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

@CLIMethod("--remove-dangling-annotations")
public void removeDangningAnnotations(Opts opts) throws Exception {
	OWLOntology ont = g.getSourceOntology();
	int n = 0;
	Set<OWLAxiom> rmAxioms = new HashSet<OWLAxiom>();
	for (OWLNamedIndividual i : ont.getIndividualsInSignature()) {
		for (OWLClassAssertionAxiom ca : ont.getClassAssertionAxioms(i)) {
			OWLClassExpression cx = ca.getClassExpression();
			if (cx instanceof OWLClass) {
				OWLClass c = (OWLClass) cx;
				String label = g.getLabel(c);
				if (label == null)
					rmAxioms.add(ca);
				else
					n++;
			}
		}
	}
	LOG.info("Removing " + rmAxioms.size() + " axioms");
	ont.getOWLOntologyManager().removeAxioms(ont, rmAxioms);
	LOG.info("Remaining: " + n + " axioms");
}
 

public static void randomizeClassAssertions(OWLOntology ont, int num) {
	Set<OWLClassAssertionAxiom> caas = new HashSet<OWLClassAssertionAxiom>();
	Set<OWLClassAssertionAxiom> caasNew = new HashSet<OWLClassAssertionAxiom>();
		Set<OWLNamedIndividual> inds = ont.getIndividualsInSignature(Imports.INCLUDED);
	OWLNamedIndividual[] indArr = (OWLNamedIndividual[]) inds.toArray();
	for (OWLNamedIndividual ind : inds) {
		caas.addAll( ont.getClassAssertionAxioms(ind) );
	}
	for (OWLClassAssertionAxiom caa : caas) {
		OWLIndividual randomIndividual = null;
		caasNew.add(ont.getOWLOntologyManager().getOWLDataFactory().getOWLClassAssertionAxiom(caa.getClassExpression(), 
				randomIndividual));
	}
	ont.getOWLOntologyManager().removeAxioms(ont, caas);
	ont.getOWLOntologyManager().addAxioms(ont, caasNew);
}
 

/**
 * Find all edges of the form [i INST c] in the graph closure.
 * (this includes both direct assertions, plus assertions to objects
 *  that link to c via a chain of SubClassOf assertions)
 * <p> 
 * the semantics are the same as inferred ClassAssertion axioms
 * 
 * @param c owlClass
 * @return all individuals classified here via basic graph traversal
 */
public Set<OWLIndividual> getInstancesFromClosure(OWLClass c) {
	Set<OWLIndividual> ins = new HashSet<OWLIndividual>();
	for (OWLOntology o : getAllOntologies()) {
		// iterate through all individuals; sequential scan may be slow for
		// large knowledge bases
		for (OWLIndividual in : o.getIndividualsInSignature()) {
			for (OWLGraphEdge e : getEdgesBetween(in, c)) {
				List<OWLQuantifiedProperty> qps = e.getQuantifiedPropertyList();
				// check for edges of the form < i INSTANCE_OF c >
				// we exclude relation chaims, e.g. <i [INSTANCE_OF PART_OF-some] c>
				if (qps.size() == 1 && qps.get(0).isInstanceOf()) {
					ins.add(in);
					break;
				}
			}
		}
	}
	return ins;
}
 

public static OWLOntology createOWLThingTypeDeclForIndividuals(OWLOntology ont) throws OWLOntologyCreationException, IOException  {
	OWLOntology ret = ont.getOntologyID()!=null && ont.getOntologyID().getOntologyIRI()!=null?
				ont.getOWLOntologyManager().createOntology(ont.getOntologyID().getOntologyIRI()):
				ont.getOWLOntologyManager().createOntology();
	
				OWLDataFactory fac = ret.getOWLOntologyManager().getOWLDataFactory();
	OWLClass owlThing = ret.getOWLOntologyManager().getOWLDataFactory().getOWLThing();
	for (OWLNamedIndividual ind: ont.getIndividualsInSignature()) {
		OWLNamedIndividual ni = fac.getOWLNamedIndividual(ind.getIRI());
		OWLAxiom ax = fac.getOWLClassAssertionAxiom(owlThing, ni);
		ret.getOWLOntologyManager().addAxiom(ret, ax);
	}
	return ret;
	
	
}
 

public Set<GeneAnnotation> generateAssociations(OWLOntology ont) {
	Set<GeneAnnotation> assocs = new HashSet<GeneAnnotation>();
	for (OWLNamedIndividual i : ont.getIndividualsInSignature(Imports.INCLUDED)) {
		assocs.addAll(generateAssociations(i, ont));
	}
	return assocs;
}
 

/**
 * Finds all edges between an instance i and he given class c.
 * <p>
 * this includes inferred class assertions, as well as chains such as
 * <p>
 * i has_part j, j inst_of k, k part_of some c
 * 
 * @param c owlClass
 * @return all edges in closure between an instance and owlClass
 */
public Set<OWLGraphEdge> getInstanceChainsFromClosure(OWLClass c) {
	Set<OWLGraphEdge> edges = new OWLGraphEdgeSet();
	for (OWLOntology o : getAllOntologies()) {
		// iterate through all individuals; sequential scan may be slow for
		// large knowledge bases
		for (OWLIndividual in : o.getIndividualsInSignature()) {
		    edges.addAll(getEdgesBetween(in, c));
		}
	}
	return edges;
}
 

/**
 * Experimental method for trying out the loading of complex_annotation doc type
 * 
 * @param opts
 * @throws Exception
 */
@CLIMethod("--solr-load-complex-annotations")
public void experimentalLoadComplexAnnotationSolr(Opts opts) throws Exception {

	// Check to see if the global url has been set.
	String url = sortOutSolrURL(globalSolrURL);				

	// Only proceed if our environment was well-defined.
	if( legoCatalogs == null || legoFiles == null || legoCatalogs.isEmpty() || legoFiles.isEmpty() ){
		LOG.warn("Lego environment not well defined--skipping.");
	}else{

		// Ready the environment for every pass.
		ParserWrapper pw = new ParserWrapper();
		// Add all of the catalogs.
		for( File legoCatalog : legoCatalogs ){
			pw.addIRIMapper(new CatalogXmlIRIMapper(legoCatalog));				
		}
		OWLOntologyManager manager = pw.getManager();
		OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();

		// Actual loading--iterate over our list and load individually.
		for( File legoFile : legoFiles ){
			String fname = legoFile.getName();
			OWLReasoner currentReasoner = null;
			OWLOntology ontology = null;

			// TODO: Temp cover for missing group labels and IDs.
			//String agID = legoFile.getCanonicalPath();
			String agLabel = StringUtils.removeEnd(fname, ".owl");
			String agID = new String(agLabel);

			try {
				ontology = pw.parseOWL(IRI.create(legoFile));
				currentReasoner = reasonerFactory.createReasoner(ontology);

				// Some sanity checks--some of the genereated ones are problematic.
				boolean consistent = currentReasoner.isConsistent();
				if( consistent == false ){
					LOG.info("Skip since inconsistent: " + fname);
					continue;
				}
				Set<OWLClass> unsatisfiable = currentReasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();

				// TODO - make configurable to allow fail fast
				if (unsatisfiable.isEmpty() == false) {
					LOG.info("Skip since unsatisfiable: " + fname);
					continue;
				}

				Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
				Set<OWLAnnotation> modelAnnotations = ontology.getAnnotations();

				OWLGraphWrapper currentGraph = new OWLGraphWrapper(ontology);						
				try {
					LOG.info("Trying complex annotation load of: " + fname);
					ComplexAnnotationSolrDocumentLoader loader =
							new ComplexAnnotationSolrDocumentLoader(url, currentGraph, currentReasoner, individuals, modelAnnotations, agID, agLabel, fname);
					loader.load();
				} catch (SolrServerException e) {
					LOG.info("Complex annotation load of " + fname + " at " + url + " failed!");
					e.printStackTrace();
					System.exit(1);
				}
			} finally {
				// Cleanup reasoner and ontology.
				if (currentReasoner != null) {
					currentReasoner.dispose();
				}
				if (ontology != null) {
					manager.removeOntology(ontology);
				}
			}
		}
	}
}
 

/**
 * Experimental method for trying out the loading of complex_annotation doc type.
 * Works with --read-ca-list <file>.
 * 
 * @param opts
 * @throws Exception
 */
@CLIMethod("--solr-load-complex-exp")
public void loadComplexAnnotationSolr(Opts opts) throws Exception {

	// Check to see if the global url has been set.
	String url = sortOutSolrURL(globalSolrURL);				

	// Only proceed if our environment was well-defined.
	if( caFiles == null || caFiles.isEmpty() ){
		LOG.warn("LEGO environment not well defined--will skip loading LEGO/CA.");
	}else{

		// NOTE: These two lines are remainders from old code, and I'm not sure of their place in this world of ours.
		// I wish there was an arcitecture diagram somehwere...
		OWLOntologyManager manager = pw.getManager();
		OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();

		// Actual loading--iterate over our list and load individually.
		for( String fname : caFiles ){
			OWLReasoner currentReasoner = null;
			OWLOntology ontology = null;

			// TODO: Temp cover for missing group labels and IDs.
			//String agID = legoFile.getCanonicalPath();
			String pretmp = StringUtils.removeEnd(fname, ".owl");
			String[] bits = StringUtils.split(pretmp, "/");
			String agID = bits[bits.length -1];
			String agLabel = new String(StringUtils.replaceOnce(agID, ":", "_"));

			try {
				ontology = pw.parseOWL(IRI.create(fname));
				currentReasoner = reasonerFactory.createReasoner(ontology);

				// Some sanity checks--some of the genereated ones are problematic.
				boolean consistent = currentReasoner.isConsistent();
				if( consistent == false ){
					LOG.info("Skip since inconsistent: " + fname);
					continue;
				}
				Set<OWLClass> unsatisfiable = currentReasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
				if (unsatisfiable.isEmpty() == false) {
					LOG.info("Skip since unsatisfiable: " + fname);
					continue;
				}

				Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
				Set<OWLAnnotation> modelAnnotations = ontology.getAnnotations();
				OWLGraphWrapper currentGraph = new OWLGraphWrapper(ontology);						
				try {
					LOG.info("Trying complex annotation load of: " + fname);
					ComplexAnnotationSolrDocumentLoader loader =
							new ComplexAnnotationSolrDocumentLoader(url, currentGraph, currentReasoner, individuals, modelAnnotations, agID, agLabel, fname);
					loader.load();
				} catch (SolrServerException e) {
					LOG.info("Complex annotation load of " + fname + " at " + url + " failed!");
					e.printStackTrace();
					System.exit(1);
				}
			} finally {
				// Cleanup reasoner and ontology.
				if (currentReasoner != null) {
					currentReasoner.dispose();
				}
				if (ontology != null) {
					manager.removeOntology(ontology);
				}
			}
		}
	}
}