Summarisation before Skolemisation. Added Reactome testcase.

8 files changed, 71 insertions, 26 deletions

diff --git a/src/resources/pagoda.properties b/src/resources/pagoda.properties
index 0401d64..64de225 100644
--- a/src/resources/pagoda.properties
+++ b/src/resources/pagoda.properties
@@ -1,5 +1,5 @@
 debug=true
 useAlwaysSimpleUpperBound=false
-useSkolemUpperBound=false
+useSkolemUpperBound=true
 
 statisticsDir=/home/alessandro/Dropbox/Oxford/PAGOdA/statistics
\ No newline at end of file
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
diff --git a/test/resources/LightTests.xml b/test/resources/LightTests.xml
index 69cb572..544833b 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/LightTests.xml
@@ -7,13 +7,15 @@
             <run>
                 <include name="light"/>
                 <!--<include name="justExecute"/>-->
+                <exclude name="nonOriginal"/>
             </run>
         </groups>
         <classes>
-            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaReactome"/>-->
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>-->
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>-->
             <!--Fly does not terminate: query-5 looks really hard-->
-            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>
         </classes>
     </test>
 </suite>
\ No newline at end of file
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
index caaad35..31d2eac 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -52,7 +52,7 @@ public class TestPagodaFLY {
         CheckAnswers.assertSameAnswers(answers, givenAnswers);
     }
 
-    @Test(groups = {"light", "justExecute"})
+    @Test(groups = {"light", "justExecute", "nonOriginal"})
     public void justExecute_newQueries() throws IOException {
         String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
 
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
new file mode 100644
index 0000000..5c05b94
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
@@ -0,0 +1,26 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+public class TestPagodaReactome {
+
+    @Test(groups = {"light"})
+    public void justExecute() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
+              .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
+              .query(Paths.get(ontoDir, "reactome/test.sparql"))
+              .classify(true)
+              .hermit(true)
+              .build()
+              .run();
+    }
+
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
index d0f0b9a..9fb6cbe 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
@@ -87,7 +87,8 @@ public class TestPagodaUOBM {
                           .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia_all-blanks.sparql"))
                           .classify(true)
                           .hermit(true)
-                          .build().run();
+                          .build()
+                          .run();
         }
 
         @Test(groups = {"justExecute"})
diff --git a/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java b/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
index 97e3a57..71730c3 100644
--- a/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
+++ b/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
@@ -25,8 +25,7 @@ public class CheckAnswers {
 
         Gson gson = QueryRecord.GsonCreator.getInstance();
 
-        Type cqType = new TypeToken<Set<QueryRecord>>() {
-        }.getType();
+        Type cqType = new TypeToken<Set<QueryRecord>>() {}.getType();
         Set<QueryRecord> computedAnswersRecords = gson.fromJson(computedReader, cqType);
         Set<QueryRecord> givenAnswersRecords = gson.fromJson(givenReader, cqType);