1 files changed, 464 insertions, 0 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java b/test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java
new file mode 100644
index 0000000..4b0c1d4
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/ore/PagodaOWLReasoner.java
@@ -0,0 +1,464 @@
+package uk.ac.ox.cs.pagoda.ore;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataPropertyExpression;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyChange;
+import org.semanticweb.owlapi.reasoner.AxiomNotInProfileException;
+import org.semanticweb.owlapi.reasoner.BufferingMode;
+import org.semanticweb.owlapi.reasoner.ClassExpressionNotInProfileException;
+import org.semanticweb.owlapi.reasoner.FreshEntitiesException;
+import org.semanticweb.owlapi.reasoner.FreshEntityPolicy;
+import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
+import org.semanticweb.owlapi.reasoner.IndividualNodeSetPolicy;
+import org.semanticweb.owlapi.reasoner.InferenceType;
+import org.semanticweb.owlapi.reasoner.Node;
+import org.semanticweb.owlapi.reasoner.NodeSet;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.ReasonerInterruptedException;
+import org.semanticweb.owlapi.reasoner.TimeOutException;
+import org.semanticweb.owlapi.reasoner.UnsupportedEntailmentTypeException;
+import org.semanticweb.owlapi.reasoner.impl.OWLClassNodeSet;
+import org.semanticweb.owlapi.util.Version;
+
+import uk.ac.ox.cs.JRDFox.model.GroundTerm;
+import uk.ac.ox.cs.JRDFox.model.Individual;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+
+public class PagodaOWLReasoner implements OWLReasoner {
+        
+        QueryReasoner reasoner; 
+        OWLOntology ontology; 
+        OWLDataFactory factory;
+        boolean sat; 
+
+        public PagodaOWLReasoner(OWLOntology ontology) {
+                this.ontology = ontology; 
+                factory = ontology.getOWLOntologyManager().getOWLDataFactory();                                 
+                reasoner = QueryReasoner.getInstance(ontology);
+                reasoner.setToClassify(false);
+                reasoner.loadOntology(ontology);
+                sat = reasoner.preprocess();
+                thing = new OWLClassNodeSet(factory.getOWLThing());
+        }
+
+        @Override
+        public String getReasonerName() {
+                return "PAGOdA";
+        }
+
+        @Override
+        public Version getReasonerVersion() {
+                return null; 
+        }
+
+        @Override
+        public BufferingMode getBufferingMode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public void flush() {
+                // TODO Auto-generated method stub
+                
+        }
+
+        @Override
+        public List<OWLOntologyChange> getPendingChanges() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Set<OWLAxiom> getPendingAxiomAdditions() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Set<OWLAxiom> getPendingAxiomRemovals() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public OWLOntology getRootOntology() {
+                return ontology;
+        }
+
+        @Override
+        public void interrupt() {
+                // TODO Auto-generated method stub
+                
+        }
+        
+        @Override
+        public void precomputeInferences(InferenceType... inferenceTypes) throws ReasonerInterruptedException, TimeOutException, InconsistentOntologyException {
+                if (inferenceTypes.length == 1 && inferenceTypes[0].equals(InferenceType.CLASS_ASSERTIONS) && types.isEmpty()) {
+                        Set<OWLClass> queriedClasses = new HashSet<OWLClass>(); 
+                        for (OWLOntology onto: ontology.getImportsClosure())
+                                for (OWLClass cls: onto.getClassesInSignature(true)) {
+//                                      if (cls.toStringID().equals("http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Meritage")); 
+//                                      else continue; 
+                                        if (!cls.equals(factory.getOWLThing()) && !queriedClasses.contains(cls)) {
+                                                queriedClasses.add(cls);
+                                                AnswerTuples tuples = null; 
+                                                try {
+                                                        tuples = reasoner.evaluate(String.format("select distinct ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <%s> .}", cls.toStringID()));
+                                                        int cnt = 0; 
+                                                        for (GroundTerm t; tuples.isValid(); tuples.moveNext()) {
+                                                                t = tuples.getTuple().getGroundTerm(0);
+                                                                if (t instanceof Individual) {
+                                                                        addType(((Individual) t).getIRI(), cls);
+                                                                        ++cnt; 
+                                                                }
+                                                        }
+                                                        System.out.println("The number of answers: " + cnt); 
+                                                } finally {
+                                                        if (tuples != null) tuples.dispose();
+                                                }
+                                        }
+                                }
+                }               
+        }
+
+        private void addType(String iri, OWLClass cls) {
+                OWLNamedIndividual ind = factory.getOWLNamedIndividual(IRI.create(iri));
+                OWLClassNodeSet set; 
+                if (types.containsKey(ind)) {
+                        set = types.get(ind); 
+                }
+                else {
+                        set = new OWLClassNodeSet(factory.getOWLThing()); 
+                        types.put(ind, set); 
+                }
+                set.addEntity(cls);
+        }
+
+        @Override
+        public boolean isPrecomputed(InferenceType inferenceType) {
+                // TODO Auto-generated method stub
+                return false;
+        }
+
+        @Override
+        public Set<InferenceType> getPrecomputableInferenceTypes() {
+                return java.util.Collections.singleton(InferenceType.CLASS_ASSERTIONS);
+        }
+
+        @Override
+        public boolean isConsistent() throws ReasonerInterruptedException, TimeOutException {
+                return sat;
+        }
+
+        @Override
+        public boolean isSatisfiable(OWLClassExpression classExpression) throws ReasonerInterruptedException, TimeOutException, ClassExpressionNotInProfileException, FreshEntitiesException, InconsistentOntologyException {
+                // TODO Auto-generated method stub
+                return false;
+        }
+
+        @Override
+        public Node<OWLClass> getUnsatisfiableClasses() throws ReasonerInterruptedException, TimeOutException, InconsistentOntologyException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public boolean isEntailed(OWLAxiom axiom)
+                        throws ReasonerInterruptedException,
+                        UnsupportedEntailmentTypeException, TimeOutException,
+                        AxiomNotInProfileException, FreshEntitiesException,
+                        InconsistentOntologyException {
+                // TODO Auto-generated method stub
+                return false;
+        }
+
+        @Override
+        public boolean isEntailed(Set<? extends OWLAxiom> axioms)
+                        throws ReasonerInterruptedException,
+                        UnsupportedEntailmentTypeException, TimeOutException,
+                        AxiomNotInProfileException, FreshEntitiesException,
+                        InconsistentOntologyException {
+                // TODO Auto-generated method stub
+                return false;
+        }
+
+        @Override
+        public boolean isEntailmentCheckingSupported(AxiomType<?> axiomType) {
+                // TODO Auto-generated method stub
+                return false;
+        }
+
+        @Override
+        public Node<OWLClass> getTopClassNode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLClass> getBottomClassNode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLClass> getSubClasses(OWLClassExpression ce, boolean direct)
+                        throws ReasonerInterruptedException, TimeOutException,
+                        FreshEntitiesException, InconsistentOntologyException,
+                        ClassExpressionNotInProfileException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLClass> getSuperClasses(OWLClassExpression ce,
+                        boolean direct) throws InconsistentOntologyException,
+                        ClassExpressionNotInProfileException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLClass> getEquivalentClasses(OWLClassExpression ce)
+                        throws InconsistentOntologyException,
+                        ClassExpressionNotInProfileException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLClass> getDisjointClasses(OWLClassExpression ce)
+                        throws ReasonerInterruptedException, TimeOutException,
+                        FreshEntitiesException, InconsistentOntologyException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLObjectPropertyExpression> getTopObjectPropertyNode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLObjectPropertyExpression> getBottomObjectPropertyNode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLObjectPropertyExpression> getSubObjectProperties(
+                        OWLObjectPropertyExpression pe, boolean direct)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLObjectPropertyExpression> getSuperObjectProperties(
+                        OWLObjectPropertyExpression pe, boolean direct)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLObjectPropertyExpression> getEquivalentObjectProperties(
+                        OWLObjectPropertyExpression pe)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLObjectPropertyExpression> getDisjointObjectProperties(
+                        OWLObjectPropertyExpression pe)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLObjectPropertyExpression> getInverseObjectProperties(
+                        OWLObjectPropertyExpression pe)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLClass> getObjectPropertyDomains(
+                        OWLObjectPropertyExpression pe, boolean direct)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLClass> getObjectPropertyRanges(
+                        OWLObjectPropertyExpression pe, boolean direct)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLDataProperty> getTopDataPropertyNode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLDataProperty> getBottomDataPropertyNode() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLDataProperty> getSubDataProperties(OWLDataProperty pe,
+                        boolean direct) throws InconsistentOntologyException,
+                        FreshEntitiesException, ReasonerInterruptedException,
+                        TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLDataProperty> getSuperDataProperties(OWLDataProperty pe,
+                        boolean direct) throws InconsistentOntologyException,
+                        FreshEntitiesException, ReasonerInterruptedException,
+                        TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLDataProperty> getEquivalentDataProperties(OWLDataProperty pe)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLDataProperty> getDisjointDataProperties(
+                        OWLDataPropertyExpression pe) throws InconsistentOntologyException,
+                        FreshEntitiesException, ReasonerInterruptedException,
+                        TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLClass> getDataPropertyDomains(OWLDataProperty pe,
+                        boolean direct) throws InconsistentOntologyException,
+                        FreshEntitiesException, ReasonerInterruptedException,
+                        TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+        
+        private Map<OWLNamedIndividual, OWLClassNodeSet> types = new HashMap<OWLNamedIndividual, OWLClassNodeSet>();
+        private OWLClassNodeSet thing; 
+        
+        @Override
+        public NodeSet<OWLClass> getTypes(OWLNamedIndividual ind, boolean direct) throws InconsistentOntologyException, FreshEntitiesException, ReasonerInterruptedException, TimeOutException {
+                if (types.containsKey(ind)) return types.get(ind); 
+                return thing; 
+        }
+
+        @Override
+        public NodeSet<OWLNamedIndividual> getInstances(OWLClassExpression ce,
+                        boolean direct) throws InconsistentOntologyException,
+                        ClassExpressionNotInProfileException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLNamedIndividual> getObjectPropertyValues(
+                        OWLNamedIndividual ind, OWLObjectPropertyExpression pe)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Set<OWLLiteral> getDataPropertyValues(OWLNamedIndividual ind,
+                        OWLDataProperty pe) throws InconsistentOntologyException,
+                        FreshEntitiesException, ReasonerInterruptedException,
+                        TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public Node<OWLNamedIndividual> getSameIndividuals(OWLNamedIndividual ind)
+                        throws InconsistentOntologyException, FreshEntitiesException,
+                        ReasonerInterruptedException, TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public NodeSet<OWLNamedIndividual> getDifferentIndividuals(
+                        OWLNamedIndividual ind) throws InconsistentOntologyException,
+                        FreshEntitiesException, ReasonerInterruptedException,
+                        TimeOutException {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public long getTimeOut() {
+                // TODO Auto-generated method stub
+                return 0;
+        }
+
+        @Override
+        public FreshEntityPolicy getFreshEntityPolicy() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public IndividualNodeSetPolicy getIndividualNodeSetPolicy() {
+                // TODO Auto-generated method stub
+                return null;
+        }
+
+        @Override
+        public void dispose() {
+                // TODO Auto-generated method stub
+                
+        }
+
+}