public int resolveReferences() { return model.resolveReferences(); }
public void setDatasetExperimenterGroupRef(String experimenterGroup, int datasetIndex) { // Parents: {u'OME': None} // ExperimenterGroupRef is reference and occurs more than once ExperimenterGroupRef experimenterGroup_reference = new ExperimenterGroupRef(); experimenterGroup_reference.setID(experimenterGroup); model.addReference( root.getDataset(datasetIndex), experimenterGroup_reference); }
public void setDatasetID(String id, int datasetIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfDatasetList() == datasetIndex) { o0.addDataset(new Dataset()); } Dataset o1 = o0.getDataset(datasetIndex); model.addModelObject(id, o1); o1.setID(id); }
@Test(groups={"disabled"}) public static void main(String[] args) throws Exception { InOutCurrentTest t = new InOutCurrentTest(); t.setUp("loci.formats.utests.ObjectBasedOMEModelMock"); System.out.println("###\n### XML\n###"); System.out.println(t.asString); t.testValidOMENode(); System.out.println("###\n### Model Objects\n###"); Map<String, OMEModelObject> objects = t.model.getModelObjects(); for (Entry<String, OMEModelObject> entry : objects.entrySet()) { System.out.println(String.format( "%s -- %s", entry.getKey(), entry.getValue().toString())); } System.out.println("###\n### References\n###"); Map<OMEModelObject, List<Reference>> references = t.model.getReferences(); for (Entry<OMEModelObject, List<Reference>> entry : references.entrySet()) { System.out.println(String.format( "%s -- %s", entry.getKey(), entry.getValue().toString())); } } }
public void setPlateID(String id, int plateIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfPlateList() == plateIndex) { o0.addPlate(new Plate()); } Plate o1 = o0.getPlate(plateIndex); model.addModelObject(id, o1); o1.setID(id); }
public int resolveReferences() { return model.resolveReferences(); }
public void setFolderROIRef(String roi, int folderIndex, int ROIRefIndex) { // Parents: {u'OME': None} // ROIRef is reference and occurs more than once ROIRef roiLinks_reference = new ROIRef(); roiLinks_reference.setID(roi); model.addReference( root.getFolder(folderIndex), roiLinks_reference); }
public void setProjectID(String id, int projectIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfProjectList() == projectIndex) { o0.addProject(new Project()); } Project o1 = o0.getProject(projectIndex); model.addModelObject(id, o1); o1.setID(id); }
@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(); }
public void setScreenAnnotationRef(String annotation, int screenIndex, int annotationRefIndex) { // Parents: {u'OME': None} // AnnotationRef is reference and occurs more than once AnnotationRef annotationLinks_reference = new AnnotationRef(); annotationLinks_reference.setID(annotation); model.addReference( root.getScreen(screenIndex), annotationLinks_reference); }
public void setScreenID(String id, int screenIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfScreenList() == screenIndex) { o0.addScreen(new Screen()); } Screen o1 = o0.getScreen(screenIndex); model.addModelObject(id, o1); o1.setID(id); }
/** * 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); } }
public void setDatasetExperimenterRef(String experimenter, int datasetIndex) { // Parents: {u'OME': None} // ExperimenterRef is reference and occurs more than once ExperimenterRef experimenter_reference = new ExperimenterRef(); experimenter_reference.setID(experimenter); model.addReference( root.getDataset(datasetIndex), experimenter_reference); }
public void setExperimenterGroupID(String id, int experimenterGroupIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfExperimenterGroupList() == experimenterGroupIndex) { o0.addExperimenterGroup(new ExperimenterGroup()); } ExperimenterGroup o1 = o0.getExperimenterGroup(experimenterGroupIndex); model.addModelObject(id, o1); o1.setID(id); }
/** * 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); } }
public void setFolderROIRef(String roi, int folderIndex, int ROIRefIndex) { // Parents: {u'OME': None} // ROIRef is reference and occurs more than once ROIRef roiLinks_reference = new ROIRef(); roiLinks_reference.setID(roi); model.addReference( root.getFolder(folderIndex), roiLinks_reference); }
public void setScreenID(String id, int screenIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfScreenList() == screenIndex) { o0.addScreen(new Screen()); } Screen o1 = o0.getScreen(screenIndex); model.addModelObject(id, o1); o1.setID(id); }
@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(); }
public void setImageROIRef(String roi, int imageIndex, int ROIRefIndex) { // Parents: {u'OME': None} // ROIRef is reference and occurs more than once ROIRef roiLinks_reference = new ROIRef(); roiLinks_reference.setID(roi); model.addReference( root.getImage(imageIndex), roiLinks_reference); }
public void setExperimentID(String id, int experimentIndex) { // Parents: {u'OME': None} // ID is not a reference OME o0 = root; if (o0.sizeOfExperimentList() == experimentIndex) { o0.addExperiment(new Experiment()); } Experiment o1 = o0.getExperiment(experimentIndex); model.addModelObject(id, o1); o1.setID(id); }