Java Code Examples for org.semanticweb.owlapi.apibinding.OWLManager#getOWLDataFactory()

/**
 * Create a new report object with a QuotedEntityChecker loaded with entries from the label map.
 * Use labels for report output.
 *
 * @param labelMap Map of IRI to label for all entities in the ontology
 * @throws IOException on problem creating IOHelper
 */
public Report(Map<IRI, String> labelMap) throws IOException {
  this.ioHelper = new IOHelper();
  checker = new QuotedEntityChecker();
  checker.setIOHelper(ioHelper);
  checker.addProvider(new SimpleShortFormProvider());
  checker.addProperty(OWLManager.getOWLDataFactory().getRDFSLabel());
  if (labelMap != null) {
    useLabels = true;
    OWLDataFactory df = OWLManager.getOWLDataFactory();
    for (Entry<IRI, String> entry : labelMap.entrySet()) {
      // Set all the entities as class - will not matter for retrieving label
      OWLEntity e = df.getOWLEntity(EntityType.CLASS, entry.getKey());
      checker.add(e, entry.getValue());
    }
  }
}
 

private static OWLAxiom getEntailment() {
	// Let's pick some class subsumption we want to explain
	OWLDataFactory factory = OWLManager.getOWLDataFactory();
	
	OWLClass subsumee = factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#LiquidFood"));
	OWLClass subsumer = factory.getOWLClass(IRI.create("http://www.co-ode.org/ontologies/galen#Food"));
	
	return factory.getOWLSubClassOfAxiom(subsumee, subsumer);
}
 

static public void main (String[] args) throws OWLException,
        InstantiationException, IllegalAccessException,
        ClassNotFoundException {
    String reasonerFactoryClassName = null;

    String pathToOwlOntology = "/Users/piek/Desktop/NWR/NWR-ontology/version-0.6/ESO_version_0.6.owl";
    OWLOntologyManager m = (OWLOntologyManager) OWLManager.getOWLDataFactory();
    @SuppressWarnings("null")
    //@Nonnull
    IRI documentIRI = IRI.create(pathToOwlOntology);
    OWLOntology ontology = m
            .loadOntologyFromOntologyDocument(documentIRI);
    // Report information about the ontology
    System.out.println("Ontology Loaded...");
    System.out.println("Document IRI: " + documentIRI);
    System.out.println("Ontology : " + ontology.getOntologyID());
    System.out.println("Format      : "
            + m.getOntologyFormat(ontology));

    @SuppressWarnings("null")

    OwlReader2 simpleHierarchy = new OwlReader2(
            (OWLReasonerFactory) Class.forName(reasonerFactoryClassName)
                    .newInstance(), ontology);
    // Get Thing
    OWLClass clazz = m.getOWLDataFactory().getOWLThing();
    System.out.println("Class       : " + clazz);
    // Print the hierarchy below thing
    simpleHierarchy.printHierarchy(clazz);
}
 

@Before
public void initialize() {
	factory = OWLManager.getOWLDataFactory();
}
 

@Override
public CommandState execute(CommandState state, String[] args) throws Exception {
  CommandLine line = CommandLineHelper.getCommandLine(getUsage(), getOptions(), args);
  if (line == null) {
    return null;
  }
  if (state == null) {
    state = new CommandState();
  }
  IOHelper ioHelper = CommandLineHelper.getIOHelper(line);
  state = CommandLineHelper.updateInputOntology(ioHelper, state, line);
  OWLOntology ontology = state.getOntology();
  QuotedEntityChecker checker = new QuotedEntityChecker();
  checker.setIOHelper(ioHelper);
  checker.addProvider(new SimpleShortFormProvider());
  checker.addProperty(OWLManager.getOWLDataFactory().getRDFSLabel());
  checker.addAll(ontology);

  String maxString = CommandLineHelper.getDefaultValue(line, "max", "1");
  final int max;
  try {
    max = Integer.parseInt(maxString);
  } catch (NumberFormatException e) {
    throw new Exception(String.format(maxTypeError, maxString));
  }
  OWLReasonerFactory reasonerFactory = CommandLineHelper.getReasonerFactory(line, true);
  ManchesterOWLSyntaxInlineAxiomParser parser =
      new ManchesterOWLSyntaxInlineAxiomParser(OWLManager.getOWLDataFactory(), checker);
  String expression = CommandLineHelper.getRequiredValue(line, "axiom", "an --axiom is required");
  OWLAxiom axiom = parser.parse(expression);

  Set<Explanation<OWLAxiom>> explanations =
      ExplainOperation.explain(axiom, ontology, reasonerFactory, max);

  if (line.hasOption("explanation")) {
    File output = new File(line.getOptionValue("explanation"));
    String result =
        explanations
            .stream()
            .map(
                e ->
                    ExplainOperation.renderExplanationAsMarkdown(
                        e, ontology.getOWLOntologyManager()))
            .collect(Collectors.joining("\n\n\n"));
    Writer writer = Files.newBufferedWriter(output.toPath(), StandardCharsets.UTF_8);
    writer.write(result);
    writer.close();
  }

  Set<OWLAxiom> explanationsAxioms =
      explanations.stream().flatMap(e -> e.getAxioms().stream()).collect(Collectors.toSet());
  Set<IRI> explanationTerms =
      explanationsAxioms
          .stream()
          .flatMap(ax -> ax.getSignature().stream().map(e -> e.getIRI()))
          .collect(Collectors.toSet());
  Set<OWLAnnotationAssertionAxiom> annotations =
      OntologyHelper.getAnnotationAxioms(
          ontology,
          Collections.singleton(OWLManager.getOWLDataFactory().getRDFSLabel()),
          explanationTerms);
  explanationsAxioms.addAll(annotations);
  state.setOntology(ontology.getOWLOntologyManager().createOntology(explanationsAxioms));
  CommandLineHelper.maybeSaveOutput(line, ontology);
  return state;
}
 

/**
 * Creates an {@link AbstractElkObjectConverter} that uses the default
 * {@link OWLDataFactory} for creating the corresponding {@link OWLObject}s
 */
public AbstractElkObjectConverter() {
	this(OWLManager.getOWLDataFactory());
}