public String setXmlContent() {
// if (!xmlContent.equals("")) {
// return "";
// }
// calling getTermInfo to get the xml content
try {
GetTermInfoType termInfoType = new GetTermInfoType();
termInfoType.setMax(null); // Integer.parseInt(System.getProperty(
// "OntMax")));
termInfoType.setHiddens(Boolean.parseBoolean("true"));
termInfoType.setSynonyms(Boolean.parseBoolean("false"));
// log.info("sent : " + parentType.getMax() +
// System.getProperty("OntMax") + System.getProperty("OntHiddens")
// + System.getProperty("OntSynonyms") );
// parentType.setMax(150);
termInfoType.setBlob(true);
// parentType.setType("all");
termInfoType.setSelf(fullname());
// Long time = System.currentTimeMillis();
// log.info("making web service call " + time);
GetTermInfoResponseMessage msg = new GetTermInfoResponseMessage();
StatusType procStatus = null;
// while(procStatus == null ||
// !procStatus.getType().equals("DONE")){
String response = OntServiceDriver.getTermInfo(termInfoType, "");
log.debug("Ontology service getTermInfo response: " + response);
procStatus = msg.processResult(response);
// log.info(procStatus.getType());
// log.info(procStatus.getValue());
if (!procStatus.getType().equals("DONE")) {
return "error";
}
ConceptsType allConcepts = msg.doReadConcepts();
// List<ConceptType> concepts = allConcepts.getConcept();
StringWriter strWriter = new StringWriter();
try {
// strWriter = new StringWriter();
DndType dnd = new DndType();
edu.harvard.i2b2.crcxmljaxb.datavo.vdo.ObjectFactory vdoOf =
new edu.harvard.i2b2.crcxmljaxb.datavo.vdo.ObjectFactory();
dnd.getAny().add(vdoOf.createConcepts(allConcepts));
edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory of =
new edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory();
PatientMappingJAXBUtil.getJAXBUtil().marshaller(of.createPluginDragDrop(dnd), strWriter);
} catch (JAXBUtilException e) {
// log.error("Error marshalling Ont drag text");
return "error";
}
log.debug("Node xml set to: " + strWriter.toString());
xmlContent(strWriter.toString());
return "";
} catch (Exception e) {
e.printStackTrace();
return "error";
}
}
public void updateNodeMetaDataXML() {
try {
boolean hasValue = false;
SAXBuilder parser = new SAXBuilder();
GetTermInfoType vocab = new GetTermInfoType();
vocab.setHiddens(true);
vocab.setSynonyms(false);
vocab.setMax(200);
vocab.setType("default");
vocab.setBlob(true);
vocab.setSelf(this.fullname());
String xmlContent = OntServiceDriver.getTermInfo(vocab, "");
GetTermInfoResponseMessage msg = new GetTermInfoResponseMessage();
StatusType procStatus = null;
// while(procStatus == null ||
// !procStatus.getType().equals("DONE")){
// String response = OntServiceDriver.getTermInfo(termInfoType, "");
// log.debug("Ontology service getTermInfo response: " + response);
procStatus = msg.processResult(xmlContent);
// log.info(procStatus.getType());
// log.info(procStatus.getValue());
// if (!procStatus.getType().equals("DONE")) {
// return "error";
// }
ConceptsType allConcepts = msg.doReadConcepts();
StringWriter strWriter = new StringWriter();
try {
// strWriter = new StringWriter();
DndType dnd = new DndType();
edu.harvard.i2b2.crcxmljaxb.datavo.vdo.ObjectFactory vdoOf =
new edu.harvard.i2b2.crcxmljaxb.datavo.vdo.ObjectFactory();
dnd.getAny().add(vdoOf.createConcepts(allConcepts));
edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory of =
new edu.harvard.i2b2.crcxmljaxb.datavo.dnd.ObjectFactory();
PatientMappingJAXBUtil.getJAXBUtil().marshaller(of.createPluginDragDrop(dnd), strWriter);
} catch (JAXBUtilException e) {
// log.error("Error marshalling Ont drag text");
// return "error";
}
log.debug("Node xml set to: " + strWriter.toString());
xmlContent(strWriter.toString());
java.io.StringReader xmlStringReader = new java.io.StringReader(xmlContent);
org.jdom.Document tableDoc = parser.build(xmlStringReader);
org.jdom.Element elementMsgBody =
tableDoc.getRootElement().getChild("message_body"); // , Namespace.getNamespace(
// "http://www.i2b2.org/xsd/cell/ont/1.1/"
// ));
org.jdom.Element tableXml =
elementMsgBody.getChild(
"concepts", Namespace.getNamespace("http://www.i2b2.org/xsd/cell/ont/1.1/"));
List conceptChildren = tableXml.getChildren();
for (Iterator itr = conceptChildren.iterator(); itr.hasNext(); ) {
Element conceptXml = (org.jdom.Element) itr.next();
// String conceptText = conceptXml.getText().trim();
Element conTableXml = conceptXml; // .getChildren().get(0);
org.jdom.Element nameXml = conTableXml.getChild("name");
String c_name = nameXml.getText();
// titleName(c_name);
// Element visualAttribs = conTableXml
// .getChild("visualattributes");
// String sVisualAttribs = visualAttribs.getText().trim();
Element metadataAttribs = conTableXml.getChild("metadataxml");
Element valuedataAttribs = metadataAttribs.getChild("ValueMetadata");
if ((metadataAttribs != null) && (valuedataAttribs != null)) {
log.debug("Has value");
hasValue = true;
this.hasValue(hasValue);
Element dataTypeElement = valuedataAttribs.getChild("DataType");
if (dataTypeElement != null && dataTypeElement.getTextTrim().equalsIgnoreCase("Enum")) {
// add text values to node data
this.valueModel().hasEnumValue(true);
Element enumElement = valuedataAttribs.getChild("EnumValues");
for (int i = 0; i < enumElement.getChildren().size(); i++) {
Element valElement = (Element) enumElement.getChildren().get(i);
String valString = new String(valElement.getTextTrim());
this.valueModel().enumValues.add(valString);
}
log.debug("Got vals: " + this.valueModel().enumValues.size());
} else if (dataTypeElement != null
&& (dataTypeElement.getTextTrim().equalsIgnoreCase("String")
|| dataTypeElement.getTextTrim().equalsIgnoreCase("LargeString"))) {
// add text values to node data
this.valueModel().hasStringValue(true);
Element maxLengthElement = valuedataAttribs.getChild("MaxStringLength");
String valString = new String(maxLengthElement.getTextTrim());
if (!valString.equalsIgnoreCase("")) {
valueModel().searchStrLength(Integer.parseInt(valString));
}
if (dataTypeElement.getTextTrim().equalsIgnoreCase("LargeString")) {
this.valueModel().isLongText(true);
}
/*Element enumElement = valuedataAttribs
.getChild("EnumValues");
for (int i = 0; i < enumElement.getChildren().size(); i++) {
Element valElement = (Element) enumElement
.getChildren().get(i);
String valString = new String(valElement
.getTextTrim());
String valDisplayString = new String(valElement
.getAttributeValue("description"));
if(valDisplayString.equalsIgnoreCase("")) {
valDisplayString = valString;
}
modifierValuePropertyData.enumValues.add(valString);
modifierValuePropertyData.enumValueNames.add(valDisplayString);
}
log.debug("Got vals: "
+ this.modifierValuePropertyData.enumValues.size());*/
}
if (valuedataAttribs.getChild("Oktousevalues") != null
&& valuedataAttribs.getChild("Oktousevalues").getText().equalsIgnoreCase("Y")) {
this.valueModel().okToUseValue(true);
}
if (valuedataAttribs.getChild("Flagstouse") == null
|| valuedataAttribs.getChild("Flagstouse").getText().equalsIgnoreCase("")) {
this.valueModel().okToUseValueFlag(false);
}
Element unitElement = valuedataAttribs.getChild("UnitValues");
if (unitElement != null) {
for (int i = 0; i < unitElement.getChildren().size(); i++) {
Element element = (Element) unitElement.getChildren().get(i);
if (element.getName().equalsIgnoreCase("NormalUnits")
|| element.getName().equalsIgnoreCase("EqualUnits")) {
String unitString = new String(element.getTextTrim());
// this.valueModel().units.add(new UnitsData(unitString, 1, false));
} else if (element.getName().equalsIgnoreCase("ConvertingUnits")) {
Element cunitElement = element.getChild("Units");
String unitString = new String(cunitElement.getTextTrim());
Element mfElement = element.getChild("MultiplyingFactor");
// double mf = Double.parseDouble(mfElement.getTextTrim());
// this.valueModel.units.add(new UnitsData(unitString, mf, true));
}
}
log.debug("Got vals: " + this.valueModel().enumValues.size());
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
