Examples with OWLOntologyChange org.semanticweb.owlapi.model.OWLOntologyChange used on opensource projects

Example 1 with OWLOntologyChange

use of org.semanticweb.owlapi.model.OWLOntologyChange in project stanbol by apache.

the class SessionManagerResource method listSessions.

@GET
@Produces(value = { RDF_XML, OWL_XML, TURTLE, X_TURTLE, FUNCTIONAL_OWL, MANCHESTER_OWL, RDF_JSON, N3, N_TRIPLE, TEXT_PLAIN })
public Response listSessions(@Context UriInfo uriInfo, @Context HttpHeaders headers) {
    OWLOntologyManager ontMgr = OWLManager.createOWLOntologyManager();
    OWLDataFactory df = ontMgr.getOWLDataFactory();
    OWLClass cSession = df.getOWLClass(IRI.create("http://stanbol.apache.org/ontologies/meta/Session"));
    OWLOntology o;
    try {
        o = ontMgr.createOntology(IRI.create(uriInfo.getRequestUri()));
        List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
        for (String id : sessionManager.getRegisteredSessionIDs()) {
            IRI sessionid = IRI.create(sessionManager.getDefaultNamespace() + sessionManager.getID() + "/" + id);
            OWLNamedIndividual ind = df.getOWLNamedIndividual(sessionid);
            changes.add(new AddAxiom(o, df.getOWLClassAssertionAxiom(cSession, ind)));
        }
        ontMgr.applyChanges(changes);
    } catch (OWLOntologyCreationException e) {
        throw new WebApplicationException(e, INTERNAL_SERVER_ERROR);
    }
    ResponseBuilder rb = Response.ok(o);
    MediaType mediaType = MediaTypeUtil.getAcceptableMediaType(headers, null);
    if (mediaType != null)
        rb.header(HttpHeaders.CONTENT_TYPE, mediaType);
    //        addCORSOrigin(servletContext, rb, headers);
    return rb.build();
}

Example 2 with OWLOntologyChange

use of org.semanticweb.owlapi.model.OWLOntologyChange in project stanbol by apache.

the class AbstractOntologyCollectorImpl method getOntologyAsOWLOntology.

protected OWLOntology getOntologyAsOWLOntology(OWLOntologyID ontologyId, boolean merge, org.semanticweb.owlapi.model.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];
            org.semanticweb.owlapi.model.IRI target = org.semanticweb.owlapi.model.IRI.create((managed ? universalPrefix + "/" + tid + "/" : URIUtils.upOne(universalPrefix) + "/") + s);
            changes.add(new AddImport(o, df.getOWLImportsDeclaration(target)));
        }
        o.getOWLOntologyManager().applyChanges(changes);
    }
    return o;
}

Example 3 with OWLOntologyChange

use of org.semanticweb.owlapi.model.OWLOntologyChange in project stanbol by apache.

the class AbstractOntologyCollectorImpl method exportToOWLOntology.

/**
     * This method has no conversion calls, to it can be invoked by subclasses that wish to modify it
     * afterwards.
     * 
     * FIXME not merging yet FIXME not including imported ontologies unless they are merged *before* storage.
     * 
     * @param merge
     * @return
     */
protected OWLOntology exportToOWLOntology(boolean merge, org.semanticweb.owlapi.model.IRI prefix) {
    long before = System.currentTimeMillis();
    // Create a new ontology
    OWLOntology root;
    OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
    org.semanticweb.owlapi.model.IRI iri = org.semanticweb.owlapi.model.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
                org.semanticweb.owlapi.model.IRI physIRI = org.semanticweb.owlapi.model.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;
}

Example 4 with OWLOntologyChange

use of org.semanticweb.owlapi.model.OWLOntologyChange in project stanbol by apache.

the class ScopeImpl method exportToOWLOntology.

/**
     * Get an OWL API {@link OWLOntology} representation of the scope.
     * 
     * @param merge
     *            if true the core and custom spaces will be recursively merged with the scope ontology,
     *            otherwise owl:imports statements will be added.
     * @return the OWL representation of the scope.
     */
protected OWLOntology exportToOWLOntology(boolean merge, org.semanticweb.owlapi.model.IRI universalPrefix) {
    // if (merge) throw new UnsupportedOperationException(
    // "Ontology merging only implemented for managed ontologies, not for collectors. "
    // + "Please set merge parameter to false.");
    // Create an ontology manager on the fly. We don't really need a permanent one.
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    OWLDataFactory df = mgr.getOWLDataFactory();
    OWLOntology ont = null;
    try {
        if (merge) {
            final Set<OWLOntology> set = new HashSet<OWLOntology>();
            log.debug("Merging custom space of {}.", getID());
            set.add(this.getCustomSpace().export(OWLOntology.class, merge));
            log.debug("Merging core space of {}.", getID());
            set.add(this.getCoreSpace().export(OWLOntology.class, merge));
            OWLOntologySetProvider provider = new OWLOntologySetProvider() {

                @Override
                public Set<OWLOntology> getOntologies() {
                    return set;
                }
            };
            OWLOntologyMerger merger = new OWLOntologyMerger(provider);
            try {
                ont = merger.createMergedOntology(OWLManager.createOWLOntologyManager(), org.semanticweb.owlapi.model.IRI.create(getDefaultNamespace() + getID()));
            } catch (OWLOntologyCreationException e) {
                log.error("Failed to merge imports for ontology.", e);
                ont = null;
            }
        } else {
            // The root ontology ID is in the form [namespace][scopeId]
            ont = mgr.createOntology(org.semanticweb.owlapi.model.IRI.create(universalPrefix + getID()));
            List<OWLOntologyChange> additions = new LinkedList<OWLOntologyChange>();
            // Add the import statement for the custom space, if existing and not empty
            OntologySpace spc = getCustomSpace();
            if (spc != null && spc.listManagedOntologies().size() > 0) {
                org.semanticweb.owlapi.model.IRI spaceIri = org.semanticweb.owlapi.model.IRI.create(universalPrefix + spc.getID());
                additions.add(new AddImport(ont, df.getOWLImportsDeclaration(spaceIri)));
            }
            // Add the import statement for the core space, if existing and not empty
            spc = getCoreSpace();
            if (spc != null && spc.listManagedOntologies().size() > 0) {
                org.semanticweb.owlapi.model.IRI spaceIri = org.semanticweb.owlapi.model.IRI.create(universalPrefix + spc.getID());
                additions.add(new AddImport(ont, df.getOWLImportsDeclaration(spaceIri)));
            }
            mgr.applyChanges(additions);
        }
    } catch (OWLOntologyCreationException e) {
        log.error("Failed to generate an OWL form of scope " + getID(), e);
        ont = null;
    }
    return ont;
}

Example 5 with OWLOntologyChange

use of org.semanticweb.owlapi.model.OWLOntologyChange in project stanbol by apache.

the class ClerezzaOntologyProvider method toOWLOntology.

/**
     * 
     * @param graphName
     * @param forceMerge
     *            if set to false, the selected import management policy will be applied.
     * @return
     * @throws OWLOntologyCreationException
     */
protected OWLOntology toOWLOntology(IRI graphName, boolean forceMerge) throws OWLOntologyCreationException {
    log.debug("Exporting graph to OWLOntology");
    log.debug(" -- ImmutableGraph name : {}", graphName);
    OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
    // Never try to import
    mgr.addIRIMapper(new PhonyIRIMapper(Collections.<org.semanticweb.owlapi.model.IRI>emptySet()));
    Set<OWLOntologyID> loaded = new HashSet<OWLOntologyID>();
    Graph graph = store.getGraph(graphName);
    IRI ontologyId = null;
    // Get the id of this ontology.
    Iterator<Triple> itt = graph.filter(null, RDF.type, OWL.Ontology);
    if (itt.hasNext()) {
        BlankNodeOrIRI nl = itt.next().getSubject();
        if (nl instanceof IRI)
            ontologyId = (IRI) nl;
    }
    List<OWLOntologyID> revImps = new Stack<OWLOntologyID>();
    List<OWLOntologyID> lvl1 = new Stack<OWLOntologyID>();
    fillImportsReverse(keymap.getReverseMapping(graphName), revImps, lvl1);
    // If not set to merge (either by policy of by force), adopt the set import policy.
    if (!forceMerge && !ImportManagementPolicy.MERGE.equals(getImportManagementPolicy())) {
        OWLOntology o = OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(graph, mgr);
        // TODO make it not flat.
        // Examining the reverse imports stack will flatten all imports.
        List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
        OWLDataFactory df = OWLManager.getOWLDataFactory();
        List<OWLOntologyID> listToUse;
        switch(getImportManagementPolicy()) {
            case FLATTEN:
                listToUse = revImps;
                break;
            case PRESERVE:
                listToUse = lvl1;
                break;
            default:
                listToUse = lvl1;
                break;
        }
        for (OWLOntologyID ref : listToUse) if (!loaded.contains(ref) && !ref.equals(keymap.getReverseMapping(graphName))) {
            changes.add(new AddImport(o, df.getOWLImportsDeclaration(ref.getOntologyIRI())));
            loaded.add(ref);
        }
        o.getOWLOntologyManager().applyChanges(changes);
        return o;
    } else {
        // If there is just the root ontology, convert it straight away.
        if (revImps.size() == 1 && revImps.contains(graphName)) {
            OWLOntology o = OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(graph, mgr);
            return o;
        }
        // FIXME when there's more than one ontology, this way of merging them seems inefficient...
        Graph tempGraph = new IndexedGraph();
        // The set of triples that will be excluded from the merge
        Set<Triple> exclusions = new HashSet<Triple>();
        // Examine all reverse imports
        for (OWLOntologyID ref : revImps) if (!loaded.contains(ref)) {
            // Get the triples
            Graph imported = // store.getTriples(ref);
            getStoredOntology(getKey(ref), Graph.class, false);
            // For each owl:Ontology
            Iterator<Triple> remove = imported.filter(null, RDF.type, OWL.Ontology);
            while (remove.hasNext()) {
                BlankNodeOrIRI subj = remove.next().getSubject();
                /*
                         * If it's not the root ontology, trash all its triples. If the root ontology is
                         * anonymous, all ontology annotations are to be trashed without distinction.
                         */
                if (ontologyId == null || !subj.equals(ontologyId)) {
                    Iterator<Triple> it = imported.filter(subj, null, null);
                    while (it.hasNext()) {
                        Triple t = it.next();
                        exclusions.add(t);
                    }
                }
            }
            Iterator<Triple> it = imported.iterator();
            while (it.hasNext()) {
                Triple t = it.next();
                if (!exclusions.contains(t))
                    tempGraph.add(t);
            }
            loaded.add(ref);
        }
        // online.
        return OWLAPIToClerezzaConverter.clerezzaGraphToOWLOntology(tempGraph, mgr);
    }
}