@Override
public KuabaRepository load(String url) throws RepositoryLoadException {
IRI iri;
File f = new File(url);
if (!url.contains(":/")) {
iri = IRI.create(f);
} else iri = IRI.create(url);
try {
OWLOntology inst = manager.loadOntologyFromOntologyDocument(iri);
if (inst == null) throw new RepositoryLoadException(url, "Invalid Location.");
if (inst.getOntologyID().getOntologyIRI() == null) {
// An anonymous Ontology was loaded, and they are not supported by the Kuaba Subsystem
manager.removeOntology(inst);
throw new RepositoryLoadException(url, "It is probably an incompatible or malformed file.");
}
KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
fileMap.put(repo, f);
return repo;
} catch (OWLOntologyAlreadyExistsException ex) {
OWLOntologyID id = ex.getOntologyID();
// System.err.println("Ontologia "+id.getOntologyIRI().toString()+" já está
// carregada, esta será retornada.");
return repoMap.get(id.getOntologyIRI());
} catch (OWLOntologyCreationException ex) {
throw new RepositoryLoadException(url, "Invalid Location.");
// Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
}
}
public DLOntology_withMaps preprocessAndClausify(OWLOntology rootOntology) {
OWLDataFactory factory = rootOntology.getOWLOntologyManager().getOWLDataFactory();
String ontologyIRI =
rootOntology.getOntologyID().getDefaultDocumentIRI() == null
? "urn:hermit:kb"
: rootOntology.getOntologyID().getDefaultDocumentIRI().toString();
Collection<OWLOntology> importClosure = rootOntology.getImportsClosure();
OWLAxioms_withMaps axioms = new OWLAxioms_withMaps();
OWLNormalization_withMaps normalization =
new OWLNormalization_withMaps(factory, axioms, 0, m_datatypeManager);
for (OWLOntology ontology : importClosure) normalization.processOntology(ontology);
BuiltInPropertyManager_withMaps builtInPropertyManager =
new BuiltInPropertyManager_withMaps(factory);
builtInPropertyManager.axiomatizeBuiltInPropertiesAsNeeded(axioms);
ObjectPropertyInclusionManager_withMaps objectPropertyInclusionManager =
new ObjectPropertyInclusionManager_withMaps(axioms);
// now object property inclusion manager added all non-simple properties to
// axioms.m_complexObjectPropertyExpressions
// now that we know which roles are non-simple, we can decide which negative object property
// assertions have to be
// expressed as concept assertions so that transitivity rewriting applies properly.
objectPropertyInclusionManager.rewriteNegativeObjectPropertyAssertions(
factory, axioms, normalization.getDefinitions().size());
objectPropertyInclusionManager.rewriteAxioms(factory, axioms, 0);
OWLAxiomsExpressivity_withMaps axiomsExpressivity = new OWLAxiomsExpressivity_withMaps(axioms);
DLOntology_withMaps dlOntology =
clausify_withMaps(factory, ontologyIRI, axioms, axiomsExpressivity);
return dlOntology;
}
public OWLOntology getMergedOntology() {
final IRI mergedOntologyIRI =
IRI.create(queryOntology.getOntologyID().getDefaultDocumentIRI() + "-merged");
final OWLOntologyManager mm = controller.getOWLOntologyManager();
if (mm.contains(mergedOntologyIRI)) {
return mm.getOntology(mergedOntologyIRI);
} else {
try {
final OWLOntology mergedOntology = mm.createOntology(mergedOntologyIRI);
mm.setOntologyFormat(mergedOntology, new RDFXMLOntologyFormat());
final String mergedOntologyFileName =
mergedOntologyIRI
.toURI()
.toString()
.substring(mergedOntologyIRI.toURI().toString().lastIndexOf("/") + 1)
+ ".owl";
mm.setOntologyDocumentIRI(
mergedOntology,
IRI.create(
controller.getRuleSpec().getOutputDir().toURI() + "/" + mergedOntologyFileName));
mm.applyChange(
new AddImport(
mergedOntology,
mm.getOWLDataFactory()
.getOWLImportsDeclaration(
queryOntology.getOntologyID().getDefaultDocumentIRI())));
return mergedOntology;
} catch (OWLOntologyCreationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return null;
}
}
}
public void writeOntologyHeader(OWLOntology ontology) {
event = new RendererEvent(this, ontology);
fireFrameRenderingPrepared(ONTOLOGY.toString());
write(ONTOLOGY.toString());
write(":");
writeSpace();
if (!ontology.isAnonymous()) {
int indent = getIndent();
writeFullURI(ontology.getOntologyID().getOntologyIRI().toString());
writeNewLine();
pushTab(indent);
if (ontology.getOntologyID().getVersionIRI() != null) {
writeFullURI(ontology.getOntologyID().getVersionIRI().toString());
}
popTab();
}
fireFrameRenderingStarted(ONTOLOGY.toString());
writeNewLine();
for (OWLImportsDeclaration decl : ontology.getImportsDeclarations()) {
fireSectionItemPrepared(IMPORT.toString());
write(IMPORT.toString());
write(":");
writeSpace();
fireSectionRenderingStarted(IMPORT.toString());
writeFullURI(decl.getURI().toString());
writeNewLine();
fireSectionRenderingFinished(IMPORT.toString());
}
writeNewLine();
writeSection(ANNOTATIONS, ontology.getAnnotations(), ",", true);
fireFrameRenderingFinished(ONTOLOGY.toString());
}
@Test
public void testCreateAnonymousOntology() throws Exception {
OWLOntologyManager manager = Factory.getManager();
OWLOntology ontology = manager.createOntology();
assertNotNull("ontology should not be null", ontology);
assertNotNull("ontology id should not be null", ontology.getOntologyID());
assertNull(ontology.getOntologyID().getDefaultDocumentIRI());
assertNull(ontology.getOntologyID().getOntologyIRI());
assertNull(ontology.getOntologyID().getVersionIRI());
assertNotNull("iri should not be null", manager.getOntologyDocumentIRI(ontology));
}
@Test
public void testCreateOntologyWithIRI() throws Exception {
OWLOntologyManager manager = Factory.getManager();
IRI ontologyIRI = IRI("http://www.semanticweb.org/ontologies/ontology");
OWLOntology ontology = manager.createOntology(ontologyIRI);
assertNotNull("ontology should not be null", ontology);
assertNotNull("ontology id should not be null", ontology.getOntologyID());
assertEquals(ontologyIRI, ontology.getOntologyID().getDefaultDocumentIRI());
assertEquals(ontologyIRI, ontology.getOntologyID().getOntologyIRI());
assertNull(ontology.getOntologyID().getVersionIRI());
assertEquals(ontologyIRI, manager.getOntologyDocumentIRI(ontology));
}
/**
* This method makes sure is used to setup a new/fresh OBDA model. This is done by replacing the
* instance this.obdacontroller (the OBDA model) with a new object. On creation listeners for the
* datasources, mappings and queries are setup so that changes in these trigger and ontology
* change.
*
* <p>Additionally, this method configures all available OBDAOWLReasonerFacotry objects to have a
* reference to the newly created OBDA model and to the global preference object. This is
* necessary so that the factories are able to pass the OBDA model to the reasoner instances when
* they are created.
*/
private void setupNewOBDAModel() {
OBDAModel activeOBDAModel = getActiveOBDAModel();
if (activeOBDAModel != null) {
return;
}
activeOBDAModel = dfac.getOBDAModel();
activeOBDAModel.addSourcesListener(dlistener);
activeOBDAModel.addMappingsListener(mlistener);
queryController.addListener(qlistener);
OWLModelManager mmgr = owlEditorKit.getOWLWorkspace().getOWLModelManager();
Set<OWLOntology> ontologies = mmgr.getOntologies();
for (OWLOntology ontology : ontologies) {
// Setup the entity declarations
for (OWLClass c : ontology.getClassesInSignature()) {
OClass pred = ofac.createClass(c.getIRI().toString());
activeOBDAModel.declareClass(pred);
}
for (OWLObjectProperty r : ontology.getObjectPropertiesInSignature()) {
ObjectPropertyExpression pred = ofac.createObjectProperty(r.getIRI().toString());
activeOBDAModel.declareObjectProperty(pred);
}
for (OWLDataProperty p : ontology.getDataPropertiesInSignature()) {
DataPropertyExpression pred = ofac.createDataProperty(p.getIRI().toString());
activeOBDAModel.declareDataProperty(pred);
}
}
// Setup the prefixes
PrefixOWLOntologyFormat prefixManager =
PrefixUtilities.getPrefixOWLOntologyFormat(mmgr.getActiveOntology());
// addOBDACommonPrefixes(prefixManager);
PrefixManagerWrapper prefixwrapper = new PrefixManagerWrapper(prefixManager);
activeOBDAModel.setPrefixManager(prefixwrapper);
OWLOntology activeOntology = mmgr.getActiveOntology();
String defaultPrefix = prefixManager.getDefaultPrefix();
if (defaultPrefix == null) {
OWLOntologyID ontologyID = activeOntology.getOntologyID();
defaultPrefix = ontologyID.getOntologyIRI().toURI().toString();
}
activeOBDAModel.getPrefixManager().addPrefix(PrefixManager.DEFAULT_PREFIX, defaultPrefix);
// Add the model
URI modelUri = activeOntology.getOntologyID().getOntologyIRI().toURI();
obdamodels.put(modelUri, activeOBDAModel);
}
public boolean assertDataPropertyInstance(String ind, String prop, int value) {
OWLDataProperty dataProp =
OWLFactory.getOWLDataProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + prop));
OWLDataPropertyAssertionAxiom tmpAx =
OWLFactory.getOWLDataPropertyAssertionAxiom(
dataProp,
OWLFactory.getOWLNamedIndividual(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + ind)),
OWLFactory.getOWLLiteral(value));
manager.addAxiom(topIxOnt, tmpAx);
return true;
}
////////////////////////////////
// INDIVIDUAL ASSERTION METHODS//
////////////////////////////////
public boolean assertSiteIndividual(String siteNameHash, String siteNameAnnotation) {
OWLClassExpression tmpCE = OWLFactory.getOWLClass(":Site", topIxPrefixManager);
OWLIndividual tmpInd = OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
manager.addAxiom(topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tmpCE, tmpInd));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + siteNameHash),
OWLFactory.getOWLLiteral(siteNameAnnotation)));
return true;
}
public KuabaRepository createNewRepository(String url, File destination) {
IRI iri;
if (url == null) iri = IRI.generateDocumentIRI();
else iri = IRI.create(url);
try {
OWLOntology inst = manager.createOntology(iri);
OWLImportsDeclaration imp =
manager.getOWLDataFactory().getOWLImportsDeclaration(IRI.create(ONTOLOGY_URL));
AddImport addi = new AddImport(inst, imp);
manager.applyChange(addi);
KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
fileMap.put(repo, destination);
TemplateGenerator.generateRootQuestion(repo);
if (destination != null) this.save(repo);
return repo;
} catch (OWLOntologyCreationException ex) {
Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
}
return null;
}
@Test
public void testCreateOntologyWithIRIAndVersionIRIWithMapper() throws Exception {
OWLOntologyManager manager = Factory.getManager();
IRI ontologyIRI = IRI("http://www.semanticweb.org/ontologies/ontology");
IRI versionIRI = IRI("http://www.semanticweb.org/ontologies/ontology/version");
IRI documentIRI = IRI("file:documentIRI");
SimpleIRIMapper mapper = new SimpleIRIMapper(versionIRI, documentIRI);
manager.addIRIMapper(mapper);
OWLOntology ontology = manager.createOntology(new OWLOntologyID(ontologyIRI, versionIRI));
assertNotNull("ontology should not be null", ontology);
assertNotNull("ontology id should not be null", ontology.getOntologyID());
assertEquals(versionIRI, ontology.getOntologyID().getDefaultDocumentIRI());
assertEquals(ontologyIRI, ontology.getOntologyID().getOntologyIRI());
assertEquals(versionIRI, ontology.getOntologyID().getVersionIRI());
assertEquals(documentIRI, manager.getOntologyDocumentIRI(ontology));
}
OntologyDataProperty(
OWLOntologyManager manager, OWLOntology localContext, OntologyChangeManager changeManager) {
this.manager = manager;
this.localContext = localContext;
this.changeManager = changeManager;
prefix = localContext.getOntologyID().getOntologyIRI() + "#";
}
public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) {
ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.values());
long time = System.currentTimeMillis();
boolean isConsistent = reasoner.isConsistent();
int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size();
time = System.currentTimeMillis() - time;
DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
String e = checker.getDescriptionLogicName();
String name = ontology.getOntologyID().getOntologyIRI().getFragment();
logger.info(
"ontology: "
+ name
+ ", reasoner: "
+ factory.getReasonerName()
+ ", expressivity: "
+ e
+ ", consistent: "
+ isConsistent
+ ", unsat classes: "
+ numOfUnsatClasses
+ ", time: "
+ time);
}
@Deprecated
protected boolean isInternal(OWLEntity ent) {
return ent.getIRI()
.toURI()
.getPath()
.equals(_ontology.getOntologyID().getOntologyIRI().get().toURI().getPath());
}
public static Map<EdamUri, Concept> load(String edamPath) throws OWLOntologyCreationException {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(new File(edamPath));
String prefix = ontology.getOntologyID().getOntologyIRI().get().toString();
return ontology
.classesInSignature()
.filter(c -> EdamUri.isEdamUri(c.getIRI().toString(), prefix))
.collect(
Collectors.toMap(
c -> new EdamUri(c.getIRI().toString(), prefix),
c -> {
Concept concept = new Concept();
EntitySearcher.getAnnotations(c, ontology)
.forEachOrdered(
a -> {
if (a.getProperty().isLabel())
concept.setLabel(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty().isDeprecated()) concept.setObsolete(true);
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addExactSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addNarrowSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addBroadSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasDefinition")
&& a.getValue().asLiteral().isPresent())
concept.setDefinition(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty().isComment()
&& a.getValue().asLiteral().isPresent())
concept.setComment(a.getValue().asLiteral().get().getLiteral());
});
if (concept.getLabel().isEmpty())
throw new IllegalStateException(
String.format("Label of concept %s is empty", c.getIRI()));
return concept;
},
(u, v) -> {
throw new IllegalStateException(String.format("Duplicate key %s", u));
},
LinkedHashMap::new));
}
private OWLOntology findOntology(List<OWLOntology> loadedOntologies, IRI documentIRI) {
for (OWLOntology o : loadedOntologies) {
if (documentIRI.equals(o.getOntologyID().getOntologyIRI())) {
return o;
}
}
return null;
}
public boolean assertHouseIndividual(String houseEntryHash, String houseEntryAnnotation) {
OWLClassExpression tempClassExpression = OWLFactory.getOWLClass(":House", topIxPrefixManager);
OWLIndividual tempIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + houseEntryHash),
OWLFactory.getOWLLiteral(houseEntryAnnotation)));
return true;
}
/**
* Initialization consists of:
*
* <ul>
* <li>Setting aboxOntology, if not set - defaults to a new ontology using tbox.IRI as base.
* Adds import to tbox.
* <li>Setting queryOntology, if not set. Adds abox imports queryOntology declaration
* </ul>
*
* @throws OWLOntologyCreationException
*/
private void init() throws OWLOntologyCreationException {
// reasoner -> query -> abox -> tbox
if (aboxOntology == null) {
LOG.debug("Creating abox ontology. mgr = " + getOWLOntologyManager());
IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI() + "__abox");
aboxOntology = getOWLOntologyManager().getOntology(ontologyIRI);
if (aboxOntology != null) {
LOG.warn("Clearing existing abox ontology");
getOWLOntologyManager().removeOntology(aboxOntology);
}
aboxOntology = getOWLOntologyManager().createOntology(ontologyIRI);
AddImport ai =
new AddImport(
aboxOntology,
getOWLDataFactory()
.getOWLImportsDeclaration(tboxOntology.getOntologyID().getOntologyIRI()));
getOWLOntologyManager().applyChange(ai);
}
// add listener to abox to set modified flag
OWLOntologyChangeBroadcastStrategy strategy =
new SpecificOntologyChangeBroadcastStrategy(aboxOntology);
OWLOntologyChangeListener listener =
new OWLOntologyChangeListener() {
@Override
public void ontologiesChanged(List<? extends OWLOntologyChange> changes)
throws OWLException {
for (OWLOntologyChange owlOntologyChange : changes) {
if (aboxOntology.equals(owlOntologyChange.getOntology())) {
setAboxModified(true);
}
}
}
};
aboxOntology.getOWLOntologyManager().addOntologyChangeListener(listener, strategy);
if (queryOntology == null) {
// Imports: {q imports a, a imports t}
LOG.debug("Creating query ontology");
IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI() + "__query");
queryOntology = getOWLOntologyManager().getOntology(ontologyIRI);
if (queryOntology == null) {
queryOntology = getOWLOntologyManager().createOntology(ontologyIRI);
}
AddImport ai =
new AddImport(
queryOntology,
getOWLDataFactory()
.getOWLImportsDeclaration(aboxOntology.getOntologyID().getOntologyIRI()));
getOWLOntologyManager().applyChange(ai);
}
if (LOG.isDebugEnabled()) {
LOG.debug(modelId + " manager(T) = " + tboxOntology.getOWLOntologyManager());
LOG.debug(modelId + " manager(A) = " + aboxOntology.getOWLOntologyManager());
LOG.debug(modelId + " manager(Q) = " + queryOntology.getOWLOntologyManager());
LOG.debug(modelId + " id(T) = " + tboxOntology.getOntologyID().getOntologyIRI());
LOG.debug(modelId + " id(A) = " + aboxOntology.getOntologyID().getOntologyIRI());
LOG.debug(modelId + " id(Q) = " + queryOntology.getOntologyID().getOntologyIRI());
}
}
@Override
protected Set<? extends OWLAxiom> createAxioms() {
OWLOntology ont = getOWLOntology("Ont");
OWLClass cls =
getFactory().getOWLClass(IRI.create(ont.getOntologyID().getOntologyIRI() + "/Office"));
Set<OWLAxiom> axs = new HashSet<OWLAxiom>();
axs.add(getFactory().getOWLDeclarationAxiom(cls));
return axs;
}
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);
}
}
// asserts a hasHouse property instance between a house and its corresponding
// site
public boolean assertHasHousePropertyInstance(String houseEntryHash, String siteNameHash) {
OWLObjectProperty objProp =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasHouse"));
OWLIndividual houseIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
OWLIndividual siteIndividual =
OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(objProp, siteIndividual, houseIndividual));
return true;
}
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;
}
public void executeRuleSpec(final RuleSpec r) {
this.controller.clearResults();
IRI id = queryOntology.getOntologyID().getDefaultDocumentIRI();
int i = 0;
for (final Rule rule : r.getRuleList()) {
if (rule.isActive()) {
if (rule.getException() != null) {
log.info("The query " + rule.getName() + " is not valid, execution cancelled.");
controller.setStatus(rule.getException().getMessage());
return;
}
id = executeRule(rule, id);
}
}
}
public boolean assertHasRoomPropertyInstance(
String houseIndividualHash, String roomIndividualHash) {
OWLObjectProperty tempOWLbjectProperty =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasRoom"));
OWLIndividual houseIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseIndividualHash, topIxPrefixManager);
OWLIndividual roomIndividual =
OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(
tempOWLbjectProperty, houseIndividual, roomIndividual));
return true;
}
public boolean assertRoomIndividual(
String roomName, String roomIndividualHash, String roomIndividualAnnotation) {
OWLClassExpression tempClassExpression =
OWLFactory.getOWLClass(
IRI.create(
roomToIRI.get(
roomName))); // retrieves the Room Class IRI fron the roomToIRI map, using
// roomID as a key.
OWLIndividual tempIndividual =
OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + roomIndividualHash),
OWLFactory.getOWLLiteral(String.format(roomIndividualAnnotation))));
return true;
}
public OBDAModel getActiveOBDAModel() {
OWLOntology ontology = owlEditorKit.getOWLModelManager().getActiveOntology();
if (ontology != null) {
OWLOntologyID ontologyID = ontology.getOntologyID();
IRI ontologyIRI = ontologyID.getOntologyIRI();
URI uri = null;
if (ontologyIRI != null) {
uri = ontologyIRI.toURI();
} else {
uri = URI.create(ontologyID.toString());
}
return obdamodels.get(uri);
}
return null;
}
@Test
public void testNamedOntologyToString() throws Exception {
OWLOntologyManager man = Factory.getManager();
IRI ontIRI = IRI("http://owlapi.sourceforge.net/ont");
OWLOntology ont = man.createOntology(ontIRI);
String s = ont.toString();
String expected =
"Ontology("
+ ont.getOntologyID().toString()
+ ") [Axioms: "
+ ont.getAxiomCount()
+ " Logical Axioms: "
+ ont.getLogicalAxiomCount()
+ "]";
assertEquals(expected, s);
}
public TurtleRenderer(
OWLOntology ontology, OWLOntologyManager manager, Writer writer, OWLOntologyFormat format) {
super(ontology, manager, format);
this.writer = new PrintWriter(writer);
pending = new HashSet<RDFResourceNode>();
pm = new DefaultPrefixManager();
if (!ontology.isAnonymous()) {
pm.setDefaultPrefix(ontology.getOntologyID().getOntologyIRI() + "#");
}
if (format instanceof PrefixOWLOntologyFormat) {
PrefixOWLOntologyFormat prefixFormat = (PrefixOWLOntologyFormat) format;
for (String prefixName : prefixFormat.getPrefixNames()) {
pm.setPrefix(prefixName, prefixFormat.getPrefix(prefixName));
}
}
base = "";
}
public HGDBOntology createOntologyInDatabase(IRI ontologyIRI)
throws OWLOntologyCreationException {
try {
HGDBOntologyFormat format = new HGDBOntologyFormat();
IRI hgdbDocumentIRI = HGDBOntologyFormat.convertToHGDBDocumentIRI(ontologyIRI);
OWLOntology o = super.createOntology(ontologyIRI);
setOntologyFormat(o, format);
setOntologyDocumentIRI(o, hgdbDocumentIRI);
saveOntology(o, format, hgdbDocumentIRI);
HGDBOntology result = ontologyRepository.getOntologyByDocumentIRI(hgdbDocumentIRI);
result.setOWLOntologyManager(this);
this.ontologiesByID.put(o.getOntologyID(), result);
return result;
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
public void loadOntology() {
try {
/*
* --apaitoymena vimata gia th dhmioyrgia mapped ontologias:
* 1.dhmioyrgoyme ena toBeMappedIRI me skopo toy thn antistoixish me
* to local File. 2.dhmioyrgoyme ena File me th dieythynsh ths
* ontologias sto topiko apothikeytiko meso. 3.dhmioyrgoyme enan
* SimpleIRIMapper kai ton prosthetoyme mesw toy manager. o
* SimpleIRIMapper syndeei to toBeMappedIRI poy dwsame arxika, me
* thn fysikh topothesia ths ontologias sto topiko apothikeytiko
* meso. 4.dhmioyrgoyme ena ontologyIRI me akrivws thn idia arxiki
* timh me to toBeMappedIRI to opoio tha einai to IRI ths ontologias
* mas 5.dhmioyrgoyme thn ontologia mas xrhsimopoiwntas to
* manager.loadOntology(ontologyIRI);
*/
String sep = File.separator;
manager = OWLManager.createOWLOntologyManager();
toBeMappedIRI =
IRI.create(
"http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl");
// ontFile = new File("../src/ontologyresources/ptyxiaki_v0.8.owl");
ontFile = new File("src/ontologyresources/ptyxiaki_v0.8.owl");
// in case of alternative location on load time when the application is jar'ed!
if (!ontFile.canRead()) {
ontFile = new File("ontologyresources/ptyxiaki_v0.8.owl");
}
manager.addIRIMapper(new SimpleIRIMapper(toBeMappedIRI, IRI.create(ontFile)));
ontologyIRI =
IRI.create(
"http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl");
topIxOnt = manager.loadOntology(ontologyIRI);
OWLFactory = manager.getOWLDataFactory();
topIxFormat = manager.getOntologyFormat(topIxOnt);
topIxPrefixManager =
new DefaultPrefixManager(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#');
System.out.println("loaded ontology: " + this.topIxOnt);
System.out.println("from: " + this.manager.getOntologyDocumentIRI(this.topIxOnt));
} catch (OWLException oex) {
logger.info(oex.getMessage());
}
}