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

Example 1 with OWLOntologyFormat

use of org.semanticweb.owlapi.model.OWLOntologyFormat 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 2 with OWLOntologyFormat

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

Example 3 with OWLOntologyFormat

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

the class JenaToOwlConvert method ModelOwlToJenaConvert.

// //////////////////////////////////////////////////////////////////////////////
/**
     * This function converts an ontology object from OWLapi to Jena
     * 
     * @param owlmodel
     *            {An OWLOntology object}
     * @param format
     *            {RDF/XML or TURTLE}
     * @return {An OntModel that is a Jena object}
     */
public synchronized OntModel ModelOwlToJenaConvert(OWLOntology owlmodel, String format) {
    while (availablemain == false) {
        try {
            wait();
        } catch (InterruptedException e) {
            System.err.println("ModelOwlToJenaConvert::: " + e);
        }
    }
    availablemain = false;
    OWLOntologyID id;
    try {
        ByteArrayOutputStream out = new ByteArrayOutputStream();
        OWLOntologyManager owlmanager = owlmodel.getOWLOntologyManager();
        format = format.trim();
        if (format.equals("TURTLE") || format.equals("RDF/XML")) {
            if (format.equals("TURTLE"))
                owlmanager.setOntologyFormat(owlmodel, new TurtleOntologyFormat());
            if (format.equals("RDF/XML"))
                owlmanager.setOntologyFormat(owlmodel, new RDFXMLOntologyFormat());
            OWLOntologyFormat owlformat = owlmanager.getOntologyFormat(owlmodel);
            owlmanager.saveOntology(owlmodel, owlformat, out);
            OntModel jenamodel = ModelFactory.createOntologyModel();
            id = owlmodel.getOntologyID();
            jenamodel.read(new ByteArrayInputStream(out.toByteArray()), id.toString().replace("<", "").replace(">", ""), format);
            availablemain = true;
            notifyAll();
            return jenamodel;
        } else {
            System.err.println("The only format supported is RDF/XML or TURTLE. Please check the format!");
            availablemain = true;
            notifyAll();
            return null;
        }
    } catch (OWLOntologyStorageException eos) {
        System.err.print("ModelOwlToJenaConvert::: ");
        eos.printStackTrace();
        return null;
    }
}