Java Code Examples for org.semanticweb.owlapi.model.OWLOntology#equals()

/**
 * Each ontology in the import closure of the source ontology
 * (and the import closure of each existing support ontology, if
 * doForAllSupportOntologies is true) is added to
 * the list of support ontologies
 * 
 * @param doForAllSupportOntologies
 */
public void addSupportOntologiesFromImportsClosure(boolean doForAllSupportOntologies) {
	Set<OWLOntology> ios = new HashSet<OWLOntology>();
	ios.add(sourceOntology);

	if (doForAllSupportOntologies) {
		ios.addAll(getSupportOntologySet());
	}
	for (OWLOntology so : ios) {
		for (OWLOntology o : so.getImportsClosure()) {
			if (o.equals(sourceOntology))
				continue;
			addSupportOntology(o);
		}
	}
}
 

public void mergeImportClosure(boolean isRemovedImportsDeclarations) throws OWLOntologyCreationException {
	OWLOntologyManager manager = getManager();
	Set<OWLOntology> imports = sourceOntology.getImportsClosure();
	for (OWLOntology o : imports) {
		if (o.equals(sourceOntology))
			continue;

		String comment = "Includes "+summarizeOntology(o);
		LOG.info(comment);
		addCommentToOntology(sourceOntology, comment);

		manager.addAxioms(sourceOntology, o.getAxioms());
	}
	Set<OWLImportsDeclaration> oids = sourceOntology.getImportsDeclarations();
	for (OWLImportsDeclaration oid : oids) {
		RemoveImport ri = new RemoveImport(sourceOntology, oid);
		getManager().applyChange(ri);
	}
}
 

/**
 * Merge a specific ontology from the import closure into the main ontology.
 * Removes the import statement.
 * 
 * @param ontologyIRI id of the ontology to merge
 * @throws OWLOntologyCreationException
 */
public void mergeSpecificImport(IRI ontologyIRI) throws OWLOntologyCreationException {
	OWLOntologyManager manager = getManager();
	Set<OWLOntology> imports = sourceOntology.getImportsClosure();
	for (OWLOntology o : imports) {
		if (o.equals(sourceOntology))
			continue;
		Optional<IRI> currentIRI = o.getOntologyID().getOntologyIRI();
		if (currentIRI.isPresent() && currentIRI.get().equals(ontologyIRI)) {
			String comment = "Includes "+summarizeOntology(o);
			LOG.info(comment);
			addCommentToOntology(sourceOntology, comment);
			manager.addAxioms(sourceOntology, o.getAxioms());	
		}
	}
	Set<OWLImportsDeclaration> oids = sourceOntology.getImportsDeclarations();
	for (OWLImportsDeclaration oid : oids) {
		if (ontologyIRI.equals(oid.getIRI())) {
			RemoveImport ri = new RemoveImport(sourceOntology, oid);
			getManager().applyChange(ri);
		}
	}
}
 

@Override
public void ontologiesChanged(List<? extends OWLOntologyChange> changes) {
	Set<OWLOntology> importClosure = null;
	for (OWLOntologyChange change : changes) {
		OWLOntology changedOntology = change.getOntology();
		if (!changedOntology.equals(owlOntology_)) {
			if (importClosure == null) {
				importClosure = owlOntology_.getImportsClosure();
			}
			if (!importClosure.contains(changedOntology)) {
				LOGGER_.trace(
						"Ignoring the change not applicable to the current ontology: {}"
								+ change);
				continue;
			}
		}

		if (!change.isAxiomChange()) {
			LOGGER_.trace(
					"Non-axiom change: {}\n The ontology will be reloaded.",
					change);
			// cannot handle non-axiom changes incrementally
			ontologyReloadRequired_ = true;
		} else {
			bufferedChangesLoader_.registerChange(change);
		}
	}
	if (!isBufferingMode_)
		flush();
}
 

public OntologySetMetadata(OWLOntology ont) {
	ontologies = new HashSet<OntologyMetadata>();
	for (OWLOntology io : ont.getImportsClosure()) {
		OntologyMetadata om = new OntologyMetadata(io);
		ontologies.add(om);
		if (io.equals(ont)) {
			om.isRoot = true;
		}
	}
}
 

public void reasonLeavingOneOut(OWLOntology leaveOutOntology) throws OWLOntologyCreationException {
	OWLOntologyManager m = getManager();
	OWLOntology ont2 = m.createOntology();
	
	LOG.info("LEAVE ONE OUT: "+leaveOutOntology);
	for (OWLOntology io : ontology.getImportsClosure()) {
		if (io.equals(leaveOutOntology)) {
			LOG.info("SKIPPING:"+io);
			continue;
		}
		m.addAxioms(ont2, io.getAxioms());
		
	}
	
	OWLReasoner reasoner = rf.createReasoner(ont2);
	for (OWLEdge e : edges) {
		if (!e.isJustified) {
			// there is no point checking unjustified edges;
			// these are edges that when removed cannot be re-inferred using the entire ontology set.
			// as reasoning is monotonic, removing imports cannot bring it back.
			continue;
		}
		//LOG.info("Testing "+e); 
		if (!isEdgeEntailed(e, ont2, reasoner)) {
			IRI req = leaveOutOntology.getOntologyID().getOntologyIRI().orNull();
			LOG.info(e + " requires "+req);
			e.requires.add(req);
			
		}
	}
	reasoner.dispose();
}
 

/**
     * Merges {@code OWLAxiom}s from the import ontology closure, with the source ontology.
     * This method is similar to {@link OWLGraphWrapperBasic#mergeImportClosure(boolean)}, 
     * except that: i) an {@code OWLAxiom} will be added to the source ontology only if 
     * it is not already present in the source (without taking annotations into account); 
     * ii) a check is performed to ensure that there will not be more than 
     * one annotation axiom for a given subject, when the annotation property 
     * corresponds to a tag with max cardinality one in OBO format 
     * (see {@code org.obolibrary.oboformat.model.Frame#check()}). As for 
     * {@link OWLGraphWrapperBasic#mergeImportClosure(boolean)}, annotations on the ontology 
     * itself are not imported, and the import declarations are removed after execution. 
     */
    private void mergeImportClosure() {
        log.info("Merging axioms from import closure with source ontology...");
        OWLOntology sourceOnt = this.getOwlGraphWrapper().getSourceOntology();
        
        //the method OWLOntology.containsAxiomIgnoreAnnotations is really 
        //not well optimized, so we get all OWLAxioms without annotations 
        //from the source ontology. 
        log.debug("Retrieving OWLAxioms without annotations from source ontology...");
        Set<OWLAxiom> sourceAxiomsNoAnnots = new HashSet<OWLAxiom>();
        for (OWLAxiom ax: sourceOnt.getAxioms()) {
            sourceAxiomsNoAnnots.add(ax.getAxiomWithoutAnnotations());
        }
        if (log.isDebugEnabled()) {
            log.debug(sourceAxiomsNoAnnots.size() + " axioms without annotations retrieved " +
            		"over " + sourceOnt.getAxiomCount() + " axioms.");
        }
        
        for (OWLOntology importedOnt: sourceOnt.getImportsClosure()) {
            if (importedOnt.equals(sourceOnt)) {
                continue;
            }
            log.info("Merging " + importedOnt);
            
//            OWLDataFactory df = sourceOnt.getOWLOntologyManager().getOWLDataFactory();
//            OWLAnnotationProperty p = 
//                    df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI());
//            OWLLiteral v = df.getOWLLiteral("Imported " + importedOnt);
//            OWLAnnotation ann = df.getOWLAnnotation(p, v);
//            AddOntologyAnnotation addAnn = 
//                    new AddOntologyAnnotation(sourceOnt, ann);
//            sourceOnt.getOWLOntologyManager().applyChange(addAnn);
            
            //filter the axioms imported to avoid redundancy (too bad there is not 
            //a method OWLOntology.getAxiomsIgnoreAnnotations())
            int importedAxiomCount = 0;
            importAxioms: for (OWLAxiom importedAx: importedOnt.getAxioms()) {
                if (sourceAxiomsNoAnnots.contains(importedAx.getAxiomWithoutAnnotations())) {
                    continue importAxioms;
                }
                    
                //if it is an annotation axion, we need to ensure that 
                //there will not be more than one axiom for a given subject, 
                //when the annotation corresponds to a tag with max cardinality one 
                //in OBO format (see org.obolibrary.oboformat.model.Frame#check()).
                if (importedAx instanceof OWLAnnotationAssertionAxiom) {
                    OWLAnnotationAssertionAxiom castAx = 
                            (OWLAnnotationAssertionAxiom) importedAx;

                    if (maxOneCardinalityAnnots.contains(
                            castAx.getProperty().getIRI().toString()) || 
                            maxOneCardinalityAnnots.contains(
                                    this.getOwlGraphWrapper().getIdentifier(
                                            castAx.getProperty()))) {

                        //check whether we have an annotation for the same subject 
                        //in the source ontology.
                        for (OWLAnnotationAssertionAxiom sourceAnnotAx: 
                            sourceOnt.getAnnotationAssertionAxioms(
                                    castAx.getSubject())) {
                            if (sourceAnnotAx.getProperty().equals(
                                    castAx.getProperty())) {
                                //discard the axiom from import ontology, there is already 
                                //an annotation with same property on same subject
                                log.trace("Discarding axiom: " + castAx);
                                continue importAxioms;
                            }
                        }
                    }
                }
                
                //all verifications passed, include the axiom
                importedAxiomCount++;
                sourceAxiomsNoAnnots.add(importedAx.getAxiomWithoutAnnotations());
                sourceOnt.getOWLOntologyManager().addAxiom(sourceOnt, importedAx);
            }
            log.info(importedAxiomCount + " axioms imported.");
        }

        //remove the import declarations
        Set<OWLImportsDeclaration> oids = sourceOnt.getImportsDeclarations();
        for (OWLImportsDeclaration oid : oids) {
            RemoveImport ri = new RemoveImport(sourceOnt, oid);
            sourceOnt.getOWLOntologyManager().applyChange(ri);
        }
        
        log.info("Done merging axioms.");
    }