Fixed marking original individuals in the relevant upper store.

7 files changed, 28 insertions, 5 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/uk/ac/ox/cs/pagoda/Pagoda.java
index aeb85a7..f5dce15 100644
--- a/src/uk/ac/ox/cs/pagoda/Pagoda.java
+++ b/src/uk/ac/ox/cs/pagoda/Pagoda.java
@@ -177,6 +177,12 @@ public class Pagoda implements Runnable {
             return this;
         }
 
+        public PagodaBuilder skolem(Boolean isEnabled) {
+            if(instance == null) return null;
+            instance.properties.setUseSkolemUpperBound(isEnabled);
+            return this;
+        }
+
         public Pagoda build() {
             Pagoda builtInstance = instance;
             instance = null;
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index 479905d..2471c80 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -10,6 +10,7 @@ import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.rules.Program;
+import uk.ac.ox.cs.pagoda.rules.approximators.SkolemTermsManager;
 import uk.ac.ox.cs.pagoda.util.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
@@ -216,6 +217,9 @@ public class MultiStageQueryEngine extends StageQueryEngine {
                 Utility.logDebug(name + " store after adding facts for violations: " + (tripleCount =
                         store.getTriplesCount()) + " (" + (tripleCount - oldTripleCount) + " new)");
                 Utility.logDebug("Time to add triples for violations: " + subTimer.duration());
+
+                Utility.logDebug("Number of Skolem individuals: " + SkolemTermsManager.getInstance()
+                                                                                      .getSkolemIndividualsCount());
             }
         } catch(JRDFStoreException e) {
             e.printStackTrace();
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 7f02741..5878a57 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -2,6 +2,7 @@ package uk.ac.ox.cs.pagoda.query;
 
 import com.google.gson.*;
 import com.google.gson.reflect.TypeToken;
+import org.apache.commons.lang.WordUtils;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
@@ -713,7 +714,12 @@ public class QueryRecord extends Disposable {
         FRAGMENT_REFINEMENT,
         SUMMARISATION,
         DEPENDENCY,
-        FULL_REASONING
+        FULL_REASONING;
+
+        @Override
+        public String toString() {
+            return WordUtils.capitalizeFully(super.toString(), new char[]{'_'}).replace("_", "");
+        }
     }
 
     /**
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index e6e508a..e689de6 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -19,7 +19,6 @@ import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
-import uk.ac.ox.cs.pagoda.util.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
 import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
@@ -192,7 +191,7 @@ class MyQueryReasoner extends QueryReasoner {
         OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
 //        queryRecord.saveRelevantOntology("./fragment_query" + queryRecord.getQueryID() + ".owl");
 
-        if(PagodaProperties.getDefaultUseSkolemUpperBound() &&
+        if(properties.getUseSkolemUpperBound() &&
                 querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
             return;
 
@@ -297,7 +296,7 @@ class MyQueryReasoner extends QueryReasoner {
 
         Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
 
-        if(PagodaProperties.getDefaultUseAlwaysSimpleUpperBound() || lazyUpperStore == null) {
+        if(properties.getUseAlwaysSimpleUpperBound() || lazyUpperStore == null) {
             Utility.logDebug("Tracking store");
             if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
                 return true;
@@ -369,8 +368,10 @@ class MyQueryReasoner extends QueryReasoner {
                 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
 
         relevantStore.importDataFromABoxOf(relevantSubset);
+        String relevantOriginalMarkProgram = OWLHelper.getOriginalMarkProgram(relevantSubset);
 
         int queryDependentMaxTermDepth = 5; // TODO make it dynamic
+        relevantStore.materialise("Mark original individuals", relevantOriginalMarkProgram);
         int materialisationTag = relevantStore.materialiseSkolemly(relevantProgram, null,
                                                                    queryDependentMaxTermDepth);
         queryRecord.addProcessingTime(Step.SKOLEM_UPPER_BOUND, t.duration());
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index eab6a1b..3a057ec 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -193,6 +193,7 @@ public abstract class QueryReasoner extends Disposable {
                 if(!record.isProcessed())
                     evaluate(record);
                 Utility.logInfo("Total time to answer this query: " + t.duration());
+                Utility.logInfo("Difficulty of this query: " + record.getDifficulty());
                 if(!fullReasoner && !record.isProcessed()) {
                     Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds.");
                     continue;
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
index 44daf7a..a78aabe 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
@@ -83,7 +83,7 @@ public class SkolemTermsManager {
     /**
      * Get the number of individuals generated by this manager.
      */
-    public int getNumberOfSkolemisedIndividual() {
+    public int getSkolemIndividualsCount() {
         return individualToDepth_map.keySet().size();
     }
 
diff --git a/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java b/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
index 9139a5d..0a5983c 100644
--- a/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
+++ b/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
@@ -46,4 +46,9 @@ public class Tuple<T> implements Iterable<T> {
     public int hashCode() {
         return elements.hashCode() + getClass().hashCode();
     }
+
+    @Override
+    public String toString() {
+        return elements.toString();
+    }
 }