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

Example 61 with OWLOntology

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

the class SessionImpl method exportToOWLOntology.

/**
     * TODO support merging for attached scopes as well?
     */
@Override
protected OWLOntology exportToOWLOntology(boolean merge, org.semanticweb.owlapi.model.IRI universalPrefix) {
    OWLOntology o = super.exportToOWLOntology(merge, universalPrefix);
    org.semanticweb.owlapi.model.IRI iri = o.getOntologyID().getOntologyIRI();
    if (merge) {
        // Re-merge
        // FIXME try to avoid this.
        ScopeManager onm = ScopeManagerImpl.get();
        final Set<OWLOntology> set = new HashSet<OWLOntology>();
        set.add(o);
        for (String scopeID : attachedScopes) {
            log.debug(" ... Merging with attached scope {}.", scopeID);
            Scope sc = onm.getScope(scopeID);
            if (sc != null)
                set.add(sc.export(OWLOntology.class, merge));
            for (OWLOntologyID ontologyId : managedOntologies) {
                set.add(getOntology(ontologyId, OWLOntology.class, true));
            }
            OWLOntologySetProvider provider = new OWLOntologySetProvider() {

                @Override
                public Set<OWLOntology> getOntologies() {
                    return set;
                }
            };
            OWLOntologyMerger merger = new OWLOntologyMerger(provider);
            try {
                o = merger.createMergedOntology(OWLManager.createOWLOntologyManager(), iri);
            } catch (OWLOntologyCreationException e) {
                log.error("Failed to merge imports for ontology " + iri, e);
                o = null;
            }
        }
    } else
        attachScopeImportsOwlApi(o, universalPrefix);
    return o;
}

Example 62 with OWLOntology

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

the class ClerezzaOntologyProvider method loadInStore.

@Override
public OWLOntologyID loadInStore(Object ontology, final boolean force, Origin<?>... origins) {
    if (ontology == null)
        throw new IllegalArgumentException("No ontology supplied.");
    checkReplaceability(origins);
    long before = System.currentTimeMillis();
    // The final graph
    Graph targetGraph;
    // The supplied ontology converted to Graph
    Graph rdfData;
    if (ontology instanceof OWLOntology) {
        // This will be in memory!
        rdfData = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph((OWLOntology) ontology);
    } else if (ontology instanceof Graph) {
        // This might be in memory or in persistent storage.
        rdfData = (Graph) ontology;
    } else
        throw new UnsupportedOperationException("This ontology provider can only accept objects assignable to " + Graph.class + " or " + OWLOntology.class);
    // XXX Force is ignored for the content, but the imports?
    // Now we proceed to assign the primary key to the ontology.
    OWLOntologyID primaryKey = null;
    /*
         * Compute aliases
         */
    IRI graphName = null;
    // Priority aliases.
    List<OWLOntologyID> overrides = new ArrayList<OWLOntologyID>();
    // Second-choice aliases.
    List<org.semanticweb.owlapi.model.IRI> sources = new ArrayList<org.semanticweb.owlapi.model.IRI>();
    // Scan origins ONCE.
    for (int i = 0; i < origins.length; i++) {
        Origin<?> origin = origins[i];
        log.debug("Found origin at index {}", i);
        if (origin == null) {
            log.warn("Null origin at index {}. Skipping.", i);
            continue;
        }
        Object ref = origin.getReference();
        if (ref == null) {
            log.warn("Null reference at index {}. Skipping.", i);
            continue;
        }
        log.debug(" ... Reference is a {}", ref.getClass().getCanonicalName());
        log.debug(" ... Value : {}", ref);
        if (ref instanceof OWLOntologyID) {
            OWLOntologyID key = (OWLOntologyID) ref;
            if (primaryKey == null) {
                primaryKey = key;
                log.debug(" ... assigned as primary key.");
            } else if (primaryKey.equals(key)) {
                log.debug(" ... matches primary key. Skipping.");
            } else {
                overrides.add(key);
                log.debug(" ... assigned as a priority alias for {}", primaryKey);
            }
        } else if (ref instanceof org.semanticweb.owlapi.model.IRI) {
            sources.add((org.semanticweb.owlapi.model.IRI) ref);
            log.debug(" ... assigned as a secondary alias (source) for {}", primaryKey);
        } else if (ref instanceof IRI) {
            if (graphName != null)
                log.warn("ImmutableGraph name already assigned as {}. Skipping.", graphName);
            else {
                graphName = (IRI) ref;
                log.debug(" ... assigned as a graph name for {}", primaryKey);
            }
        } else {
            log.warn("Unhandled type for origin at index {} : {}. Skipping.", i, ref.getClass());
        }
    }
    // The actual logical ID will be dereferenceable no matter what.
    OWLOntologyID extractedId = OWLUtils.extractOntologyID(rdfData);
    if (// Not overridden: set as primary key.
    primaryKey == null)
        // Not overridden: set as primary key.
        primaryKey = extractedId;
    else
        // Overridden: must be an alias anyway.
        overrides.add(extractedId);
    if (// No overrides, no extracted ID.
    primaryKey == null) {
        org.semanticweb.owlapi.model.IRI z;
        // The first IRI found becomes the primary key.
        if (!sources.isEmpty())
            z = sources.iterator().next();
        else // Try the graph name
        if (graphName != null)
            z = org.semanticweb.owlapi.model.IRI.create(graphName.getUnicodeString());
        else
            // Extrema ratio : compute a timestamped primary key.
            z = org.semanticweb.owlapi.model.IRI.create(getClass().getCanonicalName() + "-time:" + System.currentTimeMillis());
        primaryKey = new OWLOntologyID(z);
    }
    // Check if it is possible to avoid reloading the ontology content from its source.
    boolean mustLoad = true;
    if (!force && graphName != null && store.listGraphs().contains(graphName)) {
        // Any failed check will abort the scan.
        boolean condition = true;
        // Check if the extracted ontology ID matches that of the supplied graph.
        // XXX note that anonymous ontologies should be considered a match... or should they not?
        Graph tc = store.getGraph(graphName);
        OWLOntologyID idFromStore = OWLUtils.extractOntologyID(tc);
        condition &= (extractedId == null && idFromStore == null) || extractedId.equals(idFromStore);
        // FIXME not a good policy for graphs that change without altering the size.
        if (condition && rdfData instanceof Graph)
            condition &= tc.size() == rdfData.size();
        mustLoad &= !condition;
    }
    if (!mustLoad && graphName != null) {
        log.debug("ImmutableGraph with ID {} already in store. Default action is to skip storage.", graphName);
        targetGraph = store.getGraph(graphName);
    } else {
        String iri = null;
        if (primaryKey.getOntologyIRI() != null)
            iri = primaryKey.getOntologyIRI().toString();
        if (primaryKey.getVersionIRI() != null)
            iri += ":::" + primaryKey.getVersionIRI().toString();
        // s will become the graph name
        String s = (iri.startsWith(prefix + "::")) ? "" : (prefix + "::");
        s += iri;
        graphName = new IRI(URIUtils.sanitize(s));
        log.debug("Storing ontology with graph ID {}", graphName);
        try {
            targetGraph = store.createGraph(graphName);
        } catch (EntityAlreadyExistsException e) {
            if (graphName.equals(e.getEntityName()))
                targetGraph = store.getGraph(graphName);
            else
                targetGraph = store.createGraph(graphName);
        }
        targetGraph.addAll(rdfData);
    }
    // All is already sanitized by the time we get here.
    // Now do the mappings
    String mappedIds = "";
    // Discard unconventional ontology IDs with only the version IRI
    if (primaryKey != null && primaryKey.getOntologyIRI() != null) {
        // Versioned or not, the real ID mapping is always added
        keymap.setMapping(primaryKey, graphName);
        mappedIds += primaryKey;
        // TODO map unversioned ID as well?
        Triple t = new TripleImpl(keymap.buildResource(primaryKey), SIZE_IN_TRIPLES_URIREF, LiteralFactory.getInstance().createTypedLiteral(Integer.valueOf(rdfData.size())));
        getMetaGraph(Graph.class).add(t);
    }
    // Add aliases.
    for (org.semanticweb.owlapi.model.IRI source : sources) if (source != null)
        overrides.add(new OWLOntologyID(source));
    for (OWLOntologyID alias : overrides) if (alias != null && !alias.equals(primaryKey)) {
        addAlias(primaryKey, alias);
        mappedIds += " , " + alias;
    }
    // Do this AFTER registering the ontology, otherwise import cycles will cause infinite loops.
    if (resolveImports) {
        // Scan resources of type owl:Ontology, but only get the first.
        Iterator<Triple> it = targetGraph.filter(null, RDF.type, OWL.Ontology);
        if (it.hasNext()) {
            // Scan import statements for the one owl:Ontology considered.
            Iterator<Triple> it2 = targetGraph.filter(it.next().getSubject(), OWL.imports, null);
            while (it2.hasNext()) {
                RDFTerm obj = it2.next().getObject();
                log.info("Resolving import target {}", obj);
                if (obj instanceof IRI)
                    try {
                        // TODO try locals first
                        IRI target = (IRI) obj;
                        OWLOntologyID id = new OWLOntologyID(org.semanticweb.owlapi.model.IRI.create(target.getUnicodeString()));
                        if (keymap.getMapping(id) == null) {
                            // Check if it's not there already.
                            if (isOfflineMode())
                                throw new RuntimeException("Cannot load imported ontology " + obj + " while Stanbol is in offline mode.");
                            // TODO manage origins for imported ontologies too?
                            OWLOntologyID id2 = loadInStore(org.semanticweb.owlapi.model.IRI.create(((IRI) obj).getUnicodeString()), null, false);
                            if (id2 != null)
                                id = id2;
                            log.info("Import {} resolved.", obj);
                            log.debug("");
                        } else {
                            log.info("Requested import already stored. Setting dependency only.");
                        }
                        descriptor.setDependency(primaryKey, id);
                    } catch (UnsupportedFormatException e) {
                        log.warn("Failed to parse format for resource " + obj, e);
                    // / XXX configure to continue?
                    } catch (IOException e) {
                        log.warn("Failed to load ontology from resource " + obj, e);
                    // / XXX configure to continue?
                    }
            }
        }
    }
    log.debug(" Ontology {}", mappedIds);
    if (targetGraph != null)
        log.debug(" ... ({} triples)", targetGraph.size());
    log.debug(" ... primary public key : {}", primaryKey);
    // log.debug("--- {}", URIUtils.sanitize(s));
    log.debug("Time: {} ms", (System.currentTimeMillis() - before));
    // return URIUtils.sanitize(s);
    return primaryKey;
}

Example 63 with OWLOntology

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

the class RegistryManagerImpl method activate.

protected void activate(Dictionary<String, Object> configuration) {
    // Parse configuration.
    try {
        lazyLoading = (Boolean) (configuration.get(RegistryManager.LAZY_LOADING));
    } catch (Exception ex) {
        lazyLoading = _LAZY_LOADING_DEFAULT;
    }
    try {
        retainIncomplete = (Boolean) (configuration.get(RegistryManager.RETAIN_INCOMPLETE));
    } catch (Exception ex) {
        retainIncomplete = _RETAIN_INCOMPLETE_DEFAULT;
    }
    Object obj = configuration.get(RegistryManager.REGISTRY_LOCATIONS);
    if (obj instanceof String[])
        locations = (String[]) obj;
    else if (obj instanceof String)
        locations = new String[] { (String) obj };
    if (locations == null)
        locations = new String[] { "stanbol_network.owl" };
    Object cachingPolicy = configuration.get(RegistryManager.CACHING_POLICY);
    if (cachingPolicy == null) {
        this.cachingPolicyString = _CACHING_POLICY_DEFAULT.name();
    } else {
        this.cachingPolicyString = cachingPolicy.toString();
    }
    final IRI[] offlineResources;
    if (this.offline != null) {
        List<IRI> paths = offline.getOntologySourceLocations();
        if (paths != null)
            offlineResources = paths.toArray(new IRI[0]);
        else
            // There are no offline paths.
            offlineResources = new IRI[0];
    } else
        // There's no offline configuration at all.
        offlineResources = new IRI[0];
    // Used only for creating the registry model, do not use for caching.
    OWLOntologyManager mgr = OWLOntologyManagerFactory.createOWLOntologyManager(offlineResources);
    OWLOntologyLoaderConfiguration conf = new OWLOntologyLoaderConfiguration();
    // If we are retaining incomplete registries, do not throw exceptions if imports fail.
    conf.setSilentMissingImportsHandling(retainIncomplete);
    // Load registries
    Set<OWLOntology> regOnts = new HashSet<OWLOntology>();
    for (String loc : locations) {
        try {
            IRI iri = IRI.create(loc);
            OWLOntologyDocumentSource src = null;
            OWLOntology o = null;
            if (iri.isAbsolute())
                src = new IRIDocumentSource(iri);
            else {
                // Relative IRI : use data file provider
                log.debug("Found relative IRI {} . Will try to retrieve from data file providers.", iri);
                Map<String, String> info = new HashMap<String, String>();
                if (dataFileProvider != null && dataFileProvider.isAvailable(null, loc, info))
                    src = new StreamDocumentSource(dataFileProvider.getInputStream(null, loc, info));
            }
            if (src != null)
                o = mgr.loadOntologyFromOntologyDocument(src, conf);
            if (o != null)
                regOnts.add(o);
            else
                log.warn("Failed to obtain OWL ontology from resource {}", loc);
        } catch (OWLOntologyAlreadyExistsException e) {
            log.info("Skipping cached ontology {}.", e.getOntologyID());
            continue;
        } catch (OWLOntologyCreationException e) {
            log.warn("Failed to load ontology " + loc + " - Skipping...", e);
            continue;
        } catch (Exception e) {
            log.warn("Invalid registry configuration " + loc + " - Skipping...", e);
            continue;
        }
    }
    // Create and set the cache.
    if (cachingPolicyString.equals(CachingPolicy.CENTRALISED.name())) {
        // this.cache = OWLOntologyManagerFactory.createOWLOntologyManager(offlineResources);
        if (cache == null) {
            log.warn("Caching policy is set as Centralised, but no ontology provider is supplied. Will use new in-memory tcProvider.");
            cache = new ClerezzaOntologyProvider(TcManager.getInstance(), offline, Parser.getInstance());
        }
    // else sta bene cosi'
    } else if (cachingPolicyString.equals(CachingPolicy.DISTRIBUTED.name())) {
        this.cache = null;
    }
    riFactory = new RegistryItemFactoryImpl(cache);
    // Build the model.
    createModel(regOnts);
    // Set the cache on libraries.
    Set<RegistryItem> visited = new HashSet<RegistryItem>();
    for (Registry reg : getRegistries()) for (RegistryItem child : reg.getChildren()) if (!visited.contains(child)) {
        if (child instanceof Library) {
            if (this.cache != null)
                ((Library) child).setCache(this.cache);
            else
                ((Library) child).setCache(new ClerezzaOntologyProvider(TcManager.getInstance(), offline, Parser.getInstance()));
        }
        visited.add(child);
    }
    if (isLazyLoading()) {
    // Nothing to do about it at the moment.
    } else {
        loadEager();
    }
}

Example 64 with OWLOntology

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

the class RegistryManagerImpl method populateLibrary.

protected Library populateLibrary(OWLNamedObject ind, Set<OWLOntology> registries) throws RegistryContentException {
    IRI libId = ind.getIRI();
    RegistryItem lib = null;
    if (population.containsKey(libId)) {
        // We are not allowing multityping either.
        lib = population.get(libId);
        if (!(lib instanceof Library))
            throw new RegistryContentException("Inconsistent multityping: for item " + libId + " : {" + Library.class + ", " + lib.getClass() + "}");
    } else {
        lib = riFactory.createLibrary(ind);
        try {
            population.put(lib.getIRI(), lib);
        } catch (Exception e) {
            log.error("Invalid identifier for library item " + lib, e);
            return null;
        }
    }
    // EXIT nodes.
    Set<OWLNamedObject> ironts = new HashSet<OWLNamedObject>();
    OWLDataFactory df = OWLManager.getOWLDataFactory();
    for (OWLOntology o : registries) {
        if (ind instanceof OWLIndividual) {
            // Get usages of hasOntology as an object property
            for (OWLIndividual value : ((OWLIndividual) ind).getObjectPropertyValues(hasOntology, o)) if (value.isNamed())
                ironts.add(value.asOWLNamedIndividual());
            // Get usages of hasOntology as an annotation property
            for (OWLAnnotationAssertionAxiom ann : o.getAnnotationAssertionAxioms(ind.getIRI())) if (hasOntologyAnn.equals(ann.getProperty())) {
                OWLAnnotationValue value = ann.getValue();
                if (value instanceof OWLNamedObject)
                    ironts.add((OWLNamedObject) value);
                else if (value instanceof IRI)
                    ironts.add(df.getOWLNamedIndividual((IRI) value));
            }
        }
    }
    for (OWLNamedObject iront : ironts) {
        IRI childId = iront.getIRI();
        // If some populate*() method has created it, it will be there.
        RegistryItem ront = population.get(childId);
        // Otherwise populating it will also put it in population.
        if (ront == null)
            ront = populateOntology(iront, registries);
        lib.addChild(ront);
        if (ontologyIndex.get(childId) == null)
            ontologyIndex.put(childId, new HashSet<IRI>());
        ontologyIndex.get(childId).add(libId);
    }
    return (Library) lib;
}

Example 65 with OWLOntology

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

the class RegistryManagerImpl method populateRegistry.

protected Registry populateRegistry(OWLOntology registry) throws RegistryContentException {
    log.debug("Populating registry content from ontology {}", registry);
    Registry reg = riFactory.createRegistry(registry);
    Set<OWLOntology> closure = registry.getOWLOntologyManager().getImportsClosure(registry);
    // Just scan all individuals. Recurse in case the registry imports more registries.
    for (OWLIndividual ind : registry.getIndividualsInSignature(true)) {
        // We do not allow anonymous registry items.
        if (ind.isAnonymous())
            continue;
        RegistryItem item = null;
        // IRI id = ind.asOWLNamedIndividual().getIRI();
        Type t = RegistryUtils.getType(ind, closure);
        if (t == null) {
            log.warn("Undetermined type for registry ontology individual {}", ind);
            continue;
        }
        switch(t) {
            case LIBRARY:
                log.debug("Found library for individual {}", ind);
                // Create the library and attach to parent and children
                item = populateLibrary(ind.asOWLNamedIndividual(), closure);
                reg.addChild(item);
                item.addRegistryContentListener(this);
                break;
            case ONTOLOGY:
                log.debug("Found ontology for individual {}", ind);
                // Create the ontology and attach to parent
                item = populateOntology(ind.asOWLNamedIndividual(), closure);
                item.addRegistryContentListener(this);
                // We don't know where to attach it within this method.
                break;
            default:
                break;
        }
    }
    try {
        reg.addRegistryContentListener(this);
        log.info("Registry {} added.", reg.getIRI());
        population.put(reg.getIRI(), reg);
    } catch (Exception e) {
        log.error("Invalid identifier for library item " + reg, e);
        return null;
    }
    return reg;
}