Testing and fixing. Executed successfully on UOBM{1,2,3,4,5,6,7,8}.

14 files changed, 925 insertions, 0 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java b/test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java
new file mode 100644
index 0000000..abd0741
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/ClauseTester.java
@@ -0,0 +1,158 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.semanticweb.HermiT.model.*;
+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/global_tests/CostEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
new file mode 100644
index 0000000..01e8203
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
@@ -0,0 +1,115 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+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.TestUtil;
+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;
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/test_all_pagoda.sparql")
+                ); 
+//              AllTests.copy("output/log4j.log", "results-backup/jair/lubm" + number + ".out"); 
+        }
+        
+        public void lubm1000() {
+                int number = 1000;
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "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 ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "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 ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "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 ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "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) {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "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/global_tests/JAIR_PAGOdA.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
new file mode 100644
index 0000000..0d77fdb
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
@@ -0,0 +1,193 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+
+public class JAIR_PAGOdA {
+
+        @Test
+        public void lubm1() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql")
+                };
+                PagodaTester.main(args);
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda");
+        }
+
+        @Test
+        public void lubm1_conj() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/test_pellet.sparql")
+                };
+                PagodaTester.main(args);
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_conj");
+        }
+
+        @Test
+        public void lubm1_rolledUp() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                "/home/yzhou/backup/20141212/univ-bench-queries.owl",
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm1.ttl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql")
+                                );
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/lubm1/pagoda_rolledUp");
+        }
+
+        @Test
+        public void uobm1() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
+                };
+                PagodaTester.main(args);
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda");
+        }
+
+        @Test
+        public void uobm1_conj() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/standard_pellet.sparql")
+                };
+                PagodaTester.main(args);
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_conj");
+        }
+
+        @Test
+        public void uobm1_rolledUp() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl",
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm1.ttl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql")
+                };
+                PagodaTester.main(args);
+//              TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/uobm1/pagoda_rolledUp");
+        }
+
+        @Test
+        public void fly() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
+                                null,
+                                TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql")
+                };
+                PagodaTester.main(args);
+//              TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda");
+        }
+
+        @Test
+        public void fly_conj() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
+                                null,
+                                TestUtil.combinePaths(ontoDir, "fly/queries/fly_pellet.sparql")
+                };
+                PagodaTester.main(args);
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_conj");
+        }
+
+
+        public void fly_rolledUp() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+//                              TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
+                                TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"),
+                                null,
+                                TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql")
+                );
+//              TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/fly/pagoda_rolledUp");
+        }
+
+        public void dbpedia() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/queries/atomic_ground.sparql"),
+                                "dbpedia.ans"
+                );
+
+//              TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/dbpedia/pagoda");
+        }
+
+        public void npd() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "npd/queries/atomic_ground.sparql")
+                                , "npd.ans"
+                );
+
+//              TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/npd/pagoda");
+        }
+
+        public void reactome() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"),
+//                              null,
+//                              TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql")
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/example.sparql")
+                                , "pagoda_reactome.ans"
+                );
+                TestUtil.copyFile("log4j.log", "output/jair/pagoda_reactome.example");
+
+//              TestUtil.copyFile(("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/reactome/pagoda_10p");
+        }
+
+        public void chembl() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"),
+//                              TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/example.sparql")
+                                , "pagoda_chembl.ans"
+                );
+                TestUtil.copyFile("log4j.log", "output/jair/pagoda_chembl.example");
+//              TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/test-share/results_new/chembl/pagoda_1p");
+        }
+
+        public void uniprot() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"),
+//                              null,
+//                              TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/example.sparql")
+                                , "pagoda_uniprot.ans"
+                );
+                TestUtil.copyFile("log4j.log", "output/jair/pagoda_uniprot.example");
+//              TestUtil.copyFile("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/global_tests/JAIR_Scalability.java b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
new file mode 100644
index 0000000..cdf55bd
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
@@ -0,0 +1,91 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+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.TestUtil;
+
+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 ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/simplifed_sample_" + percentage + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/test.sparql")
+                                , "reactome.ans"
+                }; 
+                if (percentage == 10)
+                        args[1] = args[1].replace("simplifed", "reactome");
+                
+                PagodaTester.main(args); 
+                if (save)
+                        TestUtil.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 ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/sample_" + percentage + ".nt"),
+//                              TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
+                                TestUtil.combinePaths(ontoDir, "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)
+                        TestUtil.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 ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat-processed.owl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/sample_" + percentage + ".nt"),
+//                              TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
+                                TestUtil.combinePaths(ontoDir, "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)
+                        TestUtil.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/global_tests/LightEvaluation.java b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
new file mode 100644
index 0000000..3ee268e
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
@@ -0,0 +1,67 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+
+public class LightEvaluation {
+
+        @Test
+        public void uobm1() throws IOException {
+                int number = 1;
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
+                );
+                TestUtil.copyFile("log4j.log", "output/jair/uobm1.out");
+        }
+        
+        @Test
+        public void lubm100() throws IOException {
+                int number = 100;
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql")
+                );
+                TestUtil.copyFile("log4j.log", "results-backup/current/lubm100.out");
+        }
+        
+        @Test
+        public void fly() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
+                                TestUtil.combinePaths(ontoDir, "fly/queries/fly.sparql")
+                );
+                TestUtil.copyFile("log4j.log", "results-backup/current/fly.out");
+        }
+        
+        @Test 
+        public void dbpedia() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/atomic.sparql")
+                );
+                TestUtil.copyFile("log4j.log", "results-backup/current/dbpedia.out");
+        }
+        
+        @Test
+        public void npdWithoutDataType() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "npd/queries/atomic.sparql")
+                );
+                TestUtil.copyFile("log4j.log", "results-backup/current/npd_minus.out");
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java
new file mode 100644
index 0000000..2b9cdbd
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaDBPedia.java
@@ -0,0 +1,30 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+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.TestUtil;
+
+import java.io.IOException;
+
+import static org.junit.Assert.fail;
+
+public class PagodaDBPedia {
+
+        @Test 
+        public void test() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "dbpedia/atomic.sparql")
+                );
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                String diff = stat.diff("results-backup/benchmark/dbpedia.out");
+                TestUtil.copyFile("output/log4j.log", "results-backup/current/dbpedia.out");
+                if (!diff.isEmpty())
+                        fail(diff);
+        }
+
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java
new file mode 100644
index 0000000..da059f9
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaELU.java
@@ -0,0 +1,20 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+public class PagodaELU {
+
+        @Test void test() {
+                int number = 1;
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
+                ); 
+        }
+        
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java
new file mode 100644
index 0000000..d558e0f
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaFLY.java
@@ -0,0 +1,25 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+public class PagodaFLY {
+
+        @Test
+        public void test() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"),
+                                TestUtil.combinePaths(ontoDir, "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/global_tests/PagodaLUBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java
new file mode 100644
index 0000000..2014ec1
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaLUBM.java
@@ -0,0 +1,24 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+public class PagodaLUBM {
+
+        private void testN(int number ) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                TestGlobalCorrectness.test(Paths.get(ontoDir, "lubm/univ-bench.owl"),
+                                                                   Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"),
+                                                                   Paths.get(ontoDir, "lubm/queries/test.sparql"),
+                                                                   Paths.get(ontoDir, "lubm/lubm" + number + ".json"));
+        }
+
+        @Test
+        public void test1() throws IOException {
+                testN(1);
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java
new file mode 100644
index 0000000..17d1e82
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD.java
@@ -0,0 +1,46 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+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.TestUtil;
+
+import java.io.IOException;
+
+import static org.junit.Assert.fail;
+
+public class PagodaNPD {
+
+        @Test
+        public void testNPDwithoutDataType() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "npd/npd-all-minus-datatype.owl"),
+                                TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"),
+                                TestUtil.combinePaths(ontoDir, "npd/queries/atomic.sparql")
+                ); 
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                String diff = stat.diff("results-backup/benchmark/npd_minus.out");
+                TestUtil.copyFile("output/log4j.log", "results-backup/current/npd_minus.out");
+                if (!diff.isEmpty())
+                        fail(diff);
+        }
+        
+        @Test
+        public void testNPD() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "npd/npd-all.owl"),
+                                TestUtil.combinePaths(ontoDir, "npd/data/npd-data-dump-processed.ttl"),
+                                TestUtil.combinePaths(ontoDir, "npd/queries/atomic.sparql")
+                );
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                String diff = stat.diff("results-backup/benchmark/npd.out");
+                TestUtil.copyFile("output/log4j.log", "results-backup/current/npd.out");
+                if (!diff.isEmpty())
+                        fail(diff);
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java
new file mode 100644
index 0000000..c908cb4
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaNPD_bench.java
@@ -0,0 +1,30 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+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.TestUtil;
+
+import java.io.IOException;
+
+import static org.junit.Assert.fail;
+
+public class PagodaNPD_bench {
+        
+        @Test
+        public void test() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "npd-benchmark/npd-v2-ql_a.owl"),
+                                TestUtil.combinePaths(ontoDir, "npd-benchmark/npd-v2-ql_a.ttl"),
+                                TestUtil.combinePaths(ontoDir, "npd-benchmark/queries/all.sparql")
+                ); 
+                
+                Statistics stat = new Statistics("output/log4j.log");
+                String diff = stat.diff("results-backup/benchmark/npd-bench.out");
+                TestUtil.copyFile("output/log4j.log", "results-backup/current/npd-bench.out");
+                if (!diff.isEmpty())
+                        fail(diff);
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java
new file mode 100644
index 0000000..88e0835
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaRLU.java
@@ -0,0 +1,20 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+public class PagodaRLU {
+
+        @Test 
+        public void testRL() {
+                int number = 1;
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
+                );
+        }
+
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java
new file mode 100644
index 0000000..065fb29
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/PagodaUOBM.java
@@ -0,0 +1,53 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+import static uk.ac.ox.cs.pagoda.util.TestUtil.combinePaths;
+
+public class PagodaUOBM {
+
+        private void testN(int number ) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                TestGlobalCorrectness.test(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"),
+                                                                   Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                                                   Paths.get(ontoDir, "uobm/queries/test.sparql"),
+                                                                   Paths.get(ontoDir, "uobm/uobm" + number + ".json"));
+        }
+
+        @Test
+        public void test1() throws IOException {
+                testN(1);
+        }
+
+        private static final int N_1 = 8;
+        private static final int N_2 = 10;
+
+
+        @DataProvider(name = "uobmNumbers")
+        public static Object[][] uobmNumbers() {
+                Integer[][] integers = new Integer[N_2 - N_1 + 1][1];
+                for (int i = 0; i < N_2 - N_1 + 1; i++)
+                        integers[i][0]= N_1 + i;
+                return integers;
+        }
+
+//      @Test
+//      public void justExecute3() {
+//              justExecute(1);
+//      }
+
+        @Test(dataProvider = "uobmNumbers")
+        public void justExecute(int number) {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                PagodaTester.main(combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                                  combinePaths(ontoDir, "uobm/data/uobm" + number + ".ttl"),
+                                                  combinePaths(ontoDir, "uobm/queries/test.sparql"));
+        }
+        
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java
new file mode 100644
index 0000000..dff2366
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestGlobalCorrectness.java
@@ -0,0 +1,53 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import org.apache.log4j.Level;
+import org.testng.Assert;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.tester.PagodaTester;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.lang.reflect.Type;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Set;
+
+/**
+ * This is a unit test for TestNG.
+ * <p>
+ * It tests the correctness on the final output.
+ * */
+public class TestGlobalCorrectness {
+
+    public static void test(Path ontology, Path data, Path queries, Path givenAnswers) {
+        try {
+            Utility.setLogLevel(Level.DEBUG);
+            Path computedAnswers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+            new File(computedAnswers.toString()).deleteOnExit();
+            PagodaTester.main(ontology.toString(), data.toString(), queries.toString(), computedAnswers.toString());
+            assertSameContent(computedAnswers, givenAnswers);
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    private static void assertSameContent(Path computedAnswersFile, Path givenAnswersFile) throws IOException {
+        BufferedReader computedReader = Files.newBufferedReader(computedAnswersFile);
+        BufferedReader givenReader = Files.newBufferedReader(givenAnswersFile);
+
+        Gson gson = QueryRecord.GsonCreator.getInstance();
+
+        Type cqType = new TypeToken<Set<QueryRecord>>() {}.getType();
+        Set<QueryRecord> computedAnswers = gson.fromJson(computedReader, cqType);
+        Set<QueryRecord> givenAnswers = gson.fromJson(givenReader, cqType);
+
+        Assert.assertEquals(computedAnswers, givenAnswers);
+    }
+
+
+}