Switch from JUnit to TestNG.

Plus minor fixes.

20 files changed, 334 insertions, 285 deletions

diff --git a/test/AllTests.xml b/test/AllTests.xml
new file mode 100644
index 0000000..8ce5fcf
--- /dev/null
+++ b/test/AllTests.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd" >
+
+<suite name="AllTests">
+
+    <test name="PagodaUOBM">
+        <classes>
+            <class name="uk.ac.ox.cs.pagoda.test_units.PagodaUOBM" />
+        </classes>
+    </test>
+
+</suite>
\ No newline at end of file
diff --git a/test/FullEvaluation.xml b/test/FullEvaluation.xml
new file mode 100644
index 0000000..f0f047d
--- /dev/null
+++ b/test/FullEvaluation.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd" >
+
+<suite name="AllTests">
+
+    <test name="LightEvaluation">
+        <classes>
+            <class name="uk.ac.ox.cs.pagoda.test_units.LightEvaluation" />
+        </classes>
+    </test>
+
+    <test name="CostEvaluation">
+        <classes>
+            <class name="uk.ac.ox.cs.pagoda.test_units.CostEvaluation" />
+        </classes>
+    </test>
+
+</suite>
\ No newline at end of file
diff --git a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java b/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
deleted file mode 100644
index fb38787..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/AllTests.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package uk.ac.ox.cs.pagoda.junit;
-
-import java.io.BufferedWriter;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ PagodaUOBM.class
-        })
-public class AllTests {
-
-        public static void copy(String source, String dest) {
-            InputStream is = null;
-            OutputStream os = null;
-            try {
-                is = new FileInputStream(source);
-                os = new FileOutputStream(dest);
-                byte[] buffer = new byte[1024];
-                int length;
-                while ((length = is.read(buffer)) > 0) {
-                    os.write(buffer, 0, length);
-                }
-                is.close();
-                os.close();
-                
-                    BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(source))); 
-                    writer.write("");
-                    writer.close();
-            } catch (FileNotFoundException e) {
-                        e.printStackTrace();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                }       
-            
-//          File src = new File(source);
-//          src.delete(); 
-        }
-        
-}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java b/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
deleted file mode 100644
index 3406ed2..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/FullEvaluation.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package uk.ac.ox.cs.pagoda.junit;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ LightEvaluation.class, 
-        CostEvaluation.class
-        })
-
-public class FullEvaluation {
-        
-}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
deleted file mode 100644
index f8fef0e..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaLUBM.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package uk.ac.ox.cs.pagoda.junit;
-
-import static org.junit.Assert.*;
-
-import org.junit.Test;
-
-import uk.ac.ox.cs.pagoda.tester.PagodaTester;
-import uk.ac.ox.cs.pagoda.tester.Statistics;
-
-public class PagodaLUBM {
-
-        public void test_all(int number) {
-                PagodaTester.main(
-                                PagodaTester.onto_dir + "lubm/univ-bench.owl",
-                                PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
-                                PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql" 
-                ); 
-                
-                AllTests.copy("log4j.log", "output/jair/lubm" + number + ".out"); 
-        }
-        
-        @Test
-        public void test1() { test_all(1); }
-        
-        public void test() {
-                int number = 100;
-                test_all(number); 
-        }
-        
-        public void check(int number) {
-                Statistics stat = new Statistics("output/log4j.log");
-                String diff = stat.diff("results-backup/benchmark/lubm" + number + ".out"); 
-                AllTests.copy("output/log4j.log", "results-backup/current/lubm" + number + ".out"); 
-                if (!diff.isEmpty()) 
-                        fail(diff);
-        }
-        
-}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
deleted file mode 100644
index 5b56c6d..0000000
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaUOBM.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package uk.ac.ox.cs.pagoda.junit;
-
-import org.junit.Test;
-
-import uk.ac.ox.cs.pagoda.tester.PagodaTester;
-import uk.ac.ox.cs.pagoda.tester.Statistics;
-
-public class PagodaUOBM {
-
-        public void test_all(int number ) {
-                PagodaTester.main(
-                                PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
-                                PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
-                                PagodaTester.onto_dir + "uobm/queries/standard_all_pagoda.sparql" 
-//                              PagodaTester.onto_dir + "uobm/queries/standard_group3_all_less.sparql;" + 
-//                              PagodaTester.onto_dir + "uobm/queries/G3.sparql;" +
-//                              PagodaTester.onto_dir + "uobm/queries/last.sparql" 
-                ); 
-                
-                AllTests.copy("log4j.log", "output/jair/newuobm/uobm" + number + ".out"); 
-        }
-        
-        public void test_upToSum(int number) {
-                PagodaTester.main(
-                                PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
-                                PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
-                                PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql" 
-                ); 
-                
-//              AllTests.copy("log4j.log", "output/jair/uobm" + number + ".out"); 
-        }
-        
-        @Test
-        public void test1() {   test_all(1); }
-        
-        public void test500() { test_upToSum(500); }
-        
-        public static void main(String... args) {
-                new PagodaUOBM().test_all(1); 
-        }
-        
-        public void check() {
-                Statistics stat = new Statistics("results-backup/current/uobm1.out"); 
-                String diff = stat.diff("results-backup/benchmark/uobm1.out"); 
-                System.out.println(diff); 
-        }
-        
-}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java
index d23f186..a0f16d4 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java
@@ -1,8 +1,5 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
-import static org.junit.Assert.*;
-
-import org.junit.Test;
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicConcept;
 import org.semanticweb.HermiT.model.AtomicRole;
@@ -13,6 +10,8 @@ import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 
+import org.testng.Assert;
+import org.testng.annotations.Test;
 import uk.ac.ox.cs.pagoda.approx.Clause;
 import uk.ac.ox.cs.pagoda.approx.Clausifier;
 
@@ -39,7 +38,7 @@ public class ClauseTester {
                         emptyOntology = m.createOntology(); 
                 } catch (Exception e) {
                         e.printStackTrace();
-                        fail("failed to create a new ontology"); 
+                        Assert.fail("failed to create a new ontology");
                 }
                 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
                 System.out.println(c.toString()); 
@@ -69,7 +68,7 @@ public class ClauseTester {
                         emptyOntology = m.createOntology(); 
                 } catch (Exception e) {
                         e.printStackTrace();
-                        fail("failed to create a new ontology"); 
+                        Assert.fail("failed to create a new ontology");
                 }
                 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
                 System.out.println(c.toString()); 
@@ -96,7 +95,7 @@ public class ClauseTester {
                         emptyOntology = m.createOntology(); 
                 } catch (Exception e) {
                         e.printStackTrace();
-                        fail("failed to create a new ontology"); 
+                        Assert.fail("failed to create a new ontology");
                 }
                 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
                 System.out.println(c.toString()); 
@@ -126,7 +125,7 @@ public class ClauseTester {
                         emptyOntology = m.createOntology(); 
                 } catch (Exception e) {
                         e.printStackTrace();
-                        fail("failed to create a new ontology"); 
+                        Assert.fail("failed to create a new ontology");
                 }
                 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
                 System.out.println(c.toString()); 
@@ -156,7 +155,7 @@ public class ClauseTester {
                         emptyOntology = m.createOntology(); 
                 } catch (Exception e) {
                         e.printStackTrace();
-                        fail("failed to create a new ontology"); 
+                        Assert.fail("failed to create a new ontology");
                 }
                 Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
                 System.out.println(c.toString()); 
diff --git a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java
index 87b01ed..4e32297 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/CostEvaluation.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java
@@ -1,8 +1,8 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
-import org.junit.Test;
 import org.semanticweb.owlapi.model.OWLOntology;
 
+import org.testng.annotations.Test;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
 import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner.Type;
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java
index 2a148cc..ff616f7 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_PAGOdA.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java
@@ -1,173 +1,180 @@
-package uk.ac.ox.cs.pagoda.junit;
-
-import org.junit.Test;
+package uk.ac.ox.cs.pagoda.test_units;
 
+import org.testng.annotations.Test;
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.IOException;
 
 public class JAIR_PAGOdA {
 
-        public void lubm1() {
+        @Test
+        public void lubm1() throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "lubm/univ-bench.owl",
                                 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
                                 PagodaTester.onto_dir + "lubm/queries/test.sparql" 
                 };
                 PagodaTester.main(args);
-                AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda"); 
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda");
         }
-        
-        
-        public void lubm1_conj() {
+
+        @Test
+        public void lubm1_conj() throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "lubm/univ-bench.owl",
                                 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
-                                PagodaTester.onto_dir + "lubm/queries/test_pellet.sparql" 
+                                PagodaTester.onto_dir + "lubm/queries/test_pellet.sparql"
                 };
                 PagodaTester.main(args);
-                AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj"); 
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj");
         }
-        
-        
-        public void lubm1_rolledUp() {
+
+        @Test
+        public void lubm1_rolledUp() throws IOException {
                 String[] args = new String[] {
                                 "/home/yzhou/backup/20141212/univ-bench-queries.owl",
                                 PagodaTester.onto_dir + "lubm/data/lubm1.ttl",
-                                PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql" 
+                                PagodaTester.onto_dir + "lubm/queries/atomic_lubm.sparql"
                 };
                 PagodaTester.main(args);
-                AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp"); 
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp");
         }
-        
-        
-        public void uobm1() {
+
+        @Test
+        public void uobm1() throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
                                 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
-                                PagodaTester.onto_dir + "uobm/queries/standard.sparql" 
+                                PagodaTester.onto_dir + "uobm/queries/standard.sparql"
                 };
                 PagodaTester.main(args);
-                AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda"); 
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda");
         }
-        
-        
-        public void uobm1_conj() {
+
+        @Test
+        public void uobm1_conj() throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
                                 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
-                                PagodaTester.onto_dir + "uobm/queries/standard_pellet.sparql" 
+                                PagodaTester.onto_dir + "uobm/queries/standard_pellet.sparql"
                 };
                 PagodaTester.main(args);
-                AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj"); 
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj");
         }
 
-        
+        @Test
         public void uobm1_rolledUp() {
                 String[] args = new String[] {
                                 "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
                                 PagodaTester.onto_dir + "uobm/data/uobm1.ttl",
-                                PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql" 
+                                PagodaTester.onto_dir + "uobm/queries/atomic_uobm.sparql"
                 };
                 PagodaTester.main(args);
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp"); 
+//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp");
         }
-        
-        
+
+        @Test
         public void fly() {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
-                                null, 
-                                PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql" 
+                                null,
+                                PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
                 };
                 PagodaTester.main(args);
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda"); 
+//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda");
         }
-        
+
         @Test
-        public void fly_conj() {
+        public void fly_conj() throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
-                                null, 
-                                PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql" 
+                                null,
+                                PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql"
                 };
                 PagodaTester.main(args);
-                AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj"); 
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj");
         }
-        
-        
+
+
         public void fly_rolledUp() {
                 PagodaTester.main(new String[] {
 //                              PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
                                 PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl",
-                                null, 
-                                PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql" 
+                                null,
+                                PagodaTester.onto_dir + "fly/queries/fly_atomic.sparql"
                 });
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp"); 
+//              Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp");
         }
-        
+
         public void dbpedia() {
                 PagodaTester.main(
-                                PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 
+                                PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl",
                                 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
                                 PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql"
                                 , "dbpedia.ans"
                 );
-                
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda"); 
+
+//              Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda");
         }
 
         public void npd() {
                 PagodaTester.main(
-                                PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 
-                                PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 
+                                PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl",
+                                PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl",
                                 PagodaTester.onto_dir + "npd/queries/atomic_ground.sparql"
                                 , "npd.ans"
-                ); 
-                
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda"); 
+                );
+
+//              Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda");
         }
 
-        public void reactome() {
+        public void reactome() throws IOException {
                 PagodaTester.main(
-                                PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", 
+                                PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
                                 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl",
-//                              null, 
+//                              null,
 //                              PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql"
                                 PagodaTester.onto_dir + "bio2rdf/reactome/queries/example.sparql"
                                 , "pagoda_reactome.ans"
                 );
-                AllTests.copy("log4j.log", "output/jair/pagoda_reactome.example");
-                
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p"); 
+                Utility.copyFile("log4j.log", "output/jair/pagoda_reactome.example");
+
+//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p");
         }
-        
-        public void chembl() {
+
+        public void chembl() throws IOException {
                 PagodaTester.main(
-                                PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", 
-                                PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt", 
+                                PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl",
+                                PagodaTester.onto_dir + "bio2rdf/chembl/graph sampling/sample_1.nt",
 //                              PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
                                 PagodaTester.onto_dir + "bio2rdf/chembl/queries/example.sparql"
                                 , "pagoda_chembl.ans"
-                ); 
-                AllTests.copy("log4j.log", "output/jair/pagoda_chembl.example"); 
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p"); 
+                );
+                Utility.copyFile("log4j.log", "output/jair/pagoda_chembl.example");
+//              Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p");
         }
 
-        public void uniprot() {
+        public void uniprot() throws IOException {
                 PagodaTester.main(
-                                PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl", 
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
                                 PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt",
-//                              null, 
+//                              null,
 //                              PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
                                 PagodaTester.onto_dir + "bio2rdf/uniprot/queries/example.sparql"
                                 , "pagoda_uniprot.ans"
-                ); 
-                AllTests.copy("log4j.log", "output/jair/pagoda_uniprot.example"); 
-//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p"); 
+                );
+                Utility.copyFile("log4j.log", "output/jair/pagoda_uniprot.example");
+//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_1p");
         }
 
         
         public static void main(String... args) {
-                new JAIR_PAGOdA().fly();
+                try {
+                        new JAIR_PAGOdA().lubm1();
+                } catch (IOException e) {
+                        e.printStackTrace();
+                }
         }
 
 }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java
index 5e2b1d7..43cb810 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/JAIR_Scalability.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java
@@ -1,30 +1,32 @@
-package uk.ac.ox.cs.pagoda.junit;
-
-import org.junit.Test;
+package uk.ac.ox.cs.pagoda.test_units;
 
+import org.testng.annotations.Test;
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
 import uk.ac.ox.cs.pagoda.util.Properties;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.IOException;
 
 public class JAIR_Scalability {
         
         private static final String date = "_0123"; 
 
         @Test
-        public void reactome() {
+        public void reactome() throws IOException {
                 testReactome(10, false);
         }
         
         @Test
-        public void chembl() {
+        public void chembl() throws IOException {
                 testChEMBL(1, false);
         }
 
         @Test
-        public void uniprot() {
+        public void uniprot() throws IOException {
                 testUniProt(1, false);
         }
 
-        public void testReactome(int percentage, boolean save) {
+        public void testReactome(int percentage, boolean save) throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl", 
                                 PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl", 
@@ -36,10 +38,10 @@ public class JAIR_Scalability {
                 
                 PagodaTester.main(args); 
                 if (save)
-                        AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date); 
+                        Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date);
         }
         
-        public void testChEMBL(int percentage, boolean save) {
+        public void testChEMBL(int percentage, boolean save) throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl", 
                                 PagodaTester.onto_dir + "bio2rdf/chembl/sample_" + percentage + ".nt",
@@ -55,10 +57,10 @@ public class JAIR_Scalability {
                 
                 PagodaTester.main(args);
                 if (save)
-                AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date); 
+                        Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date);
         }
         
-        public void testUniProt(int percentage, boolean save) {
+        public void testUniProt(int percentage, boolean save) throws IOException {
                 String[] args = new String[] {
                                 PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl", 
                                 PagodaTester.onto_dir + "bio2rdf/uniprot/sample_" + percentage + ".nt",
@@ -75,10 +77,10 @@ public class JAIR_Scalability {
                 
                 PagodaTester.main(args); 
                 if (save)
-                        AllTests.copy("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date); 
+                        Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
         }
         
-        public static void main(String... args) {
+        public static void main(String... args) throws IOException {
                 Properties.ShellModeDefault = true; 
                 new JAIR_Scalability().testUniProt(50, false);
         }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java
index 1ddca15..29006de 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/LightEvaluation.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java
@@ -1,59 +1,62 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import org.junit.Test;
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.IOException;
 
 public class LightEvaluation {
 
         @Test
-        public void uobm1() {
+        public void uobm1() throws IOException {
                 int number = 1;
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
                                 PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
                                 PagodaTester.onto_dir + "uobm/queries/standard.sparql"
-                ); 
-                AllTests.copy("log4j.log", "output/jair/uobm1.out"); 
+                );
+                Utility.copyFile("log4j.log", "output/jair/uobm1.out");
         }
         
         @Test
-        public void lubm100() {
+        public void lubm100() throws IOException {
                 int number = 100;
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "lubm/univ-bench.owl",
                                 PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
                                 PagodaTester.onto_dir + "lubm/queries/test.sparql"
-                ); 
-                AllTests.copy("log4j.log", "results-backup/current/lubm100.out"); 
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/lubm100.out");
         }
         
         @Test
-        public void fly() {
+        public void fly() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
                                 PagodaTester.onto_dir + "fly/queries/fly.sparql" 
-                ); 
-                AllTests.copy("log4j.log", "results-backup/current/fly.out"); 
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/fly.out");
         }
         
         @Test 
-        public void dbpedia() {
+        public void dbpedia() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 
                                 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
                                 PagodaTester.onto_dir + "dbpedia/atomic.sparql"
                 );
-                AllTests.copy("log4j.log", "results-backup/current/dbpedia.out"); 
+                Utility.copyFile("log4j.log", "results-backup/current/dbpedia.out");
         }
         
         @Test
-        public void npdWithoutDataType() {
+        public void npdWithoutDataType() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 
                                 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 
                                 PagodaTester.onto_dir + "npd/queries/atomic.sparql"
-                ); 
-                AllTests.copy("log4j.log", "results-backup/current/npd_minus.out"); 
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/npd_minus.out");
         }
         
 }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java
index 37ffb44..aaf542e 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaDBPedia.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java
@@ -1,4 +1,4 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import static org.junit.Assert.fail;
 
@@ -6,11 +6,14 @@ import org.junit.Test;
 
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
 import uk.ac.ox.cs.pagoda.tester.Statistics;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.IOException;
 
 public class PagodaDBPedia {
 
         @Test 
-        public void test() {
+        public void test() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl", 
                                 PagodaTester.onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl",
@@ -18,8 +21,8 @@ public class PagodaDBPedia {
                 );
                 
                 Statistics stat = new Statistics("output/log4j.log");
-                String diff = stat.diff("results-backup/benchmark/dbpedia.out"); 
-                AllTests.copy("output/log4j.log", "results-backup/current/dbpedia.out"); 
+                String diff = stat.diff("results-backup/benchmark/dbpedia.out");
+                Utility.copyFile("output/log4j.log", "results-backup/current/dbpedia.out");
                 if (!diff.isEmpty())
                         fail(diff);
         }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java
index d999a6e..c2fa838 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaELU.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java
@@ -1,4 +1,4 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import org.junit.Test;
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java
index 4631837..2fe07f0 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaFLY.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java
@@ -1,4 +1,4 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import org.junit.Test;
 
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java
new file mode 100644
index 0000000..f40e41b
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaLUBM.java
@@ -0,0 +1,68 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.tester.Statistics;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Properties;
+
+public class PagodaLUBM {
+
+        public static final String CONFIG_FILE = "config/test.properties";
+
+        private static boolean isInit = false;
+        private static String ontoDir;
+
+        private static void init() {
+                if(isInit) return;
+                isInit = true;
+
+                Properties config = new Properties();
+
+                try(FileInputStream in = new FileInputStream(CONFIG_FILE)) {
+                        config.load(in);
+                        in.close();
+                } catch (IOException e) {
+                        e.printStackTrace();
+                }
+
+                ontoDir = config.getProperty("ontoDir");
+        }
+
+        private void test_all(int number) {
+                init();
+                PagodaTester.main(
+                                Utility.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                Utility.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
+                                Utility.combinePaths(ontoDir, "lubm/queries/test.sparql")
+                );
+
+//              assertTrue(false);
+//              AllTests.copy("log4j.log", "output/jair/lubm" + number + ".out");
+        }
+
+        @Test
+        public void test1() {
+                test_all(1);
+        }
+
+//      @Test
+//      public void test() {
+//              int number = 100;
+//              test_all(number);
+//      }
+        
+        private void check(int number) throws IOException {
+                Statistics stat = new Statistics("output/log4j.log");
+                // TODO insert proper file
+                String diff = stat.diff("results-backup/benchmark/lubm" + number + ".out");
+                Utility.copyFile("output/log4j.log", "results-backup/current/lubm" + number + ".out");
+                if (!diff.isEmpty())
+                        Assert.fail(diff);
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java
index 96edbb4..8fbe793 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java
@@ -1,4 +1,4 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import static org.junit.Assert.fail;
 
@@ -6,11 +6,14 @@ import org.junit.Test;
 
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
 import uk.ac.ox.cs.pagoda.tester.Statistics;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.IOException;
 
 public class PagodaNPD {
 
         @Test
-        public void testNPDwithoutDataType() {
+        public void testNPDwithoutDataType() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl", 
                                 PagodaTester.onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl", 
@@ -18,14 +21,14 @@ public class PagodaNPD {
                 ); 
                 
                 Statistics stat = new Statistics("output/log4j.log");
-                String diff = stat.diff("results-backup/benchmark/npd_minus.out"); 
-                AllTests.copy("output/log4j.log", "results-backup/current/npd_minus.out"); 
+                String diff = stat.diff("results-backup/benchmark/npd_minus.out");
+                Utility.copyFile("output/log4j.log", "results-backup/current/npd_minus.out");
                 if (!diff.isEmpty())
                         fail(diff);
         }
         
         @Test
-        public void testNPD() {
+        public void testNPD() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "npd/npd-all.owl", 
                                 PagodaTester.onto_dir + "npd/data/npd-data-dump-processed.ttl", 
@@ -33,8 +36,8 @@ public class PagodaNPD {
                 );
                 
                 Statistics stat = new Statistics("output/log4j.log");
-                String diff = stat.diff("results-backup/benchmark/npd.out"); 
-                AllTests.copy("output/log4j.log", "results-backup/current/npd.out"); 
+                String diff = stat.diff("results-backup/benchmark/npd.out");
+                Utility.copyFile("output/log4j.log", "results-backup/current/npd.out");
                 if (!diff.isEmpty())
                         fail(diff);
         }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java
index df1a57d..1243180 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaNPD_bench.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java
@@ -1,4 +1,4 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import static org.junit.Assert.fail;
 
@@ -6,11 +6,14 @@ import org.junit.Test;
 
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
 import uk.ac.ox.cs.pagoda.tester.Statistics;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.IOException;
 
 public class PagodaNPD_bench {
         
         @Test
-        public void test() {
+        public void test() throws IOException {
                 PagodaTester.main(
                                 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.owl", 
                                 PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.ttl", 
@@ -18,8 +21,8 @@ public class PagodaNPD_bench {
                 ); 
                 
                 Statistics stat = new Statistics("output/log4j.log");
-                String diff = stat.diff("results-backup/benchmark/npd-bench.out"); 
-                AllTests.copy("output/log4j.log", "results-backup/current/npd-bench.out"); 
+                String diff = stat.diff("results-backup/benchmark/npd-bench.out");
+                Utility.copyFile("output/log4j.log", "results-backup/current/npd-bench.out");
                 if (!diff.isEmpty())
                         fail(diff);
         }
diff --git a/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java
index 5d93302..8b31c99 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/PagodaRLU.java
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java
@@ -1,4 +1,4 @@
-package uk.ac.ox.cs.pagoda.junit;
+package uk.ac.ox.cs.pagoda.test_units;
 
 import org.junit.Test;
 import uk.ac.ox.cs.pagoda.tester.PagodaTester;
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java
new file mode 100644
index 0000000..29a9056
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaUOBM.java
@@ -0,0 +1,79 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.tester.Statistics;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.Properties;
+
+public class PagodaUOBM {
+
+        public static final String CONFIG_FILE = "config/test.properties";
+
+        private static boolean isInit = false;
+        private static String ontoDir;
+
+        private static void init() {
+                if(isInit) return;
+                isInit = true;
+
+                Properties config = new Properties();
+
+                try(FileInputStream in = new FileInputStream(CONFIG_FILE)) {
+                        config.load(in);
+                        in.close();
+                } catch (IOException e) {
+                        e.printStackTrace();
+                }
+
+                ontoDir = config.getProperty("ontoDir");
+        }
+
+        private void test_all(int number ) {
+                init();
+
+                PagodaTester.main(
+                                Utility.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                Utility.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                Utility.combinePaths(ontoDir, "uobm/queries/test.sparql")
+//                              + ";" +
+//                              Utility.combinePaths(ontoDir, "uobm/queries/standard_group3_all_less.sparql") + ";" +
+//                              Utility.combinePaths(ontoDir, "uobm/queries/G3.sparql") + ";" +
+//                              Utility.combinePaths(ontoDir, "uobm/queries/last.sparql")
+                );
+
+//              AllTests.copy("log4j.log", "output/jair/newuobm/uobm" + number + ".out");
+        }
+        
+        private void test_upToSum(int number) {
+                init();
+
+                PagodaTester.main(
+                                PagodaTester.onto_dir + "uobm/univ-bench-dl.owl",
+                                PagodaTester.onto_dir + "uobm/data/uobm" + number + ".ttl",
+                                PagodaTester.onto_dir + "uobm/queries/standard_group3_all.sparql" 
+                ); 
+                
+//              AllTests.copy("log4j.log", "output/jair/uobm" + number + ".out"); 
+        }
+
+        @Test
+        public void test1() { test_all(1); }
+
+//      @Test
+        public void test500() { test_upToSum(500); }
+        
+//      public static void main(String... args) {
+//              new PagodaUOBM().test_all(1);
+//      }
+        
+        private void check() {
+                Statistics stat = new Statistics("results-backup/current/uobm1.out"); 
+                String diff = stat.diff("results-backup/benchmark/uobm1.out"); 
+                System.out.println(diff); 
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index 05a7d70..51b41f9 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -17,7 +17,7 @@ public class PagodaTester {
 //      public static final String onto_dir = "/media/RDFData/yzhou/";
 //      public static final String onto_dir = "/users/yzhou/ontologies/";
 //      public static final String onto_dir = "/home/scratch/yzhou/ontologies/";
-        public static final String onto_dir = "/home/yzhou/krr-nas-share/Yujiao/ontologies/"; 
+        public static final String onto_dir = "/home/alessandro/Big_files/Ontologies/";
 
         public static final String fly = onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl";
         public static final String fly_query = onto_dir + "fly/queries/fly.sparql";
@@ -88,12 +88,12 @@ public class PagodaTester {
         
         public static final String atlas_tbox = onto_dir + "bio2rdf/atlas/gxaterms.owl"; 
         public static final String atlas_abox = onto_dir + "bio2rdf/atlas/graph sampling/sample_1.nt"; 
-        public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql"; 
-        
+        public static final String atlas_queries = onto_dir + "bio2rdf/atlas/queries/atomic_one.sparql";
+
         public static void main(String... args) {
                 if (args.length == 0) {
 //                      args = new String[] {test_tbox, test_abox, test_query};
-//                      args = new String[] {lubm_tbox, lubm_abox, lubm_query.replace(".sparql", "_all_pagoda.sparql")}; 
+                        args = new String[] {lubm_tbox, lubm_abox, lubm_query};
 //                      args = new String[] {uobm_tbox, uobm_abox, uobm_query.replace(".sparql", "_all_pagoda.sparql")};
 //                      args = new String[] {fly, "null", fly_query.replace(".sparql", "_pellet.sparql") };
 //                      args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
@@ -129,10 +129,10 @@ public class PagodaTester {
                 if (args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));   
                 if (args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));   
         
-                System.out.println("Ontology file: " + properties.getOntologyPath()); 
-                System.out.println("Data files: " + properties.getDataPath());  
-                System.out.println("Query files: " + properties.getQueryPath()); 
-                System.out.println("Answer file: " + properties.getAnswerPath());
+                Utility.logInfo("Ontology file: " + properties.getOntologyPath());
+                Utility.logInfo("Data files: " + properties.getDataPath());
+                Utility.logInfo("Query files: " + properties.getQueryPath());
+                Utility.logInfo("Answer file: " + properties.getAnswerPath());
                 
                 QueryReasoner pagoda = null;