private void collectGlobalVariables() { StudyBean study = studyBase.getStudy(); String sn = study.getName(); String sd = study.getSummary().trim(); String pn = study.getIdentifier(); if (parentStudy.getId() > 0) { sn = parentStudy.getName() + " - " + study.getName(); sd = parentStudy.getSummary().trim() + " - " + study.getSummary().trim(); pn = parentStudy.getIdentifier() + " - " + study.getIdentifier(); } GlobalVariablesBean gv = this.odmStudy.getGlobalVariables(); gv.setStudyName(sn); gv.setStudyDescription(sd); gv.setProtocolName(pn); }
/** * 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; }
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; }
/** Inserts the new study into database */ private void submitStudy() { FormProcessor fp = new FormProcessor(request); StudyDAO sdao = new StudyDAO(sm.getDataSource()); StudyBean study = (StudyBean) session.getAttribute("newStudy"); ArrayList parameters = study.getStudyParameters(); logger.info("study bean to be created:\n"); logger.info( study.getName() + "\n" + study.getIdentifier() + "\n" + study.getParentStudyId() + "\n" + study.getSummary() + "\n" + study.getPrincipalInvestigator() + "\n" + study.getDatePlannedStart() + "\n" + study.getDatePlannedEnd() + "\n" + study.getFacilityName() + "\n" + study.getFacilityCity() + "\n" + study.getFacilityState() + "\n" + study.getFacilityZip() + "\n" + study.getFacilityCountry() + "\n" + study.getFacilityRecruitmentStatus() + "\n" + study.getFacilityContactName() + "\n" + study.getFacilityContactEmail() + "\n" + study.getFacilityContactPhone() + "\n" + study.getFacilityContactDegree()); study.setOwner(ub); study.setCreatedDate(new Date()); StudyBean parent = (StudyBean) sdao.findByPK(study.getParentStudyId()); study.setType(parent.getType()); // YW 10-10-2007, enable setting site status study.setStatus(study.getStatus()); // YW >> study.setGenetic(parent.isGenetic()); study = (StudyBean) sdao.create(study); StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource()); for (int i = 0; i < parameters.size(); i++) { StudyParamsConfig config = (StudyParamsConfig) parameters.get(i); StudyParameterValueBean spv = config.getValue(); spv.setStudyId(study.getId()); spv = (StudyParameterValueBean) spvdao.create(config.getValue()); } // YW << here only "collectDob" and "genderRequired" have been corrected // for sites. StudyParameterValueBean spv = new StudyParameterValueBean(); StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parent.getId(), "collectDob"); spv.setStudyId(study.getId()); spv.setParameter("collectDob"); spv.setValue(parentSPV.getValue()); spvdao.create(spv); parentSPV = spvdao.findByHandleAndStudy(parent.getId(), "genderRequired"); spv.setParameter("genderRequired"); spv.setValue(parentSPV.getValue()); spvdao.create(spv); // YW >> // switch user to the newly created site session.setAttribute("study", session.getAttribute("newStudy")); currentStudy = (StudyBean) session.getAttribute("study"); session.removeAttribute("newStudy"); addPageMessage(respage.getString("the_new_site_created_succesfully_current")); forwardPage(Page.SITE_LIST_SERVLET); }
private void submitStudy() { StudyDAO sdao = new StudyDAO(sm.getDataSource()); StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource()); StudyBean study1 = (StudyBean) session.getAttribute("newStudy"); logger.info("study bean to be updated:" + study1.getName()); study1.setUpdatedDate(new Date()); study1.setUpdater((UserAccountBean) session.getAttribute("userBean")); System.out.println("study's parentId=" + study1.getParentStudyId()); sdao.update(study1); StudyParameterValueBean spv = new StudyParameterValueBean(); spv.setStudyId(study1.getId()); spv.setParameter("collectDob"); spv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString()); updateParameter(spvdao, spv); spv.setParameter("discrepancyManagement"); spv.setValue(study1.getStudyParameterConfig().getDiscrepancyManagement()); updateParameter(spvdao, spv); spv.setParameter("genderRequired"); spv.setValue(study1.getStudyParameterConfig().getGenderRequired()); updateParameter(spvdao, spv); spv.setParameter("subjectPersonIdRequired"); spv.setValue(study1.getStudyParameterConfig().getSubjectPersonIdRequired()); updateParameter(spvdao, spv); spv.setParameter("interviewerNameRequired"); spv.setValue(study1.getStudyParameterConfig().getInterviewerNameRequired()); updateParameter(spvdao, spv); spv.setParameter("interviewerNameDefault"); spv.setValue(study1.getStudyParameterConfig().getInterviewerNameDefault()); updateParameter(spvdao, spv); spv.setParameter("interviewerNameEditable"); spv.setValue(study1.getStudyParameterConfig().getInterviewerNameEditable()); updateParameter(spvdao, spv); spv.setParameter("interviewDateRequired"); spv.setValue(study1.getStudyParameterConfig().getInterviewDateRequired()); updateParameter(spvdao, spv); spv.setParameter("interviewDateDefault"); spv.setValue(study1.getStudyParameterConfig().getInterviewDateDefault()); updateParameter(spvdao, spv); spv.setParameter("interviewDateEditable"); spv.setValue(study1.getStudyParameterConfig().getInterviewDateEditable()); updateParameter(spvdao, spv); spv.setParameter("subjectIdGeneration"); spv.setValue(study1.getStudyParameterConfig().getSubjectIdGeneration()); updateParameter(spvdao, spv); spv.setParameter("subjectIdPrefixSuffix"); spv.setValue(study1.getStudyParameterConfig().getSubjectIdPrefixSuffix()); updateParameter(spvdao, spv); spv.setParameter("personIdShownOnCRF"); spv.setValue(study1.getStudyParameterConfig().getPersonIdShownOnCRF()); updateParameter(spvdao, spv); StudyBean curStudy = (StudyBean) session.getAttribute("study"); if (curStudy != null && study1.getId() == curStudy.getId()) { super.currentStudy = study1; session.setAttribute("study", study1); } // update manage_pedigrees for all sites ArrayList children = (ArrayList) sdao.findAllByParent(study1.getId()); for (int i = 0; i < children.size(); i++) { StudyBean child = (StudyBean) children.get(i); child.setType(study1.getType()); // same as parent's type child.setUpdatedDate(new Date()); child.setUpdater(ub); sdao.update(child); // YW << update "collectDob" and "genderRequired" for sites StudyParameterValueBean childspv = new StudyParameterValueBean(); childspv.setStudyId(child.getId()); childspv.setParameter("collectDob"); childspv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString()); updateParameter(spvdao, childspv); childspv.setParameter("genderRequired"); childspv.setValue(study1.getStudyParameterConfig().getGenderRequired()); updateParameter(spvdao, childspv); // YW >> } session.removeAttribute("newStudy"); session.removeAttribute("interventions"); }
@RequestMapping(method = RequestMethod.GET) public ModelMap handleMainPage(HttpServletRequest request) { ModelMap map = new ModelMap(); // setUpSidebar(request); StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study"); eventDefinitionCRFDao = new EventDefinitionCRFDAO(dataSource); studyEventDefinitionDao = new StudyEventDefinitionDAO(dataSource); crfDao = new CRFDAO(dataSource); studyGroupClassDao = new StudyGroupClassDAO(dataSource); studyDao = new StudyDAO(dataSource); userDao = new UserAccountDAO(dataSource); ruleDao = new RuleDAO(dataSource); StudyModuleStatus sms = studyModuleStatusDao.findByStudyId(currentStudy.getId()); if (sms == null) { sms = new StudyModuleStatus(); sms.setStudyId(currentStudy.getId()); } int crfCount = crfDao.findAllByStudy(currentStudy.getId()).size(); int crfWithEventDefinition = crfDao.findAllActiveByDefinitions(currentStudy.getId()).size(); int totalCrf = crfCount + crfWithEventDefinition; // int eventDefinitionCount = eventDefinitionCRFDao.findAllActiveByStudy(currentStudy).size(); int eventDefinitionCount = studyEventDefinitionDao.findAllActiveByStudy(currentStudy).size(); int subjectGroupCount = studyGroupClassDao.findAllActiveByStudy(currentStudy).size(); List<RuleSetBean> ruleSets = ruleSetService.getRuleSetsByStudy(currentStudy); ruleSets = ruleSetService.filterByStatusEqualsAvailableOnlyRuleSetRules(ruleSets); int ruleCount = ruleSets != null ? ruleSets.size() : 0; int siteCount = studyDao.findOlnySiteIdsByStudy(currentStudy).size(); int userCount = userDao.findAllUsersByStudy(currentStudy.getId()).size(); Collection childStudies = studyDao.findAllByParent(currentStudy.getId()); Map childStudyUserCount = new HashMap(); for (Object sb : childStudies) { StudyBean childStudy = (StudyBean) sb; childStudyUserCount.put( childStudy.getName(), userDao.findAllUsersByStudy(childStudy.getId()).size()); } if (sms.getCrf() == 0) { sms.setCrf(StudyModuleStatus.NOT_STARTED); } if (sms.getCrf() != 3 && totalCrf > 0) { sms.setCrf(StudyModuleStatus.IN_PROGRESS); } if (sms.getEventDefinition() == 0) { sms.setEventDefinition(StudyModuleStatus.NOT_STARTED); } if (sms.getEventDefinition() != 3 && eventDefinitionCount > 0) { sms.setEventDefinition(StudyModuleStatus.IN_PROGRESS); } if (sms.getSubjectGroup() == 0) { sms.setSubjectGroup(StudyModuleStatus.NOT_STARTED); } if (sms.getSubjectGroup() != 3 && subjectGroupCount > 0) { sms.setSubjectGroup(StudyModuleStatus.IN_PROGRESS); } if (sms.getRule() == 0) { sms.setRule(StudyModuleStatus.NOT_STARTED); } if (sms.getRule() != 3 && ruleCount > 0) { sms.setRule(StudyModuleStatus.IN_PROGRESS); } if (sms.getSite() == 0) { sms.setSite(StudyModuleStatus.NOT_STARTED); } if (sms.getSite() != 3 && siteCount > 0) { sms.setSite(StudyModuleStatus.IN_PROGRESS); } if (sms.getUsers() == 0) { sms.setUsers(StudyModuleStatus.NOT_STARTED); } if (sms.getUsers() != 3 && userCount > 0) { sms.setUsers(StudyModuleStatus.IN_PROGRESS); } map.addObject(sms); map.addAttribute("crfCount", totalCrf); map.addAttribute("eventDefinitionCount", eventDefinitionCount); map.addAttribute("subjectGroupCount", subjectGroupCount); map.addAttribute("ruleCount", ruleCount); map.addAttribute("siteCount", siteCount); map.addAttribute("userCount", userCount); map.addAttribute("childStudyUserCount", childStudyUserCount); map.addAttribute("studyId", currentStudy.getId()); map.addAttribute("currentStudy", currentStudy); UserAccountBean userBean = (UserAccountBean) request.getSession().getAttribute("userBean"); request.setAttribute("userBean", userBean); request.setAttribute("statusMap", Status.toStudyUpdateMembersList()); ArrayList pageMessages = new ArrayList(); if (request.getSession().getAttribute("pageMessages") != null) { pageMessages.addAll((ArrayList) request.getSession().getAttribute("pageMessages")); request.setAttribute("pageMessages", pageMessages); request.getSession().removeAttribute("pageMessages"); } return map; }
private void submitStudy(StudyBean newStudy) { StudyDAO sdao = new StudyDAO(sm.getDataSource()); StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource()); StudyBean study1 = newStudy; logger.info("study bean to be updated:" + study1.getName()); study1.setUpdatedDate(new Date()); study1.setUpdater((UserAccountBean) session.getAttribute("userBean")); sdao.update(study1); ArrayList siteList = (ArrayList) sdao.findAllByParent(newStudy.getId()); if (siteList.size() > 0) { sdao.updateSitesStatus(study1); } StudyParameterValueBean spv = new StudyParameterValueBean(); spv.setStudyId(study1.getId()); spv.setParameter("collectDob"); spv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString()); updateParameter(spvdao, spv); spv.setParameter("discrepancyManagement"); spv.setValue(study1.getStudyParameterConfig().getDiscrepancyManagement()); updateParameter(spvdao, spv); spv.setParameter("genderRequired"); spv.setValue(study1.getStudyParameterConfig().getGenderRequired()); updateParameter(spvdao, spv); spv.setParameter("subjectPersonIdRequired"); spv.setValue(study1.getStudyParameterConfig().getSubjectPersonIdRequired()); updateParameter(spvdao, spv); spv.setParameter("interviewerNameRequired"); spv.setValue(study1.getStudyParameterConfig().getInterviewerNameRequired()); updateParameter(spvdao, spv); spv.setParameter("interviewerNameDefault"); spv.setValue(study1.getStudyParameterConfig().getInterviewerNameDefault()); updateParameter(spvdao, spv); spv.setParameter("interviewerNameEditable"); spv.setValue(study1.getStudyParameterConfig().getInterviewerNameEditable()); updateParameter(spvdao, spv); // BWP 1/12/2009 3169 Update interviewerNameEditable and // interviewDateEditable parameters for all sites>> List<StudyBean> sites = new ArrayList<StudyBean>(); sites = (ArrayList) sdao.findAllByParent(newStudy.getId()); if (sites != null && (!sites.isEmpty())) { updateInterviewerForSites(newStudy, sites, spvdao, "interviewerNameEditable"); } // >> spv.setParameter("interviewDateRequired"); spv.setValue(study1.getStudyParameterConfig().getInterviewDateRequired()); updateParameter(spvdao, spv); spv.setParameter("interviewDateDefault"); spv.setValue(study1.getStudyParameterConfig().getInterviewDateDefault()); updateParameter(spvdao, spv); spv.setParameter("interviewDateEditable"); spv.setValue(study1.getStudyParameterConfig().getInterviewDateEditable()); updateParameter(spvdao, spv); // BWP 1/12/2009 3169>> if (sites != null && (!sites.isEmpty())) { updateInterviewerForSites(newStudy, sites, spvdao, "interviewDateEditable"); } // >> spv.setParameter("subjectIdGeneration"); spv.setValue(study1.getStudyParameterConfig().getSubjectIdGeneration()); updateParameter(spvdao, spv); spv.setParameter("subjectIdPrefixSuffix"); spv.setValue(study1.getStudyParameterConfig().getSubjectIdPrefixSuffix()); updateParameter(spvdao, spv); spv.setParameter("personIdShownOnCRF"); spv.setValue(study1.getStudyParameterConfig().getPersonIdShownOnCRF()); updateParameter(spvdao, spv); spv.setParameter("secondaryLabelViewable"); spv.setValue(study1.getStudyParameterConfig().getSecondaryLabelViewable()); updateParameter(spvdao, spv); // tbh, 06/04/2009 3684>> spv.setParameter("adminForcedReasonForChange"); spv.setValue(study1.getStudyParameterConfig().getAdminForcedReasonForChange()); updateParameter(spvdao, spv); // >> StudyBean curStudy = (StudyBean) session.getAttribute("study"); if (curStudy != null && study1.getId() == curStudy.getId()) { super.currentStudy = study1; session.setAttribute("study", study1); } // update manage_pedigrees for all sites ArrayList children = (ArrayList) sdao.findAllByParent(study1.getId()); for (int i = 0; i < children.size(); i++) { StudyBean child = (StudyBean) children.get(i); child.setType(study1.getType()); // same as parent's type child.setUpdatedDate(new Date()); child.setUpdater(ub); sdao.update(child); // YW << update "collectDob" and "genderRequired" for sites StudyParameterValueBean childspv = new StudyParameterValueBean(); childspv.setStudyId(child.getId()); childspv.setParameter("collectDob"); childspv.setValue(new Integer(study1.getStudyParameterConfig().getCollectDob()).toString()); updateParameter(spvdao, childspv); childspv.setParameter("genderRequired"); childspv.setValue(study1.getStudyParameterConfig().getGenderRequired()); updateParameter(spvdao, childspv); } }
@Override public void processRequest() throws Exception { 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); } } }
public boolean validate(SubjectTransferBean subjectTransferBean) throws OpenClinicaSystemException { StudyDAO stdao = new StudyDAO(this.getDataSource()); StudyBean study = stdao.findByUniqueIdentifier(subjectTransferBean.getStudyOid()); if (study == null) { throw new OpenClinicaSystemException("Study you specified does not exist"); } UserAccountBean ua = subjectTransferBean.getOwner(); StudyUserRoleBean role = ua.getRoleByStudy(study); if (role.getId() == 0 || role.getRole().equals(Role.MONITOR)) { throw new OpenClinicaSystemException( "You do not have sufficient priviliges to run this service"); } if (subjectTransferBean.getSiteIdentifier() != null) { study = stdao.findSiteByUniqueIdentifier( subjectTransferBean.getStudyOid(), subjectTransferBean.getSiteIdentifier()); } subjectTransferBean.setStudy(study); if (study == null) { throw new OpenClinicaSystemException("Site you specified does not exist"); } int handleStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId(); org.akaza.openclinica.dao.service.StudyParameterValueDAO spvdao = new StudyParameterValueDAO(this.getDataSource()); StudyParameterValueBean studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "subjectPersonIdRequired"); String personId = subjectTransferBean.getPersonId(); if ("required".equals(studyParameter.getValue()) && (personId == null || personId.length() < 1)) { throw new OpenClinicaSystemException( "personId is required for the study: " + study.getName()); // return false; } if (personId != null && personId.length() > 255) { throw new OpenClinicaSystemException("personId should not be longer than 255."); // return false; } String idSetting = ""; StudyParameterValueBean subjectIdGenerationParameter = spvdao.findByHandleAndStudy(handleStudyId, "subjectIdGeneration"); idSetting = subjectIdGenerationParameter.getValue(); if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) { int nextLabel = getStudySubjectDao().findTheGreatestLabel() + 1; subjectTransferBean.setStudySubjectId(new Integer(nextLabel).toString()); } String studySubjectId = subjectTransferBean.getStudySubjectId(); if (studySubjectId == null || studySubjectId.length() < 1) { logger.info("studySubjectId is required."); throw new OpenClinicaSystemException("studySubjectId is required."); // return false; } else if (studySubjectId.length() > 30) { throw new OpenClinicaSystemException("studySubjectId should not be longer than 30."); // return false; } String secondaryId = subjectTransferBean.getSecondaryId(); if (secondaryId != null && secondaryId.length() > 30) { throw new OpenClinicaSystemException("secondaryId should not be longer than 30."); // return false; } String gender = subjectTransferBean.getGender() + ""; studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "genderRequired"); if ("true".equals(studyParameter.getValue()) && (gender == null || gender.length() < 1)) { throw new OpenClinicaSystemException("gender is required for the study:" + study.getName()); // return false; } Date dateOfBirth = subjectTransferBean.getDateOfBirth(); String yearOfBirth = subjectTransferBean.getYearOfBirth(); studyParameter = spvdao.findByHandleAndStudy(handleStudyId, "collectDob"); if ("1".equals(studyParameter.getValue()) && (dateOfBirth == null)) { throw new OpenClinicaSystemException("date Of Birth is required:" + study.getName()); // return false; } else if ("2".equals(studyParameter.getValue()) && (yearOfBirth == null)) { throw new OpenClinicaSystemException("Year Of Birth is required:" + study.getName()); } else if ("2".equals(studyParameter.getValue()) && (yearOfBirth != null)) { try { SimpleDateFormat sdf = new SimpleDateFormat("yyyy"); subjectTransferBean.setDateOfBirth(sdf.parse(subjectTransferBean.getYearOfBirth())); } catch (ParseException e) { throw new OpenClinicaSystemException("Year Of Birth not Valid:" + study.getName()); } } Date enrollmentDate = subjectTransferBean.getEnrollmentDate(); if (enrollmentDate == null) { throw new OpenClinicaSystemException("enrollmentDate is required."); // return false; } else { if ((new Date()).compareTo(enrollmentDate) < 0) { throw new OpenClinicaSystemException("enrollmentDate should be in the past."); // return false; } } return true; }
@Override protected void executeInternal(JobExecutionContext context) throws JobExecutionException { // need to generate a Locale so that user beans and other things will // generate normally Locale locale = new Locale("en-US"); ResourceBundleProvider.updateLocale(locale); ResourceBundle pageMessages = ResourceBundleProvider.getPageMessagesBundle(); // logger.debug("--"); // logger.debug("-- executing a job " + message + " at " + new // java.util.Date().toString()); JobDataMap dataMap = context.getMergedJobDataMap(); SimpleTrigger trigger = (SimpleTrigger) context.getTrigger(); try { ApplicationContext appContext = (ApplicationContext) context.getScheduler().getContext().get("applicationContext"); String studySubjectNumber = ((CoreResources) appContext.getBean("coreResources")).getField("extract.number"); coreResources = (CoreResources) appContext.getBean("coreResources"); ruleSetRuleDao = (RuleSetRuleDao) appContext.getBean("ruleSetRuleDao"); dataSource = (DataSource) appContext.getBean("dataSource"); mailSender = (OpenClinicaMailSender) appContext.getBean("openClinicaMailSender"); AuditEventDAO auditEventDAO = new AuditEventDAO(dataSource); // Scheduler scheduler = context.getScheduler(); // JobDetail detail = context.getJobDetail(); // jobDetailBean = (JobDetailBean) detail; /* * data map here should coincide with the job data map found in * CreateJobExportServlet, with the following code: jobDataMap = new * JobDataMap(); jobDataMap.put(DATASET_ID, datasetId); * jobDataMap.put(PERIOD, period); jobDataMap.put(EMAIL, email); * jobDataMap.put(TAB, tab); jobDataMap.put(CDISC, cdisc); * jobDataMap.put(SPSS, spss); */ String alertEmail = dataMap.getString(EMAIL); String localeStr = dataMap.getString(LOCALE); if (localeStr != null) { locale = new Locale(localeStr); ResourceBundleProvider.updateLocale(locale); pageMessages = ResourceBundleProvider.getPageMessagesBundle(); } int dsId = dataMap.getInt(DATASET_ID); String tab = dataMap.getString(TAB); String cdisc = dataMap.getString(CDISC); String cdisc12 = dataMap.getString(CDISC12); if (cdisc12 == null) { cdisc12 = "0"; } String cdisc13 = dataMap.getString(CDISC13); if (cdisc13 == null) { cdisc13 = "0"; } String cdisc13oc = dataMap.getString(CDISC13OC); if (cdisc13oc == null) { cdisc13oc = "0"; } String spss = dataMap.getString(SPSS); int userId = dataMap.getInt(USER_ID); int studyId = dataMap.getInt(STUDY_ID); // String datasetId = dataMap.getString(DATASET_ID); // int dsId = new Integer(datasetId).intValue(); // String userAcctId = dataMap.getString(USER_ID); // int userId = new Integer(userAcctId).intValue(); // why the flip-flop? if one property is set to 'true' we can // see jobs in another screen but all properties have to be // strings logger.debug("-- found the job: " + dsId + " dataset id"); // for (Iterator it = dataMap.entrySet().iterator(); it.hasNext();) // { // java.util.Map.Entry entry = (java.util.Map.Entry) it.next(); // Object key = entry.getKey(); // Object value = entry.getValue(); // // logger.debug("-- found datamap property: " + key.toString() + // // " : " + value.toString()); // } HashMap fileName = new HashMap<String, Integer>(); if (dsId > 0) { // trying to not throw an error if there's no dataset id DatasetDAO dsdao = new DatasetDAO(dataSource); DatasetBean datasetBean = (DatasetBean) dsdao.findByPK(dsId); StudyDAO studyDao = new StudyDAO(dataSource); UserAccountDAO userAccountDAO = new UserAccountDAO(dataSource); // hmm, three lines in the if block DRY? String generalFileDir = ""; String generalFileDirCopy = ""; String exportFilePath = SQLInitServlet.getField("exportFilePath"); String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator; SimpleDateFormat sdfDir = new SimpleDateFormat(pattern); generalFileDir = DATASET_DIR + datasetBean.getId() + File.separator + sdfDir.format(new java.util.Date()); if (!"".equals(exportFilePath)) { generalFileDirCopy = SQLInitServlet.getField("filePath") + exportFilePath + File.separator; } // logger.debug("-- created the following dir: " + // generalFileDir); long sysTimeBegin = System.currentTimeMillis(); // set up the user bean here, tbh // logger.debug("-- gen tab file 00"); userBean = (UserAccountBean) userAccountDAO.findByPK(userId); // needs to also be captured by the servlet, tbh // logger.debug("-- gen tab file 00"); generateFileService = new GenerateExtractFileService(dataSource, userBean, coreResources, ruleSetRuleDao); // logger.debug("-- gen tab file 00"); // tbh #5796 - covers a bug when the user changes studies, 10/2010 StudyBean activeStudy = (StudyBean) studyDao.findByPK(studyId); StudyBean parentStudy = new StudyBean(); logger.debug( "active study: " + studyId + " parent study: " + activeStudy.getParentStudyId()); if (activeStudy.getParentStudyId() > 0) { // StudyDAO sdao = new StudyDAO(sm.getDataSource()); parentStudy = (StudyBean) studyDao.findByPK(activeStudy.getParentStudyId()); } else { parentStudy = activeStudy; // covers a bug in tab file creation, tbh 01/2009 } logger.debug("-- found extract bean "); ExtractBean eb = generateFileService.generateExtractBean(datasetBean, activeStudy, parentStudy); MessageFormat mf = new MessageFormat(""); StringBuffer message = new StringBuffer(); StringBuffer auditMessage = new StringBuffer(); // use resource bundle page messages to generate the email, tbh // 02/2009 // message.append(pageMessages.getString("html_email_header_1") // + " " + alertEmail + // pageMessages.getString("html_email_header_2") + "<br/>"); message.append( "<p>" + pageMessages.getString("email_header_1") + " " + EmailEngine.getAdminEmail() + " " + pageMessages.getString("email_header_2") + " Job Execution " + pageMessages.getString("email_header_3") + "</p>"); message.append("<P>Dataset: " + datasetBean.getName() + "</P>"); message.append("<P>Study: " + activeStudy.getName() + "</P>"); message.append( "<p>" + pageMessages.getString("html_email_body_1") + datasetBean.getName() + pageMessages.getString("html_email_body_2") + SQLInitServlet.getField("sysURL") + pageMessages.getString("html_email_body_3") + "</p>"); // logger.debug("-- gen tab file 00"); if ("1".equals(tab)) { logger.debug("-- gen tab file 01"); fileName = generateFileService.createTabFile( eb, sysTimeBegin, generalFileDir, datasetBean, activeStudy.getId(), parentStudy.getId(), generalFileDirCopy); message.append( "<p>" + pageMessages.getString("html_email_body_4") + " " + getFileNameStr(fileName) + pageMessages.getString("html_email_body_4_5") + SQLInitServlet.getField("sysURL.base") + "AccessFile?fileId=" + getFileIdInt(fileName) + pageMessages.getString("html_email_body_3") + "</p>"); // MessageFormat mf = new MessageFormat(""); // mf.applyPattern(pageMessages.getString( // "you_can_access_tab_delimited")); // Object[] arguments = { getFileIdInt(fileName) }; // auditMessage.append(mf.format(arguments)); // auditMessage.append( // "You can access your tab-delimited file <a href='AccessFile?fileId=" // + getFileIdInt(fileName) + "'>here</a>.<br/>"); auditMessage.append( pageMessages.getString("you_can_access_tab_delimited") + getFileIdInt(fileName) + pageMessages.getString("access_end")); } if ("1".equals(cdisc)) { String odmVersion = "oc1.2"; fileName = generateFileService.createODMFile( odmVersion, sysTimeBegin, generalFileDir, datasetBean, activeStudy, generalFileDirCopy, eb, activeStudy.getId(), parentStudy.getId(), studySubjectNumber, true, true, true, null); logger.debug("-- gen odm file"); message.append( "<p>" + pageMessages.getString("html_email_body_4") + " " + getFileNameStr(fileName) + pageMessages.getString("html_email_body_4_5") + SQLInitServlet.getField("sysURL.base") + "AccessFile?fileId=" + getFileIdInt(fileName) + pageMessages.getString("html_email_body_3") + "</p>"); // MessageFormat mf = new MessageFormat(""); // mf.applyPattern(pageMessages.getString( // "you_can_access_odm_12")); // Object[] arguments = { getFileIdInt(fileName) }; // auditMessage.append(mf.format(arguments)); // auditMessage.append( // "You can access your ODM 1.2 w/OpenClinica Extension XML file <a // href='AccessFile?fileId=" // + getFileIdInt(fileName) // + "'>here</a>.<br/>"); auditMessage.append( pageMessages.getString("you_can_access_odm_12") + getFileIdInt(fileName) + pageMessages.getString("access_end")); } if ("1".equals(cdisc12)) { String odmVersion = "1.2"; fileName = generateFileService.createODMFile( odmVersion, sysTimeBegin, generalFileDir, datasetBean, activeStudy, generalFileDirCopy, eb, activeStudy.getId(), parentStudy.getId(), studySubjectNumber, true, true, true, null); logger.debug("-- gen odm file 1.2 default"); message.append( "<p>" + pageMessages.getString("html_email_body_4") + " " + getFileNameStr(fileName) + pageMessages.getString("html_email_body_4_5") + SQLInitServlet.getField("sysURL.base") + "AccessFile?fileId=" + getFileIdInt(fileName) + pageMessages.getString("html_email_body_3") + "</p>"); // mf.applyPattern(pageMessages.getString( // "you_can_access_odm_12_xml")); // Object[] arguments = { getFileIdInt(fileName) }; // auditMessage.append(mf.format(arguments)); // // auditMessage.append( // "You can access your ODM 1.2 XML file <a href='AccessFile?fileId=" // + getFileIdInt(fileName) + "'>here</a>.<br/>"); auditMessage.append( pageMessages.getString("you_can_access_odm_12_xml") + getFileIdInt(fileName) + pageMessages.getString("access_end")); } if ("1".equals(cdisc13)) { String odmVersion = "1.3"; fileName = generateFileService.createODMFile( odmVersion, sysTimeBegin, generalFileDir, datasetBean, activeStudy, generalFileDirCopy, eb, activeStudy.getId(), parentStudy.getId(), studySubjectNumber, true, true, true, null); logger.debug("-- gen odm file 1.3"); message.append( "<p>" + pageMessages.getString("html_email_body_4") + " " + getFileNameStr(fileName) + pageMessages.getString("html_email_body_4_5") + SQLInitServlet.getField("sysURL.base") + "AccessFile?fileId=" + getFileIdInt(fileName) + pageMessages.getString("html_email_body_3") + "</p>"); // MessageFormat mf = new MessageFormat(""); // mf.applyPattern(pageMessages.getString( // "you_can_access_odm_13")); // Object[] arguments = { getFileIdInt(fileName) }; // auditMessage.append(mf.format(arguments)); // auditMessage.append( // "You can access your ODM 1.3 XML file <a href='AccessFile?fileId=" // + getFileIdInt(fileName) + "'>here</a>.<br/>"); auditMessage.append( pageMessages.getString("you_can_access_odm_13") + getFileIdInt(fileName) + pageMessages.getString("access_end")); } if ("1".equals(cdisc13oc)) { String odmVersion = "oc1.3"; fileName = generateFileService.createODMFile( odmVersion, sysTimeBegin, generalFileDir, datasetBean, activeStudy, generalFileDirCopy, eb, activeStudy.getId(), parentStudy.getId(), studySubjectNumber, true, true, true, null); logger.debug("-- gen odm file 1.3 oc"); message.append( "<p>" + pageMessages.getString("html_email_body_4") + " " + getFileNameStr(fileName) + pageMessages.getString("html_email_body_4_5") + SQLInitServlet.getField("sysURL.base") + "AccessFile?fileId=" + getFileIdInt(fileName) + pageMessages.getString("html_email_body_3") + "</p>"); // MessageFormat mf = new MessageFormat(""); // mf.applyPattern(pageMessages.getString( // "you_can_access_odm_13_xml")); // Object[] arguments = { getFileIdInt(fileName) }; // auditMessage.append(mf.format(arguments)); // auditMessage.append( // "You can access your ODM 1.3 w/OpenClinica Extension XML file <a // href='AccessFile?fileId=" // + getFileIdInt(fileName) // + "'>here</a>.<br/>"); auditMessage.append( pageMessages.getString("you_can_access_odm_13_xml") + getFileIdInt(fileName) + pageMessages.getString("access_end")); } if ("1".equals(spss)) { SPSSReportBean answer = new SPSSReportBean(); fileName = generateFileService.createSPSSFile( datasetBean, eb, activeStudy, parentStudy, sysTimeBegin, generalFileDir, answer, generalFileDirCopy); logger.debug("-- gen spss file"); message.append( "<p>" + pageMessages.getString("html_email_body_4") + " " + getFileNameStr(fileName) + pageMessages.getString("html_email_body_4_5") + SQLInitServlet.getField("sysURL.base") + "AccessFile?fileId=" + getFileIdInt(fileName) + pageMessages.getString("html_email_body_3") + "</p>"); // MessageFormat mf = new MessageFormat(""); // mf.applyPattern(pageMessages.getString( // "you_can_access_spss")); // Object[] arguments = { getFileIdInt(fileName) }; // auditMessage.append(mf.format(arguments)); // auditMessage.append( // "You can access your SPSS files <a href='AccessFile?fileId=" // + getFileIdInt(fileName) + "'>here</a>.<br/>"); auditMessage.append( pageMessages.getString("you_can_access_spss") + getFileIdInt(fileName) + pageMessages.getString("access_end")); } // wrap up the message, and send the email message.append( "<p>" + pageMessages.getString("html_email_body_5") + "</P><P>" + pageMessages.getString("email_footer")); try { mailSender.sendEmail( alertEmail.trim(), pageMessages.getString("job_ran_for") + " " + datasetBean.getName(), message.toString(), true); } catch (OpenClinicaSystemException ose) { // Do Nothing, In the future we might want to have an email // status added to system. } TriggerBean triggerBean = new TriggerBean(); triggerBean.setDataset(datasetBean); triggerBean.setUserAccount(userBean); triggerBean.setFullName(trigger.getName()); auditEventDAO.createRowForExtractDataJobSuccess(triggerBean, auditMessage.toString()); } else { TriggerBean triggerBean = new TriggerBean(); // triggerBean.setDataset(datasetBean); triggerBean.setUserAccount(userBean); triggerBean.setFullName(trigger.getName()); auditEventDAO.createRowForExtractDataJobFailure(triggerBean); // logger.debug("-- made it here for some reason, ds id: " // + dsId); } // logger.debug("-- generated file: " + fileNameStr); // dataSource. } catch (Exception e) { // TODO Auto-generated catch block -- ideally should generate a fail // msg here, tbh 02/2009 logger.debug("-- found exception: " + e.getMessage()); e.printStackTrace(); } }
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 { 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); } } }