Open Source Projects Europe

/**

 * Copyright (c) 2013/2014 Verein zur Foerderung der IT-Sicherheit in Oesterreich (SBA).

 * The work has been developed in the TIMBUS Project and the above-mentioned are Members of the TIMBUS Consortium.

 * TIMBUS is supported by the European Union under the 7th Framework Programme for research and technological

 * development and demonstration activities (FP7/2007-2013) under grant agreement no. 269940.

 *

 * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with

 * the License. You may obtain a copy of the License at: http://www.apache.org/licenses/LICENSE-2.0

 * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on

 * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including without

 * limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTIBITLY, or FITNESS FOR A PARTICULAR

 * PURPOSE. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise,

 * unless required by applicable law or agreed to in writing, shall any Contributor be liable for damages, including

 * any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this

 * License or out of the use or inability to use the Work.

 * See the License for the specific language governing permissions and limitation under the License.

 */

package net.timbusproject.dpes.alternative.AlternativesBuilder;

import ch.lambdaj.function.convert.Converter;

import com.hp.hpl.jena.query.QuerySolution;

import net.timbusproject.dpes.alternative.PreservationAlternative;

import net.timbusproject.dpes.alternative.PreservationIdentifierException;

import net.timbusproject.dpes.alternative.Risk;

import org.apache.commons.lang3.tuple.ImmutablePair;

import org.apache.commons.lang3.tuple.Pair;

import org.sba_research.timbus.kb.ToolKnowledgeBase;

import org.sbaresearch.owl.AlternativesBuilder;

import org.sbaresearch.owl.JenaQueryFacade;

import org.sbaresearch.owl.OwlApiFacade;

import org.sbaresearch.owl.OwlElementNotFoundException;

import org.semanticweb.owlapi.model.*;

import java.io.IOException;

import java.util.ArrayList;

import java.util.List;

import static ch.lambdaj.Lambda.convert;

/**

 * Creates alternative ontologies where tools at risk are replaced.

 */

public class ToolAlternativesBuilder implements PreservationAlternativesBuilder {

    private final ToolKnowledgeBase knowledgeBase;

    private final String baseURL;

    private final OwlApiFacade originalModelFacade;

    private final String identifier;

    public ToolAlternativesBuilder(ToolKnowledgeBase knowledgeBase, String baseURL, OwlApiFacade originalModelFacade, String identifier) {

        this.knowledgeBase = knowledgeBase;

        this.baseURL = baseURL;

        this.originalModelFacade = originalModelFacade;

        this.identifier = identifier;

    }

    @Override

    public List<PreservationAlternative> createAlternatives(Risk identifiedRisk, IRI individualAtRisk) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {

        List<PreservationAlternative> alternatives = new ArrayList<>();

        String affectedResourceName = identifiedRisk.getAffectedResource();

        List<String> alternativeTools = getAlternativeTools(originalModelFacade, affectedResourceName);

        ChangesOntologyBuilder changesOntologyBuilder = new ChangesOntologyBuilder(

                originalModelFacade.getOntology(), originalModelFacade.getIndividual(individualAtRisk.toString()), "SoftwareReplacement");

        if (alternativeTools.size() < 1) {

            System.out.println("No alternatives found for risk: " + identifiedRisk.getRiskIdentifier());

            System.out.println("Using fake alternatives for test purposes...");

            for (int i = 0; i < 3; ++i) {

                System.out.println("Replacing identified software " + affectedResourceName);

                String replacingIndividual = affectedResourceName + "-replacement_" + i;

                String alternativeOntologyIri = createIriFragment(baseURL, identifier, identifiedRisk, i);//, originalModel.getOntologyID().getOntologyIRI());

                String iriSuffix = identifier + "/" + i;

                alternatives.add(createAlternativeOntology(originalModelFacade.getOntology(), identifiedRisk,

                        individualAtRisk, replacingIndividual, alternativeOntologyIri, changesOntologyBuilder, iriSuffix));

            }

        } else {

            for (int i = 0; i < alternativeTools.size(); ++i) {

                System.out.println("Replacing identified software " + affectedResourceName);

                String alternativeOntologyIri = createIriFragment(baseURL, identifier, identifiedRisk, i);//, originalModel.getOntologyID().getOntologyIRI());

                String iriSuffix = identifier + "/" + i;

                alternatives.add(createAlternativeOntology(originalModelFacade.getOntology(), identifiedRisk,

                        individualAtRisk, alternativeTools.get(i), alternativeOntologyIri, changesOntologyBuilder, iriSuffix));

            }

        }

        return alternatives;

    }

    private List<String> getAlternativeTools(OwlApiFacade originalModelFacade, String affectedResourceName) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException {

        // get alternatives based on the tool

        List<String> alternativeTools = knowledgeBase.getAlternativeTools(affectedResourceName);

        // get alternatives based on the formats

        JenaQueryFacade originalModelQueryFacade = new JenaQueryFacade(originalModelFacade.getJenaModel(false));

        List<Pair<String, String>> formatPairs = convertToIDs(originalModelQueryFacade.query(QueryHelper.getQueryFormatPairs(affectedResourceName)), originalModelQueryFacade);

        for (Pair<String, String> formatPair : formatPairs) {

            alternativeTools.addAll(JenaQueryFacade.removeNamespace(knowledgeBase.getSupportingTools(formatPair)));

        }

        return alternativeTools;

    }

    private PreservationAlternative createAlternativeOntology(OWLOntology originalModel,

                                                              Risk identifiedRisk, IRI individualAtRisk,

                                                              String replacingIndividual, String alternativeOntologyIriPrefix, ChangesOntologyBuilder changesOntologyBuilder, String iriSuffix) throws OWLOntologyCreationException, OwlElementNotFoundException, OWLOntologyStorageException {

        AlternativesBuilder alternativesBuilder = new AlternativesBuilder(new OwlApiFacade(originalModel));

        OWLOntology modifiedModel = alternativesBuilder.copyOntology(IRI.create(alternativeOntologyIriPrefix, originalModel.getOntologyID().getOntologyIRI().getFragment()));

        OWLOntologyManager modifiedModelOntologyManager = modifiedModel.getOWLOntologyManager();

        IRI individualInModifiedModelModifiedIRI = null;

        if (originalModel.containsIndividualInSignature(individualAtRisk)) {

            individualInModifiedModelModifiedIRI = renameIndividual(individualAtRisk, replacingIndividual, modifiedModel);

        }

        List<String> changedOntologies = new ArrayList<>();

        for (OWLOntology ontology : originalModel.getDirectImports()) {

            if (!ontology.containsIndividualInSignature(individualAtRisk)) continue;

            AlternativesBuilder alternativesBuilderImportedOntology = new AlternativesBuilder(new OwlApiFacade(ontology));

            OWLOntology modifiedOntology = alternativesBuilderImportedOntology.copyOntology(

                    IRI.create(alternativeOntologyIriPrefix, ontology.getOntologyID().getOntologyIRI().getFragment()),

                    modifiedModel.getOWLOntologyManager()

            );

            individualInModifiedModelModifiedIRI = renameIndividual(individualAtRisk, replacingIndividual, modifiedOntology);

            modifiedModelOntologyManager.applyChange(new RemoveImport(modifiedModel,

                    modifiedModelOntologyManager.getOWLDataFactory().getOWLImportsDeclaration(ontology.getOntologyID().getOntologyIRI())));

            modifiedModelOntologyManager.applyChange(new AddImport(modifiedModel,

                    modifiedModelOntologyManager.getOWLDataFactory().getOWLImportsDeclaration(modifiedOntology.getOntologyID().getOntologyIRI())));

            changedOntologies.add(OwlApiFacade.toOwlXml(modifiedOntology));

        }

        OWLNamedIndividual modifiedIndividual = modifiedModelOntologyManager.getOWLDataFactory().getOWLNamedIndividual(individualInModifiedModelModifiedIRI);

        OWLOntology eventsOntology = changesOntologyBuilder.createChangesOntology(iriSuffix, modifiedModel, modifiedIndividual);

        return new PreservationAlternative(

                OwlApiFacade.toOwlXml(originalModel), OwlApiFacade.toOwlXml(modifiedModel),

                OwlApiFacade.toOwlXml(eventsOntology), identifiedRisk.getRiskIdentifier(), changedOntologies);

    }

    private String createIriFragment(String baseURL, String identifier, Risk identifiedRisk, int count) {

        return baseURL + "/" + identifier + "/" + identifiedRisk.getRiskIdentifier() + "/" + count + "/";

    }

    private IRI renameIndividual(IRI individualAtRisk, String replacingIndividual, OWLOntology modifiedModel) throws OwlElementNotFoundException {

        OwlApiFacade model = new OwlApiFacade(modifiedModel);

        IRI sourceIRI = model.createIri(OwlApiFacade.getFragment(individualAtRisk));

        if (!model.containsIndividual(sourceIRI.toString())) {

            throw new PreservationIdentifierException("Original individual not found in modified model: " + sourceIRI);

        }

        AlternativesBuilder alternativesBuilder = new AlternativesBuilder(model);

        alternativesBuilder.renameIndividualByIRI(model.createIri(OwlApiFacade.getFragment(individualAtRisk)), replacingIndividual); // TODO: not sure why fragment only does not work... bug!

        IRI targetIRI = model.createIri(replacingIndividual);

        if (!model.containsIndividual(targetIRI.toString())) {

            throw new PreservationIdentifierException("Modified individual not found in modified model: " + targetIRI);

        }

        System.out.println("\tReplaced " + sourceIRI + " with " + targetIRI);

        return targetIRI;

    }

    private List<Pair<String, String>> convertToIDs(List<QuerySolution> query, final JenaQueryFacade queryFacade) {

        return convert(query, new Converter<QuerySolution, Pair<String, String>>() {

            public Pair<String, String> convert(QuerySolution solution) {

                return new ImmutablePair<>(getID(solution, "readFormat", queryFacade), getID(solution, "writeFormat", queryFacade));

            }

        });

    }

    private String getID(QuerySolution solution, String formatIndex, JenaQueryFacade queryFacade) {

        String format = solution.contains(formatIndex) ? solution.get(formatIndex).toString() : null;

        if (format == null) return null;

        List<String> pronomIDs = JenaQueryFacade.extractColumn(queryFacade.query(QueryHelper.getQueryGetFormatID(format)), "pronom_id");

        return (pronomIDs.size() > 0 ? pronomIDs.get(0) : format);

    }

}