[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, 53 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
deleted file mode 100644
index 8a8a596..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
+++ /dev/null
@@ -1,53 +0,0 @@
-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();
-    }
-
-}