/**
* Updates Screen recursively from an XML DOM tree. <b>NOTE:</b> No properties are removed, only
* added or updated.
*
* @param element Root of the XML DOM tree to construct a model object graph from.
* @param model Handler for the OME model which keeps track of instances and references seen
* during object population.
* @throws EnumerationException If there is an error instantiating an enumeration during model
* object creation.
*/
public void update(Element element, OMEModel model) throws EnumerationException {
super.update(element, model);
String tagName = element.getTagName();
if (!"Screen".equals(tagName)) {
LOGGER.debug("Expecting node name of Screen got {}", tagName);
}
if (element.hasAttribute("Name")) {
// Attribute property Name
setName(String.valueOf(element.getAttribute("Name")));
}
if (element.hasAttribute("ProtocolDescription")) {
// Attribute property ProtocolDescription
setProtocolDescription(String.valueOf(element.getAttribute("ProtocolDescription")));
}
if (element.hasAttribute("ProtocolIdentifier")) {
// Attribute property ProtocolIdentifier
setProtocolIdentifier(String.valueOf(element.getAttribute("ProtocolIdentifier")));
}
if (element.hasAttribute("ReagentSetDescription")) {
// Attribute property ReagentSetDescription
setReagentSetDescription(String.valueOf(element.getAttribute("ReagentSetDescription")));
}
if (element.hasAttribute("Type")) {
// Attribute property Type
setType(String.valueOf(element.getAttribute("Type")));
}
if (!element.hasAttribute("ID") && getID() == null) {
// TODO: Should be its own exception
throw new RuntimeException(String.format("Screen missing required ID property."));
}
if (element.hasAttribute("ID")) {
// ID property
setID(String.valueOf(element.getAttribute("ID")));
// Adding this model object to the model handler
model.addModelObject(getID(), this);
}
if (element.hasAttribute("ReagentSetIdentifier")) {
// Attribute property ReagentSetIdentifier
setReagentSetIdentifier(String.valueOf(element.getAttribute("ReagentSetIdentifier")));
}
List<Element> Description_nodeList = getChildrenByTagName(element, "Description");
if (Description_nodeList.size() > 1) {
// TODO: Should be its own Exception
throw new RuntimeException(
String.format("Description node list size %d != 1", Description_nodeList.size()));
} else if (Description_nodeList.size() != 0) {
// Element property Description which is not complex (has no
// sub-elements)
setDescription(String.valueOf(Description_nodeList.get(0).getTextContent()));
}
// Element property Reagent which is complex (has
// sub-elements) and occurs more than once
List<Element> Reagent_nodeList = getChildrenByTagName(element, "Reagent");
for (Element Reagent_element : Reagent_nodeList) {
addReagent(new Reagent(Reagent_element, model));
}
// Element reference PlateRef
List<Element> PlateRef_nodeList = getChildrenByTagName(element, "PlateRef");
for (Element PlateRef_element : PlateRef_nodeList) {
PlateRef plateLinks_reference = new PlateRef();
plateLinks_reference.setID(PlateRef_element.getAttribute("ID"));
model.addReference(this, plateLinks_reference);
}
// Element reference AnnotationRef
List<Element> AnnotationRef_nodeList = getChildrenByTagName(element, "AnnotationRef");
for (Element AnnotationRef_element : AnnotationRef_nodeList) {
AnnotationRef annotationLinks_reference = new AnnotationRef();
annotationLinks_reference.setID(AnnotationRef_element.getAttribute("ID"));
model.addReference(this, annotationLinks_reference);
}
}
/**
* Updates OME recursively from an XML DOM tree. <b>NOTE:</b> No properties are removed, only
* added or updated.
*
* @param element Root of the XML DOM tree to construct a model object graph from.
* @param model Handler for the OME model which keeps track of instances and references seen
* during object population.
* @throws EnumerationException If there is an error instantiating an enumeration during model
* object creation.
*/
public void update(Element element, OMEModel model) throws EnumerationException {
super.update(element, model);
String tagName = element.getTagName();
if (!"OME".equals(tagName)) {
LOGGER.debug("Expecting node name of OME got {}", tagName);
}
if (element.hasAttribute("UUID")) {
// Attribute property UUID
setUUID(String.valueOf(element.getAttribute("UUID")));
}
if (element.hasAttribute("Creator")) {
// Attribute property Creator
setCreator(String.valueOf(element.getAttribute("Creator")));
}
// Element property Project which is complex (has
// sub-elements) and occurs more than once
List<Element> Project_nodeList = getChildrenByTagName(element, "Project");
for (Element Project_element : Project_nodeList) {
addProject(new Project(Project_element, model));
}
// Element property Dataset which is complex (has
// sub-elements) and occurs more than once
List<Element> Dataset_nodeList = getChildrenByTagName(element, "Dataset");
for (Element Dataset_element : Dataset_nodeList) {
addDataset(new Dataset(Dataset_element, model));
}
// Element property Experiment which is complex (has
// sub-elements) and occurs more than once
List<Element> Experiment_nodeList = getChildrenByTagName(element, "Experiment");
for (Element Experiment_element : Experiment_nodeList) {
addExperiment(new Experiment(Experiment_element, model));
}
// Element property Plate which is complex (has
// sub-elements) and occurs more than once
List<Element> Plate_nodeList = getChildrenByTagName(element, "Plate");
for (Element Plate_element : Plate_nodeList) {
addPlate(new Plate(Plate_element, model));
}
// Element property Screen which is complex (has
// sub-elements) and occurs more than once
List<Element> Screen_nodeList = getChildrenByTagName(element, "Screen");
for (Element Screen_element : Screen_nodeList) {
addScreen(new Screen(Screen_element, model));
}
// Element property Experimenter which is complex (has
// sub-elements) and occurs more than once
List<Element> Experimenter_nodeList = getChildrenByTagName(element, "Experimenter");
for (Element Experimenter_element : Experimenter_nodeList) {
addExperimenter(new Experimenter(Experimenter_element, model));
}
// Element property ExperimenterGroup which is complex (has
// sub-elements) and occurs more than once
List<Element> ExperimenterGroup_nodeList = getChildrenByTagName(element, "ExperimenterGroup");
for (Element ExperimenterGroup_element : ExperimenterGroup_nodeList) {
addExperimenterGroup(new ExperimenterGroup(ExperimenterGroup_element, model));
}
// Element property Instrument which is complex (has
// sub-elements) and occurs more than once
List<Element> Instrument_nodeList = getChildrenByTagName(element, "Instrument");
for (Element Instrument_element : Instrument_nodeList) {
addInstrument(new Instrument(Instrument_element, model));
}
// Element property Image which is complex (has
// sub-elements) and occurs more than once
List<Element> Image_nodeList = getChildrenByTagName(element, "Image");
for (Element Image_element : Image_nodeList) {
addImage(new Image(Image_element, model));
}
List<Element> StructuredAnnotations_nodeList =
getChildrenByTagName(element, "StructuredAnnotations");
if (StructuredAnnotations_nodeList.size() > 1) {
// TODO: Should be its own Exception
throw new RuntimeException(
String.format(
"StructuredAnnotations node list size %d != 1",
StructuredAnnotations_nodeList.size()));
} else if (StructuredAnnotations_nodeList.size() != 0) {
// Element property StructuredAnnotations which is complex (has
// sub-elements)
setStructuredAnnotations(
new StructuredAnnotations((Element) StructuredAnnotations_nodeList.get(0), model));
}
// Element property ROI which is complex (has
// sub-elements) and occurs more than once
List<Element> ROI_nodeList = getChildrenByTagName(element, "ROI");
for (Element ROI_element : ROI_nodeList) {
addROI(new ROI(ROI_element, model));
}
List<Element> BinaryOnly_nodeList = getChildrenByTagName(element, "BinaryOnly");
if (BinaryOnly_nodeList.size() > 1) {
// TODO: Should be its own Exception
throw new RuntimeException(
String.format("BinaryOnly node list size %d != 1", BinaryOnly_nodeList.size()));
} else if (BinaryOnly_nodeList.size() != 0) {
// Element property BinaryOnly which is complex (has
// sub-elements)
setBinaryOnly(new BinaryOnly((Element) BinaryOnly_nodeList.get(0), model));
}
}
