Many little changes.

8 files changed, 136 insertions, 41 deletions

diff --git a/test/resources/BugTests.xml b/test/resources/BugTests.xml
index 5782bd4..c7a80ba 100644
--- a/test/resources/BugTests.xml
+++ b/test/resources/BugTests.xml
@@ -4,13 +4,8 @@
 <suite name="BugTests">
 
     <test name="BugTest">
-        <groups>
-            <run>
-                <include name="BugTesters"/>
-            </run>
-        </groups>
         <classes>
-            <class name="uk.ac.ox.cs.pagoda.global_tests.MinimumCardinalityTest"/>
+            <class name="uk.ac.ox.cs.pagoda.global_tests.BugTests"/>
         </classes>
     </test>
 
diff --git a/test/resources/LightTests.xml b/test/resources/MainTests.xml
index bcdc4af..255b68e 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/MainTests.xml
@@ -1,21 +1,25 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd" >
 
-<suite name="LightTests">
-    <test name="light">
+<suite name="MainTests">
+    <test name="main">
         <groups>
             <run>
-                <include name="light"/>
+                <!--<include name="correctness"/>-->
+                <!--<include name="light"/>-->
                 <!--<include name="justExecute"/>-->
-                <exclude name="nonOriginal"/>
+                <!--&lt;!&ndash;<include name="heavy"/>&ndash;&gt;-->
+                <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.TestPagodaFLY"/>
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.SkolemisationTests"/>-->
+            <!--<class name="uk.ac.ox.cs.pagoda.util.SimpleProgressBarTester" />-->
         </classes>
     </test>
 </suite>
\ No newline at end of file
diff --git a/test/resources/SygeniaTests.xml b/test/resources/SygeniaTests.xml
index 01c4eab..4daecf5 100644
--- a/test/resources/SygeniaTests.xml
+++ b/test/resources/SygeniaTests.xml
@@ -11,9 +11,10 @@
         </groups>
 
         <classes>
-            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>-->
+            <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.TestPagodaFLY"/>-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaReactome"/>
         </classes>
     </test>
 
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();
         }
diff --git a/test/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java b/test/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
new file mode 100644
index 0000000..3de30e4
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
@@ -0,0 +1,16 @@
+package uk.ac.ox.cs.pagoda.util;
+
+import org.testng.annotations.Test;
+
+public class SimpleProgressBarTester {
+
+    @Test
+    public void test() throws InterruptedException {
+        SimpleProgressBar simpleProgressBar = new SimpleProgressBar("TestBar", 1000);
+        for(int i = 0; i < 1000; i++) {
+            simpleProgressBar.update(i);
+            Thread.sleep(10);
+        }
+        simpleProgressBar.dispose();
+    }
+}