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;
}
@Override
protected boolean exec() {
Timer t = new Timer();
if (ontology == null) {
extractor = null;
return true;
}
IRI iri =
IRI.create("http://www.cs.ox.ac.uk/isg/tools/MORe/ontologies/inverseRewritingModule.owl");
extractor.findLsignature(ontology, LogicFragment.SHOIQ);
if (containsNonInternalClasses(
extractor
.getCompSignature())) { // then the ontology goes beyond SHOIQ and we need to work
// with a SHOIQ module rather than the whole ontology
Set<OWLEntity> aux = getNonInternalClasses(extractor.getLsignature());
if (aux.isEmpty()) {
extractor = null;
Logger_MORe.logDebug(
t.duration()
+ "s to find Lsignature with inverseRewriting (failed - empty SHOIQ-signature)");
return true;
}
SyntacticLocalityModuleExtractor moduleExtractor =
new SyntacticLocalityModuleExtractor(manager, ontology, ModuleType.BOT);
try {
// ontology = manager.createOntology(iri);
// manager.addAxioms(ontology, moduleExtractor.extract(aux));
ontology = moduleExtractor.extractAsOntology(aux, iri);
} catch (OWLOntologyCreationException e1) {
extractor = null;
e1.printStackTrace();
Logger_MORe.logDebug(
t.duration()
+ "s to find Lsignature with inverseRewriting (failed - exception creating a SHOIQ module)");
return true;
}
}
// if we get this far then we have a nonempty ontology (maybe module) that we need to
// normalize and then rewrite
OWLNormalization4MORe normalization = new OWLNormalization4MORe(ontology, true, true, true);
Rewriter rewriter =
new Rewriter(normalization.getNormalizedOntology(), normalization.getSortedGCIs());
if (manager.contains(iri)) manager.removeOntology(ontology);
Set<OWLAxiom> rewrittenAxioms = rewriter.getRewrittenOntology();
if (!rewriter.anyRewrittenRoles()) {
extractor = null;
Logger_MORe.logDebug(
t.duration()
+ "s to find Lsignature with inverseRewriting (failed - could not rewrite any roles)");
return true;
}
try {
ontology = manager.createOntology();
manager.addAxioms(ontology, rewrittenAxioms);
extractor = new LsignatureExtractor_reducedGreedyness();
extractor.findLsignature(ontology, fragment);
} catch (OWLOntologyCreationException e1) {
extractor = null;
e1.printStackTrace();
Logger_MORe.logDebug(
t.duration()
+ "s to find Lsignature with inverseRewriting (failed - exception creating ontology for rewritten axioms)");
return true;
}
Logger_MORe.logDebug(t.duration() + "s to find Lsignature with inverseRewriting");
return true;
}
/** @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);
}
}
