@Override
public boolean preprocess() {
t.reset();
Utility.logInfo("Preprocessing ... checking satisfiability ... ");
String name = "data", datafile = importedData.toString();
rlLowerStore.importRDFData(name, datafile);
rlLowerStore.materialise("lower program", program.getLower().toString());
// program.getLower().save();
if (!consistency.checkRLLowerBound()) return false;
Utility.logInfo(
"The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
elLowerStore.importRDFData(name, datafile);
elLowerStore.materialise("saturate named individuals", originalMarkProgram);
elLowerStore.materialise("lower program", program.getLower().toString());
elLowerStore.initialiseKarma();
if (!consistency.checkELLowerBound()) return false;
if (lazyUpperStore != null) {
lazyUpperStore.importRDFData(name, datafile);
lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
int tag = lazyUpperStore.materialiseRestrictedly(program, null);
if (tag != 1) {
lazyUpperStore.dispose();
lazyUpperStore = null;
}
if (tag == -1) return false;
}
if (consistency.checkLazyUpper()) {
satisfiable = true;
Utility.logInfo("time for satisfiability checking: " + t.duration());
}
trackingStore.importRDFData(name, datafile);
trackingStore.materialise("saturate named individuals", originalMarkProgram);
// materialiseFullUpper();
// GapByStore4ID gap = new GapByStore4ID(trackingStore);
GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
trackingStore.materialiseFoldedly(program, gap);
predicatesWithGap = gap.getPredicatesWithGap();
gap.clear();
if (program.getGeneral().isHorn())
encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
else encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
// encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore);
// encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore);
// encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore);
program.deleteABoxTurtleFile();
if (!isConsistent()) return false;
consistency.extractBottomFragment();
return true;
}
@Override
public void loadOntology(OWLOntology o) {
if (!equalityTag) {
EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
o = eliminator.getOutputOntology();
eliminator.save();
}
ontology = o;
program = new DatalogProgram(ontology, properties.getToClassify());
// program.getLower().save();
// program.getUpper().save();
// program.getGeneral().save();
if (multiStageTag && !program.getGeneral().isHorn()) {
lazyUpperStore =
getUpperStore(
"lazy-upper-bound", true); // new MultiStageQueryEngine("lazy-upper-bound", true); //
}
importData(program.getAdditionalDataFile());
elho_ontology = new ELHOProfile().getFragment(ontology);
elLowerStore.processOntology(elho_ontology);
}
protected void internal_importDataFile(String name, String datafile) {
// addDataFile(datafile);
rlLowerStore.importRDFData(name, datafile);
if (lazyUpperStore != null) lazyUpperStore.importRDFData(name, datafile);
elLowerStore.importRDFData(name, datafile);
trackingStore.importRDFData(name, datafile);
}
@Override
public void dispose() {
if (encoder != null) encoder.dispose();
if (rlLowerStore != null) rlLowerStore.dispose();
if (lazyUpperStore != null) lazyUpperStore.dispose();
if (elLowerStore != null) elLowerStore.dispose();
if (trackingStore != null) trackingStore.dispose();
super.dispose();
}
private OWLOntology relevantPart(QueryRecord queryRecord) {
AnswerTuples rlAnswer = null, elAnswer = null;
t.reset();
try {
rlAnswer =
rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
Utility.logDebug(t.duration());
queryRecord.updateLowerBoundAnswers(rlAnswer);
} finally {
if (rlAnswer != null) rlAnswer.dispose();
}
queryRecord.addProcessingTime(Step.LowerBound, t.duration());
rlAnswer = null;
t.reset();
BasicQueryEngine upperStore =
queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
String[] extendedQuery = queryRecord.getExtendedQueryText();
queryUpperBound(
upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
if (!queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery[0]))
queryUpperBound(upperStore, queryRecord, extendedQuery[0], queryRecord.getAnswerVariables());
if (!queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables())
queryUpperBound(
upperStore, queryRecord, extendedQuery[1], queryRecord.getDistinguishedVariables());
queryRecord.addProcessingTime(Step.UpperBound, t.duration());
if (queryRecord.processed()) {
queryRecord.setDifficulty(Step.UpperBound);
return null;
}
t.reset();
try {
elAnswer =
elLowerStore.evaluate(
extendedQuery[0],
queryRecord.getAnswerVariables(),
queryRecord.getLowerBoundAnswers());
Utility.logDebug(t.duration());
queryRecord.updateLowerBoundAnswers(elAnswer);
} finally {
if (elAnswer != null) elAnswer.dispose();
}
queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
if (queryRecord.processed()) {
queryRecord.setDifficulty(Step.ELLowerBound);
return null;
}
t.reset();
QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
OWLOntology knowledgebase;
t.reset();
// if (program.getGeneral().isHorn()) {
// knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
// queryRecord.addProcessingTime(Step.Fragment, t.duration());
// return knowledgebase;
// }
// else {
knowledgebase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
queryRecord.addProcessingTime(Step.Fragment, t.duration());
// }
if (knowledgebase.isEmpty() || queryRecord.isBottom()) return knowledgebase;
if (program.getGeneral().isHorn()) return knowledgebase;
// t.reset();
// if (queryRecord.isHorn() && lazyUpperStore != null) {
//// knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
// } else if (queryRecord.getArity() < 3) {
// IterativeRefinement iterativeRefinement = new IterativeRefinement(queryRecord, tracker,
// trackingStore, consistency.getQueryRecords());
// knowledgebase = iterativeRefinement.extractWithFullABox(importedData.toString(),
// program.getUpperBottomStrategy());
// }
//
// queryRecord.addProcessingTime(Step.FragmentRefinement, t.duration());
//
// if (knowledgebase == null)
// queryRecord.setDifficulty(Step.FragmentRefinement);
return knowledgebase;
}