Merge pull request #249 from owlcollab/bugfix-get-identifier

Fixed the null exception error in GetIdentifier
owlcollab · Apr 24, 2018 · a2d32ee · a2d32ee
2 parents c498f85 + 8a676df
commit a2d32ee
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Showing 4 changed files with 21 additions and 13 deletions.
diff --git a/OWLTools-Core/.settings/org.eclipse.jdt.core.prefs b/OWLTools-Core/.settings/org.eclipse.jdt.core.prefs
diff --git a/OWLTools-Core/src/main/java/owltools/graph/OWLGraphWrapperExtended.java b/OWLTools-Core/src/main/java/owltools/graph/OWLGraphWrapperExtended.java
@@ -1,6 +1,7 @@
 package owltools.graph;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -893,30 +894,36 @@ public String getIdentifier(IRI iriId) {
 			return (String) SerializationUtils.clone(Owl2Obo.getIdentifier(iriId));
 
 		final OWLAnnotationProperty oboIdInOwl = getDataFactory().getOWLAnnotationProperty(Obo2Owl.trTagToIRI(OboFormatTag.TAG_ID.getTag()));
-		OWLClass oc = getOWLClass(iriId);
 		for (OWLOntology o : getAllOntologies()) {
-			for (OWLAnnotation oa: EntitySearcher.getAnnotations(oc.getIRI(), o)) {
-				if (oa.getProperty().equals(oboIdInOwl) != true) 
+			Collection<OWLAnnotation> oas = EntitySearcher.getAnnotations(iriId, o);
+			if (oas == null) continue;
+
+			for (OWLAnnotation oa: oas) {
+				// We specifically look for the annotation property, oboInOwl:id; ignore others.
+				if (oa.getProperty().equals(oboIdInOwl) != true)
 					continue;
 
+				// We then get the object value of this property, which is supposed to be a literal.
 				OWLAnnotationValue objValue = oa.getValue();
 				if (objValue.isLiteral() != true) {
-					LOG.warn(objValue + " is supposed to be an literal, but it is not?!");
+					LOG.warn("Odd. " + objValue + " of oboInOw#id for "+ iriId + ", is supposed to be an literal, but it is not.");
 					continue;
 				}
 
 				Optional<OWLLiteral> literalOpt = objValue.asLiteral();
 				if (literalOpt.isPresent() != true) {
-					LOG.warn("Is the literal value of oboInOw#id, " + objValue + ", null?");
+					LOG.warn("Odd. " + objValue + " of oboInOw#id for "+ iriId + ", does not exist.");
 					continue;
 				}
 
 				OWLLiteral literal = literalOpt.get();
 				return (String) SerializationUtils.clone(literal.getLiteral());
 			}
-		} 
+		}
 
-		throw new RuntimeException("The IRI " + iriId + " does not start with the obolib prefix nor have any oboInOw#id?!");
+		// In the case where the input class does not have oboInOwl#id, we return its original URL.
+		LOG.warn("Unable to retrieve the value of oboInOw#id as the identifier for " + iriId + "; we will use an original iri as the identifier.");
+		return (String) SerializationUtils.clone(iriId.toString());
 	}
 
 	public IRI getIRIByIdentifier(String id) {

diff --git a/OWLTools-Core/src/test/java/owltools/graph/OWLGraphWrapperExtendedTest.java b/OWLTools-Core/src/test/java/owltools/graph/OWLGraphWrapperExtendedTest.java
@@ -43,9 +43,11 @@ public void testGetIdentifier() throws Exception {
 		String id1 = wrapper.getIdentifier(IRI.create("http://purl.obolibrary.org/obo/GO_0000001"));
 		String id2 = wrapper.getIdentifier(IRI.create("http://purl.obolibrary.org/obo/GO_0000002"));
 		String id3 = wrapper.getIdentifier(IRI.create("http://example.com/X_005"));
+		String id4 = wrapper.getIdentifier(IRI.create("http://example.com/X_010"));
 
 		assertEquals(id1, "GO:0000001");
 		assertEquals(id2, "GO:0000002");
 		assertEquals(id3, "X:5");
+		assertEquals(id4, "http://example.com/X_010");
 	}
 }
diff --git a/OWLTools-Core/src/test/resources/graph/dummy-ontology.owl b/OWLTools-Core/src/test/resources/graph/dummy-ontology.owl
@@ -28,4 +28,8 @@
     <owl:Class rdf:about="http://example.com/X_005">
         <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X:5</oboInOwl:id>
     </owl:Class>
-</rdf:RDF>
+
+    <owl:Class rdf:about="http://example.com/X_010">
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">test4</rdfs:label>
+    </owl:Class>
+</rdf:RDF>