[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, 101 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
deleted file mode 100644
index cc2c4c0..0000000
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ /dev/null
@@ -1,101 +0,0 @@
-package uk.ac.ox.cs.pagoda.reasoner;
-
-import org.semanticweb.karma2.profile.ELHOProfile;
-import org.semanticweb.owlapi.model.OWLOntology;
-import uk.ac.ox.cs.pagoda.constraints.UnaryBottom;
-import uk.ac.ox.cs.pagoda.query.AnswerTuples;
-import uk.ac.ox.cs.pagoda.query.QueryRecord;
-import uk.ac.ox.cs.pagoda.query.QueryRecord.Step;
-import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
-import uk.ac.ox.cs.pagoda.util.Timer;
-import uk.ac.ox.cs.pagoda.util.Utility;
-import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
-
-class ELHOQueryReasoner extends QueryReasoner {
-
-    LowerDatalogProgram program;
-
-    OWLOntology elho_ontology;
-    KarmaQueryEngine elLowerStore = null;
-
-    private Timer t = new Timer();
-
-    public ELHOQueryReasoner() {
-        elLowerStore = new KarmaQueryEngine("el");
-    }
-
-    @Override
-    public void evaluate(QueryRecord queryRecord) {
-        if(isDisposed()) throw new DisposedException();
-        AnswerTuples elAnswer = null;
-        t.reset();
-        try {
-            elAnswer = elLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-            queryRecord.updateLowerBoundAnswers(elAnswer);
-        } finally {
-            if(elAnswer != null) elAnswer.dispose();
-        }
-        queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
-
-        queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
-        queryRecord.markAsProcessed();
-    }
-
-    @Override
-    public void evaluateUpper(QueryRecord queryRecord) {
-        if(isDisposed()) throw new DisposedException();
-        evaluate(queryRecord);
-    }
-
-    @Override
-    public void dispose() {
-        super.dispose();
-        if(elLowerStore != null) elLowerStore.dispose();
-    }
-
-    @Override
-    public void loadOntology(OWLOntology ontology) {
-        if(isDisposed()) throw new DisposedException();
-        program = new LowerDatalogProgram(properties.getToClassify());
-        program.load(ontology, new UnaryBottom());
-        program.transform();
-
-        importData(program.getAdditionalDataFile());
-
-        elho_ontology = new ELHOProfile().getFragment(ontology);
-        elLowerStore.processOntology(elho_ontology);
-    }
-
-    @Override
-    public boolean preprocess() {
-        if(isDisposed()) throw new DisposedException();
-        elLowerStore.importRDFData("data", getImportedData());
-        String rlLowerProgramText = program.toString();
-//              program.save();
-        elLowerStore.materialise("lower program", rlLowerProgramText);
-        elLowerStore.initialiseKarma();
-
-        if(!isConsistent()) {
-            Utility.logDebug("The dataset is not consistent with the ontology.");
-            return false;
-        }
-        return true;
-    }
-
-    @Override
-    public boolean isConsistent() {
-        if(isDisposed()) throw new DisposedException();
-        String[] X = new String[]{"X"};
-        AnswerTuples ans = null;
-        try {
-            ans = elLowerStore.evaluate(QueryRecord.botQueryText, X);
-            if(ans.isValid()) return false;
-        } finally {
-            if(ans != null) ans.dispose();
-        }
-
-        return true;
-    }
-
-}