added top answers optimisation back

5 files changed, 46 insertions, 42 deletions

diff --git a/config/fly.conf b/config/fly.conf
index 68c36b6..88c85c3 100644
--- a/config/fly.conf
+++ b/config/fly.conf
@@ -1,5 +1,6 @@
 #ONTOLOGY variable points to the file that stores ontology of interest
 ONTOLOGY=data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl
+#ONTOLOGY=data/fly/fbbt_vfb_ind_pr_nr.owl
 
 #QUERY variable points to the file that stores all queries
 QUERY=data/fly/fly.sparql
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index 63fe246..9b862ce 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -23,6 +23,7 @@ import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
 
 public class ConsistencyManager {
 
@@ -218,7 +219,7 @@ public class ConsistencyManager {
                         Timer t1 = new Timer();
                         oldTripleCount = store.getTriplesCount();
                         for (String program: programs) 
-                                store.importRules(program);
+                                store.importRules(program, UpdateType.ScheduleForAddition);
                         store.applyReasoning(true);
                         tripleCount = store.getTriplesCount(); 
                         
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 4970e7a..d5796ad 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -21,7 +21,10 @@ import uk.ac.ox.cs.pagoda.util.Utility;
 public abstract class QueryReasoner {
         
 //      protected boolean forSemFacet = false;
-        Properties properties; 
+        Properties properties;
+        
+        private static boolean defaultMultiStages = true; 
+        private static boolean defaultEqualities = true; 
 
         public static enum Type { Full, RLU, ELHOU };  
         
@@ -43,7 +46,7 @@ public abstract class QueryReasoner {
         }
         
         public static QueryReasoner getInstance(OWLOntology o) {
-                QueryReasoner pagoda = getInstance(Type.Full, o, true, true);
+                QueryReasoner pagoda = getInstance(Type.Full, o, defaultMultiStages, defaultEqualities);
                 pagoda.properties = new Properties(); 
                 return pagoda; 
         }
@@ -57,7 +60,7 @@ public abstract class QueryReasoner {
         }
         
         private static QueryReasoner getInstance(OWLOntology o, Properties p) {
-                return getInstance(Type.Full, o, true, true); 
+                return getInstance(Type.Full, o, defaultMultiStages, defaultEqualities); 
         }
         
         public static QueryReasoner getInstance(Type type, OWLOntology o, boolean performMultiStages, boolean considerEqualities) {
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
index 4dd11d8..5dcf0f8 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -77,8 +77,7 @@ public class HermitChecker implements Checker {
         }
         
         private int tag = 0;
-//      AnswerTuple topAnswerTuple = null; 
-        AnswerTuple botAnswerTuple = null; 
+        AnswerTuple topAnswerTuple = null, botAnswerTuple = null; 
         
         private void initialiseReasoner() {
                 qGraph = new QueryGraph(queryClause.getBodyAtoms(), answerVariable[1], ontology); 
@@ -88,17 +87,20 @@ public class HermitChecker implements Checker {
                 if (hermit != null)     hermit.dispose();
                 
                 if (dGraph != null && answerVariable[1].length == 1 && (dGraph.getExits().size() > 1 || dGraph.getEntrances().size() > 1)) {
-                        Set<OWLAxiom> axioms = new HashSet<OWLAxiom>(); 
-                        addTopAndBotTuple(axioms);
-                        manager.addAxioms(ontology, axioms); 
+                        Set<OWLAxiom> topAxioms = new HashSet<OWLAxiom>(); 
+                        Set<OWLAxiom> botAxioms = new HashSet<OWLAxiom>(); 
+                        addTopAndBotTuple(topAxioms, botAxioms);
+                        manager.addAxioms(ontology, topAxioms); 
+                        manager.addAxioms(ontology, botAxioms); 
                         hermit = new Reasoner(ontology);
-                        if (!hermit.isConsistent()) {
+                        boolean topValid = true; 
+                        if (!hermit.isConsistent() || topAnswerTuple != null && (topValid = check(topAnswerTuple))) {
                                 hermit.dispose();
-                                manager.removeAxioms(ontology, axioms); 
+                                manager.removeAxioms(ontology, topAxioms); 
                                 hermit = new Reasoner(ontology); 
                         } else {
-//                              if (topAnswerTuple != null && !check(topAnswerTuple)) tag = -1; 
-//                              else 
+                                if (!topValid) tag = -1; 
+                                else 
                                         if (botAnswerTuple != null && check(botAnswerTuple)) tag = 1; 
                         }
                 }
@@ -106,23 +108,20 @@ public class HermitChecker implements Checker {
                         hermit = new Reasoner(ontology);
         }
         
-        private void addTopAndBotTuple(Set<OWLAxiom> axioms) {
-//              String top_str = Namespace.PAGODA_ANONY + "top";
-                String bot_str = Namespace.PAGODA_ANONY + "bot";
-//              topAnswerTuple = new AnswerTuple(new uk.ac.ox.cs.JRDFox.model.Individual[] { uk.ac.ox.cs.JRDFox.model.Individual.create(top_str) } ); 
+        private void addTopAndBotTuple(Set<OWLAxiom> topAxioms, Set<OWLAxiom> botAxioms) {
+                String top_str = Namespace.PAGODA_ANONY + "top", bot_str = Namespace.PAGODA_ANONY + "bot";
+                topAnswerTuple = new AnswerTuple(new uk.ac.ox.cs.JRDFox.model.Individual[] { uk.ac.ox.cs.JRDFox.model.Individual.create(top_str) } ); 
                 botAnswerTuple = new AnswerTuple(new uk.ac.ox.cs.JRDFox.model.Individual[] { uk.ac.ox.cs.JRDFox.model.Individual.create(bot_str) } );  
-//              OWLIndividual top_ind = factory.getOWLNamedIndividual(IRI.create(top_str));
-                OWLIndividual bot_ind = factory.getOWLNamedIndividual(IRI.create(bot_str));
+                OWLIndividual top_ind = factory.getOWLNamedIndividual(IRI.create(top_str)), bot_ind = factory.getOWLNamedIndividual(IRI.create(bot_str));
                 Map<OWLAxiom, Integer> counter = new HashMap<OWLAxiom, Integer>(); 
                 
-//              Set<String> topAnswers = new HashSet<String>();
-                Set<String> botAnswers = new HashSet<String>();
+                Set<String> topAnswers = new HashSet<String>(), botAnswers = new HashSet<String>();
                 OWLIndividual sub, obj; 
-//              if (dGraph.getExits().size() > 1) {
-//                      for (Clique answerClique: dGraph.getExits())  
-//                              topAnswers.add(((uk.ac.ox.cs.JRDFox.model.Individual) answerClique.getRepresentative().getAnswerTuple().getGroundTerm(0)).getIRI());
-//              }
-//              else topAnswerTuple = null; 
+                if (dGraph.getExits().size() > 1) {
+                        for (Clique answerClique: dGraph.getExits())  
+                                topAnswers.add(((uk.ac.ox.cs.JRDFox.model.Individual) answerClique.getRepresentative().getAnswerTuple().getGroundTerm(0)).getIRI());
+                }
+                else topAnswerTuple = null; 
                 
                 if (dGraph.getEntrances().size() > 1) {
                         for (Clique answerClique: dGraph.getEntrances()) 
@@ -134,23 +133,23 @@ public class HermitChecker implements Checker {
                         if (axiom instanceof OWLClassAssertionAxiom) {
                                 OWLClassAssertionAxiom ca = (OWLClassAssertionAxiom) axiom;
                                 sub = ca.getIndividual();
-//                              if (topAnswers.contains(sub.toStringID())) 
-//                                      axioms.add(factory.getOWLClassAssertionAxiom(ca.getClassExpression(), top_ind));
+                                if (topAnswers.contains(sub.toStringID())) 
+                                        topAxioms.add(factory.getOWLClassAssertionAxiom(ca.getClassExpression(), top_ind));
                                 if (botAnswers.contains(sub.toStringID())) 
                                         inc(counter, factory.getOWLClassAssertionAxiom(ca.getClassExpression(), bot_ind));
                         }
                         else if (axiom instanceof OWLObjectPropertyAssertionAxiom) {
                                 OWLObjectPropertyAssertionAxiom oa = (OWLObjectPropertyAssertionAxiom) axiom; 
                                 sub = oa.getSubject(); obj = oa.getObject(); 
-////                            if (topAnswers.contains(sub.toStringID()))
-////                                    if (topAnswers.contains(obj.toStringID()))
-////                                            axioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), top_ind, top_ind));
-////                                    else 
-////                                            axioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), top_ind, obj));
-////                            else {
-////                                    if (topAnswers.contains(obj.toStringID()))
-////                                            axioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), sub, top_ind));
-////                            }
+                                if (topAnswers.contains(sub.toStringID()))
+                                        if (topAnswers.contains(obj.toStringID()))
+                                                topAxioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), top_ind, top_ind));
+                                        else 
+                                                topAxioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), top_ind, obj));
+                                else {
+                                        if (topAnswers.contains(obj.toStringID()))
+                                                topAxioms.add(factory.getOWLObjectPropertyAssertionAxiom(oa.getProperty(), sub, top_ind));
+                                }
                                 
                                 if (botAnswers.contains(sub.toStringID()))
                                         if (botAnswers.contains(obj.toStringID()))
@@ -166,8 +165,8 @@ public class HermitChecker implements Checker {
                         else if (axiom instanceof OWLDataPropertyAssertionAxiom) {
                                 OWLDataPropertyAssertionAxiom da = (OWLDataPropertyAssertionAxiom) axiom; 
                                 sub = da.getSubject(); 
-//                              if (topAnswers.contains(sub.toStringID())) 
-//                                      axioms.add(factory.getOWLDataPropertyAssertionAxiom(da.getProperty(), top_ind, da.getObject()));
+                                if (topAnswers.contains(sub.toStringID())) 
+                                        topAxioms.add(factory.getOWLDataPropertyAssertionAxiom(da.getProperty(), top_ind, da.getObject()));
                                 
                                 if (botAnswers.contains(sub.toStringID())) 
                                         inc(counter, factory.getOWLDataPropertyAssertionAxiom(da.getProperty(), bot_ind, da.getObject()));
@@ -176,7 +175,7 @@ public class HermitChecker implements Checker {
                 int number = botAnswers.size(); 
                 for (Map.Entry<OWLAxiom, Integer> entry: counter.entrySet()) {
                         if (entry.getValue() == number) 
-                                axioms.add(entry.getKey());
+                                botAxioms.add(entry.getKey());
                 }
         }
 
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index d50a18b..a803d63 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -99,7 +99,7 @@ public class PagodaTester {
 //                      args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
 //                      args = new String[] {travel_tbox, null, dbpedia_query274};
 //                      args = new String[] {fly, null, fly_query};
-                        args = new String[] {npd_tbox, npd_abox, npd_query};
+//                      args = new String[] {npd_tbox, npd_abox, npd_query};
 //                      args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
 //                      args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null}; 
 //                      args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null}; 
@@ -119,7 +119,7 @@ public class PagodaTester {
 //                      args[2] = args[2].replace(".sparql", "_pellet.sparql");
                 }
 
-                Properties properties = new Properties("config/uobm.conf"); 
+                Properties properties = new Properties("config/fly.conf"); 
                 
                 int index = 0; 
                 if (args.length > index) properties.setOntologyPath(args[index++]);