Rules parsing.

13 files changed, 151 insertions, 57 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java b/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
index 81c99a4..43c5849 100644
--- a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
+++ b/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
@@ -2,9 +2,16 @@ package uk.ac.ox.cs.pagoda.hermit;
 
 import org.semanticweb.HermiT.model.*;
 import uk.ac.ox.cs.pagoda.MyPrefixes;
+import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 
+import java.security.InvalidParameterException;
+import java.util.ArrayList;
+
 public class RuleHelper {
+    private static final String OR = "|";
+    private static final String IF = ":-";
+    private static final String AND = ",";
 
 //      public static String abbreviateIRI(String text) {
 //              String prefixName, prefixIRI; 
@@ -37,16 +44,16 @@ public class RuleHelper {
                 boolean lastSpace = true;
                 for (Atom headAtom: clause.getHeadAtoms()) {
                         if ((atomText = getText(headAtom)) == null) continue; 
-                        if (!lastSpace) buf.append(" v ");
+                        if (!lastSpace) buf.append(" ").append(OR).append(" ");
                         buf.append(atomText);
                         lastSpace = false;
                 }
-                buf.append(" :- ");
+        buf.append(" ").append(IF).append(" ");
                 lastSpace = true;
                 for (Atom bodyAtom: clause.getBodyAtoms()) {
 //              for (String str: strs[1].split(", ")) {
                         if ((atomText = getText(bodyAtom)) == null) continue; 
-                        if (!lastSpace) buf.append(", ");
+                        if (!lastSpace) buf.append(AND).append(" ");
                         buf.append(atomText);
                         lastSpace = false;
                 }
@@ -74,7 +81,7 @@ public class RuleHelper {
                         else builder.append(getText(p));
                         builder.append("("); 
                         builder.append(getText(atom.getArgument(0))); 
-                        builder.append(","); 
+                        builder.append(",");
                         builder.append(getText(atom.getArgument(1))); 
                         builder.append(")"); 
                 }
@@ -95,4 +102,72 @@ public class RuleHelper {
                 return MyPrefixes.PAGOdAPrefixes.abbreviateIRI(t.toString());
         }
 
+        public static Term parseTerm(String s) {
+                s = s.trim();
+                if(s.startsWith("?")) return Variable.create(s.substring(1));
+                return Individual.create(MyPrefixes.PAGOdAPrefixes.expandIRI(s));
+        }
+
+    public static Atom parseAtom(String s) {
+        s = s.trim();
+
+        String[] split = s.split("\\(");
+        String predicateIri = OWLHelper.removeAngles(MyPrefixes.PAGOdAPrefixes.expandText(split[0]));
+        String[] predicateArgs = split[1].substring(0, split[1].length() - 1).split(",");
+        int numOfargs = predicateArgs.length;
+        Term terms[] = new Term[predicateArgs.length];
+        for (int i = 0; i < terms.length; i++)
+            terms[i] = parseTerm(predicateArgs[i]);
+        if(numOfargs == 1) {
+            AtomicConcept atomicConcept = AtomicConcept.create(predicateIri);
+            return Atom.create(atomicConcept, terms);
+        }
+        else if(numOfargs == 2) {
+            AtomicRole atomicRole = AtomicRole.create(predicateIri);
+            return Atom.create(atomicRole, terms);
+        }
+        else
+            throw new InvalidParameterException();
+        // TODO? add equality (owl:sameAs)?
+    }
+
+    public static DLClause parseClause(String s) {
+        s = s.trim();
+        if(s.endsWith(".")) s = s.substring(0, s.length()-1).trim();
+
+        String[] headAndBody = s.split(IF);
+        String[] headAtomsStr = splitAtoms(headAndBody[0], OR);
+        String[] bodyAtomsStr = splitAtoms(headAndBody[1], AND);
+
+        Atom[] headAtoms = new Atom[headAtomsStr.length];
+        Atom[] bodyAtoms = new Atom[bodyAtomsStr.length];
+        for (int i = 0; i < headAtoms.length; i++)
+            headAtoms[i] = parseAtom(headAtomsStr[i]);
+        for (int i = 0; i < bodyAtoms.length; i++)
+            bodyAtoms[i] = parseAtom(bodyAtomsStr[i]);
+
+        return DLClause.create(headAtoms, bodyAtoms);
+    }
+
+    private static String[] splitAtoms(String s, String operator) {
+        char op = operator.charAt(0);
+        ArrayList<String> result = new ArrayList<>();
+
+        int b = 0;
+        boolean betweenParenthesis = false;
+        for (int i = 0; i < s.length(); i++) {
+            if(s.charAt(i) == '(')
+                betweenParenthesis = true;
+            else if(s.charAt(i) == ')')
+                betweenParenthesis = false;
+            else if(s.charAt(i) == op && !betweenParenthesis) {
+                result.add(s.substring(b, i));
+                b = i + 1;
+            }
+        }
+        if(b < s.length()) result.add(s.substring(b));
+
+        return result.toArray(new String[0]);
+    }
+
 }
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
index 1664c99..e64c5e6 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
@@ -193,6 +193,7 @@ public abstract class MultiStageUpperProgram {
 
         public abstract Collection<Violation> isIntegrated(MultiStageQueryEngine engine, boolean incrementally);
 
+        // TODO -RULE-
         protected Violation violate(MultiStageQueryEngine engine, DLClause clause, boolean incrementally) {
                 Utility.logTrace("checking constraint: " + clause);
 
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
index 687fa4a..3528788 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
@@ -49,6 +49,7 @@ public abstract class Pick4NegativeConcept extends Treatment {
             tripleManager.addTripleByID(tripleManager.getInstance(gapAtom, assignment));
     }
 
+    // TODO -RULE-
     protected boolean makeSatisfied(Violation violation, Comparator<Atom> comp) {
         LinkedList<AnswerTupleID> tuples = violation.getTuples();
         DLClause constraint = violation.getConstraint();
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index a56a793..15dfa03 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -117,7 +117,7 @@ class ELHOUQueryReasoner extends QueryReasoner {
         }
 
         OWLOntology ontology = o;
-        program = new DatalogProgram(ontology, properties.getToClassify());
+        program = new DatalogProgram(ontology);
 
         importData(program.getAdditionalDataFile());
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
index 15eb9e8..ac62488 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
@@ -52,7 +52,7 @@ class HermiTReasoner extends QueryReasoner {
             e.printStackTrace();
         }
 
-        DatalogProgram datalogProgram = new DatalogProgram(tbox, false);
+        DatalogProgram datalogProgram = new DatalogProgram(tbox);
         importData(datalogProgram.getAdditionalDataFile());
         upperStore = new MultiStageQueryEngine("rl-upper", false);
         upperStore.importRDFData("data", getImportedData());
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 8e28142..71d5752 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -68,7 +68,7 @@ class MyQueryReasoner extends QueryReasoner {
         }
 
         ontology = o;
-        program = new DatalogProgram(ontology, properties.getToClassify());
+        program = new DatalogProgram(ontology);
 //              program.getLower().save();
 //              program.getUpper().save();
 //              program.getGeneral().save();
@@ -154,7 +154,7 @@ class MyQueryReasoner extends QueryReasoner {
 //                      encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore);
 
-        // TODO add consistency check by Skolem-upper-bound
+        // TODO? add consistency check by Skolem-upper-bound
 
         if(!isConsistent())
             return false;
@@ -225,7 +225,7 @@ class MyQueryReasoner extends QueryReasoner {
     @Override
     public void evaluateUpper(QueryRecord queryRecord) {
         if(isDisposed()) throw new DisposedException();
-        // TODO add new upper store
+        // TODO? add new upper store
         AnswerTuples rlAnswer = null;
         boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
         try {
@@ -388,7 +388,7 @@ class MyQueryReasoner extends QueryReasoner {
         Utility.logInfo(">> Semi-Skolemisation <<");
         t.reset();
 
-        DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
+        DatalogProgram relevantProgram = new DatalogProgram(relevantSubset);
 
         MultiStageQueryEngine relevantStore =
                 new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
diff --git a/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java b/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
index 29e74c2..e2a171d 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
@@ -2,11 +2,12 @@ package uk.ac.ox.cs.pagoda.rules;
 
 import org.semanticweb.owlapi.model.OWLOntology;
 import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
-import uk.ac.ox.cs.pagoda.constraints.PredicateDependency;
 import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom;
 import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
 import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
+import java.io.InputStream;
+
 public class DatalogProgram extends Disposable {
 
     UpperDatalogProgram upperProgram = new UpperDatalogProgram();
@@ -15,14 +16,36 @@ public class DatalogProgram extends Disposable {
 
     BottomStrategy upperBottom;
 
-    public DatalogProgram(OWLOntology o) {
+    public DatalogProgram(InputStream inputStream) {
         lowerProgram = new LowerDatalogProgram();
-        init(o, false);
+
+        upperProgram.load(inputStream, upperBottom = new UpperUnaryBottom());
+        lowerProgram.clone(upperProgram);
+        program.clone(upperProgram);
+
+        upperProgram.transform();
+        lowerProgram.transform();
+        program.transform();
+
+        program.buildDependencyGraph();
+        lowerProgram.dependencyGraph = upperProgram.buildDependencyGraph();
     }
 
-    public DatalogProgram(OWLOntology o, boolean toClassify) {
-        lowerProgram = new LowerDatalogProgram(toClassify);
-        init(o, toClassify);
+    public DatalogProgram(OWLOntology o) {
+        lowerProgram = new LowerDatalogProgram();
+
+        upperProgram.load(o, upperBottom = new UpperUnaryBottom());
+//              upperProgram.load(o, upperBottom = new UnaryBottom());
+        lowerProgram.clone(upperProgram);
+        program.clone(upperProgram);
+//              program.botStrategy = new UnaryBottom();
+
+        upperProgram.transform();
+        lowerProgram.transform();
+        program.transform();
+
+        program.buildDependencyGraph();
+        lowerProgram.dependencyGraph = upperProgram.buildDependencyGraph();
     }
 
     public LowerDatalogProgram getLower() {
@@ -55,20 +78,4 @@ public class DatalogProgram extends Disposable {
         super.dispose();
         if(upperProgram != null) upperProgram.deleteABoxTurtleFile();
     }
-
-    private void init(OWLOntology o, boolean forSemFacet) {
-        upperProgram.load(o, upperBottom = new UpperUnaryBottom());
-//              upperProgram.load(o, upperBottom = new UnaryBottom());
-        lowerProgram.clone(upperProgram);
-        program.clone(upperProgram);
-//              program.botStrategy = new UnaryBottom();
-
-        upperProgram.transform();
-        lowerProgram.transform();
-        program.transform();
-
-        program.buildDependencyGraph();
-        PredicateDependency graph = upperProgram.buildDependencyGraph();
-        lowerProgram.dependencyGraph = graph;
-    }
 }
diff --git a/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java b/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
index 01ab427..e390a29 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
@@ -15,7 +15,7 @@ public class GeneralProgram extends Program {
                 ontology = relevantOntology;
                 
                 ontologyDirectory = null; 
-                dlOntology = null; 
+//              dlOntology = null;
                 botStrategy = new UnaryBottom(); 
                 
                 clauses = botStrategy.process(relevantClauses); 
diff --git a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index 9930009..a2676e8 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
@@ -39,6 +39,7 @@ public class LowerDatalogProgram extends ApproxProgram implements IncrementalPro
         }
 
 
+        // TODO -RULE- filter out unsafe rules
         @Override
         public void transform() {
                 if (m_toClassify) {
@@ -56,7 +57,7 @@ public class LowerDatalogProgram extends ApproxProgram implements IncrementalPro
                 else 
                         super.transform();
                 
-                Normalisation norm = new Normalisation(dlOntology.getDLClauses(), ontology, new NullaryBottom());
+                Normalisation norm = new Normalisation(dlClauses, ontology, new NullaryBottom());
                 BottomStrategy tBottom = new NullaryBottom(); 
                 norm.process();
                 for (DLClause nClause: norm.getNormlisedClauses()) {
diff --git a/src/uk/ac/ox/cs/pagoda/rules/Program.java b/src/uk/ac/ox/cs/pagoda/rules/Program.java
index a0edf85..de06f52 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -4,6 +4,7 @@ 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;
@@ -13,6 +14,7 @@ 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;
 
@@ -23,7 +25,9 @@ public abstract class Program implements KnowledgeBase {
         
         protected String ontologyDirectory = null;
         protected OWLOntology ontology; 
-        protected DLOntology dlOntology;
+//      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>();
@@ -40,6 +44,24 @@ protected PredicateDependency dependencyGraph;
                 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();
@@ -57,7 +79,7 @@ protected PredicateDependency dependencyGraph;
                 OWLOntology abox = OWLHelper.loadOntology(aboxOWLFile);
                 OWLOntologyManager manager = abox.getOWLOntologyManager();
                 OWLAxiom axiom;
-                for (Atom atom: dlOntology.getPositiveFacts()) {
+                for (Atom atom: positiveFacts) {
                         if ((axiom = OWLHelper.getABoxAssertion(manager.getOWLDataFactory(), atom)) != null)
                                 manager.addAxiom(abox, axiom);
                 }
@@ -90,7 +112,7 @@ protected PredicateDependency dependencyGraph;
 
         @Override
         public void transform() {
-                for(DLClause dlClause : dlOntology.getDLClauses()) {
+                for(DLClause dlClause : dlClauses) {
                         DLClause simplifiedDLClause = DLClauseHelper.removeNominalConcept(dlClause);
                         simplifiedDLClause = removeAuxiliaryBodyAtoms(simplifiedDLClause);
                         simplifiedDLClause = DLClauseHelper.replaceWithDataValue(simplifiedDLClause);
@@ -190,7 +212,9 @@ protected PredicateDependency dependencyGraph;
         void clone(Program program) {
                 this.ontologyDirectory = program.ontologyDirectory;
                 this.ontology = program.ontology;
-                this.dlOntology = program.dlOntology;
+//              this.dlOntology = program.dlOntology;
+        this.dlClauses = program.dlClauses;
+        this.positiveFacts = program.positiveFacts;
                 this.botStrategy = program.botStrategy;
                 this.additionalDataFile = program.additionalDataFile;
                 this.transitiveAxioms = program.transitiveAxioms;
@@ -248,8 +272,9 @@ protected PredicateDependency dependencyGraph;
                         }
                 Utility.logInfo("The number of data property range axioms that are ignored: " + noOfDataPropertyRangeAxioms + "(" + noOfAxioms + ")");
 
-                dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
-                clausifier = null;
+        DLOntology dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
+        dlClauses = dlOntology.getDLClauses();
+        positiveFacts = dlOntology.getPositiveFacts();
         }
 
         private DLClause removeAuxiliaryBodyAtoms(DLClause dlClause) {
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java b/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
index 7d29c74..a140225 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
@@ -9,7 +9,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 
-/**
+/***
  * Approximates existential rules through a limited form of Skolemisation.
  * <p>
  * Given a rule and a ground substitution,
diff --git a/src/uk/ac/ox/cs/pagoda/rules/clauses/Conjunction.java b/src/uk/ac/ox/cs/pagoda/rules/clauses/Conjunction.java
deleted file mode 100644
index 91bb3e7..0000000
--- a/src/uk/ac/ox/cs/pagoda/rules/clauses/Conjunction.java
+++ /dev/null
@@ -1,4 +0,0 @@
-package uk.ac.ox.cs.pagoda.rules.clauses;
-
-public class Conjunction {
-}
diff --git a/src/uk/ac/ox/cs/pagoda/rules/clauses/DLClause.java b/src/uk/ac/ox/cs/pagoda/rules/clauses/DLClause.java
deleted file mode 100644
index 7394be0..0000000
--- a/src/uk/ac/ox/cs/pagoda/rules/clauses/DLClause.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package uk.ac.ox.cs.pagoda.rules.clauses;
-
-public class DLClause extends Clause {
-
-//    private DLClause(Atom[] headAtoms, Atom[] bodyAtoms) {
-//        super(headAtoms, bodyAtoms);
-//    }
-//
-//    public static DLClause create(Atom[] headAtoms, Atom[] bodyAtoms) {
-//        return s_interningManager.intern(new DLClause(headAtoms, bodyAtoms));
-//    }
-}