Switch from JUnit to TestNG.

Plus minor fixes.

13 files changed, 915 insertions, 0 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java
new file mode 100644
index 0000000..a0f16d4
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/ClauseTester.java
@@ -0,0 +1,164 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import org.semanticweb.HermiT.model.Atom;
+import org.semanticweb.HermiT.model.AtomicConcept;
+import org.semanticweb.HermiT.model.AtomicRole;
+import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.HermiT.model.Equality;
+import org.semanticweb.HermiT.model.Variable;
+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;
+
+public class ClauseTester {
+
+        @Test
+        public void test_simple() {
+                Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
+                AtomicConcept A = AtomicConcept.create("A"); 
+                AtomicRole r = AtomicRole.create("r"); 
+                Atom[] bodyAtoms = new Atom[] {
+                                Atom.create(A, x),
+                                Atom.create(r, x, y1),
+                                Atom.create(r, x, y2)
+                }; 
+                
+                Atom[] headAtoms = new Atom[] {
+                                Atom.create(Equality.INSTANCE, y1, y2) 
+                }; 
+                
+                OWLOntologyManager m = OWLManager.createOWLOntologyManager(); 
+                OWLOntology emptyOntology = null; 
+                try {
+                        emptyOntology = m.createOntology(); 
+                } catch (Exception e) {
+                        e.printStackTrace();
+                        Assert.fail("failed to create a new ontology");
+                }
+                Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
+                System.out.println(c.toString()); 
+        }
+        
+        @Test
+        public void test_more() {
+                Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2"), y3 = Variable.create("y3");
+                AtomicConcept A = AtomicConcept.create("A"); 
+                AtomicRole r = AtomicRole.create("r"); 
+                Atom[] bodyAtoms = new Atom[] {
+                                Atom.create(A, x),
+                                Atom.create(r, x, y1),
+                                Atom.create(r, x, y2), 
+                                Atom.create(r, x, y3), 
+                }; 
+                
+                Atom[] headAtoms = new Atom[] {
+                                Atom.create(Equality.INSTANCE, y1, y2), 
+                                Atom.create(Equality.INSTANCE, y1, y3), 
+                                Atom.create(Equality.INSTANCE, y2, y3)
+                }; 
+                
+                OWLOntologyManager m = OWLManager.createOWLOntologyManager(); 
+                OWLOntology emptyOntology = null; 
+                try {
+                        emptyOntology = m.createOntology(); 
+                } catch (Exception e) {
+                        e.printStackTrace();
+                        Assert.fail("failed to create a new ontology");
+                }
+                Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
+                System.out.println(c.toString()); 
+        }
+        
+        @Test
+        public void test_inverse() {
+                Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
+                AtomicConcept A = AtomicConcept.create("A"); 
+                AtomicRole r = AtomicRole.create("r"); 
+                Atom[] bodyAtoms = new Atom[] {
+                                Atom.create(A, x),
+                                Atom.create(r, y1, x),
+                                Atom.create(r, y2, x)
+                }; 
+                
+                Atom[] headAtoms = new Atom[] {
+                                Atom.create(Equality.INSTANCE, y1, y2) 
+                }; 
+                
+                OWLOntologyManager m = OWLManager.createOWLOntologyManager(); 
+                OWLOntology emptyOntology = null; 
+                try {
+                        emptyOntology = m.createOntology(); 
+                } catch (Exception e) {
+                        e.printStackTrace();
+                        Assert.fail("failed to create a new ontology");
+                }
+                Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
+                System.out.println(c.toString()); 
+        }
+        
+        @Test
+        public void test_fillter() {
+                Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
+                AtomicConcept A = AtomicConcept.create("A"); 
+                AtomicConcept B = AtomicConcept.create("B"); 
+                AtomicRole r = AtomicRole.create("r"); 
+                Atom[] bodyAtoms = new Atom[] {
+                                Atom.create(A, x),
+                                Atom.create(r, y1, x),
+                                Atom.create(r, y2, x), 
+                                Atom.create(B, y1), 
+                                Atom.create(B, y2) 
+                }; 
+                
+                Atom[] headAtoms = new Atom[] {
+                                Atom.create(Equality.INSTANCE, y1, y2) 
+                }; 
+                
+                OWLOntologyManager m = OWLManager.createOWLOntologyManager(); 
+                OWLOntology emptyOntology = null; 
+                try {
+                        emptyOntology = m.createOntology(); 
+                } catch (Exception e) {
+                        e.printStackTrace();
+                        Assert.fail("failed to create a new ontology");
+                }
+                Clause c = new Clause(Clausifier.getInstance(emptyOntology), DLClause.create(headAtoms, bodyAtoms));
+                System.out.println(c.toString()); 
+        }
+        
+        @Test
+        public void test_negFillter() {
+                Variable x = Variable.create("X"), y1 = Variable.create("y1"), y2 = Variable.create("y2");
+                AtomicConcept A = AtomicConcept.create("A"); 
+                AtomicConcept B = AtomicConcept.create("B"); 
+                AtomicRole r = AtomicRole.create("r"); 
+                Atom[] bodyAtoms = new Atom[] {
+                                Atom.create(A, x),
+                                Atom.create(r, y1, x),
+                                Atom.create(r, y2, x)
+                }; 
+                
+                Atom[] headAtoms = new Atom[] {
+                                Atom.create(Equality.INSTANCE, y1, y2), 
+                                Atom.create(B, y1), 
+                                Atom.create(B, y2)  
+                }; 
+                
+                OWLOntologyManager m = OWLManager.createOWLOntologyManager(); 
+                OWLOntology emptyOntology = null; 
+                try {
+                        emptyOntology = m.createOntology(); 
+                } catch (Exception e) {
+                        e.printStackTrace();
+                        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/test_units/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java
new file mode 100644
index 0000000..4e32297
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/CostEvaluation.java
@@ -0,0 +1,109 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+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;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class CostEvaluation {   
+        
+        @Test
+        public void lubm100() {
+                int number = 1;
+                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("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); 
+        }
+        
+        public void lubm1000() {
+                int number = 1000;
+                String[] args = new String[] {
+                                PagodaTester.onto_dir + "lubm/univ-bench.owl",
+                                PagodaTester.onto_dir + "lubm/data/lubm" + number + ".ttl",
+                                PagodaTester.onto_dir + "lubm/queries/test_all_pagoda.sparql" 
+                }; 
+                OWLOntology ontology = OWLHelper.loadOntology(args[0]); 
+                QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true); 
+                Timer t = new Timer(); 
+                reasoner.loadOntology(ontology);
+                reasoner.importData(args[1]);
+                if (!reasoner.preprocess())
+                        return ; 
+                Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
+                
+                reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
+//              AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); 
+        }
+
+        @Test
+        public void uobm5() {
+                int number = 1;
+                String[] args = new String[] {
+                                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.main(args);
+//              AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); 
+        }
+        
+        public void uobm100() {
+                int number = 200;
+                String[] args = new String[] {
+                                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" 
+                }; 
+                PagodaTester.main(args);
+//              AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); 
+        }
+        
+        public void uobm500() {
+                int number = 500;
+                String[] args = new String[] {
+                                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" 
+                }; 
+                
+                OWLOntology ontology = OWLHelper.loadOntology(args[0]); 
+                QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
+                Timer t = new Timer(); 
+                reasoner.loadOntology(ontology);
+                reasoner.importData(args[1]);
+                if (!reasoner.preprocess())
+                        return ; 
+                Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
+                
+                reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
+//              AllTests.copy("output/log4j.log", "results-backup/jair/uobm" + number + ".out"); 
+        }
+        
+        
+        public static void main(String... args) {
+                args = new String[] {
+                                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"
+                }; 
+                
+                OWLOntology ontology = OWLHelper.loadOntology(args[0]); 
+                QueryReasoner reasoner = QueryReasoner.getInstance(Type.ELHOU, ontology, true, true);
+                Timer t = new Timer(); 
+                reasoner.loadOntology(ontology);
+                reasoner.importData(args[1]);
+                if (!reasoner.preprocess())
+                        return ; 
+                Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
+                
+                reasoner.evaluate(reasoner.getQueryManager().collectQueryRecords(args[2]));
+        }
+}
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java
new file mode 100644
index 0000000..ff616f7
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_PAGOdA.java
@@ -0,0 +1,180 @@
+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 {
+
+        @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);
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda");
+        }
+
+        @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.main(args);
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj");
+        }
+
+        @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.main(args);
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp");
+        }
+
+        @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.main(args);
+                Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda");
+        }
+
+        @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.main(args);
+                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.main(args);
+//              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"
+                };
+                PagodaTester.main(args);
+//              AllTests.copy("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda");
+        }
+
+        @Test
+        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"
+                };
+                PagodaTester.main(args);
+                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"
+                });
+//              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/data/dbpedia-minus-datatype-new.ttl",
+                                PagodaTester.onto_dir + "dbpedia/queries/atomic_ground.sparql"
+                                , "dbpedia.ans"
+                );
+
+//              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/queries/atomic_ground.sparql"
+                                , "npd.ans"
+                );
+
+//              Utility.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda");
+        }
+
+        public void reactome() throws IOException {
+                PagodaTester.main(
+                                PagodaTester.onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl",
+                                PagodaTester.onto_dir + "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl",
+//                              null,
+//                              PagodaTester.onto_dir + "bio2rdf/reactome/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/reactome/queries/example.sparql"
+                                , "pagoda_reactome.ans"
+                );
+                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() 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/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/chembl/queries/example.sparql"
+                                , "pagoda_chembl.ans"
+                );
+                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() throws IOException {
+                PagodaTester.main(
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/core-sat-processed.owl",
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt",
+//                              null,
+//                              PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/queries/example.sparql"
+                                , "pagoda_uniprot.ans"
+                );
+                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) {
+                try {
+                        new JAIR_PAGOdA().lubm1();
+                } catch (IOException e) {
+                        e.printStackTrace();
+                }
+        }
+
+}
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java
new file mode 100644
index 0000000..43cb810
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/JAIR_Scalability.java
@@ -0,0 +1,88 @@
+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() throws IOException {
+                testReactome(10, false);
+        }
+        
+        @Test
+        public void chembl() throws IOException {
+                testChEMBL(1, false);
+        }
+
+        @Test
+        public void uniprot() throws IOException {
+                testUniProt(1, false);
+        }
+
+        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", 
+                                PagodaTester.onto_dir + "bio2rdf/reactome/queries/test.sparql"
+                                , "reactome.ans"
+                }; 
+                if (percentage == 10)
+                        args[1] = args[1].replace("simplifed", "reactome");
+                
+                PagodaTester.main(args); 
+                if (save)
+                        Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_" + percentage + "p" + date);
+        }
+        
+        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",
+//                              PagodaTester.onto_dir + "bio2rdf/chembl/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/chembl/queries/test.sparql"
+                                , "chembl.ans"
+                }; 
+                if (percentage == 1 || percentage == 10 || percentage == 50)
+                        args[1] = args[1].replace("chembl", "chembl/graph sampling");
+                else 
+                        if (percentage == 100)
+                                args[1] = "/home/yzhou/RDFData/ChEMBL/facts/ChEMBL.ttl"; 
+                
+                PagodaTester.main(args);
+                if (save)
+                        Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_" + percentage + "p" + date);
+        }
+        
+        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",
+//                              PagodaTester.onto_dir + "bio2rdf/uniprot/queries/atomic_ground.sparql"
+                                PagodaTester.onto_dir + "bio2rdf/uniprot/queries/test.sparql"
+                                , "uniprot.ans"
+                }; 
+                
+                if (percentage == 1 || percentage == 10 || percentage == 50)
+                        args[1] = args[1].replace("uniprot", "uniprot/graph sampling");
+                else 
+                        if (percentage == 100)
+                                args[1] = "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/data/uniprot_cleaned.nt"; 
+                
+                PagodaTester.main(args); 
+                if (save)
+                        Utility.copyFile("log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
+        }
+        
+        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/test_units/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java
new file mode 100644
index 0000000..29006de
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/LightEvaluation.java
@@ -0,0 +1,62 @@
+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() 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"
+                );
+                Utility.copyFile("log4j.log", "output/jair/uobm1.out");
+        }
+        
+        @Test
+        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"
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/lubm100.out");
+        }
+        
+        @Test
+        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" 
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/fly.out");
+        }
+        
+        @Test 
+        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"
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/dbpedia.out");
+        }
+        
+        @Test
+        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"
+                );
+                Utility.copyFile("log4j.log", "results-backup/current/npd_minus.out");
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java
new file mode 100644
index 0000000..aaf542e
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaDBPedia.java
@@ -0,0 +1,30 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import static org.junit.Assert.fail;
+
+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() 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"
+                );
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                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/test_units/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java
new file mode 100644
index 0000000..c2fa838
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaELU.java
@@ -0,0 +1,18 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+
+public class PagodaELU {
+
+        @Test void test() {
+                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" 
+                ); 
+        }
+        
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java
new file mode 100644
index 0000000..2fe07f0
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaFLY.java
@@ -0,0 +1,24 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import org.junit.Test;
+
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+
+public class PagodaFLY {
+
+        @Test
+        public void test() {
+                PagodaTester.main(
+                                PagodaTester.onto_dir + "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
+                                PagodaTester.onto_dir + "fly/queries/fly_pellet.sparql" 
+                ); 
+                
+//              Statistics stat = new Statistics("output/log4j.log");
+//              String diff = stat.diff("results-backup/benchmark/fly.out"); 
+//              AllTests.copy("output/log4j.log", "results-backup/current/fly.out"); 
+//              if (!diff.isEmpty())
+//                      fail(diff);
+        }
+        
+
+}
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/test_units/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java
new file mode 100644
index 0000000..8fbe793
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD.java
@@ -0,0 +1,45 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import static org.junit.Assert.fail;
+
+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() 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"
+                ); 
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                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() throws IOException {
+                PagodaTester.main(
+                                PagodaTester.onto_dir + "npd/npd-all.owl", 
+                                PagodaTester.onto_dir + "npd/data/npd-data-dump-processed.ttl", 
+                                PagodaTester.onto_dir + "npd/queries/atomic.sparql"
+                );
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                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/test_units/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java
new file mode 100644
index 0000000..1243180
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaNPD_bench.java
@@ -0,0 +1,30 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import static org.junit.Assert.fail;
+
+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() throws IOException {
+                PagodaTester.main(
+                                PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.owl", 
+                                PagodaTester.onto_dir + "npd-benchmark/npd-v2-ql_a.ttl", 
+                                PagodaTester.onto_dir + "npd-benchmark/queries/all.sparql"
+                ); 
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                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/test_units/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java
new file mode 100644
index 0000000..8b31c99
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/test_units/PagodaRLU.java
@@ -0,0 +1,18 @@
+package uk.ac.ox.cs.pagoda.test_units;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+
+public class PagodaRLU {
+
+        @Test 
+        public void testRL() {
+                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" 
+                ); 
+        }
+
+}
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); 
+        }
+        
+}