[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, 314 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
deleted file mode 100644
index 3fd2fbd..0000000
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ /dev/null
@@ -1,314 +0,0 @@
-package uk.ac.ox.cs.pagoda.reasoner;
-
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.Variable;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import uk.ac.ox.cs.JRDFox.JRDFStoreException;
-import uk.ac.ox.cs.JRDFox.store.DataStore;
-import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
-import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
-import uk.ac.ox.cs.pagoda.query.AnswerTuples;
-import uk.ac.ox.cs.pagoda.query.QueryManager;
-import uk.ac.ox.cs.pagoda.query.QueryRecord;
-import uk.ac.ox.cs.pagoda.reasoner.full.Checker;
-import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
-import uk.ac.ox.cs.pagoda.summary.HermitSummaryFilter;
-import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
-import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
-import uk.ac.ox.cs.pagoda.util.Timer;
-import uk.ac.ox.cs.pagoda.util.Utility;
-import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
-import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
-
-import java.util.LinkedList;
-
-public class ConsistencyManager extends Disposable {
-
-        protected MyQueryReasoner m_reasoner;
-        protected QueryManager m_queryManager;  
-        
-        Timer t = new Timer();
-        QueryRecord fullQueryRecord;
-        QueryRecord[] botQueryRecords;
-        LinkedList<DLClause> toAddClauses;
-        boolean fragmentExtracted = false;
-        
-        public ConsistencyManager(MyQueryReasoner reasoner) {
-                m_reasoner = reasoner;
-                m_queryManager = reasoner.getQueryManager();
-        }
-
-        @Override
-        public void dispose() {
-                super.dispose();
-                fullQueryRecord.dispose();
-        }
-
-        public void extractBottomFragment() {
-                if(isDisposed()) throw new DisposedException();
-
-                if(fragmentExtracted) return;
-                fragmentExtracted = true;
-
-                UpperDatalogProgram upperProgram = m_reasoner.program.getUpper();
-                int number = upperProgram.getBottomNumber();
-
-                if(number <= 1) {
-                        botQueryRecords = new QueryRecord[]{fullQueryRecord};
-                }
-                else {
-                        QueryRecord[] tempQueryRecords = new QueryRecord[number - 1];
-                        QueryRecord record;
-                        for(int i = 0; i < number - 1; ++i) {
-                                tempQueryRecords[i] = record =
-                                                m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1);
-                                AnswerTuples iter = null;
-                                try {
-                                        iter = m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables());
-                                        record.updateUpperBoundAnswers(iter);
-                                } finally {
-                                        if(iter != null) iter.dispose();
-                                        iter = null;
-                                }
-                        }
-
-                        int bottomNumber = 0;
-                        int[] group = new int[number - 1];
-                        for(int i = 0; i < number - 1; ++i) group[i] = i;
-                        for(int i = 0; i < number - 1; ++i)
-                                if(tempQueryRecords[i].isProcessed()) tempQueryRecords[i].dispose();
-                                else if(group[i] == i) {
-                                        ++bottomNumber;
-                                        record = tempQueryRecords[i];
-                                        for(int j = i + 1; j < number - 1; ++j)
-                                                if(record.hasSameGapAnswers(tempQueryRecords[j]))
-                                                        group[j] = i;
-                                }
-
-                        Utility.logInfo("There are " + bottomNumber + " different bottom fragments.");
-                        toAddClauses = new LinkedList<DLClause>();
-                        int bottomCounter = 0;
-                        botQueryRecords = new QueryRecord[bottomNumber];
-                        Variable X = Variable.create("X");
-                        for(int i = 0; i < number - 1; ++i)
-                                if(!tempQueryRecords[i].isDisposed() && !tempQueryRecords[i].isProcessed())
-                                        if(group[i] == i) {
-                                                botQueryRecords[bottomCounter] = record = tempQueryRecords[i];
-                                                record.resetInfo(QueryRecord.botQueryText.replace("Nothing", "Nothing_final" + (++bottomCounter)), 0,
-                                                                                 group[i] = bottomCounter);
-                                                toAddClauses.add(
-                                                                DLClause.create(
-                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + bottomCounter), X)},
-                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
-                                        }
-                                        else {
-                                                toAddClauses.add(
-                                                                DLClause.create(
-                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + group[group[i]]), X)},
-                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
-                                                tempQueryRecords[i].dispose();
-                                        }
-
-                        upperProgram.updateDependencyGraph(toAddClauses);
-                }
-
-                String[] programs = collectTrackingProgramAndImport();
-                if(programs.length == 0)
-                        return;
-
-                DataStore store = m_reasoner.trackingStore.getDataStore();
-                long oldTripleCount, tripleCount;
-                try {
-                        Timer t1 = new Timer();
-                        oldTripleCount = store.getTriplesCount();
-                        for(String program : programs)
-                                store.importRules(program, UpdateType.ScheduleForAddition);
-                        store.applyReasoning(true);
-                        tripleCount = store.getTriplesCount();
-
-                        Utility.logDebug("tracking store after materialising tracking program: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)",
-                                                        "tracking store finished the materialisation of tracking program in " + t1.duration() + " seconds.");
-
-                        extractAxioms();
-                        store.clearRulesAndMakeFactsExplicit();
-                } catch(JRDFStoreException e) {
-                        e.printStackTrace();
-                } catch(OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                }
-        }
-
-        public QueryRecord[] getQueryRecords() {
-                if(isDisposed()) throw new DisposedException();
-
-                return botQueryRecords;
-        }
-
-        boolean checkRLLowerBound() {
-                if(isDisposed()) throw new DisposedException();
-
-                fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0);
-                AnswerTuples iter = null;
-
-                try {
-                        iter = m_reasoner.rlLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
-                        fullQueryRecord.updateLowerBoundAnswers(iter);
-                } finally {
-                        iter.dispose();
-                }
-
-                if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
-                        Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple());
-                        return false;
-                }
-                return true;
-        }
-
-//      protected boolean unsatisfiability(double duration) {
-//              fullQueryRecord.dispose();
-//              Utility.logDebug("The ontology and dataset is unsatisfiable.");
-//              return false;
-//      }
-
-//      protected boolean satisfiability(double duration) {
-//              fullQueryRecord.dispose();
-//              Utility.logDebug("The ontology and dataset is satisfiable.");
-//              return true;
-//      }
-
-        boolean checkELLowerBound() {
-                if(isDisposed()) throw new DisposedException();
-
-                fullQueryRecord.updateLowerBoundAnswers(m_reasoner.elLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord
-                                .getAnswerVariables()));
-                if(fullQueryRecord.getNoOfSoundAnswers() > 0) {
-                        Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple());
-                        return true;
-                }
-                return true;
-        }
-
-        boolean checkUpper(BasicQueryEngine upperStore) {
-                if(isDisposed()) throw new DisposedException();
-
-                if(upperStore != null) {
-                        AnswerTuples tuples = null;
-                        try {
-                                tuples = upperStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
-                                if(!tuples.isValid()) {
-                                        Utility.logInfo("There are no contradictions derived in " + upperStore.getName() + " materialisation.");
-                                        Utility.logDebug("The ontology and dataset is satisfiable.");
-                                        return true;
-                                }
-                        } finally {
-                                if(tuples != null) tuples.dispose();
-                        }
-                }
-                return false;
-        }
-
-        boolean check() {
-                if(isDisposed()) throw new DisposedException();
-
-//              if (!checkRLLowerBound()) return false;
-//              if (!checkELLowerBound()) return false;
-//              if (checkLazyUpper()) return true;
-                AnswerTuples iter = null;
-
-                try {
-                        iter =
-                                        m_reasoner.trackingStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
-                        fullQueryRecord.updateUpperBoundAnswers(iter);
-                } finally {
-                        if(iter != null) iter.dispose();
-                }
-
-                if(fullQueryRecord.getNoOfCompleteAnswers() == 0)
-                        return true;
-
-                extractBottomFragment();
-
-                try {
-                        extractAxioms4Full();
-                } catch(OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                }
-//              fullQueryRecord.saveRelevantClause();
-
-                boolean satisfiability;
-
-                Checker checker;
-                for(QueryRecord r : getQueryRecords()) {
-                        // TODO to be removed ...
-//                      r.saveRelevantOntology("bottom" + r.getQueryID() + ".owl");
-                        checker = new HermitSummaryFilter(r, true); // m_reasoner.factory.getSummarisedReasoner(r);
-                        satisfiability = checker.isConsistent();
-                        checker.dispose();
-                        if(!satisfiability) return false;
-                }
-
-//              Checker checker = m_reasoner.factory.getSummarisedReasoner(fullQueryRecord);
-//              boolean satisfiable = checker.isConsistent();
-//              checker.dispose();
-//              if (!satisfiable) return unsatisfiability(t.duration());
-
-                return true;
-        }
-
-        private void extractAxioms4Full() throws OWLOntologyCreationException {
-                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager();
-                OWLOntology fullOntology = manager.createOntology();
-                for (QueryRecord record: botQueryRecords) {
-                        for (DLClause clause: record.getRelevantClauses()) {
-                                fullQueryRecord.addRelevantClauses(clause);
-                        }
-                        manager.addAxioms(fullOntology, record.getRelevantOntology().getAxioms());
-                }
-                fullQueryRecord.setRelevantOntology(fullOntology);
-        }
-
-        private void extractAxioms() throws OWLOntologyCreationException {
-                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager();
-                for (QueryRecord record: botQueryRecords) {
-                        record.setRelevantOntology(manager.createOntology());
-                        QueryTracker tracker = new QueryTracker(m_reasoner.encoder, m_reasoner.rlLowerStore, record);
-                        m_reasoner.encoder.setCurrentQuery(record);
-                        tracker.extractAxioms(m_reasoner.trackingStore);
-//                      record.saveRelevantClause();
-//                      record.saveRelevantOntology("bottom" + record.getQueryID() + ".owl");
-                        Utility.logInfo("finish extracting axioms for bottom " + record.getQueryID());
-                }
-        }
-
-        private String[] collectTrackingProgramAndImport() {
-                String[] programs = new String[botQueryRecords.length];
-                TrackingRuleEncoder encoder = m_reasoner.encoder;
-
-                StringBuilder builder;
-                LinkedList<DLClause> currentClauses = new LinkedList<DLClause>();
-
-                for (int i = 0; i < botQueryRecords.length; ++i) {
-                        encoder.setCurrentQuery(botQueryRecords[i]);
-                        builder = new StringBuilder(encoder.getTrackingProgram());
-//                      encoder.saveTrackingRules("tracking_bottom" + (i + 1) + ".dlog");
-
-                        for (DLClause clause: toAddClauses)
-                                if (clause.getHeadAtom(0).getDLPredicate().toString().contains("_final" + (i + 1)))
-                                        currentClauses.add(clause);
-
-                        builder.append(DLClauseHelper.toString(currentClauses));
-                        programs[i] = builder.toString();
-
-                        currentClauses.clear();
-                }
-
-                return programs;
-        }
-
-
-}