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Removed some unnecessary RDF properties #87

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merged 6 commits into from
Mar 18, 2021
Merged

Removed some unnecessary RDF properties #87

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c0233e6
Removed testcase:internal_specifier and testcase:external_specifier.
gaurav Mar 15, 2021
5c44bbb
Removed `testcase:malformed_phyloreference`.
gaurav Mar 15, 2021
c345485
Replaced `hasComponentClass` with `subClasses` for direct subclasses.
gaurav Mar 18, 2021
fd3f42f
`createComponentClass` no longer appends to phyloref.hasComponentClass.
gaurav Mar 18, 2021
e7d33c3
Updated component class caches to be Phyloref specific, not global.
gaurav Mar 18, 2021
1e7ae16
Regenerated expected example files.
gaurav Mar 18, 2021
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24 changes: 4 additions & 20 deletions docs/context/development/phyx.json
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,10 @@
"phyloref": "http://ontology.phyloref.org/phyloref.owl#",
"opentree": "http://purl.org/opentree/nexson#",

"subClasses": {
"@reverse": "rdfs:subClassOf"
},

"label": {
"@id": "rdfs:label",
"@type": "xsd:string"
Expand All @@ -38,21 +42,6 @@
"@type": "xsd:string"
},

"internalSpecifiers": {
"@id": "testcase:internal_specifier",
"@container": "@set"
},

"externalSpecifiers": {
"@id": "testcase:external_specifier",
"@container": "@set"
},

"hasComponentClass": {
"@id": "testcase:has_component_class",
"@container": "@set"
},

"hasName": {
"@id": "http://rs.tdwg.org/ontology/voc/TaxonConcept#hasName",
"@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName"
Expand Down Expand Up @@ -176,11 +165,6 @@
"@container": "@set"
},

"malformedPhyloreference": {
"@id": "testcase:malformed_phyloreference",
"@type": "xsd:string"
},

"title": "dct:title",
"source": "dct:source",
"bibliographicCitation": "dct:bibliographicCitation",
Expand Down
24 changes: 13 additions & 11 deletions src/wrappers/PhylorefWrapper.js
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Expand Up @@ -408,15 +408,15 @@ class PhylorefWrapper {

// TODO We need to replace this with an actual object-based comparison,
// rather than trusting the labels to tell us everything.
if (reusePrevious && has(PhylorefWrapper.componentClassesByLabel, componentClassLabel)) {
if (reusePrevious && has(this.componentClassesByLabel, componentClassLabel)) {
// If we see the same label again, return the previously defined component class.
return { '@id': PhylorefWrapper.componentClassesByLabel[componentClassLabel]['@id'] };
return { '@id': this.componentClassesByLabel[componentClassLabel]['@id'] };
}

// Create a new component class for this set of internal and external specifiers.
PhylorefWrapper.componentClassCount += 1;
this.componentClassCount += 1;
const componentClass = {};
componentClass['@id'] = `${jsonld['@id']}_component${PhylorefWrapper.componentClassCount}`;
componentClass['@id'] = `${jsonld['@id']}_component${this.componentClassCount}`;
// process.stderr.write(`Creating new componentClass with id: ${componentClass['@id']}`);

componentClass['@type'] = 'owl:Class';
Expand All @@ -431,10 +431,13 @@ class PhylorefWrapper {
});
}

jsonld.hasComponentClass.push(componentClass);
PhylorefWrapper.componentClassesByLabel[componentClassLabel] = componentClass;
// Save it in the cache for later usage.
this.componentClassesByLabel[componentClassLabel] = componentClass;

return { '@id': componentClass['@id'] };
// The first time we create a componentClass, we include it into the logical
// expression directly. On subsequent calls, we'll only return the `@id`
// (see above).
return componentClass;
}

getIncludesRestrictionForTU(tu) {
Expand Down Expand Up @@ -633,9 +636,8 @@ class PhylorefWrapper {

// We might need to make component classes.
// So we reset our component class counts and records.
PhylorefWrapper.componentClassCount = 0;
PhylorefWrapper.componentClassesByLabel = {};
phylorefAsJSONLD.hasComponentClass = [];
this.componentClassCount = 0;
this.componentClassesByLabel = {};

// The type of this phyloreference.
let calculatedPhylorefType;
Expand Down Expand Up @@ -748,7 +750,7 @@ class PhylorefWrapper {
// 2. We need to set each of these component classes to be a subclass of
// this phyloreference so that it can include instances from each of the
// logical expressions.
logicalExpressions.forEach(classExpr => this.createComponentClass(
phylorefAsJSONLD.subClasses = logicalExpressions.map(classExpr => this.createComponentClass(
phylorefAsJSONLD,
internalSpecifiers,
externalSpecifiers,
Expand Down
1 change: 0 additions & 1 deletion test/examples/correct/alligatoridae_default_nomen_code.jsonld
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Expand Up @@ -1535,7 +1535,6 @@
"externalSpecifiers": [],
"@id": "http://example.org/phyx.js/example#phyloref0",
"@type": "owl:Class",
"hasComponentClass": [],
"equivalentClass": {
"@type": "owl:Restriction",
"onProperty": "obo:CDAO_0000149",
Expand Down
237 changes: 110 additions & 127 deletions test/examples/correct/alligatoridae_default_nomen_code.nq
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1 change: 0 additions & 1 deletion test/examples/correct/alligatoridae_inferred_nomen_code.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -1536,7 +1536,6 @@
"externalSpecifiers": [],
"@id": "http://example.org/phyx.js/example#phyloref0",
"@type": "owl:Class",
"hasComponentClass": [],
"equivalentClass": {
"@type": "owl:Restriction",
"onProperty": "obo:CDAO_0000149",
Expand Down
238 changes: 110 additions & 128 deletions test/examples/correct/alligatoridae_inferred_nomen_code.nq
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8 changes: 2 additions & 6 deletions test/examples/correct/brochu_2003.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -1632,7 +1632,6 @@
"externalSpecifiers": [],
"@id": "http://example.org/phyx.js/example#phyloref0",
"@type": "owl:Class",
"hasComponentClass": [],
"equivalentClass": {
"@type": "owl:Restriction",
"onProperty": "obo:CDAO_0000149",
Expand Down Expand Up @@ -1775,7 +1774,6 @@
},
"@id": "http://example.org/phyx.js/example#phyloref1",
"@type": "owl:Class",
"hasComponentClass": [],
"equivalentClass": {
"@type": "owl:Class",
"intersectionOf": [
Expand Down Expand Up @@ -1913,7 +1911,6 @@
},
"@id": "http://example.org/phyx.js/example#phyloref2",
"@type": "owl:Class",
"hasComponentClass": [],
"equivalentClass": {
"@type": "owl:Class",
"intersectionOf": [
Expand Down Expand Up @@ -2024,7 +2021,7 @@
},
"@id": "http://example.org/phyx.js/example#phyloref3",
"@type": "owl:Class",
"hasComponentClass": [
"subClasses": [
{
"@id": "http://example.org/phyx.js/example#phyloref3_component1",
"@type": "owl:Class",
Expand Down Expand Up @@ -2305,7 +2302,7 @@
"externalSpecifiers": [],
"@id": "http://example.org/phyx.js/example#phyloref4",
"@type": "owl:Class",
"hasComponentClass": [
"subClasses": [
{
"@id": "http://example.org/phyx.js/example#phyloref4_component1",
"@type": "owl:Class",
Expand Down Expand Up @@ -3362,7 +3359,6 @@
},
"@id": "http://example.org/phyx.js/example#phyloref5",
"@type": "owl:Class",
"hasComponentClass": [],
"equivalentClass": {
"@type": "owl:Class",
"intersectionOf": [
Expand Down
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