@Override
public void removeSubDataProperty(String subDataPropertyName, String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDataProperty subDataProperty =
factory.getOWLDataProperty(IRI.create(prefix + subDataPropertyName));
OWLAxiom axiom = factory.getOWLSubDataPropertyOfAxiom(subDataProperty, dataProperty);
axiom = changeManager.getAnnotatedAxiom(axiom);
RemoveAxiom removeAxiom = new RemoveAxiom(localContext, axiom);
try {
synchronized (this) {
changeManager.validateRemovalChange(axiom);
manager.applyChange(removeAxiom);
}
} catch (RemovalException ex) {
logger.severe(
ex.getMessage()
+ " Change ( removeSubDataProperty "
+ subDataPropertyName
+ " of "
+ dataPropertyName
+ ") will not be applied.");
}
}
@SuppressWarnings("javadoc")
public class BadDataPropertyRT extends TestCase {
private static final OWLDataFactory factory = Factory.getFactory();
public static final String NS = "http://test.org/DataPropertyRestriction.owl";
public static final OWLDataProperty P = factory.getOWLDataProperty(IRI.create(NS + "#p"));
public static final OWLClass A = factory.getOWLClass(IRI.create(NS + "#A"));
@Test
public void testBadDataproperty() throws Exception {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.createOntology(IRI.create(NS));
OWLClassExpression restriction =
factory.getOWLDataSomeValuesFrom(
P, factory.getOWLDatatype(XSDVocabulary.DURATION.getIRI()));
OWLAxiom axiom = factory.getOWLSubClassOfAxiom(A, restriction);
manager.addAxiom(ontology, axiom);
assertTrue(ontology.containsDataPropertyInSignature(P.getIRI()));
StringDocumentTarget t = new StringDocumentTarget();
manager.saveOntology(ontology, new RDFXMLOntologyFormat(), t);
manager.removeOntology(ontology);
ontology = manager.loadOntologyFromOntologyDocument(new StringDocumentSource(t.toString()));
assertTrue(ontology.containsDataPropertyInSignature(P.getIRI()));
}
}
/**
* Gets the IconBox for the specified image IRI.
*
* @param iri The IRI pointing to the image.
* @return The icon box containing the image.
* @throws MalformedURLException
*/
private IconBox getImageBox(IRI iri) throws MalformedURLException {
ImageIcon imageIcon = new ImageIcon(iri.toURI().toURL());
imageIcon.getImageLoadStatus();
IconBox iconBox = new IconBox(imageIcon, new HTTPLink(iri.toURI()));
iconBox.setMaxHeight(50);
return iconBox;
}
private void translateTaxon(Taxon taxon, OWLNamedIndividual otu) {
this.taxonOTUToOWLMap.put(taxon, otu);
this.addClass(otu, this.factory.getOWLClass(IRI.create(CDAO.OTU)));
if (StringUtils.isNotBlank(taxon.getPublicationName())) {
final OWLLiteral label = this.factory.getOWLLiteral(taxon.getPublicationName());
this.addAnnotation(OWLRDFVocabulary.RDFS_LABEL.getIRI(), otu.getIRI(), label);
}
if (taxon.getValidName() != null) {
final IRI taxonIRI = this.convertOBOIRI(taxon.getValidName().getID());
this.addClass(
this.factory.getOWLNamedIndividual(taxonIRI),
this.factory.getOWLClass(IRI.create(PHENOSCAPE.TAXON)));
this.addPropertyAssertion(
IRI.create(CDAO.HAS_EXTERNAL_REFERENCE),
otu,
this.factory.getOWLNamedIndividual(taxonIRI));
}
if (StringUtils.isNotBlank(taxon.getComment())) {
final OWLLiteral comment = factory.getOWLLiteral(taxon.getComment());
this.addAnnotation(OWLRDFVocabulary.RDFS_COMMENT.getIRI(), otu.getIRI(), comment);
}
for (Specimen specimen : taxon.getSpecimens()) {
final OWLAnonymousIndividual owlSpecimen = this.factory.getOWLAnonymousIndividual();
this.addPropertyAssertion(IRI.create(DWC.HAS_SPECIMEN), otu, owlSpecimen);
this.translateSpecimen(specimen, owlSpecimen);
}
}
@Test
public void fragmentGetLocalNameTest() {
assertEquals("path", OwlUtils.getLocalName(IRI.create("http://host/path#")));
assertEquals("f", OwlUtils.getLocalName(IRI.create("http://host/path#f")));
assertEquals("fragment", OwlUtils.getLocalName(IRI.create("http://host/path#fragment")));
assertEquals("fragment#", OwlUtils.getLocalName(IRI.create("http://host/path#fragment#")));
}
public void testIgnoreAnnotations() throws Exception {
OWLOntologyManager man = getManager(); // OWLManager.createOWLOntologyManager();
OWLOntology ont = man.createOntology();
OWLDataFactory df = man.getOWLDataFactory();
OWLClass clsA = df.getOWLClass(IRI.create("http://ont.com#A"));
OWLClass clsB = df.getOWLClass(IRI.create("http://ont.com#B"));
OWLSubClassOfAxiom sca = df.getOWLSubClassOfAxiom(clsA, clsB);
man.addAxiom(ont, sca);
OWLAnnotationProperty rdfsComment = df.getRDFSComment();
OWLLiteral lit = df.getOWLLiteral("Hello world");
OWLAnnotationAssertionAxiom annoAx1 =
df.getOWLAnnotationAssertionAxiom(rdfsComment, clsA.getIRI(), lit);
man.addAxiom(ont, annoAx1);
OWLAnnotationPropertyDomainAxiom annoAx2 =
df.getOWLAnnotationPropertyDomainAxiom(rdfsComment, clsA.getIRI());
man.addAxiom(ont, annoAx2);
OWLAnnotationPropertyRangeAxiom annoAx3 =
df.getOWLAnnotationPropertyRangeAxiom(rdfsComment, clsB.getIRI());
man.addAxiom(ont, annoAx3);
OWLAnnotationProperty myComment =
df.getOWLAnnotationProperty(IRI.create("http://ont.com#myComment"));
OWLSubAnnotationPropertyOfAxiom annoAx4 =
df.getOWLSubAnnotationPropertyOfAxiom(myComment, rdfsComment);
man.addAxiom(ont, annoAx4);
reload(ont, new RDFXMLOntologyFormat());
reload(ont, new OWLXMLOntologyFormat());
reload(ont, new TurtleOntologyFormat());
reload(ont, new OWLFunctionalSyntaxOntologyFormat());
}
@Override
public KuabaRepository load(String url) throws RepositoryLoadException {
IRI iri;
File f = new File(url);
if (!url.contains(":/")) {
iri = IRI.create(f);
} else iri = IRI.create(url);
try {
OWLOntology inst = manager.loadOntologyFromOntologyDocument(iri);
if (inst == null) throw new RepositoryLoadException(url, "Invalid Location.");
if (inst.getOntologyID().getOntologyIRI() == null) {
// An anonymous Ontology was loaded, and they are not supported by the Kuaba Subsystem
manager.removeOntology(inst);
throw new RepositoryLoadException(url, "It is probably an incompatible or malformed file.");
}
KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
fileMap.put(repo, f);
return repo;
} catch (OWLOntologyAlreadyExistsException ex) {
OWLOntologyID id = ex.getOntologyID();
// System.err.println("Ontologia "+id.getOntologyIRI().toString()+" já está
// carregada, esta será retornada.");
return repoMap.get(id.getOntologyIRI());
} catch (OWLOntologyCreationException ex) {
throw new RepositoryLoadException(url, "Invalid Location.");
// Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
}
}
private void getPelletIncrementalClassifierRunTime(String baseOnt, String ontDir)
throws Exception {
System.out.println("Using Pellet Incremental Classifier...");
GregorianCalendar start = new GregorianCalendar();
File ontFile = new File(baseOnt);
IRI documentIRI = IRI.create(ontFile);
OWLOntology baseOntology = OWL.manager.loadOntology(documentIRI);
IncrementalClassifier classifier = new IncrementalClassifier(baseOntology);
classifier.classify();
System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
System.out.println("Time taken for base ontology (millis): " + Util.getElapsedTime(start));
File ontDirPath = new File(ontDir);
File[] allFiles = ontDirPath.listFiles();
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
addTripsBaseOntologies(manager);
int count = 1;
for (File owlFile : allFiles) {
IRI owlDocumentIRI = IRI.create(owlFile);
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(owlDocumentIRI);
Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
for (OWLLogicalAxiom axiom : axioms)
OWL.manager.applyChange(new AddAxiom(baseOntology, axiom));
System.out.println("\nLogical axioms: " + baseOntology.getLogicalAxiomCount());
System.out.println(count + " file: " + owlFile.getName());
// System.out.println("" + count + " file: " + owlFile.getName());
// GregorianCalendar start2 = new GregorianCalendar();
classifier.classify();
// System.out.println("Time taken (millis): " +
// Util.getElapsedTime(start2));
manager.removeOntology(ontology);
count++;
}
System.out.println("\nTotal time taken (millis): " + Util.getElapsedTime(start));
}
public KuabaRepository createNewRepository(String url, File destination) {
IRI iri;
if (url == null) iri = IRI.generateDocumentIRI();
else iri = IRI.create(url);
try {
OWLOntology inst = manager.createOntology(iri);
OWLImportsDeclaration imp =
manager.getOWLDataFactory().getOWLImportsDeclaration(IRI.create(ONTOLOGY_URL));
AddImport addi = new AddImport(inst, imp);
manager.applyChange(addi);
KuabaRepository repo = new OwlApiKuabaRepository(inst, manager.getOWLDataFactory());
repoMap.put(inst.getOntologyID().getOntologyIRI(), repo);
fileMap.put(repo, destination);
TemplateGenerator.generateRootQuestion(repo);
if (destination != null) this.save(repo);
return repo;
} catch (OWLOntologyCreationException ex) {
Logger.getLogger(OwlApiFileGateway.class.getName()).log(Level.SEVERE, null, ex);
}
return null;
}
/**
* Initialization consists of:
*
* <ul>
* <li>Setting aboxOntology, if not set - defaults to a new ontology using tbox.IRI as base.
* Adds import to tbox.
* <li>Setting queryOntology, if not set. Adds abox imports queryOntology declaration
* </ul>
*
* @throws OWLOntologyCreationException
*/
private void init() throws OWLOntologyCreationException {
// reasoner -> query -> abox -> tbox
if (aboxOntology == null) {
LOG.debug("Creating abox ontology. mgr = " + getOWLOntologyManager());
IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI() + "__abox");
aboxOntology = getOWLOntologyManager().getOntology(ontologyIRI);
if (aboxOntology != null) {
LOG.warn("Clearing existing abox ontology");
getOWLOntologyManager().removeOntology(aboxOntology);
}
aboxOntology = getOWLOntologyManager().createOntology(ontologyIRI);
AddImport ai =
new AddImport(
aboxOntology,
getOWLDataFactory()
.getOWLImportsDeclaration(tboxOntology.getOntologyID().getOntologyIRI()));
getOWLOntologyManager().applyChange(ai);
}
// add listener to abox to set modified flag
OWLOntologyChangeBroadcastStrategy strategy =
new SpecificOntologyChangeBroadcastStrategy(aboxOntology);
OWLOntologyChangeListener listener =
new OWLOntologyChangeListener() {
@Override
public void ontologiesChanged(List<? extends OWLOntologyChange> changes)
throws OWLException {
for (OWLOntologyChange owlOntologyChange : changes) {
if (aboxOntology.equals(owlOntologyChange.getOntology())) {
setAboxModified(true);
}
}
}
};
aboxOntology.getOWLOntologyManager().addOntologyChangeListener(listener, strategy);
if (queryOntology == null) {
// Imports: {q imports a, a imports t}
LOG.debug("Creating query ontology");
IRI ontologyIRI = IRI.create(tboxOntology.getOntologyID().getOntologyIRI() + "__query");
queryOntology = getOWLOntologyManager().getOntology(ontologyIRI);
if (queryOntology == null) {
queryOntology = getOWLOntologyManager().createOntology(ontologyIRI);
}
AddImport ai =
new AddImport(
queryOntology,
getOWLDataFactory()
.getOWLImportsDeclaration(aboxOntology.getOntologyID().getOntologyIRI()));
getOWLOntologyManager().applyChange(ai);
}
if (LOG.isDebugEnabled()) {
LOG.debug(modelId + " manager(T) = " + tboxOntology.getOWLOntologyManager());
LOG.debug(modelId + " manager(A) = " + aboxOntology.getOWLOntologyManager());
LOG.debug(modelId + " manager(Q) = " + queryOntology.getOWLOntologyManager());
LOG.debug(modelId + " id(T) = " + tboxOntology.getOntologyID().getOntologyIRI());
LOG.debug(modelId + " id(A) = " + aboxOntology.getOntologyID().getOntologyIRI());
LOG.debug(modelId + " id(Q) = " + queryOntology.getOntologyID().getOntologyIRI());
}
}
public OWLOntology getMergedOntology() {
final IRI mergedOntologyIRI =
IRI.create(queryOntology.getOntologyID().getDefaultDocumentIRI() + "-merged");
final OWLOntologyManager mm = controller.getOWLOntologyManager();
if (mm.contains(mergedOntologyIRI)) {
return mm.getOntology(mergedOntologyIRI);
} else {
try {
final OWLOntology mergedOntology = mm.createOntology(mergedOntologyIRI);
mm.setOntologyFormat(mergedOntology, new RDFXMLOntologyFormat());
final String mergedOntologyFileName =
mergedOntologyIRI
.toURI()
.toString()
.substring(mergedOntologyIRI.toURI().toString().lastIndexOf("/") + 1)
+ ".owl";
mm.setOntologyDocumentIRI(
mergedOntology,
IRI.create(
controller.getRuleSpec().getOutputDir().toURI() + "/" + mergedOntologyFileName));
mm.applyChange(
new AddImport(
mergedOntology,
mm.getOWLDataFactory()
.getOWLImportsDeclaration(
queryOntology.getOntologyID().getDefaultDocumentIRI())));
return mergedOntology;
} catch (OWLOntologyCreationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return null;
}
}
}
private void translatePhenotype(Phenotype phenotype, OWLClass owlPhenotype) {
this.phenotypeToOWLMap.put(phenotype, owlPhenotype);
if (phenotype.getEntity() == null || phenotype.getQuality() == null) {
return;
}
final OWLObjectProperty inheresIn =
this.factory.getOWLObjectProperty(IRI.create(OBO_REL.INHERES_IN));
final OWLClassExpression entity = this.convertOBOClass(phenotype.getEntity());
final OWLClassExpression qualityTerm = this.convertOBOClass(phenotype.getQuality());
final OWLClassExpression quality;
if (phenotype.getRelatedEntity() != null) {
final OWLClassExpression relatedEntity = this.convertOBOClass(phenotype.getRelatedEntity());
final OWLObjectProperty towards =
this.factory.getOWLObjectProperty(IRI.create(OBO_REL.TOWARDS));
quality =
this.factory.getOWLObjectIntersectionOf(
qualityTerm, this.factory.getOWLObjectSomeValuesFrom(towards, relatedEntity));
} else {
quality = qualityTerm;
}
final OWLClassExpression eq =
this.factory.getOWLObjectIntersectionOf(
quality, this.factory.getOWLObjectSomeValuesFrom(inheresIn, entity));
// TODO measurements, counts, etc.
this.ontologyManager.addAxiom(
this.ontology, this.factory.getOWLEquivalentClassesAxiom(owlPhenotype, eq));
}
private void translateState(State state, OWLNamedIndividual owlState) {
this.stateToOWLMap.put(state, owlState);
this.addClass(owlState, this.factory.getOWLClass(IRI.create(CDAO.STANDARD_STATE)));
if (StringUtils.isNotBlank(state.getLabel())) {
final OWLLiteral label = this.factory.getOWLLiteral(state.getLabel());
this.addAnnotation(OWLRDFVocabulary.RDFS_LABEL.getIRI(), owlState.getIRI(), label);
}
if (StringUtils.isNotBlank(state.getComment())) {
final OWLLiteral comment = factory.getOWLLiteral(state.getComment());
this.addAnnotation(OWLRDFVocabulary.RDFS_COMMENT.getIRI(), owlState.getIRI(), comment);
}
int phenotypeIndex = 0;
final OWLObjectProperty denotes = this.factory.getOWLObjectProperty(IRI.create(IAO.DENOTES));
for (Phenotype phenotype : state.getPhenotypes()) {
phenotypeIndex++;
final IRI phenotypeIRI =
IRI.create(owlState.getIRI().toURI().toString() + "/phenotype/" + phenotypeIndex);
final OWLClass owlPhenotype = this.factory.getOWLClass(phenotypeIRI);
final OWLObjectAllValuesFrom denotesOnlyPhenotype =
this.factory.getOWLObjectAllValuesFrom(denotes, owlPhenotype);
this.ontologyManager.addAxiom(
ontology, this.factory.getOWLClassAssertionAxiom(denotesOnlyPhenotype, owlState));
this.translatePhenotype(phenotype, owlPhenotype);
}
}
public void retrieveRoomsMap() {
// this method retrieves the rooms to be insserted in the two rooms lists.
// it deposits the retrieved data in a map where the key is the room name (String) and the value
// is the corresponding entity IRI.
// the above data structure will be used in passing the entity IRIs in the jess working memory
// when constructing the facts
// when the respective room name (String) is selected in the rooms list combo box.
for (OWLSubClassOfAxiom scoAx :
topIxOnt.getSubClassAxiomsForSuperClass(
OWLFactory.getOWLClass(
IRI.create(
"http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl#Room")))) {
String tmpS = scoAx.getSubClass().toString();
Set<OWLAnnotationAssertionAxiom> tmpAnnSet =
topIxOnt.getAnnotationAssertionAxioms(
IRI.create(tmpS.substring(tmpS.indexOf('<') + 1, tmpS.indexOf('>'))));
for (OWLAnnotationAssertionAxiom aaAx : tmpAnnSet) {
if (aaAx.getProperty()
.toString()
.equals(
"<http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl#classID>")) {
roomToIRI.put(
aaAx.getValue().toString().substring(1, aaAx.getValue().toString().indexOf('^') - 1),
tmpS.substring(tmpS.indexOf('<') + 1, tmpS.indexOf('>')));
}
}
}
}
@Override
public boolean hasDataPropertyStringRange(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDatatype stringDatatype = factory.getOWLDatatype(IRI.create(prefix + "string"));
OWLAxiom axiom = factory.getOWLDataPropertyRangeAxiom(dataProperty, stringDatatype);
return localContext.containsAxiomIgnoreAnnotations(axiom);
}
/**
* Renders an IRI as a full IRI rather than as an IRI that represents an entity in the signature
* of the imports closure of the active ontology.
*
* @param page The page that the IRI should be rendered into.
* @param iri The IRI to be rendered.
* @return A list of paragraphs that represent the rendering of the annotation value.
*/
private List<Paragraph> renderExternalIRI(Page page, IRI iri) {
Paragraph paragraph;
if (isLinkableAddress(iri)) {
paragraph = page.addParagraph(iri.toString(), new HTTPLink(iri.toURI()));
} else {
paragraph = page.addParagraph(iri.toString());
}
return Arrays.asList(paragraph);
}
protected OWLClass getFreshQueryClass(String base) {
long cnt = 0;
String iriString = base;
while (m_ontologyOperator.getOntology().containsClassInSignature(IRI.create(iriString))) {
iriString =
base + (cnt++); // not guaranteed to succeed.. however |long| amount of possibilities
}
return OWLManager.getOWLDataFactory().getOWLClass(IRI.create(iriString));
}
@Override
public boolean hasDataPropertyDomain(String dataPropertyName, String domainName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLClass cls = factory.getOWLClass(IRI.create(prefix + domainName));
OWLAxiom axiom = factory.getOWLDataPropertyDomainAxiom(dataProperty, cls);
return localContext.containsAxiomIgnoreAnnotations(axiom);
}
@Override
public boolean hasSubDataProperty(String subDataPropertyName, String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDataProperty subDataProperty =
factory.getOWLDataProperty(IRI.create(prefix + subDataPropertyName));
OWLAxiom axiom = factory.getOWLSubDataPropertyOfAxiom(subDataProperty, dataProperty);
return localContext.containsAxiomIgnoreAnnotations(axiom);
}
@Test
public void testNonCycle3() throws Exception {
ParserWrapper parser = new ParserWrapper();
IRI iri = IRI.create(getResource("verification/self_references.obo").getAbsoluteFile());
OWLGraphWrapper graph = parser.parseToOWLGraph(iri.toString());
OntologyCheck check = new CycleCheck();
Collection<CheckWarning> warnings = check.check(graph, graph.getAllOWLObjects());
assertTrue(warnings.isEmpty());
}
@Override
public void addDataPropertyDomain(String dataPropertyName, String domainName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLClass domain = factory.getOWLClass(IRI.create(prefix + domainName));
OWLAxiom axiom = factory.getOWLDataPropertyDomainAxiom(dataProperty, domain);
axiom = changeManager.getAnnotatedAxiom(axiom);
AddAxiom addAxiom = new AddAxiom(localContext, axiom);
manager.applyChange(addAxiom);
}
@Override
public void addDataPropertyStringRange(String dataPropertyName) {
OWLDataFactory factory = manager.getOWLDataFactory();
OWLDataProperty dataProperty =
factory.getOWLDataProperty(IRI.create(prefix + dataPropertyName));
OWLDatatype stringDatatype = factory.getOWLDatatype(IRI.create(prefix + "string"));
OWLAxiom axiom = factory.getOWLDataPropertyRangeAxiom(dataProperty, stringDatatype);
axiom = changeManager.getAnnotatedAxiom(axiom);
AddAxiom addAxiom = new AddAxiom(localContext, axiom);
manager.applyChange(addAxiom);
}
public static void insertSystemTriples(
ISparulExecutor executor, String dataGraphName, String metaGraphName) throws Exception {
logger.info("Inserting Annotation Properties.");
List<RDFTriple> triples = new ArrayList<RDFTriple>();
MyVocabulary[] vocabs = {
MyVocabulary.DC_MODIFIED,
MyVocabulary.DBM_EDIT_LINK,
MyVocabulary.DBM_PAGE_ID,
MyVocabulary.DBM_REVISION,
MyVocabulary.DBM_OAIIDENTIFIER
};
for (MyVocabulary item : vocabs) {
triples.add(
new RDFTriple(
new RDFResourceNode(item.getIRI()),
new RDFResourceNode(OWLRDFVocabulary.RDF_TYPE.getIRI()),
new RDFResourceNode(OWLRDFVocabulary.OWL_ANNOTATION_PROPERTY.getIRI())));
}
List<RDFTriple> metaTriples = new ArrayList<RDFTriple>();
for (RDFTriple item : triples) {
URI uri = RDFUtil.generateMD5HashUri("http://dbpedia.org/sysvocab/", item);
RDFResourceNode reifier = new RDFResourceNode(IRI.create(uri));
metaTriples.add(
new RDFTriple(
reifier,
new RDFResourceNode(OWLRDFVocabulary.OWL_ANNOTATED_SOURCE.getIRI()),
item.getSubject()));
metaTriples.add(
new RDFTriple(
reifier,
new RDFResourceNode(OWLRDFVocabulary.OWL_ANNOTATED_PROPERTY.getIRI()),
item.getProperty()));
metaTriples.add(
new RDFTriple(
reifier,
new RDFResourceNode(OWLRDFVocabulary.OWL_ANNOTATED_TARGET.getIRI()),
item.getObject()));
metaTriples.add(
new RDFTriple(
reifier,
new RDFResourceNode(MyVocabulary.DBM_EXTRACTED_BY.getIRI()),
new RDFResourceNode(IRI.create(TBoxExtractor.extractorUri))));
}
executor.insert(metaTriples, metaGraphName);
executor.insert(triples, dataGraphName);
}
public KuabaRepository getSourceRepository(IRI iri) {
IRI repoIRI = IRI.create(iri.getStart().replaceAll("#", ""));
KuabaRepository repo = repoMap.get(repoIRI);
try {
if (repo == null) repo = this.load(repoIRI.toString());
} catch (Exception e) {
System.err.println("Error when trying to get the source repository of " + iri.toString());
System.err.println("Source repository not found.");
}
return repo;
}
public void retrieveSubObjectPropertyAxioms() {
// this method is to perform a dual operation; it shall retrieve all the declarative object
// properties categories' annotations,
// thus filling the objPropCategories Set, while parallelly will, for each category entry
// retrieve the object properties themselves
// and adding their entries in the objPropEntries Set.
Set<OWLSubObjectPropertyOfAxiom> tmpSet;
OWLObjectPropertyExpression tempDeclarativePropertyClass =
OWLFactory.getOWLObjectProperty(":DeclarativeProperty", topIxPrefixManager);
tmpSet =
topIxOnt.getObjectSubPropertyAxiomsForSuperProperty(
tempDeclarativePropertyClass); // OWLFactory.getOWLObjectProperty(IRI.create("http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl#DeclarativeProperty")));
Set<OWLSubObjectPropertyOfAxiom> tmpSet2;
Set<OWLAnnotationAssertionAxiom> tmpAnnSet1;
Set<OWLAnnotationAssertionAxiom> tmpAnnSet2;
// to become class variables.
for (OWLSubObjectPropertyOfAxiom sopAx : tmpSet) {
String tmpS = sopAx.getSubProperty().toString();
// categories...
tmpAnnSet1 =
topIxOnt.getAnnotationAssertionAxioms(
IRI.create(
tmpS.substring(
1, tmpS.indexOf('>')))); // this set only contains one annotation per entry
for (OWLAnnotationAssertionAxiom aaAx : tmpAnnSet1) {
String currentObjPropCatName =
aaAx.getValue().toString().substring(1, aaAx.getValue().toString().indexOf('^') - 1);
tmpSet2 =
topIxOnt.getObjectSubPropertyAxiomsForSuperProperty(
OWLFactory.getOWLObjectProperty(IRI.create(tmpS.substring(1, tmpS.length() - 1))));
for (OWLSubObjectPropertyOfAxiom sopAx2 : tmpSet2) {
String tmpS2 = sopAx2.getSubProperty().toString();
tmpAnnSet2 =
topIxOnt.getAnnotationAssertionAxioms(
IRI.create(tmpS2.substring(1, tmpS2.length() - 1)));
for (OWLAnnotationAssertionAxiom aaAx2 : tmpAnnSet2) {
String currentObjPropEntryName =
aaAx2
.getValue()
.toString()
.substring(1, aaAx2.getValue().toString().indexOf('^') - 1);
propEntryNameToPropCatName.put(currentObjPropEntryName, currentObjPropCatName);
propEntryNametoPropEntryIRI.put(
currentObjPropEntryName, tmpS2.substring(1, tmpS2.length() - 1));
}
}
}
}
}
@Override
public boolean equals(Object obj) {
if (super.equals(obj)) {
if (!(obj instanceof OWLDataProperty)) {
return false;
}
IRI otherIRI = ((OWLDataProperty) obj).getIRI();
return otherIRI.equals(iri);
}
return false;
}
public void applyChanges() {
EntityCreationPreferences.setUseDefaultBaseIRI(iriBaseSpecifiedIri.isSelected());
try {
IRI defaultBase = IRI.create(new URI(iriDefaultBaseField.getText()));
EntityCreationPreferences.setDefaultBaseIRI(defaultBase);
} catch (URISyntaxException e) {
logger.error("Ignoring invalid base IRI ({})", iriDefaultBaseField.getText(), e);
}
if (hashButton.isSelected()) {
EntityCreationPreferences.setDefaultSeparator(SEP_HASH);
} else if (slashButton.isSelected()) {
EntityCreationPreferences.setDefaultSeparator(SEP_SLASH);
} else if (colonButton.isSelected()) {
EntityCreationPreferences.setDefaultSeparator(SEP_COLON);
}
EntityCreationPreferences.setFragmentAutoGenerated(autoIDIriFragment.isSelected());
EntityCreationPreferences.setGenerateNameLabel(autoIDIriFragment.isSelected());
EntityCreationPreferences.setGenerateIDLabel(false);
if (sameAsRendererLabelButton.isSelected()) {
EntityCreationPreferences.setLabelDescriptorClass(MatchRendererLabelDescriptor.class);
}
if (customLabelButton.isSelected()) {
EntityCreationPreferences.setLabelDescriptorClass(CustomLabelDescriptor.class);
}
EntityCreationPreferences.setNameLabelIRI(IRI.create(annotationIriLabel.getText()));
Object lang = annotationLangSelector.getSelectedItem();
if (lang != null && !lang.equals("")) {
EntityCreationPreferences.setNameLabelLang((String) lang);
} else {
EntityCreationPreferences.setNameLabelLang(null);
}
if (iterativeButton.isSelected()) {
EntityCreationPreferences.setAutoIDGeneratorClass(IterativeAutoIDGenerator.class);
}
if (uniqueIdButton.isSelected()) {
EntityCreationPreferences.setAutoIDGeneratorClass(UniqueIdGenerator.class);
}
EntityCreationPreferences.setAutoIDStart((Integer) autoIDStart.getValue());
EntityCreationPreferences.setAutoIDEnd((Integer) autoIDEnd.getValue());
EntityCreationPreferences.setAutoIDDigitCount((Integer) autoIDDigitCount.getValue());
EntityCreationPreferences.setPrefix(autoIDPrefix.getText());
EntityCreationPreferences.setSuffix(autoIDSuffix.getText());
EntityCreationPreferences.setSaveAutoIDStart(saveIterativeIds.isSelected());
}
public boolean assertDataPropertyInstance(String ind, String prop, int value) {
OWLDataProperty dataProp =
OWLFactory.getOWLDataProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + prop));
OWLDataPropertyAssertionAxiom tmpAx =
OWLFactory.getOWLDataPropertyAssertionAxiom(
dataProp,
OWLFactory.getOWLNamedIndividual(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + ind)),
OWLFactory.getOWLLiteral(value));
manager.addAxiom(topIxOnt, tmpAx);
return true;
}
public void mergeAndCompare(String dirPath) throws Exception {
File dir = new File(dirPath);
File[] files = dir.listFiles();
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntologyMerger merger = new OWLOntologyMerger(manager);
for (File f : files) manager.loadOntologyFromOntologyDocument(IRI.create(f));
String s = "norm-merged-base+300.owl";
IRI iri = IRI.create(new File(s));
OWLOntology mergedOntology = merger.createMergedOntology(manager, iri);
manager.saveOntology(mergedOntology, iri);
System.out.println("Done creating merged ontology");
// precomputeAndCheckResults(mergedOntology);
}
public static void callLogMap() throws OWLOntologyCreationException {
String onto1_iri = "http://oaei.ontologymatching.org/tests/101/onto.rdf";
String onto2_iri = "http://oaei.ontologymatching.org/tests/304/onto.rdf";
OWLOntologyManager onto_manager = OWLManager.createOWLOntologyManager();
OWLOntology onto1 = onto_manager.loadOntology(IRI.create(onto1_iri));
OWLOntology onto2 = onto_manager.loadOntology(IRI.create(onto2_iri));
LogMap2_Matcher logmap2 = new LogMap2_Matcher(onto1, onto2);
Set<MappingObjectStr> logmap2_mappings = logmap2.getLogmap2_Mappings();
for (MappingObjectStr mappingObject : logmap2_mappings) {
System.out.println(" test des mots : " + mappingObject.toString());
}
System.out.println("Num.mappings: " + logmap2_mappings.size());
}
