Java OWLOntologyCreationException类代码示例

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * Returns a list of rules extracted from the given OWL-2 ontology document.
 * 
 * @param src an ontology document
 * @return a list of rules
 */
public static List<Rule> fromOntology(OWLOntologyDocumentSource src) {
	try {
		// use OWL-API to get a OWLOntology document from source
		OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
		manager.loadOntologyFromOntologyDocument(src);
		Set<OWLOntology> ontologies = manager.getOntologies();
		if (ontologies.isEmpty()) {
			return Collections.EMPTY_LIST;
		} else {
			// use first ontology from given source
			return fromOntology(ontologies.iterator().next());
		}
	} catch (OWLOntologyCreationException ex) {
		throw new IllegalArgumentException(
				"Loading ontology stream failed", ex);
	}
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * Open the OWL ontology (from the ontology resources of CartAGen) whose name
 * is passed as parameter.
 * @param name
 * @return
 * @throws OWLOntologyCreationException
 */
public static OWLOntology getOntologyFromName(String name)
    throws OWLOntologyCreationException {
  // create the URI from the name and the CartAGen ontologies folder path
  String uri = FOLDER_PATH + "/" + name + ".owl";
  InputStream stream = OwlUtil.class.getResourceAsStream(uri);
  File file = new File(stream.toString());
  String path = file.getAbsolutePath().substring(0,
      file.getAbsolutePath().lastIndexOf('\\'));
  path = path.replaceAll(new String("\\\\"), new String("//"));
  path = path + "//src/main//resources//ontologies//" + name + ".owl";
  // create the ontology from the URI using an OWLOntologyManager
  OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
  IRI physicalURI = IRI.create(new File(path));
  OWLOntology ontology = manager
      .loadOntologyFromOntologyDocument(physicalURI);

  return ontology;
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * @param filename
 * @return
 */
private static OWLOntology getOntology(String filename) {
	File file = new File(filename);
	
	OWLOntologyManager m = OWLManager.createOWLOntologyManager();

	OWLOntology o;
	try {
		o = m.loadOntologyFromOntologyDocument(IRI.create(file.toURI()));
	} catch (OWLOntologyCreationException e) {
		fail("Cannot load ontology.");
		return null;
	}
	assertNotNull(o);

	return o;
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * Creates a dictionary for use by the ConceptMapper that includes GO terms
 * from the namespaces defined in the namespacesToInclude set.
 * 
 * @param namespacesToInclude
 * @param workDirectory
 * @param cleanWorkDirectory
 * @param synonymType
 * @return
 * @throws IOException
 * @throws OWLOntologyCreationException
 * @throws IllegalAccessException
 * @throws IllegalArgumentException
 * @throws OBOParseException
 */
public static File buildConceptMapperDictionary(EnumSet<GoNamespace> namespacesToInclude, File workDirectory,
		CleanDirectory cleanWorkDirectory, SynonymType synonymType) throws IOException, IllegalArgumentException,
		IllegalAccessException, OWLOntologyCreationException {
	if (namespacesToInclude.isEmpty())
		return null;

	boolean doClean = cleanWorkDirectory.equals(CleanDirectory.YES);
	GeneOntologyClassIterator goIter = new GeneOntologyClassIterator(workDirectory, doClean);

	File geneOntologyOboFile = goIter.getGeneOntologyOboFile();
	goIter.close();

	return buildConceptMapperDictionary(namespacesToInclude, workDirectory, geneOntologyOboFile, doClean,
			synonymType);
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
@Test
public void testExactSynonymOnly_SO_OBO() throws IOException, OWLOntologyCreationException {
	File oboFile = ClassPathUtil.copyClasspathResourceToDirectory(getClass(), SAMPLE_SO_OBO_FILE_NAME,
			folder.newFolder("input"));
	OntologyUtil ontUtil = new OntologyUtil(oboFile);
	File outputFile = folder.newFile("dict.xml");
	OboToDictionary.buildDictionary(outputFile, ontUtil, null, SynonymType.EXACT);
	/* @formatter:off */
	List<String> expectedLines = CollectionsUtil.createList(
			"<?xml version=\"1.0\" encoding=\"UTF-8\" ?>",
			"<synonym>", 
			"<token id=\"http://purl.obolibrary.org/obo/SO_0000012\" canonical=\"scRNA_primary_transcript\">",
			"<variant base=\"scRNA_primary_transcript\"/>", 
			"<variant base=\"scRNA primary transcript\"/>", 
			"<variant base=\"scRNA primary transcript\"/>", // this entry ends up in there twice due to underscore removal
			"<variant base=\"scRNA transcript\"/>",
			"<variant base=\"small cytoplasmic RNA transcript\"/>", 
			"</token>", 
			"</synonym>");
	/* @formatter:on */
	assertTrue(FileComparisonUtil.hasExpectedLines(outputFile, CharacterEncoding.UTF_8, expectedLines, null,
			LineOrder.ANY_ORDER, ColumnOrder.AS_IN_FILE, LineTrim.ON, ShowWhiteSpace.ON));
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
	super.initialize(context);
	try {
		ontUtil = new OntologyUtil(ontologyFile);

		/*
		 * check that the term to remove is in the ontology -- if it is not,
		 * it could be a format issue
		 */
		OWLClass cls = ontUtil.getOWLClassFromId(termIdToRemove);
		if (cls == null) {
			String errorMessage = "Ontology term ID selected for removal is not in the given ontology. "
					+ "This could be a formatting issue. Term selected for removal: " + termIdToRemove
					+ " Example term ID from the ontology: " + ontUtil.getClassIterator().next().toStringID();
			throw new ResourceInitializationException(new IllegalArgumentException(errorMessage));
		}

	} catch (OWLOntologyCreationException e) {
		throw new ResourceInitializationException(e);
	}
	annotationDataExtractor = (AnnotationDataExtractor) ConstructorUtil
			.invokeConstructor(annotationDataExtractorClassName);
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
@Override
public InferenceProvider create(final ModelContainer model) throws OWLOntologyCreationException, InterruptedException {
	synchronized (model.getAboxOntology()) {
		InferenceProvider inferenceProvider = inferenceCache.get(model);
		if (inferenceProvider == null) {
			addMiss();
			inferenceProvider = super.create(model);
			model.registerListener(new ModelChangeListenerImplementation(model));
			inferenceCache.put(model, inferenceProvider);
		}
		else {
			addHit();
		}
		return inferenceProvider;
	}
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
@Deprecated
public void deleteFactCommand() throws IOException, OWLOntologyCreationException, OWLOntologyStorageException, UnknownOWLClassException {
	if (isHelp()) {
		info("generates ClassAssertion");
		return;
	}
	OWLOntology ont = resolveOntology(Param.ontology);
	OWLIndividual i = resolveIndividual(Param.individualId);
	OWLIndividual j = resolveIndividual(Param.fillerId);
	OWLObjectProperty p = resolveObjectProperty(Param.propertyId);
	for (OWLObjectPropertyAssertionAxiom ax : ont.getAxioms(AxiomType.OBJECT_PROPERTY_ASSERTION)) {
		if (ax.getSubject().equals(i)) {
			if (p == null || ax.getProperty().equals(p)) {
				if (j == null || ax.getObject().equals(j)) {
					removeAxiom(ont, graph.getDataFactory().getOWLObjectPropertyAssertionAxiom(p, i, j));
				}
			}
		}
	}
	String jsonStr = "";
	response.getWriter().write(jsonStr);
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
@Test
public void testUnion() throws OWLOntologyCreationException, IOException, FrameMergeException {
	OWLObject cls = gw.getOWLObjectByIdentifier("NCBITaxon:6239"); // C elegans
	OWLObject uc = gw.getOWLObjectByIdentifier("NCBITaxon_Union:0000005"); // C elegans
	Set<OWLGraphEdge> edges = gw.getOutgoingEdgesClosure(cls);
	// TODO - test includes union
	boolean ok = false;
	for (OWLGraphEdge e : edges) {
		System.out.println(e);
		OWLObject t = e.getTarget();
		String tid = gw.getIdentifier(t);
		System.out.println(" "+tid);
		// Nematoda or Protostomia
		if ("NCBITaxon_Union:0000005".equals(tid)) {
			ok = true;
		}
	}
	assertTrue(ok);
	
	assertTrue(gw.getAncestorsReflexive(cls).contains(uc));
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * 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);
		}
	}
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * Read a data file, create an OWL representation, and save an OWL file.
 * Create alternate identifiers from the merge.dmp file information
 *
 * @param inputPath the path to the input data file (e.g. taxonomy.dat)
 * @param outputPath the path to the output OWL file
 *	(e.g. ncbi_taxonomy.owl).
 * @param mergeInfo the input stream of the merged information
 * @param citationInfo the input stream of the citation information
 * @param uniqueNames
 * @return OWL ontology
 * @throws IOException if the paths do not resolve
 * @throws OWLOntologyCreationException if OWLAPI fails to create an
 *	empty ontology
 * @throws OWLOntologyStorageException if OWLAPI can't save the file
 */
public static OWLOntology convertToOWL(String inputPath,
		String outputPath, InputStream mergeInfo,
		InputStream citationInfo,
		Map<String, String> uniqueNames) throws IOException,
		OWLOntologyCreationException,
		OWLOntologyStorageException {
	File outputFile = new File(outputPath);
	IRI outputIRI = IRI.create(outputFile);
	OWLOntology ontology = convertToOWL(inputPath, uniqueNames);
	
	if (mergeInfo != null) {
		addAltIds(ontology, mergeInfo);
	}
	
	if (citationInfo != null) {
		addCitationInfo(ontology, citationInfo);
	}
	
	logger.debug("Saving ontology...");

	ontology.getOWLOntologyManager().saveOntology(
		ontology, outputIRI);
	return ontology;
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * Classifies a given ontology and checks whether another ontology is
 * entailed by the former.
 *
 * @param premiseFile
 *            ontology file to be classified and used as premise
 * @param conclusionFile
 *            file with the conclusion
 * @throws FileNotFoundException
 *             if the file was not found
 * @throws OWLOntologyCreationException
 *             if the ontology could not be created
 * @throws OWLRendererException
 *             if a renderer error occurs
 * @return <code>true</code> if and only if the premise ontology entails the
 *         conclusion ontology
 */
public boolean checkEntailment(File premiseFile, File conclusionFile)
		throws OWLOntologyCreationException, OWLRendererException, FileNotFoundException {
	Objects.requireNonNull(premiseFile);
	Objects.requireNonNull(conclusionFile);
	logger.fine("starting jcel console ...");

	OWLOntologyManager manager = OWLManager.createOWLOntologyManager();

	logger.fine("loading premise ontology using the OWL API ...");
	OWLOntology premiseOntology = manager.loadOntologyFromOntologyDocument(premiseFile);

	logger.fine("loading conclusion ontology using the OWL API ...");
	OWLOntology conclusionOntology = manager.loadOntologyFromOntologyDocument(conclusionFile);

	logger.fine("starting reasoner ...");
	JcelReasoner reasoner = new JcelReasoner(premiseOntology, false);

	logger.fine("precomputing inferences ...");
	reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);

	boolean ret = conclusionOntology.getAxioms().stream().allMatch(axiom -> reasoner.isEntailed(axiom));

	logger.fine("jcel console finished.");
	return ret;
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
@Test
public void testDiffInCommon() throws OWLOntologyCreationException {
    ParserWrapper pw = new ParserWrapper();
    OWLOntology ont1 = pw.parseOWL(getResourceIRIString("difftest1.obo"));
    OWLOntology ont2 = pw.parseOWL(getResourceIRIString("difftest2.obo"));
    Diff diff = new Diff();
    diff.ontology1 = ont1;
    diff.ontology2 = ont2;
    diff.isCompareClassesInCommon = true;
    DiffUtil.getDiff(diff);
    System.out.println(diff.ontology1remaining.getAxioms());
    System.out.println(diff.ontology2remaining.getAxioms());
    System.out.println(diff.intersectionOntology.getAxioms());
    assertEquals(4, diff.intersectionOntology.getAxiomCount());
    assertEquals(5, diff.ontology1remaining.getAxiomCount());
    assertEquals(6, diff.ontology2remaining.getAxiomCount());
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
/**
 * Returns a list of example configurations based on a list of files.
 * 
 * @param list
 *            list of files
 * @return a list of example configurations based on a list of files
 * @throws IOException
 *             if something goes wrong with I/O
 * @throws OWLOntologyCreationException
 *             if something goes wrong with the creation of the ontologies
 */
public List<ExampleConfiguration> getOntologyAndNetworkFiles(List<String> list)
		throws IOException, OWLOntologyCreationException {
	Objects.requireNonNull(list);
	List<ExampleConfiguration> ret = new ArrayList<>();
	List<String> owlFiles = getFilesWithExtension(list, OWL_EXTENSION);

	for (String fileName : owlFiles) {
		String fileNamePrefix = fileName.substring(0, fileName.length() - OWL_EXTENSION.length());
		String bayesianNetworkFileName = fileNamePrefix + NETWORK_EXTENSION;
		String queryFileName = fileNamePrefix + QUERY_EXTENSION;

		String owlOntologyName = fileName;
		OWLOntology owlOntology = readOntology(getInputStreamForFile(owlOntologyName));
		String bayesianNetwork = getFile(getInputStreamForFile(bayesianNetworkFileName));
		String query = getFile(getInputStreamForFile(queryFileName));

		ExampleConfiguration exampleConf = new ExampleConfigurationImpl(getFileName(fileNamePrefix),
				owlOntologyName, owlOntology, bayesianNetworkFileName, bayesianNetwork, query);

		ret.add(exampleConf);
	}
	return ret;
}
 

import org.semanticweb.owlapi.model.OWLOntologyCreationException; //导入依赖的package包/类
public static void main(String[] args) throws OWLOntologyCreationException {
	// Creation of a new Querier = Motor running the query
	System.out.println("Initialization of the querier...");

	QueryingWithNamedClasses querier = new QueryingWithNamedClasses();
	// Actual query:
	// "In our ontology, what are the subclasses of the named class MeatEater?"
	// It will work only if you use a reference to a class already present
	// in your ontology (named class).
	Set<OWLClass> results = querier.getSubClasses("MeatEater");
	// The result is the set of classes satisfying the query.
	for (OWLClass owlClass : results) {
		// Just iterates over it and print the name of the class
		System.out.println("Subclass: "
				+ querier.shortFormProvider.getShortForm(owlClass));
	}
}