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Remove node ref from Warning
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@alexander-myltsev
alexander-myltsev committed Apr 10, 2018
1 parent f118d82 commit d1683da
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Showing 3 changed files with 28 additions and 82 deletions.
58 changes: 24 additions & 34 deletions parser/src/main/scala/org/globalnames/parser/Parser.scala
View file
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
val r = FactoryAST.name(uninomial = uninomial1M,
species = sp.some,
infraspecies = ig)
.changeWarningsRef((n1M.node, n2M.node), (n1M.node.uninomial, uninomial1M.node))
(hc, r.some)
case Right((hc, n)) => (hc, n)
}
Expand Down Expand Up @@ -136,7 +135,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
val u1 = FactoryAST.uninomial(u)
val nm = FactoryAST.name(uninomial = u1, species = s, comparison = c.some)
nm.add(warnings = Seq((3, "Name comparison")))
.changeWarningsRef((u.node, u1.node))
}
}

Expand Down Expand Up @@ -165,9 +163,9 @@ class Parser(preprocessorResult: Preprocessor.Result,
infrOpt <- lift(maybeInfraspeciesGroupM) }
yield Name(u1, comparison = cmp,
species = species.some, infraspecies = infrOpt)
nm.changeWarningsRef((ssM.node, uM1.node))
nm
}
name.changeWarningsRef((uwM.node, uM1.node))
name
}
}

Expand Down Expand Up @@ -276,15 +274,15 @@ class Parser(preprocessorResult: Preprocessor.Result,
(uninomial ~ softSpace ~ rankUninomial ~ softSpace ~ uninomial) ~> {
(u1M: NodeMeta[Uninomial], rM: NodeMeta[Rank], u2M: NodeMeta[Uninomial]) =>
val r = for { u1 <- u1M; r <- rM; u2 <- u2M } yield u2.copy(rank = r.some, parent = u1.some)
r.changeWarningsRef((u2M.node, r.node))
r
}
}

def uninomial: RuleNodeMeta[Uninomial] = rule {
uninomialWord ~ (space ~ authorship).? ~> {
(uM: NodeMeta[UninomialWord], aM: Option[NodeMeta[Authorship]]) =>
val r = for { u <- uM; a <- lift(aM) } yield Uninomial(u, a)
r.changeWarningsRef((uM.node, r.node))
r
}
}

Expand Down Expand Up @@ -324,7 +322,7 @@ class Parser(preprocessorResult: Preprocessor.Result,
(uwM: NodeMeta[UninomialWord], wM: NodeMeta[UninomialWord]) =>
val uw1M = for { uw <- uwM; w <- wM }
yield uw.copy(pos = CapturePosition(uw.pos.start, w.pos.end))
uw1M.changeWarningsRef((uwM.node, uw1M.node), (wM.node, uw1M.node))
uw1M
}
}

Expand Down Expand Up @@ -429,8 +427,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
yield bau.copy(authors = authors1)

bau1M.add(warnings = Seq((2, "Ex authors are not required")))
.changeWarningsRef((bauM.node.authors, authors1M.node), (bauM.node, bau1M.node),
(exM.node, bau1M.node))
}
}

Expand All @@ -442,8 +438,7 @@ class Parser(preprocessorResult: Preprocessor.Result,
val bau1M = for { bau <- bauM; authors1 <- authors1M; _ <- emendM }
yield bau.copy(authors = authors1)

bau1M.changeWarningsRef((bauM.node.authors, authors1M.node), (bauM.node, bau1M.node),
(emendauM.node, bau1M.node))
bau1M
}
}

Expand All @@ -452,7 +447,7 @@ class Parser(preprocessorResult: Preprocessor.Result,
(bauM: NodeMeta[Authorship], cauM: NodeMeta[Authorship]) =>
val r = for { bau <- bauM; cau <- cauM }
yield bau.copy(combination = cau.authors.some, basionymParsed = true)
r.changeWarningsRef((bauM.node, r.node))
r
}
}

Expand All @@ -462,7 +457,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
val authors1 = aM.map { a => a.copy(authors = a.authors.copy(year = yM.node.some)) }
FactoryAST.authorship(authors = authors1, inparenthesis = true, basionymParsed = true)
.add(warnings = Seq((2, "Misformed basionym year")))
.changeWarningsRef((aM.node, authors1.node))
}
}

Expand All @@ -474,7 +468,7 @@ class Parser(preprocessorResult: Preprocessor.Result,
'(' ~ softSpace ~ authorship1 ~ softSpace ~ ')' ~> {
(aM: NodeMeta[Authorship]) =>
val r = aM.map { a => a.copy(basionymParsed = true, inparenthesis = true) }
r.changeWarningsRef((aM.node, r.node))
r
}
}

Expand All @@ -483,12 +477,20 @@ class Parser(preprocessorResult: Preprocessor.Result,
(aM: NodeMeta[Authorship]) =>
val r = aM.map { a => a.copy(basionymParsed = true, inparenthesis = true) }
r.add(warnings = Seq((3, "Authroship in double parentheses")))
.changeWarningsRef((aM.node, r.node))
}
}

def authorship1: RuleNodeMeta[Authorship] = rule {
authorsGroup ~> { (a: NodeMeta[AuthorsGroup]) => FactoryAST.authorship(a) }
(authorsYear | authorsGroup) ~> { (a: NodeMeta[AuthorsGroup]) => FactoryAST.authorship(a) }
}

def authorsYear: RuleNodeMeta[AuthorsGroup] = rule {
authorsGroup ~ softSpace ~ (',' ~ softSpace).? ~ year ~> {
(aM: NodeMeta[AuthorsGroup], yM: NodeMeta[Year]) =>
val a1 = for { a <- aM; y <- yM }
yield a.copy(authors = a.authors.copy(year = y.some))
a1
}
}

def authorsGroup: RuleNodeMeta[AuthorsGroup] = rule {
Expand Down Expand Up @@ -528,7 +530,7 @@ class Parser(preprocessorResult: Preprocessor.Result,
}) ~ (softSpace ~ (',' ~ softSpace).? ~ year).? ~> {
(atM: NodeMeta[AuthorsTeam], yM: Option[NodeMeta[Year]]) =>
val at1M = for { at <- atM; y <- lift(yM) } yield at.copy(year = y)
at1M.changeWarningsRef((atM.node, at1M.node))
at1M
}
}

Expand Down Expand Up @@ -561,7 +563,7 @@ class Parser(preprocessorResult: Preprocessor.Result,
author2 ~ softSpace ~ filius ~> {
(auM: NodeMeta[Author], filiusM: NodeMeta[AuthorWord]) =>
val au1M = for { au <- auM; filius <- filiusM } yield au.copy(filius = filius.some)
au1M.changeWarningsRef((auM.node, au1M.node))
au1M
}
}

Expand All @@ -583,11 +585,11 @@ class Parser(preprocessorResult: Preprocessor.Result,
def authorWordSep: RuleNodeMeta[AuthorWord] = rule {
(ch(dash) ~ authorWordSoft ~> { (awM: NodeMeta[AuthorWord]) =>
val aw1M = for (aw <- awM) yield aw.copy(separator = AuthorWordSeparator.Dash)
aw1M.changeWarningsRef((awM.node, aw1M.node))
aw1M
}) |
(softSpace ~ authorWord ~> { (awM: NodeMeta[AuthorWord]) =>
val aw1M = awM.node.copy(separator = AuthorWordSeparator.Space)
aw1M.changeWarningsRef((awM.node, aw1M.node))
val aw1M = for (aw <- awM) yield { aw.copy(separator = AuthorWordSeparator.Space) }
aw1M
})
}

Expand Down Expand Up @@ -657,7 +659,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
(yStartM: NodeMeta[Year], yEnd: CapturePosition) =>
val yrM = yStartM.map { yStart => yStart.copy(approximate = true, rangeEnd = Some(yEnd)) }
yrM.add(warnings = Seq((3, "Years range")))
.changeWarningsRef((yStartM.node, yrM.node))
}
}

Expand All @@ -670,7 +671,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
(yM: NodeMeta[Year]) =>
val yrM = yM.map { y => y.copy(approximate = true) }
yrM.add(warnings = Seq((3, "Year with square brakets")))
.changeWarningsRef((yM.node, yrM.node))
}
}

Expand All @@ -685,7 +685,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
(yM: NodeMeta[Year]) =>
val y1M = yM.map { y => y.copy(approximate = true) }
y1M.add(warnings = Seq((2, "Year with parentheses")))
.changeWarningsRef((yM.node, y1M.node))
}
}

Expand All @@ -694,7 +693,6 @@ class Parser(preprocessorResult: Preprocessor.Result,
(yM: NodeMeta[Year], pos: CapturePosition) =>
val y1M = yM.map { y => y.copy(alpha = pos.some) }
y1M.add(warnings = Seq((2, "Year with latin character")))
.changeWarningsRef((yM.node, y1M.node))
}
}

Expand Down Expand Up @@ -763,15 +761,7 @@ object Parser {
case class NodeMeta[T <: AstNode](node: T, warnings: Vector[Warning] = Vector.empty)
extends NodeMetaBase[T] {

val rawWarnings = warnings.map { w => (w.level, w.message) }

def changeWarningsRef(substitutions: (AstNode, AstNode)*): NodeMeta[T] = {
val substWarnsMap = substitutions.toMap
val ws = warnings.map { w =>
substWarnsMap.get(w.node).map { subst => w.copy(node = subst) }.getOrElse(w)
}
this.copy(warnings = ws)
}
val rawWarnings: Vector[(Int, String)] = warnings.map { w => (w.level, w.message) }

def add(warnings: Seq[(Int, String)] = Seq.empty): NodeMeta[T] = {
if (warnings.isEmpty) this
Expand Down
8 changes: 4 additions & 4 deletions parser/src/test/resources/test_data.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -1969,16 +1969,16 @@ Anthoscopus Cabanis [1851?]
6b12b541-b58b-5f11-ba66-bb314b53813f|Anthoscopus Cabanis [1851?]|Anthoscopus|Anthoscopus|Cabanis (1851?)|(1851?)|3

Trismegistia monodii Ando, 1973 [1974]
{"name_string_id":"f396d2d0-b14e-537f-ae8f-c383310f813e","parsed":true,"quality":3,"quality_warnings":[[3,"Unparseable tail"]],"parser_version":"test_version","verbatim":"Trismegistia monodii Ando, 1973 [1974]","normalized":"Trismegistia monodii Ando 1973","canonical_name":{"value":"Trismegistia monodii","value_ranked":"Trismegistia monodii"},"hybrid":false,"surrogate":false,"unparsed_tail":" [1974]","virus":false,"bacteria":false,"details":[{"genus":{"value":"Trismegistia"},"specific_epithet":{"value":"monodii","authorship":{"value":"Ando 1973","basionym_authorship":{"authors":["Ando"],"year":{"value":"1973"}}}}}],"positions":[["genus",0,12],["specific_epithet",13,20],["author_word",21,25],["year",27,31]]}
f396d2d0-b14e-537f-ae8f-c383310f813e|Trismegistia monodii Ando, 1973 [1974]|Trismegistia monodii|Trismegistia monodii|Ando 1973|1973|3
{"name_string_id":"f396d2d0-b14e-537f-ae8f-c383310f813e","parsed":true,"quality":3,"quality_warnings":[[3,"Year with square brakets"]],"parser_version":"test_version","verbatim":"Trismegistia monodii Ando, 1973 [1974]","normalized":"Trismegistia monodii Ando (1974)","canonical_name":{"value":"Trismegistia monodii","value_ranked":"Trismegistia monodii"},"hybrid":false,"surrogate":false,"virus":false,"bacteria":false,"details":[{"genus":{"value":"Trismegistia"},"specific_epithet":{"value":"monodii","authorship":{"value":"Ando (1974)","basionym_authorship":{"authors":["Ando"],"year":{"value":"1974","approximate":true}}}}}],"positions":[["genus",0,12],["specific_epithet",13,20],["author_word",21,25],["approximate_year",33,37]]}
f396d2d0-b14e-537f-ae8f-c383310f813e|Trismegistia monodii Ando, 1973 [1974]|Trismegistia monodii|Trismegistia monodii|Ando (1974)|(1974)|3

Zygaena witti Wiegel [1973]
{"name_string_id":"76eef612-f125-54f9-b241-6b3a9be0a6c6","parsed":true,"quality":3,"quality_warnings":[[3,"Year with square brakets"]],"parser_version":"test_version","verbatim":"Zygaena witti Wiegel [1973]","normalized":"Zygaena witti Wiegel (1973)","canonical_name":{"value":"Zygaena witti","value_ranked":"Zygaena witti"},"hybrid":false,"surrogate":false,"virus":false,"bacteria":false,"details":[{"genus":{"value":"Zygaena"},"specific_epithet":{"value":"witti","authorship":{"value":"Wiegel (1973)","basionym_authorship":{"authors":["Wiegel"],"year":{"value":"1973","approximate":true}}}}}],"positions":[["genus",0,7],["specific_epithet",8,13],["author_word",14,20],["approximate_year",22,26]]}
76eef612-f125-54f9-b241-6b3a9be0a6c6|Zygaena witti Wiegel [1973]|Zygaena witti|Zygaena witti|Wiegel (1973)|(1973)|3

Deyeuxia coarctata Kunth, 1815 [1816]
{"name_string_id":"2f479365-40be-5181-b194-8a24fc743f73","parsed":true,"quality":3,"quality_warnings":[[3,"Unparseable tail"]],"parser_version":"test_version","verbatim":"Deyeuxia coarctata Kunth, 1815 [1816]","normalized":"Deyeuxia coarctata Kunth 1815","canonical_name":{"value":"Deyeuxia coarctata","value_ranked":"Deyeuxia coarctata"},"hybrid":false,"surrogate":false,"unparsed_tail":" [1816]","virus":false,"bacteria":false,"details":[{"genus":{"value":"Deyeuxia"},"specific_epithet":{"value":"coarctata","authorship":{"value":"Kunth 1815","basionym_authorship":{"authors":["Kunth"],"year":{"value":"1815"}}}}}],"positions":[["genus",0,8],["specific_epithet",9,18],["author_word",19,24],["year",26,30]]}
2f479365-40be-5181-b194-8a24fc743f73|Deyeuxia coarctata Kunth, 1815 [1816]|Deyeuxia coarctata|Deyeuxia coarctata|Kunth 1815|1815|3
{"name_string_id":"2f479365-40be-5181-b194-8a24fc743f73","parsed":true,"quality":3,"quality_warnings":[[3,"Year with square brakets"]],"parser_version":"test_version","verbatim":"Deyeuxia coarctata Kunth, 1815 [1816]","normalized":"Deyeuxia coarctata Kunth (1816)","canonical_name":{"value":"Deyeuxia coarctata","value_ranked":"Deyeuxia coarctata"},"hybrid":false,"surrogate":false,"virus":false,"bacteria":false,"details":[{"genus":{"value":"Deyeuxia"},"specific_epithet":{"value":"coarctata","authorship":{"value":"Kunth (1816)","basionym_authorship":{"authors":["Kunth"],"year":{"value":"1816","approximate":true}}}}}],"positions":[["genus",0,8],["specific_epithet",9,18],["author_word",19,24],["approximate_year",32,36]]}
2f479365-40be-5181-b194-8a24fc743f73|Deyeuxia coarctata Kunth, 1815 [1816]|Deyeuxia coarctata|Deyeuxia coarctata|Kunth (1816)|(1816)|3
#>

#SECTION: Names with broken conversion between encodings<
Expand Down
44 changes: 0 additions & 44 deletions parser/src/test/scala/org/globalnames/parser/ScientificNameParserSpec.scala
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,49 +73,5 @@ class ScientificNameParserSpec extends Specification {
val pr = scientificNameParser.fromString(expectedName.verbatim)
Set(pr.warnings: _*).size === pr.warnings.size
}

s"contain no orphans in warnings" in {
def hasRefNode(sourceNode: AstNode, targetNode: AstNode): Boolean = targetNode match {
case tn if tn == sourceNode => true
case sn: ScientificName => sn.namesGroup.exists { ng => hasRefNode(sourceNode, ng) }
case ng: NamesGroup =>
hasRefNode(sourceNode, ng.name) ||
ng.hybridParts.exists { case (hc, name) =>
hasRefNode(sourceNode, hc) || name.exists { n => hasRefNode(sourceNode, n) }
}
case n: Name => hasRefNode(sourceNode, n.uninomial) ||
n.subgenus.exists { sg => hasRefNode(sourceNode, sg) } ||
n.species.exists { sp => hasRefNode(sourceNode, sp) } ||
n.infraspecies.exists { is => hasRefNode(sourceNode, is) } ||
n.comparison.exists { cmp => hasRefNode(sourceNode, cmp) } ||
n.approximation.exists { aprx => hasRefNode(sourceNode, aprx) }
case sg: SubGenus => hasRefNode(sourceNode, sg.word)
case u: Uninomial => u.authorship.exists { auth => hasRefNode(sourceNode, auth)} ||
u.rank.exists { rk => hasRefNode(sourceNode, rk) } ||
u.parent.exists { par => hasRefNode(sourceNode, par) }
case ig: InfraspeciesGroup => ig.group.exists { is => hasRefNode(sourceNode, is) }
case is: Infraspecies => hasRefNode(sourceNode, is.word) ||
is.rank.exists { rk => hasRefNode(sourceNode, rk) } ||
is.authorship.exists { a => hasRefNode(sourceNode, a) }
case sp: Species => hasRefNode(sourceNode, sp.word) ||
sp.authorship.exists { a => hasRefNode(sourceNode, a) }
case auth: Authorship => hasRefNode(sourceNode, auth.authors) ||
auth.combination.exists { cmb => hasRefNode(sourceNode, cmb) }
case ag: AuthorsGroup => hasRefNode(sourceNode, ag.authors) ||
ag.authorsEx.exists { auEx => hasRefNode(sourceNode, auEx) } ||
ag.authorsEmend.exists { auEm => hasRefNode(sourceNode, auEm) }
case at: AuthorsTeam => at.authors.exists { a => hasRefNode(sourceNode, a) } ||
at.year.exists { y => hasRefNode(sourceNode, y) }
case au: Author => au.words.exists { aw => hasRefNode(sourceNode, aw) } ||
au.filius.exists { f => hasRefNode(sourceNode, f) }
case _ => false
}

val pr = scientificNameParser.fromString(expectedName.verbatim)

pr.warnings.filterNot {
warning => hasRefNode(warning.node, pr.scientificName)
} should beEmpty
}
}
}

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