private StudyBean getParentStudy(String studyOid) {
StudyBean study = getStudy(studyOid);
if (study.getParentStudyId() == 0) {
return study;
} else {
StudyBean parentStudy = (StudyBean) sdao.findByPK(study.getParentStudyId());
return parentStudy;
}
}
public MetadataUnit(DataSource ds, StudyBean study, int category) {
super(ds, study, category);
this.odmStudy = new OdmStudyBean();
if (study.getParentStudyId() > 0) {
this.parentStudy = (StudyBean) new StudyDAO(ds).findByPK(study.getParentStudyId());
} else {
this.parentStudy = new StudyBean();
}
}
public String getInputUsername(StudyBean studyBean, StudySubjectBean studySubjectBean) {
String inputUserName = null;
if (studySubjectBean != null) {
if (studyBean.getParentStudyId() > 0) studyBean = getStudy(studyBean.getParentStudyId());
inputUserName = studyBean.getOid() + "." + studySubjectBean.getOid();
}
return inputUserName;
}
private StudyUserRoleBean getRole(UserAccountBean userAccount, StudyBean study) throws Exception {
StudyUserRoleBean role = new StudyUserRoleBean();
if (study == null || userAccount == null || study.getId() == 0) {
throw new Exception();
}
if (userAccount.getId() > 0
&& study.getId() > 0
&& !study.getStatus().getName().equals("removed")) {
role = userAccount.getRoleByStudy(study.getId());
if (study.getParentStudyId() > 0) {
StudyUserRoleBean roleInParent = userAccount.getRoleByStudy(study.getParentStudyId());
role.setRole(Role.max(role.getRole(), roleInParent.getRole()));
}
} else {
throw new Exception();
}
return role;
}
private ArrayList<StudyEventDefinitionBean> initDefinitions(StudyBean site) {
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
StudyBean parentStudy =
(StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId());
seds = sedDao.findAllByStudy(parentStudy);
int start = 0;
for (StudyEventDefinitionBean sed : seds) {
int defId = sed.getId();
ArrayList<EventDefinitionCRFBean> edcs =
(ArrayList<EventDefinitionCRFBean>)
edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(
defId, site.getId(), parentStudy.getId());
ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
// sed.setCrfNum(edcs.size());
for (EventDefinitionCRFBean edcBean : edcs) {
int edcStatusId = edcBean.getStatus().getId();
CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId());
int crfStatusId = crf.getStatusId();
if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) {
} else {
ArrayList<CRFVersionBean> versions =
(ArrayList<CRFVersionBean>) cvdao.findAllActiveByCRF(edcBean.getCrfId());
edcBean.setVersions(versions);
edcBean.setCrfName(crf.getName());
CRFVersionBean defaultVersion =
(CRFVersionBean) cvdao.findByPK(edcBean.getDefaultVersionId());
edcBean.setDefaultVersionName(defaultVersion.getName());
String sversionIds = edcBean.getSelectedVersionIds();
ArrayList<Integer> idList = new ArrayList<Integer>();
if (sversionIds.length() > 0) {
String[] ids = sversionIds.split("\\,");
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
}
edcBean.setSelectedVersionIdList(idList);
defCrfs.add(edcBean);
++start;
}
}
logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size());
sed.setCrfs(defCrfs);
sed.setCrfNum(defCrfs.size());
}
return seds;
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(
@ModelAttribute("studyModuleStatus") StudyModuleStatus studyModuleStatus,
BindingResult result,
SessionStatus status,
HttpServletRequest request) {
StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
studyModuleStatusDao.saveOrUpdate(studyModuleStatus);
status.setComplete();
currentStudy.setStatus(Status.get(studyModuleStatus.getStudyStatus()));
if (currentStudy.getParentStudyId() > 0) {
studyDao.updateStudyStatus(currentStudy);
} else {
studyDao.updateStudyStatus(currentStudy);
}
return "redirect:studymodule";
}
private void setUpServlet(Trigger trigger) throws Exception {
FormProcessor fp2 = new FormProcessor(request);
request.setAttribute(CreateJobImportServlet.JOB_NAME, trigger.getName());
request.setAttribute(CreateJobImportServlet.JOB_DESC, trigger.getDescription());
dataMap = trigger.getJobDataMap();
String contactEmail = dataMap.getString(ImportSpringJob.EMAIL);
System.out.println("found email: " + contactEmail);
int userId = dataMap.getInt(ImportSpringJob.USER_ID);
int hours = dataMap.getInt(CreateJobImportServlet.HOURS);
int minutes = dataMap.getInt(CreateJobImportServlet.MINUTES);
String directory = dataMap.getString(ImportSpringJob.DIRECTORY);
String studyName = dataMap.getString(ImportSpringJob.STUDY_NAME);
request.setAttribute(ImportSpringJob.EMAIL, contactEmail);
request.setAttribute(ImportSpringJob.STUDY_NAME, studyName);
request.setAttribute("filePath", directory);
request.setAttribute("firstFilePath", IMPORT_DIR);
request.setAttribute("hours", new Integer(hours).toString());
request.setAttribute("minutes", new Integer(minutes).toString());
Date jobDate = trigger.getNextFireTime();
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
// ArrayList studies = udao.findStudyByUser(ub.getName(), (ArrayList)
// sdao.findAll());
// request.setAttribute("studies", studies);
ArrayList<StudyBean> all = (ArrayList<StudyBean>) sdao.findAll();
ArrayList<StudyBean> finalList = new ArrayList<StudyBean>();
for (StudyBean sb : all) {
if (!(sb.getParentStudyId() > 0)) {
finalList.add(sb);
// System.out.println("found study name: " + sb.getName());
finalList.addAll(sdao.findAllByParent(sb.getId()));
}
}
// System.out.println("found list of studies: " + finalList.toString());
addEntityList(
"studies",
finalList,
respage.getString("a_user_cannot_be_created_no_study_as_active"),
Page.ADMIN_SYSTEM);
// tbh >>
// HashMap presetValues = new HashMap();
// Calendar calendar = new GregorianCalendar();
// calendar.setTime(jobDate);
// presetValues.put(CreateJobImportServlet.DATE_START_JOB + "Hour",
// calendar.get(Calendar.HOUR_OF_DAY));
// presetValues.put(CreateJobImportServlet.DATE_START_JOB + "Minute",
// calendar.get(Calendar.MINUTE));
// // TODO this will have to match l10n formatting
// presetValues.put(CreateJobImportServlet.DATE_START_JOB + "Date",
// (calendar.get(Calendar.MONTH) + 1) + "/" +
// calendar.get(Calendar.DATE) + "/"
// + calendar.get(Calendar.YEAR));
// fp2.setPresetValues(presetValues);
// setPresetValues(fp2.getPresetValues());
}
private void collectMetaDataVersion() {
ArrayList<StudyEventDefinitionBean> sedBeansInStudy =
(ArrayList<StudyEventDefinitionBean>) studyBase.getSedBeansInStudy();
if (sedBeansInStudy == null || sedBeansInStudy.size() < 1) {
logger.info("null, because there is no study event definition in this study.");
return;
}
StudyBean study = studyBase.getStudy();
MetaDataVersionBean metadata = this.odmStudy.getMetaDataVersion();
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(this.ds);
int parentId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
StudyParameterValueBean spv = spvdao.findByHandleAndStudy(parentId, "discrepancyManagement");
metadata.setSoftHard(spv.getValue().equalsIgnoreCase("true") ? "Hard" : "Soft");
OdmExtractDAO oedao = new OdmExtractDAO(this.ds);
int studyId = study.getId();
int parentStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : studyId;
if (this.getCategory() == 1 && study.isSite(study.getParentStudyId())) {
// populate MetaDataVersion attributes
if (dataset != null) {
metadata.setOid(dataset.getODMMetaDataVersionOid() + "-" + study.getOid());
metadata.setName(dataset.getODMMetaDataVersionName() + "-" + study.getOid());
this.setParentMetaDataVersionOid(dataset.getODMMetaDataVersionOid());
}
if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
metadata.setOid("v1.0.0" + "-" + study.getOid());
this.setParentMetaDataVersionOid("v1.0.0");
}
if (metadata.getName() == null || metadata.getName().length() <= 0) {
metadata.setName("MetaDataVersion_v1.0.0" + "-" + study.getOid());
}
// populate Include
this.collectIncludeFromParentInSameFile();
// populate protocol
oedao.getUpdatedSiteMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
} else {
if (dataset != null) {
metadata.setOid(dataset.getODMMetaDataVersionOid());
metadata.setName(dataset.getODMMetaDataVersionName());
}
if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
metadata.setOid("v1.0.0");
}
if (metadata.getName() == null || metadata.getName().length() <= 0) {
metadata.setName("MetaDataVersion_v1.0.0");
}
// populate Include
String psOid = new String();
String pmOid = new String();
if (dataset != null) {
psOid = dataset.getODMPriorStudyOid();
pmOid = dataset.getODMPriorMetaDataVersionOid();
}
if (pmOid != null && pmOid.length() > 0) {
MetaDataVersionIncludeBean ib = metadata.getInclude();
ib.setMetaDataVersionOID(pmOid);
if (psOid != null && psOid.length() > 0) {
ib.setStudyOID(psOid);
} else {
ib.setStudyOID(study.getOid());
}
}
// populate protocol
// Set<Integer> nullCodeSet = oedao.getMetadata(parentStudyId,
// studyId,
// metadata, this.getODMBean().getODMVersion());
// studyBase.setNullClSet(nullCodeSet);
oedao.getMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
}
}
@Override
public void processRequest() throws Exception {
resetPanel();
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
int studyId = fp.getInt("id");
studyId = studyId == 0 ? fp.getInt("studyId") : studyId;
String action = fp.getString("action");
StudyDAO sdao = new StudyDAO(sm.getDataSource());
boolean isInterventional = false;
study = (StudyBean) sdao.findByPK(studyId);
if (study.getId() != currentStudy.getId()) {
addPageMessage(
respage.getString("not_current_study")
+ respage.getString("change_study_contact_sysadmin"));
forwardPage(Page.MENU_SERVLET);
return;
}
study.setId(studyId);
StudyConfigService scs = new StudyConfigService(sm.getDataSource());
study = scs.setParametersForStudy(study);
request.setAttribute("studyToView", study);
request.setAttribute("studyId", studyId + "");
request.setAttribute("studyPhaseMap", CreateStudyServlet.studyPhaseMap);
ArrayList statuses = Status.toStudyUpdateMembersList();
statuses.add(Status.PENDING);
request.setAttribute("statuses", statuses);
String interventional = resadmin.getString("interventional");
isInterventional = interventional.equalsIgnoreCase(study.getProtocolType());
request.setAttribute("isInterventional", isInterventional ? "1" : "0");
String protocolType = study.getProtocolTypeKey();
// A. Hamid. 5001
if (study.getParentStudyId() > 0) {
StudyBean parentStudy = (StudyBean) sdao.findByPK(study.getParentStudyId());
request.setAttribute("parentStudy", parentStudy);
}
ArrayList interventionArray = new ArrayList();
if (isInterventional) {
interventionArray = parseInterventions((study));
setMaps(isInterventional, interventionArray);
} else {
setMaps(isInterventional, interventionArray);
}
if (!action.equals("submit")) {
// First Load First Form
if (study.getDatePlannedStart() != null) {
fp.addPresetValue(INPUT_START_DATE, local_df.format(study.getDatePlannedStart()));
}
if (study.getDatePlannedEnd() != null) {
fp.addPresetValue(INPUT_END_DATE, local_df.format(study.getDatePlannedEnd()));
}
if (study.getProtocolDateVerification() != null) {
fp.addPresetValue(INPUT_VER_DATE, local_df.format(study.getProtocolDateVerification()));
}
setPresetValues(fp.getPresetValues());
// first load 2nd form
}
if (study == null) {
addPageMessage(respage.getString("please_choose_a_study_to_edit"));
forwardPage(Page.STUDY_LIST_SERVLET);
return;
}
if (action.equals("submit")) {
validateStudy1(fp, v);
validateStudy2(fp, v);
validateStudy3(isInterventional, v, fp);
validateStudy4(fp, v);
validateStudy5(fp, v);
validateStudy6(fp, v);
confirmWholeStudy(fp, v);
request.setAttribute("studyToView", study);
if (!errors.isEmpty()) {
System.out.println("found errors : " + errors.toString());
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY_NEW);
} else {
study.setProtocolType(protocolType);
submitStudy(study);
addPageMessage(respage.getString("the_study_has_been_updated_succesfully"));
ArrayList pageMessages = (ArrayList) request.getAttribute(PAGE_MESSAGE);
session.setAttribute("pageMessages", pageMessages);
response.sendRedirect(request.getContextPath() + "/pages/studymodule");
// forwardPage(Page.MANAGE_STUDY_MODULE);
}
} else {
forwardPage(Page.UPDATE_STUDY_NEW);
}
}
/*
* Purpose: Iterates over ODM to populate 2 objects: 1. importCRFList: A List of EventCRFs and information on how to
* process them. 2. importCRFMap: A Map multi-layer map of Subject/Event/Form only populated when the subsequent
* EventCRF passes the UpsertOn rules.
*/
public ImportCRFInfoContainer(ODMContainer odmContainer, DataSource ds) {
importCRFList = new ArrayList<ImportCRFInfo>();
ArrayList<EventCRFBean> eventCRFBeans = new ArrayList<EventCRFBean>();
ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
UpsertOnBean upsert = odmContainer.getCrfDataPostImportContainer().getUpsertOn();
// If Upsert bean is not present, create one with default settings
if (upsert == null) upsert = new UpsertOnBean();
String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOID);
ArrayList<SubjectDataBean> subjectDataBeans =
odmContainer.getCrfDataPostImportContainer().getSubjectData();
Map<String, Map<String, Map<String, String>>> subjectMap =
new HashMap<String, Map<String, Map<String, String>>>();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
StudySubjectBean studySubjectBean =
studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
Map<String, Map<String, String>> eventMap = new HashMap<String, Map<String, String>>();
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
String sampleOrdinal =
studyEventDataBean.getStudyEventRepeatKey() == null
? "1"
: studyEventDataBean.getStudyEventRepeatKey();
StudyEventDefinitionBean studyEventDefinitionBean =
studyEventDefinitionDAO.findByOidAndStudy(
studyEventDataBean.getStudyEventOID(),
studyBean.getId(),
studyBean.getParentStudyId());
logger.info(
"find all by def and subject "
+ studyEventDefinitionBean.getName()
+ " study subject "
+ studySubjectBean.getName());
StudyEventBean studyEventBean =
(StudyEventBean)
studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(
studySubjectBean.getId(),
studyEventDefinitionBean.getId(),
Integer.parseInt(sampleOrdinal));
// @pgawade 16-March-2011 Do not allow the data import
// if event status is one of the - stopped, signed,
// locked
Map<String, String> formMap = new HashMap<String, String>();
for (FormDataBean formDataBean : formDataBeans) {
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans =
crfVersionDAO.findAllByOid(formDataBean.getFormOID());
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
ArrayList<EventCRFBean> eventCrfBeans =
eventCrfDAO.findByEventSubjectVersion(
studyEventBean, studySubjectBean, crfVersionBean);
// what if we have begun with creating a study
// event, but haven't entered data yet? this would
// have us with a study event, but no corresponding
// event crf, yet.
if (eventCrfBeans.isEmpty()) {
logger.debug(
" found no event crfs from Study Event id "
+ studyEventBean.getId()
+ ", location "
+ studyEventBean.getLocation());
ImportCRFInfo importCrfInfo =
new ImportCRFInfo(
studyOID,
subjectDataBean.getSubjectOID(),
studyEventDataBean.getStudyEventOID(),
formDataBean.getFormOID());
importCrfInfo.setPreImportStage(DataEntryStage.UNCOMPLETED);
String crfStatus = formDataBean.getEventCRFStatus();
if (crfStatus != null
&& crfStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()))
importCrfInfo.setPostImportStage(DataEntryStage.INITIAL_DATA_ENTRY);
if ((studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SCHEDULED)
|| studyEventBean
.getSubjectEventStatus()
.equals(SubjectEventStatus.DATA_ENTRY_STARTED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.COMPLETED))) {
if (!upsert.isNotStarted()) {
importCrfInfo.setProcessImport(false);
importCrfInfo.setEventCRFID(null);
}
}
importCRFList.add(importCrfInfo);
if (importCrfInfo.isProcessImport()) formMap.put(formDataBean.getFormOID(), "true");
}
for (EventCRFBean ecb : eventCrfBeans) {
ImportCRFInfo importCrfInfo =
new ImportCRFInfo(
studyOID,
subjectDataBean.getSubjectOID(),
studyEventDataBean.getStudyEventOID(),
formDataBean.getFormOID());
importCrfInfo.setPreImportStage(ecb.getStage());
String crfStatus = formDataBean.getEventCRFStatus();
if (crfStatus != null
&& crfStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()))
importCrfInfo.setPostImportStage(DataEntryStage.INITIAL_DATA_ENTRY);
importCrfInfo.setEventCRFID(new Integer(ecb.getId()));
if (!(ecb.getStage().equals(DataEntryStage.INITIAL_DATA_ENTRY)
&& upsert.isDataEntryStarted())
&& !(ecb.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE)
&& upsert.isDataEntryComplete())) importCrfInfo.setProcessImport(false);
importCRFList.add(importCrfInfo);
if (importCrfInfo.isProcessImport()) formMap.put(formDataBean.getFormOID(), "true");
}
}
} // formdata loop
if (formMap.size() > 0) eventMap.put(studyEventDataBean.getStudyEventOID(), formMap);
} // study event loop
if (eventMap.size() > 0) subjectMap.put(subjectDataBean.getSubjectOID(), eventMap);
} // subject data loop
importCRFMap = subjectMap;
}
private ArrayList<StudyEventDefinitionBean> createSiteEventDefinitions(StudyBean site) {
FormProcessor fp = new FormProcessor(request);
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
StudyBean parentStudy =
(StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId());
seds = (ArrayList<StudyEventDefinitionBean>) session.getAttribute("definitions");
if (seds == null || seds.size() <= 0) {
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
seds = sedDao.findAllByStudy(parentStudy);
}
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
HashMap<String, Boolean> changes = new HashMap<String, Boolean>();
for (StudyEventDefinitionBean sed : seds) {
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
ArrayList<EventDefinitionCRFBean> edcs = sed.getCrfs();
int start = 0;
for (EventDefinitionCRFBean edcBean : edcs) {
int edcStatusId = edcBean.getStatus().getId();
if (edcStatusId == 5 || edcStatusId == 7) {
} else {
String order = start + "-" + edcBean.getId();
int defaultVersionId = fp.getInt("defaultVersionId" + order);
String requiredCRF = fp.getString("requiredCRF" + order);
String doubleEntry = fp.getString("doubleEntry" + order);
String electronicSignature = fp.getString("electronicSignature" + order);
String hideCRF = fp.getString("hideCRF" + order);
int sdvId = fp.getInt("sdvOption" + order);
ArrayList<String> selectedVersionIdList = fp.getStringArray("versionSelection" + order);
int selectedVersionIdListSize = selectedVersionIdList.size();
String selectedVersionIds = "";
if (selectedVersionIdListSize > 0) {
for (String id : selectedVersionIdList) {
selectedVersionIds += id + ",";
}
selectedVersionIds = selectedVersionIds.substring(0, selectedVersionIds.length() - 1);
}
boolean changed = false;
boolean isRequired =
!StringUtil.isBlank(requiredCRF) && "yes".equalsIgnoreCase(requiredCRF.trim())
? true
: false;
boolean isDouble =
!StringUtil.isBlank(doubleEntry) && "yes".equalsIgnoreCase(doubleEntry.trim())
? true
: false;
boolean hasPassword =
!StringUtil.isBlank(electronicSignature)
&& "yes".equalsIgnoreCase(electronicSignature.trim())
? true
: false;
boolean isHide =
!StringUtil.isBlank(hideCRF) && "yes".equalsIgnoreCase(hideCRF.trim()) ? true : false;
if (edcBean.getParentId() > 0) {
int dbDefaultVersionId = edcBean.getDefaultVersionId();
if (defaultVersionId != dbDefaultVersionId) {
changed = true;
CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(defaultVersionId);
edcBean.setDefaultVersionId(defaultVersionId);
edcBean.setDefaultVersionName(defaultVersion.getName());
}
if (isRequired != edcBean.isRequiredCRF()) {
changed = true;
edcBean.setRequiredCRF(isRequired);
}
if (isDouble != edcBean.isDoubleEntry()) {
changed = true;
edcBean.setDoubleEntry(isDouble);
}
if (hasPassword != edcBean.isElectronicSignature()) {
changed = true;
edcBean.setElectronicSignature(hasPassword);
}
if (isHide != edcBean.isHideCrf()) {
changed = true;
edcBean.setHideCrf(isHide);
}
if (!StringUtil.isBlank(selectedVersionIds)
&& !selectedVersionIds.equals(edcBean.getSelectedVersionIds())) {
changed = true;
String[] ids = selectedVersionIds.split(",");
ArrayList<Integer> idList = new ArrayList<Integer>();
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
edcBean.setSelectedVersionIdList(idList);
edcBean.setSelectedVersionIds(selectedVersionIds);
}
if (sdvId > 0 && sdvId != edcBean.getSourceDataVerification().getCode()) {
changed = true;
edcBean.setSourceDataVerification(SourceDataVerification.getByCode(sdvId));
}
} else {
// only if definition-crf has been modified, will it be
// saved for the site
int defaultId = defaultVersionId > 0 ? defaultVersionId : edcBean.getDefaultVersionId();
if (defaultId == defaultVersionId) {
if (isRequired == edcBean.isRequiredCRF()) {
if (isDouble == edcBean.isDoubleEntry()) {
if (hasPassword == edcBean.isElectronicSignature()) {
if (isHide == edcBean.isHideCrf()) {
if (selectedVersionIdListSize > 0) {
if (selectedVersionIdListSize == edcBean.getVersions().size()) {
if (sdvId > 0) {
if (sdvId != edcBean.getSourceDataVerification().getCode()) {
changed = true;
edcBean.setSourceDataVerification(
SourceDataVerification.getByCode(sdvId));
}
}
} else {
changed = true;
String[] ids = selectedVersionIds.split(",");
ArrayList<Integer> idList = new ArrayList<Integer>();
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
edcBean.setSelectedVersionIdList(idList);
edcBean.setSelectedVersionIds(selectedVersionIds);
}
}
} else {
changed = true;
edcBean.setHideCrf(isHide);
}
} else {
changed = true;
edcBean.setElectronicSignature(hasPassword);
}
} else {
changed = true;
edcBean.setDoubleEntry(isDouble);
}
} else {
changed = true;
edcBean.setRequiredCRF(isRequired);
}
} else {
changed = true;
CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(defaultVersionId);
edcBean.setDefaultVersionId(defaultVersionId);
edcBean.setDefaultVersionName(defaultVersion.getName());
}
}
changes.put(sed.getId() + "-" + edcBean.getId(), changed);
++start;
}
}
}
session.setAttribute("changed", changes);
return seds;
}
public boolean validate(SubjectTransferBean subjectTransferBean)
throws OpenClinicaSystemException {
StudyDAO stdao = new StudyDAO(this.getDataSource());
StudyBean study = stdao.findByUniqueIdentifier(subjectTransferBean.getStudyOid());
if (study == null) {
throw new OpenClinicaSystemException("Study you specified does not exist");
}
UserAccountBean ua = subjectTransferBean.getOwner();
StudyUserRoleBean role = ua.getRoleByStudy(study);
if (role.getId() == 0 || role.getRole().equals(Role.MONITOR)) {
throw new OpenClinicaSystemException(
"You do not have sufficient priviliges to run this service");
}
if (subjectTransferBean.getSiteIdentifier() != null) {
study =
stdao.findSiteByUniqueIdentifier(
subjectTransferBean.getStudyOid(), subjectTransferBean.getSiteIdentifier());
}
subjectTransferBean.setStudy(study);
if (study == null) {
throw new OpenClinicaSystemException("Site you specified does not exist");
}
int handleStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
org.akaza.openclinica.dao.service.StudyParameterValueDAO spvdao =
new StudyParameterValueDAO(this.getDataSource());
StudyParameterValueBean studyParameter =
spvdao.findByHandleAndStudy(handleStudyId, "subjectPersonIdRequired");
String personId = subjectTransferBean.getPersonId();
if ("required".equals(studyParameter.getValue())
&& (personId == null || personId.length() < 1)) {
throw new OpenClinicaSystemException(
"personId is required for the study: " + study.getName());
// return false;
}
if (personId != null && personId.length() > 255) {
throw new OpenClinicaSystemException("personId should not be longer than 255.");
// return false;
}
String idSetting = "";
StudyParameterValueBean subjectIdGenerationParameter =
spvdao.findByHandleAndStudy(handleStudyId, "subjectIdGeneration");
idSetting = subjectIdGenerationParameter.getValue();
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
int nextLabel = getStudySubjectDao().findTheGreatestLabel() + 1;
subjectTransferBean.setStudySubjectId(new Integer(nextLabel).toString());
}
String studySubjectId = subjectTransferBean.getStudySubjectId();
if (studySubjectId == null || studySubjectId.length() < 1) {
logger.info("studySubjectId is required.");
throw new OpenClinicaSystemException("studySubjectId is required.");
// return false;
} else if (studySubjectId.length() > 30) {
throw new OpenClinicaSystemException("studySubjectId should not be longer than 30.");
// return false;
}
String secondaryId = subjectTransferBean.getSecondaryId();
if (secondaryId != null && secondaryId.length() > 30) {
throw new OpenClinicaSystemException("secondaryId should not be longer than 30.");
// return false;
}
String gender = subjectTransferBean.getGender() + "";
studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "genderRequired");
if ("true".equals(studyParameter.getValue()) && (gender == null || gender.length() < 1)) {
throw new OpenClinicaSystemException("gender is required for the study:" + study.getName());
// return false;
}
Date dateOfBirth = subjectTransferBean.getDateOfBirth();
String yearOfBirth = subjectTransferBean.getYearOfBirth();
studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "collectDob");
if ("1".equals(studyParameter.getValue()) && (dateOfBirth == null)) {
throw new OpenClinicaSystemException("date Of Birth is required:" + study.getName());
// return false;
} else if ("2".equals(studyParameter.getValue()) && (yearOfBirth == null)) {
throw new OpenClinicaSystemException("Year Of Birth is required:" + study.getName());
} else if ("2".equals(studyParameter.getValue()) && (yearOfBirth != null)) {
try {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy");
subjectTransferBean.setDateOfBirth(sdf.parse(subjectTransferBean.getYearOfBirth()));
} catch (ParseException e) {
throw new OpenClinicaSystemException("Year Of Birth not Valid:" + study.getName());
}
}
Date enrollmentDate = subjectTransferBean.getEnrollmentDate();
if (enrollmentDate == null) {
throw new OpenClinicaSystemException("enrollmentDate is required.");
// return false;
} else {
if ((new Date()).compareTo(enrollmentDate) < 0) {
throw new OpenClinicaSystemException("enrollmentDate should be in the past.");
// return false;
}
}
return true;
}
@Override
protected void executeInternal(JobExecutionContext context) throws JobExecutionException {
// need to generate a Locale so that user beans and other things will
// generate normally
Locale locale = new Locale("en-US");
ResourceBundleProvider.updateLocale(locale);
ResourceBundle pageMessages = ResourceBundleProvider.getPageMessagesBundle();
// logger.debug("--");
// logger.debug("-- executing a job " + message + " at " + new
// java.util.Date().toString());
JobDataMap dataMap = context.getMergedJobDataMap();
SimpleTrigger trigger = (SimpleTrigger) context.getTrigger();
try {
ApplicationContext appContext =
(ApplicationContext) context.getScheduler().getContext().get("applicationContext");
String studySubjectNumber =
((CoreResources) appContext.getBean("coreResources")).getField("extract.number");
coreResources = (CoreResources) appContext.getBean("coreResources");
ruleSetRuleDao = (RuleSetRuleDao) appContext.getBean("ruleSetRuleDao");
dataSource = (DataSource) appContext.getBean("dataSource");
mailSender = (OpenClinicaMailSender) appContext.getBean("openClinicaMailSender");
AuditEventDAO auditEventDAO = new AuditEventDAO(dataSource);
// Scheduler scheduler = context.getScheduler();
// JobDetail detail = context.getJobDetail();
// jobDetailBean = (JobDetailBean) detail;
/*
* data map here should coincide with the job data map found in
* CreateJobExportServlet, with the following code: jobDataMap = new
* JobDataMap(); jobDataMap.put(DATASET_ID, datasetId);
* jobDataMap.put(PERIOD, period); jobDataMap.put(EMAIL, email);
* jobDataMap.put(TAB, tab); jobDataMap.put(CDISC, cdisc);
* jobDataMap.put(SPSS, spss);
*/
String alertEmail = dataMap.getString(EMAIL);
String localeStr = dataMap.getString(LOCALE);
if (localeStr != null) {
locale = new Locale(localeStr);
ResourceBundleProvider.updateLocale(locale);
pageMessages = ResourceBundleProvider.getPageMessagesBundle();
}
int dsId = dataMap.getInt(DATASET_ID);
String tab = dataMap.getString(TAB);
String cdisc = dataMap.getString(CDISC);
String cdisc12 = dataMap.getString(CDISC12);
if (cdisc12 == null) {
cdisc12 = "0";
}
String cdisc13 = dataMap.getString(CDISC13);
if (cdisc13 == null) {
cdisc13 = "0";
}
String cdisc13oc = dataMap.getString(CDISC13OC);
if (cdisc13oc == null) {
cdisc13oc = "0";
}
String spss = dataMap.getString(SPSS);
int userId = dataMap.getInt(USER_ID);
int studyId = dataMap.getInt(STUDY_ID);
// String datasetId = dataMap.getString(DATASET_ID);
// int dsId = new Integer(datasetId).intValue();
// String userAcctId = dataMap.getString(USER_ID);
// int userId = new Integer(userAcctId).intValue();
// why the flip-flop? if one property is set to 'true' we can
// see jobs in another screen but all properties have to be
// strings
logger.debug("-- found the job: " + dsId + " dataset id");
// for (Iterator it = dataMap.entrySet().iterator(); it.hasNext();)
// {
// java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
// Object key = entry.getKey();
// Object value = entry.getValue();
// // logger.debug("-- found datamap property: " + key.toString() +
// // " : " + value.toString());
// }
HashMap fileName = new HashMap<String, Integer>();
if (dsId > 0) {
// trying to not throw an error if there's no dataset id
DatasetDAO dsdao = new DatasetDAO(dataSource);
DatasetBean datasetBean = (DatasetBean) dsdao.findByPK(dsId);
StudyDAO studyDao = new StudyDAO(dataSource);
UserAccountDAO userAccountDAO = new UserAccountDAO(dataSource);
// hmm, three lines in the if block DRY?
String generalFileDir = "";
String generalFileDirCopy = "";
String exportFilePath = SQLInitServlet.getField("exportFilePath");
String pattern =
"yyyy"
+ File.separator
+ "MM"
+ File.separator
+ "dd"
+ File.separator
+ "HHmmssSSS"
+ File.separator;
SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
generalFileDir =
DATASET_DIR
+ datasetBean.getId()
+ File.separator
+ sdfDir.format(new java.util.Date());
if (!"".equals(exportFilePath)) {
generalFileDirCopy =
SQLInitServlet.getField("filePath") + exportFilePath + File.separator;
}
// logger.debug("-- created the following dir: " +
// generalFileDir);
long sysTimeBegin = System.currentTimeMillis();
// set up the user bean here, tbh
// logger.debug("-- gen tab file 00");
userBean = (UserAccountBean) userAccountDAO.findByPK(userId);
// needs to also be captured by the servlet, tbh
// logger.debug("-- gen tab file 00");
generateFileService =
new GenerateExtractFileService(dataSource, userBean, coreResources, ruleSetRuleDao);
// logger.debug("-- gen tab file 00");
// tbh #5796 - covers a bug when the user changes studies, 10/2010
StudyBean activeStudy = (StudyBean) studyDao.findByPK(studyId);
StudyBean parentStudy = new StudyBean();
logger.debug(
"active study: " + studyId + " parent study: " + activeStudy.getParentStudyId());
if (activeStudy.getParentStudyId() > 0) {
// StudyDAO sdao = new StudyDAO(sm.getDataSource());
parentStudy = (StudyBean) studyDao.findByPK(activeStudy.getParentStudyId());
} else {
parentStudy = activeStudy;
// covers a bug in tab file creation, tbh 01/2009
}
logger.debug("-- found extract bean ");
ExtractBean eb =
generateFileService.generateExtractBean(datasetBean, activeStudy, parentStudy);
MessageFormat mf = new MessageFormat("");
StringBuffer message = new StringBuffer();
StringBuffer auditMessage = new StringBuffer();
// use resource bundle page messages to generate the email, tbh
// 02/2009
// message.append(pageMessages.getString("html_email_header_1")
// + " " + alertEmail +
// pageMessages.getString("html_email_header_2") + "<br/>");
message.append(
"<p>"
+ pageMessages.getString("email_header_1")
+ " "
+ EmailEngine.getAdminEmail()
+ " "
+ pageMessages.getString("email_header_2")
+ " Job Execution "
+ pageMessages.getString("email_header_3")
+ "</p>");
message.append("<P>Dataset: " + datasetBean.getName() + "</P>");
message.append("<P>Study: " + activeStudy.getName() + "</P>");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_1")
+ datasetBean.getName()
+ pageMessages.getString("html_email_body_2")
+ SQLInitServlet.getField("sysURL")
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// logger.debug("-- gen tab file 00");
if ("1".equals(tab)) {
logger.debug("-- gen tab file 01");
fileName =
generateFileService.createTabFile(
eb,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy.getId(),
parentStudy.getId(),
generalFileDirCopy);
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_tab_delimited"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your tab-delimited file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_tab_delimited")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc)) {
String odmVersion = "oc1.2";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_12"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.2 w/OpenClinica Extension XML file <a
// href='AccessFile?fileId="
// + getFileIdInt(fileName)
// + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_12")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc12)) {
String odmVersion = "1.2";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.2 default");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_12_xml"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// // auditMessage.append(
// "You can access your ODM 1.2 XML file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_12_xml")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc13)) {
String odmVersion = "1.3";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.3");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_13"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.3 XML file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_13")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc13oc)) {
String odmVersion = "oc1.3";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.3 oc");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_13_xml"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.3 w/OpenClinica Extension XML file <a
// href='AccessFile?fileId="
// + getFileIdInt(fileName)
// + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_13_xml")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(spss)) {
SPSSReportBean answer = new SPSSReportBean();
fileName =
generateFileService.createSPSSFile(
datasetBean,
eb,
activeStudy,
parentStudy,
sysTimeBegin,
generalFileDir,
answer,
generalFileDirCopy);
logger.debug("-- gen spss file");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_spss"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your SPSS files <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_spss")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
// wrap up the message, and send the email
message.append(
"<p>"
+ pageMessages.getString("html_email_body_5")
+ "</P><P>"
+ pageMessages.getString("email_footer"));
try {
mailSender.sendEmail(
alertEmail.trim(),
pageMessages.getString("job_ran_for") + " " + datasetBean.getName(),
message.toString(),
true);
} catch (OpenClinicaSystemException ose) {
// Do Nothing, In the future we might want to have an email
// status added to system.
}
TriggerBean triggerBean = new TriggerBean();
triggerBean.setDataset(datasetBean);
triggerBean.setUserAccount(userBean);
triggerBean.setFullName(trigger.getName());
auditEventDAO.createRowForExtractDataJobSuccess(triggerBean, auditMessage.toString());
} else {
TriggerBean triggerBean = new TriggerBean();
// triggerBean.setDataset(datasetBean);
triggerBean.setUserAccount(userBean);
triggerBean.setFullName(trigger.getName());
auditEventDAO.createRowForExtractDataJobFailure(triggerBean);
// logger.debug("-- made it here for some reason, ds id: "
// + dsId);
}
// logger.debug("-- generated file: " + fileNameStr);
// dataSource.
} catch (Exception e) {
// TODO Auto-generated catch block -- ideally should generate a fail
// msg here, tbh 02/2009
logger.debug("-- found exception: " + e.getMessage());
e.printStackTrace();
}
}
@Override
public void processRequest() throws Exception {
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
String name = request.getParameter("name");
String studyIdString = request.getParameter("studyId");
if (StringUtil.isBlank(name) || StringUtil.isBlank(studyIdString)) {
addPageMessage(respage.getString("please_choose_a_user_to_set_role_for"));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
} else {
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
UserAccountBean user = (UserAccountBean) udao.findByUserName(name);
StudyBean userStudy = (StudyBean) sdao.findByPK(fp.getInt("studyId"));
if ("confirm".equalsIgnoreCase(action)) {
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
request.setAttribute("user", user);
StudyUserRoleBean uRole = udao.findRoleByUserNameAndStudyId(name, studyId);
uRole.setStudyName(userStudy.getName());
request.setAttribute("uRole", uRole);
ArrayList roles = Role.toArrayList();
roles.remove(Role.ADMIN); // admin is not a user role, only used for tomcat
StudyBean studyBean = (StudyBean) sdao.findByPK(uRole.getStudyId());
if (currentStudy.getParentStudyId() > 0) {
roles.remove(Role.COORDINATOR);
roles.remove(Role.STUDYDIRECTOR);
} else if (studyBean.getParentStudyId() > 0) {
roles.remove(Role.COORDINATOR);
roles.remove(Role.STUDYDIRECTOR);
// TODO: redo this fix
Role r = Role.RESEARCHASSISTANT;
r.setDescription("site_Data_Entry_Person");
roles.remove(Role.RESEARCHASSISTANT);
roles.add(r);
Role ri = Role.INVESTIGATOR;
ri.setDescription("site_investigator");
roles.remove(Role.INVESTIGATOR);
roles.add(ri);
}
request.setAttribute("roles", roles);
forwardPage(Page.SET_USER_ROLE_IN_STUDY);
} else {
// set role
String userName = fp.getString("name");
int studyId = fp.getInt("studyId");
int roleId = fp.getInt("roleId");
StudyUserRoleBean sur = new StudyUserRoleBean();
sur.setName(userName);
sur.setRole(Role.get(roleId));
sur.setStudyId(studyId);
sur.setStudyName(userStudy.getName());
sur.setStatus(Status.AVAILABLE);
sur.setUpdater(ub);
sur.setUpdatedDate(new Date());
udao.updateStudyUserRole(sur, userName);
addPageMessage(sendEmail(user, sur));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
}
}
}
private void submitStudy() {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyBean study1 = (StudyBean) session.getAttribute("newStudy");
logger.info("study bean to be updated:" + study1.getName());
study1.setUpdatedDate(new Date());
study1.setUpdater((UserAccountBean) session.getAttribute("userBean"));
System.out.println("study's parentId=" + study1.getParentStudyId());
sdao.update(study1);
StudyParameterValueBean spv = new StudyParameterValueBean();
spv.setStudyId(study1.getId());
spv.setParameter("collectDob");
spv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString());
updateParameter(spvdao, spv);
spv.setParameter("discrepancyManagement");
spv.setValue(study1.getStudyParameterConfig().getDiscrepancyManagement());
updateParameter(spvdao, spv);
spv.setParameter("genderRequired");
spv.setValue(study1.getStudyParameterConfig().getGenderRequired());
updateParameter(spvdao, spv);
spv.setParameter("subjectPersonIdRequired");
spv.setValue(study1.getStudyParameterConfig().getSubjectPersonIdRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameRequired");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameDefault");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameDefault());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameEditable");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameEditable());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateRequired");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateDefault");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateDefault());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateEditable");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateEditable());
updateParameter(spvdao, spv);
spv.setParameter("subjectIdGeneration");
spv.setValue(study1.getStudyParameterConfig().getSubjectIdGeneration());
updateParameter(spvdao, spv);
spv.setParameter("subjectIdPrefixSuffix");
spv.setValue(study1.getStudyParameterConfig().getSubjectIdPrefixSuffix());
updateParameter(spvdao, spv);
spv.setParameter("personIdShownOnCRF");
spv.setValue(study1.getStudyParameterConfig().getPersonIdShownOnCRF());
updateParameter(spvdao, spv);
StudyBean curStudy = (StudyBean) session.getAttribute("study");
if (curStudy != null && study1.getId() == curStudy.getId()) {
super.currentStudy = study1;
session.setAttribute("study", study1);
}
// update manage_pedigrees for all sites
ArrayList children = (ArrayList) sdao.findAllByParent(study1.getId());
for (int i = 0; i < children.size(); i++) {
StudyBean child = (StudyBean) children.get(i);
child.setType(study1.getType()); // same as parent's type
child.setUpdatedDate(new Date());
child.setUpdater(ub);
sdao.update(child);
// YW << update "collectDob" and "genderRequired" for sites
StudyParameterValueBean childspv = new StudyParameterValueBean();
childspv.setStudyId(child.getId());
childspv.setParameter("collectDob");
childspv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString());
updateParameter(spvdao, childspv);
childspv.setParameter("genderRequired");
childspv.setValue(study1.getStudyParameterConfig().getGenderRequired());
updateParameter(spvdao, childspv);
// YW >>
}
session.removeAttribute("newStudy");
session.removeAttribute("interventions");
}
/** Inserts the new study into database */
private void submitStudy() {
FormProcessor fp = new FormProcessor(request);
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) session.getAttribute("newStudy");
ArrayList parameters = study.getStudyParameters();
logger.info("study bean to be created:\n");
logger.info(
study.getName()
+ "\n"
+ study.getIdentifier()
+ "\n"
+ study.getParentStudyId()
+ "\n"
+ study.getSummary()
+ "\n"
+ study.getPrincipalInvestigator()
+ "\n"
+ study.getDatePlannedStart()
+ "\n"
+ study.getDatePlannedEnd()
+ "\n"
+ study.getFacilityName()
+ "\n"
+ study.getFacilityCity()
+ "\n"
+ study.getFacilityState()
+ "\n"
+ study.getFacilityZip()
+ "\n"
+ study.getFacilityCountry()
+ "\n"
+ study.getFacilityRecruitmentStatus()
+ "\n"
+ study.getFacilityContactName()
+ "\n"
+ study.getFacilityContactEmail()
+ "\n"
+ study.getFacilityContactPhone()
+ "\n"
+ study.getFacilityContactDegree());
study.setOwner(ub);
study.setCreatedDate(new Date());
StudyBean parent = (StudyBean) sdao.findByPK(study.getParentStudyId());
study.setType(parent.getType());
// YW 10-10-2007, enable setting site status
study.setStatus(study.getStatus());
// YW >>
study.setGenetic(parent.isGenetic());
study = (StudyBean) sdao.create(study);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
for (int i = 0; i < parameters.size(); i++) {
StudyParamsConfig config = (StudyParamsConfig) parameters.get(i);
StudyParameterValueBean spv = config.getValue();
spv.setStudyId(study.getId());
spv = (StudyParameterValueBean) spvdao.create(config.getValue());
}
// YW << here only "collectDob" and "genderRequired" have been corrected
// for sites.
StudyParameterValueBean spv = new StudyParameterValueBean();
StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parent.getId(), "collectDob");
spv.setStudyId(study.getId());
spv.setParameter("collectDob");
spv.setValue(parentSPV.getValue());
spvdao.create(spv);
parentSPV = spvdao.findByHandleAndStudy(parent.getId(), "genderRequired");
spv.setParameter("genderRequired");
spv.setValue(parentSPV.getValue());
spvdao.create(spv);
// YW >>
// switch user to the newly created site
session.setAttribute("study", session.getAttribute("newStudy"));
currentStudy = (StudyBean) session.getAttribute("study");
session.removeAttribute("newStudy");
addPageMessage(respage.getString("the_new_site_created_succesfully_current"));
forwardPage(Page.SITE_LIST_SERVLET);
}
/**
* Validates the first section of study and save it into study bean
*
* @throws Exception
*/
private void confirmStudy() throws Exception {
Validator v = new Validator(request);
FormProcessor fp = new FormProcessor(request);
v.addValidation("name", Validator.NO_BLANKS);
v.addValidation("uniqueProId", Validator.NO_BLANKS);
// >> tbh
// v.addValidation("description", Validator.NO_BLANKS);
// << tbh, #3943, 07/2009
v.addValidation("prinInvestigator", Validator.NO_BLANKS);
if (!StringUtil.isBlank(fp.getString(INPUT_START_DATE))) {
v.addValidation(INPUT_START_DATE, Validator.IS_A_DATE);
}
if (!StringUtil.isBlank(fp.getString(INPUT_END_DATE))) {
v.addValidation(INPUT_END_DATE, Validator.IS_A_DATE);
}
if (!StringUtil.isBlank(fp.getString("facConEmail"))) {
v.addValidation("facConEmail", Validator.IS_A_EMAIL);
}
if (!StringUtil.isBlank(fp.getString(INPUT_VER_DATE))) {
v.addValidation(INPUT_VER_DATE, Validator.IS_A_DATE);
}
// v.addValidation("statusId", Validator.IS_VALID_TERM);
v.addValidation(
"secondProId",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facCity",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facState",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
20);
v.addValidation(
"facZip",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facCountry",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facConName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConDegree",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConPhone",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConEmail",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
// >> tbh
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
ArrayList<StudyBean> allStudies = (ArrayList<StudyBean>) studyDAO.findAll();
for (StudyBean thisBean : allStudies) {
if (fp.getString("uniqueProId").trim().equals(thisBean.getIdentifier())) {
Validator.addError(
errors, "uniqueProId", resexception.getString("unique_protocol_id_existed"));
}
}
// << tbh #3999 08/2009
if (fp.getString("name").trim().length() > 100) {
Validator.addError(errors, "name", resexception.getString("maximum_lenght_name_100"));
}
if (fp.getString("uniqueProId").trim().length() > 30) {
Validator.addError(
errors, "uniqueProId", resexception.getString("maximum_lenght_unique_protocol_30"));
}
if (fp.getString("description").trim().length() > 255) {
Validator.addError(
errors, "description", resexception.getString("maximum_lenght_brief_summary_255"));
}
if (fp.getString("prinInvestigator").trim().length() > 255) {
Validator.addError(
errors,
"prinInvestigator",
resexception.getString("maximum_lenght_principal_investigator_255"));
}
if (fp.getInt("expectedTotalEnrollment") <= 0) {
Validator.addError(
errors,
"expectedTotalEnrollment",
respage.getString("expected_total_enrollment_must_be_a_positive_number"));
}
StudyBean newSite = this.createStudyBean();
StudyBean parentStudy =
(StudyBean) new StudyDAO(sm.getDataSource()).findByPK(newSite.getParentStudyId());
session.setAttribute("newStudy", newSite);
session.setAttribute("definitions", this.createSiteEventDefinitions(parentStudy));
if (errors.isEmpty()) {
logger.info("no errors");
forwardPage(Page.CONFIRM_CREATE_SUB_STUDY);
} else {
try {
local_df.parse(fp.getString(INPUT_START_DATE));
fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE));
}
try {
local_df.parse(fp.getString(INPUT_END_DATE));
fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE));
}
try {
local_df.parse(fp.getString(INPUT_VER_DATE));
fp.addPresetValue(INPUT_VER_DATE, local_df.format(fp.getDate(INPUT_VER_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_VER_DATE, fp.getString(INPUT_VER_DATE));
}
setPresetValues(fp.getPresetValues());
logger.info("has validation errors");
request.setAttribute("formMessages", errors);
// request.setAttribute("facRecruitStatusMap",
// CreateStudyServlet.facRecruitStatusMap);
request.setAttribute("statuses", Status.toActiveArrayList());
forwardPage(Page.CREATE_SUB_STUDY);
}
}
