": 9716, + "end": 9727, "loc": { "start": { - "line": 292, + "line": 311, "column": 8 }, "end": { - "line": 292, + "line": 311, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 9083, - "end": 9087, + "start": 9716, + "end": 9720, "loc": { "start": { - "line": 292, + "line": 311, "column": 8 }, "end": { - "line": 292, + "line": 311, "column": 12 } } }, "property": { "type": "Identifier", - "start": 9088, - "end": 9094, + "start": 9721, + "end": 9727, "loc": { "start": { - "line": 292, + "line": 311, "column": 13 }, "end": { - "line": 292, + "line": 311, "column": 19 }, "identifierName": "txname" @@ -34449,15 +36683,15 @@ }, "property": { "type": "Identifier", - "start": 9095, - "end": 9107, + "start": 9728, + "end": 9740, "loc": { "start": { - "line": 292, + "line": 311, "column": 20 }, "end": { - "line": 292, + "line": 311, "column": 32 }, "identifierName": "nameComplete" @@ -34468,44 +36702,44 @@ }, { "type": "MemberExpression", - "start": 9117, - "end": 9139, + "start": 9750, + "end": 9772, "loc": { "start": { - "line": 293, + "line": 312, "column": 8 }, "end": { - "line": 293, + "line": 312, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 9117, - "end": 9121, + "start": 9750, + "end": 9754, "loc": { "start": { - "line": 293, + "line": 312, "column": 8 }, "end": { - "line": 293, + "line": 312, "column": 12 } } }, "property": { "type": "Identifier", - "start": 9122, - "end": 9139, + "start": 9755, + "end": 9772, "loc": { "start": { - "line": 293, + "line": 312, "column": 13 }, "end": { - "line": 293, + "line": 312, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -34522,43 +36756,43 @@ }, { "type": "IfStatement", - "start": 9155, - "end": 9209, + "start": 9788, + "end": 9842, "loc": { "start": { - "line": 295, + "line": 314, "column": 6 }, "end": { - "line": 295, + "line": 314, "column": 60 } }, "test": { "type": "CallExpression", - "start": 9159, - "end": 9183, + "start": 9792, + "end": 9816, "loc": { "start": { - "line": 295, + "line": 314, "column": 10 }, "end": { - "line": 295, + "line": 314, "column": 34 } }, "callee": { "type": "Identifier", - "start": 9159, - "end": 9162, + "start": 9792, + "end": 9795, "loc": { "start": { - "line": 295, + "line": 314, "column": 10 }, "end": { - "line": 295, + "line": 314, "column": 13 }, "identifierName": "has" @@ -34568,15 +36802,15 @@ "arguments": [ { "type": "Identifier", - "start": 9163, - "end": 9169, + "start": 9796, + "end": 9802, "loc": { "start": { - "line": 295, + "line": 314, "column": 14 }, "end": { - "line": 295, + "line": 314, "column": 20 }, "identifierName": "txname" @@ -34585,15 +36819,15 @@ }, { "type": "StringLiteral", - "start": 9171, - "end": 9182, + "start": 9804, + "end": 9815, "loc": { "start": { - "line": 295, + "line": 314, "column": 22 }, "end": { - "line": 295, + "line": 314, "column": 33 } }, @@ -34607,43 +36841,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 9185, - "end": 9209, + "start": 9818, + "end": 9842, "loc": { "start": { - "line": 295, + "line": 314, "column": 36 }, "end": { - "line": 295, + "line": 314, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 9192, - "end": 9208, + "start": 9825, + "end": 9841, "loc": { "start": { - "line": 295, + "line": 314, "column": 43 }, "end": { - "line": 295, + "line": 314, "column": 59 } }, "object": { "type": "Identifier", - "start": 9192, - "end": 9198, + "start": 9825, + "end": 9831, "loc": { "start": { - "line": 295, + "line": 314, "column": 43 }, "end": { - "line": 295, + "line": 314, "column": 49 }, "identifierName": "txname" @@ -34652,15 +36886,15 @@ }, "property": { "type": "Identifier", - "start": 9199, - "end": 9208, + "start": 9832, + "end": 9841, "loc": { "start": { - "line": 295, + "line": 314, "column": 50 }, "end": { - "line": 295, + "line": 314, "column": 59 }, "identifierName": "uninomial" @@ -34680,15 +36914,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 8889, - "end": 8966, + "start": 9522, + "end": 9599, "loc": { "start": { - "line": 288, + "line": 307, "column": 4 }, "end": { - "line": 288, + "line": 307, "column": 81 } } @@ -34696,15 +36930,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 8971, - "end": 8982, + "start": 9604, + "end": 9615, "loc": { "start": { - "line": 289, + "line": 308, "column": 4 }, "end": { - "line": 289, + "line": 308, "column": 15 } } @@ -34713,29 +36947,29 @@ }, { "type": "ReturnStatement", - "start": 9221, - "end": 9238, + "start": 9854, + "end": 9871, "loc": { "start": { - "line": 298, + "line": 317, "column": 4 }, "end": { - "line": 298, + "line": 317, "column": 21 } }, "argument": { "type": "Identifier", - "start": 9228, - "end": 9237, + "start": 9861, + "end": 9870, "loc": { "start": { - "line": 298, + "line": 317, "column": 11 }, "end": { - "line": 298, + "line": 317, "column": 20 }, "identifierName": "undefined" @@ -34751,15 +36985,15 @@ { "type": "CommentBlock", "value": "* Return the uninomial name if there is one. ", - "start": 8753, - "end": 8802, + "start": 9386, + "end": 9435, "loc": { "start": { - "line": 284, + "line": 303, "column": 2 }, "end": { - "line": 284, + "line": 303, "column": 51 } } @@ -34769,15 +37003,15 @@ { "type": "CommentBlock", "value": "* Set the uninomial name. ", - "start": 9246, - "end": 9276, + "start": 9879, + "end": 9909, "loc": { "start": { - "line": 301, + "line": 320, "column": 2 }, "end": { - "line": 301, + "line": 320, "column": 32 } } @@ -34786,15 +37020,15 @@ }, { "type": "ClassMethod", - "start": 9279, - "end": 9381, + "start": 9912, + "end": 10014, "loc": { "start": { - "line": 302, + "line": 321, "column": 2 }, "end": { - "line": 305, + "line": 324, "column": 3 } }, @@ -34802,15 +37036,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9283, - "end": 9292, + "start": 9916, + "end": 9925, "loc": { "start": { - "line": 302, + "line": 321, "column": 6 }, "end": { - "line": 302, + "line": 321, "column": 15 }, "identifierName": "uninomial" @@ -34825,15 +37059,15 @@ "params": [ { "type": "Identifier", - "start": 9293, - "end": 9299, + "start": 9926, + "end": 9932, "loc": { "start": { - "line": 302, + "line": 321, "column": 16 }, "end": { - "line": 302, + "line": 321, "column": 22 }, "identifierName": "uninom" @@ -34843,102 +37077,102 @@ ], "body": { "type": "BlockStatement", - "start": 9301, - "end": 9381, + "start": 9934, + "end": 10014, "loc": { "start": { - "line": 302, + "line": 321, "column": 24 }, "end": { - "line": 305, + "line": 324, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 9307, - "end": 9338, + "start": 9940, + "end": 9971, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 35 } }, "expression": { "type": "AssignmentExpression", - "start": 9307, - "end": 9337, + "start": 9940, + "end": 9970, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 34 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9307, - "end": 9328, + "start": 9940, + "end": 9961, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 9307, - "end": 9318, + "start": 9940, + "end": 9951, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9307, - "end": 9311, + "start": 9940, + "end": 9944, "loc": { "start": { - "line": 303, + "line": 322, "column": 4 }, "end": { - "line": 303, + "line": 322, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9312, - "end": 9318, + "start": 9945, + "end": 9951, "loc": { "start": { - "line": 303, + "line": 322, "column": 9 }, "end": { - "line": 303, + "line": 322, "column": 15 }, "identifierName": "txname" @@ -34949,15 +37183,15 @@ }, "property": { "type": "Identifier", - "start": 9319, - "end": 9328, + "start": 9952, + "end": 9961, "loc": { "start": { - "line": 303, + "line": 322, "column": 16 }, "end": { - "line": 303, + "line": 322, "column": 25 }, "identifierName": "uninomial" @@ -34968,15 +37202,15 @@ }, "right": { "type": "Identifier", - "start": 9331, - "end": 9337, + "start": 9964, + "end": 9970, "loc": { "start": { - "line": 303, + "line": 322, "column": 28 }, "end": { - "line": 303, + "line": 322, "column": 34 }, "identifierName": "uninom" @@ -34987,87 +37221,87 @@ }, { "type": "ExpressionStatement", - "start": 9343, - "end": 9377, + "start": 9976, + "end": 10010, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 9343, - "end": 9376, + "start": 9976, + "end": 10009, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9343, - "end": 9367, + "start": 9976, + "end": 10000, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 9343, - "end": 9354, + "start": 9976, + "end": 9987, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9343, - "end": 9347, + "start": 9976, + "end": 9980, "loc": { "start": { - "line": 304, + "line": 323, "column": 4 }, "end": { - "line": 304, + "line": 323, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9348, - "end": 9354, + "start": 9981, + "end": 9987, "loc": { "start": { - "line": 304, + "line": 323, "column": 9 }, "end": { - "line": 304, + "line": 323, "column": 15 }, "identifierName": "txname" @@ -35078,15 +37312,15 @@ }, "property": { "type": "Identifier", - "start": 9355, - "end": 9367, + "start": 9988, + "end": 10000, "loc": { "start": { - "line": 304, + "line": 323, "column": 16 }, "end": { - "line": 304, + "line": 323, "column": 28 }, "identifierName": "nameComplete" @@ -35097,15 +37331,15 @@ }, "right": { "type": "Identifier", - "start": 9370, - "end": 9376, + "start": 10003, + "end": 10009, "loc": { "start": { - "line": 304, + "line": 323, "column": 31 }, "end": { - "line": 304, + "line": 323, "column": 37 }, "identifierName": "uninom" @@ -35122,15 +37356,15 @@ { "type": "CommentBlock", "value": "* Set the uninomial name. ", - "start": 9246, - "end": 9276, + "start": 9879, + "end": 9909, "loc": { "start": { - "line": 301, + "line": 320, "column": 2 }, "end": { - "line": 301, + "line": 320, "column": 32 } } @@ -35140,15 +37374,15 @@ { "type": "CommentBlock", "value": "* Return the binomial name if available. ", - "start": 9385, - "end": 9430, + "start": 10018, + "end": 10063, "loc": { "start": { - "line": 307, + "line": 326, "column": 2 }, "end": { - "line": 307, + "line": 326, "column": 47 } } @@ -35157,15 +37391,15 @@ }, { "type": "ClassMethod", - "start": 9433, - "end": 9706, + "start": 10066, + "end": 10339, "loc": { "start": { - "line": 308, + "line": 327, "column": 2 }, "end": { - "line": 313, + "line": 332, "column": 3 } }, @@ -35173,15 +37407,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9437, - "end": 9449, + "start": 10070, + "end": 10082, "loc": { "start": { - "line": 308, + "line": 327, "column": 6 }, "end": { - "line": 308, + "line": 327, "column": 18 }, "identifierName": "binomialName" @@ -35196,86 +37430,86 @@ "params": [], "body": { "type": "BlockStatement", - "start": 9452, - "end": 9706, + "start": 10085, + "end": 10339, "loc": { "start": { - "line": 308, + "line": 327, "column": 21 }, "end": { - "line": 313, + "line": 332, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 9557, - "end": 9646, + "start": 10190, + "end": 10279, "loc": { "start": { - "line": 311, + "line": 330, "column": 4 }, "end": { - "line": 311, + "line": 330, "column": 93 } }, "test": { "type": "LogicalExpression", - "start": 9561, - "end": 9627, + "start": 10194, + "end": 10260, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 74 } }, "left": { "type": "BinaryExpression", - "start": 9561, - "end": 9589, + "start": 10194, + "end": 10222, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 36 } }, "left": { "type": "MemberExpression", - "start": 9561, - "end": 9575, + "start": 10194, + "end": 10208, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 9561, - "end": 9565, + "start": 10194, + "end": 10198, "loc": { "start": { - "line": 311, + "line": 330, "column": 8 }, "end": { - "line": 311, + "line": 330, "column": 12 } }, @@ -35283,15 +37517,15 @@ }, "property": { "type": "Identifier", - "start": 9566, - "end": 9575, + "start": 10199, + "end": 10208, "loc": { "start": { - "line": 311, + "line": 330, "column": 13 }, "end": { - "line": 311, + "line": 330, "column": 22 }, "identifierName": "genusPart" @@ -35304,15 +37538,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 9580, - "end": 9589, + "start": 10213, + "end": 10222, "loc": { "start": { - "line": 311, + "line": 330, "column": 27 }, "end": { - "line": 311, + "line": 330, "column": 36 }, "identifierName": "undefined" @@ -35324,58 +37558,58 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 9593, - "end": 9627, + "start": 10226, + "end": 10260, "loc": { "start": { - "line": 311, + "line": 330, "column": 40 }, "end": { - "line": 311, + "line": 330, "column": 74 } }, "left": { "type": "MemberExpression", - "start": 9593, - "end": 9613, + "start": 10226, + "end": 10246, "loc": { "start": { - "line": 311, + "line": 330, "column": 40 }, "end": { - "line": 311, + "line": 330, "column": 60 } }, "object": { "type": "ThisExpression", - "start": 9593, - "end": 9597, + "start": 10226, + "end": 10230, "loc": { "start": { - "line": 311, + "line": 330, "column": 40 }, "end": { - "line": 311, + "line": 330, "column": 44 } } }, "property": { "type": "Identifier", - "start": 9598, - "end": 9613, + "start": 10231, + "end": 10246, "loc": { "start": { - "line": 311, + "line": 330, "column": 45 }, "end": { - "line": 311, + "line": 330, "column": 60 }, "identifierName": "specificEpithet" @@ -35387,15 +37621,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 9618, - "end": 9627, + "start": 10251, + "end": 10260, "loc": { "start": { - "line": 311, + "line": 330, "column": 65 }, "end": { - "line": 311, + "line": 330, "column": 74 }, "identifierName": "undefined" @@ -35407,29 +37641,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 9629, - "end": 9646, + "start": 10262, + "end": 10279, "loc": { "start": { - "line": 311, + "line": 330, "column": 76 }, "end": { - "line": 311, + "line": 330, "column": 93 } }, "argument": { "type": "Identifier", - "start": 9636, - "end": 9645, + "start": 10269, + "end": 10278, "loc": { "start": { - "line": 311, + "line": 330, "column": 83 }, "end": { - "line": 311, + "line": 330, "column": 92 }, "identifierName": "undefined" @@ -35442,15 +37676,15 @@ { "type": "CommentLine", "value": " Get the binomial name. Constructed from the genus and specific epithet", - "start": 9458, - "end": 9531, + "start": 10091, + "end": 10164, "loc": { "start": { - "line": 309, + "line": 328, "column": 4 }, "end": { - "line": 309, + "line": 328, "column": 77 } } @@ -35458,15 +37692,15 @@ { "type": "CommentLine", "value": " if available.", - "start": 9536, - "end": 9552, + "start": 10169, + "end": 10185, "loc": { "start": { - "line": 310, + "line": 329, "column": 4 }, "end": { - "line": 310, + "line": 329, "column": 20 } } @@ -35475,73 +37709,73 @@ }, { "type": "ReturnStatement", - "start": 9651, - "end": 9702, + "start": 10284, + "end": 10335, "loc": { "start": { - "line": 312, + "line": 331, "column": 4 }, "end": { - "line": 312, + "line": 331, "column": 55 } }, "argument": { "type": "TemplateLiteral", - "start": 9658, - "end": 9701, + "start": 10291, + "end": 10334, "loc": { "start": { - "line": 312, + "line": 331, "column": 11 }, "end": { - "line": 312, + "line": 331, "column": 54 } }, "expressions": [ { "type": "MemberExpression", - "start": 9661, - "end": 9675, + "start": 10294, + "end": 10308, "loc": { "start": { - "line": 312, + "line": 331, "column": 14 }, "end": { - "line": 312, + "line": 331, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 9661, - "end": 9665, + "start": 10294, + "end": 10298, "loc": { "start": { - "line": 312, + "line": 331, "column": 14 }, "end": { - "line": 312, + "line": 331, "column": 18 } } }, "property": { "type": "Identifier", - "start": 9666, - "end": 9675, + "start": 10299, + "end": 10308, "loc": { "start": { - "line": 312, + "line": 331, "column": 19 }, "end": { - "line": 312, + "line": 331, "column": 28 }, "identifierName": "genusPart" @@ -35552,44 +37786,44 @@ }, { "type": "MemberExpression", - "start": 9679, - "end": 9699, + "start": 10312, + "end": 10332, "loc": { "start": { - "line": 312, + "line": 331, "column": 32 }, "end": { - "line": 312, + "line": 331, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 9679, - "end": 9683, + "start": 10312, + "end": 10316, "loc": { "start": { - "line": 312, + "line": 331, "column": 32 }, "end": { - "line": 312, + "line": 331, "column": 36 } } }, "property": { "type": "Identifier", - "start": 9684, - "end": 9699, + "start": 10317, + "end": 10332, "loc": { "start": { - "line": 312, + "line": 331, "column": 37 }, "end": { - "line": 312, + "line": 331, "column": 52 }, "identifierName": "specificEpithet" @@ -35602,15 +37836,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 9659, - "end": 9659, + "start": 10292, + "end": 10292, "loc": { "start": { - "line": 312, + "line": 331, "column": 12 }, "end": { - "line": 312, + "line": 331, "column": 12 } }, @@ -35622,15 +37856,15 @@ }, { "type": "TemplateElement", - "start": 9676, - "end": 9677, + "start": 10309, + "end": 10310, "loc": { "start": { - "line": 312, + "line": 331, "column": 29 }, "end": { - "line": 312, + "line": 331, "column": 30 } }, @@ -35642,15 +37876,15 @@ }, { "type": "TemplateElement", - "start": 9700, - "end": 9700, + "start": 10333, + "end": 10333, "loc": { "start": { - "line": 312, + "line": 331, "column": 53 }, "end": { - "line": 312, + "line": 331, "column": 53 } }, @@ -35671,15 +37905,15 @@ { "type": "CommentBlock", "value": "* Return the binomial name if available. ", - "start": 9385, - "end": 9430, + "start": 10018, + "end": 10063, "loc": { "start": { - "line": 307, + "line": 326, "column": 2 }, "end": { - "line": 307, + "line": 326, "column": 47 } } @@ -35689,15 +37923,15 @@ { "type": "CommentBlock", "value": "* Set the binomial name. ", - "start": 9710, - "end": 9739, + "start": 10343, + "end": 10372, "loc": { "start": { - "line": 315, + "line": 334, "column": 2 }, "end": { - "line": 315, + "line": 334, "column": 31 } } @@ -35706,15 +37940,15 @@ }, { "type": "ClassMethod", - "start": 9742, - "end": 9848, + "start": 10375, + "end": 10481, "loc": { "start": { - "line": 316, + "line": 335, "column": 2 }, "end": { - "line": 319, + "line": 338, "column": 3 } }, @@ -35722,15 +37956,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9746, - "end": 9758, + "start": 10379, + "end": 10391, "loc": { "start": { - "line": 316, + "line": 335, "column": 6 }, "end": { - "line": 316, + "line": 335, "column": 18 }, "identifierName": "binomialName" @@ -35745,15 +37979,15 @@ "params": [ { "type": "Identifier", - "start": 9759, - "end": 9764, + "start": 10392, + "end": 10397, "loc": { "start": { - "line": 316, + "line": 335, "column": 19 }, "end": { - "line": 316, + "line": 335, "column": 24 }, "identifierName": "binom" @@ -35763,102 +37997,102 @@ ], "body": { "type": "BlockStatement", - "start": 9766, - "end": 9848, + "start": 10399, + "end": 10481, "loc": { "start": { - "line": 316, + "line": 335, "column": 26 }, "end": { - "line": 319, + "line": 338, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 9772, - "end": 9806, + "start": 10405, + "end": 10439, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 9772, - "end": 9805, + "start": 10405, + "end": 10438, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9772, - "end": 9793, + "start": 10405, + "end": 10426, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 9772, - "end": 9783, + "start": 10405, + "end": 10416, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9772, - "end": 9776, + "start": 10405, + "end": 10409, "loc": { "start": { - "line": 317, + "line": 336, "column": 4 }, "end": { - "line": 317, + "line": 336, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9777, - "end": 9783, + "start": 10410, + "end": 10416, "loc": { "start": { - "line": 317, + "line": 336, "column": 9 }, "end": { - "line": 317, + "line": 336, "column": 15 }, "identifierName": "txname" @@ -35869,15 +38103,15 @@ }, "property": { "type": "Identifier", - "start": 9784, - "end": 9793, + "start": 10417, + "end": 10426, "loc": { "start": { - "line": 317, + "line": 336, "column": 16 }, "end": { - "line": 317, + "line": 336, "column": 25 }, "identifierName": "uninomial" @@ -35888,15 +38122,15 @@ }, "right": { "type": "Identifier", - "start": 9796, - "end": 9805, + "start": 10429, + "end": 10438, "loc": { "start": { - "line": 317, + "line": 336, "column": 28 }, "end": { - "line": 317, + "line": 336, "column": 37 }, "identifierName": "undefined" @@ -35907,87 +38141,87 @@ }, { "type": "ExpressionStatement", - "start": 9811, - "end": 9844, + "start": 10444, + "end": 10477, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 37 } }, "expression": { "type": "AssignmentExpression", - "start": 9811, - "end": 9843, + "start": 10444, + "end": 10476, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 36 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 9811, - "end": 9835, + "start": 10444, + "end": 10468, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 9811, - "end": 9822, + "start": 10444, + "end": 10455, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 9811, - "end": 9815, + "start": 10444, + "end": 10448, "loc": { "start": { - "line": 318, + "line": 337, "column": 4 }, "end": { - "line": 318, + "line": 337, "column": 8 } } }, "property": { "type": "Identifier", - "start": 9816, - "end": 9822, + "start": 10449, + "end": 10455, "loc": { "start": { - "line": 318, + "line": 337, "column": 9 }, "end": { - "line": 318, + "line": 337, "column": 15 }, "identifierName": "txname" @@ -35998,15 +38232,15 @@ }, "property": { "type": "Identifier", - "start": 9823, - "end": 9835, + "start": 10456, + "end": 10468, "loc": { "start": { - "line": 318, + "line": 337, "column": 16 }, "end": { - "line": 318, + "line": 337, "column": 28 }, "identifierName": "nameComplete" @@ -36017,15 +38251,15 @@ }, "right": { "type": "Identifier", - "start": 9838, - "end": 9843, + "start": 10471, + "end": 10476, "loc": { "start": { - "line": 318, + "line": 337, "column": 31 }, "end": { - "line": 318, + "line": 337, "column": 36 }, "identifierName": "binom" @@ -36042,15 +38276,15 @@ { "type": "CommentBlock", "value": "* Set the binomial name. ", - "start": 9710, - "end": 9739, + "start": 10343, + "end": 10372, "loc": { "start": { - "line": 315, + "line": 334, "column": 2 }, "end": { - "line": 315, + "line": 334, "column": 31 } } @@ -36060,15 +38294,15 @@ { "type": "CommentBlock", "value": "* Return the trinomial name if available. ", - "start": 9852, - "end": 9898, + "start": 10485, + "end": 10531, "loc": { "start": { - "line": 321, + "line": 340, "column": 2 }, "end": { - "line": 321, + "line": 340, "column": 48 } } @@ -36077,15 +38311,15 @@ }, { "type": "ClassMethod", - "start": 9901, - "end": 10172, + "start": 10534, + "end": 10805, "loc": { "start": { - "line": 322, + "line": 341, "column": 2 }, "end": { - "line": 329, + "line": 348, "column": 3 } }, @@ -36093,15 +38327,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 9905, - "end": 9918, + "start": 10538, + "end": 10551, "loc": { "start": { - "line": 322, + "line": 341, "column": 6 }, "end": { - "line": 322, + "line": 341, "column": 19 }, "identifierName": "trinomialName" @@ -36116,115 +38350,115 @@ "params": [], "body": { "type": "BlockStatement", - "start": 9921, - "end": 10172, + "start": 10554, + "end": 10805, "loc": { "start": { - "line": 322, + "line": 341, "column": 22 }, "end": { - "line": 329, + "line": 348, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 9927, - "end": 10083, + "start": 10560, + "end": 10716, "loc": { "start": { - "line": 323, + "line": 342, "column": 4 }, "end": { - "line": 327, + "line": 346, "column": 23 } }, "test": { "type": "LogicalExpression", - "start": 9938, - "end": 10059, + "start": 10571, + "end": 10692, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 326, + "line": 345, "column": 37 } }, "left": { "type": "LogicalExpression", - "start": 9938, - "end": 10021, + "start": 10571, + "end": 10654, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 325, + "line": 344, "column": 43 } }, "left": { "type": "BinaryExpression", - "start": 9938, - "end": 9977, + "start": 10571, + "end": 10610, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 324, + "line": 343, "column": 45 } }, "left": { "type": "MemberExpression", - "start": 9938, - "end": 9963, + "start": 10571, + "end": 10596, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 324, + "line": 343, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 9938, - "end": 9942, + "start": 10571, + "end": 10575, "loc": { "start": { - "line": 324, + "line": 343, "column": 6 }, "end": { - "line": 324, + "line": 343, "column": 10 } } }, "property": { "type": "Identifier", - "start": 9943, - "end": 9963, + "start": 10576, + "end": 10596, "loc": { "start": { - "line": 324, + "line": 343, "column": 11 }, "end": { - "line": 324, + "line": 343, "column": 31 }, "identifierName": "infraspecificEpithet" @@ -36236,15 +38470,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 9968, - "end": 9977, + "start": 10601, + "end": 10610, "loc": { "start": { - "line": 324, + "line": 343, "column": 36 }, "end": { - "line": 324, + "line": 343, "column": 45 }, "identifierName": "undefined" @@ -36255,58 +38489,58 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 9987, - "end": 10021, + "start": 10620, + "end": 10654, "loc": { "start": { - "line": 325, + "line": 344, "column": 9 }, "end": { - "line": 325, + "line": 344, "column": 43 } }, "left": { "type": "MemberExpression", - "start": 9987, - "end": 10007, + "start": 10620, + "end": 10640, "loc": { "start": { - "line": 325, + "line": 344, "column": 9 }, "end": { - "line": 325, + "line": 344, "column": 29 } }, "object": { "type": "ThisExpression", - "start": 9987, - "end": 9991, + "start": 10620, + "end": 10624, "loc": { "start": { - "line": 325, + "line": 344, "column": 9 }, "end": { - "line": 325, + "line": 344, "column": 13 } } }, "property": { "type": "Identifier", - "start": 9992, - "end": 10007, + "start": 10625, + "end": 10640, "loc": { "start": { - "line": 325, + "line": 344, "column": 14 }, "end": { - "line": 325, + "line": 344, "column": 29 }, "identifierName": "specificEpithet" @@ -36318,15 +38552,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 10012, - "end": 10021, + "start": 10645, + "end": 10654, "loc": { "start": { - "line": 325, + "line": 344, "column": 34 }, "end": { - "line": 325, + "line": 344, "column": 43 }, "identifierName": "undefined" @@ -36338,58 +38572,58 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 10031, - "end": 10059, + "start": 10664, + "end": 10692, "loc": { "start": { - "line": 326, + "line": 345, "column": 9 }, "end": { - "line": 326, + "line": 345, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 10031, - "end": 10045, + "start": 10664, + "end": 10678, "loc": { "start": { - "line": 326, + "line": 345, "column": 9 }, "end": { - "line": 326, + "line": 345, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 10031, - "end": 10035, + "start": 10664, + "end": 10668, "loc": { "start": { - "line": 326, + "line": 345, "column": 9 }, "end": { - "line": 326, + "line": 345, "column": 13 } } }, "property": { "type": "Identifier", - "start": 10036, - "end": 10045, + "start": 10669, + "end": 10678, "loc": { "start": { - "line": 326, + "line": 345, "column": 14 }, "end": { - "line": 326, + "line": 345, "column": 23 }, "identifierName": "genusPart" @@ -36401,15 +38635,15 @@ "operator": "===", "right": { "type": "Identifier", - 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"start": 10095, - "end": 10167, + "start": 10728, + "end": 10800, "loc": { "start": { - "line": 328, + "line": 347, "column": 11 }, "end": { - "line": 328, + "line": 347, "column": 83 } }, "expressions": [ { "type": "MemberExpression", - "start": 10098, - "end": 10112, + "start": 10731, + "end": 10745, "loc": { "start": { - "line": 328, + "line": 347, "column": 14 }, "end": { - "line": 328, + "line": 347, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 10098, - "end": 10102, + "start": 10731, + "end": 10735, "loc": { "start": { - "line": 328, + "line": 347, "column": 14 }, "end": { - "line": 328, + "line": 347, "column": 18 } } }, "property": { "type": "Identifier", - "start": 10103, - "end": 10112, + "start": 10736, + "end": 10745, "loc": { "start": { - "line": 328, + "line": 347, "column": 19 }, "end": { - "line": 328, + "line": 347, "column": 28 }, "identifierName": "genusPart" @@ -36531,44 +38765,44 @@ }, { "type": "MemberExpression", - "start": 10116, - "end": 10136, + "start": 10749, + "end": 10769, "loc": { "start": { - "line": 328, + "line": 347, "column": 32 }, "end": { - "line": 328, + "line": 347, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 10116, - "end": 10120, + "start": 10749, + "end": 10753, "loc": { "start": { - "line": 328, + "line": 347, "column": 32 }, "end": { - "line": 328, + "line": 347, "column": 36 } } }, "property": { "type": "Identifier", - "start": 10121, - "end": 10136, + "start": 10754, + "end": 10769, "loc": { "start": { - "line": 328, + "line": 347, "column": 37 }, "end": { - "line": 328, + "line": 347, "column": 52 }, "identifierName": "specificEpithet" @@ -36579,44 +38813,44 @@ }, { "type": "MemberExpression", - "start": 10140, - "end": 10165, + "start": 10773, + "end": 10798, "loc": { "start": { - "line": 328, + "line": 347, "column": 56 }, "end": { - "line": 328, + "line": 347, "column": 81 } }, "object": { "type": "ThisExpression", - "start": 10140, - "end": 10144, + "start": 10773, + "end": 10777, "loc": { "start": { - "line": 328, + "line": 347, "column": 56 }, "end": { - "line": 328, + "line": 347, "column": 60 } } }, "property": { "type": "Identifier", - "start": 10145, - "end": 10165, + "start": 10778, + "end": 10798, "loc": { "start": { - "line": 328, + "line": 347, "column": 61 }, "end": { - "line": 328, + "line": 347, "column": 81 }, "identifierName": "infraspecificEpithet" @@ -36629,15 +38863,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 10096, - "end": 10096, + "start": 10729, + "end": 10729, "loc": { "start": { - "line": 328, + "line": 347, "column": 12 }, "end": { - "line": 328, + "line": 347, "column": 12 } }, @@ -36649,15 +38883,15 @@ }, { "type": "TemplateElement", - "start": 10113, - "end": 10114, + "start": 10746, + "end": 10747, "loc": { "start": { - "line": 328, + "line": 347, "column": 29 }, "end": { - "line": 328, + "line": 347, "column": 30 } }, @@ -36669,15 +38903,15 @@ }, { "type": "TemplateElement", - "start": 10137, - "end": 10138, + "start": 10770, + "end": 10771, "loc": { "start": { - "line": 328, + "line": 347, "column": 53 }, "end": { - "line": 328, + "line": 347, "column": 54 } }, @@ -36689,15 +38923,15 @@ }, { "type": "TemplateElement", - "start": 10166, - "end": 10166, + "start": 10799, + "end": 10799, "loc": { "start": { - "line": 328, + "line": 347, "column": 82 }, "end": { - "line": 328, + "line": 347, "column": 82 } }, @@ -36718,15 +38952,15 @@ { "type": "CommentBlock", "value": "* Return the trinomial name if available. ", - "start": 9852, - "end": 9898, + "start": 10485, + "end": 10531, "loc": { "start": { - "line": 321, + "line": 340, "column": 2 }, "end": { - "line": 321, + "line": 340, "column": 48 } } @@ -36736,15 +38970,15 @@ { "type": "CommentBlock", "value": "* Set the trinomial name. ", - "start": 10176, - "end": 10206, + "start": 10809, + "end": 10839, "loc": { "start": { - "line": 331, + "line": 350, "column": 2 }, "end": { - "line": 331, + "line": 350, "column": 32 } } @@ -36753,15 +38987,15 @@ }, { "type": "ClassMethod", - "start": 10209, - "end": 10318, + "start": 10842, + "end": 10951, "loc": { "start": { - "line": 332, + "line": 351, "column": 2 }, "end": { - "line": 335, + "line": 354, "column": 3 } }, @@ -36769,15 +39003,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10213, - "end": 10226, + "start": 10846, + "end": 10859, "loc": { "start": { - "line": 332, + "line": 351, "column": 6 }, "end": { - "line": 332, + "line": 351, "column": 19 }, "identifierName": "trinomialName" @@ -36792,15 +39026,15 @@ "params": [ { "type": "Identifier", - "start": 10227, - "end": 10233, + "start": 10860, + "end": 10866, "loc": { "start": { - "line": 332, + "line": 351, "column": 20 }, "end": { - "line": 332, + "line": 351, "column": 26 }, "identifierName": "trinom" @@ -36810,102 +39044,102 @@ ], "body": { "type": "BlockStatement", - 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"line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 10241, - "end": 10245, + "start": 10874, + "end": 10878, "loc": { "start": { - "line": 333, + "line": 352, "column": 4 }, "end": { - "line": 333, + "line": 352, "column": 8 } } }, "property": { "type": "Identifier", - "start": 10246, - "end": 10252, + "start": 10879, + "end": 10885, "loc": { "start": { - "line": 333, + "line": 352, "column": 9 }, "end": { - "line": 333, + "line": 352, "column": 15 }, "identifierName": "txname" @@ -36916,15 +39150,15 @@ }, "property": { "type": "Identifier", - "start": 10253, - "end": 10262, + "start": 10886, + "end": 10895, "loc": { "start": { - "line": 333, + "line": 352, "column": 16 }, "end": { - "line": 333, + "line": 352, "column": 25 }, "identifierName": "uninomial" @@ -36935,15 +39169,15 @@ }, "right": { "type": "Identifier", - "start": 10265, - "end": 10274, + "start": 10898, + "end": 10907, "loc": { "start": { - "line": 333, + "line": 352, "column": 28 }, "end": { - "line": 333, + "line": 352, "column": 37 }, "identifierName": "undefined" @@ -36954,87 +39188,87 @@ }, { "type": "ExpressionStatement", - "start": 10280, - "end": 10314, + "start": 10913, + "end": 10947, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 10280, - "end": 10313, + "start": 10913, + "end": 10946, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10280, - "end": 10304, + "start": 10913, + "end": 10937, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 28 } }, "object": { "type": "MemberExpression", - "start": 10280, - "end": 10291, + "start": 10913, + "end": 10924, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 10280, - "end": 10284, + "start": 10913, + "end": 10917, "loc": { "start": { - "line": 334, + "line": 353, "column": 4 }, "end": { - "line": 334, + "line": 353, "column": 8 } } }, "property": { "type": "Identifier", - "start": 10285, - "end": 10291, + "start": 10918, + "end": 10924, "loc": { "start": { - "line": 334, + "line": 353, "column": 9 }, "end": { - "line": 334, + "line": 353, "column": 15 }, "identifierName": "txname" @@ -37045,15 +39279,15 @@ }, "property": { "type": "Identifier", - "start": 10292, - "end": 10304, + "start": 10925, + "end": 10937, "loc": { "start": { - "line": 334, + "line": 353, "column": 16 }, "end": { - "line": 334, + "line": 353, "column": 28 }, "identifierName": "nameComplete" @@ -37064,15 +39298,15 @@ }, "right": { "type": "Identifier", - "start": 10307, - "end": 10313, + "start": 10940, + "end": 10946, "loc": { "start": { - "line": 334, + "line": 353, "column": 31 }, "end": { - "line": 334, + "line": 353, "column": 37 }, "identifierName": "trinom" @@ -37089,15 +39323,15 @@ { "type": "CommentBlock", "value": "* Set the trinomial name. ", - "start": 10176, - "end": 10206, + "start": 10809, + "end": 10839, "loc": { "start": { - "line": 331, + "line": 350, "column": 2 }, "end": { - "line": 331, + "line": 350, "column": 32 } } @@ -37107,15 +39341,15 @@ { "type": "CommentBlock", "value": "* Return the genus part of this scientific name if available. ", - "start": 10322, - "end": 10388, + "start": 10955, + "end": 11021, "loc": { "start": { - "line": 337, + "line": 356, "column": 2 }, "end": { - "line": 337, + "line": 356, "column": 68 } } @@ -37124,15 +39358,15 @@ }, { "type": "ClassMethod", - "start": 10391, - "end": 10879, + "start": 11024, + "end": 11512, "loc": { "start": { - "line": 338, + "line": 357, "column": 2 }, "end": { - "line": 353, + "line": 372, "column": 3 } }, @@ -37140,15 +39374,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10395, - "end": 10404, + "start": 11028, + "end": 11037, "loc": { "start": { - "line": 338, + "line": 357, "column": 6 }, "end": { - "line": 338, + "line": 357, "column": 15 }, "identifierName": "genusPart" @@ -37163,58 +39397,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 10407, - "end": 10879, + "start": 11040, + "end": 11512, "loc": { "start": { - "line": 338, + "line": 357, "column": 18 }, "end": { - "line": 353, + "line": 372, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 10456, - "end": 10520, + "start": 11089, + "end": 11153, "loc": { "start": { - "line": 340, + "line": 359, "column": 4 }, "end": { - "line": 340, + "line": 359, "column": 68 } }, "test": { "type": "CallExpression", - "start": 10460, - "end": 10489, + "start": 11093, + "end": 11122, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 37 } }, "callee": { "type": "Identifier", - "start": 10460, - "end": 10463, + "start": 11093, + "end": 11096, "loc": { "start": { - "line": 340, + "line": 359, "column": 8 }, "end": { - "line": 340, + "line": 359, "column": 11 }, "identifierName": "has" @@ -37225,44 +39459,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 10464, - "end": 10475, + "start": 11097, + "end": 11108, "loc": { "start": { - "line": 340, + "line": 359, "column": 12 }, "end": { - "line": 340, + "line": 359, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 10464, - "end": 10468, + "start": 11097, + "end": 11101, "loc": { "start": { - "line": 340, + "line": 359, "column": 12 }, "end": { - "line": 340, + "line": 359, "column": 16 } } }, "property": { "type": "Identifier", - "start": 10469, - "end": 10475, + "start": 11102, + "end": 11108, "loc": { "start": { - "line": 340, + "line": 359, "column": 17 }, "end": { - "line": 340, + "line": 359, "column": 23 }, "identifierName": "txname" @@ -37273,15 +39507,15 @@ }, { "type": "StringLiteral", - "start": 10477, - "end": 10488, + "start": 11110, + "end": 11121, "loc": { "start": { - "line": 340, + "line": 359, "column": 25 }, "end": { - "line": 340, + "line": 359, "column": 36 } }, @@ -37296,72 +39530,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 10491, - "end": 10520, + "start": 11124, + "end": 11153, "loc": { "start": { - "line": 340, + "line": 359, "column": 39 }, "end": { - "line": 340, + "line": 359, "column": 68 } }, "argument": { "type": "MemberExpression", - "start": 10498, - "end": 10519, + "start": 11131, + "end": 11152, "loc": { "start": { - "line": 340, + "line": 359, "column": 46 }, "end": { - "line": 340, + "line": 359, "column": 67 } }, "object": { "type": "MemberExpression", - "start": 10498, - "end": 10509, + "start": 11131, + "end": 11142, "loc": { "start": { - "line": 340, + "line": 359, "column": 46 }, "end": { - "line": 340, + "line": 359, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 10498, - "end": 10502, + "start": 11131, + "end": 11135, "loc": { "start": { - "line": 340, + "line": 359, "column": 46 }, "end": { - "line": 340, + "line": 359, "column": 50 } } }, "property": { "type": "Identifier", - "start": 10503, - "end": 10509, + "start": 11136, + "end": 11142, "loc": { "start": { - "line": 340, + "line": 359, "column": 51 }, "end": { - "line": 340, + "line": 359, "column": 57 }, "identifierName": "txname" @@ -37372,15 +39606,15 @@ }, "property": { "type": "Identifier", - "start": 10510, - "end": 10519, + "start": 11143, + "end": 11152, "loc": { "start": { - "line": 340, + "line": 359, "column": 58 }, "end": { - "line": 340, + "line": 359, "column": 67 }, "identifierName": "genusPart" @@ -37396,15 +39630,15 @@ { "type": "CommentLine", "value": " Try to read the genus if available.", - "start": 10413, - "end": 10451, + "start": 11046, + "end": 11084, "loc": { "start": { - "line": 339, + "line": 358, "column": 4 }, "end": { - "line": 339, + "line": 358, "column": 42 } } @@ -37414,15 +39648,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 10526, - "end": 10603, + "start": 11159, + "end": 11236, "loc": { "start": { - "line": 342, + "line": 361, "column": 4 }, "end": { - "line": 342, + "line": 361, "column": 81 } } @@ -37430,15 +39664,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 10608, - "end": 10619, + "start": 11241, + "end": 11252, "loc": { "start": { - "line": 343, + "line": 362, "column": 4 }, "end": { - "line": 343, + "line": 362, "column": 15 } } @@ -37447,57 +39681,57 @@ }, { "type": "IfStatement", - "start": 10624, - "end": 10852, + "start": 11257, + "end": 11485, "loc": { "start": { - "line": 344, + "line": 363, "column": 4 }, "end": { - "line": 350, + "line": 369, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 10628, - "end": 10652, + "start": 11261, + "end": 11285, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 10628, - "end": 10639, + "start": 11261, + "end": 11272, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 10628, - "end": 10632, + "start": 11261, + "end": 11265, "loc": { "start": { - "line": 344, + "line": 363, "column": 8 }, "end": { - "line": 344, + "line": 363, "column": 12 } }, @@ -37505,15 +39739,15 @@ }, "property": { "type": "Identifier", - "start": 10633, - "end": 10639, + "start": 11266, + "end": 11272, "loc": { "start": { - "line": 344, + "line": 363, "column": 13 }, "end": { - "line": 344, + "line": 363, "column": 19 }, "identifierName": "txname" @@ -37525,15 +39759,15 @@ }, "property": { "type": "Identifier", - "start": 10640, - "end": 10652, + "start": 11273, + "end": 11285, "loc": { "start": { - "line": 344, + "line": 363, "column": 20 }, "end": { - "line": 344, + "line": 363, "column": 32 }, "identifierName": "nameComplete" @@ -37545,59 +39779,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 10654, - "end": 10852, + "start": 11287, + "end": 11485, "loc": { "start": { - "line": 344, + "line": 363, "column": 34 }, "end": { - "line": 350, + "line": 369, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 10662, - "end": 10785, + "start": 11295, + "end": 11418, "loc": { "start": { - "line": 345, + "line": 364, "column": 6 }, "end": { - "line": 348, + "line": 367, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 10668, - "end": 10784, + "start": 11301, + "end": 11417, "loc": { "start": { - "line": 345, + "line": 364, "column": 12 }, "end": { - "line": 348, + "line": 367, "column": 7 } }, "id": { "type": "Identifier", - "start": 10668, - "end": 10674, + "start": 11301, + "end": 11307, "loc": { "start": { - "line": 345, + "line": 364, "column": 12 }, "end": { - "line": 345, + "line": 364, "column": 18 }, "identifierName": "txname" @@ -37606,43 +39840,43 @@ }, "init": { "type": "CallExpression", - "start": 10677, - "end": 10784, + "start": 11310, + "end": 11417, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 348, + "line": 367, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 10677, - "end": 10710, + "start": 11310, + "end": 11343, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 54 } }, "object": { "type": "Identifier", - "start": 10677, - "end": 10693, + "start": 11310, + "end": 11326, "loc": { "start": { - "line": 345, + "line": 364, "column": 21 }, "end": { - "line": 345, + "line": 364, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -37651,15 +39885,15 @@ }, "property": { "type": "Identifier", - "start": 10694, - "end": 10710, + "start": 11327, + "end": 11343, "loc": { "start": { - 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"line": 346, + "line": 365, "column": 19 }, "identifierName": "txname" @@ -37733,15 +39967,15 @@ }, "property": { "type": "Identifier", - "start": 10732, - "end": 10744, + "start": 11365, + "end": 11377, "loc": { "start": { - "line": 346, + "line": 365, "column": 20 }, "end": { - "line": 346, + "line": 365, "column": 32 }, "identifierName": "nameComplete" @@ -37752,44 +39986,44 @@ }, { "type": "MemberExpression", - "start": 10754, - "end": 10776, + "start": 11387, + "end": 11409, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 10754, - "end": 10758, + "start": 11387, + "end": 11391, "loc": { "start": { - "line": 347, + "line": 366, "column": 8 }, "end": { - "line": 347, + "line": 366, "column": 12 } } }, "property": { "type": "Identifier", - "start": 10759, - "end": 10776, + "start": 11392, + "end": 11409, "loc": { "start": { - "line": 347, + "line": 366, "column": 13 }, "end": { - "line": 347, + "line": 366, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -37806,43 +40040,43 @@ }, { "type": "IfStatement", - "start": 10792, - "end": 10846, + "start": 11425, + "end": 11479, "loc": { "start": { - "line": 349, + "line": 368, "column": 6 }, "end": { - "line": 349, + "line": 368, "column": 60 } }, "test": { "type": "CallExpression", - "start": 10796, - "end": 10820, + "start": 11429, + "end": 11453, "loc": { "start": { - "line": 349, + "line": 368, "column": 10 }, "end": { - "line": 349, + "line": 368, "column": 34 } }, "callee": { "type": "Identifier", - "start": 10796, - "end": 10799, + "start": 11429, + "end": 11432, "loc": { "start": { - "line": 349, + "line": 368, "column": 10 }, "end": { - "line": 349, + "line": 368, "column": 13 }, "identifierName": "has" @@ -37852,15 +40086,15 @@ "arguments": [ { "type": "Identifier", - "start": 10800, - "end": 10806, + "start": 11433, + "end": 11439, "loc": { "start": { - "line": 349, + "line": 368, "column": 14 }, "end": { - "line": 349, + "line": 368, "column": 20 }, "identifierName": "txname" @@ -37869,15 +40103,15 @@ }, { "type": "StringLiteral", - "start": 10808, - "end": 10819, + "start": 11441, + "end": 11452, "loc": { "start": { - "line": 349, + "line": 368, "column": 22 }, "end": { - "line": 349, + "line": 368, "column": 33 } }, @@ -37891,43 +40125,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 10822, - "end": 10846, + "start": 11455, + "end": 11479, "loc": { "start": { - "line": 349, + "line": 368, "column": 36 }, "end": { - "line": 349, + "line": 368, "column": 60 } }, "argument": { "type": "MemberExpression", - "start": 10829, - "end": 10845, + "start": 11462, + "end": 11478, "loc": { "start": { - "line": 349, + "line": 368, "column": 43 }, "end": { - "line": 349, + "line": 368, "column": 59 } }, "object": { "type": "Identifier", - "start": 10829, - "end": 10835, + "start": 11462, + "end": 11468, "loc": { "start": { - "line": 349, + "line": 368, "column": 43 }, "end": { - "line": 349, + "line": 368, "column": 49 }, "identifierName": "txname" @@ -37936,15 +40170,15 @@ }, "property": { "type": "Identifier", - "start": 10836, - "end": 10845, + "start": 11469, + "end": 11478, "loc": { "start": { - "line": 349, + "line": 368, "column": 50 }, "end": { - "line": 349, + "line": 368, "column": 59 }, "identifierName": "genusPart" @@ -37964,15 +40198,15 @@ { "type": "CommentLine", "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 10526, - "end": 10603, + "start": 11159, + "end": 11236, "loc": { "start": { - "line": 342, + "line": 361, "column": 4 }, "end": { - "line": 342, + "line": 361, "column": 81 } } @@ -37980,15 +40214,15 @@ { "type": "CommentLine", "value": " from it.", - "start": 10608, - "end": 10619, + "start": 11241, + "end": 11252, "loc": { "start": { - "line": 343, + "line": 362, "column": 4 }, "end": { - "line": 343, + "line": 362, "column": 15 } } @@ -37997,29 +40231,29 @@ }, { "type": "ReturnStatement", - "start": 10858, - "end": 10875, + "start": 11491, + "end": 11508, "loc": { "start": { - "line": 352, + "line": 371, "column": 4 }, "end": { - "line": 352, + "line": 371, "column": 21 } }, "argument": { "type": "Identifier", - "start": 10865, - "end": 10874, + "start": 11498, + "end": 11507, "loc": { "start": { - "line": 352, + "line": 371, "column": 11 }, "end": { - "line": 352, + "line": 371, "column": 20 }, "identifierName": "undefined" @@ -38035,15 +40269,15 @@ { "type": "CommentBlock", "value": "* Return the genus part of this scientific name if available. ", - "start": 10322, - "end": 10388, + "start": 10955, + "end": 11021, "loc": { "start": { - "line": 337, + "line": 356, "column": 2 }, "end": { - "line": 337, + "line": 356, "column": 68 } } @@ -38053,15 +40287,15 @@ { "type": "CommentBlock", "value": "* Set the genus part of this name. ", - "start": 10883, - "end": 10922, + "start": 11516, + "end": 11555, "loc": { "start": { - "line": 355, + "line": 374, "column": 2 }, "end": { - "line": 355, + "line": 374, "column": 41 } } @@ -38070,15 +40304,15 @@ }, { "type": "ClassMethod", - "start": 10925, - "end": 11257, + "start": 11558, + "end": 11890, "loc": { "start": { - "line": 356, + "line": 375, "column": 2 }, "end": { - "line": 365, + "line": 384, "column": 3 } }, @@ -38086,15 +40320,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 10929, - "end": 10938, + "start": 11562, + "end": 11571, "loc": { "start": { - "line": 356, + "line": 375, "column": 6 }, "end": { - "line": 356, + "line": 375, "column": 15 }, "identifierName": "genusPart" @@ -38109,15 +40343,15 @@ "params": [ { "type": "Identifier", - "start": 10939, - "end": 10944, + "start": 11572, + "end": 11577, "loc": { "start": { - "line": 356, + "line": 375, "column": 16 }, "end": { - "line": 356, + "line": 375, "column": 21 }, "identifierName": "genus" @@ -38127,102 +40361,102 @@ ], "body": { "type": "BlockStatement", - "start": 10946, - "end": 11257, + "start": 11579, + "end": 11890, "loc": { "start": { - "line": 356, + "line": 375, "column": 23 }, "end": { - "line": 365, + "line": 384, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 10952, - "end": 10982, + "start": 11585, + "end": 11615, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 34 } }, "expression": { "type": "AssignmentExpression", - "start": 10952, - "end": 10981, + "start": 11585, + "end": 11614, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 33 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 10952, - "end": 10973, + "start": 11585, + "end": 11606, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 25 } }, "object": { "type": "MemberExpression", - "start": 10952, - "end": 10963, + "start": 11585, + "end": 11596, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 10952, - "end": 10956, + "start": 11585, + "end": 11589, "loc": { "start": { - "line": 357, + "line": 376, "column": 4 }, "end": { - "line": 357, + "line": 376, "column": 8 } } }, "property": { "type": "Identifier", - "start": 10957, - "end": 10963, + "start": 11590, + "end": 11596, "loc": { "start": { - "line": 357, + "line": 376, "column": 9 }, "end": { - "line": 357, + "line": 376, "column": 15 }, "identifierName": "txname" @@ -38233,15 +40467,15 @@ }, "property": { "type": "Identifier", - "start": 10964, - "end": 10973, + "start": 11597, + "end": 11606, "loc": { "start": { - "line": 357, + "line": 376, "column": 16 }, "end": { - "line": 357, + "line": 376, "column": 25 }, "identifierName": "genusPart" @@ -38252,15 +40486,15 @@ }, "right": { "type": "Identifier", - "start": 10976, - "end": 10981, + "start": 11609, + "end": 11614, "loc": { "start": { - "line": 357, + "line": 376, "column": 28 }, "end": { - "line": 357, + "line": 376, "column": 33 }, "identifierName": "genus" @@ -38271,58 +40505,58 @@ }, { "type": "IfStatement", - "start": 10987, - "end": 11253, + "start": 11620, + "end": 11886, "loc": { "start": { - "line": 358, + "line": 377, "column": 4 }, "end": { - "line": 364, + "line": 383, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 10991, - "end": 11011, + "start": 11624, + "end": 11644, "loc": { "start": { - "line": 358, + "line": 377, "column": 8 }, "end": { - "line": 358, + "line": 377, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 10991, - "end": 10995, + "start": 11624, + "end": 11628, "loc": { "start": { - "line": 358, + "line": 377, "column": 8 }, "end": { - "line": 358, + "line": 377, "column": 12 } } }, "property": { "type": "Identifier", - "start": 10996, - "end": 11011, + "start": 11629, + "end": 11644, "loc": { "start": { - "line": 358, + "line": 377, "column": 13 }, "end": { - "line": 358, + "line": 377, "column": 28 }, "identifierName": "specificEpithet" @@ -38333,73 +40567,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 11013, - "end": 11253, + "start": 11646, + "end": 11886, "loc": { "start": { - "line": 358, + "line": 377, "column": 30 }, "end": { - "line": 364, + "line": 383, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 11021, - "end": 11247, + "start": 11654, + "end": 11880, "loc": { "start": { - "line": 359, + "line": 378, "column": 6 }, "end": { - "line": 363, + "line": 382, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 11025, - "end": 11050, + "start": 11658, + "end": 11683, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 11025, - "end": 11029, + "start": 11658, + "end": 11662, "loc": { "start": { - "line": 359, + "line": 378, "column": 10 }, "end": { - "line": 359, + "line": 378, "column": 14 } } }, "property": { "type": "Identifier", - "start": 11030, - "end": 11050, + "start": 11663, + "end": 11683, "loc": { "start": { - "line": 359, + "line": 378, "column": 15 }, "end": { - "line": 359, + "line": 378, "column": 35 }, "identifierName": "infraspecificEpithet" @@ -38410,102 +40644,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 11052, - "end": 11161, + "start": 11685, + "end": 11794, "loc": { "start": { - "line": 359, + "line": 378, "column": 37 }, "end": { - "line": 361, + "line": 380, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 11062, - "end": 11153, + "start": 11695, + "end": 11786, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 99 } }, "expression": { "type": "AssignmentExpression", - "start": 11062, - "end": 11152, + "start": 11695, + "end": 11785, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 98 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11062, - "end": 11086, + "start": 11695, + "end": 11719, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 11062, - "end": 11073, + "start": 11695, + "end": 11706, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 11062, - "end": 11066, + "start": 11695, + "end": 11699, "loc": { "start": { - "line": 360, + "line": 379, "column": 8 }, "end": { - "line": 360, + "line": 379, "column": 12 } } }, "property": { "type": "Identifier", - "start": 11067, - "end": 11073, + "start": 11700, + "end": 11706, "loc": { "start": { - "line": 360, + "line": 379, "column": 13 }, "end": { - "line": 360, + "line": 379, "column": 19 }, "identifierName": "txname" @@ -38516,15 +40750,15 @@ }, "property": { "type": "Identifier", - "start": 11074, - "end": 11086, + "start": 11707, + "end": 11719, "loc": { "start": { - "line": 360, + "line": 379, "column": 20 }, "end": { - "line": 360, + "line": 379, "column": 32 }, "identifierName": "nameComplete" @@ -38535,30 +40769,30 @@ }, "right": { "type": "TemplateLiteral", - "start": 11089, - "end": 11152, + "start": 11722, + "end": 11785, "loc": { "start": { - "line": 360, + "line": 379, "column": 35 }, "end": { - "line": 360, + "line": 379, "column": 98 } }, "expressions": [ { "type": "Identifier", - "start": 11092, - "end": 11097, + "start": 11725, + "end": 11730, "loc": { "start": { - "line": 360, + "line": 379, "column": 38 }, "end": { - "line": 360, + "line": 379, "column": 43 }, "identifierName": "genus" @@ -38567,44 +40801,44 @@ }, { "type": "MemberExpression", - "start": 11101, - "end": 11121, + "start": 11734, + "end": 11754, "loc": { "start": { - "line": 360, + "line": 379, "column": 47 }, "end": { - "line": 360, + "line": 379, "column": 67 } }, "object": { "type": "ThisExpression", - "start": 11101, - "end": 11105, + "start": 11734, + "end": 11738, "loc": { "start": { - "line": 360, + "line": 379, "column": 47 }, "end": { - "line": 360, + "line": 379, "column": 51 } } }, "property": { "type": "Identifier", - "start": 11106, - "end": 11121, + "start": 11739, + "end": 11754, "loc": { "start": { - "line": 360, + "line": 379, "column": 52 }, "end": { - "line": 360, + "line": 379, "column": 67 }, "identifierName": "specificEpithet" @@ -38615,44 +40849,44 @@ }, { "type": "MemberExpression", - "start": 11125, - "end": 11150, + "start": 11758, + "end": 11783, "loc": { "start": { - "line": 360, + "line": 379, "column": 71 }, "end": { - "line": 360, + "line": 379, "column": 96 } }, "object": { "type": "ThisExpression", - "start": 11125, - "end": 11129, + "start": 11758, + "end": 11762, "loc": { "start": { - "line": 360, + "line": 379, "column": 71 }, "end": { - "line": 360, + "line": 379, "column": 75 } } }, "property": { "type": "Identifier", - "start": 11130, - "end": 11150, + "start": 11763, + "end": 11783, "loc": { "start": { - "line": 360, + "line": 379, "column": 76 }, "end": { - "line": 360, + "line": 379, "column": 96 }, "identifierName": "infraspecificEpithet" @@ -38665,15 +40899,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 11090, - "end": 11090, + "start": 11723, + "end": 11723, "loc": { "start": { - "line": 360, + "line": 379, "column": 36 }, "end": { - "line": 360, + "line": 379, "column": 36 } }, @@ -38685,15 +40919,15 @@ }, { "type": "TemplateElement", - "start": 11098, - "end": 11099, + "start": 11731, + "end": 11732, "loc": { "start": { - "line": 360, + "line": 379, "column": 44 }, "end": { - "line": 360, + "line": 379, "column": 45 } }, @@ -38705,15 +40939,15 @@ }, { "type": "TemplateElement", - "start": 11122, - "end": 11123, + "start": 11755, + "end": 11756, "loc": { "start": { - "line": 360, + "line": 379, "column": 68 }, "end": { - "line": 360, + "line": 379, "column": 69 } }, @@ -38725,15 +40959,15 @@ }, { "type": "TemplateElement", - "start": 11151, - "end": 11151, + "start": 11784, + "end": 11784, "loc": { "start": { - "line": 360, + "line": 379, "column": 97 }, "end": { - "line": 360, + "line": 379, "column": 97 } }, @@ -38752,102 +40986,102 @@ }, "alternate": { "type": "BlockStatement", - "start": 11167, - "end": 11247, + "start": 11800, + "end": 11880, "loc": { "start": { - "line": 361, + "line": 380, "column": 13 }, "end": { - "line": 363, + "line": 382, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 11177, - "end": 11239, + "start": 11810, + "end": 11872, "loc": { "start": { - "line": 362, + "line": 381, "column": 8 }, "end": { - "line": 362, + "line": 381, "column": 70 } }, "expression": { "type": "AssignmentExpression", - "start": 11177, - "end": 11238, + "start": 11810, + "end": 11871, "loc": { "start": { - "line": 362, + "line": 381, "column": 8 }, "end": { - "line": 362, + "line": 381, "column": 69 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 11177, - "end": 11201, + "start": 11810, + "end": 11834, "loc": { "start": { - "line": 362, + "line": 381, "column": 8 }, "end": { - "line": 362, + "line": 381, "column": 32 } }, "object": { "type": "MemberExpression", - 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"start": 11204, - "end": 11238, + "start": 11837, + "end": 11871, "loc": { "start": { - "line": 362, + "line": 381, "column": 35 }, "end": { - "line": 362, + "line": 381, "column": 69 } }, "expressions": [ { "type": "Identifier", - "start": 11207, - "end": 11212, + "start": 11840, + "end": 11845, "loc": { "start": { - "line": 362, + "line": 381, "column": 38 }, "end": { - "line": 362, + "line": 381, "column": 43 }, "identifierName": "genus" @@ -38909,44 +41143,44 @@ }, { "type": "MemberExpression", - "start": 11216, - "end": 11236, + "start": 11849, + "end": 11869, "loc": { "start": { - "line": 362, + "line": 381, "column": 47 }, "end": { - "line": 362, + "line": 381, "column": 67 } }, "object": { "type": "ThisExpression", - "start": 11216, - "end": 11220, + "start": 11849, + "end": 11853, "loc": { "start": { - "line": 362, + "line": 381, "column": 47 }, "end": { - "line": 362, + "line": 381, "column": 51 } } }, "property": { "type": "Identifier", - "start": 11221, - "end": 11236, + "start": 11854, + "end": 11869, "loc": { "start": { - "line": 362, + "line": 381, "column": 52 }, "end": { - "line": 362, + "line": 381, "column": 67 }, "identifierName": "specificEpithet" @@ -38959,15 +41193,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 11205, - "end": 11205, + "start": 11838, + "end": 11838, "loc": { "start": { - "line": 362, + "line": 381, "column": 36 }, "end": { - "line": 362, + "line": 381, "column": 36 } }, @@ -38979,15 +41213,15 @@ }, { "type": "TemplateElement", - "start": 11213, - "end": 11214, + "start": 11846, + "end": 11847, "loc": { "start": { - "line": 362, + "line": 381, "column": 44 }, "end": { - "line": 362, + "line": 381, "column": 45 } }, @@ -38999,15 +41233,15 @@ }, { "type": "TemplateElement", - "start": 11237, - "end": 11237, + "start": 11870, + "end": 11870, "loc": { "start": { - "line": 362, + "line": 381, "column": 68 }, "end": { - "line": 362, + "line": 381, "column": 68 } }, @@ -39038,15 +41272,15 @@ { "type": "CommentBlock", "value": "* Set the genus part of this name. ", - "start": 10883, - "end": 10922, + "start": 11516, + "end": 11555, "loc": { "start": { - "line": 355, + "line": 374, "column": 2 }, "end": { - "line": 355, + "line": 374, "column": 41 } } @@ -39056,15 +41290,15 @@ { "type": "CommentBlock", "value": "* Return the specific epithet of this scientific name if available. ", - "start": 11261, - "end": 11333, + "start": 11894, + "end": 11966, "loc": { "start": { - "line": 367, + "line": 386, "column": 2 }, "end": { - "line": 367, + "line": 386, "column": 74 } } @@ -39073,15 +41307,15 @@ }, { "type": "ClassMethod", - "start": 11336, - "end": 11873, + "start": 11969, + "end": 12506, "loc": { "start": { - "line": 368, + "line": 387, "column": 2 }, "end": { - "line": 383, + "line": 402, "column": 3 } }, @@ -39089,15 +41323,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11340, - "end": 11355, + "start": 11973, + "end": 11988, "loc": { "start": { - "line": 368, + "line": 387, "column": 6 }, "end": { - "line": 368, + "line": 387, "column": 21 }, "identifierName": "specificEpithet" @@ -39112,58 +41346,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 11358, - "end": 11873, + "start": 11991, + "end": 12506, "loc": { "start": { - "line": 368, + "line": 387, "column": 24 }, "end": { - "line": 383, + "line": 402, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 11418, - "end": 11494, + "start": 12051, + "end": 12127, "loc": { "start": { - "line": 370, + "line": 389, "column": 4 }, "end": { - "line": 370, + "line": 389, "column": 80 } }, "test": { "type": "CallExpression", - "start": 11422, - "end": 11457, + "start": 12055, + "end": 12090, "loc": { "start": { - "line": 370, + "line": 389, "column": 8 }, "end": { - "line": 370, + "line": 389, "column": 43 } }, "callee": { "type": "Identifier", - "start": 11422, - "end": 11425, + "start": 12055, + "end": 12058, "loc": { "start": { - "line": 370, + "line": 389, "column": 8 }, "end": { - "line": 370, + "line": 389, "column": 11 }, "identifierName": "has" @@ -39174,44 +41408,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 11426, - "end": 11437, + "start": 12059, + "end": 12070, "loc": { "start": { - "line": 370, + "line": 389, "column": 12 }, "end": { - "line": 370, + "line": 389, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 11426, - "end": 11430, + "start": 12059, + "end": 12063, "loc": { "start": { - "line": 370, + "line": 389, "column": 12 }, "end": { - "line": 370, + "line": 389, "column": 16 } } }, "property": { "type": "Identifier", - "start": 11431, - "end": 11437, + "start": 12064, + "end": 12070, "loc": { "start": { - "line": 370, + "line": 389, "column": 17 }, "end": { - "line": 370, + "line": 389, "column": 23 }, "identifierName": "txname" @@ -39222,15 +41456,15 @@ }, { "type": "StringLiteral", - "start": 11439, - "end": 11456, + "start": 12072, + "end": 12089, "loc": { "start": { - "line": 370, + "line": 389, "column": 25 }, "end": { - "line": 370, + "line": 389, "column": 42 } }, @@ -39245,72 +41479,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 11459, - "end": 11494, + "start": 12092, + "end": 12127, "loc": { "start": { - "line": 370, + "line": 389, "column": 45 }, "end": { - "line": 370, + "line": 389, "column": 80 } }, "argument": { "type": "MemberExpression", - "start": 11466, - "end": 11493, + "start": 12099, + "end": 12126, "loc": { "start": { - "line": 370, + "line": 389, "column": 52 }, "end": { - "line": 370, + "line": 389, "column": 79 } }, "object": { "type": "MemberExpression", - "start": 11466, - "end": 11477, + "start": 12099, + "end": 12110, "loc": { "start": { - "line": 370, + "line": 389, "column": 52 }, "end": { - "line": 370, + "line": 389, "column": 63 } }, "object": { "type": "ThisExpression", - "start": 11466, - "end": 11470, + "start": 12099, + "end": 12103, "loc": { "start": { - "line": 370, + "line": 389, "column": 52 }, "end": { - "line": 370, + "line": 389, "column": 56 } } }, "property": { "type": "Identifier", - "start": 11471, - "end": 11477, + "start": 12104, + "end": 12110, "loc": { "start": { - "line": 370, + "line": 389, "column": 57 }, "end": { - "line": 370, + "line": 389, "column": 63 }, "identifierName": "txname" @@ -39321,15 +41555,15 @@ }, "property": { "type": "Identifier", - "start": 11478, - "end": 11493, + "start": 12111, + "end": 12126, "loc": { "start": { - "line": 370, + "line": 389, "column": 64 }, "end": { - "line": 370, + "line": 389, "column": 79 }, "identifierName": "specificEpithet" @@ -39345,15 +41579,15 @@ { "type": "CommentLine", "value": " Try to read the specific epithet if available.", - "start": 11364, - "end": 11413, + "start": 11997, + "end": 12046, "loc": { "start": { - "line": 369, + "line": 388, "column": 4 }, "end": { - "line": 369, + "line": 388, "column": 53 } } @@ -39363,15 +41597,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 11500, - "end": 11572, + "start": 12133, + "end": 12205, "loc": { "start": { - "line": 372, + "line": 391, "column": 4 }, "end": { - "line": 372, + "line": 391, "column": 76 } } @@ -39379,15 +41613,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 11577, - "end": 11615, + "start": 12210, + "end": 12248, "loc": { "start": { - "line": 373, + "line": 392, "column": 4 }, "end": { - "line": 373, + "line": 392, "column": 42 } } @@ -39396,43 +41630,43 @@ }, { "type": "IfStatement", - "start": 11620, - "end": 11846, + "start": 12253, + "end": 12479, "loc": { "start": { - "line": 374, + "line": 393, "column": 4 }, "end": { - "line": 380, + "line": 399, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 11624, - "end": 11641, + "start": 12257, + "end": 12274, "loc": { "start": { - "line": 374, + "line": 393, "column": 8 }, "end": { - "line": 374, + "line": 393, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 11624, - "end": 11628, + "start": 12257, + "end": 12261, "loc": { "start": { - "line": 374, + "line": 393, "column": 8 }, "end": { - "line": 374, + "line": 393, "column": 12 } }, @@ -39440,15 +41674,15 @@ }, "property": { "type": "Identifier", - "start": 11629, - "end": 11641, + "start": 12262, + "end": 12274, "loc": { "start": { - "line": 374, + "line": 393, "column": 13 }, "end": { - "line": 374, + "line": 393, "column": 25 }, "identifierName": "nameComplete" @@ -39460,59 +41694,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 11643, - "end": 11846, + "start": 12276, + "end": 12479, "loc": { "start": { - "line": 374, + "line": 393, "column": 27 }, "end": { - "line": 380, + "line": 399, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 11651, - "end": 11767, + "start": 12284, + "end": 12400, "loc": { "start": { - "line": 375, + "line": 394, "column": 6 }, "end": { - "line": 378, + "line": 397, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 11657, - "end": 11766, + "start": 12290, + "end": 12399, "loc": { "start": { - "line": 375, + "line": 394, "column": 12 }, "end": { - "line": 378, + "line": 397, "column": 7 } }, "id": { "type": "Identifier", - "start": 11657, - "end": 11663, + "start": 12290, + "end": 12296, "loc": { "start": { - "line": 375, + "line": 394, "column": 12 }, "end": { - "line": 375, + "line": 394, "column": 18 }, "identifierName": "txname" @@ -39521,43 +41755,43 @@ }, "init": { "type": "CallExpression", - "start": 11666, - "end": 11766, + "start": 12299, + "end": 12399, "loc": { "start": { - "line": 375, + "line": 394, "column": 21 }, "end": { - "line": 378, + "line": 397, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 11666, - "end": 11699, + "start": 12299, + "end": 12332, "loc": { "start": { - "line": 375, + "line": 394, "column": 21 }, "end": { - "line": 375, + "line": 394, "column": 54 } }, "object": { "type": "Identifier", - "start": 11666, - "end": 11682, + "start": 12299, + "end": 12315, "loc": { "start": { - "line": 375, + "line": 394, "column": 21 }, "end": { - "line": 375, + "line": 394, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -39566,15 +41800,15 @@ }, "property": { "type": "Identifier", - "start": 11683, - "end": 11699, + "start": 12316, + "end": 12332, "loc": { "start": { - "line": 375, + "line": 394, "column": 38 }, "end": { - "line": 375, + "line": 394, "column": 54 }, "identifierName": "fromVerbatimName" @@ -39586,44 +41820,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 11709, - "end": 11726, + "start": 12342, + "end": 12359, "loc": { "start": { - "line": 376, + "line": 395, "column": 8 }, "end": { - "line": 376, + "line": 395, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 11709, - "end": 11713, + "start": 12342, + "end": 12346, "loc": { "start": { - "line": 376, + "line": 395, "column": 8 }, "end": { - "line": 376, + "line": 395, "column": 12 } } }, "property": { "type": "Identifier", - "start": 11714, - "end": 11726, + "start": 12347, + "end": 12359, "loc": { "start": { - "line": 376, + "line": 395, "column": 13 }, "end": { - "line": 376, + "line": 395, "column": 25 }, "identifierName": "nameComplete" @@ -39634,44 +41868,44 @@ }, { "type": "MemberExpression", - "start": 11736, - "end": 11758, + "start": 12369, + "end": 12391, "loc": { "start": { - "line": 377, + "line": 396, "column": 8 }, "end": { - "line": 377, + "line": 396, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 11736, - "end": 11740, + "start": 12369, + "end": 12373, "loc": { "start": { - "line": 377, + "line": 396, "column": 8 }, "end": { - "line": 377, + "line": 396, "column": 12 } } }, "property": { "type": "Identifier", - "start": 11741, - "end": 11758, + "start": 12374, + "end": 12391, "loc": { "start": { - "line": 377, + "line": 396, "column": 13 }, "end": { - "line": 377, + "line": 396, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -39688,43 +41922,43 @@ }, { "type": "IfStatement", - "start": 11774, - "end": 11840, + "start": 12407, + "end": 12473, "loc": { "start": { - "line": 379, + "line": 398, "column": 6 }, "end": { - "line": 379, + "line": 398, "column": 72 } }, "test": { "type": "CallExpression", - "start": 11778, - "end": 11808, + "start": 12411, + "end": 12441, "loc": { "start": { - "line": 379, + "line": 398, "column": 10 }, "end": { - "line": 379, + "line": 398, "column": 40 } }, "callee": { "type": "Identifier", - "start": 11778, - "end": 11781, + "start": 12411, + "end": 12414, "loc": { "start": { - "line": 379, + "line": 398, "column": 10 }, "end": { - "line": 379, + "line": 398, "column": 13 }, "identifierName": "has" @@ -39734,15 +41968,15 @@ "arguments": [ { "type": "Identifier", - "start": 11782, - "end": 11788, + "start": 12415, + "end": 12421, "loc": { "start": { - "line": 379, + "line": 398, "column": 14 }, "end": { - "line": 379, + "line": 398, "column": 20 }, "identifierName": "txname" @@ -39751,15 +41985,15 @@ }, { "type": "StringLiteral", - "start": 11790, - "end": 11807, + "start": 12423, + "end": 12440, "loc": { "start": { - "line": 379, + "line": 398, "column": 22 }, "end": { - "line": 379, + "line": 398, "column": 39 } }, @@ -39773,43 +42007,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 11810, - "end": 11840, + "start": 12443, + "end": 12473, "loc": { "start": { - "line": 379, + "line": 398, "column": 42 }, "end": { - "line": 379, + "line": 398, "column": 72 } }, "argument": { "type": "MemberExpression", - "start": 11817, - "end": 11839, + "start": 12450, + "end": 12472, "loc": { "start": { - "line": 379, + "line": 398, "column": 49 }, "end": { - "line": 379, + "line": 398, "column": 71 } }, "object": { "type": "Identifier", - "start": 11817, - "end": 11823, + "start": 12450, + "end": 12456, "loc": { "start": { - "line": 379, + "line": 398, "column": 49 }, "end": { - "line": 379, + "line": 398, "column": 55 }, "identifierName": "txname" @@ -39818,15 +42052,15 @@ }, "property": { "type": "Identifier", - "start": 11824, - "end": 11839, + "start": 12457, + "end": 12472, "loc": { "start": { - "line": 379, + "line": 398, "column": 56 }, "end": { - "line": 379, + "line": 398, "column": 71 }, "identifierName": "specificEpithet" @@ -39846,15 +42080,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 11500, - "end": 11572, + "start": 12133, + "end": 12205, "loc": { "start": { - "line": 372, + "line": 391, "column": 4 }, "end": { - "line": 372, + "line": 391, "column": 76 } } @@ -39862,15 +42096,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 11577, - "end": 11615, + "start": 12210, + "end": 12248, "loc": { "start": { - "line": 373, + "line": 392, "column": 4 }, "end": { - "line": 373, + "line": 392, "column": 42 } } @@ -39879,29 +42113,29 @@ }, { "type": "ReturnStatement", - "start": 11852, - "end": 11869, + "start": 12485, + "end": 12502, "loc": { "start": { - "line": 382, + "line": 401, "column": 4 }, "end": { - "line": 382, + "line": 401, "column": 21 } }, "argument": { "type": "Identifier", - "start": 11859, - "end": 11868, + "start": 12492, + "end": 12501, "loc": { "start": { - "line": 382, + "line": 401, "column": 11 }, "end": { - "line": 382, + "line": 401, "column": 20 }, "identifierName": "undefined" @@ -39917,15 +42151,15 @@ { "type": "CommentBlock", "value": "* Return the specific epithet of this scientific name if available. ", - "start": 11261, - "end": 11333, + "start": 11894, + "end": 11966, "loc": { "start": { - "line": 367, + "line": 386, "column": 2 }, "end": { - "line": 367, + "line": 386, "column": 74 } } @@ -39935,15 +42169,15 @@ { "type": "CommentBlock", "value": "* Set the specificEpithet part of this name. ", - "start": 11877, - "end": 11926, + "start": 12510, + "end": 12559, "loc": { "start": { - "line": 385, + "line": 404, "column": 2 }, "end": { - "line": 385, + "line": 404, "column": 51 } } @@ -39952,15 +42186,15 @@ }, { "type": "ClassMethod", - "start": 11929, - "end": 12263, + "start": 12562, + "end": 12896, "loc": { "start": { - "line": 386, + "line": 405, "column": 2 }, "end": { - "line": 395, + "line": 414, "column": 3 } }, @@ -39968,15 +42202,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 11933, - "end": 11948, + "start": 12566, + "end": 12581, "loc": { "start": { - "line": 386, + "line": 405, "column": 6 }, "end": { - "line": 386, + "line": 405, "column": 21 }, "identifierName": "specificEpithet" @@ -39991,15 +42225,15 @@ "params": [ { "type": "Identifier", - "start": 11949, - "end": 11956, + "start": 12582, + "end": 12589, "loc": { "start": { - "line": 386, + "line": 405, "column": 22 }, "end": { - "line": 386, + "line": 405, "column": 29 }, "identifierName": "epithet" @@ -40009,102 +42243,102 @@ ], "body": { "type": "BlockStatement", - 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"line": 388, + "line": 407, "column": 22 }, "identifierName": "genusPart" @@ -40215,73 +42449,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 12027, - "end": 12259, + "start": 12660, + "end": 12892, "loc": { "start": { - "line": 388, + "line": 407, "column": 24 }, "end": { - "line": 394, + "line": 413, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 12035, - "end": 12253, + "start": 12668, + "end": 12886, "loc": { "start": { - "line": 389, + "line": 408, "column": 6 }, "end": { - "line": 393, + "line": 412, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 12039, - "end": 12064, + "start": 12672, + "end": 12697, "loc": { "start": { - "line": 389, + "line": 408, "column": 10 }, "end": { - "line": 389, + "line": 408, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 12039, - "end": 12043, + "start": 12672, + "end": 12676, "loc": { "start": { - "line": 389, + "line": 408, "column": 10 }, "end": { - "line": 389, + "line": 408, "column": 14 } } }, "property": { "type": "Identifier", - "start": 12044, - "end": 12064, + "start": 12677, + "end": 12697, "loc": { "start": { - "line": 389, + "line": 408, "column": 15 }, "end": { - "line": 389, + "line": 408, "column": 35 }, "identifierName": "infraspecificEpithet" @@ -40292,102 +42526,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 12066, - "end": 12171, + "start": 12699, + "end": 12804, "loc": { "start": { - "line": 389, + "line": 408, "column": 37 }, "end": { - "line": 391, + "line": 410, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 12076, - "end": 12163, + "start": 12709, + "end": 12796, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 95 } }, "expression": { "type": "AssignmentExpression", - "start": 12076, - "end": 12162, + "start": 12709, + "end": 12795, "loc": { "start": { - "line": 390, + "line": 409, "column": 8 }, "end": { - "line": 390, + "line": 409, "column": 94 } }, "operator": "=", "left": { "type": "MemberExpression", - 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"line": 390, + "line": 409, "column": 20 }, "end": { - "line": 390, + "line": 409, "column": 32 }, "identifierName": "nameComplete" @@ -40417,59 +42651,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 12103, - "end": 12162, + "start": 12736, + "end": 12795, "loc": { "start": { - "line": 390, + "line": 409, "column": 35 }, "end": { - "line": 390, + "line": 409, "column": 94 } }, "expressions": [ { "type": "MemberExpression", - "start": 12106, - "end": 12120, + "start": 12739, + "end": 12753, "loc": { "start": { - "line": 390, + "line": 409, "column": 38 }, "end": { - "line": 390, + "line": 409, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 12106, - "end": 12110, + "start": 12739, + "end": 12743, "loc": { "start": { - "line": 390, + "line": 409, "column": 38 }, "end": { - "line": 390, + "line": 409, "column": 42 } } }, "property": { "type": "Identifier", - "start": 12111, - "end": 12120, + "start": 12744, + "end": 12753, "loc": { "start": { - "line": 390, + "line": 409, "column": 43 }, "end": { - "line": 390, + "line": 409, "column": 52 }, "identifierName": "genusPart" @@ -40480,15 +42714,15 @@ }, { "type": "Identifier", - "start": 12124, - "end": 12131, + "start": 12757, + "end": 12764, "loc": { "start": { - "line": 390, + "line": 409, "column": 56 }, "end": { - "line": 390, + "line": 409, "column": 63 }, "identifierName": "epithet" @@ -40497,44 +42731,44 @@ }, { "type": "MemberExpression", - "start": 12135, - "end": 12160, + "start": 12768, + "end": 12793, "loc": { "start": { - "line": 390, + "line": 409, "column": 67 }, "end": { - "line": 390, + "line": 409, "column": 92 } }, "object": { "type": "ThisExpression", - "start": 12135, - "end": 12139, + "start": 12768, + "end": 12772, "loc": { "start": { - "line": 390, + "line": 409, "column": 67 }, "end": { - "line": 390, + "line": 409, "column": 71 } } }, "property": { "type": "Identifier", - "start": 12140, - "end": 12160, + "start": 12773, + "end": 12793, "loc": { "start": { - "line": 390, + "line": 409, "column": 72 }, "end": { - "line": 390, + "line": 409, "column": 92 }, "identifierName": "infraspecificEpithet" @@ -40547,15 +42781,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 12104, - "end": 12104, + "start": 12737, + "end": 12737, "loc": { "start": { - "line": 390, + "line": 409, "column": 36 }, "end": { - "line": 390, + "line": 409, "column": 36 } }, @@ -40567,15 +42801,15 @@ }, { "type": "TemplateElement", - "start": 12121, - "end": 12122, + "start": 12754, + "end": 12755, "loc": { "start": { - "line": 390, + "line": 409, "column": 53 }, "end": { - "line": 390, + "line": 409, "column": 54 } }, @@ -40587,15 +42821,15 @@ }, { "type": "TemplateElement", - "start": 12132, - "end": 12133, + "start": 12765, + "end": 12766, "loc": { "start": { - "line": 390, + "line": 409, "column": 64 }, "end": { - "line": 390, + "line": 409, "column": 65 } }, @@ -40607,15 +42841,15 @@ }, { "type": "TemplateElement", - "start": 12161, - "end": 12161, + "start": 12794, + "end": 12794, "loc": { "start": { - "line": 390, + "line": 409, "column": 93 }, "end": { - "line": 390, + "line": 409, "column": 93 } }, @@ -40634,102 +42868,102 @@ }, "alternate": { "type": "BlockStatement", - "start": 12177, - "end": 12253, + "start": 12810, + "end": 12886, "loc": { "start": { - "line": 391, + "line": 410, "column": 13 }, "end": { - "line": 393, + "line": 412, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 12187, - "end": 12245, + "start": 12820, + "end": 12878, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 66 } }, "expression": { "type": "AssignmentExpression", - "start": 12187, - "end": 12244, + "start": 12820, + "end": 12877, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 65 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 12187, - "end": 12211, + "start": 12820, + "end": 12844, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 12187, - "end": 12198, + "start": 12820, + "end": 12831, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 12187, - "end": 12191, + "start": 12820, + "end": 12824, "loc": { "start": { - "line": 392, + "line": 411, "column": 8 }, "end": { - "line": 392, + "line": 411, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12192, - "end": 12198, + "start": 12825, + "end": 12831, "loc": { "start": { - "line": 392, + "line": 411, "column": 13 }, "end": { - "line": 392, + "line": 411, "column": 19 }, "identifierName": "txname" @@ -40740,15 +42974,15 @@ }, "property": { "type": "Identifier", - "start": 12199, - "end": 12211, + "start": 12832, + "end": 12844, "loc": { "start": { - "line": 392, + "line": 411, "column": 20 }, "end": { - "line": 392, + "line": 411, "column": 32 }, "identifierName": "nameComplete" @@ -40759,59 +42993,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 12214, - "end": 12244, + "start": 12847, + "end": 12877, "loc": { "start": { - "line": 392, + "line": 411, "column": 35 }, "end": { - "line": 392, + "line": 411, "column": 65 } }, "expressions": [ { "type": "MemberExpression", - "start": 12217, - "end": 12231, + "start": 12850, + "end": 12864, "loc": { "start": { - "line": 392, + "line": 411, "column": 38 }, "end": { - "line": 392, + "line": 411, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 12217, - "end": 12221, + "start": 12850, + "end": 12854, "loc": { "start": { - "line": 392, + "line": 411, "column": 38 }, "end": { - "line": 392, + "line": 411, "column": 42 } } }, "property": { "type": "Identifier", - "start": 12222, - "end": 12231, + "start": 12855, + "end": 12864, "loc": { "start": { - "line": 392, + "line": 411, "column": 43 }, "end": { - "line": 392, + "line": 411, "column": 52 }, "identifierName": "genusPart" @@ -40822,15 +43056,15 @@ }, { "type": "Identifier", - "start": 12235, - "end": 12242, + "start": 12868, + "end": 12875, "loc": { "start": { - "line": 392, + "line": 411, "column": 56 }, "end": { - "line": 392, + "line": 411, "column": 63 }, "identifierName": "epithet" @@ -40841,15 +43075,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 12215, - "end": 12215, + "start": 12848, + "end": 12848, "loc": { "start": { - "line": 392, + "line": 411, "column": 36 }, "end": { - "line": 392, + "line": 411, "column": 36 } }, @@ -40861,15 +43095,15 @@ }, { "type": "TemplateElement", - "start": 12232, - "end": 12233, + "start": 12865, + "end": 12866, "loc": { "start": { - "line": 392, + "line": 411, "column": 53 }, "end": { - "line": 392, + "line": 411, "column": 54 } }, @@ -40881,15 +43115,15 @@ }, { "type": "TemplateElement", - "start": 12243, - "end": 12243, + "start": 12876, + "end": 12876, "loc": { "start": { - "line": 392, + "line": 411, "column": 64 }, "end": { - "line": 392, + "line": 411, "column": 64 } }, @@ -40920,15 +43154,15 @@ { "type": "CommentBlock", "value": "* Set the specificEpithet part of this name. ", - "start": 11877, - "end": 11926, + "start": 12510, + "end": 12559, "loc": { "start": { - "line": 385, + "line": 404, "column": 2 }, "end": { - "line": 385, + "line": 404, "column": 51 } } @@ -40938,15 +43172,15 @@ { "type": "CommentBlock", "value": "* Return the infraspecific epithet of this scientific name if available. ", - "start": 12267, - "end": 12344, + "start": 12900, + "end": 12977, "loc": { "start": { - "line": 397, + "line": 416, "column": 2 }, "end": { - "line": 397, + "line": 416, "column": 79 } } @@ -40955,15 +43189,15 @@ }, { "type": "ClassMethod", - "start": 12347, - "end": 12916, + "start": 12980, + "end": 13549, "loc": { "start": { - "line": 398, + "line": 417, "column": 2 }, "end": { - "line": 413, + "line": 432, "column": 3 } }, @@ -40971,15 +43205,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12351, - "end": 12371, + "start": 12984, + "end": 13004, "loc": { "start": { - "line": 398, + "line": 417, "column": 6 }, "end": { - "line": 398, + "line": 417, "column": 26 }, "identifierName": "infraspecificEpithet" @@ -40994,58 +43228,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 12374, - "end": 12916, + "start": 13007, + "end": 13549, "loc": { "start": { - "line": 398, + "line": 417, "column": 29 }, "end": { - "line": 413, + "line": 432, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 12434, - "end": 12520, + "start": 13067, + "end": 13153, "loc": { "start": { - "line": 400, + "line": 419, "column": 4 }, "end": { - "line": 400, + "line": 419, "column": 90 } }, "test": { "type": "CallExpression", - "start": 12438, - "end": 12478, + "start": 13071, + "end": 13111, "loc": { "start": { - "line": 400, + "line": 419, "column": 8 }, "end": { - "line": 400, + "line": 419, "column": 48 } }, "callee": { "type": "Identifier", - "start": 12438, - "end": 12441, + "start": 13071, + "end": 13074, "loc": { "start": { - "line": 400, + "line": 419, "column": 8 }, "end": { - "line": 400, + "line": 419, "column": 11 }, "identifierName": "has" @@ -41056,44 +43290,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 12442, - "end": 12453, + "start": 13075, + "end": 13086, "loc": { "start": { - "line": 400, + "line": 419, "column": 12 }, "end": { - "line": 400, + "line": 419, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 12442, - "end": 12446, + "start": 13075, + "end": 13079, "loc": { "start": { - "line": 400, + "line": 419, "column": 12 }, "end": { - "line": 400, + "line": 419, "column": 16 } } }, "property": { "type": "Identifier", - "start": 12447, - "end": 12453, + "start": 13080, + "end": 13086, "loc": { "start": { - "line": 400, + "line": 419, "column": 17 }, "end": { - "line": 400, + "line": 419, "column": 23 }, "identifierName": "txname" @@ -41104,15 +43338,15 @@ }, { "type": "StringLiteral", - "start": 12455, - "end": 12477, + "start": 13088, + "end": 13110, "loc": { "start": { - "line": 400, + "line": 419, "column": 25 }, "end": { - "line": 400, + "line": 419, "column": 47 } }, @@ -41127,72 +43361,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12480, - "end": 12520, + "start": 13113, + "end": 13153, "loc": { "start": { - "line": 400, + "line": 419, "column": 50 }, "end": { - "line": 400, + "line": 419, "column": 90 } }, "argument": { "type": "MemberExpression", - "start": 12487, - "end": 12519, + "start": 13120, + "end": 13152, "loc": { "start": { - "line": 400, + "line": 419, "column": 57 }, "end": { - "line": 400, + "line": 419, "column": 89 } }, "object": { "type": "MemberExpression", - "start": 12487, - "end": 12498, + "start": 13120, + "end": 13131, "loc": { "start": { - "line": 400, + "line": 419, "column": 57 }, "end": { - "line": 400, + "line": 419, "column": 68 } }, "object": { "type": "ThisExpression", - "start": 12487, - "end": 12491, + "start": 13120, + "end": 13124, "loc": { "start": { - "line": 400, + "line": 419, "column": 57 }, "end": { - "line": 400, + "line": 419, "column": 61 } } }, "property": { "type": "Identifier", - "start": 12492, - "end": 12498, + "start": 13125, + "end": 13131, "loc": { "start": { - "line": 400, + "line": 419, "column": 62 }, "end": { - "line": 400, + "line": 419, "column": 68 }, "identifierName": "txname" @@ -41203,15 +43437,15 @@ }, "property": { "type": "Identifier", - "start": 12499, - "end": 12519, + "start": 13132, + "end": 13152, "loc": { "start": { - "line": 400, + "line": 419, "column": 69 }, "end": { - "line": 400, + "line": 419, "column": 89 }, "identifierName": "infraspecificEpithet" @@ -41227,15 +43461,15 @@ { "type": "CommentLine", "value": " Try to read the specific epithet if available.", - "start": 12380, - "end": 12429, + "start": 13013, + "end": 13062, "loc": { "start": { - "line": 399, + "line": 418, "column": 4 }, "end": { - "line": 399, + "line": 418, "column": 53 } } @@ -41245,15 +43479,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 12526, - "end": 12598, + "start": 13159, + "end": 13231, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 76 } } @@ -41261,15 +43495,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 12603, - "end": 12641, + "start": 13236, + "end": 13274, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 42 } } @@ -41278,57 +43512,57 @@ }, { "type": "IfStatement", - "start": 12646, - "end": 12889, + "start": 13279, + "end": 13522, "loc": { "start": { - "line": 404, + "line": 423, "column": 4 }, "end": { - "line": 410, + "line": 429, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 12650, - "end": 12674, + "start": 13283, + "end": 13307, "loc": { "start": { - "line": 404, + "line": 423, "column": 8 }, "end": { - "line": 404, + "line": 423, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 12650, - "end": 12661, + "start": 13283, + "end": 13294, "loc": { "start": { - "line": 404, + "line": 423, "column": 8 }, "end": { - "line": 404, + "line": 423, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 12650, - "end": 12654, + "start": 13283, + "end": 13287, "loc": { "start": { - "line": 404, + "line": 423, "column": 8 }, "end": { - "line": 404, + "line": 423, "column": 12 } }, @@ -41336,15 +43570,15 @@ }, "property": { "type": "Identifier", - "start": 12655, - "end": 12661, + "start": 13288, + "end": 13294, "loc": { "start": { - "line": 404, + "line": 423, "column": 13 }, "end": { - "line": 404, + "line": 423, "column": 19 }, "identifierName": "txname" @@ -41356,15 +43590,15 @@ }, "property": { "type": "Identifier", - "start": 12662, - "end": 12674, + "start": 13295, + "end": 13307, "loc": { "start": { - "line": 404, + "line": 423, "column": 20 }, "end": { - "line": 404, + "line": 423, "column": 32 }, "identifierName": "nameComplete" @@ -41376,59 +43610,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 12676, - "end": 12889, + "start": 13309, + "end": 13522, "loc": { "start": { - "line": 404, + "line": 423, "column": 34 }, "end": { - "line": 410, + "line": 429, "column": 5 } }, "body": [ { "type": "VariableDeclaration", - "start": 12684, - "end": 12800, + "start": 13317, + "end": 13433, "loc": { "start": { - "line": 405, + "line": 424, "column": 6 }, "end": { - "line": 408, + "line": 427, "column": 8 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 12690, - "end": 12799, + "start": 13323, + "end": 13432, "loc": { "start": { - "line": 405, + "line": 424, "column": 12 }, "end": { - "line": 408, + "line": 427, "column": 7 } }, "id": { "type": "Identifier", - "start": 12690, - "end": 12696, + "start": 13323, + "end": 13329, "loc": { "start": { - "line": 405, + "line": 424, "column": 12 }, "end": { - "line": 405, + "line": 424, "column": 18 }, "identifierName": "txname" @@ -41437,43 +43671,43 @@ }, "init": { "type": "CallExpression", - "start": 12699, - "end": 12799, + "start": 13332, + "end": 13432, "loc": { "start": { - "line": 405, + "line": 424, "column": 21 }, "end": { - "line": 408, + "line": 427, "column": 7 } }, "callee": { "type": "MemberExpression", - "start": 12699, - "end": 12732, + "start": 13332, + "end": 13365, "loc": { "start": { - "line": 405, + "line": 424, "column": 21 }, "end": { - "line": 405, + "line": 424, "column": 54 } }, "object": { "type": "Identifier", - "start": 12699, - "end": 12715, + "start": 13332, + "end": 13348, "loc": { "start": { - "line": 405, + "line": 424, "column": 21 }, "end": { - "line": 405, + "line": 424, "column": 37 }, "identifierName": "TaxonNameWrapper" @@ -41482,15 +43716,15 @@ }, "property": { "type": "Identifier", - "start": 12716, - "end": 12732, + "start": 13349, + "end": 13365, "loc": { "start": { - "line": 405, + "line": 424, "column": 38 }, "end": { - "line": 405, + "line": 424, "column": 54 }, "identifierName": "fromVerbatimName" @@ -41502,44 +43736,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 12742, - "end": 12759, + "start": 13375, + "end": 13392, "loc": { "start": { - "line": 406, + "line": 425, "column": 8 }, "end": { - "line": 406, + "line": 425, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 12742, - "end": 12746, + "start": 13375, + "end": 13379, "loc": { "start": { - "line": 406, + "line": 425, "column": 8 }, "end": { - "line": 406, + "line": 425, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12747, - "end": 12759, + "start": 13380, + "end": 13392, "loc": { "start": { - "line": 406, + "line": 425, "column": 13 }, "end": { - "line": 406, + "line": 425, "column": 25 }, "identifierName": "nameComplete" @@ -41550,44 +43784,44 @@ }, { "type": "MemberExpression", - "start": 12769, - "end": 12791, + "start": 13402, + "end": 13424, "loc": { "start": { - "line": 407, + "line": 426, "column": 8 }, "end": { - "line": 407, + "line": 426, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 12769, - "end": 12773, + "start": 13402, + "end": 13406, "loc": { "start": { - "line": 407, + "line": 426, "column": 8 }, "end": { - "line": 407, + "line": 426, "column": 12 } } }, "property": { "type": "Identifier", - "start": 12774, - "end": 12791, + "start": 13407, + "end": 13424, "loc": { "start": { - "line": 407, + "line": 426, "column": 13 }, "end": { - "line": 407, + "line": 426, "column": 30 }, "identifierName": "nomenclaturalCode" @@ -41604,43 +43838,43 @@ }, { "type": "IfStatement", - "start": 12807, - "end": 12883, + "start": 13440, + "end": 13516, "loc": { "start": { - "line": 409, + "line": 428, "column": 6 }, "end": { - "line": 409, + "line": 428, "column": 82 } }, "test": { "type": "CallExpression", - "start": 12811, - "end": 12846, + "start": 13444, + "end": 13479, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 45 } }, "callee": { "type": "Identifier", - "start": 12811, - "end": 12814, + "start": 13444, + "end": 13447, "loc": { "start": { - "line": 409, + "line": 428, "column": 10 }, "end": { - "line": 409, + "line": 428, "column": 13 }, "identifierName": "has" @@ -41650,15 +43884,15 @@ "arguments": [ { "type": "Identifier", - "start": 12815, - "end": 12821, + "start": 13448, + "end": 13454, "loc": { "start": { - "line": 409, + "line": 428, "column": 14 }, "end": { - "line": 409, + "line": 428, "column": 20 }, "identifierName": "txname" @@ -41667,15 +43901,15 @@ }, { "type": "StringLiteral", - "start": 12823, - "end": 12845, + "start": 13456, + "end": 13478, "loc": { "start": { - "line": 409, + "line": 428, "column": 22 }, "end": { - "line": 409, + "line": 428, "column": 44 } }, @@ -41689,43 +43923,43 @@ }, "consequent": { "type": "ReturnStatement", - "start": 12848, - "end": 12883, + "start": 13481, + "end": 13516, "loc": { "start": { - "line": 409, + "line": 428, "column": 47 }, "end": { - "line": 409, + "line": 428, "column": 82 } }, "argument": { "type": "MemberExpression", - "start": 12855, - "end": 12882, + "start": 13488, + "end": 13515, "loc": { "start": { - "line": 409, + "line": 428, "column": 54 }, "end": { - "line": 409, + "line": 428, "column": 81 } }, "object": { "type": "Identifier", - "start": 12855, - "end": 12861, + "start": 13488, + "end": 13494, "loc": { "start": { - "line": 409, + "line": 428, "column": 54 }, "end": { - "line": 409, + "line": 428, "column": 60 }, "identifierName": "txname" @@ -41734,15 +43968,15 @@ }, "property": { "type": "Identifier", - "start": 12862, - "end": 12882, + "start": 13495, + "end": 13515, "loc": { "start": { - "line": 409, + "line": 428, "column": 61 }, "end": { - "line": 409, + "line": 428, "column": 81 }, "identifierName": "infraspecificEpithet" @@ -41762,15 +43996,15 @@ { "type": "CommentLine", "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 12526, - "end": 12598, + "start": 13159, + "end": 13231, "loc": { "start": { - "line": 402, + "line": 421, "column": 4 }, "end": { - "line": 402, + "line": 421, "column": 76 } } @@ -41778,15 +44012,15 @@ { "type": "CommentLine", "value": " extract a specific epithet from it.", - "start": 12603, - "end": 12641, + "start": 13236, + "end": 13274, "loc": { "start": { - "line": 403, + "line": 422, "column": 4 }, "end": { - "line": 403, + "line": 422, "column": 42 } } @@ -41795,29 +44029,29 @@ }, { "type": "ReturnStatement", - "start": 12895, - "end": 12912, + "start": 13528, + "end": 13545, "loc": { "start": { - "line": 412, + "line": 431, "column": 4 }, "end": { - "line": 412, + "line": 431, "column": 21 } }, "argument": { "type": "Identifier", - "start": 12902, - "end": 12911, + "start": 13535, + "end": 13544, "loc": { "start": { - "line": 412, + "line": 431, "column": 11 }, "end": { - "line": 412, + "line": 431, "column": 20 }, "identifierName": "undefined" @@ -41833,15 +44067,15 @@ { "type": "CommentBlock", "value": "* Return the infraspecific epithet of this scientific name if available. ", - "start": 12267, - "end": 12344, + "start": 12900, + "end": 12977, "loc": { "start": { - "line": 397, + "line": 416, "column": 2 }, "end": { - "line": 397, + "line": 416, "column": 79 } } @@ -41851,15 +44085,15 @@ { "type": "CommentBlock", "value": "* Set the infraspecificEpithet part of this name. ", - "start": 12920, - "end": 12974, + "start": 13553, + "end": 13607, "loc": { "start": { - "line": 415, + "line": 434, "column": 2 }, "end": { - "line": 415, + "line": 434, "column": 56 } } @@ -41868,15 +44102,15 @@ }, { "type": "ClassMethod", - "start": 12977, - "end": 13315, + "start": 13610, + "end": 13948, "loc": { "start": { - "line": 416, + "line": 435, "column": 2 }, "end": { - "line": 425, + "line": 444, "column": 3 } }, @@ -41884,15 +44118,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 12981, - "end": 13001, + "start": 13614, + "end": 13634, "loc": { "start": { - "line": 416, + "line": 435, "column": 6 }, "end": { - "line": 416, + "line": 435, "column": 26 }, "identifierName": "infraspecificEpithet" @@ -41907,15 +44141,15 @@ "params": [ { "type": "Identifier", - "start": 13002, - "end": 13009, + "start": 13635, + "end": 13642, "loc": { "start": { - "line": 416, + "line": 435, "column": 27 }, "end": { - "line": 416, + "line": 435, "column": 34 }, "identifierName": "epithet" @@ -41925,102 +44159,102 @@ ], "body": { "type": "BlockStatement", - "start": 13011, - "end": 13315, + "start": 13644, + "end": 13948, "loc": { "start": { - "line": 416, + "line": 435, "column": 36 }, "end": { - "line": 425, + "line": 444, "column": 3 } }, "body": [ { "type": "ExpressionStatement", - "start": 13017, - "end": 13060, + "start": 13650, + "end": 13693, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 47 } }, "expression": { "type": "AssignmentExpression", - "start": 13017, - "end": 13059, + "start": 13650, + "end": 13692, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 46 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13017, - "end": 13049, + "start": 13650, + "end": 13682, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 36 } }, "object": { "type": "MemberExpression", - "start": 13017, - "end": 13028, + "start": 13650, + "end": 13661, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 15 } }, "object": { "type": "ThisExpression", - "start": 13017, - "end": 13021, + "start": 13650, + "end": 13654, "loc": { "start": { - "line": 417, + "line": 436, "column": 4 }, "end": { - "line": 417, + "line": 436, "column": 8 } } }, "property": { "type": "Identifier", - "start": 13022, - "end": 13028, + "start": 13655, + "end": 13661, "loc": { "start": { - "line": 417, + "line": 436, "column": 9 }, "end": { - "line": 417, + "line": 436, "column": 15 }, "identifierName": "txname" @@ -42031,15 +44265,15 @@ }, "property": { "type": "Identifier", - "start": 13029, - "end": 13049, + "start": 13662, + "end": 13682, "loc": { "start": { - "line": 417, + "line": 436, "column": 16 }, "end": { - "line": 417, + "line": 436, "column": 36 }, "identifierName": "infraspecificEpithet" @@ -42050,15 +44284,15 @@ }, "right": { "type": "Identifier", - "start": 13052, - "end": 13059, + "start": 13685, + "end": 13692, "loc": { "start": { - "line": 417, + "line": 436, "column": 39 }, "end": { - "line": 417, + "line": 436, "column": 46 }, "identifierName": "epithet" @@ -42069,58 +44303,58 @@ }, { "type": "IfStatement", - "start": 13065, - "end": 13311, + "start": 13698, + "end": 13944, "loc": { "start": { - "line": 418, + "line": 437, "column": 4 }, "end": { - "line": 424, + "line": 443, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 13069, - "end": 13083, + "start": 13702, + "end": 13716, "loc": { "start": { - "line": 418, + "line": 437, "column": 8 }, "end": { - "line": 418, + "line": 437, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 13069, - "end": 13073, + "start": 13702, + "end": 13706, "loc": { "start": { - "line": 418, + "line": 437, "column": 8 }, "end": { - "line": 418, + "line": 437, "column": 12 } } }, "property": { "type": "Identifier", - "start": 13074, - "end": 13083, + "start": 13707, + "end": 13716, "loc": { "start": { - "line": 418, + "line": 437, "column": 13 }, "end": { - "line": 418, + "line": 437, "column": 22 }, "identifierName": "genusPart" @@ -42131,73 +44365,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 13085, - "end": 13311, + "start": 13718, + "end": 13944, "loc": { "start": { - "line": 418, + "line": 437, "column": 24 }, "end": { - "line": 424, + "line": 443, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 13093, - "end": 13305, + "start": 13726, + "end": 13938, "loc": { "start": { - "line": 419, + "line": 438, "column": 6 }, "end": { - "line": 423, + "line": 442, "column": 7 } }, "test": { "type": "MemberExpression", - "start": 13097, - "end": 13117, + "start": 13730, + "end": 13750, "loc": { "start": { - "line": 419, + "line": 438, "column": 10 }, "end": { - "line": 419, + "line": 438, "column": 30 } }, "object": { "type": "ThisExpression", - "start": 13097, - "end": 13101, + "start": 13730, + "end": 13734, "loc": { "start": { - "line": 419, + "line": 438, "column": 10 }, "end": { - "line": 419, + "line": 438, "column": 14 } } }, "property": { "type": "Identifier", - "start": 13102, - "end": 13117, + "start": 13735, + "end": 13750, "loc": { "start": { - "line": 419, + "line": 438, "column": 15 }, "end": { - "line": 419, + "line": 438, "column": 30 }, "identifierName": "specificEpithet" @@ -42208,102 +44442,102 @@ }, "consequent": { "type": "BlockStatement", - "start": 13119, - "end": 13219, + "start": 13752, + "end": 13852, "loc": { "start": { - "line": 419, + "line": 438, "column": 32 }, "end": { - "line": 421, + "line": 440, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 13129, - "end": 13211, + "start": 13762, + "end": 13844, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 90 } }, "expression": { "type": "AssignmentExpression", - "start": 13129, - "end": 13210, + "start": 13762, + "end": 13843, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 89 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13129, - "end": 13153, + "start": 13762, + "end": 13786, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 13129, - "end": 13140, + "start": 13762, + "end": 13773, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 13129, - "end": 13133, + "start": 13762, + "end": 13766, "loc": { "start": { - "line": 420, + "line": 439, "column": 8 }, "end": { - "line": 420, + "line": 439, "column": 12 } } }, "property": { "type": "Identifier", - "start": 13134, - "end": 13140, + "start": 13767, + "end": 13773, "loc": { "start": { - "line": 420, + "line": 439, "column": 13 }, "end": { - "line": 420, + "line": 439, "column": 19 }, "identifierName": "txname" @@ -42314,15 +44548,15 @@ }, "property": { "type": "Identifier", - "start": 13141, - "end": 13153, + "start": 13774, + "end": 13786, "loc": { "start": { - "line": 420, + "line": 439, "column": 20 }, "end": { - "line": 420, + "line": 439, "column": 32 }, "identifierName": "nameComplete" @@ -42333,59 +44567,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 13156, - "end": 13210, + "start": 13789, + "end": 13843, "loc": { "start": { - "line": 420, + "line": 439, "column": 35 }, "end": { - "line": 420, + "line": 439, "column": 89 } }, "expressions": [ { "type": "MemberExpression", - "start": 13159, - "end": 13173, + "start": 13792, + "end": 13806, "loc": { "start": { - "line": 420, + "line": 439, "column": 38 }, "end": { - "line": 420, + "line": 439, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 13159, - "end": 13163, + "start": 13792, + "end": 13796, "loc": { "start": { - "line": 420, + "line": 439, "column": 38 }, "end": { - "line": 420, + "line": 439, "column": 42 } } }, "property": { "type": "Identifier", - "start": 13164, - "end": 13173, + "start": 13797, + "end": 13806, "loc": { "start": { - "line": 420, + "line": 439, "column": 43 }, "end": { - "line": 420, + "line": 439, "column": 52 }, "identifierName": "genusPart" @@ -42396,44 +44630,44 @@ }, { "type": "MemberExpression", - "start": 13177, - "end": 13197, + "start": 13810, + "end": 13830, "loc": { "start": { - "line": 420, + "line": 439, "column": 56 }, "end": { - "line": 420, + "line": 439, "column": 76 } }, "object": { "type": "ThisExpression", - "start": 13177, - "end": 13181, + "start": 13810, + "end": 13814, "loc": { "start": { - "line": 420, + "line": 439, "column": 56 }, "end": { - "line": 420, + "line": 439, "column": 60 } } }, "property": { "type": "Identifier", - "start": 13182, - "end": 13197, + "start": 13815, + "end": 13830, "loc": { "start": { - "line": 420, + "line": 439, "column": 61 }, "end": { - "line": 420, + "line": 439, "column": 76 }, "identifierName": "specificEpithet" @@ -42444,15 +44678,15 @@ }, { "type": "Identifier", - "start": 13201, - "end": 13208, + "start": 13834, + "end": 13841, "loc": { "start": { - "line": 420, + "line": 439, "column": 80 }, "end": { - "line": 420, + "line": 439, "column": 87 }, "identifierName": "epithet" @@ -42463,15 +44697,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 13157, - "end": 13157, + "start": 13790, + "end": 13790, "loc": { "start": { - "line": 420, + "line": 439, "column": 36 }, "end": { - "line": 420, + "line": 439, "column": 36 } }, @@ -42483,15 +44717,15 @@ }, { "type": "TemplateElement", - "start": 13174, - "end": 13175, + "start": 13807, + "end": 13808, "loc": { "start": { - "line": 420, + "line": 439, "column": 53 }, "end": { - "line": 420, + "line": 439, "column": 54 } }, @@ -42503,15 +44737,15 @@ }, { "type": "TemplateElement", - "start": 13198, - "end": 13199, + "start": 13831, + "end": 13832, "loc": { "start": { - "line": 420, + "line": 439, "column": 77 }, "end": { - "line": 420, + "line": 439, "column": 78 } }, @@ -42523,15 +44757,15 @@ }, { "type": "TemplateElement", - "start": 13209, - "end": 13209, + "start": 13842, + "end": 13842, "loc": { "start": { - "line": 420, + "line": 439, "column": 88 }, "end": { - "line": 420, + "line": 439, "column": 88 } }, @@ -42550,102 +44784,102 @@ }, "alternate": { "type": "BlockStatement", - "start": 13225, - "end": 13305, + "start": 13858, + "end": 13938, "loc": { "start": { - "line": 421, + "line": 440, "column": 13 }, "end": { - "line": 423, + "line": 442, "column": 7 } }, "body": [ { "type": "ExpressionStatement", - "start": 13235, - "end": 13297, + "start": 13868, + "end": 13930, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 70 } }, "expression": { "type": "AssignmentExpression", - "start": 13235, - "end": 13296, + "start": 13868, + "end": 13929, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 69 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13235, - "end": 13259, + "start": 13868, + "end": 13892, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 32 } }, "object": { "type": "MemberExpression", - "start": 13235, - "end": 13246, + "start": 13868, + "end": 13879, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 19 } }, "object": { "type": "ThisExpression", - "start": 13235, - "end": 13239, + "start": 13868, + "end": 13872, "loc": { "start": { - "line": 422, + "line": 441, "column": 8 }, "end": { - "line": 422, + "line": 441, "column": 12 } } }, "property": { "type": "Identifier", - "start": 13240, - "end": 13246, + "start": 13873, + "end": 13879, "loc": { "start": { - "line": 422, + "line": 441, "column": 13 }, "end": { - "line": 422, + "line": 441, "column": 19 }, "identifierName": "txname" @@ -42656,15 +44890,15 @@ }, "property": { "type": "Identifier", - "start": 13247, - "end": 13259, + "start": 13880, + "end": 13892, "loc": { "start": { - "line": 422, + "line": 441, "column": 20 }, "end": { - "line": 422, + "line": 441, "column": 32 }, "identifierName": "nameComplete" @@ -42675,59 +44909,59 @@ }, "right": { "type": "TemplateLiteral", - "start": 13262, - "end": 13296, + "start": 13895, + "end": 13929, "loc": { "start": { - "line": 422, + "line": 441, "column": 35 }, "end": { - "line": 422, + "line": 441, "column": 69 } }, "expressions": [ { "type": "MemberExpression", - "start": 13265, - "end": 13279, + "start": 13898, + "end": 13912, "loc": { "start": { - "line": 422, + "line": 441, "column": 38 }, "end": { - "line": 422, + "line": 441, "column": 52 } }, "object": { "type": "ThisExpression", - "start": 13265, - "end": 13269, + "start": 13898, + "end": 13902, "loc": { "start": { - "line": 422, + "line": 441, "column": 38 }, "end": { - "line": 422, + "line": 441, "column": 42 } } }, "property": { "type": "Identifier", - "start": 13270, - "end": 13279, + "start": 13903, + "end": 13912, "loc": { "start": { - "line": 422, + "line": 441, "column": 43 }, "end": { - "line": 422, + "line": 441, "column": 52 }, "identifierName": "genusPart" @@ -42738,15 +44972,15 @@ }, { "type": "Identifier", - "start": 13287, - "end": 13294, + "start": 13920, + "end": 13927, "loc": { "start": { - "line": 422, + "line": 441, "column": 60 }, "end": { - "line": 422, + "line": 441, "column": 67 }, "identifierName": "epithet" @@ -42757,15 +44991,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 13263, - "end": 13263, + "start": 13896, + "end": 13896, "loc": { "start": { - "line": 422, + "line": 441, "column": 36 }, "end": { - "line": 422, + "line": 441, "column": 36 } }, @@ -42777,15 +45011,15 @@ }, { "type": "TemplateElement", - "start": 13280, - "end": 13285, + "start": 13913, + "end": 13918, "loc": { "start": { - "line": 422, + "line": 441, "column": 53 }, "end": { - "line": 422, + "line": 441, "column": 58 } }, @@ -42797,15 +45031,15 @@ }, { "type": "TemplateElement", - "start": 13295, - "end": 13295, + "start": 13928, + "end": 13928, "loc": { "start": { - "line": 422, + "line": 441, "column": 68 }, "end": { - "line": 422, + "line": 441, "column": 68 } }, @@ -42836,15 +45070,15 @@ { "type": "CommentBlock", "value": "* Set the infraspecificEpithet part of this name. ", - "start": 12920, - "end": 12974, + "start": 13553, + "end": 13607, "loc": { "start": { - "line": 415, + "line": 434, "column": 2 }, "end": { - "line": 415, + "line": 434, "column": 56 } } @@ -42854,15 +45088,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name in an JSON-LD representation.\n ", - "start": 13319, - "end": 13386, + "start": 13952, + "end": 14019, "loc": { "start": { - "line": 427, + "line": 446, "column": 2 }, "end": { - "line": 429, + "line": 448, "column": 5 } } @@ -42871,15 +45105,15 @@ }, { "type": "ClassMethod", - "start": 13389, - "end": 13832, + "start": 14022, + "end": 14465, "loc": { "start": { - "line": 430, + "line": 449, "column": 2 }, "end": { - "line": 442, + "line": 461, "column": 3 } }, @@ -42887,15 +45121,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 13393, - "end": 13401, + "start": 14026, + "end": 14034, "loc": { "start": { - "line": 430, + "line": 449, "column": 6 }, "end": { - "line": 430, + "line": 449, "column": 14 }, "identifierName": "asJSONLD" @@ -42910,59 +45144,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 13404, - "end": 13832, + "start": 14037, + "end": 14465, "loc": { "start": { - "line": 430, + "line": 449, "column": 17 }, "end": { - "line": 442, + "line": 461, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 13410, - "end": 13448, + "start": 14043, + "end": 14081, "loc": { "start": { - "line": 431, + "line": 450, "column": 4 }, "end": { - "line": 431, + "line": 450, "column": 42 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13416, - "end": 13447, + "start": 14049, + "end": 14080, "loc": { "start": { - "line": 431, + "line": 450, "column": 10 }, "end": { - "line": 431, + "line": 450, "column": 41 } }, "id": { "type": "Identifier", - "start": 13416, - "end": 13422, + "start": 14049, + "end": 14055, "loc": { "start": { - "line": 431, + "line": 450, "column": 10 }, "end": { - "line": 431, + "line": 450, "column": 16 }, "identifierName": "jsonld" @@ -42971,29 +45205,29 @@ }, "init": { "type": "CallExpression", - "start": 13425, - "end": 13447, + "start": 14058, + "end": 14080, "loc": { "start": { - "line": 431, + "line": 450, "column": 19 }, "end": { - "line": 431, + "line": 450, "column": 41 } }, "callee": { "type": "Identifier", - "start": 13425, - "end": 13434, + "start": 14058, + "end": 14067, "loc": { "start": { - "line": 431, + "line": 450, "column": 19 }, "end": { - "line": 431, + "line": 450, "column": 28 }, "identifierName": "cloneDeep" @@ -43003,44 +45237,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 13435, - "end": 13446, + "start": 14068, + "end": 14079, "loc": { "start": { - "line": 431, + "line": 450, "column": 29 }, "end": { - "line": 431, + "line": 450, "column": 40 } }, "object": { "type": "ThisExpression", - "start": 13435, - "end": 13439, + "start": 14068, + "end": 14072, "loc": { "start": { - "line": 431, + "line": 450, "column": 29 }, "end": { - "line": 431, + "line": 450, "column": 33 } } }, "property": { "type": "Identifier", - "start": 13440, - "end": 13446, + "start": 14073, + "end": 14079, "loc": { "start": { - "line": 431, + "line": 450, "column": 34 }, "end": { - "line": 431, + "line": 450, "column": 40 }, "identifierName": "txname" @@ -43058,15 +45292,15 @@ { "type": "CommentLine", "value": " Make sure '@type' is an array.", - "start": 13454, - "end": 13487, + "start": 14087, + "end": 14120, "loc": { "start": { - "line": 433, + "line": 452, "column": 4 }, "end": { - "line": 433, + "line": 452, "column": 37 } } @@ -43075,29 +45309,29 @@ }, { "type": "IfStatement", - "start": 13492, - "end": 13540, + "start": 14125, + "end": 14173, "loc": { "start": { - "line": 434, + "line": 453, "column": 4 }, "end": { - "line": 434, + "line": 453, "column": 52 } }, "test": { "type": "UnaryExpression", - "start": 13496, - "end": 13517, + "start": 14129, + "end": 14150, "loc": { "start": { - "line": 434, + "line": 453, "column": 8 }, "end": { - "line": 434, + "line": 453, "column": 29 } }, @@ -43105,29 +45339,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 13497, - "end": 13517, + "start": 14130, + "end": 14150, "loc": { "start": { - "line": 434, + "line": 453, "column": 9 }, "end": { - "line": 434, + "line": 453, "column": 29 } }, "callee": { "type": "Identifier", - "start": 13497, - "end": 13500, + "start": 14130, + "end": 14133, "loc": { "start": { - "line": 434, + "line": 453, "column": 9 }, "end": { - "line": 434, + "line": 453, "column": 12 }, "identifierName": "has" @@ -43138,15 +45372,15 @@ "arguments": [ { "type": "Identifier", - "start": 13501, - "end": 13507, + "start": 14134, + "end": 14140, "loc": { "start": { - "line": 434, + "line": 453, "column": 13 }, "end": { - "line": 434, + "line": 453, "column": 19 }, "identifierName": "jsonld" @@ -43155,15 +45389,15 @@ }, { "type": "StringLiteral", - "start": 13509, - "end": 13516, + "start": 14142, + "end": 14149, "loc": { "start": { - "line": 434, + "line": 453, "column": 21 }, "end": { - "line": 434, + "line": 453, "column": 28 } }, @@ -43183,58 +45417,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 13519, - "end": 13540, + "start": 14152, + "end": 14173, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 52 } }, "expression": { "type": "AssignmentExpression", - "start": 13519, - "end": 13539, + "start": 14152, + "end": 14172, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 51 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13519, - "end": 13534, + "start": 14152, + "end": 14167, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 46 } }, "object": { "type": "Identifier", - "start": 13519, - "end": 13525, + "start": 14152, + "end": 14158, "loc": { "start": { - "line": 434, + "line": 453, "column": 31 }, "end": { - "line": 434, + "line": 453, "column": 37 }, "identifierName": "jsonld" @@ -43243,15 +45477,15 @@ }, "property": { "type": "StringLiteral", - "start": 13526, - "end": 13533, + "start": 14159, + "end": 14166, "loc": { "start": { - "line": 434, + "line": 453, "column": 38 }, "end": { - "line": 434, + "line": 453, "column": 45 } }, @@ -43265,15 +45499,15 @@ }, "right": { "type": "ArrayExpression", - "start": 13537, - "end": 13539, + "start": 14170, + "end": 14172, "loc": { "start": { - "line": 434, + "line": 453, "column": 49 }, "end": { - "line": 434, + "line": 453, "column": 51 } }, @@ -43286,15 +45520,15 @@ { "type": "CommentLine", "value": " Make sure '@type' is an array.", - "start": 13454, - "end": 13487, + "start": 14087, + "end": 14120, "loc": { "start": { - "line": 433, + "line": 452, "column": 4 }, "end": { - "line": 433, + "line": 452, "column": 37 } } @@ -43303,29 +45537,29 @@ }, { "type": "IfStatement", - "start": 13545, - "end": 13612, + "start": 14178, + "end": 14245, "loc": { "start": { - "line": 435, + "line": 454, "column": 4 }, "end": { - "line": 435, + "line": 454, "column": 71 } }, "test": { "type": "UnaryExpression", - "start": 13549, - "end": 13574, + "start": 14182, + "end": 14207, "loc": { "start": { - "line": 435, + "line": 454, "column": 8 }, "end": { - "line": 435, + "line": 454, "column": 33 } }, @@ -43333,29 +45567,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 13550, - "end": 13574, + "start": 14183, + "end": 14207, "loc": { "start": { - "line": 435, + "line": 454, "column": 9 }, "end": { - "line": 435, + "line": 454, "column": 33 } }, "callee": { "type": "Identifier", - "start": 13550, - "end": 13557, + "start": 14183, + "end": 14190, "loc": { "start": { - "line": 435, + "line": 454, "column": 9 }, "end": { - "line": 435, + "line": 454, "column": 16 }, "identifierName": "isArray" @@ -43365,29 +45599,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 13558, - "end": 13573, + "start": 14191, + "end": 14206, "loc": { "start": { - "line": 435, + "line": 454, "column": 17 }, "end": { - "line": 435, + "line": 454, "column": 32 } }, "object": { "type": "Identifier", - "start": 13558, - "end": 13564, + "start": 14191, + "end": 14197, "loc": { "start": { - "line": 435, + "line": 454, "column": 17 }, "end": { - "line": 435, + "line": 454, "column": 23 }, "identifierName": "jsonld" @@ -43396,15 +45630,15 @@ }, "property": { "type": "StringLiteral", - "start": 13565, - "end": 13572, + "start": 14198, + "end": 14205, "loc": { "start": { - "line": 435, + "line": 454, "column": 24 }, "end": { - "line": 435, + "line": 454, "column": 31 } }, @@ -43424,58 +45658,58 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 13576, - "end": 13612, + "start": 14209, + "end": 14245, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 13576, - "end": 13611, + "start": 14209, + "end": 14244, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 70 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 13576, - "end": 13591, + "start": 14209, + "end": 14224, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 50 } }, "object": { "type": "Identifier", - "start": 13576, - "end": 13582, + "start": 14209, + "end": 14215, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 41 }, "identifierName": "jsonld" @@ -43484,15 +45718,15 @@ }, "property": { "type": "StringLiteral", - "start": 13583, - "end": 13590, + "start": 14216, + "end": 14223, "loc": { "start": { - "line": 435, + "line": 454, "column": 42 }, "end": { - "line": 435, + "line": 454, "column": 49 } }, @@ -43506,44 +45740,44 @@ }, "right": { "type": "ArrayExpression", - "start": 13594, - "end": 13611, + "start": 14227, + "end": 14244, "loc": { "start": { - "line": 435, + "line": 454, "column": 53 }, "end": { - "line": 435, + "line": 454, "column": 70 } }, "elements": [ { "type": "MemberExpression", - "start": 13595, - "end": 13610, + "start": 14228, + "end": 14243, "loc": { "start": { - "line": 435, + "line": 454, "column": 54 }, "end": { - "line": 435, + "line": 454, "column": 69 } }, "object": { "type": "Identifier", - "start": 13595, - "end": 13601, + "start": 14228, + "end": 14234, "loc": { "start": { - "line": 435, + "line": 454, "column": 54 }, "end": { - "line": 435, + "line": 454, "column": 60 }, "identifierName": "jsonld" @@ -43552,15 +45786,15 @@ }, "property": { "type": "StringLiteral", - "start": 13602, - "end": 13609, + "start": 14235, + "end": 14242, "loc": { "start": { - "line": 435, + "line": 454, "column": 61 }, "end": { - "line": 435, + "line": 454, "column": 68 } }, @@ -43582,15 +45816,15 @@ { "type": "CommentLine", "value": " Make it explicit that the type includes the nomenclaturalCode.", - "start": 13618, - "end": 13683, + "start": 14251, + "end": 14316, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 69 } } @@ -43599,44 +45833,44 @@ }, { "type": "VariableDeclaration", - "start": 13688, - "end": 13729, + "start": 14321, + "end": 14362, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 45 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 13694, - "end": 13728, + "start": 14327, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 10 }, "end": { - "line": 438, + "line": 457, "column": 44 } }, "id": { "type": "Identifier", - "start": 13694, - "end": 13703, + "start": 14327, + "end": 14336, "loc": { "start": { - "line": 438, + "line": 457, "column": 10 }, "end": { - "line": 438, + "line": 457, "column": 19 }, "identifierName": "nomenCode" @@ -43646,44 +45880,44 @@ }, "init": { "type": "MemberExpression", - "start": 13706, - "end": 13728, + "start": 14339, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 44 } }, "object": { "type": "ThisExpression", - "start": 13706, - "end": 13710, + "start": 14339, + "end": 14343, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 26 } } }, "property": { "type": "Identifier", - "start": 13711, - "end": 13728, + "start": 14344, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 27 }, "end": { - "line": 438, + "line": 457, "column": 44 }, "identifierName": "nomenclaturalCode" @@ -43700,15 +45934,15 @@ { "type": "CommentLine", "value": " Make it explicit that the type includes the nomenclaturalCode.", - "start": 13618, - "end": 13683, + "start": 14251, + "end": 14316, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 69 } } @@ -43717,29 +45951,29 @@ }, { "type": "IfStatement", - "start": 13734, - "end": 13808, + "start": 14367, + "end": 14441, "loc": { "start": { - "line": 439, + "line": 458, "column": 4 }, "end": { - "line": 439, + "line": 458, "column": 78 } }, "test": { "type": "UnaryExpression", - "start": 13738, - "end": 13774, + "start": 14371, + "end": 14407, "loc": { "start": { - "line": 439, + "line": 458, "column": 8 }, "end": { - "line": 439, + "line": 458, "column": 44 } }, @@ -43747,57 +45981,57 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 13739, - "end": 13774, + "start": 14372, + "end": 14407, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 44 } }, "callee": { "type": "MemberExpression", - "start": 13739, - "end": 13763, + "start": 14372, + "end": 14396, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 33 } }, "object": { "type": "MemberExpression", - "start": 13739, - "end": 13754, + "start": 14372, + "end": 14387, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 24 } }, "object": { "type": "Identifier", - "start": 13739, - "end": 13745, + "start": 14372, + "end": 14378, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 15 }, "identifierName": "jsonld" @@ -43806,15 +46040,15 @@ }, "property": { "type": "StringLiteral", - "start": 13746, - "end": 13753, + "start": 14379, + "end": 14386, "loc": { "start": { - "line": 439, + "line": 458, "column": 16 }, "end": { - "line": 439, + "line": 458, "column": 23 } }, @@ -43828,15 +46062,15 @@ }, "property": { "type": "Identifier", - "start": 13755, - "end": 13763, + "start": 14388, + "end": 14396, "loc": { "start": { - "line": 439, + "line": 458, "column": 25 }, "end": { - "line": 439, + "line": 458, "column": 33 }, "identifierName": "includes" @@ -43848,15 +46082,15 @@ "arguments": [ { "type": "Identifier", - "start": 13764, - "end": 13773, + "start": 14397, + "end": 14406, "loc": { "start": { - "line": 439, + "line": 458, "column": 34 }, "end": { - "line": 439, + "line": 458, "column": 43 }, "identifierName": "nomenCode" @@ -43871,71 +46105,71 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 13776, - "end": 13808, + "start": 14409, + "end": 14441, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 78 } }, "expression": { "type": "CallExpression", - "start": 13776, - "end": 13807, + "start": 14409, + "end": 14440, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 77 } }, "callee": { "type": "MemberExpression", - "start": 13776, - "end": 13796, + "start": 14409, + "end": 14429, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 66 } }, "object": { "type": "MemberExpression", - "start": 13776, - "end": 13791, + "start": 14409, + "end": 14424, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 61 } }, "object": { "type": "Identifier", - "start": 13776, - "end": 13782, + "start": 14409, + "end": 14415, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 52 }, "identifierName": "jsonld" @@ -43944,15 +46178,15 @@ }, "property": { "type": "StringLiteral", - "start": 13783, - "end": 13790, + "start": 14416, + "end": 14423, "loc": { "start": { - "line": 439, + "line": 458, "column": 53 }, "end": { - "line": 439, + "line": 458, "column": 60 } }, @@ -43966,15 +46200,15 @@ }, "property": { "type": "Identifier", - "start": 13792, - "end": 13796, + "start": 14425, + "end": 14429, "loc": { "start": { - "line": 439, + "line": 458, "column": 62 }, "end": { - "line": 439, + "line": 458, "column": 66 }, "identifierName": "push" @@ -43986,15 +46220,15 @@ "arguments": [ { "type": "Identifier", - "start": 13797, - "end": 13806, + "start": 14430, + "end": 14439, "loc": { "start": { - "line": 439, + "line": 458, "column": 67 }, "end": { - "line": 439, + "line": 458, "column": 76 }, "identifierName": "nomenCode" @@ -44008,29 +46242,29 @@ }, { "type": "ReturnStatement", - "start": 13814, - "end": 13828, + "start": 14447, + "end": 14461, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 18 } }, "argument": { "type": "Identifier", - "start": 13821, - "end": 13827, + "start": 14454, + "end": 14460, "loc": { "start": { - "line": 441, + "line": 460, "column": 11 }, "end": { - "line": 441, + "line": 460, "column": 17 }, "identifierName": "jsonld" @@ -44046,15 +46280,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name in an JSON-LD representation.\n ", - "start": 13319, - "end": 13386, + "start": 13952, + "end": 14019, "loc": { "start": { - "line": 427, + "line": 446, "column": 2 }, "end": { - "line": 429, + "line": 448, "column": 5 } } @@ -44064,15 +46298,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", - "start": 13836, - "end": 13911, + "start": 14469, + "end": 14544, "loc": { "start": { - "line": 444, + "line": 463, "column": 2 }, "end": { - "line": 446, + "line": 465, "column": 5 } } @@ -44081,15 +46315,15 @@ }, { "type": "ClassMethod", - "start": 13914, - "end": 14748, + "start": 14547, + "end": 15381, "loc": { "start": { - "line": 447, + "line": 466, "column": 2 }, "end": { - "line": 476, + "line": 495, "column": 3 } }, @@ -44097,15 +46331,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 13918, - "end": 13933, + "start": 14551, + "end": 14566, "loc": { "start": { - "line": 447, + "line": 466, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 21 }, "identifierName": "asOWLEquivClass" @@ -44120,44 +46354,44 @@ "params": [], "body": { "type": "BlockStatement", - "start": 13936, - "end": 14748, + "start": 14569, + "end": 15381, "loc": { "start": { - "line": 447, + "line": 466, "column": 24 }, "end": { - "line": 476, + "line": 495, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 13990, - "end": 14031, + "start": 14623, + "end": 14664, "loc": { "start": { - "line": 449, + "line": 468, "column": 4 }, "end": { - "line": 449, + "line": 468, "column": 45 } }, "test": { "type": "UnaryExpression", - "start": 13994, - "end": 14012, + "start": 14627, + "end": 14645, "loc": { "start": { - "line": 449, + "line": 468, "column": 8 }, "end": { - "line": 449, + "line": 468, "column": 26 } }, @@ -44165,29 +46399,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 13995, - "end": 14012, + "start": 14628, + "end": 14645, "loc": { "start": { - "line": 449, + "line": 468, "column": 9 }, "end": { - "line": 449, + "line": 468, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 13995, - "end": 13999, + "start": 14628, + "end": 14632, "loc": { "start": { - "line": 449, + "line": 468, "column": 9 }, "end": { - "line": 449, + "line": 468, "column": 13 } }, @@ -44195,15 +46429,15 @@ }, "property": { "type": "Identifier", - "start": 14000, - "end": 14012, + "start": 14633, + "end": 14645, "loc": { "start": { - "line": 449, + "line": 468, "column": 14 }, "end": { - "line": 449, + "line": 468, "column": 26 }, "identifierName": "nameComplete" @@ -44220,29 +46454,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 14014, - "end": 14031, + "start": 14647, + "end": 14664, "loc": { "start": { - "line": 449, + "line": 468, "column": 28 }, "end": { - "line": 449, + "line": 468, "column": 45 } }, "argument": { "type": "Identifier", - "start": 14021, - "end": 14030, + "start": 14654, + "end": 14663, "loc": { "start": { - "line": 449, + "line": 468, "column": 35 }, "end": { - "line": 449, + "line": 468, "column": 44 }, "identifierName": "undefined" @@ -44256,15 +46490,15 @@ { "type": "CommentLine", "value": " No complete name, can't return anything.", - "start": 13942, - "end": 13985, + "start": 14575, + "end": 14618, "loc": { "start": { - "line": 448, + "line": 467, "column": 4 }, "end": { - "line": 448, + "line": 467, "column": 47 } } @@ -44274,15 +46508,15 @@ { "type": "CommentLine", "value": " Do we have a nomenclaturalCode?", - "start": 14037, - "end": 14071, + "start": 14670, + "end": 14704, "loc": { "start": { - "line": 451, + "line": 470, "column": 4 }, "end": { - "line": 451, + "line": 470, "column": 38 } } @@ -44291,29 +46525,29 @@ }, { "type": "IfStatement", - "start": 14076, - "end": 14262, + "start": 14709, + "end": 14895, "loc": { "start": { - "line": 452, + "line": 471, "column": 4 }, "end": { - "line": 458, + "line": 477, "column": 5 } }, "test": { "type": "UnaryExpression", - "start": 14080, - "end": 14103, + "start": 14713, + "end": 14736, "loc": { "start": { - "line": 452, + "line": 471, "column": 8 }, "end": { - "line": 452, + "line": 471, "column": 31 } }, @@ -44321,29 +46555,29 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 14081, - "end": 14103, + "start": 14714, + "end": 14736, "loc": { "start": { - "line": 452, + "line": 471, "column": 9 }, "end": { - "line": 452, + "line": 471, "column": 31 } }, "object": { "type": "ThisExpression", - "start": 14081, - "end": 14085, + "start": 14714, + "end": 14718, "loc": { "start": { - "line": 452, + "line": 471, "column": 9 }, "end": { - "line": 452, + "line": 471, "column": 13 } }, @@ -44351,15 +46585,15 @@ }, "property": { "type": "Identifier", - "start": 14086, - "end": 14103, + "start": 14719, + "end": 14736, "loc": { "start": { - "line": 452, + "line": 471, "column": 14 }, "end": { - "line": 452, + "line": 471, "column": 31 }, "identifierName": "nomenclaturalCode" @@ -44376,59 +46610,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 14105, - "end": 14262, + "start": 14738, + "end": 14895, "loc": { "start": { - "line": 452, + "line": 471, "column": 33 }, "end": { - "line": 458, + "line": 477, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 14113, - "end": 14256, + "start": 14746, + "end": 14889, "loc": { "start": { - "line": 453, + "line": 472, "column": 6 }, "end": { - "line": 457, + "line": 476, "column": 8 } }, "argument": { "type": "ObjectExpression", - "start": 14120, - "end": 14255, + "start": 14753, + "end": 14888, "loc": { "start": { - "line": 453, + "line": 472, "column": 13 }, "end": { - "line": 457, + "line": 476, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 14130, - "end": 14156, + "start": 14763, + "end": 14789, "loc": { "start": { - "line": 454, + "line": 473, "column": 8 }, "end": { - "line": 454, + "line": 473, "column": 34 } }, @@ -44437,15 +46671,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14130, - "end": 14137, + "start": 14763, + "end": 14770, "loc": { "start": { - "line": 454, + "line": 473, "column": 8 }, "end": { - "line": 454, + "line": 473, "column": 15 } }, @@ -44457,15 +46691,15 @@ }, "value": { "type": "StringLiteral", - "start": 14139, - "end": 14156, + "start": 14772, + "end": 14789, "loc": { "start": { - "line": 454, + "line": 473, "column": 17 }, "end": { - "line": 454, + "line": 473, "column": 34 } }, @@ -44478,15 +46712,15 @@ }, { "type": "ObjectProperty", - "start": 14166, - "end": 14209, + "start": 14799, + "end": 14842, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 51 } }, @@ -44495,15 +46729,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14166, - "end": 14176, + "start": 14799, + "end": 14809, "loc": { "start": { - "line": 455, + "line": 474, "column": 8 }, "end": { - "line": 455, + "line": 474, "column": 18 }, "identifierName": "onProperty" @@ -44512,29 +46746,29 @@ }, "value": { "type": "MemberExpression", - "start": 14178, - "end": 14209, + "start": 14811, + "end": 14842, "loc": { "start": { - "line": 455, + "line": 474, "column": 20 }, "end": { - "line": 455, + "line": 474, "column": 51 } }, "object": { "type": "Identifier", - "start": 14178, - "end": 14186, + "start": 14811, + "end": 14819, "loc": { "start": { - "line": 455, + "line": 474, "column": 20 }, "end": { - "line": 455, + "line": 474, "column": 28 }, "identifierName": "owlterms" @@ -44543,15 +46777,15 @@ }, "property": { "type": "Identifier", - "start": 14187, - "end": 14209, + "start": 14820, + "end": 14842, "loc": { "start": { - "line": 455, + "line": 474, "column": 29 }, "end": { - "line": 455, + "line": 474, "column": 51 }, "identifierName": "TDWG_VOC_NAME_COMPLETE" @@ -44563,15 +46797,15 @@ }, { "type": "ObjectProperty", - "start": 14219, - "end": 14246, + "start": 14852, + "end": 14879, "loc": { "start": { - "line": 456, + "line": 475, "column": 8 }, "end": { - "line": 456, + "line": 475, "column": 35 } }, @@ -44580,15 +46814,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14219, - "end": 14227, + "start": 14852, + "end": 14860, "loc": { "start": { - "line": 456, + "line": 475, "column": 8 }, "end": { - "line": 456, + "line": 475, "column": 16 }, "identifierName": "hasValue" @@ -44597,44 +46831,44 @@ }, "value": { "type": "MemberExpression", - "start": 14229, - "end": 14246, + "start": 14862, + "end": 14879, "loc": { "start": { - "line": 456, + "line": 475, "column": 18 }, "end": { - "line": 456, + "line": 475, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 14229, - "end": 14233, + "start": 14862, + "end": 14866, "loc": { "start": { - "line": 456, + "line": 475, "column": 18 }, "end": { - "line": 456, + "line": 475, "column": 22 } } }, "property": { "type": "Identifier", - "start": 14234, - "end": 14246, + "start": 14867, + "end": 14879, "loc": { "start": { - "line": 456, + "line": 475, "column": 23 }, "end": { - "line": 456, + "line": 475, "column": 35 }, "identifierName": "nameComplete" @@ -44656,15 +46890,15 @@ { "type": "CommentLine", "value": " Do we have a nomenclaturalCode?", - "start": 14037, - "end": 14071, + "start": 14670, + "end": 14704, "loc": { "start": { - "line": 451, + "line": 470, "column": 4 }, "end": { - "line": 451, + "line": 470, "column": 38 } } @@ -44674,15 +46908,15 @@ { "type": "CommentLine", "value": " If we do have a nomenclatural code, incorporate that into the logical", - "start": 14268, - "end": 14340, + "start": 14901, + "end": 14973, "loc": { "start": { - "line": 460, + "line": 479, "column": 4 }, "end": { - "line": 460, + "line": 479, "column": 76 } } @@ -44690,15 +46924,15 @@ { "type": "CommentLine", "value": " expression as well.", - "start": 14345, - "end": 14367, + "start": 14978, + "end": 15000, "loc": { "start": { - "line": 461, + "line": 480, "column": 4 }, "end": { - "line": 461, + "line": 480, "column": 26 } } @@ -44707,44 +46941,44 @@ }, { "type": "ReturnStatement", - "start": 14372, - "end": 14744, + "start": 15005, + "end": 15377, "loc": { "start": { - "line": 462, + "line": 481, "column": 4 }, "end": { - "line": 475, + "line": 494, "column": 6 } }, "argument": { "type": "ObjectExpression", - "start": 14379, - "end": 14743, + "start": 15012, + "end": 15376, "loc": { "start": { - "line": 462, + "line": 481, "column": 11 }, "end": { - "line": 475, + "line": 494, "column": 5 } }, "properties": [ { "type": "ObjectProperty", - "start": 14387, - "end": 14407, + "start": 15020, + "end": 15040, "loc": { "start": { - "line": 463, + "line": 482, "column": 6 }, "end": { - "line": 463, + "line": 482, "column": 26 } }, @@ -44753,15 +46987,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14387, - "end": 14394, + "start": 15020, + "end": 15027, "loc": { "start": { - "line": 463, + "line": 482, "column": 6 }, "end": { - "line": 463, + "line": 482, "column": 13 } }, @@ -44774,15 +47008,15 @@ }, "value": { "type": "StringLiteral", - "start": 14396, - "end": 14407, + "start": 15029, + "end": 15040, "loc": { "start": { - "line": 463, + "line": 482, "column": 15 }, "end": { - "line": 463, + "line": 482, "column": 26 } }, @@ -44796,15 +47030,15 @@ }, { "type": "ObjectProperty", - "start": 14415, - "end": 14736, + "start": 15048, + "end": 15369, "loc": { "start": { - "line": 464, + "line": 483, "column": 6 }, "end": { - "line": 474, + "line": 493, "column": 8 } }, @@ -44813,15 +47047,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14415, - "end": 14429, + "start": 15048, + "end": 15062, "loc": { "start": { - "line": 464, + "line": 483, "column": 6 }, "end": { - "line": 464, + "line": 483, "column": 20 }, "identifierName": "intersectionOf" @@ -44830,45 +47064,45 @@ }, "value": { "type": "ArrayExpression", - "start": 14431, - "end": 14736, + "start": 15064, + "end": 15369, "loc": { "start": { - "line": 464, + "line": 483, "column": 22 }, "end": { - "line": 474, + "line": 493, "column": 8 } }, "elements": [ { "type": "ObjectExpression", - "start": 14432, - "end": 14567, + "start": 15065, + "end": 15200, "loc": { "start": { - "line": 464, + "line": 483, "column": 23 }, "end": { - "line": 468, + "line": 487, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 14442, - "end": 14468, + "start": 15075, + "end": 15101, "loc": { "start": { - "line": 465, + "line": 484, "column": 8 }, "end": { - "line": 465, + "line": 484, "column": 34 } }, @@ -44877,15 +47111,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14442, - "end": 14449, + "start": 15075, + "end": 15082, "loc": { "start": { - "line": 465, + "line": 484, "column": 8 }, "end": { - "line": 465, + "line": 484, "column": 15 } }, @@ -44897,15 +47131,15 @@ }, "value": { "type": "StringLiteral", - "start": 14451, - "end": 14468, + "start": 15084, + "end": 15101, "loc": { "start": { - "line": 465, + "line": 484, "column": 17 }, "end": { - "line": 465, + "line": 484, "column": 34 } }, @@ -44918,15 +47152,15 @@ }, { "type": "ObjectProperty", - "start": 14478, - "end": 14521, + "start": 15111, + "end": 15154, "loc": { "start": { - "line": 466, + "line": 485, "column": 8 }, "end": { - "line": 466, + "line": 485, "column": 51 } }, @@ -44935,15 +47169,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14478, - "end": 14488, + "start": 15111, + "end": 15121, "loc": { "start": { - "line": 466, + "line": 485, "column": 8 }, "end": { - "line": 466, + "line": 485, "column": 18 }, "identifierName": "onProperty" @@ -44952,29 +47186,29 @@ }, "value": { "type": "MemberExpression", - "start": 14490, - "end": 14521, + "start": 15123, + "end": 15154, "loc": { "start": { - "line": 466, + "line": 485, "column": 20 }, "end": { - "line": 466, + "line": 485, "column": 51 } }, "object": { "type": "Identifier", - "start": 14490, - "end": 14498, + "start": 15123, + "end": 15131, "loc": { "start": { - "line": 466, + "line": 485, "column": 20 }, "end": { - "line": 466, + "line": 485, "column": 28 }, "identifierName": "owlterms" @@ -44983,15 +47217,15 @@ }, "property": { "type": "Identifier", - "start": 14499, - "end": 14521, + "start": 15132, + "end": 15154, "loc": { "start": { - "line": 466, + "line": 485, "column": 29 }, "end": { - "line": 466, + "line": 485, "column": 51 }, "identifierName": "TDWG_VOC_NAME_COMPLETE" @@ -45003,15 +47237,15 @@ }, { "type": "ObjectProperty", - "start": 14531, - "end": 14558, + "start": 15164, + "end": 15191, "loc": { "start": { - "line": 467, + "line": 486, "column": 8 }, "end": { - "line": 467, + "line": 486, "column": 35 } }, @@ -45020,15 +47254,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14531, - "end": 14539, + "start": 15164, + "end": 15172, "loc": { "start": { - "line": 467, + "line": 486, "column": 8 }, "end": { - "line": 467, + "line": 486, "column": 16 }, "identifierName": "hasValue" @@ -45037,44 +47271,44 @@ }, "value": { "type": "MemberExpression", - "start": 14541, - "end": 14558, + "start": 15174, + "end": 15191, "loc": { "start": { - "line": 467, + "line": 486, "column": 18 }, "end": { - "line": 467, + "line": 486, "column": 35 } }, "object": { "type": "ThisExpression", - "start": 14541, - "end": 14545, + "start": 15174, + "end": 15178, "loc": { "start": { - "line": 467, + "line": 486, "column": 18 }, "end": { - "line": 467, + "line": 486, "column": 22 } } }, "property": { "type": "Identifier", - "start": 14546, - "end": 14558, + "start": 15179, + "end": 15191, "loc": { "start": { - "line": 467, + "line": 486, "column": 23 }, "end": { - "line": 467, + "line": 486, "column": 35 }, "identifierName": "nameComplete" @@ -45088,30 +47322,30 @@ }, { "type": "ObjectExpression", - "start": 14569, - "end": 14735, + "start": 15202, + "end": 15368, "loc": { "start": { - "line": 468, + "line": 487, "column": 9 }, "end": { - "line": 474, + "line": 493, "column": 7 } }, "properties": [ { "type": "ObjectProperty", - "start": 14579, - "end": 14605, + "start": 15212, + "end": 15238, "loc": { "start": { - "line": 469, + "line": 488, "column": 8 }, "end": { - "line": 469, + "line": 488, "column": 34 } }, @@ -45120,15 +47354,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14579, - "end": 14586, + "start": 15212, + "end": 15219, "loc": { "start": { - "line": 469, + "line": 488, "column": 8 }, "end": { - "line": 469, + "line": 488, "column": 15 } }, @@ -45140,15 +47374,15 @@ }, "value": { "type": "StringLiteral", - "start": 14588, - "end": 14605, + "start": 15221, + "end": 15238, "loc": { "start": { - "line": 469, + "line": 488, "column": 17 }, "end": { - "line": 469, + "line": 488, "column": 34 } }, @@ -45161,15 +47395,15 @@ }, { "type": "ObjectProperty", - "start": 14615, - "end": 14654, + "start": 15248, + "end": 15287, "loc": { "start": { - "line": 470, + "line": 489, "column": 8 }, "end": { - "line": 470, + "line": 489, "column": 47 } }, @@ -45178,15 +47412,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14615, - "end": 14625, + "start": 15248, + "end": 15258, "loc": { "start": { - "line": 470, + "line": 489, "column": 8 }, "end": { - "line": 470, + "line": 489, "column": 18 }, "identifierName": "onProperty" @@ -45195,29 +47429,29 @@ }, "value": { "type": "MemberExpression", - "start": 14627, - "end": 14654, + "start": 15260, + "end": 15287, "loc": { "start": { - "line": 470, + "line": 489, "column": 20 }, "end": { - "line": 470, + "line": 489, "column": 47 } }, "object": { "type": "Identifier", - "start": 14627, - "end": 14635, + "start": 15260, + "end": 15268, "loc": { "start": { - "line": 470, + "line": 489, "column": 20 }, "end": { - "line": 470, + "line": 489, "column": 28 }, "identifierName": "owlterms" @@ -45226,15 +47460,15 @@ }, "property": { "type": "Identifier", - "start": 14636, - "end": 14654, + "start": 15269, + "end": 15287, "loc": { "start": { - "line": 470, + "line": 489, "column": 29 }, "end": { - "line": 470, + "line": 489, "column": 47 }, "identifierName": "NOMENCLATURAL_CODE" @@ -45246,15 +47480,15 @@ }, { "type": "ObjectProperty", - "start": 14664, - "end": 14726, + "start": 15297, + "end": 15359, "loc": { "start": { - "line": 471, + "line": 490, "column": 8 }, "end": { - "line": 473, + "line": 492, "column": 9 } }, @@ -45263,15 +47497,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 14664, - "end": 14672, + "start": 15297, + "end": 15305, "loc": { "start": { - "line": 471, + "line": 490, "column": 8 }, "end": { - "line": 471, + "line": 490, "column": 16 }, "identifierName": "hasValue" @@ -45280,30 +47514,30 @@ }, "value": { "type": "ObjectExpression", - "start": 14674, - "end": 14726, + "start": 15307, + "end": 15359, "loc": { "start": { - "line": 471, + "line": 490, "column": 18 }, "end": { - "line": 473, + "line": 492, "column": 9 } }, "properties": [ { "type": "ObjectProperty", - "start": 14686, - "end": 14715, + "start": 15319, + "end": 15348, "loc": { "start": { - "line": 472, + "line": 491, "column": 10 }, "end": { - "line": 472, + "line": 491, "column": 39 } }, @@ -45312,15 +47546,15 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 14686, - "end": 14691, + "start": 15319, + "end": 15324, "loc": { "start": { - "line": 472, + "line": 491, "column": 10 }, "end": { - "line": 472, + "line": 491, "column": 15 } }, @@ -45332,44 +47566,44 @@ }, "value": { "type": "MemberExpression", - "start": 14693, - "end": 14715, + "start": 15326, + "end": 15348, "loc": { "start": { - "line": 472, + "line": 491, "column": 17 }, "end": { - "line": 472, + "line": 491, "column": 39 } }, "object": { "type": "ThisExpression", - "start": 14693, - "end": 14697, + "start": 15326, + "end": 15330, "loc": { "start": { - "line": 472, + "line": 491, "column": 17 }, "end": { - "line": 472, + "line": 491, "column": 21 } } }, "property": { "type": "Identifier", - "start": 14698, - "end": 14715, + "start": 15331, + "end": 15348, "loc": { "start": { - "line": 472, + "line": 491, "column": 22 }, "end": { - "line": 472, + "line": 491, "column": 39 }, "identifierName": "nomenclaturalCode" @@ -45394,15 +47628,15 @@ { "type": "CommentLine", "value": " If we do have a nomenclatural code, incorporate that into the logical", - "start": 14268, - "end": 14340, + "start": 14901, + "end": 14973, "loc": { "start": { - "line": 460, + "line": 479, "column": 4 }, "end": { - "line": 460, + "line": 479, "column": 76 } } @@ -45410,15 +47644,15 @@ { "type": "CommentLine", "value": " expression as well.", - "start": 14345, - "end": 14367, + "start": 14978, + "end": 15000, "loc": { "start": { - "line": 461, + "line": 480, "column": 4 }, "end": { - "line": 461, + "line": 480, "column": 26 } } @@ -45432,15 +47666,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", - "start": 13836, - "end": 13911, + "start": 14469, + "end": 14544, "loc": { "start": { - "line": 444, + "line": 463, "column": 2 }, "end": { - "line": 446, + "line": 465, "column": 5 } } @@ -45501,1100 +47735,3292 @@ "end": 141, "loc": { "start": { - "line": 5, - "column": 0 + "line": 5, + "column": 0 + }, + "end": { + "line": 5, + "column": 21 + } + } + }, + { + "type": "CommentBlock", + "value": "* We need the cache manager to memoize parsing scientific names. ", + "start": 185, + "end": 254, + "loc": { + "start": { + "line": 8, + "column": 0 + }, + "end": { + "line": 8, + "column": 69 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n ", + "start": 361, + "end": 1751, + "loc": { + "start": { + "line": 12, + "column": 0 + }, + "end": { + "line": 39, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n ", + "start": 1779, + "end": 1878, + "loc": { + "start": { + "line": 41, + "column": 2 + }, + "end": { + "line": 44, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The type associated with these taxonName objects.\n ", + "start": 2115, + "end": 2179, + "loc": { + "start": { + "line": 51, + "column": 2 + }, + "end": { + "line": 53, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n ", + "start": 2261, + "end": 2368, + "loc": { + "start": { + "line": 58, + "column": 2 + }, + "end": { + "line": 60, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": " Directly access IRIs for nomenclatural codes. ", + "start": 2440, + "end": 2491, + "loc": { + "start": { + "line": 65, + "column": 2 + }, + "end": { + "line": 65, + "column": 53 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n ", + "start": 2779, + "end": 3281, + "loc": { + "start": { + "line": 76, + "column": 2 + }, + "end": { + "line": 86, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Note: the unknown code needs to be the first one in this list.", + "start": 3336, + "end": 3401, + "loc": { + "start": { + "line": 89, + "column": 6 + }, + "end": { + "line": 89, + "column": 71 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Returns the nomenclatural code entry for a code.\n ", + "start": 4534, + "end": 4597, + "loc": { + "start": { + "line": 129, + "column": 2 + }, + "end": { + "line": 131, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " If the nomenCode provided is owlterms.UNKNOWN_CODE,", + "start": 4705, + "end": 4759, + "loc": { + "start": { + "line": 135, + "column": 4 + }, + "end": { + "line": 135, + "column": 58 + } + } + }, + { + "type": "CommentLine", + "value": " return that entry.", + "start": 4764, + "end": 4785, + "loc": { + "start": { + "line": 136, + "column": 4 + }, + "end": { + "line": 136, + "column": 25 + } + } + }, + { + "type": "CommentLine", + "value": " Look for the entry with the same IRI as the provided IRI.", + "start": 4867, + "end": 4927, + "loc": { + "start": { + "line": 141, + "column": 4 + }, + "end": { + "line": 141, + "column": 64 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Normalize the specified taxon name.\n * @param txname A taxon name to be normalized.\n ", + "start": 5112, + "end": 5212, + "loc": { + "start": { + "line": 148, + "column": 2 + }, + "end": { + "line": 151, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Returns the nomenclatural code of this taxon name.\n ", + "start": 5745, + "end": 5810, + "loc": { + "start": { + "line": 167, + "column": 2 + }, + "end": { + "line": 169, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Returns the nomenclatural code of this taxon name as a IRI.\n ", + "start": 5913, + "end": 5987, + "loc": { + "start": { + "line": 174, + "column": 2 + }, + "end": { + "line": 176, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Set the nomenclatural code of this taxon name.\n ", + "start": 6205, + "end": 6266, + "loc": { + "start": { + "line": 185, + "column": 2 + }, + "end": { + "line": 187, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n ", + "start": 6358, + "end": 6432, + "loc": { + "start": { + "line": 192, + "column": 2 + }, + "end": { + "line": 194, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Have we already parsed this verbatim name?", + "start": 6514, + "end": 6559, + "loc": { + "start": { + "line": 196, + "column": 4 + }, + "end": { + "line": 196, + "column": 49 + } + } + }, + { + "type": "CommentLine", + "value": " Use a regular expression to parse the verbatimName.", + "start": 6762, + "end": 6816, + "loc": { + "start": { + "line": 201, + "column": 4 + }, + "end": { + "line": 201, + "column": 58 + } + } + }, + { + "type": "CommentLine", + "value": " Attempt 1. Look for a trinomial name.", + "start": 6822, + "end": 6862, + "loc": { + "start": { + "line": 203, + "column": 4 + }, + "end": { + "line": 203, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " Attempt 2. Look for a binomial name.", + "start": 7293, + "end": 7332, + "loc": { + "start": { + "line": 218, + "column": 4 + }, + "end": { + "line": 218, + "column": 43 + } + } + }, + { + "type": "CommentLine", + "value": " Attempt 3. Look for a uninomial name.", + "start": 7718, + "end": 7758, + "loc": { + "start": { + "line": 233, + "column": 4 + }, + "end": { + "line": 233, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " Is it a uninomial name?", + "start": 7784, + "end": 7810, + "loc": { + "start": { + "line": 235, + "column": 6 + }, + "end": { + "line": 235, + "column": 32 + } + } + }, + { + "type": "CommentLine", + "value": " Add a nomenclatural code if possible.", + "start": 8099, + "end": 8139, + "loc": { + "start": { + "line": 247, + "column": 4 + }, + "end": { + "line": 247, + "column": 44 + } + } + }, + { + "type": "CommentLine", + "value": " Store in the cache.", + "start": 8226, + "end": 8248, + "loc": { + "start": { + "line": 252, + "column": 4 + }, + "end": { + "line": 252, + "column": 26 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the label of this scientific name.\n ", + "start": 8412, + "end": 8468, + "loc": { + "start": { + "line": 260, + "column": 2 + }, + "end": { + "line": 262, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Set the label of this scientific name.\n ", + "start": 8543, + "end": 8596, + "loc": { + "start": { + "line": 267, + "column": 2 + }, + "end": { + "line": 269, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " If we don't have a nameComplete, treat this as the name complete.", + "start": 8681, + "end": 8749, + "loc": { + "start": { + "line": 273, + "column": 6 + }, + "end": { + "line": 273, + "column": 74 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the verbatim name of this taxon name.\n ", + "start": 8794, + "end": 8853, + "loc": { + "start": { + "line": 278, + "column": 2 + }, + "end": { + "line": 280, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", + "start": 8914, + "end": 9037, + "loc": { + "start": { + "line": 285, + "column": 2 + }, + "end": { + "line": 288, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", + "start": 9188, + "end": 9268, + "loc": { + "start": { + "line": 296, + "column": 2 + }, + "end": { + "line": 298, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the uninomial name if there is one. ", + "start": 9386, + "end": 9435, + "loc": { + "start": { + "line": 303, + "column": 2 + }, + "end": { + "line": 303, + "column": 51 + } + } + }, + { + "type": "CommentLine", + "value": " If there is no genus but there is a scientificName, try to extract a genus", + "start": 9522, + "end": 9599, + "loc": { + "start": { + "line": 307, + "column": 4 + }, + "end": { + "line": 307, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " from it.", + "start": 9604, + "end": 9615, + "loc": { + "start": { + "line": 308, + "column": 4 + }, + "end": { + "line": 308, + "column": 15 + } + } + }, + { + "type": "CommentBlock", + "value": "* Set the uninomial name. ", + "start": 9879, + "end": 9909, + "loc": { + "start": { + "line": 320, + "column": 2 + }, + "end": { + "line": 320, + "column": 32 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the binomial name if available. ", + "start": 10018, + "end": 10063, + "loc": { + "start": { + "line": 326, + "column": 2 + }, + "end": { + "line": 326, + "column": 47 + } + } + }, + { + "type": "CommentLine", + "value": " Get the binomial name. Constructed from the genus and specific epithet", + "start": 10091, + "end": 10164, + "loc": { + "start": { + "line": 328, + "column": 4 + }, + "end": { + "line": 328, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " if available.", + "start": 10169, + "end": 10185, + "loc": { + "start": { + "line": 329, + "column": 4 + }, + "end": { + "line": 329, + "column": 20 + } + } + }, + { + "type": "CommentBlock", + "value": "* Set the binomial name. ", + "start": 10343, + "end": 10372, + "loc": { + "start": { + "line": 334, + "column": 2 + }, + "end": { + "line": 334, + "column": 31 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the trinomial name if available. ", + "start": 10485, + "end": 10531, + "loc": { + "start": { + "line": 340, + "column": 2 + }, + "end": { + "line": 340, + "column": 48 + } + } + }, + { + "type": "CommentBlock", + "value": "* Set the trinomial name. ", + "start": 10809, + "end": 10839, + "loc": { + "start": { + "line": 350, + "column": 2 + }, + "end": { + "line": 350, + "column": 32 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the genus part of this scientific name if available. ", + "start": 10955, + "end": 11021, + "loc": { + "start": { + "line": 356, + "column": 2 + }, + "end": { + "line": 356, + "column": 68 + } + } + }, + { + "type": "CommentLine", + "value": " Try to read the genus if available.", + "start": 11046, + "end": 11084, + "loc": { + "start": { + "line": 358, + "column": 4 + }, + "end": { + "line": 358, + "column": 42 + } + } + }, + { + "type": "CommentLine", + "value": " If there is no genus but there is a scientificName, try to extract a genus", + "start": 11159, + "end": 11236, + "loc": { + "start": { + "line": 361, + "column": 4 + }, + "end": { + "line": 361, + "column": 81 + } + } + }, + { + "type": "CommentLine", + "value": " from it.", + "start": 11241, + "end": 11252, + "loc": { + "start": { + "line": 362, + "column": 4 + }, + "end": { + "line": 362, + "column": 15 + } + } + }, + { + "type": "CommentBlock", + "value": "* Set the genus part of this name. ", + "start": 11516, + "end": 11555, + "loc": { + "start": { + "line": 374, + "column": 2 + }, + "end": { + "line": 374, + "column": 41 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the specific epithet of this scientific name if available. ", + "start": 11894, + "end": 11966, + "loc": { + "start": { + "line": 386, + "column": 2 + }, + "end": { + "line": 386, + "column": 74 + } + } + }, + { + "type": "CommentLine", + "value": " Try to read the specific epithet if available.", + "start": 11997, + "end": 12046, + "loc": { + "start": { + "line": 388, + "column": 4 + }, + "end": { + "line": 388, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": " If there is no specific epithet but there is a scientificName, try to", + "start": 12133, + "end": 12205, + "loc": { + "start": { + "line": 391, + "column": 4 + }, + "end": { + "line": 391, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " extract a specific epithet from it.", + "start": 12210, + "end": 12248, + "loc": { + "start": { + "line": 392, + "column": 4 + }, + "end": { + "line": 392, + "column": 42 + } + } + }, + { + "type": "CommentBlock", + "value": "* Set the specificEpithet part of this name. ", + "start": 12510, + "end": 12559, + "loc": { + "start": { + "line": 404, + "column": 2 + }, + "end": { + "line": 404, + "column": 51 + } + } + }, + { + "type": "CommentBlock", + "value": "* Return the infraspecific epithet of this scientific name if available. ", + "start": 12900, + "end": 12977, + "loc": { + "start": { + "line": 416, + "column": 2 + }, + "end": { + "line": 416, + "column": 79 + } + } + }, + { + "type": "CommentLine", + "value": " Try to read the specific epithet if available.", + "start": 13013, + "end": 13062, + "loc": { + "start": { + "line": 418, + "column": 4 + }, + "end": { + "line": 418, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": " If there is no specific epithet but there is a scientificName, try to", + "start": 13159, + "end": 13231, + "loc": { + "start": { + "line": 421, + "column": 4 + }, + "end": { + "line": 421, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " extract a specific epithet from it.", + "start": 13236, + "end": 13274, + "loc": { + "start": { + "line": 422, + "column": 4 + }, + "end": { + "line": 422, + "column": 42 + } + } + }, + { + "type": "CommentBlock", + "value": "* Set the infraspecificEpithet part of this name. ", + "start": 13553, + "end": 13607, + "loc": { + "start": { + "line": 434, + "column": 2 + }, + "end": { + "line": 434, + "column": 56 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return this taxon name in an JSON-LD representation.\n ", + "start": 13952, + "end": 14019, + "loc": { + "start": { + "line": 446, + "column": 2 + }, + "end": { + "line": 448, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Make sure '@type' is an array.", + "start": 14087, + "end": 14120, + "loc": { + "start": { + "line": 452, + "column": 4 + }, + "end": { + "line": 452, + "column": 37 + } + } + }, + { + "type": "CommentLine", + "value": " Make it explicit that the type includes the nomenclaturalCode.", + "start": 14251, + "end": 14316, + "loc": { + "start": { + "line": 456, + "column": 4 + }, + "end": { + "line": 456, + "column": 69 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", + "start": 14469, + "end": 14544, + "loc": { + "start": { + "line": 463, + "column": 2 + }, + "end": { + "line": 465, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " No complete name, can't return anything.", + "start": 14575, + "end": 14618, + "loc": { + "start": { + "line": 467, + "column": 4 + }, + "end": { + "line": 467, + "column": 47 + } + } + }, + { + "type": "CommentLine", + "value": " Do we have a nomenclaturalCode?", + "start": 14670, + "end": 14704, + "loc": { + "start": { + "line": 470, + "column": 4 + }, + "end": { + "line": 470, + "column": 38 + } + } + }, + { + "type": "CommentLine", + "value": " If we do have a nomenclatural code, incorporate that into the logical", + "start": 14901, + "end": 14973, + "loc": { + "start": { + "line": 479, + "column": 4 + }, + "end": { + "line": 479, + "column": 76 + } + } + }, + { + "type": "CommentLine", + "value": " expression as well.", + "start": 14978, + "end": 15000, + "loc": { + "start": { + "line": 480, + "column": 4 + }, + "end": { + "line": 480, + "column": 26 + } + } + } + ], + "tokens": [ + { + "type": "CommentBlock", + "value": "* Utility functions. ", + "start": 0, + "end": 25, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 25 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 26, + "end": 32, + "loc": { + "start": { + "line": 2, + "column": 0 + }, + "end": { + "line": 2, + "column": 6 + } + } + }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 33, + "end": 34, + "loc": { + "start": { + "line": 2, + "column": 7 + }, + "end": { + "line": 2, + "column": 8 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 35, + "end": 37, + "loc": { + "start": { + "line": 2, + "column": 9 + }, + "end": { + "line": 2, + "column": 11 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9A559BE", + "start": 38, + "end": 51, + "loc": { + "start": { + "line": 2, + "column": 12 + }, + "end": { + "line": 2, + "column": 25 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 52, + "end": 56, + "loc": { + "start": { + "line": 2, + "column": 26 + }, + "end": { 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"column": 23 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "isArray", + "start": 92, + "end": 99, + "loc": { + "start": { + "line": 3, + "column": 24 + }, + "end": { + "line": 3, + "column": 31 + } + } + }, + { + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 100, + "end": 101, + "loc": { + "start": { + "line": 3, + "column": 32 + }, + "end": { + "line": 3, + "column": 33 + } + } + }, + { + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 102, + "end": 103, + "loc": { + "start": { + "line": 3, + "column": 34 + }, + "end": { + "line": 3, + "column": 35 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9A559BE", + "start": 104, + "end": 117, + "loc": { + "start": { + "line": 3, + "column": 36 + }, + "end": { + "line": 3, + "column": 49 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 117, + "end": 118, + "loc": { + "start": { + "line": 3, + "column": 49 + }, + "end": { + "line": 3, + "column": 50 + } + } + }, + { + "type": "CommentBlock", + "value": "* OWL/RDF terms. ", + "start": 120, + "end": 141, + "loc": { + "start": { + "line": 5, + "column": 0 + }, + "end": { + "line": 5, + "column": 21 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 142, + "end": 148, + "loc": { + "start": { + "line": 6, + "column": 0 + }, + "end": { + "line": 6, + "column": 6 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 149, + "end": 157, + "loc": { + "start": { + "line": 6, + "column": 7 }, "end": { - "line": 5, - "column": 21 + "line": 6, + "column": 15 } } }, { - "type": "CommentBlock", - "value": "* We need the cache manager to memoize parsing scientific names. ", - "start": 185, - "end": 254, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 158, + "end": 162, "loc": { "start": { - "line": 8, - "column": 0 + "line": 6, + "column": 16 }, "end": { - "line": 8, - "column": 69 + "line": 6, + "column": 20 } } }, { - "type": "CommentBlock", - "value": "*\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n ", - "start": 361, - "end": 1751, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/owlterms", + "start": 163, + "end": 182, "loc": { "start": { - "line": 12, - "column": 0 + "line": 6, + "column": 21 }, "end": { - "line": 39, - "column": 3 + "line": 6, + "column": 40 } } }, { - "type": "CommentBlock", - "value": "*\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n ", - "start": 1779, - "end": 1878, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 182, + "end": 183, "loc": { "start": { - "line": 41, - "column": 2 + "line": 6, + "column": 40 }, "end": { - "line": 44, - "column": 5 + "line": 6, + "column": 41 } } }, { "type": "CommentBlock", - "value": "*\n * The type associated with these taxonName objects.\n ", - "start": 2115, - "end": 2179, + "value": "* We need the cache manager to memoize parsing scientific names. ", + "start": 185, + "end": 254, "loc": { "start": { - "line": 51, - "column": 2 + "line": 8, + "column": 0 }, "end": { - "line": 53, - "column": 5 + "line": 8, + "column": 69 } } }, { - "type": "CommentBlock", - "value": "*\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n ", - "start": 2261, - "end": 2368, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 255, + "end": 261, "loc": { "start": { - "line": 58, - "column": 2 + "line": 9, + "column": 0 }, "end": { - "line": 60, - "column": 5 + "line": 9, + "column": 6 } } }, { - "type": "CommentBlock", - "value": " Directly access IRIs for nomenclatural codes. ", - "start": 2440, - "end": 2491, + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 262, + "end": 263, "loc": { "start": { - "line": 65, - "column": 2 + "line": 9, + "column": 7 }, "end": { - "line": 65, - "column": 53 + "line": 9, + "column": 8 } } }, { - "type": "CommentBlock", - "value": "*\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n ", - "start": 2779, - "end": 3281, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 264, + "end": 266, "loc": { "start": { - "line": 76, - "column": 2 + "line": 9, + "column": 9 }, "end": { - "line": 86, - "column": 5 + "line": 9, + "column": 11 } } }, { - "type": "CommentLine", - "value": " Note: the unknown code needs to be the first one in this list.", - "start": 3336, - "end": 3401, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9AF9PKK", + "start": 267, + "end": 280, "loc": { "start": { - "line": 89, - "column": 6 + "line": 9, + "column": 12 }, "end": { - "line": 89, - "column": 71 + "line": 9, + "column": 25 } } }, { - "type": "CommentBlock", - "value": "*\n * Returns the nomenclatural code entry for a code.\n ", - "start": 4534, - "end": 4597, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 281, + "end": 285, "loc": { "start": { - "line": 129, - "column": 2 + "line": 9, + "column": 26 }, "end": { - "line": 131, - "column": 5 + "line": 9, + "column": 30 } } }, { - "type": "CommentLine", - "value": " If the nomenCode provided is owlterms.UNKNOWN_CODE,", - "start": 4705, - "end": 4759, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/PhyxCacheManager", + "start": 286, + "end": 313, "loc": { "start": { - "line": 135, - "column": 4 + "line": 9, + "column": 31 }, "end": { - "line": 135, + "line": 9, "column": 58 } } }, { - "type": "CommentLine", - "value": " return that entry.", - "start": 4764, - "end": 4785, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 313, + "end": 314, "loc": { "start": { - "line": 136, - "column": 4 + "line": 9, + "column": 58 }, "end": { - "line": 136, - "column": 25 + "line": 9, + "column": 59 } } }, { - "type": "CommentLine", - "value": " Look for the entry with the same IRI as the provided IRI.", - "start": 4867, - "end": 4927, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 316, + "end": 321, "loc": { "start": { - "line": 141, - "column": 4 + "line": 10, + "column": 0 }, "end": { - "line": 141, - "column": 64 + "line": 10, + "column": 5 } } }, { - "type": "CommentBlock", - "value": "*\n * Returns the nomenclatural code of this taxon name.\n ", - "start": 5112, - "end": 5177, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 322, + "end": 323, "loc": { "start": { - "line": 148, - "column": 2 + "line": 10, + "column": 6 }, "end": { - "line": 150, - "column": 5 + "line": 10, + "column": 7 } } }, { - "type": "CommentBlock", - "value": "*\n * Returns the nomenclatural code of this taxon name as a IRI.\n ", - "start": 5280, - "end": 5354, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "PhyxCacheManager", + "start": 324, + "end": 340, "loc": { "start": { - "line": 155, - "column": 2 + "line": 10, + "column": 8 }, "end": { - "line": 157, - "column": 5 + "line": 10, + "column": 24 } } }, { - "type": "CommentBlock", - "value": "*\n * Set the nomenclatural code of this taxon name.\n ", - "start": 5572, - "end": 5633, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 341, + "end": 342, "loc": { "start": { - "line": 166, - "column": 2 + "line": 10, + "column": 25 }, "end": { - "line": 168, - "column": 5 + "line": 10, + "column": 26 } } }, { - "type": "CommentBlock", - "value": "*\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n ", - "start": 5725, - "end": 5799, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 343, + "end": 344, "loc": { "start": { - "line": 173, - "column": 2 + "line": 10, + "column": 27 }, "end": { - "line": 175, - "column": 5 + "line": 10, + "column": 28 } } }, { - "type": "CommentLine", - "value": " Have we already parsed this verbatim name?", - "start": 5881, - "end": 5926, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9AF9PKK", + "start": 345, + "end": 358, "loc": { "start": { - "line": 177, - "column": 4 + "line": 10, + "column": 29 }, "end": { - "line": 177, - "column": 49 + "line": 10, + "column": 42 } } }, { - "type": "CommentLine", - "value": " Use a regular expression to parse the verbatimName.", - "start": 6129, - "end": 6183, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 358, + "end": 359, "loc": { "start": { - "line": 182, - "column": 4 + "line": 10, + "column": 42 }, "end": { - "line": 182, - "column": 58 + "line": 10, + "column": 43 } } }, { - "type": "CommentLine", - "value": " Attempt 1. Look for a trinomial name.", - "start": 6189, - "end": 6229, + "type": "CommentBlock", + "value": "*\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n ", + "start": 361, + "end": 1751, "loc": { "start": { - "line": 184, - "column": 4 + "line": 12, + "column": 0 }, "end": { - "line": 184, - "column": 44 + "line": 39, + "column": 3 } } }, { - "type": "CommentLine", - "value": " Attempt 2. Look for a binomial name.", - "start": 6660, - "end": 6699, + "type": { + "label": "class", + "keyword": "class", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "class", + "start": 1752, + "end": 1757, "loc": { "start": { - "line": 199, - "column": 4 + "line": 40, + "column": 0 }, "end": { - "line": 199, - "column": 43 + "line": 40, + "column": 5 } } }, { - "type": "CommentLine", - "value": " Attempt 3. Look for a uninomial name.", - "start": 7085, - "end": 7125, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "TaxonNameWrapper", + "start": 1758, + "end": 1774, "loc": { "start": { - "line": 214, - "column": 4 + "line": 40, + "column": 6 }, "end": { - "line": 214, - "column": 44 + "line": 40, + "column": 22 } } }, { - "type": "CommentLine", - "value": " Is it a uninomial name?", - "start": 7151, - "end": 7177, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1775, + "end": 1776, "loc": { "start": { - "line": 216, - "column": 6 + "line": 40, + "column": 23 }, "end": { - "line": 216, - "column": 32 + "line": 40, + "column": 24 } } }, { - "type": "CommentLine", - "value": " Add a nomenclatural code if possible.", - "start": 7466, - "end": 7506, + "type": "CommentBlock", + "value": "*\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n ", + "start": 1779, + "end": 1878, "loc": { "start": { - "line": 228, - "column": 4 + "line": 41, + "column": 2 }, "end": { - "line": 228, - "column": 44 + "line": 44, + "column": 5 } } }, { - "type": "CommentLine", - "value": " Store in the cache.", - "start": 7593, - "end": 7615, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "constructor", + "start": 1881, + "end": 1892, "loc": { "start": { - "line": 233, - "column": 4 + "line": 45, + "column": 2 }, "end": { - "line": 233, - "column": 26 + "line": 45, + "column": 13 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the label of this scientific name.\n ", - "start": 7779, - "end": 7835, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1892, + "end": 1893, "loc": { "start": { - "line": 241, - "column": 2 + "line": 45, + "column": 13 }, "end": { - "line": 243, - "column": 5 + "line": 45, + "column": 14 } } }, { - "type": "CommentBlock", - "value": "*\n * Set the label of this scientific name.\n ", - "start": 7910, - "end": 7963, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "txname", + "start": 1893, + "end": 1899, "loc": { "start": { - "line": 248, - "column": 2 + "line": 45, + "column": 14 }, "end": { - "line": 250, - "column": 5 + "line": 45, + "column": 20 } } }, { - "type": "CommentLine", - "value": " If we don't have a nameComplete, treat this as the name complete.", - "start": 8048, - "end": 8116, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1899, + "end": 1900, "loc": { "start": { - "line": 254, - "column": 6 + "line": 45, + "column": 20 }, "end": { - "line": 254, - "column": 74 + "line": 45, + "column": 21 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the verbatim name of this taxon name.\n ", - "start": 8161, - "end": 8220, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "defaultNomenCode", + "start": 1901, + "end": 1917, "loc": { "start": { - "line": 259, - "column": 2 + "line": 45, + "column": 22 }, "end": { - "line": 261, - "column": 5 + "line": 45, + "column": 38 } } }, { - "type": "CommentBlock", - "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", - "start": 8281, - "end": 8404, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 1918, + "end": 1919, "loc": { "start": { - "line": 266, - "column": 2 + "line": 45, + "column": 39 }, "end": { - "line": 269, - "column": 5 + "line": 45, + "column": 40 } } }, { - "type": "CommentBlock", - "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", - "start": 8555, - "end": 8635, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 1920, + "end": 1928, "loc": { "start": { - "line": 277, - "column": 2 + "line": 45, + "column": 41 }, "end": { - "line": 279, - "column": 5 + "line": 45, + "column": 49 } } }, { - "type": "CommentBlock", - "value": "* Return the uninomial name if there is one. ", - "start": 8753, - "end": 8802, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 1928, + "end": 1929, "loc": { "start": { - "line": 284, - "column": 2 + "line": 45, + "column": 49 }, "end": { - "line": 284, - "column": 51 + "line": 45, + "column": 50 } } }, { - "type": "CommentLine", - "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 8889, - "end": 8966, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "UNKNOWN_CODE", + "start": 1929, + "end": 1941, "loc": { "start": { - "line": 288, - "column": 4 + "line": 45, + "column": 50 }, "end": { - "line": 288, - "column": 81 + "line": 45, + "column": 62 } } }, { - "type": "CommentLine", - "value": " from it.", - "start": 8971, - "end": 8982, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1941, + "end": 1942, "loc": { "start": { - "line": 289, - "column": 4 + "line": 45, + "column": 62 }, "end": { - "line": 289, - "column": 15 + "line": 45, + "column": 63 } } }, { - "type": "CommentBlock", - "value": "* Set the uninomial name. ", - "start": 9246, - "end": 9276, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1943, + "end": 1944, "loc": { "start": { - "line": 301, - "column": 2 + "line": 45, + "column": 64 }, "end": { - "line": 301, - "column": 32 + "line": 45, + "column": 65 } } }, { - "type": "CommentBlock", - "value": "* Return the binomial name if available. ", - "start": 9385, - "end": 9430, + "type": { + "label": "if", + "keyword": "if", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "if", + "start": 1949, + "end": 1951, "loc": { "start": { - "line": 307, - "column": 2 + "line": 46, + "column": 4 }, "end": { - "line": 307, - "column": 47 + "line": 46, + "column": 6 } } }, { - "type": "CommentLine", - "value": " Get the binomial name. Constructed from the genus and specific epithet", - "start": 9458, - "end": 9531, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1952, + "end": 1953, "loc": { "start": { - "line": 309, - "column": 4 + "line": 46, + "column": 7 }, "end": { - "line": 309, - "column": 77 + "line": 46, + "column": 8 } } }, { - "type": "CommentLine", - "value": " if available.", - "start": 9536, - "end": 9552, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "txname", + "start": 1953, + "end": 1959, "loc": { "start": { - "line": 310, - "column": 4 + "line": 46, + "column": 8 }, "end": { - "line": 310, - "column": 20 + "line": 46, + "column": 14 } } }, { - "type": "CommentBlock", - "value": "* Set the binomial name. ", - "start": 9710, - "end": 9739, + "type": { + "label": "==/!=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 6, + "updateContext": null + }, + "value": "===", + "start": 1960, + "end": 1963, "loc": { "start": { - "line": 315, - "column": 2 + "line": 46, + "column": 15 }, "end": { - "line": 315, - "column": 31 + "line": 46, + "column": 18 } } }, { - "type": "CommentBlock", - "value": "* Return the trinomial name if available. ", - "start": 9852, - "end": 9898, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "undefined", + "start": 1964, + "end": 1973, "loc": { "start": { - "line": 321, - "column": 2 + "line": 46, + "column": 19 }, "end": { - "line": 321, - "column": 48 + "line": 46, + "column": 28 } } }, { - "type": "CommentBlock", - "value": "* Set the trinomial name. ", - "start": 10176, - "end": 10206, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1973, + "end": 1974, "loc": { "start": { - "line": 331, - "column": 2 + "line": 46, + "column": 28 }, "end": { - "line": 331, - "column": 32 + "line": 46, + "column": 29 } } }, { - "type": "CommentBlock", - "value": "* Return the genus part of this scientific name if available. ", - "start": 10322, - "end": 10388, + "type": { + "label": "throw", + "keyword": "throw", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "throw", + "start": 1975, + "end": 1980, "loc": { "start": { - "line": 337, - "column": 2 + "line": 46, + "column": 30 }, "end": { - "line": 337, - "column": 68 + "line": 46, + "column": 35 } } }, { - "type": "CommentLine", - "value": " Try to read the genus if available.", - "start": 10413, - "end": 10451, + "type": { + "label": "new", + "keyword": "new", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "new", + "start": 1981, + "end": 1984, "loc": { "start": { - "line": 339, - "column": 4 + "line": 46, + "column": 36 }, "end": { - "line": 339, - "column": 42 + "line": 46, + "column": 39 } } }, { - "type": "CommentLine", - "value": " If there is no genus but there is a scientificName, try to extract a genus", - "start": 10526, - "end": 10603, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "Error", + "start": 1985, + "end": 1990, "loc": { "start": { - "line": 342, - "column": 4 + "line": 46, + "column": 40 }, "end": { - "line": 342, - "column": 81 + "line": 46, + "column": 45 } } }, { - "type": "CommentLine", - "value": " from it.", - "start": 10608, - "end": 10619, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1990, + "end": 1991, "loc": { "start": { - "line": 343, - "column": 4 + "line": 46, + "column": 45 }, "end": { - "line": 343, - "column": 15 + "line": 46, + "column": 46 } } }, { - "type": "CommentBlock", - "value": "* Set the genus part of this name. ", - "start": 10883, - "end": 10922, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "TaxonNameWrapper tried to wrap undefined", + "start": 1991, + "end": 2033, "loc": { "start": { - "line": 355, - "column": 2 + "line": 46, + "column": 46 }, "end": { - "line": 355, - "column": 41 + "line": 46, + "column": 88 } } }, { - "type": "CommentBlock", - "value": "* Return the specific epithet of this scientific name if available. ", - "start": 11261, - "end": 11333, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 2033, + "end": 2034, "loc": { "start": { - "line": 367, - "column": 2 + "line": 46, + "column": 88 }, "end": { - "line": 367, - "column": 74 + "line": 46, + "column": 89 } } }, { - "type": "CommentLine", - "value": " Try to read the specific epithet if available.", - "start": 11364, - "end": 11413, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2034, + "end": 2035, "loc": { "start": { - "line": 369, - "column": 4 + "line": 46, + "column": 89 }, "end": { - "line": 369, - "column": 53 + "line": 46, + "column": 90 } } }, { - "type": "CommentLine", - "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 11500, - "end": 11572, + "type": { + "label": "this", + "keyword": "this", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "this", + "start": 2040, + "end": 2044, "loc": { "start": { - "line": 372, + "line": 47, "column": 4 }, "end": { - "line": 372, - "column": 76 + "line": 47, + "column": 8 } } }, { - "type": "CommentLine", - "value": " extract a specific epithet from it.", - "start": 11577, - "end": 11615, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2044, + "end": 2045, "loc": { "start": { - "line": 373, - "column": 4 + "line": 47, + "column": 8 }, "end": { - "line": 373, - "column": 42 + "line": 47, + "column": 9 } } }, { - "type": "CommentBlock", - "value": "* Set the specificEpithet part of this name. ", - "start": 11877, - "end": 11926, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "txname", + "start": 2045, + "end": 2051, "loc": { "start": { - "line": 385, - "column": 2 + "line": 47, + "column": 9 }, "end": { - "line": 385, - "column": 51 + "line": 47, + "column": 15 } } }, { - "type": "CommentBlock", - "value": "* Return the infraspecific epithet of this scientific name if available. ", - "start": 12267, - "end": 12344, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 2052, + "end": 2053, "loc": { "start": { - "line": 397, - "column": 2 + "line": 47, + "column": 16 }, "end": { - "line": 397, - "column": 79 + "line": 47, + "column": 17 } } }, { - "type": "CommentLine", - "value": " Try to read the specific epithet if available.", - "start": 12380, - "end": 12429, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "txname", + "start": 2054, + "end": 2060, "loc": { "start": { - "line": 399, - "column": 4 + "line": 47, + "column": 18 }, "end": { - "line": 399, - "column": 53 + "line": 47, + "column": 24 } } }, { - "type": "CommentLine", - "value": " If there is no specific epithet but there is a scientificName, try to", - "start": 12526, - "end": 12598, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2060, + "end": 2061, "loc": { "start": { - "line": 402, - "column": 4 + "line": 47, + "column": 24 }, "end": { - "line": 402, - "column": 76 + "line": 47, + "column": 25 } } }, { - "type": "CommentLine", - "value": " extract a specific epithet from it.", - "start": 12603, - "end": 12641, + "type": { + "label": "this", + "keyword": "this", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "this", + "start": 2066, + "end": 2070, "loc": { "start": { - "line": 403, + "line": 48, "column": 4 }, "end": { - "line": 403, - "column": 42 + "line": 48, + "column": 8 } } }, { - "type": "CommentBlock", - "value": "* Set the infraspecificEpithet part of this name. ", - "start": 12920, - "end": 12974, + "type": { + "label": ".", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2070, + "end": 2071, "loc": { "start": { - "line": 415, - "column": 2 + "line": 48, + "column": 8 }, "end": { - "line": 415, - "column": 56 + "line": 48, + "column": 9 } } }, { - "type": "CommentBlock", - "value": "*\n * Return this taxon name in an JSON-LD representation.\n ", - "start": 13319, - "end": 13386, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "defaultNomenCode", + "start": 2071, + "end": 2087, "loc": { "start": { - "line": 427, - "column": 2 + "line": 48, + "column": 9 }, "end": { - "line": 429, - "column": 5 + "line": 48, + "column": 25 } } }, { - "type": "CommentLine", - "value": " Make sure '@type' is an array.", - "start": 13454, - "end": 13487, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 2088, + "end": 2089, "loc": { "start": { - "line": 433, - "column": 4 + "line": 48, + "column": 26 }, "end": { - "line": 433, - "column": 37 + "line": 48, + "column": 27 } } }, { - "type": "CommentLine", - "value": " Make it explicit that the type includes the nomenclaturalCode.", - "start": 13618, - "end": 13683, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "defaultNomenCode", + "start": 2090, + "end": 2106, "loc": { "start": { - "line": 437, - "column": 4 + "line": 48, + "column": 28 }, "end": { - "line": 437, - "column": 69 + "line": 48, + "column": 44 } } }, { - "type": "CommentBlock", - "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", - "start": 13836, - "end": 13911, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2106, + "end": 2107, "loc": { "start": { - "line": 444, - "column": 2 + "line": 48, + "column": 44 }, "end": { - "line": 446, - "column": 5 + "line": 48, + "column": 45 } } }, { - "type": "CommentLine", - "value": " No complete name, can't return anything.", - "start": 13942, - "end": 13985, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 2110, + "end": 2111, "loc": { "start": { - "line": 448, - "column": 4 + "line": 49, + "column": 2 }, "end": { - "line": 448, - "column": 47 + "line": 49, + "column": 3 } } }, { - "type": "CommentLine", - "value": " Do we have a nomenclaturalCode?", - "start": 14037, - "end": 14071, + "type": "CommentBlock", + "value": "*\n * The type associated with these taxonName objects.\n ", + "start": 2115, + "end": 2179, "loc": { "start": { - "line": 451, - "column": 4 + "line": 51, + "column": 2 }, "end": { - "line": 451, - "column": 38 + "line": 53, + "column": 5 } } }, { - "type": "CommentLine", - "value": " If we do have a nomenclatural code, incorporate that into the logical", - "start": 14268, - "end": 14340, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "static", + "start": 2182, + "end": 2188, "loc": { "start": { - "line": 460, - "column": 4 + "line": 54, + "column": 2 }, "end": { - "line": 460, - "column": 76 + "line": 54, + "column": 8 } } }, { - "type": "CommentLine", - "value": " expression as well.", - "start": 14345, - "end": 14367, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "get", + "start": 2189, + "end": 2192, "loc": { "start": { - "line": 461, - "column": 4 + "line": 54, + "column": 9 }, "end": { - "line": 461, - "column": 26 + "line": 54, + "column": 12 } } - } - ], - "tokens": [ + }, { - "type": "CommentBlock", - "value": "* Utility functions. ", - "start": 0, - "end": 25, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "TYPE_TAXON_NAME", + "start": 2193, + "end": 2208, "loc": { "start": { - "line": 1, - "column": 0 + "line": 54, + "column": 13 }, "end": { - "line": 1, - "column": 25 + "line": 54, + "column": 28 } } }, { "type": { - "label": "import", - "keyword": "import", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 26, - "end": 32, + "start": 2208, + "end": 2209, "loc": { "start": { - "line": 2, - "column": 0 + "line": 54, + "column": 28 }, "end": { - "line": 2, - "column": 6 + "line": 54, + "column": 29 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 33, - "end": 34, + "start": 2209, + "end": 2210, "loc": { "start": { - "line": 2, - "column": 7 + "line": 54, + "column": 29 }, "end": { - "line": 2, - "column": 8 + "line": 54, + "column": 30 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -46603,43 +51029,44 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 35, - "end": 37, + "start": 2211, + "end": 2212, "loc": { "start": { - "line": 2, - "column": 9 + "line": 54, + "column": 31 }, "end": { - "line": 2, - "column": 11 + "line": 54, + "column": 32 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H19CBL1UQ", - "start": 38, - "end": 51, + "value": "return", + "start": 2217, + "end": 2223, "loc": { "start": { - "line": 2, - "column": 12 + "line": 55, + "column": 4 }, "end": { - "line": 2, - "column": 25 + "line": 55, + "column": 10 } } }, @@ -46655,25 +51082,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 52, - "end": 56, + "value": "owlterms", + "start": 2224, + "end": 2232, "loc": { "start": { - "line": 2, - "column": 26 + "line": 55, + "column": 11 }, "end": { - "line": 2, - "column": 30 + "line": 55, + "column": 19 } } }, { "type": { - "label": "string", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -46682,51 +51109,49 @@ "binop": null, "updateContext": null }, - "value": "lodash", - "start": 57, - "end": 65, + "start": 2232, + "end": 2233, "loc": { "start": { - "line": 2, - "column": 31 + "line": 55, + "column": 19 }, "end": { - "line": 2, - "column": 39 + "line": 55, + "column": 20 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 65, - "end": 66, + "value": "TDWG_VOC_TAXON_NAME", + "start": 2233, + "end": 2252, "loc": { "start": { - "line": 2, - "column": 39 + "line": 55, + "column": 20 }, "end": { - "line": 2, - "column": 40 + "line": 55, + "column": 39 } } }, { "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -46736,25 +51161,24 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 68, - "end": 73, + "start": 2252, + "end": 2253, "loc": { "start": { - "line": 3, - "column": 0 + "line": 55, + "column": 39 }, "end": { - "line": 3, - "column": 5 + "line": 55, + "column": 40 } } }, { "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, + "label": "}", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -46762,16 +51186,32 @@ "postfix": false, "binop": null }, - "start": 74, - "end": 75, + "start": 2256, + "end": 2257, "loc": { "start": { - "line": 3, - "column": 6 + "line": 56, + "column": 2 }, "end": { - "line": 3, - "column": 7 + "line": 56, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n ", + "start": 2261, + "end": 2368, + "loc": { + "start": { + "line": 58, + "column": 2 + }, + "end": { + "line": 60, + "column": 5 } } }, @@ -46787,42 +51227,42 @@ "postfix": false, "binop": null }, - "value": "has", - "start": 76, - "end": 79, + "value": "static", + "start": 2371, + "end": 2377, "loc": { "start": { - "line": 3, - "column": 8 + "line": 61, + "column": 2 }, "end": { - "line": 3, - "column": 11 + "line": 61, + "column": 8 } } }, { "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 79, - "end": 80, + "value": "get", + "start": 2378, + "end": 2381, "loc": { "start": { - "line": 3, - "column": 11 + "line": 61, + "column": 9 }, "end": { - "line": 3, + "line": 61, "column": 12 } } @@ -46839,51 +51279,50 @@ "postfix": false, "binop": null }, - "value": "cloneDeep", - "start": 81, - "end": 90, + "value": "UNKNOWN_CODE", + "start": 2382, + "end": 2394, "loc": { "start": { - "line": 3, + "line": 61, "column": 13 }, "end": { - "line": 3, - "column": 22 + "line": 61, + "column": 25 } } }, { "type": { - "label": ",", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 90, - "end": 91, + "start": 2394, + "end": 2395, "loc": { "start": { - "line": 3, - "column": 22 + "line": 61, + "column": 25 }, "end": { - "line": 3, - "column": 23 + "line": 61, + "column": 26 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -46891,25 +51330,24 @@ "postfix": false, "binop": null }, - "value": "isArray", - "start": 92, - "end": 99, + "start": 2395, + "end": 2396, "loc": { "start": { - "line": 3, - "column": 24 + "line": 61, + "column": 26 }, "end": { - "line": 3, - "column": 31 + "line": 61, + "column": 27 } } }, { "type": { - "label": "}", - "beforeExpr": false, - "startsExpr": false, + "label": "{", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -46917,43 +51355,44 @@ "postfix": false, "binop": null }, - "start": 100, - "end": 101, + "start": 2397, + "end": 2398, "loc": { "start": { - "line": 3, - "column": 32 + "line": 61, + "column": 28 }, "end": { - "line": 3, - "column": 33 + "line": 61, + "column": 29 } } }, { "type": { - "label": "=", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 102, - "end": 103, + "value": "return", + "start": 2403, + "end": 2409, "loc": { "start": { - "line": 3, - "column": 34 + "line": 62, + "column": 4 }, "end": { - "line": 3, - "column": 35 + "line": 62, + "column": 10 } } }, @@ -46969,24 +51408,24 @@ "postfix": false, "binop": null }, - "value": "LKT4H19CBL1UQ", - "start": 104, - "end": 117, + "value": "owlterms", + "start": 2410, + "end": 2418, "loc": { "start": { - "line": 3, - "column": 36 + "line": 62, + "column": 11 }, "end": { - "line": 3, - "column": 49 + "line": 62, + "column": 19 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -46996,41 +51435,50 @@ "binop": null, "updateContext": null }, - "start": 117, - "end": 118, + "start": 2418, + "end": 2419, "loc": { "start": { - "line": 3, - "column": 49 + "line": 62, + "column": 19 }, "end": { - "line": 3, - "column": 50 + "line": 62, + "column": 20 } } }, { - "type": "CommentBlock", - "value": "* OWL/RDF terms. ", - "start": 120, - "end": 141, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "UNKNOWN_CODE", + "start": 2419, + "end": 2431, "loc": { "start": { - "line": 5, - "column": 0 + "line": 62, + "column": 20 }, "end": { - "line": 5, - "column": 21 + "line": 62, + "column": 32 } } }, { "type": { - "label": "import", - "keyword": "import", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -47039,25 +51487,24 @@ "binop": null, "updateContext": null }, - "value": "import", - "start": 142, - "end": 148, + "start": 2431, + "end": 2432, "loc": { "start": { - "line": 6, - "column": 0 + "line": 62, + "column": 32 }, "end": { - "line": 6, - "column": 6 + "line": 62, + "column": 33 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -47065,17 +51512,32 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 149, - "end": 157, + "start": 2435, + "end": 2436, "loc": { "start": { - "line": 6, - "column": 7 + "line": 63, + "column": 2 }, "end": { - "line": 6, - "column": 15 + "line": 63, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": " Directly access IRIs for nomenclatural codes. ", + "start": 2440, + "end": 2491, + "loc": { + "start": { + "line": 65, + "column": 2 + }, + "end": { + "line": 65, + "column": 53 } } }, @@ -47091,23 +51553,23 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 158, - "end": 162, + "value": "static", + "start": 2494, + "end": 2500, "loc": { "start": { - "line": 6, - "column": 16 + "line": 66, + "column": 2 }, "end": { - "line": 6, - "column": 20 + "line": 66, + "column": 8 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -47115,143 +51577,148 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "../utils/owlterms", - "start": 163, - "end": 182, + "value": "get", + "start": 2501, + "end": 2504, "loc": { "start": { - "line": 6, - "column": 21 + "line": 66, + "column": 9 }, "end": { - "line": 6, - "column": 40 + "line": 66, + "column": 12 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 182, - "end": 183, + "value": "ICZN_CODE", + "start": 2505, + "end": 2514, "loc": { "start": { - "line": 6, - "column": 40 + "line": 66, + "column": 13 }, "end": { - "line": 6, - "column": 41 + "line": 66, + "column": 22 } } }, { - "type": "CommentBlock", - "value": "* We need the cache manager to memoize parsing scientific names. ", - "start": 185, - "end": 254, + "type": { + "label": "(", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 2514, + "end": 2515, "loc": { "start": { - "line": 8, - "column": 0 + "line": 66, + "column": 22 }, "end": { - "line": 8, - "column": 69 + "line": 66, + "column": 23 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "import", - "start": 255, - "end": 261, + "binop": null + }, + "start": 2515, + "end": 2516, "loc": { "start": { - "line": 9, - "column": 0 + "line": 66, + "column": 23 }, "end": { - "line": 9, - "column": 6 + "line": 66, + "column": 24 } } }, { "type": { - "label": "*", + "label": "{", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, - "updateContext": null + "binop": null }, - "value": "*", - "start": 262, - "end": 263, + "start": 2517, + "end": 2518, "loc": { "start": { - "line": 9, - "column": 7 + "line": 66, + "column": 25 }, "end": { - "line": 9, - "column": 8 + "line": 66, + "column": 26 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "as", - "start": 264, - "end": 266, + "value": "return", + "start": 2519, + "end": 2525, "loc": { "start": { - "line": 9, - "column": 9 + "line": 66, + "column": 27 }, "end": { - "line": 9, - "column": 11 + "line": 66, + "column": 33 } } }, @@ -47267,49 +51734,49 @@ "postfix": false, "binop": null }, - "value": "LKT4H19CB2PO4", - "start": 267, - "end": 280, + "value": "owlterms", + "start": 2526, + "end": 2534, "loc": { "start": { - "line": 9, - "column": 12 + "line": 66, + "column": 34 }, "end": { - "line": 9, - "column": 25 + "line": 66, + "column": 42 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "from", - "start": 281, - "end": 285, + "start": 2534, + "end": 2535, "loc": { "start": { - "line": 9, - "column": 26 + "line": 66, + "column": 42 }, "end": { - "line": 9, - "column": 30 + "line": 66, + "column": 43 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -47317,20 +51784,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "../utils/PhyxCacheManager", - "start": 286, - "end": 313, + "value": "ICZN_CODE", + "start": 2535, + "end": 2544, "loc": { "start": { - "line": 9, - "column": 31 + "line": 66, + "column": 43 }, "end": { - "line": 9, - "column": 58 + "line": 66, + "column": 52 } } }, @@ -47347,23 +51813,22 @@ "binop": null, "updateContext": null }, - "start": 313, - "end": 314, + "start": 2544, + "end": 2545, "loc": { "start": { - "line": 9, - "column": 58 + "line": 66, + "column": 52 }, "end": { - "line": 9, - "column": 59 + "line": 66, + "column": 53 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "}", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -47371,27 +51836,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 316, - "end": 321, + "start": 2546, + "end": 2547, "loc": { "start": { - "line": 10, - "column": 0 + "line": 66, + "column": 54 }, "end": { - "line": 10, - "column": 5 + "line": 66, + "column": 55 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -47400,16 +51863,17 @@ "postfix": false, "binop": null }, - "start": 322, - "end": 323, + "value": "static", + "start": 2551, + "end": 2557, "loc": { "start": { - "line": 10, - "column": 6 + "line": 68, + "column": 2 }, "end": { - "line": 10, - "column": 7 + "line": 68, + "column": 8 } } }, @@ -47425,25 +51889,25 @@ "postfix": false, "binop": null }, - "value": "PhyxCacheManager", - "start": 324, - "end": 340, + "value": "get", + "start": 2558, + "end": 2561, "loc": { "start": { - "line": 10, - "column": 8 + "line": 68, + "column": 9 }, "end": { - "line": 10, - "column": 24 + "line": 68, + "column": 12 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -47451,51 +51915,50 @@ "postfix": false, "binop": null }, - "start": 341, - "end": 342, + "value": "ICN_CODE", + "start": 2562, + "end": 2570, "loc": { "start": { - "line": 10, - "column": 25 + "line": 68, + "column": 13 }, "end": { - "line": 10, - "column": 26 + "line": 68, + "column": 21 } } }, { "type": { - "label": "=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 343, - "end": 344, + "start": 2570, + "end": 2571, "loc": { "start": { - "line": 10, - "column": 27 + "line": 68, + "column": 21 }, "end": { - "line": 10, - "column": 28 + "line": 68, + "column": 22 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -47503,67 +51966,49 @@ "postfix": false, "binop": null }, - "value": "LKT4H19CB2PO4", - "start": 345, - "end": 358, + "start": 2571, + "end": 2572, "loc": { "start": { - "line": 10, - "column": 29 + "line": 68, + "column": 22 }, "end": { - "line": 10, - "column": 42 + "line": 68, + "column": 23 } } }, { "type": { - "label": ";", + "label": "{", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 358, - "end": 359, - "loc": { - "start": { - "line": 10, - "column": 42 - }, - "end": { - "line": 10, - "column": 43 - } - } - }, - { - "type": "CommentBlock", - "value": "*\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n ", - "start": 361, - "end": 1751, + "start": 2573, + "end": 2574, "loc": { "start": { - "line": 12, - "column": 0 + "line": 68, + "column": 24 }, "end": { - "line": 39, - "column": 3 + "line": 68, + "column": 25 } } }, { "type": { - "label": "class", - "keyword": "class", - "beforeExpr": false, + "label": "return", + "keyword": "return", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -47573,17 +52018,17 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 1752, - "end": 1757, + "value": "return", + "start": 2575, + "end": 2581, "loc": { "start": { - "line": 40, - "column": 0 + "line": 68, + "column": 26 }, "end": { - "line": 40, - "column": 5 + "line": 68, + "column": 32 } } }, @@ -47599,58 +52044,43 @@ "postfix": false, "binop": null }, - "value": "TaxonNameWrapper", - "start": 1758, - "end": 1774, + "value": "owlterms", + "start": 2582, + "end": 2590, "loc": { "start": { - "line": 40, - "column": 6 + "line": 68, + "column": 33 }, "end": { - "line": 40, - "column": 22 + "line": 68, + "column": 41 } } }, { "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, + "label": ".", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1775, - "end": 1776, - "loc": { - "start": { - "line": 40, - "column": 23 - }, - "end": { - "line": 40, - "column": 24 - } - } - }, - { - "type": "CommentBlock", - "value": "*\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n ", - "start": 1779, - "end": 1878, + "start": 2590, + "end": 2591, "loc": { "start": { - "line": 41, - "column": 2 + "line": 68, + "column": 41 }, "end": { - "line": 44, - "column": 5 + "line": 68, + "column": 42 } } }, @@ -47666,50 +52096,51 @@ "postfix": false, "binop": null }, - "value": "constructor", - "start": 1881, - "end": 1892, + "value": "ICN_CODE", + "start": 2591, + "end": 2599, "loc": { "start": { - "line": 45, - "column": 2 + "line": 68, + "column": 42 }, "end": { - "line": 45, - "column": 13 + "line": 68, + "column": 50 } } }, { "type": { - "label": "(", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1892, - "end": 1893, + "start": 2599, + "end": 2600, "loc": { "start": { - "line": 45, - "column": 13 + "line": 68, + "column": 50 }, "end": { - "line": 45, - "column": 14 + "line": 68, + "column": 51 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -47717,43 +52148,42 @@ "postfix": false, "binop": null }, - "value": "txname", - "start": 1893, - "end": 1899, + "start": 2601, + "end": 2602, "loc": { "start": { - "line": 45, - "column": 14 + "line": 68, + "column": 52 }, "end": { - "line": 45, - "column": 20 + "line": 68, + "column": 53 } } }, { "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 1899, - "end": 1900, + "value": "static", + "start": 2606, + "end": 2612, "loc": { "start": { - "line": 45, - "column": 20 + "line": 70, + "column": 2 }, "end": { - "line": 45, - "column": 21 + "line": 70, + "column": 8 } } }, @@ -47769,51 +52199,50 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 1901, - "end": 1917, + "value": "get", + "start": 2613, + "end": 2616, "loc": { "start": { - "line": 45, - "column": 22 + "line": 70, + "column": 9 }, "end": { - "line": 45, - "column": 38 + "line": 70, + "column": 12 } } }, { "type": { - "label": "=", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 1918, - "end": 1919, + "value": "ICNP_CODE", + "start": 2617, + "end": 2626, "loc": { "start": { - "line": 45, - "column": 39 + "line": 70, + "column": 13 }, "end": { - "line": 45, - "column": 40 + "line": 70, + "column": 22 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -47822,23 +52251,22 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 1920, - "end": 1928, + "start": 2626, + "end": 2627, "loc": { "start": { - "line": 45, - "column": 41 + "line": 70, + "column": 22 }, "end": { - "line": 45, - "column": 49 + "line": 70, + "column": 23 } } }, { "type": { - "label": ".", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -47846,26 +52274,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 1928, - "end": 1929, + "start": 2627, + "end": 2628, "loc": { "start": { - "line": 45, - "column": 49 + "line": 70, + "column": 23 }, "end": { - "line": 45, - "column": 50 + "line": 70, + "column": 24 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -47874,49 +52301,51 @@ "postfix": false, "binop": null }, - "value": "UNKNOWN_CODE", - "start": 1929, - "end": 1941, + "start": 2629, + "end": 2630, "loc": { "start": { - "line": 45, - "column": 50 + "line": 70, + "column": 25 }, "end": { - "line": 45, - "column": 62 + "line": 70, + "column": 26 } } }, { "type": { - "label": ")", - "beforeExpr": false, + "label": "return", + "keyword": "return", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1941, - "end": 1942, + "value": "return", + "start": 2631, + "end": 2637, "loc": { "start": { - "line": 45, - "column": 62 + "line": 70, + "column": 27 }, "end": { - "line": 45, - "column": 63 + "line": 70, + "column": 33 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -47925,23 +52354,23 @@ "postfix": false, "binop": null }, - "start": 1943, - "end": 1944, + "value": "owlterms", + "start": 2638, + "end": 2646, "loc": { "start": { - "line": 45, - "column": 64 + "line": 70, + "column": 34 }, "end": { - "line": 45, - "column": 65 + "line": 70, + "column": 42 } } }, { "type": { - "label": "if", - "keyword": "if", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -47952,24 +52381,23 @@ "binop": null, "updateContext": null }, - "value": "if", - "start": 1949, - "end": 1951, + "start": 2646, + "end": 2647, "loc": { "start": { - "line": 46, - "column": 4 + "line": 70, + "column": 42 }, "end": { - "line": 46, - "column": 6 + "line": 70, + "column": 43 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -47978,69 +52406,68 @@ "postfix": false, "binop": null }, - "start": 1952, - "end": 1953, + "value": "ICNP_CODE", + "start": 2647, + "end": 2656, "loc": { "start": { - "line": 46, - "column": 7 + "line": 70, + "column": 43 }, "end": { - "line": 46, - "column": 8 + "line": 70, + "column": 52 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "txname", - "start": 1953, - "end": 1959, + "start": 2656, + "end": 2657, "loc": { "start": { - "line": 46, - "column": 8 + "line": 70, + "column": 52 }, "end": { - "line": 46, - "column": 14 + "line": 70, + "column": 53 } } }, { "type": { - "label": "==/!=", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 6, - "updateContext": null + "binop": null }, - "value": "===", - "start": 1960, - "end": 1963, + "start": 2658, + "end": 2659, "loc": { "start": { - "line": 46, - "column": 15 + "line": 70, + "column": 54 }, "end": { - "line": 46, - "column": 18 + "line": 70, + "column": 55 } } }, @@ -48056,25 +52483,25 @@ "postfix": false, "binop": null }, - "value": "undefined", - "start": 1964, - "end": 1973, + "value": "static", + "start": 2663, + "end": 2669, "loc": { "start": { - "line": 46, - "column": 19 + "line": 72, + "column": 2 }, "end": { - "line": 46, - "column": 28 + "line": 72, + "column": 8 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48082,51 +52509,49 @@ "postfix": false, "binop": null }, - "start": 1973, - "end": 1974, + "value": "get", + "start": 2670, + "end": 2673, "loc": { "start": { - "line": 46, - "column": 28 + "line": 72, + "column": 9 }, "end": { - "line": 46, - "column": 29 + "line": 72, + "column": 12 } } }, { "type": { - "label": "throw", - "keyword": "throw", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "throw", - "start": 1975, - "end": 1980, + "value": "ICTV_CODE", + "start": 2674, + "end": 2683, "loc": { "start": { - "line": 46, - "column": 30 + "line": 72, + "column": 13 }, "end": { - "line": 46, - "column": 35 + "line": 72, + "column": 22 } } }, { "type": { - "label": "new", - "keyword": "new", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -48134,28 +52559,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "new", - "start": 1981, - "end": 1984, + "start": 2683, + "end": 2684, "loc": { "start": { - "line": 46, - "column": 36 + "line": 72, + "column": 22 }, "end": { - "line": 46, - "column": 39 + "line": 72, + "column": 23 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48163,23 +52586,22 @@ "postfix": false, "binop": null }, - "value": "Error", - "start": 1985, - "end": 1990, + "start": 2684, + "end": 2685, "loc": { "start": { - "line": 46, - "column": 40 + "line": 72, + "column": 23 }, "end": { - "line": 46, - "column": 45 + "line": 72, + "column": 24 } } }, { "type": { - "label": "(", + "label": "{", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -48189,24 +52611,25 @@ "postfix": false, "binop": null }, - "start": 1990, - "end": 1991, + "start": 2686, + "end": 2687, "loc": { "start": { - "line": 46, - "column": 45 + "line": 72, + "column": 25 }, "end": { - "line": 46, - "column": 46 + "line": 72, + "column": 26 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48215,25 +52638,25 @@ "binop": null, "updateContext": null }, - "value": "TaxonNameWrapper tried to wrap undefined", - "start": 1991, - "end": 2033, + "value": "return", + "start": 2688, + "end": 2694, "loc": { "start": { - "line": 46, - "column": 46 + "line": 72, + "column": 27 }, "end": { - "line": 46, - "column": 88 + "line": 72, + "column": 33 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48241,23 +52664,24 @@ "postfix": false, "binop": null }, - "start": 2033, - "end": 2034, + "value": "owlterms", + "start": 2695, + "end": 2703, "loc": { "start": { - "line": 46, - "column": 88 + "line": 72, + "column": 34 }, "end": { - "line": 46, - "column": 89 + "line": 72, + "column": 42 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -48267,23 +52691,22 @@ "binop": null, "updateContext": null }, - "start": 2034, - "end": 2035, + "start": 2703, + "end": 2704, "loc": { "start": { - "line": 46, - "column": 89 + "line": 72, + "column": 42 }, "end": { - "line": 46, - "column": 90 + "line": 72, + "column": 43 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -48291,27 +52714,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 2040, - "end": 2044, + "value": "ICTV_CODE", + "start": 2704, + "end": 2713, "loc": { "start": { - "line": 47, - "column": 4 + "line": 72, + "column": 43 }, "end": { - "line": 47, - "column": 8 + "line": 72, + "column": 52 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -48321,24 +52743,24 @@ "binop": null, "updateContext": null }, - "start": 2044, - "end": 2045, + "start": 2713, + "end": 2714, "loc": { "start": { - "line": 47, - "column": 8 + "line": 72, + "column": 52 }, "end": { - "line": 47, - "column": 9 + "line": 72, + "column": 53 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48346,44 +52768,42 @@ "postfix": false, "binop": null }, - "value": "txname", - "start": 2045, - "end": 2051, + "start": 2715, + "end": 2716, "loc": { "start": { - "line": 47, - "column": 9 + "line": 72, + "column": 54 }, "end": { - "line": 47, - "column": 15 + "line": 72, + "column": 55 } } }, { "type": { - "label": "=", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 2052, - "end": 2053, + "value": "static", + "start": 2720, + "end": 2726, "loc": { "start": { - "line": 47, - "column": 16 + "line": 74, + "column": 2 }, "end": { - "line": 47, - "column": 17 + "line": 74, + "column": 8 } } }, @@ -48399,77 +52819,74 @@ "postfix": false, "binop": null }, - "value": "txname", - "start": 2054, - "end": 2060, + "value": "get", + "start": 2727, + "end": 2730, "loc": { "start": { - "line": 47, - "column": 18 + "line": 74, + "column": 9 }, "end": { - "line": 47, - "column": 24 + "line": 74, + "column": 12 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2060, - "end": 2061, + "value": "ICNCP_CODE", + "start": 2731, + "end": 2741, "loc": { "start": { - "line": 47, - "column": 24 + "line": 74, + "column": 13 }, "end": { - "line": 47, - "column": 25 + "line": 74, + "column": 23 } } }, { "type": { - "label": "this", - "keyword": "this", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 2066, - "end": 2070, + "start": 2741, + "end": 2742, "loc": { "start": { - "line": 48, - "column": 4 + "line": 74, + "column": 23 }, "end": { - "line": 48, - "column": 8 + "line": 74, + "column": 24 } } }, { "type": { - "label": ".", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -48477,26 +52894,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2070, - "end": 2071, + "start": 2742, + "end": 2743, "loc": { "start": { - "line": 48, - "column": 8 + "line": 74, + "column": 24 }, "end": { - "line": 48, - "column": 9 + "line": 74, + "column": 25 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -48505,44 +52921,44 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 2071, - "end": 2087, + "start": 2744, + "end": 2745, "loc": { "start": { - "line": 48, - "column": 9 + "line": 74, + "column": 26 }, "end": { - "line": 48, - "column": 25 + "line": 74, + "column": 27 } } }, { "type": { - "label": "=", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 2088, - "end": 2089, + "value": "return", + "start": 2746, + "end": 2752, "loc": { "start": { - "line": 48, - "column": 26 + "line": 74, + "column": 28 }, "end": { - "line": 48, - "column": 27 + "line": 74, + "column": 34 } } }, @@ -48558,24 +52974,24 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 2090, - "end": 2106, + "value": "owlterms", + "start": 2753, + "end": 2761, "loc": { "start": { - "line": 48, - "column": 28 + "line": 74, + "column": 35 }, "end": { - "line": 48, - "column": 44 + "line": 74, + "column": 43 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -48585,24 +53001,24 @@ "binop": null, "updateContext": null }, - "start": 2106, - "end": 2107, + "start": 2761, + "end": 2762, "loc": { "start": { - "line": 48, - "column": 44 + "line": 74, + "column": 43 }, "end": { - "line": 48, - "column": 45 + "line": 74, + "column": 44 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48610,40 +53026,51 @@ "postfix": false, "binop": null }, - "start": 2110, - "end": 2111, + "value": "ICNCP_CODE", + "start": 2762, + "end": 2772, "loc": { "start": { - "line": 49, - "column": 2 + "line": 74, + "column": 44 }, "end": { - "line": 49, - "column": 3 + "line": 74, + "column": 54 } } }, { - "type": "CommentBlock", - "value": "*\n * The type associated with these taxonName objects.\n ", - "start": 2115, - "end": 2179, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 2772, + "end": 2773, "loc": { "start": { - "line": 51, - "column": 2 + "line": 74, + "column": 54 }, "end": { - "line": 53, - "column": 5 + "line": 74, + "column": 55 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48651,17 +53078,32 @@ "postfix": false, "binop": null }, - "value": "static", - "start": 2182, - "end": 2188, + "start": 2774, + "end": 2775, "loc": { "start": { - "line": 54, + "line": 74, + "column": 56 + }, + "end": { + "line": 74, + "column": 57 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n ", + "start": 2779, + "end": 3281, + "loc": { + "start": { + "line": 76, "column": 2 }, "end": { - "line": 54, - "column": 8 + "line": 86, + "column": 5 } } }, @@ -48677,17 +53119,17 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 2189, - "end": 2192, + "value": "static", + "start": 3284, + "end": 3290, "loc": { "start": { - "line": 54, - "column": 9 + "line": 87, + "column": 2 }, "end": { - "line": 54, - "column": 12 + "line": 87, + "column": 8 } } }, @@ -48703,17 +53145,17 @@ "postfix": false, "binop": null }, - "value": "TYPE_TAXON_NAME", - "start": 2193, - "end": 2208, + "value": "getNomenclaturalCodes", + "start": 3291, + "end": 3312, "loc": { "start": { - "line": 54, - "column": 13 + "line": 87, + "column": 9 }, "end": { - "line": 54, - "column": 28 + "line": 87, + "column": 30 } } }, @@ -48729,16 +53171,16 @@ "postfix": false, "binop": null }, - "start": 2208, - "end": 2209, + "start": 3312, + "end": 3313, "loc": { "start": { - "line": 54, - "column": 28 + "line": 87, + "column": 30 }, "end": { - "line": 54, - "column": 29 + "line": 87, + "column": 31 } } }, @@ -48754,16 +53196,16 @@ "postfix": false, "binop": null }, - "start": 2209, - "end": 2210, + "start": 3313, + "end": 3314, "loc": { "start": { - "line": 54, - "column": 29 + "line": 87, + "column": 31 }, "end": { - "line": 54, - "column": 30 + "line": 87, + "column": 32 } } }, @@ -48779,16 +53221,16 @@ "postfix": false, "binop": null }, - "start": 2211, - "end": 2212, + "start": 3315, + "end": 3316, "loc": { "start": { - "line": 54, - "column": 31 + "line": 87, + "column": 33 }, "end": { - "line": 54, - "column": 32 + "line": 87, + "column": 34 } } }, @@ -48807,68 +53249,83 @@ "updateContext": null }, "value": "return", - "start": 2217, - "end": 2223, + "start": 3321, + "end": 3327, "loc": { "start": { - "line": 55, + "line": 88, "column": 4 }, "end": { - "line": 55, + "line": 88, "column": 10 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "[", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "owlterms", - "start": 2224, - "end": 2232, + "start": 3328, + "end": 3329, "loc": { "start": { - "line": 55, + "line": 88, "column": 11 }, "end": { - "line": 55, - "column": 19 + "line": 88, + "column": 12 + } + } + }, + { + "type": "CommentLine", + "value": " Note: the unknown code needs to be the first one in this list.", + "start": 3336, + "end": 3401, + "loc": { + "start": { + "line": 89, + "column": 6 + }, + "end": { + "line": 89, + "column": 71 } } }, { "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, + "label": "{", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 2232, - "end": 2233, + "start": 3408, + "end": 3409, "loc": { "start": { - "line": 55, - "column": 19 + "line": 90, + "column": 6 }, "end": { - "line": 55, - "column": 20 + "line": 90, + "column": 7 } } }, @@ -48884,23 +53341,23 @@ "postfix": false, "binop": null }, - "value": "TDWG_VOC_TAXON_NAME", - "start": 2233, - "end": 2252, + "value": "iri", + "start": 3418, + "end": 3421, "loc": { "start": { - "line": 55, - "column": 20 + "line": 91, + "column": 8 }, "end": { - "line": 55, - "column": 39 + "line": 91, + "column": 11 } } }, { "type": { - "label": ";", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -48911,24 +53368,24 @@ "binop": null, "updateContext": null }, - "start": 2252, - "end": 2253, + "start": 3421, + "end": 3422, "loc": { "start": { - "line": 55, - "column": 39 + "line": 91, + "column": 11 }, "end": { - "line": 55, - "column": 40 + "line": 91, + "column": 12 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -48936,58 +53393,43 @@ "postfix": false, "binop": null }, - "start": 2256, - "end": 2257, - "loc": { - "start": { - "line": 56, - "column": 2 - }, - "end": { - "line": 56, - "column": 3 - } - } - }, - { - "type": "CommentBlock", - "value": "*\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n ", - "start": 2261, - "end": 2368, + "value": "owlterms", + "start": 3423, + "end": 3431, "loc": { "start": { - "line": 58, - "column": 2 + "line": 91, + "column": 13 }, "end": { - "line": 60, - "column": 5 + "line": 91, + "column": 21 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 2371, - "end": 2377, + "start": 3431, + "end": 3432, "loc": { "start": { - "line": 61, - "column": 2 + "line": 91, + "column": 21 }, "end": { - "line": 61, - "column": 8 + "line": 91, + "column": 22 } } }, @@ -49003,50 +53445,50 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 2378, - "end": 2381, + "value": "UNKNOWN_CODE", + "start": 3432, + "end": 3444, "loc": { "start": { - "line": 61, - "column": 9 + "line": 91, + "column": 22 }, "end": { - "line": 61, - "column": 12 + "line": 91, + "column": 34 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "UNKNOWN_CODE", - "start": 2382, - "end": 2394, + "start": 3444, + "end": 3445, "loc": { "start": { - "line": 61, - "column": 13 + "line": 91, + "column": 34 }, "end": { - "line": 61, - "column": 25 + "line": 91, + "column": 35 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -49055,73 +53497,76 @@ "postfix": false, "binop": null }, - "start": 2394, - "end": 2395, + "value": "shortName", + "start": 3454, + "end": 3463, "loc": { "start": { - "line": 61, - "column": 25 + "line": 92, + "column": 8 }, "end": { - "line": 61, - "column": 26 + "line": 92, + "column": 17 } } }, { "type": { - "label": ")", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2395, - "end": 2396, + "start": 3463, + "end": 3464, "loc": { "start": { - "line": 61, - "column": 26 + "line": 92, + "column": 17 }, "end": { - "line": 61, - "column": 27 + "line": 92, + "column": 18 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "string", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2397, - "end": 2398, + "value": "Code not known", + "start": 3465, + "end": 3481, "loc": { "start": { - "line": 61, - "column": 28 + "line": 92, + "column": 19 }, "end": { - "line": 61, - "column": 29 + "line": 92, + "column": 35 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -49132,17 +53577,16 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2403, - "end": 2409, + "start": 3481, + "end": 3482, "loc": { "start": { - "line": 62, - "column": 4 + "line": 92, + "column": 35 }, "end": { - "line": 62, - "column": 10 + "line": 92, + "column": 36 } } }, @@ -49158,24 +53602,24 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 2410, - "end": 2418, + "value": "label", + "start": 3491, + "end": 3496, "loc": { "start": { - "line": 62, - "column": 11 + "line": 93, + "column": 8 }, "end": { - "line": 62, - "column": 19 + "line": 93, + "column": 13 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -49185,22 +53629,22 @@ "binop": null, "updateContext": null }, - "start": 2418, - "end": 2419, + "start": 3496, + "end": 3497, "loc": { "start": { - "line": 62, - "column": 19 + "line": 93, + "column": 13 }, "end": { - "line": 62, - "column": 20 + "line": 93, + "column": 14 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -49208,25 +53652,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "UNKNOWN_CODE", - "start": 2419, - "end": 2431, + "value": "Nomenclatural code not known", + "start": 3498, + "end": 3528, "loc": { "start": { - "line": 62, - "column": 20 + "line": 93, + "column": 15 }, "end": { - "line": 62, - "column": 32 + "line": 93, + "column": 45 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -49237,24 +53682,24 @@ "binop": null, "updateContext": null }, - "start": 2431, - "end": 2432, + "start": 3528, + "end": 3529, "loc": { "start": { - "line": 62, - "column": 32 + "line": 93, + "column": 45 }, "end": { - "line": 62, - "column": 33 + "line": 93, + "column": 46 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -49262,38 +53707,49 @@ "postfix": false, "binop": null }, - "start": 2435, - "end": 2436, + "value": "title", + "start": 3538, + "end": 3543, "loc": { "start": { - "line": 63, - "column": 2 + "line": 94, + "column": 8 }, "end": { - "line": 63, - "column": 3 + "line": 94, + "column": 13 } } }, { - "type": "CommentBlock", - "value": " Directly access IRIs for nomenclatural codes. ", - "start": 2440, - "end": 2491, + "type": { + "label": ":", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 3543, + "end": 3544, "loc": { "start": { - "line": 65, - "column": 2 + "line": 94, + "column": 13 }, "end": { - "line": 65, - "column": 53 + "line": 94, + "column": 14 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -49301,53 +53757,54 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 2494, - "end": 2500, + "value": "Nomenclatural code not known", + "start": 3545, + "end": 3575, "loc": { "start": { - "line": 66, - "column": 2 + "line": 94, + "column": 15 }, "end": { - "line": 66, - "column": 8 + "line": 94, + "column": 45 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "get", - "start": 2501, - "end": 2504, + "start": 3575, + "end": 3576, "loc": { "start": { - "line": 66, - "column": 9 + "line": 94, + "column": 45 }, "end": { - "line": 66, - "column": 12 + "line": 94, + "column": 46 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -49355,50 +53812,50 @@ "postfix": false, "binop": null }, - "value": "ICZN_CODE", - "start": 2505, - "end": 2514, + "start": 3583, + "end": 3584, "loc": { "start": { - "line": 66, - "column": 13 + "line": 95, + "column": 6 }, "end": { - "line": 66, - "column": 22 + "line": 95, + "column": 7 } } }, { "type": { - "label": "(", + "label": ",", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2514, - "end": 2515, + "start": 3584, + "end": 3585, "loc": { "start": { - "line": 66, - "column": 22 + "line": 95, + "column": 7 }, "end": { - "line": 66, - "column": 23 + "line": 95, + "column": 8 } } }, { "type": { - "label": ")", - "beforeExpr": false, - "startsExpr": false, + "label": "{", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -49406,23 +53863,23 @@ "postfix": false, "binop": null }, - "start": 2515, - "end": 2516, + "start": 3592, + "end": 3593, "loc": { "start": { - "line": 66, - "column": 23 + "line": 96, + "column": 6 }, "end": { - "line": 66, - "column": 24 + "line": 96, + "column": 7 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -49431,23 +53888,23 @@ "postfix": false, "binop": null }, - "start": 2517, - "end": 2518, + "value": "iri", + "start": 3602, + "end": 3605, "loc": { "start": { - "line": 66, - "column": 25 + "line": 97, + "column": 8 }, "end": { - "line": 66, - "column": 26 + "line": 97, + "column": 11 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -49458,17 +53915,16 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2519, - "end": 2525, + "start": 3605, + "end": 3606, "loc": { "start": { - "line": 66, - "column": 27 + "line": 97, + "column": 11 }, "end": { - "line": 66, - "column": 33 + "line": 97, + "column": 12 } } }, @@ -49485,16 +53941,16 @@ "binop": null }, "value": "owlterms", - "start": 2526, - "end": 2534, + "start": 3607, + "end": 3615, "loc": { "start": { - "line": 66, - "column": 34 + "line": 97, + "column": 13 }, "end": { - "line": 66, - "column": 42 + "line": 97, + "column": 21 } } }, @@ -49511,16 +53967,16 @@ "binop": null, "updateContext": null }, - "start": 2534, - "end": 2535, + "start": 3615, + "end": 3616, "loc": { "start": { - "line": 66, - "column": 42 + "line": 97, + "column": 21 }, "end": { - "line": 66, - "column": 43 + "line": 97, + "column": 22 } } }, @@ -49537,22 +53993,22 @@ "binop": null }, "value": "ICZN_CODE", - "start": 2535, - "end": 2544, + "start": 3616, + "end": 3625, "loc": { "start": { - "line": 66, - "column": 43 + "line": 97, + "column": 22 }, "end": { - "line": 66, - "column": 52 + "line": 97, + "column": 31 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -49563,24 +54019,24 @@ "binop": null, "updateContext": null }, - "start": 2544, - "end": 2545, + "start": 3625, + "end": 3626, "loc": { "start": { - "line": 66, - "column": 52 + "line": 97, + "column": 31 }, "end": { - "line": 66, - "column": 53 + "line": 97, + "column": 32 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -49588,48 +54044,49 @@ "postfix": false, "binop": null }, - "start": 2546, - "end": 2547, + "value": "shortName", + "start": 3635, + "end": 3644, "loc": { "start": { - "line": 66, - "column": 54 + "line": 98, + "column": 8 }, "end": { - "line": 66, - "column": 55 + "line": 98, + "column": 17 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 2551, - "end": 2557, + "start": 3644, + "end": 3645, "loc": { "start": { - "line": 68, - "column": 2 + "line": 98, + "column": 17 }, "end": { - "line": 68, - "column": 8 + "line": 98, + "column": 18 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -49637,52 +54094,53 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "get", - "start": 2558, - "end": 2561, + "value": "ICZN", + "start": 3646, + "end": 3652, "loc": { "start": { - "line": 68, - "column": 9 + "line": 98, + "column": 19 }, "end": { - "line": 68, - "column": 12 + "line": 98, + "column": 25 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "ICN_CODE", - "start": 2562, - "end": 2570, + "start": 3652, + "end": 3653, "loc": { "start": { - "line": 68, - "column": 13 + "line": 98, + "column": 25 }, "end": { - "line": 68, - "column": 21 + "line": 98, + "column": 26 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -49691,73 +54149,76 @@ "postfix": false, "binop": null }, - "start": 2570, - "end": 2571, + "value": "label", + "start": 3662, + "end": 3667, "loc": { "start": { - "line": 68, - "column": 21 + "line": 99, + "column": 8 }, "end": { - "line": 68, - "column": 22 + "line": 99, + "column": 13 } } }, { "type": { - "label": ")", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2571, - "end": 2572, + "start": 3667, + "end": 3668, "loc": { "start": { - "line": 68, - "column": 22 + "line": 99, + "column": 13 }, "end": { - "line": 68, - "column": 23 + "line": 99, + "column": 14 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "string", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2573, - "end": 2574, + "value": "Animals (ICZN)", + "start": 3669, + "end": 3685, "loc": { "start": { - "line": 68, - "column": 24 + "line": 99, + "column": 15 }, "end": { - "line": 68, - "column": 25 + "line": 99, + "column": 31 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -49768,16 +54229,15 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2575, - "end": 2581, + "start": 3685, + "end": 3686, "loc": { "start": { - "line": 68, - "column": 26 + "line": 99, + "column": 31 }, "end": { - "line": 68, + "line": 99, "column": 32 } } @@ -49794,24 +54254,24 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 2582, - "end": 2590, + "value": "title", + "start": 3695, + "end": 3700, "loc": { "start": { - "line": 68, - "column": 33 + "line": 100, + "column": 8 }, "end": { - "line": 68, - "column": 41 + "line": 100, + "column": 13 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -49821,22 +54281,22 @@ "binop": null, "updateContext": null }, - "start": 2590, - "end": 2591, + "start": 3700, + "end": 3701, "loc": { "start": { - "line": 68, - "column": 41 + "line": 100, + "column": 13 }, "end": { - "line": 68, - "column": 42 + "line": 100, + "column": 14 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -49844,25 +54304,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "ICN_CODE", - "start": 2591, - "end": 2599, + "value": "International Code of Zoological Nomenclature", + "start": 3702, + "end": 3749, "loc": { "start": { - "line": 68, - "column": 42 + "line": 100, + "column": 15 }, "end": { - "line": 68, - "column": 50 + "line": 100, + "column": 62 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -49873,16 +54334,16 @@ "binop": null, "updateContext": null }, - "start": 2599, - "end": 2600, + "start": 3749, + "end": 3750, "loc": { "start": { - "line": 68, - "column": 50 + "line": 100, + "column": 62 }, "end": { - "line": 68, - "column": 51 + "line": 100, + "column": 63 } } }, @@ -49898,49 +54359,49 @@ "postfix": false, "binop": null }, - "start": 2601, - "end": 2602, + "start": 3757, + "end": 3758, "loc": { "start": { - "line": 68, - "column": 52 + "line": 101, + "column": 6 }, "end": { - "line": 68, - "column": 53 + "line": 101, + "column": 7 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 2606, - "end": 2612, + "start": 3758, + "end": 3759, "loc": { "start": { - "line": 70, - "column": 2 + "line": 101, + "column": 7 }, "end": { - "line": 70, + "line": 101, "column": 8 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -49949,17 +54410,16 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 2613, - "end": 2616, + "start": 3766, + "end": 3767, "loc": { "start": { - "line": 70, - "column": 9 + "line": 102, + "column": 6 }, "end": { - "line": 70, - "column": 12 + "line": 102, + "column": 7 } } }, @@ -49975,74 +54435,50 @@ "postfix": false, "binop": null }, - "value": "ICNP_CODE", - "start": 2617, - "end": 2626, + "value": "iri", + "start": 3776, + "end": 3779, "loc": { "start": { - "line": 70, - "column": 13 + "line": 103, + "column": 8 }, "end": { - "line": 70, - "column": 22 + "line": 103, + "column": 11 } } }, { "type": { - "label": "(", + "label": ":", "beforeExpr": true, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "start": 2626, - "end": 2627, - "loc": { - "start": { - "line": 70, - "column": 22 - }, - "end": { - "line": 70, - "column": 23 - } - } - }, - { - "type": { - "label": ")", - "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2627, - "end": 2628, + "start": 3779, + "end": 3780, "loc": { "start": { - "line": 70, - "column": 23 + "line": 103, + "column": 11 }, "end": { - "line": 70, - "column": 24 + "line": 103, + "column": 12 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -50051,24 +54487,24 @@ "postfix": false, "binop": null }, - "start": 2629, - "end": 2630, + "value": "owlterms", + "start": 3781, + "end": 3789, "loc": { "start": { - "line": 70, - "column": 25 + "line": 103, + "column": 13 }, "end": { - "line": 70, - "column": 26 + "line": 103, + "column": 21 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -50078,17 +54514,16 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2631, - "end": 2637, + "start": 3789, + "end": 3790, "loc": { "start": { - "line": 70, - "column": 27 + "line": 103, + "column": 21 }, "end": { - "line": 70, - "column": 33 + "line": 103, + "column": 22 } } }, @@ -50104,24 +54539,24 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 2638, - "end": 2646, + "value": "ICN_CODE", + "start": 3790, + "end": 3798, "loc": { "start": { - "line": 70, - "column": 34 + "line": 103, + "column": 22 }, "end": { - "line": 70, - "column": 42 + "line": 103, + "column": 30 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -50131,16 +54566,16 @@ "binop": null, "updateContext": null }, - "start": 2646, - "end": 2647, + "start": 3798, + "end": 3799, "loc": { "start": { - "line": 70, - "column": 42 + "line": 103, + "column": 30 }, "end": { - "line": 70, - "column": 43 + "line": 103, + "column": 31 } } }, @@ -50156,23 +54591,23 @@ "postfix": false, "binop": null }, - "value": "ICNP_CODE", - "start": 2647, - "end": 2656, + "value": "shortName", + "start": 3808, + "end": 3817, "loc": { "start": { - "line": 70, - "column": 43 + "line": 104, + "column": 8 }, "end": { - "line": 70, - "column": 52 + "line": 104, + "column": 17 } } }, { "type": { - "label": ";", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -50183,67 +54618,69 @@ "binop": null, "updateContext": null }, - "start": 2656, - "end": 2657, + "start": 3817, + "end": 3818, "loc": { "start": { - "line": 70, - "column": 52 + "line": 104, + "column": 17 }, "end": { - "line": 70, - "column": 53 + "line": 104, + "column": 18 } } }, { "type": { - "label": "}", + "label": "string", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2658, - "end": 2659, + "value": "ICN", + "start": 3819, + "end": 3824, "loc": { "start": { - "line": 70, - "column": 54 + "line": 104, + "column": 19 }, "end": { - "line": 70, - "column": 55 + "line": 104, + "column": 24 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 2663, - "end": 2669, + "start": 3824, + "end": 3825, "loc": { "start": { - "line": 72, - "column": 2 + "line": 104, + "column": 24 }, "end": { - "line": 72, - "column": 8 + "line": 104, + "column": 25 } } }, @@ -50259,100 +54696,103 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 2670, - "end": 2673, + "value": "label", + "start": 3834, + "end": 3839, "loc": { "start": { - "line": 72, - "column": 9 + "line": 105, + "column": 8 }, "end": { - "line": 72, - "column": 12 + "line": 105, + "column": 13 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "ICTV_CODE", - "start": 2674, - "end": 2683, + "start": 3839, + "end": 3840, "loc": { "start": { - "line": 72, + "line": 105, "column": 13 }, "end": { - "line": 72, - "column": 22 + "line": 105, + "column": 14 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "string", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2683, - "end": 2684, + "value": "Algae, fungi and plants (ICN, previously ICBN)", + "start": 3841, + "end": 3889, "loc": { "start": { - "line": 72, - "column": 22 + "line": 105, + "column": 15 }, "end": { - "line": 72, - "column": 23 + "line": 105, + "column": 63 } } }, { "type": { - "label": ")", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2684, - "end": 2685, + "start": 3889, + "end": 3890, "loc": { "start": { - "line": 72, - "column": 23 + "line": 105, + "column": 63 }, "end": { - "line": 72, - "column": 24 + "line": 105, + "column": 64 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -50361,23 +54801,23 @@ "postfix": false, "binop": null }, - "start": 2686, - "end": 2687, + "value": "title", + "start": 3899, + "end": 3904, "loc": { "start": { - "line": 72, - "column": 25 + "line": 106, + "column": 8 }, "end": { - "line": 72, - "column": 26 + "line": 106, + "column": 13 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -50388,23 +54828,22 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2688, - "end": 2694, + "start": 3904, + "end": 3905, "loc": { "start": { - "line": 72, - "column": 27 + "line": 106, + "column": 13 }, "end": { - "line": 72, - "column": 33 + "line": 106, + "column": 14 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -50412,26 +54851,27 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "owlterms", - "start": 2695, - "end": 2703, + "value": "International Code of Nomenclature for algae, fungi, and plants", + "start": 3906, + "end": 3971, "loc": { "start": { - "line": 72, - "column": 34 + "line": 106, + "column": 15 }, "end": { - "line": 72, - "column": 42 + "line": 106, + "column": 80 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -50441,24 +54881,24 @@ "binop": null, "updateContext": null }, - "start": 2703, - "end": 2704, + "start": 3971, + "end": 3972, "loc": { "start": { - "line": 72, - "column": 42 + "line": 106, + "column": 80 }, "end": { - "line": 72, - "column": 43 + "line": 106, + "column": 81 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50466,23 +54906,22 @@ "postfix": false, "binop": null }, - "value": "ICTV_CODE", - "start": 2704, - "end": 2713, + "start": 3979, + "end": 3980, "loc": { "start": { - "line": 72, - "column": 43 + "line": 107, + "column": 6 }, "end": { - "line": 72, - "column": 52 + "line": 107, + "column": 7 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -50493,24 +54932,24 @@ "binop": null, "updateContext": null }, - "start": 2713, - "end": 2714, + "start": 3980, + "end": 3981, "loc": { "start": { - "line": 72, - "column": 52 + "line": 107, + "column": 7 }, "end": { - "line": 72, - "column": 53 + "line": 107, + "column": 8 } } }, { "type": { - "label": "}", - "beforeExpr": false, - "startsExpr": false, + "label": "{", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50518,16 +54957,16 @@ "postfix": false, "binop": null }, - "start": 2715, - "end": 2716, + "start": 3988, + "end": 3989, "loc": { "start": { - "line": 72, - "column": 54 + "line": 108, + "column": 6 }, "end": { - "line": 72, - "column": 55 + "line": 108, + "column": 7 } } }, @@ -50543,42 +54982,42 @@ "postfix": false, "binop": null }, - "value": "static", - "start": 2720, - "end": 2726, + "value": "iri", + "start": 3998, + "end": 4001, "loc": { "start": { - "line": 74, - "column": 2 + "line": 109, + "column": 8 }, "end": { - "line": 74, - "column": 8 + "line": 109, + "column": 11 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "get", - "start": 2727, - "end": 2730, + "start": 4001, + "end": 4002, "loc": { "start": { - "line": 74, - "column": 9 + "line": 109, + "column": 11 }, "end": { - "line": 74, + "line": 109, "column": 12 } } @@ -50595,50 +55034,51 @@ "postfix": false, "binop": null }, - "value": "ICNCP_CODE", - "start": 2731, - "end": 2741, + "value": "owlterms", + "start": 4003, + "end": 4011, "loc": { "start": { - "line": 74, + "line": 109, "column": 13 }, "end": { - "line": 74, - "column": 23 + "line": 109, + "column": 21 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": ".", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2741, - "end": 2742, + "start": 4011, + "end": 4012, "loc": { "start": { - "line": 74, - "column": 23 + "line": 109, + "column": 21 }, "end": { - "line": 74, - "column": 24 + "line": 109, + "column": 22 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -50646,23 +55086,50 @@ "postfix": false, "binop": null }, - "start": 2742, - "end": 2743, + "value": "ICNP_CODE", + "start": 4012, + "end": 4021, "loc": { "start": { - "line": 74, - "column": 24 + "line": 109, + "column": 22 }, "end": { - "line": 74, - "column": 25 + "line": 109, + "column": 31 } } }, { "type": { - "label": "{", + "label": ",", "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 4021, + "end": 4022, + "loc": { + "start": { + "line": 109, + "column": 31 + }, + "end": { + "line": 109, + "column": 32 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -50671,23 +55138,23 @@ "postfix": false, "binop": null }, - "start": 2744, - "end": 2745, + "value": "shortName", + "start": 4031, + "end": 4040, "loc": { "start": { - "line": 74, - "column": 26 + "line": 110, + "column": 8 }, "end": { - "line": 74, - "column": 27 + "line": 110, + "column": 17 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -50698,23 +55165,22 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 2746, - "end": 2752, + "start": 4040, + "end": 4041, "loc": { "start": { - "line": 74, - "column": 28 + "line": 110, + "column": 17 }, "end": { - "line": 74, - "column": 34 + "line": 110, + "column": 18 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -50722,26 +55188,27 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "owlterms", - "start": 2753, - "end": 2761, + "value": "ICNP", + "start": 4042, + "end": 4048, "loc": { "start": { - "line": 74, - "column": 35 + "line": 110, + "column": 19 }, "end": { - "line": 74, - "column": 43 + "line": 110, + "column": 25 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -50751,16 +55218,16 @@ "binop": null, "updateContext": null }, - "start": 2761, - "end": 2762, + "start": 4048, + "end": 4049, "loc": { "start": { - "line": 74, - "column": 43 + "line": 110, + "column": 25 }, "end": { - "line": 74, - "column": 44 + "line": 110, + "column": 26 } } }, @@ -50776,23 +55243,23 @@ "postfix": false, "binop": null }, - "value": "ICNCP_CODE", - "start": 2762, - "end": 2772, + "value": "label", + "start": 4058, + "end": 4063, "loc": { "start": { - "line": 74, - "column": 44 + "line": 111, + "column": 8 }, "end": { - "line": 74, - "column": 54 + "line": 111, + "column": 13 } } }, { "type": { - "label": ";", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -50803,83 +55270,69 @@ "binop": null, "updateContext": null }, - "start": 2772, - "end": 2773, + "start": 4063, + "end": 4064, "loc": { "start": { - "line": 74, - "column": 54 + "line": 111, + "column": 13 }, "end": { - "line": 74, - "column": 55 + "line": 111, + "column": 14 } } }, { "type": { - "label": "}", + "label": "string", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2774, - "end": 2775, - "loc": { - "start": { - "line": 74, - "column": 56 - }, - "end": { - "line": 74, - "column": 57 - } - } - }, - { - "type": "CommentBlock", - "value": "*\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n ", - "start": 2779, - "end": 3281, + "value": "Prokaryotes (ICNP)", + "start": 4065, + "end": 4085, "loc": { "start": { - "line": 76, - "column": 2 + "line": 111, + "column": 15 }, "end": { - "line": 86, - "column": 5 + "line": 111, + "column": 35 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 3284, - "end": 3290, + "start": 4085, + "end": 4086, "loc": { "start": { - "line": 87, - "column": 2 + "line": 111, + "column": 35 }, "end": { - "line": 87, - "column": 8 + "line": 111, + "column": 36 } } }, @@ -50895,128 +55348,129 @@ "postfix": false, "binop": null }, - "value": "getNomenclaturalCodes", - "start": 3291, - "end": 3312, + "value": "title", + "start": 4095, + "end": 4100, "loc": { "start": { - "line": 87, - "column": 9 + "line": 112, + "column": 8 }, "end": { - "line": 87, - "column": 30 + "line": 112, + "column": 13 } } }, { "type": { - "label": "(", + "label": ":", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 3312, - "end": 3313, + "start": 4100, + "end": 4101, "loc": { "start": { - "line": 87, - "column": 30 + "line": 112, + "column": 13 }, "end": { - "line": 87, - "column": 31 + "line": 112, + "column": 14 } } }, { "type": { - "label": ")", + "label": "string", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 3313, - "end": 3314, + "value": "International Code of Nomenclature of Prokaryotes", + "start": 4102, + "end": 4153, "loc": { "start": { - "line": 87, - "column": 31 + "line": 112, + "column": 15 }, "end": { - "line": 87, - "column": 32 + "line": 112, + "column": 66 } } }, { "type": { - "label": "{", + "label": ",", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 3315, - "end": 3316, + "start": 4153, + "end": 4154, "loc": { "start": { - "line": 87, - "column": 33 + "line": 112, + "column": 66 }, "end": { - "line": 87, - "column": 34 + "line": 112, + "column": 67 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "return", - "start": 3321, - "end": 3327, + "start": 4161, + "end": 4162, "loc": { "start": { - "line": 88, - "column": 4 + "line": 113, + "column": 6 }, "end": { - "line": 88, - "column": 10 + "line": 113, + "column": 7 } } }, { "type": { - "label": "[", + "label": ",", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -51025,32 +55479,16 @@ "binop": null, "updateContext": null }, - "start": 3328, - "end": 3329, - "loc": { - "start": { - "line": 88, - "column": 11 - }, - "end": { - "line": 88, - "column": 12 - } - } - }, - { - "type": "CommentLine", - "value": " Note: the unknown code needs to be the first one in this list.", - "start": 3336, - "end": 3401, + "start": 4162, + "end": 4163, "loc": { "start": { - "line": 89, - "column": 6 + "line": 113, + "column": 7 }, "end": { - "line": 89, - "column": 71 + "line": 113, + "column": 8 } } }, @@ -51066,15 +55504,15 @@ "postfix": false, "binop": null }, - "start": 3408, - "end": 3409, + "start": 4170, + "end": 4171, "loc": { "start": { - "line": 90, + "line": 114, "column": 6 }, "end": { - "line": 90, + "line": 114, "column": 7 } } @@ -51092,15 +55530,15 @@ "binop": null }, "value": "iri", - "start": 3418, - "end": 3421, + "start": 4180, + "end": 4183, "loc": { "start": { - "line": 91, + "line": 115, "column": 8 }, "end": { - "line": 91, + "line": 115, "column": 11 } } @@ -51118,15 +55556,15 @@ "binop": null, "updateContext": null }, - "start": 3421, - "end": 3422, + "start": 4183, + "end": 4184, "loc": { "start": { - "line": 91, + "line": 115, "column": 11 }, "end": { - "line": 91, + "line": 115, "column": 12 } } @@ -51144,15 +55582,15 @@ "binop": null }, "value": "owlterms", - "start": 3423, - "end": 3431, + "start": 4185, + "end": 4193, "loc": { "start": { - "line": 91, + "line": 115, "column": 13 }, "end": { - "line": 91, + "line": 115, "column": 21 } } @@ -51170,15 +55608,15 @@ "binop": null, "updateContext": null }, - "start": 3431, - "end": 3432, + "start": 4193, + "end": 4194, "loc": { "start": { - "line": 91, + "line": 115, "column": 21 }, "end": { - "line": 91, + "line": 115, "column": 22 } } @@ -51195,17 +55633,17 @@ "postfix": false, "binop": null }, - "value": "UNKNOWN_CODE", - "start": 3432, - "end": 3444, + "value": "ICTV_CODE", + "start": 4194, + "end": 4203, "loc": { "start": { - "line": 91, + "line": 115, "column": 22 }, "end": { - "line": 91, - "column": 34 + "line": 115, + "column": 31 } } }, @@ -51222,16 +55660,16 @@ "binop": null, "updateContext": null }, - "start": 3444, - "end": 3445, + "start": 4203, + "end": 4204, "loc": { "start": { - "line": 91, - "column": 34 + "line": 115, + "column": 31 }, "end": { - "line": 91, - "column": 35 + "line": 115, + "column": 32 } } }, @@ -51248,15 +55686,15 @@ "binop": null }, "value": "shortName", - "start": 3454, - "end": 3463, + "start": 4213, + "end": 4222, "loc": { "start": { - "line": 92, + "line": 116, "column": 8 }, "end": { - "line": 92, + "line": 116, "column": 17 } } @@ -51274,15 +55712,15 @@ "binop": null, "updateContext": null }, - "start": 3463, - "end": 3464, + "start": 4222, + "end": 4223, "loc": { "start": { - "line": 92, + "line": 116, "column": 17 }, "end": { - "line": 92, + "line": 116, "column": 18 } } @@ -51300,17 +55738,17 @@ "binop": null, "updateContext": null }, - "value": "Code not known", - "start": 3465, - "end": 3481, + "value": "ICTV", + "start": 4224, + "end": 4230, "loc": { "start": { - "line": 92, + "line": 116, "column": 19 }, "end": { - "line": 92, - "column": 35 + "line": 116, + "column": 25 } } }, @@ -51327,16 +55765,16 @@ "binop": null, "updateContext": null }, - "start": 3481, - "end": 3482, + "start": 4230, + "end": 4231, "loc": { "start": { - "line": 92, - "column": 35 + "line": 116, + "column": 25 }, "end": { - "line": 92, - "column": 36 + "line": 116, + "column": 26 } } }, @@ -51353,15 +55791,15 @@ "binop": null }, "value": "label", - "start": 3491, - "end": 3496, + "start": 4240, + "end": 4245, "loc": { "start": { - "line": 93, + "line": 117, "column": 8 }, "end": { - "line": 93, + "line": 117, "column": 13 } } @@ -51379,15 +55817,15 @@ "binop": null, "updateContext": null }, - "start": 3496, - "end": 3497, + "start": 4245, + "end": 4246, "loc": { "start": { - "line": 93, + "line": 117, "column": 13 }, "end": { - "line": 93, + "line": 117, "column": 14 } } @@ -51405,17 +55843,17 @@ "binop": null, "updateContext": null }, - "value": "Nomenclatural code not known", - "start": 3498, - "end": 3528, + "value": "Viruses (ICTV)", + "start": 4247, + "end": 4263, "loc": { "start": { - "line": 93, + "line": 117, "column": 15 }, "end": { - "line": 93, - "column": 45 + "line": 117, + "column": 31 } } }, @@ -51432,16 +55870,16 @@ "binop": null, "updateContext": null }, - "start": 3528, - "end": 3529, + "start": 4263, + "end": 4264, "loc": { "start": { - "line": 93, - "column": 45 + "line": 117, + "column": 31 }, "end": { - "line": 93, - "column": 46 + "line": 117, + "column": 32 } } }, @@ -51458,15 +55896,15 @@ "binop": null }, "value": "title", - "start": 3538, - "end": 3543, + "start": 4273, + "end": 4278, "loc": { "start": { - "line": 94, + "line": 118, "column": 8 }, "end": { - "line": 94, + "line": 118, "column": 13 } } @@ -51484,15 +55922,15 @@ "binop": null, "updateContext": null }, - "start": 3543, - "end": 3544, + "start": 4278, + "end": 4279, "loc": { "start": { - "line": 94, + "line": 118, "column": 13 }, "end": { - "line": 94, + "line": 118, "column": 14 } } @@ -51510,17 +55948,17 @@ "binop": null, "updateContext": null }, - "value": "Nomenclatural code not known", - "start": 3545, - "end": 3575, + "value": "International Committee on Taxonomy of Viruses", + "start": 4280, + "end": 4328, "loc": { "start": { - "line": 94, + "line": 118, "column": 15 }, "end": { - "line": 94, - "column": 45 + "line": 118, + "column": 63 } } }, @@ -51537,16 +55975,16 @@ "binop": null, "updateContext": null }, - "start": 3575, - "end": 3576, + "start": 4328, + "end": 4329, "loc": { "start": { - "line": 94, - "column": 45 + "line": 118, + "column": 63 }, "end": { - "line": 94, - "column": 46 + "line": 118, + "column": 64 } } }, @@ -51562,15 +56000,15 @@ "postfix": false, "binop": null }, - "start": 3583, - "end": 3584, + "start": 4336, + "end": 4337, "loc": { "start": { - "line": 95, + "line": 119, "column": 6 }, "end": { - "line": 95, + "line": 119, "column": 7 } } @@ -51588,15 +56026,15 @@ "binop": null, "updateContext": null }, - "start": 3584, - "end": 3585, + "start": 4337, + "end": 4338, "loc": { "start": { - "line": 95, + "line": 119, "column": 7 }, "end": { - "line": 95, + "line": 119, "column": 8 } } @@ -51613,15 +56051,15 @@ "postfix": false, "binop": null }, - "start": 3592, - "end": 3593, + "start": 4345, + "end": 4346, "loc": { "start": { - "line": 96, + "line": 120, "column": 6 }, "end": { - "line": 96, + "line": 120, "column": 7 } } @@ -51639,15 +56077,15 @@ "binop": null }, "value": "iri", - "start": 3602, - "end": 3605, + "start": 4355, + "end": 4358, "loc": { "start": { - "line": 97, + "line": 121, "column": 8 }, "end": { - "line": 97, + "line": 121, "column": 11 } } @@ -51665,15 +56103,15 @@ "binop": null, "updateContext": null }, - "start": 3605, - "end": 3606, + "start": 4358, + "end": 4359, "loc": { "start": { - "line": 97, + "line": 121, "column": 11 }, "end": { - "line": 97, + "line": 121, "column": 12 } } @@ -51691,15 +56129,15 @@ "binop": null }, "value": "owlterms", - "start": 3607, - "end": 3615, + "start": 4360, + "end": 4368, "loc": { "start": { - "line": 97, + "line": 121, "column": 13 }, "end": { - "line": 97, + "line": 121, "column": 21 } } @@ -51717,15 +56155,15 @@ "binop": null, "updateContext": null }, - "start": 3615, - "end": 3616, + "start": 4368, + "end": 4369, "loc": { "start": { - "line": 97, + "line": 121, "column": 21 }, "end": { - "line": 97, + "line": 121, "column": 22 } } @@ -51742,17 +56180,17 @@ "postfix": false, "binop": null }, - "value": "ICZN_CODE", - "start": 3616, - "end": 3625, + "value": "ICNCP_CODE", + "start": 4369, + "end": 4379, "loc": { "start": { - "line": 97, + "line": 121, "column": 22 }, "end": { - "line": 97, - "column": 31 + "line": 121, + "column": 32 } } }, @@ -51769,16 +56207,16 @@ "binop": null, "updateContext": null }, - "start": 3625, - "end": 3626, + "start": 4379, + "end": 4380, "loc": { "start": { - "line": 97, - "column": 31 + "line": 121, + "column": 32 }, "end": { - "line": 97, - "column": 32 + "line": 121, + "column": 33 } } }, @@ -51795,15 +56233,15 @@ "binop": null }, "value": "shortName", - "start": 3635, - "end": 3644, + "start": 4389, + "end": 4398, "loc": { "start": { - "line": 98, + "line": 122, "column": 8 }, "end": { - "line": 98, + "line": 122, "column": 17 } } @@ -51821,121 +56259,16 @@ "binop": null, "updateContext": null }, - "start": 3644, - "end": 3645, + "start": 4398, + "end": 4399, "loc": { "start": { - "line": 98, + "line": 122, "column": 17 }, "end": { - "line": 98, - "column": 18 - } - } - }, - { - "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "ICZN", - "start": 3646, - "end": 3652, - "loc": { - "start": { - "line": 98, - "column": 19 - }, - "end": { - "line": 98, - "column": 25 - } - } - }, - { - "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 3652, - "end": 3653, - "loc": { - "start": { - "line": 98, - "column": 25 - }, - "end": { - "line": 98, - "column": 26 - } - } - }, - { - "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "value": "label", - "start": 3662, - "end": 3667, - "loc": { - "start": { - "line": 99, - "column": 8 - }, - "end": { - "line": 99, - "column": 13 - } - } - }, - { - "type": { - "label": ":", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 3667, - "end": 3668, - "loc": { - "start": { - "line": 99, - "column": 13 - }, - "end": { - "line": 99, - "column": 14 + "line": 122, + "column": 18 } } }, @@ -51952,17 +56285,17 @@ "binop": null, "updateContext": null }, - "value": "Animals (ICZN)", - "start": 3669, - "end": 3685, + "value": "ICNCP", + "start": 4400, + "end": 4407, "loc": { "start": { - "line": 99, - "column": 15 + "line": 122, + "column": 19 }, "end": { - "line": 99, - "column": 31 + "line": 122, + "column": 26 } } }, @@ -51979,16 +56312,16 @@ "binop": null, "updateContext": null }, - "start": 3685, - "end": 3686, + "start": 4407, + "end": 4408, "loc": { "start": { - "line": 99, - "column": 31 + "line": 122, + "column": 26 }, "end": { - "line": 99, - "column": 32 + "line": 122, + "column": 27 } } }, @@ -52004,16 +56337,16 @@ "postfix": false, "binop": null }, - "value": "title", - "start": 3695, - "end": 3700, + "value": "label", + "start": 4417, + "end": 4422, "loc": { "start": { - "line": 100, + "line": 123, "column": 8 }, "end": { - "line": 100, + "line": 123, "column": 13 } } @@ -52031,15 +56364,15 @@ "binop": null, "updateContext": null }, - "start": 3700, - "end": 3701, + "start": 4422, + "end": 4423, "loc": { "start": { - "line": 100, + "line": 123, "column": 13 }, "end": { - "line": 100, + "line": 123, "column": 14 } } @@ -52057,17 +56390,17 @@ "binop": null, "updateContext": null }, - "value": "International Code of Zoological Nomenclature", - "start": 3702, - "end": 3749, + "value": "Cultivated plants (ICNCP)", + "start": 4424, + "end": 4451, "loc": { "start": { - "line": 100, + "line": 123, "column": 15 }, "end": { - "line": 100, - "column": 62 + "line": 123, + "column": 42 } } }, @@ -52084,24 +56417,24 @@ "binop": null, "updateContext": null }, - "start": 3749, - "end": 3750, + "start": 4451, + "end": 4452, "loc": { "start": { - "line": 100, - "column": 62 + "line": 123, + "column": 42 }, "end": { - "line": 100, - "column": 63 + "line": 123, + "column": 43 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -52109,22 +56442,23 @@ "postfix": false, "binop": null }, - "start": 3757, - "end": 3758, + "value": "title", + "start": 4461, + "end": 4466, "loc": { "start": { - "line": 101, - "column": 6 + "line": 124, + "column": 8 }, "end": { - "line": 101, - "column": 7 + "line": 124, + "column": 13 } } }, { "type": { - "label": ",", + "label": ":", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -52135,47 +56469,22 @@ "binop": null, "updateContext": null }, - "start": 3758, - "end": 3759, - "loc": { - "start": { - "line": 101, - "column": 7 - }, - "end": { - "line": 101, - "column": 8 - } - } - }, - { - "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "start": 3766, - "end": 3767, + "start": 4466, + "end": 4467, "loc": { "start": { - "line": 102, - "column": 6 + "line": 124, + "column": 13 }, "end": { - "line": 102, - "column": 7 + "line": 124, + "column": 14 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -52183,25 +56492,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "iri", - "start": 3776, - "end": 3779, + "value": "International Code of Cultivated Plants", + "start": 4468, + "end": 4509, "loc": { "start": { - "line": 103, - "column": 8 + "line": 124, + "column": 15 }, "end": { - "line": 103, - "column": 11 + "line": 124, + "column": 56 } } }, { "type": { - "label": ":", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -52212,24 +56522,24 @@ "binop": null, "updateContext": null }, - "start": 3779, - "end": 3780, + "start": 4509, + "end": 4510, "loc": { "start": { - "line": 103, - "column": 11 + "line": 124, + "column": 56 }, "end": { - "line": 103, - "column": 12 + "line": 124, + "column": 57 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -52237,24 +56547,23 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 3781, - "end": 3789, + "start": 4517, + "end": 4518, "loc": { "start": { - "line": 103, - "column": 13 + "line": 125, + "column": 6 }, "end": { - "line": 103, - "column": 21 + "line": 125, + "column": 7 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -52264,48 +56573,48 @@ "binop": null, "updateContext": null }, - "start": 3789, - "end": 3790, + "start": 4518, + "end": 4519, "loc": { "start": { - "line": 103, - "column": 21 + "line": 125, + "column": 7 }, "end": { - "line": 103, - "column": 22 + "line": 125, + "column": 8 } } }, { "type": { - "label": "name", + "label": "]", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "ICN_CODE", - "start": 3790, - "end": 3798, + "start": 4524, + "end": 4525, "loc": { "start": { - "line": 103, - "column": 22 + "line": 126, + "column": 4 }, "end": { - "line": 103, - "column": 30 + "line": 126, + "column": 5 } } }, { "type": { - "label": ",", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -52316,24 +56625,24 @@ "binop": null, "updateContext": null }, - "start": 3798, - "end": 3799, + "start": 4525, + "end": 4526, "loc": { "start": { - "line": 103, - "column": 30 + "line": 126, + "column": 5 }, "end": { - "line": 103, - "column": 31 + "line": 126, + "column": 6 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -52341,49 +56650,64 @@ "postfix": false, "binop": null }, - "value": "shortName", - "start": 3808, - "end": 3817, + "start": 4529, + "end": 4530, "loc": { "start": { - "line": 104, - "column": 8 + "line": 127, + "column": 2 }, "end": { - "line": 104, - "column": 17 + "line": 127, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Returns the nomenclatural code entry for a code.\n ", + "start": 4534, + "end": 4597, + "loc": { + "start": { + "line": 129, + "column": 2 + }, + "end": { + "line": 131, + "column": 5 } } }, { "type": { - "label": ":", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 3817, - "end": 3818, + "value": "static", + "start": 4600, + "end": 4606, "loc": { "start": { - "line": 104, - "column": 17 + "line": 132, + "column": 2 }, "end": { - "line": 104, - "column": 18 + "line": 132, + "column": 8 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -52391,46 +56715,44 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "ICN", - "start": 3819, - "end": 3824, + "value": "getNomenCodeDetails", + "start": 4607, + "end": 4626, "loc": { "start": { - "line": 104, - "column": 19 + "line": 132, + "column": 9 }, "end": { - "line": 104, - "column": 24 + "line": 132, + "column": 28 } } }, { "type": { - "label": ",", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 3824, - "end": 3825, + "start": 4626, + "end": 4627, "loc": { "start": { - "line": 104, - "column": 24 + "line": 132, + "column": 28 }, "end": { - "line": 104, - "column": 25 + "line": 132, + "column": 29 } } }, @@ -52446,77 +56768,75 @@ "postfix": false, "binop": null }, - "value": "label", - "start": 3834, - "end": 3839, + "value": "nomenCode", + "start": 4627, + "end": 4636, "loc": { "start": { - "line": 105, - "column": 8 + "line": 132, + "column": 29 }, "end": { - "line": 105, - "column": 13 + "line": 132, + "column": 38 } } }, { "type": { - "label": ":", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 3839, - "end": 3840, + "start": 4636, + "end": 4637, "loc": { "start": { - "line": 105, - "column": 13 + "line": 132, + "column": 38 }, "end": { - "line": 105, - "column": 14 + "line": 132, + "column": 39 } } }, { "type": { - "label": "string", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "Algae, fungi and plants (ICN, previously ICBN)", - "start": 3841, - "end": 3889, + "start": 4638, + "end": 4639, "loc": { "start": { - "line": 105, - "column": 15 + "line": 132, + "column": 40 }, "end": { - "line": 105, - "column": 63 + "line": 132, + "column": 41 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": "const", + "keyword": "const", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -52526,16 +56846,17 @@ "binop": null, "updateContext": null }, - "start": 3889, - "end": 3890, + "value": "const", + "start": 4644, + "end": 4649, "loc": { "start": { - "line": 105, - "column": 63 + "line": 133, + "column": 4 }, "end": { - "line": 105, - "column": 64 + "line": 133, + "column": 9 } } }, @@ -52551,49 +56872,50 @@ "postfix": false, "binop": null }, - "value": "title", - "start": 3899, - "end": 3904, + "value": "codes", + "start": 4650, + "end": 4655, "loc": { "start": { - "line": 106, - "column": 8 + "line": 133, + "column": 10 }, "end": { - "line": 106, - "column": 13 + "line": 133, + "column": 15 } } }, { "type": { - "label": ":", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 3904, - "end": 3905, + "value": "=", + "start": 4656, + "end": 4657, "loc": { "start": { - "line": 106, - "column": 13 + "line": 133, + "column": 16 }, "end": { - "line": 106, - "column": 14 + "line": 133, + "column": 17 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -52601,27 +56923,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "International Code of Nomenclature for algae, fungi, and plants", - "start": 3906, - "end": 3971, + "value": "TaxonNameWrapper", + "start": 4658, + "end": 4674, "loc": { "start": { - "line": 106, - "column": 15 + "line": 133, + "column": 18 }, "end": { - "line": 106, - "column": 80 + "line": 133, + "column": 34 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -52631,24 +56952,24 @@ "binop": null, "updateContext": null }, - "start": 3971, - "end": 3972, + "start": 4674, + "end": 4675, "loc": { "start": { - "line": 106, - "column": 80 + "line": 133, + "column": 34 }, "end": { - "line": 106, - "column": 81 + "line": 133, + "column": 35 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -52656,48 +56977,23 @@ "postfix": false, "binop": null }, - "start": 3979, - "end": 3980, - "loc": { - "start": { - "line": 107, - "column": 6 - }, - "end": { - "line": 107, - "column": 7 - } - } - }, - { - "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 3980, - "end": 3981, + "value": "getNomenclaturalCodes", + "start": 4675, + "end": 4696, "loc": { "start": { - "line": 107, - "column": 7 + "line": 133, + "column": 35 }, "end": { - "line": 107, - "column": 8 + "line": 133, + "column": 56 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -52707,24 +57003,24 @@ "postfix": false, "binop": null }, - "start": 3988, - "end": 3989, + "start": 4696, + "end": 4697, "loc": { "start": { - "line": 108, - "column": 6 + "line": 133, + "column": 56 }, - "end": { - "line": 108, - "column": 7 + "end": { + "line": 133, + "column": 57 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -52732,23 +57028,22 @@ "postfix": false, "binop": null }, - "value": "iri", - "start": 3998, - "end": 4001, + "start": 4697, + "end": 4698, "loc": { "start": { - "line": 109, - "column": 8 + "line": 133, + "column": 57 }, "end": { - "line": 109, - "column": 11 + "line": 133, + "column": 58 } } }, { "type": { - "label": ":", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -52759,120 +57054,101 @@ "binop": null, "updateContext": null }, - "start": 4001, - "end": 4002, + "start": 4698, + "end": 4699, "loc": { "start": { - "line": 109, - "column": 11 + "line": 133, + "column": 58 }, "end": { - "line": 109, - "column": 12 + "line": 133, + "column": 59 } } }, { - "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "value": "owlterms", - "start": 4003, - "end": 4011, + "type": "CommentLine", + "value": " If the nomenCode provided is owlterms.UNKNOWN_CODE,", + "start": 4705, + "end": 4759, "loc": { "start": { - "line": 109, - "column": 13 + "line": 135, + "column": 4 }, "end": { - "line": 109, - "column": 21 + "line": 135, + "column": 58 } } }, { - "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 4011, - "end": 4012, + "type": "CommentLine", + "value": " return that entry.", + "start": 4764, + "end": 4785, "loc": { "start": { - "line": 109, - "column": 21 + "line": 136, + "column": 4 }, "end": { - "line": 109, - "column": 22 + "line": 136, + "column": 25 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "ICNP_CODE", - "start": 4012, - "end": 4021, + "value": "if", + "start": 4790, + "end": 4792, "loc": { "start": { - "line": 109, - "column": 22 + "line": 137, + "column": 4 }, "end": { - "line": 109, - "column": 31 + "line": 137, + "column": 6 } } }, { "type": { - "label": ",", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4021, - "end": 4022, + "start": 4793, + "end": 4794, "loc": { "start": { - "line": 109, - "column": 31 + "line": 137, + "column": 7 }, "end": { - "line": 109, - "column": 32 + "line": 137, + "column": 8 } } }, @@ -52888,23 +57164,23 @@ "postfix": false, "binop": null }, - "value": "shortName", - "start": 4031, - "end": 4040, + "value": "nomenCode", + "start": 4794, + "end": 4803, "loc": { "start": { - "line": 110, + "line": 137, "column": 8 }, "end": { - "line": 110, + "line": 137, "column": 17 } } }, { "type": { - "label": ":", + "label": "==/!=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -52912,25 +57188,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 6, "updateContext": null }, - "start": 4040, - "end": 4041, + "value": "===", + "start": 4804, + "end": 4807, "loc": { "start": { - "line": 110, - "column": 17 + "line": 137, + "column": 18 }, "end": { - "line": 110, - "column": 18 + "line": 137, + "column": 21 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -52938,27 +57215,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "ICNP", - "start": 4042, - "end": 4048, + "value": "owlterms", + "start": 4808, + "end": 4816, "loc": { "start": { - "line": 110, - "column": 19 + "line": 137, + "column": 22 }, "end": { - "line": 110, - "column": 25 + "line": 137, + "column": 30 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -52968,16 +57244,16 @@ "binop": null, "updateContext": null }, - "start": 4048, - "end": 4049, + "start": 4816, + "end": 4817, "loc": { "start": { - "line": 110, - "column": 25 + "line": 137, + "column": 30 }, "end": { - "line": 110, - "column": 26 + "line": 137, + "column": 31 } } }, @@ -52993,76 +57269,74 @@ "postfix": false, "binop": null }, - "value": "label", - "start": 4058, - "end": 4063, + "value": "UNKNOWN_CODE", + "start": 4817, + "end": 4829, "loc": { "start": { - "line": 111, - "column": 8 + "line": 137, + "column": 31 }, "end": { - "line": 111, - "column": 13 + "line": 137, + "column": 43 } } }, { "type": { - "label": ":", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4063, - "end": 4064, + "start": 4829, + "end": 4830, "loc": { "start": { - "line": 111, - "column": 13 + "line": 137, + "column": 43 }, "end": { - "line": 111, - "column": 14 + "line": 137, + "column": 44 } } }, { "type": { - "label": "string", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "Prokaryotes (ICNP)", - "start": 4065, - "end": 4085, + "start": 4831, + "end": 4832, "loc": { "start": { - "line": 111, - "column": 15 + "line": 137, + "column": 45 }, "end": { - "line": 111, - "column": 35 + "line": 137, + "column": 46 } } }, { "type": { - "label": ",", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -53073,16 +57347,17 @@ "binop": null, "updateContext": null }, - "start": 4085, - "end": 4086, + "value": "return", + "start": 4839, + "end": 4845, "loc": { "start": { - "line": 111, - "column": 35 + "line": 138, + "column": 6 }, "end": { - "line": 111, - "column": 36 + "line": 138, + "column": 12 } } }, @@ -53098,25 +57373,25 @@ "postfix": false, "binop": null }, - "value": "title", - "start": 4095, - "end": 4100, + "value": "codes", + "start": 4846, + "end": 4851, "loc": { "start": { - "line": 112, - "column": 8 + "line": 138, + "column": 13 }, "end": { - "line": 112, - "column": 13 + "line": 138, + "column": 18 } } }, { "type": { - "label": ":", + "label": "[", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -53125,22 +57400,22 @@ "binop": null, "updateContext": null }, - "start": 4100, - "end": 4101, + "start": 4851, + "end": 4852, "loc": { "start": { - "line": 112, - "column": 13 + "line": 138, + "column": 18 }, "end": { - "line": 112, - "column": 14 + "line": 138, + "column": 19 } } }, { "type": { - "label": "string", + "label": "num", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -53151,24 +57426,24 @@ "binop": null, "updateContext": null }, - "value": "International Code of Nomenclature of Prokaryotes", - "start": 4102, - "end": 4153, + "value": 0, + "start": 4852, + "end": 4853, "loc": { "start": { - "line": 112, - "column": 15 + "line": 138, + "column": 19 }, "end": { - "line": 112, - "column": 66 + "line": 138, + "column": 20 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": "]", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -53178,92 +57453,111 @@ "binop": null, "updateContext": null }, - "start": 4153, - "end": 4154, + "start": 4853, + "end": 4854, "loc": { "start": { - "line": 112, - "column": 66 + "line": 138, + "column": 20 }, "end": { - "line": 112, - "column": 67 + "line": 138, + "column": 21 } } }, { "type": { - "label": "}", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4161, - "end": 4162, + "start": 4854, + "end": 4855, "loc": { "start": { - "line": 113, - "column": 6 + "line": 138, + "column": 21 }, "end": { - "line": 113, - "column": 7 + "line": 138, + "column": 22 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4162, - "end": 4163, + "start": 4860, + "end": 4861, "loc": { "start": { - "line": 113, - "column": 7 + "line": 139, + "column": 4 }, "end": { - "line": 113, - "column": 8 + "line": 139, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Look for the entry with the same IRI as the provided IRI.", + "start": 4867, + "end": 4927, + "loc": { + "start": { + "line": 141, + "column": 4 + }, + "end": { + "line": 141, + "column": 64 } } }, { "type": { - "label": "{", - "beforeExpr": true, - "startsExpr": true, + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4170, - "end": 4171, + "value": "const", + "start": 4932, + "end": 4937, "loc": { "start": { - "line": 114, - "column": 6 + "line": 142, + "column": 4 }, "end": { - "line": 114, - "column": 7 + "line": 142, + "column": 9 } } }, @@ -53279,43 +57573,44 @@ "postfix": false, "binop": null }, - "value": "iri", - "start": 4180, - "end": 4183, + "value": "matchingCode", + "start": 4938, + "end": 4950, "loc": { "start": { - "line": 115, - "column": 8 + "line": 142, + "column": 10 }, "end": { - "line": 115, - "column": 11 + "line": 142, + "column": 22 } } }, { "type": { - "label": ":", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 4183, - "end": 4184, + "value": "=", + "start": 4951, + "end": 4952, "loc": { "start": { - "line": 115, - "column": 11 + "line": 142, + "column": 23 }, "end": { - "line": 115, - "column": 12 + "line": 142, + "column": 24 } } }, @@ -53331,17 +57626,17 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 4185, - "end": 4193, + "value": "codes", + "start": 4953, + "end": 4958, "loc": { "start": { - "line": 115, - "column": 13 + "line": 142, + "column": 25 }, "end": { - "line": 115, - "column": 21 + "line": 142, + "column": 30 } } }, @@ -53358,16 +57653,16 @@ "binop": null, "updateContext": null }, - "start": 4193, - "end": 4194, + "start": 4965, + "end": 4966, "loc": { "start": { - "line": 115, - "column": 21 + "line": 143, + "column": 6 }, "end": { - "line": 115, - "column": 22 + "line": 143, + "column": 7 } } }, @@ -53383,43 +57678,42 @@ "postfix": false, "binop": null }, - "value": "ICTV_CODE", - "start": 4194, - "end": 4203, + "value": "find", + "start": 4966, + "end": 4970, "loc": { "start": { - "line": 115, - "column": 22 + "line": 143, + "column": 7 }, "end": { - "line": 115, - "column": 31 + "line": 143, + "column": 11 } } }, { "type": { - "label": ",", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4203, - "end": 4204, + "start": 4970, + "end": 4971, "loc": { "start": { - "line": 115, - "column": 31 + "line": 143, + "column": 11 }, "end": { - "line": 115, - "column": 32 + "line": 143, + "column": 12 } } }, @@ -53433,51 +57727,76 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null + }, + "value": "code", + "start": 4971, + "end": 4975, + "loc": { + "start": { + "line": 143, + "column": 12 + }, + "end": { + "line": 143, + "column": 16 + } + } + }, + { + "type": { + "label": "=>", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null }, - "value": "shortName", - "start": 4213, - "end": 4222, + "start": 4976, + "end": 4978, "loc": { "start": { - "line": 116, - "column": 8 + "line": 143, + "column": 17 }, "end": { - "line": 116, - "column": 17 + "line": 143, + "column": 19 } } }, { "type": { - "label": ":", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4222, - "end": 4223, + "start": 4979, + "end": 4980, "loc": { "start": { - "line": 116, - "column": 17 + "line": 143, + "column": 20 }, "end": { - "line": 116, - "column": 18 + "line": 143, + "column": 21 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -53485,27 +57804,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "ICTV", - "start": 4224, - "end": 4230, + "value": "code", + "start": 4980, + "end": 4984, "loc": { "start": { - "line": 116, - "column": 19 + "line": 143, + "column": 21 }, "end": { - "line": 116, + "line": 143, "column": 25 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -53515,15 +57833,15 @@ "binop": null, "updateContext": null }, - "start": 4230, - "end": 4231, + "start": 4984, + "end": 4985, "loc": { "start": { - "line": 116, + "line": 143, "column": 25 }, "end": { - "line": 116, + "line": 143, "column": 26 } } @@ -53540,23 +57858,23 @@ "postfix": false, "binop": null }, - "value": "label", - "start": 4240, - "end": 4245, + "value": "iri", + "start": 4985, + "end": 4988, "loc": { "start": { - "line": 117, - "column": 8 + "line": 143, + "column": 26 }, "end": { - "line": 117, - "column": 13 + "line": 143, + "column": 29 } } }, { "type": { - "label": ":", + "label": "||", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -53564,19 +57882,20 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 1, "updateContext": null }, - "start": 4245, - "end": 4246, + "value": "||", + "start": 4989, + "end": 4991, "loc": { "start": { - "line": 117, - "column": 13 + "line": 143, + "column": 30 }, "end": { - "line": 117, - "column": 14 + "line": 143, + "column": 32 } } }, @@ -53593,24 +57912,49 @@ "binop": null, "updateContext": null }, - "value": "Viruses (ICTV)", - "start": 4247, - "end": 4263, + "value": "", + "start": 4992, + "end": 4994, "loc": { "start": { - "line": 117, - "column": 15 + "line": 143, + "column": 33 }, "end": { - "line": 117, - "column": 31 + "line": 143, + "column": 35 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 4994, + "end": 4995, + "loc": { + "start": { + "line": 143, + "column": 35 + }, + "end": { + "line": 143, + "column": 36 + } + } + }, + { + "type": { + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -53620,16 +57964,16 @@ "binop": null, "updateContext": null }, - "start": 4263, - "end": 4264, + "start": 4995, + "end": 4996, "loc": { "start": { - "line": 117, - "column": 31 + "line": 143, + "column": 36 }, "end": { - "line": 117, - "column": 32 + "line": 143, + "column": 37 } } }, @@ -53645,76 +57989,73 @@ "postfix": false, "binop": null }, - "value": "title", - "start": 4273, - "end": 4278, + "value": "toLowerCase", + "start": 4996, + "end": 5007, "loc": { "start": { - "line": 118, - "column": 8 + "line": 143, + "column": 37 }, "end": { - "line": 118, - "column": 13 + "line": 143, + "column": 48 } } }, { "type": { - "label": ":", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4278, - "end": 4279, + "start": 5007, + "end": 5008, "loc": { "start": { - "line": 118, - "column": 13 + "line": 143, + "column": 48 }, "end": { - "line": 118, - "column": 14 + "line": 143, + "column": 49 } } }, { "type": { - "label": "string", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "International Committee on Taxonomy of Viruses", - "start": 4280, - "end": 4328, + "start": 5008, + "end": 5009, "loc": { "start": { - "line": 118, - "column": 15 + "line": 143, + "column": 49 }, "end": { - "line": 118, - "column": 63 + "line": 143, + "column": 50 } } }, { "type": { - "label": ",", + "label": "==/!=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -53722,27 +58063,28 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 6, "updateContext": null }, - "start": 4328, - "end": 4329, + "value": "===", + "start": 5010, + "end": 5013, "loc": { "start": { - "line": 118, - "column": 63 + "line": 143, + "column": 51 }, "end": { - "line": 118, - "column": 64 + "line": 143, + "column": 54 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -53750,23 +58092,24 @@ "postfix": false, "binop": null }, - "start": 4336, - "end": 4337, + "value": "nomenCode", + "start": 5014, + "end": 5023, "loc": { "start": { - "line": 119, - "column": 6 + "line": 143, + "column": 55 }, "end": { - "line": 119, - "column": 7 + "line": 143, + "column": 64 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -53776,23 +58119,23 @@ "binop": null, "updateContext": null }, - "start": 4337, - "end": 4338, + "start": 5023, + "end": 5024, "loc": { "start": { - "line": 119, - "column": 7 + "line": 143, + "column": 64 }, "end": { - "line": 119, - "column": 8 + "line": 143, + "column": 65 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -53801,23 +58144,24 @@ "postfix": false, "binop": null }, - "start": 4345, - "end": 4346, + "value": "toLowerCase", + "start": 5024, + "end": 5035, "loc": { "start": { - "line": 120, - "column": 6 + "line": 143, + "column": 65 }, "end": { - "line": 120, - "column": 7 + "line": 143, + "column": 76 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -53826,51 +58170,49 @@ "postfix": false, "binop": null }, - "value": "iri", - "start": 4355, - "end": 4358, + "start": 5035, + "end": 5036, "loc": { "start": { - "line": 121, - "column": 8 + "line": 143, + "column": 76 }, "end": { - "line": 121, - "column": 11 + "line": 143, + "column": 77 } } }, { "type": { - "label": ":", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4358, - "end": 4359, + "start": 5036, + "end": 5037, "loc": { "start": { - "line": 121, - "column": 11 + "line": 143, + "column": 77 }, "end": { - "line": 121, - "column": 12 + "line": 143, + "column": 78 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -53878,24 +58220,23 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 4360, - "end": 4368, + "start": 5037, + "end": 5038, "loc": { "start": { - "line": 121, - "column": 13 + "line": 143, + "column": 78 }, "end": { - "line": 121, - "column": 21 + "line": 143, + "column": 79 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -53905,68 +58246,69 @@ "binop": null, "updateContext": null }, - "start": 4368, - "end": 4369, + "start": 5038, + "end": 5039, "loc": { "start": { - "line": 121, - "column": 21 + "line": 143, + "column": 79 }, "end": { - "line": 121, - "column": 22 + "line": 143, + "column": 80 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "ICNCP_CODE", - "start": 4369, - "end": 4379, + "value": "if", + "start": 5044, + "end": 5046, "loc": { "start": { - "line": 121, - "column": 22 + "line": 144, + "column": 4 }, "end": { - "line": 121, - "column": 32 + "line": 144, + "column": 6 } } }, { "type": { - "label": ",", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4379, - "end": 4380, + "start": 5047, + "end": 5048, "loc": { "start": { - "line": 121, - "column": 32 + "line": 144, + "column": 7 }, "end": { - "line": 121, - "column": 33 + "line": 144, + "column": 8 } } }, @@ -53982,51 +58324,51 @@ "postfix": false, "binop": null }, - "value": "shortName", - "start": 4389, - "end": 4398, + "value": "matchingCode", + "start": 5048, + "end": 5060, "loc": { "start": { - "line": 122, + "line": 144, "column": 8 }, "end": { - "line": 122, - "column": 17 + "line": 144, + "column": 20 } } }, { "type": { - "label": ":", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4398, - "end": 4399, + "start": 5060, + "end": 5061, "loc": { "start": { - "line": 122, - "column": 17 + "line": 144, + "column": 20 }, "end": { - "line": 122, - "column": 18 + "line": 144, + "column": 21 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": "return", + "keyword": "return", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -54035,75 +58377,76 @@ "binop": null, "updateContext": null }, - "value": "ICNCP", - "start": 4400, - "end": 4407, + "value": "return", + "start": 5062, + "end": 5068, "loc": { "start": { - "line": 122, - "column": 19 + "line": 144, + "column": 22 }, "end": { - "line": 122, - "column": 26 + "line": 144, + "column": 28 } } }, { "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4407, - "end": 4408, + "value": "matchingCode", + "start": 5069, + "end": 5081, "loc": { "start": { - "line": 122, - "column": 26 + "line": 144, + "column": 29 }, "end": { - "line": 122, - "column": 27 + "line": 144, + "column": 41 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "label", - "start": 4417, - "end": 4422, + "start": 5081, + "end": 5082, "loc": { "start": { - "line": 123, - "column": 8 + "line": 144, + "column": 41 }, "end": { - "line": 123, - "column": 13 + "line": 144, + "column": 42 } } }, { "type": { - "label": ":", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -54114,22 +58457,23 @@ "binop": null, "updateContext": null }, - "start": 4422, - "end": 4423, + "value": "return", + "start": 5087, + "end": 5093, "loc": { "start": { - "line": 123, - "column": 13 + "line": 145, + "column": 4 }, "end": { - "line": 123, - "column": 14 + "line": 145, + "column": 10 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -54137,26 +58481,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "Cultivated plants (ICNCP)", - "start": 4424, - "end": 4451, + "value": "undefined", + "start": 5094, + "end": 5103, "loc": { "start": { - "line": 123, - "column": 15 + "line": 145, + "column": 11 }, "end": { - "line": 123, - "column": 42 + "line": 145, + "column": 20 } } }, { "type": { - "label": ",", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -54167,24 +58510,24 @@ "binop": null, "updateContext": null }, - "start": 4451, - "end": 4452, + "start": 5103, + "end": 5104, "loc": { "start": { - "line": 123, - "column": 42 + "line": 145, + "column": 20 }, "end": { - "line": 123, - "column": 43 + "line": 145, + "column": 21 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -54192,49 +58535,64 @@ "postfix": false, "binop": null }, - "value": "title", - "start": 4461, - "end": 4466, + "start": 5107, + "end": 5108, "loc": { "start": { - "line": 124, - "column": 8 + "line": 146, + "column": 2 }, "end": { - "line": 124, - "column": 13 + "line": 146, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Normalize the specified taxon name.\n * @param txname A taxon name to be normalized.\n ", + "start": 5112, + "end": 5212, + "loc": { + "start": { + "line": 148, + "column": 2 + }, + "end": { + "line": 151, + "column": 5 } } }, { "type": { - "label": ":", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4466, - "end": 4467, + "value": "static", + "start": 5215, + "end": 5221, "loc": { "start": { - "line": 124, - "column": 13 + "line": 152, + "column": 2 }, "end": { - "line": 124, - "column": 14 + "line": 152, + "column": 8 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -54242,54 +58600,52 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "International Code of Cultivated Plants", - "start": 4468, - "end": 4509, + "value": "normalize", + "start": 5222, + "end": 5231, "loc": { "start": { - "line": 124, - "column": 15 + "line": 152, + "column": 9 }, "end": { - "line": 124, - "column": 56 + "line": 152, + "column": 18 } } }, { "type": { - "label": ",", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4509, - "end": 4510, + "start": 5231, + "end": 5232, "loc": { "start": { - "line": 124, - "column": 56 + "line": 152, + "column": 18 }, "end": { - "line": 124, - "column": 57 + "line": 152, + "column": 19 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -54297,75 +58653,75 @@ "postfix": false, "binop": null }, - "start": 4517, - "end": 4518, + "value": "txname", + "start": 5232, + "end": 5238, "loc": { "start": { - "line": 125, - "column": 6 + "line": 152, + "column": 19 }, "end": { - "line": 125, - "column": 7 + "line": 152, + "column": 25 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4518, - "end": 4519, + "start": 5238, + "end": 5239, "loc": { "start": { - "line": 125, - "column": 7 + "line": 152, + "column": 25 }, "end": { - "line": 125, - "column": 8 + "line": 152, + "column": 26 } } }, { "type": { - "label": "]", - "beforeExpr": false, - "startsExpr": false, + "label": "{", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4524, - "end": 4525, + "start": 5240, + "end": 5241, "loc": { "start": { - "line": 126, - "column": 4 + "line": 152, + "column": 27 }, "end": { - "line": 126, - "column": 5 + "line": 152, + "column": 28 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": "const", + "keyword": "const", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -54375,24 +58731,25 @@ "binop": null, "updateContext": null }, - "start": 4525, - "end": 4526, + "value": "const", + "start": 5246, + "end": 5251, "loc": { "start": { - "line": 126, - "column": 5 + "line": 153, + "column": 4 }, "end": { - "line": 126, - "column": 6 + "line": 153, + "column": 9 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -54400,58 +58757,72 @@ "postfix": false, "binop": null }, - "start": 4529, - "end": 4530, + "value": "wrapped", + "start": 5252, + "end": 5259, "loc": { "start": { - "line": 127, - "column": 2 + "line": 153, + "column": 10 }, "end": { - "line": 127, - "column": 3 + "line": 153, + "column": 17 } } }, { - "type": "CommentBlock", - "value": "*\n * Returns the nomenclatural code entry for a code.\n ", - "start": 4534, - "end": 4597, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 5260, + "end": 5261, "loc": { "start": { - "line": 129, - "column": 2 + "line": 153, + "column": 18 }, "end": { - "line": 131, - "column": 5 + "line": 153, + "column": 19 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "new", + "keyword": "new", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 4600, - "end": 4606, + "value": "new", + "start": 5262, + "end": 5265, "loc": { "start": { - "line": 132, - "column": 2 + "line": 153, + "column": 20 }, "end": { - "line": 132, - "column": 8 + "line": 153, + "column": 23 } } }, @@ -54467,17 +58838,17 @@ "postfix": false, "binop": null }, - "value": "getNomenCodeDetails", - "start": 4607, - "end": 4626, + "value": "TaxonNameWrapper", + "start": 5266, + "end": 5282, "loc": { "start": { - "line": 132, - "column": 9 + "line": 153, + "column": 24 }, "end": { - "line": 132, - "column": 28 + "line": 153, + "column": 40 } } }, @@ -54493,16 +58864,16 @@ "postfix": false, "binop": null }, - "start": 4626, - "end": 4627, + "start": 5282, + "end": 5283, "loc": { "start": { - "line": 132, - "column": 28 + "line": 153, + "column": 40 }, "end": { - "line": 132, - "column": 29 + "line": 153, + "column": 41 } } }, @@ -54518,17 +58889,17 @@ "postfix": false, "binop": null }, - "value": "nomenCode", - "start": 4627, - "end": 4636, + "value": "txname", + "start": 5283, + "end": 5289, "loc": { "start": { - "line": 132, - "column": 29 + "line": 153, + "column": 41 }, "end": { - "line": 132, - "column": 38 + "line": 153, + "column": 47 } } }, @@ -54544,41 +58915,42 @@ "postfix": false, "binop": null }, - "start": 4636, - "end": 4637, + "start": 5289, + "end": 5290, "loc": { "start": { - "line": 132, - "column": 38 + "line": 153, + "column": 47 }, "end": { - "line": 132, - "column": 39 + "line": 153, + "column": 48 } } }, { "type": { - "label": "{", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4638, - "end": 4639, + "start": 5290, + "end": 5291, "loc": { "start": { - "line": 132, - "column": 40 + "line": 153, + "column": 48 }, "end": { - "line": 132, - "column": 41 + "line": 153, + "column": 49 } } }, @@ -54597,15 +58969,15 @@ "updateContext": null }, "value": "const", - "start": 4644, - "end": 4649, + "start": 5296, + "end": 5301, "loc": { "start": { - "line": 133, + "line": 154, "column": 4 }, "end": { - "line": 133, + "line": 154, "column": 9 } } @@ -54622,17 +58994,17 @@ "postfix": false, "binop": null }, - "value": "codes", - "start": 4650, - "end": 4655, + "value": "normalizedTxname", + "start": 5302, + "end": 5318, "loc": { "start": { - "line": 133, + "line": 154, "column": 10 }, "end": { - "line": 133, - "column": 15 + "line": 154, + "column": 26 } } }, @@ -54650,23 +59022,23 @@ "updateContext": null }, "value": "=", - "start": 4656, - "end": 4657, + "start": 5319, + "end": 5320, "loc": { "start": { - "line": 133, - "column": 16 + "line": 154, + "column": 27 }, "end": { - "line": 133, - "column": 17 + "line": 154, + "column": 28 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -54675,24 +59047,50 @@ "postfix": false, "binop": null }, - "value": "TaxonNameWrapper", - "start": 4658, - "end": 4674, + "start": 5321, + "end": 5322, "loc": { "start": { - "line": 133, - "column": 18 + "line": 154, + "column": 29 }, "end": { - "line": 133, - "column": 34 + "line": 154, + "column": 30 } } }, { "type": { - "label": ".", + "label": "string", "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "@type", + "start": 5329, + "end": 5336, + "loc": { + "start": { + "line": 155, + "column": 6 + }, + "end": { + "line": 155, + "column": 13 + } + } + }, + { + "type": { + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -54702,16 +59100,16 @@ "binop": null, "updateContext": null }, - "start": 4674, - "end": 4675, + "start": 5336, + "end": 5337, "loc": { "start": { - "line": 133, - "column": 34 + "line": 155, + "column": 13 }, "end": { - "line": 133, - "column": 35 + "line": 155, + "column": 14 } } }, @@ -54727,50 +59125,51 @@ "postfix": false, "binop": null }, - "value": "getNomenclaturalCodes", - "start": 4675, - "end": 4696, + "value": "TaxonNameWrapper", + "start": 5338, + "end": 5354, "loc": { "start": { - "line": 133, - "column": 35 + "line": 155, + "column": 15 }, "end": { - "line": 133, - "column": 56 + "line": 155, + "column": 31 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": ".", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4696, - "end": 4697, + "start": 5354, + "end": 5355, "loc": { "start": { - "line": 133, - "column": 56 + "line": 155, + "column": 31 }, "end": { - "line": 133, - "column": 57 + "line": 155, + "column": 32 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -54778,22 +59177,23 @@ "postfix": false, "binop": null }, - "start": 4697, - "end": 4698, + "value": "TYPE_TAXON_NAME", + "start": 5355, + "end": 5370, "loc": { "start": { - "line": 133, - "column": 57 + "line": 155, + "column": 32 }, "end": { - "line": 133, - "column": 58 + "line": 155, + "column": 47 } } }, { "type": { - "label": ";", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -54804,101 +59204,120 @@ "binop": null, "updateContext": null }, - "start": 4698, - "end": 4699, + "start": 5370, + "end": 5371, "loc": { "start": { - "line": 133, - "column": 58 + "line": 155, + "column": 47 }, "end": { - "line": 133, - "column": 59 + "line": 155, + "column": 48 } } }, { - "type": "CommentLine", - "value": " If the nomenCode provided is owlterms.UNKNOWN_CODE,", - "start": 4705, - "end": 4759, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "nomenclaturalCode", + "start": 5378, + "end": 5395, "loc": { "start": { - "line": 135, - "column": 4 + "line": 156, + "column": 6 }, "end": { - "line": 135, - "column": 58 + "line": 156, + "column": 23 } } }, { - "type": "CommentLine", - "value": " return that entry.", - "start": 4764, - "end": 4785, + "type": { + "label": ":", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 5395, + "end": 5396, "loc": { "start": { - "line": 136, - "column": 4 + "line": 156, + "column": 23 }, "end": { - "line": 136, - "column": 25 + "line": 156, + "column": 24 } } }, { "type": { - "label": "if", - "keyword": "if", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "if", - "start": 4790, - "end": 4792, + "value": "wrapped", + "start": 5397, + "end": 5404, "loc": { "start": { - "line": 137, - "column": 4 + "line": 156, + "column": 25 }, "end": { - "line": 137, - "column": 6 + "line": 156, + "column": 32 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": ".", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4793, - "end": 4794, + "start": 5404, + "end": 5405, "loc": { "start": { - "line": 137, - "column": 7 + "line": 156, + "column": 32 }, "end": { - "line": 137, - "column": 8 + "line": 156, + "column": 33 } } }, @@ -54914,23 +59333,23 @@ "postfix": false, "binop": null }, - "value": "nomenCode", - "start": 4794, - "end": 4803, + "value": "nomenclaturalCode", + "start": 5405, + "end": 5422, "loc": { "start": { - "line": 137, - "column": 8 + "line": 156, + "column": 33 }, "end": { - "line": 137, - "column": 17 + "line": 156, + "column": 50 } } }, { "type": { - "label": "==/!=", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -54938,20 +59357,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": 6, + "binop": null, "updateContext": null }, - "value": "===", - "start": 4804, - "end": 4807, + "start": 5422, + "end": 5423, "loc": { "start": { - "line": 137, - "column": 18 + "line": 156, + "column": 50 }, "end": { - "line": 137, - "column": 21 + "line": 156, + "column": 51 } } }, @@ -54967,24 +59385,24 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 4808, - "end": 4816, + "value": "label", + "start": 5430, + "end": 5435, "loc": { "start": { - "line": 137, - "column": 22 + "line": 157, + "column": 6 }, "end": { - "line": 137, - "column": 30 + "line": 157, + "column": 11 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -54994,16 +59412,16 @@ "binop": null, "updateContext": null }, - "start": 4816, - "end": 4817, + "start": 5435, + "end": 5436, "loc": { "start": { - "line": 137, - "column": 30 + "line": 157, + "column": 11 }, "end": { - "line": 137, - "column": 31 + "line": 157, + "column": 12 } } }, @@ -55019,23 +59437,23 @@ "postfix": false, "binop": null }, - "value": "UNKNOWN_CODE", - "start": 4817, - "end": 4829, + "value": "wrapped", + "start": 5437, + "end": 5444, "loc": { "start": { - "line": 137, - "column": 31 + "line": 157, + "column": 13 }, "end": { - "line": 137, - "column": 43 + "line": 157, + "column": 20 } } }, { "type": { - "label": ")", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -55043,25 +59461,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4829, - "end": 4830, + "start": 5444, + "end": 5445, "loc": { "start": { - "line": 137, - "column": 43 + "line": 157, + "column": 20 }, "end": { - "line": 137, - "column": 44 + "line": 157, + "column": 21 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -55070,23 +59489,23 @@ "postfix": false, "binop": null }, - "start": 4831, - "end": 4832, + "value": "label", + "start": 5445, + "end": 5450, "loc": { "start": { - "line": 137, - "column": 45 + "line": 157, + "column": 21 }, "end": { - "line": 137, - "column": 46 + "line": 157, + "column": 26 } } }, { "type": { - "label": "return", - "keyword": "return", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -55097,17 +59516,16 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 4839, - "end": 4845, + "start": 5450, + "end": 5451, "loc": { "start": { - "line": 138, - "column": 6 + "line": 157, + "column": 26 }, "end": { - "line": 138, - "column": 12 + "line": 157, + "column": 27 } } }, @@ -55123,25 +59541,25 @@ "postfix": false, "binop": null }, - "value": "codes", - "start": 4846, - "end": 4851, + "value": "nameComplete", + "start": 5458, + "end": 5470, "loc": { "start": { - "line": 138, - "column": 13 + "line": 158, + "column": 6 }, "end": { - "line": 138, + "line": 158, "column": 18 } } }, { "type": { - "label": "[", + "label": ":", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55150,22 +59568,22 @@ "binop": null, "updateContext": null }, - "start": 4851, - "end": 4852, + "start": 5470, + "end": 5471, "loc": { "start": { - "line": 138, + "line": 158, "column": 18 }, "end": { - "line": 138, + "line": 158, "column": 19 } } }, { "type": { - "label": "num", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -55173,26 +59591,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": 0, - "start": 4852, - "end": 4853, + "value": "wrapped", + "start": 5472, + "end": 5479, "loc": { "start": { - "line": 138, - "column": 19 + "line": 158, + "column": 20 }, "end": { - "line": 138, - "column": 20 + "line": 158, + "column": 27 } } }, { "type": { - "label": "]", + "label": ".", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -55203,91 +59620,101 @@ "binop": null, "updateContext": null }, - "start": 4853, - "end": 4854, + "start": 5479, + "end": 5480, "loc": { "start": { - "line": 138, - "column": 20 + "line": 158, + "column": 27 }, "end": { - "line": 138, - "column": 21 + "line": 158, + "column": 28 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4854, - "end": 4855, + "value": "nameComplete", + "start": 5480, + "end": 5492, "loc": { "start": { - "line": 138, - "column": 21 + "line": 158, + "column": 28 }, "end": { - "line": 138, - "column": 22 + "line": 158, + "column": 40 } } }, { "type": { - "label": "}", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4860, - "end": 4861, + "start": 5492, + "end": 5493, "loc": { "start": { - "line": 139, - "column": 4 + "line": 158, + "column": 40 }, "end": { - "line": 139, - "column": 5 + "line": 158, + "column": 41 } } }, { - "type": "CommentLine", - "value": " Look for the entry with the same IRI as the provided IRI.", - "start": 4867, - "end": 4927, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "genusPart", + "start": 5500, + "end": 5509, "loc": { "start": { - "line": 141, - "column": 4 + "line": 159, + "column": 6 }, "end": { - "line": 141, - "column": 64 + "line": 159, + "column": 15 } } }, { "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, + "label": ":", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -55297,17 +59724,16 @@ "binop": null, "updateContext": null }, - "value": "const", - "start": 4932, - "end": 4937, + "start": 5509, + "end": 5510, "loc": { "start": { - "line": 142, - "column": 4 + "line": 159, + "column": 15 }, "end": { - "line": 142, - "column": 9 + "line": 159, + "column": 16 } } }, @@ -55323,44 +59749,43 @@ "postfix": false, "binop": null }, - "value": "matchingCode", - "start": 4938, - "end": 4950, + "value": "wrapped", + "start": 5511, + "end": 5518, "loc": { "start": { - "line": 142, - "column": 10 + "line": 159, + "column": 17 }, "end": { - "line": 142, - "column": 22 + "line": 159, + "column": 24 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 4951, - "end": 4952, + "start": 5518, + "end": 5519, "loc": { "start": { - "line": 142, - "column": 23 + "line": 159, + "column": 24 }, "end": { - "line": 142, - "column": 24 + "line": 159, + "column": 25 } } }, @@ -55376,24 +59801,24 @@ "postfix": false, "binop": null }, - "value": "codes", - "start": 4953, - "end": 4958, + "value": "genusPart", + "start": 5519, + "end": 5528, "loc": { "start": { - "line": 142, + "line": 159, "column": 25 }, "end": { - "line": 142, - "column": 30 + "line": 159, + "column": 34 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -55403,16 +59828,16 @@ "binop": null, "updateContext": null }, - "start": 4965, - "end": 4966, + "start": 5528, + "end": 5529, "loc": { "start": { - "line": 143, - "column": 6 + "line": 159, + "column": 34 }, "end": { - "line": 143, - "column": 7 + "line": 159, + "column": 35 } } }, @@ -55428,42 +59853,43 @@ "postfix": false, "binop": null }, - "value": "find", - "start": 4966, - "end": 4970, + "value": "specificEpithet", + "start": 5536, + "end": 5551, "loc": { "start": { - "line": 143, - "column": 7 + "line": 160, + "column": 6 }, "end": { - "line": 143, - "column": 11 + "line": 160, + "column": 21 } } }, { "type": { - "label": "(", + "label": ":", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 4970, - "end": 4971, + "start": 5551, + "end": 5552, "loc": { "start": { - "line": 143, - "column": 11 + "line": 160, + "column": 21 }, "end": { - "line": 143, - "column": 12 + "line": 160, + "column": 22 } } }, @@ -55479,24 +59905,24 @@ "postfix": false, "binop": null }, - "value": "code", - "start": 4971, - "end": 4975, + "value": "wrapped", + "start": 5553, + "end": 5560, "loc": { "start": { - "line": 143, - "column": 12 + "line": 160, + "column": 23 }, "end": { - "line": 143, - "column": 16 + "line": 160, + "column": 30 } } }, { "type": { - "label": "=>", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -55506,23 +59932,23 @@ "binop": null, "updateContext": null }, - "start": 4976, - "end": 4978, + "start": 5560, + "end": 5561, "loc": { "start": { - "line": 143, - "column": 17 + "line": 160, + "column": 30 }, "end": { - "line": 143, - "column": 19 + "line": 160, + "column": 31 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -55531,129 +59957,129 @@ "postfix": false, "binop": null }, - "start": 4979, - "end": 4980, + "value": "specificEpithet", + "start": 5561, + "end": 5576, "loc": { "start": { - "line": 143, - "column": 20 + "line": 160, + "column": 31 }, "end": { - "line": 143, - "column": 21 + "line": 160, + "column": 46 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ",", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "code", - "start": 4980, - "end": 4984, + "start": 5576, + "end": 5577, "loc": { "start": { - "line": 143, - "column": 21 + "line": 160, + "column": 46 }, "end": { - "line": 143, - "column": 25 + "line": 160, + "column": 47 } } }, { "type": { - "label": ".", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 4984, - "end": 4985, + "value": "infraspecificEpithet", + "start": 5584, + "end": 5604, "loc": { "start": { - "line": 143, - "column": 25 + "line": 161, + "column": 6 }, "end": { - "line": 143, + "line": 161, "column": 26 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ":", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "iri", - "start": 4985, - "end": 4988, + "start": 5604, + "end": 5605, "loc": { "start": { - "line": 143, + "line": 161, "column": 26 }, "end": { - "line": 143, - "column": 29 + "line": 161, + "column": 27 } } }, { "type": { - "label": "||", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 1, - "updateContext": null + "binop": null }, - "value": "||", - "start": 4989, - "end": 4991, + "value": "wrapped", + "start": 5606, + "end": 5613, "loc": { "start": { - "line": 143, - "column": 30 + "line": 161, + "column": 28 }, "end": { - "line": 143, - "column": 32 + "line": 161, + "column": 35 } } }, { "type": { - "label": "string", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55662,25 +60088,24 @@ "binop": null, "updateContext": null }, - "value": "", - "start": 4992, - "end": 4994, + "start": 5613, + "end": 5614, "loc": { "start": { - "line": 143, - "column": 33 + "line": 161, + "column": 35 }, "end": { - "line": 143, - "column": 35 + "line": 161, + "column": 36 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55688,23 +60113,24 @@ "postfix": false, "binop": null }, - "start": 4994, - "end": 4995, + "value": "infraspecificEpithet", + "start": 5614, + "end": 5634, "loc": { "start": { - "line": 143, - "column": 35 + "line": 161, + "column": 36 }, "end": { - "line": 143, - "column": 36 + "line": 161, + "column": 56 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -55714,24 +60140,24 @@ "binop": null, "updateContext": null }, - "start": 4995, - "end": 4996, + "start": 5634, + "end": 5635, "loc": { "start": { - "line": 143, - "column": 36 + "line": 161, + "column": 56 }, "end": { - "line": 143, - "column": 37 + "line": 161, + "column": 57 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55739,48 +60165,49 @@ "postfix": false, "binop": null }, - "value": "toLowerCase", - "start": 4996, - "end": 5007, + "start": 5640, + "end": 5641, "loc": { "start": { - "line": 143, - "column": 37 + "line": 162, + "column": 4 }, "end": { - "line": 143, - "column": 48 + "line": 162, + "column": 5 } } }, { "type": { - "label": "(", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 5007, - "end": 5008, + "start": 5641, + "end": 5642, "loc": { "start": { - "line": 143, - "column": 48 + "line": 162, + "column": 5 }, "end": { - "line": 143, - "column": 49 + "line": 162, + "column": 6 } } }, { "type": { - "label": ")", + "label": "if", + "keyword": "if", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -55788,51 +60215,51 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 5008, - "end": 5009, + "value": "if", + "start": 5647, + "end": 5649, "loc": { "start": { - "line": 143, - "column": 49 + "line": 163, + "column": 4 }, "end": { - "line": 143, - "column": 50 + "line": 163, + "column": 6 } } }, { "type": { - "label": "==/!=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 6, - "updateContext": null + "binop": null }, - "value": "===", - "start": 5010, - "end": 5013, + "start": 5650, + "end": 5651, "loc": { "start": { - "line": 143, - "column": 51 + "line": 163, + "column": 7 }, "end": { - "line": 143, - "column": 54 + "line": 163, + "column": 8 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -55840,45 +60267,48 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "nomenCode", - "start": 5014, - "end": 5023, + "value": "@id", + "start": 5651, + "end": 5656, "loc": { "start": { - "line": 143, - "column": 55 + "line": 163, + "column": 8 }, "end": { - "line": 143, - "column": 64 + "line": 163, + "column": 13 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": "in", + "keyword": "in", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, + "binop": 7, "updateContext": null }, - "start": 5023, - "end": 5024, + "value": "in", + "start": 5657, + "end": 5659, "loc": { "start": { - "line": 143, - "column": 64 + "line": 163, + "column": 14 }, "end": { - "line": 143, - "column": 65 + "line": 163, + "column": 16 } } }, @@ -55894,25 +60324,25 @@ "postfix": false, "binop": null }, - "value": "toLowerCase", - "start": 5024, - "end": 5035, + "value": "txname", + "start": 5660, + "end": 5666, "loc": { "start": { - "line": 143, - "column": 65 + "line": 163, + "column": 17 }, "end": { - "line": 143, - "column": 76 + "line": 163, + "column": 23 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": ")", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55920,24 +60350,24 @@ "postfix": false, "binop": null }, - "start": 5035, - "end": 5036, + "start": 5666, + "end": 5667, "loc": { "start": { - "line": 143, - "column": 76 + "line": 163, + "column": 23 }, "end": { - "line": 143, - "column": 77 + "line": 163, + "column": 24 } } }, { "type": { - "label": ")", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55945,49 +60375,51 @@ "postfix": false, "binop": null }, - "start": 5036, - "end": 5037, + "value": "normalizedTxname", + "start": 5668, + "end": 5684, "loc": { "start": { - "line": 143, - "column": 77 + "line": 163, + "column": 25 }, "end": { - "line": 143, - "column": 78 + "line": 163, + "column": 41 } } }, { "type": { - "label": ")", - "beforeExpr": false, - "startsExpr": false, + "label": "[", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 5037, - "end": 5038, + "start": 5684, + "end": 5685, "loc": { "start": { - "line": 143, - "column": 78 + "line": 163, + "column": 41 }, "end": { - "line": 143, - "column": 79 + "line": 163, + "column": 42 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "string", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -55996,23 +60428,23 @@ "binop": null, "updateContext": null }, - "start": 5038, - "end": 5039, + "value": "@id", + "start": 5685, + "end": 5690, "loc": { "start": { - "line": 143, - "column": 79 + "line": 163, + "column": 42 }, "end": { - "line": 143, - "column": 80 + "line": 163, + "column": 47 } } }, { "type": { - "label": "if", - "keyword": "if", + "label": "]", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -56023,42 +60455,43 @@ "binop": null, "updateContext": null }, - "value": "if", - "start": 5044, - "end": 5046, + "start": 5690, + "end": 5691, "loc": { "start": { - "line": 144, - "column": 4 + "line": 163, + "column": 47 }, "end": { - "line": 144, - "column": 6 + "line": 163, + "column": 48 } } }, { "type": { - "label": "(", + "label": "=", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 5047, - "end": 5048, + "value": "=", + "start": 5692, + "end": 5693, "loc": { "start": { - "line": 144, - "column": 7 + "line": 163, + "column": 49 }, "end": { - "line": 144, - "column": 8 + "line": 163, + "column": 50 } } }, @@ -56074,51 +60507,51 @@ "postfix": false, "binop": null }, - "value": "matchingCode", - "start": 5048, - "end": 5060, + "value": "txname", + "start": 5694, + "end": 5700, "loc": { "start": { - "line": 144, - "column": 8 + "line": 163, + "column": 51 }, "end": { - "line": 144, - "column": 20 + "line": 163, + "column": 57 } } }, { "type": { - "label": ")", - "beforeExpr": false, - "startsExpr": false, + "label": "[", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 5060, - "end": 5061, + "start": 5700, + "end": 5701, "loc": { "start": { - "line": 144, - "column": 20 + "line": 163, + "column": 57 }, "end": { - "line": 144, - "column": 21 + "line": 163, + "column": 58 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, - "startsExpr": false, + "label": "string", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -56127,43 +60560,43 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 5062, - "end": 5068, + "value": "@id", + "start": 5701, + "end": 5706, "loc": { "start": { - "line": 144, - "column": 22 + "line": 163, + "column": 58 }, "end": { - "line": 144, - "column": 28 + "line": 163, + "column": 63 } } }, { "type": { - "label": "name", + "label": "]", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "matchingCode", - "start": 5069, - "end": 5081, + "start": 5706, + "end": 5707, "loc": { "start": { - "line": 144, - "column": 29 + "line": 163, + "column": 63 }, "end": { - "line": 144, - "column": 41 + "line": 163, + "column": 64 } } }, @@ -56180,16 +60613,16 @@ "binop": null, "updateContext": null }, - "start": 5081, - "end": 5082, + "start": 5707, + "end": 5708, "loc": { "start": { - "line": 144, - "column": 41 + "line": 163, + "column": 64 }, "end": { - "line": 144, - "column": 42 + "line": 163, + "column": 65 } } }, @@ -56208,15 +60641,15 @@ "updateContext": null }, "value": "return", - "start": 5087, - "end": 5093, + "start": 5713, + "end": 5719, "loc": { "start": { - "line": 145, + "line": 164, "column": 4 }, "end": { - "line": 145, + "line": 164, "column": 10 } } @@ -56233,17 +60666,17 @@ "postfix": false, "binop": null }, - "value": "undefined", - "start": 5094, - "end": 5103, + "value": "normalizedTxname", + "start": 5720, + "end": 5736, "loc": { "start": { - "line": 145, + "line": 164, "column": 11 }, "end": { - "line": 145, - "column": 20 + "line": 164, + "column": 27 } } }, @@ -56260,16 +60693,16 @@ "binop": null, "updateContext": null }, - "start": 5103, - "end": 5104, + "start": 5736, + "end": 5737, "loc": { "start": { - "line": 145, - "column": 20 + "line": 164, + "column": 27 }, "end": { - "line": 145, - "column": 21 + "line": 164, + "column": 28 } } }, @@ -56285,15 +60718,15 @@ "postfix": false, "binop": null }, - "start": 5107, - "end": 5108, + "start": 5740, + "end": 5741, "loc": { "start": { - "line": 146, + "line": 165, "column": 2 }, "end": { - "line": 146, + "line": 165, "column": 3 } } @@ -56301,15 +60734,15 @@ { "type": "CommentBlock", "value": "*\n * Returns the nomenclatural code of this taxon name.\n ", - "start": 5112, - "end": 5177, + "start": 5745, + "end": 5810, "loc": { "start": { - "line": 148, + "line": 167, "column": 2 }, "end": { - "line": 150, + "line": 169, "column": 5 } } @@ -56327,15 +60760,15 @@ "binop": null }, "value": "get", - "start": 5180, - "end": 5183, + "start": 5813, + "end": 5816, "loc": { "start": { - "line": 151, + "line": 170, "column": 2 }, "end": { - "line": 151, + "line": 170, "column": 5 } } @@ -56353,15 +60786,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 5184, - "end": 5201, + "start": 5817, + "end": 5834, "loc": { "start": { - "line": 151, + "line": 170, "column": 6 }, "end": { - "line": 151, + "line": 170, "column": 23 } } @@ -56378,15 +60811,15 @@ "postfix": false, "binop": null }, - "start": 5201, - "end": 5202, + "start": 5834, + "end": 5835, "loc": { "start": { - "line": 151, + "line": 170, "column": 23 }, "end": { - "line": 151, + "line": 170, "column": 24 } } @@ -56403,15 +60836,15 @@ "postfix": false, "binop": null }, - "start": 5202, - "end": 5203, + "start": 5835, + "end": 5836, "loc": { "start": { - "line": 151, + "line": 170, "column": 24 }, "end": { - "line": 151, + "line": 170, "column": 25 } } @@ -56428,15 +60861,15 @@ "postfix": false, "binop": null }, - "start": 5204, - "end": 5205, + "start": 5837, + "end": 5838, "loc": { "start": { - "line": 151, + "line": 170, "column": 26 }, "end": { - "line": 151, + "line": 170, "column": 27 } } @@ -56456,15 +60889,15 @@ "updateContext": null }, "value": "return", - "start": 5210, - "end": 5216, + "start": 5843, + "end": 5849, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 10 } } @@ -56484,15 +60917,15 @@ "updateContext": null }, "value": "this", - "start": 5217, - "end": 5221, + "start": 5850, + "end": 5854, "loc": { "start": { - "line": 152, + "line": 171, "column": 11 }, "end": { - "line": 152, + "line": 171, "column": 15 } } @@ -56510,15 +60943,15 @@ "binop": null, "updateContext": null }, - "start": 5221, - "end": 5222, + "start": 5854, + "end": 5855, "loc": { "start": { - "line": 152, + "line": 171, "column": 15 }, "end": { - "line": 152, + "line": 171, "column": 16 } } @@ -56536,15 +60969,15 @@ "binop": null }, "value": "txname", - "start": 5222, - "end": 5228, + "start": 5855, + "end": 5861, "loc": { "start": { - "line": 152, + "line": 171, "column": 16 }, "end": { - "line": 152, + "line": 171, "column": 22 } } @@ -56562,15 +60995,15 @@ "binop": null, "updateContext": null }, - "start": 5228, - "end": 5229, + "start": 5861, + "end": 5862, "loc": { "start": { - "line": 152, + "line": 171, "column": 22 }, "end": { - "line": 152, + "line": 171, "column": 23 } } @@ -56588,15 +61021,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 5229, - "end": 5246, + "start": 5862, + "end": 5879, "loc": { "start": { - "line": 152, + "line": 171, "column": 23 }, "end": { - "line": 152, + "line": 171, "column": 40 } } @@ -56615,15 +61048,15 @@ "updateContext": null }, "value": "||", - "start": 5247, - "end": 5249, + "start": 5880, + "end": 5882, "loc": { "start": { - "line": 152, + "line": 171, "column": 41 }, "end": { - "line": 152, + "line": 171, "column": 43 } } @@ -56643,15 +61076,15 @@ "updateContext": null }, "value": "this", - "start": 5250, - "end": 5254, + "start": 5883, + "end": 5887, "loc": { "start": { - "line": 152, + "line": 171, "column": 44 }, "end": { - "line": 152, + "line": 171, "column": 48 } } @@ -56669,15 +61102,15 @@ "binop": null, "updateContext": null }, - "start": 5254, - "end": 5255, + "start": 5887, + "end": 5888, "loc": { "start": { - "line": 152, + "line": 171, "column": 48 }, "end": { - "line": 152, + "line": 171, "column": 49 } } @@ -56695,15 +61128,15 @@ "binop": null }, "value": "defaultNomenCode", - "start": 5255, - "end": 5271, + "start": 5888, + "end": 5904, "loc": { "start": { - "line": 152, + "line": 171, "column": 49 }, "end": { - "line": 152, + "line": 171, "column": 65 } } @@ -56721,15 +61154,15 @@ "binop": null, "updateContext": null }, - "start": 5271, - "end": 5272, + "start": 5904, + "end": 5905, "loc": { "start": { - "line": 152, + "line": 171, "column": 65 }, "end": { - "line": 152, + "line": 171, "column": 66 } } @@ -56746,15 +61179,15 @@ "postfix": false, "binop": null }, - "start": 5275, - "end": 5276, + "start": 5908, + "end": 5909, "loc": { "start": { - "line": 153, + "line": 172, "column": 2 }, "end": { - "line": 153, + "line": 172, "column": 3 } } @@ -56762,15 +61195,15 @@ { "type": "CommentBlock", "value": "*\n * Returns the nomenclatural code of this taxon name as a IRI.\n ", - "start": 5280, - "end": 5354, + "start": 5913, + "end": 5987, "loc": { "start": { - "line": 155, + "line": 174, "column": 2 }, "end": { - "line": 157, + "line": 176, "column": 5 } } @@ -56788,15 +61221,15 @@ "binop": null }, "value": "get", - "start": 5357, - "end": 5360, + "start": 5990, + "end": 5993, "loc": { "start": { - "line": 158, + "line": 177, "column": 2 }, "end": { - "line": 158, + "line": 177, "column": 5 } } @@ -56814,15 +61247,15 @@ "binop": null }, "value": "nomenclaturalCodeDetails", - "start": 5361, - "end": 5385, + "start": 5994, + "end": 6018, "loc": { "start": { - "line": 158, + "line": 177, "column": 6 }, "end": { - "line": 158, + "line": 177, "column": 30 } } @@ -56839,15 +61272,15 @@ "postfix": false, "binop": null }, - "start": 5385, - "end": 5386, + "start": 6018, + "end": 6019, "loc": { "start": { - "line": 158, + "line": 177, "column": 30 }, "end": { - "line": 158, + "line": 177, "column": 31 } } @@ -56864,15 +61297,15 @@ "postfix": false, "binop": null }, - "start": 5386, - "end": 5387, + "start": 6019, + "end": 6020, "loc": { "start": { - "line": 158, + "line": 177, "column": 31 }, "end": { - "line": 158, + "line": 177, "column": 32 } } @@ -56889,15 +61322,15 @@ "postfix": false, "binop": null }, - "start": 5388, - "end": 5389, + "start": 6021, + "end": 6022, "loc": { "start": { - "line": 158, + "line": 177, "column": 33 }, "end": { - "line": 158, + "line": 177, "column": 34 } } @@ -56917,15 +61350,15 @@ "updateContext": null }, "value": "const", - "start": 5394, - "end": 5399, + "start": 6027, + "end": 6032, "loc": { "start": { - "line": 159, + "line": 178, "column": 4 }, "end": { - "line": 159, + "line": 178, "column": 9 } } @@ -56943,15 +61376,15 @@ "binop": null }, "value": "nomenCode", - "start": 5400, - "end": 5409, + "start": 6033, + "end": 6042, "loc": { "start": { - "line": 159, + "line": 178, "column": 10 }, "end": { - "line": 159, + "line": 178, "column": 19 } } @@ -56970,15 +61403,15 @@ "updateContext": null }, "value": "=", - "start": 5410, - "end": 5411, + "start": 6043, + "end": 6044, "loc": { "start": { - "line": 159, + "line": 178, "column": 20 }, "end": { - "line": 159, + "line": 178, "column": 21 } } @@ -56998,15 +61431,15 @@ "updateContext": null }, "value": "this", - "start": 5412, - "end": 5416, + "start": 6045, + "end": 6049, "loc": { "start": { - "line": 159, + "line": 178, "column": 22 }, "end": { - "line": 159, + "line": 178, "column": 26 } } @@ -57024,15 +61457,15 @@ "binop": null, "updateContext": null }, - "start": 5416, - "end": 5417, + "start": 6049, + "end": 6050, "loc": { "start": { - "line": 159, + "line": 178, "column": 26 }, "end": { - "line": 159, + "line": 178, "column": 27 } } @@ -57050,15 +61483,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 5417, - "end": 5434, + "start": 6050, + "end": 6067, "loc": { "start": { - "line": 159, + "line": 178, "column": 27 }, "end": { - "line": 159, + "line": 178, "column": 44 } } @@ -57076,15 +61509,15 @@ "binop": null, "updateContext": null }, - "start": 5434, - "end": 5435, + "start": 6067, + "end": 6068, "loc": { "start": { - "line": 159, + "line": 178, "column": 44 }, "end": { - "line": 159, + "line": 178, "column": 45 } } @@ -57104,15 +61537,15 @@ "updateContext": null }, "value": "const", - "start": 5440, - "end": 5445, + "start": 6073, + "end": 6078, "loc": { "start": { - "line": 160, + "line": 179, "column": 4 }, "end": { - "line": 160, + "line": 179, "column": 9 } } @@ -57130,15 +61563,15 @@ "binop": null }, "value": "nomenObj", - "start": 5446, - "end": 5454, + "start": 6079, + "end": 6087, "loc": { "start": { - "line": 160, + "line": 179, "column": 10 }, "end": { - "line": 160, + "line": 179, "column": 18 } } @@ -57157,15 +61590,15 @@ "updateContext": null }, "value": "=", - "start": 5455, - "end": 5456, + "start": 6088, + "end": 6089, "loc": { "start": { - "line": 160, + "line": 179, "column": 19 }, "end": { - "line": 160, + "line": 179, "column": 20 } } @@ -57183,15 +61616,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 5457, - "end": 5473, + "start": 6090, + "end": 6106, "loc": { "start": { - "line": 160, + "line": 179, "column": 21 }, "end": { - "line": 160, + "line": 179, "column": 37 } } @@ -57209,15 +61642,15 @@ "binop": null, "updateContext": null }, - "start": 5473, - "end": 5474, + "start": 6106, + "end": 6107, "loc": { "start": { - "line": 160, + "line": 179, "column": 37 }, "end": { - "line": 160, + "line": 179, "column": 38 } } @@ -57235,15 +61668,15 @@ "binop": null }, "value": "getNomenCodeDetails", - "start": 5474, - "end": 5493, + "start": 6107, + "end": 6126, "loc": { "start": { - "line": 160, + "line": 179, "column": 38 }, "end": { - "line": 160, + "line": 179, "column": 57 } } @@ -57260,15 +61693,15 @@ "postfix": false, "binop": null }, - "start": 5493, - "end": 5494, + "start": 6126, + "end": 6127, "loc": { "start": { - "line": 160, + "line": 179, "column": 57 }, "end": { - "line": 160, + "line": 179, "column": 58 } } @@ -57286,15 +61719,15 @@ "binop": null }, "value": "nomenCode", - "start": 5494, - "end": 5503, + "start": 6127, + "end": 6136, "loc": { "start": { - "line": 160, + "line": 179, "column": 58 }, "end": { - "line": 160, + "line": 179, "column": 67 } } @@ -57311,15 +61744,15 @@ "postfix": false, "binop": null }, - "start": 5503, - "end": 5504, + "start": 6136, + "end": 6137, "loc": { "start": { - "line": 160, + "line": 179, "column": 67 }, "end": { - "line": 160, + "line": 179, "column": 68 } } @@ -57337,15 +61770,15 @@ "binop": null, "updateContext": null }, - "start": 5504, - "end": 5505, + "start": 6137, + "end": 6138, "loc": { "start": { - "line": 160, + "line": 179, "column": 68 }, "end": { - "line": 160, + "line": 179, "column": 69 } } @@ -57365,15 +61798,15 @@ "updateContext": null }, "value": "if", - "start": 5510, - "end": 5512, + "start": 6143, + "end": 6145, "loc": { "start": { - "line": 161, + "line": 180, "column": 4 }, "end": { - "line": 161, + "line": 180, "column": 6 } } @@ -57390,15 +61823,15 @@ "postfix": false, "binop": null }, - "start": 5513, - "end": 5514, + "start": 6146, + "end": 6147, "loc": { "start": { - "line": 161, + "line": 180, "column": 7 }, "end": { - "line": 161, + "line": 180, "column": 8 } } @@ -57417,15 +61850,15 @@ "updateContext": null }, "value": "!", - "start": 5514, - "end": 5515, + "start": 6147, + "end": 6148, "loc": { "start": { - "line": 161, + "line": 180, "column": 8 }, "end": { - "line": 161, + "line": 180, "column": 9 } } @@ -57443,15 +61876,15 @@ "binop": null }, "value": "nomenObj", - "start": 5515, - "end": 5523, + "start": 6148, + "end": 6156, "loc": { "start": { - "line": 161, + "line": 180, "column": 9 }, "end": { - "line": 161, + "line": 180, "column": 17 } } @@ -57468,15 +61901,15 @@ "postfix": false, "binop": null }, - "start": 5523, - "end": 5524, + "start": 6156, + "end": 6157, "loc": { "start": { - "line": 161, + "line": 180, "column": 17 }, "end": { - "line": 161, + "line": 180, "column": 18 } } @@ -57496,15 +61929,15 @@ "updateContext": null }, "value": "return", - "start": 5525, - "end": 5531, + "start": 6158, + "end": 6164, "loc": { "start": { - "line": 161, + "line": 180, "column": 19 }, "end": { - "line": 161, + "line": 180, "column": 25 } } @@ -57522,15 +61955,15 @@ "binop": null }, "value": "undefined", - "start": 5532, - "end": 5541, + "start": 6165, + "end": 6174, "loc": { "start": { - "line": 161, + "line": 180, "column": 26 }, "end": { - "line": 161, + "line": 180, "column": 35 } } @@ -57548,15 +61981,15 @@ "binop": null, "updateContext": null }, - "start": 5541, - "end": 5542, + "start": 6174, + "end": 6175, "loc": { "start": { - "line": 161, + "line": 180, "column": 35 }, "end": { - "line": 161, + "line": 180, "column": 36 } } @@ -57576,15 +62009,15 @@ "updateContext": null }, "value": "return", - "start": 5548, - "end": 5554, + "start": 6181, + "end": 6187, "loc": { "start": { - "line": 163, + "line": 182, "column": 4 }, "end": { - "line": 163, + "line": 182, "column": 10 } } @@ -57602,15 +62035,15 @@ "binop": null }, "value": "nomenObj", - "start": 5555, - "end": 5563, + "start": 6188, + "end": 6196, "loc": { "start": { - "line": 163, + "line": 182, "column": 11 }, "end": { - "line": 163, + "line": 182, "column": 19 } } @@ -57628,15 +62061,15 @@ "binop": null, "updateContext": null }, - "start": 5563, - "end": 5564, + "start": 6196, + "end": 6197, "loc": { "start": { - "line": 163, + "line": 182, "column": 19 }, "end": { - "line": 163, + "line": 182, "column": 20 } } @@ -57653,15 +62086,15 @@ "postfix": false, "binop": null }, - "start": 5567, - "end": 5568, + "start": 6200, + "end": 6201, "loc": { "start": { - "line": 164, + "line": 183, "column": 2 }, "end": { - "line": 164, + "line": 183, "column": 3 } } @@ -57669,15 +62102,15 @@ { "type": "CommentBlock", "value": "*\n * Set the nomenclatural code of this taxon name.\n ", - "start": 5572, - "end": 5633, + "start": 6205, + "end": 6266, "loc": { "start": { - "line": 166, + "line": 185, "column": 2 }, "end": { - "line": 168, + "line": 187, "column": 5 } } @@ -57695,15 +62128,15 @@ "binop": null }, "value": "set", - "start": 5636, - "end": 5639, + "start": 6269, + "end": 6272, "loc": { "start": { - "line": 169, + "line": 188, "column": 2 }, "end": { - "line": 169, + "line": 188, "column": 5 } } @@ -57721,15 +62154,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 5640, - "end": 5657, + "start": 6273, + "end": 6290, "loc": { "start": { - "line": 169, + "line": 188, "column": 6 }, "end": { - "line": 169, + "line": 188, "column": 23 } } @@ -57746,15 +62179,15 @@ "postfix": false, "binop": null }, - "start": 5657, - "end": 5658, + "start": 6290, + "end": 6291, "loc": { "start": { - "line": 169, + "line": 188, "column": 23 }, "end": { - "line": 169, + "line": 188, "column": 24 } } @@ -57772,15 +62205,15 @@ "binop": null }, "value": "nomenCode", - "start": 5658, - "end": 5667, + "start": 6291, + "end": 6300, "loc": { "start": { - "line": 169, + "line": 188, "column": 24 }, "end": { - "line": 169, + "line": 188, "column": 33 } } @@ -57797,15 +62230,15 @@ "postfix": false, "binop": null }, - "start": 5667, - "end": 5668, + "start": 6300, + "end": 6301, "loc": { "start": { - "line": 169, + "line": 188, "column": 33 }, "end": { - "line": 169, + "line": 188, "column": 34 } } @@ -57822,15 +62255,15 @@ "postfix": false, "binop": null }, - "start": 5669, - "end": 5670, + "start": 6302, + "end": 6303, "loc": { "start": { - "line": 169, + "line": 188, "column": 35 }, "end": { - "line": 169, + "line": 188, "column": 36 } } @@ -57850,15 +62283,15 @@ "updateContext": null }, "value": "this", - "start": 5675, - "end": 5679, + "start": 6308, + "end": 6312, "loc": { "start": { - "line": 170, + "line": 189, "column": 4 }, "end": { - "line": 170, + "line": 189, "column": 8 } } @@ -57876,15 +62309,15 @@ "binop": null, "updateContext": null }, - "start": 5679, - "end": 5680, + "start": 6312, + "end": 6313, "loc": { "start": { - "line": 170, + "line": 189, "column": 8 }, "end": { - "line": 170, + "line": 189, "column": 9 } } @@ -57902,15 +62335,15 @@ "binop": null }, "value": "txname", - "start": 5680, - "end": 5686, + "start": 6313, + "end": 6319, "loc": { "start": { - "line": 170, + "line": 189, "column": 9 }, "end": { - "line": 170, + "line": 189, "column": 15 } } @@ -57928,15 +62361,15 @@ "binop": null, "updateContext": null }, - "start": 5686, - "end": 5687, + "start": 6319, + "end": 6320, "loc": { "start": { - "line": 170, + "line": 189, "column": 15 }, "end": { - "line": 170, + "line": 189, "column": 16 } } @@ -57954,15 +62387,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 5687, - "end": 5704, + "start": 6320, + "end": 6337, "loc": { "start": { - "line": 170, + "line": 189, "column": 16 }, "end": { - "line": 170, + "line": 189, "column": 33 } } @@ -57981,15 +62414,15 @@ "updateContext": null }, "value": "=", - "start": 5705, - "end": 5706, + "start": 6338, + "end": 6339, "loc": { "start": { - "line": 170, + "line": 189, "column": 34 }, "end": { - "line": 170, + "line": 189, "column": 35 } } @@ -58007,15 +62440,15 @@ "binop": null }, "value": "nomenCode", - "start": 5707, - "end": 5716, + "start": 6340, + "end": 6349, "loc": { "start": { - "line": 170, + "line": 189, "column": 36 }, "end": { - "line": 170, + "line": 189, "column": 45 } } @@ -58033,15 +62466,15 @@ "binop": null, "updateContext": null }, - "start": 5716, - "end": 5717, + "start": 6349, + "end": 6350, "loc": { "start": { - "line": 170, + "line": 189, "column": 45 }, "end": { - "line": 170, + "line": 189, "column": 46 } } @@ -58058,15 +62491,15 @@ "postfix": false, "binop": null }, - "start": 5720, - "end": 5721, + "start": 6353, + "end": 6354, "loc": { "start": { - "line": 171, + "line": 190, "column": 2 }, "end": { - "line": 171, + "line": 190, "column": 3 } } @@ -58074,15 +62507,15 @@ { "type": "CommentBlock", "value": "*\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n ", - "start": 5725, - 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"line": 244, + "line": 263, "column": 11 }, "end": { - "line": 244, + "line": 263, "column": 12 } } @@ -66164,15 +70597,15 @@ "postfix": false, "binop": null }, - "start": 7848, - "end": 7849, + "start": 8481, + "end": 8482, "loc": { "start": { - "line": 244, + "line": 263, "column": 12 }, "end": { - "line": 244, + "line": 263, "column": 13 } } @@ -66189,15 +70622,15 @@ "postfix": false, "binop": null }, - "start": 7850, - "end": 7851, + "start": 8483, + "end": 8484, "loc": { "start": { - "line": 244, + "line": 263, "column": 14 }, "end": { - "line": 244, + "line": 263, "column": 15 } } @@ -66217,15 +70650,15 @@ "updateContext": null }, "value": "return", - "start": 7856, - "end": 7862, + "start": 8489, + "end": 8495, "loc": { "start": { - "line": 245, + "line": 264, "column": 4 }, "end": { - "line": 245, + "line": 264, "column": 10 } } @@ -66245,15 +70678,15 @@ "updateContext": null }, "value": "this", - "start": 7863, - "end": 7867, + "start": 8496, + "end": 8500, "loc": { "start": { - "line": 245, + "line": 264, "column": 11 }, "end": { - "line": 245, + "line": 264, "column": 15 } } @@ -66271,15 +70704,15 @@ "binop": null, "updateContext": null }, - "start": 7867, - "end": 7868, + "start": 8500, + "end": 8501, "loc": { "start": { - "line": 245, + "line": 264, "column": 15 }, "end": { - "line": 245, + "line": 264, "column": 16 } } @@ -66297,15 +70730,15 @@ "binop": null }, "value": "txname", - "start": 7868, - "end": 7874, + "start": 8501, + "end": 8507, "loc": { "start": { - "line": 245, + "line": 264, "column": 16 }, "end": { - "line": 245, + "line": 264, "column": 22 } } @@ -66323,15 +70756,15 @@ "binop": null, "updateContext": null }, - "start": 7874, - "end": 7875, + "start": 8507, + "end": 8508, "loc": { "start": { - "line": 245, + "line": 264, "column": 22 }, "end": { - "line": 245, + "line": 264, "column": 23 } } @@ -66349,15 +70782,15 @@ "binop": null }, "value": "label", - "start": 7875, - "end": 7880, + "start": 8508, + "end": 8513, "loc": { "start": { - "line": 245, + "line": 264, "column": 23 }, "end": { - "line": 245, + "line": 264, "column": 28 } } @@ -66376,15 +70809,15 @@ "updateContext": null }, "value": "||", - "start": 7881, - "end": 7883, + "start": 8514, + "end": 8516, "loc": { "start": { - "line": 245, + "line": 264, "column": 29 }, "end": { - "line": 245, + "line": 264, "column": 31 } } @@ -66404,15 +70837,15 @@ "updateContext": null }, "value": "this", - "start": 7884, - "end": 7888, + "start": 8517, + "end": 8521, "loc": { "start": { - "line": 245, + "line": 264, "column": 32 }, "end": { - "line": 245, + "line": 264, "column": 36 } } @@ -66430,15 +70863,15 @@ "binop": null, "updateContext": null }, - "start": 7888, - "end": 7889, + "start": 8521, + "end": 8522, "loc": { "start": { - "line": 245, + "line": 264, "column": 36 }, "end": { - "line": 245, + "line": 264, "column": 37 } } @@ -66456,15 +70889,15 @@ "binop": null }, "value": "nameComplete", - "start": 7889, - "end": 7901, + "start": 8522, + "end": 8534, "loc": { "start": { - "line": 245, + "line": 264, "column": 37 }, "end": { - "line": 245, + "line": 264, "column": 49 } } @@ -66482,15 +70915,15 @@ "binop": null, "updateContext": null }, - "start": 7901, - "end": 7902, + "start": 8534, + "end": 8535, "loc": { "start": { - "line": 245, + "line": 264, "column": 49 }, "end": { - "line": 245, + "line": 264, "column": 50 } } @@ -66507,15 +70940,15 @@ "postfix": false, "binop": null }, - "start": 7905, - "end": 7906, + "start": 8538, + "end": 8539, "loc": { "start": { - "line": 246, + "line": 265, "column": 2 }, "end": { - "line": 246, + "line": 265, "column": 3 } } @@ -66523,15 +70956,15 @@ { "type": "CommentBlock", "value": "*\n * Set the label of this scientific name.\n ", - "start": 7910, - "end": 7963, + "start": 8543, + "end": 8596, "loc": { "start": { - "line": 248, + "line": 267, "column": 2 }, "end": { - "line": 250, + "line": 269, "column": 5 } } @@ -66549,15 +70982,15 @@ "binop": null }, "value": "set", - "start": 7966, - "end": 7969, + "start": 8599, + "end": 8602, "loc": { "start": { - "line": 251, + "line": 270, "column": 2 }, "end": { - "line": 251, + "line": 270, "column": 5 } } @@ -66575,15 +71008,15 @@ "binop": null }, "value": "label", - "start": 7970, - "end": 7975, + "start": 8603, + "end": 8608, "loc": { "start": { - "line": 251, + "line": 270, "column": 6 }, "end": { - "line": 251, + "line": 270, "column": 11 } } @@ -66600,15 +71033,15 @@ "postfix": false, "binop": null }, - "start": 7975, - "end": 7976, + "start": 8608, + "end": 8609, "loc": { "start": { - "line": 251, + "line": 270, "column": 11 }, "end": { - "line": 251, + "line": 270, "column": 12 } } @@ -66626,15 +71059,15 @@ "binop": null }, "value": "lab", - "start": 7976, - "end": 7979, + "start": 8609, + "end": 8612, "loc": { "start": { - "line": 251, + "line": 270, "column": 12 }, "end": { - "line": 251, + "line": 270, "column": 15 } } @@ -66651,15 +71084,15 @@ "postfix": false, "binop": null }, - "start": 7979, - "end": 7980, + "start": 8612, + "end": 8613, "loc": { "start": { - "line": 251, + "line": 270, "column": 15 }, "end": { - "line": 251, + "line": 270, "column": 16 } } @@ -66676,15 +71109,15 @@ "postfix": false, "binop": null }, - "start": 7981, - "end": 7982, + "start": 8614, + "end": 8615, "loc": { "start": { - "line": 251, + "line": 270, "column": 17 }, "end": { - "line": 251, + "line": 270, "column": 18 } } @@ -66704,15 +71137,15 @@ "updateContext": null }, "value": "this", - "start": 7987, - "end": 7991, + "start": 8620, + "end": 8624, "loc": { "start": { - "line": 252, + "line": 271, "column": 4 }, "end": { - "line": 252, + "line": 271, "column": 8 } } @@ -66730,15 +71163,15 @@ "binop": null, "updateContext": null }, - "start": 7991, - "end": 7992, + "start": 8624, + "end": 8625, "loc": { "start": { - "line": 252, + "line": 271, "column": 8 }, "end": { - "line": 252, + "line": 271, "column": 9 } } @@ -66756,15 +71189,15 @@ "binop": null }, "value": "txname", - "start": 7992, - "end": 7998, + "start": 8625, + "end": 8631, "loc": { "start": { - "line": 252, + "line": 271, "column": 9 }, "end": { - "line": 252, + "line": 271, "column": 15 } } @@ -66782,15 +71215,15 @@ "binop": null, "updateContext": null }, - "start": 7998, - "end": 7999, + "start": 8631, + "end": 8632, "loc": { "start": { - "line": 252, + "line": 271, "column": 15 }, "end": { - "line": 252, + "line": 271, "column": 16 } } @@ -66808,15 +71241,15 @@ "binop": null }, "value": "label", - "start": 7999, - "end": 8004, + "start": 8632, + "end": 8637, "loc": { "start": { - "line": 252, + "line": 271, "column": 16 }, "end": { - "line": 252, + "line": 271, "column": 21 } } @@ -66835,15 +71268,15 @@ "updateContext": null }, "value": "=", - "start": 8005, - "end": 8006, + "start": 8638, + "end": 8639, "loc": { "start": { - "line": 252, + "line": 271, "column": 22 }, "end": { - "line": 252, + "line": 271, "column": 23 } } @@ -66861,15 +71294,15 @@ "binop": null }, "value": "lab", - "start": 8007, - "end": 8010, + "start": 8640, + "end": 8643, "loc": { "start": { - "line": 252, + "line": 271, "column": 24 }, "end": { - "line": 252, + "line": 271, "column": 27 } } @@ -66887,15 +71320,15 @@ "binop": null, "updateContext": null }, - "start": 8010, - "end": 8011, + "start": 8643, + "end": 8644, "loc": { "start": { - "line": 252, + "line": 271, "column": 27 }, "end": { - "line": 252, + "line": 271, "column": 28 } } @@ -66915,15 +71348,15 @@ "updateContext": null }, "value": "if", - "start": 8016, - "end": 8018, + "start": 8649, + "end": 8651, "loc": { "start": { - "line": 253, + "line": 272, "column": 4 }, "end": { - "line": 253, + "line": 272, "column": 6 } } @@ -66940,15 +71373,15 @@ "postfix": false, "binop": null }, - "start": 8019, - "end": 8020, + "start": 8652, + "end": 8653, "loc": { "start": { - "line": 253, + "line": 272, "column": 7 }, "end": { - "line": 253, + "line": 272, "column": 8 } } @@ -66967,15 +71400,15 @@ "updateContext": null }, "value": "!", - "start": 8020, - "end": 8021, + "start": 8653, + "end": 8654, "loc": { "start": { - "line": 253, + "line": 272, "column": 8 }, "end": { - "line": 253, + "line": 272, "column": 9 } } @@ -66995,15 +71428,15 @@ "updateContext": null }, "value": "this", - "start": 8021, - "end": 8025, + "start": 8654, + "end": 8658, "loc": { "start": { - "line": 253, + "line": 272, "column": 9 }, "end": { - "line": 253, + "line": 272, "column": 13 } } @@ -67021,15 +71454,15 @@ "binop": null, "updateContext": null }, - "start": 8025, - "end": 8026, + "start": 8658, + "end": 8659, "loc": { "start": { - "line": 253, + "line": 272, "column": 13 }, "end": { - "line": 253, + "line": 272, "column": 14 } } @@ -67047,15 +71480,15 @@ "binop": null }, "value": "nameComplete", - "start": 8026, - "end": 8038, + "start": 8659, + "end": 8671, "loc": { "start": { - "line": 253, + "line": 272, "column": 14 }, "end": { - "line": 253, + "line": 272, "column": 26 } } @@ -67072,15 +71505,15 @@ "postfix": false, "binop": null }, - "start": 8038, - "end": 8039, + "start": 8671, + "end": 8672, "loc": { "start": { - "line": 253, + "line": 272, "column": 26 }, "end": { - "line": 253, + "line": 272, "column": 27 } } @@ -67097,15 +71530,15 @@ "postfix": false, "binop": null }, - "start": 8040, - "end": 8041, + "start": 8673, + "end": 8674, "loc": { "start": { - "line": 253, + "line": 272, "column": 28 }, "end": { - "line": 253, + "line": 272, "column": 29 } } @@ -67113,15 +71546,15 @@ { "type": "CommentLine", "value": " If we don't have a nameComplete, treat this as the name complete.", - "start": 8048, - "end": 8116, + "start": 8681, + "end": 8749, "loc": { "start": { - "line": 254, + "line": 273, "column": 6 }, "end": { - "line": 254, + "line": 273, "column": 74 } } @@ -67141,15 +71574,15 @@ "updateContext": null }, "value": "this", - "start": 8123, - "end": 8127, + "start": 8756, + "end": 8760, "loc": { "start": { - "line": 255, + "line": 274, "column": 6 }, "end": { - "line": 255, + "line": 274, "column": 10 } } @@ -67167,15 +71600,15 @@ "binop": null, "updateContext": null }, - "start": 8127, - "end": 8128, + "start": 8760, + "end": 8761, "loc": { "start": { - "line": 255, + "line": 274, "column": 10 }, "end": { - "line": 255, + "line": 274, "column": 11 } } @@ -67193,15 +71626,15 @@ "binop": null }, "value": "nameComplete", - "start": 8128, - "end": 8140, + "start": 8761, + "end": 8773, "loc": { "start": { - "line": 255, + "line": 274, "column": 11 }, "end": { - "line": 255, + "line": 274, "column": 23 } } @@ -67220,15 +71653,15 @@ "updateContext": null }, "value": "=", - "start": 8141, - "end": 8142, + "start": 8774, + "end": 8775, "loc": { "start": { - "line": 255, + "line": 274, "column": 24 }, "end": { - "line": 255, + "line": 274, "column": 25 } } @@ -67246,15 +71679,15 @@ "binop": null }, "value": "lab", - "start": 8143, - "end": 8146, + "start": 8776, + "end": 8779, "loc": { "start": { - "line": 255, + "line": 274, "column": 26 }, "end": { - "line": 255, + "line": 274, "column": 29 } } @@ -67272,15 +71705,15 @@ "binop": null, "updateContext": null }, - "start": 8146, - "end": 8147, + "start": 8779, + "end": 8780, "loc": { "start": { - "line": 255, + "line": 274, "column": 29 }, "end": { - "line": 255, + "line": 274, "column": 30 } } @@ -67297,15 +71730,15 @@ "postfix": false, "binop": null }, - "start": 8152, - "end": 8153, + "start": 8785, + "end": 8786, "loc": { "start": { - "line": 256, + "line": 275, "column": 4 }, "end": { - "line": 256, + "line": 275, "column": 5 } } @@ -67322,15 +71755,15 @@ "postfix": false, "binop": null }, - "start": 8156, - "end": 8157, + "start": 8789, + "end": 8790, "loc": { "start": { - "line": 257, + "line": 276, "column": 2 }, "end": { - "line": 257, + "line": 276, "column": 3 } } @@ -67338,15 +71771,15 @@ { "type": "CommentBlock", "value": "*\n * Return the verbatim name of this taxon name.\n ", - "start": 8161, - "end": 8220, + "start": 8794, + "end": 8853, "loc": { "start": { - "line": 259, + "line": 278, "column": 2 }, "end": { - "line": 261, + "line": 280, "column": 5 } } @@ -67364,15 +71797,15 @@ "binop": null }, "value": "get", - "start": 8223, - "end": 8226, + "start": 8856, + "end": 8859, "loc": { "start": { - "line": 262, + "line": 281, "column": 2 }, "end": { - "line": 262, + "line": 281, "column": 5 } } @@ -67390,15 +71823,15 @@ "binop": null }, "value": "verbatimName", - "start": 8227, - "end": 8239, + "start": 8860, + "end": 8872, "loc": { "start": { - "line": 262, + "line": 281, "column": 6 }, "end": { - "line": 262, + "line": 281, "column": 18 } } @@ -67415,15 +71848,15 @@ "postfix": false, "binop": null }, - "start": 8239, - "end": 8240, + "start": 8872, + "end": 8873, "loc": { "start": { - "line": 262, + "line": 281, "column": 18 }, "end": { - "line": 262, + "line": 281, "column": 19 } } @@ -67440,15 +71873,15 @@ "postfix": false, "binop": null }, - "start": 8240, - "end": 8241, + "start": 8873, + "end": 8874, "loc": { "start": { - "line": 262, + "line": 281, "column": 19 }, "end": { - "line": 262, + "line": 281, "column": 20 } } @@ -67465,15 +71898,15 @@ "postfix": false, "binop": null }, - "start": 8242, - "end": 8243, + "start": 8875, + "end": 8876, "loc": { "start": { - "line": 262, + "line": 281, "column": 21 }, "end": { - "line": 262, + "line": 281, "column": 22 } } @@ -67493,15 +71926,15 @@ "updateContext": null }, "value": "return", - "start": 8248, - "end": 8254, + "start": 8881, + "end": 8887, "loc": { "start": { - "line": 263, + "line": 282, "column": 4 }, "end": { - "line": 263, + "line": 282, "column": 10 } } @@ -67521,15 +71954,15 @@ "updateContext": null }, "value": "this", - "start": 8255, - "end": 8259, + "start": 8888, + "end": 8892, "loc": { "start": { - "line": 263, + "line": 282, "column": 11 }, "end": { - "line": 263, + "line": 282, "column": 15 } } @@ -67547,15 +71980,15 @@ "binop": null, "updateContext": null }, - "start": 8259, - "end": 8260, + "start": 8892, + "end": 8893, "loc": { "start": { - "line": 263, + "line": 282, "column": 15 }, "end": { - "line": 263, + "line": 282, "column": 16 } } @@ -67573,15 +72006,15 @@ "binop": null }, "value": "txname", - "start": 8260, - "end": 8266, + "start": 8893, + "end": 8899, "loc": { "start": { - "line": 263, + "line": 282, "column": 16 }, "end": { - "line": 263, + "line": 282, "column": 22 } } @@ -67599,15 +72032,15 @@ "binop": null, "updateContext": null }, - "start": 8266, - "end": 8267, + "start": 8899, + "end": 8900, "loc": { "start": { - "line": 263, + "line": 282, "column": 22 }, "end": { - "line": 263, + "line": 282, "column": 23 } } @@ -67625,15 +72058,15 @@ "binop": null }, "value": "label", - "start": 8267, - "end": 8272, + "start": 8900, + "end": 8905, "loc": { "start": { - "line": 263, + "line": 282, "column": 23 }, "end": { - "line": 263, + "line": 282, "column": 28 } } @@ -67651,15 +72084,15 @@ "binop": null, "updateContext": null }, - "start": 8272, - "end": 8273, + "start": 8905, + "end": 8906, "loc": { "start": { - "line": 263, + "line": 282, "column": 28 }, "end": { - "line": 263, + "line": 282, "column": 29 } } @@ -67676,15 +72109,15 @@ "postfix": false, "binop": null }, - "start": 8276, - "end": 8277, + "start": 8909, + "end": 8910, "loc": { "start": { - "line": 264, + "line": 283, "column": 2 }, "end": { - "line": 264, + "line": 283, "column": 3 } } @@ -67692,15 +72125,15 @@ { "type": "CommentBlock", "value": "\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n ", - "start": 8281, - "end": 8404, + "start": 8914, + "end": 9037, "loc": { "start": { - "line": 266, + "line": 285, "column": 2 }, "end": { - "line": 269, + "line": 288, "column": 5 } } @@ -67718,15 +72151,15 @@ "binop": null }, "value": "get", - "start": 8407, - "end": 8410, + "start": 9040, + "end": 9043, "loc": { "start": { - "line": 270, + "line": 289, "column": 2 }, "end": { - "line": 270, + "line": 289, "column": 5 } } @@ -67744,15 +72177,15 @@ "binop": null }, "value": "nameComplete", - "start": 8411, - "end": 8423, + "start": 9044, + "end": 9056, "loc": { "start": { - "line": 270, + "line": 289, "column": 6 }, "end": { - "line": 270, + "line": 289, "column": 18 } } @@ -67769,15 +72202,15 @@ "postfix": false, "binop": null }, - "start": 8423, - "end": 8424, + "start": 9056, + "end": 9057, "loc": { "start": { - "line": 270, + "line": 289, "column": 18 }, "end": { - "line": 270, + "line": 289, "column": 19 } } @@ -67794,15 +72227,15 @@ "postfix": false, "binop": null }, - "start": 8424, - "end": 8425, + "start": 9057, + "end": 9058, "loc": { "start": { - "line": 270, + "line": 289, "column": 19 }, "end": { - "line": 270, + "line": 289, "column": 20 } } @@ -67819,15 +72252,15 @@ "postfix": false, "binop": null }, - "start": 8426, - "end": 8427, + "start": 9059, + "end": 9060, "loc": { "start": { - "line": 270, + "line": 289, "column": 21 }, "end": { - "line": 270, + "line": 289, "column": 22 } } @@ -67847,15 +72280,15 @@ "updateContext": null }, "value": "return", - "start": 8432, - "end": 8438, + "start": 9065, + "end": 9071, "loc": { "start": { - "line": 271, + "line": 290, "column": 4 }, "end": { - "line": 271, + "line": 290, "column": 10 } } @@ -67875,15 +72308,15 @@ "updateContext": null }, "value": "this", - "start": 8439, - "end": 8443, + "start": 9072, + "end": 9076, "loc": { "start": { - "line": 271, + "line": 290, "column": 11 }, "end": { - "line": 271, + "line": 290, "column": 15 } } @@ -67901,15 +72334,15 @@ "binop": null, "updateContext": null }, - "start": 8443, - "end": 8444, + "start": 9076, + "end": 9077, "loc": { "start": { - "line": 271, + "line": 290, "column": 15 }, "end": { - "line": 271, + "line": 290, "column": 16 } } @@ -67927,15 +72360,15 @@ "binop": null }, "value": "txname", - "start": 8444, - "end": 8450, + "start": 9077, + "end": 9083, "loc": { "start": { - "line": 271, + "line": 290, "column": 16 }, "end": { - "line": 271, + "line": 290, "column": 22 } } @@ -67953,15 +72386,15 @@ "binop": null, "updateContext": null }, - "start": 8450, - "end": 8451, + "start": 9083, + "end": 9084, "loc": { "start": { - "line": 271, + "line": 290, "column": 22 }, "end": { - "line": 271, + "line": 290, "column": 23 } } @@ -67979,15 +72412,15 @@ "binop": null }, "value": "nameComplete", - "start": 8451, - "end": 8463, + "start": 9084, + "end": 9096, "loc": { "start": { - "line": 271, + "line": 290, "column": 23 }, "end": { - "line": 271, + "line": 290, "column": 35 } } @@ -68006,15 +72439,15 @@ "updateContext": null }, "value": "||", - "start": 8470, - "end": 8472, + "start": 9103, + "end": 9105, "loc": { "start": { - "line": 272, + "line": 291, "column": 6 }, "end": { - "line": 272, + "line": 291, "column": 8 } } @@ -68034,15 +72467,15 @@ "updateContext": null }, "value": "this", - "start": 8473, - "end": 8477, + "start": 9106, + "end": 9110, "loc": { "start": { - "line": 272, + "line": 291, "column": 9 }, "end": { - "line": 272, + "line": 291, "column": 13 } } @@ -68060,15 +72493,15 @@ "binop": null, "updateContext": null }, - "start": 8477, - "end": 8478, + "start": 9110, + "end": 9111, "loc": { "start": { - "line": 272, + "line": 291, "column": 13 }, "end": { - "line": 272, + "line": 291, "column": 14 } } @@ -68086,15 +72519,15 @@ "binop": null }, "value": "trinomialName", - "start": 8478, - "end": 8491, + "start": 9111, + "end": 9124, "loc": { "start": { - "line": 272, + "line": 291, "column": 14 }, "end": { - "line": 272, + "line": 291, "column": 27 } } @@ -68113,15 +72546,15 @@ "updateContext": null }, "value": "||", - "start": 8498, - "end": 8500, + "start": 9131, + "end": 9133, "loc": { "start": { - "line": 273, + "line": 292, "column": 6 }, "end": { - "line": 273, + "line": 292, "column": 8 } } @@ -68141,15 +72574,15 @@ "updateContext": null }, "value": "this", - "start": 8501, - "end": 8505, + "start": 9134, + "end": 9138, "loc": { "start": { - "line": 273, + "line": 292, "column": 9 }, "end": { - "line": 273, + "line": 292, "column": 13 } } @@ -68167,15 +72600,15 @@ "binop": null, "updateContext": null }, - "start": 8505, - "end": 8506, + "start": 9138, + "end": 9139, "loc": { "start": { - "line": 273, + "line": 292, "column": 13 }, "end": { - "line": 273, + "line": 292, "column": 14 } } @@ -68193,15 +72626,15 @@ "binop": null }, "value": "binomialName", - "start": 8506, - "end": 8518, + "start": 9139, + "end": 9151, "loc": { "start": { - "line": 273, + "line": 292, "column": 14 }, "end": { - "line": 273, + "line": 292, "column": 26 } } @@ -68220,15 +72653,15 @@ "updateContext": null }, "value": "||", - "start": 8525, - "end": 8527, + "start": 9158, + "end": 9160, "loc": { "start": { - "line": 274, + "line": 293, "column": 6 }, "end": { - "line": 274, + "line": 293, "column": 8 } } @@ -68248,15 +72681,15 @@ "updateContext": null }, "value": "this", - "start": 8528, - "end": 8532, + "start": 9161, + "end": 9165, "loc": { "start": { - "line": 274, + "line": 293, "column": 9 }, "end": { - "line": 274, + "line": 293, "column": 13 } } @@ -68274,15 +72707,15 @@ "binop": null, "updateContext": null }, - "start": 8532, - "end": 8533, + "start": 9165, + "end": 9166, "loc": { "start": { - "line": 274, + "line": 293, "column": 13 }, "end": { - "line": 274, + "line": 293, "column": 14 } } @@ -68300,15 +72733,15 @@ "binop": null }, "value": "uninomialName", - "start": 8533, - "end": 8546, + "start": 9166, + "end": 9179, "loc": { "start": { - "line": 274, + "line": 293, "column": 14 }, "end": { - "line": 274, + "line": 293, "column": 27 } } @@ -68326,15 +72759,15 @@ "binop": null, "updateContext": null }, - "start": 8546, - "end": 8547, + "start": 9179, + "end": 9180, "loc": { "start": { - "line": 274, + "line": 293, "column": 27 }, "end": { - "line": 274, + "line": 293, "column": 28 } } @@ -68351,15 +72784,15 @@ "postfix": false, "binop": null }, - "start": 8550, - "end": 8551, + "start": 9183, + "end": 9184, "loc": { "start": { - "line": 275, + "line": 294, "column": 2 }, "end": { - "line": 275, + "line": 294, "column": 3 } } @@ -68367,15 +72800,15 @@ { "type": "CommentBlock", "value": "*\n * Set the complete name. To do this, we re-parse the provided name.\n ", - "start": 8555, - "end": 8635, + "start": 9188, + "end": 9268, "loc": { "start": { - "line": 277, + "line": 296, "column": 2 }, "end": { - "line": 279, + "line": 298, "column": 5 } } @@ -68393,15 +72826,15 @@ "binop": null }, "value": "set", - "start": 8638, - "end": 8641, + "start": 9271, + "end": 9274, "loc": { "start": { - "line": 280, + "line": 299, "column": 2 }, "end": { - "line": 280, + "line": 299, "column": 5 } } @@ -68419,15 +72852,15 @@ "binop": null }, "value": "nameComplete", - "start": 8642, - "end": 8654, + "start": 9275, + "end": 9287, "loc": { "start": { - "line": 280, + "line": 299, "column": 6 }, "end": { - "line": 280, + "line": 299, "column": 18 } } @@ -68444,15 +72877,15 @@ "postfix": false, "binop": null }, - "start": 8654, - "end": 8655, + "start": 9287, + "end": 9288, "loc": { "start": { - "line": 280, + "line": 299, "column": 18 }, "end": { - "line": 280, + "line": 299, "column": 19 } } @@ -68470,15 +72903,15 @@ "binop": null }, "value": "name", - "start": 8655, - "end": 8659, + "start": 9288, + "end": 9292, "loc": { "start": { - "line": 280, + "line": 299, "column": 19 }, "end": { - "line": 280, + "line": 299, "column": 23 } } @@ -68495,15 +72928,15 @@ "postfix": false, "binop": null }, - "start": 8659, - "end": 8660, + "start": 9292, + "end": 9293, "loc": { "start": { - "line": 280, + "line": 299, "column": 23 }, "end": { - "line": 280, + "line": 299, "column": 24 } } @@ -68520,15 +72953,15 @@ "postfix": false, "binop": null }, - "start": 8661, - "end": 8662, + "start": 9294, + "end": 9295, "loc": { "start": { - "line": 280, + "line": 299, "column": 25 }, "end": { - "line": 280, + "line": 299, "column": 26 } } @@ -68548,15 +72981,15 @@ "updateContext": null }, "value": "this", - "start": 8667, - "end": 8671, + "start": 9300, + "end": 9304, "loc": { "start": { - "line": 281, + "line": 300, "column": 4 }, "end": { - "line": 281, + "line": 300, "column": 8 } } @@ -68574,15 +73007,15 @@ "binop": null, "updateContext": null }, - "start": 8671, - "end": 8672, + "start": 9304, + "end": 9305, "loc": { "start": { - "line": 281, + "line": 300, "column": 8 }, "end": { - "line": 281, + "line": 300, "column": 9 } } @@ -68600,15 +73033,15 @@ "binop": null }, "value": "txname", - "start": 8672, - "end": 8678, + "start": 9305, + "end": 9311, "loc": { "start": { - "line": 281, + "line": 300, "column": 9 }, "end": { - "line": 281, + "line": 300, "column": 15 } } @@ -68627,15 +73060,15 @@ "updateContext": null }, "value": "=", - "start": 8679, - "end": 8680, + "start": 9312, + "end": 9313, "loc": { "start": { - "line": 281, + "line": 300, "column": 16 }, "end": { - "line": 281, + "line": 300, "column": 17 } } @@ -68653,15 +73086,15 @@ "binop": null }, "value": "TaxonNameWrapper", - "start": 8681, - "end": 8697, + "start": 9314, + "end": 9330, "loc": { "start": { - "line": 281, + "line": 300, "column": 18 }, "end": { - "line": 281, + "line": 300, "column": 34 } } @@ -68679,15 +73112,15 @@ "binop": null, "updateContext": null }, - "start": 8697, - "end": 8698, + "start": 9330, + "end": 9331, "loc": { "start": { - "line": 281, + "line": 300, "column": 34 }, "end": { - "line": 281, + "line": 300, "column": 35 } } @@ -68705,15 +73138,15 @@ "binop": null }, "value": "fromVerbatimName", - "start": 8698, - "end": 8714, + "start": 9331, + "end": 9347, "loc": { "start": { - "line": 281, + "line": 300, "column": 35 }, "end": { - "line": 281, + "line": 300, "column": 51 } } @@ -68730,15 +73163,15 @@ "postfix": false, "binop": null }, - "start": 8714, - "end": 8715, + "start": 9347, + "end": 9348, "loc": { "start": { - "line": 281, + "line": 300, "column": 51 }, "end": { - "line": 281, + "line": 300, "column": 52 } } @@ -68756,15 +73189,15 @@ "binop": null }, "value": "name", - "start": 8715, - "end": 8719, + "start": 9348, + "end": 9352, "loc": { "start": { - "line": 281, + "line": 300, "column": 52 }, "end": { - "line": 281, + "line": 300, "column": 56 } } @@ -68782,15 +73215,15 @@ "binop": null, "updateContext": null }, - "start": 8719, - "end": 8720, + "start": 9352, + "end": 9353, "loc": { "start": { - "line": 281, + "line": 300, "column": 56 }, "end": { - "line": 281, + "line": 300, "column": 57 } } @@ -68810,15 +73243,15 @@ "updateContext": null }, "value": "this", - "start": 8721, - "end": 8725, + "start": 9354, + "end": 9358, "loc": { "start": { - "line": 281, + "line": 300, "column": 58 }, "end": { - "line": 281, + "line": 300, "column": 62 } } @@ -68836,15 +73269,15 @@ "binop": null, "updateContext": null }, - "start": 8725, - "end": 8726, + "start": 9358, + "end": 9359, "loc": { "start": { - "line": 281, + "line": 300, "column": 62 }, "end": { - "line": 281, + "line": 300, "column": 63 } } @@ -68862,15 +73295,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 8726, - "end": 8743, + "start": 9359, + "end": 9376, "loc": { "start": { - "line": 281, + "line": 300, "column": 63 }, "end": { - "line": 281, + "line": 300, "column": 80 } } @@ -68887,15 +73320,15 @@ "postfix": false, "binop": null }, - "start": 8743, - "end": 8744, + "start": 9376, + "end": 9377, "loc": { "start": { - "line": 281, + "line": 300, "column": 80 }, "end": { - "line": 281, + "line": 300, "column": 81 } } @@ -68913,15 +73346,15 @@ "binop": null, "updateContext": null }, - "start": 8744, - "end": 8745, + "start": 9377, + "end": 9378, "loc": { "start": { - "line": 281, + "line": 300, "column": 81 }, "end": { - "line": 281, + "line": 300, "column": 82 } } @@ -68938,15 +73371,15 @@ "postfix": false, "binop": null }, - "start": 8748, - "end": 8749, + "start": 9381, + "end": 9382, "loc": { "start": { - "line": 282, + "line": 301, "column": 2 }, "end": { - "line": 282, + "line": 301, "column": 3 } } @@ -68954,15 +73387,15 @@ { "type": "CommentBlock", "value": "* Return the uninomial name if there is one. 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"start": 13576, - "end": 13582, + "start": 14209, + "end": 14215, "loc": { "start": { - "line": 435, + "line": 454, "column": 35 }, "end": { - "line": 435, + "line": 454, "column": 41 } } @@ -88012,15 +92445,15 @@ "binop": null, "updateContext": null }, - "start": 13582, - "end": 13583, + "start": 14215, + "end": 14216, "loc": { "start": { - "line": 435, + "line": 454, "column": 41 }, "end": { - "line": 435, + "line": 454, "column": 42 } } @@ -88039,15 +92472,15 @@ "updateContext": null }, "value": "@type", - "start": 13583, - "end": 13590, + "start": 14216, + "end": 14223, "loc": { "start": { - "line": 435, + "line": 454, "column": 42 }, "end": { - "line": 435, + "line": 454, "column": 49 } } @@ -88065,15 +92498,15 @@ "binop": null, "updateContext": null }, - "start": 13590, - "end": 13591, + "start": 14223, + "end": 14224, "loc": { "start": { - "line": 435, + "line": 454, "column": 49 }, "end": { - "line": 435, + "line": 454, "column": 50 } } @@ -88092,15 +92525,15 @@ "updateContext": null }, "value": "=", - "start": 13592, - "end": 13593, + "start": 14225, + "end": 14226, "loc": { "start": { - "line": 435, + "line": 454, "column": 51 }, "end": { - "line": 435, + "line": 454, "column": 52 } } @@ -88118,15 +92551,15 @@ "binop": null, "updateContext": null }, - "start": 13594, - "end": 13595, + "start": 14227, + "end": 14228, "loc": { "start": { - "line": 435, + "line": 454, "column": 53 }, "end": { - "line": 435, + "line": 454, "column": 54 } } @@ -88144,15 +92577,15 @@ "binop": null }, "value": "jsonld", - "start": 13595, - "end": 13601, + "start": 14228, + "end": 14234, "loc": { "start": { - "line": 435, + "line": 454, "column": 54 }, "end": { - "line": 435, + "line": 454, "column": 60 } } @@ -88170,15 +92603,15 @@ "binop": null, "updateContext": null }, - "start": 13601, - "end": 13602, + "start": 14234, + "end": 14235, "loc": { "start": { - "line": 435, + "line": 454, "column": 60 }, "end": { - "line": 435, + "line": 454, "column": 61 } } @@ -88197,15 +92630,15 @@ "updateContext": null }, "value": "@type", - 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"start": 13618, - "end": 13683, + "start": 14251, + "end": 14316, "loc": { "start": { - "line": 437, + "line": 456, "column": 4 }, "end": { - "line": 437, + "line": 456, "column": 69 } } @@ -88319,15 +92752,15 @@ "updateContext": null }, "value": "const", - "start": 13688, - "end": 13693, + "start": 14321, + "end": 14326, "loc": { "start": { - "line": 438, + "line": 457, "column": 4 }, "end": { - "line": 438, + "line": 457, "column": 9 } } @@ -88345,15 +92778,15 @@ "binop": null }, "value": "nomenCode", - "start": 13694, - "end": 13703, + "start": 14327, + "end": 14336, "loc": { "start": { - "line": 438, + "line": 457, "column": 10 }, "end": { - "line": 438, + "line": 457, "column": 19 } } @@ -88372,15 +92805,15 @@ "updateContext": null }, "value": "=", - "start": 13704, - "end": 13705, + "start": 14337, + "end": 14338, "loc": { "start": { - "line": 438, + "line": 457, "column": 20 }, "end": { - "line": 438, + "line": 457, "column": 21 } } @@ -88400,15 +92833,15 @@ "updateContext": null }, "value": "this", - "start": 13706, - "end": 13710, + "start": 14339, + "end": 14343, "loc": { "start": { - "line": 438, + "line": 457, "column": 22 }, "end": { - "line": 438, + "line": 457, "column": 26 } } @@ -88426,15 +92859,15 @@ "binop": null, "updateContext": null }, - "start": 13710, - "end": 13711, + "start": 14343, + "end": 14344, "loc": { "start": { - "line": 438, + "line": 457, "column": 26 }, "end": { - "line": 438, + "line": 457, "column": 27 } } @@ -88452,15 +92885,15 @@ "binop": null }, "value": "nomenclaturalCode", - "start": 13711, - "end": 13728, + "start": 14344, + "end": 14361, "loc": { "start": { - "line": 438, + "line": 457, "column": 27 }, "end": { - "line": 438, + "line": 457, "column": 44 } } @@ -88478,15 +92911,15 @@ "binop": null, "updateContext": null }, - "start": 13728, - "end": 13729, + "start": 14361, + "end": 14362, "loc": { "start": { - "line": 438, + "line": 457, "column": 44 }, "end": { - "line": 438, + "line": 457, "column": 45 } } @@ -88506,15 +92939,15 @@ "updateContext": null }, "value": "if", - "start": 13734, - "end": 13736, + "start": 14367, + "end": 14369, "loc": { "start": { - "line": 439, + "line": 458, "column": 4 }, "end": { - "line": 439, + "line": 458, "column": 6 } } @@ -88531,15 +92964,15 @@ "postfix": false, "binop": null }, - "start": 13737, - "end": 13738, + "start": 14370, + "end": 14371, "loc": { "start": { - "line": 439, + "line": 458, "column": 7 }, "end": { - "line": 439, + "line": 458, "column": 8 } } @@ -88558,15 +92991,15 @@ "updateContext": null }, "value": "!", - "start": 13738, - "end": 13739, + "start": 14371, + "end": 14372, "loc": { "start": { - "line": 439, + "line": 458, "column": 8 }, "end": { - "line": 439, + "line": 458, "column": 9 } } @@ -88584,15 +93017,15 @@ "binop": null }, "value": "jsonld", - "start": 13739, - "end": 13745, + "start": 14372, + "end": 14378, "loc": { "start": { - "line": 439, + "line": 458, "column": 9 }, "end": { - "line": 439, + "line": 458, "column": 15 } } @@ -88610,15 +93043,15 @@ "binop": null, "updateContext": null }, - "start": 13745, - "end": 13746, + "start": 14378, + "end": 14379, "loc": { "start": { - "line": 439, + "line": 458, "column": 15 }, "end": { - "line": 439, + "line": 458, "column": 16 } } @@ -88637,15 +93070,15 @@ "updateContext": null }, "value": "@type", - "start": 13746, - "end": 13753, + "start": 14379, + "end": 14386, "loc": { "start": { - "line": 439, + "line": 458, "column": 16 }, "end": { - "line": 439, + "line": 458, "column": 23 } } @@ -88663,15 +93096,15 @@ "binop": null, "updateContext": null }, - "start": 13753, - "end": 13754, + "start": 14386, + "end": 14387, "loc": { "start": { - "line": 439, + "line": 458, "column": 23 }, "end": { - "line": 439, + "line": 458, "column": 24 } } @@ -88689,15 +93122,15 @@ "binop": null, "updateContext": null }, - "start": 13754, - "end": 13755, + "start": 14387, + "end": 14388, "loc": { "start": { - "line": 439, + "line": 458, "column": 24 }, "end": { - "line": 439, + "line": 458, "column": 25 } } @@ -88715,15 +93148,15 @@ "binop": null }, "value": "includes", - "start": 13755, - "end": 13763, + "start": 14388, + "end": 14396, "loc": { "start": { - "line": 439, + "line": 458, "column": 25 }, "end": { - "line": 439, + "line": 458, "column": 33 } } @@ -88740,15 +93173,15 @@ "postfix": false, "binop": null }, - "start": 13763, - "end": 13764, + "start": 14396, + "end": 14397, "loc": { "start": { - "line": 439, + "line": 458, "column": 33 }, "end": { - "line": 439, + "line": 458, "column": 34 } } @@ -88766,15 +93199,15 @@ "binop": null }, "value": "nomenCode", - "start": 13764, - "end": 13773, + "start": 14397, + "end": 14406, "loc": { "start": { - "line": 439, + "line": 458, "column": 34 }, "end": { - "line": 439, + "line": 458, "column": 43 } } @@ -88791,15 +93224,15 @@ "postfix": false, "binop": null }, - "start": 13773, - "end": 13774, + "start": 14406, + "end": 14407, "loc": { "start": { - "line": 439, + "line": 458, "column": 43 }, "end": { - "line": 439, + "line": 458, "column": 44 } } @@ -88816,15 +93249,15 @@ "postfix": false, "binop": null }, - "start": 13774, - "end": 13775, + "start": 14407, + "end": 14408, "loc": { "start": { - "line": 439, + "line": 458, "column": 44 }, "end": { - "line": 439, + "line": 458, "column": 45 } } @@ -88842,15 +93275,15 @@ "binop": null }, "value": "jsonld", - "start": 13776, - "end": 13782, + "start": 14409, + "end": 14415, "loc": { "start": { - "line": 439, + "line": 458, "column": 46 }, "end": { - "line": 439, + "line": 458, "column": 52 } } @@ -88868,15 +93301,15 @@ "binop": null, "updateContext": null }, - "start": 13782, - "end": 13783, + "start": 14415, + "end": 14416, "loc": { "start": { - "line": 439, + "line": 458, "column": 52 }, "end": { - "line": 439, + "line": 458, "column": 53 } } @@ -88895,15 +93328,15 @@ "updateContext": null }, "value": "@type", - "start": 13783, - "end": 13790, + "start": 14416, + "end": 14423, "loc": { "start": { - "line": 439, + "line": 458, "column": 53 }, "end": { - "line": 439, + "line": 458, "column": 60 } } @@ -88921,15 +93354,15 @@ "binop": null, "updateContext": null }, - "start": 13790, - "end": 13791, + "start": 14423, + "end": 14424, "loc": { "start": { - "line": 439, + "line": 458, "column": 60 }, "end": { - "line": 439, + "line": 458, "column": 61 } } @@ -88947,15 +93380,15 @@ "binop": null, "updateContext": null }, - "start": 13791, - "end": 13792, + "start": 14424, + "end": 14425, "loc": { "start": { - "line": 439, + "line": 458, "column": 61 }, "end": { - "line": 439, + "line": 458, "column": 62 } } @@ -88973,15 +93406,15 @@ "binop": null }, "value": "push", - "start": 13792, - "end": 13796, + "start": 14425, + "end": 14429, "loc": { "start": { - "line": 439, + "line": 458, "column": 62 }, "end": { - "line": 439, + "line": 458, "column": 66 } } @@ -88998,15 +93431,15 @@ "postfix": false, "binop": null }, - "start": 13796, - "end": 13797, + "start": 14429, + "end": 14430, "loc": { "start": { - "line": 439, + "line": 458, "column": 66 }, "end": { - "line": 439, + "line": 458, "column": 67 } } @@ -89024,15 +93457,15 @@ "binop": null }, "value": "nomenCode", - "start": 13797, - "end": 13806, + "start": 14430, + "end": 14439, "loc": { "start": { - "line": 439, + "line": 458, "column": 67 }, "end": { - "line": 439, + "line": 458, "column": 76 } } @@ -89049,15 +93482,15 @@ "postfix": false, "binop": null }, - "start": 13806, - "end": 13807, + "start": 14439, + "end": 14440, "loc": { "start": { - "line": 439, + "line": 458, "column": 76 }, "end": { - "line": 439, + "line": 458, "column": 77 } } @@ -89075,15 +93508,15 @@ "binop": null, "updateContext": null }, - "start": 13807, - "end": 13808, + "start": 14440, + "end": 14441, "loc": { "start": { - "line": 439, + "line": 458, "column": 77 }, "end": { - "line": 439, + "line": 458, "column": 78 } } @@ -89103,15 +93536,15 @@ "updateContext": null }, "value": "return", - "start": 13814, - "end": 13820, + "start": 14447, + "end": 14453, "loc": { "start": { - "line": 441, + "line": 460, "column": 4 }, "end": { - "line": 441, + "line": 460, "column": 10 } } @@ -89129,15 +93562,15 @@ "binop": null }, "value": "jsonld", - "start": 13821, - "end": 13827, + "start": 14454, + "end": 14460, "loc": { "start": { - "line": 441, + "line": 460, "column": 11 }, "end": { - "line": 441, + "line": 460, "column": 17 } } @@ -89155,15 +93588,15 @@ "binop": null, "updateContext": null }, - "start": 13827, - "end": 13828, + "start": 14460, + "end": 14461, "loc": { "start": { - "line": 441, + "line": 460, "column": 17 }, "end": { - "line": 441, + "line": 460, "column": 18 } } @@ -89180,15 +93613,15 @@ "postfix": false, "binop": null }, - "start": 13831, - "end": 13832, + "start": 14464, + "end": 14465, "loc": { "start": { - "line": 442, + "line": 461, "column": 2 }, "end": { - "line": 442, + "line": 461, "column": 3 } } @@ -89196,15 +93629,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxon name as an OWL equivalentClass expression.\n ", - "start": 13836, - "end": 13911, + "start": 14469, + "end": 14544, "loc": { "start": { - "line": 444, + "line": 463, "column": 2 }, "end": { - "line": 446, + "line": 465, "column": 5 } } @@ -89222,15 +93655,15 @@ "binop": null }, "value": "get", - "start": 13914, - "end": 13917, + "start": 14547, + "end": 14550, "loc": { "start": { - "line": 447, + "line": 466, "column": 2 }, "end": { - "line": 447, + "line": 466, "column": 5 } } @@ -89248,15 +93681,15 @@ "binop": null }, "value": "asOWLEquivClass", - "start": 13918, - "end": 13933, + "start": 14551, + "end": 14566, "loc": { "start": { - "line": 447, + "line": 466, "column": 6 }, "end": { - "line": 447, + "line": 466, "column": 21 } } @@ -89273,15 +93706,15 @@ "postfix": false, "binop": null }, - "start": 13933, - "end": 13934, + "start": 14566, + "end": 14567, "loc": { "start": { - "line": 447, + "line": 466, "column": 21 }, "end": { - "line": 447, + "line": 466, "column": 22 } } @@ -89298,15 +93731,15 @@ "postfix": false, "binop": null }, - "start": 13934, - "end": 13935, + "start": 14567, + "end": 14568, "loc": { "start": { - "line": 447, + "line": 466, "column": 22 }, "end": { - "line": 447, + "line": 466, "column": 23 } } @@ -89323,15 +93756,15 @@ "postfix": false, "binop": null }, - 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"line": 101, - "column": 31 - } - }, - "operator": "!", - "prefix": true, - "argument": { - "type": "CallExpression", - "start": 3283, - "end": 3305, - "loc": { - "start": { - "line": 101, - "column": 9 - }, - "end": { - "line": 101, - "column": 31 - } - }, - "callee": { - "type": "Identifier", - "start": 3283, - "end": 3286, - "loc": { - "start": { - "line": 101, - "column": 9 - }, - "end": { - "line": 101, - "column": 12 - }, - "identifierName": "has" - }, - "name": "has" - }, - "arguments": [ - { - "type": "MemberExpression", - "start": 3287, - "end": 3297, - "loc": { - "start": { - "line": 101, - "column": 13 - }, - "end": { - "line": 101, - "column": 23 - } - }, - "object": { - "type": "ThisExpression", - "start": 3287, - "end": 3291, - "loc": { - "start": { - "line": 101, - "column": 13 - }, - "end": { - "line": 101, - "column": 17 - } - } - }, - "property": { - "type": "Identifier", - "start": 3292, - "end": 3297, - "loc": { - "start": { - "line": 101, - "column": 18 - }, - "end": { - "line": 101, - "column": 23 - }, - "identifierName": "tunit" - }, - "name": "tunit" - }, - "computed": false - }, - { - "type": "StringLiteral", - "start": 3299, - "end": 3304, - "loc": { - "start": { - "line": 101, - "column": 25 - }, - "end": { - "line": 101, - "column": 30 - } - }, - "extra": { - "rawValue": "@id", - "raw": "'@id'" - }, - "value": "@id" - } - ] - }, - "extra": { - "parenthesizedArgument": false - } - }, - "consequent": { - "type": "ReturnStatement", - "start": 3307, - "end": 3317, - "loc": { - "start": { - "line": 101, - "column": 33 - }, - "end": { - "line": 101, - "column": 43 - } - }, - "argument": { - "type": "ArrayExpression", - "start": 3314, - "end": 3316, - "loc": { - "start": { - "line": 101, - "column": 40 - }, - "end": { - "line": 101, - "column": 42 - } - }, - "elements": [] - } - }, - "alternate": null - }, - { - "type": "IfStatement", - "start": 3322, - "end": 3379, - "loc": { - "start": { - "line": 102, - "column": 4 - }, - "end": { - "line": 102, - "column": 61 + "column": 65 } }, "test": { "type": "CallExpression", - "start": 3326, - "end": 3352, + "start": 3072, + "end": 3100, "loc": { "start": { - "line": 102, + "line": 93, "column": 8 }, "end": { - "line": 102, - "column": 34 + "line": 93, + "column": 36 } }, "callee": { "type": "Identifier", - "start": 3326, - "end": 3333, + "start": 3072, + "end": 3079, "loc": { "start": { - "line": 102, + "line": 93, "column": 8 }, "end": { - "line": 102, + "line": 93, "column": 15 }, "identifierName": "isArray" @@ -3602,58 +3006,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 3334, - "end": 3351, + "start": 3080, + "end": 3099, "loc": { "start": { - "line": 102, + "line": 93, "column": 16 }, "end": { - "line": 102, - "column": 33 + "line": 93, + "column": 35 } }, "object": { "type": "MemberExpression", - "start": 3334, - "end": 3344, + "start": 3080, + "end": 3090, "loc": { "start": { - "line": 102, + "line": 93, "column": 16 }, "end": { - "line": 102, + "line": 93, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 3334, - "end": 3338, + "start": 3080, + "end": 3084, "loc": { "start": { - "line": 102, + "line": 93, "column": 16 }, "end": { - "line": 102, + "line": 93, "column": 20 } } }, "property": { "type": "Identifier", - "start": 3339, - "end": 3344, + "start": 3085, + "end": 3090, "loc": { "start": { - "line": 102, + "line": 93, "column": 21 }, "end": { - "line": 102, + "line": 93, "column": 26 }, "identifierName": "tunit" @@ -3664,23 +3068,23 @@ }, "property": { "type": "StringLiteral", - "start": 3345, - "end": 3350, + "start": 3091, + "end": 3098, "loc": { "start": { - "line": 102, + "line": 93, "column": 27 }, "end": { - "line": 102, - "column": 32 + "line": 93, + "column": 34 } }, "extra": { - "rawValue": "@id", - "raw": "'@id'" + "rawValue": "@type", + "raw": "'@type'" }, - "value": "@id" + "value": "@type" }, "computed": true } @@ -3688,73 +3092,73 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3354, - "end": 3379, + "start": 3102, + "end": 3129, "loc": { "start": { - "line": 102, - "column": 36 + "line": 93, + "column": 38 }, "end": { - "line": 102, - "column": 61 + "line": 93, + "column": 65 } }, "argument": { "type": "MemberExpression", - "start": 3361, - "end": 3378, + "start": 3109, + "end": 3128, "loc": { "start": { - "line": 102, - "column": 43 + "line": 93, + "column": 45 }, "end": { - "line": 102, - "column": 60 + "line": 93, + "column": 64 } }, "object": { "type": "MemberExpression", - "start": 3361, - "end": 3371, + "start": 3109, + "end": 3119, "loc": { "start": { - "line": 102, - "column": 43 + "line": 93, + "column": 45 }, "end": { - "line": 102, - "column": 53 + "line": 93, + "column": 55 } }, "object": { "type": "ThisExpression", - "start": 3361, - "end": 3365, + "start": 3109, + "end": 3113, "loc": { "start": { - "line": 102, - "column": 43 + "line": 93, + "column": 45 }, "end": { - "line": 102, - "column": 47 + "line": 93, + "column": 49 } } }, "property": { "type": "Identifier", - "start": 3366, - "end": 3371, + "start": 3114, + "end": 3119, "loc": { "start": { - "line": 102, - "column": 48 + "line": 93, + "column": 50 }, "end": { - "line": 102, - "column": 53 + "line": 93, + "column": 55 }, "identifierName": "tunit" }, @@ -3764,23 +3168,23 @@ }, "property": { "type": "StringLiteral", - "start": 3372, - "end": 3377, + "start": 3120, + "end": 3127, "loc": { "start": { - "line": 102, - "column": 54 + "line": 93, + "column": 56 }, "end": { - "line": 102, - "column": 59 + "line": 93, + "column": 63 } }, "extra": { - "rawValue": "@id", - "raw": "'@id'" + "rawValue": "@type", + "raw": "'@type'" }, - "value": "@id" + "value": "@type" }, "computed": true } @@ -3789,87 +3193,87 @@ }, { "type": "ReturnStatement", - "start": 3384, - "end": 3411, + "start": 3134, + "end": 3163, "loc": { "start": { - "line": 103, + "line": 94, "column": 4 }, "end": { - "line": 103, - "column": 31 + "line": 94, + "column": 33 } }, "argument": { "type": "ArrayExpression", - "start": 3391, - "end": 3410, + "start": 3141, + "end": 3162, "loc": { "start": { - "line": 103, + "line": 94, "column": 11 }, "end": { - "line": 103, - "column": 30 + "line": 94, + "column": 32 } }, "elements": [ { "type": "MemberExpression", - "start": 3392, - "end": 3409, + "start": 3142, + "end": 3161, "loc": { "start": { - "line": 103, + "line": 94, "column": 12 }, "end": { - "line": 103, - "column": 29 + "line": 94, + "column": 31 } }, "object": { "type": "MemberExpression", - "start": 3392, - "end": 3402, + "start": 3142, + "end": 3152, "loc": { "start": { - "line": 103, + "line": 94, "column": 12 }, "end": { - "line": 103, + "line": 94, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3392, - "end": 3396, + "start": 3142, + "end": 3146, "loc": { "start": { - "line": 103, + "line": 94, "column": 12 }, "end": { - "line": 103, + "line": 94, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3397, - "end": 3402, + "start": 3147, + "end": 3152, "loc": { "start": { - "line": 103, + "line": 94, "column": 17 }, "end": { - "line": 103, + "line": 94, "column": 22 }, "identifierName": "tunit" @@ -3880,23 +3284,23 @@ }, "property": { "type": "StringLiteral", - "start": 3403, - "end": 3408, + "start": 3153, + "end": 3160, "loc": { "start": { - "line": 103, + "line": 94, "column": 23 }, "end": { - "line": 103, - "column": 28 + "line": 94, + "column": 30 } }, "extra": { - "rawValue": "@id", - "raw": "'@id'" + "rawValue": "@type", + "raw": "'@type'" }, - "value": "@id" + "value": "@type" }, "computed": true } @@ -3910,16 +3314,16 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n ", - "start": 3117, - "end": 3244, + "value": "*\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n ", + "start": 2804, + "end": 3001, "loc": { "start": { - "line": 96, + "line": 85, "column": 2 }, "end": { - "line": 99, + "line": 90, "column": 5 } } @@ -3928,16 +3332,16 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * Return the label of this taxonomic unit.\n ", - "start": 3419, - "end": 3474, + "value": "*\n * Return this taxonomic unit if it is a taxon concept.\n ", + "start": 3171, + "end": 3238, "loc": { "start": { - "line": 106, + "line": 97, "column": 2 }, "end": { - "line": 108, + "line": 99, "column": 5 } } @@ -3946,15 +3350,15 @@ }, { "type": "ClassMethod", - "start": 3477, - "end": 4317, + "start": 3241, + "end": 3376, "loc": { "start": { - "line": 109, + "line": 100, "column": 2 }, "end": { - "line": 135, + "line": 103, "column": 3 } }, @@ -3962,20 +3366,20 @@ "computed": false, "key": { "type": "Identifier", - 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110, + "column": 48 + }, + "identifierName": "TaxonomicUnitWrapper" + }, + "name": "TaxonomicUnitWrapper" + }, + "property": { + "type": "Identifier", + "start": 3556, + "end": 3569, + "loc": { + "start": { + "line": 110, + "column": 49 + }, + "end": { + "line": 110, + "column": 62 + }, + "identifierName": "TYPE_SPECIMEN" + }, + "name": "TYPE_SPECIMEN" + }, + "computed": false + } + ], + "leadingComments": null + }, + "consequent": { + "type": "ReturnStatement", + "start": 3572, + "end": 3590, + "loc": { + "start": { + "line": 110, "column": 65 }, "end": { - "line": 91, + "line": 110, "column": 83 } }, "argument": { "type": "MemberExpression", - "start": 3075, - "end": 3085, + "start": 3579, + "end": 3589, "loc": { "start": { - "line": 91, + "line": 110, "column": 72 }, "end": { - "line": 91, + "line": 110, "column": 82 } }, "object": { "type": "ThisExpression", - "start": 3075, - "end": 3079, + "start": 3579, + "end": 3583, "loc": { "start": { - "line": 91, + "line": 110, "column": 72 }, "end": { - "line": 91, + "line": 110, "column": 76 } } }, "property": { "type": "Identifier", - "start": 3080, - "end": 3085, + "start": 3584, + "end": 3589, "loc": { "start": { - "line": 91, + "line": 110, "column": 77 }, "end": { - "line": 91, + "line": 110, "column": 82 }, "identifierName": "tunit" @@ -13274,15 +14768,15 @@ { "type": "CommentLine", "value": " Only specimens have scientific names.", - "start": 2962, - "end": 3002, + "start": 3466, + "end": 3506, "loc": { "start": { - "line": 90, + "line": 109, "column": 4 }, "end": { - "line": 90, + "line": 109, "column": 44 } } @@ -13291,29 +14785,29 @@ }, { "type": "ReturnStatement", - "start": 3092, - "end": 3109, + "start": 3596, + "end": 3613, "loc": { "start": { - "line": 93, + "line": 112, "column": 4 }, "end": { - "line": 93, + "line": 112, "column": 21 } }, "argument": { "type": "Identifier", - "start": 3099, - "end": 3108, + "start": 3603, + "end": 3612, "loc": { "start": { - "line": 93, + "line": 112, "column": 11 }, "end": { - "line": 93, + "line": 112, "column": 20 }, "identifierName": "undefined" @@ -13329,15 +14823,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxonomic unit if it is a specimen.\n ", - "start": 2876, - "end": 2938, + "start": 3380, + "end": 3442, "loc": { "start": { - "line": 86, + "line": 105, "column": 2 }, "end": { - "line": 88, + "line": 107, "column": 5 } } @@ -13347,15 +14841,15 @@ { "type": "CommentBlock", "value": "*\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n ", - "start": 3117, - "end": 3244, + "start": 3621, + "end": 3748, "loc": { "start": { - "line": 96, + "line": 115, "column": 2 }, "end": { - "line": 99, + "line": 118, "column": 5 } } @@ -13364,15 +14858,15 @@ }, { "type": "ClassMethod", - "start": 3247, - "end": 3415, + "start": 3751, + "end": 3919, "loc": { "start": { - "line": 100, + "line": 119, "column": 2 }, "end": { - "line": 104, + "line": 123, "column": 3 } }, @@ -13380,15 +14874,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3251, - "end": 3269, + "start": 3755, + "end": 3773, "loc": { "start": { - "line": 100, + "line": 119, "column": 6 }, "end": { - "line": 100, + "line": 119, "column": 24 }, "identifierName": "externalReferences" @@ -13403,44 +14897,44 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3272, - "end": 3415, + "start": 3776, + "end": 3919, "loc": { "start": { - "line": 100, + "line": 119, "column": 27 }, "end": { - "line": 104, + "line": 123, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 3278, - "end": 3317, + "start": 3782, + "end": 3821, "loc": { "start": { - "line": 101, + "line": 120, "column": 4 }, "end": { - "line": 101, + "line": 120, "column": 43 } }, "test": { "type": "UnaryExpression", - "start": 3282, - "end": 3305, + "start": 3786, + "end": 3809, "loc": { "start": { - "line": 101, + "line": 120, "column": 8 }, "end": { - "line": 101, + "line": 120, "column": 31 } }, @@ -13448,29 +14942,29 @@ "prefix": true, "argument": { "type": "CallExpression", - "start": 3283, - "end": 3305, + "start": 3787, + "end": 3809, "loc": { "start": { - "line": 101, + "line": 120, "column": 9 }, "end": { - "line": 101, + "line": 120, "column": 31 } }, "callee": { "type": "Identifier", - "start": 3283, - "end": 3286, + "start": 3787, + "end": 3790, "loc": { "start": { - "line": 101, + "line": 120, "column": 9 }, "end": { - "line": 101, + "line": 120, "column": 12 }, "identifierName": "has" @@ -13480,44 +14974,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3287, - "end": 3297, + "start": 3791, + "end": 3801, "loc": { "start": { - "line": 101, + "line": 120, "column": 13 }, "end": { - "line": 101, + "line": 120, "column": 23 } }, "object": { "type": "ThisExpression", - "start": 3287, - "end": 3291, + "start": 3791, + "end": 3795, "loc": { "start": { - "line": 101, + "line": 120, "column": 13 }, "end": { - "line": 101, + "line": 120, "column": 17 } } }, "property": { "type": "Identifier", - "start": 3292, - "end": 3297, + "start": 3796, + "end": 3801, "loc": { "start": { - "line": 101, + "line": 120, "column": 18 }, "end": { - "line": 101, + "line": 120, "column": 23 }, "identifierName": "tunit" @@ -13528,15 +15022,15 @@ }, { "type": "StringLiteral", - "start": 3299, - "end": 3304, + "start": 3803, + "end": 3808, "loc": { "start": { - "line": 101, + "line": 120, "column": 25 }, "end": { - "line": 101, + "line": 120, "column": 30 } }, @@ -13554,29 +15048,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3307, - "end": 3317, + "start": 3811, + "end": 3821, "loc": { "start": { - "line": 101, + "line": 120, "column": 33 }, "end": { - "line": 101, + "line": 120, "column": 43 } }, "argument": { "type": "ArrayExpression", - "start": 3314, - "end": 3316, + "start": 3818, + "end": 3820, "loc": { "start": { - "line": 101, + "line": 120, "column": 40 }, "end": { - "line": 101, + "line": 120, "column": 42 } }, @@ -13587,43 +15081,43 @@ }, { "type": "IfStatement", - "start": 3322, - "end": 3379, + "start": 3826, + "end": 3883, "loc": { "start": { - "line": 102, + "line": 121, "column": 4 }, "end": { - "line": 102, + "line": 121, "column": 61 } }, "test": { "type": "CallExpression", - "start": 3326, - "end": 3352, + "start": 3830, + "end": 3856, "loc": { "start": { - "line": 102, + "line": 121, "column": 8 }, "end": { - "line": 102, + "line": 121, "column": 34 } }, "callee": { "type": "Identifier", - "start": 3326, - "end": 3333, + "start": 3830, + "end": 3837, "loc": { "start": { - "line": 102, + "line": 121, "column": 8 }, "end": { - "line": 102, + "line": 121, "column": 15 }, "identifierName": "isArray" @@ -13633,58 +15127,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 3334, - "end": 3351, + "start": 3838, + "end": 3855, "loc": { "start": { - "line": 102, + "line": 121, "column": 16 }, "end": { - "line": 102, + "line": 121, "column": 33 } }, "object": { "type": "MemberExpression", - "start": 3334, - "end": 3344, + "start": 3838, + "end": 3848, "loc": { "start": { - "line": 102, + "line": 121, "column": 16 }, "end": { - "line": 102, + "line": 121, "column": 26 } }, "object": { "type": "ThisExpression", - "start": 3334, - "end": 3338, + "start": 3838, + "end": 3842, "loc": { "start": { - "line": 102, + "line": 121, "column": 16 }, "end": { - "line": 102, + "line": 121, "column": 20 } } }, "property": { "type": "Identifier", - "start": 3339, - "end": 3344, + "start": 3843, + "end": 3848, "loc": { "start": { - "line": 102, + "line": 121, "column": 21 }, "end": { - "line": 102, + "line": 121, "column": 26 }, "identifierName": "tunit" @@ -13695,15 +15189,15 @@ }, "property": { "type": "StringLiteral", - "start": 3345, - "end": 3350, + "start": 3849, + "end": 3854, "loc": { "start": { - "line": 102, + "line": 121, "column": 27 }, "end": { - "line": 102, + "line": 121, "column": 32 } }, @@ -13719,72 +15213,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3354, - "end": 3379, + "start": 3858, + "end": 3883, "loc": { "start": { - "line": 102, + "line": 121, "column": 36 }, "end": { - "line": 102, + "line": 121, "column": 61 } }, "argument": { "type": "MemberExpression", - "start": 3361, - "end": 3378, + "start": 3865, + "end": 3882, "loc": { "start": { - "line": 102, + "line": 121, "column": 43 }, "end": { - "line": 102, + "line": 121, "column": 60 } }, "object": { "type": "MemberExpression", - "start": 3361, - "end": 3371, + "start": 3865, + "end": 3875, "loc": { "start": { - "line": 102, + "line": 121, "column": 43 }, "end": { - "line": 102, + "line": 121, "column": 53 } }, "object": { "type": "ThisExpression", - "start": 3361, - "end": 3365, + "start": 3865, + "end": 3869, "loc": { "start": { - "line": 102, + "line": 121, "column": 43 }, "end": { - "line": 102, + "line": 121, "column": 47 } } }, "property": { "type": "Identifier", - "start": 3366, - "end": 3371, + "start": 3870, + "end": 3875, "loc": { "start": { - "line": 102, + "line": 121, "column": 48 }, "end": { - "line": 102, + "line": 121, "column": 53 }, "identifierName": "tunit" @@ -13795,15 +15289,15 @@ }, "property": { "type": "StringLiteral", - "start": 3372, - "end": 3377, + "start": 3876, + "end": 3881, "loc": { "start": { - "line": 102, + "line": 121, "column": 54 }, "end": { - "line": 102, + "line": 121, "column": 59 } }, @@ -13820,87 +15314,87 @@ }, { "type": "ReturnStatement", - "start": 3384, - "end": 3411, + "start": 3888, + "end": 3915, "loc": { "start": { - "line": 103, + "line": 122, "column": 4 }, "end": { - "line": 103, + "line": 122, "column": 31 } }, "argument": { "type": "ArrayExpression", - "start": 3391, - "end": 3410, + "start": 3895, + "end": 3914, "loc": { "start": { - "line": 103, + "line": 122, "column": 11 }, "end": { - "line": 103, + "line": 122, "column": 30 } }, "elements": [ { "type": "MemberExpression", - "start": 3392, - "end": 3409, + "start": 3896, + "end": 3913, "loc": { "start": { - "line": 103, + "line": 122, "column": 12 }, "end": { - "line": 103, + "line": 122, "column": 29 } }, "object": { "type": "MemberExpression", - "start": 3392, - "end": 3402, + "start": 3896, + "end": 3906, "loc": { "start": { - "line": 103, + "line": 122, "column": 12 }, "end": { - "line": 103, + "line": 122, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3392, - "end": 3396, + "start": 3896, + "end": 3900, "loc": { "start": { - "line": 103, + "line": 122, "column": 12 }, "end": { - "line": 103, + "line": 122, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3397, - "end": 3402, + "start": 3901, + "end": 3906, "loc": { "start": { - "line": 103, + "line": 122, "column": 17 }, "end": { - "line": 103, + "line": 122, "column": 22 }, "identifierName": "tunit" @@ -13911,15 +15405,15 @@ }, "property": { "type": "StringLiteral", - "start": 3403, - "end": 3408, + "start": 3907, + "end": 3912, "loc": { "start": { - "line": 103, + "line": 122, "column": 23 }, "end": { - "line": 103, + "line": 122, "column": 28 } }, @@ -13942,15 +15436,15 @@ { "type": "CommentBlock", "value": "*\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n ", - "start": 3117, - "end": 3244, + "start": 3621, + "end": 3748, "loc": { "start": { - "line": 96, + "line": 115, "column": 2 }, "end": { - "line": 99, + "line": 118, "column": 5 } } @@ -13960,15 +15454,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this taxonomic unit.\n ", - "start": 3419, - "end": 3474, + "start": 3923, + "end": 3978, "loc": { "start": { - "line": 106, + "line": 125, "column": 2 }, "end": { - "line": 108, + "line": 127, "column": 5 } } @@ -13977,15 +15471,15 @@ }, { "type": "ClassMethod", - "start": 3477, - "end": 4317, + "start": 3981, + "end": 4821, "loc": { "start": { - "line": 109, + "line": 128, "column": 2 }, "end": { - "line": 135, + "line": 154, "column": 3 } }, @@ -13993,15 +15487,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 3481, - "end": 3486, + "start": 3985, + "end": 3990, "loc": { "start": { - "line": 109, + "line": 128, "column": 6 }, "end": { - "line": 109, + "line": 128, "column": 11 }, "identifierName": "label" @@ -14016,58 +15510,58 @@ "params": [], "body": { "type": "BlockStatement", - "start": 3489, - "end": 4317, + "start": 3993, + "end": 4821, "loc": { "start": { - "line": 109, + "line": 128, "column": 14 }, "end": { - "line": 135, + "line": 154, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 3538, - "end": 3592, + "start": 4042, + "end": 4096, "loc": { "start": { - "line": 111, + "line": 130, "column": 4 }, "end": { - "line": 111, + "line": 130, "column": 58 } }, "test": { "type": "CallExpression", - "start": 3542, - "end": 3566, + "start": 4046, + "end": 4070, "loc": { "start": { - "line": 111, + "line": 130, "column": 8 }, "end": { - "line": 111, + "line": 130, "column": 32 } }, "callee": { "type": "Identifier", - "start": 3542, - "end": 3545, + "start": 4046, + "end": 4049, "loc": { "start": { - "line": 111, + "line": 130, "column": 8 }, "end": { - "line": 111, + "line": 130, "column": 11 }, "identifierName": "has" @@ -14078,44 +15572,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3546, - "end": 3556, + "start": 4050, + "end": 4060, "loc": { "start": { - "line": 111, + "line": 130, "column": 12 }, "end": { - "line": 111, + "line": 130, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3546, - "end": 3550, + "start": 4050, + "end": 4054, "loc": { "start": { - "line": 111, + "line": 130, "column": 12 }, "end": { - "line": 111, + "line": 130, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3551, - "end": 3556, + "start": 4055, + "end": 4060, "loc": { "start": { - "line": 111, + "line": 130, "column": 17 }, "end": { - "line": 111, + "line": 130, "column": 22 }, "identifierName": "tunit" @@ -14126,15 +15620,15 @@ }, { "type": "StringLiteral", - "start": 3558, - "end": 3565, + "start": 4062, + "end": 4069, "loc": { "start": { - "line": 111, + "line": 130, "column": 24 }, "end": { - "line": 111, + "line": 130, "column": 31 } }, @@ -14149,72 +15643,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3568, - "end": 3592, + "start": 4072, + "end": 4096, "loc": { "start": { - "line": 111, + "line": 130, "column": 34 }, "end": { - "line": 111, + "line": 130, "column": 58 } }, "argument": { "type": "MemberExpression", - "start": 3575, - "end": 3591, + "start": 4079, + "end": 4095, "loc": { "start": { - "line": 111, + "line": 130, "column": 41 }, "end": { - "line": 111, + "line": 130, "column": 57 } }, "object": { "type": "MemberExpression", - "start": 3575, - "end": 3585, + "start": 4079, + "end": 4089, "loc": { "start": { - "line": 111, + "line": 130, "column": 41 }, "end": { - "line": 111, + "line": 130, "column": 51 } }, "object": { "type": "ThisExpression", - "start": 3575, - "end": 3579, + "start": 4079, + "end": 4083, "loc": { "start": { - "line": 111, + "line": 130, "column": 41 }, "end": { - "line": 111, + "line": 130, "column": 45 } } }, "property": { "type": "Identifier", - "start": 3580, - "end": 3585, + "start": 4084, + "end": 4089, "loc": { "start": { - "line": 111, + "line": 130, "column": 46 }, "end": { - "line": 111, + "line": 130, "column": 51 }, "identifierName": "tunit" @@ -14225,15 +15719,15 @@ }, "property": { "type": "Identifier", - "start": 3586, - "end": 3591, + "start": 4090, + "end": 4095, "loc": { "start": { - "line": 111, + "line": 130, "column": 52 }, "end": { - "line": 111, + "line": 130, "column": 57 }, "identifierName": "label" @@ -14248,15 +15742,15 @@ { "type": "CommentLine", "value": " A label or description for this TU?", - "start": 3495, - "end": 3533, + "start": 3999, + "end": 4037, "loc": { "start": { - "line": 110, + "line": 129, "column": 4 }, "end": { - "line": 110, + "line": 129, "column": 42 } } @@ -14265,43 +15759,43 @@ }, { "type": "IfStatement", - "start": 3597, - "end": 3663, + "start": 4101, + "end": 4167, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 70 } }, "test": { "type": "CallExpression", - "start": 3601, - "end": 3631, + "start": 4105, + "end": 4135, "loc": { "start": { - "line": 112, + "line": 131, "column": 8 }, "end": { - "line": 112, + "line": 131, "column": 38 } }, "callee": { "type": "Identifier", - "start": 3601, - "end": 3604, + "start": 4105, + "end": 4108, "loc": { "start": { - "line": 112, + "line": 131, "column": 8 }, "end": { - "line": 112, + "line": 131, "column": 11 }, "identifierName": "has" @@ -14311,44 +15805,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3605, - "end": 3615, + "start": 4109, + "end": 4119, "loc": { "start": { - "line": 112, + "line": 131, "column": 12 }, "end": { - "line": 112, + "line": 131, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 3605, - "end": 3609, + "start": 4109, + "end": 4113, "loc": { "start": { - "line": 112, + "line": 131, "column": 12 }, "end": { - "line": 112, + "line": 131, "column": 16 } } }, "property": { "type": "Identifier", - "start": 3610, - "end": 3615, + "start": 4114, + "end": 4119, "loc": { "start": { - "line": 112, + "line": 131, "column": 17 }, "end": { - "line": 112, + "line": 131, "column": 22 }, "identifierName": "tunit" @@ -14359,15 +15853,15 @@ }, { "type": "StringLiteral", - "start": 3617, - "end": 3630, + "start": 4121, + "end": 4134, "loc": { "start": { - "line": 112, + "line": 131, "column": 24 }, "end": { - "line": 112, + "line": 131, "column": 37 } }, @@ -14381,72 +15875,72 @@ }, "consequent": { "type": "ReturnStatement", - "start": 3633, - "end": 3663, + "start": 4137, + "end": 4167, "loc": { "start": { - "line": 112, + "line": 131, "column": 40 }, "end": { - "line": 112, + "line": 131, "column": 70 } }, "argument": { "type": "MemberExpression", - "start": 3640, - "end": 3662, + "start": 4144, + "end": 4166, "loc": { "start": { - "line": 112, + "line": 131, "column": 47 }, "end": { - "line": 112, + "line": 131, "column": 69 } }, "object": { "type": "MemberExpression", - "start": 3640, - "end": 3650, + "start": 4144, + "end": 4154, "loc": { "start": { - "line": 112, + "line": 131, "column": 47 }, "end": { - "line": 112, + "line": 131, "column": 57 } }, "object": { "type": "ThisExpression", - "start": 3640, - "end": 3644, + "start": 4144, + "end": 4148, "loc": { "start": { - "line": 112, + "line": 131, "column": 47 }, "end": { - "line": 112, + "line": 131, "column": 51 } } }, "property": { "type": "Identifier", - "start": 3645, - "end": 3650, + "start": 4149, + "end": 4154, "loc": { "start": { - "line": 112, + "line": 131, "column": 52 }, "end": { - "line": 112, + "line": 131, "column": 57 }, "identifierName": "tunit" @@ -14457,15 +15951,15 @@ }, "property": { "type": "Identifier", - "start": 3651, - "end": 3662, + "start": 4155, + "end": 4166, "loc": { "start": { - "line": 112, + "line": 131, "column": 58 }, "end": { - "line": 112, + "line": 131, "column": 69 }, "identifierName": "description" @@ -14481,15 +15975,15 @@ { "type": "CommentLine", "value": " Is this a specimen?", - "start": 3669, - "end": 3691, + "start": 4173, + "end": 4195, "loc": { "start": { - "line": 114, + "line": 133, "column": 4 }, "end": { - "line": 114, + "line": 133, "column": 26 } } @@ -14498,43 +15992,43 @@ }, { "type": "IfStatement", - "start": 3696, - "end": 3777, + "start": 4200, + "end": 4281, "loc": { "start": { - "line": 115, + "line": 134, "column": 4 }, "end": { - "line": 117, + "line": 136, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 3700, - "end": 3713, + "start": 4204, + "end": 4217, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 21 } }, "object": { "type": "ThisExpression", - "start": 3700, - "end": 3704, + "start": 4204, + "end": 4208, "loc": { "start": { - "line": 115, + "line": 134, "column": 8 }, "end": { - "line": 115, + "line": 134, "column": 12 } }, @@ -14542,15 +16036,15 @@ }, "property": { "type": "Identifier", - "start": 3705, - "end": 3713, + "start": 4209, + "end": 4217, "loc": { "start": { - "line": 115, + "line": 134, "column": 13 }, "end": { - "line": 115, + "line": 134, "column": 21 }, "identifierName": "specimen" @@ -14562,72 +16056,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 3715, - "end": 3777, + "start": 4219, + "end": 4281, "loc": { "start": { - "line": 115, + "line": 134, "column": 23 }, "end": { - "line": 117, + "line": 136, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 3723, - "end": 3771, + "start": 4227, + "end": 4275, "loc": { "start": { - "line": 116, + "line": 135, "column": 6 }, "end": { - "line": 116, + "line": 135, "column": 54 } }, "argument": { "type": "MemberExpression", - "start": 3730, - "end": 3770, + "start": 4234, + "end": 4274, "loc": { "start": { - "line": 116, + "line": 135, "column": 13 }, "end": { - "line": 116, + "line": 135, "column": 53 } }, "object": { "type": "NewExpression", - "start": 3730, - "end": 3764, + "start": 4234, + "end": 4268, "loc": { "start": { - "line": 116, + "line": 135, "column": 13 }, "end": { - "line": 116, + "line": 135, "column": 47 } }, "callee": { "type": "Identifier", - "start": 3734, - "end": 3749, + "start": 4238, + "end": 4253, "loc": { "start": { - "line": 116, + "line": 135, "column": 17 }, "end": { - "line": 116, + "line": 135, "column": 32 }, "identifierName": "SpecimenWrapper" @@ -14637,44 +16131,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3750, - "end": 3763, + "start": 4254, + "end": 4267, "loc": { "start": { - "line": 116, + "line": 135, "column": 33 }, "end": { - "line": 116, + "line": 135, "column": 46 } }, "object": { "type": "ThisExpression", - "start": 3750, - "end": 3754, + "start": 4254, + "end": 4258, "loc": { "start": { - "line": 116, + "line": 135, "column": 33 }, "end": { - "line": 116, + "line": 135, "column": 37 } } }, "property": { "type": "Identifier", - "start": 3755, - "end": 3763, + "start": 4259, + "end": 4267, "loc": { "start": { - "line": 116, + "line": 135, "column": 38 }, "end": { - "line": 116, + "line": 135, "column": 46 }, "identifierName": "specimen" @@ -14687,15 +16181,15 @@ }, "property": { "type": "Identifier", - "start": 3765, - "end": 3770, + "start": 4269, + "end": 4274, "loc": { "start": { - "line": 116, + "line": 135, "column": 48 }, "end": { - "line": 116, + "line": 135, "column": 53 }, "identifierName": "label" @@ -14714,15 +16208,15 @@ { "type": "CommentLine", "value": " Is this a specimen?", - "start": 3669, - "end": 3691, + "start": 4173, + "end": 4195, "loc": { "start": { - "line": 114, + "line": 133, "column": 4 }, "end": { - "line": 114, + "line": 133, "column": 26 } } @@ -14732,15 +16226,15 @@ { "type": "CommentLine", "value": " Is this a taxon concept?", - "start": 3783, - "end": 3810, + "start": 4287, + "end": 4314, "loc": { "start": { - "line": 119, + "line": 138, "column": 4 }, "end": { - "line": 119, + "line": 138, "column": 31 } } @@ -14749,43 +16243,43 @@ }, { "type": "IfStatement", - "start": 3815, - "end": 3908, + "start": 4319, + "end": 4412, "loc": { "start": { - "line": 120, + "line": 139, "column": 4 }, "end": { - "line": 122, + "line": 141, "column": 5 } }, "test": { "type": "MemberExpression", - "start": 3819, - "end": 3836, + "start": 4323, + "end": 4340, "loc": { "start": { - "line": 120, + "line": 139, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 25 } }, "object": { "type": "ThisExpression", - "start": 3819, - "end": 3823, + "start": 4323, + "end": 4327, "loc": { "start": { - "line": 120, + "line": 139, "column": 8 }, "end": { - "line": 120, + "line": 139, "column": 12 } }, @@ -14793,15 +16287,15 @@ }, "property": { "type": "Identifier", - "start": 3824, - "end": 3836, + "start": 4328, + "end": 4340, "loc": { "start": { - "line": 120, + "line": 139, "column": 13 }, "end": { - "line": 120, + "line": 139, "column": 25 }, "identifierName": "taxonConcept" @@ -14813,72 +16307,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 3838, - "end": 3908, + "start": 4342, + "end": 4412, "loc": { "start": { - "line": 120, + "line": 139, "column": 27 }, "end": { - "line": 122, + "line": 141, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 3846, - "end": 3902, + "start": 4350, + "end": 4406, "loc": { "start": { - "line": 121, + "line": 140, "column": 6 }, "end": { - "line": 121, + "line": 140, "column": 62 } }, "argument": { "type": "MemberExpression", - "start": 3853, - "end": 3901, + "start": 4357, + "end": 4405, "loc": { "start": { - "line": 121, + "line": 140, "column": 13 }, "end": { - "line": 121, + "line": 140, "column": 61 } }, "object": { "type": "NewExpression", - "start": 3853, - "end": 3895, + "start": 4357, + "end": 4399, "loc": { "start": { - "line": 121, + "line": 140, "column": 13 }, "end": { - "line": 121, + "line": 140, "column": 55 } }, "callee": { "type": "Identifier", - "start": 3857, - "end": 3876, + "start": 4361, + "end": 4380, "loc": { "start": { - "line": 121, + "line": 140, "column": 17 }, "end": { - "line": 121, + "line": 140, "column": 36 }, "identifierName": "TaxonConceptWrapper" @@ -14888,44 +16382,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 3877, - "end": 3894, + "start": 4381, + "end": 4398, "loc": { "start": { - "line": 121, + "line": 140, "column": 37 }, "end": { - "line": 121, + "line": 140, "column": 54 } }, "object": { "type": "ThisExpression", - "start": 3877, - "end": 3881, + "start": 4381, + "end": 4385, "loc": { "start": { - "line": 121, + "line": 140, "column": 37 }, "end": { - "line": 121, + "line": 140, "column": 41 } } }, "property": { "type": "Identifier", - "start": 3882, - "end": 3894, + "start": 4386, + "end": 4398, "loc": { "start": { - "line": 121, + "line": 140, "column": 42 }, "end": { - "line": 121, + "line": 140, "column": 54 }, "identifierName": "taxonConcept" @@ -14938,15 +16432,15 @@ }, "property": { "type": "Identifier", - "start": 3896, - "end": 3901, + "start": 4400, + "end": 4405, "loc": { "start": { - "line": 121, + "line": 140, "column": 56 }, "end": { - "line": 121, + "line": 140, "column": 61 }, "identifierName": "label" @@ -14965,15 +16459,15 @@ { "type": "CommentLine", "value": " Is this a taxon concept?", - "start": 3783, - "end": 3810, + "start": 4287, + "end": 4314, "loc": { "start": { - "line": 119, + "line": 138, "column": 4 }, "end": { - "line": 119, + "line": 138, "column": 31 } } @@ -14983,15 +16477,15 @@ { "type": "CommentLine", "value": " If its neither a specimen nor a taxon concept, just list the", - "start": 3914, - "end": 3977, + "start": 4418, + "end": 4481, "loc": { "start": { - "line": 124, + "line": 143, "column": 4 }, "end": { - "line": 124, + "line": 143, "column": 67 } } @@ -14999,15 +16493,15 @@ { "type": "CommentLine", "value": " external references.", - "start": 3982, - "end": 4005, + "start": 4486, + "end": 4509, "loc": { "start": { - "line": 125, + "line": 144, "column": 4 }, "end": { - "line": 125, + "line": 144, "column": 27 } } @@ -15016,44 +16510,44 @@ }, { "type": "VariableDeclaration", - "start": 4010, - "end": 4061, + "start": 4514, + "end": 4565, "loc": { "start": { - "line": 126, + "line": 145, "column": 4 }, "end": { - "line": 126, + "line": 145, "column": 55 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 4016, - "end": 4060, + "start": 4520, + "end": 4564, "loc": { "start": { - "line": 126, + "line": 145, "column": 10 }, "end": { - "line": 126, + "line": 145, "column": 54 } }, "id": { "type": "Identifier", - "start": 4016, - "end": 4034, + "start": 4520, + "end": 4538, "loc": { "start": { - "line": 126, + "line": 145, "column": 10 }, "end": { - "line": 126, + "line": 145, "column": 28 }, "identifierName": "externalReferences" @@ -15063,44 +16557,44 @@ }, "init": { "type": "MemberExpression", - "start": 4037, - "end": 4060, + "start": 4541, + "end": 4564, "loc": { "start": { - "line": 126, + "line": 145, "column": 31 }, "end": { - "line": 126, + "line": 145, "column": 54 } }, "object": { "type": "ThisExpression", - "start": 4037, - "end": 4041, + "start": 4541, + "end": 4545, "loc": { "start": { - "line": 126, + "line": 145, "column": 31 }, "end": { - "line": 126, + "line": 145, "column": 35 } } }, "property": { "type": "Identifier", - "start": 4042, - "end": 4060, + "start": 4546, + "end": 4564, "loc": { "start": { - "line": 126, + "line": 145, "column": 36 }, "end": { - "line": 126, + "line": 145, "column": 54 }, "identifierName": "externalReferences" @@ -15117,15 +16611,15 @@ { "type": "CommentLine", "value": " If its neither a specimen nor a taxon concept, just list the", - "start": 3914, - "end": 3977, + "start": 4418, + "end": 4481, "loc": { "start": { - "line": 124, + "line": 143, "column": 4 }, "end": { - "line": 124, + "line": 143, "column": 67 } } @@ -15133,15 +16627,15 @@ { "type": "CommentLine", "value": " external references.", - "start": 3982, - "end": 4005, + "start": 4486, + "end": 4509, "loc": { "start": { - "line": 125, + "line": 144, "column": 4 }, "end": { - "line": 125, + "line": 144, "column": 27 } } @@ -15150,57 +16644,57 @@ }, { "type": "IfStatement", - "start": 4066, - "end": 4212, + "start": 4570, + "end": 4716, "loc": { "start": { - "line": 127, + "line": 146, "column": 4 }, "end": { - "line": 131, + "line": 150, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 4070, - "end": 4099, + "start": 4574, + "end": 4603, "loc": { "start": { - "line": 127, + "line": 146, "column": 8 }, "end": { - "line": 127, + "line": 146, "column": 37 } }, "left": { "type": "MemberExpression", - "start": 4070, - "end": 4095, + "start": 4574, + "end": 4599, "loc": { "start": { - "line": 127, + "line": 146, "column": 8 }, "end": { - "line": 127, + "line": 146, "column": 33 } }, "object": { "type": "Identifier", - "start": 4070, - "end": 4088, + "start": 4574, + "end": 4592, "loc": { "start": { - "line": 127, + "line": 146, "column": 8 }, "end": { - "line": 127, + "line": 146, "column": 26 }, "identifierName": "externalReferences" @@ -15209,15 +16703,15 @@ }, "property": { "type": "Identifier", - "start": 4089, - "end": 4095, + "start": 4593, + "end": 4599, "loc": { "start": { - "line": 127, + "line": 146, "column": 27 }, "end": { - "line": 127, + "line": 146, "column": 33 }, "identifierName": "length" @@ -15229,15 +16723,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 4098, - "end": 4099, + "start": 4602, + "end": 4603, "loc": { "start": { - "line": 127, + "line": 146, "column": 36 }, "end": { - "line": 127, + "line": 146, "column": 37 } }, @@ -15250,100 +16744,100 @@ }, "consequent": { "type": "BlockStatement", - "start": 4101, - "end": 4212, + "start": 4605, + "end": 4716, "loc": { "start": { - "line": 127, + "line": 146, "column": 39 }, "end": { - "line": 131, + "line": 150, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 4109, - "end": 4206, + "start": 4613, + "end": 4710, "loc": { "start": { - "line": 128, + "line": 147, "column": 6 }, "end": { - "line": 130, + "line": 149, "column": 23 } }, "argument": { "type": "CallExpression", - "start": 4116, - "end": 4205, + "start": 4620, + "end": 4709, "loc": { "start": { - "line": 128, + "line": 147, "column": 13 }, "end": { - "line": 130, + "line": 149, "column": 22 } }, "callee": { "type": "MemberExpression", - "start": 4116, - "end": 4196, + "start": 4620, + "end": 4700, "loc": { "start": { - "line": 128, + "line": 147, "column": 13 }, "end": { - "line": 130, + "line": 149, "column": 13 } }, "object": { "type": "CallExpression", - "start": 4116, - "end": 4182, + "start": 4620, + "end": 4686, "loc": { "start": { - "line": 128, + "line": 147, "column": 13 }, "end": { - "line": 129, + "line": 148, "column": 47 } }, "callee": { "type": "MemberExpression", - "start": 4116, - "end": 4147, + "start": 4620, + "end": 4651, "loc": { "start": { - "line": 128, + "line": 147, "column": 13 }, "end": { - "line": 129, + "line": 148, "column": 12 } }, "object": { "type": "Identifier", - "start": 4116, - "end": 4134, + "start": 4620, + "end": 4638, "loc": { "start": { - "line": 128, + "line": 147, "column": 13 }, "end": { - "line": 128, + "line": 147, "column": 31 }, "identifierName": "externalReferences" @@ -15352,15 +16846,15 @@ }, "property": { "type": "Identifier", - "start": 4144, - "end": 4147, + "start": 4648, + "end": 4651, "loc": { "start": { - "line": 129, + "line": 148, "column": 9 }, "end": { - "line": 129, + "line": 148, "column": 12 }, "identifierName": "map" @@ -15372,15 +16866,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 4148, - "end": 4181, + "start": 4652, + "end": 4685, "loc": { "start": { - "line": 129, + "line": 148, "column": 13 }, "end": { - "line": 129, + "line": 148, "column": 46 } }, @@ -15391,15 +16885,15 @@ "params": [ { "type": "Identifier", - "start": 4148, - "end": 4159, + "start": 4652, + "end": 4663, "loc": { "start": { - "line": 129, + "line": 148, "column": 13 }, "end": { - "line": 129, + "line": 148, "column": 24 }, "identifierName": "externalRef" @@ -15409,30 +16903,30 @@ ], "body": { "type": "TemplateLiteral", - "start": 4163, - "end": 4181, + "start": 4667, + "end": 4685, "loc": { "start": { - "line": 129, + "line": 148, "column": 28 }, "end": { - "line": 129, + "line": 148, "column": 46 } }, "expressions": [ { "type": "Identifier", - "start": 4167, - "end": 4178, + "start": 4671, + "end": 4682, "loc": { "start": { - "line": 129, + "line": 148, "column": 32 }, "end": { - "line": 129, + "line": 148, "column": 43 }, "identifierName": "externalRef" @@ -15443,15 +16937,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 4164, - "end": 4165, + "start": 4668, + "end": 4669, "loc": { "start": { - "line": 129, + "line": 148, "column": 29 }, "end": { - "line": 129, + "line": 148, "column": 30 } }, @@ -15463,15 +16957,15 @@ }, { "type": "TemplateElement", - "start": 4179, - "end": 4180, + "start": 4683, + "end": 4684, "loc": { "start": { - "line": 129, + "line": 148, "column": 44 }, "end": { - "line": 129, + "line": 148, "column": 45 } }, @@ -15488,15 +16982,15 @@ }, "property": { "type": "Identifier", - "start": 4192, - "end": 4196, + "start": 4696, + "end": 4700, "loc": { "start": { - "line": 130, + "line": 149, "column": 9 }, "end": { - "line": 130, + "line": 149, "column": 13 }, "identifierName": "join" @@ -15508,15 +17002,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 4197, - "end": 4204, + "start": 4701, + "end": 4708, "loc": { "start": { - "line": 130, + "line": 149, "column": 14 }, "end": { - "line": 130, + "line": 149, "column": 21 } }, @@ -15538,15 +17032,15 @@ { "type": "CommentLine", "value": " If we don't have any properties of a taxonomic unit, return undefined.", - "start": 4218, - "end": 4291, + "start": 4722, + "end": 4795, "loc": { "start": { - "line": 133, + "line": 152, "column": 4 }, "end": { - "line": 133, + "line": 152, "column": 77 } } @@ -15555,29 +17049,29 @@ }, { "type": "ReturnStatement", - "start": 4296, - "end": 4313, + "start": 4800, + "end": 4817, "loc": { "start": { - "line": 134, + "line": 153, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 21 } }, "argument": { "type": "Identifier", - "start": 4303, - "end": 4312, + "start": 4807, + "end": 4816, "loc": { "start": { - "line": 134, + "line": 153, "column": 11 }, "end": { - "line": 134, + "line": 153, "column": 20 }, "identifierName": "undefined" @@ -15589,15 +17083,15 @@ { "type": "CommentLine", "value": " If we don't have any properties of a taxonomic unit, return undefined.", - "start": 4218, - "end": 4291, + "start": 4722, + "end": 4795, "loc": { "start": { - "line": 133, + "line": 152, "column": 4 }, "end": { - "line": 133, + "line": 152, "column": 77 } } @@ -15612,15 +17106,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this taxonomic unit.\n ", - "start": 3419, - "end": 3474, + "start": 3923, + "end": 3978, "loc": { "start": { - "line": 106, + "line": 125, "column": 2 }, "end": { - "line": 108, + "line": 127, "column": 5 } } @@ -15630,15 +17124,15 @@ { "type": "CommentBlock", "value": "*\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n ", - "start": 4321, - "end": 4562, + "start": 4825, + "end": 5066, "loc": { "start": { - "line": 137, + "line": 156, "column": 2 }, "end": { - "line": 142, + "line": 161, "column": 5 } } @@ -15647,15 +17141,15 @@ }, { "type": "ClassMethod", - "start": 4565, - "end": 6726, + "start": 5069, + "end": 7230, "loc": { "start": { - "line": 143, + "line": 162, "column": 2 }, "end": { - "line": 203, + "line": 222, "column": 3 } }, @@ -15663,15 +17157,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 4572, - "end": 4581, + "start": 5076, + "end": 5085, "loc": { "start": { - "line": 143, + "line": 162, "column": 9 }, "end": { - "line": 143, + "line": 162, "column": 18 }, "identifierName": "fromLabel" @@ -15686,15 +17180,15 @@ "params": [ { "type": "Identifier", - "start": 4582, - "end": 4591, + "start": 5086, + "end": 5095, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 28 }, "identifierName": "nodeLabel" @@ -15703,29 +17197,29 @@ }, { "type": "AssignmentPattern", - "start": 4593, - "end": 4634, + "start": 5097, + "end": 5138, "loc": { "start": { - "line": 143, + "line": 162, "column": 30 }, "end": { - "line": 143, + "line": 162, "column": 71 } }, "left": { "type": "Identifier", - "start": 4593, - "end": 4602, + "start": 5097, + "end": 5106, "loc": { "start": { - "line": 143, + "line": 162, "column": 30 }, "end": { - "line": 143, + "line": 162, "column": 39 }, "identifierName": "nomenCode" @@ -15734,29 +17228,29 @@ }, "right": { "type": "MemberExpression", - "start": 4605, - "end": 4634, + "start": 5109, + "end": 5138, "loc": { "start": { - "line": 143, + "line": 162, "column": 42 }, "end": { - "line": 143, + "line": 162, "column": 71 } }, "object": { "type": "Identifier", - "start": 4605, - "end": 4613, + "start": 5109, + "end": 5117, "loc": { "start": { - "line": 143, + "line": 162, "column": 42 }, "end": { - "line": 143, + "line": 162, "column": 50 }, "identifierName": "owlterms" @@ -15765,15 +17259,15 @@ }, "property": { "type": "Identifier", - "start": 4614, - "end": 4634, + "start": 5118, + "end": 5138, "loc": { "start": { - "line": 143, + "line": 162, "column": 51 }, "end": { - "line": 143, + "line": 162, "column": 71 }, "identifierName": "NAME_IN_UNKNOWN_CODE" @@ -15786,86 +17280,86 @@ ], "body": { "type": "BlockStatement", - "start": 4636, - "end": 6726, + "start": 5140, + "end": 7230, "loc": { "start": { - "line": 143, + "line": 162, "column": 73 }, "end": { - "line": 203, + "line": 222, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 4642, - "end": 4737, + "start": 5146, + "end": 5241, "loc": { "start": { - "line": 144, + "line": 163, "column": 4 }, "end": { - "line": 144, + "line": 163, "column": 99 } }, "test": { "type": "LogicalExpression", - "start": 4646, - "end": 4718, + "start": 5150, + "end": 5222, "loc": { "start": { - "line": 144, + "line": 163, "column": 8 }, "end": { - "line": 144, + "line": 163, "column": 80 } }, "left": { "type": "LogicalExpression", - "start": 4646, - "end": 4691, + "start": 5150, + "end": 5195, "loc": { "start": { - "line": 144, + "line": 163, "column": 8 }, "end": { - "line": 144, + "line": 163, "column": 53 } }, "left": { "type": "BinaryExpression", - "start": 4646, - "end": 4669, + "start": 5150, + "end": 5173, "loc": { "start": { - "line": 144, + "line": 163, "column": 8 }, "end": { - "line": 144, + "line": 163, "column": 31 } }, "left": { "type": "Identifier", - "start": 4646, - "end": 4655, + "start": 5150, + "end": 5159, "loc": { "start": { - "line": 144, + "line": 163, "column": 8 }, "end": { - "line": 144, + "line": 163, "column": 17 }, "identifierName": "nodeLabel" @@ -15875,15 +17369,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 4660, - "end": 4669, + "start": 5164, + "end": 5173, "loc": { "start": { - "line": 144, + "line": 163, "column": 22 }, "end": { - "line": 144, + "line": 163, "column": 31 }, "identifierName": "undefined" @@ -15894,29 +17388,29 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 4673, - "end": 4691, + "start": 5177, + "end": 5195, "loc": { "start": { - "line": 144, + "line": 163, "column": 35 }, "end": { - "line": 144, + "line": 163, "column": 53 } }, "left": { "type": "Identifier", - "start": 4673, - "end": 4682, + "start": 5177, + "end": 5186, "loc": { "start": { - "line": 144, + "line": 163, "column": 35 }, "end": { - "line": 144, + "line": 163, "column": 44 }, "identifierName": "nodeLabel" @@ -15926,15 +17420,15 @@ "operator": "===", "right": { "type": "NullLiteral", - "start": 4687, - "end": 4691, + "start": 5191, + "end": 5195, "loc": { "start": { - "line": 144, + "line": 163, "column": 49 }, "end": { - "line": 144, + "line": 163, "column": 53 } } @@ -15944,57 +17438,57 @@ "operator": "||", "right": { "type": "BinaryExpression", - "start": 4695, - "end": 4718, + "start": 5199, + "end": 5222, "loc": { "start": { - "line": 144, + "line": 163, "column": 57 }, "end": { - "line": 144, + "line": 163, "column": 80 } }, "left": { "type": "CallExpression", - "start": 4695, - "end": 4711, + "start": 5199, + "end": 5215, "loc": { "start": { - "line": 144, + "line": 163, "column": 57 }, "end": { - "line": 144, + "line": 163, "column": 73 } }, "callee": { "type": "MemberExpression", - "start": 4695, - "end": 4709, + "start": 5199, + "end": 5213, "loc": { "start": { - "line": 144, + "line": 163, "column": 57 }, "end": { - "line": 144, + "line": 163, "column": 71 } }, "object": { "type": "Identifier", - "start": 4695, - "end": 4704, + "start": 5199, + "end": 5208, "loc": { "start": { - "line": 144, + "line": 163, "column": 57 }, "end": { - "line": 144, + "line": 163, "column": 66 }, "identifierName": "nodeLabel" @@ -16003,15 +17497,15 @@ }, "property": { "type": "Identifier", - "start": 4705, - "end": 4709, + "start": 5209, + "end": 5213, "loc": { "start": { - "line": 144, + "line": 163, "column": 67 }, "end": { - "line": 144, + "line": 163, "column": 71 }, "identifierName": "trim" @@ -16025,15 +17519,15 @@ "operator": "===", "right": { "type": "StringLiteral", - "start": 4716, - "end": 4718, + "start": 5220, + "end": 5222, "loc": { "start": { - "line": 144, + "line": 163, "column": 78 }, "end": { - "line": 144, + "line": 163, "column": 80 } }, @@ -16047,29 +17541,29 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4720, - "end": 4737, + "start": 5224, + "end": 5241, "loc": { "start": { - "line": 144, + "line": 163, "column": 82 }, "end": { - "line": 144, + "line": 163, "column": 99 } }, "argument": { "type": "Identifier", - "start": 4727, - "end": 4736, + "start": 5231, + "end": 5240, "loc": { "start": { - "line": 144, + "line": 163, "column": 89 }, "end": { - "line": 144, + "line": 163, "column": 98 }, "identifierName": "undefined" @@ -16083,15 +17577,15 @@ { "type": "CommentLine", "value": " Rather than figuring out with this label, check to see if we've parsed", - "start": 4743, - "end": 4816, + "start": 5247, + "end": 5320, "loc": { "start": { - "line": 146, + "line": 165, "column": 4 }, "end": { - "line": 146, + "line": 165, "column": 77 } } @@ -16099,15 +17593,15 @@ { "type": "CommentLine", "value": " this before.", - "start": 4821, - "end": 4836, + "start": 5325, + "end": 5340, "loc": { "start": { - "line": 147, + "line": 166, "column": 4 }, "end": { - "line": 147, + "line": 166, "column": 19 } } @@ -16116,57 +17610,57 @@ }, { "type": "IfStatement", - "start": 4841, - "end": 5071, + "start": 5345, + "end": 5575, "loc": { "start": { - "line": 148, + "line": 167, "column": 4 }, "end": { - "line": 150, + "line": 169, "column": 5 } }, "test": { "type": "CallExpression", - "start": 4845, - "end": 4946, + "start": 5349, + "end": 5450, "loc": { "start": { - "line": 148, + "line": 167, "column": 8 }, "end": { - "line": 148, + "line": 167, "column": 109 } }, "callee": { "type": "MemberExpression", - "start": 4845, - "end": 4865, + "start": 5349, + "end": 5369, "loc": { "start": { - "line": 148, + "line": 167, "column": 8 }, "end": { - "line": 148, + "line": 167, "column": 28 } }, "object": { "type": "Identifier", - "start": 4845, - "end": 4861, + "start": 5349, + "end": 5365, "loc": { "start": { - "line": 148, + "line": 167, "column": 8 }, "end": { - "line": 148, + "line": 167, "column": 24 }, "identifierName": "PhyxCacheManager" @@ -16176,15 +17670,15 @@ }, "property": { "type": "Identifier", - "start": 4862, - "end": 4865, + "start": 5366, + "end": 5369, "loc": { "start": { - "line": 148, + "line": 167, "column": 25 }, "end": { - "line": 148, + "line": 167, "column": 28 }, "identifierName": "has" @@ -16197,30 +17691,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 4866, - "end": 4934, + "start": 5370, + "end": 5438, "loc": { "start": { - "line": 148, + "line": 167, "column": 29 }, "end": { - "line": 148, + "line": 167, "column": 97 } }, "expressions": [ { "type": "Identifier", - "start": 4923, - "end": 4932, + "start": 5427, + "end": 5436, "loc": { "start": { - "line": 148, + "line": 167, "column": 86 }, "end": { - "line": 148, + "line": 167, "column": 95 }, "identifierName": "nomenCode" @@ -16231,15 +17725,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 4867, - "end": 4921, + "start": 5371, + "end": 5425, "loc": { "start": { - "line": 148, + "line": 167, "column": 30 }, "end": { - "line": 148, + "line": 167, "column": 84 } }, @@ -16251,15 +17745,15 @@ }, { "type": "TemplateElement", - "start": 4933, - "end": 4933, + "start": 5437, + "end": 5437, "loc": { "start": { - "line": 148, + "line": 167, "column": 96 }, "end": { - "line": 148, + "line": 167, "column": 96 } }, @@ -16273,15 +17767,15 @@ }, { "type": "Identifier", - "start": 4936, - "end": 4945, + "start": 5440, + "end": 5449, "loc": { "start": { - "line": 148, + "line": 167, "column": 99 }, "end": { - "line": 148, + "line": 167, "column": 108 }, "identifierName": "nodeLabel" @@ -16293,72 +17787,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 4948, - "end": 5071, + "start": 5452, + "end": 5575, "loc": { "start": { - "line": 148, + "line": 167, "column": 111 }, "end": { - "line": 150, + "line": 169, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 4956, - "end": 5065, + "start": 5460, + "end": 5569, "loc": { "start": { - "line": 149, + "line": 168, "column": 6 }, "end": { - "line": 149, + "line": 168, "column": 115 } }, "argument": { "type": "CallExpression", - "start": 4963, - "end": 5064, + "start": 5467, + "end": 5568, "loc": { "start": { - "line": 149, + "line": 168, "column": 13 }, "end": { - "line": 149, + "line": 168, "column": 114 } }, "callee": { "type": "MemberExpression", - "start": 4963, - "end": 4983, + "start": 5467, + "end": 5487, "loc": { "start": { - "line": 149, + "line": 168, "column": 13 }, "end": { - "line": 149, + "line": 168, "column": 33 } }, "object": { "type": "Identifier", - "start": 4963, - "end": 4979, + "start": 5467, + "end": 5483, "loc": { "start": { - "line": 149, + "line": 168, "column": 13 }, "end": { - "line": 149, + "line": 168, "column": 29 }, "identifierName": "PhyxCacheManager" @@ -16367,15 +17861,15 @@ }, "property": { "type": "Identifier", - "start": 4980, - "end": 4983, + "start": 5484, + "end": 5487, "loc": { "start": { - "line": 149, + "line": 168, "column": 30 }, "end": { - "line": 149, + "line": 168, "column": 33 }, "identifierName": "get" @@ -16387,30 +17881,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 4984, - "end": 5052, + "start": 5488, + "end": 5556, "loc": { "start": { - "line": 149, + "line": 168, "column": 34 }, "end": { - "line": 149, + "line": 168, "column": 102 } }, "expressions": [ { "type": "Identifier", - "start": 5041, - "end": 5050, + "start": 5545, + "end": 5554, "loc": { "start": { - "line": 149, + "line": 168, "column": 91 }, "end": { - "line": 149, + "line": 168, "column": 100 }, "identifierName": "nomenCode" @@ -16421,15 +17915,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 4985, - "end": 5039, + "start": 5489, + "end": 5543, "loc": { "start": { - "line": 149, + "line": 168, "column": 35 }, "end": { - "line": 149, + "line": 168, "column": 89 } }, @@ -16441,15 +17935,15 @@ }, { "type": "TemplateElement", - "start": 5051, - "end": 5051, + "start": 5555, + "end": 5555, "loc": { "start": { - "line": 149, + "line": 168, "column": 101 }, "end": { - "line": 149, + "line": 168, "column": 101 } }, @@ -16463,15 +17957,15 @@ }, { "type": "Identifier", - "start": 5054, - "end": 5063, + "start": 5558, + "end": 5567, "loc": { "start": { - "line": 149, + "line": 168, "column": 104 }, "end": { - "line": 149, + "line": 168, "column": 113 }, "identifierName": "nodeLabel" @@ -16490,15 +17984,15 @@ { "type": "CommentLine", "value": " Rather than figuring out with this label, check to see if we've parsed", - "start": 4743, - "end": 4816, + "start": 5247, + "end": 5320, "loc": { "start": { - "line": 146, + "line": 165, "column": 4 }, "end": { - "line": 146, + "line": 165, "column": 77 } } @@ -16506,15 +18000,15 @@ { "type": "CommentLine", "value": " this before.", - "start": 4821, - "end": 4836, + "start": 5325, + "end": 5340, "loc": { "start": { - "line": 147, + "line": 166, "column": 4 }, "end": { - "line": 147, + "line": 166, "column": 19 } } @@ -16524,15 +18018,15 @@ { "type": "CommentLine", "value": " Look for taxon concept.", - "start": 5077, - "end": 5103, + "start": 5581, + "end": 5607, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 30 } } @@ -16541,44 +18035,44 @@ }, { "type": "VariableDeclaration", - "start": 5108, - "end": 5181, + "start": 5612, + "end": 5685, "loc": { "start": { - "line": 153, + "line": 172, "column": 4 }, "end": { - "line": 153, + "line": 172, "column": 77 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5114, - "end": 5180, + "start": 5618, + "end": 5684, "loc": { "start": { - "line": 153, + "line": 172, "column": 10 }, "end": { - "line": 153, + "line": 172, "column": 76 } }, "id": { "type": "Identifier", - "start": 5114, - "end": 5126, + "start": 5618, + "end": 5630, "loc": { "start": { - "line": 153, + "line": 172, "column": 10 }, "end": { - "line": 153, + "line": 172, "column": 22 }, "identifierName": "taxonConcept" @@ -16588,43 +18082,43 @@ }, "init": { "type": "CallExpression", - "start": 5129, - "end": 5180, + "start": 5633, + "end": 5684, "loc": { "start": { - "line": 153, + "line": 172, "column": 25 }, "end": { - "line": 153, + "line": 172, "column": 76 } }, "callee": { "type": "MemberExpression", - "start": 5129, - "end": 5158, + "start": 5633, + "end": 5662, "loc": { "start": { - "line": 153, + "line": 172, "column": 25 }, "end": { - "line": 153, + "line": 172, "column": 54 } }, "object": { "type": "Identifier", - "start": 5129, - "end": 5148, + "start": 5633, + "end": 5652, "loc": { "start": { - "line": 153, + "line": 172, "column": 25 }, "end": { - "line": 153, + "line": 172, "column": 44 }, "identifierName": "TaxonConceptWrapper" @@ -16633,15 +18127,15 @@ }, "property": { "type": "Identifier", - "start": 5149, - "end": 5158, + "start": 5653, + "end": 5662, "loc": { "start": { - "line": 153, + "line": 172, "column": 45 }, "end": { - "line": 153, + "line": 172, "column": 54 }, "identifierName": "fromLabel" @@ -16653,15 +18147,15 @@ "arguments": [ { "type": "Identifier", - "start": 5159, - "end": 5168, + "start": 5663, + "end": 5672, "loc": { "start": { - "line": 153, + "line": 172, "column": 55 }, "end": { - "line": 153, + "line": 172, "column": 64 }, "identifierName": "nodeLabel" @@ -16670,15 +18164,15 @@ }, { "type": "Identifier", - "start": 5170, - "end": 5179, + "start": 5674, + "end": 5683, "loc": { "start": { - "line": 153, + "line": 172, "column": 66 }, "end": { - "line": 153, + "line": 172, "column": 75 }, "identifierName": "nomenCode" @@ -16695,15 +18189,15 @@ { "type": "CommentLine", "value": " Look for taxon concept.", - "start": 5077, - "end": 5103, + "start": 5581, + "end": 5607, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 30 } } @@ -16713,15 +18207,15 @@ { "type": "CommentLine", "value": " Look for specimen information.", - "start": 5187, - "end": 5220, + "start": 5691, + "end": 5724, "loc": { "start": { - "line": 155, + "line": 174, "column": 4 }, "end": { - "line": 155, + "line": 174, "column": 37 } } @@ -16730,44 +18224,44 @@ }, { "type": "VariableDeclaration", - "start": 5225, - "end": 5238, + "start": 5729, + "end": 5742, "loc": { "start": { - "line": 156, + "line": 175, "column": 4 }, "end": { - "line": 156, + "line": 175, "column": 17 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5229, - "end": 5237, + "start": 5733, + "end": 5741, "loc": { "start": { - "line": 156, + "line": 175, "column": 8 }, "end": { - "line": 156, + "line": 175, "column": 16 } }, "id": { "type": "Identifier", - "start": 5229, - "end": 5237, + "start": 5733, + "end": 5741, "loc": { "start": { - "line": 156, + "line": 175, "column": 8 }, "end": { - "line": 156, + "line": 175, "column": 16 }, "identifierName": "specimen" @@ -16784,15 +18278,15 @@ { "type": "CommentLine", "value": " Look for specimen information.", - "start": 5187, - "end": 5220, + "start": 5691, + "end": 5724, "loc": { "start": { - "line": 155, + "line": 174, "column": 4 }, "end": { - "line": 155, + "line": 174, "column": 37 } } @@ -16801,85 +18295,85 @@ }, { "type": "IfStatement", - "start": 5243, - "end": 5429, + "start": 5747, + "end": 5933, "loc": { "start": { - "line": 157, + "line": 176, "column": 4 }, "end": { - "line": 160, + "line": 179, "column": 5 } }, "test": { "type": "CallExpression", - "start": 5247, - "end": 5294, + "start": 5751, + "end": 5798, "loc": { "start": { - "line": 157, + "line": 176, "column": 8 }, "end": { - "line": 157, + "line": 176, "column": 55 } }, "callee": { "type": "MemberExpression", - "start": 5247, - "end": 5281, + "start": 5751, + "end": 5785, "loc": { "start": { - "line": 157, + "line": 176, "column": 8 }, "end": { - "line": 157, + "line": 176, "column": 42 } }, "object": { "type": "CallExpression", - "start": 5247, - "end": 5270, + "start": 5751, + "end": 5774, "loc": { "start": { - "line": 157, + "line": 176, "column": 8 }, "end": { - "line": 157, + "line": 176, "column": 31 } }, "callee": { "type": "MemberExpression", - "start": 5247, - "end": 5268, + "start": 5751, + "end": 5772, "loc": { "start": { - "line": 157, + "line": 176, "column": 8 }, "end": { - "line": 157, + "line": 176, "column": 29 } }, "object": { "type": "Identifier", - "start": 5247, - "end": 5256, + "start": 5751, + "end": 5760, "loc": { "start": { - "line": 157, + "line": 176, "column": 8 }, "end": { - "line": 157, + "line": 176, "column": 17 }, "identifierName": "nodeLabel" @@ -16888,15 +18382,15 @@ }, "property": { "type": "Identifier", - "start": 5257, - "end": 5268, + "start": 5761, + "end": 5772, "loc": { "start": { - "line": 157, + "line": 176, "column": 18 }, "end": { - "line": 157, + "line": 176, "column": 29 }, "identifierName": "toLowerCase" @@ -16909,15 +18403,15 @@ }, "property": { "type": "Identifier", - "start": 5271, - "end": 5281, + "start": 5775, + "end": 5785, "loc": { "start": { - "line": 157, + "line": 176, "column": 32 }, "end": { - "line": 157, + "line": 176, "column": 42 }, "identifierName": "startsWith" @@ -16929,15 +18423,15 @@ "arguments": [ { "type": "StringLiteral", - "start": 5282, - "end": 5293, + "start": 5786, + "end": 5797, "loc": { "start": { - "line": 157, + "line": 176, "column": 43 }, "end": { - "line": 157, + "line": 176, "column": 54 } }, @@ -16951,59 +18445,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5296, - "end": 5429, + "start": 5800, + "end": 5933, "loc": { "start": { - "line": 157, + "line": 176, "column": 57 }, "end": { - "line": 160, + "line": 179, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 5358, - "end": 5423, + "start": 5862, + "end": 5927, "loc": { "start": { - "line": 159, + "line": 178, "column": 6 }, "end": { - "line": 159, + "line": 178, "column": 71 } }, "expression": { "type": "AssignmentExpression", - "start": 5358, - "end": 5422, + "start": 5862, + "end": 5926, "loc": { "start": { - "line": 159, + "line": 178, "column": 6 }, "end": { - "line": 159, + "line": 178, "column": 70 } }, "operator": "=", "left": { "type": "Identifier", - "start": 5358, - "end": 5366, + "start": 5862, + "end": 5870, "loc": { "start": { - "line": 159, + "line": 178, "column": 6 }, "end": { - "line": 159, + "line": 178, "column": 14 }, "identifierName": "specimen" @@ -17013,43 +18507,43 @@ }, "right": { "type": "CallExpression", - "start": 5369, - "end": 5422, + "start": 5873, + "end": 5926, "loc": { "start": { - "line": 159, + "line": 178, "column": 17 }, "end": { - "line": 159, + "line": 178, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 5369, - "end": 5401, + "start": 5873, + "end": 5905, "loc": { "start": { - "line": 159, + "line": 178, "column": 17 }, "end": { - "line": 159, + "line": 178, "column": 49 } }, "object": { "type": "Identifier", - "start": 5369, - "end": 5384, + "start": 5873, + "end": 5888, "loc": { "start": { - "line": 159, + "line": 178, "column": 17 }, "end": { - "line": 159, + "line": 178, "column": 32 }, "identifierName": "SpecimenWrapper" @@ -17058,15 +18552,15 @@ }, "property": { "type": "Identifier", - "start": 5385, - "end": 5401, + "start": 5889, + "end": 5905, "loc": { "start": { - "line": 159, + "line": 178, "column": 33 }, "end": { - "line": 159, + "line": 178, "column": 49 }, "identifierName": "fromOccurrenceID" @@ -17078,43 +18572,43 @@ "arguments": [ { "type": "CallExpression", - "start": 5402, - "end": 5421, + "start": 5906, + "end": 5925, "loc": { "start": { - "line": 159, + "line": 178, "column": 50 }, "end": { - "line": 159, + "line": 178, "column": 69 } }, "callee": { "type": "MemberExpression", - "start": 5402, - "end": 5418, + "start": 5906, + "end": 5922, "loc": { "start": { - "line": 159, + "line": 178, "column": 50 }, "end": { - "line": 159, + "line": 178, "column": 66 } }, "object": { "type": "Identifier", - "start": 5402, - "end": 5411, + "start": 5906, + "end": 5915, "loc": { "start": { - "line": 159, + "line": 178, "column": 50 }, "end": { - "line": 159, + "line": 178, "column": 59 }, "identifierName": "nodeLabel" @@ -17123,15 +18617,15 @@ }, "property": { "type": "Identifier", - "start": 5412, - "end": 5418, + "start": 5916, + "end": 5922, "loc": { "start": { - "line": 159, + "line": 178, "column": 60 }, "end": { - "line": 159, + "line": 178, "column": 66 }, "identifierName": "substr" @@ -17143,15 +18637,15 @@ "arguments": [ { "type": "NumericLiteral", - "start": 5419, - "end": 5420, + "start": 5923, + "end": 5924, "loc": { "start": { - "line": 159, + "line": 178, "column": 67 }, "end": { - "line": 159, + "line": 178, "column": 68 } }, @@ -17171,15 +18665,15 @@ { "type": "CommentLine", "value": " Eliminate a 'Specimen ' prefix if it exists.", - "start": 5304, - "end": 5351, + "start": 5808, + "end": 5855, "loc": { "start": { - "line": 158, + "line": 177, "column": 6 }, "end": { - "line": 158, + "line": 177, "column": 53 } } @@ -17193,44 +18687,44 @@ }, { "type": "VariableDeclaration", - "start": 5435, - "end": 5445, + "start": 5939, + "end": 5949, "loc": { "start": { - "line": 162, + "line": 181, "column": 4 }, "end": { - "line": 162, + "line": 181, "column": 14 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 5439, - "end": 5444, + "start": 5943, + "end": 5948, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 13 } }, "id": { "type": "Identifier", - "start": 5439, - "end": 5444, + "start": 5943, + "end": 5948, "loc": { "start": { - "line": 162, + "line": 181, "column": 8 }, "end": { - "line": 162, + "line": 181, "column": 13 }, "identifierName": "tunit" @@ -17244,43 +18738,43 @@ }, { "type": "IfStatement", - "start": 5450, - "end": 5827, + "start": 5954, + "end": 6331, "loc": { "start": { - "line": 163, + "line": 182, "column": 4 }, "end": { - "line": 173, + "line": 192, "column": 5 } }, "test": { "type": "LogicalExpression", - "start": 5454, - "end": 5478, + "start": 5958, + "end": 5982, "loc": { "start": { - "line": 163, + "line": 182, "column": 8 }, "end": { - "line": 163, + "line": 182, "column": 32 } }, "left": { "type": "Identifier", - "start": 5454, - "end": 5466, + "start": 5958, + "end": 5970, "loc": { "start": { - "line": 163, + "line": 182, "column": 8 }, "end": { - "line": 163, + "line": 182, "column": 20 }, "identifierName": "taxonConcept" @@ -17290,15 +18784,15 @@ "operator": "&&", "right": { "type": "Identifier", - "start": 5470, - "end": 5478, + "start": 5974, + "end": 5982, "loc": { "start": { - "line": 163, + "line": 182, "column": 24 }, "end": { - "line": 163, + "line": 182, "column": 32 }, "identifierName": "specimen" @@ -17308,59 +18802,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5480, - "end": 5717, + "start": 5984, + "end": 6221, "loc": { "start": { - "line": 163, + "line": 182, "column": 34 }, "end": { - "line": 169, + "line": 188, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 5608, - "end": 5651, + "start": 6112, + "end": 6155, "loc": { "start": { - "line": 166, + "line": 185, "column": 6 }, "end": { - "line": 166, + "line": 185, "column": 49 } }, "expression": { "type": "AssignmentExpression", - "start": 5608, - "end": 5650, + "start": 6112, + "end": 6154, "loc": { "start": { - "line": 166, + "line": 185, "column": 6 }, "end": { - "line": 166, + "line": 185, "column": 48 } }, "operator": "=", "left": { "type": "Identifier", - "start": 5608, - "end": 5613, + "start": 6112, + "end": 6117, "loc": { "start": { - "line": 166, + "line": 185, "column": 6 }, "end": { - "line": 166, + "line": 185, "column": 11 }, "identifierName": "tunit" @@ -17370,29 +18864,29 @@ }, "right": { "type": "CallExpression", - "start": 5616, - "end": 5650, + "start": 6120, + "end": 6154, "loc": { "start": { - "line": 166, + "line": 185, "column": 14 }, "end": { - "line": 166, + "line": 185, "column": 48 } }, "callee": { "type": "Identifier", - "start": 5616, - "end": 5622, + "start": 6120, + "end": 6126, "loc": { "start": { - "line": 166, + "line": 185, "column": 14 }, "end": { - "line": 166, + "line": 185, "column": 20 }, "identifierName": "assign" @@ -17402,15 +18896,15 @@ "arguments": [ { "type": "ObjectExpression", - "start": 5623, - "end": 5625, + "start": 6127, + "end": 6129, "loc": { "start": { - "line": 166, + "line": 185, "column": 21 }, "end": { - "line": 166, + "line": 185, "column": 23 } }, @@ -17418,15 +18912,15 @@ }, { "type": "Identifier", - "start": 5627, - "end": 5639, + "start": 6131, + "end": 6143, "loc": { "start": { - "line": 166, + "line": 185, "column": 25 }, "end": { - "line": 166, + "line": 185, "column": 37 }, "identifierName": "taxonConcept" @@ -17435,15 +18929,15 @@ }, { "type": "Identifier", - "start": 5641, - "end": 5649, + "start": 6145, + "end": 6153, "loc": { "start": { - "line": 166, + "line": 185, "column": 39 }, "end": { - "line": 166, + "line": 185, "column": 47 }, "identifierName": "specimen" @@ -17458,15 +18952,15 @@ { "type": "CommentLine", "value": " If we have both, then treat it as a specimen that has been identified", - "start": 5488, - "end": 5560, + "start": 5992, + "end": 6064, "loc": { "start": { - "line": 164, + "line": 183, "column": 6 }, "end": { - "line": 164, + "line": 183, "column": 78 } } @@ -17474,15 +18968,15 @@ { "type": "CommentLine", "value": " to a particular taxonomic name.", - "start": 5567, - "end": 5601, + "start": 6071, + "end": 6105, "loc": { "start": { - "line": 165, + "line": 184, "column": 6 }, "end": { - "line": 165, + "line": 184, "column": 40 } } @@ -17491,58 +18985,58 @@ }, { "type": "ExpressionStatement", - "start": 5659, - "end": 5711, + "start": 6163, + "end": 6215, "loc": { "start": { - "line": 168, + "line": 187, "column": 6 }, "end": { - "line": 168, + "line": 187, "column": 58 } }, "expression": { "type": "AssignmentExpression", - "start": 5659, - "end": 5710, + "start": 6163, + "end": 6214, "loc": { "start": { - "line": 168, + "line": 187, "column": 6 }, "end": { - "line": 168, + "line": 187, "column": 57 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 5659, - "end": 5673, + "start": 6163, + "end": 6177, "loc": { "start": { - "line": 168, + "line": 187, "column": 6 }, "end": { - "line": 168, + "line": 187, "column": 20 } }, "object": { "type": "Identifier", - "start": 5659, - "end": 5664, + "start": 6163, + "end": 6168, "loc": { "start": { - "line": 168, + "line": 187, "column": 6 }, "end": { - "line": 168, + "line": 187, "column": 11 }, "identifierName": "tunit" @@ -17551,15 +19045,15 @@ }, "property": { "type": "StringLiteral", - "start": 5665, - "end": 5672, + "start": 6169, + "end": 6176, "loc": { "start": { - "line": 168, + "line": 187, "column": 12 }, "end": { - "line": 168, + "line": 187, "column": 19 } }, @@ -17573,29 +19067,29 @@ }, "right": { "type": "MemberExpression", - "start": 5676, - "end": 5710, + "start": 6180, + "end": 6214, "loc": { "start": { - "line": 168, + "line": 187, "column": 23 }, "end": { - "line": 168, + "line": 187, "column": 57 } }, "object": { "type": "Identifier", - "start": 5676, - "end": 5696, + "start": 6180, + "end": 6200, "loc": { "start": { - "line": 168, + "line": 187, "column": 23 }, "end": { - "line": 168, + "line": 187, "column": 43 }, "identifierName": "TaxonomicUnitWrapper" @@ -17604,15 +19098,15 @@ }, "property": { "type": "Identifier", - "start": 5697, - "end": 5710, + "start": 6201, + "end": 6214, "loc": { "start": { - "line": 168, + "line": 187, "column": 44 }, "end": { - "line": 168, + "line": 187, "column": 57 }, "identifierName": "TYPE_SPECIMEN" @@ -17628,29 +19122,29 @@ }, "alternate": { "type": "IfStatement", - "start": 5723, - "end": 5827, + "start": 6227, + "end": 6331, "loc": { "start": { - "line": 169, + "line": 188, "column": 11 }, "end": { - "line": 173, + "line": 192, "column": 5 } }, "test": { "type": "Identifier", - "start": 5727, - "end": 5739, + "start": 6231, + "end": 6243, "loc": { "start": { - "line": 169, + "line": 188, "column": 15 }, "end": { - "line": 169, + "line": 188, "column": 27 }, "identifierName": "taxonConcept" @@ -17659,59 +19153,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5741, - "end": 5776, + "start": 6245, + "end": 6280, "loc": { "start": { - "line": 169, + "line": 188, "column": 29 }, "end": { - "line": 171, + "line": 190, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 5749, - "end": 5770, + "start": 6253, + "end": 6274, "loc": { "start": { - "line": 170, + "line": 189, "column": 6 }, "end": { - "line": 170, + "line": 189, "column": 27 } }, "expression": { "type": "AssignmentExpression", - "start": 5749, - "end": 5769, + "start": 6253, + "end": 6273, "loc": { "start": { - "line": 170, + "line": 189, "column": 6 }, "end": { - "line": 170, + "line": 189, "column": 26 } }, "operator": "=", "left": { "type": "Identifier", - "start": 5749, - "end": 5754, + "start": 6253, + "end": 6258, "loc": { "start": { - "line": 170, + "line": 189, "column": 6 }, "end": { - "line": 170, + "line": 189, "column": 11 }, "identifierName": "tunit" @@ -17720,15 +19214,15 @@ }, "right": { "type": "Identifier", - "start": 5757, - "end": 5769, + "start": 6261, + "end": 6273, "loc": { "start": { - "line": 170, + "line": 189, "column": 14 }, "end": { - "line": 170, + "line": 189, "column": 26 }, "identifierName": "taxonConcept" @@ -17742,29 +19236,29 @@ }, "alternate": { "type": "IfStatement", - "start": 5782, - "end": 5827, + "start": 6286, + "end": 6331, "loc": { "start": { - "line": 171, + "line": 190, "column": 11 }, "end": { - "line": 173, + "line": 192, "column": 5 } }, "test": { "type": "Identifier", - "start": 5786, - "end": 5794, + "start": 6290, + "end": 6298, "loc": { "start": { - "line": 171, + "line": 190, "column": 15 }, "end": { - "line": 171, + "line": 190, "column": 23 }, "identifierName": "specimen" @@ -17773,59 +19267,59 @@ }, "consequent": { "type": "BlockStatement", - "start": 5796, - "end": 5827, + "start": 6300, + "end": 6331, "loc": { "start": { - "line": 171, + "line": 190, "column": 25 }, "end": { - "line": 173, + "line": 192, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 5804, - "end": 5821, + "start": 6308, + "end": 6325, "loc": { "start": { - "line": 172, + "line": 191, "column": 6 }, "end": { - "line": 172, + "line": 191, "column": 23 } }, "expression": { "type": "AssignmentExpression", - "start": 5804, - "end": 5820, + "start": 6308, + "end": 6324, "loc": { "start": { - "line": 172, + "line": 191, "column": 6 }, "end": { - "line": 172, + "line": 191, "column": 22 } }, "operator": "=", "left": { "type": "Identifier", - "start": 5804, - "end": 5809, + "start": 6308, + "end": 6313, "loc": { "start": { - "line": 172, + "line": 191, "column": 6 }, "end": { - "line": 172, + "line": 191, "column": 11 }, "identifierName": "tunit" @@ -17834,15 +19328,15 @@ }, "right": { "type": "Identifier", - "start": 5812, - "end": 5820, + "start": 6316, + "end": 6324, "loc": { "start": { - "line": 172, + "line": 191, "column": 14 }, "end": { - "line": 172, + "line": 191, "column": 22 }, "identifierName": "specimen" @@ -17864,15 +19358,15 @@ { "type": "CommentLine", "value": " Look for external references. For now, we only check to see if the entire", - "start": 5833, - "end": 5909, + "start": 6337, + "end": 6413, "loc": { "start": { - "line": 175, + "line": 194, "column": 4 }, "end": { - "line": 175, + "line": 194, "column": 80 } } @@ -17880,15 +19374,15 @@ { "type": "CommentLine", "value": " nodeLabel starts with URL/URNs, but we should eventually just look for", - "start": 5914, - "end": 5987, + "start": 6418, + "end": 6491, "loc": { "start": { - "line": 176, + "line": 195, "column": 4 }, "end": { - "line": 176, + "line": 195, "column": 77 } } @@ -17896,15 +19390,15 @@ { "type": "CommentLine", "value": " them inside the label.", - "start": 5992, - "end": 6017, + "start": 6496, + "end": 6521, "loc": { "start": { - "line": 177, + "line": 196, "column": 4 }, "end": { - "line": 177, + "line": 196, "column": 29 } } @@ -17913,44 +19407,44 @@ }, { "type": "VariableDeclaration", - "start": 6022, - "end": 6154, + "start": 6526, + "end": 6658, "loc": { "start": { - "line": 178, + "line": 197, "column": 4 }, "end": { - "line": 185, + "line": 204, "column": 6 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6028, - "end": 6153, + "start": 6532, + "end": 6657, "loc": { "start": { - "line": 178, + "line": 197, "column": 10 }, "end": { - "line": 185, + "line": 204, "column": 5 } }, "id": { "type": "Identifier", - "start": 6028, - "end": 6044, + "start": 6532, + "end": 6548, "loc": { "start": { - "line": 178, + "line": 197, "column": 10 }, "end": { - "line": 178, + "line": 197, "column": 26 }, "identifierName": "URL_URN_PREFIXES" @@ -17960,30 +19454,30 @@ }, "init": { "type": "ArrayExpression", - "start": 6047, - "end": 6153, + "start": 6551, + "end": 6657, "loc": { "start": { - "line": 178, + "line": 197, "column": 29 }, "end": { - "line": 185, + "line": 204, "column": 5 } }, "elements": [ { "type": "StringLiteral", - "start": 6055, - "end": 6064, + "start": 6559, + "end": 6568, "loc": { "start": { - "line": 179, + "line": 198, "column": 6 }, "end": { - "line": 179, + "line": 198, "column": 15 } }, @@ -17995,15 +19489,15 @@ }, { "type": "StringLiteral", - "start": 6072, - "end": 6082, + "start": 6576, + "end": 6586, "loc": { "start": { - "line": 180, + "line": 199, "column": 6 }, "end": { - "line": 180, + "line": 199, "column": 16 } }, @@ -18015,15 +19509,15 @@ }, { "type": "StringLiteral", - "start": 6090, - "end": 6098, + "start": 6594, + "end": 6602, "loc": { "start": { - "line": 181, + "line": 200, "column": 6 }, "end": { - "line": 181, + "line": 200, "column": 14 } }, @@ -18035,15 +19529,15 @@ }, { "type": "StringLiteral", - "start": 6106, - "end": 6115, + "start": 6610, + "end": 6619, "loc": { "start": { - "line": 182, + "line": 201, "column": 6 }, "end": { - "line": 182, + "line": 201, "column": 15 } }, @@ -18055,15 +19549,15 @@ }, { "type": "StringLiteral", - "start": 6123, - "end": 6132, + "start": 6627, + "end": 6636, "loc": { "start": { - "line": 183, + "line": 202, "column": 6 }, "end": { - "line": 183, + "line": 202, "column": 15 } }, @@ -18075,15 +19569,15 @@ }, { "type": "StringLiteral", - "start": 6140, - "end": 6146, + "start": 6644, + "end": 6650, "loc": { "start": { - "line": 184, + "line": 203, "column": 6 }, "end": { - "line": 184, + "line": 203, "column": 12 } }, @@ -18103,15 +19597,15 @@ { "type": "CommentLine", "value": " Look for external references. For now, we only check to see if the entire", - "start": 5833, - "end": 5909, + "start": 6337, + "end": 6413, "loc": { "start": { - "line": 175, + "line": 194, "column": 4 }, "end": { - "line": 175, + "line": 194, "column": 80 } } @@ -18119,15 +19613,15 @@ { "type": "CommentLine", "value": " nodeLabel starts with URL/URNs, but we should eventually just look for", - "start": 5914, - "end": 5987, + "start": 6418, + "end": 6491, "loc": { "start": { - "line": 176, + "line": 195, "column": 4 }, "end": { - "line": 176, + "line": 195, "column": 77 } } @@ -18135,15 +19629,15 @@ { "type": "CommentLine", "value": " them inside the label.", - "start": 5992, - "end": 6017, + "start": 6496, + "end": 6521, "loc": { "start": { - "line": 177, + "line": 196, "column": 4 }, "end": { - "line": 177, + "line": 196, "column": 29 } } @@ -18152,85 +19646,85 @@ }, { "type": "IfStatement", - "start": 6160, - "end": 6435, + "start": 6664, + "end": 6939, "loc": { "start": { - "line": 187, + "line": 206, "column": 4 }, "end": { - "line": 192, + "line": 211, "column": 5 } }, "test": { "type": "BinaryExpression", - "start": 6164, - "end": 6238, + "start": 6668, + "end": 6742, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 82 } }, "left": { "type": "MemberExpression", - "start": 6164, - "end": 6234, + "start": 6668, + "end": 6738, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 78 } }, "object": { "type": "CallExpression", - "start": 6164, - "end": 6227, + "start": 6668, + "end": 6731, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 71 } }, "callee": { "type": "MemberExpression", - "start": 6164, - "end": 6187, + "start": 6668, + "end": 6691, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 31 } }, "object": { "type": "Identifier", - "start": 6164, - "end": 6180, + "start": 6668, + "end": 6684, "loc": { "start": { - "line": 187, + "line": 206, "column": 8 }, "end": { - "line": 187, + "line": 206, "column": 24 }, "identifierName": "URL_URN_PREFIXES" @@ -18239,15 +19733,15 @@ }, "property": { "type": "Identifier", - "start": 6181, - "end": 6187, + "start": 6685, + "end": 6691, "loc": { "start": { - "line": 187, + "line": 206, "column": 25 }, "end": { - "line": 187, + "line": 206, "column": 31 }, "identifierName": "filter" @@ -18259,15 +19753,15 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 6188, - "end": 6226, + "start": 6692, + "end": 6730, "loc": { "start": { - "line": 187, + "line": 206, "column": 32 }, "end": { - "line": 187, + "line": 206, "column": 70 } }, @@ -18278,15 +19772,15 @@ "params": [ { "type": "Identifier", - "start": 6188, - "end": 6194, + "start": 6692, + "end": 6698, "loc": { "start": { - "line": 187, + "line": 206, "column": 32 }, "end": { - "line": 187, + "line": 206, "column": 38 }, "identifierName": "prefix" @@ -18296,43 +19790,43 @@ ], "body": { "type": "CallExpression", - "start": 6198, - "end": 6226, + "start": 6702, + "end": 6730, "loc": { "start": { - "line": 187, + "line": 206, "column": 42 }, "end": { - "line": 187, + "line": 206, "column": 70 } }, "callee": { "type": "MemberExpression", - "start": 6198, - "end": 6218, + "start": 6702, + "end": 6722, "loc": { "start": { - "line": 187, + "line": 206, "column": 42 }, "end": { - "line": 187, + "line": 206, "column": 62 } }, "object": { "type": "Identifier", - "start": 6198, - "end": 6207, + "start": 6702, + "end": 6711, "loc": { "start": { - "line": 187, + "line": 206, "column": 42 }, "end": { - "line": 187, + "line": 206, "column": 51 }, "identifierName": "nodeLabel" @@ -18341,15 +19835,15 @@ }, "property": { "type": "Identifier", - "start": 6208, - "end": 6218, + "start": 6712, + "end": 6722, "loc": { "start": { - "line": 187, + "line": 206, "column": 52 }, "end": { - "line": 187, + "line": 206, "column": 62 }, "identifierName": "startsWith" @@ -18361,15 +19855,15 @@ "arguments": [ { "type": "Identifier", - "start": 6219, - "end": 6225, + "start": 6723, + "end": 6729, "loc": { "start": { - "line": 187, + "line": 206, "column": 63 }, "end": { - "line": 187, + "line": 206, "column": 69 }, "identifierName": "prefix" @@ -18383,15 +19877,15 @@ }, "property": { "type": "Identifier", - "start": 6228, - "end": 6234, + "start": 6732, + "end": 6738, "loc": { "start": { - "line": 187, + "line": 206, "column": 72 }, "end": { - "line": 187, + "line": 206, "column": 78 }, "identifierName": "length" @@ -18403,15 +19897,15 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 6237, - "end": 6238, + "start": 6741, + "end": 6742, "loc": { "start": { - "line": 187, + "line": 206, "column": 81 }, "end": { - "line": 187, + "line": 206, "column": 82 } }, @@ -18424,58 +19918,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 6240, - "end": 6435, + "start": 6744, + "end": 6939, "loc": { "start": { - "line": 187, + "line": 206, "column": 84 }, "end": { - "line": 192, + "line": 211, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 6361, - "end": 6397, + "start": 6865, + "end": 6901, "loc": { "start": { - "line": 190, + "line": 209, "column": 6 }, "end": { - "line": 190, + "line": 209, "column": 42 } }, "test": { "type": "BinaryExpression", - "start": 6365, - "end": 6384, + "start": 6869, + "end": 6888, "loc": { "start": { - "line": 190, + "line": 209, "column": 10 }, "end": { - "line": 190, + "line": 209, "column": 29 } }, "left": { "type": "Identifier", - "start": 6365, - "end": 6370, + "start": 6869, + "end": 6874, "loc": { "start": { - "line": 190, + "line": 209, "column": 10 }, "end": { - "line": 190, + "line": 209, "column": 15 }, "identifierName": "tunit" @@ -18486,15 +19980,15 @@ "operator": "===", "right": { "type": "Identifier", - "start": 6375, - "end": 6384, + "start": 6879, + "end": 6888, "loc": { "start": { - "line": 190, + "line": 209, "column": 20 }, "end": { - "line": 190, + "line": 209, "column": 29 }, "identifierName": "undefined" @@ -18505,44 +19999,44 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 6386, - "end": 6397, + "start": 6890, + "end": 6901, "loc": { "start": { - "line": 190, + "line": 209, "column": 31 }, "end": { - "line": 190, + "line": 209, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 6386, - "end": 6396, + "start": 6890, + "end": 6900, "loc": { "start": { - "line": 190, + "line": 209, "column": 31 }, "end": { - "line": 190, + "line": 209, "column": 41 } }, "operator": "=", "left": { "type": "Identifier", - "start": 6386, - "end": 6391, + "start": 6890, + "end": 6895, "loc": { "start": { - "line": 190, + "line": 209, "column": 31 }, "end": { - "line": 190, + "line": 209, "column": 36 }, "identifierName": "tunit" @@ -18551,15 +20045,15 @@ }, "right": { "type": "ObjectExpression", - "start": 6394, - "end": 6396, + "start": 6898, + "end": 6900, "loc": { "start": { - "line": 190, + "line": 209, "column": 39 }, "end": { - "line": 190, + "line": 209, "column": 41 } }, @@ -18572,15 +20066,15 @@ { "type": "CommentLine", "value": " The node label starts with something that looks like a URL!", - "start": 6248, - "end": 6310, + "start": 6752, + "end": 6814, "loc": { "start": { - "line": 188, + "line": 207, "column": 6 }, "end": { - "line": 188, + "line": 207, "column": 68 } } @@ -18588,15 +20082,15 @@ { "type": "CommentLine", "value": " Treat it as an external reference.", - "start": 6317, - "end": 6354, + "start": 6821, + "end": 6858, "loc": { "start": { - "line": 189, + "line": 208, "column": 6 }, "end": { - "line": 189, + "line": 208, "column": 43 } } @@ -18605,58 +20099,58 @@ }, { "type": "ExpressionStatement", - "start": 6404, - "end": 6429, + "start": 6908, + "end": 6933, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 31 } }, "expression": { "type": "AssignmentExpression", - "start": 6404, - "end": 6428, + "start": 6908, + "end": 6932, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 30 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 6404, - "end": 6416, + "start": 6908, + "end": 6920, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 18 } }, "object": { "type": "Identifier", - "start": 6404, - "end": 6409, + "start": 6908, + "end": 6913, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 11 }, "identifierName": "tunit" @@ -18665,15 +20159,15 @@ }, "property": { "type": "StringLiteral", - "start": 6410, - "end": 6415, + "start": 6914, + "end": 6919, "loc": { "start": { - "line": 191, + "line": 210, "column": 12 }, "end": { - "line": 191, + "line": 210, "column": 17 } }, @@ -18687,15 +20181,15 @@ }, "right": { "type": "Identifier", - "start": 6419, - "end": 6428, + "start": 6923, + "end": 6932, "loc": { "start": { - "line": 191, + "line": 210, "column": 21 }, "end": { - "line": 191, + "line": 210, "column": 30 }, "identifierName": "nodeLabel" @@ -18713,15 +20207,15 @@ { "type": "CommentLine", "value": " Finally, let's record the label we parsed to get to this tunit!", - "start": 6441, - "end": 6507, + "start": 6945, + "end": 7011, "loc": { "start": { - "line": 194, + "line": 213, "column": 4 }, "end": { - "line": 194, + "line": 213, "column": 70 } } @@ -18730,29 +20224,29 @@ }, { "type": "IfStatement", - "start": 6512, - "end": 6561, + "start": 7016, + "end": 7065, "loc": { "start": { - "line": 195, + "line": 214, "column": 4 }, "end": { - "line": 197, + "line": 216, "column": 5 } }, "test": { "type": "Identifier", - "start": 6516, - "end": 6521, + "start": 7020, + "end": 7025, "loc": { "start": { - "line": 195, + "line": 214, "column": 8 }, "end": { - "line": 195, + "line": 214, "column": 13 }, "identifierName": "tunit" @@ -18762,73 +20256,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 6523, - "end": 6561, + "start": 7027, + "end": 7065, "loc": { "start": { - "line": 195, + "line": 214, "column": 15 }, "end": { - "line": 197, + "line": 216, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 6531, - "end": 6555, + "start": 7035, + "end": 7059, "loc": { "start": { - "line": 196, + "line": 215, "column": 6 }, "end": { - "line": 196, + "line": 215, "column": 30 } }, "expression": { "type": "AssignmentExpression", - "start": 6531, - "end": 6554, + "start": 7035, + "end": 7058, "loc": { "start": { - "line": 196, + "line": 215, "column": 6 }, "end": { - "line": 196, + "line": 215, "column": 29 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 6531, - "end": 6542, + "start": 7035, + "end": 7046, "loc": { "start": { - "line": 196, + "line": 215, "column": 6 }, "end": { - "line": 196, + "line": 215, "column": 17 } }, "object": { "type": "Identifier", - "start": 6531, - "end": 6536, + "start": 7035, + "end": 7040, "loc": { "start": { - "line": 196, + "line": 215, "column": 6 }, "end": { - "line": 196, + "line": 215, "column": 11 }, "identifierName": "tunit" @@ -18837,15 +20331,15 @@ }, "property": { "type": "Identifier", - "start": 6537, - "end": 6542, + "start": 7041, + "end": 7046, "loc": { "start": { - "line": 196, + "line": 215, "column": 12 }, "end": { - "line": 196, + "line": 215, "column": 17 }, "identifierName": "label" @@ -18856,15 +20350,15 @@ }, "right": { "type": "Identifier", - "start": 6545, - "end": 6554, + "start": 7049, + "end": 7058, "loc": { "start": { - "line": 196, + "line": 215, "column": 20 }, "end": { - "line": 196, + "line": 215, "column": 29 }, "identifierName": "nodeLabel" @@ -18882,15 +20376,15 @@ { "type": "CommentLine", "value": " Finally, let's record the label we parsed to get to this tunit!", - "start": 6441, - "end": 6507, + "start": 6945, + "end": 7011, "loc": { "start": { - "line": 194, + "line": 213, "column": 4 }, "end": { - "line": 194, + "line": 213, "column": 70 } } @@ -18900,15 +20394,15 @@ { "type": "CommentLine", "value": " Record in the cache", - "start": 6567, - "end": 6589, + "start": 7071, + "end": 7093, "loc": { "start": { - "line": 199, + "line": 218, "column": 4 }, "end": { - "line": 199, + "line": 218, "column": 26 } } @@ -18917,57 +20411,57 @@ }, { "type": "ExpressionStatement", - "start": 6594, - "end": 6703, + "start": 7098, + "end": 7207, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 113 } }, "expression": { "type": "CallExpression", - "start": 6594, - "end": 6702, + "start": 7098, + "end": 7206, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 112 } }, "callee": { "type": "MemberExpression", - "start": 6594, - "end": 6614, + "start": 7098, + "end": 7118, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 24 } }, "object": { "type": "Identifier", - "start": 6594, - "end": 6610, + "start": 7098, + "end": 7114, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 20 }, "identifierName": "PhyxCacheManager" @@ -18977,15 +20471,15 @@ }, "property": { "type": "Identifier", - "start": 6611, - "end": 6614, + "start": 7115, + "end": 7118, "loc": { "start": { - "line": 200, + "line": 219, "column": 21 }, "end": { - "line": 200, + "line": 219, "column": 24 }, "identifierName": "put" @@ -18998,30 +20492,30 @@ "arguments": [ { "type": "TemplateLiteral", - "start": 6615, - "end": 6683, + "start": 7119, + "end": 7187, "loc": { "start": { - "line": 200, + "line": 219, "column": 25 }, "end": { - "line": 200, + "line": 219, "column": 93 } }, "expressions": [ { "type": "Identifier", - "start": 6672, - "end": 6681, + "start": 7176, + "end": 7185, "loc": { "start": { - "line": 200, + "line": 219, "column": 82 }, "end": { - "line": 200, + "line": 219, "column": 91 }, "identifierName": "nomenCode" @@ -19032,15 +20526,15 @@ "quasis": [ { "type": "TemplateElement", - "start": 6616, - "end": 6670, + "start": 7120, + "end": 7174, "loc": { "start": { - "line": 200, + "line": 219, "column": 26 }, "end": { - "line": 200, + "line": 219, "column": 80 } }, @@ -19052,15 +20546,15 @@ }, { "type": "TemplateElement", - "start": 6682, - "end": 6682, + "start": 7186, + "end": 7186, "loc": { "start": { - "line": 200, + "line": 219, "column": 92 }, "end": { - "line": 200, + "line": 219, "column": 92 } }, @@ -19074,15 +20568,15 @@ }, { "type": "Identifier", - "start": 6685, - "end": 6694, + "start": 7189, + "end": 7198, "loc": { "start": { - "line": 200, + "line": 219, "column": 95 }, "end": { - "line": 200, + "line": 219, "column": 104 }, "identifierName": "nodeLabel" @@ -19091,15 +20585,15 @@ }, { "type": "Identifier", - "start": 6696, - "end": 6701, + "start": 7200, + "end": 7205, "loc": { "start": { - "line": 200, + "line": 219, "column": 106 }, "end": { - "line": 200, + "line": 219, "column": 111 }, "identifierName": "tunit" @@ -19113,15 +20607,15 @@ { "type": "CommentLine", "value": " Record in the cache", - "start": 6567, - "end": 6589, + "start": 7071, + "end": 7093, "loc": { "start": { - "line": 199, + "line": 218, "column": 4 }, "end": { - "line": 199, + "line": 218, "column": 26 } } @@ -19130,29 +20624,29 @@ }, { "type": "ReturnStatement", - "start": 6709, - "end": 6722, + "start": 7213, + "end": 7226, "loc": { "start": { - "line": 202, + "line": 221, "column": 4 }, "end": { - "line": 202, + "line": 221, "column": 17 } }, "argument": { "type": "Identifier", - "start": 6716, - "end": 6721, + "start": 7220, + "end": 7225, "loc": { "start": { - "line": 202, + "line": 221, "column": 11 }, "end": { - "line": 202, + "line": 221, "column": 16 }, "identifierName": "tunit" @@ -19168,15 +20662,15 @@ { "type": "CommentBlock", "value": "*\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n ", - "start": 4321, - "end": 4562, + "start": 4825, + "end": 5066, "loc": { "start": { - "line": 137, + "line": 156, "column": 2 }, "end": { - "line": 142, + "line": 161, "column": 5 } } @@ -19186,15 +20680,15 @@ { "type": "CommentBlock", "value": "*\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n ", - "start": 6730, - "end": 6831, + "start": 7234, + "end": 7335, "loc": { "start": { - "line": 205, + "line": 224, "column": 2 }, "end": { - "line": 207, + "line": 226, "column": 5 } } @@ -19203,15 +20697,15 @@ }, { "type": "ClassMethod", - "start": 6834, - "end": 6875, + "start": 7338, + "end": 7379, "loc": { "start": { - "line": 208, + "line": 227, "column": 2 }, "end": { - "line": 210, + "line": 229, "column": 3 } }, @@ -19219,15 +20713,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6838, - "end": 6844, + "start": 7342, + "end": 7348, "loc": { "start": { - "line": 208, + "line": 227, "column": 6 }, "end": { - "line": 208, + "line": 227, "column": 12 }, "identifierName": "asJSON" @@ -19242,73 +20736,73 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6847, - "end": 6875, + "start": 7351, + "end": 7379, "loc": { "start": { - "line": 208, + "line": 227, "column": 15 }, "end": { - "line": 210, + "line": 229, "column": 3 } }, "body": [ { "type": "ReturnStatement", - "start": 6853, - "end": 6871, + "start": 7357, + "end": 7375, "loc": { "start": { - "line": 209, + "line": 228, "column": 4 }, "end": { - "line": 209, + "line": 228, "column": 22 } }, "argument": { "type": "MemberExpression", - "start": 6860, - "end": 6870, + "start": 7364, + "end": 7374, "loc": { "start": { - "line": 209, + "line": 228, "column": 11 }, "end": { - "line": 209, + "line": 228, "column": 21 } }, "object": { "type": "ThisExpression", - "start": 6860, - "end": 6864, + "start": 7364, + "end": 7368, "loc": { "start": { - "line": 209, + "line": 228, "column": 11 }, "end": { - "line": 209, + "line": 228, "column": 15 } } }, "property": { "type": "Identifier", - "start": 6865, - "end": 6870, + "start": 7369, + "end": 7374, "loc": { "start": { - "line": 209, + "line": 228, "column": 16 }, "end": { - "line": 209, + "line": 228, "column": 21 }, "identifierName": "tunit" @@ -19326,15 +20820,15 @@ { "type": "CommentBlock", "value": "*\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n ", - "start": 6730, - "end": 6831, + "start": 7234, + "end": 7335, "loc": { "start": { - "line": 205, + "line": 224, "column": 2 }, "end": { - "line": 207, + "line": 226, "column": 5 } } @@ -19344,15 +20838,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxonomic unit as an OWL/JSON-LD object.\n ", - "start": 6879, - "end": 6946, + "start": 7383, + "end": 7450, "loc": { "start": { - "line": 212, + "line": 231, "column": 2 }, "end": { - "line": 214, + "line": 233, "column": 5 } } @@ -19361,15 +20855,15 @@ }, { "type": "ClassMethod", - "start": 6949, - "end": 7327, + "start": 7453, + "end": 7831, "loc": { "start": { - "line": 215, + "line": 234, "column": 2 }, "end": { - "line": 229, + "line": 248, "column": 3 } }, @@ -19377,15 +20871,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 6953, - "end": 6961, + "start": 7457, + "end": 7465, "loc": { "start": { - "line": 215, + "line": 234, "column": 6 }, "end": { - "line": 215, + "line": 234, "column": 14 }, "identifierName": "asJSONLD" @@ -19400,59 +20894,59 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6964, - "end": 7327, + "start": 7468, + "end": 7831, "loc": { "start": { - "line": 215, + "line": 234, "column": 17 }, "end": { - "line": 229, + "line": 248, "column": 3 } }, "body": [ { "type": "VariableDeclaration", - "start": 6970, - "end": 7007, + "start": 7474, + "end": 7511, "loc": { "start": { - "line": 216, + "line": 235, "column": 4 }, "end": { - "line": 216, + "line": 235, "column": 41 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 6976, - "end": 7006, + "start": 7480, + "end": 7510, "loc": { "start": { - "line": 216, + "line": 235, "column": 10 }, "end": { - "line": 216, + "line": 235, "column": 40 } }, "id": { "type": "Identifier", - "start": 6976, - "end": 6982, + "start": 7480, + "end": 7486, "loc": { "start": { - "line": 216, + "line": 235, "column": 10 }, "end": { - "line": 216, + "line": 235, "column": 16 }, "identifierName": "jsonld" @@ -19461,29 +20955,29 @@ }, "init": { "type": "CallExpression", - "start": 6985, - "end": 7006, + "start": 7489, + "end": 7510, "loc": { "start": { - "line": 216, + "line": 235, "column": 19 }, "end": { - "line": 216, + "line": 235, "column": 40 } }, "callee": { "type": "Identifier", - "start": 6985, - "end": 6994, + "start": 7489, + "end": 7498, "loc": { "start": { - "line": 216, + "line": 235, "column": 19 }, "end": { - "line": 216, + "line": 235, "column": 28 }, "identifierName": "cloneDeep" @@ -19493,44 +20987,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 6995, - "end": 7005, + "start": 7499, + "end": 7509, "loc": { "start": { - "line": 216, + "line": 235, "column": 29 }, "end": { - "line": 216, + "line": 235, "column": 39 } }, "object": { "type": "ThisExpression", - "start": 6995, - "end": 6999, + "start": 7499, + "end": 7503, "loc": { "start": { - "line": 216, + "line": 235, "column": 29 }, "end": { - "line": 216, + "line": 235, "column": 33 } } }, "property": { "type": "Identifier", - "start": 7000, - "end": 7005, + "start": 7504, + "end": 7509, "loc": { "start": { - "line": 216, + "line": 235, "column": 34 }, "end": { - "line": 216, + "line": 235, "column": 39 }, "identifierName": "tunit" @@ -19548,15 +21042,15 @@ { "type": "CommentLine", "value": " Add CDAO_TU as a type to the existing types.", - "start": 7013, - "end": 7060, + "start": 7517, + "end": 7564, "loc": { "start": { - "line": 218, + "line": 237, "column": 4 }, "end": { - "line": 218, + "line": 237, "column": 51 } } @@ -19565,43 +21059,43 @@ }, { "type": "IfStatement", - "start": 7065, - "end": 7186, + "start": 7569, + "end": 7690, "loc": { "start": { - "line": 219, + "line": 238, "column": 4 }, "end": { - "line": 221, + "line": 240, "column": 5 } }, "test": { "type": "CallExpression", - "start": 7069, - "end": 7093, + "start": 7573, + "end": 7597, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 219, + "line": 238, "column": 32 } }, "callee": { "type": "Identifier", - "start": 7069, - "end": 7072, + "start": 7573, + "end": 7576, "loc": { "start": { - "line": 219, + "line": 238, "column": 8 }, "end": { - "line": 219, + "line": 238, "column": 11 }, "identifierName": "has" @@ -19612,44 +21106,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7073, - "end": 7083, + "start": 7577, + "end": 7587, "loc": { "start": { - "line": 219, + "line": 238, "column": 12 }, "end": { - "line": 219, + "line": 238, "column": 22 } }, "object": { "type": "ThisExpression", - "start": 7073, - "end": 7077, + "start": 7577, + "end": 7581, "loc": { "start": { - "line": 219, + "line": 238, "column": 12 }, "end": { - "line": 219, + "line": 238, "column": 16 } } }, "property": { "type": "Identifier", - "start": 7078, - "end": 7083, + "start": 7582, + "end": 7587, "loc": { "start": { - "line": 219, + "line": 238, "column": 17 }, "end": { - "line": 219, + "line": 238, "column": 22 }, "identifierName": "tunit" @@ -19660,15 +21154,15 @@ }, { "type": "StringLiteral", - "start": 7085, - "end": 7092, + "start": 7589, + "end": 7596, "loc": { "start": { - "line": 219, + "line": 238, "column": 24 }, "end": { - "line": 219, + "line": 238, "column": 31 } }, @@ -19683,58 +21177,58 @@ }, "consequent": { "type": "BlockStatement", - "start": 7095, - "end": 7186, + "start": 7599, + "end": 7690, "loc": { "start": { - "line": 219, + "line": 238, "column": 34 }, "end": { - "line": 221, + "line": 240, "column": 5 } }, "body": [ { "type": "IfStatement", - "start": 7103, - "end": 7180, + "start": 7607, + "end": 7684, "loc": { "start": { - "line": 220, + "line": 239, "column": 6 }, "end": { - "line": 220, + "line": 239, "column": 83 } }, "test": { "type": "CallExpression", - "start": 7107, - "end": 7135, + "start": 7611, + "end": 7639, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 38 } }, "callee": { "type": "Identifier", - "start": 7107, - "end": 7114, + "start": 7611, + "end": 7618, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 17 }, "identifierName": "isArray" @@ -19744,58 +21238,58 @@ "arguments": [ { "type": "MemberExpression", - "start": 7115, - "end": 7134, + "start": 7619, + "end": 7638, "loc": { "start": { - "line": 220, + "line": 239, "column": 18 }, "end": { - "line": 220, + "line": 239, "column": 37 } }, "object": { "type": "MemberExpression", - "start": 7115, - "end": 7125, + "start": 7619, + "end": 7629, "loc": { "start": { - "line": 220, + "line": 239, "column": 18 }, "end": { - "line": 220, + "line": 239, "column": 28 } }, "object": { "type": "ThisExpression", - "start": 7115, - "end": 7119, + "start": 7619, + "end": 7623, "loc": { "start": { - "line": 220, + "line": 239, "column": 18 }, "end": { - "line": 220, + "line": 239, "column": 22 } } }, "property": { "type": "Identifier", - "start": 7120, - "end": 7125, + "start": 7624, + "end": 7629, "loc": { "start": { - "line": 220, + "line": 239, "column": 23 }, "end": { - "line": 220, + "line": 239, "column": 28 }, "identifierName": "tunit" @@ -19806,15 +21300,15 @@ }, "property": { "type": "StringLiteral", - "start": 7126, - "end": 7133, + "start": 7630, + "end": 7637, "loc": { "start": { - "line": 220, + "line": 239, "column": 29 }, "end": { - "line": 220, + "line": 239, "column": 36 } }, @@ -19830,100 +21324,100 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 7137, - "end": 7180, + "start": 7641, + "end": 7684, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 83 } }, "expression": { "type": "CallExpression", - "start": 7137, - "end": 7179, + "start": 7641, + "end": 7683, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 82 } }, "callee": { "type": "MemberExpression", - "start": 7137, - "end": 7161, + "start": 7641, + "end": 7665, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 64 } }, "object": { "type": "MemberExpression", - "start": 7137, - "end": 7156, + "start": 7641, + "end": 7660, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 59 } }, "object": { "type": "MemberExpression", - "start": 7137, - "end": 7147, + "start": 7641, + "end": 7651, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 50 } }, "object": { "type": "ThisExpression", - "start": 7137, - "end": 7141, + "start": 7641, + "end": 7645, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 44 } } }, "property": { "type": "Identifier", - "start": 7142, - "end": 7147, + "start": 7646, + "end": 7651, "loc": { "start": { - "line": 220, + "line": 239, "column": 45 }, "end": { - "line": 220, + "line": 239, "column": 50 }, "identifierName": "tunit" @@ -19934,15 +21428,15 @@ }, "property": { "type": "StringLiteral", - "start": 7148, - "end": 7155, + "start": 7652, + "end": 7659, "loc": { "start": { - "line": 220, + "line": 239, "column": 51 }, "end": { - "line": 220, + "line": 239, "column": 58 } }, @@ -19956,15 +21450,15 @@ }, "property": { "type": "Identifier", - "start": 7157, - "end": 7161, + "start": 7661, + "end": 7665, "loc": { "start": { - "line": 220, + "line": 239, "column": 60 }, "end": { - "line": 220, + "line": 239, "column": 64 }, "identifierName": "push" @@ -19976,29 +21470,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 7162, - "end": 7178, + "start": 7666, + "end": 7682, "loc": { "start": { - "line": 220, + "line": 239, "column": 65 }, "end": { - "line": 220, + "line": 239, "column": 81 } }, "object": { "type": "Identifier", - "start": 7162, - "end": 7170, + "start": 7666, + "end": 7674, "loc": { "start": { - "line": 220, + "line": 239, "column": 65 }, "end": { - "line": 220, + "line": 239, "column": 73 }, "identifierName": "owlterms" @@ -20007,15 +21501,15 @@ }, "property": { "type": "Identifier", - "start": 7171, - "end": 7178, + "start": 7675, + "end": 7682, "loc": { "start": { - "line": 220, + "line": 239, "column": 74 }, "end": { - "line": 220, + "line": 239, "column": 81 }, "identifierName": "CDAO_TU" @@ -20037,15 +21531,15 @@ { "type": "CommentLine", "value": " Add CDAO_TU as a type to the existing types.", - "start": 7013, - "end": 7060, + "start": 7517, + "end": 7564, "loc": { "start": { - "line": 218, + "line": 237, "column": 4 }, "end": { - "line": 218, + "line": 237, "column": 51 } } @@ -20054,44 +21548,44 @@ }, { "type": "VariableDeclaration", - "start": 7192, - "end": 7232, + "start": 7696, + "end": 7736, "loc": { "start": { - "line": 223, + "line": 242, "column": 4 }, "end": { - "line": 223, + "line": 242, "column": 44 } }, "declarations": [ { "type": "VariableDeclarator", - "start": 7198, - "end": 7231, + "start": 7702, + "end": 7735, "loc": { "start": { - "line": 223, + "line": 242, "column": 10 }, "end": { - "line": 223, + "line": 242, "column": 43 } }, "id": { "type": "Identifier", - "start": 7198, - "end": 7208, + "start": 7702, + "end": 7712, "loc": { "start": { - "line": 223, + "line": 242, "column": 10 }, "end": { - "line": 223, + "line": 242, "column": 20 }, "identifierName": "equivClass" @@ -20100,44 +21594,44 @@ }, "init": { "type": "MemberExpression", - "start": 7211, - "end": 7231, + "start": 7715, + "end": 7735, "loc": { "start": { - "line": 223, + "line": 242, "column": 23 }, "end": { - "line": 223, + "line": 242, "column": 43 } }, "object": { "type": "ThisExpression", - "start": 7211, - "end": 7215, + "start": 7715, + "end": 7719, "loc": { "start": { - "line": 223, + "line": 242, "column": 23 }, "end": { - "line": 223, + "line": 242, "column": 27 } } }, "property": { "type": "Identifier", - "start": 7216, - "end": 7231, + "start": 7720, + "end": 7735, "loc": { "start": { - "line": 223, + "line": 242, "column": 28 }, "end": { - "line": 223, + "line": 242, "column": 43 }, "identifierName": "asOWLEquivClass" @@ -20152,29 +21646,29 @@ }, { "type": "IfStatement", - "start": 7237, - "end": 7303, + "start": 7741, + "end": 7807, "loc": { "start": { - "line": 224, + "line": 243, "column": 4 }, "end": { - "line": 226, + "line": 245, "column": 5 } }, "test": { "type": "Identifier", - "start": 7241, - "end": 7251, + "start": 7745, + "end": 7755, "loc": { "start": { - "line": 224, + "line": 243, "column": 8 }, "end": { - "line": 224, + "line": 243, "column": 18 }, "identifierName": "equivClass" @@ -20183,73 +21677,73 @@ }, "consequent": { "type": "BlockStatement", - "start": 7253, - "end": 7303, + "start": 7757, + "end": 7807, "loc": { "start": { - "line": 224, + "line": 243, "column": 20 }, "end": { - "line": 226, + "line": 245, "column": 5 } }, "body": [ { "type": "ExpressionStatement", - "start": 7261, - "end": 7297, + "start": 7765, + "end": 7801, "loc": { "start": { - "line": 225, + "line": 244, "column": 6 }, "end": { - "line": 225, + "line": 244, "column": 42 } }, "expression": { "type": "AssignmentExpression", - "start": 7261, - "end": 7296, + "start": 7765, + "end": 7800, "loc": { "start": { - "line": 225, + "line": 244, "column": 6 }, "end": { - "line": 225, + "line": 244, "column": 41 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7261, - "end": 7283, + "start": 7765, + "end": 7787, "loc": { "start": { - "line": 225, + "line": 244, "column": 6 }, "end": { - "line": 225, + "line": 244, "column": 28 } }, "object": { "type": "Identifier", - "start": 7261, - "end": 7267, + "start": 7765, + "end": 7771, "loc": { "start": { - "line": 225, + "line": 244, "column": 6 }, "end": { - "line": 225, + "line": 244, "column": 12 }, "identifierName": "jsonld" @@ -20258,15 +21752,15 @@ }, "property": { "type": "Identifier", - "start": 7268, - "end": 7283, + "start": 7772, + "end": 7787, "loc": { "start": { - "line": 225, + "line": 244, "column": 13 }, "end": { - "line": 225, + "line": 244, "column": 28 }, "identifierName": "equivalentClass" @@ -20277,15 +21771,15 @@ }, "right": { "type": "Identifier", - "start": 7286, - "end": 7296, + "start": 7790, + "end": 7800, "loc": { "start": { - "line": 225, + "line": 244, "column": 31 }, "end": { - "line": 225, + "line": 244, "column": 41 }, "identifierName": "equivClass" @@ -20301,29 +21795,29 @@ }, { "type": "ReturnStatement", - "start": 7309, - "end": 7323, + "start": 7813, + "end": 7827, "loc": { "start": { - "line": 228, + "line": 247, "column": 4 }, "end": { - "line": 228, + "line": 247, "column": 18 } }, "argument": { "type": "Identifier", - "start": 7316, - "end": 7322, + "start": 7820, + "end": 7826, "loc": { "start": { - "line": 228, + "line": 247, "column": 11 }, "end": { - "line": 228, + "line": 247, "column": 17 }, "identifierName": "jsonld" @@ -20339,15 +21833,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxonomic unit as an OWL/JSON-LD object.\n ", - "start": 6879, - "end": 6946, + "start": 7383, + "end": 7450, "loc": { "start": { - "line": 212, + "line": 231, "column": 2 }, "end": { - "line": 214, + "line": 233, "column": 5 } } @@ -20357,15 +21851,15 @@ { "type": "CommentBlock", "value": "*\n * Return the equivalent class expression for this taxonomic unit.\n ", - "start": 7331, - "end": 7409, + "start": 7835, + "end": 7913, "loc": { "start": { - "line": 231, + "line": 250, "column": 2 }, "end": { - "line": 233, + "line": 252, "column": 5 } } @@ -20374,15 +21868,15 @@ }, { "type": "ClassMethod", - "start": 7412, - "end": 7813, + "start": 7916, + "end": 8317, "loc": { "start": { - "line": 234, + "line": 253, "column": 2 }, "end": { - "line": 245, + "line": 264, "column": 3 } }, @@ -20390,15 +21884,15 @@ "computed": false, "key": { "type": "Identifier", - "start": 7416, - "end": 7431, + "start": 7920, + "end": 7935, "loc": { "start": { - "line": 234, + "line": 253, "column": 6 }, "end": { - "line": 234, + "line": 253, "column": 21 }, "identifierName": "asOWLEquivClass" @@ -20413,101 +21907,101 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7434, - "end": 7813, + "start": 7938, + "end": 8317, "loc": { "start": { - "line": 234, + "line": 253, "column": 24 }, "end": { - "line": 245, + "line": 264, "column": 3 } }, "body": [ { "type": "IfStatement", - "start": 7440, - "end": 7602, + "start": 7944, + "end": 8106, "loc": { "start": { - "line": 235, + "line": 254, "column": 4 }, "end": { - "line": 237, + "line": 256, "column": 5 } }, "test": { "type": "CallExpression", - "start": 7444, - "end": 7504, + "start": 7948, + "end": 8008, "loc": { "start": { - "line": 235, + "line": 254, "column": 8 }, "end": { - "line": 235, + "line": 254, "column": 68 } }, "callee": { "type": "MemberExpression", - "start": 7444, - "end": 7463, + "start": 7948, + "end": 7967, "loc": { "start": { - "line": 235, + "line": 254, "column": 8 }, "end": { - "line": 235, + "line": 254, "column": 27 } }, "object": { "type": "MemberExpression", - "start": 7444, - "end": 7454, + "start": 7948, + "end": 7958, "loc": { "start": { - "line": 235, + "line": 254, "column": 8 }, "end": { - "line": 235, + "line": 254, "column": 18 } }, "object": { "type": "ThisExpression", - "start": 7444, - "end": 7448, + "start": 7948, + "end": 7952, "loc": { "start": { - "line": 235, + "line": 254, "column": 8 }, "end": { - "line": 235, + "line": 254, "column": 12 } } }, "property": { "type": "Identifier", - "start": 7449, - "end": 7454, + "start": 7953, + "end": 7958, "loc": { "start": { - "line": 235, + "line": 254, "column": 13 }, "end": { - "line": 235, + "line": 254, "column": 18 }, "identifierName": "types" @@ -20518,15 +22012,15 @@ }, "property": { "type": "Identifier", - "start": 7455, - "end": 7463, + "start": 7959, + "end": 7967, "loc": { "start": { - "line": 235, + "line": 254, "column": 19 }, "end": { - "line": 235, + "line": 254, "column": 27 }, "identifierName": "includes" @@ -20538,29 +22032,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 7464, - "end": 7503, + "start": 7968, + "end": 8007, "loc": { "start": { - "line": 235, + "line": 254, "column": 28 }, "end": { - "line": 235, + "line": 254, "column": 67 } }, "object": { "type": "Identifier", - "start": 7464, - "end": 7484, + "start": 7968, + "end": 7988, "loc": { "start": { - "line": 235, + "line": 254, "column": 28 }, "end": { - "line": 235, + "line": 254, "column": 48 }, "identifierName": "TaxonomicUnitWrapper" @@ -20569,15 +22063,15 @@ }, "property": { "type": "Identifier", - "start": 7485, - "end": 7503, + "start": 7989, + "end": 8007, "loc": { "start": { - "line": 235, + "line": 254, "column": 49 }, "end": { - "line": 235, + "line": 254, "column": 67 }, "identifierName": "TYPE_TAXON_CONCEPT" @@ -20590,72 +22084,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 7506, - "end": 7602, + "start": 8010, + "end": 8106, "loc": { "start": { - "line": 235, + "line": 254, "column": 70 }, "end": { - "line": 237, + "line": 256, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 7514, - "end": 7596, + "start": 8018, + "end": 8100, "loc": { "start": { - "line": 236, + "line": 255, "column": 6 }, "end": { - "line": 236, + "line": 255, "column": 88 } }, "argument": { "type": "MemberExpression", - "start": 7521, - "end": 7595, + "start": 8025, + "end": 8099, "loc": { "start": { - "line": 236, + "line": 255, "column": 13 }, "end": { - "line": 236, + "line": 255, "column": 87 } }, "object": { "type": "NewExpression", - "start": 7521, - "end": 7579, + "start": 8025, + "end": 8083, "loc": { "start": { - "line": 236, + "line": 255, "column": 13 }, "end": { - "line": 236, + "line": 255, "column": 71 } }, "callee": { "type": "Identifier", - "start": 7525, - "end": 7544, + "start": 8029, + "end": 8048, "loc": { "start": { - "line": 236, + "line": 255, "column": 17 }, "end": { - "line": 236, + "line": 255, "column": 36 }, "identifierName": "TaxonConceptWrapper" @@ -20665,44 +22159,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7545, - "end": 7555, + "start": 8049, + "end": 8059, "loc": { "start": { - "line": 236, + "line": 255, "column": 37 }, "end": { - "line": 236, + "line": 255, "column": 47 } }, "object": { "type": "ThisExpression", - "start": 7545, - "end": 7549, + "start": 8049, + "end": 8053, "loc": { "start": { - "line": 236, + "line": 255, "column": 37 }, "end": { - "line": 236, + "line": 255, "column": 41 } } }, "property": { "type": "Identifier", - "start": 7550, - "end": 7555, + "start": 8054, + "end": 8059, "loc": { "start": { - "line": 236, + "line": 255, "column": 42 }, "end": { - "line": 236, + "line": 255, "column": 47 }, "identifierName": "tunit" @@ -20713,44 +22207,44 @@ }, { "type": "MemberExpression", - "start": 7557, - "end": 7578, + "start": 8061, + "end": 8082, "loc": { "start": { - "line": 236, + "line": 255, "column": 49 }, "end": { - "line": 236, + "line": 255, "column": 70 } }, "object": { "type": "ThisExpression", - "start": 7557, - "end": 7561, + "start": 8061, + "end": 8065, "loc": { "start": { - "line": 236, + "line": 255, "column": 49 }, "end": { - "line": 236, + "line": 255, "column": 53 } } }, "property": { "type": "Identifier", - "start": 7562, - "end": 7578, + "start": 8066, + "end": 8082, "loc": { "start": { - "line": 236, + "line": 255, "column": 54 }, "end": { - "line": 236, + "line": 255, "column": 70 }, "identifierName": "defaultNomenCode" @@ -20763,15 +22257,15 @@ }, "property": { "type": "Identifier", - "start": 7580, - "end": 7595, + "start": 8084, + "end": 8099, "loc": { "start": { - "line": 236, + "line": 255, "column": 72 }, "end": { - "line": 236, + "line": 255, "column": 87 }, "identifierName": "asOWLEquivClass" @@ -20788,86 +22282,86 @@ }, { "type": "IfStatement", - "start": 7608, - "end": 7741, + "start": 8112, + "end": 8245, "loc": { "start": { - "line": 239, + "line": 258, "column": 4 }, "end": { - "line": 241, + "line": 260, "column": 5 } }, "test": { "type": "CallExpression", - "start": 7612, - "end": 7667, + "start": 8116, + "end": 8171, "loc": { "start": { - "line": 239, + "line": 258, "column": 8 }, "end": { - "line": 239, + "line": 258, "column": 63 } }, "callee": { "type": "MemberExpression", - "start": 7612, - "end": 7631, + "start": 8116, + "end": 8135, "loc": { "start": { - "line": 239, + "line": 258, "column": 8 }, "end": { - "line": 239, + "line": 258, "column": 27 } }, "object": { "type": "MemberExpression", - "start": 7612, - "end": 7622, + "start": 8116, + "end": 8126, "loc": { "start": { - "line": 239, + "line": 258, "column": 8 }, "end": { - "line": 239, + "line": 258, "column": 18 } }, "object": { "type": "ThisExpression", - "start": 7612, - "end": 7616, + "start": 8116, + "end": 8120, "loc": { "start": { - "line": 239, + "line": 258, "column": 8 }, "end": { - "line": 239, + "line": 258, "column": 12 } } }, "property": { "type": "Identifier", - "start": 7617, - "end": 7622, + "start": 8121, + "end": 8126, "loc": { "start": { - "line": 239, + "line": 258, "column": 13 }, "end": { - "line": 239, + "line": 258, "column": 18 }, "identifierName": "types" @@ -20878,15 +22372,15 @@ }, "property": { "type": "Identifier", - "start": 7623, - "end": 7631, + "start": 8127, + "end": 8135, "loc": { "start": { - "line": 239, + "line": 258, "column": 19 }, "end": { - "line": 239, + "line": 258, "column": 27 }, "identifierName": "includes" @@ -20898,29 +22392,29 @@ "arguments": [ { "type": "MemberExpression", - "start": 7632, - "end": 7666, + "start": 8136, + "end": 8170, "loc": { "start": { - "line": 239, + "line": 258, "column": 28 }, "end": { - "line": 239, + "line": 258, "column": 62 } }, "object": { "type": "Identifier", - "start": 7632, - "end": 7652, + "start": 8136, + "end": 8156, "loc": { "start": { - "line": 239, + "line": 258, "column": 28 }, "end": { - "line": 239, + "line": 258, "column": 48 }, "identifierName": "TaxonomicUnitWrapper" @@ -20929,15 +22423,15 @@ }, "property": { "type": "Identifier", - "start": 7653, - "end": 7666, + "start": 8157, + "end": 8170, "loc": { "start": { - "line": 239, + "line": 258, "column": 49 }, "end": { - "line": 239, + "line": 258, "column": 62 }, "identifierName": "TYPE_SPECIMEN" @@ -20950,72 +22444,72 @@ }, "consequent": { "type": "BlockStatement", - "start": 7669, - "end": 7741, + "start": 8173, + "end": 8245, "loc": { "start": { - "line": 239, + "line": 258, "column": 65 }, "end": { - "line": 241, + "line": 260, "column": 5 } }, "body": [ { "type": "ReturnStatement", - "start": 7677, - "end": 7735, + "start": 8181, + "end": 8239, "loc": { "start": { - "line": 240, + "line": 259, "column": 6 }, "end": { - "line": 240, + "line": 259, "column": 64 } }, "argument": { "type": "MemberExpression", - "start": 7684, - "end": 7734, + "start": 8188, + "end": 8238, "loc": { "start": { - "line": 240, + "line": 259, "column": 13 }, "end": { - "line": 240, + "line": 259, "column": 63 } }, "object": { "type": "NewExpression", - "start": 7684, - "end": 7718, + "start": 8188, + "end": 8222, "loc": { "start": { - "line": 240, + "line": 259, "column": 13 }, "end": { - "line": 240, + "line": 259, "column": 47 } }, "callee": { "type": "Identifier", - "start": 7688, - "end": 7703, + "start": 8192, + "end": 8207, "loc": { "start": { - "line": 240, + "line": 259, "column": 17 }, "end": { - "line": 240, + "line": 259, "column": 32 }, "identifierName": "SpecimenWrapper" @@ -21025,44 +22519,44 @@ "arguments": [ { "type": "MemberExpression", - "start": 7704, - "end": 7717, + "start": 8208, + "end": 8221, "loc": { "start": { - "line": 240, + "line": 259, "column": 33 }, "end": { - "line": 240, + "line": 259, "column": 46 } }, "object": { "type": "ThisExpression", - "start": 7704, - "end": 7708, + "start": 8208, + "end": 8212, "loc": { "start": { - "line": 240, + "line": 259, "column": 33 }, "end": { - "line": 240, + "line": 259, "column": 37 } } }, "property": { "type": "Identifier", - "start": 7709, - "end": 7717, + "start": 8213, + "end": 8221, "loc": { "start": { - "line": 240, + "line": 259, "column": 38 }, "end": { - "line": 240, + "line": 259, "column": 46 }, "identifierName": "specimen" @@ -21075,15 +22569,15 @@ }, "property": { "type": "Identifier", - "start": 7719, - "end": 7734, + "start": 8223, + "end": 8238, "loc": { "start": { - "line": 240, + "line": 259, "column": 48 }, "end": { - "line": 240, + "line": 259, "column": 63 }, "identifierName": "asOWLEquivClass" @@ -21102,15 +22596,15 @@ { "type": "CommentLine", "value": " Nothing we can do, so just ignore it.", - "start": 7747, - "end": 7787, + "start": 8251, + "end": 8291, "loc": { "start": { - "line": 243, + "line": 262, "column": 4 }, "end": { - "line": 243, + "line": 262, "column": 44 } } @@ -21119,29 +22613,29 @@ }, { "type": "ReturnStatement", - "start": 7792, - "end": 7809, + "start": 8296, + "end": 8313, "loc": { "start": { - "line": 244, + "line": 263, "column": 4 }, "end": { - "line": 244, + "line": 263, "column": 21 } }, "argument": { "type": "Identifier", - "start": 7799, - "end": 7808, + "start": 8303, + "end": 8312, "loc": { "start": { - "line": 244, + "line": 263, "column": 11 }, "end": { - "line": 244, + "line": 263, "column": 20 }, "identifierName": "undefined" @@ -21153,15 +22647,15 @@ { "type": "CommentLine", "value": " Nothing we can do, so just ignore it.", - "start": 7747, - "end": 7787, + "start": 8251, + "end": 8291, "loc": { "start": { - "line": 243, + "line": 262, "column": 4 }, "end": { - "line": 243, + "line": 262, "column": 44 } } @@ -21175,15 +22669,15 @@ { "type": "CommentBlock", "value": "*\n * Return the equivalent class expression for this taxonomic unit.\n ", - "start": 7331, - "end": 7409, + "start": 7835, + "end": 7913, "loc": { "start": { - "line": 231, + "line": 250, "column": 2 }, "end": { - "line": 233, + "line": 252, "column": 5 } } @@ -21213,701 +22707,2219 @@ "__PseudoExport__": false, "trailingComments": [] }, - "specifiers": null, - "source": null, - "leadingComments": null + "specifiers": null, + "source": null, + "leadingComments": null + } + ], + "directives": [] + }, + "comments": [ + { + "type": "CommentBlock", + "value": "* Utility functions. ", + "start": 0, + "end": 25, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 25 + } + } + }, + { + "type": "CommentBlock", + "value": "* List of OWL/RDF terms we use. ", + "start": 137, + "end": 173, + "loc": { + "start": { + "line": 10, + "column": 0 + }, + "end": { + "line": 10, + "column": 36 + } + } + }, + { + "type": "CommentBlock", + "value": "* We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. ", + "start": 217, + "end": 312, + "loc": { + "start": { + "line": 13, + "column": 0 + }, + "end": { + "line": 13, + "column": 95 + } + } + }, + { + "type": "CommentBlock", + "value": "* For parsing specimen identifiers. ", + "start": 419, + "end": 459, + "loc": { + "start": { + "line": 17, + "column": 0 + }, + "end": { + "line": 17, + "column": 40 + } + } + }, + { + "type": "CommentBlock", + "value": "* For parsing scientific names. ", + "start": 557, + "end": 593, + "loc": { + "start": { + "line": 21, + "column": 0 + }, + "end": { + "line": 21, + "column": 36 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n ", + "start": 699, + "end": 1789, + "loc": { + "start": { + "line": 25, + "column": 0 + }, + "end": { + "line": 45, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": " Types of taxonomic units we support (see documentation above). ", + "start": 1822, + "end": 1890, + "loc": { + "start": { + "line": 48, + "column": 2 + }, + "end": { + "line": 48, + "column": 70 + } + } + }, + { + "type": "CommentBlock", + "value": "* A taxon or taxon concept. ", + "start": 1894, + "end": 1926, + "loc": { + "start": { + "line": 50, + "column": 2 + }, + "end": { + "line": 50, + "column": 34 + } + } + }, + { + "type": "CommentBlock", + "value": "* A specimen. ", + "start": 2021, + "end": 2039, + "loc": { + "start": { + "line": 55, + "column": 2 + }, + "end": { + "line": 55, + "column": 20 + } + } + }, + { + "type": "CommentBlock", + "value": "* Wrap a taxonomic unit. ", + "start": 2120, + "end": 2149, + "loc": { + "start": { + "line": 60, + "column": 2 + }, + "end": { + "line": 60, + "column": 31 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Normalize the specified taxonomic unit.\n * @param tunit A taxonomic unit to be normalized.\n ", + "start": 2300, + "end": 2407, + "loc": { + "start": { + "line": 66, + "column": 2 + }, + "end": { + "line": 69, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " External references should only have an `@id`.", + "start": 2703, + "end": 2752, + "loc": { + "start": { + "line": 79, + "column": 6 + }, + "end": { + "line": 79, + "column": 55 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n ", + "start": 2804, + "end": 3001, + "loc": { + "start": { + "line": 85, + "column": 2 + }, + "end": { + "line": 90, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return this taxonomic unit if it is a taxon concept.\n ", + "start": 3171, + "end": 3238, + "loc": { + "start": { + "line": 97, + "column": 2 + }, + "end": { + "line": 99, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return this taxonomic unit if it is a specimen.\n ", + "start": 3380, + "end": 3442, + "loc": { + "start": { + "line": 105, + "column": 2 + }, + "end": { + "line": 107, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Only specimens have scientific names.", + "start": 3466, + "end": 3506, + "loc": { + "start": { + "line": 109, + "column": 4 + }, + "end": { + "line": 109, + "column": 44 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n ", + "start": 3621, + "end": 3748, + "loc": { + "start": { + "line": 115, + "column": 2 + }, + "end": { + "line": 118, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the label of this taxonomic unit.\n ", + "start": 3923, + "end": 3978, + "loc": { + "start": { + "line": 125, + "column": 2 + }, + "end": { + "line": 127, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " A label or description for this TU?", + "start": 3999, + "end": 4037, + "loc": { + "start": { + "line": 129, + "column": 4 + }, + "end": { + "line": 129, + "column": 42 + } + } + }, + { + "type": "CommentLine", + "value": " Is this a specimen?", + "start": 4173, + "end": 4195, + "loc": { + "start": { + "line": 133, + "column": 4 + }, + "end": { + "line": 133, + "column": 26 + } + } + }, + { + "type": "CommentLine", + "value": " Is this a taxon concept?", + "start": 4287, + "end": 4314, + "loc": { + "start": { + "line": 138, + "column": 4 + }, + "end": { + "line": 138, + "column": 31 + } + } + }, + { + "type": "CommentLine", + "value": " If its neither a specimen nor a taxon concept, just list the", + "start": 4418, + "end": 4481, + "loc": { + "start": { + "line": 143, + "column": 4 + }, + "end": { + "line": 143, + "column": 67 + } + } + }, + { + "type": "CommentLine", + "value": " external references.", + "start": 4486, + "end": 4509, + "loc": { + "start": { + "line": 144, + "column": 4 + }, + "end": { + "line": 144, + "column": 27 + } + } + }, + { + "type": "CommentLine", + "value": " If we don't have any properties of a taxonomic unit, return undefined.", + "start": 4722, + "end": 4795, + "loc": { + "start": { + "line": 152, + "column": 4 + }, + "end": { + "line": 152, + "column": 77 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n ", + "start": 4825, + "end": 5066, + "loc": { + "start": { + "line": 156, + "column": 2 + }, + "end": { + "line": 161, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Rather than figuring out with this label, check to see if we've parsed", + "start": 5247, + "end": 5320, + "loc": { + "start": { + "line": 165, + "column": 4 + }, + "end": { + "line": 165, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " this before.", + "start": 5325, + "end": 5340, + "loc": { + "start": { + "line": 166, + "column": 4 + }, + "end": { + "line": 166, + "column": 19 + } + } + }, + { + "type": "CommentLine", + "value": " Look for taxon concept.", + "start": 5581, + "end": 5607, + "loc": { + "start": { + "line": 171, + "column": 4 + }, + "end": { + "line": 171, + "column": 30 + } + } + }, + { + "type": "CommentLine", + "value": " Look for specimen information.", + "start": 5691, + "end": 5724, + "loc": { + "start": { + "line": 174, + "column": 4 + }, + "end": { + "line": 174, + "column": 37 + } + } + }, + { + "type": "CommentLine", + "value": " Eliminate a 'Specimen ' prefix if it exists.", + "start": 5808, + "end": 5855, + "loc": { + "start": { + "line": 177, + "column": 6 + }, + "end": { + "line": 177, + "column": 53 + } + } + }, + { + "type": "CommentLine", + "value": " If we have both, then treat it as a specimen that has been identified", + "start": 5992, + "end": 6064, + "loc": { + "start": { + "line": 183, + "column": 6 + }, + "end": { + "line": 183, + "column": 78 + } + } + }, + { + "type": "CommentLine", + "value": " to a particular taxonomic name.", + "start": 6071, + "end": 6105, + "loc": { + "start": { + "line": 184, + "column": 6 + }, + "end": { + "line": 184, + "column": 40 + } + } + }, + { + "type": "CommentLine", + "value": " Look for external references. For now, we only check to see if the entire", + "start": 6337, + "end": 6413, + "loc": { + "start": { + "line": 194, + "column": 4 + }, + "end": { + "line": 194, + "column": 80 + } + } + }, + { + "type": "CommentLine", + "value": " nodeLabel starts with URL/URNs, but we should eventually just look for", + "start": 6418, + "end": 6491, + "loc": { + "start": { + "line": 195, + "column": 4 + }, + "end": { + "line": 195, + "column": 77 + } + } + }, + { + "type": "CommentLine", + "value": " them inside the label.", + "start": 6496, + "end": 6521, + "loc": { + "start": { + "line": 196, + "column": 4 + }, + "end": { + "line": 196, + "column": 29 + } + } + }, + { + "type": "CommentLine", + "value": " The node label starts with something that looks like a URL!", + "start": 6752, + "end": 6814, + "loc": { + "start": { + "line": 207, + "column": 6 + }, + "end": { + "line": 207, + "column": 68 + } + } + }, + { + "type": "CommentLine", + "value": " Treat it as an external reference.", + "start": 6821, + "end": 6858, + "loc": { + "start": { + "line": 208, + "column": 6 + }, + "end": { + "line": 208, + "column": 43 + } + } + }, + { + "type": "CommentLine", + "value": " Finally, let's record the label we parsed to get to this tunit!", + "start": 6945, + "end": 7011, + "loc": { + "start": { + "line": 213, + "column": 4 + }, + "end": { + "line": 213, + "column": 70 + } + } + }, + { + "type": "CommentLine", + "value": " Record in the cache", + "start": 7071, + "end": 7093, + "loc": { + "start": { + "line": 218, + "column": 4 + }, + "end": { + "line": 218, + "column": 26 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n ", + "start": 7234, + "end": 7335, + "loc": { + "start": { + "line": 224, + "column": 2 + }, + "end": { + "line": 226, + "column": 5 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return this taxonomic unit as an OWL/JSON-LD object.\n ", + "start": 7383, + "end": 7450, + "loc": { + "start": { + "line": 231, + "column": 2 + }, + "end": { + "line": 233, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Add CDAO_TU as a type to the existing types.", + "start": 7517, + "end": 7564, + "loc": { + "start": { + "line": 237, + "column": 4 + }, + "end": { + "line": 237, + "column": 51 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Return the equivalent class expression for this taxonomic unit.\n ", + "start": 7835, + "end": 7913, + "loc": { + "start": { + "line": 250, + "column": 2 + }, + "end": { + "line": 252, + "column": 5 + } + } + }, + { + "type": "CommentLine", + "value": " Nothing we can do, so just ignore it.", + "start": 8251, + "end": 8291, + "loc": { + "start": { + "line": 262, + "column": 4 + }, + "end": { + "line": 262, + "column": 44 + } + } + } + ], + "tokens": [ + { + "type": "CommentBlock", + "value": "* Utility functions. ", + "start": 0, + "end": 25, + "loc": { + "start": { + "line": 1, + "column": 0 + }, + "end": { + "line": 1, + "column": 25 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 26, + "end": 32, + "loc": { + "start": { + "line": 2, + "column": 0 + }, + "end": { + "line": 2, + "column": 6 + } + } + }, + { + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 33, + "end": 34, + "loc": { + "start": { + "line": 2, + "column": 7 + }, + "end": { + "line": 2, + "column": 8 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 35, + "end": 37, + "loc": { + "start": { + "line": 2, + "column": 9 + }, + "end": { + "line": 2, + "column": 11 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZA8O5P", + "start": 38, + "end": 51, + "loc": { + "start": { + "line": 2, + "column": 12 + }, + "end": { + "line": 2, + "column": 25 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 52, + "end": 56, + "loc": { + "start": { + "line": 2, + "column": 26 + }, + "end": { + "line": 2, + "column": 30 + } + } + }, + { + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "lodash", + "start": 57, + "end": 65, + "loc": { + "start": { + "line": 2, + "column": 31 + }, + "end": { + "line": 2, + "column": 39 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 65, + "end": 66, + "loc": { + "start": { + "line": 2, + "column": 39 + }, + "end": { + "line": 2, + "column": 40 + } + } + }, + { + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 68, + "end": 73, + "loc": { + "start": { + "line": 3, + "column": 0 + }, + "end": { + "line": 3, + "column": 5 + } + } + }, + { + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 74, + "end": 75, + "loc": { + "start": { + "line": 3, + "column": 6 + }, + "end": { + "line": 3, + "column": 7 + } } - ], - "directives": [] - }, - "comments": [ + }, { - "type": "CommentBlock", - "value": "* Utility functions. ", - "start": 0, - "end": 25, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "has", + "start": 78, + "end": 81, "loc": { "start": { - "line": 1, - "column": 0 + "line": 4, + "column": 2 }, "end": { - "line": 1, - "column": 25 + "line": 4, + "column": 5 } } }, { - "type": "CommentBlock", - "value": "* List of OWL/RDF terms we use. ", - "start": 137, - "end": 173, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 81, + "end": 82, "loc": { "start": { - "line": 10, - "column": 0 + "line": 4, + "column": 5 }, "end": { - "line": 10, - "column": 36 + "line": 4, + "column": 6 } } }, { - "type": "CommentBlock", - "value": "* We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. ", - "start": 217, - "end": 312, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "isArray", + "start": 85, + "end": 92, "loc": { "start": { - "line": 13, - "column": 0 + "line": 5, + "column": 2 }, "end": { - "line": 13, - "column": 95 + "line": 5, + "column": 9 } } }, { - "type": "CommentBlock", - "value": "* For parsing specimen identifiers. ", - "start": 419, - "end": 459, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 92, + "end": 93, "loc": { "start": { - "line": 17, - "column": 0 + "line": 5, + "column": 9 }, "end": { - "line": 17, - "column": 40 + "line": 5, + "column": 10 } } }, { - "type": "CommentBlock", - "value": "* For parsing scientific names. ", - "start": 557, - "end": 593, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "cloneDeep", + "start": 96, + "end": 105, "loc": { "start": { - "line": 21, - "column": 0 + "line": 6, + "column": 2 }, "end": { - "line": 21, - "column": 36 + "line": 6, + "column": 11 } } }, { - "type": "CommentBlock", - "value": "*\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n ", - "start": 699, - "end": 1789, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 105, + "end": 106, "loc": { "start": { - "line": 25, - "column": 0 + "line": 6, + "column": 11 }, "end": { - "line": 45, - "column": 3 + "line": 6, + "column": 12 } } }, { - "type": "CommentBlock", - "value": " Types of taxonomic units we support (see documentation above). ", - "start": 1822, - "end": 1890, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "assign", + "start": 109, + "end": 115, "loc": { "start": { - "line": 48, + "line": 7, "column": 2 }, "end": { - "line": 48, - "column": 70 + "line": 7, + "column": 8 } } }, { - "type": "CommentBlock", - "value": "* A taxon or taxon concept. ", - "start": 1894, - "end": 1926, + "type": { + "label": ",", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 115, + "end": 116, "loc": { "start": { - "line": 50, + "line": 7, + "column": 8 + }, + "end": { + "line": 7, + "column": 9 + } + } + }, + { + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 117, + "end": 118, + "loc": { + "start": { + "line": 8, + "column": 0 + }, + "end": { + "line": 8, + "column": 1 + } + } + }, + { + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 119, + "end": 120, + "loc": { + "start": { + "line": 8, "column": 2 }, "end": { - "line": 50, - "column": 34 + "line": 8, + "column": 3 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZA8O5P", + "start": 121, + "end": 134, + "loc": { + "start": { + "line": 8, + "column": 4 + }, + "end": { + "line": 8, + "column": 17 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 134, + "end": 135, + "loc": { + "start": { + "line": 8, + "column": 17 + }, + "end": { + "line": 8, + "column": 18 } } }, { "type": "CommentBlock", - "value": "* A specimen. ", - "start": 2021, - "end": 2039, + "value": "* List of OWL/RDF terms we use. ", + "start": 137, + "end": 173, "loc": { "start": { - "line": 55, - "column": 2 + "line": 10, + "column": 0 }, "end": { - "line": 55, + "line": 10, + "column": 36 + } + } + }, + { + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 174, + "end": 180, + "loc": { + "start": { + "line": 11, + "column": 0 + }, + "end": { + "line": 11, + "column": 6 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "owlterms", + "start": 181, + "end": 189, + "loc": { + "start": { + "line": 11, + "column": 7 + }, + "end": { + "line": 11, + "column": 15 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 190, + "end": 194, + "loc": { + "start": { + "line": 11, + "column": 16 + }, + "end": { + "line": 11, "column": 20 } } }, { - "type": "CommentBlock", - "value": "* Wrap a taxonomic unit. ", - "start": 2120, - "end": 2149, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/owlterms", + "start": 195, + "end": 214, "loc": { "start": { - "line": 60, - "column": 2 + "line": 11, + "column": 21 }, "end": { - "line": 60, - "column": 31 + "line": 11, + "column": 40 } } }, { - "type": "CommentBlock", - "value": "*\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n ", - "start": 2300, - "end": 2497, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 214, + "end": 215, "loc": { "start": { - "line": 66, - "column": 2 + "line": 11, + "column": 40 }, "end": { - "line": 71, - "column": 5 + "line": 11, + "column": 41 } } }, { "type": "CommentBlock", - "value": "*\n * Return this taxonomic unit if it is a taxon concept.\n ", - "start": 2667, - "end": 2734, + "value": "* We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. ", + "start": 217, + "end": 312, "loc": { "start": { - "line": 78, - "column": 2 + "line": 13, + "column": 0 }, "end": { - "line": 80, - "column": 5 + "line": 13, + "column": 95 } } }, { - "type": "CommentBlock", - "value": "*\n * Return this taxonomic unit if it is a specimen.\n ", - "start": 2876, - "end": 2938, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 313, + "end": 319, "loc": { "start": { - "line": 86, - "column": 2 + "line": 14, + "column": 0 }, "end": { - "line": 88, - "column": 5 + "line": 14, + "column": 6 } } }, { - "type": "CommentLine", - "value": " Only specimens have scientific names.", - "start": 2962, - "end": 3002, + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 320, + "end": 321, "loc": { "start": { - "line": 90, - "column": 4 + "line": 14, + "column": 7 }, "end": { - "line": 90, - "column": 44 + "line": 14, + "column": 8 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n ", - "start": 3117, - "end": 3244, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 322, + "end": 324, "loc": { "start": { - "line": 96, - "column": 2 + "line": 14, + "column": 9 }, "end": { - "line": 99, - "column": 5 + "line": 14, + "column": 11 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the label of this taxonomic unit.\n ", - "start": 3419, - "end": 3474, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZRPNL2", + "start": 325, + "end": 338, "loc": { "start": { - "line": 106, - "column": 2 + "line": 14, + "column": 12 }, "end": { - "line": 108, - "column": 5 + "line": 14, + "column": 25 } } }, { - "type": "CommentLine", - "value": " A label or description for this TU?", - "start": 3495, - "end": 3533, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 339, + "end": 343, "loc": { "start": { - "line": 110, - "column": 4 + "line": 14, + "column": 26 }, "end": { - "line": 110, - "column": 42 + "line": 14, + "column": 30 } } }, { - "type": "CommentLine", - "value": " Is this a specimen?", - "start": 3669, - "end": 3691, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "../utils/PhyxCacheManager", + "start": 344, + "end": 371, "loc": { "start": { - "line": 114, - "column": 4 + "line": 14, + "column": 31 }, "end": { - "line": 114, - "column": 26 + "line": 14, + "column": 58 } } }, { - "type": "CommentLine", - "value": " Is this a taxon concept?", - "start": 3783, - "end": 3810, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 371, + "end": 372, "loc": { "start": { - "line": 119, - "column": 4 + "line": 14, + "column": 58 }, "end": { - "line": 119, - "column": 31 + "line": 14, + "column": 59 } } }, { - "type": "CommentLine", - "value": " If its neither a specimen nor a taxon concept, just list the", - "start": 3914, - "end": 3977, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 374, + "end": 379, "loc": { "start": { - "line": 124, - "column": 4 + "line": 15, + "column": 0 }, "end": { - "line": 124, - "column": 67 + "line": 15, + "column": 5 } } }, { - "type": "CommentLine", - "value": " external references.", - "start": 3982, - "end": 4005, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 380, + "end": 381, "loc": { "start": { - "line": 125, - "column": 4 + "line": 15, + "column": 6 }, "end": { - "line": 125, - "column": 27 + "line": 15, + "column": 7 } } }, { - "type": "CommentLine", - "value": " If we don't have any properties of a taxonomic unit, return undefined.", - "start": 4218, - "end": 4291, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "PhyxCacheManager", + "start": 382, + "end": 398, "loc": { "start": { - "line": 133, - "column": 4 + "line": 15, + "column": 8 }, "end": { - "line": 133, - "column": 77 + "line": 15, + "column": 24 } } }, { - "type": "CommentBlock", - "value": "*\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n ", - "start": 4321, - "end": 4562, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 399, + "end": 400, "loc": { "start": { - "line": 137, - "column": 2 + "line": 15, + "column": 25 }, "end": { - "line": 142, - "column": 5 + "line": 15, + "column": 26 } } }, { - "type": "CommentLine", - "value": " Rather than figuring out with this label, check to see if we've parsed", - "start": 4743, - "end": 4816, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 401, + "end": 402, "loc": { "start": { - "line": 146, - "column": 4 + "line": 15, + "column": 27 }, "end": { - "line": 146, - "column": 77 + "line": 15, + "column": 28 } } }, { - "type": "CommentLine", - "value": " this before.", - "start": 4821, - "end": 4836, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZRPNL2", + "start": 403, + "end": 416, "loc": { "start": { - "line": 147, - "column": 4 + "line": 15, + "column": 29 }, "end": { - "line": 147, - "column": 19 + "line": 15, + "column": 42 } } }, { - "type": "CommentLine", - "value": " Look for taxon concept.", - "start": 5077, - "end": 5103, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 416, + "end": 417, "loc": { "start": { - "line": 152, - "column": 4 + "line": 15, + "column": 42 }, "end": { - "line": 152, - "column": 30 + "line": 15, + "column": 43 } } }, { - "type": "CommentLine", - "value": " Look for specimen information.", - "start": 5187, - "end": 5220, + "type": "CommentBlock", + "value": "* For parsing specimen identifiers. ", + "start": 419, + "end": 459, "loc": { "start": { - "line": 155, - "column": 4 + "line": 17, + "column": 0 }, "end": { - "line": 155, - "column": 37 + "line": 17, + "column": 40 } } }, { - "type": "CommentLine", - "value": " Eliminate a 'Specimen ' prefix if it exists.", - "start": 5304, - "end": 5351, + "type": { + "label": "import", + "keyword": "import", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "import", + "start": 460, + "end": 466, "loc": { "start": { - "line": 158, - "column": 6 + "line": 18, + "column": 0 }, "end": { - "line": 158, - "column": 53 - } - } - }, - { - "type": "CommentLine", - "value": " If we have both, then treat it as a specimen that has been identified", - "start": 5488, - "end": 5560, - "loc": { - "start": { - "line": 164, + "line": 18, "column": 6 - }, - "end": { - "line": 164, - "column": 78 } } }, { - "type": "CommentLine", - "value": " to a particular taxonomic name.", - "start": 5567, - "end": 5601, + "type": { + "label": "*", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": 10, + "updateContext": null + }, + "value": "*", + "start": 467, + "end": 468, "loc": { "start": { - "line": 165, - "column": 6 + "line": 18, + "column": 7 }, "end": { - "line": 165, - "column": 40 + "line": 18, + "column": 8 } } }, { - "type": "CommentLine", - "value": " Look for external references. For now, we only check to see if the entire", - "start": 5833, - "end": 5909, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "as", + "start": 469, + "end": 471, "loc": { "start": { - "line": 175, - "column": 4 + "line": 18, + "column": 9 }, "end": { - "line": 175, - "column": 80 + "line": 18, + "column": 11 } } }, { - "type": "CommentLine", - "value": " nodeLabel starts with URL/URNs, but we should eventually just look for", - "start": 5914, - "end": 5987, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZO9F5X", + "start": 472, + "end": 485, "loc": { "start": { - "line": 176, - "column": 4 + "line": 18, + "column": 12 }, "end": { - "line": 176, - "column": 77 + "line": 18, + "column": 25 } } }, { - "type": "CommentLine", - "value": " them inside the label.", - "start": 5992, - "end": 6017, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "from", + "start": 486, + "end": 490, "loc": { "start": { - "line": 177, - "column": 4 + "line": 18, + "column": 26 }, "end": { - "line": 177, - "column": 29 + "line": 18, + "column": 30 } } }, { - "type": "CommentLine", - "value": " The node label starts with something that looks like a URL!", - "start": 6248, - "end": 6310, + "type": { + "label": "string", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "./SpecimenWrapper", + "start": 491, + "end": 510, "loc": { "start": { - "line": 188, - "column": 6 + "line": 18, + "column": 31 }, "end": { - "line": 188, - "column": 68 + "line": 18, + "column": 50 } } }, { - "type": "CommentLine", - "value": " Treat it as an external reference.", - "start": 6317, - "end": 6354, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 510, + "end": 511, "loc": { "start": { - "line": 189, - "column": 6 + "line": 18, + "column": 50 }, "end": { - "line": 189, - "column": 43 + "line": 18, + "column": 51 } } }, { - "type": "CommentLine", - "value": " Finally, let's record the label we parsed to get to this tunit!", - "start": 6441, - "end": 6507, + "type": { + "label": "const", + "keyword": "const", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "const", + "start": 513, + "end": 518, "loc": { "start": { - "line": 194, - "column": 4 + "line": 19, + "column": 0 }, "end": { - "line": 194, - "column": 70 + "line": 19, + "column": 5 } } }, { - "type": "CommentLine", - "value": " Record in the cache", - "start": 6567, - "end": 6589, + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 519, + "end": 520, "loc": { "start": { - "line": 199, - "column": 4 + "line": 19, + "column": 6 }, "end": { - "line": 199, - "column": 26 + "line": 19, + "column": 7 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n ", - "start": 6730, - "end": 6831, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "SpecimenWrapper", + "start": 521, + "end": 536, "loc": { "start": { - "line": 205, - "column": 2 + "line": 19, + "column": 8 }, "end": { - "line": 207, - "column": 5 + "line": 19, + "column": 23 } } }, { - "type": "CommentBlock", - "value": "*\n * Return this taxonomic unit as an OWL/JSON-LD object.\n ", - "start": 6879, - "end": 6946, + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 537, + "end": 538, "loc": { "start": { - "line": 212, - "column": 2 + "line": 19, + "column": 24 }, "end": { - "line": 214, - "column": 5 + "line": 19, + "column": 25 } } }, { - "type": "CommentLine", - "value": " Add CDAO_TU as a type to the existing types.", - "start": 7013, - "end": 7060, + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 539, + "end": 540, "loc": { "start": { - "line": 218, - "column": 4 + "line": 19, + "column": 26 }, "end": { - "line": 218, - "column": 51 + "line": 19, + "column": 27 } } }, { - "type": "CommentBlock", - "value": "*\n * Return the equivalent class expression for this taxonomic unit.\n ", - "start": 7331, - "end": 7409, + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZO9F5X", + "start": 541, + "end": 554, "loc": { "start": { - "line": 231, - "column": 2 + "line": 19, + "column": 28 }, "end": { - "line": 233, - "column": 5 + "line": 19, + "column": 41 } } }, { - "type": "CommentLine", - "value": " Nothing we can do, so just ignore it.", - "start": 7747, - "end": 7787, + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "start": 554, + "end": 555, "loc": { "start": { - "line": 243, - "column": 4 + "line": 19, + "column": 41 }, "end": { - "line": 243, - "column": 44 + "line": 19, + "column": 42 } } - } - ], - "tokens": [ + }, { "type": "CommentBlock", - "value": "* Utility functions. ", - "start": 0, - "end": 25, + "value": "* For parsing scientific names. ", + "start": 557, + "end": 593, "loc": { "start": { - "line": 1, + "line": 21, "column": 0 }, "end": { - "line": 1, - "column": 25 + "line": 21, + "column": 36 } } }, @@ -21926,15 +24938,15 @@ "updateContext": null }, "value": "import", - "start": 26, - "end": 32, + "start": 594, + "end": 600, "loc": { "start": { - "line": 2, + "line": 22, "column": 0 }, "end": { - "line": 2, + "line": 22, "column": 6 } } @@ -21953,15 +24965,15 @@ "updateContext": null }, "value": "*", - "start": 33, - "end": 34, + "start": 601, + "end": 602, "loc": { "start": { - "line": 2, + "line": 22, "column": 7 }, "end": { - "line": 2, + "line": 22, "column": 8 } } @@ -21979,15 +24991,15 @@ "binop": null }, "value": "as", - "start": 35, - "end": 37, + "start": 603, + "end": 605, "loc": { "start": { - "line": 2, + "line": 22, "column": 9 }, "end": { - "line": 2, + "line": 22, "column": 11 } } @@ -22004,16 +25016,16 @@ "postfix": false, "binop": null }, - "value": "LKT4H1A2LDSKB", - "start": 38, - "end": 51, + "value": "LXL9JK9ZJD9PZ", + "start": 606, + "end": 619, "loc": { "start": { - "line": 2, + "line": 22, "column": 12 }, "end": { - "line": 2, + "line": 22, "column": 25 } } @@ -22031,15 +25043,15 @@ "binop": null }, "value": "from", - "start": 52, - "end": 56, + "start": 620, + "end": 624, "loc": { "start": { - "line": 2, + "line": 22, "column": 26 }, "end": { - "line": 2, + "line": 22, "column": 30 } } @@ -22057,17 +25069,17 @@ "binop": null, "updateContext": null }, - "value": "lodash", - "start": 57, - "end": 65, + "value": "./TaxonConceptWrapper", + "start": 625, + "end": 648, "loc": { "start": { - "line": 2, + "line": 22, "column": 31 }, "end": { - "line": 2, - "column": 39 + "line": 22, + "column": 54 } } }, @@ -22084,16 +25096,16 @@ "binop": null, "updateContext": null }, - "start": 65, - "end": 66, + "start": 648, + "end": 649, "loc": { "start": { - "line": 2, - "column": 39 + "line": 22, + "column": 54 }, "end": { - "line": 2, - "column": 40 + "line": 22, + "column": 55 } } }, @@ -22112,15 +25124,15 @@ "updateContext": null }, "value": "const", - "start": 68, - "end": 73, + "start": 651, + "end": 656, "loc": { "start": { - "line": 3, + "line": 23, "column": 0 }, "end": { - "line": 3, + "line": 23, "column": 5 } } @@ -22137,15 +25149,15 @@ "postfix": false, "binop": null }, - "start": 74, - "end": 75, + "start": 657, + "end": 658, "loc": { "start": { - "line": 3, + "line": 23, "column": 6 }, "end": { - "line": 3, + "line": 23, "column": 7 } } @@ -22162,23 +25174,101 @@ "postfix": false, "binop": null }, - "value": "has", - "start": 78, - "end": 81, + "value": "TaxonConceptWrapper", + "start": 659, + "end": 678, "loc": { "start": { - "line": 4, - "column": 2 + "line": 23, + "column": 8 }, "end": { - "line": 4, - "column": 5 + "line": 23, + "column": 27 } } }, { "type": { - "label": ",", + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 679, + "end": 680, + "loc": { + "start": { + "line": 23, + "column": 28 + }, + "end": { + "line": 23, + "column": 29 + } + } + }, + { + "type": { + "label": "=", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": true, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "=", + "start": 681, + "end": 682, + "loc": { + "start": { + "line": 23, + "column": 30 + }, + "end": { + "line": 23, + "column": 31 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "LXL9JK9ZJD9PZ", + "start": 683, + "end": 696, + "loc": { + "start": { + "line": 23, + "column": 32 + }, + "end": { + "line": 23, + "column": 45 + } + } + }, + { + "type": { + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -22186,19 +25276,172 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null, + "updateContext": null + }, + "start": 696, + "end": 697, + "loc": { + "start": { + "line": 23, + "column": 45 + }, + "end": { + "line": 23, + "column": 46 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n ", + "start": 699, + "end": 1789, + "loc": { + "start": { + "line": 25, + "column": 0 + }, + "end": { + "line": 45, + "column": 3 + } + } + }, + { + "type": { + "label": "class", + "keyword": "class", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null, + "updateContext": null + }, + "value": "class", + "start": 1791, + "end": 1796, + "loc": { + "start": { + "line": 47, + "column": 0 + }, + "end": { + "line": 47, + "column": 5 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "value": "TaxonomicUnitWrapper", + "start": 1797, + "end": 1817, + "loc": { + "start": { + "line": 47, + "column": 6 + }, + "end": { + "line": 47, + "column": 26 + } + } + }, + { + "type": { + "label": "{", + "beforeExpr": true, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 1818, + "end": 1819, + "loc": { + "start": { + "line": 47, + "column": 27 + }, + "end": { + "line": 47, + "column": 28 + } + } + }, + { + "type": "CommentBlock", + "value": " Types of taxonomic units we support (see documentation above). ", + "start": 1822, + "end": 1890, + "loc": { + "start": { + "line": 48, + "column": 2 + }, + "end": { + "line": 48, + "column": 70 + } + } + }, + { + "type": "CommentBlock", + "value": "* A taxon or taxon concept. ", + "start": 1894, + "end": 1926, + "loc": { + "start": { + "line": 50, + "column": 2 + }, + "end": { + "line": 50, + "column": 34 + } + } + }, + { + "type": { + "label": "name", + "beforeExpr": false, + "startsExpr": true, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null }, - "start": 81, - "end": 82, + "value": "static", + "start": 1929, + "end": 1935, "loc": { "start": { - "line": 4, - "column": 5 + "line": 51, + "column": 2 }, "end": { - "line": 4, - "column": 6 + "line": 51, + "column": 8 } } }, @@ -22214,50 +25457,50 @@ "postfix": false, "binop": null }, - "value": "isArray", - "start": 85, - "end": 92, + "value": "get", + "start": 1936, + "end": 1939, "loc": { "start": { - "line": 5, - "column": 2 + "line": 51, + "column": 9 }, "end": { - "line": 5, - "column": 9 + "line": 51, + "column": 12 } } }, { "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 92, - "end": 93, + "value": "TYPE_TAXON_CONCEPT", + "start": 1940, + "end": 1958, "loc": { "start": { - "line": 5, - "column": 9 + "line": 51, + "column": 13 }, "end": { - "line": 5, - "column": 10 + "line": 51, + "column": 31 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -22266,50 +25509,48 @@ "postfix": false, "binop": null }, - "value": "cloneDeep", - "start": 96, - "end": 105, + "start": 1958, + "end": 1959, "loc": { "start": { - "line": 6, - "column": 2 + "line": 51, + "column": 31 }, "end": { - "line": 6, - "column": 11 + "line": 51, + "column": 32 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 105, - "end": 106, + "start": 1959, + "end": 1960, "loc": { "start": { - "line": 6, - "column": 11 + "line": 51, + "column": 32 }, "end": { - "line": 6, - "column": 12 + "line": 51, + "column": 33 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -22318,23 +25559,23 @@ "postfix": false, "binop": null }, - "value": "assign", - "start": 109, - "end": 115, + "start": 1961, + "end": 1962, "loc": { "start": { - "line": 7, - "column": 2 + "line": 51, + "column": 34 }, "end": { - "line": 7, - "column": 8 + "line": 51, + "column": 35 } } }, { "type": { - "label": ",", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -22345,24 +25586,25 @@ "binop": null, "updateContext": null }, - "start": 115, - "end": 116, + "value": "return", + "start": 1967, + "end": 1973, "loc": { "start": { - "line": 7, - "column": 8 + "line": 52, + "column": 4 }, "end": { - "line": 7, - "column": 9 + "line": 52, + "column": 10 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -22370,43 +25612,43 @@ "postfix": false, "binop": null }, - "start": 117, - "end": 118, + "value": "TaxonConceptWrapper", + "start": 1974, + "end": 1993, "loc": { "start": { - "line": 8, - "column": 0 + "line": 52, + "column": 11 }, "end": { - "line": 8, - "column": 1 + "line": 52, + "column": 30 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 119, - "end": 120, + "start": 1993, + "end": 1994, "loc": { "start": { - "line": 8, - "column": 2 + "line": 52, + "column": 30 }, "end": { - "line": 8, - "column": 3 + "line": 52, + "column": 31 } } }, @@ -22422,17 +25664,17 @@ "postfix": false, "binop": null }, - "value": "LKT4H1A2LDSKB", - "start": 121, - "end": 134, + "value": "TYPE_TAXON_CONCEPT", + "start": 1994, + "end": 2012, "loc": { "start": { - "line": 8, - "column": 4 + "line": 52, + "column": 31 }, "end": { - "line": 8, - "column": 17 + "line": 52, + "column": 49 } } }, @@ -22449,39 +25691,63 @@ "binop": null, "updateContext": null }, - "start": 134, - "end": 135, + "start": 2012, + "end": 2013, "loc": { "start": { - "line": 8, - "column": 17 + "line": 52, + "column": 49 }, "end": { - "line": 8, - "column": 18 + "line": 52, + "column": 50 + } + } + }, + { + "type": { + "label": "}", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 2016, + "end": 2017, + "loc": { + "start": { + "line": 53, + "column": 2 + }, + "end": { + "line": 53, + "column": 3 } } }, { "type": "CommentBlock", - "value": "* List of OWL/RDF terms we use. ", - "start": 137, - "end": 173, + "value": "* A specimen. ", + "start": 2021, + "end": 2039, "loc": { "start": { - "line": 10, - "column": 0 + "line": 55, + "column": 2 }, "end": { - "line": 10, - "column": 36 + "line": 55, + "column": 20 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -22489,20 +25755,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 174, - "end": 180, + "value": "static", + "start": 2042, + "end": 2048, "loc": { "start": { - "line": 11, - "column": 0 + "line": 56, + "column": 2 }, "end": { - "line": 11, - "column": 6 + "line": 56, + "column": 8 } } }, @@ -22518,17 +25783,17 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 181, - "end": 189, + "value": "get", + "start": 2049, + "end": 2052, "loc": { "start": { - "line": 11, - "column": 7 + "line": 56, + "column": 9 }, "end": { - "line": 11, - "column": 15 + "line": 56, + "column": 12 } } }, @@ -22544,120 +25809,99 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 190, - "end": 194, + "value": "TYPE_SPECIMEN", + "start": 2053, + "end": 2066, "loc": { "start": { - "line": 11, - "column": 16 + "line": 56, + "column": 13 }, "end": { - "line": 11, - "column": 20 + "line": 56, + "column": 26 } } }, { "type": { - "label": "string", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "../utils/owlterms", - "start": 195, - "end": 214, + "start": 2066, + "end": 2067, "loc": { "start": { - "line": 11, - "column": 21 + "line": 56, + "column": 26 }, "end": { - "line": 11, - "column": 40 + "line": 56, + "column": 27 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 214, - "end": 215, - "loc": { - "start": { - "line": 11, - "column": 40 - }, - "end": { - "line": 11, - "column": 41 - } - } - }, - { - "type": "CommentBlock", - "value": "* We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. ", - "start": 217, - "end": 312, + "start": 2067, + "end": 2068, "loc": { "start": { - "line": 13, - "column": 0 + "line": 56, + "column": 27 }, "end": { - "line": 13, - "column": 95 + "line": 56, + "column": 28 } } }, { "type": { - "label": "import", - "keyword": "import", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 313, - "end": 319, + "start": 2069, + "end": 2070, "loc": { "start": { - "line": 14, - "column": 0 + "line": 56, + "column": 29 }, "end": { - "line": 14, - "column": 6 + "line": 56, + "column": 30 } } }, { "type": { - "label": "*", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -22665,20 +25909,20 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 320, - "end": 321, + "value": "return", + "start": 2075, + "end": 2081, "loc": { "start": { - "line": 14, - "column": 7 + "line": 57, + "column": 4 }, "end": { - "line": 14, - "column": 8 + "line": 57, + "column": 10 } } }, @@ -22694,43 +25938,43 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 322, - "end": 324, + "value": "SpecimenWrapper", + "start": 2082, + "end": 2097, "loc": { "start": { - "line": 14, - "column": 9 + "line": 57, + "column": 11 }, "end": { - "line": 14, - "column": 11 + "line": 57, + "column": 26 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H1A2OMXOJ", - "start": 325, - "end": 338, + "start": 2097, + "end": 2098, "loc": { "start": { - "line": 14, - "column": 12 + "line": 57, + "column": 26 }, "end": { - "line": 14, - "column": 25 + "line": 57, + "column": 27 } } }, @@ -22746,25 +25990,25 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 339, - "end": 343, + "value": "TYPE_SPECIMEN", + "start": 2098, + "end": 2111, "loc": { "start": { - "line": 14, - "column": 26 + "line": 57, + "column": 27 }, "end": { - "line": 14, - "column": 30 + "line": 57, + "column": 40 } } }, { "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -22773,78 +26017,64 @@ "binop": null, "updateContext": null }, - "value": "../utils/PhyxCacheManager", - "start": 344, - "end": 371, + "start": 2111, + "end": 2112, "loc": { "start": { - "line": 14, - "column": 31 + "line": 57, + "column": 40 }, "end": { - "line": 14, - "column": 58 + "line": 57, + "column": 41 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 371, - "end": 372, + "start": 2115, + "end": 2116, "loc": { "start": { - "line": 14, - "column": 58 + "line": 58, + "column": 2 }, "end": { - "line": 14, - "column": 59 + "line": 58, + "column": 3 } } }, { - "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "const", - "start": 374, - "end": 379, + "type": "CommentBlock", + "value": "* Wrap a taxonomic unit. ", + "start": 2120, + "end": 2149, "loc": { "start": { - "line": 15, - "column": 0 + "line": 60, + "column": 2 }, "end": { - "line": 15, - "column": 5 + "line": 60, + "column": 31 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -22853,23 +26083,24 @@ "postfix": false, "binop": null }, - "start": 380, - "end": 381, + "value": "constructor", + "start": 2152, + "end": 2163, "loc": { "start": { - "line": 15, - "column": 6 + "line": 61, + "column": 2 }, "end": { - "line": 15, - "column": 7 + "line": 61, + "column": 13 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -22878,25 +26109,24 @@ "postfix": false, "binop": null }, - "value": "PhyxCacheManager", - "start": 382, - "end": 398, + "start": 2163, + "end": 2164, "loc": { "start": { - "line": 15, - "column": 8 + "line": 61, + "column": 13 }, "end": { - "line": 15, - "column": 24 + "line": 61, + "column": 14 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -22904,43 +26134,43 @@ "postfix": false, "binop": null }, - "start": 399, - "end": 400, + "value": "tunit", + "start": 2164, + "end": 2169, "loc": { "start": { - "line": 15, - "column": 25 + "line": 61, + "column": 14 }, "end": { - "line": 15, - "column": 26 + "line": 61, + "column": 19 } } }, { "type": { - "label": "=", + "label": ",", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 401, - "end": 402, + "start": 2169, + "end": 2170, "loc": { "start": { - "line": 15, - "column": 27 + "line": 61, + "column": 19 }, "end": { - "line": 15, - "column": 28 + "line": 61, + "column": 20 } } }, @@ -22956,66 +26186,50 @@ "postfix": false, "binop": null }, - "value": "LKT4H1A2OMXOJ", - "start": 403, - "end": 416, + "value": "defaultNomenCode", + "start": 2171, + "end": 2187, "loc": { "start": { - "line": 15, - "column": 29 + "line": 61, + "column": 21 }, "end": { - "line": 15, - "column": 42 + "line": 61, + "column": 37 } } }, { "type": { - "label": ";", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 416, - "end": 417, - "loc": { - "start": { - "line": 15, - "column": 42 - }, - "end": { - "line": 15, - "column": 43 - } - } - }, - { - "type": "CommentBlock", - "value": "* For parsing specimen identifiers. ", - "start": 419, - "end": 459, + "value": "=", + "start": 2188, + "end": 2189, "loc": { "start": { - "line": 17, - "column": 0 + "line": 61, + "column": 38 }, "end": { - "line": 17, - "column": 40 + "line": 61, + "column": 39 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -23023,47 +26237,45 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 460, - "end": 466, + "value": "owlterms", + "start": 2190, + "end": 2198, "loc": { "start": { - "line": 18, - "column": 0 + "line": 61, + "column": 40 }, "end": { - "line": 18, - "column": 6 + "line": 61, + "column": 48 } } }, { "type": { - "label": "*", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 467, - "end": 468, + "start": 2198, + "end": 2199, "loc": { "start": { - "line": 18, - "column": 7 + "line": 61, + "column": 48 }, "end": { - "line": 18, - "column": 8 + "line": 61, + "column": 49 } } }, @@ -23079,25 +26291,25 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 469, - "end": 471, + "value": "NAME_IN_UNKNOWN_CODE", + "start": 2199, + "end": 2219, "loc": { "start": { - "line": 18, - "column": 9 + "line": 61, + "column": 49 }, "end": { - "line": 18, - "column": 11 + "line": 61, + "column": 69 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23105,24 +26317,23 @@ "postfix": false, "binop": null }, - "value": "LKT4H1A22T3E0", - "start": 472, - "end": 485, + "start": 2219, + "end": 2220, "loc": { "start": { - "line": 18, - "column": 12 + "line": 61, + "column": 69 }, "end": { - "line": 18, - "column": 25 + "line": 61, + "column": 70 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -23131,23 +26342,23 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 486, - "end": 490, + "start": 2221, + "end": 2222, "loc": { "start": { - "line": 18, - "column": 26 + "line": 61, + "column": 71 }, "end": { - "line": 18, - "column": 30 + "line": 61, + "column": 72 } } }, { "type": { - "label": "string", + "label": "this", + "keyword": "this", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -23158,24 +26369,24 @@ "binop": null, "updateContext": null }, - "value": "./SpecimenWrapper", - "start": 491, - "end": 510, + "value": "this", + "start": 2227, + "end": 2231, "loc": { "start": { - "line": 18, - "column": 31 + "line": 62, + "column": 4 }, "end": { - "line": 18, - "column": 50 + "line": 62, + "column": 8 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -23185,69 +26396,69 @@ "binop": null, "updateContext": null }, - "start": 510, - "end": 511, + "start": 2231, + "end": 2232, "loc": { "start": { - "line": 18, - "column": 50 + "line": 62, + "column": 8 }, "end": { - "line": 18, - "column": 51 + "line": 62, + "column": 9 } } }, { "type": { - "label": "const", - "keyword": "const", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 513, - "end": 518, + "value": "tunit", + "start": 2232, + "end": 2237, "loc": { "start": { - "line": 19, - "column": 0 + "line": 62, + "column": 9 }, "end": { - "line": 19, - "column": 5 + "line": 62, + "column": 14 } } }, { "type": { - "label": "{", + "label": "=", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 519, - "end": 520, + "value": "=", + "start": 2238, + "end": 2239, "loc": { "start": { - "line": 19, - "column": 6 + "line": 62, + "column": 15 }, "end": { - "line": 19, - "column": 7 + "line": 62, + "column": 16 } } }, @@ -23263,75 +26474,50 @@ "postfix": false, "binop": null }, - "value": "SpecimenWrapper", - "start": 521, - "end": 536, - "loc": { - "start": { - "line": 19, - "column": 8 - }, - "end": { - "line": 19, - "column": 23 - } - } - }, - { - "type": { - "label": "}", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "start": 537, - "end": 538, + "value": "tunit", + "start": 2240, + "end": 2245, "loc": { "start": { - "line": 19, - "column": 24 + "line": 62, + "column": 17 }, "end": { - "line": 19, - "column": 25 + "line": 62, + "column": 22 } } }, { "type": { - "label": "=", + "label": ";", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 539, - "end": 540, + "start": 2245, + "end": 2246, "loc": { "start": { - "line": 19, - "column": 26 + "line": 62, + "column": 22 }, "end": { - "line": 19, - "column": 27 + "line": 62, + "column": 23 } } }, { "type": { - "label": "name", + "label": "this", + "keyword": "this", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -23339,26 +26525,27 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H1A22T3E0", - "start": 541, - "end": 554, + "value": "this", + "start": 2251, + "end": 2255, "loc": { "start": { - "line": 19, - "column": 28 + "line": 63, + "column": 4 }, "end": { - "line": 19, - "column": 41 + "line": 63, + "column": 8 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -23368,39 +26555,22 @@ "binop": null, "updateContext": null }, - "start": 554, - "end": 555, - "loc": { - "start": { - "line": 19, - "column": 41 - }, - "end": { - "line": 19, - "column": 42 - } - } - }, - { - "type": "CommentBlock", - "value": "* For parsing scientific names. ", - "start": 557, - "end": 593, + "start": 2255, + "end": 2256, "loc": { "start": { - "line": 21, - "column": 0 + "line": 63, + "column": 8 }, "end": { - "line": 21, - "column": 36 + "line": 63, + "column": 9 } } }, { "type": { - "label": "import", - "keyword": "import", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -23408,47 +26578,46 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "import", - "start": 594, - "end": 600, + "value": "defaultNomenCode", + "start": 2256, + "end": 2272, "loc": { "start": { - "line": 22, - "column": 0 + "line": 63, + "column": 9 }, "end": { - "line": 22, - "column": 6 + "line": 63, + "column": 25 } } }, { "type": { - "label": "*", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, - "binop": 10, + "binop": null, "updateContext": null }, - "value": "*", - "start": 601, - "end": 602, + "value": "=", + "start": 2273, + "end": 2274, "loc": { "start": { - "line": 22, - "column": 7 + "line": 63, + "column": 26 }, "end": { - "line": 22, - "column": 8 + "line": 63, + "column": 27 } } }, @@ -23464,51 +26633,51 @@ "postfix": false, "binop": null }, - "value": "as", - "start": 603, - "end": 605, + "value": "defaultNomenCode", + "start": 2275, + "end": 2291, "loc": { "start": { - "line": 22, - "column": 9 + "line": 63, + "column": 28 }, "end": { - "line": 22, - "column": 11 + "line": 63, + "column": 44 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "LKT4H1A2K7H5M", - "start": 606, - "end": 619, + "start": 2291, + "end": 2292, "loc": { "start": { - "line": 22, - "column": 12 + "line": 63, + "column": 44 }, "end": { - "line": 22, - "column": 25 + "line": 63, + "column": 45 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23516,23 +26685,38 @@ "postfix": false, "binop": null }, - "value": "from", - "start": 620, - "end": 624, + "start": 2295, + "end": 2296, "loc": { "start": { - "line": 22, - "column": 26 + "line": 64, + "column": 2 }, "end": { - "line": 22, - "column": 30 + "line": 64, + "column": 3 + } + } + }, + { + "type": "CommentBlock", + "value": "*\n * Normalize the specified taxonomic unit.\n * @param tunit A taxonomic unit to be normalized.\n ", + "start": 2300, + "end": 2407, + "loc": { + "start": { + "line": 66, + "column": 2 + }, + "end": { + "line": 69, + "column": 5 } } }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -23540,81 +26724,77 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "./TaxonConceptWrapper", - "start": 625, - "end": 648, + "value": "static", + "start": 2410, + "end": 2416, "loc": { "start": { - "line": 22, - "column": 31 + "line": 70, + "column": 2 }, "end": { - "line": 22, - "column": 54 + "line": 70, + "column": 8 } } }, { "type": { - "label": ";", - "beforeExpr": true, - "startsExpr": false, + "label": "name", + "beforeExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 648, - "end": 649, + "value": "normalize", + "start": 2417, + "end": 2426, "loc": { "start": { - "line": 22, - "column": 54 + "line": 70, + "column": 9 }, "end": { - "line": 22, - "column": 55 + "line": 70, + "column": 18 } } }, { "type": { - "label": "const", - "keyword": "const", - "beforeExpr": false, - "startsExpr": false, + "label": "(", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "const", - "start": 651, - "end": 656, + "start": 2426, + "end": 2427, "loc": { "start": { - "line": 23, - "column": 0 + "line": 70, + "column": 18 }, "end": { - "line": 23, - "column": 5 + "line": 70, + "column": 19 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -23623,24 +26803,25 @@ "postfix": false, "binop": null }, - "start": 657, - "end": 658, + "value": "tunit", + "start": 2427, + "end": 2432, "loc": { "start": { - "line": 23, - "column": 6 + "line": 70, + "column": 19 }, "end": { - "line": 23, - "column": 7 + "line": 70, + "column": 24 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23648,25 +26829,24 @@ "postfix": false, "binop": null }, - "value": "TaxonConceptWrapper", - "start": 659, - "end": 678, + "start": 2432, + "end": 2433, "loc": { "start": { - "line": 23, - "column": 8 + "line": 70, + "column": 24 }, "end": { - "line": 23, - "column": 27 + "line": 70, + "column": 25 } } }, { "type": { - "label": "}", - "beforeExpr": false, - "startsExpr": false, + "label": "{", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23674,43 +26854,44 @@ "postfix": false, "binop": null }, - "start": 679, - "end": 680, + "start": 2434, + "end": 2435, "loc": { "start": { - "line": 23, - "column": 28 + "line": 70, + "column": 26 }, "end": { - "line": 23, - "column": 29 + "line": 70, + "column": 27 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": "const", + "keyword": "const", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 681, - "end": 682, + "value": "const", + "start": 2440, + "end": 2445, "loc": { "start": { - "line": 23, - "column": 30 + "line": 71, + "column": 4 }, "end": { - "line": 23, - "column": 31 + "line": 71, + "column": 9 } } }, @@ -23726,68 +26907,53 @@ "postfix": false, "binop": null }, - "value": "LKT4H1A2K7H5M", - "start": 683, - "end": 696, + "value": "wrapped", + "start": 2446, + "end": 2453, "loc": { "start": { - "line": 23, - "column": 32 + "line": 71, + "column": 10 }, "end": { - "line": 23, - "column": 45 + "line": 71, + "column": 17 } } }, { "type": { - "label": ";", + "label": "=", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": false, + "isAssign": true, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "start": 696, - "end": 697, - "loc": { - "start": { - "line": 23, - "column": 45 - }, - "end": { - "line": 23, - "column": 46 - } - } - }, - { - "type": "CommentBlock", - "value": "*\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n ", - "start": 699, - "end": 1789, + "value": "=", + "start": 2454, + "end": 2455, "loc": { "start": { - "line": 25, - "column": 0 + "line": 71, + "column": 18 }, "end": { - "line": 45, - "column": 3 + "line": 71, + "column": 19 } } }, { "type": { - "label": "class", - "keyword": "class", - "beforeExpr": false, - "startsExpr": false, + "label": "new", + "keyword": "new", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23796,17 +26962,17 @@ "binop": null, "updateContext": null }, - "value": "class", - "start": 1791, - "end": 1796, + "value": "new", + "start": 2456, + "end": 2459, "loc": { "start": { - "line": 47, - "column": 0 + "line": 71, + "column": 20 }, "end": { - "line": 47, - "column": 5 + "line": 71, + "column": 23 } } }, @@ -23823,22 +26989,22 @@ "binop": null }, "value": "TaxonomicUnitWrapper", - "start": 1797, - "end": 1817, + "start": 2460, + "end": 2480, "loc": { "start": { - "line": 47, - "column": 6 + "line": 71, + "column": 24 }, "end": { - "line": 47, - "column": 26 + "line": 71, + "column": 44 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -23848,48 +27014,16 @@ "postfix": false, "binop": null }, - "start": 1818, - "end": 1819, - "loc": { - "start": { - "line": 47, - "column": 27 - }, - "end": { - "line": 47, - "column": 28 - } - } - }, - { - "type": "CommentBlock", - "value": " Types of taxonomic units we support (see documentation above). ", - "start": 1822, - "end": 1890, - "loc": { - "start": { - "line": 48, - "column": 2 - }, - "end": { - "line": 48, - "column": 70 - } - } - }, - { - "type": "CommentBlock", - "value": "* A taxon or taxon concept. ", - "start": 1894, - "end": 1926, + "start": 2480, + "end": 2481, "loc": { "start": { - "line": 50, - "column": 2 + "line": 71, + "column": 44 }, "end": { - "line": 50, - "column": 34 + "line": 71, + "column": 45 } } }, @@ -23905,25 +27039,25 @@ "postfix": false, "binop": null }, - "value": "static", - "start": 1929, - "end": 1935, + "value": "tunit", + "start": 2481, + "end": 2486, "loc": { "start": { - "line": 51, - "column": 2 + "line": 71, + "column": 45 }, "end": { - "line": 51, - "column": 8 + "line": 71, + "column": 50 } } }, { "type": { - "label": "name", + "label": ")", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -23931,76 +27065,78 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 1936, - "end": 1939, + "start": 2486, + "end": 2487, "loc": { "start": { - "line": 51, - "column": 9 + "line": 71, + "column": 50 }, "end": { - "line": 51, - "column": 12 + "line": 71, + "column": 51 } } }, { "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, + "label": ";", + "beforeExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "TYPE_TAXON_CONCEPT", - "start": 1940, - "end": 1958, + "start": 2487, + "end": 2488, "loc": { "start": { - "line": 51, - "column": 13 + "line": 71, + "column": 51 }, "end": { - "line": 51, - "column": 31 + "line": 71, + "column": 52 } } }, { "type": { - "label": "(", - "beforeExpr": true, - "startsExpr": true, + "label": "if", + "keyword": "if", + "beforeExpr": false, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 1958, - "end": 1959, + "value": "if", + "start": 2493, + "end": 2495, "loc": { "start": { - "line": 51, - "column": 31 + "line": 72, + "column": 4 }, "end": { - "line": 51, - "column": 32 + "line": 72, + "column": 6 } } }, { "type": { - "label": ")", - "beforeExpr": false, - "startsExpr": false, + "label": "(", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -24008,23 +27144,23 @@ "postfix": false, "binop": null }, - "start": 1959, - "end": 1960, + "start": 2496, + "end": 2497, "loc": { "start": { - "line": 51, - "column": 32 + "line": 72, + "column": 7 }, "end": { - "line": 51, - "column": 33 + "line": 72, + "column": 8 } } }, { "type": { - "label": "{", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24033,24 +27169,24 @@ "postfix": false, "binop": null }, - "start": 1961, - "end": 1962, + "value": "wrapped", + "start": 2497, + "end": 2504, "loc": { "start": { - "line": 51, - "column": 34 + "line": 72, + "column": 8 }, "end": { - "line": 51, - "column": 35 + "line": 72, + "column": 15 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -24060,17 +27196,16 @@ "binop": null, "updateContext": null }, - "value": "return", - "start": 1967, - "end": 1973, + "start": 2504, + "end": 2505, "loc": { "start": { - "line": 52, - "column": 4 + "line": 72, + "column": 15 }, "end": { - "line": 52, - "column": 10 + "line": 72, + "column": 16 } } }, @@ -24086,23 +27221,23 @@ "postfix": false, "binop": null }, - "value": "TaxonConceptWrapper", - "start": 1974, - "end": 1993, + "value": "taxonConcept", + "start": 2505, + "end": 2517, "loc": { "start": { - "line": 52, - "column": 11 + "line": 72, + "column": 16 }, "end": { - "line": 52, - "column": 30 + "line": 72, + "column": 28 } } }, { "type": { - "label": ".", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -24110,26 +27245,25 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "start": 1993, - "end": 1994, + "start": 2517, + "end": 2518, "loc": { "start": { - "line": 52, - "column": 30 + "line": 72, + "column": 28 }, "end": { - "line": 52, - "column": 31 + "line": 72, + "column": 29 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24138,23 +27272,23 @@ "postfix": false, "binop": null }, - "value": "TYPE_TAXON_CONCEPT", - "start": 1994, - "end": 2012, + "start": 2519, + "end": 2520, "loc": { "start": { - "line": 52, - "column": 31 + "line": 72, + "column": 30 }, "end": { - "line": 52, - "column": 49 + "line": 72, + "column": 31 } } }, { "type": { - "label": ";", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -24165,24 +27299,25 @@ "binop": null, "updateContext": null }, - "start": 2012, - "end": 2013, + "value": "return", + "start": 2527, + "end": 2533, "loc": { "start": { - "line": 52, - "column": 49 + "line": 73, + "column": 6 }, "end": { - "line": 52, - "column": 50 + "line": 73, + "column": 12 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -24190,58 +27325,43 @@ "postfix": false, "binop": null }, - "start": 2016, - "end": 2017, - "loc": { - "start": { - "line": 53, - "column": 2 - }, - "end": { - "line": 53, - "column": 3 - } - } - }, - { - "type": "CommentBlock", - "value": "* A specimen. ", - "start": 2021, - "end": 2039, + "value": "TaxonConceptWrapper", + "start": 2534, + "end": 2553, "loc": { "start": { - "line": 55, - "column": 2 + "line": 73, + "column": 13 }, "end": { - "line": 55, - "column": 20 + "line": 73, + "column": 32 } } }, { "type": { - "label": "name", + "label": ".", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "static", - "start": 2042, - "end": 2048, + "start": 2553, + "end": 2554, "loc": { "start": { - "line": 56, - "column": 2 + "line": 73, + "column": 32 }, "end": { - "line": 56, - "column": 8 + "line": 73, + "column": 33 } } }, @@ -24257,24 +27377,24 @@ "postfix": false, "binop": null }, - "value": "get", - "start": 2049, - "end": 2052, + "value": "normalize", + "start": 2554, + "end": 2563, "loc": { "start": { - "line": 56, - "column": 9 + "line": 73, + "column": 33 }, "end": { - "line": 56, - "column": 12 + "line": 73, + "column": 42 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "(", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24283,24 +27403,23 @@ "postfix": false, "binop": null }, - "value": "TYPE_SPECIMEN", - "start": 2053, - "end": 2066, + "start": 2563, + "end": 2564, "loc": { "start": { - "line": 56, - "column": 13 + "line": 73, + "column": 42 }, "end": { - "line": 56, - "column": 26 + "line": 73, + "column": 43 } } }, { "type": { - "label": "(", - "beforeExpr": true, + "label": "name", + "beforeExpr": false, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24309,16 +27428,17 @@ "postfix": false, "binop": null }, - "start": 2066, - "end": 2067, + "value": "tunit", + "start": 2564, + "end": 2569, "loc": { "start": { - "line": 56, - "column": 26 + "line": 73, + "column": 43 }, "end": { - "line": 56, - "column": 27 + "line": 73, + "column": 48 } } }, @@ -24334,121 +27454,120 @@ "postfix": false, "binop": null }, - "start": 2067, - "end": 2068, + "start": 2569, + "end": 2570, "loc": { "start": { - "line": 56, - "column": 27 + "line": 73, + "column": 48 }, "end": { - "line": 56, - "column": 28 + "line": 73, + "column": 49 } } }, { "type": { - "label": "{", + "label": ";", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2069, - "end": 2070, + "start": 2570, + "end": 2571, "loc": { "start": { - "line": 56, - "column": 29 + "line": 73, + "column": 49 }, "end": { - "line": 56, - "column": 30 + "line": 73, + "column": 50 } } }, { "type": { - "label": "return", - "keyword": "return", - "beforeExpr": true, + "label": "}", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "return", - "start": 2075, - "end": 2081, + "start": 2576, + "end": 2577, "loc": { "start": { - "line": 57, + "line": 74, "column": 4 }, "end": { - "line": 57, - "column": 10 + "line": 74, + "column": 5 } } }, { "type": { - "label": "name", + "label": "if", + "keyword": "if", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "value": "SpecimenWrapper", - "start": 2082, - "end": 2097, + "value": "if", + "start": 2582, + "end": 2584, "loc": { "start": { - "line": 57, - "column": 11 + "line": 75, + "column": 4 }, "end": { - "line": 57, - "column": 26 + "line": 75, + "column": 6 } } }, { "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, + "label": "(", + "beforeExpr": true, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 2097, - "end": 2098, + "binop": null + }, + "start": 2585, + "end": 2586, "loc": { "start": { - "line": 57, - "column": 26 + "line": 75, + "column": 7 }, "end": { - "line": 57, - "column": 27 + "line": 75, + "column": 8 } } }, @@ -24464,24 +27583,24 @@ "postfix": false, "binop": null }, - "value": "TYPE_SPECIMEN", - "start": 2098, - "end": 2111, + "value": "wrapped", + "start": 2586, + "end": 2593, "loc": { "start": { - "line": 57, - "column": 27 + "line": 75, + "column": 8 }, "end": { - "line": 57, - "column": 40 + "line": 75, + "column": 15 } } }, { "type": { - "label": ";", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -24491,24 +27610,24 @@ "binop": null, "updateContext": null }, - "start": 2111, - "end": 2112, + "start": 2593, + "end": 2594, "loc": { "start": { - "line": 57, - "column": 40 + "line": 75, + "column": 15 }, "end": { - "line": 57, - "column": 41 + "line": 75, + "column": 16 } } }, { "type": { - "label": "}", + "label": "name", "beforeExpr": false, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -24516,39 +27635,49 @@ "postfix": false, "binop": null }, - "start": 2115, - "end": 2116, + "value": "specimen", + "start": 2594, + "end": 2602, "loc": { "start": { - "line": 58, - "column": 2 + "line": 75, + "column": 16 }, "end": { - "line": 58, - "column": 3 + "line": 75, + "column": 24 } } }, { - "type": "CommentBlock", - "value": "* Wrap a taxonomic unit. ", - "start": 2120, - "end": 2149, + "type": { + "label": ")", + "beforeExpr": false, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, + "binop": null + }, + "start": 2602, + "end": 2603, "loc": { "start": { - "line": 60, - "column": 2 + "line": 75, + "column": 24 }, "end": { - "line": 60, - "column": 31 + "line": 75, + "column": 25 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24557,42 +27686,44 @@ "postfix": false, "binop": null }, - "value": "constructor", - "start": 2152, - "end": 2163, + "start": 2604, + "end": 2605, "loc": { "start": { - "line": 61, - "column": 2 + "line": 75, + "column": 26 }, "end": { - "line": 61, - "column": 13 + "line": 75, + "column": 27 } } }, { "type": { - "label": "(", + "label": "return", + "keyword": "return", "beforeExpr": true, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2163, - "end": 2164, + "value": "return", + "start": 2612, + "end": 2618, "loc": { "start": { - "line": 61, - "column": 13 + "line": 76, + "column": 6 }, "end": { - "line": 61, - "column": 14 + "line": 76, + "column": 12 } } }, @@ -24608,24 +27739,24 @@ "postfix": false, "binop": null }, - "value": "tunit", - "start": 2164, - "end": 2169, + "value": "SpecimenWrapper", + "start": 2619, + "end": 2634, "loc": { "start": { - "line": 61, - "column": 14 + "line": 76, + "column": 13 }, "end": { - "line": 61, - "column": 19 + "line": 76, + "column": 28 } } }, { "type": { - "label": ",", - "beforeExpr": true, + "label": ".", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -24635,16 +27766,16 @@ "binop": null, "updateContext": null }, - "start": 2169, - "end": 2170, + "start": 2634, + "end": 2635, "loc": { "start": { - "line": 61, - "column": 19 + "line": 76, + "column": 28 }, "end": { - "line": 61, - "column": 20 + "line": 76, + "column": 29 } } }, @@ -24660,43 +27791,41 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 2171, - "end": 2187, + "value": "normalize", + "start": 2635, + "end": 2644, "loc": { "start": { - "line": 61, - "column": 21 + "line": 76, + "column": 29 }, "end": { - "line": 61, - "column": 37 + "line": 76, + "column": 38 } } }, { "type": { - "label": "=", + "label": "(", "beforeExpr": true, - "startsExpr": false, + "startsExpr": true, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 2188, - "end": 2189, + "start": 2644, + "end": 2645, "loc": { "start": { - "line": 61, + "line": 76, "column": 38 }, "end": { - "line": 61, + "line": 76, "column": 39 } } @@ -24713,23 +27842,23 @@ "postfix": false, "binop": null }, - "value": "owlterms", - "start": 2190, - "end": 2198, + "value": "tunit", + "start": 2645, + "end": 2650, "loc": { "start": { - "line": 61, - "column": 40 + "line": 76, + "column": 39 }, "end": { - "line": 61, - "column": 48 + "line": 76, + "column": 44 } } }, { "type": { - "label": ".", + "label": ")", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -24737,27 +27866,52 @@ "isAssign": false, "prefix": false, "postfix": false, + "binop": null + }, + "start": 2650, + "end": 2651, + "loc": { + "start": { + "line": 76, + "column": 44 + }, + "end": { + "line": 76, + "column": 45 + } + } + }, + { + "type": { + "label": ";", + "beforeExpr": true, + "startsExpr": false, + "rightAssociative": false, + "isLoop": false, + "isAssign": false, + "prefix": false, + "postfix": false, "binop": null, "updateContext": null }, - "start": 2198, - "end": 2199, + "start": 2651, + "end": 2652, "loc": { "start": { - "line": 61, - "column": 48 + "line": 76, + "column": 45 }, "end": { - "line": 61, - "column": 49 + "line": 76, + "column": 46 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -24765,23 +27919,23 @@ "postfix": false, "binop": null }, - "value": "NAME_IN_UNKNOWN_CODE", - "start": 2199, - "end": 2219, + "start": 2657, + "end": 2658, "loc": { "start": { - "line": 61, - "column": 49 + "line": 77, + "column": 4 }, "end": { - "line": 61, - "column": 69 + "line": 77, + "column": 5 } } }, { "type": { - "label": ")", + "label": "if", + "keyword": "if", "beforeExpr": false, "startsExpr": false, "rightAssociative": false, @@ -24789,24 +27943,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null + "binop": null, + "updateContext": null }, - "start": 2219, - "end": 2220, + "value": "if", + "start": 2663, + "end": 2665, "loc": { "start": { - "line": 61, - "column": 69 + "line": 78, + "column": 4 }, "end": { - "line": 61, - "column": 70 + "line": 78, + "column": 6 } } }, { "type": { - "label": "{", + "label": "(", "beforeExpr": true, "startsExpr": true, "rightAssociative": false, @@ -24816,23 +27972,22 @@ "postfix": false, "binop": null }, - "start": 2221, - "end": 2222, + "start": 2666, + "end": 2667, "loc": { "start": { - "line": 61, - "column": 71 + "line": 78, + "column": 7 }, "end": { - "line": 61, - "column": 72 + "line": 78, + "column": 8 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -24840,20 +27995,19 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 2227, - "end": 2231, + "value": "wrapped", + "start": 2667, + "end": 2674, "loc": { "start": { - "line": 62, - "column": 4 + "line": 78, + "column": 8 }, "end": { - "line": 62, - "column": 8 + "line": 78, + "column": 15 } } }, @@ -24870,16 +28024,16 @@ "binop": null, "updateContext": null }, - "start": 2231, - "end": 2232, + "start": 2674, + "end": 2675, "loc": { "start": { - "line": 62, - "column": 8 + "line": 78, + "column": 15 }, "end": { - "line": 62, - "column": 9 + "line": 78, + "column": 16 } } }, @@ -24895,51 +28049,49 @@ "postfix": false, "binop": null }, - "value": "tunit", - "start": 2232, - "end": 2237, + "value": "externalReferences", + "start": 2675, + "end": 2693, "loc": { "start": { - "line": 62, - "column": 9 + "line": 78, + "column": 16 }, "end": { - "line": 62, - "column": 14 + "line": 78, + "column": 34 } } }, { "type": { - "label": "=", - "beforeExpr": true, + "label": ")", + "beforeExpr": false, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "=", - "start": 2238, - "end": 2239, + "start": 2693, + "end": 2694, "loc": { "start": { - "line": 62, - "column": 15 + "line": 78, + "column": 34 }, "end": { - "line": 62, - "column": 16 + "line": 78, + "column": 35 } } }, { "type": { - "label": "name", - "beforeExpr": false, + "label": "{", + "beforeExpr": true, "startsExpr": true, "rightAssociative": false, "isLoop": false, @@ -24948,23 +28100,39 @@ "postfix": false, "binop": null }, - "value": "tunit", - "start": 2240, - "end": 2245, + "start": 2695, + "end": 2696, "loc": { "start": { - "line": 62, - "column": 17 + "line": 78, + "column": 36 }, "end": { - "line": 62, - "column": 22 + "line": 78, + "column": 37 + } + } + }, + { + "type": "CommentLine", + "value": " External references should only have an `@id`.", + "start": 2703, + "end": 2752, + "loc": { + "start": { + "line": 79, + "column": 6 + }, + "end": { + "line": 79, + "column": 55 } } }, { "type": { - "label": ";", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, @@ -24975,23 +28143,23 @@ "binop": null, "updateContext": null }, - "start": 2245, - "end": 2246, + "value": "return", + "start": 2759, + "end": 2765, "loc": { "start": { - "line": 62, - "column": 22 + "line": 80, + "column": 6 }, "end": { - "line": 62, - "column": 23 + "line": 80, + "column": 12 } } }, { "type": { - "label": "this", - "keyword": "this", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -24999,27 +28167,26 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "this", - "start": 2251, - "end": 2255, + "value": "tunit", + "start": 2766, + "end": 2771, "loc": { "start": { - "line": 63, - "column": 4 + "line": 80, + "column": 13 }, "end": { - "line": 63, - "column": 8 + "line": 80, + "column": 18 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ";", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -25029,24 +28196,24 @@ "binop": null, "updateContext": null }, - "start": 2255, - "end": 2256, + "start": 2771, + "end": 2772, "loc": { "start": { - "line": 63, - "column": 8 + "line": 80, + "column": 18 }, "end": { - "line": 63, - "column": 9 + "line": 80, + "column": 19 } } }, { "type": { - "label": "name", + "label": "}", "beforeExpr": false, - "startsExpr": true, + "startsExpr": false, "rightAssociative": false, "isLoop": false, "isAssign": false, @@ -25054,44 +28221,44 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 2256, - "end": 2272, + "start": 2777, + "end": 2778, "loc": { "start": { - "line": 63, - "column": 9 + "line": 81, + "column": 4 }, "end": { - "line": 63, - "column": 25 + "line": 81, + "column": 5 } } }, { "type": { - "label": "=", + "label": "return", + "keyword": "return", "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, - "isAssign": true, + "isAssign": false, "prefix": false, "postfix": false, "binop": null, "updateContext": null }, - "value": "=", - "start": 2273, - "end": 2274, + "value": "return", + "start": 2783, + "end": 2789, "loc": { "start": { - "line": 63, - "column": 26 + "line": 82, + "column": 4 }, "end": { - "line": 63, - "column": 27 + "line": 82, + "column": 10 } } }, @@ -25107,17 +28274,17 @@ "postfix": false, "binop": null }, - "value": "defaultNomenCode", - "start": 2275, - "end": 2291, + "value": "tunit", + "start": 2790, + "end": 2795, "loc": { "start": { - "line": 63, - "column": 28 + "line": 82, + "column": 11 }, "end": { - "line": 63, - "column": 44 + "line": 82, + "column": 16 } } }, @@ -25134,16 +28301,16 @@ "binop": null, "updateContext": null }, - "start": 2291, - "end": 2292, + "start": 2795, + "end": 2796, "loc": { "start": { - "line": 63, - "column": 44 + "line": 82, + "column": 16 }, "end": { - "line": 63, - "column": 45 + "line": 82, + "column": 17 } } }, @@ -25159,15 +28326,15 @@ "postfix": false, "binop": null }, - "start": 2295, - "end": 2296, + "start": 2799, + "end": 2800, "loc": { "start": { - "line": 64, + "line": 83, "column": 2 }, "end": { - "line": 64, + "line": 83, "column": 3 } } @@ -25175,15 +28342,15 @@ { "type": "CommentBlock", "value": "*\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n ", - "start": 2300, - "end": 2497, + "start": 2804, + "end": 3001, "loc": { "start": { - "line": 66, + "line": 85, "column": 2 }, "end": { - "line": 71, + "line": 90, "column": 5 } } @@ -25201,15 +28368,15 @@ "binop": null }, "value": "get", - "start": 2500, - "end": 2503, + "start": 3004, + "end": 3007, "loc": { "start": { - "line": 72, + "line": 91, "column": 2 }, "end": { - "line": 72, + "line": 91, "column": 5 } } @@ -25227,15 +28394,15 @@ "binop": null }, "value": "types", - "start": 2504, - "end": 2509, + "start": 3008, + "end": 3013, "loc": { "start": { - "line": 72, + "line": 91, "column": 6 }, "end": { - "line": 72, + "line": 91, "column": 11 } } @@ -25252,15 +28419,15 @@ "postfix": false, "binop": null }, - "start": 2509, - "end": 2510, + "start": 3013, + "end": 3014, "loc": { "start": { - "line": 72, + "line": 91, "column": 11 }, "end": { - "line": 72, + "line": 91, "column": 12 } } @@ -25277,15 +28444,15 @@ "postfix": false, "binop": null }, - "start": 2510, - "end": 2511, + "start": 3014, + "end": 3015, "loc": { "start": { - "line": 72, + "line": 91, "column": 12 }, "end": { - "line": 72, + "line": 91, "column": 13 } } @@ -25302,15 +28469,15 @@ "postfix": false, "binop": null }, - "start": 2512, - "end": 2513, + "start": 3016, + "end": 3017, "loc": { "start": { - "line": 72, + "line": 91, "column": 14 }, "end": { - "line": 72, + "line": 91, "column": 15 } } @@ -25330,15 +28497,15 @@ "updateContext": null }, "value": "if", - "start": 2518, - "end": 2520, + "start": 3022, + "end": 3024, "loc": { "start": { - "line": 73, + "line": 92, "column": 4 }, "end": { - "line": 73, + "line": 92, "column": 6 } } @@ -25355,15 +28522,15 @@ "postfix": false, "binop": null }, - "start": 2521, - "end": 2522, + "start": 3025, + "end": 3026, "loc": { "start": { - "line": 73, + "line": 92, "column": 7 }, "end": { - "line": 73, + "line": 92, "column": 8 } } @@ -25382,15 +28549,15 @@ "updateContext": null }, "value": "!", - "start": 2522, - "end": 2523, + "start": 3026, + "end": 3027, "loc": { "start": { - "line": 73, + "line": 92, "column": 8 }, "end": { - "line": 73, + "line": 92, "column": 9 } } @@ -25408,15 +28575,15 @@ "binop": null }, "value": "has", - "start": 2523, - "end": 2526, + "start": 3027, + "end": 3030, "loc": { "start": { - "line": 73, + "line": 92, "column": 9 }, "end": { - "line": 73, + "line": 92, "column": 12 } } @@ -25433,15 +28600,15 @@ "postfix": false, "binop": null }, - "start": 2526, - "end": 2527, + "start": 3030, + "end": 3031, "loc": { "start": { - "line": 73, + "line": 92, "column": 12 }, "end": { - "line": 73, + "line": 92, "column": 13 } } @@ -25461,15 +28628,15 @@ "updateContext": null }, "value": "this", - "start": 2527, - "end": 2531, + "start": 3031, + "end": 3035, "loc": { "start": { - "line": 73, + "line": 92, "column": 13 }, "end": { - "line": 73, + "line": 92, "column": 17 } } @@ -25487,15 +28654,15 @@ "binop": null, "updateContext": null }, - "start": 2531, - "end": 2532, + "start": 3035, + "end": 3036, "loc": { "start": { - "line": 73, + "line": 92, "column": 17 }, "end": { - "line": 73, + "line": 92, "column": 18 } } @@ -25513,15 +28680,15 @@ "binop": null }, "value": "tunit", - "start": 2532, - "end": 2537, + "start": 3036, + "end": 3041, "loc": { "start": { - "line": 73, + "line": 92, "column": 18 }, "end": { - "line": 73, + "line": 92, "column": 23 } } @@ -25539,15 +28706,15 @@ "binop": null, "updateContext": null }, - "start": 2537, - "end": 2538, + "start": 3041, + "end": 3042, "loc": { "start": { - "line": 73, + "line": 92, "column": 23 }, "end": { - "line": 73, + "line": 92, "column": 24 } } @@ -25566,15 +28733,15 @@ "updateContext": null }, "value": "@type", - "start": 2539, - "end": 2546, + "start": 3043, + "end": 3050, "loc": { "start": { - "line": 73, + "line": 92, "column": 25 }, "end": { - "line": 73, + "line": 92, "column": 32 } } @@ -25591,15 +28758,15 @@ "postfix": false, "binop": null }, - "start": 2546, - "end": 2547, + "start": 3050, + "end": 3051, "loc": { "start": { - "line": 73, + "line": 92, "column": 32 }, "end": { - "line": 73, + "line": 92, "column": 33 } } @@ -25616,15 +28783,15 @@ "postfix": false, "binop": null }, - "start": 2547, - "end": 2548, + "start": 3051, + "end": 3052, "loc": { "start": { - "line": 73, + "line": 92, "column": 33 }, "end": { - "line": 73, + "line": 92, "column": 34 } } @@ -25644,15 +28811,15 @@ "updateContext": null }, "value": "return", - "start": 2549, - "end": 2555, + "start": 3053, + "end": 3059, "loc": { "start": { - "line": 73, + "line": 92, "column": 35 }, "end": { - "line": 73, + "line": 92, "column": 41 } } @@ -25670,15 +28837,15 @@ "binop": null, "updateContext": null }, - "start": 2556, - "end": 2557, + "start": 3060, + "end": 3061, "loc": { "start": { - "line": 73, + "line": 92, "column": 42 }, "end": { - "line": 73, + "line": 92, "column": 43 } } @@ -25696,15 +28863,15 @@ "binop": null, "updateContext": null }, - "start": 2557, - "end": 2558, + "start": 3061, + "end": 3062, "loc": { "start": { - "line": 73, + "line": 92, "column": 43 }, "end": { - "line": 73, + "line": 92, "column": 44 } } @@ -25722,15 +28889,15 @@ "binop": null, "updateContext": null }, - "start": 2558, - "end": 2559, + "start": 3062, + "end": 3063, "loc": { "start": { - "line": 73, + "line": 92, "column": 44 }, "end": { - "line": 73, + "line": 92, "column": 45 } } @@ -25750,15 +28917,15 @@ "updateContext": null }, "value": "if", - "start": 2564, - "end": 2566, + "start": 3068, + "end": 3070, "loc": { "start": { - "line": 74, + "line": 93, "column": 4 }, "end": { - "line": 74, + "line": 93, "column": 6 } } @@ -25775,15 +28942,15 @@ "postfix": false, "binop": null }, - "start": 2567, - "end": 2568, + "start": 3071, + "end": 3072, "loc": { "start": { - "line": 74, + "line": 93, "column": 7 }, "end": { - "line": 74, + "line": 93, "column": 8 } } @@ -25801,15 +28968,15 @@ "binop": null }, "value": "isArray", - "start": 2568, - "end": 2575, + "start": 3072, + "end": 3079, "loc": { "start": { - "line": 74, + "line": 93, "column": 8 }, "end": { - "line": 74, + "line": 93, "column": 15 } } @@ -25826,15 +28993,15 @@ "postfix": false, "binop": null }, - "start": 2575, - "end": 2576, + "start": 3079, + "end": 3080, "loc": { "start": { - "line": 74, + "line": 93, "column": 15 }, "end": { - "line": 74, + "line": 93, "column": 16 } } @@ -25854,15 +29021,15 @@ "updateContext": null }, "value": "this", - "start": 2576, - "end": 2580, + "start": 3080, + "end": 3084, "loc": { "start": { - "line": 74, + "line": 93, "column": 16 }, "end": { - "line": 74, + "line": 93, "column": 20 } } @@ -25880,15 +29047,15 @@ "binop": null, "updateContext": null }, - "start": 2580, - "end": 2581, + "start": 3084, + "end": 3085, "loc": { "start": { - "line": 74, + "line": 93, "column": 20 }, "end": { - "line": 74, + "line": 93, "column": 21 } } @@ -25906,15 +29073,15 @@ "binop": null }, "value": "tunit", - "start": 2581, - "end": 2586, + "start": 3085, + "end": 3090, "loc": { "start": { - "line": 74, + "line": 93, "column": 21 }, "end": { - "line": 74, + "line": 93, "column": 26 } } @@ -25932,15 +29099,15 @@ "binop": null, "updateContext": null }, - "start": 2586, - "end": 2587, + "start": 3090, + "end": 3091, "loc": { "start": { - "line": 74, + "line": 93, "column": 26 }, "end": { - "line": 74, + "line": 93, "column": 27 } } @@ -25959,15 +29126,15 @@ "updateContext": null }, "value": "@type", - "start": 2587, - "end": 2594, + "start": 3091, + "end": 3098, "loc": { "start": { - "line": 74, + "line": 93, "column": 27 }, "end": { - "line": 74, + "line": 93, "column": 34 } } @@ -25985,15 +29152,15 @@ "binop": null, "updateContext": null }, - "start": 2594, - "end": 2595, + "start": 3098, + "end": 3099, "loc": { "start": { - "line": 74, + "line": 93, "column": 34 }, "end": { - "line": 74, + "line": 93, "column": 35 } } @@ -26010,15 +29177,15 @@ "postfix": false, "binop": null }, - "start": 2595, - "end": 2596, + "start": 3099, + "end": 3100, "loc": { "start": { - "line": 74, + "line": 93, "column": 35 }, "end": { - "line": 74, + "line": 93, "column": 36 } } @@ -26035,15 +29202,15 @@ "postfix": false, "binop": null }, - "start": 2596, - "end": 2597, + "start": 3100, + "end": 3101, "loc": { "start": { - "line": 74, + "line": 93, "column": 36 }, "end": { - "line": 74, + "line": 93, "column": 37 } } @@ -26063,15 +29230,15 @@ "updateContext": null }, "value": "return", - "start": 2598, - "end": 2604, + "start": 3102, + "end": 3108, "loc": { "start": { - "line": 74, + "line": 93, "column": 38 }, "end": { - "line": 74, + "line": 93, "column": 44 } } @@ -26091,15 +29258,15 @@ "updateContext": null }, "value": "this", - "start": 2605, - "end": 2609, + "start": 3109, + "end": 3113, "loc": { "start": { - "line": 74, + "line": 93, "column": 45 }, "end": { - "line": 74, + "line": 93, "column": 49 } } @@ -26117,15 +29284,15 @@ "binop": null, "updateContext": null }, - "start": 2609, - "end": 2610, + "start": 3113, + "end": 3114, "loc": { "start": { - "line": 74, + "line": 93, "column": 49 }, "end": { - "line": 74, + "line": 93, "column": 50 } } @@ -26143,15 +29310,15 @@ "binop": null }, "value": "tunit", - "start": 2610, - "end": 2615, + "start": 3114, + "end": 3119, "loc": { "start": { - "line": 74, + "line": 93, "column": 50 }, "end": { - "line": 74, + "line": 93, "column": 55 } } @@ -26169,15 +29336,15 @@ "binop": null, "updateContext": null }, - "start": 2615, - "end": 2616, + "start": 3119, + "end": 3120, "loc": { "start": { - "line": 74, + "line": 93, "column": 55 }, "end": { - "line": 74, + "line": 93, "column": 56 } } @@ -26196,15 +29363,15 @@ "updateContext": null }, "value": "@type", - "start": 2616, - "end": 2623, + "start": 3120, + "end": 3127, "loc": { "start": { - "line": 74, + "line": 93, "column": 56 }, "end": { - "line": 74, + "line": 93, "column": 63 } } @@ -26222,15 +29389,15 @@ "binop": null, "updateContext": null }, - "start": 2623, - "end": 2624, + "start": 3127, + "end": 3128, "loc": { "start": { - "line": 74, + "line": 93, "column": 63 }, "end": { - "line": 74, + "line": 93, "column": 64 } } @@ -26248,15 +29415,15 @@ "binop": null, "updateContext": null }, - "start": 2624, - "end": 2625, + "start": 3128, + "end": 3129, "loc": { "start": { - "line": 74, + "line": 93, "column": 64 }, "end": { - "line": 74, + "line": 93, "column": 65 } } @@ -26276,15 +29443,15 @@ "updateContext": null }, "value": "return", - "start": 2630, - "end": 2636, + "start": 3134, + "end": 3140, "loc": { "start": { - "line": 75, + "line": 94, "column": 4 }, "end": { - "line": 75, + "line": 94, "column": 10 } } @@ -26302,15 +29469,15 @@ "binop": null, "updateContext": null }, - "start": 2637, - "end": 2638, + "start": 3141, + "end": 3142, "loc": { "start": { - "line": 75, + "line": 94, "column": 11 }, "end": { - "line": 75, + "line": 94, "column": 12 } } @@ -26330,15 +29497,15 @@ "updateContext": null }, "value": "this", - "start": 2638, - "end": 2642, + "start": 3142, + "end": 3146, "loc": { "start": { - "line": 75, + "line": 94, "column": 12 }, "end": { - "line": 75, + "line": 94, "column": 16 } } @@ -26356,15 +29523,15 @@ "binop": null, "updateContext": null }, - "start": 2642, - "end": 2643, + "start": 3146, + "end": 3147, "loc": { "start": { - "line": 75, + "line": 94, "column": 16 }, "end": { - "line": 75, + "line": 94, "column": 17 } } @@ -26382,15 +29549,15 @@ "binop": null }, "value": "tunit", - "start": 2643, - "end": 2648, + "start": 3147, + "end": 3152, "loc": { "start": { - "line": 75, + "line": 94, "column": 17 }, "end": { - "line": 75, + "line": 94, "column": 22 } } @@ -26408,15 +29575,15 @@ "binop": null, "updateContext": null }, - "start": 2648, - "end": 2649, + "start": 3152, + "end": 3153, "loc": { "start": { - "line": 75, + "line": 94, "column": 22 }, "end": { - "line": 75, + "line": 94, "column": 23 } } @@ -26435,15 +29602,15 @@ "updateContext": null }, "value": "@type", - "start": 2649, - "end": 2656, + "start": 3153, + "end": 3160, "loc": { "start": { - "line": 75, + "line": 94, "column": 23 }, "end": { - "line": 75, + "line": 94, "column": 30 } } @@ -26461,15 +29628,15 @@ "binop": null, "updateContext": null }, - "start": 2656, - "end": 2657, + "start": 3160, + "end": 3161, "loc": { "start": { - "line": 75, + "line": 94, "column": 30 }, "end": { - "line": 75, + "line": 94, "column": 31 } } @@ -26487,15 +29654,15 @@ "binop": null, "updateContext": null }, - "start": 2657, - "end": 2658, + "start": 3161, + "end": 3162, "loc": { "start": { - "line": 75, + "line": 94, "column": 31 }, "end": { - "line": 75, + "line": 94, "column": 32 } } @@ -26513,15 +29680,15 @@ "binop": null, "updateContext": null }, - "start": 2658, - "end": 2659, + "start": 3162, + "end": 3163, "loc": { "start": { - "line": 75, + "line": 94, "column": 32 }, "end": { - "line": 75, + "line": 94, "column": 33 } } @@ -26538,15 +29705,15 @@ "postfix": false, "binop": null }, - "start": 2662, - "end": 2663, + "start": 3166, + "end": 3167, "loc": { "start": { - "line": 76, + "line": 95, "column": 2 }, "end": { - "line": 76, + "line": 95, "column": 3 } } @@ -26554,15 +29721,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxonomic unit if it is a taxon concept.\n ", - "start": 2667, - "end": 2734, + "start": 3171, + "end": 3238, "loc": { "start": { - "line": 78, + "line": 97, "column": 2 }, "end": { - "line": 80, + "line": 99, "column": 5 } } @@ -26580,15 +29747,15 @@ "binop": null }, "value": "get", - "start": 2737, - "end": 2740, + "start": 3241, + "end": 3244, "loc": { "start": { - "line": 81, + "line": 100, "column": 2 }, "end": { - "line": 81, + "line": 100, "column": 5 } } @@ -26606,15 +29773,15 @@ "binop": null }, "value": "taxonConcept", - "start": 2741, - "end": 2753, + "start": 3245, + "end": 3257, "loc": { "start": { - "line": 81, + "line": 100, "column": 6 }, "end": { - "line": 81, + "line": 100, "column": 18 } } @@ -26631,15 +29798,15 @@ "postfix": false, "binop": null }, - "start": 2753, - "end": 2754, + "start": 3257, + "end": 3258, "loc": { "start": { - "line": 81, + "line": 100, "column": 18 }, "end": { - "line": 81, + "line": 100, "column": 19 } } @@ -26656,15 +29823,15 @@ "postfix": false, "binop": null }, - "start": 2754, - "end": 2755, + "start": 3258, + "end": 3259, "loc": { "start": { - "line": 81, + "line": 100, "column": 19 }, "end": { - "line": 81, + "line": 100, "column": 20 } } @@ -26681,15 +29848,15 @@ "postfix": false, "binop": null }, - "start": 2756, - "end": 2757, + "start": 3260, + "end": 3261, "loc": { "start": { - "line": 81, + "line": 100, "column": 21 }, "end": { - "line": 81, + "line": 100, "column": 22 } } @@ -26709,15 +29876,15 @@ "updateContext": null }, "value": "if", - "start": 2762, - "end": 2764, + "start": 3266, + "end": 3268, "loc": { "start": { - "line": 82, + "line": 101, "column": 4 }, "end": { - "line": 82, + "line": 101, "column": 6 } } @@ -26734,15 +29901,15 @@ "postfix": false, "binop": null }, - "start": 2765, - "end": 2766, + "start": 3269, + "end": 3270, "loc": { "start": { - "line": 82, + "line": 101, "column": 7 }, "end": { - "line": 82, + "line": 101, "column": 8 } } @@ -26762,15 +29929,15 @@ "updateContext": null }, "value": "this", - "start": 2766, - "end": 2770, + "start": 3270, + "end": 3274, "loc": { "start": { - "line": 82, + "line": 101, "column": 8 }, "end": { - "line": 82, + "line": 101, "column": 12 } } @@ -26788,15 +29955,15 @@ "binop": null, "updateContext": null }, - "start": 2770, - "end": 2771, + "start": 3274, + "end": 3275, "loc": { "start": { - "line": 82, + "line": 101, "column": 12 }, "end": { - "line": 82, + "line": 101, "column": 13 } } @@ -26814,15 +29981,15 @@ "binop": null }, "value": "types", - "start": 2771, - "end": 2776, + "start": 3275, + "end": 3280, "loc": { "start": { - "line": 82, + "line": 101, "column": 13 }, "end": { - "line": 82, + "line": 101, "column": 18 } } @@ -26840,15 +30007,15 @@ "binop": null, "updateContext": null }, - "start": 2776, - "end": 2777, + "start": 3280, + "end": 3281, "loc": { "start": { - "line": 82, + "line": 101, "column": 18 }, "end": { - "line": 82, + "line": 101, "column": 19 } } @@ -26866,15 +30033,15 @@ "binop": null }, "value": "includes", - "start": 2777, - "end": 2785, + "start": 3281, + "end": 3289, "loc": { "start": { - "line": 82, + "line": 101, "column": 19 }, "end": { - "line": 82, + "line": 101, "column": 27 } } @@ -26891,15 +30058,15 @@ "postfix": false, "binop": null }, - "start": 2785, - "end": 2786, + "start": 3289, + "end": 3290, "loc": { "start": { - "line": 82, + "line": 101, "column": 27 }, "end": { - "line": 82, + "line": 101, "column": 28 } } @@ -26917,15 +30084,15 @@ "binop": null }, "value": "TaxonomicUnitWrapper", - "start": 2786, - "end": 2806, + "start": 3290, + "end": 3310, "loc": { "start": { - "line": 82, + "line": 101, "column": 28 }, "end": { - "line": 82, + "line": 101, "column": 48 } } @@ -26943,15 +30110,15 @@ "binop": null, "updateContext": null }, - "start": 2806, - "end": 2807, + "start": 3310, + "end": 3311, "loc": { "start": { - "line": 82, + "line": 101, "column": 48 }, "end": { - "line": 82, + "line": 101, "column": 49 } } @@ -26969,15 +30136,15 @@ "binop": null }, "value": "TYPE_TAXON_CONCEPT", - "start": 2807, - "end": 2825, + "start": 3311, + "end": 3329, "loc": { "start": { - "line": 82, + "line": 101, "column": 49 }, "end": { - "line": 82, + "line": 101, "column": 67 } } @@ -26994,15 +30161,15 @@ "postfix": false, "binop": null }, - "start": 2825, - "end": 2826, + "start": 3329, + "end": 3330, "loc": { "start": { - "line": 82, + "line": 101, "column": 67 }, "end": { - "line": 82, + "line": 101, "column": 68 } } @@ -27019,15 +30186,15 @@ "postfix": false, "binop": null }, - "start": 2826, - "end": 2827, + "start": 3330, + "end": 3331, "loc": { "start": { - "line": 82, + "line": 101, "column": 68 }, "end": { - "line": 82, + "line": 101, "column": 69 } } @@ -27047,15 +30214,15 @@ "updateContext": null }, "value": "return", - "start": 2828, - "end": 2834, + "start": 3332, + "end": 3338, "loc": { "start": { - "line": 82, + "line": 101, "column": 70 }, "end": { - "line": 82, + "line": 101, "column": 76 } } @@ -27075,15 +30242,15 @@ "updateContext": null }, "value": "this", - "start": 2835, - "end": 2839, + "start": 3339, + "end": 3343, "loc": { "start": { - "line": 82, + "line": 101, "column": 77 }, "end": { - "line": 82, + "line": 101, "column": 81 } } @@ -27101,15 +30268,15 @@ "binop": null, "updateContext": null }, - "start": 2839, - "end": 2840, + "start": 3343, + "end": 3344, "loc": { "start": { - "line": 82, + "line": 101, "column": 81 }, "end": { - "line": 82, + "line": 101, "column": 82 } } @@ -27127,15 +30294,15 @@ "binop": null }, "value": "tunit", - "start": 2840, - "end": 2845, + "start": 3344, + "end": 3349, "loc": { "start": { - "line": 82, + "line": 101, "column": 82 }, "end": { - "line": 82, + "line": 101, "column": 87 } } @@ -27153,15 +30320,15 @@ "binop": null, "updateContext": null }, - "start": 2845, - "end": 2846, + "start": 3349, + "end": 3350, "loc": { "start": { - "line": 82, + "line": 101, "column": 87 }, "end": { - "line": 82, + "line": 101, "column": 88 } } @@ -27181,15 +30348,15 @@ "updateContext": null }, "value": "return", - "start": 2851, - "end": 2857, + "start": 3355, + "end": 3361, "loc": { "start": { - "line": 83, + "line": 102, "column": 4 }, "end": { - "line": 83, + "line": 102, "column": 10 } } @@ -27207,15 +30374,15 @@ "binop": null }, "value": "undefined", - "start": 2858, - "end": 2867, + "start": 3362, + "end": 3371, "loc": { "start": { - "line": 83, + "line": 102, "column": 11 }, "end": { - "line": 83, + "line": 102, "column": 20 } } @@ -27233,15 +30400,15 @@ "binop": null, "updateContext": null }, - "start": 2867, - "end": 2868, + "start": 3371, + "end": 3372, "loc": { "start": { - "line": 83, + "line": 102, "column": 20 }, "end": { - "line": 83, + "line": 102, "column": 21 } } @@ -27258,15 +30425,15 @@ "postfix": false, "binop": null }, - "start": 2871, - "end": 2872, + "start": 3375, + "end": 3376, "loc": { "start": { - "line": 84, + "line": 103, "column": 2 }, "end": { - "line": 84, + "line": 103, "column": 3 } } @@ -27274,15 +30441,15 @@ { "type": "CommentBlock", "value": "*\n * Return this taxonomic unit if it is a specimen.\n ", - "start": 2876, - "end": 2938, + "start": 3380, + "end": 3442, "loc": { "start": { - "line": 86, + "line": 105, "column": 2 }, "end": { - "line": 88, + "line": 107, "column": 5 } } @@ -27300,15 +30467,15 @@ "binop": null }, "value": "get", - "start": 2941, - "end": 2944, + "start": 3445, + "end": 3448, "loc": { "start": { - "line": 89, + "line": 108, "column": 2 }, "end": { - "line": 89, + "line": 108, "column": 5 } } @@ -27326,15 +30493,15 @@ "binop": null }, "value": "specimen", - "start": 2945, - "end": 2953, + "start": 3449, + "end": 3457, "loc": { "start": { - "line": 89, + "line": 108, "column": 6 }, "end": { - "line": 89, + "line": 108, "column": 14 } } @@ -27351,15 +30518,15 @@ "postfix": false, "binop": null }, - "start": 2953, - "end": 2954, + "start": 3457, + "end": 3458, "loc": { "start": { - "line": 89, + "line": 108, "column": 14 }, "end": { - "line": 89, + "line": 108, "column": 15 } } @@ -27376,15 +30543,15 @@ "postfix": false, "binop": null }, - "start": 2954, - "end": 2955, + "start": 3458, + "end": 3459, "loc": { "start": { - "line": 89, + "line": 108, "column": 15 }, "end": { - "line": 89, + "line": 108, "column": 16 } } @@ -27401,15 +30568,15 @@ "postfix": false, "binop": null }, - "start": 2956, - "end": 2957, + "start": 3460, + "end": 3461, "loc": { "start": { - "line": 89, + "line": 108, "column": 17 }, "end": { - "line": 89, + "line": 108, "column": 18 } } @@ -27417,15 +30584,15 @@ { "type": "CommentLine", "value": " Only specimens have scientific names.", - "start": 2962, - "end": 3002, + "start": 3466, + "end": 3506, "loc": { "start": { - "line": 90, + "line": 109, "column": 4 }, "end": { - "line": 90, + "line": 109, "column": 44 } } @@ -27445,15 +30612,15 @@ "updateContext": null }, "value": "if", - "start": 3007, - "end": 3009, + "start": 3511, + "end": 3513, "loc": { "start": { - "line": 91, + "line": 110, "column": 4 }, "end": { - "line": 91, + "line": 110, "column": 6 } } @@ -27470,15 +30637,15 @@ "postfix": false, "binop": null }, - "start": 3010, - "end": 3011, + "start": 3514, + "end": 3515, "loc": { "start": { - "line": 91, + "line": 110, "column": 7 }, "end": { - "line": 91, + "line": 110, "column": 8 } } @@ -27498,15 +30665,15 @@ "updateContext": null }, "value": "this", - "start": 3011, - "end": 3015, + "start": 3515, + "end": 3519, "loc": { "start": { - "line": 91, + "line": 110, "column": 8 }, "end": { - "line": 91, + "line": 110, "column": 12 } } @@ -27524,15 +30691,15 @@ "binop": null, "updateContext": null }, - "start": 3015, - "end": 3016, + "start": 3519, + "end": 3520, "loc": { "start": { - "line": 91, + "line": 110, "column": 12 }, "end": { - "line": 91, + "line": 110, "column": 13 } } @@ -27550,15 +30717,15 @@ "binop": null }, "value": "types", - "start": 3016, - "end": 3021, + "start": 3520, + "end": 3525, "loc": { "start": { - "line": 91, + "line": 110, "column": 13 }, "end": { - "line": 91, + "line": 110, "column": 18 } } @@ -27576,15 +30743,15 @@ "binop": null, "updateContext": null }, - "start": 3021, - "end": 3022, + "start": 3525, + "end": 3526, "loc": { "start": { - "line": 91, + "line": 110, "column": 18 }, "end": { - "line": 91, + "line": 110, "column": 19 } } @@ -27602,15 +30769,15 @@ "binop": null }, "value": "includes", - "start": 3022, - "end": 3030, + "start": 3526, + "end": 3534, "loc": { "start": { - "line": 91, + "line": 110, "column": 19 }, "end": { - "line": 91, + "line": 110, "column": 27 } } @@ -27627,15 +30794,15 @@ "postfix": false, "binop": null }, - "start": 3030, - "end": 3031, + "start": 3534, + "end": 3535, "loc": { "start": { - "line": 91, + "line": 110, "column": 27 }, "end": { - "line": 91, + "line": 110, "column": 28 } } @@ -27653,15 +30820,15 @@ "binop": null }, "value": "TaxonomicUnitWrapper", - "start": 3031, - "end": 3051, + "start": 3535, + "end": 3555, "loc": { "start": { - "line": 91, + "line": 110, "column": 28 }, "end": { - "line": 91, + "line": 110, "column": 48 } } @@ -27679,15 +30846,15 @@ "binop": null, "updateContext": null }, - "start": 3051, - "end": 3052, + "start": 3555, + "end": 3556, "loc": { "start": { - "line": 91, + "line": 110, "column": 48 }, "end": { - "line": 91, + "line": 110, "column": 49 } } @@ -27705,15 +30872,15 @@ "binop": null }, "value": "TYPE_SPECIMEN", - "start": 3052, - "end": 3065, + "start": 3556, + "end": 3569, "loc": { "start": { - "line": 91, + "line": 110, "column": 49 }, "end": { - "line": 91, + "line": 110, "column": 62 } } @@ -27730,15 +30897,15 @@ "postfix": false, "binop": null }, - "start": 3065, - "end": 3066, + "start": 3569, + "end": 3570, "loc": { "start": { - "line": 91, + "line": 110, "column": 62 }, "end": { - "line": 91, + "line": 110, "column": 63 } } @@ -27755,15 +30922,15 @@ "postfix": false, "binop": null }, - "start": 3066, - "end": 3067, + "start": 3570, + "end": 3571, "loc": { "start": { - "line": 91, + "line": 110, "column": 63 }, "end": { - "line": 91, + "line": 110, "column": 64 } } @@ -27783,15 +30950,15 @@ "updateContext": null }, "value": "return", - "start": 3068, - "end": 3074, + "start": 3572, + "end": 3578, "loc": { "start": { - "line": 91, + "line": 110, "column": 65 }, "end": { - "line": 91, + "line": 110, "column": 71 } } @@ -27811,15 +30978,15 @@ "updateContext": null }, "value": "this", - "start": 3075, - "end": 3079, + "start": 3579, + "end": 3583, "loc": { "start": { - "line": 91, + "line": 110, "column": 72 }, "end": { - "line": 91, + "line": 110, "column": 76 } } @@ -27837,15 +31004,15 @@ "binop": null, "updateContext": null }, - "start": 3079, - "end": 3080, + "start": 3583, + "end": 3584, "loc": { "start": { - "line": 91, + "line": 110, "column": 76 }, "end": { - "line": 91, + "line": 110, "column": 77 } } @@ -27863,15 +31030,15 @@ "binop": null }, "value": "tunit", - "start": 3080, - "end": 3085, + "start": 3584, + "end": 3589, "loc": { "start": { - "line": 91, + "line": 110, "column": 77 }, "end": { - "line": 91, + "line": 110, "column": 82 } } @@ -27889,15 +31056,15 @@ "binop": null, "updateContext": null }, - "start": 3085, - "end": 3086, + "start": 3589, + "end": 3590, "loc": { "start": { - "line": 91, + "line": 110, "column": 82 }, "end": { - "line": 91, + "line": 110, "column": 83 } } @@ -27917,15 +31084,15 @@ "updateContext": null }, "value": "return", - "start": 3092, - "end": 3098, + "start": 3596, + "end": 3602, "loc": { "start": { - "line": 93, + "line": 112, "column": 4 }, "end": { - "line": 93, + "line": 112, "column": 10 } } @@ -27943,15 +31110,15 @@ "binop": null }, "value": "undefined", - "start": 3099, - "end": 3108, + "start": 3603, + "end": 3612, "loc": { "start": { - "line": 93, + "line": 112, "column": 11 }, "end": { - "line": 93, + "line": 112, "column": 20 } } @@ -27969,15 +31136,15 @@ "binop": null, "updateContext": null }, - "start": 3108, - "end": 3109, + "start": 3612, + "end": 3613, "loc": { "start": { - "line": 93, + "line": 112, "column": 20 }, "end": { - "line": 93, + "line": 112, "column": 21 } } @@ -27994,15 +31161,15 @@ "postfix": false, "binop": null }, - "start": 3112, - "end": 3113, + "start": 3616, + "end": 3617, "loc": { "start": { - "line": 94, + "line": 113, "column": 2 }, "end": { - "line": 94, + "line": 113, "column": 3 } } @@ -28010,15 +31177,15 @@ { "type": "CommentBlock", "value": "*\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n ", - "start": 3117, - "end": 3244, + "start": 3621, + "end": 3748, "loc": { "start": { - "line": 96, + "line": 115, "column": 2 }, "end": { - "line": 99, + "line": 118, "column": 5 } } @@ -28036,15 +31203,15 @@ "binop": null }, "value": "get", - "start": 3247, - "end": 3250, + "start": 3751, + "end": 3754, "loc": { "start": { - "line": 100, + "line": 119, "column": 2 }, "end": { - "line": 100, + "line": 119, "column": 5 } } @@ -28062,15 +31229,15 @@ "binop": null }, "value": "externalReferences", - "start": 3251, - "end": 3269, + "start": 3755, + "end": 3773, "loc": { "start": { - "line": 100, + "line": 119, "column": 6 }, "end": { - "line": 100, + "line": 119, "column": 24 } } @@ -28087,15 +31254,15 @@ "postfix": false, "binop": null }, - "start": 3269, - "end": 3270, + "start": 3773, + "end": 3774, "loc": { "start": { - "line": 100, + "line": 119, "column": 24 }, "end": { - "line": 100, + "line": 119, "column": 25 } } @@ -28112,15 +31279,15 @@ "postfix": false, "binop": null }, - "start": 3270, - "end": 3271, + "start": 3774, + "end": 3775, "loc": { "start": { - "line": 100, + "line": 119, "column": 25 }, "end": { - "line": 100, + "line": 119, "column": 26 } } @@ -28137,15 +31304,15 @@ "postfix": false, "binop": null }, - "start": 3272, - "end": 3273, + "start": 3776, + "end": 3777, "loc": { "start": { - "line": 100, + "line": 119, "column": 27 }, "end": { - "line": 100, + "line": 119, "column": 28 } } @@ -28165,15 +31332,15 @@ "updateContext": null }, "value": "if", - "start": 3278, - "end": 3280, + "start": 3782, + "end": 3784, "loc": { "start": { - "line": 101, + "line": 120, "column": 4 }, "end": { - "line": 101, + "line": 120, "column": 6 } } @@ -28190,15 +31357,15 @@ "postfix": false, "binop": null }, - "start": 3281, - "end": 3282, + "start": 3785, + "end": 3786, "loc": { "start": { - "line": 101, + "line": 120, "column": 7 }, "end": { - "line": 101, + "line": 120, "column": 8 } } @@ -28217,15 +31384,15 @@ "updateContext": null }, "value": "!", - "start": 3282, - "end": 3283, + "start": 3786, + "end": 3787, "loc": { "start": { - "line": 101, + "line": 120, "column": 8 }, "end": { - "line": 101, + "line": 120, "column": 9 } } @@ -28243,15 +31410,15 @@ "binop": null }, "value": "has", - "start": 3283, - "end": 3286, + "start": 3787, + "end": 3790, "loc": { "start": { - "line": 101, + "line": 120, "column": 9 }, "end": { - "line": 101, + "line": 120, "column": 12 } } @@ -28268,15 +31435,15 @@ "postfix": false, "binop": null }, - "start": 3286, - "end": 3287, + "start": 3790, + "end": 3791, "loc": { "start": { - "line": 101, + "line": 120, "column": 12 }, "end": { - "line": 101, + "line": 120, "column": 13 } } @@ -28296,15 +31463,15 @@ "updateContext": null }, "value": "this", - "start": 3287, - "end": 3291, + "start": 3791, + "end": 3795, "loc": { "start": { - "line": 101, + "line": 120, "column": 13 }, "end": { - "line": 101, + "line": 120, "column": 17 } } @@ -28322,15 +31489,15 @@ "binop": null, "updateContext": null }, - "start": 3291, - "end": 3292, + "start": 3795, + "end": 3796, "loc": { "start": { - "line": 101, + "line": 120, "column": 17 }, "end": { - "line": 101, + "line": 120, "column": 18 } } @@ -28348,15 +31515,15 @@ "binop": null }, "value": "tunit", - "start": 3292, - "end": 3297, + "start": 3796, + "end": 3801, "loc": { "start": { - "line": 101, + "line": 120, "column": 18 }, "end": { - "line": 101, + "line": 120, "column": 23 } } @@ -28374,15 +31541,15 @@ "binop": null, "updateContext": null }, - "start": 3297, - "end": 3298, + "start": 3801, + "end": 3802, "loc": { "start": { - "line": 101, + "line": 120, "column": 23 }, "end": { - "line": 101, + "line": 120, "column": 24 } } @@ -28401,15 +31568,15 @@ "updateContext": null }, "value": "@id", - "start": 3299, - "end": 3304, + "start": 3803, + "end": 3808, "loc": { "start": { - "line": 101, + "line": 120, "column": 25 }, "end": { - "line": 101, + "line": 120, "column": 30 } } @@ -28426,15 +31593,15 @@ "postfix": false, "binop": null }, - "start": 3304, - "end": 3305, + "start": 3808, + "end": 3809, "loc": { "start": { - "line": 101, + "line": 120, "column": 30 }, "end": { - "line": 101, + "line": 120, "column": 31 } } @@ -28451,15 +31618,15 @@ "postfix": false, "binop": null }, - "start": 3305, - "end": 3306, + "start": 3809, + "end": 3810, "loc": { "start": { - "line": 101, + "line": 120, "column": 31 }, "end": { - "line": 101, + "line": 120, "column": 32 } } @@ -28479,15 +31646,15 @@ "updateContext": null }, "value": "return", - "start": 3307, - "end": 3313, + "start": 3811, + "end": 3817, "loc": { "start": { - "line": 101, + "line": 120, "column": 33 }, "end": { - "line": 101, + "line": 120, "column": 39 } } @@ -28505,15 +31672,15 @@ "binop": null, "updateContext": null }, - "start": 3314, - "end": 3315, + "start": 3818, + "end": 3819, "loc": { "start": { - "line": 101, + "line": 120, "column": 40 }, "end": { - "line": 101, + "line": 120, "column": 41 } } @@ -28531,15 +31698,15 @@ "binop": null, "updateContext": null }, - "start": 3315, - "end": 3316, + "start": 3819, + "end": 3820, "loc": { "start": { - "line": 101, + "line": 120, "column": 41 }, "end": { - "line": 101, + "line": 120, "column": 42 } } @@ -28557,15 +31724,15 @@ "binop": null, "updateContext": null }, - "start": 3316, - "end": 3317, + "start": 3820, + "end": 3821, "loc": { "start": { - "line": 101, + "line": 120, "column": 42 }, "end": { - "line": 101, + "line": 120, "column": 43 } } @@ -28585,15 +31752,15 @@ "updateContext": null }, "value": "if", - "start": 3322, - "end": 3324, + "start": 3826, + "end": 3828, "loc": { "start": { - "line": 102, + "line": 121, "column": 4 }, "end": { - "line": 102, + "line": 121, "column": 6 } } @@ -28610,15 +31777,15 @@ "postfix": false, "binop": null }, - "start": 3325, - "end": 3326, + "start": 3829, + "end": 3830, "loc": { "start": { - "line": 102, + "line": 121, "column": 7 }, "end": { - "line": 102, + "line": 121, "column": 8 } } @@ -28636,15 +31803,15 @@ "binop": null }, "value": "isArray", - "start": 3326, - "end": 3333, + "start": 3830, + "end": 3837, "loc": { "start": { - "line": 102, + "line": 121, "column": 8 }, "end": { - "line": 102, + "line": 121, "column": 15 } } @@ -28661,15 +31828,15 @@ "postfix": false, "binop": null }, - "start": 3333, - "end": 3334, + "start": 3837, + "end": 3838, "loc": { "start": { - "line": 102, + "line": 121, "column": 15 }, "end": { - "line": 102, + "line": 121, "column": 16 } } @@ -28689,15 +31856,15 @@ "updateContext": null }, "value": "this", - "start": 3334, - "end": 3338, + "start": 3838, + "end": 3842, "loc": { "start": { - "line": 102, + "line": 121, "column": 16 }, "end": { - "line": 102, + "line": 121, "column": 20 } } @@ -28715,15 +31882,15 @@ "binop": null, "updateContext": null }, - "start": 3338, - "end": 3339, + "start": 3842, + "end": 3843, "loc": { "start": { - "line": 102, + "line": 121, "column": 20 }, "end": { - "line": 102, + "line": 121, "column": 21 } } @@ -28741,15 +31908,15 @@ "binop": null }, "value": "tunit", - "start": 3339, - "end": 3344, + "start": 3843, + "end": 3848, "loc": { "start": { - "line": 102, + "line": 121, "column": 21 }, "end": { - "line": 102, + "line": 121, "column": 26 } } @@ -28767,15 +31934,15 @@ "binop": null, "updateContext": null }, - "start": 3344, - "end": 3345, + "start": 3848, + "end": 3849, "loc": { "start": { - "line": 102, + "line": 121, "column": 26 }, "end": { - "line": 102, + "line": 121, "column": 27 } } @@ -28794,15 +31961,15 @@ "updateContext": null }, "value": "@id", - "start": 3345, - "end": 3350, + "start": 3849, + "end": 3854, "loc": { "start": { - "line": 102, + "line": 121, "column": 27 }, "end": { - "line": 102, + "line": 121, "column": 32 } } @@ -28820,15 +31987,15 @@ "binop": null, "updateContext": null }, - "start": 3350, - "end": 3351, + "start": 3854, + "end": 3855, "loc": { "start": { - "line": 102, + "line": 121, "column": 32 }, "end": { - "line": 102, + "line": 121, "column": 33 } } @@ -28845,15 +32012,15 @@ "postfix": false, "binop": null }, - "start": 3351, - "end": 3352, + "start": 3855, + "end": 3856, "loc": { "start": { - "line": 102, + "line": 121, "column": 33 }, "end": { - "line": 102, + "line": 121, "column": 34 } } @@ -28870,15 +32037,15 @@ "postfix": false, "binop": null }, - "start": 3352, - "end": 3353, + "start": 3856, + "end": 3857, "loc": { "start": { - "line": 102, + "line": 121, "column": 34 }, "end": { - "line": 102, + "line": 121, "column": 35 } } @@ -28898,15 +32065,15 @@ "updateContext": null }, "value": "return", - "start": 3354, - "end": 3360, + "start": 3858, + "end": 3864, "loc": { "start": { - "line": 102, + "line": 121, "column": 36 }, "end": { - "line": 102, + "line": 121, "column": 42 } } @@ -28926,15 +32093,15 @@ "updateContext": null }, "value": "this", - "start": 3361, - "end": 3365, + "start": 3865, + "end": 3869, "loc": { "start": { - "line": 102, + "line": 121, "column": 43 }, "end": { - "line": 102, + "line": 121, "column": 47 } } @@ -28952,15 +32119,15 @@ "binop": null, "updateContext": null }, - "start": 3365, - "end": 3366, + "start": 3869, + "end": 3870, "loc": { "start": { - "line": 102, + "line": 121, "column": 47 }, "end": { - "line": 102, + "line": 121, "column": 48 } } @@ -28978,15 +32145,15 @@ "binop": null }, "value": "tunit", - "start": 3366, - "end": 3371, + "start": 3870, + "end": 3875, "loc": { "start": { - "line": 102, + "line": 121, "column": 48 }, "end": { - "line": 102, + "line": 121, "column": 53 } } @@ -29004,15 +32171,15 @@ "binop": null, "updateContext": null }, - "start": 3371, - "end": 3372, + "start": 3875, + "end": 3876, "loc": { "start": { - "line": 102, + "line": 121, "column": 53 }, "end": { - "line": 102, + "line": 121, "column": 54 } } @@ -29031,15 +32198,15 @@ "updateContext": null }, "value": "@id", - "start": 3372, - "end": 3377, + "start": 3876, + "end": 3881, "loc": { "start": { - "line": 102, + "line": 121, "column": 54 }, "end": { - "line": 102, + "line": 121, "column": 59 } } @@ -29057,15 +32224,15 @@ "binop": null, "updateContext": null }, - "start": 3377, - "end": 3378, + "start": 3881, + "end": 3882, "loc": { "start": { - "line": 102, + "line": 121, "column": 59 }, "end": { - "line": 102, + "line": 121, "column": 60 } } @@ -29083,15 +32250,15 @@ "binop": null, "updateContext": null }, - "start": 3378, - "end": 3379, + "start": 3882, + "end": 3883, "loc": { "start": { - "line": 102, + "line": 121, "column": 60 }, "end": { - "line": 102, + "line": 121, "column": 61 } } @@ -29111,15 +32278,15 @@ "updateContext": null }, "value": "return", - "start": 3384, - "end": 3390, + "start": 3888, + "end": 3894, "loc": { "start": { - "line": 103, + "line": 122, "column": 4 }, "end": { - "line": 103, + "line": 122, "column": 10 } } @@ -29137,15 +32304,15 @@ "binop": null, "updateContext": null }, - "start": 3391, - "end": 3392, + "start": 3895, + "end": 3896, "loc": { "start": { - "line": 103, + "line": 122, "column": 11 }, "end": { - "line": 103, + "line": 122, "column": 12 } } @@ -29165,15 +32332,15 @@ "updateContext": null }, "value": "this", - "start": 3392, - "end": 3396, + "start": 3896, + "end": 3900, "loc": { "start": { - "line": 103, + "line": 122, "column": 12 }, "end": { - "line": 103, + "line": 122, "column": 16 } } @@ -29191,15 +32358,15 @@ "binop": null, "updateContext": null }, - "start": 3396, - "end": 3397, + "start": 3900, + "end": 3901, "loc": { "start": { - "line": 103, + "line": 122, "column": 16 }, "end": { - "line": 103, + "line": 122, "column": 17 } } @@ -29217,15 +32384,15 @@ "binop": null }, "value": "tunit", - "start": 3397, - "end": 3402, + "start": 3901, + "end": 3906, "loc": { "start": { - "line": 103, + "line": 122, "column": 17 }, "end": { - "line": 103, + "line": 122, "column": 22 } } @@ -29243,15 +32410,15 @@ "binop": null, "updateContext": null }, - "start": 3402, - "end": 3403, + "start": 3906, + "end": 3907, "loc": { "start": { - "line": 103, + "line": 122, "column": 22 }, "end": { - "line": 103, + "line": 122, "column": 23 } } @@ -29270,15 +32437,15 @@ "updateContext": null }, "value": "@id", - "start": 3403, - "end": 3408, + "start": 3907, + "end": 3912, "loc": { "start": { - "line": 103, + "line": 122, "column": 23 }, "end": { - "line": 103, + "line": 122, "column": 28 } } @@ -29296,15 +32463,15 @@ "binop": null, "updateContext": null }, - "start": 3408, - "end": 3409, + "start": 3912, + "end": 3913, "loc": { "start": { - "line": 103, + "line": 122, "column": 28 }, "end": { - "line": 103, + "line": 122, "column": 29 } } @@ -29322,15 +32489,15 @@ "binop": null, "updateContext": null }, - "start": 3409, - "end": 3410, + "start": 3913, + "end": 3914, "loc": { "start": { - "line": 103, + "line": 122, "column": 29 }, "end": { - "line": 103, + "line": 122, "column": 30 } } @@ -29348,15 +32515,15 @@ "binop": null, "updateContext": null }, - "start": 3410, - "end": 3411, + "start": 3914, + "end": 3915, "loc": { "start": { - "line": 103, + "line": 122, "column": 30 }, "end": { - "line": 103, + "line": 122, "column": 31 } } @@ -29373,15 +32540,15 @@ "postfix": false, "binop": null }, - "start": 3414, - "end": 3415, + "start": 3918, + "end": 3919, "loc": { "start": { - "line": 104, + "line": 123, "column": 2 }, "end": { - "line": 104, + "line": 123, "column": 3 } } @@ -29389,15 +32556,15 @@ { "type": "CommentBlock", "value": "*\n * Return the label of this taxonomic unit.\n ", - "start": 3419, - "end": 3474, + "start": 3923, + "end": 3978, "loc": { "start": { - "line": 106, + "line": 125, "column": 2 }, "end": { - "line": 108, + "line": 127, "column": 5 } } @@ -29415,15 +32582,15 @@ "binop": null }, "value": "get", - "start": 3477, - "end": 3480, + "start": 3981, + "end": 3984, "loc": { "start": { - "line": 109, + "line": 128, "column": 2 }, "end": { - "line": 109, + "line": 128, "column": 5 } } @@ -29441,15 +32608,15 @@ "binop": null }, "value": "label", - "start": 3481, - "end": 3486, + "start": 3985, + "end": 3990, "loc": { "start": { - "line": 109, + "line": 128, "column": 6 }, "end": { - "line": 109, + "line": 128, "column": 11 } } @@ -29466,15 +32633,15 @@ "postfix": false, "binop": null }, - "start": 3486, - "end": 3487, + "start": 3990, + "end": 3991, "loc": { "start": { - "line": 109, + "line": 128, "column": 11 }, "end": { - "line": 109, + "line": 128, "column": 12 } } @@ -29491,15 +32658,15 @@ "postfix": false, "binop": null }, - "start": 3487, - "end": 3488, + "start": 3991, + "end": 3992, "loc": { "start": { - "line": 109, + "line": 128, "column": 12 }, "end": { - "line": 109, + "line": 128, "column": 13 } } @@ -29516,15 +32683,15 @@ "postfix": false, "binop": null }, - "start": 3489, - "end": 3490, + "start": 3993, + "end": 3994, "loc": { "start": { - "line": 109, + "line": 128, "column": 14 }, "end": { - "line": 109, + "line": 128, "column": 15 } } @@ -29532,15 +32699,15 @@ { "type": "CommentLine", "value": " A label or description for this TU?", - "start": 3495, - "end": 3533, + "start": 3999, + "end": 4037, "loc": { "start": { - "line": 110, + "line": 129, "column": 4 }, "end": { - "line": 110, + "line": 129, "column": 42 } } @@ -29560,15 +32727,15 @@ "updateContext": null }, "value": "if", - "start": 3538, - "end": 3540, + "start": 4042, + "end": 4044, "loc": { "start": { - "line": 111, + "line": 130, "column": 4 }, "end": { - "line": 111, + "line": 130, "column": 6 } } @@ -29585,15 +32752,15 @@ "postfix": false, "binop": null }, - "start": 3541, - "end": 3542, + "start": 4045, + "end": 4046, "loc": { "start": { - "line": 111, + "line": 130, "column": 7 }, "end": { - "line": 111, + "line": 130, "column": 8 } } @@ -29611,15 +32778,15 @@ "binop": null }, "value": "has", - "start": 3542, - "end": 3545, + "start": 4046, + "end": 4049, "loc": { "start": { - "line": 111, + "line": 130, "column": 8 }, "end": { - "line": 111, + "line": 130, "column": 11 } } @@ -29636,15 +32803,15 @@ "postfix": false, "binop": null }, - "start": 3545, - "end": 3546, + "start": 4049, + "end": 4050, "loc": { "start": { - "line": 111, + "line": 130, "column": 11 }, "end": { - "line": 111, + "line": 130, "column": 12 } } @@ -29664,15 +32831,15 @@ "updateContext": null }, "value": "this", - "start": 3546, - "end": 3550, + "start": 4050, + "end": 4054, "loc": { "start": { - "line": 111, + "line": 130, "column": 12 }, "end": { - "line": 111, + "line": 130, "column": 16 } } @@ -29690,15 +32857,15 @@ "binop": null, "updateContext": null }, - "start": 3550, - "end": 3551, + "start": 4054, + "end": 4055, "loc": { "start": { - "line": 111, + "line": 130, "column": 16 }, "end": { - "line": 111, + "line": 130, "column": 17 } } @@ -29716,15 +32883,15 @@ "binop": null }, "value": "tunit", - "start": 3551, - "end": 3556, + "start": 4055, + "end": 4060, "loc": { "start": { - "line": 111, + "line": 130, "column": 17 }, "end": { - "line": 111, + "line": 130, "column": 22 } } @@ -29742,15 +32909,15 @@ "binop": null, "updateContext": null }, - "start": 3556, - "end": 3557, + "start": 4060, + "end": 4061, "loc": { "start": { - "line": 111, + "line": 130, "column": 22 }, "end": { - "line": 111, + "line": 130, "column": 23 } } @@ -29769,15 +32936,15 @@ "updateContext": null }, "value": "label", - "start": 3558, - "end": 3565, + "start": 4062, + "end": 4069, "loc": { "start": { - "line": 111, + "line": 130, "column": 24 }, "end": { - "line": 111, + "line": 130, "column": 31 } } @@ -29794,15 +32961,15 @@ "postfix": false, "binop": null }, - "start": 3565, - "end": 3566, + "start": 4069, + "end": 4070, "loc": { "start": { - "line": 111, + "line": 130, "column": 31 }, "end": { - "line": 111, + "line": 130, "column": 32 } } @@ -29819,15 +32986,15 @@ "postfix": false, "binop": null }, - "start": 3566, - "end": 3567, + "start": 4070, + "end": 4071, "loc": { "start": { - "line": 111, + "line": 130, "column": 32 }, "end": { - "line": 111, + "line": 130, "column": 33 } } @@ -29847,15 +33014,15 @@ "updateContext": null }, "value": "return", - "start": 3568, - 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"end": 3586, + "start": 4089, + "end": 4090, "loc": { "start": { - "line": 111, + "line": 130, "column": 51 }, "end": { - "line": 111, + "line": 130, "column": 52 } } @@ -29979,15 +33146,15 @@ "binop": null }, "value": "label", - "start": 3586, - "end": 3591, + "start": 4090, + "end": 4095, "loc": { "start": { - "line": 111, + "line": 130, "column": 52 }, "end": { - "line": 111, + "line": 130, "column": 57 } } @@ -30005,15 +33172,15 @@ "binop": null, "updateContext": null }, - "start": 3591, - "end": 3592, + "start": 4095, + "end": 4096, "loc": { "start": { - "line": 111, + "line": 130, "column": 57 }, "end": { - "line": 111, + "line": 130, "column": 58 } } @@ -30033,15 +33200,15 @@ "updateContext": null }, "value": "if", - "start": 3597, - "end": 3599, + "start": 4101, + "end": 4103, "loc": { "start": { - "line": 112, + "line": 131, "column": 4 }, "end": { - "line": 112, + "line": 131, "column": 6 } } @@ -30058,15 +33225,15 @@ "postfix": false, "binop": null }, - "start": 3600, - "end": 3601, + "start": 4104, + "end": 4105, "loc": { "start": { - 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"line": 129, + "line": 148, "column": 25 }, "end": { - "line": 129, + "line": 148, "column": 27 } } @@ -32168,15 +35335,15 @@ "postfix": false, "binop": null }, - "start": 4163, - "end": 4164, + "start": 4667, + "end": 4668, "loc": { "start": { - "line": 129, + "line": 148, "column": 28 }, "end": { - "line": 129, + "line": 148, "column": 29 } } @@ -32195,15 +35362,15 @@ "updateContext": null }, "value": "<", - "start": 4164, - "end": 4165, + "start": 4668, + "end": 4669, "loc": { "start": { - "line": 129, + "line": 148, "column": 29 }, "end": { - "line": 129, + "line": 148, "column": 30 } } @@ -32220,15 +35387,15 @@ "postfix": false, "binop": null }, - "start": 4165, - "end": 4167, + "start": 4669, + "end": 4671, "loc": { "start": { - "line": 129, + "line": 148, "column": 30 }, "end": { - "line": 129, + "line": 148, "column": 32 } } @@ -32246,15 +35413,15 @@ "binop": null }, "value": "externalRef", - "start": 4167, - "end": 4178, + "start": 4671, + "end": 4682, "loc": { "start": { - "line": 129, + "line": 148, "column": 32 }, "end": { - "line": 129, + "line": 148, "column": 43 } } @@ -32271,15 +35438,15 @@ "postfix": false, "binop": null }, - "start": 4178, - "end": 4179, + "start": 4682, + "end": 4683, "loc": { "start": { - "line": 129, + "line": 148, "column": 43 }, "end": { - "line": 129, + "line": 148, "column": 44 } } @@ -32298,15 +35465,15 @@ "updateContext": null }, "value": ">", - "start": 4179, - "end": 4180, + "start": 4683, + "end": 4684, "loc": { "start": { - "line": 129, + "line": 148, "column": 44 }, "end": { - "line": 129, + "line": 148, "column": 45 } } @@ -32323,15 +35490,15 @@ "postfix": false, "binop": null }, - "start": 4180, - "end": 4181, + "start": 4684, + "end": 4685, "loc": { "start": { - "line": 129, + "line": 148, "column": 45 }, "end": { - "line": 129, + "line": 148, "column": 46 } } @@ -32348,15 +35515,15 @@ "postfix": false, "binop": null }, - "start": 4181, - "end": 4182, + "start": 4685, + "end": 4686, "loc": { "start": { - "line": 129, + "line": 148, "column": 46 }, "end": { - "line": 129, + "line": 148, "column": 47 } } @@ -32374,15 +35541,15 @@ "binop": null, "updateContext": null }, - 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"end": 4205, + "start": 4708, + "end": 4709, "loc": { "start": { - "line": 130, + "line": 149, "column": 21 }, "end": { - "line": 130, + "line": 149, "column": 22 } } @@ -32503,15 +35670,15 @@ "binop": null, "updateContext": null }, - "start": 4205, - "end": 4206, + "start": 4709, + "end": 4710, "loc": { "start": { - "line": 130, + "line": 149, "column": 22 }, "end": { - "line": 130, + "line": 149, "column": 23 } } @@ -32528,15 +35695,15 @@ "postfix": false, "binop": null }, - "start": 4211, - "end": 4212, + "start": 4715, + "end": 4716, "loc": { "start": { - "line": 131, + "line": 150, "column": 4 }, "end": { - "line": 131, + "line": 150, "column": 5 } } @@ -32544,15 +35711,15 @@ { "type": "CommentLine", "value": " If we don't have any properties of a taxonomic unit, return undefined.", - "start": 4218, - "end": 4291, + "start": 4722, + "end": 4795, "loc": { "start": { - "line": 133, + "line": 152, "column": 4 }, "end": { - "line": 133, + "line": 152, "column": 77 } } @@ -32572,15 +35739,15 @@ "updateContext": null }, "value": "return", - "start": 4296, - "end": 4302, + "start": 4800, + "end": 4806, "loc": { "start": { - "line": 134, + "line": 153, "column": 4 }, "end": { - "line": 134, + "line": 153, "column": 10 } } @@ -32598,15 +35765,15 @@ "binop": null }, "value": "undefined", - "start": 4303, - "end": 4312, + "start": 4807, + "end": 4816, "loc": { "start": { - "line": 134, + "line": 153, "column": 11 }, "end": { - "line": 134, + "line": 153, "column": 20 } } @@ -32624,15 +35791,15 @@ "binop": null, "updateContext": null }, - "start": 4312, - "end": 4313, + "start": 4816, + "end": 4817, "loc": { "start": { - "line": 134, + "line": 153, "column": 20 }, "end": { - "line": 134, + "line": 153, "column": 21 } } @@ -32649,15 +35816,15 @@ "postfix": false, "binop": null }, - "start": 4316, - "end": 4317, + "start": 4820, + "end": 4821, "loc": { "start": { - "line": 135, + "line": 154, "column": 2 }, "end": { - "line": 135, + "line": 154, "column": 3 } } @@ -32665,15 +35832,15 @@ { "type": "CommentBlock", "value": "*\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n ", - "start": 4321, - "end": 4562, + "start": 4825, + "end": 5066, "loc": { "start": { - "line": 137, + "line": 156, "column": 2 }, "end": { - "line": 142, + "line": 161, "column": 5 } } @@ -32691,15 +35858,15 @@ "binop": null }, "value": "static", - "start": 4565, - "end": 4571, + "start": 5069, + "end": 5075, "loc": { "start": { - "line": 143, + "line": 162, "column": 2 }, "end": { - "line": 143, + "line": 162, "column": 8 } } @@ -32717,15 +35884,15 @@ "binop": null }, "value": "fromLabel", - "start": 4572, - "end": 4581, + "start": 5076, + "end": 5085, "loc": { "start": { - "line": 143, + "line": 162, "column": 9 }, "end": { - "line": 143, + "line": 162, "column": 18 } } @@ -32742,15 +35909,15 @@ "postfix": false, "binop": null }, - "start": 4581, - "end": 4582, + "start": 5085, + "end": 5086, "loc": { "start": { - "line": 143, + "line": 162, "column": 18 }, "end": { - "line": 143, + "line": 162, "column": 19 } } @@ -32768,15 +35935,15 @@ "binop": null }, "value": "nodeLabel", - "start": 4582, - "end": 4591, + "start": 5086, + "end": 5095, "loc": { "start": { - "line": 143, + "line": 162, "column": 19 }, "end": { - "line": 143, + "line": 162, "column": 28 } } @@ -32794,15 +35961,15 @@ "binop": null, "updateContext": null }, - "start": 4591, - "end": 4592, + "start": 5095, + "end": 5096, "loc": { "start": { - "line": 143, + "line": 162, "column": 28 }, "end": { - "line": 143, + "line": 162, "column": 29 } } @@ -32820,15 +35987,15 @@ "binop": null }, "value": "nomenCode", - "start": 4593, - "end": 4602, + "start": 5097, + "end": 5106, "loc": { "start": { - "line": 143, + "line": 162, "column": 30 }, "end": { - "line": 143, + "line": 162, "column": 39 } } @@ -32847,15 +36014,15 @@ "updateContext": null }, "value": "=", - "start": 4603, - "end": 4604, + "start": 5107, + "end": 5108, "loc": { "start": { - "line": 143, + "line": 162, "column": 40 }, "end": { - "line": 143, + "line": 162, "column": 41 } } @@ -32873,15 +36040,15 @@ "binop": null }, "value": "owlterms", - "start": 4605, - "end": 4613, + "start": 5109, + "end": 5117, "loc": { "start": { - "line": 143, + "line": 162, "column": 42 }, "end": { - "line": 143, + "line": 162, "column": 50 } } @@ -32899,15 +36066,15 @@ "binop": null, "updateContext": null }, - "start": 4613, - "end": 4614, + "start": 5117, + "end": 5118, "loc": { "start": { - "line": 143, + "line": 162, "column": 50 }, "end": { - "line": 143, + "line": 162, "column": 51 } } @@ -32925,15 +36092,15 @@ "binop": null }, "value": "NAME_IN_UNKNOWN_CODE", - "start": 4614, - "end": 4634, + "start": 5118, + "end": 5138, "loc": { "start": { - "line": 143, + "line": 162, "column": 51 }, "end": { - "line": 143, + "line": 162, "column": 71 } } @@ -32950,15 +36117,15 @@ "postfix": false, "binop": null }, - "start": 4634, - "end": 4635, + "start": 5138, + "end": 5139, "loc": { "start": { - "line": 143, + "line": 162, "column": 71 }, "end": { - "line": 143, + "line": 162, "column": 72 } } @@ -32975,15 +36142,15 @@ "postfix": false, "binop": null }, - "start": 4636, - "end": 4637, + "start": 5140, + "end": 5141, "loc": { "start": { - "line": 143, + "line": 162, "column": 73 }, "end": { - "line": 143, + "line": 162, "column": 74 } } @@ -33003,15 +36170,15 @@ "updateContext": null }, "value": "if", - "start": 4642, - "end": 4644, + "start": 5146, + "end": 5148, "loc": { "start": { - "line": 144, + "line": 163, "column": 4 }, "end": { - "line": 144, + "line": 163, "column": 6 } } @@ -33028,15 +36195,15 @@ "postfix": false, "binop": null }, - "start": 4645, - "end": 4646, + "start": 5149, + "end": 5150, "loc": { "start": { - "line": 144, + "line": 163, "column": 7 }, "end": { - "line": 144, + "line": 163, "column": 8 } } @@ -33054,15 +36221,15 @@ "binop": null }, "value": "nodeLabel", - "start": 4646, - "end": 4655, + "start": 5150, + "end": 5159, "loc": { "start": { - "line": 144, + "line": 163, "column": 8 }, "end": { - "line": 144, + "line": 163, "column": 17 } } @@ -33081,15 +36248,15 @@ "updateContext": null }, "value": "===", - "start": 4656, - "end": 4659, + "start": 5160, + "end": 5163, "loc": { "start": { - "line": 144, + "line": 163, "column": 18 }, "end": { - "line": 144, + "line": 163, "column": 21 } } @@ -33107,15 +36274,15 @@ "binop": null }, "value": "undefined", - "start": 4660, - "end": 4669, + "start": 5164, + "end": 5173, "loc": { "start": { - "line": 144, + "line": 163, "column": 22 }, "end": { - "line": 144, + "line": 163, "column": 31 } } @@ -33134,15 +36301,15 @@ "updateContext": null }, "value": "||", - "start": 4670, - "end": 4672, + "start": 5174, + "end": 5176, "loc": { "start": { - "line": 144, + "line": 163, "column": 32 }, "end": { - "line": 144, + "line": 163, "column": 34 } } @@ -33160,15 +36327,15 @@ "binop": null }, "value": "nodeLabel", - "start": 4673, - "end": 4682, + "start": 5177, + "end": 5186, "loc": { "start": { - "line": 144, + "line": 163, "column": 35 }, "end": { - "line": 144, + "line": 163, "column": 44 } } @@ -33187,15 +36354,15 @@ "updateContext": null }, "value": "===", - "start": 4683, - "end": 4686, + "start": 5187, + "end": 5190, "loc": { "start": { - "line": 144, + "line": 163, "column": 45 }, "end": { - "line": 144, + "line": 163, "column": 48 } } @@ -33215,15 +36382,15 @@ "updateContext": null }, "value": "null", - "start": 4687, - "end": 4691, + "start": 5191, + "end": 5195, "loc": { "start": { - "line": 144, + "line": 163, "column": 49 }, "end": { - "line": 144, + "line": 163, "column": 53 } } @@ -33242,15 +36409,15 @@ "updateContext": null }, "value": "||", - "start": 4692, - "end": 4694, + "start": 5196, + "end": 5198, "loc": { "start": { - "line": 144, + "line": 163, "column": 54 }, "end": { - "line": 144, + "line": 163, "column": 56 } } @@ -33268,15 +36435,15 @@ "binop": null }, "value": "nodeLabel", - "start": 4695, - "end": 4704, + "start": 5199, + "end": 5208, "loc": { "start": { - "line": 144, + "line": 163, "column": 57 }, "end": { - "line": 144, + "line": 163, "column": 66 } } @@ -33294,15 +36461,15 @@ "binop": null, "updateContext": null }, - "start": 4704, - "end": 4705, + "start": 5208, + "end": 5209, "loc": { "start": { - "line": 144, + "line": 163, "column": 66 }, "end": { - "line": 144, + "line": 163, "column": 67 } } @@ -33320,15 +36487,15 @@ "binop": null }, "value": "trim", - "start": 4705, - "end": 4709, + "start": 5209, + "end": 5213, "loc": { "start": { - "line": 144, + "line": 163, "column": 67 }, "end": { - "line": 144, + "line": 163, "column": 71 } } @@ -33345,15 +36512,15 @@ "postfix": false, "binop": null }, - "start": 4709, - "end": 4710, + "start": 5213, + "end": 5214, "loc": { "start": { - "line": 144, + "line": 163, "column": 71 }, "end": { - "line": 144, + "line": 163, "column": 72 } } @@ -33370,15 +36537,15 @@ "postfix": false, "binop": null }, - "start": 4710, - "end": 4711, + "start": 5214, + "end": 5215, "loc": { "start": { - "line": 144, + "line": 163, "column": 72 }, "end": { - "line": 144, + "line": 163, "column": 73 } } @@ -33397,15 +36564,15 @@ "updateContext": null }, "value": "===", - "start": 4712, - "end": 4715, + "start": 5216, + "end": 5219, "loc": { "start": { - "line": 144, + "line": 163, "column": 74 }, "end": { - "line": 144, + "line": 163, "column": 77 } } @@ -33424,15 +36591,15 @@ "updateContext": null }, "value": "", - "start": 4716, - "end": 4718, + "start": 5220, + "end": 5222, "loc": { "start": { - "line": 144, + "line": 163, "column": 78 }, "end": { - "line": 144, + "line": 163, "column": 80 } } @@ -33449,15 +36616,15 @@ "postfix": false, "binop": null }, - "start": 4718, - "end": 4719, + "start": 5222, + "end": 5223, "loc": { "start": { - "line": 144, + "line": 163, "column": 80 }, "end": { - "line": 144, + "line": 163, "column": 81 } } @@ -33477,15 +36644,15 @@ "updateContext": null }, "value": "return", - "start": 4720, - "end": 4726, + "start": 5224, + "end": 5230, "loc": { "start": { - "line": 144, + "line": 163, "column": 82 }, "end": { - "line": 144, + "line": 163, "column": 88 } } @@ -33503,15 +36670,15 @@ "binop": null }, "value": "undefined", - "start": 4727, - "end": 4736, + "start": 5231, + "end": 5240, "loc": { "start": { - "line": 144, + "line": 163, "column": 89 }, "end": { - "line": 144, + "line": 163, "column": 98 } } @@ -33529,15 +36696,15 @@ "binop": null, "updateContext": null }, - "start": 4736, - "end": 4737, + "start": 5240, + "end": 5241, "loc": { "start": { - "line": 144, + "line": 163, "column": 98 }, "end": { - "line": 144, + "line": 163, "column": 99 } } @@ -33545,15 +36712,15 @@ { "type": "CommentLine", "value": " Rather than figuring out with this label, check to see if we've parsed", - "start": 4743, - "end": 4816, + "start": 5247, + "end": 5320, "loc": { "start": { - "line": 146, + "line": 165, "column": 4 }, "end": { - "line": 146, + "line": 165, "column": 77 } } @@ -33561,15 +36728,15 @@ { "type": "CommentLine", "value": " this before.", - "start": 4821, - "end": 4836, + "start": 5325, + "end": 5340, "loc": { "start": { - "line": 147, + "line": 166, "column": 4 }, "end": { - "line": 147, + "line": 166, "column": 19 } } @@ -33589,15 +36756,15 @@ "updateContext": null }, "value": "if", - "start": 4841, - "end": 4843, + "start": 5345, + "end": 5347, "loc": { "start": { - "line": 148, + "line": 167, "column": 4 }, "end": { - "line": 148, + "line": 167, "column": 6 } } @@ -33614,15 +36781,15 @@ "postfix": false, "binop": null }, - "start": 4844, - "end": 4845, + "start": 5348, + "end": 5349, "loc": { "start": { - "line": 148, + "line": 167, "column": 7 }, "end": { - "line": 148, + "line": 167, "column": 8 } } @@ -33640,15 +36807,15 @@ "binop": null }, "value": "PhyxCacheManager", - "start": 4845, - "end": 4861, + "start": 5349, + "end": 5365, "loc": { "start": { - "line": 148, + "line": 167, "column": 8 }, "end": { - "line": 148, + "line": 167, "column": 24 } } @@ -33666,15 +36833,15 @@ "binop": null, "updateContext": null }, - "start": 4861, - "end": 4862, + "start": 5365, + "end": 5366, "loc": { "start": { - "line": 148, + "line": 167, "column": 24 }, "end": { - "line": 148, + "line": 167, "column": 25 } } @@ -33692,15 +36859,15 @@ "binop": null }, "value": "has", - "start": 4862, - "end": 4865, + "start": 5366, + "end": 5369, "loc": { "start": { - "line": 148, + "line": 167, "column": 25 }, "end": { - "line": 148, + "line": 167, "column": 28 } } @@ -33717,15 +36884,15 @@ "postfix": false, "binop": null }, - "start": 4865, - "end": 4866, + "start": 5369, + "end": 5370, "loc": { "start": { - "line": 148, + "line": 167, "column": 28 }, "end": { - "line": 148, + "line": 167, "column": 29 } } @@ -33742,15 +36909,15 @@ "postfix": false, "binop": null }, - "start": 4866, - "end": 4867, + "start": 5370, + "end": 5371, "loc": { "start": { - "line": 148, + "line": 167, "column": 29 }, "end": { - "line": 148, + "line": 167, "column": 30 } } @@ -33769,15 +36936,15 @@ "updateContext": null }, "value": "TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.", - "start": 4867, - "end": 4921, + "start": 5371, + "end": 5425, "loc": { "start": { - "line": 148, + "line": 167, "column": 30 }, "end": { - "line": 148, + "line": 167, "column": 84 } } @@ -33794,15 +36961,15 @@ "postfix": false, "binop": null }, - 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"end": 4980, + "start": 5483, + "end": 5484, "loc": { "start": { - "line": 149, + "line": 168, "column": 29 }, "end": { - "line": 149, + "line": 168, "column": 30 } } @@ -34130,15 +37297,15 @@ "binop": null }, "value": "get", - "start": 4980, - "end": 4983, + "start": 5484, + "end": 5487, "loc": { "start": { - "line": 149, + "line": 168, "column": 30 }, "end": { - "line": 149, + "line": 168, "column": 33 } } @@ -34155,15 +37322,15 @@ "postfix": false, "binop": null }, - "start": 4983, - "end": 4984, + "start": 5487, + "end": 5488, "loc": { "start": { - "line": 149, + "line": 168, "column": 33 }, "end": { - "line": 149, + "line": 168, "column": 34 } } @@ -34180,15 +37347,15 @@ "postfix": false, "binop": null }, - "start": 4984, - "end": 4985, + "start": 5488, + "end": 5489, "loc": { "start": { - "line": 149, + "line": 168, "column": 34 }, "end": { - "line": 149, + "line": 168, "column": 35 } } @@ -34207,15 +37374,15 @@ "updateContext": null }, "value": "TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.", - "start": 4985, - "end": 5039, + "start": 5489, + "end": 5543, "loc": { "start": { - "line": 149, + "line": 168, "column": 35 }, "end": { - "line": 149, + "line": 168, "column": 89 } } @@ -34232,15 +37399,15 @@ "postfix": false, "binop": null }, - "start": 5039, - "end": 5041, + "start": 5543, + "end": 5545, "loc": { "start": { - "line": 149, + "line": 168, "column": 89 }, "end": { - "line": 149, + "line": 168, "column": 91 } } @@ -34258,15 +37425,15 @@ "binop": null }, "value": "nomenCode", - "start": 5041, - "end": 5050, + "start": 5545, + "end": 5554, "loc": { "start": { - "line": 149, + "line": 168, "column": 91 }, "end": { - "line": 149, + "line": 168, "column": 100 } } @@ -34283,15 +37450,15 @@ "postfix": false, "binop": null }, - "start": 5050, - "end": 5051, + "start": 5554, + "end": 5555, "loc": { "start": { - "line": 149, + "line": 168, "column": 100 }, "end": { - "line": 149, + "line": 168, "column": 101 } } @@ -34310,15 +37477,15 @@ "updateContext": null }, "value": "", - "start": 5051, - "end": 5051, + "start": 5555, + "end": 5555, "loc": { "start": { - "line": 149, + "line": 168, "column": 101 }, "end": { - "line": 149, + "line": 168, "column": 101 } } @@ -34335,15 +37502,15 @@ "postfix": false, "binop": null }, - "start": 5051, - "end": 5052, + "start": 5555, + "end": 5556, "loc": { "start": { - "line": 149, + "line": 168, "column": 101 }, "end": { - "line": 149, + "line": 168, "column": 102 } } @@ -34361,15 +37528,15 @@ "binop": null, "updateContext": null }, - "start": 5052, - "end": 5053, + "start": 5556, + "end": 5557, "loc": { "start": { - "line": 149, + "line": 168, "column": 102 }, "end": { - "line": 149, + "line": 168, "column": 103 } } @@ -34387,15 +37554,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5054, - "end": 5063, + "start": 5558, + "end": 5567, "loc": { "start": { - "line": 149, + "line": 168, "column": 104 }, "end": { - "line": 149, + "line": 168, "column": 113 } } @@ -34412,15 +37579,15 @@ "postfix": false, "binop": null }, - "start": 5063, - "end": 5064, + "start": 5567, + "end": 5568, "loc": { "start": { - "line": 149, + "line": 168, "column": 113 }, "end": { - "line": 149, + "line": 168, "column": 114 } } @@ -34438,15 +37605,15 @@ "binop": null, "updateContext": null }, - "start": 5064, - "end": 5065, + "start": 5568, + "end": 5569, "loc": { "start": { - "line": 149, + "line": 168, "column": 114 }, "end": { - "line": 149, + "line": 168, "column": 115 } } @@ -34463,15 +37630,15 @@ "postfix": false, "binop": null }, - "start": 5070, - "end": 5071, + "start": 5574, + "end": 5575, "loc": { "start": { - "line": 150, + "line": 169, "column": 4 }, "end": { - "line": 150, + "line": 169, "column": 5 } } @@ -34479,15 +37646,15 @@ { "type": "CommentLine", "value": " Look for taxon concept.", - "start": 5077, - "end": 5103, + "start": 5581, + "end": 5607, "loc": { "start": { - "line": 152, + "line": 171, "column": 4 }, "end": { - "line": 152, + "line": 171, "column": 30 } } @@ -34507,15 +37674,15 @@ "updateContext": null }, "value": "const", - "start": 5108, - "end": 5113, + "start": 5612, + "end": 5617, "loc": { "start": { - "line": 153, + "line": 172, "column": 4 }, "end": { - "line": 153, + "line": 172, "column": 9 } } @@ -34533,15 +37700,15 @@ "binop": null }, "value": "taxonConcept", - "start": 5114, - "end": 5126, + "start": 5618, + "end": 5630, "loc": { "start": { - "line": 153, + "line": 172, "column": 10 }, "end": { - "line": 153, + "line": 172, "column": 22 } } @@ -34560,15 +37727,15 @@ "updateContext": null }, "value": "=", - "start": 5127, - "end": 5128, + "start": 5631, + "end": 5632, "loc": { "start": { - "line": 153, + "line": 172, "column": 23 }, "end": { - "line": 153, + "line": 172, "column": 24 } } @@ -34586,15 +37753,15 @@ "binop": null }, "value": "TaxonConceptWrapper", - "start": 5129, - "end": 5148, + "start": 5633, + "end": 5652, "loc": { "start": { - "line": 153, + "line": 172, "column": 25 }, "end": { - "line": 153, + "line": 172, "column": 44 } } @@ -34612,15 +37779,15 @@ "binop": null, "updateContext": null }, - "start": 5148, - "end": 5149, + "start": 5652, + "end": 5653, "loc": { "start": { - "line": 153, + "line": 172, "column": 44 }, "end": { - "line": 153, + "line": 172, "column": 45 } } @@ -34638,15 +37805,15 @@ "binop": null }, "value": "fromLabel", - "start": 5149, - "end": 5158, + "start": 5653, + "end": 5662, "loc": { "start": { - "line": 153, + "line": 172, "column": 45 }, "end": { - "line": 153, + "line": 172, "column": 54 } } @@ -34663,15 +37830,15 @@ "postfix": false, "binop": null }, - "start": 5158, - "end": 5159, + "start": 5662, + "end": 5663, "loc": { "start": { - "line": 153, + "line": 172, "column": 54 }, "end": { - "line": 153, + "line": 172, "column": 55 } } @@ -34689,15 +37856,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5159, - "end": 5168, + "start": 5663, + "end": 5672, "loc": { "start": { - "line": 153, + "line": 172, "column": 55 }, "end": { - "line": 153, + "line": 172, "column": 64 } } @@ -34715,15 +37882,15 @@ "binop": null, "updateContext": null }, - "start": 5168, - "end": 5169, + "start": 5672, + "end": 5673, "loc": { "start": { - "line": 153, + "line": 172, "column": 64 }, "end": { - "line": 153, + "line": 172, "column": 65 } } @@ -34741,15 +37908,15 @@ "binop": null }, "value": "nomenCode", - "start": 5170, - "end": 5179, + "start": 5674, + "end": 5683, "loc": { "start": { - "line": 153, + "line": 172, "column": 66 }, "end": { - "line": 153, + "line": 172, "column": 75 } } @@ -34766,15 +37933,15 @@ "postfix": false, "binop": null }, - "start": 5179, - "end": 5180, + "start": 5683, + "end": 5684, "loc": { "start": { - "line": 153, + "line": 172, "column": 75 }, "end": { - "line": 153, + "line": 172, "column": 76 } } @@ -34792,15 +37959,15 @@ "binop": null, "updateContext": null }, - "start": 5180, - "end": 5181, + "start": 5684, + "end": 5685, "loc": { "start": { - "line": 153, + "line": 172, "column": 76 }, "end": { - "line": 153, + "line": 172, "column": 77 } } @@ -34808,15 +37975,15 @@ { "type": "CommentLine", "value": " Look for specimen information.", - "start": 5187, - "end": 5220, + "start": 5691, + "end": 5724, "loc": { "start": { - "line": 155, + "line": 174, "column": 4 }, "end": { - "line": 155, + "line": 174, "column": 37 } } @@ -34836,15 +38003,15 @@ "updateContext": null }, "value": "let", - "start": 5225, - "end": 5228, + "start": 5729, + "end": 5732, "loc": { "start": { - "line": 156, + "line": 175, "column": 4 }, "end": { - "line": 156, + "line": 175, "column": 7 } } @@ -34862,15 +38029,15 @@ "binop": null }, "value": "specimen", - "start": 5229, - "end": 5237, + "start": 5733, + "end": 5741, "loc": { "start": { - "line": 156, + "line": 175, "column": 8 }, "end": { - "line": 156, + "line": 175, "column": 16 } } @@ -34888,15 +38055,15 @@ "binop": null, "updateContext": null }, - "start": 5237, - "end": 5238, + "start": 5741, + "end": 5742, "loc": { "start": { - "line": 156, + "line": 175, "column": 16 }, "end": { - "line": 156, + "line": 175, "column": 17 } } @@ -34916,15 +38083,15 @@ "updateContext": null }, "value": "if", - "start": 5243, - "end": 5245, + "start": 5747, + "end": 5749, "loc": { "start": { - "line": 157, + "line": 176, "column": 4 }, "end": { - "line": 157, + "line": 176, "column": 6 } } @@ -34941,15 +38108,15 @@ "postfix": false, "binop": null }, - "start": 5246, - "end": 5247, + "start": 5750, + "end": 5751, "loc": { "start": { - "line": 157, + "line": 176, "column": 7 }, "end": { - "line": 157, + "line": 176, "column": 8 } } @@ -34967,15 +38134,15 @@ "binop": null }, "value": "nodeLabel", - "start": 5247, - "end": 5256, + "start": 5751, + "end": 5760, "loc": { "start": { - "line": 157, + "line": 176, "column": 8 }, "end": { - "line": 157, + "line": 176, "column": 17 } } @@ -34993,15 +38160,15 @@ "binop": null, "updateContext": null }, - "start": 5256, - "end": 5257, + "start": 5760, + "end": 5761, "loc": { "start": { - "line": 157, + "line": 176, "column": 17 }, "end": { - "line": 157, + "line": 176, "column": 18 } } @@ -35019,15 +38186,15 @@ "binop": null }, "value": "toLowerCase", - "start": 5257, - "end": 5268, + "start": 5761, + "end": 5772, "loc": { "start": { - "line": 157, + "line": 176, "column": 18 }, "end": { - "line": 157, + "line": 176, "column": 29 } } @@ -35044,15 +38211,15 @@ "postfix": false, "binop": null }, - "start": 5268, - "end": 5269, + "start": 5772, + "end": 5773, "loc": { "start": { - "line": 157, + "line": 176, "column": 29 }, "end": { - "line": 157, + "line": 176, "column": 30 } } @@ -35069,15 +38236,15 @@ "postfix": false, "binop": null }, - "start": 5269, - "end": 5270, + "start": 5773, + "end": 5774, "loc": { "start": { - "line": 157, + "line": 176, "column": 30 }, "end": { - "line": 157, + "line": 176, "column": 31 } } @@ -35095,15 +38262,15 @@ "binop": null, "updateContext": null }, - "start": 5270, - "end": 5271, + "start": 5774, + "end": 5775, "loc": { "start": { - "line": 157, + "line": 176, "column": 31 }, "end": { - "line": 157, + "line": 176, "column": 32 } } @@ -35121,15 +38288,15 @@ "binop": null }, "value": "startsWith", - "start": 5271, - "end": 5281, + "start": 5775, + "end": 5785, "loc": { "start": { - "line": 157, + "line": 176, "column": 32 }, "end": { - "line": 157, + "line": 176, "column": 42 } } @@ -35146,15 +38313,15 @@ "postfix": false, "binop": null }, - "start": 5281, - "end": 5282, + "start": 5785, + "end": 5786, "loc": { "start": { - "line": 157, + "line": 176, "column": 42 }, "end": { - "line": 157, + "line": 176, "column": 43 } } @@ -35173,15 +38340,15 @@ "updateContext": null }, "value": "specimen ", - "start": 5282, - "end": 5293, + "start": 5786, + "end": 5797, "loc": { "start": { - "line": 157, + "line": 176, "column": 43 }, "end": { - "line": 157, + "line": 176, "column": 54 } } @@ -35198,15 +38365,15 @@ "postfix": false, "binop": null }, - "start": 5293, - "end": 5294, + "start": 5797, + "end": 5798, "loc": { "start": { - "line": 157, + "line": 176, "column": 54 }, "end": { - "line": 157, + "line": 176, "column": 55 } } @@ -35223,15 +38390,15 @@ "postfix": false, "binop": null }, - "start": 5294, - "end": 5295, + "start": 5798, + "end": 5799, "loc": { "start": { - "line": 157, + "line": 176, "column": 55 }, "end": { - "line": 157, + "line": 176, "column": 56 } } @@ -35248,15 +38415,15 @@ "postfix": false, "binop": null }, - "start": 5296, - "end": 5297, + "start": 5800, + "end": 5801, "loc": { "start": { - "line": 157, + "line": 176, "column": 57 }, "end": { - "line": 157, + "line": 176, "column": 58 } } @@ -35264,15 +38431,15 @@ { "type": "CommentLine", "value": " Eliminate a 'Specimen ' prefix if it exists.", - "start": 5304, - "end": 5351, + "start": 5808, + "end": 5855, "loc": { "start": { - "line": 158, + "line": 177, "column": 6 }, "end": { - "line": 158, + "line": 177, "column": 53 } } @@ -35290,15 +38457,15 @@ "binop": null }, "value": "specimen", - "start": 5358, - "end": 5366, + "start": 5862, + "end": 5870, "loc": { "start": { - "line": 159, + "line": 178, "column": 6 }, "end": { - "line": 159, + "line": 178, "column": 14 } } @@ -35317,15 +38484,15 @@ "updateContext": null }, "value": "=", - "start": 5367, - "end": 5368, + "start": 5871, + "end": 5872, "loc": { "start": { - "line": 159, + "line": 178, "column": 15 }, "end": { - "line": 159, + "line": 178, "column": 16 } } @@ -35343,15 +38510,15 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 5369, - "end": 5384, + "start": 5873, + "end": 5888, "loc": { "start": { - "line": 159, + "line": 178, "column": 17 }, "end": { - "line": 159, + "line": 178, "column": 32 } } @@ -35369,15 +38536,15 @@ "binop": null, "updateContext": null }, - "start": 5384, - "end": 5385, + "start": 5888, + "end": 5889, "loc": { "start": { - "line": 159, + "line": 178, "column": 32 }, "end": { - "line": 159, + "line": 178, "column": 33 } } @@ -35395,15 +38562,15 @@ "binop": null }, "value": "fromOccurrenceID", - "start": 5385, - "end": 5401, + "start": 5889, + "end": 5905, "loc": { "start": { - "line": 159, + "line": 178, "column": 33 }, "end": { - "line": 159, + "line": 178, "column": 49 } } @@ -35420,15 +38587,15 @@ "postfix": false, "binop": null }, - "start": 5401, - "end": 5402, + "start": 5905, + "end": 5906, "loc": { "start": { - 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"line": 190, + "line": 209, "column": 39 }, "end": { - "line": 190, + "line": 209, "column": 40 } } @@ -38449,15 +41616,15 @@ "postfix": false, "binop": null }, - "start": 6395, - "end": 6396, + "start": 6899, + "end": 6900, "loc": { "start": { - "line": 190, + "line": 209, "column": 40 }, "end": { - "line": 190, + "line": 209, "column": 41 } } @@ -38475,15 +41642,15 @@ "binop": null, "updateContext": null }, - "start": 6396, - "end": 6397, + "start": 6900, + "end": 6901, "loc": { "start": { - "line": 190, + "line": 209, "column": 41 }, "end": { - "line": 190, + "line": 209, "column": 42 } } @@ -38501,15 +41668,15 @@ "binop": null }, "value": "tunit", - "start": 6404, - "end": 6409, + "start": 6908, + "end": 6913, "loc": { "start": { - "line": 191, + "line": 210, "column": 6 }, "end": { - "line": 191, + "line": 210, "column": 11 } } @@ -38527,15 +41694,15 @@ "binop": null, "updateContext": null }, - "start": 6409, - "end": 6410, + "start": 6913, + "end": 6914, "loc": { "start": { - "line": 191, + "line": 210, "column": 11 }, "end": { - "line": 191, + "line": 210, "column": 12 } } @@ -38554,15 +41721,15 @@ "updateContext": null }, "value": "@id", - "start": 6410, - "end": 6415, + "start": 6914, + "end": 6919, "loc": { "start": { - "line": 191, + "line": 210, "column": 12 }, "end": { - "line": 191, + "line": 210, "column": 17 } } @@ -38580,15 +41747,15 @@ "binop": null, "updateContext": null }, - "start": 6415, - "end": 6416, + "start": 6919, + "end": 6920, "loc": { "start": { - "line": 191, + "line": 210, "column": 17 }, "end": { - "line": 191, + "line": 210, "column": 18 } } @@ -38607,15 +41774,15 @@ "updateContext": null }, "value": "=", - "start": 6417, - "end": 6418, + "start": 6921, + "end": 6922, "loc": { "start": { - "line": 191, + "line": 210, "column": 19 }, "end": { - "line": 191, + "line": 210, "column": 20 } } @@ -38633,15 +41800,15 @@ "binop": null }, "value": "nodeLabel", - "start": 6419, - "end": 6428, + "start": 6923, + "end": 6932, "loc": { "start": { - "line": 191, + "line": 210, "column": 21 }, "end": { - "line": 191, + "line": 210, "column": 30 } } @@ -38659,15 +41826,15 @@ "binop": null, "updateContext": null }, - "start": 6428, - "end": 6429, + "start": 6932, + "end": 6933, "loc": { "start": { - "line": 191, + "line": 210, "column": 30 }, "end": { - "line": 191, + "line": 210, "column": 31 } } @@ -38684,15 +41851,15 @@ "postfix": false, "binop": null }, - "start": 6434, - "end": 6435, + "start": 6938, + "end": 6939, "loc": { "start": { - "line": 192, + "line": 211, "column": 4 }, "end": { - "line": 192, + "line": 211, "column": 5 } } @@ -38700,15 +41867,15 @@ { "type": "CommentLine", "value": " Finally, let's record the label we parsed to get to this tunit!", - "start": 6441, - "end": 6507, + "start": 6945, + "end": 7011, "loc": { "start": { - "line": 194, + "line": 213, "column": 4 }, "end": { - "line": 194, + "line": 213, "column": 70 } } @@ -38728,15 +41895,15 @@ "updateContext": null }, "value": "if", - "start": 6512, - "end": 6514, + "start": 7016, + "end": 7018, "loc": { "start": { - "line": 195, + "line": 214, "column": 4 }, "end": { - "line": 195, + "line": 214, "column": 6 } } @@ -38753,15 +41920,15 @@ "postfix": false, "binop": null }, - "start": 6515, - "end": 6516, + "start": 7019, + "end": 7020, "loc": { "start": { - "line": 195, + "line": 214, "column": 7 }, "end": { - "line": 195, + "line": 214, "column": 8 } } @@ -38779,15 +41946,15 @@ "binop": null }, "value": "tunit", - "start": 6516, - "end": 6521, + "start": 7020, + "end": 7025, "loc": { "start": { - "line": 195, + "line": 214, "column": 8 }, "end": { - "line": 195, + "line": 214, "column": 13 } } @@ -38804,15 +41971,15 @@ "postfix": false, "binop": null }, - "start": 6521, - "end": 6522, + "start": 7025, + "end": 7026, "loc": { "start": { - "line": 195, + "line": 214, "column": 13 }, "end": { - "line": 195, + "line": 214, "column": 14 } } @@ -38829,15 +41996,15 @@ "postfix": false, "binop": null }, - "start": 6523, - "end": 6524, + "start": 7027, + "end": 7028, "loc": { "start": { - "line": 195, + "line": 214, "column": 15 }, "end": { - "line": 195, + "line": 214, "column": 16 } } @@ -38855,15 +42022,15 @@ "binop": null }, "value": "tunit", - "start": 6531, - "end": 6536, + "start": 7035, + "end": 7040, "loc": { "start": { - "line": 196, + "line": 215, "column": 6 }, "end": { - "line": 196, + "line": 215, "column": 11 } } @@ -38881,15 +42048,15 @@ "binop": null, "updateContext": null }, - "start": 6536, - "end": 6537, + "start": 7040, + "end": 7041, "loc": { "start": { - "line": 196, + "line": 215, "column": 11 }, "end": { - "line": 196, + "line": 215, "column": 12 } } @@ -38907,15 +42074,15 @@ "binop": null }, "value": "label", - "start": 6537, - "end": 6542, + "start": 7041, + "end": 7046, "loc": { "start": { - "line": 196, + "line": 215, "column": 12 }, "end": { - "line": 196, + "line": 215, "column": 17 } } @@ -38934,15 +42101,15 @@ "updateContext": null }, "value": "=", - "start": 6543, - "end": 6544, + "start": 7047, + "end": 7048, "loc": { "start": { - "line": 196, + "line": 215, "column": 18 }, "end": { - "line": 196, + "line": 215, "column": 19 } } @@ -38960,15 +42127,15 @@ "binop": null }, "value": "nodeLabel", - "start": 6545, - "end": 6554, + "start": 7049, + "end": 7058, "loc": { "start": { - "line": 196, + "line": 215, "column": 20 }, "end": { - "line": 196, + "line": 215, "column": 29 } } @@ -38986,15 +42153,15 @@ "binop": null, "updateContext": null }, - "start": 6554, - "end": 6555, + "start": 7058, + "end": 7059, "loc": { "start": { - "line": 196, + "line": 215, "column": 29 }, "end": { - "line": 196, + "line": 215, "column": 30 } } @@ -39011,15 +42178,15 @@ "postfix": false, "binop": null }, - "start": 6560, - "end": 6561, + "start": 7064, + "end": 7065, "loc": { "start": { - "line": 197, + "line": 216, "column": 4 }, "end": { - "line": 197, + "line": 216, "column": 5 } } @@ -39027,15 +42194,15 @@ { "type": "CommentLine", "value": " Record in the cache", - "start": 6567, - "end": 6589, + "start": 7071, + "end": 7093, "loc": { "start": { - "line": 199, + "line": 218, "column": 4 }, "end": { - "line": 199, + "line": 218, "column": 26 } } @@ -39053,15 +42220,15 @@ "binop": null }, "value": "PhyxCacheManager", - "start": 6594, - "end": 6610, + "start": 7098, + "end": 7114, "loc": { "start": { - "line": 200, + "line": 219, "column": 4 }, "end": { - "line": 200, + "line": 219, "column": 20 } } @@ -39079,15 +42246,15 @@ "binop": null, "updateContext": null }, - "start": 6610, - "end": 6611, + "start": 7114, + "end": 7115, "loc": { "start": { - "line": 200, + "line": 219, "column": 20 }, "end": { - "line": 200, + "line": 219, "column": 21 } } @@ -39105,15 +42272,15 @@ "binop": null }, "value": "put", - "start": 6611, - "end": 6614, + "start": 7115, + "end": 7118, "loc": { "start": { - "line": 200, + "line": 219, "column": 21 }, "end": { - "line": 200, + "line": 219, "column": 24 } } @@ -39130,15 +42297,15 @@ "postfix": false, "binop": null }, - "start": 6614, - "end": 6615, + "start": 7118, + "end": 7119, "loc": { "start": { - "line": 200, + "line": 219, "column": 24 }, "end": { - "line": 200, + "line": 219, "column": 25 } } @@ -39155,15 +42322,15 @@ "postfix": false, "binop": null }, - "start": 6615, - 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"start": 6681, - "end": 6682, + "start": 7185, + "end": 7186, "loc": { "start": { - "line": 200, + "line": 219, "column": 91 }, "end": { - "line": 200, + "line": 219, "column": 92 } } @@ -39285,15 +42452,15 @@ "updateContext": null }, "value": "", - "start": 6682, - "end": 6682, + "start": 7186, + "end": 7186, "loc": { "start": { - "line": 200, + "line": 219, "column": 92 }, "end": { - "line": 200, + "line": 219, "column": 92 } } @@ -39310,15 +42477,15 @@ "postfix": false, "binop": null }, - "start": 6682, - "end": 6683, + "start": 7186, + "end": 7187, "loc": { "start": { - "line": 200, + "line": 219, "column": 92 }, "end": { - "line": 200, + "line": 219, "column": 93 } } @@ -39336,15 +42503,15 @@ "binop": null, "updateContext": null }, - "start": 6683, - "end": 6684, + "start": 7187, + "end": 7188, "loc": { "start": { - "line": 200, + "line": 219, "column": 93 }, "end": { - "line": 200, + "line": 219, "column": 94 } } @@ -39362,15 +42529,15 @@ "binop": null }, "value": "nodeLabel", - 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"line": 219, + "line": 238, "column": 22 } } @@ -40504,15 +43671,15 @@ "binop": null, "updateContext": null }, - "start": 7083, - "end": 7084, + "start": 7587, + "end": 7588, "loc": { "start": { - "line": 219, + "line": 238, "column": 22 }, "end": { - "line": 219, + "line": 238, "column": 23 } } @@ -40531,15 +43698,15 @@ "updateContext": null }, "value": "@type", - "start": 7085, - "end": 7092, + "start": 7589, + "end": 7596, "loc": { "start": { - "line": 219, + "line": 238, "column": 24 }, "end": { - "line": 219, + "line": 238, "column": 31 } } @@ -40556,15 +43723,15 @@ "postfix": false, "binop": null }, - "start": 7092, - "end": 7093, + "start": 7596, + "end": 7597, "loc": { "start": { - "line": 219, + "line": 238, "column": 31 }, "end": { - "line": 219, + "line": 238, "column": 32 } } @@ -40581,15 +43748,15 @@ "postfix": false, "binop": null }, - "start": 7093, - "end": 7094, + "start": 7597, + "end": 7598, "loc": { "start": { - "line": 219, + "line": 238, "column": 32 }, "end": { - "line": 219, + "line": 238, "column": 33 } } @@ -40606,15 +43773,15 @@ "postfix": false, "binop": null }, - "start": 7095, - "end": 7096, + "start": 7599, + "end": 7600, "loc": { "start": { - "line": 219, + "line": 238, "column": 34 }, "end": { - "line": 219, + "line": 238, "column": 35 } } @@ -40634,15 +43801,15 @@ "updateContext": null }, "value": "if", - "start": 7103, - "end": 7105, + "start": 7607, + "end": 7609, "loc": { "start": { - "line": 220, + "line": 239, "column": 6 }, "end": { - "line": 220, + "line": 239, "column": 8 } } @@ -40659,15 +43826,15 @@ "postfix": false, "binop": null }, - "start": 7106, - "end": 7107, + "start": 7610, + "end": 7611, "loc": { "start": { - "line": 220, + "line": 239, "column": 9 }, "end": { - "line": 220, + "line": 239, "column": 10 } } @@ -40685,15 +43852,15 @@ "binop": null }, "value": "isArray", - "start": 7107, - "end": 7114, + "start": 7611, + "end": 7618, "loc": { "start": { - "line": 220, + "line": 239, "column": 10 }, "end": { - "line": 220, + "line": 239, "column": 17 } } @@ -40710,15 +43877,15 @@ "postfix": false, "binop": null }, - 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"start": 7135, - "end": 7136, + "start": 7639, + "end": 7640, "loc": { "start": { - "line": 220, + "line": 239, "column": 38 }, "end": { - "line": 220, + "line": 239, "column": 39 } } @@ -40947,15 +44114,15 @@ "updateContext": null }, "value": "this", - "start": 7137, - "end": 7141, + "start": 7641, + "end": 7645, "loc": { "start": { - "line": 220, + "line": 239, "column": 40 }, "end": { - "line": 220, + "line": 239, "column": 44 } } @@ -40973,15 +44140,15 @@ "binop": null, "updateContext": null }, - "start": 7141, - "end": 7142, + "start": 7645, + "end": 7646, "loc": { "start": { - "line": 220, + "line": 239, "column": 44 }, "end": { - "line": 220, + "line": 239, "column": 45 } } @@ -40999,15 +44166,15 @@ "binop": null }, "value": "tunit", - "start": 7142, - "end": 7147, + "start": 7646, + "end": 7651, "loc": { "start": { - "line": 220, + "line": 239, "column": 45 }, "end": { - "line": 220, + "line": 239, "column": 50 } } @@ -41025,15 +44192,15 @@ "binop": null, "updateContext": null }, - 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"end": 7616, + "start": 8116, + "end": 8120, "loc": { "start": { - "line": 239, + "line": 258, "column": 8 }, "end": { - "line": 239, + "line": 258, "column": 12 } } @@ -42946,15 +46113,15 @@ "binop": null, "updateContext": null }, - "start": 7616, - "end": 7617, + "start": 8120, + "end": 8121, "loc": { "start": { - "line": 239, + "line": 258, "column": 12 }, "end": { - "line": 239, + "line": 258, "column": 13 } } @@ -42972,15 +46139,15 @@ "binop": null }, "value": "types", - "start": 7617, - "end": 7622, + "start": 8121, + "end": 8126, "loc": { "start": { - "line": 239, + "line": 258, "column": 13 }, "end": { - "line": 239, + "line": 258, "column": 18 } } @@ -42998,15 +46165,15 @@ "binop": null, "updateContext": null }, - "start": 7622, - "end": 7623, + "start": 8126, + "end": 8127, "loc": { "start": { - "line": 239, + "line": 258, "column": 18 }, "end": { - "line": 239, + "line": 258, "column": 19 } } @@ -43024,15 +46191,15 @@ "binop": null }, "value": "includes", - "start": 7623, - "end": 7631, + "start": 8127, + "end": 8135, "loc": { "start": { - "line": 239, + "line": 258, "column": 19 }, "end": { - "line": 239, + "line": 258, "column": 27 } } @@ -43049,15 +46216,15 @@ "postfix": false, "binop": null }, - "start": 7631, - "end": 7632, + "start": 8135, + "end": 8136, "loc": { "start": { - "line": 239, + "line": 258, "column": 27 }, "end": { - "line": 239, + "line": 258, "column": 28 } } @@ -43075,15 +46242,15 @@ "binop": null }, "value": "TaxonomicUnitWrapper", - "start": 7632, - "end": 7652, + "start": 8136, + "end": 8156, "loc": { "start": { - "line": 239, + "line": 258, "column": 28 }, "end": { - "line": 239, + "line": 258, "column": 48 } } @@ -43101,15 +46268,15 @@ "binop": null, "updateContext": null }, - "start": 7652, - "end": 7653, + "start": 8156, + "end": 8157, "loc": { "start": { - "line": 239, + "line": 258, "column": 48 }, "end": { - "line": 239, + "line": 258, "column": 49 } } @@ -43127,15 +46294,15 @@ "binop": null }, "value": "TYPE_SPECIMEN", - "start": 7653, - "end": 7666, + "start": 8157, + "end": 8170, "loc": { "start": { - "line": 239, + "line": 258, "column": 49 }, "end": { - "line": 239, + "line": 258, "column": 62 } } @@ -43152,15 +46319,15 @@ "postfix": false, "binop": null }, - "start": 7666, - "end": 7667, + "start": 8170, + "end": 8171, "loc": { "start": { - "line": 239, + "line": 258, "column": 62 }, "end": { - "line": 239, + "line": 258, "column": 63 } } @@ -43177,15 +46344,15 @@ "postfix": false, "binop": null }, - "start": 7667, - "end": 7668, + "start": 8171, + "end": 8172, "loc": { "start": { - "line": 239, + "line": 258, "column": 63 }, "end": { - "line": 239, + "line": 258, "column": 64 } } @@ -43202,15 +46369,15 @@ "postfix": false, "binop": null }, - "start": 7669, - "end": 7670, + "start": 8173, + "end": 8174, "loc": { "start": { - "line": 239, + "line": 258, "column": 65 }, "end": { - "line": 239, + "line": 258, "column": 66 } } @@ -43230,15 +46397,15 @@ "updateContext": null }, "value": "return", - "start": 7677, - "end": 7683, + "start": 8181, + "end": 8187, "loc": { "start": { - "line": 240, + "line": 259, "column": 6 }, "end": { - "line": 240, + "line": 259, "column": 12 } } @@ -43258,15 +46425,15 @@ "updateContext": null }, "value": "new", - "start": 7684, - "end": 7687, + "start": 8188, + "end": 8191, "loc": { "start": { - "line": 240, + "line": 259, "column": 13 }, "end": { - "line": 240, + "line": 259, "column": 16 } } @@ -43284,15 +46451,15 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 7688, - "end": 7703, + "start": 8192, + "end": 8207, "loc": { "start": { - "line": 240, + "line": 259, "column": 17 }, "end": { - "line": 240, + "line": 259, "column": 32 } } @@ -43309,15 +46476,15 @@ "postfix": false, "binop": null }, - "start": 7703, - "end": 7704, + "start": 8207, + "end": 8208, "loc": { "start": { - "line": 240, + "line": 259, "column": 32 }, "end": { - "line": 240, + "line": 259, "column": 33 } } @@ -43337,15 +46504,15 @@ "updateContext": null }, "value": "this", - "start": 7704, - "end": 7708, + "start": 8208, + "end": 8212, "loc": { "start": { - "line": 240, + "line": 259, "column": 33 }, "end": { - "line": 240, + "line": 259, "column": 37 } } @@ -43363,15 +46530,15 @@ "binop": null, "updateContext": null }, - "start": 7708, - "end": 7709, + "start": 8212, + "end": 8213, "loc": { "start": { - "line": 240, + "line": 259, "column": 37 }, "end": { - "line": 240, + "line": 259, "column": 38 } } @@ -43389,15 +46556,15 @@ "binop": null }, "value": "specimen", - "start": 7709, - "end": 7717, + "start": 8213, + "end": 8221, "loc": { "start": { - "line": 240, + "line": 259, "column": 38 }, "end": { - "line": 240, + "line": 259, "column": 46 } } @@ -43414,15 +46581,15 @@ "postfix": false, "binop": null }, - "start": 7717, - "end": 7718, + "start": 8221, + "end": 8222, "loc": { "start": { - "line": 240, + "line": 259, "column": 46 }, "end": { - "line": 240, + "line": 259, "column": 47 } } @@ -43440,15 +46607,15 @@ "binop": null, "updateContext": null }, - "start": 7718, - "end": 7719, + "start": 8222, + "end": 8223, "loc": { "start": { - "line": 240, + "line": 259, "column": 47 }, "end": { - "line": 240, + "line": 259, "column": 48 } } @@ -43466,15 +46633,15 @@ "binop": null }, "value": "asOWLEquivClass", - "start": 7719, - "end": 7734, + "start": 8223, + "end": 8238, "loc": { "start": { - "line": 240, + "line": 259, "column": 48 }, "end": { - "line": 240, + "line": 259, "column": 63 } } @@ -43492,15 +46659,15 @@ "binop": null, "updateContext": null }, - "start": 7734, - "end": 7735, + "start": 8238, + "end": 8239, "loc": { "start": { - "line": 240, + "line": 259, "column": 63 }, "end": { - "line": 240, + "line": 259, "column": 64 } } @@ -43517,15 +46684,15 @@ "postfix": false, "binop": null }, - "start": 7740, - "end": 7741, + "start": 8244, + "end": 8245, "loc": { "start": { - "line": 241, + "line": 260, "column": 4 }, "end": { - "line": 241, + "line": 260, "column": 5 } } @@ -43533,15 +46700,15 @@ { "type": "CommentLine", "value": " Nothing we can do, so just ignore it.", - "start": 7747, - "end": 7787, + "start": 8251, + "end": 8291, "loc": { "start": { - "line": 243, + "line": 262, "column": 4 }, "end": { - "line": 243, + "line": 262, "column": 44 } } @@ -43561,15 +46728,15 @@ "updateContext": null }, "value": "return", - "start": 7792, - "end": 7798, + "start": 8296, + "end": 8302, "loc": { "start": { - "line": 244, + "line": 263, "column": 4 }, "end": { - "line": 244, + "line": 263, "column": 10 } } @@ -43587,15 +46754,15 @@ "binop": null }, "value": "undefined", - "start": 7799, - "end": 7808, + "start": 8303, + "end": 8312, "loc": { "start": { - "line": 244, + "line": 263, "column": 11 }, "end": { - "line": 244, + "line": 263, "column": 20 } } @@ -43613,15 +46780,15 @@ "binop": null, "updateContext": null }, - "start": 7808, - "end": 7809, + "start": 8312, + "end": 8313, "loc": { "start": { - "line": 244, + "line": 263, "column": 20 }, "end": { - "line": 244, + "line": 263, "column": 21 } } @@ -43638,15 +46805,15 @@ "postfix": false, "binop": null }, - "start": 7812, - "end": 7813, + "start": 8316, + "end": 8317, "loc": { "start": { - "line": 245, + "line": 264, "column": 2 }, "end": { - "line": 245, + "line": 264, "column": 3 } } @@ -43663,15 +46830,15 @@ "postfix": false, "binop": null }, - "start": 7814, - "end": 7815, + "start": 8318, + "end": 8319, "loc": { "start": { - "line": 246, + "line": 265, "column": 0 }, "end": { - "line": 246, + "line": 265, "column": 1 } } @@ -43691,15 +46858,15 @@ "updateContext": null }, "value": "export", - "start": 7817, - "end": 7823, + "start": 8321, + "end": 8327, "loc": { "start": { - "line": 248, + "line": 267, "column": 0 }, "end": { - "line": 248, + "line": 267, "column": 6 } } @@ -43716,15 +46883,15 @@ "postfix": false, "binop": null }, - "start": 7824, - "end": 7825, + "start": 8328, + "end": 8329, "loc": { "start": { - "line": 248, + "line": 267, "column": 7 }, "end": { - "line": 248, + "line": 267, "column": 8 } } @@ -43742,15 +46909,15 @@ "binop": null }, "value": "TaxonomicUnitWrapper", - "start": 7826, - "end": 7846, + "start": 8330, + "end": 8350, "loc": { "start": { - "line": 248, + "line": 267, "column": 9 }, "end": { - "line": 248, + "line": 267, "column": 29 } } @@ -43768,15 +46935,15 @@ "binop": null, "updateContext": null }, - "start": 7846, - "end": 7847, + "start": 8350, + "end": 8351, "loc": { "start": { - "line": 248, + "line": 267, "column": 29 }, "end": { - "line": 248, + "line": 267, "column": 30 } } @@ -43793,15 +46960,15 @@ "postfix": false, "binop": null }, - "start": 7848, - "end": 7849, + "start": 8352, + "end": 8353, "loc": { "start": { - "line": 248, + "line": 267, "column": 31 }, "end": { - "line": 248, + "line": 267, "column": 32 } } @@ -43819,15 +46986,15 @@ "binop": null, "updateContext": null }, - "start": 7849, - "end": 7850, + "start": 8353, + "end": 8354, "loc": { "start": { - "line": 248, + "line": 267, "column": 32 }, "end": { - "line": 248, + "line": 267, "column": 33 } } @@ -43845,15 +47012,15 @@ "binop": null, "updateContext": null }, - "start": 7851, - "end": 7851, + "start": 8355, + "end": 8355, "loc": { "start": { - "line": 249, + "line": 268, "column": 0 }, "end": { - "line": 249, + "line": 268, "column": 0 } } diff --git a/docs/badge.svg b/docs/badge.svg index 303f6c6d..8d64e854 100644 --- a/docs/badge.svg +++ b/docs/badge.svg @@ -11,7 +11,7 @@ document document - 52% - 52% + 54% + 54% diff --git a/docs/class/src/wrappers/CitationWrapper.js~CitationWrapper.html b/docs/class/src/wrappers/CitationWrapper.js~CitationWrapper.html index bd1e7338..5c1fed55 100644 --- a/docs/class/src/wrappers/CitationWrapper.js~CitationWrapper.html +++ b/docs/class/src/wrappers/CitationWrapper.js~CitationWrapper.html @@ -113,6 +113,35 @@

CitationWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(citation: *): * +

+
+
+ + +

Return a normalized form of a citation.

+
+
+ + + + @@ -243,7 +272,7 @@

- source + source

@@ -307,6 +336,81 @@

Return:

+ +
+

+ public + static + + + + + normalize(citation: *): * + + + + source + +

+ + + + +

Return a normalized form of a citation.

+

I'm not really sure how to normalize a citation, but the main thing we can do is delete any key +that is equivalent to ''. We could interconvert between name and +firstname/lastname/middlename, but that's not really equivalent, is it?

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
citation*
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

Public Constructors

@@ -416,7 +520,7 @@

- source + source

diff --git a/docs/class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html b/docs/class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html index 299d418f..c332fb24 100644 --- a/docs/class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html +++ b/docs/class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html @@ -43,13 +43,13 @@
- 
import {PhylogenyWrapper} from '@phyloref/phyx/src/wrappers/PhylogenyWrapper.js'
+ 
import {PhylogenyWrapper} from '@phyloref/phyx/src/wrappers/PhylogenyWrapper.js'
public class - | source + | source
@@ -140,6 +140,35 @@

PhylogenyWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(phylogeny: *): * +

+
+
+ + +

Return a normalized form of the phylogeny.

+
+
+ + + + @@ -493,7 +522,7 @@

- source + source

@@ -564,7 +593,7 @@

- source + source

@@ -622,6 +651,78 @@

Return:

+
+
+

+ public + static + + + + + normalize(phylogeny: *): * + + + + source + +

+ + + + +

Return a normalized form of the phylogeny.

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
phylogeny*
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

@@ -635,7 +736,7 @@

- source + source

@@ -729,7 +830,7 @@

- source + source

@@ -775,7 +876,7 @@

- source + source

@@ -818,7 +919,7 @@

- source + source

@@ -864,7 +965,7 @@

- source + source

@@ -941,7 +1042,7 @@

- source + source

@@ -1013,7 +1114,7 @@

- source + source

@@ -1084,7 +1185,7 @@

- source + source

@@ -1161,7 +1262,7 @@

- source + source

@@ -1238,7 +1339,7 @@

- source + source

@@ -1310,7 +1411,7 @@

- source + source

diff --git a/docs/class/src/wrappers/PhylorefWrapper.js~PhylorefWrapper.html b/docs/class/src/wrappers/PhylorefWrapper.js~PhylorefWrapper.html index 7de3e3ad..0087683b 100644 --- a/docs/class/src/wrappers/PhylorefWrapper.js~PhylorefWrapper.html +++ b/docs/class/src/wrappers/PhylorefWrapper.js~PhylorefWrapper.html @@ -113,6 +113,35 @@

PhylorefWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(phyloref: *): * +

+
+
+ + +

Normalize a phyloreference.

+
+
+ + + + @@ -837,7 +866,7 @@

- source + source

@@ -879,6 +908,78 @@

Return:

+
+
+

+ public + static + + + + + normalize(phyloref: *): * + + + + source + +

+ + + + +

Normalize a phyloreference.

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
phyloref*
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

Public Constructors

@@ -941,7 +1042,7 @@

- source + source

@@ -984,7 +1085,7 @@

- source + source

@@ -1027,7 +1128,7 @@

- source + source

@@ -1074,7 +1175,7 @@

- source + source

@@ -1162,7 +1263,7 @@

- source + source

@@ -1205,7 +1306,7 @@

- source + source

@@ -1334,7 +1435,7 @@

- source + source

@@ -1378,7 +1479,7 @@

- source + source

@@ -1429,7 +1530,7 @@

- source + source

@@ -1500,7 +1601,7 @@

- source + source

@@ -1583,7 +1684,7 @@

- source + source

@@ -1703,7 +1804,7 @@

- source + source

@@ -1762,7 +1863,7 @@

- source + source

@@ -1817,7 +1918,7 @@

- source + source

@@ -1888,7 +1989,7 @@

- source + source

@@ -1959,7 +2060,7 @@

- source + source

@@ -2038,7 +2139,7 @@

- source + source

@@ -2109,7 +2210,7 @@

- source + source

@@ -2164,7 +2265,7 @@

- source + source

@@ -2229,7 +2330,7 @@

- source + source

diff --git a/docs/class/src/wrappers/PhyxWrapper.js~PhyxWrapper.html b/docs/class/src/wrappers/PhyxWrapper.js~PhyxWrapper.html index 32f38b5a..14f5207f 100644 --- a/docs/class/src/wrappers/PhyxWrapper.js~PhyxWrapper.html +++ b/docs/class/src/wrappers/PhyxWrapper.js~PhyxWrapper.html @@ -83,7 +83,42 @@

PhyxWrapper

- +

Static Method Summary

+ + + + + + + + + +
Static Public Methods
+ public + static + + + + +
+

+ + + + normalize(phyxDocument: *): * +

+
+
+ + +

Return a provided Phyx document as a normalized JSON document.

+
+
+ 		+ + +
+

Constructor Summary

@@ -280,7 +315,89 @@

PhyxWrapper

+

Static Public Methods

+ +
+

+ public + static + + + + + normalize(phyxDocument: *): * + + + + source + +

+ + + + +

Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including +keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this +package will be wrapped and normalized before being returned.

+

Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses +(TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially +identical ways. But if we implement it at every level, we can implement comparison code in +Klados easily.

+

Two Phyx documents should -- upon being normalized -- be comparable with each other with +lodash.deepEqual().

+
+ + + +
+

Params:

+
Public Constructor
+ + + + + + + + + + + + +
NameTypeAttributeDescription
phyxDocument*
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + + +

Public Constructors

@@ -504,7 +621,7 @@

- source + source

@@ -591,7 +708,7 @@

- source + source

diff --git a/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html b/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html index c7f2c929..c18fddf1 100644 --- a/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html +++ b/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html @@ -163,6 +163,35 @@

SpecimenWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(specimen: *): * +

+
+
+ + +

Normalize the specified specimen.

+
+
+ + + + @@ -565,7 +594,7 @@

- source + source

@@ -636,6 +665,79 @@

Return:

+
+
+

+ public + static + + + + + normalize(specimen: *): * + + + + source + +

+ + + + +

Normalize the specified specimen.

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
specimen*

A specimen to be normalized.

+
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

Public Constructors

@@ -699,7 +801,7 @@

- source + source

@@ -743,7 +845,7 @@

- source + source

@@ -787,7 +889,7 @@

- source + source

@@ -832,7 +934,7 @@

- source + source

@@ -876,7 +978,7 @@

- source + source

@@ -920,7 +1022,7 @@

- source + source

@@ -964,7 +1066,7 @@

- source + source

@@ -1008,7 +1110,7 @@

- source + source

@@ -1098,7 +1200,7 @@

- source + source

diff --git a/docs/class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html b/docs/class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html index 87f238ee..67cc4ac6 100644 --- a/docs/class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html +++ b/docs/class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html @@ -161,6 +161,35 @@

TaxonConceptWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(tc: *): * +

+
+
+ + +

Normalize the specified taxon concept.

+
+
+ + + + @@ -592,7 +621,7 @@

- source + source

@@ -661,6 +690,79 @@

Return:

+
+
+

+ public + static + + + + + normalize(tc: *): * + + + + source + +

+ + + + +

Normalize the specified taxon concept.

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
tc*

A taxon concept to be normalized.

+
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

@@ -674,7 +776,7 @@

- source + source

@@ -802,7 +904,7 @@

- source + source

@@ -848,7 +950,7 @@

- source + source

@@ -894,7 +996,7 @@

- source + source

@@ -983,7 +1085,7 @@

- source + source

@@ -1027,7 +1129,7 @@

- source + source

@@ -1072,7 +1174,7 @@

- source + source

@@ -1116,7 +1218,7 @@

- source + source

@@ -1160,7 +1262,7 @@

- source + source

diff --git a/docs/class/src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.html b/docs/class/src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.html index 64fe590e..d4712942 100644 --- a/docs/class/src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.html +++ b/docs/class/src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.html @@ -401,6 +401,35 @@

TaxonNameWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(txname: *): * +

+
+
+ + +

Normalize the specified taxon name.

+
+
+ + + + @@ -1467,7 +1496,7 @@

- source + source

@@ -1669,6 +1698,79 @@

Return:

+
+
+

+ public + static + + + + + normalize(txname: *): * + + + + source + +

+ + + + +

Normalize the specified taxon name.

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
txname*

A taxon name to be normalized.

+
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

Public Constructors

@@ -1733,7 +1835,7 @@

- source + source

@@ -1777,7 +1879,7 @@

- source + source

@@ -1821,7 +1923,7 @@

- source + source

@@ -1865,7 +1967,7 @@

- source + source

@@ -1952,7 +2054,7 @@

- source + source

@@ -1996,7 +2098,7 @@

- source + source

@@ -2040,7 +2142,7 @@

- source + source

@@ -2084,7 +2186,7 @@

- source + source

@@ -2128,7 +2230,7 @@

- source + source

@@ -2172,7 +2274,7 @@

- source + source

@@ -2216,7 +2318,7 @@

- source + source

@@ -2259,7 +2361,7 @@

- source + source

@@ -2303,7 +2405,7 @@

- source + source

@@ -2347,7 +2449,7 @@

- source + source

@@ -2391,7 +2493,7 @@

- source + source

@@ -2435,7 +2537,7 @@

- source + source

@@ -2479,7 +2581,7 @@

- source + source

@@ -2523,7 +2625,7 @@

- source + source

@@ -2567,7 +2669,7 @@

- source + source

@@ -2654,7 +2756,7 @@

- source + source

@@ -2698,7 +2800,7 @@

- source + source

@@ -2742,7 +2844,7 @@

- source + source

diff --git a/docs/class/src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.html b/docs/class/src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.html index 5162d59e..47436c7f 100644 --- a/docs/class/src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.html +++ b/docs/class/src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.html @@ -196,6 +196,35 @@

TaxonomicUnitWrapper

+ + + + + public + static + + + + + +
+

+ + + + normalize(tunit: *): * +

+
+
+ + +

Normalize the specified taxonomic unit.

+
+
+ + + + @@ -646,7 +675,7 @@

- source + source

@@ -713,6 +742,79 @@

Return:

+
+
+

+ public + static + + + + + normalize(tunit: *): * + + + + source + +

+ + + + +

Normalize the specified taxonomic unit.

+
+ + + +
+

Params:

+ + + + + + + + + + + + + +
NameTypeAttributeDescription
tunit*

A taxonomic unit to be normalized.

+
+
+
+ +
+

Return:

+ + + + + + + +
*
+
+
+
+ + + + + + + + + + + + + + +

Public Constructors

@@ -776,7 +878,7 @@

- source + source

@@ -820,7 +922,7 @@

- source + source

@@ -864,7 +966,7 @@

- source + source

@@ -951,7 +1053,7 @@

- source + source

@@ -996,7 +1098,7 @@

- source + source

@@ -1040,7 +1142,7 @@

- source + source

@@ -1084,7 +1186,7 @@

- source + source

@@ -1171,7 +1273,7 @@

- source + source

diff --git a/docs/coverage.json b/docs/coverage.json index 8ecb4642..84f22da8 100644 --- a/docs/coverage.json +++ b/docs/coverage.json @@ -1,7 +1,7 @@ { - "coverage": "52.63%", - "expectCount": 171, - "actualCount": 90, + "coverage": "54.74%", + "expectCount": 179, + "actualCount": 98, "files": { "src/matchers/TaxonomicUnitMatcher.js": { "expectCount": 14, @@ -17,8 +17,8 @@ ] }, "src/wrappers/CitationWrapper.js": { - "expectCount": 6, - "actualCount": 3, + "expectCount": 7, + "actualCount": 4, "undocumentLines": [ 7, 9, @@ -26,31 +26,31 @@ ] }, "src/wrappers/PhylogenyWrapper.js": { - "expectCount": 18, - "actualCount": 1, + "expectCount": 19, + "actualCount": 2, "undocumentLines": [ 6, - 15, - 17, - 19, - 21, - 27, - 37, - 38, + 18, + 20, + 22, + 24, + 30, + 40, 41, - 93, - 127, - 150, - 236, - 253, - 284, - 308, - 424 + 60, + 112, + 146, + 169, + 255, + 272, + 303, + 327, + 443 ] }, "src/wrappers/PhylorefWrapper.js": { - "expectCount": 31, - "actualCount": 8, + "expectCount": 32, + "actualCount": 9, "undocumentLines": [ 4, 8, @@ -60,26 +60,26 @@ 24, 26, 27, - 52, - 61, - 81, - 90, - 121, + 68, + 77, + 97, + 106, 137, - 177, - 189, - 232, - 266, - 430, - 456, - 512, - 607, - 653 + 153, + 193, + 205, + 248, + 282, + 446, + 472, + 528, + 623, + 669 ] }, "src/wrappers/PhyxWrapper.js": { - "expectCount": 11, - "actualCount": 4, + "expectCount": 12, + "actualCount": 5, "undocumentLines": [ 6, 14, @@ -91,8 +91,8 @@ ] }, "src/wrappers/SpecimenWrapper.js": { - "expectCount": 17, - "actualCount": 13, + "expectCount": 18, + "actualCount": 14, "undocumentLines": [ 2, 4, @@ -101,8 +101,8 @@ ] }, "src/wrappers/TaxonConceptWrapper.js": { - "expectCount": 17, - "actualCount": 13, + "expectCount": 18, + "actualCount": 14, "undocumentLines": [ 3, 10, @@ -111,8 +111,8 @@ ] }, "src/wrappers/TaxonNameWrapper.js": { - "expectCount": 38, - "actualCount": 28, + "expectCount": 39, + "actualCount": 29, "undocumentLines": [ 3, 10, @@ -123,12 +123,12 @@ 70, 72, 74, - 270 + 289 ] }, "src/wrappers/TaxonomicUnitWrapper.js": { - "expectCount": 19, - "actualCount": 13, + "expectCount": 20, + "actualCount": 14, "undocumentLines": [ 3, 15, diff --git a/docs/file/src/wrappers/CitationWrapper.js.html b/docs/file/src/wrappers/CitationWrapper.js.html index 7cd2be3c..e7f15d25 100644 --- a/docs/file/src/wrappers/CitationWrapper.js.html +++ b/docs/file/src/wrappers/CitationWrapper.js.html @@ -58,6 +58,24 @@ this.citation = citation; } + /** + * Return a normalized form of a citation. + * + * I'm not really sure how to normalize a citation, but the main thing we can do is delete any key + * that is equivalent to ''. We could interconvert between `name` and + * `firstname/lastname/middlename`, but that's not really equivalent, is it? + */ + static normalize(citation) { + const normalizedCitation = {}; + Object.keys(citation).forEach((key) => { + // As long as citation[key] has a reasonable value, we copy it into the normalized citation. + if (citation[key]) { + normalizedCitation[key] = citation[key]; + } + }); + return normalizedCitation; + } + /** * Helper method to return a single name for a given agent entry. * The algorithm we use is: diff --git a/docs/file/src/wrappers/PhylogenyWrapper.js.html b/docs/file/src/wrappers/PhylogenyWrapper.js.html index ef4cdc16..eb4aada5 100644 --- a/docs/file/src/wrappers/PhylogenyWrapper.js.html +++ b/docs/file/src/wrappers/PhylogenyWrapper.js.html @@ -47,7 +47,10 @@ * PhylogenyWrapper */ -const { has } = require('lodash'); +const { + has, + cloneDeep, +} = require('lodash'); /** Used to parse Newick strings. */ const newickJs = require('newick-js'); @@ -79,6 +82,22 @@ this.defaultNomenCode = defaultNomenCode; } + /** + * Return a normalized form of the phylogeny. + */ + static normalize(phylogeny) { + const normalizedPhylogeny = cloneDeep(phylogeny); + + // We could normalize the Newick string, but that doesn't seem very nice. + + // Normalize the source if there is one. + if ('source' in phylogeny) { + normalizedPhylogeny.source = CitationWrapper.normalize(phylogeny.source || {}); + } + + return normalizedPhylogeny; + } + static getErrorsInNewickString(newick) { // Given a Newick string, return a list of errors found in parsing this // string. The errors are returned as a list of objects, each of which diff --git a/docs/file/src/wrappers/PhylorefWrapper.js.html b/docs/file/src/wrappers/PhylorefWrapper.js.html index 9ccaf366..882c4f90 100644 --- a/docs/file/src/wrappers/PhylorefWrapper.js.html +++ b/docs/file/src/wrappers/PhylorefWrapper.js.html @@ -78,6 +78,22 @@ return this.phyloref.internalSpecifiers; } + /** + * Normalize a phyloreference. + * + * @param phyloref + */ + static normalize(phyloref) { + const normalizedPhyloref = cloneDeep(phyloref); + + normalizedPhyloref.internalSpecifiers = (phyloref.internalSpecifiers || []) + .map(TaxonomicUnitWrapper.normalize); + normalizedPhyloref.externalSpecifiers = (phyloref.externalSpecifiers || []) + .map(TaxonomicUnitWrapper.normalize); + + return normalizedPhyloref; + } + /** Return the external specifiers of this phyloref (if any). */ get externalSpecifiers() { if (!has(this.phyloref, 'externalSpecifiers')) { diff --git a/docs/file/src/wrappers/PhyxWrapper.js.html b/docs/file/src/wrappers/PhyxWrapper.js.html index 05de1d09..0c951d94 100644 --- a/docs/file/src/wrappers/PhyxWrapper.js.html +++ b/docs/file/src/wrappers/PhyxWrapper.js.html @@ -96,6 +96,32 @@ return owlterms.UNKNOWN_CODE; } + /** + * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including + * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this + * package will be wrapped and normalized before being returned. + * + * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses + * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially + * identical ways. But if we implement it at every level, we can implement comparison code in + * Klados easily. + * + * Two Phyx documents should -- upon being normalized -- be comparable with each other with + * lodash.deepEqual(). + */ + static normalize(phyxDocument) { + const normalizedDocument = cloneDeep(phyxDocument); + + normalizedDocument.phylorefs = (phyxDocument.phylorefs || []).map(PhylorefWrapper.normalize); + normalizedDocument.phylogenies = (phyxDocument.phylogenies || []) + .map(PhylogenyWrapper.normalize); + if ('source' in phyxDocument) { + normalizedDocument.source = CitationWrapper.normalize(phyxDocument.source); + } + + return normalizedDocument; + } + /** * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD * already, except for three important things: diff --git a/docs/file/src/wrappers/SpecimenWrapper.js.html b/docs/file/src/wrappers/SpecimenWrapper.js.html index 980da1a8..d0c956f6 100644 --- a/docs/file/src/wrappers/SpecimenWrapper.js.html +++ b/docs/file/src/wrappers/SpecimenWrapper.js.html @@ -74,6 +74,25 @@ this.specimen = specimen; } + /** + * Normalize the specified specimen. + * @param specimen A specimen to be normalized. + */ + static normalize(specimen) { + const wrapped = new SpecimenWrapper(specimen); + const normalizedSpecimen = { + '@type': SpecimenWrapper.TYPE_SPECIMEN, + label: wrapped.label, + 'dwc:basisOfRecord': wrapped.basisOfRecord, + occurrenceID: wrapped.occurrenceID, + catalogNumber: wrapped.catalogNumber, + institutionCode: wrapped.institutionCode, + collectionCode: wrapped.collectionCode, + }; + if ('@id' in specimen) normalizedSpecimen['@id'] = specimen['@id']; + return normalizedSpecimen; + } + /** * Parse the provided occurrence ID. The two expected formats are: * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]' diff --git a/docs/file/src/wrappers/TaxonConceptWrapper.js.html b/docs/file/src/wrappers/TaxonConceptWrapper.js.html index 9873deaf..9db1d76c 100644 --- a/docs/file/src/wrappers/TaxonConceptWrapper.js.html +++ b/docs/file/src/wrappers/TaxonConceptWrapper.js.html @@ -79,6 +79,23 @@ this.defaultNomenCode = defaultNomenCode; } + /** + * Normalize the specified taxon concept. + * @param tc A taxon concept to be normalized. + */ + static normalize(tc) { + const wrapped = new TaxonConceptWrapper(tc); + const normalizedTC = { + '@type': TaxonConceptWrapper.TYPE_TAXON_CONCEPT, + label: wrapped.label, + hasName: TaxonNameWrapper.normalize(wrapped.taxonName), + nameString: wrapped.taxonName.nameComplete, + accordingTo: wrapped.accordingTo, + }; + if ('@id' in tc) normalizedTC['@id'] = tc['@id']; + return normalizedTC; + } + /** * Return the taxon name of this taxon concept (if any) as an object. */ @@ -134,10 +151,10 @@ */ get accordingTo() { // Do we have any accordingTo information? - if (has(this.tunit, 'accordingTo')) return this.type.accordingTo; + if (has(this.tunit, 'accordingTo')) return this.tunit.accordingTo; // Do we have an accordingToString? - if (has(this.tunit, 'accordingToString')) return this.type.accordingToString; + if (has(this.tunit, 'accordingToString')) return this.tunit.accordingToString; // If not, we have no accodingTo information! return undefined; @@ -151,10 +168,10 @@ */ get accordingToString() { // Do we have any accordingTo information? - if (has(this.tunit, 'accordingTo')) return JSON.stringify(this.type.accordingTo); + if (has(this.tunit, 'accordingTo')) return JSON.stringify(this.tunit.accordingTo); // Do we have an accordingToString? - if (has(this.tunit, 'accordingToString')) return this.type.accordingToString; + if (has(this.tunit, 'accordingToString')) return this.tunit.accordingToString; // If not, we have no accodingTo information! return undefined; diff --git a/docs/file/src/wrappers/TaxonNameWrapper.js.html b/docs/file/src/wrappers/TaxonNameWrapper.js.html index a6f83f37..458fc58c 100644 --- a/docs/file/src/wrappers/TaxonNameWrapper.js.html +++ b/docs/file/src/wrappers/TaxonNameWrapper.js.html @@ -188,6 +188,25 @@ return undefined; } + /** + * Normalize the specified taxon name. + * @param txname A taxon name to be normalized. + */ + static normalize(txname) { + const wrapped = new TaxonNameWrapper(txname); + const normalizedTxname = { + '@type': TaxonNameWrapper.TYPE_TAXON_NAME, + nomenclaturalCode: wrapped.nomenclaturalCode, + label: wrapped.label, + nameComplete: wrapped.nameComplete, + genusPart: wrapped.genusPart, + specificEpithet: wrapped.specificEpithet, + infraspecificEpithet: wrapped.infraspecificEpithet, + }; + if ('@id' in txname) normalizedTxname['@id'] = txname['@id']; + return normalizedTxname; + } + /** * Returns the nomenclatural code of this taxon name. */ diff --git a/docs/file/src/wrappers/TaxonomicUnitWrapper.js.html b/docs/file/src/wrappers/TaxonomicUnitWrapper.js.html index 3b5bfac7..c060ea0f 100644 --- a/docs/file/src/wrappers/TaxonomicUnitWrapper.js.html +++ b/docs/file/src/wrappers/TaxonomicUnitWrapper.js.html @@ -104,6 +104,25 @@ this.defaultNomenCode = defaultNomenCode; } + /** + * Normalize the specified taxonomic unit. + * @param tunit A taxonomic unit to be normalized. + */ + static normalize(tunit) { + const wrapped = new TaxonomicUnitWrapper(tunit); + if (wrapped.taxonConcept) { + return TaxonConceptWrapper.normalize(tunit); + } + if (wrapped.specimen) { + return SpecimenWrapper.normalize(tunit); + } + if (wrapped.externalReferences) { + // External references should only have an `@id`. + return tunit; + } + return tunit; + } + /** * What type of specifier is this? This is an array that could contain multiple * classes, but should contain one of: diff --git a/docs/index.json b/docs/index.json index cd0b403a..4b90575b 100644 --- a/docs/index.json +++ b/docs/index.json @@ -835,7 +835,7 @@ "__docId__": 69, "kind": "file", "name": "src/wrappers/CitationWrapper.js", - "content": "/**\n * The CitationWrapper wraps a single citation in the Phyx document.\n * Based on BibJSON (http://okfnlabs.org/bibjson/).\n */\n\nconst { has, isEmpty } = require('lodash');\n\nclass CitationWrapper {\n /**\n * Construct a CitationWrapper.\n */\n constructor(citation) {\n this.citation = citation;\n }\n\n /**\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n */\n static getAgentName(agent) {\n if (has(agent, 'name')) return agent.name;\n if (has(agent, 'lastname')) {\n if (has(agent, 'firstname')) {\n if (has(agent, 'middlename')) {\n return `${agent.firstname} ${agent.middlename} ${agent.lastname}`;\n }\n\n return `${agent.firstname} ${agent.lastname}`;\n }\n return `${agent.lastname}`;\n }\n return '(Unable to read name)';\n }\n\n /** Returns a single string with the entire bibliographic citation. */\n toString() {\n if (!this.citation || isEmpty(this.citation)) return undefined;\n\n // If we already have a bibliographic citation, we can just return that.\n if (has(this.citation, 'bibliographicCitation')) return this.citation.bibliographicCitation;\n\n let authors = (this.citation.authors || []).map(CitationWrapper.getAgentName);\n if (authors.length === 0) authors = ['Anonymous'];\n if (authors.length > 2) authors = [`${authors[0]} et al`];\n\n // The title is based on citation.title, but may include citation.section as well.\n let title = this.citation.title || 'Untitled';\n if (has(this.citation, 'booktitle')) title = `${title} in ${this.citation.booktitle || 'Untitled book'}`;\n let authorsAndTitle = `${authors.join(' and ')} (${this.citation.year || 'n.d.'}) ${title}`;\n\n const editorLists = [];\n const editors = (this.citation.editors || []).map(CitationWrapper.getAgentName);\n if (editors.length > 0) editorLists.push(`eds: ${editors.join(' and ')}`);\n\n const seriesEditors = (this.citation.series_editors || []).map(CitationWrapper.getAgentName);\n if (seriesEditors.length > 0) editorLists.push(`series eds: ${seriesEditors.join(' and ')}`);\n\n if (editorLists.length > 0) authorsAndTitle += ` [${editorLists.join(', ')}]`;\n\n if (has(this.citation, 'section_title')) {\n authorsAndTitle += ` (section: ${this.citation.section_title})`;\n }\n\n // Additional info stores details that should be at the end of the figure number,\n // DOIs, URLs, ISBNs and so on.\n let additionalInfo = ' ';\n if (has(this.citation, 'figure')) additionalInfo += ` fig ${this.citation.figure}`;\n\n // Add DOIs and URLs.\n additionalInfo += (this.citation.identifier || [])\n .filter(id => id.type === 'doi')\n .map(doi => ` doi: ${doi.id}`)\n .join('');\n additionalInfo += (this.citation.link || []).map(link => ` URL: ${link.url}`).join('');\n\n additionalInfo += (this.citation.identifier || [])\n .filter(id => id.type === 'isbn')\n .map(isbn => ` ISBN: ${isbn.id}`)\n .join('');\n\n // A citation for a journal article should be different from others.\n if (has(this.citation, 'journal') && this.citation.type === 'article') {\n const journal = this.citation.journal;\n const journalIssue = (has(journal, 'number')) ? `(${journal.number})` : '';\n const pages = (has(journal, 'pages')) ? `:${journal.pages}` : '';\n additionalInfo += (journal.identifier || [])\n .filter(id => id.type === 'issn')\n .map(issn => `ISSN: ${issn.id} `)\n .join('');\n return `${authorsAndTitle} ${journal.name || 'Unknown journal'} ${journal.volume || 'Unknown volume'}${journalIssue}${pages}${additionalInfo}`;\n }\n\n // If we are here, this must be a book or a book_section.\n if (has(this.citation, 'pages')) additionalInfo += ` pages: ${this.citation.pages}`;\n\n if (has(this.citation, 'publisher') && has(this.citation, 'city')) {\n return `${authorsAndTitle} ${this.citation.publisher}, ${this.citation.city}${additionalInfo}`;\n }\n\n if (has(this.citation, 'publisher')) {\n return `${authorsAndTitle} ${this.citation.publisher}${additionalInfo}`;\n }\n\n return `${authorsAndTitle}${additionalInfo}`.trim();\n }\n}\n\nmodule.exports = {\n CitationWrapper,\n};\n", + "content": "/**\n * The CitationWrapper wraps a single citation in the Phyx document.\n * Based on BibJSON (http://okfnlabs.org/bibjson/).\n */\n\nconst { has, isEmpty } = require('lodash');\n\nclass CitationWrapper {\n /**\n * Construct a CitationWrapper.\n */\n constructor(citation) {\n this.citation = citation;\n }\n\n /**\n * Return a normalized form of a citation.\n *\n * I'm not really sure how to normalize a citation, but the main thing we can do is delete any key\n * that is equivalent to ''. We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n */\n static normalize(citation) {\n const normalizedCitation = {};\n Object.keys(citation).forEach((key) => {\n // As long as citation[key] has a reasonable value, we copy it into the normalized citation.\n if (citation[key]) {\n normalizedCitation[key] = citation[key];\n }\n });\n return normalizedCitation;\n }\n\n /**\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n */\n static getAgentName(agent) {\n if (has(agent, 'name')) return agent.name;\n if (has(agent, 'lastname')) {\n if (has(agent, 'firstname')) {\n if (has(agent, 'middlename')) {\n return `${agent.firstname} ${agent.middlename} ${agent.lastname}`;\n }\n\n return `${agent.firstname} ${agent.lastname}`;\n }\n return `${agent.lastname}`;\n }\n return '(Unable to read name)';\n }\n\n /** Returns a single string with the entire bibliographic citation. */\n toString() {\n if (!this.citation || isEmpty(this.citation)) return undefined;\n\n // If we already have a bibliographic citation, we can just return that.\n if (has(this.citation, 'bibliographicCitation')) return this.citation.bibliographicCitation;\n\n let authors = (this.citation.authors || []).map(CitationWrapper.getAgentName);\n if (authors.length === 0) authors = ['Anonymous'];\n if (authors.length > 2) authors = [`${authors[0]} et al`];\n\n // The title is based on citation.title, but may include citation.section as well.\n let title = this.citation.title || 'Untitled';\n if (has(this.citation, 'booktitle')) title = `${title} in ${this.citation.booktitle || 'Untitled book'}`;\n let authorsAndTitle = `${authors.join(' and ')} (${this.citation.year || 'n.d.'}) ${title}`;\n\n const editorLists = [];\n const editors = (this.citation.editors || []).map(CitationWrapper.getAgentName);\n if (editors.length > 0) editorLists.push(`eds: ${editors.join(' and ')}`);\n\n const seriesEditors = (this.citation.series_editors || []).map(CitationWrapper.getAgentName);\n if (seriesEditors.length > 0) editorLists.push(`series eds: ${seriesEditors.join(' and ')}`);\n\n if (editorLists.length > 0) authorsAndTitle += ` [${editorLists.join(', ')}]`;\n\n if (has(this.citation, 'section_title')) {\n authorsAndTitle += ` (section: ${this.citation.section_title})`;\n }\n\n // Additional info stores details that should be at the end of the figure number,\n // DOIs, URLs, ISBNs and so on.\n let additionalInfo = ' ';\n if (has(this.citation, 'figure')) additionalInfo += ` fig ${this.citation.figure}`;\n\n // Add DOIs and URLs.\n additionalInfo += (this.citation.identifier || [])\n .filter(id => id.type === 'doi')\n .map(doi => ` doi: ${doi.id}`)\n .join('');\n additionalInfo += (this.citation.link || []).map(link => ` URL: ${link.url}`).join('');\n\n additionalInfo += (this.citation.identifier || [])\n .filter(id => id.type === 'isbn')\n .map(isbn => ` ISBN: ${isbn.id}`)\n .join('');\n\n // A citation for a journal article should be different from others.\n if (has(this.citation, 'journal') && this.citation.type === 'article') {\n const journal = this.citation.journal;\n const journalIssue = (has(journal, 'number')) ? `(${journal.number})` : '';\n const pages = (has(journal, 'pages')) ? `:${journal.pages}` : '';\n additionalInfo += (journal.identifier || [])\n .filter(id => id.type === 'issn')\n .map(issn => `ISSN: ${issn.id} `)\n .join('');\n return `${authorsAndTitle} ${journal.name || 'Unknown journal'} ${journal.volume || 'Unknown volume'}${journalIssue}${pages}${additionalInfo}`;\n }\n\n // If we are here, this must be a book or a book_section.\n if (has(this.citation, 'pages')) additionalInfo += ` pages: ${this.citation.pages}`;\n\n if (has(this.citation, 'publisher') && has(this.citation, 'city')) {\n return `${authorsAndTitle} ${this.citation.publisher}, ${this.citation.city}${additionalInfo}`;\n }\n\n if (has(this.citation, 'publisher')) {\n return `${authorsAndTitle} ${this.citation.publisher}${additionalInfo}`;\n }\n\n return `${authorsAndTitle}${additionalInfo}`.trim();\n }\n}\n\nmodule.exports = {\n CitationWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/CitationWrapper.js", "access": "public", @@ -912,6 +912,32 @@ { "__docId__": 74, "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/CitationWrapper.js~CitationWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/CitationWrapper.js~CitationWrapper.normalize", + "access": "public", + "description": "Return a normalized form of a citation.\n\nI'm not really sure how to normalize a citation, but the main thing we can do is delete any key\nthat is equivalent to ''. We could interconvert between `name` and\n`firstname/lastname/middlename`, but that's not really equivalent, is it?", + "lineNumber": 24, + "params": [ + { + "name": "citation", + "types": [ + "*" + ] + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 75, + "kind": "method", "name": "getAgentName", "memberof": "src/wrappers/CitationWrapper.js~CitationWrapper", "generator": false, @@ -920,7 +946,7 @@ "longname": "src/wrappers/CitationWrapper.js~CitationWrapper.getAgentName", "access": "public", "description": "Helper method to return a single name for a given agent entry.\nThe algorithm we use is:\n - `name`, if one is present.\n - Some combination of `lastname`, `firstname` and `middlename`, if present.", - "lineNumber": 23, + "lineNumber": 41, "params": [ { "name": "agent", @@ -936,7 +962,7 @@ } }, { - "__docId__": 75, + "__docId__": 76, "kind": "method", "name": "toString", "memberof": "src/wrappers/CitationWrapper.js~CitationWrapper", @@ -946,7 +972,7 @@ "longname": "src/wrappers/CitationWrapper.js~CitationWrapper#toString", "access": "public", "description": "Returns a single string with the entire bibliographic citation.", - "lineNumber": 39, + "lineNumber": 57, "params": [], "return": { "types": [ @@ -955,10 +981,10 @@ } }, { - "__docId__": 76, + "__docId__": 77, "kind": "file", "name": "src/wrappers/PhylogenyWrapper.js", - "content": "/**\n * PhylogenyWrapper\n */\n\nconst { has } = require('lodash');\n\n/** Used to parse Newick strings. */\nconst newickJs = require('newick-js');\n\n/** OWL terms to be used here. */\nconst owlterms = require('../utils/owlterms');\n\nconst { TaxonomicUnitWrapper } = require('./TaxonomicUnitWrapper');\nconst { TaxonomicUnitMatcher } = require('../matchers/TaxonomicUnitMatcher');\nconst { CitationWrapper } = require('./CitationWrapper');\n\nclass PhylogenyWrapper {\n // Wraps a Phylogeny in a PHYX file and provides access to node, node labels\n // and other information. Remember that a Phylogeny also has the\n // additionalNodeProperties object which provides additional properties for\n // nodes.\n\n constructor(phylogeny, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n // Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.\n // Note that this version ONLY uses the `newick` property to determine the\n // phylogeny: if other representations are included (such as a node-based\n // format, as used in JSON-LD), they will be ignored and possibly overwritten\n // during export. So, to update the phylogeny, please only update the newick\n // string!\n //\n // This ensures that we don't need to reconcile between different\n // possible representations of a phylogeny.\n this.phylogeny = phylogeny;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n static getErrorsInNewickString(newick) {\n // Given a Newick string, return a list of errors found in parsing this\n // string. The errors are returned as a list of objects, each of which\n // has two properties:\n // - title: A short title of the error, distinct for each type of error.\n // - message: A longer description of the error, which might include\n // information specific to a particular error.\n //\n // We try to order errors from most helpful ('Unbalanced parentheses in\n // Newick string') to least helpful ('Error parsing phylogeny').\n const newickTrimmed = newick.trim();\n const errors = [];\n\n // Look for an empty Newick string.\n if (newickTrimmed === '' || newickTrimmed === '()' || newickTrimmed === '();') {\n // None of the later errors are relevant here, so bail out now.\n return [{\n title: 'No phylogeny entered',\n message: 'Click on \"Edit as Newick\" to enter a phylogeny below.',\n }];\n }\n\n // Look for an unbalanced Newick string.\n let parenLevels = 0;\n for (let x = 0; x < newickTrimmed.length; x += 1) {\n if (newickTrimmed[x] === '(') parenLevels += 1;\n if (newickTrimmed[x] === ')') parenLevels -= 1;\n }\n\n if (parenLevels !== 0) {\n errors.push({\n title: 'Unbalanced parentheses in Newick string',\n message: (parenLevels > 0\n ? `You have ${parenLevels} too many open parentheses`\n : `You have ${-parenLevels} too few open parentheses`\n ),\n });\n }\n\n // Finally, try parsing it with newickJs.parse() and see if we get an error.\n try {\n newickJs.parse(newickTrimmed);\n } catch (ex) {\n errors.push({\n title: 'Error parsing phylogeny',\n message: `An error occured while parsing this phylogeny: ${ex.message}`,\n });\n }\n\n return errors;\n }\n\n static recurseNodes(node, func, nodeCount = 0, parentCount = undefined) {\n // Recurse through PhyloTree nodes, executing function on each node.\n // - node: The node to recurse from. The function will be called on node\n // *before* being called on its children.\n // - func: The function to call on `node` and all of its children.\n // - nodeCount: `node` will be called with this nodeCount. All of its\n // children will be called with consecutively increasing nodeCounts.\n // - parentCount: The nodeCount associated with the parent of this node\n // within this run of recurseNodes. For instance, immediate children\n // of `node` will have a parentCount of 0. By default, `node` itself\n // will have a parentCount of `undefined`.\n // When the function `func` is called, it is given three arguments:\n // - The current node object (initially: `node`)\n // - The count of the current node object (initially: `nodeCount`)\n // - The parent count of the current node object (initially: `parentCount`)\n func(node, nodeCount, parentCount);\n\n let nextID = nodeCount + 1;\n\n // Recurse through all children of this node.\n if (has(node, 'children')) {\n node.children.forEach((child) => {\n nextID = PhylogenyWrapper.recurseNodes(\n child,\n func,\n nextID,\n nodeCount\n );\n });\n }\n\n return nextID;\n }\n\n getTaxonomicUnits(nodeType = 'both') {\n // Return a list of all taxonomic units in this phylogeny.\n // Node labels will be extracted from:\n // - internal nodes only (if nodeType == 'internal')\n // - terminal nodes only (if nodeType == 'terminal')\n // - both internal and terminal nodes (if nodeType == 'both')\n //\n // See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted\n // into node labels, but in brief:\n // 1. We look for taxonomic units in the additionalNodeProperties.\n // 2. If none are found, we attempt to parse the node label as a scientific name.\n //\n const nodeLabels = this.getNodeLabels(nodeType);\n const tunits = new Set();\n\n nodeLabels.forEach(\n nodeLabel => this.getTaxonomicUnitsForNodeLabel(nodeLabel)\n .forEach(tunit => tunits.add(tunit))\n );\n\n return tunits;\n }\n\n getNodeLabels(nodeType = 'both') {\n // Return a list of all the node labels in this phylogeny.\n //\n // nodeType can be one of:\n // - 'internal': Return node labels on internal nodes.\n // - 'terminal': Return node labels on terminal nodes.\n // - 'both': Return node labels on both internal and terminal nodes.\n\n // Parse the phylogeny (will throw an exception if parsing failed).\n const { graph } = newickJs.parse(this.phylogeny.newick || '()');\n const [vertices, arcs] = graph;\n\n if (nodeType === 'both') {\n // Return all node labels.\n return Array.from(\n new Set(\n Array.from(vertices)\n .map(vertex => vertex.label)\n .filter(label => label !== undefined)\n )\n );\n }\n\n if (nodeType === 'internal') {\n // Return the internal nodes (those with atleast one child).\n return Array.from(new Set(\n Array.from(arcs)\n .map(arc => arc[0].label) // Retrieve the label of the parent vertex in this arc.\n .filter(label => label !== undefined)\n ));\n }\n\n if (nodeType === 'terminal') {\n // Return the terminal nodes. This would require calculating the children\n // of every vertex in the graph and then identifying vertices without any\n // children.\n //\n // A quicker and dirtier way to do this is by removing internal labels\n // from the list of all node labels. This will report an incorrect result\n // if an internal node has the same label as a terminal node, but at that\n // point a lot of other assumptions are going to fail, too, so this is\n // probably good enough for now.\n const allLabels = this.getNodeLabels('both');\n const internalLabels = new Set(this.getNodeLabels('internal'));\n\n return allLabels.filter(label => !internalLabels.has(label));\n }\n\n throw new Error(`Unknown nodeType: '${nodeType}'`);\n }\n\n /**\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n */\n getTaxonomicUnitsForNodeLabel(nodeLabel) {\n // Look up additional node properties.\n let additionalNodeProperties = {};\n if (\n has(this.phylogeny, 'additionalNodeProperties')\n && has(this.phylogeny.additionalNodeProperties, nodeLabel)\n ) {\n additionalNodeProperties = this.phylogeny.additionalNodeProperties[nodeLabel];\n }\n\n // If there are explicit taxonomic units in the\n // representsTaxonomicUnits property, we need to use those.\n if (has(additionalNodeProperties, 'representsTaxonomicUnits')) {\n return additionalNodeProperties.representsTaxonomicUnits;\n }\n\n // If that doesn't work, we can try to extract scientific names from\n // the node label. Note that taxonomic units will NOT be extracted from\n // the label if there is a taxonomic unit present!\n //\n // Note that old-style taxonomic units were lists while new-style taxonomic\n // units are single objects. So we turn it into a single entry list here.\n const tunit = TaxonomicUnitWrapper.fromLabel(nodeLabel.trim(), this.defaultNomenCode);\n if (tunit) return [tunit];\n return []; // No TUnit? Return the empty list.\n }\n\n getNodeLabelsMatchedBySpecifier(specifier) {\n // Return a list of node labels matched by a given specifier on\n // a given phylogeny.\n\n return this.getNodeLabels().filter((nodeLabel) => {\n // Find all the taxonomic units associated with the specifier and\n // with the node.\n const nodeTUnits = this.getTaxonomicUnitsForNodeLabel(nodeLabel);\n\n // Attempt pairwise matches between taxonomic units in the specifier\n // and associated with the node.\n return nodeTUnits.some(\n tunit => new TaxonomicUnitMatcher(specifier, tunit).matched\n );\n });\n }\n\n static getParsedNewick(newick) {\n // We previously used phylotree.js's Newick parser to parse Newick into a\n // tree-like structure. However, this is difficult to integrate using NPM.\n // This method provides a similar facility using the newick-js library.\n //\n // Throws an exception if the Newick could not be parsed.\n const { graph, root, rootWeight } = newickJs.parse(newick);\n const [, arcs] = graph;\n\n // Go through the arcs, assigning 'children' to the appropriate parent node.\n arcs.forEach((arc) => {\n const [parent, child, weight] = arc;\n\n // Add child to parent.children.\n if (!has(parent, 'children')) parent.children = [];\n parent.children.push(child);\n\n // Phylotree.js uses 'name' instead of 'label'.\n if (has(parent, 'label')) { parent.name = parent.label; }\n if (has(child, 'label')) { child.name = child.label; }\n\n // Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.\n if (!has(child, 'attribute') && !Number.isNaN(weight)) child.attribute = weight;\n });\n\n // Set root 'attribute' to root weight.\n if (!has(root, 'attribute') && !Number.isNaN(rootWeight)) root.attribute = rootWeight;\n\n return { json: root };\n }\n\n getParsedNewickWithIRIs(baseIRI, newickParser = PhylogenyWrapper.getParsedNewick) {\n // Return the parsed Newick string, but with EVERY node given an IRI.\n // - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').\n // Node IDs are generated by concatenating `_node${number}` to the end of\n // the baseIRI.\n // - newickParser: A method for converting a Newick string to a object-based\n // representation. The static method PhylogenyWrapper.getParsedNewick() is\n // used if none is provided.\n\n const parsed = newickParser(this.phylogeny.newick || '()');\n if (has(parsed, 'json')) {\n PhylogenyWrapper.recurseNodes(parsed.json, (node, nodeCount) => {\n // Start with the additional node properties.\n const nodeAsJSONLD = node;\n\n // Set @id and @type.\n const nodeIRI = `${baseIRI}_node${nodeCount}`;\n nodeAsJSONLD['@id'] = nodeIRI;\n });\n }\n\n return parsed;\n }\n\n getNodesAsJSONLD(baseIRI, newickParser) {\n // Returns a list of all nodes in this phylogeny as a series of nodes.\n // - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').\n // Node IDs are generated by concatenating `_node${number}` to the end of\n // the baseIRI.\n // - newickParser: A method for converting a Newick string to a object-based\n // representation. See PhylogenyWrapper.getParsedNewick() for an example\n // implementation.\n\n // List of nodes we have identified.\n const nodes = [];\n\n // We need to track the identifiers we give each node as we go.\n const nodesById = {};\n const nodeIdsByParentId = {};\n\n // Extract the newick string.\n const { additionalNodeProperties } = this.phylogeny;\n\n // Parse the Newick string; if parseable, recurse through the nodes,\n // added them to the list of JSON-LD nodes as we go.\n\n const parsed = this.getParsedNewickWithIRIs(baseIRI, newickParser);\n if (has(parsed, 'json')) {\n PhylogenyWrapper.recurseNodes(parsed.json, (node, nodeCount, parentCount) => {\n // Start with the additional node properties.\n const nodeAsJSONLD = {};\n\n // Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!\n const nodeIRI = node['@id'];\n nodeAsJSONLD['@id'] = nodeIRI;\n\n // Since we may need to add multiple classes into the rdf:type, we need\n // to make @type an array. However, the JSON-LD library we use in JPhyloRef\n // can't support @type being an array (despite that being in the standard,\n // see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),\n // so we fall back to using rdf:type instead.\n nodeAsJSONLD[owlterms.RDF_TYPE] = [{ '@id': owlterms.CDAO_NODE }];\n\n // Add labels, additional node properties and taxonomic units.\n if (has(node, 'name') && node.name !== '') {\n // Add node label.\n nodeAsJSONLD.labels = [node.name];\n\n // Add additional node properties, if any.\n if (additionalNodeProperties && has(additionalNodeProperties, node.name)) {\n Object.keys(additionalNodeProperties[node.name]).forEach((key) => {\n nodeAsJSONLD[key] = additionalNodeProperties[node.name][key];\n });\n }\n\n // Add taxonomic units into the metadata.\n nodeAsJSONLD.representsTaxonomicUnits = this.getTaxonomicUnitsForNodeLabel(node.name);\n\n // Add it into the @type so we can reason over it.\n nodeAsJSONLD.representsTaxonomicUnits.forEach((tu) => {\n const wrappedTUnit = new TaxonomicUnitWrapper(tu);\n\n if (wrappedTUnit) {\n const equivClass = wrappedTUnit.asOWLEquivClass;\n if (equivClass) {\n nodeAsJSONLD[owlterms.RDF_TYPE].push(\n {\n '@type': 'owl:Restriction',\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: equivClass,\n }\n );\n }\n }\n });\n }\n\n // Add references to parents and siblings.\n if (parentCount !== undefined) {\n const parentIRI = `${baseIRI}_node${parentCount}`;\n nodeAsJSONLD.parent = parentIRI;\n\n // Update list of nodes by parent IDs.\n if (!has(nodeIdsByParentId, parentIRI)) {\n nodeIdsByParentId[parentIRI] = new Set();\n }\n nodeIdsByParentId[parentIRI].add(nodeIRI);\n }\n\n // Add nodeAsJSONLD to list\n if (has(nodesById, nodeIRI)) {\n throw new Error(`Error in programming: duplicate node IRI generated (${nodeIRI})`);\n }\n nodesById[nodeIRI] = nodeAsJSONLD;\n nodes.push(nodeAsJSONLD);\n });\n }\n\n // Go through nodes again and set children and sibling relationships.\n Object.keys(nodeIdsByParentId).forEach((parentId) => {\n // What are the children of this parentId?\n const childrenIDs = Array.from(nodeIdsByParentId[parentId]);\n const children = childrenIDs.map(childId => nodesById[childId]);\n\n // Is this the root node?\n if (has(nodesById, parentId)) {\n const parent = nodesById[parentId];\n parent.children = childrenIDs;\n }\n\n children.forEach((child) => {\n const childToModify = child;\n // Add all other sibling to node.siblings, but don't add this node itself!\n childToModify.siblings = childrenIDs.filter(childId => childId !== child['@id']);\n });\n });\n\n return nodes;\n }\n\n asJSONLD(fallbackIRI, newickParser) {\n // Export this phylogeny as JSON-LD.\n // - fallbackIRI: The fallback IRI to use for this phylogeny if it does not\n // already have an '@id' set.\n // - newickParser: A function that parses a Newick string and returns a\n // an object based representation of this phylogeny. If not set, the\n // static method PhylogenyWrapper.getParsedNewick will be used instead.\n\n // Create a copy to export.\n const phylogenyAsJSONLD = JSON.parse(JSON.stringify(this.phylogeny));\n\n // Set name and class for phylogeny. If no '@id' is set, use the provided\n // fallbackIRI.\n if (!has(phylogenyAsJSONLD, '@id')) phylogenyAsJSONLD['@id'] = fallbackIRI;\n phylogenyAsJSONLD['@type'] = 'phyloref:ReferencePhylogenyEvidence';\n\n // Translate nodes into JSON-LD objects.\n phylogenyAsJSONLD.nodes = this.getNodesAsJSONLD(phylogenyAsJSONLD['@id'], newickParser);\n if (phylogenyAsJSONLD.nodes.length > 0) {\n // We don't have a better way to identify the root node, so we just\n // default to the first one.\n phylogenyAsJSONLD.hasRootNode = {\n '@id': phylogenyAsJSONLD.nodes[0]['@id'],\n };\n }\n\n // Add a bibliographicCitation to the source if it is a Citation.\n if (has(phylogenyAsJSONLD, 'source')) {\n const source = phylogenyAsJSONLD.source;\n\n if (!has(source, 'bibliographicCitation')) {\n source.bibliographicCitation = new CitationWrapper(source).toString();\n }\n }\n\n return phylogenyAsJSONLD;\n }\n}\n\nmodule.exports = {\n PhylogenyWrapper,\n};\n", + "content": "/**\n * PhylogenyWrapper\n */\n\nconst {\n has,\n cloneDeep,\n} = require('lodash');\n\n/** Used to parse Newick strings. */\nconst newickJs = require('newick-js');\n\n/** OWL terms to be used here. */\nconst owlterms = require('../utils/owlterms');\n\nconst { TaxonomicUnitWrapper } = require('./TaxonomicUnitWrapper');\nconst { TaxonomicUnitMatcher } = require('../matchers/TaxonomicUnitMatcher');\nconst { CitationWrapper } = require('./CitationWrapper');\n\nclass PhylogenyWrapper {\n // Wraps a Phylogeny in a PHYX file and provides access to node, node labels\n // and other information. Remember that a Phylogeny also has the\n // additionalNodeProperties object which provides additional properties for\n // nodes.\n\n constructor(phylogeny, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n // Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.\n // Note that this version ONLY uses the `newick` property to determine the\n // phylogeny: if other representations are included (such as a node-based\n // format, as used in JSON-LD), they will be ignored and possibly overwritten\n // during export. So, to update the phylogeny, please only update the newick\n // string!\n //\n // This ensures that we don't need to reconcile between different\n // possible representations of a phylogeny.\n this.phylogeny = phylogeny;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Return a normalized form of the phylogeny.\n */\n static normalize(phylogeny) {\n const normalizedPhylogeny = cloneDeep(phylogeny);\n\n // We could normalize the Newick string, but that doesn't seem very nice.\n\n // Normalize the source if there is one.\n if ('source' in phylogeny) {\n normalizedPhylogeny.source = CitationWrapper.normalize(phylogeny.source || {});\n }\n\n return normalizedPhylogeny;\n }\n\n static getErrorsInNewickString(newick) {\n // Given a Newick string, return a list of errors found in parsing this\n // string. The errors are returned as a list of objects, each of which\n // has two properties:\n // - title: A short title of the error, distinct for each type of error.\n // - message: A longer description of the error, which might include\n // information specific to a particular error.\n //\n // We try to order errors from most helpful ('Unbalanced parentheses in\n // Newick string') to least helpful ('Error parsing phylogeny').\n const newickTrimmed = newick.trim();\n const errors = [];\n\n // Look for an empty Newick string.\n if (newickTrimmed === '' || newickTrimmed === '()' || newickTrimmed === '();') {\n // None of the later errors are relevant here, so bail out now.\n return [{\n title: 'No phylogeny entered',\n message: 'Click on \"Edit as Newick\" to enter a phylogeny below.',\n }];\n }\n\n // Look for an unbalanced Newick string.\n let parenLevels = 0;\n for (let x = 0; x < newickTrimmed.length; x += 1) {\n if (newickTrimmed[x] === '(') parenLevels += 1;\n if (newickTrimmed[x] === ')') parenLevels -= 1;\n }\n\n if (parenLevels !== 0) {\n errors.push({\n title: 'Unbalanced parentheses in Newick string',\n message: (parenLevels > 0\n ? `You have ${parenLevels} too many open parentheses`\n : `You have ${-parenLevels} too few open parentheses`\n ),\n });\n }\n\n // Finally, try parsing it with newickJs.parse() and see if we get an error.\n try {\n newickJs.parse(newickTrimmed);\n } catch (ex) {\n errors.push({\n title: 'Error parsing phylogeny',\n message: `An error occured while parsing this phylogeny: ${ex.message}`,\n });\n }\n\n return errors;\n }\n\n static recurseNodes(node, func, nodeCount = 0, parentCount = undefined) {\n // Recurse through PhyloTree nodes, executing function on each node.\n // - node: The node to recurse from. The function will be called on node\n // *before* being called on its children.\n // - func: The function to call on `node` and all of its children.\n // - nodeCount: `node` will be called with this nodeCount. All of its\n // children will be called with consecutively increasing nodeCounts.\n // - parentCount: The nodeCount associated with the parent of this node\n // within this run of recurseNodes. For instance, immediate children\n // of `node` will have a parentCount of 0. By default, `node` itself\n // will have a parentCount of `undefined`.\n // When the function `func` is called, it is given three arguments:\n // - The current node object (initially: `node`)\n // - The count of the current node object (initially: `nodeCount`)\n // - The parent count of the current node object (initially: `parentCount`)\n func(node, nodeCount, parentCount);\n\n let nextID = nodeCount + 1;\n\n // Recurse through all children of this node.\n if (has(node, 'children')) {\n node.children.forEach((child) => {\n nextID = PhylogenyWrapper.recurseNodes(\n child,\n func,\n nextID,\n nodeCount\n );\n });\n }\n\n return nextID;\n }\n\n getTaxonomicUnits(nodeType = 'both') {\n // Return a list of all taxonomic units in this phylogeny.\n // Node labels will be extracted from:\n // - internal nodes only (if nodeType == 'internal')\n // - terminal nodes only (if nodeType == 'terminal')\n // - both internal and terminal nodes (if nodeType == 'both')\n //\n // See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted\n // into node labels, but in brief:\n // 1. We look for taxonomic units in the additionalNodeProperties.\n // 2. If none are found, we attempt to parse the node label as a scientific name.\n //\n const nodeLabels = this.getNodeLabels(nodeType);\n const tunits = new Set();\n\n nodeLabels.forEach(\n nodeLabel => this.getTaxonomicUnitsForNodeLabel(nodeLabel)\n .forEach(tunit => tunits.add(tunit))\n );\n\n return tunits;\n }\n\n getNodeLabels(nodeType = 'both') {\n // Return a list of all the node labels in this phylogeny.\n //\n // nodeType can be one of:\n // - 'internal': Return node labels on internal nodes.\n // - 'terminal': Return node labels on terminal nodes.\n // - 'both': Return node labels on both internal and terminal nodes.\n\n // Parse the phylogeny (will throw an exception if parsing failed).\n const { graph } = newickJs.parse(this.phylogeny.newick || '()');\n const [vertices, arcs] = graph;\n\n if (nodeType === 'both') {\n // Return all node labels.\n return Array.from(\n new Set(\n Array.from(vertices)\n .map(vertex => vertex.label)\n .filter(label => label !== undefined)\n )\n );\n }\n\n if (nodeType === 'internal') {\n // Return the internal nodes (those with atleast one child).\n return Array.from(new Set(\n Array.from(arcs)\n .map(arc => arc[0].label) // Retrieve the label of the parent vertex in this arc.\n .filter(label => label !== undefined)\n ));\n }\n\n if (nodeType === 'terminal') {\n // Return the terminal nodes. This would require calculating the children\n // of every vertex in the graph and then identifying vertices without any\n // children.\n //\n // A quicker and dirtier way to do this is by removing internal labels\n // from the list of all node labels. This will report an incorrect result\n // if an internal node has the same label as a terminal node, but at that\n // point a lot of other assumptions are going to fail, too, so this is\n // probably good enough for now.\n const allLabels = this.getNodeLabels('both');\n const internalLabels = new Set(this.getNodeLabels('internal'));\n\n return allLabels.filter(label => !internalLabels.has(label));\n }\n\n throw new Error(`Unknown nodeType: '${nodeType}'`);\n }\n\n /**\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n */\n getTaxonomicUnitsForNodeLabel(nodeLabel) {\n // Look up additional node properties.\n let additionalNodeProperties = {};\n if (\n has(this.phylogeny, 'additionalNodeProperties')\n && has(this.phylogeny.additionalNodeProperties, nodeLabel)\n ) {\n additionalNodeProperties = this.phylogeny.additionalNodeProperties[nodeLabel];\n }\n\n // If there are explicit taxonomic units in the\n // representsTaxonomicUnits property, we need to use those.\n if (has(additionalNodeProperties, 'representsTaxonomicUnits')) {\n return additionalNodeProperties.representsTaxonomicUnits;\n }\n\n // If that doesn't work, we can try to extract scientific names from\n // the node label. Note that taxonomic units will NOT be extracted from\n // the label if there is a taxonomic unit present!\n //\n // Note that old-style taxonomic units were lists while new-style taxonomic\n // units are single objects. So we turn it into a single entry list here.\n const tunit = TaxonomicUnitWrapper.fromLabel(nodeLabel.trim(), this.defaultNomenCode);\n if (tunit) return [tunit];\n return []; // No TUnit? Return the empty list.\n }\n\n getNodeLabelsMatchedBySpecifier(specifier) {\n // Return a list of node labels matched by a given specifier on\n // a given phylogeny.\n\n return this.getNodeLabels().filter((nodeLabel) => {\n // Find all the taxonomic units associated with the specifier and\n // with the node.\n const nodeTUnits = this.getTaxonomicUnitsForNodeLabel(nodeLabel);\n\n // Attempt pairwise matches between taxonomic units in the specifier\n // and associated with the node.\n return nodeTUnits.some(\n tunit => new TaxonomicUnitMatcher(specifier, tunit).matched\n );\n });\n }\n\n static getParsedNewick(newick) {\n // We previously used phylotree.js's Newick parser to parse Newick into a\n // tree-like structure. However, this is difficult to integrate using NPM.\n // This method provides a similar facility using the newick-js library.\n //\n // Throws an exception if the Newick could not be parsed.\n const { graph, root, rootWeight } = newickJs.parse(newick);\n const [, arcs] = graph;\n\n // Go through the arcs, assigning 'children' to the appropriate parent node.\n arcs.forEach((arc) => {\n const [parent, child, weight] = arc;\n\n // Add child to parent.children.\n if (!has(parent, 'children')) parent.children = [];\n parent.children.push(child);\n\n // Phylotree.js uses 'name' instead of 'label'.\n if (has(parent, 'label')) { parent.name = parent.label; }\n if (has(child, 'label')) { child.name = child.label; }\n\n // Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.\n if (!has(child, 'attribute') && !Number.isNaN(weight)) child.attribute = weight;\n });\n\n // Set root 'attribute' to root weight.\n if (!has(root, 'attribute') && !Number.isNaN(rootWeight)) root.attribute = rootWeight;\n\n return { json: root };\n }\n\n getParsedNewickWithIRIs(baseIRI, newickParser = PhylogenyWrapper.getParsedNewick) {\n // Return the parsed Newick string, but with EVERY node given an IRI.\n // - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').\n // Node IDs are generated by concatenating `_node${number}` to the end of\n // the baseIRI.\n // - newickParser: A method for converting a Newick string to a object-based\n // representation. The static method PhylogenyWrapper.getParsedNewick() is\n // used if none is provided.\n\n const parsed = newickParser(this.phylogeny.newick || '()');\n if (has(parsed, 'json')) {\n PhylogenyWrapper.recurseNodes(parsed.json, (node, nodeCount) => {\n // Start with the additional node properties.\n const nodeAsJSONLD = node;\n\n // Set @id and @type.\n const nodeIRI = `${baseIRI}_node${nodeCount}`;\n nodeAsJSONLD['@id'] = nodeIRI;\n });\n }\n\n return parsed;\n }\n\n getNodesAsJSONLD(baseIRI, newickParser) {\n // Returns a list of all nodes in this phylogeny as a series of nodes.\n // - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').\n // Node IDs are generated by concatenating `_node${number}` to the end of\n // the baseIRI.\n // - newickParser: A method for converting a Newick string to a object-based\n // representation. See PhylogenyWrapper.getParsedNewick() for an example\n // implementation.\n\n // List of nodes we have identified.\n const nodes = [];\n\n // We need to track the identifiers we give each node as we go.\n const nodesById = {};\n const nodeIdsByParentId = {};\n\n // Extract the newick string.\n const { additionalNodeProperties } = this.phylogeny;\n\n // Parse the Newick string; if parseable, recurse through the nodes,\n // added them to the list of JSON-LD nodes as we go.\n\n const parsed = this.getParsedNewickWithIRIs(baseIRI, newickParser);\n if (has(parsed, 'json')) {\n PhylogenyWrapper.recurseNodes(parsed.json, (node, nodeCount, parentCount) => {\n // Start with the additional node properties.\n const nodeAsJSONLD = {};\n\n // Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!\n const nodeIRI = node['@id'];\n nodeAsJSONLD['@id'] = nodeIRI;\n\n // Since we may need to add multiple classes into the rdf:type, we need\n // to make @type an array. However, the JSON-LD library we use in JPhyloRef\n // can't support @type being an array (despite that being in the standard,\n // see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),\n // so we fall back to using rdf:type instead.\n nodeAsJSONLD[owlterms.RDF_TYPE] = [{ '@id': owlterms.CDAO_NODE }];\n\n // Add labels, additional node properties and taxonomic units.\n if (has(node, 'name') && node.name !== '') {\n // Add node label.\n nodeAsJSONLD.labels = [node.name];\n\n // Add additional node properties, if any.\n if (additionalNodeProperties && has(additionalNodeProperties, node.name)) {\n Object.keys(additionalNodeProperties[node.name]).forEach((key) => {\n nodeAsJSONLD[key] = additionalNodeProperties[node.name][key];\n });\n }\n\n // Add taxonomic units into the metadata.\n nodeAsJSONLD.representsTaxonomicUnits = this.getTaxonomicUnitsForNodeLabel(node.name);\n\n // Add it into the @type so we can reason over it.\n nodeAsJSONLD.representsTaxonomicUnits.forEach((tu) => {\n const wrappedTUnit = new TaxonomicUnitWrapper(tu);\n\n if (wrappedTUnit) {\n const equivClass = wrappedTUnit.asOWLEquivClass;\n if (equivClass) {\n nodeAsJSONLD[owlterms.RDF_TYPE].push(\n {\n '@type': 'owl:Restriction',\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: equivClass,\n }\n );\n }\n }\n });\n }\n\n // Add references to parents and siblings.\n if (parentCount !== undefined) {\n const parentIRI = `${baseIRI}_node${parentCount}`;\n nodeAsJSONLD.parent = parentIRI;\n\n // Update list of nodes by parent IDs.\n if (!has(nodeIdsByParentId, parentIRI)) {\n nodeIdsByParentId[parentIRI] = new Set();\n }\n nodeIdsByParentId[parentIRI].add(nodeIRI);\n }\n\n // Add nodeAsJSONLD to list\n if (has(nodesById, nodeIRI)) {\n throw new Error(`Error in programming: duplicate node IRI generated (${nodeIRI})`);\n }\n nodesById[nodeIRI] = nodeAsJSONLD;\n nodes.push(nodeAsJSONLD);\n });\n }\n\n // Go through nodes again and set children and sibling relationships.\n Object.keys(nodeIdsByParentId).forEach((parentId) => {\n // What are the children of this parentId?\n const childrenIDs = Array.from(nodeIdsByParentId[parentId]);\n const children = childrenIDs.map(childId => nodesById[childId]);\n\n // Is this the root node?\n if (has(nodesById, parentId)) {\n const parent = nodesById[parentId];\n parent.children = childrenIDs;\n }\n\n children.forEach((child) => {\n const childToModify = child;\n // Add all other sibling to node.siblings, but don't add this node itself!\n childToModify.siblings = childrenIDs.filter(childId => childId !== child['@id']);\n });\n });\n\n return nodes;\n }\n\n asJSONLD(fallbackIRI, newickParser) {\n // Export this phylogeny as JSON-LD.\n // - fallbackIRI: The fallback IRI to use for this phylogeny if it does not\n // already have an '@id' set.\n // - newickParser: A function that parses a Newick string and returns a\n // an object based representation of this phylogeny. If not set, the\n // static method PhylogenyWrapper.getParsedNewick will be used instead.\n\n // Create a copy to export.\n const phylogenyAsJSONLD = JSON.parse(JSON.stringify(this.phylogeny));\n\n // Set name and class for phylogeny. If no '@id' is set, use the provided\n // fallbackIRI.\n if (!has(phylogenyAsJSONLD, '@id')) phylogenyAsJSONLD['@id'] = fallbackIRI;\n phylogenyAsJSONLD['@type'] = 'phyloref:ReferencePhylogenyEvidence';\n\n // Translate nodes into JSON-LD objects.\n phylogenyAsJSONLD.nodes = this.getNodesAsJSONLD(phylogenyAsJSONLD['@id'], newickParser);\n if (phylogenyAsJSONLD.nodes.length > 0) {\n // We don't have a better way to identify the root node, so we just\n // default to the first one.\n phylogenyAsJSONLD.hasRootNode = {\n '@id': phylogenyAsJSONLD.nodes[0]['@id'],\n };\n }\n\n // Add a bibliographicCitation to the source if it is a Citation.\n if (has(phylogenyAsJSONLD, 'source')) {\n const source = phylogenyAsJSONLD.source;\n\n if (!has(source, 'bibliographicCitation')) {\n source.bibliographicCitation = new CitationWrapper(source).toString();\n }\n }\n\n return phylogenyAsJSONLD;\n }\n}\n\nmodule.exports = {\n PhylogenyWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/PhylogenyWrapper.js", "access": "public", @@ -966,7 +992,7 @@ "lineNumber": 1 }, { - "__docId__": 77, + "__docId__": 78, "kind": "variable", "name": "has", "memberof": "src/wrappers/PhylogenyWrapper.js", @@ -987,7 +1013,7 @@ "ignore": true }, { - "__docId__": 78, + "__docId__": 79, "kind": "variable", "name": "TaxonomicUnitWrapper", "memberof": "src/wrappers/PhylogenyWrapper.js", @@ -998,7 +1024,7 @@ "importPath": "@phyloref/phyx/src/wrappers/PhylogenyWrapper.js", "importStyle": null, "description": null, - "lineNumber": 15, + "lineNumber": 18, "undocument": true, "type": { "types": [ @@ -1008,7 +1034,7 @@ "ignore": true }, { - "__docId__": 79, + "__docId__": 80, "kind": "variable", "name": "TaxonomicUnitMatcher", "memberof": "src/wrappers/PhylogenyWrapper.js", @@ -1019,7 +1045,7 @@ "importPath": "@phyloref/phyx/src/wrappers/PhylogenyWrapper.js", "importStyle": null, "description": null, - "lineNumber": 17, + "lineNumber": 20, "undocument": true, "type": { "types": [ @@ -1029,7 +1055,7 @@ "ignore": true }, { - "__docId__": 80, + "__docId__": 81, "kind": "variable", "name": "CitationWrapper", "memberof": "src/wrappers/PhylogenyWrapper.js", @@ -1040,7 +1066,7 @@ "importPath": "@phyloref/phyx/src/wrappers/PhylogenyWrapper.js", "importStyle": null, "description": null, - "lineNumber": 19, + "lineNumber": 22, "undocument": true, "type": { "types": [ @@ -1050,7 +1076,7 @@ "ignore": true }, { - "__docId__": 81, + "__docId__": 82, "kind": "class", "name": "PhylogenyWrapper", "memberof": "src/wrappers/PhylogenyWrapper.js", @@ -1061,12 +1087,12 @@ "importPath": "@phyloref/phyx/src/wrappers/PhylogenyWrapper.js", "importStyle": "{PhylogenyWrapper}", "description": null, - "lineNumber": 21, + "lineNumber": 24, "undocument": true, "interface": false }, { - "__docId__": 82, + "__docId__": 83, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1076,11 +1102,11 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#constructor", "access": "public", "description": null, - "lineNumber": 27, + "lineNumber": 30, "undocument": true }, { - "__docId__": 83, + "__docId__": 84, "kind": "member", "name": "phylogeny", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1088,7 +1114,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#phylogeny", "access": "public", "description": null, - "lineNumber": 37, + "lineNumber": 40, "undocument": true, "type": { "types": [ @@ -1097,7 +1123,7 @@ } }, { - "__docId__": 84, + "__docId__": 85, "kind": "member", "name": "defaultNomenCode", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1105,7 +1131,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#defaultNomenCode", "access": "public", "description": null, - "lineNumber": 38, + "lineNumber": 41, "undocument": true, "type": { "types": [ @@ -1114,7 +1140,33 @@ } }, { - "__docId__": 85, + "__docId__": 86, + "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.normalize", + "access": "public", + "description": "Return a normalized form of the phylogeny.", + "lineNumber": 47, + "params": [ + { + "name": "phylogeny", + "types": [ + "*" + ] + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 87, "kind": "method", "name": "getErrorsInNewickString", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1124,7 +1176,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.getErrorsInNewickString", "access": "public", "description": null, - "lineNumber": 41, + "lineNumber": 60, "undocument": true, "params": [ { @@ -1141,7 +1193,7 @@ } }, { - "__docId__": 86, + "__docId__": 88, "kind": "method", "name": "recurseNodes", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1151,7 +1203,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.recurseNodes", "access": "public", "description": null, - "lineNumber": 93, + "lineNumber": 112, "undocument": true, "params": [ { @@ -1192,7 +1244,7 @@ } }, { - "__docId__": 87, + "__docId__": 89, "kind": "method", "name": "getTaxonomicUnits", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1202,7 +1254,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#getTaxonomicUnits", "access": "public", "description": null, - "lineNumber": 127, + "lineNumber": 146, "undocument": true, "params": [ { @@ -1222,7 +1274,7 @@ } }, { - "__docId__": 88, + "__docId__": 90, "kind": "method", "name": "getNodeLabels", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1232,7 +1284,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#getNodeLabels", "access": "public", "description": null, - "lineNumber": 150, + "lineNumber": 169, "undocument": true, "params": [ { @@ -1252,7 +1304,7 @@ } }, { - "__docId__": 89, + "__docId__": 91, "kind": "method", "name": "getTaxonomicUnitsForNodeLabel", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1262,7 +1314,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#getTaxonomicUnitsForNodeLabel", "access": "public", "description": "Return a list of taxonomic units for a node label.\n\nIf the additionalNodeProperties for this node label includes taxonomic units\n(using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\nunits are used. Otherwise, one will be constructed using the default\nnomenclatural code set up when this PhylogenyWrapper was set up.", - "lineNumber": 209, + "lineNumber": 228, "params": [ { "name": "nodeLabel", @@ -1278,7 +1330,7 @@ } }, { - "__docId__": 90, + "__docId__": 92, "kind": "method", "name": "getNodeLabelsMatchedBySpecifier", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1288,7 +1340,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#getNodeLabelsMatchedBySpecifier", "access": "public", "description": null, - "lineNumber": 236, + "lineNumber": 255, "undocument": true, "params": [ { @@ -1305,7 +1357,7 @@ } }, { - "__docId__": 91, + "__docId__": 93, "kind": "method", "name": "getParsedNewick", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1315,7 +1367,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.getParsedNewick", "access": "public", "description": null, - "lineNumber": 253, + "lineNumber": 272, "undocument": true, "params": [ { @@ -1332,7 +1384,7 @@ } }, { - "__docId__": 92, + "__docId__": 94, "kind": "method", "name": "getParsedNewickWithIRIs", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1342,7 +1394,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#getParsedNewickWithIRIs", "access": "public", "description": null, - "lineNumber": 284, + "lineNumber": 303, "undocument": true, "params": [ { @@ -1366,7 +1418,7 @@ } }, { - "__docId__": 93, + "__docId__": 95, "kind": "method", "name": "getNodesAsJSONLD", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1376,7 +1428,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#getNodesAsJSONLD", "access": "public", "description": null, - "lineNumber": 308, + "lineNumber": 327, "undocument": true, "params": [ { @@ -1399,7 +1451,7 @@ } }, { - "__docId__": 94, + "__docId__": 96, "kind": "method", "name": "asJSONLD", "memberof": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper", @@ -1409,7 +1461,7 @@ "longname": "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper#asJSONLD", "access": "public", "description": null, - "lineNumber": 424, + "lineNumber": 443, "undocument": true, "params": [ { @@ -1432,10 +1484,10 @@ } }, { - "__docId__": 95, + "__docId__": 97, "kind": "file", "name": "src/wrappers/PhylorefWrapper.js", - "content": "/** Used to parse timestamps for phyloref statuses. */\nconst moment = require('moment');\nconst { has, cloneDeep, uniq } = require('lodash');\n\nconst owlterms = require('../utils/owlterms');\nconst { TaxonomicUnitWrapper } = require('./TaxonomicUnitWrapper');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst { PhylogenyWrapper } = require('./PhylogenyWrapper');\nconst { CitationWrapper } = require('./CitationWrapper');\n\n/**\n * PhylorefWrapper\n *\n */\n\nclass PhylorefWrapper {\n // Wraps a phyloreference in a PHYX model.\n\n constructor(phyloref, phyxDefaultNomenCode = owlterms.UNKNOWN_CODE) {\n // Wraps the provided phyloreference\n this.phyloref = phyloref;\n this.phyxDefaultNomenCode = phyxDefaultNomenCode;\n }\n\n /** Return the internal specifiers of this phyloref (if any). */\n get internalSpecifiers() {\n if (!has(this.phyloref, 'internalSpecifiers')) {\n // If there isn't one, create an empty list so that the caller can do\n // `wrappedPhyloref.internalSpecifiers.push({...})`.\n this.phyloref.internalSpecifiers = [];\n }\n\n return this.phyloref.internalSpecifiers;\n }\n\n /** Return the external specifiers of this phyloref (if any). */\n get externalSpecifiers() {\n if (!has(this.phyloref, 'externalSpecifiers')) {\n // If there isn't one, create an empty list so that the caller can do\n // `wrappedPhyloref.externalSpecifiers.push({...})`.\n this.phyloref.externalSpecifiers = [];\n }\n\n return this.phyloref.externalSpecifiers;\n }\n\n get label() {\n // Return a label for this phyloreference.\n if (has(this.phyloref, 'label')) return this.phyloref.label;\n if (has(this.phyloref, 'labels') && this.phyloref.labels.length > 0) return this.phyloref.labels[0];\n if (has(this.phyloref, 'title')) return this.phyloref.title;\n\n return undefined;\n }\n\n set label(newLabel) {\n // Set a label for this phyloreference.\n if (has(this.phyloref, 'label')) {\n this.phyloref.label = newLabel;\n } else {\n // Vue.set(this.phyloref, 'label', newLabel);\n this.phyloref.label = newLabel;\n }\n }\n\n /** Return all the specifiers of this phyloref (if any). */\n get specifiers() {\n // Returns a list of all specifiers by combining the internal and external\n // specifiers into a single list, with internal specifiers before\n // external specifiers.\n let specifiers = this.internalSpecifiers;\n specifiers = specifiers.concat(this.externalSpecifiers);\n return specifiers;\n }\n\n getSpecifierType(specifier) {\n // For a given specifier, return a string indicating whether it is\n // an 'Internal' or 'External' specifier.\n\n if (this.internalSpecifiers.includes(specifier)) return 'Internal';\n if (this.externalSpecifiers.includes(specifier)) return 'External';\n return 'Specifier';\n }\n\n setSpecifierType(specifier, specifierType) {\n // Change the type of a given specifier. To do this, we first need\n // to determine if it was originally an internal or external\n // specifier, then move it into the other list.\n\n let index;\n if (specifierType === 'Internal') {\n // To set a specifier to 'Internal', we might need to delete it from the\n // list of external specifiers first.\n index = this.externalSpecifiers.indexOf(specifier);\n if (index !== -1) this.externalSpecifiers.splice(index, 1);\n\n // Don't add it to the list of internal specifiers if it's already there.\n if (!this.internalSpecifiers.includes(specifier)) {\n this.phyloref.internalSpecifiers.unshift(specifier);\n }\n } else if (specifierType === 'External') {\n // To set a specifier to 'External', we might need to delete it from the\n // list of internal specifiers first.\n index = this.phyloref.internalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.internalSpecifiers.splice(index, 1);\n\n // Don't add it to the list of internal specifiers if it's already there.\n if (!this.phyloref.externalSpecifiers.includes(specifier)) {\n this.phyloref.externalSpecifiers.unshift(specifier);\n }\n } else {\n // Neither internal nor external? Ignore.\n }\n }\n\n deleteSpecifier(specifier) {\n // Since the user interface combines specifiers into a single list,\n // it doesn't remember if the specifier to be deleted is internal\n // or external. We delete the intended specifier from both arrays.\n\n if (has(this.phyloref, 'internalSpecifiers') && this.phyloref.internalSpecifiers.length > 0) {\n const index = this.phyloref.internalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.internalSpecifiers.splice(index, 1);\n }\n\n if (has(this.phyloref, 'externalSpecifiers') && this.phyloref.externalSpecifiers.length > 0) {\n const index = this.phyloref.externalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.externalSpecifiers.splice(index, 1);\n }\n }\n\n getExpectedNodeLabels(phylogeny) {\n // Given a phylogeny, determine which node labels we expect this phyloref to\n // resolve to. To do this, we:\n // 1. Find all node labels that are case-sensitively identical\n // to the phyloreference.\n // 2. Find all node labels that have additionalNodeProperties with\n // expectedPhyloreferenceNamed case-sensitively identical to\n // the phyloreference.\n const phylorefLabel = this.label;\n const nodeLabels = new Set();\n\n new PhylogenyWrapper(\n phylogeny,\n this.defaultNomenCode\n ).getNodeLabels().forEach((nodeLabel) => {\n // Is this node label identical to the phyloreference name?\n if (nodeLabel === phylorefLabel) {\n nodeLabels.add(nodeLabel);\n } else if (\n has(phylogeny, 'additionalNodeProperties')\n && has(phylogeny.additionalNodeProperties, nodeLabel)\n && has(phylogeny.additionalNodeProperties[nodeLabel], 'expectedPhyloreferenceNamed')\n ) {\n // Does this node label have an expectedPhyloreferenceNamed that\n // includes this phyloreference name?\n\n const expectedPhylorefs = phylogeny\n .additionalNodeProperties[nodeLabel]\n .expectedPhyloreferenceNamed;\n\n if (expectedPhylorefs.includes(phylorefLabel)) {\n nodeLabels.add(nodeLabel);\n }\n }\n });\n\n // Return node labels sorted alphabetically.\n return Array.from(nodeLabels).sort();\n }\n\n static getStatusCURIEsInEnglish() {\n // Return dictionary of all phyloref statuses in English\n return {\n 'pso:draft': 'Draft',\n 'pso:final-draft': 'Final draft',\n 'pso:under-review': 'Under review',\n 'pso:submitted': 'Tested',\n 'pso:published': 'Published',\n 'pso:retracted-from-publication': 'Retracted',\n };\n }\n\n getCurrentStatus() {\n // Return a result object that contains:\n // - status: phyloreference status as a short URI (CURIE)\n // - statusInEnglish: an English representation of the phyloref status\n // - intervalStart: the start of the interval\n // - intervalEnd: the end of the interval\n\n if (\n has(this.phyloref, 'pso:holdsStatusInTime')\n && Array.isArray(this.phyloref['pso:holdsStatusInTime'])\n && this.phyloref['pso:holdsStatusInTime'].length > 0\n ) {\n // If we have any pso:holdsStatusInTime entries, pick the first one and\n // extract the CURIE and time interval information from it.\n const lastStatusInTime = this.phyloref['pso:holdsStatusInTime'][this.phyloref['pso:holdsStatusInTime'].length - 1];\n const statusCURIE = lastStatusInTime['pso:withStatus']['@id'];\n\n // Look for time interval information\n let intervalStart;\n let intervalEnd;\n\n if (has(lastStatusInTime, 'tvc:atTime')) {\n const atTime = lastStatusInTime['tvc:atTime'];\n if (has(atTime, 'timeinterval:hasIntervalStartDate')) intervalStart = atTime['timeinterval:hasIntervalStartDate'];\n if (has(atTime, 'timeinterval:hasIntervalEndDate')) intervalEnd = atTime['timeinterval:hasIntervalEndDate'];\n }\n\n // Return result object\n return {\n statusCURIE,\n statusInEnglish: PhylorefWrapper.getStatusCURIEsInEnglish()[statusCURIE],\n intervalStart,\n intervalEnd,\n };\n }\n\n // If we couldn't figure out a status for this phyloref, assume it's a draft.\n return {\n statusCURIE: 'pso:draft',\n statusInEnglish: PhylorefWrapper.getStatusCURIEsInEnglish()['pso:draft'],\n };\n }\n\n getStatusChanges() {\n // Return a list of status changes for a particular phyloreference\n if (has(this.phyloref, 'pso:holdsStatusInTime')) {\n return this.phyloref['pso:holdsStatusInTime'].map((entry) => {\n const result = {};\n\n // Create a statusCURIE convenience field.\n if (has(entry, 'pso:withStatus')) {\n result.statusCURIE = entry['pso:withStatus']['@id'];\n result.statusInEnglish = PhylorefWrapper.getStatusCURIEsInEnglish()[result.statusCURIE];\n }\n\n // Create intervalStart/intervalEnd convenient fields\n if (has(entry, 'tvc:atTime')) {\n const atTime = entry['tvc:atTime'];\n if (has(atTime, 'timeinterval:hasIntervalStartDate')) {\n result.intervalStart = atTime['timeinterval:hasIntervalStartDate'];\n result.intervalStartAsCalendar = moment(result.intervalStart).calendar();\n }\n\n if (has(atTime, 'timeinterval:hasIntervalEndDate')) {\n result.intervalEnd = atTime['timeinterval:hasIntervalEndDate'];\n result.intervalEndAsCalendar = moment(result.intervalEnd).calendar();\n }\n }\n\n return result;\n });\n }\n\n // No changes? Return an empty list.\n return [];\n }\n\n setStatus(status) {\n // Set the status of a phyloreference\n //\n // Check whether we have a valid status CURIE.\n if (!has(PhylorefWrapper.getStatusCURIEsInEnglish(), status)) {\n throw new TypeError(`setStatus() called with invalid status CURIE '${status}'`);\n }\n\n // See if we can end the previous interval.\n const currentTime = new Date(Date.now()).toISOString();\n\n if (!has(this.phyloref, 'pso:holdsStatusInTime')) {\n // Vue.set(this.phyloref, 'pso:holdsStatusInTime', []);\n this.phyloref['pso:holdsStatusInTime'] = [];\n }\n\n // Check to see if there's a previous time interval we should end.\n if (\n Array.isArray(this.phyloref['pso:holdsStatusInTime'])\n && this.phyloref['pso:holdsStatusInTime'].length > 0\n ) {\n const lastStatusInTime = this.phyloref['pso:holdsStatusInTime'][this.phyloref['pso:holdsStatusInTime'].length - 1];\n\n // if (!has(lastStatusInTime, 'tvc:atTime'))\n // Vue.set(lastStatusInTime, 'tvc:atTime', {});\n if (!has(lastStatusInTime, 'tvc:atTime')) {\n lastStatusInTime['tvc:atTime'] = {};\n }\n if (!has(lastStatusInTime['tvc:atTime'], 'timeinterval:hasIntervalEndDate')) {\n // If the last time entry doesn't already have an interval end date, set it to now.\n lastStatusInTime['tvc:atTime']['timeinterval:hasIntervalEndDate'] = currentTime;\n }\n }\n\n // Create new entry.\n this.phyloref['pso:holdsStatusInTime'].push({\n '@type': 'http://purl.org/spar/pso/StatusInTime',\n 'pso:withStatus': { '@id': status },\n 'tvc:atTime': {\n 'timeinterval:hasIntervalStartDate': currentTime,\n },\n });\n }\n\n /**\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n */\n get uniqNomenCodes() {\n return uniq(this.specifiers.map((specifier) => {\n const taxonConcept = new TaxonomicUnitWrapper(\n specifier,\n this.phyxDefaultNomenCode\n ).taxonConcept;\n if (!taxonConcept) return owlterms.UNKNOWN_CODE;\n\n const nomenCode = new TaxonConceptWrapper(\n taxonConcept,\n this.phyxDefaultNomenCode\n ).nomenCode;\n if (!nomenCode) return owlterms.UNKNOWN_CODE;\n\n return nomenCode;\n }));\n }\n\n /**\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n */\n get defaultNomenCode() {\n // Check to see if we have a single nomenclatural code to use.\n if (this.uniqNomenCodes.length === 1) return this.uniqNomenCodes[0];\n\n // If one or more of our specifiers have no nomenclatural code (e.g. if\n // they are specimens), they will show up as owlterms.UNKNOWN_CODE.\n // If we have a single nomenclatural code *apart* from all the\n // owlterms.UNKNOWN_CODEs, then that is still usable as a default\n // nomenclatural code for this phyloreference.\n const uniqNomenCodesNoUnknowns = this.uniqNomenCodes\n .filter(code => code !== owlterms.UNKNOWN_CODE);\n if (uniqNomenCodesNoUnknowns.length === 1) return uniqNomenCodesNoUnknowns[0];\n\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n */\n createComponentClass(\n jsonld,\n internalSpecifiers,\n externalSpecifiers,\n equivClass,\n reusePrevious = true,\n parentClass = undefined\n ) {\n if (internalSpecifiers.length === 0) throw new Error('Cannot create component class without any internal specifiers');\n if (internalSpecifiers.length === 1 && externalSpecifiers.length === 0) throw new Error('Cannot create component class with a single internal specifiers and no external specifiers');\n\n /* Generate a label that represents this component class. */\n\n // By default, taxonomic unit labels don't include the nomenclatural code.\n // However, we should include that here in order to distinguish between\n // taxonomic names in different taxonomic codes. This method generates that\n // name for a specifier.\n const outerThis = this;\n function generateSpecifierName(specifier) {\n const wrapped = new TaxonomicUnitWrapper(specifier, outerThis.defaultNomenCode);\n if (!wrapped) return '(error)';\n if (wrapped.taxonConcept) {\n const nomenCodeDetails = new TaxonConceptWrapper(wrapped.taxonConcept).nomenCodeDetails;\n if (nomenCodeDetails) return `${wrapped.label} (${nomenCodeDetails.shortName})`;\n }\n return wrapped.label;\n }\n\n // Start with the internal specifiers, concatenated with '&'.\n const internalSpecifierLabel = internalSpecifiers\n .map(generateSpecifierName)\n .sort()\n .join(' & ');\n let componentClassLabel = `(${internalSpecifierLabel}`;\n\n if (externalSpecifiers.length === 0) {\n componentClassLabel += ')';\n } else {\n // Add the external specifiers, concatenated with 'V'.\n const externalSpecifierLabel = externalSpecifiers\n .map(generateSpecifierName)\n .sort()\n .join(' V ');\n componentClassLabel += ` ~ ${externalSpecifierLabel})`;\n }\n\n // process.stderr.write(`component class label: ${componentClassLabel}\\n`);\n\n // TODO We need to replace this with an actual object-based comparison,\n // rather than trusting the labels to tell us everything.\n if (reusePrevious && has(this.componentClassesByLabel, componentClassLabel)) {\n // If we see the same label again, return the previously defined component class.\n return { '@id': this.componentClassesByLabel[componentClassLabel]['@id'] };\n }\n\n // Create a new component class for this set of internal and external specifiers.\n this.componentClassCount += 1;\n const componentClass = {};\n componentClass['@id'] = `${jsonld['@id']}_component${this.componentClassCount}`;\n // process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);\n\n componentClass['@type'] = 'owl:Class';\n componentClass.label = componentClassLabel;\n componentClass.equivalentClass = equivClass;\n if (externalSpecifiers.length > 0) componentClass.subClassOf = ['phyloref:PhyloreferenceUsingMaximumClade'];\n else componentClass.subClassOf = ['phyloref:PhyloreferenceUsingMinimumClade'];\n\n if (parentClass) {\n componentClass.subClassOf.push({\n '@id': parentClass['@id'],\n });\n }\n\n // Save it in the cache for later usage.\n this.componentClassesByLabel[componentClassLabel] = componentClass;\n\n // The first time we create a componentClass, we include it into the logical\n // expression directly. On subsequent calls, we'll only return the `@id`\n // (see above).\n return componentClass;\n }\n\n getIncludesRestrictionForTU(tu) {\n return {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:includes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(tu, this.defaultNomenCode).asOWLEquivClass,\n };\n }\n\n /**\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n */\n getMRCARestrictionOfTwoTUs(tu1, tu2) {\n return {\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000149', // cdao:has_Child\n someValuesFrom: {\n '@type': 'owl:Class',\n intersectionOf: [\n {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(tu1, this.defaultNomenCode).asOWLEquivClass,\n },\n this.getIncludesRestrictionForTU(tu2),\n ],\n },\n };\n }\n\n /*\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n */\n createClassExpressionsForInternals(jsonld, remainingInternals, selected) {\n // process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:\n // ${remainingInternals.length}, selected: ${selected.length}\\n`);\n\n // Quick special case: if we have two 'remainingInternals' and zero selecteds,\n // we can just return the MRCA for two internal specifiers.\n if (selected.length === 0) {\n if (remainingInternals.length === 2) {\n return [\n this.getMRCARestrictionOfTwoTUs(remainingInternals[0], remainingInternals[1]),\n ];\n } if (remainingInternals.length === 1) {\n throw new Error('Cannot determine class expression for a single specifier');\n } else if (remainingInternals.length === 0) {\n throw new Error('Cannot determine class expression for zero specifiers');\n }\n }\n\n // Step 1. If we've already selected something, create an expression for it.\n const classExprs = [];\n if (selected.length > 0) {\n let remainingInternalsExpr = [];\n if (remainingInternals.length === 1) {\n remainingInternalsExpr = this.getIncludesRestrictionForTU(remainingInternals[0]);\n } else if (remainingInternals.length === 2) {\n remainingInternalsExpr = this.getMRCARestrictionOfTwoTUs(\n remainingInternals[0],\n remainingInternals[1]\n );\n } else {\n remainingInternalsExpr = this.createComponentClass(\n jsonld,\n remainingInternals,\n [],\n this.createClassExpressionsForInternals(jsonld, remainingInternals, [])\n );\n }\n\n let selectedExpr = [];\n if (selected.length === 1) {\n selectedExpr = this.getIncludesRestrictionForTU(selected[0]);\n } else if (selected.length === 2) {\n selectedExpr = this.getMRCARestrictionOfTwoTUs(selected[0], selected[1]);\n } else {\n selectedExpr = this.createComponentClass(\n jsonld,\n selected,\n [],\n this.createClassExpressionsForInternals(jsonld, selected, [])\n );\n }\n\n classExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000149', // cdao:has_Child\n someValuesFrom: {\n '@type': 'owl:Class',\n intersectionOf: [{\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_lineage_to',\n someValuesFrom: remainingInternalsExpr,\n }, selectedExpr],\n },\n });\n }\n\n // Step 2. Now select everything from remaining once, and start recursing through\n // every possibility.\n // Note that we only process cases where there are more remainingInternals than\n // selected internals -- when there are fewer, we'll just end up with the inverses\n // of the previous comparisons, which we'll already have covered.\n if (remainingInternals.length > 1 && selected.length <= remainingInternals.length) {\n remainingInternals.map(newlySelected => this.createClassExpressionsForInternals(\n jsonld,\n // The new remaining is the old remaining minus the selected TU.\n remainingInternals.filter(i => i !== newlySelected),\n // The new selected is the old selected plus the selected TU.\n selected.concat([newlySelected])\n ))\n .reduce((acc, val) => acc.concat(val), [])\n .forEach(expr => classExprs.push(expr));\n }\n\n return classExprs;\n }\n\n /*\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n */\n asJSONLD(fallbackIRI) {\n // Keep all currently extant data.\n const phylorefAsJSONLD = cloneDeep(this.phyloref);\n\n // Set the @id and @type. If we don't already have an '@id', use the\n // fallbackIRI.\n if (!has(phylorefAsJSONLD, '@id')) phylorefAsJSONLD['@id'] = fallbackIRI;\n phylorefAsJSONLD['@type'] = 'owl:Class';\n\n // If we don't have a bibliographicCitation but we do have a definition source,\n // then generate a bibliographicCitation for the source.\n if (has(phylorefAsJSONLD, 'definitionSource')) {\n const definitionSource = phylorefAsJSONLD.definitionSource;\n if (!has(definitionSource, 'bibliographicCitation')) {\n definitionSource.bibliographicCitation = new CitationWrapper(definitionSource).toString();\n }\n }\n\n // Construct a class expression for this phyloreference.\n const internalSpecifiers = phylorefAsJSONLD.internalSpecifiers || [];\n const externalSpecifiers = phylorefAsJSONLD.externalSpecifiers || [];\n\n // If it is an apomorphy-based class expression, we should generate a\n // logical expression that describes the apomorphy.\n const phylorefType = phylorefAsJSONLD.phylorefType;\n if (\n (phylorefType && phylorefType === 'phyloref:PhyloreferenceUsingApomorphy')\n || (has(phylorefAsJSONLD, 'apomorphy'))\n ) {\n // This is an apomorphy-based definition!\n phylorefAsJSONLD.subClassOf = [\n 'phyloref:Phyloreference',\n 'phyloref:PhyloreferenceUsingApomorphy',\n ];\n\n // Someday, we will probably want to turn this apomorphy into a\n // logical expression so that it can be computed alongside other\n // OWL ontologies. This is outside our scope for the moment, so\n // we will simply pass on the phyloreference as-is.\n\n return phylorefAsJSONLD;\n }\n\n // We might need to make component classes.\n // So we reset our component class counts and records.\n this.componentClassCount = 0;\n this.componentClassesByLabel = {};\n\n // The type of this phyloreference.\n let calculatedPhylorefType;\n\n // The list of logical expressions generated for this phyloref.\n let logicalExpressions = [];\n\n if (internalSpecifiers.length === 0) {\n // We can't handle phyloreferences without at least one internal specifier.\n calculatedPhylorefType = 'phyloref:MalformedPhyloreference';\n phylorefAsJSONLD.malformedPhyloreference = 'No internal specifiers provided';\n } else if (externalSpecifiers.length > 0) {\n calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMaximumClade';\n\n // If the phyloreference has at least one external specifier, we\n // can provide a simplified expression for the internal specifier,\n // in the form:\n // phyloref:includes_TU some [internal1] and\n // phyloref:includes_TU some [internal2] and ...\n // phyloref:excludes_TU some [exclusion1] and\n // has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...\n //\n // Since we don't know which of the external specifiers will actually\n // be the one that will be used, we need to generate logical expressions\n // for every possibility.\n\n logicalExpressions = externalSpecifiers.map((selectedExternal) => {\n // Add the internal specifiers.\n const intersectionExprs = internalSpecifiers.map(\n sp => this.getIncludesRestrictionForTU(sp)\n );\n\n // Add the selected external specifier.\n intersectionExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(\n selectedExternal,\n this.defaultNomenCode\n ).asOWLEquivClass,\n });\n\n // Collect all of the externals that are not selected.\n const remainingExternals = externalSpecifiers.filter(ex => ex !== selectedExternal);\n\n // Add the remaining externals, which we assume will resolve outside of\n // this clade.\n remainingExternals.forEach((externalTU) => {\n intersectionExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000144', // has_Ancestor\n someValuesFrom: {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(\n externalTU,\n this.defaultNomenCode\n ).asOWLEquivClass,\n },\n });\n });\n\n return {\n '@type': 'owl:Class',\n intersectionOf: intersectionExprs,\n };\n });\n } else {\n calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMinimumClade';\n\n // We only have internal specifiers. We therefore need to use the algorithm in\n // this.createClassExpressionsForInternals() to create this expression.\n logicalExpressions = this.createClassExpressionsForInternals(\n phylorefAsJSONLD, internalSpecifiers, []\n );\n }\n\n // If we have a single logical expression, we set that as an equivalentClass\n // expression. If we have more than one, we produce multiple component classes\n // to represent it.\n if (logicalExpressions.length === 0) {\n // This is fine, as long as there is an explanation in\n // phyloref.malformedPhyloreference explaining why no logical expressions\n // could be generated. Otherwise, throw an error.\n if (!has(phylorefAsJSONLD, 'malformedPhyloreference')) {\n throw new Error(\n `Phyloref ${this.label} was generated by Phyx.js with neither logical expressions nor an explanation for the lack of logical expressions. `\n + 'This indicates an error in the Phyx.js library. Please report this bug at https://github.com/phyloref/phyx.js/issues.'\n );\n }\n } else if (logicalExpressions.length === 1) {\n // If we have a single logical expression, then that is what this phyloref\n // is equivalent to.\n phylorefAsJSONLD.equivalentClass = logicalExpressions[0];\n } else {\n // If we have multiple logical expressions, the phyloreference can be\n // represented by any of them. We model this by creating subclasses of\n // the phyloreference for each logical expression -- that way, it's clear\n // that these expressions aren't equivalent to each other (which is what\n // caused https://github.com/phyloref/phyx.js/issues/57), but nodes\n // resolved by any of those expressions will also be included in the\n // phyloreference itself.\n //\n // Note that there are two differences from the way in which we usually call\n // this.createComponentClass():\n // 1. Usually, createComponentClass() reuses logical expressions with the\n // same sets of internal and external specifiers. That won't work here,\n // since *all* these logical expressions have the same specifiers. So,\n // we turn off caching.\n // 2. We need to set each of these component classes to be a subclass of\n // this phyloreference so that it can include instances from each of the\n // logical expressions.\n phylorefAsJSONLD.subClasses = logicalExpressions.map(classExpr => this.createComponentClass(\n phylorefAsJSONLD,\n internalSpecifiers,\n externalSpecifiers,\n classExpr,\n // False in order to turn off caching by internal and external specifiers.\n false,\n // Make the new component class a subclass of this phyloreference.\n phylorefAsJSONLD\n ));\n }\n\n // Every phyloreference is a subclass of phyloref:Phyloreference.\n if (!phylorefAsJSONLD.subClassOf) phylorefAsJSONLD.subClassOf = [];\n if (!Array.isArray(phylorefAsJSONLD.subClassOf)) {\n phylorefAsJSONLD.subClassOf = [phylorefAsJSONLD.subClassOf];\n }\n phylorefAsJSONLD.subClassOf.push('phyloref:Phyloreference');\n\n // If the this Phyloref has a phylorefType that differs from the calculated\n // phyloref type, throw an error.\n if (has(phylorefAsJSONLD, 'phylorefType') && phylorefAsJSONLD.phylorefType !== calculatedPhylorefType) {\n throw new Error(\n `Phyloref ${this.label} has phylorefType set to '${phylorefAsJSONLD.phylorefType}', but it appears to be a '${calculatedPhylorefType}'.`\n );\n }\n phylorefAsJSONLD.subClassOf.push(calculatedPhylorefType);\n\n return phylorefAsJSONLD;\n }\n}\n\nmodule.exports = {\n PhylorefWrapper,\n};\n", + "content": "/** Used to parse timestamps for phyloref statuses. */\nconst moment = require('moment');\nconst { has, cloneDeep, uniq } = require('lodash');\n\nconst owlterms = require('../utils/owlterms');\nconst { TaxonomicUnitWrapper } = require('./TaxonomicUnitWrapper');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst { PhylogenyWrapper } = require('./PhylogenyWrapper');\nconst { CitationWrapper } = require('./CitationWrapper');\n\n/**\n * PhylorefWrapper\n *\n */\n\nclass PhylorefWrapper {\n // Wraps a phyloreference in a PHYX model.\n\n constructor(phyloref, phyxDefaultNomenCode = owlterms.UNKNOWN_CODE) {\n // Wraps the provided phyloreference\n this.phyloref = phyloref;\n this.phyxDefaultNomenCode = phyxDefaultNomenCode;\n }\n\n /** Return the internal specifiers of this phyloref (if any). */\n get internalSpecifiers() {\n if (!has(this.phyloref, 'internalSpecifiers')) {\n // If there isn't one, create an empty list so that the caller can do\n // `wrappedPhyloref.internalSpecifiers.push({...})`.\n this.phyloref.internalSpecifiers = [];\n }\n\n return this.phyloref.internalSpecifiers;\n }\n\n /**\n * Normalize a phyloreference.\n *\n * @param phyloref\n */\n static normalize(phyloref) {\n const normalizedPhyloref = cloneDeep(phyloref);\n\n normalizedPhyloref.internalSpecifiers = (phyloref.internalSpecifiers || [])\n .map(TaxonomicUnitWrapper.normalize);\n normalizedPhyloref.externalSpecifiers = (phyloref.externalSpecifiers || [])\n .map(TaxonomicUnitWrapper.normalize);\n\n return normalizedPhyloref;\n }\n\n /** Return the external specifiers of this phyloref (if any). */\n get externalSpecifiers() {\n if (!has(this.phyloref, 'externalSpecifiers')) {\n // If there isn't one, create an empty list so that the caller can do\n // `wrappedPhyloref.externalSpecifiers.push({...})`.\n this.phyloref.externalSpecifiers = [];\n }\n\n return this.phyloref.externalSpecifiers;\n }\n\n get label() {\n // Return a label for this phyloreference.\n if (has(this.phyloref, 'label')) return this.phyloref.label;\n if (has(this.phyloref, 'labels') && this.phyloref.labels.length > 0) return this.phyloref.labels[0];\n if (has(this.phyloref, 'title')) return this.phyloref.title;\n\n return undefined;\n }\n\n set label(newLabel) {\n // Set a label for this phyloreference.\n if (has(this.phyloref, 'label')) {\n this.phyloref.label = newLabel;\n } else {\n // Vue.set(this.phyloref, 'label', newLabel);\n this.phyloref.label = newLabel;\n }\n }\n\n /** Return all the specifiers of this phyloref (if any). */\n get specifiers() {\n // Returns a list of all specifiers by combining the internal and external\n // specifiers into a single list, with internal specifiers before\n // external specifiers.\n let specifiers = this.internalSpecifiers;\n specifiers = specifiers.concat(this.externalSpecifiers);\n return specifiers;\n }\n\n getSpecifierType(specifier) {\n // For a given specifier, return a string indicating whether it is\n // an 'Internal' or 'External' specifier.\n\n if (this.internalSpecifiers.includes(specifier)) return 'Internal';\n if (this.externalSpecifiers.includes(specifier)) return 'External';\n return 'Specifier';\n }\n\n setSpecifierType(specifier, specifierType) {\n // Change the type of a given specifier. To do this, we first need\n // to determine if it was originally an internal or external\n // specifier, then move it into the other list.\n\n let index;\n if (specifierType === 'Internal') {\n // To set a specifier to 'Internal', we might need to delete it from the\n // list of external specifiers first.\n index = this.externalSpecifiers.indexOf(specifier);\n if (index !== -1) this.externalSpecifiers.splice(index, 1);\n\n // Don't add it to the list of internal specifiers if it's already there.\n if (!this.internalSpecifiers.includes(specifier)) {\n this.phyloref.internalSpecifiers.unshift(specifier);\n }\n } else if (specifierType === 'External') {\n // To set a specifier to 'External', we might need to delete it from the\n // list of internal specifiers first.\n index = this.phyloref.internalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.internalSpecifiers.splice(index, 1);\n\n // Don't add it to the list of internal specifiers if it's already there.\n if (!this.phyloref.externalSpecifiers.includes(specifier)) {\n this.phyloref.externalSpecifiers.unshift(specifier);\n }\n } else {\n // Neither internal nor external? Ignore.\n }\n }\n\n deleteSpecifier(specifier) {\n // Since the user interface combines specifiers into a single list,\n // it doesn't remember if the specifier to be deleted is internal\n // or external. We delete the intended specifier from both arrays.\n\n if (has(this.phyloref, 'internalSpecifiers') && this.phyloref.internalSpecifiers.length > 0) {\n const index = this.phyloref.internalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.internalSpecifiers.splice(index, 1);\n }\n\n if (has(this.phyloref, 'externalSpecifiers') && this.phyloref.externalSpecifiers.length > 0) {\n const index = this.phyloref.externalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.externalSpecifiers.splice(index, 1);\n }\n }\n\n getExpectedNodeLabels(phylogeny) {\n // Given a phylogeny, determine which node labels we expect this phyloref to\n // resolve to. To do this, we:\n // 1. Find all node labels that are case-sensitively identical\n // to the phyloreference.\n // 2. Find all node labels that have additionalNodeProperties with\n // expectedPhyloreferenceNamed case-sensitively identical to\n // the phyloreference.\n const phylorefLabel = this.label;\n const nodeLabels = new Set();\n\n new PhylogenyWrapper(\n phylogeny,\n this.defaultNomenCode\n ).getNodeLabels().forEach((nodeLabel) => {\n // Is this node label identical to the phyloreference name?\n if (nodeLabel === phylorefLabel) {\n nodeLabels.add(nodeLabel);\n } else if (\n has(phylogeny, 'additionalNodeProperties')\n && has(phylogeny.additionalNodeProperties, nodeLabel)\n && has(phylogeny.additionalNodeProperties[nodeLabel], 'expectedPhyloreferenceNamed')\n ) {\n // Does this node label have an expectedPhyloreferenceNamed that\n // includes this phyloreference name?\n\n const expectedPhylorefs = phylogeny\n .additionalNodeProperties[nodeLabel]\n .expectedPhyloreferenceNamed;\n\n if (expectedPhylorefs.includes(phylorefLabel)) {\n nodeLabels.add(nodeLabel);\n }\n }\n });\n\n // Return node labels sorted alphabetically.\n return Array.from(nodeLabels).sort();\n }\n\n static getStatusCURIEsInEnglish() {\n // Return dictionary of all phyloref statuses in English\n return {\n 'pso:draft': 'Draft',\n 'pso:final-draft': 'Final draft',\n 'pso:under-review': 'Under review',\n 'pso:submitted': 'Tested',\n 'pso:published': 'Published',\n 'pso:retracted-from-publication': 'Retracted',\n };\n }\n\n getCurrentStatus() {\n // Return a result object that contains:\n // - status: phyloreference status as a short URI (CURIE)\n // - statusInEnglish: an English representation of the phyloref status\n // - intervalStart: the start of the interval\n // - intervalEnd: the end of the interval\n\n if (\n has(this.phyloref, 'pso:holdsStatusInTime')\n && Array.isArray(this.phyloref['pso:holdsStatusInTime'])\n && this.phyloref['pso:holdsStatusInTime'].length > 0\n ) {\n // If we have any pso:holdsStatusInTime entries, pick the first one and\n // extract the CURIE and time interval information from it.\n const lastStatusInTime = this.phyloref['pso:holdsStatusInTime'][this.phyloref['pso:holdsStatusInTime'].length - 1];\n const statusCURIE = lastStatusInTime['pso:withStatus']['@id'];\n\n // Look for time interval information\n let intervalStart;\n let intervalEnd;\n\n if (has(lastStatusInTime, 'tvc:atTime')) {\n const atTime = lastStatusInTime['tvc:atTime'];\n if (has(atTime, 'timeinterval:hasIntervalStartDate')) intervalStart = atTime['timeinterval:hasIntervalStartDate'];\n if (has(atTime, 'timeinterval:hasIntervalEndDate')) intervalEnd = atTime['timeinterval:hasIntervalEndDate'];\n }\n\n // Return result object\n return {\n statusCURIE,\n statusInEnglish: PhylorefWrapper.getStatusCURIEsInEnglish()[statusCURIE],\n intervalStart,\n intervalEnd,\n };\n }\n\n // If we couldn't figure out a status for this phyloref, assume it's a draft.\n return {\n statusCURIE: 'pso:draft',\n statusInEnglish: PhylorefWrapper.getStatusCURIEsInEnglish()['pso:draft'],\n };\n }\n\n getStatusChanges() {\n // Return a list of status changes for a particular phyloreference\n if (has(this.phyloref, 'pso:holdsStatusInTime')) {\n return this.phyloref['pso:holdsStatusInTime'].map((entry) => {\n const result = {};\n\n // Create a statusCURIE convenience field.\n if (has(entry, 'pso:withStatus')) {\n result.statusCURIE = entry['pso:withStatus']['@id'];\n result.statusInEnglish = PhylorefWrapper.getStatusCURIEsInEnglish()[result.statusCURIE];\n }\n\n // Create intervalStart/intervalEnd convenient fields\n if (has(entry, 'tvc:atTime')) {\n const atTime = entry['tvc:atTime'];\n if (has(atTime, 'timeinterval:hasIntervalStartDate')) {\n result.intervalStart = atTime['timeinterval:hasIntervalStartDate'];\n result.intervalStartAsCalendar = moment(result.intervalStart).calendar();\n }\n\n if (has(atTime, 'timeinterval:hasIntervalEndDate')) {\n result.intervalEnd = atTime['timeinterval:hasIntervalEndDate'];\n result.intervalEndAsCalendar = moment(result.intervalEnd).calendar();\n }\n }\n\n return result;\n });\n }\n\n // No changes? Return an empty list.\n return [];\n }\n\n setStatus(status) {\n // Set the status of a phyloreference\n //\n // Check whether we have a valid status CURIE.\n if (!has(PhylorefWrapper.getStatusCURIEsInEnglish(), status)) {\n throw new TypeError(`setStatus() called with invalid status CURIE '${status}'`);\n }\n\n // See if we can end the previous interval.\n const currentTime = new Date(Date.now()).toISOString();\n\n if (!has(this.phyloref, 'pso:holdsStatusInTime')) {\n // Vue.set(this.phyloref, 'pso:holdsStatusInTime', []);\n this.phyloref['pso:holdsStatusInTime'] = [];\n }\n\n // Check to see if there's a previous time interval we should end.\n if (\n Array.isArray(this.phyloref['pso:holdsStatusInTime'])\n && this.phyloref['pso:holdsStatusInTime'].length > 0\n ) {\n const lastStatusInTime = this.phyloref['pso:holdsStatusInTime'][this.phyloref['pso:holdsStatusInTime'].length - 1];\n\n // if (!has(lastStatusInTime, 'tvc:atTime'))\n // Vue.set(lastStatusInTime, 'tvc:atTime', {});\n if (!has(lastStatusInTime, 'tvc:atTime')) {\n lastStatusInTime['tvc:atTime'] = {};\n }\n if (!has(lastStatusInTime['tvc:atTime'], 'timeinterval:hasIntervalEndDate')) {\n // If the last time entry doesn't already have an interval end date, set it to now.\n lastStatusInTime['tvc:atTime']['timeinterval:hasIntervalEndDate'] = currentTime;\n }\n }\n\n // Create new entry.\n this.phyloref['pso:holdsStatusInTime'].push({\n '@type': 'http://purl.org/spar/pso/StatusInTime',\n 'pso:withStatus': { '@id': status },\n 'tvc:atTime': {\n 'timeinterval:hasIntervalStartDate': currentTime,\n },\n });\n }\n\n /**\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n */\n get uniqNomenCodes() {\n return uniq(this.specifiers.map((specifier) => {\n const taxonConcept = new TaxonomicUnitWrapper(\n specifier,\n this.phyxDefaultNomenCode\n ).taxonConcept;\n if (!taxonConcept) return owlterms.UNKNOWN_CODE;\n\n const nomenCode = new TaxonConceptWrapper(\n taxonConcept,\n this.phyxDefaultNomenCode\n ).nomenCode;\n if (!nomenCode) return owlterms.UNKNOWN_CODE;\n\n return nomenCode;\n }));\n }\n\n /**\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n */\n get defaultNomenCode() {\n // Check to see if we have a single nomenclatural code to use.\n if (this.uniqNomenCodes.length === 1) return this.uniqNomenCodes[0];\n\n // If one or more of our specifiers have no nomenclatural code (e.g. if\n // they are specimens), they will show up as owlterms.UNKNOWN_CODE.\n // If we have a single nomenclatural code *apart* from all the\n // owlterms.UNKNOWN_CODEs, then that is still usable as a default\n // nomenclatural code for this phyloreference.\n const uniqNomenCodesNoUnknowns = this.uniqNomenCodes\n .filter(code => code !== owlterms.UNKNOWN_CODE);\n if (uniqNomenCodesNoUnknowns.length === 1) return uniqNomenCodesNoUnknowns[0];\n\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n */\n createComponentClass(\n jsonld,\n internalSpecifiers,\n externalSpecifiers,\n equivClass,\n reusePrevious = true,\n parentClass = undefined\n ) {\n if (internalSpecifiers.length === 0) throw new Error('Cannot create component class without any internal specifiers');\n if (internalSpecifiers.length === 1 && externalSpecifiers.length === 0) throw new Error('Cannot create component class with a single internal specifiers and no external specifiers');\n\n /* Generate a label that represents this component class. */\n\n // By default, taxonomic unit labels don't include the nomenclatural code.\n // However, we should include that here in order to distinguish between\n // taxonomic names in different taxonomic codes. This method generates that\n // name for a specifier.\n const outerThis = this;\n function generateSpecifierName(specifier) {\n const wrapped = new TaxonomicUnitWrapper(specifier, outerThis.defaultNomenCode);\n if (!wrapped) return '(error)';\n if (wrapped.taxonConcept) {\n const nomenCodeDetails = new TaxonConceptWrapper(wrapped.taxonConcept).nomenCodeDetails;\n if (nomenCodeDetails) return `${wrapped.label} (${nomenCodeDetails.shortName})`;\n }\n return wrapped.label;\n }\n\n // Start with the internal specifiers, concatenated with '&'.\n const internalSpecifierLabel = internalSpecifiers\n .map(generateSpecifierName)\n .sort()\n .join(' & ');\n let componentClassLabel = `(${internalSpecifierLabel}`;\n\n if (externalSpecifiers.length === 0) {\n componentClassLabel += ')';\n } else {\n // Add the external specifiers, concatenated with 'V'.\n const externalSpecifierLabel = externalSpecifiers\n .map(generateSpecifierName)\n .sort()\n .join(' V ');\n componentClassLabel += ` ~ ${externalSpecifierLabel})`;\n }\n\n // process.stderr.write(`component class label: ${componentClassLabel}\\n`);\n\n // TODO We need to replace this with an actual object-based comparison,\n // rather than trusting the labels to tell us everything.\n if (reusePrevious && has(this.componentClassesByLabel, componentClassLabel)) {\n // If we see the same label again, return the previously defined component class.\n return { '@id': this.componentClassesByLabel[componentClassLabel]['@id'] };\n }\n\n // Create a new component class for this set of internal and external specifiers.\n this.componentClassCount += 1;\n const componentClass = {};\n componentClass['@id'] = `${jsonld['@id']}_component${this.componentClassCount}`;\n // process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);\n\n componentClass['@type'] = 'owl:Class';\n componentClass.label = componentClassLabel;\n componentClass.equivalentClass = equivClass;\n if (externalSpecifiers.length > 0) componentClass.subClassOf = ['phyloref:PhyloreferenceUsingMaximumClade'];\n else componentClass.subClassOf = ['phyloref:PhyloreferenceUsingMinimumClade'];\n\n if (parentClass) {\n componentClass.subClassOf.push({\n '@id': parentClass['@id'],\n });\n }\n\n // Save it in the cache for later usage.\n this.componentClassesByLabel[componentClassLabel] = componentClass;\n\n // The first time we create a componentClass, we include it into the logical\n // expression directly. On subsequent calls, we'll only return the `@id`\n // (see above).\n return componentClass;\n }\n\n getIncludesRestrictionForTU(tu) {\n return {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:includes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(tu, this.defaultNomenCode).asOWLEquivClass,\n };\n }\n\n /**\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n */\n getMRCARestrictionOfTwoTUs(tu1, tu2) {\n return {\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000149', // cdao:has_Child\n someValuesFrom: {\n '@type': 'owl:Class',\n intersectionOf: [\n {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(tu1, this.defaultNomenCode).asOWLEquivClass,\n },\n this.getIncludesRestrictionForTU(tu2),\n ],\n },\n };\n }\n\n /*\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n */\n createClassExpressionsForInternals(jsonld, remainingInternals, selected) {\n // process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:\n // ${remainingInternals.length}, selected: ${selected.length}\\n`);\n\n // Quick special case: if we have two 'remainingInternals' and zero selecteds,\n // we can just return the MRCA for two internal specifiers.\n if (selected.length === 0) {\n if (remainingInternals.length === 2) {\n return [\n this.getMRCARestrictionOfTwoTUs(remainingInternals[0], remainingInternals[1]),\n ];\n } if (remainingInternals.length === 1) {\n throw new Error('Cannot determine class expression for a single specifier');\n } else if (remainingInternals.length === 0) {\n throw new Error('Cannot determine class expression for zero specifiers');\n }\n }\n\n // Step 1. If we've already selected something, create an expression for it.\n const classExprs = [];\n if (selected.length > 0) {\n let remainingInternalsExpr = [];\n if (remainingInternals.length === 1) {\n remainingInternalsExpr = this.getIncludesRestrictionForTU(remainingInternals[0]);\n } else if (remainingInternals.length === 2) {\n remainingInternalsExpr = this.getMRCARestrictionOfTwoTUs(\n remainingInternals[0],\n remainingInternals[1]\n );\n } else {\n remainingInternalsExpr = this.createComponentClass(\n jsonld,\n remainingInternals,\n [],\n this.createClassExpressionsForInternals(jsonld, remainingInternals, [])\n );\n }\n\n let selectedExpr = [];\n if (selected.length === 1) {\n selectedExpr = this.getIncludesRestrictionForTU(selected[0]);\n } else if (selected.length === 2) {\n selectedExpr = this.getMRCARestrictionOfTwoTUs(selected[0], selected[1]);\n } else {\n selectedExpr = this.createComponentClass(\n jsonld,\n selected,\n [],\n this.createClassExpressionsForInternals(jsonld, selected, [])\n );\n }\n\n classExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000149', // cdao:has_Child\n someValuesFrom: {\n '@type': 'owl:Class',\n intersectionOf: [{\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_lineage_to',\n someValuesFrom: remainingInternalsExpr,\n }, selectedExpr],\n },\n });\n }\n\n // Step 2. Now select everything from remaining once, and start recursing through\n // every possibility.\n // Note that we only process cases where there are more remainingInternals than\n // selected internals -- when there are fewer, we'll just end up with the inverses\n // of the previous comparisons, which we'll already have covered.\n if (remainingInternals.length > 1 && selected.length <= remainingInternals.length) {\n remainingInternals.map(newlySelected => this.createClassExpressionsForInternals(\n jsonld,\n // The new remaining is the old remaining minus the selected TU.\n remainingInternals.filter(i => i !== newlySelected),\n // The new selected is the old selected plus the selected TU.\n selected.concat([newlySelected])\n ))\n .reduce((acc, val) => acc.concat(val), [])\n .forEach(expr => classExprs.push(expr));\n }\n\n return classExprs;\n }\n\n /*\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n */\n asJSONLD(fallbackIRI) {\n // Keep all currently extant data.\n const phylorefAsJSONLD = cloneDeep(this.phyloref);\n\n // Set the @id and @type. If we don't already have an '@id', use the\n // fallbackIRI.\n if (!has(phylorefAsJSONLD, '@id')) phylorefAsJSONLD['@id'] = fallbackIRI;\n phylorefAsJSONLD['@type'] = 'owl:Class';\n\n // If we don't have a bibliographicCitation but we do have a definition source,\n // then generate a bibliographicCitation for the source.\n if (has(phylorefAsJSONLD, 'definitionSource')) {\n const definitionSource = phylorefAsJSONLD.definitionSource;\n if (!has(definitionSource, 'bibliographicCitation')) {\n definitionSource.bibliographicCitation = new CitationWrapper(definitionSource).toString();\n }\n }\n\n // Construct a class expression for this phyloreference.\n const internalSpecifiers = phylorefAsJSONLD.internalSpecifiers || [];\n const externalSpecifiers = phylorefAsJSONLD.externalSpecifiers || [];\n\n // If it is an apomorphy-based class expression, we should generate a\n // logical expression that describes the apomorphy.\n const phylorefType = phylorefAsJSONLD.phylorefType;\n if (\n (phylorefType && phylorefType === 'phyloref:PhyloreferenceUsingApomorphy')\n || (has(phylorefAsJSONLD, 'apomorphy'))\n ) {\n // This is an apomorphy-based definition!\n phylorefAsJSONLD.subClassOf = [\n 'phyloref:Phyloreference',\n 'phyloref:PhyloreferenceUsingApomorphy',\n ];\n\n // Someday, we will probably want to turn this apomorphy into a\n // logical expression so that it can be computed alongside other\n // OWL ontologies. This is outside our scope for the moment, so\n // we will simply pass on the phyloreference as-is.\n\n return phylorefAsJSONLD;\n }\n\n // We might need to make component classes.\n // So we reset our component class counts and records.\n this.componentClassCount = 0;\n this.componentClassesByLabel = {};\n\n // The type of this phyloreference.\n let calculatedPhylorefType;\n\n // The list of logical expressions generated for this phyloref.\n let logicalExpressions = [];\n\n if (internalSpecifiers.length === 0) {\n // We can't handle phyloreferences without at least one internal specifier.\n calculatedPhylorefType = 'phyloref:MalformedPhyloreference';\n phylorefAsJSONLD.malformedPhyloreference = 'No internal specifiers provided';\n } else if (externalSpecifiers.length > 0) {\n calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMaximumClade';\n\n // If the phyloreference has at least one external specifier, we\n // can provide a simplified expression for the internal specifier,\n // in the form:\n // phyloref:includes_TU some [internal1] and\n // phyloref:includes_TU some [internal2] and ...\n // phyloref:excludes_TU some [exclusion1] and\n // has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...\n //\n // Since we don't know which of the external specifiers will actually\n // be the one that will be used, we need to generate logical expressions\n // for every possibility.\n\n logicalExpressions = externalSpecifiers.map((selectedExternal) => {\n // Add the internal specifiers.\n const intersectionExprs = internalSpecifiers.map(\n sp => this.getIncludesRestrictionForTU(sp)\n );\n\n // Add the selected external specifier.\n intersectionExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(\n selectedExternal,\n this.defaultNomenCode\n ).asOWLEquivClass,\n });\n\n // Collect all of the externals that are not selected.\n const remainingExternals = externalSpecifiers.filter(ex => ex !== selectedExternal);\n\n // Add the remaining externals, which we assume will resolve outside of\n // this clade.\n remainingExternals.forEach((externalTU) => {\n intersectionExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000144', // has_Ancestor\n someValuesFrom: {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(\n externalTU,\n this.defaultNomenCode\n ).asOWLEquivClass,\n },\n });\n });\n\n return {\n '@type': 'owl:Class',\n intersectionOf: intersectionExprs,\n };\n });\n } else {\n calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMinimumClade';\n\n // We only have internal specifiers. We therefore need to use the algorithm in\n // this.createClassExpressionsForInternals() to create this expression.\n logicalExpressions = this.createClassExpressionsForInternals(\n phylorefAsJSONLD, internalSpecifiers, []\n );\n }\n\n // If we have a single logical expression, we set that as an equivalentClass\n // expression. If we have more than one, we produce multiple component classes\n // to represent it.\n if (logicalExpressions.length === 0) {\n // This is fine, as long as there is an explanation in\n // phyloref.malformedPhyloreference explaining why no logical expressions\n // could be generated. Otherwise, throw an error.\n if (!has(phylorefAsJSONLD, 'malformedPhyloreference')) {\n throw new Error(\n `Phyloref ${this.label} was generated by Phyx.js with neither logical expressions nor an explanation for the lack of logical expressions. `\n + 'This indicates an error in the Phyx.js library. Please report this bug at https://github.com/phyloref/phyx.js/issues.'\n );\n }\n } else if (logicalExpressions.length === 1) {\n // If we have a single logical expression, then that is what this phyloref\n // is equivalent to.\n phylorefAsJSONLD.equivalentClass = logicalExpressions[0];\n } else {\n // If we have multiple logical expressions, the phyloreference can be\n // represented by any of them. We model this by creating subclasses of\n // the phyloreference for each logical expression -- that way, it's clear\n // that these expressions aren't equivalent to each other (which is what\n // caused https://github.com/phyloref/phyx.js/issues/57), but nodes\n // resolved by any of those expressions will also be included in the\n // phyloreference itself.\n //\n // Note that there are two differences from the way in which we usually call\n // this.createComponentClass():\n // 1. Usually, createComponentClass() reuses logical expressions with the\n // same sets of internal and external specifiers. That won't work here,\n // since *all* these logical expressions have the same specifiers. So,\n // we turn off caching.\n // 2. We need to set each of these component classes to be a subclass of\n // this phyloreference so that it can include instances from each of the\n // logical expressions.\n phylorefAsJSONLD.subClasses = logicalExpressions.map(classExpr => this.createComponentClass(\n phylorefAsJSONLD,\n internalSpecifiers,\n externalSpecifiers,\n classExpr,\n // False in order to turn off caching by internal and external specifiers.\n false,\n // Make the new component class a subclass of this phyloreference.\n phylorefAsJSONLD\n ));\n }\n\n // Every phyloreference is a subclass of phyloref:Phyloreference.\n if (!phylorefAsJSONLD.subClassOf) phylorefAsJSONLD.subClassOf = [];\n if (!Array.isArray(phylorefAsJSONLD.subClassOf)) {\n phylorefAsJSONLD.subClassOf = [phylorefAsJSONLD.subClassOf];\n }\n phylorefAsJSONLD.subClassOf.push('phyloref:Phyloreference');\n\n // If the this Phyloref has a phylorefType that differs from the calculated\n // phyloref type, throw an error.\n if (has(phylorefAsJSONLD, 'phylorefType') && phylorefAsJSONLD.phylorefType !== calculatedPhylorefType) {\n throw new Error(\n `Phyloref ${this.label} has phylorefType set to '${phylorefAsJSONLD.phylorefType}', but it appears to be a '${calculatedPhylorefType}'.`\n );\n }\n phylorefAsJSONLD.subClassOf.push(calculatedPhylorefType);\n\n return phylorefAsJSONLD;\n }\n}\n\nmodule.exports = {\n PhylorefWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/PhylorefWrapper.js", "access": "public", @@ -1443,7 +1495,7 @@ "lineNumber": 1 }, { - "__docId__": 96, + "__docId__": 98, "kind": "variable", "name": "has", "memberof": "src/wrappers/PhylorefWrapper.js", @@ -1464,7 +1516,7 @@ "ignore": true }, { - "__docId__": 97, + "__docId__": 99, "kind": "variable", "name": "TaxonomicUnitWrapper", "memberof": "src/wrappers/PhylorefWrapper.js", @@ -1485,7 +1537,7 @@ "ignore": true }, { - "__docId__": 98, + "__docId__": 100, "kind": "variable", "name": "TaxonConceptWrapper", "memberof": "src/wrappers/PhylorefWrapper.js", @@ -1506,7 +1558,7 @@ "ignore": true }, { - "__docId__": 99, + "__docId__": 101, "kind": "variable", "name": "PhylogenyWrapper", "memberof": "src/wrappers/PhylorefWrapper.js", @@ -1527,7 +1579,7 @@ "ignore": true }, { - "__docId__": 100, + "__docId__": 102, "kind": "variable", "name": "CitationWrapper", "memberof": "src/wrappers/PhylorefWrapper.js", @@ -1548,7 +1600,7 @@ "ignore": true }, { - "__docId__": 101, + "__docId__": 103, "kind": "class", "name": "PhylorefWrapper", "memberof": "src/wrappers/PhylorefWrapper.js", @@ -1563,7 +1615,7 @@ "interface": false }, { - "__docId__": 102, + "__docId__": 104, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1577,7 +1629,7 @@ "undocument": true }, { - "__docId__": 103, + "__docId__": 105, "kind": "member", "name": "phyloref", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1594,7 +1646,7 @@ } }, { - "__docId__": 104, + "__docId__": 106, "kind": "member", "name": "phyxDefaultNomenCode", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1611,7 +1663,7 @@ } }, { - "__docId__": 105, + "__docId__": 107, "kind": "get", "name": "internalSpecifiers", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1629,7 +1681,37 @@ } }, { - "__docId__": 106, + "__docId__": 108, + "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper.normalize", + "access": "public", + "description": "Normalize a phyloreference.", + "lineNumber": 46, + "params": [ + { + "nullable": null, + "types": [ + "*" + ], + "spread": false, + "optional": false, + "name": "phyloref", + "description": "" + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 109, "kind": "get", "name": "externalSpecifiers", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1639,7 +1721,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#externalSpecifiers", "access": "public", "description": "Return the external specifiers of this phyloref (if any).", - "lineNumber": 42, + "lineNumber": 58, "type": { "types": [ "*" @@ -1647,7 +1729,7 @@ } }, { - "__docId__": 107, + "__docId__": 110, "kind": "get", "name": "label", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1657,7 +1739,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#label", "access": "public", "description": null, - "lineNumber": 52, + "lineNumber": 68, "undocument": true, "type": { "types": [ @@ -1666,7 +1748,7 @@ } }, { - "__docId__": 108, + "__docId__": 111, "kind": "set", "name": "label", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1676,11 +1758,11 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#label", "access": "public", "description": null, - "lineNumber": 61, + "lineNumber": 77, "undocument": true }, { - "__docId__": 109, + "__docId__": 112, "kind": "get", "name": "specifiers", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1690,7 +1772,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#specifiers", "access": "public", "description": "Return all the specifiers of this phyloref (if any).", - "lineNumber": 72, + "lineNumber": 88, "type": { "types": [ "*" @@ -1698,7 +1780,7 @@ } }, { - "__docId__": 110, + "__docId__": 113, "kind": "method", "name": "getSpecifierType", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1708,7 +1790,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#getSpecifierType", "access": "public", "description": null, - "lineNumber": 81, + "lineNumber": 97, "undocument": true, "params": [ { @@ -1725,7 +1807,7 @@ } }, { - "__docId__": 111, + "__docId__": 114, "kind": "method", "name": "setSpecifierType", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1735,7 +1817,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#setSpecifierType", "access": "public", "description": null, - "lineNumber": 90, + "lineNumber": 106, "undocument": true, "params": [ { @@ -1754,7 +1836,7 @@ "return": null }, { - "__docId__": 112, + "__docId__": 115, "kind": "method", "name": "deleteSpecifier", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1764,7 +1846,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#deleteSpecifier", "access": "public", "description": null, - "lineNumber": 121, + "lineNumber": 137, "undocument": true, "params": [ { @@ -1777,7 +1859,7 @@ "return": null }, { - "__docId__": 113, + "__docId__": 116, "kind": "method", "name": "getExpectedNodeLabels", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1787,7 +1869,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#getExpectedNodeLabels", "access": "public", "description": null, - "lineNumber": 137, + "lineNumber": 153, "undocument": true, "params": [ { @@ -1804,7 +1886,7 @@ } }, { - "__docId__": 114, + "__docId__": 117, "kind": "method", "name": "getStatusCURIEsInEnglish", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1814,7 +1896,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper.getStatusCURIEsInEnglish", "access": "public", "description": null, - "lineNumber": 177, + "lineNumber": 193, "undocument": true, "params": [], "return": { @@ -1824,7 +1906,7 @@ } }, { - "__docId__": 115, + "__docId__": 118, "kind": "method", "name": "getCurrentStatus", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1834,7 +1916,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#getCurrentStatus", "access": "public", "description": null, - "lineNumber": 189, + "lineNumber": 205, "undocument": true, "params": [], "return": { @@ -1844,7 +1926,7 @@ } }, { - "__docId__": 116, + "__docId__": 119, "kind": "method", "name": "getStatusChanges", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1854,7 +1936,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#getStatusChanges", "access": "public", "description": null, - "lineNumber": 232, + "lineNumber": 248, "undocument": true, "params": [], "return": { @@ -1864,7 +1946,7 @@ } }, { - "__docId__": 117, + "__docId__": 120, "kind": "method", "name": "setStatus", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1874,7 +1956,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#setStatus", "access": "public", "description": null, - "lineNumber": 266, + "lineNumber": 282, "undocument": true, "params": [ { @@ -1887,7 +1969,7 @@ "return": null }, { - "__docId__": 118, + "__docId__": 121, "kind": "get", "name": "uniqNomenCodes", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1897,7 +1979,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#uniqNomenCodes", "access": "public", "description": "Return a list of all the unique nomenclatural codes used by this phyloreference.\nThe default nomenclatural code used in creating the PhylorefWrapper will be used\nfor any taxonomic units that don't have any nomenclatural code set. If any\nspecifiers are not taxon concepts, they will be represented in the returned\nlist as owlterms.UNKNOWN_CODE.", - "lineNumber": 317, + "lineNumber": 333, "type": { "types": [ "*" @@ -1905,7 +1987,7 @@ } }, { - "__docId__": 119, + "__docId__": 122, "kind": "get", "name": "defaultNomenCode", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1915,7 +1997,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#defaultNomenCode", "access": "public", "description": "Returns a summarized nomenclatural code for this phyloref. If all of the\nspecifiers have either the same nomenclatural code or `undefined`,\nthis getter will return that nomenclatural code. Otherwise, this method\nwill return owlterms.UNKNOWN_CODE.", - "lineNumber": 341, + "lineNumber": 357, "type": { "types": [ "*" @@ -1923,7 +2005,7 @@ } }, { - "__docId__": 120, + "__docId__": 123, "kind": "method", "name": "createComponentClass", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1933,7 +2015,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#createComponentClass", "access": "public", "description": "Create a component class for the set of internal and external specifiers provided.\nWe turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\nwe don't create more than one class for a particular set of internal and external\nspecifiers.\n- jsonld: The JSON-LD representation of the Phyloreference this is an component class\n for. We mainly use this to retrieve its '@id'.\n- internalSpecifiers: The set of internal specifiers for this component class.\n- externalSpecifiers: The set of external specifiers for this component class.\n- equivClass: The equivalent class expression for this component class as a function\n that returns the expression as a string.\n- reusePrevious (default: true): If true, we reuse previous expressions with the\n same set of included and excluded specifiers. If false, we always generate a new\n component class for this expression.\n- parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n parent class of this component class. We only use the ['@id'].", - "lineNumber": 374, + "lineNumber": 390, "params": [ { "name": "jsonld", @@ -1985,7 +2067,7 @@ } }, { - "__docId__": 121, + "__docId__": 124, "kind": "member", "name": "componentClassCount", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -1993,7 +2075,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#componentClassCount", "access": "public", "description": null, - "lineNumber": 430, + "lineNumber": 446, "undocument": true, "type": { "types": [ @@ -2002,7 +2084,7 @@ } }, { - "__docId__": 122, + "__docId__": 125, "kind": "method", "name": "getIncludesRestrictionForTU", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -2012,7 +2094,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#getIncludesRestrictionForTU", "access": "public", "description": null, - "lineNumber": 456, + "lineNumber": 472, "undocument": true, "params": [ { @@ -2029,7 +2111,7 @@ } }, { - "__docId__": 123, + "__docId__": 126, "kind": "method", "name": "getMRCARestrictionOfTwoTUs", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -2039,7 +2121,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#getMRCARestrictionOfTwoTUs", "access": "public", "description": "Return an OWL restriction for the most recent common ancestor (MRCA)\nof two taxonomic units.", - "lineNumber": 468, + "lineNumber": 484, "params": [ { "name": "tu1", @@ -2061,7 +2143,7 @@ } }, { - "__docId__": 124, + "__docId__": 127, "kind": "method", "name": "createClassExpressionsForInternals", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -2071,7 +2153,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#createClassExpressionsForInternals", "access": "public", "description": null, - "lineNumber": 512, + "lineNumber": 528, "undocument": true, "params": [ { @@ -2100,7 +2182,7 @@ } }, { - "__docId__": 125, + "__docId__": 128, "kind": "method", "name": "asJSONLD", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -2110,7 +2192,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#asJSONLD", "access": "public", "description": null, - "lineNumber": 607, + "lineNumber": 623, "undocument": true, "params": [ { @@ -2127,7 +2209,7 @@ } }, { - "__docId__": 127, + "__docId__": 130, "kind": "member", "name": "componentClassesByLabel", "memberof": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper", @@ -2135,7 +2217,7 @@ "longname": "src/wrappers/PhylorefWrapper.js~PhylorefWrapper#componentClassesByLabel", "access": "public", "description": null, - "lineNumber": 653, + "lineNumber": 669, "undocument": true, "type": { "types": [ @@ -2144,10 +2226,10 @@ } }, { - "__docId__": 128, + "__docId__": 131, "kind": "file", "name": "src/wrappers/PhyxWrapper.js", - "content": "const fs = require('fs');\nconst path = require('path');\n\n/** Helper methods from lodash. */\nconst { has, cloneDeep, uniq } = require('lodash');\n\n/** For NQuads export. */\nconst JSONLD = require('jsonld');\n\nconst owlterms = require('../utils/owlterms');\n\nconst { PhylorefWrapper } = require('./PhylorefWrapper');\nconst { PhylogenyWrapper } = require('./PhylogenyWrapper');\nconst { CitationWrapper } = require('./CitationWrapper');\n\n/**\n * The PhyxWrapper wraps an entire Phyx document.\n */\n\nclass PhyxWrapper {\n /**\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n */\n constructor(phyx, newickParser = PhylogenyWrapper.getParsedNewick) {\n //\n this.phyx = phyx;\n this.newickParser = newickParser;\n }\n\n // Determine a 'default nomenclatural code' for this Phyx file. There are\n // two ways to do this:\n // 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.\n // 2. Otherwise, we check to see if every phyloref in this file has the same\n // nomenclatural code. If so, we can use that code. If not, i.e. if any of\n // the phylorefs are missing a nomenclatural code or include a specifier,\n // we default to owlterms.UNKNOWN_CODE.\n get defaultNomenCode() {\n if (has(this.phyx, 'defaultNomenclaturalCodeIRI')) return this.phyx.defaultNomenclaturalCodeIRI;\n const nomenCodes = (this.phyx.phylorefs || [])\n .map(phyloref => new PhylorefWrapper(phyloref).defaultNomenCode);\n const uniqNomenCodes = uniq(nomenCodes);\n if (uniqNomenCodes.length === 1) return uniqNomenCodes[0];\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n */\n asJSONLD(baseIRI = '') {\n const jsonld = cloneDeep(this.phyx);\n\n // Some helper methods for generating base IRIs for phylorefs and phylogenies.\n function getBaseIRIForPhyloref(index) {\n if (baseIRI) return `${baseIRI}phyloref${index}`;\n return `#phyloref${index}`;\n }\n\n function getBaseIRIForPhylogeny(index) {\n if (baseIRI) return `${baseIRI}phylogeny${index}`;\n return `#phylogeny${index}`;\n }\n\n // Given a relative ID (e.g. '#phylo1') make it absolute (`${baseIRI}phylo1`).\n function makeIDAbsolute(phylogenyId) {\n if (baseIRI && phylogenyId.startsWith('#')) return `${baseIRI}${phylogenyId.substring(1)}`; // Remove the initial '#'.\n return phylogenyId;\n }\n\n // Given an absolute ID (`${baseIRI}phylo1`) make it relative (e.g. '#phylo1').\n function makeIDRelative(phylogenyId) {\n if (phylogenyId.startsWith(baseIRI)) return `#${phylogenyId.substring(baseIRI.length)}`;\n return phylogenyId;\n }\n\n if (has(jsonld, 'phylorefs')) {\n // We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").\n // If the baseIRI is set to '', that's fine. But if not, we'll add it\n // to the relative IRI to make it absolute. This seems to avoid problems\n // with some JSON-LD parsers.\n if (baseIRI) {\n jsonld.phylorefs = jsonld.phylorefs.map((phyloref) => {\n if ((phyloref['@id'] || '').startsWith('#')) {\n const modifiedPhyloref = cloneDeep(phyloref);\n modifiedPhyloref['@id'] = makeIDAbsolute(phyloref['@id']);\n return modifiedPhyloref;\n }\n return phyloref;\n });\n }\n\n // Convert phyloreferences into an OWL class restriction\n jsonld.phylorefs = jsonld.phylorefs.map(\n (phyloref, countPhyloref) => new PhylorefWrapper(phyloref, this.defaultNomenCode)\n .asJSONLD(getBaseIRIForPhyloref(countPhyloref))\n );\n }\n\n if (has(jsonld, 'phylogenies')) {\n // We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").\n // If the baseIRI is set to '', that's fine. But if not, we'll add it\n // to the relative IRI to make it absolute. This seems to avoid problems\n // with some JSON-LD parsers.\n if (baseIRI) {\n jsonld.phylogenies = jsonld.phylogenies.map((phylogeny) => {\n if ((phylogeny['@id'] || '').startsWith('#')) {\n const modifiedPhylogeny = cloneDeep(phylogeny);\n modifiedPhylogeny['@id'] = makeIDAbsolute(phylogeny['@id']);\n return modifiedPhylogeny;\n }\n return phylogeny;\n });\n }\n\n // Add descriptions for individual nodes in each phylogeny.\n jsonld.phylogenies = jsonld.phylogenies.map(\n (phylogeny, countPhylogeny) => new PhylogenyWrapper(phylogeny, this.defaultNomenCode)\n .asJSONLD(getBaseIRIForPhylogeny(countPhylogeny), this.newickParser)\n );\n\n // Go through all the nodes and add information on expected resolution.\n jsonld.phylogenies.forEach((phylogeny) => {\n const phylogenyId = phylogeny['@id'];\n (phylogeny.nodes || []).forEach((node) => {\n // We can't set expected resolution information on unlabeled nodes.\n if (!node.labels) return;\n\n jsonld.phylorefs.forEach((phyloref) => {\n const phylorefId = phyloref['@id'];\n\n // There are two ways in which we determine that a phyloreference\n // is expected to resolve to a node:\n // (1) If nodeLabel is set, then that must be one of the node's labels.\n // (2) If nodeLabel is not set, then one of the node's label should be\n // identical to the phyloreference's label.\n //\n // We set flagNodeExpectsPhyloref in all cases where we should note\n // that this node expects to resolve to this phyloreference.\n let flagNodeExpectsPhyloref = false;\n\n // console.log(`Testing expected resolution of '${phylorefId}' on `\n // + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);\n\n if (\n has(phyloref, 'expectedResolution')\n && (\n // The user might have used the absolute phylogeny ID here.\n has(phyloref.expectedResolution, phylogenyId)\n\n // Or they might have used a relative phylogeny ID.\n || has(phyloref.expectedResolution, makeIDRelative(phylogenyId))\n )\n ) {\n // Expected resolution information set! The node label mentioned in that\n // information must be identical to one of the labels of this phylogeny node.\n\n // Figure out which phylogenyId was matched here.\n const nodeLabel = has(phyloref.expectedResolution, phylogenyId)\n ? phyloref.expectedResolution[phylogenyId].nodeLabel\n : phyloref.expectedResolution[makeIDRelative(phylogenyId)].nodeLabel;\n\n if (nodeLabel && (node.labels || []).includes(nodeLabel)) {\n flagNodeExpectsPhyloref = true;\n }\n } else if ((node.labels || []).includes(phyloref.label)) {\n // No expected resolution information, so we just check whether\n // the phyloref label is one of the labels on this phylogeny node.\n flagNodeExpectsPhyloref = true;\n }\n\n if (flagNodeExpectsPhyloref) {\n // Modify this phylogeny node's type to include that it is a type\n // of:\n // obi:is_specified_output_of some (\n // obi:Prediction and obi:has_specified_output some #phyloref_id\n // )\n node[owlterms.RDF_TYPE].push({\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.OBI_IS_SPECIFIED_OUTPUT_OF,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n { '@id': owlterms.OBI_PREDICTION },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.OBI_HAS_SPECIFIED_INPUT,\n someValuesFrom: {\n '@id': phylorefId,\n },\n },\n ],\n },\n });\n }\n });\n });\n });\n }\n\n // Earlier, we used to generate a list of taxonomic matches here (stored in\n // jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic\n // units in phyloref specifiers were related to taxonomic units in phylogeny\n // nodes. This is no longer necessary, since phyloref specifiers are now logical\n // expressions that directly evaluate to phylogeny nodes. However, if in the\n // future we decide that we need to perform more advanced TU matching, this\n // would be the place to implement that.\n\n // If there is a top-level source, generate a bibliographicCitation for it.\n if (has(jsonld, 'source')) {\n jsonld.source.bibliographicCitation = new CitationWrapper(jsonld.source).toString();\n }\n\n // Set up the top-level object '@type'. If one is present, we add our terms to that.\n if (!has(jsonld, '@type')) jsonld['@type'] = [];\n if (!Array.isArray(jsonld['@type'])) jsonld['@type'] = [jsonld['@type']];\n jsonld['@type'].push('owl:Ontology');\n\n // Set up the ontology imports. If one is present, we add our imports to that.\n if (!has(jsonld, 'owl:imports')) jsonld['owl:imports'] = [];\n if (!Array.isArray(jsonld['owl:imports'])) jsonld['owl:imports'] = [jsonld['owl:imports']];\n jsonld['owl:imports'].push('http://ontology.phyloref.org/2018-12-14/phyloref.owl');\n jsonld['owl:imports'].push('http://ontology.phyloref.org/2018-12-14/tcan.owl');\n\n // If the '@context' is missing, add it here.\n if (!has(jsonld, '@context')) {\n jsonld['@context'] = owlterms.PHYX_CONTEXT_JSON;\n }\n\n return jsonld;\n }\n\n /**\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n */\n toRDF(baseIRI = '', filePath = undefined) {\n const owlJSONLD = this.asJSONLD(baseIRI);\n\n // For the purposes of testing, we are sometimes given a relative path to `@context`,\n // but the JSONLD package does not support this. Instead, we'll import the contents\n // of the relative path on the fly.\n if (filePath && has(owlJSONLD, '@context') && owlJSONLD['@context'].startsWith('.')) {\n owlJSONLD['@context'] = JSON.parse(fs.readFileSync(\n path.resolve(filePath, owlJSONLD['@context'])\n ));\n }\n\n return JSONLD.toRDF(owlJSONLD, { format: 'application/n-quads' });\n }\n}\n\nmodule.exports = {\n PhyxWrapper,\n};\n", + "content": "const fs = require('fs');\nconst path = require('path');\n\n/** Helper methods from lodash. */\nconst { has, cloneDeep, uniq } = require('lodash');\n\n/** For NQuads export. */\nconst JSONLD = require('jsonld');\n\nconst owlterms = require('../utils/owlterms');\n\nconst { PhylorefWrapper } = require('./PhylorefWrapper');\nconst { PhylogenyWrapper } = require('./PhylogenyWrapper');\nconst { CitationWrapper } = require('./CitationWrapper');\n\n/**\n * The PhyxWrapper wraps an entire Phyx document.\n */\n\nclass PhyxWrapper {\n /**\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n */\n constructor(phyx, newickParser = PhylogenyWrapper.getParsedNewick) {\n //\n this.phyx = phyx;\n this.newickParser = newickParser;\n }\n\n // Determine a 'default nomenclatural code' for this Phyx file. There are\n // two ways to do this:\n // 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.\n // 2. Otherwise, we check to see if every phyloref in this file has the same\n // nomenclatural code. If so, we can use that code. If not, i.e. if any of\n // the phylorefs are missing a nomenclatural code or include a specifier,\n // we default to owlterms.UNKNOWN_CODE.\n get defaultNomenCode() {\n if (has(this.phyx, 'defaultNomenclaturalCodeIRI')) return this.phyx.defaultNomenclaturalCodeIRI;\n const nomenCodes = (this.phyx.phylorefs || [])\n .map(phyloref => new PhylorefWrapper(phyloref).defaultNomenCode);\n const uniqNomenCodes = uniq(nomenCodes);\n if (uniqNomenCodes.length === 1) return uniqNomenCodes[0];\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\n * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\n * package will be wrapped and normalized before being returned.\n *\n * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\n * identical ways. But if we implement it at every level, we can implement comparison code in\n * Klados easily.\n *\n * Two Phyx documents should -- upon being normalized -- be comparable with each other with\n * lodash.deepEqual().\n */\n static normalize(phyxDocument) {\n const normalizedDocument = cloneDeep(phyxDocument);\n\n normalizedDocument.phylorefs = (phyxDocument.phylorefs || []).map(PhylorefWrapper.normalize);\n normalizedDocument.phylogenies = (phyxDocument.phylogenies || [])\n .map(PhylogenyWrapper.normalize);\n if ('source' in phyxDocument) {\n normalizedDocument.source = CitationWrapper.normalize(phyxDocument.source);\n }\n\n return normalizedDocument;\n }\n\n /**\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n */\n asJSONLD(baseIRI = '') {\n const jsonld = cloneDeep(this.phyx);\n\n // Some helper methods for generating base IRIs for phylorefs and phylogenies.\n function getBaseIRIForPhyloref(index) {\n if (baseIRI) return `${baseIRI}phyloref${index}`;\n return `#phyloref${index}`;\n }\n\n function getBaseIRIForPhylogeny(index) {\n if (baseIRI) return `${baseIRI}phylogeny${index}`;\n return `#phylogeny${index}`;\n }\n\n // Given a relative ID (e.g. '#phylo1') make it absolute (`${baseIRI}phylo1`).\n function makeIDAbsolute(phylogenyId) {\n if (baseIRI && phylogenyId.startsWith('#')) return `${baseIRI}${phylogenyId.substring(1)}`; // Remove the initial '#'.\n return phylogenyId;\n }\n\n // Given an absolute ID (`${baseIRI}phylo1`) make it relative (e.g. '#phylo1').\n function makeIDRelative(phylogenyId) {\n if (phylogenyId.startsWith(baseIRI)) return `#${phylogenyId.substring(baseIRI.length)}`;\n return phylogenyId;\n }\n\n if (has(jsonld, 'phylorefs')) {\n // We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").\n // If the baseIRI is set to '', that's fine. But if not, we'll add it\n // to the relative IRI to make it absolute. This seems to avoid problems\n // with some JSON-LD parsers.\n if (baseIRI) {\n jsonld.phylorefs = jsonld.phylorefs.map((phyloref) => {\n if ((phyloref['@id'] || '').startsWith('#')) {\n const modifiedPhyloref = cloneDeep(phyloref);\n modifiedPhyloref['@id'] = makeIDAbsolute(phyloref['@id']);\n return modifiedPhyloref;\n }\n return phyloref;\n });\n }\n\n // Convert phyloreferences into an OWL class restriction\n jsonld.phylorefs = jsonld.phylorefs.map(\n (phyloref, countPhyloref) => new PhylorefWrapper(phyloref, this.defaultNomenCode)\n .asJSONLD(getBaseIRIForPhyloref(countPhyloref))\n );\n }\n\n if (has(jsonld, 'phylogenies')) {\n // We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").\n // If the baseIRI is set to '', that's fine. But if not, we'll add it\n // to the relative IRI to make it absolute. This seems to avoid problems\n // with some JSON-LD parsers.\n if (baseIRI) {\n jsonld.phylogenies = jsonld.phylogenies.map((phylogeny) => {\n if ((phylogeny['@id'] || '').startsWith('#')) {\n const modifiedPhylogeny = cloneDeep(phylogeny);\n modifiedPhylogeny['@id'] = makeIDAbsolute(phylogeny['@id']);\n return modifiedPhylogeny;\n }\n return phylogeny;\n });\n }\n\n // Add descriptions for individual nodes in each phylogeny.\n jsonld.phylogenies = jsonld.phylogenies.map(\n (phylogeny, countPhylogeny) => new PhylogenyWrapper(phylogeny, this.defaultNomenCode)\n .asJSONLD(getBaseIRIForPhylogeny(countPhylogeny), this.newickParser)\n );\n\n // Go through all the nodes and add information on expected resolution.\n jsonld.phylogenies.forEach((phylogeny) => {\n const phylogenyId = phylogeny['@id'];\n (phylogeny.nodes || []).forEach((node) => {\n // We can't set expected resolution information on unlabeled nodes.\n if (!node.labels) return;\n\n jsonld.phylorefs.forEach((phyloref) => {\n const phylorefId = phyloref['@id'];\n\n // There are two ways in which we determine that a phyloreference\n // is expected to resolve to a node:\n // (1) If nodeLabel is set, then that must be one of the node's labels.\n // (2) If nodeLabel is not set, then one of the node's label should be\n // identical to the phyloreference's label.\n //\n // We set flagNodeExpectsPhyloref in all cases where we should note\n // that this node expects to resolve to this phyloreference.\n let flagNodeExpectsPhyloref = false;\n\n // console.log(`Testing expected resolution of '${phylorefId}' on `\n // + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);\n\n if (\n has(phyloref, 'expectedResolution')\n && (\n // The user might have used the absolute phylogeny ID here.\n has(phyloref.expectedResolution, phylogenyId)\n\n // Or they might have used a relative phylogeny ID.\n || has(phyloref.expectedResolution, makeIDRelative(phylogenyId))\n )\n ) {\n // Expected resolution information set! The node label mentioned in that\n // information must be identical to one of the labels of this phylogeny node.\n\n // Figure out which phylogenyId was matched here.\n const nodeLabel = has(phyloref.expectedResolution, phylogenyId)\n ? phyloref.expectedResolution[phylogenyId].nodeLabel\n : phyloref.expectedResolution[makeIDRelative(phylogenyId)].nodeLabel;\n\n if (nodeLabel && (node.labels || []).includes(nodeLabel)) {\n flagNodeExpectsPhyloref = true;\n }\n } else if ((node.labels || []).includes(phyloref.label)) {\n // No expected resolution information, so we just check whether\n // the phyloref label is one of the labels on this phylogeny node.\n flagNodeExpectsPhyloref = true;\n }\n\n if (flagNodeExpectsPhyloref) {\n // Modify this phylogeny node's type to include that it is a type\n // of:\n // obi:is_specified_output_of some (\n // obi:Prediction and obi:has_specified_output some #phyloref_id\n // )\n node[owlterms.RDF_TYPE].push({\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.OBI_IS_SPECIFIED_OUTPUT_OF,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n { '@id': owlterms.OBI_PREDICTION },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.OBI_HAS_SPECIFIED_INPUT,\n someValuesFrom: {\n '@id': phylorefId,\n },\n },\n ],\n },\n });\n }\n });\n });\n });\n }\n\n // Earlier, we used to generate a list of taxonomic matches here (stored in\n // jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic\n // units in phyloref specifiers were related to taxonomic units in phylogeny\n // nodes. This is no longer necessary, since phyloref specifiers are now logical\n // expressions that directly evaluate to phylogeny nodes. However, if in the\n // future we decide that we need to perform more advanced TU matching, this\n // would be the place to implement that.\n\n // If there is a top-level source, generate a bibliographicCitation for it.\n if (has(jsonld, 'source')) {\n jsonld.source.bibliographicCitation = new CitationWrapper(jsonld.source).toString();\n }\n\n // Set up the top-level object '@type'. If one is present, we add our terms to that.\n if (!has(jsonld, '@type')) jsonld['@type'] = [];\n if (!Array.isArray(jsonld['@type'])) jsonld['@type'] = [jsonld['@type']];\n jsonld['@type'].push('owl:Ontology');\n\n // Set up the ontology imports. If one is present, we add our imports to that.\n if (!has(jsonld, 'owl:imports')) jsonld['owl:imports'] = [];\n if (!Array.isArray(jsonld['owl:imports'])) jsonld['owl:imports'] = [jsonld['owl:imports']];\n jsonld['owl:imports'].push('http://ontology.phyloref.org/2018-12-14/phyloref.owl');\n jsonld['owl:imports'].push('http://ontology.phyloref.org/2018-12-14/tcan.owl');\n\n // If the '@context' is missing, add it here.\n if (!has(jsonld, '@context')) {\n jsonld['@context'] = owlterms.PHYX_CONTEXT_JSON;\n }\n\n return jsonld;\n }\n\n /**\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n */\n toRDF(baseIRI = '', filePath = undefined) {\n const owlJSONLD = this.asJSONLD(baseIRI);\n\n // For the purposes of testing, we are sometimes given a relative path to `@context`,\n // but the JSONLD package does not support this. Instead, we'll import the contents\n // of the relative path on the fly.\n if (filePath && has(owlJSONLD, '@context') && owlJSONLD['@context'].startsWith('.')) {\n owlJSONLD['@context'] = JSON.parse(fs.readFileSync(\n path.resolve(filePath, owlJSONLD['@context'])\n ));\n }\n\n return JSONLD.toRDF(owlJSONLD, { format: 'application/n-quads' });\n }\n}\n\nmodule.exports = {\n PhyxWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/PhyxWrapper.js", "access": "public", @@ -2155,7 +2237,7 @@ "lineNumber": 1 }, { - "__docId__": 129, + "__docId__": 132, "kind": "variable", "name": "has", "memberof": "src/wrappers/PhyxWrapper.js", @@ -2176,7 +2258,7 @@ "ignore": true }, { - "__docId__": 130, + "__docId__": 133, "kind": "variable", "name": "PhylorefWrapper", "memberof": "src/wrappers/PhyxWrapper.js", @@ -2197,7 +2279,7 @@ "ignore": true }, { - "__docId__": 131, + "__docId__": 134, "kind": "variable", "name": "PhylogenyWrapper", "memberof": "src/wrappers/PhyxWrapper.js", @@ -2218,7 +2300,7 @@ "ignore": true }, { - "__docId__": 132, + "__docId__": 135, "kind": "variable", "name": "CitationWrapper", "memberof": "src/wrappers/PhyxWrapper.js", @@ -2239,7 +2321,7 @@ "ignore": true }, { - "__docId__": 133, + "__docId__": 136, "kind": "class", "name": "PhyxWrapper", "memberof": "src/wrappers/PhyxWrapper.js", @@ -2254,7 +2336,7 @@ "interface": false }, { - "__docId__": 134, + "__docId__": 137, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", @@ -2291,7 +2373,7 @@ ] }, { - "__docId__": 135, + "__docId__": 138, "kind": "member", "name": "phyx", "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", @@ -2308,7 +2390,7 @@ } }, { - "__docId__": 136, + "__docId__": 139, "kind": "member", "name": "newickParser", "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", @@ -2325,7 +2407,7 @@ } }, { - "__docId__": 137, + "__docId__": 140, "kind": "get", "name": "defaultNomenCode", "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", @@ -2344,7 +2426,33 @@ } }, { - "__docId__": 138, + "__docId__": 141, + "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/PhyxWrapper.js~PhyxWrapper.normalize", + "access": "public", + "description": "Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\nkeys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\npackage will be wrapped and normalized before being returned.\n\nNormalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n(TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\nidentical ways. But if we implement it at every level, we can implement comparison code in\nKlados easily.\n\nTwo Phyx documents should -- upon being normalized -- be comparable with each other with\nlodash.deepEqual().", + "lineNumber": 71, + "params": [ + { + "name": "phyxDocument", + "types": [ + "*" + ] + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 142, "kind": "method", "name": "asJSONLD", "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", @@ -2354,7 +2462,7 @@ "longname": "src/wrappers/PhyxWrapper.js~PhyxWrapper#asJSONLD", "access": "public", "description": "Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\nalready, except for three important things:\n 1. We have to convert all phylogenies into a series of statements relating to the nodes\n inside these phylogenies.\n 2. We have to convert phylogenies into OWL restrictions.\n 3. Insert all matches between taxonomic units in this file.", - "lineNumber": 74, + "lineNumber": 100, "params": [ { "nullable": null, @@ -2379,7 +2487,7 @@ } }, { - "__docId__": 139, + "__docId__": 143, "kind": "method", "name": "toRDF", "memberof": "src/wrappers/PhyxWrapper.js~PhyxWrapper", @@ -2389,7 +2497,7 @@ "longname": "src/wrappers/PhyxWrapper.js~PhyxWrapper#toRDF", "access": "public", "description": "Generate an executable ontology from this Phyx document as N-Quads. Under the\nhood, we generate an OWL/JSON-LD representation of this Phyx document, and then\nconvert it into N-Quads so that OWLAPI-supporting tools can directly consume it.", - "lineNumber": 272, + "lineNumber": 298, "params": [ { "nullable": null, @@ -2426,10 +2534,10 @@ } }, { - "__docId__": 140, + "__docId__": 144, "kind": "file", "name": "src/wrappers/SpecimenWrapper.js", - "content": "const { has } = require('lodash');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst owlterms = require('../utils/owlterms');\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n */\nclass SpecimenWrapper {\n /** The '@type' of specimens in JSON-LD document. */\n static get TYPE_SPECIMEN() {\n return owlterms.DWC_OCCURRENCE;\n }\n\n /** Construct a wrapper around a specimen. */\n constructor(specimen) {\n this.specimen = specimen;\n }\n\n /**\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n */\n static fromOccurrenceID(occurrenceID, basisOfRecord = 'PreservedSpecimen') {\n // Copy the occurrence ID so we can truncate it if necessary.\n let occurID = occurrenceID;\n if (occurID.startsWith('urn:catalog:')) occurID = occurID.substr(12);\n\n // Prepare the specimen.\n const specimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n 'dwc:basisOfRecord': basisOfRecord,\n occurrenceID: occurID,\n };\n\n // Look for certain prefixes that suggest that we've been passed a URN or\n // URL instead. If so, don't do any further processing!\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n if (URL_URN_PREFIXES.filter(prefix => occurID.toLowerCase().startsWith(prefix)).length > 0) {\n return specimen;\n }\n\n // Parsing an occurrence ID takes some time, so we should memoize it.\n if (PhyxCacheManager.has('SpecimenWrapper.occurrenceIDCache', occurID)) {\n return PhyxCacheManager.get('SpecimenWrapper.occurrenceIDCache', occurID);\n }\n\n // Split the occurrence ID into components, and store them in the appropriate fields.\n const comps = occurID.split(/:/);\n if (comps.length === 1) {\n // specimen.institutionCode = undefined;\n // specimen.collectionCode = undefined;\n [specimen.catalogNumber] = comps;\n } else if (comps.length === 2) {\n [specimen.institutionCode, specimen.catalogNumber] = comps;\n } else if (comps.length >= 3) {\n let catalogNumValues = []; // Store all split catalog number values.\n [specimen.institutionCode, specimen.collectionCode, ...catalogNumValues] = comps;\n specimen.catalogNumber = catalogNumValues.join(':');\n }\n\n PhyxCacheManager.put('SpecimenWrapper.occurrenceIDCache', occurID, specimen);\n return specimen;\n }\n\n /**\n * Get the catalogNumber if present.\n */\n get catalogNumber() {\n // Get the catalog number from the specimen object if present.\n if (has(this.specimen, 'catalogNumber')) return this.specimen.catalogNumber;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract a\n // catalogNumber from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'catalogNumber')) return specimen.catalogNumber;\n }\n return undefined;\n }\n\n /**\n * Get the institutionCode if present.\n */\n get institutionCode() {\n // Get the institution code from the specimen object if present.\n if (has(this.specimen, 'institutionCode')) return this.specimen.institutionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'institutionCode')) return specimen.institutionCode;\n }\n return undefined;\n }\n\n /**\n * Get the collectionCode if present.\n */\n get collectionCode() {\n // Get the collection code from the specimen object if present.\n if (has(this.specimen, 'collectionCode')) return this.specimen.collectionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'collectionCode')) return specimen.collectionCode;\n }\n return undefined;\n }\n\n /**\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n */\n get occurrenceID() {\n // Return the occurrenceID if it exists.\n if (has(this.specimen, 'occurrenceID') && this.specimen.occurrenceID.trim() !== '') {\n return this.specimen.occurrenceID.trim();\n }\n\n // Otherwise, we could try to construct the occurrenceID from its components.\n if (has(this.specimen, 'catalogNumber')) {\n if (has(this.specimen, 'institutionCode')) {\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog:${this.specimen.institutionCode.trim()}:${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:${this.specimen.institutionCode.trim()}::${this.specimen.catalogNumber.trim()}`;\n }\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog::${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:::${this.specimen.catalogNumber.trim()}`;\n }\n\n // None of our specimen identifier schemes worked.\n return undefined;\n }\n\n /**\n * Return the basis of record, if one is present.\n */\n get basisOfRecord() {\n if (has(this.specimen, 'dwc:basisOfRecord')) return this.specimen['dwc:basisOfRecord'];\n return undefined;\n }\n\n /**\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n */\n set basisOfRecord(bor) {\n this.specimen['dwc:basisOfRecord'] = bor;\n }\n\n /** Return this specimen as a taxon concept if it contains taxon name information. */\n get taxonConcept() {\n if (has(this.specimen, 'hasName')) return this.specimen;\n if (has(this.specimen, 'nameString')) return this.specimen;\n return undefined;\n }\n\n /** Return a label for this specimen. */\n get label() {\n // We can't return anything without an occurrenceID.\n if (!this.occurrenceID) return undefined;\n\n // Note that specimens may be identified to a taxon concept. If so, we should\n // include that information in the label.\n if (this.taxonConcept) {\n return `Specimen ${this.occurrenceID} identified as ${new TaxonConceptWrapper(this.taxonConcept).label}`;\n }\n\n // Return a label for this specimen.\n return `Specimen ${this.occurrenceID}`;\n }\n\n /** Return this specimen as an equivalentClass expression. */\n get asOWLEquivClass() {\n // We can't do anything without an occurrence ID!\n if (!this.occurrenceID) return undefined;\n\n // TODO: Should we also match by this.taxonConcept is one is available?\n // Technically no, but it might be useful. Hmm.\n\n // Return as an OWL restriction.\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n hasValue: this.occurrenceID,\n };\n }\n}\n\nmodule.exports = {\n SpecimenWrapper,\n};\n", + "content": "const { has } = require('lodash');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst owlterms = require('../utils/owlterms');\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n */\nclass SpecimenWrapper {\n /** The '@type' of specimens in JSON-LD document. */\n static get TYPE_SPECIMEN() {\n return owlterms.DWC_OCCURRENCE;\n }\n\n /** Construct a wrapper around a specimen. */\n constructor(specimen) {\n this.specimen = specimen;\n }\n\n /**\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n */\n static normalize(specimen) {\n const wrapped = new SpecimenWrapper(specimen);\n const normalizedSpecimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n label: wrapped.label,\n 'dwc:basisOfRecord': wrapped.basisOfRecord,\n occurrenceID: wrapped.occurrenceID,\n catalogNumber: wrapped.catalogNumber,\n institutionCode: wrapped.institutionCode,\n collectionCode: wrapped.collectionCode,\n };\n if ('@id' in specimen) normalizedSpecimen['@id'] = specimen['@id'];\n return normalizedSpecimen;\n }\n\n /**\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n */\n static fromOccurrenceID(occurrenceID, basisOfRecord = 'PreservedSpecimen') {\n // Copy the occurrence ID so we can truncate it if necessary.\n let occurID = occurrenceID;\n if (occurID.startsWith('urn:catalog:')) occurID = occurID.substr(12);\n\n // Prepare the specimen.\n const specimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n 'dwc:basisOfRecord': basisOfRecord,\n occurrenceID: occurID,\n };\n\n // Look for certain prefixes that suggest that we've been passed a URN or\n // URL instead. If so, don't do any further processing!\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n if (URL_URN_PREFIXES.filter(prefix => occurID.toLowerCase().startsWith(prefix)).length > 0) {\n return specimen;\n }\n\n // Parsing an occurrence ID takes some time, so we should memoize it.\n if (PhyxCacheManager.has('SpecimenWrapper.occurrenceIDCache', occurID)) {\n return PhyxCacheManager.get('SpecimenWrapper.occurrenceIDCache', occurID);\n }\n\n // Split the occurrence ID into components, and store them in the appropriate fields.\n const comps = occurID.split(/:/);\n if (comps.length === 1) {\n // specimen.institutionCode = undefined;\n // specimen.collectionCode = undefined;\n [specimen.catalogNumber] = comps;\n } else if (comps.length === 2) {\n [specimen.institutionCode, specimen.catalogNumber] = comps;\n } else if (comps.length >= 3) {\n let catalogNumValues = []; // Store all split catalog number values.\n [specimen.institutionCode, specimen.collectionCode, ...catalogNumValues] = comps;\n specimen.catalogNumber = catalogNumValues.join(':');\n }\n\n PhyxCacheManager.put('SpecimenWrapper.occurrenceIDCache', occurID, specimen);\n return specimen;\n }\n\n /**\n * Get the catalogNumber if present.\n */\n get catalogNumber() {\n // Get the catalog number from the specimen object if present.\n if (has(this.specimen, 'catalogNumber')) return this.specimen.catalogNumber;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract a\n // catalogNumber from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'catalogNumber')) return specimen.catalogNumber;\n }\n return undefined;\n }\n\n /**\n * Get the institutionCode if present.\n */\n get institutionCode() {\n // Get the institution code from the specimen object if present.\n if (has(this.specimen, 'institutionCode')) return this.specimen.institutionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'institutionCode')) return specimen.institutionCode;\n }\n return undefined;\n }\n\n /**\n * Get the collectionCode if present.\n */\n get collectionCode() {\n // Get the collection code from the specimen object if present.\n if (has(this.specimen, 'collectionCode')) return this.specimen.collectionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'collectionCode')) return specimen.collectionCode;\n }\n return undefined;\n }\n\n /**\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n */\n get occurrenceID() {\n // Return the occurrenceID if it exists.\n if (has(this.specimen, 'occurrenceID') && this.specimen.occurrenceID.trim() !== '') {\n return this.specimen.occurrenceID.trim();\n }\n\n // Otherwise, we could try to construct the occurrenceID from its components.\n if (has(this.specimen, 'catalogNumber')) {\n if (has(this.specimen, 'institutionCode')) {\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog:${this.specimen.institutionCode.trim()}:${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:${this.specimen.institutionCode.trim()}::${this.specimen.catalogNumber.trim()}`;\n }\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog::${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:::${this.specimen.catalogNumber.trim()}`;\n }\n\n // None of our specimen identifier schemes worked.\n return undefined;\n }\n\n /**\n * Return the basis of record, if one is present.\n */\n get basisOfRecord() {\n if (has(this.specimen, 'dwc:basisOfRecord')) return this.specimen['dwc:basisOfRecord'];\n return undefined;\n }\n\n /**\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n */\n set basisOfRecord(bor) {\n this.specimen['dwc:basisOfRecord'] = bor;\n }\n\n /** Return this specimen as a taxon concept if it contains taxon name information. */\n get taxonConcept() {\n if (has(this.specimen, 'hasName')) return this.specimen;\n if (has(this.specimen, 'nameString')) return this.specimen;\n return undefined;\n }\n\n /** Return a label for this specimen. */\n get label() {\n // We can't return anything without an occurrenceID.\n if (!this.occurrenceID) return undefined;\n\n // Note that specimens may be identified to a taxon concept. If so, we should\n // include that information in the label.\n if (this.taxonConcept) {\n return `Specimen ${this.occurrenceID} identified as ${new TaxonConceptWrapper(this.taxonConcept).label}`;\n }\n\n // Return a label for this specimen.\n return `Specimen ${this.occurrenceID}`;\n }\n\n /** Return this specimen as an equivalentClass expression. */\n get asOWLEquivClass() {\n // We can't do anything without an occurrence ID!\n if (!this.occurrenceID) return undefined;\n\n // TODO: Should we also match by this.taxonConcept is one is available?\n // Technically no, but it might be useful. Hmm.\n\n // Return as an OWL restriction.\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n hasValue: this.occurrenceID,\n };\n }\n}\n\nmodule.exports = {\n SpecimenWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/SpecimenWrapper.js", "access": "public", @@ -2437,7 +2545,7 @@ "lineNumber": 1 }, { - "__docId__": 141, + "__docId__": 145, "kind": "variable", "name": "has", "memberof": "src/wrappers/SpecimenWrapper.js", @@ -2458,7 +2566,7 @@ "ignore": true }, { - "__docId__": 142, + "__docId__": 146, "kind": "variable", "name": "TaxonConceptWrapper", "memberof": "src/wrappers/SpecimenWrapper.js", @@ -2479,7 +2587,7 @@ "ignore": true }, { - "__docId__": 143, + "__docId__": 147, "kind": "variable", "name": "PhyxCacheManager", "memberof": "src/wrappers/SpecimenWrapper.js", @@ -2500,7 +2608,7 @@ "ignore": true }, { - "__docId__": 144, + "__docId__": 148, "kind": "class", "name": "SpecimenWrapper", "memberof": "src/wrappers/SpecimenWrapper.js", @@ -2515,7 +2623,7 @@ "interface": false }, { - "__docId__": 145, + "__docId__": 149, "kind": "get", "name": "TYPE_SPECIMEN", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2533,7 +2641,7 @@ } }, { - "__docId__": 146, + "__docId__": 150, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2546,7 +2654,7 @@ "lineNumber": 31 }, { - "__docId__": 147, + "__docId__": 151, "kind": "member", "name": "specimen", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2563,7 +2671,37 @@ } }, { - "__docId__": 148, + "__docId__": 152, + "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper.normalize", + "access": "public", + "description": "Normalize the specified specimen.", + "lineNumber": 39, + "params": [ + { + "nullable": null, + "types": [ + "*" + ], + "spread": false, + "optional": false, + "name": "specimen", + "description": "A specimen to be normalized." + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 153, "kind": "method", "name": "fromOccurrenceID", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2573,7 +2711,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper.fromOccurrenceID", "access": "public", "description": "Parse the provided occurrence ID. The two expected formats are:\n - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n (in which case, we ignore the first two \"components\" here)\n - '[institutionCode]:[collectionCode]:[catalogNumber]'", - "lineNumber": 41, + "lineNumber": 60, "params": [ { "name": "occurrenceID", @@ -2598,7 +2736,7 @@ } }, { - "__docId__": 149, + "__docId__": 154, "kind": "get", "name": "catalogNumber", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2608,7 +2746,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#catalogNumber", "access": "public", "description": "Get the catalogNumber if present.", - "lineNumber": 93, + "lineNumber": 112, "type": { "types": [ "*" @@ -2616,7 +2754,7 @@ } }, { - "__docId__": 150, + "__docId__": 155, "kind": "get", "name": "institutionCode", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2626,7 +2764,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#institutionCode", "access": "public", "description": "Get the institutionCode if present.", - "lineNumber": 109, + "lineNumber": 128, "type": { "types": [ "*" @@ -2634,7 +2772,7 @@ } }, { - "__docId__": 151, + "__docId__": 156, "kind": "get", "name": "collectionCode", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2644,7 +2782,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#collectionCode", "access": "public", "description": "Get the collectionCode if present.", - "lineNumber": 125, + "lineNumber": 144, "type": { "types": [ "*" @@ -2652,7 +2790,7 @@ } }, { - "__docId__": 152, + "__docId__": 157, "kind": "get", "name": "occurrenceID", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2662,7 +2800,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#occurrenceID", "access": "public", "description": "Return the occurrence ID of this specimen, if we have one. Otherwise, we\nattempt to construct one in the form:\n \"urn:catalog:\" + institutionCode (if present) + ':' +\n collectionCode (if present) + ':' + catalogNumber (if present)", - "lineNumber": 144, + "lineNumber": 163, "type": { "types": [ "*" @@ -2670,7 +2808,7 @@ } }, { - "__docId__": 153, + "__docId__": 158, "kind": "get", "name": "basisOfRecord", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2680,7 +2818,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#basisOfRecord", "access": "public", "description": "Return the basis of record, if one is present.", - "lineNumber": 171, + "lineNumber": 190, "type": { "types": [ "*" @@ -2688,7 +2826,7 @@ } }, { - "__docId__": 154, + "__docId__": 159, "kind": "set", "name": "basisOfRecord", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2698,10 +2836,10 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#basisOfRecord", "access": "public", "description": "Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\nrecommended values.", - "lineNumber": 180 + "lineNumber": 199 }, { - "__docId__": 155, + "__docId__": 160, "kind": "get", "name": "taxonConcept", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2711,7 +2849,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#taxonConcept", "access": "public", "description": "Return this specimen as a taxon concept if it contains taxon name information.", - "lineNumber": 185, + "lineNumber": 204, "type": { "types": [ "*" @@ -2719,7 +2857,7 @@ } }, { - "__docId__": 156, + "__docId__": 161, "kind": "get", "name": "label", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2729,7 +2867,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#label", "access": "public", "description": "Return a label for this specimen.", - "lineNumber": 192, + "lineNumber": 211, "type": { "types": [ "string" @@ -2737,7 +2875,7 @@ } }, { - "__docId__": 157, + "__docId__": 162, "kind": "get", "name": "asOWLEquivClass", "memberof": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper", @@ -2747,7 +2885,7 @@ "longname": "src/wrappers/SpecimenWrapper.js~SpecimenWrapper#asOWLEquivClass", "access": "public", "description": "Return this specimen as an equivalentClass expression.", - "lineNumber": 207, + "lineNumber": 226, "type": { "types": [ "{\"@type\": string, \"onProperty\": *, \"hasValue\": *}" @@ -2755,10 +2893,10 @@ } }, { - "__docId__": 158, + "__docId__": 163, "kind": "file", "name": "src/wrappers/TaxonConceptWrapper.js", - "content": "/** Utility functions. */\nconst { has } = require('lodash');\n\n/** List of OWL/RDF terms we use. */\nconst owlterms = require('../utils/owlterms');\n\n/** For parsing scientific names. */\nconst { TaxonNameWrapper } = require('./TaxonNameWrapper');\n\n/**\n * The TaxonConceptWrapper wraps taxon concepts. These are taxonomic units with\n * a type of TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT. They are based on the\n * Taxon Concept ontology at https://github.com/tdwg/ontology/tree/master/ontology/voc.\n *\n * A taxon concept:\n * - SHOULD have a hasName property indicating the name this taxon refers to.\n * - MAY have accordingTo, describedBy or circumscribedBy to indicate how this\n * taxon concept should be circumscribed. If none of these are present,\n * this taxonomic unit will be considered a taxon rather than a taxon concept\n * (i.e. as a nominal taxon concept, as in https://github.com/darwin-sw/dsw/wiki/ClassTaxon).\n * - MAY have nameString and accordingToString properties. We will fall back\n * to these properties if hasName or accordingTo are missing.\n */\n\nclass TaxonConceptWrapper {\n /** The @type of a taxon or taxon concept. */\n static get TYPE_TAXON_CONCEPT() {\n return owlterms.TDWG_VOC_TAXON_CONCEPT;\n }\n\n /** Create a TaxonConceptWrapper around a taxon concept. */\n constructor(tunit, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n this.tunit = tunit;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Return the taxon name of this taxon concept (if any) as an object.\n */\n get taxonName() {\n // Do we have any names as taxon name objects?\n if (has(this.tunit, 'hasName')) return this.tunit.hasName;\n\n // Do we have a nameString with a taxon name as string?\n if (has(this.tunit, 'nameString')) return TaxonNameWrapper.fromVerbatimName(this.tunit.nameString, this.defaultNomenCode);\n\n // If not, we have no name!\n return undefined;\n }\n\n /**\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n */\n get nameComplete() {\n // Do we have any names as taxon name objects?\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nameComplete;\n\n // Do we have a nameString with a taxon name as string?\n if (has(this.tunit, 'nameString')) return TaxonNameWrapper.fromVerbatimName(this.tunit.nameString, this.defaultNomenCode).nameComplete;\n\n // If not, we have no name!\n return undefined;\n }\n\n /**\n * Return the nomenclatural code of this taxon concept as a string.\n */\n get nomenCode() {\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nomenclaturalCode;\n\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Return the nomenclatural code of this taxon concept as an object.\n */\n get nomenCodeDetails() {\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nomenclaturalCodeDetails;\n\n return TaxonNameWrapper.getNomenCodeDetails(owlterms.UNKNOWN_CODE);\n }\n\n /**\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n */\n get accordingTo() {\n // Do we have any accordingTo information?\n if (has(this.tunit, 'accordingTo')) return this.type.accordingTo;\n\n // Do we have an accordingToString?\n if (has(this.tunit, 'accordingToString')) return this.type.accordingToString;\n\n // If not, we have no accodingTo information!\n return undefined;\n }\n\n /**\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n */\n get accordingToString() {\n // Do we have any accordingTo information?\n if (has(this.tunit, 'accordingTo')) return JSON.stringify(this.type.accordingTo);\n\n // Do we have an accordingToString?\n if (has(this.tunit, 'accordingToString')) return this.type.accordingToString;\n\n // If not, we have no accodingTo information!\n return undefined;\n }\n\n /**\n * Return the label of this taxon concept.\n */\n get label() {\n // If we're wrapping a taxonName, use its label.\n if (this.taxonName) {\n // Do we also have accordingTo information?\n if (this.accordingToString) {\n return `${new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).label} sensu ${this.accordingToString}`;\n }\n\n return new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).label;\n }\n\n return undefined;\n }\n\n /**\n * Given a node label, attempt to parse it as a scientific name.\n *\n * Note that this is NOT memoized -- you should really be using\n * TaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\n * than calling this directly.\n *\n * @return A taxonomic unit that corresponds to this taxon concept.\n */\n static fromLabel(nodeLabel, nomenCode = owlterms.UNKNOWN_CODE) {\n if (nodeLabel === undefined || nodeLabel === null || nodeLabel.trim() === '') return undefined;\n\n // Check if this label can be divided into a name and a sensu/sec component.\n const match = /^\\s*(.*)\\s+(?:sec|sensu)\\.?\\s+(.*)\\s*$/.exec(nodeLabel);\n let accordingTo;\n if (match) {\n accordingTo = match[2];\n }\n\n // Can we parse it as a taxon name? If not, we will return undefined.\n const taxonName = TaxonNameWrapper.fromVerbatimName(nodeLabel, nomenCode);\n if (taxonName) {\n return TaxonConceptWrapper.wrapTaxonName(taxonName, accordingTo);\n }\n\n // Couldn't parse it at all.\n return undefined;\n }\n\n /** Wrap a taxon name with a particular TaxonName object and an accordingTo (string). */\n static wrapTaxonName(taxonName, accordingTo) {\n const result = {\n '@type': TaxonConceptWrapper.TYPE_TAXON_CONCEPT,\n hasName: taxonName,\n };\n if (accordingTo) result.accordingTo = accordingTo;\n return result;\n }\n\n /**\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n */\n get asOWLEquivClass() {\n // Without a taxonomicName, we can't do anything.\n if (!this.taxonName) return undefined;\n\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).asOWLEquivClass,\n };\n }\n}\n\nmodule.exports = {\n TaxonConceptWrapper,\n};\n", + "content": "/** Utility functions. */\nconst { has } = require('lodash');\n\n/** List of OWL/RDF terms we use. */\nconst owlterms = require('../utils/owlterms');\n\n/** For parsing scientific names. */\nconst { TaxonNameWrapper } = require('./TaxonNameWrapper');\n\n/**\n * The TaxonConceptWrapper wraps taxon concepts. These are taxonomic units with\n * a type of TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT. They are based on the\n * Taxon Concept ontology at https://github.com/tdwg/ontology/tree/master/ontology/voc.\n *\n * A taxon concept:\n * - SHOULD have a hasName property indicating the name this taxon refers to.\n * - MAY have accordingTo, describedBy or circumscribedBy to indicate how this\n * taxon concept should be circumscribed. If none of these are present,\n * this taxonomic unit will be considered a taxon rather than a taxon concept\n * (i.e. as a nominal taxon concept, as in https://github.com/darwin-sw/dsw/wiki/ClassTaxon).\n * - MAY have nameString and accordingToString properties. We will fall back\n * to these properties if hasName or accordingTo are missing.\n */\n\nclass TaxonConceptWrapper {\n /** The @type of a taxon or taxon concept. */\n static get TYPE_TAXON_CONCEPT() {\n return owlterms.TDWG_VOC_TAXON_CONCEPT;\n }\n\n /** Create a TaxonConceptWrapper around a taxon concept. */\n constructor(tunit, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n this.tunit = tunit;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Normalize the specified taxon concept.\n * @param tc A taxon concept to be normalized.\n */\n static normalize(tc) {\n const wrapped = new TaxonConceptWrapper(tc);\n const normalizedTC = {\n '@type': TaxonConceptWrapper.TYPE_TAXON_CONCEPT,\n label: wrapped.label,\n hasName: TaxonNameWrapper.normalize(wrapped.taxonName),\n nameString: wrapped.taxonName.nameComplete,\n accordingTo: wrapped.accordingTo,\n };\n if ('@id' in tc) normalizedTC['@id'] = tc['@id'];\n return normalizedTC;\n }\n\n /**\n * Return the taxon name of this taxon concept (if any) as an object.\n */\n get taxonName() {\n // Do we have any names as taxon name objects?\n if (has(this.tunit, 'hasName')) return this.tunit.hasName;\n\n // Do we have a nameString with a taxon name as string?\n if (has(this.tunit, 'nameString')) return TaxonNameWrapper.fromVerbatimName(this.tunit.nameString, this.defaultNomenCode);\n\n // If not, we have no name!\n return undefined;\n }\n\n /**\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n */\n get nameComplete() {\n // Do we have any names as taxon name objects?\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nameComplete;\n\n // Do we have a nameString with a taxon name as string?\n if (has(this.tunit, 'nameString')) return TaxonNameWrapper.fromVerbatimName(this.tunit.nameString, this.defaultNomenCode).nameComplete;\n\n // If not, we have no name!\n return undefined;\n }\n\n /**\n * Return the nomenclatural code of this taxon concept as a string.\n */\n get nomenCode() {\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nomenclaturalCode;\n\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Return the nomenclatural code of this taxon concept as an object.\n */\n get nomenCodeDetails() {\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nomenclaturalCodeDetails;\n\n return TaxonNameWrapper.getNomenCodeDetails(owlterms.UNKNOWN_CODE);\n }\n\n /**\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n */\n get accordingTo() {\n // Do we have any accordingTo information?\n if (has(this.tunit, 'accordingTo')) return this.tunit.accordingTo;\n\n // Do we have an accordingToString?\n if (has(this.tunit, 'accordingToString')) return this.tunit.accordingToString;\n\n // If not, we have no accodingTo information!\n return undefined;\n }\n\n /**\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n */\n get accordingToString() {\n // Do we have any accordingTo information?\n if (has(this.tunit, 'accordingTo')) return JSON.stringify(this.tunit.accordingTo);\n\n // Do we have an accordingToString?\n if (has(this.tunit, 'accordingToString')) return this.tunit.accordingToString;\n\n // If not, we have no accodingTo information!\n return undefined;\n }\n\n /**\n * Return the label of this taxon concept.\n */\n get label() {\n // If we're wrapping a taxonName, use its label.\n if (this.taxonName) {\n // Do we also have accordingTo information?\n if (this.accordingToString) {\n return `${new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).label} sensu ${this.accordingToString}`;\n }\n\n return new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).label;\n }\n\n return undefined;\n }\n\n /**\n * Given a node label, attempt to parse it as a scientific name.\n *\n * Note that this is NOT memoized -- you should really be using\n * TaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\n * than calling this directly.\n *\n * @return A taxonomic unit that corresponds to this taxon concept.\n */\n static fromLabel(nodeLabel, nomenCode = owlterms.UNKNOWN_CODE) {\n if (nodeLabel === undefined || nodeLabel === null || nodeLabel.trim() === '') return undefined;\n\n // Check if this label can be divided into a name and a sensu/sec component.\n const match = /^\\s*(.*)\\s+(?:sec|sensu)\\.?\\s+(.*)\\s*$/.exec(nodeLabel);\n let accordingTo;\n if (match) {\n accordingTo = match[2];\n }\n\n // Can we parse it as a taxon name? If not, we will return undefined.\n const taxonName = TaxonNameWrapper.fromVerbatimName(nodeLabel, nomenCode);\n if (taxonName) {\n return TaxonConceptWrapper.wrapTaxonName(taxonName, accordingTo);\n }\n\n // Couldn't parse it at all.\n return undefined;\n }\n\n /** Wrap a taxon name with a particular TaxonName object and an accordingTo (string). */\n static wrapTaxonName(taxonName, accordingTo) {\n const result = {\n '@type': TaxonConceptWrapper.TYPE_TAXON_CONCEPT,\n hasName: taxonName,\n };\n if (accordingTo) result.accordingTo = accordingTo;\n return result;\n }\n\n /**\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n */\n get asOWLEquivClass() {\n // Without a taxonomicName, we can't do anything.\n if (!this.taxonName) return undefined;\n\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).asOWLEquivClass,\n };\n }\n}\n\nmodule.exports = {\n TaxonConceptWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/TaxonConceptWrapper.js", "access": "public", @@ -2766,7 +2904,7 @@ "lineNumber": 1 }, { - "__docId__": 159, + "__docId__": 164, "kind": "variable", "name": "has", "memberof": "src/wrappers/TaxonConceptWrapper.js", @@ -2787,7 +2925,7 @@ "ignore": true }, { - "__docId__": 160, + "__docId__": 165, "kind": "variable", "name": "TaxonNameWrapper", "memberof": "src/wrappers/TaxonConceptWrapper.js", @@ -2808,7 +2946,7 @@ "ignore": true }, { - "__docId__": 161, + "__docId__": 166, "kind": "class", "name": "TaxonConceptWrapper", "memberof": "src/wrappers/TaxonConceptWrapper.js", @@ -2823,7 +2961,7 @@ "interface": false }, { - "__docId__": 162, + "__docId__": 167, "kind": "get", "name": "TYPE_TAXON_CONCEPT", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2841,7 +2979,7 @@ } }, { - "__docId__": 163, + "__docId__": 168, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2854,7 +2992,7 @@ "lineNumber": 34 }, { - "__docId__": 164, + "__docId__": 169, "kind": "member", "name": "tunit", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2871,7 +3009,7 @@ } }, { - "__docId__": 165, + "__docId__": 170, "kind": "member", "name": "defaultNomenCode", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2888,7 +3026,37 @@ } }, { - "__docId__": 166, + "__docId__": 171, + "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.normalize", + "access": "public", + "description": "Normalize the specified taxon concept.", + "lineNumber": 43, + "params": [ + { + "nullable": null, + "types": [ + "*" + ], + "spread": false, + "optional": false, + "name": "tc", + "description": "A taxon concept to be normalized." + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 172, "kind": "get", "name": "taxonName", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2898,7 +3066,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#taxonName", "access": "public", "description": "Return the taxon name of this taxon concept (if any) as an object.", - "lineNumber": 42, + "lineNumber": 59, "type": { "types": [ "*" @@ -2906,7 +3074,7 @@ } }, { - "__docId__": 167, + "__docId__": 173, "kind": "get", "name": "nameComplete", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2916,7 +3084,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#nameComplete", "access": "public", "description": "Return the complete taxon name of this taxon concept (if any), which is the\nuninomial, binomial or trinomial name.", - "lineNumber": 57, + "lineNumber": 74, "type": { "types": [ "*" @@ -2924,7 +3092,7 @@ } }, { - "__docId__": 168, + "__docId__": 174, "kind": "get", "name": "nomenCode", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2934,7 +3102,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#nomenCode", "access": "public", "description": "Return the nomenclatural code of this taxon concept as a string.", - "lineNumber": 71, + "lineNumber": 88, "type": { "types": [ "*" @@ -2942,7 +3110,7 @@ } }, { - "__docId__": 169, + "__docId__": 175, "kind": "get", "name": "nomenCodeDetails", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2952,7 +3120,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#nomenCodeDetails", "access": "public", "description": "Return the nomenclatural code of this taxon concept as an object.", - "lineNumber": 80, + "lineNumber": 97, "type": { "types": [ "*" @@ -2960,7 +3128,7 @@ } }, { - "__docId__": 170, + "__docId__": 176, "kind": "get", "name": "accordingTo", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2970,7 +3138,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#accordingTo", "access": "public", "description": "Return the accordingTo information (if any) as an object.\n\nFor now, we return this verbatim. Once we close #15, we should parse raw labels\nwith a CitationWrapper.", - "lineNumber": 92, + "lineNumber": 109, "type": { "types": [ "*" @@ -2978,7 +3146,7 @@ } }, { - "__docId__": 171, + "__docId__": 177, "kind": "get", "name": "accordingToString", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -2988,7 +3156,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#accordingToString", "access": "public", "description": "Return the accordingTo information (if any) as a string.\n\nFor now, we stringify objects by converting them into JSON strings. Once we\nclose #15, we will be able to generate a label using CitationWrapper.", - "lineNumber": 109, + "lineNumber": 126, "type": { "types": [ "*" @@ -2996,7 +3164,7 @@ } }, { - "__docId__": 172, + "__docId__": 178, "kind": "get", "name": "label", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -3006,7 +3174,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#label", "access": "public", "description": "Return the label of this taxon concept.", - "lineNumber": 123, + "lineNumber": 140, "type": { "types": [ "*" @@ -3014,7 +3182,7 @@ } }, { - "__docId__": 173, + "__docId__": 179, "kind": "method", "name": "fromLabel", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -3024,7 +3192,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.fromLabel", "access": "public", "description": "Given a node label, attempt to parse it as a scientific name.\n\nNote that this is NOT memoized -- you should really be using\nTaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\nthan calling this directly.", - "lineNumber": 146, + "lineNumber": 163, "return": { "nullable": null, "types": [ @@ -3050,7 +3218,7 @@ ] }, { - "__docId__": 174, + "__docId__": 180, "kind": "method", "name": "wrapTaxonName", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -3060,7 +3228,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.wrapTaxonName", "access": "public", "description": "Wrap a taxon name with a particular TaxonName object and an accordingTo (string).", - "lineNumber": 167, + "lineNumber": 184, "params": [ { "name": "taxonName", @@ -3082,7 +3250,7 @@ } }, { - "__docId__": 175, + "__docId__": 181, "kind": "get", "name": "asOWLEquivClass", "memberof": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper", @@ -3092,7 +3260,7 @@ "longname": "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper#asOWLEquivClass", "access": "public", "description": "Return how this class should look in an OWL equivalentClass expression.\n\nNote that we don't include the accordingTo information in this\nquery, since we don't have a useful way to use that during OWL reasoning.", - "lineNumber": 182, + "lineNumber": 199, "type": { "types": [ "{\"@type\": string, \"onProperty\": *, \"someValuesFrom\": *}" @@ -3100,10 +3268,10 @@ } }, { - "__docId__": 176, + "__docId__": 182, "kind": "file", "name": "src/wrappers/TaxonNameWrapper.js", - "content": "/** Utility functions. */\nconst { has, cloneDeep, isArray } = require('lodash');\n\n/** OWL/RDF terms. */\nconst owlterms = require('../utils/owlterms');\n\n/** We need the cache manager to memoize parsing scientific names. */\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n */\nclass TaxonNameWrapper {\n /**\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n */\n constructor(txname, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n if (txname === undefined) throw new Error('TaxonNameWrapper tried to wrap undefined');\n this.txname = txname;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * The type associated with these taxonName objects.\n */\n static get TYPE_TAXON_NAME() {\n return owlterms.TDWG_VOC_TAXON_NAME;\n }\n\n /**\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n */\n static get UNKNOWN_CODE() {\n return owlterms.UNKNOWN_CODE;\n }\n\n /* Directly access IRIs for nomenclatural codes. */\n static get ICZN_CODE() { return owlterms.ICZN_CODE; }\n\n static get ICN_CODE() { return owlterms.ICN_CODE; }\n\n static get ICNP_CODE() { return owlterms.ICNP_CODE; }\n\n static get ICTV_CODE() { return owlterms.ICTV_CODE; }\n\n static get ICNCP_CODE() { return owlterms.ICNCP_CODE; }\n\n /**\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n */\n static getNomenclaturalCodes() {\n return [\n // Note: the unknown code needs to be the first one in this list.\n {\n iri: owlterms.UNKNOWN_CODE,\n shortName: 'Code not known',\n label: 'Nomenclatural code not known',\n title: 'Nomenclatural code not known',\n },\n {\n iri: owlterms.ICZN_CODE,\n shortName: 'ICZN',\n label: 'Animals (ICZN)',\n title: 'International Code of Zoological Nomenclature',\n },\n {\n iri: owlterms.ICN_CODE,\n shortName: 'ICN',\n label: 'Algae, fungi and plants (ICN, previously ICBN)',\n title: 'International Code of Nomenclature for algae, fungi, and plants',\n },\n {\n iri: owlterms.ICNP_CODE,\n shortName: 'ICNP',\n label: 'Prokaryotes (ICNP)',\n title: 'International Code of Nomenclature of Prokaryotes',\n },\n {\n iri: owlterms.ICTV_CODE,\n shortName: 'ICTV',\n label: 'Viruses (ICTV)',\n title: 'International Committee on Taxonomy of Viruses',\n },\n {\n iri: owlterms.ICNCP_CODE,\n shortName: 'ICNCP',\n label: 'Cultivated plants (ICNCP)',\n title: 'International Code of Cultivated Plants',\n },\n ];\n }\n\n /**\n * Returns the nomenclatural code entry for a code.\n */\n static getNomenCodeDetails(nomenCode) {\n const codes = TaxonNameWrapper.getNomenclaturalCodes();\n\n // If the nomenCode provided is owlterms.UNKNOWN_CODE,\n // return that entry.\n if (nomenCode === owlterms.UNKNOWN_CODE) {\n return codes[0];\n }\n\n // Look for the entry with the same IRI as the provided IRI.\n const matchingCode = codes\n .find(code => (code.iri || '').toLowerCase() === nomenCode.toLowerCase());\n if (matchingCode) return matchingCode;\n return undefined;\n }\n\n /**\n * Returns the nomenclatural code of this taxon name.\n */\n get nomenclaturalCode() {\n return this.txname.nomenclaturalCode || this.defaultNomenCode;\n }\n\n /**\n * Returns the nomenclatural code of this taxon name as a IRI.\n */\n get nomenclaturalCodeDetails() {\n const nomenCode = this.nomenclaturalCode;\n const nomenObj = TaxonNameWrapper.getNomenCodeDetails(nomenCode);\n if (!nomenObj) return undefined;\n\n return nomenObj;\n }\n\n /**\n * Set the nomenclatural code of this taxon name.\n */\n set nomenclaturalCode(nomenCode) {\n this.txname.nomenclaturalCode = nomenCode;\n }\n\n /**\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n */\n static fromVerbatimName(verbatimName, nomenCode = owlterms.UNKNOWN_CODE) {\n // Have we already parsed this verbatim name?\n if (PhyxCacheManager.has(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName)) {\n return PhyxCacheManager.get(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName);\n }\n\n // Use a regular expression to parse the verbatimName.\n\n // Attempt 1. Look for a trinomial name.\n let txname;\n let results = /^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)\\s*([a-z-]+)\\b/.exec(verbatimName);\n\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: `${results[1]} ${results[2]} ${results[3]}`.trim(),\n genusPart: results[1],\n specificEpithet: results[2],\n infraspecificEpithet: results[3],\n };\n }\n\n // Attempt 2. Look for a binomial name.\n if (!txname) {\n results = /^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)/.exec(verbatimName);\n\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: `${results[1]} ${results[2]}`.trim(),\n genusPart: results[1],\n specificEpithet: results[2],\n };\n }\n }\n\n // Attempt 3. Look for a uninomial name.\n if (!txname) {\n // Is it a uninomial name?\n results = /^([A-Z][a-z]+)(?:[_\\s]|\\b)/.exec(verbatimName);\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: results[1],\n uninomial: results[1],\n };\n }\n }\n\n // Add a nomenclatural code if possible.\n if (txname && nomenCode) {\n txname.nomenclaturalCode = nomenCode;\n }\n\n // Store in the cache.\n if (txname !== undefined) {\n PhyxCacheManager.put(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName, txname);\n }\n\n return txname;\n }\n\n /**\n * Return the label of this scientific name.\n */\n get label() {\n return this.txname.label || this.nameComplete;\n }\n\n /**\n * Set the label of this scientific name.\n */\n set label(lab) {\n this.txname.label = lab;\n if (!this.nameComplete) {\n // If we don't have a nameComplete, treat this as the name complete.\n this.nameComplete = lab;\n }\n }\n\n /**\n * Return the verbatim name of this taxon name.\n */\n get verbatimName() {\n return this.txname.label;\n }\n\n /*\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n */\n get nameComplete() {\n return this.txname.nameComplete\n || this.trinomialName\n || this.binomialName\n || this.uninomialName;\n }\n\n /**\n * Set the complete name. To do this, we re-parse the provided name.\n */\n set nameComplete(name) {\n this.txname = TaxonNameWrapper.fromVerbatimName(name, this.nomenclaturalCode);\n }\n\n /** Return the uninomial name if there is one. */\n get uninomial() {\n if (this.txname.uninomial) return this.txname.uninomial;\n\n // If there is no genus but there is a scientificName, try to extract a genus\n // from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.txname.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'uninomial')) return txname.uninomial;\n }\n\n return undefined;\n }\n\n /** Set the uninomial name. */\n set uninomial(uninom) {\n this.txname.uninomial = uninom;\n this.txname.nameComplete = uninom;\n }\n\n /** Return the binomial name if available. */\n get binomialName() {\n // Get the binomial name. Constructed from the genus and specific epithet\n // if available.\n if (this.genusPart === undefined || this.specificEpithet === undefined) return undefined;\n return `${this.genusPart} ${this.specificEpithet}`;\n }\n\n /** Set the binomial name. */\n set binomialName(binom) {\n this.txname.uninomial = undefined;\n this.txname.nameComplete = binom;\n }\n\n /** Return the trinomial name if available. */\n get trinomialName() {\n if (\n this.infraspecificEpithet === undefined\n || this.specificEpithet === undefined\n || this.genusPart === undefined\n ) return undefined;\n return `${this.genusPart} ${this.specificEpithet} ${this.infraspecificEpithet}`;\n }\n\n /** Set the trinomial name. */\n set trinomialName(trinom) {\n this.txname.uninomial = undefined;\n this.txname.nameComplete = trinom;\n }\n\n /** Return the genus part of this scientific name if available. */\n get genusPart() {\n // Try to read the genus if available.\n if (has(this.txname, 'genusPart')) return this.txname.genusPart;\n\n // If there is no genus but there is a scientificName, try to extract a genus\n // from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.txname.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'genusPart')) return txname.genusPart;\n }\n\n return undefined;\n }\n\n /** Set the genus part of this name. */\n set genusPart(genus) {\n this.txname.genusPart = genus;\n if (this.specificEpithet) {\n if (this.infraspecificEpithet) {\n this.txname.nameComplete = `${genus} ${this.specificEpithet} ${this.infraspecificEpithet}`;\n } else {\n this.txname.nameComplete = `${genus} ${this.specificEpithet}`;\n }\n }\n }\n\n /** Return the specific epithet of this scientific name if available. */\n get specificEpithet() {\n // Try to read the specific epithet if available.\n if (has(this.txname, 'specificEpithet')) return this.txname.specificEpithet;\n\n // If there is no specific epithet but there is a scientificName, try to\n // extract a specific epithet from it.\n if (this.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'specificEpithet')) return txname.specificEpithet;\n }\n\n return undefined;\n }\n\n /** Set the specificEpithet part of this name. */\n set specificEpithet(epithet) {\n this.txname.specificEpithet = epithet;\n if (this.genusPart) {\n if (this.infraspecificEpithet) {\n this.txname.nameComplete = `${this.genusPart} ${epithet} ${this.infraspecificEpithet}`;\n } else {\n this.txname.nameComplete = `${this.genusPart} ${epithet}`;\n }\n }\n }\n\n /** Return the infraspecific epithet of this scientific name if available. */\n get infraspecificEpithet() {\n // Try to read the specific epithet if available.\n if (has(this.txname, 'infraspecificEpithet')) return this.txname.infraspecificEpithet;\n\n // If there is no specific epithet but there is a scientificName, try to\n // extract a specific epithet from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'infraspecificEpithet')) return txname.infraspecificEpithet;\n }\n\n return undefined;\n }\n\n /** Set the infraspecificEpithet part of this name. */\n set infraspecificEpithet(epithet) {\n this.txname.infraspecificEpithet = epithet;\n if (this.genusPart) {\n if (this.specificEpithet) {\n this.txname.nameComplete = `${this.genusPart} ${this.specificEpithet} ${epithet}`;\n } else {\n this.txname.nameComplete = `${this.genusPart} sp. ${epithet}`;\n }\n }\n }\n\n /**\n * Return this taxon name in an JSON-LD representation.\n */\n get asJSONLD() {\n const jsonld = cloneDeep(this.txname);\n\n // Make sure '@type' is an array.\n if (!has(jsonld, '@type')) jsonld['@type'] = [];\n if (!isArray(jsonld['@type'])) jsonld['@type'] = [jsonld['@type']];\n\n // Make it explicit that the type includes the nomenclaturalCode.\n const nomenCode = this.nomenclaturalCode;\n if (!jsonld['@type'].includes(nomenCode)) jsonld['@type'].push(nomenCode);\n\n return jsonld;\n }\n\n /**\n * Return this taxon name as an OWL equivalentClass expression.\n */\n get asOWLEquivClass() {\n // No complete name, can't return anything.\n if (!this.nameComplete) return undefined;\n\n // Do we have a nomenclaturalCode?\n if (!this.nomenclaturalCode) {\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n hasValue: this.nameComplete,\n };\n }\n\n // If we do have a nomenclatural code, incorporate that into the logical\n // expression as well.\n return {\n '@type': 'owl:Class',\n intersectionOf: [{\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n hasValue: this.nameComplete,\n }, {\n '@type': 'owl:Restriction',\n onProperty: owlterms.NOMENCLATURAL_CODE,\n hasValue: {\n '@id': this.nomenclaturalCode,\n },\n }],\n };\n }\n}\n\nmodule.exports = {\n TaxonNameWrapper,\n};\n", + "content": "/** Utility functions. */\nconst { has, cloneDeep, isArray } = require('lodash');\n\n/** OWL/RDF terms. */\nconst owlterms = require('../utils/owlterms');\n\n/** We need the cache manager to memoize parsing scientific names. */\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n */\nclass TaxonNameWrapper {\n /**\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n */\n constructor(txname, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n if (txname === undefined) throw new Error('TaxonNameWrapper tried to wrap undefined');\n this.txname = txname;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * The type associated with these taxonName objects.\n */\n static get TYPE_TAXON_NAME() {\n return owlterms.TDWG_VOC_TAXON_NAME;\n }\n\n /**\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n */\n static get UNKNOWN_CODE() {\n return owlterms.UNKNOWN_CODE;\n }\n\n /* Directly access IRIs for nomenclatural codes. */\n static get ICZN_CODE() { return owlterms.ICZN_CODE; }\n\n static get ICN_CODE() { return owlterms.ICN_CODE; }\n\n static get ICNP_CODE() { return owlterms.ICNP_CODE; }\n\n static get ICTV_CODE() { return owlterms.ICTV_CODE; }\n\n static get ICNCP_CODE() { return owlterms.ICNCP_CODE; }\n\n /**\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n */\n static getNomenclaturalCodes() {\n return [\n // Note: the unknown code needs to be the first one in this list.\n {\n iri: owlterms.UNKNOWN_CODE,\n shortName: 'Code not known',\n label: 'Nomenclatural code not known',\n title: 'Nomenclatural code not known',\n },\n {\n iri: owlterms.ICZN_CODE,\n shortName: 'ICZN',\n label: 'Animals (ICZN)',\n title: 'International Code of Zoological Nomenclature',\n },\n {\n iri: owlterms.ICN_CODE,\n shortName: 'ICN',\n label: 'Algae, fungi and plants (ICN, previously ICBN)',\n title: 'International Code of Nomenclature for algae, fungi, and plants',\n },\n {\n iri: owlterms.ICNP_CODE,\n shortName: 'ICNP',\n label: 'Prokaryotes (ICNP)',\n title: 'International Code of Nomenclature of Prokaryotes',\n },\n {\n iri: owlterms.ICTV_CODE,\n shortName: 'ICTV',\n label: 'Viruses (ICTV)',\n title: 'International Committee on Taxonomy of Viruses',\n },\n {\n iri: owlterms.ICNCP_CODE,\n shortName: 'ICNCP',\n label: 'Cultivated plants (ICNCP)',\n title: 'International Code of Cultivated Plants',\n },\n ];\n }\n\n /**\n * Returns the nomenclatural code entry for a code.\n */\n static getNomenCodeDetails(nomenCode) {\n const codes = TaxonNameWrapper.getNomenclaturalCodes();\n\n // If the nomenCode provided is owlterms.UNKNOWN_CODE,\n // return that entry.\n if (nomenCode === owlterms.UNKNOWN_CODE) {\n return codes[0];\n }\n\n // Look for the entry with the same IRI as the provided IRI.\n const matchingCode = codes\n .find(code => (code.iri || '').toLowerCase() === nomenCode.toLowerCase());\n if (matchingCode) return matchingCode;\n return undefined;\n }\n\n /**\n * Normalize the specified taxon name.\n * @param txname A taxon name to be normalized.\n */\n static normalize(txname) {\n const wrapped = new TaxonNameWrapper(txname);\n const normalizedTxname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n nomenclaturalCode: wrapped.nomenclaturalCode,\n label: wrapped.label,\n nameComplete: wrapped.nameComplete,\n genusPart: wrapped.genusPart,\n specificEpithet: wrapped.specificEpithet,\n infraspecificEpithet: wrapped.infraspecificEpithet,\n };\n if ('@id' in txname) normalizedTxname['@id'] = txname['@id'];\n return normalizedTxname;\n }\n\n /**\n * Returns the nomenclatural code of this taxon name.\n */\n get nomenclaturalCode() {\n return this.txname.nomenclaturalCode || this.defaultNomenCode;\n }\n\n /**\n * Returns the nomenclatural code of this taxon name as a IRI.\n */\n get nomenclaturalCodeDetails() {\n const nomenCode = this.nomenclaturalCode;\n const nomenObj = TaxonNameWrapper.getNomenCodeDetails(nomenCode);\n if (!nomenObj) return undefined;\n\n return nomenObj;\n }\n\n /**\n * Set the nomenclatural code of this taxon name.\n */\n set nomenclaturalCode(nomenCode) {\n this.txname.nomenclaturalCode = nomenCode;\n }\n\n /**\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n */\n static fromVerbatimName(verbatimName, nomenCode = owlterms.UNKNOWN_CODE) {\n // Have we already parsed this verbatim name?\n if (PhyxCacheManager.has(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName)) {\n return PhyxCacheManager.get(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName);\n }\n\n // Use a regular expression to parse the verbatimName.\n\n // Attempt 1. Look for a trinomial name.\n let txname;\n let results = /^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)\\s*([a-z-]+)\\b/.exec(verbatimName);\n\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: `${results[1]} ${results[2]} ${results[3]}`.trim(),\n genusPart: results[1],\n specificEpithet: results[2],\n infraspecificEpithet: results[3],\n };\n }\n\n // Attempt 2. Look for a binomial name.\n if (!txname) {\n results = /^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)/.exec(verbatimName);\n\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: `${results[1]} ${results[2]}`.trim(),\n genusPart: results[1],\n specificEpithet: results[2],\n };\n }\n }\n\n // Attempt 3. Look for a uninomial name.\n if (!txname) {\n // Is it a uninomial name?\n results = /^([A-Z][a-z]+)(?:[_\\s]|\\b)/.exec(verbatimName);\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: results[1],\n uninomial: results[1],\n };\n }\n }\n\n // Add a nomenclatural code if possible.\n if (txname && nomenCode) {\n txname.nomenclaturalCode = nomenCode;\n }\n\n // Store in the cache.\n if (txname !== undefined) {\n PhyxCacheManager.put(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName, txname);\n }\n\n return txname;\n }\n\n /**\n * Return the label of this scientific name.\n */\n get label() {\n return this.txname.label || this.nameComplete;\n }\n\n /**\n * Set the label of this scientific name.\n */\n set label(lab) {\n this.txname.label = lab;\n if (!this.nameComplete) {\n // If we don't have a nameComplete, treat this as the name complete.\n this.nameComplete = lab;\n }\n }\n\n /**\n * Return the verbatim name of this taxon name.\n */\n get verbatimName() {\n return this.txname.label;\n }\n\n /*\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n */\n get nameComplete() {\n return this.txname.nameComplete\n || this.trinomialName\n || this.binomialName\n || this.uninomialName;\n }\n\n /**\n * Set the complete name. To do this, we re-parse the provided name.\n */\n set nameComplete(name) {\n this.txname = TaxonNameWrapper.fromVerbatimName(name, this.nomenclaturalCode);\n }\n\n /** Return the uninomial name if there is one. */\n get uninomial() {\n if (this.txname.uninomial) return this.txname.uninomial;\n\n // If there is no genus but there is a scientificName, try to extract a genus\n // from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.txname.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'uninomial')) return txname.uninomial;\n }\n\n return undefined;\n }\n\n /** Set the uninomial name. */\n set uninomial(uninom) {\n this.txname.uninomial = uninom;\n this.txname.nameComplete = uninom;\n }\n\n /** Return the binomial name if available. */\n get binomialName() {\n // Get the binomial name. Constructed from the genus and specific epithet\n // if available.\n if (this.genusPart === undefined || this.specificEpithet === undefined) return undefined;\n return `${this.genusPart} ${this.specificEpithet}`;\n }\n\n /** Set the binomial name. */\n set binomialName(binom) {\n this.txname.uninomial = undefined;\n this.txname.nameComplete = binom;\n }\n\n /** Return the trinomial name if available. */\n get trinomialName() {\n if (\n this.infraspecificEpithet === undefined\n || this.specificEpithet === undefined\n || this.genusPart === undefined\n ) return undefined;\n return `${this.genusPart} ${this.specificEpithet} ${this.infraspecificEpithet}`;\n }\n\n /** Set the trinomial name. */\n set trinomialName(trinom) {\n this.txname.uninomial = undefined;\n this.txname.nameComplete = trinom;\n }\n\n /** Return the genus part of this scientific name if available. */\n get genusPart() {\n // Try to read the genus if available.\n if (has(this.txname, 'genusPart')) return this.txname.genusPart;\n\n // If there is no genus but there is a scientificName, try to extract a genus\n // from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.txname.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'genusPart')) return txname.genusPart;\n }\n\n return undefined;\n }\n\n /** Set the genus part of this name. */\n set genusPart(genus) {\n this.txname.genusPart = genus;\n if (this.specificEpithet) {\n if (this.infraspecificEpithet) {\n this.txname.nameComplete = `${genus} ${this.specificEpithet} ${this.infraspecificEpithet}`;\n } else {\n this.txname.nameComplete = `${genus} ${this.specificEpithet}`;\n }\n }\n }\n\n /** Return the specific epithet of this scientific name if available. */\n get specificEpithet() {\n // Try to read the specific epithet if available.\n if (has(this.txname, 'specificEpithet')) return this.txname.specificEpithet;\n\n // If there is no specific epithet but there is a scientificName, try to\n // extract a specific epithet from it.\n if (this.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'specificEpithet')) return txname.specificEpithet;\n }\n\n return undefined;\n }\n\n /** Set the specificEpithet part of this name. */\n set specificEpithet(epithet) {\n this.txname.specificEpithet = epithet;\n if (this.genusPart) {\n if (this.infraspecificEpithet) {\n this.txname.nameComplete = `${this.genusPart} ${epithet} ${this.infraspecificEpithet}`;\n } else {\n this.txname.nameComplete = `${this.genusPart} ${epithet}`;\n }\n }\n }\n\n /** Return the infraspecific epithet of this scientific name if available. */\n get infraspecificEpithet() {\n // Try to read the specific epithet if available.\n if (has(this.txname, 'infraspecificEpithet')) return this.txname.infraspecificEpithet;\n\n // If there is no specific epithet but there is a scientificName, try to\n // extract a specific epithet from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'infraspecificEpithet')) return txname.infraspecificEpithet;\n }\n\n return undefined;\n }\n\n /** Set the infraspecificEpithet part of this name. */\n set infraspecificEpithet(epithet) {\n this.txname.infraspecificEpithet = epithet;\n if (this.genusPart) {\n if (this.specificEpithet) {\n this.txname.nameComplete = `${this.genusPart} ${this.specificEpithet} ${epithet}`;\n } else {\n this.txname.nameComplete = `${this.genusPart} sp. ${epithet}`;\n }\n }\n }\n\n /**\n * Return this taxon name in an JSON-LD representation.\n */\n get asJSONLD() {\n const jsonld = cloneDeep(this.txname);\n\n // Make sure '@type' is an array.\n if (!has(jsonld, '@type')) jsonld['@type'] = [];\n if (!isArray(jsonld['@type'])) jsonld['@type'] = [jsonld['@type']];\n\n // Make it explicit that the type includes the nomenclaturalCode.\n const nomenCode = this.nomenclaturalCode;\n if (!jsonld['@type'].includes(nomenCode)) jsonld['@type'].push(nomenCode);\n\n return jsonld;\n }\n\n /**\n * Return this taxon name as an OWL equivalentClass expression.\n */\n get asOWLEquivClass() {\n // No complete name, can't return anything.\n if (!this.nameComplete) return undefined;\n\n // Do we have a nomenclaturalCode?\n if (!this.nomenclaturalCode) {\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n hasValue: this.nameComplete,\n };\n }\n\n // If we do have a nomenclatural code, incorporate that into the logical\n // expression as well.\n return {\n '@type': 'owl:Class',\n intersectionOf: [{\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n hasValue: this.nameComplete,\n }, {\n '@type': 'owl:Restriction',\n onProperty: owlterms.NOMENCLATURAL_CODE,\n hasValue: {\n '@id': this.nomenclaturalCode,\n },\n }],\n };\n }\n}\n\nmodule.exports = {\n TaxonNameWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/TaxonNameWrapper.js", "access": "public", @@ -3111,7 +3279,7 @@ "lineNumber": 1 }, { - "__docId__": 177, + "__docId__": 183, "kind": "variable", "name": "has", "memberof": "src/wrappers/TaxonNameWrapper.js", @@ -3132,7 +3300,7 @@ "ignore": true }, { - "__docId__": 178, + "__docId__": 184, "kind": "variable", "name": "PhyxCacheManager", "memberof": "src/wrappers/TaxonNameWrapper.js", @@ -3153,7 +3321,7 @@ "ignore": true }, { - "__docId__": 179, + "__docId__": 185, "kind": "class", "name": "TaxonNameWrapper", "memberof": "src/wrappers/TaxonNameWrapper.js", @@ -3168,7 +3336,7 @@ "interface": false }, { - "__docId__": 180, + "__docId__": 186, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3181,7 +3349,7 @@ "lineNumber": 45 }, { - "__docId__": 181, + "__docId__": 187, "kind": "member", "name": "txname", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3198,7 +3366,7 @@ } }, { - "__docId__": 182, + "__docId__": 188, "kind": "member", "name": "defaultNomenCode", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3215,7 +3383,7 @@ } }, { - "__docId__": 183, + "__docId__": 189, "kind": "get", "name": "TYPE_TAXON_NAME", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3233,7 +3401,7 @@ } }, { - "__docId__": 184, + "__docId__": 190, "kind": "get", "name": "UNKNOWN_CODE", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3251,7 +3419,7 @@ } }, { - "__docId__": 185, + "__docId__": 191, "kind": "get", "name": "ICZN_CODE", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3270,7 +3438,7 @@ } }, { - "__docId__": 186, + "__docId__": 192, "kind": "get", "name": "ICN_CODE", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3289,7 +3457,7 @@ } }, { - "__docId__": 187, + "__docId__": 193, "kind": "get", "name": "ICNP_CODE", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3308,7 +3476,7 @@ } }, { - "__docId__": 188, + "__docId__": 194, "kind": "get", "name": "ICTV_CODE", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3327,7 +3495,7 @@ } }, { - "__docId__": 189, + "__docId__": 195, "kind": "get", "name": "ICNCP_CODE", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3346,7 +3514,7 @@ } }, { - "__docId__": 190, + "__docId__": 196, "kind": "method", "name": "getNomenclaturalCodes", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3365,7 +3533,7 @@ } }, { - "__docId__": 191, + "__docId__": 197, "kind": "method", "name": "getNomenCodeDetails", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3391,7 +3559,37 @@ } }, { - "__docId__": 192, + "__docId__": 198, + "kind": "method", + "name": "normalize", + "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", + "generator": false, + "async": false, + "static": true, + "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.normalize", + "access": "public", + "description": "Normalize the specified taxon name.", + "lineNumber": 152, + "params": [ + { + "nullable": null, + "types": [ + "*" + ], + "spread": false, + "optional": false, + "name": "txname", + "description": "A taxon name to be normalized." + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 199, "kind": "get", "name": "nomenclaturalCode", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3401,7 +3599,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#nomenclaturalCode", "access": "public", "description": "Returns the nomenclatural code of this taxon name.", - "lineNumber": 151, + "lineNumber": 170, "type": { "types": [ "*" @@ -3409,7 +3607,7 @@ } }, { - "__docId__": 193, + "__docId__": 200, "kind": "get", "name": "nomenclaturalCodeDetails", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3419,7 +3617,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#nomenclaturalCodeDetails", "access": "public", "description": "Returns the nomenclatural code of this taxon name as a IRI.", - "lineNumber": 158, + "lineNumber": 177, "type": { "types": [ "*" @@ -3427,7 +3625,7 @@ } }, { - "__docId__": 194, + "__docId__": 201, "kind": "set", "name": "nomenclaturalCode", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3437,10 +3635,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#nomenclaturalCode", "access": "public", "description": "Set the nomenclatural code of this taxon name.", - "lineNumber": 169 + "lineNumber": 188 }, { - "__docId__": 195, + "__docId__": 202, "kind": "method", "name": "fromVerbatimName", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3450,7 +3648,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.fromVerbatimName", "access": "public", "description": "Parses a verbatim taxon name into an (unwrapped) TaxonName.", - "lineNumber": 176, + "lineNumber": 195, "params": [ { "name": "verbatimName", @@ -3473,7 +3671,7 @@ } }, { - "__docId__": 196, + "__docId__": 203, "kind": "get", "name": "label", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3483,7 +3681,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#label", "access": "public", "description": "Return the label of this scientific name.", - "lineNumber": 244, + "lineNumber": 263, "type": { "types": [ "*" @@ -3491,7 +3689,7 @@ } }, { - "__docId__": 197, + "__docId__": 204, "kind": "set", "name": "label", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3501,10 +3699,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#label", "access": "public", "description": "Set the label of this scientific name.", - "lineNumber": 251 + "lineNumber": 270 }, { - "__docId__": 199, + "__docId__": 206, "kind": "get", "name": "verbatimName", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3514,7 +3712,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#verbatimName", "access": "public", "description": "Return the verbatim name of this taxon name.", - "lineNumber": 262, + "lineNumber": 281, "type": { "types": [ "*" @@ -3522,7 +3720,7 @@ } }, { - "__docId__": 200, + "__docId__": 207, "kind": "get", "name": "nameComplete", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3532,7 +3730,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#nameComplete", "access": "public", "description": null, - "lineNumber": 270, + "lineNumber": 289, "undocument": true, "type": { "types": [ @@ -3541,7 +3739,7 @@ } }, { - "__docId__": 201, + "__docId__": 208, "kind": "set", "name": "nameComplete", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3551,10 +3749,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#nameComplete", "access": "public", "description": "Set the complete name. To do this, we re-parse the provided name.", - "lineNumber": 280 + "lineNumber": 299 }, { - "__docId__": 203, + "__docId__": 210, "kind": "get", "name": "uninomial", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3564,7 +3762,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#uninomial", "access": "public", "description": "Return the uninomial name if there is one.", - "lineNumber": 285, + "lineNumber": 304, "type": { "types": [ "*" @@ -3572,7 +3770,7 @@ } }, { - "__docId__": 204, + "__docId__": 211, "kind": "set", "name": "uninomial", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3582,10 +3780,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#uninomial", "access": "public", "description": "Set the uninomial name.", - "lineNumber": 302 + "lineNumber": 321 }, { - "__docId__": 205, + "__docId__": 212, "kind": "get", "name": "binomialName", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3595,7 +3793,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#binomialName", "access": "public", "description": "Return the binomial name if available.", - "lineNumber": 308, + "lineNumber": 327, "type": { "types": [ "string" @@ -3603,7 +3801,7 @@ } }, { - "__docId__": 206, + "__docId__": 213, "kind": "set", "name": "binomialName", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3613,10 +3811,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#binomialName", "access": "public", "description": "Set the binomial name.", - "lineNumber": 316 + "lineNumber": 335 }, { - "__docId__": 207, + "__docId__": 214, "kind": "get", "name": "trinomialName", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3626,7 +3824,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#trinomialName", "access": "public", "description": "Return the trinomial name if available.", - "lineNumber": 322, + "lineNumber": 341, "type": { "types": [ "string" @@ -3634,7 +3832,7 @@ } }, { - "__docId__": 208, + "__docId__": 215, "kind": "set", "name": "trinomialName", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3644,10 +3842,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#trinomialName", "access": "public", "description": "Set the trinomial name.", - "lineNumber": 332 + "lineNumber": 351 }, { - "__docId__": 209, + "__docId__": 216, "kind": "get", "name": "genusPart", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3657,7 +3855,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#genusPart", "access": "public", "description": "Return the genus part of this scientific name if available.", - "lineNumber": 338, + "lineNumber": 357, "type": { "types": [ "*" @@ -3665,7 +3863,7 @@ } }, { - "__docId__": 210, + "__docId__": 217, "kind": "set", "name": "genusPart", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3675,10 +3873,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#genusPart", "access": "public", "description": "Set the genus part of this name.", - "lineNumber": 356 + "lineNumber": 375 }, { - "__docId__": 211, + "__docId__": 218, "kind": "get", "name": "specificEpithet", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3688,7 +3886,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#specificEpithet", "access": "public", "description": "Return the specific epithet of this scientific name if available.", - "lineNumber": 368, + "lineNumber": 387, "type": { "types": [ "*" @@ -3696,7 +3894,7 @@ } }, { - "__docId__": 212, + "__docId__": 219, "kind": "set", "name": "specificEpithet", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3706,10 +3904,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#specificEpithet", "access": "public", "description": "Set the specificEpithet part of this name.", - "lineNumber": 386 + "lineNumber": 405 }, { - "__docId__": 213, + "__docId__": 220, "kind": "get", "name": "infraspecificEpithet", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3719,7 +3917,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#infraspecificEpithet", "access": "public", "description": "Return the infraspecific epithet of this scientific name if available.", - "lineNumber": 398, + "lineNumber": 417, "type": { "types": [ "*" @@ -3727,7 +3925,7 @@ } }, { - "__docId__": 214, + "__docId__": 221, "kind": "set", "name": "infraspecificEpithet", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3737,10 +3935,10 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#infraspecificEpithet", "access": "public", "description": "Set the infraspecificEpithet part of this name.", - "lineNumber": 416 + "lineNumber": 435 }, { - "__docId__": 215, + "__docId__": 222, "kind": "get", "name": "asJSONLD", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3750,7 +3948,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#asJSONLD", "access": "public", "description": "Return this taxon name in an JSON-LD representation.", - "lineNumber": 430, + "lineNumber": 449, "type": { "types": [ "*" @@ -3758,7 +3956,7 @@ } }, { - "__docId__": 216, + "__docId__": 223, "kind": "get", "name": "asOWLEquivClass", "memberof": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper", @@ -3768,7 +3966,7 @@ "longname": "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper#asOWLEquivClass", "access": "public", "description": "Return this taxon name as an OWL equivalentClass expression.", - "lineNumber": 447, + "lineNumber": 466, "type": { "types": [ "{\"@type\": string, \"intersectionOf\": *}" @@ -3776,10 +3974,10 @@ } }, { - "__docId__": 217, + "__docId__": 224, "kind": "file", "name": "src/wrappers/TaxonomicUnitWrapper.js", - "content": "/** Utility functions. */\nconst {\n has,\n isArray,\n cloneDeep,\n assign,\n} = require('lodash');\n\n/** List of OWL/RDF terms we use. */\nconst owlterms = require('../utils/owlterms');\n\n/** We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. */\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/** For parsing specimen identifiers. */\nconst { SpecimenWrapper } = require('./SpecimenWrapper');\n\n/** For parsing scientific names. */\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\n\n/**\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n */\n\nclass TaxonomicUnitWrapper {\n /* Types of taxonomic units we support (see documentation above). */\n\n /** A taxon or taxon concept. */\n static get TYPE_TAXON_CONCEPT() {\n return TaxonConceptWrapper.TYPE_TAXON_CONCEPT;\n }\n\n /** A specimen. */\n static get TYPE_SPECIMEN() {\n return SpecimenWrapper.TYPE_SPECIMEN;\n }\n\n /** Wrap a taxonomic unit. */\n constructor(tunit, defaultNomenCode = owlterms.NAME_IN_UNKNOWN_CODE) {\n this.tunit = tunit;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n */\n get types() {\n if (!has(this.tunit, '@type')) return [];\n if (isArray(this.tunit['@type'])) return this.tunit['@type'];\n return [this.tunit['@type']];\n }\n\n /**\n * Return this taxonomic unit if it is a taxon concept.\n */\n get taxonConcept() {\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT)) return this.tunit;\n return undefined;\n }\n\n /**\n * Return this taxonomic unit if it is a specimen.\n */\n get specimen() {\n // Only specimens have scientific names.\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) return this.tunit;\n\n return undefined;\n }\n\n /**\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n */\n get externalReferences() {\n if (!has(this.tunit, '@id')) return [];\n if (isArray(this.tunit['@id'])) return this.tunit['@id'];\n return [this.tunit['@id']];\n }\n\n /**\n * Return the label of this taxonomic unit.\n */\n get label() {\n // A label or description for this TU?\n if (has(this.tunit, 'label')) return this.tunit.label;\n if (has(this.tunit, 'description')) return this.tunit.description;\n\n // Is this a specimen?\n if (this.specimen) {\n return new SpecimenWrapper(this.specimen).label;\n }\n\n // Is this a taxon concept?\n if (this.taxonConcept) {\n return new TaxonConceptWrapper(this.taxonConcept).label;\n }\n\n // If its neither a specimen nor a taxon concept, just list the\n // external references.\n const externalReferences = this.externalReferences;\n if (externalReferences.length > 0) {\n return externalReferences\n .map(externalRef => `<${externalRef}>`)\n .join(' and ');\n }\n\n // If we don't have any properties of a taxonomic unit, return undefined.\n return undefined;\n }\n\n /**\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n */\n static fromLabel(nodeLabel, nomenCode = owlterms.NAME_IN_UNKNOWN_CODE) {\n if (nodeLabel === undefined || nodeLabel === null || nodeLabel.trim() === '') return undefined;\n\n // Rather than figuring out with this label, check to see if we've parsed\n // this before.\n if (PhyxCacheManager.has(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel)) {\n return PhyxCacheManager.get(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel);\n }\n\n // Look for taxon concept.\n const taxonConcept = TaxonConceptWrapper.fromLabel(nodeLabel, nomenCode);\n\n // Look for specimen information.\n let specimen;\n if (nodeLabel.toLowerCase().startsWith('specimen ')) {\n // Eliminate a 'Specimen ' prefix if it exists.\n specimen = SpecimenWrapper.fromOccurrenceID(nodeLabel.substr(9));\n }\n\n let tunit;\n if (taxonConcept && specimen) {\n // If we have both, then treat it as a specimen that has been identified\n // to a particular taxonomic name.\n tunit = assign({}, taxonConcept, specimen);\n\n tunit['@type'] = TaxonomicUnitWrapper.TYPE_SPECIMEN;\n } else if (taxonConcept) {\n tunit = taxonConcept;\n } else if (specimen) {\n tunit = specimen;\n }\n\n // Look for external references. For now, we only check to see if the entire\n // nodeLabel starts with URL/URNs, but we should eventually just look for\n // them inside the label.\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n\n if (URL_URN_PREFIXES.filter(prefix => nodeLabel.startsWith(prefix)).length > 0) {\n // The node label starts with something that looks like a URL!\n // Treat it as an external reference.\n if (tunit === undefined) tunit = {};\n tunit['@id'] = nodeLabel;\n }\n\n // Finally, let's record the label we parsed to get to this tunit!\n if (tunit) {\n tunit.label = nodeLabel;\n }\n\n // Record in the cache\n PhyxCacheManager.put(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel, tunit);\n\n return tunit;\n }\n\n /**\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n */\n get asJSON() {\n return this.tunit;\n }\n\n /**\n * Return this taxonomic unit as an OWL/JSON-LD object.\n */\n get asJSONLD() {\n const jsonld = cloneDeep(this.tunit);\n\n // Add CDAO_TU as a type to the existing types.\n if (has(this.tunit, '@type')) {\n if (isArray(this.tunit['@type'])) this.tunit['@type'].push(owlterms.CDAO_TU);\n }\n\n const equivClass = this.asOWLEquivClass;\n if (equivClass) {\n jsonld.equivalentClass = equivClass;\n }\n\n return jsonld;\n }\n\n /**\n * Return the equivalent class expression for this taxonomic unit.\n */\n get asOWLEquivClass() {\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT)) {\n return new TaxonConceptWrapper(this.tunit, this.defaultNomenCode).asOWLEquivClass;\n }\n\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) {\n return new SpecimenWrapper(this.specimen).asOWLEquivClass;\n }\n\n // Nothing we can do, so just ignore it.\n return undefined;\n }\n}\n\nmodule.exports = {\n TaxonomicUnitWrapper,\n};\n", + "content": "/** Utility functions. */\nconst {\n has,\n isArray,\n cloneDeep,\n assign,\n} = require('lodash');\n\n/** List of OWL/RDF terms we use. */\nconst owlterms = require('../utils/owlterms');\n\n/** We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. */\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/** For parsing specimen identifiers. */\nconst { SpecimenWrapper } = require('./SpecimenWrapper');\n\n/** For parsing scientific names. */\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\n\n/**\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n */\n\nclass TaxonomicUnitWrapper {\n /* Types of taxonomic units we support (see documentation above). */\n\n /** A taxon or taxon concept. */\n static get TYPE_TAXON_CONCEPT() {\n return TaxonConceptWrapper.TYPE_TAXON_CONCEPT;\n }\n\n /** A specimen. */\n static get TYPE_SPECIMEN() {\n return SpecimenWrapper.TYPE_SPECIMEN;\n }\n\n /** Wrap a taxonomic unit. */\n constructor(tunit, defaultNomenCode = owlterms.NAME_IN_UNKNOWN_CODE) {\n this.tunit = tunit;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Normalize the specified taxonomic unit.\n * @param tunit A taxonomic unit to be normalized.\n */\n static normalize(tunit) {\n const wrapped = new TaxonomicUnitWrapper(tunit);\n if (wrapped.taxonConcept) {\n return TaxonConceptWrapper.normalize(tunit);\n }\n if (wrapped.specimen) {\n return SpecimenWrapper.normalize(tunit);\n }\n if (wrapped.externalReferences) {\n // External references should only have an `@id`.\n return tunit;\n }\n return tunit;\n }\n\n /**\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n */\n get types() {\n if (!has(this.tunit, '@type')) return [];\n if (isArray(this.tunit['@type'])) return this.tunit['@type'];\n return [this.tunit['@type']];\n }\n\n /**\n * Return this taxonomic unit if it is a taxon concept.\n */\n get taxonConcept() {\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT)) return this.tunit;\n return undefined;\n }\n\n /**\n * Return this taxonomic unit if it is a specimen.\n */\n get specimen() {\n // Only specimens have scientific names.\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) return this.tunit;\n\n return undefined;\n }\n\n /**\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n */\n get externalReferences() {\n if (!has(this.tunit, '@id')) return [];\n if (isArray(this.tunit['@id'])) return this.tunit['@id'];\n return [this.tunit['@id']];\n }\n\n /**\n * Return the label of this taxonomic unit.\n */\n get label() {\n // A label or description for this TU?\n if (has(this.tunit, 'label')) return this.tunit.label;\n if (has(this.tunit, 'description')) return this.tunit.description;\n\n // Is this a specimen?\n if (this.specimen) {\n return new SpecimenWrapper(this.specimen).label;\n }\n\n // Is this a taxon concept?\n if (this.taxonConcept) {\n return new TaxonConceptWrapper(this.taxonConcept).label;\n }\n\n // If its neither a specimen nor a taxon concept, just list the\n // external references.\n const externalReferences = this.externalReferences;\n if (externalReferences.length > 0) {\n return externalReferences\n .map(externalRef => `<${externalRef}>`)\n .join(' and ');\n }\n\n // If we don't have any properties of a taxonomic unit, return undefined.\n return undefined;\n }\n\n /**\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n */\n static fromLabel(nodeLabel, nomenCode = owlterms.NAME_IN_UNKNOWN_CODE) {\n if (nodeLabel === undefined || nodeLabel === null || nodeLabel.trim() === '') return undefined;\n\n // Rather than figuring out with this label, check to see if we've parsed\n // this before.\n if (PhyxCacheManager.has(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel)) {\n return PhyxCacheManager.get(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel);\n }\n\n // Look for taxon concept.\n const taxonConcept = TaxonConceptWrapper.fromLabel(nodeLabel, nomenCode);\n\n // Look for specimen information.\n let specimen;\n if (nodeLabel.toLowerCase().startsWith('specimen ')) {\n // Eliminate a 'Specimen ' prefix if it exists.\n specimen = SpecimenWrapper.fromOccurrenceID(nodeLabel.substr(9));\n }\n\n let tunit;\n if (taxonConcept && specimen) {\n // If we have both, then treat it as a specimen that has been identified\n // to a particular taxonomic name.\n tunit = assign({}, taxonConcept, specimen);\n\n tunit['@type'] = TaxonomicUnitWrapper.TYPE_SPECIMEN;\n } else if (taxonConcept) {\n tunit = taxonConcept;\n } else if (specimen) {\n tunit = specimen;\n }\n\n // Look for external references. For now, we only check to see if the entire\n // nodeLabel starts with URL/URNs, but we should eventually just look for\n // them inside the label.\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n\n if (URL_URN_PREFIXES.filter(prefix => nodeLabel.startsWith(prefix)).length > 0) {\n // The node label starts with something that looks like a URL!\n // Treat it as an external reference.\n if (tunit === undefined) tunit = {};\n tunit['@id'] = nodeLabel;\n }\n\n // Finally, let's record the label we parsed to get to this tunit!\n if (tunit) {\n tunit.label = nodeLabel;\n }\n\n // Record in the cache\n PhyxCacheManager.put(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel, tunit);\n\n return tunit;\n }\n\n /**\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n */\n get asJSON() {\n return this.tunit;\n }\n\n /**\n * Return this taxonomic unit as an OWL/JSON-LD object.\n */\n get asJSONLD() {\n const jsonld = cloneDeep(this.tunit);\n\n // Add CDAO_TU as a type to the existing types.\n if (has(this.tunit, '@type')) {\n if (isArray(this.tunit['@type'])) this.tunit['@type'].push(owlterms.CDAO_TU);\n }\n\n const equivClass = this.asOWLEquivClass;\n if (equivClass) {\n jsonld.equivalentClass = equivClass;\n }\n\n return jsonld;\n }\n\n /**\n * Return the equivalent class expression for this taxonomic unit.\n */\n get asOWLEquivClass() {\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT)) {\n return new TaxonConceptWrapper(this.tunit, this.defaultNomenCode).asOWLEquivClass;\n }\n\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) {\n return new SpecimenWrapper(this.specimen).asOWLEquivClass;\n }\n\n // Nothing we can do, so just ignore it.\n return undefined;\n }\n}\n\nmodule.exports = {\n TaxonomicUnitWrapper,\n};\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/TaxonomicUnitWrapper.js", "access": "public", @@ -3787,7 +3985,7 @@ "lineNumber": 1 }, { - "__docId__": 218, + "__docId__": 225, "kind": "variable", "name": "has", "memberof": "src/wrappers/TaxonomicUnitWrapper.js", @@ -3808,7 +4006,7 @@ "ignore": true }, { - "__docId__": 219, + "__docId__": 226, "kind": "variable", "name": "PhyxCacheManager", "memberof": "src/wrappers/TaxonomicUnitWrapper.js", @@ -3829,7 +4027,7 @@ "ignore": true }, { - "__docId__": 220, + "__docId__": 227, "kind": "variable", "name": "SpecimenWrapper", "memberof": "src/wrappers/TaxonomicUnitWrapper.js", @@ -3850,7 +4048,7 @@ "ignore": true }, { - "__docId__": 221, + "__docId__": 228, "kind": "variable", "name": "TaxonConceptWrapper", "memberof": "src/wrappers/TaxonomicUnitWrapper.js", @@ -3871,7 +4069,7 @@ "ignore": true }, { - "__docId__": 222, + "__docId__": 229, "kind": "class", "name": "TaxonomicUnitWrapper", "memberof": "src/wrappers/TaxonomicUnitWrapper.js", @@ -3886,7 +4084,7 @@ "interface": false }, { - "__docId__": 223, + "__docId__": 230, "kind": "get", "name": "TYPE_TAXON_CONCEPT", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -3904,7 +4102,7 @@ } }, { - "__docId__": 224, + "__docId__": 231, "kind": "get", "name": "TYPE_SPECIMEN", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -3922,7 +4120,7 @@ } }, { - "__docId__": 225, + "__docId__": 232, "kind": "constructor", "name": "constructor", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -3935,7 +4133,7 @@ "lineNumber": 61 }, { - "__docId__": 226, + "__docId__": 233, "kind": "member", "name": "tunit", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -3952,7 +4150,7 @@ } }, { - "__docId__": 227, + "__docId__": 234, "kind": "member", "name": "defaultNomenCode", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -3969,25 +4167,55 @@ } }, { - "__docId__": 228, - "kind": "get", - "name": "types", + "__docId__": 235, + "kind": "method", + "name": "normalize", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", "generator": false, "async": false, - "static": false, - "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#types", + "static": true, + "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.normalize", "access": "public", - "description": "What type of specifier is this? This is an array that could contain multiple\nclasses, but should contain one of:\n - {@link TYPE_TAXON_CONCEPT}\n - {@link TYPE_SPECIMEN}", - "lineNumber": 72, - "type": { - "types": [ + "description": "Normalize the specified taxonomic unit.", + "lineNumber": 70, + "params": [ + { + "nullable": null, + "types": [ + "*" + ], + "spread": false, + "optional": false, + "name": "tunit", + "description": "A taxonomic unit to be normalized." + } + ], + "return": { + "types": [ + "*" + ] + } + }, + { + "__docId__": 236, + "kind": "get", + "name": "types", + "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", + "generator": false, + "async": false, + "static": false, + "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#types", + "access": "public", + "description": "What type of specifier is this? This is an array that could contain multiple\nclasses, but should contain one of:\n - {@link TYPE_TAXON_CONCEPT}\n - {@link TYPE_SPECIMEN}", + "lineNumber": 91, + "type": { + "types": [ "undefined[]" ] } }, { - "__docId__": 229, + "__docId__": 237, "kind": "get", "name": "taxonConcept", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -3997,7 +4225,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#taxonConcept", "access": "public", "description": "Return this taxonomic unit if it is a taxon concept.", - "lineNumber": 81, + "lineNumber": 100, "type": { "types": [ "*" @@ -4005,7 +4233,7 @@ } }, { - "__docId__": 230, + "__docId__": 238, "kind": "get", "name": "specimen", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4015,7 +4243,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#specimen", "access": "public", "description": "Return this taxonomic unit if it is a specimen.", - "lineNumber": 89, + "lineNumber": 108, "type": { "types": [ "*" @@ -4023,7 +4251,7 @@ } }, { - "__docId__": 231, + "__docId__": 239, "kind": "get", "name": "externalReferences", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4033,7 +4261,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#externalReferences", "access": "public", "description": "Return the list of external references for this taxonomic unit.\nThis is just all the '@ids' of this object.", - "lineNumber": 100, + "lineNumber": 119, "type": { "types": [ "undefined[]" @@ -4041,7 +4269,7 @@ } }, { - "__docId__": 232, + "__docId__": 240, "kind": "get", "name": "label", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4051,7 +4279,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#label", "access": "public", "description": "Return the label of this taxonomic unit.", - "lineNumber": 109, + "lineNumber": 128, "type": { "types": [ "*" @@ -4059,7 +4287,7 @@ } }, { - "__docId__": 233, + "__docId__": 241, "kind": "method", "name": "fromLabel", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4069,7 +4297,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.fromLabel", "access": "public", "description": "Given a label, attempt to parse it into a taxonomic unit, whether a scientific\nname or a specimen identifier. The provided nomenclatural code is used.", - "lineNumber": 143, + "lineNumber": 162, "return": { "nullable": null, "types": [ @@ -4095,7 +4323,7 @@ ] }, { - "__docId__": 234, + "__docId__": 242, "kind": "get", "name": "asJSON", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4105,7 +4333,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#asJSON", "access": "public", "description": "Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.", - "lineNumber": 208, + "lineNumber": 227, "type": { "types": [ "*" @@ -4113,7 +4341,7 @@ } }, { - "__docId__": 235, + "__docId__": 243, "kind": "get", "name": "asJSONLD", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4123,7 +4351,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#asJSONLD", "access": "public", "description": "Return this taxonomic unit as an OWL/JSON-LD object.", - "lineNumber": 215, + "lineNumber": 234, "type": { "types": [ "*" @@ -4131,7 +4359,7 @@ } }, { - "__docId__": 236, + "__docId__": 244, "kind": "get", "name": "asOWLEquivClass", "memberof": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper", @@ -4141,7 +4369,7 @@ "longname": "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper#asOWLEquivClass", "access": "public", "description": "Return the equivalent class expression for this taxonomic unit.", - "lineNumber": 234, + "lineNumber": 253, "type": { "types": [ "*" @@ -4158,7 +4386,7 @@ }, { "kind": "packageJSON", - "content": "{\n \"name\": \"@phyloref/phyx\",\n \"version\": \"1.1.1\",\n \"description\": \"Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files\",\n \"keywords\": [\n \"phylogenetics\",\n \"phylogeny\",\n \"phylogenetic definitions\",\n \"clade definitions\"\n ],\n \"homepage\": \"https://github.com/phyloref/phyx.js#readme\",\n \"bugs\": {\n \"url\": \"https://github.com/phyloref/phyx.js/issues\"\n },\n \"repository\": {\n \"type\": \"git\",\n \"url\": \"git+https://github.com/phyloref/phyx.js.git\"\n },\n \"license\": \"MIT\",\n \"author\": \"Gaurav Vaidya \",\n \"main\": \"src/index.js\",\n \"bin\": {\n \"phyx2owl\": \"bin/phyx2owl.js\",\n \"resolve\": \"bin/resolve.js\"\n },\n \"scripts\": {\n \"docs\": \"esdoc\",\n \"generate-every-topology\": \"every-topology-testing/generate-topologies.js\",\n \"lint\": \"eslint \\\"src/**/*.js\\\" \\\"test/**/*.js\\\" \\\"**/*.json\\\"\",\n \"phyx2owl\": \"node bin/phyx2owl.js\",\n \"resolve\": \"node bin/resolve.js\",\n \"pretest\": \"npm run lint\",\n \"test\": \"mocha --recursive\"\n },\n \"dependencies\": {\n \"jsonld\": \"^5.0.0\",\n \"lodash\": \"^4.17.20\",\n \"moment\": \"^2.27.0\",\n \"newick-js\": \"^1.2.1\",\n \"retus\": \"^1.1.1\",\n \"yargs\": \"^15.4.1\"\n },\n \"devDependencies\": {\n \"ajv\": \"^6.12.2\",\n \"chai\": \"^4.2.0\",\n \"esdoc\": \"^1.1.0\",\n \"esdoc-node\": \"^1.0.5\",\n \"esdoc-standard-plugin\": \"^1.0.0\",\n \"eslint\": \"^5.16.0\",\n \"eslint-config-airbnb-base\": \"^13.2.0\",\n \"eslint-plugin-import\": \"^2.22.1\",\n \"eslint-plugin-json-format\": \"^2.0.1\",\n \"eslint-plugin-mocha\": \"^5.3.0\",\n \"mocha\": \"^5.2.0\",\n \"nodejs-file-downloader\": \"^4.1.1\",\n \"yargs\": \"^15.3.1\"\n },\n \"esdoc\": {\n \"source\": \"./src\",\n \"destination\": \"./docs\",\n \"plugins\": [\n {\n \"name\": \"esdoc-standard-plugin\",\n \"option\": {\n \"manual\": {\n \"files\": [\n \"./CHANGELOG.md\",\n \"./tutorials/Introduction.md\"\n ]\n },\n \"test\": {\n \"source\": \"./test/\",\n \"includes\": [\n \"\\\\.js$\"\n ]\n }\n }\n },\n {\n \"name\": \"esdoc-node\"\n }\n ]\n }\n}\n", + "content": "{\n \"name\": \"@phyloref/phyx\",\n \"version\": \"1.2.0-alpha1\",\n \"description\": \"Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files\",\n \"keywords\": [\n \"phylogenetics\",\n \"phylogeny\",\n \"phylogenetic definitions\",\n \"clade definitions\"\n ],\n \"homepage\": \"https://github.com/phyloref/phyx.js#readme\",\n \"bugs\": {\n \"url\": \"https://github.com/phyloref/phyx.js/issues\"\n },\n \"repository\": {\n \"type\": \"git\",\n \"url\": \"git+https://github.com/phyloref/phyx.js.git\"\n },\n \"license\": \"MIT\",\n \"author\": \"Gaurav Vaidya \",\n \"main\": \"src/index.js\",\n \"bin\": {\n \"phyx2owl\": \"bin/phyx2owl.js\",\n \"resolve\": \"bin/resolve.js\"\n },\n \"scripts\": {\n \"docs\": \"esdoc\",\n \"generate-every-topology\": \"every-topology-testing/generate-topologies.js\",\n \"lint\": \"eslint \\\"src/**/*.js\\\" \\\"test/**/*.js\\\" \\\"**/*.json\\\"\",\n \"phyx2owl\": \"node bin/phyx2owl.js\",\n \"resolve\": \"node bin/resolve.js\",\n \"pretest\": \"npm run lint\",\n \"test\": \"mocha --recursive\"\n },\n \"dependencies\": {\n \"jsonld\": \"^5.0.0\",\n \"lodash\": \"^4.17.20\",\n \"moment\": \"^2.27.0\",\n \"newick-js\": \"^1.2.1\",\n \"retus\": \"^1.1.1\",\n \"yargs\": \"^15.4.1\"\n },\n \"devDependencies\": {\n \"ajv\": \"^6.12.2\",\n \"chai\": \"^4.2.0\",\n \"esdoc\": \"^1.1.0\",\n \"esdoc-node\": \"^1.0.5\",\n \"esdoc-standard-plugin\": \"^1.0.0\",\n \"eslint\": \"^5.16.0\",\n \"eslint-config-airbnb-base\": \"^13.2.0\",\n \"eslint-plugin-import\": \"^2.22.1\",\n \"eslint-plugin-json-format\": \"^2.0.1\",\n \"eslint-plugin-mocha\": \"^5.3.0\",\n \"mocha\": \"^5.2.0\",\n \"nodejs-file-downloader\": \"^4.1.1\",\n \"yargs\": \"^15.3.1\"\n },\n \"esdoc\": {\n \"source\": \"./src\",\n \"destination\": \"./docs\",\n \"plugins\": [\n {\n \"name\": \"esdoc-standard-plugin\",\n \"option\": {\n \"manual\": {\n \"files\": [\n \"./CHANGELOG.md\",\n \"./tutorials/Introduction.md\"\n ]\n },\n \"test\": {\n \"source\": \"./test/\",\n \"includes\": [\n \"\\\\.js$\"\n ]\n }\n }\n },\n {\n \"name\": \"esdoc-node\"\n }\n ]\n }\n}\n", "longname": "/Users/gaurav/Development/phyloref/phyx.js/package.json", "name": "package.json", "static": true, @@ -4176,7 +4404,7 @@ "kind": "manual", "longname": "/Users/gaurav/Development/phyloref/phyx.js/CHANGELOG.md", "name": "./CHANGELOG.md", - "content": "# Changelog\nAll notable changes to this library will be documented in this file.\n\nThe format is based on [Keep a Changelog] and this project adheres to [Semantic Versioning].\n\n## [Unreleased]\n\n## [1.1.1] - 2023-08-01\n- PR #133: Add guards to some usages of `phyloref.internalSpecifiers/phyloref.externalSpecifiers`.\n- PR #136: Improved GitHub test action, including changing Node versions.\n- PR #127: Upgraded Newick.js to ^1.2.1. This means that we no longer\n support Node.js v10.x, which end-of-lifed on April 30, 2021.\n\n## [1.1.0] - 2023-05-11\n- PR #129: Added curator notes to phylorefs and phylogenies.\n- PR #128: Added citation to README and a CITATION.CFF file.\n- PR #125: Added curator information as contributors to Phyx file.\n\n## [1.0.1] - 2021-10-15\n- Created a tutorial for using phyx.js, including:\n - PR #99: Add tutorial.\n - PR #103: Improve integration of the tutorial.\n - PR #109: Add resolve.js instructions to Introduction tutorial.\n- Improvements to README files, including:\n - PR #108: Added links to published JSON-LD contexts and JSON schemas.\n - PR #110: Added note that Binder cannot be used.\n - PR #111: Changes link to tutorials to directory.\n- PR #106: Fixed typo in resolve.js.\n- Updated timeout to 60s as 20s was timing out on GitHub Actions.\n- Updated NPM packages and resorted packages in package.json.\n\n## [1.0.0] - 2021-03-16\n- Many changes across the entire library.\n- Two new scripts: `bin/phyx2owl.js` for converting a Phyx file into OWL/JSON-LD\n and `bin/resolve.js` to resolve a Phyx file on the Open Tree of Life.\n- Incorporation of JPhyloRef into testing.\n- Fixed a bug in which phyloref and phylogeny `@id` values were being overwritten when generating JSON-LD.\n- Added scripts to generate every possible topology from n=2 to n=6 with expected resolution and to test them with JPhyloRef.\n\n## [0.2.1] - 2019-08-15\n- Updated all NPM packages to their latest version.\n- Fixed a bug in which node's types were not being correctly set to obo:CDAO\\_0000140.\n\n## [0.2.0] - 2019-07-18\n### Changed\n- The single index.js has been split into multiple files, one per class, with documentation using ESdocs (#21).\n- Added support for generating \"model 2.0\" ontologies, which can be reasoned over in an OWL 2 EL reasoner such as Elk (#4). As part of this change, specifiers have been changed so that they are taxonomic units, rather than containing taxonomic units and a new Phyx context file has been created (#19).\n- Taxonomic units have been cleaned up, are clearly typed, and taxonomic names now include nomenclatural codes (#18) and support trinomial names (#22).\n\n## [0.1.2] - 2019-02-08\n### Added\n- Moved Phyx context file for JSON-LD into this repository from the Curation Tool and changed URI to point to it.\n\n## [0.1.1] - 2019-02-06\n### Added\n- A replacement for the Phylotree.js Newick parser.\n\n## [0.1.0] - 2019-01-27\n### Added\n- Transfered initial code from the [Phyloreference Curation Tool]. The initial\nrelease of this package was based on [commit 14d2c3d5d1] in that repository.\n\n### Changed\n- Replaced references to the [phylotree] library with the [newick-js] library.\n- Made other changes to the initial code as needed to work as an independent NPM package.\n\n [Unreleased]: https://github.com/phyloref/phyx.js/compare/v1.1.1...master\n [1.1.1]: https://github.com/phyloref/phyx.js/compare/v1.1.0...v1.1.1\n [1.1.0]: https://github.com/phyloref/phyx.js/compare/v1.0.1...v1.1.0\n [1.0.1]: https://github.com/phyloref/phyx.js/compare/v1.0.0...v1.0.1\n [1.0.0]: https://github.com/phyloref/phyx.js/compare/v0.2.1...v1.0.0\n [0.2.1]: https://github.com/phyloref/phyx.js/compare/v0.2.0...v0.2.1\n [0.2.0]: https://github.com/phyloref/phyx.js/compare/v0.1.2...v0.2.0\n [0.1.2]: https://github.com/phyloref/phyx.js/compare/v0.1.1...v0.1.2\n [0.1.1]: https://github.com/phyloref/phyx.js/compare/v0.1.0...v0.1.1\n [0.1.0]: https://github.com/phyloref/phyx.js/releases/tag/v0.1.0\n [Keep a Changelog]: https://keepachangelog.com/en/1.0.0/\n [Semantic Versioning]: https://semver.org/spec/v2.0.0.html\n [Phyloreference Curation Tool]: http://github.com/phyloref/curation-tool\n [commit 14d2c3d5d1]: https://github.com/phyloref/curation-tool/commit/14d2c3d5d12ee4e925e29961bd46587aabfb8cd4\n [phylotree]: https://www.npmjs.com/package/phylotree\n [newick-js]: https://www.npmjs.com/package/newick-js\n", + "content": "# Changelog\nAll notable changes to this library will be documented in this file.\n\nThe format is based on [Keep a Changelog] and this project adheres to [Semantic Versioning].\n\n## [Unreleased]\n\n## [1.2.0] - 2024-06-18\n- PR #138: Added normalization methods so that Phyx objects can be normalized.\n- PR #139: upgraded NPM packages and minor test fixes\n\n## [1.1.1] - 2023-08-01\n- PR #133: Add guards to some usages of `phyloref.internalSpecifiers/phyloref.externalSpecifiers`.\n- PR #136: Improved GitHub test action, including changing Node versions.\n- PR #127: Upgraded Newick.js to ^1.2.1. This means that we no longer\n support Node.js v10.x, which end-of-lifed on April 30, 2021.\n\n## [1.1.0] - 2023-05-11\n- PR #129: Added curator notes to phylorefs and phylogenies.\n- PR #128: Added citation to README and a CITATION.CFF file.\n- PR #125: Added curator information as contributors to Phyx file.\n\n## [1.0.1] - 2021-10-15\n- Created a tutorial for using phyx.js, including:\n - PR #99: Add tutorial.\n - PR #103: Improve integration of the tutorial.\n - PR #109: Add resolve.js instructions to Introduction tutorial.\n- Improvements to README files, including:\n - PR #108: Added links to published JSON-LD contexts and JSON schemas.\n - PR #110: Added note that Binder cannot be used.\n - PR #111: Changes link to tutorials to directory.\n- PR #106: Fixed typo in resolve.js.\n- Updated timeout to 60s as 20s was timing out on GitHub Actions.\n- Updated NPM packages and resorted packages in package.json.\n\n## [1.0.0] - 2021-03-16\n- Many changes across the entire library.\n- Two new scripts: `bin/phyx2owl.js` for converting a Phyx file into OWL/JSON-LD\n and `bin/resolve.js` to resolve a Phyx file on the Open Tree of Life.\n- Incorporation of JPhyloRef into testing.\n- Fixed a bug in which phyloref and phylogeny `@id` values were being overwritten when generating JSON-LD.\n- Added scripts to generate every possible topology from n=2 to n=6 with expected resolution and to test them with JPhyloRef.\n\n## [0.2.1] - 2019-08-15\n- Updated all NPM packages to their latest version.\n- Fixed a bug in which node's types were not being correctly set to obo:CDAO\\_0000140.\n\n## [0.2.0] - 2019-07-18\n### Changed\n- The single index.js has been split into multiple files, one per class, with documentation using ESdocs (#21).\n- Added support for generating \"model 2.0\" ontologies, which can be reasoned over in an OWL 2 EL reasoner such as Elk (#4). As part of this change, specifiers have been changed so that they are taxonomic units, rather than containing taxonomic units and a new Phyx context file has been created (#19).\n- Taxonomic units have been cleaned up, are clearly typed, and taxonomic names now include nomenclatural codes (#18) and support trinomial names (#22).\n\n## [0.1.2] - 2019-02-08\n### Added\n- Moved Phyx context file for JSON-LD into this repository from the Curation Tool and changed URI to point to it.\n\n## [0.1.1] - 2019-02-06\n### Added\n- A replacement for the Phylotree.js Newick parser.\n\n## [0.1.0] - 2019-01-27\n### Added\n- Transfered initial code from the [Phyloreference Curation Tool]. The initial\nrelease of this package was based on [commit 14d2c3d5d1] in that repository.\n\n### Changed\n- Replaced references to the [phylotree] library with the [newick-js] library.\n- Made other changes to the initial code as needed to work as an independent NPM package.\n\n [Unreleased]: https://github.com/phyloref/phyx.js/compare/v1.2.0...master\n [1.2.0]: https://github.com/phyloref/phyx.js/compare/v1.1.1...v1.2.0\n [1.1.1]: https://github.com/phyloref/phyx.js/compare/v1.1.0...v1.1.1\n [1.1.0]: https://github.com/phyloref/phyx.js/compare/v1.0.1...v1.1.0\n [1.0.1]: https://github.com/phyloref/phyx.js/compare/v1.0.0...v1.0.1\n [1.0.0]: https://github.com/phyloref/phyx.js/compare/v0.2.1...v1.0.0\n [0.2.1]: https://github.com/phyloref/phyx.js/compare/v0.2.0...v0.2.1\n [0.2.0]: https://github.com/phyloref/phyx.js/compare/v0.1.2...v0.2.0\n [0.1.2]: https://github.com/phyloref/phyx.js/compare/v0.1.1...v0.1.2\n [0.1.1]: https://github.com/phyloref/phyx.js/compare/v0.1.0...v0.1.1\n [0.1.0]: https://github.com/phyloref/phyx.js/releases/tag/v0.1.0\n [Keep a Changelog]: https://keepachangelog.com/en/1.0.0/\n [Semantic Versioning]: https://semver.org/spec/v2.0.0.html\n [Phyloreference Curation Tool]: http://github.com/phyloref/curation-tool\n [commit 14d2c3d5d1]: https://github.com/phyloref/curation-tool/commit/14d2c3d5d12ee4e925e29961bd46587aabfb8cd4\n [phylotree]: https://www.npmjs.com/package/phylotree\n [newick-js]: https://www.npmjs.com/package/newick-js\n", "static": true, "access": "public" }, @@ -4189,7 +4417,7 @@ "access": "public" }, { - "__docId__": 237, + "__docId__": 245, "kind": "testFile", "name": "test/citations.js", "content": "/*\n * Test citations.\n */\n\n// Require phyx.js, our PHYX library, and Chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// We use Chai's Expect API.\nconst expect = chai.expect;\n\n/*\n * Citation tests check to see if the CitationWrapper works correctly.\n */\n\ndescribe('CitationWrapper', function () {\n // Some citations to use in testing.\n const citations = [{\n bibliographicCitation: 'Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308',\n citation: {\n type: 'article',\n title: 'Phylogenetic approaches toward crocodylian history',\n authors: [\n {\n name: 'Christopher A. Brochu',\n alternate: ['Brochu, Christopher A.'],\n firstname: 'Christopher',\n middlename: 'A.',\n lastname: 'Brochu',\n },\n ],\n year: 2003,\n figure: 1,\n identifier: [\n {\n type: 'doi',\n id: '10.1146/annurev.earth.31.100901.141308',\n },\n ],\n link: [\n {\n url: 'https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308',\n },\n ],\n journal: {\n name: 'Annual Review of Earth and Planetary Sciences',\n volume: '31',\n pages: '357--397',\n identifier: [{\n type: 'eISSN',\n id: '1545-4495',\n }],\n },\n },\n }];\n\n describe('given an empty citation', function () {\n const wrapper = new phyx.CitationWrapper({});\n\n describe('#constructor', function () {\n it('should return a CitationWrapper', function () {\n expect(wrapper).to.be.an.instanceOf(phyx.CitationWrapper);\n });\n });\n\n describe('#toString', function () {\n it('should return undefined', function () {\n expect(wrapper.toString()).to.be.undefined;\n });\n\n it('should be settable by changing the title', function () {\n wrapper.citation.title = 'Title';\n expect(wrapper.toString()).equals('Anonymous (n.d.) Title');\n });\n });\n });\n\n citations.forEach((test, index) => {\n describe(`for test citation #${index + 1}`, function () {\n const wrapper = new phyx.CitationWrapper(test.citation);\n\n describe('#constructor', function () {\n it('should return a CitationWrapper', function () {\n expect(wrapper).to.be.an.instanceOf(phyx.CitationWrapper);\n });\n });\n\n describe('#toString', function () {\n it('should return the expected string', function () {\n expect(wrapper.toString()).to.equal(test.bibliographicCitation);\n });\n });\n });\n });\n});\n", @@ -4200,7 +4428,7 @@ "lineNumber": 1 }, { - "__docId__": 238, + "__docId__": 246, "kind": "test", "name": "describe0", "testId": 0, @@ -4213,7 +4441,7 @@ "lineNumber": 16 }, { - "__docId__": 239, + "__docId__": 247, "kind": "test", "name": "describe1", "testId": 1, @@ -4226,7 +4454,7 @@ "lineNumber": 57 }, { - "__docId__": 240, + "__docId__": 248, "kind": "test", "name": "describe2", "testId": 2, @@ -4239,7 +4467,7 @@ "lineNumber": 60 }, { - "__docId__": 241, + "__docId__": 249, "kind": "test", "name": "it3", "testId": 3, @@ -4252,7 +4480,7 @@ "lineNumber": 61 }, { - "__docId__": 242, + "__docId__": 250, "kind": "test", "name": "describe4", "testId": 4, @@ -4265,7 +4493,7 @@ "lineNumber": 66 }, { - "__docId__": 243, + "__docId__": 251, "kind": "test", "name": "it5", "testId": 5, @@ -4278,7 +4506,7 @@ "lineNumber": 67 }, { - "__docId__": 244, + "__docId__": 252, "kind": "test", "name": "it6", "testId": 6, @@ -4291,7 +4519,7 @@ "lineNumber": 71 }, { - "__docId__": 245, + "__docId__": 253, "kind": "test", "name": "describe7", "testId": 7, @@ -4303,7 +4531,7 @@ "lineNumber": 79 }, { - "__docId__": 246, + "__docId__": 254, "kind": "test", "name": "describe8", "testId": 8, @@ -4316,7 +4544,7 @@ "lineNumber": 82 }, { - "__docId__": 247, + "__docId__": 255, "kind": "test", "name": "it9", "testId": 9, @@ -4329,7 +4557,7 @@ "lineNumber": 83 }, { - "__docId__": 248, + "__docId__": 256, "kind": "test", "name": "describe10", "testId": 10, @@ -4342,7 +4570,7 @@ "lineNumber": 88 }, { - "__docId__": 249, + "__docId__": 257, "kind": "test", "name": "it11", "testId": 11, @@ -4355,7 +4583,7 @@ "lineNumber": 89 }, { - "__docId__": 250, + "__docId__": 258, "kind": "testFile", "name": "test/examples.js", "content": "/*\n * Test conversion on example files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\n\nconst chai = require('chai');\nconst Ajv = require('ajv');\n\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/*\n * Constants\n */\n// If REPLACE_EXISTING is set to true, we replace the existing JSON-LD and N-Quads\n// files rather than comparing them -- not a good way to test, but useful when\n// the output has changed.\nconst REPLACE_EXISTING = false;\n\n/**\n * Test whether conversion of Phyx files to an OWL ontology occurs predictably.\n */\n\ndescribe('PhyxWrapper', function () {\n const ajv = new Ajv({\n allErrors: true, // Display all error messages, not just the first.\n });\n const validator = ajv.compile(\n JSON.parse(\n fs.readFileSync(\n path.resolve(__dirname, '../docs/context/development/schema.json')\n )\n )\n );\n\n describe('Test all correct example Phyx files', function () {\n const examples = fs.readdirSync(path.resolve(__dirname, './examples/correct'))\n .filter(filename => filename.endsWith('.json'));\n\n examples.forEach((example) => {\n const basename = path.resolve(__dirname, './examples/correct', path.parse(example).name);\n const jsonFilename = `${basename}.json`;\n const jsonldFilename = `${basename}.jsonld`;\n const nqFilename = `${basename}.nq`;\n\n let json;\n let jsonld;\n let nq;\n\n describe(`Test file '${example}'`, function () {\n it('should be loadable', function () {\n json = JSON.parse(fs.readFileSync(jsonFilename));\n expect(json).to.be.an('object');\n });\n\n it('should validate against our JSON schema', function () {\n const valid = validator(json);\n expect(\n validator.errors,\n `The following validation errors were generated: ${JSON.stringify(validator.errors, null, 2)}`\n ).to.be.null;\n expect(valid).to.be.true;\n });\n\n it('should be able to convertible to an OWL Ontology', function () {\n this.timeout(10000);\n jsonld = new phyx.PhyxWrapper(json)\n .asJSONLD('http://example.org/phyx.js/example#');\n if (REPLACE_EXISTING) {\n fs.writeFileSync(\n jsonldFilename,\n JSON.stringify(jsonld, null, 2)\n );\n }\n expect(jsonld).to.be.an('object');\n });\n\n it('should generate the same OWL ontology as it generated earlier', function () {\n const expectedJSONLD = JSON.parse(fs.readFileSync(jsonldFilename));\n expect(jsonld).to.deep.equal(expectedJSONLD);\n });\n\n it('should be convertible to n-quads', function () {\n this.timeout(10000);\n\n return new phyx.PhyxWrapper(json)\n .toRDF('http://example.org/phyx.js/example#', path.resolve(__dirname, 'examples', 'correct'))\n .then((rdf) => {\n nq = rdf;\n if (REPLACE_EXISTING) fs.writeFileSync(nqFilename, nq);\n expect(nq).to.be.a('string');\n });\n });\n\n it('should generate the same n-quads ontology as it generated earlier', function () {\n const expectedNQ = fs.readFileSync(nqFilename).toString();\n expect(nq).to.deep.equal(expectedNQ);\n });\n });\n });\n });\n\n describe('Test incorrect example Phyx files that should fail validation', function () {\n const filesThatShouldFailValidation = [\n {\n fileName: 'examples/incorrect/no-context.json',\n expectedErrors: [{\n dataPath: '',\n keyword: 'required',\n message: \"should have required property '@context'\",\n params: {\n missingProperty: '@context',\n },\n schemaPath: '#/required',\n }],\n },\n {\n fileName: 'examples/incorrect/invalid-specifier.json',\n expectedErrors: [\n {\n dataPath: '.phylorefs[0].internalSpecifiers',\n keyword: 'minItems',\n message: 'should NOT have fewer than 1 items',\n params: {\n limit: 1,\n },\n schemaPath: '#/properties/phylorefs/items/properties/internalSpecifiers/minItems',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0].hasName',\n keyword: 'required',\n message: \"should have required property 'nameComplete'\",\n params: {\n missingProperty: 'nameComplete',\n },\n schemaPath: '#/required',\n },\n {\n dataPath: \".phylorefs[0].externalSpecifiers[0]['@type']\",\n keyword: 'enum',\n message: 'should be equal to one of the allowed values',\n params: {\n allowedValues: [\n 'http://rs.tdwg.org/dwc/terms/Occurrence',\n ],\n },\n schemaPath: '#/properties/%40type/enum',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0].hasName',\n keyword: 'required',\n message: \"should have required property 'nameComplete'\",\n params: {\n missingProperty: 'nameComplete',\n },\n schemaPath: '#/required',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: '@type',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/additionalProperties',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'hasName',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/additionalProperties',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'label',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/additionalProperties',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'required',\n message: \"should have required property '@id'\",\n params: {\n missingProperty: '@id',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/required',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'anyOf',\n message: 'should match some schema in anyOf',\n params: {},\n schemaPath: '#/anyOf',\n },\n ],\n },\n {\n fileName: 'examples/incorrect/unexpected-field-in-contributor.json',\n expectedErrors: [{\n dataPath: '.contributors[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'first_name',\n },\n schemaPath: '#/definitions/contributor/additionalProperties',\n }, {\n dataPath: '.contributors[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'last_name',\n },\n schemaPath: '#/definitions/contributor/additionalProperties',\n },\n ],\n },\n ];\n\n filesThatShouldFailValidation.forEach((entry) => {\n describe(`Example file ${entry.fileName}`, function () {\n it('should not validate against our JSON schema', function () {\n const phyxContent = JSON.parse(\n fs.readFileSync(\n path.resolve(__dirname, entry.fileName)\n )\n );\n const valid = validator(phyxContent);\n expect(validator.errors).to.deep.equal(entry.expectedErrors);\n expect(valid).to.not.be.true;\n });\n });\n });\n });\n});\n", @@ -4366,7 +4594,7 @@ "lineNumber": 1 }, { - "__docId__": 251, + "__docId__": 259, "kind": "test", "name": "describe12", "testId": 12, @@ -4379,7 +4607,7 @@ "lineNumber": 27 }, { - "__docId__": 252, + "__docId__": 260, "kind": "test", "name": "describe13", "testId": 13, @@ -4392,7 +4620,7 @@ "lineNumber": 39 }, { - "__docId__": 253, + "__docId__": 261, "kind": "test", "name": "describe14", "testId": 14, @@ -4404,7 +4632,7 @@ "lineNumber": 53 }, { - "__docId__": 254, + "__docId__": 262, "kind": "test", "name": "it15", "testId": 15, @@ -4417,7 +4645,7 @@ "lineNumber": 54 }, { - "__docId__": 255, + "__docId__": 263, "kind": "test", "name": "it16", "testId": 16, @@ -4430,7 +4658,7 @@ "lineNumber": 59 }, { - "__docId__": 256, + "__docId__": 264, "kind": "test", "name": "it17", "testId": 17, @@ -4443,7 +4671,7 @@ "lineNumber": 68 }, { - "__docId__": 257, + "__docId__": 265, "kind": "test", "name": "it18", "testId": 18, @@ -4456,7 +4684,7 @@ "lineNumber": 81 }, { - "__docId__": 258, + "__docId__": 266, "kind": "test", "name": "it19", "testId": 19, @@ -4469,7 +4697,7 @@ "lineNumber": 86 }, { - "__docId__": 259, + "__docId__": 267, "kind": "test", "name": "it20", "testId": 20, @@ -4482,7 +4710,7 @@ "lineNumber": 98 }, { - "__docId__": 260, + "__docId__": 268, "kind": "test", "name": "describe21", "testId": 21, @@ -4495,7 +4723,7 @@ "lineNumber": 106 }, { - "__docId__": 261, + "__docId__": 269, "kind": "test", "name": "describe22", "testId": 22, @@ -4507,7 +4735,7 @@ "lineNumber": 230 }, { - "__docId__": 262, + "__docId__": 270, "kind": "test", "name": "it23", "testId": 23, @@ -4520,10 +4748,10 @@ "lineNumber": 231 }, { - "__docId__": 263, + "__docId__": 271, "kind": "testFile", "name": "test/jphyloref.js", - "content": "/*\n * Use JPhyloRef to ensure that the expected JSON-LD files pass testing.\n * A different test, `examples.js`, will then test whether the current Phyx.js\n * produces a file identical to the expected JSON-LD files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\nconst childProcess = require('child_process');\n\nconst Downloader = require('nodejs-file-downloader');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Constants\n */\n// The version of JPhyloRef to download.\nconst JPHYLOREF_VERSION = '0.4.0';\n\n// The URL from where JPhyloRef should be downloaded.\nconst JPHYLOREF_URL = `https://repo.maven.apache.org/maven2/org/phyloref/jphyloref/${JPHYLOREF_VERSION}/jphyloref-${JPHYLOREF_VERSION}.jar`;\n// Where should the JPhyloRef be stored?\nconst JPHYLOREF_PATH = path.resolve(__dirname, `jphyloref-${JPHYLOREF_VERSION}.jar`);\n\n/**\n * Test whether the expected JSON-LD files pass testing using JPhyloRef.\n */\n\ndescribe('JPhyloRef', function () {\n describe('download JPhyloRef', function () {\n // TODO: we should eventually use SHA to ensure that we have the expected file.\n if (\n fs.existsSync(JPHYLOREF_PATH)\n && fs.statSync(JPHYLOREF_PATH).size > 0\n ) {\n it('has already been downloaded', function () {\n expect(true);\n });\n } else {\n it('should be downloadable', function () {\n this.timeout(10000);\n // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.\n return new Downloader({\n url: JPHYLOREF_URL,\n directory: path.dirname(JPHYLOREF_PATH),\n fileName: path.basename(JPHYLOREF_PATH),\n }).download();\n });\n }\n });\n\n describe('test example JSON-LD files using JPhyloRef', function () {\n fs.readdirSync(path.resolve(__dirname, 'examples', 'correct'))\n .filter(filename => filename.endsWith('.nq'))\n .forEach((filename) => {\n it(`testing ${filename}`, function () {\n this.timeout(60000);\n\n // Start JPhyloRef to test filename.\n const filePath = path.resolve(__dirname, 'examples', 'correct', filename);\n const child = childProcess.spawnSync(\n 'java',\n [\n '-jar', JPHYLOREF_PATH,\n 'test', filePath,\n ],\n {\n encoding: 'utf8',\n shell: true,\n }\n );\n const matches = /Testing complete:(\\d+) successes, (\\d+) failures, (\\d+) failures marked TODO, (\\d+) skipped./.exec(child.stderr);\n\n expect(matches, `Test result line not found in STDERR <${child.stderr}>`).to.have.lengthOf(5);\n\n // const countSuccess = Number(matches[1]);\n const countFailure = Number(matches[2]);\n const countTODOs = Number(matches[3]);\n // const countSkipped = Number(matches[4]);\n\n // We can't test for one or more successes since some example Phyx file\n // such as apomorphy-based phyloreferences don't have any successes at all.\n // expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);\n expect(countFailure, 'Expected zero failures').to.equal(0);\n expect(countTODOs, 'Expected zero TODOs').to.equal(0);\n\n // An exit code of 0 means success. An exit code of 255 means that while\n // there were no successes, there were also no failures. Either is acceptable here.\n expect(child.status).to.be.oneOf([0, 255]);\n });\n });\n });\n});\n", + "content": "/*\n * Use JPhyloRef to ensure that the expected JSON-LD files pass testing.\n * A different test, `examples.js`, will then test whether the current Phyx.js\n * produces a file identical to the expected JSON-LD files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\nconst childProcess = require('child_process');\n\nconst Downloader = require('nodejs-file-downloader');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Constants\n */\n// The version of JPhyloRef to download.\nconst JPHYLOREF_VERSION = '1.1.1';\n\n// The URL from where JPhyloRef should be downloaded.\nconst JPHYLOREF_URL = `https://repo.maven.apache.org/maven2/org/phyloref/jphyloref/${JPHYLOREF_VERSION}/jphyloref-${JPHYLOREF_VERSION}.jar`;\n// Where should the JPhyloRef be stored?\nconst JPHYLOREF_PATH = path.resolve(__dirname, `jphyloref-${JPHYLOREF_VERSION}.jar`);\n\n/**\n * Test whether the expected JSON-LD files pass testing using JPhyloRef.\n */\n\ndescribe('JPhyloRef', function () {\n describe('download JPhyloRef', function () {\n // TODO: we should eventually use SHA to ensure that we have the expected file.\n if (\n fs.existsSync(JPHYLOREF_PATH)\n && fs.statSync(JPHYLOREF_PATH).size > 0\n ) {\n it('has already been downloaded', function () {\n expect(true);\n });\n } else {\n it('should be downloadable', function () {\n this.timeout(10000);\n // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.\n return new Downloader({\n url: JPHYLOREF_URL,\n directory: path.dirname(JPHYLOREF_PATH),\n fileName: path.basename(JPHYLOREF_PATH),\n }).download();\n });\n }\n });\n\n describe('test example JSON-LD files using JPhyloRef', function () {\n fs.readdirSync(path.resolve(__dirname, 'examples', 'correct'))\n .filter(filename => filename.endsWith('.nq'))\n .forEach((filename) => {\n it(`testing ${filename}`, function () {\n this.timeout(60000);\n\n // Start JPhyloRef to test filename.\n const filePath = path.resolve(__dirname, 'examples', 'correct', filename);\n const child = childProcess.spawnSync(\n 'java',\n [\n '-jar', JPHYLOREF_PATH,\n 'test', filePath,\n ],\n {\n encoding: 'utf8',\n shell: true,\n }\n );\n const matches = /Testing complete:(\\d+) successes, (\\d+) failures, (\\d+) failures marked TODO, (\\d+) skipped./.exec(child.stderr);\n\n expect(matches, `Test result line not found in STDERR <${child.stderr}>`).to.have.lengthOf(5);\n\n // const countSuccess = Number(matches[1]);\n const countFailure = Number(matches[2]);\n const countTODOs = Number(matches[3]);\n // const countSkipped = Number(matches[4]);\n\n // We can't test for one or more successes since some example Phyx file\n // such as apomorphy-based phyloreferences don't have any successes at all.\n // expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);\n expect(countFailure, 'Expected zero failures').to.equal(0);\n expect(countTODOs, 'Expected zero TODOs').to.equal(0);\n\n // An exit code of 0 means success. An exit code of 255 means that while\n // there were no successes, there were also no failures. Either is acceptable here.\n expect(child.status).to.be.oneOf([0, 255]);\n });\n });\n });\n});\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/jphyloref.js", "access": null, @@ -4531,7 +4759,7 @@ "lineNumber": 1 }, { - "__docId__": 264, + "__docId__": 272, "kind": "test", "name": "describe24", "testId": 24, @@ -4544,7 +4772,7 @@ "lineNumber": 31 }, { - "__docId__": 265, + "__docId__": 273, "kind": "test", "name": "describe25", "testId": 25, @@ -4557,7 +4785,7 @@ "lineNumber": 32 }, { - "__docId__": 266, + "__docId__": 274, "kind": "test", "name": "it26", "testId": 26, @@ -4570,7 +4798,7 @@ "lineNumber": 38 }, { - "__docId__": 267, + "__docId__": 275, "kind": "test", "name": "it27", "testId": 27, @@ -4583,7 +4811,7 @@ "lineNumber": 42 }, { - "__docId__": 268, + "__docId__": 276, "kind": "test", "name": "describe28", "testId": 28, @@ -4596,7 +4824,7 @@ "lineNumber": 54 }, { - "__docId__": 269, + "__docId__": 277, "kind": "test", "name": "it29", "testId": 29, @@ -4608,7 +4836,7 @@ "lineNumber": 58 }, { - "__docId__": 270, + "__docId__": 278, "kind": "testFile", "name": "test/nomenclatural-codes.js", "content": "/*\n * Test nomenclatural code lookups and fallback behavior. While most of the\n * nomenclatural code logic is in TaxonNameWrapper, we need to provide fallback\n * nomenclatural codes in TaxonConceptWrapper, TaxonomicUnitWrapper and\n * PhylorefWrapper as well. This test file makes sure that this functionality\n * works correctly at all of these levels.\n */\n\nconst fs = require('fs');\nconst path = require('path');\n\nconst { cloneDeep } = require('lodash');\n\nconst chai = require('chai');\nconst phyx = require('../src');\nconst owlterms = require('../src/utils/owlterms');\n\n// Use Chai's expect API.\nconst expect = chai.expect;\n\n/* The list of expected fields in nomenclatural details. */\nconst EXPECTED_NOMEN_DETAIL_FIELDS = ['iri', 'shortName', 'label', 'title'];\n\n/* Some example taxon names to use. */\nconst ranaLuteiventris = {\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n hasName: {\n label: 'Rana luteiventris',\n },\n occurrenceID: 'MVZ 225749',\n};\n\n/*\n * The nomenclatural codes are set up in TaxonNameWrapper, so that's where\n * most of the nomenclatural code behavior code exists.\n */\ndescribe('TaxonNameWrapper', function () {\n describe('#getNomenclaturalCodes', function () {\n it('should provide a non-empty list with the expected keys', function () {\n const nomenCodes = phyx.TaxonNameWrapper.getNomenclaturalCodes();\n\n expect(nomenCodes)\n .to.be.an('array')\n .that.is.not.empty;\n\n nomenCodes.forEach((nomenCode) => {\n expect(nomenCode).to.have.all.keys(EXPECTED_NOMEN_DETAIL_FIELDS);\n });\n });\n });\n\n describe('#getNomenCodeDetails', function () {\n it('should provide details for some built-in codes', function () {\n const codesToTest = {\n 'Code not known': owlterms.UNKNOWN_CODE,\n ICZN: owlterms.ICZN_CODE,\n ICN: owlterms.ICN_CODE,\n ICNP: owlterms.ICNP_CODE,\n ICTV: owlterms.ICTV_CODE,\n ICNCP: owlterms.ICNCP_CODE,\n };\n\n Object.keys(codesToTest).forEach((code) => {\n const uri = codesToTest[code];\n const details = phyx.TaxonNameWrapper.getNomenCodeDetails(uri);\n expect(details).to.have.all.keys(EXPECTED_NOMEN_DETAIL_FIELDS);\n expect(details.shortName).to.equal(code);\n });\n });\n });\n\n describe('#nomenclaturalCodeDetails', function () {\n it('should provide nomenclatural code details for an example taxon name', function () {\n const wrapper = new phyx.TaxonNameWrapper(ranaLuteiventris.hasName);\n expect(wrapper.nomenclaturalCode).to.equal(owlterms.UNKNOWN_CODE);\n expect(wrapper.nomenclaturalCodeDetails.shortName).to.equal('Code not known');\n\n const wrapperWithDefault = new phyx.TaxonNameWrapper(\n ranaLuteiventris.hasName,\n owlterms.ICZN_CODE\n );\n expect(wrapperWithDefault.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n expect(wrapperWithDefault.nomenclaturalCodeDetails.shortName).to.equal('ICZN');\n\n const nameWithNomenCode = cloneDeep(ranaLuteiventris.hasName);\n nameWithNomenCode.nomenclaturalCode = owlterms.ICZN_CODE;\n const wrapperWithExplicit = new phyx.TaxonNameWrapper(nameWithNomenCode, owlterms.ICN_CODE);\n expect(wrapperWithExplicit.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n expect(wrapperWithExplicit.nomenclaturalCodeDetails.shortName).to.equal('ICZN');\n });\n });\n});\n\n/*\n * Make sure we can set a default nomenclatural code in TaxonConceptWrapper.\n */\ndescribe('TaxonConceptWrapper', function () {\n describe('#nomenCode', function () {\n const wrapper = new phyx.TaxonConceptWrapper(ranaLuteiventris);\n\n it('should return UNKNOWN_CODE if one is not set', function () {\n expect(wrapper.nomenCode).to.equal(owlterms.UNKNOWN_CODE);\n });\n\n it('should return the default nomenclatural code if one is provided', function () {\n const wrapperWithDefault = new phyx.TaxonConceptWrapper(ranaLuteiventris, owlterms.ICZN_CODE);\n expect(wrapperWithDefault.nomenCode).to.equal(owlterms.ICZN_CODE);\n expect(wrapperWithDefault.nomenCodeDetails.shortName).to.equal('ICZN');\n });\n });\n});\n\n/*\n * There are two ways in which nomenclatural codes can be set at the Phyx level:\n * (1) If there is a `defaultNomenclaturalCodeIRI` field at the Phyx level,\n * that will be used to provide a nomenclatural code for all specifiers\n * without a nomenclatural code as well as for all the phylogeny nodes.\n * (2) If no `defaultNomenclaturalCodeIRI` is provided, but all the specifiers\n * on all the phylorefs in the file have the same nomenclatural code, then\n * that code will be used on all the phylogeny nodes.\n */\ndescribe('PhyxWrapper', function () {\n it('should use the defaultNomenclaturalCodeIRI for phylogeny nodes', function () {\n // The examples/correct/alligatoridae_default_nomen_code.json file has\n // a `defaultNomenclaturalCodeIRI`.\n const json = JSON.parse(fs.readFileSync(\n path.resolve(__dirname, './examples/correct/alligatoridae_default_nomen_code.json')\n ));\n\n // Make sure this is the right example file.\n expect(json, 'Expected alligatoridae_default_nomen_code.json to include a defaultNomenclaturalCodeIRI value.')\n .to.include.key('defaultNomenclaturalCodeIRI');\n const defaultNomenclaturalCodeIRI = json.defaultNomenclaturalCodeIRI;\n\n const jsonld = new phyx.PhyxWrapper(json).asJSONLD();\n\n // Step 1. Check the phyloreferences. Neither specifier has a nomenclatural code,\n // but they should pick up the default nomenclatural code for the Phyx file.\n expect(jsonld.phylorefs).to.be.an('array').of.length(1);\n const phyloref1 = jsonld.phylorefs[0];\n expect(phyloref1).to.be.an('object').and.to.include.key('equivalentClass');\n\n const equivalentClass = phyloref1.equivalentClass;\n const specifierExprs = equivalentClass.someValuesFrom.intersectionOf;\n expect(specifierExprs).to.be.an('array').with.length(2);\n\n specifierExprs.forEach((specifierExpr) => {\n const nameExprs = specifierExpr.someValuesFrom.someValuesFrom.intersectionOf;\n\n expect(nameExprs).to.be.an('array').with.length(2).and.to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': defaultNomenclaturalCodeIRI,\n },\n }\n );\n });\n\n // Step 2. Check the phylogenies.\n expect(jsonld).to.include.key('phylogenies');\n expect(jsonld.phylogenies).to.be.an('array').with.length(1);\n\n const phylogeny1 = jsonld.phylogenies[0];\n expect(phylogeny1).to.include.key('nodes');\n\n phylogeny1.nodes.forEach((node) => {\n const nodeType = node['rdf:type'];\n\n // There should be at least one type definition: obo:CDAO_0000140.\n expect(nodeType[0]).to.deep.equal({\n '@id': 'obo:CDAO_0000140',\n });\n\n // The second type definition -- if it exists -- must be a name entry,\n // which should include the appropriate nomenclatural code.\n if (nodeType.length > 1) {\n const nameEntry = nodeType[1];\n expect(nameEntry.someValuesFrom.someValuesFrom.intersectionOf).to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': defaultNomenclaturalCodeIRI,\n },\n }\n );\n }\n });\n });\n\n it('should use the inferred nomenclatural code for phylogeny nodes', function () {\n // The examples/correct/alligatoridae_inferred_nomen_code.json file does not have\n // a `defaultNomenclaturalCodeIRI`, but the nomenclatural code can be inferred from\n // its specifiers.\n const json = JSON.parse(fs.readFileSync(\n path.resolve(__dirname, './examples/correct/alligatoridae_inferred_nomen_code.json')\n ));\n\n // Make sure this is the right example file.\n expect(json, 'Expected alligatoridae_inferred_nomen_code.json to not include a defaultNomenclaturalCodeIRI value.')\n .to.not.include.key('defaultNomenclaturalCodeIRI');\n\n const wrapped = new phyx.PhyxWrapper(json);\n const inferredNomenCode = wrapped.defaultNomenCode;\n expect(inferredNomenCode).to.equal(owlterms.ICZN_CODE);\n\n const jsonld = wrapped.asJSONLD();\n\n // Step 1. Check the phyloreferences. Since only *Caiman crocodilus* has a\n // nomenclatural code set, we should make sure that the other specifier\n // picks up the inferred nomenclatural code of the entire file.\n expect(jsonld.phylorefs).to.be.an('array').of.length(1);\n const phyloref1 = jsonld.phylorefs[0];\n expect(phyloref1).to.be.an('object').and.to.include.key('equivalentClass');\n\n const equivalentClass = phyloref1.equivalentClass;\n const specifierExprs = equivalentClass.someValuesFrom.intersectionOf;\n expect(specifierExprs).to.be.an('array').with.length(2);\n\n specifierExprs.forEach((specifierExpr) => {\n const nameExprs = specifierExpr.someValuesFrom.someValuesFrom.intersectionOf;\n\n expect(nameExprs).to.be.an('array').with.length(2).and.to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': inferredNomenCode,\n },\n }\n );\n });\n\n // Step 2. Check the phylogenies.\n expect(jsonld).to.include.key('phylogenies');\n expect(jsonld.phylogenies).to.be.an('array').with.length(1);\n\n const phylogeny1 = jsonld.phylogenies[0];\n expect(phylogeny1).to.include.key('nodes');\n\n phylogeny1.nodes.forEach((node) => {\n const nodeType = node['rdf:type'];\n\n // There should be at least one type definition: obo:CDAO_0000140.\n expect(nodeType[0]).to.deep.equal({\n '@id': 'obo:CDAO_0000140',\n });\n\n // The second type definition -- if it exists -- must be a name entry,\n // which should include the appropriate nomenclatural code.\n if (nodeType.length > 1) {\n const nameEntry = nodeType[1];\n expect(nameEntry.someValuesFrom.someValuesFrom.intersectionOf).to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': inferredNomenCode,\n },\n }\n );\n }\n });\n });\n});\n", @@ -4619,7 +4847,7 @@ "lineNumber": 1 }, { - "__docId__": 271, + "__docId__": 279, "kind": "test", "name": "describe30", "testId": 30, @@ -4632,7 +4860,7 @@ "lineNumber": 41 }, { - "__docId__": 272, + "__docId__": 280, "kind": "test", "name": "describe31", "testId": 31, @@ -4645,7 +4873,7 @@ "lineNumber": 42 }, { - "__docId__": 273, + "__docId__": 281, "kind": "test", "name": "it32", "testId": 32, @@ -4658,7 +4886,7 @@ "lineNumber": 43 }, { - "__docId__": 274, + "__docId__": 282, "kind": "test", "name": "describe33", "testId": 33, @@ -4671,7 +4899,7 @@ "lineNumber": 56 }, { - "__docId__": 275, + "__docId__": 283, "kind": "test", "name": "it34", "testId": 34, @@ -4684,7 +4912,7 @@ "lineNumber": 57 }, { - "__docId__": 276, + "__docId__": 284, "kind": "test", "name": "describe35", "testId": 35, @@ -4697,7 +4925,7 @@ "lineNumber": 76 }, { - "__docId__": 277, + "__docId__": 285, "kind": "test", "name": "it36", "testId": 36, @@ -4710,7 +4938,7 @@ "lineNumber": 77 }, { - "__docId__": 278, + "__docId__": 286, "kind": "test", "name": "describe37", "testId": 37, @@ -4723,7 +4951,7 @@ "lineNumber": 101 }, { - "__docId__": 279, + "__docId__": 287, "kind": "test", "name": "describe38", "testId": 38, @@ -4736,7 +4964,7 @@ "lineNumber": 102 }, { - "__docId__": 280, + "__docId__": 288, "kind": "test", "name": "it39", "testId": 39, @@ -4749,7 +4977,7 @@ "lineNumber": 105 }, { - "__docId__": 281, + "__docId__": 289, "kind": "test", "name": "it40", "testId": 40, @@ -4762,7 +4990,7 @@ "lineNumber": 109 }, { - "__docId__": 282, + "__docId__": 290, "kind": "test", "name": "describe41", "testId": 41, @@ -4775,7 +5003,7 @@ "lineNumber": 126 }, { - "__docId__": 283, + "__docId__": 291, "kind": "test", "name": "it42", "testId": 42, @@ -4788,7 +5016,7 @@ "lineNumber": 127 }, { - "__docId__": 284, + "__docId__": 292, "kind": "test", "name": "it43", "testId": 43, @@ -4801,447 +5029,587 @@ "lineNumber": 197 }, { - "__docId__": 285, + "__docId__": 293, "kind": "testFile", - "name": "test/phylogenies.js", - "content": "/*\n * Test phylogenies.\n */\n\n// Load phyx.js, our PHYX library, and chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Make it easier to access owlterms.\nconst owlterms = require('../src/utils/owlterms');\n\n// Use Chai's expect API for testing.\nconst expect = chai.expect;\n\n/*\n * These tests focus on three aspects of PhylogenyWrapper:\n * - Whether it can detect errors in an input Newick string.\n * - Retrieve taxonomic units from the phylogeny based on either their node label\n * or on the additional properties associated with the phylogeny.\n * - Whether we can match specifiers with nodes on the phylogeny if they share\n * taxonomic units that match.\n */\n\ndescribe('PhylogenyWrapper', function () {\n describe('#constructor', function () {\n describe('when used to wrap an empty object', function () {\n it('should return a PhylogenyWrapper object', function () {\n expect(new phyx.PhylogenyWrapper({}))\n .to.be.an.instanceOf(phyx.PhylogenyWrapper);\n });\n });\n });\n\n describe('#getErrorsInNewickString', function () {\n describe('when given a correct Newick string', function () {\n const correctNewickStrings = [\n '(A:3, B:5, (C:6, N:7));',\n ];\n\n it('should return an empty list of errors', function () {\n correctNewickStrings.forEach((str) => {\n expect(phyx.PhylogenyWrapper.getErrorsInNewickString(str)).to.be.empty;\n });\n });\n });\n\n describe('when given an empty Newick string', function () {\n const emptyNewickStrings = [\n '()',\n '(); ',\n ];\n\n it('should return a single \"No phylogeny entered\" error', function () {\n emptyNewickStrings.forEach((newick) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(newick);\n expect(errors).to.have.length(1);\n expect(errors[0].title).to.equal('No phylogeny entered');\n });\n });\n });\n\n describe('when given an unbalanced Newick string', function () {\n const unbalancedNewickString = [\n {\n newick: '(A, B))',\n expected: 'You have 1 too few open parentheses',\n },\n {\n newick: '(A, (B, (C, D))',\n expected: 'You have 1 too many open parentheses',\n },\n {\n newick: '(A, (B, (C, (((D))',\n expected: 'You have 4 too many open parentheses',\n },\n ];\n\n it('should report how many parentheses are missing', function () {\n unbalancedNewickString.forEach((entry) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(entry.newick);\n\n // We should get two errors.\n expect(errors).to.have.lengthOf(2);\n\n // Should include an error about the unbalanced parentheses.\n expect(errors[0].title).to.equal('Unbalanced parentheses in Newick string');\n expect(errors[0].message).to.equal(entry.expected);\n\n // Should include an error passed on from the Newick parser.\n expect(errors[1].title).to.equal('Error parsing phylogeny');\n expect(errors[1].message).to.include('An error occured while parsing this phylogeny:');\n });\n });\n });\n\n describe('when given an incomplete Newick string', function () {\n const incompleteNewickStrings = [\n ';',\n '))(A, (B, ',\n ];\n\n it('should report an error parsing the phylogeny', function () {\n incompleteNewickStrings.forEach((newick) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(newick);\n\n expect(errors).to.have.lengthOf(1);\n expect(errors[0].title).to.equal('Error parsing phylogeny');\n expect(errors[0].message).to.include('An error occured while parsing this phylogeny:');\n });\n });\n });\n });\n\n describe('#getNodeLabels', function () {\n const tests = [\n {\n // Note that 'newick' is the input for this test.\n newick: '(A, (B, (C, D))E, F, (G, (H, I, J)K, L)M, N)O',\n // The following keys indicate the expected all/internal/terminal node labels\n // for the given Newick string.\n nodeLabels: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O'],\n internalNodeLabels: ['E', 'K', 'M', 'O'],\n terminalNodeLabels: ['A', 'B', 'C', 'D', 'F', 'G', 'H', 'I', 'J', 'L', 'N'],\n },\n ];\n\n tests.forEach((test) => {\n const wrapper = new phyx.PhylogenyWrapper({ newick: test.newick });\n\n describe('For a particular Newick phylogeny', function () {\n it('should return a list of all node labels by default', function () {\n expect(wrapper.getNodeLabels().sort())\n .to.have.members(test.nodeLabels.sort());\n });\n\n it('should return a list of internal labels when asked for internal labels', function () {\n expect(wrapper.getNodeLabels('internal').sort())\n .to.have.members(test.internalNodeLabels.sort());\n });\n\n it('should return a list of terminal labels when asked for terminal labels', function () {\n expect(wrapper.getNodeLabels('terminal').sort())\n .to.have.members(test.terminalNodeLabels.sort());\n });\n });\n });\n });\n\n describe('given a particular phylogeny with additional node properties', function () {\n const wrapper = new phyx.PhylogenyWrapper({\n newick: '((MVZ225749, MVZ191016), Rana boylii)',\n additionalNodeProperties: {\n MVZ225749: {\n representsTaxonomicUnits: [{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:225749',\n }],\n },\n MVZ191016: {\n representsTaxonomicUnits: [{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:191016',\n }],\n },\n },\n });\n\n describe('#getNodeLabels', function () {\n it('should return the list of node labels from the Newick string', function () {\n expect(wrapper.getNodeLabels().sort())\n .to.have.members([\n 'MVZ191016',\n 'MVZ225749',\n 'Rana boylii',\n ]);\n });\n });\n\n describe('#getTaxonomicUnitsForNodeLabel', function () {\n it('should return the list of taxonomic units using information from additional node properties', function () {\n expect(wrapper.getTaxonomicUnitsForNodeLabel('MVZ191016')).to.deep.equal([{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:191016',\n }]);\n\n expect(wrapper.getTaxonomicUnitsForNodeLabel('MVZ225749')).to.deep.equal([{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:225749',\n }]);\n\n expect(wrapper.getTaxonomicUnitsForNodeLabel('Rana boylii')).to.deep.equal([{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n label: 'Rana boylii',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana boylii',\n nameComplete: 'Rana boylii',\n genusPart: 'Rana',\n specificEpithet: 'boylii',\n },\n }]);\n });\n });\n\n describe('#getNodeLabelsMatchedBySpecifier', function () {\n it('should match a specifier to MVZ225749 based on occurrence ID', function () {\n const specifier1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:225749',\n };\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier1))\n .to.have.members(['MVZ225749']);\n });\n\n it('should match a specifier to MVZ191016 based on occurrence ID', function () {\n const specifier2 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:191016',\n };\n\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier2))\n .to.have.members(['MVZ191016']);\n });\n\n it('should match a specifier to node \"Rana boylii\" based on the parsed scientific name', function () {\n const specifier3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana boylii',\n };\n\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier3))\n .to.have.members(['Rana boylii']);\n });\n });\n });\n\n describe('#asJSONLD', function () {\n it('should preserve an existing @id on input phylogenies', function () {\n const jsonld = new phyx.PhylogenyWrapper({\n '@id': '#providedId',\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n }).asJSONLD('#phylogeny0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#providedId');\n });\n it('should generate a new @id on input phylorefs', function () {\n const jsonld = new phyx.PhylogenyWrapper({\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n }, owlterms.ICZN_CODE).asJSONLD('#phylogeny0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#phylogeny0');\n });\n it('should generate the phylogeny in JSON-LD as expected', function () {\n const expectedResults = [\n {\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n jsonld: {\n '@id': '#',\n '@type': 'phyloref:ReferencePhylogenyEvidence',\n hasRootNode: { '@id': '#_node0' },\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n nodes: [\n {\n '@id': '#_node0',\n children: ['#_node1', '#_node2'],\n 'rdf:type': [{ '@id': owlterms.CDAO_NODE }],\n },\n {\n '@id': '#_node1',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Mus musculus',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Mus_musculus'],\n parent: '#_node0',\n representsTaxonomicUnits: [{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Mus',\n label: 'Mus_musculus',\n nameComplete: 'Mus musculus',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'musculus',\n },\n label: 'Mus_musculus',\n }],\n siblings: ['#_node2'],\n },\n {\n '@id': '#_node2',\n children: ['#_node3', '#_node4'],\n 'rdf:type': [{ '@id': owlterms.CDAO_NODE }],\n parent: '#_node0',\n siblings: ['#_node1'],\n },\n {\n '@id': '#_node3',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Panthera tigris',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Panthera_tigris'],\n parent: '#_node2',\n representsTaxonomicUnits: [{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Panthera',\n label: 'Panthera_tigris',\n nameComplete: 'Panthera tigris',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'tigris',\n },\n label: 'Panthera_tigris',\n }],\n siblings: ['#_node4'],\n },\n {\n '@id': '#_node4',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Homo sapiens',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Homo_sapiens'],\n parent: '#_node2',\n representsTaxonomicUnits: [\n {\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Homo',\n label: 'Homo_sapiens',\n nameComplete: 'Homo sapiens',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'sapiens',\n },\n label: 'Homo_sapiens',\n },\n ],\n siblings: ['#_node3'],\n },\n ],\n },\n },\n ];\n\n expectedResults.forEach((expected) => {\n const wrapper = new phyx.PhylogenyWrapper({\n '@id': '#',\n newick: expected.newick,\n }, owlterms.ICZN_CODE);\n expect(wrapper.asJSONLD('#phylogeny0')).to.deep.equal(expected.jsonld);\n });\n });\n });\n\n describe('#getParsedNewickWithIRIs', function () {\n const tests = [\n {\n newick: '(((A, B)C, D)E, F)G',\n result: {\n json: {\n '@id': '_node0',\n name: 'G',\n label: 'G',\n children: [\n { '@id': '_node1', name: 'F', label: 'F' },\n {\n '@id': '_node2',\n name: 'E',\n label: 'E',\n children: [\n { '@id': '_node3', name: 'D', label: 'D' },\n {\n '@id': '_node4',\n name: 'C',\n label: 'C',\n children: [\n { '@id': '_node5', name: 'B', label: 'B' },\n { '@id': '_node6', name: 'A', label: 'A' },\n ],\n },\n ],\n },\n ],\n },\n },\n },\n ];\n\n tests.forEach((test) => {\n it('should be able to parse a provided Newick string as expected', function () {\n expect(new phyx.PhylogenyWrapper({ newick: test.newick }).getParsedNewickWithIRIs(''))\n .to.deep.equal(test.result);\n });\n });\n });\n});\n", + "name": "test/normalization.js", + "content": "/*\n * Test normalization on examples/correct/normalization files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\n\nconst chai = require('chai');\n\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/**\n * When making the comparisons, we need to remove the `@id`s which would otherwise be different\n * between the phylorefs being compared.\n *\n * @param phyloref The phyloref whose '@id' needs to be removed.\n */\nfunction removeId(phyloref) {\n // Shallow copy the phyloref.\n const copiedPhyloref = Object.assign({}, phyloref);\n // Delete the '@id'.\n delete copiedPhyloref['@id'];\n return copiedPhyloref;\n}\n\n\n/**\n * Test whether normalization of phyloreferences and phylogenies work as expected.\n * This test does not cover Phyx normalization.\n */\n\ndescribe('Phyloref and phylogeny normalization', function () {\n describe('Test all normalization Phyx files', function () {\n /*\n * Normalization Phyx files consist of a number of phyloreferences and phylogenies. We can\n * test them by confirming:\n * - every phyloref or phylogeny should be DIFFERENT from every other.\n * - every phyloref or phylogeny whose `@id` ends with `_same` should be IDENTICAL to\n * every other phyloref or phylogeny whose `@id` ends with `_same` after NORMALIZATION (to\n * test non-same phyloref or phylogeny files, they should be placed in different files).\n * - every phyloref or phylogeny whose `@id` ends with `_different` should be DIFFERENT to\n * every phyloref or phylogeny whose `@id` ends with `_same` even after NORMALIZATION.\n */\n const normalizationExamples = fs\n .readdirSync(path.resolve(__dirname, './examples/correct/normalization'))\n .filter(filename => filename.endsWith('.json'));\n\n normalizationExamples.forEach((example) => {\n const basename = path.resolve(__dirname, './examples/correct/normalization', path.parse(example).name);\n const jsonFilename = `${basename}.json`;\n\n describe(`Normalization test file '${example}'`, function () {\n const phyxDoc = JSON.parse(fs.readFileSync(jsonFilename));\n const phylorefs = phyxDoc.phylorefs || [];\n const samePhylorefs = phylorefs.filter(p => (p['@id'] || '').endsWith('_same'));\n const differentPhylorefs = phylorefs.filter(p => (p['@id'] || '').endsWith('_different'));\n\n // We don't need phylogeny normalization yet, so there's no point in testing them.\n describe('Test phylogenies', function () {\n it(\"These tests have not yet been implemented since we don't have an urgent need for them.\");\n });\n\n // So we only focus on phyloreference normalization.\n describe('Test phyloreferences', function () {\n it('should have multiple same phyloreferences for testing', function () {\n expect(samePhylorefs).to.not.be.empty;\n });\n\n it('should not have any duplicate phylorefs (which would be pointless)', function () {\n // No two phyloreferences in a normalization file should be deeply identical to each\n // other, otherwise the test will be pointless.\n phylorefs.forEach((phyloref1) => {\n phylorefs.forEach((phyloref2) => {\n if (phyloref1 === phyloref2) return;\n expect(removeId(phyloref1))\n .to\n .not\n .deep\n .equal(removeId(phyloref2),\n 'No two phyloreferences in a single normalization file should be identical.');\n });\n });\n });\n\n it('should have pairs of `_same` phylorefs that are different, but are identical after normalization', function () {\n // Every pair of `_same` phyloreferences should be different.\n samePhylorefs.forEach((phyloref1) => {\n samePhylorefs.forEach((phyloref2) => {\n if (phyloref1 === phyloref2) return;\n expect(\n removeId(phyx.PhylorefWrapper.normalize(phyloref1))\n )\n .to\n .deep\n .equal(\n removeId(phyx.PhylorefWrapper.normalize(phyloref2)),\n `Expected phyloref ${phyloref1['@id']} to deeply equal ${phyloref2['@id']} `\n + 'after normalization'\n );\n });\n });\n });\n\n it('should have pairs of `_different` phylorefs that are different before and after normalization', function () {\n // Every pair of `_different` phyloreferences should be different from every `_same`\n // phyloreference, even after normalization.\n differentPhylorefs.forEach((phyloref1) => {\n samePhylorefs.forEach((phyloref2) => {\n if (phyloref1 === phyloref2) return;\n expect(\n removeId(phyx.PhylorefWrapper.normalize(phyloref1))\n )\n .to\n .not\n .deep\n .equal(\n removeId(phyx.PhylorefWrapper.normalize(phyloref2)),\n `Expected phyloref ${phyloref1['@id']} to not deeply equal ${phyloref2['@id']} `\n + 'after normalization'\n );\n });\n });\n });\n });\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/phylogenies.js", + "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/normalization.js", "access": null, "description": null, "lineNumber": 1 }, { - "__docId__": 286, + "__docId__": 294, "kind": "test", "name": "describe44", "testId": 44, - "memberof": "test/phylogenies.js", + "memberof": "test/normalization.js", "testDepth": 0, "static": true, - "longname": "test/phylogenies.js~describe44", + "longname": "test/normalization.js~describe44", "access": null, - "description": "PhylogenyWrapper", - "lineNumber": 24 + "description": "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization.", + "lineNumber": 34 }, { - "__docId__": 287, + "__docId__": 295, "kind": "test", "name": "describe45", "testId": 45, - "memberof": "test/phylogenies.js~describe44", + "memberof": "test/normalization.js~describe44", "testDepth": 1, "static": true, - "longname": "test/phylogenies.js~describe44.describe45", + "longname": "test/normalization.js~describe44.describe45", "access": null, - "description": "#constructor", - "lineNumber": 25 + "description": "Test all normalization Phyx files", + "lineNumber": 35 }, { - "__docId__": 288, + "__docId__": 296, "kind": "test", "name": "describe46", "testId": 46, - "memberof": "test/phylogenies.js~describe44.describe45", + "memberof": "test/normalization.js~describe44.describe45", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe45.describe46", + "longname": "test/normalization.js~describe44.describe45.describe46", "access": null, - "description": "when used to wrap an empty object", - "lineNumber": 26 + "lineNumber": 54 }, { - "__docId__": 289, + "__docId__": 297, "kind": "test", - "name": "it47", + "name": "describe47", "testId": 47, - "memberof": "test/phylogenies.js~describe44.describe45.describe46", + "memberof": "test/normalization.js~describe44.describe45.describe46", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe45.describe46.it47", + "longname": "test/normalization.js~describe44.describe45.describe46.describe47", "access": null, - "description": "should return a PhylogenyWrapper object", - "lineNumber": 27 + "description": "Test phylogenies", + "lineNumber": 61 }, { - "__docId__": 290, + "__docId__": 298, "kind": "test", - "name": "describe48", + "name": "it48", "testId": 48, - "memberof": "test/phylogenies.js~describe44", - "testDepth": 1, + "memberof": "test/normalization.js~describe44.describe45.describe46.describe47", + "testDepth": 4, "static": true, - "longname": "test/phylogenies.js~describe44.describe48", + "longname": "test/normalization.js~describe44.describe45.describe46.describe47.it48", "access": null, - "description": "#getErrorsInNewickString", - "lineNumber": 34 + "description": "These tests have not yet been implemented since we don't have an urgent need for them.", + "lineNumber": 62 }, { - "__docId__": 291, + "__docId__": 299, "kind": "test", "name": "describe49", "testId": 49, - "memberof": "test/phylogenies.js~describe44.describe48", - "testDepth": 2, + "memberof": "test/normalization.js~describe44.describe45.describe46", + "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe49", + "longname": "test/normalization.js~describe44.describe45.describe46.describe49", "access": null, - "description": "when given a correct Newick string", - "lineNumber": 35 + "description": "Test phyloreferences", + "lineNumber": 66 }, { - "__docId__": 292, + "__docId__": 300, "kind": "test", "name": "it50", "testId": 50, - "memberof": "test/phylogenies.js~describe44.describe48.describe49", - "testDepth": 3, + "memberof": "test/normalization.js~describe44.describe45.describe46.describe49", + "testDepth": 4, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe49.it50", + "longname": "test/normalization.js~describe44.describe45.describe46.describe49.it50", "access": null, - "description": "should return an empty list of errors", - "lineNumber": 40 + "description": "should have multiple same phyloreferences for testing", + "lineNumber": 67 }, { - "__docId__": 293, + "__docId__": 301, "kind": "test", - "name": "describe51", + "name": "it51", "testId": 51, - "memberof": "test/phylogenies.js~describe44.describe48", - "testDepth": 2, + "memberof": "test/normalization.js~describe44.describe45.describe46.describe49", + "testDepth": 4, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe51", + "longname": "test/normalization.js~describe44.describe45.describe46.describe49.it51", "access": null, - "description": "when given an empty Newick string", - "lineNumber": 47 + "description": "should not have any duplicate phylorefs (which would be pointless)", + "lineNumber": 71 }, { - "__docId__": 294, + "__docId__": 302, "kind": "test", "name": "it52", "testId": 52, - "memberof": "test/phylogenies.js~describe44.describe48.describe51", - "testDepth": 3, + "memberof": "test/normalization.js~describe44.describe45.describe46.describe49", + "testDepth": 4, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe51.it52", + "longname": "test/normalization.js~describe44.describe45.describe46.describe49.it52", "access": null, - "description": "should return a single \"No phylogeny entered\" error", - "lineNumber": 53 + "description": "should have pairs of `_same` phylorefs that are different, but are identical after normalization", + "lineNumber": 87 }, { - "__docId__": 295, + "__docId__": 303, "kind": "test", - "name": "describe53", + "name": "it53", "testId": 53, - "memberof": "test/phylogenies.js~describe44.describe48", - "testDepth": 2, + "memberof": "test/normalization.js~describe44.describe45.describe46.describe49", + "testDepth": 4, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe53", + "longname": "test/normalization.js~describe44.describe45.describe46.describe49.it53", "access": null, - "description": "when given an unbalanced Newick string", - "lineNumber": 62 + "description": "should have pairs of `_different` phylorefs that are different before and after normalization", + "lineNumber": 106 }, { - "__docId__": 296, + "__docId__": 304, + "kind": "testFile", + "name": "test/phylogenies.js", + "content": "/*\n * Test phylogenies.\n */\n\n// Load phyx.js, our PHYX library, and chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Make it easier to access owlterms.\nconst owlterms = require('../src/utils/owlterms');\n\n// Use Chai's expect API for testing.\nconst expect = chai.expect;\n\n/*\n * These tests focus on three aspects of PhylogenyWrapper:\n * - Whether it can detect errors in an input Newick string.\n * - Retrieve taxonomic units from the phylogeny based on either their node label\n * or on the additional properties associated with the phylogeny.\n * - Whether we can match specifiers with nodes on the phylogeny if they share\n * taxonomic units that match.\n */\n\ndescribe('PhylogenyWrapper', function () {\n describe('#constructor', function () {\n describe('when used to wrap an empty object', function () {\n it('should return a PhylogenyWrapper object', function () {\n expect(new phyx.PhylogenyWrapper({}))\n .to.be.an.instanceOf(phyx.PhylogenyWrapper);\n });\n });\n });\n\n describe('#getErrorsInNewickString', function () {\n describe('when given a correct Newick string', function () {\n const correctNewickStrings = [\n '(A:3, B:5, (C:6, N:7));',\n ];\n\n it('should return an empty list of errors', function () {\n correctNewickStrings.forEach((str) => {\n expect(phyx.PhylogenyWrapper.getErrorsInNewickString(str)).to.be.empty;\n });\n });\n });\n\n describe('when given an empty Newick string', function () {\n const emptyNewickStrings = [\n '()',\n '(); ',\n ];\n\n it('should return a single \"No phylogeny entered\" error', function () {\n emptyNewickStrings.forEach((newick) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(newick);\n expect(errors).to.have.length(1);\n expect(errors[0].title).to.equal('No phylogeny entered');\n });\n });\n });\n\n describe('when given an unbalanced Newick string', function () {\n const unbalancedNewickString = [\n {\n newick: '(A, B))',\n expected: 'You have 1 too few open parentheses',\n },\n {\n newick: '(A, (B, (C, D))',\n expected: 'You have 1 too many open parentheses',\n },\n {\n newick: '(A, (B, (C, (((D))',\n expected: 'You have 4 too many open parentheses',\n },\n ];\n\n it('should report how many parentheses are missing', function () {\n unbalancedNewickString.forEach((entry) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(entry.newick);\n\n // We should get two errors.\n expect(errors).to.have.lengthOf(2);\n\n // Should include an error about the unbalanced parentheses.\n expect(errors[0].title).to.equal('Unbalanced parentheses in Newick string');\n expect(errors[0].message).to.equal(entry.expected);\n\n // Should include an error passed on from the Newick parser.\n expect(errors[1].title).to.equal('Error parsing phylogeny');\n expect(errors[1].message).to.include('An error occured while parsing this phylogeny:');\n });\n });\n });\n\n describe('when given an incomplete Newick string', function () {\n const incompleteNewickStrings = [\n ';',\n '))(A, (B, ',\n ];\n\n it('should report an error parsing the phylogeny', function () {\n incompleteNewickStrings.forEach((newick) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(newick);\n\n expect(errors).to.have.lengthOf(1);\n expect(errors[0].title).to.equal('Error parsing phylogeny');\n expect(errors[0].message).to.include('An error occured while parsing this phylogeny:');\n });\n });\n });\n });\n\n describe('#getNodeLabels', function () {\n const tests = [\n {\n // Note that 'newick' is the input for this test.\n newick: '(A, (B, (C, D))E, F, (G, (H, I, J)K, L)M, N)O',\n // The following keys indicate the expected all/internal/terminal node labels\n // for the given Newick string.\n nodeLabels: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O'],\n internalNodeLabels: ['E', 'K', 'M', 'O'],\n terminalNodeLabels: ['A', 'B', 'C', 'D', 'F', 'G', 'H', 'I', 'J', 'L', 'N'],\n },\n ];\n\n tests.forEach((test) => {\n const wrapper = new phyx.PhylogenyWrapper({ newick: test.newick });\n\n describe('For a particular Newick phylogeny', function () {\n it('should return a list of all node labels by default', function () {\n expect(wrapper.getNodeLabels().sort())\n .to.have.members(test.nodeLabels.sort());\n });\n\n it('should return a list of internal labels when asked for internal labels', function () {\n expect(wrapper.getNodeLabels('internal').sort())\n .to.have.members(test.internalNodeLabels.sort());\n });\n\n it('should return a list of terminal labels when asked for terminal labels', function () {\n expect(wrapper.getNodeLabels('terminal').sort())\n .to.have.members(test.terminalNodeLabels.sort());\n });\n });\n });\n });\n\n describe('given a particular phylogeny with additional node properties', function () {\n const wrapper = new phyx.PhylogenyWrapper({\n newick: '((MVZ225749, MVZ191016), Rana boylii)',\n additionalNodeProperties: {\n MVZ225749: {\n representsTaxonomicUnits: [{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:225749',\n }],\n },\n MVZ191016: {\n representsTaxonomicUnits: [{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:191016',\n }],\n },\n },\n });\n\n describe('#getNodeLabels', function () {\n it('should return the list of node labels from the Newick string', function () {\n expect(wrapper.getNodeLabels().sort())\n .to.have.members([\n 'MVZ191016',\n 'MVZ225749',\n 'Rana boylii',\n ]);\n });\n });\n\n describe('#getTaxonomicUnitsForNodeLabel', function () {\n it('should return the list of taxonomic units using information from additional node properties', function () {\n expect(wrapper.getTaxonomicUnitsForNodeLabel('MVZ191016')).to.deep.equal([{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:191016',\n }]);\n\n expect(wrapper.getTaxonomicUnitsForNodeLabel('MVZ225749')).to.deep.equal([{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:225749',\n }]);\n\n expect(wrapper.getTaxonomicUnitsForNodeLabel('Rana boylii')).to.deep.equal([{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n label: 'Rana boylii',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana boylii',\n nameComplete: 'Rana boylii',\n genusPart: 'Rana',\n specificEpithet: 'boylii',\n },\n }]);\n });\n });\n\n describe('#getNodeLabelsMatchedBySpecifier', function () {\n it('should match a specifier to MVZ225749 based on occurrence ID', function () {\n const specifier1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:225749',\n };\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier1))\n .to.have.members(['MVZ225749']);\n });\n\n it('should match a specifier to MVZ191016 based on occurrence ID', function () {\n const specifier2 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:191016',\n };\n\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier2))\n .to.have.members(['MVZ191016']);\n });\n\n it('should match a specifier to node \"Rana boylii\" based on the parsed scientific name', function () {\n const specifier3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana boylii',\n };\n\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier3))\n .to.have.members(['Rana boylii']);\n });\n });\n });\n\n describe('#asJSONLD', function () {\n it('should preserve an existing @id on input phylogenies', function () {\n const jsonld = new phyx.PhylogenyWrapper({\n '@id': '#providedId',\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n }).asJSONLD('#phylogeny0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#providedId');\n });\n it('should generate a new @id on input phylorefs', function () {\n const jsonld = new phyx.PhylogenyWrapper({\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n }, owlterms.ICZN_CODE).asJSONLD('#phylogeny0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#phylogeny0');\n });\n it('should generate the phylogeny in JSON-LD as expected', function () {\n const expectedResults = [\n {\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n jsonld: {\n '@id': '#',\n '@type': 'phyloref:ReferencePhylogenyEvidence',\n hasRootNode: { '@id': '#_node0' },\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n nodes: [\n {\n '@id': '#_node0',\n children: ['#_node1', '#_node2'],\n 'rdf:type': [{ '@id': owlterms.CDAO_NODE }],\n },\n {\n '@id': '#_node1',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Mus musculus',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Mus_musculus'],\n parent: '#_node0',\n representsTaxonomicUnits: [{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Mus',\n label: 'Mus_musculus',\n nameComplete: 'Mus musculus',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'musculus',\n },\n label: 'Mus_musculus',\n }],\n siblings: ['#_node2'],\n },\n {\n '@id': '#_node2',\n children: ['#_node3', '#_node4'],\n 'rdf:type': [{ '@id': owlterms.CDAO_NODE }],\n parent: '#_node0',\n siblings: ['#_node1'],\n },\n {\n '@id': '#_node3',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Panthera tigris',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Panthera_tigris'],\n parent: '#_node2',\n representsTaxonomicUnits: [{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Panthera',\n label: 'Panthera_tigris',\n nameComplete: 'Panthera tigris',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'tigris',\n },\n label: 'Panthera_tigris',\n }],\n siblings: ['#_node4'],\n },\n {\n '@id': '#_node4',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Homo sapiens',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Homo_sapiens'],\n parent: '#_node2',\n representsTaxonomicUnits: [\n {\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Homo',\n label: 'Homo_sapiens',\n nameComplete: 'Homo sapiens',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'sapiens',\n },\n label: 'Homo_sapiens',\n },\n ],\n siblings: ['#_node3'],\n },\n ],\n },\n },\n ];\n\n expectedResults.forEach((expected) => {\n const wrapper = new phyx.PhylogenyWrapper({\n '@id': '#',\n newick: expected.newick,\n }, owlterms.ICZN_CODE);\n expect(wrapper.asJSONLD('#phylogeny0')).to.deep.equal(expected.jsonld);\n });\n });\n });\n\n describe('#getParsedNewickWithIRIs', function () {\n const tests = [\n {\n newick: '(((A, B)C, D)E, F)G',\n result: {\n json: {\n '@id': '_node0',\n name: 'G',\n label: 'G',\n children: [\n { '@id': '_node1', name: 'F', label: 'F' },\n {\n '@id': '_node2',\n name: 'E',\n label: 'E',\n children: [\n { '@id': '_node3', name: 'D', label: 'D' },\n {\n '@id': '_node4',\n name: 'C',\n label: 'C',\n children: [\n { '@id': '_node5', name: 'B', label: 'B' },\n { '@id': '_node6', name: 'A', label: 'A' },\n ],\n },\n ],\n },\n ],\n },\n },\n },\n ];\n\n tests.forEach((test) => {\n it('should be able to parse a provided Newick string as expected', function () {\n expect(new phyx.PhylogenyWrapper({ newick: test.newick }).getParsedNewickWithIRIs(''))\n .to.deep.equal(test.result);\n });\n });\n });\n});\n", + "static": true, + "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/phylogenies.js", + "access": null, + "description": null, + "lineNumber": 1 + }, + { + "__docId__": 305, "kind": "test", - "name": "it54", + "name": "describe54", "testId": 54, - "memberof": "test/phylogenies.js~describe44.describe48.describe53", - "testDepth": 3, + "memberof": "test/phylogenies.js", + "testDepth": 0, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe53.it54", + "longname": "test/phylogenies.js~describe54", "access": null, - "description": "should report how many parentheses are missing", - "lineNumber": 78 + "description": "PhylogenyWrapper", + "lineNumber": 24 }, { - "__docId__": 297, + "__docId__": 306, "kind": "test", "name": "describe55", "testId": 55, - "memberof": "test/phylogenies.js~describe44.describe48", - "testDepth": 2, + "memberof": "test/phylogenies.js~describe54", + "testDepth": 1, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe55", + "longname": "test/phylogenies.js~describe54.describe55", "access": null, - "description": "when given an incomplete Newick string", - "lineNumber": 96 + "description": "#constructor", + "lineNumber": 25 }, { - "__docId__": 298, + "__docId__": 307, "kind": "test", - "name": "it56", + "name": "describe56", "testId": 56, - "memberof": "test/phylogenies.js~describe44.describe48.describe55", - "testDepth": 3, + "memberof": "test/phylogenies.js~describe54.describe55", + "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe48.describe55.it56", + "longname": "test/phylogenies.js~describe54.describe55.describe56", "access": null, - "description": "should report an error parsing the phylogeny", - "lineNumber": 102 + "description": "when used to wrap an empty object", + "lineNumber": 26 }, { - "__docId__": 299, + "__docId__": 308, "kind": "test", - "name": "describe57", + "name": "it57", "testId": 57, - "memberof": "test/phylogenies.js~describe44", - "testDepth": 1, + "memberof": "test/phylogenies.js~describe54.describe55.describe56", + "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe57", + "longname": "test/phylogenies.js~describe54.describe55.describe56.it57", "access": null, - "description": "#getNodeLabels", - "lineNumber": 114 + "description": "should return a PhylogenyWrapper object", + "lineNumber": 27 }, { - "__docId__": 300, + "__docId__": 309, "kind": "test", "name": "describe58", "testId": 58, - "memberof": "test/phylogenies.js~describe44.describe57", + "memberof": "test/phylogenies.js~describe54", + "testDepth": 1, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58", + "access": null, + "description": "#getErrorsInNewickString", + "lineNumber": 34 + }, + { + "__docId__": 310, + "kind": "test", + "name": "describe59", + "testId": 59, + "memberof": "test/phylogenies.js~describe54.describe58", + "testDepth": 2, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe59", + "access": null, + "description": "when given a correct Newick string", + "lineNumber": 35 + }, + { + "__docId__": 311, + "kind": "test", + "name": "it60", + "testId": 60, + "memberof": "test/phylogenies.js~describe54.describe58.describe59", + "testDepth": 3, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe59.it60", + "access": null, + "description": "should return an empty list of errors", + "lineNumber": 40 + }, + { + "__docId__": 312, + "kind": "test", + "name": "describe61", + "testId": 61, + "memberof": "test/phylogenies.js~describe54.describe58", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe57.describe58", + "longname": "test/phylogenies.js~describe54.describe58.describe61", + "access": null, + "description": "when given an empty Newick string", + "lineNumber": 47 + }, + { + "__docId__": 313, + "kind": "test", + "name": "it62", + "testId": 62, + "memberof": "test/phylogenies.js~describe54.describe58.describe61", + "testDepth": 3, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe61.it62", + "access": null, + "description": "should return a single \"No phylogeny entered\" error", + "lineNumber": 53 + }, + { + "__docId__": 314, + "kind": "test", + "name": "describe63", + "testId": 63, + "memberof": "test/phylogenies.js~describe54.describe58", + "testDepth": 2, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe63", + "access": null, + "description": "when given an unbalanced Newick string", + "lineNumber": 62 + }, + { + "__docId__": 315, + "kind": "test", + "name": "it64", + "testId": 64, + "memberof": "test/phylogenies.js~describe54.describe58.describe63", + "testDepth": 3, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe63.it64", + "access": null, + "description": "should report how many parentheses are missing", + "lineNumber": 78 + }, + { + "__docId__": 316, + "kind": "test", + "name": "describe65", + "testId": 65, + "memberof": "test/phylogenies.js~describe54.describe58", + "testDepth": 2, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe65", + "access": null, + "description": "when given an incomplete Newick string", + "lineNumber": 96 + }, + { + "__docId__": 317, + "kind": "test", + "name": "it66", + "testId": 66, + "memberof": "test/phylogenies.js~describe54.describe58.describe65", + "testDepth": 3, + "static": true, + "longname": "test/phylogenies.js~describe54.describe58.describe65.it66", + "access": null, + "description": "should report an error parsing the phylogeny", + "lineNumber": 102 + }, + { + "__docId__": 318, + "kind": "test", + "name": "describe67", + "testId": 67, + "memberof": "test/phylogenies.js~describe54", + "testDepth": 1, + "static": true, + "longname": "test/phylogenies.js~describe54.describe67", + "access": null, + "description": "#getNodeLabels", + "lineNumber": 114 + }, + { + "__docId__": 319, + "kind": "test", + "name": "describe68", + "testId": 68, + "memberof": "test/phylogenies.js~describe54.describe67", + "testDepth": 2, + "static": true, + "longname": "test/phylogenies.js~describe54.describe67.describe68", "access": null, "description": "For a particular Newick phylogeny", "lineNumber": 130 }, { - "__docId__": 301, + "__docId__": 320, "kind": "test", - "name": "it59", - "testId": 59, - "memberof": "test/phylogenies.js~describe44.describe57.describe58", + "name": "it69", + "testId": 69, + "memberof": "test/phylogenies.js~describe54.describe67.describe68", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe57.describe58.it59", + "longname": "test/phylogenies.js~describe54.describe67.describe68.it69", "access": null, "description": "should return a list of all node labels by default", "lineNumber": 131 }, { - "__docId__": 302, + "__docId__": 321, "kind": "test", - "name": "it60", - "testId": 60, - "memberof": "test/phylogenies.js~describe44.describe57.describe58", + "name": "it70", + "testId": 70, + "memberof": "test/phylogenies.js~describe54.describe67.describe68", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe57.describe58.it60", + "longname": "test/phylogenies.js~describe54.describe67.describe68.it70", "access": null, "description": "should return a list of internal labels when asked for internal labels", "lineNumber": 136 }, { - "__docId__": 303, + "__docId__": 322, "kind": "test", - "name": "it61", - "testId": 61, - "memberof": "test/phylogenies.js~describe44.describe57.describe58", + "name": "it71", + "testId": 71, + "memberof": "test/phylogenies.js~describe54.describe67.describe68", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe57.describe58.it61", + "longname": "test/phylogenies.js~describe54.describe67.describe68.it71", "access": null, "description": "should return a list of terminal labels when asked for terminal labels", "lineNumber": 141 }, { - "__docId__": 304, + "__docId__": 323, "kind": "test", - "name": "describe62", - "testId": 62, - "memberof": "test/phylogenies.js~describe44", + "name": "describe72", + "testId": 72, + "memberof": "test/phylogenies.js~describe54", "testDepth": 1, "static": true, - "longname": "test/phylogenies.js~describe44.describe62", + "longname": "test/phylogenies.js~describe54.describe72", "access": null, "description": "given a particular phylogeny with additional node properties", "lineNumber": 149 }, { - "__docId__": 305, + "__docId__": 324, "kind": "test", - "name": "describe63", - "testId": 63, - "memberof": "test/phylogenies.js~describe44.describe62", + "name": "describe73", + "testId": 73, + "memberof": "test/phylogenies.js~describe54.describe72", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe63", + "longname": "test/phylogenies.js~describe54.describe72.describe73", "access": null, "description": "#getNodeLabels", "lineNumber": 174 }, { - "__docId__": 306, + "__docId__": 325, "kind": "test", - "name": "it64", - "testId": 64, - "memberof": "test/phylogenies.js~describe44.describe62.describe63", + "name": "it74", + "testId": 74, + "memberof": "test/phylogenies.js~describe54.describe72.describe73", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe63.it64", + "longname": "test/phylogenies.js~describe54.describe72.describe73.it74", "access": null, "description": "should return the list of node labels from the Newick string", "lineNumber": 175 }, { - "__docId__": 307, + "__docId__": 326, "kind": "test", - "name": "describe65", - "testId": 65, - "memberof": "test/phylogenies.js~describe44.describe62", + "name": "describe75", + "testId": 75, + "memberof": "test/phylogenies.js~describe54.describe72", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe65", + "longname": "test/phylogenies.js~describe54.describe72.describe75", "access": null, "description": "#getTaxonomicUnitsForNodeLabel", "lineNumber": 185 }, { - "__docId__": 308, + "__docId__": 327, "kind": "test", - "name": "it66", - "testId": 66, - "memberof": "test/phylogenies.js~describe44.describe62.describe65", + "name": "it76", + "testId": 76, + "memberof": "test/phylogenies.js~describe54.describe72.describe75", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe65.it66", + "longname": "test/phylogenies.js~describe54.describe72.describe75.it76", "access": null, "description": "should return the list of taxonomic units using information from additional node properties", "lineNumber": 186 }, { - "__docId__": 309, + "__docId__": 328, "kind": "test", - "name": "describe67", - "testId": 67, - "memberof": "test/phylogenies.js~describe44.describe62", + "name": "describe77", + "testId": 77, + "memberof": "test/phylogenies.js~describe54.describe72", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe67", + "longname": "test/phylogenies.js~describe54.describe72.describe77", "access": null, "description": "#getNodeLabelsMatchedBySpecifier", "lineNumber": 217 }, { - "__docId__": 310, + "__docId__": 329, "kind": "test", - "name": "it68", - "testId": 68, - "memberof": "test/phylogenies.js~describe44.describe62.describe67", + "name": "it78", + "testId": 78, + "memberof": "test/phylogenies.js~describe54.describe72.describe77", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe67.it68", + "longname": "test/phylogenies.js~describe54.describe72.describe77.it78", "access": null, "description": "should match a specifier to MVZ225749 based on occurrence ID", "lineNumber": 218 }, { - "__docId__": 311, + "__docId__": 330, "kind": "test", - "name": "it69", - "testId": 69, - "memberof": "test/phylogenies.js~describe44.describe62.describe67", + "name": "it79", + "testId": 79, + "memberof": "test/phylogenies.js~describe54.describe72.describe77", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe67.it69", + "longname": "test/phylogenies.js~describe54.describe72.describe77.it79", "access": null, "description": "should match a specifier to MVZ191016 based on occurrence ID", "lineNumber": 227 }, { - "__docId__": 312, + "__docId__": 331, "kind": "test", - "name": "it70", - "testId": 70, - "memberof": "test/phylogenies.js~describe44.describe62.describe67", + "name": "it80", + "testId": 80, + "memberof": "test/phylogenies.js~describe54.describe72.describe77", "testDepth": 3, "static": true, - "longname": "test/phylogenies.js~describe44.describe62.describe67.it70", + "longname": "test/phylogenies.js~describe54.describe72.describe77.it80", "access": null, "description": "should match a specifier to node \"Rana boylii\" based on the parsed scientific name", "lineNumber": 237 }, { - "__docId__": 313, + "__docId__": 332, "kind": "test", - "name": "describe71", - "testId": 71, - "memberof": "test/phylogenies.js~describe44", + "name": "describe81", + "testId": 81, + "memberof": "test/phylogenies.js~describe54", "testDepth": 1, "static": true, - "longname": "test/phylogenies.js~describe44.describe71", + "longname": "test/phylogenies.js~describe54.describe81", "access": null, "description": "#asJSONLD", "lineNumber": 249 }, { - "__docId__": 314, + "__docId__": 333, "kind": "test", - "name": "it72", - "testId": 72, - "memberof": "test/phylogenies.js~describe44.describe71", + "name": "it82", + "testId": 82, + "memberof": "test/phylogenies.js~describe54.describe81", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe71.it72", + "longname": "test/phylogenies.js~describe54.describe81.it82", "access": null, "description": "should preserve an existing @id on input phylogenies", "lineNumber": 250 }, { - "__docId__": 315, + "__docId__": 334, "kind": "test", - "name": "it73", - "testId": 73, - "memberof": "test/phylogenies.js~describe44.describe71", + "name": "it83", + "testId": 83, + "memberof": "test/phylogenies.js~describe54.describe81", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe71.it73", + "longname": "test/phylogenies.js~describe54.describe81.it83", "access": null, "description": "should generate a new @id on input phylorefs", "lineNumber": 258 }, { - "__docId__": 316, + "__docId__": 335, "kind": "test", - "name": "it74", - "testId": 74, - "memberof": "test/phylogenies.js~describe44.describe71", + "name": "it84", + "testId": 84, + "memberof": "test/phylogenies.js~describe54.describe81", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe71.it74", + "longname": "test/phylogenies.js~describe54.describe81.it84", "access": null, "description": "should generate the phylogeny in JSON-LD as expected", "lineNumber": 265 }, { - "__docId__": 317, + "__docId__": 336, "kind": "test", - "name": "describe75", - "testId": 75, - "memberof": "test/phylogenies.js~describe44", + "name": "describe85", + "testId": 85, + "memberof": "test/phylogenies.js~describe54", "testDepth": 1, "static": true, - "longname": "test/phylogenies.js~describe44.describe75", + "longname": "test/phylogenies.js~describe54.describe85", "access": null, "description": "#getParsedNewickWithIRIs", "lineNumber": 433 }, { - "__docId__": 318, + "__docId__": 337, "kind": "test", - "name": "it76", - "testId": 76, - "memberof": "test/phylogenies.js~describe44.describe75", + "name": "it86", + "testId": 86, + "memberof": "test/phylogenies.js~describe54.describe85", "testDepth": 2, "static": true, - "longname": "test/phylogenies.js~describe44.describe75.it76", + "longname": "test/phylogenies.js~describe54.describe85.it86", "access": null, "description": "should be able to parse a provided Newick string as expected", "lineNumber": 468 }, { - "__docId__": 319, + "__docId__": 338, "kind": "testFile", "name": "test/phylorefs.js", "content": "/*\n * Test phyloreferences.\n */\n\n// Require phyx.js, our PHYX library, and Chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Use owlterms so we don't have to repeat OWL terms.\nconst owlterms = require('../src/utils/owlterms');\n\n// We use Chai's Expect API.\nconst expect = chai.expect;\n\n/*\n * Phyloref tests cover three aspects of phyloreferences:\n * - Whether we can create a phyloref with a particular set of specifiers,\n * and whether we can correctly change the type of a specifer (from 'External'\n * to 'Internal'), delete specifiers, and retrieve specifier labels.\n * - Whether we can determine to which node a phyloref is expected to resolve to\n * by using additionalNodeProperties.\n * - Whether we can update the phyloref's status several times and retrieve the\n * full history of its status changes.\n */\n\ndescribe('PhylorefWrapper', function () {\n // Some specifiers to use in testing.\n const specifier1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:225749',\n };\n const specifier2 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:191016',\n };\n const specifier3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n '@type': phyx.TaxonNameWrapper.TYPE_TAXON_NAME,\n nomenclaturalCode: owlterms.ICZN_CODE,\n nameComplete: 'Rana boylii',\n },\n };\n const specifier4 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n '@type': phyx.TaxonNameWrapper.TYPE_TAXON_NAME,\n nomenclaturalCode: owlterms.ICN_CODE,\n nameComplete: 'Mangifera indica',\n },\n };\n\n describe('given an empty phyloreference', function () {\n const wrapper = new phyx.PhylorefWrapper({});\n\n describe('#constructor', function () {\n it('should return a PhylorefWrapper', function () {\n expect(wrapper).to.be.an.instanceOf(phyx.PhylorefWrapper);\n });\n });\n\n describe('#label', function () {\n it('should return undefined', function () {\n expect(wrapper.label).to.be.undefined;\n });\n\n it('should be settable by assigning to .label', function () {\n wrapper.label = 'phyloref1';\n expect(wrapper.label).equals('phyloref1');\n });\n });\n\n describe('#specifiers', function () {\n it('should initially return an empty list', function () {\n expect(wrapper.specifiers).to.be.empty;\n });\n\n it('should initially return a nomenclatural code of unknown', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.UNKNOWN_CODE);\n });\n\n describe('when a new external specifier is added using .externalSpecifiers', function () {\n it('should return a list with the new specifier', function () {\n wrapper.externalSpecifiers.push(specifier3);\n expect(wrapper.specifiers).to.deep.equal([specifier3]);\n });\n\n it('should return a nomenclatural code of ICZN', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.ICZN_CODE);\n });\n });\n\n describe('when a new external specifier is added using .externalSpecifiers', function () {\n it('should return a list with the new specifier', function () {\n wrapper.externalSpecifiers.push(specifier2);\n expect(wrapper.specifiers).to.deep.equal([specifier3, specifier2]);\n });\n\n it('should return two nomenclatural codes, one for each specifier', function () {\n expect(wrapper.uniqNomenCodes).to.have.lengthOf(2);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.ICZN_CODE);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.UNKNOWN_CODE);\n });\n\n it('should still return a nomenclatural code of ICZN', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.ICZN_CODE);\n });\n });\n\n describe('when a new internal specifier is added using .internalSpecifiers', function () {\n it('should return a list with the new specifier', function () {\n wrapper.internalSpecifiers.push(specifier4);\n expect(wrapper.specifiers).to.deep.equal([specifier4, specifier3, specifier2]);\n });\n\n it('should return three nomenclatural codes, one for each specifier', function () {\n expect(wrapper.uniqNomenCodes).to.have.lengthOf(3);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.ICZN_CODE);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.UNKNOWN_CODE);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.ICN_CODE);\n });\n\n it('should change to a default nomenclatural code of owlterms.UNKNOWN_CODE', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.UNKNOWN_CODE);\n });\n });\n\n describe('when specifiers are deleted using .deleteSpecifier', function () {\n it('should return the updated list', function () {\n // Delete an external specifier.\n wrapper.deleteSpecifier(specifier2);\n // Delete an internal specifier.\n wrapper.deleteSpecifier(specifier4);\n\n // Only the first specifier should be left.\n expect(wrapper.specifiers).to.deep.equal([specifier3]);\n });\n });\n\n describe('when a specifier is added using .externalSpecifiers', function () {\n it('should return the updated list', function () {\n wrapper.externalSpecifiers.push(specifier1);\n expect(wrapper.specifiers).to.deep.equal([specifier3, specifier1]);\n });\n });\n\n describe('when a specifier is changed to an internal specifier using .setSpecifierType', function () {\n it('should remain in the list of specifiers', function () {\n wrapper.setSpecifierType(specifier1, 'Internal');\n expect(wrapper.specifiers).to.deep.equal([specifier1, specifier3]);\n });\n });\n\n describe('when a specifier is added using .internalSpecifiers', function () {\n it('should be included in the list of all specifiers', function () {\n wrapper.internalSpecifiers.push(specifier2);\n expect(wrapper.specifiers).to.deep.equal([specifier1, specifier2, specifier3]);\n });\n });\n });\n\n describe('#getSpecifierType', function () {\n it('should return the correct specifier type for each specifier', function () {\n expect(wrapper.getSpecifierType(specifier1)).to.equal('Internal');\n expect(wrapper.getSpecifierType(specifier2)).to.equal('Internal');\n expect(wrapper.getSpecifierType(specifier3)).to.equal('External');\n });\n });\n\n describe('#getSpecifierLabel as TaxonomicUnitWrapper', function () {\n it('should return the correct label for each specifier', function () {\n expect((new phyx.TaxonomicUnitWrapper(specifier1)).label).to.equal('Specimen MVZ:225749');\n expect((new phyx.TaxonomicUnitWrapper(specifier2)).label).to.equal('Specimen MVZ:191016');\n expect((new phyx.TaxonomicUnitWrapper(specifier3)).label).to.equal('Rana boylii');\n });\n });\n });\n\n describe('given a particular phylogeny', function () {\n // Some phylogenies to use in testing.\n const phylogeny1 = {\n newick: '((MVZ225749, MVZ191016)Test, \"Rana boylii\")',\n additionalNodeProperties: {\n Test: {\n expectedPhyloreferenceNamed: 'phyloref1',\n },\n },\n };\n\n describe('#getExpectedNodeLabels', function () {\n it('should be able to determine expected node labels for a phylogeny', function () {\n const phyloref1 = new phyx.PhylorefWrapper({\n label: 'phyloref1',\n internalSpecifiers: [specifier1, specifier2],\n externalSpecifiers: [specifier3],\n });\n\n expect(phyloref1.getExpectedNodeLabels(phylogeny1))\n .to.deep.equal(['Test']);\n });\n });\n });\n\n describe('given an empty phyloreference', function () {\n const wrapper = new phyx.PhylorefWrapper({});\n\n describe('#getCurrentStatus', function () {\n it('should return \"pso:draft\" as the default initial status', function () {\n // Initially, an empty phyloref should report a status of 'pso:draft'.\n expect(wrapper.getCurrentStatus().statusCURIE).to.equal('pso:draft');\n });\n });\n\n describe('#setStatus', function () {\n it('should throw an error if given a mistyped status', function () {\n expect(function () { wrapper.setStatus('pso:retracted-from_publication'); })\n .to.throw(\n TypeError,\n 'setStatus() called with invalid status CURIE \\'pso:retracted-from_publication\\'',\n 'PhylorefWrapper throws TypeError on a mistyped status'\n );\n });\n });\n\n describe('#getStatusChanges', function () {\n it('should return the empty list', function () {\n expect(wrapper.getStatusChanges()).to.be.empty;\n });\n\n describe('when modified by using .setStatus', function () {\n it('should return the updated list', function () {\n wrapper.setStatus('pso:final-draft');\n wrapper.setStatus('pso:under-review');\n wrapper.setStatus('pso:submitted');\n wrapper.setStatus('pso:published');\n wrapper.setStatus('pso:retracted-from-publication');\n\n // And see if we get the statuses back in the correct order.\n const statusChanges = wrapper.getStatusChanges();\n expect(statusChanges.length, 'number of status changes should be 5').to.equal(5);\n expect(statusChanges[0].statusCURIE, 'first status change should be \"pso:final-draft\"').to.equal('pso:final-draft');\n expect(statusChanges[1].statusCURIE, 'second status change should be \"pso:under-review\"').to.equal('pso:under-review');\n expect(statusChanges[2].statusCURIE, 'third status change should be a \"pso:submitted\"').to.equal('pso:submitted');\n expect(statusChanges[3].statusCURIE, 'fourth status change should be a \"pso:published\"').to.equal('pso:published');\n expect(statusChanges[4].statusCURIE, 'fifth status change should be a \"pso:retracted-from-publication\"').to.equal('pso:retracted-from-publication');\n });\n });\n });\n });\n\n describe('#asJSONLD', function () {\n it('should preserve an existing @id on input phylorefs', function () {\n const jsonld = new phyx.PhylorefWrapper({\n '@id': '#providedId',\n internalSpecifiers: [specifier1],\n externalSpecifiers: [specifier2],\n }).asJSONLD('#phyloref0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#providedId');\n });\n it('should generate a new @id on input phylorefs', function () {\n const jsonld = new phyx.PhylorefWrapper({\n internalSpecifiers: [specifier1],\n externalSpecifiers: [specifier2],\n }).asJSONLD('#phyloref0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#phyloref0');\n });\n it('should generate the expected equivClass expression for 1 int, 1 ext phyloref', function () {\n const jsonld = new phyx.PhylorefWrapper({\n internalSpecifiers: [specifier1],\n externalSpecifiers: [specifier2],\n }).asJSONLD('#');\n expect(jsonld).to.have.property('equivalentClass');\n expect(jsonld.equivalentClass).to.deep.equal({\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_INCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'MVZ:225749',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n },\n },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_EXCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'MVZ:191016',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n },\n },\n ],\n });\n });\n\n it('should generate the expected equivClass expression for 2 int phyloref', function () {\n const jsonld = new phyx.PhylorefWrapper({\n internalSpecifiers: [specifier2, specifier3],\n }).asJSONLD('#');\n expect(jsonld).to.have.property('equivalentClass');\n expect(jsonld.equivalentClass).to.deep.equal({\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_HAS_CHILD,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_EXCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'MVZ:191016',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n },\n },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_INCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Rana boylii',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n },\n });\n });\n });\n});\n", @@ -5252,660 +5620,660 @@ "lineNumber": 1 }, { - "__docId__": 320, + "__docId__": 339, "kind": "test", - "name": "describe77", - "testId": 77, + "name": "describe87", + "testId": 87, "memberof": "test/phylorefs.js", "testDepth": 0, "static": true, - "longname": "test/phylorefs.js~describe77", + "longname": "test/phylorefs.js~describe87", "access": null, "description": "PhylorefWrapper", "lineNumber": 26 }, { - "__docId__": 321, + "__docId__": 340, "kind": "test", - "name": "describe78", - "testId": 78, - "memberof": "test/phylorefs.js~describe77", + 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.externalSpecifiers", "lineNumber": 82 }, { - "__docId__": 331, + "__docId__": 350, "kind": "test", - "name": "it88", - "testId": 88, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe87", + "name": "it98", + "testId": 98, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe97", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe87.it88", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe97.it98", "access": null, "description": "should return a list with the new specifier", "lineNumber": 83 }, { - "__docId__": 332, + "__docId__": 351, "kind": "test", - "name": "it89", - "testId": 89, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe87", + "name": "it99", + "testId": 99, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe97", "testDepth": 4, "static": true, - "longname": 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"test/phylorefs.js~describe77.describe78.describe84.describe90", + "name": "it101", + "testId": 101, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe100", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe90.it91", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe100.it101", "access": null, "description": "should return a list with the new specifier", "lineNumber": 94 }, { - "__docId__": 335, + "__docId__": 354, "kind": "test", - "name": "it92", - "testId": 92, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe90", + "name": "it102", + "testId": 102, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe100", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe90.it92", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe100.it102", "access": null, "description": "should return two nomenclatural codes, one for each specifier", "lineNumber": 99 }, { - "__docId__": 336, + "__docId__": 355, "kind": "test", - "name": "it93", - "testId": 93, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe90", + "name": "it103", + "testId": 103, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe100", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe90.it93", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe100.it103", "access": null, "description": "should still return a nomenclatural code of ICZN", "lineNumber": 105 }, { - "__docId__": 337, + "__docId__": 356, "kind": "test", - "name": "describe94", - "testId": 94, - "memberof": "test/phylorefs.js~describe77.describe78.describe84", + "name": "describe104", + "testId": 104, + "memberof": "test/phylorefs.js~describe87.describe88.describe94", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe94", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe104", "access": null, "description": "when a new internal specifier is added using .internalSpecifiers", "lineNumber": 110 }, { - "__docId__": 338, + "__docId__": 357, "kind": "test", - "name": "it95", - "testId": 95, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe94", + "name": "it105", + "testId": 105, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe104", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe94.it95", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe104.it105", "access": null, "description": "should return a list with the new specifier", "lineNumber": 111 }, { - "__docId__": 339, + "__docId__": 358, "kind": "test", - "name": "it96", - "testId": 96, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe94", + "name": "it106", + "testId": 106, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe104", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe94.it96", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe104.it106", "access": null, "description": "should return three nomenclatural codes, one for each specifier", "lineNumber": 116 }, { - "__docId__": 340, + "__docId__": 359, "kind": "test", - "name": "it97", - "testId": 97, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe94", + "name": "it107", + "testId": 107, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe104", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe94.it97", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe104.it107", "access": null, "description": "should change to a default nomenclatural code of owlterms.UNKNOWN_CODE", "lineNumber": 123 }, { - "__docId__": 341, + "__docId__": 360, "kind": "test", - "name": "describe98", - "testId": 98, - "memberof": "test/phylorefs.js~describe77.describe78.describe84", + "name": "describe108", + "testId": 108, + "memberof": "test/phylorefs.js~describe87.describe88.describe94", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe98", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe108", "access": null, "description": "when specifiers are deleted using .deleteSpecifier", "lineNumber": 128 }, { - "__docId__": 342, + "__docId__": 361, "kind": "test", - "name": "it99", - "testId": 99, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe98", + "name": "it109", + "testId": 109, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe108", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe98.it99", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe108.it109", "access": null, "description": "should return the updated list", "lineNumber": 129 }, { - "__docId__": 343, + "__docId__": 362, "kind": "test", - "name": "describe100", - "testId": 100, - "memberof": "test/phylorefs.js~describe77.describe78.describe84", + "name": "describe110", + "testId": 110, + "memberof": "test/phylorefs.js~describe87.describe88.describe94", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe100", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe110", "access": null, "description": "when a specifier is added using .externalSpecifiers", "lineNumber": 140 }, { - "__docId__": 344, + "__docId__": 363, "kind": "test", - "name": "it101", - "testId": 101, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe100", + "name": "it111", + "testId": 111, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe110", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe100.it101", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe110.it111", "access": null, "description": "should return the updated list", "lineNumber": 141 }, { - "__docId__": 345, + "__docId__": 364, "kind": "test", - "name": "describe102", - "testId": 102, - "memberof": "test/phylorefs.js~describe77.describe78.describe84", + "name": "describe112", + "testId": 112, + "memberof": "test/phylorefs.js~describe87.describe88.describe94", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe102", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe112", "access": null, "description": "when a specifier is changed to an internal specifier using .setSpecifierType", "lineNumber": 147 }, { - "__docId__": 346, + "__docId__": 365, "kind": "test", - "name": "it103", - "testId": 103, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe102", + "name": "it113", + "testId": 113, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe112", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe102.it103", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe112.it113", "access": null, "description": "should remain in the list of specifiers", "lineNumber": 148 }, { - "__docId__": 347, + "__docId__": 366, "kind": "test", - "name": "describe104", - "testId": 104, - "memberof": "test/phylorefs.js~describe77.describe78.describe84", + "name": "describe114", + "testId": 114, + "memberof": "test/phylorefs.js~describe87.describe88.describe94", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe104", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe114", "access": null, "description": "when a specifier is added using .internalSpecifiers", "lineNumber": 154 }, { - "__docId__": 348, + "__docId__": 367, "kind": "test", - "name": "it105", - "testId": 105, - "memberof": "test/phylorefs.js~describe77.describe78.describe84.describe104", + "name": "it115", + "testId": 115, + "memberof": "test/phylorefs.js~describe87.describe88.describe94.describe114", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe84.describe104.it105", + "longname": "test/phylorefs.js~describe87.describe88.describe94.describe114.it115", "access": null, "description": "should be included in the list of all specifiers", "lineNumber": 155 }, { - "__docId__": 349, + "__docId__": 368, "kind": "test", - "name": "describe106", - "testId": 106, - "memberof": "test/phylorefs.js~describe77.describe78", + "name": "describe116", + "testId": 116, + "memberof": "test/phylorefs.js~describe87.describe88", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe106", + "longname": "test/phylorefs.js~describe87.describe88.describe116", "access": null, "description": "#getSpecifierType", "lineNumber": 162 }, { - "__docId__": 350, + "__docId__": 369, "kind": "test", - "name": "it107", - "testId": 107, - "memberof": "test/phylorefs.js~describe77.describe78.describe106", + "name": "it117", + "testId": 117, + "memberof": "test/phylorefs.js~describe87.describe88.describe116", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe106.it107", + "longname": "test/phylorefs.js~describe87.describe88.describe116.it117", "access": null, "description": "should return the correct specifier type for each specifier", "lineNumber": 163 }, { - "__docId__": 351, + "__docId__": 370, "kind": "test", - "name": "describe108", - "testId": 108, - "memberof": "test/phylorefs.js~describe77.describe78", + "name": "describe118", + "testId": 118, + "memberof": "test/phylorefs.js~describe87.describe88", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe108", + "longname": "test/phylorefs.js~describe87.describe88.describe118", "access": null, "description": "#getSpecifierLabel as TaxonomicUnitWrapper", "lineNumber": 170 }, { - "__docId__": 352, + "__docId__": 371, "kind": "test", - "name": "it109", - "testId": 109, - "memberof": "test/phylorefs.js~describe77.describe78.describe108", + "name": "it119", + "testId": 119, + "memberof": "test/phylorefs.js~describe87.describe88.describe118", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe78.describe108.it109", + "longname": "test/phylorefs.js~describe87.describe88.describe118.it119", "access": null, "description": "should return the correct label for each specifier", "lineNumber": 171 }, { - "__docId__": 353, + "__docId__": 372, "kind": "test", - "name": "describe110", - "testId": 110, - "memberof": "test/phylorefs.js~describe77", + "name": "describe120", + "testId": 120, + "memberof": "test/phylorefs.js~describe87", "testDepth": 1, "static": true, - "longname": "test/phylorefs.js~describe77.describe110", + "longname": "test/phylorefs.js~describe87.describe120", "access": null, "description": "given a particular phylogeny", "lineNumber": 179 }, { - "__docId__": 354, + "__docId__": 373, "kind": "test", - "name": "describe111", - "testId": 111, - "memberof": "test/phylorefs.js~describe77.describe110", + "name": "describe121", + "testId": 121, + "memberof": "test/phylorefs.js~describe87.describe120", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe110.describe111", + "longname": "test/phylorefs.js~describe87.describe120.describe121", "access": null, "description": "#getExpectedNodeLabels", "lineNumber": 190 }, { - "__docId__": 355, + "__docId__": 374, "kind": "test", - "name": "it112", - "testId": 112, - "memberof": "test/phylorefs.js~describe77.describe110.describe111", + "name": "it122", + "testId": 122, + "memberof": "test/phylorefs.js~describe87.describe120.describe121", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe110.describe111.it112", + "longname": "test/phylorefs.js~describe87.describe120.describe121.it122", "access": null, "description": "should be able to determine expected node labels for a phylogeny", "lineNumber": 191 }, { - "__docId__": 356, + "__docId__": 375, "kind": "test", - "name": "describe113", - "testId": 113, - "memberof": "test/phylorefs.js~describe77", + "name": "describe123", + "testId": 123, + "memberof": "test/phylorefs.js~describe87", "testDepth": 1, "static": true, - "longname": "test/phylorefs.js~describe77.describe113", + "longname": "test/phylorefs.js~describe87.describe123", "access": null, "description": "given an empty phyloreference", "lineNumber": 204 }, { - "__docId__": 357, + "__docId__": 376, "kind": "test", - "name": "describe114", - "testId": 114, - "memberof": "test/phylorefs.js~describe77.describe113", + "name": "describe124", + "testId": 124, + "memberof": "test/phylorefs.js~describe87.describe123", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe114", + "longname": "test/phylorefs.js~describe87.describe123.describe124", "access": null, "description": "#getCurrentStatus", "lineNumber": 207 }, { - "__docId__": 358, + "__docId__": 377, "kind": "test", - "name": "it115", - "testId": 115, - "memberof": "test/phylorefs.js~describe77.describe113.describe114", + "name": "it125", + "testId": 125, + "memberof": "test/phylorefs.js~describe87.describe123.describe124", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe114.it115", + "longname": "test/phylorefs.js~describe87.describe123.describe124.it125", "access": null, "description": "should return \"pso:draft\" as the default initial status", "lineNumber": 208 }, { - "__docId__": 359, + "__docId__": 378, "kind": "test", - "name": "describe116", - "testId": 116, - "memberof": "test/phylorefs.js~describe77.describe113", + "name": "describe126", + "testId": 126, + "memberof": "test/phylorefs.js~describe87.describe123", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe116", + "longname": "test/phylorefs.js~describe87.describe123.describe126", "access": null, "description": "#setStatus", "lineNumber": 214 }, { - "__docId__": 360, + "__docId__": 379, "kind": "test", - "name": "it117", - "testId": 117, - "memberof": "test/phylorefs.js~describe77.describe113.describe116", + "name": "it127", + "testId": 127, + "memberof": "test/phylorefs.js~describe87.describe123.describe126", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe116.it117", + "longname": "test/phylorefs.js~describe87.describe123.describe126.it127", "access": null, "description": "should throw an error if given a mistyped status", "lineNumber": 215 }, { - "__docId__": 361, + "__docId__": 380, "kind": "test", - "name": "describe118", - "testId": 118, - "memberof": "test/phylorefs.js~describe77.describe113", + "name": "describe128", + "testId": 128, + "memberof": "test/phylorefs.js~describe87.describe123", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe118", + "longname": "test/phylorefs.js~describe87.describe123.describe128", "access": null, "description": "#getStatusChanges", "lineNumber": 225 }, { - "__docId__": 362, + "__docId__": 381, "kind": "test", - "name": "it119", - "testId": 119, - "memberof": "test/phylorefs.js~describe77.describe113.describe118", + "name": "it129", + "testId": 129, + "memberof": "test/phylorefs.js~describe87.describe123.describe128", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe118.it119", + "longname": "test/phylorefs.js~describe87.describe123.describe128.it129", "access": null, "description": "should return the empty list", "lineNumber": 226 }, { - "__docId__": 363, + "__docId__": 382, "kind": "test", - "name": "describe120", - "testId": 120, - "memberof": "test/phylorefs.js~describe77.describe113.describe118", + "name": "describe130", + "testId": 130, + "memberof": "test/phylorefs.js~describe87.describe123.describe128", "testDepth": 3, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe118.describe120", + "longname": "test/phylorefs.js~describe87.describe123.describe128.describe130", "access": null, "description": "when modified by using .setStatus", "lineNumber": 230 }, { - "__docId__": 364, + "__docId__": 383, "kind": "test", - "name": "it121", - "testId": 121, - "memberof": "test/phylorefs.js~describe77.describe113.describe118.describe120", + "name": "it131", + "testId": 131, + "memberof": "test/phylorefs.js~describe87.describe123.describe128.describe130", "testDepth": 4, "static": true, - "longname": "test/phylorefs.js~describe77.describe113.describe118.describe120.it121", + "longname": "test/phylorefs.js~describe87.describe123.describe128.describe130.it131", "access": null, "description": "should return the updated list", "lineNumber": 231 }, { - "__docId__": 365, + "__docId__": 384, "kind": "test", - "name": "describe122", - "testId": 122, - "memberof": "test/phylorefs.js~describe77", + "name": "describe132", + "testId": 132, + "memberof": "test/phylorefs.js~describe87", "testDepth": 1, "static": true, - "longname": "test/phylorefs.js~describe77.describe122", + "longname": "test/phylorefs.js~describe87.describe132", "access": null, "description": "#asJSONLD", "lineNumber": 251 }, { - "__docId__": 366, + "__docId__": 385, "kind": "test", - "name": "it123", - "testId": 123, - "memberof": "test/phylorefs.js~describe77.describe122", + "name": "it133", + "testId": 133, + "memberof": "test/phylorefs.js~describe87.describe132", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe122.it123", + "longname": "test/phylorefs.js~describe87.describe132.it133", "access": null, "description": "should preserve an existing @id on input phylorefs", "lineNumber": 252 }, { - "__docId__": 367, + "__docId__": 386, "kind": "test", - "name": "it124", - "testId": 124, - "memberof": "test/phylorefs.js~describe77.describe122", + "name": "it134", + "testId": 134, + "memberof": "test/phylorefs.js~describe87.describe132", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe122.it124", + "longname": "test/phylorefs.js~describe87.describe132.it134", "access": null, "description": "should generate a new @id on input phylorefs", "lineNumber": 261 }, { - "__docId__": 368, + "__docId__": 387, "kind": "test", - "name": "it125", - "testId": 125, - "memberof": "test/phylorefs.js~describe77.describe122", + "name": "it135", + "testId": 135, + "memberof": "test/phylorefs.js~describe87.describe132", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe122.it125", + "longname": "test/phylorefs.js~describe87.describe132.it135", "access": null, "description": "should generate the expected equivClass expression for 1 int, 1 ext phyloref", "lineNumber": 269 }, { - "__docId__": 369, + "__docId__": 388, "kind": "test", - "name": "it126", - "testId": 126, - "memberof": "test/phylorefs.js~describe77.describe122", + "name": "it136", + "testId": 136, + "memberof": "test/phylorefs.js~describe87.describe132", "testDepth": 2, "static": true, - "longname": "test/phylorefs.js~describe77.describe122.it126", + "longname": "test/phylorefs.js~describe87.describe132.it136", "access": null, "description": "should generate the expected equivClass expression for 2 int phyloref", "lineNumber": 300 }, { - "__docId__": 370, + "__docId__": 389, "kind": "testFile", "name": "test/scripts/phyx2owl.js", - "content": "/*\n * Test conversion to OWL using the phyx2owl.js script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\nconst fs = require('fs');\n\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can convert Phyx files to OWL in JSON-LD using phyx2owl.js.\n */\n\nconst PHYX2OWL_JS = 'bin/phyx2owl.js';\n\ndescribe(PHYX2OWL_JS, function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(PHYX2OWL_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(PHYX2OWL_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('phyx2owl.js [files or directories to convert into OWL ontologies]');\n });\n it('should be able to convert `brochu_2003.json`', function () {\n const PHYX_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.json');\n const NQ_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.nq');\n const OWL_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.owl');\n\n // If there is already a '../examples/brochu_2003.owl' file, we should delete it.\n if (fs.existsSync(OWL_FILE)) fs.unlinkSync(OWL_FILE);\n expect(fs.existsSync(OWL_FILE)).to.be.false;\n\n // Convert brochu_2003.json to brochu_2003.owl.\n // Because of the way in which we test brochu_2003.owl in test/examples.js,\n // we need to set a base IRI as well.\n const result = child.spawnSync(PHYX2OWL_JS, [PHYX_FILE, '--base-iri', 'http://example.org/phyx.js/example#'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('1 files converted successfully.');\n expect(result.status).to.equal(0);\n\n expect(fs.existsSync(OWL_FILE), `File ${OWL_FILE} was not generated.`).to.be.true;\n\n // Make sure that the generated file is identical to the N-Quads file expected./\n const nqGenerated = fs.readFileSync(OWL_FILE, 'utf8');\n const nqExpected = fs.readFileSync(NQ_FILE, 'utf8');\n expect(nqGenerated).to.equal(nqExpected);\n });\n it('should be able to convert the entire `test/examples/correct` directory', function () {\n const EXAMPLE_DIR = path.resolve(__dirname, '../examples/correct');\n const jsonFilesInExamples = fs.readdirSync(EXAMPLE_DIR, 'utf8')\n .filter(fileName => fileName.toLowerCase().endsWith('.json'));\n\n const result = child.spawnSync(PHYX2OWL_JS, [EXAMPLE_DIR, '--base-iri', 'http://example.org/phyx.js/example#'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stdout).to.match(/\\d+ files converted successfully./);\n expect(result.stderr).to.be.empty;\n\n const regexMatch = result.stdout.match(/(\\d+) files converted successfully./);\n const fileCount = Number(regexMatch[1]);\n expect(fileCount).to.be.greaterThan(0);\n expect(fileCount).to.equal(jsonFilesInExamples.length);\n\n // Make sure that the generated files *look* like JSON-LD files.\n fs.readdirSync(EXAMPLE_DIR, 'utf8')\n .filter(fileName => fileName.toLowerCase().endsWith('.owl'))\n .forEach((owlFilename) => {\n const nqGenerated = fs.readFileSync(path.resolve(EXAMPLE_DIR, owlFilename), 'utf8');\n\n // If there's an .owl file, there should an .nq file with the expected content.\n const nqFilename = `${owlFilename.substring(0, owlFilename.length - 4)}.nq`;\n const nqExpected = fs.readFileSync(path.resolve(EXAMPLE_DIR, nqFilename), 'utf8');\n\n expect(nqGenerated).to.equal(nqExpected);\n });\n });\n // This is where we should test the recursive directory functionality. However,\n // doing that would require using `test/examples` (which isn't recursive),\n // using `test/` or the root project directory (potentially messing with other\n // test scripts). We could potentially create a separate recursive hierarchy to\n // test this, but that seems unnecessary. So we won't test this functionality\n // for now, but will add a test if we find a replicable bug in the future.\n it('should give an error if no JSON files could be found', function () {\n const result = child.spawnSync(PHYX2OWL_JS, [__dirname], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('Input files do not exist or consist of directories that do not contain JSON files: ');\n });\n});\n", + "content": "/*\n * Test conversion to OWL using the phyx2owl.js script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\nconst fs = require('fs');\n\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can convert Phyx files to OWL in JSON-LD using phyx2owl.js.\n */\n\nconst PHYX2OWL_JS = 'bin/phyx2owl.js';\n\ndescribe(PHYX2OWL_JS, function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(PHYX2OWL_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(PHYX2OWL_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('phyx2owl.js [files or directories to convert into OWL ontologies]');\n });\n it('should be able to convert `brochu_2003.json`', function () {\n const PHYX_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.json');\n const NQ_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.nq');\n const OWL_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.owl');\n\n // If there is already a '../examples/brochu_2003.owl' file, we should delete it.\n if (fs.existsSync(OWL_FILE)) fs.unlinkSync(OWL_FILE);\n expect(fs.existsSync(OWL_FILE)).to.be.false;\n\n // Convert brochu_2003.json to brochu_2003.owl.\n // Because of the way in which we test brochu_2003.owl in test/examples.js,\n // we need to set a base IRI as well.\n const result = child.spawnSync(PHYX2OWL_JS, [PHYX_FILE, '--base-iri', 'http://example.org/phyx.js/example#'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('1 files converted successfully.');\n expect(result.status).to.equal(0);\n\n expect(fs.existsSync(OWL_FILE), `File ${OWL_FILE} was not generated.`).to.be.true;\n\n // Make sure that the generated file is identical to the N-Quads file expected./\n const nqGenerated = fs.readFileSync(OWL_FILE, 'utf8');\n const nqExpected = fs.readFileSync(NQ_FILE, 'utf8');\n expect(nqGenerated).to.equal(nqExpected);\n });\n it('should be able to convert the entire `test/examples/correct` directory', function () {\n const EXAMPLE_DIR = path.resolve(__dirname, '../examples/correct');\n const jsonFilesInExamples = fs.readdirSync(EXAMPLE_DIR, { recursive: true })\n .filter(fileName => fileName.toLowerCase().endsWith('.json'));\n\n const result = child.spawnSync(PHYX2OWL_JS, [EXAMPLE_DIR, '--base-iri', 'http://example.org/phyx.js/example#'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stdout).to.match(/\\d+ files converted successfully./);\n expect(result.stderr).to.be.empty;\n\n const regexMatch = result.stdout.match(/(\\d+) files converted successfully./);\n const fileCount = Number(regexMatch[1]);\n expect(fileCount).to.be.greaterThan(0);\n expect(fileCount).to.equal(jsonFilesInExamples.length);\n\n // Make sure that the generated files *look* like JSON-LD files.\n fs.readdirSync(EXAMPLE_DIR, 'utf8')\n .filter(fileName => fileName.toLowerCase().endsWith('.owl'))\n .forEach((owlFilename) => {\n const nqGenerated = fs.readFileSync(path.resolve(EXAMPLE_DIR, owlFilename), 'utf8');\n\n // If there's an .owl file, there should an .nq file with the expected content.\n const nqFilename = `${owlFilename.substring(0, owlFilename.length - 4)}.nq`;\n const nqExpected = fs.readFileSync(path.resolve(EXAMPLE_DIR, nqFilename), 'utf8');\n\n expect(nqGenerated).to.equal(nqExpected);\n });\n });\n // This is where we should test the recursive directory functionality. However,\n // doing that would require using `test/examples` (which isn't recursive),\n // using `test/` or the root project directory (potentially messing with other\n // test scripts). We could potentially create a separate recursive hierarchy to\n // test this, but that seems unnecessary. So we won't test this functionality\n // for now, but will add a test if we find a replicable bug in the future.\n it('should give an error if no JSON files could be found', function () {\n const result = child.spawnSync(PHYX2OWL_JS, [__dirname], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('Input files do not exist or consist of directories that do not contain JSON files: ');\n });\n});\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/scripts/phyx2owl.js", "access": null, @@ -5913,87 +6281,87 @@ "lineNumber": 1 }, { - "__docId__": 371, + "__docId__": 390, "kind": "test", - "name": "describe127", - "testId": 127, + "name": "describe137", + "testId": 137, "memberof": "test/scripts/phyx2owl.js", "testDepth": 0, "static": true, - "longname": "test/scripts/phyx2owl.js~describe127", + "longname": "test/scripts/phyx2owl.js~describe137", "access": null, "lineNumber": 19 }, { - "__docId__": 372, + "__docId__": 391, "kind": "test", - "name": "it128", - "testId": 128, - "memberof": "test/scripts/phyx2owl.js~describe127", + "name": "it138", + "testId": 138, + "memberof": "test/scripts/phyx2owl.js~describe137", "testDepth": 1, "static": true, - "longname": "test/scripts/phyx2owl.js~describe127.it128", + "longname": "test/scripts/phyx2owl.js~describe137.it138", "access": null, "description": "should work without any arguments", "lineNumber": 20 }, { - "__docId__": 373, + "__docId__": 392, "kind": "test", - "name": "it129", - "testId": 129, - "memberof": "test/scripts/phyx2owl.js~describe127", + "name": "it139", + "testId": 139, + "memberof": "test/scripts/phyx2owl.js~describe137", "testDepth": 1, "static": true, - "longname": "test/scripts/phyx2owl.js~describe127.it129", + "longname": "test/scripts/phyx2owl.js~describe137.it139", "access": null, "description": "should support `--help`", "lineNumber": 29 }, { - "__docId__": 374, + "__docId__": 393, "kind": "test", - "name": "it130", - "testId": 130, - "memberof": "test/scripts/phyx2owl.js~describe127", + "name": "it140", + "testId": 140, + "memberof": "test/scripts/phyx2owl.js~describe137", "testDepth": 1, "static": true, - "longname": "test/scripts/phyx2owl.js~describe127.it130", + "longname": "test/scripts/phyx2owl.js~describe137.it140", "access": null, "description": "should be able to convert `brochu_2003.json`", "lineNumber": 38 }, { - "__docId__": 375, + "__docId__": 394, "kind": "test", - "name": "it131", - "testId": 131, - "memberof": "test/scripts/phyx2owl.js~describe127", + "name": "it141", + "testId": 141, + "memberof": "test/scripts/phyx2owl.js~describe137", "testDepth": 1, "static": true, - "longname": "test/scripts/phyx2owl.js~describe127.it131", + "longname": "test/scripts/phyx2owl.js~describe137.it141", "access": null, "description": "should be able to convert the entire `test/examples/correct` directory", "lineNumber": 65 }, { - "__docId__": 376, + "__docId__": 395, "kind": "test", - "name": "it132", - "testId": 132, - "memberof": "test/scripts/phyx2owl.js~describe127", + "name": "it142", + "testId": 142, + "memberof": "test/scripts/phyx2owl.js~describe137", "testDepth": 1, "static": true, - "longname": "test/scripts/phyx2owl.js~describe127.it132", + "longname": "test/scripts/phyx2owl.js~describe137.it142", "access": null, "description": "should give an error if no JSON files could be found", "lineNumber": 102 }, { - "__docId__": 377, + "__docId__": 396, "kind": "testFile", "name": "test/scripts/resolve.js", - "content": "/*\n * Test resolution against the Open Tree of Life via the resolve script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\n\nconst lodash = require('lodash');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can use the resolve script to resolve phylorefs against\n * the Open Tree of Life.\n */\n\nconst RESOLVE_JS = 'bin/resolve.js';\n\ndescribe('bin/resolve.js', function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(RESOLVE_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(RESOLVE_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('resolve.js [files to resolve on the Open Tree of Life]');\n });\n it('should provide the expected results on the `brochu_2003.json` example file', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/correct/brochu_2003.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'Alligatoridae',\n 'Alligatorinae',\n 'Caimaninae',\n 'Crocodyloidea',\n 'Crocodylidae',\n 'Diplocynodontinae',\n ]);\n\n expect(resultObj.Alligatoridae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.7@ott195670',\n label: 'Alligatoridae',\n });\n expect(resultObj.Alligatorinae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.7@ott151255',\n label: 'Alligatorinae',\n });\n expect(resultObj.Crocodylidae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.7@ott1092501',\n label: 'Longirostres',\n });\n expect(resultObj.Diplocynodontinae[0]).to.include({\n error: 'no_mrca_found:400',\n });\n });\n it('should correctly report errors with certain phyloreferences', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/incorrect/otl-resolution-errors.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'SingleSpecifier',\n 'TaxonNameNotFound',\n 'Produces404OnOTR',\n ]);\n\n // console.log(JSON.stringify(resultObj, null, 2));\n\n expect(resultObj.SingleSpecifier[0]).to.include({\n error: 'one_internal_specifier_with_no_external_specifiers',\n });\n\n expect(resultObj.TaxonNameNotFound[0]).to.include({\n error: 'internal_specifiers_missing',\n });\n\n expect(resultObj.Produces404OnOTR[0]).to.include({\n error: 'no_mrca_found:404',\n });\n });\n});\n", + "content": "/*\n * Test resolution against the Open Tree of Life via the resolve script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\n\nconst lodash = require('lodash');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can use the resolve script to resolve phylorefs against\n * the Open Tree of Life.\n */\n\nconst RESOLVE_JS = 'bin/resolve.js';\n\ndescribe('bin/resolve.js', function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(RESOLVE_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(RESOLVE_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('resolve.js [files to resolve on the Open Tree of Life]');\n });\n it('should provide the expected results on the `brochu_2003.json` example file', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/correct/brochu_2003.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'Alligatoridae',\n 'Alligatorinae',\n 'Caimaninae',\n 'Crocodyloidea',\n 'Crocodylidae',\n 'Diplocynodontinae',\n ]);\n\n expect(resultObj.Alligatoridae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott195670',\n label: 'Alligatoridae',\n });\n expect(resultObj.Alligatorinae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott151255',\n label: 'Alligatorinae',\n });\n expect(resultObj.Crocodylidae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott1092501',\n label: 'Longirostres',\n });\n expect(resultObj.Diplocynodontinae[0]).to.include({\n error: 'no_mrca_found:400',\n });\n });\n it('should correctly report errors with certain phyloreferences', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/incorrect/otl-resolution-errors.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'SingleSpecifier',\n 'TaxonNameNotFound',\n 'Produces404OnOTR',\n ]);\n\n // console.log(JSON.stringify(resultObj, null, 2));\n\n expect(resultObj.SingleSpecifier[0]).to.include({\n error: 'one_internal_specifier_with_no_external_specifiers',\n });\n\n expect(resultObj.TaxonNameNotFound[0]).to.include({\n error: 'internal_specifiers_missing',\n });\n\n expect(resultObj.Produces404OnOTR[0]).to.include({\n error: 'no_mrca_found:404',\n });\n });\n});\n", "static": true, "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/scripts/resolve.js", "access": null, @@ -6001,72 +6369,72 @@ "lineNumber": 1 }, { - "__docId__": 378, + "__docId__": 397, "kind": "test", - "name": "describe133", - "testId": 133, + "name": "describe143", + "testId": 143, "memberof": "test/scripts/resolve.js", "testDepth": 0, "static": true, - "longname": "test/scripts/resolve.js~describe133", + "longname": "test/scripts/resolve.js~describe143", "access": null, "description": "bin/resolve.js", "lineNumber": 20 }, { - "__docId__": 379, + "__docId__": 398, "kind": "test", - "name": "it134", - "testId": 134, - "memberof": "test/scripts/resolve.js~describe133", + "name": "it144", + "testId": 144, + "memberof": "test/scripts/resolve.js~describe143", "testDepth": 1, "static": true, - "longname": "test/scripts/resolve.js~describe133.it134", + "longname": "test/scripts/resolve.js~describe143.it144", "access": null, "description": "should work without any arguments", "lineNumber": 21 }, { - "__docId__": 380, + "__docId__": 399, "kind": "test", - "name": "it135", - "testId": 135, - "memberof": "test/scripts/resolve.js~describe133", + "name": "it145", + "testId": 145, + "memberof": "test/scripts/resolve.js~describe143", "testDepth": 1, "static": true, - "longname": "test/scripts/resolve.js~describe133.it135", + "longname": "test/scripts/resolve.js~describe143.it145", "access": null, "description": "should support `--help`", "lineNumber": 30 }, { - "__docId__": 381, + "__docId__": 400, "kind": "test", - "name": "it136", - "testId": 136, - "memberof": "test/scripts/resolve.js~describe133", + "name": "it146", + "testId": 146, + "memberof": "test/scripts/resolve.js~describe143", "testDepth": 1, "static": true, - "longname": "test/scripts/resolve.js~describe133.it136", + "longname": "test/scripts/resolve.js~describe143.it146", "access": null, "description": "should provide the expected results on the `brochu_2003.json` example file", "lineNumber": 39 }, { - "__docId__": 382, + "__docId__": 401, "kind": "test", - "name": "it137", - "testId": 137, - "memberof": "test/scripts/resolve.js~describe133", + "name": "it147", + "testId": 147, + "memberof": "test/scripts/resolve.js~describe143", "testDepth": 1, "static": true, - "longname": "test/scripts/resolve.js~describe133.it137", + "longname": "test/scripts/resolve.js~describe143.it147", "access": null, "description": "should correctly report errors with certain phyloreferences", "lineNumber": 80 }, { - "__docId__": 383, + "__docId__": 402, "kind": "testFile", "name": "test/specimens.js", "content": "/*\n * Test specimen processing.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/*\n * Test whether SpecimenWrapper can parse specimen identifiers from simple specimen\n * identifiers, from institutionCode:catalogNumber format, and from Darwin Core triples.\n * However, URNs and HTTP URLs should not be accidentally parsed as Darwin Core triples.\n */\n\ndescribe('SpecimenWrapper', function () {\n describe('#constructor', function () {\n it('should be able to wrap an empty specimen', function () {\n const wrapped = new phyx.SpecimenWrapper({});\n\n expect(wrapped).to.be.an.instanceOf(phyx.SpecimenWrapper);\n expect(wrapped.occurrenceID).to.be.undefined;\n });\n it('should be able to extract an occurenceID and catalogNumber from simple specimen IDs', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'Wall 2527, Fiji (uc)',\n 'dwc:basisOfRecord': 'PreservedSpecimen',\n });\n expect(wrapper.occurrenceID).to.equal('Wall 2527, Fiji (uc)');\n expect(wrapper.catalogNumber).to.equal('Wall 2527, Fiji (uc)');\n expect(wrapper.basisOfRecord).to.equal('PreservedSpecimen');\n });\n it('should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'FMNH:PR 2081',\n 'dwc:basisOfRecord': 'PreservedSpecimen',\n });\n expect(wrapper.occurrenceID).to.equal('FMNH:PR 2081');\n expect(wrapper.institutionCode).to.equal('FMNH');\n expect(wrapper.catalogNumber).to.equal('PR 2081');\n expect(wrapper.basisOfRecord).to.equal('PreservedSpecimen');\n });\n it('should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'FMNH:PR:2081',\n });\n expect(wrapper.occurrenceID).to.equal('FMNH:PR:2081');\n expect(wrapper.institutionCode).to.equal('FMNH');\n expect(wrapper.collectionCode).to.equal('PR');\n expect(wrapper.catalogNumber).to.equal('2081');\n expect(wrapper.basisOfRecord).to.be.undefined;\n });\n it('should be able to extract the same occurrenceID from different representations', function () {\n expect(new phyx.SpecimenWrapper({ occurrenceID: 'urn:catalog:::MVZ225749' }).occurrenceID)\n .to.equal('urn:catalog:::MVZ225749');\n expect(new phyx.SpecimenWrapper({ catalogNumber: 'MVZ225749' }).occurrenceID)\n .to.equal('urn:catalog:::MVZ225749');\n });\n it('should not attempt to split a URN into occurenceID, institutionCode and catalogNumber', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'urn:lsid:biocol.org:col:34777',\n });\n expect(wrapper.occurrenceID).to.equal('urn:lsid:biocol.org:col:34777');\n expect(wrapper.institutionCode).to.be.undefined;\n expect(wrapper.collectionCode).to.be.undefined;\n expect(wrapper.catalogNumber).to.be.undefined;\n });\n it('should not attempt to split a URL into occurenceID, institutionCode and catalogNumber', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'http://arctos.database.museum/guid/MVZ:Herp:148929?seid=886464',\n });\n expect(wrapper.occurrenceID).to.equal('http://arctos.database.museum/guid/MVZ:Herp:148929?seid=886464');\n expect(wrapper.institutionCode).to.be.undefined;\n expect(wrapper.collectionCode).to.be.undefined;\n expect(wrapper.catalogNumber).to.be.undefined;\n });\n it('should be able to create a specimen JSON record from an occurrence ID', function () {\n const specimen = phyx.SpecimenWrapper.fromOccurrenceID('FMNH:PR:2081');\n expect(specimen.occurrenceID).to.equal('FMNH:PR:2081');\n expect(specimen.institutionCode).to.equal('FMNH');\n expect(specimen.collectionCode).to.equal('PR');\n expect(specimen.catalogNumber).to.equal('2081');\n expect(specimen['dwc:basisOfRecord']).to.equal('PreservedSpecimen');\n });\n });\n});\n", @@ -6077,137 +6445,137 @@ "lineNumber": 1 }, { - "__docId__": 384, + "__docId__": 403, "kind": "test", - "name": "describe138", - "testId": 138, + "name": "describe148", + "testId": 148, "memberof": "test/specimens.js", "testDepth": 0, "static": true, - "longname": "test/specimens.js~describe138", + "longname": "test/specimens.js~describe148", "access": null, "description": "SpecimenWrapper", "lineNumber": 16 }, { - "__docId__": 385, + "__docId__": 404, "kind": "test", - "name": "describe139", - "testId": 139, - "memberof": "test/specimens.js~describe138", + "name": "describe149", + "testId": 149, + "memberof": "test/specimens.js~describe148", "testDepth": 1, "static": true, - "longname": "test/specimens.js~describe138.describe139", + "longname": "test/specimens.js~describe148.describe149", "access": null, "description": "#constructor", "lineNumber": 17 }, { - "__docId__": 386, + "__docId__": 405, "kind": "test", - "name": "it140", - "testId": 140, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it150", + "testId": 150, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it140", + "longname": "test/specimens.js~describe148.describe149.it150", "access": null, "description": "should be able to wrap an empty specimen", "lineNumber": 18 }, { - "__docId__": 387, + "__docId__": 406, "kind": "test", - "name": "it141", - "testId": 141, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it151", + "testId": 151, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it141", + "longname": "test/specimens.js~describe148.describe149.it151", "access": null, "description": "should be able to extract an occurenceID and catalogNumber from simple specimen IDs", "lineNumber": 24 }, { - "__docId__": 388, + "__docId__": 407, "kind": "test", - "name": "it142", - "testId": 142, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it152", + "testId": 152, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it142", + "longname": "test/specimens.js~describe148.describe149.it152", "access": null, "description": "should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination", "lineNumber": 33 }, { - "__docId__": 389, + "__docId__": 408, "kind": "test", - "name": "it143", - "testId": 143, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it153", + "testId": 153, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it143", + "longname": "test/specimens.js~describe148.describe149.it153", "access": null, "description": "should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples", "lineNumber": 43 }, { - "__docId__": 390, + "__docId__": 409, "kind": "test", - "name": "it144", - "testId": 144, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it154", + "testId": 154, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it144", + "longname": "test/specimens.js~describe148.describe149.it154", "access": null, "description": "should be able to extract the same occurrenceID from different representations", "lineNumber": 53 }, { - "__docId__": 391, + "__docId__": 410, "kind": "test", - "name": "it145", - "testId": 145, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it155", + "testId": 155, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it145", + "longname": "test/specimens.js~describe148.describe149.it155", "access": null, "description": "should not attempt to split a URN into occurenceID, institutionCode and catalogNumber", "lineNumber": 59 }, { - "__docId__": 392, + "__docId__": 411, "kind": "test", - "name": "it146", - "testId": 146, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it156", + "testId": 156, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it146", + "longname": "test/specimens.js~describe148.describe149.it156", "access": null, "description": "should not attempt to split a URL into occurenceID, institutionCode and catalogNumber", "lineNumber": 68 }, { - "__docId__": 393, + "__docId__": 412, "kind": "test", - "name": "it147", - "testId": 147, - "memberof": "test/specimens.js~describe138.describe139", + "name": "it157", + "testId": 157, + "memberof": "test/specimens.js~describe148.describe149", "testDepth": 2, "static": true, - "longname": "test/specimens.js~describe138.describe139.it147", + "longname": "test/specimens.js~describe148.describe149.it157", "access": null, "description": "should be able to create a specimen JSON record from an occurrence ID", "lineNumber": 77 }, { - "__docId__": 394, + "__docId__": 413, "kind": "testFile", "name": "test/taxon-names.js", "content": "/*\n * Test taxon name processing.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\nconst owlterms = require('../src/utils/owlterms');\n\nconst expect = chai.expect;\n\n/*\n * Test whether TaxonNameWrapper parses taxon names correctly.\n */\n\ndescribe('TaxonNameWrapper', function () {\n describe('#constructor', function () {\n it('should accept empty taxon names without errors', function () {\n const wrapper = new phyx.TaxonNameWrapper({});\n\n expect(wrapper).to.be.an.instanceOf(phyx.TaxonNameWrapper);\n expect(wrapper.nameComplete).to.be.undefined;\n });\n it('should be able to parse uninomial names as such', function () {\n const wrapper = new phyx.TaxonNameWrapper({\n nameComplete: 'Mus',\n });\n\n expect(wrapper.uninomial).to.equal('Mus');\n expect(wrapper.genusPart).to.be.undefined;\n expect(wrapper.specificEpithet).to.be.undefined;\n });\n it('should be able to parse binomial names into genus and specific epithet', function () {\n const wrapper = new phyx.TaxonNameWrapper({\n nameComplete: 'Mus musculus',\n });\n\n expect(wrapper.genusPart).to.equal('Mus');\n expect(wrapper.specificEpithet).to.equal('musculus');\n });\n it('should be able to parse trinomial names into genus, specific epithet and infraspecific epithet', function () {\n const wrapper = new phyx.TaxonNameWrapper({\n nameComplete: 'Mus musculus domesticus',\n });\n\n expect(wrapper.genusPart).to.equal('Mus');\n expect(wrapper.specificEpithet).to.equal('musculus');\n expect(wrapper.infraspecificEpithet).to.equal('domesticus');\n });\n it('should ignore authority after a binomial name', function () {\n const taxonName = phyx.TaxonNameWrapper.fromVerbatimName('Mus musculus Linnaeus, 1758');\n expect(taxonName.nameComplete).to.equal('Mus musculus');\n expect(taxonName.genusPart).to.equal('Mus');\n expect(taxonName.specificEpithet).to.equal('musculus');\n expect(taxonName.infraspecificEpithet).to.be.undefined;\n expect(taxonName.uninomial).to.be.undefined;\n });\n it('should be able to use default nomenclatural codes', function () {\n const taxonName = phyx.TaxonNameWrapper.fromVerbatimName('Mus musculus Linnaeus, 1758', owlterms.ICZN_CODE);\n expect(taxonName.nameComplete).to.equal('Mus musculus');\n expect(taxonName.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n\n const wrappedTaxonName = new phyx.TaxonNameWrapper(taxonName);\n expect(wrappedTaxonName.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n expect(wrappedTaxonName.nomenclaturalCodeDetails).to.have.own.property('title');\n expect(wrappedTaxonName.nomenclaturalCodeDetails.title).to.equal('International Code of Zoological Nomenclature');\n });\n });\n});\n", @@ -6218,111 +6586,111 @@ "lineNumber": 1 }, { - "__docId__": 395, + "__docId__": 414, "kind": "test", - "name": "describe148", - "testId": 148, + "name": "describe158", + "testId": 158, "memberof": "test/taxon-names.js", "testDepth": 0, "static": true, - "longname": "test/taxon-names.js~describe148", + "longname": "test/taxon-names.js~describe158", "access": null, "description": "TaxonNameWrapper", "lineNumber": 15 }, { - "__docId__": 396, + "__docId__": 415, "kind": "test", - "name": "describe149", - "testId": 149, - "memberof": "test/taxon-names.js~describe148", + "name": "describe159", + "testId": 159, + "memberof": "test/taxon-names.js~describe158", "testDepth": 1, "static": true, - "longname": "test/taxon-names.js~describe148.describe149", + "longname": "test/taxon-names.js~describe158.describe159", "access": null, "description": "#constructor", "lineNumber": 16 }, { - "__docId__": 397, + "__docId__": 416, "kind": "test", - "name": "it150", - "testId": 150, - "memberof": "test/taxon-names.js~describe148.describe149", + "name": "it160", + "testId": 160, + "memberof": "test/taxon-names.js~describe158.describe159", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe148.describe149.it150", + "longname": "test/taxon-names.js~describe158.describe159.it160", "access": null, "description": "should accept empty taxon names without errors", "lineNumber": 17 }, { - "__docId__": 398, + "__docId__": 417, "kind": "test", - "name": "it151", - "testId": 151, - "memberof": "test/taxon-names.js~describe148.describe149", + "name": "it161", + "testId": 161, + "memberof": "test/taxon-names.js~describe158.describe159", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe148.describe149.it151", + "longname": "test/taxon-names.js~describe158.describe159.it161", "access": null, "description": "should be able to parse uninomial names as such", "lineNumber": 23 }, { - "__docId__": 399, + "__docId__": 418, "kind": "test", - "name": "it152", - "testId": 152, - "memberof": "test/taxon-names.js~describe148.describe149", + "name": "it162", + "testId": 162, + "memberof": "test/taxon-names.js~describe158.describe159", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe148.describe149.it152", + "longname": "test/taxon-names.js~describe158.describe159.it162", "access": null, "description": "should be able to parse binomial names into genus and specific epithet", "lineNumber": 32 }, { - "__docId__": 400, + "__docId__": 419, "kind": "test", - "name": "it153", - "testId": 153, - "memberof": "test/taxon-names.js~describe148.describe149", + "name": "it163", + "testId": 163, + "memberof": "test/taxon-names.js~describe158.describe159", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe148.describe149.it153", + "longname": "test/taxon-names.js~describe158.describe159.it163", "access": null, "description": "should be able to parse trinomial names into genus, specific epithet and infraspecific epithet", "lineNumber": 40 }, { - "__docId__": 401, + "__docId__": 420, "kind": "test", - "name": "it154", - "testId": 154, - "memberof": "test/taxon-names.js~describe148.describe149", + "name": "it164", + "testId": 164, + "memberof": "test/taxon-names.js~describe158.describe159", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe148.describe149.it154", + "longname": "test/taxon-names.js~describe158.describe159.it164", "access": null, "description": "should ignore authority after a binomial name", "lineNumber": 49 }, { - "__docId__": 402, + "__docId__": 421, "kind": "test", - "name": "it155", - "testId": 155, - "memberof": "test/taxon-names.js~describe148.describe149", + "name": "it165", + "testId": 165, + "memberof": "test/taxon-names.js~describe158.describe159", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe148.describe149.it155", + "longname": "test/taxon-names.js~describe158.describe159.it165", "access": null, "description": "should be able to use default nomenclatural codes", "lineNumber": 57 }, { - "__docId__": 403, + "__docId__": 422, "kind": "testFile", "name": "test/taxonomic-units.js", "content": "/*\n * Test taxonomic unit construction and matching.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Use Chai's expect API.\nconst expect = chai.expect;\n\n/*\n * We primarily test two classes here:\n * - TaxonomicUnitWrapper, which wraps a taxonomic unit and determines if it\n * refers to a scientific name, specimen identifier or external reference,\n * or a combination of these.\n * - TaxonomicUnitMatcher, which accepts two taxonomic units and determines\n * whether and for what reason the two can be matched.\n */\n\ndescribe('TaxonomicUnitWrapper', function () {\n describe('#constructor given no arguments', function () {\n it('should create an empty TaxonomicUnitWrapper without a defined label', function () {\n // Empty TU without @type.\n let wrapper = new phyx.TaxonomicUnitWrapper({});\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n\n // Empty TU with type TYPE_TAXON_CONCEPT.\n wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n });\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n\n // Empty TU with type TYPE_SPECIMEN.\n wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n });\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n\n // Empty TU with type TYPE_SPECIMEN and a taxonomic name.\n wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n nameString: 'Taxonomic name',\n });\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n });\n });\n describe('#label given a taxonomic unit', function () {\n it('should return a wrapped scientific name', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n label: 'Ornithorhynchus anatinus (Shaw, 1799)',\n nameComplete: 'Ornithorhynchus anatinus',\n },\n });\n expect(wrapper.label).to.equal('Ornithorhynchus anatinus (Shaw, 1799)');\n });\n it('should return a wrapped specimen identifier preceded by \"Specimen\"', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Specimen MVZ 225749');\n });\n it('should return specimens with an occurrenceID as well as a taxon concept', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Specimen MVZ 225749 identified as Rana luteiventris');\n });\n it('should ignore occurrence ID if typed as a taxon concept', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Rana luteiventris');\n });\n it('should return a wrapped external reference by surrounding it with \"<>\"', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@id': [\n 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n ],\n });\n expect(wrapper.label).to.equal('');\n });\n it('should provide both taxon name and occurrence ID in label, but ignore external reference', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@id': [\n 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n ],\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Specimen MVZ 225749 identified as Rana luteiventris');\n });\n });\n describe('#fromLabel', function () {\n it('should return empty lists when inputs are empty or undefined', function () {\n expect(phyx.TaxonomicUnitWrapper.fromLabel()).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel(undefined)).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel(null)).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel('')).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel(' ')).to.be.undefined;\n });\n it('when given a scientific name, it should return a list of a single TU wrapping a scientific name', function () {\n expect(phyx.TaxonomicUnitWrapper.fromLabel('Rana luteiventris MVZ225749'))\n .to.be.deep.equal({\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept',\n label: 'Rana luteiventris MVZ225749',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana luteiventris MVZ225749',\n genusPart: 'Rana',\n specificEpithet: 'luteiventris',\n nameComplete: 'Rana luteiventris',\n },\n });\n });\n it('when given a scientific name separated with underscores, it should return a list of a single TU wrapping the scientific name', function () {\n expect(phyx.TaxonomicUnitWrapper.fromLabel('Rana_luteiventris_MVZ_225749'))\n .to.be.deep.equal({\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept',\n label: 'Rana_luteiventris_MVZ_225749',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana_luteiventris_MVZ_225749',\n nameComplete: 'Rana luteiventris',\n genusPart: 'Rana',\n specificEpithet: 'luteiventris',\n },\n });\n });\n });\n describe('#asOWLEquivClass', function () {\n it('when given a taxon concept, only the complete name should be present in the equivClass', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana luteiventris Thompson, 1913',\n });\n expect(wrapper.asOWLEquivClass).to.deep.equal({\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName',\n someValuesFrom: {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete',\n hasValue: 'Rana luteiventris',\n },\n });\n });\n it('when given a specimen, only the occurrence ID should be present in the equivClass', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.asOWLEquivClass).to.deep.equal({\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/dwc/terms/occurrenceID',\n hasValue: 'MVZ 225749',\n });\n });\n });\n});\n\ndescribe('TaxonomicUnitMatcher', function () {\n // To test matching, let's set up some taxonomic units.\n // Note that:\n // tunit1 and tunit2 should match by scientific name.\n // tunit2 and tunit3 should match by specimen identifier.\n // tunit3 and tunit4 should match by external references.\n const tunit1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n nameComplete: 'Rana luteiventris',\n },\n };\n const tunit2 = {\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris MVZ225749',\n occurrenceID: 'MVZ225749',\n };\n const tunit3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ225749',\n '@id': 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n };\n const tunit4 = {\n '@id': 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n };\n\n describe('#matchByNameComplete', function () {\n it('should be able to match tunit1 and tunit2 by complete name', function () {\n expect(new phyx.TaxonomicUnitMatcher(tunit1, tunit2).matchByExternalReferences()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit1, tunit2).matchByOccurrenceID()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit1, tunit2).matchByNameComplete()).to.be.true;\n });\n });\n describe('#matchByExternalReferences', function () {\n it('should be able to match tunit3 and tunit4 by external references', function () {\n expect(new phyx.TaxonomicUnitMatcher(tunit3, tunit4).matchByExternalReferences()).to.be.true;\n expect(new phyx.TaxonomicUnitMatcher(tunit3, tunit4).matchByOccurrenceID()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit3, tunit4).matchByNameComplete()).to.be.false;\n });\n });\n describe('#matchByOccurrenceID', function () {\n it('should be able to match tunit2 and tunit3 by specimen identifiers', function () {\n expect(new phyx.TaxonomicUnitMatcher(tunit2, tunit3).matchByExternalReferences()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit2, tunit3).matchByOccurrenceID()).to.be.true;\n expect(new phyx.TaxonomicUnitMatcher(tunit2, tunit3).matchByNameComplete()).to.be.false;\n });\n });\n describe('#matched and #matchReason', function () {\n it('should match tunit1 and tunit2 on the basis of identical complete names', function () {\n const matcher = new phyx.TaxonomicUnitMatcher(tunit1, tunit2);\n expect(matcher.matched).to.be.true;\n expect(matcher.matchReason).to.include('share the same complete name');\n });\n\n it('should match tunit3 and tunit4 by identical external reference', function () {\n const matcher = new phyx.TaxonomicUnitMatcher(tunit3, tunit4);\n expect(matcher.matched).to.be.true;\n expect(matcher.matchReason).to.include('External reference');\n });\n\n it('should match tunit2 and tunit3 by identical specimen identifier', function () {\n const matcher = new phyx.TaxonomicUnitMatcher(tunit2, tunit3);\n expect(matcher.matched).to.be.true;\n expect(matcher.matchReason).to.include('Specimen identifier');\n });\n });\n});\n", @@ -6333,365 +6701,365 @@ "lineNumber": 1 }, { - "__docId__": 404, + "__docId__": 423, "kind": "test", - "name": "describe156", - "testId": 156, + "name": "describe166", + "testId": 166, "memberof": "test/taxonomic-units.js", "testDepth": 0, "static": true, - "longname": "test/taxonomic-units.js~describe156", + "longname": "test/taxonomic-units.js~describe166", "access": null, "description": "TaxonomicUnitWrapper", "lineNumber": 20 }, { - "__docId__": 405, + "__docId__": 424, "kind": "test", - "name": "describe157", - "testId": 157, - "memberof": "test/taxonomic-units.js~describe156", + "name": "describe167", + "testId": 167, + "memberof": "test/taxonomic-units.js~describe166", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe157", 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2, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe159.it161", + "longname": "test/taxonomic-units.js~describe166.describe169.it171", "access": null, "description": "should return a wrapped specimen identifier preceded by \"Specimen\"", "lineNumber": 62 }, { - "__docId__": 410, + "__docId__": 429, "kind": "test", - "name": "it162", - "testId": 162, - "memberof": "test/taxonomic-units.js~describe156.describe159", + "name": "it172", + "testId": 172, + "memberof": "test/taxonomic-units.js~describe166.describe169", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe159.it162", + "longname": "test/taxonomic-units.js~describe166.describe169.it172", "access": null, "description": "should return specimens with an occurrenceID as well as a taxon concept", "lineNumber": 69 }, { - "__docId__": 411, + "__docId__": 430, "kind": "test", - "name": "it163", - "testId": 163, - "memberof": "test/taxonomic-units.js~describe156.describe159", + "name": "it173", + "testId": 173, + "memberof": "test/taxonomic-units.js~describe166.describe169", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe159.it163", + "longname": "test/taxonomic-units.js~describe166.describe169.it173", "access": null, "description": "should ignore occurrence ID if typed as a taxon concept", "lineNumber": 79 }, { - "__docId__": 412, + "__docId__": 431, "kind": "test", - "name": "it164", - "testId": 164, - "memberof": "test/taxonomic-units.js~describe156.describe159", + "name": "it174", + "testId": 174, + "memberof": "test/taxonomic-units.js~describe166.describe169", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe159.it164", + "longname": "test/taxonomic-units.js~describe166.describe169.it174", "access": null, "description": "should return a wrapped external reference by surrounding it with \"<>\"", "lineNumber": 87 }, { - "__docId__": 413, + "__docId__": 432, "kind": "test", - "name": "it165", - "testId": 165, - "memberof": "test/taxonomic-units.js~describe156.describe159", + "name": "it175", + "testId": 175, + "memberof": "test/taxonomic-units.js~describe166.describe169", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe159.it165", + "longname": "test/taxonomic-units.js~describe166.describe169.it175", "access": null, "description": "should provide both taxon name and occurrence ID in label, but ignore external reference", "lineNumber": 95 }, { - "__docId__": 414, + "__docId__": 433, "kind": "test", - "name": "describe166", - "testId": 166, - "memberof": "test/taxonomic-units.js~describe156", + "name": "describe176", + "testId": 176, + "memberof": "test/taxonomic-units.js~describe166", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe156.describe166", + "longname": "test/taxonomic-units.js~describe166.describe176", "access": null, 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"lineNumber": 218 }, { - "__docId__": 428, + "__docId__": 447, "kind": "test", - "name": "describe180", - "testId": 180, - "memberof": "test/taxonomic-units.js~describe173", + "name": "describe190", + "testId": 190, + "memberof": "test/taxonomic-units.js~describe183", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe173.describe180", + "longname": "test/taxonomic-units.js~describe183.describe190", "access": null, "description": "#matched and #matchReason", "lineNumber": 224 }, { - "__docId__": 429, + "__docId__": 448, "kind": "test", - "name": "it181", - "testId": 181, - "memberof": "test/taxonomic-units.js~describe173.describe180", + "name": "it191", + "testId": 191, + "memberof": "test/taxonomic-units.js~describe183.describe190", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe173.describe180.it181", + "longname": "test/taxonomic-units.js~describe183.describe190.it191", "access": null, "description": "should match tunit1 and tunit2 on the basis of identical complete names", "lineNumber": 225 }, { - "__docId__": 430, + "__docId__": 449, "kind": "test", - "name": "it182", - "testId": 182, - "memberof": "test/taxonomic-units.js~describe173.describe180", + "name": "it192", + "testId": 192, + "memberof": "test/taxonomic-units.js~describe183.describe190", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe173.describe180.it182", + "longname": "test/taxonomic-units.js~describe183.describe190.it192", "access": null, "description": "should match tunit3 and tunit4 by identical external reference", "lineNumber": 231 }, { - "__docId__": 431, + "__docId__": 450, "kind": "test", - "name": "it183", - "testId": 183, - "memberof": "test/taxonomic-units.js~describe173.describe180", + "name": "it193", + "testId": 193, + "memberof": "test/taxonomic-units.js~describe183.describe190", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe173.describe180.it183", + "longname": "test/taxonomic-units.js~describe183.describe190.it193", "access": null, "description": "should match tunit2 and tunit3 by identical specimen identifier", "lineNumber": 237 diff --git a/docs/manual/CHANGELOG.html b/docs/manual/CHANGELOG.html index 12986ea5..cdad46ff 100644 --- a/docs/manual/CHANGELOG.html +++ b/docs/manual/CHANGELOG.html @@ -32,7 +32,8 @@
  • Changelog
    • -
  • Unreleased
    • +
  • Unreleased
    • +
  • 1.2.0 - 2024-06-18
  • 1.1.1 - 2023-08-01
  • 1.1.0 - 2023-05-11
  • 1.0.1 - 2021-10-15
    • @@ -70,7 +71,11 @@

    Changelog

    All notable changes to this library will be documented in this file.

    The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

    -

    Unreleased

    1.1.1 - 2023-08-01

      +

      Unreleased

      1.2.0 - 2024-06-18

        +
      • PR #138: Added normalization methods so that Phyx objects can be normalized.
        • +
      • PR #139: upgraded NPM packages and minor test fixes
        • +
      +

      1.1.1 - 2023-08-01

      • PR #133: Add guards to some usages of phyloref.internalSpecifiers/phyloref.externalSpecifiers.
      • PR #136: Improved GitHub test action, including changing Node versions.
      • PR #127: Upgraded Newick.js to ^1.2.1. This means that we no longer diff --git a/docs/manual/Introduction.html b/docs/manual/Introduction.html index c265ae39..f1874fe3 100644 --- a/docs/manual/Introduction.html +++ b/docs/manual/Introduction.html @@ -32,7 +32,8 @@
        • Changelog
          • -
        • Unreleased
          • +
        • Unreleased
          • +
        • 1.2.0 - 2024-06-18
        • 1.1.1 - 2023-08-01
        • 1.1.0 - 2023-05-11
        • 1.0.1 - 2021-10-15
          • diff --git a/docs/manual/index.html b/docs/manual/index.html index e3cdcd60..8ae3d044 100644 --- a/docs/manual/index.html +++ b/docs/manual/index.html @@ -32,7 +32,8 @@
          • Changelog
            • -
          • Unreleased
            • +
          • Unreleased
            • +
          • 1.2.0 - 2024-06-18
          • 1.1.1 - 2023-08-01
          • 1.1.0 - 2023-05-11
          • 1.0.1 - 2021-10-15
            • @@ -77,7 +78,10 @@
            -

            Changelog

            All notable changes to this library will be documented in this file.

            The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

            Unreleased

            1.1.1 - 2023-08-01

              +

              Changelog

              All notable changes to this library will be documented in this file.

              The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

              Unreleased

              1.2.0 - 2024-06-18

                +
              • PR #138: Added normalization methods so that Phyx objects can be normalized.
                • +
              • PR #139: upgraded NPM packages and minor test fixes
                • +

              1.1.1 - 2023-08-01

              • PR #133: Add guards to some usages of phyloref.internalSpecifiers/phyloref.externalSpecifiers.
              • PR #136: Improved GitHub test action, including changing Node versions.
              • PR #127: Upgraded Newick.js to ^1.2.1. 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Test all normalization Phyx files ", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber61", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phylogenies", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber62", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phylogenies These tests have not yet been implemented since we don't have an urgent need for them.", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber66", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phyloreferences", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber67", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phyloreferences should have multiple same phyloreferences for testing", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber106", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phyloreferences should have pairs of `_different` phylorefs that are different before and after normalization", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber87", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phyloreferences should have pairs of `_same` phylorefs that are different, but are identical after normalization", + "test" + ], + [ + "", + "test-file/test/normalization.js.html#lineNumber71", + "Test whether normalization of phyloreferences and phylogenies work as expected.\nThis test does not cover Phyx normalization. Test all normalization Phyx files Test phyloreferences should not have any duplicate phylorefs (which would be pointless)", + "test" + ], [ "", "test-file/test/jphyloref.js.html#lineNumber31", @@ -1535,6 +1595,12 @@ window.esdocSearchIndex = [ "src/wrappers/CitationWrapper.js~CitationWrapper.getAgentName", "method" ], + [ + "src/wrappers/citationwrapper.js~citationwrapper.normalize", + "class/src/wrappers/CitationWrapper.js~CitationWrapper.html#static-method-normalize", + "src/wrappers/CitationWrapper.js~CitationWrapper.normalize", + "method" + ], [ "src/wrappers/phylogenywrapper.js", "file/src/wrappers/PhylogenyWrapper.js.html", @@ -1613,6 +1679,12 @@ window.esdocSearchIndex = [ "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.getParsedNewick", "method" ], + [ + "src/wrappers/phylogenywrapper.js~phylogenywrapper.normalize", + "class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html#static-method-normalize", + "src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.normalize", + "method" + ], [ "src/wrappers/phylogenywrapper.js~phylogenywrapper.recursenodes", "class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html#static-method-recurseNodes", @@ -1775,6 +1847,12 @@ window.esdocSearchIndex = [ "src/wrappers/PhylorefWrapper.js~PhylorefWrapper.getStatusCURIEsInEnglish", "method" ], + [ + "src/wrappers/phylorefwrapper.js~phylorefwrapper.normalize", + "class/src/wrappers/PhylorefWrapper.js~PhylorefWrapper.html#static-method-normalize", + "src/wrappers/PhylorefWrapper.js~PhylorefWrapper.normalize", + "method" + ], [ "src/wrappers/phyxwrapper.js", "file/src/wrappers/PhyxWrapper.js.html", @@ -1817,6 +1895,12 @@ window.esdocSearchIndex = [ "src/wrappers/PhyxWrapper.js~PhyxWrapper#toRDF", "method" ], + [ + "src/wrappers/phyxwrapper.js~phyxwrapper.normalize", + "class/src/wrappers/PhyxWrapper.js~PhyxWrapper.html#static-method-normalize", + "src/wrappers/PhyxWrapper.js~PhyxWrapper.normalize", + "method" + ], [ "src/wrappers/specimenwrapper.js", "file/src/wrappers/SpecimenWrapper.js.html", @@ -1901,6 +1985,12 @@ window.esdocSearchIndex = [ "src/wrappers/SpecimenWrapper.js~SpecimenWrapper.fromOccurrenceID", "method" ], + [ + "src/wrappers/specimenwrapper.js~specimenwrapper.normalize", + "class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html#static-method-normalize", + "src/wrappers/SpecimenWrapper.js~SpecimenWrapper.normalize", + "method" + ], [ "src/wrappers/taxonconceptwrapper.js", "file/src/wrappers/TaxonConceptWrapper.js.html", @@ -1985,6 +2075,12 @@ window.esdocSearchIndex = [ "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.fromLabel", "method" ], + [ + "src/wrappers/taxonconceptwrapper.js~taxonconceptwrapper.normalize", + "class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html#static-method-normalize", + "src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.normalize", + "method" + ], [ "src/wrappers/taxonconceptwrapper.js~taxonconceptwrapper.wraptaxonname", "class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html#static-method-wrapTaxonName", @@ -2207,6 +2303,12 @@ window.esdocSearchIndex = [ "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.getNomenclaturalCodes", "method" ], + [ + "src/wrappers/taxonnamewrapper.js~taxonnamewrapper.normalize", + "class/src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.html#static-method-normalize", + "src/wrappers/TaxonNameWrapper.js~TaxonNameWrapper.normalize", + "method" + ], [ "src/wrappers/taxonomicunitwrapper.js", "file/src/wrappers/TaxonomicUnitWrapper.js.html", @@ -2297,6 +2399,12 @@ window.esdocSearchIndex = [ "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.fromLabel", "method" ], + [ + "src/wrappers/taxonomicunitwrapper.js~taxonomicunitwrapper.normalize", + "class/src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.html#static-method-normalize", + "src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.normalize", + "method" + ], [ "test/citations.js", "test-file/test/citations.js.html", @@ -2321,6 +2429,12 @@ window.esdocSearchIndex = [ "test/nomenclatural-codes.js", "testFile" ], + [ + "test/normalization.js", + "test-file/test/normalization.js.html", + "test/normalization.js", + "testFile" + ], [ "test/phylogenies.js", "test-file/test/phylogenies.js.html", diff --git a/docs/source.html b/docs/source.html index da86b9b9..67bc01fe 100644 --- a/docs/source.html +++ b/docs/source.html @@ -42,7 +42,7 @@
              -

              Source 90/171

              +

              Source 98/179

              @@ -68,66 +68,66 @@ - - - - + + + + - + - - - - + + + + - + - - - - + + + + - - - - + + + + - - - - + + + + - - - - + + + + - + - - - - + + + + - - - - + + + +
              src/wrappers/CitationWrapper.js CitationWrapper50 %3/64322 byte1122021-03-02 04:08:18 (UTC)57 %4/74974 byte1302024-06-04 03:09:07 (UTC)
              src/wrappers/PhylogenyWrapper.jssrc/wrappers/PhylogenyWrapper.js PhylogenyWrapper5 %1/1818006 byte4612023-08-04 02:25:29 (UTC)10 %2/1918456 byte4802024-06-04 03:09:07 (UTC)
              src/wrappers/PhylorefWrapper.jssrc/wrappers/PhylorefWrapper.js PhylorefWrapper25 %8/3132228 byte7952023-08-04 02:25:29 (UTC)28 %9/3232668 byte8112024-06-04 03:09:07 (UTC)
              src/wrappers/PhyxWrapper.js PhyxWrapper36 %4/1112874 byte2862021-03-06 17:38:06 (UTC)41 %5/1214037 byte3122024-06-04 03:09:07 (UTC)
              src/wrappers/SpecimenWrapper.js SpecimenWrapper76 %13/178135 byte2222020-10-06 03:01:31 (UTC)77 %14/188770 byte2412024-06-04 03:09:07 (UTC)
              src/wrappers/TaxonConceptWrapper.js TaxonConceptWrapper76 %13/176711 byte1942021-03-03 17:34:35 (UTC)77 %14/187247 byte2112024-06-04 03:09:07 (UTC)
              src/wrappers/TaxonNameWrapper.jssrc/wrappers/TaxonNameWrapper.js TaxonNameWrapper73 %28/3814723 byte4792021-03-03 17:34:35 (UTC)74 %29/3915356 byte4982024-06-04 03:09:07 (UTC)
              src/wrappers/TaxonomicUnitWrapper.js TaxonomicUnitWrapper68 %13/197716 byte2462021-03-02 03:23:12 (UTC)70 %14/208220 byte2652024-06-04 03:09:07 (UTC)
              diff --git a/docs/test-file/test/jphyloref.js.html b/docs/test-file/test/jphyloref.js.html index 377ff490..ffbb825b 100644 --- a/docs/test-file/test/jphyloref.js.html +++ b/docs/test-file/test/jphyloref.js.html @@ -62,7 +62,7 @@ * Constants */ // The version of JPhyloRef to download. -const JPHYLOREF_VERSION = '0.4.0'; +const JPHYLOREF_VERSION = '1.1.1'; // The URL from where JPhyloRef should be downloaded. const JPHYLOREF_URL = `https://repo.maven.apache.org/maven2/org/phyloref/jphyloref/${JPHYLOREF_VERSION}/jphyloref-${JPHYLOREF_VERSION}.jar`; diff --git a/docs/test-file/test/scripts/phyx2owl.js.html b/docs/test-file/test/scripts/phyx2owl.js.html index 817d4eac..ec360e2e 100644 --- a/docs/test-file/test/scripts/phyx2owl.js.html +++ b/docs/test-file/test/scripts/phyx2owl.js.html @@ -109,7 +109,7 @@ }); it('should be able to convert the entire `test/examples/correct` directory', function () { const EXAMPLE_DIR = path.resolve(__dirname, '../examples/correct'); - const jsonFilesInExamples = fs.readdirSync(EXAMPLE_DIR, 'utf8') + const jsonFilesInExamples = fs.readdirSync(EXAMPLE_DIR, { recursive: true }) .filter(fileName => fileName.toLowerCase().endsWith('.json')); const result = child.spawnSync(PHYX2OWL_JS, [EXAMPLE_DIR, '--base-iri', 'http://example.org/phyx.js/example#'], { diff --git a/docs/test-file/test/scripts/resolve.js.html b/docs/test-file/test/scripts/resolve.js.html index a2207371..2855db5d 100644 --- a/docs/test-file/test/scripts/resolve.js.html +++ b/docs/test-file/test/scripts/resolve.js.html @@ -107,15 +107,15 @@ ]); expect(resultObj.Alligatoridae[0].resolved).to.include({ - '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.7@ott195670', + '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott195670', label: 'Alligatoridae', }); expect(resultObj.Alligatorinae[0].resolved).to.include({ - '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.7@ott151255', + '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott151255', label: 'Alligatorinae', }); expect(resultObj.Crocodylidae[0].resolved).to.include({ - '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.7@ott1092501', + '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott1092501', label: 'Longirostres', }); expect(resultObj.Diplocynodontinae[0]).to.include({ diff --git a/docs/test.html b/docs/test.html index 42d5cbe0..0df675a3 100644 --- a/docs/test.html +++ b/docs/test.html @@ -311,6 +311,66 @@ - + +

              Test whether normalization of phyloreferences and phylogenies work as expected. +This test does not cover Phyx normalization.

              +               + - + + + +

              Test all normalization Phyx files

              +               + - + + + + test/normalization.js + - + + + +

              Test phylogenies

              +               + - + + + +

              These tests have not yet been implemented since we don't have an urgent need for them.

              +               + - + + + +

              Test phyloreferences

              +               + - + + + +

              should have multiple same phyloreferences for testing

              +               + - + + + +

              should not have any duplicate phylorefs (which would be pointless)

              +               + - + + + +

              should have pairs of _same phylorefs that are different, but are identical after normalization

              +               + - + + + +

              should have pairs of _different phylorefs that are different before and after normalization

              +               + - + +

              PhylogenyWrapper

               From c4b608c5fc6145521c329201786c42f002c380dd Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Sun, 22 Dec 2024 22:29:35 -0500 Subject: [PATCH 4/6] Updated version to v1.2.0-alpha2. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 161407c5..2d6a5d8e 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@phyloref/phyx", - "version": "1.2.0-alpha1", + "version": "1.2.0-alpha2", "description": "Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files", "keywords": [ "phylogenetics", From 1b6d75f71e143a01cdc0ee6dbe049b016d28479d Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Sun, 22 Dec 2024 22:33:43 -0500 Subject: [PATCH 5/6] Updated docs. --- .../matchers/TaxonomicUnitMatcher.js.json | 36 +- .../source/wrappers/CitationWrapper.js.json | 12 +- .../source/wrappers/PhylogenyWrapper.js.json | 48 +- .../source/wrappers/PhylorefWrapper.js.json | 60 +- docs/ast/source/wrappers/PhyxWrapper.js.json | 48 +- .../source/wrappers/SpecimenWrapper.js.json | 11313 +++++++--------- .../wrappers/TaxonConceptWrapper.js.json | 24 +- .../source/wrappers/TaxonNameWrapper.js.json | 24 +- .../wrappers/TaxonomicUnitWrapper.js.json | 48 +- .../SpecimenWrapper.js~SpecimenWrapper.html | 4 +- .../file/src/wrappers/SpecimenWrapper.js.html | 16 +- docs/index.html | 6 +- docs/index.json | 455 +- docs/script/search_index.js | 20 +- docs/source.html | 20 +- docs/test-file/test/scripts/resolve.js.html | 6 +- docs/test-file/test/specimens.js.html | 12 +- docs/test.html | 20 +- 18 files changed, 5700 insertions(+), 6472 deletions(-) diff --git a/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json b/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json index 6f3d7491..41ed6f2c 100644 --- a/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json +++ b/docs/ast/source/matchers/TaxonomicUnitMatcher.js.json @@ -70,9 +70,9 @@ "line": 1, "column": 25 }, - "identifierName": "LXL9JK4849P6M" + "identifierName": "M50HFXTXLX50B" }, - "name": "LXL9JK4849P6M" + "name": "M50HFXTXLX50B" } } ], @@ -211,9 +211,9 @@ "line": 2, "column": 46 }, - "identifierName": "LXL9JK4849P6M" + "identifierName": "M50HFXTXLX50B" }, - "name": "LXL9JK4849P6M" + "name": "M50HFXTXLX50B" } } ], @@ -261,9 +261,9 @@ "line": 3, "column": 25 }, - "identifierName": "LXL9JK48UIGO0" + "identifierName": "M50HFXTXWY9DG" }, - "name": "LXL9JK48UIGO0" + "name": "M50HFXTXWY9DG" } } ], @@ -402,9 +402,9 @@ "line": 4, "column": 45 }, - "identifierName": "LXL9JK48UIGO0" + "identifierName": "M50HFXTXWY9DG" }, - "name": "LXL9JK48UIGO0" + "name": "M50HFXTXWY9DG" } } ], @@ -452,9 +452,9 @@ "line": 5, "column": 25 }, - "identifierName": "LXL9JK48T1OMI" + "identifierName": "M50HFXTXA2PM8" }, - "name": "LXL9JK48T1OMI" + "name": "M50HFXTXA2PM8" } } ], @@ -593,9 +593,9 @@ "line": 6, "column": 41 }, - "identifierName": "LXL9JK48T1OMI" + "identifierName": "M50HFXTXA2PM8" }, - "name": "LXL9JK48T1OMI" + "name": "M50HFXTXA2PM8" } } ], @@ -13549,7 +13549,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK4849P6M", + "value": "M50HFXTXLX50B", "start": 12, "end": 25, "loc": { @@ -13785,7 +13785,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK4849P6M", + "value": "M50HFXTXLX50B", "start": 101, "end": 114, "loc": { @@ -13918,7 +13918,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK48UIGO0", + "value": "M50HFXTXWY9DG", "start": 128, "end": 141, "loc": { @@ -14154,7 +14154,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK48UIGO0", + "value": "M50HFXTXWY9DG", "start": 215, "end": 228, "loc": { @@ -14287,7 +14287,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK48T1OMI", + "value": "M50HFXTXA2PM8", "start": 242, "end": 255, "loc": { @@ -14523,7 +14523,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK48T1OMI", + "value": "M50HFXTXA2PM8", "start": 321, "end": 334, "loc": { diff --git a/docs/ast/source/wrappers/CitationWrapper.js.json b/docs/ast/source/wrappers/CitationWrapper.js.json index 249461ff..f2422e7f 100644 --- a/docs/ast/source/wrappers/CitationWrapper.js.json +++ b/docs/ast/source/wrappers/CitationWrapper.js.json @@ -70,9 +70,9 @@ "line": 6, "column": 25 }, - "identifierName": "LXL9JK4VB2TPD" + "identifierName": "M50HFXU6F0NKU" }, - "name": "LXL9JK4VB2TPD", + "name": "M50HFXU6F0NKU", "leadingComments": null }, "leadingComments": null @@ -286,9 +286,9 @@ "line": 7, "column": 38 }, - "identifierName": "LXL9JK4VB2TPD" + "identifierName": "M50HFXU6F0NKU" }, - "name": "LXL9JK4VB2TPD" + "name": "M50HFXU6F0NKU" } } ], @@ -24283,7 +24283,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK4VB2TPD", + "value": "M50HFXU6F0NKU", "start": 142, "end": 155, "loc": { @@ -24571,7 +24571,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK4VB2TPD", + "value": "M50HFXU6F0NKU", "start": 197, "end": 210, "loc": { diff --git a/docs/ast/source/wrappers/PhylogenyWrapper.js.json b/docs/ast/source/wrappers/PhylogenyWrapper.js.json index 173f9f75..07a62bbe 100644 --- a/docs/ast/source/wrappers/PhylogenyWrapper.js.json +++ b/docs/ast/source/wrappers/PhylogenyWrapper.js.json @@ -70,9 +70,9 @@ "line": 5, "column": 25 }, - "identifierName": "LXL9JK5MY9Z3Z" + "identifierName": "M50HFXUGMZEIO" }, - "name": "LXL9JK5MY9Z3Z", + "name": "M50HFXUGMZEIO", "leadingComments": null }, "leadingComments": null @@ -286,9 +286,9 @@ "line": 9, "column": 17 }, - "identifierName": "LXL9JK5MY9Z3Z" + "identifierName": "M50HFXUGMZEIO" }, - "name": "LXL9JK5MY9Z3Z" + "name": "M50HFXUGMZEIO" } } ], @@ -550,9 +550,9 @@ "line": 17, "column": 25 }, - "identifierName": "LXL9JK5M3VRPM" + "identifierName": "M50HFXUGA4T4Y" }, - "name": "LXL9JK5M3VRPM" + "name": "M50HFXUGA4T4Y" } } ], @@ -691,9 +691,9 @@ "line": 18, "column": 46 }, - "identifierName": "LXL9JK5M3VRPM" + "identifierName": "M50HFXUGA4T4Y" }, - "name": "LXL9JK5M3VRPM" + "name": "M50HFXUGA4T4Y" } } ], @@ -741,9 +741,9 @@ "line": 19, "column": 25 }, - "identifierName": "LXL9JK5M475GC" + "identifierName": "M50HFXUGG4ABQ" }, - "name": "LXL9JK5M475GC" + "name": "M50HFXUGG4ABQ" } } ], @@ -882,9 +882,9 @@ "line": 20, "column": 46 }, - "identifierName": "LXL9JK5M475GC" + "identifierName": "M50HFXUGG4ABQ" }, - "name": "LXL9JK5M475GC" + "name": "M50HFXUGG4ABQ" } } ], @@ -932,9 +932,9 @@ "line": 21, "column": 25 }, - "identifierName": "LXL9JK5MUANAE" + "identifierName": "M50HFXUGUZ2JB" }, - "name": "LXL9JK5MUANAE" + "name": "M50HFXUGUZ2JB" } } ], @@ -1073,9 +1073,9 @@ "line": 22, "column": 41 }, - "identifierName": "LXL9JK5MUANAE" + "identifierName": "M50HFXUGUZ2JB" }, - "name": "LXL9JK5MUANAE" + "name": "M50HFXUGUZ2JB" } } ], @@ -51102,7 +51102,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5MY9Z3Z", + "value": "M50HFXUGMZEIO", "start": 41, "end": 54, "loc": { @@ -51416,7 +51416,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5MY9Z3Z", + "value": "M50HFXUGMZEIO", "start": 103, "end": 116, "loc": { @@ -51847,7 +51847,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5M3VRPM", + "value": "M50HFXUGA4T4Y", "start": 280, "end": 293, "loc": { @@ -52083,7 +52083,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5M3VRPM", + "value": "M50HFXUGA4T4Y", "start": 359, "end": 372, "loc": { @@ -52216,7 +52216,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5M475GC", + "value": "M50HFXUGG4ABQ", "start": 386, "end": 399, "loc": { @@ -52452,7 +52452,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5M475GC", + "value": "M50HFXUGG4ABQ", "start": 475, "end": 488, "loc": { @@ -52585,7 +52585,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5MUANAE", + "value": "M50HFXUGUZ2JB", "start": 502, "end": 515, "loc": { @@ -52821,7 +52821,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK5MUANAE", + "value": "M50HFXUGUZ2JB", "start": 571, "end": 584, "loc": { diff --git a/docs/ast/source/wrappers/PhylorefWrapper.js.json b/docs/ast/source/wrappers/PhylorefWrapper.js.json index f5ecc04b..bed7e903 100644 --- a/docs/ast/source/wrappers/PhylorefWrapper.js.json +++ b/docs/ast/source/wrappers/PhylorefWrapper.js.json @@ -159,9 +159,9 @@ "line": 3, "column": 25 }, - "identifierName": "LXL9JK6ODIPBD" + "identifierName": "M50HFXUVFVB42" }, - "name": "LXL9JK6ODIPBD" + "name": "M50HFXUVFVB42" } } ], @@ -410,9 +410,9 @@ "line": 4, "column": 46 }, - "identifierName": "LXL9JK6ODIPBD" + "identifierName": "M50HFXUVFVB42" }, - "name": "LXL9JK6ODIPBD" + "name": "M50HFXUVFVB42" } } ], @@ -529,9 +529,9 @@ "line": 7, "column": 25 }, - "identifierName": "LXL9JK6OWJB6S" + "identifierName": "M50HFXUVZ5Q9F" }, - "name": "LXL9JK6OWJB6S" + "name": "M50HFXUVZ5Q9F" } } ], @@ -670,9 +670,9 @@ "line": 8, "column": 46 }, - "identifierName": "LXL9JK6OWJB6S" + "identifierName": "M50HFXUVZ5Q9F" }, - "name": "LXL9JK6OWJB6S" + "name": "M50HFXUVZ5Q9F" } } ], @@ -720,9 +720,9 @@ "line": 9, "column": 25 }, - "identifierName": "LXL9JK6OL1ASK" + "identifierName": "M50HFXUVBS4RX" }, - "name": "LXL9JK6OL1ASK" + "name": "M50HFXUVBS4RX" } } ], @@ -861,9 +861,9 @@ "line": 10, "column": 45 }, - "identifierName": "LXL9JK6OL1ASK" + "identifierName": "M50HFXUVBS4RX" }, - "name": "LXL9JK6OL1ASK" + "name": "M50HFXUVBS4RX" } } ], @@ -911,9 +911,9 @@ "line": 11, "column": 25 }, - "identifierName": "LXL9JK6ORWVVE" + "identifierName": "M50HFXUV9876D" }, - "name": "LXL9JK6ORWVVE" + "name": "M50HFXUV9876D" } } ], @@ -1052,9 +1052,9 @@ "line": 12, "column": 42 }, - "identifierName": "LXL9JK6ORWVVE" + "identifierName": "M50HFXUV9876D" }, - "name": "LXL9JK6ORWVVE" + "name": "M50HFXUV9876D" } } ], @@ -1102,9 +1102,9 @@ "line": 13, "column": 25 }, - "identifierName": "LXL9JK6O9OPUJ" + "identifierName": "M50HFXUVEI6GD" }, - "name": "LXL9JK6O9OPUJ" + "name": "M50HFXUVEI6GD" } } ], @@ -1243,9 +1243,9 @@ "line": 14, "column": 41 }, - "identifierName": "LXL9JK6O9OPUJ" + "identifierName": "M50HFXUVEI6GD" }, - "name": "LXL9JK6O9OPUJ" + "name": "M50HFXUVEI6GD" } } ], @@ -85266,7 +85266,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6ODIPBD", + "value": "M50HFXUVFVB42", "start": 96, "end": 109, "loc": { @@ -85606,7 +85606,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6ODIPBD", + "value": "M50HFXUVFVB42", "start": 159, "end": 172, "loc": { @@ -85872,7 +85872,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6OWJB6S", + "value": "M50HFXUVZ5Q9F", "start": 229, "end": 242, "loc": { @@ -86108,7 +86108,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6OWJB6S", + "value": "M50HFXUVZ5Q9F", "start": 308, "end": 321, "loc": { @@ -86241,7 +86241,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6OL1ASK", + "value": "M50HFXUVBS4RX", "start": 335, "end": 348, "loc": { @@ -86477,7 +86477,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6OL1ASK", + "value": "M50HFXUVBS4RX", "start": 412, "end": 425, "loc": { @@ -86610,7 +86610,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6ORWVVE", + "value": "M50HFXUV9876D", "start": 439, "end": 452, "loc": { @@ -86846,7 +86846,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6ORWVVE", + "value": "M50HFXUV9876D", "start": 510, "end": 523, "loc": { @@ -86979,7 +86979,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6O9OPUJ", + "value": "M50HFXUVEI6GD", "start": 537, "end": 550, "loc": { @@ -87215,7 +87215,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK6O9OPUJ", + "value": "M50HFXUVEI6GD", "start": 606, "end": 619, "loc": { diff --git a/docs/ast/source/wrappers/PhyxWrapper.js.json b/docs/ast/source/wrappers/PhyxWrapper.js.json index 13fa994e..52f46b8d 100644 --- a/docs/ast/source/wrappers/PhyxWrapper.js.json +++ b/docs/ast/source/wrappers/PhyxWrapper.js.json @@ -226,9 +226,9 @@ "line": 5, "column": 25 }, - "identifierName": "LXL9JK83PH1BW" + "identifierName": "M50HFXVL6ZOI3" }, - "name": "LXL9JK83PH1BW", + "name": "M50HFXVL6ZOI3", "leadingComments": null }, "leadingComments": null @@ -497,9 +497,9 @@ "line": 6, "column": 46 }, - "identifierName": "LXL9JK83PH1BW" + "identifierName": "M50HFXVL6ZOI3" }, - "name": "LXL9JK83PH1BW" + "name": "M50HFXVL6ZOI3" } } ], @@ -723,9 +723,9 @@ "line": 13, "column": 25 }, - "identifierName": "LXL9JK836PI9S" + "identifierName": "M50HFXVL4VN6M" }, - "name": "LXL9JK836PI9S" + "name": "M50HFXVL4VN6M" } } ], @@ -864,9 +864,9 @@ "line": 14, "column": 41 }, - "identifierName": "LXL9JK836PI9S" + "identifierName": "M50HFXVL4VN6M" }, - "name": "LXL9JK836PI9S" + "name": "M50HFXVL4VN6M" } } ], @@ -914,9 +914,9 @@ "line": 15, "column": 25 }, - "identifierName": "LXL9JK830DC8M" + "identifierName": "M50HFXVLNRV2S" }, - "name": "LXL9JK830DC8M" + "name": "M50HFXVLNRV2S" } } ], @@ -1055,9 +1055,9 @@ "line": 16, "column": 42 }, - "identifierName": "LXL9JK830DC8M" + "identifierName": "M50HFXVLNRV2S" }, - "name": "LXL9JK830DC8M" + "name": "M50HFXVLNRV2S" } } ], @@ -1105,9 +1105,9 @@ "line": 17, "column": 25 }, - "identifierName": "LXL9JK83OXXQ2" + "identifierName": "M50HFXVLF02HT" }, - "name": "LXL9JK83OXXQ2" + "name": "M50HFXVLF02HT" } } ], @@ -1246,9 +1246,9 @@ "line": 18, "column": 41 }, - "identifierName": "LXL9JK83OXXQ2" + "identifierName": "M50HFXVLF02HT" }, - "name": "LXL9JK83OXXQ2" + "name": "M50HFXVLF02HT" } } ], @@ -33226,7 +33226,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK83PH1BW", + "value": "M50HFXVL6ZOI3", "start": 94, "end": 107, "loc": { @@ -33566,7 +33566,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK83PH1BW", + "value": "M50HFXVL6ZOI3", "start": 157, "end": 170, "loc": { @@ -33981,7 +33981,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK836PI9S", + "value": "M50HFXVL4VN6M", "start": 284, "end": 297, "loc": { @@ -34217,7 +34217,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK836PI9S", + "value": "M50HFXVL4VN6M", "start": 353, "end": 366, "loc": { @@ -34350,7 +34350,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK830DC8M", + "value": "M50HFXVLNRV2S", "start": 380, "end": 393, "loc": { @@ -34586,7 +34586,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK830DC8M", + "value": "M50HFXVLNRV2S", "start": 451, "end": 464, "loc": { @@ -34719,7 +34719,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK83OXXQ2", + "value": "M50HFXVLF02HT", "start": 478, "end": 491, "loc": { @@ -34955,7 +34955,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK83OXXQ2", + "value": "M50HFXVLF02HT", "start": 547, "end": 560, "loc": { diff --git a/docs/ast/source/wrappers/SpecimenWrapper.js.json b/docs/ast/source/wrappers/SpecimenWrapper.js.json index 5b102473..af4a2f6d 100644 --- a/docs/ast/source/wrappers/SpecimenWrapper.js.json +++ b/docs/ast/source/wrappers/SpecimenWrapper.js.json @@ -1,7 +1,7 @@ { "type": "File", "start": 0, - "end": 8867, + "end": 8773, "loc": { "start": { "line": 1, @@ -15,7 +15,7 @@ "program": { "type": "Program", "start": 0, - "end": 8867, + "end": 8773, "loc": { "start": { "line": 1, @@ -70,9 +70,9 @@ "line": 1, "column": 25 }, - "identifierName": "LXL9JK8J7MTDE" + "identifierName": "M50HFXVTJPWM5" }, - "name": "LXL9JK8J7MTDE" + "name": "M50HFXVTJPWM5" } } ], @@ -211,9 +211,9 @@ "line": 2, "column": 29 }, - "identifierName": "LXL9JK8J7MTDE" + "identifierName": "M50HFXVTJPWM5" }, - "name": "LXL9JK8J7MTDE" + "name": "M50HFXVTJPWM5" } } ], @@ -261,9 +261,9 @@ "line": 3, "column": 25 }, - "identifierName": "LXL9JK8JTNLQE" + "identifierName": "M50HFXVT2CD2B" }, - "name": "LXL9JK8JTNLQE" + "name": "M50HFXVT2CD2B" } } ], @@ -402,9 +402,9 @@ "line": 4, "column": 45 }, - "identifierName": "LXL9JK8JTNLQE" + "identifierName": "M50HFXVT2CD2B" }, - "name": "LXL9JK8JTNLQE" + "name": "M50HFXVT2CD2B" } } ], @@ -521,9 +521,9 @@ "line": 6, "column": 25 }, - "identifierName": "LXL9JK8JDZPL7" + "identifierName": "M50HFXVT6MY40" }, - "name": "LXL9JK8JDZPL7" + "name": "M50HFXVT6MY40" } } ], @@ -662,9 +662,9 @@ "line": 7, "column": 42 }, - "identifierName": "LXL9JK8JDZPL7" + "identifierName": "M50HFXVT6MY40" }, - "name": "LXL9JK8JDZPL7" + "name": "M50HFXVT6MY40" } } ], @@ -672,9 +672,9 @@ "trailingComments": [ { "type": "CommentBlock", - "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", + "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a occurrenceID with the occurrence identifier.\n * - Should have a basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", "start": 325, - "end": 1088, + "end": 1080, "loc": { "start": { "line": 9, @@ -690,8 +690,8 @@ }, { "type": "Identifier", - "start": 1089, - "end": 8836, + "start": 1081, + "end": 8742, "loc": { "start": { "line": 24, @@ -704,8 +704,8 @@ }, "id": { "type": "Identifier", - "start": 1095, - "end": 1110, + "start": 1087, + "end": 1102, "loc": { "start": { "line": 24, @@ -723,8 +723,8 @@ "superClass": null, "body": { "type": "ClassBody", - "start": 1111, - "end": 8836, + "start": 1103, + "end": 8742, "loc": { "start": { "line": 24, @@ -738,8 +738,8 @@ "body": [ { "type": "ClassMethod", - "start": 1170, - "end": 1238, + "start": 1162, + "end": 1230, "loc": { "start": { "line": 26, @@ -754,8 +754,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1181, - "end": 1194, + "start": 1173, + "end": 1186, "loc": { "start": { "line": 26, @@ -777,8 +777,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 1197, - "end": 1238, + "start": 1189, + "end": 1230, "loc": { "start": { "line": 26, @@ -792,8 +792,8 @@ "body": [ { "type": "ReturnStatement", - "start": 1203, - "end": 1234, + "start": 1195, + "end": 1226, "loc": { "start": { "line": 27, @@ -806,8 +806,8 @@ }, "argument": { "type": "MemberExpression", - "start": 1210, - "end": 1233, + "start": 1202, + "end": 1225, "loc": { "start": { "line": 27, @@ -820,8 +820,8 @@ }, "object": { "type": "Identifier", - "start": 1210, - "end": 1218, + "start": 1202, + "end": 1210, "loc": { "start": { "line": 27, @@ -837,8 +837,8 @@ }, "property": { "type": "Identifier", - "start": 1219, - "end": 1233, + "start": 1211, + "end": 1225, "loc": { "start": { "line": 27, @@ -863,8 +863,8 @@ { "type": "CommentBlock", "value": "* The '@type' of specimens in JSON-LD document. ", - "start": 1115, - "end": 1167, + "start": 1107, + "end": 1159, "loc": { "start": { "line": 25, @@ -881,8 +881,8 @@ { "type": "CommentBlock", "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "start": 1234, + "end": 1279, "loc": { "start": { "line": 30, @@ -898,8 +898,8 @@ }, { "type": "ClassMethod", - "start": 1290, - "end": 1347, + "start": 1282, + "end": 1339, "loc": { "start": { "line": 31, @@ -914,8 +914,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1290, - "end": 1301, + "start": 1282, + "end": 1293, "loc": { "start": { "line": 31, @@ -938,8 +938,8 @@ "params": [ { "type": "Identifier", - "start": 1302, - "end": 1310, + "start": 1294, + "end": 1302, "loc": { "start": { "line": 31, @@ -956,8 +956,8 @@ ], "body": { "type": "BlockStatement", - "start": 1312, - "end": 1347, + "start": 1304, + "end": 1339, "loc": { "start": { "line": 31, @@ -971,8 +971,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 1318, - "end": 1343, + "start": 1310, + "end": 1335, "loc": { "start": { "line": 32, @@ -985,8 +985,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 1318, - "end": 1342, + "start": 1310, + "end": 1334, "loc": { "start": { "line": 32, @@ -1000,8 +1000,8 @@ "operator": "=", "left": { "type": "MemberExpression", - "start": 1318, - "end": 1331, + "start": 1310, + "end": 1323, "loc": { "start": { "line": 32, @@ -1014,8 +1014,8 @@ }, "object": { "type": "ThisExpression", - "start": 1318, - "end": 1322, + "start": 1310, + "end": 1314, "loc": { "start": { "line": 32, @@ -1029,8 +1029,8 @@ }, "property": { "type": "Identifier", - "start": 1323, - "end": 1331, + "start": 1315, + "end": 1323, "loc": { "start": { "line": 32, @@ -1048,8 +1048,8 @@ }, "right": { "type": "Identifier", - "start": 1334, - "end": 1342, + "start": 1326, + "end": 1334, "loc": { "start": { "line": 32, @@ -1073,8 +1073,8 @@ { "type": "CommentBlock", "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "start": 1234, + "end": 1279, "loc": { "start": { "line": 30, @@ -1091,8 +1091,8 @@ { "type": "CommentBlock", "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", - "start": 1351, - "end": 1449, + "start": 1343, + "end": 1441, "loc": { "start": { "line": 35, @@ -1108,8 +1108,8 @@ }, { "type": "ClassMethod", - "start": 1452, - "end": 1982, + "start": 1444, + "end": 1968, "loc": { "start": { "line": 39, @@ -1124,8 +1124,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1459, - "end": 1468, + "start": 1451, + "end": 1460, "loc": { "start": { "line": 39, @@ -1147,8 +1147,8 @@ "params": [ { "type": "Identifier", - "start": 1469, - "end": 1477, + "start": 1461, + "end": 1469, "loc": { "start": { "line": 39, @@ -1165,8 +1165,8 @@ ], "body": { "type": "BlockStatement", - "start": 1479, - "end": 1982, + "start": 1471, + "end": 1968, "loc": { "start": { "line": 39, @@ -1180,8 +1180,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 1485, - "end": 1531, + "start": 1477, + "end": 1523, "loc": { "start": { "line": 40, @@ -1195,8 +1195,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 1491, - "end": 1530, + "start": 1483, + "end": 1522, "loc": { "start": { "line": 40, @@ -1209,8 +1209,8 @@ }, "id": { "type": "Identifier", - "start": 1491, - "end": 1498, + "start": 1483, + "end": 1490, "loc": { "start": { "line": 40, @@ -1226,8 +1226,8 @@ }, "init": { "type": "NewExpression", - "start": 1501, - "end": 1530, + "start": 1493, + "end": 1522, "loc": { "start": { "line": 40, @@ -1240,8 +1240,8 @@ }, "callee": { "type": "Identifier", - "start": 1505, - "end": 1520, + "start": 1497, + "end": 1512, "loc": { "start": { "line": 40, @@ -1258,8 +1258,8 @@ "arguments": [ { "type": "Identifier", - "start": 1521, - "end": 1529, + "start": 1513, + "end": 1521, "loc": { "start": { "line": 40, @@ -1281,8 +1281,8 @@ }, { "type": "VariableDeclaration", - "start": 1536, - "end": 1875, + "start": 1528, + "end": 1861, "loc": { "start": { "line": 41, @@ -1296,8 +1296,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 1542, - "end": 1874, + "start": 1534, + "end": 1860, "loc": { "start": { "line": 41, @@ -1310,8 +1310,8 @@ }, "id": { "type": "Identifier", - "start": 1542, - "end": 1560, + "start": 1534, + "end": 1552, "loc": { "start": { "line": 41, @@ -1327,8 +1327,8 @@ }, "init": { "type": "ObjectExpression", - "start": 1563, - "end": 1874, + "start": 1555, + "end": 1860, "loc": { "start": { "line": 41, @@ -1342,8 +1342,8 @@ "properties": [ { "type": "ObjectProperty", - "start": 1571, - "end": 1609, + "start": 1563, + "end": 1601, "loc": { "start": { "line": 42, @@ -1359,8 +1359,8 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 1571, - "end": 1578, + "start": 1563, + "end": 1570, "loc": { "start": { "line": 42, @@ -1379,8 +1379,8 @@ }, "value": { "type": "MemberExpression", - "start": 1580, - "end": 1609, + "start": 1572, + "end": 1601, "loc": { "start": { "line": 42, @@ -1393,8 +1393,8 @@ }, "object": { "type": "Identifier", - "start": 1580, - "end": 1595, + "start": 1572, + "end": 1587, "loc": { "start": { "line": 42, @@ -1410,8 +1410,8 @@ }, "property": { "type": "Identifier", - "start": 1596, - "end": 1609, + "start": 1588, + "end": 1601, "loc": { "start": { "line": 42, @@ -1430,8 +1430,8 @@ }, { "type": "ObjectProperty", - "start": 1617, - "end": 1637, + "start": 1609, + "end": 1629, "loc": { "start": { "line": 43, @@ -1447,8 +1447,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1617, - "end": 1622, + "start": 1609, + "end": 1614, "loc": { "start": { "line": 43, @@ -1464,8 +1464,8 @@ }, "value": { "type": "MemberExpression", - "start": 1624, - "end": 1637, + "start": 1616, + "end": 1629, "loc": { "start": { "line": 43, @@ -1478,8 +1478,8 @@ }, "object": { "type": "Identifier", - "start": 1624, - "end": 1631, + "start": 1616, + "end": 1623, "loc": { "start": { "line": 43, @@ -1495,8 +1495,8 @@ }, "property": { "type": "Identifier", - "start": 1632, - "end": 1637, + "start": 1624, + "end": 1629, "loc": { "start": { "line": 43, @@ -1515,8 +1515,8 @@ }, { "type": "ObjectProperty", - "start": 1645, - "end": 1687, + "start": 1637, + "end": 1673, "loc": { "start": { "line": 44, @@ -1524,16 +1524,16 @@ }, "end": { "line": 44, - "column": 48 + "column": 42 } }, "method": false, "shorthand": false, "computed": false, "key": { - "type": "StringLiteral", - "start": 1645, - "end": 1664, + "type": "Identifier", + "start": 1637, + "end": 1650, "loc": { "start": { "line": 44, @@ -1541,41 +1541,38 @@ }, "end": { "line": 44, - "column": 25 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 19 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, "value": { "type": "MemberExpression", - "start": 1666, - "end": 1687, + "start": 1652, + "end": 1673, "loc": { "start": { "line": 44, - "column": 27 + "column": 21 }, "end": { "line": 44, - "column": 48 + "column": 42 } }, "object": { "type": "Identifier", - "start": 1666, - "end": 1673, + "start": 1652, + "end": 1659, "loc": { "start": { "line": 44, - "column": 27 + "column": 21 }, "end": { "line": 44, - "column": 34 + "column": 28 }, "identifierName": "wrapped" }, @@ -1583,16 +1580,16 @@ }, "property": { "type": "Identifier", - "start": 1674, - "end": 1687, + "start": 1660, + "end": 1673, "loc": { "start": { "line": 44, - "column": 35 + "column": 29 }, "end": { "line": 44, - "column": 48 + "column": 42 }, "identifierName": "basisOfRecord" }, @@ -1603,8 +1600,8 @@ }, { "type": "ObjectProperty", - "start": 1695, - "end": 1729, + "start": 1681, + "end": 1715, "loc": { "start": { "line": 45, @@ -1620,8 +1617,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1695, - "end": 1707, + "start": 1681, + "end": 1693, "loc": { "start": { "line": 45, @@ -1637,8 +1634,8 @@ }, "value": { "type": "MemberExpression", - "start": 1709, - "end": 1729, + "start": 1695, + "end": 1715, "loc": { "start": { "line": 45, @@ -1651,8 +1648,8 @@ }, "object": { "type": "Identifier", - "start": 1709, - "end": 1716, + "start": 1695, + "end": 1702, "loc": { "start": { "line": 45, @@ -1668,8 +1665,8 @@ }, "property": { "type": "Identifier", - "start": 1717, - "end": 1729, + "start": 1703, + "end": 1715, "loc": { "start": { "line": 45, @@ -1688,8 +1685,8 @@ }, { "type": "ObjectProperty", - "start": 1737, - "end": 1773, + "start": 1723, + "end": 1759, "loc": { "start": { "line": 46, @@ -1705,8 +1702,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1737, - "end": 1750, + "start": 1723, + "end": 1736, "loc": { "start": { "line": 46, @@ -1722,8 +1719,8 @@ }, "value": { "type": "MemberExpression", - "start": 1752, - "end": 1773, + "start": 1738, + "end": 1759, "loc": { "start": { "line": 46, @@ -1736,8 +1733,8 @@ }, "object": { "type": "Identifier", - "start": 1752, - "end": 1759, + "start": 1738, + "end": 1745, "loc": { "start": { "line": 46, @@ -1753,8 +1750,8 @@ }, "property": { "type": "Identifier", - "start": 1760, - "end": 1773, + "start": 1746, + "end": 1759, "loc": { "start": { "line": 46, @@ -1773,8 +1770,8 @@ }, { "type": "ObjectProperty", - "start": 1781, - "end": 1821, + "start": 1767, + "end": 1807, "loc": { "start": { "line": 47, @@ -1790,8 +1787,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1781, - "end": 1796, + "start": 1767, + "end": 1782, "loc": { "start": { "line": 47, @@ -1807,8 +1804,8 @@ }, "value": { "type": "MemberExpression", - "start": 1798, - "end": 1821, + "start": 1784, + "end": 1807, "loc": { "start": { "line": 47, @@ -1821,8 +1818,8 @@ }, "object": { "type": "Identifier", - "start": 1798, - "end": 1805, + "start": 1784, + "end": 1791, "loc": { "start": { "line": 47, @@ -1838,8 +1835,8 @@ }, "property": { "type": "Identifier", - "start": 1806, - "end": 1821, + "start": 1792, + "end": 1807, "loc": { "start": { "line": 47, @@ -1858,8 +1855,8 @@ }, { "type": "ObjectProperty", - "start": 1829, - "end": 1867, + "start": 1815, + "end": 1853, "loc": { "start": { "line": 48, @@ -1875,8 +1872,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1829, - "end": 1843, + "start": 1815, + "end": 1829, "loc": { "start": { "line": 48, @@ -1892,8 +1889,8 @@ }, "value": { "type": "MemberExpression", - "start": 1845, - "end": 1867, + "start": 1831, + "end": 1853, "loc": { "start": { "line": 48, @@ -1906,8 +1903,8 @@ }, "object": { "type": "Identifier", - "start": 1845, - "end": 1852, + "start": 1831, + "end": 1838, "loc": { "start": { "line": 48, @@ -1923,8 +1920,8 @@ }, "property": { "type": "Identifier", - "start": 1853, - "end": 1867, + "start": 1839, + "end": 1853, "loc": { "start": { "line": 48, @@ -1949,8 +1946,8 @@ }, { "type": "IfStatement", - "start": 1880, - "end": 1947, + "start": 1866, + "end": 1933, "loc": { "start": { "line": 50, @@ -1963,8 +1960,8 @@ }, "test": { "type": "BinaryExpression", - "start": 1884, - "end": 1901, + "start": 1870, + "end": 1887, "loc": { "start": { "line": 50, @@ -1977,8 +1974,8 @@ }, "left": { "type": "StringLiteral", - "start": 1884, - "end": 1889, + "start": 1870, + "end": 1875, "loc": { "start": { "line": 50, @@ -1998,8 +1995,8 @@ "operator": "in", "right": { "type": "Identifier", - "start": 1893, - "end": 1901, + "start": 1879, + "end": 1887, "loc": { "start": { "line": 50, @@ -2016,8 +2013,8 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 1903, - "end": 1947, + "start": 1889, + "end": 1933, "loc": { "start": { "line": 50, @@ -2030,8 +2027,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 1903, - "end": 1946, + "start": 1889, + "end": 1932, "loc": { "start": { "line": 50, @@ -2045,8 +2042,8 @@ "operator": "=", "left": { "type": "MemberExpression", - "start": 1903, - "end": 1928, + "start": 1889, + "end": 1914, "loc": { "start": { "line": 50, @@ -2059,8 +2056,8 @@ }, "object": { "type": "Identifier", - "start": 1903, - "end": 1921, + "start": 1889, + "end": 1907, "loc": { "start": { "line": 50, @@ -2076,8 +2073,8 @@ }, "property": { "type": "StringLiteral", - "start": 1922, - "end": 1927, + "start": 1908, + "end": 1913, "loc": { "start": { "line": 50, @@ -2098,8 +2095,8 @@ }, "right": { "type": "MemberExpression", - "start": 1931, - "end": 1946, + "start": 1917, + "end": 1932, "loc": { "start": { "line": 50, @@ -2112,8 +2109,8 @@ }, "object": { "type": "Identifier", - "start": 1931, - "end": 1939, + "start": 1917, + "end": 1925, "loc": { "start": { "line": 50, @@ -2129,8 +2126,8 @@ }, "property": { "type": "StringLiteral", - "start": 1940, - "end": 1945, + "start": 1926, + "end": 1931, "loc": { "start": { "line": 50, @@ -2155,8 +2152,8 @@ }, { "type": "ReturnStatement", - "start": 1952, - "end": 1978, + "start": 1938, + "end": 1964, "loc": { "start": { "line": 51, @@ -2169,8 +2166,8 @@ }, "argument": { "type": "Identifier", - "start": 1959, - "end": 1977, + "start": 1945, + "end": 1963, "loc": { "start": { "line": 51, @@ -2193,8 +2190,8 @@ { "type": "CommentBlock", "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", - "start": 1351, - "end": 1449, + "start": 1343, + "end": 1441, "loc": { "start": { "line": 35, @@ -2211,8 +2208,8 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1986, - "end": 2267, + "start": 1972, + "end": 2253, "loc": { "start": { "line": 54, @@ -2228,8 +2225,8 @@ }, { "type": "ClassMethod", - "start": 2270, - "end": 4105, + "start": 2256, + "end": 4073, "loc": { "start": { "line": 60, @@ -2244,8 +2241,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 2277, - "end": 2293, + "start": 2263, + "end": 2279, "loc": { "start": { "line": 60, @@ -2267,8 +2264,8 @@ "params": [ { "type": "Identifier", - "start": 2294, - "end": 2306, + "start": 2280, + "end": 2292, "loc": { "start": { "line": 60, @@ -2284,8 +2281,8 @@ }, { "type": "AssignmentPattern", - "start": 2308, - "end": 2343, + "start": 2294, + "end": 2329, "loc": { "start": { "line": 60, @@ -2298,8 +2295,8 @@ }, "left": { "type": "Identifier", - "start": 2308, - "end": 2321, + "start": 2294, + "end": 2307, "loc": { "start": { "line": 60, @@ -2315,8 +2312,8 @@ }, "right": { "type": "StringLiteral", - "start": 2324, - "end": 2343, + "start": 2310, + "end": 2329, "loc": { "start": { "line": 60, @@ -2337,8 +2334,8 @@ ], "body": { "type": "BlockStatement", - "start": 2345, - "end": 4105, + "start": 2331, + "end": 4073, "loc": { "start": { "line": 60, @@ -2352,8 +2349,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 2417, - "end": 2444, + "start": 2403, + "end": 2430, "loc": { "start": { "line": 62, @@ -2367,8 +2364,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 2421, - "end": 2443, + "start": 2407, + "end": 2429, "loc": { "start": { "line": 62, @@ -2381,8 +2378,8 @@ }, "id": { "type": "Identifier", - "start": 2421, - "end": 2428, + "start": 2407, + "end": 2414, "loc": { "start": { "line": 62, @@ -2399,8 +2396,8 @@ }, "init": { "type": "Identifier", - "start": 2431, - "end": 2443, + "start": 2417, + "end": 2429, "loc": { "start": { "line": 62, @@ -2422,8 +2419,8 @@ { "type": "CommentLine", "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 2351, - "end": 2412, + "start": 2337, + "end": 2398, "loc": { "start": { "line": 61, @@ -2439,8 +2436,8 @@ }, { "type": "IfStatement", - "start": 2449, - "end": 2518, + "start": 2435, + "end": 2507, "loc": { "start": { "line": 63, @@ -2448,13 +2445,13 @@ }, "end": { "line": 63, - "column": 73 + "column": 76 } }, "test": { "type": "CallExpression", - "start": 2453, - "end": 2487, + "start": 2439, + "end": 2473, "loc": { "start": { "line": 63, @@ -2467,8 +2464,8 @@ }, "callee": { "type": "MemberExpression", - "start": 2453, - "end": 2471, + "start": 2439, + "end": 2457, "loc": { "start": { "line": 63, @@ -2481,8 +2478,8 @@ }, "object": { "type": "Identifier", - "start": 2453, - "end": 2460, + "start": 2439, + "end": 2446, "loc": { "start": { "line": 63, @@ -2498,8 +2495,8 @@ }, "property": { "type": "Identifier", - "start": 2461, - "end": 2471, + "start": 2447, + "end": 2457, "loc": { "start": { "line": 63, @@ -2518,8 +2515,8 @@ "arguments": [ { "type": "StringLiteral", - "start": 2472, - "end": 2486, + "start": 2458, + "end": 2472, "loc": { "start": { "line": 63, @@ -2540,8 +2537,8 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 2489, - "end": 2518, + "start": 2475, + "end": 2507, "loc": { "start": { "line": 63, @@ -2549,13 +2546,13 @@ }, "end": { "line": 63, - "column": 73 + "column": 76 } }, "expression": { "type": "AssignmentExpression", - "start": 2489, - "end": 2517, + "start": 2475, + "end": 2506, "loc": { "start": { "line": 63, @@ -2563,14 +2560,14 @@ }, "end": { "line": 63, - "column": 72 + "column": 75 } }, "operator": "=", "left": { "type": "Identifier", - "start": 2489, - "end": 2496, + "start": 2475, + "end": 2482, "loc": { "start": { "line": 63, @@ -2586,8 +2583,8 @@ }, "right": { "type": "CallExpression", - "start": 2499, - "end": 2517, + "start": 2485, + "end": 2506, "loc": { "start": { "line": 63, @@ -2595,13 +2592,13 @@ }, "end": { "line": 63, - "column": 72 + "column": 75 } }, "callee": { "type": "MemberExpression", - "start": 2499, - "end": 2513, + "start": 2485, + "end": 2502, "loc": { "start": { "line": 63, @@ -2609,13 +2606,13 @@ }, "end": { "line": 63, - "column": 68 + "column": 71 } }, "object": { "type": "Identifier", - "start": 2499, - "end": 2506, + "start": 2485, + "end": 2492, "loc": { "start": { "line": 63, @@ -2631,8 +2628,8 @@ }, "property": { "type": "Identifier", - "start": 2507, - "end": 2513, + "start": 2493, + "end": 2502, "loc": { "start": { "line": 63, @@ -2640,27 +2637,27 @@ }, "end": { "line": 63, - "column": 68 + "column": 71 }, - "identifierName": "substr" + "identifierName": "substring" }, - "name": "substr" + "name": "substring" }, "computed": false }, "arguments": [ { "type": "NumericLiteral", - "start": 2514, - "end": 2516, + "start": 2503, + "end": 2505, "loc": { "start": { "line": 63, - "column": 69 + "column": 72 }, "end": { "line": 63, - "column": 71 + "column": 74 } }, "extra": { @@ -2679,8 +2676,8 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 2524, - "end": 2548, + "start": 2513, + "end": 2537, "loc": { "start": { "line": 65, @@ -2696,8 +2693,8 @@ }, { "type": "VariableDeclaration", - "start": 2553, - "end": 2695, + "start": 2542, + "end": 2663, "loc": { "start": { "line": 66, @@ -2711,8 +2708,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 2559, - "end": 2694, + "start": 2548, + "end": 2662, "loc": { "start": { "line": 66, @@ -2725,8 +2722,8 @@ }, "id": { "type": "Identifier", - "start": 2559, - "end": 2567, + "start": 2548, + "end": 2556, "loc": { "start": { "line": 66, @@ -2743,8 +2740,8 @@ }, "init": { "type": "ObjectExpression", - "start": 2570, - "end": 2694, + "start": 2559, + "end": 2662, "loc": { "start": { "line": 66, @@ -2758,8 +2755,8 @@ "properties": [ { "type": "ObjectProperty", - "start": 2578, - "end": 2616, + "start": 2567, + "end": 2605, "loc": { "start": { "line": 67, @@ -2775,8 +2772,8 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 2578, - "end": 2585, + "start": 2567, + "end": 2574, "loc": { "start": { "line": 67, @@ -2795,8 +2792,8 @@ }, "value": { "type": "MemberExpression", - "start": 2587, - "end": 2616, + "start": 2576, + "end": 2605, "loc": { "start": { "line": 67, @@ -2809,8 +2806,8 @@ }, "object": { "type": "Identifier", - "start": 2587, - "end": 2602, + "start": 2576, + "end": 2591, "loc": { "start": { "line": 67, @@ -2826,8 +2823,8 @@ }, "property": { "type": "Identifier", - "start": 2603, - "end": 2616, + "start": 2592, + "end": 2605, "loc": { "start": { "line": 67, @@ -2846,8 +2843,8 @@ }, { "type": "ObjectProperty", - "start": 2624, - "end": 2658, + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, @@ -2855,16 +2852,16 @@ }, "end": { "line": 68, - "column": 40 + "column": 19 } }, "method": false, - "shorthand": false, + "shorthand": true, "computed": false, "key": { - "type": "StringLiteral", - "start": 2624, - "end": 2643, + "type": "Identifier", + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, @@ -2872,37 +2869,37 @@ }, "end": { "line": 68, - "column": 25 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 19 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, "value": { "type": "Identifier", - "start": 2645, - "end": 2658, + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, - "column": 27 + "column": 6 }, "end": { "line": 68, - "column": 40 + "column": 19 }, "identifierName": "basisOfRecord" }, "name": "basisOfRecord" + }, + "extra": { + "shorthand": true } }, { "type": "ObjectProperty", - "start": 2666, - "end": 2687, + "start": 2634, + "end": 2655, "loc": { "start": { "line": 69, @@ -2918,8 +2915,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 2666, - "end": 2678, + "start": 2634, + "end": 2646, "loc": { "start": { "line": 69, @@ -2935,8 +2932,8 @@ }, "value": { "type": "Identifier", - "start": 2680, - "end": 2687, + "start": 2648, + "end": 2655, "loc": { "start": { "line": 69, @@ -2961,8 +2958,8 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 2524, - "end": 2548, + "start": 2513, + "end": 2537, "loc": { "start": { "line": 65, @@ -2979,8 +2976,8 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2701, - "end": 2774, + "start": 2669, + "end": 2742, "loc": { "start": { "line": 72, @@ -2995,8 +2992,8 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2779, - "end": 2834, + "start": 2747, + "end": 2802, "loc": { "start": { "line": 73, @@ -3012,8 +3009,8 @@ }, { "type": "VariableDeclaration", - "start": 2839, - "end": 2971, + "start": 2807, + "end": 2939, "loc": { "start": { "line": 74, @@ -3027,8 +3024,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 2845, - "end": 2970, + "start": 2813, + "end": 2938, "loc": { "start": { "line": 74, @@ -3041,8 +3038,8 @@ }, "id": { "type": "Identifier", - "start": 2845, - "end": 2861, + "start": 2813, + "end": 2829, "loc": { "start": { "line": 74, @@ -3059,8 +3056,8 @@ }, "init": { "type": "ArrayExpression", - "start": 2864, - "end": 2970, + "start": 2832, + "end": 2938, "loc": { "start": { "line": 74, @@ -3074,8 +3071,8 @@ "elements": [ { "type": "StringLiteral", - "start": 2872, - "end": 2881, + "start": 2840, + "end": 2849, "loc": { "start": { "line": 75, @@ -3094,8 +3091,8 @@ }, { "type": "StringLiteral", - "start": 2889, - "end": 2899, + "start": 2857, + "end": 2867, "loc": { "start": { "line": 76, @@ -3114,8 +3111,8 @@ }, { "type": "StringLiteral", - "start": 2907, - "end": 2915, + "start": 2875, + "end": 2883, "loc": { "start": { "line": 77, @@ -3134,8 +3131,8 @@ }, { "type": "StringLiteral", - "start": 2923, - "end": 2932, + "start": 2891, + "end": 2900, "loc": { "start": { "line": 78, @@ -3154,8 +3151,8 @@ }, { "type": "StringLiteral", - "start": 2940, - "end": 2949, + "start": 2908, + "end": 2917, "loc": { "start": { "line": 79, @@ -3174,8 +3171,8 @@ }, { "type": "StringLiteral", - "start": 2957, - "end": 2963, + "start": 2925, + "end": 2931, "loc": { "start": { "line": 80, @@ -3202,8 +3199,8 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2701, - "end": 2774, + "start": 2669, + "end": 2742, "loc": { "start": { "line": 72, @@ -3218,8 +3215,8 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2779, - "end": 2834, + "start": 2747, + "end": 2802, "loc": { "start": { "line": 73, @@ -3235,8 +3232,8 @@ }, { "type": "IfStatement", - "start": 2976, - "end": 3098, + "start": 2944, + "end": 3066, "loc": { "start": { "line": 82, @@ -3249,8 +3246,8 @@ }, "test": { "type": "BinaryExpression", - "start": 2980, - "end": 3066, + "start": 2948, + "end": 3034, "loc": { "start": { "line": 82, @@ -3263,8 +3260,8 @@ }, "left": { "type": "MemberExpression", - "start": 2980, - "end": 3062, + "start": 2948, + "end": 3030, "loc": { "start": { "line": 82, @@ -3277,8 +3274,8 @@ }, "object": { "type": "CallExpression", - "start": 2980, - "end": 3055, + "start": 2948, + "end": 3023, "loc": { "start": { "line": 82, @@ -3291,8 +3288,8 @@ }, "callee": { "type": "MemberExpression", - "start": 2980, - "end": 3003, + "start": 2948, + "end": 2971, "loc": { "start": { "line": 82, @@ -3305,8 +3302,8 @@ }, "object": { "type": "Identifier", - "start": 2980, - "end": 2996, + "start": 2948, + "end": 2964, "loc": { "start": { "line": 82, @@ -3322,8 +3319,8 @@ }, "property": { "type": "Identifier", - "start": 2997, - "end": 3003, + "start": 2965, + "end": 2971, "loc": { "start": { "line": 82, @@ -3342,8 +3339,8 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 3004, - "end": 3054, + "start": 2972, + "end": 3022, "loc": { "start": { "line": 82, @@ -3361,8 +3358,8 @@ "params": [ { "type": "Identifier", - "start": 3004, - "end": 3010, + "start": 2972, + "end": 2978, "loc": { "start": { "line": 82, @@ -3379,8 +3376,8 @@ ], "body": { "type": "CallExpression", - "start": 3014, - "end": 3054, + "start": 2982, + "end": 3022, "loc": { "start": { "line": 82, @@ -3393,8 +3390,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3014, - "end": 3046, + "start": 2982, + "end": 3014, "loc": { "start": { "line": 82, @@ -3407,8 +3404,8 @@ }, "object": { "type": "CallExpression", - "start": 3014, - "end": 3035, + "start": 2982, + "end": 3003, "loc": { "start": { "line": 82, @@ -3421,8 +3418,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3014, - "end": 3033, + "start": 2982, + "end": 3001, "loc": { "start": { "line": 82, @@ -3435,8 +3432,8 @@ }, "object": { "type": "Identifier", - "start": 3014, - "end": 3021, + "start": 2982, + "end": 2989, "loc": { "start": { "line": 82, @@ -3452,8 +3449,8 @@ }, "property": { "type": "Identifier", - "start": 3022, - "end": 3033, + "start": 2990, + "end": 3001, "loc": { "start": { "line": 82, @@ -3473,8 +3470,8 @@ }, "property": { "type": "Identifier", - "start": 3036, - "end": 3046, + "start": 3004, + "end": 3014, "loc": { "start": { "line": 82, @@ -3493,8 +3490,8 @@ "arguments": [ { "type": "Identifier", - "start": 3047, - "end": 3053, + "start": 3015, + "end": 3021, "loc": { "start": { "line": 82, @@ -3515,8 +3512,8 @@ }, "property": { "type": "Identifier", - "start": 3056, - "end": 3062, + "start": 3024, + "end": 3030, "loc": { "start": { "line": 82, @@ -3535,8 +3532,8 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 3065, - "end": 3066, + "start": 3033, + "end": 3034, "loc": { "start": { "line": 82, @@ -3556,8 +3553,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3068, - "end": 3098, + "start": 3036, + "end": 3066, "loc": { "start": { "line": 82, @@ -3571,8 +3568,8 @@ "body": [ { "type": "ReturnStatement", - "start": 3076, - "end": 3092, + "start": 3044, + "end": 3060, "loc": { "start": { "line": 83, @@ -3585,8 +3582,8 @@ }, "argument": { "type": "Identifier", - "start": 3083, - "end": 3091, + "start": 3051, + "end": 3059, "loc": { "start": { "line": 83, @@ -3610,8 +3607,8 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 3104, - "end": 3173, + "start": 3072, + "end": 3141, "loc": { "start": { "line": 86, @@ -3627,8 +3624,8 @@ }, { "type": "IfStatement", - "start": 3178, - "end": 3338, + "start": 3146, + "end": 3306, "loc": { "start": { "line": 87, @@ -3641,8 +3638,8 @@ }, "test": { "type": "CallExpression", - "start": 3182, - "end": 3248, + "start": 3150, + "end": 3216, "loc": { "start": { "line": 87, @@ -3655,8 +3652,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3182, - "end": 3202, + "start": 3150, + "end": 3170, "loc": { "start": { "line": 87, @@ -3669,8 +3666,8 @@ }, "object": { "type": "Identifier", - "start": 3182, - "end": 3198, + "start": 3150, + "end": 3166, "loc": { "start": { "line": 87, @@ -3687,8 +3684,8 @@ }, "property": { "type": "Identifier", - "start": 3199, - "end": 3202, + "start": 3167, + "end": 3170, "loc": { "start": { "line": 87, @@ -3708,8 +3705,8 @@ "arguments": [ { "type": "StringLiteral", - "start": 3203, - "end": 3238, + "start": 3171, + "end": 3206, "loc": { "start": { "line": 87, @@ -3728,8 +3725,8 @@ }, { "type": "Identifier", - "start": 3240, - "end": 3247, + "start": 3208, + "end": 3215, "loc": { "start": { "line": 87, @@ -3748,8 +3745,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3250, - "end": 3338, + "start": 3218, + "end": 3306, "loc": { "start": { "line": 87, @@ -3763,8 +3760,8 @@ "body": [ { "type": "ReturnStatement", - "start": 3258, - "end": 3332, + "start": 3226, + "end": 3300, "loc": { "start": { "line": 88, @@ -3777,8 +3774,8 @@ }, "argument": { "type": "CallExpression", - "start": 3265, - "end": 3331, + "start": 3233, + "end": 3299, "loc": { "start": { "line": 88, @@ -3791,8 +3788,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3265, - "end": 3285, + "start": 3233, + "end": 3253, "loc": { "start": { "line": 88, @@ -3805,8 +3802,8 @@ }, "object": { "type": "Identifier", - "start": 3265, - "end": 3281, + "start": 3233, + "end": 3249, "loc": { "start": { "line": 88, @@ -3822,8 +3819,8 @@ }, "property": { "type": "Identifier", - "start": 3282, - "end": 3285, + "start": 3250, + "end": 3253, "loc": { "start": { "line": 88, @@ -3842,8 +3839,8 @@ "arguments": [ { "type": "StringLiteral", - "start": 3286, - "end": 3321, + "start": 3254, + "end": 3289, "loc": { "start": { "line": 88, @@ -3862,8 +3859,8 @@ }, { "type": "Identifier", - "start": 3323, - "end": 3330, + "start": 3291, + "end": 3298, "loc": { "start": { "line": 88, @@ -3889,8 +3886,8 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 3104, - "end": 3173, + "start": 3072, + "end": 3141, "loc": { "start": { "line": 86, @@ -3907,8 +3904,8 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 3344, - "end": 3429, + "start": 3312, + "end": 3397, "loc": { "start": { "line": 91, @@ -3924,8 +3921,8 @@ }, { "type": "VariableDeclaration", - "start": 3434, - "end": 3467, + "start": 3402, + "end": 3435, "loc": { "start": { "line": 92, @@ -3939,8 +3936,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 3440, - "end": 3466, + "start": 3408, + "end": 3434, "loc": { "start": { "line": 92, @@ -3953,8 +3950,8 @@ }, "id": { "type": "Identifier", - "start": 3440, - "end": 3445, + "start": 3408, + "end": 3413, "loc": { "start": { "line": 92, @@ -3971,8 +3968,8 @@ }, "init": { "type": "CallExpression", - "start": 3448, - "end": 3466, + "start": 3416, + "end": 3434, "loc": { "start": { "line": 92, @@ -3985,8 +3982,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3448, - "end": 3461, + "start": 3416, + "end": 3429, "loc": { "start": { "line": 92, @@ -3999,8 +3996,8 @@ }, "object": { "type": "Identifier", - "start": 3448, - "end": 3455, + "start": 3416, + "end": 3423, "loc": { "start": { "line": 92, @@ -4016,8 +4013,8 @@ }, "property": { "type": "Identifier", - "start": 3456, - "end": 3461, + "start": 3424, + "end": 3429, "loc": { "start": { "line": 92, @@ -4036,8 +4033,8 @@ "arguments": [ { "type": "RegExpLiteral", - "start": 3462, - "end": 3465, + "start": 3430, + "end": 3433, "loc": { "start": { "line": 92, @@ -4064,8 +4061,8 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 3344, - "end": 3429, + "start": 3312, + "end": 3397, "loc": { "start": { "line": 91, @@ -4081,8 +4078,8 @@ }, { "type": "IfStatement", - "start": 3472, - "end": 3997, + "start": 3440, + "end": 3965, "loc": { "start": { "line": 93, @@ -4095,8 +4092,8 @@ }, "test": { "type": "BinaryExpression", - "start": 3476, - "end": 3494, + "start": 3444, + "end": 3462, "loc": { "start": { "line": 93, @@ -4109,8 +4106,8 @@ }, "left": { "type": "MemberExpression", - "start": 3476, - "end": 3488, + "start": 3444, + "end": 3456, "loc": { "start": { "line": 93, @@ -4123,8 +4120,8 @@ }, "object": { "type": "Identifier", - "start": 3476, - "end": 3481, + "start": 3444, + "end": 3449, "loc": { "start": { "line": 93, @@ -4140,8 +4137,8 @@ }, "property": { "type": "Identifier", - "start": 3482, - "end": 3488, + "start": 3450, + "end": 3456, "loc": { "start": { "line": 93, @@ -4160,8 +4157,8 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 3493, - "end": 3494, + "start": 3461, + "end": 3462, "loc": { "start": { "line": 93, @@ -4181,8 +4178,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3496, - "end": 3636, + "start": 3464, + "end": 3604, "loc": { "start": { "line": 93, @@ -4196,8 +4193,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 3597, - "end": 3630, + "start": 3565, + "end": 3598, "loc": { "start": { "line": 96, @@ -4210,8 +4207,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 3597, - "end": 3629, + "start": 3565, + "end": 3597, "loc": { "start": { "line": 96, @@ -4225,8 +4222,8 @@ "operator": "=", "left": { "type": "ArrayPattern", - "start": 3597, - "end": 3621, + "start": 3565, + "end": 3589, "loc": { "start": { "line": 96, @@ -4240,8 +4237,8 @@ "elements": [ { "type": "MemberExpression", - "start": 3598, - "end": 3620, + "start": 3566, + "end": 3588, "loc": { "start": { "line": 96, @@ -4254,8 +4251,8 @@ }, "object": { "type": "Identifier", - "start": 3598, - "end": 3606, + "start": 3566, + "end": 3574, "loc": { "start": { "line": 96, @@ -4272,8 +4269,8 @@ }, "property": { "type": "Identifier", - "start": 3607, - "end": 3620, + "start": 3575, + "end": 3588, "loc": { "start": { "line": 96, @@ -4295,8 +4292,8 @@ }, "right": { "type": "Identifier", - "start": 3624, - "end": 3629, + "start": 3592, + "end": 3597, "loc": { "start": { "line": 96, @@ -4316,8 +4313,8 @@ { "type": "CommentLine", "value": " specimen.institutionCode = undefined;", - "start": 3504, - "end": 3544, + "start": 3472, + "end": 3512, "loc": { "start": { "line": 94, @@ -4332,8 +4329,8 @@ { "type": "CommentLine", "value": " specimen.collectionCode = undefined;", - "start": 3551, - "end": 3590, + "start": 3519, + "end": 3558, "loc": { "start": { "line": 95, @@ -4352,8 +4349,8 @@ }, "alternate": { "type": "IfStatement", - "start": 3642, - "end": 3997, + "start": 3610, + "end": 3965, "loc": { "start": { "line": 97, @@ -4366,8 +4363,8 @@ }, "test": { "type": "BinaryExpression", - "start": 3646, - "end": 3664, + "start": 3614, + "end": 3632, "loc": { "start": { "line": 97, @@ -4380,8 +4377,8 @@ }, "left": { "type": "MemberExpression", - "start": 3646, - "end": 3658, + "start": 3614, + "end": 3626, "loc": { "start": { "line": 97, @@ -4394,8 +4391,8 @@ }, "object": { "type": "Identifier", - "start": 3646, - "end": 3651, + "start": 3614, + "end": 3619, "loc": { "start": { "line": 97, @@ -4411,8 +4408,8 @@ }, "property": { "type": "Identifier", - "start": 3652, - "end": 3658, + "start": 3620, + "end": 3626, "loc": { "start": { "line": 97, @@ -4431,8 +4428,8 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 3663, - "end": 3664, + "start": 3631, + "end": 3632, "loc": { "start": { "line": 97, @@ -4452,8 +4449,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3666, - "end": 3739, + "start": 3634, + "end": 3707, "loc": { "start": { "line": 97, @@ -4467,8 +4464,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 3674, - "end": 3733, + "start": 3642, + "end": 3701, "loc": { "start": { "line": 98, @@ -4481,8 +4478,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 3674, - "end": 3732, + "start": 3642, + "end": 3700, "loc": { "start": { "line": 98, @@ -4496,8 +4493,8 @@ "operator": "=", "left": { "type": "ArrayPattern", - "start": 3674, - "end": 3724, + "start": 3642, + "end": 3692, "loc": { "start": { "line": 98, @@ -4511,8 +4508,8 @@ "elements": [ { "type": "MemberExpression", - "start": 3675, - "end": 3699, + "start": 3643, + "end": 3667, "loc": { "start": { "line": 98, @@ -4525,8 +4522,8 @@ }, "object": { "type": "Identifier", - "start": 3675, - "end": 3683, + "start": 3643, + "end": 3651, "loc": { "start": { "line": 98, @@ -4542,8 +4539,8 @@ }, "property": { "type": "Identifier", - "start": 3684, - "end": 3699, + "start": 3652, + "end": 3667, "loc": { "start": { "line": 98, @@ -4561,8 +4558,8 @@ }, { "type": "MemberExpression", - "start": 3701, - "end": 3723, + "start": 3669, + "end": 3691, "loc": { "start": { "line": 98, @@ -4575,8 +4572,8 @@ }, "object": { "type": "Identifier", - "start": 3701, - "end": 3709, + "start": 3669, + "end": 3677, "loc": { "start": { "line": 98, @@ -4592,8 +4589,8 @@ }, "property": { "type": "Identifier", - "start": 3710, - "end": 3723, + "start": 3678, + "end": 3691, "loc": { "start": { "line": 98, @@ -4613,8 +4610,8 @@ }, "right": { "type": "Identifier", - "start": 3727, - "end": 3732, + "start": 3695, + "end": 3700, "loc": { "start": { "line": 98, @@ -4635,8 +4632,8 @@ }, "alternate": { "type": "IfStatement", - "start": 3745, - "end": 3997, + "start": 3713, + "end": 3965, "loc": { "start": { "line": 99, @@ -4649,8 +4646,8 @@ }, "test": { "type": "BinaryExpression", - "start": 3749, - "end": 3766, + "start": 3717, + "end": 3734, "loc": { "start": { "line": 99, @@ -4663,8 +4660,8 @@ }, "left": { "type": "MemberExpression", - "start": 3749, - "end": 3761, + "start": 3717, + "end": 3729, "loc": { "start": { "line": 99, @@ -4677,8 +4674,8 @@ }, "object": { "type": "Identifier", - "start": 3749, - "end": 3754, + "start": 3717, + "end": 3722, "loc": { "start": { "line": 99, @@ -4694,8 +4691,8 @@ }, "property": { "type": "Identifier", - "start": 3755, - "end": 3761, + "start": 3723, + "end": 3729, "loc": { "start": { "line": 99, @@ -4714,8 +4711,8 @@ "operator": ">=", "right": { "type": "NumericLiteral", - "start": 3765, - "end": 3766, + "start": 3733, + "end": 3734, "loc": { "start": { "line": 99, @@ -4735,8 +4732,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3768, - "end": 3997, + "start": 3736, + "end": 3965, "loc": { "start": { "line": 99, @@ -4750,8 +4747,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 3776, - "end": 3802, + "start": 3744, + "end": 3770, "loc": { "start": { "line": 100, @@ -4765,8 +4762,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 3780, - "end": 3801, + "start": 3748, + "end": 3769, "loc": { "start": { "line": 100, @@ -4779,8 +4776,8 @@ }, "id": { "type": "Identifier", - "start": 3780, - "end": 3796, + "start": 3748, + "end": 3764, "loc": { "start": { "line": 100, @@ -4796,8 +4793,8 @@ }, "init": { "type": "ArrayExpression", - "start": 3799, - "end": 3801, + "start": 3767, + "end": 3769, "loc": { "start": { "line": 100, @@ -4817,8 +4814,8 @@ { "type": "CommentLine", "value": " Store all split catalog number values.", - "start": 3803, - "end": 3844, + "start": 3771, + "end": 3812, "loc": { "start": { "line": 100, @@ -4834,8 +4831,8 @@ }, { "type": "ExpressionStatement", - "start": 3851, - "end": 3932, + "start": 3819, + "end": 3900, "loc": { "start": { "line": 101, @@ -4848,8 +4845,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 3851, - "end": 3931, + "start": 3819, + "end": 3899, "loc": { "start": { "line": 101, @@ -4863,8 +4860,8 @@ "operator": "=", "left": { "type": "ArrayPattern", - "start": 3851, - "end": 3923, + "start": 3819, + "end": 3891, "loc": { "start": { "line": 101, @@ -4878,8 +4875,8 @@ "elements": [ { "type": "MemberExpression", - "start": 3852, - "end": 3876, + "start": 3820, + "end": 3844, "loc": { "start": { "line": 101, @@ -4892,8 +4889,8 @@ }, "object": { "type": "Identifier", - "start": 3852, - "end": 3860, + "start": 3820, + "end": 3828, "loc": { "start": { "line": 101, @@ -4910,8 +4907,8 @@ }, "property": { "type": "Identifier", - "start": 3861, - "end": 3876, + "start": 3829, + "end": 3844, "loc": { "start": { "line": 101, @@ -4930,8 +4927,8 @@ }, { "type": "MemberExpression", - "start": 3878, - "end": 3901, + "start": 3846, + "end": 3869, "loc": { "start": { "line": 101, @@ -4944,8 +4941,8 @@ }, "object": { "type": "Identifier", - "start": 3878, - "end": 3886, + "start": 3846, + "end": 3854, "loc": { "start": { "line": 101, @@ -4961,8 +4958,8 @@ }, "property": { "type": "Identifier", - "start": 3887, - "end": 3901, + "start": 3855, + "end": 3869, "loc": { "start": { "line": 101, @@ -4980,8 +4977,8 @@ }, { "type": "RestElement", - "start": 3903, - "end": 3922, + "start": 3871, + "end": 3890, "loc": { "start": { "line": 101, @@ -4994,8 +4991,8 @@ }, "argument": { "type": "Identifier", - "start": 3906, - "end": 3922, + "start": 3874, + "end": 3890, "loc": { "start": { "line": 101, @@ -5015,8 +5012,8 @@ }, "right": { "type": "Identifier", - "start": 3926, - "end": 3931, + "start": 3894, + "end": 3899, "loc": { "start": { "line": 101, @@ -5036,8 +5033,8 @@ { "type": "CommentLine", "value": " Store all split catalog number values.", - "start": 3803, - "end": 3844, + "start": 3771, + "end": 3812, "loc": { "start": { "line": 100, @@ -5053,8 +5050,8 @@ }, { "type": "ExpressionStatement", - "start": 3939, - "end": 3991, + "start": 3907, + "end": 3959, "loc": { "start": { "line": 102, @@ -5067,8 +5064,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 3939, - "end": 3990, + "start": 3907, + "end": 3958, "loc": { "start": { "line": 102, @@ -5082,8 +5079,8 @@ "operator": "=", "left": { "type": "MemberExpression", - "start": 3939, - "end": 3961, + "start": 3907, + "end": 3929, "loc": { "start": { "line": 102, @@ -5096,8 +5093,8 @@ }, "object": { "type": "Identifier", - "start": 3939, - "end": 3947, + "start": 3907, + "end": 3915, "loc": { "start": { "line": 102, @@ -5113,8 +5110,8 @@ }, "property": { "type": "Identifier", - "start": 3948, - "end": 3961, + "start": 3916, + "end": 3929, "loc": { "start": { "line": 102, @@ -5132,8 +5129,8 @@ }, "right": { "type": "CallExpression", - "start": 3964, - "end": 3990, + "start": 3932, + "end": 3958, "loc": { "start": { "line": 102, @@ -5146,8 +5143,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3964, - "end": 3985, + "start": 3932, + "end": 3953, "loc": { "start": { "line": 102, @@ -5160,8 +5157,8 @@ }, "object": { "type": "Identifier", - "start": 3964, - "end": 3980, + "start": 3932, + "end": 3948, "loc": { "start": { "line": 102, @@ -5177,8 +5174,8 @@ }, "property": { "type": "Identifier", - "start": 3981, - "end": 3985, + "start": 3949, + "end": 3953, "loc": { "start": { "line": 102, @@ -5197,8 +5194,8 @@ "arguments": [ { "type": "StringLiteral", - "start": 3986, - "end": 3989, + "start": 3954, + "end": 3957, "loc": { "start": { "line": 102, @@ -5228,8 +5225,8 @@ }, { "type": "ExpressionStatement", - "start": 4003, - "end": 4080, + "start": 3971, + "end": 4048, "loc": { "start": { "line": 105, @@ -5242,8 +5239,8 @@ }, "expression": { "type": "CallExpression", - "start": 4003, - "end": 4079, + "start": 3971, + "end": 4047, "loc": { "start": { "line": 105, @@ -5256,8 +5253,8 @@ }, "callee": { "type": "MemberExpression", - "start": 4003, - "end": 4023, + "start": 3971, + "end": 3991, "loc": { "start": { "line": 105, @@ -5270,8 +5267,8 @@ }, "object": { "type": "Identifier", - "start": 4003, - "end": 4019, + "start": 3971, + "end": 3987, "loc": { "start": { "line": 105, @@ -5287,8 +5284,8 @@ }, "property": { "type": "Identifier", - "start": 4020, - "end": 4023, + "start": 3988, + "end": 3991, "loc": { "start": { "line": 105, @@ -5307,8 +5304,8 @@ "arguments": [ { "type": "StringLiteral", - "start": 4024, - "end": 4059, + "start": 3992, + "end": 4027, "loc": { "start": { "line": 105, @@ -5327,8 +5324,8 @@ }, { "type": "Identifier", - "start": 4061, - "end": 4068, + "start": 4029, + "end": 4036, "loc": { "start": { "line": 105, @@ -5344,8 +5341,8 @@ }, { "type": "Identifier", - "start": 4070, - "end": 4078, + "start": 4038, + "end": 4046, "loc": { "start": { "line": 105, @@ -5364,8 +5361,8 @@ }, { "type": "ReturnStatement", - "start": 4085, - "end": 4101, + "start": 4053, + "end": 4069, "loc": { "start": { "line": 106, @@ -5378,8 +5375,8 @@ }, "argument": { "type": "Identifier", - "start": 4092, - "end": 4100, + "start": 4060, + "end": 4068, "loc": { "start": { "line": 106, @@ -5402,8 +5399,8 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1986, - "end": 2267, + "start": 1972, + "end": 2253, "loc": { "start": { "line": 54, @@ -5420,8 +5417,8 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 4109, - "end": 4157, + "start": 4077, + "end": 4125, "loc": { "start": { "line": 109, @@ -5437,8 +5434,8 @@ }, { "type": "ClassMethod", - "start": 4160, - "end": 4675, + "start": 4128, + "end": 4643, "loc": { "start": { "line": 112, @@ -5453,8 +5450,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 4164, - "end": 4177, + "start": 4132, + "end": 4145, "loc": { "start": { "line": 112, @@ -5476,8 +5473,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4180, - "end": 4675, + "start": 4148, + "end": 4643, "loc": { "start": { "line": 112, @@ -5491,8 +5488,8 @@ "body": [ { "type": "IfStatement", - "start": 4253, - "end": 4329, + "start": 4221, + "end": 4297, "loc": { "start": { "line": 114, @@ -5505,8 +5502,8 @@ }, "test": { "type": "CallExpression", - "start": 4257, - "end": 4292, + "start": 4225, + "end": 4260, "loc": { "start": { "line": 114, @@ -5519,8 +5516,8 @@ }, "callee": { "type": "Identifier", - "start": 4257, - "end": 4260, + "start": 4225, + "end": 4228, "loc": { "start": { "line": 114, @@ -5538,8 +5535,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 4261, - "end": 4274, + "start": 4229, + "end": 4242, "loc": { "start": { "line": 114, @@ -5552,8 +5549,8 @@ }, "object": { "type": "ThisExpression", - "start": 4261, - "end": 4265, + "start": 4229, + "end": 4233, "loc": { "start": { "line": 114, @@ -5567,8 +5564,8 @@ }, "property": { "type": "Identifier", - "start": 4266, - "end": 4274, + "start": 4234, + "end": 4242, "loc": { "start": { "line": 114, @@ -5586,8 +5583,8 @@ }, { "type": "StringLiteral", - "start": 4276, - "end": 4291, + "start": 4244, + "end": 4259, "loc": { "start": { "line": 114, @@ -5609,8 +5606,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4294, - "end": 4329, + "start": 4262, + "end": 4297, "loc": { "start": { "line": 114, @@ -5623,8 +5620,8 @@ }, "argument": { "type": "MemberExpression", - "start": 4301, - "end": 4328, + "start": 4269, + "end": 4296, "loc": { "start": { "line": 114, @@ -5637,8 +5634,8 @@ }, "object": { "type": "MemberExpression", - "start": 4301, - "end": 4314, + "start": 4269, + "end": 4282, "loc": { "start": { "line": 114, @@ -5651,8 +5648,8 @@ }, "object": { "type": "ThisExpression", - "start": 4301, - "end": 4305, + "start": 4269, + "end": 4273, "loc": { "start": { "line": 114, @@ -5666,8 +5663,8 @@ }, "property": { "type": "Identifier", - "start": 4306, - "end": 4314, + "start": 4274, + "end": 4282, "loc": { "start": { "line": 114, @@ -5685,8 +5682,8 @@ }, "property": { "type": "Identifier", - "start": 4315, - "end": 4328, + "start": 4283, + "end": 4296, "loc": { "start": { "line": 114, @@ -5709,8 +5706,8 @@ { "type": "CommentLine", "value": " Get the catalog number from the specimen object if present.", - "start": 4186, - "end": 4248, + "start": 4154, + "end": 4216, "loc": { "start": { "line": 113, @@ -5727,8 +5724,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 4335, - "end": 4406, + "start": 4303, + "end": 4374, "loc": { "start": { "line": 116, @@ -5743,8 +5740,8 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 4411, - "end": 4439, + "start": 4379, + "end": 4407, "loc": { "start": { "line": 117, @@ -5760,8 +5757,8 @@ }, { "type": "IfStatement", - "start": 4444, - "end": 4649, + "start": 4412, + "end": 4617, "loc": { "start": { "line": 118, @@ -5774,8 +5771,8 @@ }, "test": { "type": "CallExpression", - "start": 4448, - "end": 4482, + "start": 4416, + "end": 4450, "loc": { "start": { "line": 118, @@ -5788,8 +5785,8 @@ }, "callee": { "type": "Identifier", - "start": 4448, - "end": 4451, + "start": 4416, + "end": 4419, "loc": { "start": { "line": 118, @@ -5807,8 +5804,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 4452, - "end": 4465, + "start": 4420, + "end": 4433, "loc": { "start": { "line": 118, @@ -5821,8 +5818,8 @@ }, "object": { "type": "ThisExpression", - "start": 4452, - "end": 4456, + "start": 4420, + "end": 4424, "loc": { "start": { "line": 118, @@ -5836,8 +5833,8 @@ }, "property": { "type": "Identifier", - "start": 4457, - "end": 4465, + "start": 4425, + "end": 4433, "loc": { "start": { "line": 118, @@ -5855,8 +5852,8 @@ }, { "type": "StringLiteral", - "start": 4467, - "end": 4481, + "start": 4435, + "end": 4449, "loc": { "start": { "line": 118, @@ -5878,8 +5875,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 4484, - "end": 4649, + "start": 4452, + "end": 4617, "loc": { "start": { "line": 118, @@ -5893,8 +5890,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 4492, - "end": 4570, + "start": 4460, + "end": 4538, "loc": { "start": { "line": 119, @@ -5908,8 +5905,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 4498, - "end": 4569, + "start": 4466, + "end": 4537, "loc": { "start": { "line": 119, @@ -5922,8 +5919,8 @@ }, "id": { "type": "Identifier", - "start": 4498, - "end": 4506, + "start": 4466, + "end": 4474, "loc": { "start": { "line": 119, @@ -5939,8 +5936,8 @@ }, "init": { "type": "CallExpression", - "start": 4509, - "end": 4569, + "start": 4477, + "end": 4537, "loc": { "start": { "line": 119, @@ -5953,8 +5950,8 @@ }, "callee": { "type": "MemberExpression", - "start": 4509, - "end": 4541, + "start": 4477, + "end": 4509, "loc": { "start": { "line": 119, @@ -5967,8 +5964,8 @@ }, "object": { "type": "Identifier", - "start": 4509, - "end": 4524, + "start": 4477, + "end": 4492, "loc": { "start": { "line": 119, @@ -5984,8 +5981,8 @@ }, "property": { "type": "Identifier", - "start": 4525, - "end": 4541, + "start": 4493, + "end": 4509, "loc": { "start": { "line": 119, @@ -6004,8 +6001,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 4542, - "end": 4568, + "start": 4510, + "end": 4536, "loc": { "start": { "line": 119, @@ -6018,8 +6015,8 @@ }, "object": { "type": "MemberExpression", - "start": 4542, - "end": 4555, + "start": 4510, + "end": 4523, "loc": { "start": { "line": 119, @@ -6032,8 +6029,8 @@ }, "object": { "type": "ThisExpression", - "start": 4542, - "end": 4546, + "start": 4510, + "end": 4514, "loc": { "start": { "line": 119, @@ -6047,8 +6044,8 @@ }, "property": { "type": "Identifier", - "start": 4547, - "end": 4555, + "start": 4515, + "end": 4523, "loc": { "start": { "line": 119, @@ -6066,8 +6063,8 @@ }, "property": { "type": "Identifier", - "start": 4556, - "end": 4568, + "start": 4524, + "end": 4536, "loc": { "start": { "line": 119, @@ -6091,8 +6088,8 @@ }, { "type": "IfStatement", - "start": 4577, - "end": 4643, + "start": 4545, + "end": 4611, "loc": { "start": { "line": 120, @@ -6105,8 +6102,8 @@ }, "test": { "type": "CallExpression", - "start": 4581, - "end": 4611, + "start": 4549, + "end": 4579, "loc": { "start": { "line": 120, @@ -6119,8 +6116,8 @@ }, "callee": { "type": "Identifier", - "start": 4581, - "end": 4584, + "start": 4549, + "end": 4552, "loc": { "start": { "line": 120, @@ -6137,8 +6134,8 @@ "arguments": [ { "type": "Identifier", - "start": 4585, - "end": 4593, + "start": 4553, + "end": 4561, "loc": { "start": { "line": 120, @@ -6154,8 +6151,8 @@ }, { "type": "StringLiteral", - "start": 4595, - "end": 4610, + "start": 4563, + "end": 4578, "loc": { "start": { "line": 120, @@ -6176,8 +6173,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4613, - "end": 4643, + "start": 4581, + "end": 4611, "loc": { "start": { "line": 120, @@ -6190,8 +6187,8 @@ }, "argument": { "type": "MemberExpression", - "start": 4620, - "end": 4642, + "start": 4588, + "end": 4610, "loc": { "start": { "line": 120, @@ -6204,8 +6201,8 @@ }, "object": { "type": "Identifier", - "start": 4620, - "end": 4628, + "start": 4588, + "end": 4596, "loc": { "start": { "line": 120, @@ -6221,8 +6218,8 @@ }, "property": { "type": "Identifier", - "start": 4629, - "end": 4642, + "start": 4597, + "end": 4610, "loc": { "start": { "line": 120, @@ -6249,8 +6246,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 4335, - "end": 4406, + "start": 4303, + "end": 4374, "loc": { "start": { "line": 116, @@ -6265,8 +6262,8 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 4411, - "end": 4439, + "start": 4379, + "end": 4407, "loc": { "start": { "line": 117, @@ -6282,8 +6279,8 @@ }, { "type": "ReturnStatement", - "start": 4654, - "end": 4671, + "start": 4622, + "end": 4639, "loc": { "start": { "line": 122, @@ -6296,8 +6293,8 @@ }, "argument": { "type": "Identifier", - "start": 4661, - "end": 4670, + "start": 4629, + "end": 4638, "loc": { "start": { "line": 122, @@ -6320,8 +6317,8 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 4109, - "end": 4157, + "start": 4077, + "end": 4125, "loc": { "start": { "line": 109, @@ -6338,8 +6335,8 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4679, - "end": 4729, + "start": 4647, + "end": 4697, "loc": { "start": { "line": 125, @@ -6355,8 +6352,8 @@ }, { "type": "ClassMethod", - "start": 4732, - "end": 5259, + "start": 4700, + "end": 5227, "loc": { "start": { "line": 128, @@ -6371,8 +6368,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 4736, - "end": 4751, + "start": 4704, + "end": 4719, "loc": { "start": { "line": 128, @@ -6394,8 +6391,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4754, - "end": 5259, + "start": 4722, + "end": 5227, "loc": { "start": { "line": 128, @@ -6409,8 +6406,8 @@ "body": [ { "type": "IfStatement", - "start": 4829, - "end": 4909, + "start": 4797, + "end": 4877, "loc": { "start": { "line": 130, @@ -6423,8 +6420,8 @@ }, "test": { "type": "CallExpression", - "start": 4833, - "end": 4870, + "start": 4801, + "end": 4838, "loc": { "start": { "line": 130, @@ -6437,8 +6434,8 @@ }, "callee": { "type": "Identifier", - "start": 4833, - "end": 4836, + "start": 4801, + "end": 4804, "loc": { "start": { "line": 130, @@ -6456,8 +6453,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 4837, - "end": 4850, + "start": 4805, + "end": 4818, "loc": { "start": { "line": 130, @@ -6470,8 +6467,8 @@ }, "object": { "type": "ThisExpression", - "start": 4837, - "end": 4841, + "start": 4805, + "end": 4809, "loc": { "start": { "line": 130, @@ -6485,8 +6482,8 @@ }, "property": { "type": "Identifier", - "start": 4842, - "end": 4850, + "start": 4810, + "end": 4818, "loc": { "start": { "line": 130, @@ -6504,8 +6501,8 @@ }, { "type": "StringLiteral", - "start": 4852, - "end": 4869, + "start": 4820, + "end": 4837, "loc": { "start": { "line": 130, @@ -6527,8 +6524,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4872, - "end": 4909, + "start": 4840, + "end": 4877, "loc": { "start": { "line": 130, @@ -6541,8 +6538,8 @@ }, "argument": { "type": "MemberExpression", - "start": 4879, - "end": 4908, + "start": 4847, + "end": 4876, "loc": { "start": { "line": 130, @@ -6555,8 +6552,8 @@ }, "object": { "type": "MemberExpression", - "start": 4879, - "end": 4892, + "start": 4847, + "end": 4860, "loc": { "start": { "line": 130, @@ -6569,8 +6566,8 @@ }, "object": { "type": "ThisExpression", - "start": 4879, - "end": 4883, + "start": 4847, + "end": 4851, "loc": { "start": { "line": 130, @@ -6584,8 +6581,8 @@ }, "property": { "type": "Identifier", - "start": 4884, - "end": 4892, + "start": 4852, + "end": 4860, "loc": { "start": { "line": 130, @@ -6603,8 +6600,8 @@ }, "property": { "type": "Identifier", - "start": 4893, - "end": 4908, + "start": 4861, + "end": 4876, "loc": { "start": { "line": 130, @@ -6627,8 +6624,8 @@ { "type": "CommentLine", "value": " Get the institution code from the specimen object if present.", - "start": 4760, - "end": 4824, + "start": 4728, + "end": 4792, "loc": { "start": { "line": 129, @@ -6645,8 +6642,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4915, - "end": 4987, + "start": 4883, + "end": 4955, "loc": { "start": { "line": 132, @@ -6661,8 +6658,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4992, - "end": 5019, + "start": 4960, + "end": 4987, "loc": { "start": { "line": 133, @@ -6678,8 +6675,8 @@ }, { "type": "IfStatement", - "start": 5024, - "end": 5233, + "start": 4992, + "end": 5201, "loc": { "start": { "line": 134, @@ -6692,8 +6689,8 @@ }, "test": { "type": "CallExpression", - "start": 5028, - "end": 5062, + "start": 4996, + "end": 5030, "loc": { "start": { "line": 134, @@ -6706,8 +6703,8 @@ }, "callee": { "type": "Identifier", - "start": 5028, - "end": 5031, + "start": 4996, + "end": 4999, "loc": { "start": { "line": 134, @@ -6725,8 +6722,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5032, - "end": 5045, + "start": 5000, + "end": 5013, "loc": { "start": { "line": 134, @@ -6739,8 +6736,8 @@ }, "object": { "type": "ThisExpression", - "start": 5032, - "end": 5036, + "start": 5000, + "end": 5004, "loc": { "start": { "line": 134, @@ -6754,8 +6751,8 @@ }, "property": { "type": "Identifier", - "start": 5037, - "end": 5045, + "start": 5005, + "end": 5013, "loc": { "start": { "line": 134, @@ -6773,8 +6770,8 @@ }, { "type": "StringLiteral", - "start": 5047, - "end": 5061, + "start": 5015, + "end": 5029, "loc": { "start": { "line": 134, @@ -6796,8 +6793,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 5064, - "end": 5233, + "start": 5032, + "end": 5201, "loc": { "start": { "line": 134, @@ -6811,8 +6808,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 5072, - "end": 5150, + "start": 5040, + "end": 5118, "loc": { "start": { "line": 135, @@ -6826,8 +6823,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 5078, - "end": 5149, + "start": 5046, + "end": 5117, "loc": { "start": { "line": 135, @@ -6840,8 +6837,8 @@ }, "id": { "type": "Identifier", - "start": 5078, - "end": 5086, + "start": 5046, + "end": 5054, "loc": { "start": { "line": 135, @@ -6857,8 +6854,8 @@ }, "init": { "type": "CallExpression", - "start": 5089, - "end": 5149, + "start": 5057, + "end": 5117, "loc": { "start": { "line": 135, @@ -6871,8 +6868,8 @@ }, "callee": { "type": "MemberExpression", - "start": 5089, - "end": 5121, + "start": 5057, + "end": 5089, "loc": { "start": { "line": 135, @@ -6885,8 +6882,8 @@ }, "object": { "type": "Identifier", - "start": 5089, - "end": 5104, + "start": 5057, + "end": 5072, "loc": { "start": { "line": 135, @@ -6902,8 +6899,8 @@ }, "property": { "type": "Identifier", - "start": 5105, - "end": 5121, + "start": 5073, + "end": 5089, "loc": { "start": { "line": 135, @@ -6922,8 +6919,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5122, - "end": 5148, + "start": 5090, + "end": 5116, "loc": { "start": { "line": 135, @@ -6936,8 +6933,8 @@ }, "object": { "type": "MemberExpression", - "start": 5122, - "end": 5135, + "start": 5090, + "end": 5103, "loc": { "start": { "line": 135, @@ -6950,8 +6947,8 @@ }, "object": { "type": "ThisExpression", - "start": 5122, - "end": 5126, + "start": 5090, + "end": 5094, "loc": { "start": { "line": 135, @@ -6965,8 +6962,8 @@ }, "property": { "type": "Identifier", - "start": 5127, - "end": 5135, + "start": 5095, + "end": 5103, "loc": { "start": { "line": 135, @@ -6984,8 +6981,8 @@ }, "property": { "type": "Identifier", - "start": 5136, - "end": 5148, + "start": 5104, + "end": 5116, "loc": { "start": { "line": 135, @@ -7009,8 +7006,8 @@ }, { "type": "IfStatement", - "start": 5157, - "end": 5227, + "start": 5125, + "end": 5195, "loc": { "start": { "line": 136, @@ -7023,8 +7020,8 @@ }, "test": { "type": "CallExpression", - "start": 5161, - "end": 5193, + "start": 5129, + "end": 5161, "loc": { "start": { "line": 136, @@ -7037,8 +7034,8 @@ }, "callee": { "type": "Identifier", - "start": 5161, - "end": 5164, + "start": 5129, + "end": 5132, "loc": { "start": { "line": 136, @@ -7055,8 +7052,8 @@ "arguments": [ { "type": "Identifier", - "start": 5165, - "end": 5173, + "start": 5133, + "end": 5141, "loc": { "start": { "line": 136, @@ -7072,8 +7069,8 @@ }, { "type": "StringLiteral", - "start": 5175, - "end": 5192, + "start": 5143, + "end": 5160, "loc": { "start": { "line": 136, @@ -7094,8 +7091,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5195, - "end": 5227, + "start": 5163, + "end": 5195, "loc": { "start": { "line": 136, @@ -7108,8 +7105,8 @@ }, "argument": { "type": "MemberExpression", - "start": 5202, - "end": 5226, + "start": 5170, + "end": 5194, "loc": { "start": { "line": 136, @@ -7122,8 +7119,8 @@ }, "object": { "type": "Identifier", - "start": 5202, - "end": 5210, + "start": 5170, + "end": 5178, "loc": { "start": { "line": 136, @@ -7139,8 +7136,8 @@ }, "property": { "type": "Identifier", - "start": 5211, - "end": 5226, + "start": 5179, + "end": 5194, "loc": { "start": { "line": 136, @@ -7167,8 +7164,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4915, - "end": 4987, + "start": 4883, + "end": 4955, "loc": { "start": { "line": 132, @@ -7183,8 +7180,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4992, - "end": 5019, + "start": 4960, + "end": 4987, "loc": { "start": { "line": 133, @@ -7200,8 +7197,8 @@ }, { "type": "ReturnStatement", - "start": 5238, - "end": 5255, + "start": 5206, + "end": 5223, "loc": { "start": { "line": 138, @@ -7214,8 +7211,8 @@ }, "argument": { "type": "Identifier", - "start": 5245, - "end": 5254, + "start": 5213, + "end": 5222, "loc": { "start": { "line": 138, @@ -7238,8 +7235,8 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4679, - "end": 4729, + "start": 4647, + "end": 4697, "loc": { "start": { "line": 125, @@ -7256,8 +7253,8 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 5263, - "end": 5312, + "start": 5231, + "end": 5280, "loc": { "start": { "line": 141, @@ -7273,8 +7270,8 @@ }, { "type": "ClassMethod", - "start": 5315, - "end": 5836, + "start": 5283, + "end": 5804, "loc": { "start": { "line": 144, @@ -7289,8 +7286,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 5319, - "end": 5333, + "start": 5287, + "end": 5301, "loc": { "start": { "line": 144, @@ -7312,8 +7309,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 5336, - "end": 5836, + "start": 5304, + "end": 5804, "loc": { "start": { "line": 144, @@ -7327,8 +7324,8 @@ "body": [ { "type": "IfStatement", - "start": 5410, - "end": 5488, + "start": 5378, + "end": 5456, "loc": { "start": { "line": 146, @@ -7341,8 +7338,8 @@ }, "test": { "type": "CallExpression", - "start": 5414, - "end": 5450, + "start": 5382, + "end": 5418, "loc": { "start": { "line": 146, @@ -7355,8 +7352,8 @@ }, "callee": { "type": "Identifier", - "start": 5414, - "end": 5417, + "start": 5382, + "end": 5385, "loc": { "start": { "line": 146, @@ -7374,8 +7371,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5418, - "end": 5431, + "start": 5386, + "end": 5399, "loc": { "start": { "line": 146, @@ -7388,8 +7385,8 @@ }, "object": { "type": "ThisExpression", - "start": 5418, - "end": 5422, + "start": 5386, + "end": 5390, "loc": { "start": { "line": 146, @@ -7403,8 +7400,8 @@ }, "property": { "type": "Identifier", - "start": 5423, - "end": 5431, + "start": 5391, + "end": 5399, "loc": { "start": { "line": 146, @@ -7422,8 +7419,8 @@ }, { "type": "StringLiteral", - "start": 5433, - "end": 5449, + "start": 5401, + "end": 5417, "loc": { "start": { "line": 146, @@ -7445,8 +7442,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5452, - "end": 5488, + "start": 5420, + "end": 5456, "loc": { "start": { "line": 146, @@ -7459,8 +7456,8 @@ }, "argument": { "type": "MemberExpression", - "start": 5459, - "end": 5487, + "start": 5427, + "end": 5455, "loc": { "start": { "line": 146, @@ -7473,8 +7470,8 @@ }, "object": { "type": "MemberExpression", - "start": 5459, - "end": 5472, + "start": 5427, + "end": 5440, "loc": { "start": { "line": 146, @@ -7487,8 +7484,8 @@ }, "object": { "type": "ThisExpression", - "start": 5459, - "end": 5463, + "start": 5427, + "end": 5431, "loc": { "start": { "line": 146, @@ -7502,8 +7499,8 @@ }, "property": { "type": "Identifier", - "start": 5464, - "end": 5472, + "start": 5432, + "end": 5440, "loc": { "start": { "line": 146, @@ -7521,8 +7518,8 @@ }, "property": { "type": "Identifier", - "start": 5473, - "end": 5487, + "start": 5441, + "end": 5455, "loc": { "start": { "line": 146, @@ -7545,8 +7542,8 @@ { "type": "CommentLine", "value": " Get the collection code from the specimen object if present.", - "start": 5342, - "end": 5405, + "start": 5310, + "end": 5373, "loc": { "start": { "line": 145, @@ -7563,8 +7560,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 5494, - "end": 5566, + "start": 5462, + "end": 5534, "loc": { "start": { "line": 148, @@ -7579,8 +7576,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 5571, - "end": 5598, + "start": 5539, + "end": 5566, "loc": { "start": { "line": 149, @@ -7596,8 +7593,8 @@ }, { "type": "IfStatement", - "start": 5603, - "end": 5810, + "start": 5571, + "end": 5778, "loc": { "start": { "line": 150, @@ -7610,8 +7607,8 @@ }, "test": { "type": "CallExpression", - "start": 5607, - "end": 5641, + "start": 5575, + "end": 5609, "loc": { "start": { "line": 150, @@ -7624,8 +7621,8 @@ }, "callee": { "type": "Identifier", - "start": 5607, - "end": 5610, + "start": 5575, + "end": 5578, "loc": { "start": { "line": 150, @@ -7643,8 +7640,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5611, - "end": 5624, + "start": 5579, + "end": 5592, "loc": { "start": { "line": 150, @@ -7657,8 +7654,8 @@ }, "object": { "type": "ThisExpression", - "start": 5611, - "end": 5615, + "start": 5579, + "end": 5583, "loc": { "start": { "line": 150, @@ -7672,8 +7669,8 @@ }, "property": { "type": "Identifier", - "start": 5616, - "end": 5624, + "start": 5584, + "end": 5592, "loc": { "start": { "line": 150, @@ -7691,8 +7688,8 @@ }, { "type": "StringLiteral", - "start": 5626, - "end": 5640, + "start": 5594, + "end": 5608, "loc": { "start": { "line": 150, @@ -7714,8 +7711,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 5643, - "end": 5810, + "start": 5611, + "end": 5778, "loc": { "start": { "line": 150, @@ -7729,8 +7726,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 5651, - "end": 5729, + "start": 5619, + "end": 5697, "loc": { "start": { "line": 151, @@ -7744,8 +7741,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 5657, - "end": 5728, + "start": 5625, + "end": 5696, "loc": { "start": { "line": 151, @@ -7758,8 +7755,8 @@ }, "id": { "type": "Identifier", - "start": 5657, - "end": 5665, + "start": 5625, + "end": 5633, "loc": { "start": { "line": 151, @@ -7775,8 +7772,8 @@ }, "init": { "type": "CallExpression", - "start": 5668, - "end": 5728, + "start": 5636, + "end": 5696, "loc": { "start": { "line": 151, @@ -7789,8 +7786,8 @@ }, "callee": { "type": "MemberExpression", - "start": 5668, - "end": 5700, + "start": 5636, + "end": 5668, "loc": { "start": { "line": 151, @@ -7803,8 +7800,8 @@ }, "object": { "type": "Identifier", - "start": 5668, - "end": 5683, + "start": 5636, + "end": 5651, "loc": { "start": { "line": 151, @@ -7820,8 +7817,8 @@ }, "property": { "type": "Identifier", - "start": 5684, - "end": 5700, + "start": 5652, + "end": 5668, "loc": { "start": { "line": 151, @@ -7840,8 +7837,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5701, - "end": 5727, + "start": 5669, + "end": 5695, "loc": { "start": { "line": 151, @@ -7854,8 +7851,8 @@ }, "object": { "type": "MemberExpression", - "start": 5701, - "end": 5714, + "start": 5669, + "end": 5682, "loc": { "start": { "line": 151, @@ -7868,8 +7865,8 @@ }, "object": { "type": "ThisExpression", - "start": 5701, - "end": 5705, + "start": 5669, + "end": 5673, "loc": { "start": { "line": 151, @@ -7883,8 +7880,8 @@ }, "property": { "type": "Identifier", - "start": 5706, - "end": 5714, + "start": 5674, + "end": 5682, "loc": { "start": { "line": 151, @@ -7902,8 +7899,8 @@ }, "property": { "type": "Identifier", - "start": 5715, - "end": 5727, + "start": 5683, + "end": 5695, "loc": { "start": { "line": 151, @@ -7927,8 +7924,8 @@ }, { "type": "IfStatement", - "start": 5736, - "end": 5804, + "start": 5704, + "end": 5772, "loc": { "start": { "line": 152, @@ -7941,8 +7938,8 @@ }, "test": { "type": "CallExpression", - "start": 5740, - "end": 5771, + "start": 5708, + "end": 5739, "loc": { "start": { "line": 152, @@ -7955,8 +7952,8 @@ }, "callee": { "type": "Identifier", - "start": 5740, - "end": 5743, + "start": 5708, + "end": 5711, "loc": { "start": { "line": 152, @@ -7973,8 +7970,8 @@ "arguments": [ { "type": "Identifier", - "start": 5744, - "end": 5752, + "start": 5712, + "end": 5720, "loc": { "start": { "line": 152, @@ -7990,8 +7987,8 @@ }, { "type": "StringLiteral", - "start": 5754, - "end": 5770, + "start": 5722, + "end": 5738, "loc": { "start": { "line": 152, @@ -8012,8 +8009,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5773, - "end": 5804, + "start": 5741, + "end": 5772, "loc": { "start": { "line": 152, @@ -8026,8 +8023,8 @@ }, "argument": { "type": "MemberExpression", - "start": 5780, - "end": 5803, + "start": 5748, + "end": 5771, "loc": { "start": { "line": 152, @@ -8040,8 +8037,8 @@ }, "object": { "type": "Identifier", - "start": 5780, - "end": 5788, + "start": 5748, + "end": 5756, "loc": { "start": { "line": 152, @@ -8057,8 +8054,8 @@ }, "property": { "type": "Identifier", - "start": 5789, - "end": 5803, + "start": 5757, + "end": 5771, "loc": { "start": { "line": 152, @@ -8085,8 +8082,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 5494, - "end": 5566, + "start": 5462, + "end": 5534, "loc": { "start": { "line": 148, @@ -8101,8 +8098,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 5571, - "end": 5598, + "start": 5539, + "end": 5566, "loc": { "start": { "line": 149, @@ -8118,8 +8115,8 @@ }, { "type": "ReturnStatement", - "start": 5815, - "end": 5832, + "start": 5783, + "end": 5800, "loc": { "start": { "line": 154, @@ -8132,8 +8129,8 @@ }, "argument": { "type": "Identifier", - "start": 5822, - "end": 5831, + "start": 5790, + "end": 5799, "loc": { "start": { "line": 154, @@ -8156,8 +8153,8 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 5263, - "end": 5312, + "start": 5231, + "end": 5280, "loc": { "start": { "line": 141, @@ -8174,8 +8171,8 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5840, - "end": 6099, + "start": 5808, + "end": 6067, "loc": { "start": { "line": 157, @@ -8191,8 +8188,8 @@ }, { "type": "ClassMethod", - "start": 6102, - "end": 7142, + "start": 6070, + "end": 7066, "loc": { "start": { "line": 163, @@ -8207,8 +8204,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 6106, - "end": 6118, + "start": 6074, + "end": 6086, "loc": { "start": { "line": 163, @@ -8230,8 +8227,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6121, - "end": 7142, + "start": 6089, + "end": 7066, "loc": { "start": { "line": 163, @@ -8245,8 +8242,8 @@ "body": [ { "type": "IfStatement", - "start": 6172, - "end": 6311, + "start": 6140, + "end": 6235, "loc": { "start": { "line": 165, @@ -8258,9 +8255,9 @@ } }, "test": { - "type": "LogicalExpression", - "start": 6176, - "end": 6254, + "type": "CallExpression", + "start": 6144, + "end": 6178, "loc": { "start": { "line": 165, @@ -8268,13 +8265,13 @@ }, "end": { "line": 165, - "column": 86 + "column": 42 } }, - "left": { - "type": "CallExpression", - "start": 6176, - "end": 6210, + "callee": { + "type": "Identifier", + "start": 6144, + "end": 6147, "loc": { "start": { "line": 165, @@ -8282,32 +8279,32 @@ }, "end": { "line": 165, - "column": 42 - } + "column": 11 + }, + "identifierName": "has" }, - "callee": { - "type": "Identifier", - "start": 6176, - "end": 6179, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 6148, + "end": 6161, "loc": { "start": { "line": 165, - "column": 8 + "column": 12 }, "end": { "line": 165, - "column": 11 - }, - "identifierName": "has" + "column": 25 + } }, - "name": "has", - "leadingComments": null - }, - "arguments": [ - { - "type": "MemberExpression", - "start": 6180, - "end": 6193, + "object": { + "type": "ThisExpression", + "start": 6148, + "end": 6152, "loc": { "start": { "line": 165, @@ -8315,243 +8312,60 @@ }, "end": { "line": 165, - "column": 25 - } - }, - "object": { - "type": "ThisExpression", - "start": 6180, - "end": 6184, - "loc": { - "start": { - "line": 165, - "column": 12 - }, - "end": { - "line": 165, - "column": 16 - } - } - }, - "property": { - "type": "Identifier", - "start": 6185, - "end": 6193, - "loc": { - "start": { - "line": 165, - "column": 17 - }, - "end": { - "line": 165, - "column": 25 - }, - "identifierName": "specimen" - }, - "name": "specimen" - }, - "computed": false - }, - { - "type": "StringLiteral", - "start": 6195, - "end": 6209, - "loc": { - "start": { - "line": 165, - "column": 27 - }, - "end": { - "line": 165, - "column": 41 + "column": 16 } - }, - "extra": { - "rawValue": "occurrenceID", - "raw": "'occurrenceID'" - }, - "value": "occurrenceID" - } - ], - "leadingComments": null - }, - "operator": "&&", - "right": { - "type": "BinaryExpression", - "start": 6214, - "end": 6254, - "loc": { - "start": { - "line": 165, - "column": 46 - }, - "end": { - "line": 165, - "column": 86 - } - }, - "left": { - "type": "CallExpression", - "start": 6214, - "end": 6247, - "loc": { - "start": { - "line": 165, - "column": 46 - }, - "end": { - "line": 165, - "column": 79 } }, - "callee": { - "type": "MemberExpression", - "start": 6214, - "end": 6245, + "property": { + "type": "Identifier", + "start": 6153, + "end": 6161, "loc": { "start": { "line": 165, - "column": 46 + "column": 17 }, "end": { "line": 165, - "column": 77 - } - }, - "object": { - "type": "MemberExpression", - "start": 6214, - "end": 6240, - "loc": { - "start": { - "line": 165, - "column": 46 - }, - "end": { - "line": 165, - "column": 72 - } - }, - "object": { - "type": "MemberExpression", - "start": 6214, - "end": 6227, - "loc": { - "start": { - "line": 165, - "column": 46 - }, - "end": { - "line": 165, - "column": 59 - } - }, - "object": { - "type": "ThisExpression", - "start": 6214, - "end": 6218, - "loc": { - "start": { - "line": 165, - "column": 46 - }, - "end": { - "line": 165, - "column": 50 - } - } - }, - "property": { - 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"column": 84 + "column": 27 }, "end": { "line": 165, - "column": 86 + "column": 41 } }, "extra": { - "rawValue": "", - "raw": "''" + "rawValue": "occurrenceID", + "raw": "'occurrenceID'" }, - "value": "" + "value": "occurrenceID" } - }, + ], "leadingComments": null }, "consequent": { "type": "BlockStatement", - "start": 6256, - "end": 6311, + "start": 6180, + "end": 6235, "loc": { "start": { "line": 165, - "column": 88 + "column": 44 }, "end": { "line": 167, @@ -8561,8 +8375,8 @@ "body": [ { "type": "ReturnStatement", - "start": 6264, - "end": 6305, + "start": 6188, + "end": 6229, "loc": { "start": { "line": 166, @@ -8575,8 +8389,8 @@ }, "argument": { "type": "CallExpression", - "start": 6271, - "end": 6304, + "start": 6195, + "end": 6228, "loc": { "start": { "line": 166, @@ -8589,8 +8403,8 @@ }, "callee": { "type": "MemberExpression", - "start": 6271, - "end": 6302, + "start": 6195, + "end": 6226, "loc": { "start": { "line": 166, @@ -8603,8 +8417,8 @@ }, "object": { "type": "MemberExpression", - 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"start": 6941, - "end": 6968, + "start": 6865, + "end": 6892, "loc": { "start": { "line": 178, @@ -10343,8 +10157,8 @@ }, "object": { "type": "MemberExpression", - "start": 6941, - "end": 6954, + "start": 6865, + "end": 6878, "loc": { "start": { "line": 178, @@ -10357,8 +10171,8 @@ }, "object": { "type": "ThisExpression", - "start": 6941, - "end": 6945, + "start": 6865, + "end": 6869, "loc": { "start": { "line": 178, @@ -10372,8 +10186,8 @@ }, "property": { "type": "Identifier", - "start": 6946, - "end": 6954, + "start": 6870, + "end": 6878, "loc": { "start": { "line": 178, @@ -10391,8 +10205,8 @@ }, "property": { "type": "Identifier", - "start": 6955, - "end": 6968, + "start": 6879, + "end": 6892, "loc": { "start": { "line": 178, @@ -10410,8 +10224,8 @@ }, "property": { "type": "Identifier", - "start": 6969, - "end": 6973, + "start": 6893, + "end": 6897, "loc": { "start": { "line": 178, @@ -10433,8 +10247,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 6887, - "end": 6900, + "start": 6811, + "end": 6824, "loc": { "start": { "line": 178, @@ -10453,8 +10267,8 @@ }, { "type": "TemplateElement", - "start": 6938, - "end": 6939, + "start": 6862, + "end": 6863, "loc": { "start": { "line": 178, @@ -10473,8 +10287,8 @@ }, { "type": "TemplateElement", - "start": 6976, - "end": 6976, + "start": 6900, + "end": 6900, "loc": { "start": { "line": 178, @@ -10501,8 +10315,8 @@ }, { "type": "ReturnStatement", - "start": 6993, - "end": 7054, + "start": 6917, + "end": 6978, "loc": { "start": { "line": 180, @@ -10515,8 +10329,8 @@ }, "argument": { "type": "TemplateLiteral", - "start": 7000, - "end": 7053, + "start": 6924, + "end": 6977, "loc": { "start": { "line": 180, @@ -10530,8 +10344,8 @@ "expressions": [ { "type": "CallExpression", - "start": 7017, - "end": 7051, + "start": 6941, + "end": 6975, "loc": { "start": { "line": 180, @@ -10544,8 +10358,8 @@ }, "callee": { "type": "MemberExpression", - "start": 7017, - "end": 7049, + "start": 6941, + "end": 6973, "loc": { "start": { "line": 180, @@ -10558,8 +10372,8 @@ }, "object": { "type": "MemberExpression", - "start": 7017, - "end": 7044, + "start": 6941, + "end": 6968, "loc": { "start": { "line": 180, @@ -10572,8 +10386,8 @@ }, "object": { "type": "MemberExpression", - "start": 7017, - "end": 7030, + "start": 6941, + "end": 6954, "loc": { "start": { "line": 180, @@ -10586,8 +10400,8 @@ }, "object": { "type": "ThisExpression", - "start": 7017, - "end": 7021, + "start": 6941, + "end": 6945, "loc": { "start": { "line": 180, @@ -10601,8 +10415,8 @@ }, "property": { "type": "Identifier", - "start": 7022, - "end": 7030, + "start": 6946, + "end": 6954, "loc": { "start": { "line": 180, @@ -10620,8 +10434,8 @@ }, "property": { "type": "Identifier", - "start": 7031, - "end": 7044, + "start": 6955, + "end": 6968, "loc": { "start": { "line": 180, @@ -10639,8 +10453,8 @@ }, "property": { "type": "Identifier", - "start": 7045, - "end": 7049, + "start": 6969, + "end": 6973, "loc": { "start": { "line": 180, @@ -10662,8 +10476,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 7001, - "end": 7015, + "start": 6925, + "end": 6939, "loc": { "start": { "line": 180, @@ -10682,8 +10496,8 @@ }, { "type": "TemplateElement", - "start": 7052, - "end": 7052, + "start": 6976, + "end": 6976, "loc": { "start": { "line": 180, @@ -10712,8 +10526,8 @@ { "type": "CommentLine", "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 6317, - "end": 6394, + "start": 6241, + "end": 6318, "loc": { "start": { "line": 169, @@ -10730,8 +10544,8 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 7066, - "end": 7116, + "start": 6990, + "end": 7040, "loc": { "start": { "line": 183, @@ -10747,8 +10561,8 @@ }, { "type": "ReturnStatement", - "start": 7121, - "end": 7138, + "start": 7045, + "end": 7062, "loc": { "start": { "line": 184, @@ -10761,8 +10575,8 @@ }, "argument": { "type": "Identifier", - "start": 7128, - "end": 7137, + "start": 7052, + "end": 7061, "loc": { "start": { "line": 184, @@ -10781,8 +10595,8 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 7066, - "end": 7116, + "start": 6990, + "end": 7040, "loc": { "start": { "line": 183, @@ -10804,8 +10618,8 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5840, - "end": 6099, + "start": 5808, + "end": 6067, "loc": { "start": { "line": 157, @@ -10822,8 +10636,8 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 7146, - "end": 7207, + "start": 7070, + "end": 7131, "loc": { "start": { "line": 187, @@ -10839,8 +10653,8 @@ }, { "type": "ClassMethod", - "start": 7210, - "end": 7349, + "start": 7134, + "end": 7262, "loc": { "start": { "line": 190, @@ -10855,8 +10669,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7214, - "end": 7227, + "start": 7138, + "end": 7151, "loc": { "start": { "line": 190, @@ -10878,8 +10692,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7230, - "end": 7349, + "start": 7154, + "end": 7262, "loc": { "start": { "line": 190, @@ -10893,8 +10707,8 @@ "body": [ { "type": "IfStatement", - "start": 7236, - "end": 7323, + "start": 7160, + "end": 7236, "loc": { "start": { "line": 191, @@ -10902,13 +10716,13 @@ }, "end": { "line": 191, - "column": 91 + "column": 80 } }, "test": { "type": "CallExpression", - "start": 7240, - "end": 7279, + "start": 7164, + "end": 7199, "loc": { "start": { "line": 191, @@ -10916,13 +10730,13 @@ }, "end": { "line": 191, - "column": 47 + "column": 43 } }, "callee": { "type": "Identifier", - "start": 7240, - "end": 7243, + "start": 7164, + "end": 7167, "loc": { "start": { "line": 191, @@ -10939,8 +10753,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 7244, - "end": 7257, + "start": 7168, + "end": 7181, "loc": { "start": { "line": 191, @@ -10953,8 +10767,8 @@ }, "object": { "type": "ThisExpression", - "start": 7244, - "end": 7248, + "start": 7168, + "end": 7172, "loc": { "start": { "line": 191, @@ -10968,8 +10782,8 @@ }, "property": { "type": "Identifier", - "start": 7249, - "end": 7257, + "start": 7173, + "end": 7181, "loc": { "start": { "line": 191, @@ -10987,8 +10801,8 @@ }, { "type": "StringLiteral", - "start": 7259, - "end": 7278, + "start": 7183, + "end": 7198, "loc": { "start": { "line": 191, @@ -10996,86 +10810,86 @@ }, "end": { "line": 191, - "column": 46 + "column": 42 } }, "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "rawValue": "basisOfRecord", + "raw": "'basisOfRecord'" }, - "value": "dwc:basisOfRecord" + "value": "basisOfRecord" } ] }, "consequent": { "type": "ReturnStatement", - "start": 7281, - "end": 7323, + "start": 7201, + "end": 7236, "loc": { "start": { "line": 191, - "column": 49 + "column": 45 }, "end": { "line": 191, - "column": 91 + "column": 80 } }, "argument": { "type": "MemberExpression", - "start": 7288, - "end": 7322, + "start": 7208, + "end": 7235, "loc": { "start": { "line": 191, - "column": 56 + "column": 52 }, "end": { "line": 191, - "column": 90 + "column": 79 } }, "object": { "type": "MemberExpression", - "start": 7288, - "end": 7301, + "start": 7208, + "end": 7221, "loc": { "start": { "line": 191, - "column": 56 + "column": 52 }, "end": { "line": 191, - "column": 69 + "column": 65 } }, "object": { "type": "ThisExpression", - "start": 7288, - "end": 7292, + "start": 7208, + "end": 7212, "loc": { "start": { "line": 191, - "column": 56 + "column": 52 }, "end": { "line": 191, - "column": 60 + "column": 56 } } }, "property": { "type": "Identifier", - "start": 7293, - "end": 7301, + "start": 7213, + "end": 7221, "loc": { "start": { "line": 191, - "column": 61 + "column": 57 }, "end": { "line": 191, - "column": 69 + "column": 65 }, "identifierName": "specimen" }, @@ -11084,34 +10898,31 @@ "computed": false }, "property": { - "type": "StringLiteral", - "start": 7302, - "end": 7321, + "type": "Identifier", + "start": 7222, + "end": 7235, "loc": { "start": { "line": 191, - "column": 70 + "column": 66 }, "end": { "line": 191, - "column": 89 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 79 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, - "computed": true + "computed": false } }, "alternate": null }, { "type": "ReturnStatement", - "start": 7328, - "end": 7345, + "start": 7241, + "end": 7258, "loc": { "start": { "line": 192, @@ -11124,8 +10935,8 @@ }, "argument": { "type": "Identifier", - "start": 7335, - "end": 7344, + "start": 7248, + "end": 7257, "loc": { "start": { "line": 192, @@ -11148,8 +10959,8 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 7146, - "end": 7207, + "start": 7070, + "end": 7131, "loc": { "start": { "line": 187, @@ -11166,8 +10977,8 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 7353, - "end": 7468, + "start": 7266, + "end": 7381, "loc": { "start": { "line": 195, @@ -11183,8 +10994,8 @@ }, { "type": "ClassMethod", - "start": 7471, - "end": 7545, + "start": 7384, + "end": 7451, "loc": { "start": { "line": 199, @@ -11199,8 +11010,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7475, - "end": 7488, + "start": 7388, + "end": 7401, "loc": { "start": { "line": 199, @@ -11222,8 +11033,8 @@ "params": [ { "type": "Identifier", - "start": 7489, - "end": 7492, + "start": 7402, + "end": 7405, "loc": { "start": { "line": 199, @@ -11240,8 +11051,8 @@ ], "body": { "type": "BlockStatement", - "start": 7494, - "end": 7545, + "start": 7407, + "end": 7451, "loc": { "start": { "line": 199, @@ -11255,8 +11066,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 7500, - "end": 7541, + "start": 7413, + "end": 7447, "loc": { "start": { "line": 200, @@ -11264,13 +11075,13 @@ }, "end": { "line": 200, - "column": 45 + "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 7500, - "end": 7540, + "start": 7413, + "end": 7446, "loc": { "start": { "line": 200, @@ -11278,14 +11089,14 @@ }, "end": { "line": 200, - "column": 44 + "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7500, - "end": 7534, + "start": 7413, + "end": 7440, "loc": { "start": { "line": 200, @@ -11293,13 +11104,13 @@ }, "end": { "line": 200, - "column": 38 + "column": 31 } }, "object": { "type": "MemberExpression", - "start": 7500, - "end": 7513, + "start": 7413, + "end": 7426, "loc": { "start": { "line": 200, @@ -11312,8 +11123,8 @@ }, "object": { "type": "ThisExpression", - "start": 7500, - "end": 7504, + "start": 7413, + "end": 7417, "loc": { "start": { "line": 200, @@ -11327,8 +11138,8 @@ }, "property": { "type": "Identifier", - "start": 7505, - "end": 7513, + "start": 7418, + "end": 7426, "loc": { "start": { "line": 200, @@ -11345,9 +11156,9 @@ "computed": false }, "property": { - "type": "StringLiteral", - "start": 7514, - "end": 7533, + "type": "Identifier", + "start": 7427, + "end": 7440, "loc": { "start": { "line": 200, @@ -11355,29 +11166,26 @@ }, "end": { "line": 200, - "column": 37 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 31 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, - "computed": true + "computed": false }, "right": { "type": "Identifier", - "start": 7537, - "end": 7540, + "start": 7443, + "end": 7446, "loc": { "start": { "line": 200, - "column": 41 + "column": 34 }, "end": { "line": 200, - "column": 44 + "column": 37 }, "identifierName": "bor" }, @@ -11393,8 +11201,8 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 7353, - "end": 7468, + "start": 7266, + "end": 7381, "loc": { "start": { "line": 195, @@ -11411,8 +11219,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 7549, - "end": 7634, + "start": 7455, + "end": 7540, "loc": { "start": { "line": 203, @@ -11428,8 +11236,8 @@ }, { "type": "ClassMethod", - "start": 7637, - "end": 7808, + "start": 7543, + "end": 7714, "loc": { "start": { "line": 204, @@ -11444,8 +11252,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7641, - "end": 7653, + "start": 7547, + "end": 7559, "loc": { "start": { "line": 204, @@ -11467,8 +11275,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7656, - "end": 7808, + "start": 7562, + "end": 7714, "loc": { "start": { "line": 204, @@ -11482,8 +11290,8 @@ "body": [ { "type": "IfStatement", - "start": 7662, - "end": 7718, + "start": 7568, + "end": 7624, "loc": { "start": { "line": 205, @@ -11496,8 +11304,8 @@ }, "test": { "type": "CallExpression", - "start": 7666, - "end": 7695, + "start": 7572, + "end": 7601, "loc": { "start": { "line": 205, @@ -11510,8 +11318,8 @@ }, "callee": { "type": "Identifier", - "start": 7666, - "end": 7669, + "start": 7572, + "end": 7575, "loc": { "start": { "line": 205, @@ -11528,8 +11336,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 7670, - "end": 7683, + "start": 7576, + "end": 7589, "loc": { "start": { "line": 205, @@ -11542,8 +11350,8 @@ }, "object": { "type": "ThisExpression", - "start": 7670, - "end": 7674, + "start": 7576, + "end": 7580, "loc": { "start": { "line": 205, @@ -11557,8 +11365,8 @@ }, "property": { "type": "Identifier", - "start": 7675, - "end": 7683, + "start": 7581, + "end": 7589, "loc": { "start": { "line": 205, @@ -11576,8 +11384,8 @@ }, { "type": "StringLiteral", - "start": 7685, - "end": 7694, + "start": 7591, + "end": 7600, "loc": { "start": { "line": 205, @@ -11598,8 +11406,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7697, - "end": 7718, + "start": 7603, + "end": 7624, "loc": { "start": { "line": 205, @@ -11612,8 +11420,8 @@ }, "argument": { "type": "MemberExpression", - "start": 7704, - "end": 7717, + "start": 7610, + "end": 7623, "loc": { "start": { "line": 205, @@ -11626,8 +11434,8 @@ }, "object": { "type": "ThisExpression", - "start": 7704, - "end": 7708, + "start": 7610, + "end": 7614, "loc": { "start": { "line": 205, @@ -11641,8 +11449,8 @@ }, "property": { "type": "Identifier", - "start": 7709, - "end": 7717, + "start": 7615, + "end": 7623, "loc": { "start": { "line": 205, @@ -11663,8 +11471,8 @@ }, { "type": "IfStatement", - "start": 7723, - "end": 7782, + "start": 7629, + "end": 7688, "loc": { "start": { "line": 206, @@ -11677,8 +11485,8 @@ }, "test": { "type": "CallExpression", - "start": 7727, - "end": 7759, + "start": 7633, + "end": 7665, "loc": { "start": { "line": 206, @@ -11691,8 +11499,8 @@ }, "callee": { "type": "Identifier", - "start": 7727, - "end": 7730, + "start": 7633, + "end": 7636, "loc": { "start": { "line": 206, @@ -11709,8 +11517,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 7731, - "end": 7744, + "start": 7637, + "end": 7650, "loc": { "start": { "line": 206, @@ -11723,8 +11531,8 @@ }, "object": { "type": "ThisExpression", - "start": 7731, - "end": 7735, + "start": 7637, + "end": 7641, "loc": { "start": { "line": 206, @@ -11738,8 +11546,8 @@ }, "property": { "type": "Identifier", - "start": 7736, - "end": 7744, + "start": 7642, + "end": 7650, "loc": { "start": { "line": 206, @@ -11757,8 +11565,8 @@ }, { "type": "StringLiteral", - "start": 7746, - "end": 7758, + "start": 7652, + "end": 7664, "loc": { "start": { "line": 206, @@ -11779,8 +11587,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7761, - "end": 7782, + "start": 7667, + "end": 7688, "loc": { "start": { "line": 206, @@ -11793,8 +11601,8 @@ }, "argument": { "type": "MemberExpression", - "start": 7768, - "end": 7781, + "start": 7674, + "end": 7687, "loc": { "start": { "line": 206, @@ -11807,8 +11615,8 @@ }, "object": { "type": "ThisExpression", - "start": 7768, - "end": 7772, + "start": 7674, + "end": 7678, "loc": { "start": { "line": 206, @@ -11822,8 +11630,8 @@ }, "property": { "type": "Identifier", - "start": 7773, - "end": 7781, + "start": 7679, + "end": 7687, "loc": { "start": { "line": 206, @@ -11844,8 +11652,8 @@ }, { "type": "ReturnStatement", - "start": 7787, - "end": 7804, + "start": 7693, + "end": 7710, "loc": { "start": { "line": 207, @@ -11858,8 +11666,8 @@ }, "argument": { "type": "Identifier", - "start": 7794, - "end": 7803, + "start": 7700, + "end": 7709, "loc": { "start": { "line": 207, @@ -11882,8 +11690,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 7549, - "end": 7634, + "start": 7455, + "end": 7540, "loc": { "start": { "line": 203, @@ -11900,8 +11708,8 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7812, - "end": 7852, + "start": 7718, + "end": 7758, "loc": { "start": { "line": 210, @@ -11917,8 +11725,8 @@ }, { "type": "ClassMethod", - "start": 7855, - "end": 8337, + "start": 7761, + "end": 8243, "loc": { "start": { "line": 211, @@ -11933,8 +11741,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7859, - "end": 7864, + "start": 7765, + "end": 7770, "loc": { "start": { "line": 211, @@ -11956,8 +11764,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7867, - "end": 8337, + "start": 7773, + "end": 8243, "loc": { "start": { "line": 211, @@ -11971,8 +11779,8 @@ "body": [ { "type": "IfStatement", - "start": 7930, - "end": 7971, + "start": 7836, + "end": 7877, "loc": { "start": { "line": 213, @@ -11985,8 +11793,8 @@ }, "test": { "type": "UnaryExpression", - "start": 7934, - "end": 7952, + "start": 7840, + "end": 7858, "loc": { "start": { "line": 213, @@ -12001,8 +11809,8 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 7935, - "end": 7952, + "start": 7841, + "end": 7858, "loc": { "start": { "line": 213, @@ -12015,8 +11823,8 @@ }, "object": { "type": "ThisExpression", - "start": 7935, - "end": 7939, + "start": 7841, + "end": 7845, "loc": { "start": { "line": 213, @@ -12031,8 +11839,8 @@ }, "property": { "type": "Identifier", - "start": 7940, - "end": 7952, + "start": 7846, + "end": 7858, "loc": { "start": { "line": 213, @@ -12056,8 +11864,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7954, - "end": 7971, + "start": 7860, + "end": 7877, "loc": { "start": { "line": 213, @@ -12070,8 +11878,8 @@ }, "argument": { "type": "Identifier", - "start": 7961, - "end": 7970, + "start": 7867, + "end": 7876, "loc": { "start": { "line": 213, @@ -12092,8 +11900,8 @@ { "type": "CommentLine", "value": " We can't return anything without an occurrenceID.", - "start": 7873, - "end": 7925, + "start": 7779, + "end": 7831, "loc": { "start": { "line": 212, @@ -12110,8 +11918,8 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7977, - "end": 8054, + "start": 7883, + "end": 7960, "loc": { "start": { "line": 215, @@ -12126,8 +11934,8 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 8059, - "end": 8100, + "start": 7965, + "end": 8006, "loc": { "start": { "line": 216, @@ -12143,8 +11951,8 @@ }, { "type": "IfStatement", - "start": 8105, - "end": 8247, + "start": 8011, + "end": 8153, "loc": { "start": { "line": 217, @@ -12157,8 +11965,8 @@ }, "test": { "type": "MemberExpression", - "start": 8109, - "end": 8126, + "start": 8015, + "end": 8032, "loc": { "start": { "line": 217, @@ -12171,8 +11979,8 @@ }, "object": { "type": "ThisExpression", - "start": 8109, - "end": 8113, + "start": 8015, + "end": 8019, "loc": { "start": { "line": 217, @@ -12187,8 +11995,8 @@ }, "property": { "type": "Identifier", - "start": 8114, - "end": 8126, + "start": 8020, + "end": 8032, "loc": { "start": { "line": 217, @@ -12207,8 +12015,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 8128, - "end": 8247, + "start": 8034, + "end": 8153, "loc": { "start": { "line": 217, @@ -12222,8 +12030,8 @@ "body": [ { "type": "ReturnStatement", - "start": 8136, - "end": 8241, + "start": 8042, + "end": 8147, "loc": { "start": { "line": 218, @@ -12236,8 +12044,8 @@ }, "argument": { "type": "TemplateLiteral", - "start": 8143, - "end": 8240, + "start": 8049, + "end": 8146, "loc": { "start": { "line": 218, @@ -12251,8 +12059,8 @@ "expressions": [ { "type": "MemberExpression", - "start": 8155, - "end": 8172, + "start": 8061, + "end": 8078, "loc": { "start": { "line": 218, @@ -12265,8 +12073,8 @@ }, "object": { "type": "ThisExpression", - "start": 8155, - "end": 8159, + "start": 8061, + "end": 8065, "loc": { "start": { "line": 218, @@ -12280,8 +12088,8 @@ }, "property": { "type": "Identifier", - "start": 8160, - "end": 8172, + "start": 8066, + "end": 8078, "loc": { "start": { "line": 218, @@ -12299,8 +12107,8 @@ }, { "type": "MemberExpression", - "start": 8190, - "end": 8238, + "start": 8096, + "end": 8144, "loc": { "start": { "line": 218, @@ -12313,8 +12121,8 @@ }, "object": { "type": "NewExpression", - "start": 8190, - "end": 8232, + "start": 8096, + "end": 8138, "loc": { "start": { "line": 218, @@ -12327,8 +12135,8 @@ }, "callee": { "type": "Identifier", - "start": 8194, - "end": 8213, + "start": 8100, + "end": 8119, "loc": { "start": { "line": 218, @@ -12345,8 +12153,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 8214, - "end": 8231, + "start": 8120, + "end": 8137, "loc": { "start": { "line": 218, @@ -12359,8 +12167,8 @@ }, "object": { "type": "ThisExpression", - "start": 8214, - "end": 8218, + "start": 8120, + "end": 8124, "loc": { "start": { "line": 218, @@ -12374,8 +12182,8 @@ }, "property": { "type": "Identifier", - "start": 8219, - "end": 8231, + "start": 8125, + "end": 8137, "loc": { "start": { "line": 218, @@ -12395,8 +12203,8 @@ }, "property": { "type": "Identifier", - "start": 8233, - "end": 8238, + "start": 8139, + "end": 8144, "loc": { "start": { "line": 218, @@ -12416,8 +12224,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 8144, - "end": 8153, + "start": 8050, + "end": 8059, "loc": { "start": { "line": 218, @@ -12436,8 +12244,8 @@ }, { "type": "TemplateElement", - "start": 8173, - "end": 8188, + "start": 8079, + "end": 8094, "loc": { "start": { "line": 218, @@ -12456,8 +12264,8 @@ }, { "type": "TemplateElement", - "start": 8239, - "end": 8239, + "start": 8145, + "end": 8145, "loc": { "start": { "line": 218, @@ -12486,8 +12294,8 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7977, - "end": 8054, + "start": 7883, + "end": 7960, "loc": { "start": { "line": 215, @@ -12502,8 +12310,8 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 8059, - "end": 8100, + "start": 7965, + "end": 8006, "loc": { "start": { "line": 216, @@ -12520,8 +12328,8 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 8253, - "end": 8289, + "start": 8159, + "end": 8195, "loc": { "start": { "line": 221, @@ -12537,8 +12345,8 @@ }, { "type": "ReturnStatement", - "start": 8294, - "end": 8333, + "start": 8200, + "end": 8239, "loc": { "start": { "line": 222, @@ -12551,8 +12359,8 @@ }, "argument": { "type": "TemplateLiteral", - "start": 8301, - "end": 8332, + "start": 8207, + "end": 8238, "loc": { "start": { "line": 222, @@ -12566,8 +12374,8 @@ "expressions": [ { "type": "MemberExpression", - "start": 8313, - "end": 8330, + "start": 8219, + "end": 8236, "loc": { "start": { "line": 222, @@ -12580,8 +12388,8 @@ }, "object": { "type": "ThisExpression", - "start": 8313, - "end": 8317, + "start": 8219, + "end": 8223, "loc": { "start": { "line": 222, @@ -12595,8 +12403,8 @@ }, "property": { "type": "Identifier", - "start": 8318, - "end": 8330, + "start": 8224, + "end": 8236, "loc": { "start": { "line": 222, @@ -12616,8 +12424,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 8302, - "end": 8311, + "start": 8208, + "end": 8217, "loc": { "start": { "line": 222, @@ -12637,8 +12445,8 @@ }, { "type": "TemplateElement", - "start": 8331, - "end": 8331, + "start": 8237, + "end": 8237, "loc": { "start": { "line": 222, @@ -12662,8 +12470,8 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 8253, - "end": 8289, + "start": 8159, + "end": 8195, "loc": { "start": { "line": 221, @@ -12685,8 +12493,8 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7812, - "end": 7852, + "start": 7718, + "end": 7758, "loc": { "start": { "line": 210, @@ -12703,8 +12511,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 8341, - "end": 8402, + "start": 8247, + "end": 8308, "loc": { "start": { "line": 225, @@ -12720,8 +12528,8 @@ }, { "type": "ClassMethod", - "start": 8405, - "end": 8834, + "start": 8311, + "end": 8740, "loc": { "start": { "line": 226, @@ -12736,8 +12544,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 8409, - "end": 8424, + "start": 8315, + "end": 8330, "loc": { "start": { "line": 226, @@ -12759,8 +12567,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8427, - "end": 8834, + "start": 8333, + "end": 8740, "loc": { "start": { "line": 226, @@ -12774,8 +12582,8 @@ "body": [ { "type": "IfStatement", - "start": 8487, - "end": 8528, + "start": 8393, + "end": 8434, "loc": { "start": { "line": 228, @@ -12788,8 +12596,8 @@ }, "test": { "type": "UnaryExpression", - "start": 8491, - "end": 8509, + "start": 8397, + "end": 8415, "loc": { "start": { "line": 228, @@ -12804,8 +12612,8 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 8492, - "end": 8509, + "start": 8398, + "end": 8415, "loc": { "start": { "line": 228, @@ -12818,8 +12626,8 @@ }, "object": { "type": "ThisExpression", - "start": 8492, - "end": 8496, + "start": 8398, + "end": 8402, "loc": { "start": { "line": 228, @@ -12834,8 +12642,8 @@ }, "property": { "type": "Identifier", - "start": 8497, - "end": 8509, + "start": 8403, + "end": 8415, "loc": { "start": { "line": 228, @@ -12859,8 +12667,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 8511, - "end": 8528, + "start": 8417, + "end": 8434, "loc": { "start": { "line": 228, @@ -12873,8 +12681,8 @@ }, "argument": { "type": "Identifier", - "start": 8518, - "end": 8527, + "start": 8424, + "end": 8433, "loc": { "start": { "line": 228, @@ -12895,8 +12703,8 @@ { "type": "CommentLine", "value": " We can't do anything without an occurrence ID!", - "start": 8433, - "end": 8482, + "start": 8339, + "end": 8388, "loc": { "start": { "line": 227, @@ -12913,8 +12721,8 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 8534, - "end": 8605, + "start": 8440, + "end": 8511, "loc": { "start": { "line": 230, @@ -12929,8 +12737,8 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 8610, - "end": 8657, + "start": 8516, + "end": 8563, "loc": { "start": { "line": 231, @@ -12945,8 +12753,8 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8663, - "end": 8695, + "start": 8569, + "end": 8601, "loc": { "start": { "line": 233, @@ -12962,8 +12770,8 @@ }, { "type": "ReturnStatement", - "start": 8700, - "end": 8830, + "start": 8606, + "end": 8736, "loc": { "start": { "line": 234, @@ -12976,8 +12784,8 @@ }, "argument": { "type": "ObjectExpression", - "start": 8707, - "end": 8829, + "start": 8613, + "end": 8735, "loc": { "start": { "line": 234, @@ -12991,8 +12799,8 @@ "properties": [ { "type": "ObjectProperty", - "start": 8715, - "end": 8741, + "start": 8621, + "end": 8647, "loc": { "start": { "line": 235, @@ -13008,8 +12816,8 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 8715, - "end": 8722, + "start": 8621, + "end": 8628, "loc": { "start": { "line": 235, @@ -13029,8 +12837,8 @@ }, "value": { "type": "StringLiteral", - "start": 8724, - "end": 8741, + "start": 8630, + "end": 8647, "loc": { "start": { "line": 235, @@ -13051,8 +12859,8 @@ }, { "type": "ObjectProperty", - "start": 8749, - "end": 8787, + "start": 8655, + "end": 8693, "loc": { "start": { "line": 236, @@ -13068,8 +12876,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 8749, - "end": 8759, + "start": 8655, + "end": 8665, "loc": { "start": { "line": 236, @@ -13085,8 +12893,8 @@ }, "value": { "type": "MemberExpression", - "start": 8761, - "end": 8787, + "start": 8667, + "end": 8693, "loc": { "start": { "line": 236, @@ -13099,8 +12907,8 @@ }, "object": { "type": "Identifier", - "start": 8761, - "end": 8769, + "start": 8667, + "end": 8675, "loc": { "start": { "line": 236, @@ -13116,8 +12924,8 @@ }, "property": { "type": "Identifier", - "start": 8770, - "end": 8787, + "start": 8676, + "end": 8693, "loc": { "start": { "line": 236, @@ -13136,8 +12944,8 @@ }, { "type": "ObjectProperty", - "start": 8795, - "end": 8822, + "start": 8701, + "end": 8728, "loc": { "start": { "line": 237, @@ -13153,8 +12961,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 8795, - "end": 8803, + "start": 8701, + "end": 8709, "loc": { "start": { "line": 237, @@ -13170,8 +12978,8 @@ }, "value": { "type": "MemberExpression", - "start": 8805, - "end": 8822, + "start": 8711, + "end": 8728, "loc": { "start": { "line": 237, @@ -13184,8 +12992,8 @@ }, "object": { "type": "ThisExpression", - "start": 8805, - "end": 8809, + "start": 8711, + "end": 8715, "loc": { "start": { "line": 237, @@ -13199,8 +13007,8 @@ }, "property": { "type": "Identifier", - "start": 8810, - "end": 8822, + "start": 8716, + "end": 8728, "loc": { "start": { "line": 237, @@ -13224,8 +13032,8 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 8534, - "end": 8605, + "start": 8440, + "end": 8511, "loc": { "start": { "line": 230, @@ -13240,8 +13048,8 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 8610, - "end": 8657, + "start": 8516, + "end": 8563, "loc": { "start": { "line": 231, @@ -13256,8 +13064,8 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8663, - "end": 8695, + "start": 8569, + "end": 8601, "loc": { "start": { "line": 233, @@ -13278,8 +13086,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 8341, - "end": 8402, + "start": 8247, + "end": 8308, "loc": { "start": { "line": 225, @@ -13301,8 +13109,8 @@ }, { "type": "ExportNamedDeclaration", - "start": 8838, - "end": 8866, + "start": 8744, + "end": 8772, "loc": { "start": { "line": 242, @@ -13317,8 +13125,8 @@ "specifiers": [ { "type": "ExportSpecifier", - "start": 8847, - "end": 8862, + "start": 8753, + "end": 8768, "loc": { "start": { "line": 242, @@ -13331,8 +13139,8 @@ }, "local": { "type": "Identifier", - "start": 8847, - "end": 8862, + "start": 8753, + "end": 8768, "loc": { "start": { "line": 242, @@ -13348,8 +13156,8 @@ }, "exported": { "type": "Identifier", - "start": 8847, - "end": 8862, + "start": 8753, + "end": 8768, "loc": { "start": { "line": 242, @@ -13369,8 +13177,8 @@ }, { "type": "ExportNamedDeclaration", - "start": 8838, - "end": 8866, + "start": 8744, + "end": 8772, "loc": { "start": { "line": 242, @@ -13383,8 +13191,8 @@ }, "declaration": { "type": "ClassDeclaration", - "start": 1089, - "end": 8836, + "start": 1081, + "end": 8742, "loc": { "start": { "line": 24, @@ -13397,8 +13205,8 @@ }, "id": { "type": "Identifier", - "start": 1095, - "end": 1110, + "start": 1087, + "end": 1102, "loc": { "start": { "line": 24, @@ -13416,8 +13224,8 @@ "superClass": null, "body": { "type": "ClassBody", - "start": 1111, - "end": 8836, + "start": 1103, + "end": 8742, "loc": { "start": { "line": 24, @@ -13431,8 +13239,8 @@ "body": [ { "type": "ClassMethod", - "start": 1170, - "end": 1238, + "start": 1162, + "end": 1230, "loc": { "start": { "line": 26, @@ -13447,8 +13255,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1181, - "end": 1194, + "start": 1173, + "end": 1186, "loc": { "start": { "line": 26, @@ -13470,8 +13278,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 1197, - "end": 1238, + "start": 1189, + "end": 1230, "loc": { "start": { "line": 26, @@ -13485,8 +13293,8 @@ "body": [ { "type": "ReturnStatement", - "start": 1203, - "end": 1234, + "start": 1195, + "end": 1226, "loc": { "start": { "line": 27, @@ -13499,8 +13307,8 @@ }, "argument": { "type": "MemberExpression", - "start": 1210, - "end": 1233, + "start": 1202, + "end": 1225, "loc": { "start": { "line": 27, @@ -13513,8 +13321,8 @@ }, "object": { "type": "Identifier", - "start": 1210, - "end": 1218, + "start": 1202, + "end": 1210, "loc": { "start": { "line": 27, @@ -13530,8 +13338,8 @@ }, "property": { "type": "Identifier", - "start": 1219, - "end": 1233, + "start": 1211, + "end": 1225, "loc": { "start": { "line": 27, @@ -13556,8 +13364,8 @@ { "type": "CommentBlock", "value": "* The '@type' of specimens in JSON-LD document. ", - "start": 1115, - "end": 1167, + "start": 1107, + "end": 1159, "loc": { "start": { "line": 25, @@ -13574,8 +13382,8 @@ { "type": "CommentBlock", "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "start": 1234, + "end": 1279, "loc": { "start": { "line": 30, @@ -13591,8 +13399,8 @@ }, { "type": "ClassMethod", - "start": 1290, - "end": 1347, + "start": 1282, + "end": 1339, "loc": { "start": { "line": 31, @@ -13607,8 +13415,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1290, - "end": 1301, + "start": 1282, + "end": 1293, "loc": { "start": { "line": 31, @@ -13631,8 +13439,8 @@ "params": [ { "type": "Identifier", - "start": 1302, - "end": 1310, + "start": 1294, + "end": 1302, "loc": { "start": { "line": 31, @@ -13649,8 +13457,8 @@ ], "body": { "type": "BlockStatement", - "start": 1312, - "end": 1347, + "start": 1304, + "end": 1339, "loc": { "start": { "line": 31, @@ -13664,8 +13472,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 1318, - "end": 1343, + "start": 1310, + "end": 1335, "loc": { "start": { "line": 32, @@ -13678,8 +13486,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 1318, - "end": 1342, + "start": 1310, + "end": 1334, "loc": { "start": { "line": 32, @@ -13693,8 +13501,8 @@ "operator": "=", "left": { "type": "MemberExpression", - "start": 1318, - "end": 1331, + "start": 1310, + "end": 1323, "loc": { "start": { "line": 32, @@ -13707,8 +13515,8 @@ }, "object": { "type": "ThisExpression", - "start": 1318, - "end": 1322, + "start": 1310, + "end": 1314, "loc": { "start": { "line": 32, @@ -13722,8 +13530,8 @@ }, "property": { "type": "Identifier", - "start": 1323, - "end": 1331, + "start": 1315, + "end": 1323, "loc": { "start": { "line": 32, @@ -13741,8 +13549,8 @@ }, "right": { "type": "Identifier", - "start": 1334, - "end": 1342, + "start": 1326, + "end": 1334, "loc": { "start": { "line": 32, @@ -13766,8 +13574,8 @@ { "type": "CommentBlock", "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "start": 1234, + "end": 1279, "loc": { "start": { "line": 30, @@ -13784,8 +13592,8 @@ { "type": "CommentBlock", "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", - "start": 1351, - "end": 1449, + "start": 1343, + "end": 1441, "loc": { "start": { "line": 35, @@ -13801,8 +13609,8 @@ }, { "type": "ClassMethod", - "start": 1452, - "end": 1982, + "start": 1444, + "end": 1968, "loc": { "start": { "line": 39, @@ -13817,8 +13625,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1459, - "end": 1468, + "start": 1451, + "end": 1460, "loc": { "start": { "line": 39, @@ -13840,8 +13648,8 @@ "params": [ { "type": "Identifier", - "start": 1469, - "end": 1477, + "start": 1461, + "end": 1469, "loc": { "start": { "line": 39, @@ -13858,8 +13666,8 @@ ], "body": { "type": "BlockStatement", - "start": 1479, - "end": 1982, + "start": 1471, + "end": 1968, "loc": { "start": { "line": 39, @@ -13873,8 +13681,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 1485, - "end": 1531, + "start": 1477, + "end": 1523, "loc": { "start": { "line": 40, @@ -13888,8 +13696,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 1491, - "end": 1530, + "start": 1483, + "end": 1522, "loc": { "start": { "line": 40, @@ -13902,8 +13710,8 @@ }, "id": { "type": "Identifier", - "start": 1491, - "end": 1498, + "start": 1483, + "end": 1490, "loc": { "start": { "line": 40, @@ -13919,8 +13727,8 @@ }, "init": { "type": "NewExpression", - "start": 1501, - "end": 1530, + "start": 1493, + "end": 1522, "loc": { "start": { "line": 40, @@ -13933,8 +13741,8 @@ }, "callee": { "type": "Identifier", - "start": 1505, - "end": 1520, + "start": 1497, + "end": 1512, "loc": { "start": { "line": 40, @@ -13951,8 +13759,8 @@ "arguments": [ { "type": "Identifier", - "start": 1521, - "end": 1529, + "start": 1513, + "end": 1521, "loc": { "start": { "line": 40, @@ -13974,8 +13782,8 @@ }, { "type": "VariableDeclaration", - "start": 1536, - "end": 1875, + "start": 1528, + "end": 1861, "loc": { "start": { "line": 41, @@ -13989,8 +13797,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 1542, - "end": 1874, + "start": 1534, + "end": 1860, "loc": { "start": { "line": 41, @@ -14003,8 +13811,8 @@ }, "id": { "type": "Identifier", - "start": 1542, - "end": 1560, + "start": 1534, + "end": 1552, "loc": { "start": { "line": 41, @@ -14020,8 +13828,8 @@ }, "init": { "type": "ObjectExpression", - "start": 1563, - "end": 1874, + "start": 1555, + "end": 1860, "loc": { "start": { "line": 41, @@ -14035,8 +13843,8 @@ "properties": [ { "type": "ObjectProperty", - "start": 1571, - "end": 1609, + "start": 1563, + "end": 1601, "loc": { "start": { "line": 42, @@ -14052,8 +13860,8 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 1571, - "end": 1578, + "start": 1563, + "end": 1570, "loc": { "start": { "line": 42, @@ -14072,8 +13880,8 @@ }, "value": { "type": "MemberExpression", - "start": 1580, - "end": 1609, + "start": 1572, + "end": 1601, "loc": { "start": { "line": 42, @@ -14086,8 +13894,8 @@ }, "object": { "type": "Identifier", - "start": 1580, - "end": 1595, + "start": 1572, + "end": 1587, "loc": { "start": { "line": 42, @@ -14103,8 +13911,8 @@ }, "property": { "type": "Identifier", - "start": 1596, - "end": 1609, + "start": 1588, + "end": 1601, "loc": { "start": { "line": 42, @@ -14123,8 +13931,8 @@ }, { "type": "ObjectProperty", - "start": 1617, - "end": 1637, + "start": 1609, + "end": 1629, "loc": { "start": { "line": 43, @@ -14140,8 +13948,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1617, - "end": 1622, + "start": 1609, + "end": 1614, "loc": { "start": { "line": 43, @@ -14157,8 +13965,8 @@ }, "value": { "type": "MemberExpression", - "start": 1624, - "end": 1637, + "start": 1616, + "end": 1629, "loc": { "start": { "line": 43, @@ -14171,8 +13979,8 @@ }, "object": { "type": "Identifier", - "start": 1624, - "end": 1631, + "start": 1616, + "end": 1623, "loc": { "start": { "line": 43, @@ -14188,8 +13996,8 @@ }, "property": { "type": "Identifier", - "start": 1632, - "end": 1637, + "start": 1624, + "end": 1629, "loc": { "start": { "line": 43, @@ -14208,8 +14016,8 @@ }, { "type": "ObjectProperty", - "start": 1645, - "end": 1687, + "start": 1637, + "end": 1673, "loc": { "start": { "line": 44, @@ -14217,16 +14025,16 @@ }, "end": { "line": 44, - "column": 48 + "column": 42 } }, "method": false, "shorthand": false, "computed": false, "key": { - "type": "StringLiteral", - "start": 1645, - "end": 1664, + "type": "Identifier", + "start": 1637, + "end": 1650, "loc": { "start": { "line": 44, @@ -14234,41 +14042,38 @@ }, "end": { "line": 44, - "column": 25 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 19 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, "value": { "type": "MemberExpression", - "start": 1666, - "end": 1687, + "start": 1652, + "end": 1673, "loc": { "start": { "line": 44, - "column": 27 + "column": 21 }, "end": { "line": 44, - "column": 48 + "column": 42 } }, "object": { "type": "Identifier", - "start": 1666, - "end": 1673, + "start": 1652, + "end": 1659, "loc": { "start": { "line": 44, - "column": 27 + "column": 21 }, "end": { "line": 44, - "column": 34 + "column": 28 }, "identifierName": "wrapped" }, @@ -14276,16 +14081,16 @@ }, "property": { "type": "Identifier", - "start": 1674, - "end": 1687, + "start": 1660, + "end": 1673, "loc": { "start": { "line": 44, - "column": 35 + "column": 29 }, "end": { "line": 44, - "column": 48 + "column": 42 }, "identifierName": "basisOfRecord" }, @@ -14296,8 +14101,8 @@ }, { "type": "ObjectProperty", - "start": 1695, - "end": 1729, + "start": 1681, + "end": 1715, "loc": { "start": { "line": 45, @@ -14313,8 +14118,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1695, - "end": 1707, + "start": 1681, + "end": 1693, "loc": { "start": { "line": 45, @@ -14330,8 +14135,8 @@ }, "value": { "type": "MemberExpression", - "start": 1709, - "end": 1729, + "start": 1695, + "end": 1715, "loc": { "start": { "line": 45, @@ -14344,8 +14149,8 @@ }, "object": { "type": "Identifier", - "start": 1709, - "end": 1716, + "start": 1695, + "end": 1702, "loc": { "start": { "line": 45, @@ -14361,8 +14166,8 @@ }, "property": { "type": "Identifier", - "start": 1717, - "end": 1729, + "start": 1703, + "end": 1715, "loc": { "start": { "line": 45, @@ -14381,8 +14186,8 @@ }, { "type": "ObjectProperty", - "start": 1737, - "end": 1773, + "start": 1723, + "end": 1759, "loc": { "start": { "line": 46, @@ -14398,8 +14203,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1737, - "end": 1750, + "start": 1723, + "end": 1736, "loc": { "start": { "line": 46, @@ -14415,8 +14220,8 @@ }, "value": { "type": "MemberExpression", - "start": 1752, - "end": 1773, + "start": 1738, + "end": 1759, "loc": { "start": { "line": 46, @@ -14429,8 +14234,8 @@ }, "object": { "type": "Identifier", - "start": 1752, - "end": 1759, + "start": 1738, + "end": 1745, "loc": { "start": { "line": 46, @@ -14446,8 +14251,8 @@ }, "property": { "type": "Identifier", - "start": 1760, - "end": 1773, + "start": 1746, + "end": 1759, "loc": { "start": { "line": 46, @@ -14466,8 +14271,8 @@ }, { "type": "ObjectProperty", - "start": 1781, - "end": 1821, + "start": 1767, + "end": 1807, "loc": { "start": { "line": 47, @@ -14483,8 +14288,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1781, - "end": 1796, + "start": 1767, + "end": 1782, "loc": { "start": { "line": 47, @@ -14500,8 +14305,8 @@ }, "value": { "type": "MemberExpression", - "start": 1798, - "end": 1821, + "start": 1784, + "end": 1807, "loc": { "start": { "line": 47, @@ -14514,8 +14319,8 @@ }, "object": { "type": "Identifier", - "start": 1798, - "end": 1805, + "start": 1784, + "end": 1791, "loc": { "start": { "line": 47, @@ -14531,8 +14336,8 @@ }, "property": { "type": "Identifier", - "start": 1806, - "end": 1821, + "start": 1792, + "end": 1807, "loc": { "start": { "line": 47, @@ -14551,8 +14356,8 @@ }, { "type": "ObjectProperty", - "start": 1829, - "end": 1867, + "start": 1815, + "end": 1853, "loc": { "start": { "line": 48, @@ -14568,8 +14373,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 1829, - "end": 1843, + "start": 1815, + "end": 1829, "loc": { "start": { "line": 48, @@ -14585,8 +14390,8 @@ }, "value": { "type": "MemberExpression", - "start": 1845, - "end": 1867, + "start": 1831, + "end": 1853, "loc": { "start": { "line": 48, @@ -14599,8 +14404,8 @@ }, "object": { "type": "Identifier", - "start": 1845, - "end": 1852, + "start": 1831, + "end": 1838, "loc": { "start": { "line": 48, @@ -14616,8 +14421,8 @@ }, "property": { "type": "Identifier", - "start": 1853, - "end": 1867, + "start": 1839, + "end": 1853, "loc": { "start": { "line": 48, @@ -14642,8 +14447,8 @@ }, { "type": "IfStatement", - "start": 1880, - "end": 1947, + "start": 1866, + "end": 1933, "loc": { "start": { "line": 50, @@ -14656,8 +14461,8 @@ }, "test": { "type": "BinaryExpression", - "start": 1884, - "end": 1901, + "start": 1870, + "end": 1887, "loc": { "start": { "line": 50, @@ -14670,8 +14475,8 @@ }, "left": { "type": "StringLiteral", - "start": 1884, - "end": 1889, + "start": 1870, + "end": 1875, "loc": { "start": { "line": 50, @@ -14691,8 +14496,8 @@ "operator": "in", "right": { "type": "Identifier", - "start": 1893, - "end": 1901, + "start": 1879, + "end": 1887, "loc": { "start": { "line": 50, @@ -14709,8 +14514,8 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 1903, - "end": 1947, + "start": 1889, + "end": 1933, "loc": { "start": { "line": 50, @@ -14723,8 +14528,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 1903, - "end": 1946, + "start": 1889, + "end": 1932, "loc": { "start": { "line": 50, @@ -14738,8 +14543,8 @@ "operator": "=", "left": { "type": "MemberExpression", - "start": 1903, - "end": 1928, + "start": 1889, + "end": 1914, "loc": { "start": { "line": 50, @@ -14752,8 +14557,8 @@ }, "object": { "type": "Identifier", - "start": 1903, - "end": 1921, + "start": 1889, + "end": 1907, "loc": { "start": { "line": 50, @@ -14769,8 +14574,8 @@ }, "property": { "type": "StringLiteral", - "start": 1922, - "end": 1927, + "start": 1908, + "end": 1913, "loc": { "start": { "line": 50, @@ -14791,8 +14596,8 @@ }, "right": { "type": "MemberExpression", - "start": 1931, - "end": 1946, + "start": 1917, + "end": 1932, "loc": { "start": { "line": 50, @@ -14805,8 +14610,8 @@ }, "object": { "type": "Identifier", - "start": 1931, - "end": 1939, + "start": 1917, + "end": 1925, "loc": { "start": { "line": 50, @@ -14822,8 +14627,8 @@ }, "property": { "type": "StringLiteral", - "start": 1940, - "end": 1945, + "start": 1926, + "end": 1931, "loc": { "start": { "line": 50, @@ -14848,8 +14653,8 @@ }, { "type": "ReturnStatement", - "start": 1952, - "end": 1978, + "start": 1938, + "end": 1964, "loc": { "start": { "line": 51, @@ -14862,8 +14667,8 @@ }, "argument": { "type": "Identifier", - "start": 1959, - "end": 1977, + "start": 1945, + "end": 1963, "loc": { "start": { "line": 51, @@ -14886,8 +14691,8 @@ { "type": "CommentBlock", "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", - "start": 1351, - "end": 1449, + "start": 1343, + "end": 1441, "loc": { "start": { "line": 35, @@ -14904,8 +14709,8 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1986, - "end": 2267, + "start": 1972, + "end": 2253, "loc": { "start": { "line": 54, @@ -14921,8 +14726,8 @@ }, { "type": "ClassMethod", - "start": 2270, - "end": 4105, + "start": 2256, + "end": 4073, "loc": { "start": { "line": 60, @@ -14937,8 +14742,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 2277, - "end": 2293, + "start": 2263, + "end": 2279, "loc": { "start": { "line": 60, @@ -14960,8 +14765,8 @@ "params": [ { "type": "Identifier", - "start": 2294, - "end": 2306, + "start": 2280, + "end": 2292, "loc": { "start": { "line": 60, @@ -14977,8 +14782,8 @@ }, { "type": "AssignmentPattern", - "start": 2308, - "end": 2343, + "start": 2294, + "end": 2329, "loc": { "start": { "line": 60, @@ -14991,8 +14796,8 @@ }, "left": { "type": "Identifier", - "start": 2308, - "end": 2321, + "start": 2294, + "end": 2307, "loc": { "start": { "line": 60, @@ -15008,8 +14813,8 @@ }, "right": { "type": "StringLiteral", - "start": 2324, - "end": 2343, + "start": 2310, + "end": 2329, "loc": { "start": { "line": 60, @@ -15030,8 +14835,8 @@ ], "body": { "type": "BlockStatement", - "start": 2345, - "end": 4105, + "start": 2331, + "end": 4073, "loc": { "start": { "line": 60, @@ -15045,8 +14850,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 2417, - "end": 2444, + "start": 2403, + "end": 2430, "loc": { "start": { "line": 62, @@ -15060,8 +14865,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 2421, - "end": 2443, + "start": 2407, + "end": 2429, "loc": { "start": { "line": 62, @@ -15074,8 +14879,8 @@ }, "id": { "type": "Identifier", - "start": 2421, - "end": 2428, + "start": 2407, + "end": 2414, "loc": { "start": { "line": 62, @@ -15092,8 +14897,8 @@ }, "init": { "type": "Identifier", - "start": 2431, - "end": 2443, + "start": 2417, + "end": 2429, "loc": { "start": { "line": 62, @@ -15115,8 +14920,8 @@ { "type": "CommentLine", "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 2351, - "end": 2412, + "start": 2337, + "end": 2398, "loc": { "start": { "line": 61, @@ -15132,8 +14937,8 @@ }, { "type": "IfStatement", - "start": 2449, - "end": 2518, + "start": 2435, + "end": 2507, "loc": { "start": { "line": 63, @@ -15141,13 +14946,13 @@ }, "end": { "line": 63, - "column": 73 + "column": 76 } }, "test": { "type": "CallExpression", - "start": 2453, - "end": 2487, + "start": 2439, + "end": 2473, "loc": { "start": { "line": 63, @@ -15160,8 +14965,8 @@ }, "callee": { "type": "MemberExpression", - "start": 2453, - "end": 2471, + "start": 2439, + "end": 2457, "loc": { "start": { "line": 63, @@ -15174,8 +14979,8 @@ }, "object": { "type": "Identifier", - "start": 2453, - "end": 2460, + "start": 2439, + "end": 2446, "loc": { "start": { "line": 63, @@ -15191,8 +14996,8 @@ }, "property": { "type": "Identifier", - "start": 2461, - "end": 2471, + "start": 2447, + "end": 2457, "loc": { "start": { "line": 63, @@ -15211,8 +15016,8 @@ "arguments": [ { "type": "StringLiteral", - "start": 2472, - "end": 2486, + "start": 2458, + "end": 2472, "loc": { "start": { "line": 63, @@ -15233,8 +15038,8 @@ }, "consequent": { "type": "ExpressionStatement", - "start": 2489, - "end": 2518, + "start": 2475, + "end": 2507, "loc": { "start": { "line": 63, @@ -15242,13 +15047,13 @@ }, "end": { "line": 63, - "column": 73 + "column": 76 } }, "expression": { "type": "AssignmentExpression", - "start": 2489, - "end": 2517, + "start": 2475, + "end": 2506, "loc": { "start": { "line": 63, @@ -15256,14 +15061,14 @@ }, "end": { "line": 63, - "column": 72 + "column": 75 } }, "operator": "=", "left": { "type": "Identifier", - "start": 2489, - "end": 2496, + "start": 2475, + "end": 2482, "loc": { "start": { "line": 63, @@ -15279,8 +15084,8 @@ }, "right": { "type": "CallExpression", - "start": 2499, - "end": 2517, + "start": 2485, + "end": 2506, "loc": { "start": { "line": 63, @@ -15288,13 +15093,13 @@ }, "end": { "line": 63, - "column": 72 + "column": 75 } }, "callee": { "type": "MemberExpression", - "start": 2499, - "end": 2513, + "start": 2485, + "end": 2502, "loc": { "start": { "line": 63, @@ -15302,13 +15107,13 @@ }, "end": { "line": 63, - "column": 68 + "column": 71 } }, "object": { "type": "Identifier", - "start": 2499, - "end": 2506, + "start": 2485, + "end": 2492, "loc": { "start": { "line": 63, @@ -15324,8 +15129,8 @@ }, "property": { "type": "Identifier", - "start": 2507, - "end": 2513, + "start": 2493, + "end": 2502, "loc": { "start": { "line": 63, @@ -15333,27 +15138,27 @@ }, "end": { "line": 63, - "column": 68 + "column": 71 }, - "identifierName": "substr" + "identifierName": "substring" }, - "name": "substr" + "name": "substring" }, "computed": false }, "arguments": [ { "type": "NumericLiteral", - "start": 2514, - "end": 2516, + "start": 2503, + "end": 2505, "loc": { "start": { "line": 63, - "column": 69 + "column": 72 }, "end": { "line": 63, - "column": 71 + "column": 74 } }, "extra": { @@ -15372,8 +15177,8 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 2524, - "end": 2548, + "start": 2513, + "end": 2537, "loc": { "start": { "line": 65, @@ -15389,8 +15194,8 @@ }, { "type": "VariableDeclaration", - "start": 2553, - "end": 2695, + "start": 2542, + "end": 2663, "loc": { "start": { "line": 66, @@ -15404,8 +15209,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 2559, - "end": 2694, + "start": 2548, + "end": 2662, "loc": { "start": { "line": 66, @@ -15418,8 +15223,8 @@ }, "id": { "type": "Identifier", - "start": 2559, - "end": 2567, + "start": 2548, + "end": 2556, "loc": { "start": { "line": 66, @@ -15436,8 +15241,8 @@ }, "init": { "type": "ObjectExpression", - "start": 2570, - "end": 2694, + "start": 2559, + "end": 2662, "loc": { "start": { "line": 66, @@ -15451,8 +15256,8 @@ "properties": [ { "type": "ObjectProperty", - "start": 2578, - "end": 2616, + "start": 2567, + "end": 2605, "loc": { "start": { "line": 67, @@ -15468,8 +15273,8 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 2578, - "end": 2585, + "start": 2567, + "end": 2574, "loc": { "start": { "line": 67, @@ -15488,8 +15293,8 @@ }, "value": { "type": "MemberExpression", - "start": 2587, - "end": 2616, + "start": 2576, + "end": 2605, "loc": { "start": { "line": 67, @@ -15502,8 +15307,8 @@ }, "object": { "type": "Identifier", - "start": 2587, - "end": 2602, + "start": 2576, + "end": 2591, "loc": { "start": { "line": 67, @@ -15519,8 +15324,8 @@ }, "property": { "type": "Identifier", - "start": 2603, - "end": 2616, + "start": 2592, + "end": 2605, "loc": { "start": { "line": 67, @@ -15539,8 +15344,8 @@ }, { "type": "ObjectProperty", - "start": 2624, - "end": 2658, + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, @@ -15548,16 +15353,16 @@ }, "end": { "line": 68, - "column": 40 + "column": 19 } }, "method": false, - "shorthand": false, + "shorthand": true, "computed": false, "key": { - "type": "StringLiteral", - "start": 2624, - "end": 2643, + "type": "Identifier", + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, @@ -15565,37 +15370,37 @@ }, "end": { "line": 68, - "column": 25 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 19 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, "value": { "type": "Identifier", - "start": 2645, - "end": 2658, + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, - "column": 27 + "column": 6 }, "end": { "line": 68, - "column": 40 + "column": 19 }, "identifierName": "basisOfRecord" }, "name": "basisOfRecord" + }, + "extra": { + "shorthand": true } }, { "type": "ObjectProperty", - "start": 2666, - "end": 2687, + "start": 2634, + "end": 2655, "loc": { "start": { "line": 69, @@ -15611,8 +15416,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 2666, - "end": 2678, + "start": 2634, + "end": 2646, "loc": { "start": { "line": 69, @@ -15628,8 +15433,8 @@ }, "value": { "type": "Identifier", - "start": 2680, - "end": 2687, + "start": 2648, + "end": 2655, "loc": { "start": { "line": 69, @@ -15654,8 +15459,8 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 2524, - "end": 2548, + "start": 2513, + "end": 2537, "loc": { "start": { "line": 65, @@ -15672,8 +15477,8 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2701, - "end": 2774, + "start": 2669, + "end": 2742, "loc": { "start": { "line": 72, @@ -15688,8 +15493,8 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2779, - "end": 2834, + "start": 2747, + "end": 2802, "loc": { "start": { "line": 73, @@ -15705,8 +15510,8 @@ }, { "type": "VariableDeclaration", - "start": 2839, - "end": 2971, + "start": 2807, + "end": 2939, "loc": { "start": { "line": 74, @@ -15720,8 +15525,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 2845, - "end": 2970, + "start": 2813, + "end": 2938, "loc": { "start": { "line": 74, @@ -15734,8 +15539,8 @@ }, "id": { "type": "Identifier", - "start": 2845, - "end": 2861, + "start": 2813, + "end": 2829, "loc": { "start": { "line": 74, @@ -15752,8 +15557,8 @@ }, "init": { "type": "ArrayExpression", - "start": 2864, - "end": 2970, + "start": 2832, + "end": 2938, "loc": { "start": { "line": 74, @@ -15767,8 +15572,8 @@ "elements": [ { "type": "StringLiteral", - "start": 2872, - "end": 2881, + "start": 2840, + "end": 2849, "loc": { "start": { "line": 75, @@ -15787,8 +15592,8 @@ }, { "type": "StringLiteral", - "start": 2889, - "end": 2899, + "start": 2857, + "end": 2867, "loc": { "start": { "line": 76, @@ -15807,8 +15612,8 @@ }, { "type": "StringLiteral", - "start": 2907, - "end": 2915, + "start": 2875, + "end": 2883, "loc": { "start": { "line": 77, @@ -15827,8 +15632,8 @@ }, { "type": "StringLiteral", - "start": 2923, - "end": 2932, + "start": 2891, + "end": 2900, "loc": { "start": { "line": 78, @@ -15847,8 +15652,8 @@ }, { "type": "StringLiteral", - "start": 2940, - "end": 2949, + "start": 2908, + "end": 2917, "loc": { "start": { "line": 79, @@ -15867,8 +15672,8 @@ }, { "type": "StringLiteral", - "start": 2957, - "end": 2963, + "start": 2925, + "end": 2931, "loc": { "start": { "line": 80, @@ -15895,8 +15700,8 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2701, - "end": 2774, + "start": 2669, + "end": 2742, "loc": { "start": { "line": 72, @@ -15911,8 +15716,8 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2779, - "end": 2834, + "start": 2747, + "end": 2802, "loc": { "start": { "line": 73, @@ -15928,8 +15733,8 @@ }, { "type": "IfStatement", - "start": 2976, - "end": 3098, + "start": 2944, + "end": 3066, "loc": { "start": { "line": 82, @@ -15942,8 +15747,8 @@ }, "test": { "type": "BinaryExpression", - "start": 2980, - "end": 3066, + "start": 2948, + "end": 3034, "loc": { "start": { "line": 82, @@ -15956,8 +15761,8 @@ }, "left": { "type": "MemberExpression", - "start": 2980, - "end": 3062, + "start": 2948, + "end": 3030, "loc": { "start": { "line": 82, @@ -15970,8 +15775,8 @@ }, "object": { "type": "CallExpression", - "start": 2980, - "end": 3055, + "start": 2948, + "end": 3023, "loc": { "start": { "line": 82, @@ -15984,8 +15789,8 @@ }, "callee": { "type": "MemberExpression", - "start": 2980, - "end": 3003, + "start": 2948, + "end": 2971, "loc": { "start": { "line": 82, @@ -15998,8 +15803,8 @@ }, "object": { "type": "Identifier", - "start": 2980, - "end": 2996, + "start": 2948, + "end": 2964, "loc": { "start": { "line": 82, @@ -16015,8 +15820,8 @@ }, "property": { "type": "Identifier", - "start": 2997, - "end": 3003, + "start": 2965, + "end": 2971, "loc": { "start": { "line": 82, @@ -16035,8 +15840,8 @@ "arguments": [ { "type": "ArrowFunctionExpression", - "start": 3004, - "end": 3054, + "start": 2972, + "end": 3022, "loc": { "start": { "line": 82, @@ -16054,8 +15859,8 @@ "params": [ { "type": "Identifier", - "start": 3004, - "end": 3010, + "start": 2972, + "end": 2978, "loc": { "start": { "line": 82, @@ -16072,8 +15877,8 @@ ], "body": { "type": "CallExpression", - "start": 3014, - "end": 3054, + "start": 2982, + "end": 3022, "loc": { "start": { "line": 82, @@ -16086,8 +15891,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3014, - "end": 3046, + "start": 2982, + "end": 3014, "loc": { "start": { "line": 82, @@ -16100,8 +15905,8 @@ }, "object": { "type": "CallExpression", - "start": 3014, - "end": 3035, + "start": 2982, + "end": 3003, "loc": { "start": { "line": 82, @@ -16114,8 +15919,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3014, - "end": 3033, + "start": 2982, + "end": 3001, "loc": { "start": { "line": 82, @@ -16128,8 +15933,8 @@ }, "object": { "type": "Identifier", - "start": 3014, - "end": 3021, + "start": 2982, + "end": 2989, "loc": { "start": { "line": 82, @@ -16145,8 +15950,8 @@ }, "property": { "type": "Identifier", - "start": 3022, - "end": 3033, + "start": 2990, + "end": 3001, "loc": { "start": { "line": 82, @@ -16166,8 +15971,8 @@ }, "property": { "type": "Identifier", - "start": 3036, - "end": 3046, + "start": 3004, + "end": 3014, "loc": { "start": { "line": 82, @@ -16186,8 +15991,8 @@ "arguments": [ { "type": "Identifier", - "start": 3047, - "end": 3053, + "start": 3015, + "end": 3021, "loc": { "start": { "line": 82, @@ -16208,8 +16013,8 @@ }, "property": { "type": "Identifier", - "start": 3056, - "end": 3062, + "start": 3024, + "end": 3030, "loc": { "start": { "line": 82, @@ -16228,8 +16033,8 @@ "operator": ">", "right": { "type": "NumericLiteral", - "start": 3065, - "end": 3066, + "start": 3033, + "end": 3034, "loc": { "start": { "line": 82, @@ -16249,8 +16054,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3068, - "end": 3098, + "start": 3036, + "end": 3066, "loc": { "start": { "line": 82, @@ -16264,8 +16069,8 @@ "body": [ { "type": "ReturnStatement", - "start": 3076, - "end": 3092, + "start": 3044, + "end": 3060, "loc": { "start": { "line": 83, @@ -16278,8 +16083,8 @@ }, "argument": { "type": "Identifier", - "start": 3083, - "end": 3091, + "start": 3051, + "end": 3059, "loc": { "start": { "line": 83, @@ -16303,8 +16108,8 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 3104, - "end": 3173, + "start": 3072, + "end": 3141, "loc": { "start": { "line": 86, @@ -16320,8 +16125,8 @@ }, { "type": "IfStatement", - "start": 3178, - "end": 3338, + "start": 3146, + "end": 3306, "loc": { "start": { "line": 87, @@ -16334,8 +16139,8 @@ }, "test": { "type": "CallExpression", - "start": 3182, - "end": 3248, + "start": 3150, + "end": 3216, "loc": { "start": { "line": 87, @@ -16348,8 +16153,8 @@ }, "callee": { "type": "MemberExpression", - 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"start": 3104, - "end": 3173, + "start": 3072, + "end": 3141, "loc": { "start": { "line": 86, @@ -16600,8 +16405,8 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 3344, - "end": 3429, + "start": 3312, + "end": 3397, "loc": { "start": { "line": 91, @@ -16617,8 +16422,8 @@ }, { "type": "VariableDeclaration", - "start": 3434, - "end": 3467, + "start": 3402, + "end": 3435, "loc": { "start": { "line": 92, @@ -16632,8 +16437,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 3440, - "end": 3466, + "start": 3408, + "end": 3434, "loc": { "start": { "line": 92, @@ -16646,8 +16451,8 @@ }, "id": { "type": "Identifier", - "start": 3440, - "end": 3445, + "start": 3408, + "end": 3413, "loc": { "start": { "line": 92, @@ -16664,8 +16469,8 @@ }, "init": { "type": "CallExpression", - "start": 3448, - "end": 3466, + "start": 3416, + "end": 3434, "loc": { "start": { "line": 92, @@ -16678,8 +16483,8 @@ }, "callee": { "type": "MemberExpression", - "start": 3448, - "end": 3461, + "start": 3416, + "end": 3429, "loc": { "start": { "line": 92, @@ -16692,8 +16497,8 @@ }, "object": { "type": "Identifier", - "start": 3448, - "end": 3455, + "start": 3416, + "end": 3423, "loc": { "start": { "line": 92, @@ -16709,8 +16514,8 @@ }, "property": { "type": "Identifier", - "start": 3456, - "end": 3461, + "start": 3424, + "end": 3429, "loc": { "start": { "line": 92, @@ -16729,8 +16534,8 @@ "arguments": [ { "type": "RegExpLiteral", - "start": 3462, - "end": 3465, + "start": 3430, + "end": 3433, "loc": { "start": { "line": 92, @@ -16757,8 +16562,8 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 3344, - "end": 3429, + "start": 3312, + "end": 3397, "loc": { "start": { "line": 91, @@ -16774,8 +16579,8 @@ }, { "type": "IfStatement", - "start": 3472, - "end": 3997, + "start": 3440, + "end": 3965, "loc": { "start": { "line": 93, @@ -16788,8 +16593,8 @@ }, "test": { "type": "BinaryExpression", - 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"start": 3597, - "end": 3629, + "start": 3565, + "end": 3597, "loc": { "start": { "line": 96, @@ -16918,8 +16723,8 @@ "operator": "=", "left": { "type": "ArrayPattern", - "start": 3597, - "end": 3621, + "start": 3565, + "end": 3589, "loc": { "start": { "line": 96, @@ -16933,8 +16738,8 @@ "elements": [ { "type": "MemberExpression", - "start": 3598, - "end": 3620, + "start": 3566, + "end": 3588, "loc": { "start": { "line": 96, @@ -16947,8 +16752,8 @@ }, "object": { "type": "Identifier", - "start": 3598, - "end": 3606, + "start": 3566, + "end": 3574, "loc": { "start": { "line": 96, @@ -16965,8 +16770,8 @@ }, "property": { "type": "Identifier", - "start": 3607, - "end": 3620, + "start": 3575, + "end": 3588, "loc": { "start": { "line": 96, @@ -16988,8 +16793,8 @@ }, "right": { "type": "Identifier", - "start": 3624, - "end": 3629, + "start": 3592, + "end": 3597, "loc": { "start": { "line": 96, @@ -17009,8 +16814,8 @@ { "type": "CommentLine", "value": " specimen.institutionCode = undefined;", - "start": 3504, - "end": 3544, + "start": 3472, + "end": 3512, "loc": { "start": { "line": 94, @@ -17025,8 +16830,8 @@ { "type": "CommentLine", "value": " specimen.collectionCode = undefined;", - "start": 3551, - "end": 3590, + "start": 3519, + "end": 3558, "loc": { "start": { "line": 95, @@ -17045,8 +16850,8 @@ }, "alternate": { "type": "IfStatement", - "start": 3642, - "end": 3997, + "start": 3610, + "end": 3965, "loc": { "start": { "line": 97, @@ -17059,8 +16864,8 @@ }, "test": { "type": "BinaryExpression", - "start": 3646, - "end": 3664, + "start": 3614, + "end": 3632, "loc": { "start": { "line": 97, @@ -17073,8 +16878,8 @@ }, "left": { "type": "MemberExpression", - "start": 3646, - "end": 3658, + "start": 3614, + "end": 3626, "loc": { "start": { "line": 97, @@ -17087,8 +16892,8 @@ }, "object": { "type": "Identifier", - "start": 3646, - "end": 3651, + "start": 3614, + "end": 3619, "loc": { "start": { "line": 97, @@ -17104,8 +16909,8 @@ }, "property": { "type": "Identifier", - "start": 3652, - "end": 3658, + "start": 3620, + "end": 3626, "loc": { "start": { "line": 97, @@ -17124,8 +16929,8 @@ "operator": "===", "right": { "type": "NumericLiteral", - "start": 3663, - "end": 3664, + "start": 3631, + "end": 3632, "loc": { "start": { "line": 97, @@ -17145,8 +16950,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3666, - "end": 3739, + "start": 3634, + "end": 3707, "loc": { "start": { "line": 97, @@ -17160,8 +16965,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 3674, - "end": 3733, + "start": 3642, + "end": 3701, "loc": { "start": { "line": 98, @@ -17174,8 +16979,8 @@ }, "expression": { "type": "AssignmentExpression", - "start": 3674, - "end": 3732, + "start": 3642, + "end": 3700, "loc": { "start": { "line": 98, @@ -17189,8 +16994,8 @@ "operator": "=", "left": { "type": "ArrayPattern", - "start": 3674, - "end": 3724, + "start": 3642, + "end": 3692, "loc": { "start": { "line": 98, @@ -17204,8 +17009,8 @@ "elements": [ { "type": "MemberExpression", - "start": 3675, - 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"start": 3745, - "end": 3997, + "start": 3713, + "end": 3965, "loc": { "start": { "line": 99, @@ -17342,8 +17147,8 @@ }, "test": { "type": "BinaryExpression", - "start": 3749, - "end": 3766, + "start": 3717, + "end": 3734, "loc": { "start": { "line": 99, @@ -17356,8 +17161,8 @@ }, "left": { "type": "MemberExpression", - "start": 3749, - "end": 3761, + "start": 3717, + "end": 3729, "loc": { "start": { "line": 99, @@ -17370,8 +17175,8 @@ }, "object": { "type": "Identifier", - "start": 3749, - "end": 3754, + "start": 3717, + "end": 3722, "loc": { "start": { "line": 99, @@ -17387,8 +17192,8 @@ }, "property": { "type": "Identifier", - "start": 3755, - "end": 3761, + "start": 3723, + "end": 3729, "loc": { "start": { "line": 99, @@ -17407,8 +17212,8 @@ "operator": ">=", "right": { "type": "NumericLiteral", - "start": 3765, - "end": 3766, + "start": 3733, + "end": 3734, "loc": { "start": { "line": 99, @@ -17428,8 +17233,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 3768, - "end": 3997, + "start": 3736, + "end": 3965, "loc": { "start": { "line": 99, @@ -17443,8 +17248,8 @@ "body": [ { "type": "VariableDeclaration", - 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"start": 3851, - "end": 3931, + "start": 3819, + "end": 3899, "loc": { "start": { "line": 101, @@ -17556,8 +17361,8 @@ "operator": "=", "left": { "type": "ArrayPattern", - "start": 3851, - "end": 3923, + "start": 3819, + "end": 3891, "loc": { "start": { "line": 101, @@ -17571,8 +17376,8 @@ "elements": [ { "type": "MemberExpression", - "start": 3852, - "end": 3876, + "start": 3820, + "end": 3844, "loc": { "start": { "line": 101, @@ -17585,8 +17390,8 @@ }, "object": { "type": "Identifier", - "start": 3852, - "end": 3860, + "start": 3820, + "end": 3828, "loc": { "start": { "line": 101, @@ -17603,8 +17408,8 @@ }, "property": { "type": "Identifier", - "start": 3861, - "end": 3876, + "start": 3829, + "end": 3844, "loc": { "start": { "line": 101, @@ -17623,8 +17428,8 @@ }, { "type": "MemberExpression", - "start": 3878, - "end": 3901, + "start": 3846, + "end": 3869, "loc": { "start": { "line": 101, @@ -17637,8 +17442,8 @@ }, "object": { "type": "Identifier", - "start": 3878, - "end": 3886, + "start": 3846, + "end": 3854, "loc": { "start": { "line": 101, @@ -17654,8 +17459,8 @@ }, "property": { "type": "Identifier", - 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The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1986, - "end": 2267, + "start": 1972, + "end": 2253, "loc": { "start": { "line": 54, @@ -18113,8 +17918,8 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 4109, - "end": 4157, + "start": 4077, + "end": 4125, "loc": { "start": { "line": 109, @@ -18130,8 +17935,8 @@ }, { "type": "ClassMethod", - "start": 4160, - "end": 4675, + "start": 4128, + "end": 4643, "loc": { "start": { "line": 112, @@ -18146,8 +17951,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 4164, - "end": 4177, + "start": 4132, + "end": 4145, "loc": { "start": { "line": 112, @@ -18169,8 +17974,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4180, - "end": 4675, + "start": 4148, + "end": 4643, "loc": { "start": { "line": 112, @@ -18184,8 +17989,8 @@ "body": [ { "type": "IfStatement", - 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"start": 4186, - "end": 4248, + "start": 4154, + "end": 4216, "loc": { "start": { "line": 113, @@ -18420,8 +18225,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 4335, - "end": 4406, + "start": 4303, + "end": 4374, "loc": { "start": { "line": 116, @@ -18436,8 +18241,8 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 4411, - "end": 4439, + "start": 4379, + "end": 4407, "loc": { "start": { "line": 117, @@ -18453,8 +18258,8 @@ }, { "type": "IfStatement", - "start": 4444, - "end": 4649, + "start": 4412, + "end": 4617, "loc": { "start": { "line": 118, @@ -18467,8 +18272,8 @@ }, "test": { "type": "CallExpression", - "start": 4448, - "end": 4482, + "start": 4416, + "end": 4450, "loc": { "start": { "line": 118, @@ -18481,8 +18286,8 @@ }, "callee": { "type": "Identifier", - "start": 4448, - "end": 4451, + "start": 4416, + "end": 4419, "loc": { "start": { "line": 118, @@ -18500,8 +18305,8 @@ "arguments": [ { "type": "MemberExpression", - 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"start": 4498, - "end": 4506, + "start": 4466, + "end": 4474, "loc": { "start": { "line": 119, @@ -18632,8 +18437,8 @@ }, "init": { "type": "CallExpression", - "start": 4509, - "end": 4569, + "start": 4477, + "end": 4537, "loc": { "start": { "line": 119, @@ -18646,8 +18451,8 @@ }, "callee": { "type": "MemberExpression", - "start": 4509, - "end": 4541, + "start": 4477, + "end": 4509, "loc": { "start": { "line": 119, @@ -18660,8 +18465,8 @@ }, "object": { "type": "Identifier", - "start": 4509, - "end": 4524, + "start": 4477, + "end": 4492, "loc": { "start": { "line": 119, @@ -18677,8 +18482,8 @@ }, "property": { "type": "Identifier", - "start": 4525, - "end": 4541, + "start": 4493, + "end": 4509, "loc": { "start": { "line": 119, @@ -18697,8 +18502,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 4542, - "end": 4568, + "start": 4510, + "end": 4536, "loc": { "start": { "line": 119, @@ -18711,8 +18516,8 @@ }, "object": { "type": "MemberExpression", - "start": 4542, - "end": 4555, + "start": 4510, + "end": 4523, "loc": { "start": { "line": 119, @@ -18725,8 +18530,8 @@ }, "object": { "type": "ThisExpression", - "start": 4542, - "end": 4546, + "start": 4510, + "end": 4514, "loc": { "start": { "line": 119, @@ -18740,8 +18545,8 @@ }, "property": { "type": "Identifier", - "start": 4547, - "end": 4555, + "start": 4515, + "end": 4523, "loc": { "start": { "line": 119, @@ -18759,8 +18564,8 @@ }, "property": { "type": "Identifier", - "start": 4556, - "end": 4568, + "start": 4524, + "end": 4536, "loc": { "start": { "line": 119, @@ -18784,8 +18589,8 @@ }, { "type": "IfStatement", - "start": 4577, - "end": 4643, + "start": 4545, + "end": 4611, "loc": { "start": { "line": 120, @@ -18798,8 +18603,8 @@ }, "test": { "type": "CallExpression", - "start": 4581, - "end": 4611, + "start": 4549, + "end": 4579, "loc": { "start": { "line": 120, @@ -18812,8 +18617,8 @@ }, "callee": { "type": "Identifier", - "start": 4581, - "end": 4584, + "start": 4549, + "end": 4552, "loc": { "start": { "line": 120, @@ -18830,8 +18635,8 @@ "arguments": [ { "type": "Identifier", - "start": 4585, - "end": 4593, + "start": 4553, + "end": 4561, "loc": { "start": { "line": 120, @@ -18847,8 +18652,8 @@ }, { "type": "StringLiteral", - "start": 4595, - "end": 4610, + "start": 4563, + "end": 4578, "loc": { "start": { "line": 120, @@ -18869,8 +18674,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4613, - "end": 4643, + "start": 4581, + "end": 4611, "loc": { "start": { "line": 120, @@ -18883,8 +18688,8 @@ }, "argument": { "type": "MemberExpression", - "start": 4620, - "end": 4642, + "start": 4588, + "end": 4610, "loc": { "start": { "line": 120, @@ -18897,8 +18702,8 @@ }, "object": { "type": "Identifier", - "start": 4620, - "end": 4628, + "start": 4588, + "end": 4596, "loc": { "start": { "line": 120, @@ -18914,8 +18719,8 @@ }, "property": { "type": "Identifier", - "start": 4629, - "end": 4642, + "start": 4597, + "end": 4610, "loc": { "start": { "line": 120, @@ -18942,8 +18747,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 4335, - "end": 4406, + "start": 4303, + "end": 4374, "loc": { "start": { "line": 116, @@ -18958,8 +18763,8 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 4411, - "end": 4439, + "start": 4379, + "end": 4407, "loc": { "start": { "line": 117, @@ -18975,8 +18780,8 @@ }, { "type": "ReturnStatement", - "start": 4654, - "end": 4671, + "start": 4622, + "end": 4639, "loc": { "start": { "line": 122, @@ -18989,8 +18794,8 @@ }, "argument": { "type": "Identifier", - "start": 4661, - "end": 4670, + "start": 4629, + "end": 4638, "loc": { "start": { "line": 122, @@ -19013,8 +18818,8 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 4109, - "end": 4157, + "start": 4077, + "end": 4125, "loc": { "start": { "line": 109, @@ -19031,8 +18836,8 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4679, - "end": 4729, + "start": 4647, + "end": 4697, "loc": { "start": { "line": 125, @@ -19048,8 +18853,8 @@ }, { "type": "ClassMethod", - "start": 4732, - "end": 5259, + "start": 4700, + "end": 5227, "loc": { "start": { "line": 128, @@ -19064,8 +18869,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 4736, - "end": 4751, + "start": 4704, + "end": 4719, "loc": { "start": { "line": 128, @@ -19087,8 +18892,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 4754, - "end": 5259, + "start": 4722, + "end": 5227, "loc": { "start": { "line": 128, @@ -19102,8 +18907,8 @@ "body": [ { "type": "IfStatement", - "start": 4829, - "end": 4909, + "start": 4797, + "end": 4877, "loc": { "start": { "line": 130, @@ -19116,8 +18921,8 @@ }, "test": { "type": "CallExpression", - "start": 4833, - "end": 4870, + "start": 4801, + "end": 4838, "loc": { "start": { "line": 130, @@ -19130,8 +18935,8 @@ }, "callee": { "type": "Identifier", - "start": 4833, - "end": 4836, + "start": 4801, + "end": 4804, "loc": { "start": { "line": 130, @@ -19149,8 +18954,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 4837, - "end": 4850, + "start": 4805, + "end": 4818, "loc": { "start": { "line": 130, @@ -19163,8 +18968,8 @@ }, "object": { "type": "ThisExpression", - "start": 4837, - "end": 4841, + "start": 4805, + "end": 4809, "loc": { "start": { "line": 130, @@ -19178,8 +18983,8 @@ }, "property": { "type": "Identifier", - "start": 4842, - "end": 4850, + "start": 4810, + "end": 4818, "loc": { "start": { "line": 130, @@ -19197,8 +19002,8 @@ }, { "type": "StringLiteral", - "start": 4852, - "end": 4869, + "start": 4820, + "end": 4837, "loc": { "start": { "line": 130, @@ -19220,8 +19025,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 4872, - "end": 4909, + "start": 4840, + "end": 4877, "loc": { "start": { "line": 130, @@ -19234,8 +19039,8 @@ }, "argument": { "type": "MemberExpression", - "start": 4879, - "end": 4908, + "start": 4847, + "end": 4876, "loc": { "start": { "line": 130, @@ -19248,8 +19053,8 @@ }, "object": { "type": "MemberExpression", - "start": 4879, - "end": 4892, + "start": 4847, + "end": 4860, "loc": { "start": { "line": 130, @@ -19262,8 +19067,8 @@ }, "object": { "type": "ThisExpression", - "start": 4879, - "end": 4883, + "start": 4847, + "end": 4851, "loc": { "start": { "line": 130, @@ -19277,8 +19082,8 @@ }, "property": { "type": "Identifier", - "start": 4884, - "end": 4892, + "start": 4852, + "end": 4860, "loc": { "start": { "line": 130, @@ -19296,8 +19101,8 @@ }, "property": { "type": "Identifier", - "start": 4893, - "end": 4908, + "start": 4861, + "end": 4876, "loc": { "start": { "line": 130, @@ -19320,8 +19125,8 @@ { "type": "CommentLine", "value": " Get the institution code from the specimen object if present.", - "start": 4760, - "end": 4824, + "start": 4728, + "end": 4792, "loc": { "start": { "line": 129, @@ -19338,8 +19143,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4915, - "end": 4987, + "start": 4883, + "end": 4955, "loc": { "start": { "line": 132, @@ -19354,8 +19159,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4992, - "end": 5019, + "start": 4960, + "end": 4987, "loc": { "start": { "line": 133, @@ -19371,8 +19176,8 @@ }, { "type": "IfStatement", - "start": 5024, - "end": 5233, + "start": 4992, + "end": 5201, "loc": { "start": { "line": 134, @@ -19385,8 +19190,8 @@ }, "test": { "type": "CallExpression", - "start": 5028, - "end": 5062, + "start": 4996, + "end": 5030, "loc": { "start": { "line": 134, @@ -19399,8 +19204,8 @@ }, "callee": { "type": "Identifier", - "start": 5028, - "end": 5031, + "start": 4996, + "end": 4999, "loc": { "start": { "line": 134, @@ -19418,8 +19223,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5032, - "end": 5045, + "start": 5000, + "end": 5013, "loc": { "start": { "line": 134, @@ -19432,8 +19237,8 @@ }, "object": { "type": "ThisExpression", - "start": 5032, - "end": 5036, + "start": 5000, + "end": 5004, "loc": { "start": { "line": 134, @@ -19447,8 +19252,8 @@ }, "property": { "type": "Identifier", - "start": 5037, - "end": 5045, + "start": 5005, + "end": 5013, "loc": { "start": { "line": 134, @@ -19466,8 +19271,8 @@ }, { "type": "StringLiteral", - "start": 5047, - "end": 5061, + "start": 5015, + "end": 5029, "loc": { "start": { "line": 134, @@ -19489,8 +19294,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 5064, - "end": 5233, + "start": 5032, + "end": 5201, "loc": { "start": { "line": 134, @@ -19504,8 +19309,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 5072, - "end": 5150, + "start": 5040, + "end": 5118, "loc": { "start": { "line": 135, @@ -19519,8 +19324,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 5078, - "end": 5149, + "start": 5046, + "end": 5117, "loc": { "start": { "line": 135, @@ -19533,8 +19338,8 @@ }, "id": { "type": "Identifier", - "start": 5078, - "end": 5086, + "start": 5046, + "end": 5054, "loc": { "start": { "line": 135, @@ -19550,8 +19355,8 @@ }, "init": { "type": "CallExpression", - "start": 5089, - "end": 5149, + "start": 5057, + "end": 5117, "loc": { "start": { "line": 135, @@ -19564,8 +19369,8 @@ }, "callee": { "type": "MemberExpression", - "start": 5089, - "end": 5121, + "start": 5057, + "end": 5089, "loc": { "start": { "line": 135, @@ -19578,8 +19383,8 @@ }, "object": { "type": "Identifier", - "start": 5089, - "end": 5104, + "start": 5057, + "end": 5072, "loc": { "start": { "line": 135, @@ -19595,8 +19400,8 @@ }, "property": { "type": "Identifier", - "start": 5105, - "end": 5121, + "start": 5073, + "end": 5089, "loc": { "start": { "line": 135, @@ -19615,8 +19420,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5122, - "end": 5148, + "start": 5090, + "end": 5116, "loc": { "start": { "line": 135, @@ -19629,8 +19434,8 @@ }, "object": { "type": "MemberExpression", - "start": 5122, - "end": 5135, + "start": 5090, + "end": 5103, "loc": { "start": { "line": 135, @@ -19643,8 +19448,8 @@ }, "object": { "type": "ThisExpression", - "start": 5122, - "end": 5126, + "start": 5090, + "end": 5094, "loc": { "start": { "line": 135, @@ -19658,8 +19463,8 @@ }, "property": { "type": "Identifier", - "start": 5127, - "end": 5135, + "start": 5095, + "end": 5103, "loc": { "start": { "line": 135, @@ -19677,8 +19482,8 @@ }, "property": { "type": "Identifier", - "start": 5136, - "end": 5148, + "start": 5104, + "end": 5116, "loc": { "start": { "line": 135, @@ -19702,8 +19507,8 @@ }, { "type": "IfStatement", - "start": 5157, - "end": 5227, + "start": 5125, + "end": 5195, "loc": { "start": { "line": 136, @@ -19716,8 +19521,8 @@ }, "test": { "type": "CallExpression", - "start": 5161, - "end": 5193, + "start": 5129, + "end": 5161, "loc": { "start": { "line": 136, @@ -19730,8 +19535,8 @@ }, "callee": { "type": "Identifier", - "start": 5161, - "end": 5164, + "start": 5129, + "end": 5132, "loc": { "start": { "line": 136, @@ -19748,8 +19553,8 @@ "arguments": [ { "type": "Identifier", - "start": 5165, - "end": 5173, + "start": 5133, + "end": 5141, "loc": { "start": { "line": 136, @@ -19765,8 +19570,8 @@ }, { "type": "StringLiteral", - "start": 5175, - "end": 5192, + "start": 5143, + "end": 5160, "loc": { "start": { "line": 136, @@ -19787,8 +19592,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5195, - "end": 5227, + "start": 5163, + "end": 5195, "loc": { "start": { "line": 136, @@ -19801,8 +19606,8 @@ }, "argument": { "type": "MemberExpression", - "start": 5202, - "end": 5226, + "start": 5170, + "end": 5194, "loc": { "start": { "line": 136, @@ -19815,8 +19620,8 @@ }, "object": { "type": "Identifier", - "start": 5202, - "end": 5210, + "start": 5170, + "end": 5178, "loc": { "start": { "line": 136, @@ -19832,8 +19637,8 @@ }, "property": { "type": "Identifier", - "start": 5211, - "end": 5226, + "start": 5179, + "end": 5194, "loc": { "start": { "line": 136, @@ -19860,8 +19665,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4915, - "end": 4987, + "start": 4883, + "end": 4955, "loc": { "start": { "line": 132, @@ -19876,8 +19681,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4992, - "end": 5019, + "start": 4960, + "end": 4987, "loc": { "start": { "line": 133, @@ -19893,8 +19698,8 @@ }, { "type": "ReturnStatement", - "start": 5238, - "end": 5255, + "start": 5206, + "end": 5223, "loc": { "start": { "line": 138, @@ -19907,8 +19712,8 @@ }, "argument": { "type": "Identifier", - "start": 5245, - "end": 5254, + "start": 5213, + "end": 5222, "loc": { "start": { "line": 138, @@ -19931,8 +19736,8 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4679, - "end": 4729, + "start": 4647, + "end": 4697, "loc": { "start": { "line": 125, @@ -19949,8 +19754,8 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 5263, - "end": 5312, + "start": 5231, + "end": 5280, "loc": { "start": { "line": 141, @@ -19966,8 +19771,8 @@ }, { "type": "ClassMethod", - "start": 5315, - "end": 5836, + "start": 5283, + "end": 5804, "loc": { "start": { "line": 144, @@ -19982,8 +19787,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 5319, - "end": 5333, + "start": 5287, + "end": 5301, "loc": { "start": { "line": 144, @@ -20005,8 +19810,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 5336, - "end": 5836, + "start": 5304, + "end": 5804, "loc": { "start": { "line": 144, @@ -20020,8 +19825,8 @@ "body": [ { "type": "IfStatement", - "start": 5410, - "end": 5488, + "start": 5378, + "end": 5456, "loc": { "start": { "line": 146, @@ -20034,8 +19839,8 @@ }, "test": { "type": "CallExpression", - "start": 5414, - "end": 5450, + "start": 5382, + "end": 5418, "loc": { "start": { "line": 146, @@ -20048,8 +19853,8 @@ }, "callee": { "type": "Identifier", - "start": 5414, - "end": 5417, + "start": 5382, + "end": 5385, "loc": { "start": { "line": 146, @@ -20067,8 +19872,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5418, - "end": 5431, + "start": 5386, + "end": 5399, "loc": { "start": { "line": 146, @@ -20081,8 +19886,8 @@ }, "object": { "type": "ThisExpression", - "start": 5418, - "end": 5422, + "start": 5386, + "end": 5390, "loc": { "start": { "line": 146, @@ -20096,8 +19901,8 @@ }, "property": { "type": "Identifier", - "start": 5423, - "end": 5431, + "start": 5391, + "end": 5399, "loc": { "start": { "line": 146, @@ -20115,8 +19920,8 @@ }, { "type": "StringLiteral", - "start": 5433, - "end": 5449, + "start": 5401, + "end": 5417, "loc": { "start": { "line": 146, @@ -20138,8 +19943,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5452, - "end": 5488, + "start": 5420, + "end": 5456, "loc": { "start": { "line": 146, @@ -20152,8 +19957,8 @@ }, "argument": { "type": "MemberExpression", - "start": 5459, - "end": 5487, + "start": 5427, + "end": 5455, "loc": { "start": { "line": 146, @@ -20166,8 +19971,8 @@ }, "object": { "type": "MemberExpression", - "start": 5459, - "end": 5472, + "start": 5427, + "end": 5440, "loc": { "start": { "line": 146, @@ -20180,8 +19985,8 @@ }, "object": { "type": "ThisExpression", - "start": 5459, - "end": 5463, + "start": 5427, + "end": 5431, "loc": { "start": { "line": 146, @@ -20195,8 +20000,8 @@ }, "property": { "type": "Identifier", - "start": 5464, - "end": 5472, + "start": 5432, + "end": 5440, "loc": { "start": { "line": 146, @@ -20214,8 +20019,8 @@ }, "property": { "type": "Identifier", - "start": 5473, - "end": 5487, + "start": 5441, + "end": 5455, "loc": { "start": { "line": 146, @@ -20238,8 +20043,8 @@ { "type": "CommentLine", "value": " Get the collection code from the specimen object if present.", - "start": 5342, - "end": 5405, + "start": 5310, + "end": 5373, "loc": { "start": { "line": 145, @@ -20256,8 +20061,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 5494, - "end": 5566, + "start": 5462, + "end": 5534, "loc": { "start": { "line": 148, @@ -20272,8 +20077,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 5571, - "end": 5598, + "start": 5539, + "end": 5566, "loc": { "start": { "line": 149, @@ -20289,8 +20094,8 @@ }, { "type": "IfStatement", - "start": 5603, - "end": 5810, + "start": 5571, + "end": 5778, "loc": { "start": { "line": 150, @@ -20303,8 +20108,8 @@ }, "test": { "type": "CallExpression", - "start": 5607, - "end": 5641, + "start": 5575, + "end": 5609, "loc": { "start": { "line": 150, @@ -20317,8 +20122,8 @@ }, "callee": { "type": "Identifier", - "start": 5607, - "end": 5610, + "start": 5575, + "end": 5578, "loc": { "start": { "line": 150, @@ -20336,8 +20141,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5611, - "end": 5624, + "start": 5579, + "end": 5592, "loc": { "start": { "line": 150, @@ -20350,8 +20155,8 @@ }, "object": { "type": "ThisExpression", - "start": 5611, - "end": 5615, + "start": 5579, + "end": 5583, "loc": { "start": { "line": 150, @@ -20365,8 +20170,8 @@ }, "property": { "type": "Identifier", - "start": 5616, - "end": 5624, + "start": 5584, + "end": 5592, "loc": { "start": { "line": 150, @@ -20384,8 +20189,8 @@ }, { "type": "StringLiteral", - "start": 5626, - "end": 5640, + "start": 5594, + "end": 5608, "loc": { "start": { "line": 150, @@ -20407,8 +20212,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 5643, - "end": 5810, + "start": 5611, + "end": 5778, "loc": { "start": { "line": 150, @@ -20422,8 +20227,8 @@ "body": [ { "type": "VariableDeclaration", - "start": 5651, - "end": 5729, + "start": 5619, + "end": 5697, "loc": { "start": { "line": 151, @@ -20437,8 +20242,8 @@ "declarations": [ { "type": "VariableDeclarator", - "start": 5657, - "end": 5728, + "start": 5625, + "end": 5696, "loc": { "start": { "line": 151, @@ -20451,8 +20256,8 @@ }, "id": { "type": "Identifier", - "start": 5657, - "end": 5665, + "start": 5625, + "end": 5633, "loc": { "start": { "line": 151, @@ -20468,8 +20273,8 @@ }, "init": { "type": "CallExpression", - "start": 5668, - "end": 5728, + "start": 5636, + "end": 5696, "loc": { "start": { "line": 151, @@ -20482,8 +20287,8 @@ }, "callee": { "type": "MemberExpression", - "start": 5668, - "end": 5700, + "start": 5636, + "end": 5668, "loc": { "start": { "line": 151, @@ -20496,8 +20301,8 @@ }, "object": { "type": "Identifier", - "start": 5668, - "end": 5683, + "start": 5636, + "end": 5651, "loc": { "start": { "line": 151, @@ -20513,8 +20318,8 @@ }, "property": { "type": "Identifier", - "start": 5684, - "end": 5700, + "start": 5652, + "end": 5668, "loc": { "start": { "line": 151, @@ -20533,8 +20338,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 5701, - "end": 5727, + "start": 5669, + "end": 5695, "loc": { "start": { "line": 151, @@ -20547,8 +20352,8 @@ }, "object": { "type": "MemberExpression", - "start": 5701, - "end": 5714, + "start": 5669, + "end": 5682, "loc": { "start": { "line": 151, @@ -20561,8 +20366,8 @@ }, "object": { "type": "ThisExpression", - "start": 5701, - "end": 5705, + "start": 5669, + "end": 5673, "loc": { "start": { "line": 151, @@ -20576,8 +20381,8 @@ }, "property": { "type": "Identifier", - "start": 5706, - "end": 5714, + "start": 5674, + "end": 5682, "loc": { "start": { "line": 151, @@ -20595,8 +20400,8 @@ }, "property": { "type": "Identifier", - "start": 5715, - "end": 5727, + "start": 5683, + "end": 5695, "loc": { "start": { "line": 151, @@ -20620,8 +20425,8 @@ }, { "type": "IfStatement", - "start": 5736, - "end": 5804, + "start": 5704, + "end": 5772, "loc": { "start": { "line": 152, @@ -20634,8 +20439,8 @@ }, "test": { "type": "CallExpression", - "start": 5740, - "end": 5771, + "start": 5708, + "end": 5739, "loc": { "start": { "line": 152, @@ -20648,8 +20453,8 @@ }, "callee": { "type": "Identifier", - "start": 5740, - "end": 5743, + "start": 5708, + "end": 5711, "loc": { "start": { "line": 152, @@ -20666,8 +20471,8 @@ "arguments": [ { "type": "Identifier", - "start": 5744, - "end": 5752, + "start": 5712, + "end": 5720, "loc": { "start": { "line": 152, @@ -20683,8 +20488,8 @@ }, { "type": "StringLiteral", - "start": 5754, - "end": 5770, + "start": 5722, + "end": 5738, "loc": { "start": { "line": 152, @@ -20705,8 +20510,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 5773, - "end": 5804, + "start": 5741, + "end": 5772, "loc": { "start": { "line": 152, @@ -20719,8 +20524,8 @@ }, "argument": { "type": "MemberExpression", - "start": 5780, - "end": 5803, + "start": 5748, + "end": 5771, "loc": { "start": { "line": 152, @@ -20733,8 +20538,8 @@ }, "object": { "type": "Identifier", - "start": 5780, - "end": 5788, + "start": 5748, + "end": 5756, "loc": { "start": { "line": 152, @@ -20750,8 +20555,8 @@ }, "property": { "type": "Identifier", - "start": 5789, - "end": 5803, + "start": 5757, + "end": 5771, "loc": { "start": { "line": 152, @@ -20778,8 +20583,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 5494, - "end": 5566, + "start": 5462, + "end": 5534, "loc": { "start": { "line": 148, @@ -20794,8 +20599,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 5571, - "end": 5598, + "start": 5539, + "end": 5566, "loc": { "start": { "line": 149, @@ -20811,8 +20616,8 @@ }, { "type": "ReturnStatement", - "start": 5815, - "end": 5832, + "start": 5783, + "end": 5800, "loc": { "start": { "line": 154, @@ -20825,8 +20630,8 @@ }, "argument": { "type": "Identifier", - "start": 5822, - "end": 5831, + "start": 5790, + "end": 5799, "loc": { "start": { "line": 154, @@ -20849,8 +20654,8 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 5263, - "end": 5312, + "start": 5231, + "end": 5280, "loc": { "start": { "line": 141, @@ -20867,8 +20672,8 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5840, - "end": 6099, + "start": 5808, + "end": 6067, "loc": { "start": { "line": 157, @@ -20884,8 +20689,8 @@ }, { "type": "ClassMethod", - "start": 6102, - "end": 7142, + "start": 6070, + "end": 7066, "loc": { "start": { "line": 163, @@ -20900,8 +20705,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 6106, - "end": 6118, + "start": 6074, + "end": 6086, "loc": { "start": { "line": 163, @@ -20923,8 +20728,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 6121, - "end": 7142, + "start": 6089, + "end": 7066, "loc": { "start": { "line": 163, @@ -20938,8 +20743,8 @@ "body": [ { "type": "IfStatement", - "start": 6172, - "end": 6311, + "start": 6140, + "end": 6235, "loc": { "start": { "line": 165, @@ -20951,9 +20756,9 @@ } }, "test": { - "type": "LogicalExpression", - "start": 6176, - "end": 6254, + "type": "CallExpression", + "start": 6144, + "end": 6178, "loc": { "start": { "line": 165, @@ -20961,13 +20766,13 @@ }, "end": { "line": 165, - "column": 86 + "column": 42 } }, - "left": { - "type": "CallExpression", - "start": 6176, - "end": 6210, + "callee": { + "type": "Identifier", + "start": 6144, + "end": 6147, "loc": { "start": { "line": 165, @@ -20975,32 +20780,32 @@ }, "end": { "line": 165, - "column": 42 - } + "column": 11 + }, + "identifierName": "has" }, - "callee": { - "type": "Identifier", - "start": 6176, - "end": 6179, + "name": "has", + "leadingComments": null + }, + "arguments": [ + { + "type": "MemberExpression", + "start": 6148, + "end": 6161, "loc": { "start": { "line": 165, - "column": 8 + "column": 12 }, "end": { "line": 165, - "column": 11 - }, - "identifierName": "has" + "column": 25 + } }, - "name": "has", - "leadingComments": null - }, - "arguments": [ - { - "type": "MemberExpression", - "start": 6180, - "end": 6193, + "object": { + "type": "ThisExpression", + "start": 6148, + "end": 6152, "loc": { "start": { "line": 165, @@ -21008,243 +20813,60 @@ }, "end": { "line": 165, - "column": 25 - } - }, - "object": { - "type": "ThisExpression", - "start": 6180, - "end": 6184, - "loc": { - "start": { - "line": 165, - "column": 12 - }, - "end": { - "line": 165, - "column": 16 - } - } - }, - "property": { - "type": "Identifier", - "start": 6185, - "end": 6193, - "loc": { - "start": { - "line": 165, - "column": 17 - }, - "end": { - "line": 165, - "column": 25 - }, - "identifierName": "specimen" - }, - "name": "specimen" - }, - "computed": false - }, - { - "type": "StringLiteral", - "start": 6195, - "end": 6209, - "loc": { - "start": { - "line": 165, - "column": 27 - }, - "end": { - "line": 165, - "column": 41 + "column": 16 } - }, - "extra": { - "rawValue": "occurrenceID", - "raw": "'occurrenceID'" - }, - "value": "occurrenceID" - } - ], - "leadingComments": null - }, - "operator": "&&", - "right": { - "type": "BinaryExpression", - "start": 6214, - "end": 6254, - "loc": { - "start": { - "line": 165, - "column": 46 - }, - "end": { - "line": 165, - "column": 86 - } - }, - 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"start": 6941, - "end": 6973, + "start": 6865, + "end": 6897, "loc": { "start": { "line": 178, @@ -23022,8 +22644,8 @@ }, "object": { "type": "MemberExpression", - "start": 6941, - "end": 6968, + "start": 6865, + "end": 6892, "loc": { "start": { "line": 178, @@ -23036,8 +22658,8 @@ }, "object": { "type": "MemberExpression", - "start": 6941, - "end": 6954, + "start": 6865, + "end": 6878, "loc": { "start": { "line": 178, @@ -23050,8 +22672,8 @@ }, "object": { "type": "ThisExpression", - "start": 6941, - "end": 6945, + "start": 6865, + "end": 6869, "loc": { "start": { "line": 178, @@ -23065,8 +22687,8 @@ }, "property": { "type": "Identifier", - "start": 6946, - "end": 6954, + "start": 6870, + "end": 6878, "loc": { "start": { "line": 178, @@ -23084,8 +22706,8 @@ }, "property": { "type": "Identifier", - "start": 6955, - "end": 6968, + "start": 6879, + "end": 6892, "loc": { "start": { "line": 178, @@ -23103,8 +22725,8 @@ }, "property": { "type": "Identifier", - "start": 6969, - "end": 6973, + "start": 6893, + "end": 6897, "loc": { "start": { "line": 178, @@ -23126,8 +22748,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 6887, - "end": 6900, + "start": 6811, + "end": 6824, "loc": { "start": { "line": 178, @@ -23146,8 +22768,8 @@ }, { "type": "TemplateElement", - "start": 6938, - "end": 6939, + "start": 6862, + "end": 6863, "loc": { "start": { "line": 178, @@ -23166,8 +22788,8 @@ }, { "type": "TemplateElement", - "start": 6976, - "end": 6976, + "start": 6900, + "end": 6900, "loc": { "start": { "line": 178, @@ -23194,8 +22816,8 @@ }, { "type": "ReturnStatement", - "start": 6993, - "end": 7054, + "start": 6917, + "end": 6978, "loc": { "start": { "line": 180, @@ -23208,8 +22830,8 @@ }, "argument": { "type": "TemplateLiteral", - "start": 7000, - "end": 7053, + "start": 6924, + "end": 6977, "loc": { "start": { "line": 180, @@ -23223,8 +22845,8 @@ "expressions": [ { "type": "CallExpression", - "start": 7017, - "end": 7051, + "start": 6941, + "end": 6975, "loc": { "start": { "line": 180, @@ -23237,8 +22859,8 @@ }, "callee": { "type": "MemberExpression", - "start": 7017, - "end": 7049, + "start": 6941, + "end": 6973, "loc": { "start": { "line": 180, @@ -23251,8 +22873,8 @@ }, "object": { "type": "MemberExpression", - "start": 7017, - "end": 7044, + "start": 6941, + "end": 6968, "loc": { "start": { "line": 180, @@ -23265,8 +22887,8 @@ }, "object": { "type": "MemberExpression", - "start": 7017, - "end": 7030, + "start": 6941, + "end": 6954, "loc": { "start": { "line": 180, @@ -23279,8 +22901,8 @@ }, "object": { "type": "ThisExpression", - "start": 7017, - "end": 7021, + "start": 6941, + "end": 6945, "loc": { "start": { "line": 180, @@ -23294,8 +22916,8 @@ }, "property": { "type": "Identifier", - "start": 7022, - "end": 7030, + "start": 6946, + "end": 6954, "loc": { "start": { "line": 180, @@ -23313,8 +22935,8 @@ }, "property": { "type": "Identifier", - "start": 7031, - "end": 7044, + "start": 6955, + "end": 6968, "loc": { "start": { "line": 180, @@ -23332,8 +22954,8 @@ }, "property": { "type": "Identifier", - "start": 7045, - "end": 7049, + "start": 6969, + "end": 6973, "loc": { "start": { "line": 180, @@ -23355,8 +22977,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 7001, - "end": 7015, + "start": 6925, + "end": 6939, "loc": { "start": { "line": 180, @@ -23375,8 +22997,8 @@ }, { "type": "TemplateElement", - "start": 7052, - "end": 7052, + "start": 6976, + "end": 6976, "loc": { "start": { "line": 180, @@ -23405,8 +23027,8 @@ { "type": "CommentLine", "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 6317, - "end": 6394, + "start": 6241, + "end": 6318, "loc": { "start": { "line": 169, @@ -23423,8 +23045,8 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 7066, - "end": 7116, + "start": 6990, + "end": 7040, "loc": { "start": { "line": 183, @@ -23440,8 +23062,8 @@ }, { "type": "ReturnStatement", - "start": 7121, - "end": 7138, + "start": 7045, + "end": 7062, "loc": { "start": { "line": 184, @@ -23454,8 +23076,8 @@ }, "argument": { "type": "Identifier", - "start": 7128, - "end": 7137, + "start": 7052, + "end": 7061, "loc": { "start": { "line": 184, @@ -23474,8 +23096,8 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 7066, - "end": 7116, + "start": 6990, + "end": 7040, "loc": { "start": { "line": 183, @@ -23497,8 +23119,8 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5840, - "end": 6099, + "start": 5808, + "end": 6067, "loc": { "start": { "line": 157, @@ -23515,8 +23137,8 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 7146, - "end": 7207, + "start": 7070, + "end": 7131, "loc": { "start": { "line": 187, @@ -23532,8 +23154,8 @@ }, { "type": "ClassMethod", - "start": 7210, - "end": 7349, + "start": 7134, + "end": 7262, "loc": { "start": { "line": 190, @@ -23548,8 +23170,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7214, - "end": 7227, + "start": 7138, + "end": 7151, "loc": { "start": { "line": 190, @@ -23571,8 +23193,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7230, - "end": 7349, + "start": 7154, + "end": 7262, "loc": { "start": { "line": 190, @@ -23586,8 +23208,8 @@ "body": [ { "type": "IfStatement", - "start": 7236, - "end": 7323, + "start": 7160, + "end": 7236, "loc": { "start": { "line": 191, @@ -23595,13 +23217,13 @@ }, "end": { "line": 191, - "column": 91 + "column": 80 } }, "test": { "type": "CallExpression", - "start": 7240, - "end": 7279, + "start": 7164, + "end": 7199, "loc": { "start": { "line": 191, @@ -23609,13 +23231,13 @@ }, "end": { "line": 191, - "column": 47 + "column": 43 } }, "callee": { "type": "Identifier", - "start": 7240, - "end": 7243, + "start": 7164, + "end": 7167, "loc": { "start": { "line": 191, @@ -23632,8 +23254,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 7244, - "end": 7257, + "start": 7168, + "end": 7181, "loc": { "start": { "line": 191, @@ -23646,8 +23268,8 @@ }, "object": { "type": "ThisExpression", - "start": 7244, - "end": 7248, + "start": 7168, + "end": 7172, "loc": { "start": { "line": 191, @@ -23661,8 +23283,8 @@ }, "property": { "type": "Identifier", - "start": 7249, - "end": 7257, + "start": 7173, + "end": 7181, "loc": { "start": { "line": 191, @@ -23680,8 +23302,8 @@ }, { "type": "StringLiteral", - "start": 7259, - "end": 7278, + "start": 7183, + "end": 7198, "loc": { "start": { "line": 191, @@ -23689,86 +23311,86 @@ }, "end": { "line": 191, - "column": 46 + "column": 42 } }, "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "rawValue": "basisOfRecord", + "raw": "'basisOfRecord'" }, - "value": "dwc:basisOfRecord" + "value": "basisOfRecord" } ] }, "consequent": { "type": "ReturnStatement", - "start": 7281, - "end": 7323, + "start": 7201, + "end": 7236, "loc": { "start": { "line": 191, - "column": 49 + "column": 45 }, "end": { "line": 191, - "column": 91 + "column": 80 } }, "argument": { "type": "MemberExpression", - "start": 7288, - "end": 7322, + "start": 7208, + "end": 7235, "loc": { "start": { "line": 191, - "column": 56 + "column": 52 }, "end": { "line": 191, - "column": 90 + "column": 79 } }, "object": { "type": "MemberExpression", - "start": 7288, - "end": 7301, + "start": 7208, + "end": 7221, "loc": { "start": { "line": 191, - "column": 56 + "column": 52 }, "end": { "line": 191, - "column": 69 + "column": 65 } }, "object": { "type": "ThisExpression", - "start": 7288, - "end": 7292, + "start": 7208, + "end": 7212, "loc": { "start": { "line": 191, - "column": 56 + "column": 52 }, "end": { "line": 191, - "column": 60 + "column": 56 } } }, "property": { "type": "Identifier", - "start": 7293, - "end": 7301, + "start": 7213, + "end": 7221, "loc": { "start": { "line": 191, - "column": 61 + "column": 57 }, "end": { "line": 191, - "column": 69 + "column": 65 }, "identifierName": "specimen" }, @@ -23777,34 +23399,31 @@ "computed": false }, "property": { - "type": "StringLiteral", - "start": 7302, - "end": 7321, + "type": "Identifier", + "start": 7222, + "end": 7235, "loc": { "start": { "line": 191, - "column": 70 + "column": 66 }, "end": { "line": 191, - "column": 89 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 79 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, - "computed": true + "computed": false } }, "alternate": null }, { "type": "ReturnStatement", - "start": 7328, - "end": 7345, + "start": 7241, + "end": 7258, "loc": { "start": { "line": 192, @@ -23817,8 +23436,8 @@ }, "argument": { "type": "Identifier", - "start": 7335, - "end": 7344, + "start": 7248, + "end": 7257, "loc": { "start": { "line": 192, @@ -23841,8 +23460,8 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 7146, - "end": 7207, + "start": 7070, + "end": 7131, "loc": { "start": { "line": 187, @@ -23859,8 +23478,8 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 7353, - "end": 7468, + "start": 7266, + "end": 7381, "loc": { "start": { "line": 195, @@ -23876,8 +23495,8 @@ }, { "type": "ClassMethod", - "start": 7471, - "end": 7545, + "start": 7384, + "end": 7451, "loc": { "start": { "line": 199, @@ -23892,8 +23511,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7475, - "end": 7488, + "start": 7388, + "end": 7401, "loc": { "start": { "line": 199, @@ -23915,8 +23534,8 @@ "params": [ { "type": "Identifier", - "start": 7489, - "end": 7492, + "start": 7402, + "end": 7405, "loc": { "start": { "line": 199, @@ -23933,8 +23552,8 @@ ], "body": { "type": "BlockStatement", - "start": 7494, - "end": 7545, + "start": 7407, + "end": 7451, "loc": { "start": { "line": 199, @@ -23948,8 +23567,8 @@ "body": [ { "type": "ExpressionStatement", - "start": 7500, - "end": 7541, + "start": 7413, + "end": 7447, "loc": { "start": { "line": 200, @@ -23957,13 +23576,13 @@ }, "end": { "line": 200, - "column": 45 + "column": 38 } }, "expression": { "type": "AssignmentExpression", - "start": 7500, - "end": 7540, + "start": 7413, + "end": 7446, "loc": { "start": { "line": 200, @@ -23971,14 +23590,14 @@ }, "end": { "line": 200, - "column": 44 + "column": 37 } }, "operator": "=", "left": { "type": "MemberExpression", - "start": 7500, - "end": 7534, + "start": 7413, + "end": 7440, "loc": { "start": { "line": 200, @@ -23986,13 +23605,13 @@ }, "end": { "line": 200, - "column": 38 + "column": 31 } }, "object": { "type": "MemberExpression", - "start": 7500, - "end": 7513, + "start": 7413, + "end": 7426, "loc": { "start": { "line": 200, @@ -24005,8 +23624,8 @@ }, "object": { "type": "ThisExpression", - "start": 7500, - "end": 7504, + "start": 7413, + "end": 7417, "loc": { "start": { "line": 200, @@ -24020,8 +23639,8 @@ }, "property": { "type": "Identifier", - "start": 7505, - "end": 7513, + "start": 7418, + "end": 7426, "loc": { "start": { "line": 200, @@ -24038,9 +23657,9 @@ "computed": false }, "property": { - "type": "StringLiteral", - "start": 7514, - "end": 7533, + "type": "Identifier", + "start": 7427, + "end": 7440, "loc": { "start": { "line": 200, @@ -24048,29 +23667,26 @@ }, "end": { "line": 200, - "column": 37 - } - }, - "extra": { - "rawValue": "dwc:basisOfRecord", - "raw": "'dwc:basisOfRecord'" + "column": 31 + }, + "identifierName": "basisOfRecord" }, - "value": "dwc:basisOfRecord" + "name": "basisOfRecord" }, - "computed": true + "computed": false }, "right": { "type": "Identifier", - "start": 7537, - "end": 7540, + "start": 7443, + "end": 7446, "loc": { "start": { "line": 200, - "column": 41 + "column": 34 }, "end": { "line": 200, - "column": 44 + "column": 37 }, "identifierName": "bor" }, @@ -24086,8 +23702,8 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 7353, - "end": 7468, + "start": 7266, + "end": 7381, "loc": { "start": { "line": 195, @@ -24104,8 +23720,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 7549, - "end": 7634, + "start": 7455, + "end": 7540, "loc": { "start": { "line": 203, @@ -24121,8 +23737,8 @@ }, { "type": "ClassMethod", - "start": 7637, - "end": 7808, + "start": 7543, + "end": 7714, "loc": { "start": { "line": 204, @@ -24137,8 +23753,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7641, - "end": 7653, + "start": 7547, + "end": 7559, "loc": { "start": { "line": 204, @@ -24160,8 +23776,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7656, - "end": 7808, + "start": 7562, + "end": 7714, "loc": { "start": { "line": 204, @@ -24175,8 +23791,8 @@ "body": [ { "type": "IfStatement", - "start": 7662, - "end": 7718, + "start": 7568, + "end": 7624, "loc": { "start": { "line": 205, @@ -24189,8 +23805,8 @@ }, "test": { "type": "CallExpression", - "start": 7666, - "end": 7695, + "start": 7572, + "end": 7601, "loc": { "start": { "line": 205, @@ -24203,8 +23819,8 @@ }, "callee": { "type": "Identifier", - "start": 7666, - "end": 7669, + "start": 7572, + "end": 7575, "loc": { "start": { "line": 205, @@ -24221,8 +23837,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 7670, - "end": 7683, + "start": 7576, + "end": 7589, "loc": { "start": { "line": 205, @@ -24235,8 +23851,8 @@ }, "object": { "type": "ThisExpression", - "start": 7670, - "end": 7674, + "start": 7576, + "end": 7580, "loc": { "start": { "line": 205, @@ -24250,8 +23866,8 @@ }, "property": { "type": "Identifier", - "start": 7675, - "end": 7683, + "start": 7581, + "end": 7589, "loc": { "start": { "line": 205, @@ -24269,8 +23885,8 @@ }, { "type": "StringLiteral", - "start": 7685, - "end": 7694, + "start": 7591, + "end": 7600, "loc": { "start": { "line": 205, @@ -24291,8 +23907,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7697, - "end": 7718, + "start": 7603, + "end": 7624, "loc": { "start": { "line": 205, @@ -24305,8 +23921,8 @@ }, "argument": { "type": "MemberExpression", - "start": 7704, - "end": 7717, + "start": 7610, + "end": 7623, "loc": { "start": { "line": 205, @@ -24319,8 +23935,8 @@ }, "object": { "type": "ThisExpression", - "start": 7704, - "end": 7708, + "start": 7610, + "end": 7614, "loc": { "start": { "line": 205, @@ -24334,8 +23950,8 @@ }, "property": { "type": "Identifier", - "start": 7709, - "end": 7717, + "start": 7615, + "end": 7623, "loc": { "start": { "line": 205, @@ -24356,8 +23972,8 @@ }, { "type": "IfStatement", - "start": 7723, - "end": 7782, + "start": 7629, + "end": 7688, "loc": { "start": { "line": 206, @@ -24370,8 +23986,8 @@ }, "test": { "type": "CallExpression", - "start": 7727, - "end": 7759, + "start": 7633, + "end": 7665, "loc": { "start": { "line": 206, @@ -24384,8 +24000,8 @@ }, "callee": { "type": "Identifier", - "start": 7727, - "end": 7730, + "start": 7633, + "end": 7636, "loc": { "start": { "line": 206, @@ -24402,8 +24018,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 7731, - "end": 7744, + "start": 7637, + "end": 7650, "loc": { "start": { "line": 206, @@ -24416,8 +24032,8 @@ }, "object": { "type": "ThisExpression", - "start": 7731, - "end": 7735, + "start": 7637, + "end": 7641, "loc": { "start": { "line": 206, @@ -24431,8 +24047,8 @@ }, "property": { "type": "Identifier", - "start": 7736, - "end": 7744, + "start": 7642, + "end": 7650, "loc": { "start": { "line": 206, @@ -24450,8 +24066,8 @@ }, { "type": "StringLiteral", - "start": 7746, - "end": 7758, + "start": 7652, + "end": 7664, "loc": { "start": { "line": 206, @@ -24472,8 +24088,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7761, - "end": 7782, + "start": 7667, + "end": 7688, "loc": { "start": { "line": 206, @@ -24486,8 +24102,8 @@ }, "argument": { "type": "MemberExpression", - "start": 7768, - "end": 7781, + "start": 7674, + "end": 7687, "loc": { "start": { "line": 206, @@ -24500,8 +24116,8 @@ }, "object": { "type": "ThisExpression", - "start": 7768, - "end": 7772, + "start": 7674, + "end": 7678, "loc": { "start": { "line": 206, @@ -24515,8 +24131,8 @@ }, "property": { "type": "Identifier", - "start": 7773, - "end": 7781, + "start": 7679, + "end": 7687, "loc": { "start": { "line": 206, @@ -24537,8 +24153,8 @@ }, { "type": "ReturnStatement", - "start": 7787, - "end": 7804, + "start": 7693, + "end": 7710, "loc": { "start": { "line": 207, @@ -24551,8 +24167,8 @@ }, "argument": { "type": "Identifier", - "start": 7794, - "end": 7803, + "start": 7700, + "end": 7709, "loc": { "start": { "line": 207, @@ -24575,8 +24191,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 7549, - "end": 7634, + "start": 7455, + "end": 7540, "loc": { "start": { "line": 203, @@ -24593,8 +24209,8 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7812, - "end": 7852, + "start": 7718, + "end": 7758, "loc": { "start": { "line": 210, @@ -24610,8 +24226,8 @@ }, { "type": "ClassMethod", - "start": 7855, - "end": 8337, + "start": 7761, + "end": 8243, "loc": { "start": { "line": 211, @@ -24626,8 +24242,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 7859, - "end": 7864, + "start": 7765, + "end": 7770, "loc": { "start": { "line": 211, @@ -24649,8 +24265,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 7867, - "end": 8337, + "start": 7773, + "end": 8243, "loc": { "start": { "line": 211, @@ -24664,8 +24280,8 @@ "body": [ { "type": "IfStatement", - "start": 7930, - "end": 7971, + "start": 7836, + "end": 7877, "loc": { "start": { "line": 213, @@ -24678,8 +24294,8 @@ }, "test": { "type": "UnaryExpression", - "start": 7934, - "end": 7952, + "start": 7840, + "end": 7858, "loc": { "start": { "line": 213, @@ -24694,8 +24310,8 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 7935, - "end": 7952, + "start": 7841, + "end": 7858, "loc": { "start": { "line": 213, @@ -24708,8 +24324,8 @@ }, "object": { "type": "ThisExpression", - "start": 7935, - "end": 7939, + "start": 7841, + "end": 7845, "loc": { "start": { "line": 213, @@ -24724,8 +24340,8 @@ }, "property": { "type": "Identifier", - "start": 7940, - "end": 7952, + "start": 7846, + "end": 7858, "loc": { "start": { "line": 213, @@ -24749,8 +24365,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 7954, - "end": 7971, + "start": 7860, + "end": 7877, "loc": { "start": { "line": 213, @@ -24763,8 +24379,8 @@ }, "argument": { "type": "Identifier", - "start": 7961, - "end": 7970, + "start": 7867, + "end": 7876, "loc": { "start": { "line": 213, @@ -24785,8 +24401,8 @@ { "type": "CommentLine", "value": " We can't return anything without an occurrenceID.", - "start": 7873, - "end": 7925, + "start": 7779, + "end": 7831, "loc": { "start": { "line": 212, @@ -24803,8 +24419,8 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7977, - "end": 8054, + "start": 7883, + "end": 7960, "loc": { "start": { "line": 215, @@ -24819,8 +24435,8 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 8059, - "end": 8100, + "start": 7965, + "end": 8006, "loc": { "start": { "line": 216, @@ -24836,8 +24452,8 @@ }, { "type": "IfStatement", - "start": 8105, - "end": 8247, + "start": 8011, + "end": 8153, "loc": { "start": { "line": 217, @@ -24850,8 +24466,8 @@ }, "test": { "type": "MemberExpression", - "start": 8109, - "end": 8126, + "start": 8015, + "end": 8032, "loc": { "start": { "line": 217, @@ -24864,8 +24480,8 @@ }, "object": { "type": "ThisExpression", - "start": 8109, - "end": 8113, + "start": 8015, + "end": 8019, "loc": { "start": { "line": 217, @@ -24880,8 +24496,8 @@ }, "property": { "type": "Identifier", - "start": 8114, - "end": 8126, + "start": 8020, + "end": 8032, "loc": { "start": { "line": 217, @@ -24900,8 +24516,8 @@ }, "consequent": { "type": "BlockStatement", - "start": 8128, - "end": 8247, + "start": 8034, + "end": 8153, "loc": { "start": { "line": 217, @@ -24915,8 +24531,8 @@ "body": [ { "type": "ReturnStatement", - "start": 8136, - "end": 8241, + "start": 8042, + "end": 8147, "loc": { "start": { "line": 218, @@ -24929,8 +24545,8 @@ }, "argument": { "type": "TemplateLiteral", - "start": 8143, - "end": 8240, + "start": 8049, + "end": 8146, "loc": { "start": { "line": 218, @@ -24944,8 +24560,8 @@ "expressions": [ { "type": "MemberExpression", - "start": 8155, - "end": 8172, + "start": 8061, + "end": 8078, "loc": { "start": { "line": 218, @@ -24958,8 +24574,8 @@ }, "object": { "type": "ThisExpression", - "start": 8155, - "end": 8159, + "start": 8061, + "end": 8065, "loc": { "start": { "line": 218, @@ -24973,8 +24589,8 @@ }, "property": { "type": "Identifier", - "start": 8160, - "end": 8172, + "start": 8066, + "end": 8078, "loc": { "start": { "line": 218, @@ -24992,8 +24608,8 @@ }, { "type": "MemberExpression", - "start": 8190, - "end": 8238, + "start": 8096, + "end": 8144, "loc": { "start": { "line": 218, @@ -25006,8 +24622,8 @@ }, "object": { "type": "NewExpression", - "start": 8190, - "end": 8232, + "start": 8096, + "end": 8138, "loc": { "start": { "line": 218, @@ -25020,8 +24636,8 @@ }, "callee": { "type": "Identifier", - "start": 8194, - "end": 8213, + "start": 8100, + "end": 8119, "loc": { "start": { "line": 218, @@ -25038,8 +24654,8 @@ "arguments": [ { "type": "MemberExpression", - "start": 8214, - "end": 8231, + "start": 8120, + "end": 8137, "loc": { "start": { "line": 218, @@ -25052,8 +24668,8 @@ }, "object": { "type": "ThisExpression", - "start": 8214, - "end": 8218, + "start": 8120, + "end": 8124, "loc": { "start": { "line": 218, @@ -25067,8 +24683,8 @@ }, "property": { "type": "Identifier", - "start": 8219, - "end": 8231, + "start": 8125, + "end": 8137, "loc": { "start": { "line": 218, @@ -25088,8 +24704,8 @@ }, "property": { "type": "Identifier", - "start": 8233, - "end": 8238, + "start": 8139, + "end": 8144, "loc": { "start": { "line": 218, @@ -25109,8 +24725,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 8144, - "end": 8153, + "start": 8050, + "end": 8059, "loc": { "start": { "line": 218, @@ -25129,8 +24745,8 @@ }, { "type": "TemplateElement", - "start": 8173, - "end": 8188, + "start": 8079, + "end": 8094, "loc": { "start": { "line": 218, @@ -25149,8 +24765,8 @@ }, { "type": "TemplateElement", - "start": 8239, - "end": 8239, + "start": 8145, + "end": 8145, "loc": { "start": { "line": 218, @@ -25179,8 +24795,8 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7977, - "end": 8054, + "start": 7883, + "end": 7960, "loc": { "start": { "line": 215, @@ -25195,8 +24811,8 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 8059, - "end": 8100, + "start": 7965, + "end": 8006, "loc": { "start": { "line": 216, @@ -25213,8 +24829,8 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 8253, - "end": 8289, + "start": 8159, + "end": 8195, "loc": { "start": { "line": 221, @@ -25230,8 +24846,8 @@ }, { "type": "ReturnStatement", - "start": 8294, - "end": 8333, + "start": 8200, + "end": 8239, "loc": { "start": { "line": 222, @@ -25244,8 +24860,8 @@ }, "argument": { "type": "TemplateLiteral", - "start": 8301, - "end": 8332, + "start": 8207, + "end": 8238, "loc": { "start": { "line": 222, @@ -25259,8 +24875,8 @@ "expressions": [ { "type": "MemberExpression", - "start": 8313, - "end": 8330, + "start": 8219, + "end": 8236, "loc": { "start": { "line": 222, @@ -25273,8 +24889,8 @@ }, "object": { "type": "ThisExpression", - "start": 8313, - "end": 8317, + "start": 8219, + "end": 8223, "loc": { "start": { "line": 222, @@ -25288,8 +24904,8 @@ }, "property": { "type": "Identifier", - "start": 8318, - "end": 8330, + "start": 8224, + "end": 8236, "loc": { "start": { "line": 222, @@ -25309,8 +24925,8 @@ "quasis": [ { "type": "TemplateElement", - "start": 8302, - "end": 8311, + "start": 8208, + "end": 8217, "loc": { "start": { "line": 222, @@ -25330,8 +24946,8 @@ }, { "type": "TemplateElement", - "start": 8331, - "end": 8331, + "start": 8237, + "end": 8237, "loc": { "start": { "line": 222, @@ -25355,8 +24971,8 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 8253, - "end": 8289, + "start": 8159, + "end": 8195, "loc": { "start": { "line": 221, @@ -25378,8 +24994,8 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7812, - "end": 7852, + "start": 7718, + "end": 7758, "loc": { "start": { "line": 210, @@ -25396,8 +25012,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 8341, - "end": 8402, + "start": 8247, + "end": 8308, "loc": { "start": { "line": 225, @@ -25413,8 +25029,8 @@ }, { "type": "ClassMethod", - "start": 8405, - "end": 8834, + "start": 8311, + "end": 8740, "loc": { "start": { "line": 226, @@ -25429,8 +25045,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 8409, - "end": 8424, + "start": 8315, + "end": 8330, "loc": { "start": { "line": 226, @@ -25452,8 +25068,8 @@ "params": [], "body": { "type": "BlockStatement", - "start": 8427, - "end": 8834, + "start": 8333, + "end": 8740, "loc": { "start": { "line": 226, @@ -25467,8 +25083,8 @@ "body": [ { "type": "IfStatement", - "start": 8487, - "end": 8528, + "start": 8393, + "end": 8434, "loc": { "start": { "line": 228, @@ -25481,8 +25097,8 @@ }, "test": { "type": "UnaryExpression", - "start": 8491, - "end": 8509, + "start": 8397, + "end": 8415, "loc": { "start": { "line": 228, @@ -25497,8 +25113,8 @@ "prefix": true, "argument": { "type": "MemberExpression", - "start": 8492, - "end": 8509, + "start": 8398, + "end": 8415, "loc": { "start": { "line": 228, @@ -25511,8 +25127,8 @@ }, "object": { "type": "ThisExpression", - "start": 8492, - "end": 8496, + "start": 8398, + "end": 8402, "loc": { "start": { "line": 228, @@ -25527,8 +25143,8 @@ }, "property": { "type": "Identifier", - "start": 8497, - "end": 8509, + "start": 8403, + "end": 8415, "loc": { "start": { "line": 228, @@ -25552,8 +25168,8 @@ }, "consequent": { "type": "ReturnStatement", - "start": 8511, - "end": 8528, + "start": 8417, + "end": 8434, "loc": { "start": { "line": 228, @@ -25566,8 +25182,8 @@ }, "argument": { "type": "Identifier", - "start": 8518, - "end": 8527, + "start": 8424, + "end": 8433, "loc": { "start": { "line": 228, @@ -25588,8 +25204,8 @@ { "type": "CommentLine", "value": " We can't do anything without an occurrence ID!", - "start": 8433, - "end": 8482, + "start": 8339, + "end": 8388, "loc": { "start": { "line": 227, @@ -25606,8 +25222,8 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 8534, - "end": 8605, + "start": 8440, + "end": 8511, "loc": { "start": { "line": 230, @@ -25622,8 +25238,8 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 8610, - "end": 8657, + "start": 8516, + "end": 8563, "loc": { "start": { "line": 231, @@ -25638,8 +25254,8 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8663, - "end": 8695, + "start": 8569, + "end": 8601, "loc": { "start": { "line": 233, @@ -25655,8 +25271,8 @@ }, { "type": "ReturnStatement", - "start": 8700, - "end": 8830, + "start": 8606, + "end": 8736, "loc": { "start": { "line": 234, @@ -25669,8 +25285,8 @@ }, "argument": { "type": "ObjectExpression", - "start": 8707, - "end": 8829, + "start": 8613, + "end": 8735, "loc": { "start": { "line": 234, @@ -25684,8 +25300,8 @@ "properties": [ { "type": "ObjectProperty", - "start": 8715, - "end": 8741, + "start": 8621, + "end": 8647, "loc": { "start": { "line": 235, @@ -25701,8 +25317,8 @@ "computed": false, "key": { "type": "StringLiteral", - "start": 8715, - "end": 8722, + "start": 8621, + "end": 8628, "loc": { "start": { "line": 235, @@ -25722,8 +25338,8 @@ }, "value": { "type": "StringLiteral", - "start": 8724, - "end": 8741, + "start": 8630, + "end": 8647, "loc": { "start": { "line": 235, @@ -25744,8 +25360,8 @@ }, { "type": "ObjectProperty", - "start": 8749, - "end": 8787, + "start": 8655, + "end": 8693, "loc": { "start": { "line": 236, @@ -25761,8 +25377,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 8749, - "end": 8759, + "start": 8655, + "end": 8665, "loc": { "start": { "line": 236, @@ -25778,8 +25394,8 @@ }, "value": { "type": "MemberExpression", - "start": 8761, - "end": 8787, + "start": 8667, + "end": 8693, "loc": { "start": { "line": 236, @@ -25792,8 +25408,8 @@ }, "object": { "type": "Identifier", - "start": 8761, - "end": 8769, + "start": 8667, + "end": 8675, "loc": { "start": { "line": 236, @@ -25809,8 +25425,8 @@ }, "property": { "type": "Identifier", - "start": 8770, - "end": 8787, + "start": 8676, + "end": 8693, "loc": { "start": { "line": 236, @@ -25829,8 +25445,8 @@ }, { "type": "ObjectProperty", - "start": 8795, - "end": 8822, + "start": 8701, + "end": 8728, "loc": { "start": { "line": 237, @@ -25846,8 +25462,8 @@ "computed": false, "key": { "type": "Identifier", - "start": 8795, - "end": 8803, + "start": 8701, + "end": 8709, "loc": { "start": { "line": 237, @@ -25863,8 +25479,8 @@ }, "value": { "type": "MemberExpression", - "start": 8805, - "end": 8822, + "start": 8711, + "end": 8728, "loc": { "start": { "line": 237, @@ -25877,8 +25493,8 @@ }, "object": { "type": "ThisExpression", - "start": 8805, - "end": 8809, + "start": 8711, + "end": 8715, "loc": { "start": { "line": 237, @@ -25892,8 +25508,8 @@ }, "property": { "type": "Identifier", - "start": 8810, - "end": 8822, + "start": 8716, + "end": 8728, "loc": { "start": { "line": 237, @@ -25917,8 +25533,8 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 8534, - "end": 8605, + "start": 8440, + "end": 8511, "loc": { "start": { "line": 230, @@ -25933,8 +25549,8 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 8610, - "end": 8657, + "start": 8516, + "end": 8563, "loc": { "start": { "line": 231, @@ -25949,8 +25565,8 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8663, - "end": 8695, + "start": 8569, + "end": 8601, "loc": { "start": { "line": 233, @@ -25971,8 +25587,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 8341, - "end": 8402, + "start": 8247, + "end": 8308, "loc": { "start": { "line": 225, @@ -25991,9 +25607,9 @@ "leadingComments": [ { "type": "CommentBlock", - "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", + "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a occurrenceID with the occurrence identifier.\n * - Should have a basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", "start": 325, - "end": 1088, + "end": 1080, "loc": { "start": { "line": 9, @@ -26019,9 +25635,9 @@ "comments": [ { "type": "CommentBlock", - "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", + "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a occurrenceID with the occurrence identifier.\n * - Should have a basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", "start": 325, - "end": 1088, + "end": 1080, "loc": { "start": { "line": 9, @@ -26036,8 +25652,8 @@ { "type": "CommentBlock", "value": "* The '@type' of specimens in JSON-LD document. ", - "start": 1115, - "end": 1167, + "start": 1107, + "end": 1159, "loc": { "start": { "line": 25, @@ -26052,8 +25668,8 @@ { "type": "CommentBlock", "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "start": 1234, + "end": 1279, "loc": { "start": { "line": 30, @@ -26068,8 +25684,8 @@ { "type": "CommentBlock", "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", - "start": 1351, - "end": 1449, + "start": 1343, + "end": 1441, "loc": { "start": { "line": 35, @@ -26084,8 +25700,8 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1986, - "end": 2267, + "start": 1972, + "end": 2253, "loc": { "start": { "line": 54, @@ -26100,8 +25716,8 @@ { "type": "CommentLine", "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 2351, - "end": 2412, + "start": 2337, + "end": 2398, "loc": { "start": { "line": 61, @@ -26116,8 +25732,8 @@ { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 2524, - "end": 2548, + "start": 2513, + "end": 2537, "loc": { "start": { "line": 65, @@ -26132,8 +25748,8 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2701, - "end": 2774, + "start": 2669, + "end": 2742, "loc": { "start": { "line": 72, @@ -26148,8 +25764,8 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2779, - "end": 2834, + "start": 2747, + "end": 2802, "loc": { "start": { "line": 73, @@ -26164,8 +25780,8 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 3104, - "end": 3173, + "start": 3072, + "end": 3141, "loc": { "start": { "line": 86, @@ -26180,8 +25796,8 @@ { "type": "CommentLine", "value": " Split the occurrence ID into components, and store them in the appropriate fields.", - "start": 3344, - "end": 3429, + "start": 3312, + "end": 3397, "loc": { "start": { "line": 91, @@ -26196,8 +25812,8 @@ { "type": "CommentLine", "value": " specimen.institutionCode = undefined;", - "start": 3504, - "end": 3544, + "start": 3472, + "end": 3512, "loc": { "start": { "line": 94, @@ -26212,8 +25828,8 @@ { "type": "CommentLine", "value": " specimen.collectionCode = undefined;", - "start": 3551, - "end": 3590, + "start": 3519, + "end": 3558, "loc": { "start": { "line": 95, @@ -26228,8 +25844,8 @@ { "type": "CommentLine", "value": " Store all split catalog number values.", - "start": 3803, - "end": 3844, + "start": 3771, + "end": 3812, "loc": { "start": { "line": 100, @@ -26244,8 +25860,8 @@ { "type": "CommentBlock", "value": "*\n * Get the catalogNumber if present.\n ", - "start": 4109, - "end": 4157, + "start": 4077, + "end": 4125, "loc": { "start": { "line": 109, @@ -26260,8 +25876,8 @@ { "type": "CommentLine", "value": " Get the catalog number from the specimen object if present.", - "start": 4186, - "end": 4248, + "start": 4154, + "end": 4216, "loc": { "start": { "line": 113, @@ -26276,8 +25892,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract a", - "start": 4335, - "end": 4406, + "start": 4303, + "end": 4374, "loc": { "start": { "line": 116, @@ -26292,8 +25908,8 @@ { "type": "CommentLine", "value": " catalogNumber from there.", - "start": 4411, - "end": 4439, + "start": 4379, + "end": 4407, "loc": { "start": { "line": 117, @@ -26308,8 +25924,8 @@ { "type": "CommentBlock", "value": "*\n * Get the institutionCode if present.\n ", - "start": 4679, - "end": 4729, + "start": 4647, + "end": 4697, "loc": { "start": { "line": 125, @@ -26324,8 +25940,8 @@ { "type": "CommentLine", "value": " Get the institution code from the specimen object if present.", - "start": 4760, - "end": 4824, + "start": 4728, + "end": 4792, "loc": { "start": { "line": 129, @@ -26340,8 +25956,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 4915, - "end": 4987, + "start": 4883, + "end": 4955, "loc": { "start": { "line": 132, @@ -26356,8 +25972,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 4992, - "end": 5019, + "start": 4960, + "end": 4987, "loc": { "start": { "line": 133, @@ -26372,8 +25988,8 @@ { "type": "CommentBlock", "value": "*\n * Get the collectionCode if present.\n ", - "start": 5263, - "end": 5312, + "start": 5231, + "end": 5280, "loc": { "start": { "line": 141, @@ -26388,8 +26004,8 @@ { "type": "CommentLine", "value": " Get the collection code from the specimen object if present.", - "start": 5342, - "end": 5405, + "start": 5310, + "end": 5373, "loc": { "start": { "line": 145, @@ -26404,8 +26020,8 @@ { "type": "CommentLine", "value": " Otherwise, try to parse the occurrenceID and see if we can extract an", - "start": 5494, - "end": 5566, + "start": 5462, + "end": 5534, "loc": { "start": { "line": 148, @@ -26420,8 +26036,8 @@ { "type": "CommentLine", "value": " occurrenceID from there.", - "start": 5571, - "end": 5598, + "start": 5539, + "end": 5566, "loc": { "start": { "line": 149, @@ -26436,8 +26052,8 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5840, - "end": 6099, + "start": 5808, + "end": 6067, "loc": { "start": { "line": 157, @@ -26452,8 +26068,8 @@ { "type": "CommentLine", "value": " Return the occurrenceID if it exists.", - "start": 6127, - "end": 6167, + "start": 6095, + "end": 6135, "loc": { "start": { "line": 164, @@ -26468,8 +26084,8 @@ { "type": "CommentLine", "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 6317, - "end": 6394, + "start": 6241, + "end": 6318, "loc": { "start": { "line": 169, @@ -26484,8 +26100,8 @@ { "type": "CommentLine", "value": " None of our specimen identifier schemes worked.", - "start": 7066, - "end": 7116, + "start": 6990, + "end": 7040, "loc": { "start": { "line": 183, @@ -26500,8 +26116,8 @@ { "type": "CommentBlock", "value": "*\n * Return the basis of record, if one is present.\n ", - "start": 7146, - "end": 7207, + "start": 7070, + "end": 7131, "loc": { "start": { "line": 187, @@ -26516,8 +26132,8 @@ { "type": "CommentBlock", "value": "*\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n ", - "start": 7353, - "end": 7468, + "start": 7266, + "end": 7381, "loc": { "start": { "line": 195, @@ -26532,8 +26148,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as a taxon concept if it contains taxon name information. ", - "start": 7549, - "end": 7634, + "start": 7455, + "end": 7540, "loc": { "start": { "line": 203, @@ -26548,8 +26164,8 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7812, - "end": 7852, + "start": 7718, + "end": 7758, "loc": { "start": { "line": 210, @@ -26564,8 +26180,8 @@ { "type": "CommentLine", "value": " We can't return anything without an occurrenceID.", - "start": 7873, - "end": 7925, + "start": 7779, + "end": 7831, "loc": { "start": { "line": 212, @@ -26580,8 +26196,8 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7977, - "end": 8054, + "start": 7883, + "end": 7960, "loc": { "start": { "line": 215, @@ -26596,8 +26212,8 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 8059, - "end": 8100, + "start": 7965, + "end": 8006, "loc": { "start": { "line": 216, @@ -26612,8 +26228,8 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 8253, - "end": 8289, + "start": 8159, + "end": 8195, "loc": { "start": { "line": 221, @@ -26628,8 +26244,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 8341, - "end": 8402, + "start": 8247, + "end": 8308, "loc": { "start": { "line": 225, @@ -26644,8 +26260,8 @@ { "type": "CommentLine", "value": " We can't do anything without an occurrence ID!", - "start": 8433, - "end": 8482, + "start": 8339, + "end": 8388, "loc": { "start": { "line": 227, @@ -26660,8 +26276,8 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 8534, - "end": 8605, + "start": 8440, + "end": 8511, "loc": { "start": { "line": 230, @@ -26676,8 +26292,8 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 8610, - "end": 8657, + "start": 8516, + "end": 8563, "loc": { "start": { "line": 231, @@ -26692,8 +26308,8 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8663, - "end": 8695, + "start": 8569, + "end": 8601, "loc": { "start": { "line": 233, @@ -26800,7 +26416,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8J7MTDE", + "value": "M50HFXVTJPWM5", "start": 12, "end": 25, "loc": { @@ -27036,7 +26652,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8J7MTDE", + "value": "M50HFXVTJPWM5", "start": 58, "end": 71, "loc": { @@ -27169,7 +26785,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8JTNLQE", + "value": "M50HFXVT2CD2B", "start": 85, "end": 98, "loc": { @@ -27405,7 +27021,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8JTNLQE", + "value": "M50HFXVT2CD2B", "start": 162, "end": 175, "loc": { @@ -27671,7 +27287,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8JDZPL7", + "value": "M50HFXVT6MY40", "start": 231, "end": 244, "loc": { @@ -27907,7 +27523,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8JDZPL7", + "value": "M50HFXVT6MY40", "start": 309, "end": 322, "loc": { @@ -27949,9 +27565,9 @@ }, { "type": "CommentBlock", - "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", + "value": "*\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a occurrenceID with the occurrence identifier.\n * - Should have a basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n ", "start": 325, - "end": 1088, + "end": 1080, "loc": { "start": { "line": 9, @@ -27978,8 +27594,8 @@ "updateContext": null }, "value": "class", - "start": 1089, - "end": 1094, + "start": 1081, + "end": 1086, "loc": { "start": { "line": 24, @@ -28004,8 +27620,8 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 1095, - "end": 1110, + "start": 1087, + "end": 1102, "loc": { "start": { "line": 24, @@ -28029,8 +27645,8 @@ "postfix": false, "binop": null }, - "start": 1111, - "end": 1112, + "start": 1103, + "end": 1104, "loc": { "start": { "line": 24, @@ -28045,8 +27661,8 @@ { "type": "CommentBlock", "value": "* The '@type' of specimens in JSON-LD document. ", - "start": 1115, - "end": 1167, + "start": 1107, + "end": 1159, "loc": { "start": { "line": 25, @@ -28071,8 +27687,8 @@ "binop": null }, "value": "static", - "start": 1170, - "end": 1176, + "start": 1162, + "end": 1168, "loc": { "start": { "line": 26, @@ -28097,8 +27713,8 @@ "binop": null }, "value": "get", - "start": 1177, - "end": 1180, + "start": 1169, + "end": 1172, "loc": { "start": { "line": 26, @@ -28123,8 +27739,8 @@ "binop": null }, "value": "TYPE_SPECIMEN", - "start": 1181, - "end": 1194, + "start": 1173, + "end": 1186, "loc": { "start": { "line": 26, @@ -28148,8 +27764,8 @@ "postfix": false, "binop": null }, - "start": 1194, - "end": 1195, + "start": 1186, + "end": 1187, "loc": { "start": { "line": 26, @@ -28173,8 +27789,8 @@ "postfix": false, "binop": null }, - "start": 1195, - "end": 1196, + "start": 1187, + "end": 1188, "loc": { "start": { "line": 26, @@ -28198,8 +27814,8 @@ "postfix": false, "binop": null }, - "start": 1197, - "end": 1198, + "start": 1189, + "end": 1190, "loc": { "start": { "line": 26, @@ -28226,8 +27842,8 @@ "updateContext": null }, "value": "return", - "start": 1203, - "end": 1209, + "start": 1195, + "end": 1201, "loc": { "start": { "line": 27, @@ -28252,8 +27868,8 @@ "binop": null }, "value": "owlterms", - "start": 1210, - "end": 1218, + "start": 1202, + "end": 1210, "loc": { "start": { "line": 27, @@ -28278,8 +27894,8 @@ "binop": null, "updateContext": null }, - "start": 1218, - "end": 1219, + "start": 1210, + "end": 1211, "loc": { "start": { "line": 27, @@ -28304,8 +27920,8 @@ "binop": null }, "value": "DWC_OCCURRENCE", - "start": 1219, - "end": 1233, + "start": 1211, + "end": 1225, "loc": { "start": { "line": 27, @@ -28330,8 +27946,8 @@ "binop": null, "updateContext": null }, - "start": 1233, - "end": 1234, + "start": 1225, + "end": 1226, "loc": { "start": { "line": 27, @@ -28355,8 +27971,8 @@ "postfix": false, "binop": null }, - "start": 1237, - "end": 1238, + "start": 1229, + "end": 1230, "loc": { "start": { "line": 28, @@ -28371,8 +27987,8 @@ { "type": "CommentBlock", "value": "* Construct a wrapper around a specimen. ", - "start": 1242, - "end": 1287, + "start": 1234, + "end": 1279, "loc": { "start": { "line": 30, @@ -28397,8 +28013,8 @@ "binop": null }, "value": "constructor", - "start": 1290, - "end": 1301, + "start": 1282, + "end": 1293, "loc": { "start": { "line": 31, @@ -28422,8 +28038,8 @@ "postfix": false, "binop": null }, - "start": 1301, - "end": 1302, + "start": 1293, + "end": 1294, "loc": { "start": { "line": 31, @@ -28448,8 +28064,8 @@ "binop": null }, "value": "specimen", - "start": 1302, - "end": 1310, + "start": 1294, + "end": 1302, "loc": { "start": { "line": 31, @@ -28473,8 +28089,8 @@ "postfix": false, "binop": null }, - "start": 1310, - "end": 1311, + "start": 1302, + "end": 1303, "loc": { "start": { "line": 31, @@ -28498,8 +28114,8 @@ "postfix": false, "binop": null }, - "start": 1312, - "end": 1313, + "start": 1304, + "end": 1305, "loc": { "start": { "line": 31, @@ -28526,8 +28142,8 @@ "updateContext": null }, "value": "this", - "start": 1318, - "end": 1322, + "start": 1310, + "end": 1314, "loc": { "start": { "line": 32, @@ -28552,8 +28168,8 @@ "binop": null, "updateContext": null }, - "start": 1322, - "end": 1323, + "start": 1314, + "end": 1315, "loc": { "start": { "line": 32, @@ -28578,8 +28194,8 @@ "binop": null }, "value": "specimen", - "start": 1323, - "end": 1331, + "start": 1315, + "end": 1323, "loc": { "start": { "line": 32, @@ -28605,8 +28221,8 @@ "updateContext": null }, "value": "=", - "start": 1332, - "end": 1333, + "start": 1324, + "end": 1325, "loc": { "start": { "line": 32, @@ -28631,8 +28247,8 @@ "binop": null }, "value": "specimen", - "start": 1334, - "end": 1342, + "start": 1326, + "end": 1334, "loc": { "start": { "line": 32, @@ -28657,8 +28273,8 @@ "binop": null, "updateContext": null }, - "start": 1342, - "end": 1343, + "start": 1334, + "end": 1335, "loc": { "start": { "line": 32, @@ -28682,8 +28298,8 @@ "postfix": false, "binop": null }, - "start": 1346, - "end": 1347, + "start": 1338, + "end": 1339, "loc": { "start": { "line": 33, @@ -28698,8 +28314,8 @@ { "type": "CommentBlock", "value": "*\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n ", - "start": 1351, - "end": 1449, + "start": 1343, + "end": 1441, "loc": { "start": { "line": 35, @@ -28724,8 +28340,8 @@ "binop": null }, "value": "static", - "start": 1452, - "end": 1458, + "start": 1444, + "end": 1450, "loc": { "start": { "line": 39, @@ -28750,8 +28366,8 @@ "binop": null }, "value": "normalize", - "start": 1459, - "end": 1468, + "start": 1451, + "end": 1460, "loc": { "start": { "line": 39, @@ -28775,8 +28391,8 @@ "postfix": false, "binop": null }, - "start": 1468, - "end": 1469, + "start": 1460, + "end": 1461, "loc": { "start": { "line": 39, @@ -28801,8 +28417,8 @@ "binop": null }, "value": "specimen", - "start": 1469, - "end": 1477, + "start": 1461, + "end": 1469, "loc": { "start": { "line": 39, @@ -28826,8 +28442,8 @@ "postfix": false, "binop": null }, - "start": 1477, - "end": 1478, + "start": 1469, + "end": 1470, "loc": { "start": { "line": 39, @@ -28851,8 +28467,8 @@ "postfix": false, "binop": null }, - "start": 1479, - "end": 1480, + "start": 1471, + "end": 1472, "loc": { "start": { "line": 39, @@ -28879,8 +28495,8 @@ "updateContext": null }, "value": "const", - "start": 1485, - "end": 1490, + "start": 1477, + "end": 1482, "loc": { "start": { "line": 40, @@ -28905,8 +28521,8 @@ "binop": null }, "value": "wrapped", - "start": 1491, - "end": 1498, + "start": 1483, + "end": 1490, "loc": { "start": { "line": 40, @@ -28932,8 +28548,8 @@ "updateContext": null }, "value": "=", - "start": 1499, - "end": 1500, + "start": 1491, + "end": 1492, "loc": { "start": { "line": 40, @@ -28960,8 +28576,8 @@ "updateContext": null }, "value": "new", - "start": 1501, - "end": 1504, + "start": 1493, + "end": 1496, "loc": { "start": { "line": 40, @@ -28986,8 +28602,8 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 1505, - "end": 1520, + "start": 1497, + "end": 1512, "loc": { "start": { "line": 40, @@ -29011,8 +28627,8 @@ "postfix": false, "binop": null }, - "start": 1520, - "end": 1521, + "start": 1512, + "end": 1513, "loc": { "start": { "line": 40, @@ -29037,8 +28653,8 @@ "binop": null }, "value": "specimen", - "start": 1521, - "end": 1529, + "start": 1513, + "end": 1521, "loc": { "start": { "line": 40, @@ -29062,8 +28678,8 @@ "postfix": false, "binop": null }, - "start": 1529, - "end": 1530, + "start": 1521, + "end": 1522, "loc": { "start": { "line": 40, @@ -29088,8 +28704,8 @@ "binop": null, "updateContext": null }, - "start": 1530, - "end": 1531, + "start": 1522, + "end": 1523, "loc": { "start": { "line": 40, @@ -29116,8 +28732,8 @@ "updateContext": null }, "value": "const", - "start": 1536, - "end": 1541, + "start": 1528, + "end": 1533, "loc": { "start": { "line": 41, @@ -29142,8 +28758,8 @@ "binop": null }, "value": "normalizedSpecimen", - "start": 1542, - "end": 1560, + "start": 1534, + "end": 1552, "loc": { "start": { "line": 41, @@ -29169,8 +28785,8 @@ "updateContext": null }, "value": "=", - "start": 1561, - "end": 1562, + "start": 1553, + "end": 1554, "loc": { "start": { "line": 41, @@ -29194,8 +28810,8 @@ "postfix": false, "binop": null }, - "start": 1563, - "end": 1564, + "start": 1555, + "end": 1556, "loc": { "start": { "line": 41, @@ -29221,8 +28837,8 @@ "updateContext": null }, "value": "@type", - "start": 1571, - "end": 1578, + "start": 1563, + "end": 1570, "loc": { "start": { "line": 42, @@ -29247,8 +28863,8 @@ "binop": null, "updateContext": null }, - "start": 1578, - "end": 1579, + "start": 1570, + "end": 1571, "loc": { "start": { "line": 42, @@ -29273,8 +28889,8 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 1580, - "end": 1595, + "start": 1572, + "end": 1587, "loc": { "start": { "line": 42, @@ -29299,8 +28915,8 @@ "binop": null, "updateContext": null }, - "start": 1595, - "end": 1596, + "start": 1587, + "end": 1588, "loc": { "start": { "line": 42, @@ -29325,8 +28941,8 @@ "binop": null }, "value": "TYPE_SPECIMEN", - "start": 1596, - "end": 1609, + "start": 1588, + "end": 1601, "loc": { "start": { "line": 42, @@ -29351,8 +28967,8 @@ "binop": null, "updateContext": null }, - "start": 1609, - "end": 1610, + "start": 1601, + "end": 1602, "loc": { "start": { "line": 42, @@ -29377,8 +28993,8 @@ "binop": null }, "value": "label", - "start": 1617, - "end": 1622, + "start": 1609, + "end": 1614, "loc": { "start": { "line": 43, @@ -29403,8 +29019,8 @@ "binop": null, "updateContext": null }, - "start": 1622, - "end": 1623, + "start": 1614, + "end": 1615, "loc": { "start": { "line": 43, @@ -29429,8 +29045,8 @@ "binop": null }, "value": "wrapped", - "start": 1624, - "end": 1631, + "start": 1616, + "end": 1623, "loc": { "start": { "line": 43, @@ -29455,8 +29071,8 @@ "binop": null, "updateContext": null }, - "start": 1631, - "end": 1632, + "start": 1623, + "end": 1624, "loc": { "start": { "line": 43, @@ -29481,8 +29097,8 @@ "binop": null }, "value": "label", - "start": 1632, - "end": 1637, + "start": 1624, + "end": 1629, "loc": { "start": { "line": 43, @@ -29507,8 +29123,8 @@ "binop": null, "updateContext": null }, - "start": 1637, - "end": 1638, + "start": 1629, + "end": 1630, "loc": { "start": { "line": 43, @@ -29522,7 +29138,7 @@ }, { "type": { - "label": "string", + "label": "name", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -29530,12 +29146,11 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null, - "updateContext": null + "binop": null }, - "value": "dwc:basisOfRecord", - "start": 1645, - "end": 1664, + "value": "basisOfRecord", + "start": 1637, + "end": 1650, "loc": { "start": { "line": 44, @@ -29543,7 +29158,7 @@ }, "end": { "line": 44, - "column": 25 + "column": 19 } } }, @@ -29560,16 +29175,16 @@ "binop": null, "updateContext": null }, - "start": 1664, - "end": 1665, + "start": 1650, + "end": 1651, "loc": { "start": { "line": 44, - "column": 25 + "column": 19 }, "end": { "line": 44, - "column": 26 + "column": 20 } } }, @@ -29586,16 +29201,16 @@ "binop": null }, "value": "wrapped", - "start": 1666, - "end": 1673, + "start": 1652, + "end": 1659, "loc": { "start": { "line": 44, - "column": 27 + "column": 21 }, "end": { "line": 44, - "column": 34 + "column": 28 } } }, @@ -29612,16 +29227,16 @@ "binop": null, "updateContext": null }, - "start": 1673, - "end": 1674, + "start": 1659, + "end": 1660, "loc": { "start": { "line": 44, - "column": 34 + "column": 28 }, "end": { "line": 44, - "column": 35 + "column": 29 } } }, @@ -29638,16 +29253,16 @@ "binop": null }, "value": "basisOfRecord", - "start": 1674, - "end": 1687, + "start": 1660, + "end": 1673, "loc": { "start": { "line": 44, - "column": 35 + "column": 29 }, "end": { "line": 44, - "column": 48 + "column": 42 } } }, @@ -29664,16 +29279,16 @@ "binop": null, "updateContext": null }, - "start": 1687, - "end": 1688, + "start": 1673, + "end": 1674, "loc": { "start": { "line": 44, - "column": 48 + "column": 42 }, "end": { "line": 44, - "column": 49 + "column": 43 } } }, @@ -29690,8 +29305,8 @@ "binop": null }, "value": "occurrenceID", - "start": 1695, - "end": 1707, + "start": 1681, + "end": 1693, "loc": { "start": { "line": 45, @@ -29716,8 +29331,8 @@ "binop": null, "updateContext": null }, - "start": 1707, - "end": 1708, + "start": 1693, + "end": 1694, "loc": { "start": { "line": 45, @@ -29742,8 +29357,8 @@ "binop": null }, "value": "wrapped", - "start": 1709, - "end": 1716, + "start": 1695, + "end": 1702, "loc": { "start": { "line": 45, @@ -29768,8 +29383,8 @@ "binop": null, "updateContext": null }, - "start": 1716, - "end": 1717, + "start": 1702, + "end": 1703, "loc": { "start": { "line": 45, @@ -29794,8 +29409,8 @@ "binop": null }, "value": "occurrenceID", - "start": 1717, - "end": 1729, + "start": 1703, + "end": 1715, "loc": { "start": { "line": 45, @@ -29820,8 +29435,8 @@ "binop": null, "updateContext": null }, - "start": 1729, - "end": 1730, + "start": 1715, + "end": 1716, "loc": { "start": { "line": 45, @@ -29846,8 +29461,8 @@ "binop": null }, "value": "catalogNumber", - "start": 1737, - "end": 1750, + "start": 1723, + "end": 1736, "loc": { "start": { "line": 46, @@ -29872,8 +29487,8 @@ "binop": null, "updateContext": null }, - "start": 1750, - "end": 1751, + "start": 1736, + "end": 1737, "loc": { "start": { "line": 46, @@ -29898,8 +29513,8 @@ "binop": null }, "value": "wrapped", - "start": 1752, - "end": 1759, + "start": 1738, + "end": 1745, "loc": { "start": { "line": 46, @@ -29924,8 +29539,8 @@ "binop": null, "updateContext": null }, - "start": 1759, - "end": 1760, + "start": 1745, + "end": 1746, "loc": { "start": { "line": 46, @@ -29950,8 +29565,8 @@ "binop": null }, "value": "catalogNumber", - "start": 1760, - "end": 1773, + "start": 1746, + "end": 1759, "loc": { "start": { "line": 46, @@ -29976,8 +29591,8 @@ "binop": null, "updateContext": null }, - "start": 1773, - "end": 1774, + "start": 1759, + "end": 1760, "loc": { "start": { "line": 46, @@ -30002,8 +29617,8 @@ "binop": null }, "value": "institutionCode", - "start": 1781, - "end": 1796, + "start": 1767, + "end": 1782, "loc": { "start": { "line": 47, @@ -30028,8 +29643,8 @@ "binop": null, "updateContext": null }, - "start": 1796, - "end": 1797, + "start": 1782, + "end": 1783, "loc": { "start": { "line": 47, @@ -30054,8 +29669,8 @@ "binop": null }, "value": "wrapped", - "start": 1798, - "end": 1805, + "start": 1784, + "end": 1791, "loc": { "start": { "line": 47, @@ -30080,8 +29695,8 @@ "binop": null, "updateContext": null }, - "start": 1805, - "end": 1806, + "start": 1791, + "end": 1792, "loc": { "start": { "line": 47, @@ -30106,8 +29721,8 @@ "binop": null }, "value": "institutionCode", - "start": 1806, - "end": 1821, + "start": 1792, + "end": 1807, "loc": { "start": { "line": 47, @@ -30132,8 +29747,8 @@ "binop": null, "updateContext": null }, - "start": 1821, - "end": 1822, + "start": 1807, + "end": 1808, "loc": { "start": { "line": 47, @@ -30158,8 +29773,8 @@ "binop": null }, "value": "collectionCode", - "start": 1829, - "end": 1843, + "start": 1815, + "end": 1829, "loc": { "start": { "line": 48, @@ -30184,8 +29799,8 @@ "binop": null, "updateContext": null }, - "start": 1843, - "end": 1844, + "start": 1829, + "end": 1830, "loc": { "start": { "line": 48, @@ -30210,8 +29825,8 @@ "binop": null }, "value": "wrapped", - "start": 1845, - "end": 1852, + "start": 1831, + "end": 1838, "loc": { "start": { "line": 48, @@ -30236,8 +29851,8 @@ "binop": null, "updateContext": null }, - "start": 1852, - "end": 1853, + "start": 1838, + "end": 1839, "loc": { "start": { "line": 48, @@ -30262,8 +29877,8 @@ "binop": null }, "value": "collectionCode", - "start": 1853, - "end": 1867, + "start": 1839, + "end": 1853, "loc": { "start": { "line": 48, @@ -30288,8 +29903,8 @@ "binop": null, "updateContext": null }, - "start": 1867, - "end": 1868, + "start": 1853, + "end": 1854, "loc": { "start": { "line": 48, @@ -30313,8 +29928,8 @@ "postfix": false, "binop": null }, - "start": 1873, - "end": 1874, + "start": 1859, + "end": 1860, "loc": { "start": { "line": 49, @@ -30339,8 +29954,8 @@ "binop": null, "updateContext": null }, - "start": 1874, - "end": 1875, + "start": 1860, + "end": 1861, "loc": { "start": { "line": 49, @@ -30367,8 +29982,8 @@ "updateContext": null }, "value": "if", - "start": 1880, - "end": 1882, + "start": 1866, + "end": 1868, "loc": { "start": { "line": 50, @@ -30392,8 +30007,8 @@ "postfix": false, "binop": null }, - "start": 1883, - "end": 1884, + "start": 1869, + "end": 1870, "loc": { "start": { "line": 50, @@ -30419,8 +30034,8 @@ "updateContext": null }, "value": "@id", - "start": 1884, - "end": 1889, + "start": 1870, + "end": 1875, "loc": { "start": { "line": 50, @@ -30447,8 +30062,8 @@ "updateContext": null }, "value": "in", - "start": 1890, - "end": 1892, + "start": 1876, + "end": 1878, "loc": { "start": { "line": 50, @@ -30473,8 +30088,8 @@ "binop": null }, "value": "specimen", - "start": 1893, - "end": 1901, + "start": 1879, + "end": 1887, "loc": { "start": { "line": 50, @@ -30498,8 +30113,8 @@ "postfix": false, "binop": null }, - "start": 1901, - "end": 1902, + "start": 1887, + "end": 1888, "loc": { "start": { "line": 50, @@ -30524,8 +30139,8 @@ "binop": null }, "value": "normalizedSpecimen", - "start": 1903, - "end": 1921, + "start": 1889, + "end": 1907, "loc": { "start": { "line": 50, @@ -30550,8 +30165,8 @@ "binop": null, "updateContext": null }, - "start": 1921, - "end": 1922, + "start": 1907, + "end": 1908, "loc": { "start": { "line": 50, @@ -30577,8 +30192,8 @@ "updateContext": null }, "value": "@id", - "start": 1922, - "end": 1927, + "start": 1908, + "end": 1913, "loc": { "start": { "line": 50, @@ -30603,8 +30218,8 @@ "binop": null, "updateContext": null }, - "start": 1927, - "end": 1928, + "start": 1913, + "end": 1914, "loc": { "start": { "line": 50, @@ -30630,8 +30245,8 @@ "updateContext": null }, "value": "=", - "start": 1929, - "end": 1930, + "start": 1915, + "end": 1916, "loc": { "start": { "line": 50, @@ -30656,8 +30271,8 @@ "binop": null }, "value": "specimen", - "start": 1931, - "end": 1939, + "start": 1917, + "end": 1925, "loc": { "start": { "line": 50, @@ -30682,8 +30297,8 @@ "binop": null, "updateContext": null }, - "start": 1939, - "end": 1940, + "start": 1925, + "end": 1926, "loc": { "start": { "line": 50, @@ -30709,8 +30324,8 @@ "updateContext": null }, "value": "@id", - "start": 1940, - "end": 1945, + "start": 1926, + "end": 1931, "loc": { "start": { "line": 50, @@ -30735,8 +30350,8 @@ "binop": null, "updateContext": null }, - "start": 1945, - "end": 1946, + "start": 1931, + "end": 1932, "loc": { "start": { "line": 50, @@ -30761,8 +30376,8 @@ "binop": null, "updateContext": null }, - "start": 1946, - "end": 1947, + "start": 1932, + "end": 1933, "loc": { "start": { "line": 50, @@ -30789,8 +30404,8 @@ "updateContext": null }, "value": "return", - "start": 1952, - "end": 1958, + "start": 1938, + "end": 1944, "loc": { "start": { "line": 51, @@ -30815,8 +30430,8 @@ "binop": null }, "value": "normalizedSpecimen", - "start": 1959, - "end": 1977, + "start": 1945, + "end": 1963, "loc": { "start": { "line": 51, @@ -30841,8 +30456,8 @@ "binop": null, "updateContext": null }, - "start": 1977, - "end": 1978, + "start": 1963, + "end": 1964, "loc": { "start": { "line": 51, @@ -30866,8 +30481,8 @@ "postfix": false, "binop": null }, - "start": 1981, - "end": 1982, + "start": 1967, + "end": 1968, "loc": { "start": { "line": 52, @@ -30882,8 +30497,8 @@ { "type": "CommentBlock", "value": "*\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n ", - "start": 1986, - "end": 2267, + "start": 1972, + "end": 2253, "loc": { "start": { "line": 54, @@ -30908,8 +30523,8 @@ "binop": null }, "value": "static", - "start": 2270, - "end": 2276, + "start": 2256, + "end": 2262, "loc": { "start": { "line": 60, @@ -30934,8 +30549,8 @@ "binop": null }, "value": "fromOccurrenceID", - "start": 2277, - "end": 2293, + "start": 2263, + "end": 2279, "loc": { "start": { "line": 60, @@ -30959,8 +30574,8 @@ "postfix": false, "binop": null }, - "start": 2293, - "end": 2294, + "start": 2279, + "end": 2280, "loc": { "start": { "line": 60, @@ -30985,8 +30600,8 @@ "binop": null }, "value": "occurrenceID", - "start": 2294, - "end": 2306, + "start": 2280, + "end": 2292, "loc": { "start": { "line": 60, @@ -31011,8 +30626,8 @@ "binop": null, "updateContext": null }, - "start": 2306, - "end": 2307, + "start": 2292, + "end": 2293, "loc": { "start": { "line": 60, @@ -31037,8 +30652,8 @@ "binop": null }, "value": "basisOfRecord", - "start": 2308, - "end": 2321, + "start": 2294, + "end": 2307, "loc": { "start": { "line": 60, @@ -31064,8 +30679,8 @@ "updateContext": null }, "value": "=", - "start": 2322, - "end": 2323, + "start": 2308, + "end": 2309, "loc": { "start": { "line": 60, @@ -31091,8 +30706,8 @@ "updateContext": null }, "value": "PreservedSpecimen", - "start": 2324, - "end": 2343, + "start": 2310, + "end": 2329, "loc": { "start": { "line": 60, @@ -31116,8 +30731,8 @@ "postfix": false, "binop": null }, - "start": 2343, - "end": 2344, + "start": 2329, + "end": 2330, "loc": { "start": { "line": 60, @@ -31141,8 +30756,8 @@ "postfix": false, "binop": null }, - "start": 2345, - "end": 2346, + "start": 2331, + "end": 2332, "loc": { "start": { "line": 60, @@ -31157,8 +30772,8 @@ { "type": "CommentLine", "value": " Copy the occurrence ID so we can truncate it if necessary.", - "start": 2351, - "end": 2412, + "start": 2337, + "end": 2398, "loc": { "start": { "line": 61, @@ -31185,8 +30800,8 @@ "updateContext": null }, "value": "let", - "start": 2417, - "end": 2420, + "start": 2403, + "end": 2406, "loc": { "start": { "line": 62, @@ -31211,8 +30826,8 @@ "binop": null }, "value": "occurID", - "start": 2421, - "end": 2428, + "start": 2407, + "end": 2414, "loc": { "start": { "line": 62, @@ -31238,8 +30853,8 @@ "updateContext": null }, "value": "=", - "start": 2429, - "end": 2430, + "start": 2415, + "end": 2416, "loc": { "start": { "line": 62, @@ -31264,8 +30879,8 @@ "binop": null }, "value": "occurrenceID", - "start": 2431, - "end": 2443, + "start": 2417, + "end": 2429, "loc": { "start": { "line": 62, @@ -31290,8 +30905,8 @@ "binop": null, "updateContext": null }, - "start": 2443, - "end": 2444, + "start": 2429, + "end": 2430, "loc": { "start": { "line": 62, @@ -31318,8 +30933,8 @@ "updateContext": null }, "value": "if", - "start": 2449, - "end": 2451, + "start": 2435, + "end": 2437, "loc": { "start": { "line": 63, @@ -31343,8 +30958,8 @@ "postfix": false, "binop": null }, - "start": 2452, - "end": 2453, + "start": 2438, + "end": 2439, "loc": { "start": { "line": 63, @@ -31369,8 +30984,8 @@ "binop": null }, "value": "occurID", - "start": 2453, - "end": 2460, + "start": 2439, + "end": 2446, "loc": { "start": { "line": 63, @@ -31395,8 +31010,8 @@ "binop": null, "updateContext": null }, - "start": 2460, - "end": 2461, + "start": 2446, + "end": 2447, "loc": { "start": { "line": 63, @@ -31421,8 +31036,8 @@ "binop": null }, "value": "startsWith", - "start": 2461, - "end": 2471, + "start": 2447, + "end": 2457, "loc": { "start": { "line": 63, @@ -31446,8 +31061,8 @@ "postfix": false, "binop": null }, - "start": 2471, - "end": 2472, + "start": 2457, + "end": 2458, "loc": { "start": { "line": 63, @@ -31473,8 +31088,8 @@ "updateContext": null }, "value": "urn:catalog:", - "start": 2472, - "end": 2486, + "start": 2458, + "end": 2472, "loc": { "start": { "line": 63, @@ -31498,8 +31113,8 @@ "postfix": false, "binop": null }, - "start": 2486, - "end": 2487, + "start": 2472, + "end": 2473, "loc": { "start": { "line": 63, @@ -31523,8 +31138,8 @@ "postfix": false, "binop": null }, - "start": 2487, - "end": 2488, + "start": 2473, + "end": 2474, "loc": { "start": { "line": 63, @@ -31549,8 +31164,8 @@ "binop": null }, "value": "occurID", - "start": 2489, - "end": 2496, + "start": 2475, + "end": 2482, "loc": { "start": { "line": 63, @@ -31576,8 +31191,8 @@ "updateContext": null }, "value": "=", - "start": 2497, - "end": 2498, + "start": 2483, + "end": 2484, "loc": { "start": { "line": 63, @@ -31602,8 +31217,8 @@ "binop": null }, "value": "occurID", - "start": 2499, - "end": 2506, + "start": 2485, + "end": 2492, "loc": { "start": { "line": 63, @@ -31628,8 +31243,8 @@ "binop": null, "updateContext": null }, - "start": 2506, - "end": 2507, + "start": 2492, + "end": 2493, "loc": { "start": { "line": 63, @@ -31653,9 +31268,9 @@ "postfix": false, "binop": null }, - "value": "substr", - "start": 2507, - "end": 2513, + "value": "substring", + "start": 2493, + "end": 2502, "loc": { "start": { "line": 63, @@ -31663,7 +31278,7 @@ }, "end": { "line": 63, - "column": 68 + "column": 71 } } }, @@ -31679,16 +31294,16 @@ "postfix": false, "binop": null }, - "start": 2513, - "end": 2514, + "start": 2502, + "end": 2503, "loc": { "start": { "line": 63, - "column": 68 + "column": 71 }, "end": { "line": 63, - "column": 69 + "column": 72 } } }, @@ -31706,16 +31321,16 @@ "updateContext": null }, "value": 12, - "start": 2514, - "end": 2516, + "start": 2503, + "end": 2505, "loc": { "start": { "line": 63, - "column": 69 + "column": 72 }, "end": { "line": 63, - "column": 71 + "column": 74 } } }, @@ -31731,16 +31346,16 @@ "postfix": false, "binop": null }, - "start": 2516, - "end": 2517, + "start": 2505, + "end": 2506, "loc": { "start": { "line": 63, - "column": 71 + "column": 74 }, "end": { "line": 63, - "column": 72 + "column": 75 } } }, @@ -31757,24 +31372,24 @@ "binop": null, "updateContext": null }, - "start": 2517, - "end": 2518, + "start": 2506, + "end": 2507, "loc": { "start": { "line": 63, - "column": 72 + "column": 75 }, "end": { "line": 63, - "column": 73 + "column": 76 } } }, { "type": "CommentLine", "value": " Prepare the specimen.", - "start": 2524, - "end": 2548, + "start": 2513, + "end": 2537, "loc": { "start": { "line": 65, @@ -31801,8 +31416,8 @@ "updateContext": null }, "value": "const", - "start": 2553, - "end": 2558, + "start": 2542, + "end": 2547, "loc": { "start": { "line": 66, @@ -31827,8 +31442,8 @@ "binop": null }, "value": "specimen", - "start": 2559, - "end": 2567, + "start": 2548, + "end": 2556, "loc": { "start": { "line": 66, @@ -31854,8 +31469,8 @@ "updateContext": null }, "value": "=", - "start": 2568, - "end": 2569, + "start": 2557, + "end": 2558, "loc": { "start": { "line": 66, @@ -31879,8 +31494,8 @@ "postfix": false, "binop": null }, - "start": 2570, - "end": 2571, + "start": 2559, + "end": 2560, "loc": { "start": { "line": 66, @@ -31906,8 +31521,8 @@ "updateContext": null }, "value": "@type", - "start": 2578, - "end": 2585, + "start": 2567, + "end": 2574, "loc": { "start": { "line": 67, @@ -31932,8 +31547,8 @@ "binop": null, "updateContext": null }, - "start": 2585, - "end": 2586, + "start": 2574, + "end": 2575, "loc": { "start": { "line": 67, @@ -31958,8 +31573,8 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 2587, - "end": 2602, + "start": 2576, + "end": 2591, "loc": { "start": { "line": 67, @@ -31984,8 +31599,8 @@ "binop": null, "updateContext": null }, - "start": 2602, - "end": 2603, + "start": 2591, + "end": 2592, "loc": { "start": { "line": 67, @@ -32010,8 +31625,8 @@ "binop": null }, "value": "TYPE_SPECIMEN", - "start": 2603, - "end": 2616, + "start": 2592, + "end": 2605, "loc": { "start": { "line": 67, @@ -32036,8 +31651,8 @@ "binop": null, "updateContext": null }, - "start": 2616, - "end": 2617, + "start": 2605, + "end": 2606, "loc": { "start": { "line": 67, @@ -32049,59 +31664,6 @@ } } }, - { - "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "dwc:basisOfRecord", - "start": 2624, - "end": 2643, - "loc": { - "start": { - "line": 68, - "column": 6 - }, - "end": { - "line": 68, - "column": 25 - } - } - }, - { - "type": { - "label": ":", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 2643, - "end": 2644, - "loc": { - "start": { - "line": 68, - "column": 25 - }, - "end": { - "line": 68, - "column": 26 - } - } - }, { "type": { "label": "name", @@ -32115,16 +31677,16 @@ "binop": null }, "value": "basisOfRecord", - "start": 2645, - "end": 2658, + "start": 2613, + "end": 2626, "loc": { "start": { "line": 68, - "column": 27 + "column": 6 }, "end": { "line": 68, - "column": 40 + "column": 19 } } }, @@ -32141,16 +31703,16 @@ "binop": null, "updateContext": null }, - "start": 2658, - "end": 2659, + "start": 2626, + "end": 2627, "loc": { "start": { "line": 68, - "column": 40 + "column": 19 }, "end": { "line": 68, - "column": 41 + "column": 20 } } }, @@ -32167,8 +31729,8 @@ "binop": null }, "value": "occurrenceID", - "start": 2666, - "end": 2678, + "start": 2634, + "end": 2646, "loc": { "start": { "line": 69, @@ -32193,8 +31755,8 @@ "binop": null, "updateContext": null }, - "start": 2678, - "end": 2679, + "start": 2646, + "end": 2647, "loc": { "start": { "line": 69, @@ -32219,8 +31781,8 @@ "binop": null }, "value": "occurID", - "start": 2680, - "end": 2687, + "start": 2648, + "end": 2655, "loc": { "start": { "line": 69, @@ -32245,8 +31807,8 @@ "binop": null, "updateContext": null }, - "start": 2687, - "end": 2688, + "start": 2655, + "end": 2656, "loc": { "start": { "line": 69, @@ -32270,8 +31832,8 @@ "postfix": false, "binop": null }, - "start": 2693, - "end": 2694, + "start": 2661, + "end": 2662, "loc": { "start": { "line": 70, @@ -32296,8 +31858,8 @@ "binop": null, "updateContext": null }, - "start": 2694, - "end": 2695, + "start": 2662, + "end": 2663, "loc": { "start": { "line": 70, @@ -32312,8 +31874,8 @@ { "type": "CommentLine", "value": " Look for certain prefixes that suggest that we've been passed a URN or", - "start": 2701, - "end": 2774, + "start": 2669, + "end": 2742, "loc": { "start": { "line": 72, @@ -32328,8 +31890,8 @@ { "type": "CommentLine", "value": " URL instead. If so, don't do any further processing!", - "start": 2779, - "end": 2834, + "start": 2747, + "end": 2802, "loc": { "start": { "line": 73, @@ -32356,8 +31918,8 @@ "updateContext": null }, "value": "const", - "start": 2839, - "end": 2844, + "start": 2807, + "end": 2812, "loc": { "start": { "line": 74, @@ -32382,8 +31944,8 @@ "binop": null }, "value": "URL_URN_PREFIXES", - "start": 2845, - "end": 2861, + "start": 2813, + "end": 2829, "loc": { "start": { "line": 74, @@ -32409,8 +31971,8 @@ "updateContext": null }, "value": "=", - "start": 2862, - "end": 2863, + "start": 2830, + "end": 2831, "loc": { "start": { "line": 74, @@ -32435,8 +31997,8 @@ "binop": null, "updateContext": null }, - "start": 2864, - "end": 2865, + "start": 2832, + "end": 2833, "loc": { "start": { "line": 74, @@ -32462,8 +32024,8 @@ "updateContext": null }, "value": "http://", - "start": 2872, - "end": 2881, + "start": 2840, + "end": 2849, "loc": { "start": { "line": 75, @@ -32488,8 +32050,8 @@ "binop": null, "updateContext": null }, - "start": 2881, - "end": 2882, + "start": 2849, + "end": 2850, "loc": { "start": { "line": 75, @@ -32515,8 +32077,8 @@ "updateContext": null }, "value": "https://", - "start": 2889, - "end": 2899, + "start": 2857, + "end": 2867, "loc": { "start": { "line": 76, @@ -32541,8 +32103,8 @@ "binop": null, "updateContext": null }, - "start": 2899, - "end": 2900, + "start": 2867, + "end": 2868, "loc": { "start": { "line": 76, @@ -32568,8 +32130,8 @@ "updateContext": null }, "value": "ftp://", - "start": 2907, - "end": 2915, + "start": 2875, + "end": 2883, "loc": { "start": { "line": 77, @@ -32594,8 +32156,8 @@ "binop": null, "updateContext": null }, - "start": 2915, - "end": 2916, + "start": 2883, + "end": 2884, "loc": { "start": { "line": 77, @@ -32621,8 +32183,8 @@ "updateContext": null }, "value": "sftp://", - "start": 2923, - "end": 2932, + "start": 2891, + "end": 2900, "loc": { "start": { "line": 78, @@ -32647,8 +32209,8 @@ "binop": null, "updateContext": null }, - "start": 2932, - "end": 2933, + "start": 2900, + "end": 2901, "loc": { "start": { "line": 78, @@ -32674,8 +32236,8 @@ "updateContext": null }, "value": "file://", - 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"start": 2979, - "end": 2980, + "start": 2947, + "end": 2948, "loc": { "start": { "line": 82, @@ -32884,8 +32446,8 @@ "binop": null }, "value": "URL_URN_PREFIXES", - "start": 2980, - "end": 2996, + "start": 2948, + "end": 2964, "loc": { "start": { "line": 82, @@ -32910,8 +32472,8 @@ "binop": null, "updateContext": null }, - "start": 2996, - "end": 2997, + "start": 2964, + "end": 2965, "loc": { "start": { "line": 82, @@ -32936,8 +32498,8 @@ "binop": null }, "value": "filter", - "start": 2997, - "end": 3003, + "start": 2965, + "end": 2971, "loc": { "start": { "line": 82, @@ -32961,8 +32523,8 @@ "postfix": false, "binop": null }, - "start": 3003, - "end": 3004, + "start": 2971, + "end": 2972, "loc": { "start": { "line": 82, @@ -32987,8 +32549,8 @@ "binop": null }, "value": "prefix", - "start": 3004, - "end": 3010, + "start": 2972, + "end": 2978, "loc": { "start": { "line": 82, @@ -33013,8 +32575,8 @@ "binop": null, "updateContext": null }, - "start": 3011, - "end": 3013, + "start": 2979, + "end": 2981, "loc": { "start": { "line": 82, @@ -33039,8 +32601,8 @@ "binop": null }, "value": "occurID", - "start": 3014, - "end": 3021, + "start": 2982, + "end": 2989, "loc": { "start": { "line": 82, @@ -33065,8 +32627,8 @@ "binop": null, "updateContext": null }, - "start": 3021, - "end": 3022, + "start": 2989, + "end": 2990, "loc": { "start": { "line": 82, @@ -33091,8 +32653,8 @@ "binop": null }, "value": "toLowerCase", - "start": 3022, - "end": 3033, + "start": 2990, + "end": 3001, "loc": { "start": { "line": 82, @@ -33116,8 +32678,8 @@ "postfix": false, "binop": null }, - "start": 3033, - "end": 3034, + "start": 3001, + "end": 3002, "loc": { "start": { "line": 82, @@ -33141,8 +32703,8 @@ "postfix": false, "binop": null }, - "start": 3034, - "end": 3035, + "start": 3002, + "end": 3003, "loc": { "start": { "line": 82, @@ -33167,8 +32729,8 @@ "binop": null, "updateContext": null }, - "start": 3035, - "end": 3036, + "start": 3003, + "end": 3004, "loc": { "start": { "line": 82, @@ -33193,8 +32755,8 @@ "binop": null }, "value": "startsWith", - "start": 3036, - "end": 3046, + "start": 3004, + "end": 3014, "loc": { "start": { "line": 82, @@ -33218,8 +32780,8 @@ "postfix": false, "binop": null }, - "start": 3046, - "end": 3047, + "start": 3014, + "end": 3015, "loc": { "start": { "line": 82, @@ -33244,8 +32806,8 @@ "binop": null }, "value": "prefix", - "start": 3047, - "end": 3053, + "start": 3015, + "end": 3021, "loc": { "start": { "line": 82, @@ -33269,8 +32831,8 @@ "postfix": false, "binop": null }, - "start": 3053, - "end": 3054, + "start": 3021, + "end": 3022, "loc": { "start": { "line": 82, @@ -33294,8 +32856,8 @@ "postfix": false, "binop": null }, - "start": 3054, - "end": 3055, + "start": 3022, + "end": 3023, "loc": { "start": { "line": 82, @@ -33320,8 +32882,8 @@ "binop": null, "updateContext": null }, - "start": 3055, - "end": 3056, + "start": 3023, + "end": 3024, "loc": { "start": { "line": 82, @@ -33346,8 +32908,8 @@ "binop": null }, "value": "length", - "start": 3056, - "end": 3062, + "start": 3024, + "end": 3030, "loc": { "start": { "line": 82, @@ -33373,8 +32935,8 @@ "updateContext": null }, "value": ">", - "start": 3063, - "end": 3064, + "start": 3031, + "end": 3032, "loc": { "start": { "line": 82, @@ -33400,8 +32962,8 @@ "updateContext": null }, "value": 0, - "start": 3065, - "end": 3066, + "start": 3033, + "end": 3034, "loc": { "start": { "line": 82, @@ -33425,8 +32987,8 @@ "postfix": false, "binop": null }, - "start": 3066, - "end": 3067, + "start": 3034, + "end": 3035, "loc": { "start": { "line": 82, @@ -33450,8 +33012,8 @@ "postfix": false, "binop": null }, - "start": 3068, - "end": 3069, + "start": 3036, + "end": 3037, "loc": { "start": { "line": 82, @@ -33478,8 +33040,8 @@ "updateContext": null }, "value": "return", - "start": 3076, - "end": 3082, + "start": 3044, + "end": 3050, "loc": { "start": { "line": 83, @@ -33504,8 +33066,8 @@ "binop": null }, "value": "specimen", - "start": 3083, - "end": 3091, + "start": 3051, + "end": 3059, "loc": { "start": { "line": 83, @@ -33530,8 +33092,8 @@ "binop": null, "updateContext": null }, - "start": 3091, - "end": 3092, + "start": 3059, + "end": 3060, "loc": { "start": { "line": 83, @@ -33555,8 +33117,8 @@ "postfix": false, "binop": null }, - "start": 3097, - "end": 3098, + "start": 3065, + "end": 3066, "loc": { "start": { "line": 84, @@ -33571,8 +33133,8 @@ { "type": "CommentLine", "value": " Parsing an occurrence ID takes some time, so we should memoize it.", - "start": 3104, - "end": 3173, + "start": 3072, + "end": 3141, "loc": { "start": { "line": 86, @@ -33599,8 +33161,8 @@ "updateContext": null }, "value": "if", - "start": 3178, - "end": 3180, + "start": 3146, + "end": 3148, "loc": { "start": { "line": 87, @@ -33624,8 +33186,8 @@ "postfix": false, "binop": null }, - "start": 3181, - "end": 3182, + "start": 3149, + "end": 3150, "loc": { "start": { "line": 87, @@ -33650,8 +33212,8 @@ "binop": null }, "value": "PhyxCacheManager", - "start": 3182, - "end": 3198, + "start": 3150, + "end": 3166, "loc": { "start": { "line": 87, @@ -33676,8 +33238,8 @@ "binop": null, "updateContext": null }, - "start": 3198, - "end": 3199, + "start": 3166, + "end": 3167, "loc": { "start": { "line": 87, @@ -33702,8 +33264,8 @@ "binop": null }, "value": "has", - "start": 3199, - "end": 3202, + "start": 3167, + "end": 3170, "loc": { "start": { "line": 87, @@ -33727,8 +33289,8 @@ "postfix": false, "binop": null }, - "start": 3202, - "end": 3203, + "start": 3170, + "end": 3171, "loc": { "start": { "line": 87, @@ -33754,8 +33316,8 @@ "updateContext": null }, "value": "SpecimenWrapper.occurrenceIDCache", - "start": 3203, - "end": 3238, + "start": 3171, + "end": 3206, "loc": { "start": { "line": 87, @@ -33780,8 +33342,8 @@ "binop": null, "updateContext": null }, - "start": 3238, - "end": 3239, + "start": 3206, + "end": 3207, "loc": { "start": { "line": 87, @@ -33806,8 +33368,8 @@ "binop": null }, "value": "occurID", - "start": 3240, - "end": 3247, + "start": 3208, + "end": 3215, "loc": { "start": { "line": 87, @@ -33831,8 +33393,8 @@ "postfix": false, "binop": null }, - "start": 3247, - "end": 3248, + "start": 3215, + "end": 3216, "loc": { "start": { "line": 87, @@ -33856,8 +33418,8 @@ "postfix": false, "binop": null }, - "start": 3248, - "end": 3249, + "start": 3216, + "end": 3217, "loc": { "start": { "line": 87, @@ -33881,8 +33443,8 @@ "postfix": false, "binop": null }, - "start": 3250, - "end": 3251, + "start": 3218, + "end": 3219, "loc": { "start": { "line": 87, @@ -33909,8 +33471,8 @@ "updateContext": null }, "value": "return", - "start": 3258, - "end": 3264, + "start": 3226, + "end": 3232, "loc": { "start": { "line": 88, @@ -33935,8 +33497,8 @@ "binop": null }, "value": "PhyxCacheManager", - 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"start": 5789, - "end": 5803, + "start": 5757, + "end": 5771, "loc": { "start": { "line": 152, @@ -42464,8 +42026,8 @@ "binop": null, "updateContext": null }, - "start": 5803, - "end": 5804, + "start": 5771, + "end": 5772, "loc": { "start": { "line": 152, @@ -42489,8 +42051,8 @@ "postfix": false, "binop": null }, - "start": 5809, - "end": 5810, + "start": 5777, + "end": 5778, "loc": { "start": { "line": 153, @@ -42517,8 +42079,8 @@ "updateContext": null }, "value": "return", - "start": 5815, - "end": 5821, + "start": 5783, + "end": 5789, "loc": { "start": { "line": 154, @@ -42543,8 +42105,8 @@ "binop": null }, "value": "undefined", - "start": 5822, - "end": 5831, + "start": 5790, + "end": 5799, "loc": { "start": { "line": 154, @@ -42569,8 +42131,8 @@ "binop": null, "updateContext": null }, - "start": 5831, - "end": 5832, + "start": 5799, + "end": 5800, "loc": { "start": { "line": 154, @@ -42594,8 +42156,8 @@ "postfix": false, "binop": null }, - "start": 5835, - "end": 5836, + "start": 5803, + "end": 5804, "loc": { "start": { "line": 155, @@ -42610,8 +42172,8 @@ { "type": "CommentBlock", "value": "*\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n ", - "start": 5840, - "end": 6099, + "start": 5808, + "end": 6067, "loc": { "start": { "line": 157, @@ -42636,8 +42198,8 @@ "binop": null }, "value": "get", - "start": 6102, - "end": 6105, + "start": 6070, + "end": 6073, "loc": { "start": { "line": 163, @@ -42662,8 +42224,8 @@ "binop": null }, "value": "occurrenceID", - "start": 6106, - "end": 6118, + "start": 6074, + "end": 6086, "loc": { "start": { "line": 163, @@ -42687,8 +42249,8 @@ "postfix": false, "binop": null }, - "start": 6118, - "end": 6119, + "start": 6086, + "end": 6087, "loc": { "start": { "line": 163, @@ -42712,8 +42274,8 @@ "postfix": false, "binop": null }, - "start": 6119, - "end": 6120, + "start": 6087, + "end": 6088, "loc": { "start": { "line": 163, @@ -42737,8 +42299,8 @@ "postfix": false, "binop": null }, - "start": 6121, - "end": 6122, + "start": 6089, + "end": 6090, "loc": { "start": { "line": 163, @@ -42753,8 +42315,8 @@ { "type": "CommentLine", "value": " Return the occurrenceID if it exists.", - "start": 6127, - "end": 6167, + "start": 6095, + "end": 6135, "loc": { "start": { "line": 164, @@ -42781,8 +42343,8 @@ "updateContext": null }, "value": "if", - "start": 6172, - "end": 6174, + "start": 6140, + "end": 6142, "loc": { "start": { "line": 165, @@ -42806,8 +42368,8 @@ "postfix": false, "binop": null }, - "start": 6175, - "end": 6176, + "start": 6143, + "end": 6144, "loc": { "start": { "line": 165, @@ -42832,8 +42394,8 @@ "binop": null }, "value": "has", - "start": 6176, - "end": 6179, + "start": 6144, + "end": 6147, "loc": { "start": { "line": 165, @@ -42857,8 +42419,8 @@ "postfix": false, "binop": null }, - "start": 6179, - "end": 6180, + "start": 6147, + "end": 6148, "loc": { "start": { "line": 165, @@ -42885,201 +42447,16 @@ "updateContext": null }, "value": "this", - "start": 6180, - "end": 6184, - "loc": { - "start": { - "line": 165, - "column": 12 - }, - "end": { - "line": 165, - "column": 16 - } - } - }, - { - "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 6184, - "end": 6185, - "loc": { - "start": { - "line": 165, - "column": 16 - }, - "end": { - "line": 165, - "column": 17 - } - } - }, - { - "type": { - "label": "name", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "value": "specimen", - "start": 6185, - "end": 6193, - "loc": { - "start": { - "line": 165, - "column": 17 - }, - "end": { - "line": 165, - "column": 25 - } - } - }, - { - "type": { - "label": ",", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "start": 6193, - "end": 6194, - "loc": { - "start": { - "line": 165, - "column": 25 - }, - "end": { - "line": 165, - "column": 26 - } - } - }, - { - "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "occurrenceID", - "start": 6195, - "end": 6209, - "loc": { - "start": { - "line": 165, - "column": 27 - }, - "end": { - "line": 165, - "column": 41 - } - } - }, - { - "type": { - "label": ")", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null - }, - "start": 6209, - "end": 6210, - "loc": { - "start": { - "line": 165, - "column": 41 - }, - "end": { - "line": 165, - "column": 42 - } - } - }, - { - "type": { - "label": "&&", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": 2, - "updateContext": null - }, - "value": "&&", - "start": 6211, - "end": 6213, - "loc": { - "start": { - "line": 165, - "column": 43 - }, - "end": { - "line": 165, - "column": 45 - } - } - }, - { - "type": { - "label": "this", - "keyword": "this", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "this", - "start": 6214, - "end": 6218, + "start": 6148, + "end": 6152, "loc": { "start": { "line": 165, - "column": 46 + "column": 12 }, "end": { "line": 165, - "column": 50 + "column": 16 } } }, @@ -43096,16 +42473,16 @@ "binop": null, "updateContext": null }, - "start": 6218, - "end": 6219, + "start": 6152, + "end": 6153, "loc": { "start": { "line": 165, - "column": 50 + "column": 16 }, "end": { "line": 165, - "column": 51 + "column": 17 } } }, @@ -43122,23 +42499,23 @@ "binop": null }, "value": "specimen", - "start": 6219, - "end": 6227, + "start": 6153, + "end": 6161, "loc": { "start": { "line": 165, - "column": 51 + "column": 17 }, "end": { "line": 165, - "column": 59 + "column": 25 } } }, { "type": { - "label": ".", - "beforeExpr": false, + "label": ",", + "beforeExpr": true, "startsExpr": false, "rightAssociative": false, "isLoop": false, @@ -43148,22 +42525,22 @@ "binop": null, "updateContext": null }, - "start": 6227, - "end": 6228, + "start": 6161, + "end": 6162, "loc": { "start": { "line": 165, - "column": 59 + "column": 25 }, "end": { "line": 165, - "column": 60 + "column": 26 } } }, { "type": { - "label": "name", + "label": "string", "beforeExpr": false, "startsExpr": true, "rightAssociative": false, @@ -43171,96 +42548,20 @@ "isAssign": false, "prefix": false, "postfix": false, - "binop": null - }, - "value": "occurrenceID", - "start": 6228, - "end": 6240, - "loc": { - "start": { - "line": 165, - "column": 60 - }, - "end": { - "line": 165, - "column": 72 - } - } - }, - { - "type": { - "label": ".", - "beforeExpr": false, - "startsExpr": false, - "rightAssociative": false, - 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"column": 78 + "column": 41 } } }, @@ -43276,70 +42577,16 @@ "postfix": false, "binop": null }, - "start": 6246, - "end": 6247, - "loc": { - "start": { - "line": 165, - "column": 78 - }, - "end": { - "line": 165, - "column": 79 - } - } - }, - { - "type": { - "label": "==/!=", - "beforeExpr": true, - "startsExpr": false, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": 6, - "updateContext": null - }, - "value": "!==", - "start": 6248, - "end": 6251, + "start": 6177, + "end": 6178, "loc": { "start": { "line": 165, - "column": 80 - }, - "end": { - "line": 165, - "column": 83 - } - } - }, - { - "type": { - "label": "string", - "beforeExpr": false, - "startsExpr": true, - "rightAssociative": false, - "isLoop": false, - "isAssign": false, - "prefix": false, - "postfix": false, - "binop": null, - "updateContext": null - }, - "value": "", - "start": 6252, - "end": 6254, - "loc": { - "start": { - "line": 165, - "column": 84 + "column": 41 }, "end": { "line": 165, - "column": 86 + "column": 42 } } }, @@ -43355,16 +42602,16 @@ "postfix": false, "binop": null }, - "start": 6254, - "end": 6255, + "start": 6178, + "end": 6179, "loc": { "start": { "line": 165, - "column": 86 + "column": 42 }, "end": { "line": 165, - "column": 87 + "column": 43 } } }, @@ -43380,16 +42627,16 @@ "postfix": false, "binop": null }, - "start": 6256, - "end": 6257, + "start": 6180, + "end": 6181, "loc": { "start": { "line": 165, - "column": 88 + "column": 44 }, "end": { "line": 165, - "column": 89 + "column": 45 } } }, @@ -43408,8 +42655,8 @@ "updateContext": null }, "value": "return", - "start": 6264, - "end": 6270, + "start": 6188, + "end": 6194, "loc": { "start": { "line": 166, @@ -43436,8 +42683,8 @@ "updateContext": null }, "value": "this", - "start": 6271, - "end": 6275, + "start": 6195, + "end": 6199, "loc": { "start": { "line": 166, @@ -43462,8 +42709,8 @@ "binop": null, "updateContext": null }, - "start": 6275, - "end": 6276, + "start": 6199, + "end": 6200, "loc": { "start": { "line": 166, @@ -43488,8 +42735,8 @@ "binop": null }, "value": "specimen", - "start": 6276, - "end": 6284, + "start": 6200, + "end": 6208, "loc": { "start": { "line": 166, @@ -43514,8 +42761,8 @@ "binop": null, "updateContext": null }, - "start": 6284, - "end": 6285, + "start": 6208, + "end": 6209, "loc": { "start": { "line": 166, @@ -43540,8 +42787,8 @@ "binop": null }, "value": "occurrenceID", - "start": 6285, - "end": 6297, + "start": 6209, + "end": 6221, "loc": { "start": { "line": 166, @@ -43566,8 +42813,8 @@ "binop": null, "updateContext": null }, - "start": 6297, - "end": 6298, + "start": 6221, + "end": 6222, "loc": { "start": { "line": 166, @@ -43592,8 +42839,8 @@ "binop": null }, "value": "trim", - "start": 6298, - "end": 6302, + "start": 6222, + "end": 6226, "loc": { "start": { "line": 166, @@ -43617,8 +42864,8 @@ "postfix": false, "binop": null }, - "start": 6302, - "end": 6303, + "start": 6226, + "end": 6227, "loc": { "start": { "line": 166, @@ -43642,8 +42889,8 @@ "postfix": false, "binop": null }, - "start": 6303, - "end": 6304, + "start": 6227, + "end": 6228, "loc": { "start": { "line": 166, @@ -43668,8 +42915,8 @@ "binop": null, "updateContext": null }, - "start": 6304, - "end": 6305, + "start": 6228, + "end": 6229, "loc": { "start": { "line": 166, @@ -43693,8 +42940,8 @@ "postfix": false, "binop": null }, - "start": 6310, - "end": 6311, + "start": 6234, + "end": 6235, "loc": { "start": { "line": 167, @@ -43709,8 +42956,8 @@ { "type": "CommentLine", "value": " Otherwise, we could try to construct the occurrenceID from its components.", - "start": 6317, - "end": 6394, + "start": 6241, + "end": 6318, "loc": { "start": { "line": 169, @@ -43737,8 +42984,8 @@ "updateContext": null }, "value": "if", - "start": 6399, - "end": 6401, + "start": 6323, + "end": 6325, "loc": { "start": { "line": 170, @@ -43762,8 +43009,8 @@ "postfix": false, "binop": null }, - "start": 6402, - "end": 6403, + "start": 6326, + "end": 6327, "loc": { "start": { "line": 170, @@ -43788,8 +43035,8 @@ "binop": null }, "value": "has", - "start": 6403, - "end": 6406, + "start": 6327, + "end": 6330, "loc": { "start": { "line": 170, @@ -43813,8 +43060,8 @@ "postfix": false, "binop": null }, - 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"start": 6460, - "end": 6461, + "start": 6384, + "end": 6385, "loc": { "start": { "line": 171, @@ -44205,8 +43452,8 @@ "binop": null }, "value": "specimen", - "start": 6461, - "end": 6469, + "start": 6385, + "end": 6393, "loc": { "start": { "line": 171, @@ -44231,8 +43478,8 @@ "binop": null, "updateContext": null }, - "start": 6469, - "end": 6470, + "start": 6393, + "end": 6394, "loc": { "start": { "line": 171, @@ -44258,8 +43505,8 @@ "updateContext": null }, "value": "institutionCode", - "start": 6471, - "end": 6488, + "start": 6395, + "end": 6412, "loc": { "start": { "line": 171, @@ -44283,8 +43530,8 @@ "postfix": false, "binop": null }, - "start": 6488, - "end": 6489, + "start": 6412, + "end": 6413, "loc": { "start": { "line": 171, @@ -44308,8 +43555,8 @@ "postfix": false, "binop": null }, - "start": 6489, - "end": 6490, + "start": 6413, + "end": 6414, "loc": { "start": { "line": 171, @@ -44333,8 +43580,8 @@ "postfix": false, "binop": null }, - "start": 6491, - "end": 6492, + "start": 6415, + "end": 6416, "loc": { "start": { "line": 171, @@ -44361,8 +43608,8 @@ "updateContext": null }, "value": "if", - 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"start": 7717, - "end": 7718, + "start": 7623, + "end": 7624, "loc": { "start": { "line": 205, @@ -49962,8 +49155,8 @@ "updateContext": null }, "value": "if", - "start": 7723, - "end": 7725, + "start": 7629, + "end": 7631, "loc": { "start": { "line": 206, @@ -49987,8 +49180,8 @@ "postfix": false, "binop": null }, - "start": 7726, - "end": 7727, + "start": 7632, + "end": 7633, "loc": { "start": { "line": 206, @@ -50013,8 +49206,8 @@ "binop": null }, "value": "has", - "start": 7727, - "end": 7730, + "start": 7633, + "end": 7636, "loc": { "start": { "line": 206, @@ -50038,8 +49231,8 @@ "postfix": false, "binop": null }, - "start": 7730, - "end": 7731, + "start": 7636, + "end": 7637, "loc": { "start": { "line": 206, @@ -50066,8 +49259,8 @@ "updateContext": null }, "value": "this", - "start": 7731, - "end": 7735, + "start": 7637, + "end": 7641, "loc": { "start": { "line": 206, @@ -50092,8 +49285,8 @@ "binop": null, "updateContext": null }, - "start": 7735, - "end": 7736, + "start": 7641, + "end": 7642, "loc": { "start": { "line": 206, @@ -50118,8 +49311,8 @@ "binop": null }, "value": "specimen", - "start": 7736, - "end": 7744, + "start": 7642, + "end": 7650, "loc": { "start": { "line": 206, @@ -50144,8 +49337,8 @@ "binop": null, "updateContext": null }, - "start": 7744, - "end": 7745, + "start": 7650, + "end": 7651, "loc": { "start": { "line": 206, @@ -50171,8 +49364,8 @@ "updateContext": null }, "value": "nameString", - "start": 7746, - "end": 7758, + "start": 7652, + "end": 7664, "loc": { "start": { "line": 206, @@ -50196,8 +49389,8 @@ "postfix": false, "binop": null }, - "start": 7758, - "end": 7759, + "start": 7664, + "end": 7665, "loc": { "start": { "line": 206, @@ -50221,8 +49414,8 @@ "postfix": false, "binop": null }, - "start": 7759, - "end": 7760, + "start": 7665, + "end": 7666, "loc": { "start": { "line": 206, @@ -50249,8 +49442,8 @@ "updateContext": null }, "value": "return", - "start": 7761, - "end": 7767, + "start": 7667, + "end": 7673, "loc": { "start": { "line": 206, @@ -50277,8 +49470,8 @@ "updateContext": null }, "value": "this", - "start": 7768, - "end": 7772, + "start": 7674, + "end": 7678, "loc": { "start": { "line": 206, @@ -50303,8 +49496,8 @@ "binop": null, "updateContext": null }, - "start": 7772, - "end": 7773, + "start": 7678, + "end": 7679, "loc": { "start": { "line": 206, @@ -50329,8 +49522,8 @@ "binop": null }, "value": "specimen", - "start": 7773, - "end": 7781, + "start": 7679, + "end": 7687, "loc": { "start": { "line": 206, @@ -50355,8 +49548,8 @@ "binop": null, "updateContext": null }, - "start": 7781, - "end": 7782, + "start": 7687, + "end": 7688, "loc": { "start": { "line": 206, @@ -50383,8 +49576,8 @@ "updateContext": null }, "value": "return", - "start": 7787, - "end": 7793, + "start": 7693, + "end": 7699, "loc": { "start": { "line": 207, @@ -50409,8 +49602,8 @@ "binop": null }, "value": "undefined", - "start": 7794, - "end": 7803, + "start": 7700, + "end": 7709, "loc": { "start": { "line": 207, @@ -50435,8 +49628,8 @@ "binop": null, "updateContext": null }, - "start": 7803, - "end": 7804, + "start": 7709, + "end": 7710, "loc": { "start": { "line": 207, @@ -50460,8 +49653,8 @@ "postfix": false, "binop": null }, - "start": 7807, - "end": 7808, + "start": 7713, + "end": 7714, "loc": { "start": { "line": 208, @@ -50476,8 +49669,8 @@ { "type": "CommentBlock", "value": "* Return a label for this specimen. ", - "start": 7812, - "end": 7852, + "start": 7718, + "end": 7758, "loc": { "start": { "line": 210, @@ -50502,8 +49695,8 @@ "binop": null }, "value": "get", - "start": 7855, - "end": 7858, + "start": 7761, + "end": 7764, "loc": { "start": { "line": 211, @@ -50528,8 +49721,8 @@ "binop": null }, "value": "label", - "start": 7859, - "end": 7864, + "start": 7765, + "end": 7770, "loc": { "start": { "line": 211, @@ -50553,8 +49746,8 @@ "postfix": false, "binop": null }, - "start": 7864, - "end": 7865, + "start": 7770, + "end": 7771, "loc": { "start": { "line": 211, @@ -50578,8 +49771,8 @@ "postfix": false, "binop": null }, - "start": 7865, - "end": 7866, + "start": 7771, + "end": 7772, "loc": { "start": { "line": 211, @@ -50603,8 +49796,8 @@ "postfix": false, "binop": null }, - "start": 7867, - "end": 7868, + "start": 7773, + "end": 7774, "loc": { "start": { "line": 211, @@ -50619,8 +49812,8 @@ { "type": "CommentLine", "value": " We can't return anything without an occurrenceID.", - "start": 7873, - "end": 7925, + "start": 7779, + "end": 7831, "loc": { "start": { "line": 212, @@ -50647,8 +49840,8 @@ "updateContext": null }, "value": "if", - "start": 7930, - "end": 7932, + "start": 7836, + "end": 7838, "loc": { "start": { "line": 213, @@ -50672,8 +49865,8 @@ "postfix": false, "binop": null }, - "start": 7933, - "end": 7934, + "start": 7839, + "end": 7840, "loc": { "start": { "line": 213, @@ -50699,8 +49892,8 @@ "updateContext": null }, "value": "!", - "start": 7934, - "end": 7935, + "start": 7840, + "end": 7841, "loc": { "start": { "line": 213, @@ -50727,8 +49920,8 @@ "updateContext": null }, "value": "this", - "start": 7935, - "end": 7939, + "start": 7841, + "end": 7845, "loc": { "start": { "line": 213, @@ -50753,8 +49946,8 @@ "binop": null, "updateContext": null }, - "start": 7939, - "end": 7940, + "start": 7845, + "end": 7846, "loc": { "start": { "line": 213, @@ -50779,8 +49972,8 @@ "binop": null }, "value": "occurrenceID", - "start": 7940, - "end": 7952, + "start": 7846, + "end": 7858, "loc": { "start": { "line": 213, @@ -50804,8 +49997,8 @@ "postfix": false, "binop": null }, - "start": 7952, - "end": 7953, + "start": 7858, + "end": 7859, "loc": { "start": { "line": 213, @@ -50832,8 +50025,8 @@ "updateContext": null }, "value": "return", - "start": 7954, - "end": 7960, + "start": 7860, + "end": 7866, "loc": { "start": { "line": 213, @@ -50858,8 +50051,8 @@ "binop": null }, "value": "undefined", - "start": 7961, - "end": 7970, + "start": 7867, + "end": 7876, "loc": { "start": { "line": 213, @@ -50884,8 +50077,8 @@ "binop": null, "updateContext": null }, - "start": 7970, - "end": 7971, + "start": 7876, + "end": 7877, "loc": { "start": { "line": 213, @@ -50900,8 +50093,8 @@ { "type": "CommentLine", "value": " Note that specimens may be identified to a taxon concept. If so, we should", - "start": 7977, - "end": 8054, + "start": 7883, + "end": 7960, "loc": { "start": { "line": 215, @@ -50916,8 +50109,8 @@ { "type": "CommentLine", "value": " include that information in the label.", - "start": 8059, - "end": 8100, + "start": 7965, + "end": 8006, "loc": { "start": { "line": 216, @@ -50944,8 +50137,8 @@ "updateContext": null }, "value": "if", - "start": 8105, - "end": 8107, + "start": 8011, + "end": 8013, "loc": { "start": { "line": 217, @@ -50969,8 +50162,8 @@ "postfix": false, "binop": null }, - "start": 8108, - "end": 8109, + "start": 8014, + "end": 8015, "loc": { "start": { "line": 217, @@ -50997,8 +50190,8 @@ "updateContext": null }, "value": "this", - "start": 8109, - "end": 8113, + "start": 8015, + "end": 8019, "loc": { "start": { "line": 217, @@ -51023,8 +50216,8 @@ "binop": null, "updateContext": null }, - "start": 8113, - "end": 8114, + "start": 8019, + "end": 8020, "loc": { "start": { "line": 217, @@ -51049,8 +50242,8 @@ "binop": null }, "value": "taxonConcept", - "start": 8114, - "end": 8126, + "start": 8020, + "end": 8032, "loc": { "start": { "line": 217, @@ -51074,8 +50267,8 @@ "postfix": false, "binop": null }, - "start": 8126, - "end": 8127, + "start": 8032, + "end": 8033, "loc": { "start": { "line": 217, @@ -51099,8 +50292,8 @@ "postfix": false, "binop": null }, - "start": 8128, - "end": 8129, + "start": 8034, + "end": 8035, "loc": { "start": { "line": 217, @@ -51127,8 +50320,8 @@ "updateContext": null }, "value": "return", - "start": 8136, - "end": 8142, + "start": 8042, + "end": 8048, "loc": { "start": { "line": 218, @@ -51152,8 +50345,8 @@ "postfix": false, "binop": null }, - "start": 8143, - "end": 8144, + "start": 8049, + "end": 8050, "loc": { "start": { "line": 218, @@ -51179,8 +50372,8 @@ "updateContext": null }, "value": "Specimen ", - "start": 8144, - "end": 8153, + "start": 8050, + "end": 8059, "loc": { "start": { "line": 218, @@ -51204,8 +50397,8 @@ "postfix": false, "binop": null }, - "start": 8153, - "end": 8155, + "start": 8059, + "end": 8061, "loc": { "start": { "line": 218, @@ -51232,8 +50425,8 @@ "updateContext": null }, "value": "this", - "start": 8155, - "end": 8159, + "start": 8061, + "end": 8065, "loc": { "start": { "line": 218, @@ -51258,8 +50451,8 @@ "binop": null, "updateContext": null }, - "start": 8159, - "end": 8160, + "start": 8065, + "end": 8066, "loc": { "start": { "line": 218, @@ -51284,8 +50477,8 @@ "binop": null }, "value": "occurrenceID", - "start": 8160, - "end": 8172, + "start": 8066, + "end": 8078, "loc": { "start": { "line": 218, @@ -51309,8 +50502,8 @@ "postfix": false, "binop": null }, - "start": 8172, - "end": 8173, + "start": 8078, + "end": 8079, "loc": { "start": { "line": 218, @@ -51336,8 +50529,8 @@ "updateContext": null }, "value": " identified as ", - "start": 8173, - "end": 8188, + "start": 8079, + "end": 8094, "loc": { "start": { "line": 218, @@ -51361,8 +50554,8 @@ "postfix": false, "binop": null }, - "start": 8188, - "end": 8190, + "start": 8094, + "end": 8096, "loc": { "start": { "line": 218, @@ -51389,8 +50582,8 @@ "updateContext": null }, "value": "new", - "start": 8190, - "end": 8193, + "start": 8096, + "end": 8099, "loc": { "start": { "line": 218, @@ -51415,8 +50608,8 @@ "binop": null }, "value": "TaxonConceptWrapper", - "start": 8194, - "end": 8213, + "start": 8100, + "end": 8119, "loc": { "start": { "line": 218, @@ -51440,8 +50633,8 @@ "postfix": false, "binop": null }, - "start": 8213, - "end": 8214, + "start": 8119, + "end": 8120, "loc": { "start": { "line": 218, @@ -51468,8 +50661,8 @@ "updateContext": null }, "value": "this", - "start": 8214, - "end": 8218, + "start": 8120, + "end": 8124, "loc": { "start": { "line": 218, @@ -51494,8 +50687,8 @@ "binop": null, "updateContext": null }, - "start": 8218, - "end": 8219, + "start": 8124, + "end": 8125, "loc": { "start": { "line": 218, @@ -51520,8 +50713,8 @@ "binop": null }, "value": "taxonConcept", - "start": 8219, - "end": 8231, + "start": 8125, + "end": 8137, "loc": { "start": { "line": 218, @@ -51545,8 +50738,8 @@ "postfix": false, "binop": null }, - "start": 8231, - "end": 8232, + "start": 8137, + "end": 8138, "loc": { "start": { "line": 218, @@ -51571,8 +50764,8 @@ "binop": null, "updateContext": null }, - "start": 8232, - "end": 8233, + "start": 8138, + "end": 8139, "loc": { "start": { "line": 218, @@ -51597,8 +50790,8 @@ "binop": null }, "value": "label", - "start": 8233, - "end": 8238, + "start": 8139, + "end": 8144, "loc": { "start": { "line": 218, @@ -51622,8 +50815,8 @@ "postfix": false, "binop": null }, - "start": 8238, - "end": 8239, + "start": 8144, + "end": 8145, "loc": { "start": { "line": 218, @@ -51649,8 +50842,8 @@ "updateContext": null }, "value": "", - "start": 8239, - "end": 8239, + "start": 8145, + "end": 8145, "loc": { "start": { "line": 218, @@ -51674,8 +50867,8 @@ "postfix": false, "binop": null }, - "start": 8239, - "end": 8240, + "start": 8145, + "end": 8146, "loc": { "start": { "line": 218, @@ -51700,8 +50893,8 @@ "binop": null, "updateContext": null }, - "start": 8240, - "end": 8241, + "start": 8146, + "end": 8147, "loc": { "start": { "line": 218, @@ -51725,8 +50918,8 @@ "postfix": false, "binop": null }, - "start": 8246, - "end": 8247, + "start": 8152, + "end": 8153, "loc": { "start": { "line": 219, @@ -51741,8 +50934,8 @@ { "type": "CommentLine", "value": " Return a label for this specimen.", - "start": 8253, - "end": 8289, + "start": 8159, + "end": 8195, "loc": { "start": { "line": 221, @@ -51769,8 +50962,8 @@ "updateContext": null }, "value": "return", - "start": 8294, - "end": 8300, + "start": 8200, + "end": 8206, "loc": { "start": { "line": 222, @@ -51794,8 +50987,8 @@ "postfix": false, "binop": null }, - "start": 8301, - "end": 8302, + "start": 8207, + "end": 8208, "loc": { "start": { "line": 222, @@ -51821,8 +51014,8 @@ "updateContext": null }, "value": "Specimen ", - "start": 8302, - "end": 8311, + "start": 8208, + "end": 8217, "loc": { "start": { "line": 222, @@ -51846,8 +51039,8 @@ "postfix": false, "binop": null }, - "start": 8311, - "end": 8313, + "start": 8217, + "end": 8219, "loc": { "start": { "line": 222, @@ -51874,8 +51067,8 @@ "updateContext": null }, "value": "this", - "start": 8313, - "end": 8317, + "start": 8219, + "end": 8223, "loc": { "start": { "line": 222, @@ -51900,8 +51093,8 @@ "binop": null, "updateContext": null }, - "start": 8317, - "end": 8318, + "start": 8223, + "end": 8224, "loc": { "start": { "line": 222, @@ -51926,8 +51119,8 @@ "binop": null }, "value": "occurrenceID", - "start": 8318, - "end": 8330, + "start": 8224, + "end": 8236, "loc": { "start": { "line": 222, @@ -51951,8 +51144,8 @@ "postfix": false, "binop": null }, - "start": 8330, - "end": 8331, + "start": 8236, + "end": 8237, "loc": { "start": { "line": 222, @@ -51978,8 +51171,8 @@ "updateContext": null }, "value": "", - "start": 8331, - "end": 8331, + "start": 8237, + "end": 8237, "loc": { "start": { "line": 222, @@ -52003,8 +51196,8 @@ "postfix": false, "binop": null }, - "start": 8331, - "end": 8332, + "start": 8237, + "end": 8238, "loc": { "start": { "line": 222, @@ -52029,8 +51222,8 @@ "binop": null, "updateContext": null }, - "start": 8332, - "end": 8333, + "start": 8238, + "end": 8239, "loc": { "start": { "line": 222, @@ -52054,8 +51247,8 @@ "postfix": false, "binop": null }, - "start": 8336, - "end": 8337, + "start": 8242, + "end": 8243, "loc": { "start": { "line": 223, @@ -52070,8 +51263,8 @@ { "type": "CommentBlock", "value": "* Return this specimen as an equivalentClass expression. ", - "start": 8341, - "end": 8402, + "start": 8247, + "end": 8308, "loc": { "start": { "line": 225, @@ -52096,8 +51289,8 @@ "binop": null }, "value": "get", - "start": 8405, - "end": 8408, + "start": 8311, + "end": 8314, "loc": { "start": { "line": 226, @@ -52122,8 +51315,8 @@ "binop": null }, "value": "asOWLEquivClass", - "start": 8409, - "end": 8424, + "start": 8315, + "end": 8330, "loc": { "start": { "line": 226, @@ -52147,8 +51340,8 @@ "postfix": false, "binop": null }, - "start": 8424, - "end": 8425, + "start": 8330, + "end": 8331, "loc": { "start": { "line": 226, @@ -52172,8 +51365,8 @@ "postfix": false, "binop": null }, - "start": 8425, - "end": 8426, + "start": 8331, + "end": 8332, "loc": { "start": { "line": 226, @@ -52197,8 +51390,8 @@ "postfix": false, "binop": null }, - "start": 8427, - "end": 8428, + "start": 8333, + "end": 8334, "loc": { "start": { "line": 226, @@ -52213,8 +51406,8 @@ { "type": "CommentLine", "value": " We can't do anything without an occurrence ID!", - "start": 8433, - "end": 8482, + "start": 8339, + "end": 8388, "loc": { "start": { "line": 227, @@ -52241,8 +51434,8 @@ "updateContext": null }, "value": "if", - "start": 8487, - "end": 8489, + "start": 8393, + "end": 8395, "loc": { "start": { "line": 228, @@ -52266,8 +51459,8 @@ "postfix": false, "binop": null }, - "start": 8490, - "end": 8491, + "start": 8396, + "end": 8397, "loc": { "start": { "line": 228, @@ -52293,8 +51486,8 @@ "updateContext": null }, "value": "!", - "start": 8491, - "end": 8492, + "start": 8397, + "end": 8398, "loc": { "start": { "line": 228, @@ -52321,8 +51514,8 @@ "updateContext": null }, "value": "this", - "start": 8492, - "end": 8496, + "start": 8398, + "end": 8402, "loc": { "start": { "line": 228, @@ -52347,8 +51540,8 @@ "binop": null, "updateContext": null }, - "start": 8496, - "end": 8497, + "start": 8402, + "end": 8403, "loc": { "start": { "line": 228, @@ -52373,8 +51566,8 @@ "binop": null }, "value": "occurrenceID", - "start": 8497, - "end": 8509, + "start": 8403, + "end": 8415, "loc": { "start": { "line": 228, @@ -52398,8 +51591,8 @@ "postfix": false, "binop": null }, - "start": 8509, - "end": 8510, + "start": 8415, + "end": 8416, "loc": { "start": { "line": 228, @@ -52426,8 +51619,8 @@ "updateContext": null }, "value": "return", - "start": 8511, - "end": 8517, + "start": 8417, + "end": 8423, "loc": { "start": { "line": 228, @@ -52452,8 +51645,8 @@ "binop": null }, "value": "undefined", - "start": 8518, - "end": 8527, + "start": 8424, + "end": 8433, "loc": { "start": { "line": 228, @@ -52478,8 +51671,8 @@ "binop": null, "updateContext": null }, - "start": 8527, - "end": 8528, + "start": 8433, + "end": 8434, "loc": { "start": { "line": 228, @@ -52494,8 +51687,8 @@ { "type": "CommentLine", "value": " TODO: Should we also match by this.taxonConcept is one is available?", - "start": 8534, - "end": 8605, + "start": 8440, + "end": 8511, "loc": { "start": { "line": 230, @@ -52510,8 +51703,8 @@ { "type": "CommentLine", "value": " Technically no, but it might be useful. Hmm.", - "start": 8610, - "end": 8657, + "start": 8516, + "end": 8563, "loc": { "start": { "line": 231, @@ -52526,8 +51719,8 @@ { "type": "CommentLine", "value": " Return as an OWL restriction.", - "start": 8663, - "end": 8695, + "start": 8569, + "end": 8601, "loc": { "start": { "line": 233, @@ -52554,8 +51747,8 @@ "updateContext": null }, "value": "return", - "start": 8700, - "end": 8706, + "start": 8606, + "end": 8612, "loc": { "start": { "line": 234, @@ -52579,8 +51772,8 @@ "postfix": false, "binop": null }, - "start": 8707, - "end": 8708, + "start": 8613, + "end": 8614, "loc": { "start": { "line": 234, @@ -52606,8 +51799,8 @@ "updateContext": null }, "value": "@type", - "start": 8715, - "end": 8722, + "start": 8621, + "end": 8628, "loc": { "start": { "line": 235, @@ -52632,8 +51825,8 @@ "binop": null, "updateContext": null }, - "start": 8722, - "end": 8723, + "start": 8628, + "end": 8629, "loc": { "start": { "line": 235, @@ -52659,8 +51852,8 @@ "updateContext": null }, "value": "owl:Restriction", - "start": 8724, - "end": 8741, + "start": 8630, + "end": 8647, "loc": { "start": { "line": 235, @@ -52685,8 +51878,8 @@ "binop": null, "updateContext": null }, - "start": 8741, - "end": 8742, + "start": 8647, + "end": 8648, "loc": { "start": { "line": 235, @@ -52711,8 +51904,8 @@ "binop": null }, "value": "onProperty", - "start": 8749, - "end": 8759, + "start": 8655, + "end": 8665, "loc": { "start": { "line": 236, @@ -52737,8 +51930,8 @@ "binop": null, "updateContext": null }, - "start": 8759, - "end": 8760, + "start": 8665, + "end": 8666, "loc": { "start": { "line": 236, @@ -52763,8 +51956,8 @@ "binop": null }, "value": "owlterms", - "start": 8761, - "end": 8769, + "start": 8667, + "end": 8675, "loc": { "start": { "line": 236, @@ -52789,8 +51982,8 @@ "binop": null, "updateContext": null }, - "start": 8769, - "end": 8770, + "start": 8675, + "end": 8676, "loc": { "start": { "line": 236, @@ -52815,8 +52008,8 @@ "binop": null }, "value": "DWC_OCCURRENCE_ID", - "start": 8770, - "end": 8787, + "start": 8676, + "end": 8693, "loc": { "start": { "line": 236, @@ -52841,8 +52034,8 @@ "binop": null, "updateContext": null }, - "start": 8787, - "end": 8788, + "start": 8693, + "end": 8694, "loc": { "start": { "line": 236, @@ -52867,8 +52060,8 @@ "binop": null }, "value": "hasValue", - "start": 8795, - "end": 8803, + "start": 8701, + "end": 8709, "loc": { "start": { "line": 237, @@ -52893,8 +52086,8 @@ "binop": null, "updateContext": null }, - "start": 8803, - "end": 8804, + "start": 8709, + "end": 8710, "loc": { "start": { "line": 237, @@ -52921,8 +52114,8 @@ "updateContext": null }, "value": "this", - "start": 8805, - "end": 8809, + "start": 8711, + "end": 8715, "loc": { "start": { "line": 237, @@ -52947,8 +52140,8 @@ "binop": null, "updateContext": null }, - "start": 8809, - "end": 8810, + "start": 8715, + "end": 8716, "loc": { "start": { "line": 237, @@ -52973,8 +52166,8 @@ "binop": null }, "value": "occurrenceID", - "start": 8810, - "end": 8822, + "start": 8716, + "end": 8728, "loc": { "start": { "line": 237, @@ -52999,8 +52192,8 @@ "binop": null, "updateContext": null }, - "start": 8822, - "end": 8823, + "start": 8728, + "end": 8729, "loc": { "start": { "line": 237, @@ -53024,8 +52217,8 @@ "postfix": false, "binop": null }, - "start": 8828, - "end": 8829, + "start": 8734, + "end": 8735, "loc": { "start": { "line": 238, @@ -53050,8 +52243,8 @@ "binop": null, "updateContext": null }, - "start": 8829, - "end": 8830, + "start": 8735, + "end": 8736, "loc": { "start": { "line": 238, @@ -53075,8 +52268,8 @@ "postfix": false, "binop": null }, - "start": 8833, - "end": 8834, + "start": 8739, + "end": 8740, "loc": { "start": { "line": 239, @@ -53100,8 +52293,8 @@ "postfix": false, "binop": null }, - "start": 8835, - "end": 8836, + "start": 8741, + "end": 8742, "loc": { "start": { "line": 240, @@ -53128,8 +52321,8 @@ "updateContext": null }, "value": "export", - "start": 8838, - "end": 8844, + "start": 8744, + "end": 8750, "loc": { "start": { "line": 242, @@ -53153,8 +52346,8 @@ "postfix": false, "binop": null }, - "start": 8845, - "end": 8846, + "start": 8751, + "end": 8752, "loc": { "start": { "line": 242, @@ -53179,8 +52372,8 @@ "binop": null }, "value": "SpecimenWrapper", - "start": 8847, - "end": 8862, + "start": 8753, + "end": 8768, "loc": { "start": { "line": 242, @@ -53205,8 +52398,8 @@ "binop": null, "updateContext": null }, - "start": 8862, - "end": 8863, + "start": 8768, + "end": 8769, "loc": { "start": { "line": 242, @@ -53230,8 +52423,8 @@ "postfix": false, "binop": null }, - "start": 8864, - "end": 8865, + "start": 8770, + "end": 8771, "loc": { "start": { "line": 242, @@ -53256,8 +52449,8 @@ "binop": null, "updateContext": null }, - "start": 8865, - "end": 8866, + "start": 8771, + "end": 8772, "loc": { "start": { "line": 242, @@ -53282,8 +52475,8 @@ "binop": null, "updateContext": null }, - "start": 8867, - "end": 8867, + "start": 8773, + "end": 8773, "loc": { "start": { "line": 243, diff --git a/docs/ast/source/wrappers/TaxonConceptWrapper.js.json b/docs/ast/source/wrappers/TaxonConceptWrapper.js.json index 10a9b9c5..3833c768 100644 --- a/docs/ast/source/wrappers/TaxonConceptWrapper.js.json +++ b/docs/ast/source/wrappers/TaxonConceptWrapper.js.json @@ -70,9 +70,9 @@ "line": 2, "column": 25 }, - "identifierName": "LXL9JK8W7XYSP" + "identifierName": "M50HFXW0VO944" }, - "name": "LXL9JK8W7XYSP", + "name": "M50HFXW0VO944", "leadingComments": null }, "leadingComments": null @@ -231,9 +231,9 @@ "line": 3, "column": 29 }, - "identifierName": "LXL9JK8W7XYSP" + "identifierName": "M50HFXW0VO944" }, - "name": "LXL9JK8W7XYSP" + "name": "M50HFXW0VO944" } } ], @@ -406,9 +406,9 @@ "line": 9, "column": 25 }, - "identifierName": "LXL9JK8W1GXXG" + "identifierName": "M50HFXW0K82UI" }, - "name": "LXL9JK8W1GXXG", + "name": "M50HFXW0K82UI", "leadingComments": null }, "leadingComments": null @@ -567,9 +567,9 @@ "line": 10, "column": 42 }, - "identifierName": "LXL9JK8W1GXXG" + "identifierName": "M50HFXW0K82UI" }, - "name": "LXL9JK8W1GXXG" + "name": "M50HFXW0K82UI" } } ], @@ -19227,7 +19227,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8W7XYSP", + "value": "M50HFXW0VO944", "start": 38, "end": 51, "loc": { @@ -19463,7 +19463,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8W7XYSP", + "value": "M50HFXW0VO944", "start": 84, "end": 97, "loc": { @@ -19761,7 +19761,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8W1GXXG", + "value": "M50HFXW0K82UI", "start": 229, "end": 242, "loc": { @@ -19997,7 +19997,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK8W1GXXG", + "value": "M50HFXW0K82UI", "start": 300, "end": 313, "loc": { diff --git a/docs/ast/source/wrappers/TaxonNameWrapper.js.json b/docs/ast/source/wrappers/TaxonNameWrapper.js.json index ac091e95..31f767f7 100644 --- a/docs/ast/source/wrappers/TaxonNameWrapper.js.json +++ b/docs/ast/source/wrappers/TaxonNameWrapper.js.json @@ -70,9 +70,9 @@ "line": 2, "column": 25 }, - "identifierName": "LXL9JK9A559BE" + "identifierName": "M50HFXW61ZY4F" }, - "name": "LXL9JK9A559BE", + "name": "M50HFXW61ZY4F", "leadingComments": null }, "leadingComments": null @@ -341,9 +341,9 @@ "line": 3, "column": 49 }, - "identifierName": "LXL9JK9A559BE" + "identifierName": "M50HFXW61ZY4F" }, - "name": "LXL9JK9A559BE" + "name": "M50HFXW61ZY4F" } } ], @@ -516,9 +516,9 @@ "line": 9, "column": 25 }, - "identifierName": "LXL9JK9AF9PKK" + "identifierName": "M50HFXW6GFFF3" }, - "name": "LXL9JK9AF9PKK", + "name": "M50HFXW6GFFF3", "leadingComments": null }, "leadingComments": null @@ -677,9 +677,9 @@ "line": 10, "column": 42 }, - "identifierName": "LXL9JK9AF9PKK" + "identifierName": "M50HFXW6GFFF3" }, - "name": "LXL9JK9AF9PKK" + "name": "M50HFXW6GFFF3" } } ], @@ -48879,7 +48879,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9A559BE", + "value": "M50HFXW61ZY4F", "start": 38, "end": 51, "loc": { @@ -49219,7 +49219,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9A559BE", + "value": "M50HFXW61ZY4F", "start": 104, "end": 117, "loc": { @@ -49517,7 +49517,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9AF9PKK", + "value": "M50HFXW6GFFF3", "start": 267, "end": 280, "loc": { @@ -49753,7 +49753,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9AF9PKK", + "value": "M50HFXW6GFFF3", "start": 345, "end": 358, "loc": { diff --git a/docs/ast/source/wrappers/TaxonomicUnitWrapper.js.json b/docs/ast/source/wrappers/TaxonomicUnitWrapper.js.json index dbe66c65..58c55e56 100644 --- a/docs/ast/source/wrappers/TaxonomicUnitWrapper.js.json +++ b/docs/ast/source/wrappers/TaxonomicUnitWrapper.js.json @@ -70,9 +70,9 @@ "line": 2, "column": 25 }, - "identifierName": "LXL9JK9ZA8O5P" + "identifierName": "M50HFXWHOXJ4P" }, - "name": "LXL9JK9ZA8O5P", + "name": "M50HFXWHOXJ4P", "leadingComments": null }, "leadingComments": null @@ -396,9 +396,9 @@ "line": 8, "column": 17 }, - "identifierName": "LXL9JK9ZA8O5P" + "identifierName": "M50HFXWHOXJ4P" }, - "name": "LXL9JK9ZA8O5P" + "name": "M50HFXWHOXJ4P" } } ], @@ -571,9 +571,9 @@ "line": 14, "column": 25 }, - "identifierName": "LXL9JK9ZRPNL2" + "identifierName": "M50HFXWH1YK6A" }, - "name": "LXL9JK9ZRPNL2", + "name": "M50HFXWH1YK6A", "leadingComments": null }, "leadingComments": null @@ -732,9 +732,9 @@ "line": 15, "column": 42 }, - "identifierName": "LXL9JK9ZRPNL2" + "identifierName": "M50HFXWH1YK6A" }, - "name": "LXL9JK9ZRPNL2" + "name": "M50HFXWH1YK6A" } } ], @@ -800,9 +800,9 @@ "line": 18, "column": 25 }, - "identifierName": "LXL9JK9ZO9F5X" + "identifierName": "M50HFXWHPZ8F9" }, - "name": "LXL9JK9ZO9F5X", + "name": "M50HFXWHPZ8F9", "leadingComments": null }, "leadingComments": null @@ -961,9 +961,9 @@ "line": 19, "column": 41 }, - "identifierName": "LXL9JK9ZO9F5X" + "identifierName": "M50HFXWHPZ8F9" }, - "name": "LXL9JK9ZO9F5X" + "name": "M50HFXWHPZ8F9" } } ], @@ -1029,9 +1029,9 @@ "line": 22, "column": 25 }, - "identifierName": "LXL9JK9ZJD9PZ" + "identifierName": "M50HFXWHN2L13" }, - "name": "LXL9JK9ZJD9PZ", + "name": "M50HFXWHN2L13", "leadingComments": null }, "leadingComments": null @@ -1190,9 +1190,9 @@ "line": 23, "column": 45 }, - "identifierName": "LXL9JK9ZJD9PZ" + "identifierName": "M50HFXWHN2L13" }, - "name": "LXL9JK9ZJD9PZ" + "name": "M50HFXWHN2L13" } } ], @@ -23530,7 +23530,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZA8O5P", + "value": "M50HFXWHOXJ4P", "start": 38, "end": 51, "loc": { @@ -23948,7 +23948,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZA8O5P", + "value": "M50HFXWHOXJ4P", "start": 121, "end": 134, "loc": { @@ -24246,7 +24246,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZRPNL2", + "value": "M50HFXWH1YK6A", "start": 325, "end": 338, "loc": { @@ -24482,7 +24482,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZRPNL2", + "value": "M50HFXWH1YK6A", "start": 403, "end": 416, "loc": { @@ -24631,7 +24631,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZO9F5X", + "value": "M50HFXWHPZ8F9", "start": 472, "end": 485, "loc": { @@ -24867,7 +24867,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZO9F5X", + "value": "M50HFXWHPZ8F9", "start": 541, "end": 554, "loc": { @@ -25016,7 +25016,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZJD9PZ", + "value": "M50HFXWHN2L13", "start": 606, "end": 619, "loc": { @@ -25252,7 +25252,7 @@ "postfix": false, "binop": null }, - "value": "LXL9JK9ZJD9PZ", + "value": "M50HFXWHN2L13", "start": 683, "end": 696, "loc": { diff --git a/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html b/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html index c18fddf1..bb5730fe 100644 --- a/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html +++ b/docs/class/src/wrappers/SpecimenWrapper.js~SpecimenWrapper.html @@ -75,8 +75,8 @@

              SpecimenWrapper

              • TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.
                • Based on http://rs.tdwg.org/dwc/terms/Occurrence
                  • -
                • Should have a dwc:occurrenceID with the occurrence identifier.
                  • -
                • Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.
                  • +
                • Should have a occurrenceID with the occurrence identifier.
                  • +
                • Should have a basisOfRecord to indicate what sort of occurrence this is.
              diff --git a/docs/file/src/wrappers/SpecimenWrapper.js.html b/docs/file/src/wrappers/SpecimenWrapper.js.html index d0c956f6..ac477418 100644 --- a/docs/file/src/wrappers/SpecimenWrapper.js.html +++ b/docs/file/src/wrappers/SpecimenWrapper.js.html @@ -55,8 +55,8 @@ * * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen. * - Based on http://rs.tdwg.org/dwc/terms/Occurrence - * - Should have a dwc:occurrenceID with the occurrence identifier. - * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is. + * - Should have a occurrenceID with the occurrence identifier. + * - Should have a basisOfRecord to indicate what sort of occurrence this is. * * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated @@ -83,7 +83,7 @@ const normalizedSpecimen = { '@type': SpecimenWrapper.TYPE_SPECIMEN, label: wrapped.label, - 'dwc:basisOfRecord': wrapped.basisOfRecord, + basisOfRecord: wrapped.basisOfRecord, occurrenceID: wrapped.occurrenceID, catalogNumber: wrapped.catalogNumber, institutionCode: wrapped.institutionCode, @@ -102,12 +102,12 @@ static fromOccurrenceID(occurrenceID, basisOfRecord = 'PreservedSpecimen') { // Copy the occurrence ID so we can truncate it if necessary. let occurID = occurrenceID; - if (occurID.startsWith('urn:catalog:')) occurID = occurID.substr(12); + if (occurID.startsWith('urn:catalog:')) occurID = occurID.substring(12); // Prepare the specimen. const specimen = { '@type': SpecimenWrapper.TYPE_SPECIMEN, - 'dwc:basisOfRecord': basisOfRecord, + basisOfRecord, occurrenceID: occurID, }; @@ -204,7 +204,7 @@ */ get occurrenceID() { // Return the occurrenceID if it exists. - if (has(this.specimen, 'occurrenceID') && this.specimen.occurrenceID.trim() !== '') { + if (has(this.specimen, 'occurrenceID')) { return this.specimen.occurrenceID.trim(); } @@ -230,7 +230,7 @@ * Return the basis of record, if one is present. */ get basisOfRecord() { - if (has(this.specimen, 'dwc:basisOfRecord')) return this.specimen['dwc:basisOfRecord']; + if (has(this.specimen, 'basisOfRecord')) return this.specimen.basisOfRecord; return undefined; } @@ -239,7 +239,7 @@ * recommended values. */ set basisOfRecord(bor) { - this.specimen['dwc:basisOfRecord'] = bor; + this.specimen.basisOfRecord = bor; } /** Return this specimen as a taxon concept if it contains taxon name information. */ diff --git a/docs/index.html b/docs/index.html index b5fa5447..42896916 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,13 +43,17 @@

              phyx.js

              Build Status -DOI

              +DOI +NPM Version

              The Phyloreference Exchange (PHYX) format is a JSON representation that can be used to store and transfer definitions of phyloreferences. This library provides classes to help interpret some parts of these files, and for transforming an entire Phyx file into a JSON-LD representation that can be reasoned over with an OWL 2 DL reasoner. See the Phyloreference Curation Tool or the Clade Ontology for examples of its usage.

              +

              Usage

              You can install phyx.js using npm:

              +
              $ npm install @phyloref/phyx
+

              Tutorials demonstrating the use of phyx.js are available.

              Citation

              phyx.js should be cited by citing our publication documenting the Phyx format and phyx.js.

              diff --git a/docs/index.json b/docs/index.json index 4b90575b..e6c2d1fc 100644 --- a/docs/index.json +++ b/docs/index.json @@ -569,7 +569,7 @@ "name": "src/matchers/TaxonomicUnitMatcher.js", "content": "const { TaxonomicUnitWrapper } = require('../wrappers/TaxonomicUnitWrapper');\nconst { TaxonConceptWrapper } = require('../wrappers/TaxonConceptWrapper');\nconst { SpecimenWrapper } = require('../wrappers/SpecimenWrapper');\n\n/**\n * The TaxonomicUnitMatcher matches pairs of taxonomic units and provides\n * a consistent report on:\n * - Which taxonomic units have matched, and\n * - Why the match occurred.\n *\n * In Model 2.0, we start by using direct matching in OWL, so this should no longer\n * be needed. However, I'll leave this around to provide matching in the\n * Curation Tool UI and in case it's needed again later.\n */\nclass TaxonomicUnitMatcher {\n /**\n * Create a Taxonomic Unit Matcher to match two taxonomic units. Matching\n * will occur immediately, so when this method returns, you can check\n * tuMatch.matched and tuMatch.matchReason to determine if the two TUs matched\n * and why.\n */\n constructor(tunit1, tunit2) {\n this.tunit1 = tunit1;\n this.tunit2 = tunit2;\n\n // Set up places to store the match results.\n this.matched = undefined; // Boolean variable for storing whether these TUnits matched.\n this.matchReason = undefined; // The reason provided for this match.\n\n // Execute the match.\n this.match();\n }\n\n /** Return this TUMatch as a JSON object for insertion into the PHYX file. */\n asJSONLD(idIRI) {\n if (!this.matched) return undefined;\n\n return {\n '@id': idIRI,\n reason: this.matchReason,\n matchesTaxonomicUnits: [\n { '@id': this.tunit1['@id'] },\n { '@id': this.tunit2['@id'] },\n ],\n };\n }\n\n /** Try to match the two taxonomic units using a number of matching methods. */\n match() {\n if (\n this.matchByNameComplete()\n || this.matchByExternalReferences()\n || this.matchByOccurrenceID()\n ) {\n this.matched = true;\n } else {\n this.matched = false;\n this.matchReason = undefined;\n }\n }\n\n /** Try to match by nameComplete, and return true if it could be matched. */\n matchByNameComplete() {\n // Note that this doesn't apply just to taxon concepts -- we try to match\n // any taxonomic units that have nameComplete, which might be taxon concepts\n // OR specimens with taxonomic units.\n const wrappedTName1 = new TaxonConceptWrapper(this.tunit1);\n const wrappedTName2 = new TaxonConceptWrapper(this.tunit2);\n\n if (\n wrappedTName1.nameComplete && wrappedTName2.nameComplete\n && wrappedTName1.nameComplete === wrappedTName2.nameComplete\n ) {\n this.matchReason = `Taxon name '${wrappedTName1.label}' and taxon name '${wrappedTName2.label}' share the same complete name`;\n return true;\n }\n\n return false;\n }\n\n /** Match by external references. */\n matchByExternalReferences() {\n const wrappedTUnit1 = new TaxonomicUnitWrapper(this.tunit1);\n const wrappedTUnit2 = new TaxonomicUnitWrapper(this.tunit2);\n\n const externalRefs1 = wrappedTUnit1.externalReferences;\n const externalRefs2 = wrappedTUnit2.externalReferences;\n\n return externalRefs1.some(\n extref1 => externalRefs2.some(\n (extref2) => {\n if (\n extref1\n && extref2\n && (extref1.toLowerCase() === extref2.toLowerCase())\n ) {\n this.matchReason = `External reference '${extref1}' is shared by taxonomic unit ${this.tunit1} and ${this.tunit2}`;\n return true;\n }\n\n return false;\n }\n )\n );\n }\n\n /** Match by occurrence ID */\n matchByOccurrenceID() {\n // Are both TUs specimens?\n const wrappedTUnit1 = new TaxonomicUnitWrapper(this.tunit1);\n const wrappedTUnit2 = new TaxonomicUnitWrapper(this.tunit2);\n\n if (!wrappedTUnit1.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) return false;\n if (!wrappedTUnit2.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) return false;\n\n // Occurrence IDs from both taxonomic units.\n const wrappedSpecimen1 = new SpecimenWrapper(this.tunit1);\n const wrappedSpecimen2 = new SpecimenWrapper(this.tunit2);\n\n if (\n wrappedSpecimen1.occurrenceID && wrappedSpecimen2.occurrenceID\n && wrappedSpecimen1.occurrenceID === wrappedSpecimen2.occurrenceID\n ) {\n this.matchReason = `Specimen identifier '${wrappedSpecimen1.occurrenceID}' is shared by taxonomic units`;\n\n return true;\n }\n\n return false;\n }\n}\n\nmodule.exports = {\n TaxonomicUnitMatcher,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/matchers/TaxonomicUnitMatcher.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/matchers/TaxonomicUnitMatcher.js", "access": "public", "description": null, "lineNumber": 1 @@ -837,7 +837,7 @@ "name": "src/wrappers/CitationWrapper.js", "content": "/**\n * The CitationWrapper wraps a single citation in the Phyx document.\n * Based on BibJSON (http://okfnlabs.org/bibjson/).\n */\n\nconst { has, isEmpty } = require('lodash');\n\nclass CitationWrapper {\n /**\n * Construct a CitationWrapper.\n */\n constructor(citation) {\n this.citation = citation;\n }\n\n /**\n * Return a normalized form of a citation.\n *\n * I'm not really sure how to normalize a citation, but the main thing we can do is delete any key\n * that is equivalent to ''. We could interconvert between `name` and\n * `firstname/lastname/middlename`, but that's not really equivalent, is it?\n */\n static normalize(citation) {\n const normalizedCitation = {};\n Object.keys(citation).forEach((key) => {\n // As long as citation[key] has a reasonable value, we copy it into the normalized citation.\n if (citation[key]) {\n normalizedCitation[key] = citation[key];\n }\n });\n return normalizedCitation;\n }\n\n /**\n * Helper method to return a single name for a given agent entry.\n * The algorithm we use is:\n * - `name`, if one is present.\n * - Some combination of `lastname`, `firstname` and `middlename`, if present.\n */\n static getAgentName(agent) {\n if (has(agent, 'name')) return agent.name;\n if (has(agent, 'lastname')) {\n if (has(agent, 'firstname')) {\n if (has(agent, 'middlename')) {\n return `${agent.firstname} ${agent.middlename} ${agent.lastname}`;\n }\n\n return `${agent.firstname} ${agent.lastname}`;\n }\n return `${agent.lastname}`;\n }\n return '(Unable to read name)';\n }\n\n /** Returns a single string with the entire bibliographic citation. */\n toString() {\n if (!this.citation || isEmpty(this.citation)) return undefined;\n\n // If we already have a bibliographic citation, we can just return that.\n if (has(this.citation, 'bibliographicCitation')) return this.citation.bibliographicCitation;\n\n let authors = (this.citation.authors || []).map(CitationWrapper.getAgentName);\n if (authors.length === 0) authors = ['Anonymous'];\n if (authors.length > 2) authors = [`${authors[0]} et al`];\n\n // The title is based on citation.title, but may include citation.section as well.\n let title = this.citation.title || 'Untitled';\n if (has(this.citation, 'booktitle')) title = `${title} in ${this.citation.booktitle || 'Untitled book'}`;\n let authorsAndTitle = `${authors.join(' and ')} (${this.citation.year || 'n.d.'}) ${title}`;\n\n const editorLists = [];\n const editors = (this.citation.editors || []).map(CitationWrapper.getAgentName);\n if (editors.length > 0) editorLists.push(`eds: ${editors.join(' and ')}`);\n\n const seriesEditors = (this.citation.series_editors || []).map(CitationWrapper.getAgentName);\n if (seriesEditors.length > 0) editorLists.push(`series eds: ${seriesEditors.join(' and ')}`);\n\n if (editorLists.length > 0) authorsAndTitle += ` [${editorLists.join(', ')}]`;\n\n if (has(this.citation, 'section_title')) {\n authorsAndTitle += ` (section: ${this.citation.section_title})`;\n }\n\n // Additional info stores details that should be at the end of the figure number,\n // DOIs, URLs, ISBNs and so on.\n let additionalInfo = ' ';\n if (has(this.citation, 'figure')) additionalInfo += ` fig ${this.citation.figure}`;\n\n // Add DOIs and URLs.\n additionalInfo += (this.citation.identifier || [])\n .filter(id => id.type === 'doi')\n .map(doi => ` doi: ${doi.id}`)\n .join('');\n additionalInfo += (this.citation.link || []).map(link => ` URL: ${link.url}`).join('');\n\n additionalInfo += (this.citation.identifier || [])\n .filter(id => id.type === 'isbn')\n .map(isbn => ` ISBN: ${isbn.id}`)\n .join('');\n\n // A citation for a journal article should be different from others.\n if (has(this.citation, 'journal') && this.citation.type === 'article') {\n const journal = this.citation.journal;\n const journalIssue = (has(journal, 'number')) ? `(${journal.number})` : '';\n const pages = (has(journal, 'pages')) ? `:${journal.pages}` : '';\n additionalInfo += (journal.identifier || [])\n .filter(id => id.type === 'issn')\n .map(issn => `ISSN: ${issn.id} `)\n .join('');\n return `${authorsAndTitle} ${journal.name || 'Unknown journal'} ${journal.volume || 'Unknown volume'}${journalIssue}${pages}${additionalInfo}`;\n }\n\n // If we are here, this must be a book or a book_section.\n if (has(this.citation, 'pages')) additionalInfo += ` pages: ${this.citation.pages}`;\n\n if (has(this.citation, 'publisher') && has(this.citation, 'city')) {\n return `${authorsAndTitle} ${this.citation.publisher}, ${this.citation.city}${additionalInfo}`;\n }\n\n if (has(this.citation, 'publisher')) {\n return `${authorsAndTitle} ${this.citation.publisher}${additionalInfo}`;\n }\n\n return `${authorsAndTitle}${additionalInfo}`.trim();\n }\n}\n\nmodule.exports = {\n CitationWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/CitationWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/CitationWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -986,7 +986,7 @@ "name": "src/wrappers/PhylogenyWrapper.js", "content": "/**\n * PhylogenyWrapper\n */\n\nconst {\n has,\n cloneDeep,\n} = require('lodash');\n\n/** Used to parse Newick strings. */\nconst newickJs = require('newick-js');\n\n/** OWL terms to be used here. */\nconst owlterms = require('../utils/owlterms');\n\nconst { TaxonomicUnitWrapper } = require('./TaxonomicUnitWrapper');\nconst { TaxonomicUnitMatcher } = require('../matchers/TaxonomicUnitMatcher');\nconst { CitationWrapper } = require('./CitationWrapper');\n\nclass PhylogenyWrapper {\n // Wraps a Phylogeny in a PHYX file and provides access to node, node labels\n // and other information. Remember that a Phylogeny also has the\n // additionalNodeProperties object which provides additional properties for\n // nodes.\n\n constructor(phylogeny, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n // Construct a phylogeny based on a Phylogeny object in a PHYX phylogeny.\n // Note that this version ONLY uses the `newick` property to determine the\n // phylogeny: if other representations are included (such as a node-based\n // format, as used in JSON-LD), they will be ignored and possibly overwritten\n // during export. So, to update the phylogeny, please only update the newick\n // string!\n //\n // This ensures that we don't need to reconcile between different\n // possible representations of a phylogeny.\n this.phylogeny = phylogeny;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Return a normalized form of the phylogeny.\n */\n static normalize(phylogeny) {\n const normalizedPhylogeny = cloneDeep(phylogeny);\n\n // We could normalize the Newick string, but that doesn't seem very nice.\n\n // Normalize the source if there is one.\n if ('source' in phylogeny) {\n normalizedPhylogeny.source = CitationWrapper.normalize(phylogeny.source || {});\n }\n\n return normalizedPhylogeny;\n }\n\n static getErrorsInNewickString(newick) {\n // Given a Newick string, return a list of errors found in parsing this\n // string. The errors are returned as a list of objects, each of which\n // has two properties:\n // - title: A short title of the error, distinct for each type of error.\n // - message: A longer description of the error, which might include\n // information specific to a particular error.\n //\n // We try to order errors from most helpful ('Unbalanced parentheses in\n // Newick string') to least helpful ('Error parsing phylogeny').\n const newickTrimmed = newick.trim();\n const errors = [];\n\n // Look for an empty Newick string.\n if (newickTrimmed === '' || newickTrimmed === '()' || newickTrimmed === '();') {\n // None of the later errors are relevant here, so bail out now.\n return [{\n title: 'No phylogeny entered',\n message: 'Click on \"Edit as Newick\" to enter a phylogeny below.',\n }];\n }\n\n // Look for an unbalanced Newick string.\n let parenLevels = 0;\n for (let x = 0; x < newickTrimmed.length; x += 1) {\n if (newickTrimmed[x] === '(') parenLevels += 1;\n if (newickTrimmed[x] === ')') parenLevels -= 1;\n }\n\n if (parenLevels !== 0) {\n errors.push({\n title: 'Unbalanced parentheses in Newick string',\n message: (parenLevels > 0\n ? `You have ${parenLevels} too many open parentheses`\n : `You have ${-parenLevels} too few open parentheses`\n ),\n });\n }\n\n // Finally, try parsing it with newickJs.parse() and see if we get an error.\n try {\n newickJs.parse(newickTrimmed);\n } catch (ex) {\n errors.push({\n title: 'Error parsing phylogeny',\n message: `An error occured while parsing this phylogeny: ${ex.message}`,\n });\n }\n\n return errors;\n }\n\n static recurseNodes(node, func, nodeCount = 0, parentCount = undefined) {\n // Recurse through PhyloTree nodes, executing function on each node.\n // - node: The node to recurse from. The function will be called on node\n // *before* being called on its children.\n // - func: The function to call on `node` and all of its children.\n // - nodeCount: `node` will be called with this nodeCount. All of its\n // children will be called with consecutively increasing nodeCounts.\n // - parentCount: The nodeCount associated with the parent of this node\n // within this run of recurseNodes. For instance, immediate children\n // of `node` will have a parentCount of 0. By default, `node` itself\n // will have a parentCount of `undefined`.\n // When the function `func` is called, it is given three arguments:\n // - The current node object (initially: `node`)\n // - The count of the current node object (initially: `nodeCount`)\n // - The parent count of the current node object (initially: `parentCount`)\n func(node, nodeCount, parentCount);\n\n let nextID = nodeCount + 1;\n\n // Recurse through all children of this node.\n if (has(node, 'children')) {\n node.children.forEach((child) => {\n nextID = PhylogenyWrapper.recurseNodes(\n child,\n func,\n nextID,\n nodeCount\n );\n });\n }\n\n return nextID;\n }\n\n getTaxonomicUnits(nodeType = 'both') {\n // Return a list of all taxonomic units in this phylogeny.\n // Node labels will be extracted from:\n // - internal nodes only (if nodeType == 'internal')\n // - terminal nodes only (if nodeType == 'terminal')\n // - both internal and terminal nodes (if nodeType == 'both')\n //\n // See `getTaxonomicUnitsForNodeLabel` to see how node labels are converted\n // into node labels, but in brief:\n // 1. We look for taxonomic units in the additionalNodeProperties.\n // 2. If none are found, we attempt to parse the node label as a scientific name.\n //\n const nodeLabels = this.getNodeLabels(nodeType);\n const tunits = new Set();\n\n nodeLabels.forEach(\n nodeLabel => this.getTaxonomicUnitsForNodeLabel(nodeLabel)\n .forEach(tunit => tunits.add(tunit))\n );\n\n return tunits;\n }\n\n getNodeLabels(nodeType = 'both') {\n // Return a list of all the node labels in this phylogeny.\n //\n // nodeType can be one of:\n // - 'internal': Return node labels on internal nodes.\n // - 'terminal': Return node labels on terminal nodes.\n // - 'both': Return node labels on both internal and terminal nodes.\n\n // Parse the phylogeny (will throw an exception if parsing failed).\n const { graph } = newickJs.parse(this.phylogeny.newick || '()');\n const [vertices, arcs] = graph;\n\n if (nodeType === 'both') {\n // Return all node labels.\n return Array.from(\n new Set(\n Array.from(vertices)\n .map(vertex => vertex.label)\n .filter(label => label !== undefined)\n )\n );\n }\n\n if (nodeType === 'internal') {\n // Return the internal nodes (those with atleast one child).\n return Array.from(new Set(\n Array.from(arcs)\n .map(arc => arc[0].label) // Retrieve the label of the parent vertex in this arc.\n .filter(label => label !== undefined)\n ));\n }\n\n if (nodeType === 'terminal') {\n // Return the terminal nodes. This would require calculating the children\n // of every vertex in the graph and then identifying vertices without any\n // children.\n //\n // A quicker and dirtier way to do this is by removing internal labels\n // from the list of all node labels. This will report an incorrect result\n // if an internal node has the same label as a terminal node, but at that\n // point a lot of other assumptions are going to fail, too, so this is\n // probably good enough for now.\n const allLabels = this.getNodeLabels('both');\n const internalLabels = new Set(this.getNodeLabels('internal'));\n\n return allLabels.filter(label => !internalLabels.has(label));\n }\n\n throw new Error(`Unknown nodeType: '${nodeType}'`);\n }\n\n /**\n * Return a list of taxonomic units for a node label.\n *\n * If the additionalNodeProperties for this node label includes taxonomic units\n * (using `representsTaxonomicUnits` = obo:CDAO_0000187), then those taxonomic\n * units are used. Otherwise, one will be constructed using the default\n * nomenclatural code set up when this PhylogenyWrapper was set up.\n */\n getTaxonomicUnitsForNodeLabel(nodeLabel) {\n // Look up additional node properties.\n let additionalNodeProperties = {};\n if (\n has(this.phylogeny, 'additionalNodeProperties')\n && has(this.phylogeny.additionalNodeProperties, nodeLabel)\n ) {\n additionalNodeProperties = this.phylogeny.additionalNodeProperties[nodeLabel];\n }\n\n // If there are explicit taxonomic units in the\n // representsTaxonomicUnits property, we need to use those.\n if (has(additionalNodeProperties, 'representsTaxonomicUnits')) {\n return additionalNodeProperties.representsTaxonomicUnits;\n }\n\n // If that doesn't work, we can try to extract scientific names from\n // the node label. Note that taxonomic units will NOT be extracted from\n // the label if there is a taxonomic unit present!\n //\n // Note that old-style taxonomic units were lists while new-style taxonomic\n // units are single objects. So we turn it into a single entry list here.\n const tunit = TaxonomicUnitWrapper.fromLabel(nodeLabel.trim(), this.defaultNomenCode);\n if (tunit) return [tunit];\n return []; // No TUnit? Return the empty list.\n }\n\n getNodeLabelsMatchedBySpecifier(specifier) {\n // Return a list of node labels matched by a given specifier on\n // a given phylogeny.\n\n return this.getNodeLabels().filter((nodeLabel) => {\n // Find all the taxonomic units associated with the specifier and\n // with the node.\n const nodeTUnits = this.getTaxonomicUnitsForNodeLabel(nodeLabel);\n\n // Attempt pairwise matches between taxonomic units in the specifier\n // and associated with the node.\n return nodeTUnits.some(\n tunit => new TaxonomicUnitMatcher(specifier, tunit).matched\n );\n });\n }\n\n static getParsedNewick(newick) {\n // We previously used phylotree.js's Newick parser to parse Newick into a\n // tree-like structure. However, this is difficult to integrate using NPM.\n // This method provides a similar facility using the newick-js library.\n //\n // Throws an exception if the Newick could not be parsed.\n const { graph, root, rootWeight } = newickJs.parse(newick);\n const [, arcs] = graph;\n\n // Go through the arcs, assigning 'children' to the appropriate parent node.\n arcs.forEach((arc) => {\n const [parent, child, weight] = arc;\n\n // Add child to parent.children.\n if (!has(parent, 'children')) parent.children = [];\n parent.children.push(child);\n\n // Phylotree.js uses 'name' instead of 'label'.\n if (has(parent, 'label')) { parent.name = parent.label; }\n if (has(child, 'label')) { child.name = child.label; }\n\n // Phylotree.js uses 'attribute' to store weights, so we'll store it there as well.\n if (!has(child, 'attribute') && !Number.isNaN(weight)) child.attribute = weight;\n });\n\n // Set root 'attribute' to root weight.\n if (!has(root, 'attribute') && !Number.isNaN(rootWeight)) root.attribute = rootWeight;\n\n return { json: root };\n }\n\n getParsedNewickWithIRIs(baseIRI, newickParser = PhylogenyWrapper.getParsedNewick) {\n // Return the parsed Newick string, but with EVERY node given an IRI.\n // - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').\n // Node IDs are generated by concatenating `_node${number}` to the end of\n // the baseIRI.\n // - newickParser: A method for converting a Newick string to a object-based\n // representation. The static method PhylogenyWrapper.getParsedNewick() is\n // used if none is provided.\n\n const parsed = newickParser(this.phylogeny.newick || '()');\n if (has(parsed, 'json')) {\n PhylogenyWrapper.recurseNodes(parsed.json, (node, nodeCount) => {\n // Start with the additional node properties.\n const nodeAsJSONLD = node;\n\n // Set @id and @type.\n const nodeIRI = `${baseIRI}_node${nodeCount}`;\n nodeAsJSONLD['@id'] = nodeIRI;\n });\n }\n\n return parsed;\n }\n\n getNodesAsJSONLD(baseIRI, newickParser) {\n // Returns a list of all nodes in this phylogeny as a series of nodes.\n // - baseIRI: The base IRI to use for node elements (e.g. ':phylogeny1').\n // Node IDs are generated by concatenating `_node${number}` to the end of\n // the baseIRI.\n // - newickParser: A method for converting a Newick string to a object-based\n // representation. See PhylogenyWrapper.getParsedNewick() for an example\n // implementation.\n\n // List of nodes we have identified.\n const nodes = [];\n\n // We need to track the identifiers we give each node as we go.\n const nodesById = {};\n const nodeIdsByParentId = {};\n\n // Extract the newick string.\n const { additionalNodeProperties } = this.phylogeny;\n\n // Parse the Newick string; if parseable, recurse through the nodes,\n // added them to the list of JSON-LD nodes as we go.\n\n const parsed = this.getParsedNewickWithIRIs(baseIRI, newickParser);\n if (has(parsed, 'json')) {\n PhylogenyWrapper.recurseNodes(parsed.json, (node, nodeCount, parentCount) => {\n // Start with the additional node properties.\n const nodeAsJSONLD = {};\n\n // Set @id and @type. '@id' should already be set by getParsedNewickWithIRIs()!\n const nodeIRI = node['@id'];\n nodeAsJSONLD['@id'] = nodeIRI;\n\n // Since we may need to add multiple classes into the rdf:type, we need\n // to make @type an array. However, the JSON-LD library we use in JPhyloRef\n // can't support @type being an array (despite that being in the standard,\n // see https://w3c.github.io/json-ld-syntax/#example-14-specifying-multiple-types-for-a-node),\n // so we fall back to using rdf:type instead.\n nodeAsJSONLD[owlterms.RDF_TYPE] = [{ '@id': owlterms.CDAO_NODE }];\n\n // Add labels, additional node properties and taxonomic units.\n if (has(node, 'name') && node.name !== '') {\n // Add node label.\n nodeAsJSONLD.labels = [node.name];\n\n // Add additional node properties, if any.\n if (additionalNodeProperties && has(additionalNodeProperties, node.name)) {\n Object.keys(additionalNodeProperties[node.name]).forEach((key) => {\n nodeAsJSONLD[key] = additionalNodeProperties[node.name][key];\n });\n }\n\n // Add taxonomic units into the metadata.\n nodeAsJSONLD.representsTaxonomicUnits = this.getTaxonomicUnitsForNodeLabel(node.name);\n\n // Add it into the @type so we can reason over it.\n nodeAsJSONLD.representsTaxonomicUnits.forEach((tu) => {\n const wrappedTUnit = new TaxonomicUnitWrapper(tu);\n\n if (wrappedTUnit) {\n const equivClass = wrappedTUnit.asOWLEquivClass;\n if (equivClass) {\n nodeAsJSONLD[owlterms.RDF_TYPE].push(\n {\n '@type': 'owl:Restriction',\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: equivClass,\n }\n );\n }\n }\n });\n }\n\n // Add references to parents and siblings.\n if (parentCount !== undefined) {\n const parentIRI = `${baseIRI}_node${parentCount}`;\n nodeAsJSONLD.parent = parentIRI;\n\n // Update list of nodes by parent IDs.\n if (!has(nodeIdsByParentId, parentIRI)) {\n nodeIdsByParentId[parentIRI] = new Set();\n }\n nodeIdsByParentId[parentIRI].add(nodeIRI);\n }\n\n // Add nodeAsJSONLD to list\n if (has(nodesById, nodeIRI)) {\n throw new Error(`Error in programming: duplicate node IRI generated (${nodeIRI})`);\n }\n nodesById[nodeIRI] = nodeAsJSONLD;\n nodes.push(nodeAsJSONLD);\n });\n }\n\n // Go through nodes again and set children and sibling relationships.\n Object.keys(nodeIdsByParentId).forEach((parentId) => {\n // What are the children of this parentId?\n const childrenIDs = Array.from(nodeIdsByParentId[parentId]);\n const children = childrenIDs.map(childId => nodesById[childId]);\n\n // Is this the root node?\n if (has(nodesById, parentId)) {\n const parent = nodesById[parentId];\n parent.children = childrenIDs;\n }\n\n children.forEach((child) => {\n const childToModify = child;\n // Add all other sibling to node.siblings, but don't add this node itself!\n childToModify.siblings = childrenIDs.filter(childId => childId !== child['@id']);\n });\n });\n\n return nodes;\n }\n\n asJSONLD(fallbackIRI, newickParser) {\n // Export this phylogeny as JSON-LD.\n // - fallbackIRI: The fallback IRI to use for this phylogeny if it does not\n // already have an '@id' set.\n // - newickParser: A function that parses a Newick string and returns a\n // an object based representation of this phylogeny. If not set, the\n // static method PhylogenyWrapper.getParsedNewick will be used instead.\n\n // Create a copy to export.\n const phylogenyAsJSONLD = JSON.parse(JSON.stringify(this.phylogeny));\n\n // Set name and class for phylogeny. If no '@id' is set, use the provided\n // fallbackIRI.\n if (!has(phylogenyAsJSONLD, '@id')) phylogenyAsJSONLD['@id'] = fallbackIRI;\n phylogenyAsJSONLD['@type'] = 'phyloref:ReferencePhylogenyEvidence';\n\n // Translate nodes into JSON-LD objects.\n phylogenyAsJSONLD.nodes = this.getNodesAsJSONLD(phylogenyAsJSONLD['@id'], newickParser);\n if (phylogenyAsJSONLD.nodes.length > 0) {\n // We don't have a better way to identify the root node, so we just\n // default to the first one.\n phylogenyAsJSONLD.hasRootNode = {\n '@id': phylogenyAsJSONLD.nodes[0]['@id'],\n };\n }\n\n // Add a bibliographicCitation to the source if it is a Citation.\n if (has(phylogenyAsJSONLD, 'source')) {\n const source = phylogenyAsJSONLD.source;\n\n if (!has(source, 'bibliographicCitation')) {\n source.bibliographicCitation = new CitationWrapper(source).toString();\n }\n }\n\n return phylogenyAsJSONLD;\n }\n}\n\nmodule.exports = {\n PhylogenyWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/PhylogenyWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/PhylogenyWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -1489,7 +1489,7 @@ "name": "src/wrappers/PhylorefWrapper.js", "content": "/** Used to parse timestamps for phyloref statuses. */\nconst moment = require('moment');\nconst { has, cloneDeep, uniq } = require('lodash');\n\nconst owlterms = require('../utils/owlterms');\nconst { TaxonomicUnitWrapper } = require('./TaxonomicUnitWrapper');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst { PhylogenyWrapper } = require('./PhylogenyWrapper');\nconst { CitationWrapper } = require('./CitationWrapper');\n\n/**\n * PhylorefWrapper\n *\n */\n\nclass PhylorefWrapper {\n // Wraps a phyloreference in a PHYX model.\n\n constructor(phyloref, phyxDefaultNomenCode = owlterms.UNKNOWN_CODE) {\n // Wraps the provided phyloreference\n this.phyloref = phyloref;\n this.phyxDefaultNomenCode = phyxDefaultNomenCode;\n }\n\n /** Return the internal specifiers of this phyloref (if any). */\n get internalSpecifiers() {\n if (!has(this.phyloref, 'internalSpecifiers')) {\n // If there isn't one, create an empty list so that the caller can do\n // `wrappedPhyloref.internalSpecifiers.push({...})`.\n this.phyloref.internalSpecifiers = [];\n }\n\n return this.phyloref.internalSpecifiers;\n }\n\n /**\n * Normalize a phyloreference.\n *\n * @param phyloref\n */\n static normalize(phyloref) {\n const normalizedPhyloref = cloneDeep(phyloref);\n\n normalizedPhyloref.internalSpecifiers = (phyloref.internalSpecifiers || [])\n .map(TaxonomicUnitWrapper.normalize);\n normalizedPhyloref.externalSpecifiers = (phyloref.externalSpecifiers || [])\n .map(TaxonomicUnitWrapper.normalize);\n\n return normalizedPhyloref;\n }\n\n /** Return the external specifiers of this phyloref (if any). */\n get externalSpecifiers() {\n if (!has(this.phyloref, 'externalSpecifiers')) {\n // If there isn't one, create an empty list so that the caller can do\n // `wrappedPhyloref.externalSpecifiers.push({...})`.\n this.phyloref.externalSpecifiers = [];\n }\n\n return this.phyloref.externalSpecifiers;\n }\n\n get label() {\n // Return a label for this phyloreference.\n if (has(this.phyloref, 'label')) return this.phyloref.label;\n if (has(this.phyloref, 'labels') && this.phyloref.labels.length > 0) return this.phyloref.labels[0];\n if (has(this.phyloref, 'title')) return this.phyloref.title;\n\n return undefined;\n }\n\n set label(newLabel) {\n // Set a label for this phyloreference.\n if (has(this.phyloref, 'label')) {\n this.phyloref.label = newLabel;\n } else {\n // Vue.set(this.phyloref, 'label', newLabel);\n this.phyloref.label = newLabel;\n }\n }\n\n /** Return all the specifiers of this phyloref (if any). */\n get specifiers() {\n // Returns a list of all specifiers by combining the internal and external\n // specifiers into a single list, with internal specifiers before\n // external specifiers.\n let specifiers = this.internalSpecifiers;\n specifiers = specifiers.concat(this.externalSpecifiers);\n return specifiers;\n }\n\n getSpecifierType(specifier) {\n // For a given specifier, return a string indicating whether it is\n // an 'Internal' or 'External' specifier.\n\n if (this.internalSpecifiers.includes(specifier)) return 'Internal';\n if (this.externalSpecifiers.includes(specifier)) return 'External';\n return 'Specifier';\n }\n\n setSpecifierType(specifier, specifierType) {\n // Change the type of a given specifier. To do this, we first need\n // to determine if it was originally an internal or external\n // specifier, then move it into the other list.\n\n let index;\n if (specifierType === 'Internal') {\n // To set a specifier to 'Internal', we might need to delete it from the\n // list of external specifiers first.\n index = this.externalSpecifiers.indexOf(specifier);\n if (index !== -1) this.externalSpecifiers.splice(index, 1);\n\n // Don't add it to the list of internal specifiers if it's already there.\n if (!this.internalSpecifiers.includes(specifier)) {\n this.phyloref.internalSpecifiers.unshift(specifier);\n }\n } else if (specifierType === 'External') {\n // To set a specifier to 'External', we might need to delete it from the\n // list of internal specifiers first.\n index = this.phyloref.internalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.internalSpecifiers.splice(index, 1);\n\n // Don't add it to the list of internal specifiers if it's already there.\n if (!this.phyloref.externalSpecifiers.includes(specifier)) {\n this.phyloref.externalSpecifiers.unshift(specifier);\n }\n } else {\n // Neither internal nor external? Ignore.\n }\n }\n\n deleteSpecifier(specifier) {\n // Since the user interface combines specifiers into a single list,\n // it doesn't remember if the specifier to be deleted is internal\n // or external. We delete the intended specifier from both arrays.\n\n if (has(this.phyloref, 'internalSpecifiers') && this.phyloref.internalSpecifiers.length > 0) {\n const index = this.phyloref.internalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.internalSpecifiers.splice(index, 1);\n }\n\n if (has(this.phyloref, 'externalSpecifiers') && this.phyloref.externalSpecifiers.length > 0) {\n const index = this.phyloref.externalSpecifiers.indexOf(specifier);\n if (index !== -1) this.phyloref.externalSpecifiers.splice(index, 1);\n }\n }\n\n getExpectedNodeLabels(phylogeny) {\n // Given a phylogeny, determine which node labels we expect this phyloref to\n // resolve to. To do this, we:\n // 1. Find all node labels that are case-sensitively identical\n // to the phyloreference.\n // 2. Find all node labels that have additionalNodeProperties with\n // expectedPhyloreferenceNamed case-sensitively identical to\n // the phyloreference.\n const phylorefLabel = this.label;\n const nodeLabels = new Set();\n\n new PhylogenyWrapper(\n phylogeny,\n this.defaultNomenCode\n ).getNodeLabels().forEach((nodeLabel) => {\n // Is this node label identical to the phyloreference name?\n if (nodeLabel === phylorefLabel) {\n nodeLabels.add(nodeLabel);\n } else if (\n has(phylogeny, 'additionalNodeProperties')\n && has(phylogeny.additionalNodeProperties, nodeLabel)\n && has(phylogeny.additionalNodeProperties[nodeLabel], 'expectedPhyloreferenceNamed')\n ) {\n // Does this node label have an expectedPhyloreferenceNamed that\n // includes this phyloreference name?\n\n const expectedPhylorefs = phylogeny\n .additionalNodeProperties[nodeLabel]\n .expectedPhyloreferenceNamed;\n\n if (expectedPhylorefs.includes(phylorefLabel)) {\n nodeLabels.add(nodeLabel);\n }\n }\n });\n\n // Return node labels sorted alphabetically.\n return Array.from(nodeLabels).sort();\n }\n\n static getStatusCURIEsInEnglish() {\n // Return dictionary of all phyloref statuses in English\n return {\n 'pso:draft': 'Draft',\n 'pso:final-draft': 'Final draft',\n 'pso:under-review': 'Under review',\n 'pso:submitted': 'Tested',\n 'pso:published': 'Published',\n 'pso:retracted-from-publication': 'Retracted',\n };\n }\n\n getCurrentStatus() {\n // Return a result object that contains:\n // - status: phyloreference status as a short URI (CURIE)\n // - statusInEnglish: an English representation of the phyloref status\n // - intervalStart: the start of the interval\n // - intervalEnd: the end of the interval\n\n if (\n has(this.phyloref, 'pso:holdsStatusInTime')\n && Array.isArray(this.phyloref['pso:holdsStatusInTime'])\n && this.phyloref['pso:holdsStatusInTime'].length > 0\n ) {\n // If we have any pso:holdsStatusInTime entries, pick the first one and\n // extract the CURIE and time interval information from it.\n const lastStatusInTime = this.phyloref['pso:holdsStatusInTime'][this.phyloref['pso:holdsStatusInTime'].length - 1];\n const statusCURIE = lastStatusInTime['pso:withStatus']['@id'];\n\n // Look for time interval information\n let intervalStart;\n let intervalEnd;\n\n if (has(lastStatusInTime, 'tvc:atTime')) {\n const atTime = lastStatusInTime['tvc:atTime'];\n if (has(atTime, 'timeinterval:hasIntervalStartDate')) intervalStart = atTime['timeinterval:hasIntervalStartDate'];\n if (has(atTime, 'timeinterval:hasIntervalEndDate')) intervalEnd = atTime['timeinterval:hasIntervalEndDate'];\n }\n\n // Return result object\n return {\n statusCURIE,\n statusInEnglish: PhylorefWrapper.getStatusCURIEsInEnglish()[statusCURIE],\n intervalStart,\n intervalEnd,\n };\n }\n\n // If we couldn't figure out a status for this phyloref, assume it's a draft.\n return {\n statusCURIE: 'pso:draft',\n statusInEnglish: PhylorefWrapper.getStatusCURIEsInEnglish()['pso:draft'],\n };\n }\n\n getStatusChanges() {\n // Return a list of status changes for a particular phyloreference\n if (has(this.phyloref, 'pso:holdsStatusInTime')) {\n return this.phyloref['pso:holdsStatusInTime'].map((entry) => {\n const result = {};\n\n // Create a statusCURIE convenience field.\n if (has(entry, 'pso:withStatus')) {\n result.statusCURIE = entry['pso:withStatus']['@id'];\n result.statusInEnglish = PhylorefWrapper.getStatusCURIEsInEnglish()[result.statusCURIE];\n }\n\n // Create intervalStart/intervalEnd convenient fields\n if (has(entry, 'tvc:atTime')) {\n const atTime = entry['tvc:atTime'];\n if (has(atTime, 'timeinterval:hasIntervalStartDate')) {\n result.intervalStart = atTime['timeinterval:hasIntervalStartDate'];\n result.intervalStartAsCalendar = moment(result.intervalStart).calendar();\n }\n\n if (has(atTime, 'timeinterval:hasIntervalEndDate')) {\n result.intervalEnd = atTime['timeinterval:hasIntervalEndDate'];\n result.intervalEndAsCalendar = moment(result.intervalEnd).calendar();\n }\n }\n\n return result;\n });\n }\n\n // No changes? Return an empty list.\n return [];\n }\n\n setStatus(status) {\n // Set the status of a phyloreference\n //\n // Check whether we have a valid status CURIE.\n if (!has(PhylorefWrapper.getStatusCURIEsInEnglish(), status)) {\n throw new TypeError(`setStatus() called with invalid status CURIE '${status}'`);\n }\n\n // See if we can end the previous interval.\n const currentTime = new Date(Date.now()).toISOString();\n\n if (!has(this.phyloref, 'pso:holdsStatusInTime')) {\n // Vue.set(this.phyloref, 'pso:holdsStatusInTime', []);\n this.phyloref['pso:holdsStatusInTime'] = [];\n }\n\n // Check to see if there's a previous time interval we should end.\n if (\n Array.isArray(this.phyloref['pso:holdsStatusInTime'])\n && this.phyloref['pso:holdsStatusInTime'].length > 0\n ) {\n const lastStatusInTime = this.phyloref['pso:holdsStatusInTime'][this.phyloref['pso:holdsStatusInTime'].length - 1];\n\n // if (!has(lastStatusInTime, 'tvc:atTime'))\n // Vue.set(lastStatusInTime, 'tvc:atTime', {});\n if (!has(lastStatusInTime, 'tvc:atTime')) {\n lastStatusInTime['tvc:atTime'] = {};\n }\n if (!has(lastStatusInTime['tvc:atTime'], 'timeinterval:hasIntervalEndDate')) {\n // If the last time entry doesn't already have an interval end date, set it to now.\n lastStatusInTime['tvc:atTime']['timeinterval:hasIntervalEndDate'] = currentTime;\n }\n }\n\n // Create new entry.\n this.phyloref['pso:holdsStatusInTime'].push({\n '@type': 'http://purl.org/spar/pso/StatusInTime',\n 'pso:withStatus': { '@id': status },\n 'tvc:atTime': {\n 'timeinterval:hasIntervalStartDate': currentTime,\n },\n });\n }\n\n /**\n * Return a list of all the unique nomenclatural codes used by this phyloreference.\n * The default nomenclatural code used in creating the PhylorefWrapper will be used\n * for any taxonomic units that don't have any nomenclatural code set. If any\n * specifiers are not taxon concepts, they will be represented in the returned\n * list as owlterms.UNKNOWN_CODE.\n */\n get uniqNomenCodes() {\n return uniq(this.specifiers.map((specifier) => {\n const taxonConcept = new TaxonomicUnitWrapper(\n specifier,\n this.phyxDefaultNomenCode\n ).taxonConcept;\n if (!taxonConcept) return owlterms.UNKNOWN_CODE;\n\n const nomenCode = new TaxonConceptWrapper(\n taxonConcept,\n this.phyxDefaultNomenCode\n ).nomenCode;\n if (!nomenCode) return owlterms.UNKNOWN_CODE;\n\n return nomenCode;\n }));\n }\n\n /**\n * Returns a summarized nomenclatural code for this phyloref. If all of the\n * specifiers have either the same nomenclatural code or `undefined`,\n * this getter will return that nomenclatural code. Otherwise, this method\n * will return owlterms.UNKNOWN_CODE.\n */\n get defaultNomenCode() {\n // Check to see if we have a single nomenclatural code to use.\n if (this.uniqNomenCodes.length === 1) return this.uniqNomenCodes[0];\n\n // If one or more of our specifiers have no nomenclatural code (e.g. if\n // they are specimens), they will show up as owlterms.UNKNOWN_CODE.\n // If we have a single nomenclatural code *apart* from all the\n // owlterms.UNKNOWN_CODEs, then that is still usable as a default\n // nomenclatural code for this phyloreference.\n const uniqNomenCodesNoUnknowns = this.uniqNomenCodes\n .filter(code => code !== owlterms.UNKNOWN_CODE);\n if (uniqNomenCodesNoUnknowns.length === 1) return uniqNomenCodesNoUnknowns[0];\n\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Create a component class for the set of internal and external specifiers provided.\n * We turn this into a label (in the form `A & B ~ C V D`), which we use to ensure that\n * we don't create more than one class for a particular set of internal and external\n * specifiers.\n * - jsonld: The JSON-LD representation of the Phyloreference this is an component class\n * for. We mainly use this to retrieve its '@id'.\n * - internalSpecifiers: The set of internal specifiers for this component class.\n * - externalSpecifiers: The set of external specifiers for this component class.\n * - equivClass: The equivalent class expression for this component class as a function\n * that returns the expression as a string.\n * - reusePrevious (default: true): If true, we reuse previous expressions with the\n * same set of included and excluded specifiers. If false, we always generate a new\n * component class for this expression.\n * - parentClass: If not undefined, provides a JSON-LD definition of the class to set as the\n * parent class of this component class. We only use the ['@id'].\n */\n createComponentClass(\n jsonld,\n internalSpecifiers,\n externalSpecifiers,\n equivClass,\n reusePrevious = true,\n parentClass = undefined\n ) {\n if (internalSpecifiers.length === 0) throw new Error('Cannot create component class without any internal specifiers');\n if (internalSpecifiers.length === 1 && externalSpecifiers.length === 0) throw new Error('Cannot create component class with a single internal specifiers and no external specifiers');\n\n /* Generate a label that represents this component class. */\n\n // By default, taxonomic unit labels don't include the nomenclatural code.\n // However, we should include that here in order to distinguish between\n // taxonomic names in different taxonomic codes. This method generates that\n // name for a specifier.\n const outerThis = this;\n function generateSpecifierName(specifier) {\n const wrapped = new TaxonomicUnitWrapper(specifier, outerThis.defaultNomenCode);\n if (!wrapped) return '(error)';\n if (wrapped.taxonConcept) {\n const nomenCodeDetails = new TaxonConceptWrapper(wrapped.taxonConcept).nomenCodeDetails;\n if (nomenCodeDetails) return `${wrapped.label} (${nomenCodeDetails.shortName})`;\n }\n return wrapped.label;\n }\n\n // Start with the internal specifiers, concatenated with '&'.\n const internalSpecifierLabel = internalSpecifiers\n .map(generateSpecifierName)\n .sort()\n .join(' & ');\n let componentClassLabel = `(${internalSpecifierLabel}`;\n\n if (externalSpecifiers.length === 0) {\n componentClassLabel += ')';\n } else {\n // Add the external specifiers, concatenated with 'V'.\n const externalSpecifierLabel = externalSpecifiers\n .map(generateSpecifierName)\n .sort()\n .join(' V ');\n componentClassLabel += ` ~ ${externalSpecifierLabel})`;\n }\n\n // process.stderr.write(`component class label: ${componentClassLabel}\\n`);\n\n // TODO We need to replace this with an actual object-based comparison,\n // rather than trusting the labels to tell us everything.\n if (reusePrevious && has(this.componentClassesByLabel, componentClassLabel)) {\n // If we see the same label again, return the previously defined component class.\n return { '@id': this.componentClassesByLabel[componentClassLabel]['@id'] };\n }\n\n // Create a new component class for this set of internal and external specifiers.\n this.componentClassCount += 1;\n const componentClass = {};\n componentClass['@id'] = `${jsonld['@id']}_component${this.componentClassCount}`;\n // process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);\n\n componentClass['@type'] = 'owl:Class';\n componentClass.label = componentClassLabel;\n componentClass.equivalentClass = equivClass;\n if (externalSpecifiers.length > 0) componentClass.subClassOf = ['phyloref:PhyloreferenceUsingMaximumClade'];\n else componentClass.subClassOf = ['phyloref:PhyloreferenceUsingMinimumClade'];\n\n if (parentClass) {\n componentClass.subClassOf.push({\n '@id': parentClass['@id'],\n });\n }\n\n // Save it in the cache for later usage.\n this.componentClassesByLabel[componentClassLabel] = componentClass;\n\n // The first time we create a componentClass, we include it into the logical\n // expression directly. On subsequent calls, we'll only return the `@id`\n // (see above).\n return componentClass;\n }\n\n getIncludesRestrictionForTU(tu) {\n return {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:includes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(tu, this.defaultNomenCode).asOWLEquivClass,\n };\n }\n\n /**\n * Return an OWL restriction for the most recent common ancestor (MRCA)\n * of two taxonomic units.\n */\n getMRCARestrictionOfTwoTUs(tu1, tu2) {\n return {\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000149', // cdao:has_Child\n someValuesFrom: {\n '@type': 'owl:Class',\n intersectionOf: [\n {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(tu1, this.defaultNomenCode).asOWLEquivClass,\n },\n this.getIncludesRestrictionForTU(tu2),\n ],\n },\n };\n }\n\n /*\n * Create an OWL restriction for a phyloreference made up entirely of internal\n * specifiers.\n * - jsonld: the JSON-LD representation of this phyloreference in model 1.0.\n * We mainly use this to access the '@id' and internal and external specifiers.\n * - remainingInternals: all internal specifiers that have not yet been selected.\n * - selected: internal specifiers have been seen selected. This should initially\n * be [], and will be filled in when this method calls itself recursively.\n *\n * This method works like this:\n * 1. We have several special cases: we fail if 0 or 1 specifiers are\n * provided, and we have a special representation for 2 specifiers.\n * 2. Create an expression for the currently selected specifiers. This expression\n * is in the form:\n * has_Child some (\n * excludes_lineage_to some [remaining specifiers]\n * and [selected specifiers]\n * )\n * We generate the expressions for remaining specifiers and selected specifiers by calling\n * this method recursively.\n * 3. Finally, we select another internal from the remainingInternals and generate an\n * expression for that selection by calling this method recursively. Note that we\n * only process cases where there are more remainingInternals than selected\n * internals -- when there are fewer, we'll just end up with the inverses of the\n * previous comparisons, which we'll already have covered.\n */\n createClassExpressionsForInternals(jsonld, remainingInternals, selected) {\n // process.stderr.write(`@id [${jsonld['@id']}] Remaining internals:\n // ${remainingInternals.length}, selected: ${selected.length}\\n`);\n\n // Quick special case: if we have two 'remainingInternals' and zero selecteds,\n // we can just return the MRCA for two internal specifiers.\n if (selected.length === 0) {\n if (remainingInternals.length === 2) {\n return [\n this.getMRCARestrictionOfTwoTUs(remainingInternals[0], remainingInternals[1]),\n ];\n } if (remainingInternals.length === 1) {\n throw new Error('Cannot determine class expression for a single specifier');\n } else if (remainingInternals.length === 0) {\n throw new Error('Cannot determine class expression for zero specifiers');\n }\n }\n\n // Step 1. If we've already selected something, create an expression for it.\n const classExprs = [];\n if (selected.length > 0) {\n let remainingInternalsExpr = [];\n if (remainingInternals.length === 1) {\n remainingInternalsExpr = this.getIncludesRestrictionForTU(remainingInternals[0]);\n } else if (remainingInternals.length === 2) {\n remainingInternalsExpr = this.getMRCARestrictionOfTwoTUs(\n remainingInternals[0],\n remainingInternals[1]\n );\n } else {\n remainingInternalsExpr = this.createComponentClass(\n jsonld,\n remainingInternals,\n [],\n this.createClassExpressionsForInternals(jsonld, remainingInternals, [])\n );\n }\n\n let selectedExpr = [];\n if (selected.length === 1) {\n selectedExpr = this.getIncludesRestrictionForTU(selected[0]);\n } else if (selected.length === 2) {\n selectedExpr = this.getMRCARestrictionOfTwoTUs(selected[0], selected[1]);\n } else {\n selectedExpr = this.createComponentClass(\n jsonld,\n selected,\n [],\n this.createClassExpressionsForInternals(jsonld, selected, [])\n );\n }\n\n classExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000149', // cdao:has_Child\n someValuesFrom: {\n '@type': 'owl:Class',\n intersectionOf: [{\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_lineage_to',\n someValuesFrom: remainingInternalsExpr,\n }, selectedExpr],\n },\n });\n }\n\n // Step 2. Now select everything from remaining once, and start recursing through\n // every possibility.\n // Note that we only process cases where there are more remainingInternals than\n // selected internals -- when there are fewer, we'll just end up with the inverses\n // of the previous comparisons, which we'll already have covered.\n if (remainingInternals.length > 1 && selected.length <= remainingInternals.length) {\n remainingInternals.map(newlySelected => this.createClassExpressionsForInternals(\n jsonld,\n // The new remaining is the old remaining minus the selected TU.\n remainingInternals.filter(i => i !== newlySelected),\n // The new selected is the old selected plus the selected TU.\n selected.concat([newlySelected])\n ))\n .reduce((acc, val) => acc.concat(val), [])\n .forEach(expr => classExprs.push(expr));\n }\n\n return classExprs;\n }\n\n /*\n * Phyloref.asJSONLD(fallbackIRI)\n *\n * Export this phylogeny as JSON-LD.\n *\n * Arguments:\n * - fallbackIRI: The base IRI to use for this phyloref if it does not have\n * an '@id'.\n */\n asJSONLD(fallbackIRI) {\n // Keep all currently extant data.\n const phylorefAsJSONLD = cloneDeep(this.phyloref);\n\n // Set the @id and @type. If we don't already have an '@id', use the\n // fallbackIRI.\n if (!has(phylorefAsJSONLD, '@id')) phylorefAsJSONLD['@id'] = fallbackIRI;\n phylorefAsJSONLD['@type'] = 'owl:Class';\n\n // If we don't have a bibliographicCitation but we do have a definition source,\n // then generate a bibliographicCitation for the source.\n if (has(phylorefAsJSONLD, 'definitionSource')) {\n const definitionSource = phylorefAsJSONLD.definitionSource;\n if (!has(definitionSource, 'bibliographicCitation')) {\n definitionSource.bibliographicCitation = new CitationWrapper(definitionSource).toString();\n }\n }\n\n // Construct a class expression for this phyloreference.\n const internalSpecifiers = phylorefAsJSONLD.internalSpecifiers || [];\n const externalSpecifiers = phylorefAsJSONLD.externalSpecifiers || [];\n\n // If it is an apomorphy-based class expression, we should generate a\n // logical expression that describes the apomorphy.\n const phylorefType = phylorefAsJSONLD.phylorefType;\n if (\n (phylorefType && phylorefType === 'phyloref:PhyloreferenceUsingApomorphy')\n || (has(phylorefAsJSONLD, 'apomorphy'))\n ) {\n // This is an apomorphy-based definition!\n phylorefAsJSONLD.subClassOf = [\n 'phyloref:Phyloreference',\n 'phyloref:PhyloreferenceUsingApomorphy',\n ];\n\n // Someday, we will probably want to turn this apomorphy into a\n // logical expression so that it can be computed alongside other\n // OWL ontologies. This is outside our scope for the moment, so\n // we will simply pass on the phyloreference as-is.\n\n return phylorefAsJSONLD;\n }\n\n // We might need to make component classes.\n // So we reset our component class counts and records.\n this.componentClassCount = 0;\n this.componentClassesByLabel = {};\n\n // The type of this phyloreference.\n let calculatedPhylorefType;\n\n // The list of logical expressions generated for this phyloref.\n let logicalExpressions = [];\n\n if (internalSpecifiers.length === 0) {\n // We can't handle phyloreferences without at least one internal specifier.\n calculatedPhylorefType = 'phyloref:MalformedPhyloreference';\n phylorefAsJSONLD.malformedPhyloreference = 'No internal specifiers provided';\n } else if (externalSpecifiers.length > 0) {\n calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMaximumClade';\n\n // If the phyloreference has at least one external specifier, we\n // can provide a simplified expression for the internal specifier,\n // in the form:\n // phyloref:includes_TU some [internal1] and\n // phyloref:includes_TU some [internal2] and ...\n // phyloref:excludes_TU some [exclusion1] and\n // has_Ancestor some (phyloref:excludesTU some [exclusion2]) ...\n //\n // Since we don't know which of the external specifiers will actually\n // be the one that will be used, we need to generate logical expressions\n // for every possibility.\n\n logicalExpressions = externalSpecifiers.map((selectedExternal) => {\n // Add the internal specifiers.\n const intersectionExprs = internalSpecifiers.map(\n sp => this.getIncludesRestrictionForTU(sp)\n );\n\n // Add the selected external specifier.\n intersectionExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(\n selectedExternal,\n this.defaultNomenCode\n ).asOWLEquivClass,\n });\n\n // Collect all of the externals that are not selected.\n const remainingExternals = externalSpecifiers.filter(ex => ex !== selectedExternal);\n\n // Add the remaining externals, which we assume will resolve outside of\n // this clade.\n remainingExternals.forEach((externalTU) => {\n intersectionExprs.push({\n '@type': 'owl:Restriction',\n onProperty: 'obo:CDAO_0000144', // has_Ancestor\n someValuesFrom: {\n '@type': 'owl:Restriction',\n onProperty: 'phyloref:excludes_TU',\n someValuesFrom: new TaxonomicUnitWrapper(\n externalTU,\n this.defaultNomenCode\n ).asOWLEquivClass,\n },\n });\n });\n\n return {\n '@type': 'owl:Class',\n intersectionOf: intersectionExprs,\n };\n });\n } else {\n calculatedPhylorefType = 'phyloref:PhyloreferenceUsingMinimumClade';\n\n // We only have internal specifiers. We therefore need to use the algorithm in\n // this.createClassExpressionsForInternals() to create this expression.\n logicalExpressions = this.createClassExpressionsForInternals(\n phylorefAsJSONLD, internalSpecifiers, []\n );\n }\n\n // If we have a single logical expression, we set that as an equivalentClass\n // expression. If we have more than one, we produce multiple component classes\n // to represent it.\n if (logicalExpressions.length === 0) {\n // This is fine, as long as there is an explanation in\n // phyloref.malformedPhyloreference explaining why no logical expressions\n // could be generated. Otherwise, throw an error.\n if (!has(phylorefAsJSONLD, 'malformedPhyloreference')) {\n throw new Error(\n `Phyloref ${this.label} was generated by Phyx.js with neither logical expressions nor an explanation for the lack of logical expressions. `\n + 'This indicates an error in the Phyx.js library. Please report this bug at https://github.com/phyloref/phyx.js/issues.'\n );\n }\n } else if (logicalExpressions.length === 1) {\n // If we have a single logical expression, then that is what this phyloref\n // is equivalent to.\n phylorefAsJSONLD.equivalentClass = logicalExpressions[0];\n } else {\n // If we have multiple logical expressions, the phyloreference can be\n // represented by any of them. We model this by creating subclasses of\n // the phyloreference for each logical expression -- that way, it's clear\n // that these expressions aren't equivalent to each other (which is what\n // caused https://github.com/phyloref/phyx.js/issues/57), but nodes\n // resolved by any of those expressions will also be included in the\n // phyloreference itself.\n //\n // Note that there are two differences from the way in which we usually call\n // this.createComponentClass():\n // 1. Usually, createComponentClass() reuses logical expressions with the\n // same sets of internal and external specifiers. That won't work here,\n // since *all* these logical expressions have the same specifiers. So,\n // we turn off caching.\n // 2. We need to set each of these component classes to be a subclass of\n // this phyloreference so that it can include instances from each of the\n // logical expressions.\n phylorefAsJSONLD.subClasses = logicalExpressions.map(classExpr => this.createComponentClass(\n phylorefAsJSONLD,\n internalSpecifiers,\n externalSpecifiers,\n classExpr,\n // False in order to turn off caching by internal and external specifiers.\n false,\n // Make the new component class a subclass of this phyloreference.\n phylorefAsJSONLD\n ));\n }\n\n // Every phyloreference is a subclass of phyloref:Phyloreference.\n if (!phylorefAsJSONLD.subClassOf) phylorefAsJSONLD.subClassOf = [];\n if (!Array.isArray(phylorefAsJSONLD.subClassOf)) {\n phylorefAsJSONLD.subClassOf = [phylorefAsJSONLD.subClassOf];\n }\n phylorefAsJSONLD.subClassOf.push('phyloref:Phyloreference');\n\n // If the this Phyloref has a phylorefType that differs from the calculated\n // phyloref type, throw an error.\n if (has(phylorefAsJSONLD, 'phylorefType') && phylorefAsJSONLD.phylorefType !== calculatedPhylorefType) {\n throw new Error(\n `Phyloref ${this.label} has phylorefType set to '${phylorefAsJSONLD.phylorefType}', but it appears to be a '${calculatedPhylorefType}'.`\n );\n }\n phylorefAsJSONLD.subClassOf.push(calculatedPhylorefType);\n\n return phylorefAsJSONLD;\n }\n}\n\nmodule.exports = {\n PhylorefWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/PhylorefWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/PhylorefWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -2231,7 +2231,7 @@ "name": "src/wrappers/PhyxWrapper.js", "content": "const fs = require('fs');\nconst path = require('path');\n\n/** Helper methods from lodash. */\nconst { has, cloneDeep, uniq } = require('lodash');\n\n/** For NQuads export. */\nconst JSONLD = require('jsonld');\n\nconst owlterms = require('../utils/owlterms');\n\nconst { PhylorefWrapper } = require('./PhylorefWrapper');\nconst { PhylogenyWrapper } = require('./PhylogenyWrapper');\nconst { CitationWrapper } = require('./CitationWrapper');\n\n/**\n * The PhyxWrapper wraps an entire Phyx document.\n */\n\nclass PhyxWrapper {\n /**\n * Wraps an entire PHYX document.\n * @param {Object} phyx - The Phyx structure to wrap.\n * @param {function(newick: string): {name: string, children: Object[]}}\n * [newickParser=PhylogenyWrapper.getParsedNewick] - A method\n * that accepts a Newick string and returns a list of nodes. Each node should have a\n * 'children' key with its children and optionally a 'name' key with its label. This\n * code previously depended on phylotree.js, whose newick_parser() function works exactly\n * like this. This option allows you to drop in Phylotree's newick_parser() or -- if you\n * prefer -- any other option.\n */\n constructor(phyx, newickParser = PhylogenyWrapper.getParsedNewick) {\n //\n this.phyx = phyx;\n this.newickParser = newickParser;\n }\n\n // Determine a 'default nomenclatural code' for this Phyx file. There are\n // two ways to do this:\n // 1. If the Phyx file has a 'defaultNomenclaturalCodeIRI' property, we use that.\n // 2. Otherwise, we check to see if every phyloref in this file has the same\n // nomenclatural code. If so, we can use that code. If not, i.e. if any of\n // the phylorefs are missing a nomenclatural code or include a specifier,\n // we default to owlterms.UNKNOWN_CODE.\n get defaultNomenCode() {\n if (has(this.phyx, 'defaultNomenclaturalCodeIRI')) return this.phyx.defaultNomenclaturalCodeIRI;\n const nomenCodes = (this.phyx.phylorefs || [])\n .map(phyloref => new PhylorefWrapper(phyloref).defaultNomenCode);\n const uniqNomenCodes = uniq(nomenCodes);\n if (uniqNomenCodes.length === 1) return uniqNomenCodes[0];\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Return a provided Phyx document as a normalized JSON document. We ignore most keys -- including\n * keys we don't know -- but any key that can be wrapped by one of the other Wrappers in this\n * package will be wrapped and normalized before being returned.\n *\n * Normalization is mostly needed for TaxonomicUnitWrappers and its subclasses\n * (TaxonConceptWrapper, TaxonNameWrapper), since these can be represented in several essentially\n * identical ways. But if we implement it at every level, we can implement comparison code in\n * Klados easily.\n *\n * Two Phyx documents should -- upon being normalized -- be comparable with each other with\n * lodash.deepEqual().\n */\n static normalize(phyxDocument) {\n const normalizedDocument = cloneDeep(phyxDocument);\n\n normalizedDocument.phylorefs = (phyxDocument.phylorefs || []).map(PhylorefWrapper.normalize);\n normalizedDocument.phylogenies = (phyxDocument.phylogenies || [])\n .map(PhylogenyWrapper.normalize);\n if ('source' in phyxDocument) {\n normalizedDocument.source = CitationWrapper.normalize(phyxDocument.source);\n }\n\n return normalizedDocument;\n }\n\n /**\n * Generate an executable ontology from this Phyx document. The document is mostly in JSON-LD\n * already, except for three important things:\n * 1. We have to convert all phylogenies into a series of statements relating to the nodes\n * inside these phylogenies.\n * 2. We have to convert phylogenies into OWL restrictions.\n * 3. Insert all matches between taxonomic units in this file.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @return {Object} This Phyx document as an OWL ontology as a JSON-LD object.\n */\n asJSONLD(baseIRI = '') {\n const jsonld = cloneDeep(this.phyx);\n\n // Some helper methods for generating base IRIs for phylorefs and phylogenies.\n function getBaseIRIForPhyloref(index) {\n if (baseIRI) return `${baseIRI}phyloref${index}`;\n return `#phyloref${index}`;\n }\n\n function getBaseIRIForPhylogeny(index) {\n if (baseIRI) return `${baseIRI}phylogeny${index}`;\n return `#phylogeny${index}`;\n }\n\n // Given a relative ID (e.g. '#phylo1') make it absolute (`${baseIRI}phylo1`).\n function makeIDAbsolute(phylogenyId) {\n if (baseIRI && phylogenyId.startsWith('#')) return `${baseIRI}${phylogenyId.substring(1)}`; // Remove the initial '#'.\n return phylogenyId;\n }\n\n // Given an absolute ID (`${baseIRI}phylo1`) make it relative (e.g. '#phylo1').\n function makeIDRelative(phylogenyId) {\n if (phylogenyId.startsWith(baseIRI)) return `#${phylogenyId.substring(baseIRI.length)}`;\n return phylogenyId;\n }\n\n if (has(jsonld, 'phylorefs')) {\n // We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").\n // If the baseIRI is set to '', that's fine. But if not, we'll add it\n // to the relative IRI to make it absolute. This seems to avoid problems\n // with some JSON-LD parsers.\n if (baseIRI) {\n jsonld.phylorefs = jsonld.phylorefs.map((phyloref) => {\n if ((phyloref['@id'] || '').startsWith('#')) {\n const modifiedPhyloref = cloneDeep(phyloref);\n modifiedPhyloref['@id'] = makeIDAbsolute(phyloref['@id']);\n return modifiedPhyloref;\n }\n return phyloref;\n });\n }\n\n // Convert phyloreferences into an OWL class restriction\n jsonld.phylorefs = jsonld.phylorefs.map(\n (phyloref, countPhyloref) => new PhylorefWrapper(phyloref, this.defaultNomenCode)\n .asJSONLD(getBaseIRIForPhyloref(countPhyloref))\n );\n }\n\n if (has(jsonld, 'phylogenies')) {\n // We might have phyloref IDs set to relative IRIs (e.g. \"#phyloref0\").\n // If the baseIRI is set to '', that's fine. But if not, we'll add it\n // to the relative IRI to make it absolute. This seems to avoid problems\n // with some JSON-LD parsers.\n if (baseIRI) {\n jsonld.phylogenies = jsonld.phylogenies.map((phylogeny) => {\n if ((phylogeny['@id'] || '').startsWith('#')) {\n const modifiedPhylogeny = cloneDeep(phylogeny);\n modifiedPhylogeny['@id'] = makeIDAbsolute(phylogeny['@id']);\n return modifiedPhylogeny;\n }\n return phylogeny;\n });\n }\n\n // Add descriptions for individual nodes in each phylogeny.\n jsonld.phylogenies = jsonld.phylogenies.map(\n (phylogeny, countPhylogeny) => new PhylogenyWrapper(phylogeny, this.defaultNomenCode)\n .asJSONLD(getBaseIRIForPhylogeny(countPhylogeny), this.newickParser)\n );\n\n // Go through all the nodes and add information on expected resolution.\n jsonld.phylogenies.forEach((phylogeny) => {\n const phylogenyId = phylogeny['@id'];\n (phylogeny.nodes || []).forEach((node) => {\n // We can't set expected resolution information on unlabeled nodes.\n if (!node.labels) return;\n\n jsonld.phylorefs.forEach((phyloref) => {\n const phylorefId = phyloref['@id'];\n\n // There are two ways in which we determine that a phyloreference\n // is expected to resolve to a node:\n // (1) If nodeLabel is set, then that must be one of the node's labels.\n // (2) If nodeLabel is not set, then one of the node's label should be\n // identical to the phyloreference's label.\n //\n // We set flagNodeExpectsPhyloref in all cases where we should note\n // that this node expects to resolve to this phyloreference.\n let flagNodeExpectsPhyloref = false;\n\n // console.log(`Testing expected resolution of '${phylorefId}' on `\n // + `'${phylogenyId}' (${makeIDRelative(phylogenyId)}).`);\n\n if (\n has(phyloref, 'expectedResolution')\n && (\n // The user might have used the absolute phylogeny ID here.\n has(phyloref.expectedResolution, phylogenyId)\n\n // Or they might have used a relative phylogeny ID.\n || has(phyloref.expectedResolution, makeIDRelative(phylogenyId))\n )\n ) {\n // Expected resolution information set! The node label mentioned in that\n // information must be identical to one of the labels of this phylogeny node.\n\n // Figure out which phylogenyId was matched here.\n const nodeLabel = has(phyloref.expectedResolution, phylogenyId)\n ? phyloref.expectedResolution[phylogenyId].nodeLabel\n : phyloref.expectedResolution[makeIDRelative(phylogenyId)].nodeLabel;\n\n if (nodeLabel && (node.labels || []).includes(nodeLabel)) {\n flagNodeExpectsPhyloref = true;\n }\n } else if ((node.labels || []).includes(phyloref.label)) {\n // No expected resolution information, so we just check whether\n // the phyloref label is one of the labels on this phylogeny node.\n flagNodeExpectsPhyloref = true;\n }\n\n if (flagNodeExpectsPhyloref) {\n // Modify this phylogeny node's type to include that it is a type\n // of:\n // obi:is_specified_output_of some (\n // obi:Prediction and obi:has_specified_output some #phyloref_id\n // )\n node[owlterms.RDF_TYPE].push({\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.OBI_IS_SPECIFIED_OUTPUT_OF,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n { '@id': owlterms.OBI_PREDICTION },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.OBI_HAS_SPECIFIED_INPUT,\n someValuesFrom: {\n '@id': phylorefId,\n },\n },\n ],\n },\n });\n }\n });\n });\n });\n }\n\n // Earlier, we used to generate a list of taxonomic matches here (stored in\n // jsonld.hasTaxonomicUnitMatches) that logically expressed how taxonomic\n // units in phyloref specifiers were related to taxonomic units in phylogeny\n // nodes. This is no longer necessary, since phyloref specifiers are now logical\n // expressions that directly evaluate to phylogeny nodes. However, if in the\n // future we decide that we need to perform more advanced TU matching, this\n // would be the place to implement that.\n\n // If there is a top-level source, generate a bibliographicCitation for it.\n if (has(jsonld, 'source')) {\n jsonld.source.bibliographicCitation = new CitationWrapper(jsonld.source).toString();\n }\n\n // Set up the top-level object '@type'. If one is present, we add our terms to that.\n if (!has(jsonld, '@type')) jsonld['@type'] = [];\n if (!Array.isArray(jsonld['@type'])) jsonld['@type'] = [jsonld['@type']];\n jsonld['@type'].push('owl:Ontology');\n\n // Set up the ontology imports. If one is present, we add our imports to that.\n if (!has(jsonld, 'owl:imports')) jsonld['owl:imports'] = [];\n if (!Array.isArray(jsonld['owl:imports'])) jsonld['owl:imports'] = [jsonld['owl:imports']];\n jsonld['owl:imports'].push('http://ontology.phyloref.org/2018-12-14/phyloref.owl');\n jsonld['owl:imports'].push('http://ontology.phyloref.org/2018-12-14/tcan.owl');\n\n // If the '@context' is missing, add it here.\n if (!has(jsonld, '@context')) {\n jsonld['@context'] = owlterms.PHYX_CONTEXT_JSON;\n }\n\n return jsonld;\n }\n\n /**\n * Generate an executable ontology from this Phyx document as N-Quads. Under the\n * hood, we generate an OWL/JSON-LD representation of this Phyx document, and then\n * convert it into N-Quads so that OWLAPI-supporting tools can directly consume it.\n *\n * @param {string} [baseIRI=\"\"] - The base IRI to use when generating this Phyx document.\n * This should include a trailing '#' or '/'. Use '' to indicate that relative IDs\n * should be generated in the produced ontology (e.g. '#phylogeny1'). Note that if a\n * baseIRI is provided, then relative IDs already in the Phyx file (identified by an\n * initial '#') will be turned into absolute IDs by removing the initial `#` and\n * prepending them with the baseIRI.\n * @param {string} [filePath=undefined] - The path of the Phyx file being converted.\n * Used only if the `@context` of the file is a relative path.\n * @return {Promise[string]} A Promise to return this Phyx document as a string that can\n * be written to an N-Quads file.\n */\n toRDF(baseIRI = '', filePath = undefined) {\n const owlJSONLD = this.asJSONLD(baseIRI);\n\n // For the purposes of testing, we are sometimes given a relative path to `@context`,\n // but the JSONLD package does not support this. Instead, we'll import the contents\n // of the relative path on the fly.\n if (filePath && has(owlJSONLD, '@context') && owlJSONLD['@context'].startsWith('.')) {\n owlJSONLD['@context'] = JSON.parse(fs.readFileSync(\n path.resolve(filePath, owlJSONLD['@context'])\n ));\n }\n\n return JSONLD.toRDF(owlJSONLD, { format: 'application/n-quads' });\n }\n}\n\nmodule.exports = {\n PhyxWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/PhyxWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/PhyxWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -2537,9 +2537,9 @@ "__docId__": 144, "kind": "file", "name": "src/wrappers/SpecimenWrapper.js", - "content": "const { has } = require('lodash');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst owlterms = require('../utils/owlterms');\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a dwc:occurrenceID with the occurrence identifier.\n * - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n */\nclass SpecimenWrapper {\n /** The '@type' of specimens in JSON-LD document. */\n static get TYPE_SPECIMEN() {\n return owlterms.DWC_OCCURRENCE;\n }\n\n /** Construct a wrapper around a specimen. */\n constructor(specimen) {\n this.specimen = specimen;\n }\n\n /**\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n */\n static normalize(specimen) {\n const wrapped = new SpecimenWrapper(specimen);\n const normalizedSpecimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n label: wrapped.label,\n 'dwc:basisOfRecord': wrapped.basisOfRecord,\n occurrenceID: wrapped.occurrenceID,\n catalogNumber: wrapped.catalogNumber,\n institutionCode: wrapped.institutionCode,\n collectionCode: wrapped.collectionCode,\n };\n if ('@id' in specimen) normalizedSpecimen['@id'] = specimen['@id'];\n return normalizedSpecimen;\n }\n\n /**\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n */\n static fromOccurrenceID(occurrenceID, basisOfRecord = 'PreservedSpecimen') {\n // Copy the occurrence ID so we can truncate it if necessary.\n let occurID = occurrenceID;\n if (occurID.startsWith('urn:catalog:')) occurID = occurID.substr(12);\n\n // Prepare the specimen.\n const specimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n 'dwc:basisOfRecord': basisOfRecord,\n occurrenceID: occurID,\n };\n\n // Look for certain prefixes that suggest that we've been passed a URN or\n // URL instead. If so, don't do any further processing!\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n if (URL_URN_PREFIXES.filter(prefix => occurID.toLowerCase().startsWith(prefix)).length > 0) {\n return specimen;\n }\n\n // Parsing an occurrence ID takes some time, so we should memoize it.\n if (PhyxCacheManager.has('SpecimenWrapper.occurrenceIDCache', occurID)) {\n return PhyxCacheManager.get('SpecimenWrapper.occurrenceIDCache', occurID);\n }\n\n // Split the occurrence ID into components, and store them in the appropriate fields.\n const comps = occurID.split(/:/);\n if (comps.length === 1) {\n // specimen.institutionCode = undefined;\n // specimen.collectionCode = undefined;\n [specimen.catalogNumber] = comps;\n } else if (comps.length === 2) {\n [specimen.institutionCode, specimen.catalogNumber] = comps;\n } else if (comps.length >= 3) {\n let catalogNumValues = []; // Store all split catalog number values.\n [specimen.institutionCode, specimen.collectionCode, ...catalogNumValues] = comps;\n specimen.catalogNumber = catalogNumValues.join(':');\n }\n\n PhyxCacheManager.put('SpecimenWrapper.occurrenceIDCache', occurID, specimen);\n return specimen;\n }\n\n /**\n * Get the catalogNumber if present.\n */\n get catalogNumber() {\n // Get the catalog number from the specimen object if present.\n if (has(this.specimen, 'catalogNumber')) return this.specimen.catalogNumber;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract a\n // catalogNumber from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'catalogNumber')) return specimen.catalogNumber;\n }\n return undefined;\n }\n\n /**\n * Get the institutionCode if present.\n */\n get institutionCode() {\n // Get the institution code from the specimen object if present.\n if (has(this.specimen, 'institutionCode')) return this.specimen.institutionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'institutionCode')) return specimen.institutionCode;\n }\n return undefined;\n }\n\n /**\n * Get the collectionCode if present.\n */\n get collectionCode() {\n // Get the collection code from the specimen object if present.\n if (has(this.specimen, 'collectionCode')) return this.specimen.collectionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'collectionCode')) return specimen.collectionCode;\n }\n return undefined;\n }\n\n /**\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n */\n get occurrenceID() {\n // Return the occurrenceID if it exists.\n if (has(this.specimen, 'occurrenceID') && this.specimen.occurrenceID.trim() !== '') {\n return this.specimen.occurrenceID.trim();\n }\n\n // Otherwise, we could try to construct the occurrenceID from its components.\n if (has(this.specimen, 'catalogNumber')) {\n if (has(this.specimen, 'institutionCode')) {\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog:${this.specimen.institutionCode.trim()}:${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:${this.specimen.institutionCode.trim()}::${this.specimen.catalogNumber.trim()}`;\n }\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog::${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:::${this.specimen.catalogNumber.trim()}`;\n }\n\n // None of our specimen identifier schemes worked.\n return undefined;\n }\n\n /**\n * Return the basis of record, if one is present.\n */\n get basisOfRecord() {\n if (has(this.specimen, 'dwc:basisOfRecord')) return this.specimen['dwc:basisOfRecord'];\n return undefined;\n }\n\n /**\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n */\n set basisOfRecord(bor) {\n this.specimen['dwc:basisOfRecord'] = bor;\n }\n\n /** Return this specimen as a taxon concept if it contains taxon name information. */\n get taxonConcept() {\n if (has(this.specimen, 'hasName')) return this.specimen;\n if (has(this.specimen, 'nameString')) return this.specimen;\n return undefined;\n }\n\n /** Return a label for this specimen. */\n get label() {\n // We can't return anything without an occurrenceID.\n if (!this.occurrenceID) return undefined;\n\n // Note that specimens may be identified to a taxon concept. If so, we should\n // include that information in the label.\n if (this.taxonConcept) {\n return `Specimen ${this.occurrenceID} identified as ${new TaxonConceptWrapper(this.taxonConcept).label}`;\n }\n\n // Return a label for this specimen.\n return `Specimen ${this.occurrenceID}`;\n }\n\n /** Return this specimen as an equivalentClass expression. */\n get asOWLEquivClass() {\n // We can't do anything without an occurrence ID!\n if (!this.occurrenceID) return undefined;\n\n // TODO: Should we also match by this.taxonConcept is one is available?\n // Technically no, but it might be useful. Hmm.\n\n // Return as an OWL restriction.\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n hasValue: this.occurrenceID,\n };\n }\n}\n\nmodule.exports = {\n SpecimenWrapper,\n};\n", + "content": "const { has } = require('lodash');\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\nconst owlterms = require('../utils/owlterms');\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * The SpecimenWrapper wraps specimen taxonomic units. These can be identified\n * with a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\n * https://dwc.tdwg.org/terms/#occurrence).\n *\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n * - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n * - Should have a occurrenceID with the occurrence identifier.\n * - Should have a basisOfRecord to indicate what sort of occurrence this is.\n *\n * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\n * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n * (see https://github.com/tdwg/ontology). Therefore, it instead improvises a\n * representation based on dwc:Occurrence.\n */\nclass SpecimenWrapper {\n /** The '@type' of specimens in JSON-LD document. */\n static get TYPE_SPECIMEN() {\n return owlterms.DWC_OCCURRENCE;\n }\n\n /** Construct a wrapper around a specimen. */\n constructor(specimen) {\n this.specimen = specimen;\n }\n\n /**\n * Normalize the specified specimen.\n * @param specimen A specimen to be normalized.\n */\n static normalize(specimen) {\n const wrapped = new SpecimenWrapper(specimen);\n const normalizedSpecimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n label: wrapped.label,\n basisOfRecord: wrapped.basisOfRecord,\n occurrenceID: wrapped.occurrenceID,\n catalogNumber: wrapped.catalogNumber,\n institutionCode: wrapped.institutionCode,\n collectionCode: wrapped.collectionCode,\n };\n if ('@id' in specimen) normalizedSpecimen['@id'] = specimen['@id'];\n return normalizedSpecimen;\n }\n\n /**\n * Parse the provided occurrence ID. The two expected formats are:\n * - 'urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]'\n * (in which case, we ignore the first two \"components\" here)\n * - '[institutionCode]:[collectionCode]:[catalogNumber]'\n */\n static fromOccurrenceID(occurrenceID, basisOfRecord = 'PreservedSpecimen') {\n // Copy the occurrence ID so we can truncate it if necessary.\n let occurID = occurrenceID;\n if (occurID.startsWith('urn:catalog:')) occurID = occurID.substring(12);\n\n // Prepare the specimen.\n const specimen = {\n '@type': SpecimenWrapper.TYPE_SPECIMEN,\n basisOfRecord,\n occurrenceID: occurID,\n };\n\n // Look for certain prefixes that suggest that we've been passed a URN or\n // URL instead. If so, don't do any further processing!\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n if (URL_URN_PREFIXES.filter(prefix => occurID.toLowerCase().startsWith(prefix)).length > 0) {\n return specimen;\n }\n\n // Parsing an occurrence ID takes some time, so we should memoize it.\n if (PhyxCacheManager.has('SpecimenWrapper.occurrenceIDCache', occurID)) {\n return PhyxCacheManager.get('SpecimenWrapper.occurrenceIDCache', occurID);\n }\n\n // Split the occurrence ID into components, and store them in the appropriate fields.\n const comps = occurID.split(/:/);\n if (comps.length === 1) {\n // specimen.institutionCode = undefined;\n // specimen.collectionCode = undefined;\n [specimen.catalogNumber] = comps;\n } else if (comps.length === 2) {\n [specimen.institutionCode, specimen.catalogNumber] = comps;\n } else if (comps.length >= 3) {\n let catalogNumValues = []; // Store all split catalog number values.\n [specimen.institutionCode, specimen.collectionCode, ...catalogNumValues] = comps;\n specimen.catalogNumber = catalogNumValues.join(':');\n }\n\n PhyxCacheManager.put('SpecimenWrapper.occurrenceIDCache', occurID, specimen);\n return specimen;\n }\n\n /**\n * Get the catalogNumber if present.\n */\n get catalogNumber() {\n // Get the catalog number from the specimen object if present.\n if (has(this.specimen, 'catalogNumber')) return this.specimen.catalogNumber;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract a\n // catalogNumber from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'catalogNumber')) return specimen.catalogNumber;\n }\n return undefined;\n }\n\n /**\n * Get the institutionCode if present.\n */\n get institutionCode() {\n // Get the institution code from the specimen object if present.\n if (has(this.specimen, 'institutionCode')) return this.specimen.institutionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'institutionCode')) return specimen.institutionCode;\n }\n return undefined;\n }\n\n /**\n * Get the collectionCode if present.\n */\n get collectionCode() {\n // Get the collection code from the specimen object if present.\n if (has(this.specimen, 'collectionCode')) return this.specimen.collectionCode;\n\n // Otherwise, try to parse the occurrenceID and see if we can extract an\n // occurrenceID from there.\n if (has(this.specimen, 'occurrenceID')) {\n const specimen = SpecimenWrapper.fromOccurrenceID(this.specimen.occurrenceID);\n if (has(specimen, 'collectionCode')) return specimen.collectionCode;\n }\n return undefined;\n }\n\n /**\n * Return the occurrence ID of this specimen, if we have one. Otherwise, we\n * attempt to construct one in the form:\n * \"urn:catalog:\" + institutionCode (if present) + ':' +\n * collectionCode (if present) + ':' + catalogNumber (if present)\n */\n get occurrenceID() {\n // Return the occurrenceID if it exists.\n if (has(this.specimen, 'occurrenceID')) {\n return this.specimen.occurrenceID.trim();\n }\n\n // Otherwise, we could try to construct the occurrenceID from its components.\n if (has(this.specimen, 'catalogNumber')) {\n if (has(this.specimen, 'institutionCode')) {\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog:${this.specimen.institutionCode.trim()}:${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:${this.specimen.institutionCode.trim()}::${this.specimen.catalogNumber.trim()}`;\n }\n if (has(this.specimen, 'collectionCode')) {\n return `urn:catalog::${this.specimen.collectionCode.trim()}:${this.specimen.catalogNumber.trim()}`;\n }\n return `urn:catalog:::${this.specimen.catalogNumber.trim()}`;\n }\n\n // None of our specimen identifier schemes worked.\n return undefined;\n }\n\n /**\n * Return the basis of record, if one is present.\n */\n get basisOfRecord() {\n if (has(this.specimen, 'basisOfRecord')) return this.specimen.basisOfRecord;\n return undefined;\n }\n\n /**\n * Set the basis of record. See http://rs.tdwg.org/dwc/terms/basisOfRecord for\n * recommended values.\n */\n set basisOfRecord(bor) {\n this.specimen.basisOfRecord = bor;\n }\n\n /** Return this specimen as a taxon concept if it contains taxon name information. */\n get taxonConcept() {\n if (has(this.specimen, 'hasName')) return this.specimen;\n if (has(this.specimen, 'nameString')) return this.specimen;\n return undefined;\n }\n\n /** Return a label for this specimen. */\n get label() {\n // We can't return anything without an occurrenceID.\n if (!this.occurrenceID) return undefined;\n\n // Note that specimens may be identified to a taxon concept. If so, we should\n // include that information in the label.\n if (this.taxonConcept) {\n return `Specimen ${this.occurrenceID} identified as ${new TaxonConceptWrapper(this.taxonConcept).label}`;\n }\n\n // Return a label for this specimen.\n return `Specimen ${this.occurrenceID}`;\n }\n\n /** Return this specimen as an equivalentClass expression. */\n get asOWLEquivClass() {\n // We can't do anything without an occurrence ID!\n if (!this.occurrenceID) return undefined;\n\n // TODO: Should we also match by this.taxonConcept is one is available?\n // Technically no, but it might be useful. Hmm.\n\n // Return as an OWL restriction.\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n hasValue: this.occurrenceID,\n };\n }\n}\n\nmodule.exports = {\n SpecimenWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/SpecimenWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/SpecimenWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -2618,7 +2618,7 @@ "export": true, "importPath": "@phyloref/phyx/src/wrappers/SpecimenWrapper.js", "importStyle": "{SpecimenWrapper}", - "description": "The SpecimenWrapper wraps specimen taxonomic units. These can be identified\nwith a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\nhttps://dwc.tdwg.org/terms/#occurrence).\n\n- TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n - Should have a dwc:occurrenceID with the occurrence identifier.\n - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.\n\nSince TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\nSpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n(see https://github.com/tdwg/ontology). Therefore, it instead improvises a\nrepresentation based on dwc:Occurrence.", + "description": "The SpecimenWrapper wraps specimen taxonomic units. These can be identified\nwith a '@type' of SpecimenWrapper.TYPE_SPECIMEN (which is currently\nhttps://dwc.tdwg.org/terms/#occurrence).\n\n- TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.\n - Based on http://rs.tdwg.org/dwc/terms/Occurrence\n - Should have a occurrenceID with the occurrence identifier.\n - Should have a basisOfRecord to indicate what sort of occurrence this is.\n\nSince TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for\nSpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated\n(see https://github.com/tdwg/ontology). Therefore, it instead improvises a\nrepresentation based on dwc:Occurrence.", "lineNumber": 24, "interface": false }, @@ -2898,7 +2898,7 @@ "name": "src/wrappers/TaxonConceptWrapper.js", "content": "/** Utility functions. */\nconst { has } = require('lodash');\n\n/** List of OWL/RDF terms we use. */\nconst owlterms = require('../utils/owlterms');\n\n/** For parsing scientific names. */\nconst { TaxonNameWrapper } = require('./TaxonNameWrapper');\n\n/**\n * The TaxonConceptWrapper wraps taxon concepts. These are taxonomic units with\n * a type of TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT. They are based on the\n * Taxon Concept ontology at https://github.com/tdwg/ontology/tree/master/ontology/voc.\n *\n * A taxon concept:\n * - SHOULD have a hasName property indicating the name this taxon refers to.\n * - MAY have accordingTo, describedBy or circumscribedBy to indicate how this\n * taxon concept should be circumscribed. If none of these are present,\n * this taxonomic unit will be considered a taxon rather than a taxon concept\n * (i.e. as a nominal taxon concept, as in https://github.com/darwin-sw/dsw/wiki/ClassTaxon).\n * - MAY have nameString and accordingToString properties. We will fall back\n * to these properties if hasName or accordingTo are missing.\n */\n\nclass TaxonConceptWrapper {\n /** The @type of a taxon or taxon concept. */\n static get TYPE_TAXON_CONCEPT() {\n return owlterms.TDWG_VOC_TAXON_CONCEPT;\n }\n\n /** Create a TaxonConceptWrapper around a taxon concept. */\n constructor(tunit, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n this.tunit = tunit;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Normalize the specified taxon concept.\n * @param tc A taxon concept to be normalized.\n */\n static normalize(tc) {\n const wrapped = new TaxonConceptWrapper(tc);\n const normalizedTC = {\n '@type': TaxonConceptWrapper.TYPE_TAXON_CONCEPT,\n label: wrapped.label,\n hasName: TaxonNameWrapper.normalize(wrapped.taxonName),\n nameString: wrapped.taxonName.nameComplete,\n accordingTo: wrapped.accordingTo,\n };\n if ('@id' in tc) normalizedTC['@id'] = tc['@id'];\n return normalizedTC;\n }\n\n /**\n * Return the taxon name of this taxon concept (if any) as an object.\n */\n get taxonName() {\n // Do we have any names as taxon name objects?\n if (has(this.tunit, 'hasName')) return this.tunit.hasName;\n\n // Do we have a nameString with a taxon name as string?\n if (has(this.tunit, 'nameString')) return TaxonNameWrapper.fromVerbatimName(this.tunit.nameString, this.defaultNomenCode);\n\n // If not, we have no name!\n return undefined;\n }\n\n /**\n * Return the complete taxon name of this taxon concept (if any), which is the\n * uninomial, binomial or trinomial name.\n */\n get nameComplete() {\n // Do we have any names as taxon name objects?\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nameComplete;\n\n // Do we have a nameString with a taxon name as string?\n if (has(this.tunit, 'nameString')) return TaxonNameWrapper.fromVerbatimName(this.tunit.nameString, this.defaultNomenCode).nameComplete;\n\n // If not, we have no name!\n return undefined;\n }\n\n /**\n * Return the nomenclatural code of this taxon concept as a string.\n */\n get nomenCode() {\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nomenclaturalCode;\n\n return owlterms.UNKNOWN_CODE;\n }\n\n /**\n * Return the nomenclatural code of this taxon concept as an object.\n */\n get nomenCodeDetails() {\n if (has(this.tunit, 'hasName')) return new TaxonNameWrapper(this.tunit.hasName, this.defaultNomenCode).nomenclaturalCodeDetails;\n\n return TaxonNameWrapper.getNomenCodeDetails(owlterms.UNKNOWN_CODE);\n }\n\n /**\n * Return the accordingTo information (if any) as an object.\n *\n * For now, we return this verbatim. Once we close #15, we should parse raw labels\n * with a CitationWrapper.\n */\n get accordingTo() {\n // Do we have any accordingTo information?\n if (has(this.tunit, 'accordingTo')) return this.tunit.accordingTo;\n\n // Do we have an accordingToString?\n if (has(this.tunit, 'accordingToString')) return this.tunit.accordingToString;\n\n // If not, we have no accodingTo information!\n return undefined;\n }\n\n /**\n * Return the accordingTo information (if any) as a string.\n *\n * For now, we stringify objects by converting them into JSON strings. Once we\n * close #15, we will be able to generate a label using CitationWrapper.\n */\n get accordingToString() {\n // Do we have any accordingTo information?\n if (has(this.tunit, 'accordingTo')) return JSON.stringify(this.tunit.accordingTo);\n\n // Do we have an accordingToString?\n if (has(this.tunit, 'accordingToString')) return this.tunit.accordingToString;\n\n // If not, we have no accodingTo information!\n return undefined;\n }\n\n /**\n * Return the label of this taxon concept.\n */\n get label() {\n // If we're wrapping a taxonName, use its label.\n if (this.taxonName) {\n // Do we also have accordingTo information?\n if (this.accordingToString) {\n return `${new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).label} sensu ${this.accordingToString}`;\n }\n\n return new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).label;\n }\n\n return undefined;\n }\n\n /**\n * Given a node label, attempt to parse it as a scientific name.\n *\n * Note that this is NOT memoized -- you should really be using\n * TaxonomicUnitWrapper.fromLabel() or TaxonNameWrapper.fromVerbatimName() rather\n * than calling this directly.\n *\n * @return A taxonomic unit that corresponds to this taxon concept.\n */\n static fromLabel(nodeLabel, nomenCode = owlterms.UNKNOWN_CODE) {\n if (nodeLabel === undefined || nodeLabel === null || nodeLabel.trim() === '') return undefined;\n\n // Check if this label can be divided into a name and a sensu/sec component.\n const match = /^\\s*(.*)\\s+(?:sec|sensu)\\.?\\s+(.*)\\s*$/.exec(nodeLabel);\n let accordingTo;\n if (match) {\n accordingTo = match[2];\n }\n\n // Can we parse it as a taxon name? If not, we will return undefined.\n const taxonName = TaxonNameWrapper.fromVerbatimName(nodeLabel, nomenCode);\n if (taxonName) {\n return TaxonConceptWrapper.wrapTaxonName(taxonName, accordingTo);\n }\n\n // Couldn't parse it at all.\n return undefined;\n }\n\n /** Wrap a taxon name with a particular TaxonName object and an accordingTo (string). */\n static wrapTaxonName(taxonName, accordingTo) {\n const result = {\n '@type': TaxonConceptWrapper.TYPE_TAXON_CONCEPT,\n hasName: taxonName,\n };\n if (accordingTo) result.accordingTo = accordingTo;\n return result;\n }\n\n /**\n * Return how this class should look in an OWL equivalentClass expression.\n *\n * Note that we don't include the accordingTo information in this\n * query, since we don't have a useful way to use that during OWL reasoning.\n */\n get asOWLEquivClass() {\n // Without a taxonomicName, we can't do anything.\n if (!this.taxonName) return undefined;\n\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: new TaxonNameWrapper(this.taxonName, this.defaultNomenCode).asOWLEquivClass,\n };\n }\n}\n\nmodule.exports = {\n TaxonConceptWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/TaxonConceptWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/TaxonConceptWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -3273,7 +3273,7 @@ "name": "src/wrappers/TaxonNameWrapper.js", "content": "/** Utility functions. */\nconst { has, cloneDeep, isArray } = require('lodash');\n\n/** OWL/RDF terms. */\nconst owlterms = require('../utils/owlterms');\n\n/** We need the cache manager to memoize parsing scientific names. */\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/**\n * Wraps a taxon name to provide access to components of\n * the taxon name. This is based on the TDWG TaxonName standard, as at\n * https://github.com/tdwg/ontology/blob/master/ontology/voc/TaxonName.rdf.\n *\n * Every instance of this class is expected to have some combination of the\n * following fields:\n * - rdfs:label -- the verbatim taxon name\n * - nameComplete -- the complete uninomial, binomial or trinomial name.\n * - nomenclaturalCode -- the nomenclatural code under which the complete name\n * should be interpreted.\n *\n * We will also read the following fields if they are present:\n * - uninomial: The uninomial name of this taxon, if one is present.\n * - genusPart: The genus name.\n * - specificEpithet: The specific epithet.\n * - infraspecificEpithet: The infraspecific epithet.\n *\n * We wrap whatever we're given, so we won't assume that these fields are actually\n * consistent with each other. However, when one of these fields are set, we\n * overwrite the nameComplete to ensure that they are consistent. Similarly,\n * changing the nameComplete will overwrite the genusPart, specificEpithet and\n * infraspecificEpithet.\n *\n * Note that the TaxonName ontology recommends dc:title instead of rdfs:label;\n * however, I like the idea of using dc:title for documents and rdfs:label for\n * vocabulary terms, so I'm okay with using rdfs:label for the verbatim name.\n */\nclass TaxonNameWrapper {\n /**\n * Create a new taxon name wrapper around the JSON representation of\n * a taxon name.\n */\n constructor(txname, defaultNomenCode = owlterms.UNKNOWN_CODE) {\n if (txname === undefined) throw new Error('TaxonNameWrapper tried to wrap undefined');\n this.txname = txname;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * The type associated with these taxonName objects.\n */\n static get TYPE_TAXON_NAME() {\n return owlterms.TDWG_VOC_TAXON_NAME;\n }\n\n /**\n * The IRI for an unknown nomenclatural code (i.e. all we know is that it's a scientific name).\n */\n static get UNKNOWN_CODE() {\n return owlterms.UNKNOWN_CODE;\n }\n\n /* Directly access IRIs for nomenclatural codes. */\n static get ICZN_CODE() { return owlterms.ICZN_CODE; }\n\n static get ICN_CODE() { return owlterms.ICN_CODE; }\n\n static get ICNP_CODE() { return owlterms.ICNP_CODE; }\n\n static get ICTV_CODE() { return owlterms.ICTV_CODE; }\n\n static get ICNCP_CODE() { return owlterms.ICNCP_CODE; }\n\n /**\n * Return a list of all supported nomenclatural code. Each entry will have\n * the following keys:\n * - code: A list of short names that can be used to represent this nomenclatural code.\n * - label: An informal name of this nomenclatural code in English.\n * - title: The formal name of this nomenclatural code in English.\n * - iri: The IRI of this nomenclatural code.\n *\n * This will be used in drawing user interfaces, so this should be in order\n * of likelihood of use.\n */\n static getNomenclaturalCodes() {\n return [\n // Note: the unknown code needs to be the first one in this list.\n {\n iri: owlterms.UNKNOWN_CODE,\n shortName: 'Code not known',\n label: 'Nomenclatural code not known',\n title: 'Nomenclatural code not known',\n },\n {\n iri: owlterms.ICZN_CODE,\n shortName: 'ICZN',\n label: 'Animals (ICZN)',\n title: 'International Code of Zoological Nomenclature',\n },\n {\n iri: owlterms.ICN_CODE,\n shortName: 'ICN',\n label: 'Algae, fungi and plants (ICN, previously ICBN)',\n title: 'International Code of Nomenclature for algae, fungi, and plants',\n },\n {\n iri: owlterms.ICNP_CODE,\n shortName: 'ICNP',\n label: 'Prokaryotes (ICNP)',\n title: 'International Code of Nomenclature of Prokaryotes',\n },\n {\n iri: owlterms.ICTV_CODE,\n shortName: 'ICTV',\n label: 'Viruses (ICTV)',\n title: 'International Committee on Taxonomy of Viruses',\n },\n {\n iri: owlterms.ICNCP_CODE,\n shortName: 'ICNCP',\n label: 'Cultivated plants (ICNCP)',\n title: 'International Code of Cultivated Plants',\n },\n ];\n }\n\n /**\n * Returns the nomenclatural code entry for a code.\n */\n static getNomenCodeDetails(nomenCode) {\n const codes = TaxonNameWrapper.getNomenclaturalCodes();\n\n // If the nomenCode provided is owlterms.UNKNOWN_CODE,\n // return that entry.\n if (nomenCode === owlterms.UNKNOWN_CODE) {\n return codes[0];\n }\n\n // Look for the entry with the same IRI as the provided IRI.\n const matchingCode = codes\n .find(code => (code.iri || '').toLowerCase() === nomenCode.toLowerCase());\n if (matchingCode) return matchingCode;\n return undefined;\n }\n\n /**\n * Normalize the specified taxon name.\n * @param txname A taxon name to be normalized.\n */\n static normalize(txname) {\n const wrapped = new TaxonNameWrapper(txname);\n const normalizedTxname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n nomenclaturalCode: wrapped.nomenclaturalCode,\n label: wrapped.label,\n nameComplete: wrapped.nameComplete,\n genusPart: wrapped.genusPart,\n specificEpithet: wrapped.specificEpithet,\n infraspecificEpithet: wrapped.infraspecificEpithet,\n };\n if ('@id' in txname) normalizedTxname['@id'] = txname['@id'];\n return normalizedTxname;\n }\n\n /**\n * Returns the nomenclatural code of this taxon name.\n */\n get nomenclaturalCode() {\n return this.txname.nomenclaturalCode || this.defaultNomenCode;\n }\n\n /**\n * Returns the nomenclatural code of this taxon name as a IRI.\n */\n get nomenclaturalCodeDetails() {\n const nomenCode = this.nomenclaturalCode;\n const nomenObj = TaxonNameWrapper.getNomenCodeDetails(nomenCode);\n if (!nomenObj) return undefined;\n\n return nomenObj;\n }\n\n /**\n * Set the nomenclatural code of this taxon name.\n */\n set nomenclaturalCode(nomenCode) {\n this.txname.nomenclaturalCode = nomenCode;\n }\n\n /**\n * Parses a verbatim taxon name into an (unwrapped) TaxonName.\n */\n static fromVerbatimName(verbatimName, nomenCode = owlterms.UNKNOWN_CODE) {\n // Have we already parsed this verbatim name?\n if (PhyxCacheManager.has(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName)) {\n return PhyxCacheManager.get(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName);\n }\n\n // Use a regular expression to parse the verbatimName.\n\n // Attempt 1. Look for a trinomial name.\n let txname;\n let results = /^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)\\s*([a-z-]+)\\b/.exec(verbatimName);\n\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: `${results[1]} ${results[2]} ${results[3]}`.trim(),\n genusPart: results[1],\n specificEpithet: results[2],\n infraspecificEpithet: results[3],\n };\n }\n\n // Attempt 2. Look for a binomial name.\n if (!txname) {\n results = /^([A-Z][a-z]+)[ _]([a-z-]+\\.?)(?:\\b|_)/.exec(verbatimName);\n\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: `${results[1]} ${results[2]}`.trim(),\n genusPart: results[1],\n specificEpithet: results[2],\n };\n }\n }\n\n // Attempt 3. Look for a uninomial name.\n if (!txname) {\n // Is it a uninomial name?\n results = /^([A-Z][a-z]+)(?:[_\\s]|\\b)/.exec(verbatimName);\n if (results) {\n txname = {\n '@type': TaxonNameWrapper.TYPE_TAXON_NAME,\n label: verbatimName,\n nameComplete: results[1],\n uninomial: results[1],\n };\n }\n }\n\n // Add a nomenclatural code if possible.\n if (txname && nomenCode) {\n txname.nomenclaturalCode = nomenCode;\n }\n\n // Store in the cache.\n if (txname !== undefined) {\n PhyxCacheManager.put(`TaxonNameWrapper.taxonNameCache.${nomenCode}`, verbatimName, txname);\n }\n\n return txname;\n }\n\n /**\n * Return the label of this scientific name.\n */\n get label() {\n return this.txname.label || this.nameComplete;\n }\n\n /**\n * Set the label of this scientific name.\n */\n set label(lab) {\n this.txname.label = lab;\n if (!this.nameComplete) {\n // If we don't have a nameComplete, treat this as the name complete.\n this.nameComplete = lab;\n }\n }\n\n /**\n * Return the verbatim name of this taxon name.\n */\n get verbatimName() {\n return this.txname.label;\n }\n\n /*\n * Return the complete name (i.e. the uninomial, binomial or trinomial name\n * without authority information).\n */\n get nameComplete() {\n return this.txname.nameComplete\n || this.trinomialName\n || this.binomialName\n || this.uninomialName;\n }\n\n /**\n * Set the complete name. To do this, we re-parse the provided name.\n */\n set nameComplete(name) {\n this.txname = TaxonNameWrapper.fromVerbatimName(name, this.nomenclaturalCode);\n }\n\n /** Return the uninomial name if there is one. */\n get uninomial() {\n if (this.txname.uninomial) return this.txname.uninomial;\n\n // If there is no genus but there is a scientificName, try to extract a genus\n // from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.txname.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'uninomial')) return txname.uninomial;\n }\n\n return undefined;\n }\n\n /** Set the uninomial name. */\n set uninomial(uninom) {\n this.txname.uninomial = uninom;\n this.txname.nameComplete = uninom;\n }\n\n /** Return the binomial name if available. */\n get binomialName() {\n // Get the binomial name. Constructed from the genus and specific epithet\n // if available.\n if (this.genusPart === undefined || this.specificEpithet === undefined) return undefined;\n return `${this.genusPart} ${this.specificEpithet}`;\n }\n\n /** Set the binomial name. */\n set binomialName(binom) {\n this.txname.uninomial = undefined;\n this.txname.nameComplete = binom;\n }\n\n /** Return the trinomial name if available. */\n get trinomialName() {\n if (\n this.infraspecificEpithet === undefined\n || this.specificEpithet === undefined\n || this.genusPart === undefined\n ) return undefined;\n return `${this.genusPart} ${this.specificEpithet} ${this.infraspecificEpithet}`;\n }\n\n /** Set the trinomial name. */\n set trinomialName(trinom) {\n this.txname.uninomial = undefined;\n this.txname.nameComplete = trinom;\n }\n\n /** Return the genus part of this scientific name if available. */\n get genusPart() {\n // Try to read the genus if available.\n if (has(this.txname, 'genusPart')) return this.txname.genusPart;\n\n // If there is no genus but there is a scientificName, try to extract a genus\n // from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.txname.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'genusPart')) return txname.genusPart;\n }\n\n return undefined;\n }\n\n /** Set the genus part of this name. */\n set genusPart(genus) {\n this.txname.genusPart = genus;\n if (this.specificEpithet) {\n if (this.infraspecificEpithet) {\n this.txname.nameComplete = `${genus} ${this.specificEpithet} ${this.infraspecificEpithet}`;\n } else {\n this.txname.nameComplete = `${genus} ${this.specificEpithet}`;\n }\n }\n }\n\n /** Return the specific epithet of this scientific name if available. */\n get specificEpithet() {\n // Try to read the specific epithet if available.\n if (has(this.txname, 'specificEpithet')) return this.txname.specificEpithet;\n\n // If there is no specific epithet but there is a scientificName, try to\n // extract a specific epithet from it.\n if (this.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'specificEpithet')) return txname.specificEpithet;\n }\n\n return undefined;\n }\n\n /** Set the specificEpithet part of this name. */\n set specificEpithet(epithet) {\n this.txname.specificEpithet = epithet;\n if (this.genusPart) {\n if (this.infraspecificEpithet) {\n this.txname.nameComplete = `${this.genusPart} ${epithet} ${this.infraspecificEpithet}`;\n } else {\n this.txname.nameComplete = `${this.genusPart} ${epithet}`;\n }\n }\n }\n\n /** Return the infraspecific epithet of this scientific name if available. */\n get infraspecificEpithet() {\n // Try to read the specific epithet if available.\n if (has(this.txname, 'infraspecificEpithet')) return this.txname.infraspecificEpithet;\n\n // If there is no specific epithet but there is a scientificName, try to\n // extract a specific epithet from it.\n if (this.txname.nameComplete) {\n const txname = TaxonNameWrapper.fromVerbatimName(\n this.nameComplete,\n this.nomenclaturalCode\n );\n if (has(txname, 'infraspecificEpithet')) return txname.infraspecificEpithet;\n }\n\n return undefined;\n }\n\n /** Set the infraspecificEpithet part of this name. */\n set infraspecificEpithet(epithet) {\n this.txname.infraspecificEpithet = epithet;\n if (this.genusPart) {\n if (this.specificEpithet) {\n this.txname.nameComplete = `${this.genusPart} ${this.specificEpithet} ${epithet}`;\n } else {\n this.txname.nameComplete = `${this.genusPart} sp. ${epithet}`;\n }\n }\n }\n\n /**\n * Return this taxon name in an JSON-LD representation.\n */\n get asJSONLD() {\n const jsonld = cloneDeep(this.txname);\n\n // Make sure '@type' is an array.\n if (!has(jsonld, '@type')) jsonld['@type'] = [];\n if (!isArray(jsonld['@type'])) jsonld['@type'] = [jsonld['@type']];\n\n // Make it explicit that the type includes the nomenclaturalCode.\n const nomenCode = this.nomenclaturalCode;\n if (!jsonld['@type'].includes(nomenCode)) jsonld['@type'].push(nomenCode);\n\n return jsonld;\n }\n\n /**\n * Return this taxon name as an OWL equivalentClass expression.\n */\n get asOWLEquivClass() {\n // No complete name, can't return anything.\n if (!this.nameComplete) return undefined;\n\n // Do we have a nomenclaturalCode?\n if (!this.nomenclaturalCode) {\n return {\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n hasValue: this.nameComplete,\n };\n }\n\n // If we do have a nomenclatural code, incorporate that into the logical\n // expression as well.\n return {\n '@type': 'owl:Class',\n intersectionOf: [{\n '@type': 'owl:Restriction',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n hasValue: this.nameComplete,\n }, {\n '@type': 'owl:Restriction',\n onProperty: owlterms.NOMENCLATURAL_CODE,\n hasValue: {\n '@id': this.nomenclaturalCode,\n },\n }],\n };\n }\n}\n\nmodule.exports = {\n TaxonNameWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/TaxonNameWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/TaxonNameWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -3979,7 +3979,7 @@ "name": "src/wrappers/TaxonomicUnitWrapper.js", "content": "/** Utility functions. */\nconst {\n has,\n isArray,\n cloneDeep,\n assign,\n} = require('lodash');\n\n/** List of OWL/RDF terms we use. */\nconst owlterms = require('../utils/owlterms');\n\n/** We store the taxonomic units we extract from phylogeny labels in the Phyx Cache Manager. */\nconst { PhyxCacheManager } = require('../utils/PhyxCacheManager');\n\n/** For parsing specimen identifiers. */\nconst { SpecimenWrapper } = require('./SpecimenWrapper');\n\n/** For parsing scientific names. */\nconst { TaxonConceptWrapper } = require('./TaxonConceptWrapper');\n\n/**\n * The TaxonomicUnitWrapper wraps taxonomic units, whether on a node or being used\n * as a specifier on a phyloreference. Every taxonomic unit can additionally be\n * wrapped by more specific classes, such as {@link TaxonConceptWrapper} or\n * {@link SpecimenWrapper}. We can determine which type it is based on its\n * '@type' and whether it includes:\n * - TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT => {@link TaxonConceptWrapper}\n * - TaxonomicUnitWrapper.TYPE_SPECIMEN => {@link SpecimenWrapper}\n * - TaxonomicUnitWrapper.TYPE_APOMORPHY => reserved for future use\n * - TaxonomicUnitWrapper.TYPE_PHYLOREF => reserved for future use\n *\n * It also contains static methods for extracting\n * taxonomic units from arbitrary strings, such as phylogeny labels.\n *\n * Every taxonomic unit SHOULD have an rdfs:label and MAY include a dcterm:description\n * to describe it in human-readable terms. It MUST include a '@type' that specifies\n * what type of taxonomic unit it is.\n *\n * Taxonomic units may be specified with only an '@id' or a set of '@id's, which\n * indicate external references.\n */\n\nclass TaxonomicUnitWrapper {\n /* Types of taxonomic units we support (see documentation above). */\n\n /** A taxon or taxon concept. */\n static get TYPE_TAXON_CONCEPT() {\n return TaxonConceptWrapper.TYPE_TAXON_CONCEPT;\n }\n\n /** A specimen. */\n static get TYPE_SPECIMEN() {\n return SpecimenWrapper.TYPE_SPECIMEN;\n }\n\n /** Wrap a taxonomic unit. */\n constructor(tunit, defaultNomenCode = owlterms.NAME_IN_UNKNOWN_CODE) {\n this.tunit = tunit;\n this.defaultNomenCode = defaultNomenCode;\n }\n\n /**\n * Normalize the specified taxonomic unit.\n * @param tunit A taxonomic unit to be normalized.\n */\n static normalize(tunit) {\n const wrapped = new TaxonomicUnitWrapper(tunit);\n if (wrapped.taxonConcept) {\n return TaxonConceptWrapper.normalize(tunit);\n }\n if (wrapped.specimen) {\n return SpecimenWrapper.normalize(tunit);\n }\n if (wrapped.externalReferences) {\n // External references should only have an `@id`.\n return tunit;\n }\n return tunit;\n }\n\n /**\n * What type of specifier is this? This is an array that could contain multiple\n * classes, but should contain one of:\n * - {@link TYPE_TAXON_CONCEPT}\n * - {@link TYPE_SPECIMEN}\n */\n get types() {\n if (!has(this.tunit, '@type')) return [];\n if (isArray(this.tunit['@type'])) return this.tunit['@type'];\n return [this.tunit['@type']];\n }\n\n /**\n * Return this taxonomic unit if it is a taxon concept.\n */\n get taxonConcept() {\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT)) return this.tunit;\n return undefined;\n }\n\n /**\n * Return this taxonomic unit if it is a specimen.\n */\n get specimen() {\n // Only specimens have scientific names.\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) return this.tunit;\n\n return undefined;\n }\n\n /**\n * Return the list of external references for this taxonomic unit.\n * This is just all the '@ids' of this object.\n */\n get externalReferences() {\n if (!has(this.tunit, '@id')) return [];\n if (isArray(this.tunit['@id'])) return this.tunit['@id'];\n return [this.tunit['@id']];\n }\n\n /**\n * Return the label of this taxonomic unit.\n */\n get label() {\n // A label or description for this TU?\n if (has(this.tunit, 'label')) return this.tunit.label;\n if (has(this.tunit, 'description')) return this.tunit.description;\n\n // Is this a specimen?\n if (this.specimen) {\n return new SpecimenWrapper(this.specimen).label;\n }\n\n // Is this a taxon concept?\n if (this.taxonConcept) {\n return new TaxonConceptWrapper(this.taxonConcept).label;\n }\n\n // If its neither a specimen nor a taxon concept, just list the\n // external references.\n const externalReferences = this.externalReferences;\n if (externalReferences.length > 0) {\n return externalReferences\n .map(externalRef => `<${externalRef}>`)\n .join(' and ');\n }\n\n // If we don't have any properties of a taxonomic unit, return undefined.\n return undefined;\n }\n\n /**\n * Given a label, attempt to parse it into a taxonomic unit, whether a scientific\n * name or a specimen identifier. The provided nomenclatural code is used.\n *\n * @return A taxonomic unit that this label could be parsed as.\n */\n static fromLabel(nodeLabel, nomenCode = owlterms.NAME_IN_UNKNOWN_CODE) {\n if (nodeLabel === undefined || nodeLabel === null || nodeLabel.trim() === '') return undefined;\n\n // Rather than figuring out with this label, check to see if we've parsed\n // this before.\n if (PhyxCacheManager.has(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel)) {\n return PhyxCacheManager.get(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel);\n }\n\n // Look for taxon concept.\n const taxonConcept = TaxonConceptWrapper.fromLabel(nodeLabel, nomenCode);\n\n // Look for specimen information.\n let specimen;\n if (nodeLabel.toLowerCase().startsWith('specimen ')) {\n // Eliminate a 'Specimen ' prefix if it exists.\n specimen = SpecimenWrapper.fromOccurrenceID(nodeLabel.substr(9));\n }\n\n let tunit;\n if (taxonConcept && specimen) {\n // If we have both, then treat it as a specimen that has been identified\n // to a particular taxonomic name.\n tunit = assign({}, taxonConcept, specimen);\n\n tunit['@type'] = TaxonomicUnitWrapper.TYPE_SPECIMEN;\n } else if (taxonConcept) {\n tunit = taxonConcept;\n } else if (specimen) {\n tunit = specimen;\n }\n\n // Look for external references. For now, we only check to see if the entire\n // nodeLabel starts with URL/URNs, but we should eventually just look for\n // them inside the label.\n const URL_URN_PREFIXES = [\n 'http://',\n 'https://',\n 'ftp://',\n 'sftp://',\n 'file://',\n 'urn:',\n ];\n\n if (URL_URN_PREFIXES.filter(prefix => nodeLabel.startsWith(prefix)).length > 0) {\n // The node label starts with something that looks like a URL!\n // Treat it as an external reference.\n if (tunit === undefined) tunit = {};\n tunit['@id'] = nodeLabel;\n }\n\n // Finally, let's record the label we parsed to get to this tunit!\n if (tunit) {\n tunit.label = nodeLabel;\n }\n\n // Record in the cache\n PhyxCacheManager.put(`TaxonomicUnitWrapper.taxonomicUnitsFromNodeLabelCache.${nomenCode}`, nodeLabel, tunit);\n\n return tunit;\n }\n\n /**\n * Return the JSON representation of this taxonomic unit, i.e. the object we're wrapping.\n */\n get asJSON() {\n return this.tunit;\n }\n\n /**\n * Return this taxonomic unit as an OWL/JSON-LD object.\n */\n get asJSONLD() {\n const jsonld = cloneDeep(this.tunit);\n\n // Add CDAO_TU as a type to the existing types.\n if (has(this.tunit, '@type')) {\n if (isArray(this.tunit['@type'])) this.tunit['@type'].push(owlterms.CDAO_TU);\n }\n\n const equivClass = this.asOWLEquivClass;\n if (equivClass) {\n jsonld.equivalentClass = equivClass;\n }\n\n return jsonld;\n }\n\n /**\n * Return the equivalent class expression for this taxonomic unit.\n */\n get asOWLEquivClass() {\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT)) {\n return new TaxonConceptWrapper(this.tunit, this.defaultNomenCode).asOWLEquivClass;\n }\n\n if (this.types.includes(TaxonomicUnitWrapper.TYPE_SPECIMEN)) {\n return new SpecimenWrapper(this.specimen).asOWLEquivClass;\n }\n\n // Nothing we can do, so just ignore it.\n return undefined;\n }\n}\n\nmodule.exports = {\n TaxonomicUnitWrapper,\n};\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/src/wrappers/TaxonomicUnitWrapper.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/src/wrappers/TaxonomicUnitWrapper.js", "access": "public", "description": null, "lineNumber": 1 @@ -4378,16 +4378,16 @@ }, { "kind": "index", - "content": "# phyx.js\n\n[![Build Status](https://github.com/phyloref/phyx.js/workflows/Build%20and%20Test/badge.svg)](https://github.com/phyloref/phyx.js/actions?query=workflow%3A%22Build+and+Test%22)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5576556.svg)](https://doi.org/10.5281/zenodo.5576556)\n\nThe Phyloreference Exchange (PHYX) format is a JSON representation that can be\nused to store and transfer definitions of [phyloreferences]. This library provides\nclasses to help interpret some parts of these files, and for transforming an\nentire Phyx file into a [JSON-LD] representation that can be reasoned over with\nan [OWL 2 DL] reasoner. See the [Phyloreference Curation Tool] or the [Clade Ontology]\nfor examples of its usage.\n\n[Tutorials demonstrating the use of phyx.js](./tutorials/) are available.\n\n## Citation\n\nphyx.js should be cited by citing our publication documenting the Phyx format and phyx.js.\n\n> Vaidya G, Cellinese N, Lapp H. 2022. A new phylogenetic data standard for computable clade definitions: the\n> Phyloreference Exchange Format (Phyx) PeerJ 10:e12618 [doi:10.7717/peerj.12618](https://doi.org/10.7717/peerj.12618)\n\n## Funding\nFunded by the US National Science Foundation through collaborative grants [DBI-1458484]\nand [DBI-1458604]. See [Funding] for details.\n\n [phyloreferences]: http://phyloref.org\n [JSON-LD]: https://en.wikipedia.org/wiki/JSON-LD\n [OWL 2 DL]: https://www.w3.org/TR/owl2-overview/\n [Phyloreference Curation Tool]: https://github.com/phyloref/curation-tool\n [Clade Ontology]: https://github.com/phyloref/clade-ontology\n [DBI-1458484]: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458484\n [DBI-1458604]: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458604\n [Funding]: http://www.phyloref.org/about/#funding\n", - "longname": "/Users/gaurav/Development/phyloref/phyx.js/README.md", + "content": "# phyx.js\n\n[![Build Status](https://github.com/phyloref/phyx.js/workflows/Build%20and%20Test/badge.svg)](https://github.com/phyloref/phyx.js/actions?query=workflow%3A%22Build+and+Test%22)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5576556.svg)](https://doi.org/10.5281/zenodo.5576556)\n[![NPM Version](https://img.shields.io/npm/v/@phyloref/phyx)](https://www.npmjs.com/package/@phyloref/phyx)\n\nThe Phyloreference Exchange (PHYX) format is a JSON representation that can be\nused to store and transfer definitions of [phyloreferences]. This library provides\nclasses to help interpret some parts of these files, and for transforming an\nentire Phyx file into a [JSON-LD] representation that can be reasoned over with\nan [OWL 2 DL] reasoner. See the [Phyloreference Curation Tool] or the [Clade Ontology]\nfor examples of its usage.\n\n## Usage\n\nYou can install [phyx.js using npm](https://www.npmjs.com/package/@phyloref/phyx):\n\n```shell\n$ npm install @phyloref/phyx\n```\n\n[Tutorials demonstrating the use of phyx.js](./tutorials/) are available.\n\n## Citation\n\nphyx.js should be cited by citing our publication documenting the Phyx format and phyx.js.\n\n> Vaidya G, Cellinese N, Lapp H. 2022. A new phylogenetic data standard for computable clade definitions: the\n> Phyloreference Exchange Format (Phyx) PeerJ 10:e12618 [doi:10.7717/peerj.12618](https://doi.org/10.7717/peerj.12618)\n\n## Funding\nFunded by the US National Science Foundation through collaborative grants [DBI-1458484]\nand [DBI-1458604]. See [Funding] for details.\n\n [phyloreferences]: http://phyloref.org\n [JSON-LD]: https://en.wikipedia.org/wiki/JSON-LD\n [OWL 2 DL]: https://www.w3.org/TR/owl2-overview/\n [Phyloreference Curation Tool]: https://github.com/phyloref/curation-tool\n [Clade Ontology]: https://github.com/phyloref/clade-ontology\n [DBI-1458484]: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458484\n [DBI-1458604]: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1458604\n [Funding]: http://www.phyloref.org/about/#funding\n", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/README.md", "name": "./README.md", "static": true, "access": "public" }, { "kind": "packageJSON", - "content": "{\n \"name\": \"@phyloref/phyx\",\n \"version\": \"1.2.0-alpha1\",\n \"description\": \"Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files\",\n \"keywords\": [\n \"phylogenetics\",\n \"phylogeny\",\n \"phylogenetic definitions\",\n \"clade definitions\"\n ],\n \"homepage\": \"https://github.com/phyloref/phyx.js#readme\",\n \"bugs\": {\n \"url\": \"https://github.com/phyloref/phyx.js/issues\"\n },\n \"repository\": {\n \"type\": \"git\",\n \"url\": \"git+https://github.com/phyloref/phyx.js.git\"\n },\n \"license\": \"MIT\",\n \"author\": \"Gaurav Vaidya \",\n \"main\": \"src/index.js\",\n \"bin\": {\n \"phyx2owl\": \"bin/phyx2owl.js\",\n \"resolve\": \"bin/resolve.js\"\n },\n \"scripts\": {\n \"docs\": \"esdoc\",\n \"generate-every-topology\": \"every-topology-testing/generate-topologies.js\",\n \"lint\": \"eslint \\\"src/**/*.js\\\" \\\"test/**/*.js\\\" \\\"**/*.json\\\"\",\n \"phyx2owl\": \"node bin/phyx2owl.js\",\n \"resolve\": \"node bin/resolve.js\",\n \"pretest\": \"npm run lint\",\n \"test\": \"mocha --recursive\"\n },\n \"dependencies\": {\n \"jsonld\": \"^5.0.0\",\n \"lodash\": \"^4.17.20\",\n \"moment\": \"^2.27.0\",\n \"newick-js\": \"^1.2.1\",\n \"retus\": \"^1.1.1\",\n \"yargs\": \"^15.4.1\"\n },\n \"devDependencies\": {\n \"ajv\": \"^6.12.2\",\n \"chai\": \"^4.2.0\",\n \"esdoc\": \"^1.1.0\",\n \"esdoc-node\": \"^1.0.5\",\n \"esdoc-standard-plugin\": \"^1.0.0\",\n \"eslint\": \"^5.16.0\",\n \"eslint-config-airbnb-base\": \"^13.2.0\",\n \"eslint-plugin-import\": \"^2.22.1\",\n \"eslint-plugin-json-format\": \"^2.0.1\",\n \"eslint-plugin-mocha\": \"^5.3.0\",\n \"mocha\": \"^5.2.0\",\n \"nodejs-file-downloader\": \"^4.1.1\",\n \"yargs\": \"^15.3.1\"\n },\n \"esdoc\": {\n \"source\": \"./src\",\n \"destination\": \"./docs\",\n \"plugins\": [\n {\n \"name\": \"esdoc-standard-plugin\",\n \"option\": {\n \"manual\": {\n \"files\": [\n \"./CHANGELOG.md\",\n \"./tutorials/Introduction.md\"\n ]\n },\n \"test\": {\n \"source\": \"./test/\",\n \"includes\": [\n \"\\\\.js$\"\n ]\n }\n }\n },\n {\n \"name\": \"esdoc-node\"\n }\n ]\n }\n}\n", - "longname": "/Users/gaurav/Development/phyloref/phyx.js/package.json", + "content": "{\n \"name\": \"@phyloref/phyx\",\n \"version\": \"1.2.0-alpha2\",\n \"description\": \"Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files\",\n \"keywords\": [\n \"phylogenetics\",\n \"phylogeny\",\n \"phylogenetic definitions\",\n \"clade definitions\"\n ],\n \"homepage\": \"https://github.com/phyloref/phyx.js#readme\",\n \"bugs\": {\n \"url\": \"https://github.com/phyloref/phyx.js/issues\"\n },\n \"repository\": {\n \"type\": \"git\",\n \"url\": \"git+https://github.com/phyloref/phyx.js.git\"\n },\n \"license\": \"MIT\",\n \"author\": \"Gaurav Vaidya \",\n \"main\": \"src/index.js\",\n \"bin\": {\n \"phyx2owl\": \"bin/phyx2owl.js\",\n \"resolve\": \"bin/resolve.js\"\n },\n \"scripts\": {\n \"docs\": \"esdoc\",\n \"generate-every-topology\": \"every-topology-testing/generate-topologies.js\",\n \"lint\": \"eslint \\\"src/**/*.js\\\" \\\"test/**/*.js\\\" \\\"**/*.json\\\"\",\n \"phyx2owl\": \"node bin/phyx2owl.js\",\n \"resolve\": \"node bin/resolve.js\",\n \"pretest\": \"npm run lint\",\n \"test\": \"mocha --recursive\"\n },\n \"dependencies\": {\n \"jsonld\": \"^5.0.0\",\n \"lodash\": \"^4.17.20\",\n \"moment\": \"^2.27.0\",\n \"newick-js\": \"^1.2.1\",\n \"retus\": \"^1.1.1\",\n \"yargs\": \"^15.4.1\"\n },\n \"devDependencies\": {\n \"@shinnn/eslint-config\": \"^7.0.0\",\n \"ajv\": \"^6.12.2\",\n \"chai\": \"^4.2.0\",\n \"esdoc\": \"^1.1.0\",\n \"esdoc-node\": \"^1.0.5\",\n \"esdoc-standard-plugin\": \"^1.0.0\",\n \"eslint\": \"^5.16.0\",\n \"eslint-config-airbnb-base\": \"^13.2.0\",\n \"eslint-plugin-import\": \"^2.22.1\",\n \"eslint-plugin-json-format\": \"^2.0.1\",\n \"eslint-plugin-mocha\": \"^5.3.0\",\n \"mocha\": \"^5.2.0\",\n \"nodejs-file-downloader\": \"^4.1.1\",\n \"yargs\": \"^15.3.1\"\n },\n \"esdoc\": {\n \"source\": \"./src\",\n \"destination\": \"./docs\",\n \"plugins\": [\n {\n \"name\": \"esdoc-standard-plugin\",\n \"option\": {\n \"manual\": {\n \"files\": [\n \"./CHANGELOG.md\",\n \"./tutorials/Introduction.md\"\n ]\n },\n \"test\": {\n \"source\": \"./test/\",\n \"includes\": [\n \"\\\\.js$\"\n ]\n }\n }\n },\n {\n \"name\": \"esdoc-node\"\n }\n ]\n }\n}\n", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/package.json", "name": "package.json", "static": true, "access": "public" @@ -4402,7 +4402,7 @@ }, { "kind": "manual", - "longname": "/Users/gaurav/Development/phyloref/phyx.js/CHANGELOG.md", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/CHANGELOG.md", "name": "./CHANGELOG.md", "content": "# Changelog\nAll notable changes to this library will be documented in this file.\n\nThe format is based on [Keep a Changelog] and this project adheres to [Semantic Versioning].\n\n## [Unreleased]\n\n## [1.2.0] - 2024-06-18\n- PR #138: Added normalization methods so that Phyx objects can be normalized.\n- PR #139: upgraded NPM packages and minor test fixes\n\n## [1.1.1] - 2023-08-01\n- PR #133: Add guards to some usages of `phyloref.internalSpecifiers/phyloref.externalSpecifiers`.\n- PR #136: Improved GitHub test action, including changing Node versions.\n- PR #127: Upgraded Newick.js to ^1.2.1. This means that we no longer\n support Node.js v10.x, which end-of-lifed on April 30, 2021.\n\n## [1.1.0] - 2023-05-11\n- PR #129: Added curator notes to phylorefs and phylogenies.\n- PR #128: Added citation to README and a CITATION.CFF file.\n- PR #125: Added curator information as contributors to Phyx file.\n\n## [1.0.1] - 2021-10-15\n- Created a tutorial for using phyx.js, including:\n - PR #99: Add tutorial.\n - PR #103: Improve integration of the tutorial.\n - PR #109: Add resolve.js instructions to Introduction tutorial.\n- Improvements to README files, including:\n - PR #108: Added links to published JSON-LD contexts and JSON schemas.\n - PR #110: Added note that Binder cannot be used.\n - PR #111: Changes link to tutorials to directory.\n- PR #106: Fixed typo in resolve.js.\n- Updated timeout to 60s as 20s was timing out on GitHub Actions.\n- Updated NPM packages and resorted packages in package.json.\n\n## [1.0.0] - 2021-03-16\n- Many changes across the entire library.\n- Two new scripts: `bin/phyx2owl.js` for converting a Phyx file into OWL/JSON-LD\n and `bin/resolve.js` to resolve a Phyx file on the Open Tree of Life.\n- Incorporation of JPhyloRef into testing.\n- Fixed a bug in which phyloref and phylogeny `@id` values were being overwritten when generating JSON-LD.\n- Added scripts to generate every possible topology from n=2 to n=6 with expected resolution and to test them with JPhyloRef.\n\n## [0.2.1] - 2019-08-15\n- Updated all NPM packages to their latest version.\n- Fixed a bug in which node's types were not being correctly set to obo:CDAO\\_0000140.\n\n## [0.2.0] - 2019-07-18\n### Changed\n- The single index.js has been split into multiple files, one per class, with documentation using ESdocs (#21).\n- Added support for generating \"model 2.0\" ontologies, which can be reasoned over in an OWL 2 EL reasoner such as Elk (#4). As part of this change, specifiers have been changed so that they are taxonomic units, rather than containing taxonomic units and a new Phyx context file has been created (#19).\n- Taxonomic units have been cleaned up, are clearly typed, and taxonomic names now include nomenclatural codes (#18) and support trinomial names (#22).\n\n## [0.1.2] - 2019-02-08\n### Added\n- Moved Phyx context file for JSON-LD into this repository from the Curation Tool and changed URI to point to it.\n\n## [0.1.1] - 2019-02-06\n### Added\n- A replacement for the Phylotree.js Newick parser.\n\n## [0.1.0] - 2019-01-27\n### Added\n- Transfered initial code from the [Phyloreference Curation Tool]. The initial\nrelease of this package was based on [commit 14d2c3d5d1] in that repository.\n\n### Changed\n- Replaced references to the [phylotree] library with the [newick-js] library.\n- Made other changes to the initial code as needed to work as an independent NPM package.\n\n [Unreleased]: https://github.com/phyloref/phyx.js/compare/v1.2.0...master\n [1.2.0]: https://github.com/phyloref/phyx.js/compare/v1.1.1...v1.2.0\n [1.1.1]: https://github.com/phyloref/phyx.js/compare/v1.1.0...v1.1.1\n [1.1.0]: https://github.com/phyloref/phyx.js/compare/v1.0.1...v1.1.0\n [1.0.1]: https://github.com/phyloref/phyx.js/compare/v1.0.0...v1.0.1\n [1.0.0]: https://github.com/phyloref/phyx.js/compare/v0.2.1...v1.0.0\n [0.2.1]: https://github.com/phyloref/phyx.js/compare/v0.2.0...v0.2.1\n [0.2.0]: https://github.com/phyloref/phyx.js/compare/v0.1.2...v0.2.0\n [0.1.2]: https://github.com/phyloref/phyx.js/compare/v0.1.1...v0.1.2\n [0.1.1]: https://github.com/phyloref/phyx.js/compare/v0.1.0...v0.1.1\n [0.1.0]: https://github.com/phyloref/phyx.js/releases/tag/v0.1.0\n [Keep a Changelog]: https://keepachangelog.com/en/1.0.0/\n [Semantic Versioning]: https://semver.org/spec/v2.0.0.html\n [Phyloreference Curation Tool]: http://github.com/phyloref/curation-tool\n [commit 14d2c3d5d1]: https://github.com/phyloref/curation-tool/commit/14d2c3d5d12ee4e925e29961bd46587aabfb8cd4\n [phylotree]: https://www.npmjs.com/package/phylotree\n [newick-js]: https://www.npmjs.com/package/newick-js\n", "static": true, @@ -4410,7 +4410,7 @@ }, { "kind": "manual", - "longname": "/Users/gaurav/Development/phyloref/phyx.js/tutorials/Introduction.md", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/tutorials/Introduction.md", "name": "./tutorials/Introduction.md", "content": "---\ntitle: Introduction to phyx.js\nauthor: Gaurav Vaidya\ndate: August 24, 2021\ncode-block-font-size: \\footnotesize\n---\n# Introduction to phyx.js\n\n*Written by Gaurav Vaidya. Last updated August 24, 2021*\n\nThis tutorial provides an introduction to the phyx.js library, and shows you how it can be used to read a Phyx file, check it for validity, examine [phyloreferences](https://www.phyloref.org/), phylogenies and specifiers, and describe how to convert the file into RDF.\n\n## Starting with Phyx files\n\nPhyx files are digitized clade definitions in a JSON-LD format. While you can use an editor like [Klados](https://github.com/phyloref/klados#readme) to create Phyx files, you can also write one by yourself as a JSON document.\n\n\n```javascript\nvar alligatoridae_brochu2003 = {\n \"@context\": \"https://www.phyloref.org/phyx.js/context/v1.0.0/phyx.json\",\n \n // Phylogeny from Brochu 2003: https://doi.org/10.1146/annurev.earth.31.100901.141308\n \"phylogenies\": [{\n \"newick\": \"(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha));\",\n \"source\": {\n \"type\": \"article\",\n \"title\": \"Phylogenetic approaches toward crocodylian history\",\n \"authors\": [{\n \"firstname\": \"Christopher\",\n \"middlename\": \"A.\",\n \"lastname\": \"Brochu\"\n }],\n \"year\": 2003,\n \"figure\": \"1\",\n \"identifier\": [{\n \"type\": \"doi\",\n \"id\": \"10.1146/annurev.earth.31.100901.141308\"\n }],\n \"journal\": {\n \"name\": \"Annual Review of Earth and Planetary Sciences\",\n \"volume\": \"31\",\n \"pages\": \"357--397\",\n \"identifier\": [{ \"type\": \"eISSN\", \"id\": \"1545-4495\" }]\n }\n }\n }],\n \n // Clade definition from Brochu 2003: Alligatoridae\n \"phylorefs\": [{\n \"label\": \"Alligatoridae\",\n \"scientificNameAuthorship\": { \"bibliographicCitation\": \"(Cuvier 1807)\" },\n \"phylorefType\": \"phyloref:PhyloreferenceUsingMinimumClade\",\n \"definition\": \"Alligatoridae (Cuvier 1807).\\n\\nLast common ancestor of Alligator mississippiensis and Caiman crocodilus and all of its descendents.\",\n \"definitionSource\": {\n \"bibliographicCitation\": \"Brochu (2003) Phylogenetic approaches toward crocodylian history. Annual Review of Earth and Planetary Sciences 31:1, 357-397. doi: 10.1146/annurev.earth.31.100901.141308\"\n },\n \"internalSpecifiers\": [\n {\n \"@type\": \"http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept\",\n \"hasName\": {\n \"@type\": \"http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName\",\n \"nomenclaturalCode\": \"http://rs.tdwg.org/ontology/voc/TaxonName#ICZN\",\n \"label\": \"Caiman crocodilus Linnaeus, 1758\",\n \"nameComplete\": \"Caiman crocodilus\",\n \"genusPart\": \"Caiman\",\n \"specificEpithet\": \"crocodilus\"\n }\n }, {\n \"@type\": \"http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept\",\n \"hasName\": {\n \"@type\": \"http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName\",\n \"nomenclaturalCode\": \"http://rs.tdwg.org/ontology/voc/TaxonName#ICZN\",\n \"label\": \"Alligator mississippiensis (Daudin, 1802)\",\n \"nameComplete\": \"Alligator mississippiensis\",\n \"genusPart\": \"Alligator\",\n \"specificEpithet\": \"mississippiensis\"\n }\n }\n ]\n }]\n}\n```\n\n## Validating a Phyx document using JSON Schema\n\nWe publish a [JSON Schema](https://json-schema.org/) with phyx.js, which can be used to validate that a Phyx document is correctly formed. We use [Ajv](https://ajv.js.org/), a JSON Schema validator for JavaScript. Note that we use the copy of the context file that is included in this repository, but you can also [download it from our website](https://www.phyloref.org/phyx.js/context/v1.0.0/schema.json).\n\n\n```javascript\nvar fs = require('fs');\nvar Ajv = require('ajv');\n\n// Configure Ajv.\nvar ajv = new Ajv({\n allErrors: true, // Display all error messages, not just the first.\n});\n\n// We use the JSON Schema included with this repository, but you can download the\n// Phyx JSON Schema from https://www.phyloref.org/phyx.js/context/v1.0.0/schema.json\nvar validator = ajv.compile(JSON.parse(fs.readFileSync('../docs/context/v1.0.0/schema.json')));\n\n// Attempt to validate the Brochu 2003 example file.\nvar result = validator(alligatoridae_brochu2003);\nconsole.log(`Is alligatoridae_brochu2003 valid? ${result}`);\nconsole.log('Errors:', validator.errors || 'none');\n\n// Let's make an invalid copy of the Brochu 2003 example file to make sure this is working.\nvar alligatoridae_brochu2003copy = {...alligatoridae_brochu2003};\ndelete alligatoridae_brochu2003copy['@context']; // @context is required for successful validation\n\nvar result = validator(alligatoridae_brochu2003copy);\nconsole.log(`Is alligatoridae_brochu2003copy valid? ${result}`);\nconsole.log('Errors:', validator.errors);\n```\n\n Is alligatoridae_brochu2003 valid? true\n Errors: none\n Is alligatoridae_brochu2003copy valid? false\n Errors: [\n {\n keyword: 'required',\n dataPath: '',\n schemaPath: '#/required',\n params: { missingProperty: '@context' },\n message: \"should have required property '@context'\"\n }\n ]\n\n\n## Examining phyloreferences, taxonomic units and taxon concepts\n\nThe phyx.js library was built in order to simplify the process of working with individual components of Phyx documents, and to facilitate the conversion of a Phyx document into OWL. The library consists of a series of [wrappers](https://www.phyloref.org/phyx.js/identifiers.html#wrappers), each of which wraps part of the document. For example, we can wrap every specifier that is a [taxonomic unit](http://purl.obolibrary.org/obo/CDAO_0000138) using the [TaxonomicUnitWrapper](https://www.phyloref.org/phyx.js/class/src/wrappers/TaxonomicUnitWrapper.js~TaxonomicUnitWrapper.html).\n\nThis provides a number of convenience methods: for example, `.internalSpecifiers` and `.externalSpecifiers` will always return lists, whether or not these are defined in the underlying phyloreference (if undefined, the methods return empty lists). There is also a `.specifiers` method that lists both internal and external specifiers.\n\nFurthermore, taxonomic units that are taxon concepts can be wrapped by a [TaxonConceptWrapper](https://www.phyloref.org/phyx.js/class/src/wrappers/TaxonConceptWrapper.js~TaxonConceptWrapper.html), which have methods for accessing the \"complete name\" (i.e. the monomial, binomial or trinomial name) and the nomenclatural code.\n\n\n```javascript\n// Load the Phyx library.\nvar phyx = require('..');\n\n// List all the phyloreferences along with their specifiers.\nalligatoridae_brochu2003.phylorefs.forEach(phyloref => {\n let wrappedPhyloref = new phyx.PhylorefWrapper(phyloref);\n \n console.log(wrappedPhyloref.label);\n \n // Extract the \"complete name\" and the nomenclatural code short name for each specifier that is a taxonomic unit.\n wrappedPhyloref.internalSpecifiers.forEach(specifier => {\n let wrappedSpecifier = new phyx.TaxonomicUnitWrapper(specifier);\n if (wrappedSpecifier.taxonConcept) {\n let wrappedTaxonConcept = new phyx.TaxonConceptWrapper(wrappedSpecifier.taxonConcept);\n console.log(` - Internal: ${wrappedTaxonConcept.nameComplete} (${wrappedTaxonConcept.nomenCodeDetails.shortName})`);\n } else {\n console.log(` - Internal: ${wrappedSpecifier.label}`);\n }\n });\n \n // Note that the phyloref doesn't have an `externalSpecifiers` key, but the wrapper provides it as an empty list\n // for ease of use.\n wrappedPhyloref.externalSpecifiers.forEach(specifier => {\n let wrappedSpecifier = new phyx.TaxonomicUnitWrapper(specifier);\n if (wrappedSpecifier.taxonConcept) {\n let wrappedTaxonConcept = new phyx.TaxonConceptWrapper(wrappedSpecifier.taxonConcept);\n console.log(` - External: ${wrappedTaxonConcept.nameComplete} (${wrappedTaxonConcept.nomenCodeDetails.shortName})`);\n } else {\n console.log(` - External: ${wrappedSpecifier.label}`);\n }\n });\n \n console.log();\n});\n```\n\n Alligatoridae\n - Internal: Caiman crocodilus (ICZN)\n - Internal: Alligator mississippiensis (ICZN)\n \n\n\n### Examining phylogenies\n\nPhylogenies are stored in JSON files as Newick strings, but the [PhylogenyWrapper](https://www.phyloref.org/phyx.js/class/src/wrappers/PhylogenyWrapper.js~PhylogenyWrapper.html) can be used to look at internal and terminal node labels and to translate the Newick string into a JSON structure for use by downstream programs.\n\n\n```javascript\nvar phylogeny = alligatoridae_brochu2003.phylogenies[0];\nconsole.log(`The phylogeny is represented by the Newick string: ${phylogeny.newick}`);\nconsole.log();\n\n// Display internal and external nodes.\nvar wrappedPhylogeny = new phyx.PhylogenyWrapper(phylogeny);\nconsole.log(`This consists of the following nodes:\\n - Internal nodes: ${wrappedPhylogeny.getNodeLabels('internal').join(', ')}`);\nconsole.log(` - Terminal nodes: ${wrappedPhylogeny.getNodeLabels('terminal').join(', ')}`);\nconsole.log();\n\n// Convert the Newick string into a JSON structure for examination.\nconsole.log(`Newick string as a JSON structure: ${JSON.stringify(phyx.PhylogenyWrapper.getParsedNewick(phylogeny.newick), undefined, 2)}`);\nconsole.log();\n```\n\n The phylogeny is represented by the Newick string: (Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha));\n \n This consists of the following nodes:\n - Internal nodes: Alligatoridae, Alligatoroidea, Crocodylinae, Crocodylidae, Brevirostres, Crocodylia, Eusuchia, Mesoeucrocodylia, Crocodyliformes, Crocodylomorpha\n - Terminal nodes: Parasuchia, rauisuchians, Aetosauria, sphenosuchians, protosuchians, mesosuchians, Hylaeochampsa, Aegyptosuchus, Stomatosuchus, Allodaposuchus, Gavialis gangeticus, Diplocynodon ratelii, Alligator mississippiensis, Caiman crocodilus, Tomistoma schlegelii, Osteolaemus tetraspis, Crocodylus niloticus\n \n Newick string as a JSON structure: {\n \"json\": {\n \"children\": [\n {\n \"children\": [\n {\n \"label\": \"Crocodylomorpha\",\n \"children\": [\n {\n \"label\": \"Crocodyliformes\",\n \"children\": [\n {\n \"label\": \"Mesoeucrocodylia\",\n \"children\": [\n {\n \"label\": \"Eusuchia\",\n \"children\": [\n {\n \"children\": [\n {\n \"label\": \"Crocodylia\",\n \"children\": [\n {\n \"label\": \"Brevirostres\",\n \"children\": [\n {\n \"label\": \"Crocodylidae\",\n \"children\": [\n {\n \"label\": \"Crocodylinae\",\n \"children\": [\n {\n \"label\": \"Crocodylus niloticus\",\n \"name\": \"Crocodylus niloticus\"\n },\n {\n \"label\": \"Osteolaemus tetraspis\",\n \"name\": \"Osteolaemus tetraspis\"\n }\n ],\n \"name\": \"Crocodylinae\"\n },\n {\n \"label\": \"Tomistoma schlegelii\",\n \"name\": \"Tomistoma schlegelii\"\n }\n ],\n \"name\": \"Crocodylidae\"\n },\n {\n \"label\": \"Alligatoroidea\",\n \"children\": [\n {\n \"label\": \"Alligatoridae\",\n \"children\": [\n {\n \"label\": \"Caiman crocodilus\",\n \"name\": \"Caiman crocodilus\"\n },\n {\n \"label\": \"Alligator mississippiensis\",\n \"name\": \"Alligator mississippiensis\"\n }\n ],\n \"name\": \"Alligatoridae\"\n },\n {\n \"label\": \"Diplocynodon ratelii\",\n \"name\": \"Diplocynodon ratelii\"\n }\n ],\n \"name\": \"Alligatoroidea\"\n }\n ],\n \"name\": \"Brevirostres\"\n },\n {\n \"label\": \"Gavialis gangeticus\",\n \"name\": \"Gavialis gangeticus\"\n }\n ],\n \"name\": \"Crocodylia\"\n },\n {\n \"label\": \"Allodaposuchus\",\n \"name\": \"Allodaposuchus\"\n }\n ]\n },\n {\n \"label\": \"Stomatosuchus\",\n \"name\": \"Stomatosuchus\"\n },\n {\n \"label\": \"Aegyptosuchus\",\n \"name\": \"Aegyptosuchus\"\n },\n {\n \"label\": \"Hylaeochampsa\",\n \"name\": \"Hylaeochampsa\"\n }\n ],\n \"name\": \"Eusuchia\"\n },\n {\n \"label\": \"mesosuchians\",\n \"name\": \"mesosuchians\"\n }\n ],\n \"name\": \"Mesoeucrocodylia\"\n },\n {\n \"label\": \"protosuchians\",\n \"name\": \"protosuchians\"\n }\n ],\n \"name\": \"Crocodyliformes\"\n },\n {\n \"label\": \"sphenosuchians\",\n \"name\": \"sphenosuchians\"\n }\n ],\n \"name\": \"Crocodylomorpha\"\n },\n {\n \"label\": \"Aetosauria\",\n \"name\": \"Aetosauria\"\n },\n {\n \"label\": \"rauisuchians\",\n \"name\": \"rauisuchians\"\n }\n ]\n },\n {\n \"label\": \"Parasuchia\",\n \"name\": \"Parasuchia\"\n }\n ]\n }\n }\n \n\n\n### Accessing citations\n\nAnother example of a wrapper that can be used for wrapping a part of a Phyx file is the [CitationWrapper](https://www.phyloref.org/phyx.js/class/src/wrappers/CitationWrapper.js~CitationWrapper.html). This can be used to wrap citations anywhere in the Phyx file to provide a full bibliographic citation for the citation.\n\n\n```javascript\nvar wrappedPhylogenyCitation = new phyx.CitationWrapper(alligatoridae_brochu2003.phylogenies[0].source);\nconsole.log(`The source of the phylogeny in this Phyx document is: ${wrappedPhylogenyCitation.toString()}`);\n\nvar wrappedPhylorefCitation = new phyx.CitationWrapper(alligatoridae_brochu2003.phylorefs[0].definitionSource);\nconsole.log(`The definition source of the phyloreference in this Phyx document is: ${wrappedPhylorefCitation.toString()}`);\n```\n\n The source of the phylogeny in this Phyx document is: Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308\n The definition source of the phyloreference in this Phyx document is: Brochu (2003) Phylogenetic approaches toward crocodylian history. Annual Review of Earth and Planetary Sciences 31:1, 357-397. doi: 10.1146/annurev.earth.31.100901.141308\n\n\n### Converting a Phyx document into OWL\n\nA Phyx document (which is in JSON-LD format) can be converted into OWL/RDF in the form of [N-Quads](https://www.w3.org/TR/n-quads/) by using the `PhyxWrapper` to wrap the entire Phyx document. A base URL can be specified.\n\n\n```javascript\nnQuads = new phyx.PhyxWrapper(alligatoridae_brochu2003).toRDF('http://example.org/phyx-tutorial#');\nnQuads.then(nq => console.log(nq.slice(0, 2500) + '...'));\n```\n\n \"(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha));\" .\n .\n _:b165 .\n .\n _:b0 .\n .\n .\n .\n .\n .\n .\n .\n .\n _:b50 .\n {\n someNqs = nq.slice(0, 1071)\n\n var streamParser = new N3.StreamParser(),\n inputStream = Readable.from([someNqs]),\n streamWriter = new N3.StreamWriter();\n\n inputStream.pipe(streamParser);\n streamParser.pipe(streamWriter);\n streamWriter.pipe(process.stdout);\n});\n\nundefined;\n```\n\n## Navigating a Phyx document as a JSON file\n\nMost phyx.js wrappers have been designed to help interpret the more complex parts of a Phyx file, such as the phyloreferences, specifiers, phylogenies, citations and the entire Phyx document. However, since every Phyx document is also a JSON document, much of the information in the Phyx document can be accessed sufficiently easily using standard JSON libraries. In some cases, as in the demonstration below, this requires more complex code than would be necessary by using the phyx.js wrappers.\n\n\n```javascript\n// List all the phylorefs in a Phyx document.\nalligatoridae_brochu2003copy.phylorefs.forEach((phyloref, index) => {\n console.log(`- Phyloref ${index + 1}. ${phyloref.label}:`);\n (phyloref.internalSpecifiers || []).forEach(specifier => {\n console.log(` - Internal specifier: ${(specifier.hasName || {}).nameComplete}`);\n });\n (phyloref.externalSpecifiers || []).forEach(specifier => {\n console.log(` - External specifier: ${(specifier.hasName || {}).nameComplete}`);\n });\n console.log();\n});\n```\n\n \"(Parasuchia,(rauisuchians,Aetosauria,(sphenosuchians,(protosuchians,(mesosuchians,(Hylaeochampsa,Aegyptosuchus,Stomatosuchus,(Allodaposuchus,('Gavialis gangeticus',(('Diplocynodon ratelii',('Alligator mississippiensis','Caiman crocodilus')Alligatoridae)Alligatoroidea,('Tomistoma schlegelii',('Osteolaemus tetraspis','Crocodylus niloticus')Crocodylinae)Crocodylidae)Brevirostres)Crocodylia))Eusuchia)Mesoeucrocodylia)Crocodyliformes)Crocodylomorpha));\";\n ;\n _:b0_b165;\n a ;\n _:b0_b0.\n - Phyloref 1. Alligatoridae:\n - Internal specifier: Caiman crocodilus\n - Internal specifier: Alligator mississippiensis\n \n\n\n## Looking up phyloreferences on the Open Tree of Life\n\nAn included script, `resolve.js`, can be used to resolve a phyloreference on the Open Tree of Life. This can be executed from the command line by running:\n\n```bash\n$ npm run resolve test/examples/correct/brochu_2003.json\n```\n\nHowever, this script can also be invoked from within Node.js.\n\n\n```javascript\nvar child_process = require('child_process');\n\nchild = child_process.spawnSync('../bin/resolve.js', ['../test/examples/correct/brochu_2003.json'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n});\nresults = JSON.parse(child.output.join('\\n'));\n\nObject.keys(results).forEach(key => {\n console.log(`- ${key}:`);\n values = results[key];\n values.forEach(value => {\n if('status' in value) {\n resolved = value['resolved'];\n console.log(` - Resolved ${value['cladeType']} clade-type phylorefence`);\n console.log(` to: ${resolved['@id']} (label: ${resolved['label']})`);\n } else if ('error' in value) {\n console.log(` - Could not resolve: ${value['error']}`);\n } else {\n console.log(` - Unable to interpret: ${JSON.stringify(value, undefined, 2)}`);\n }\n })\n});\n```\n\n - Alligatoridae:\n - Resolved minimum phylorefence\n to: https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott195670 (label: Alligatoridae)\n - Alligatorinae:\n - Resolved maximum phylorefence\n to: https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott151255 (label: Alligatorinae)\n - Caimaninae:\n - Resolved maximum phylorefence\n to: https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott195671 (label: Caimaninae)\n - Crocodyloidea:\n - Resolved maximum phylorefence\n to: https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott335582 (label: Crocodylidae)\n - Crocodylidae:\n - Resolved minimum phylorefence\n to: https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott1092501 (label: Longirostres)\n - Diplocynodontinae:\n - Could not resolve: no_mrca_found:400\n\n\n## About this notebook\n\nThis document was created as a [Jupyter Notebook](https://jupyter.org/), and the source file is available in our GitHub repository. We recommend installing [Jupyterlab via Homebrew on Mac](https://formulae.brew.sh/formula/jupyterlab#default), but [other installation options are available](https://jupyter.org/install). Once Jupyter Notebook is set up, you should be able to open this notebook for editing by running `jupyter notebook Introduction\\ to\\ phyx.js.ipynb` from the command line.\n\nWe use [IJavascript](https://github.com/n-riesco/ijavascript) to use Javascript as a kernel in Jupyter Notebook. If you would like to edit this notebook, you will need to [install this](https://github.com/n-riesco/ijavascript#installation) as well.\n", "static": true, @@ -4422,7 +4422,7 @@ "name": "test/citations.js", "content": "/*\n * Test citations.\n */\n\n// Require phyx.js, our PHYX library, and Chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// We use Chai's Expect API.\nconst expect = chai.expect;\n\n/*\n * Citation tests check to see if the CitationWrapper works correctly.\n */\n\ndescribe('CitationWrapper', function () {\n // Some citations to use in testing.\n const citations = [{\n bibliographicCitation: 'Christopher A. Brochu (2003) Phylogenetic approaches toward crocodylian history Annual Review of Earth and Planetary Sciences 31:357--397 fig 1 doi: 10.1146/annurev.earth.31.100901.141308 URL: https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308',\n citation: {\n type: 'article',\n title: 'Phylogenetic approaches toward crocodylian history',\n authors: [\n {\n name: 'Christopher A. Brochu',\n alternate: ['Brochu, Christopher A.'],\n firstname: 'Christopher',\n middlename: 'A.',\n lastname: 'Brochu',\n },\n ],\n year: 2003,\n figure: 1,\n identifier: [\n {\n type: 'doi',\n id: '10.1146/annurev.earth.31.100901.141308',\n },\n ],\n link: [\n {\n url: 'https://www.annualreviews.org/doi/10.1146/annurev.earth.31.100901.141308',\n },\n ],\n journal: {\n name: 'Annual Review of Earth and Planetary Sciences',\n volume: '31',\n pages: '357--397',\n identifier: [{\n type: 'eISSN',\n id: '1545-4495',\n }],\n },\n },\n }];\n\n describe('given an empty citation', function () {\n const wrapper = new phyx.CitationWrapper({});\n\n describe('#constructor', function () {\n it('should return a CitationWrapper', function () {\n expect(wrapper).to.be.an.instanceOf(phyx.CitationWrapper);\n });\n });\n\n describe('#toString', function () {\n it('should return undefined', function () {\n expect(wrapper.toString()).to.be.undefined;\n });\n\n it('should be settable by changing the title', function () {\n wrapper.citation.title = 'Title';\n expect(wrapper.toString()).equals('Anonymous (n.d.) Title');\n });\n });\n });\n\n citations.forEach((test, index) => {\n describe(`for test citation #${index + 1}`, function () {\n const wrapper = new phyx.CitationWrapper(test.citation);\n\n describe('#constructor', function () {\n it('should return a CitationWrapper', function () {\n expect(wrapper).to.be.an.instanceOf(phyx.CitationWrapper);\n });\n });\n\n describe('#toString', function () {\n it('should return the expected string', function () {\n expect(wrapper.toString()).to.equal(test.bibliographicCitation);\n });\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/citations.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/citations.js", "access": null, "description": null, "lineNumber": 1 @@ -4588,7 +4588,7 @@ "name": "test/examples.js", "content": "/*\n * Test conversion on example files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\n\nconst chai = require('chai');\nconst Ajv = require('ajv');\n\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/*\n * Constants\n */\n// If REPLACE_EXISTING is set to true, we replace the existing JSON-LD and N-Quads\n// files rather than comparing them -- not a good way to test, but useful when\n// the output has changed.\nconst REPLACE_EXISTING = false;\n\n/**\n * Test whether conversion of Phyx files to an OWL ontology occurs predictably.\n */\n\ndescribe('PhyxWrapper', function () {\n const ajv = new Ajv({\n allErrors: true, // Display all error messages, not just the first.\n });\n const validator = ajv.compile(\n JSON.parse(\n fs.readFileSync(\n path.resolve(__dirname, '../docs/context/development/schema.json')\n )\n )\n );\n\n describe('Test all correct example Phyx files', function () {\n const examples = fs.readdirSync(path.resolve(__dirname, './examples/correct'))\n .filter(filename => filename.endsWith('.json'));\n\n examples.forEach((example) => {\n const basename = path.resolve(__dirname, './examples/correct', path.parse(example).name);\n const jsonFilename = `${basename}.json`;\n const jsonldFilename = `${basename}.jsonld`;\n const nqFilename = `${basename}.nq`;\n\n let json;\n let jsonld;\n let nq;\n\n describe(`Test file '${example}'`, function () {\n it('should be loadable', function () {\n json = JSON.parse(fs.readFileSync(jsonFilename));\n expect(json).to.be.an('object');\n });\n\n it('should validate against our JSON schema', function () {\n const valid = validator(json);\n expect(\n validator.errors,\n `The following validation errors were generated: ${JSON.stringify(validator.errors, null, 2)}`\n ).to.be.null;\n expect(valid).to.be.true;\n });\n\n it('should be able to convertible to an OWL Ontology', function () {\n this.timeout(10000);\n jsonld = new phyx.PhyxWrapper(json)\n .asJSONLD('http://example.org/phyx.js/example#');\n if (REPLACE_EXISTING) {\n fs.writeFileSync(\n jsonldFilename,\n JSON.stringify(jsonld, null, 2)\n );\n }\n expect(jsonld).to.be.an('object');\n });\n\n it('should generate the same OWL ontology as it generated earlier', function () {\n const expectedJSONLD = JSON.parse(fs.readFileSync(jsonldFilename));\n expect(jsonld).to.deep.equal(expectedJSONLD);\n });\n\n it('should be convertible to n-quads', function () {\n this.timeout(10000);\n\n return new phyx.PhyxWrapper(json)\n .toRDF('http://example.org/phyx.js/example#', path.resolve(__dirname, 'examples', 'correct'))\n .then((rdf) => {\n nq = rdf;\n if (REPLACE_EXISTING) fs.writeFileSync(nqFilename, nq);\n expect(nq).to.be.a('string');\n });\n });\n\n it('should generate the same n-quads ontology as it generated earlier', function () {\n const expectedNQ = fs.readFileSync(nqFilename).toString();\n expect(nq).to.deep.equal(expectedNQ);\n });\n });\n });\n });\n\n describe('Test incorrect example Phyx files that should fail validation', function () {\n const filesThatShouldFailValidation = [\n {\n fileName: 'examples/incorrect/no-context.json',\n expectedErrors: [{\n dataPath: '',\n keyword: 'required',\n message: \"should have required property '@context'\",\n params: {\n missingProperty: '@context',\n },\n schemaPath: '#/required',\n }],\n },\n {\n fileName: 'examples/incorrect/invalid-specifier.json',\n expectedErrors: [\n {\n dataPath: '.phylorefs[0].internalSpecifiers',\n keyword: 'minItems',\n message: 'should NOT have fewer than 1 items',\n params: {\n limit: 1,\n },\n schemaPath: '#/properties/phylorefs/items/properties/internalSpecifiers/minItems',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0].hasName',\n keyword: 'required',\n message: \"should have required property 'nameComplete'\",\n params: {\n missingProperty: 'nameComplete',\n },\n schemaPath: '#/required',\n },\n {\n dataPath: \".phylorefs[0].externalSpecifiers[0]['@type']\",\n keyword: 'enum',\n message: 'should be equal to one of the allowed values',\n params: {\n allowedValues: [\n 'http://rs.tdwg.org/dwc/terms/Occurrence',\n ],\n },\n schemaPath: '#/properties/%40type/enum',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0].hasName',\n keyword: 'required',\n message: \"should have required property 'nameComplete'\",\n params: {\n missingProperty: 'nameComplete',\n },\n schemaPath: '#/required',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: '@type',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/additionalProperties',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'hasName',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/additionalProperties',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'label',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/additionalProperties',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'required',\n message: \"should have required property '@id'\",\n params: {\n missingProperty: '@id',\n },\n schemaPath: '#/definitions/taxonomic_unit_by_id/required',\n },\n {\n dataPath: '.phylorefs[0].externalSpecifiers[0]',\n keyword: 'anyOf',\n message: 'should match some schema in anyOf',\n params: {},\n schemaPath: '#/anyOf',\n },\n ],\n },\n {\n fileName: 'examples/incorrect/unexpected-field-in-contributor.json',\n expectedErrors: [{\n dataPath: '.contributors[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'first_name',\n },\n schemaPath: '#/definitions/contributor/additionalProperties',\n }, {\n dataPath: '.contributors[0]',\n keyword: 'additionalProperties',\n message: 'should NOT have additional properties',\n params: {\n additionalProperty: 'last_name',\n },\n schemaPath: '#/definitions/contributor/additionalProperties',\n },\n ],\n },\n ];\n\n filesThatShouldFailValidation.forEach((entry) => {\n describe(`Example file ${entry.fileName}`, function () {\n it('should not validate against our JSON schema', function () {\n const phyxContent = JSON.parse(\n fs.readFileSync(\n path.resolve(__dirname, entry.fileName)\n )\n );\n const valid = validator(phyxContent);\n expect(validator.errors).to.deep.equal(entry.expectedErrors);\n expect(valid).to.not.be.true;\n });\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/examples.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/examples.js", "access": null, "description": null, "lineNumber": 1 @@ -4753,7 +4753,7 @@ "name": "test/jphyloref.js", "content": "/*\n * Use JPhyloRef to ensure that the expected JSON-LD files pass testing.\n * A different test, `examples.js`, will then test whether the current Phyx.js\n * produces a file identical to the expected JSON-LD files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\nconst childProcess = require('child_process');\n\nconst Downloader = require('nodejs-file-downloader');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Constants\n */\n// The version of JPhyloRef to download.\nconst JPHYLOREF_VERSION = '1.1.1';\n\n// The URL from where JPhyloRef should be downloaded.\nconst JPHYLOREF_URL = `https://repo.maven.apache.org/maven2/org/phyloref/jphyloref/${JPHYLOREF_VERSION}/jphyloref-${JPHYLOREF_VERSION}.jar`;\n// Where should the JPhyloRef be stored?\nconst JPHYLOREF_PATH = path.resolve(__dirname, `jphyloref-${JPHYLOREF_VERSION}.jar`);\n\n/**\n * Test whether the expected JSON-LD files pass testing using JPhyloRef.\n */\n\ndescribe('JPhyloRef', function () {\n describe('download JPhyloRef', function () {\n // TODO: we should eventually use SHA to ensure that we have the expected file.\n if (\n fs.existsSync(JPHYLOREF_PATH)\n && fs.statSync(JPHYLOREF_PATH).size > 0\n ) {\n it('has already been downloaded', function () {\n expect(true);\n });\n } else {\n it('should be downloadable', function () {\n this.timeout(10000);\n // Download JPhyloRef from Maven and save it to JPHYLOREF_PATH.\n return new Downloader({\n url: JPHYLOREF_URL,\n directory: path.dirname(JPHYLOREF_PATH),\n fileName: path.basename(JPHYLOREF_PATH),\n }).download();\n });\n }\n });\n\n describe('test example JSON-LD files using JPhyloRef', function () {\n fs.readdirSync(path.resolve(__dirname, 'examples', 'correct'))\n .filter(filename => filename.endsWith('.nq'))\n .forEach((filename) => {\n it(`testing ${filename}`, function () {\n this.timeout(60000);\n\n // Start JPhyloRef to test filename.\n const filePath = path.resolve(__dirname, 'examples', 'correct', filename);\n const child = childProcess.spawnSync(\n 'java',\n [\n '-jar', JPHYLOREF_PATH,\n 'test', filePath,\n ],\n {\n encoding: 'utf8',\n shell: true,\n }\n );\n const matches = /Testing complete:(\\d+) successes, (\\d+) failures, (\\d+) failures marked TODO, (\\d+) skipped./.exec(child.stderr);\n\n expect(matches, `Test result line not found in STDERR <${child.stderr}>`).to.have.lengthOf(5);\n\n // const countSuccess = Number(matches[1]);\n const countFailure = Number(matches[2]);\n const countTODOs = Number(matches[3]);\n // const countSkipped = Number(matches[4]);\n\n // We can't test for one or more successes since some example Phyx file\n // such as apomorphy-based phyloreferences don't have any successes at all.\n // expect(countSuccess, 'Expected one or more successes').to.be.greaterThan(0);\n expect(countFailure, 'Expected zero failures').to.equal(0);\n expect(countTODOs, 'Expected zero TODOs').to.equal(0);\n\n // An exit code of 0 means success. An exit code of 255 means that while\n // there were no successes, there were also no failures. Either is acceptable here.\n expect(child.status).to.be.oneOf([0, 255]);\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/jphyloref.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/jphyloref.js", "access": null, "description": null, "lineNumber": 1 @@ -4841,7 +4841,7 @@ "name": "test/nomenclatural-codes.js", "content": "/*\n * Test nomenclatural code lookups and fallback behavior. While most of the\n * nomenclatural code logic is in TaxonNameWrapper, we need to provide fallback\n * nomenclatural codes in TaxonConceptWrapper, TaxonomicUnitWrapper and\n * PhylorefWrapper as well. This test file makes sure that this functionality\n * works correctly at all of these levels.\n */\n\nconst fs = require('fs');\nconst path = require('path');\n\nconst { cloneDeep } = require('lodash');\n\nconst chai = require('chai');\nconst phyx = require('../src');\nconst owlterms = require('../src/utils/owlterms');\n\n// Use Chai's expect API.\nconst expect = chai.expect;\n\n/* The list of expected fields in nomenclatural details. */\nconst EXPECTED_NOMEN_DETAIL_FIELDS = ['iri', 'shortName', 'label', 'title'];\n\n/* Some example taxon names to use. */\nconst ranaLuteiventris = {\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n hasName: {\n label: 'Rana luteiventris',\n },\n occurrenceID: 'MVZ 225749',\n};\n\n/*\n * The nomenclatural codes are set up in TaxonNameWrapper, so that's where\n * most of the nomenclatural code behavior code exists.\n */\ndescribe('TaxonNameWrapper', function () {\n describe('#getNomenclaturalCodes', function () {\n it('should provide a non-empty list with the expected keys', function () {\n const nomenCodes = phyx.TaxonNameWrapper.getNomenclaturalCodes();\n\n expect(nomenCodes)\n .to.be.an('array')\n .that.is.not.empty;\n\n nomenCodes.forEach((nomenCode) => {\n expect(nomenCode).to.have.all.keys(EXPECTED_NOMEN_DETAIL_FIELDS);\n });\n });\n });\n\n describe('#getNomenCodeDetails', function () {\n it('should provide details for some built-in codes', function () {\n const codesToTest = {\n 'Code not known': owlterms.UNKNOWN_CODE,\n ICZN: owlterms.ICZN_CODE,\n ICN: owlterms.ICN_CODE,\n ICNP: owlterms.ICNP_CODE,\n ICTV: owlterms.ICTV_CODE,\n ICNCP: owlterms.ICNCP_CODE,\n };\n\n Object.keys(codesToTest).forEach((code) => {\n const uri = codesToTest[code];\n const details = phyx.TaxonNameWrapper.getNomenCodeDetails(uri);\n expect(details).to.have.all.keys(EXPECTED_NOMEN_DETAIL_FIELDS);\n expect(details.shortName).to.equal(code);\n });\n });\n });\n\n describe('#nomenclaturalCodeDetails', function () {\n it('should provide nomenclatural code details for an example taxon name', function () {\n const wrapper = new phyx.TaxonNameWrapper(ranaLuteiventris.hasName);\n expect(wrapper.nomenclaturalCode).to.equal(owlterms.UNKNOWN_CODE);\n expect(wrapper.nomenclaturalCodeDetails.shortName).to.equal('Code not known');\n\n const wrapperWithDefault = new phyx.TaxonNameWrapper(\n ranaLuteiventris.hasName,\n owlterms.ICZN_CODE\n );\n expect(wrapperWithDefault.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n expect(wrapperWithDefault.nomenclaturalCodeDetails.shortName).to.equal('ICZN');\n\n const nameWithNomenCode = cloneDeep(ranaLuteiventris.hasName);\n nameWithNomenCode.nomenclaturalCode = owlterms.ICZN_CODE;\n const wrapperWithExplicit = new phyx.TaxonNameWrapper(nameWithNomenCode, owlterms.ICN_CODE);\n expect(wrapperWithExplicit.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n expect(wrapperWithExplicit.nomenclaturalCodeDetails.shortName).to.equal('ICZN');\n });\n });\n});\n\n/*\n * Make sure we can set a default nomenclatural code in TaxonConceptWrapper.\n */\ndescribe('TaxonConceptWrapper', function () {\n describe('#nomenCode', function () {\n const wrapper = new phyx.TaxonConceptWrapper(ranaLuteiventris);\n\n it('should return UNKNOWN_CODE if one is not set', function () {\n expect(wrapper.nomenCode).to.equal(owlterms.UNKNOWN_CODE);\n });\n\n it('should return the default nomenclatural code if one is provided', function () {\n const wrapperWithDefault = new phyx.TaxonConceptWrapper(ranaLuteiventris, owlterms.ICZN_CODE);\n expect(wrapperWithDefault.nomenCode).to.equal(owlterms.ICZN_CODE);\n expect(wrapperWithDefault.nomenCodeDetails.shortName).to.equal('ICZN');\n });\n });\n});\n\n/*\n * There are two ways in which nomenclatural codes can be set at the Phyx level:\n * (1) If there is a `defaultNomenclaturalCodeIRI` field at the Phyx level,\n * that will be used to provide a nomenclatural code for all specifiers\n * without a nomenclatural code as well as for all the phylogeny nodes.\n * (2) If no `defaultNomenclaturalCodeIRI` is provided, but all the specifiers\n * on all the phylorefs in the file have the same nomenclatural code, then\n * that code will be used on all the phylogeny nodes.\n */\ndescribe('PhyxWrapper', function () {\n it('should use the defaultNomenclaturalCodeIRI for phylogeny nodes', function () {\n // The examples/correct/alligatoridae_default_nomen_code.json file has\n // a `defaultNomenclaturalCodeIRI`.\n const json = JSON.parse(fs.readFileSync(\n path.resolve(__dirname, './examples/correct/alligatoridae_default_nomen_code.json')\n ));\n\n // Make sure this is the right example file.\n expect(json, 'Expected alligatoridae_default_nomen_code.json to include a defaultNomenclaturalCodeIRI value.')\n .to.include.key('defaultNomenclaturalCodeIRI');\n const defaultNomenclaturalCodeIRI = json.defaultNomenclaturalCodeIRI;\n\n const jsonld = new phyx.PhyxWrapper(json).asJSONLD();\n\n // Step 1. Check the phyloreferences. Neither specifier has a nomenclatural code,\n // but they should pick up the default nomenclatural code for the Phyx file.\n expect(jsonld.phylorefs).to.be.an('array').of.length(1);\n const phyloref1 = jsonld.phylorefs[0];\n expect(phyloref1).to.be.an('object').and.to.include.key('equivalentClass');\n\n const equivalentClass = phyloref1.equivalentClass;\n const specifierExprs = equivalentClass.someValuesFrom.intersectionOf;\n expect(specifierExprs).to.be.an('array').with.length(2);\n\n specifierExprs.forEach((specifierExpr) => {\n const nameExprs = specifierExpr.someValuesFrom.someValuesFrom.intersectionOf;\n\n expect(nameExprs).to.be.an('array').with.length(2).and.to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': defaultNomenclaturalCodeIRI,\n },\n }\n );\n });\n\n // Step 2. Check the phylogenies.\n expect(jsonld).to.include.key('phylogenies');\n expect(jsonld.phylogenies).to.be.an('array').with.length(1);\n\n const phylogeny1 = jsonld.phylogenies[0];\n expect(phylogeny1).to.include.key('nodes');\n\n phylogeny1.nodes.forEach((node) => {\n const nodeType = node['rdf:type'];\n\n // There should be at least one type definition: obo:CDAO_0000140.\n expect(nodeType[0]).to.deep.equal({\n '@id': 'obo:CDAO_0000140',\n });\n\n // The second type definition -- if it exists -- must be a name entry,\n // which should include the appropriate nomenclatural code.\n if (nodeType.length > 1) {\n const nameEntry = nodeType[1];\n expect(nameEntry.someValuesFrom.someValuesFrom.intersectionOf).to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': defaultNomenclaturalCodeIRI,\n },\n }\n );\n }\n });\n });\n\n it('should use the inferred nomenclatural code for phylogeny nodes', function () {\n // The examples/correct/alligatoridae_inferred_nomen_code.json file does not have\n // a `defaultNomenclaturalCodeIRI`, but the nomenclatural code can be inferred from\n // its specifiers.\n const json = JSON.parse(fs.readFileSync(\n path.resolve(__dirname, './examples/correct/alligatoridae_inferred_nomen_code.json')\n ));\n\n // Make sure this is the right example file.\n expect(json, 'Expected alligatoridae_inferred_nomen_code.json to not include a defaultNomenclaturalCodeIRI value.')\n .to.not.include.key('defaultNomenclaturalCodeIRI');\n\n const wrapped = new phyx.PhyxWrapper(json);\n const inferredNomenCode = wrapped.defaultNomenCode;\n expect(inferredNomenCode).to.equal(owlterms.ICZN_CODE);\n\n const jsonld = wrapped.asJSONLD();\n\n // Step 1. Check the phyloreferences. Since only *Caiman crocodilus* has a\n // nomenclatural code set, we should make sure that the other specifier\n // picks up the inferred nomenclatural code of the entire file.\n expect(jsonld.phylorefs).to.be.an('array').of.length(1);\n const phyloref1 = jsonld.phylorefs[0];\n expect(phyloref1).to.be.an('object').and.to.include.key('equivalentClass');\n\n const equivalentClass = phyloref1.equivalentClass;\n const specifierExprs = equivalentClass.someValuesFrom.intersectionOf;\n expect(specifierExprs).to.be.an('array').with.length(2);\n\n specifierExprs.forEach((specifierExpr) => {\n const nameExprs = specifierExpr.someValuesFrom.someValuesFrom.intersectionOf;\n\n expect(nameExprs).to.be.an('array').with.length(2).and.to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': inferredNomenCode,\n },\n }\n );\n });\n\n // Step 2. Check the phylogenies.\n expect(jsonld).to.include.key('phylogenies');\n expect(jsonld.phylogenies).to.be.an('array').with.length(1);\n\n const phylogeny1 = jsonld.phylogenies[0];\n expect(phylogeny1).to.include.key('nodes');\n\n phylogeny1.nodes.forEach((node) => {\n const nodeType = node['rdf:type'];\n\n // There should be at least one type definition: obo:CDAO_0000140.\n expect(nodeType[0]).to.deep.equal({\n '@id': 'obo:CDAO_0000140',\n });\n\n // The second type definition -- if it exists -- must be a name entry,\n // which should include the appropriate nomenclatural code.\n if (nodeType.length > 1) {\n const nameEntry = nodeType[1];\n expect(nameEntry.someValuesFrom.someValuesFrom.intersectionOf).to.deep.include(\n {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nomenclaturalCode',\n hasValue: {\n '@id': inferredNomenCode,\n },\n }\n );\n }\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/nomenclatural-codes.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/nomenclatural-codes.js", "access": null, "description": null, "lineNumber": 1 @@ -5034,7 +5034,7 @@ "name": "test/normalization.js", "content": "/*\n * Test normalization on examples/correct/normalization files.\n */\n\nconst fs = require('fs');\nconst path = require('path');\n\nconst chai = require('chai');\n\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/**\n * When making the comparisons, we need to remove the `@id`s which would otherwise be different\n * between the phylorefs being compared.\n *\n * @param phyloref The phyloref whose '@id' needs to be removed.\n */\nfunction removeId(phyloref) {\n // Shallow copy the phyloref.\n const copiedPhyloref = Object.assign({}, phyloref);\n // Delete the '@id'.\n delete copiedPhyloref['@id'];\n return copiedPhyloref;\n}\n\n\n/**\n * Test whether normalization of phyloreferences and phylogenies work as expected.\n * This test does not cover Phyx normalization.\n */\n\ndescribe('Phyloref and phylogeny normalization', function () {\n describe('Test all normalization Phyx files', function () {\n /*\n * Normalization Phyx files consist of a number of phyloreferences and phylogenies. We can\n * test them by confirming:\n * - every phyloref or phylogeny should be DIFFERENT from every other.\n * - every phyloref or phylogeny whose `@id` ends with `_same` should be IDENTICAL to\n * every other phyloref or phylogeny whose `@id` ends with `_same` after NORMALIZATION (to\n * test non-same phyloref or phylogeny files, they should be placed in different files).\n * - every phyloref or phylogeny whose `@id` ends with `_different` should be DIFFERENT to\n * every phyloref or phylogeny whose `@id` ends with `_same` even after NORMALIZATION.\n */\n const normalizationExamples = fs\n .readdirSync(path.resolve(__dirname, './examples/correct/normalization'))\n .filter(filename => filename.endsWith('.json'));\n\n normalizationExamples.forEach((example) => {\n const basename = path.resolve(__dirname, './examples/correct/normalization', path.parse(example).name);\n const jsonFilename = `${basename}.json`;\n\n describe(`Normalization test file '${example}'`, function () {\n const phyxDoc = JSON.parse(fs.readFileSync(jsonFilename));\n const phylorefs = phyxDoc.phylorefs || [];\n const samePhylorefs = phylorefs.filter(p => (p['@id'] || '').endsWith('_same'));\n const differentPhylorefs = phylorefs.filter(p => (p['@id'] || '').endsWith('_different'));\n\n // We don't need phylogeny normalization yet, so there's no point in testing them.\n describe('Test phylogenies', function () {\n it(\"These tests have not yet been implemented since we don't have an urgent need for them.\");\n });\n\n // So we only focus on phyloreference normalization.\n describe('Test phyloreferences', function () {\n it('should have multiple same phyloreferences for testing', function () {\n expect(samePhylorefs).to.not.be.empty;\n });\n\n it('should not have any duplicate phylorefs (which would be pointless)', function () {\n // No two phyloreferences in a normalization file should be deeply identical to each\n // other, otherwise the test will be pointless.\n phylorefs.forEach((phyloref1) => {\n phylorefs.forEach((phyloref2) => {\n if (phyloref1 === phyloref2) return;\n expect(removeId(phyloref1))\n .to\n .not\n .deep\n .equal(removeId(phyloref2),\n 'No two phyloreferences in a single normalization file should be identical.');\n });\n });\n });\n\n it('should have pairs of `_same` phylorefs that are different, but are identical after normalization', function () {\n // Every pair of `_same` phyloreferences should be different.\n samePhylorefs.forEach((phyloref1) => {\n samePhylorefs.forEach((phyloref2) => {\n if (phyloref1 === phyloref2) return;\n expect(\n removeId(phyx.PhylorefWrapper.normalize(phyloref1))\n )\n .to\n .deep\n .equal(\n removeId(phyx.PhylorefWrapper.normalize(phyloref2)),\n `Expected phyloref ${phyloref1['@id']} to deeply equal ${phyloref2['@id']} `\n + 'after normalization'\n );\n });\n });\n });\n\n it('should have pairs of `_different` phylorefs that are different before and after normalization', function () {\n // Every pair of `_different` phyloreferences should be different from every `_same`\n // phyloreference, even after normalization.\n differentPhylorefs.forEach((phyloref1) => {\n samePhylorefs.forEach((phyloref2) => {\n if (phyloref1 === phyloref2) return;\n expect(\n removeId(phyx.PhylorefWrapper.normalize(phyloref1))\n )\n .to\n .not\n .deep\n .equal(\n removeId(phyx.PhylorefWrapper.normalize(phyloref2)),\n `Expected phyloref ${phyloref1['@id']} to not deeply equal ${phyloref2['@id']} `\n + 'after normalization'\n );\n });\n });\n });\n });\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/normalization.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/normalization.js", "access": null, "description": null, "lineNumber": 1 @@ -5174,7 +5174,7 @@ "name": "test/phylogenies.js", "content": "/*\n * Test phylogenies.\n */\n\n// Load phyx.js, our PHYX library, and chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Make it easier to access owlterms.\nconst owlterms = require('../src/utils/owlterms');\n\n// Use Chai's expect API for testing.\nconst expect = chai.expect;\n\n/*\n * These tests focus on three aspects of PhylogenyWrapper:\n * - Whether it can detect errors in an input Newick string.\n * - Retrieve taxonomic units from the phylogeny based on either their node label\n * or on the additional properties associated with the phylogeny.\n * - Whether we can match specifiers with nodes on the phylogeny if they share\n * taxonomic units that match.\n */\n\ndescribe('PhylogenyWrapper', function () {\n describe('#constructor', function () {\n describe('when used to wrap an empty object', function () {\n it('should return a PhylogenyWrapper object', function () {\n expect(new phyx.PhylogenyWrapper({}))\n .to.be.an.instanceOf(phyx.PhylogenyWrapper);\n });\n });\n });\n\n describe('#getErrorsInNewickString', function () {\n describe('when given a correct Newick string', function () {\n const correctNewickStrings = [\n '(A:3, B:5, (C:6, N:7));',\n ];\n\n it('should return an empty list of errors', function () {\n correctNewickStrings.forEach((str) => {\n expect(phyx.PhylogenyWrapper.getErrorsInNewickString(str)).to.be.empty;\n });\n });\n });\n\n describe('when given an empty Newick string', function () {\n const emptyNewickStrings = [\n '()',\n '(); ',\n ];\n\n it('should return a single \"No phylogeny entered\" error', function () {\n emptyNewickStrings.forEach((newick) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(newick);\n expect(errors).to.have.length(1);\n expect(errors[0].title).to.equal('No phylogeny entered');\n });\n });\n });\n\n describe('when given an unbalanced Newick string', function () {\n const unbalancedNewickString = [\n {\n newick: '(A, B))',\n expected: 'You have 1 too few open parentheses',\n },\n {\n newick: '(A, (B, (C, D))',\n expected: 'You have 1 too many open parentheses',\n },\n {\n newick: '(A, (B, (C, (((D))',\n expected: 'You have 4 too many open parentheses',\n },\n ];\n\n it('should report how many parentheses are missing', function () {\n unbalancedNewickString.forEach((entry) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(entry.newick);\n\n // We should get two errors.\n expect(errors).to.have.lengthOf(2);\n\n // Should include an error about the unbalanced parentheses.\n expect(errors[0].title).to.equal('Unbalanced parentheses in Newick string');\n expect(errors[0].message).to.equal(entry.expected);\n\n // Should include an error passed on from the Newick parser.\n expect(errors[1].title).to.equal('Error parsing phylogeny');\n expect(errors[1].message).to.include('An error occured while parsing this phylogeny:');\n });\n });\n });\n\n describe('when given an incomplete Newick string', function () {\n const incompleteNewickStrings = [\n ';',\n '))(A, (B, ',\n ];\n\n it('should report an error parsing the phylogeny', function () {\n incompleteNewickStrings.forEach((newick) => {\n const errors = phyx.PhylogenyWrapper.getErrorsInNewickString(newick);\n\n expect(errors).to.have.lengthOf(1);\n expect(errors[0].title).to.equal('Error parsing phylogeny');\n expect(errors[0].message).to.include('An error occured while parsing this phylogeny:');\n });\n });\n });\n });\n\n describe('#getNodeLabels', function () {\n const tests = [\n {\n // Note that 'newick' is the input for this test.\n newick: '(A, (B, (C, D))E, F, (G, (H, I, J)K, L)M, N)O',\n // The following keys indicate the expected all/internal/terminal node labels\n // for the given Newick string.\n nodeLabels: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O'],\n internalNodeLabels: ['E', 'K', 'M', 'O'],\n terminalNodeLabels: ['A', 'B', 'C', 'D', 'F', 'G', 'H', 'I', 'J', 'L', 'N'],\n },\n ];\n\n tests.forEach((test) => {\n const wrapper = new phyx.PhylogenyWrapper({ newick: test.newick });\n\n describe('For a particular Newick phylogeny', function () {\n it('should return a list of all node labels by default', function () {\n expect(wrapper.getNodeLabels().sort())\n .to.have.members(test.nodeLabels.sort());\n });\n\n it('should return a list of internal labels when asked for internal labels', function () {\n expect(wrapper.getNodeLabels('internal').sort())\n .to.have.members(test.internalNodeLabels.sort());\n });\n\n it('should return a list of terminal labels when asked for terminal labels', function () {\n expect(wrapper.getNodeLabels('terminal').sort())\n .to.have.members(test.terminalNodeLabels.sort());\n });\n });\n });\n });\n\n describe('given a particular phylogeny with additional node properties', function () {\n const wrapper = new phyx.PhylogenyWrapper({\n newick: '((MVZ225749, MVZ191016), Rana boylii)',\n additionalNodeProperties: {\n MVZ225749: {\n representsTaxonomicUnits: [{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:225749',\n }],\n },\n MVZ191016: {\n representsTaxonomicUnits: [{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:191016',\n }],\n },\n },\n });\n\n describe('#getNodeLabels', function () {\n it('should return the list of node labels from the Newick string', function () {\n expect(wrapper.getNodeLabels().sort())\n .to.have.members([\n 'MVZ191016',\n 'MVZ225749',\n 'Rana boylii',\n ]);\n });\n });\n\n describe('#getTaxonomicUnitsForNodeLabel', function () {\n it('should return the list of taxonomic units using information from additional node properties', function () {\n expect(wrapper.getTaxonomicUnitsForNodeLabel('MVZ191016')).to.deep.equal([{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:191016',\n }]);\n\n expect(wrapper.getTaxonomicUnitsForNodeLabel('MVZ225749')).to.deep.equal([{\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ:225749',\n }]);\n\n expect(wrapper.getTaxonomicUnitsForNodeLabel('Rana boylii')).to.deep.equal([{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n label: 'Rana boylii',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana boylii',\n nameComplete: 'Rana boylii',\n genusPart: 'Rana',\n specificEpithet: 'boylii',\n },\n }]);\n });\n });\n\n describe('#getNodeLabelsMatchedBySpecifier', function () {\n it('should match a specifier to MVZ225749 based on occurrence ID', function () {\n const specifier1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:225749',\n };\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier1))\n .to.have.members(['MVZ225749']);\n });\n\n it('should match a specifier to MVZ191016 based on occurrence ID', function () {\n const specifier2 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:191016',\n };\n\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier2))\n .to.have.members(['MVZ191016']);\n });\n\n it('should match a specifier to node \"Rana boylii\" based on the parsed scientific name', function () {\n const specifier3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana boylii',\n };\n\n expect(wrapper.getNodeLabelsMatchedBySpecifier(specifier3))\n .to.have.members(['Rana boylii']);\n });\n });\n });\n\n describe('#asJSONLD', function () {\n it('should preserve an existing @id on input phylogenies', function () {\n const jsonld = new phyx.PhylogenyWrapper({\n '@id': '#providedId',\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n }).asJSONLD('#phylogeny0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#providedId');\n });\n it('should generate a new @id on input phylorefs', function () {\n const jsonld = new phyx.PhylogenyWrapper({\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n }, owlterms.ICZN_CODE).asJSONLD('#phylogeny0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#phylogeny0');\n });\n it('should generate the phylogeny in JSON-LD as expected', function () {\n const expectedResults = [\n {\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n jsonld: {\n '@id': '#',\n '@type': 'phyloref:ReferencePhylogenyEvidence',\n hasRootNode: { '@id': '#_node0' },\n newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',\n nodes: [\n {\n '@id': '#_node0',\n children: ['#_node1', '#_node2'],\n 'rdf:type': [{ '@id': owlterms.CDAO_NODE }],\n },\n {\n '@id': '#_node1',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Mus musculus',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Mus_musculus'],\n parent: '#_node0',\n representsTaxonomicUnits: [{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Mus',\n label: 'Mus_musculus',\n nameComplete: 'Mus musculus',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'musculus',\n },\n label: 'Mus_musculus',\n }],\n siblings: ['#_node2'],\n },\n {\n '@id': '#_node2',\n children: ['#_node3', '#_node4'],\n 'rdf:type': [{ '@id': owlterms.CDAO_NODE }],\n parent: '#_node0',\n siblings: ['#_node1'],\n },\n {\n '@id': '#_node3',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Panthera tigris',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Panthera_tigris'],\n parent: '#_node2',\n representsTaxonomicUnits: [{\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Panthera',\n label: 'Panthera_tigris',\n nameComplete: 'Panthera tigris',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'tigris',\n },\n label: 'Panthera_tigris',\n }],\n siblings: ['#_node4'],\n },\n {\n '@id': '#_node4',\n 'rdf:type': [\n { '@id': owlterms.CDAO_NODE },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_REPRESENTS_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Homo sapiens',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n labels: ['Homo_sapiens'],\n parent: '#_node2',\n representsTaxonomicUnits: [\n {\n '@type': owlterms.TDWG_VOC_TAXON_CONCEPT,\n hasName: {\n '@type': owlterms.TDWG_VOC_TAXON_NAME,\n genusPart: 'Homo',\n label: 'Homo_sapiens',\n nameComplete: 'Homo sapiens',\n nomenclaturalCode: owlterms.ICZN_CODE,\n specificEpithet: 'sapiens',\n },\n label: 'Homo_sapiens',\n },\n ],\n siblings: ['#_node3'],\n },\n ],\n },\n },\n ];\n\n expectedResults.forEach((expected) => {\n const wrapper = new phyx.PhylogenyWrapper({\n '@id': '#',\n newick: expected.newick,\n }, owlterms.ICZN_CODE);\n expect(wrapper.asJSONLD('#phylogeny0')).to.deep.equal(expected.jsonld);\n });\n });\n });\n\n describe('#getParsedNewickWithIRIs', function () {\n const tests = [\n {\n newick: '(((A, B)C, D)E, F)G',\n result: {\n json: {\n '@id': '_node0',\n name: 'G',\n label: 'G',\n children: [\n { '@id': '_node1', name: 'F', label: 'F' },\n {\n '@id': '_node2',\n name: 'E',\n label: 'E',\n children: [\n { '@id': '_node3', name: 'D', label: 'D' },\n {\n '@id': '_node4',\n name: 'C',\n label: 'C',\n children: [\n { '@id': '_node5', name: 'B', label: 'B' },\n { '@id': '_node6', name: 'A', label: 'A' },\n ],\n },\n ],\n },\n ],\n },\n },\n },\n ];\n\n tests.forEach((test) => {\n it('should be able to parse a provided Newick string as expected', function () {\n expect(new phyx.PhylogenyWrapper({ newick: test.newick }).getParsedNewickWithIRIs(''))\n .to.deep.equal(test.result);\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/phylogenies.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/phylogenies.js", "access": null, "description": null, "lineNumber": 1 @@ -5614,7 +5614,7 @@ "name": "test/phylorefs.js", "content": "/*\n * Test phyloreferences.\n */\n\n// Require phyx.js, our PHYX library, and Chai for testing.\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Use owlterms so we don't have to repeat OWL terms.\nconst owlterms = require('../src/utils/owlterms');\n\n// We use Chai's Expect API.\nconst expect = chai.expect;\n\n/*\n * Phyloref tests cover three aspects of phyloreferences:\n * - Whether we can create a phyloref with a particular set of specifiers,\n * and whether we can correctly change the type of a specifer (from 'External'\n * to 'Internal'), delete specifiers, and retrieve specifier labels.\n * - Whether we can determine to which node a phyloref is expected to resolve to\n * by using additionalNodeProperties.\n * - Whether we can update the phyloref's status several times and retrieve the\n * full history of its status changes.\n */\n\ndescribe('PhylorefWrapper', function () {\n // Some specifiers to use in testing.\n const specifier1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:225749',\n };\n const specifier2 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ:191016',\n };\n const specifier3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n '@type': phyx.TaxonNameWrapper.TYPE_TAXON_NAME,\n nomenclaturalCode: owlterms.ICZN_CODE,\n nameComplete: 'Rana boylii',\n },\n };\n const specifier4 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n '@type': phyx.TaxonNameWrapper.TYPE_TAXON_NAME,\n nomenclaturalCode: owlterms.ICN_CODE,\n nameComplete: 'Mangifera indica',\n },\n };\n\n describe('given an empty phyloreference', function () {\n const wrapper = new phyx.PhylorefWrapper({});\n\n describe('#constructor', function () {\n it('should return a PhylorefWrapper', function () {\n expect(wrapper).to.be.an.instanceOf(phyx.PhylorefWrapper);\n });\n });\n\n describe('#label', function () {\n it('should return undefined', function () {\n expect(wrapper.label).to.be.undefined;\n });\n\n it('should be settable by assigning to .label', function () {\n wrapper.label = 'phyloref1';\n expect(wrapper.label).equals('phyloref1');\n });\n });\n\n describe('#specifiers', function () {\n it('should initially return an empty list', function () {\n expect(wrapper.specifiers).to.be.empty;\n });\n\n it('should initially return a nomenclatural code of unknown', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.UNKNOWN_CODE);\n });\n\n describe('when a new external specifier is added using .externalSpecifiers', function () {\n it('should return a list with the new specifier', function () {\n wrapper.externalSpecifiers.push(specifier3);\n expect(wrapper.specifiers).to.deep.equal([specifier3]);\n });\n\n it('should return a nomenclatural code of ICZN', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.ICZN_CODE);\n });\n });\n\n describe('when a new external specifier is added using .externalSpecifiers', function () {\n it('should return a list with the new specifier', function () {\n wrapper.externalSpecifiers.push(specifier2);\n expect(wrapper.specifiers).to.deep.equal([specifier3, specifier2]);\n });\n\n it('should return two nomenclatural codes, one for each specifier', function () {\n expect(wrapper.uniqNomenCodes).to.have.lengthOf(2);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.ICZN_CODE);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.UNKNOWN_CODE);\n });\n\n it('should still return a nomenclatural code of ICZN', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.ICZN_CODE);\n });\n });\n\n describe('when a new internal specifier is added using .internalSpecifiers', function () {\n it('should return a list with the new specifier', function () {\n wrapper.internalSpecifiers.push(specifier4);\n expect(wrapper.specifiers).to.deep.equal([specifier4, specifier3, specifier2]);\n });\n\n it('should return three nomenclatural codes, one for each specifier', function () {\n expect(wrapper.uniqNomenCodes).to.have.lengthOf(3);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.ICZN_CODE);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.UNKNOWN_CODE);\n expect(wrapper.uniqNomenCodes).to.include(owlterms.ICN_CODE);\n });\n\n it('should change to a default nomenclatural code of owlterms.UNKNOWN_CODE', function () {\n expect(wrapper.defaultNomenCode).to.equal(owlterms.UNKNOWN_CODE);\n });\n });\n\n describe('when specifiers are deleted using .deleteSpecifier', function () {\n it('should return the updated list', function () {\n // Delete an external specifier.\n wrapper.deleteSpecifier(specifier2);\n // Delete an internal specifier.\n wrapper.deleteSpecifier(specifier4);\n\n // Only the first specifier should be left.\n expect(wrapper.specifiers).to.deep.equal([specifier3]);\n });\n });\n\n describe('when a specifier is added using .externalSpecifiers', function () {\n it('should return the updated list', function () {\n wrapper.externalSpecifiers.push(specifier1);\n expect(wrapper.specifiers).to.deep.equal([specifier3, specifier1]);\n });\n });\n\n describe('when a specifier is changed to an internal specifier using .setSpecifierType', function () {\n it('should remain in the list of specifiers', function () {\n wrapper.setSpecifierType(specifier1, 'Internal');\n expect(wrapper.specifiers).to.deep.equal([specifier1, specifier3]);\n });\n });\n\n describe('when a specifier is added using .internalSpecifiers', function () {\n it('should be included in the list of all specifiers', function () {\n wrapper.internalSpecifiers.push(specifier2);\n expect(wrapper.specifiers).to.deep.equal([specifier1, specifier2, specifier3]);\n });\n });\n });\n\n describe('#getSpecifierType', function () {\n it('should return the correct specifier type for each specifier', function () {\n expect(wrapper.getSpecifierType(specifier1)).to.equal('Internal');\n expect(wrapper.getSpecifierType(specifier2)).to.equal('Internal');\n expect(wrapper.getSpecifierType(specifier3)).to.equal('External');\n });\n });\n\n describe('#getSpecifierLabel as TaxonomicUnitWrapper', function () {\n it('should return the correct label for each specifier', function () {\n expect((new phyx.TaxonomicUnitWrapper(specifier1)).label).to.equal('Specimen MVZ:225749');\n expect((new phyx.TaxonomicUnitWrapper(specifier2)).label).to.equal('Specimen MVZ:191016');\n expect((new phyx.TaxonomicUnitWrapper(specifier3)).label).to.equal('Rana boylii');\n });\n });\n });\n\n describe('given a particular phylogeny', function () {\n // Some phylogenies to use in testing.\n const phylogeny1 = {\n newick: '((MVZ225749, MVZ191016)Test, \"Rana boylii\")',\n additionalNodeProperties: {\n Test: {\n expectedPhyloreferenceNamed: 'phyloref1',\n },\n },\n };\n\n describe('#getExpectedNodeLabels', function () {\n it('should be able to determine expected node labels for a phylogeny', function () {\n const phyloref1 = new phyx.PhylorefWrapper({\n label: 'phyloref1',\n internalSpecifiers: [specifier1, specifier2],\n externalSpecifiers: [specifier3],\n });\n\n expect(phyloref1.getExpectedNodeLabels(phylogeny1))\n .to.deep.equal(['Test']);\n });\n });\n });\n\n describe('given an empty phyloreference', function () {\n const wrapper = new phyx.PhylorefWrapper({});\n\n describe('#getCurrentStatus', function () {\n it('should return \"pso:draft\" as the default initial status', function () {\n // Initially, an empty phyloref should report a status of 'pso:draft'.\n expect(wrapper.getCurrentStatus().statusCURIE).to.equal('pso:draft');\n });\n });\n\n describe('#setStatus', function () {\n it('should throw an error if given a mistyped status', function () {\n expect(function () { wrapper.setStatus('pso:retracted-from_publication'); })\n .to.throw(\n TypeError,\n 'setStatus() called with invalid status CURIE \\'pso:retracted-from_publication\\'',\n 'PhylorefWrapper throws TypeError on a mistyped status'\n );\n });\n });\n\n describe('#getStatusChanges', function () {\n it('should return the empty list', function () {\n expect(wrapper.getStatusChanges()).to.be.empty;\n });\n\n describe('when modified by using .setStatus', function () {\n it('should return the updated list', function () {\n wrapper.setStatus('pso:final-draft');\n wrapper.setStatus('pso:under-review');\n wrapper.setStatus('pso:submitted');\n wrapper.setStatus('pso:published');\n wrapper.setStatus('pso:retracted-from-publication');\n\n // And see if we get the statuses back in the correct order.\n const statusChanges = wrapper.getStatusChanges();\n expect(statusChanges.length, 'number of status changes should be 5').to.equal(5);\n expect(statusChanges[0].statusCURIE, 'first status change should be \"pso:final-draft\"').to.equal('pso:final-draft');\n expect(statusChanges[1].statusCURIE, 'second status change should be \"pso:under-review\"').to.equal('pso:under-review');\n expect(statusChanges[2].statusCURIE, 'third status change should be a \"pso:submitted\"').to.equal('pso:submitted');\n expect(statusChanges[3].statusCURIE, 'fourth status change should be a \"pso:published\"').to.equal('pso:published');\n expect(statusChanges[4].statusCURIE, 'fifth status change should be a \"pso:retracted-from-publication\"').to.equal('pso:retracted-from-publication');\n });\n });\n });\n });\n\n describe('#asJSONLD', function () {\n it('should preserve an existing @id on input phylorefs', function () {\n const jsonld = new phyx.PhylorefWrapper({\n '@id': '#providedId',\n internalSpecifiers: [specifier1],\n externalSpecifiers: [specifier2],\n }).asJSONLD('#phyloref0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#providedId');\n });\n it('should generate a new @id on input phylorefs', function () {\n const jsonld = new phyx.PhylorefWrapper({\n internalSpecifiers: [specifier1],\n externalSpecifiers: [specifier2],\n }).asJSONLD('#phyloref0');\n expect(jsonld).to.have.property('@id');\n expect(jsonld['@id']).to.equal('#phyloref0');\n });\n it('should generate the expected equivClass expression for 1 int, 1 ext phyloref', function () {\n const jsonld = new phyx.PhylorefWrapper({\n internalSpecifiers: [specifier1],\n externalSpecifiers: [specifier2],\n }).asJSONLD('#');\n expect(jsonld).to.have.property('equivalentClass');\n expect(jsonld.equivalentClass).to.deep.equal({\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_INCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'MVZ:225749',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n },\n },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_EXCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'MVZ:191016',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n },\n },\n ],\n });\n });\n\n it('should generate the expected equivClass expression for 2 int phyloref', function () {\n const jsonld = new phyx.PhylorefWrapper({\n internalSpecifiers: [specifier2, specifier3],\n }).asJSONLD('#');\n expect(jsonld).to.have.property('equivalentClass');\n expect(jsonld.equivalentClass).to.deep.equal({\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.CDAO_HAS_CHILD,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_EXCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'MVZ:191016',\n onProperty: owlterms.DWC_OCCURRENCE_ID,\n },\n },\n {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.PHYLOREF_INCLUDES_TU,\n someValuesFrom: {\n '@type': owlterms.OWL_RESTRICTION,\n onProperty: owlterms.TDWG_VOC_HAS_NAME,\n someValuesFrom: {\n '@type': owlterms.OWL_CLASS,\n intersectionOf: [{\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: 'Rana boylii',\n onProperty: owlterms.TDWG_VOC_NAME_COMPLETE,\n }, {\n '@type': owlterms.OWL_RESTRICTION,\n hasValue: {\n '@id': owlterms.ICZN_CODE,\n },\n onProperty: owlterms.NOMENCLATURAL_CODE,\n }],\n },\n },\n },\n ],\n },\n });\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/phylorefs.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/phylorefs.js", "access": null, "description": null, "lineNumber": 1 @@ -6275,7 +6275,7 @@ "name": "test/scripts/phyx2owl.js", "content": "/*\n * Test conversion to OWL using the phyx2owl.js script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\nconst fs = require('fs');\n\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can convert Phyx files to OWL in JSON-LD using phyx2owl.js.\n */\n\nconst PHYX2OWL_JS = 'bin/phyx2owl.js';\n\ndescribe(PHYX2OWL_JS, function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(PHYX2OWL_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(PHYX2OWL_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('phyx2owl.js [files or directories to convert into OWL ontologies]');\n });\n it('should be able to convert `brochu_2003.json`', function () {\n const PHYX_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.json');\n const NQ_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.nq');\n const OWL_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.owl');\n\n // If there is already a '../examples/brochu_2003.owl' file, we should delete it.\n if (fs.existsSync(OWL_FILE)) fs.unlinkSync(OWL_FILE);\n expect(fs.existsSync(OWL_FILE)).to.be.false;\n\n // Convert brochu_2003.json to brochu_2003.owl.\n // Because of the way in which we test brochu_2003.owl in test/examples.js,\n // we need to set a base IRI as well.\n const result = child.spawnSync(PHYX2OWL_JS, [PHYX_FILE, '--base-iri', 'http://example.org/phyx.js/example#'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('1 files converted successfully.');\n expect(result.status).to.equal(0);\n\n expect(fs.existsSync(OWL_FILE), `File ${OWL_FILE} was not generated.`).to.be.true;\n\n // Make sure that the generated file is identical to the N-Quads file expected./\n const nqGenerated = fs.readFileSync(OWL_FILE, 'utf8');\n const nqExpected = fs.readFileSync(NQ_FILE, 'utf8');\n expect(nqGenerated).to.equal(nqExpected);\n });\n it('should be able to convert the entire `test/examples/correct` directory', function () {\n const EXAMPLE_DIR = path.resolve(__dirname, '../examples/correct');\n const jsonFilesInExamples = fs.readdirSync(EXAMPLE_DIR, { recursive: true })\n .filter(fileName => fileName.toLowerCase().endsWith('.json'));\n\n const result = child.spawnSync(PHYX2OWL_JS, [EXAMPLE_DIR, '--base-iri', 'http://example.org/phyx.js/example#'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stdout).to.match(/\\d+ files converted successfully./);\n expect(result.stderr).to.be.empty;\n\n const regexMatch = result.stdout.match(/(\\d+) files converted successfully./);\n const fileCount = Number(regexMatch[1]);\n expect(fileCount).to.be.greaterThan(0);\n expect(fileCount).to.equal(jsonFilesInExamples.length);\n\n // Make sure that the generated files *look* like JSON-LD files.\n fs.readdirSync(EXAMPLE_DIR, 'utf8')\n .filter(fileName => fileName.toLowerCase().endsWith('.owl'))\n .forEach((owlFilename) => {\n const nqGenerated = fs.readFileSync(path.resolve(EXAMPLE_DIR, owlFilename), 'utf8');\n\n // If there's an .owl file, there should an .nq file with the expected content.\n const nqFilename = `${owlFilename.substring(0, owlFilename.length - 4)}.nq`;\n const nqExpected = fs.readFileSync(path.resolve(EXAMPLE_DIR, nqFilename), 'utf8');\n\n expect(nqGenerated).to.equal(nqExpected);\n });\n });\n // This is where we should test the recursive directory functionality. However,\n // doing that would require using `test/examples` (which isn't recursive),\n // using `test/` or the root project directory (potentially messing with other\n // test scripts). We could potentially create a separate recursive hierarchy to\n // test this, but that seems unnecessary. So we won't test this functionality\n // for now, but will add a test if we find a replicable bug in the future.\n it('should give an error if no JSON files could be found', function () {\n const result = child.spawnSync(PHYX2OWL_JS, [__dirname], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('Input files do not exist or consist of directories that do not contain JSON files: ');\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/scripts/phyx2owl.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/scripts/phyx2owl.js", "access": null, "description": null, "lineNumber": 1 @@ -6361,9 +6361,9 @@ "__docId__": 396, "kind": "testFile", "name": "test/scripts/resolve.js", - "content": "/*\n * Test resolution against the Open Tree of Life via the resolve script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\n\nconst lodash = require('lodash');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can use the resolve script to resolve phylorefs against\n * the Open Tree of Life.\n */\n\nconst RESOLVE_JS = 'bin/resolve.js';\n\ndescribe('bin/resolve.js', function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(RESOLVE_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(RESOLVE_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('resolve.js [files to resolve on the Open Tree of Life]');\n });\n it('should provide the expected results on the `brochu_2003.json` example file', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/correct/brochu_2003.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'Alligatoridae',\n 'Alligatorinae',\n 'Caimaninae',\n 'Crocodyloidea',\n 'Crocodylidae',\n 'Diplocynodontinae',\n ]);\n\n expect(resultObj.Alligatoridae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott195670',\n label: 'Alligatoridae',\n });\n expect(resultObj.Alligatorinae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott151255',\n label: 'Alligatorinae',\n });\n expect(resultObj.Crocodylidae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott1092501',\n label: 'Longirostres',\n });\n expect(resultObj.Diplocynodontinae[0]).to.include({\n error: 'no_mrca_found:400',\n });\n });\n it('should correctly report errors with certain phyloreferences', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/incorrect/otl-resolution-errors.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'SingleSpecifier',\n 'TaxonNameNotFound',\n 'Produces404OnOTR',\n ]);\n\n // console.log(JSON.stringify(resultObj, null, 2));\n\n expect(resultObj.SingleSpecifier[0]).to.include({\n error: 'one_internal_specifier_with_no_external_specifiers',\n });\n\n expect(resultObj.TaxonNameNotFound[0]).to.include({\n error: 'internal_specifiers_missing',\n });\n\n expect(resultObj.Produces404OnOTR[0]).to.include({\n error: 'no_mrca_found:404',\n });\n });\n});\n", + "content": "/*\n * Test resolution against the Open Tree of Life via the resolve script.\n */\n\nconst child = require('child_process');\nconst path = require('path');\n\nconst lodash = require('lodash');\nconst chai = require('chai');\n\nconst expect = chai.expect;\n\n/*\n * Test whether we can use the resolve script to resolve phylorefs against\n * the Open Tree of Life.\n */\n\nconst RESOLVE_JS = 'bin/resolve.js';\n\ndescribe('bin/resolve.js', function () {\n it('should work without any arguments', function () {\n const result = child.spawnSync(RESOLVE_JS, [], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(1);\n expect(result.stdout).to.be.empty;\n expect(result.stderr).to.contain('No input files provided.');\n });\n it('should support `--help`', function () {\n const result = child.spawnSync(RESOLVE_JS, ['--help'], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n expect(result.stdout).to.contain('resolve.js [files to resolve on the Open Tree of Life]');\n });\n it('should provide the expected results on the `brochu_2003.json` example file', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/correct/brochu_2003.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'Alligatoridae',\n 'Alligatorinae',\n 'Caimaninae',\n 'Crocodyloidea',\n 'Crocodylidae',\n 'Diplocynodontinae',\n ]);\n\n expect(resultObj.Alligatoridae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott195670',\n label: 'Alligatoridae',\n });\n expect(resultObj.Alligatorinae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott151255',\n label: 'Alligatorinae',\n });\n expect(resultObj.Crocodylidae[0].resolved).to.include({\n '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott1092501',\n label: 'Longirostres',\n });\n expect(resultObj.Diplocynodontinae[0]).to.include({\n error: 'no_mrca_found:400',\n });\n });\n it('should correctly report errors with certain phyloreferences', function () {\n var resultObj; // eslint-disable-line no-var\n\n this.timeout(20000); // Take up to 20 seconds to run this.\n\n const result = child.spawnSync(RESOLVE_JS, [path.resolve(__dirname, '../examples/incorrect/otl-resolution-errors.json')], {\n encoding: 'utf-8',\n stdio: 'pipe',\n });\n expect(result.status).to.equal(0);\n expect(result.stderr).to.be.empty;\n\n expect(function () {\n resultObj = JSON.parse(result.stdout);\n }).to.not.throw(SyntaxError);\n\n expect(lodash.keys(resultObj)).to.have.members([\n 'SingleSpecifier',\n 'TaxonNameNotFound',\n 'Produces404OnOTR',\n ]);\n\n // console.log(JSON.stringify(resultObj, null, 2));\n\n expect(resultObj.SingleSpecifier[0]).to.include({\n error: 'one_internal_specifier_with_no_external_specifiers',\n });\n\n expect(resultObj.TaxonNameNotFound[0]).to.include({\n error: 'internal_specifiers_missing',\n });\n\n expect(resultObj.Produces404OnOTR[0]).to.include({\n error: 'no_mrca_found:404',\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/scripts/resolve.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/scripts/resolve.js", "access": null, "description": null, "lineNumber": 1 @@ -6437,9 +6437,9 @@ "__docId__": 402, "kind": "testFile", "name": "test/specimens.js", - "content": "/*\n * Test specimen processing.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/*\n * Test whether SpecimenWrapper can parse specimen identifiers from simple specimen\n * identifiers, from institutionCode:catalogNumber format, and from Darwin Core triples.\n * However, URNs and HTTP URLs should not be accidentally parsed as Darwin Core triples.\n */\n\ndescribe('SpecimenWrapper', function () {\n describe('#constructor', function () {\n it('should be able to wrap an empty specimen', function () {\n const wrapped = new phyx.SpecimenWrapper({});\n\n expect(wrapped).to.be.an.instanceOf(phyx.SpecimenWrapper);\n expect(wrapped.occurrenceID).to.be.undefined;\n });\n it('should be able to extract an occurenceID and catalogNumber from simple specimen IDs', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'Wall 2527, Fiji (uc)',\n 'dwc:basisOfRecord': 'PreservedSpecimen',\n });\n expect(wrapper.occurrenceID).to.equal('Wall 2527, Fiji (uc)');\n expect(wrapper.catalogNumber).to.equal('Wall 2527, Fiji (uc)');\n expect(wrapper.basisOfRecord).to.equal('PreservedSpecimen');\n });\n it('should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'FMNH:PR 2081',\n 'dwc:basisOfRecord': 'PreservedSpecimen',\n });\n expect(wrapper.occurrenceID).to.equal('FMNH:PR 2081');\n expect(wrapper.institutionCode).to.equal('FMNH');\n expect(wrapper.catalogNumber).to.equal('PR 2081');\n expect(wrapper.basisOfRecord).to.equal('PreservedSpecimen');\n });\n it('should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'FMNH:PR:2081',\n });\n expect(wrapper.occurrenceID).to.equal('FMNH:PR:2081');\n expect(wrapper.institutionCode).to.equal('FMNH');\n expect(wrapper.collectionCode).to.equal('PR');\n expect(wrapper.catalogNumber).to.equal('2081');\n expect(wrapper.basisOfRecord).to.be.undefined;\n });\n it('should be able to extract the same occurrenceID from different representations', function () {\n expect(new phyx.SpecimenWrapper({ occurrenceID: 'urn:catalog:::MVZ225749' }).occurrenceID)\n .to.equal('urn:catalog:::MVZ225749');\n expect(new phyx.SpecimenWrapper({ catalogNumber: 'MVZ225749' }).occurrenceID)\n .to.equal('urn:catalog:::MVZ225749');\n });\n it('should not attempt to split a URN into occurenceID, institutionCode and catalogNumber', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'urn:lsid:biocol.org:col:34777',\n });\n expect(wrapper.occurrenceID).to.equal('urn:lsid:biocol.org:col:34777');\n expect(wrapper.institutionCode).to.be.undefined;\n expect(wrapper.collectionCode).to.be.undefined;\n expect(wrapper.catalogNumber).to.be.undefined;\n });\n it('should not attempt to split a URL into occurenceID, institutionCode and catalogNumber', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'http://arctos.database.museum/guid/MVZ:Herp:148929?seid=886464',\n });\n expect(wrapper.occurrenceID).to.equal('http://arctos.database.museum/guid/MVZ:Herp:148929?seid=886464');\n expect(wrapper.institutionCode).to.be.undefined;\n expect(wrapper.collectionCode).to.be.undefined;\n expect(wrapper.catalogNumber).to.be.undefined;\n });\n it('should be able to create a specimen JSON record from an occurrence ID', function () {\n const specimen = phyx.SpecimenWrapper.fromOccurrenceID('FMNH:PR:2081');\n expect(specimen.occurrenceID).to.equal('FMNH:PR:2081');\n expect(specimen.institutionCode).to.equal('FMNH');\n expect(specimen.collectionCode).to.equal('PR');\n expect(specimen.catalogNumber).to.equal('2081');\n expect(specimen['dwc:basisOfRecord']).to.equal('PreservedSpecimen');\n });\n });\n});\n", + "content": "/*\n * Test specimen processing.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\n\nconst expect = chai.expect;\n\n/*\n * Test whether SpecimenWrapper can parse specimen identifiers from simple specimen\n * identifiers, from institutionCode:catalogNumber format, and from Darwin Core triples.\n * However, URNs and HTTP URLs should not be accidentally parsed as Darwin Core triples.\n */\n\ndescribe('SpecimenWrapper', function () {\n describe('#constructor', function () {\n it('should be able to wrap an empty specimen', function () {\n const wrapped = new phyx.SpecimenWrapper({});\n\n expect(wrapped).to.be.an.instanceOf(phyx.SpecimenWrapper);\n expect(wrapped.occurrenceID).to.be.undefined;\n });\n it('should be able to wrap a specimen with an empty occurenceID', function () {\n const wrapped = new phyx.SpecimenWrapper(phyx.SpecimenWrapper.fromOccurrenceID(''));\n\n expect(wrapped).to.be.an.instanceOf(phyx.SpecimenWrapper);\n expect(wrapped.occurrenceID).to.equal('');\n });\n it('should be able to extract an occurenceID and catalogNumber from simple specimen IDs', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'Wall 2527, Fiji (uc)',\n basisOfRecord: 'PreservedSpecimen',\n });\n expect(wrapper.occurrenceID).to.equal('Wall 2527, Fiji (uc)');\n expect(wrapper.catalogNumber).to.equal('Wall 2527, Fiji (uc)');\n expect(wrapper.basisOfRecord).to.equal('PreservedSpecimen');\n });\n it('should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'FMNH:PR 2081',\n basisOfRecord: 'PreservedSpecimen',\n });\n expect(wrapper.occurrenceID).to.equal('FMNH:PR 2081');\n expect(wrapper.institutionCode).to.equal('FMNH');\n expect(wrapper.catalogNumber).to.equal('PR 2081');\n expect(wrapper.basisOfRecord).to.equal('PreservedSpecimen');\n });\n it('should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'FMNH:PR:2081',\n });\n expect(wrapper.occurrenceID).to.equal('FMNH:PR:2081');\n expect(wrapper.institutionCode).to.equal('FMNH');\n expect(wrapper.collectionCode).to.equal('PR');\n expect(wrapper.catalogNumber).to.equal('2081');\n expect(wrapper.basisOfRecord).to.be.undefined;\n });\n it('should be able to extract the same occurrenceID from different representations', function () {\n expect(new phyx.SpecimenWrapper({ occurrenceID: 'urn:catalog:::MVZ225749' }).occurrenceID)\n .to.equal('urn:catalog:::MVZ225749');\n expect(new phyx.SpecimenWrapper({ catalogNumber: 'MVZ225749' }).occurrenceID)\n .to.equal('urn:catalog:::MVZ225749');\n });\n it('should not attempt to split a URN into occurenceID, institutionCode and catalogNumber', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'urn:lsid:biocol.org:col:34777',\n });\n expect(wrapper.occurrenceID).to.equal('urn:lsid:biocol.org:col:34777');\n expect(wrapper.institutionCode).to.be.undefined;\n expect(wrapper.collectionCode).to.be.undefined;\n expect(wrapper.catalogNumber).to.be.undefined;\n });\n it('should not attempt to split a URL into occurenceID, institutionCode and catalogNumber', function () {\n const wrapper = new phyx.SpecimenWrapper({\n occurrenceID: 'http://arctos.database.museum/guid/MVZ:Herp:148929?seid=886464',\n });\n expect(wrapper.occurrenceID).to.equal('http://arctos.database.museum/guid/MVZ:Herp:148929?seid=886464');\n expect(wrapper.institutionCode).to.be.undefined;\n expect(wrapper.collectionCode).to.be.undefined;\n expect(wrapper.catalogNumber).to.be.undefined;\n });\n it('should be able to create a specimen JSON record from an occurrence ID', function () {\n const specimen = phyx.SpecimenWrapper.fromOccurrenceID('FMNH:PR:2081');\n expect(specimen.occurrenceID).to.equal('FMNH:PR:2081');\n expect(specimen.institutionCode).to.equal('FMNH');\n expect(specimen.collectionCode).to.equal('PR');\n expect(specimen.catalogNumber).to.equal('2081');\n expect(specimen.basisOfRecord).to.equal('PreservedSpecimen');\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/specimens.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/specimens.js", "access": null, "description": null, "lineNumber": 1 @@ -6493,7 +6493,7 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it151", "access": null, - "description": "should be able to extract an occurenceID and catalogNumber from simple specimen IDs", + "description": "should be able to wrap a specimen with an empty occurenceID", "lineNumber": 24 }, { @@ -6506,8 +6506,8 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it152", "access": null, - "description": "should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination", - "lineNumber": 33 + "description": "should be able to extract an occurenceID and catalogNumber from simple specimen IDs", + "lineNumber": 30 }, { "__docId__": 408, @@ -6519,8 +6519,8 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it153", "access": null, - "description": "should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples", - "lineNumber": 43 + "description": "should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination", + "lineNumber": 39 }, { "__docId__": 409, @@ -6532,8 +6532,8 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it154", "access": null, - "description": "should be able to extract the same occurrenceID from different representations", - "lineNumber": 53 + "description": "should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples", + "lineNumber": 49 }, { "__docId__": 410, @@ -6545,7 +6545,7 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it155", "access": null, - "description": "should not attempt to split a URN into occurenceID, institutionCode and catalogNumber", + "description": "should be able to extract the same occurrenceID from different representations", "lineNumber": 59 }, { @@ -6558,8 +6558,8 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it156", "access": null, - "description": "should not attempt to split a URL into occurenceID, institutionCode and catalogNumber", - "lineNumber": 68 + "description": "should not attempt to split a URN into occurenceID, institutionCode and catalogNumber", + "lineNumber": 65 }, { "__docId__": 412, @@ -6571,495 +6571,508 @@ "static": true, "longname": "test/specimens.js~describe148.describe149.it157", "access": null, - "description": "should be able to create a specimen JSON record from an occurrence ID", - "lineNumber": 77 + "description": "should not attempt to split a URL into occurenceID, institutionCode and catalogNumber", + "lineNumber": 74 }, { "__docId__": 413, + "kind": "test", + "name": "it158", + "testId": 158, + "memberof": "test/specimens.js~describe148.describe149", + "testDepth": 2, + "static": true, + "longname": "test/specimens.js~describe148.describe149.it158", + "access": null, + "description": "should be able to create a specimen JSON record from an occurrence ID", + "lineNumber": 83 + }, + { + "__docId__": 414, "kind": "testFile", "name": "test/taxon-names.js", "content": "/*\n * Test taxon name processing.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\nconst owlterms = require('../src/utils/owlterms');\n\nconst expect = chai.expect;\n\n/*\n * Test whether TaxonNameWrapper parses taxon names correctly.\n */\n\ndescribe('TaxonNameWrapper', function () {\n describe('#constructor', function () {\n it('should accept empty taxon names without errors', function () {\n const wrapper = new phyx.TaxonNameWrapper({});\n\n expect(wrapper).to.be.an.instanceOf(phyx.TaxonNameWrapper);\n expect(wrapper.nameComplete).to.be.undefined;\n });\n it('should be able to parse uninomial names as such', function () {\n const wrapper = new phyx.TaxonNameWrapper({\n nameComplete: 'Mus',\n });\n\n expect(wrapper.uninomial).to.equal('Mus');\n expect(wrapper.genusPart).to.be.undefined;\n expect(wrapper.specificEpithet).to.be.undefined;\n });\n it('should be able to parse binomial names into genus and specific epithet', function () {\n const wrapper = new phyx.TaxonNameWrapper({\n nameComplete: 'Mus musculus',\n });\n\n expect(wrapper.genusPart).to.equal('Mus');\n expect(wrapper.specificEpithet).to.equal('musculus');\n });\n it('should be able to parse trinomial names into genus, specific epithet and infraspecific epithet', function () {\n const wrapper = new phyx.TaxonNameWrapper({\n nameComplete: 'Mus musculus domesticus',\n });\n\n expect(wrapper.genusPart).to.equal('Mus');\n expect(wrapper.specificEpithet).to.equal('musculus');\n expect(wrapper.infraspecificEpithet).to.equal('domesticus');\n });\n it('should ignore authority after a binomial name', function () {\n const taxonName = phyx.TaxonNameWrapper.fromVerbatimName('Mus musculus Linnaeus, 1758');\n expect(taxonName.nameComplete).to.equal('Mus musculus');\n expect(taxonName.genusPart).to.equal('Mus');\n expect(taxonName.specificEpithet).to.equal('musculus');\n expect(taxonName.infraspecificEpithet).to.be.undefined;\n expect(taxonName.uninomial).to.be.undefined;\n });\n it('should be able to use default nomenclatural codes', function () {\n const taxonName = phyx.TaxonNameWrapper.fromVerbatimName('Mus musculus Linnaeus, 1758', owlterms.ICZN_CODE);\n expect(taxonName.nameComplete).to.equal('Mus musculus');\n expect(taxonName.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n\n const wrappedTaxonName = new phyx.TaxonNameWrapper(taxonName);\n expect(wrappedTaxonName.nomenclaturalCode).to.equal(owlterms.ICZN_CODE);\n expect(wrappedTaxonName.nomenclaturalCodeDetails).to.have.own.property('title');\n expect(wrappedTaxonName.nomenclaturalCodeDetails.title).to.equal('International Code of Zoological Nomenclature');\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/taxon-names.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/taxon-names.js", "access": null, "description": null, "lineNumber": 1 }, { - "__docId__": 414, + "__docId__": 415, "kind": "test", - "name": "describe158", - "testId": 158, + "name": "describe159", + "testId": 159, "memberof": "test/taxon-names.js", "testDepth": 0, "static": true, - "longname": "test/taxon-names.js~describe158", + "longname": "test/taxon-names.js~describe159", "access": null, "description": "TaxonNameWrapper", "lineNumber": 15 }, { - "__docId__": 415, + "__docId__": 416, "kind": "test", - "name": "describe159", - "testId": 159, - "memberof": "test/taxon-names.js~describe158", + "name": "describe160", + "testId": 160, + "memberof": "test/taxon-names.js~describe159", "testDepth": 1, "static": true, - "longname": "test/taxon-names.js~describe158.describe159", + "longname": "test/taxon-names.js~describe159.describe160", "access": null, "description": "#constructor", "lineNumber": 16 }, { - "__docId__": 416, + "__docId__": 417, "kind": "test", - "name": "it160", - "testId": 160, - "memberof": "test/taxon-names.js~describe158.describe159", + "name": "it161", + "testId": 161, + "memberof": "test/taxon-names.js~describe159.describe160", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe158.describe159.it160", + "longname": "test/taxon-names.js~describe159.describe160.it161", "access": null, "description": "should accept empty taxon names without errors", "lineNumber": 17 }, { - "__docId__": 417, + "__docId__": 418, "kind": "test", - "name": "it161", - "testId": 161, - "memberof": "test/taxon-names.js~describe158.describe159", + "name": "it162", + "testId": 162, + "memberof": "test/taxon-names.js~describe159.describe160", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe158.describe159.it161", + "longname": "test/taxon-names.js~describe159.describe160.it162", "access": null, "description": "should be able to parse uninomial names as such", "lineNumber": 23 }, { - "__docId__": 418, + "__docId__": 419, "kind": "test", - "name": "it162", - "testId": 162, - "memberof": "test/taxon-names.js~describe158.describe159", + "name": "it163", + "testId": 163, + "memberof": "test/taxon-names.js~describe159.describe160", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe158.describe159.it162", + "longname": "test/taxon-names.js~describe159.describe160.it163", "access": null, "description": "should be able to parse binomial names into genus and specific epithet", "lineNumber": 32 }, { - "__docId__": 419, + "__docId__": 420, "kind": "test", - "name": "it163", - "testId": 163, - "memberof": "test/taxon-names.js~describe158.describe159", + "name": "it164", + "testId": 164, + "memberof": "test/taxon-names.js~describe159.describe160", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe158.describe159.it163", + "longname": "test/taxon-names.js~describe159.describe160.it164", "access": null, "description": "should be able to parse trinomial names into genus, specific epithet and infraspecific epithet", "lineNumber": 40 }, { - "__docId__": 420, + "__docId__": 421, "kind": "test", - "name": "it164", - "testId": 164, - "memberof": "test/taxon-names.js~describe158.describe159", + "name": "it165", + "testId": 165, + "memberof": "test/taxon-names.js~describe159.describe160", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe158.describe159.it164", + "longname": "test/taxon-names.js~describe159.describe160.it165", "access": null, "description": "should ignore authority after a binomial name", "lineNumber": 49 }, { - "__docId__": 421, + "__docId__": 422, "kind": "test", - "name": "it165", - "testId": 165, - "memberof": "test/taxon-names.js~describe158.describe159", + "name": "it166", + "testId": 166, + "memberof": "test/taxon-names.js~describe159.describe160", "testDepth": 2, "static": true, - "longname": "test/taxon-names.js~describe158.describe159.it165", + "longname": "test/taxon-names.js~describe159.describe160.it166", "access": null, "description": "should be able to use default nomenclatural codes", "lineNumber": 57 }, { - "__docId__": 422, + "__docId__": 423, "kind": "testFile", "name": "test/taxonomic-units.js", "content": "/*\n * Test taxonomic unit construction and matching.\n */\n\nconst chai = require('chai');\nconst phyx = require('../src');\n\n// Use Chai's expect API.\nconst expect = chai.expect;\n\n/*\n * We primarily test two classes here:\n * - TaxonomicUnitWrapper, which wraps a taxonomic unit and determines if it\n * refers to a scientific name, specimen identifier or external reference,\n * or a combination of these.\n * - TaxonomicUnitMatcher, which accepts two taxonomic units and determines\n * whether and for what reason the two can be matched.\n */\n\ndescribe('TaxonomicUnitWrapper', function () {\n describe('#constructor given no arguments', function () {\n it('should create an empty TaxonomicUnitWrapper without a defined label', function () {\n // Empty TU without @type.\n let wrapper = new phyx.TaxonomicUnitWrapper({});\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n\n // Empty TU with type TYPE_TAXON_CONCEPT.\n wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n });\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n\n // Empty TU with type TYPE_SPECIMEN.\n wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n });\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n\n // Empty TU with type TYPE_SPECIMEN and a taxonomic name.\n wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n nameString: 'Taxonomic name',\n });\n expect(wrapper).to.be.instanceOf(phyx.TaxonomicUnitWrapper);\n expect(wrapper.label).to.be.undefined;\n });\n });\n describe('#label given a taxonomic unit', function () {\n it('should return a wrapped scientific name', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n label: 'Ornithorhynchus anatinus (Shaw, 1799)',\n nameComplete: 'Ornithorhynchus anatinus',\n },\n });\n expect(wrapper.label).to.equal('Ornithorhynchus anatinus (Shaw, 1799)');\n });\n it('should return a wrapped specimen identifier preceded by \"Specimen\"', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Specimen MVZ 225749');\n });\n it('should return specimens with an occurrenceID as well as a taxon concept', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Specimen MVZ 225749 identified as Rana luteiventris');\n });\n it('should ignore occurrence ID if typed as a taxon concept', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Rana luteiventris');\n });\n it('should return a wrapped external reference by surrounding it with \"<>\"', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@id': [\n 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n ],\n });\n expect(wrapper.label).to.equal('');\n });\n it('should provide both taxon name and occurrence ID in label, but ignore external reference', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@id': [\n 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n ],\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.label).to.equal('Specimen MVZ 225749 identified as Rana luteiventris');\n });\n });\n describe('#fromLabel', function () {\n it('should return empty lists when inputs are empty or undefined', function () {\n expect(phyx.TaxonomicUnitWrapper.fromLabel()).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel(undefined)).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel(null)).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel('')).to.be.undefined;\n expect(phyx.TaxonomicUnitWrapper.fromLabel(' ')).to.be.undefined;\n });\n it('when given a scientific name, it should return a list of a single TU wrapping a scientific name', function () {\n expect(phyx.TaxonomicUnitWrapper.fromLabel('Rana luteiventris MVZ225749'))\n .to.be.deep.equal({\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept',\n label: 'Rana luteiventris MVZ225749',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana luteiventris MVZ225749',\n genusPart: 'Rana',\n specificEpithet: 'luteiventris',\n nameComplete: 'Rana luteiventris',\n },\n });\n });\n it('when given a scientific name separated with underscores, it should return a list of a single TU wrapping the scientific name', function () {\n expect(phyx.TaxonomicUnitWrapper.fromLabel('Rana_luteiventris_MVZ_225749'))\n .to.be.deep.equal({\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept',\n label: 'Rana_luteiventris_MVZ_225749',\n hasName: {\n '@type': 'http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName',\n label: 'Rana_luteiventris_MVZ_225749',\n nameComplete: 'Rana luteiventris',\n genusPart: 'Rana',\n specificEpithet: 'luteiventris',\n },\n });\n });\n });\n describe('#asOWLEquivClass', function () {\n it('when given a taxon concept, only the complete name should be present in the equivClass', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n nameString: 'Rana luteiventris Thompson, 1913',\n });\n expect(wrapper.asOWLEquivClass).to.deep.equal({\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName',\n someValuesFrom: {\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/ontology/voc/TaxonName#nameComplete',\n hasValue: 'Rana luteiventris',\n },\n });\n });\n it('when given a specimen, only the occurrence ID should be present in the equivClass', function () {\n const wrapper = new phyx.TaxonomicUnitWrapper({\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n nameString: 'Rana luteiventris',\n occurrenceID: 'MVZ 225749',\n });\n expect(wrapper.asOWLEquivClass).to.deep.equal({\n '@type': 'owl:Restriction',\n onProperty: 'http://rs.tdwg.org/dwc/terms/occurrenceID',\n hasValue: 'MVZ 225749',\n });\n });\n });\n});\n\ndescribe('TaxonomicUnitMatcher', function () {\n // To test matching, let's set up some taxonomic units.\n // Note that:\n // tunit1 and tunit2 should match by scientific name.\n // tunit2 and tunit3 should match by specimen identifier.\n // tunit3 and tunit4 should match by external references.\n const tunit1 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_TAXON_CONCEPT,\n hasName: {\n nameComplete: 'Rana luteiventris',\n },\n };\n const tunit2 = {\n '@type': [\n phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n ],\n nameString: 'Rana luteiventris MVZ225749',\n occurrenceID: 'MVZ225749',\n };\n const tunit3 = {\n '@type': phyx.TaxonomicUnitWrapper.TYPE_SPECIMEN,\n occurrenceID: 'MVZ225749',\n '@id': 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n };\n const tunit4 = {\n '@id': 'http://arctos.database.museum/guid/MVZ:Herp:225749',\n };\n\n describe('#matchByNameComplete', function () {\n it('should be able to match tunit1 and tunit2 by complete name', function () {\n expect(new phyx.TaxonomicUnitMatcher(tunit1, tunit2).matchByExternalReferences()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit1, tunit2).matchByOccurrenceID()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit1, tunit2).matchByNameComplete()).to.be.true;\n });\n });\n describe('#matchByExternalReferences', function () {\n it('should be able to match tunit3 and tunit4 by external references', function () {\n expect(new phyx.TaxonomicUnitMatcher(tunit3, tunit4).matchByExternalReferences()).to.be.true;\n expect(new phyx.TaxonomicUnitMatcher(tunit3, tunit4).matchByOccurrenceID()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit3, tunit4).matchByNameComplete()).to.be.false;\n });\n });\n describe('#matchByOccurrenceID', function () {\n it('should be able to match tunit2 and tunit3 by specimen identifiers', function () {\n expect(new phyx.TaxonomicUnitMatcher(tunit2, tunit3).matchByExternalReferences()).to.be.false;\n expect(new phyx.TaxonomicUnitMatcher(tunit2, tunit3).matchByOccurrenceID()).to.be.true;\n expect(new phyx.TaxonomicUnitMatcher(tunit2, tunit3).matchByNameComplete()).to.be.false;\n });\n });\n describe('#matched and #matchReason', function () {\n it('should match tunit1 and tunit2 on the basis of identical complete names', function () {\n const matcher = new phyx.TaxonomicUnitMatcher(tunit1, tunit2);\n expect(matcher.matched).to.be.true;\n expect(matcher.matchReason).to.include('share the same complete name');\n });\n\n it('should match tunit3 and tunit4 by identical external reference', function () {\n const matcher = new phyx.TaxonomicUnitMatcher(tunit3, tunit4);\n expect(matcher.matched).to.be.true;\n expect(matcher.matchReason).to.include('External reference');\n });\n\n it('should match tunit2 and tunit3 by identical specimen identifier', function () {\n const matcher = new phyx.TaxonomicUnitMatcher(tunit2, tunit3);\n expect(matcher.matched).to.be.true;\n expect(matcher.matchReason).to.include('Specimen identifier');\n });\n });\n});\n", "static": true, - "longname": "/Users/gaurav/Development/phyloref/phyx.js/test/taxonomic-units.js", + "longname": "/Users/gaurav/Developer/phyloref/phyx.js/test/taxonomic-units.js", "access": null, "description": null, "lineNumber": 1 }, { - "__docId__": 423, + "__docId__": 424, "kind": "test", - "name": "describe166", - "testId": 166, + "name": "describe167", + "testId": 167, "memberof": "test/taxonomic-units.js", "testDepth": 0, "static": true, - "longname": "test/taxonomic-units.js~describe166", + "longname": "test/taxonomic-units.js~describe167", "access": null, "description": "TaxonomicUnitWrapper", "lineNumber": 20 }, { - "__docId__": 424, + "__docId__": 425, "kind": "test", - "name": "describe167", - "testId": 167, - "memberof": "test/taxonomic-units.js~describe166", + "name": "describe168", + "testId": 168, + "memberof": "test/taxonomic-units.js~describe167", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe167", + "longname": "test/taxonomic-units.js~describe167.describe168", "access": null, "description": "#constructor given no arguments", "lineNumber": 21 }, { - "__docId__": 425, + "__docId__": 426, "kind": "test", - "name": "it168", - "testId": 168, - "memberof": "test/taxonomic-units.js~describe166.describe167", + "name": "it169", + "testId": 169, + "memberof": "test/taxonomic-units.js~describe167.describe168", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe167.it168", + "longname": "test/taxonomic-units.js~describe167.describe168.it169", "access": null, "description": "should create an empty TaxonomicUnitWrapper without a defined label", "lineNumber": 22 }, { - "__docId__": 426, + "__docId__": 427, "kind": "test", - "name": "describe169", - "testId": 169, - "memberof": "test/taxonomic-units.js~describe166", + "name": "describe170", + "testId": 170, + "memberof": "test/taxonomic-units.js~describe167", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169", + "longname": "test/taxonomic-units.js~describe167.describe170", "access": null, "description": "#label given a taxonomic unit", "lineNumber": 51 }, { - "__docId__": 427, + "__docId__": 428, "kind": "test", - "name": "it170", - "testId": 170, - "memberof": "test/taxonomic-units.js~describe166.describe169", + "name": "it171", + "testId": 171, + "memberof": "test/taxonomic-units.js~describe167.describe170", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169.it170", + "longname": "test/taxonomic-units.js~describe167.describe170.it171", "access": null, "description": "should return a wrapped scientific name", "lineNumber": 52 }, { - "__docId__": 428, + "__docId__": 429, "kind": "test", - "name": "it171", - "testId": 171, - "memberof": "test/taxonomic-units.js~describe166.describe169", + "name": "it172", + "testId": 172, + "memberof": "test/taxonomic-units.js~describe167.describe170", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169.it171", + "longname": "test/taxonomic-units.js~describe167.describe170.it172", "access": null, "description": "should return a wrapped specimen identifier preceded by \"Specimen\"", "lineNumber": 62 }, { - "__docId__": 429, + "__docId__": 430, "kind": "test", - "name": "it172", - "testId": 172, - "memberof": "test/taxonomic-units.js~describe166.describe169", + "name": "it173", + "testId": 173, + "memberof": "test/taxonomic-units.js~describe167.describe170", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169.it172", + "longname": "test/taxonomic-units.js~describe167.describe170.it173", "access": null, "description": "should return specimens with an occurrenceID as well as a taxon concept", "lineNumber": 69 }, { - "__docId__": 430, + "__docId__": 431, "kind": "test", - "name": "it173", - "testId": 173, - "memberof": "test/taxonomic-units.js~describe166.describe169", + "name": "it174", + "testId": 174, + "memberof": "test/taxonomic-units.js~describe167.describe170", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169.it173", + "longname": "test/taxonomic-units.js~describe167.describe170.it174", "access": null, "description": "should ignore occurrence ID if typed as a taxon concept", "lineNumber": 79 }, { - "__docId__": 431, + "__docId__": 432, "kind": "test", - "name": "it174", - "testId": 174, - "memberof": "test/taxonomic-units.js~describe166.describe169", + "name": "it175", + "testId": 175, + "memberof": "test/taxonomic-units.js~describe167.describe170", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169.it174", + "longname": "test/taxonomic-units.js~describe167.describe170.it175", "access": null, "description": "should return a wrapped external reference by surrounding it with \"<>\"", "lineNumber": 87 }, { - "__docId__": 432, + "__docId__": 433, "kind": "test", - "name": "it175", - "testId": 175, - "memberof": "test/taxonomic-units.js~describe166.describe169", + "name": "it176", + "testId": 176, + "memberof": "test/taxonomic-units.js~describe167.describe170", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe169.it175", + "longname": "test/taxonomic-units.js~describe167.describe170.it176", "access": null, "description": "should provide both taxon name and occurrence ID in label, but ignore external reference", "lineNumber": 95 }, { - "__docId__": 433, + "__docId__": 434, "kind": "test", - "name": "describe176", - "testId": 176, - "memberof": "test/taxonomic-units.js~describe166", + "name": "describe177", + "testId": 177, + "memberof": "test/taxonomic-units.js~describe167", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe176", + "longname": "test/taxonomic-units.js~describe167.describe177", "access": null, "description": "#fromLabel", "lineNumber": 107 }, { - "__docId__": 434, + "__docId__": 435, "kind": "test", - "name": "it177", - "testId": 177, - "memberof": "test/taxonomic-units.js~describe166.describe176", + "name": "it178", + "testId": 178, + "memberof": "test/taxonomic-units.js~describe167.describe177", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe176.it177", + "longname": "test/taxonomic-units.js~describe167.describe177.it178", "access": null, "description": "should return empty lists when inputs are empty or undefined", "lineNumber": 108 }, { - "__docId__": 435, + "__docId__": 436, "kind": "test", - "name": "it178", - "testId": 178, - "memberof": "test/taxonomic-units.js~describe166.describe176", + "name": "it179", + "testId": 179, + "memberof": "test/taxonomic-units.js~describe167.describe177", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe176.it178", + "longname": "test/taxonomic-units.js~describe167.describe177.it179", "access": null, "description": "when given a scientific name, it should return a list of a single TU wrapping a scientific name", "lineNumber": 115 }, { - "__docId__": 436, + "__docId__": 437, "kind": "test", - "name": "it179", - "testId": 179, - "memberof": "test/taxonomic-units.js~describe166.describe176", + "name": "it180", + "testId": 180, + "memberof": "test/taxonomic-units.js~describe167.describe177", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe176.it179", + "longname": "test/taxonomic-units.js~describe167.describe177.it180", "access": null, "description": "when given a scientific name separated with underscores, it should return a list of a single TU wrapping the scientific name", "lineNumber": 129 }, { - "__docId__": 437, + "__docId__": 438, "kind": "test", - "name": "describe180", - "testId": 180, - "memberof": "test/taxonomic-units.js~describe166", + "name": "describe181", + "testId": 181, + "memberof": "test/taxonomic-units.js~describe167", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe180", + "longname": "test/taxonomic-units.js~describe167.describe181", "access": null, "description": "#asOWLEquivClass", "lineNumber": 144 }, { - "__docId__": 438, + "__docId__": 439, "kind": "test", - "name": "it181", - "testId": 181, - "memberof": "test/taxonomic-units.js~describe166.describe180", + "name": "it182", + "testId": 182, + "memberof": "test/taxonomic-units.js~describe167.describe181", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe180.it181", + "longname": "test/taxonomic-units.js~describe167.describe181.it182", "access": null, "description": "when given a taxon concept, only the complete name should be present in the equivClass", "lineNumber": 145 }, { - "__docId__": 439, + "__docId__": 440, "kind": "test", - "name": "it182", - "testId": 182, - "memberof": "test/taxonomic-units.js~describe166.describe180", + "name": "it183", + "testId": 183, + "memberof": "test/taxonomic-units.js~describe167.describe181", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe166.describe180.it182", + "longname": "test/taxonomic-units.js~describe167.describe181.it183", "access": null, "description": "when given a specimen, only the occurrence ID should be present in the equivClass", "lineNumber": 160 }, { - "__docId__": 440, + "__docId__": 441, "kind": "test", - "name": "describe183", - "testId": 183, + "name": "describe184", + "testId": 184, "memberof": "test/taxonomic-units.js", "testDepth": 0, "static": true, - "longname": "test/taxonomic-units.js~describe183", + "longname": "test/taxonomic-units.js~describe184", "access": null, "description": "TaxonomicUnitMatcher", "lineNumber": 175 }, { - "__docId__": 441, + "__docId__": 442, "kind": "test", - "name": "describe184", - "testId": 184, - "memberof": "test/taxonomic-units.js~describe183", + "name": "describe185", + "testId": 185, + "memberof": "test/taxonomic-units.js~describe184", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe184", + "longname": "test/taxonomic-units.js~describe184.describe185", "access": null, "description": "#matchByNameComplete", "lineNumber": 203 }, { - "__docId__": 442, + "__docId__": 443, "kind": "test", - "name": "it185", - "testId": 185, - "memberof": "test/taxonomic-units.js~describe183.describe184", + "name": "it186", + "testId": 186, + "memberof": "test/taxonomic-units.js~describe184.describe185", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe184.it185", + "longname": "test/taxonomic-units.js~describe184.describe185.it186", "access": null, "description": "should be able to match tunit1 and tunit2 by complete name", "lineNumber": 204 }, { - "__docId__": 443, + "__docId__": 444, "kind": "test", - "name": "describe186", - "testId": 186, - "memberof": "test/taxonomic-units.js~describe183", + "name": "describe187", + "testId": 187, + "memberof": "test/taxonomic-units.js~describe184", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe186", + "longname": "test/taxonomic-units.js~describe184.describe187", "access": null, "description": "#matchByExternalReferences", "lineNumber": 210 }, { - "__docId__": 444, + "__docId__": 445, "kind": "test", - "name": "it187", - "testId": 187, - "memberof": "test/taxonomic-units.js~describe183.describe186", + "name": "it188", + "testId": 188, + "memberof": "test/taxonomic-units.js~describe184.describe187", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe186.it187", + "longname": "test/taxonomic-units.js~describe184.describe187.it188", "access": null, "description": "should be able to match tunit3 and tunit4 by external references", "lineNumber": 211 }, { - "__docId__": 445, + "__docId__": 446, "kind": "test", - "name": "describe188", - "testId": 188, - "memberof": "test/taxonomic-units.js~describe183", + "name": "describe189", + "testId": 189, + "memberof": "test/taxonomic-units.js~describe184", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe188", + "longname": "test/taxonomic-units.js~describe184.describe189", "access": null, "description": "#matchByOccurrenceID", "lineNumber": 217 }, { - "__docId__": 446, + "__docId__": 447, "kind": "test", - "name": "it189", - "testId": 189, - "memberof": "test/taxonomic-units.js~describe183.describe188", + "name": "it190", + "testId": 190, + "memberof": "test/taxonomic-units.js~describe184.describe189", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe188.it189", + "longname": "test/taxonomic-units.js~describe184.describe189.it190", "access": null, "description": "should be able to match tunit2 and tunit3 by specimen identifiers", "lineNumber": 218 }, { - "__docId__": 447, + "__docId__": 448, "kind": "test", - "name": "describe190", - "testId": 190, - "memberof": "test/taxonomic-units.js~describe183", + "name": "describe191", + "testId": 191, + "memberof": "test/taxonomic-units.js~describe184", "testDepth": 1, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe190", + "longname": "test/taxonomic-units.js~describe184.describe191", "access": null, "description": "#matched and #matchReason", "lineNumber": 224 }, { - "__docId__": 448, + "__docId__": 449, "kind": "test", - "name": "it191", - "testId": 191, - "memberof": "test/taxonomic-units.js~describe183.describe190", + "name": "it192", + "testId": 192, + "memberof": "test/taxonomic-units.js~describe184.describe191", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe190.it191", + "longname": "test/taxonomic-units.js~describe184.describe191.it192", "access": null, "description": "should match tunit1 and tunit2 on the basis of identical complete names", "lineNumber": 225 }, { - "__docId__": 449, + "__docId__": 450, "kind": "test", - "name": "it192", - "testId": 192, - "memberof": "test/taxonomic-units.js~describe183.describe190", + "name": "it193", + "testId": 193, + "memberof": "test/taxonomic-units.js~describe184.describe191", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe190.it192", + "longname": "test/taxonomic-units.js~describe184.describe191.it193", "access": null, "description": "should match tunit3 and tunit4 by identical external reference", "lineNumber": 231 }, { - "__docId__": 450, + "__docId__": 451, "kind": "test", - "name": "it193", - "testId": 193, - "memberof": "test/taxonomic-units.js~describe183.describe190", + "name": "it194", + "testId": 194, + "memberof": "test/taxonomic-units.js~describe184.describe191", "testDepth": 2, "static": true, - "longname": "test/taxonomic-units.js~describe183.describe190.it193", + "longname": "test/taxonomic-units.js~describe184.describe191.it194", "access": null, "description": "should match tunit2 and tunit3 by identical specimen identifier", "lineNumber": 237 diff --git a/docs/script/search_index.js b/docs/script/search_index.js index 100214e9..5dee36ad 100644 --- a/docs/script/search_index.js +++ b/docs/script/search_index.js @@ -691,22 +691,28 @@ window.esdocSearchIndex = [ ], [ "", - "test-file/test/specimens.js.html#lineNumber77", + "test-file/test/specimens.js.html#lineNumber83", "SpecimenWrapper #constructor should be able to create a specimen JSON record from an occurrence ID", "test" ], [ "", - "test-file/test/specimens.js.html#lineNumber24", + "test-file/test/specimens.js.html#lineNumber30", "SpecimenWrapper #constructor should be able to extract an occurenceID and catalogNumber from simple specimen IDs", "test" ], [ "", - "test-file/test/specimens.js.html#lineNumber53", + "test-file/test/specimens.js.html#lineNumber59", "SpecimenWrapper #constructor should be able to extract the same occurrenceID from different representations", "test" ], + [ + "", + "test-file/test/specimens.js.html#lineNumber24", + "SpecimenWrapper #constructor should be able to wrap a specimen with an empty occurenceID", + "test" + ], [ "", "test-file/test/specimens.js.html#lineNumber18", @@ -715,25 +721,25 @@ window.esdocSearchIndex = [ ], [ "", - "test-file/test/specimens.js.html#lineNumber33", + "test-file/test/specimens.js.html#lineNumber39", "SpecimenWrapper #constructor should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination", "test" ], [ "", - "test-file/test/specimens.js.html#lineNumber43", + "test-file/test/specimens.js.html#lineNumber49", "SpecimenWrapper #constructor should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples", "test" ], [ "", - "test-file/test/specimens.js.html#lineNumber68", + "test-file/test/specimens.js.html#lineNumber74", "SpecimenWrapper #constructor should not attempt to split a URL into occurenceID, institutionCode and catalogNumber", "test" ], [ "", - "test-file/test/specimens.js.html#lineNumber59", + "test-file/test/specimens.js.html#lineNumber65", "SpecimenWrapper #constructor should not attempt to split a URN into occurenceID, institutionCode and catalogNumber", "test" ], diff --git a/docs/source.html b/docs/source.html index 67bc01fe..467b60c1 100644 --- a/docs/source.html +++ b/docs/source.html @@ -63,7 +63,7 @@ 50 %7/14 4411 byte 135 - 2021-03-02 04:00:27 (UTC) + 2024-12-03 05:49:05 (UTC) src/wrappers/CitationWrapper.js @@ -71,7 +71,7 @@ 57 %4/7 4974 byte 130 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:49:05 (UTC) src/wrappers/PhylogenyWrapper.js @@ -79,7 +79,7 @@ 10 %2/19 18456 byte 480 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:49:05 (UTC) src/wrappers/PhylorefWrapper.js @@ -87,7 +87,7 @@ 28 %9/32 32668 byte 811 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:49:05 (UTC) src/wrappers/PhyxWrapper.js @@ -95,15 +95,15 @@ 41 %5/12 14037 byte 312 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:49:05 (UTC) src/wrappers/SpecimenWrapper.js SpecimenWrapper 77 %14/18 - 8770 byte + 8676 byte 241 - 2024-06-04 03:09:07 (UTC) + 2024-12-02 03:27:18 (UTC) src/wrappers/TaxonConceptWrapper.js @@ -111,7 +111,7 @@ 77 %14/18 7247 byte 211 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:26:12 (UTC) src/wrappers/TaxonNameWrapper.js @@ -119,7 +119,7 @@ 74 %29/39 15356 byte 498 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:49:05 (UTC) src/wrappers/TaxonomicUnitWrapper.js @@ -127,7 +127,7 @@ 70 %14/20 8220 byte 265 - 2024-06-04 03:09:07 (UTC) + 2024-12-03 05:49:05 (UTC) diff --git a/docs/test-file/test/scripts/resolve.js.html b/docs/test-file/test/scripts/resolve.js.html index 2855db5d..709c3259 100644 --- a/docs/test-file/test/scripts/resolve.js.html +++ b/docs/test-file/test/scripts/resolve.js.html @@ -107,15 +107,15 @@ ]); expect(resultObj.Alligatoridae[0].resolved).to.include({ - '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott195670', + '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott195670', label: 'Alligatoridae', }); expect(resultObj.Alligatorinae[0].resolved).to.include({ - '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott151255', + '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott151255', label: 'Alligatorinae', }); expect(resultObj.Crocodylidae[0].resolved).to.include({ - '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree14.9@ott1092501', + '@id': 'https://tree.opentreeoflife.org/opentree/argus/opentree15.1@ott1092501', label: 'Longirostres', }); expect(resultObj.Diplocynodontinae[0]).to.include({ diff --git a/docs/test-file/test/specimens.js.html b/docs/test-file/test/specimens.js.html index 2bd4ac66..5cbdfaa6 100644 --- a/docs/test-file/test/specimens.js.html +++ b/docs/test-file/test/specimens.js.html @@ -66,10 +66,16 @@ expect(wrapped).to.be.an.instanceOf(phyx.SpecimenWrapper); expect(wrapped.occurrenceID).to.be.undefined; }); + it('should be able to wrap a specimen with an empty occurenceID', function () { + const wrapped = new phyx.SpecimenWrapper(phyx.SpecimenWrapper.fromOccurrenceID('')); + + expect(wrapped).to.be.an.instanceOf(phyx.SpecimenWrapper); + expect(wrapped.occurrenceID).to.equal(''); + }); it('should be able to extract an occurenceID and catalogNumber from simple specimen IDs', function () { const wrapper = new phyx.SpecimenWrapper({ occurrenceID: 'Wall 2527, Fiji (uc)', - 'dwc:basisOfRecord': 'PreservedSpecimen', + basisOfRecord: 'PreservedSpecimen', }); expect(wrapper.occurrenceID).to.equal('Wall 2527, Fiji (uc)'); expect(wrapper.catalogNumber).to.equal('Wall 2527, Fiji (uc)'); @@ -78,7 +84,7 @@ it('should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination', function () { const wrapper = new phyx.SpecimenWrapper({ occurrenceID: 'FMNH:PR 2081', - 'dwc:basisOfRecord': 'PreservedSpecimen', + basisOfRecord: 'PreservedSpecimen', }); expect(wrapper.occurrenceID).to.equal('FMNH:PR 2081'); expect(wrapper.institutionCode).to.equal('FMNH'); @@ -125,7 +131,7 @@ expect(specimen.institutionCode).to.equal('FMNH'); expect(specimen.collectionCode).to.equal('PR'); expect(specimen.catalogNumber).to.equal('2081'); - expect(specimen['dwc:basisOfRecord']).to.equal('PreservedSpecimen'); + expect(specimen.basisOfRecord).to.equal('PreservedSpecimen'); }); }); }); diff --git a/docs/test.html b/docs/test.html index 0df675a3..d984eb9b 100644 --- a/docs/test.html +++ b/docs/test.html @@ -953,43 +953,49 @@ -

              should be able to extract an occurenceID and catalogNumber from simple specimen IDs

              +

              should be able to wrap a specimen with an empty occurenceID

               - -

              should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination

              +

              should be able to extract an occurenceID and catalogNumber from simple specimen IDs

               - -

              should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples

              +

              should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination

               - -

              should be able to extract the same occurrenceID from different representations

              +

              should extract occurenceID, institutionCode and catalogNumber from Darwin Core triples

               - -

              should not attempt to split a URN into occurenceID, institutionCode and catalogNumber

              +

              should be able to extract the same occurrenceID from different representations

               - -

              should not attempt to split a URL into occurenceID, institutionCode and catalogNumber

              +

              should not attempt to split a URN into occurenceID, institutionCode and catalogNumber

               - -

              should be able to create a specimen JSON record from an occurrence ID

              +

              should not attempt to split a URL into occurenceID, institutionCode and catalogNumber

              +               + - + + + +

              should be able to create a specimen JSON record from an occurrence ID

               - From 3df414e218dd8f4b94d554463f33a82eb51d4b16 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Sun, 22 Dec 2024 22:39:57 -0500 Subject: [PATCH 6/6] Updated version to v1.2.0-alpha3. Apparently we already released an alpha2 six months ago? --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 2d6a5d8e..41d39793 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@phyloref/phyx", - "version": "1.2.0-alpha2", + "version": "1.2.0-alpha3", "description": "Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files", "keywords": [ "phylogenetics",