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API-TEST: Update Curie Formation Logic #755

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API-TEST: Update Curie Formation Logic #755

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3422b93
- Update curie formation logic
haideriqbal Oct 1, 2024
4eb0e5f
- Improve code logic
haideriqbal Oct 1, 2024
5e161a1
- Improve code logic to handle edge cases
haideriqbal Oct 2, 2024
44a9fcc
- Update testcases
haideriqbal Oct 2, 2024
eeb03c5
- Update API testcase
haideriqbal Oct 3, 2024
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5 changes: 1 addition & 4 deletions apitester4/src/main/java/uk/ac/ebi/ols/apitester/RecursiveJsonDiff.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,13 +63,10 @@ public boolean diff() throws FileNotFoundException {
continue;
}

if(jsonA.equals(jsonB)) {
System.out.println(inputDir + filename + " was equal to " + expectedDir + filename);
} else {
if(!jsonA.equals(jsonB)) {
System.out.println(inputDir + filename + " differed from " + expectedDir + filename);
success = false;
}

}

return success;
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11 changes: 8 additions & 3 deletions dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
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Expand Up @@ -36,16 +36,21 @@ public static void annotateShortForms(OntologyGraph graph) {
}

String shortForm = extractShortForm(graph, ontologyBaseUris, preferredPrefix, c.uri);
String curie = shortForm.replaceFirst("_", ":");

/*
CURIEs are formed by following rules:
If there is only one underscore "_" AND the characters after the underscore are numbers then replace the underscore with colon ":"
If there is only one underscore "_" and the characters after the underscore are not just numbers then just keep the curie same as shortform
If there are multiple underscore but has only digits after the last underscore then the code replaces the last underscore with a colon
*/

String curie = shortForm.replaceFirst("_(\\d+)$", ":$1");
c.properties.addProperty("shortForm", PropertyValueLiteral.fromString(shortForm));
c.properties.addProperty("curie", PropertyValueLiteral.fromString(curie));
}
}
long endTime3 = System.nanoTime();
logger.info("annotate short forms: {}", ((endTime3 - startTime3) / 1000 / 1000 / 1000));


}

private static String extractShortForm(OntologyGraph graph, Set<String> ontologyBaseUris, String preferredPrefix,
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594 changes: 297 additions & 297 deletions testcases_expected_output/annotation-properties/gitIssue502/classes.jsonl
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498 changes: 249 additions & 249 deletions testcases_expected_output/annotation-properties/gitIssue502/gitissue502_classes.csv
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304 changes: 152 additions & 152 deletions testcases_expected_output/annotation-properties/gitIssue502/gitissue502_properties.csv
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12 changes: 6 additions & 6 deletions testcases_expected_output/annotation-properties/gitIssue502/oio_classes.csv
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2 changes: 1 addition & 1 deletion testcases_expected_output/annotation-properties/gitIssue502/oio_ontologies.csv
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@@ -1,5 +1,5 @@
"id:ID",":LABEL","_json","iri","numberOfIndividuals:string[]","linkedEntities:string[]","ontology_purl:string[]","numDescendants:string[]","numberOfProperties:string[]","numberOfClasses:string[]","language:string[]","numHierarchicalDescendants:string[]","isObsolete:string[]","label:string[]","importsFrom:string[]","type:string[]","directAncestor:string[]","exportsTo:string[]","base_uri:string[]","http__//www.w3.org/2000/01/rdf-schema#comment:string[]","imported:string[]","numberOfEntities:string[]","ontologyId:string[]","http__//www.w3.org/2000/01/rdf-schema#label:string[]","definition:string[]","http__//www.w3.org/1999/02/22-rdf-syntax-ns#type:string[]"
"oio+ontology+http://www.geneontology.org/formats/oboInOwl","Ontology","{""ontologyId"":""oio"",""importsFrom"":[],""exportsTo"":[""gitissue502""],""iri"":""http://www.geneontology.org/formats/oboInOwl"",""ontology_purl"":""https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl"",""base_uri"":[""http://www.geneontology.org/formats/oboInOwl#""],""type"":[""ontology""],""definition"":[{""type"":[""literal""],""value"":""OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties""},{""type"":[""literal""],""value"":""\n This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n ""}],""directAncestor"":[],""http://www.w3.org/1999/02/22-rdf-syntax-ns#type"":""http://www.w3.org/2002/07/owl#Ontology"",""http://www.w3.org/2000/01/rdf-schema#comment"":[{""type"":[""literal""],""value"":""OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties""},{""type"":[""literal""],""value"":""\n This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n ""}],""http://www.w3.org/2000/01/rdf-schema#label"":{""type"":[""literal""],""value"":""""},""imported"":false,""isObsolete"":false,""label"":{""type"":[""literal""],""value"":""""},""language"":{""type"":[""literal""],""value"":""en""},""numDescendants"":0.0,""numHierarchicalDescendants"":0.0,""numberOfClasses"":{""type"":[""literal""],""value"":""12""},""numberOfEntities"":{""type"":[""literal""],""value"":""56""},""numberOfIndividuals"":{""type"":[""literal""],""value"":""0""},""numberOfProperties"":{""type"":[""literal""],""value"":""44""},""searchableAnnotationValues"":[false,{""type"":[""literal""],""value"":""en""},{""type"":[""literal""],""value"":""12""},{""type"":[""literal""],""value"":""56""},{""type"":[""literal""],""value"":""0""},{""type"":[""literal""],""value"":""44""}],""linkedEntities"":{""http://www.w3.org/2000/01/rdf-schema#comment"":{""definedBy"":[""rdfs""],""numAppearsIn"":2.0,""hasLocalDefinition"":false,""label"":{""type"":[""literal""],""value"":""comment""},""curie"":{""type"":[""literal""],""value"":""RDFS:comment""},""type"":[""property"",""entity""]},""http://www.w3.org/2000/01/rdf-schema#label"":{""definedBy"":[""rdfs""],""numAppearsIn"":3.0,""hasLocalDefinition"":false,""label"":{""type"":[""literal""],""value"":""label""},""curie"":{""type"":[""literal""],""value"":""RDFS:label""},""type"":[""property"",""entity""]}}}","http://www.geneontology.org/formats/oboInOwl","0","","https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl","0.0","44","12","en","0.0","false","","","ontology","","gitissue502","http://www.geneontology.org/formats/oboInOwl#","OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties|
"oio+ontology+http://www.geneontology.org/formats/oboInOwl","Ontology","{""ontologyId"":""oio"",""importsFrom"":[],""exportsTo"":[""gitissue502""],""iri"":""http://www.geneontology.org/formats/oboInOwl"",""ontology_purl"":""https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl"",""base_uri"":[""http://www.geneontology.org/formats/oboInOwl#""],""type"":[""ontology""],""definition"":[{""type"":[""literal""],""value"":""OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties""},{""type"":[""literal""],""value"":""\n This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n ""}],""directAncestor"":[],""http://www.w3.org/1999/02/22-rdf-syntax-ns#type"":""http://www.w3.org/2002/07/owl#Ontology"",""http://www.w3.org/2000/01/rdf-schema#comment"":[{""type"":[""literal""],""value"":""OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties""},{""type"":[""literal""],""value"":""\n This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi\n ""}],""http://www.w3.org/2000/01/rdf-schema#label"":{""type"":[""literal""],""value"":""""},""imported"":false,""isObsolete"":false,""label"":{""type"":[""literal""],""value"":""""},""language"":{""type"":[""literal""],""value"":""en""},""numDescendants"":0.0,""numHierarchicalDescendants"":0.0,""numberOfClasses"":{""type"":[""literal""],""value"":""12""},""numberOfEntities"":{""type"":[""literal""],""value"":""56""},""numberOfIndividuals"":{""type"":[""literal""],""value"":""0""},""numberOfProperties"":{""type"":[""literal""],""value"":""44""},""searchableAnnotationValues"":[false,{""type"":[""literal""],""value"":""en""},{""type"":[""literal""],""value"":""12""},{""type"":[""literal""],""value"":""56""},{""type"":[""literal""],""value"":""0""},{""type"":[""literal""],""value"":""44""}],""linkedEntities"":{""http://www.w3.org/2000/01/rdf-schema#comment"":{""definedBy"":[""rdfs""],""numAppearsIn"":2.0,""hasLocalDefinition"":false,""label"":{""type"":[""literal""],""value"":""comment""},""curie"":{""type"":[""literal""],""value"":""RDFS_comment""},""type"":[""property"",""entity""]},""http://www.w3.org/2000/01/rdf-schema#label"":{""definedBy"":[""rdfs""],""numAppearsIn"":3.0,""hasLocalDefinition"":false,""label"":{""type"":[""literal""],""value"":""label""},""curie"":{""type"":[""literal""],""value"":""RDFS_label""},""type"":[""property"",""entity""]}}}","http://www.geneontology.org/formats/oboInOwl","0","","https://gist.githubusercontent.com/haideriqbal/4a2b1a9aa81d9fa26cae81e0b0b7730b/raw/527665128b9be9d7d6133f9a796379600151c737/oboInOwl.owl","0.0","44","12","en","0.0","false","","","ontology","","gitissue502","http://www.geneontology.org/formats/oboInOwl#","OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties|
This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi
","false","56","oio","","OBO Format metamodel. This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties|
This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi
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