1 files changed, 89 insertions, 87 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 1f435b7..dfbcb4d 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -37,21 +37,19 @@ public class MyQueryReasoner extends QueryReasoner {
         BasicQueryEngine limitedSkolemUpperStore;
 //      boolean[] namedIndividuals_lazyUpper; 
         
-        OWLOntology elho_ontology; 
-        KarmaQueryEngine elLowerStore = null; 
+        OWLOntology elho_ontology;
+        KarmaQueryEngine elLowerStore = null;
         
         BasicQueryEngine trackingStore = null;
 //      boolean[] namedIndividuals_tracking; 
-        
-        boolean equalityTag; 
-        boolean multiStageTag;
         TrackingRuleEncoder encoder;
-        Timer t = new Timer();
+        private boolean equalityTag;
+        private boolean multiStageTag;
+        private Timer t = new Timer();
         private Collection<String> predicatesWithGap = null;
-        private Boolean satisfiable;
+        private SatisfiabilityStatus satisfiable;
         private ConsistencyManager consistency = new ConsistencyManager(this);
         private boolean useUpperStores = false;
-
         public MyQueryReasoner() {
                 setup(true, true);
         }
@@ -59,7 +57,7 @@ public class MyQueryReasoner extends QueryReasoner {
         public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
                 setup(multiStageTag, considerEqualities);
         }
-        
+
         private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
                 if (multiStageTag)
                         return new MultiStageQueryEngine(name, checkValidity);
@@ -69,7 +67,7 @@ public class MyQueryReasoner extends QueryReasoner {
         }
         
         public void setup(boolean multiStageTag, boolean considerEqualities) {
-                satisfiable = null;
+                satisfiable = SatisfiabilityStatus.UNCHECKED;
                 this.multiStageTag = multiStageTag;
                 this.equalityTag = considerEqualities;
 
@@ -90,7 +88,7 @@ public class MyQueryReasoner extends QueryReasoner {
 
         @Override
         public void loadOntology(OWLOntology o) {
-                if (!equalityTag) {
+                if(!equalityTag) {
                         EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
                         o = eliminator.getOutputOntology();
                         eliminator.save();
@@ -103,9 +101,9 @@ public class MyQueryReasoner extends QueryReasoner {
 //              program.getGeneral().save();
 
                 useUpperStores = multiStageTag && !program.getGeneral().isHorn();
-                if (useUpperStores) {
-                        lazyUpperStore =  getUpperStore("lazy-upper-bound", true); // new MultiStageQueryEngine("lazy-upper-bound", true); //
-                        limitedSkolemUpperStore =  getUpperStore("limited-skolem-upper-bound", true);
+                if(useUpperStores) {
+                        lazyUpperStore = getUpperStore("lazy-upper-bound", true);
+                        limitedSkolemUpperStore = getUpperStore("limited-skolem-upper-bound", true);
                 }
 
                 importData(program.getAdditionalDataFile());
@@ -113,11 +111,11 @@ public class MyQueryReasoner extends QueryReasoner {
                 elho_ontology = new ELHOProfile().getFragment(ontology);
                 elLowerStore.processOntology(elho_ontology);
         }
-        
+
         public Collection<String> getPredicatesWithGap() {
                 return predicatesWithGap;
         }
-
+        
         @Override
         public boolean preprocess() {
                 t.reset();
@@ -127,7 +125,7 @@ public class MyQueryReasoner extends QueryReasoner {
                 rlLowerStore.importRDFData(name, datafile);
                 rlLowerStore.materialise("lower program", program.getLower().toString());
 //              program.getLower().save();
-                if (!consistency.checkRLLowerBound()) return false;
+                if(!consistency.checkRLLowerBound()) return false;
                 Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
 
                 String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
@@ -136,35 +134,35 @@ public class MyQueryReasoner extends QueryReasoner {
                 elLowerStore.materialise("saturate named individuals", originalMarkProgram);
                 elLowerStore.materialise("lower program", program.getLower().toString());
                 elLowerStore.initialiseKarma();
-                if (!consistency.checkELLowerBound()) return false;
+                if(!consistency.checkELLowerBound()) return false;
 
-                if (lazyUpperStore != null) {
+                if(lazyUpperStore != null) {
                         lazyUpperStore.importRDFData(name, datafile);
                         lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
                         int tag = lazyUpperStore.materialiseRestrictedly(program, null);
-                        if (tag != 1) {
+                        if(tag != 1) {
                                 lazyUpperStore.dispose();
                                 lazyUpperStore = null;
                         }
-                        if (tag == -1) return false;
+                        if(tag == -1) return false;
                 }
-                if (consistency.checkUpper(lazyUpperStore)) {
-                        satisfiable = true;
+                if(consistency.checkUpper(lazyUpperStore)) {
+                        satisfiable = SatisfiabilityStatus.SATISFIABLE;
                         Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
 
-                if (limitedSkolemUpperStore != null) {
+                if(limitedSkolemUpperStore != null) {
                         limitedSkolemUpperStore.importRDFData(name, datafile);
                         limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
                         int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
-                        if (tag != 1) {
+                        if(tag != 1) {
                                 limitedSkolemUpperStore.dispose();
                                 limitedSkolemUpperStore = null;
                         }
-                        if (tag == -1) return false;
+                        if(tag == -1) return false;
                 }
-                if (consistency.checkUpper(limitedSkolemUpperStore)) {
-                        satisfiable = true;
+                if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
+                        satisfiable = SatisfiabilityStatus.SATISFIABLE;
                         Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
 
@@ -176,7 +174,7 @@ public class MyQueryReasoner extends QueryReasoner {
                 predicatesWithGap = gap.getPredicatesWithGap();
                 gap.clear();
 
-                if (program.getGeneral().isHorn())
+                if(program.getGeneral().isHorn())
                         encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
                 else
                         encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
@@ -186,21 +184,22 @@ public class MyQueryReasoner extends QueryReasoner {
 
                 program.deleteABoxTurtleFile();
 
-                if (!isConsistent())
+                if(!isConsistent())
                         return false;
 
                 consistency.extractBottomFragment();
                 consistency.dispose();
+
                 return true;
         }
-        
+
         @Override
         public boolean isConsistent() {
-                if (satisfiable == null) {
-                        satisfiable = consistency.check();
+                if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
+                        satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
                         Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
-                return satisfiable;
+                return satisfiable == SatisfiabilityStatus.SATISFIABLE ? true : false;
         }
 
         /**
@@ -208,8 +207,8 @@ public class MyQueryReasoner extends QueryReasoner {
          * */
         private OWLOntology relevantPart(QueryRecord queryRecord) {
                 AnswerTuples rlAnswer = null, elAnswer = null;
-                
-                t.reset(); 
+
+                t.reset();
                 try {
                         rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
                         Utility.logDebug(t.duration());
@@ -218,11 +217,11 @@ public class MyQueryReasoner extends QueryReasoner {
                         if (rlAnswer != null) rlAnswer.dispose();
                 }
                 queryRecord.addProcessingTime(Step.LowerBound, t.duration());
-                
+
                 t.reset();
-                BasicQueryEngine upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;  
-                        
-                String[] extendedQuery = queryRecord.getExtendedQueryText(); 
+                BasicQueryEngine upperStore = queryRecord.isBottom() || lazyUpperStore == null ? trackingStore : lazyUpperStore;
+
+                String[] extendedQuery = queryRecord.getExtendedQueryText();
 
                 // TODO why the following???
                 queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
@@ -246,10 +245,10 @@ public class MyQueryReasoner extends QueryReasoner {
 
                 queryRecord.addProcessingTime(Step.UpperBound, t.duration());
                 if (queryRecord.processed()) {
-                        queryRecord.setDifficulty(Step.UpperBound); 
+                        queryRecord.setDifficulty(Step.UpperBound);
                         return null;
                 }
-                
+
                 t.reset();
                 try {
                         elAnswer = elLowerStore.evaluate(extendedQuery[0], queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
@@ -261,48 +260,46 @@ public class MyQueryReasoner extends QueryReasoner {
                 queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
 
                 if (queryRecord.processed()) {
-                        queryRecord.setDifficulty(Step.ELLowerBound); 
-                        return null; 
+                        queryRecord.setDifficulty(Step.ELLowerBound);
+                        return null;
                 }
-                
-                t.reset(); 
-                
+
+                t.reset();
+
                 QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
-                
-                OWLOntology knowledgebase; 
-                t.reset(); 
+
+                OWLOntology knowledgebase;
+                t.reset();
 //              if (program.getGeneral().isHorn()) {
 //                      knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
 //                      queryRecord.addProcessingTime(Step.Fragment, t.duration());
-//                      return knowledgebase; 
+//                      return knowledgebase;
 //              }
-//              else { 
+//              else {
                         knowledgebase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
                         queryRecord.addProcessingTime(Step.Fragment, t.duration());
 //              }
-                
-                        if (knowledgebase.isEmpty() || queryRecord.isBottom()) 
-                                return knowledgebase; 
-                        
-                if (program.getGeneral().isHorn()) return knowledgebase; 
-
-//              t.reset(); 
-//              if (queryRecord.isHorn() && lazyUpperStore != null) { 
-////                    knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true); 
+
+                if(knowledgebase.isEmpty() || queryRecord.isBottom())
+                        return knowledgebase;
+
+                if(program.getGeneral().isHorn()) return knowledgebase;
+
+//              t.reset();
+//              if (queryRecord.isHorn() && lazyUpperStore != null) {
+////                    knowledgebase = tracker.extract(lazyUpperStore, consistency.getQueryRecords(), true);
 //              } else if (queryRecord.getArity() < 3) {
 //                      IterativeRefinement iterativeRefinement = new IterativeRefinement(queryRecord, tracker, trackingStore, consistency.getQueryRecords());
 //                      knowledgebase = iterativeRefinement.extractWithFullABox(importedData.toString(), program.getUpperBottomStrategy());
 //              }
-//              
+//
 //              queryRecord.addProcessingTime(Step.FragmentRefinement, t.duration());
-//              
+//
 //              if (knowledgebase == null)
 //                      queryRecord.setDifficulty(Step.FragmentRefinement);
-                
-                return knowledgebase; 
-        }
 
-//      int counter = 0; 
+                return knowledgebase;
+        }
 
         private String toJsonKeyValuePair(String key, Object value) {
                 HashMap<String, Object> map = new HashMap<>();
@@ -310,8 +307,10 @@ 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; 
+                AnswerTuples rlAnswer = null;
                 try {
                         Utility.logDebug(queryText);
                         rlAnswer = upperStore.evaluate(queryText, answerVariables);
@@ -326,37 +325,38 @@ public class MyQueryReasoner extends QueryReasoner {
         @Override
         public void evaluate(QueryRecord queryRecord) {
                 OWLOntology knowledgeBase = relevantPart(queryRecord);
-                
-                if (knowledgeBase == null) {
+
+                if(knowledgeBase == null) {
                         Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
-                        return ; 
+                        return;
                 }
-                
+
                 int aBoxCount = knowledgeBase.getABoxAxioms(true).size();
                 Utility.logDebug("ABox axioms: " + aBoxCount + " TBox axioms: " + (knowledgeBase.getAxiomCount() - aBoxCount));
-//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl"); 
-                
-                Timer t = new Timer(); 
-                Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT()); 
-//              int validNumber = 
-                summarisedChecker.check(queryRecord.getGapAnswers()); 
+//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
+
+                Timer t = new Timer();
+                Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
+//              int validNumber =
+                summarisedChecker.check(queryRecord.getGapAnswers());
                 summarisedChecker.dispose();
                 Utility.logDebug("Total time for full reasoner: " + t.duration());
-//              if (validNumber == 0) { 
-                        queryRecord.markAsProcessed(); 
-                        Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
+//              if (validNumber == 0) {
+                queryRecord.markAsProcessed();
+                Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
 //              }
         }
-        
+
         @Override
         public void evaluateUpper(QueryRecord queryRecord) {
-                AnswerTuples rlAnswer = null; 
-                boolean useFull = queryRecord.isBottom() || lazyUpperStore == null; 
+                AnswerTuples rlAnswer = null;
+                boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
                 try {
-                        rlAnswer = (useFull ? trackingStore: lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        queryRecord.updateUpperBoundAnswers(rlAnswer, true); 
+                        rlAnswer =
+                                        (useFull ? trackingStore : lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                        queryRecord.updateUpperBoundAnswers(rlAnswer, true);
                 } finally {
-                        if (rlAnswer != null) rlAnswer.dispose();
+                        if(rlAnswer != null) rlAnswer.dispose();
                 }
         }
         
@@ -370,4 +370,6 @@ public class MyQueryReasoner extends QueryReasoner {
                 super.dispose();
         }
 
+        enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED}
+
 }