[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, 163 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java b/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
deleted file mode 100644
index eaa629b..0000000
--- a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
+++ /dev/null
@@ -1,163 +0,0 @@
-package uk.ac.ox.cs.pagoda.query;
-
-import org.semanticweb.HermiT.model.*;
-import uk.ac.ox.cs.JRDFox.JRDFStoreException;
-import uk.ac.ox.cs.JRDFox.Prefixes;
-import uk.ac.ox.cs.JRDFox.store.DataStore;
-import uk.ac.ox.cs.JRDFox.store.Parameters;
-import uk.ac.ox.cs.JRDFox.store.TupleIterator;
-import uk.ac.ox.cs.pagoda.MyPrefixes;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
-import uk.ac.ox.cs.pagoda.util.Namespace;
-import uk.ac.ox.cs.pagoda.util.Utility;
-
-import java.io.BufferedWriter;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.util.Collection;
-
-public class GapByTriple extends GapTupleIterator<String> {
-        
-        static final String allTripleQuery = "SELECT ?X ?Y ?Z WHERE { ?X ?Y ?Z }";
-        private static final String RDF_TYPE = Namespace.RDF_NS + "type";
-        private static final String BRIEF_RDF_TYPE = "rdf:type";
-        DataStore lowerStore, upperStore;
-        long multi; 
-        TupleIterator iterator;
-        String sub, obj, predicate; 
-//      GroundTerm subTerm, objTerm; 
-        Prefixes prefixes; 
-        Parameters parameters;
-
-        public GapByTriple(BasicQueryEngine lowerStore, BasicQueryEngine upperStore) {
-                this.lowerStore = lowerStore.getDataStore(); 
-                this.upperStore = upperStore.getDataStore();
-                prefixes = MyPrefixes.PAGOdAPrefixes.getRDFoxPrefixes();
-                parameters = new Parameters();
-        }
-        
-        public void compile(Collection<DLClause> clauses) throws JRDFStoreException {
-                iterator = this.upperStore.compileQuery(allTripleQuery, prefixes, parameters);
-                multi = iterator.open();
-        }
-        
-        @Override
-        public boolean hasNext() {
-                TupleIterator iter = null;
-                boolean inGap; 
-                StringBuffer queryBuffer = new StringBuffer();
-                try {
-                        for (; multi != 0; multi = iterator.getNext()) {
-//                      iterator.getRawGroundTerm(0); 
-//                      iterator.getRawGroundTerm(1); 
-//                      iterator.getRawGroundTerm(2); 
-                                
-                                sub = RDFoxTripleManager.getQuotedTerm(iterator.getResource(0)); 
-                                predicate = RDFoxTripleManager.getQuotedTerm(iterator.getResource(1));
-                                obj = RDFoxTripleManager.getQuotedTerm(iterator.getResource(2));
-                                                        
-                                if (!obj.startsWith("<")) {
-                                        // This fragment of code ignores data types assertions.
-//                                      Utility.LOGS.info(sub + " " + predicate + " " + obj); 
-                                        continue;
-                                }
-                                
-                                queryBuffer.setLength(0);
-                                queryBuffer.append("SELECT WHERE { ").append(sub).append(" ").append(predicate).append(" ").append(obj).append(" }");
-
-                                try {
-                                        iter = lowerStore.compileQuery(queryBuffer.toString(), prefixes, parameters);
-                                        inGap = iter.open() != 0;
-                                } finally {
-                                        if (iter != null) iter.dispose();
-                                        iter = null; 
-                                }
-                                if (inGap) 
-                                        return true;
-                        }
-                } catch (JRDFStoreException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                }
-                return false;
-        }
-        
-        @Override
-        public String next() {
-                try {
-                        multi = iterator.getNext();
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                }
-                StringBuilder sb = new StringBuilder(); 
-                if (isRDF_TYPE()) {
-                        sb.append(sub).append(" ").append(predicate).append(" ").append(getGapPredicate(obj)).append(".");
-                }
-                else sb.append(sub).append(" ").append(getGapPredicate(predicate)).append(" ").append(obj).append(".");  
-                return sb.toString(); 
-        }
-        
-        private boolean isRDF_TYPE() {
-                return predicate.equals(RDF_TYPE) || predicate.equals(BRIEF_RDF_TYPE);
-        }
-
-        @Override
-        public void remove() {
-                Utility.logError("Unsupported operation!"); 
-        }
-        
-        public void save(String file) {
-                int tupleCounter = 0; 
-                try {
-                        BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(file)));
-                        String tuple; 
-                        while (hasNext()) {
-                                tuple = next(); 
-                                writer.write(tuple);
-                                writer.newLine(); 
-                                ++tupleCounter; 
-                        }
-                        writer.close(); 
-                } catch (IOException e) {
-                        e.printStackTrace();
-                } 
-                
-                Utility.logError("There are " + tupleCounter + " tuples in the gap between lower and upper bound materialisation."); 
-        }
-
-        public void addTo(DataStore store) throws JRDFStoreException {
-                int tupleCounter = 0; 
-                RDFoxTripleManager tripleManager = new RDFoxTripleManager(store, false); 
-                while (hasNext()) {
-                        multi = iterator.getNext();
-                        ++tupleCounter; 
-                        if (isRDF_TYPE()) {
-                                obj = OWLHelper.removeAngles(obj); 
-                                tripleManager.addTripleByTerm(
-                                                        Atom.create(AtomicConcept.create(getGapPredicate(obj)), Individual.create(sub))); 
-                        }
-                        else {
-                                predicate = OWLHelper.removeAngles(predicate);
-                                tripleManager.addTripleByTerm(
-                                                        Atom.create(AtomicRole.create(getGapPredicate(predicate)), Individual.create(sub), Individual.create(obj))); 
-                        }
-                        if (tupleCounter % 10000 == 0)
-                                Utility.logDebug(tupleCounter); 
-                }
-                
-                Utility.logDebug("There are " + tupleCounter + " tuples in the gap between lower and upper bound materialisation."); 
-        }
-
-        @Override
-        public void addBackTo() throws JRDFStoreException {
-                addTo(upperStore);
-        }
-        
-        @Override
-        public void clear() {
-                iterator.dispose();             
-        }
-}