
...

package net.timbusproject.dpes.alternative.AlternativesBuilder;

import ch.lambdaj.function.convert.Converter;

import ch.lambdaj.function.matcher.Predicate;
import com.hp.hpl.jena.query.QuerySolution;

import net.timbusproject.dpes.alternative.PreservationAlternative;
import net.timbusproject.dpes.alternative.Risk;

...
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import static ch.lambdaj.Lambda.convert;
import static ch.lambdaj.Lambda.filter;

/**
 * Creates alternative ontologies where tools at risk are replaced.
 */
public class ToolAlternativesBuilder implements PreservationAlternativesBuilder {
...

    @Override
    public List<PreservationAlternative> createAlternatives(Risk identifiedRisk, IRI individualAtRisk) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {
        LOG.info("Searching for tool alternatives...");
        List<PreservationAlternative> alternatives = new ArrayList<>();
        String affectedResourceName = AlternativesBuilderHelper.getFragmentOfResource(originalModelFacade, identifiedRisk.getAffectedResource());
        List<String> alternativeTools = getAlternativeTools(originalModelFacade, affectedResourceName);
        ChangesOntologyBuilder changesOntologyBuilder = new ChangesOntologyBuilder(
                originalModelFacade.getOntology(), originalModelFacade.getIndividual(individualAtRisk.toString()), "SoftwareReplacement");
        if (alternativeTools.size() < 1) {
            LOG.warn("No alternatives found for risk: " + identifiedRisk.getRiskIdentifier());
...
        return alternatives;
    }

    private List<String> getAlternativeTools(OwlApiFacade originalModelFacade, String affectedResourceName) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {
        // get alternatives based on the tool
        IRI individualByFragmentAndLabel = originalModelFacade.findIndividualByFragmentAndLabel(affectedResourceName);
        if (individualByFragmentAndLabel == null) return new ArrayList<>();
        OWLNamedIndividual affectedIndiv = originalModelFacade.getIndividual(individualByFragmentAndLabel.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.");
...
        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 filter(new Predicate<String>() {
            @Override
            public boolean apply(String s) {
                if (s == null || s.isEmpty()) return false;
                return true;
            }
        }, alternativeTools);
    }

    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) {

	a/src/net/timbusproject/dpes/alternative/AlternativesBuilder/ToolAlternativesBuilder.java		b/src/net/timbusproject/dpes/alternative/AlternativesBuilder/ToolAlternativesBuilder.java
	...		...
18		18
19	package net.timbusproject.dpes.alternative.AlternativesBuilder;	19	package net.timbusproject.dpes.alternative.AlternativesBuilder;
20		20
21	import ch.lambdaj.function.convert.Converter;	21	import ch.lambdaj.function.convert.Converter;
22		22
		23	import ch.lambdaj.function.matcher.Predicate;
23	import com.hp.hpl.jena.query.QuerySolution;	24	import com.hp.hpl.jena.query.QuerySolution;
24		25
25	import net.timbusproject.dpes.alternative.PreservationAlternative;	26	import net.timbusproject.dpes.alternative.PreservationAlternative;
26	import net.timbusproject.dpes.alternative.Risk;	27	import net.timbusproject.dpes.alternative.Risk;
27		28
	...		...
41	import java.io.IOException;	42	import java.io.IOException;
42	import java.util.ArrayList;	43	import java.util.ArrayList;
43	import java.util.List;	44	import java.util.List;
44		45
45	import static ch.lambdaj.Lambda.convert;	46	import static ch.lambdaj.Lambda.convert;
		47	import static ch.lambdaj.Lambda.filter;
46		48
47	/**	49	/**
48	* Creates alternative ontologies where tools at risk are replaced.	50	* Creates alternative ontologies where tools at risk are replaced.
49	*/	51	*/
50	public class ToolAlternativesBuilder implements PreservationAlternativesBuilder {	52	public class ToolAlternativesBuilder implements PreservationAlternativesBuilder {
	...		...
64		66
65	@Override	67	@Override
66	public List<PreservationAlternative> createAlternatives(Risk identifiedRisk, IRI individualAtRisk) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {	68	public List<PreservationAlternative> createAlternatives(Risk identifiedRisk, IRI individualAtRisk) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {
67	LOG.info("Searching for tool alternatives...");	69	LOG.info("Searching for tool alternatives...");
68	List<PreservationAlternative> alternatives = new ArrayList<>();	70	List<PreservationAlternative> alternatives = new ArrayList<>();
69	String affectedResourceName = identifiedRisk.getAffectedResource();	71	String affectedResourceName = AlternativesBuilderHelper.getFragmentOfResource(originalModelFacade, identifiedRisk.getAffectedResource());
70	List<String> alternativeTools = getAlternativeTools(originalModelFacade, affectedResourceName);	72	List<String> alternativeTools = getAlternativeTools(originalModelFacade, affectedResourceName);
71	ChangesOntologyBuilder changesOntologyBuilder = new ChangesOntologyBuilder(	73	ChangesOntologyBuilder changesOntologyBuilder = new ChangesOntologyBuilder(
72	originalModelFacade.getOntology(), originalModelFacade.getIndividual(individualAtRisk.toString()), "SoftwareReplacement");	74	originalModelFacade.getOntology(), originalModelFacade.getIndividual(individualAtRisk.toString()), "SoftwareReplacement");
73	if (alternativeTools.size() < 1) {	75	if (alternativeTools.size() < 1) {
74	LOG.warn("No alternatives found for risk: " + identifiedRisk.getRiskIdentifier());	76	LOG.warn("No alternatives found for risk: " + identifiedRisk.getRiskIdentifier());
	...		...
98	return alternatives;	100	return alternatives;
99	}	101	}
100		102
101	private List<String> getAlternativeTools(OwlApiFacade originalModelFacade, String affectedResourceName) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {	103	private List<String> getAlternativeTools(OwlApiFacade originalModelFacade, String affectedResourceName) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {
102	// get alternatives based on the tool	104	// get alternatives based on the tool
		105	IRI individualByFragmentAndLabel = originalModelFacade.findIndividualByFragmentAndLabel(affectedResourceName);
		106	if (individualByFragmentAndLabel == null) return new ArrayList<>();
103	OWLNamedIndividual affectedIndiv = originalModelFacade.getIndividual(originalModelFacade.findIndividualByFragmentAndLabel(affectedResourceName).toString());	107	OWLNamedIndividual affectedIndiv = originalModelFacade.getIndividual(individualByFragmentAndLabel.toString());
104	String affectedResourceFragment = originalModelFacade.createIri(affectedResourceName).getFragment();	108	String affectedResourceFragment = originalModelFacade.createIri(affectedResourceName).getFragment();
105	try {	109	try {
106	affectedResourceFragment = originalModelFacade.hasLabel(affectedIndiv) ? originalModelFacade.getLabel(affectedIndiv) : affectedResourceFragment;	110	affectedResourceFragment = originalModelFacade.hasLabel(affectedIndiv) ? originalModelFacade.getLabel(affectedIndiv) : affectedResourceFragment;
107	} catch (AnnotationNotFoundException e) {	111	} catch (AnnotationNotFoundException e) {
108	LOG.error("Unable to get label for resource: " + affectedResourceName + ". Using resource name as fallback.");	112	LOG.error("Unable to get label for resource: " + affectedResourceName + ". Using resource name as fallback.");
	...		...
113	JenaQueryFacade originalModelQueryFacade = new JenaQueryFacade(originalModelFacade.getJenaModel(false));	117	JenaQueryFacade originalModelQueryFacade = new JenaQueryFacade(originalModelFacade.getJenaModel(false));
114	List<Pair<String, String>> formatPairs = convertToIDs(originalModelQueryFacade.query(QueryHelper.getQueryFormatPairs(affectedResourceName)), originalModelQueryFacade);	118	List<Pair<String, String>> formatPairs = convertToIDs(originalModelQueryFacade.query(QueryHelper.getQueryFormatPairs(affectedResourceName)), originalModelQueryFacade);
115	for (Pair<String, String> formatPair : formatPairs) {	119	for (Pair<String, String> formatPair : formatPairs) {
116	alternativeTools.addAll(JenaQueryFacade.removeNamespace(knowledgeBase.getSupportingTools(formatPair)));	120	alternativeTools.addAll(JenaQueryFacade.removeNamespace(knowledgeBase.getSupportingTools(formatPair)));
117	}	121	}
		122	return filter(new Predicate<String>() {
		123	@Override
		124	public boolean apply(String s) {
		125	if (s == null \|\| s.isEmpty()) return false;
		126	return true;
		127	}
118	return alternativeTools;	128	}, alternativeTools);
119	}	129	}
120		130
121	private List<Pair<String, String>> convertToIDs(List<QuerySolution> query, final JenaQueryFacade queryFacade) {	131	private List<Pair<String, String>> convertToIDs(List<QuerySolution> query, final JenaQueryFacade queryFacade) {
122	return convert(query, new Converter<QuerySolution, Pair<String, String>>() {	132	return convert(query, new Converter<QuerySolution, Pair<String, String>>() {
123	public Pair<String, String> convert(QuerySolution solution) {	133	public Pair<String, String> convert(QuerySolution solution) {