Examples with OntologyInputSource org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource used on opensource projects

Example 1 with OntologyInputSource

use of org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource in project stanbol by apache.

the class SessionResource method manageOntology.

/**
     * Tells the session that it should manage the ontology obtained by parsing the supplied content.<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 content
     * @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 = { RDF_XML, OWL_XML, N_TRIPLE, N3, TURTLE, X_TURTLE, FUNCTIONAL_OWL, MANCHESTER_OWL, RDF_JSON })
public Response manageOntology(InputStream content, @PathParam("id") String sessionId, @Context HttpHeaders headers) {
    long before = System.currentTimeMillis();
    ResponseBuilder rb;
    session = sesMgr.getSession(sessionId);
    String mt = headers.getMediaType().toString();
    if (// Always check session first
    session == null)
        // Always check session first
        rb = Response.status(NOT_FOUND);
    else
        try {
            log.debug("POST content claimed to be of type {}.", mt);
            OntologyInputSource<?> src;
            if (OWL_XML.equals(mt) || FUNCTIONAL_OWL.equals(mt) || MANCHESTER_OWL.equals(mt))
                src = new OntologyContentInputSource(content);
            else
                // content = new BufferedInputStream(content);
                src = new GraphContentInputSource(content, mt, ontologyProvider.getStore());
            log.debug("SUCCESS parse with media type {}.", mt);
            OWLOntologyID key = session.addOntology(src);
            if (key == null || key.isAnonymous()) {
                log.error("FAILED parse with media type {}.", mt);
                throw new WebApplicationException(INTERNAL_SERVER_ERROR);
            }
            // FIXME ugly but will have to do for the time being
            log.debug("SUCCESS add ontology to session {}.", session.getID());
            log.debug("Storage key : {}", key);
            // key.split("::")[1];
            String uri = OntologyUtils.encode(key);
            // uri = uri.substring((ontologyProvider.getGraphPrefix() + "::").length());
            URI created = null;
            if (uri != null && !uri.isEmpty()) {
                created = getCreatedResource(uri);
                rb = Response.created(created);
            } else
                rb = Response.ok();
            log.info("POST request for ontology addition completed in {} ms.", (System.currentTimeMillis() - before));
            log.info("New resource URL is {}", created);
        } catch (UnmodifiableOntologyCollectorException e) {
            throw new WebApplicationException(e, FORBIDDEN);
        } catch (OWLOntologyCreationException e) {
            log.error("FAILED parse with media type {}.", mt);
            throw new WebApplicationException(e, BAD_REQUEST);
        }
    //        addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 2 with OntologyInputSource

use of org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource in project stanbol by apache.

the class ScopeManagerImpl method rebuildScopes.

private void rebuildScopes() {
    OntologyNetworkConfiguration struct = ontologyProvider.getOntologyNetworkConfiguration();
    for (String scopeId : struct.getScopeIDs()) {
        long before = System.currentTimeMillis();
        log.debug("Rebuilding scope with ID \"{}\".", scopeId);
        Collection<OWLOntologyID> coreOnts = struct.getCoreOntologyKeysForScope(scopeId);
        OntologyInputSource<?>[] srcs = new OntologyInputSource<?>[coreOnts.size()];
        int i = 0;
        for (OWLOntologyID coreOnt : coreOnts) {
            log.debug("Core ontology key : {}", coreOnts);
            srcs[i++] = new StoredOntologySource(coreOnt);
        }
        Scope scope;
        try {
            scope = createOntologyScope(scopeId, srcs);
        } catch (DuplicateIDException e) {
            String dupe = e.getDuplicateID();
            log.warn("Scope \"{}\" already exists and will be reused.", dupe);
            scope = getScope(dupe);
        }
        OntologySpace custom = scope.getCustomSpace();
        // Register even if some ontologies were to fail to be restored afterwards.
        scopeMap.put(scopeId, scope);
        for (OWLOntologyID key : struct.getCustomOntologyKeysForScope(scopeId)) try {
            log.debug("Custom ontology key : {}", key);
            custom.addOntology(new StoredOntologySource(key));
        } catch (MissingOntologyException ex) {
            log.error("Could not find an ontology with public key {} to be managed by scope \"{}\". Proceeding to next ontology.", key, scopeId);
            continue;
        } catch (Exception ex) {
            log.error("Exception caught while trying to add ontology with public key " + key + " to rebuilt scope \"" + scopeId + "\". proceeding to next ontology", ex);
            continue;
        }
        log.info("Scope \"{}\" rebuilt in {} ms.", scopeId, System.currentTimeMillis() - before);
    }
}

Example 3 with OntologyInputSource

use of org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource in project stanbol by apache.

the class RootResource method storeOntology.

/**
     * POSTs an ontology content as application/x-www-form-urlencoded
     * 
     * @param content
     * @param headers
     * @return
     */
@POST
@Consumes(value = { RDF_XML, TURTLE, X_TURTLE, N3, N_TRIPLE, OWL_XML, FUNCTIONAL_OWL, MANCHESTER_OWL, RDF_JSON })
public Response storeOntology(InputStream content, @Context HttpHeaders headers) {
    long before = System.currentTimeMillis();
    ResponseBuilder rb;
    MediaType mt = headers.getMediaType();
    if (RDF_XML_TYPE.equals(mt) || TURTLE_TYPE.equals(mt) || X_TURTLE_TYPE.equals(mt) || N3_TYPE.equals(mt) || N_TRIPLE_TYPE.equals(mt) || RDF_JSON_TYPE.equals(mt)) {
        OWLOntologyID key = null;
        try {
            key = ontologyProvider.loadInStore(content, headers.getMediaType().toString(), true);
            rb = Response.ok();
        } catch (UnsupportedFormatException e) {
            log.warn("POST method failed for media type {}. This should not happen (should fail earlier)", headers.getMediaType());
            rb = Response.status(UNSUPPORTED_MEDIA_TYPE);
        } catch (IOException e) {
            throw new WebApplicationException(e, BAD_REQUEST);
        }
        // An exception should have been thrown earlier, but just in case.
        if (key == null || key.isAnonymous()) {
            rb = Response.status(Status.INTERNAL_SERVER_ERROR);
        }
    } else if (OWL_XML_TYPE.equals(mt) || FUNCTIONAL_OWL_TYPE.equals(mt) || MANCHESTER_OWL_TYPE.equals(mt)) {
        try {
            OntologyInputSource<OWLOntology> src = new OntologyContentInputSource(content);
            ontologyProvider.loadInStore(src.getRootOntology(), true);
            rb = Response.ok();
        } catch (OWLOntologyCreationException e) {
            throw new WebApplicationException(e, INTERNAL_SERVER_ERROR);
        }
    } else {
        rb = Response.status(UNSUPPORTED_MEDIA_TYPE);
    }
    // addCORSOrigin(servletContext, rb, headers);
    Response r = rb.build();
    log.debug("POST request for ontology addition completed in {} ms with status {}.", (System.currentTimeMillis() - before), r.getStatus());
    return r;
}

Example 4 with OntologyInputSource

use of org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource in project stanbol by apache.

the class ScopeResource method registerScope.

/**
     * At least one between corereg and coreont must be present. Registry iris supersede ontology iris.
     * 
     * @param scopeid
     * @param coreRegistry
     *            a. If it is a well-formed IRI it supersedes <code>coreOntology</code>.
     * @param coreOntologies
     * @param customRegistry
     *            a. If it is a well-formed IRI it supersedes <code>customOntology</code>.
     * @param customOntologies
     * @param activate
     *            if true, the new scope will be activated upon creation.
     * @param uriInfo
     * @param headers
     * @return
     */
@PUT
@Consumes(MediaType.WILDCARD)
public Response registerScope(@PathParam("scopeid") String scopeid, @QueryParam("corereg") final List<String> coreRegistries, @QueryParam("coreont") final List<String> coreOntologies, @DefaultValue("false") @QueryParam("activate") boolean activate, @Context HttpHeaders headers) {
    log.debug("Request URI {}", uriInfo.getRequestUri());
    scope = onm.getScope(scopeid);
    List<OntologyInputSource<?>> srcs = new ArrayList<OntologyInputSource<?>>(coreOntologies.size() + coreRegistries.size());
    // First thing, check registry sources.
    if (coreRegistries != null)
        for (String reg : coreRegistries) if (reg != null && !reg.isEmpty())
            try {
                // Library IDs are sanitized differently
                srcs.add(new LibrarySource(URIUtils.desanitize(IRI.create(reg)), regMgr));
            } catch (Exception e1) {
                throw new WebApplicationException(e1, BAD_REQUEST);
            // Bad or not supplied core registry, try the ontology.
            }
    // Then ontology sources
    if (coreOntologies != null)
        for (String ont : coreOntologies) if (ont != null && !ont.isEmpty())
            try {
                srcs.add(new RootOntologySource(IRI.create(ont)));
            } catch (OWLOntologyCreationException e2) {
                // If this fails too, throw a bad request.
                throw new WebApplicationException(e2, BAD_REQUEST);
            }
    // Now the creation.
    try {
        // Expand core sources
        List<OntologyInputSource<?>> expanded = new ArrayList<OntologyInputSource<?>>();
        for (OntologyInputSource<?> coreSrc : srcs) if (coreSrc != null) {
            if (coreSrc instanceof SetInputSource) {
                for (Object o : ((SetInputSource<?>) coreSrc).getOntologies()) {
                    OntologyInputSource<?> src = null;
                    if (o instanceof OWLOntology)
                        src = new RootOntologySource((OWLOntology) o);
                    else if (o instanceof Graph)
                        src = new GraphSource((Graph) o);
                    if (src != null)
                        expanded.add(src);
                }
            } else
                // Must be denoting a single ontology
                expanded.add(coreSrc);
        }
        scope = onm.createOntologyScope(scopeid, expanded.toArray(new OntologyInputSource[0]));
        // Setup and register the scope. If no custom space was set, it will
        // still be open for modification.
        scope.setUp();
        onm.setScopeActive(scopeid, activate);
    } catch (DuplicateIDException e) {
        throw new WebApplicationException(e, CONFLICT);
    } catch (Exception ex) {
        throw new WebApplicationException(ex, INTERNAL_SERVER_ERROR);
    }
    ResponseBuilder rb = Response.created(uriInfo.getAbsolutePath());
    // addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 5 with OntologyInputSource

use of org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource 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());
    }
}