10 files changed, 32 insertions, 28 deletions

diff --git a/src/resources/pagoda.properties b/src/resources/pagoda.properties
index 64de225..0401d64 100644
--- a/src/resources/pagoda.properties
+++ b/src/resources/pagoda.properties
@@ -1,5 +1,5 @@
 debug=true
 useAlwaysSimpleUpperBound=false
-useSkolemUpperBound=true
+useSkolemUpperBound=false
 
 statisticsDir=/home/alessandro/Dropbox/Oxford/PAGOdA/statistics
\ No newline at end of file
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index 2471c80..33f9f03 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -83,21 +83,6 @@ public class MultiStageQueryEngine extends StageQueryEngine {
         return materialise(program, treatment, gap);
     }
 
-    /**
-     * delta-chase with fixed mad term depth
-     */
-    @Override
-    public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) {
-        if(isDisposed()) throw new DisposedException();
-
-        materialise("lower program", dProgram.getLower().toString());
-        Program generalProgram = dProgram.getGeneral();
-        LimitedSkolemisationApplication program =
-                new LimitedSkolemisationApplication(generalProgram, dProgram.getUpperBottomStrategy());
-        Treatment treatment = new Pick4NegativeConceptNaive(this, program);
-        return materialise(program, treatment, gap);
-    }
-
     public int materialise4SpecificQuery(Program generalProgram, QueryRecord record, BottomStrategy upperBottom) {
         if(isDisposed()) throw new DisposedException();
 
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
index ffca55a..65184ee 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
@@ -21,8 +21,6 @@ public abstract class StageQueryEngine extends BasicQueryEngine {
 
         public abstract int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap);
 
-        public abstract int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap);
-
         public boolean isValid() {
                 if (!checkValidity) return true; 
                 if (validMaterialisation != null) return validMaterialisation; 
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 5878a57..291af27 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -188,6 +188,10 @@ public class QueryRecord extends Disposable {
         return new AnswerTuplesImp(answerVariables[0], gapAnswerTuples);
     }
 
+    public int getGapAnswersCount() {
+        return gapAnswerTuples.size();
+    }
+
     public String toString() {
         if(isDisposed()) throw new DisposedException();
 
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java b/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
index a567699..01336ba 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
+++ b/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
@@ -88,10 +88,20 @@ public class QueryGraph {
                 Visitor visitor = new Visitor(factory, assignment);
                 Set<OWLAxiom> axioms = getPropertyAssertions(assignment);
                 for(Map.Entry<Term, Set<OWLClassExpression>> entry : concepts.map.entrySet()) {
-                        if(existVars.contains(entry.getKey())) continue;
-                        sub = factory.getOWLNamedIndividual(IRI.create(getIndividual(entry.getKey(), assignment).getIRI()));
-                        for(OWLClassExpression clsExp : entry.getValue()) {
-                                axioms.add(factory.getOWLClassAssertionAxiom(clsExp.accept(visitor), sub));
+                        // TODO check correctness!!!
+                        if(existVars.contains(entry.getKey())) {
+                                OWLClassExpression conjunction =
+                                                factory.getOWLObjectIntersectionOf(factory.getOWLThing());
+                                for(OWLClassExpression owlClassExpression : entry.getValue()) {
+                                        conjunction = factory.getOWLObjectIntersectionOf(conjunction, owlClassExpression.accept(visitor));
+                                }
+                                axioms.add(factory.getOWLSubClassOfAxiom(conjunction, factory.getOWLNothing()));
+                        }
+                        else {
+                                sub = factory.getOWLNamedIndividual(IRI.create(getIndividual(entry.getKey(), assignment).getIRI()));
+                                for(OWLClassExpression clsExp : entry.getValue()) {
+                                        axioms.add(factory.getOWLClassAssertionAxiom(clsExp.accept(visitor), sub));
+                                }
                         }
                 }
                 return axioms;
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 93fbc98..0b02e5a 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -189,12 +189,18 @@ class MyQueryReasoner extends QueryReasoner {
             return;
 
         OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
-//        queryRecord.saveRelevantOntology("./fragment_query" + queryRecord.getQueryID() + ".owl");
+        queryRecord.saveRelevantOntology("/home/alessandro/Desktop/test-relevant-ontology.owl");
 
+//        int gapAnswersCount = queryRecord.getGapAnswersCount();
         if(properties.getUseSkolemUpperBound() &&
                 querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
             return;
 
+//        // TODO extract from the previous relevant ontology
+//        // TODO implement details or remove it
+//        if(queryRecord.getGapAnswersCount() < gapAnswersCount)
+//            extractRelevantOntologySubset(queryRecord); // takes the relevant ontology from the record
+
         Timer t = new Timer();
         Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
         summarisedChecker.check(queryRecord.getGapAnswers());
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 3a057ec..e8daa3b 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -206,7 +206,7 @@ public abstract class QueryReasoner extends Disposable {
                    if you call twice, you will end up with a json file with multiple roots */
         if(answerWriter != null) gson.toJson(queryRecords, answerWriter);
 //              queryRecords.stream().forEach(record -> Utility.logDebug(gson.toJson(record)));
-        queryRecords.stream().forEach(record -> record.dispose());
+        queryRecords.stream().forEach(QueryRecord::dispose);
     }
 
     @Override
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 35db0f2..9cfc773 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -101,6 +101,7 @@ public class HermitChecker extends Checker {
 
 //              for (OWLAxiom axiom: toCheckAxioms)     System.out.println(axiom.toString());
 
+//              Utility.logInfo(toCheckAxioms);
                 if(hermit.isEntailed(toCheckAxioms)) {
                         Utility.logDebug("@TIME to check one tuple: " + t.duration());
                         return true;
diff --git a/src/uk/ac/ox/cs/pagoda/rules/Program.java b/src/uk/ac/ox/cs/pagoda/rules/Program.java
index afc32d4..85000e3 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -119,7 +119,7 @@ protected PredicateDependency dependencyGraph;
                 } catch(IOException e) {
                         e.printStackTrace();
                 }
-                Utility.logDebug("The rules are saved in " + getOutputPath() + ".");
+                Utility.logInfo("The rules are saved in " + getOutputPath() + ".");
         }
 
         @Override
diff --git a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
index e501821..4991d0d 100644
--- a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
+++ b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
@@ -43,14 +43,14 @@ public class PagodaProperties {
                                 defaultUseAlwaysSimpleUpperBound =
                                                 Boolean.parseBoolean(config.getProperty("useAlwaysSimpleUpperBound"));
                                 if(defaultUseAlwaysSimpleUpperBound)
-                                        logger.info("By default the simple upper bound is always used");
+                                        logger.debug("By default the simple upper bound is always used");
                         }
                         if(config.containsKey("useSkolemUpperBound")) {
                                 defaultUseSkolemUpperBound = Boolean.parseBoolean(config.getProperty("useSkolemUpperBound"));
                                 if(defaultUseSkolemUpperBound)
-                                        logger.info("By default the Skolem upper bound is enabled");
+                                        logger.debug("By default the Skolem upper bound is enabled");
                                 else
-                                        logger.info("By default the Skolem upper bound is disabled");
+                                        logger.debug("By default the Skolem upper bound is disabled");
                         }
 
                 } catch(IOException e) {