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

Example 1 with OWLOntologyStorageException

use of org.semanticweb.owlapi.model.OWLOntologyStorageException in project webprotege by protegeproject.

the class CreateNewProjectActionHandler method execute.

@Nonnull
@Override
public CreateNewProjectResult execute(@Nonnull CreateNewProjectAction action, @Nonnull ExecutionContext executionContext) {
    try {
        UserId userId = executionContext.getUserId();
        if (!accessManager.hasPermission(forUser(userId), ApplicationResource.get(), CREATE_EMPTY_PROJECT)) {
            throw new PermissionDeniedException("You do not have permission to create new projects", userInSessionFactory.getUserInSession(userId));
        }
        NewProjectSettings newProjectSettings = action.getNewProjectSettings();
        if (newProjectSettings.hasSourceDocument()) {
            if (!accessManager.hasPermission(forUser(userId), ApplicationResource.get(), UPLOAD_PROJECT)) {
                throw new PermissionDeniedException("You do not have permission to upload projects", userInSessionFactory.getUserInSession(userId));
            }
        }
        ProjectId projectId = pm.createNewProject(newProjectSettings);
        if (!projectDetailsManager.isExistingProject(projectId)) {
            projectDetailsManager.registerProject(projectId, newProjectSettings);
            applyDefaultPermissions(projectId, userId);
        }
        return new CreateNewProjectResult(projectDetailsManager.getProjectDetails(projectId));
    } catch (OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
        throw new RuntimeException(e);
    }
}

Example 2 with OWLOntologyStorageException

use of org.semanticweb.owlapi.model.OWLOntologyStorageException in project webprotege by protegeproject.

the class RootOntologyLoader method loadRootOntology.

public OWLOntology loadRootOntology() {
    // The delegate - we use the concurrent ontology manager
    OWLOntologyManager delegateManager = WebProtegeOWLManager.createConcurrentOWLOntologyManager();
    // We only support the binary format for speed
    delegateManager.getOntologyStorers().add(new RDFXMLStorerFactory());
    delegateManager.getOntologyStorers().add(new OWLXMLStorerFactory());
    delegateManager.getOntologyStorers().add(new FunctionalSyntaxStorerFactory());
    delegateManager.getOntologyStorers().add(new ManchesterSyntaxStorerFactory());
    delegateManager.getOntologyParsers().add(new BinaryOWLOntologyDocumentParserFactory());
    // The wrapper manager
    ProjectOWLOntologyManager manager = new ProjectOWLOntologyManager();
    manager.setDelegate(delegateManager);
    int threadPriority = Thread.currentThread().getPriority();
    try {
        Thread.currentThread().setPriority(3);
        OWLOntology rootOntology = documentStore.initialiseOntologyManagerWithProject(manager.getDelegate());
        manager.sealDelegate();
        return rootOntology;
    } catch (OWLOntologyCreationException | OWLOntologyStorageException e) {
        throw new RuntimeException("Failed to load project: " + e.getMessage(), e);
    } finally {
        Thread.currentThread().setPriority(threadPriority);
    }
}

Example 3 with OWLOntologyStorageException

use of org.semanticweb.owlapi.model.OWLOntologyStorageException in project goci by EBISPOT.

the class DefaultGWASOWLPublisher method saveGWASDataInferredView.

public void saveGWASDataInferredView(OWLReasoner reasoner, File outputFile) throws OWLConversionException {
    try {
        // create new ontology to hold inferred axioms
        OWLOntology inferredOntology = getConverter().createConversionOntology();
        getLog().info("Saving inferred view...");
        List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
        // we require all inferred stuff except for disjoints...
        gens.add(new InferredClassAssertionAxiomGenerator());
        gens.add(new InferredDataPropertyCharacteristicAxiomGenerator());
        gens.add(new InferredEquivalentClassAxiomGenerator());
        gens.add(new InferredEquivalentDataPropertiesAxiomGenerator());
        gens.add(new InferredEquivalentObjectPropertyAxiomGenerator());
        gens.add(new InferredInverseObjectPropertiesAxiomGenerator());
        gens.add(new InferredObjectPropertyCharacteristicAxiomGenerator());
        gens.add(new InferredPropertyAssertionGenerator());
        gens.add(new InferredSubClassAxiomGenerator());
        gens.add(new InferredSubDataPropertyAxiomGenerator());
        gens.add(new InferredSubObjectPropertyAxiomGenerator());
        // now create the target ontology and save
        OWLOntologyManager inferredManager = inferredOntology.getOWLOntologyManager();
        InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
        iog.fillOntology(inferredManager, inferredOntology);
        inferredManager.saveOntology(inferredOntology, IRI.create(outputFile));
        getLog().info("Inferred view saved ok");
    } catch (OWLOntologyStorageException e) {
        throw new OWLConversionException("Failed to save GWAS data (inferred view)", e);
    }
}

Example 4 with OWLOntologyStorageException

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

the class ODPRegistryCacheManager method retrieveRemoteResource.

/**
 * Gets the remote ontology and saves it locally
 *
 * @param uri
 * @return
 * @throws OWLOntologyCreationException
 * @throws UnknownOWLOntologyException
 * @throws OWLOntologyStorageException
 */
private static synchronized OWLOntology retrieveRemoteResource(URI uri) throws OWLOntologyCreationException, UnknownOWLOntologyException, OWLOntologyStorageException {
    manager.setSilentMissingImportsHandling(true);
    manager.addMissingImportListener(new MissingImportListener() {

        public void importMissing(MissingImportEvent arg0) {
            if (!getUnresolvedURIs().contains(arg0.getImportedOntologyURI()))
                getUnresolvedURIs().add(arg0.getImportedOntologyURI().toURI());
        }
    });
    manager.addOntologyLoaderListener(new OWLOntologyLoaderListener() {

        @Override
        public void startedLoadingOntology(LoadingStartedEvent event) {
        // Nothing to do
        }

        @Override
        public void finishedLoadingOntology(LoadingFinishedEvent event) {
            URI onturi = event.getDocumentIRI().toURI();
            if (event.getException() != null) {
                getUnresolvedURIs().add(onturi);
                LoggerFactory.getLogger(ODPRegistryCacheManager.class).warn("Failed to resolve ontology at " + onturi + " . Skipping.", event.getException());
                return;
            }
            try {
                if (!uris.containsKey(onturi)) {
                    cacheOntology(onturi, newFile(), manager.getOntology(event.getOntologyID()));
                }
            } catch (UnknownOWLOntologyException e) {
                LoggerFactory.getLogger(ODPRegistryCacheManager.class).warn("Failed to cache ontology at " + onturi + " . Skipping.", e);
                getUnresolvedURIs().add(onturi);
            } catch (OWLOntologyStorageException e) {
                LoggerFactory.getLogger(ODPRegistryCacheManager.class).warn("Failed to cache ontology at " + onturi + " . Skipping.", e);
                getUnresolvedURIs().add(onturi);
            }
        }
    });
    OWLOntology ont;
    try {
        ont = manager.loadOntologyFromOntologyDocument(IRI.create(uri));
    } catch (OWLOntologyAlreadyExistsException e) {
        ont = manager.getOntology(e.getOntologyID().getOntologyIRI());
    }
    File file = newFile();
    cacheOntology(uri, file, ont);
    return ont;
}

Example 5 with OWLOntologyStorageException

use of org.semanticweb.owlapi.model.OWLOntologyStorageException 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();
}