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.
---
 .../ac/ox/cs/pagoda/reasoner/HermiTReasoner.java   | 122 ---------------------
 1 file changed, 122 deletions(-)
 delete mode 100644 src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java

(limited to 'src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java')

diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
deleted file mode 100644
index ac62488..0000000
--- a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package uk.ac.ox.cs.pagoda.reasoner;
-
-import org.semanticweb.HermiT.Reasoner;
-import org.semanticweb.owlapi.model.*;
-import uk.ac.ox.cs.JRDFox.model.Individual;
-import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
-import uk.ac.ox.cs.pagoda.owl.OWLHelper;
-import uk.ac.ox.cs.pagoda.owl.QueryRoller;
-import uk.ac.ox.cs.pagoda.query.*;
-import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
-import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
-import uk.ac.ox.cs.pagoda.util.Utility;
-import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.HashSet;
-import java.util.Set;
-
-class HermiTReasoner extends QueryReasoner {
-
-    Reasoner hermit;
-
-    BasicQueryEngine upperStore = null;
-
-    OWLOntology onto;
-    OWLDataFactory factory;
-
-    String importedOntologyPath = null;
-
-    QueryRoller roller;
-    boolean toCheckSatisfiability;
-
-    public HermiTReasoner(boolean toCheckSatisfiability) {
-        this.toCheckSatisfiability = toCheckSatisfiability;
-    }
-
-    @Override
-    public void loadOntology(OWLOntology ontology) {
-        if(isDisposed()) throw new DisposedException();
-        onto = ontology;
-    }
-
-    @Override
-    public boolean preprocess() {
-        if(isDisposed()) throw new DisposedException();
-        OWLOntology tbox = onto;
-        try {
-            onto = OWLHelper.getImportedOntology(tbox, getImportedData().split(ImportDataFileSeparator));
-            importedOntologyPath = OWLHelper.getOntologyPath(onto);
-        } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
-            e.printStackTrace();
-        }
-
-        DatalogProgram datalogProgram = new DatalogProgram(tbox);
-        importData(datalogProgram.getAdditionalDataFile());
-        upperStore = new MultiStageQueryEngine("rl-upper", false);
-        upperStore.importRDFData("data", getImportedData());
-        GapByStore4ID gap = new GapByStore4ID(upperStore);
-        upperStore.materialiseFoldedly(datalogProgram, gap);
-        gap.clear();
-
-        factory = onto.getOWLOntologyManager().getOWLDataFactory();
-        roller = new QueryRoller(factory);
-
-        hermit = new Reasoner(onto);
-        return isConsistent();
-    }
-
-    @Override
-    public boolean isConsistent() {
-        if(isDisposed()) throw new DisposedException();
-        if(toCheckSatisfiability)
-            return hermit.isConsistent();
-        return true;
-    }
-
-    @Override
-    public void evaluate(QueryRecord record) {
-        if(isDisposed()) throw new DisposedException();
-        String[] disVars = record.getDistinguishedVariables();
-        Set<OWLNamedIndividual> individuals = onto.getIndividualsInSignature(true);
-        if(disVars.length == 1) {
-            OWLClassExpression clsExp = roller.rollUp(record.getClause(), record.getAnswerVariables()[0]);
-            Set<AnswerTuple> answers = new HashSet<AnswerTuple>();
-            for(OWLNamedIndividual individual : individuals) {
-                Utility.logDebug("checking ... " + individual);
-                if(hermit.isEntailed(factory.getOWLClassAssertionAxiom(clsExp, individual))) {
-                    answers.add(new AnswerTuple(new Individual[]{Individual.create(individual.toStringID())}));
-                }
-            }
-            record.updateLowerBoundAnswers(new AnswerTuplesImp(record.getAnswerVariables(), answers));
-            record.markAsProcessed();
-        }
-        else {
-            // FIXME join here
-            record.markAsProcessed();
-        }
-    }
-
-    @Override
-    public void evaluateUpper(QueryRecord record) {
-        if(isDisposed()) throw new DisposedException();
-        AnswerTuples rlAnswer = null;
-        try {
-            rlAnswer = upperStore.evaluate(record.getQueryText(), record.getAnswerVariables());
-            record.updateUpperBoundAnswers(rlAnswer, true);
-        } finally {
-            if(rlAnswer != null) rlAnswer.dispose();
-        }
-    }
-
-    @Override
-    public void dispose() {
-        super.dispose();
-        if(importedOntologyPath != null) {
-            File tmp = new File(importedOntologyPath);
-            if(tmp.exists()) tmp.delete();
-        }
-    }
-
-}
-- 
cgit v1.2.3