[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, 107 deletions

diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
deleted file mode 100644
index 3eb956f..0000000
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ /dev/null
@@ -1,107 +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.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...");
-    }
-}