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;
}
/**
* This method has no conversion calls, to it can be invoked by subclasses that wish to modify it
* afterwards.
*
* <p>FIXME not merging yet FIXME not including imported ontologies unless they are merged
* *before* storage.
*
* @param merge
* @return
*/
protected OWLOntology exportToOWLOntology(boolean merge, IRI prefix) {
long before = System.currentTimeMillis();
// Create a new ontology
OWLOntology root;
OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
IRI iri = IRI.create(prefix + _id);
try {
root = ontologyManager.createOntology(iri);
} catch (OWLOntologyAlreadyExistsException e) {
// It should be impossible, but just in case.
ontologyManager.removeOntology(ontologyManager.getOntology(iri));
try {
root = ontologyManager.createOntology(iri);
} catch (OWLOntologyAlreadyExistsException e1) {
root = ontologyManager.getOntology(iri);
} catch (OWLOntologyCreationException e1) {
log.error("Failed to assemble root ontology for scope " + iri, e);
root = null;
}
} catch (OWLOntologyCreationException e) {
log.error("Failed to assemble root ontology for scope " + _id, e);
root = null;
}
// Add the import declarations for directly managed ontologies.
if (root != null) {
if (merge) {
final Set<OWLOntology> set = new HashSet<OWLOntology>();
log.debug("Merging {} with its imports.", root);
set.add(root);
for (OWLOntologyID ontologyId : managedOntologies) {
log.debug("Merging {} with {}.", ontologyId, root);
set.add(getOntology(ontologyId, OWLOntology.class, true));
}
OWLOntologySetProvider provider =
new OWLOntologySetProvider() {
@Override
public Set<OWLOntology> getOntologies() {
return set;
}
};
OWLOntologyMerger merger = new OWLOntologyMerger(provider);
try {
root = merger.createMergedOntology(OWLManager.createOWLOntologyManager(), iri);
} catch (OWLOntologyCreationException e) {
log.error("Failed to merge imports for ontology " + iri, e);
root = null;
}
} else {
// Add the import declarations for directly managed ontologies.
List<OWLOntologyChange> changes = new LinkedList<OWLOntologyChange>();
OWLDataFactory df = ontologyManager.getOWLDataFactory();
String base = prefix + getID();
for (int i = 0; i < backwardPathLength; i++)
base = URIUtils.upOne(URI.create(base)).toString();
base += "/";
// The key set of managedOntologies contains the ontology IRIs, not their storage keys.
for (OWLOntologyID ontologyId : managedOntologies) {
// XXX some day the versionIRI will be the only physical reference for the ontology
IRI physIRI = IRI.create(base + OntologyUtils.encode(ontologyId));
changes.add(new AddImport(root, df.getOWLImportsDeclaration(physIRI)));
}
ontologyManager.applyChanges(changes);
}
}
log.debug("OWL export of {} completed in {} ms.", getID(), System.currentTimeMillis() - before);
return root;
}
/**
* This method has no conversion calls, to it can be invoked by subclasses that wish to modify it
* afterwards.
*
* @param merge
* @return
*/
protected MGraph exportToMGraph(boolean merge, IRI prefix) {
// if (merge) throw new UnsupportedOperationException(
// "Merge not implemented yet for Clerezza triple collections.");
long before = System.currentTimeMillis();
// No need to store, give it a name, or anything.
MGraph root = new SimpleMGraph();
UriRef iri = new UriRef(prefix + _id);
// Add the import declarations for directly managed ontologies.
if (root != null) {
// Set the ontology ID
root.add(new TripleImpl(iri, RDF.type, OWL.Ontology));
if (merge) {
log.warn(
"Merging of Clerezza triple collections is only implemented one level down. Import statements will be preserved for further levels.");
Iterator<Triple> it;
Set<Resource> importTargets = new HashSet<Resource>();
for (OWLOntologyID ontologyId : managedOntologies) {
Graph g = getOntology(ontologyId, Graph.class, false);
root.addAll(g);
it = g.filter(null, OWL.imports, null);
while (it.hasNext()) {
IRI tgt;
Resource r = it.next().getObject();
try {
if (r instanceof UriRef) tgt = IRI.create(((UriRef) r).getUnicodeString());
else if (r instanceof Literal) tgt = IRI.create(((Literal) r).getLexicalForm());
else tgt = IRI.create(r.toString());
tgt = URIUtils.sanitize(tgt);
importTargets.add(new UriRef(tgt.toString()));
} catch (Exception ex) {
log.error("FAILED to obtain import target from resource {}", r);
continue;
}
}
it = g.filter(null, RDF.type, OWL.Ontology);
while (it.hasNext()) {
NonLiteral ontology = it.next().getSubject();
log.debug("Removing all triples related to {} from {}", ontology, iri);
Iterator<Triple> it2 = g.filter(ontology, null, null);
while (it2.hasNext()) root.remove(it2.next());
}
/*
* Reinstate import statements, though. If imported ontologies were not merged earlier, we
* are not doing it now anyway.
*/
for (Resource target : importTargets) root.add(new TripleImpl(iri, OWL.imports, target));
}
} else {
String base = prefix + getID();
for (int i = 0; i < backwardPathLength; i++)
base = URIUtils.upOne(URI.create(base)).toString();
base += "/";
// The key set of managedOntologies contains the ontology IRIs, not their storage keys.
for (OWLOntologyID ontologyId : managedOntologies) {
IRI physIRI =
// ontologyId.getVersionIRI() == null ? URIUtils.sanitize(IRI
// .create(base + ontologyId.getOntologyIRI())) : URIUtils.sanitize(IRI
// .create(base + ontologyId.getVersionIRI()));
IRI.create(base + OntologyUtils.encode(ontologyId));
root.add(new TripleImpl(iri, OWL.imports, new UriRef(physIRI.toString())));
}
}
log.debug(
"Clerezza export of {} completed in {} ms.",
getID(),
System.currentTimeMillis() - before);
}
return root;
}