Examples with BlankNodeOrIRI org.apache.clerezza.commons.rdf.BlankNodeOrIRI used on opensource projects

Example 31 with BlankNodeOrIRI

use of org.apache.clerezza.commons.rdf.BlankNodeOrIRI 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);
    }
}

Example 32 with BlankNodeOrIRI

use of org.apache.clerezza.commons.rdf.BlankNodeOrIRI in project stanbol by apache.

the class ClerezzaOntologyProvider method getOntologyNetworkConfiguration.

public OntologyNetworkConfiguration getOntologyNetworkConfiguration() {
    Map<String, Collection<OWLOntologyID>> coreOntologies = new HashMap<String, Collection<OWLOntologyID>>(), customOntologies = new HashMap<String, Collection<OWLOntologyID>>();
    Map<String, Collection<String>> attachedScopes = new HashMap<String, Collection<String>>();
    final Graph meta = store.getGraph(new IRI(metaGraphId));
    // Scopes first
    for (Iterator<Triple> it = meta.filter(null, RDF.type, SCOPE_URIREF); it.hasNext(); ) {
        // for each
        // scope
        Triple ta = it.next();
        BlankNodeOrIRI sub = ta.getSubject();
        if (sub instanceof IRI) {
            String s = ((IRI) sub).getUnicodeString(), prefix = _NS_STANBOL_INTERNAL + Scope.shortName + "/";
            if (s.startsWith(prefix)) {
                String scopeId = s.substring(prefix.length());
                log.info("Rebuilding scope \"{}\".", scopeId);
                coreOntologies.put(scopeId, new TreeSet<OWLOntologyID>());
                customOntologies.put(scopeId, new TreeSet<OWLOntologyID>());
                IRI core_ur = null, custom_ur = null;
                RDFTerm r;
                // Check core space
                Iterator<Triple> it2 = meta.filter(sub, HAS_SPACE_CORE_URIREF, null);
                if (it2.hasNext()) {
                    r = it2.next().getObject();
                    if (r instanceof IRI)
                        core_ur = (IRI) r;
                } else {
                    it2 = meta.filter(null, IS_SPACE_CORE_OF_URIREF, sub);
                    if (it2.hasNext()) {
                        r = it2.next().getSubject();
                        if (r instanceof IRI)
                            core_ur = (IRI) r;
                    }
                }
                // Check custom space
                it2 = meta.filter(sub, HAS_SPACE_CUSTOM_URIREF, null);
                if (it2.hasNext()) {
                    r = it2.next().getObject();
                    if (r instanceof IRI)
                        custom_ur = (IRI) r;
                } else {
                    it2 = meta.filter(null, IS_SPACE_CUSTOM_OF_URIREF, sub);
                    if (it2.hasNext()) {
                        r = it2.next().getSubject();
                        if (r instanceof IRI)
                            custom_ur = (IRI) r;
                    }
                }
                // retrieve the ontologies
                if (core_ur != null) {
                    for (it2 = meta.filter(core_ur, null, null); it2.hasNext(); ) {
                        Triple t = it2.next();
                        IRI predicate = t.getPredicate();
                        if (predicate.equals(MANAGES_URIREF)) {
                            if (t.getObject() instanceof IRI)
                                coreOntologies.get(scopeId).add(// FIXME must be very
                                keymap.buildPublicKey((IRI) t.getObject()));
                        }
                    }
                    for (it2 = meta.filter(null, null, core_ur); it2.hasNext(); ) {
                        Triple t = it2.next();
                        IRI predicate = t.getPredicate();
                        if (predicate.equals(IS_MANAGED_BY_URIREF)) {
                            if (t.getSubject() instanceof IRI)
                                coreOntologies.get(scopeId).add(// FIXME must be very
                                keymap.buildPublicKey((IRI) t.getSubject()));
                        }
                    }
                }
                if (custom_ur != null) {
                    for (it2 = meta.filter(custom_ur, null, null); it2.hasNext(); ) {
                        Triple t = it2.next();
                        IRI predicate = t.getPredicate();
                        if (predicate.equals(MANAGES_URIREF)) {
                            if (t.getObject() instanceof IRI)
                                customOntologies.get(scopeId).add(// FIXME must be very
                                keymap.buildPublicKey((IRI) t.getObject()));
                        }
                    }
                    for (it2 = meta.filter(null, null, custom_ur); it2.hasNext(); ) {
                        Triple t = it2.next();
                        IRI predicate = t.getPredicate();
                        if (predicate.equals(IS_MANAGED_BY_URIREF)) {
                            if (t.getSubject() instanceof IRI)
                                customOntologies.get(scopeId).add(// FIXME must be very
                                keymap.buildPublicKey((IRI) t.getSubject()));
                        }
                    }
                }
            }
        }
    }
    // Sessions next
    Map<String, Collection<OWLOntologyID>> sessionOntologies = new HashMap<String, Collection<OWLOntologyID>>();
    for (Iterator<Triple> it = meta.filter(null, RDF.type, SESSION_URIREF); it.hasNext(); ) {
        // for each
        // scope
        Triple ta = it.next();
        BlankNodeOrIRI sub = ta.getSubject();
        if (sub instanceof IRI) {
            IRI ses_ur = (IRI) sub;
            String s = ((IRI) sub).getUnicodeString();
            String prefix = _NS_STANBOL_INTERNAL + Session.shortName + "/";
            if (s.startsWith(prefix)) {
                String sessionId = s.substring(prefix.length());
                log.info("Rebuilding session \"{}\".", sessionId);
                sessionOntologies.put(sessionId, new TreeSet<OWLOntologyID>());
                attachedScopes.put(sessionId, new TreeSet<String>());
                // retrieve the ontologies
                if (ses_ur != null) {
                    for (Iterator<Triple> it2 = meta.filter(ses_ur, MANAGES_URIREF, null); it2.hasNext(); ) {
                        RDFTerm obj = it2.next().getObject();
                        if (obj instanceof IRI)
                            sessionOntologies.get(sessionId).add(// FIXME must be very temporary!
                            keymap.buildPublicKey((IRI) obj));
                    }
                    for (Iterator<Triple> it2 = meta.filter(null, IS_MANAGED_BY_URIREF, ses_ur); it2.hasNext(); ) {
                        RDFTerm subj = it2.next().getSubject();
                        if (subj instanceof IRI)
                            sessionOntologies.get(sessionId).add(// FIXME must be very temporary!
                            keymap.buildPublicKey((IRI) subj));
                    }
                    for (Iterator<Triple> it2 = meta.filter(null, APPENDED_TO_URIREF, ses_ur); it2.hasNext(); ) {
                        RDFTerm subj = it2.next().getSubject();
                        if (subj instanceof IRI) {
                            String s1 = ((IRI) subj).getUnicodeString();
                            String prefix1 = _NS_STANBOL_INTERNAL + Scope.shortName + "/";
                            if (s1.startsWith(prefix1)) {
                                String scopeId = s1.substring(prefix1.length());
                                attachedScopes.get(sessionId).add(scopeId);
                            }
                        }
                    }
                    for (Iterator<Triple> it2 = meta.filter(ses_ur, HAS_APPENDED_URIREF, null); it2.hasNext(); ) {
                        RDFTerm obj = it2.next().getObject();
                        if (obj instanceof IRI) {
                            String s1 = ((IRI) obj).getUnicodeString();
                            String prefix1 = _NS_STANBOL_INTERNAL + Scope.shortName + "/";
                            if (s1.startsWith(prefix1)) {
                                String scopeId = s1.substring(prefix1.length());
                                attachedScopes.get(sessionId).add(scopeId);
                            }
                        }
                    }
                }
            }
        }
    }
    return new OntologyNetworkConfiguration(coreOntologies, customOntologies, sessionOntologies, attachedScopes);
}

Example 33 with BlankNodeOrIRI

use of org.apache.clerezza.commons.rdf.BlankNodeOrIRI in project stanbol by apache.

the class AuthenticationCheckerImpl method authenticate.

/**
	 * Checks if the provided username and password matches a username and
	 * password stored in the system graph
	 *
	 * @param userName
	 * @param password
	 * @return true if the password matched, false otherwise
	 * @throws org.apache.stanbol.commons.security.auth.NoSuchAgent
	 */
@Override
public boolean authenticate(String userName, String password) throws NoSuchAgent {
    SecurityManager security = System.getSecurityManager();
    if (security != null) {
        AccessController.checkPermission(new CheckAuthenticationPermission());
    }
    BlankNodeOrIRI agent = getAgentFromGraph(userName);
    String storedPassword = getPasswordOfAgent(agent);
    if (storedPassword.equals(PasswordUtil.convertPassword(password))) {
        logger.debug("user {} successfully authenticated", userName);
        return true;
    } else {
        logger.debug("unsuccessful authentication attempt as user {}", userName);
        return false;
    }
}

Example 34 with BlankNodeOrIRI

use of org.apache.clerezza.commons.rdf.BlankNodeOrIRI in project stanbol by apache.

the class AuthenticationCheckerImpl method getAgentFromGraph.

private BlankNodeOrIRI getAgentFromGraph(String userName) throws NoSuchAgent {
    BlankNodeOrIRI agent;
    Lock l = systemGraph.getLock().readLock();
    l.lock();
    try {
        Iterator<Triple> agents = systemGraph.filter(null, PLATFORM.userName, new PlainLiteralImpl(userName));
        if (agents.hasNext()) {
            agent = agents.next().getSubject();
        } else {
            logger.debug("unsuccessful authentication attempt as non-existent user {}", userName);
            throw new NoSuchAgent();
        }
    } finally {
        l.unlock();
    }
    return agent;
}

Example 35 with BlankNodeOrIRI

use of org.apache.clerezza.commons.rdf.BlankNodeOrIRI in project stanbol by apache.

the class OWLUtils method extractOntologyID.

/**
     * Returns the logical identifier of the supplied RDF graph, which is interpreted as an OWL ontology.
     * 
     * @param graph
     *            the RDF graph
     * @return the OWL ontology ID of the supplied graph, or null if it denotes an anonymous ontology.
     */
public static OWLOntologyID extractOntologyID(Graph graph) {
    IRI ontologyIri = null, versionIri = null;
    Iterator<Triple> it = graph.filter(null, RDF.type, OWL.Ontology);
    if (it.hasNext()) {
        BlankNodeOrIRI subj = it.next().getSubject();
        if (it.hasNext()) {
            log.warn("Multiple OWL ontology definitions found.");
            log.warn("Ignoring all but {}", subj);
        }
        if (subj instanceof org.apache.clerezza.commons.rdf.IRI) {
            ontologyIri = IRI.create(((org.apache.clerezza.commons.rdf.IRI) subj).getUnicodeString());
            Iterator<Triple> it2 = graph.filter(subj, new org.apache.clerezza.commons.rdf.IRI(OWL2Constants.OWL_VERSION_IRI), null);
            if (it2.hasNext())
                versionIri = IRI.create(((org.apache.clerezza.commons.rdf.IRI) it2.next().getObject()).getUnicodeString());
        }
    }
    if (ontologyIri == null) {
        // Note that OWL 2 does not allow ontologies with a version IRI and no ontology IRI.
        log.debug("Ontology is anonymous. Returning null ID.");
        return null;
    }
    if (versionIri == null)
        return new OWLOntologyID(ontologyIri);
    else
        return new OWLOntologyID(ontologyIri, versionIri);
}