protected MGraph getOntologyAsMGraph( OWLOntologyID ontologyId, boolean merge, IRI universalPrefix) { if (merge) throw new UnsupportedOperationException( "Merge not implemented yet for Clerezza triple collections."); /* * 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. */ // if (!merge) { // TODO MGraph o = new IndexedMGraph(ontologyProvider.getStoredOntology(ontologyId, MGraph.class, merge)); // Now rewrite import statements // Scan import statements for each owl:Ontology instance (hopefully one). String tid = getID(); // Bit of a hack : since ontology spaces are named like {scopeid}/{core|custom}, in that // particular // case we go back to {scopeid}, whereas for sessions we maintain their original id. if (backwardPathLength > 0) tid = tid.split("/")[0]; Iterator<Triple> it; List<Triple> newImports = new LinkedList<Triple>(); synchronized (o) { it = o.filter(null, OWL.imports, null); // We use this list to avoid concurrent modification exceptions. List<Triple> replaceUs = new LinkedList<Triple>(); while (it.hasNext()) replaceUs.add(it.next()); for (Triple t : replaceUs) { String s = ((UriRef) (t.getObject())).getUnicodeString(); // FIXME note the different import targets in the OWLOntology and TripleColllection objects! // s = s.substring(s.indexOf("::") + 2, s.length()); boolean managed = managedOntologies.contains(IRI.create(s)); UriRef target = new UriRef( (managed ? universalPrefix + "/" + tid + "/" : URIUtils.upOne(universalPrefix) + "/") + s); o.remove(t); newImports.add(new TripleImpl(t.getSubject(), OWL.imports, target)); } } for (Triple t : newImports) o.add(t); // } // TODO else if (merge) return o; }
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; }