public HashMap validateImportJobForm(
FormProcessor fp, HttpServletRequest request, String[] triggerNames, String properName) {
Validator v = new Validator(request);
v.addValidation(JOB_NAME, Validator.NO_BLANKS);
// need to be unique too
v.addValidation(JOB_DESC, Validator.NO_BLANKS);
if (!"".equals(fp.getString(EMAIL))) {
v.addValidation(EMAIL, Validator.IS_A_EMAIL);
}
// << tbh we are now allowing email to be optional
// v.addValidation(PERIOD, Validator.NO_BLANKS);
// v.addValidation(DIRECTORY, Validator.NO_BLANKS);
// v.addValidation(DATE_START_JOB + "Date", Validator.IS_A_DATE);
// TODO job names will have to be unique, tbh
String hours = fp.getString("hours");
String minutes = fp.getString("minutes");
HashMap errors = v.validate();
if ((hours.equals("0")) && (minutes.equals("0"))) {
// System.out.println("got in the ERROR LOOP");
// throw an error here, at least one should be greater than zero
// errors.put(TAB, "Error Message - Pick one of the below");
v.addError(errors, "hours", "At least one of the following should be greater than zero.");
}
for (String triggerName : triggerNames) {
if (triggerName.equals(fp.getString(JOB_NAME)) && (!triggerName.equals(properName))) {
v.addError(
errors, JOB_NAME, "A job with that name already exists. Please pick another name.");
}
}
return errors;
}
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);
}
}
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
TriggerService triggerService = new TriggerService();
String action = fp.getString("action");
String triggerName = fp.getString("tname");
scheduler = getScheduler();
System.out.println("found trigger name " + triggerName);
Trigger trigger = scheduler.getTrigger(triggerName.trim(), TRIGGER_IMPORT_GROUP);
System.out.println("found trigger from the other side " + trigger.getFullName());
if (StringUtil.isBlank(action)) {
setUpServlet(trigger);
forwardPage(Page.UPDATE_JOB_IMPORT);
} else if ("confirmall".equalsIgnoreCase(action)) {
HashMap errors =
triggerService.validateImportJobForm(
fp, request, scheduler.getTriggerNames("DEFAULT"), trigger.getName());
if (!errors.isEmpty()) {
// send back
addPageMessage(
"Your modifications caused an error, please see the messages for more information.");
setUpServlet(trigger);
forwardPage(Page.UPDATE_JOB_IMPORT);
} else {
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
int studyId = fp.getInt(CreateJobImportServlet.STUDY_ID);
StudyBean study = (StudyBean) studyDAO.findByPK(studyId);
// in the place of a users' current study, tbh
Date startDate = trigger.getStartTime();
trigger =
triggerService.generateImportTrigger(
fp, sm.getUserBean(), study, startDate, request.getLocale().getLanguage());
// scheduler = getScheduler();
JobDetailBean jobDetailBean = new JobDetailBean();
jobDetailBean.setGroup(TRIGGER_IMPORT_GROUP);
jobDetailBean.setName(trigger.getName());
jobDetailBean.setJobClass(org.akaza.openclinica.web.job.ImportStatefulJob.class);
jobDetailBean.setJobDataMap(trigger.getJobDataMap());
jobDetailBean.setDurability(true); // need durability?
jobDetailBean.setVolatility(false);
try {
scheduler.deleteJob(triggerName, TRIGGER_IMPORT_GROUP);
Date dateStart = scheduler.scheduleJob(jobDetailBean, trigger);
addPageMessage("Your job has been successfully modified.");
forwardPage(Page.VIEW_IMPORT_JOB_SERVLET);
} catch (SchedulerException se) {
se.printStackTrace();
// set a message here with the exception message
setUpServlet(trigger);
addPageMessage(
"There was an unspecified error with your creation, please contact an administrator.");
forwardPage(Page.UPDATE_JOB_IMPORT);
}
}
}
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
// YW <<
StudyDAO stdao = new StudyDAO(sm.getDataSource());
int parentStudyId = currentStudy.getParentStudyId();
ArrayList groups = new ArrayList();
if (parentStudyId > 0) {
StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
groups = sgcdao.findAllByStudy(parentStudy);
} else {
groups = sgcdao.findAllByStudy(currentStudy);
}
// YW >>
String isReadOnly = request.getParameter("read");
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
for (int i = 0; i < groups.size(); i++) {
StudyGroupClassBean group = (StudyGroupClassBean) groups.get(i);
ArrayList studyGroups = sgdao.findAllByGroupClass(group);
group.setStudyGroups(studyGroups);
}
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allGroupRows = StudyGroupClassRow.generateRowsFromBeans(groups);
boolean isParentStudy = currentStudy.getParentStudyId() > 0 ? false : true;
request.setAttribute("isParentStudy", isParentStudy);
String[] columns = {
resword.getString("subject_group_class"),
resword.getString("type"),
resword.getString("subject_assignment"),
resword.getString("study_name"),
resword.getString("subject_groups"),
resword.getString("status"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(4);
table.hideColumnLink(6);
table.setQuery("ListSubjectGroupClass", new HashMap());
// if (isParentStudy && (!currentStudy.getStatus().isLocked())) {
// table.addLink(resword.getString("create_a_subject_group_class"),
// "CreateSubjectGroupClass");
// }
table.setRows(allGroupRows);
table.computeDisplay();
request.setAttribute("table", table);
if (request.getParameter("read") != null && request.getParameter("read").equals("true")) {
request.setAttribute("readOnly", true);
}
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST);
}
/**
* 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());
}
/**
* 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;
}
/**
* Confirms the third input block of study info
*
* @throws Exception
*/
private void confirmStudy3(boolean isInterventional) throws Exception {
Validator v = new Validator(request);
FormProcessor fp = new FormProcessor(request);
v.addValidation("purpose", Validator.NO_BLANKS);
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)) {
v.addValidation("interName", Validator.NO_BLANKS);
request.setAttribute(
"interventionError", respage.getString("name_cannot_be_blank_if_type"));
break;
}
if (!StringUtil.isBlank(name) && StringUtil.isBlank(type)) {
v.addValidation("interType", Validator.NO_BLANKS);
request.setAttribute(
"interventionError", respage.getString("name_cannot_be_blank_if_name"));
break;
}
}
errors = v.validate();
updateStudy3(isInterventional);
if (errors.isEmpty()) {
logger.info("no errors");
request.setAttribute("interventions", session.getAttribute("interventions"));
forwardPage(Page.UPDATE_STUDY5);
} else {
logger.info("has validation errors");
request.setAttribute("formMessages", errors);
setMaps(isInterventional, (ArrayList) session.getAttribute("interventions"));
if (isInterventional) {
forwardPage(Page.UPDATE_STUDY3);
} else {
forwardPage(Page.UPDATE_STUDY4);
}
}
}
/*
* (non-Javadoc)
*
* @see
* org.akaza.openclinica.control.submit.DataEntryServlet#getServletPage()
*/
@Override
protected Page getServletPage(HttpServletRequest request) {
FormProcessor fp = new FormProcessor(request);
String tabId = fp.getString("tab", true);
String sectionId = fp.getString(DataEntryServlet.INPUT_SECTION_ID, true);
String eventCRFId = fp.getString(INPUT_EVENT_CRF_ID, true);
if (StringUtil.isBlank(sectionId) || StringUtil.isBlank(tabId)) {
return Page.DOUBLE_DATA_ENTRY_SERVLET;
} else {
Page target = Page.DOUBLE_DATA_ENTRY_SERVLET;
target.setFileName(
target.getFileName()
+ "?eventCRFId="
+ eventCRFId
+ "§ionId="
+ sectionId
+ "&tab="
+ tabId);
return target;
}
}
/**
* 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);
}
}
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 HashMap validateForm(
FormProcessor fp, HttpServletRequest request, String[] triggerNames, String properName) {
Validator v = new Validator(request);
v.addValidation(JOB_NAME, Validator.NO_BLANKS);
// need to be unique too
v.addValidation(JOB_DESC, Validator.NO_BLANKS);
v.addValidation(EMAIL, Validator.IS_A_EMAIL);
v.addValidation(PERIOD, Validator.NO_BLANKS);
v.addValidation(DATE_START_JOB + "Date", Validator.IS_A_DATE);
// v.addValidation(DATE_START_JOB + "Date", new Date(), Validator.DATE_IS_AFTER_OR_EQUAL);
// TODO job names will have to be unique, tbh
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);
String spss = fp.getString(SPSS);
Date jobDate = fp.getDateTime(DATE_START_JOB);
HashMap errors = v.validate();
if ((tab == "")
&& (cdisc == "")
&& (spss == "")
&& (cdisc12 == "")
&& (cdisc13 == "")
&& (cdisc13oc == "")) {
// throw an error here, at least one should work
// errors.put(TAB, "Error Message - Pick one of the below");
v.addError(errors, TAB, "Please pick at least one of the below.");
}
for (String triggerName : triggerNames) {
if (triggerName.equals(fp.getString(JOB_NAME)) && (!triggerName.equals(properName))) {
v.addError(
errors, JOB_NAME, "A job with that name already exists. Please pick another name.");
}
}
if (jobDate.before(new Date())) {
v.addError(
errors, DATE_START_JOB + "Date", "This date needs to be later than the present time.");
}
return errors;
}
@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);
}
}
}
private void confirmWholeStudy() throws Exception {
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
errors = v.validate();
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
newStudy.getStudyParameterConfig().setCollectDob(fp.getString("collectDob"));
newStudy
.getStudyParameterConfig()
.setDiscrepancyManagement(fp.getString("discrepancyManagement"));
newStudy.getStudyParameterConfig().setGenderRequired(fp.getString("genderRequired"));
newStudy
.getStudyParameterConfig()
.setInterviewerNameRequired(fp.getString("interviewerNameRequired"));
newStudy
.getStudyParameterConfig()
.setInterviewerNameDefault(fp.getString("interviewerNameDefault"));
newStudy
.getStudyParameterConfig()
.setInterviewDateEditable(fp.getString("interviewDateEditable"));
newStudy
.getStudyParameterConfig()
.setInterviewDateRequired(fp.getString("interviewDateRequired"));
newStudy
.getStudyParameterConfig()
.setInterviewerNameEditable(fp.getString("interviewerNameEditable"));
newStudy
.getStudyParameterConfig()
.setInterviewDateDefault(fp.getString("interviewDateDefault"));
newStudy.getStudyParameterConfig().setSubjectIdGeneration(fp.getString("subjectIdGeneration"));
newStudy
.getStudyParameterConfig()
.setSubjectPersonIdRequired(fp.getString("subjectPersonIdRequired"));
newStudy
.getStudyParameterConfig()
.setSubjectIdPrefixSuffix(fp.getString("subjectIdPrefixSuffix"));
newStudy.getStudyParameterConfig().setPersonIdShownOnCRF(fp.getString("personIdShownOnCRF"));
session.setAttribute("newStudy", newStudy);
if (errors.isEmpty()) {
forwardPage(Page.STUDY_UPDATE_CONFIRM);
} else {
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY8);
}
}
/**
* Validates the forth section of study and save it into study bean
*
* @param request
* @param response
* @throws Exception
*/
private void confirmStudy5() throws Exception {
FormProcessor fp = new FormProcessor(request);
Validator v = new Validator(request);
if (!StringUtil.isBlank(fp.getString("facConEmail"))) {
v.addValidation("facConEmail", Validator.IS_A_EMAIL);
}
v.addValidation(
"facName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facCity",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facState",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
20);
v.addValidation(
"facZip",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facCountry",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
64);
v.addValidation(
"facConName",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConDegree",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConPhone",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"facConEmail",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
errors = v.validate();
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
newStudy.setFacilityCity(fp.getString("facCity"));
newStudy.setFacilityContactDegree(fp.getString("facConDrgree"));
newStudy.setFacilityName(fp.getString("facName"));
newStudy.setFacilityContactEmail(fp.getString("facConEmail"));
newStudy.setFacilityContactPhone(fp.getString("facConPhone"));
newStudy.setFacilityContactName(fp.getString("facConName"));
newStudy.setFacilityCountry(fp.getString("facCountry"));
newStudy.setFacilityContactDegree(fp.getString("facConDegree"));
// newStudy.setFacilityRecruitmentStatus(fp.getString("facRecStatus"));
newStudy.setFacilityState(fp.getString("facState"));
newStudy.setFacilityZip(fp.getString("facZip"));
session.setAttribute("newStudy", newStudy);
if (errors.isEmpty()) {
forwardPage(Page.UPDATE_STUDY7);
} else {
request.setAttribute("formMessages", errors);
request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
forwardPage(Page.UPDATE_STUDY6);
}
}
private void confirmStudy2() throws Exception {
Validator v = new Validator(request);
FormProcessor fp = new FormProcessor(request);
v.addValidation(INPUT_START_DATE, Validator.IS_A_DATE);
if (!StringUtil.isBlank(fp.getString(INPUT_END_DATE))) {
v.addValidation(INPUT_END_DATE, Validator.IS_A_DATE);
}
v.addValidation(INPUT_VER_DATE, Validator.IS_A_DATE);
errors = v.validate();
boolean isInterventional = updateStudy2();
if (errors.isEmpty()) {
logger.info("no errors");
ArrayList interventionArray = new ArrayList();
if (isInterventional) {
interventionArray = parseInterventions((StudyBean) session.getAttribute("newStudy"));
setMaps(isInterventional, interventionArray);
forwardPage(Page.UPDATE_STUDY3);
} else {
setMaps(isInterventional, interventionArray);
forwardPage(Page.UPDATE_STUDY4);
}
} else {
logger.info("has validation errors");
try {
local_df.parse(fp.getString(INPUT_START_DATE));
fp.addPresetValue(INPUT_START_DATE, local_df.format(fp.getDate(INPUT_START_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_START_DATE, fp.getString(INPUT_START_DATE));
}
try {
local_df.parse(fp.getString(INPUT_VER_DATE));
fp.addPresetValue(INPUT_VER_DATE, local_df.format(fp.getDate(INPUT_VER_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_VER_DATE, fp.getString(INPUT_VER_DATE));
}
try {
local_df.parse(fp.getString(INPUT_END_DATE));
fp.addPresetValue(INPUT_END_DATE, local_df.format(fp.getDate(INPUT_END_DATE)));
} catch (ParseException pe) {
fp.addPresetValue(INPUT_END_DATE, fp.getString(INPUT_END_DATE));
}
setPresetValues(fp.getPresetValues());
request.setAttribute("formMessages", errors);
request.setAttribute("studyPhaseMap", CreateStudyServlet.studyPhaseMap);
request.setAttribute("statuses", Status.toActiveArrayList());
forwardPage(Page.UPDATE_STUDY2);
}
}
/**
* Validates the first section of study and save it into study bean
*
* @param request
* @param response
* @throws Exception
*/
private void confirmStudy1() throws Exception {
Validator v = new Validator(request);
FormProcessor fp = new FormProcessor(request);
v.addValidation("name", Validator.NO_BLANKS);
v.addValidation("uniqueProId", Validator.NO_BLANKS);
v.addValidation("description", Validator.NO_BLANKS);
v.addValidation("prinInvestigator", Validator.NO_BLANKS);
v.addValidation("sponsor", Validator.NO_BLANKS);
v.addValidation(
"secondProId",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
255);
v.addValidation(
"collaborators",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
1000);
v.addValidation(
"protocolDescription",
Validator.LENGTH_NUMERIC_COMPARISON,
NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO,
1000);
errors = v.validate();
if (fp.getString("name").trim().length() > 100) {
Validator.addError(errors, "name", resexception.getString("maximum_lenght_name_100"));
}
if (fp.getString("uniqueProId").trim().length() > 30) {
Validator.addError(
errors, "uniqueProId", resexception.getString("maximum_lenght_unique_protocol_30"));
}
if (fp.getString("description").trim().length() > 255) {
Validator.addError(
errors, "description", resexception.getString("maximum_lenght_brief_summary_255"));
}
if (fp.getString("prinInvestigator").trim().length() > 255) {
Validator.addError(
errors,
"prinInvestigator",
resexception.getString("maximum_lenght_principal_investigator_255"));
}
if (fp.getString("sponsor").trim().length() > 255) {
Validator.addError(errors, "sponsor", resexception.getString("maximum_lenght_sponsor_255"));
}
if (fp.getString("officialTitle").trim().length() > 255) {
Validator.addError(
errors, "officialTitle", resexception.getString("maximum_lenght_official_title_255"));
}
session.setAttribute("newStudy", createStudyBean());
if (errors.isEmpty()) {
logger.info("no errors in the first section");
request.setAttribute("studyPhaseMap", CreateStudyServlet.studyPhaseMap);
request.setAttribute("statuses", Status.toActiveArrayList());
StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
fp.addPresetValue(INPUT_START_DATE, local_df.format(newStudy.getDatePlannedStart()));
if (newStudy.getDatePlannedEnd() != null) {
fp.addPresetValue(INPUT_END_DATE, local_df.format(newStudy.getDatePlannedEnd()));
}
fp.addPresetValue(INPUT_VER_DATE, local_df.format(newStudy.getProtocolDateVerification()));
setPresetValues(fp.getPresetValues());
forwardPage(Page.UPDATE_STUDY2);
} else {
logger.info("has validation errors in the first section");
request.setAttribute("formMessages", errors);
forwardPage(Page.UPDATE_STUDY1);
}
}
@Override
public void processRequest() throws Exception {
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
String name = request.getParameter("name");
String studyIdString = request.getParameter("studyId");
if (StringUtil.isBlank(name) || StringUtil.isBlank(studyIdString)) {
addPageMessage(respage.getString("please_choose_a_user_to_set_role_for"));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
} else {
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
UserAccountBean user = (UserAccountBean) udao.findByUserName(name);
StudyBean userStudy = (StudyBean) sdao.findByPK(fp.getInt("studyId"));
if ("confirm".equalsIgnoreCase(action)) {
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
request.setAttribute("user", user);
StudyUserRoleBean uRole = udao.findRoleByUserNameAndStudyId(name, studyId);
uRole.setStudyName(userStudy.getName());
request.setAttribute("uRole", uRole);
ArrayList roles = Role.toArrayList();
roles.remove(Role.ADMIN); // admin is not a user role, only used for tomcat
StudyBean studyBean = (StudyBean) sdao.findByPK(uRole.getStudyId());
if (currentStudy.getParentStudyId() > 0) {
roles.remove(Role.COORDINATOR);
roles.remove(Role.STUDYDIRECTOR);
} else if (studyBean.getParentStudyId() > 0) {
roles.remove(Role.COORDINATOR);
roles.remove(Role.STUDYDIRECTOR);
// TODO: redo this fix
Role r = Role.RESEARCHASSISTANT;
r.setDescription("site_Data_Entry_Person");
roles.remove(Role.RESEARCHASSISTANT);
roles.add(r);
Role ri = Role.INVESTIGATOR;
ri.setDescription("site_investigator");
roles.remove(Role.INVESTIGATOR);
roles.add(ri);
}
request.setAttribute("roles", roles);
forwardPage(Page.SET_USER_ROLE_IN_STUDY);
} else {
// set role
String userName = fp.getString("name");
int studyId = fp.getInt("studyId");
int roleId = fp.getInt("roleId");
StudyUserRoleBean sur = new StudyUserRoleBean();
sur.setName(userName);
sur.setRole(Role.get(roleId));
sur.setStudyId(studyId);
sur.setStudyName(userStudy.getName());
sur.setStatus(Status.AVAILABLE);
sur.setUpdater(ub);
sur.setUpdatedDate(new Date());
udao.updateStudyUserRole(sur, userName);
addPageMessage(sendEmail(user, sur));
forwardPage(Page.LIST_USER_IN_STUDY_SERVLET);
}
}
}
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;
}
@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);
}
}
}
@Override
@SuppressWarnings(value = "unchecked")
public void processRequest() throws Exception {
ItemDataDAO itemDataDao = new ItemDataDAO(sm.getDataSource());
EventCRFDAO eventCrfDao = new EventCRFDAO(sm.getDataSource());
CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(sm.getDataSource());
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from
String module = fp.getString(MODULE);
request.setAttribute(MODULE, module);
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering"));
setToPanel(
resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading"));
setToPanel(
resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version"));
setToPanel(
resword.getString("CRF_spreadsheet_template"),
respage.getString("br_download_blank_CRF_spreadsheet_from"));
setToPanel(
resword.getString("example_CRF_br_spreadsheets"),
respage.getString("br_download_example_CRF_instructions_from"));
if ("confirm".equalsIgnoreCase(action)) {
List<DisplayItemBeanWrapper> displayItemBeanWrappers =
(List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
logger.info("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());
forwardPage(Page.VERIFY_IMPORT_CRF_DATA);
}
if ("save".equalsIgnoreCase(action)) {
List<DisplayItemBeanWrapper> displayItemBeanWrappers =
(List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
// System.out.println("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());
for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
int eventCrfBeanId = -1;
EventCRFBean eventCrfBean = new EventCRFBean();
// TODO : tom , the wrapper object has all the necessary data -
// as you see we check the
// is to see if this data is Savable if it is then we go ahead
// and save it. if not we discard.
// So the change needs to happen here , instead of discarding we
// need to file discrepancy notes
// and save the data. If you look in the
// Page.VERIFY_IMPORT_CRF_DATA jsp file you can see how I am
// pulling the errors. and use that in the same way.
logger.info("right before we check to make sure it is savable: " + wrapper.isSavable());
if (wrapper.isSavable()) {
ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
// based on the use case: "If any of the data does not meet
// validations specified in the CRF
// Template, a discrepancy note is automatically logged.
// The DN will have a type of Failed Validation Check, and
// a message of Failed Validation check."
// System.out.println("wrapper problems found : " +
// wrapper.getValidationErrors().toString());
for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
eventCrfBeanId = displayItemBean.getData().getEventCRFId();
eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
logger.info("found value here: " + displayItemBean.getData().getValue());
logger.info("found status here: " + eventCrfBean.getStatus().getName());
// System.out.println("found event crf bean name here: "
// +
// eventCrfBean.getEventName()+" id "+eventCrfBean.getId
// ());
// SO, items can be created in a wrapper which is set to
// overwrite
// we get around this by checking the bean first, to
// make sure it's not null
ItemDataBean itemDataBean = new ItemDataBean();
itemDataBean =
itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
displayItemBean.getItem().getId(),
eventCrfBean.getId(),
displayItemBean.getData().getOrdinal());
if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
// ItemDataBean itemDataBean = new ItemDataBean();
// itemDataBean =
// itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
// displayItemBean.getItem().getId(),
// eventCrfBean.getId(), displayItemBean
// .getData().getOrdinal());
// itemDataBean =
// itemDataDao.findByEventCRFIdAndItemName(
// eventCrfBean,
// displayItemBean.getItem().getName());
logger.info(
"just tried to find item data bean on item name "
+ displayItemBean.getItem().getName());
itemDataBean.setUpdatedDate(new Date());
itemDataBean.setUpdater(ub);
itemDataBean.setValue(displayItemBean.getData().getValue());
// set status?
itemDataDao.update(itemDataBean);
logger.info("updated: " + itemDataBean.getItemId());
// need to set pk here in order to create dn
displayItemBean.getData().setId(itemDataBean.getId());
} else {
itemDataDao.create(displayItemBean.getData());
logger.info(
"created: "
+ displayItemBean.getData().getItemId()
+ "event CRF ID = "
+ eventCrfBean.getId()
+ "CRF VERSION ID ="
+ eventCrfBean.getCRFVersionId());
// does this dao function work for repeating
// events/groups?
// ItemDataBean itemDataBean =
// itemDataDao.findByEventCRFIdAndItemName(
// eventCrfBean,
// displayItemBean.getItem().getName());
ItemDataBean itemDataBean2 =
itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
displayItemBean.getItem().getId(),
eventCrfBean.getId(),
displayItemBean.getData().getOrdinal());
logger.info(
"found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
displayItemBean.getData().setId(itemDataBean2.getId());
}
// logger.info("created item data bean:
// "+displayItemBean.getData().getId());
// logger.info("created:
// "+displayItemBean.getData().getName());
// logger.info("continued:
// "+displayItemBean.getData().getItemId());
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
// logger.info("continued2: getName " +
// ibean.getName());
// System.out.println("*** checking for validation errors: " + ibean.getName());
String itemOid =
displayItemBean.getItem().getOid()
+ "_"
+ wrapper.getStudyEventRepeatKey()
+ "_"
+ displayItemBean.getData().getOrdinal()
+ "_"
+ wrapper.getStudySubjectOid();
if (wrapper.getValidationErrors().containsKey(itemOid)) {
ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
// if
// (wrapper.getValidationErrors().containsKey(ibean
// .getName())) {
// ArrayList messageList = (ArrayList)
// wrapper.getValidationErrors
// ().get(ibean.getName());
// could be more then one will have to iterate
// could it be more than one? tbh 08/2008
for (int iter = 0; iter < messageList.size(); iter++) {
String message = (String) messageList.get(iter);
DiscrepancyNoteBean parentDn =
ImportSpringJob.createDiscrepancyNote(
ibean,
message,
eventCrfBean,
displayItemBean,
null,
ub,
sm.getDataSource(),
currentStudy);
ImportSpringJob.createDiscrepancyNote(
ibean,
message,
eventCrfBean,
displayItemBean,
parentDn.getId(),
ub,
sm.getDataSource(),
currentStudy);
// System.out.println("*** created disc note with message: " + message);
// displayItemBean);
}
}
// logger.info("created:
// "+displayItemBean.getDbData().getName());
if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
// System.out.println("*** just updated event crf bean: " + eventCrfBean.getId());
eventCrfInts.add(new Integer(eventCrfBean.getId()));
}
}
// end of item datas, tbh
// crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
// System .out.println("*** just updated event crf bean: "+
// eventCrfBean.getId());
// need to update the study event status as well, tbh
// crfBusinessLogicHelper.updateStudyEvent(eventCrfBean,
// ub);
// above should do it for us, tbh 08/2008
}
}
addPageMessage(respage.getString("data_has_been_successfully_import"));
// forwardPage(Page.SUBMIT_DATA_SERVLET);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
// replaced tbh, 06/2009
}
}
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
// changes to this servlet, we now look at group name too, tbh 05/2009
String triggerName = fp.getString("tname");
String gName = fp.getString("gname");
String groupName = "";
if (gName.equals("") || gName.equals("0")) {
groupName = TRIGGER_GROUP;
} else { // if (gName.equals("1")) {
groupName = TRIGGER_IMPORT_GROUP;
}
// << tbh 09/03/2009 #4143
scheduler = getScheduler();
Trigger trigger = scheduler.getTrigger(triggerName.trim(), groupName);
// trigger bean is a wrapper for the trigger, to serve as a link btw
// quartz classes and oc classes
// is it really necessary? DRY
if (trigger == null) {
System.out.println("*** reset trigger group name");
groupName = TRIGGER_GROUP;
trigger = scheduler.getTrigger(triggerName.trim(), groupName);
}
// << tbh 09/03/2009 #4143
// above is a hack, if we add more trigger groups this will have
// to be redone
System.out.println("found trigger name: " + triggerName);
System.out.println("found group name: " + groupName);
// System.out.println("found trigger on the other side, full name: " +
// trigger.getFullName());
TriggerBean triggerBean = new TriggerBean();
JobDataMap dataMap = new JobDataMap();
AuditEventDAO auditEventDAO = new AuditEventDAO(sm.getDataSource());
try {
triggerBean.setFullName(trigger.getName());
triggerBean.setPreviousDate(trigger.getPreviousFireTime());
triggerBean.setNextDate(trigger.getNextFireTime());
// >> set active here, tbh 10/08/2009
if (scheduler.getTriggerState(triggerName, groupName) == Trigger.STATE_PAUSED) {
triggerBean.setActive(false);
System.out.println("setting active to false for trigger: " + trigger.getName());
} else {
triggerBean.setActive(true);
System.out.println("setting active to TRUE for trigger: " + trigger.getName());
}
// <<
if (trigger.getDescription() != null) {
triggerBean.setDescription(trigger.getDescription());
}
if (trigger.getJobDataMap().size() > 0) {
dataMap = trigger.getJobDataMap();
String contactEmail = dataMap.getString(ExampleSpringJob.EMAIL);
System.out.println("found email: " + contactEmail);
// String datasetId =
// dataMap.getString(ExampleSpringJob.DATASET_ID);
// int dsId = new Integer(datasetId).intValue();
if (gName.equals("") || gName.equals("0")) {
String tab = dataMap.getString(ExampleSpringJob.TAB);
String cdisc = dataMap.getString(ExampleSpringJob.CDISC);
String spss = dataMap.getString(ExampleSpringJob.SPSS);
String periodToRun = dataMap.getString(ExampleSpringJob.PERIOD);
// int userId = new Integer(userAcctId).intValue();
int dsId = dataMap.getInt(ExampleSpringJob.DATASET_ID);
triggerBean.setCdisc(cdisc);
triggerBean.setSpss(spss);
triggerBean.setTab(tab);
triggerBean.setPeriodToRun(periodToRun);
DatasetDAO datasetDAO = new DatasetDAO(sm.getDataSource());
DatasetBean dataset = (DatasetBean) datasetDAO.findByPK(dsId);
triggerBean.setDataset(dataset);
}
int userId = dataMap.getInt(ExampleSpringJob.USER_ID);
// need to set information, extract bean, user account bean
UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
triggerBean.setContactEmail(contactEmail);
UserAccountBean userAccount = (UserAccountBean) userAccountDAO.findByPK(userId);
triggerBean.setUserAccount(userAccount);
ArrayList<AuditEventBean> triggerLogs =
auditEventDAO.findAllByAuditTable(trigger.getName());
// set the table for the audit event beans here
ArrayList allRows = AuditEventRow.generateRowsFromBeans(triggerLogs);
EntityBeanTable table = fp.getEntityBeanTable();
String[] columns = {
resword.getString("date_and_time"),
resword.getString("action_message"),
resword.getString("entity_operation"),
// resword.getString("study_site"),
// resword.getString("study_subject_ID"),
resword.getString("changes_and_additions"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.setAscendingSort(false);
table.hideColumnLink(1);
table.hideColumnLink(3);
table.hideColumnLink(4);
table.setQuery("ViewSingleJob?tname=" + triggerName + "&gname=" + gName, new HashMap());
table.setRows(allRows);
table.computeDisplay();
request.setAttribute("table", table);
}
} catch (NullPointerException e) {
// TODO Auto-generated catch block
System.out.println(" found NPE " + e.getMessage());
e.printStackTrace();
}
// need to show the extract for which this runs, which files, etc
// in other words the job data map
request.setAttribute("triggerBean", triggerBean);
request.setAttribute("groupName", groupName);
forwardPage(Page.VIEW_SINGLE_JOB);
}
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#mayProceed()
*/
@Override
protected void mayProceed(HttpServletRequest request, HttpServletResponse response)
throws InsufficientPermissionException {
checkStudyLocked(
Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_locked"), request, response);
checkStudyFrozen(
Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_frozen"), request, response);
UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME);
StudyUserRoleBean currentRole =
(StudyUserRoleBean) request.getSession().getAttribute("userRole");
HttpSession session = request.getSession();
locale = request.getLocale();
// < respage =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.page_messages",
// locale);
// < restext =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.notes",locale);
// <
// resexception=ResourceBundle.getBundle(
// "org.akaza.openclinica.i18n.exceptions",locale);
// < resword =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
getInputBeans(request);
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
FormProcessor fp = new FormProcessor(request);
SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN);
// BWP 12/2/07>> The following COUNT_VALIDATE session attribute is not
// accessible,
// for unknown reasons (threading problems?), when
// double-data entry displays error messages; it's value is always 0; so
// I have to create my
// own session variable here to keep track of DDE stages
// We'll go by the SectionBean's ordinal first
int tabNumber = 1;
if (sb != null) {
tabNumber = sb.getOrdinal();
}
// if tabNumber still isn't valid, check the "tab" parameter
if (tabNumber < 1) {
if (fp == null) {
fp = new FormProcessor(request);
}
String tab = fp.getString("tab");
if (tab == null || tab.length() < 1) {
tabNumber = 1;
} else {
tabNumber = fp.getInt("tab");
}
}
SectionDAO sectionDao = new SectionDAO(getDataSource());
int crfVersionId = ecb.getCRFVersionId();
int eventCRFId = ecb.getId();
ArrayList sections = sectionDao.findAllByCRFVersionId(crfVersionId);
int sectionSize = sections.size();
HttpSession mySession = request.getSession();
DoubleDataProgress doubleDataProgress =
(DoubleDataProgress) mySession.getAttribute(DDE_PROGESS);
if (doubleDataProgress == null || doubleDataProgress.getEventCRFId() != eventCRFId) {
doubleDataProgress = new DoubleDataProgress(sectionSize, eventCRFId);
mySession.setAttribute(DDE_PROGESS, doubleDataProgress);
}
boolean hasVisitedSection = doubleDataProgress.getSectionVisited(tabNumber, eventCRFId);
// setting up one-time validation here
// admit that it's an odd place to put it, but where else?
// placing it in dataentryservlet is creating too many counts
int keyId = ecb.getId();
Integer count = (Integer) session.getAttribute(COUNT_VALIDATE + keyId);
if (count != null) {
count++;
session.setAttribute(COUNT_VALIDATE + keyId, count);
logger.info("^^^just set count to session: " + count);
} else {
count = 0;
session.setAttribute(COUNT_VALIDATE + keyId, count);
logger.info("***count not found, set to session: " + count);
}
DataEntryStage stage = ecb.getStage();
if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) && !hasVisitedSection) {
// if the user has not entered this section yet in Double Data
// Entry, then
// set a flag that default values should be shown in the form
request.setAttribute(DDE_ENTERED, true);
}
// Now update the session attribute
doubleDataProgress.setSectionVisited(eventCRFId, tabNumber, true);
mySession.setAttribute("doubleDataProgress", doubleDataProgress);
// StudyEventStatus status =
Role r = currentRole.getRole();
session.setAttribute("mayProcessUploading", "true");
// if (!SubmitDataServlet.maySubmitData(ub, currentRole)) {
// this.session.setAttribute("mayProcessUploading", "false");
// String exceptionName = resexception.getString("no_permission_validation");
// String noAccessMessage =
// resexception.getString("not_perfom_validation_syscontact");
//
// addPageMessage(noAccessMessage);
// throw new InsufficientPermissionException(Page.MENU, exceptionName, "1");
// }
//
// if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE)) {
// if (userIsOwnerAndLessThanTwelveHoursHavePassed() && !r.equals(Role.STUDYDIRECTOR)
// && !r.equals(Role.COORDINATOR)) {
// this.session.setAttribute("mayProcessUploading", "false");
// addPageMessage(respage.getString("since_perform_data_entry"));
// throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET,
// resexception.getString("owner_attempting_double_data_entry"), "1");
// }
// } else if (stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
// if (ub.getId() != ecb.getValidatorId() && !r.equals(Role.STUDYDIRECTOR) &&
// !r.equals(Role.COORDINATOR)) {
// this.session.setAttribute("mayProcessUploading", "false");
// addPageMessage(respage.getString("validation_has_already_begun"));
// throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET,
// resexception
// .getString("non_validator_attempting_double_data_entry"), "1");
// }
// } else {
// this.session.setAttribute("mayProcessUploading", "false");
// addPageMessage(respage.getString("not_perform_validation"));
// throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET,
// resexception.getString("using_double_data_entry_CRF_completed"), "1");
// }
return;
}
private void updateStudy3(boolean isInterventional) {
FormProcessor fp = new FormProcessor(request);
StudyBean study = (StudyBean) session.getAttribute("newStudy");
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"));
// Handle Interventions-type and name
// repeat 10 times for each pair on the web page
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"));
}
session.setAttribute("newStudy", study);
session.setAttribute("interventions", interventionArray);
}
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#processRequest()
*/
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int noteId = fp.getInt(INPUT_NOTE_ID);
String module = (String) session.getAttribute("module");
// Integer subjectId = (Integer) session.getAttribute("subjectId");
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(sm.getDataSource());
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
dndao.setFetchMapping(true);
// check that the note exists
DiscrepancyNoteBean discrepancyNoteBean = (DiscrepancyNoteBean) dndao.findByPK(noteId);
if (!discrepancyNoteBean.isActive()) {
throw new InconsistentStateException(
Page.MANAGE_STUDY_SERVLET,
resexception.getString("you_are_trying_resolve_discrepancy_not_exist"));
}
// check that the note has not already been closed
ArrayList children = dndao.findAllByParent(discrepancyNoteBean);
discrepancyNoteBean.setChildren(children);
// This logic has been reverted, issue-7459
// if (parentNoteIsClosed(discrepancyNoteBean)) {
// throw new InconsistentStateException(Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET,
// respage
// .getString("the_discrepancy_choose_has_been_closed_resolved_create_new"));
// }
// all clear, send the user to the resolved screen
String entityType = discrepancyNoteBean.getEntityType().toLowerCase();
discrepancyNoteBean.setResStatus(
ResolutionStatus.get(discrepancyNoteBean.getResolutionStatusId()));
discrepancyNoteBean.setDisType(
DiscrepancyNoteType.get(discrepancyNoteBean.getDiscrepancyNoteTypeId()));
// BWP 03/17/2009 3166: if it's not an ItemData type note, redirect
// Monitors to View Subject or
// View Study Events <<
if (currentRole.getRole().equals(Role.MONITOR)
&& !"itemdata".equalsIgnoreCase(entityType)
&& !"eventcrf".equalsIgnoreCase(entityType)) {
redirectMonitor(module, discrepancyNoteBean);
return;
}
// >>
// If Study is Frozen or Locked
if (currentStudy.getStatus().isFrozen()
&& !"itemdata".equalsIgnoreCase(entityType)
&& !"eventcrf".equalsIgnoreCase(entityType)) {
redirectMonitor(module, discrepancyNoteBean);
return;
}
boolean toView = false;
boolean isCompleted = false;
if ("itemdata".equalsIgnoreCase(entityType)) {
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
ItemDataBean idb = (ItemDataBean) iddao.findByPK(discrepancyNoteBean.getEntityId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(idb.getEventCRFId());
StudySubjectBean studySubjectBean =
(StudySubjectBean) studySubjectDAO.findByPK(ecb.getStudySubjectId());
discrepancyNoteBean.setSubjectId(studySubjectBean.getId());
discrepancyNoteBean.setItemId(idb.getItemId());
if (ecb.getStatus().equals(Status.UNAVAILABLE)) {
isCompleted = true;
}
toView = true; // we want to go to view note page if the note is
// for item data
}
// logger.info("set up pop up url: " + createNoteURL);
// System.out.println("set up pop up url: " + createNoteURL);
boolean goNext =
prepareRequestForResolution(
request, sm.getDataSource(), currentStudy, discrepancyNoteBean, isCompleted);
Page p = getPageForForwarding(discrepancyNoteBean, isCompleted);
// logger.info("found page for forwarding: " + p.getFileName());
if (p == null) {
throw new InconsistentStateException(
Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET,
resexception.getString("the_discrepancy_note_triying_resolve_has_invalid_type"));
} else {
if (p.getFileName().contains("?")) {
if (!p.getFileName().contains("fromViewNotes=1")) {
p.setFileName(p.getFileName() + "&fromViewNotes=1");
}
} else {
p.setFileName(p.getFileName() + "?fromViewNotes=1");
}
String createNoteURL =
CreateDiscrepancyNoteServlet.getAddChildURL(
discrepancyNoteBean, ResolutionStatus.CLOSED, true);
setPopUpURL(createNoteURL);
}
if (!goNext) {
setPopUpURL("");
addPageMessage(
respage.getString("you_may_not_perform_admin_edit_on_CRF_not_completed_by_user"));
p = Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET;
}
forwardPage(p);
}