Summarisation before Skolemisation. Added Reactome testcase.

2 files changed, 36 insertions, 19 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 51cb44d..04b2c65 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -43,6 +43,7 @@ class MyQueryReasoner extends QueryReasoner {
     private Collection<String> predicatesWithGap = null;
     private ConsistencyStatus isConsistent;
     private ConsistencyManager consistency = new ConsistencyManager(this);
+    private int relevantOntologiesCounter = 0;
 
     public MyQueryReasoner() {
         setup(true);
@@ -188,17 +189,22 @@ class MyQueryReasoner extends QueryReasoner {
             return;
 
         OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
-//        queryRecord.saveRelevantOntology("/home/alessandro/Desktop/test-relevant-ontology.owl");
+
+        queryRecord.saveRelevantOntology("/home/alessandro/Desktop/test-relevant-ontology-"+relevantOntologiesCounter+".owl");
+        relevantOntologiesCounter++;
+
+        Utility.logInfo("Summarisation...");
+        HermitSummaryFilter summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
+        if(summarisedChecker.check(queryRecord.getGapAnswers()) == 0)
+            return;
 
         if(properties.getUseSkolemUpperBound() &&
-                querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord)) {
+                querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
             return;
-        }
 
+        Utility.logInfo("Full reasoning...");
         Timer t = new Timer();
-        HermitSummaryFilter summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
-        summarisedChecker.check(queryRecord.getGapAnswers());
-//        summarisedChecker.checkByFullReasoner(queryRecord.getGapAnswers());
+        summarisedChecker.checkByFullReasoner(queryRecord.getGapAnswers());
         Utility.logDebug("Total time for full reasoner: " + t.duration());
 
         queryRecord.markAsProcessed();
@@ -360,7 +366,7 @@ class MyQueryReasoner extends QueryReasoner {
     }
 
     private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
-        Utility.logInfo("Evaluating semi-Skolemised relevant upper store...");
+        Utility.logInfo("Evaluating semi-Skolemised relevant upper store");
         t.reset();
 
         DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
@@ -371,7 +377,7 @@ class MyQueryReasoner extends QueryReasoner {
         relevantStore.importDataFromABoxOf(relevantSubset);
         String relevantOriginalMarkProgram = OWLHelper.getOriginalMarkProgram(relevantSubset);
 
-        int queryDependentMaxTermDepth = 10; // TODO make it dynamic
+        int queryDependentMaxTermDepth = 5; // TODO make it dynamic
         relevantStore.materialise("Mark original individuals", relevantOriginalMarkProgram);
         int materialisationTag = relevantStore.materialiseSkolemly(relevantProgram, null,
                                                                    queryDependentMaxTermDepth);
diff --git a/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java b/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
index 95f2cbb..2d2198f 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
+++ b/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
@@ -27,7 +27,9 @@ public class HermitSummaryFilter extends Checker {
         HermitChecker summarisedHermiT = null;
         boolean summarisedConsistency;
         Endomorph endomorphismChecker = null;
-        
+        private HashSet<AnswerTuple> passed;
+        private int counter;
+
         public HermitSummaryFilter(QueryRecord record, boolean toCallHermiT) {
                 m_record = record;
                 HermitChecker hermitChecker = new HermitChecker(record.getRelevantOntology(), record, toCallHermiT);
@@ -115,6 +117,20 @@ public class HermitSummaryFilter extends Checker {
                 return summarisedHermiT.getNoOfCalls() + endomorphismChecker.getNoOfCalls();
         }
 
+        public int checkByFullReasoner(AnswerTuples answers) {
+                if(isDisposed()) throw new DisposedException();
+                if(m_record.isProcessed())
+                        return 0;
+
+                Utility.logDebug("The number of answers to be checked with HermiT: " + passed.size() + "/" + counter);
+                m_record.setDifficulty(Step.FULL_REASONING);
+
+                if(summarisedConsistency)
+                        return endomorphismChecker.check(new AnswerTuplesImp(m_record.getAnswerVariables(), passed));
+                else
+                        return endomorphismChecker.check(answers);
+        }
+
         @Override
         public int check(AnswerTuples answers) {
                 if(isDisposed()) throw new DisposedException();
@@ -125,10 +141,11 @@ public class HermitSummaryFilter extends Checker {
                 initialiseSummarisedReasoner();
 
                 if(summarisedConsistency) {
-                        Set<AnswerTuple> passed = new HashSet<AnswerTuple>(), succ = new HashSet<AnswerTuple>();
+                        passed = new HashSet<AnswerTuple>();
+                        Set<AnswerTuple> succ = new HashSet<AnswerTuple>();
                         Set<AnswerTuple> falsified = new HashSet<AnswerTuple>(), fail = new HashSet<AnswerTuple>();
 
-                        int counter = 0;
+                        counter = 0;
                         AnswerTuple representative;
                         for(AnswerTuple answer; answers.isValid(); answers.moveNext()) {
                                 ++counter;
@@ -158,20 +175,14 @@ public class HermitSummaryFilter extends Checker {
                                 m_record.addProcessingTime(Step.SUMMARISATION, t.duration());
                                 return 0;
                         }
-
-                        Utility.logDebug("The number of answers to be checked with HermiT: " + passed.size() + "/" + counter);
-
-                        m_record.setDifficulty(Step.FULL_REASONING);
                         m_record.addProcessingTime(Step.SUMMARISATION, t.duration());
-
-                        return endomorphismChecker.check(new AnswerTuplesImp(m_record.getAnswerVariables(), passed));
                 }
                 else {
                         m_record.addProcessingTime(Step.SUMMARISATION, t.duration());
 //                      m_record.saveRelevantOntology("fragment.owl");
-                        m_record.setDifficulty(Step.FULL_REASONING);
-                        return endomorphismChecker.check(answers);
                 }
+
+                return 1;
         }
 
         @Override