[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

31 files changed, 3577 insertions, 0 deletions

diff --git a/src/test/java/uk/ac/ox/cs/hermit/HermitQueryReasoner.java b/src/test/java/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
new file mode 100644
index 0000000..957790f
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
@@ -0,0 +1,200 @@
+package uk.ac.ox.cs.hermit;
+
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.HermiT.model.Atom;
+import org.semanticweb.HermiT.model.AtomicRole;
+import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.Imports;
+import org.semanticweb.owlapi.reasoner.Node;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.owl.QueryRoller;
+import uk.ac.ox.cs.pagoda.query.QueryManager;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.util.Timer;
+
+import java.io.*;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.concurrent.*;
+
+public class HermitQueryReasoner {
+
+        public static void main(String... args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException {
+                if (args.length == 0) {
+//                      args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/lubm/lubm1_merged.owl", null, PagodaTester.lubm_query};
+//                      args = new String[] {"/users/yzhou/ontologies/uobm/uobm1_merged.owl", null, "/users/yzhou/ontologies/uobm/queries/standard.sparql"};
+//                      args = new String[] {"/users/yzhou/ontologies/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", null, "/users/yzhou/ontologies/fly/queries/fly.sparql"};
+//                      args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all-minus-datatype.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-minus-datatype-new.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"};
+//                      args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/npd/npd-all.owl", "/media/krr-nas-share/Yujiao/ontologies/npd/data/npd-data-dump-processed.ttl", "/users/yzhou/ontologies/npd/queries/atomic.sparql"};
+//                      args = new String[] {PagodaTester.dbpedia_tbox, PagodaTester.dbpedia_abox, PagodaTester.dbpedia_query};
+//                      args = new String[] {"/users/yzhou/ontologies/answersCorrectness/unsatisfiable.owl", null, "/users/yzhou/ontologies/answersCorrectness/unsatisfiable_queries.sparql"};
+
+//                      args = new String[] {"/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/graph sampling/sample_100.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/queries/atomic_one_filtered.sparql", "../answersCorrectness-share/results/chembl/hermit_1p"};
+                        args =
+                                        new String[]{"/users/yzhou/temp/uniprot_debug/core-processed-noDis.owl", "/users/yzhou/temp/uniprot_debug/sample_1_removed.nt", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../answersCorrectness-share/results/uniprot/hermit_1p"};
+                }
+//                      args = new String[] {"imported.owl", "", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../answersCorrectness-share/results/uniprot/hermit_1p"};          }
+                
+                
+                PrintStream ps = args.length < 4 ? null : new PrintStream(new File(args[3])); 
+                for (int i = 0; i < args.length; ++i) {
+                        if (args[i] == null || args[i].equalsIgnoreCase("null")) args[i] = ""; 
+                        System.out.println("Argument " + i + ": " + args[i]); 
+                }
+
+//              PrintStream ps = null; // new PrintStream(new File("../answersCorrectness-share/results/reactome/ "));
+                if (ps != null) System.setOut(ps);
+                
+                Timer t = new Timer(); 
+                OWLOntology onto = OWLHelper.loadOntology(args[0]);
+                OWLOntologyManager man = onto.getOWLOntologyManager();
+                
+                OWLDatatype date = man.getOWLDataFactory().getOWLDatatype(IRI.create("http://www.w3.org/2001/XMLSchema#date"));
+                
+                if (onto.containsEntityInSignature(date)) {
+                        for (OWLOntology o: onto.getImportsClosure())
+                                for (OWLAxiom axiom: o.getAxioms())
+                                        if (axiom.getDatatypesInSignature().contains(date)) {
+                                                System.out.println("The axiom: " + axiom + " is being ingored. ");
+                                                man.removeAxiom(onto, axiom); 
+                                        }
+                        man.saveOntology(onto, new FileOutputStream(args[0] = "tbox_hermit.owl"));
+                        man.removeOntology(onto);
+                        onto = OWLHelper.loadOntology(man, args[0]); 
+                        System.out.println("TBox processed in " + t.duration());
+                }
+                
+                try {
+                        onto = OWLHelper.getImportedOntology(onto, args[1]); 
+                } catch (IOException e) {
+                        e.printStackTrace();
+                }
+                System.out.println("Ontology loaded in " + t.duration()); 
+                System.out.println("ABox axioms:" + onto.getABoxAxioms(Imports.INCLUDED).size()); 
+//              for (OWLOntology o: onto.getImportsClosure())
+//                      for (OWLAxiom axiom: o.getAxioms())
+//                              System.out.println(axiom); 
+                
+                Reasoner hermit = new Reasoner(onto);
+                if (!hermit.isConsistent()) {
+                        System.out.println("The ontology is inconsistent."); 
+                        return ; 
+                }
+                System.out.println("Preprocessing DONE in " + t.duration()); 
+
+//              System.out.println(hermit.isConsistent()); 
+                
+                QueryManager queryManager = new QueryManager(); 
+                QueryRoller roller = new QueryRoller(onto.getOWLOntologyManager().getOWLDataFactory());
+                int failedCounter = 0; 
+                Timer total = new Timer(); 
+                for (QueryRecord record: queryManager.collectQueryRecords(args[2])) {
+                        if (Integer.parseInt(record.getQueryID()) < 10) continue; 
+                        if (total.duration() > 18000) {
+                                System.out.println("Time out 5h."); 
+                                return ; 
+                        }
+                        System.out.println("--------------------- Query " + record.getQueryID() + " -----------------------");
+                        System.out.println(record.getQueryText());
+                        ExecutorService exec = Executors.newSingleThreadExecutor();
+                        try {
+                        Future<Boolean> succ = exec.submit(new QueryThread(record, onto, hermit, roller));
+                        try {
+                                try {
+                                        if (record.getQueryID().equals("1"))
+                                                System.out.println(succ.get(60, TimeUnit.MINUTES));
+                                        else 
+                                                System.out.println(succ.get(20, TimeUnit.MINUTES));
+                                } catch (InterruptedException e) {
+//                                      e.printStackTrace();
+                                } catch (ExecutionException e) {
+//                                      e.printStackTrace();
+                                } catch (TimeoutException e) {
+//                                      e.printStackTrace();
+                                } 
+                        } finally {
+                                if (succ.cancel(true)) {
+                                        System.out.println("Trying to cancel the current query thread " + (++failedCounter));
+                                }
+                        } 
+                        } finally {
+                                exec.shutdownNow(); 
+                        }
+                }
+                
+                if (ps != null) ps.close();
+                System.exit(0);
+        }
+
+}
+
+class QueryThread implements Callable<Boolean> {
+
+        QueryRecord record;
+        OWLOntology onto; 
+        Reasoner hermit; 
+        QueryRoller roller; 
+        
+        public QueryThread(QueryRecord record2, OWLOntology onto2, Reasoner hermit2, QueryRoller roller2) {
+                record = record2; onto = onto2; hermit = hermit2; roller = roller2; 
+        }
+
+        @Override
+        public Boolean call() throws Exception {
+                Set<String> answers = new HashSet<String>(); 
+                Timer t = new Timer(); 
+                if (record.getDistinguishedVariables().length > 1) {
+                        if (record.getDistinguishedVariables().length == 2 && record.getClause().getBodyLength() == 1) {
+                                dealWithAtomicBinaryQuery(record.getClause().getBodyAtom(0), answers);
+                                System.out.println("Query " + record.getQueryID() + " The number of answers: " + answers.size());
+                                System.out.println("Query " + record.getQueryID() + " Total time: " + t.duration());
+                        }
+                        else {
+                                System.out.println("Query " + record.getQueryID() + " The number of answers: Query cannot be processsed.");
+                                System.out.println("Query " + record.getQueryID() + " Total time: Query cannot be processsed."); 
+                        }
+                        return false;  
+                }
+
+                OWLClassExpression exp = null;
+
+                try {
+                        exp = roller.rollUp(record.getClause(), record.getAnswerVariables()[0]); 
+                } catch (Exception e) {
+                        System.out.println("Query " + record.getQueryID() + " The number of answers: Query cannot be processsed.");
+                        System.out.println("Query " + record.getQueryID() + " Total time: Query cannot be processsed."); 
+                        return false;
+                }                       
+                System.out.println(exp); 
+                for (Node<OWLNamedIndividual> node: hermit.getInstances(exp, false)) {
+                        for (OWLIndividual ind: node.getEntities()) {
+                                answers.add(ind.toStringID()); 
+                        }
+                }
+                System.out.println("Query " + record.getQueryID() + " The number of answers: " + answers.size());
+                System.out.println("Query " + record.getQueryID() + " Total time: " + t.duration());
+                return true; 
+        }
+
+        private void dealWithAtomicBinaryQuery(Atom bodyAtom, Set<String> answers) {
+                StringBuilder sb = new StringBuilder(); 
+                OWLDataFactory f = onto.getOWLOntologyManager().getOWLDataFactory(); 
+                OWLObjectProperty p = f.getOWLObjectProperty(IRI.create(((AtomicRole) bodyAtom.getDLPredicate()).getIRI()));
+                for (Node<OWLNamedIndividual> sub: hermit.getInstances(f.getOWLObjectMinCardinality(1, p), false)) {
+                        for (Node<OWLNamedIndividual> obj: hermit.getObjectPropertyValues(sub.getRepresentativeElement(), p)) {
+                                for (OWLNamedIndividual subInd: sub.getEntities()) {
+                                        sb.setLength(0);
+                                        sb.append(subInd.toString()).append(" ");
+                                        int len = sb.length();
+                                        for (OWLNamedIndividual objInd: obj.getEntities()) {
+                                                sb.setLength(len);
+                                                sb.append(objInd.toString()); 
+                                                answers.add(sb.toString()); 
+                                        }
+                                }
+                        }
+                }
+        }
+        
+}
+
diff --git a/src/test/java/uk/ac/ox/cs/hermit/HermitTester.java b/src/test/java/uk/ac/ox/cs/hermit/HermitTester.java
new file mode 100644
index 0000000..dc70284
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/hermit/HermitTester.java
@@ -0,0 +1,55 @@
+package uk.ac.ox.cs.hermit;
+
+import org.semanticweb.HermiT.Configuration;
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.HermiT.model.Atom;
+import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.HermiT.model.DLOntology;
+import org.semanticweb.HermiT.structural.OWLClausification;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.reasoner.Node;
+
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+
+public class HermitTester {
+
+        public static void main(String[] args) {
+                OWLOntology onto = OWLHelper.loadOntology("imported.owl");
+                Reasoner hermit = new Reasoner(onto);
+                OWLDataFactory f = onto.getOWLOntologyManager().getOWLDataFactory();
+                OWLClass concept = f.getOWLClass(IRI.create("http://semantics.crl.ibm.com/univ-bench-dl.owl#Query12")); 
+                
+                for (OWLOntology o: onto.getImportsClosure()) {
+                        System.out.println(o.containsEntityInSignature(concept));
+                        for (OWLAxiom axiom: o.getAxioms())
+                                if (axiom.getClassesInSignature().contains(concept))
+                                        System.out.println(axiom); 
+                }
+                
+                for (Node<OWLNamedIndividual> node : hermit.getInstances(concept, false))
+                        for (OWLNamedIndividual i: node.getEntities()) {
+                                System.out.println(i.toStringID()); 
+                        }
+        
+//              clausifierTest(); 
+        }
+
+        @SuppressWarnings("unused")
+        private static void clausifierTest() {
+                OWLOntology onto = OWLHelper.loadOntology("/users/yzhou/ontologies/travel.owl");
+                OWLClausification clausifier = new OWLClausification(new Configuration());
+                DLOntology dlOntology = (DLOntology)clausifier.preprocessAndClausify(onto, null)[1];
+                
+                for (DLClause clause: dlOntology.getDLClauses())
+                        System.out.println(clause); 
+                for (Atom atom : dlOntology.getPositiveFacts())
+                        System.out.println(atom); 
+
+        }
+        
+}
diff --git a/src/test/java/uk/ac/ox/cs/hermit/JAIR_HermiT.java b/src/test/java/uk/ac/ox/cs/hermit/JAIR_HermiT.java
new file mode 100644
index 0000000..72e7af8
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/hermit/JAIR_HermiT.java
@@ -0,0 +1,129 @@
+package uk.ac.ox.cs.hermit;
+
+import org.junit.Test;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+public class JAIR_HermiT {
+
+        @Test
+        public void lubm1() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/answersCorrectness.sparql")
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/hermit"
+                };
+                HermitQueryReasoner.main(args);
+        }
+        
+        @Test
+        public void lubm1_rolledUp() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                "/home/yzhou/backup/20141212/univ-bench-queries.owl",
+                                TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"),
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/atomic_lubm.sparql")
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/hermit_rolledUp"
+                };
+                HermitQueryReasoner.main(args);
+        }
+        
+        @Test
+        public void uobm1() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                String[] args = new String[] {
+                                TestUtil.combinePaths(ontoDir, "uobm/univ-bench-dl.owl"),
+                                TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
+//                              , "hermit_uobm1.out"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/hermit"
+                };
+                HermitQueryReasoner.main(args);
+        }
+        
+        @Test
+        public void uobm1_rolledUp() throws Exception {
+                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_owl_withDeclaration"),
+                                TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql")
+                                , "hermit_uobm1_rolledUp.out"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/hermit_rolledUp"
+                };
+                HermitQueryReasoner.main(args);
+        }
+        
+        @Test
+        public void fly_rolledUp() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                HermitQueryReasoner.main(
+                                TestUtil.combinePaths(ontoDir, "fly/fly-all-in-one_rolledUp.owl"),
+//                              TestUtil.combinePaths(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl",
+                                null, 
+                                TestUtil.combinePaths(ontoDir, "fly/queries/fly_atomic.sparql")
+                                , "hermit_fly.out"
+                );
+        }
+        
+        @Test 
+        public void npd() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                HermitQueryReasoner.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")
+                                , "hermit_npd.out"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/npd/hermit"
+                ); 
+        }
+
+        @Test 
+        public void dbpedia() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                HermitQueryReasoner.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")
+                                , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/dbpedia/hermit"
+                );
+        }
+
+        @Test 
+        public void reactome() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                HermitQueryReasoner.main(
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/biopax-level3-processed.owl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/graph sampling/reactome_sample_10.ttl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/reactome/queries/atomic_ground.sparql")
+                                , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/hermit_10p"
+                ); 
+        }
+
+        @Test 
+        public void chembl() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                HermitQueryReasoner.main(
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/cco-noDPR.ttl"),
+//                              null,
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/graph sampling/sample_1.nt"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/chembl/queries/atomic_ground.sparql")
+                                , "hermit_chembl.out"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/hermit_1p"
+                ); 
+        }
+
+        @Test 
+        public void uniprot() throws Exception {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                HermitQueryReasoner.main(
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/core-sat.owl"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/graph sampling/sample_1.nt"),
+                                TestUtil.combinePaths(ontoDir, "bio2rdf/uniprot/queries/atomic_ground.sparql")
+                                , "hermit_uniprot.out"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/hermit_1p"
+                ); 
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java b/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java
new file mode 100644
index 0000000..94f5401
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java
@@ -0,0 +1,195 @@
+package uk.ac.ox.cs.jrdfox;
+
+import java.io.File;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.Prefixes;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+import uk.ac.ox.cs.JRDFox.store.Parameters;
+import uk.ac.ox.cs.JRDFox.store.TripleStatus;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+import uk.ac.ox.cs.JRDFox.store.DataStore.StoreType;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxQueryEngine;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.Timer;
+
+public class Tester {
+        
+        public static void main(String[] args) throws JRDFStoreException {
+                Tester tester = new Tester();
+                tester.testCrash();
+        }
+        
+        private void evaluate_againstIDs(String queryText) throws JRDFStoreException {
+                int number = 0; 
+                Timer t = new Timer(); 
+                TupleIterator iter = null; 
+                try {
+                        iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
+                                ++number; 
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                System.out.println(number); 
+                System.out.println(t.duration());
+
+        }
+
+        DataStore store; 
+        Prefixes prefixes = new Prefixes(); 
+        Parameters parameters; 
+        
+        public Tester() {
+                try {
+                        store = new DataStore(StoreType.NarrowParallelHead);
+                        store.setNumberOfThreads(RDFoxQueryEngine.matNoOfThreads);
+                        store.initialize();
+                        System.out.println("data store created.");
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                parameters = new Parameters();
+                parameters.m_allAnswersInRoot = true; 
+                parameters.m_useBushy = true; 
+        }
+        
+        public Tester(String path) {
+                try {
+                        store = new DataStore(new File(path));
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }
+                parameters = new Parameters(); 
+//              parameters.m_allAnswersInRoot = true; 
+//              parameters.m_useBushy = true;
+        }
+        
+        public void applyReasoning(boolean incremental) {
+                Timer t = new Timer(); 
+                try {
+                        store.applyReasoning(incremental);
+                } catch (JRDFStoreException e) {
+                        e.printStackTrace();
+                }  
+                System.out.println("reasoning done: " + t.duration()); 
+        }
+        
+        public void dispose() {
+                store.dispose();
+        }
+        
+        public void testCrash() throws JRDFStoreException {
+//              DataStore lowerStore = new DataStore(StoreType.NarrowParallelHead);
+//              lowerStore.setNumberOfThreads(RDFoxQueryEngine.matNoOfThreads);
+//              lowerStore.initialize();
+//              System.out.println("lower data store created.");
+                OWLOntology ontology = OWLHelper.loadOntology("data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl");
+                System.out.println("ontology loaded ... " + ontology.getAxiomCount());
+                
+                store.importTurtleFile(new File("testcase/fly.ttl"));
+                System.out.println("data loaded. " + store.getTriplesCount());
+                
+                store.importRules(new File[] {new File("testcase/lower.dlog")});
+                System.out.println("rules loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning();
+                System.out.println("materialised. " + store.getTriplesCount());
+                
+                store.clearRulesAndMakeFactsExplicit();
+                
+                store.importRules(new File[] {new File("testcase/multi.dlog")});
+                System.out.println("rules loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning();
+                System.out.println("materialised. " + store.getTriplesCount());
+                
+                store.makeFactsExplicit();
+                
+                store.importTurtleFiles(new File[] {new File("testcase/first.ttl")}, UpdateType.ScheduleForAddition);
+                System.out.println("first data loaded. " + store.getTriplesCount());
+                
+                store.applyReasoning(true);
+                System.out.println("incremental reasoning done. " + store.getTriplesCount());
+                
+                store.clearRulesAndMakeFactsExplicit();
+                
+                store.importTurtleFiles(new File[] {new File("testcase/second.ttl")}, UpdateType.ScheduleForAddition);
+                store.importRules(new File[] {new File("testcase/tracking.dlog")}, UpdateType.ScheduleForAddition);
+                store.applyReasoning(true);
+                System.out.println("incremental reasoning done. " + store.getTriplesCount());
+                
+                evaluate_againstIDs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
+                System.out.println("done."); 
+//              tester.applyReasoning(true);
+//              tester.evaluate_againstIDs("select distinct ?z where { ?x <" + Namespace.RDF_TYPE + "> ?z . }");
+//              System.out.println("done."); 
+                
+                store.dispose();
+//              lowerStore.dispose();
+        }
+        
+        public void test() throws JRDFStoreException {
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?x a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }");
+                
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> ."
+                                + "?x a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
+
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?x a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . "
+                                + "?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
+                
+                evaluate("PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> " 
+                                + "SELECT distinct ?x WHERE { "
+                                + "?x a benchmark:Person . "
+                                + "?x benchmark:like ?y . "
+                                + "?z a benchmark:Chair . "
+                                + "?z benchmark:isHeadOf <http://www.Department0.University0.edu> . "
+                                + "?z benchmark:like ?y . "
+                                + "?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }"); 
+        }
+        
+        public void evaluate(String query) throws JRDFStoreException {
+                int number = 0; 
+                Timer t = new Timer(); 
+                TupleIterator iter = null; 
+                try {
+                        iter = store.compileQuery(query, prefixes, parameters);
+                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
+                                ++number; 
+                } finally {
+                        if (iter != null) iter.dispose();
+                }
+                System.out.println(number); 
+                System.out.println(t.duration());
+        }
+        
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/approx/ApproxTester.java b/src/test/java/uk/ac/ox/cs/pagoda/approx/ApproxTester.java
new file mode 100644
index 0000000..63fe7b7
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/approx/ApproxTester.java
@@ -0,0 +1,158 @@
+package uk.ac.ox.cs.pagoda.approx;
+
+import java.io.IOException;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.approx.KnowledgeBase;
+import uk.ac.ox.cs.pagoda.approx.RLOntology;
+import uk.ac.ox.cs.pagoda.approx.RLPlusOntology;
+import uk.ac.ox.cs.pagoda.constraints.NullaryBottom;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.rules.DisjunctiveProgram;
+import uk.ac.ox.cs.pagoda.rules.ExistentialProgram;
+import uk.ac.ox.cs.pagoda.rules.ExistentialToDisjunctive;
+import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
+import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
+import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+public class ApproxTester {
+        
+        private static ApproxType description = ApproxType.DATALOGPMOR; 
+        
+        private static String ontoFile = null;
+        
+        public static void main(String[] args) throws IOException
+        {
+                args = new String[] {
+                                "-tbox", 
+//                              "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-noDPR.ttl", 
+//                              "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/reactome/biopax-level3-processed.owl", 
+//                              "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/atlas/gxaterms.owl", 
+//                              "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/core-sat-processed.owl",
+//                              PagodaTester.npd_tbox,
+//                              "/users/yzhou/temp/ontologies/core.RLor.rdf",
+                                "datatype.owl", 
+                                "-dest", ApproxType.DATALOGPMOR.toString() 
+                }; 
+
+                long startTime = System.currentTimeMillis();
+                
+                if (args.length > 0) {
+                        if (args.length % 2 != 0) {
+                                System.out.println("arguments error..."); 
+                                return ;
+                        }
+                        for (int i = 0; i < args.length ; i = i + 2) 
+                                if (!setArgument(args[i], args[i + 1])) {
+                                        System.out.println("arguments error..."); 
+                                        return ;
+                                }
+                }
+                
+//              Utility.redirectSystemOut();
+                
+                System.setProperty("entityExpansionLimit", String.valueOf(Integer.MAX_VALUE));
+                
+                String directory = ontoFile.substring(0, ontoFile.lastIndexOf(Utility.FILE_SEPARATOR) + 1); 
+                
+                KnowledgeBase program = null;
+                switch (description) {
+                case OWL2RLPLUS: program = new RLPlusOntology(); break; 
+                case OWL2RL: program = new RLOntology(); break;
+                case DATALOG_UPPER: program = new UpperDatalogProgram(); break; 
+                case DATALOG_LOWER: program = new LowerDatalogProgram(); break; 
+                case EXISTENTIAL: program = new ExistentialProgram(); break;
+                case DISJUNCTIVE: program = new DisjunctiveProgram(); break;  
+                case DATALOGPMOR: program = new GeneralProgram(); break;
+                case EXIST2DISJ: program = new ExistentialToDisjunctive(); break;
+                default: 
+                        System.exit(0);
+                }
+
+                if (program instanceof RLPlusOntology)
+                        ((RLPlusOntology) program).setCorrespondenceFileLoc(directory + "correspondence");
+                OWLOntology ontology = OWLHelper.loadOntology(ontoFile);  
+                program.load(ontology, new NullaryBottom());
+
+                program.transform();
+
+                program.save();
+                
+                System.out.println("Time to transform the rules: " + (System.currentTimeMillis() - startTime) / 1000.);
+                
+                Utility.closeCurrentOut();
+        }
+
+        private static boolean setArgument(String key, String value) {
+                if (key.equalsIgnoreCase("-dest")) 
+                        if (value.equalsIgnoreCase("OWL2RL+")) description = ApproxType.OWL2RLPLUS;
+                        else if (value.equalsIgnoreCase("OWL2RL")) description = ApproxType.OWL2RL; 
+                        else if (value.equalsIgnoreCase("UPPERDATALOG")) description = ApproxType.DATALOG_UPPER;
+                        else if (value.equalsIgnoreCase("LOWERDATALOG")) description = ApproxType.DATALOG_LOWER;
+                        else if (value.equalsIgnoreCase("DATALOGPMOR")) description = ApproxType.DATALOGPMOR;
+                        else if (value.equalsIgnoreCase("EXISTENTIALRULES")) description = ApproxType.EXISTENTIAL;
+                        else if (value.equalsIgnoreCase("DISJUNCTIVE")) description = ApproxType.DISJUNCTIVE;
+                        else if (value.equalsIgnoreCase("EXIST2DISJ")) description = ApproxType.EXIST2DISJ; 
+                        else {
+                                System.out.println("illegal destination argument..."); 
+                                return false;
+                        }
+                else if (key.equalsIgnoreCase("-tbox")) 
+                        ontoFile = value;
+                else {
+                        System.out.println("unrecognisable type of argument..."); 
+                        return false;
+                }
+                
+                return true;
+        }
+        
+        public enum ApproxType {
+                /**
+                 * approx to (RL + self + top being the subClassExp)
+                 */
+                OWL2RLPLUS,     
+                
+                /**
+                 * approx to RL
+                 */
+                OWL2RL,                 
+                
+                /**
+                 * approx to datalog by replacing existential quantified variables 
+                 * by fresh constants and replacing disjunctions by conjunctions
+                 */
+                DATALOG_UPPER,          
+                
+                /**
+                 * approx to datalog by ignoring existential and disjunctive axiom
+                 */
+                DATALOG_LOWER,          
+                
+                /**
+                 * approx to existential rules by replacing disjunctions by 
+                 * conjunctions
+                 */
+                EXISTENTIAL,
+                
+                /**
+                 * approx to disjunctive datalog program by replacing existential 
+                 * quantified variables by fresh constants (DNF)
+                 */
+                DISJUNCTIVE, 
+                
+                /**
+                 * transform into rules, no approximation at all
+                 */
+                DATALOGPMOR,    
+                
+                /**
+                 * approx existential quantifiers by disjunctions
+                 */
+                EXIST2DISJ              
+
+        }; 
+        
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/approx/ClauseTester.java b/src/test/java/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
new file mode 100644
index 0000000..cff1d1c
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
@@ -0,0 +1,38 @@
+package uk.ac.ox.cs.pagoda.approx;
+
+import org.semanticweb.HermiT.model.DLClause;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+import uk.ac.ox.cs.pagoda.constraints.NullaryBottom;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
+
+public class ClauseTester {
+
+        public static void main(String... args) {
+                args = new String[] {
+//                              "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/chembl/cco-noDPR.ttl", 
+                                "/home/yzhou/krr-nas-share/Yujiao/ontologies/bio2rdf/reactome/biopax-level3-processed.owl", 
+//                              "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/atlas/gxaterms.owl", 
+//                              "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/core-sat-processed.owl",
+//                              PagodaTester.npd_tbox,
+//                              "/users/yzhou/temp/ontologies/core.RLor.rdf",
+//                              "datatype.owl" 
+                }; 
+                
+                String ontoFile = args[0];   
+                OWLOntology ontology = OWLHelper.loadOntology(ontoFile);  
+                GeneralProgram program = new GeneralProgram();; 
+                program.load(ontology, new NullaryBottom());
+                program.transform();
+                program.save();
+                if (program instanceof GeneralProgram) {
+                        GeneralProgram gp = ((GeneralProgram) program); 
+                        for (DLClause clause: gp.getClauses()) {
+                                System.out.println(clause);
+                                System.out.println(OWLHelper.getOWLAxiom(ontology, clause)); 
+                        }
+                }
+        }
+        
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java b/src/test/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java
new file mode 100644
index 0000000..a4579a3
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java
@@ -0,0 +1,60 @@
+package uk.ac.ox.cs.pagoda.endomorph;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.JRDFox.model.GroundTerm;
+import uk.ac.ox.cs.JRDFox.model.Individual;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.summary.Graph;
+import uk.ac.ox.cs.pagoda.summary.NodeTuple;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.util.HashSet;
+
+import static uk.ac.ox.cs.pagoda.util.TestUtil.getEntityIRI;
+
+public class DependencyGraphTest {
+
+    private OWLOntology getOntology() throws OWLOntologyCreationException {
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass hardWorkingStudent = factory.getOWLClass(getEntityIRI("HardWorkingStudent"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(hardWorkingStudent));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLObjectProperty takesCourse = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "takesCourse")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(takesCourse));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, a));    // HardWorkingStudent(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, b));    // HardWorkingStudent(b)
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology,
+                factory.getOWLEquivalentClassesAxiom(hardWorkingStudent,
+                        factory.getOWLObjectMinCardinality(3,
+                                takesCourse)));
+        return ontology;
+    }
+
+    @Test
+    public void test() throws OWLOntologyCreationException {
+        OWLOntology ontology = getOntology();
+        Graph graph = new Graph(ontology);
+        DependencyGraph dependencyGraph = new DependencyGraph(graph);
+
+        HashSet<NodeTuple> tuples = new HashSet<>();
+        tuples.add(graph.getNodeTuple(new AnswerTuple(new GroundTerm[]{Individual.create(String.format(TestUtil.NS, "a")), Individual.create(String.format(TestUtil.NS, "a"))})));
+        tuples.add(graph.getNodeTuple(new AnswerTuple(new GroundTerm[]{Individual.create(String.format(TestUtil.NS, "a")), Individual.create(String.format(TestUtil.NS, "b"))})));
+        tuples.add(graph.getNodeTuple(new AnswerTuple(new GroundTerm[]{Individual.create(String.format(TestUtil.NS, "b")), Individual.create(String.format(TestUtil.NS, "a"))})));
+        tuples.add(graph.getNodeTuple(new AnswerTuple(new GroundTerm[]{Individual.create(String.format(TestUtil.NS, "b")), Individual.create(String.format(TestUtil.NS, "b"))})));
+
+        dependencyGraph.build(tuples);
+
+        Assert.assertTrue(dependencyGraph.getTopologicalOrder().size() >= 2);
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/BugTests.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
new file mode 100644
index 0000000..3f14ec7
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
@@ -0,0 +1,240 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+import static uk.ac.ox.cs.pagoda.util.TestUtil.getEntityIRI;
+
+public class BugTests {
+
+
+
+    @Test
+    public void minimumCardinalityAxiom2() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+//        OWLClass student = factory.getOWLClass(getEntityIRI("Student"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(student));
+//        OWLClass course = factory.getOWLClass(getEntityIRI("Course"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(course));
+        OWLClass hardWorkingStudent = factory.getOWLClass(getEntityIRI("HardWorkingStudent"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(hardWorkingStudent));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLObjectProperty takesCourse = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "takesCourse")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(takesCourse));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, a));   // HardWorkingStudent(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(hardWorkingStudent, b));   // HardWorkingStudent(b)
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology,
+                factory.getOWLEquivalentClassesAxiom(hardWorkingStudent,
+                        factory.getOWLObjectMinCardinality(3,
+                                takesCourse)));
+
+//        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if (pagoda.preprocess()) {
+            String query = "select distinct ?x ?y " +
+                    " where { "
+                    + " ?x <" + takesCourse.toStringID() + "> _:z . "
+                    + " ?y <" + takesCourse.toStringID() + "> _:z " +
+                    " }";
+            AnswerTuples answers = pagoda.evaluate(query);
+            int count = 0;
+            for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+            Assert.assertEquals(count, 2);
+        }
+        pagoda.dispose();
+    }
+
+//    @Test
+    public void minimumCardinalityAxiom() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass student = factory.getOWLClass(getEntityIRI("Student"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(student));
+        OWLClass course = factory.getOWLClass(getEntityIRI("Course"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(course));
+        OWLClass hardWorkingStudent = factory.getOWLClass(getEntityIRI("HardWorkingStudent"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(hardWorkingStudent));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c1 = factory.getOWLNamedIndividual(getEntityIRI("c1"));
+        OWLNamedIndividual c2 = factory.getOWLNamedIndividual(getEntityIRI("c2"));
+        OWLNamedIndividual c3 = factory.getOWLNamedIndividual(getEntityIRI("c3"));
+        OWLNamedIndividual d1 = factory.getOWLNamedIndividual(getEntityIRI("d1"));
+        OWLNamedIndividual d2 = factory.getOWLNamedIndividual(getEntityIRI("d2"));
+        OWLNamedIndividual d3 = factory.getOWLNamedIndividual(getEntityIRI("d3"));
+        OWLObjectProperty takesCourse = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "takesCourse")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(takesCourse));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(student, a));      // Student(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(student, b));      // Student(b)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, c1));      // Course(c1)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, c2));      // Course(c2)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, c3));      // Course(c3)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, d1));      // Course(d1)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, d2));      // Course(d2)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(course, d3));      // Course(d3)
+
+        // Role assertions
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, a, c1));     // takesCourse(a,c1)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, a, c2));     // takesCourse(a,c2)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, a, c3));     // takesCourse(a,c3)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, b, d1));     // takesCourse(b,d1)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, b, d2));     // takesCourse(b,d2)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(takesCourse, b, d3));     // takesCourse(b,d3)
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology,
+                         factory.getOWLEquivalentClassesAxiom(hardWorkingStudent,
+                                                              factory.getOWLObjectMinCardinality(3,
+                                                                                                 takesCourse)));
+
+        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if (pagoda.preprocess()) {
+            String query = "select distinct ?x ?y " +
+                    " where { "
+                    + " ?x <" + takesCourse.toStringID() + "> _:z . "
+                    + " ?y <" + takesCourse.toStringID() + "> _:z " +
+                    " }";
+            AnswerTuples answers = pagoda.evaluate(query);
+            int count = 0;
+            for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+            Assert.assertEquals(count, 2);
+        }
+        pagoda.dispose();
+    }
+
+    /**
+     * Bug: the relevant ontology is not a subset of the original one.
+     *
+     * @throws OWLOntologyCreationException
+     * @throws IOException
+     * @throws OWLOntologyStorageException
+     */
+//    @Test
+    public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+        OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "P")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a));    // A(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b));    // A(b)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
+
+        // Axioms
+        // subsetOf(A someValuesFrom(R owl:Thing))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classA,
+                                                       factory.getOWLObjectSomeValuesFrom(roleR,
+                                                                                          factory.getOWLThing())));
+
+        // inverseFunctional(R)
+        manager.addAxiom(ontology,
+                         factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
+
+        // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       classB));
+        /*
+         * Save the ontology
+         * */
+
+//        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+                    "select distinct ?x" +
+                    " where { "
+                    + " ?x rdf:type " + classB +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            System.out.println(queryRecord);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+            }
+        }
+        pagoda.dispose();
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
new file mode 100644
index 0000000..01e8203
--- /dev/null
+++ b/src/test/java/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/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
new file mode 100644
index 0000000..18f6cf9
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
@@ -0,0 +1,191 @@
+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 {
+
+        public static void main(String... args) {
+                try {
+                        new JAIR_PAGOdA().lubm1();
+                } catch(IOException e) {
+                        e.printStackTrace();
+                }
+        }
+
+        @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/answersCorrectness.sparql")
+                };
+                PagodaTester.main(args);
+                TestUtil.copyFile("output/log4j.log", "/home/yzhou/java-workspace/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-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/answersCorrectness-share/results_new/uniprot/pagoda_1p");
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
new file mode 100644
index 0000000..01f3568
--- /dev/null
+++ b/src/test/java/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.PagodaProperties;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+
+public class JAIR_Scalability {
+        
+        private static final String date = "_0123";
+
+        public static void main(String... args) throws IOException {
+                PagodaProperties.shellModeDefault = true;
+                new JAIR_Scalability().testUniProt(50, false);
+        }
+        
+        @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/answersCorrectness.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/answersCorrectness-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/answersCorrectness.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/answersCorrectness-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/answersCorrectness.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/answersCorrectness-share/results_new/uniprot/pagoda_" + percentage + "p" + date);
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
new file mode 100644
index 0000000..3551b9b
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
@@ -0,0 +1,18 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+
+import java.io.IOException;
+
+@Deprecated
+public class LightEvaluation {
+
+        @Test
+        public void evaluation() throws IOException {
+                new TestPagodaUOBM().answersCorrectness(1);
+                new TestPagodaLUBM().answersCorrectness(100);
+//              new TestPagodaFLY().answersCorrectness();
+                new TestPagodaDBPedia().answersCorrectness();
+                new TestPagodaNPD().testNPDwithoutDataType();
+        }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
new file mode 100644
index 0000000..3d154cb
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
@@ -0,0 +1,77 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+
+import static uk.ac.ox.cs.pagoda.util.TestUtil.getEntityIRI;
+
+public class MadeUpCases {
+
+    @Test(groups = {"existential"})
+    public void someTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass A1 = factory.getOWLClass(getEntityIRI("A1"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A1));
+        OWLClass A2 = factory.getOWLClass(getEntityIRI("A2"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A2));
+        OWLClass A3 = factory.getOWLClass(getEntityIRI("A3"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A3));
+        OWLClass A4 = factory.getOWLClass(getEntityIRI("A4"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A4));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLObjectProperty R = factory.getOWLObjectProperty(IRI.create(String.format(TestUtil.NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(R));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A1, a));
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A1, b));
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A1, factory.getOWLObjectSomeValuesFrom(R, A2)));
+        manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A2, factory.getOWLObjectSomeValuesFrom(R, A3)));
+        manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A3, factory.getOWLObjectSomeValuesFrom(R, A4)));
+        manager.addAxiom(ontology, factory.getOWLTransitiveObjectPropertyAxiom(R));
+
+//        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if (pagoda.preprocess()) {
+            String query = "select distinct ?x ?y " +
+                    " where { "
+                    + " ?x <" + R.toStringID() + "> _:z . "
+                    + " ?y <" + R.toStringID() + "> _:z " +
+                    " }";
+            AnswerTuples answers = pagoda.evaluate(query);
+            int count = 0;
+            for (AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+            Assert.assertEquals(count, 2);
+        }
+        pagoda.dispose();
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
new file mode 100644
index 0000000..2fc682b
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
@@ -0,0 +1,269 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+public class SkolemisationTests {
+
+    public static final String NS = "http://example.org/test#%s";
+
+    private IRI getEntityIRI(String name) {
+        return IRI.create(String.format(NS, name));
+    }
+
+//    @Test
+    public void commonSuccessorTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+        OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+        OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, c));    // A(c)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, d));    // A(d)
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classA,
+                                                       factory.getOWLObjectUnionOf(
+                                                               factory.getOWLObjectSomeValuesFrom(roleR, classB),
+                                                               factory.getOWLObjectSomeValuesFrom(roleR, classC))));
+
+        /*
+         * Save the ontology
+         * */
+
+//        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "select distinct ?x ?y " +
+                    " where { "
+                    + " ?x <" + roleR.toStringID() + "> _:z . "
+                    + " ?y <" + roleR.toStringID() + "> _:z " +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            int count = 0;
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+            Assert.assertEquals(count, 2);
+        }
+        pagoda.dispose();
+    }
+
+//    @Test
+    public void yTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+        OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
+        OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+        OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+        OWLObjectProperty roleS = factory.getOWLObjectProperty(IRI.create(String.format(NS, "S")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleS));
+        OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, a));    // D(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, b));    // D(b)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleS, c, a)); // S(c,a)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, d, b)); // P(d,b)
+
+        // Axioms
+        // subsetOf(D someValuesFrom(R owl:Thing))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classD,
+                                                       factory.getOWLObjectSomeValuesFrom(roleR,
+                                                                                          factory.getOWLThing())));
+        // subsetOf(someValuesFrom(inverseOf(S) owl:Thing) allValuesFrom(R A))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleS.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       factory.getOWLObjectAllValuesFrom(roleR, classA)));
+        // subsetOf(someValuesFrom(inverseOf(P) owl:Thing) B)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       classB));
+        // subsetOf(someValuesFrom(R A) C)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleR, classA), classC));
+
+        /*
+         * Save the ontology
+         * */
+
+        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+                    "select distinct ?x" +
+                    " where { "
+//                    + " ?x rdf:type " + classB + " ."
+//                    + " ?x " + roleR + " "+ "_:y . "
+                    + " ?x rdf:type " + classC +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            System.out.println(queryRecord);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            int count = 0;
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+//            Assert.assertEquals(count, 1);
+        }
+        pagoda.dispose();
+    }
+
+    @Test
+    public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+//        OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
+//        OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+//        OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+//        OWLObjectProperty roleF = factory.getOWLObjectProperty(IRI.create(String.format(NS, "F")));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleF));
+        OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
+//        OWLObjectProperty roleL = factory.getOWLObjectProperty(IRI.create(String.format(NS, "L")));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleL));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a));    // A(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b));    // A(b)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
+
+        // Axioms
+        // subsetOf(A someValuesFrom(R owl:Thing))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classA,
+                                                       factory.getOWLObjectSomeValuesFrom(roleR,
+                                                                                          factory.getOWLThing())));
+
+        // inverseFunctional(R)
+        manager.addAxiom(ontology,
+                         factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
+
+        // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       classB));
+        /*
+         * Save the ontology
+         * */
+
+        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+                    "select distinct ?x" +
+                    " where { "
+                    + " ?x rdf:type " + classB +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            System.out.println(queryRecord);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            int count = 0;
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+//            Assert.assertEquals(count, 1);
+        }
+        pagoda.dispose();
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
new file mode 100644
index 0000000..4b1ec6d
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
@@ -0,0 +1,68 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import junit.framework.Assert;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.Namespace;
+
+public class TestGapMappedToLower {
+
+        public static final String ns = "http://example.org/test#%s";
+        
+        public IRI getEntityIRI(String name) {
+                return IRI.create(String.format(ns, name)); 
+        }
+        
+        @Test
+        public void test() throws OWLOntologyCreationException {
+                OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 
+                OWLDataFactory factory = manager.getOWLDataFactory(); 
+                OWLOntology ontology = manager.createOntology(); 
+                OWLClass A = factory.getOWLClass(getEntityIRI("A"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A)); 
+                OWLClass B = factory.getOWLClass(getEntityIRI("B"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(B)); 
+                OWLClass C = factory.getOWLClass(getEntityIRI("C"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(C)); 
+                OWLClass A1 = factory.getOWLClass(getEntityIRI("A1"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A1)); 
+                OWLClass A2 = factory.getOWLClass(getEntityIRI("A2"));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(A2)); 
+                OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a")); 
+                OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+                OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c")); 
+                OWLObjectProperty r = factory.getOWLObjectProperty(IRI.create(String.format(ns, "r")));
+                manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(r));
+
+                manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(A, a));    // A(a)
+                manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(B, b));    // B(b)
+                manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(C, c));    // C(c)
+                manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, b));        // r(a,b)
+                manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(r, a, c));        // r(a,c)
+                manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A, factory.getOWLObjectUnionOf(A1, A2)));      // A \sqsubseteq A1 \sqcup A2
+                manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A1, factory.getOWLObjectMaxCardinality(1, r)));        // A1 \sqsubseteq \leq 1 r.\top 
+                manager.addAxiom(ontology, factory.getOWLSubClassOfAxiom(A2, factory.getOWLObjectMaxCardinality(1, r)));        // A2 \sqsubseteq \leq 1 r.\top 
+
+                QueryReasoner pagoda = QueryReasoner.getInstance(ontology); 
+                pagoda.loadOntology(ontology);
+                if (pagoda.preprocess()) {
+                        String sparql = "select ?x where { "
+                                        + "?x <" + r.toStringID() + "> ?y . "
+                                        + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + B.toStringID() + "> . "
+                                        + "?y " + Namespace.RDF_TYPE_QUOTED + " <" + C.toStringID() + "> . } ";
+                        AnswerTuples rs = pagoda.evaluate(sparql);
+                        int count = 0; 
+                        for (AnswerTuple ans; rs.isValid(); rs.moveNext()) {
+                                ans = rs.getTuple(); 
+                                System.out.println(ans.getGroundTerm(0)); 
+                                ++count; 
+                        }
+                        Assert.assertEquals(1, count);
+                }
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
new file mode 100644
index 0000000..3642147
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
@@ -0,0 +1,33 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+public class TestPagodaDBPedia {
+
+        public static final String ANSWER_PATH = "~/TestPagodaDEBPedia.json";
+
+        @Test
+        public void just_execute() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "dbpedia/integratedOntology-all-in-one-minus-datatype.owl"))
+                                                          .data(Paths.get(ontoDir, "dbpedia/data/dbpedia-minus-datatype-new.ttl"))
+                                                          .query(Paths.get(ontoDir, "dbpedia/atomic.sparql"))
+                                                          .answer(ANSWER_PATH)
+                                                          .classify(true)
+                                                          .hermit(true)
+                                                          .build();
+                pagoda.run();
+        }
+
+        @Test
+        public void answersCorrectness() {
+                // TODO implement
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
new file mode 100644
index 0000000..3eb956f
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
@@ -0,0 +1,107 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.query.CheckAnswers;
+import uk.ac.ox.cs.pagoda.util.PagodaProperties;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+import uk.ac.ox.cs.pagoda.util.Timer;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class TestPagodaFLY {
+
+    //  @Test(groups = {"light"})
+    public void answersCorrectness_withGJFC() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+        Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+        new File(answers.toString()).deleteOnExit();
+        Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-with-GJ-FC-individuals.json");
+
+        Pagoda pagoda = Pagoda.builder()
+                              .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
+                              .query(Paths.get(ontoDir, "fly/queries/fly.sparql"))
+                              .answer(answers)
+                              .classify(false)
+                              .build();
+
+        pagoda.run();
+        CheckAnswers.assertSameAnswers(answers, givenAnswers);
+    }
+
+    @Test(groups = {"light", "correctness"})
+    public void answersCorrectness_rolledUp() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+        Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+        new File(answers.toString()).deleteOnExit();
+        Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-fly-rolledup.json");
+
+        Pagoda pagoda = Pagoda.builder()
+                              .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+                              .query(Paths.get(ontoDir, "fly/queries/fly_rolledUp.sparql"))
+                              .answer(answers)
+//                              .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
+                              .classify(false)
+                              .build();
+
+        pagoda.run();
+        CheckAnswers.assertSameAnswers(answers, givenAnswers);
+    }
+
+    @Test(groups = {"light", "justExecute", "nonOriginal", "existential"})
+    public void justExecute_newQueries() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+//                .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+                          .ontology(Paths.get(ontoDir, "fly/fly_anatomy_XP_with_GJ_FC_individuals.owl"))
+//                .query(Paths.get(ontoDir, "fly/queries/fly_rolledUp.sparql"))
+//                .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
+                .query("/home/alessandro/Desktop/query-8.sparql")
+//                        .answer(Paths.get("/home/alessandro/Desktop/answers.json"))
+                .classify(false)
+                .hermit(true)
+                .skolemDepth(3)
+                .skolem(PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION)
+                .build()
+                .run();
+    }
+
+    @Test(groups = {"comparison"})
+    public void compare_newQueries() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Timer timer = new Timer();
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+              .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
+              .classify(false)
+              .hermit(true)
+                .skolem(PagodaProperties.SkolemUpperBoundOptions.AFTER_SUMMARISATION) // <----<< Skolem upper bound is ENABLED <<<
+                .build()
+                .run();
+        double t1 = timer.duration();
+
+        timer.reset();
+
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "fly/fly_rolledUp.owl"))
+              .query(Paths.get(ontoDir, "fly/queries/new_queries.sparql"))
+              .classify(false)
+              .hermit(true)
+                .skolem(PagodaProperties.SkolemUpperBoundOptions.DISABLED) // <----<< Skolem upper bound is DISABLED <<<
+                .build()
+                .run();
+        double t2 = timer.duration();
+
+        if(t1 < t2)
+            TestUtil.logInfo(
+                    "Overall reasoning with Skolem upper bound was " + (int) (t2 / t1 * 100 - 100) + "x faster!");
+        else
+            TestUtil.logInfo(
+                    "Overall reasoning with Skolem upper bound was " + (int) (t1 / t2 * 100 - 100) + "x slower...");
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
new file mode 100644
index 0000000..019fafa
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
@@ -0,0 +1,92 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.query.CheckAnswers;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class TestPagodaLUBM {
+
+        public void answersCorrectness(int number) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+                new File(answers.toString()).deleteOnExit();
+                Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
+
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
+                                                          .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
+                                                          .query(Paths.get(ontoDir, "lubm/queries/test.sparql"))
+                                                          .answer(answers)
+                                                          .build();
+
+                pagoda.run();
+                CheckAnswers.assertSameAnswers(answers, givenAnswers);
+        }
+
+        @Test(groups = {"light", "correctness"})
+        public void answersCorrectness_1() throws IOException {
+                answersCorrectness(1);
+        }
+
+        public void justExecute_sygenia(int number) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+//              Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+//              new File(answers.toString()).deleteOnExit();
+//              Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
+
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
+                                                          .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
+                                              .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia.sparql"))
+//                                                        .answer(answers)
+                                              .build();
+
+                pagoda.run();
+//              CheckAnswers.assertSameAnswers(answers, givenAnswers);
+        }
+
+        @Test(groups = {"sygenia"})
+        public void justExecute_sygenia_1() throws IOException {
+                justExecute_sygenia(1);
+        }
+
+        public void justExecute_sygenia_allBlanks(int number) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+//              Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+//              new File(answers.toString()).deleteOnExit();
+//              Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-lubm" + number + ".json");
+
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
+                                                          .data(Paths.get(ontoDir, "lubm/data/lubm" + number + ".ttl"))
+                                .query(Paths.get(ontoDir, "lubm/queries/lubm_sygenia_all-blanks.sparql"))
+//                                                        .answer(answers)
+                                .build();
+
+                pagoda.run();
+//              CheckAnswers.assertSameAnswers(answers, givenAnswers);
+        }
+
+        @Test(groups = {"sygenia"})
+        public void justExecute_sygenia_1_allBlanks() throws IOException {
+                justExecute_sygenia_allBlanks(1);
+        }
+
+    @Test(groups = {"existential"})
+    public void justExecute_feier() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "lubm/univ-bench.owl"))
+              .data(Paths.get(ontoDir, "lubm/data/lubm1.ttl"))
+              .query(Paths.get(ontoDir, "lubm/queries/queries_from_rules.sparql"))
+              .build()
+              .run();
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
new file mode 100644
index 0000000..939ee6e
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
@@ -0,0 +1,38 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+public class TestPagodaNPD {
+
+        public static final String ANSWER_PATH = "~/PagodaNPDWithoutDatatype.json";
+
+        @Test
+        public void justExecuteNPDWithoutDataType() {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "npd/npd-all-minus-datatype.owl"))
+                                                          .data(Paths.get(ontoDir, "npd/data/npd-data-dump-minus-datatype-new.ttl"))
+                                                          .query(Paths.get(ontoDir, "npd/queries/atomic.sparql"))
+                                                          .answer(ANSWER_PATH)
+                                                          .classify(true)
+                                                          .hermit(true)
+                                                          .build();
+                pagoda.run();
+        }
+
+        @Test
+        public void testNPDwithoutDataType() throws IOException {
+                // TODO implement
+        }
+        
+        @Test
+        public void testNPD() throws IOException {
+                // TODO implement
+        }
+        
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
new file mode 100644
index 0000000..8a8a596
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
@@ -0,0 +1,53 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+
+public class TestPagodaReactome {
+
+    @Test(groups = {"justExecute"})
+    public void justExecute() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
+              .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
+              .query(Paths.get(ontoDir, "reactome/test.sparql"))
+              .classify(true)
+              .hermit(true)
+              .build()
+              .run();
+    }
+
+    @Test(groups = {"sygenia"})
+    public void justExecute_sygenia() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
+              .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
+              .query(Paths.get(ontoDir, "reactome/reactome_sygenia_queries.sparql"))
+              .classify(true)
+              .hermit(true)
+              .build()
+              .run();
+    }
+
+    @Test(groups = {"existential"})
+    public void justExecute_existential() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+                .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
+                .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
+                .query(Paths.get(ontoDir, "reactome/existential_queries.sparql"))
+//                .query(Paths.get(ontoDir, "reactome/Queries_by_Feier-et-al.sparql"))
+                .build()
+                .run();
+    }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
new file mode 100644
index 0000000..4dae223
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
@@ -0,0 +1,122 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.Pagoda;
+import uk.ac.ox.cs.pagoda.query.CheckAnswers;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class TestPagodaUOBM {
+
+        private static final int N_1 = 1;
+        private static final int N_2 = 4;
+
+        @DataProvider(name = "UOBMNumbers")
+        private 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(groups = {"light", "correctness"})
+        public void answersCorrectness_1() throws IOException {
+                answersCorrectness(1);
+        }
+
+        @Test(groups = {"heavy", "correctness"}, dataProvider = "UOBMNumbers")
+        public void answersCorrectness(int number) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+                new File(answers.toString()).deleteOnExit();
+                Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-uobm" + number + ".json");
+
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
+                                                          .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
+                                                          .query(Paths.get(ontoDir, "uobm/queries/test.sparql"))
+                                                          .answer(answers)
+                                                          .build();
+
+                pagoda.run();
+                CheckAnswers.assertSameAnswers(answers, givenAnswers);
+        }
+
+        @Test(groups = {"sygenia"})
+        public void answersCorrectness_sygenia_1() throws IOException {
+                answersCorrectness_sygenia(1);
+        }
+
+        @Test(groups = {"heavy",}, dataProvider = "UOBMNumbers")
+        public void answersCorrectness_sygenia(int number) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+//              Path answers = Paths.get(File.createTempFile("answers", ".json").getAbsolutePath());
+//              new File(answers.toString()).deleteOnExit();
+//              Path givenAnswers = TestUtil.getAnswersFilePath("answers/pagoda-uobm" + number + ".json");
+
+                Pagoda pagoda = Pagoda.builder()
+                                                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
+                                                          .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
+                                .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia.sparql"))
+                                .build();
+
+                pagoda.run();
+        }
+
+        @Test(groups = {"sygenia"})
+        public void answersCorrectness_sygenia_allBlanks_1() throws IOException {
+                answersCorrectness_sygenia(1);
+        }
+
+        @Test(groups = {"heavy"}, dataProvider = "UOBMNumbers")
+        public void answersCorrectness_sygenia_allBlanks(int number) throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
+                          .data(Paths.get(ontoDir, "uobm/data/uobm" + number + ".ttl"))
+                          .query(Paths.get(ontoDir, "uobm/queries/uobm_sygenia_all-blanks.sparql"))
+                          .build()
+                          .run();
+        }
+
+        @Test(groups = {"justExecute", "heavy", "nonOriginal", "existential"})
+        public void justExecute_modifiedUOBM() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "uobm_modified/univ-bench-dl-modified.owl"))
+                          .data(Paths.get(ontoDir, "uobm_modified/data/uobm1.ttl"))
+                          .query(Paths.get(ontoDir, "uobm_modified/queries/additional_queries.sparql"))
+                          .build()
+                          .run();
+        }
+
+        @Test(groups = {"justExecute"})
+        public void justExecute_additionalQueries() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
+                          .data(Paths.get(ontoDir, "uobm/data/uobm1.ttl"))
+                          .query(Paths.get(ontoDir, "uobm/queries/additional_queries.sparql"))
+                          .build()
+                          .run();
+        }
+
+        @Test(groups = {"justExecute", "UOBM50"})
+        public void justExecuteUOBM_50() throws IOException {
+                String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+                Pagoda.builder()
+                          .ontology(Paths.get(ontoDir, "uobm/univ-bench-dl.owl"))
+                          .data(Paths.get(ontoDir, "uobm/data/uobm50.ttl"))
+                          .query(Paths.get(ontoDir, "uobm/queries/test.sparql"))
+                          .build()
+                          .run();
+        }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java b/src/test/java/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java
new file mode 100644
index 0000000..3a2cad8
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java
@@ -0,0 +1,319 @@
+package uk.ac.ox.cs.pagoda.hermit;
+
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.MyPrefixes;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.Charset;
+
+public class TestRuleHelper {
+
+    @Test
+    public static void someTest() {
+        String prefixes = "PREFIX anony: <http://www.cs.ox.ac.uk/PAGOdA/skolemised#>\n" +
+                "PREFIX aux: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#>\n" +
+                "PREFIX owl: <http://www.w3.org/2002/07/owl#>\n" +
+                "PREFIX prefix0: <http://semantics.crl.ibm.com/univ-bench-dl.owl#>\n" +
+                "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n" +
+                "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n" +
+                "PREFIX ruleml: <http://www.w3.org/2003/11/ruleml#>\n" +
+                "PREFIX swrl: <http://www.w3.org/2003/11/swrl#>\n" +
+                "PREFIX swrlb: <http://www.w3.org/2003/11/swrlb#>\n" +
+                "PREFIX swrlx: <http://www.w3.org/2003/11/swrlx#>\n" +
+                "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>\n";
+        String rule = "owl:Nothing(?X) :- owl:Nothing2(?X).\n" +
+                "prefix0:WomanCollege(?X) :- prefix0:College(?X).\n" +
+                "owl:Nothing5(?X) :- prefix0:WomanCollege(?X), prefix0:hasStudent(?X,?Y), prefix0:Man(?Y).\n" +
+                "prefix0:SportsFan(?X) :- prefix0:Person(?X), prefix0:isCrazyAbout(?X,?Y), prefix0:Sports(?Y).\n" +
+                "prefix0:Organization(?X) :- prefix0:isAffiliateOf(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:lastName(?X,?Y).\n" +
+                "owl:sameAs(?Y1,?Y2) :- prefix0:isHeadOf(?Y1,?X), prefix0:isHeadOf(?Y2,?X).\n" +
+                "prefix0:isMemberOf(?Y,?X) :- prefix0:hasMember(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:hasMasterDegreeFrom(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:TeachingAssistant(?X).\n" +
+                "prefix0:Employee(?X) :- prefix0:Person(?X), prefix0:worksFor(?X,?Y), prefix0:Organization(?Y).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Media_Arts_And_ciencesClass(?X).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Medieval_ArtsClass(?X).\n" +
+                "prefix0:Professor(?X) :- prefix0:Chair(?X).\n" +
+                "prefix0:Faculty(?Y) :- prefix0:isTaughtBy(?X,?Y).\n" +
+                "prefix0:worksFor(?X,anony:individual25) :- prefix0:Employee(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Chemical_EngineeringClass(?X).\n" +
+                "prefix0:BaseballClass(anony:individual1) :- prefix0:BaseballLover(?X).\n" +
+                "prefix0:Course(?Y) :- prefix0:listedCourse(?X,?Y).\n" +
+                "prefix0:worksFor(?X,?Y) :- prefix0:isHeadOf(?X,?Y).\n" +
+                "prefix0:Faculty(?X) :- prefix0:teacherOf(?X,?Y).\n" +
+                "prefix0:Course(?Y) :- prefix0:teachingAssistantOf(?X,?Y).\n" +
+                "owl:Nothing(?X) :- owl:Nothing1(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:Student(?X).\n" +
+                "prefix0:isFriendOf(?Y,?X) :- prefix0:isFriendOf(?X,?Y).\n" +
+                "prefix0:Student(?X) :- prefix0:UndergraduateStudent(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:BasketBallLover(?X).\n" +
+                "prefix0:Person(?Y) :- prefix0:hasSameHomeTownWith(?X,?Y).\n" +
+                "prefix0:Employee(?X) :- prefix0:Faculty(?X).\n" +
+                "prefix0:Insterest(?X) :- prefix0:Music(?X).\n" +
+                "owl:Nothing1(?X) :- prefix0:NonScienceStudent(?X), prefix0:hasMajor(?X,?Y), prefix0:Science(?Y).\n" +
+                "owl:sameAs(?Y1,?Y2) :- prefix0:isTaughtBy(?X,?Y1), prefix0:isTaughtBy(?X,?Y2).\n" +
+                "prefix0:hasStudent(?Y,?X) :- prefix0:isStudentOf(?X,?Y).\n" +
+                "prefix0:Student(?X) :- prefix0:ScienceStudent(?X).\n" +
+                "prefix0:like(?X,anony:individual7) :- prefix0:PeopleWithHobby(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:Article(?X).\n" +
+                "prefix0:isTaughtBy(?Y,?X) :- prefix0:teacherOf(?X,?Y).\n" +
+                "prefix0:isCrazyAbout(?X,anony:individual19) :- prefix0:TennisFan(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:Marine_ScienceClass(?X).\n" +
+                "prefix0:SupportingStaff(?X) :- prefix0:SystemsStaff(?X).\n" +
+                "prefix0:hasStudent(?X,anony:individual10) :- prefix0:College(?X).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Theatre_and_DanceClass(?X).\n" +
+                "prefix0:Organization(?Y) :- prefix0:subOrganizationOf(?X,?Y).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Materical_Science_EngineeringClass(?X).\n" +
+                "prefix0:hasMember(?Y,?X) :- prefix0:isMemberOf(?X,?Y).\n" +
+                "prefix0:Student(?Y) :- prefix0:hasStudent(?X,?Y).\n" +
+                "owl:Nothing(?X) :- owl:Nothing5(?X).\n" +
+                "prefix0:isCrazyAbout(?X,anony:individual18) :- prefix0:SwimmingFan(?X).\n" +
+                "prefix0:Publication(?Y) :- prefix0:orgPublication(?X,?Y).\n" +
+                "prefix0:Chair(?X) :- prefix0:Person(?X), prefix0:isHeadOf(?X,?Y), prefix0:Department(?Y).\n" +
+                "prefix0:isStudentOf(?Y,?X) :- prefix0:hasStudent(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:isAdvisedBy(?X,?Y).\n" +
+                "prefix0:hasMajor(?X,anony:individual2) :- prefix0:Student(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:publicationDate(?X,?Y).\n" +
+                "owl:Nothing(?X) :- owl:Nothing6(?X).\n" +
+                "prefix0:Director(?X) :- prefix0:Person(?X), prefix0:isHeadOf(?X,?Y), prefix0:Program(?Y).\n" +
+                "prefix0:Professor(?X) :- prefix0:AssociateProfessor(?X).\n" +
+                "prefix0:TeachingAssistant(?X) :- prefix0:Person(?X), prefix0:teachingAssistantOf(?X,?Y), prefix0:Course(?Y).\n" +
+                "prefix0:Research(?Y) :- prefix0:researchProject(?X,?Y).\n" +
+                "prefix0:TeachingAssistant(?X) :- prefix0:teachingAssistantOf(?X,?Y).\n" +
+                "prefix0:University(?X) :- prefix0:hasAlumnus(?X,?Y).\n" +
+                "prefix0:Faculty(?X) :- prefix0:Lecturer(?X).\n" +
+                "prefix0:isHeadOf(?X,anony:individual21) :- prefix0:Dean(?X).\n" +
+                "prefix0:like(?X,?Y) :- prefix0:isCrazyAbout(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:hasSameHomeTownWith(?X,?Y).\n" +
+                "prefix0:Organization(?X) :- prefix0:orgPublication(?X,?Y).\n" +
+                "prefix0:Person(?Y) :- prefix0:hasMember(?X,?Y).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:LinguisticsClass(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Aeronautical_EngineeringClass(?X).\n" +
+                "owl:Nothing(?X) :- owl:Nothing3(?X).\n" +
+                "prefix0:isHeadOf(?X,anony:individual12) :- prefix0:Director(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:publicationAuthor(?X,?Y).\n" +
+                "prefix0:Organization(?X) :- prefix0:College(?X).\n" +
+                "prefix0:isCrazyAbout(?X,anony:individual24) :- prefix0:BaseballFan(?X).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Performing_ArtsClass(?X).\n" +
+                "prefix0:Sports(?X) :- prefix0:BasketBallClass(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:PsychologyClass(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:Employee(?X).\n" +
+                "prefix0:FineArts(?X) :- prefix0:DramaClass(?X).\n" +
+                "prefix0:Faculty(?X) :- prefix0:PostDoc(?X).\n" +
+                "prefix0:University(?Y) :- prefix0:hasDoctoralDegreeFrom(?X,?Y).\n" +
+                "prefix0:Sports(anony:individual0) :- prefix0:SportsLover(?X).\n" +
+                "prefix0:Person(?Y) :- prefix0:hasAlumnus(?X,?Y).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Modern_ArtsClass(?X).\n" +
+                "prefix0:hasMember(?X,?Y) :- prefix0:hasStudent(?X,?Y).\n" +
+                "prefix0:Course(?X) :- prefix0:isTaughtBy(?X,?Y).\n" +
+                "prefix0:NonScienceStudent(?X) :- prefix0:Student(?X).\n" +
+                "prefix0:BasketBallLover(?X) :- prefix0:Person(?X), prefix0:like(?X,?Y), prefix0:BasketBallClass(?Y).\n" +
+                "prefix0:Professor(?X) :- prefix0:VisitingProfessor(?X).\n" +
+                "prefix0:GraduateCourse(?Y) :- prefix0:GraduateStudent(?X), prefix0:takesCourse(?X,?Y).\n" +
+                "prefix0:TennisClass(anony:individual19) :- prefix0:TennisFan(?X).\n" +
+                "prefix0:Work(?X) :- prefix0:Research(?X).\n" +
+                "prefix0:TennisFan(?X) :- prefix0:Person(?X), prefix0:isCrazyAbout(?X,?Y), prefix0:TennisClass(?Y).\n" +
+                "prefix0:ScienceStudent(?X) :- prefix0:Student(?X), prefix0:hasMajor(?X,?Y), prefix0:Science(?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:Woman(?X).\n" +
+                "prefix0:Man(?X) :- prefix0:Person(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:hasUndergraduateDegreeFrom(?X,?Y).\n" +
+                "prefix0:ResearchGroup(?X) :- prefix0:researchProject(?X,?Y).\n" +
+                "prefix0:hasSameHomeTownWith(?X,?Z) :- prefix0:hasSameHomeTownWith(?X,?Y), prefix0:hasSameHomeTownWith(?Y,?Z).\n" +
+                "prefix0:Person(?X) :- prefix0:isFriendOf(?X,?Y).\n" +
+                "prefix0:Person(?Y) :- prefix0:publicationAuthor(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:Chair(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:Manual(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:UnofficialPublication(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Industry_EngineeringClass(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:StatisticsClass(?X).\n" +
+                "prefix0:Organization(?Y) :- prefix0:isStudentOf(?X,?Y).\n" +
+                "prefix0:SwimmingFan(?X) :- prefix0:Person(?X), prefix0:isCrazyAbout(?X,?Y), prefix0:SwimmingClass(?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:emailAddress(?X,?Y).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Latin_ArtsClass(?X).\n" +
+                "prefix0:Organization(?X) :- prefix0:ResearchGroup(?X).\n" +
+                "prefix0:AcademicSubject(?X) :- prefix0:HumanitiesAndSocial(?X).\n" +
+                "prefix0:Professor(?X) :- prefix0:Dean(?X).\n" +
+                "prefix0:SwimmingClass(anony:individual8) :- prefix0:SwimmingLover(?X).\n" +
+                "prefix0:University(?Y) :- prefix0:hasMasterDegreeFrom(?X,?Y).\n" +
+                "prefix0:Article(?X) :- prefix0:ConferencePaper(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:BasketBallFan(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:ReligionsClass(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:PhysicsClass(?X).\n" +
+                "prefix0:Dean(?X) :- prefix0:isHeadOf(?X,?Y), prefix0:College(?Y).\n" +
+                "prefix0:University(?Y) :- prefix0:hasDegreeFrom(?X,?Y).\n" +
+                "prefix0:Organization(?X) :- prefix0:hasMember(?X,?Y).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Computer_EngineeringClass(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:Software(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:GeosciencesClass(?X).\n" +
+                "prefix0:hasMajor(?X,anony:individual9) :- prefix0:ScienceStudent(?X).\n" +
+                "prefix0:hasDegreeFrom(?Y,?X) :- prefix0:hasAlumnus(?X,?Y).\n" +
+                "prefix0:Software(?X) :- prefix0:softwareDocumentation(?X,?Y).\n" +
+                "prefix0:isMemberOf(?X,?Y) :- prefix0:isStudentOf(?X,?Y).\n" +
+                "prefix0:Organization(?X) :- prefix0:hasStudent(?X,?Y).\n" +
+                "owl:Nothing2(?X) :- prefix0:GraduateCourse(?X), prefix0:GraduateCourse_neg(?X).\n" +
+                "prefix0:BaseballFan(?X) :- prefix0:Person(?X), prefix0:isCrazyAbout(?X,?Y), prefix0:BaseballClass(?Y).\n" +
+                "prefix0:Publication(?X) :- prefix0:publicationResearch(?X,?Y).\n" +
+                "prefix0:like(?X,anony:individual14) :- prefix0:PeopleWithManyHobbies(?X).\n" +
+                "prefix0:SportsLover(?X) :- prefix0:Person(?X), prefix0:like(?X,?Y), prefix0:Sports(?Y).\n" +
+                "prefix0:Organization(?X) :- prefix0:University(?X).\n" +
+                "prefix0:hasAlumnus(?Y,?X) :- prefix0:hasDegreeFrom(?X,?Y).\n" +
+                "prefix0:Science(?X) :- prefix0:Materials_ScienceClass(?X).\n" +
+                "prefix0:Professor(?X) :- prefix0:tenured(?X,?Y).\n" +
+                "prefix0:Faculty(?X) :- prefix0:Professor(?X).\n" +
+                "prefix0:Student(?X) :- prefix0:NonScienceStudent(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:telephone(?X,?Y).\n" +
+                "prefix0:FineArts(?X) :- prefix0:ArchitectureClass(?X).\n" +
+                "prefix0:University(?Y) :- prefix0:hasUndergraduateDegreeFrom(?X,?Y).\n" +
+                "prefix0:Man(anony:individual10) :- prefix0:College(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:Man(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:title(?X,?Y).\n" +
+                "prefix0:subOrganizationOf(?X,?Z) :- prefix0:subOrganizationOf(?X,?Y), prefix0:subOrganizationOf(?Y,?Z).\n" +
+                "owl:sameAs(?Y1,?Y2) :- prefix0:like(?X,?Y1), prefix0:like(?X,?Y2).\n" +
+                "prefix0:takesCourse(?X,anony:individual4) :- prefix0:GraduateStudent(?X).\n" +
+                "prefix0:Sports(?X) :- prefix0:TennisClass(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Petroleuml_EngineeringClass(?X).\n" +
+                "prefix0:Organization(?X) :- prefix0:Institute(?X).\n" +
+                "prefix0:isCrazyAbout(?X,anony:individual16) :- prefix0:BasketBallFan(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:BiologyClass(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:SportsFan(?X).\n" +
+                "prefix0:Course(?X) :- prefix0:GraduateCourse(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:Director(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:EconomicsClass(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:BaseballLover(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:HistoryClass(?X).\n" +
+                "prefix0:FineArts(?X) :- prefix0:Asian_ArtsClass(?X).\n" +
+                "prefix0:isStudentOf(?X,?Y) :- prefix0:enrollIn(?X,?Y).\n" +
+                "prefix0:isHeadOf(?X,anony:individual20) :- prefix0:Chair(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:PeopleWithHobby(?X).\n" +
+                "prefix0:Sports(anony:individual5) :- prefix0:SportsFan(?X).\n" +
+                "prefix0:Science(anony:individual9) :- prefix0:ScienceStudent(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Biomedical_EngineeringClass(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:Modern_LanguagesClass(?X).\n" +
+                "prefix0:like(?X,?Y) :- prefix0:love(?X,?Y).\n" +
+                "prefix0:hasStudent(?X,anony:individual11) :- prefix0:College(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:ChemistryClass(?X).\n" +
+                "prefix0:Student(?X) :- prefix0:takesCourse(?X,?Y).\n" +
+                "prefix0:teacherOf(?Y,?X) :- prefix0:isTaughtBy(?X,?Y).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:AnthropologyClass(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:hasDegreeFrom(?X,?Y).\n" +
+                "prefix0:Person(?X) :- prefix0:hasDoctoralDegreeFrom(?X,?Y).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Electrical_EngineeringClass(?X).\n" +
+                "owl:differentFrom(anony:individual13,anony:individual14) :- prefix0:PeopleWithManyHobbies(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:SportsLover(?X).\n" +
+                "prefix0:Organization(?X) :- prefix0:subOrganizationOf(?X,?Y).\n" +
+                "prefix0:SwimmingLover(?X) :- prefix0:Person(?X), prefix0:like(?X,?Y), prefix0:SwimmingClass(?Y).\n" +
+                "prefix0:BaseballLover(?X) :- prefix0:Person(?X), prefix0:like(?X,?Y), prefix0:BaseballClass(?Y).\n" +
+                "prefix0:Science(?X) :- prefix0:Computer_ScienceClass(?X).\n" +
+                "prefix0:Sports(?X) :- prefix0:SwimmingClass(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:AstronomyClass(?X).\n" +
+                "prefix0:Work(?X) :- prefix0:Course(?X).\n" +
+                "prefix0:Science(?X) :- prefix0:MathematicsClass(?X).\n" +
+                "prefix0:AcademicSubject(?X) :- prefix0:Engineering(?X).\n" +
+                "prefix0:hasDegreeFrom(?X,?Y) :- prefix0:hasUndergraduateDegreeFrom(?X,?Y).\n" +
+                "prefix0:like(?X,anony:individual15) :- prefix0:PeopleWithManyHobbies(?X).\n" +
+                "prefix0:Sports(?X) :- prefix0:BaseballClass(?X).\n" +
+                "prefix0:Student(?X) :- prefix0:isStudentOf(?X,?Y).\n" +
+                "prefix0:Professor(?Y) :- prefix0:isAdvisedBy(?X,?Y).\n" +
+                "prefix0:SwimmingClass(anony:individual18) :- prefix0:SwimmingFan(?X).\n" +
+                "prefix0:like(?X,anony:individual22) :- prefix0:BasketBallLover(?X).\n" +
+                "prefix0:like(?X,anony:individual1) :- prefix0:BaseballLover(?X).\n" +
+                "prefix0:Schedule(?X) :- prefix0:listedCourse(?X,?Y).\n" +
+                "owl:Nothing6(?X) :- owl:differentFrom(?X,?X).\n" +
+                "prefix0:PeopleWithManyHobbies(?X) :- prefix0:like(?X,?Y3).\n" +
+                "prefix0:Course(anony:individual23) :- prefix0:TeachingAssistant(?X).\n" +
+                "prefix0:takesCourse(?X,anony:individual3) :- prefix0:takesCourse(?X,?Y).\n" +
+                "prefix0:love(?X,?Y) :- prefix0:like(?X,?Y).\n" +
+                "prefix0:AcademicSubject(?X) :- prefix0:Science(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:ResearchAssistant(?X).\n" +
+                "prefix0:Insterest(?X) :- prefix0:Sports(?X).\n" +
+                "prefix0:Article(?X) :- prefix0:TechnicalReport(?X).\n" +
+                "prefix0:UndergraduateStudent(?Y) :- prefix0:WomanCollege(?X), prefix0:hasStudent(?X,?Y).\n" +
+                "prefix0:Department(anony:individual20) :- prefix0:Chair(?X).\n" +
+                "prefix0:Woman(?X) :- prefix0:Person(?X).\n" +
+                "owl:Nothing4(?X) :- prefix0:UndergraduateStudent(?X), prefix0:UndergraduateStudent_neg(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:HumanitiesClass(?X).\n" +
+                "prefix0:GraduateCourse_neg(anony:individual3) :- prefix0:takesCourse(?X,?Y).\n" +
+                "prefix0:Organization(?Y) :- prefix0:isAffiliatedOrganizationOf(?X,?Y).\n" +
+                "owl:Nothing(?X) :- owl:Nothing4(?X).\n" +
+                "prefix0:like(?X,anony:individual0) :- prefix0:SportsLover(?X).\n" +
+                "prefix0:Research(?Y) :- prefix0:publicationResearch(?X,?Y).\n" +
+                "prefix0:Professor(?X) :- prefix0:AssistantProfessor(?X).\n" +
+                "prefix0:Program(anony:individual12) :- prefix0:Director(?X).\n" +
+                "prefix0:isMemberOf(?X,?Y) :- prefix0:worksFor(?X,?Y).\n" +
+                "prefix0:Organization(anony:individual25) :- prefix0:Employee(?X).\n" +
+                "prefix0:hasDegreeFrom(?X,?Y) :- prefix0:hasDoctoralDegreeFrom(?X,?Y).\n" +
+                "prefix0:Person(?Y) :- prefix0:isAffiliateOf(?X,?Y).\n" +
+                "prefix0:Student(?X) :- prefix0:Person(?X), prefix0:isStudentOf(?X,?Y), prefix0:Organization(?Y).\n" +
+                "prefix0:PeopleWithHobby(?X) :- prefix0:Person(?X), prefix0:like(?X,?Y).\n" +
+                "prefix0:Organization(anony:individual17) :- prefix0:Student(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Mechanical_EngineeringClass(?X).\n" +
+                "prefix0:Employee(?X) :- prefix0:SupportingStaff(?X).\n" +
+                "prefix0:Organization(?X) :- prefix0:Department(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:PhilosophyClass(?X).\n" +
+                "prefix0:College(anony:individual21) :- prefix0:Dean(?X).\n" +
+                "prefix0:UndergraduateStudent_neg(anony:individual11) :- prefix0:College(?X).\n" +
+                "owl:Nothing3(?X) :- prefix0:Man(?X), prefix0:Woman(?X).\n" +
+                "owl:sameAs(?Y1,?Y2) :- prefix0:takesCourse(?X,?Y1), prefix0:LeisureStudent(?X), prefix0:takesCourse(?X,?Y2).\n" +
+                "prefix0:Organization(?X) :- prefix0:isAffiliatedOrganizationOf(?X,?Y).\n" +
+                "prefix0:isCrazyAbout(?X,anony:individual5) :- prefix0:SportsFan(?X).\n" +
+                "prefix0:Software(?X) :- prefix0:softwareVersion(?X,?Y).\n" +
+                "prefix0:Science(anony:individual2) :- prefix0:Student(?X).\n" +
+                "prefix0:SupportingStaff(?X) :- prefix0:ClericalStaff(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:SwimmingLover(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:age(?X,?Y).\n" +
+                "prefix0:BasketBallClass(anony:individual22) :- prefix0:BasketBallLover(?X).\n" +
+                "prefix0:like(?X,anony:individual8) :- prefix0:SwimmingLover(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:firstName(?X,?Y).\n" +
+                "prefix0:Department(?Y) :- prefix0:enrollIn(?X,?Y).\n" +
+                "prefix0:Publication(?Y) :- prefix0:softwareDocumentation(?X,?Y).\n" +
+                "prefix0:hasDegreeFrom(?X,?Y) :- prefix0:hasMasterDegreeFrom(?X,?Y).\n" +
+                "prefix0:AcademicSubject(?Y) :- prefix0:hasMajor(?X,?Y).\n" +
+                "prefix0:Article(?X) :- prefix0:JournalArticle(?X).\n" +
+                "prefix0:Organization(?X) :- prefix0:Program(?X).\n" +
+                "prefix0:Course(?Y) :- prefix0:teacherOf(?X,?Y).\n" +
+                "prefix0:AcademicSubject(?X) :- prefix0:FineArts(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:TennisFan(?X).\n" +
+                "prefix0:GraduateStudent(?X) :- prefix0:takesCourse(?X,?Y).\n" +
+                "prefix0:BasketBallFan(?X) :- prefix0:Person(?X), prefix0:isCrazyAbout(?X,?Y), prefix0:BasketBallClass(?Y).\n" +
+                "prefix0:Publication(?X) :- prefix0:Specification(?X).\n" +
+                "prefix0:worksFor(?X,anony:individual6) :- prefix0:ResearchAssistant(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:SwimmingFan(?X).\n" +
+                "prefix0:BasketBallClass(anony:individual16) :- prefix0:BasketBallFan(?X).\n" +
+                "prefix0:Person(?X) :- prefix0:BaseballFan(?X).\n" +
+                "prefix0:Person(?Y) :- prefix0:isFriendOf(?X,?Y).\n" +
+                "prefix0:like(?X,anony:individual13) :- prefix0:PeopleWithManyHobbies(?X).\n" +
+                "owl:differentFrom(anony:individual14,anony:individual15) :- prefix0:PeopleWithManyHobbies(?X).\n" +
+                "prefix0:hasSameHomeTownWith(?Y,?X) :- prefix0:hasSameHomeTownWith(?X,?Y).\n" +
+                "prefix0:ResearchGroup(anony:individual6) :- prefix0:ResearchAssistant(?X).\n" +
+                "prefix0:College(?X) :- prefix0:WomanCollege(?X).\n" +
+                "prefix0:BaseballClass(anony:individual24) :- prefix0:BaseballFan(?X).\n" +
+                "owl:differentFrom(anony:individual13,anony:individual15) :- prefix0:PeopleWithManyHobbies(?X).\n" +
+                "prefix0:Publication(?X) :- prefix0:Book(?X).\n" +
+                "prefix0:Professor(?X) :- prefix0:FullProfessor(?X).\n" +
+                "prefix0:Engineering(?X) :- prefix0:Civil_EngineeringClass(?X).\n" +
+                "prefix0:isStudentOf(?X,anony:individual17) :- prefix0:Student(?X).\n" +
+                "prefix0:HumanitiesAndSocial(?X) :- prefix0:EnglishClass(?X).\n" +
+                "prefix0:teachingAssistantOf(?X,anony:individual23) :- prefix0:TeachingAssistant(?X).\n" +
+                "prefix0:woman(?X) | prefix0:man(?X) :- prefix0:human(?X).\n" +
+                "prefix0:FineArts(?X) :- prefix0:MusicsClass(?X).\n";
+
+        for(String line: prefixes.split("\n")) {
+            String[] split = line.split(" ");
+            MyPrefixes.PAGOdAPrefixes.declarePrefix(split[1], OWLHelper.removeAngles(split[2]));
+        }
+
+        InputStream is = new ByteArrayInputStream(rule.getBytes(Charset.defaultCharset()));
+        DatalogProgram datalogProgram = new DatalogProgram(is);
+        System.out.println(">> General <<");
+        System.out.println(datalogProgram.getGeneral().toString());
+        System.out.println(">> Lower <<");
+        System.out.println(datalogProgram.getLower().toString());
+        System.out.println(">> Upper <<");
+        System.out.println(datalogProgram.getUpper().toString());
+        System.out.flush();
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/junit/ClauseTester.java b/src/test/java/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
new file mode 100644
index 0000000..ad4b2de
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
@@ -0,0 +1,183 @@
+package uk.ac.ox.cs.pagoda.junit;
+
+import org.junit.Test;
+import org.semanticweb.HermiT.model.*;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import uk.ac.ox.cs.pagoda.approx.Clause;
+import uk.ac.ox.cs.pagoda.approx.Clausifier;
+
+import static org.junit.Assert.fail;
+
+public class ClauseTester {
+
+        public void test_clause(Atom[] headAtoms, Atom[] bodyAtoms) {
+                OWLOntologyManager m = OWLManager.createOWLOntologyManager();
+                OWLOntology emptyOntology = null;
+                try {
+                        emptyOntology = m.createOntology();
+                } catch(Exception e) {
+                        e.printStackTrace();
+                        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_nominal() {
+                Variable x = Variable.create("X");
+                AtomicRole r = AtomicRole.create("r");
+                Individual o = Individual.create("o");
+                Atom[] bodyAtoms = new Atom[]{Atom.create(r, x, o)};
+                AtomicConcept A = AtomicConcept.create("A");
+                Atom[] headAtoms = new Atom[]{Atom.create(A, x)};
+                test_clause(headAtoms, bodyAtoms);
+        }
+
+        @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();
+                        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();
+                        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();
+                        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();
+                        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();
+                        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/src/test/java/uk/ac/ox/cs/pagoda/query/CheckAnswers.java b/src/test/java/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
new file mode 100644
index 0000000..71730c3
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
@@ -0,0 +1,51 @@
+package uk.ac.ox.cs.pagoda.query;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import org.testng.Assert;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.lang.reflect.Type;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Set;
+
+/**
+ * It provides auxiliary methods for checking answers.
+ */
+public class CheckAnswers {
+
+    private CheckAnswers() {
+    }
+
+    public static void assertSameAnswers(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> computedAnswersRecords = gson.fromJson(computedReader, cqType);
+        Set<QueryRecord> givenAnswersRecords = gson.fromJson(givenReader, cqType);
+
+        for(QueryRecord computedAnswersRecord : computedAnswersRecords) {
+            Set<AnswerTuple> givenAnswers = null;
+            for(QueryRecord givenAnswersRecord : givenAnswersRecords) {
+                if(givenAnswersRecord.queryID == computedAnswersRecord.queryID) {
+                    givenAnswers = givenAnswersRecord.soundAnswerTuples;
+                    break;
+                }
+            }
+
+            Assert.assertNotNull(givenAnswers, "Missing given answer for query no. " + computedAnswersRecord.queryID);
+
+            Set<AnswerTuple> computedAnswers = computedAnswersRecord.soundAnswerTuples;
+            Assert.assertEquals(computedAnswers.size(), givenAnswers.size(),
+                                "Different number of sound answers for query " + computedAnswersRecord.queryID + "!"
+                                        + "Expected " + givenAnswers.size() + ", got " + computedAnswers.size());
+            Assert.assertEquals(computedAnswers, givenAnswers,
+                                "Different sound answers for query " + computedAnswersRecord.queryID + "!");
+        }
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java b/src/test/java/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
new file mode 100644
index 0000000..6bd8f05
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
@@ -0,0 +1,14 @@
+package uk.ac.ox.cs.pagoda.rules.approximators;
+
+import org.testng.annotations.Test;
+
+/**
+ * Tests for the class <tt>SkolemTermsManager</tt>
+ */
+public class TestSkolemTermsManager {
+
+    @Test
+    public void test() {
+        // TODO some test
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/summary/SummaryTester.java b/src/test/java/uk/ac/ox/cs/pagoda/summary/SummaryTester.java
new file mode 100644
index 0000000..60c8ed4
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/summary/SummaryTester.java
@@ -0,0 +1,140 @@
+package uk.ac.ox.cs.pagoda.summary;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Scanner;
+
+import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.parameters.Imports;
+
+import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+import uk.ac.ox.cs.pagoda.owl.QueryRoller;
+import uk.ac.ox.cs.pagoda.query.QueryManager;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.summary.Summary;
+
+public class SummaryTester {
+
+        static String FILE_BREAK = System.getProperty("file.separator");
+        static String LINE_BREAK = System.getProperty("line.separator");
+        
+        public static void main(String[] args) throws Exception {
+//              String arg = "ontologies/claros/all-in-one-manually.owl"; 
+//              String arg = "ontologies/claros/Claros.owl ontologies/claros/data"; 
+                String arg =  "../uobmGenerator/univ-bench-dl.owl " + 
+                                "../uobmGenerator/uobm1 " + //"a " + 
+                                "ontologies/uobm/queries/uobm_standard_less.sparql"; 
+                                
+                testSummarisedUpperBound(arg.split("\\ ")); 
+        }
+        
+        /**
+         * args[0] ontology file location
+         * args[1] data directory
+         * args[2] sparql query file location
+         * 
+         * @param args 
+         * @throws OWLOntologyCreationException
+         * @throws FileNotFoundException
+         * @throws OWLOntologyStorageException 
+         */
+        public static void testSummarisedUpperBound(String[] args) throws OWLOntologyCreationException, FileNotFoundException, OWLOntologyStorageException {
+                OWLOntology onto = OWLHelper.loadOntology(args[0]); 
+                try {
+                        onto = OWLHelper.getImportedOntology(onto, args[1]); 
+                } catch (IOException e) {
+                        e.printStackTrace();
+                } 
+                 
+                Summary sum = testSummary(onto);
+                System.out.println("Summarisation Done."); 
+                
+                System.out.println(args[2]); 
+                Scanner scanner = new Scanner(new File(args[2])); 
+                OWLOntology summary = sum.getSummary();
+                OWLDataFactory factory = summary.getOWLOntologyManager().getOWLDataFactory(); 
+                QueryRoller r = new QueryRoller(factory);
+                OWLClassExpression summarisedQueryExp;
+                Reasoner reasoner = new Reasoner(summary); 
+                QueryManager queryManager = new QueryManager(); 
+                int upperBoundCounter, queryID = 0;
+                StringBuilder queryText = new StringBuilder();
+                String[] vars; 
+                
+                for (String line; ; ) {
+                        queryText.setLength(0);
+                        while (scanner.hasNextLine() && (line = scanner.nextLine()) != null && !line.startsWith("^[query"));
+                        if (!scanner.hasNextLine()) break; 
+                        
+                        while (scanner.hasNextLine() && (line = scanner.nextLine()) != null && !line.isEmpty())
+                                queryText.append(line).append(LINE_BREAK);
+                        if (!scanner.hasNextLine()) break; 
+                                
+                        System.out.println("------------ starting computing for Query " + ++queryID + "------------"); 
+                        
+                        System.out.println(queryText); 
+                        
+                        QueryRecord record = queryManager.create(queryText.toString(), queryID);
+                        vars = record.getAnswerVariables(); 
+                        if (vars.length > 1) {
+                                System.out.println("The query cannot be processed by HermiT ... More than one answer variable"); 
+                                continue; 
+                        }
+                        
+                        summarisedQueryExp = r.rollUp(DLClauseHelper.getQuery(sum.getSummary(record), null), vars[0]);
+                        
+                        upperBoundCounter = 0; 
+                        for (String representative: sum.getRepresentatives()) 
+                                if (reasoner.isEntailed(factory.getOWLClassAssertionAxiom(summarisedQueryExp, factory.getOWLNamedIndividual(IRI.create(representative))))) {
+                                        upperBoundCounter += sum.getGroup(representative).size(); 
+                                }
+                        
+                        System.out.println("There are " + upperBoundCounter + " individual(s) in the upper bound computed by summary."); 
+                }
+                scanner.close();
+        }
+        
+        public static Summary testSummary(OWLOntology ontology) throws OWLOntologyCreationException, FileNotFoundException {
+                Summary sum = new Summary(ontology);
+                
+                System.out.println("original ontology data: "); 
+                outputStatistics(ontology); 
+                
+                OWLOntology summary = sum.getSummary();
+                
+                System.out.println("summarised ontology data: "); 
+                outputStatistics(summary);
+                
+                try {
+                        FileOutputStream out = new FileOutputStream("summary.owl"); 
+                        summary.getOWLOntologyManager().saveOntology(summary, out);
+                        out.close();
+                } catch (OWLOntologyStorageException e) {
+                        e.printStackTrace();
+                } catch (IOException e) {
+                        // TODO Auto-generated catch block
+                        e.printStackTrace();
+                }
+                
+                return sum; 
+        }
+
+        private static void outputStatistics(OWLOntology onto) {
+                System.out.println("TBox: " + onto.getTBoxAxioms(Imports.INCLUDED).size() +
+                                "\tRBox: " + onto.getRBoxAxioms(Imports.INCLUDED).size() + 
+                                "\tABox: " + onto.getABoxAxioms(Imports.INCLUDED).size());
+                System.out.println("Class Assertions: " + onto.getAxiomCount(AxiomType.CLASS_ASSERTION, Imports.INCLUDED) + 
+                                "\tObject Property Assertions: " + onto.getAxiomCount(AxiomType.OBJECT_PROPERTY_ASSERTION, Imports.INCLUDED)); 
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/tester/OWLTester.java b/src/test/java/uk/ac/ox/cs/pagoda/tester/OWLTester.java
new file mode 100644
index 0000000..25162c8
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/tester/OWLTester.java
@@ -0,0 +1,30 @@
+package uk.ac.ox.cs.pagoda.tester;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.parameters.Imports;
+
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
+
+public class OWLTester {
+
+        public static void main(String[] args) throws OWLOntologyCreationException {
+//              OWLOntology onto = OWLHelper.loadOntology("dbpedia_imported.owl");
+                OWLOntology onto = OWLHelper.loadOntology("reactome_imported.owl");
+                OWLOntologyManager manager = onto.getOWLOntologyManager();
+//              OWLOntology data = manager.loadOntology(IRI.create("file:/media/krr-nas-share/Yujiao/ontologies/bio2rdf/reactome/graph\ sampling/sample_1_new.ttl"));
+//              System.out.println("data: " + data.getAxiomCount() + " " + data.getABoxAxioms(true).size()); 
+                for (OWLOntology t: manager.getOntologies()) {
+                        System.out.println(t.getOntologyID());
+                        System.out.println(t.getAxiomCount() + " " + onto.getABoxAxioms(Imports.INCLUDED).size()); 
+                }
+                System.out.println("In closure: " + onto.getImportsClosure().size()); 
+                for (OWLOntology t: onto.getImportsClosure())
+                        System.out.println(t.getOntologyID());
+                
+                System.out.println(onto.getAxiomCount() + " " + onto.getABoxAxioms(Imports.INCLUDED).size()); 
+        }
+
+}
+
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/src/test/java/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
new file mode 100644
index 0000000..d741d3b
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
@@ -0,0 +1,318 @@
+package uk.ac.ox.cs.pagoda.tester;
+
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.PagodaProperties;
+import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.Utility;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Scanner;
+
+@Deprecated
+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/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";
+
+        public static final String test_tbox = onto_dir + "smallExampleFromAna/dummy.owl";
+        public static final String test_abox = onto_dir + "smallExampleFromAna/initialABox.ttl";
+        public static final String test_query = onto_dir + "smallExampleFromAna/queries.dlog";
+
+        public static final int lubm_number = 1;
+        public static final String lubm_tbox = onto_dir + "lubm/univ-bench.owl";
+        public static final String lubm_abox = onto_dir + "lubm/data/lubm" + lubm_number + ".ttl";
+        public static final String lubm_abox_copy = onto_dir + "lubm/data/lubm" + lubm_number + " (copy).ttl";
+        public static final String lubm_query = onto_dir + "lubm/queries/test.sparql";
+        public static final String lubm_query6 = onto_dir + "lubm/queries/test_q6.sparql";
+        public static final String lubm_query20 = onto_dir + "lubm/queries/test_q16.sparql";
+
+        public static final int uobm_number = 1;
+        public static final String uobm_tbox = onto_dir + "uobm/univ-bench-dl.owl";
+        public static final String uobm_abox = onto_dir + "uobm/data/uobm" + uobm_number + ".ttl";
+        public static final String uobm_query = onto_dir + "uobm/queries/test.sparql";
+        public static final String uobm_query_temp = onto_dir + "uobm/queries/temp.sparql";
+        public static final String uobm_query2 = onto_dir + "uobm/queries/standard_q2.sparql";
+        public static final String uobm_query9 = onto_dir + "uobm/queries/standard_q9.sparql";
+        public static final String uobm_query11 = onto_dir + "uobm/queries/standard_q11.sparql";
+        public static final String uobm_query12 = onto_dir + "uobm/queries/standard_q12.sparql";
+        public static final String uobm_query14 = onto_dir + "uobm/queries/standard_q14.sparql";
+        public static final String uobm_query15 = onto_dir + "uobm/queries/standard_q15.sparql";
+        public static final String uobm_query_multi = onto_dir + "uobm/queries/standard_multi.sparql";
+        public static final String uobm_generated_query1 = onto_dir + "uobm/queries/generated_q1.sparql";
+        public static final String uobm_query_group3 = onto_dir + "uobm/queries/standard_group3.sparql";
+
+        public static final String npd_tbox = onto_dir + "npd/npd-all-minus-datatype.owl";
+        // "npd/npd-all.owl";
+        // "npd-all-minus-datatype.owl";
+        public static final String npd_abox = onto_dir + "npd/data/npd-data-dump-minus-datatype-new.ttl";
+        // "npd/data/npd-data-dump-processed.ttl";
+        // "npd-data-dump-minus-datatype-old.ttl";
+        public static final String npd_query = onto_dir + "npd/queries/atomic.sparql";
+
+        public static final String npd_bench_tbox = onto_dir + "npd-benchmark/npd-v2-ql_a.owl";
+                        // npd-all-minus-datatype.owl";
+        public static final String npd_bench_abox = onto_dir + "npd-benchmark/npd-v2-ql_a.ttl";
+                        // npd-data-dump-minus-datatype-old.ttl";
+        public static final String npd_bench_query = onto_dir + "npd-benchmark/queries/all.sparql";
+
+        public static final String dbpedia_tbox = onto_dir + "dbpedia/integratedOntology-all-in-one-minus-datatype.owl";
+        public static final String dbpedia_abox = onto_dir + "dbpedia/data/dbpedia-minus-datatype-new.ttl";
+        public static final String dbpedia_query = onto_dir + "dbpedia/queries/atomic_ground.sparql";
+        public static final String dbpedia_query274 = onto_dir + "dbpedia/atomic_q274.sparql";
+
+        public static final String dbpedia_latest_tbox = onto_dir + "dbpedia/dbpedia_2014.owl";
+        public static final String travel_tbox = onto_dir + "dbpedia/travel.owl";
+        public static final String dbpedia_tbox_simple = onto_dir + "dbpedia/dbpedia_simple.owl";
+
+        public static final String bioModels_tbox = onto_dir + "biomodels/biomodels-21.owl";
+        public static final String bioModels_abox = onto_dir + "biomodels/data_processed_1.ttl";
+        public static final String bioModels_queries = onto_dir + "biomodels/queries/queries.sparql";
+
+        public static final String chembl_tbox = onto_dir + "bio2rdf/chembl/cco-processed-noDPR-noDPD.ttl";
+        public static final String chembl_abox = onto_dir + "bio2rdf/chembl/graph sampling old/sample_100.nt";
+        public static final String chembl_queries = onto_dir + "bio2rdf/chembl/queries/problematic.sparql";
+                        //"bio2rdf/chembl/queries/atomic_one_filtered.sparql"; //
+
+        public static final String reactome_tbox = onto_dir + "bio2rdf/reactome/biopax-level3-processed.owl";
+        public static final String reactome_abox = onto_dir + "bio2rdf/reactome/graph sampling old/sample.ttl";
+                        //data/data.ttl"; //graph sampling old/reactome_sample_10.ttl"; //
+        public static final String reactome_queries = onto_dir + "bio2rdf/reactome/queries/atomic.sparql";
+
+        public static final String uniprot_tbox = onto_dir + "bio2rdf/uniprot/core-processed.owl";
+        public static final String uniprot_abox = onto_dir + "bio2rdf/uniprot/graph sampling/sample_1.nt";
+        public static final String uniprot_queries = onto_dir + "bio2rdf/uniprot/queries/atomic_one.sparql";
+
+        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";
+        QueryReasoner pagoda;
+
+        //      private void printPredicatesWithGap() {
+//              for (String p: ((MyQueryReasoner) pagoda).getPredicatesWithGap()) {
+//                      System.out.println(p); 
+//              }
+//      }
+        Timer timer = new Timer();
+
+        public PagodaTester(QueryReasoner reasoner) {
+                pagoda = reasoner;
+        }
+
+        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};
+//                      args = new String[] {uobm_tbox, uobm_abox, uobm_query};
+//                      args = new String[] {fly, "null", fly_query};
+//                      args = new String[] {dbpedia_tbox, dbpedia_abox, dbpedia_query};
+//                      args = new String[] {travel_tbox, null, dbpedia_query274};
+                        args = new String[]{fly, fly_query};
+//                      args = new String[] {npd_tbox, npd_abox, npd_query};
+//                      args = new String[] {npd_bench_tbox, npd_bench_abox, npd_bench_query};
+//                      args = new String[] {"../SemFacet/WebContent/WEB-INF/data/dbpedia.owl", "../SemFacet/WebContent/WEB-INF/data/dbpediaA.nt", null};
+//                      args = new String[] {"../core/WebContent/WEB-INF/data/fly.owl", "../core/WebContent/WEB-INF/data/fly-data.nt", null};
+//                      args = new String[] {"data/lubm/univ-bench.owl", "data/lubm/lubm1.ttl", "data/lubm/lubm.sparql", "lubm.ans"};
+//                      args = new String[] {"data/uobm/univ-bench-dl.owl", "data/uobm/uobm1.ttl", "data/uobm/uobm.sparql", "uobm.ans"};
+//                      args = new String[] {"data/fly/fly_anatomy_XP_with_GJ_FC_individuals.owl", "data/fly/fly.sparql", "fly.ans"};
+//                      args = new String[] {bioModels_tbox, bioModels_abox, bioModels_queries};
+//                      args = new String[] {chembl_tbox, chembl_abox, chembl_queries};
+//                      args = new String[] {reactome_tbox, reactome_abox, reactome_queries};
+//                      args = new String[] {reactome_tbox, "/users/yzhou/temp/reactome_debug.ttl", onto_dir +"bio2rdf/reactome/queries/atomic_one_q65.sparql"};
+//                      args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), "/users/yzhou/temp/uniprot_debug/sample_1_string.nt", uniprot_queries};
+//                      args = new String[] {uniprot_tbox.replace(".owl", "-noDis.owl"), uniprot_abox, uniprot_queries};
+//                      args = new String[] {atlas_tbox, atlas_abox, atlas_queries};
+//                      args = new String[] {onto_dir + "test/unsatisfiable.owl", null, onto_dir + "test/unsatisfiable_queries.sparql"};
+//                      args = new String[] {onto_dir + "test/jair-example.owl", null, onto_dir + "test/jair-example_query.sparql"};
+//                      args[2] = args[2].replace(".sparql", "_all_pagoda.sparql");
+//                      args[2] = args[2].replace(".sparql", "_pellet.sparql");
+                }
+
+                PagodaProperties properties = new PagodaProperties("config/uobm.properties");
+
+                int index = 0;
+                if(args.length > index) properties.setOntologyPath(args[index++]);
+                if(args.length > index && (args[index].endsWith(".ttl") || args[index].endsWith(".nt")))
+                        properties.setDataPath(args[index++]);
+                if(args.length > index && args[index].endsWith(".sparql")) properties.setQueryPath(args[index++]);
+                if(args.length > index && !args[index].startsWith("-")) properties.setAnswerPath(args[index++]);
+                if(args.length > index) properties.setToClassify(Boolean.parseBoolean(args[index++].substring(1)));
+                if(args.length > index) properties.setToCallHermiT(Boolean.parseBoolean(args[index++].substring(1)));
+
+                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;
+
+                try {
+                        Timer t = new Timer();
+                        pagoda = QueryReasoner.getInstance(properties);
+                        if (pagoda == null) return;
+
+                        Utility.logInfo("Preprocessing Done in " + t.duration() + " seconds.");
+
+                        if (properties.getQueryPath() != null)
+                                for (String queryFile: properties.getQueryPath().split(";"))
+                                        pagoda.evaluate(pagoda.getQueryManager().collectQueryRecords(queryFile));
+
+                        if(properties.getShellMode())
+                                try {
+                                        evaluateConsoleQuery(pagoda);
+                                } catch(IOException e) {
+                                        e.printStackTrace();
+                                }
+                } finally {
+                        if (pagoda != null) pagoda.dispose();
+                }
+
+//              Utility.closeCurrentOut();
+
+                if(properties.getShellMode()) System.exit(0);
+        }
+
+        private static void evaluateConsoleQuery(QueryReasoner pagoda) throws IOException {
+                int ending = (int) '$', symbol;
+                while(true) {
+                        Utility.logInfo("Input your query ending with $");
+                        StringBuilder queryBuilder = new StringBuilder();
+                        while((symbol = System.in.read()) != ending) {
+                                queryBuilder.append((char) symbol);
+                        }
+                        System.in.read();
+                        if(queryBuilder.length() == 0) return;
+                        pagoda.evaluate_shell(queryBuilder.toString());
+                }
+        }
+
+        void testReactomeQueries() {
+                evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.biopax.org/release/biopax-level3.owl#DnaReference> . }");
+                evaluate("select ?y ?z where { <http://identifiers.org/ensembl/ENSG00000157557> ?y ?z . }");
+                evaluate("select ?y where { <http://identifiers.org/ensembl/ENSG00000157557> <http://www.biopax.org/release/biopax-level3.owl#name> ?y . }", true);
+
+        }
+
+        void testSemFacetQueries() {
+//              try {
+//                      BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream("query.line")));
+//                      for (String line; (line = reader.readLine()) != null && !line.isEmpty(); )
+//                              evaluate(line, true);
+//                      reader.close();
+//              } catch (FileNotFoundException e) {
+//                      e.printStackTrace();
+//              } catch (IOException e) {
+//                      e.printStackTrace();
+//              }
+                evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
+                evaluate("select distinct ?y where { ?x ?y ?z }", true);
+                evaluate("select distinct ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z }", true);
+                evaluate("select ?y ?z where { <http://www.reactome.org/biopax/46/49633#Protein3885> ?y ?z .}", true);
+        }
+
+        void testISGQueries() {
+                evaluate("select ?z where {<http://cs.ox.ac.uk/Evgeny_Kharlamov> <http://cs.ox.ac.uk/lat> ?z .}", false);
+                evaluate("select ?x where {?x <http://cs.ox.ac.uk/type> <http://cs.ox.ac.uk/person> .}", false);
+        }
+
+        void testSomeTravelQueries() {
+                evaluate("select ?y ?z where {<http://www.owl-ontologies.com/travel.owl#BlueMountains> ?y ?z. }", true);
+                evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#RetireeDestination>. }");
+                evaluate("select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.owl-ontologies.com/travel.owl#BackpackersDestination>. }");
+        }
+
+        void testSomeFlyQueries() {
+                evaluate("select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00005106> . }", false);
+
+                evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . ?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z .  ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00067123> . } ", true);
+
+                evaluate("Select ?x where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00067123>. ?x "
+                                                 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
+                                                 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
+
+                evaluate("Select ?x where {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00067363> . ?x "
+                                                 + "<http://purl.obolibrary.org/obo/RO_0002131> ?any . ?any "
+                                                 + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "
+                                                 + "<http://purl.obolibrary.org/obo/FBbt_00005140> . }", true);
+
+//              evaluate("Select ?x where { "
+//                              + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00003660>. "
+//                              + "?x <http://purl.obolibrary.org/obo/FBbt#develops_from> ?any . "
+//                              + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00001446> . }", true);
+
+                evaluate("select DISTINCT ?z where { ?x <http://purl.obolibrary.org/obo/RO_0002110> ?any . "
+                                                 + "?any <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z . "
+                                                 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007016>  . } ", true);
+
+                evaluate("Select * where {"
+                                                 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>. "
+                                                 + "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100607> <http://www.w3.org/2002/07/owl#sameAs> ?z }", true);
+
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/2002/07/owl#sameAs> ?z}", true);
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://purl.obolibrary.org/obo/BFO_0000051> ?z}", true);
+
+                evaluate("select DISTINCT ?y where { ?x ?y ?z . "
+                                                 + "?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/FBbt_00007364>  }", true);
+
+                evaluateQueriesFromFile("/users/yzhou/Downloads/logs(1).log");
+                evaluateQueriesFromFile("/users/yzhou/Downloads/logs.log");
+
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z}", true);
+                evaluate("SELECT DISTINCT ?x ?z WHERE {?x <http://xmlns.com/foaf/0.1/depicts> ?z}", true);
+
+                evaluate("select ?x ?z where { ?x <http://www.w3.org/2002/07/owl#sameAs> ?z } ", true);
+                evaluate("select ?x ?z where { ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?z } ", true);
+        }
+
+        public void evaluateQueriesFromFile(String fileName) {
+                Scanner scanner = null;
+                try {
+                        scanner = new Scanner(new File(fileName));
+                        String line;
+                        while(scanner.hasNextLine()) {
+                                line = scanner.nextLine();
+                                if(line.startsWith("select"))
+                                        evaluate(line, true);
+                        }
+                } catch(FileNotFoundException e) {
+                        e.printStackTrace();
+                } finally {
+                        if(scanner != null)
+                                scanner.close();
+                }
+        }
+
+        private void evaluate(String query) {
+                evaluate(query, false);
+        }
+
+        private void evaluate(String query, boolean tag) {
+                timer.reset();
+                AnswerTuples tuples = pagoda.evaluate(query, tag);
+                int arity = tuples.getArity();
+                int count = 0;
+                for(AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
+                        tuple = tuples.getTuple();
+                        for(int i = 0; i < arity; ++i)
+                                tuple.getGroundTerm(i).toString();
+//                              System.out.print(tuple.getGroundTerm(i).toString() + "\t");
+//                      System.out.println();
+                        ++count;
+                }
+                tuples.dispose();
+                Utility.logInfo("The number of answers for this SemFacet query: " + count);
+                Utility.logInfo("Total time for this SemFacet query: " + timer.duration());
+        }
+
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/tester/Statistics.java b/src/test/java/uk/ac/ox/cs/pagoda/tester/Statistics.java
new file mode 100644
index 0000000..13d7f90
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/tester/Statistics.java
@@ -0,0 +1,60 @@
+package uk.ac.ox.cs.pagoda.tester;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Scanner;
+
+@Deprecated
+public class Statistics {
+        
+        double satCheckTime; 
+        double preprocessTime;
+        LinkedList<Integer> number = new LinkedList<Integer>(); 
+        LinkedList<Double> time = new LinkedList<Double>(); 
+        
+        public Statistics(String file) {
+                Scanner scanner = null; 
+                try {
+                        scanner = new Scanner(new File(file));
+                        for (String line; scanner.hasNextLine(); ) {
+                                line = scanner.nextLine(); 
+                                if (line.contains("time for satisfiability checking"))
+                                        satCheckTime = Double.parseDouble(line.substring(line.indexOf(": ") + 2));
+                                else if (line.contains("Preprocessing Done in"))
+                                        preprocessTime = Double.parseDouble(line.substring(line.indexOf("in ") + 3, line.indexOf(" second")));
+                                else if (line.contains("The number of answer tuples:"))
+                                        number.add(Integer.parseInt(line.substring(line.indexOf(": ") + 2))); 
+                                else if (line.contains("Total time to answer this query:")) 
+                                        time.add(Double.parseDouble(line.substring(line.indexOf(": ") + 2))); 
+                        }
+                } catch (FileNotFoundException e) {
+                        e.printStackTrace();
+                } finally {
+                        if (scanner != null)
+                                scanner.close();
+                }
+        }
+        
+        public String diff(String other) {
+                return diff(new Statistics(other)); 
+        }
+        
+        public String diff(Statistics other) {
+                if (other.number.size() != number.size()) 
+                        return "The number of query is different! " + this.number.size() + " v.s. " + other.number.size();  
+                int i = 0; 
+                Iterator<Integer> iter1 = number.iterator(), iter2 = other.number.iterator();
+                StringBuilder diff = new StringBuilder(); 
+                int a, b; 
+                while (iter1.hasNext()) {
+                        ++i; 
+                        if ((a = iter1.next()) != (b = iter2.next())) {
+                                diff.append("Query ").append(i).append(": ").append(a).append(", reference ").append(b).append("\n"); 
+                        }
+                }
+                return diff.toString(); 
+        }
+        
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java b/src/test/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
new file mode 100644
index 0000000..3de30e4
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
@@ -0,0 +1,16 @@
+package uk.ac.ox.cs.pagoda.util;
+
+import org.testng.annotations.Test;
+
+public class SimpleProgressBarTester {
+
+    @Test
+    public void test() throws InterruptedException {
+        SimpleProgressBar simpleProgressBar = new SimpleProgressBar("TestBar", 1000);
+        for(int i = 0; i < 1000; i++) {
+            simpleProgressBar.update(i);
+            Thread.sleep(10);
+        }
+        simpleProgressBar.dispose();
+    }
+}
diff --git a/src/test/java/uk/ac/ox/cs/pagoda/util/TestUtil.java b/src/test/java/uk/ac/ox/cs/pagoda/util/TestUtil.java
new file mode 100644
index 0000000..c7f024a
--- /dev/null
+++ b/src/test/java/uk/ac/ox/cs/pagoda/util/TestUtil.java
@@ -0,0 +1,97 @@
+package uk.ac.ox.cs.pagoda.util;
+
+import org.apache.log4j.Appender;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.Logger;
+import org.semanticweb.owlapi.model.IRI;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Enumeration;
+import java.util.Properties;
+
+import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
+
+/**
+ * A collection of utility methods for testing.
+ */
+public class TestUtil {
+
+    public static final String CONFIG_FILE = "test.properties";
+    private static final Logger LOGGER = Logger.getLogger("Tester");
+    private static boolean isConfigLoaded = false;
+    private static Properties config;
+
+    public static Properties getConfig() {
+        if(!isConfigLoaded) {
+            try(InputStream in = TestUtil.class.getClassLoader().getResourceAsStream(CONFIG_FILE)) {
+                config = new java.util.Properties();
+                config.load(in);
+                in.close();
+                isConfigLoaded = true;
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        }
+        return config;
+    }
+
+    public static String combinePaths(String path1, String path2) {
+        File file1 = new File(path1);
+        File file2 = new File(file1, path2);
+        return file2.getPath();
+    }
+
+    public static void copyFile(String src, String dst) throws IOException {
+        Files.copy(Paths.get(src), Paths.get(dst), REPLACE_EXISTING);
+    }
+
+    /**
+     * Get the log file, which is assumed unique.
+     * */
+    public static String getLogFileName() {
+        Enumeration e = Logger.getRootLogger().getAllAppenders();
+        while (e.hasMoreElements()){
+            Appender app = (Appender)e.nextElement();
+            if (app instanceof FileAppender){
+                return ((FileAppender)app).getFile();
+            }
+        }
+        return null;
+    }
+
+    public static Path getAnswersFilePath(String name) {
+        URL givenAnswersURL = TestUtil.class.getClassLoader()
+                                            .getResource(name);
+        if(givenAnswersURL == null) throw new RuntimeException("Missing answers file:" + name);
+        return Paths.get(givenAnswersURL.getPath());
+    }
+
+    public static void logInfo(Object msg) {
+        LOGGER.info(msg);
+    }
+
+    public static void logDebug(Object msg) {
+        LOGGER.debug(msg);
+    }
+
+    public static void logError(Object msg) {
+        LOGGER.error(msg);
+    }
+
+    public static void logError(Object msg, Throwable t) {
+        LOGGER.error(msg, t);
+    }
+
+    public static final String NS = "http://example.org/test#%s";
+
+    public static IRI getEntityIRI(String name) {
+        return IRI.create(String.format(NS, name));
+    }
+
+}