private void runWithSeparateFiles() {
if (owlFile == null) {
throw new NullPointerException("You have to specify an ontology file!");
}
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = null;
OBDADataFactory obdaDataFactory = OBDADataFactoryImpl.getInstance();
try {
ontology = manager.loadOntologyFromOntologyDocument((new File(owlFile)));
if (disableReasoning) {
/*
* when reasoning is disabled, we extract only the declaration assertions for the vocabulary
*/
ontology = extractDeclarations(manager, ontology);
}
Collection<Predicate> predicates = new ArrayList<>();
for (OWLClass owlClass : ontology.getClassesInSignature()) {
Predicate predicate = obdaDataFactory.getClassPredicate(owlClass.getIRI().toString());
predicates.add(predicate);
}
for (OWLDataProperty owlDataProperty : ontology.getDataPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getDataPropertyPredicate(owlDataProperty.getIRI().toString());
predicates.add(predicate);
}
for (OWLObjectProperty owlObjectProperty : ontology.getObjectPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getObjectPropertyPredicate(owlObjectProperty.getIRI().toString());
predicates.add(predicate);
}
OBDAModel obdaModel = loadMappingFile(mappingFile);
Ontology inputOntology = OWLAPI3TranslatorUtility.translate(ontology);
obdaModel.declareAll(inputOntology.getVocabulary());
int numPredicates = predicates.size();
int i = 1;
for (Predicate predicate : predicates) {
System.err.println(String.format("Materializing %s (%d/%d)", predicate, i, numPredicates));
serializePredicate(ontology, inputOntology, obdaModel, predicate, outputFile, format);
i++;
}
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
}
public boolean isOntologyDefined() {
try {
Concept concept = getConceptByIRI(OntologyRepository.ROOT_CONCEPT_IRI);
return concept != null; // todo should check for more
} catch (Exception e) {
if (e.getMessage() != null
&& e.getMessage().contains(OntologyLumifyProperties.ONTOLOGY_TITLE.getPropertyName())) {
return false;
}
throw new RuntimeException(e);
}
}
public void runWithSingleFile() {
BufferedOutputStream output = null;
BufferedWriter writer = null;
try {
final long startTime = System.currentTimeMillis();
if (outputFile != null) {
output = new BufferedOutputStream(new FileOutputStream(outputFile));
} else {
output = new BufferedOutputStream(System.out);
}
writer = new BufferedWriter(new OutputStreamWriter(output, "UTF-8"));
OBDAModel obdaModel = loadMappingFile(mappingFile);
OWLOntology ontology = null;
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLAPI3Materializer materializer = null;
if (owlFile != null) {
// Loading the OWL ontology from the file as with normal OWLReasoners
ontology = manager.loadOntologyFromOntologyDocument((new File(owlFile)));
if (disableReasoning) {
/*
* when reasoning is disabled, we extract only the declaration assertions for the vocabulary
*/
ontology = extractDeclarations(manager, ontology);
}
Ontology onto = OWLAPI3TranslatorUtility.translate(ontology);
obdaModel.declareAll(onto.getVocabulary());
materializer = new OWLAPI3Materializer(obdaModel, onto, DO_STREAM_RESULTS);
} else {
ontology = manager.createOntology();
materializer = new OWLAPI3Materializer(obdaModel, DO_STREAM_RESULTS);
}
// OBDAModelSynchronizer.declarePredicates(ontology, obdaModel);
QuestOWLIndividualAxiomIterator iterator = materializer.getIterator();
while (iterator.hasNext()) manager.addAxiom(ontology, iterator.next());
OWLOntologyFormat ontologyFormat = getOntologyFormat(format);
manager.saveOntology(ontology, ontologyFormat, new WriterDocumentTarget(writer));
System.err.println("NR of TRIPLES: " + materializer.getTriplesCount());
System.err.println("VOCABULARY SIZE (NR of QUERIES): " + materializer.getVocabularySize());
materializer.disconnect();
if (outputFile != null) output.close();
final long endTime = System.currentTimeMillis();
final long time = endTime - startTime;
System.out.println("Elapsed time to materialize: " + time + " {ms}");
} catch (Exception e) {
System.out.println("Error materializing ontology:");
e.printStackTrace();
}
}