@Override public Individual getIndividual(String uri) { return inner.getIndividual(uri); }
public static void main(String[] arges){ //note local path below. OntModel m = ModelUtils.loadModel("C:\\Users\\dgarijo\\Dropbox (OEG-UPM)\\NetBeansProjects\\WingsToOPMWMapper\\NEW_TEST\\concreteWorkflow\\MpileupVariantCallerV1.owl"); OntModel taxonomy = ModelUtils.loadModel("http://www.wings-workflows.org/wings-omics-portal/export/users/ravali/genomics/components/library.owl"); Individual templateInstance = m.getIndividual("http://www.wings-workflows.org/wings-omics-portal/export/users/ravali/genomics/workflows/MpileupVariantCaller.owl#MpileupVariantCaller"); System.out.println(HashUtils.createMD5ForTemplate(templateInstance,m, taxonomy)); } }
private Individual findRO(OntModel model, URI base) { try (ClosableIterable<? extends OntResource> instances = iterate(aggregation .listInstances())) { for (OntResource o : instances) // System.out.println("Woo " + o); return o.asIndividual(); } // Fallback - resolve as "/" // TODO: Ensure it's an Aggregation? return model.getIndividual(base.toString()); }
public void markModified(Individual ind, OntModel ontModel) { ontModel.enterCriticalSection(Lock.WRITE); try { org.apache.jena.ontology.Individual jind = ontModel.getIndividual(ind.getURI()); if (jind != null) { updatePropertyDateTimeValue(jind,MODTIME,Calendar.getInstance().getTime(),ontModel); } } finally { ontModel.leaveCriticalSection(); } }
private void doExecuteWorkflow(VitroRequest vreq) { String workflowURI = vreq.getParameter("workflowURI"); String workflowStepURI = vreq.getParameter("workflowStepURI"); OntModel jenaOntModel = (OntModel) getModel("vitro:jenaOntModel",vreq); new JenaIngestWorkflowProcessor( jenaOntModel.getIndividual(workflowURI),getModelMaker( vreq)).run(jenaOntModel.getIndividual(workflowStepURI)); }
/** * Method that given a WINGS canonical instance, it will query the local catalog for its type. * This method is added because in workflow templates, components are bound to canonical instances. * @param canonicalInstanceURI instance of a component in the WINGS component library * @return */ public String getCatalogTypeForComponentInstanceURI(String canonicalInstanceURI){ //each canonical instance has 1 direct class String compType = this.getCatalogTypeForComponentURI(this.WINGSDomainTaxonomy.getIndividual(canonicalInstanceURI).getOntClass(true).getURI()); //We return the type. return compType; }
private ObjectProperty addRelationToModel(OntModel model, Edge e) { Individual source = model.getIndividual(namespace + e.outVertex().id()); Individual target = model.getIndividual(namespace + e.inVertex().id()); ObjectProperty property = model.getObjectProperty(namespace + e.label()); source.addProperty(property, target); return property; }
private ObjectProperty addRelationToModel(OntModel model, Edge e) { Individual source = model.getIndividual(namespace + e.outVertex().id()); Individual target = model.getIndividual(namespace + e.inVertex().id()); ObjectProperty property = model.getObjectProperty(namespace + e.label()); source.addProperty(property, target); return property; }
private Individual getCountry(String countryCode) { ResIterator hasCountryCode = getCountries().listSubjectsWithProperty(Geonames.countryCode, countryCode); if (hasCountryCode.hasNext()) { return getCountries().getIndividual(hasCountryCode.next().getURI()); } return null; }
@Test public void testTransitive2() { final OntModel model = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); model.read(_base + "cyclic_transitive.owl"); model.prepare(); final String ns = "http://www.example.org/test#"; final OntClass Probe = model.getOntClass(ns + "Probe"); final Individual Instance1 = model.getIndividual(ns + "Instance1"); final Individual Instance2 = model.getIndividual(ns + "Instance2"); final Individual Instance3 = model.getIndividual(ns + "Instance3"); assertIteratorValues(Probe.listInstances(), new Resource[] { Instance1, Instance2, Instance3 }); }
@Test public void testSibling() { final String ns = "http://www.example.org/test#"; final OntModel model = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); model.read(_base + "sibling.owl"); final Individual Bob = model.getIndividual(ns + "Bob"); final Individual John = model.getIndividual(ns + "John"); final Individual Jane = model.getIndividual(ns + "Jane"); final Property hasBrother = model.getProperty(ns + "hasBrother"); final Property hasSister = model.getProperty(ns + "hasSister"); assertPropertyValues(model, Bob, hasBrother, John); assertPropertyValues(model, Bob, hasSister, Jane); }
public VClassGroup getGroupByURI(String uri) { if (uri == null) { return null; } getOntModel().enterCriticalSection(Lock.READ); try { Individual group = getOntModel().getIndividual(uri); return groupFromGroupIndividual(group); } catch (IllegalArgumentException ex) { return null; } finally { getOntModel().leaveCriticalSection(); } }
public void testGetIndividual() { OntModel m = ModelFactory.createOntologyModel(); OntClass c = m.createClass( NS +"c" ); Resource r = m.getResource( NS + "r" ); m.add( r, RDF.type, r ); Resource s = m.createIndividual( NS + "s", c ); assertEquals( "Result of get s", s, m.getIndividual( NS + "s" ) ); assertNull( "result of get q", m.getIndividual( NS+"q") ); }
public void testGetIndividual() { OntModel m = ModelFactory.createOntologyModel(); OntClass c = m.createClass( NS +"c" ); Resource r = m.getResource( NS + "r" ); m.add( r, RDF.type, r ); Resource s = m.createIndividual( NS + "s", c ); assertEquals( "Result of get s", s, m.getIndividual( NS + "s" ) ); assertNull( "result of get q", m.getIndividual( NS+"q") ); }
@Test public void testUncle() { final String ns = "http://www.example.org/test#"; final OntModel model = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); model.read(_base + "uncle.owl"); final Individual Bob = model.getIndividual(ns + "Bob"); final Individual Sam = model.getIndividual(ns + "Sam"); final Property uncleOf = model.getProperty(ns + "uncleOf"); final Model uncleValues = ModelFactory.createDefaultModel(); addStatements(uncleValues, Bob, uncleOf, Sam); assertPropertyValues(model, uncleOf, uncleValues); }
@Test public void dataAssertionTest() { _model.read(MiscTests.class.getResourceAsStream("/decimal-int.owl"), null); final Individual entity = _model.getIndividual(NAMESPACE + "/dataAssertion.owl#ENTITY"); final DatatypeProperty value = _model.getDatatypeProperty(NAMESPACE + "/dataAssertion.owl#dataAssertionValue"); Assert.assertTrue(value.isFunctionalProperty()); Assert.assertEquals(1, entity.listPropertyValues(value).toSet().size()); }
@Test public void dataAssertionTest() { _model.read(MiscTests.class.getResourceAsStream("/decimal-int.owl"), null); final Individual entity = _model.getIndividual(NAMESPACE + "/dataAssertion.owl#ENTITY"); final DatatypeProperty value = _model.getDatatypeProperty(NAMESPACE + "/dataAssertion.owl#dataAssertionValue"); Assert.assertTrue(value.isFunctionalProperty()); Assert.assertEquals(1, entity.listPropertyValues(value).toSet().size()); }
/** * Test for a reported bug in delete */ public void testDeleteBug() { Model modelo = ModelFactory.createDefaultModel(); modelo.read("file:testing/reasoners/bugs/deleteBug.owl"); OntModel modeloOnt = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM_RULE_INF, modelo ); Individual indi = modeloOnt.getIndividual("http://decsai.ugr.es/~ontoserver/bacarex2.owl#JS"); indi.remove(); ClosableIterator<Statement> it = modeloOnt.listStatements(indi, null, (RDFNode) null); boolean ok = ! it.hasNext(); it.close(); assertTrue(ok); }
/** * Test for a reported bug in delete */ public void testDeleteBug() { Model modelo = ModelFactory.createDefaultModel(); modelo.read("file:testing/reasoners/bugs/deleteBug.owl"); OntModel modeloOnt = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM_RULE_INF, modelo ); Individual indi = modeloOnt.getIndividual("http://decsai.ugr.es/~ontoserver/bacarex2.owl#JS"); indi.remove(); ClosableIterator<Statement> it = modeloOnt.listStatements(indi, null, (RDFNode) null); boolean ok = ! it.hasNext(); it.close(); assertTrue(ok); }
@Test public void testFileManagerReadOntModel() { OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM) ; FileManager.get().readModel(model, testingDir+"/data.ttl") ; // Check Individual ind = model.getIndividual("http://example.com/individual") ; String t = ind.getOntClass().getURI() ; assertEquals("http://example.com/T", t) ; long c1 = model.size() ; model.loadImports(); long c2 = model.size() ; assertEquals(c1,c2) ; }