Revised solr document loader codes to deep-copy all relevant ontologies

OWLTools-Core/src/main/java/owltools/graph/OWLGraphWrapperEdgesAdvanced.java

@@ -680,12 +680,13 @@ else if (obj instanceof OWLObjectProperty) {
 		}
 		return relation_map;
 	}
-	
+
 	private void addIdLabelClosure(OWLClass c, boolean reflexive, 
-			final Set<OWLObjectProperty> props, final Map<String,String> relation_map) {
+			final Set<OWLObjectProperty> props, final Map<String,String> relation_map) {		
 		addPropertiesForMaterialization(props);
 		ExpressionMaterializingReasoner materializingReasoner = getMaterializingReasoner();
 		Set<OWLClassExpression> classExpressions = materializingReasoner.getSuperClassExpressions(c, false);
+
 		OWLEntity owlThing = this.getManager().getOWLDataFactory().getOWLThing();
 
 		// remove owl:Thing - although logically valid, it is not of use to the consumer

OWLTools-Core/src/main/java/owltools/graph/OWLGraphWrapperExtended.java

@@ -221,6 +221,7 @@ public String getAnnotationValue(OWLObject c, OWLAnnotationProperty lap) {
 		else {
 			return null;
 		}
+
 		for (OWLAnnotation a : anns) {
 			if (a.getValue() instanceof OWLLiteral) {
 				OWLLiteral val = (OWLLiteral) a.getValue();
@@ -623,7 +624,6 @@ public OWLAnnotationProperty getAnnotationProperty(String tag){
 	 */
 	public String getNamespace(OWLObject c) {
 		OWLAnnotationProperty lap = getAnnotationProperty(OboFormatTag.TAG_NAMESPACE.getTag());
-
 		return getAnnotationValue(c, lap);
 	}
 
@@ -933,7 +933,7 @@ public String getIdentifier(IRI iriId) {
 		}
 
 		// 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.");
+		// 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());
 	}
 

OWLTools-Core/src/test/java/owltools/graph/OWLGraphWrapperExtendedTest.java

@@ -44,6 +44,7 @@ public void testGetIdentifier() throws Exception {
 		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"));
+		String id5 = wrapper.getIdentifier(IRI.create("http://purl.obolibrary.org/obo/GR_protein_Q6K4D1"));
 
 		assertEquals(id1, "GO:0000001");
 		assertEquals(id2, "GO:0000002");

OWLTools-Runner/src/main/java/owltools/cli/SolrCommandRunner.java

@@ -593,8 +593,6 @@ private void loadEachModelAnnotation(ParserWrapper pwr, File legoFile, String ur
 			boolean exitIfUnsatisfiable, boolean exitIfLoadFails) throws IOException {
 		String fname = legoFile.getName();
 		OWLReasoner currentReasoner = null;
-		OWLOntologyManager manager = pwr.getManager();
-
 		OWLOntology model = null;
 		ModelAnnotationSolrDocumentLoader loader = null;
 
@@ -609,20 +607,24 @@ private void loadEachModelAnnotation(ParserWrapper pwr, File legoFile, String ur
 			}
 
 			/**
-			 * DEEP-COPIES OWLOntology instance.
+			 * DEEP-COPIES ALL OWLOntology instances in the manager of the model.
 			 * Note that most serialization libraries such as Kryo or Cloner DO NOT work for
 			 * copying OWLOntology or reasoner instance. In other words, deep-copying ontology 
 			 * should be done via "copyOntology" method. This allows preventing memory leaks, i.e., 
 			 * running reasoners affects the model (OWLOntology instance) but the changes only happen 
 			 * over copied instance, which can be safely disposed without blowing out of memory.
+			 * See also: https://github.com/owlcollab/owltools/issues/253#issuecomment-388415035
 			 */
 			OWLOntologyManager tempOWLManager = OWLManager.createOWLOntologyManager();
-			OWLOntology tModel = tempOWLManager.copyOntology(model, OntologyCopy.DEEP);
+			for(OWLOntology o: model.getOWLOntologyManager().getOntologies())
+				tempOWLManager.copyOntology(o, OntologyCopy.DEEP);
+
+			OWLOntology dcpModel = tempOWLManager.getOntology(model.getOntologyID());
 
 			// Some sanity checks--some of the generated ones are problematic.
 			// We need a consistent ontology for the closure calculations!
 			OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
-			currentReasoner = reasonerFactory.createReasoner(tModel);
+			currentReasoner = reasonerFactory.createReasoner(dcpModel);
 			boolean consistent = currentReasoner.isConsistent();
 			if(consistent == false){
 				LOG.warn("Skip since inconsistent: " + fname);
@@ -634,12 +636,12 @@ private void loadEachModelAnnotation(ParserWrapper pwr, File legoFile, String ur
 			String modelUrl = legoModelPrefix + fname;
 
 			if (url.equals("mock")) {
-				loader = new MockModelAnnotationSolrDocumentLoader(url, tModel, currentReasoner, modelUrl, 
+				loader = new MockModelAnnotationSolrDocumentLoader(url, dcpModel, currentReasoner, modelUrl,
 						modelStateFilter, removeDeprecatedModels, removeTemplateModels);
 				isMock = true;
 			}
 			else {
-				loader = new ModelAnnotationSolrDocumentLoader(url, tModel, currentReasoner, modelUrl, 
+				loader = new ModelAnnotationSolrDocumentLoader(url, dcpModel, currentReasoner, modelUrl,
 						modelStateFilter, removeDeprecatedModels, removeTemplateModels);
 			}
 
@@ -650,19 +652,18 @@ private void loadEachModelAnnotation(ParserWrapper pwr, File legoFile, String ur
 			}
 
 			currentReasoner.dispose();
-			tempOWLManager.removeOntology(tModel);
+			tempOWLManager.removeOntology(dcpModel);
 		} catch (Exception e) {
 			LOG.info("Complex annotation load of " + fname + " at " + url + " failed!");
 			e.printStackTrace();
 
 			if (exitIfLoadFails)
 				System.exit(1);
 		} finally {
-			manager.removeOntology(model);
 			if (loader != null) {
+				LOG.info("Finalizing the current loader...");
 				loader.close();
 				loader = null;
-				LOG.info("Closing the current loader...");
 			}
 		}
 	}

OWLTools-Solr/src/main/java/owltools/solrj/ModelAnnotationSolrDocumentLoader.java

@@ -87,12 +87,12 @@ public class ModelAnnotationSolrDocumentLoader extends AbstractSolrLoader implem
 	private boolean skipDeprecatedModels;
 	private boolean skipTemplateModels;
 
-	public ModelAnnotationSolrDocumentLoader(String golrUrl, OWLOntology model, OWLReasoner r, String modelUrl, 
+	public ModelAnnotationSolrDocumentLoader(String golrUrl, OWLOntology model, OWLReasoner r, String modelUrl,
 			Set<String> modelFilter, boolean skipDeprecatedModels, boolean skipTemplateModels) throws MalformedURLException {
 		this(createDefaultServer(golrUrl), model, r, modelUrl, modelFilter, skipDeprecatedModels, skipTemplateModels);
 	}
-	
-	public ModelAnnotationSolrDocumentLoader(SolrServer server, OWLOntology model, OWLReasoner r, String modelUrl, 
+
+	public ModelAnnotationSolrDocumentLoader(SolrServer server, OWLOntology model, OWLReasoner r, String modelUrl,
 			Set<String> modelFilter, boolean skipDeprecatedModels, boolean skipTemplateModels) {
 		super(server);
 		this.model = model;
@@ -106,12 +106,12 @@ public ModelAnnotationSolrDocumentLoader(SolrServer server, OWLOntology model, O
 		OWLDataFactory df = graph.getDataFactory();
 		partOf = OBOUpperVocabulary.BFO_part_of.getObjectProperty(df);
 		occursIn = OBOUpperVocabulary.BFO_occurs_in.getObjectProperty(df);
-		
+
 		defaultClosureRelations = new ArrayList<String>(1);
 		defaultClosureRelations.add(graph.getIdentifier(partOf));
-		
+
 		enabledBy = OBOUpperVocabulary.GOREL_enabled_by.getObjectProperty(df);
-		
+
 		title = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/title"));
 		source = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/source"));
 		contributor = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/contributor"));
@@ -123,29 +123,31 @@ public ModelAnnotationSolrDocumentLoader(SolrServer server, OWLOntology model, O
 		layoutHintX = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/hint/layout/x"));
 		layoutHintY = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/hint/layout/y"));
 		templatestate = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/templatestate"));
-		
+
 		displayLabelProp = df.getRDFSLabel();
 		shortIdProp = df.getOWLAnnotationProperty(IRI.create(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX+"id"));
-
 		jsonProp = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/json-model"));
-		
+
 		bpSet = getAspect(graph, "biological_process");
 	}
 
-	static Set<OWLClass> getAspect(OWLGraphWrapper graph, String aspect) {
+	Set<OWLClass> getAspect(OWLGraphWrapper graph, String aspect) {
 		Set<OWLClass> result = new HashSet<OWLClass>();
+
+		// Literally computing all subclasses of the root class labeled with "biological process"
+		OWLClass c = model.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/GO_0008150"));
+		Set<OWLClass> subClassBPSet = reasoner.getSubClasses(c, false).getFlattened();
+
 		for(OWLClass cls : graph.getAllOWLClasses()) {
-			if (cls.isBuiltIn()) {
+			if (cls.isBuiltIn())
 				continue;
-			}
+
 			String id = graph.getIdentifier(cls);
-			if (id.startsWith("GO:") == false) {
+			if (id.startsWith("GO:") == false) 
 				continue;
-			}
-			String namespace = graph.getNamespace(cls);
-			if (namespace != null && namespace.equals(aspect)) {
+
+			if (subClassBPSet.contains(cls))
 				result.add(cls);
-			}
 		}
 		return result;
 	}
@@ -166,7 +168,7 @@ public void close() throws IOException {
 	public void load() throws SolrServerException, IOException {
 		LOG.info("Loading complex annotation document...");
 		final OWLShuntGraph shuntGraph = createShuntGraph(graph);
-		
+
 		String modelId = null;
 		String modelDate = null;
 		String title = null;
@@ -217,7 +219,7 @@ else if (p.isDeprecated()) {
 			// fallback
 			modelId = model.getOntologyID().getOntologyIRI().get().toString();
 		}
-		
+
 		if (requiredModelStates != null && state != null) {
 			boolean contains = requiredModelStates.contains(state);
 			if (contains == false) {
@@ -249,6 +251,7 @@ else if (p.isDeprecated()) {
 					final Set<OWLAnnotation> mfAnnotations = getAnnotations(null, mfNamed);
 					Map<OWLClass, Pair<OWLNamedIndividual, Set<OWLAnnotation>>> processes = findProcesses(mfNamed);
 					Map<OWLClass, Pair<OWLNamedIndividual, Set<OWLAnnotation>>> locations = findLocations(mfNamed);
+
 					for(OWLClass gpType : gpTypes) {
 						for(OWLClass mfType : mfTypes) {
 							if (processes.isEmpty() == false) {

OWLTools-Solr/src/main/java/owltools/solrj/loader/MockModelAnnotationSolrDocumentLoader.java

@@ -5,6 +5,7 @@
 
 import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.common.SolrInputDocument;
+import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 
@@ -17,17 +18,15 @@ public MockModelAnnotationSolrDocumentLoader(SolrServer server,
             OWLOntology model, OWLReasoner r, String modelUrl,
             Set<String> modelFilter, boolean skipDeprecatedModels,
             boolean skipTemplateModels) {
-        super(server, model, r, modelUrl, modelFilter, skipDeprecatedModels,
-                skipTemplateModels);
+        super(server, model, r, modelUrl, modelFilter, skipDeprecatedModels, skipTemplateModels);
         // TODO Auto-generated constructor stub
     }
 
     public MockModelAnnotationSolrDocumentLoader(String golrUrl,
             OWLOntology model, OWLReasoner r, String modelUrl,
             Set<String> modelFilter, boolean skipDeprecatedModels,
             boolean skipTemplateModels) throws MalformedURLException {
-        super((SolrServer)null, model, r, modelUrl, modelFilter, skipDeprecatedModels,
-                skipTemplateModels);
+        super((SolrServer)null, model, r, modelUrl, modelFilter, skipDeprecatedModels, skipTemplateModels);
         // TODO Auto-generated constructor stub
     }