public static void main(String[] args) { try { SimpleRenderer renderer = new SimpleRenderer(); renderer.setShortFormProvider( new DefaultPrefixManager("http://www.mindswap.org/ontologies/tambis-full.owl#")); ToStringRenderer.getInstance().setRenderer(renderer); OWLOntologyManager man = OWLManager.createOWLOntologyManager(); OWLOntology ont = man.loadOntology( IRI.create( "http://owl.cs.manchester.ac.uk/repository/download?ontology=http://www.cs.manchester.ac.uk/owl/ontologies/tambis-patched.owl")); System.out.println("Loaded!"); OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance(); OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ont); reasoner.getUnsatisfiableClasses(); ExplanationBasedRootClassFinder rdr = new ExplanationBasedRootClassFinder(man, reasoner, reasonerFactory); for (OWLClass cls : rdr.getRootUnsatisfiableClasses()) System.out.println("ROOT! " + cls); } catch (TimeOutException e) { e.printStackTrace(); } catch (ReasonerInterruptedException e) { e.printStackTrace(); } catch (OWLOntologyCreationException e) { e.printStackTrace(); } }
/** * Initialise les composants du conteneur sémantique une fois les URI des ontologies dispatchées * par OwlDistributionInitializer. */ public void semInit() throws ExceptionInInitializerError { if (isInitialized()) { /** Initialisation de l'ontologie locale. Cette ontologie n'est plus modifiée ensuite. */ // Initialisation du manager de l'ontologie locale. N'est utilisé qu'ici. OWLOntologyManager localOntoManager = OWLManager.createOWLOntologyManager(); OWLOntologyIRIMapper localOntoMapper = new SimpleIRIMapper(getOntologyIri(), getPhysicalIri()); localOntoManager.addIRIMapper(localOntoMapper); // Initialisation de l'ontologie try { // On crée l'ontologie locale. this.localOntology = localOntoManager.loadOntology(getPhysicalIri()); } catch (OWLOntologyCreationException e) { e.printStackTrace(); } // System.out.println("localOntology : " + localOntology + " ; pyhsicalIri : " + // getPhysicalIri().toString()); /** * Initialisation de l'ontologie du reasoner, qui contiendra l'ontologie locale plus d'autres * axiomes éventuels. On crée l'instance, qu'on rattache à un manager et un reasoner * accessibles par des getters. L'instance reste la même, mais le contenu change. */ // Initialisation du manager de l'ontologie du reasoner this.manager = OWLManager.createOWLOntologyManager(); // On crée une deuxième ontologie. try { IRI ontoName = IRI.create(this.nameSpace); OWLOntologyID ontoId = new OWLOntologyID(ontoName); this.reasoningOntology = this.manager.createOntology(ontoId); } catch (OWLOntologyCreationException e) { e.printStackTrace(); } // Initialisation du reasoner PelletReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance(); PelletOptions.USE_INCREMENTAL_CONSISTENCY = true; PelletOptions.USE_COMPLETION_QUEUE = true; // PelletReasoner reasoner = reasonerFactory.createReasoner(reasoningOntology); PelletReasoner reasoner = reasonerFactory.createNonBufferingReasoner(reasoningOntology); // add the reasoner as an ontology change listener this.manager.addOntologyChangeListener(reasoner); reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY); /* reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS); reasoner.precomputeInferences(InferenceType.DATA_PROPERTY_HIERARCHY); reasoner.precomputeInferences(InferenceType.DISJOINT_CLASSES); reasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY); reasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL); */ this.reasoner = reasoner; } else throw new ExceptionInInitializerError( "Paramètres de l'ontologie non initialisés ; ontoParamsInit = " + Reflection.getCallerClass(2)); // initOntoReasoner(); }
private IRI executeRule(final Rule r, final IRI inputIRI) { try { PelletOptions.USE_ANNOTATION_SUPPORT = true; PelletOptions.TREAT_ALL_VARS_DISTINGUISHED = controller.isTreatAllVariablesDistinguished(); QueryEngineType type = (QueryEngineType) controller.getQueryEngineType(); final QueryExecution qe; final ByteArrayOutputStream w = new ByteArrayOutputStream(); final Query qSelect = getSelectExampleQuery(r.getQuery()); if (type.toPellet() != null) { final OWLOntology queryOntology = getInputOntologyForRule(inputIRI); final PelletReasoner reasoner = PelletReasonerFactory.getInstance().createReasoner(queryOntology); log.info("Ontology size: " + reasoner.getKB().getInfo()); final Dataset ds = kb2ds(reasoner.getKB()); final QueryExecution qeSelect = SparqlDLExecutionFactory.create(qSelect, ds, null, type.toPellet()); final ResultSet rs = qeSelect.execSelect(); controller.setSelect(r, rs.getResultVars(), ResultSetFormatter.toList(rs)); qe = SparqlDLExecutionFactory.create( r.getQuery(), kb2ds(reasoner.getKB()), null, type.toPellet()); qe.execConstruct().write(w); } else { final ByteArrayOutputStream w2 = new ByteArrayOutputStream(); final Model model = ModelFactory.createDefaultModel(); try { controller .getOWLOntologyManager() .saveOntology(queryOntology, new TurtleOntologyFormat(), w2); model.read(new ByteArrayInputStream(w2.toByteArray()), "", "TURTLE"); final QueryExecution qeSelect = QueryExecutionFactory.create(qSelect, model); final ResultSet rs = qeSelect.execSelect(); controller.setSelect(r, rs.getResultVars(), ResultSetFormatter.toList(rs)); qe = QueryExecutionFactory.create(r.getQuery(), model); qe.execConstruct().write(w); } catch (OWLOntologyStorageException e) { // TODO Auto-generated catch block e.printStackTrace(); } } final IRI outputIRI = getOntologyIRIForRuleName(r.getName()); // loaded generated ontology final OWLOntology generatedOntology = controller .getOWLOntologyManager() .loadOntologyFromOntologyDocument(new ByteArrayInputStream(w.toByteArray())); controller.updateOntology( generatedOntology, outputIRI, inputIRI, controller.getRuleSpec().getResultFile(r).toURI()); controller.setStatus("Rule " + r.getName() + " successfully executed"); return outputIRI; } catch (OWLOntologyCreationException e1) { controller.setStatus(e1.getMessage()); return null; } }
private OWLOntology parseWithReasoner(OWLOntologyManager manager, OWLOntology ontology) { try { PelletOptions.load(new URL("http://" + cssLocation + "pellet.properties")); PelletReasoner reasoner = PelletReasonerFactory.getInstance().createReasoner(ontology); reasoner.getKB().prepare(); List<InferredAxiomGenerator<? extends OWLAxiom>> generators = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>(); generators.add(new InferredSubClassAxiomGenerator()); generators.add(new InferredClassAssertionAxiomGenerator()); generators.add(new InferredDisjointClassesAxiomGenerator()); generators.add(new InferredEquivalentClassAxiomGenerator()); generators.add(new InferredEquivalentDataPropertiesAxiomGenerator()); generators.add(new InferredEquivalentObjectPropertyAxiomGenerator()); generators.add(new InferredInverseObjectPropertiesAxiomGenerator()); generators.add(new InferredPropertyAssertionGenerator()); generators.add(new InferredSubDataPropertyAxiomGenerator()); generators.add(new InferredSubObjectPropertyAxiomGenerator()); InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, generators); OWLOntologyID id = ontology.getOntologyID(); Set<OWLImportsDeclaration> declarations = ontology.getImportsDeclarations(); Set<OWLAnnotation> annotations = ontology.getAnnotations(); Map<OWLEntity, Set<OWLAnnotationAssertionAxiom>> entityAnnotations = new HashMap<OWLEntity, Set<OWLAnnotationAssertionAxiom>>(); for (OWLClass aEntity : ontology.getClassesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLObjectProperty aEntity : ontology.getObjectPropertiesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLDataProperty aEntity : ontology.getDataPropertiesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLNamedIndividual aEntity : ontology.getIndividualsInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLAnnotationProperty aEntity : ontology.getAnnotationPropertiesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } for (OWLDatatype aEntity : ontology.getDatatypesInSignature()) { entityAnnotations.put(aEntity, aEntity.getAnnotationAssertionAxioms(ontology)); } manager.removeOntology(ontology); OWLOntology inferred = manager.createOntology(id); iog.fillOntology(manager, inferred); for (OWLImportsDeclaration decl : declarations) { manager.applyChange(new AddImport(inferred, decl)); } for (OWLAnnotation ann : annotations) { manager.applyChange(new AddOntologyAnnotation(inferred, ann)); } for (OWLClass aEntity : inferred.getClassesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLObjectProperty aEntity : inferred.getObjectPropertiesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLDataProperty aEntity : inferred.getDataPropertiesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLNamedIndividual aEntity : inferred.getIndividualsInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLAnnotationProperty aEntity : inferred.getAnnotationPropertiesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } for (OWLDatatype aEntity : inferred.getDatatypesInSignature()) { applyAnnotations(aEntity, entityAnnotations, manager, inferred); } return inferred; } catch (FileNotFoundException e1) { return ontology; } catch (MalformedURLException e1) { return ontology; } catch (IOException e1) { return ontology; } catch (OWLOntologyCreationException e) { return ontology; } }
public Set<NamingIssue> detectNonMatchingChildIssues(OWLOntology ontology, boolean directChild) { long start = System.currentTimeMillis(); // get SubClass - SuperClass pairs Set<NamingIssue> nonMatchingChildren = new HashSet<NamingIssue>(); if (directChild) { Set<OWLSubClassOfAxiom> axioms = ontology.getAxioms(AxiomType.SUBCLASS_OF); for (OWLSubClassOfAxiom ax : axioms) { OWLClassExpression subClass = ax.getSubClass(); OWLClassExpression superClass = ax.getSuperClass(); if (!subClass.isAnonymous() && !superClass.isAnonymous()) { String subClassURI = subClass.asOWLClass().toStringID(); String superClassURI = superClass.asOWLClass().toStringID(); if (ignoreSingleTokenSubClasses && !singleToken(subClassURI)) { String subClassHead = getHeadNoun(subClassURI); String superClassHead = getHeadNoun(superClassURI); boolean matching = subClassHead.equals(superClassHead) || isHypernymOf(superClassHead, subClassHead); if (!matching) { String newClassURI = buildNewURI(subClassURI, superClassHead); nonMatchingChildren.add( new NamingIssue( subClassURI, superClassURI, new RenamingInstruction(subClassURI, newClassURI))); } } } } } else { OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance(); OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ontology); Set<OWLClass> classes = ontology.getClassesInSignature(); for (OWLClass cls : classes) { Set<OWLClass> superClasses = reasoner.getSuperClasses(cls, false).getFlattened(); superClasses.remove(OWL_THING); for (OWLClass superClass : superClasses) { String subClassURI = cls.asOWLClass().toStringID(); String superClassURI = superClass.asOWLClass().toStringID(); if (ignoreSingleTokenSubClasses && !singleToken(subClassURI)) { String subClassHead = getHeadNoun(subClassURI); String superClassHead = getHeadNoun(superClassURI); boolean matching = subClassHead.equals(superClassHead) || isHypernymOf(superClassHead, subClassHead); if (!matching) { String newClassURI = buildNewURI(subClassURI, superClassHead); nonMatchingChildren.add( new NamingIssue( subClassURI, superClassURI, new RenamingInstruction(subClassURI, newClassURI))); } } } } } long end = System.currentTimeMillis(); logger.info("Operation took " + (end - start) + "ms"); return nonMatchingChildren; }