[#72] provide a resolveIri method in the KB

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcher.java

@@ -47,7 +47,7 @@ public ClassMatcher(BMKnowledgeBase kb) {
 	 */
 	public List<SimpleClassMatch> matchEntity(String entity, String tOnt) {
 		Set<String> tids = kb.getClassIdsByOntology(tOnt);
-		return matchClassSets(Sets.newHashSet(entity), tids);
+		return matchClassSets(Sets.newHashSet(kb.resolveIri(entity)), tids);
 	}
 
 	public List<SimpleClassMatch> matchClassSets(Set<String> qids, Set<String> tids) {

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java

@@ -351,9 +351,12 @@
 	public int getRootIndex();
 
 
-
-
-
+	/**
+	 * Resolves a CURIE into an IRI, if possible.
+	 * 
+	 * @return IRI version of a CURIE, or the string itself
+	 */
+	public String resolveIri(String entity);
 
 
 }

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java

@@ -172,12 +172,8 @@ public void setKbMetdata(KBMetadata kbMetdata) {
 	}
 
 	private String getShortForm(IRI iri) {
-		if (curieUtil.getCurieMap().isEmpty()) {
-			return iri.toString();
-		} else {
-			String iriString = iri.toString();
-			return curieUtil.getCurie(iriString).orElse(iriString);
-		}
+		String iriString = iri.toString();
+		return curieUtil.getCurie(iriString).orElse(iriString);
 	}
 
 	private void populateLabelsFromOntology(LabelMapper labelMapper, OWLOntology ontology) {
@@ -1037,11 +1033,7 @@ protected String getIdentifier(OWLNamedObject obj) {
 	 */
 	private OWLClass getOWLClass(String id) {
 		Preconditions.checkNotNull(id);
-		if (curieUtil.getCurieMap().isEmpty()) {
-			return getOWLClass(IRI.create(id));
-		} else {
-			return getOWLClass(IRI.create(curieUtil.getIri(id).orElse(id)));
-		}
+		return getOWLClass(IRI.create(curieUtil.getIri(id).orElse(id)));
 	}
 
 	/**
@@ -1067,12 +1059,7 @@ private OWLNamedIndividual getOWLNamedIndividual(IRI iri) {
 	 */
 	public OWLNamedIndividual getOWLNamedIndividual(String id) {
 		Preconditions.checkNotNull(id);
-		//TODO: check - this is redundant code simply return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id))); will suffice
-		if (curieUtil.getCurieMap().isEmpty()) {
-			return getOWLNamedIndividual(IRI.create(id));
-		} else {
-			return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id)));
-		}
+		return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id)));
 	}
 
 	public Attribute getAttribute(String id) {
@@ -1144,4 +1131,9 @@ public EWAHCompressedBitmap getFilteredDirectTypesBM(Set<String> classIds, Strin
 
 	}
 
+	@Override
+	public String resolveIri(String entity) {
+		return curieUtil.getIri(entity).orElse(entity);
+	}
+
 }

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/OntologyMatchResource.java

@@ -67,12 +67,8 @@
             @ApiParam(value = "ontology to be matched, e.g. HP",
             required = true) @PathParam("ontology") String ontology)
                     throws UnknownFilterException, IncoherentStateException {
-    	
-    	// TODO it's weird to resolve the curie here
-    	String resolveEntity = curieUtil.getIri(entity).orElse(entity);
-    	
         List<SimpleClassMatch> matches = 
-                classMatcher.matchEntity(resolveEntity, ontology);
+                classMatcher.matchEntity(entity, ontology);
 		return matches;
 	}