Examples with RDFXMLOntologyFormat org.semanticweb.owlapi.io.RDFXMLOntologyFormat used on opensource projects

Example 1 with RDFXMLOntologyFormat

use of org.semanticweb.owlapi.io.RDFXMLOntologyFormat 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 2 with RDFXMLOntologyFormat

use of org.semanticweb.owlapi.io.RDFXMLOntologyFormat 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();
}

Example 3 with RDFXMLOntologyFormat

use of org.semanticweb.owlapi.io.RDFXMLOntologyFormat in project stanbol by apache.

the class ODPRegistryCacheManager method cacheOntology.

private static synchronized void cacheOntology(URI physicalRemoteUri, File file, OWLOntology ont) throws UnknownOWLOntologyException, OWLOntologyStorageException {
    uris.put(physicalRemoteUri, file);
    oiri.put(physicalRemoteUri, ont.getOntologyID().getOntologyIRI());
    manager.setOntologyDocumentIRI(ont, IRI.create(file));
    manager.saveOntology(ont, new RDFXMLOntologyFormat(), IRI.create(file));
}

Example 4 with RDFXMLOntologyFormat

use of org.semanticweb.owlapi.io.RDFXMLOntologyFormat in project goci by EBISPOT.

the class DefaultGWASOWLPublisher method saveGWASData.

public void saveGWASData(OWLOntology ontology, File outputFile) throws OWLConversionException {
    try {
        getLog().info("Saving GWAS catalog data...");
        OWLOntologyFormat format = new RDFXMLOntologyFormat();
        getManager().saveOntology(ontology, format, IRI.create(outputFile));
        getLog().info("GWAS catalog data saved ok");
        getLog().info("Resulting ontology contains " + ontology.getAxiomCount() + " axioms " + "and is saved at " + outputFile.getAbsolutePath());
    } catch (OWLOntologyStorageException e) {
        throw new OWLConversionException("Failed to save GWAS data", e);
    }
}

Example 5 with RDFXMLOntologyFormat

use of org.semanticweb.owlapi.io.RDFXMLOntologyFormat in project stanbol by apache.

the class OWLOntologyWriter method writeTo.

@Override
public void writeTo(OWLOntology ontology, Class<?> arg1, Type arg2, Annotation[] arg3, MediaType mediaType, MultivaluedMap<String, Object> arg5, OutputStream out) throws IOException, WebApplicationException {
    Logger log = LoggerFactory.getLogger(getClass());
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    log.debug("Rendering ontology " + ontology.getOntologyID() + " to knowledge representation format " + mediaType);
    // Native formats first
    if (RDF_XML_TYPE.equals(mediaType) || OWL_XML_TYPE.equals(mediaType) || MANCHESTER_OWL_TYPE.equals(mediaType) || FUNCTIONAL_OWL_TYPE.equals(mediaType) || TURTLE_TYPE.equals(mediaType) || X_TURTLE_TYPE.equals(mediaType)) {
        OWLOntologyFormat format = null;
        if (RDF_XML_TYPE.equals(mediaType))
            format = new RDFXMLOntologyFormat();
        else if (OWL_XML_TYPE.equals(mediaType))
            format = new OWLXMLOntologyFormat();
        else if (MANCHESTER_OWL_TYPE.equals(mediaType))
            format = new ManchesterOWLSyntaxOntologyFormat();
        else if (FUNCTIONAL_OWL_TYPE.equals(mediaType))
            format = new OWLFunctionalSyntaxOntologyFormat();
        else if (TURTLE_TYPE.equals(mediaType) || X_TURTLE_TYPE.equals(mediaType))
            format = new TurtleOntologyFormat();
        if (format != null)
            try {
                manager.saveOntology(ontology, format, out);
            } catch (OWLOntologyStorageException e) {
                log.error("Failed to store ontology for rendering.", e);
                throw new WebApplicationException(e, Status.INTERNAL_SERVER_ERROR);
            }
        else
            throw new IOException();
    } else {
        // Non-native formats that require a conversion to Clerezza
        if (RDF_JSON_TYPE.equals(mediaType) || N3_TYPE.equals(mediaType) || TEXT_PLAIN.equals(mediaType.toString()) || N_TRIPLE_TYPE.equals(mediaType)) {
            Graph mGraph = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph(ontology);
            SerializingProvider serializer = null;
            if (RDF_JSON_TYPE.equals(mediaType))
                serializer = new RdfJsonSerializingProvider();
            else if (N3_TYPE.equals(mediaType) || N_TRIPLE_TYPE.equals(mediaType) || TEXT_PLAIN.equals(mediaType.toString()))
                serializer = new JenaSerializerProvider();
            // text/plain is interpreted as N3.
            if (serializer != null)
                serializer.serialize(out, mGraph, TEXT_PLAIN.equals(mediaType.toString()) ? N3 : mediaType.toString());
        }
    }
    // JSON_LD not supported until both parser and serializer are stable.
    out.flush();
}