@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 evaluate(QueryRecord queryRecord) {
OWLOntology knowledgebase = relevantPart(queryRecord);
if (knowledgebase == null) {
Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
return;
}
int aboxcount = knowledgebase.getABoxAxioms(true).size();
Utility.logDebug(
"ABox axioms: "
+ aboxcount
+ " TBox axioms: "
+ (knowledgebase.getAxiomCount() - aboxcount));
// queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
Timer t = new Timer();
Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
// int validNumber =
summarisedChecker.check(queryRecord.getGapAnswers());
summarisedChecker.dispose();
Utility.logDebug("Total time for full reasoner: " + t.duration());
// if (validNumber == 0) {
queryRecord.markAsProcessed();
Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
// }
}
private void queryUpperBound(
BasicQueryEngine upperStore,
QueryRecord queryRecord,
String queryText,
String[] answerVariables) {
AnswerTuples rlAnswer = null;
try {
Utility.logDebug(queryText);
rlAnswer = upperStore.evaluate(queryText, answerVariables);
Utility.logDebug(t.duration());
queryRecord.updateUpperBoundAnswers(rlAnswer);
} finally {
if (rlAnswer != null) rlAnswer.dispose();
rlAnswer = null;
}
}
@Override
public boolean isConsistent() {
if (satisfiable == null) {
satisfiable = consistency.check();
Utility.logInfo("time for satisfiability checking: " + t.duration());
}
return satisfiable;
}
@Override
public void sample() throws RDFHandlerException {
getStartNodes();
Utility.logInfo(queue.size());
int u, v, pick, index;
int individualLimit = statementLimit / queue.size(), currentLimit = 0;
RDFEdge edge;
List<RDFEdge> edges;
Stack<Integer> stack = new Stack<Integer>();
while (true) {
if (noOfStatements >= statementLimit) {
System.out.println("The number of statements in the sampling: " + noOfStatements);
return;
}
if (noOfStatements >= currentLimit) {
stack.clear();
}
if (stack.isEmpty()) {
if (queue.isEmpty()) v = rand.nextInt(m_graph.numberOfIndividuals);
else {
v = queue.poll();
currentLimit += individualLimit;
}
stack.add(v);
// Utility.logInfo(noOfStart + " new start: " + m_graph.getRawString(v));
visit(v);
}
u = stack.peek();
if (rand.nextInt(100) < 15) {
stack.pop();
continue;
}
if ((edges = m_graph.edges.get(u)) == null || edges.size() == 0) {
stack.clear();
continue;
}
index = 0;
pick = rand.nextInt(edges.size());
for (Iterator<RDFEdge> iter = edges.iterator(); iter.hasNext(); ++index) {
edge = iter.next();
if (index == pick) {
stack.add(v = edge.m_dst);
visit(v);
m_writer.handleStatement(m_graph.getStatement(u, edge.m_label, edge.m_dst));
++noOfStatements;
iter.remove();
}
}
}
}
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;
}
public static void main(String[] args) throws Exception {
if (args.length == 0) {
// args = new String[] { "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl"};
args = new String[] {PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl"};
// args = new String[] { PagodaTester.onto_dir +
// "dbpedia/integratedOntology-all-in-one-minus-datatype.owl" };
// args = new String[] { PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl" };
// args = new String[] { PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl" };
// args = new String[] { PagodaTester.onto_dir +
// "bio2rdf/reactome/biopax-level3-processed.owl" };
// args = new String[] { PagodaTester.onto_dir + "bio2rdf/uniprot/core-processed-noDis.owl"
// };
}
// OWLOntology ontology = OWLHelper.getMergedOntology(args[0], null);
// OWLHelper.correctDataTypeRangeAxioms(ontology);
OWLOntology ontology = OWLHelper.loadOntology(args[0]);
OWLOntologyManager manager = ontology.getOWLOntologyManager();
OWLDataFactory factory = manager.getOWLDataFactory();
// manager.saveOntology(ontology, new FileOutputStream(args[0].replace(".owl",
// "_owlapi.owl")));
if (outputFile != null) Utility.redirectCurrentOut(outputFile);
int queryID = 0;
for (OWLClass cls : ontology.getClassesInSignature(true)) {
if (cls.equals(factory.getOWLThing()) || cls.equals(factory.getOWLNothing())) continue;
if (!cls.toStringID().contains("Query")) continue;
System.out.println("^[Query" + ++queryID + "]");
System.out.println(template.replace("@CLASS", cls.toStringID()));
System.out.println();
}
for (OWLOntology onto : ontology.getImportsClosure())
for (OWLObjectProperty prop : onto.getObjectPropertiesInSignature()) {
// if (!prop.toStringID().contains("Query")) continue;
System.out.println("^[Query" + ++queryID + "]");
System.out.println("SELECT ?X ?Y");
System.out.println("WHERE {");
System.out.println("?X <" + prop.toStringID() + "> ?Y .");
System.out.println("}");
System.out.println();
}
String[] answerVars = new String[] {"?X", "?Y"};
for (OWLOntology onto : ontology.getImportsClosure())
for (OWLObjectProperty prop : onto.getObjectPropertiesInSignature()) {
// if (!prop.toStringID().contains("Query")) continue;
for (int i = 0; i < answerVars.length; ++i) {
System.out.println("^[Query" + ++queryID + "]");
System.out.println("SELECT " + answerVars[i]);
System.out.println("WHERE {");
System.out.println("?X <" + prop.toStringID() + "> ?Y .");
System.out.println("}");
System.out.println();
}
}
if (outputFile != null) Utility.closeCurrentOut();
}