Added classes for implementing new upper store (Limited Skolemisation).

Started implementation of the new classes.

1 files changed, 68 insertions, 61 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 7999daa..3c0a001 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -44,31 +44,36 @@ public class MyQueryReasoner extends QueryReasoner {
         
         boolean equalityTag; 
         boolean multiStageTag;
-
+        TrackingRuleEncoder encoder;
+        Timer t = new Timer();
+        private Collection<String> predicatesWithGap = null;
+        private Boolean satisfiable;
+        private ConsistencyManager consistency = new ConsistencyManager(this);
+        
         public MyQueryReasoner() {
-                setup(true, true); 
+                setup(true, true);
         }
-        
+
         public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
-                setup(multiStageTag, considerEqualities); 
+                setup(multiStageTag, considerEqualities);
         }
         
         private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
                 if (multiStageTag)
-                        return new MultiStageQueryEngine(name, checkValidity); 
+                        return new MultiStageQueryEngine(name, checkValidity);
 //                      return new TwoStageQueryEngine(name, checkValidity);
-                else 
-                        return new BasicQueryEngine(name); 
+                else
+                        return new BasicQueryEngine(name);
         }
         
         public void setup(boolean multiStageTag, boolean considerEqualities) {
-                satisfiable = null; 
-                this.multiStageTag = multiStageTag; 
+                satisfiable = null;
+                this.multiStageTag = multiStageTag;
                 this.equalityTag = considerEqualities;
 
                 rlLowerStore = new BasicQueryEngine("rl-lower-bound");
                 elLowerStore = new KarmaQueryEngine("elho-lower-bound");
-                
+
                 trackingStore = getUpperStore("tracking", false);
         }
         
@@ -80,113 +85,108 @@ public class MyQueryReasoner extends QueryReasoner {
                 elLowerStore.importRDFData(name, datafile);
                 trackingStore.importRDFData(name, datafile);
         }
-        
+
         @Override
         public void loadOntology(OWLOntology o) {
                 if (!equalityTag) {
                         EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
                         o = eliminator.getOutputOntology();
                         eliminator.save();
-                }                       
+                }
 
-                ontology = o; 
+                ontology = o;
                 program = new DatalogProgram(ontology, properties.getToClassify());
 //              program.getLower().save();
 //              program.getUpper().save();
 //              program.getGeneral().save();
-                
-                if (multiStageTag && !program.getGeneral().isHorn()) { 
+
+                if (multiStageTag && !program.getGeneral().isHorn()) {
                         lazyUpperStore =  getUpperStore("lazy-upper-bound", true); // new MultiStageQueryEngine("lazy-upper-bound", true); //
                 }
-                
+
+                // TODO add new upper store creation
+
                 importData(program.getAdditionalDataFile());
-        
+
                 elho_ontology = new ELHOProfile().getFragment(ontology);
                 elLowerStore.processOntology(elho_ontology);
         }
-
-        private Collection<String> predicatesWithGap = null; 
         
         public Collection<String> getPredicatesWithGap() {
-                return predicatesWithGap; 
-        }       
-        
+                return predicatesWithGap;
+        }
+
         @Override
         public boolean preprocess() {
-                t.reset(); 
+                t.reset();
                 Utility.logInfo("Preprocessing ... checking satisfiability ... ");
 
-                String name = "data", datafile = importedData.toString(); 
+                String name = "data", datafile = importedData.toString();
                 rlLowerStore.importRDFData(name, datafile);
                 rlLowerStore.materialise("lower program", program.getLower().toString());
 //              program.getLower().save();
                 if (!consistency.checkRLLowerBound()) return false;
                 Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
-                
+
                 String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
-                
+
                 elLowerStore.importRDFData(name, datafile);
                 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) {
                         lazyUpperStore.importRDFData(name, datafile);
                         lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
-                        int tag = lazyUpperStore.materialiseRestrictedly(program, null);  
+                        int tag = lazyUpperStore.materialiseRestrictedly(program, null);
                         if (tag != 1) {
                                 lazyUpperStore.dispose();
                                 lazyUpperStore = null;
                         }
-                        if (tag == -1) return false; 
+                        if (tag == -1) return false;
                 }
                 if (consistency.checkLazyUpper()) {
-                        satisfiable = true; 
-                        Utility.logInfo("time for satisfiability checking: " + t.duration()); 
+                        satisfiable = true;
+                        Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
-                        
+
+                // TODO add new upper store preprocessing
+
                 trackingStore.importRDFData(name, datafile);
                 trackingStore.materialise("saturate named individuals", originalMarkProgram);
-                
+
 //              materialiseFullUpper();
-                GapByStore4ID gap = new GapByStore4ID(trackingStore); 
+                GapByStore4ID gap = new GapByStore4ID(trackingStore);
                 trackingStore.materialiseFoldedly(program, gap);
-                predicatesWithGap = gap.getPredicatesWithGap(); 
+                predicatesWithGap = gap.getPredicatesWithGap();
                 gap.clear();
-                
+
                 if (program.getGeneral().isHorn())
                         encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
-                else 
-                        encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore); 
-//                      encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore); 
-//                      encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore); 
-//                      encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore); 
-                
-                program.deleteABoxTurtleFile(); 
+                else
+                        encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
+//                      encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore);
+//                      encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore);
+//                      encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore);
+
+                program.deleteABoxTurtleFile();
 
                 if (!isConsistent())
-                        return false; 
-                
+                        return false;
+
                 consistency.extractBottomFragment();
-                return true; 
+                return true;
         }
         
-        private Boolean satisfiable;
-        private ConsistencyManager consistency = new ConsistencyManager(this); 
-        
-        TrackingRuleEncoder encoder;
-
         @Override
         public boolean isConsistent() {
                 if (satisfiable == null) {
-                        satisfiable = consistency.check();              
+                        satisfiable = consistency.check();
                         Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
-                return satisfiable; 
+                return satisfiable;
         }
-        
-        Timer t = new Timer();
 
         private OWLOntology relevantPart(QueryRecord queryRecord) {
                 AnswerTuples rlAnswer = null, elAnswer = null;
@@ -209,22 +209,29 @@ public class MyQueryReasoner extends QueryReasoner {
                 
                 queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
 
-                // TODO log correct partial answers
-//              Utility.logDebug(toJson("upperBound1", queryRecord));
                 if (!queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery[0])) {
                         queryUpperBound(upperStore, queryRecord, extendedQuery[0], queryRecord.getAnswerVariables());
-//                      Utility.logDebug(toJson("upperBound2", queryRecord));
                 }
                 if (!queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables()) {
                         queryUpperBound(upperStore, queryRecord, extendedQuery[1], queryRecord.getDistinguishedVariables());
-//                      Utility.logDebug(toJson("upperBound3", queryRecord));
                 }
-                        
+
+                Utility.logDebug(toJsonKeyValuePair("upperBound1", queryRecord));
+
+                // TODO check whether it is harmful. In case is not, implement it properly
+                // BEGIN: trying to intersect
+                if (!queryRecord.isBottom() && lazyUpperStore != null) {
+                        queryUpperBound(trackingStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                }
+                // END: trying to intersect
+
                 queryRecord.addProcessingTime(Step.UpperBound, t.duration());
                 if (queryRecord.processed()) {
                         queryRecord.setDifficulty(Step.UpperBound); 
                         return null;
                 }
+
+                // TODO add evaluation on new upper store
                 
                 t.reset();
                 try {
@@ -280,7 +287,7 @@ public class MyQueryReasoner extends QueryReasoner {
 
 //      int counter = 0; 
 
-        private String toJson(String key, Object value) {
+        private String toJsonKeyValuePair(String key, Object value) {
                 HashMap<String, Object> map = new HashMap<>();
                 map.put(key, value);
                 return QueryRecord.GsonCreator.getInstance().toJson(map);