/**
* This method creates a List of DisplaySectionBeans, returning them in the order that the
* sections appear in a CRF. This List is "lazily" initialized the first time it is requested.
*
* @return A List of DisplaySectionBeans.
* @see org.akaza.openclinica.control.managestudy.PrintCRFServlet
* @see org.akaza.openclinica.control.managestudy.PrintDataEntryServlet
*/
public List<DisplaySectionBean> getDisplaySectionBeans() {
FormBeanUtil formBeanUtil;
ViewPersistanceHandler persistanceHandler;
ArrayList<SectionBean> allCrfSections;
// DAO classes for getting item definitions
SectionDAO sectionDao;
CRFVersionDAO crfVersionDao;
if (displaySectionBeans == null) {
displaySectionBeans = new ArrayList<DisplaySectionBean>();
formBeanUtil = new FormBeanUtil();
if (hasStoredData) persistanceHandler = new ViewPersistanceHandler();
// We need a CRF version id to populate the form display
if (this.crfVersionId == 0) {
return displaySectionBeans;
}
sectionDao = new SectionDAO(dataSource);
allCrfSections = (ArrayList) sectionDao.findByVersionId(this.crfVersionId);
// for the purposes of null values, try to obtain a valid
// eventCrfDefinition id
EventDefinitionCRFBean eventDefBean = null;
EventCRFBean eventCRFBean = new EventCRFBean();
if (eventCRFId > 0) {
EventCRFDAO ecdao = new EventCRFDAO(dataSource);
eventCRFBean = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudyEventDAO sedao = new StudyEventDAO(dataSource);
StudyEventBean studyEvent = (StudyEventBean) sedao.findByPK(eventCRFBean.getStudyEventId());
EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(dataSource);
StudyDAO sdao = new StudyDAO(dataSource);
StudyBean study = sdao.findByStudySubjectId(eventCRFBean.getStudySubjectId());
eventDefBean =
eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId(
study, studyEvent.getId(), this.crfVersionId);
}
eventDefBean = eventDefBean == null ? new EventDefinitionCRFBean() : eventDefBean;
// Create an array or List of DisplaySectionBeans representing each
// section
// for printing
DisplaySectionBean displaySectionBean;
for (SectionBean sectionBean : allCrfSections) {
displaySectionBean =
formBeanUtil.createDisplaySectionBWithFormGroups(
sectionBean.getId(),
this.crfVersionId,
dataSource,
eventDefBean.getId(),
eventCRFBean,
context);
displaySectionBeans.add(displaySectionBean);
}
}
return displaySectionBeans;
}
@GET
@Path("/{studyOID}/getSchedule")
@Produces(MediaType.APPLICATION_XML)
public String getSchedule(
@Context HttpServletRequest request,
@Context HttpServletResponse response,
@Context ServletContext context,
@PathParam("studyOID") String studyOID,
@RequestHeader("Authorization") String authorization)
throws Exception {
String ssoid = request.getParameter("studySubjectOID");
StudySubjectDAO ssdao = new StudySubjectDAO<String, ArrayList>(dataSource);
StudySubjectBean ssBean = ssdao.findByOid(ssoid);
if (!mayProceedSubmission(studyOID, ssBean)) return null;
HashMap<String, String> urlCache =
(HashMap<String, String>) context.getAttribute("pformURLCache");
context.getAttribute("subjectContextCache");
if (ssoid == null) {
return "<error>studySubjectOID is null :(</error>";
}
try {
// Need to retrieve crf's for next event
StudyEventDAO eventDAO = new StudyEventDAO(getDataSource());
StudyEventBean nextEvent = (StudyEventBean) eventDAO.getNextScheduledEvent(ssoid);
CRFVersionDAO versionDAO = new CRFVersionDAO(getDataSource());
ArrayList<CRFVersionBean> crfs =
versionDAO.findDefCRFVersionsByStudyEvent(nextEvent.getStudyEventDefinitionId());
PFormCache cache = PFormCache.getInstance(context);
for (CRFVersionBean crfVersion : crfs) {
String enketoURL = cache.getPFormURL(studyOID, crfVersion.getOid());
String contextHash =
cache.putSubjectContext(
ssoid,
String.valueOf(nextEvent.getStudyEventDefinitionId()),
String.valueOf(nextEvent.getSampleOrdinal()),
crfVersion.getOid());
}
} catch (Exception e) {
LOGGER.debug(e.getMessage());
LOGGER.debug(ExceptionUtils.getStackTrace(e));
return "<error>" + e.getMessage() + "</error>";
}
response.setHeader("Content-Type", "text/xml; charset=UTF-8");
response.setHeader("Content-Disposition", "attachment; filename=\"schedule.xml\";");
response.setContentType("text/xml; charset=utf-8");
return "<result>success</result>";
}
@Override
public void onApplicationEvent(final OnStudyEventUpdated event) {
LOGGER.debug("listening");
if (event.getContainer().getChangeDetails().getStartDateChanged()
|| event.getContainer().getChangeDetails().getStatusChanged()) {
StudyEvent studyEvent = event.getContainer().getEvent();
Integer studyEventDefId = studyEvent.getStudyEventDefinition().getStudyEventDefinitionId();
Integer studyEventOrdinal = studyEvent.getSampleOrdinal();
// Integer studySubjectId =
// event.getContainer().getEvent().getStudySubject().getStudySubjectId();
Integer userId = studyEvent.getUpdateId();
if (userId == null && studyEvent.getUserAccount() != null)
userId = studyEvent.getUserAccount().getUserId();
StudyEventBean studyEventBean = new StudyEventBean();
studyEventBean.setId(studyEvent.getStudyEventId());
ArrayList<RuleSetBean> ruleSets = (ArrayList<RuleSetBean>) createRuleSet(studyEventDefId);
for (RuleSetBean ruleSet : ruleSets) {
ArrayList<RuleSetBean> ruleSetBeans = new ArrayList();
ExpressionBean eBean = new ExpressionBean();
eBean.setValue(ruleSet.getTarget().getValue() + ".A.B");
ruleSet.setTarget(eBean);
ruleSet.addExpression(
getRuleSetService().replaceSEDOrdinal(ruleSet.getTarget(), studyEventBean));
ruleSetBeans.add(ruleSet);
getRuleSetService()
.runIndividualRulesInBeanProperty(
ruleSetBeans, userId, event.getContainer().getChangeDetails(), studyEventOrdinal);
}
// }
}
}
public StudyEventBean createStudyEventBean(
StudySubjectBean ssBean,
int studyEventDefinitionId,
int studyEventDefnOrdinal,
UserAccountBean uBean) {
StudyEventBean studyEventBean = new StudyEventBean();
studyEventBean.setStudySubjectId(ssBean.getId());
studyEventBean.setStudyEventDefinitionId(studyEventDefinitionId);
studyEventBean.setSampleOrdinal(studyEventDefnOrdinal);
studyEventBean.setStatus(Status.AVAILABLE);
studyEventBean.setOwner(uBean);
studyEventBean.setDateStarted(new Date());
studyEventBean.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
StudyEventDAO studyEventDao = new StudyEventDAO(dataSource);
studyEventBean = (StudyEventBean) studyEventDao.create(studyEventBean);
return studyEventBean;
}
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int studyId = fp.getInt("id");
StudyBean study = (StudyBean) sdao.findByPK(studyId);
// find all sites
ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
// find all user and roles in the study, include ones in sites
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(studyId);
// find all subjects in the study, include ones in sites
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events in the study, include ones in sites
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (studyId == 0) {
addPageMessage("Please choose a study to restore.");
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("studyToRestore", study);
request.setAttribute("sitesToRestore", sites);
request.setAttribute("userRolesToRestore", userRoles);
request.setAttribute("subjectsToRestore", subjects);
request.setAttribute("definitionsToRRestore", definitions);
forwardPage(Page.RESTORE_STUDY);
} else {
logger.info("submit to restore the study");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setStatus(Status.AVAILABLE);
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// remove all sites
for (int i = 0; i < sites.size(); i++) {
StudyBean site = (StudyBean) sites.get(i);
site.setStatus(Status.AVAILABLE);
site.setUpdater(ub);
site.setUpdatedDate(new Date());
sdao.update(site);
}
// remove all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
role.setStatus(Status.AVAILABLE);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
udao.updateStudyUserRole(role, role.getUserName());
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
subject.setStatus(Status.AVAILABLE);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
}
// remove all study_group
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
ArrayList groups = sgdao.findAllByStudy(study);
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean group = (StudyGroupBean) groups.get(i);
group.setStatus(Status.AVAILABLE);
group.setUpdater(ub);
group.setUpdatedDate(new Date());
sgdao.update(group);
// all subject_group_map
ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId());
for (int j = 0; j < subjectGroupMaps.size(); j++) {
SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
sgMap.setStatus(Status.AVAILABLE);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
// remove all event definitions and event
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < definitions.size(); i++) {
StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
definition.setStatus(Status.AVAILABLE);
definition.setUpdater(ub);
definition.setUpdatedDate(new Date());
sefdao.update(definition);
ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
for (int j = 0; j < edcs.size(); j++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
edc.setStatus(Status.AVAILABLE);
edc.setUpdater(ub);
edc.setUpdatedDate(new Date());
edcdao.update(edc);
}
ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
event.setStatus(Status.AVAILABLE);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
} // for definitions
DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
ArrayList dataset = datadao.findAllByStudyId(study.getId());
for (int i = 0; i < dataset.size(); i++) {
DatasetBean data = (DatasetBean) dataset.get(i);
data.setStatus(Status.AVAILABLE);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
addPageMessage("This study has been restored successfully.");
forwardPage(Page.STUDY_LIST_SERVLET);
}
}
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int studySubId = fp.getInt(STUDY_SUB_ID, true);
int eventCRFId = fp.getInt(EVENT_CRF_ID);
String action = request.getParameter("action");
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
if (eventCRFId == 0) {
addPageMessage(respage.getString("please_choose_an_event_CRF_to_delete"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
} else {
EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
request.setAttribute("studySub", studySub);
// construct info needed on view event crf page
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
int crfVersionId = eventCRF.getCRFVersionId();
CRFBean cb = cdao.findByVersionId(crfVersionId);
eventCRF.setCrf(cb);
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
eventCRF.setCrfVersion(cvb);
// then get the definition so we can call
// DisplayEventCRFBean.setFlags
int studyEventId = eventCRF.getStudyEventId();
StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed =
(StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
event.setStudyEventDefinition(sed);
request.setAttribute("event", event);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId());
EventDefinitionCRFBean edc =
edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());
DisplayEventCRFBean dec = new DisplayEventCRFBean();
dec.setEventCRF(eventCRF);
dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry());
// find all item data
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
dnDao = new DiscrepancyNoteDAO(sm.getDataSource());
ArrayList<ItemDataBean> itemData = iddao.findAllByEventCRFId(eventCRF.getId());
request.setAttribute("items", itemData);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("displayEventCRF", dec);
forwardPage(Page.DELETE_EVENT_CRF);
} else {
logger.info("submit to delete the event CRF from event");
// OC-6303 Deleting Event CRF resets Show / Hide logic
// delete records from DynamicItemForm and DynamicItemGroup
getDynamicsItemFormMetadataDao().delete(eventCRFId);
getDynamicsItemGroupMetadataDao().delete(eventCRFId);
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.RESET);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
for (ItemDataBean itemdata : itemData) {
// OC-6343 Rule behaviour must be reset if an Event CRF is deleted
// delete the records from ruleActionRunLogDao
getRuleActionRunLogDao().delete(itemdata.getId());
// OC-6344 Notes & Discrepancies must be set to "closed" when event CRF is deleted
// parentDiscrepancyNoteList is the list of the parent DNs records only
ArrayList<DiscrepancyNoteBean> parentDiscrepancyNoteList =
getDnDao().findParentNotesOnlyByItemData(itemdata.getId());
for (DiscrepancyNoteBean parentDiscrepancyNote : parentDiscrepancyNoteList) {
if (parentDiscrepancyNote.getResolutionStatusId()
!= 4) { // if the DN's resolution status is not set to Closed
String description = resword.getString("dn_auto-closed_description");
String detailedNotes = resword.getString("dn_auto_closed_detailed_notes");
// create new DN record , new DN Map record , also update the parent record
createDiscrepancyNoteBean(
description, detailedNotes, itemdata.getId(), study, ub, parentDiscrepancyNote);
}
}
iddao = new ItemDataDAO(sm.getDataSource());
ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
ItemDataBean idBean = (ItemDataBean) iddao.findByPK(itemdata.getId());
ItemFormMetadataBean ifmBean =
ifmdao.findByItemIdAndCRFVersionId(idBean.getItemId(), crfVersionId);
// Updating Dn_item_data_map actovated column into false for the existing DNs
ArrayList<DiscrepancyNoteBean> dnBeans =
getDnDao().findExistingNotesForItemData(itemdata.getId());
if (dnBeans.size() != 0) {
DiscrepancyNoteBean dnBean = new DiscrepancyNoteBean();
dnBean.setEntityId(itemdata.getId());
dnBean.setActivated(false);
getDnDao().updateDnMapActivation(dnBean);
}
// Default Values are not addressed
itemdata.setValue("");
itemdata.setOldStatus(itemdata.getStatus());
itemdata.setOwner(ub);
itemdata.setStatus(Status.AVAILABLE);
itemdata.setUpdater(ub);
iddao.updateUser(itemdata);
iddao.update(itemdata);
}
// OC-6291 event_crf status change
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
if (event.getSubjectEventStatus().isCompleted()
|| event.getSubjectEventStatus().isSigned()) {
event.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
event.setUpdater(ub);
sedao = new StudyEventDAO(sm.getDataSource());
sedao.update(event);
}
String emailBody =
respage.getString("the_event_CRF")
+ cb.getName()
+ respage.getString("has_been_deleted_from_the_event")
+ event.getStudyEventDefinition().getName()
+ ". "
+ respage.getString("has_been_deleted_from_the_event_cont");
addPageMessage(emailBody);
// sendEmail(emailBody);
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
}
}
@Override
public void processRequest() throws Exception {
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int subjectId = fp.getInt("id");
String action = fp.getString("action");
if (subjectId == 0 || StringUtil.isBlank(action)) {
addPageMessage(respage.getString("please_choose_a_subject_to_remove"));
forwardPage(Page.SUBJECT_LIST_SERVLET);
} else {
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
// find all study subjects
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList studySubs = ssdao.findAllBySubjectId(subjectId);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = sedao.findAllBySubjectId(subjectId);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("subjectToRemove", subject);
request.setAttribute("studySubs", studySubs);
request.setAttribute("events", events);
forwardPage(Page.REMOVE_SUBJECT);
} else {
logger.info("submit to remove the subject");
// change all statuses to deleted
subject.setStatus(Status.DELETED);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
sdao.update(subject);
// remove subject references from study
for (int i = 0; i < studySubs.size(); i++) {
StudySubjectBean studySub = (StudySubjectBean) studySubs.get(i);
if (!studySub.getStatus().equals(Status.DELETED)) {
studySub.setStatus(Status.AUTO_DELETED);
studySub.setUpdater(ub);
studySub.setUpdatedDate(new Date());
ssdao.update(studySub);
}
}
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
if (!event.getStatus().equals(Status.DELETED)) {
event.setStatus(Status.AUTO_DELETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// remove all the item data
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
String emailBody =
respage.getString("the_subject")
+ " "
+ respage.getString("has_been_removed_succesfully");
addPageMessage(emailBody);
// sendEmail(emailBody);
forwardPage(Page.SUBJECT_LIST_SERVLET);
}
}
}
/*
* 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;
}
@Override
public void processRequest() throws Exception {
String studySubIdString = request.getParameter("id"); // studySubjectId
String subIdString = request.getParameter("subjectId");
String studyIdString = request.getParameter("studyId");
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
if (StringUtil.isBlank(studySubIdString)
|| StringUtil.isBlank(subIdString)
|| StringUtil.isBlank(studyIdString)) {
addPageMessage(respage.getString("please_choose_a_study_subject_to_remove"));
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
} else {
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
int studySubId = Integer.valueOf(studySubIdString.trim()).intValue();
int subjectId = Integer.valueOf(subIdString.trim()).intValue();
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
StudyDAO studydao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) studydao.findByPK(studyId);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = sedao.findAllByStudyAndStudySubjectId(study, studySubId);
String action = request.getParameter("action");
if ("confirm".equalsIgnoreCase(action)) {
if (!studySub.getStatus().equals(Status.AVAILABLE)) {
addPageMessage(
respage.getString("this_subject_is_not_available_for_this_study")
+ " "
+ respage.getString("please_contact_sysadmin_for_more_information"));
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
return;
}
request.setAttribute("subject", subject);
request.setAttribute("study", study);
request.setAttribute("studySub", studySub);
request.setAttribute("events", events);
forwardPage(Page.REMOVE_STUDY_SUBJECT);
} else {
logger.info("submit to remove the subject from study");
// remove subject from study
studySub.setStatus(Status.DELETED);
studySub.setUpdater(ub);
studySub.setUpdatedDate(new Date());
subdao.update(studySub);
// remove all study events
// remove all event crfs
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
if (!event.getStatus().equals(Status.DELETED)) {
event.setStatus(Status.AUTO_DELETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// remove all the item data
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
String emailBody =
respage.getString("the_subject")
+ " "
+ subject.getName()
+ " "
+ respage.getString("has_been_removed_from_the_study")
+ study.getName()
+ ".";
addPageMessage(emailBody);
sendEmail(emailBody);
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
}
}
}
@Override
protected void processRequest() throws Exception {
checkStudyLocked(Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_locked"));
panel.setStudyInfoShown(false);
fp = new FormProcessor(request);
FormDiscrepancyNotes discNotes = null;
int studySubjectId = fp.getInt(INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT);
// input from manage subject matrix, user has specified definition id
int studyEventDefinitionId = fp.getInt(INPUT_STUDY_EVENT_DEFINITION);
// TODO: make this sensitive to permissions
StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
StudySubjectBean ssb;
if (studySubjectId <= 0) {
ssb = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT);
} else {
// YW 11-08-2007, << a new study event could not be added if its
// study subject has been removed
ssb = (StudySubjectBean) sdao.findByPK(studySubjectId);
Status s = ssb.getStatus();
if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
addPageMessage(
resword.getString("study_event")
+ resterm.getString("could_not_be")
+ resterm.getString("added")
+ "."
+ respage.getString("study_subject_has_been_deleted"));
request.setAttribute("id", new Integer(studySubjectId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
// YW >>
request.setAttribute(INPUT_REQUEST_STUDY_SUBJECT, "no");
}
// running this crashes the server, or so we think...instead, let's grab a count
// or remove it altogether tbh 10/2009
// ArrayList subjects = sdao.findAllActiveByStudyOrderByLabel(currentStudy);
// TODO: make this sensitive to permissions
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyBean studyWithEventDefinitions = currentStudy;
if (currentStudy.getParentStudyId() > 0) {
studyWithEventDefinitions = new StudyBean();
studyWithEventDefinitions.setId(currentStudy.getParentStudyId());
}
// find all active definitions with CRFs
ArrayList eventDefinitions = seddao.findAllActiveByStudy(studyWithEventDefinitions);
// EventDefinitionCRFDAO edcdao = new
// EventDefinitionCRFDAO(sm.getDataSource());
// ArrayList definitionsWithCRF = new ArrayList();
// for (int i=0; i<eventDefinitions.size(); i++) {
// StudyEventDefinitionBean sed =
// (StudyEventDefinitionBean)eventDefinitions.get(i);
// logger.info("StudyEventDefinition name[" + sed.getName() + "]");
// ArrayList edcs = edcdao.findAllByEventDefinitionId(sed.getId());
// if (!edcs.isEmpty()) {
// definitionsWithCRF.add(sed);
// }
// }
// Collections.sort(definitionsWithCRF);
Collections.sort(eventDefinitions);
/*
* ArrayList eventDefinitionsScheduled = new ArrayList(); for (int i =
* 0; i < eventDefinitions.size(); i++) { StudyEventDefinitionBean sed =
* (StudyEventDefinitionBean) eventDefinitions.get(i); if
* (sed.getType().equalsIgnoreCase("scheduled")) {
* eventDefinitionsScheduled.add(sed); } }
*/
// all definitions will appear in scheduled event creation box-11/26/05
ArrayList eventDefinitionsScheduled = eventDefinitions;
if (!fp.isSubmitted()) {
// StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
// sed.updateSampleOrdinals_v092();
HashMap presetValues = new HashMap();
// YW 08-16-2007 << set default as blank for time
presetValues.put(INPUT_STARTDATE_PREFIX + "Hour", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX + "Minute", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX + "Half", new String(""));
presetValues.put(INPUT_ENDDATE_PREFIX + "Hour", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX + "Minute", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX + "Half", new String(""));
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half", new String(""));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half", new String(""));
}
// SimpleDateFormat sdf = new SimpleDateFormat("MM/dd/yyyy");
// example of taking the above line and transferring to i18n on the
// below line, tbh
String dateValue = local_df.format(new Date(System.currentTimeMillis()));
presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue);
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date", dateValue);
// location
presetValues.put(INPUT_SCHEDULED_LOCATION[i], currentStudy.getFacilityCity());
presetValues.put(this.DISPLAY_SCHEDULED[i], "none");
}
presetValues.put(INPUT_LOCATION, currentStudy.getFacilityCity()); // defualt
if (ssb != null && ssb.isActive()) {
presetValues.put(INPUT_STUDY_SUBJECT, ssb);
String requestStudySubject = (String) request.getAttribute(INPUT_REQUEST_STUDY_SUBJECT);
if (requestStudySubject != null) {
presetValues.put(INPUT_REQUEST_STUDY_SUBJECT, requestStudySubject);
dateValue = local_df.format(new Date());
presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue);
}
}
if (studyEventDefinitionId > 0) {
StudyEventDefinitionBean sed =
(StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
presetValues.put(INPUT_STUDY_EVENT_DEFINITION, sed);
}
// tbh
logger.info("set preset values: " + presetValues.toString());
System.out.println("set preset values: " + presetValues.toString());
logger.info("found def.w.CRF list, size " + eventDefinitions.size());
// tbh
setPresetValues(presetValues);
ArrayList subjects = new ArrayList();
setupBeans(subjects, eventDefinitions);
discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled);
setInputMessages(new HashMap());
forwardPage(Page.CREATE_NEW_STUDY_EVENT);
} else {
// tbh
// String dateCheck = (String)request.getAttribute("startDate");
// String endCheck = (String)request.getAttribute("endDate");
// logger.info(dateCheck+"; "+endCheck);
String dateCheck2 = request.getParameter("startDate");
String endCheck2 = request.getParameter("endDate");
logger.info(dateCheck2 + "; " + endCheck2);
// YW, 3-12-2008, 2220 fix <<
String strEnd = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX);
String strEndScheduled[] = new String[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
strEndScheduled[i] = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
}
Date start = getInputStartDate();
Date end = null;
Date[] startScheduled = new Date[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
startScheduled[i] = getInputStartDateScheduled(i);
}
Date[] endScheduled = new Date[ADDITIONAL_SCHEDULED_NUM];
// YW >>
// for (java.util.Enumeration enu = request.getAttributeNames();
// enu.hasMoreElements() ;) {
// logger.info(">>> found "+enu.nextElement().toString());
// }
// tbh
discNotes =
(FormDiscrepancyNotes)
session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
if (discNotes == null) {
discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
}
DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes);
v.addValidation(INPUT_STARTDATE_PREFIX, Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX);
if (!strEnd.equals("")) {
v.addValidation(INPUT_ENDDATE_PREFIX, Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX);
}
v.addValidation(
INPUT_STUDY_EVENT_DEFINITION,
Validator.ENTITY_EXISTS_IN_STUDY,
seddao,
studyWithEventDefinitions);
// v.addValidation(INPUT_STUDY_SUBJECT, Validator.ENTITY_EXISTS_IN_STUDY, sdao, currentStudy);
// removed tbh 11/2009
v.addValidation(INPUT_LOCATION, Validator.NO_BLANKS);
v.addValidation(INPUT_STUDY_SUBJECT_LABEL, Validator.NO_BLANKS);
v.addValidation(
INPUT_LOCATION,
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
2000);
v.alwaysExecuteLastValidation(INPUT_LOCATION);
boolean hasScheduledEvent = false;
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
if (!StringUtil.isBlank(fp.getString(this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]))) {
// logger.info("has scheduled definition******");
v.addValidation(
this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i],
Validator.ENTITY_EXISTS_IN_STUDY,
seddao,
studyWithEventDefinitions);
v.addValidation(INPUT_SCHEDULED_LOCATION[i], Validator.NO_BLANKS);
v.addValidation(
INPUT_SCHEDULED_LOCATION[i],
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
2000);
v.alwaysExecuteLastValidation(INPUT_SCHEDULED_LOCATION[i]);
v.addValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i]);
if (!strEndScheduled[i].equals("")) {
v.addValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
}
hasScheduledEvent = true;
fp.addPresetValue(DISPLAY_SCHEDULED[i], "all");
} else {
fp.addPresetValue(DISPLAY_SCHEDULED[i], "none");
}
}
HashMap errors = v.validate();
// logger.info("v is not null *****");
String location = resword.getString("location");
// don't allow user to use the default value 'Location' since
// location
// is a required field
if (!StringUtil.isBlank(fp.getString(INPUT_LOCATION))
&& fp.getString(INPUT_LOCATION).equalsIgnoreCase(location)) {
Validator.addError(errors, INPUT_LOCATION, restext.getString("not_a_valid_location"));
}
StudyEventDefinitionBean definition =
(StudyEventDefinitionBean) seddao.findByPK(fp.getInt(INPUT_STUDY_EVENT_DEFINITION));
// StudySubjectBean studySubject = (StudySubjectBean)
// sdao.findByPK(fp.getInt(INPUT_STUDY_SUBJECT));
// sdao.findByLabelAndStudy(label, study)
StudySubjectBean studySubject =
(StudySubjectBean)
sdao.findByLabelAndStudy(fp.getString(INPUT_STUDY_SUBJECT_LABEL), currentStudy);
// >> 4358 tbh, 11/2009
// what if we are sent here from AddNewSubjectServlet.java??? we need to get that study
// subject bean
if (request.getAttribute(INPUT_STUDY_SUBJECT) != null) {
studySubject = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT);
}
// << tbh
if (studySubject.getLabel() == "") {
// add an error here, tbh
System.out.println("tripped the error here 20091109");
Validator.addError(
errors,
INPUT_STUDY_SUBJECT,
respage.getString("must_enter_subject_ID_for_identifying"));
}
if (!subjectMayReceiveStudyEvent(sm.getDataSource(), definition, studySubject)) {
Validator.addError(
errors,
INPUT_STUDY_EVENT_DEFINITION,
restext.getString("not_added_since_event_not_repeating"));
}
ArrayList<StudyEventDefinitionBean> definitionScheduleds =
new ArrayList<StudyEventDefinitionBean>();
int[] scheduledDefinitionIds = new int[ADDITIONAL_SCHEDULED_NUM];
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
int pk = fp.getInt(INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]);
if (pk > 0) {
StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(pk);
System.out.println(
"scheduled def:"
+ pk
+ " "
+ INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]
+ " "
+ sedb.getName());
definitionScheduleds.add(sedb);
scheduledDefinitionIds[i] = pk;
if (!subjectMayReceiveStudyEvent(sm.getDataSource(), sedb, studySubject)) {
Validator.addError(
errors,
INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i],
restext.getString("not_added_since_event_not_repeating"));
}
} else {
definitionScheduleds.add(new StudyEventDefinitionBean());
}
}
}
// YW, 3-12-2008, 2220 fix >>
if (!"".equals(strEnd)
&& !errors.containsKey(INPUT_STARTDATE_PREFIX)
&& !errors.containsKey(INPUT_ENDDATE_PREFIX)) {
end = getInputEndDate();
if (!fp.getString(INPUT_STARTDATE_PREFIX + "Date")
.equals(fp.getString(INPUT_ENDDATE_PREFIX + "Date"))) {
if (end.before(start)) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX,
resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
} else {
// if in same date, only check when both had time entered
if (fp.timeEntered(INPUT_STARTDATE_PREFIX) && fp.timeEntered(INPUT_ENDDATE_PREFIX)) {
if (end.before(start) || end.equals(start)) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX,
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
}
}
String prevStartPrefix = INPUT_STARTDATE_PREFIX;
Set<Integer> pickedSeds = new TreeSet<Integer>();
pickedSeds.add(studyEventDefinitionId);
HashMap<Integer, Integer> scheduledSeds = new HashMap<Integer, Integer>();
scheduledSeds.put(studyEventDefinitionId, -1);
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
if (scheduledDefinitionIds[i] > 0
&& !errors.containsKey(INPUT_STARTDATE_PREFIX_SCHEDULED[i])
&& !errors.containsKey(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) {
if (scheduledSeds.containsKey(scheduledDefinitionIds[i])) {
int prevStart = scheduledSeds.get(scheduledDefinitionIds[i]);
prevStartPrefix =
prevStart == -1
? INPUT_STARTDATE_PREFIX
: INPUT_STARTDATE_PREFIX_SCHEDULED[prevStart];
Date prevStartDate =
prevStart == -1
? this.getInputStartDate()
: this.getInputStartDateScheduled(
Integer.parseInt(
prevStartPrefix.charAt(prevStartPrefix.length() - 1) + ""));
if (fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date")
.equals(fp.getString(prevStartPrefix + "Date"))) {
// if in same day, only check when both have time
// inputs.
boolean schStartTime = fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i]);
boolean startTime = fp.timeEntered(prevStartPrefix);
if (schStartTime && startTime) {
if (startScheduled[i].before(prevStartDate)) {
Validator.addError(
errors,
INPUT_STARTDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
} else {
if (startScheduled[i].before(prevStartDate)) {
Validator.addError(
errors,
INPUT_STARTDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
}
scheduledSeds.put(scheduledDefinitionIds[i], i);
if (!strEndScheduled[i].equals("")) {
endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
String prevEndPrefix =
i > 0 ? INPUT_ENDDATE_PREFIX_SCHEDULED[i - 1] : INPUT_ENDDATE_PREFIX;
if (!fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date")
.equals(fp.getString(prevEndPrefix + "Date"))) {
if (endScheduled[i].before(startScheduled[i])) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
} else {
// if in same date, only check when both had time
// entered
if (fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i])
&& fp.timeEntered(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) {
if (endScheduled[i].before(startScheduled[i])
|| endScheduled[i].equals(startScheduled[i])) {
Validator.addError(
errors,
INPUT_ENDDATE_PREFIX_SCHEDULED[i],
resexception.getString(
"input_provided_not_occure_after_previous_start_date_time"));
}
}
}
}
}
}
// YW >>
System.out.println("we have errors; number of this; " + errors.size());
if (!errors.isEmpty()) {
logger.info("we have errors; number of this; " + errors.size());
System.out.println(
"found request study subject: " + fp.getString(INPUT_REQUEST_STUDY_SUBJECT));
addPageMessage(respage.getString("errors_in_submission_see_below"));
setInputMessages(errors);
fp.addPresetValue(INPUT_STUDY_EVENT_DEFINITION, definition);
fp.addPresetValue(INPUT_STUDY_SUBJECT, studySubject);
fp.addPresetValue(INPUT_STUDY_SUBJECT_LABEL, fp.getString(INPUT_STUDY_SUBJECT_LABEL));
fp.addPresetValue(INPUT_REQUEST_STUDY_SUBJECT, fp.getString(INPUT_REQUEST_STUDY_SUBJECT));
fp.addPresetValue(INPUT_LOCATION, fp.getString(INPUT_LOCATION));
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
fp.addPresetValue(INPUT_SCHEDULED_LOCATION[i], fp.getString(INPUT_SCHEDULED_LOCATION[i]));
}
String prefixes[] = new String[2 + 2 * ADDITIONAL_SCHEDULED_NUM];
prefixes[0] = INPUT_STARTDATE_PREFIX;
prefixes[1] = INPUT_ENDDATE_PREFIX;
int b = ADDITIONAL_SCHEDULED_NUM + 2;
for (int i = 2; i < b; ++i) {
prefixes[i] = INPUT_STARTDATE_PREFIX_SCHEDULED[i - 2];
}
for (int i = b; i < ADDITIONAL_SCHEDULED_NUM + b; ++i) {
prefixes[i] = INPUT_ENDDATE_PREFIX_SCHEDULED[i - b];
}
fp.setCurrentDateTimeValuesAsPreset(prefixes);
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
fp.addPresetValue(
INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], definitionScheduleds.get(i));
}
}
setPresetValues(fp.getPresetValues());
ArrayList subjects = new ArrayList();
setupBeans(subjects, eventDefinitions);
request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled);
forwardPage(Page.CREATE_NEW_STUDY_EVENT);
} else {
System.out.println("error is empty");
StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
StudyEventBean studyEvent = new StudyEventBean();
studyEvent.setStudyEventDefinitionId(definition.getId());
studyEvent.setStudySubjectId(studySubject.getId());
// YW 08-17-2007 <<
if ("-1".equals(getInputStartHour())
&& "-1".equals(getInputStartMinute())
&& "".equals(getInputStartHalf())) {
studyEvent.setStartTimeFlag(false);
} else {
studyEvent.setStartTimeFlag(true);
}
// YW >>
studyEvent.setDateStarted(start);
// comment to find bug 1389, tbh
logger.info("found start date: " + local_df.format(start));
Date startScheduled2[] = new Date[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
startScheduled2[i] = getInputStartDateScheduled(i);
}
// tbh
// YW, 3-12-2008, 2220 fix <<
if (!"".equals(strEnd)) {
// YW >>
if ("-1".equals(getInputEndHour())
&& "-1".equals(getInputEndMinute())
&& "".equals(getInputEndHalf())) {
studyEvent.setEndTimeFlag(false);
} else {
studyEvent.setEndTimeFlag(true);
}
studyEvent.setDateEnded(end);
}
studyEvent.setOwner(ub);
studyEvent.setStatus(Status.AVAILABLE);
studyEvent.setLocation(fp.getString(INPUT_LOCATION));
studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
// ArrayList subjectsExistingEvents =
// sed.findAllByStudyAndStudySubjectId(currentStudy,
// studySubject.getId());
studyEvent.setSampleOrdinal(sed.getMaxSampleOrdinal(definition, studySubject) + 1);
studyEvent = (StudyEventBean) sed.create(studyEvent);
if (!studyEvent.isActive()) {
throw new OpenClinicaException(restext.getString("event_not_created_in_database"), "2");
}
addPageMessage(
restext.getString("X_event_wiht_definition")
+ definition.getName()
+ restext.getString("X_and_subject")
+ studySubject.getName()
+ respage.getString("X_was_created_succesfully"));
// save discrepancy notes into DB
FormDiscrepancyNotes fdn =
(FormDiscrepancyNotes)
session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
String[] eventFields = {INPUT_LOCATION, INPUT_STARTDATE_PREFIX, INPUT_ENDDATE_PREFIX};
for (String element : eventFields) {
AddNewSubjectServlet.saveFieldNotes(
element, fdn, dndao, studyEvent.getId(), "studyEvent", currentStudy);
}
// logger.info("here ok 3333333333333333");
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
// should only do the following process if user inputs a
// scheduled event,
// which is scheduledDefinitionIds[i] > 0
if (scheduledDefinitionIds[i] > 0) {
if (subjectMayReceiveStudyEvent(
sm.getDataSource(), definitionScheduleds.get(i), studySubject)) {
StudyEventBean studyEventScheduled = new StudyEventBean();
studyEventScheduled.setStudyEventDefinitionId(scheduledDefinitionIds[i]);
studyEventScheduled.setStudySubjectId(studySubject.getId());
// YW 11-14-2007
if ("-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour"))
&& "-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute"))
&& "".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half"))) {
studyEventScheduled.setStartTimeFlag(false);
} else {
studyEventScheduled.setStartTimeFlag(true);
}
// YW >>
studyEventScheduled.setDateStarted(startScheduled[i]);
// YW, 3-12-2008, 2220 fix<<
if (!"".equals(strEndScheduled[i])) {
endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
if ("-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour"))
&& "-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute"))
&& "".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half"))) {
studyEventScheduled.setEndTimeFlag(false);
} else {
studyEventScheduled.setEndTimeFlag(true);
}
}
studyEventScheduled.setDateEnded(endScheduled[i]);
// YW >>
studyEventScheduled.setOwner(ub);
studyEventScheduled.setStatus(Status.AVAILABLE);
studyEventScheduled.setLocation(fp.getString(INPUT_SCHEDULED_LOCATION[i]));
studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
// subjectsExistingEvents =
// sed.findAllByStudyAndStudySubjectId(
// currentStudy,
// studySubject.getId());
studyEventScheduled.setSampleOrdinal(
sed.getMaxSampleOrdinal(definitionScheduleds.get(i), studySubject) + 1);
// System.out.println("create scheduled events");
studyEventScheduled = (StudyEventBean) sed.create(studyEventScheduled);
if (!studyEventScheduled.isActive()) {
throw new OpenClinicaException(
restext.getString("scheduled_event_not_created_in_database"), "2");
}
AddNewSubjectServlet.saveFieldNotes(
INPUT_SCHEDULED_LOCATION[i],
fdn,
dndao,
studyEventScheduled.getId(),
"studyEvent",
currentStudy);
// YW 3-12-2008, 2220 fix <<
AddNewSubjectServlet.saveFieldNotes(
INPUT_STARTDATE_PREFIX_SCHEDULED[i],
fdn,
dndao,
studyEventScheduled.getId(),
"studyEvent",
currentStudy);
AddNewSubjectServlet.saveFieldNotes(
INPUT_ENDDATE_PREFIX_SCHEDULED[i],
fdn,
dndao,
studyEventScheduled.getId(),
"studyEvent",
currentStudy);
// YW >>
} else {
addPageMessage(
restext.getString("scheduled_event_definition")
+ definitionScheduleds.get(i).getName()
+ restext.getString("X_and_subject")
+ studySubject.getName()
+ restext.getString("not_created_since_event_not_repeating")
+ restext.getString("event_type_already_exists"));
}
}
}
} // if
session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
request.setAttribute(
EnterDataForStudyEventServlet.INPUT_EVENT_ID, String.valueOf(studyEvent.getId()));
response.encodeRedirectURL("EnterDataForStudyEvent?eventId=" + studyEvent.getId());
forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET);
// we want to actually have url of entering data in browser, so
// redirecting
// response.sendRedirect(response.encodeRedirectURL(
// "EnterDataForStudyEvent?eventId="
// + studyEvent.getId()));
return;
}
}
}
/**
* Organize objects in a certain way so that we can show to Users on UI. step1 : Get StudyEvent ,
* eventCrf , crfVersion from studyEventId.
*
* @param crfViewSpecificOrderedObjects
* @param ruleSet
* @param rule
* @return
*/
private HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>>
populateForCrfBasedRulesView(
HashMap<RuleBulkExecuteContainer, HashMap<RuleBulkExecuteContainerTwo, Set<String>>>
crfViewSpecificOrderedObjects,
RuleSetBean ruleSet,
RuleBean rule,
String result,
StudyBean currentStudy,
List<RuleActionBean> actions) {
// step1
StudyEventBean studyEvent =
(StudyEventBean)
getStudyEventDao()
.findByPK(
Integer.valueOf(
getExpressionService()
.getStudyEventDefenitionOrdninalCurated(
ruleSet.getTarget().getValue())));
EventCRFBean eventCrf =
(EventCRFBean)
getEventCrfDao()
.findAllByStudyEventAndCrfOrCrfVersionOid(
studyEvent, getExpressionService().getCrfOid(ruleSet.getTarget().getValue()))
.get(0);
CRFVersionBean crfVersion =
(CRFVersionBean) getCrfVersionDao().findByPK(eventCrf.getCRFVersionId());
RuleBulkExecuteContainer key =
new RuleBulkExecuteContainer(crfVersion.getName(), rule, result, actions);
String key2String =
getExpressionService()
.getCustomExpressionUsedToCreateView(
ruleSet.getTarget().getValue(), studyEvent.getSampleOrdinal());
String studyEventDefinitionName =
getExpressionService()
.getStudyEventDefinitionFromExpression(ruleSet.getTarget().getValue(), currentStudy)
.getName();
studyEventDefinitionName += " [" + studyEvent.getSampleOrdinal() + "]";
// String itemGroupName =
// getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
// String itemName =
// getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue()).getName();
String itemGroupName =
getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
ItemGroupBean itemGroupBean =
getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue());
ItemBean itemBean =
getExpressionService().getItemExpression(ruleSet.getTarget().getValue(), itemGroupBean);
String itemName = itemBean.getName();
RuleBulkExecuteContainerTwo key2 =
new RuleBulkExecuteContainerTwo(
key2String, studyEvent, studyEventDefinitionName, itemGroupName, itemName);
StudySubjectBean studySubject =
(StudySubjectBean) getStudySubjectDao().findByPK(studyEvent.getStudySubjectId());
if (crfViewSpecificOrderedObjects.containsKey(key)) {
HashMap<RuleBulkExecuteContainerTwo, Set<String>> k = crfViewSpecificOrderedObjects.get(key);
if (k.containsKey(key2)) {
k.get(key2).add(String.valueOf(studySubject.getLabel()));
} else {
HashSet<String> values = new HashSet<String>();
values.add(String.valueOf(studySubject.getLabel()));
k.put(key2, values);
}
} else {
HashMap<RuleBulkExecuteContainerTwo, Set<String>> k =
new HashMap<RuleBulkExecuteContainerTwo, Set<String>>();
HashSet<String> values = new HashSet<String>();
values.add(String.valueOf(studySubject.getLabel()));
k.put(key2, values);
crfViewSpecificOrderedObjects.put(key, k);
}
return crfViewSpecificOrderedObjects;
}
public boolean prepareRequestForResolution(
HttpServletRequest request,
DataSource ds,
StudyBean currentStudy,
DiscrepancyNoteBean note,
boolean isCompleted) {
String entityType = note.getEntityType().toLowerCase();
int id = note.getEntityId();
if ("subject".equalsIgnoreCase(entityType)) {
StudySubjectDAO ssdao = new StudySubjectDAO(ds);
StudySubjectBean ssb = ssdao.findBySubjectIdAndStudy(id, currentStudy);
request.setAttribute("action", "show");
request.setAttribute("id", String.valueOf(note.getEntityId()));
request.setAttribute("studySubId", String.valueOf(ssb.getId()));
} else if ("studysub".equalsIgnoreCase(entityType)) {
request.setAttribute("action", "show");
request.setAttribute("id", String.valueOf(note.getEntityId()));
} else if ("eventcrf".equalsIgnoreCase(entityType)) {
request.setAttribute("editInterview", "1");
EventCRFDAO ecdao = new EventCRFDAO(ds);
EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(id);
request.setAttribute(TableOfContentsServlet.INPUT_EVENT_CRF_BEAN, ecb);
// If the request is passed along to ViewSectionDataEntryServlet,
// that code needs
// an event crf id; the (ecb.getId()+"") is necessary because
// FormProcessor throws
// a ClassCastException without the casting to a String
request.setAttribute(ViewSectionDataEntryServlet.EVENT_CRF_ID, ecb.getId() + "");
} else if ("studyevent".equalsIgnoreCase(entityType)) {
StudyEventDAO sedao = new StudyEventDAO(ds);
StudyEventBean seb = (StudyEventBean) sedao.findByPK(id);
request.setAttribute(EnterDataForStudyEventServlet.INPUT_EVENT_ID, String.valueOf(id));
request.setAttribute(UpdateStudyEventServlet.EVENT_ID, String.valueOf(id));
request.setAttribute(
UpdateStudyEventServlet.STUDY_SUBJECT_ID, String.valueOf(seb.getStudySubjectId()));
}
// this is for item data
else if ("itemdata".equalsIgnoreCase(entityType)) {
ItemDataDAO iddao = new ItemDataDAO(ds);
ItemDataBean idb = (ItemDataBean) iddao.findByPK(id);
EventCRFDAO ecdao = new EventCRFDAO(ds);
EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(idb.getEventCRFId());
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
StudySubjectBean ssb = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(ds);
ItemFormMetadataBean ifmb =
ifmdao.findByItemIdAndCRFVersionId(idb.getItemId(), ecb.getCRFVersionId());
if (currentRole.getRole().equals(Role.MONITOR) || !isCompleted) {
StudyEventDAO sedao = new StudyEventDAO(ds);
StudyEventBean seb = (StudyEventBean) sedao.findByPK(id);
request.setAttribute(EVENT_CRF_ID, String.valueOf(idb.getEventCRFId()));
request.setAttribute(STUDY_SUB_ID, String.valueOf(seb.getStudySubjectId()));
} else {
request.setAttribute(
DataEntryServlet.INPUT_EVENT_CRF_ID, String.valueOf(idb.getEventCRFId()));
request.setAttribute(
DataEntryServlet.INPUT_SECTION_ID, String.valueOf(ifmb.getSectionId()));
}
DataEntryStage stage = ecb.getStage();
// if (!stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE)) {
// return false;
// }
}
return true;
}