[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.

3 files changed, 384 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"
+                ); 
+        }
+
+}