Examples with UnmodifiableOntologyCollectorException org.apache.stanbol.ontologymanager.servicesapi.collector.UnmodifiableOntologyCollectorException used on opensource projects

Example 11 with UnmodifiableOntologyCollectorException

use of org.apache.stanbol.ontologymanager.servicesapi.collector.UnmodifiableOntologyCollectorException in project stanbol by apache.

the class AbstractOntologyCollectorImpl method addOntology.

@Override
public synchronized OWLOntologyID addOntology(OntologyInputSource<?> ontologySource) throws UnmodifiableOntologyCollectorException {
    // Check for error conditions.
    if (locked)
        throw new UnmodifiableOntologyCollectorException(this);
    if (ontologySource == null)
        throw new IllegalArgumentException("Ontology source cannot be null.");
    log.debug("Adding ontology to collector {}", getID());
    OWLOntologyID key = null;
    if (ontologySource.hasRootOntology()) {
        long before = System.currentTimeMillis();
        Object o = ontologySource.getRootOntology();
        // Check the origin anyhow, as it may be useful for setting aliases with physical locations etc.
        if (ontologySource.hasOrigin())
            key = ontologyProvider.loadInStore(o, false, ontologySource.getOrigin());
        else
            key = ontologyProvider.loadInStore(o, false);
        if (key != null) {
            managedOntologies.add(key);
            // Note that imported ontologies are not considered as managed! TODO should we change this?
            log.info("Add ontology completed in {} ms.", (System.currentTimeMillis() - before));
            // Fire the event
            fireOntologyAdded(key);
        }
    } else if (ontologySource.hasOrigin()) {
        // Just the origin : see if it is satisfiable
        log.debug("Checking origin satisfiability...");
        Origin<?> origin = ontologySource.getOrigin();
        Object ref = origin.getReference();
        log.debug("Origin wraps a {}", ref.getClass().getCanonicalName());
        if (ref instanceof org.semanticweb.owlapi.model.IRI)
            try {
                log.debug("Deferring addition to physical IRI {} (if available).", ref);
                key = addOntology(new RootOntologySource((org.semanticweb.owlapi.model.IRI) ref));
            } catch (OWLOntologyCreationException e) {
                throw new RuntimeException(e);
            }
        else if (ref instanceof IRI) {
            log.debug("Deferring addition to stored Clerezza graph {} (if available).", ref);
            key = addOntology(new GraphSource((IRI) ref));
        } else if (ref instanceof OWLOntologyID) {
            OWLOntologyID idref = (OWLOntologyID) ref;
            log.debug("Deferring addition to stored ontology with public key {} (if available).", ref);
            if (!ontologyProvider.hasOntology(idref))
                throw new MissingOntologyException(this, idref);
            key = idref;
            if (managedOntologies.add(idref))
                fireOntologyAdded(idref);
        } else
            throw new IllegalArgumentException("Invalid origin " + origin);
    } else
        throw new IllegalArgumentException("Ontology source must provide either an ontology object, or a way to reference one (i.e. an origin).");
    log.info("Public key : {}", key);
    return key;
}

Example 12 with UnmodifiableOntologyCollectorException

use of org.apache.stanbol.ontologymanager.servicesapi.collector.UnmodifiableOntologyCollectorException in project stanbol by apache.

the class RefactorEnhancementEngine method initEngine.

/**
     * Method for adding ontologies to the scope core ontology.
     * <ol>
     * <li>Get all the ontologies from the property.</li>
     * <li>Create a base scope.</li>
     * <li>Retrieve the ontology space from the scope.</li>
     * <li>Add the ontologies to the scope via ontology space.</li>
     * </ol>
     */
private void initEngine(RefactorEnhancementEngineConf engineConfiguration) {
    // IRI dulcifierScopeIRI = org.semanticweb.owlapi.model.IRI.create((String) context.getProperties().get(SCOPE));
    String scopeId = engineConfiguration.getScope();
    // Create or get the scope with the configured ID
    try {
        scope = onManager.createOntologyScope(scopeId);
    // No need to deactivate a newly created scope.
    } catch (DuplicateIDException e) {
        scope = onManager.getScope(scopeId);
        onManager.setScopeActive(scopeId, false);
    }
    // All resolvable ontologies stated in the configuration are loaded into the core space.
    OntologySpace ontologySpace = scope.getCoreSpace();
    ontologySpace.tearDown();
    String[] coreScopeOntologySet = engineConfiguration.getScopeCoreOntologies();
    List<String> success = new ArrayList<String>(), failed = new ArrayList<String>();
    try {
        log.info("Will now load requested ontology into the core space of scope '{}'.", scopeId);
        OWLOntologyManager sharedManager = OWLManager.createOWLOntologyManager();
        org.semanticweb.owlapi.model.IRI physicalIRI = null;
        for (int o = 0; o < coreScopeOntologySet.length; o++) {
            String url = coreScopeOntologySet[o];
            try {
                physicalIRI = org.semanticweb.owlapi.model.IRI.create(url);
            } catch (Exception e) {
                failed.add(url);
            }
            try {
                // TODO replace with a Clerezza equivalent
                ontologySpace.addOntology(new RootOntologySource(physicalIRI, sharedManager));
                success.add(url);
            } catch (OWLOntologyCreationException e) {
                log.error("Failed to load ontology from physical location " + physicalIRI + " Continuing with next...", e);
                failed.add(url);
            }
        }
    } catch (UnmodifiableOntologyCollectorException ex) {
        log.error("Ontology space {} was found locked for modification. Cannot populate.", ontologySpace);
    }
    for (String s : success) log.info(" >> {} : SUCCESS", s);
    for (String s : failed) log.info(" >> {} : FAILED", s);
    ontologySpace.setUp();
    // if (!onManager.containsScope(scopeId)) onManager.registerScope(scope);
    onManager.setScopeActive(scopeId, true);
    /*
         * The first thing to do is to create a recipe in the rule store that can be used by the engine to
         * refactor the enhancement graphs.
         */
    String recipeId = engineConfiguration.getRecipeId();
    Recipe recipe = null;
    try {
        recipe = ruleStore.createRecipe(new IRI(recipeId), null);
    } catch (AlreadyExistingRecipeException e1) {
        log.error("A recipe with ID {} already exists in the store.", recipeId);
    }
    if (recipe != null) {
        log.debug("Initialised blank recipe with ID {}", recipeId);
        /*
             * The set of rule to put in the recipe can be provided by the user. A default set of rules is
             * provided in /META-INF/default/seo_rules.sem. Use the property engine.refactor in the felix
             * console to pass to the engine your set of rules.
             */
        String recipeLocation = engineConfiguration.getRecipeLocation();
        InputStream recipeStream = null;
        String recipeString = null;
        if (recipeLocation != null && !recipeLocation.isEmpty()) {
            Dereferencer dereferencer = new DereferencerImpl();
            try {
                recipeStream = dereferencer.resolve(recipeLocation);
                log.debug("Loaded recipe from external source {}", recipeLocation);
            } catch (FileNotFoundException e) {
                log.error("Recipe Stream is null.", e);
            }
        } else {
            // TODO remove this part (or manage it better in the @Activate method).
            String loc = "/META-INF/default/seo_rules.sem";
            recipeStream = getClass().getResourceAsStream(loc);
            log.debug("Loaded default recipe in {}.", loc);
        }
        if (recipeStream != null) {
            BufferedReader reader = new BufferedReader(new InputStreamReader(recipeStream));
            recipeString = "";
            String line = null;
            try {
                while ((line = reader.readLine()) != null) recipeString += line;
            } catch (IOException e) {
                log.error("Failed to load Refactor Engine recipe from stream. Aborting read. ", e);
                recipeString = null;
            }
        }
        log.debug("Recipe content follows :\n{}", recipeString);
        if (recipeString != null) {
            ruleStore.addRulesToRecipe(recipe, recipeString, null);
            log.debug("Added rules to recipe {}", recipeId);
        }
    }
}

Example 13 with UnmodifiableOntologyCollectorException

use of org.apache.stanbol.ontologymanager.servicesapi.collector.UnmodifiableOntologyCollectorException in project stanbol by apache.

the class RefactorEnhancementEngine method computeEnhancements.

@Override
public void computeEnhancements(ContentItem ci) throws EngineException {
    // 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 Graph metadataGraph = ci.getMetadata(), signaturesGraph = new IndexedGraph();
    // FIXME the Stanbol Enhancer vocabulary should be retrieved from somewhere in the enhancer API.
    final IRI ENHANCER_ENTITY_REFERENCE = new IRI("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
        RDFTerm obj = tripleIt.next().getObject();
        if (!(obj instanceof IRI)) {
            log.warn("Invalid IRI for entity reference {}. Skipping.", obj);
            continue;
        }
        final String entityReference = ((IRI) 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()) {
            Graph 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<Graph> source = new GraphContentSourceWithPhysicalIRI(dereferencer.resolve(entityReference), org.semanticweb.owlapi.model.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(new IRI(engineConfiguration.getRecipeId()));
        log.debug("Recipe {} contains {} rules.", recipe, recipe.getRuleList().size());
        log.debug("The ontology to be refactor is {}", ontology);
        Graph tc = refactorer.graphRefactoring(OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology), recipe);
        /*
             * 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(tc);
    } 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
             * destroySession() method).
             */
        for (OWLOntologyID id : session.listManagedOntologies()) {
            try {
                String key = ontologyProvider.getKey(id.getOntologyIRI());
                ontologyProvider.getStore().deleteGraph(new IRI(key));
            } catch (Exception ex) {
                log.error("Failed to delete triple collection " + id, ex);
                continue;
            }
        }
        sessionManager.destroySession(session.getID());
    }
}

Example 14 with UnmodifiableOntologyCollectorException

use of org.apache.stanbol.ontologymanager.servicesapi.collector.UnmodifiableOntologyCollectorException in project stanbol by apache.

the class ScopeResource method managedOntologyUnload.

/**
     * Unloads an ontology from an ontology scope.
     * 
     * @param scopeId
     * @param ontologyid
     * @param uriInfo
     * @param headers
     */
@DELETE
@Path("/{ontologyId:.+}")
public Response managedOntologyUnload(@PathParam("scopeid") String scopeid, @PathParam("ontologyId") String ontologyId, @PathParam("scopeid") String scopeId, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
    ResponseBuilder rb;
    scope = onm.getScope(scopeid);
    if (ontologyId != null && !ontologyId.trim().isEmpty()) {
        OWLOntologyID id = OntologyUtils.decode(ontologyId);
        OntologySpace cs = scope.getCustomSpace();
        if (// ontology not managed
        !cs.hasOntology(id))
            // ontology not managed
            rb = Response.notModified();
        else
            try {
                onm.setScopeActive(scopeId, false);
                cs.removeOntology(id);
                rb = Response.ok();
            } catch (IrremovableOntologyException e) {
                throw new WebApplicationException(e, FORBIDDEN);
            } catch (UnmodifiableOntologyCollectorException e) {
                throw new WebApplicationException(e, FORBIDDEN);
            } catch (OntologyCollectorModificationException e) {
                throw new WebApplicationException(e, INTERNAL_SERVER_ERROR);
            } finally {
                onm.setScopeActive(scopeId, true);
            }
    } else
        // null/blank ontology ID
        rb = Response.status(BAD_REQUEST);
    // addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 15 with UnmodifiableOntologyCollectorException

use of org.apache.stanbol.ontologymanager.servicesapi.collector.UnmodifiableOntologyCollectorException in project stanbol by apache.

the class ScopeResource method manageOntology.

/**
     * Tells the session that it should manage the ontology obtained by dereferencing the supplied IRI.<br>
     * <br>
     * Note that the PUT method cannot be used, as it is not possible to predict what ID the ontology will
     * have until it is parsed.
     * 
     * @param content
     *            the ontology physical IRI
     * @return {@link Status#OK} if the addition was successful, {@link Status#NOT_FOUND} if there is no such
     *         session at all, {@link Status#FORBIDDEN} if the session is locked or cannot modified for some
     *         other reason, {@link Status#INTERNAL_SERVER_ERROR} if some other error occurs.
     */
@POST
@Consumes(value = MediaType.TEXT_PLAIN)
public Response manageOntology(String iri, @PathParam("scopeid") String scopeid, @Context HttpHeaders headers) {
    ResponseBuilder rb;
    scope = onm.getScope(scopeid);
    if (scope == null)
        rb = Response.status(NOT_FOUND);
    else
        try {
            OWLOntologyID key = scope.getCustomSpace().addOntology(new RootOntologySource(IRI.create(iri)));
            URI created = getCreatedResource(OntologyUtils.encode(key));
            rb = Response.created(created);
        } catch (UnmodifiableOntologyCollectorException e) {
            throw new WebApplicationException(e, FORBIDDEN);
        } catch (OWLOntologyCreationException e) {
            throw new WebApplicationException(e, INTERNAL_SERVER_ERROR);
        }
    // addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}