6 files changed, 55 insertions, 53 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
index 2285b5f..f5a8093 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -34,9 +34,9 @@ class ELHOQueryReasoner extends QueryReasoner {
                 } finally {
                         if (elAnswer != null) elAnswer.dispose();
                 }
-                queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
-                
-                queryRecord.setDifficulty(Step.ELLowerBound);
+                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
+
+                queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
                 queryRecord.markAsProcessed();
         }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index a4fa7c3..34742c8 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -50,7 +50,7 @@ class ELHOUQueryReasoner extends QueryReasoner {
                 } finally {
                         if(rlAnswer != null) rlAnswer.dispose();
                 }
-                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
 
                 String extendedQueryText = queryRecord.getExtendedQueryText().get(0);
                 String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
@@ -66,10 +66,10 @@ class ELHOUQueryReasoner extends QueryReasoner {
                         } finally {
                                 if(rlAnswer != null) rlAnswer.dispose();
                         }
-                        queryRecord.addProcessingTime(Step.UpperBound, t.duration());
+                        queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
 
                         if (queryRecord.processed()) {
-                                queryRecord.setDifficulty(Step.UpperBound);
+                                queryRecord.setDifficulty(Step.UPPER_BOUND);
                                 return;
                         }
                 }
@@ -83,7 +83,7 @@ class ELHOUQueryReasoner extends QueryReasoner {
                 } finally {
                         if (elAnswer != null) elAnswer.dispose();
                 }
-                queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
+                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
         }
 
         @Override
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 6adbd37..2a49e24 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -198,26 +198,31 @@ class MyQueryReasoner extends QueryReasoner {
                 return satisfiable == SatisfiabilityStatus.SATISFIABLE;
         }
 
-        // TODO why the following???
-        private void queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord, Tuple<String> extendedQuery) {
+        /**
+         * It deals with blanks nodes differently from variables
+         * according to SPARQL semantics for OWL2 Entailment Regime.
+         * <p>
+         * In particular variables are matched only against named individuals,
+         * and blank nodes against named and anonymous individuals.
+         */
+        private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
+                                                                        Tuple<String> extendedQuery, Step step) {
+
+                queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+
+                if(queryRecord.hasNonAnsDistinguishedVariables()) {
+                        if(!queryRecord.processed())
+                                queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
+                        if(!queryRecord.processed())
+                                queryUpperBound(upperStore, queryRecord, extendedQuery.get(1), queryRecord.getDistinguishedVariables());
+                }
 
-//              Utility.logInfo("1");
-//              queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-//
-//              boolean conditionA = !queryRecord.processed() && !queryRecord.getQueryText().equals(extendedQuery.get(0));
-//              boolean conditionB = !queryRecord.processed() && queryRecord.hasNonAnsDistinguishedVariables();
-//
-//              if(conditionA ^ conditionB)
-//                      throw new Error("It really happened! I thought it was impossible");
-//
-//              if (conditionA) {
-//                      Utility.logInfo("2");
-                queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
-//              }
-//              if (conditionB) {
-//                      Utility.logInfo("3");
-//                      queryUpperBound(upperStore, queryRecord, extendedQuery.get(1), queryRecord.getDistinguishedVariables());
-//              }
+                queryRecord.addProcessingTime(step, t.duration());
+                if(queryRecord.processed()) {
+                        queryRecord.setDifficulty(step);
+                        return true;
+                }
+                return false;
         }
 
         /**
@@ -234,7 +239,7 @@ class MyQueryReasoner extends QueryReasoner {
                 } finally {
                         if (rlAnswer != null) rlAnswer.dispose();
                 }
-                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
 
                 t.reset();
 
@@ -249,17 +254,14 @@ class MyQueryReasoner extends QueryReasoner {
 //                      queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
 //              else {
 
-                queryUpperStore(trackingStore, queryRecord, extendedQueryTexts);
-                if(!(queryRecord.isBottom() || (lazyUpperStore == null && limitedSkolemUpperStore == null))) {
-                        if(lazyUpperStore != null) queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts);
-                        if(limitedSkolemUpperStore != null)
-                                queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts);
-                }
-
-                queryRecord.addProcessingTime(Step.UpperBound, t.duration());
-                if (queryRecord.processed()) {
-                        queryRecord.setDifficulty(Step.UpperBound);
+                if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
                         return null;
+
+                if(!queryRecord.isBottom()) {
+                        if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
+                                return null;
+                        if(limitedSkolemUpperStore != null && queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts, Step.L_SKOLEM_UPPER_BOUND))
+                                return null;
                 }
 
                 t.reset();
@@ -271,10 +273,10 @@ class MyQueryReasoner extends QueryReasoner {
                 } finally {
                         if (elAnswer != null) elAnswer.dispose();
                 }
-                queryRecord.addProcessingTime(Step.ELLowerBound, t.duration());
+                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
 
                 if (queryRecord.processed()) {
-                        queryRecord.setDifficulty(Step.ELLowerBound);
+                        queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
                         return null;
                 }
 
@@ -291,7 +293,7 @@ class MyQueryReasoner extends QueryReasoner {
 //              }
 //              else {
                 knowledgeBase = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
-                        queryRecord.addProcessingTime(Step.Fragment, t.duration());
+                queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
 //              }
 
                 if(knowledgeBase.isEmpty() || queryRecord.isBottom())
@@ -307,10 +309,10 @@ class MyQueryReasoner extends QueryReasoner {
 //                      knowledgebase = iterativeRefinement.extractWithFullABox(importedData.toString(), program.getUpperBottomStrategy());
 //              }
 //
-//              queryRecord.addProcessingTime(Step.FragmentRefinement, t.duration());
+//              queryRecord.addProcessingTime(Step.FRAGMENT_REFINEMENT, t.duration());
 //
 //              if (knowledgebase == null)
-//                      queryRecord.setDifficulty(Step.FragmentRefinement);
+//                      queryRecord.setDifficulty(Step.FRAGMENT_REFINEMENT);
 
                 return knowledgeBase;
         }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index d4f4596..64945e8 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -6,7 +6,7 @@ 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.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 
@@ -26,11 +26,11 @@ public abstract class QueryReasoner {
         public boolean fullReasoner = this instanceof MyQueryReasoner;
         protected StringBuilder importedData = new StringBuilder();
 //      protected boolean forSemFacet = false;
-        Properties properties;
+PagodaProperties properties;
         BufferedWriter answerWriter = null;
         private QueryManager m_queryManager = new QueryManager();
-        
-        public static QueryReasoner getInstance(Properties p) {
+
+        public static QueryReasoner getInstance(PagodaProperties p) {
                 OWLOntology ontology = OWLHelper.loadOntology(p.getOntologyPath());
                 QueryReasoner pagoda = getInstance(ontology, p);
                 pagoda.properties = p;
@@ -49,11 +49,11 @@ public abstract class QueryReasoner {
 
         public static QueryReasoner getInstance(OWLOntology o) {
                 QueryReasoner pagoda = getInstance(Type.Full, o, DEFAULT_MULTI_STAGES, DEFAULT_EQUALITIES);
-                pagoda.properties = new Properties();
+                pagoda.properties = new PagodaProperties();
                 return pagoda;
         }
 
-        private static QueryReasoner getInstance(OWLOntology o, Properties p) {
+        private static QueryReasoner getInstance(OWLOntology o, PagodaProperties p) {
                 return getInstance(Type.Full, o, DEFAULT_MULTI_STAGES, DEFAULT_EQUALITIES);
         }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
index 60f34c6..bea5bbf 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
@@ -31,8 +31,8 @@ class RLQueryReasoner extends QueryReasoner {
                 } finally {
                         if (rlAnswer != null) rlAnswer.dispose();
                 }
-                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
-                queryRecord.setDifficulty(Step.LowerBound);
+                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
+                queryRecord.setDifficulty(Step.LOWER_BOUND);
                 queryRecord.markAsProcessed();
         }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
index e5564d9..bdef436 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
@@ -41,7 +41,7 @@ class RLUQueryReasoner extends QueryReasoner {
                 } finally {
                         if (ans != null) ans.dispose();
                 }
-                queryRecord.addProcessingTime(Step.LowerBound, t.duration());
+                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
                 
                 ans = null; 
                 t.reset(); 
@@ -52,10 +52,10 @@ class RLUQueryReasoner extends QueryReasoner {
                 } finally {
                         if (ans != null) ans.dispose();
                 }
-                queryRecord.addProcessingTime(Step.UpperBound, t.duration());
+                queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
                 
                 if (queryRecord.processed())
-                        queryRecord.setDifficulty(Step.UpperBound);
+                        queryRecord.setDifficulty(Step.UPPER_BOUND);
         }
         
         @Override