public OMEXMLMetadata getOmeXmlMetadata() { if (omeXmlMetadata == null) { try { omeXmlMetadata = getOmeXmlService().createOMEXMLMetadata(); } catch (ServiceException exc) { LOGGER.error("Could not create OME-XML metadata", exc); } } return omeXmlMetadata; }
@Override public OMEXMLMetadata createOMEXMLMetadata(final String xml) throws ServiceException { return omexmlService().createOMEXMLMetadata(xml); }
public OMEXMLMetadata getOmeXmlMetadata() { if (omeXmlMetadata == null) { try { omeXmlMetadata = getOmeXmlService().createOMEXMLMetadata(); } catch (ServiceException exc) { LOGGER.error("Could not create OME-XML metadata", exc); } } return omeXmlMetadata; }
@Override public OMEXMLMetadata createOMEXMLMetadata() throws ServiceException { return omexmlService().createOMEXMLMetadata(); }
@Override public OMEXMLMetadata createOMEXMLMetadata(final String xml, final String version) throws ServiceException { return omexmlService().createOMEXMLMetadata(xml, version); }
public IMetadata convertXml(MetadataRetrieve retrieve) throws ServiceException { IMetadata xmlMeta = service.createOMEXMLMetadata(); xmlMeta.createRoot(); service.convertMetadata(retrieve, xmlMeta); return xmlMeta; }
@Test public void testCreateOMEXMLMetadata() throws ServiceException { assertNotNull(service.createOMEXMLMetadata(xml)); }
@BeforeMethod public void setUp() throws Exception { ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); InputStream s = Upgrade201004Test.class.getResourceAsStream(XML_FILE); byte[] b = new byte[s.available()]; s.read(b); s.close(); xml = new String(b); metadata = service.createOMEXMLMetadata(xml); ome = (OME) metadata.getRoot(); }
@BeforeMethod public void setUp() throws Exception { ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); InputStream s = Upgrade201106Test.class.getResourceAsStream(XML_FILE); byte[] b = new byte[s.available()]; s.read(b); s.close(); xml = new String(b); metadata = service.createOMEXMLMetadata(xml); ome = (OME) metadata.getRoot(); }
@BeforeMethod public void setUp() throws Exception { ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); InputStream s = Upgrade200909Test.class.getResourceAsStream(XML_FILE); byte[] b = new byte[s.available()]; s.read(b); s.close(); xml = new String(b); metadata = service.createOMEXMLMetadata(xml); ome = (OME) metadata.getRoot(); }
@BeforeMethod public void setUp() throws Exception { ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); InputStream s = Upgrade200809Test.class.getResourceAsStream(XML_FILE); byte[] b = new byte[s.available()]; s.read(b); s.close(); xml = new String(b); metadata = service.createOMEXMLMetadata(xml); ome = (OME) metadata.getRoot(); }
@BeforeMethod public void setUp() throws Exception { ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); InputStream s = Upgrade201006Test.class.getResourceAsStream(XML_FILE); byte[] b = new byte[s.available()]; s.read(b); s.close(); xml = new String(b); metadata = service.createOMEXMLMetadata(xml); ome = (OME) metadata.getRoot(); }
@BeforeMethod public void setUp() throws DependencyException, ServiceException, IOException { ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); metadata = service.createOMEXMLMetadata(); }
@Test public void isOMEXMLMetadata() throws ServiceException { assertEquals(true, service.isOMEXMLMetadata(service.createOMEXMLMetadata())); }
@Parameters({"id"}) @BeforeClass public void parse(String id) throws Exception { ServiceFactory factory = new ServiceFactory(); service = factory.getInstance(OMEXMLService.class); metadata = service.createOMEXMLMetadata(); reader = new ImageReader(); reader.setMetadataStore(metadata); reader.setId(id); }
@BeforeMethod public void setUp() throws Exception { wd = Files.createTempDirectory(this.getClass().getName()); reader = new FakeReader(); ServiceFactory sf = new ServiceFactory(); service = sf.getInstance(OMEXMLService.class); reader.setMetadataStore(service.createOMEXMLMetadata()); reader.setFlattenedResolutions(false); }
private void setupServiceAndMetadata() throws DependencyException, ServiceException { // extract OME-XML string from metadata object MetadataRetrieve retrieve = getMetadataRetrieve(); ServiceFactory factory = new ServiceFactory(); service = factory.getInstance(OMEXMLService.class); OMEXMLMetadata originalOMEMeta = service.getOMEMetadata(retrieve); originalOMEMeta.resolveReferences(); String omexml = service.getOMEXML(originalOMEMeta); omeMeta = service.createOMEXMLMetadata(omexml); }
private void setupServiceAndMetadata() throws DependencyException, ServiceException { // extract OME-XML string from metadata object MetadataRetrieve retrieve = getMetadataRetrieve(); ServiceFactory factory = new ServiceFactory(); service = factory.getInstance(OMEXMLService.class); OMEXMLMetadata originalOMEMeta = service.getOMEMetadata(retrieve); originalOMEMeta.resolveReferences(); String omexml = service.getOMEXML(originalOMEMeta); omeMeta = service.createOMEXMLMetadata(omexml); }
@Test public void getOMEXMLVersion() throws ServiceException { assertEquals("2008-09", service.getOMEXMLVersion(xml)); assertEquals("2016-06", service.getOMEXMLVersion(service.createOMEXMLMetadata(xml))); }
private String getBinaryOnlyOMEXML( String file, String companion, String companionUUID) throws FormatException, IOException, DependencyException, ServiceException { ServiceFactory factory = new ServiceFactory(); OMEXMLService service = factory.getInstance(OMEXMLService.class); OMEXMLMetadata meta = service.createOMEXMLMetadata(); String uuid = "urn:uuid:" + getUUID(new Location(file).getName()); meta.setUUID(uuid); meta.setBinaryOnlyMetadataFile(new Location(companion).getName()); meta.setBinaryOnlyUUID(companionUUID); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot(); root.setCreator(FormatTools.CREATOR); return service.getOMEXML(meta); }