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;
}
}
}
/** This method gets an OWL ontology used as an input for the supplied rule. */
private OWLOntology getInputOntologyForRule(IRI iri) throws OWLOntologyCreationException {
if (iri.getScheme().equals(PREFIX)) {
iri = getOntologyIRIForRuleName(iri.toString().substring(PREFIX.length()));
}
final OWLOntologyManager m = controller.getOWLOntologyManager();
OWLOntology o;
if (m.contains(iri)) {
o = m.getOntology(iri);
} else {
o = m.loadOntology(iri);
}
return o;
}
/** @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);
}
}
/**
* 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;
}
public OWLOntology getKuabaOntology() {
return manager.getOntology(IRI.create(ONTOLOGY_URL));
}
