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;
}
/**
* this custom ispy method queries ispy based on patient clinical status and creates more
* predefined user lists based on this clinical data. At the time of this writing, only
* non-timepoint dependent groups are tallied.
*
* @throws OperationNotSupportedException
*/
public static UserListBean loadStatusGroups(UserListBean userListBean)
throws OperationNotSupportedException {
ClinicalDataService cqs = ClinicalDataServiceFactory.getInstance();
ListManager listManager = new ListManager();
/**
* set up simple ISPYclinicalDataQueryDTO with the appropriate status group enums set in the
* query to return back a list of PatientDIDs based soley on the status group.
*/
/*
* for each stage group, load the EnumSet, send the query, return a list,
* set the list into a UserList and add it to the UserListBean.
*/
List<ClinicalResponseType> crt = ClinicalResponseType.getDisplayValues();
TimepointType[] timepoints = TimepointType.values();
for (ClinicalResponseType clinicalResponse : crt) {
for (TimepointType type : timepoints) {
// no data for timepoint one right now
if (type.equals(TimepointType.T1)) {
continue;
} else {
ISPYclinicalDataQueryDTO cDTO = new ISPYclinicalDataQueryDTO();
EnumSet<ClinicalResponseType> clinicalResponses =
EnumSet.noneOf(ClinicalResponseType.class);
EnumSet<TimepointType> tp = EnumSet.noneOf(TimepointType.class);
clinicalResponses.add(clinicalResponse);
tp.add(type);
cDTO.setClinicalResponseValues(clinicalResponses);
cDTO.setTimepointValues(tp);
Set<String> clinicalResponsePatients = cqs.getPatientDIDs(cDTO);
if (!clinicalResponsePatients.isEmpty()) {
List<String> dids = new ArrayList<String>(clinicalResponsePatients);
ISPYListValidator listValidator = new ISPYListValidator(ListType.PatientDID, dids);
UserList myList =
listManager.createList(
ListType.PatientDID,
clinicalResponse.toString()
+ TimepointType.T1.toString()
+ "_"
+ type.toString(),
dids,
listValidator);
if (!myList.getList().isEmpty()) {
myList.setListOrigin(ListOrigin.Default);
userListBean.addList(myList);
}
}
}
}
}
List<ClinicalStageType> cst = ClinicalStageType.getDisplayValues();
for (ClinicalStageType clinicalStage : cst) {
ISPYclinicalDataQueryDTO cDTO = new ISPYclinicalDataQueryDTO();
EnumSet<ClinicalStageType> clinicalStages = EnumSet.noneOf(ClinicalStageType.class);
clinicalStages.add(clinicalStage);
cDTO.setClinicalStageValues(clinicalStages);
Set<String> clinicalStagePatients = cqs.getPatientDIDs(cDTO);
if (!clinicalStagePatients.isEmpty()) {
List<String> dids = new ArrayList<String>(clinicalStagePatients);
ISPYListValidator listValidator = new ISPYListValidator(ListType.PatientDID, dids);
UserList myList =
listManager.createList(
ListType.PatientDID, clinicalStage.toString(), dids, listValidator);
if (!myList.getList().isEmpty()) {
myList.setListOrigin(ListOrigin.Default);
userListBean.addList(myList);
}
}
}
List<ERstatusType> est = ERstatusType.getDisplayValues();
for (ERstatusType erStatus : est) {
ISPYclinicalDataQueryDTO cDTO = new ISPYclinicalDataQueryDTO();
EnumSet<ERstatusType> erStatuses = EnumSet.noneOf(ERstatusType.class);
erStatuses.add(erStatus);
cDTO.setErStatusValues(erStatuses);
Set<String> erStatusPatients = cqs.getPatientDIDs(cDTO);
if (!erStatusPatients.isEmpty()) {
List<String> dids = new ArrayList<String>(erStatusPatients);
ISPYListValidator listValidator = new ISPYListValidator(ListType.PatientDID, dids);
UserList myList =
listManager.createList(ListType.PatientDID, erStatus.toString(), dids, listValidator);
if (!myList.getList().isEmpty()) {
myList.setListOrigin(ListOrigin.Default);
userListBean.addList(myList);
}
}
}
List<HER2statusType> hest = HER2statusType.getDisplayValues();
for (HER2statusType her2Status : hest) {
ISPYclinicalDataQueryDTO cDTO = new ISPYclinicalDataQueryDTO();
EnumSet<HER2statusType> her2Statuses = EnumSet.noneOf(HER2statusType.class);
her2Statuses.add(her2Status);
cDTO.setHer2StatusValues(her2Statuses);
Set<String> her2StatusPatients = cqs.getPatientDIDs(cDTO);
if (!her2StatusPatients.isEmpty()) {
List<String> dids = new ArrayList<String>(her2StatusPatients);
ISPYListValidator listValidator = new ISPYListValidator(ListType.PatientDID, dids);
UserList myList =
listManager.createList(ListType.PatientDID, her2Status.toString(), dids, listValidator);
if (!myList.getList().isEmpty()) {
myList.setListOrigin(ListOrigin.Default);
userListBean.addList(myList);
}
}
}
List<PRstatusType> prst = PRstatusType.getDisplayValues();
for (PRstatusType prStatus : prst) {
ISPYclinicalDataQueryDTO cDTO = new ISPYclinicalDataQueryDTO();
EnumSet<PRstatusType> prStatuses = EnumSet.noneOf(PRstatusType.class);
prStatuses.add(prStatus);
cDTO.setPrStatusValues(prStatuses);
Set<String> prStatusPatients = cqs.getPatientDIDs(cDTO);
if (!prStatusPatients.isEmpty()) {
List<String> dids = new ArrayList<String>(prStatusPatients);
ISPYListValidator listValidator = new ISPYListValidator(ListType.PatientDID, dids);
UserList myList =
listManager.createList(ListType.PatientDID, prStatus.toString(), dids, listValidator);
if (!myList.getList().isEmpty()) {
myList.setListOrigin(ListOrigin.Default);
userListBean.addList(myList);
}
}
}
return userListBean;
}