Internalisation: added condition for existential variables (classes HermitChecker and QueryGraph).

Answer dependencies: found bug, trying to solve; excluding dependency analysis solve the problem.

6 files changed, 111 insertions, 31 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java b/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
index e7f1c96..8514808 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
@@ -114,23 +114,23 @@ public class DependencyGraph {
                 
 //              print(); 
                 
-                topolocialOrder = null;
+                topologicalOrder = null;
                 Utility.logDebug("link: " + link);
         }
         
-        LinkedList<Clique> topolocialOrder = null; 
+        LinkedList<Clique> topologicalOrder = null;
 
         public LinkedList<Clique> getTopologicalOrder() {
-                if (topolocialOrder != null) return topolocialOrder;
+                if (topologicalOrder != null) return topologicalOrder;
                 
-                topolocialOrder = new LinkedList<Clique>(); 
+                topologicalOrder = new LinkedList<Clique>();
                 Queue<Clique> toVisit = new LinkedList<Clique>(entrances); 
                 Map<Clique, Integer> toVisitedInComingDegree = new HashMap<Clique, Integer>();
                 
                 int count; 
                 while (!toVisit.isEmpty()) {
                         Clique cu = toVisit.remove();
-                        topolocialOrder.add(cu); 
+                        topologicalOrder.add(cu);
                         if (outGoingEdges.containsKey(cu))
                                 for (Clique cv: outGoingEdges.get(cu)) {
                                         if (toVisitedInComingDegree.containsKey(cv)) {
@@ -144,7 +144,7 @@ public class DependencyGraph {
                                 }
                 }
                 
-                return topolocialOrder; 
+                return topologicalOrder;
         }
 
         private void addNodeTuple(NodeTuple u) {
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java b/src/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java
index 1c853d7..9ca73a1 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java
@@ -34,7 +34,11 @@ public class Endomorph extends Checker {
                 graph = new Graph(record.getRelevantOntology());
                 dGraph = new DependencyGraph(graph); 
         }
-        
+
+    /*
+    * FIXME
+    * The result is unsound. The output is not deterministic.
+    * */
         @Override
         public int check(AnswerTuples answerTuples) {
                 if(isDisposed()) throw new DisposedException();
@@ -57,11 +61,26 @@ public class Endomorph extends Checker {
                 Utility.logInfo("The number of individuals to be checked by Homomorphism checker: " + counter);
 //              CheckPlan plan = new PlainPlan(this.checker, dGraph.cliques);
 //              CheckPlan plan = new OpenEndMultiThreadPlan(this.checker, dGraph);              
-                CheckPlan plan = new OpenEndPlan(fullReasoner, dGraph, m_record);               
-                int answerCounter = plan.check(); 
-                
+
+                CheckPlan plan = new OpenEndPlan(fullReasoner, dGraph, m_record);
+                int answerCounter = plan.check();
+
+
+//        // BEGIN: debugging code
+//        Set<AnswerTuple> validatedAnswers = new HashSet<>();
+//        for (answerTuples.reset(); answerTuples.isValid(); answerTuples.moveNext()) {
+//            if(fullReasoner.check(answerTuples.getTuple())) {
+//                validatedAnswers.add(answerTuples.getTuple());
+//            }
+//        }
+//        m_record.addLowerBoundAnswers(validatedAnswers);
+//
+//              Utility.logDebug("The number of correct answers: " + validatedAnswers.size());
+//              return validatedAnswers.size();
+////         END: debugging code
+
                 Utility.logDebug("The number of correct answers: " + answerCounter);
-                return answerCounter; 
+                return answerCounter;
         }
 
         public OWLOntology getOntology() {
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 116e724..02697b8 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
+++ b/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
@@ -109,8 +109,7 @@ public class QueryGraph {
                 Set<OWLAxiom> axioms = new HashSet<>();
                 for(Map.Entry<Term, Set<OWLClassExpression>> entry : concepts.map.entrySet()) {
                         if(existVars.contains(entry.getKey())) {
-                                OWLClassExpression conjunction =
-                                                factory.getOWLObjectIntersectionOf(factory.getOWLThing());
+                                OWLClassExpression conjunction = factory.getOWLThing();
                                 for(OWLClassExpression owlClassExpression : entry.getValue()) {
                                         conjunction = factory.getOWLObjectIntersectionOf(conjunction, owlClassExpression.accept(visitor));
                                 }
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 9574845..0362fc2 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -106,19 +106,23 @@ public class HermitChecker extends Checker {
         Map<Variable, Term> sub = answerTuple.getAssignment(answerVariable[1]);
         Set<OWLAxiom> toCheckAxioms = qGraph.getAssertions(sub);
 
-//        // TODO complete
-//        Set<OWLAxiom> toCheckExistentialAxioms = qGraph.getExistentialAxioms(sub);
-//
-//        // TODO possibly inefficient
-//        for(OWLAxiom subclassAxiom : toCheckExistentialAxioms) {
-//            Utility.logInfo("Checking consistency of ontology union " + subclassAxiom);
-//            ontology.getOWLOntologyManager().addAxiom(ontology, subclassAxiom);
-//            if(hermit.isConsistent()) {
-//                Utility.logDebug("@TIME to check one tuple: " + t.duration());
-//                return false;
-//            }
-//            ontology.getOWLOntologyManager().removeAxiom(ontology, subclassAxiom);
-//        }
+        // TODO complete
+        Set<OWLAxiom> toCheckExistentialAxioms = qGraph.getExistentialAxioms(sub);
+
+        // TODO possibly inefficient
+        for(OWLAxiom subclassAxiom : toCheckExistentialAxioms) {
+            Utility.logDebug("Checking consistency of ontology union " + subclassAxiom);
+            ontology.getOWLOntologyManager().addAxiom(ontology, subclassAxiom);
+            hermit.flush();
+            if(hermit.isConsistent()) {
+                ontology.getOWLOntologyManager().removeAxiom(ontology, subclassAxiom);
+                hermit.flush();
+                Utility.logDebug("@TIME to check one tuple: " + t.duration());
+                return false;
+            }
+            ontology.getOWLOntologyManager().removeAxiom(ontology, subclassAxiom);
+            hermit.flush();
+        }
 
 
 //              for (OWLAxiom axiom: toCheckAxioms)     System.out.println(axiom.toString());
diff --git a/test/resources/MainTests.xml b/test/resources/MainTests.xml
index cfe6184..db8d977 100644
--- a/test/resources/MainTests.xml
+++ b/test/resources/MainTests.xml
@@ -5,17 +5,17 @@
     <test name="main">
         <groups>
             <run>
-                <!--<include name="correctness"/>-->
+                <include name="correctness"/>
                 <!--<include name="light"/>-->
                 <!--<include name="justExecute"/>-->
                 <!--&lt;!&ndash;<include name="heavy"/>&ndash;&gt;-->
-                <include name="nonOriginal"/>
+                <!--<include name="nonOriginal"/>-->
             </run>
         </groups>
         <classes>
             <!--<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"/>-->
+            <!--<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.SkolemisationTests"/>-->
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java b/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
index 19e0b2a..6e60e24 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
@@ -23,6 +23,64 @@ public class BugTests {
     }
 
     @Test
+    public void minimumCardinalityAxiom2() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+//        OWLClass student = factory.getOWLClass(getEntityIRI("Student"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(student));
+//        OWLClass course = factory.getOWLClass(getEntityIRI("Course"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(course));
+        OWLClass hardWorkingStudent = factory.getOWLClass(getEntityIRI("HardWorkingStudent"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(hardWorkingStudent));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLObjectProperty takesCourse = factory.getOWLObjectProperty(IRI.create(String.format(NS, "takesCourse")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(takesCourse));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, a));   // HardWorkingStudent(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, b));   // HardWorkingStudent(b)
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology,
+                factory.getOWLEquivalentClassesAxiom(hardWorkingStudent,
+                        factory.getOWLObjectMinCardinality(3,
+                                takesCourse)));
+
+//        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if (pagoda.preprocess()) {
+            String query = "select distinct ?x ?y " +
+                    " where { "
+                    + " ?x <" + takesCourse.toStringID() + "> _:z . "
+                    + " ?y <" + takesCourse.toStringID() + "> _:z " +
+                    " }";
+            AnswerTuples answers = pagoda.evaluate(query);
+            int count = 0;
+            for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+            Assert.assertEquals(count, 2);
+        }
+        pagoda.dispose();
+    }
+
+//    @Test
     public void minimumCardinalityAxiom() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
 
         /*
@@ -107,7 +165,7 @@ public class BugTests {
      * @throws IOException
      * @throws OWLOntologyStorageException
      */
-    @Test
+//    @Test
     public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
 
         /*