public void writeOntologyHeader(OWLOntology ontology) {
event = new RendererEvent(this, ontology);
fireFrameRenderingPrepared(ONTOLOGY.toString());
write(ONTOLOGY.toString());
write(":");
writeSpace();
if (!ontology.isAnonymous()) {
int indent = getIndent();
writeFullURI(ontology.getOntologyID().getOntologyIRI().toString());
writeNewLine();
pushTab(indent);
if (ontology.getOntologyID().getVersionIRI() != null) {
writeFullURI(ontology.getOntologyID().getVersionIRI().toString());
}
popTab();
}
fireFrameRenderingStarted(ONTOLOGY.toString());
writeNewLine();
for (OWLImportsDeclaration decl : ontology.getImportsDeclarations()) {
fireSectionItemPrepared(IMPORT.toString());
write(IMPORT.toString());
write(":");
writeSpace();
fireSectionRenderingStarted(IMPORT.toString());
writeFullURI(decl.getURI().toString());
writeNewLine();
fireSectionRenderingFinished(IMPORT.toString());
}
writeNewLine();
writeSection(ANNOTATIONS, ontology.getAnnotations(), ",", true);
fireFrameRenderingFinished(ONTOLOGY.toString());
}
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);
}
}
protected OWLOntology getOntologyAsOWLOntology(
OWLOntologyID ontologyId, boolean merge, IRI universalPrefix) {
// if (merge) throw new UnsupportedOperationException("Merge not implemented yet for
// OWLOntology.");
// Remove the check below. It might be an unmanaged dependency (TODO remove from collector and
// reintroduce check?).
// if (!hasOntology(ontologyIri)) return null;
OWLOntology o;
o = ontologyProvider.getStoredOntology(ontologyId, OWLOntology.class, merge);
if (merge) {
final Set<OWLOntology> set = new HashSet<OWLOntology>();
log.debug("Merging {} with its imports, if any.", o);
set.add(o);
// Actually, if the provider already performed the merge, this won't happen
for (OWLOntology impo : o.getImportsClosure()) {
log.debug("Imported ontology {} will be merged with {}.", impo, o);
set.add(impo);
}
OWLOntologySetProvider provider =
new OWLOntologySetProvider() {
@Override
public Set<OWLOntology> getOntologies() {
return set;
}
};
OWLOntologyMerger merger = new OWLOntologyMerger(provider);
try {
o =
merger.createMergedOntology(
OWLManager.createOWLOntologyManager(), ontologyId.getOntologyIRI());
} catch (OWLOntologyCreationException e) {
log.error("Failed to merge imports for ontology " + ontologyId, e);
// do not reassign the root ontology
}
} else {
// Rewrite import statements
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
OWLDataFactory df = OWLManager.getOWLDataFactory();
/*
* TODO manage import rewrites better once the container ID is fully configurable (i.e. instead of
* going upOne() add "session" or "ontology" if needed). But only do this if we keep considering
* imported ontologies as *not* managed.
*/
for (OWLImportsDeclaration oldImp : o.getImportsDeclarations()) {
changes.add(new RemoveImport(o, oldImp));
String s = oldImp.getIRI().toString();
// FIXME Ugly way to check, but we'll get through with it
if (s.contains("::")) s = s.substring(s.indexOf("::") + 2, s.length());
boolean managed = managedOntologies.contains(oldImp.getIRI());
// For space, always go up at least one
String tid = getID();
if (backwardPathLength > 0) tid = tid.split("/")[0];
IRI target =
IRI.create(
(managed
? universalPrefix + "/" + tid + "/"
: URIUtils.upOne(universalPrefix) + "/")
+ s);
changes.add(new AddImport(o, df.getOWLImportsDeclaration(target)));
}
o.getOWLOntologyManager().applyChanges(changes);
}
return o;
}
/** @param axiom the axiom */
public void visit(OWLImportsDeclaration axiom) {
write("ImportsDeclaration");
axiom.getIRI().accept(this);
}