/**
* Updates FilterRef 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 (!"FilterRef".equals(tagName)) {
LOGGER.debug("Expecting node name of FilterRef got {}", tagName);
}
if (!element.hasAttribute("ID") && getID() == null) {
// TODO: Should be its own exception
throw new RuntimeException(String.format("FilterRef 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);
}
}
/**
* Updates Dichroic 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 (!"Dichroic".equals(tagName)) {
LOGGER.debug("Expecting node name of Dichroic got {}", tagName);
}
if (!element.hasAttribute("ID") && getID() == null) {
// TODO: Should be its own exception
throw new RuntimeException(String.format("Dichroic 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);
}
// *** IGNORING *** Skipped back reference Instrument_BackReference
// *** IGNORING *** Skipped back reference FilterSet_BackReference
// *** IGNORING *** Skipped back reference LightPath_BackReference
}
/**
* 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);
}
}
