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

Example 26 with OWLOntology

use of org.semanticweb.owlapi.model.OWLOntology 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 27 with OWLOntology

use of org.semanticweb.owlapi.model.OWLOntology 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 28 with OWLOntology

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

the class ScopeManagerImpl method activate.

/**
     * Called within both OSGi and non-OSGi environments.
     * 
     * @param configuration
     * @throws IOException
     */
protected void activate(Dictionary<String, Object> configuration) throws IOException {
    long before = System.currentTimeMillis();
    // Assign singleton instance
    me = this;
    // Parse configuration
    if (offline != null)
        ontonetNS = offline.getDefaultOntologyNetworkNamespace();
    scopeRegistryId = (String) configuration.get(ScopeManager.ID_SCOPE_REGISTRY);
    if (scopeRegistryId == null)
        scopeRegistryId = _ID_SCOPE_REGISTRY_DEFAULT;
    configPath = (String) configuration.get(ScopeManager.CONFIG_ONTOLOGY_PATH);
    if (configPath == null)
        configPath = _CONFIG_ONTOLOGY_PATH_DEFAULT;
    // Bind components, starting with the local directories.
    List<String> dirs = new ArrayList<String>();
    try {
        for (IRI iri : offline.getOntologySourceLocations()) dirs.add(iri.toString());
    } catch (NullPointerException ex) {
    // Ok, go empty
    }
    bindResources();
    // String tfile = (String) configuration.get(CONFIG_FILE_PATH);
    // if (tfile != null) this.configPath = tfile;
    // String tns = (String) configuration.get(KRES_NAMESPACE);
    // if (tns != null) this.kresNs = tns;
    // configPath = (String) configuration.get(CONFIG_FILE_PATH);
    // If there is no configuration file, just start with an empty scope set
    Object connectivityPolicy = configuration.get(ScopeManager.CONNECTIVITY_POLICY);
    if (connectivityPolicy == null) {
        this.connectivityPolicyString = _CONNECTIVITY_POLICY_DEFAULT;
    } else {
        this.connectivityPolicyString = connectivityPolicy.toString();
    }
    String configPath = getOntologyNetworkConfigurationPath();
    if (configPath != null && !configPath.trim().isEmpty()) {
        OWLOntology oConf = null;
        OWLOntologyManager tempMgr = OWLOntologyManagerFactory.createOWLOntologyManager(offline.getOntologySourceLocations().toArray(new IRI[0]));
        OWLOntologyDocumentSource oConfSrc = null;
        try {
            log.debug("Try to load the configuration ontology from a local bundle relative path");
            InputStream is = this.getClass().getResourceAsStream(configPath);
            oConfSrc = new StreamDocumentSource(is);
        } catch (Exception e1) {
            try {
                log.debug("Cannot load from a local bundle relative path", e1);
                log.debug("Try to load the configuration ontology resolving the given IRI");
                IRI iri = IRI.create(configPath);
                if (!iri.isAbsolute())
                    throw new Exception("IRI seems to be not absolute! value was: " + iri.toQuotedString());
                oConfSrc = new IRIDocumentSource(iri);
            } catch (Exception e) {
                try {
                    log.debug("Cannot load from the web", e1);
                    log.debug("Try to load the configuration ontology as full local file path");
                    oConfSrc = new FileDocumentSource(new File(configPath));
                } catch (Exception e2) {
                    log.error("Cannot load the configuration ontology from parameter value: " + configPath, e2);
                }
            }
        }
        if (oConfSrc == null) {
            log.warn("No ONM configuration file found at path " + configPath + ". Starting with blank scope set.");
        } else {
            try {
                oConf = tempMgr.loadOntologyFromOntologyDocument(oConfSrc);
            } catch (OWLOntologyCreationException e) {
                log.error("Cannot create the configuration ontology", e);
            }
        }
        // Create and populate the scopes from the config ontology.
        bootstrapOntologyNetwork(oConf);
    } else {
        // No ontology supplied. Access the local graph
        rebuildScopes();
    }
    log.debug(ScopeManager.class + " activated. Time : {} ms.", System.currentTimeMillis() - before);
}

Example 29 with OWLOntology

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

the class RecipeListWriter method writeTo.

@Override
public void writeTo(RecipeList recipeList, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLDataFactory factory = OWLManager.getOWLDataFactory();
    OWLOntology ontology;
    try {
        ontology = manager.createOntology();
        String recipeClassURI = Symbols.Recipe.toString().replace("<", "").replace(">", "");
        IRI recipeClassIRI = IRI.create(recipeClassURI);
        OWLClass owlRecipeClass = factory.getOWLClass(recipeClassIRI);
        String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
        IRI descriptionIRI = IRI.create(descriptionURI);
        OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
        if (recipeList != null) {
            log.info("Converting the recipe list to OWL.");
            for (Recipe recipe : recipeList) {
                String recipeURI = recipe.getRecipeID().toString().replace("<", "").replace(">", "");
                IRI recipeIRI = IRI.create(recipeURI);
                OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
                OWLAxiom axiom = factory.getOWLClassAssertionAxiom(owlRecipeClass, recipeIndividual);
                manager.addAxiom(ontology, axiom);
                String description = recipe.getRecipeDescription();
                if (description != null) {
                    axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, description);
                    manager.addAxiom(ontology, axiom);
                }
            }
        }
        if (mediaType.toString().equals(KRFormat.RDF_XML)) {
            try {
                manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
            try {
                manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
            try {
                manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
            try {
                manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
            try {
                manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
            }
        } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
            provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
        }
    } catch (OWLOntologyCreationException e1) {
        log.error("An error occurred.", e1);
    }
    out.flush();
}

Example 30 with OWLOntology

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

the class RecipeWriter method writeTo.

@Override
public void writeTo(Recipe recipe, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    log.debug("Rendering the list of recipes.");
    if (mediaType.toString().equals(MediaType.TEXT_PLAIN)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else if (mediaType.toString().equals(MediaType.TEXT_HTML)) {
        String recipeString = recipe.toString();
        out.write(recipeString.getBytes());
    } else {
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLDataFactory factory = OWLManager.getOWLDataFactory();
        OWLOntology ontology;
        try {
            ontology = manager.createOntology();
            RuleList rules = recipe.getRuleList();
            IRI recipeID = recipe.getRecipeID();
            String recipeURI = recipeID.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI recipeIRI = org.semanticweb.owlapi.model.IRI.create(recipeURI);
            OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI);
            String descriptionURI = Symbols.description.toString().replace("<", "").replace(">", "");
            org.semanticweb.owlapi.model.IRI descriptionIRI = org.semanticweb.owlapi.model.IRI.create(descriptionURI);
            OWLDataProperty descriptionProperty = factory.getOWLDataProperty(descriptionIRI);
            OWLAxiom axiom;
            String recipeDescription = recipe.getRecipeDescription();
            if (recipeDescription != null) {
                axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, recipeIndividual, recipeDescription);
                manager.addAxiom(ontology, axiom);
            }
            if (rules != null) {
                for (Rule rule : rules) {
                    IRI ruleID = rule.getRuleID();
                    String ruleName = rule.getRuleName();
                    String ruleDescription = rule.getDescription();
                    String ruleURI = ruleID.toString().replace("<", "").replace(">", "");
                    String ruleNameURI = Symbols.ruleName.toString().replace("<", "").replace(">", "");
                    String ruleBodyURI = Symbols.ruleBody.toString().replace("<", "").replace(">", "");
                    String ruleHeadURI = Symbols.ruleHead.toString().replace("<", "").replace(">", "");
                    String hasRuleURI = Symbols.hasRule.toString().replace("<", "").replace(">", "");
                    String ruleContent = rule.toString();
                    String[] ruleParts = ruleContent.split("\\->");
                    org.semanticweb.owlapi.model.IRI ruleIRI = org.semanticweb.owlapi.model.IRI.create(ruleURI);
                    org.semanticweb.owlapi.model.IRI ruleNameIRI = org.semanticweb.owlapi.model.IRI.create(ruleNameURI);
                    org.semanticweb.owlapi.model.IRI ruleBodyIRI = org.semanticweb.owlapi.model.IRI.create(ruleBodyURI);
                    org.semanticweb.owlapi.model.IRI ruleHeadIRI = org.semanticweb.owlapi.model.IRI.create(ruleHeadURI);
                    org.semanticweb.owlapi.model.IRI hasRuleIRI = org.semanticweb.owlapi.model.IRI.create(hasRuleURI);
                    OWLIndividual ruleIndividual = factory.getOWLNamedIndividual(ruleIRI);
                    OWLObjectProperty hasRule = factory.getOWLObjectProperty(hasRuleIRI);
                    OWLDataProperty nameProperty = factory.getOWLDataProperty(ruleNameIRI);
                    OWLDataProperty ruleBodyProperty = factory.getOWLDataProperty(ruleBodyIRI);
                    OWLDataProperty ruleHeadProperty = factory.getOWLDataProperty(ruleHeadIRI);
                    // add the name to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(nameProperty, ruleIndividual, ruleName);
                    manager.addAxiom(ontology, axiom);
                    // add the description to the rule individual
                    if (ruleDescription != null) {
                        axiom = factory.getOWLDataPropertyAssertionAxiom(descriptionProperty, ruleIndividual, ruleDescription);
                        manager.addAxiom(ontology, axiom);
                    }
                    // add the rule body to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleBodyProperty, ruleIndividual, ruleParts[0]);
                    manager.addAxiom(ontology, axiom);
                    // add the rule head to the rule individual
                    axiom = factory.getOWLDataPropertyAssertionAxiom(ruleHeadProperty, ruleIndividual, ruleParts[1]);
                    manager.addAxiom(ontology, axiom);
                    // bind the rule to the recipe
                    axiom = factory.getOWLObjectPropertyAssertionAxiom(hasRule, recipeIndividual, ruleIndividual);
                    manager.addAxiom(ontology, axiom);
                }
            }
            if (mediaType.toString().equals(KRFormat.RDF_XML)) {
                try {
                    manager.saveOntology(ontology, new RDFXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.OWL_XML)) {
                try {
                    manager.saveOntology(ontology, new OWLXMLOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.MANCHESTER_OWL)) {
                try {
                    manager.saveOntology(ontology, new ManchesterOWLSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.FUNCTIONAL_OWL)) {
                try {
                    manager.saveOntology(ontology, new OWLFunctionalSyntaxOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.TURTLE)) {
                try {
                    manager.saveOntology(ontology, new TurtleOntologyFormat(), out);
                } catch (OWLOntologyStorageException e) {
                    log.error("Failed to store ontology for rendering.", e);
                }
            } else if (mediaType.toString().equals(KRFormat.RDF_JSON)) {
                Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
                RdfJsonSerializingProvider provider = new RdfJsonSerializingProvider();
                provider.serialize(out, mGraph, SupportedFormat.RDF_JSON);
            }
        } catch (OWLOntologyCreationException e1) {
            log.error("An error occurred.", e1);
        }
    }
    out.flush();
}