@Test(expected = OWLOntologyDocumentAlreadyExistsException.class)
public void testCreateDuplicatedDocumentIRI() throws Exception {
OWLOntologyManager manager = Factory.getManager();
IRI ontologyIRI = IRI("http://www.semanticweb.org/ontologies/ontology");
IRI ontologyIRI2 = IRI("http://www.semanticweb.org/ontologies/ontology2");
IRI documentIRI = IRI("file:documentIRI");
manager.addIRIMapper(new SimpleIRIMapper(ontologyIRI, documentIRI));
manager.addIRIMapper(new SimpleIRIMapper(ontologyIRI2, documentIRI));
manager.createOntology(new OWLOntologyID(ontologyIRI));
manager.createOntology(new OWLOntologyID(ontologyIRI2));
}
/**
* 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 void addTripsBaseOntologies(OWLOntologyManager manager) throws Exception {
SimpleIRIMapper iriMapperTime =
new SimpleIRIMapper(
IRI.create("http://www.w3.org/2006/time"), IRI.create(new File("Time.owl")));
manager.addIRIMapper(iriMapperTime);
SimpleIRIMapper iriMapperCore =
new SimpleIRIMapper(
IRI.create(
"http://www.ibm.com/SCTC/ontology/" + "CoreSpatioTemporalDataSensorOntology.owl"),
IRI.create(new File("CoreSpatioTemporalDataSensorOntology.owl")));
manager.addIRIMapper(iriMapperCore);
SimpleIRIMapper iriMapperTravelTime =
new SimpleIRIMapper(
IRI.create("http://www.ibm.com/SCTC/ontology/TravelTimeOntology.owl"),
IRI.create(new File("TravelTimeOntology.owl")));
manager.addIRIMapper(iriMapperTravelTime);
}
@Test
public void testCreateOntologyWithIRIWithMapper() throws Exception {
OWLOntologyManager manager = Factory.getManager();
IRI ontologyIRI = IRI("http://www.semanticweb.org/ontologies/ontology");
IRI documentIRI = IRI("file:documentIRI");
SimpleIRIMapper mapper = new SimpleIRIMapper(ontologyIRI, documentIRI);
manager.addIRIMapper(mapper);
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(documentIRI, manager.getOntologyDocumentIRI(ontology));
}
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());
}
}
@Before
public void setup() throws Exception {
String uri = Resources.getResource("ontologies/unsat_parent.owl").toURI().toString();
IRI iri = IRI.create(uri);
manager = OWLManager.createOWLOntologyManager();
manager.addIRIMapper(
new OWLOntologyIRIMapper() {
@Override
public IRI getDocumentIRI(IRI origIri) {
String uri = null;
try {
uri = Resources.getResource("ontologies/unsat.owl").toURI().toString();
} catch (URISyntaxException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return IRI.create(uri);
}
});
ont = manager.loadOntologyFromOntologyDocument(iri);
ReasonerConfiguration config = new ReasonerConfiguration();
config.setFactory(ElkReasonerFactory.class.getCanonicalName());
util = new ReasonerUtil(config, manager, ont);
}
/** @param args */
public static void main(String[] args) {
String external = "http://purl.obolibrary.org/obo/iao/dev/external.owl";
String externalDerived = "http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl";
String externalByHand = "http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl";
String metaData = "http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl";
String reasonerName = "hermit";
String path = "C:/Documents and Settings/Jie/My Documents/Ontology/iao/releases/2012-01-05/";
String saveIaoFilename = path + "merged/iao-main-infer.owl";
String inferOntURIStr = "http://purl.obolibrary.org/obo/iao/dev/iao_inferredSuperClasses.owl";
String saveInferFilename = path + "merged/iao-inferredSuperClasses.owl";
// Get hold of an ontology manager
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
AutoIRIMapper mapper = new AutoIRIMapper(new File(path + "ontology/"), false);
manager.addIRIMapper(mapper);
OWLOntology iaoOnt = OntologyManipulator.load(path + "ontology/iao-main.owl", manager);
// OntologyManipulator.printPrefixNSs(manager, iaoOnt);
OWLDataFactory df = manager.getOWLDataFactory();
// get all imported ontologies
Set<OWLOntology> importOnts = iaoOnt.getImports();
// remove imports statements from the loaded ontology
for (OWLOntology importOnt : importOnts) {
IRI importOntIRI = importOnt.getOntologyID().getOntologyIRI();
if (importOntIRI.equals(IRI.create(metaData))
|| importOntIRI.equals(IRI.create(external))
|| importOntIRI.equals(IRI.create(externalByHand))
|| importOntIRI.equals(IRI.create(externalDerived))) {
RemoveImport ri = new RemoveImport(iaoOnt, df.getOWLImportsDeclaration(importOntIRI));
manager.applyChange(ri);
}
}
// merge the removed imported ontologies to the loaded one
for (OWLOntology importOnt : importOnts) {
IRI importOntIRI = importOnt.getOntologyID().getOntologyIRI();
if (importOntIRI.equals(IRI.create(metaData))
|| importOntIRI.equals(IRI.create(external))
|| importOntIRI.equals(IRI.create(externalByHand))
|| importOntIRI.equals(IRI.create(externalDerived))) {
// OntologyManipulator.printPrefixNSs(manager, importOnt);
iaoOnt = OntologyManipulator.mergeToTargetOnt(manager, iaoOnt, importOnt);
}
}
// generate the inferred hierarchy and clean the super classes
OWLReasoner reasoner = OWLReasonerRunner.runReasoner(manager, iaoOnt, reasonerName);
iaoOnt =
OWLReasonerRunner.getCleanedOntologyWithInferredSuperClasses(
manager, iaoOnt, inferOntURIStr, reasoner);
OntologyManipulator.saveToFile(manager, iaoOnt, saveIaoFilename);
if (manager.contains(IRI.create(inferOntURIStr))) {
OWLOntology inferOnt = manager.getOntology(IRI.create(inferOntURIStr));
OntologyManipulator.saveToFile(manager, inferOnt, saveInferFilename);
}
}