public int resolveReferences() { return model.resolveReferences(); }
public int resolveReferences() { return model.resolveReferences(); }
@BeforeClass public void setUp() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.parse( this.getClass().getResourceAsStream("XMLAnnotationTest.ome")); OMEModel model = new OMEModelImpl(); // Read string XML in as a DOM tree and parse into the object hierarchy ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); }
/** * Constructs an OME root node. <b>NOTE:</b> This method is mostly here to * ensure type safety of return values as instances of service dependency * classes should not leak out of the interface. * @param xml String of XML to create the root node from. * @return An ome.xml.model.OMEModelObject subclass root node. * @throws IOException If there is an error reading from the string. * @throws SAXException If there is an error parsing the XML. * @throws ParserConfigurationException If there is an error preparing the * parsing infrastructure. */ private OMEXMLMetadataRoot createRoot(String xml) throws ServiceException { try { OMEModel model = new OMEModelImpl(); OMEXMLMetadataRoot ome = new OMEXMLMetadataRoot(XMLTools.parseDOM(xml).getDocumentElement(), model); model.resolveReferences(); return ome; } catch (Exception e) { throw new ServiceException(e); } }
/** * Constructs an OME root node. <b>NOTE:</b> This method is mostly here to * ensure type safety of return values as instances of service dependency * classes should not leak out of the interface. * @param xml String of XML to create the root node from. * @return An ome.xml.model.OMEModelObject subclass root node. * @throws IOException If there is an error reading from the string. * @throws SAXException If there is an error parsing the XML. * @throws ParserConfigurationException If there is an error preparing the * parsing infrastructure. */ private OMEXMLMetadataRoot createRoot(String xml) throws ServiceException { try { OMEModel model = new OMEModelImpl(); OMEXMLMetadataRoot ome = new OMEXMLMetadataRoot(XMLTools.parseDOM(xml).getDocumentElement(), model); model.resolveReferences(); return ome; } catch (Exception e) { throw new ServiceException(e); } }
@Test public void testGenericExcitationSourceValid() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); }
@Test public void testLightSourceType() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); }
@Test public void testMapAnnotationValid() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); }
@Test public void testGenericExcitationSourceValid() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); }
@Test public void testValidOMENode() throws EnumerationException { model = new OMEModelImpl(); // Read string XML in as a DOM tree and parse into the object hierarchy ome = new OMEXMLMetadataRoot(document.getDocumentElement(), model); model.resolveReferences(); assertNotNull(ome); assertEquals(1, ome.sizeOfImageList()); }
@Test public void testMapAnnotationValueContent() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); assertNotNull(ome); assertEquals(ome.getImage(0).getPixels().getID(), "Pixels:0"); assertNotNull(ome.getImage(0).getLinkedAnnotation(0)); MapAnnotation mapAnnotation = (MapAnnotation) ome.getImage(0).getLinkedAnnotation(0); List<MapPair> dataMap = mapAnnotation.getValue(); assertEquals(6, dataMap.size()); assertEquals("a", dataMap.get(0).getName()); assertEquals("1", dataMap.get(0).getValue()); assertEquals("d", dataMap.get(1).getName()); assertEquals("2", dataMap.get(1).getValue()); assertEquals("c", dataMap.get(2).getName()); assertEquals("3", dataMap.get(2).getValue()); assertEquals("b", dataMap.get(3).getName()); assertEquals("4", dataMap.get(3).getValue()); assertEquals("e", dataMap.get(4).getName()); assertEquals("5", dataMap.get(4).getValue()); assertEquals("c", dataMap.get(5).getName()); assertEquals("6", dataMap.get(5).getValue()); }
@Test public void testGenericExcitationSourceMapContent() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); assertNotNull(ome); assertEquals(ome.getImage(0).getPixels().getID(), "Pixels:0"); assertNotNull(ome.getImage(0).getImagingEnvironment()); ImagingEnvironment imagingEnvironment = ome.getImage(0).getImagingEnvironment(); List<MapPair> dataMap = imagingEnvironment.getMap(); assertEquals(6, dataMap.size()); assertPair(dataMap, 0, "a", "1"); assertPair(dataMap, 1, "d", "2"); assertPair(dataMap, 2, "c", "3"); assertPair(dataMap, 3, "b", "4"); assertPair(dataMap, 4, "e", "5"); assertPair(dataMap, 5, "c", "6"); }
@Test public void testGenericExcitationSourceMapContent() throws Exception { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); Document document = parser.newDocument(); // Produce a valid OME DOM element hierarchy Element root = ome.asXMLElement(document); SPWModelMock.postProcess(root, document, false); OMEModel model = new OMEModelImpl(); ome = new OME(document.getDocumentElement(), model); model.resolveReferences(); assertNotNull(ome); assertEquals(ome.getImage(0).getPixels().getChannel(0).getLightSourceSettings().getID(), "LightSource:0"); assertNotNull(ome.getInstrument(0).getLightSource(0)); GenericExcitationSource geSource = (GenericExcitationSource) ome.getInstrument(0).getLightSource(0); List<MapPair> dataMap = geSource.getMap(); assertEquals(6, dataMap.size()); assertPair(dataMap, 0, "a", "1"); assertPair(dataMap, 1, "d", "2"); assertPair(dataMap, 2, "c", "3"); assertPair(dataMap, 3, "b", "4"); assertPair(dataMap, 4, "e", "5"); assertPair(dataMap, 5, "c", "6"); }