use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class SignStudySubjectServlet method processRequest.
@Override
public void processRequest() throws Exception {
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
String action = fp.getString("action");
// studySubjectId
int studySubId = fp.getInt("id", true);
String module = fp.getString(MODULE);
request.setAttribute(MODULE, module);
if (studySubId == 0) {
addPageMessage(respage.getString("please_choose_a_subject_to_view"));
forwardPage(Page.LIST_STUDY_SUBJECTS);
return;
}
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
if (!permitSign(studySub, sm.getDataSource())) {
addPageMessage(respage.getString("subject_event_cannot_signed"));
// forwardPage(Page.SUBMIT_DATA_SERVLET);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
// >> changed tbh, 06/2009
return;
}
if (action.equalsIgnoreCase("confirm")) {
String username = request.getParameter("j_user");
String password = request.getParameter("j_pass");
SecurityManager securityManager = ((SecurityManager) SpringServletAccess.getApplicationContext(context).getBean("securityManager"));
// String encodedUserPass =
// org.akaza.openclinica.core.SecurityManager
// .getInstance().encrytPassword(password);
UserAccountBean ub = (UserAccountBean) session.getAttribute("userBean");
if (securityManager.verifyPassword(password, getUserDetails()) && ub.getName().equals(username)) {
if (signSubjectEvents(studySub, sm.getDataSource(), ub)) {
// Making the StudySubject signed as all the events have
// become signed.
studySub.setStatus(Status.SIGNED);
studySub.setUpdater(ub);
subdao.update(studySub);
addPageMessage(respage.getString("subject_event_signed"));
// forwardPage(Page.SUBMIT_DATA_SERVLET);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
// >> changed tbh, 06/2009
return;
} else {
addPageMessage(respage.getString("errors_in_submission_see_below"));
forwardPage(Page.LIST_STUDY_SUBJECTS);
return;
}
} else {
request.setAttribute("id", new Integer(studySubId).toString());
addPageMessage(restext.getString("password_match"));
forwardPage(Page.LIST_STUDY_SUBJECTS);
return;
}
}
request.setAttribute("studySub", studySub);
int studyId = studySub.getStudyId();
int subjectId = studySub.getSubjectId();
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
Date dob = subject.getDateOfBirth();
if (dob != null) {
Calendar cal = Calendar.getInstance();
cal.setTime(dob);
int year = cal.get(Calendar.YEAR);
request.setAttribute("yearOfBirth", new Integer(year));
} else {
request.setAttribute("yearOfBirth", "");
}
}
request.setAttribute("subject", subject);
StudyDAO studydao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) studydao.findByPK(studyId);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
if (study.getParentStudyId() > 0) {
// this is a site,find parent
StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
request.setAttribute("parentStudy", parentStudy);
} else {
request.setAttribute("parentStudy", new StudyBean());
}
ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId);
request.setAttribute("children", children);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
// find all eventcrfs for each event
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
ArrayList<DisplayStudyEventBean> displayEvents = getDisplayStudyEventsForStudySubject(study, studySub, sm.getDataSource(), ub, currentRole);
DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil();
// Don't filter for now; disc note beans are returned with eventCRFId
// set
discNoteUtil.injectParentDiscNotesIntoDisplayStudyEvents(displayEvents, new HashSet(), sm.getDataSource(), 0);
// All the displaystudyevents for one subject
request.setAttribute("displayStudyEvents", displayEvents);
// Set up a Map for the JSP view, mapping the eventCRFId to another Map:
// the
// inner Map maps the resolution status name to the number of notes for
// that
// eventCRF id, as in New --> 2
Map discNoteByEventCRFid = discNoteUtil.createDiscNoteMapByEventCRF(displayEvents);
request.setAttribute("discNoteByEventCRFid", discNoteByEventCRFid);
EntityBeanTable table = fp.getEntityBeanTable();
// sort by start date,
table.setSortingIfNotExplicitlySet(1, false);
// desc
ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents);
String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("location"), resword.getString("status"), resword.getString("actions"), resword.getString("CRFs_atrib") };
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(4);
table.hideColumnLink(5);
if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) {
table.addLink(resword.getString("add_new_event"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId());
}
HashMap args = new HashMap();
args.put("id", new Integer(studySubId).toString());
table.setQuery("ViewStudySubject", args);
table.setRows(allEventRows);
table.computeDisplay();
request.setAttribute("table", table);
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId);
request.setAttribute("groups", groupMaps);
AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList eventLogs = new ArrayList();
for (int i = 0; i < logs.size(); i++) {
AuditEventBean avb = (AuditEventBean) logs.get(i);
StudyEventAuditBean sea = new StudyEventAuditBean();
sea.setAuditEvent(avb);
StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId());
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
sea.setDefinition(sed);
String old = avb.getOldValue().trim();
try {
if (!StringUtil.isBlank(old)) {
SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue());
sea.setOldSubjectEventStatus(oldStatus);
}
String newValue = avb.getNewValue().trim();
if (!StringUtil.isBlank(newValue)) {
SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue());
sea.setNewSubjectEventStatus(newStatus);
}
} catch (NumberFormatException e) {
// TODO Auto-generated catch block
e.printStackTrace();
// logger.warning("^^^ caught NFE");
}
UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
sea.setUpdater(updater);
eventLogs.add(sea);
}
// logger.warning("^^^ finished iteration");
request.setAttribute("eventLogs", eventLogs);
forwardPage(Page.SIGN_STUDY_SUBJECT);
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class ListSubjectGroupClassServlet method processRequest.
@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);
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class RemoveSiteServlet method processRequest.
@Override
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
String idString = request.getParameter("id");
logger.info("site id:" + idString);
int siteId = Integer.valueOf(idString.trim()).intValue();
StudyBean study = (StudyBean) sdao.findByPK(siteId);
if (currentStudy.getId() != study.getParentStudyId()) {
addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
forwardPage(Page.MENU_SERVLET);
return;
}
// find all user and roles
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(siteId);
// find all subjects
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (StringUtil.isBlank(idString)) {
addPageMessage(respage.getString("please_choose_a_site_to_remove"));
forwardPage(Page.SITE_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("siteToRemove", study);
request.setAttribute("userRolesToRemove", userRoles);
request.setAttribute("subjectsToRemove", subjects);
forwardPage(Page.REMOVE_SITE);
} else {
logger.info("submit to remove the site");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setOldStatus(study.getStatus());
study.setStatus(Status.DELETED);
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// remove all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
if (!role.getStatus().equals(Status.DELETED)) {
role.setStatus(Status.AUTO_DELETED);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
// YW << So study_user_role table status_id field can be
// updated
udao.updateStudyUserRole(role, role.getUserName());
}
// YW 06-18-2007 >>
}
// YW << bug fix that current active study has been deleted
if (study.getId() == currentStudy.getId()) {
currentStudy.setStatus(Status.DELETED);
// currentRole.setRole(Role.INVALID);
currentRole.setStatus(Status.DELETED);
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
}
// 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);
if (!group.getStatus().equals(Status.DELETED)) {
group.setStatus(Status.AUTO_DELETED);
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);
if (!sgMap.getStatus().equals(Status.DELETED)) {
sgMap.setStatus(Status.AUTO_DELETED);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
}
}
// remove all events
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
if (!subject.getStatus().equals(Status.DELETED)) {
subject.setStatus(Status.AUTO_DELETED);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
ArrayList events = sedao.findAllByStudySubject(subject);
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.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.AUTO_DELETED);
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);
if (!item.getStatus().equals(Status.DELETED)) {
item.setOldStatus(item.getStatus());
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
}
}
// for subjects
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);
if (!data.getStatus().equals(Status.DELETED)) {
data.setStatus(Status.AUTO_DELETED);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
}
addPageMessage(respage.getString("this_site_has_been_removed_succesfully"));
String fromListSite = (String) session.getAttribute("fromListSite");
if (fromListSite != null && fromListSite.equals("yes") && currentRole.getRole().equals(Role.STUDYDIRECTOR)) {
session.removeAttribute("fromListSite");
forwardPage(Page.SITE_LIST_SERVLET);
} else {
session.removeAttribute("fromListSite");
if (currentRole.getRole().equals(Role.ADMIN)) {
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
forwardPage(Page.SITE_LIST_SERVLET);
}
}
}
}
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class ManageStudyServlet method processRequest.
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#processRequest()
*/
@Override
protected void processRequest() throws Exception {
// for the sake of testing a prototype; 2560
if (!INSTRUCTIONS.isEmpty()) {
INSTRUCTIONS.clear();
}
INSTRUCTIONS.add(restext.getString("director_coordinator_privileges_manage"));
INSTRUCTIONS.add(restext.getString("side_tables_shows_last_modified"));
request.setAttribute("instructions", INSTRUCTIONS);
// show icon keys on the sidebar, and display the instructions and
// alert messages fields
request.setAttribute("showIcons", true);
request.setAttribute("openIcons", true);
request.setAttribute("openAlerts", true);
request.setAttribute("openInstructions", true);
// find last 5 modifed sites
StudyDAO sdao = new StudyDAO(sm.getDataSource());
// ArrayList sites = (ArrayList)
// sdao.findAllByParentAndLimit(currentStudy.getId(),true);
ArrayList allSites = (ArrayList) sdao.findAllByParent(currentStudy.getId());
ArrayList sites = new ArrayList();
for (int i = 0; i < allSites.size(); i++) {
sites.add(allSites.get(i));
if (i == 5) {
break;
}
}
request.setAttribute("sites", sites);
request.setAttribute("sitesCount", new Integer(sites.size()));
request.setAttribute("allSitesCount", new Integer(allSites.size()));
// BWP 3057: add study name to JSP
if (currentStudy != null) {
request.setAttribute("studyIdentifier", currentStudy.getIdentifier());
}
StudyEventDefinitionDAO edao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList seds = (ArrayList) edao.findAllByStudyAndLimit(currentStudy.getId());
ArrayList allSeds = edao.findAllByStudy(currentStudy);
request.setAttribute("seds", seds);
request.setAttribute("sedsCount", new Integer(seds.size()));
request.setAttribute("allSedsCount", new Integer(allSeds.size()));
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList users = udao.findAllUsersByStudyIdAndLimit(currentStudy.getId(), true);
ArrayList allUsers = udao.findAllUsersByStudy(currentStudy.getId());
request.setAttribute("users", users);
request.setAttribute("usersCount", new Integer(users.size()));
request.setAttribute("allUsersCount", new Integer(allUsers.size()));
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
// ArrayList subjects = (ArrayList)
// ssdao.findAllByStudyIdAndLimit(currentStudy.getId(),true);
ArrayList allSubjects = ssdao.findAllByStudyId(currentStudy.getId());
ArrayList subjects = new ArrayList();
for (int i = 0; i < allSubjects.size(); i++) {
subjects.add(allSubjects.get(i));
if (i == 5) {
break;
}
}
request.setAttribute("subs", subjects);
request.setAttribute("subsCount", new Integer(subjects.size()));
request.setAttribute("allSubsCount", new Integer(allSubjects.size()));
// added tbh, 9-21-2005
// AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
// ArrayList audits = (ArrayList)
// aedao.findAllByStudyIdAndLimit(currentStudy.getId());
// request.setAttribute("audits", audits);
resetPanel();
if (allSubjects.size() > 0) {
setToPanel("Subjects", new Integer(allSubjects.size()).toString());
}
if (allUsers.size() > 0) {
setToPanel("Users", new Integer(allUsers.size()).toString());
}
if (allSites.size() > 0) {
setToPanel("Sites", new Integer(allSites.size()).toString());
}
if (allSeds.size() > 0) {
setToPanel("Event Definitions", new Integer(allSeds.size()).toString());
}
String proto = request.getParameter("proto");
if (proto == null || "".equalsIgnoreCase(proto)) {
forwardPage(Page.MANAGE_STUDY);
} else {
forwardPage(Page.MANAGE_STUDY_BODY);
}
}
use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.
the class RestoreStudyUserRoleServlet method processRequest.
@Override
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
UserAccountDAO udao = new UserAccountDAO(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_restore_his_role"));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
} else {
String action = request.getParameter("action");
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
StudyBean study = (StudyBean) sdao.findByPK(studyId);
UserAccountBean user = (UserAccountBean) udao.findByUserName(name);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("user", user);
StudyUserRoleBean uRole = udao.findRoleByUserNameAndStudyId(name, studyId);
request.setAttribute("uRole", uRole);
request.setAttribute("uStudy", study);
forwardPage(Page.RESTORE_USER_ROLE_IN_STUDY);
} else {
// restore role
FormProcessor fp = new FormProcessor(request);
String userName = fp.getString("name");
int roleId = fp.getInt("roleId");
StudyUserRoleBean sur = new StudyUserRoleBean();
sur.setName(userName);
sur.setRole(Role.get(roleId));
sur.setStudyId(studyId);
sur.setStatus(Status.AVAILABLE);
sur.setUpdater(ub);
sur.setUpdatedDate(new Date());
udao.updateStudyUserRole(sur, userName);
String restoreMessage = user.getFirstName() + " " + user.getLastName() + " (" + resword.getString("username") + ": " + user.getName() + ") " + respage.getString("has_been_restored_to_the_study_site") + " " + study.getName() + " " + respage.getString("with_the_role") + " " + sur.getRoleName() + ". " + respage.getString("the_user_is_now_be_able_to_access_study");
addPageMessage(restoreMessage);
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
}
}
}
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