private StudySubjectBean createStudySubject(
SubjectBean subject, StudyBean studyBean, Date enrollmentDate, String secondaryId) {
StudySubjectBean studySubject = new StudySubjectBean();
studySubject.setSecondaryLabel(secondaryId);
studySubject.setOwner(getUserAccount());
studySubject.setEnrollmentDate(enrollmentDate);
studySubject.setLabel(subject.getLabel());
subject.setLabel(null);
studySubject.setSubjectId(subject.getId());
studySubject.setStudyId(studyBean.getId());
studySubject.setStatus(Status.AVAILABLE);
return studySubject;
}
public StudySubjectBean createStudySubjectBean(
StudyBean sBean, SubjectBean subjectBean, UserAccountBean uBean) {
StudySubjectBean ssBean = new StudySubjectBean();
subjectBean.setGender('\0'); // setting null character
ssBean.setStudyId(sBean.getId());
ssBean.setSubjectId(subjectBean.getId());
ssBean.setStatus(Status.AVAILABLE);
ssBean.setOwner(uBean);
ssBean.setEnrollmentDate(new Date());
int nextLabel = getStudySubjectDao().findTheGreatestLabel() + 1;
ssBean.setLabel(Integer.toString(nextLabel));
StudySubjectDAO ssdao = new StudySubjectDAO(dataSource);
ssBean = (StudySubjectBean) ssdao.create(ssBean, false);
return ssBean;
}
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 {
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int subjectId = fp.getInt("id");
String action = fp.getString("action");
if (subjectId == 0 || StringUtil.isBlank(action)) {
addPageMessage(respage.getString("please_choose_a_subject_to_remove"));
forwardPage(Page.SUBJECT_LIST_SERVLET);
} else {
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
// find all study subjects
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList studySubs = ssdao.findAllBySubjectId(subjectId);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = sedao.findAllBySubjectId(subjectId);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("subjectToRemove", subject);
request.setAttribute("studySubs", studySubs);
request.setAttribute("events", events);
forwardPage(Page.REMOVE_SUBJECT);
} else {
logger.info("submit to remove the subject");
// change all statuses to deleted
subject.setStatus(Status.DELETED);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
sdao.update(subject);
// remove subject references from study
for (int i = 0; i < studySubs.size(); i++) {
StudySubjectBean studySub = (StudySubjectBean) studySubs.get(i);
if (!studySub.getStatus().equals(Status.DELETED)) {
studySub.setStatus(Status.AUTO_DELETED);
studySub.setUpdater(ub);
studySub.setUpdatedDate(new Date());
ssdao.update(studySub);
}
}
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")
+ " "
+ respage.getString("has_been_removed_succesfully");
addPageMessage(emailBody);
// sendEmail(emailBody);
forwardPage(Page.SUBJECT_LIST_SERVLET);
}
}
}
@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);
}
}
}