/**
* 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();
}
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();
}
}
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;
}