3 files changed, 60 insertions, 30 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index 9b862ce..d179d14 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -1,7 +1,5 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
-import java.util.LinkedList;
-
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicConcept;
 import org.semanticweb.HermiT.model.DLClause;
@@ -9,7 +7,9 @@ import org.semanticweb.HermiT.model.Variable;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
-
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.QueryManager;
@@ -21,9 +21,8 @@ import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
 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;
+
+import java.util.LinkedList;
 
 public class ConsistencyManager {
 
@@ -85,6 +84,23 @@ public class ConsistencyManager {
                 }
                 return false; 
         }
+
+        boolean checkSkolemUpper() {
+                if (m_reasoner.limitedSkolemUpperStore != null) {
+                        AnswerTuples tuples = null;
+                        try {
+                                tuples = m_reasoner.limitedSkolemUpperStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
+                                if (!tuples.isValid()) {
+                                        Utility.logInfo("There are no contradictions derived in the limited-skolem upper bound materialisation.");
+                                        return satisfiability(t.duration());
+                                }
+                        }
+                        finally {
+                                if (tuples != null) tuples.dispose();
+                        }
+                }
+                return false;
+        }
         
         boolean check() {
 //              if (!checkRLLowerBound()) return false; 
@@ -288,5 +304,6 @@ public class ConsistencyManager {
         public QueryRecord[] getQueryRecords() {
                 return botQueryRecords; 
         }
-        
+
+
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 3c0a001..233963e 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -49,7 +49,8 @@ public class MyQueryReasoner extends QueryReasoner {
         private Collection<String> predicatesWithGap = null;
         private Boolean satisfiable;
         private ConsistencyManager consistency = new ConsistencyManager(this);
-        
+        BasicQueryEngine limitedSkolemUpperStore;
+
         public MyQueryReasoner() {
                 setup(true, true);
         }
@@ -102,10 +103,10 @@ public class MyQueryReasoner extends QueryReasoner {
 
                 if (multiStageTag && !program.getGeneral().isHorn()) {
                         lazyUpperStore =  getUpperStore("lazy-upper-bound", true); // new MultiStageQueryEngine("lazy-upper-bound", true); //
+                        // TODO CHECK
+                        limitedSkolemUpperStore =  getUpperStore("limited-skolem-upper-bound", true);
                 }
 
-                // TODO add new upper store creation
-
                 importData(program.getAdditionalDataFile());
 
                 elho_ontology = new ELHOProfile().getFragment(ontology);
@@ -151,7 +152,21 @@ public class MyQueryReasoner extends QueryReasoner {
                         Utility.logInfo("time for satisfiability checking: " + t.duration());
                 }
 
-                // TODO add new upper store preprocessing
+                // TODO check
+                if (limitedSkolemUpperStore != null) {
+                        limitedSkolemUpperStore.importRDFData(name, datafile);
+                        limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
+                        int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
+                        if (tag != 1) {
+                                limitedSkolemUpperStore.dispose();
+                                limitedSkolemUpperStore = null;
+                        }
+                        if (tag == -1) return false;
+                }
+                if (consistency.checkSkolemUpper()) {
+                        satisfiable = true;
+                        Utility.logInfo("time for satisfiability checking: " + t.duration());
+                }
 
                 trackingStore.importRDFData(name, datafile);
                 trackingStore.materialise("saturate named individuals", originalMarkProgram);
@@ -223,6 +238,9 @@ public class MyQueryReasoner extends QueryReasoner {
                 if (!queryRecord.isBottom() && lazyUpperStore != null) {
                         queryUpperBound(trackingStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
                 }
+                if (!queryRecord.isBottom() && limitedSkolemUpperStore != null) {
+                        queryUpperBound(limitedSkolemUpperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+                }
                 // END: trying to intersect
 
                 queryRecord.addProcessingTime(Step.UpperBound, t.duration());
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
index 11588ce..5d2e411 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -1,29 +1,21 @@
 package uk.ac.ox.cs.pagoda.reasoner.light;
 
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-
 import org.semanticweb.HermiT.model.DLClause;
-
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+import uk.ac.ox.cs.JRDFox.store.Parameters;
+import uk.ac.ox.cs.JRDFox.store.TripleStatus;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.rules.Program;
-import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
-import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.*;
 import uk.ac.ox.cs.pagoda.util.Timer;
-import uk.ac.ox.cs.pagoda.util.UFS;
-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.Parameters;
-import uk.ac.ox.cs.JRDFox.store.TripleStatus;
-import uk.ac.ox.cs.JRDFox.store.TupleIterator;
-import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+
+import java.util.*;
 
 public class BasicQueryEngine extends RDFoxQueryEngine {
 
@@ -74,6 +66,10 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                 
                 return 1; 
         }
+
+        public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) {
+                throw new UnsupportedOperationException();
+        }
         
         @Override
         public AnswerTuples evaluate(String queryText) {
@@ -163,8 +159,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                                 instanceTuples = null; 
                                 try {
                                         instanceTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X " + predicate + " ?Z }", prefixes, parameters);
-                                        ;
-                                        long totalCount = 0; 
+                                        long totalCount = 0;
                                         for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext())
                                                 totalCount += instanceTuples.getMultiplicity();
                                         number.add(predicate + " * " + totalCount);