Small changes.

9 files changed, 41 insertions, 47 deletions

diff --git a/pom.xml b/pom.xml
index 3b9a94a..3f1c821 100644
--- a/pom.xml
+++ b/pom.xml
@@ -44,6 +44,15 @@
                                                 <descriptorRef>jar-with-dependencies</descriptorRef>
                                         </descriptorRefs>
                                 </configuration>
+                                <executions>
+                                        <execution>
+                                                <id>make-assembly</id> <!-- this is used for inheritance merges -->
+                                                <phase>package</phase> <!-- bind to the packaging phase -->
+                                                <goals>
+                                                        <goal>single</goal>
+                                                </goals>
+                                        </execution>
+                                </executions>
                         </plugin>
                 </plugins>
         </build>
diff --git a/src/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java b/src/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java
index 81b62f0..4b3c057 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java
+++ b/src/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java
@@ -7,12 +7,12 @@ public interface KnowledgeBase {
 
         void load(OWLOntology ontology, BottomStrategy botStrategy); 
 
-        public void transform();
+        void transform();
         
-        public void save();
+        void save();
         
-        public String getOutputPath();
+        String getOutputPath();
         
-        public String getDirectory(); 
+        String getDirectory();
         
 }
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java b/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
index 307fa33..e7f1c96 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
+++ b/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
@@ -1,22 +1,13 @@
  package uk.ac.ox.cs.pagoda.endomorph;
 
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.Map;
-import java.util.Queue;
-import java.util.Set;
+ import uk.ac.ox.cs.pagoda.summary.Edge;
+ import uk.ac.ox.cs.pagoda.summary.Graph;
+ import uk.ac.ox.cs.pagoda.summary.Node;
+ import uk.ac.ox.cs.pagoda.summary.NodeTuple;
+ import uk.ac.ox.cs.pagoda.util.Timer;
+ import uk.ac.ox.cs.pagoda.util.Utility;
 
-import uk.ac.ox.cs.pagoda.summary.Edge;
-import uk.ac.ox.cs.pagoda.summary.Graph;
-import uk.ac.ox.cs.pagoda.summary.Node;
-import uk.ac.ox.cs.pagoda.summary.NodeTuple;
-import uk.ac.ox.cs.pagoda.util.Timer;
-import uk.ac.ox.cs.pagoda.util.Utility;
+ import java.util.*;
 
 public class DependencyGraph {
 
@@ -82,7 +73,7 @@ public class DependencyGraph {
         private int compareNode(Node o1, Node o2) {
                 int result = o1.getConcepts().size() - o2.getConcepts().size();
                 if (result != 0) return dir(result);
-                Edge[] edge1 = graph.getOutGoingEdges(o1), edge2 = graph.getOutGoingEdges(o2);;
+                Edge[] edge1 = graph.getOutGoingEdges(o1), edge2 = graph.getOutGoingEdges(o2);
                 int len1 = edge1 == null ? 0 : edge1.length, len2 = edge2 == null ? 0 : edge2.length; 
                 result = len1 - len2; 
                 if (result != 0) return dir(result);
@@ -124,7 +115,7 @@ public class DependencyGraph {
 //              print(); 
                 
                 topolocialOrder = null;
-                Utility.logInfo("link: " + link);
+                Utility.logDebug("link: " + link);
         }
         
         LinkedList<Clique> topolocialOrder = null; 
diff --git a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java b/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
index 476fbec..530b97f 100644
--- a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
+++ b/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
@@ -1,16 +1,6 @@
 package uk.ac.ox.cs.pagoda.hermit;
 
-import org.semanticweb.HermiT.model.AnnotatedEquality;
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.HermiT.model.Equality;
-import org.semanticweb.HermiT.model.Inequality;
-import org.semanticweb.HermiT.model.NodeIDLessEqualThan;
-import org.semanticweb.HermiT.model.NodeIDsAscendingOrEqual;
-import org.semanticweb.HermiT.model.Term;
-import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.HermiT.model.*;
 import uk.ac.ox.cs.pagoda.MyPrefixes;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 
@@ -47,7 +37,7 @@ public class RuleHelper {
                 boolean lastSpace = true;
                 for (Atom headAtom: clause.getHeadAtoms()) {
                         if ((atomText = getText(headAtom)) == null) continue; 
-                        if (!lastSpace) buf.append(" v "); 
+                        if (!lastSpace) buf.append(" | ");
                         buf.append(atomText);
                         lastSpace = false;
                 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 04b2c65..e5074d5 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -68,9 +68,9 @@ class MyQueryReasoner extends QueryReasoner {
 
         ontology = o;
         program = new DatalogProgram(ontology, properties.getToClassify());
-//              program.getLower().save();
-//              program.getUpper().save();
-//              program.getGeneral().save();
+                program.getLower().save();
+                program.getUpper().save();
+                program.getGeneral().save();
 
         if(!program.getGeneral().isHorn())
             lazyUpperStore = new MultiStageQueryEngine("lazy-upper-bound", true);
diff --git a/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java b/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
index 38fa494..01ab427 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
@@ -1,13 +1,14 @@
 package uk.ac.ox.cs.pagoda.rules;
 
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Set;
-
+import org.apache.commons.io.FilenameUtils;
 import org.semanticweb.HermiT.model.DLClause;
 import org.semanticweb.owlapi.model.OWLOntology;
 import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
 
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Set;
+
 public class GeneralProgram extends Program {
         
         public GeneralProgram(Set<DLClause> relevantClauses, OWLOntology relevantOntology) {
@@ -28,7 +29,7 @@ public class GeneralProgram extends Program {
 
         @Override
         public String getOutputPath() {
-                return getDirectory() + "rules.dlog";
+                return FilenameUtils.concat(getDirectory(), "rules.dlog");
         }
 
 //      @Override
diff --git a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index 199d167..9930009 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.rules;
 
+import org.apache.commons.io.FilenameUtils;
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
@@ -76,7 +77,7 @@ public class LowerDatalogProgram extends ApproxProgram implements IncrementalPro
 
         @Override
         public String getOutputPath() {
-                return getDirectory() + "lower.dlog";
+                return FilenameUtils.concat(getDirectory(), "lower.dlog");
         }
         
 //      @Override
diff --git a/src/uk/ac/ox/cs/pagoda/rules/UpperProgram.java b/src/uk/ac/ox/cs/pagoda/rules/UpperProgram.java
index 46f22e3..52d60b7 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/UpperProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/UpperProgram.java
@@ -1,10 +1,12 @@
 package uk.ac.ox.cs.pagoda.rules;
 
+import org.apache.commons.io.FilenameUtils;
+
 public abstract class UpperProgram extends ApproxProgram {
 
         @Override
         public String getOutputPath() {
-                return getDirectory() + "upper.dlog";
+                return FilenameUtils.concat(getDirectory(), "upper.dlog");
         }
 
 }
diff --git a/test/resources/LightTests.xml b/test/resources/LightTests.xml
index 544833b..bcdc4af 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/LightTests.xml
@@ -12,10 +12,10 @@
         </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"/>-->
         </classes>
     </test>
 </suite>
\ No newline at end of file