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Correct empty occurenceID so that it is blank, not urn:catalog::: #148

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merged 5 commits into from
Dec 23, 2024
Merged

Correct empty occurenceID so that it is blank, not urn:catalog::: #148

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86cf761
Needed to add a package to get ESLint to work.
gaurav Dec 17, 2024
01deeb7
Updated some tests.
gaurav Dec 17, 2024
1dd011d
Added a failing test with the expected behavior.
gaurav Dec 17, 2024
3c5d71a
Removed unnecessary check for empty occurrenceID.
gaurav Dec 17, 2024
0e86a9c
Replaced deprecated method with non-deprecated method.
gaurav Dec 17, 2024
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227 changes: 227 additions & 0 deletions package-lock.json
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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
"yargs": "^15.4.1"
},
"devDependencies": {
"@shinnn/eslint-config": "^7.0.0",
"ajv": "^6.12.2",
"chai": "^4.2.0",
"esdoc": "^1.1.0",
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4 changes: 2 additions & 2 deletions src/wrappers/SpecimenWrapper.js
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Expand Up @@ -57,7 +57,7 @@ class SpecimenWrapper {
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 = {
Expand Down Expand Up @@ -159,7 +159,7 @@ class SpecimenWrapper {
*/
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();
}

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6 changes: 3 additions & 3 deletions test/scripts/resolve.js
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Expand Up @@ -62,15 +62,15 @@ describe('bin/resolve.js', function () {
]);

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({
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6 changes: 6 additions & 0 deletions test/specimens.js
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Expand Up @@ -21,6 +21,12 @@ describe('SpecimenWrapper', function () {
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)',
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