[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, 199 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
deleted file mode 100644
index 15dfa03..0000000
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ /dev/null
@@ -1,199 +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.multistage.MultiStageQueryEngine;
-import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-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.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
-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 ELHOUQueryReasoner extends QueryReasoner {
-
-    DatalogProgram program;
-
-    BasicQueryEngine rlLowerStore;
-    BasicQueryEngine rlUpperStore;
-
-    OWLOntology elho_ontology;
-    KarmaQueryEngine elLowerStore = null;
-
-    boolean multiStageTag, equalityTag;
-    String originalMarkProgram;
-    private Timer t = new Timer();
-
-    public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
-        this.multiStageTag = multiStageTag;
-        this.equalityTag = considerEqualities;
-        rlLowerStore = new BasicQueryEngine("rl-lower-bound");
-        elLowerStore = new KarmaQueryEngine("el-lower-bound");
-
-        if(!multiStageTag)
-            rlUpperStore = new BasicQueryEngine("rl-upper-bound");
-        else
-            rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
-    }
-
-    @Override
-    public void evaluate(QueryRecord queryRecord) {
-        if(isDisposed()) throw new DisposedException();
-        AnswerTuples rlAnswer = null;
-        t.reset();
-        try {
-            rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-            queryRecord.updateLowerBoundAnswers(rlAnswer);
-        } finally {
-            if(rlAnswer != null) rlAnswer.dispose();
-        }
-        queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
-
-        String extendedQueryText = queryRecord.getExtendedQueryText().get(0);
-        String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
-                new String[]{queryRecord.getQueryText()} :
-                new String[]{queryRecord.getQueryText(), extendedQueryText};
-
-        for(String queryText : toQuery) {
-            rlAnswer = null;
-            t.reset();
-            try {
-                rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables());
-                queryRecord.updateUpperBoundAnswers(rlAnswer);
-            } finally {
-                if(rlAnswer != null) rlAnswer.dispose();
-            }
-            queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
-
-            if(queryRecord.isProcessed()) {
-                queryRecord.setDifficulty(Step.UPPER_BOUND);
-                return;
-            }
-        }
-
-        AnswerTuples elAnswer = null;
-        t.reset();
-        try {
-            elAnswer =
-                    elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
-            queryRecord.updateLowerBoundAnswers(elAnswer);
-        } finally {
-            if(elAnswer != null) elAnswer.dispose();
-        }
-        queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
-    }
-
-    @Override
-    public void evaluateUpper(QueryRecord queryRecord) {
-        if(isDisposed()) throw new DisposedException();
-        AnswerTuples rlAnswer = null;
-        try {
-            rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-            queryRecord.updateUpperBoundAnswers(rlAnswer, true);
-        } finally {
-            if(rlAnswer != null) rlAnswer.dispose();
-        }
-    }
-
-    @Override
-    public void dispose() {
-        super.dispose();
-        if(elLowerStore != null) elLowerStore.dispose();
-        if(rlUpperStore != null) rlUpperStore.dispose();
-    }
-
-    @Override
-    public void loadOntology(OWLOntology o) {
-        if(isDisposed()) throw new DisposedException();
-        if(!equalityTag) {
-            EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
-            o = eliminator.getOutputOntology();
-            eliminator.save();
-        }
-
-        OWLOntology ontology = o;
-        program = new DatalogProgram(ontology);
-
-        importData(program.getAdditionalDataFile());
-
-        elho_ontology = new ELHOProfile().getFragment(ontology);
-        elLowerStore.processOntology(elho_ontology);
-        originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
-    }
-
-    @Override
-    public boolean preprocess() {
-        if(isDisposed()) throw new DisposedException();
-        String name = "data", datafile = getImportedData();
-
-        String lowername = "lower program";
-        String rlLowerProgramText = program.getLower().toString();
-
-        rlUpperStore.importRDFData(name, datafile);
-        rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
-
-        int flag = rlUpperStore.materialiseRestrictedly(program, null);
-        if(flag != 1) {
-            if(flag == -1) return false;
-            rlUpperStore.dispose();
-
-            if(!multiStageTag)
-                rlUpperStore = new BasicQueryEngine("rl-upper-bound");
-            else
-                rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
-            rlUpperStore.importRDFData(name, datafile);
-            rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
-            rlUpperStore.materialiseFoldedly(program, null);
-        }
-        Utility.logInfo("upper store ready.");
-
-        rlLowerStore.importRDFData(name, datafile);
-        rlLowerStore.materialise(lowername, rlLowerProgramText);
-        Utility.logInfo("lower store ready.");
-
-        elLowerStore.importRDFData(name, datafile);
-        elLowerStore.materialise("saturate named individuals", originalMarkProgram);
-        elLowerStore.materialise(lowername, rlLowerProgramText);
-
-        elLowerStore.initialiseKarma();
-        Utility.logInfo("EL lower store ready.");
-
-        if(!isConsistent()) {
-            Utility.logInfo("The dataset is not consistent with the ontology.");
-            return false;
-        }
-        Utility.logInfo("The dataset is consistent.");
-        return true;
-    }
-
-    @Override
-    public boolean isConsistent() {
-        if(isDisposed()) throw new DisposedException();
-        Utility.logInfo("Start checking consistency... ");
-        String[] X = new String[]{"X"};
-        AnswerTuples ans = null;
-        try {
-            ans = rlUpperStore.evaluate(QueryRecord.botQueryText, X);
-            if(!ans.isValid()) return true;
-        } finally {
-            if(ans != null) ans.dispose();
-        }
-
-        ans = null;
-        try {
-            ans = elLowerStore.evaluate(QueryRecord.botQueryText, X);
-            if(ans.isValid()) return false;
-        } finally {
-            if(ans != null) ans.dispose();
-        }
-
-        Utility.logDebug("The consistency of the data has not been determined yet.");
-        return true;
-    }
-
-}