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 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;
}
/**
* Updates the study bean with inputs from second section
*
* @param request
* @return true if study type is Interventional, otherwise false
*/
private boolean updateStudy2() {
FormProcessor fp = new FormProcessor(request);
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
// this is not fully supported yet, because the system will not handle
// studies which are pending
// or private...
newStudy.setStatus(Status.get(fp.getInt("statusId")));
newStudy.setProtocolDateVerification(fp.getDate(INPUT_VER_DATE));
newStudy.setDatePlannedStart(fp.getDate(INPUT_START_DATE));
if (StringUtil.isBlank(fp.getString(INPUT_END_DATE))) {
newStudy.setDatePlannedEnd(null);
} else {
newStudy.setDatePlannedEnd(fp.getDate(INPUT_END_DATE));
}
newStudy.setPhase(fp.getString("phase"));
if (fp.getInt("genetic") == 1) {
newStudy.setGenetic(true);
} else {
newStudy.setGenetic(false);
}
session.setAttribute("newStudy", newStudy);
String interventional = resadmin.getString("interventional");
return interventional.equalsIgnoreCase(newStudy.getProtocolType());
}
private void confirmStudy6() throws Exception {
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
v.addValidation(
"medlineIdentifier",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"url",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"urlDescription",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
newStudy.setMedlineIdentifier(fp.getString("medlineIdentifier"));
newStudy.setResultsReference(fp.getBoolean("resultsReference"));
newStudy.setUrl(fp.getString("url"));
newStudy.setUrlDescription(fp.getString("urlDescription"));
session.setAttribute("newStudy", newStudy);
// request.setAttribute("interventions",session.getAttribute("interventions"));
if (errors.isEmpty()) {
forwardPage(Page.UPDATE_STUDY8);
} else {
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY7);
}
}
private void updateStudy3(boolean isInterventional, FormProcessor fp) {
study.setPurpose(fp.getString("purpose"));
ArrayList interventionArray = new ArrayList();
if (isInterventional) {
study.setAllocation(fp.getString("allocation"));
study.setMasking(fp.getString("masking"));
study.setControl(fp.getString("control"));
study.setAssignment(fp.getString("assignment"));
study.setEndpoint(fp.getString("endpoint"));
StringBuffer interventions = new StringBuffer();
for (int i = 0; i < 10; i++) {
String type = fp.getString("interType" + i);
String name = fp.getString("interName" + i);
if (!StringUtil.isBlank(type) && !StringUtil.isBlank(name)) {
InterventionBean ib =
new InterventionBean(fp.getString("interType" + i), fp.getString("interName" + i));
interventionArray.add(ib);
interventions.append(ib.toString()).append(",");
}
}
study.setInterventions(interventions.toString());
} else { // type = observational
study.setDuration(fp.getString("duration"));
study.setSelection(fp.getString("selection"));
study.setTiming(fp.getString("timing"));
}
request.setAttribute("interventions", interventionArray);
}
/**
* Send email to the user, director and administrator
*
* @param request
* @param response
*/
private String sendEmail(UserAccountBean u, StudyUserRoleBean sub) throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(sub.getStudyId());
logger.info("Sending email...");
String body =
u.getFirstName()
+ " "
+ u.getLastName()
+ " ("
+ resword.getString("username")
+ ": "
+ u.getName()
+ ") "
+ respage.getString("has_been_granted_the_role")
+ " "
+ sub.getRoleName()
+ " "
+ respage.getString("in_the_study_site")
+ " "
+ study.getName()
+ ".";
// boolean emailSent = sendEmail(u.getEmail().trim(), respage.getString("set_user_role"),
// body, false);
// if (emailSent) {
// sendEmail(ub.getEmail().trim(), respage.getString("set_user_role"), body, false);
// sendEmail(EmailEngine.getAdminEmail(), respage.getString("set_user_role"), body,
// false);
// }
return body;
}
private void validateStudy6(FormProcessor fp, Validator v) {
v.addValidation(
"medlineIdentifier",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"url",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"urlDescription",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
study.setMedlineIdentifier(fp.getString("medlineIdentifier"));
study.setResultsReference(fp.getBoolean("resultsReference"));
study.setUrl(fp.getString("url"));
study.setUrlDescription(fp.getString("urlDescription"));
// request.setAttribute("interventions",session.getAttribute(
// "interventions"));
if (!errors.isEmpty()) {
request.setAttribute("formMessages", errors);
}
}
public String getInputUsername(StudyBean studyBean, StudySubjectBean studySubjectBean) {
String inputUserName = null;
if (studySubjectBean != null) {
if (studyBean.getParentStudyId() > 0) studyBean = getStudy(studyBean.getParentStudyId());
inputUserName = studyBean.getOid() + "." + studySubjectBean.getOid();
}
return inputUserName;
}
public MetadataUnit(DataSource ds, StudyBean study, int category) {
super(ds, study, category);
this.odmStudy = new OdmStudyBean();
if (study.getParentStudyId() > 0) {
this.parentStudy = (StudyBean) new StudyDAO(ds).findByPK(study.getParentStudyId());
} else {
this.parentStudy = new StudyBean();
}
}
/** 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 StudyBean getParentStudy(String studyOid) {
StudyBean study = getStudy(studyOid);
if (study.getParentStudyId() == 0) {
return study;
} else {
StudyBean parentStudy = (StudyBean) sdao.findByPK(study.getParentStudyId());
return parentStudy;
}
}
@SuppressWarnings("unchecked")
@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
// initialize i18n
resword = ResourceBundleProvider.getWordsBundle(getLocale());
resformat = ResourceBundleProvider.getFormatBundle(getLocale());
Limit limit = tableFacade.getLimit();
ListSubjectFilter listSubjectFilter = getListSubjectFilter(limit);
if (!limit.isComplete()) {
int totalRows = getSubjectDao().getCountWithFilter(listSubjectFilter, getCurrentStudy());
tableFacade.setTotalRows(totalRows);
}
ListSubjectSort listSubjectSort = getListSubjectSort(limit);
int rowStart = limit.getRowSelect().getRowStart();
int rowEnd = limit.getRowSelect().getRowEnd();
Collection<SubjectBean> items =
getSubjectDao()
.getWithFilterAndSort(
getCurrentStudy(), listSubjectFilter, listSubjectSort, rowStart, rowEnd);
Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
for (SubjectBean subject : items) {
UserAccountBean owner = (UserAccountBean) getUserAccountDao().findByPK(subject.getOwnerId());
UserAccountBean updater =
subject.getUpdaterId() == 0
? null
: (UserAccountBean) getUserAccountDao().findByPK(subject.getUpdaterId());
HashMap<Object, Object> h = new HashMap<Object, Object>();
String studySubjectIdAndStudy = "";
List<StudySubjectBean> studySubjects =
getStudySubjectDao().findAllBySubjectId(subject.getId());
for (StudySubjectBean studySubjectBean : studySubjects) {
StudyBean study = (StudyBean) getStudyDao().findByPK(studySubjectBean.getStudyId());
studySubjectIdAndStudy += studySubjectIdAndStudy.length() == 0 ? "" : ",";
studySubjectIdAndStudy += study.getIdentifier() + "-" + studySubjectBean.getLabel();
}
h.put("studySubjectIdAndStudy", studySubjectIdAndStudy);
h.put("subject", subject);
h.put("subject.uniqueIdentifier", subject.getUniqueIdentifier());
h.put("subject.gender", subject.getGender());
h.put("subject.createdDate", subject.getCreatedDate());
h.put("subject.owner", owner);
h.put("subject.updatedDate", subject.getUpdatedDate());
h.put("subject.updater", updater);
h.put("subject.status", subject.getStatus());
theItems.add(h);
}
tableFacade.setItems(theItems);
}
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 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;
}
public SimpleTrigger generateImportTrigger(
FormProcessor fp,
UserAccountBean userAccount,
StudyBean study,
Date startDateTime,
String locale) {
String jobName = fp.getString(JOB_NAME);
String email = fp.getString(EMAIL);
String jobDesc = fp.getString(JOB_DESC);
String directory = fp.getString(DIRECTORY);
// what kinds of periods do we have? hourly, daily, weekly?
long interval = 0;
int hours = fp.getInt("hours");
int minutes = fp.getInt("minutes");
if (hours > 0) {
long hoursInt = hours * 3600000;
interval = interval + hoursInt;
}
if (minutes > 0) {
long minutesInt = minutes * 60000;
interval = interval + minutesInt;
}
SimpleTrigger trigger = new SimpleTrigger(jobName, IMPORT_TRIGGER, 64000, interval);
trigger.setDescription(jobDesc);
// set just the start date
trigger.setStartTime(startDateTime);
trigger.setName(jobName); // + datasetId);
trigger.setGroup(IMPORT_TRIGGER); // + datasetId);
trigger.setMisfireInstruction(
SimpleTrigger.MISFIRE_INSTRUCTION_RESCHEDULE_NEXT_WITH_EXISTING_COUNT);
// set job data map
JobDataMap jobDataMap = new JobDataMap();
jobDataMap.put(EMAIL, email);
jobDataMap.put(USER_ID, userAccount.getId());
jobDataMap.put(STUDY_NAME, study.getName());
jobDataMap.put(STUDY_OID, study.getOid());
jobDataMap.put(DIRECTORY, directory);
jobDataMap.put(ExampleSpringJob.LOCALE, locale);
jobDataMap.put("hours", hours);
jobDataMap.put("minutes", minutes);
trigger.setJobDataMap(jobDataMap);
trigger.setVolatility(false);
return trigger;
}
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 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
}
/**
* Constructs study bean from request-first section
*
* @param request
* @return
*/
private StudyBean createStudyBean() {
FormProcessor fp = new FormProcessor(request);
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
newStudy.setName(fp.getString("name"));
newStudy.setOfficialTitle(fp.getString("officialTitle"));
newStudy.setIdentifier(fp.getString("uniqueProId"));
newStudy.setSecondaryIdentifier(fp.getString("secondProId"));
newStudy.setPrincipalInvestigator(fp.getString("prinInvestigator"));
newStudy.setSummary(fp.getString("description"));
newStudy.setProtocolDescription(fp.getString("protocolDescription"));
newStudy.setSponsor(fp.getString("sponsor"));
newStudy.setCollaborators(fp.getString("collaborators"));
return newStudy;
}
@RequestMapping(method = RequestMethod.POST)
public String processSubmit(
@ModelAttribute("studyModuleStatus") StudyModuleStatus studyModuleStatus,
BindingResult result,
SessionStatus status,
HttpServletRequest request) {
StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
studyModuleStatusDao.saveOrUpdate(studyModuleStatus);
status.setComplete();
currentStudy.setStatus(Status.get(studyModuleStatus.getStudyStatus()));
if (currentStudy.getParentStudyId() > 0) {
studyDao.updateStudyStatus(currentStudy);
} else {
studyDao.updateStudyStatus(currentStudy);
}
return "redirect:studymodule";
}
public void testRewardForDining() {
initializeLocale();
// create a new dining of 100.00 charged to credit card '1234123412341234' by merchant
// '123457890' as test input
StudyBean studyBean = new StudyBean();
studyBean.setIdentifier("default-study");
SubjectBean subjectBean = new SubjectBean();
subjectBean.setUniqueIdentifier("krikor");
// Dining dining = Dining.createDining("100.00", "1234123412341234", "1234567890");
// call the 'rewardNetwork' to test its rewardAccountFor(Dining) method
// RewardConfirmation confirmation = rewardNetwork.rewardAccountFor(dining);
String result = rewardNetwork.createSubject(subjectBean, studyBean, null);
System.out.println(result);
assertNotNull(result);
}
/**
* Validates the forth section of study and save it into study bean
*
* @param request
* @param response
* @throws Exception
*/
private void confirmStudy4() throws Exception {
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
v.addValidation(
"conditions",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
500);
v.addValidation(
"keywords",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"eligibility",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
500);
errors = v.validate();
if (fp.getInt("expectedTotalEnrollment") <= 0) {
Validator.addError(
errors,
"expectedTotalEnrollment",
respage.getString("expected_total_enrollment_must_be_a_positive_number"));
}
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
newStudy.setConditions(fp.getString("conditions"));
newStudy.setKeywords(fp.getString("keywords"));
newStudy.setEligibility(fp.getString("eligibility"));
newStudy.setGender(fp.getString("gender"));
newStudy.setAgeMax(fp.getString("ageMax"));
newStudy.setAgeMin(fp.getString("ageMin"));
newStudy.setHealthyVolunteerAccepted(fp.getBoolean("healthyVolunteerAccepted"));
newStudy.setExpectedTotalEnrollment(fp.getInt("expectedTotalEnrollment"));
session.setAttribute("newStudy", newStudy);
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
if (errors.isEmpty()) {
forwardPage(Page.UPDATE_STUDY6);
} else {
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY5);
}
}
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;
}
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 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;
}
/**
* Parses the intetventions of a study and divides it into different type and name pairs type and
* name are separated by '/', and interventions are separated by ',' examples:
* type1/name1,type2/name2,type3/name3,
*
* @param sb
* @return
*/
private ArrayList parseInterventions(StudyBean sb) {
ArrayList inters = new ArrayList();
String interventions = sb.getInterventions();
try {
if (!StringUtil.isBlank(interventions)) {
StringTokenizer st = new StringTokenizer(interventions, ",");
while (st.hasMoreTokens()) {
String s = st.nextToken();
StringTokenizer st1 = new StringTokenizer(s, "/");
String type = st1.nextToken();
String name = st1.nextToken();
InterventionBean ib = new InterventionBean(type, name);
inters.add(ib);
}
}
} catch (NoSuchElementException nse) {
return new ArrayList();
}
return inters;
}
private void validateStudy4(FormProcessor fp, Validator v) {
v.addValidation(
"conditions",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
500);
v.addValidation(
"keywords",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"eligibility",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
500);
errors = v.validate();
if (fp.getInt("expectedTotalEnrollment") <= 0) {
Validator.addError(
errors,
"expectedTotalEnrollment",
respage.getString("expected_total_enrollment_must_be_a_positive_number"));
}
study.setConditions(fp.getString("conditions"));
study.setKeywords(fp.getString("keywords"));
study.setEligibility(fp.getString("eligibility"));
study.setGender(fp.getString("gender"));
study.setAgeMax(fp.getString("ageMax"));
study.setAgeMin(fp.getString("ageMin"));
study.setHealthyVolunteerAccepted(fp.getBoolean("healthyVolunteerAccepted"));
study.setExpectedTotalEnrollment(fp.getInt("expectedTotalEnrollment"));
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
}
