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();
}
}
private Iterable<Concept> getDomainsConcepts(OWLOntology o, OWLObjectProperty objectProperty) {
String uri = objectProperty.getIRI().toString();
if (objectProperty.getDomains(o).size() == 0) {
throw new LumifyException("Invalid number of domain properties on " + uri);
}
List<Concept> domains = new ArrayList<Concept>();
for (OWLClassExpression rangeClassExpr : objectProperty.getDomains(o)) {
OWLClass rangeClass = rangeClassExpr.asOWLClass();
String rangeClassUri = rangeClass.getIRI().toString();
Concept ontologyClass = getConceptByIRI(rangeClassUri);
checkNotNull(ontologyClass, "Could not find class with uri: " + rangeClassUri);
domains.add(ontologyClass);
}
return domains;
}
protected void importInverseOf(OWLOntology o, OWLObjectProperty objectProperty) {
String iri = objectProperty.getIRI().toString();
Relationship fromRelationship = null;
for (OWLObjectPropertyExpression inverseOf : objectProperty.getInverses(o)) {
if (inverseOf instanceof OWLObjectProperty) {
if (fromRelationship == null) {
fromRelationship = getRelationshipByIRI(iri);
}
OWLObjectProperty inverseOfOWLObjectProperty = (OWLObjectProperty) inverseOf;
String inverseOfIri = inverseOfOWLObjectProperty.getIRI().toString();
Relationship inverseOfRelationship = getRelationshipByIRI(inverseOfIri);
getOrCreateInverseOfRelationship(fromRelationship, inverseOfRelationship);
}
}
}
protected void importObjectProperty(OWLOntology o, OWLObjectProperty objectProperty) {
String iri = objectProperty.getIRI().toString();
String label = getLabel(o, objectProperty);
checkNotNull(label, "label cannot be null or empty for " + iri);
LOGGER.info("Importing ontology object property " + iri + " (label: " + label + ")");
for (Concept domain : getDomainsConcepts(o, objectProperty)) {
for (Concept range : getRangesConcepts(o, objectProperty)) {
getOrCreateRelationshipType(domain, range, iri, label);
}
}
}