/**
* 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);
}
}
}
}
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;
}
}
@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);
}
/** 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);
}
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 {
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);
}
}
}
@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 StudyBean getStudy(Integer id) {
sdao = new StudyDAO(dataSource);
StudyBean studyBean = (StudyBean) sdao.findByPK(id);
return studyBean;
}
@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);
}
}
}
@Override
protected void executeInternal(JobExecutionContext context) throws JobExecutionException {
// need to generate a Locale so that user beans and other things will
// generate normally
Locale locale = new Locale("en-US");
ResourceBundleProvider.updateLocale(locale);
ResourceBundle pageMessages = ResourceBundleProvider.getPageMessagesBundle();
// logger.debug("--");
// logger.debug("-- executing a job " + message + " at " + new
// java.util.Date().toString());
JobDataMap dataMap = context.getMergedJobDataMap();
SimpleTrigger trigger = (SimpleTrigger) context.getTrigger();
try {
ApplicationContext appContext =
(ApplicationContext) context.getScheduler().getContext().get("applicationContext");
String studySubjectNumber =
((CoreResources) appContext.getBean("coreResources")).getField("extract.number");
coreResources = (CoreResources) appContext.getBean("coreResources");
ruleSetRuleDao = (RuleSetRuleDao) appContext.getBean("ruleSetRuleDao");
dataSource = (DataSource) appContext.getBean("dataSource");
mailSender = (OpenClinicaMailSender) appContext.getBean("openClinicaMailSender");
AuditEventDAO auditEventDAO = new AuditEventDAO(dataSource);
// Scheduler scheduler = context.getScheduler();
// JobDetail detail = context.getJobDetail();
// jobDetailBean = (JobDetailBean) detail;
/*
* data map here should coincide with the job data map found in
* CreateJobExportServlet, with the following code: jobDataMap = new
* JobDataMap(); jobDataMap.put(DATASET_ID, datasetId);
* jobDataMap.put(PERIOD, period); jobDataMap.put(EMAIL, email);
* jobDataMap.put(TAB, tab); jobDataMap.put(CDISC, cdisc);
* jobDataMap.put(SPSS, spss);
*/
String alertEmail = dataMap.getString(EMAIL);
String localeStr = dataMap.getString(LOCALE);
if (localeStr != null) {
locale = new Locale(localeStr);
ResourceBundleProvider.updateLocale(locale);
pageMessages = ResourceBundleProvider.getPageMessagesBundle();
}
int dsId = dataMap.getInt(DATASET_ID);
String tab = dataMap.getString(TAB);
String cdisc = dataMap.getString(CDISC);
String cdisc12 = dataMap.getString(CDISC12);
if (cdisc12 == null) {
cdisc12 = "0";
}
String cdisc13 = dataMap.getString(CDISC13);
if (cdisc13 == null) {
cdisc13 = "0";
}
String cdisc13oc = dataMap.getString(CDISC13OC);
if (cdisc13oc == null) {
cdisc13oc = "0";
}
String spss = dataMap.getString(SPSS);
int userId = dataMap.getInt(USER_ID);
int studyId = dataMap.getInt(STUDY_ID);
// String datasetId = dataMap.getString(DATASET_ID);
// int dsId = new Integer(datasetId).intValue();
// String userAcctId = dataMap.getString(USER_ID);
// int userId = new Integer(userAcctId).intValue();
// why the flip-flop? if one property is set to 'true' we can
// see jobs in another screen but all properties have to be
// strings
logger.debug("-- found the job: " + dsId + " dataset id");
// for (Iterator it = dataMap.entrySet().iterator(); it.hasNext();)
// {
// java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
// Object key = entry.getKey();
// Object value = entry.getValue();
// // logger.debug("-- found datamap property: " + key.toString() +
// // " : " + value.toString());
// }
HashMap fileName = new HashMap<String, Integer>();
if (dsId > 0) {
// trying to not throw an error if there's no dataset id
DatasetDAO dsdao = new DatasetDAO(dataSource);
DatasetBean datasetBean = (DatasetBean) dsdao.findByPK(dsId);
StudyDAO studyDao = new StudyDAO(dataSource);
UserAccountDAO userAccountDAO = new UserAccountDAO(dataSource);
// hmm, three lines in the if block DRY?
String generalFileDir = "";
String generalFileDirCopy = "";
String exportFilePath = SQLInitServlet.getField("exportFilePath");
String pattern =
"yyyy"
+ File.separator
+ "MM"
+ File.separator
+ "dd"
+ File.separator
+ "HHmmssSSS"
+ File.separator;
SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
generalFileDir =
DATASET_DIR
+ datasetBean.getId()
+ File.separator
+ sdfDir.format(new java.util.Date());
if (!"".equals(exportFilePath)) {
generalFileDirCopy =
SQLInitServlet.getField("filePath") + exportFilePath + File.separator;
}
// logger.debug("-- created the following dir: " +
// generalFileDir);
long sysTimeBegin = System.currentTimeMillis();
// set up the user bean here, tbh
// logger.debug("-- gen tab file 00");
userBean = (UserAccountBean) userAccountDAO.findByPK(userId);
// needs to also be captured by the servlet, tbh
// logger.debug("-- gen tab file 00");
generateFileService =
new GenerateExtractFileService(dataSource, userBean, coreResources, ruleSetRuleDao);
// logger.debug("-- gen tab file 00");
// tbh #5796 - covers a bug when the user changes studies, 10/2010
StudyBean activeStudy = (StudyBean) studyDao.findByPK(studyId);
StudyBean parentStudy = new StudyBean();
logger.debug(
"active study: " + studyId + " parent study: " + activeStudy.getParentStudyId());
if (activeStudy.getParentStudyId() > 0) {
// StudyDAO sdao = new StudyDAO(sm.getDataSource());
parentStudy = (StudyBean) studyDao.findByPK(activeStudy.getParentStudyId());
} else {
parentStudy = activeStudy;
// covers a bug in tab file creation, tbh 01/2009
}
logger.debug("-- found extract bean ");
ExtractBean eb =
generateFileService.generateExtractBean(datasetBean, activeStudy, parentStudy);
MessageFormat mf = new MessageFormat("");
StringBuffer message = new StringBuffer();
StringBuffer auditMessage = new StringBuffer();
// use resource bundle page messages to generate the email, tbh
// 02/2009
// message.append(pageMessages.getString("html_email_header_1")
// + " " + alertEmail +
// pageMessages.getString("html_email_header_2") + "<br/>");
message.append(
"<p>"
+ pageMessages.getString("email_header_1")
+ " "
+ EmailEngine.getAdminEmail()
+ " "
+ pageMessages.getString("email_header_2")
+ " Job Execution "
+ pageMessages.getString("email_header_3")
+ "</p>");
message.append("<P>Dataset: " + datasetBean.getName() + "</P>");
message.append("<P>Study: " + activeStudy.getName() + "</P>");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_1")
+ datasetBean.getName()
+ pageMessages.getString("html_email_body_2")
+ SQLInitServlet.getField("sysURL")
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// logger.debug("-- gen tab file 00");
if ("1".equals(tab)) {
logger.debug("-- gen tab file 01");
fileName =
generateFileService.createTabFile(
eb,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy.getId(),
parentStudy.getId(),
generalFileDirCopy);
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_tab_delimited"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your tab-delimited file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_tab_delimited")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc)) {
String odmVersion = "oc1.2";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_12"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.2 w/OpenClinica Extension XML file <a
// href='AccessFile?fileId="
// + getFileIdInt(fileName)
// + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_12")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc12)) {
String odmVersion = "1.2";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.2 default");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_12_xml"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// // auditMessage.append(
// "You can access your ODM 1.2 XML file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_12_xml")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc13)) {
String odmVersion = "1.3";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.3");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_13"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.3 XML file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_13")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc13oc)) {
String odmVersion = "oc1.3";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.3 oc");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_13_xml"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.3 w/OpenClinica Extension XML file <a
// href='AccessFile?fileId="
// + getFileIdInt(fileName)
// + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_13_xml")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(spss)) {
SPSSReportBean answer = new SPSSReportBean();
fileName =
generateFileService.createSPSSFile(
datasetBean,
eb,
activeStudy,
parentStudy,
sysTimeBegin,
generalFileDir,
answer,
generalFileDirCopy);
logger.debug("-- gen spss file");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_spss"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your SPSS files <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_spss")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
// wrap up the message, and send the email
message.append(
"<p>"
+ pageMessages.getString("html_email_body_5")
+ "</P><P>"
+ pageMessages.getString("email_footer"));
try {
mailSender.sendEmail(
alertEmail.trim(),
pageMessages.getString("job_ran_for") + " " + datasetBean.getName(),
message.toString(),
true);
} catch (OpenClinicaSystemException ose) {
// Do Nothing, In the future we might want to have an email
// status added to system.
}
TriggerBean triggerBean = new TriggerBean();
triggerBean.setDataset(datasetBean);
triggerBean.setUserAccount(userBean);
triggerBean.setFullName(trigger.getName());
auditEventDAO.createRowForExtractDataJobSuccess(triggerBean, auditMessage.toString());
} else {
TriggerBean triggerBean = new TriggerBean();
// triggerBean.setDataset(datasetBean);
triggerBean.setUserAccount(userBean);
triggerBean.setFullName(trigger.getName());
auditEventDAO.createRowForExtractDataJobFailure(triggerBean);
// logger.debug("-- made it here for some reason, ds id: "
// + dsId);
}
// logger.debug("-- generated file: " + fileNameStr);
// dataSource.
} catch (Exception e) {
// TODO Auto-generated catch block -- ideally should generate a fail
// msg here, tbh 02/2009
logger.debug("-- found exception: " + e.getMessage());
e.printStackTrace();
}
}
@Override
public void processRequest() throws Exception {
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
String name = request.getParameter("name");
String studyIdString = request.getParameter("studyId");
if (StringUtil.isBlank(name) || StringUtil.isBlank(studyIdString)) {
addPageMessage(respage.getString("please_choose_a_user_to_set_role_for"));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
} else {
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
UserAccountBean user = (UserAccountBean) udao.findByUserName(name);
StudyBean userStudy = (StudyBean) sdao.findByPK(fp.getInt("studyId"));
if ("confirm".equalsIgnoreCase(action)) {
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
request.setAttribute("user", user);
StudyUserRoleBean uRole = udao.findRoleByUserNameAndStudyId(name, studyId);
uRole.setStudyName(userStudy.getName());
request.setAttribute("uRole", uRole);
ArrayList roles = Role.toArrayList();
roles.remove(Role.ADMIN); // admin is not a user role, only used for tomcat
StudyBean studyBean = (StudyBean) sdao.findByPK(uRole.getStudyId());
if (currentStudy.getParentStudyId() > 0) {
roles.remove(Role.COORDINATOR);
roles.remove(Role.STUDYDIRECTOR);
} else if (studyBean.getParentStudyId() > 0) {
roles.remove(Role.COORDINATOR);
roles.remove(Role.STUDYDIRECTOR);
// TODO: redo this fix
Role r = Role.RESEARCHASSISTANT;
r.setDescription("site_Data_Entry_Person");
roles.remove(Role.RESEARCHASSISTANT);
roles.add(r);
Role ri = Role.INVESTIGATOR;
ri.setDescription("site_investigator");
roles.remove(Role.INVESTIGATOR);
roles.add(ri);
}
request.setAttribute("roles", roles);
forwardPage(Page.SET_USER_ROLE_IN_STUDY);
} else {
// set role
String userName = fp.getString("name");
int studyId = fp.getInt("studyId");
int roleId = fp.getInt("roleId");
StudyUserRoleBean sur = new StudyUserRoleBean();
sur.setName(userName);
sur.setRole(Role.get(roleId));
sur.setStudyId(studyId);
sur.setStudyName(userStudy.getName());
sur.setStatus(Status.AVAILABLE);
sur.setUpdater(ub);
sur.setUpdatedDate(new Date());
udao.updateStudyUserRole(sur, userName);
addPageMessage(sendEmail(user, sur));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
}
}
}