Changes in the upper store querying (mainly in MyQueryReasoner).

2 files changed, 91 insertions, 77 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 0d24a02..6da86ac 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -2,7 +2,6 @@ package uk.ac.ox.cs.pagoda.reasoner;
 
 import org.semanticweb.karma2.profile.ELHOProfile;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
 import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
@@ -26,59 +25,60 @@ public class ELHOUQueryReasoner extends QueryReasoner {
         KarmaQueryEngine elLowerStore = null; 
         
         boolean multiStageTag, equalityTag;
-        
+        String originalMarkProgram;
+        private Timer t = new Timer();
+
         public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
                 this.multiStageTag = multiStageTag;
                 this.equalityTag = considerEqualities;
                 rlLowerStore = new BasicQueryEngine("rl-lower-bound");
                 elLowerStore = new KarmaQueryEngine("el-lower-bound");
-                
-                if (!multiStageTag) 
-                        rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 
-                else  
-                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 
+
+                if(!multiStageTag)
+                        rlUpperStore = new BasicQueryEngine("rl-upper-bound");
+                else
+                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
         }
-        
-        private Timer t = new Timer(); 
 
         @Override
         public void evaluate(QueryRecord queryRecord) {
                 AnswerTuples rlAnswer = null;
                 t.reset();
                 try {
-                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 
+                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
                         queryRecord.updateLowerBoundAnswers(rlAnswer);
                 } finally {
-                        if (rlAnswer != null) rlAnswer.dispose(); 
+                        if(rlAnswer != null) rlAnswer.dispose();
                 }
                 queryRecord.addProcessingTime(Step.LowerBound, t.duration());
-                
-                String extendedQueryText = queryRecord.getExtendedQueryText()[0];
+
+                String extendedQueryText = queryRecord.getExtendedQueryText().get(0);
                 String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
-                                new String[] {queryRecord.getQueryText()} : 
+                                new String[]{queryRecord.getQueryText()} :
                                 new String[] {queryRecord.getQueryText(), extendedQueryText};
-                                
+
                 for (String queryText: toQuery) {
-                        rlAnswer = null; 
+                        rlAnswer = null;
                         t.reset();
                         try {
-                                rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables()); 
+                                rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables());
                                 queryRecord.updateUpperBoundAnswers(rlAnswer);
                         } finally {
-                                if (rlAnswer != null) rlAnswer.dispose(); 
+                                if(rlAnswer != null) rlAnswer.dispose();
                         }
                         queryRecord.addProcessingTime(Step.UpperBound, t.duration());
-                        
+
                         if (queryRecord.processed()) {
                                 queryRecord.setDifficulty(Step.UpperBound);
-                                return ; 
+                                return;
                         }
                 }
-                
+
                 AnswerTuples elAnswer = null;
-                t.reset(); 
+                t.reset();
                 try {
-                        elAnswer = elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers()); 
+                        elAnswer =
+                                        elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
                         queryRecord.updateLowerBoundAnswers(elAnswer);
                 } finally {
                         if (elAnswer != null) elAnswer.dispose();
@@ -88,19 +88,19 @@ public class ELHOUQueryReasoner extends QueryReasoner {
 
         @Override
         public void evaluateUpper(QueryRecord queryRecord) {
-                AnswerTuples rlAnswer = null; 
+                AnswerTuples rlAnswer = null;
                 try {
-                        rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables()); 
+                        rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
                         queryRecord.updateUpperBoundAnswers(rlAnswer, true);
                 } finally {
-                        if (rlAnswer != null) rlAnswer.dispose(); 
+                        if(rlAnswer != null) rlAnswer.dispose();
                 }
         }
 
         @Override
         public void dispose() {
                 if (elLowerStore != null) elLowerStore.dispose();
-                if (rlUpperStore != null) rlUpperStore.dispose();               
+                if(rlUpperStore != null) rlUpperStore.dispose();
                 super.dispose();
         }
 
@@ -110,19 +110,17 @@ public class ELHOUQueryReasoner extends QueryReasoner {
                         EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
                         o = eliminator.getOutputOntology();
                         eliminator.save();
-                }                       
+                }
+
+                OWLOntology ontology = o;
+                program = new DatalogProgram(ontology, properties.getToClassify());
 
-                OWLOntology ontology = o; 
-                program = new DatalogProgram(ontology, properties.getToClassify()); 
-                
                 importData(program.getAdditionalDataFile());
-                
+
                 elho_ontology = new ELHOProfile().getFragment(ontology);
                 elLowerStore.processOntology(elho_ontology);
                 originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
         }
-        
-        String originalMarkProgram;  
 
         @Override
         public boolean preprocess() {
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index dfbcb4d..b10e2d1 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -20,28 +20,25 @@ import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 
 import java.util.Collection;
 import java.util.HashMap;
 
 public class MyQueryReasoner extends QueryReasoner {
 
-        OWLOntology ontology; 
+        OWLOntology ontology;
+        DatalogProgram program;
 
 //      String additonalDataFile; 
-        
-        DatalogProgram program; 
-
         BasicQueryEngine rlLowerStore = null;
         BasicQueryEngine lazyUpperStore = null;
         BasicQueryEngine limitedSkolemUpperStore;
-//      boolean[] namedIndividuals_lazyUpper; 
-        
         OWLOntology elho_ontology;
+//      boolean[] namedIndividuals_lazyUpper; 
         KarmaQueryEngine elLowerStore = null;
-        
         BasicQueryEngine trackingStore = null;
-//      boolean[] namedIndividuals_tracking; 
+        //      boolean[] namedIndividuals_tracking;
         TrackingRuleEncoder encoder;
         private boolean equalityTag;
         private boolean multiStageTag;
@@ -53,7 +50,6 @@ public class MyQueryReasoner extends QueryReasoner {
         public MyQueryReasoner() {
                 setup(true, true);
         }
-
         public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
                 setup(multiStageTag, considerEqualities);
         }
@@ -65,7 +61,7 @@ public class MyQueryReasoner extends QueryReasoner {
                 else
                         return new BasicQueryEngine(name);
         }
-        
+
         public void setup(boolean multiStageTag, boolean considerEqualities) {
                 satisfiable = SatisfiabilityStatus.UNCHECKED;
                 this.multiStageTag = multiStageTag;
@@ -115,7 +111,7 @@ public class MyQueryReasoner extends QueryReasoner {
         public Collection<String> getPredicatesWithGap() {
                 return predicatesWithGap;
         }
-        
+
         @Override
         public boolean preprocess() {
                 t.reset();
@@ -192,18 +188,40 @@ public class MyQueryReasoner extends QueryReasoner {
 
                 return true;
         }
-
+        
         @Override
         public boolean isConsistent() {
                 if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
                         satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
                         Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
-                return satisfiable == SatisfiabilityStatus.SATISFIABLE ? true : false;
+                return satisfiable == SatisfiabilityStatus.SATISFIABLE;
+        }
+
+        // TODO why the following???
+        private void queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord, Tuple<String> extendedQuery) {
+
+//              Utility.logInfo("1");
+//              queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+//
+//              boolean conditionA = !queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery.get(0));
+//              boolean conditionB = !queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables();
+//
+//              if(conditionA ^ conditionB)
+//                      throw new Error("It really happened! I thought it was impossible");
+//
+//              if (conditionA) {
+//                      Utility.logInfo("2");
+                queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
+//              }
+//              if (conditionB) {
+//                      Utility.logInfo("3");
+//                      queryUpperBound(upperStore, queryRecord, extendedQuery.get(1), queryRecord.getDistinguishedVariables());
+//              }
         }
 
         /**
-         * Returns the relevant part of the ontology, while computing the bound answers.
+         * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
          * */
         private OWLOntology relevantPart(QueryRecord queryRecord) {
                 AnswerTuples rlAnswer = null, elAnswer = null;
@@ -219,28 +237,23 @@ public class MyQueryReasoner extends QueryReasoner {
                 queryRecord.addProcessingTime(Step.LowerBound, t.duration());
 
                 t.reset();
-                BasicQueryEngine upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
 
-                String[] extendedQuery = queryRecord.getExtendedQueryText();
+                Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
 
-                // TODO why the following???
-                queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+//              BasicQueryEngine upperStore;
+//              if(queryRecord.isBottom()) upperStore = trackingStore;
+//              upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
 
-                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());
-                }
-
-//              Utility.logDebug(toJsonKeyValuePair("upperBound", queryRecord));
+                // TODO
+//              if(queryRecord.isBottom() || (lazyUpperStore == null && limitedSkolemUpperStore == null))
+//                      queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
+//              else {
 
-                // TODO test intersection and new upper bound
-                if (!queryRecord.isBottom() && lazyUpperStore != null) {
-                        queryUpperBound(trackingStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                }
-                if (!queryRecord.isBottom() && limitedSkolemUpperStore != null) {
-                        queryUpperBound(limitedSkolemUpperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
+                if(!(queryRecord.isBottom() || (lazyUpperStore == null && limitedSkolemUpperStore == null))) {
+                        if(lazyUpperStore != null) queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts);
+                        if(limitedSkolemUpperStore != null)
+                                queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts);
                 }
 
                 queryRecord.addProcessingTime(Step.UpperBound, t.duration());
@@ -251,7 +264,8 @@ public class MyQueryReasoner extends QueryReasoner {
 
                 t.reset();
                 try {
-                        elAnswer = elLowerStore.evaluate(extendedQuery[0], queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
+                        elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0), queryRecord.getAnswerVariables(),
+                                                                                         queryRecord.getLowerBoundAnswers());
                         Utility.logDebug(t.duration());
                         queryRecord.updateLowerBoundAnswers(elAnswer);
                 } finally {
@@ -268,7 +282,7 @@ public class MyQueryReasoner extends QueryReasoner {
 
                 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
 
-                OWLOntology knowledgebase;
+                OWLOntology knowledgeBase;
                 t.reset();
 //              if (program.getGeneral().isHorn()) {
 //                      knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
@@ -276,14 +290,14 @@ public class MyQueryReasoner extends QueryReasoner {
 //                      return knowledgebase;
 //              }
 //              else {
-                        knowledgebase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
+                knowledgeBase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
                         queryRecord.addProcessingTime(Step.Fragment, t.duration());
 //              }
 
-                if(knowledgebase.isEmpty() || queryRecord.isBottom())
-                        return knowledgebase;
+                if(knowledgeBase.isEmpty() || queryRecord.isBottom())
+                        return knowledgeBase;
 
-                if(program.getGeneral().isHorn()) return knowledgebase;
+                if(program.getGeneral().isHorn()) return knowledgeBase;
 
 //              t.reset();
 //              if (queryRecord.isHorn() && lazyUpperStore != null) {
@@ -298,7 +312,7 @@ public class MyQueryReasoner extends QueryReasoner {
 //              if (knowledgebase == null)
 //                      queryRecord.setDifficulty(Step.FragmentRefinement);
 
-                return knowledgebase;
+                return knowledgeBase;
         }
 
         private String toJsonKeyValuePair(String key, Object value) {
@@ -307,8 +321,6 @@ public class MyQueryReasoner extends QueryReasoner {
                 return QueryRecord.GsonCreator.getInstance().toJson(map);
         }
 
-//      int counter = 0; 
-
         private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
                 AnswerTuples rlAnswer = null;
                 try {
@@ -317,11 +329,13 @@ public class MyQueryReasoner extends QueryReasoner {
                         Utility.logDebug(t.duration());
                         queryRecord.updateUpperBoundAnswers(rlAnswer);
                 } finally {
-                        if (rlAnswer != null) rlAnswer.dispose();
+                        if(rlAnswer != null) rlAnswer.dispose();
                         rlAnswer = null;
                 }
         }
 
+//      int counter = 0; 
+
         @Override
         public void evaluate(QueryRecord queryRecord) {
                 OWLOntology knowledgeBase = relevantPart(queryRecord);
@@ -349,6 +363,7 @@ public class MyQueryReasoner extends QueryReasoner {
 
         @Override
         public void evaluateUpper(QueryRecord queryRecord) {
+                // TODO add new upper store
                 AnswerTuples rlAnswer = null;
                 boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
                 try {
@@ -359,7 +374,7 @@ public class MyQueryReasoner extends QueryReasoner {
                         if(rlAnswer != null) rlAnswer.dispose();
                 }
         }
-        
+
         @Override
         public void dispose() {
                 if (encoder != null) encoder.dispose();
@@ -367,6 +382,7 @@ public class MyQueryReasoner extends QueryReasoner {
                 if (lazyUpperStore != null) lazyUpperStore.dispose();
                 if (elLowerStore != null) elLowerStore.dispose();
                 if (trackingStore != null) trackingStore.dispose();
+                if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
                 super.dispose();
         }