use of org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO in project OpenClinica by OpenClinica.
the class SignStudySubjectServlet method getDisplayStudyEventsForStudySubject.
public static ArrayList getDisplayStudyEventsForStudySubject(StudyBean study, StudySubjectBean studySub, DataSource ds, UserAccountBean ub, StudyUserRoleBean currentRole) {
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
StudyEventDAO sedao = new StudyEventDAO(ds);
EventCRFDAO ecdao = new EventCRFDAO(ds);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds);
StudySubjectDAO ssdao = new StudySubjectDAO(ds);
ArrayList events = sedao.findAllByStudySubject(studySub);
ArrayList displayEvents = new ArrayList();
for (int i = 0; i < events.size(); i++) {
StudyEventBean event = (StudyEventBean) events.get(i);
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(event.getStudyEventDefinitionId());
event.setStudyEventDefinition(sed);
// find all active crfs in the definition
ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, sed.getId());
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
// construct info needed on view study event page
DisplayStudyEventBean de = new DisplayStudyEventBean();
de.setStudyEvent(event);
de.setDisplayEventCRFs(getDisplayEventCRFs(study, ds, eventCRFs, ub, currentRole, event.getSubjectEventStatus()));
ArrayList al = getUncompletedCRFs(ds, eventDefinitionCRFs, eventCRFs, event.getSubjectEventStatus());
populateUncompletedCRFsWithCRFAndVersions(ds, al);
de.setUncompletedCRFs(al);
StudySubjectBean studySubject = (StudySubjectBean) ssdao.findByPK(event.getStudySubjectId());
de.setMaximumSampleOrdinal(sedao.getMaxSampleOrdinal(sed, studySubject));
displayEvents.add(de);
// event.setEventCRFs(createAllEventCRFs(eventCRFs,
// eventDefinitionCRFs));
}
return displayEvents;
}
use of org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO 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.EventDefinitionCRFDAO in project OpenClinica by OpenClinica.
the class StudyAuditLogServlet method processRequest.
/*
* (non-Javadoc) Assume that we get the user id automatically. We will jump
* from the edit user page if the user is an admin, they can get to see the
* users' log
* @see org.akaza.openclinica.control.core.SecureController#processRequest()
*/
/*
* (non-Javadoc) redo this servlet to run the audits per study subject for
* the study; need to add a studyId param and then use the
* StudySubjectDAO.findAllByStudyOrderByLabel() method to grab a lot of
* study subject beans and then return them much like in
* ViewStudySubjectAuditLogServet.process() currentStudy instead of studyId?
*/
@Override
protected void processRequest() throws Exception {
int studyId = currentStudy.getId();
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
AuditDAO adao = new AuditDAO(sm.getDataSource());
UserAccountDAO uadao = new UserAccountDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyDAO studydao = new StudyDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
StudyAuditLogTableFactory factory = new StudyAuditLogTableFactory();
factory.setSubjectDao(sdao);
factory.setStudySubjectDao(subdao);
factory.setUserAccountDao(uadao);
factory.setCurrentStudy(currentStudy);
String auditLogsHtml = factory.createTable(request, response).render();
request.setAttribute("auditLogsHtml", auditLogsHtml);
forwardPage(Page.AUDIT_LOGS_STUDY);
}
use of org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO in project OpenClinica by OpenClinica.
the class UnlockEventDefinitionServlet method processRequest.
@Override
public void processRequest() throws Exception {
String idString = request.getParameter("id");
int defId = Integer.valueOf(idString.trim()).intValue();
StudyEventDefinitionDAO sdao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) sdao.findByPK(defId);
// find all CRFs
EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
ArrayList eventDefinitionCRFs = (ArrayList) edao.findAllByDefinition(defId);
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
ArrayList versions = (ArrayList) cvdao.findAllByCRF(edc.getCrfId());
edc.setVersions(versions);
CRFBean crf = (CRFBean) cdao.findByPK(edc.getCrfId());
edc.setCrfName(crf.getName());
}
// finds all events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = (ArrayList) sedao.findAllByDefinition(sed.getId());
String action = request.getParameter("action");
if (StringUtil.isBlank(idString)) {
addPageMessage(respage.getString("please_choose_a_SED_to_unlock"));
forwardPage(Page.LIST_DEFINITION_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
if (!sed.getStatus().equals(Status.LOCKED)) {
addPageMessage(respage.getString("this_SED_cannot_be_unlocked") + " " + respage.getString("please_contact_sysadmin_for_more_information"));
forwardPage(Page.LIST_DEFINITION_SERVLET);
return;
}
request.setAttribute("definitionToUnlock", sed);
request.setAttribute("eventDefinitionCRFs", eventDefinitionCRFs);
request.setAttribute("events", events);
forwardPage(Page.UNLOCK_DEFINITION);
} else {
logger.info("submit to lock the definition");
// unlock definition
sed.setStatus(Status.AVAILABLE);
sed.setUpdater(ub);
sed.setUpdatedDate(new Date());
sdao.update(sed);
// lock all crfs
for (int j = 0; j < eventDefinitionCRFs.size(); j++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(j);
edc.setStatus(Status.AVAILABLE);
edc.setUpdater(ub);
edc.setUpdatedDate(new Date());
edao.update(edc);
}
// unlock all events
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);
// unlock all the item data
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);
}
}
}
String emailBody = respage.getString("the_SED") + " " + sed.getName() + respage.getString("has_been_unlocked_for_the_study") + " " + currentStudy.getName() + ". " + respage.getString("subject_event_data_is_as_it_was_before");
addPageMessage(emailBody);
sendEmail(emailBody);
forwardPage(Page.LIST_DEFINITION_SERVLET);
}
}
}
use of org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO in project OpenClinica by OpenClinica.
the class DiscrepancyNoteUtil method getThreadedDNotesForStudy.
/**
* Get all discrepancy notes for a study, including "threads" of parent and
* child discrepancy notes.
*
* @param currentStudy
* A StudyBean object.
* @param resolutionStatusIds
* A HashSet object consisting of resolution status ids (i.e.,
* 1,2,3).
* @param dataSource
* A DataSource used for various DAO methods.
* @param discNoteType
* An int discrepancy note type id; only DiscrepancyNoteBeans
* will be returned if they have this discrepancyNoteTypeId.
* @param updateStatusOfParents
* @return A List of DiscrepancyNoteBeans.
*/
public List<DiscrepancyNoteBean> getThreadedDNotesForStudy(StudyBean currentStudy, Set<Integer> resolutionStatusIds, DataSource dataSource, int discNoteType, boolean updateStatusOfParents) {
List<DiscrepancyNoteBean> allDiscNotes = new ArrayList<DiscrepancyNoteBean>();
if (currentStudy == null)
return allDiscNotes;
// Do the returned DN's have to be filtered? A valid resolution status
// has to be between 1 and 5; 0 is "invalid";
// -1 means that no resolutionStatus parameter was passed into the
// servlet
boolean filterDiscNotes = checkResolutionStatus(resolutionStatusIds);
boolean filterforDiscNoteType = discNoteType >= 1 && discNoteType <= 4;
DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(dataSource);
StudyDAO studyDAO = new StudyDAO(dataSource);
// what is the purpose of this data member?
discrepancyNoteDAO.setFetchMapping(true);
int parentStudyId = currentStudy.getParentStudyId();
Set<String> hiddenCrfNames = new TreeSet<String>();
if (parentStudyId > 0) {
hiddenCrfNames = new EventDefinitionCRFDAO(dataSource).findHiddenCrfNamesBySite(currentStudy);
}
allDiscNotes = discrepancyNoteDAO.findAllDiscrepancyNotesDataByStudy(currentStudy);
if (filterDiscNotes) {
// filter for the resolution status
allDiscNotes = filterDiscNotes(allDiscNotes, resolutionStatusIds);
}
if (filterforDiscNoteType) {
// filter for the ddiscrepancyNoteTypeId
allDiscNotes = filterforDiscNoteType(allDiscNotes, discNoteType);
}
return allDiscNotes;
}
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