From 17bd9beaf7f358a44e5bf36a5855fe6727d506dc Mon Sep 17 00:00:00 2001
From: Federico Igne <federico.igne@cs.ox.ac.uk>
Date: Tue, 10 May 2022 18:17:06 +0100
Subject: [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.
---
 .../tracking/TrackingRuleEncoderWithGap.java       | 116 ---------------------
 1 file changed, 116 deletions(-)
 delete mode 100644 src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java

(limited to 'src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java')

diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
deleted file mode 100644
index 4ece796..0000000
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ /dev/null
@@ -1,116 +0,0 @@
-package uk.ac.ox.cs.pagoda.tracking;
-
-import org.semanticweb.HermiT.model.*;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLObjectProperty;
-import org.semanticweb.owlapi.model.OWLOntology;
-import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
-import uk.ac.ox.cs.pagoda.query.GapTupleIterator;
-import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
-import uk.ac.ox.cs.pagoda.util.Namespace;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Set;
-
-public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
-
-	public TrackingRuleEncoderWithGap(UpperDatalogProgram program, BasicQueryEngine store) {
-		super(program, store);
-	}
-
-	@Override
-	protected String getEqualityRelatedRuleText() {
-		if (equalityRelatedRuleText != null) return equalityRelatedRuleText.replace("_tn", getTrackingPredicate("")); 
-		
-		Collection<DLClause> equalityRelatedClauses = new LinkedList<DLClause>(); 
-		Variable X = Variable.create("X"); 
-		AtomicRole trackingSameAs = AtomicRole.create(Namespace.EQUALITY + "_tn");  
-		OWLOntology onto = program.getOntology();
-		Atom[] headAtom = new Atom[]{Atom.create(trackingSameAs, X, X)}, bodyAtom;
-		for(OWLOntology o : onto.getImportsClosure())
-			for(OWLClass cls : o.getClassesInSignature()) {
-			String clsIRI = cls.getIRI().toString();
-			unaryPredicates.add(clsIRI); 
-			bodyAtom = new Atom[] {
-					Atom.create(AtomicConcept.create(clsIRI + "_tn"), X),
-					Atom.create(AtomicConcept.create(GapTupleIterator.getGapPredicate(clsIRI)), X)}; 
-			equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom)); 
-		}
-
-		Variable Y = Variable.create("Y");
-		Set<OWLObjectProperty> setOfProperties = new HashSet<OWLObjectProperty>();
-		for(OWLOntology o : onto.getImportsClosure())
-			for(OWLObjectProperty prop : o.getObjectPropertiesInSignature())
-				setOfProperties.add(prop);
-		setOfProperties.add(onto.getOWLOntologyManager()
-								.getOWLDataFactory()
-								.getOWLObjectProperty(IRI.create(Namespace.INEQUALITY)));
-		for(OWLObjectProperty prop : setOfProperties) {
-			String propIRI = prop.getIRI().toString();
-			binaryPredicates.add(propIRI); 
-			AtomicRole trackingRole = AtomicRole.create(propIRI + "_tn"); 
-			AtomicRole gapRole = AtomicRole.create(GapTupleIterator.getGapPredicate(propIRI)); 
-//			AtomicRole role = AtomicRole.create(propIRI); 
-			bodyAtom = new Atom[] {
-					Atom.create(trackingRole, X, Y), 
-					Atom.create(gapRole, X, Y)}; 
-			equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom));
-			
-			bodyAtom = new Atom[] {
-					Atom.create(trackingRole, Y, X), 
-					Atom.create(gapRole, Y, X)}; 
-			equalityRelatedClauses.add(DLClause.create(headAtom, bodyAtom)); 
-		}
-		
-		equalityRelatedClauses.add(
-				DLClause.create(
-						new Atom[] {Atom.create(trackingSameAs, Y, X)}, 
-						new Atom[] {Atom.create(trackingSameAs, X, Y)}));
-		
-		equalityRelatedRuleText = DLClauseHelper.toString(equalityRelatedClauses).toString();
-		return equalityRelatedRuleText.replace("_tn", getTrackingPredicate("")); 
-	}
-
-	@Override
-	protected void encodingRule(DLClause clause) {
-		LinkedList<Atom> newHeadAtoms = new LinkedList<Atom>();
-		newHeadAtoms.add(Atom.create(selected, getIndividual4GeneralRule(clause)));
-		
-		Atom headAtom;
-		for (Atom atom: clause.getBodyAtoms()) {
-			headAtom = Atom.create(
-					getTrackingDLPredicate(atom.getDLPredicate()), 
-					DLClauseHelper.getArguments(atom));
-			newHeadAtoms.add(headAtom);
-		}
-
-		DLClause newClause;
-		headAtom = clause.getHeadAtom(0);
-		
-		boolean equalityHead = headAtom.getDLPredicate() instanceof Equality || headAtom.getDLPredicate() instanceof AnnotatedEquality; 
-		int offset = (equalityHead || (clause.getBodyLength() == 1 && clause.getBodyAtom(0).getDLPredicate().toString().contains("owl:Nothing"))) ? 1 : 2;
-		
-		Atom[] newBodyAtoms = new Atom[clause.getBodyLength() + offset];
-		newBodyAtoms[0] = Atom.create(
-				getTrackingDLPredicate(headAtom.getDLPredicate()), 
-				DLClauseHelper.getArguments(headAtom));
-		
-		if (offset == 2)
-		newBodyAtoms[1] = Atom.create(
-				getGapDLPredicate(headAtom.getDLPredicate()), 
-				DLClauseHelper.getArguments(headAtom));
-
-		for (int i = 0; i < clause.getBodyLength(); ++i)
-			newBodyAtoms[i + offset] = clause.getBodyAtom(i); 
-		
-		for (Atom atom: newHeadAtoms) {
-			newClause = DLClause.create(new Atom[] {atom}, newBodyAtoms); 
-			trackingClauses.add(newClause);
-		}
-		
-	}
-}
-- 
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