4 files changed, 105 insertions, 26 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/MinimumCardinalityTest.java b/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
index 71c20c1..19e0b2a 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/MinimumCardinalityTest.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
@@ -6,6 +6,7 @@ import org.testng.Assert;
 import org.testng.annotations.Test;
 import uk.ac.ox.cs.pagoda.query.AnswerTuple;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
 import uk.ac.ox.cs.pagoda.util.TestUtil;
 
@@ -13,7 +14,7 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 
-public class MinimumCardinalityTest {
+public class BugTests {
 
     public static final String NS = "http://example.org/test#%s";
 
@@ -21,8 +22,8 @@ public class MinimumCardinalityTest {
         return IRI.create(String.format(NS, name));
     }
 
-    @Test(groups = {"BugTesters"})
-    public void test() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+    @Test
+    public void minimumCardinalityAxiom() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
 
         /*
          * Build test ontology
@@ -98,4 +99,86 @@ public class MinimumCardinalityTest {
         }
         pagoda.dispose();
     }
+
+    /**
+     * Bug: the relevant ontology is not a subset of the original one.
+     *
+     * @throws OWLOntologyCreationException
+     * @throws IOException
+     * @throws OWLOntologyStorageException
+     */
+    @Test
+    public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+        OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a));    // A(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b));    // A(b)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
+
+        // Axioms
+        // subsetOf(A someValuesFrom(R owl:Thing))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classA,
+                                                       factory.getOWLObjectSomeValuesFrom(roleR,
+                                                                                          factory.getOWLThing())));
+
+        // inverseFunctional(R)
+        manager.addAxiom(ontology,
+                         factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
+
+        // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       classB));
+        /*
+         * Save the ontology
+         * */
+
+//        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 queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+                    "select distinct ?x" +
+                    " where { "
+                    + " ?x rdf:type " + classB +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            System.out.println(queryRecord);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+            }
+        }
+        pagoda.dispose();
+    }
 }
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 31d2eac..0ce3d69 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -25,7 +25,6 @@ public class TestPagodaFLY {
                               .query(Paths.get(ontoDir, "fly/queries/fly.sparql"))
                               .answer(answers)
                               .classify(false)
-                              .hermit(true)
                               .build();
 
         pagoda.run();
@@ -45,7 +44,6 @@ public class TestPagodaFLY {
                               .answer(answers)
 //                              .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
                               .classify(false)
-                              .hermit(true)
                               .build();
 
         pagoda.run();
@@ -57,8 +55,8 @@ public class TestPagodaFLY {
         String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
 
         Pagoda.builder()
-                .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
-//                        .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
+//                .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+                          .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
                 .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
 //                        .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
                 .classify(false)
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
index fdbfc42..c893f96 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
@@ -23,8 +23,6 @@ public class TestPagodaLUBM {
                                                           .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
                                                           .query(Paths.get(ontoDir, "lubm/queries/test.sparql"))
                                                           .answer(answers)
-                                                          .classify(true)
-                                                          .hermit(true)
                                                           .build();
 
                 pagoda.run();
@@ -45,11 +43,9 @@ public class TestPagodaLUBM {
                 Pagoda pagoda = Pagoda.builder()
                                                           .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
                                                           .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
-                                .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia.sparql"))
+                                              .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia.sparql"))
 //                                                        .answer(answers)
-                                .classify(true)
-                                .hermit(true)
-                                .build();
+                                              .build();
 
                 pagoda.run();
 //              CheckAnswers.assertSameAnswers(answers, givenAnswers);
@@ -71,8 +67,6 @@ public class TestPagodaLUBM {
                                                           .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
                                 .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia_all-blanks.sparql"))
 //                                                        .answer(answers)
-                                .classify(true)
-                                .hermit(true)
                                 .build();
 
                 pagoda.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 9fb6cbe..c5b272c 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
@@ -41,8 +41,6 @@ public class TestPagodaUOBM {
                                                           .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
                                                           .query(Paths.get(ontoDir, "uobm/queries/test.sparql"))
                                                           .answer(answers)
-                                                          .classify(true)
-                                                          .hermit(true)
                                                           .build();
 
                 pagoda.run();
@@ -65,8 +63,6 @@ public class TestPagodaUOBM {
                                                           .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
                                                           .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
                                 .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia.sparql"))
-                                .classify(true)
-                                .hermit(true)
                                 .build();
 
                 pagoda.run();
@@ -85,22 +81,30 @@ public class TestPagodaUOBM {
                           .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
                           .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
                           .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia_all-blanks.sparql"))
-                          .classify(true)
-                          .hermit(true)
+                          .build()
+                          .run();
+        }
+
+        @Test(groups = {"justExecute", "heavy", "nonOriginal"})
+        public void justExecute_modifiedUOBM() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "uobm_modified/univ-bench-dl-modified.owl"))
+                          .data(Paths.get(ontoDir, "uobm_modified/data/uobm1.ttl"))
+                          .query(Paths.get(ontoDir, "uobm_modified/queries/additional_queries.sparql"))
                           .build()
                           .run();
         }
 
         @Test(groups = {"justExecute"})
-        public void justExecute_existentialQueries() throws IOException {
+        public void justExecute_additionalQueries() throws IOException {
                 String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
 
                 Pagoda.builder()
-                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl-modified.owl"))
+                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
                           .data(Paths.get(ontoDir, "uobm/data/uobm1.ttl"))
-                          .query(Paths.get(ontoDir, "uobm/queries/existential_queries.sparql"))
-                          .classify(true)
-                          .hermit(true)
+                          .query(Paths.get(ontoDir, "uobm/queries/additional_queries.sparql"))
                           .build()
                           .run();
         }