public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) {
ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.values());
long time = System.currentTimeMillis();
boolean isConsistent = reasoner.isConsistent();
int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size();
time = System.currentTimeMillis() - time;
DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
String e = checker.getDescriptionLogicName();
String name = ontology.getOntologyID().getOntologyIRI().getFragment();
logger.info(
"ontology: "
+ name
+ ", reasoner: "
+ factory.getReasonerName()
+ ", expressivity: "
+ e
+ ", consistent: "
+ isConsistent
+ ", unsat classes: "
+ numOfUnsatClasses
+ ", time: "
+ time);
}
private void handleNotesOntologyChanged(List<OWLOntologyChange> changes) {
try {
OWLOntologyManager notesOntologyManager = notesOntology.getOWLOntologyManager();
if (notesOntologyManager.getOntologyFormat(notesOntology)
instanceof BinaryOWLOntologyDocumentFormat) {
OWLAPIProjectDocumentStore documentStore =
OWLAPIProjectDocumentStore.getProjectDocumentStore(project.getProjectId());
List<OWLOntologyChangeData> infoList = new ArrayList<OWLOntologyChangeData>();
for (OWLOntologyChange change : changes) {
OWLOntologyChangeRecord rec = change.getChangeRecord();
OWLOntologyChangeData info = rec.getData();
infoList.add(info);
}
BinaryOWLOntologyDocumentSerializer serializer = new BinaryOWLOntologyDocumentSerializer();
serializer.appendOntologyChanges(
notesOntologyDocument,
new OntologyChangeDataList(infoList, System.currentTimeMillis()));
} else {
// Swap it over
notesOntologyManager.saveOntology(notesOntology, new BinaryOWLOntologyDocumentFormat());
}
} catch (OWLOntologyStorageException e) {
throw new RuntimeException(e);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
protected OWLOntology loadBigOntology(String filename) {
File file = new File(System.getenv("bigontosdir") + filename + ".owl");
OWLOntology ontology = null;
try {
ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(file);
} catch (OWLOntologyCreationException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
return ontology;
}
/** Serializes the A-box corresponding to a predicate into one or multiple file. */
private static void serializePredicate(
OWLOntology ontology,
Ontology inputOntology,
OBDAModel obdaModel,
Predicate predicate,
String outputFile,
String format)
throws Exception {
final long startTime = System.currentTimeMillis();
OWLAPI3Materializer materializer =
new OWLAPI3Materializer(obdaModel, inputOntology, predicate, DO_STREAM_RESULTS);
QuestOWLIndividualAxiomIterator iterator = materializer.getIterator();
System.err.println("Starts writing triples into files.");
int tripleCount = 0;
int fileCount = 0;
String outputDir = outputFile;
String filePrefix =
Paths.get(outputDir, predicate.getName().replaceAll("[^a-zA-Z0-9]", "_") + "_").toString();
while (iterator.hasNext()) {
tripleCount +=
serializeTripleBatch(
ontology, iterator, filePrefix, predicate.getName(), fileCount, format);
fileCount++;
}
System.out.println("NR of TRIPLES: " + tripleCount);
System.out.println("VOCABULARY SIZE (NR of QUERIES): " + materializer.getVocabularySize());
final long endTime = System.currentTimeMillis();
final long time = endTime - startTime;
System.out.println("Elapsed time to materialize: " + time + " {ms}");
}
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();
}
}
