Backup before changes in MyQueryReasoner.

2 files changed, 24 insertions, 44 deletions

diff --git a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java b/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
index f6246f8..008fcb2 100644
--- a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
+++ b/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
@@ -1,43 +1,21 @@
 package uk.ac.ox.cs.hermit;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.HashSet;
-import java.util.Set;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.TimeoutException;
-
 import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClassExpression;
-import org.semanticweb.owlapi.model.OWLDataFactory;
-import org.semanticweb.owlapi.model.OWLDatatype;
-import org.semanticweb.owlapi.model.OWLIndividual;
-import org.semanticweb.owlapi.model.OWLNamedIndividual;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.*;
 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 {
@@ -48,11 +26,13 @@ public class HermitQueryReasoner {
 //                      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/test/unsatisfiable.owl", null, "/users/yzhou/ontologies/test/unsatisfiable_queries.sparql"}; 
+//                      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", "../test-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", "../test-share/results/uniprot/hermit_1p"};                 }
-//                      args = new String[] {"imported.owl", "", "/media/krr-nas-share/Yujiao/ontologies/bio2rdf/uniprot/queries/atomic_one.sparql", "../test-share/results/uniprot/hermit_1p"};                }
+//                      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])); 
@@ -60,8 +40,8 @@ public class HermitQueryReasoner {
                         if (args[i] == null || args[i].equalsIgnoreCase("null")) args[i] = ""; 
                         System.out.println("Argument " + i + ": " + args[i]); 
                 }
-                
-//              PrintStream ps = null; // new PrintStream(new File("../test-share/results/reactome/ "));
+
+//              PrintStream ps = null; // new PrintStream(new File("../answersCorrectness-share/results/reactome/ "));
                 if (ps != null) System.setOut(ps);
                 
                 Timer t = new Timer(); 
diff --git a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
index a3264ba..72e7af8 100644
--- a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
+++ b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
@@ -11,8 +11,8 @@ public class JAIR_HermiT {
                 String[] args = new String[] {
                                 TestUtil.combinePaths(ontoDir, "lubm/univ-bench.owl"),
                                 TestUtil.combinePaths(ontoDir, "lubm/data/lubm1_owl"),
-                                TestUtil.combinePaths(ontoDir, "lubm/queries/test.sparql")
-//                              , "/home/yzhou/java-workspace/test-share/results_new/lubm1/hermit"
+                                TestUtil.combinePaths(ontoDir, "lubm/queries/answersCorrectness.sparql")
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/hermit"
                 };
                 HermitQueryReasoner.main(args);
         }
@@ -24,7 +24,7 @@ public class JAIR_HermiT {
                                 "/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/test-share/results_new/lubm1/hermit_rolledUp"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/lubm1/hermit_rolledUp"
                 };
                 HermitQueryReasoner.main(args);
         }
@@ -37,7 +37,7 @@ public class JAIR_HermiT {
                                 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"),
                                 TestUtil.combinePaths(ontoDir, "uobm/queries/standard.sparql")
 //                              , "hermit_uobm1.out"
-//                              , "/home/yzhou/java-workspace/test-share/results_new/uobm1/hermit"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/hermit"
                 };
                 HermitQueryReasoner.main(args);
         }
@@ -50,7 +50,7 @@ public class JAIR_HermiT {
                                 TestUtil.combinePaths(ontoDir, "uobm/data/uobm1_owl_withDeclaration"),
                                 TestUtil.combinePaths(ontoDir, "uobm/queries/atomic_uobm.sparql")
                                 , "hermit_uobm1_rolledUp.out"
-//                              , "/home/yzhou/java-workspace/test-share/results_new/uobm1/hermit_rolledUp"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uobm1/hermit_rolledUp"
                 };
                 HermitQueryReasoner.main(args);
         }
@@ -75,7 +75,7 @@ public class JAIR_HermiT {
                                 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/test-share/results_new/npd/hermit"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/npd/hermit"
                 ); 
         }
 
@@ -86,7 +86,7 @@ public class JAIR_HermiT {
                                 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/test-share/results_new/dbpedia/hermit"
+                                , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/dbpedia/hermit"
                 );
         }
 
@@ -97,7 +97,7 @@ public class JAIR_HermiT {
                                 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/test-share/results_new/reactome/hermit_10p"
+                                , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/reactome/hermit_10p"
                 ); 
         }
 
@@ -110,7 +110,7 @@ public class JAIR_HermiT {
                                 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/test-share/results_new/chembl/hermit_1p"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/chembl/hermit_1p"
                 ); 
         }
 
@@ -122,7 +122,7 @@ public class JAIR_HermiT {
                                 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/test-share/results_new/uniprot/hermit_1p"
+//                              , "/home/yzhou/java-workspace/answersCorrectness-share/results_new/uniprot/hermit_1p"
                 ); 
         }