private void handleNotesOntologyChanged(List<OWLOntologyChange> changes) {
try {
OWLOntologyManager notesOntologyManager = notesOntology.getOWLOntologyManager();
if (notesOntologyManager.getOntologyFormat(notesOntology)
instanceof BinaryOWLOntologyDocumentFormat) {
OWLAPIProjectDocumentStore documentStore =
OWLAPIProjectDocumentStore.getProjectDocumentStore(project.getProjectId());
List<OWLOntologyChangeData> infoList = new ArrayList<OWLOntologyChangeData>();
for (OWLOntologyChange change : changes) {
OWLOntologyChangeRecord rec = change.getChangeRecord();
OWLOntologyChangeData info = rec.getData();
infoList.add(info);
}
BinaryOWLOntologyDocumentSerializer serializer = new BinaryOWLOntologyDocumentSerializer();
serializer.appendOntologyChanges(
notesOntologyDocument,
new OntologyChangeDataList(infoList, System.currentTimeMillis()));
} else {
// Swap it over
notesOntologyManager.saveOntology(notesOntology, new BinaryOWLOntologyDocumentFormat());
}
} catch (OWLOntologyStorageException e) {
throw new RuntimeException(e);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
@Test
public void shouldHandleNullManager_For_GetBottomClassNode() {
try {
when(ontology.getOWLOntologyManager()).thenReturn(null);
reasoner.getBottomClassNode();
} catch (NullPointerException e) {
fail("NullPointerException");
}
}
@Before
public void setUp() {
when(ontology.getOWLOntologyManager()).thenReturn(manager);
when(manager.getOWLDataFactory()).thenReturn(dataFactory);
when(dataFactory.getOWLThing()).thenReturn(owlThing);
when(dataFactory.getOWLNothing()).thenReturn(owlNothing);
when(dataFactory.getOWLTopObjectProperty()).thenReturn(owlTopObjectProperty);
when(dataFactory.getOWLBottomObjectProperty()).thenReturn(owlBottomObjectProperty);
when(dataFactory.getOWLTopDataProperty()).thenReturn(owlTopDataProperty);
when(dataFactory.getOWLBottomDataProperty()).thenReturn(owlBottomDataProperty);
reasoner = new NoOpReasoner(ontology, dataFactory);
}
public OWLProfileReport checkOntology(OWLOntology ontology) {
this.ont = ontology;
OWL2DLProfile profile = new OWL2DLProfile();
OWLProfileReport report = profile.checkOntology(ontology);
Set<OWLProfileViolation> violations = new HashSet<OWLProfileViolation>();
violations.addAll(report.getViolations());
OWLOntologyWalker ontologyWalker = new OWLOntologyWalker(ontology.getImportsClosure());
OWL2ELProfileObjectVisitor visitor =
new OWL2ELProfileObjectVisitor(ontologyWalker, ontology.getOWLOntologyManager());
ontologyWalker.walkStructure(visitor);
violations.addAll(visitor.getProfileViolations());
return new OWLProfileReport(this, violations);
}
public void mergeOntologies() {
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for (OWLOntology ont : ontologies) {
if (!ont.equals(targetOntology)) {
// move the axioms
for (OWLAxiom ax : ont.getAxioms()) {
changes.add(new AddAxiom(targetOntology, ax));
}
// move ontology annotations
for (OWLAnnotation annot : ont.getAnnotations()) {
changes.add(new AddOntologyAnnotation(targetOntology, annot));
}
if (!targetOntology.getOntologyID().isAnonymous()) {
// move ontology imports
for (OWLImportsDeclaration decl : ont.getImportsDeclarations()) {
if (ontologies.contains(ont.getOWLOntologyManager().getImportedOntology(decl))) {
continue;
}
Optional<IRI> defaultDocumentIRI =
targetOntology.getOntologyID().getDefaultDocumentIRI();
if (defaultDocumentIRI.isPresent() && !decl.getIRI().equals(defaultDocumentIRI.get())) {
changes.add(new AddImport(targetOntology, decl));
} else {
logger.warn(
"Merge: ignoring import declaration for ontology "
+ targetOntology.getOntologyID()
+ " (would result in target ontology importing itself).");
}
}
}
}
}
try {
owlOntologyManager.applyChanges(changes);
} catch (OWLOntologyChangeException e) {
ErrorLogPanel.showErrorDialog(e);
}
}
private boolean isOBOFormat(OWLOntology ontology) {
OWLOntologyManager man = ontology.getOWLOntologyManager();
return man.getOntologyFormat(ontology) instanceof OBOOntologyFormat;
}
