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

/**
 * 
 * returns set of entities that belong to a referenced ontology that are referenced in the source ontology.
 * 
 * If the source ontology is not explicitly declared, then all entities that are referenced in the source
 * ontology and declared in a reference ontology are returned.
 * 
 * Example: if the source ontology is cl, and cl contains axioms that reference go:1, go:2, ...
 * and go is in the set of referenced ontologies, then {go:1,go:2,...} will be in the returned set.
 * It is irrelevant whether go:1, ... is declared in the source (e.g. MIREOTed)
 * 
 * Note this only returns direct references. See
 * {@link #getClosureOfExternalReferencedEntities()} for closure of references
 * 
 * @return all objects referenced by source ontology
 */
public Set<OWLEntity> getExternalReferencedEntities() {
	OWLOntology ont = graph.getSourceOntology();
	Set<OWLEntity> objs = ont.getSignature(Imports.EXCLUDED);
	Set<OWLEntity> refObjs = new HashSet<OWLEntity>();
	LOG.info("testing "+objs.size()+" objs to see if they are contained in: "+getReferencedOntologies());
	for (OWLEntity obj : objs) {
		//LOG.info("considering: "+obj);
		// a reference ontology may have entities from the source ontology MIREOTed in..
		// allow a configuration with the URI prefix specified
		if (isInExternalOntology(obj)) {
			refObjs.add(obj);

		}
	}
	LOG.info("#refObjs: "+refObjs.size());

	return refObjs;
}
 

/**
 * Generate a OboGraphs JSON ontology blob for the local axioms for an object.
 * 
 * This will include
 * 
 *  - all logical axioms about the object
 *  - all annotations for all entities in the signature
 *  
 * In other words, direct parents plus labels and other metadata on all entities
 * 
 * @param obj
 * @return JSON string
 * @throws JsonProcessingException
 * @throws OWLOntologyCreationException
 */
public String getOboGraphJSONString(OWLObject obj) throws JsonProcessingException, OWLOntologyCreationException {
	FromOwl fromOwl = new FromOwl();
	OWLOntologyManager m = sourceOntology.getOWLOntologyManager();
	if (obj instanceof OWLNamedObject) {
		OWLNamedObject nobj = (OWLNamedObject)obj;
		OWLOntology ont = m.createOntology(nobj.getIRI());
		Set<OWLAxiom> axioms = new HashSet<>();
		if (nobj instanceof OWLClass) {
			axioms.addAll(sourceOntology.getAxioms((OWLClass)nobj, Imports.INCLUDED));
		}
		else if (nobj instanceof OWLObjectProperty) {
			axioms.addAll(sourceOntology.getAxioms((OWLObjectProperty)nobj, Imports.INCLUDED));
		}
		m.addAxioms(ont, axioms);
		axioms = new HashSet<>();
		for (OWLEntity e : ont.getSignature()) {
			axioms.addAll(sourceOntology.getAnnotationAssertionAxioms(e.getIRI()));
		}
		axioms.addAll(sourceOntology.getAnnotationAssertionAxioms(nobj.getIRI()));
		m.addAxioms(ont, axioms);

		GraphDocument gd = fromOwl.generateGraphDocument(ont);
		return OgJsonGenerator.render(gd);
	}
	else {
		return "{}";
	}

}
 

/**
 * removes external entities:
 *  - anything marked with IAO_0000412 is removed
 *  - if isMain is true then anything that is also present in an external ontology is removed
 * 
 * @param isMain
 * @param ont
 */
public void removeExternalEntities(boolean isMain, OWLOntology ont) {
	Set<OWLEntity> objs = ont.getSignature(Imports.EXCLUDED);
	Set<OWLClass> rmClasses = new HashSet<OWLClass>();
	Set<OWLObjectProperty> rmProperties = new HashSet<OWLObjectProperty>();
	Set<OWLIndividual> rmIndividuals = new HashSet<OWLIndividual>();
	LOG.info("removing external entities marked with IAO_0000412 from: "+ont);
	if (isMain) {
		LOG.info("testing " + objs.size()
				+ " objs to see if they are contained in the follow referenced ontologies: "
				+ getReferencedOntologies());
	}
	for (OWLEntity obj : objs) {
		final boolean isMarked = isImportMarkedEntity(obj, ont);
		if (obj instanceof OWLClass) {
			if ((isMain && isInExternalOntology(obj)) || isMarked) {
				rmClasses.add((OWLClass) obj);
			}
		}
		else if (obj instanceof OWLObjectProperty && isMarked) {
			rmProperties.add((OWLObjectProperty) obj);
		}
		else if (obj instanceof OWLIndividual  && isMarked) {
			rmIndividuals.add((OWLIndividual) obj);
		}
	}
	Set<OWLAxiom> rmAxioms = new HashSet<OWLAxiom>();
	for (OWLClass c : rmClasses) {
		rmAxioms.addAll(ont.getAnnotationAssertionAxioms(c.getIRI()));
		rmAxioms.addAll(ont.getDeclarationAxioms(c));
		rmAxioms.addAll(ont.getAxioms(c, Imports.EXCLUDED));
	}
	for (OWLObjectProperty p : rmProperties) {
		rmAxioms.addAll(ont.getAnnotationAssertionAxioms(p.getIRI()));
		rmAxioms.addAll(ont.getDeclarationAxioms(p));
		rmAxioms.addAll(ont.getAxioms(p, Imports.EXCLUDED));
	}
	for (OWLIndividual i : rmIndividuals) {
		rmAxioms.addAll(ont.getAxioms(i, Imports.EXCLUDED));
	}
	if (!rmAxioms.isEmpty()) {
		LOG.info("Removing "+rmAxioms.size()+" external axioms for: "+ ont.getOntologyID());
		ont.getOWLOntologyManager().removeAxioms(ont, rmAxioms);
	}
}