downgrade owl api and reorganised src files

28 files changed, 11 insertions, 28 deletions

diff --git a/.classpath b/.classpath
index 609d84c..1d0a725 100644
--- a/.classpath
+++ b/.classpath
@@ -13,12 +13,14 @@
                         <attribute name="maven.pomderived" value="true"/>
                 </attributes>
         </classpathentry>
+        <classpathentry kind="src" path="external"/>
         <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
                 <attributes>
                         <attribute name="maven.pomderived" value="true"/>
                 </attributes>
         </classpathentry>
         <classpathentry kind="lib" path="lib/RDFox/Linux/JRDFox.jar"/>
+        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
         <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
                 <attributes>
                         <attribute name="maven.pomderived" value="true"/>
diff --git a/test/uk/ac/ox/cs/data/AtomicQueryGenerator.java b/external/uk/ac/ox/cs/data/AtomicQueryGenerator.java
index d271e87..d271e87 100644
--- a/test/uk/ac/ox/cs/data/AtomicQueryGenerator.java
+++ b/external/uk/ac/ox/cs/data/AtomicQueryGenerator.java
diff --git a/test/uk/ac/ox/cs/data/Comparator.java b/external/uk/ac/ox/cs/data/Comparator.java
index 5b61a81..5b61a81 100644
--- a/test/uk/ac/ox/cs/data/Comparator.java
+++ b/external/uk/ac/ox/cs/data/Comparator.java
diff --git a/test/uk/ac/ox/cs/data/Fragment.java b/external/uk/ac/ox/cs/data/Fragment.java
index 1038a33..1038a33 100644
--- a/test/uk/ac/ox/cs/data/Fragment.java
+++ b/external/uk/ac/ox/cs/data/Fragment.java
diff --git a/test/uk/ac/ox/cs/data/OntologyStatistics.java b/external/uk/ac/ox/cs/data/OntologyStatistics.java
index de40dda..de40dda 100644
--- a/test/uk/ac/ox/cs/data/OntologyStatistics.java
+++ b/external/uk/ac/ox/cs/data/OntologyStatistics.java
diff --git a/test/uk/ac/ox/cs/data/PrepareQueries4Hydrowl.java b/external/uk/ac/ox/cs/data/PrepareQueries4Hydrowl.java
index 10f1ac2..10f1ac2 100644
--- a/test/uk/ac/ox/cs/data/PrepareQueries4Hydrowl.java
+++ b/external/uk/ac/ox/cs/data/PrepareQueries4Hydrowl.java
diff --git a/test/uk/ac/ox/cs/data/QueryFilter.java b/external/uk/ac/ox/cs/data/QueryFilter.java
index 36837d5..36837d5 100644
--- a/test/uk/ac/ox/cs/data/QueryFilter.java
+++ b/external/uk/ac/ox/cs/data/QueryFilter.java
diff --git a/test/uk/ac/ox/cs/data/RemoveDataPropertyRange.java b/external/uk/ac/ox/cs/data/RemoveDataPropertyRange.java
index acaa91b..acaa91b 100644
--- a/test/uk/ac/ox/cs/data/RemoveDataPropertyRange.java
+++ b/external/uk/ac/ox/cs/data/RemoveDataPropertyRange.java
diff --git a/test/uk/ac/ox/cs/data/RemoveImportInTurtle.java b/external/uk/ac/ox/cs/data/RemoveImportInTurtle.java
index 2c0fb00..2c0fb00 100644
--- a/test/uk/ac/ox/cs/data/RemoveImportInTurtle.java
+++ b/external/uk/ac/ox/cs/data/RemoveImportInTurtle.java
diff --git a/test/uk/ac/ox/cs/data/WriteIntoTurtle.java b/external/uk/ac/ox/cs/data/WriteIntoTurtle.java
index b17e035..b17e035 100644
--- a/test/uk/ac/ox/cs/data/WriteIntoTurtle.java
+++ b/external/uk/ac/ox/cs/data/WriteIntoTurtle.java
diff --git a/test/uk/ac/ox/cs/data/WriteToNTriple.java b/external/uk/ac/ox/cs/data/WriteToNTriple.java
index 27e69b9..27e69b9 100644
--- a/test/uk/ac/ox/cs/data/WriteToNTriple.java
+++ b/external/uk/ac/ox/cs/data/WriteToNTriple.java
diff --git a/test/uk/ac/ox/cs/data/datatype/DataPropertyEliminator.java b/external/uk/ac/ox/cs/data/datatype/DataPropertyEliminator.java
index 95765f3..95765f3 100644
--- a/test/uk/ac/ox/cs/data/datatype/DataPropertyEliminator.java
+++ b/external/uk/ac/ox/cs/data/datatype/DataPropertyEliminator.java
diff --git a/test/uk/ac/ox/cs/data/datatype/DataToObject.java b/external/uk/ac/ox/cs/data/datatype/DataToObject.java
index 90794fd..90794fd 100644
--- a/test/uk/ac/ox/cs/data/datatype/DataToObject.java
+++ b/external/uk/ac/ox/cs/data/datatype/DataToObject.java
diff --git a/test/uk/ac/ox/cs/data/dbpedia/DataFilter.java b/external/uk/ac/ox/cs/data/dbpedia/DataFilter.java
index dc2f3e0..dc2f3e0 100644
--- a/test/uk/ac/ox/cs/data/dbpedia/DataFilter.java
+++ b/external/uk/ac/ox/cs/data/dbpedia/DataFilter.java
diff --git a/test/uk/ac/ox/cs/data/dbpedia/DataFilterRDFHandler.java b/external/uk/ac/ox/cs/data/dbpedia/DataFilterRDFHandler.java
index 6dbac91..6dbac91 100644
--- a/test/uk/ac/ox/cs/data/dbpedia/DataFilterRDFHandler.java
+++ b/external/uk/ac/ox/cs/data/dbpedia/DataFilterRDFHandler.java
diff --git a/test/uk/ac/ox/cs/data/dbpedia/Normaliser.java b/external/uk/ac/ox/cs/data/dbpedia/Normaliser.java
index e025604..e025604 100644
--- a/test/uk/ac/ox/cs/data/dbpedia/Normaliser.java
+++ b/external/uk/ac/ox/cs/data/dbpedia/Normaliser.java
diff --git a/test/uk/ac/ox/cs/data/sample/DataSampling.java b/external/uk/ac/ox/cs/data/sample/DataSampling.java
index 1a788e3..1a788e3 100644
--- a/test/uk/ac/ox/cs/data/sample/DataSampling.java
+++ b/external/uk/ac/ox/cs/data/sample/DataSampling.java
diff --git a/test/uk/ac/ox/cs/data/sample/RandomWalk.java b/external/uk/ac/ox/cs/data/sample/RandomWalk.java
index d9f5107..d9f5107 100644
--- a/test/uk/ac/ox/cs/data/sample/RandomWalk.java
+++ b/external/uk/ac/ox/cs/data/sample/RandomWalk.java
diff --git a/test/uk/ac/ox/cs/data/sample/RandomWalkMulti.java b/external/uk/ac/ox/cs/data/sample/RandomWalkMulti.java
index 592f249..592f249 100644
--- a/test/uk/ac/ox/cs/data/sample/RandomWalkMulti.java
+++ b/external/uk/ac/ox/cs/data/sample/RandomWalkMulti.java
diff --git a/test/uk/ac/ox/cs/data/sample/Sampler.java b/external/uk/ac/ox/cs/data/sample/Sampler.java
index 205b29b..205b29b 100644
--- a/test/uk/ac/ox/cs/data/sample/Sampler.java
+++ b/external/uk/ac/ox/cs/data/sample/Sampler.java
diff --git a/pom.xml b/pom.xml
index 391e3e1..fad1545 100644
--- a/pom.xml
+++ b/pom.xml
@@ -75,7 +75,7 @@
                 <dependency>
                         <groupId>net.sourceforge.owlapi</groupId>
                         <artifactId>owlapi-distribution</artifactId>
-                        <version>3.5.0</version>
+                        <version>3.4.10</version>
                 </dependency>
                 <dependency>
                         <groupId>org.openrdf.sesame</groupId>
@@ -93,11 +93,6 @@
                         <version>3.5.2</version>
                 </dependency>
                 <dependency>
-                        <groupId>log4j</groupId>
-                        <artifactId>log4j</artifactId>
-                        <version>1.2.17</version>
-                </dependency>
-                <dependency>
                         <groupId>org.jgrapht</groupId>
                         <artifactId>jgrapht-jdk1.5</artifactId>
                         <version>0.7.3</version>
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 26b0c1a..58d7add 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
+++ b/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
@@ -304,8 +304,8 @@ class Visitor implements OWLClassExpressionVisitorEx<OWLClassExpression> {
 
         @Override
         public OWLClassExpression visit(OWLObjectHasValue ce) {
-                if (ce.getFiller() instanceof VariableIndividual) {
-                        Individual c = (Individual) assignment.get(((VariableIndividual) ce.getFiller()).var); 
+                if (ce.getValue() instanceof VariableIndividual) {
+                        Individual c = (Individual) assignment.get(((VariableIndividual) ce.getValue()).var); 
                         OWLIndividual l = factory.getOWLNamedIndividual(IRI.create(c.getIRI())); 
                         return factory.getOWLObjectHasValue(ce.getProperty(), l); 
                 }
@@ -356,8 +356,8 @@ class Visitor implements OWLClassExpressionVisitorEx<OWLClassExpression> {
 
         @Override
         public OWLClassExpression visit(OWLDataHasValue ce) {
-                if (ce.getFiller() instanceof VariableConstant) {
-                        Constant c = (Constant) assignment.get(((VariableConstant) ce.getFiller()).var); 
+                if (ce.getValue() instanceof VariableConstant) {
+                        Constant c = (Constant) assignment.get(((VariableConstant) ce.getValue()).var); 
                         OWLLiteral l = factory.getOWLLiteral(c.getLexicalForm(), c.getDatatypeURI()); 
                         return factory.getOWLDataHasValue(ce.getProperty(), l); 
                 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java b/src/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java
index 3140fa4..b8035c5 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java
+++ b/src/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java
@@ -111,12 +111,6 @@ class VariableConstant implements OWLLiteral {
         }
 
         @Override
-        public boolean containsEntityInSignature(OWLEntity owlEntity) {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
         public void accept(OWLAnnotationValueVisitor visitor) {
                 // TODO Auto-generated method stub
                 
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java b/src/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java
index 53288e5..1c924b2 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java
+++ b/src/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java
@@ -261,12 +261,6 @@ class VariableIndividual implements OWLNamedIndividual {
         }
 
         @Override
-        public boolean containsEntityInSignature(OWLEntity owlEntity) {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
         public EntityType<?> getEntityType() {
                 // TODO Auto-generated method stub
                 return null;
diff --git a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java b/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
index 6e9446d..f6246f8 100644
--- a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
+++ b/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
@@ -73,7 +73,7 @@ public class HermitQueryReasoner {
                 if (onto.containsEntityInSignature(date)) {
                         for (OWLOntology o: onto.getImportsClosure())
                                 for (OWLAxiom axiom: o.getAxioms())
-                                        if (axiom.containsEntityInSignature(date)) {
+                                        if (axiom.getDatatypesInSignature().contains(date)) {
                                                 System.out.println("The axiom: " + axiom + " is being ingored. ");
                                                 man.removeAxiom(onto, axiom); 
                                         }
diff --git a/test/uk/ac/ox/cs/hermit/HermitTester.java b/test/uk/ac/ox/cs/hermit/HermitTester.java
index 00df658..dc70284 100644
--- a/test/uk/ac/ox/cs/hermit/HermitTester.java
+++ b/test/uk/ac/ox/cs/hermit/HermitTester.java
@@ -27,7 +27,7 @@ public class HermitTester {
                 for (OWLOntology o: onto.getImportsClosure()) {
                         System.out.println(o.containsEntityInSignature(concept));
                         for (OWLAxiom axiom: o.getAxioms())
-                                if (axiom.containsEntityInSignature(concept))
+                                if (axiom.getClassesInSignature().contains(concept))
                                         System.out.println(axiom); 
                 }
                 
diff --git a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
index 6884081..fb38787 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
+++ b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
@@ -13,10 +13,8 @@ import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
-import uk.ac.ox.cs.data.WriteIntoTurtle;
-
 @RunWith(Suite.class)
-@SuiteClasses({ WriteIntoTurtle.class, PagodaUOBM.class
+@SuiteClasses({ PagodaUOBM.class
         })
 public class AllTests {
 
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index a803d63..05a7d70 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -119,7 +119,7 @@ public class PagodaTester {
 //                      args[2] = args[2].replace(".sparql", "_pellet.sparql");
                 }
 
-                Properties properties = new Properties("config/fly.conf"); 
+                Properties properties = new Properties("config/uobm.conf"); 
                 
                 int index = 0; 
                 if (args.length > index) properties.setOntologyPath(args[index++]);