Extractor Modules / Taverna Extractor / Diff of /src/main/java/net/timbusproject/extractors/modules/tavernaextractor/ExtendedOWL.java

Diff of /src/main/java/net/timbusproject/extractors/modules/tavernaextractor/ExtendedOWL.java [346c31] .. [c78deb]

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...
            IRI.create(IRI_PREMIS.toString() + "#", "File"));

    /**
     * PRONOM PUID
     */
    public static final String PRONOM_REGISTRY_KEY_URI = "http://www.loc.gov/premis/rdf/v1#hasFormatRegistryKey";
    public static final IRI PRONOM_REGISTRY_KEY_IRI = IRI.create(PRONOM_REGISTRY_KEY_URI);
    public static final String PRONOM_REGISTRY_NAME_URI = "http://www.loc.gov/premis/rdf/v1#hasFormatRegistryName";
    public static final IRI PRONOM_REGISTRY_NAME_IRI = IRI.create(PRONOM_REGISTRY_NAME_URI);

    public ExtendedOWL() {
        logger.setLevel(Level.DEBUG);
    }

...
        // (2) Read entries from DROID CSV report file
        provenanceAccessClient = new ProvenanceAccessClient();
        provenanceEntries = provenanceAccessClient.filterEntries(provenanceAccessClient.readCSV(droidCSVReport));

        if (provenanceEntries.isEmpty()) {
            logger.info("Nothing to apply due to an empty provenance entry set.");
            return;
        }

        if (ontology != null) {

...
            // iterate over all entries found in the DROID CSV report
            for (CSVEntry entry : provenanceEntries) {

                logger.debug(entry.toString());
                for (OWLNamedIndividual ind : individuals) {
                    if (hasAnnotationValue(ind, ontology, entry.getNameForExtensionUsage()) && entry.getPUID() != null
                            && !entry.getPUID().isEmpty()) {

                        logger.info("Found individual (" + ind.getIRI() + ") which has to be extended with PUID ("
                                + entry.getPUID() + ")");
                        updateOWL(ind, entry);
...
    }

    // add a new individual to existing ontology
    private void updateOWL(OWLNamedIndividual ind, CSVEntry entry) {

        Queue<AddAxiom> changes = new LinkedList<>();

        // Add File assertion
        OWLClassAssertionAxiom swoClassAxiom_File = owlDataFactory.getOWLClassAssertionAxiom(PREMIS_FILE_CLASS, ind);
        changes.add(new AddAxiom(ontology, swoClassAxiom_File));

        // Create new ObjectCharacteristics
        OWLNamedIndividual swoIndividual_ObjectCharacteristics = owlDataFactory.getOWLNamedIndividual(IRI.create("#",
                replaceWhitespace(entry.getNameForExtensionUsage()) + "Characteristics"));
        OWLClassAssertionAxiom swoClassAxiom_ObjectCharacteristics = owlDataFactory.getOWLClassAssertionAxiom(
                PREMIS_OBJECTCHAR_CLASS, swoIndividual_ObjectCharacteristics);
        changes.add(new AddAxiom(ontology, swoClassAxiom_ObjectCharacteristics));

        changes.add(linkIndividuals(PREMIS_LINKING_HASOBJECTCHARACTERISTICS, ind, swoIndividual_ObjectCharacteristics));
...

        changes.add(linkIndividuals(PREMIS_LINKING_HASFORMAT, swoIndividual_ObjectCharacteristics, swoIndividual_Format));

        // Create new FormatRegistry
        OWLNamedIndividual swoIndividual_FormatRegistry = owlDataFactory.getOWLNamedIndividual(IRI.create("#",
                "PronomRegistry[" + entry.getNameForExtensionUsage() + "]"));
        OWLClassAssertionAxiom swoClassAxiom_FormatRegistry = owlDataFactory.getOWLClassAssertionAxiom(
                PREMIS_FROMATREGISTRY_CLASS, swoIndividual_FormatRegistry);
        changes.add(new AddAxiom(ontology, swoClassAxiom_FormatRegistry));

        changes.add(linkIndividuals(PREMIS_LINKING_HASFORMATREGISTRY, swoIndividual_Format,
                swoIndividual_FormatRegistry));

        // Create new FormatRegistry Data Property Assertion
        OWLDataProperty owlp = owlDataFactory.getOWLDataProperty(PRONOM_REGISTRY_KEY_IRI);
        OWLLiteral owlLiteral = owlDataFactory.getOWLLiteral("info:pronom/" + entry.getPUID(),
                OWL2Datatype.RDFS_LITERAL);
        OWLDataPropertyAssertionAxiom addProp = owlDataFactory.getOWLDataPropertyAssertionAxiom(owlp,
                swoIndividual_FormatRegistry, owlLiteral);
        changes.add(new AddAxiom(ontology, addProp));

        OWLDataProperty owlp2 = owlDataFactory.getOWLDataProperty(PRONOM_REGISTRY_NAME_IRI);
        OWLLiteral owlLiteral2 = owlDataFactory.getOWLLiteral("http://www.nationalarchives.gov.uk/PRONOM/",
                OWL2Datatype.RDFS_LITERAL);
        OWLDataPropertyAssertionAxiom addProp2 = owlDataFactory.getOWLDataPropertyAssertionAxiom(owlp2,
                swoIndividual_FormatRegistry, owlLiteral2);
        changes.add(new AddAxiom(ontology, addProp2));

        // apply all changes to the Model
        for (AddAxiom addAxiom : changes) {
            owlManager.applyChange(addAxiom);
        }

	a/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/ExtendedOWL.java		b/src/main/java/net/timbusproject/extractors/modules/tavernaextractor/ExtendedOWL.java
	...		...
98	IRI.create(IRI_PREMIS.toString() + "#", "File"));	98	IRI.create(IRI_PREMIS.toString() + "#", "File"));
99		99
100	/**	100	/**
101	* PRONOM PUID	101	* PRONOM PUID
102	*/	102	*/
103	public static final String PRONOM_REGISTRY_URI = "http://www.loc.gov/premis/rdf/v1#hasFormatRegistryKey";	103	public static final String PRONOM_REGISTRY_KEY_URI = "http://www.loc.gov/premis/rdf/v1#hasFormatRegistryKey";
104	public static final IRI PRONOM_REGISTRY_IRI = IRI.create(PRONOM_REGISTRY_URI);	104	public static final IRI PRONOM_REGISTRY_KEY_IRI = IRI.create(PRONOM_REGISTRY_KEY_URI);
		105	public static final String PRONOM_REGISTRY_NAME_URI = "http://www.loc.gov/premis/rdf/v1#hasFormatRegistryName";
		106	public static final IRI PRONOM_REGISTRY_NAME_IRI = IRI.create(PRONOM_REGISTRY_NAME_URI);
105		107
106	public ExtendedOWL() {	108	public ExtendedOWL() {
107	logger.setLevel(Level.DEBUG);	109	logger.setLevel(Level.DEBUG);
108	}	110	}
109		111
	...		...
148	// (2) Read entries from DROID CSV report file	150	// (2) Read entries from DROID CSV report file
149	provenanceAccessClient = new ProvenanceAccessClient();	151	provenanceAccessClient = new ProvenanceAccessClient();
150	provenanceEntries = provenanceAccessClient.filterEntries(provenanceAccessClient.readCSV(droidCSVReport));	152	provenanceEntries = provenanceAccessClient.filterEntries(provenanceAccessClient.readCSV(droidCSVReport));
151		153
152	if (provenanceEntries.isEmpty()) {	154	if (provenanceEntries.isEmpty()) {
153	logger.error("ERROR: Stop processing due to an empty provenance entry list.");	155	logger.info("Nothing to apply due to an empty provenance entry set.");
154	return;	156	return;
155	}	157	}
156		158
157	if (ontology != null) {	159	if (ontology != null) {
158		160
	...		...
174	// iterate over all entries found in the DROID CSV report	176	// iterate over all entries found in the DROID CSV report
175	for (CSVEntry entry : provenanceEntries) {	177	for (CSVEntry entry : provenanceEntries) {
176		178
177	logger.debug(entry.toString());	179	logger.debug(entry.toString());
178	for (OWLNamedIndividual ind : individuals) {	180	for (OWLNamedIndividual ind : individuals) {
179	if (hasAnnotationValue(ind, ontology, entry.getNAME()) && entry.getPUID() != null	181	if (hasAnnotationValue(ind, ontology, entry.getNameForExtensionUsage()) && entry.getPUID() != null
180	&& !entry.getPUID().isEmpty()) {	182	&& !entry.getPUID().isEmpty()) {
181		183
182	logger.info("Found individual (" + ind.getIRI() + ") which has to be extended with PUID ("	184	logger.info("Found individual (" + ind.getIRI() + ") which has to be extended with PUID ("
183	+ entry.getPUID() + ")");	185	+ entry.getPUID() + ")");
184	updateOWL(ind, entry);	186	updateOWL(ind, entry);
	...		...
193	}	195	}
194		196
195	// add a new individual to existing ontology	197	// add a new individual to existing ontology
196	private void updateOWL(OWLNamedIndividual ind, CSVEntry entry) {	198	private void updateOWL(OWLNamedIndividual ind, CSVEntry entry) {
197		199
198	Queue<AddAxiom> changes = new LinkedList<AddAxiom>();	200	Queue<AddAxiom> changes = new LinkedList<>();
199		201
200	// Add File assertion	202	// Add File assertion
201	OWLClassAssertionAxiom swoClassAxiom_File = owlDataFactory.getOWLClassAssertionAxiom(PREMIS_FILE_CLASS, ind);	203	OWLClassAssertionAxiom swoClassAxiom_File = owlDataFactory.getOWLClassAssertionAxiom(PREMIS_FILE_CLASS, ind);
202	changes.add(new AddAxiom(ontology, swoClassAxiom_File));	204	changes.add(new AddAxiom(ontology, swoClassAxiom_File));
203		205
204	// Create new ObjectCharacteristics	206	// Create new ObjectCharacteristics
205	OWLNamedIndividual swoIndividual_ObjectCharacteristics = owlDataFactory.getOWLNamedIndividual(IRI.create("#",	207	OWLNamedIndividual swoIndividual_ObjectCharacteristics = owlDataFactory.getOWLNamedIndividual(IRI.create("#",
206	replaceWhitespace(entry.getNAME()) + "Characteristics"));	208	replaceWhitespace(entry.getNameForExtensionUsage()) + "Characteristics"));
207	OWLClassAssertionAxiom swoClassAxiom_ObjectCharacteristics = owlDataFactory.getOWLClassAssertionAxiom(	209	OWLClassAssertionAxiom swoClassAxiom_ObjectCharacteristics = owlDataFactory.getOWLClassAssertionAxiom(
208	PREMIS_OBJECTCHAR_CLASS, swoIndividual_ObjectCharacteristics);	210	PREMIS_OBJECTCHAR_CLASS, swoIndividual_ObjectCharacteristics);
209	changes.add(new AddAxiom(ontology, swoClassAxiom_ObjectCharacteristics));	211	changes.add(new AddAxiom(ontology, swoClassAxiom_ObjectCharacteristics));
210		212
211	changes.add(linkIndividuals(PREMIS_LINKING_HASOBJECTCHARACTERISTICS, ind, swoIndividual_ObjectCharacteristics));	213	changes.add(linkIndividuals(PREMIS_LINKING_HASOBJECTCHARACTERISTICS, ind, swoIndividual_ObjectCharacteristics));
	...		...
219		221
220	changes.add(linkIndividuals(PREMIS_LINKING_HASFORMAT, swoIndividual_ObjectCharacteristics, swoIndividual_Format));	222	changes.add(linkIndividuals(PREMIS_LINKING_HASFORMAT, swoIndividual_ObjectCharacteristics, swoIndividual_Format));
221		223
222	// Create new FormatRegistry	224	// Create new FormatRegistry
223	OWLNamedIndividual swoIndividual_FormatRegistry = owlDataFactory.getOWLNamedIndividual(IRI.create("#",	225	OWLNamedIndividual swoIndividual_FormatRegistry = owlDataFactory.getOWLNamedIndividual(IRI.create("#",
224	"PronomRegistry[" + entry.getNAME() + "]"));	226	"PronomRegistry[" + entry.getNameForExtensionUsage() + "]"));
225	OWLClassAssertionAxiom swoClassAxiom_FormatRegistry = owlDataFactory.getOWLClassAssertionAxiom(	227	OWLClassAssertionAxiom swoClassAxiom_FormatRegistry = owlDataFactory.getOWLClassAssertionAxiom(
226	PREMIS_FROMATREGISTRY_CLASS, swoIndividual_FormatRegistry);	228	PREMIS_FROMATREGISTRY_CLASS, swoIndividual_FormatRegistry);
227	changes.add(new AddAxiom(ontology, swoClassAxiom_FormatRegistry));	229	changes.add(new AddAxiom(ontology, swoClassAxiom_FormatRegistry));
228		230
229	changes.add(linkIndividuals(PREMIS_LINKING_HASFORMATREGISTRY, swoIndividual_Format,	231	changes.add(linkIndividuals(PREMIS_LINKING_HASFORMATREGISTRY, swoIndividual_Format,
230	swoIndividual_FormatRegistry));	232	swoIndividual_FormatRegistry));
231		233
232	// Create new FormatRegistry Data Property Assertion	234	// Create new FormatRegistry Data Property Assertion
233	OWLDataProperty owlp = owlDataFactory.getOWLDataProperty(PRONOM_REGISTRY_IRI);	235	OWLDataProperty owlp = owlDataFactory.getOWLDataProperty(PRONOM_REGISTRY_KEY_IRI);
234	OWLLiteral owlLiteral = owlDataFactory.getOWLLiteral("info:pronom/" + entry.getPUID(),	236	OWLLiteral owlLiteral = owlDataFactory.getOWLLiteral("info:pronom/" + entry.getPUID(),
235	OWL2Datatype.RDFS_LITERAL);	237	OWL2Datatype.RDFS_LITERAL);
236	OWLDataPropertyAssertionAxiom addProp = owlDataFactory.getOWLDataPropertyAssertionAxiom(owlp,	238	OWLDataPropertyAssertionAxiom addProp = owlDataFactory.getOWLDataPropertyAssertionAxiom(owlp,
237	swoIndividual_FormatRegistry, owlLiteral);	239	swoIndividual_FormatRegistry, owlLiteral);
238	changes.add(new AddAxiom(ontology, addProp));	240	changes.add(new AddAxiom(ontology, addProp));
		241
		242	OWLDataProperty owlp2 = owlDataFactory.getOWLDataProperty(PRONOM_REGISTRY_NAME_IRI);
		243	OWLLiteral owlLiteral2 = owlDataFactory.getOWLLiteral("http://www.nationalarchives.gov.uk/PRONOM/",
		244	OWL2Datatype.RDFS_LITERAL);
		245	OWLDataPropertyAssertionAxiom addProp2 = owlDataFactory.getOWLDataPropertyAssertionAxiom(owlp2,
		246	swoIndividual_FormatRegistry, owlLiteral2);
		247	changes.add(new AddAxiom(ontology, addProp2));
239		248
240	// apply all changes to the Model	249	// apply all changes to the Model
241	for (AddAxiom addAxiom : changes) {	250	for (AddAxiom addAxiom : changes) {
242	owlManager.applyChange(addAxiom);	251	owlManager.applyChange(addAxiom);
243	}	252	}