fixed some bugs in windows server

10 files changed, 122 insertions, 43 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index a222645..7d3e40c 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -43,7 +43,15 @@ public class ConsistencyManager {
         
         boolean checkRLLowerBound() {
                 fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0);
-                fullQueryRecord.updateLowerBoundAnswers(m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
+                AnswerTuples iter = null; 
+                
+                try {
+                        iter = m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
+                        fullQueryRecord.updateLowerBoundAnswers(iter);
+                } finally {
+                        iter.dispose();
+                }
+                
                 if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
                         Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple()); 
                         return unsatisfiability(t.duration());
@@ -81,8 +89,15 @@ public class ConsistencyManager {
 //              if (!checkRLLowerBound()) return false; 
 //              if (!checkELLowerBound()) return false;  
 //              if (checkLazyUpper()) return true; 
+                AnswerTuples iter = null; 
+                
+                try {
+                        iter = m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()); 
+                        fullQueryRecord.updateUpperBoundAnswers(iter);
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
                 
-                fullQueryRecord.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
                 if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
                         return satisfiability(t.duration()); 
                 
@@ -101,7 +116,7 @@ public class ConsistencyManager {
                 for (QueryRecord r: getQueryRecords()) {
                         // TODO to be removed ... 
 //                      r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl");
-                        checker = new HermitSummaryFilter(r); // m_reasoner.factory.getSummarisedReasoner(r);
+                        checker = new HermitSummaryFilter(r, true); // m_reasoner.factory.getSummarisedReasoner(r);
                         satisfiability = checker.isConsistent(); 
                         checker.dispose();
                         if (!satisfiability) return unsatisfiability(t.duration()); 
@@ -143,8 +158,15 @@ public class ConsistencyManager {
                         QueryRecord[] tempQueryRecords = new QueryRecord[number - 1];
                         QueryRecord record; 
                         for (int i = 0; i < number - 1; ++i) {
-                                tempQueryRecords[i] = record = m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1); 
-                                record.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables())); 
+                                tempQueryRecords[i] = record = m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1);
+                                AnswerTuples iter = null; 
+                                try {
+                                        iter = m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables());
+                                        record.updateUpperBoundAnswers(iter); 
+                                } finally {
+                                        if (iter != null) iter.dispose();
+                                        iter = null; 
+                                }
                         }
                         
                         int bottomNumber = 0; 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
index 67dc4fc..9c335f3 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager2.java
@@ -3,6 +3,7 @@ package uk.ac.ox.cs.pagoda.reasoner;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
 import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
@@ -32,8 +33,15 @@ public class ConsistencyManager2 extends ConsistencyManager {
 //              if (!checkRLLowerBound()) return false; 
 //              if (!checkELLowerBound()) return false;  
                 if (checkLazyUpper()) return true; 
+                AnswerTuples iter = null; 
+                
+                try {
+                        iter = m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
+                        fullQueryRecord.updateUpperBoundAnswers(iter);
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
                 
-                fullQueryRecord.updateUpperBoundAnswers(m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
                 if (fullQueryRecord.getNoOfCompleteAnswers() == 0)
                         return satisfiability(t.duration());
                 
@@ -43,7 +51,7 @@ public class ConsistencyManager2 extends ConsistencyManager {
                         e.printStackTrace();
                 }
                 
-                Checker checker = new HermitSummaryFilter(fullQueryRecord);  // m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
+                Checker checker = new HermitSummaryFilter(fullQueryRecord, true);  // m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
 //              fullQueryRecord.saveRelevantOntology("fragment_bottom.owl");
                 boolean satisfiable = checker.isConsistent(); 
                 checker.dispose();
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
index 4ebe5f2..ab57ccf 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -54,7 +54,7 @@ public class ELHOQueryReasoner extends QueryReasoner {
 
         @Override
         public void loadOntology(OWLOntology ontology) {
-                program = new LowerDatalogProgram(!forSemFacet); 
+                program = new LowerDatalogProgram(properties.getToClassify()); 
                 program.load(ontology, new UnaryBottom());
                 program.transform();
                 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 62d238b..0d24a02 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -113,7 +113,7 @@ public class ELHOUQueryReasoner extends QueryReasoner {
                 }                       
 
                 OWLOntology ontology = o; 
-                program = new DatalogProgram(ontology, !forSemFacet); 
+                program = new DatalogProgram(ontology, properties.getToClassify()); 
                 
                 importData(program.getAdditionalDataFile());
                 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
index ba6a4d4..447a92d 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
@@ -7,6 +7,7 @@ import org.semanticweb.owlapi.model.OWLOntology;
 import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
 import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom;
 import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
@@ -47,7 +48,13 @@ public class IterativeRefinement {
                                         return m_record.getRelevantOntology(); 
                                 }
                                 
-                                update = m_record.updateUpperBoundAnswers(tEngine.evaluate(m_record.getQueryText()));
+                                AnswerTuples ans = null; 
+                                try {
+                                        ans = tEngine.evaluate(m_record.getQueryText());
+                                        update = m_record.updateUpperBoundAnswers(ans);
+                                } finally {
+                                        if (ans != null) ans.dispose();
+                                }                               
                         } finally {
                                 tEngine.dispose();
                         }
@@ -78,7 +85,13 @@ public class IterativeRefinement {
                                         return m_record.getRelevantOntology(); 
                                 }
                                 
-                                update = m_record.updateUpperBoundAnswers(tEngine.evaluate(m_record.getQueryText()));
+                                AnswerTuples ans = null; 
+                                try {
+                                        ans = tEngine.evaluate(m_record.getQueryText()); 
+                                        update = m_record.updateUpperBoundAnswers(ans);
+                                } finally {
+                                        if (ans != null) ans.dispose();
+                                }
                         } finally {
                                 tEngine.dispose();
                         }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 2c2feae..875dcdd 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -85,7 +85,7 @@ public class MyQueryReasoner extends QueryReasoner {
                 }                       
 
                 ontology = o; 
-                program = new DatalogProgram(ontology, !forSemFacet);
+                program = new DatalogProgram(ontology, properties.getToClassify());
 //              program.getLower().save();
 //              program.getUpper().save();
 //              program.getGeneral().save();
@@ -275,11 +275,10 @@ public class MyQueryReasoner extends QueryReasoner {
                         rlAnswer = upperStore.evaluate(queryText, answerVariables);
                         Utility.logDebug(t.duration());
                         queryRecord.updateUpperBoundAnswers(rlAnswer); 
-                        rlAnswer.dispose();
                 } finally {
                         if (rlAnswer != null) rlAnswer.dispose();
+                        rlAnswer = null;
                 }
-                rlAnswer = null;
         }
 
         @Override
@@ -296,11 +295,11 @@ public class MyQueryReasoner extends QueryReasoner {
 //              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl"); 
                 
                 Timer t = new Timer(); 
-                Checker summarisedChecker = new HermitSummaryFilter(queryRecord); 
+                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 (!forSemFacet || validNumber == 0) { 
+                if (validNumber == 0) { 
                         queryRecord.markAsProcessed(); 
                         Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
                 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 0c009a2..a484444 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -14,23 +14,41 @@ import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.QueryManager;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.util.Properties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
 public abstract class QueryReasoner {
         
-        protected boolean forSemFacet = false;
-        
+//      protected boolean forSemFacet = false;
+        Properties properties; 
+
         public static enum Type { Full, RLU, ELHOU };  
         
-        public static QueryReasoner getInstanceForSemFacet(OWLOntology o) {
-                QueryReasoner reasoner = getInstance(Type.Full, o, true, true); 
-                reasoner.forSemFacet = true;            
-                return reasoner; 
+        public static QueryReasoner getInstance(Properties p) {
+                OWLOntology ontology = OWLHelper.loadOntology(p.getOntologyPath());
+                QueryReasoner pagoda = getInstance(ontology, p);
+                pagoda.properties = p; 
+                pagoda.loadOntology(ontology);
+                pagoda.importData(p.getDataPath());
+                if (pagoda.preprocess()) {
+                        System.out.println("The ontology is consistent!");
+                        return pagoda; 
+                }
+                else {
+                        System.out.println("The ontology is inconsistent!");
+                        pagoda.dispose();
+                        return null;
+                }
         }
         
-        
         public static QueryReasoner getInstance(OWLOntology o) {
+                QueryReasoner pagoda = getInstance(Type.Full, o, true, true);
+                pagoda.properties = new Properties(); 
+                return pagoda; 
+        }
+        
+        private static QueryReasoner getInstance(OWLOntology o, Properties p) {
                 return getInstance(Type.Full, o, true, true); 
         }
         
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 6f5d363..97925fc 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -43,6 +43,7 @@ public class HermitChecker implements Checker {
         protected OWLOntology ontology;
         protected QueryRecord record; 
         protected QueryGraph qGraph = null; 
+        boolean toCheck = true;
         
         public HermitChecker(Checker checker) {
                 if (checker instanceof HermitChecker) {
@@ -58,12 +59,13 @@ public class HermitChecker implements Checker {
                 hermit = new Reasoner(ontology);
         }
         
-        public HermitChecker(OWLOntology ontology, QueryRecord record) {
+        public HermitChecker(OWLOntology ontology, QueryRecord record, boolean toCheck) {
                 this.ontology = ontology;
                 queryText = record.getQueryText(); 
                 answerVariable = record.getVariables();
                 queryClause = record.getClause(); 
 //              this.record = record;  
+                this.toCheck = toCheck; 
         }
         
         public HermitChecker(OWLOntology ontology, String queryText) {
@@ -198,6 +200,8 @@ public class HermitChecker implements Checker {
         
         @Override
         public boolean check(AnswerTuple answerTuple) {
+                if (!toCheck) return false; 
+                
                 if (hermit == null) initialiseReasoner();
                 if (tag != 0) return tag == 1; 
                 ++counter; 
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 3207ff1..11588ce 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -47,8 +47,8 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                                 getDataStore().clearRulesAndMakeFactsExplicit();
                         } catch (JRDFStoreException e) {
                                 e.printStackTrace();
-                                gap.clear(); 
                         } finally {
+                                gap.clear(); 
                         }
                 }
                 else 
@@ -149,9 +149,14 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                                         if (instanceTuples != null) instanceTuples.dispose(); 
                                 }
                         }
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                } finally {                     
+                        if (predicateTuples != null) predicateTuples.dispose();
+                        predicateTuples = null; 
+                }
                         
-                        predicateTuples.dispose();
-                        
+                try {
                         predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters);
                         for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
                                 predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0)); 
@@ -172,6 +177,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                         e.printStackTrace();
                 } finally {
                         if (predicateTuples != null) predicateTuples.dispose();
+                        predicateTuples = null;
                 }
                 
                 Utility.redirectCurrentOut(filename);
@@ -184,13 +190,13 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
         
         public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException {
                 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
-                iter.open();
+//              iter.open();
                 return iter; 
         }
 
         public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
                 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
-                iter.open(); 
+//              iter.open(); 
                 return iter; 
         }
         
@@ -201,7 +207,7 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
         public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException {
                 parameters.m_expandEquality = false; 
                 TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 
-                iter.open(); 
+//              iter.open(); 
                 parameters.m_expandEquality = true; 
                 return iter;
         }
@@ -346,19 +352,22 @@ public class BasicQueryEngine extends RDFoxQueryEngine {
                         for (int[] t: collection) 
                                 store.addTriplesByResourceIDs(t, ut);
                         
-                        iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
-                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
-                                int[] triple = new int[3];
-                                for (int i = 0; i < 3; ++i)
-                                        triple[i] = iter.getResourceID(i); 
-                                store.addTriplesByResourceIDs(triple, ut);
+                        try {
+                                iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
+                                for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
+                                        int[] triple = new int[3];
+                                        for (int i = 0; i < 3; ++i)
+                                                triple[i] = iter.getResourceID(i); 
+                                        store.addTriplesByResourceIDs(triple, ut);
+                                }
+                        } finally {
+                                if (iter != null) iter.dispose();
+                                iter = null; 
                         }
                         store.applyReasoning(true);
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                } finally {
-                        if (iter != null) iter.dispose();
-                }
+                } 
                 Utility.logInfo("Time for deletion: " + timer.duration()); 
         }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
index 2280b12..c2065dc 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
@@ -2,12 +2,9 @@ package uk.ac.ox.cs.pagoda.reasoner.light;
 
 import java.util.Collection;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.Map;
 import java.util.Queue;
-import java.util.Set;
-
 import org.semanticweb.HermiT.model.AnnotatedEquality;
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicConcept;
@@ -37,7 +34,7 @@ public class RDFoxTripleManager {
 
         DataStore m_store;
         Dictionary m_dict; 
-        Set<Atom> triplesByTerm = new HashSet<Atom>();
+//      Set<Atom> triplesByTerm = new HashSet<Atom>();
         
         public RDFoxTripleManager(DataStore store, boolean incrementally) {
                 m_store = store;
@@ -63,7 +60,16 @@ public class RDFoxTripleManager {
         }
         
         public void addTripleByID(int[] tuple) {
+//              System.out.println(getRawTerm(tuple[0]) + " " + getRawTerm(tuple[1]) + " " + getRawTerm(tuple[2]) + " ."); 
                 try {
+//                      Resource[] rsc = new Resource[3]; 
+//                      m_dict.getResources(tuple, 0, 3, rsc);
+//                      
+//                      GroundTerm[] terms = new GroundTerm[3]; 
+//                      for (int i = 0; i < 3; ++i)
+//                              terms[i] = uk.ac.ox.cs.JRDFox.model.Individual.create(rsc[i].m_lexicalForm); 
+//                      m_store.addTriples(terms, m_incrementally);
+                        
                         m_store.addTriplesByResourceIDs(tuple, m_incrementally);
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();