/**
* 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 net.timbusproject.dpes.alternative.PreservationAlternative;
import net.timbusproject.dpes.alternative.PreservationIdentifierException;
import net.timbusproject.dpes.alternative.Risk;
import org.sbaresearch.owl.AlternativesBuilder;
import org.sbaresearch.owl.AnnotationNotFoundException;
import org.sbaresearch.owl.OwlApiFacade;
import org.sbaresearch.owl.OwlElementNotFoundException;
import org.semanticweb.owlapi.model.*;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.List;
public class AlternativesBuilderHelper {
private static final org.slf4j.Logger LOG = LoggerFactory.getLogger(AlternativesBuilderHelper.class);
private AlternativesBuilderHelper() {
}
public static String createIriFragment(String baseURL, String identifier, Risk identifiedRisk, int count) {
return baseURL + "/" + identifier + "/" + identifiedRisk.getRiskIdentifier() + "/" + count + "/";
}
public static PreservationAlternative createAlternativeOntology(OWLOntology originalModel,
Risk identifiedRisk, IRI individualAtRisk,
String replacingIndividual, String alternativeOntologyIriPrefix, ChangesOntologyBuilder changesOntologyBuilder, String iriSuffix) throws OWLOntologyCreationException, OwlElementNotFoundException, OWLOntologyStorageException {
String alternativeShortDescription = "Replacing identified software " + individualAtRisk + " with " + replacingIndividual;
return createAlternativeOntology(originalModel, identifiedRisk, individualAtRisk, replacingIndividual, alternativeOntologyIriPrefix, changesOntologyBuilder, iriSuffix, alternativeShortDescription);
}
public static PreservationAlternative createAlternativeOntology(OWLOntology originalModel,
Risk identifiedRisk, IRI individualAtRisk,
String replacingIndividual, String alternativeOntologyIriPrefix, ChangesOntologyBuilder changesOntologyBuilder, String iriSuffix, String alternativeShortDescription) 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, null);
return new PreservationAlternative(
OwlApiFacade.toOwlXml(originalModel), OwlApiFacade.toOwlXml(modifiedModel),
OwlApiFacade.toOwlXml(eventsOntology), identifiedRisk.getRiskIdentifier(), changedOntologies, alternativeShortDescription);
}
private static IRI renameIndividual(IRI individualAtRisk, String replacingIndividual, OWLOntology modifiedModel) throws OwlElementNotFoundException {
OwlApiFacade model = new OwlApiFacade(modifiedModel);
IRI sourceIRI = model.createIri(OwlApiFacade.getFragment(individualAtRisk)); // TODO: check why this was needed could be just: individualAtRisk;
if (!model.containsIndividual(sourceIRI.toString())) {
throw new PreservationIdentifierException("Original individual not found in modified model: " + sourceIRI);
}
AlternativesBuilder alternativesBuilder = new AlternativesBuilder(model);
String targetFragment = replacingIndividual.replaceAll("[^a-zA-Z0-9_-]", "");
alternativesBuilder.renameIndividualByIRI(
model.createIri(OwlApiFacade.getFragment(individualAtRisk)),
targetFragment,
replacingIndividual); // TODO: not sure why fragment only does not work... bug!
IRI targetIRI = model.createIri(targetFragment);
if (!model.containsIndividual(targetIRI.toString())) {
throw new PreservationIdentifierException("Modified individual not found in modified model: " + targetIRI);
}
LOG.info("\tReplaced " + sourceIRI + " with " + targetIRI);
return targetIRI;
}
public static String getFragmentOfResource(OwlApiFacade originalModelFacade, String affectedResourceName) throws OwlElementNotFoundException {
OWLNamedIndividual affectedIndiv = originalModelFacade.getIndividual(originalModelFacade.findIndividualByFragmentAndLabel(affectedResourceName).toString());
String affectedResourceFragment = originalModelFacade.createIri(affectedResourceName).getFragment();
try {
affectedResourceFragment = originalModelFacade.hasLabel(affectedIndiv) ? originalModelFacade.getLabel(affectedIndiv) : affectedResourceFragment;
} catch (AnnotationNotFoundException e) {
LOG.error("Unable to get label for resource: " + affectedResourceName + ". Using resource name as fallback.");
}
affectedResourceFragment = cleanName(affectedResourceFragment);
LOG.info("Getting alternatives for tool: " + affectedResourceFragment);
return affectedResourceFragment;
}
public static String cleanName(Object name) {
return name.toString().replace(" ", "-").replace("/", "-").replaceAll("[^a-zA-Z0-9_:-]", ""); // TODO: sync with kbgen
}
}