/**
* Send email to the user, director and administrator
*
* @param request
* @param response
*/
private String sendEmail(UserAccountBean u, StudyUserRoleBean sub) throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(sub.getStudyId());
logger.info("Sending email...");
String body =
u.getFirstName()
+ " "
+ u.getLastName()
+ " ("
+ resword.getString("username")
+ ": "
+ u.getName()
+ ") "
+ respage.getString("has_been_granted_the_role")
+ " "
+ sub.getRoleName()
+ " "
+ respage.getString("in_the_study_site")
+ " "
+ study.getName()
+ ".";
// boolean emailSent = sendEmail(u.getEmail().trim(), respage.getString("set_user_role"),
// body, false);
// if (emailSent) {
// sendEmail(ub.getEmail().trim(), respage.getString("set_user_role"), body, false);
// sendEmail(EmailEngine.getAdminEmail(), respage.getString("set_user_role"), body,
// false);
// }
return body;
}
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
TriggerService triggerService = new TriggerService();
String action = fp.getString("action");
String triggerName = fp.getString("tname");
scheduler = getScheduler();
System.out.println("found trigger name " + triggerName);
Trigger trigger = scheduler.getTrigger(triggerName.trim(), TRIGGER_IMPORT_GROUP);
System.out.println("found trigger from the other side " + trigger.getFullName());
if (StringUtil.isBlank(action)) {
setUpServlet(trigger);
forwardPage(Page.UPDATE_JOB_IMPORT);
} else if ("confirmall".equalsIgnoreCase(action)) {
HashMap errors =
triggerService.validateImportJobForm(
fp, request, scheduler.getTriggerNames("DEFAULT"), trigger.getName());
if (!errors.isEmpty()) {
// send back
addPageMessage(
"Your modifications caused an error, please see the messages for more information.");
setUpServlet(trigger);
forwardPage(Page.UPDATE_JOB_IMPORT);
} else {
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
int studyId = fp.getInt(CreateJobImportServlet.STUDY_ID);
StudyBean study = (StudyBean) studyDAO.findByPK(studyId);
// in the place of a users' current study, tbh
Date startDate = trigger.getStartTime();
trigger =
triggerService.generateImportTrigger(
fp, sm.getUserBean(), study, startDate, request.getLocale().getLanguage());
// scheduler = getScheduler();
JobDetailBean jobDetailBean = new JobDetailBean();
jobDetailBean.setGroup(TRIGGER_IMPORT_GROUP);
jobDetailBean.setName(trigger.getName());
jobDetailBean.setJobClass(org.akaza.openclinica.web.job.ImportStatefulJob.class);
jobDetailBean.setJobDataMap(trigger.getJobDataMap());
jobDetailBean.setDurability(true); // need durability?
jobDetailBean.setVolatility(false);
try {
scheduler.deleteJob(triggerName, TRIGGER_IMPORT_GROUP);
Date dateStart = scheduler.scheduleJob(jobDetailBean, trigger);
addPageMessage("Your job has been successfully modified.");
forwardPage(Page.VIEW_IMPORT_JOB_SERVLET);
} catch (SchedulerException se) {
se.printStackTrace();
// set a message here with the exception message
setUpServlet(trigger);
addPageMessage(
"There was an unspecified error with your creation, please contact an administrator.");
forwardPage(Page.UPDATE_JOB_IMPORT);
}
}
}
}
/**
* This method creates a List of DisplaySectionBeans, returning them in the order that the
* sections appear in a CRF. This List is "lazily" initialized the first time it is requested.
*
* @return A List of DisplaySectionBeans.
* @see org.akaza.openclinica.control.managestudy.PrintCRFServlet
* @see org.akaza.openclinica.control.managestudy.PrintDataEntryServlet
*/
public List<DisplaySectionBean> getDisplaySectionBeans() {
FormBeanUtil formBeanUtil;
ViewPersistanceHandler persistanceHandler;
ArrayList<SectionBean> allCrfSections;
// DAO classes for getting item definitions
SectionDAO sectionDao;
CRFVersionDAO crfVersionDao;
if (displaySectionBeans == null) {
displaySectionBeans = new ArrayList<DisplaySectionBean>();
formBeanUtil = new FormBeanUtil();
if (hasStoredData) persistanceHandler = new ViewPersistanceHandler();
// We need a CRF version id to populate the form display
if (this.crfVersionId == 0) {
return displaySectionBeans;
}
sectionDao = new SectionDAO(dataSource);
allCrfSections = (ArrayList) sectionDao.findByVersionId(this.crfVersionId);
// for the purposes of null values, try to obtain a valid
// eventCrfDefinition id
EventDefinitionCRFBean eventDefBean = null;
EventCRFBean eventCRFBean = new EventCRFBean();
if (eventCRFId > 0) {
EventCRFDAO ecdao = new EventCRFDAO(dataSource);
eventCRFBean = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudyEventDAO sedao = new StudyEventDAO(dataSource);
StudyEventBean studyEvent = (StudyEventBean) sedao.findByPK(eventCRFBean.getStudyEventId());
EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(dataSource);
StudyDAO sdao = new StudyDAO(dataSource);
StudyBean study = sdao.findByStudySubjectId(eventCRFBean.getStudySubjectId());
eventDefBean =
eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId(
study, studyEvent.getId(), this.crfVersionId);
}
eventDefBean = eventDefBean == null ? new EventDefinitionCRFBean() : eventDefBean;
// Create an array or List of DisplaySectionBeans representing each
// section
// for printing
DisplaySectionBean displaySectionBean;
for (SectionBean sectionBean : allCrfSections) {
displaySectionBean =
formBeanUtil.createDisplaySectionBWithFormGroups(
sectionBean.getId(),
this.crfVersionId,
dataSource,
eventDefBean.getId(),
eventCRFBean,
context);
displaySectionBeans.add(displaySectionBean);
}
}
return displaySectionBeans;
}
/** Finds all the studies */
@Override
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
ArrayList studies = (ArrayList) sdao.findAll();
// find all parent studies
ArrayList parents = (ArrayList) sdao.findAllParents();
ArrayList displayStudies = new ArrayList();
for (int i = 0; i < parents.size(); i++) {
StudyBean parent = (StudyBean) parents.get(i);
ArrayList children = (ArrayList) sdao.findAllByParent(parent.getId());
DisplayStudyBean displayStudy = new DisplayStudyBean();
displayStudy.setParent(parent);
displayStudy.setChildren(children);
displayStudies.add(displayStudy);
}
FormProcessor fp = new FormProcessor(request);
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allStudyRows = DisplayStudyRow.generateRowsFromBeans(displayStudies);
String[] columns = {
resword.getString("name"),
resword.getString("unique_identifier"),
resword.getString("OID"),
resword.getString("principal_investigator"),
resword.getString("facility_name"),
resword.getString("date_created"),
resword.getString("status"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(2);
table.hideColumnLink(6);
table.setQuery("ListStudy", new HashMap());
table.addLink(resword.getString("create_a_new_study"), "CreateStudy");
table.setRows(allStudyRows);
table.computeDisplay();
request.setAttribute("table", table);
// request.setAttribute("studies", studies);
session.setAttribute("fromListSite", "no");
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
setToPanel(resword.getString("in_the_application"), "");
if (parents.size() > 0) {
setToPanel(resword.getString("studies"), new Integer(parents.size()).toString());
}
if (studies.size() > 0) {
setToPanel(
resword.getString("sites"), new Integer(studies.size() - parents.size()).toString());
}
forwardPage(Page.STUDY_LIST);
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
// YW <<
StudyDAO stdao = new StudyDAO(sm.getDataSource());
int parentStudyId = currentStudy.getParentStudyId();
ArrayList groups = new ArrayList();
if (parentStudyId > 0) {
StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
groups = sgcdao.findAllByStudy(parentStudy);
} else {
groups = sgcdao.findAllByStudy(currentStudy);
}
// YW >>
String isReadOnly = request.getParameter("read");
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
for (int i = 0; i < groups.size(); i++) {
StudyGroupClassBean group = (StudyGroupClassBean) groups.get(i);
ArrayList studyGroups = sgdao.findAllByGroupClass(group);
group.setStudyGroups(studyGroups);
}
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allGroupRows = StudyGroupClassRow.generateRowsFromBeans(groups);
boolean isParentStudy = currentStudy.getParentStudyId() > 0 ? false : true;
request.setAttribute("isParentStudy", isParentStudy);
String[] columns = {
resword.getString("subject_group_class"),
resword.getString("type"),
resword.getString("subject_assignment"),
resword.getString("study_name"),
resword.getString("subject_groups"),
resword.getString("status"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(4);
table.hideColumnLink(6);
table.setQuery("ListSubjectGroupClass", new HashMap());
// if (isParentStudy && (!currentStudy.getStatus().isLocked())) {
// table.addLink(resword.getString("create_a_subject_group_class"),
// "CreateSubjectGroupClass");
// }
table.setRows(allGroupRows);
table.computeDisplay();
request.setAttribute("table", table);
if (request.getParameter("read") != null && request.getParameter("read").equals("true")) {
request.setAttribute("readOnly", true);
}
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST);
}
@RequestMapping(value = "/studies/{study}/validateAndSaveRule", method = RequestMethod.POST)
public @ResponseBody Response validateAndSave(
@RequestBody org.openclinica.ns.rules.v31.Rules rules,
Model model,
HttpSession session,
@PathVariable("study") String studyOid,
@RequestParam("ignoreDuplicates") Boolean ignoreDuplicates)
throws Exception {
ResourceBundleProvider.updateLocale(new Locale("en_US"));
RulesPostImportContainer rpic = mapRulesToRulesPostImportContainer(rules);
StudyDAO studyDao = new StudyDAO(dataSource);
StudyBean currentStudy = studyDao.findByOid(studyOid);
UserAccountBean userAccount = getUserAccount();
mayProceed(userAccount, currentStudy);
getRulePostImportContainerService(currentStudy, userAccount);
rpic = getRulePostImportContainerService(currentStudy, userAccount).validateRuleDefs(rpic);
rpic = getRulePostImportContainerService(currentStudy, userAccount).validateRuleSetDefs(rpic);
Response response = new Response();
response.setValid(Boolean.TRUE);
if (rpic.getInValidRuleDefs().size() > 0 || rpic.getInValidRuleSetDefs().size() > 0) {
response.setValid(Boolean.FALSE);
for (AuditableBeanWrapper<RuleBean> beanWrapper : rpic.getInValidRuleDefs()) {
for (String error : beanWrapper.getImportErrors()) {
org.openclinica.ns.response.v31.MessagesType messageType = new MessagesType();
messageType.setMessage(error);
response.getMessages().add(messageType);
}
}
for (AuditableBeanWrapper<RuleSetBean> beanWrapper : rpic.getInValidRuleSetDefs()) {
for (String error : beanWrapper.getImportErrors()) {
org.openclinica.ns.response.v31.MessagesType messageType = new MessagesType();
messageType.setMessage(error);
response.getMessages().add(messageType);
}
}
} else if ((rpic.getDuplicateRuleDefs().size() > 0) && !ignoreDuplicates) {
response.setValid(Boolean.FALSE);
for (AuditableBeanWrapper<RuleBean> beanWrapper : rpic.getDuplicateRuleDefs()) {
org.openclinica.ns.response.v31.MessagesType messageType = new MessagesType();
messageType.setMessage(DUPLICATE_MESSAGE);
response.getMessages().add(messageType);
}
} else {
getRuleSetService().saveImportFromDesigner(rpic);
}
logger.debug("RPIC READY");
return response;
}
public StudySubjectBean getSSBean(HashMap<String, String> userContext) throws Exception {
String studySubjectOid = userContext.get("studySubjectOID");
StudySubjectBean ssBean = null;
StudySubjectDAO ssdao = new StudySubjectDAO(dataSource);
SubjectDAO subjectdao = new SubjectDAO(dataSource);
UserAccountDAO udao = new UserAccountDAO(dataSource);
if (studySubjectOid != null) {
ssBean = ssdao.findByOid(studySubjectOid);
} else {
String studyOid = userContext.get("studyOID");
StudyBean studyBean = sdao.findByOid(studyOid);
int studyEventDefnId = Integer.valueOf(userContext.get("studyEventDefinitionID"));
int studyEventOrdinal = Integer.valueOf(userContext.get("studyEventOrdinal"));
UserAccountBean uBean = (UserAccountBean) udao.findByPK(1);
// build Subject Account
SubjectBean subjectBean = createSubjectBean(uBean);
subjectBean = (SubjectBean) subjectdao.findByPK(subjectBean.getId());
// build StudySubject Account
ssBean = createStudySubjectBean(studyBean, subjectBean, uBean);
ssBean = (StudySubjectBean) ssdao.findByPK(ssBean.getId());
System.out.println("study subject oid: " + ssBean.getOid());
// build User Account
UserAccountBean userAccountBean = createUserAccount(uBean, studyBean, ssBean);
userAccountBean = (UserAccountBean) udao.findByPK(userAccountBean.getId());
// build and schedule study Event
StudyEventBean studyEventBean =
createStudyEventBean(ssBean, studyEventDefnId, studyEventOrdinal, userAccountBean);
}
return ssBean;
}
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#processRequest()
*/
@Override
protected void processRequest() throws Exception {
// find last 5 modifed studies
StudyDAO sdao = new StudyDAO(sm.getDataSource());
ArrayList studies = (ArrayList) sdao.findAllByLimit(true);
request.setAttribute("studies", studies);
ArrayList allStudies = (ArrayList) sdao.findAll();
request.setAttribute("allStudyNumber", new Integer(allStudies.size()));
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList users = (ArrayList) udao.findAllByLimit(true);
request.setAttribute("users", users);
ArrayList allUsers = (ArrayList) udao.findAll();
request.setAttribute("allUserNumber", new Integer(allUsers.size()));
SubjectDAO subdao = new SubjectDAO(sm.getDataSource());
ArrayList subjects = (ArrayList) subdao.findAllByLimit(true);
request.setAttribute("subjects", subjects);
ArrayList allSubjects = (ArrayList) subdao.findAll();
request.setAttribute("allSubjectNumber", new Integer(allSubjects.size()));
CRFDAO cdao = new CRFDAO(sm.getDataSource());
ArrayList crfs = (ArrayList) cdao.findAllByLimit(true);
request.setAttribute("crfs", crfs);
ArrayList allCrfs = (ArrayList) cdao.findAll();
request.setAttribute("allCrfNumber", new Integer(allCrfs.size()));
resetPanel();
panel.setOrderedData(true);
setToPanel(resword.getString("in_the_application"), "");
if (allSubjects.size() > 0) {
setToPanel(resword.getString("subjects"), new Integer(allSubjects.size()).toString());
}
if (allUsers.size() > 0) {
setToPanel(resword.getString("users"), new Integer(allUsers.size()).toString());
}
if (allStudies.size() > 0) {
setToPanel(resword.getString("studies"), new Integer(allStudies.size()).toString());
}
if (allCrfs.size() > 0) {
setToPanel(resword.getString("CRFs"), new Integer(allCrfs.size()).toString());
}
panel.setStudyInfoShown(false);
forwardPage(Page.ADMIN_SYSTEM);
}
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;
}
}
@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";
}
@RequestMapping(value = "/studies/{study}/connect", method = RequestMethod.POST)
public @ResponseBody org.openclinica.ns.response.v31.Response create(
@RequestBody org.openclinica.ns.response.v31.Response responeType,
Model model,
HttpSession session,
@PathVariable("study") String studyOid)
throws Exception {
ResourceBundleProvider.updateLocale(new Locale("en_US"));
StudyDAO studyDao = new StudyDAO(dataSource);
StudyBean currentStudy = studyDao.findByOid(studyOid);
UserAccountBean userAccount = getUserAccount();
mayProceed(userAccount, currentStudy);
Response response = new Response();
response.setValid(Boolean.TRUE);
org.openclinica.ns.response.v31.MessagesType theMessageType = new MessagesType();
theMessageType.setMessage("Hello");
response.getMessages().add(theMessageType);
logger.debug("RPIC READY");
return response;
// model.addAttribute("response", response);
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int studySubId = fp.getInt(STUDY_SUB_ID, true);
int eventCRFId = fp.getInt(EVENT_CRF_ID);
String action = request.getParameter("action");
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
if (eventCRFId == 0) {
addPageMessage(respage.getString("please_choose_an_event_CRF_to_delete"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
} else {
EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
request.setAttribute("studySub", studySub);
// construct info needed on view event crf page
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
int crfVersionId = eventCRF.getCRFVersionId();
CRFBean cb = cdao.findByVersionId(crfVersionId);
eventCRF.setCrf(cb);
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
eventCRF.setCrfVersion(cvb);
// then get the definition so we can call
// DisplayEventCRFBean.setFlags
int studyEventId = eventCRF.getStudyEventId();
StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed =
(StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
event.setStudyEventDefinition(sed);
request.setAttribute("event", event);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId());
EventDefinitionCRFBean edc =
edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());
DisplayEventCRFBean dec = new DisplayEventCRFBean();
dec.setEventCRF(eventCRF);
dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry());
// find all item data
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
dnDao = new DiscrepancyNoteDAO(sm.getDataSource());
ArrayList<ItemDataBean> itemData = iddao.findAllByEventCRFId(eventCRF.getId());
request.setAttribute("items", itemData);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("displayEventCRF", dec);
forwardPage(Page.DELETE_EVENT_CRF);
} else {
logger.info("submit to delete the event CRF from event");
// OC-6303 Deleting Event CRF resets Show / Hide logic
// delete records from DynamicItemForm and DynamicItemGroup
getDynamicsItemFormMetadataDao().delete(eventCRFId);
getDynamicsItemGroupMetadataDao().delete(eventCRFId);
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.RESET);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
for (ItemDataBean itemdata : itemData) {
// OC-6343 Rule behaviour must be reset if an Event CRF is deleted
// delete the records from ruleActionRunLogDao
getRuleActionRunLogDao().delete(itemdata.getId());
// OC-6344 Notes & Discrepancies must be set to "closed" when event CRF is deleted
// parentDiscrepancyNoteList is the list of the parent DNs records only
ArrayList<DiscrepancyNoteBean> parentDiscrepancyNoteList =
getDnDao().findParentNotesOnlyByItemData(itemdata.getId());
for (DiscrepancyNoteBean parentDiscrepancyNote : parentDiscrepancyNoteList) {
if (parentDiscrepancyNote.getResolutionStatusId()
!= 4) { // if the DN's resolution status is not set to Closed
String description = resword.getString("dn_auto-closed_description");
String detailedNotes = resword.getString("dn_auto_closed_detailed_notes");
// create new DN record , new DN Map record , also update the parent record
createDiscrepancyNoteBean(
description, detailedNotes, itemdata.getId(), study, ub, parentDiscrepancyNote);
}
}
iddao = new ItemDataDAO(sm.getDataSource());
ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
ItemDataBean idBean = (ItemDataBean) iddao.findByPK(itemdata.getId());
ItemFormMetadataBean ifmBean =
ifmdao.findByItemIdAndCRFVersionId(idBean.getItemId(), crfVersionId);
// Updating Dn_item_data_map actovated column into false for the existing DNs
ArrayList<DiscrepancyNoteBean> dnBeans =
getDnDao().findExistingNotesForItemData(itemdata.getId());
if (dnBeans.size() != 0) {
DiscrepancyNoteBean dnBean = new DiscrepancyNoteBean();
dnBean.setEntityId(itemdata.getId());
dnBean.setActivated(false);
getDnDao().updateDnMapActivation(dnBean);
}
// Default Values are not addressed
itemdata.setValue("");
itemdata.setOldStatus(itemdata.getStatus());
itemdata.setOwner(ub);
itemdata.setStatus(Status.AVAILABLE);
itemdata.setUpdater(ub);
iddao.updateUser(itemdata);
iddao.update(itemdata);
}
// OC-6291 event_crf status change
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
if (event.getSubjectEventStatus().isCompleted()
|| event.getSubjectEventStatus().isSigned()) {
event.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
event.setUpdater(ub);
sedao = new StudyEventDAO(sm.getDataSource());
sedao.update(event);
}
String emailBody =
respage.getString("the_event_CRF")
+ cb.getName()
+ respage.getString("has_been_deleted_from_the_event")
+ event.getStudyEventDefinition().getName()
+ ". "
+ respage.getString("has_been_deleted_from_the_event_cont");
addPageMessage(emailBody);
// sendEmail(emailBody);
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
}
}
@RequestMapping(method = RequestMethod.GET)
public ModelMap handleMainPage(HttpServletRequest request) {
ModelMap map = new ModelMap();
// setUpSidebar(request);
StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
eventDefinitionCRFDao = new EventDefinitionCRFDAO(dataSource);
studyEventDefinitionDao = new StudyEventDefinitionDAO(dataSource);
crfDao = new CRFDAO(dataSource);
studyGroupClassDao = new StudyGroupClassDAO(dataSource);
studyDao = new StudyDAO(dataSource);
userDao = new UserAccountDAO(dataSource);
ruleDao = new RuleDAO(dataSource);
StudyModuleStatus sms = studyModuleStatusDao.findByStudyId(currentStudy.getId());
if (sms == null) {
sms = new StudyModuleStatus();
sms.setStudyId(currentStudy.getId());
}
int crfCount = crfDao.findAllByStudy(currentStudy.getId()).size();
int crfWithEventDefinition = crfDao.findAllActiveByDefinitions(currentStudy.getId()).size();
int totalCrf = crfCount + crfWithEventDefinition;
// int eventDefinitionCount = eventDefinitionCRFDao.findAllActiveByStudy(currentStudy).size();
int eventDefinitionCount = studyEventDefinitionDao.findAllActiveByStudy(currentStudy).size();
int subjectGroupCount = studyGroupClassDao.findAllActiveByStudy(currentStudy).size();
List<RuleSetBean> ruleSets = ruleSetService.getRuleSetsByStudy(currentStudy);
ruleSets = ruleSetService.filterByStatusEqualsAvailableOnlyRuleSetRules(ruleSets);
int ruleCount = ruleSets != null ? ruleSets.size() : 0;
int siteCount = studyDao.findOlnySiteIdsByStudy(currentStudy).size();
int userCount = userDao.findAllUsersByStudy(currentStudy.getId()).size();
Collection childStudies = studyDao.findAllByParent(currentStudy.getId());
Map childStudyUserCount = new HashMap();
for (Object sb : childStudies) {
StudyBean childStudy = (StudyBean) sb;
childStudyUserCount.put(
childStudy.getName(), userDao.findAllUsersByStudy(childStudy.getId()).size());
}
if (sms.getCrf() == 0) {
sms.setCrf(StudyModuleStatus.NOT_STARTED);
}
if (sms.getCrf() != 3 && totalCrf > 0) {
sms.setCrf(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getEventDefinition() == 0) {
sms.setEventDefinition(StudyModuleStatus.NOT_STARTED);
}
if (sms.getEventDefinition() != 3 && eventDefinitionCount > 0) {
sms.setEventDefinition(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getSubjectGroup() == 0) {
sms.setSubjectGroup(StudyModuleStatus.NOT_STARTED);
}
if (sms.getSubjectGroup() != 3 && subjectGroupCount > 0) {
sms.setSubjectGroup(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getRule() == 0) {
sms.setRule(StudyModuleStatus.NOT_STARTED);
}
if (sms.getRule() != 3 && ruleCount > 0) {
sms.setRule(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getSite() == 0) {
sms.setSite(StudyModuleStatus.NOT_STARTED);
}
if (sms.getSite() != 3 && siteCount > 0) {
sms.setSite(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getUsers() == 0) {
sms.setUsers(StudyModuleStatus.NOT_STARTED);
}
if (sms.getUsers() != 3 && userCount > 0) {
sms.setUsers(StudyModuleStatus.IN_PROGRESS);
}
map.addObject(sms);
map.addAttribute("crfCount", totalCrf);
map.addAttribute("eventDefinitionCount", eventDefinitionCount);
map.addAttribute("subjectGroupCount", subjectGroupCount);
map.addAttribute("ruleCount", ruleCount);
map.addAttribute("siteCount", siteCount);
map.addAttribute("userCount", userCount);
map.addAttribute("childStudyUserCount", childStudyUserCount);
map.addAttribute("studyId", currentStudy.getId());
map.addAttribute("currentStudy", currentStudy);
UserAccountBean userBean = (UserAccountBean) request.getSession().getAttribute("userBean");
request.setAttribute("userBean", userBean);
request.setAttribute("statusMap", Status.toStudyUpdateMembersList());
ArrayList pageMessages = new ArrayList();
if (request.getSession().getAttribute("pageMessages") != null) {
pageMessages.addAll((ArrayList) request.getSession().getAttribute("pageMessages"));
request.setAttribute("pageMessages", pageMessages);
request.getSession().removeAttribute("pageMessages");
}
return map;
}
@Override
public void processRequest() throws Exception {
String studySubIdString = request.getParameter("id"); // studySubjectId
String subIdString = request.getParameter("subjectId");
String studyIdString = request.getParameter("studyId");
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
if (StringUtil.isBlank(studySubIdString)
|| StringUtil.isBlank(subIdString)
|| StringUtil.isBlank(studyIdString)) {
addPageMessage(respage.getString("please_choose_a_study_subject_to_remove"));
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
} else {
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
int studySubId = Integer.valueOf(studySubIdString.trim()).intValue();
int subjectId = Integer.valueOf(subIdString.trim()).intValue();
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
StudyDAO studydao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) studydao.findByPK(studyId);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = sedao.findAllByStudyAndStudySubjectId(study, studySubId);
String action = request.getParameter("action");
if ("confirm".equalsIgnoreCase(action)) {
if (!studySub.getStatus().equals(Status.AVAILABLE)) {
addPageMessage(
respage.getString("this_subject_is_not_available_for_this_study")
+ " "
+ respage.getString("please_contact_sysadmin_for_more_information"));
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
return;
}
request.setAttribute("subject", subject);
request.setAttribute("study", study);
request.setAttribute("studySub", studySub);
request.setAttribute("events", events);
forwardPage(Page.REMOVE_STUDY_SUBJECT);
} else {
logger.info("submit to remove the subject from study");
// remove subject from study
studySub.setStatus(Status.DELETED);
studySub.setUpdater(ub);
studySub.setUpdatedDate(new Date());
subdao.update(studySub);
// remove all study events
// remove all event crfs
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
if (!event.getStatus().equals(Status.DELETED)) {
event.setStatus(Status.AUTO_DELETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// remove all the item data
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
String emailBody =
respage.getString("the_subject")
+ " "
+ subject.getName()
+ " "
+ respage.getString("has_been_removed_from_the_study")
+ study.getName()
+ ".";
addPageMessage(emailBody);
sendEmail(emailBody);
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
}
}
}
@RequestMapping(value = "/studies/{study}/validateAndTestRule", method = RequestMethod.POST)
public @ResponseBody org.openclinica.ns.rules_test.v31.RulesTest create(
@RequestBody org.openclinica.ns.rules_test.v31.RulesTest ruleTest,
Model model,
HttpSession session,
@PathVariable("study") String studyOid)
throws Exception {
ResourceBundleProvider.updateLocale(new Locale("en_US"));
RulesPostImportContainer rpic = mapRulesToRulesPostImportContainer(ruleTest.getRules());
StudyDAO studyDao = new StudyDAO(dataSource);
StudyBean currentStudy = studyDao.findByOid(studyOid);
UserAccountBean userAccount = getUserAccount();
mayProceed(userAccount, currentStudy);
getRulePostImportContainerService(currentStudy, userAccount);
rpic = getRulePostImportContainerService(currentStudy, userAccount).validateRuleDefs(rpic);
rpic = getRulePostImportContainerService(currentStudy, userAccount).validateRuleSetDefs(rpic);
Response response = new Response();
response.setValid(Boolean.TRUE);
if (rpic.getInValidRuleDefs().size() > 0 || rpic.getInValidRuleSetDefs().size() > 0) {
response.setValid(Boolean.FALSE);
for (AuditableBeanWrapper<RuleBean> beanWrapper : rpic.getInValidRuleDefs()) {
for (String error : beanWrapper.getImportErrors()) {
org.openclinica.ns.response.v31.MessagesType messageType = new MessagesType();
messageType.setMessage(error);
response.getMessages().add(messageType);
}
}
for (AuditableBeanWrapper<RuleSetBean> beanWrapper : rpic.getInValidRuleSetDefs()) {
for (String error : beanWrapper.getImportErrors()) {
org.openclinica.ns.response.v31.MessagesType messageType = new MessagesType();
messageType.setMessage(error);
response.getMessages().add(messageType);
}
}
}
HashMap<String, String> p = new HashMap<String, String>();
for (ParameterType parameterType : ruleTest.getParameters()) {
p.put(parameterType.getKey(), parameterType.getValue());
}
ExpressionObjectWrapper eow =
new ExpressionObjectWrapper(
dataSource,
currentStudy,
rpic.getRuleDefs().get(0).getExpression(),
rpic.getRuleSets().get(0));
ExpressionProcessor ep = ExpressionProcessorFactory.createExpressionProcessor(eow);
// Run expression with populated HashMap
DateTime start = new DateTime();
HashMap<String, String> result = ep.testEvaluateExpression(p);
DateTime end = new DateTime();
Duration dur = new Duration(start, end);
PeriodFormatter yearsAndMonths =
new PeriodFormatterBuilder()
.printZeroAlways()
.appendSecondsWithMillis()
.appendSuffix(" second", " seconds")
.toFormatter();
yearsAndMonths.print(dur.toPeriod());
// Run expression with empty HashMap to check rule validity, because
// using illegal test values will cause invalidity
HashMap<String, String> k = new HashMap<String, String>();
HashMap<String, String> theResult = ep.testEvaluateExpression(k);
ruleTest.getParameters().clear();
for (Map.Entry<String, String> entry : result.entrySet()) {
ParameterType parameterType = new ParameterType();
parameterType.setKey(entry.getKey());
parameterType.setValue(entry.getValue());
ruleTest.getParameters().add(parameterType);
}
// if (theResult.get("ruleValidation").equals("rule_valid") &&
// result.get("ruleValidation").equals("rule_invalid")) {
// result.put("ruleValidation", "rule_valid");
// result.put("ruleEvaluatesTo", resword.getString("test_rules_rule_fail") + " " +
// result.get("ruleValidationFailMessage"));
// result.remove("ruleValidationFailMessage");
// }
// Put on screen
// request.setAttribute("duration", yearsAndMonths.print(dur.toPeriod()));
RulesTestMessagesType messageType = new RulesTestMessagesType();
messageType.setKey("duration");
messageType.setValue(yearsAndMonths.print(dur.toPeriod()));
ruleTest.getRulesTestMessages().add(messageType);
return ruleTest;
}
/*
* 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 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());
}
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int studyId = fp.getInt("id");
StudyBean study = (StudyBean) sdao.findByPK(studyId);
// find all sites
ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
// find all user and roles in the study, include ones in sites
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(studyId);
// find all subjects in the study, include ones in sites
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events in the study, include ones in sites
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (studyId == 0) {
addPageMessage("Please choose a study to restore.");
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("studyToRestore", study);
request.setAttribute("sitesToRestore", sites);
request.setAttribute("userRolesToRestore", userRoles);
request.setAttribute("subjectsToRestore", subjects);
request.setAttribute("definitionsToRRestore", definitions);
forwardPage(Page.RESTORE_STUDY);
} else {
logger.info("submit to restore the study");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setStatus(Status.AVAILABLE);
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// remove all sites
for (int i = 0; i < sites.size(); i++) {
StudyBean site = (StudyBean) sites.get(i);
site.setStatus(Status.AVAILABLE);
site.setUpdater(ub);
site.setUpdatedDate(new Date());
sdao.update(site);
}
// remove all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
role.setStatus(Status.AVAILABLE);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
udao.updateStudyUserRole(role, role.getUserName());
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
subject.setStatus(Status.AVAILABLE);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
}
// remove all study_group
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
ArrayList groups = sgdao.findAllByStudy(study);
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean group = (StudyGroupBean) groups.get(i);
group.setStatus(Status.AVAILABLE);
group.setUpdater(ub);
group.setUpdatedDate(new Date());
sgdao.update(group);
// all subject_group_map
ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId());
for (int j = 0; j < subjectGroupMaps.size(); j++) {
SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
sgMap.setStatus(Status.AVAILABLE);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
// remove all event definitions and event
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < definitions.size(); i++) {
StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
definition.setStatus(Status.AVAILABLE);
definition.setUpdater(ub);
definition.setUpdatedDate(new Date());
sefdao.update(definition);
ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
for (int j = 0; j < edcs.size(); j++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
edc.setStatus(Status.AVAILABLE);
edc.setUpdater(ub);
edc.setUpdatedDate(new Date());
edcdao.update(edc);
}
ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
event.setStatus(Status.AVAILABLE);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
} // for definitions
DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
ArrayList dataset = datadao.findAllByStudyId(study.getId());
for (int i = 0; i < dataset.size(); i++) {
DatasetBean data = (DatasetBean) dataset.get(i);
data.setStatus(Status.AVAILABLE);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
addPageMessage("This study has been restored successfully.");
forwardPage(Page.STUDY_LIST_SERVLET);
}
}
}
@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 StudyBean getStudy(String oid) {
sdao = new StudyDAO(dataSource);
StudyBean studyBean = (StudyBean) sdao.findByOid(oid);
return studyBean;
}
@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();
}
}
/**
* @api {get} /rest2/openrosa/:studyOID/formList Get Form List
* @apiName getFormList
* @apiPermission admin
* @apiVersion 1.0.0
* @apiParam {String} studyOID Study Oid.
* @apiGroup Form
* @apiDescription Retrieves a listing of the available OpenClinica forms.
* @apiParamExample {json} Request-Example: { "studyOid": "S_SAMPLTE", }
* @apiSuccessExample {xml} Success-Response: HTTP/1.1 200 OK { <xforms
* xmlns="http://openrosa.org/xforms/xformsList"> <xform> <formID>F_FIRSTFORM_1</formID>
* <name>First Form</name> <majorMinorVersion>1</majorMinorVersion> <version>1</version>
* <hash>8678370cd92814d4e3216d58d821403f</hash>
* <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
* formId=F_FIRSTFORM_1</downloadUrl> </xform> <xform> <formID>F_SECONDFORM_1</formID>
* <name>Second Form</name> <majorMinorVersion>1</majorMinorVersion> <version>1</version>
* <hash>7ee60d1c6516b730bbe9bdbd7cad942f</hash>
* <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
* formId=F_SECONDFORM_1</downloadUrl> </xform> </xforms>
*/
@GET
@Path("/{studyOID}/formList")
@Produces(MediaType.TEXT_XML)
public String getFormList(
@Context HttpServletRequest request,
@Context HttpServletResponse response,
@PathParam("studyOID") String studyOID,
@QueryParam("formID") String crfOID,
@RequestHeader("Authorization") String authorization,
@Context ServletContext context)
throws Exception {
if (!mayProceedPreview(studyOID)) return null;
StudyDAO sdao = new StudyDAO(getDataSource());
StudyBean study = sdao.findByOid(studyOID);
CRFDAO cdao = new CRFDAO(getDataSource());
Collection<CRFBean> crfs = cdao.findAll();
CRFVersionDAO cVersionDao = new CRFVersionDAO(getDataSource());
Collection<CRFVersionBean> crfVersions = cVersionDao.findAll();
CrfVersionMediaDao mediaDao =
(CrfVersionMediaDao)
SpringServletAccess.getApplicationContext(context).getBean("crfVersionMediaDao");
try {
XFormList formList = new XFormList();
for (CRFBean crf : crfs) {
for (CRFVersionBean version : crfVersions) {
if (version.getCrfId() == crf.getId()) {
XForm form = new XForm(crf, version);
// TODO: Need to generate hash based on contents of
// XForm. Will be done in a later story.
// TODO: For now all XForms get a date based hash to
// trick Enketo into always downloading
// TODO: them.
Calendar cal = Calendar.getInstance();
cal.setTime(new Date());
form.setHash(DigestUtils.md5Hex(String.valueOf(cal.getTimeInMillis())));
String urlBase =
getCoreResources().getDataInfo().getProperty("sysURL").split("/MainMenu")[0];
form.setDownloadURL(
urlBase + "/rest2/openrosa/" + studyOID + "/formXml?formId=" + version.getOid());
List<CrfVersionMedia> mediaList = mediaDao.findByCrfVersionId(version.getId());
if (mediaList != null && mediaList.size() > 0) {
form.setManifestURL(
urlBase + "/rest2/openrosa/" + studyOID + "/manifest?formId=" + version.getOid());
}
formList.add(form);
}
}
}
// Create the XML formList using a Castor mapping file.
XMLContext xmlContext = new XMLContext();
Mapping mapping = xmlContext.createMapping();
mapping.loadMapping(getCoreResources().getURL("openRosaFormListMapping.xml"));
xmlContext.addMapping(mapping);
Marshaller marshaller = xmlContext.createMarshaller();
StringWriter writer = new StringWriter();
marshaller.setWriter(writer);
marshaller.marshal(formList);
// Set response headers
Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("GMT"));
Date currentDate = new Date();
cal.setTime(currentDate);
SimpleDateFormat format = new SimpleDateFormat("E, dd MMM yyyy HH:mm:ss zz");
format.setCalendar(cal);
response.setHeader("Content-Type", "text/xml; charset=UTF-8");
response.setHeader("Date", format.format(currentDate));
response.setHeader("X-OpenRosa-Version", "1.0");
return writer.toString();
} catch (Exception e) {
LOGGER.error(e.getMessage());
LOGGER.error(ExceptionUtils.getStackTrace(e));
return "<Error>" + e.getMessage() + "</Error>";
}
}
@RequestMapping(value = "/studies/{study}/metadata", method = RequestMethod.GET)
public ModelAndView studyMetadata(
Model model,
HttpSession session,
@PathVariable("study") String studyOid,
HttpServletResponse response)
throws Exception {
ResourceBundleProvider.updateLocale(new Locale("en_US"));
StudyBean currentStudy = (StudyBean) session.getAttribute("study");
UserAccountBean userAccount = (UserAccountBean) session.getAttribute("userBean");
UserAccountDAO userAccountDao = new UserAccountDAO(dataSource);
userAccount = (UserAccountBean) userAccountDao.findByUserName("root");
StudyDAO studyDao = new StudyDAO(dataSource);
currentStudy = studyDao.findByOid(studyOid);
MetaDataCollector mdc = new MetaDataCollector(dataSource, currentStudy, getRuleSetRuleDao());
AdminDataCollector adc = new AdminDataCollector(dataSource, currentStudy);
// RulesDataCollector rdc = new RulesDataCollector(sm.getDataSource(),
// currentStudy,getRuleSetRuleDao());
MetaDataCollector.setTextLength(200);
ODMBean odmb = mdc.getODMBean();
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC2-0.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
// xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v130/v3.1\"");
xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("oc1.3");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
// rdc.setOdmbean(odmb);
mdc.collectFileData();
MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap(), coreResources);
metaReport.setODMVersion("oc1.3");
metaReport.setOdmBean(mdc.getODMBean());
metaReport.createChunkedOdmXml(Boolean.FALSE);
adc.collectFileData();
AdminDataReportBean adminReport = new AdminDataReportBean(adc.getOdmAdminDataMap());
adminReport.setODMVersion("oc1.3");
adminReport.setOdmBean(mdc.getODMBean());
adminReport.createChunkedOdmXml(Boolean.FALSE);
// rdc.collectFileData();
// RulesDataReportBean rulesReport = new
// RulesDataReportBean(rdc.getOdmRulesDataMap(),getCoreResources());
// rulesReport.setODMVersion("oc1.3");
// rulesReport.setOdmBean(mdc.getODMBean());
// rulesReport.createChunkedOdmXml(Boolean.FALSE);
FullReportBean report = new FullReportBean();
report.setAdminDataMap(adc.getOdmAdminDataMap());
report.setOdmStudyMap(mdc.getOdmStudyMap());
report.setCoreResources(coreResources);
// report.setRulesDataMap(rdc.getOdmRulesDataMap());
report.setOdmBean(mdc.getODMBean());
report.setODMVersion("oc1.3");
report.createStudyMetaOdmXml(Boolean.FALSE);
response.setContentType("application/xml");
PrintWriter out = response.getWriter();
out.print(report.getXmlOutput().toString().trim());
return null;
}
private void submitStudy(StudyBean newStudy) {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyBean study1 = newStudy;
logger.info("study bean to be updated:" + study1.getName());
study1.setUpdatedDate(new Date());
study1.setUpdater((UserAccountBean) session.getAttribute("userBean"));
sdao.update(study1);
ArrayList siteList = (ArrayList) sdao.findAllByParent(newStudy.getId());
if (siteList.size() > 0) {
sdao.updateSitesStatus(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);
// BWP 1/12/2009 3169 Update interviewerNameEditable and
// interviewDateEditable parameters for all sites>>
List<StudyBean> sites = new ArrayList<StudyBean>();
sites = (ArrayList) sdao.findAllByParent(newStudy.getId());
if (sites != null && (!sites.isEmpty())) {
updateInterviewerForSites(newStudy, sites, spvdao, "interviewerNameEditable");
}
// >>
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);
// BWP 1/12/2009 3169>>
if (sites != null && (!sites.isEmpty())) {
updateInterviewerForSites(newStudy, sites, spvdao, "interviewDateEditable");
}
// >>
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);
spv.setParameter("secondaryLabelViewable");
spv.setValue(study1.getStudyParameterConfig().getSecondaryLabelViewable());
updateParameter(spvdao, spv);
// tbh, 06/04/2009 3684>>
spv.setParameter("adminForcedReasonForChange");
spv.setValue(study1.getStudyParameterConfig().getAdminForcedReasonForChange());
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);
}
}
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
StudyDAO sdao = new StudyDAO(sm.getDataSource());
addEntityList(
"studies",
sdao.findAll(),
"A user cannot be created, because there is no study to set as an active study for the user.",
Page.ADMIN_SYSTEM);
addEntityList(
"roles",
getRoles(),
"A user cannot be created, because there are no roles to set as a role within the active study for the user.",
Page.ADMIN_SYSTEM);
ArrayList types = UserType.toArrayList();
types.remove(UserType.INVALID);
if (!ub.isTechAdmin()) {
types.remove(UserType.TECHADMIN);
}
addEntityList(
"types",
types,
"A user cannot be created, because there are no user types within the active study for the user.",
Page.ADMIN_SYSTEM);
if (!fp.isSubmitted()) {
forwardPage(Page.CREATE_ACCOUNT);
} else {
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
Validator v = new Validator(request);
// username must not be blank,
// must be in the format specified by Validator.USERNAME,
// and must be unique
v.addValidation(INPUT_USERNAME, Validator.NO_BLANKS);
v.addValidation(
INPUT_USERNAME,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(INPUT_USERNAME, Validator.IS_A_USERNAME);
v.addValidation(INPUT_USERNAME, Validator.USERNAME_UNIQUE, udao);
v.addValidation(INPUT_FIRST_NAME, Validator.NO_BLANKS);
v.addValidation(INPUT_LAST_NAME, Validator.NO_BLANKS);
v.addValidation(
INPUT_FIRST_NAME,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
50);
v.addValidation(
INPUT_LAST_NAME,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
50);
v.addValidation(INPUT_EMAIL, Validator.NO_BLANKS);
v.addValidation(
INPUT_EMAIL,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
120);
v.addValidation(INPUT_EMAIL, Validator.IS_A_EMAIL);
v.addValidation(INPUT_INSTITUTION, Validator.NO_BLANKS);
v.addValidation(
INPUT_INSTITUTION,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(INPUT_STUDY, Validator.ENTITY_EXISTS, sdao);
v.addValidation(INPUT_ROLE, Validator.IS_VALID_TERM, TermType.ROLE);
HashMap errors = v.validate();
if (errors.isEmpty()) {
UserAccountBean createdUserAccountBean = new UserAccountBean();
createdUserAccountBean.setName(fp.getString(INPUT_USERNAME));
createdUserAccountBean.setFirstName(fp.getString(INPUT_FIRST_NAME));
createdUserAccountBean.setLastName(fp.getString(INPUT_LAST_NAME));
createdUserAccountBean.setEmail(fp.getString(INPUT_EMAIL));
createdUserAccountBean.setInstitutionalAffiliation(fp.getString(INPUT_INSTITUTION));
SecurityManager secm = SecurityManager.getInstance();
String password = secm.genPassword();
String passwordHash = secm.encrytPassword(password);
createdUserAccountBean.setPasswd(passwordHash);
createdUserAccountBean.setPasswdTimestamp(null);
createdUserAccountBean.setLastVisitDate(null);
createdUserAccountBean.setStatus(Status.AVAILABLE);
createdUserAccountBean.setPasswdChallengeQuestion("");
createdUserAccountBean.setPasswdChallengeAnswer("");
createdUserAccountBean.setPhone("");
createdUserAccountBean.setOwner(ub);
int studyId = fp.getInt(INPUT_STUDY);
Role r = Role.get(fp.getInt(INPUT_ROLE));
createdUserAccountBean = addActiveStudyRole(createdUserAccountBean, studyId, r);
UserType type = UserType.get(fp.getInt("type"));
logger.warning("*** found type: " + fp.getInt("type"));
logger.warning("*** setting type: " + type.getDescription());
createdUserAccountBean.addUserType(type);
createdUserAccountBean = (UserAccountBean) udao.create(createdUserAccountBean);
String displayPwd = fp.getString(INPUT_DISPLAY_PWD);
if (createdUserAccountBean.isActive()) {
addPageMessage(
"The user account \""
+ createdUserAccountBean.getName()
+ "\" was created successfully. ");
if ("no".equalsIgnoreCase(displayPwd)) {
try {
sendNewAccountEmail(createdUserAccountBean, password);
} catch (Exception e) {
addPageMessage(
"There was an error sending the account-creating email. Please contact the user directly regarding account creation. You may reset the user's password by editing the user's account.");
}
} else {
addPageMessage(
"User Password: "******". Please write down the password and provide it directly to the user.");
}
} else {
addPageMessage(
"The user account \""
+ createdUserAccountBean.getName()
+ "\" could not be created due to a database error.");
}
if (createdUserAccountBean.isActive()) {
request.setAttribute(
ViewUserAccountServlet.ARG_USER_ID,
new Integer(createdUserAccountBean.getId()).toString());
forwardPage(Page.VIEW_USER_ACCOUNT_SERVLET);
} else {
forwardPage(Page.LIST_USER_ACCOUNTS_SERVLET);
}
} else {
String textFields[] = {
INPUT_USERNAME,
INPUT_FIRST_NAME,
INPUT_LAST_NAME,
INPUT_EMAIL,
INPUT_INSTITUTION,
INPUT_DISPLAY_PWD
};
fp.setCurrentStringValuesAsPreset(textFields);
String ddlbFields[] = {INPUT_STUDY, INPUT_ROLE, INPUT_TYPE};
fp.setCurrentIntValuesAsPreset(ddlbFields);
HashMap presetValues = fp.getPresetValues();
setPresetValues(presetValues);
setInputMessages(errors);
addPageMessage("There were some errors in your submission. See below for details.");
forwardPage(Page.CREATE_ACCOUNT);
}
}
}
@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);
}
}
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");
}
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;
}
/** 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);
}
private StudyBean getStudy(Integer id) {
sdao = new StudyDAO(dataSource);
StudyBean studyBean = (StudyBean) sdao.findByPK(id);
return studyBean;
}
