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package uk.ac.ox.cs.hermit;
import org.semanticweb.HermiT.Reasoner;
import org.semanticweb.HermiT.model.Atom;
import org.semanticweb.HermiT.model.AtomicRole;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.reasoner.Node;
import uk.ac.ox.cs.pagoda.owl.OWLHelper;
import uk.ac.ox.cs.pagoda.owl.QueryRoller;
import uk.ac.ox.cs.pagoda.query.QueryManager;
import uk.ac.ox.cs.pagoda.query.QueryRecord;
import uk.ac.ox.cs.pagoda.util.Timer;
import java.io.*;
import java.util.HashSet;
import java.util.Set;
import java.util.concurrent.*;
public class HermitQueryReasoner {
public static void main(String... args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
if (args.length == 0) {
// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/lubm/lubm1_merged.owl", null, PagodaTester.lubm_query};
// args = new String[] {"/users/yzhou/ontologies/uobm/uobm1_merged.owl", null, "/users/yzhou/ontologies/uobm/queries/standard.sparql"};
// args = new String[] {"/users/yzhou/ontologies/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", null, "/users/yzhou/ontologies/fly/queries/fly.sparql"};
// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all-minus-datatype.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-minus-datatype-new.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"};
// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-processed.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"};
// args = new String[] {PagodaTester.dbpedia_tbox, PagodaTester.dbpedia_abox, PagodaTester.dbpedia_query};
// args = new String[] {"/users/yzhou/ontologies/answersCorrectness/unsatisfiable.owl", null, "/users/yzhou/ontologies/answersCorrectness/unsatisfiable_queries.sparql"};
// args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/graph sampling/sample_100.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/queries/atomic_one_filtered.sparql", "../answersCorrectness-share/results/chembl/hermit_1p"};
args =
new String[]{"/users/yzhou/temp/uniprot_debug/core-processed-noDis.owl", "/users/yzhou/temp/uniprot_debug/sample_1_removed.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../answersCorrectness-share/results/uniprot/hermit_1p"};
}
// args = new String[] {"imported.owl", "", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../answersCorrectness-share/results/uniprot/hermit_1p"}; }
PrintStream ps = args.length < 4 ? null : new PrintStream(new File(args[3]));
for (int i = 0; i < args.length; ++i) {
if (args[i] == null || args[i].equalsIgnoreCase("null")) args[i] = "";
System.out.println("Argument " + i + ": " + args[i]);
}
// PrintStream ps = null; // new PrintStream(new File("../answersCorrectness-share/results/reactome/ "));
if (ps != null) System.setOut(ps);
Timer t = new Timer();
OWLOntology onto = OWLHelper.loadOntology(args[0]);
OWLOntologyManager man = onto.getOWLOntologyManager();
OWLDatatype date = man.getOWLDataFactory().getOWLDatatype(IRI.create("http://www.w3.org/2001/XMLSchema#date"));
if (onto.containsEntityInSignature(date)) {
for (OWLOntology o: onto.getImportsClosure())
for (OWLAxiom axiom: o.getAxioms())
if (axiom.getDatatypesInSignature().contains(date)) {
System.out.println("The axiom: " + axiom + " is being ingored. ");
man.removeAxiom(onto, axiom);
}
man.saveOntology(onto, new FileOutputStream(args[0] = "tbox_hermit.owl"));
man.removeOntology(onto);
onto = OWLHelper.loadOntology(man, args[0]);
System.out.println("TBox processed in " + t.duration());
}
try {
onto = OWLHelper.getImportedOntology(onto, args[1]);
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("Ontology loaded in " + t.duration());
System.out.println("ABox axioms:" + onto.getABoxAxioms(true).size());
// for (OWLOntology o: onto.getImportsClosure())
// for (OWLAxiom axiom: o.getAxioms())
// System.out.println(axiom);
Reasoner hermit = new Reasoner(onto);
if (!hermit.isConsistent()) {
System.out.println("The ontology is inconsistent.");
return ;
}
System.out.println("Preprocessing DONE in " + t.duration());
// System.out.println(hermit.isConsistent());
QueryManager queryManager = new QueryManager();
QueryRoller roller = new QueryRoller(onto.getOWLOntologyManager().getOWLDataFactory());
int failedCounter = 0;
Timer total = new Timer();
for (QueryRecord record: queryManager.collectQueryRecords(args[2])) {
if (Integer.parseInt(record.getQueryID()) < 10) continue;
if (total.duration() > 18000) {
System.out.println("Time out 5h.");
return ;
}
System.out.println("--------------------- Query " + record.getQueryID() + " -----------------------");
System.out.println(record.getQueryText());
ExecutorService exec = Executors.newSingleThreadExecutor();
try {
Future<Boolean> succ = exec.submit(new QueryThread(record, onto, hermit, roller));
try {
try {
if (record.getQueryID().equals("1"))
System.out.println(succ.get(60, TimeUnit.MINUTES));
else
System.out.println(succ.get(20, TimeUnit.MINUTES));
} catch (InterruptedException e) {
// e.printStackTrace();
} catch (ExecutionException e) {
// e.printStackTrace();
} catch (TimeoutException e) {
// e.printStackTrace();
}
} finally {
if (succ.cancel(true)) {
System.out.println("Trying to cancel the current query thread " + (++failedCounter));
}
}
} finally {
exec.shutdownNow();
}
}
if (ps != null) ps.close();
System.exit(0);
}
}
class QueryThread implements Callable<Boolean> {
QueryRecord record;
OWLOntology onto;
Reasoner hermit;
QueryRoller roller;
public QueryThread(QueryRecord record2, OWLOntology onto2, Reasoner hermit2, QueryRoller roller2) {
record = record2; onto = onto2; hermit = hermit2; roller = roller2;
}
@Override
public Boolean call() throws Exception {
Set<String> answers = new HashSet<String>();
Timer t = new Timer();
if (record.getDistinguishedVariables().length > 1) {
if (record.getDistinguishedVariables().length == 2 && record.getClause().getBodyLength() == 1) {
dealWithAtomicBinaryQuery(record.getClause().getBodyAtom(0), answers);
System.out.println("Query " + record.getQueryID() + " The number of answers: " + answers.size());
System.out.println("Query " + record.getQueryID() + " Total time: " + t.duration());
}
else {
System.out.println("Query " + record.getQueryID() + " The number of answers: Query cannot be processsed.");
System.out.println("Query " + record.getQueryID() + " Total time: Query cannot be processsed.");
}
return false;
}
OWLClassExpression exp = null;
try {
exp = roller.rollUp(record.getClause(), record.getAnswerVariables()[0]);
} catch (Exception e) {
System.out.println("Query " + record.getQueryID() + " The number of answers: Query cannot be processsed.");
System.out.println("Query " + record.getQueryID() + " Total time: Query cannot be processsed.");
return false;
}
System.out.println(exp);
for (Node<OWLNamedIndividual> node: hermit.getInstances(exp, false)) {
for (OWLIndividual ind: node.getEntities()) {
answers.add(ind.toStringID());
}
}
System.out.println("Query " + record.getQueryID() + " The number of answers: " + answers.size());
System.out.println("Query " + record.getQueryID() + " Total time: " + t.duration());
return true;
}
private void dealWithAtomicBinaryQuery(Atom bodyAtom, Set<String> answers) {
StringBuilder sb = new StringBuilder();
OWLDataFactory f = onto.getOWLOntologyManager().getOWLDataFactory();
OWLObjectProperty p = f.getOWLObjectProperty(IRI.create(((AtomicRole) bodyAtom.getDLPredicate()).getIRI()));
for (Node<OWLNamedIndividual> sub: hermit.getInstances(f.getOWLObjectMinCardinality(1, p), false)) {
for (Node<OWLNamedIndividual> obj: hermit.getObjectPropertyValues(sub.getRepresentativeElement(), p)) {
for (OWLNamedIndividual subInd: sub.getEntities()) {
sb.setLength(0);
sb.append(subInd.toString()).append(" ");
int len = sb.length();
for (OWLNamedIndividual objInd: obj.getEntities()) {
sb.setLength(len);
sb.append(objInd.toString());
answers.add(sb.toString());
}
}
}
}
}
}
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