NOT-WORKING: trying to add query-dependent Skolemisation.

1 files changed, 87 insertions, 91 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
index 1e17dac..767d379 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
+++ b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
@@ -38,46 +38,51 @@ public class RLPlusOntology implements KnowledgeBase {
         LinkedList<Clause> clauses; 
         Map<OWLAxiom, OWLAxiom> correspondence;
         
-        BottomStrategy botStrategy; 
-        
+        BottomStrategy botStrategy;
+        Random random = new Random(19900114);
+        private Map<OWLClassExpression, Integer> subCounter = null;
+        private Map<OWLClass, OWLClass> atomic2negation = new HashMap<OWLClass, OWLClass>();
+
+        // FIXME multiple anonymous ontologies
         @Override
         public void load(OWLOntology o, uk.ac.ox.cs.pagoda.constraints.BottomStrategy bottomStrategy) {
                 if (bottomStrategy instanceof UnaryBottom)
-                        botStrategy = BottomStrategy.UNARY; 
+                        botStrategy = BottomStrategy.UNARY;
                 else if (bottomStrategy instanceof NullaryBottom)
-                        botStrategy = BottomStrategy.NULLARY; 
-                else 
-                        botStrategy = BottomStrategy.TOREMOVE; 
-                
-                if (corrFileName == null) 
+                        botStrategy = BottomStrategy.NULLARY;
+                else
+                        botStrategy = BottomStrategy.TOREMOVE;
+
+                if(corrFileName == null)
                         corrFileName = "rlplus.crr";
                 manager = o.getOWLOntologyManager();
 //              manager = OWLManager.createOWLOntologyManager();
-                factory = manager.getOWLDataFactory(); 
-                inputOntology = o; 
-                
+                factory = manager.getOWLDataFactory();
+                inputOntology = o;
+
                 try {
                         String path = OWLHelper.getOntologyPath(inputOntology);
-                        String name = path.substring(path.lastIndexOf(Utility.JAVA_FILE_SEPARATOR)); 
+                        String name = path.substring(path.lastIndexOf(Utility.JAVA_FILE_SEPARATOR));
                         String originalExtension = name.lastIndexOf(".") >= 0 ? name.substring(name.lastIndexOf(".")) : "";
-                        
+
                         if (inputOntology.getOntologyID().getOntologyIRI() == null)
-                                ontologyIRI = "http://www.example.org/anonymous-ontology" + originalExtension; 
-                        else 
+                                ontologyIRI = "http://www.example.org/anonymous-ontology" + originalExtension;
+                        else
                                 ontologyIRI = inputOntology.getOntologyID().getOntologyIRI().toString();
-                        
-                        String tOntoIRI = ontologyIRI; 
+
+                        String tOntoIRI = ontologyIRI;
                         if (!tOntoIRI.endsWith(originalExtension)) tOntoIRI += originalExtension;
-                        
+
                         String rlOntologyIRI = originalExtension.isEmpty() ? tOntoIRI + "-RL.owl" : tOntoIRI.replaceFirst(originalExtension, "-RL.owl");
                         String rlDocumentIRI = (outputPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "RL.owl").toString());
                         outputOntology = manager.createOntology(IRI.create(rlOntologyIRI));
                         manager.setOntologyDocumentIRI(outputOntology, IRI.create(Utility.toFileIRI(rlDocumentIRI)));
-                        
-                        String tBoxOntologyIRI, aBoxOntologyIRI; 
-                        tBoxOntologyIRI = originalExtension.isEmpty() ? tOntoIRI + "-TBox.owl" : tOntoIRI.replaceFirst(originalExtension, "-TBox.owl"); 
+
+                        String tBoxOntologyIRI, aBoxOntologyIRI;
+                        tBoxOntologyIRI =
+                                        originalExtension.isEmpty() ? tOntoIRI + "-TBox.owl" : tOntoIRI.replaceFirst(originalExtension, "-TBox.owl");
                         aBoxOntologyIRI = originalExtension.isEmpty() ? tOntoIRI + "-ABox.owl" : tOntoIRI.replaceFirst(originalExtension, "-ABox.owl");
-                        
+
                         String tBoxDocumentIRI = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "TBox.owl").toString();
                         String aBoxDocumentIRI = (aBoxPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "ABox.owl").toString());
                         tBox = manager.createOntology(IRI.create(tBoxOntologyIRI));
@@ -85,10 +90,10 @@ public class RLPlusOntology implements KnowledgeBase {
                         manager.setOntologyDocumentIRI(tBox, IRI.create(Utility.toFileIRI(tBoxDocumentIRI)));
                         manager.setOntologyDocumentIRI(aBox, IRI.create(Utility.toFileIRI(aBoxDocumentIRI)));
 
-                        FileOutputStream aBoxOut = new FileOutputStream(aBoxPath); 
+                        FileOutputStream aBoxOut = new FileOutputStream(aBoxPath);
                         manager.saveOntology(aBox, aBoxOut);
                         aBoxOut.close();
-                        
+
                         restOntology = manager.createOntology();
                 }
                 catch (OWLOntologyCreationException e) {
@@ -103,11 +108,11 @@ public class RLPlusOntology implements KnowledgeBase {
         }
         
         public OWLOntology getTBox() {
-                return tBox; 
+                return tBox;
         }
         
         public String getABoxPath() {
-                return aBoxPath; 
+                return aBoxPath;
         }
         
         private void add2SubCounter(OWLClassExpression exp) {
@@ -118,24 +123,23 @@ public class RLPlusOntology implements KnowledgeBase {
         }
         
         public void simplify() {
-                if (simplifyABox()) { 
+                if(simplifyABox()) {
                         save(aBox);
 //                      save(tBox);
-                }
-                else 
-                        tBox = inputOntology; 
+                } else
+                        tBox = inputOntology;
         }
-        
+
         @Override
         public void transform() {
                 simplify();
                 filter();
                 clausify();
-                
+
                 subCounter = new HashMap<OWLClassExpression, Integer>();
                 clauses = new LinkedList<Clause>();
-                Clausifier clausifier = Clausifier.getInstance(restOntology); 
-                
+                Clausifier clausifier = Clausifier.getInstance(restOntology);
+
                 for (DLClause c: dlOntology.getDLClauses()) {
                         Clause clause = new Clause(clausifier, c);
                         clauses.add(clause);
@@ -144,7 +148,7 @@ public class RLPlusOntology implements KnowledgeBase {
                          * count the expressions in the left
                          */
                         for (OWLClassExpression exp: clause.getSubClasses()) {
-                                if (exp instanceof OWLClass) 
+                                if(exp instanceof OWLClass)
                                         add2SubCounter(exp);
                                 else if (exp instanceof OWLObjectSomeValuesFrom) {
                                         OWLObjectSomeValuesFrom someValue = (OWLObjectSomeValuesFrom)exp;
@@ -155,8 +159,7 @@ public class RLPlusOntology implements KnowledgeBase {
                                         OWLObjectMinCardinality minCard = (OWLObjectMinCardinality)exp;
                                         add2SubCounter(factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing()));
                                         add2SubCounter(minCard.getFiller());
-                                }
-                                else 
+                                } else
                                         Utility.logError("strange class expression: " + exp);
 
                         }
@@ -170,12 +173,12 @@ public class RLPlusOntology implements KnowledgeBase {
                         addedAxioms.clear();
                         for (OWLClassExpression exp: getDisjunctionApprox0(clause.getSuperClasses())) {
                                 addedAxioms.add(factory.getOWLSubClassOfAxiom(subExp, transform(exp, addedAxioms)));
-                                for (OWLAxiom a: addedAxioms) 
-                                        addAxiom2output(a, factory.getOWLSubClassOfAxiom(subExp, 
+                                for(OWLAxiom a : addedAxioms)
+                                        addAxiom2output(a, factory.getOWLSubClassOfAxiom(subExp,
                                                         OWLHelper.getSimplifiedDisjunction(factory, clause.getSuperClasses())));
                         }
                 }
-                
+
                 subCounter.clear();
         }
         
@@ -185,7 +188,7 @@ public class RLPlusOntology implements KnowledgeBase {
                         save(correspondence, corrFileName);
                 save(outputOntology);
         }
-        
+
         private void save(Map<OWLAxiom, OWLAxiom> map, String corrFileName) {
                 if (corrFileName == null) return ;
                 ObjectOutput output;
@@ -205,63 +208,61 @@ public class RLPlusOntology implements KnowledgeBase {
                         e.printStackTrace();
                 }
         }
-        
+
         /*
          * treat disjunction as conjunction
          */
         private Set<OWLClassExpression> getDisjunctionApprox0(Set<OWLClassExpression> superClasses) {
                 return superClasses;
         }
-
+        
         /*
          * choose one simple class disjunct
          */
         @SuppressWarnings("unused")
         private Set<OWLClassExpression> getDisjunctionApprox1(Set<OWLClassExpression> superClasses) {
-                if (superClasses.isEmpty() || superClasses.size() == 1) 
+                if(superClasses.isEmpty() || superClasses.size() == 1)
                         return superClasses;
-                
+
                 OWLClassExpression rep = null;
                 int min = Integer.MAX_VALUE, o;
-                for (OWLClassExpression exp: superClasses)
-                        if (exp instanceof OWLClass && (o = getOccurrence(exp)) < min) {
+                for(OWLClassExpression exp : superClasses)
+                        if(exp instanceof OWLClass && (o = getOccurrence(exp)) < min) {
                                 min = o;
                                 rep = exp;
                         }
-                
-                if (rep == null) rep = superClasses.iterator().next();
-                
+
+                if(rep == null) rep = superClasses.iterator().next();
+
                 return Collections.singleton(rep);
         }
-        
-        Random random = new Random(19900114);
+
         /*
          * randomly choose a class expression to represent this disjunction
          */
         @SuppressWarnings("unused")
         private Set<OWLClassExpression> getDisjunctionApprox2(Set<OWLClassExpression> superClasses) {
-                if (superClasses.isEmpty() || superClasses.size() == 1) 
+                if(superClasses.isEmpty() || superClasses.size() == 1)
                         return superClasses;
-                
+
                 int index = random.nextInt() % superClasses.size();
                 if (index < 0) index += superClasses.size();
-                        
+
                 int i = 0;
-                for (OWLClassExpression exp: superClasses) 
+                for(OWLClassExpression exp : superClasses)
                         if (i++ == index)
                                 return Collections.singleton(exp);
                 return null;
         }
         
-        private Map<OWLClassExpression, Integer> subCounter = null;
         /*
          * choose the one that appears least in the l.h.s.
          */
         @SuppressWarnings("unused")
         private Set<OWLClassExpression> getDisjunctionApprox3(Set<OWLClassExpression> superClasses) {
-                if (superClasses.isEmpty() || superClasses.size() == 1) 
+                if(superClasses.isEmpty() || superClasses.size() == 1)
                         return superClasses;
-                
+
                 OWLClassExpression rep = null, exp1;
                 int occurrence = Integer.MAX_VALUE, o;
                 for (OWLClassExpression exp: superClasses) {
@@ -272,16 +273,16 @@ public class RLPlusOntology implements KnowledgeBase {
                                 if (minCard.getCardinality() == 1)
                                         exp1 = factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), minCard.getFiller());
                         }
-                        
+
                         if (!subCounter.containsKey(exp1) || (o = subCounter.get(exp1)) < occurrence) {
                                 rep = exp;
                                 occurrence = o;
                         }
                 }
-                
+
                 return Collections.singleton(rep);
         }
-        
+
         private int getOccurrence(OWLClassExpression exp) {
                 if (!subCounter.containsKey(exp))
                         return 0;
@@ -290,9 +291,9 @@ public class RLPlusOntology implements KnowledgeBase {
 
         @SuppressWarnings("unused")
         private Set<OWLClassExpression> getDisjunctionApprox4(Set<OWLClassExpression> superClasses) {
-                if (superClasses.isEmpty() || superClasses.size() == 1) 
+                if(superClasses.isEmpty() || superClasses.size() == 1)
                         return superClasses;
-                
+
                 OWLClassExpression rep = null;
                 int occurrence = Integer.MAX_VALUE, o;
                 for (OWLClassExpression exp: superClasses) {
@@ -304,10 +305,9 @@ public class RLPlusOntology implements KnowledgeBase {
                                         o += getOccurrence(minCard.getFiller());
 //                                      if (o < o1) o = o1;
                                 }
-                        }
-                        else 
+                        } else
                                 o = getOccurrence(exp);
-                        
+
                         if (o < occurrence || o == occurrence && !(rep instanceof OWLClass)) {
                                 rep = exp;
                                 occurrence = o;
@@ -320,11 +320,11 @@ public class RLPlusOntology implements KnowledgeBase {
         private boolean simplifyABox() {
                 boolean flag = false;
                 Map<OWLClassExpression, OWLClass> complex2atomic= new HashMap<OWLClassExpression, OWLClass>();
-                
-                OWLDatatype anyURI = factory.getOWLDatatype(IRI.create(Namespace.XSD_NS + "anyURI")); 
+
+                OWLDatatype anyURI = factory.getOWLDatatype(IRI.create(Namespace.XSD_NS + "anyURI"));
                 OWLObjectProperty sameAs = factory.getOWLObjectProperty(IRI.create(Namespace.EQUALITY));
                 OWLObjectProperty differentFrom = factory.getOWLObjectProperty(IRI.create(Namespace.INEQUALITY));
-                
+
                 for (OWLOntology imported: inputOntology.getImportsClosure())
                         for (OWLAxiom axiom: imported.getAxioms()) {
                                 if (axiom instanceof OWLClassAssertionAxiom) {
@@ -334,7 +334,7 @@ public class RLPlusOntology implements KnowledgeBase {
                                         OWLClass cls;
                                         if (clsExp instanceof OWLClass) {
                                                 if (((OWLClass) clsExp).toStringID().startsWith("owl:"))
-                                                        manager.addAxiom(tBox, axiom); 
+                                                        manager.addAxiom(tBox, axiom);
                                                 else manager.addAxiom(aBox, axiom);
                                         }
                                         else {
@@ -343,40 +343,38 @@ public class RLPlusOntology implements KnowledgeBase {
                                                         manager.addAxiom(tBox, factory.getOWLSubClassOfAxiom(cls, clsExp));
                                                 }
                                                 manager.addAxiom(aBox, factory.getOWLClassAssertionAxiom(cls, assertion.getIndividual()));
-                                        } 
+                                        }
                                 }
                                 else if (axiom instanceof OWLObjectPropertyAssertionAxiom || axiom instanceof OWLDataPropertyAssertionAxiom || axiom instanceof OWLAnnotationAssertionAxiom) {
-                                        if (axiom.getDataPropertiesInSignature().contains(anyURI)) continue; 
+                                        if(axiom.getDataPropertiesInSignature().contains(anyURI)) continue;
                                         flag = true;
                                         manager.addAxiom(aBox, axiom);
                                 }
                                 else if (axiom instanceof OWLSameIndividualAxiom) {
-                                        OWLIndividual firstIndividual = null, previousIndividual = null, lastIndividual = null; 
+                                        OWLIndividual firstIndividual = null, previousIndividual = null, lastIndividual = null;
                                         for (OWLIndividual next: ((OWLSameIndividualAxiom) axiom).getIndividuals()) {
-                                                if (firstIndividual == null) firstIndividual = previousIndividual = next; 
-                                                else                                            
+                                                if(firstIndividual == null) firstIndividual = previousIndividual = next;
+                                                else
                                                         manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, previousIndividual, next));
                                                 previousIndividual = lastIndividual = next;
                                         }
                                         manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, lastIndividual, firstIndividual));
                                 }
                                 else if (axiom instanceof OWLDifferentIndividualsAxiom) {
-                                        int index1 = 0, index2; 
+                                        int index1 = 0, index2;
                                         for (OWLIndividual individual1: ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
                                                 ++index1;
-                                                index2 = 0; 
+                                                index2 = 0;
                                                 for (OWLIndividual individual2: ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
                                                         if (index2++ < index1) {
-                                                                manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(differentFrom, individual1, individual2));                                                    
-                                                        }
-                                                        else break; 
+                                                                manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(differentFrom, individual1, individual2));
+                                                        } else break;
                                                 }
                                         }
-                                }
-                                else 
+                                } else
                                         manager.addAxiom(tBox, axiom);
                         }
-                
+
                 return flag;
         }
 
@@ -384,15 +382,15 @@ public class RLPlusOntology implements KnowledgeBase {
                 OWL2RLProfile profile = new OWL2RLProfile();
                 OWLProfileReport report = profile.checkOntology(tBox);
                 Set<OWLAxiom> rlAxioms = tBox.getAxioms();
-                OWLAxiom axiom; 
-                
+                OWLAxiom axiom;
+
                 for (OWLProfileViolation violation: report.getViolations()) {
                         manager.addAxiom(restOntology, axiom = violation.getAxiom());
-                        rlAxioms.remove(axiom); 
+                        rlAxioms.remove(axiom);
                 }
-                
+
                 for (Iterator<OWLAxiom> iter = rlAxioms.iterator(); iter.hasNext(); )
-                        addAxiom2output(iter.next(), null); 
+                        addAxiom2output(iter.next(), null);
         }
         
         private void clausify() {
@@ -407,8 +405,6 @@ public class RLPlusOntology implements KnowledgeBase {
                 if (correspondingAxiom != null)
                         correspondence.put(axiom, correspondingAxiom);
         }
-        
-        private Map<OWLClass, OWLClass> atomic2negation = new HashMap<OWLClass, OWLClass>();
 
         private OWLClassExpression transform(OWLClassExpression exp, Set<OWLAxiom> addedAxioms) {
                 if (exp instanceof OWLClass)