Java Code Examples for org.semanticweb.owlapi.model.OWLDataFactory#getOWLClass()

@Override
void prepare() {
	final OWLDataFactory factory = new OWLDataFactoryImpl();
	A = factory.getOWLClass(IRI.create("A"));
	B = factory.getOWLClass(IRI.create("B"));
	OWLObjectProperty R = factory.getOWLObjectProperty(IRI.create("R"));
	OWLObjectProperty S = factory.getOWLObjectProperty(IRI.create("S"));
	OWLAxiom axExSsomeAsubB = factory.getOWLSubClassOfAxiom(
			factory.getOWLObjectSomeValuesFrom(S, A), B);
	OWLAxiom axReflR = factory.getOWLReflexiveObjectPropertyAxiom(R);
	axRsubS = factory.getOWLSubObjectPropertyOfAxiom(R, S);
	// from these three axioms it should follow A subclass B
	ontologyManager = TestOWLManager.createOWLOntologyManager();
	try {
		ont = ontologyManager.createOntology(new HashSet<OWLAxiom>(Arrays
				.asList(axExSsomeAsubB, axReflR, axRsubS)));
	} catch (OWLOntologyCreationException e) {
		fail(e.toString());
	}
}
 

/**
 * Test that two {@code OWLClass}es that are equal have a same hashcode, 
 * because the OWLGraphEdge bug get me paranoid. 
 */
@Test
public void testOWLClassHashCode()
{
	 OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
	 OWLDataFactory factory = manager.getOWLDataFactory(); 
	 IRI iri = IRI.create("http://www.foo.org/#A");
	 OWLClass class1 = factory.getOWLClass(iri);
	 //get the class by another way, even if if I suspect the two references 
	 //will point to the same object
	 PrefixManager pm = new DefaultPrefixManager("http://www.foo.org/#"); 
	 OWLClass class2 = factory.getOWLClass(":A", pm);
	 
	 assertTrue("The two references point to different OWLClass objects", 
			 class1 == class2);
	 //then of course the hashcodes will be the same...
	 assertTrue("Two OWLClasses are equal but have different hashcode", 
			 class1.equals(class2) && class1.hashCode() == class2.hashCode());
}
 

public static void addElementToAttributeAssociationsFromFile(OWLOntology ont, File file) throws IOException {
	OWLOntologyManager m = OWLManager.createOWLOntologyManager();
	OWLDataFactory df = m.getOWLDataFactory();
	List<String> lines = FileUtils.readLines(file);
	for (String line : lines) {
		if (line.startsWith("#"))
			continue;
		String[] colVals = line.split("\t");
		if (colVals.length != 2) {
			throw new IOException("Incorrect number of value: "+line);
		}
		OWLNamedIndividual i = df.getOWLNamedIndividual(getIRIById(colVals[0]));
		OWLClass c = df.getOWLClass(getIRIById(colVals[1]));
		m.addAxiom(ont, df.getOWLClassAssertionAxiom(c, i));
	}
}
 

protected DescriptiveStatistics computeDescriptiveStatistics(Set<OWLClass> attributes) throws UnknownOWLClassException  {
	DescriptiveStatistics statsPerAttSet = new DescriptiveStatistics();
	OWLDataFactory g = sourceOntology.getOWLOntologyManager().getOWLDataFactory();

	for (OWLClass c : attributes) {
		Double ic;
		try {
			ic = owlsim.getInformationContentForAttribute(c);
			if (ic == null) { 
				if (g.getOWLClass(c.getIRI()) != null) {
					ic = owlsim.getSummaryStatistics().max.getMax();
				} else {
					throw new UnknownOWLClassException(c); }
			}
			if (ic.isInfinite() || ic.isNaN()) {
				ic = owlsim.getSummaryStatistics().max.getMax();
			}
			statsPerAttSet.addValue(ic);	

		} catch (UnknownOWLClassException e) {
			LOG.info("Unknown class "+c.toStringID()+" submitted for summary stats. Removed from calculation.");
			continue;
		}
	}
	return statsPerAttSet;
}
 

private static OWLAxiom getEntailment() {
	// Let's pick some class subsumption we want to explain
	OWLDataFactory factory = OWLManager.getOWLDataFactory();
	
	OWLClass subsumee = factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#LiquidFood"));
	OWLClass subsumer = factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#Food"));
	
	return factory.getOWLSubClassOfAxiom(subsumee, subsumer);
}
 

private void testActinobacteria(OWLOntology ontology) {
	String curie = "ncbi:201174";
	IRI iri = OWLConverter.format.getIRI(curie);
	OWLDataFactory df = ontology.getOWLOntologyManager().
		getOWLDataFactory();
	OWLClass taxon = df.getOWLClass(iri);
	assertTrue("Actinobacteria class in signature",
		ontology.containsClassInSignature(iri));

	// Check axioms
	Set<OWLClassAxiom> axioms = ontology.getAxioms(taxon, Imports.EXCLUDED);
	assertEquals("Count class axioms for Actinobacteria", 1, axioms.size());
	assertEquals("SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_201174> <http://purl.obolibrary.org/obo/NCBITaxon_2>)", axioms.toArray()[0].toString());

	// Check annotations
	List<String> values = new ArrayList<String>();
	values.add(expandAnnotation(curie, "ncbitaxon:has_rank", OWLConverter.format.getIRI("ncbi:phylum")));
	values.add(expandAnnotation(curie, "oio:hasOBONamespace", "ncbi_taxonomy"));
	values.add(expandAnnotation(curie, "oio:hasDbXref", "GC_ID:11"));
	values.add(expandLabel(curie, "rdfs:label", "Actinobacteria [NCBITaxon:201174]"));
	values.add(expandSynonym(curie, "ncbitaxon:scientific_name", "oio:hasExactSynonym", "Actinobacteria"));
	values.add(expandSynonym(curie, "ncbitaxon:synonym", "oio:hasRelatedSynonym", "'Actinobacteria'"));
	values.add(expandSynonym(curie, "ncbitaxon:synonym", "oio:hasRelatedSynonym", "not Actinobacteria Cavalier-Smith 2002"));
	values.add(expandSynonym(curie, "ncbitaxon:blast_name", "oio:hasRelatedSynonym", "actinobacteria"));

	Set<OWLAnnotationAssertionAxiom> annotations = 
		ontology.getAnnotationAssertionAxioms(iri);
	assertEquals("Count annotations for Actinobacteria",
			values.size(), annotations.size());

	checkAnnotations(annotations, values);
}
 

@Override
void prepare() {
	final OWLDataFactory factory = new OWLDataFactoryImpl();
	A = factory.getOWLClass(IRI.create("A"));
	B = factory.getOWLClass(IRI.create("B"));
	axAsubB = factory.getOWLSubClassOfAxiom(A, B);
	axBsubA = factory.getOWLSubClassOfAxiom(B, A);
	ontologyManager = TestOWLManager.createOWLOntologyManager();
	try {
		ont = ontologyManager.createOntology(new HashSet<OWLAxiom>(Arrays
				.asList(axAsubB, axBsubA)));
	} catch (OWLOntologyCreationException e) {
		fail(e.toString());
	}
}
 

public SummaryStatistics computeAttributeSetSimilarityStats(Set<OWLClass> atts)  {

		SummaryStatistics statsPerAttSet = new SummaryStatistics();
		//		Set<OWLClass> allClasses = getSourceOntology().getClassesInSignature(true);
		OWLDataFactory g = getSourceOntology().getOWLOntologyManager().getOWLDataFactory();

		for (OWLClass c : atts) {
			Double ic;
			try {
				ic = this.getInformationContentForAttribute(c);
				if (ic == null) { 
					//If a class hasn't been annotated in the loaded corpus, we will
					//assume that it is very rare, and assign MaxIC
					if (g.getOWLClass(c.getIRI()) != null) {
						ic = this.getSummaryStatistics().max.getMax();
					} else {
						throw new UnknownOWLClassException(c); }
				}
				if (ic.isInfinite() || ic.isNaN()) {
					//If a class hasn't been annotated in the loaded corpus, we will
					//assume that it is very rare, and assign MaxIC
					//a different option would be to skip adding this value, 
					//but i'm not sure that's wise
					ic = this.getSummaryStatistics().max.getMax();
				}
				//LOG.info("IC for "+c.toString()+"is: "+ic);
				statsPerAttSet.addValue(ic);	

			} catch (UnknownOWLClassException e) {
				//This is an extra catch here, but really it should be caught upstream.
				LOG.info("Unknown class "+c.toStringID()+" submitted for summary stats. Removed from calculation.");
				continue;
			}
		}
		return statsPerAttSet;
	}
 

@Override
public void setInformationContentFromOntology(OWLOntology o) {
	OWLOntologyManager mgr = getSourceOntology().getOWLOntologyManager();
	OWLDataFactory df = mgr.getOWLDataFactory();
	clearInformationContentCache();
	for (OWLAnnotationAssertionAxiom ax : o.getAxioms(AxiomType.ANNOTATION_ASSERTION)) {
		if (ax.getProperty().getIRI().toString().equals(icIRIString)) {
			OWLLiteral lit = (OWLLiteral) ax.getValue();
			OWLClass c = df.getOWLClass((IRI) ax.getSubject());
			Double v = lit.parseDouble();
			setInformtionContectForAttribute(c, v);
		}
	}
	assignDefaultInformationContentForAllClasses();
}
 

/**
 * Names all inner ObjectSomeValuesFrom expressions
 * 
 * @param srcOntology
 * @param tgtOntology
 * @param qmap
 * @param isAddLabels
 * @return
 */
public static Map<OWLClass, OWLClassExpression> nameObjectSomeValuesFrom(OWLOntology srcOntology,
		OWLOntology tgtOntology,
		Map<OWLClass,OWLClassExpression> qmap,
		boolean isAddLabels) {

	if (qmap == null) 
		qmap = new HashMap<OWLClass, OWLClassExpression>();
	OWLOntologyManager mgr = srcOntology.getOWLOntologyManager();
	OWLDataFactory df = mgr.getOWLDataFactory();
	for (OWLOntology ont : srcOntology.getImportsClosure()) {
		for (OWLAxiom ax : srcOntology.getAxioms()) {
			for (OWLClassExpression x : ax.getNestedClassExpressions()) {
				if (x instanceof OWLObjectSomeValuesFrom) {
					OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom)x;
					OWLClass filler = (OWLClass) svf.getFiller();
					OWLObjectProperty p = (OWLObjectProperty) svf.getProperty();
					IRI iri = getSkolemIRI(filler, p);
					OWLClass c = df.getOWLClass(iri);
					mgr.addAxiom(tgtOntology, df.getOWLEquivalentClassesAxiom(c, svf));
					qmap.put(c, svf);
					if (isAddLabels) {
						Set<OWLAnnotation> anns = OwlHelper.getAnnotations(filler, df.getRDFSLabel(), ont);
						for (OWLAnnotation ann : anns) {
							mgr.addAxiom(tgtOntology, df.getOWLAnnotationAssertionAxiom(c.getIRI(), ann));
						}
					}
				}
			}
		}
	}
	return qmap;

}
 

private void testBacteria(OWLOntology ontology) {
	String curie = "ncbi:2";
	IRI iri = OWLConverter.format.getIRI(curie);
	OWLDataFactory df = ontology.getOWLOntologyManager().
		getOWLDataFactory();
	OWLClass taxon = df.getOWLClass(iri);
	assertTrue("Bacteria class in signature",
		ontology.containsClassInSignature(iri));

	// Check axioms
	Set<OWLClassAxiom> axioms = ontology.getAxioms(taxon, Imports.EXCLUDED);
	assertEquals("Count class axioms for Bacteria", 1, axioms.size());
	assertEquals("SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_2> <http://purl.obolibrary.org/obo/NCBITaxon_131567>)", axioms.toArray()[0].toString());

	// Check annotations
	List<String> values = new ArrayList<String>();
	values.add(expandAnnotation(curie, "ncbitaxon:has_rank", OWLConverter.format.getIRI("ncbi:superkingdom")));
	values.add(expandAnnotation(curie, "oio:hasOBONamespace", "ncbi_taxonomy"));
	values.add(expandAnnotation(curie, "oio:hasDbXref", "GC_ID:11"));
	values.add(expandLabel(curie, "rdfs:label", "Bacteria"));
	values.add(expandSynonym(curie, "ncbitaxon:genbank_common_name", "oio:hasExactSynonym", "eubacteria"));
	values.add(expandSynonym(curie, "ncbitaxon:synonym", "oio:hasRelatedSynonym", "not Bacteria Haeckel 1894"));
	values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Prokaryota"));
	values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Monera"));
	values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Procaryotae"));
	values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Prokaryotae"));
	values.add(expandSynonym(curie, "ncbitaxon:blast_name", "oio:hasRelatedSynonym", "eubacteria"));

	Set<OWLAnnotationAssertionAxiom> annotations = 
		ontology.getAnnotationAssertionAxioms(iri);
	assertEquals("Count annotations for Bacteria", values.size(), annotations.size());

	checkAnnotations(annotations, values);
}
 

/**
 * Testing correctness of the reasoner with respect to ontology changes
 */
@Test
public void ignoreChangesInNonImportedOntologies() throws Exception {

	OWLOntologyManager man = TestOWLManager.createOWLOntologyManager();
	OWLDataFactory dataFactory = man.getOWLDataFactory();

	// set up resolution of prefixes
	DefaultPrefixManager pm = new DefaultPrefixManager();
	pm.setDefaultPrefix("http://www.example.com/main#");
	pm.setPrefix("A:", "http://www.example.com/A#");
	pm.setPrefix("B:", "http://www.example.com/B#");

	OWLClass extA = dataFactory.getOWLClass("A:A", pm);
	OWLClass extB = dataFactory.getOWLClass("B:B", pm);

	// loading the root ontology
	OWLOntology root = loadOntology(man, "root.owl");

	// Create an ELK reasoner.
	ElkReasoner reasoner = (ElkReasoner) new ElkReasonerFactory()
			.createReasoner(root);
	// make sure the reasoner loads the ontology
	reasoner.flush();
	reasoner.isConsistent();

	try {
		OWLOntology nonImported = loadOntology(man, "nonImported.owl");

		OWLAxiom axiom = dataFactory.getOWLSubClassOfAxiom(extA, extB);
		man.removeAxiom(nonImported, axiom);
		reasoner.flush();

		AbstractReasonerState state = reasoner.getInternalReasoner();

		assertTrue(state.stageManager.inputLoadingStage.isCompleted());
	} finally {
		reasoner.dispose();
	}
}
 

@Override
protected void translateResultsToOWLAxioms(String id, OWLNamedIndividual result, Set<OWLAxiom> axioms) {
	OWLDataFactory df = simEngine.getGraph().getDataFactory();
	
	// declare a named class for the LCS and make this equivalent to the anonymous expression
	OWLClass namedLCS = df.getOWLClass(IRI.create(id+"_LCS"));
	axioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()),
			namedLCS.getIRI(), 
			df.getOWLLiteral("LCS of "+simEngine.label(a)+" and "+simEngine.label(b))));
	axioms.add(df.getOWLEquivalentClassesAxiom(namedLCS, getLCS()));

	// link the similarity object to the named LCS
	OWLAnnotationProperty lcsp = df.getOWLAnnotationProperty(annotationIRI("has_least_common_subsumer"));
	axioms.add(df.getOWLAnnotationAssertionAxiom(lcsp, result.getIRI(), namedLCS.getIRI()));
}
 

public SummaryStatistics computeAttributeSetSimilarityStatsForSubgraph(Set<OWLClass> atts, OWLClass sub)  {
	SummaryStatistics statsPerAttSet = new SummaryStatistics();
	//		Set<OWLClass> allClasses = getSourceOntology().getClassesInSignature(true);
	OWLDataFactory g = getSourceOntology().getOWLOntologyManager().getOWLDataFactory();

	for (OWLClass c : atts) {
		Double ic;
		try {
			//check if sub is an inferred superclass of the current annotated class
			//TODO check if i need all of these; this might be expensive and unnecessary
			if (getReasoner().getSuperClasses(c, false).containsEntity(sub) ||
					getReasoner().getEquivalentClasses(c).contains(sub))  { 
				ic = this.getInformationContentForAttribute(c);

				if (ic == null) { 
					//If a class hasn't been annotated in the loaded corpus, we will
					//assume that it is very rare, and assign MaxIC
					if (g.getOWLClass(c.getIRI()) != null) {
						ic = this.getSummaryStatistics().max.getMax();
					} else {
						throw new UnknownOWLClassException(c); }
				}

				if (ic.isInfinite() || ic.isNaN()) {
					//If a class hasn't been annotated in the loaded corpus, we will
					//assume that it is very rare, and assign MaxIC
					ic = this.getSummaryStatistics().max.getMax();
				}
				//LOG.info("IC for "+c.toString()+"is: "+ic);
				statsPerAttSet.addValue(ic);	
			} else {
				//LOG.info("tossing "+c.toString()+"; not a subclass of "+sub.toString());
			}
		} catch (UnknownOWLClassException e) {
			//This is an extra catch here, but really it should be caught upstream.
			LOG.info("Unknown class "+c.toStringID()+" submitted for summary stats. Removed from calculation.");
			continue;
		}
	}
	return statsPerAttSet;
}
 

private Map<Bioentity, Set<OWLClass>> generateAxioms(OWLOntology generatedContainer, Map<Bioentity, ? extends Collection<GeneAnnotation>> annMap, Map<Bioentity, Set<OWLClass>> allExistingAnnotations, Map<OWLClass, PredicationDataContainer> sourceData) {
	final OWLGraphWrapper g = getGraph();
	final OWLDataFactory f = g.getDataFactory();
	final OWLOntologyManager m = g.getManager();
	
	Map<Bioentity, Set<OWLClass>> allGeneratedClasses = new HashMap<Bioentity, Set<OWLClass>>();
	for(Entry<Bioentity, ? extends Collection<GeneAnnotation>> entry : annMap.entrySet()) {
		Set<OWLClass> generatedClasses = new HashSet<OWLClass>();
		Set<OWLClass> existingAnnotations = new HashSet<OWLClass>();
		Bioentity e = entry.getKey();
		for (GeneAnnotation ann : entry.getValue()) {
			// skip ND evidence annotations
			String evidenceString = ann.getShortEvidence();
			if ("ND".equals(evidenceString)) {
				continue;
			}
			// parse annotation cls
			String annotatedToClassString = ann.getCls();
			OWLClass annotatedToClass = g.getOWLClassByIdentifierNoAltIds(annotatedToClassString);
			if (annotatedToClass == null) {
				LOG.warn("Skipping annotation for prediction. Could not find cls for id: "+annotatedToClassString);
				continue;
			}
			// add annotation class (and its super classes as known annotation) 
			existingAnnotations.add(annotatedToClass);
			existingAnnotations.addAll(reasoner.getSuperClasses(annotatedToClass, false).getFlattened());
			
			// parse c16 expressions
			List<List<ExtensionExpression>> extensionExpressionGroups = ann.getExtensionExpressions();
			if (extensionExpressionGroups != null && !extensionExpressionGroups.isEmpty()) {
				for (List<ExtensionExpression> group : extensionExpressionGroups) {
					Set<OWLClassExpression> units = new HashSet<OWLClassExpression>();
					for (ExtensionExpression ext : group) {
						String extClsString = ext.getCls();
						String extRelString = ext.getRelation();
						OWLClass extCls = f.getOWLClass(g.getIRIByIdentifier(extClsString));
						OWLObjectProperty extRel = g.getOWLObjectPropertyByIdentifier(extRelString);
						if (extRel == null) {
							continue;
						}
						units.add(f.getOWLObjectSomeValuesFrom(extRel, extCls));
					}
					if (units.isEmpty()) {
						continue;
					}
					units.add(annotatedToClass);
					final OWLClassExpression groupExpression = f.getOWLObjectIntersectionOf(units);
					OWLClass generatedClass = f.getOWLClass(IRI.generateDocumentIRI());
					OWLAxiom axiom = f.getOWLEquivalentClassesAxiom(generatedClass, groupExpression);
					m.addAxiom(generatedContainer, axiom);
					generatedClasses.add(generatedClass);
					sourceData.put(generatedClass, new PredicationDataContainer(ann, annotatedToClass, evidenceString, groupExpression, group));
				}
			}
		}
		if (generatedClasses.isEmpty() == false) {
			allGeneratedClasses.put(e, generatedClasses);
			allExistingAnnotations.put(e, existingAnnotations);
		}
	}
	return allGeneratedClasses;
}
 

/**
 * Testing correctness of the reasoner when changes are made to other, imported or not, ontologies
 * 
 */
@Test
public void testChangesToOtherOntologies() throws Exception {

	OWLOntologyManager man = TestOWLManager.createOWLOntologyManager();
	OWLDataFactory dataFactory = man.getOWLDataFactory();

	// set up resolution of prefixes
	PrefixManager pm = new DefaultPrefixManager();
	pm.setDefaultPrefix("http://www.example.com/main#");
	pm.setPrefix("A:", "http://www.example.com/A#");
	pm.setPrefix("B:", "http://www.example.com/B#");

	// define query classes
	OWLClass mainY = dataFactory.getOWLClass(":Y", pm);
	OWLClass extA = dataFactory.getOWLClass("A:A", pm);
	OWLClass extB = dataFactory.getOWLClass("B:B", pm);
	OWLClass extC = dataFactory.getOWLClass("B:C", pm);

	// loading the root ontology
	OWLOntology root = loadOntology(man, "root.owl");
	// the imported ontologies must be loaded
	OWLOntology ontoA = man.getOntology(IRI.create("http://www.example.com/A"));
	OWLOntology ontoB = man.getOntology(IRI.create("http://www.example.com/B"));

	// Create an ELK reasoner.
	OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
	OWLReasoner reasoner = reasonerFactory.createReasoner(root);

	try {
		
		assertTrue(reasoner.getSuperClasses(extA, false).containsEntity(
				extC));
		assertTrue(reasoner.getSuperClasses(mainY, false).containsEntity(
				extC));
		
		// ************************************
		// ** removing an axiom "A:A is-a B:B" from impA
		// ************************************
		OWLAxiom axiom = dataFactory.getOWLSubClassOfAxiom(extA, extB);
		man.removeAxiom(ontoA, axiom);
		reasoner.flush();
		
		assertFalse(reasoner.getSuperClasses(extA, false).containsEntity(
				extC));
		// put it back
		man.addAxiom(ontoA, axiom);
		reasoner.flush();
		
		assertTrue(reasoner.getSuperClasses(extA, false).containsEntity(
				extC));

		// ************************************
		// ** removing an axiom "B:B is-a B:C" from impB
		// ************************************
		axiom = dataFactory.getOWLSubClassOfAxiom(extB, extC);
		man.removeAxiom(ontoB, axiom);
		reasoner.flush();
		
		assertFalse(reasoner.getSuperClasses(mainY, false).containsEntity(
				extC));

	}
	finally {
		reasoner.dispose();
	}
}
 

/**
 * Testing correctness of the reasoner with respect to ontology changes
 * <p>
 * removing the import declaration for </impA>,
 * adding the import declaration for </impB> and removing
 * ":Y is-a B:B"
 */
@Test
public void testRemovingImpAAddingImpBRemovingYB() throws Exception {

	OWLOntologyManager man = TestOWLManager.createOWLOntologyManager();
	OWLDataFactory dataFactory = man.getOWLDataFactory();

	// set up resolution of prefixes
	PrefixManager pm = new DefaultPrefixManager();
	pm.setDefaultPrefix("http://www.example.com/main#");
	pm.setPrefix("A:", "http://www.example.com/A#");
	pm.setPrefix("B:", "http://www.example.com/B#");

	// define query classes
	OWLClass mainX = dataFactory.getOWLClass(":X", pm);
	OWLClass mainY = dataFactory.getOWLClass(":Y", pm);
	OWLClass extA = dataFactory.getOWLClass("A:A", pm);
	OWLClass extB = dataFactory.getOWLClass("B:B", pm);
	OWLClass extC = dataFactory.getOWLClass("B:C", pm);

	// loading the root ontology
	OWLOntology root = loadOntology(man, "root.owl");

	// Create an ELK reasoner.
	OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
	OWLReasoner reasoner = reasonerFactory.createReasoner(root);

	try {

		// ************************************
		// ** adding the import declaration for </impB> and removing
		// ":Y is-a B:B"
		// ************************************

		OWLImportsDeclaration importA = new OWLImportsDeclarationImpl(
				IRI.create("http://www.example.com#impA"));
		OWLOntologyChange change = new RemoveImport(root, importA);
		man.applyChange(change);
		OWLImportsDeclaration importB = new OWLImportsDeclarationImpl(
				IRI.create("http://www.example.com#impB"));
		change = new AddImport(root, importB);
		man.applyChange(change);
		OWLSubClassOfAxiom axiom = dataFactory.getOWLSubClassOfAxiom(mainY, extB);
		man.removeAxiom(root, axiom);
		reasoner.flush();

		// Now ontology should import only ontology </impB>
		assertEquals(root.getAxiomCount(), 2);
		assertEquals(root.getImportsClosure().size(), 2);
		assertEquals(getAxioms(root).size(), 4);

		// reasoner queries -- only subsumptions of the root
		// ontology </impB> and there
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				mainY));
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				extA));
		assertFalse(reasoner.getSuperClasses(mainY, true).containsEntity(
				extB));
		assertFalse(reasoner.getSuperClasses(extA, true).containsEntity(
				extB));
		assertTrue(reasoner.getSuperClasses(extB, true)
				.containsEntity(extC));

	} finally {
		reasoner.dispose();
	}

}
 

/**
 * Testing correctness of the reasoner with respect to ontology changes
 * <p>
 * trying to remove "A:A is-a B:B"
 * <p>
 * Because the removed axiom belongs to the imported ontology and
 * not main ontology, the remove does not make any effect. So, we
 * should end up with the ontology we have started with.
 * <p>
 * This test is ignored, because as of OWL API 4.1.3 the removal
 * of the axiom is broadcasted even though the axiom is not removed.
 */
@Test
public void testRemovingAB() throws Exception {

	OWLOntologyManager man = TestOWLManager.createOWLOntologyManager();
	OWLDataFactory dataFactory = man.getOWLDataFactory();

	// set up resolution of prefixes
	PrefixManager pm = new DefaultPrefixManager();
	pm.setDefaultPrefix("http://www.example.com/main#");
	pm.setPrefix("A:", "http://www.example.com/A#");
	pm.setPrefix("B:", "http://www.example.com/B#");

	// define query classes
	OWLClass mainX = dataFactory.getOWLClass(":X", pm);
	OWLClass mainY = dataFactory.getOWLClass(":Y", pm);
	OWLClass extA = dataFactory.getOWLClass("A:A", pm);
	OWLClass extB = dataFactory.getOWLClass("B:B", pm);
	OWLClass extC = dataFactory.getOWLClass("B:C", pm);

	// loading the root ontology
	OWLOntology root = loadOntology(man, "root.owl");

	// Create an ELK reasoner.
	OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
	OWLReasoner reasoner = reasonerFactory.createReasoner(root);

	try {

		// ************************************
		// ** trying to remove "A:A is-a B:B"
		// ************************************
		OWLSubClassOfAxiom axiom = dataFactory.getOWLSubClassOfAxiom(extA, extB);
		man.removeAxiom(root, axiom);
		reasoner.flush();

		// Because the removed axiom belongs to the imported ontology and
		// not main ontology, the remove does not make any effect. So, we
		// should end up with the ontology we have started with

		assertEquals(root.getAxiomCount(), 3);
		// all three ontologies should be in the closure
		assertEquals(root.getImportsClosure().size(), 3);
		// all axioms from three ontologies should be in the closure
		assertEquals(getAxioms(root).size(), 6);

		// reasoner queries -- all subsumptions are there
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				mainY));
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				extA));
		assertTrue(reasoner.getSuperClasses(mainY, true).containsEntity(
				extB));
		assertTrue(reasoner.getSuperClasses(extA, true)
				.containsEntity(extB));
		assertTrue(reasoner.getSuperClasses(extB, true)
				.containsEntity(extC));

	} finally {
		reasoner.dispose();
	}

}
 

/**
 * Testing correctness of the reasoner with respect to ontology changes
 * 
 * removing an axiom ":X is-a :Y"
 */
@Test
public void testRemovingXY() throws Exception {

	OWLOntologyManager man = TestOWLManager.createOWLOntologyManager();
	OWLDataFactory dataFactory = man.getOWLDataFactory();

	// set up resolution of prefixes
	PrefixManager pm = new DefaultPrefixManager();
	pm.setDefaultPrefix("http://www.example.com/main#");
	pm.setPrefix("A:", "http://www.example.com/A#");
	pm.setPrefix("B:", "http://www.example.com/B#");

	// define query classes
	OWLClass mainX = dataFactory.getOWLClass(":X", pm);
	OWLClass mainY = dataFactory.getOWLClass(":Y", pm);
	OWLClass extA = dataFactory.getOWLClass("A:A", pm);
	OWLClass extB = dataFactory.getOWLClass("B:B", pm);
	OWLClass extC = dataFactory.getOWLClass("B:C", pm);

	// loading the root ontology
	OWLOntology root = loadOntology(man, "root.owl");

	// Create an ELK reasoner.
	OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
	OWLReasoner reasoner = reasonerFactory.createReasoner(root);

	try {

		// ************************************
		// ** removing an axiom ":X is-a :Y"
		// ************************************
		OWLAxiom axiom = dataFactory.getOWLSubClassOfAxiom(mainX, mainY);
		man.removeAxiom(root, axiom);
		reasoner.flush();

		// the root ontology contains one fewer axioms
		assertEquals(root.getAxiomCount(), 2);
		// the number of ontologies in the import closure does not change
		assertEquals(root.getImportsClosure().size(), 3);
		// the total number of axioms reduces
		assertEquals(getAxioms(root).size(), 5);

		// reasoner queries -- first subsumption is gone
		assertFalse(reasoner.getSuperClasses(mainX, true).containsEntity(
				mainY));
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				extA));
		assertTrue(reasoner.getSuperClasses(mainY, true).containsEntity(
				extB));
		assertTrue(reasoner.getSuperClasses(extA, true)
				.containsEntity(extB));
		assertTrue(reasoner.getSuperClasses(extB, true)
				.containsEntity(extC));

	} finally {
		reasoner.dispose();
	}

}
 

/**
 * Testing correctness of the reasoner with respect to ontology changes
 * 
 */
@Test
public void testNoChanges() throws Exception {

	OWLOntologyManager man = TestOWLManager.createOWLOntologyManager();
	OWLDataFactory dataFactory = man.getOWLDataFactory();

	// set up resolution of prefixes
	PrefixManager pm = new DefaultPrefixManager();
	pm.setDefaultPrefix("http://www.example.com/main#");
	pm.setPrefix("A:", "http://www.example.com/A#");
	pm.setPrefix("B:", "http://www.example.com/B#");

	// define query classes
	OWLClass mainX = dataFactory.getOWLClass(":X", pm);
	OWLClass mainY = dataFactory.getOWLClass(":Y", pm);
	OWLClass extA = dataFactory.getOWLClass("A:A", pm);
	OWLClass extB = dataFactory.getOWLClass("B:B", pm);
	OWLClass extC = dataFactory.getOWLClass("B:C", pm);

	// loading the root ontology
	OWLOntology root = loadOntology(man, "root.owl");

	// Create an ELK reasoner.
	OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
	OWLReasoner reasoner = reasonerFactory.createReasoner(root);

	try {

		// statistics about the root ontology
		assertEquals(root.getAxiomCount(), 3);
		// all three ontologies should be in the closure
		assertEquals(root.getImportsClosure().size(), 3);
		// all axioms from three ontologies should be in the closure
		assertEquals(getAxioms(root).size(), 6);

		// reasoner queries -- all subclasses are there
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				mainY));
		assertTrue(reasoner.getSuperClasses(mainX, true).containsEntity(
				extA));
		assertTrue(reasoner.getSuperClasses(mainY, true).containsEntity(
				extB));
		assertTrue(reasoner.getSuperClasses(extA, true)
				.containsEntity(extB));
		assertTrue(reasoner.getSuperClasses(extB, true)
				.containsEntity(extC));
		
	} finally {
		reasoner.dispose();
	}

}