// Prepare the OntoNet environment. First we create the OntoNet session in which run the whole
final Session session;
try {
session = sessionManager.createSession();
} catch (SessionLimitException e1) {
throw new EngineException(
"OntoNet session quota reached. The Refactor Engine requires its own new session to execute.");
}
if (session == null) throw new EngineException(
"Failed to create OntoNet session. The Refactor Engine requires its own new session to execute.");
log.debug("Refactor enhancement job will run in session '{}'.", session.getID());
// Retrieve and filter the metadata graph for entities recognized by the engines.
final MGraph metadataGraph = ci.getMetadata(), signaturesGraph = new IndexedMGraph();
// FIXME the Stanbol Enhancer vocabulary should be retrieved from somewhere in the enhancer API.
final UriRef ENHANCER_ENTITY_REFERENCE = new UriRef(
"http://fise.iks-project.eu/ontology/entity-reference");
Iterator<Triple> tripleIt = metadataGraph.filter(null, ENHANCER_ENTITY_REFERENCE, null);
while (tripleIt.hasNext()) {
// Get the entity URI
Resource obj = tripleIt.next().getObject();
if (!(obj instanceof UriRef)) {
log.warn("Invalid UriRef for entity reference {}. Skipping.", obj);
continue;
}
final String entityReference = ((UriRef) obj).getUnicodeString();
log.debug("Trying to resolve entity {}", entityReference);
// Populate the entity signatures graph, by querying either the Entity Hub or the dereferencer.
if (engineConfiguration.isEntityHubUsed()) {
MGraph result = populateWithEntity(entityReference, signaturesGraph);
if (result != signaturesGraph && result != null) {
log.warn("Entity Hub query added triples to a new graph instead of populating the supplied one!"
+ " New signatures will be discarded.");
}
} else try {
OntologyInputSource<TripleCollection,?> source = new GraphContentSourceWithPhysicalIRI(
dereferencer.resolve(entityReference), IRI.create(entityReference));
signaturesGraph.addAll(source.getRootOntology());
} catch (FileNotFoundException e) {
log.error("Failed to dereference entity " + entityReference + ". Skipping.", e);
continue;
}
}
try {
/*
* The dedicated session for this job will store the following: (1) all the (merged) signatures
* for all detected entities; (2) the original content metadata graph returned earlier in the
* chain.
*
* There is no chance that (2) could be null, as it was previously controlled by the JobManager
* through the canEnhance() method and the computeEnhancement is always called iff the former
* returns true.
*/
session.addOntology(new GraphSource(signaturesGraph));
session.addOntology(new GraphSource(metadataGraph));
} catch (UnmodifiableOntologyCollectorException e1) {
throw new EngineException("Cannot add enhancement graph to OntoNet session for refactoring", e1);
}
try {
/*
* Export the entire session (incl. entities and enhancement graph) as a single merged ontology.
*
* TODO the refactorer should have methods to accommodate an OntologyCollector directly instead.
*/
OWLOntology ontology = session.export(OWLOntology.class, true);
log.debug("Refactoring recipe IRI is : " + engineConfiguration.getRecipeId());
/*
* We pass the ontology and the recipe IRI to the Refactor that returns the refactored graph
* expressed by using the given vocabulary.
*
* To perform the refactoring of the ontology to a given vocabulary we use the Stanbol Refactor.
*/
Recipe recipe = ruleStore.getRecipe(IRI.create(engineConfiguration.getRecipeId()));
log.debug("Recipe {} contains {} rules.", recipe, recipe.getkReSRuleList().size());
log.debug("The ontology to be refactor is {}", ontology);
ontology = refactorer
.ontologyRefactoring(ontology, IRI.create(engineConfiguration.getRecipeId()));
/*
* The newly generated ontology is converted to Clarezza format and then added os substitued to
* the old mGraph.
*/
if (engineConfiguration.isInGraphAppendMode()) {
log.debug("Metadata of the content will replace old ones.", this);
} else {
metadataGraph.clear();
log.debug("Content metadata will be appended to the existing ones.", this);
}
metadataGraph.addAll(OWLAPIToClerezzaConverter.owlOntologyToClerezzaTriples(ontology));
} catch (RefactoringException e) {
String msg = "Refactor engine execution failed on content item " + ci + ".";
log.error(msg, e);
throw new EngineException(msg, e);
} catch (NoSuchRecipeException e) {
String msg = "Refactor engine could not find recipe " + engineConfiguration.getRecipeId()
+ " to refactor content item " + ci + ".";
log.error(msg, e);
throw new EngineException(msg, e);
} catch (Exception e) {
throw new EngineException("Refactor Engine has failed.", e);
} finally {
/*
* The session needs to be destroyed anyhow.
*
* Clear contents before destroying (FIXME only do this until this is implemented in the