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API TEST - Update Curie formation logic #769

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Oct 25, 2024
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API TEST - Update Curie formation logic #769

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4ab4ca3
- Update curie formation logic
haideriqbal Oct 22, 2024
597525a
Test - Update curie formation logic
haideriqbal Oct 22, 2024
f66af0d
API Test - Update curie formation logic
haideriqbal Oct 22, 2024
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24 changes: 22 additions & 2 deletions dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package uk.ac.ebi.rdf2json.annotators;

import java.util.Set;
import java.util.regex.Pattern;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -39,16 +40,35 @@ public static void annotateShortForms(OntologyGraph graph) {

/*
CURIEs are formed by following rules:
If there is only one underscore "_" AND the characters before the underscore are PreferredPrefix then replace the underscore with colon ":"
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;
// Pattern for: single underscore, prefix matches preferredPrefix
String preferredPrefixPattern = "^(?:" + Pattern.quote(preferredPrefix) + ")_([^_]+)$";
// Pattern for: single underscore, suffix is all digits
String singleUnderscoreDigitsPattern = "^[^_]+_(\\d+)$";
// Pattern for: multiple underscores, suffix is all digits
String multipleUnderscoresDigitsPattern = "^(.*)_(\\d+)$";
if (shortForm.matches(preferredPrefixPattern)) {
curie = shortForm.replaceFirst("_", ":");
} else if (shortForm.matches(singleUnderscoreDigitsPattern)) {
curie = shortForm.replaceFirst("_", ":");
} else if (shortForm.matches(multipleUnderscoresDigitsPattern)) {
// Multiple underscores, suffix is digits
// Replace the last underscore with a colon
curie = shortForm.replaceFirst("_(?=\\d+$)", ":");
} else {
// No transformation needed
curie = shortForm;
}

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));
}
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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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300 changes: 150 additions & 150 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|
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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
Expand Down
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