@Override
public void removeDataProperty(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLAxiom axiom = factory.getOWLDeclarationAxiom(dataProperty);
axiom = changeManager.getAnnotatedAxiom(axiom);
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for (OWLAxiom ax : localContext.getReferencingAxioms(dataProperty)) {
ax = ax.getAxiomWithoutAnnotations();
ax = changeManager.getAnnotatedAxiom(ax);
changes.add(new RemoveAxiom(localContext, ax));
}
try {
synchronized (this) {
changeManager.validateRemovalChange(axiom);
manager.applyChanges(changes);
}
} catch (RemovalException ex) {
logger.severe(
ex.getMessage()
+ "Data property not defined in Ontology or not defined by "
+ "this application. Change ( removeDataProperty"
+ dataPropertyName
+ ") will not be applied. ");
}
}
public void mergeOntologies() {
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for (OWLOntology ont : ontologies) {
if (!ont.equals(targetOntology)) {
// move the axioms
for (OWLAxiom ax : ont.getAxioms()) {
changes.add(new AddAxiom(targetOntology, ax));
}
// move ontology annotations
for (OWLAnnotation annot : ont.getAnnotations()) {
changes.add(new AddOntologyAnnotation(targetOntology, annot));
}
if (!targetOntology.getOntologyID().isAnonymous()) {
// move ontology imports
for (OWLImportsDeclaration decl : ont.getImportsDeclarations()) {
if (ontologies.contains(ont.getOWLOntologyManager().getImportedOntology(decl))) {
continue;
}
Optional<IRI> defaultDocumentIRI =
targetOntology.getOntologyID().getDefaultDocumentIRI();
if (defaultDocumentIRI.isPresent() && !decl.getIRI().equals(defaultDocumentIRI.get())) {
changes.add(new AddImport(targetOntology, decl));
} else {
logger.warn(
"Merge: ignoring import declaration for ontology "
+ targetOntology.getOntologyID()
+ " (would result in target ontology importing itself).");
}
}
}
}
}
try {
owlOntologyManager.applyChanges(changes);
} catch (OWLOntologyChangeException e) {
ErrorLogPanel.showErrorDialog(e);
}
}
public void executeActions(Collection<? extends OWLOntology> ontologies)
throws LintActionException {
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
OWLOntologyManager ontologyManager = LintManagerFactory.getInstance().getOntologyManager();
OWLDataFactory dataFactory = ontologyManager.getOWLDataFactory();
LintReport<OWLObjectProperty> report;
try {
report = this.detected(ontologies);
for (OWLOntology owlOntology : ontologies) {
for (OWLObjectProperty objectProperty : report.getAffectedOWLObjects(owlOntology)) {
changes.add(
new RemoveAxiom(
owlOntology, dataFactory.getOWLTransitiveObjectPropertyAxiom(objectProperty)));
}
}
ontologyManager.applyChanges(changes);
} catch (LintException e) {
throw new LintActionException(e);
} catch (OWLOntologyChangeException e) {
throw new LintActionException(e);
}
}
public KuabaRepository copy(KuabaRepository kr, String url, File destination) {
IRI iri;
if (url == null) iri = IRI.generateDocumentIRI();
else iri = IRI.create(url);
try {
OWLOntology model = (OWLOntology) kr.getModel();
OWLOntology inst = manager.createOntology(iri);
OntologyMigrator migrator = new OntologyMigrator(manager, model, inst);
migrator.performMigration();
EntityFindAndReplaceURIRenamer renamer =
new EntityFindAndReplaceURIRenamer(
manager,
inst.getSignature(false),
Collections.singleton(inst),
model.getOntologyID().getOntologyIRI().toString(),
iri.toString());
if (renamer.hasErrors()) System.err.println("ERRO durante a cópia - rename");
manager.applyChanges(renamer.getChanges());
KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
fileMap.put(repo, destination);
return repo;
} catch (OWLOntologyCreationException ex) {
System.err.println("ERRO em copy");
Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
}
return null;
}
/**
* This method has no conversion calls, to it can be invoked by subclasses that wish to modify it
* afterwards.
*
* <p>FIXME not merging yet FIXME not including imported ontologies unless they are merged
* *before* storage.
*
* @param merge
* @return
*/
protected OWLOntology exportToOWLOntology(boolean merge, IRI prefix) {
long before = System.currentTimeMillis();
// Create a new ontology
OWLOntology root;
OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
IRI iri = IRI.create(prefix + _id);
try {
root = ontologyManager.createOntology(iri);
} catch (OWLOntologyAlreadyExistsException e) {
// It should be impossible, but just in case.
ontologyManager.removeOntology(ontologyManager.getOntology(iri));
try {
root = ontologyManager.createOntology(iri);
} catch (OWLOntologyAlreadyExistsException e1) {
root = ontologyManager.getOntology(iri);
} catch (OWLOntologyCreationException e1) {
log.error("Failed to assemble root ontology for scope " + iri, e);
root = null;
}
} catch (OWLOntologyCreationException e) {
log.error("Failed to assemble root ontology for scope " + _id, e);
root = null;
}
// Add the import declarations for directly managed ontologies.
if (root != null) {
if (merge) {
final Set<OWLOntology> set = new HashSet<OWLOntology>();
log.debug("Merging {} with its imports.", root);
set.add(root);
for (OWLOntologyID ontologyId : managedOntologies) {
log.debug("Merging {} with {}.", ontologyId, root);
set.add(getOntology(ontologyId, OWLOntology.class, true));
}
OWLOntologySetProvider provider =
new OWLOntologySetProvider() {
@Override
public Set<OWLOntology> getOntologies() {
return set;
}
};
OWLOntologyMerger merger = new OWLOntologyMerger(provider);
try {
root = merger.createMergedOntology(OWLManager.createOWLOntologyManager(), iri);
} catch (OWLOntologyCreationException e) {
log.error("Failed to merge imports for ontology " + iri, e);
root = null;
}
} else {
// Add the import declarations for directly managed ontologies.
List<OWLOntologyChange> changes = new LinkedList<OWLOntologyChange>();
OWLDataFactory df = ontologyManager.getOWLDataFactory();
String base = prefix + getID();
for (int i = 0; i < backwardPathLength; i++)
base = URIUtils.upOne(URI.create(base)).toString();
base += "/";
// The key set of managedOntologies contains the ontology IRIs, not their storage keys.
for (OWLOntologyID ontologyId : managedOntologies) {
// XXX some day the versionIRI will be the only physical reference for the ontology
IRI physIRI = IRI.create(base + OntologyUtils.encode(ontologyId));
changes.add(new AddImport(root, df.getOWLImportsDeclaration(physIRI)));
}
ontologyManager.applyChanges(changes);
}
}
log.debug("OWL export of {} completed in {} ms.", getID(), System.currentTimeMillis() - before);
return root;
}