Java 类org.semanticweb.owlapi.model.OWLDocumentFormat 实例源码

项目：owltools 文件：OWLHandler.java

public void headerOWL() {
    if (isOWLOntologyFormat()) {
        LOG.info("using OWL ontology header");
        OWLDocumentFormat ofmt = this.getOWLOntologyFormat();
        if (ofmt instanceof RDFXMLDocumentFormat) {
            response.setContentType("application/rdf+xml;charset-utf-8");
        }
        else if (ofmt instanceof OWLXMLDocumentFormat) {
            response.setContentType("application/xml;charset-utf-8");
        }
        else {
            response.setContentType("text/plain;charset-utf-8");
        }
    }
    else {
        response.setContentType("text/plain;charset-utf-8");
    }
    response.setStatus(HttpServletResponse.SC_OK);
}

项目：owltools 文件：OWLHandler.java

public void printCachedObjects() throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
    if (getFormat().equals("json")) {
        OWLGsonRenderer jsonp = new OWLGsonRenderer(response.getWriter());
        if (cachedObjects.size() > 0) {
            jsonp.render(cachedObjects);
        }
        else {
            jsonp.render(cachedAxioms);
        }
    }
    else {
        // ontology format
        if (cachedAxioms.size() == 0)
            return;
        OWLOntology tmpOnt = getTemporaryOntology();
        graph.getManager().addAxioms(tmpOnt, cachedAxioms);
        OWLDocumentFormat ofmt = getOWLOntologyFormat();
        LOG.info("Format:"+ofmt);
        ParserWrapper pw = new ParserWrapper();
        //graph.getManager().saveOntology(tmpOnt, ofmt, response.getOutputStream());
        pw.saveOWL(tmpOnt, ofmt, response.getOutputStream());
        graph.getManager().removeOntology(tmpOnt);
        cachedAxioms = new HashSet<OWLAxiom>();
    }
}

项目：owltools 文件：PombeGAFOWLBridgeTest.java

@Ignore
@Test
public void testConversion() throws Exception {
    ParserWrapper pw = new ParserWrapper();
    OWLOntology ont = pw.parse("http://purl.obolibrary.org/obo/go.owl");
    OWLGraphWrapper g = new OWLGraphWrapper(ont);

    GafObjectsBuilder builder = new GafObjectsBuilder();

    GafDocument gafdoc = builder.buildDocument("http://geneontology.org/gene-associations/gene_association.GeneDB_Spombe.gz");

    GAFOWLBridge bridge = new GAFOWLBridge(g);
    OWLOntology gafOnt = g.getManager().createOntology();
    bridge.setTargetOntology(gafOnt);
    bridge.translate(gafdoc);

    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
    g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("/tmp/gaf.owl")));

    for (OWLAxiom ax : gafOnt.getAxioms()) {
        //LOG.info("AX:"+ax);
    }

}

项目：owltools 文件：GAFOWLBridgeTest.java

@Test
public void testConversion() throws Exception{
    ParserWrapper pw = new ParserWrapper();
    OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
    OWLGraphWrapper g = new OWLGraphWrapper(ont);
    g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

    GafObjectsBuilder builder = new GafObjectsBuilder();

    GafDocument gafdoc = builder.buildDocument(getResource("xp_inference_test.gaf"));

    GAFOWLBridge bridge = new GAFOWLBridge(g);
    OWLOntology gafOnt = g.getManager().createOntology();
    bridge.setTargetOntology(gafOnt);
    bridge.translate(gafdoc);

    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
    g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("/tmp/gaf.owl")));

    for (OWLAxiom ax : gafOnt.getAxioms()) {
        LOG.info("AX:"+ax);
    }

}

项目：owltools 文件：BasicAboxBridgeTest.java

@Test
public void testConversion() throws Exception{
    ParserWrapper pw = new ParserWrapper();
    OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
    OWLGraphWrapper g = new OWLGraphWrapper(ont);
    g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

    GafObjectsBuilder builder = new GafObjectsBuilder();

    GafDocument gafdoc = builder.buildDocument(getResource("xp_inference_test.gaf"));

    BasicABox bridge = new BasicABox(g);
    OWLOntology gafOnt = g.getManager().createOntology();
    bridge.setTargetOntology(gafOnt);
    bridge.translate(gafdoc);

    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
    g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("target/foo.owl")));

    for (OWLAxiom ax : gafOnt.getAxioms()) {
        LOG.info("AX:"+ax);
    }

}

项目：owltools 文件：MgiGAFOWLBridgeTest.java

@Test
public void testConversion() throws Exception{
    ParserWrapper pw = new ParserWrapper();
    OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
    OWLGraphWrapper g = new OWLGraphWrapper(ont);
    g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

    GafObjectsBuilder builder = new GafObjectsBuilder();

    GafDocument gafdoc = builder.buildDocument(getResource("mgi-exttest.gaf"));

    GAFOWLBridge bridge = new GAFOWLBridge(g);
    bridge.setGenerateIndividuals(false);
    OWLOntology gafOnt = g.getManager().createOntology();
    bridge.setTargetOntology(gafOnt);
    bridge.translate(gafdoc);

    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
    g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("target/gaf.owl")));

    for (OWLAxiom ax : gafOnt.getAxioms()) {
        //LOG.info("AX:"+ax);
    }

}

项目：owltools 文件：MgiGAFOWLBridgeTest.java

@Test
public void testConversionToIndividuals() throws Exception{
    ParserWrapper pw = new ParserWrapper();
    OWLOntology ont = pw.parse(getResourceIRIString("go_xp_predictor_test_subset.obo"));
    OWLGraphWrapper g = new OWLGraphWrapper(ont);
    g.addSupportOntology(pw.parse(getResourceIRIString("gorel.owl")));

    GafObjectsBuilder builder = new GafObjectsBuilder();

    GafDocument gafdoc = builder.buildDocument(getResource("mgi-exttest.gaf"));

    GAFOWLBridge bridge = new GAFOWLBridge(g);
    bridge.setGenerateIndividuals(false);
    OWLOntology gafOnt = g.getManager().createOntology();
    bridge.setTargetOntology(gafOnt);
    bridge.setBasicAboxMapping(true);
    bridge.translate(gafdoc);

    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
    g.getManager().saveOntology(gafOnt, owlFormat, IRI.create(new File("target/gaf-abox.owl")));

    for (OWLAxiom ax : gafOnt.getAxioms()) {
        //LOG.info("AX:"+ax);
    }

}

项目：owltools 文件：BridgeExtractor.java

private String getSuffix(OWLDocumentFormat format) {
    if (format instanceof RDFXMLDocumentFormat) {
        return "owl";
    }
    if (format instanceof FunctionalSyntaxDocumentFormat) {
        return "ofn";
    }
    if (format instanceof OWLXMLDocumentFormat) {
        return "owx";
    }
    if (format instanceof ManchesterSyntaxDocumentFormat) {
        return "omn";
    }

    return "owl";
}

项目：owltools 文件：ParserWrapper.java

public void saveOWL(OWLOntology ont, OWLDocumentFormat owlFormat, String file) throws OWLOntologyStorageException, IOException {
    if ((owlFormat instanceof OBODocumentFormat) ||
            (owlFormat instanceof OWLOboGraphsFormat) || 
            (owlFormat instanceof OWLOboGraphsYamlFormat) || 
            (owlFormat instanceof OWLJSONFormat) || 
            (owlFormat instanceof OWLJsonLDFormat)){
        try {
            FileOutputStream os = new FileOutputStream(new File(file));
            saveOWL(ont, owlFormat, os);
        } catch (FileNotFoundException e) {
            throw new OWLOntologyStorageException("Could not open file: "+file, e);
        }
    }
    else {
        IRI iri;
        if (file.startsWith("file://")) {
            iri = IRI.create(file);
        }
        else {
            iri = IRI.create(new File(file));
        }
        manager.saveOntology(ont, owlFormat, iri);
    }
}

项目：Widoco 文件：WidocoUtils.java

/**
 * Writes a model into a file
 * @param m the manager
 * @param o the ontology to write
 * @param f the format in which should be written
 * @param outPath 
 */
public static void writeModel(OWLOntologyManager m, OWLOntology o, OWLDocumentFormat f, String outPath){
    OutputStream out=null;
    try {
        out = new FileOutputStream(outPath);
        m.saveOntology(o, f, out);
        out.close();
    } catch (Exception ex) {
        System.out.println("Error while writing the model to file "+ex.getMessage());
        if(out!=null){
            try{
                out.close();
            }catch(Exception e){}
        }
    }
}

项目：minerva 文件：CoreMolecularModelManager.java

/**
 * Export the ABox, will try to set the ontologyID to the given modelId (to
 * ensure import assumptions are met)
 * 
 * @param model
 * @param ontologyFormat
 * @return modelContent
 * @throws OWLOntologyStorageException
 */
public String exportModel(ModelContainer model, OWLDocumentFormat ontologyFormat) throws OWLOntologyStorageException {
    final OWLOntology aBox = model.getAboxOntology();
    final OWLOntologyManager manager = aBox.getOWLOntologyManager();

    // make sure the exported ontology has an ontologyId and that it maps to the modelId
    final IRI expectedABoxIRI = model.getModelId();
    Optional<IRI> currentABoxIRI = aBox.getOntologyID().getOntologyIRI();
    if (currentABoxIRI.isPresent() == false) {
        manager.applyChange(new SetOntologyID(aBox, expectedABoxIRI));
    }
    else {
        if (expectedABoxIRI.equals(currentABoxIRI) == false) {
            OWLOntologyID ontologyID = new OWLOntologyID(Optional.of(expectedABoxIRI), Optional.of(expectedABoxIRI));
            manager.applyChange(new SetOntologyID(aBox, ontologyID));
        }
    }

    // write the model into a buffer
    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
    if (ontologyFormat != null) {
        manager.saveOntology(aBox, ontologyFormat, outputStream);
    }
    else {
        manager.saveOntology(aBox, outputStream);
    }

    // extract the string from the buffer
    String modelString = outputStream.toString();
    return modelString;
}

项目：owltools 文件：GafCommandRunner.java

/**
 * Created to mimic the translation to OWL for GAF checks
 * 
 * @param opts
 * @throws Exception
 */
@CLIMethod("--gaf2owl-simple")
public void gaf2OwlSimple(Opts opts) throws Exception {
    opts.info("-o FILE", "translates previously loaded GAF document into OWL, requires a loaded ontology to lookup ids");
    String out = null;
    while (opts.hasOpts()) {
        if (opts.nextEq("-o")) {
            out = opts.nextOpt();
        }
        else
            break;

    }
    if (g == null) {
        LOG.error("An ontology is required.");
        exit(-1);
    }
    else if (gafdoc == null) {
        LOG.error("A GAF document is required.");
        exit(-1);
    }
    else if (out == null) {
        LOG.error("An output file is required.");
        exit(-1);
    }
    LOG.info("Creating OWL represenation of annotations.");
    GAFOWLBridge bridge = new GAFOWLBridge(g);
    bridge.setGenerateIndividuals(false);
    bridge.setBasicAboxMapping(false);
    bridge.setBioentityMapping(BioentityMapping.CLASS_EXPRESSION);
    bridge.setSkipNotAnnotations(true);
    OWLOntology translated = bridge.translate(gafdoc);
    File outputFile = new File(out);
    OWLOntologyManager manager = translated.getOWLOntologyManager();
    OWLDocumentFormat ontologyFormat= new FunctionalSyntaxDocumentFormat();
    manager.saveOntology(translated, ontologyFormat, IRI.create(outputFile));
}

项目：owltools 文件：BridgeExtractor.java

public void save(String fn, OWLDocumentFormat format, OWLOntology xo) throws FileNotFoundException, OWLOntologyStorageException {
    fn = fn + "." + getSuffix(format);
    File file = new File(fn);
    file.getParentFile().mkdirs();
    OutputStream os = new FileOutputStream(file);
    LOG.info("Saving: "+xo);
    ontology.getOWLOntologyManager().saveOntology(xo, format, os);
}

项目：owltools 文件：EquivalenceSetMergeUtilTest.java

@Test
public void testMerge() throws OWLOntologyCreationException, IOException, IncoherentOntologyException, OWLOntologyStorageException {
    ParserWrapper pw = new ParserWrapper();
    OWLGraphWrapper g =
            pw.parseToOWLGraph(getResourceIRIString("equivalence-set-merge-util-test.obo"));
    OWLOntology ont1 = g.getSourceOntology();
    ElkReasonerFactory rf = new ElkReasonerFactory();
    OWLReasoner reasoner = rf.createReasoner(ont1);
    EquivalenceSetMergeUtil esmu = new EquivalenceSetMergeUtil(g, reasoner);
    esmu.setPrefixScore("A", 8.0);
    esmu.setPrefixScore("B", 6.0);
    esmu.setPrefixScore("C", 4.0);
    OWLAnnotationProperty lp = g.getDataFactory().getOWLAnnotationProperty( OWLRDFVocabulary.RDFS_LABEL.getIRI() );
    esmu.setPropertyPrefixScore( lp, "C", 5.0);
    esmu.setPropertyPrefixScore( lp, "B", 4.0);
    esmu.setPropertyPrefixScore( lp, "A", 3.0);

    OWLAnnotationProperty dp = g.getDataFactory().getOWLAnnotationProperty( Obo2OWLVocabulary.IRI_IAO_0000115.getIRI() );
    esmu.setPropertyPrefixScore( dp, "B", 5.0);
    esmu.setPropertyPrefixScore( dp, "A", 4.0);
    esmu.setPropertyPrefixScore( dp, "C", 3.0);

    esmu.setRemoveAxiomatizedXRefs(true);

    esmu.merge();
    OWLDocumentFormat fmt = new OBODocumentFormat();
    pw.saveOWL(g.getSourceOntology(), "target/esmu.owl");
    //pw.setCheckOboDoc(false);
    pw.saveOWL(g.getSourceOntology(), fmt, "target/esmu.obo");

    OWLOntology ont2 = pw.parseOWL(getResourceIRIString("equivalence-set-merge-util-expected.obo"));
    assertEquals(0, compare(ont1, ont2));
}

项目：owltools 文件：OWLGsonRendererTest.java

@Test
public void testOnt() throws Exception{
    OWLGraphWrapper  wrapper = getOBO2OWLOntologyWrapper("caro.obo");
    final StringWriter stringWriter = new StringWriter();
    OWLGsonRenderer gr = new OWLGsonRenderer(new PrintWriter(stringWriter));
    gr.render(wrapper.getSourceOntology());
    if (RENDER_FLAG) {
        System.out.println(stringWriter.toString());
        ParserWrapper pw = new ParserWrapper();
        OWLDocumentFormat owlFormat = new OWLJSONFormat();
        File foo = folder.newFile("foo.json");
        pw.saveOWL(wrapper.getSourceOntology(), owlFormat , foo.getAbsolutePath());
    }
}

项目：owltools 文件：OboOntologyReleaseRunner.java

private void write(OWLOntologyManager manager, OWLOntology ont, OWLDocumentFormat format, OutputStream out) throws OWLOntologyStorageException {
    try {
        manager.saveOntology(ont, format, out);
    } finally {
        try {
            out.close();
        } catch (IOException e) {
            logWarn("Could not close stream.", e);
        } 
    }

}

项目：owlbuilder 文件：Owlbuilder.java

public Owlbuilder() throws Exception{
    config = new Config("");
    if (DBConnection.probeConnection()){
        connection = DBConnection.getDBConnection();
    }
    else{
        connection = DBConnection.getMockConnection();
    }
    testWrapper = new OWLGraphWrapper(targetIRI);
    rfactory = new Reasoner.ReasonerFactory();
    elkFactory = new ElkReasonerFactory();
    iriManager = connection.getIRIManager();
    final OWLDocumentFormat format = testWrapper.getManager().getOntologyFormat(testWrapper.getSourceOntology());
    format.asPrefixOWLOntologyFormat().setPrefix("doi", "http://dx.doi.org/");
}

项目：owlbuilder 文件：Owlbuilder.java

public Owlbuilder(AbstractConnection existingConnection) throws Exception{
    config = new Config("");
    connection = existingConnection;
    testWrapper = new OWLGraphWrapper(targetIRI);
    rfactory = new Reasoner.ReasonerFactory();
    elkFactory = new ElkReasonerFactory();
    iriManager = connection.getIRIManager();
    final OWLDocumentFormat format = testWrapper.getManager().getOntologyFormat(testWrapper.getSourceOntology());
    format.asPrefixOWLOntologyFormat().setPrefix("doi", "http://dx.doi.org/");

}

项目：neo4j-sparql-extension-yars 文件：QueryRewriterFactory.java

@Override
public OWLDocumentFormat getFormat() {
    return new TurtleDocumentFormat();
}

项目：owltools 文件：OWLHandler.java

private OWLDocumentFormat getOWLOntologyFormat() {
    return getOWLOntologyFormat(getFormat());
}

项目：owltools 文件：OldSimpleOwlSim.java

public void saveOntology(String fn) throws FileNotFoundException, OWLOntologyStorageException {
    FileOutputStream os = new FileOutputStream(new File(fn));
    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();

    owlOntologyManager.saveOntology(sourceOntology, owlFormat, os);
}

项目：owltools 文件：ParserWrapper.java

public void saveOWL(OWLOntology ont, String file) throws OWLOntologyStorageException, IOException {
    OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
    saveOWL(ont, owlFormat, file);
}

项目：owltools 文件：OortConfiguration.java

/**
 * @return the defaultFormat
 */
public OWLDocumentFormat getDefaultFormat() {
    return defaultFormat;
}

项目：owltools 文件：OortConfiguration.java

/**
 * @return the owlXMLFormat
 */
public OWLDocumentFormat getOwlXMLFormat() {
    return owlXMLFormat;
}

项目：owltools 文件：OortConfiguration.java

/**
 * @return the owlOFNFormat
 */
public OWLDocumentFormat getOwlOfnFormat() {
    return owlOFNFormat;
}

项目：neo4j-sparql-extension 文件：QueryRewriterFactory.java

@Override
public OWLDocumentFormat getFormat() {
    return new TurtleDocumentFormat();
}

项目：minerva 文件：BlazegraphMolecularModelManager.java

/**
 * Export the ABox for the given modelId in the given ontology format.<br>
 * Warning: The mapping from String to {@link OWLDocumentFormat} does not
 * map every format!
 * 
 * @param model
 * @param format
 * @return modelContent
 * @throws OWLOntologyStorageException
 */
public String exportModel(ModelContainer model, String format)
        throws OWLOntologyStorageException {
    OWLDocumentFormat ontologyFormat = getOWLOntologyFormat(format);
    if (ontologyFormat == null) {
        ontologyFormat = this.ontologyFormat;
    }
    return exportModel(model, ontologyFormat);
}