2 files changed, 34 insertions, 19 deletions

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();