Merge branch 'dev' into enhance-curie-logic

apitester4/src/main/java/uk/ac/ebi/ols/apitester/RecursiveJsonDiff.java

@@ -63,10 +63,13 @@ public boolean diff() throws FileNotFoundException {
                 continue;
             }
 
-            if(!jsonA.equals(jsonB)) {
+            if(jsonA.equals(jsonB)) {
+                System.out.println(inputDir + filename + " was equal to " + expectedDir + filename);
+            } else {
                 System.out.println(inputDir + filename + " differed from " + expectedDir + filename);
                 success = false;
             }
+
         }
 
         return success;

dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/ShortFormAnnotator.java

@@ -37,7 +37,7 @@ public static void annotateShortForms(OntologyGraph graph) {
 			}
 
 			String shortForm = extractShortForm(graph, ontologyBaseUris, preferredPrefix, c.uri);
-
+          
 			/*
 			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 ":"
@@ -71,6 +71,8 @@ public static void annotateShortForms(OntologyGraph graph) {
 	}
 		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,

testcases_expected_output/annotation-properties/gitIssue502/oio_ontologies.csv

@@ -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