[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.

1 files changed, 0 insertions, 129 deletions

diff --git a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java b/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
deleted file mode 100644
index 72e7af8..0000000
--- a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
+++ /dev/null
@@ -1,129 +0,0 @@
-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"
-                ); 
-        }
-
-}