/**
* Serializes a batch of triples corresponding to a predicate into one file. Upper bound:
* TRIPLE_LIMIT_PER_FILE.
*/
private static int serializeTripleBatch(
OWLOntology ontology,
QuestOWLIndividualAxiomIterator iterator,
String filePrefix,
String predicateName,
int fileCount,
String format)
throws Exception {
String fileName = filePrefix + fileCount + ".owl";
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
// Main buffer
OWLOntology aBox = manager.createOntology(IRI.create(predicateName));
// Add the signatures
for (OWLDeclarationAxiom axiom : ontology.getAxioms(AxiomType.DECLARATION)) {
manager.addAxiom(aBox, axiom);
}
int tripleCount = 0;
while (iterator.hasNext() && (tripleCount < TRIPLE_LIMIT_PER_FILE)) {
manager.addAxiom(aBox, iterator.next());
tripleCount++;
}
// BufferedOutputStream output = new BufferedOutputStream(new
// FileOutputStream(outputPath.toFile()));
// BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(output, "UTF-8"));
BufferedWriter writer = new BufferedWriter(new FileWriter(fileName));
manager.saveOntology(aBox, getOntologyFormat(format), new WriterDocumentTarget(writer));
return tripleCount;
}
////////////////////////////////
// INDIVIDUAL ASSERTION METHODS//
////////////////////////////////
public boolean assertSiteIndividual(String siteNameHash, String siteNameAnnotation) {
OWLClassExpression tmpCE = OWLFactory.getOWLClass(":Site", topIxPrefixManager);
OWLIndividual tmpInd = OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
manager.addAxiom(topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tmpCE, tmpInd));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + siteNameHash),
OWLFactory.getOWLLiteral(siteNameAnnotation)));
return true;
}
public boolean assertHouseIndividual(String houseEntryHash, String houseEntryAnnotation) {
OWLClassExpression tempClassExpression = OWLFactory.getOWLClass(":House", topIxPrefixManager);
OWLIndividual tempIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + houseEntryHash),
OWLFactory.getOWLLiteral(houseEntryAnnotation)));
return true;
}
public boolean assertDataPropertyInstance(String ind, String prop, int value) {
OWLDataProperty dataProp =
OWLFactory.getOWLDataProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + prop));
OWLDataPropertyAssertionAxiom tmpAx =
OWLFactory.getOWLDataPropertyAssertionAxiom(
dataProp,
OWLFactory.getOWLNamedIndividual(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + ind)),
OWLFactory.getOWLLiteral(value));
manager.addAxiom(topIxOnt, tmpAx);
return true;
}
// asserts a hasHouse property instance between a house and its corresponding
// site
public boolean assertHasHousePropertyInstance(String houseEntryHash, String siteNameHash) {
OWLObjectProperty objProp =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasHouse"));
OWLIndividual houseIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
OWLIndividual siteIndividual =
OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(objProp, siteIndividual, houseIndividual));
return true;
}
//////////////////////////////
// PROPERTY ASSERTION METHODS//
//////////////////////////////
public boolean assertPropertyInstance(
String comboBoxObjectPropertyEntry, String room1Hash, String room2Hash) {
OWLObjectProperty objProp =
OWLFactory.getOWLObjectProperty(
IRI.create(propEntryNametoPropEntryIRI.get(comboBoxObjectPropertyEntry)));
OWLIndividual room1Individual =
OWLFactory.getOWLNamedIndividual(':' + room1Hash, topIxPrefixManager);
OWLIndividual room2Individual =
OWLFactory.getOWLNamedIndividual(':' + room2Hash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(objProp, room1Individual, room2Individual));
return true;
}
public boolean assertHasRoomPropertyInstance(
String houseIndividualHash, String roomIndividualHash) {
OWLObjectProperty tempOWLbjectProperty =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasRoom"));
OWLIndividual houseIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseIndividualHash, topIxPrefixManager);
OWLIndividual roomIndividual =
OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(
tempOWLbjectProperty, houseIndividual, roomIndividual));
return true;
}
public boolean assertRoomIndividual(
String roomName, String roomIndividualHash, String roomIndividualAnnotation) {
OWLClassExpression tempClassExpression =
OWLFactory.getOWLClass(
IRI.create(
roomToIRI.get(
roomName))); // retrieves the Room Class IRI fron the roomToIRI map, using
// roomID as a key.
OWLIndividual tempIndividual =
OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + roomIndividualHash),
OWLFactory.getOWLLiteral(String.format(roomIndividualAnnotation))));
return true;
}
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();
}
}
public boolean storeSolutions(String siteNameHash) {
for (OwlSolution tempSolution : solutionsList) {
// assert Solution individual and assert Site->hasSolution
OWLClassExpression solutionClassExpression =
OWLFactory.getOWLClass(":Solution", topIxPrefixManager);
String tempSolutionID =
String.format(siteNameHash + "_S_%1$02d", tempSolution.getSolutionID().intValue());
OWLIndividual tempSolutionIndividual =
OWLFactory.getOWLNamedIndividual(":" + tempSolutionID, topIxPrefixManager);
OWLClassAssertionAxiom tempClassAssertionAxiom =
OWLFactory.getOWLClassAssertionAxiom(solutionClassExpression, tempSolutionIndividual);
manager.addAxiom(topIxOnt, tempClassAssertionAxiom);
OWLObjectProperty tempSolutionObjectProperty =
OWLFactory.getOWLObjectProperty(":hasSolution", topIxPrefixManager);
OWLIndividual tempSiteIndividual =
OWLFactory.getOWLNamedIndividual(":" + siteNameHash, topIxPrefixManager);
OWLObjectPropertyAssertionAxiom tempObjPropAssAxiom =
OWLFactory.getOWLObjectPropertyAssertionAxiom(
tempSolutionObjectProperty, tempSiteIndividual, tempSolutionIndividual);
manager.addAxiom(topIxOnt, tempObjPropAssAxiom);
// assert SolvedHouse individuals and assert Solution->hasSolvedHouse objProperty. also assert
// the DATA PROPERTIES for each solvedHouse indvidual
for (OwlSolvedHouse tempSolvedHouse : tempSolution.getSolvedHouses()) {
// logger.info("373");
// logger.info(tempSolution.getSolvedHouses().toString());
OWLClassExpression solvedHouseClassExpression =
OWLFactory.getOWLClass(":SolvedHouse", topIxPrefixManager);
OWLIndividual tempSolvedHouseIndividual =
OWLFactory.getOWLNamedIndividual(
":" + tempSolutionID + "_SH_" + tempSolvedHouse.getSolvedHouseHash(),
topIxPrefixManager);
OWLClassAssertionAxiom tempClassAssAx =
OWLFactory.getOWLClassAssertionAxiom(
solvedHouseClassExpression, tempSolvedHouseIndividual);
manager.addAxiom(topIxOnt, tempClassAssAx);
OWLObjectProperty tempSolvedHouseObjectProperty =
OWLFactory.getOWLObjectProperty(":hasSolvedHouse", topIxPrefixManager);
OWLObjectPropertyAssertionAxiom tempHouseObjPropAssAx =
OWLFactory.getOWLObjectPropertyAssertionAxiom(
tempSolvedHouseObjectProperty, tempSolutionIndividual, tempSolvedHouseIndividual);
manager.addAxiom(topIxOnt, tempHouseObjPropAssAx);
OWLDataProperty tempDataProperty;
OWLDataPropertyAssertionAxiom tempDataPropertyAssertionAxiom;
tempDataProperty = OWLFactory.getOWLDataProperty(":hasLiteral", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty,
tempSolvedHouseIndividual,
tempSolvedHouse.getSolvedHouseLiteral());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasL", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty,
tempSolvedHouseIndividual,
tempSolvedHouse.getSolvedHouseLength());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasW", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedHouseIndividual, tempSolvedHouse.getSolvedHouseWidth());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedHouseIndividual, tempSolvedHouse.getSolvedHouseX());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedHouseIndividual, tempSolvedHouse.getSolvedHouseY());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
// logger.info("asserts the house");
// logger.info(tempSolvedHouse.getSolvedHouseLiteral());
}
// assert SolvedRoom individuals and assert Solution->hasSolvedRoom objProperty. also assert
// the DATA PROPERTIES for each solvedRoom indvidual
for (OwlSolvedRoom tempSolvedRoom : tempSolution.getSolvedRooms()) {
OWLClassExpression solvedRoomClassExpression =
OWLFactory.getOWLClass(":SolvedRoom", topIxPrefixManager);
OWLIndividual tempSolvedRoomIndividual =
OWLFactory.getOWLNamedIndividual(
":" + tempSolutionID + "_SR_" + tempSolvedRoom.getSolvedRoomHash(),
topIxPrefixManager);
OWLClassAssertionAxiom tempClassAssAx =
OWLFactory.getOWLClassAssertionAxiom(
solvedRoomClassExpression, tempSolvedRoomIndividual);
manager.addAxiom(topIxOnt, tempClassAssAx);
OWLObjectProperty tempSolvedRoomObjectProperty =
OWLFactory.getOWLObjectProperty(":hasSolvedRoom", topIxPrefixManager);
OWLObjectPropertyAssertionAxiom tempRoomObjPropAssAx =
OWLFactory.getOWLObjectPropertyAssertionAxiom(
tempSolvedRoomObjectProperty, tempSolutionIndividual, tempSolvedRoomIndividual);
manager.addAxiom(topIxOnt, tempRoomObjPropAssAx);
OWLDataProperty tempDataProperty;
OWLDataPropertyAssertionAxiom tempDataPropertyAssertionAxiom;
tempDataProperty = OWLFactory.getOWLDataProperty(":hasLiteral", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomLiteral());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasL", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomLength());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasW", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomWidth());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasH", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomHeight());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomX());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomY());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
tempDataProperty = OWLFactory.getOWLDataProperty(":hasZ", topIxPrefixManager);
tempDataPropertyAssertionAxiom =
OWLFactory.getOWLDataPropertyAssertionAxiom(
tempDataProperty, tempSolvedRoomIndividual, tempSolvedRoom.getSolvedRoomZ());
manager.addAxiom(topIxOnt, tempDataPropertyAssertionAxiom);
}
}
return true;
}
