public ArrayList findAllSubjectByStudy(StudyBean study) {
this.setTypesExpected();
ArrayList alist = new ArrayList();
this.setTypeExpected(11, TypeNames.STRING); // ss.label
this.setTypeExpected(12, TypeNames.STRING); // column_name
this.setTypeExpected(13, TypeNames.INT); // subject_id
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(study.getId()));
variables.put(new Integer(2), new Integer(study.getId()));
variables.put(new Integer(3), new Integer(study.getId()));
alist = this.select(digester.getQuery("findAllSubjectByStudy"), variables);
ArrayList al = new ArrayList();
Iterator it = alist.iterator();
while (it.hasNext()) {
HashMap hm = (HashMap) it.next();
DiscrepancyNoteBean eb = (DiscrepancyNoteBean) this.getEntityFromHashMap(hm);
eb.setSubjectName((String) hm.get("label"));
eb.setColumn((String) hm.get("column_name"));
eb.setEntityId(((Integer) hm.get("subject_id")).intValue());
al.add(eb);
}
return al;
}
private UserAccountBean createUserAccount(
UserAccountBean rootUserAccount, StudyBean studyBean, StudySubjectBean studySubjectBean)
throws Exception {
UserAccountBean createdUserAccountBean = new UserAccountBean();
createdUserAccountBean.setName(getInputUsername(studyBean, studySubjectBean));
createdUserAccountBean.setFirstName(INPUT_FIRST_NAME);
createdUserAccountBean.setLastName(INPUT_LAST_NAME);
createdUserAccountBean.setEmail(INPUT_EMAIL);
createdUserAccountBean.setInstitutionalAffiliation(INPUT_INSTITUTION);
createdUserAccountBean.setActiveStudyId(studyBean.getId());
String passwordHash = UserAccountBean.LDAP_PASSWORD;
createdUserAccountBean.setPasswd(passwordHash);
createdUserAccountBean.setPasswdTimestamp(null);
createdUserAccountBean.setLastVisitDate(null);
createdUserAccountBean.setActiveStudyId(studyBean.getId());
createdUserAccountBean.setStatus(Status.DELETED);
createdUserAccountBean.setPasswdChallengeQuestion("");
createdUserAccountBean.setPasswdChallengeAnswer("");
createdUserAccountBean.setPhone("");
createdUserAccountBean.setOwner(rootUserAccount);
createdUserAccountBean.setRunWebservices(false);
Role r = Role.RESEARCHASSISTANT2;
createdUserAccountBean =
addActiveStudyRole(createdUserAccountBean, studyBean.getId(), r, rootUserAccount);
UserType type = UserType.get(2);
createdUserAccountBean.addUserType(type);
UserAccountDAO udao = new UserAccountDAO(dataSource);
createdUserAccountBean = (UserAccountBean) udao.create(createdUserAccountBean);
// authoritiesDao.saveOrUpdate(new AuthoritiesBean(createdUserAccountBean.getName()));
return createdUserAccountBean;
}
private ArrayList<StudyEventDefinitionBean> initDefinitions(StudyBean site) {
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
StudyBean parentStudy =
(StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId());
seds = sedDao.findAllByStudy(parentStudy);
int start = 0;
for (StudyEventDefinitionBean sed : seds) {
int defId = sed.getId();
ArrayList<EventDefinitionCRFBean> edcs =
(ArrayList<EventDefinitionCRFBean>)
edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(
defId, site.getId(), parentStudy.getId());
ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
// sed.setCrfNum(edcs.size());
for (EventDefinitionCRFBean edcBean : edcs) {
int edcStatusId = edcBean.getStatus().getId();
CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId());
int crfStatusId = crf.getStatusId();
if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) {
} else {
ArrayList<CRFVersionBean> versions =
(ArrayList<CRFVersionBean>) cvdao.findAllActiveByCRF(edcBean.getCrfId());
edcBean.setVersions(versions);
edcBean.setCrfName(crf.getName());
CRFVersionBean defaultVersion =
(CRFVersionBean) cvdao.findByPK(edcBean.getDefaultVersionId());
edcBean.setDefaultVersionName(defaultVersion.getName());
String sversionIds = edcBean.getSelectedVersionIds();
ArrayList<Integer> idList = new ArrayList<Integer>();
if (sversionIds.length() > 0) {
String[] ids = sversionIds.split("\\,");
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
}
edcBean.setSelectedVersionIdList(idList);
defCrfs.add(edcBean);
++start;
}
}
logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size());
sed.setCrfs(defCrfs);
sed.setCrfNum(defCrfs.size());
}
return seds;
}
private void createDiscrepancyNoteBean(
String description,
String detailedNotes,
int itemDataId,
StudyBean studyBean,
UserAccountBean ub,
DiscrepancyNoteBean parentDiscrepancyNote) {
DiscrepancyNoteBean dnb = new DiscrepancyNoteBean();
dnb.setEntityId(itemDataId); // this is needed for DN Map object
dnb.setStudyId(studyBean.getId());
dnb.setEntityType(DiscrepancyNoteBean.ITEM_DATA);
dnb.setDescription(description);
dnb.setDetailedNotes(detailedNotes);
dnb.setDiscrepancyNoteTypeId(
parentDiscrepancyNote.getDiscrepancyNoteTypeId()); // set to parent DN Type Id
dnb.setResolutionStatusId(4); // set to closed
dnb.setColumn("value"); // this is needed for DN Map object
dnb.setAssignedUserId(ub.getId());
dnb.setOwner(ub);
dnb.setParentDnId(parentDiscrepancyNote.getId());
dnb.setActivated(false);
dnb = (DiscrepancyNoteBean) getDnDao().create(dnb); // create child DN
getDnDao().createMapping(dnb); // create DN mapping
DiscrepancyNoteBean itemParentNote =
(DiscrepancyNoteBean) getDnDao().findByPK(dnb.getParentDnId());
itemParentNote.setResolutionStatusId(ResolutionStatus.CLOSED.getId());
itemParentNote.setAssignedUserId(ub.getId());
getDnDao().update(itemParentNote); // update parent DN
getDnDao().updateAssignedUser(itemParentNote); // update parent DN assigned user
}
private boolean mayProceedPreview(String studyOid) throws Exception {
boolean accessPermission = false;
StudyBean study = getParentStudy(studyOid);
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(dataSource);
StudyParameterValueBean pStatus =
spvdao.findByHandleAndStudy(study.getId(), "participantPortal");
participantPortalRegistrar = new ParticipantPortalRegistrar();
String pManageStatus =
participantPortalRegistrar.getRegistrationStatus(studyOid).toString(); // ACTIVE ,
// PENDING ,
// INACTIVE
String participateStatus = pStatus.getValue().toString(); // enabled , disabled
String studyStatus =
study.getStatus().getName().toString(); // available , pending , frozen , locked
logger.info(
"pManageStatus: "
+ pManageStatus
+ " participantStatus: "
+ participateStatus
+ " studyStatus: "
+ studyStatus);
if (participateStatus.equalsIgnoreCase("enabled")
&& (studyStatus.equalsIgnoreCase("available")
|| studyStatus.equalsIgnoreCase("pending")
|| studyStatus.equalsIgnoreCase("frozen")
|| studyStatus.equalsIgnoreCase("locked"))
&& (pManageStatus.equalsIgnoreCase("ACTIVE")
|| pManageStatus.equalsIgnoreCase("PENDING")
|| pManageStatus.equalsIgnoreCase("INACTIVE"))) {
accessPermission = true;
}
return accessPermission;
}
public ArrayList findAllByStudyAndParent(StudyBean study, int parentId) {
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(parentId));
variables.put(new Integer(2), new Integer(study.getId()));
variables.put(new Integer(3), new Integer(study.getId()));
return this.executeFindAllQuery("findAllByStudyAndParent", variables);
}
private void submitSiteEventDefinitions(StudyBean site) {
FormProcessor fp = new FormProcessor(request);
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
seds = (ArrayList<StudyEventDefinitionBean>) session.getAttribute("definitions");
HashMap<String, Boolean> changes = (HashMap<String, Boolean>) session.getAttribute("changed");
for (StudyEventDefinitionBean sed : seds) {
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
ArrayList<EventDefinitionCRFBean> edcs = sed.getCrfs();
for (EventDefinitionCRFBean edcBean : edcs) {
int edcStatusId = edcBean.getStatus().getId();
if (edcStatusId == 5 || edcStatusId == 7) {
} else {
boolean changed = changes.get(sed.getId() + "-" + edcBean.getId());
if (changed) {
edcBean.setParentId(edcBean.getId());
edcBean.setStudyId(site.getId());
edcBean.setUpdater(ub);
edcBean.setUpdatedDate(new Date());
logger.debug("create for the site");
edcdao.create(edcBean);
}
}
}
}
session.removeAttribute("definitions");
session.removeAttribute("changed");
session.removeAttribute("sdvOptions");
}
private StudyUserRoleBean getRole(UserAccountBean userAccount, StudyBean study) throws Exception {
StudyUserRoleBean role = new StudyUserRoleBean();
if (study == null || userAccount == null || study.getId() == 0) {
throw new Exception();
}
if (userAccount.getId() > 0
&& study.getId() > 0
&& !study.getStatus().getName().equals("removed")) {
role = userAccount.getRoleByStudy(study.getId());
if (study.getParentStudyId() > 0) {
StudyUserRoleBean roleInParent = userAccount.getRoleByStudy(study.getParentStudyId());
role.setRole(Role.max(role.getRole(), roleInParent.getRole()));
}
} else {
throw new Exception();
}
return role;
}
/** Finds all the studies */
@Override
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
ArrayList studies = (ArrayList) sdao.findAll();
// find all parent studies
ArrayList parents = (ArrayList) sdao.findAllParents();
ArrayList displayStudies = new ArrayList();
for (int i = 0; i < parents.size(); i++) {
StudyBean parent = (StudyBean) parents.get(i);
ArrayList children = (ArrayList) sdao.findAllByParent(parent.getId());
DisplayStudyBean displayStudy = new DisplayStudyBean();
displayStudy.setParent(parent);
displayStudy.setChildren(children);
displayStudies.add(displayStudy);
}
FormProcessor fp = new FormProcessor(request);
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allStudyRows = DisplayStudyRow.generateRowsFromBeans(displayStudies);
String[] columns = {
resword.getString("name"),
resword.getString("unique_identifier"),
resword.getString("OID"),
resword.getString("principal_investigator"),
resword.getString("facility_name"),
resword.getString("date_created"),
resword.getString("status"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(2);
table.hideColumnLink(6);
table.setQuery("ListStudy", new HashMap());
table.addLink(resword.getString("create_a_new_study"), "CreateStudy");
table.setRows(allStudyRows);
table.computeDisplay();
request.setAttribute("table", table);
// request.setAttribute("studies", studies);
session.setAttribute("fromListSite", "no");
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
setToPanel(resword.getString("in_the_application"), "");
if (parents.size() > 0) {
setToPanel(resword.getString("studies"), new Integer(parents.size()).toString());
}
if (studies.size() > 0) {
setToPanel(
resword.getString("sites"), new Integer(studies.size() - parents.size()).toString());
}
forwardPage(Page.STUDY_LIST);
}
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 void collectOdmStudy() {
StudyBean study = studyBase.getStudy();
String studyOID = study.getOid();
if (studyOID == null || studyOID.length() <= 0) {
logger.info(
"Constructed studyOID using study_id because oc_oid is missing from the table - study.");
studyOID = "" + study.getId();
}
odmStudy.setOid(studyOID);
collectGlobalVariables();
collectBasicDefinitions();
collectMetaDataVersion();
}
private void collectGlobalVariables() {
StudyBean study = studyBase.getStudy();
String sn = study.getName();
String sd = study.getSummary().trim();
String pn = study.getIdentifier();
if (parentStudy.getId() > 0) {
sn = parentStudy.getName() + " - " + study.getName();
sd = parentStudy.getSummary().trim() + " - " + study.getSummary().trim();
pn = parentStudy.getIdentifier() + " - " + study.getIdentifier();
}
GlobalVariablesBean gv = this.odmStudy.getGlobalVariables();
gv.setStudyName(sn);
gv.setStudyDescription(sd);
gv.setProtocolName(pn);
}
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 ArrayList findAllParentsByStudy(StudyBean study) {
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(study.getId()));
variables.put(new Integer(2), new Integer(study.getId()));
ArrayList notes = executeFindAllQuery("findAllParentsByStudy", variables);
if (fetchMapping) {
for (int i = 0; i < notes.size(); i++) {
DiscrepancyNoteBean dnb = (DiscrepancyNoteBean) notes.get(i);
dnb = findSingleMapping(dnb);
notes.set(i, dnb);
}
}
return notes;
}
public static DiscrepancyNoteBean createDiscrepancyNote(
ItemBean itemBean,
String message,
EventCRFBean eventCrfBean,
DisplayItemBean displayItemBean,
Integer parentId,
UserAccountBean uab,
DataSource ds,
StudyBean study) {
// DisplayItemBean displayItemBean) {
DiscrepancyNoteBean note = new DiscrepancyNoteBean();
StudySubjectDAO ssdao = new StudySubjectDAO(ds);
note.setDescription(message);
note.setDetailedNotes("Failed Validation Check");
note.setOwner(uab);
note.setCreatedDate(new Date());
note.setResolutionStatusId(ResolutionStatus.OPEN.getId());
note.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
if (parentId != null) {
note.setParentDnId(parentId);
}
note.setField(itemBean.getName());
note.setStudyId(study.getId());
note.setEntityName(itemBean.getName());
note.setEntityType("ItemData");
note.setEntityValue(displayItemBean.getData().getValue());
note.setEventName(eventCrfBean.getName());
note.setEventStart(eventCrfBean.getCreatedDate());
note.setCrfName(displayItemBean.getEventDefinitionCRF().getCrfName());
StudySubjectBean ss = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
note.setSubjectName(ss.getName());
note.setEntityId(displayItemBean.getData().getId());
note.setColumn("value");
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(ds);
note = (DiscrepancyNoteBean) dndao.create(note);
// so that the below method works, need to set the entity above
// System.out.println("trying to create mapping with " + note.getId() + " " + note.getEntityId()
// + " " + note.getColumn() + " " + note.getEntityType());
dndao.createMapping(note);
// System.out.println("just created mapping");
return note;
}
private void updateInterviewerForSites(
StudyBean studyBean,
List<StudyBean> sites,
StudyParameterValueDAO studyParameterValueDAO,
String parameterType) {
StudyParameterValueBean studyParameterValueBean = new StudyParameterValueBean();
if ("interviewerNameEditable".equalsIgnoreCase(parameterType)) {
studyParameterValueBean.setParameter("interviewerNameEditable");
studyParameterValueBean.setValue(
studyBean.getStudyParameterConfig().getInterviewerNameEditable());
} else {
studyParameterValueBean.setParameter("interviewerDateEditable");
studyParameterValueBean.setValue(
studyBean.getStudyParameterConfig().getInterviewDateEditable());
}
for (StudyBean siteBean : sites) {
studyParameterValueBean.setStudyId(siteBean.getId());
updateParameter(studyParameterValueDAO, studyParameterValueBean);
}
}
public ArrayList findAllItemDataByStudy(StudyBean study) {
this.setTypesExpected();
ArrayList alist = new ArrayList();
this.setTypeExpected(11, TypeNames.STRING); // ss.label
this.setTypeExpected(12, TypeNames.DATE); // date_start
this.setTypeExpected(13, TypeNames.STRING); // sed_name
this.setTypeExpected(14, TypeNames.STRING); // crf_name
this.setTypeExpected(15, TypeNames.STRING); // item_name
this.setTypeExpected(16, TypeNames.STRING); // value
this.setTypeExpected(17, TypeNames.INT); // item_data_id
this.setTypeExpected(18, TypeNames.INT); // item_id
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(study.getId()));
variables.put(new Integer(2), new Integer(study.getId()));
alist = this.select(digester.getQuery("findAllItemDataByStudy"), variables);
ArrayList al = new ArrayList();
Iterator it = alist.iterator();
while (it.hasNext()) {
HashMap hm = (HashMap) it.next();
DiscrepancyNoteBean eb = (DiscrepancyNoteBean) this.getEntityFromHashMap(hm);
eb.setEventName((String) hm.get("sed_name"));
eb.setEventStart((Date) hm.get("date_start"));
eb.setCrfName((String) hm.get("crf_name"));
eb.setSubjectName((String) hm.get("label"));
eb.setEntityName((String) hm.get("item_name"));
eb.setEntityValue((String) hm.get("value"));
// YW << change EntityId from item_id to item_data_id.
eb.setEntityId(((Integer) hm.get("item_data_id")).intValue());
eb.setItemId(((Integer) hm.get("item_id")).intValue());
// YW >>
al.add(eb);
}
return al;
}
/** 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);
}
}
}
private void submitStudy() {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyBean study1 = (StudyBean) session.getAttribute("newStudy");
logger.info("study bean to be updated:" + study1.getName());
study1.setUpdatedDate(new Date());
study1.setUpdater((UserAccountBean) session.getAttribute("userBean"));
System.out.println("study's parentId=" + study1.getParentStudyId());
sdao.update(study1);
StudyParameterValueBean spv = new StudyParameterValueBean();
spv.setStudyId(study1.getId());
spv.setParameter("collectDob");
spv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString());
updateParameter(spvdao, spv);
spv.setParameter("discrepancyManagement");
spv.setValue(study1.getStudyParameterConfig().getDiscrepancyManagement());
updateParameter(spvdao, spv);
spv.setParameter("genderRequired");
spv.setValue(study1.getStudyParameterConfig().getGenderRequired());
updateParameter(spvdao, spv);
spv.setParameter("subjectPersonIdRequired");
spv.setValue(study1.getStudyParameterConfig().getSubjectPersonIdRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameRequired");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameDefault");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameDefault());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameEditable");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameEditable());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateRequired");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateDefault");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateDefault());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateEditable");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateEditable());
updateParameter(spvdao, spv);
spv.setParameter("subjectIdGeneration");
spv.setValue(study1.getStudyParameterConfig().getSubjectIdGeneration());
updateParameter(spvdao, spv);
spv.setParameter("subjectIdPrefixSuffix");
spv.setValue(study1.getStudyParameterConfig().getSubjectIdPrefixSuffix());
updateParameter(spvdao, spv);
spv.setParameter("personIdShownOnCRF");
spv.setValue(study1.getStudyParameterConfig().getPersonIdShownOnCRF());
updateParameter(spvdao, spv);
StudyBean curStudy = (StudyBean) session.getAttribute("study");
if (curStudy != null && study1.getId() == curStudy.getId()) {
super.currentStudy = study1;
session.setAttribute("study", study1);
}
// update manage_pedigrees for all sites
ArrayList children = (ArrayList) sdao.findAllByParent(study1.getId());
for (int i = 0; i < children.size(); i++) {
StudyBean child = (StudyBean) children.get(i);
child.setType(study1.getType()); // same as parent's type
child.setUpdatedDate(new Date());
child.setUpdater(ub);
sdao.update(child);
// YW << update "collectDob" and "genderRequired" for sites
StudyParameterValueBean childspv = new StudyParameterValueBean();
childspv.setStudyId(child.getId());
childspv.setParameter("collectDob");
childspv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString());
updateParameter(spvdao, childspv);
childspv.setParameter("genderRequired");
childspv.setValue(study1.getStudyParameterConfig().getGenderRequired());
updateParameter(spvdao, childspv);
// YW >>
}
session.removeAttribute("newStudy");
session.removeAttribute("interventions");
}
private void setUpServlet(Trigger trigger) throws Exception {
FormProcessor fp2 = new FormProcessor(request);
request.setAttribute(CreateJobImportServlet.JOB_NAME, trigger.getName());
request.setAttribute(CreateJobImportServlet.JOB_DESC, trigger.getDescription());
dataMap = trigger.getJobDataMap();
String contactEmail = dataMap.getString(ImportSpringJob.EMAIL);
System.out.println("found email: " + contactEmail);
int userId = dataMap.getInt(ImportSpringJob.USER_ID);
int hours = dataMap.getInt(CreateJobImportServlet.HOURS);
int minutes = dataMap.getInt(CreateJobImportServlet.MINUTES);
String directory = dataMap.getString(ImportSpringJob.DIRECTORY);
String studyName = dataMap.getString(ImportSpringJob.STUDY_NAME);
request.setAttribute(ImportSpringJob.EMAIL, contactEmail);
request.setAttribute(ImportSpringJob.STUDY_NAME, studyName);
request.setAttribute("filePath", directory);
request.setAttribute("firstFilePath", IMPORT_DIR);
request.setAttribute("hours", new Integer(hours).toString());
request.setAttribute("minutes", new Integer(minutes).toString());
Date jobDate = trigger.getNextFireTime();
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
// ArrayList studies = udao.findStudyByUser(ub.getName(), (ArrayList)
// sdao.findAll());
// request.setAttribute("studies", studies);
ArrayList<StudyBean> all = (ArrayList<StudyBean>) sdao.findAll();
ArrayList<StudyBean> finalList = new ArrayList<StudyBean>();
for (StudyBean sb : all) {
if (!(sb.getParentStudyId() > 0)) {
finalList.add(sb);
// System.out.println("found study name: " + sb.getName());
finalList.addAll(sdao.findAllByParent(sb.getId()));
}
}
// System.out.println("found list of studies: " + finalList.toString());
addEntityList(
"studies",
finalList,
respage.getString("a_user_cannot_be_created_no_study_as_active"),
Page.ADMIN_SYSTEM);
// tbh >>
// HashMap presetValues = new HashMap();
// Calendar calendar = new GregorianCalendar();
// calendar.setTime(jobDate);
// presetValues.put(CreateJobImportServlet.DATE_START_JOB + "Hour",
// calendar.get(Calendar.HOUR_OF_DAY));
// presetValues.put(CreateJobImportServlet.DATE_START_JOB + "Minute",
// calendar.get(Calendar.MINUTE));
// // TODO this will have to match l10n formatting
// presetValues.put(CreateJobImportServlet.DATE_START_JOB + "Date",
// (calendar.get(Calendar.MONTH) + 1) + "/" +
// calendar.get(Calendar.DATE) + "/"
// + calendar.get(Calendar.YEAR));
// fp2.setPresetValues(presetValues);
// setPresetValues(fp2.getPresetValues());
}
public SimpleTrigger generateTrigger(
FormProcessor fp, UserAccountBean userAccount, StudyBean study, String locale) {
Date startDateTime = fp.getDateTime(DATE_START_JOB);
// check the above?
int datasetId = fp.getInt(DATASET_ID);
String period = fp.getString(PERIOD);
String email = fp.getString(EMAIL);
String jobName = fp.getString(JOB_NAME);
String jobDesc = fp.getString(JOB_DESC);
String spss = fp.getString(SPSS);
String tab = fp.getString(TAB);
String cdisc = fp.getString(CDISC);
String cdisc12 = fp.getString(ExampleSpringJob.CDISC12);
String cdisc13 = fp.getString(ExampleSpringJob.CDISC13);
String cdisc13oc = fp.getString(ExampleSpringJob.CDISC13OC);
BigInteger interval = new BigInteger("0");
if ("monthly".equalsIgnoreCase(period)) {
interval = new BigInteger("2419200000"); // how many
// milliseconds in
// a month? should
// be 24192000000
} else if ("weekly".equalsIgnoreCase(period)) {
interval = new BigInteger("604800000"); // how many
// milliseconds in
// a week? should
// be 6048000000
} else { // daily
interval = new BigInteger("86400000"); // how many
// milliseconds in a
// day?
}
// set up and commit job here
SimpleTrigger trigger = new SimpleTrigger(jobName, "DEFAULT", 64000, interval.longValue());
// set the job detail name,
// based on our choice of format above
// what if there is more than one detail?
// what is the number of times it should repeat?
// arbitrary large number, 64K should be enough :)
trigger.setDescription(jobDesc);
// set just the start date
trigger.setStartTime(startDateTime);
trigger.setName(jobName); // + datasetId);
trigger.setGroup("DEFAULT"); // + datasetId);
trigger.setMisfireInstruction(
SimpleTrigger.MISFIRE_INSTRUCTION_RESCHEDULE_NEXT_WITH_EXISTING_COUNT);
// set job data map
JobDataMap 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(ExampleSpringJob.CDISC12, cdisc12);
jobDataMap.put(ExampleSpringJob.LOCALE, locale);
// System.out.println("found 1.2: " +
// jobDataMap.get(ExampleSpringJob.CDISC12));
jobDataMap.put(ExampleSpringJob.CDISC13, cdisc13);
// System.out.println("found 1.3: " +
// jobDataMap.get(ExampleSpringJob.CDISC13));
jobDataMap.put(ExampleSpringJob.CDISC13OC, cdisc13oc);
// System.out.println("found 1.3oc: " +
// jobDataMap.get(ExampleSpringJob.CDISC13OC));
jobDataMap.put(SPSS, spss);
jobDataMap.put(USER_ID, userAccount.getId());
// StudyDAO studyDAO = new StudyDAO();
jobDataMap.put(STUDY_ID, study.getId());
jobDataMap.put(STUDY_NAME, study.getName());
jobDataMap.put(STUDY_OID, study.getOid());
trigger.setJobDataMap(jobDataMap);
// trigger.setRepeatInterval(interval.longValue());
// System.out.println("default for volatile: " + trigger.isVolatile());
trigger.setVolatility(false);
return trigger;
}
public boolean validate(SubjectTransferBean subjectTransferBean)
throws OpenClinicaSystemException {
StudyDAO stdao = new StudyDAO(this.getDataSource());
StudyBean study = stdao.findByUniqueIdentifier(subjectTransferBean.getStudyOid());
if (study == null) {
throw new OpenClinicaSystemException("Study you specified does not exist");
}
UserAccountBean ua = subjectTransferBean.getOwner();
StudyUserRoleBean role = ua.getRoleByStudy(study);
if (role.getId() == 0 || role.getRole().equals(Role.MONITOR)) {
throw new OpenClinicaSystemException(
"You do not have sufficient priviliges to run this service");
}
if (subjectTransferBean.getSiteIdentifier() != null) {
study =
stdao.findSiteByUniqueIdentifier(
subjectTransferBean.getStudyOid(), subjectTransferBean.getSiteIdentifier());
}
subjectTransferBean.setStudy(study);
if (study == null) {
throw new OpenClinicaSystemException("Site you specified does not exist");
}
int handleStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
org.akaza.openclinica.dao.service.StudyParameterValueDAO spvdao =
new StudyParameterValueDAO(this.getDataSource());
StudyParameterValueBean studyParameter =
spvdao.findByHandleAndStudy(handleStudyId, "subjectPersonIdRequired");
String personId = subjectTransferBean.getPersonId();
if ("required".equals(studyParameter.getValue())
&& (personId == null || personId.length() < 1)) {
throw new OpenClinicaSystemException(
"personId is required for the study: " + study.getName());
// return false;
}
if (personId != null && personId.length() > 255) {
throw new OpenClinicaSystemException("personId should not be longer than 255.");
// return false;
}
String idSetting = "";
StudyParameterValueBean subjectIdGenerationParameter =
spvdao.findByHandleAndStudy(handleStudyId, "subjectIdGeneration");
idSetting = subjectIdGenerationParameter.getValue();
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
int nextLabel = getStudySubjectDao().findTheGreatestLabel() + 1;
subjectTransferBean.setStudySubjectId(new Integer(nextLabel).toString());
}
String studySubjectId = subjectTransferBean.getStudySubjectId();
if (studySubjectId == null || studySubjectId.length() < 1) {
logger.info("studySubjectId is required.");
throw new OpenClinicaSystemException("studySubjectId is required.");
// return false;
} else if (studySubjectId.length() > 30) {
throw new OpenClinicaSystemException("studySubjectId should not be longer than 30.");
// return false;
}
String secondaryId = subjectTransferBean.getSecondaryId();
if (secondaryId != null && secondaryId.length() > 30) {
throw new OpenClinicaSystemException("secondaryId should not be longer than 30.");
// return false;
}
String gender = subjectTransferBean.getGender() + "";
studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "genderRequired");
if ("true".equals(studyParameter.getValue()) && (gender == null || gender.length() < 1)) {
throw new OpenClinicaSystemException("gender is required for the study:" + study.getName());
// return false;
}
Date dateOfBirth = subjectTransferBean.getDateOfBirth();
String yearOfBirth = subjectTransferBean.getYearOfBirth();
studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "collectDob");
if ("1".equals(studyParameter.getValue()) && (dateOfBirth == null)) {
throw new OpenClinicaSystemException("date Of Birth is required:" + study.getName());
// return false;
} else if ("2".equals(studyParameter.getValue()) && (yearOfBirth == null)) {
throw new OpenClinicaSystemException("Year Of Birth is required:" + study.getName());
} else if ("2".equals(studyParameter.getValue()) && (yearOfBirth != null)) {
try {
SimpleDateFormat sdf = new SimpleDateFormat("yyyy");
subjectTransferBean.setDateOfBirth(sdf.parse(subjectTransferBean.getYearOfBirth()));
} catch (ParseException e) {
throw new OpenClinicaSystemException("Year Of Birth not Valid:" + study.getName());
}
}
Date enrollmentDate = subjectTransferBean.getEnrollmentDate();
if (enrollmentDate == null) {
throw new OpenClinicaSystemException("enrollmentDate is required.");
// return false;
} else {
if ((new Date()).compareTo(enrollmentDate) < 0) {
throw new OpenClinicaSystemException("enrollmentDate should be in the past.");
// return false;
}
}
return true;
}
@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();
}
}
/*
* Purpose: Iterates over ODM to populate 2 objects: 1. importCRFList: A List of EventCRFs and information on how to
* process them. 2. importCRFMap: A Map multi-layer map of Subject/Event/Form only populated when the subsequent
* EventCRF passes the UpsertOn rules.
*/
public ImportCRFInfoContainer(ODMContainer odmContainer, DataSource ds) {
importCRFList = new ArrayList<ImportCRFInfo>();
ArrayList<EventCRFBean> eventCRFBeans = new ArrayList<EventCRFBean>();
ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
UpsertOnBean upsert = odmContainer.getCrfDataPostImportContainer().getUpsertOn();
// If Upsert bean is not present, create one with default settings
if (upsert == null) upsert = new UpsertOnBean();
String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOID);
ArrayList<SubjectDataBean> subjectDataBeans =
odmContainer.getCrfDataPostImportContainer().getSubjectData();
Map<String, Map<String, Map<String, String>>> subjectMap =
new HashMap<String, Map<String, Map<String, String>>>();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
StudySubjectBean studySubjectBean =
studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
Map<String, Map<String, String>> eventMap = new HashMap<String, Map<String, String>>();
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
String sampleOrdinal =
studyEventDataBean.getStudyEventRepeatKey() == null
? "1"
: studyEventDataBean.getStudyEventRepeatKey();
StudyEventDefinitionBean studyEventDefinitionBean =
studyEventDefinitionDAO.findByOidAndStudy(
studyEventDataBean.getStudyEventOID(),
studyBean.getId(),
studyBean.getParentStudyId());
logger.info(
"find all by def and subject "
+ studyEventDefinitionBean.getName()
+ " study subject "
+ studySubjectBean.getName());
StudyEventBean studyEventBean =
(StudyEventBean)
studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(
studySubjectBean.getId(),
studyEventDefinitionBean.getId(),
Integer.parseInt(sampleOrdinal));
// @pgawade 16-March-2011 Do not allow the data import
// if event status is one of the - stopped, signed,
// locked
Map<String, String> formMap = new HashMap<String, String>();
for (FormDataBean formDataBean : formDataBeans) {
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans =
crfVersionDAO.findAllByOid(formDataBean.getFormOID());
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
ArrayList<EventCRFBean> eventCrfBeans =
eventCrfDAO.findByEventSubjectVersion(
studyEventBean, studySubjectBean, crfVersionBean);
// what if we have begun with creating a study
// event, but haven't entered data yet? this would
// have us with a study event, but no corresponding
// event crf, yet.
if (eventCrfBeans.isEmpty()) {
logger.debug(
" found no event crfs from Study Event id "
+ studyEventBean.getId()
+ ", location "
+ studyEventBean.getLocation());
ImportCRFInfo importCrfInfo =
new ImportCRFInfo(
studyOID,
subjectDataBean.getSubjectOID(),
studyEventDataBean.getStudyEventOID(),
formDataBean.getFormOID());
importCrfInfo.setPreImportStage(DataEntryStage.UNCOMPLETED);
String crfStatus = formDataBean.getEventCRFStatus();
if (crfStatus != null
&& crfStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()))
importCrfInfo.setPostImportStage(DataEntryStage.INITIAL_DATA_ENTRY);
if ((studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SCHEDULED)
|| studyEventBean
.getSubjectEventStatus()
.equals(SubjectEventStatus.DATA_ENTRY_STARTED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.COMPLETED))) {
if (!upsert.isNotStarted()) {
importCrfInfo.setProcessImport(false);
importCrfInfo.setEventCRFID(null);
}
}
importCRFList.add(importCrfInfo);
if (importCrfInfo.isProcessImport()) formMap.put(formDataBean.getFormOID(), "true");
}
for (EventCRFBean ecb : eventCrfBeans) {
ImportCRFInfo importCrfInfo =
new ImportCRFInfo(
studyOID,
subjectDataBean.getSubjectOID(),
studyEventDataBean.getStudyEventOID(),
formDataBean.getFormOID());
importCrfInfo.setPreImportStage(ecb.getStage());
String crfStatus = formDataBean.getEventCRFStatus();
if (crfStatus != null
&& crfStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()))
importCrfInfo.setPostImportStage(DataEntryStage.INITIAL_DATA_ENTRY);
importCrfInfo.setEventCRFID(new Integer(ecb.getId()));
if (!(ecb.getStage().equals(DataEntryStage.INITIAL_DATA_ENTRY)
&& upsert.isDataEntryStarted())
&& !(ecb.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE)
&& upsert.isDataEntryComplete())) importCrfInfo.setProcessImport(false);
importCRFList.add(importCrfInfo);
if (importCrfInfo.isProcessImport()) formMap.put(formDataBean.getFormOID(), "true");
}
}
} // formdata loop
if (formMap.size() > 0) eventMap.put(studyEventDataBean.getStudyEventOID(), formMap);
} // study event loop
if (eventMap.size() > 0) subjectMap.put(subjectDataBean.getSubjectOID(), eventMap);
} // subject data loop
importCRFMap = subjectMap;
}
@RequestMapping(method = RequestMethod.GET)
public ModelMap handleMainPage(HttpServletRequest request) {
ModelMap map = new ModelMap();
// setUpSidebar(request);
StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
eventDefinitionCRFDao = new EventDefinitionCRFDAO(dataSource);
studyEventDefinitionDao = new StudyEventDefinitionDAO(dataSource);
crfDao = new CRFDAO(dataSource);
studyGroupClassDao = new StudyGroupClassDAO(dataSource);
studyDao = new StudyDAO(dataSource);
userDao = new UserAccountDAO(dataSource);
ruleDao = new RuleDAO(dataSource);
StudyModuleStatus sms = studyModuleStatusDao.findByStudyId(currentStudy.getId());
if (sms == null) {
sms = new StudyModuleStatus();
sms.setStudyId(currentStudy.getId());
}
int crfCount = crfDao.findAllByStudy(currentStudy.getId()).size();
int crfWithEventDefinition = crfDao.findAllActiveByDefinitions(currentStudy.getId()).size();
int totalCrf = crfCount + crfWithEventDefinition;
// int eventDefinitionCount = eventDefinitionCRFDao.findAllActiveByStudy(currentStudy).size();
int eventDefinitionCount = studyEventDefinitionDao.findAllActiveByStudy(currentStudy).size();
int subjectGroupCount = studyGroupClassDao.findAllActiveByStudy(currentStudy).size();
List<RuleSetBean> ruleSets = ruleSetService.getRuleSetsByStudy(currentStudy);
ruleSets = ruleSetService.filterByStatusEqualsAvailableOnlyRuleSetRules(ruleSets);
int ruleCount = ruleSets != null ? ruleSets.size() : 0;
int siteCount = studyDao.findOlnySiteIdsByStudy(currentStudy).size();
int userCount = userDao.findAllUsersByStudy(currentStudy.getId()).size();
Collection childStudies = studyDao.findAllByParent(currentStudy.getId());
Map childStudyUserCount = new HashMap();
for (Object sb : childStudies) {
StudyBean childStudy = (StudyBean) sb;
childStudyUserCount.put(
childStudy.getName(), userDao.findAllUsersByStudy(childStudy.getId()).size());
}
if (sms.getCrf() == 0) {
sms.setCrf(StudyModuleStatus.NOT_STARTED);
}
if (sms.getCrf() != 3 && totalCrf > 0) {
sms.setCrf(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getEventDefinition() == 0) {
sms.setEventDefinition(StudyModuleStatus.NOT_STARTED);
}
if (sms.getEventDefinition() != 3 && eventDefinitionCount > 0) {
sms.setEventDefinition(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getSubjectGroup() == 0) {
sms.setSubjectGroup(StudyModuleStatus.NOT_STARTED);
}
if (sms.getSubjectGroup() != 3 && subjectGroupCount > 0) {
sms.setSubjectGroup(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getRule() == 0) {
sms.setRule(StudyModuleStatus.NOT_STARTED);
}
if (sms.getRule() != 3 && ruleCount > 0) {
sms.setRule(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getSite() == 0) {
sms.setSite(StudyModuleStatus.NOT_STARTED);
}
if (sms.getSite() != 3 && siteCount > 0) {
sms.setSite(StudyModuleStatus.IN_PROGRESS);
}
if (sms.getUsers() == 0) {
sms.setUsers(StudyModuleStatus.NOT_STARTED);
}
if (sms.getUsers() != 3 && userCount > 0) {
sms.setUsers(StudyModuleStatus.IN_PROGRESS);
}
map.addObject(sms);
map.addAttribute("crfCount", totalCrf);
map.addAttribute("eventDefinitionCount", eventDefinitionCount);
map.addAttribute("subjectGroupCount", subjectGroupCount);
map.addAttribute("ruleCount", ruleCount);
map.addAttribute("siteCount", siteCount);
map.addAttribute("userCount", userCount);
map.addAttribute("childStudyUserCount", childStudyUserCount);
map.addAttribute("studyId", currentStudy.getId());
map.addAttribute("currentStudy", currentStudy);
UserAccountBean userBean = (UserAccountBean) request.getSession().getAttribute("userBean");
request.setAttribute("userBean", userBean);
request.setAttribute("statusMap", Status.toStudyUpdateMembersList());
ArrayList pageMessages = new ArrayList();
if (request.getSession().getAttribute("pageMessages") != null) {
pageMessages.addAll((ArrayList) request.getSession().getAttribute("pageMessages"));
request.setAttribute("pageMessages", pageMessages);
request.getSession().removeAttribute("pageMessages");
}
return map;
}
private void submitStudy(StudyBean newStudy) {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyBean study1 = newStudy;
logger.info("study bean to be updated:" + study1.getName());
study1.setUpdatedDate(new Date());
study1.setUpdater((UserAccountBean) session.getAttribute("userBean"));
sdao.update(study1);
ArrayList siteList = (ArrayList) sdao.findAllByParent(newStudy.getId());
if (siteList.size() > 0) {
sdao.updateSitesStatus(study1);
}
StudyParameterValueBean spv = new StudyParameterValueBean();
spv.setStudyId(study1.getId());
spv.setParameter("collectDob");
spv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString());
updateParameter(spvdao, spv);
spv.setParameter("discrepancyManagement");
spv.setValue(study1.getStudyParameterConfig().getDiscrepancyManagement());
updateParameter(spvdao, spv);
spv.setParameter("genderRequired");
spv.setValue(study1.getStudyParameterConfig().getGenderRequired());
updateParameter(spvdao, spv);
spv.setParameter("subjectPersonIdRequired");
spv.setValue(study1.getStudyParameterConfig().getSubjectPersonIdRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameRequired");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameDefault");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameDefault());
updateParameter(spvdao, spv);
spv.setParameter("interviewerNameEditable");
spv.setValue(study1.getStudyParameterConfig().getInterviewerNameEditable());
updateParameter(spvdao, spv);
// BWP 1/12/2009 3169 Update interviewerNameEditable and
// interviewDateEditable parameters for all sites>>
List<StudyBean> sites = new ArrayList<StudyBean>();
sites = (ArrayList) sdao.findAllByParent(newStudy.getId());
if (sites != null && (!sites.isEmpty())) {
updateInterviewerForSites(newStudy, sites, spvdao, "interviewerNameEditable");
}
// >>
spv.setParameter("interviewDateRequired");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateRequired());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateDefault");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateDefault());
updateParameter(spvdao, spv);
spv.setParameter("interviewDateEditable");
spv.setValue(study1.getStudyParameterConfig().getInterviewDateEditable());
updateParameter(spvdao, spv);
// BWP 1/12/2009 3169>>
if (sites != null && (!sites.isEmpty())) {
updateInterviewerForSites(newStudy, sites, spvdao, "interviewDateEditable");
}
// >>
spv.setParameter("subjectIdGeneration");
spv.setValue(study1.getStudyParameterConfig().getSubjectIdGeneration());
updateParameter(spvdao, spv);
spv.setParameter("subjectIdPrefixSuffix");
spv.setValue(study1.getStudyParameterConfig().getSubjectIdPrefixSuffix());
updateParameter(spvdao, spv);
spv.setParameter("personIdShownOnCRF");
spv.setValue(study1.getStudyParameterConfig().getPersonIdShownOnCRF());
updateParameter(spvdao, spv);
spv.setParameter("secondaryLabelViewable");
spv.setValue(study1.getStudyParameterConfig().getSecondaryLabelViewable());
updateParameter(spvdao, spv);
// tbh, 06/04/2009 3684>>
spv.setParameter("adminForcedReasonForChange");
spv.setValue(study1.getStudyParameterConfig().getAdminForcedReasonForChange());
updateParameter(spvdao, spv);
// >>
StudyBean curStudy = (StudyBean) session.getAttribute("study");
if (curStudy != null && study1.getId() == curStudy.getId()) {
super.currentStudy = study1;
session.setAttribute("study", study1);
}
// update manage_pedigrees for all sites
ArrayList children = (ArrayList) sdao.findAllByParent(study1.getId());
for (int i = 0; i < children.size(); i++) {
StudyBean child = (StudyBean) children.get(i);
child.setType(study1.getType()); // same as parent's type
child.setUpdatedDate(new Date());
child.setUpdater(ub);
sdao.update(child);
// YW << update "collectDob" and "genderRequired" for sites
StudyParameterValueBean childspv = new StudyParameterValueBean();
childspv.setStudyId(child.getId());
childspv.setParameter("collectDob");
childspv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString());
updateParameter(spvdao, childspv);
childspv.setParameter("genderRequired");
childspv.setValue(study1.getStudyParameterConfig().getGenderRequired());
updateParameter(spvdao, childspv);
}
}
@Override
public void processRequest() throws Exception {
resetPanel();
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
int studyId = fp.getInt("id");
studyId = studyId == 0 ? fp.getInt("studyId") : studyId;
String action = fp.getString("action");
StudyDAO sdao = new StudyDAO(sm.getDataSource());
boolean isInterventional = false;
study = (StudyBean) sdao.findByPK(studyId);
if (study.getId() != currentStudy.getId()) {
addPageMessage(
respage.getString("not_current_study")
+ respage.getString("change_study_contact_sysadmin"));
forwardPage(Page.MENU_SERVLET);
return;
}
study.setId(studyId);
StudyConfigService scs = new StudyConfigService(sm.getDataSource());
study = scs.setParametersForStudy(study);
request.setAttribute("studyToView", study);
request.setAttribute("studyId", studyId + "");
request.setAttribute("studyPhaseMap", CreateStudyServlet.studyPhaseMap);
ArrayList statuses = Status.toStudyUpdateMembersList();
statuses.add(Status.PENDING);
request.setAttribute("statuses", statuses);
String interventional = resadmin.getString("interventional");
isInterventional = interventional.equalsIgnoreCase(study.getProtocolType());
request.setAttribute("isInterventional", isInterventional ? "1" : "0");
String protocolType = study.getProtocolTypeKey();
// A. Hamid. 5001
if (study.getParentStudyId() > 0) {
StudyBean parentStudy = (StudyBean) sdao.findByPK(study.getParentStudyId());
request.setAttribute("parentStudy", parentStudy);
}
ArrayList interventionArray = new ArrayList();
if (isInterventional) {
interventionArray = parseInterventions((study));
setMaps(isInterventional, interventionArray);
} else {
setMaps(isInterventional, interventionArray);
}
if (!action.equals("submit")) {
// First Load First Form
if (study.getDatePlannedStart() != null) {
fp.addPresetValue(INPUT_START_DATE, local_df.format(study.getDatePlannedStart()));
}
if (study.getDatePlannedEnd() != null) {
fp.addPresetValue(INPUT_END_DATE, local_df.format(study.getDatePlannedEnd()));
}
if (study.getProtocolDateVerification() != null) {
fp.addPresetValue(INPUT_VER_DATE, local_df.format(study.getProtocolDateVerification()));
}
setPresetValues(fp.getPresetValues());
// first load 2nd form
}
if (study == null) {
addPageMessage(respage.getString("please_choose_a_study_to_edit"));
forwardPage(Page.STUDY_LIST_SERVLET);
return;
}
if (action.equals("submit")) {
validateStudy1(fp, v);
validateStudy2(fp, v);
validateStudy3(isInterventional, v, fp);
validateStudy4(fp, v);
validateStudy5(fp, v);
validateStudy6(fp, v);
confirmWholeStudy(fp, v);
request.setAttribute("studyToView", study);
if (!errors.isEmpty()) {
System.out.println("found errors : " + errors.toString());
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY_NEW);
} else {
study.setProtocolType(protocolType);
submitStudy(study);
addPageMessage(respage.getString("the_study_has_been_updated_succesfully"));
ArrayList pageMessages = (ArrayList) request.getAttribute(PAGE_MESSAGE);
session.setAttribute("pageMessages", pageMessages);
response.sendRedirect(request.getContextPath() + "/pages/studymodule");
// forwardPage(Page.MANAGE_STUDY_MODULE);
}
} else {
forwardPage(Page.UPDATE_STUDY_NEW);
}
}
private void collectMetaDataVersion() {
ArrayList<StudyEventDefinitionBean> sedBeansInStudy =
(ArrayList<StudyEventDefinitionBean>) studyBase.getSedBeansInStudy();
if (sedBeansInStudy == null || sedBeansInStudy.size() < 1) {
logger.info("null, because there is no study event definition in this study.");
return;
}
StudyBean study = studyBase.getStudy();
MetaDataVersionBean metadata = this.odmStudy.getMetaDataVersion();
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(this.ds);
int parentId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
StudyParameterValueBean spv = spvdao.findByHandleAndStudy(parentId, "discrepancyManagement");
metadata.setSoftHard(spv.getValue().equalsIgnoreCase("true") ? "Hard" : "Soft");
OdmExtractDAO oedao = new OdmExtractDAO(this.ds);
int studyId = study.getId();
int parentStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : studyId;
if (this.getCategory() == 1 && study.isSite(study.getParentStudyId())) {
// populate MetaDataVersion attributes
if (dataset != null) {
metadata.setOid(dataset.getODMMetaDataVersionOid() + "-" + study.getOid());
metadata.setName(dataset.getODMMetaDataVersionName() + "-" + study.getOid());
this.setParentMetaDataVersionOid(dataset.getODMMetaDataVersionOid());
}
if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
metadata.setOid("v1.0.0" + "-" + study.getOid());
this.setParentMetaDataVersionOid("v1.0.0");
}
if (metadata.getName() == null || metadata.getName().length() <= 0) {
metadata.setName("MetaDataVersion_v1.0.0" + "-" + study.getOid());
}
// populate Include
this.collectIncludeFromParentInSameFile();
// populate protocol
oedao.getUpdatedSiteMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
} else {
if (dataset != null) {
metadata.setOid(dataset.getODMMetaDataVersionOid());
metadata.setName(dataset.getODMMetaDataVersionName());
}
if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
metadata.setOid("v1.0.0");
}
if (metadata.getName() == null || metadata.getName().length() <= 0) {
metadata.setName("MetaDataVersion_v1.0.0");
}
// populate Include
String psOid = new String();
String pmOid = new String();
if (dataset != null) {
psOid = dataset.getODMPriorStudyOid();
pmOid = dataset.getODMPriorMetaDataVersionOid();
}
if (pmOid != null && pmOid.length() > 0) {
MetaDataVersionIncludeBean ib = metadata.getInclude();
ib.setMetaDataVersionOID(pmOid);
if (psOid != null && psOid.length() > 0) {
ib.setStudyOID(psOid);
} else {
ib.setStudyOID(study.getOid());
}
}
// populate protocol
// Set<Integer> nullCodeSet = oedao.getMetadata(parentStudyId,
// studyId,
// metadata, this.getODMBean().getODMVersion());
// studyBase.setNullClSet(nullCodeSet);
oedao.getMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
}
}
