Java OWLOntologyManager.saveOntology方法代碼示例

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
private void createModule(String ontologyId, String moduleName, Set<OWLEntity> signature)
		throws OWLOntologyCreationException, IOException, OWLOntologyStorageException 
{
	// create a new manager, avoid unnecessary change events
	final OWLOntologyManager m = OWLManager.createOWLOntologyManager();
	
	// extract module
	SyntacticLocalityModuleExtractor sme = new SyntacticLocalityModuleExtractor(m, mooncat.getOntology(), ModuleType.BOT);
	Set<OWLAxiom> moduleAxioms = sme.extract(signature);
	
	OWLOntology module = m.createOntology(IRI.generateDocumentIRI());
	m.addAxioms(module, moduleAxioms);
	
	// save module
	OutputStream moduleOutputStream = null;
	try {
		moduleOutputStream = getOutputSteam(getModuleFileName(ontologyId, moduleName));
		m.saveOntology(module, moduleOutputStream);
	}
	finally {
		IOUtils.closeQuietly(moduleOutputStream);
	}
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
private static void createModule(String moduleName, Set<OWLEntity> signature, OWLOntology ont)
		throws OWLOntologyCreationException, IOException, OWLOntologyStorageException 
{
	// create a new manager avoid unnecessary change events
	final OWLOntologyManager m = OWLManager.createOWLOntologyManager();
	
	// extract module
	SyntacticLocalityModuleExtractor sme = new SyntacticLocalityModuleExtractor(m, ont, ModuleType.BOT);
	Set<OWLAxiom> moduleAxioms = sme.extract(signature);
	
	OWLOntology module = m.createOntology(IRI.generateDocumentIRI());
	m.addAxioms(module, moduleAxioms);
	
	// save module
	OutputStream moduleOutputStream = null;
	try {
		moduleOutputStream = new FileOutputStream(getModuleFile(moduleName));
		m.saveOntology(module, moduleOutputStream);
	}
	finally {
		IOUtils.closeQuietly(moduleOutputStream);
	}
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
/**
 * Export the ABox, will try to set the ontologyID to the given modelId (to
 * ensure import assumptions are met)
 * 
 * @param model
 * @param ontologyFormat
 * @return modelContent
 * @throws OWLOntologyStorageException
 */
public String exportModel(ModelContainer model, OWLDocumentFormat ontologyFormat) throws OWLOntologyStorageException {
	final OWLOntology aBox = model.getAboxOntology();
	final OWLOntologyManager manager = aBox.getOWLOntologyManager();
	
	// make sure the exported ontology has an ontologyId and that it maps to the modelId
	final IRI expectedABoxIRI = model.getModelId();
	Optional<IRI> currentABoxIRI = aBox.getOntologyID().getOntologyIRI();
	if (currentABoxIRI.isPresent() == false) {
		manager.applyChange(new SetOntologyID(aBox, expectedABoxIRI));
	}
	else {
		if (expectedABoxIRI.equals(currentABoxIRI) == false) {
			OWLOntologyID ontologyID = new OWLOntologyID(Optional.of(expectedABoxIRI), Optional.of(expectedABoxIRI));
			manager.applyChange(new SetOntologyID(aBox, ontologyID));
		}
	}

	// write the model into a buffer
	ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
	if (ontologyFormat != null) {
		manager.saveOntology(aBox, ontologyFormat, outputStream);
	}
	else {
		manager.saveOntology(aBox, outputStream);
	}
	
	// extract the string from the buffer
	String modelString = outputStream.toString();
	return modelString;
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
public void saveExtractedModule(OWLOntologyManager manager, OWLOntology module, String physicalModuleURI) {
	//OWLOntologyManager ontologyModuleManager = OWLManager.createOWLOntologyManager();
	
    try {
    	manager.saveOntology(module, new RDFXMLOntologyFormat(), IRI.create(physicalModuleURI));
    }
    catch (Exception e) {
    	System.err.println("Error saving module\n" + e.getLocalizedMessage());
    	e.printStackTrace();
    }
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
@BeforeClass
public static void setUpBeforeClass() throws Exception {
    final URI ontologyUri = URI.create("http://krizik.felk.cvut.cz/ontologies/jopa/ConnectorFactoryTest");
    final File targetFile = Files.createTempFile("connectortest", ".owl").toFile();
    targetFile.deleteOnExit();
    final OWLOntologyManager om = OWLManager.createOWLOntologyManager();
    final OWLOntology o = om.createOntology(IRI.create(ontologyUri));
    om.saveOntology(o, IRI.create(targetFile));
    final URI physicalUri = targetFile.toURI();
    storageProperties = OntologyStorageProperties.ontologyUri(ontologyUri).physicalUri(physicalUri).driver(
            OwlapiDataSource.class.getCanonicalName()).build();
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
public static void main(String[] args) throws OWLOntologyStorageException,
		OWLOntologyCreationException {
	OWLOntologyManager inputOntologyManager = OWLManager.createOWLOntologyManager();
	OWLOntologyManager outputOntologyManager = OWLManager.createOWLOntologyManager();

	// Load your ontology.
	OWLOntology ont = inputOntologyManager.loadOntologyFromOntologyDocument(new File("path-to-ontology"));

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

	// Classify the ontology.
	reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);

	// To generate an inferred ontology we use implementations of
	// inferred axiom generators
	List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
	gens.add(new InferredSubClassAxiomGenerator());
	gens.add(new InferredEquivalentClassAxiomGenerator());

	// Put the inferred axioms into a fresh empty ontology.
	OWLOntology infOnt = outputOntologyManager.createOntology();
	InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner,
			gens);
	iog.fillOntology(outputOntologyManager.getOWLDataFactory(), infOnt);

	// Save the inferred ontology.
	outputOntologyManager.saveOntology(infOnt,
			new FunctionalSyntaxDocumentFormat(),
			IRI.create((new File("path-to-output").toURI())));

	// Terminate the worker threads used by the reasoner.
	reasoner.dispose();
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
/**
 * Created to mimic the translation to OWL for GAF checks
 * 
 * @param opts
 * @throws Exception
 */
@CLIMethod("--gaf2owl-simple")
public void gaf2OwlSimple(Opts opts) throws Exception {
	opts.info("-o FILE", "translates previously loaded GAF document into OWL, requires a loaded ontology to lookup ids");
	String out = null;
	while (opts.hasOpts()) {
		if (opts.nextEq("-o")) {
			out = opts.nextOpt();
		}
		else
			break;

	}
	if (g == null) {
		LOG.error("An ontology is required.");
		exit(-1);
	}
	else if (gafdoc == null) {
		LOG.error("A GAF document is required.");
		exit(-1);
	}
	else if (out == null) {
		LOG.error("An output file is required.");
		exit(-1);
	}
	LOG.info("Creating OWL represenation of annotations.");
	GAFOWLBridge bridge = new GAFOWLBridge(g);
	bridge.setGenerateIndividuals(false);
	bridge.setBasicAboxMapping(false);
	bridge.setBioentityMapping(BioentityMapping.CLASS_EXPRESSION);
	bridge.setSkipNotAnnotations(true);
	OWLOntology translated = bridge.translate(gafdoc);
	File outputFile = new File(out);
	OWLOntologyManager manager = translated.getOWLOntologyManager();
	OWLDocumentFormat ontologyFormat= new FunctionalSyntaxDocumentFormat();
	manager.saveOntology(translated, ontologyFormat, IRI.create(outputFile));
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
private void write(OWLOntologyManager manager, OWLOntology ont, OWLDocumentFormat format, OutputStream out) throws OWLOntologyStorageException {
	try {
		manager.saveOntology(ont, format, out);
	} finally {
		try {
			out.close();
		} catch (IOException e) {
			logWarn("Could not close stream.", e);
		} 
	}
	
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
private void saveOntologyCopy(File file) throws OWLOntologyStorageException {
	IRI newOntologyIRI = IRI.create(file.toURI());
	OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
	manager.saveOntology(ontology, new RDFXMLOntologyFormat(), newOntologyIRI);
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
public static synchronized void saveOntology(OWLOntologyManager moduleManager, OWLOntology ontology, String IRIstr) throws Exception{
	
	moduleManager.saveOntology(
			ontology, new RDFXMLOntologyFormat(), IRI.create(IRIstr));
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
protected int preCheckOntology(String inConsistentMsg, String unsatisfiableMsg, String unsatisfiableModule) throws OWLException, IOException {
	// pre-check: only try to load ontology iff:
	// * ontology is consistent 
	// * no unsatisfiable classes
	OWLReasoner currentReasoner = reasoner;
	boolean disposeReasoner = false;
	try {
		if (currentReasoner == null) {
			disposeReasoner = true;
			currentReasoner = new ElkReasonerFactory().createReasoner(g.getSourceOntology());
		}
		boolean consistent = currentReasoner.isConsistent();
		if (consistent == false) {
			LOG.error(inConsistentMsg);
			return -1;
		}
		Set<OWLClass> unsatisfiable = currentReasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
		if (unsatisfiable.isEmpty() == false) {
			LOG.error(unsatisfiableMsg);
			OWLPrettyPrinter prettyPrinter = getPrettyPrinter();
			for (OWLClass owlClass : unsatisfiable) {
				LOG.error("Unsatisfiable: "+prettyPrinter.render(owlClass));
			}
			LOG.info("Creating module for unsatisfiable classes in file: "+unsatisfiableModule);
			ModuleType mtype = ModuleType.BOT;
			OWLOntologyManager m = g.getManager();
			SyntacticLocalityModuleExtractor sme = new SyntacticLocalityModuleExtractor(m, g.getSourceOntology(), mtype );
			Set<OWLEntity> seeds = new HashSet<OWLEntity>(unsatisfiable);
			Set<OWLAxiom> axioms = sme.extract(seeds);
			OWLOntology module = m.createOntology();
			m.addAxioms(module, axioms);
			File moduleFile = new File(unsatisfiableModule).getCanonicalFile();
			m.saveOntology(module, IRI.create(moduleFile));
			return -1;
		}
	}
	finally {
		if (disposeReasoner && currentReasoner != null) {
			currentReasoner.dispose();
		}
	}
	return 0;
}
 

import org.semanticweb.owlapi.model.OWLOntologyManager; //導入方法依賴的package包/類
@Test
public void testRemove() throws Exception {
	ParserWrapper pw = new ParserWrapper();
	OWLGraphWrapper g = pw.parseToOWLGraph(getResourceIRIString("mooncat/remove-directives-test1.obo"));
	
	System.out.println(g.getSourceOntology().getAxioms(AxiomType.EQUIVALENT_CLASSES));
	OWLOntology secondary = pw.parse(getResourceIRIString("mooncat/remove-directives-test2.obo"));
       System.out.println(secondary.getAxioms(AxiomType.EQUIVALENT_CLASSES));
	g.addSupportOntology(secondary);
	
	Mooncat mooncat = new Mooncat(g);
	
	//mooncat.mergeOntologies();
	g.mergeOntology(secondary);
	
	OWLOntology merged = g.getSourceOntology();

	System.out.println(merged.getAxioms(AxiomType.EQUIVALENT_CLASSES));

	Owl2Obo owl2Obo = new Owl2Obo();
	OBODoc mergedObo = owl2Obo.convert(merged);
	
	if (USE_SYSTEM_OUT) {
		System.out.println("------------------------");
		OWLOntologyManager manager = merged.getOWLOntologyManager();
		OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
		manager.saveOntology(merged, new RDFXMLDocumentFormat(), documentTarget);
		System.out.println("------------------------");
		String oboString = renderOBOtoString(mergedObo);
		System.out.println(oboString);
		System.out.println("------------------------");
	}
	
	Frame headerFrame = mergedObo.getHeaderFrame();
	String owlAxiomString = headerFrame.getTagValue(OboFormatTag.TAG_OWL_AXIOMS, String.class);
	assertNotNull(owlAxiomString);
	
	
	Frame frame = mergedObo.getTermFrame("X:1");
	Collection<Clause> clauses = frame.getClauses(OboFormatTag.TAG_INTERSECTION_OF);
	assertEquals(2, clauses.size());
}