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);
}
private OWLOntology getFromOntoMgr() throws IOException {
try {
Scope scope = null;
synchronized (onManager) {
scope = onManager.getScope(this.scopeId);
}
if (scope == null) {
log.error("Scope {} cannot be retrieved", this.scopeId);
throw new IOException("Scope " + this.scopeId + " cannot be retrieved");
}
Session session = null;
if (sessionManager != null)
synchronized (sessionManager) {
session = sessionManager.getSession(sessionId);
}
if (session == null) log.warn("Session {} cannot be retrieved. Ignoring.", this.sessionId);
final Set<OWLOntology> set = new HashSet<OWLOntology>();
set.add(scope.export(OWLOntology.class, true));
if (session != null) set.add(session.export(OWLOntology.class, true));
if (set.size() == 1) return set.iterator().next();
OWLOntologyMerger merger =
new OWLOntologyMerger(
new OWLOntologySetProvider() {
@Override
public Set<OWLOntology> getOntologies() {
return set;
}
});
return merger.createMergedOntology(
createOWLOntologyManager(), IRI.create("reasoners:input-" + System.currentTimeMillis()));
} catch (OWLOntologyCreationException e) {
String message = "The network for scope/session cannot be retrieved";
log.error(message + ":", e);
throw new IllegalArgumentException(message);
}
}
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;
}