[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, 384 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/rules/Program.java b/src/uk/ac/ox/cs/pagoda/rules/Program.java
deleted file mode 100644
index de06f52..0000000
--- a/src/uk/ac/ox/cs/pagoda/rules/Program.java
+++ /dev/null
@@ -1,384 +0,0 @@
-package uk.ac.ox.cs.pagoda.rules;
-
-import org.apache.commons.io.FilenameUtils;
-import org.semanticweb.HermiT.Configuration;
-import org.semanticweb.HermiT.model.*;
-import org.semanticweb.HermiT.structural.OWLClausification;
-import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.*;
-import org.semanticweb.simpleETL.SimpleETL;
-import uk.ac.ox.cs.pagoda.MyPrefixes;
-import uk.ac.ox.cs.pagoda.approx.KnowledgeBase;
-import uk.ac.ox.cs.pagoda.approx.RLPlusOntology;
-import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
-import uk.ac.ox.cs.pagoda.constraints.NullaryBottom;
-import uk.ac.ox.cs.pagoda.constraints.PredicateDependency;
-import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
-import uk.ac.ox.cs.pagoda.hermit.RuleHelper;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.util.Utility;
-
-import java.io.*;
-import java.util.*;
-
-public abstract class Program implements KnowledgeBase {
-        
-        protected String ontologyDirectory = null;
-        protected OWLOntology ontology; 
-//      protected DLOntology dlOntology;
-    protected Set<DLClause> dlClauses = new HashSet<>();
-    protected Set<Atom> positiveFacts = new HashSet<>();
-        protected BottomStrategy botStrategy; 
-        protected Collection<DLClause> clauses = new HashSet<DLClause>();
-//      protected Set<DLClause> used = new HashSet<DLClause>();
-protected PredicateDependency dependencyGraph;
-        protected LinkedList<OWLTransitiveObjectPropertyAxiom> transitiveAxioms;
-        protected LinkedList<DLClause> transitiveClauses;
-        protected LinkedList<OWLSubPropertyChainOfAxiom> subPropChainAxioms;
-        protected LinkedList<DLClause> subPropChainClauses;
-        private String additionalDataFile = null;
-
-        public static String toString(Collection<DLClause> clauses) {
-                StringBuilder sb = new StringBuilder(DLClauseHelper.toString(clauses));
-                sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText());
-                return sb.toString();
-        }
-
-        public void load(InputStream rules, BottomStrategy botStrategy) {
-//        this.botStrategy = botStrategy;
-//      // fake instantiation
-        try {
-            load(OWLManager.createOWLOntologyManager().createOntology(), botStrategy);
-        } catch (OWLOntologyCreationException e) {
-            e.printStackTrace();
-        }
-
-        try(BufferedReader br = new BufferedReader(new InputStreamReader(rules))) {
-            String line;
-            while((line = br.readLine()) != null)
-                dlClauses.add(RuleHelper.parseClause(line));
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-    }
-
-        public void load(OWLOntology o, BottomStrategy botStrategy) {
-                this.botStrategy = botStrategy;
-                RLPlusOntology owlOntology = new RLPlusOntology();
-                owlOntology.load(o, new NullaryBottom());
-                owlOntology.simplify();
-
-                ontology = owlOntology.getTBox();
-//              String ontologyPath = OWLHelper.getOntologyPath(ontology);
-//              ontologyDirectory = ontologyPath.substring(0, ontologyPath.lastIndexOf(Utility.JAVA_FILE_SEPARATOR));
-                String ontologyPath = ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toURI().getPath();
-                ontologyDirectory = FilenameUtils.getFullPath(ontologyPath);
-                clausify();
-
-                String aboxOWLFile = owlOntology.getABoxPath();
-                OWLOntology abox = OWLHelper.loadOntology(aboxOWLFile);
-                OWLOntologyManager manager = abox.getOWLOntologyManager();
-                OWLAxiom axiom;
-                for (Atom atom: positiveFacts) {
-                        if ((axiom = OWLHelper.getABoxAssertion(manager.getOWLDataFactory(), atom)) != null)
-                                manager.addAxiom(abox, axiom);
-                }
-
-                try {
-                        FileOutputStream out = new FileOutputStream(aboxOWLFile);
-                        manager.saveOntology(abox, out);
-                        out.close();
-                } catch(IOException | OWLOntologyStorageException e) {
-                        e.printStackTrace();
-                        System.exit(1);
-                }
-
-                if (!abox.isEmpty()) {
-                        SimpleETL rewriter = new SimpleETL(owlOntology.getOntologyIRI(), aboxOWLFile);
-                        try {
-                                rewriter.rewrite();
-                        } catch (Exception e) {
-                                e.printStackTrace();
-                        }
-                        additionalDataFile = rewriter.getExportedFile();
-                        new File(aboxOWLFile).delete();
-                }
-
-        }
-        
-        public String getAdditionalDataFile() {
-                return additionalDataFile;
-        }
-
-        @Override
-        public void transform() {
-                for(DLClause dlClause : dlClauses) {
-                        DLClause simplifiedDLClause = DLClauseHelper.removeNominalConcept(dlClause);
-                        simplifiedDLClause = removeAuxiliaryBodyAtoms(simplifiedDLClause);
-                        simplifiedDLClause = DLClauseHelper.replaceWithDataValue(simplifiedDLClause);
-                        convert(simplifiedDLClause);
-                }
-
-                addingTransitiveAxioms();
-                addingSubPropertyChainAxioms();
-
-                Collection<DLClause> botRelated = new LinkedList<DLClause>();
-                Variable X = Variable.create("X");
-                botRelated.add(DLClause.create(new Atom[0], new Atom[]{Atom.create(Inequality.INSTANCE, X, X)}));
-                clauses.addAll(botStrategy.process(botRelated));
-
-                if(this instanceof GeneralProgram)
-                        Utility.logDebug("The number of rules: " + (clauses.size() - 1));
-        }
-        
-        @Override
-        public void save() {
-                try {
-                        BufferedWriter ruleWriter = new BufferedWriter(new OutputStreamWriter(
-                                        new FileOutputStream(getOutputPath())));
-                        ruleWriter.write(toString());
-                        ruleWriter.close();
-                } catch(IOException e) {
-                        e.printStackTrace();
-                }
-                Utility.logInfo("The rules are saved in " + getOutputPath() + ".");
-        }
-
-        @Override
-        public String toString() {
-                return toString(clauses);
-        }
-
-        public final void convert(DLClause clause) {
-                Collection<DLClause> tempClauses = convert2Clauses(clause);
-                clauses.addAll(tempClauses);
-        }
-
-        public abstract Collection<DLClause> convert2Clauses(DLClause clause);
-
-        public abstract String getOutputPath();
-
-        public OWLOntology getOntology() {
-                return ontology;
-        }
-
-        public Collection<DLClause> getClauses() {
-                return clauses;
-        }
-
-        public Collection<DLClause> getClauses(DLClause queryClause) {
-//              if (true) return new HashSet<DLClause>(clauses);
-                Set<DLPredicate> predicates = new HashSet<DLPredicate>();
-                predicates.addAll(dependencyGraph.collectPredicate(queryClause.getBodyAtoms()));
-
-                Set<DLPredicate> dependence = new HashSet<DLPredicate>();
-                for(DLPredicate predicate : predicates)
-                        dependence.addAll(dependencyGraph.getAncesters(predicate));
-
-                Collection<DLClause> relevantClauses = new LinkedList<DLClause>();
-                for(DLClause clause : clauses) {
-                        if(relevant(clause, dependence))
-                                relevantClauses.add(clause);
-
-                }
-                return relevantClauses;
-        }
-
-        public PredicateDependency buildDependencyGraph() {
-                if(dependencyGraph == null)
-                        return dependencyGraph = new PredicateDependency(clauses);
-                else
-                        return dependencyGraph;
-        }
-
-        public void getDependencyGraph(PredicateDependency g) {
-                dependencyGraph = g;
-        }
-
-        public final String getDirectory() {
-                return Utility.getGlobalTempDirAbsolutePath();
-        }
-
-        public void deleteABoxTurtleFile() {
-                if(additionalDataFile != null)
-                        new File(additionalDataFile).delete();
-        }
-
-        /**
-         * clone all information of another program after load()
-         *
-         * @param program
-         */
-        void clone(Program program) {
-                this.ontologyDirectory = program.ontologyDirectory;
-                this.ontology = program.ontology;
-//              this.dlOntology = program.dlOntology;
-        this.dlClauses = program.dlClauses;
-        this.positiveFacts = program.positiveFacts;
-                this.botStrategy = program.botStrategy;
-                this.additionalDataFile = program.additionalDataFile;
-                this.transitiveAxioms = program.transitiveAxioms;
-                this.transitiveClauses = program.transitiveClauses;
-                this.subPropChainAxioms = program.subPropChainAxioms;
-                this.subPropChainClauses = program.subPropChainClauses;
-        }
-
-        private void clausify() {
-                Configuration conf = new Configuration();
-                OWLClausification clausifier = new OWLClausification(conf);
-                OWLOntology filteredOntology = null;
-                OWLOntologyManager manager = ontology.getOWLOntologyManager();
-                try {
-                        filteredOntology = manager.createOntology();
-                } catch(OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                }
-
-                transitiveAxioms = new LinkedList<OWLTransitiveObjectPropertyAxiom>();
-                subPropChainAxioms = new LinkedList<OWLSubPropertyChainOfAxiom>();
-
-                OWLDatatype date = ontology.getOWLOntologyManager()
-                                                                   .getOWLDataFactory()
-                                                                   .getOWLDatatype(IRI.create("http://www.w3.org/2001/XMLSchema#date"));
-                int noOfDataPropertyRangeAxioms = 0, noOfAxioms = 0;
-                for(OWLOntology onto : ontology.getImportsClosure())
-                        for(OWLAxiom axiom : onto.getAxioms()) {
-                                if(axiom instanceof OWLTransitiveObjectPropertyAxiom)
-                                        transitiveAxioms.add((OWLTransitiveObjectPropertyAxiom) axiom);
-                                else if(axiom instanceof OWLSubPropertyChainOfAxiom)
-                                        subPropChainAxioms.add((OWLSubPropertyChainOfAxiom) axiom);
-                                        // TODO to filter out datatype axioms
-                                else if(axiom instanceof OWLDataPropertyRangeAxiom) {
-                                        ++noOfDataPropertyRangeAxioms;
-                                        Utility.logInfo("The axiom: " + axiom + " is being ignored.");
-                                }
-                                else {
-                                        if(axiom.getDatatypesInSignature().contains(date)) {
-                                                Utility.logInfo("The axiom: " + axiom + " is being ignored.");
-                                        }
-                                        else manager.addAxiom(filteredOntology, axiom);
-                                }
-
-                                if(axiom instanceof OWLAnnotationAssertionAxiom ||
-                                                axiom instanceof OWLSubAnnotationPropertyOfAxiom ||
-                                                axiom instanceof OWLDeclarationAxiom ||
-                                                axiom instanceof OWLDataPropertyRangeAxiom) {
-                                }
-                                else {
-//                                      System.out.println(axiom);
-                                        ++noOfAxioms;
-                                }
-
-                        }
-                Utility.logInfo("The number of data property range axioms that are ignored: " + noOfDataPropertyRangeAxioms + "(" + noOfAxioms + ")");
-
-        DLOntology dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
-        dlClauses = dlOntology.getDLClauses();
-        positiveFacts = dlOntology.getPositiveFacts();
-        }
-
-        private DLClause removeAuxiliaryBodyAtoms(DLClause dlClause) {
-                Collection<Atom> newBodyAtoms = new LinkedList<Atom>();
-                DLPredicate p;
-                for(Atom bodyAtom : dlClause.getBodyAtoms()) {
-                        p = bodyAtom.getDLPredicate();
-                        if(p instanceof AtomicConcept ||
-                                        p instanceof AtomicRole || p instanceof InverseRole ||
-                                        p instanceof Equality || p instanceof AnnotatedEquality || p instanceof Inequality)
-                                newBodyAtoms.add(bodyAtom);
-                }
-                LinkedList<Atom> newHeadAtoms = new LinkedList<Atom>();
-                Map<Variable, Term> assign = new HashMap<Variable, Term>();
-                for(Atom headAtom : dlClause.getHeadAtoms()) {
-                        p = headAtom.getDLPredicate();
-                        if(p instanceof AtomicNegationDataRange) {
-                                AtomicDataRange positive = ((AtomicNegationDataRange) p).getNegatedDataRange();
-                                if(!(positive instanceof ConstantEnumeration))
-                                        newBodyAtoms.add(Atom.create(positive, headAtom.getArgument(0)));
-                                else if(((ConstantEnumeration) positive).getNumberOfConstants() == 1) {
-                                        assign.put((Variable) headAtom.getArgument(0), ((ConstantEnumeration) positive).getConstant(0));
-//                                      newBodyAtoms.add(Atom.create(Equality.INSTANCE, headAtom.getArgument(0), ((ConstantEnumeration) positive).getConstant(0)));
-                                }
-                                else newHeadAtoms.add(headAtom);
-                        }
-                        else
-                                newHeadAtoms.add(headAtom);
-                }
-
-                if(assign.isEmpty() && newHeadAtoms.isEmpty() && newBodyAtoms.size() == dlClause.getBodyLength())
-                        return dlClause;
-
-                Atom[] headArray =
-                                newHeadAtoms.size() == dlClause.getHeadLength() ? dlClause.getHeadAtoms() : newHeadAtoms.toArray(new Atom[0]);
-                Atom[] bodyArray =
-                                newBodyAtoms.size() == dlClause.getBodyLength() ? dlClause.getBodyAtoms() : newBodyAtoms.toArray(new Atom[0]);
-                if(!assign.isEmpty()) {
-                        for(int i = 0; i < headArray.length; ++i)
-                                headArray[i] = DLClauseHelper.getInstance(headArray[i], assign);
-                        for(int i = 0; i < bodyArray.length; ++i)
-                                bodyArray[i] = DLClauseHelper.getInstance(bodyArray[i], assign);
-                }
-                return DLClause.create(headArray, bodyArray);
-        }
-
-        private void addingTransitiveAxioms() {
-                DLClause transitiveClause;
-                Atom headAtom;
-                Variable X = Variable.create("X"), Y = Variable.create("Y"), Z = Variable.create("Z");
-                transitiveClauses = new LinkedList<DLClause>();
-                for(OWLTransitiveObjectPropertyAxiom axiom : transitiveAxioms) {
-                        OWLObjectPropertyExpression objExp = axiom.getProperty();
-                        headAtom = getAtom(objExp, X, Z);
-                        Atom[] bodyAtoms = new Atom[2];
-                        bodyAtoms[0] = getAtom(objExp, X, Y);
-                        bodyAtoms[1] = getAtom(objExp, Y, Z);
-                        transitiveClause = DLClause.create(new Atom[]{headAtom}, bodyAtoms);
-                        clauses.add(transitiveClause);
-                        transitiveClauses.add(transitiveClause);
-                }
-        }
-
-        private Atom getAtom(OWLObjectPropertyExpression exp, Variable x, Variable y) {
-                if(exp instanceof OWLObjectProperty)
-                        return Atom.create(AtomicRole.create(((OWLObjectProperty) exp).toStringID()), x, y);
-                // TODO fixed, test it
-                OWLObjectPropertyExpression inverseOf;
-                if(exp instanceof OWLObjectInverseOf && (inverseOf = (
-                                (OWLObjectInverseOf) exp).getInverse()) instanceof OWLObjectProperty)
-                        return Atom.create(AtomicRole.create(((OWLObjectProperty) inverseOf).toStringID()), x, y);
-                return null;
-        }
-
-        private void addingSubPropertyChainAxioms() {
-                DLClause dlClause;
-                subPropChainClauses = new LinkedList<DLClause>();
-                Atom headAtom;
-                Iterator<OWLObjectPropertyExpression> iterExp;
-                OWLObjectPropertyExpression objExp;
-                for(OWLSubPropertyChainOfAxiom axiom : subPropChainAxioms) {
-                        objExp = axiom.getSuperProperty();
-                        List<OWLObjectPropertyExpression> objs = axiom.getPropertyChain();
-                        headAtom = getAtom(objExp, Variable.create("X"), Variable.create("X" + objs.size()));
-                        iterExp = objs.iterator();
-                        int index = 1;
-                        Atom[] bodyAtoms = new Atom[objs.size()];
-                        bodyAtoms[0] = getAtom(iterExp.next(), Variable.create("X"), Variable.create("X1"));
-                        while(index < objs.size()) {
-                                bodyAtoms[index] =
-                                                getAtom(iterExp.next(), Variable.create("X" + index), Variable.create("X" + (index + 1)));
-                                ++index;
-                        }
-                        dlClause = DLClause.create(new Atom[]{headAtom}, bodyAtoms);
-                        clauses.add(dlClause);
-                        subPropChainClauses.add(dlClause);
-                }
-        }
-
-        private boolean relevant(DLClause clause, Set<DLPredicate> set) {
-                for(DLPredicate p : dependencyGraph.collectPredicate(clause.getHeadAtoms()))
-                        if(set.contains(p))
-                                return true;
-                return false;
-        }
-
-}