private ISPYGPIntegrationQueryDTO createGPIntegrationQueryDTO(
GpIntegrationForm gpQueryForm, HttpSession session) {
ISPYGPIntegrationQueryDTO gpQueryDTO =
(ISPYGPIntegrationQueryDTO)
ApplicationFactory.newQueryDTO(QueryType.PROBESET_CLONEID_QUERY_FOR_HOA);
gpQueryDTO.setQueryName(gpQueryForm.getAnalysisResultName());
HashMap<String, UserList> patientLists = new HashMap<String, UserList>();
HashMap<String, Set<TimepointType>> timepointLists = new HashMap<String, Set<TimepointType>>();
UserListBeanHelper listHelper = new UserListBeanHelper(session);
String groupTimepoint = null;
String groupName = null;
String timePointName = null;
if (gpQueryForm.getSelectedGroups() != null && gpQueryForm.getSelectedGroups().length > 0) {
for (int i = 0; i < gpQueryForm.getSelectedGroups().length; i++) {
groupTimepoint = gpQueryForm.getSelectedGroups()[i];
int index = groupTimepoint.lastIndexOf("---");
groupName = groupTimepoint.substring(0, index);
timePointName = groupTimepoint.substring(index + 3);
UserList userList = listHelper.getUserList(groupName);
patientLists.put(groupTimepoint, userList);
String[] times = timePointName.split("-");
String fixedTimepointString = null;
Set<TimepointType> set = new HashSet<TimepointType>();
for (String time : times) {
TimepointType fixedTimepointBase; // timepoint for both queryDTOs
fixedTimepointString = EnumHelper.getEnumTypeName(time, TimepointType.values());
if (fixedTimepointString != null) {
fixedTimepointBase = TimepointType.valueOf(fixedTimepointString);
set.add(fixedTimepointBase);
}
}
timepointLists.put(groupTimepoint, set);
}
}
gpQueryDTO.setPatientLists(patientLists);
gpQueryDTO.setTimepointLists(timepointLists);
// UserListBeanHelper listHelper = new UserListBeanHelper(session);
if (gpQueryForm.getGeneSetName() != null
&& (!gpQueryForm.getGeneSetName().equals("")
&& !gpQueryForm.getGeneSetName().equals("none"))) {
geneIdentifierDECollection = listHelper.getGeneDEforList(gpQueryForm.getGeneSetName());
if (geneIdentifierDECollection != null && !geneIdentifierDECollection.isEmpty()) {
logger.debug("geneIdentifierDECollection was found");
gpQueryDTO.setGeneIdentifierDEs(geneIdentifierDECollection);
gpQueryDTO.setReportersName(gpQueryForm.getGeneSetName());
} else {
logger.debug("geneIdentifierDECollection could not be found");
}
}
// Create arrayPlatfrom DEs
if (gpQueryForm.getArrayPlatform() != "" || gpQueryForm.getArrayPlatform().length() != 0) {
ArrayPlatformDE arrayPlatformDE = new ArrayPlatformDE(gpQueryForm.getArrayPlatform());
gpQueryDTO.setArrayPlatformDE(arrayPlatformDE);
}
return gpQueryDTO;
}
public ActionForward setup(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
GpIntegrationForm gpForm = (GpIntegrationForm) form;
/*setup the defined Disease query names and the list of samples selected from a Resultset*/
ClinicalGroupRetriever clinicalGroupRetriever =
new ClinicalGroupRetriever(request.getSession());
gpForm.setExistingGroupsList(clinicalGroupRetriever.getClinicalGroupsCollection());
UserListBeanHelper listHelper = new UserListBeanHelper(request.getSession());
// fetch the users gene groups populate the dropdown
List<String> names = (List<String>) listHelper.getGenericListNames(ListType.Gene);
List<LabelValueBean> gsNameList = new ArrayList<LabelValueBean>();
for (String listName : names) {
gsNameList.add(new LabelValueBean(listName, listName));
}
gpForm.setGeneSetNameList(gsNameList);
return mapping.findForward("success");
}