本文整理汇总了Java中org.semanticweb.owlapi.model.OWLDocumentFormat类的典型用法代码示例。如果您正苦于以下问题:Java OWLDocumentFormat类的具体用法?Java OWLDocumentFormat怎么用?Java OWLDocumentFormat使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
OWLDocumentFormat类属于org.semanticweb.owlapi.model包,在下文中一共展示了OWLDocumentFormat类的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: headerOWL
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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);
}
开发者ID:owlcollab,项目名称:owltools,代码行数:20,代码来源:OWLHandler.java
示例2: printCachedObjects
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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>();
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:26,代码来源:OWLHandler.java
示例3: testConversion
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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);
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:25,代码来源:PombeGAFOWLBridgeTest.java
示例4: testConversion
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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);
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:25,代码来源:GAFOWLBridgeTest.java
示例5: testConversion
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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);
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:25,代码来源:BasicAboxBridgeTest.java
示例6: testConversion
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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);
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:26,代码来源:MgiGAFOWLBridgeTest.java
示例7: testConversionToIndividuals
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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);
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:27,代码来源:MgiGAFOWLBridgeTest.java
示例8: getSuffix
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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";
}
开发者ID:owlcollab,项目名称:owltools,代码行数:17,代码来源:BridgeExtractor.java
示例9: saveOWL
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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);
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:25,代码来源:ParserWrapper.java
示例10: writeModel
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
/**
* 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){}
}
}
}
开发者ID:dgarijo,项目名称:Widoco,代码行数:23,代码来源:WidocoUtils.java
示例11: exportModel
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
/**
* 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;
}
开发者ID:geneontology,项目名称:minerva,代码行数:40,代码来源:CoreMolecularModelManager.java
示例12: gaf2OwlSimple
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
/**
* 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));
}
开发者ID:owlcollab,项目名称:owltools,代码行数:43,代码来源:GafCommandRunner.java
示例13: save
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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);
}
开发者ID:owlcollab,项目名称:owltools,代码行数:9,代码来源:BridgeExtractor.java
示例14: testMerge
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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));
}
开发者ID:owlcollab,项目名称:owltools,代码行数:34,代码来源:EquivalenceSetMergeUtilTest.java
示例15: testOnt
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@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());
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:15,代码来源:OWLGsonRendererTest.java
示例16: write
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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);
}
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:13,代码来源:OboOntologyReleaseRunner.java
示例17: Owlbuilder
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
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/");
}
开发者ID:pmidford,项目名称:owlbuilder,代码行数:16,代码来源:Owlbuilder.java
示例18: getFormat
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
@Override
public OWLDocumentFormat getFormat() {
return new TurtleDocumentFormat();
}
开发者ID:lszeremeta,项目名称:neo4j-sparql-extension-yars,代码行数:5,代码来源:QueryRewriterFactory.java
示例19: getOWLOntologyFormat
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
private OWLDocumentFormat getOWLOntologyFormat() {
return getOWLOntologyFormat(getFormat());
}
开发者ID:owlcollab,项目名称:owltools,代码行数:4,代码来源:OWLHandler.java
示例20: saveOntology
import org.semanticweb.owlapi.model.OWLDocumentFormat; //导入依赖的package包/类
public void saveOntology(String fn) throws FileNotFoundException, OWLOntologyStorageException {
FileOutputStream os = new FileOutputStream(new File(fn));
OWLDocumentFormat owlFormat = new RDFXMLDocumentFormat();
owlOntologyManager.saveOntology(sourceOntology, owlFormat, os);
}
开发者ID:owlcollab,项目名称:owltools,代码行数:7,代码来源:OldSimpleOwlSim.java
注:本文中的org.semanticweb.owlapi.model.OWLDocumentFormat类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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