// Function to build observation fact
public ObservationFactType getObservationFactType() {
Date currentDate = new Date();
ObservationFactType obType = new ObservationFactType();
DTOFactory dtoFactory = new DTOFactory();
obType.setEndDate(dtoFactory.getXMLGregorianCalendar(currentDate.getTime()));
obType.setConceptCd("i2b2:60004");
obType.setConfidenceNum(1d);
obType.setEncounterIde(getEncounterIde());
obType.setPatientIde(getPatientIde());
obType.setSourcesystemCd("i2b2");
obType.setTvalChar("tval");
obType.setNvalNum(100.0);
obType.setObservationBlob("BLOB");
return obType;
}
public ConstrainByDate writeTimeConstrain() {
ConstrainByDate timeConstrain = new ConstrainByDate();
DTOFactory dtoFactory = new DTOFactory();
if (startTime() != -1) {
ConstrainDateType constraindateType = new ConstrainDateType();
constraindateType.setValue(
dtoFactory.getXMLGregorianCalendarDate(startYear(), startMonth(), startDay()));
timeConstrain.setDateFrom(constraindateType);
}
if (endTime() != -1) {
ConstrainDateType constraindateType = new ConstrainDateType();
constraindateType.setValue(
dtoFactory.getXMLGregorianCalendarDate(endYear(), endMonth(), endDay()));
timeConstrain.setDateTo(constraindateType);
}
return timeConstrain;
}
public ConstrainByDate writeTimeConstrain() {
ConstrainByDate timeConstrain = new ConstrainByDate();
DTOFactory dtoFactory = new DTOFactory();
TimeZone tz = Calendar.getInstance().getTimeZone();
GregorianCalendar cal = new GregorianCalendar(tz);
// cal.get(Calendar.ZONE_OFFSET);
int zt_offset = (cal.get(Calendar.ZONE_OFFSET) + cal.get(Calendar.DST_OFFSET)) / 60000;
// log.info("Timezone: "+tz.getID()+" : "+zt_offset);
if (startTime() != -1) {
ConstrainDateType constraindateType = new ConstrainDateType();
XMLGregorianCalendar xmlC =
dtoFactory.getXMLGregorianCalendarDate(startYear(), startMonth() + 1, startDay());
xmlC.setTimezone(zt_offset); // 0);//-5*60);
xmlC.setHour(0);
xmlC.setMinute(0);
xmlC.setSecond(0);
constraindateType.setValue(xmlC);
timeConstrain.setDateFrom(constraindateType);
}
if (endTime() != -1) {
ConstrainDateType constraindateType = new ConstrainDateType();
XMLGregorianCalendar xmlC =
dtoFactory.getXMLGregorianCalendarDate(endYear(), endMonth() + 1, endDay());
xmlC.setTimezone(zt_offset); // 0);//-5*60);
xmlC.setHour(0);
xmlC.setMinute(0);
xmlC.setSecond(0);
constraindateType.setValue(xmlC);
timeConstrain.setDateTo(constraindateType);
}
return timeConstrain;
}
/**
* Function to build i2b2 message header
*
* @return MessageHeader object
*/
public MessageHeaderType getMessageHeader() {
MessageHeaderType messageHeader = new MessageHeaderType();
messageHeader.setI2B2VersionCompatible(
new BigDecimal(
Messages.getString("OntologyRequestData.i2b2VersionCompatible"))); // $NON-NLS-1$
ApplicationType appType = new ApplicationType();
appType.setApplicationName(
Messages.getString("OntologyRequestData.SendingApplicationName")); // $NON-NLS-1$
appType.setApplicationVersion(
Messages.getString("OntologyRequestData.SendingApplicationVersion")); // $NON-NLS-1$
messageHeader.setSendingApplication(appType);
FacilityType facility = new FacilityType();
facility.setFacilityName(
Messages.getString("OntologyRequestData.SendingFacilityName")); // $NON-NLS-1$
messageHeader.setSendingFacility(facility);
ApplicationType appType2 = new ApplicationType();
appType2.setApplicationVersion(
Messages.getString("OntologyRequestData.ReceivingApplicationVersion")); // $NON-NLS-1$
appType2.setApplicationName(
Messages.getString("OntologyRequestData.ReceivingApplicationName")); // $NON-NLS-1$
messageHeader.setReceivingApplication(appType2);
FacilityType facility2 = new FacilityType();
facility2.setFacilityName(
Messages.getString("OntologyRequestData.ReceivingFacilityName")); // $NON-NLS-1$
messageHeader.setReceivingFacility(facility2);
Date currentDate = new Date();
DTOFactory factory = new DTOFactory();
messageHeader.setDatetimeOfMessage(factory.getXMLGregorianCalendar(currentDate.getTime()));
SecurityType secType = new SecurityType();
secType.setDomain(UserInfoBean.getInstance().getUserDomain());
secType.setUsername(UserInfoBean.getInstance().getUserName());
PasswordType ptype = new PasswordType();
ptype.setIsToken(UserInfoBean.getInstance().getUserPasswordIsToken());
ptype.setTokenMsTimeout(UserInfoBean.getInstance().getUserPasswordTimeout());
ptype.setValue(UserInfoBean.getInstance().getUserPassword());
secType.setPassword(ptype);
messageHeader.setSecurity(secType);
MessageControlIdType mcIdType = new MessageControlIdType();
mcIdType.setInstanceNum(0);
mcIdType.setMessageNum(generateMessageId());
messageHeader.setMessageControlId(mcIdType);
ProcessingIdType proc = new ProcessingIdType();
proc.setProcessingId(Messages.getString("OntologyRequestData.ProcessingId")); // $NON-NLS-1$
proc.setProcessingMode(Messages.getString("OntologyRequestData.ProcessingMode")); // $NON-NLS-1$
messageHeader.setProcessingId(proc);
messageHeader.setAcceptAcknowledgementType(
Messages.getString("OntologyRequestData.AcceptAcknowledgementType")); // $NON-NLS-1$
messageHeader.setApplicationAcknowledgementType(
Messages.getString("OntologyRequestData.ApplicationAcknowledgementType")); // $NON-NLS-1$
messageHeader.setCountryCode(
Messages.getString("OntologyRequestData.CountryCode")); // $NON-NLS-1$
messageHeader.setProjectId(UserInfoBean.getInstance().getProjectId());
return messageHeader;
}
public String wirteQueryXML() {
DTOFactory dtoFactory = new DTOFactory();
// TimeZone pdt = TimeZone.getTimeZone("EST");
// DatatypeFactory dataTypeFactory = null;
// try {
// dataTypeFactory = DatatypeFactory.newInstance();
// XMLGregorianCalendar xmlCalendar =
// dataTypeFactory.newXMLGregorianCalendarDate(2006, 9, 21, -5*60);
// TimeZone pdt = xmlCalendar.getgetTimezone();
// }
// catch (DatatypeConfigurationException e) {
// e.printStackTrace();
// }
// RequestType requestType = new RequestType();
// requestType.setSpecificityScale(specificity());
QueryDefinitionType queryDefinitionType = new QueryDefinitionType();
QueryDefinitionRequestType queryDefinitionRequestType = new QueryDefinitionRequestType();
for (int i = 0; i < panelCount; i++) {
ConceptTreePanel panel = getTreePanel(i);
ArrayList<QueryConceptTreeNodeData> nodelist = panel.data().getItems();
if ((nodelist != null) && (nodelist.size() > 0)) {
System.out.println(
"Panel: "
+ panel.getGroupName()
+ " Excluded: "
+ ((panel.data().exclude()) ? "yes" : "no"));
PanelType panelType = new PanelType();
panelType.setInvert((panel.data().exclude()) ? 1 : 0);
PanelType.TotalItemOccurrences totalItemOccurrences = new PanelType.TotalItemOccurrences();
totalItemOccurrences.setValue(panel.getOccurrenceTimes());
panelType.setTotalItemOccurrences(totalItemOccurrences);
panelType.setPanelNumber(i + 1);
// if(panel.data().startTime() != -1) {
// panelType.setPanelDateFrom(//dataTypeFactory.
// newXMLGregorianCalendarDate(
// dtoFactory.getXMLGregorianCalendarDate(panel.data().startYear(
// ),
// panel.data().startMonth(), panel.data().startDay()));
// }
// if(panel.data().endTime() != -1) {
// panelType.setPanelDateTo(//dataTypeFactory.
// newXMLGregorianCalendarDate(
// dtoFactory.getXMLGregorianCalendarDate(panel.data().endYear(),
// panel.data().endMonth(), panel.data().endDay()));
// }
for (int j = 0; j < nodelist.size(); j++) {
QueryConceptTreeNodeData node = nodelist.get(j);
System.out.println("\tItem: " + node.fullname());
// create item
ItemType itemType = new ItemType();
// itemType.setConstrainByDate(.setDateFrom(dtoFactory.
// getXMLGregorianCalendarDate(2006,
// 10, 4)));
itemType.setItemKey(node.fullname());
itemType.setItemName(node.name());
// mm removed
// itemType.setItemTable(node.lookuptable());
itemType.setTooltip(node.tooltip());
itemType.setHlevel(Integer.parseInt(node.hlevel()));
itemType.setClazz("ENC");
ConstrainByDate cDate = new ConstrainByDate();
ConstrainDateType constrinDataType = new ConstrainDateType();
constrinDataType.setValue(
dtoFactory.getXMLGregorianCalendarDate(
node.startYear(), node.startMonth(), node.startDay()));
if (node.startTime() != -1) {
cDate.setDateFrom(constrinDataType);
}
if (node.endTime() != -1) {
cDate.setDateTo(constrinDataType);
}
itemType.getConstrainByDate().add(cDate);
panelType.getItem().add(itemType);
}
queryDefinitionType.getPanel().add(panelType);
}
}
// create infotype
InfoType infoType = new InfoType();
infoType.setValue("INFO");
infoType.setUrl("http://www.ibm.com");
// create header
PsmQryHeaderType headerType = new PsmQryHeaderType();
UserType userType = new UserType();
userType.setLogin(UserInfoBean.getInstance().getUserName());
userType.setValue(UserInfoBean.getInstance().getUserName());
headerType.setUser(userType);
headerType.setRequestType(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION);
if (queryName == null) {
queryName =
getTreePanel(0).data().getItems().get(0).name()
+ "_"
+ generateMessageId().substring(0, 4);
}
queryDefinitionType.setQueryName(queryName);
queryDefinitionRequestType.setQueryDefinition(queryDefinitionType);
RequestHeaderType requestHeader = new RequestHeaderType();
requestHeader.setResultWaittimeMs(180000);
BodyType bodyType = new BodyType();
edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory psmOf =
new edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory();
bodyType.getAny().add(psmOf.createPsmheader(headerType));
bodyType.getAny().add(psmOf.createRequest(queryDefinitionRequestType));
// new QueryToolDTOFactory().buildBodyType(headerType,
// queryDefinitionRequestType, null);
MessageHeaderType messageHeader = getMessageHeader();
RequestMessageType requestMessageType = new RequestMessageType();
requestMessageType.setMessageBody(bodyType);
requestMessageType.setMessageHeader(messageHeader);
requestMessageType.setRequestHeader(requestHeader);
// dtoFactory.getRequestMessageType(messageHeader, requestHeader,
// bodyType);
JAXBUtil jaxbUtil = PreviousQueryJAXBUtil.getJAXBUtil();
StringWriter strWriter = new StringWriter();
try {
edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory of =
new edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory();
jaxbUtil.marshaller(of.createRequest(requestMessageType), strWriter);
} catch (Exception e) {
e.printStackTrace();
}
return strWriter.toString();
}