/** * Fixes ordinal values if there is any duplicates * * @param definitionId * @param dao */ private void fixDuplicates(int definitionId, EventDefinitionCRFDAO dao) { ArrayList list = dao.findAllByEventDefinitionId(definitionId); int prevOrdinal = 0; boolean incrementNextOrdinal = false; for (int i = 0; i < list.size(); i++) { EventDefinitionCRFBean edc = (EventDefinitionCRFBean) list.get(i); if (i == 0) { if (edc.getOrdinal() != 0) { edc.setOrdinal(i); dao.update(edc); } continue; } if (incrementNextOrdinal) { edc.setOrdinal(i); dao.update(edc); continue; } if (edc.getOrdinal() != i) { edc.setOrdinal(i); dao.update(edc); incrementNextOrdinal = true; } } }
private void submitSiteEventDefinitions(StudyBean site) { FormProcessor fp = new FormProcessor(request); ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>(); CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource()); seds = (ArrayList<StudyEventDefinitionBean>) session.getAttribute("definitions"); HashMap<String, Boolean> changes = (HashMap<String, Boolean>) session.getAttribute("changed"); for (StudyEventDefinitionBean sed : seds) { EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource()); ArrayList<EventDefinitionCRFBean> edcs = sed.getCrfs(); for (EventDefinitionCRFBean edcBean : edcs) { int edcStatusId = edcBean.getStatus().getId(); if (edcStatusId == 5 || edcStatusId == 7) { } else { boolean changed = changes.get(sed.getId() + "-" + edcBean.getId()); if (changed) { edcBean.setParentId(edcBean.getId()); edcBean.setStudyId(site.getId()); edcBean.setUpdater(ub); edcBean.setUpdatedDate(new Date()); logger.debug("create for the site"); edcdao.create(edcBean); } } } } session.removeAttribute("definitions"); session.removeAttribute("changed"); session.removeAttribute("sdvOptions"); }
/** * This method creates a List of DisplaySectionBeans, returning them in the order that the * sections appear in a CRF. This List is "lazily" initialized the first time it is requested. * * @return A List of DisplaySectionBeans. * @see org.akaza.openclinica.control.managestudy.PrintCRFServlet * @see org.akaza.openclinica.control.managestudy.PrintDataEntryServlet */ public List<DisplaySectionBean> getDisplaySectionBeans() { FormBeanUtil formBeanUtil; ViewPersistanceHandler persistanceHandler; ArrayList<SectionBean> allCrfSections; // DAO classes for getting item definitions SectionDAO sectionDao; CRFVersionDAO crfVersionDao; if (displaySectionBeans == null) { displaySectionBeans = new ArrayList<DisplaySectionBean>(); formBeanUtil = new FormBeanUtil(); if (hasStoredData) persistanceHandler = new ViewPersistanceHandler(); // We need a CRF version id to populate the form display if (this.crfVersionId == 0) { return displaySectionBeans; } sectionDao = new SectionDAO(dataSource); allCrfSections = (ArrayList) sectionDao.findByVersionId(this.crfVersionId); // for the purposes of null values, try to obtain a valid // eventCrfDefinition id EventDefinitionCRFBean eventDefBean = null; EventCRFBean eventCRFBean = new EventCRFBean(); if (eventCRFId > 0) { EventCRFDAO ecdao = new EventCRFDAO(dataSource); eventCRFBean = (EventCRFBean) ecdao.findByPK(eventCRFId); StudyEventDAO sedao = new StudyEventDAO(dataSource); StudyEventBean studyEvent = (StudyEventBean) sedao.findByPK(eventCRFBean.getStudyEventId()); EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(dataSource); StudyDAO sdao = new StudyDAO(dataSource); StudyBean study = sdao.findByStudySubjectId(eventCRFBean.getStudySubjectId()); eventDefBean = eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId( study, studyEvent.getId(), this.crfVersionId); } eventDefBean = eventDefBean == null ? new EventDefinitionCRFBean() : eventDefBean; // Create an array or List of DisplaySectionBeans representing each // section // for printing DisplaySectionBean displaySectionBean; for (SectionBean sectionBean : allCrfSections) { displaySectionBean = formBeanUtil.createDisplaySectionBWithFormGroups( sectionBean.getId(), this.crfVersionId, dataSource, eventDefBean.getId(), eventCRFBean, context); displaySectionBeans.add(displaySectionBean); } } return displaySectionBeans; }
private ArrayList<StudyEventDefinitionBean> initDefinitions(StudyBean site) { ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>(); StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource()); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource()); CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource()); CRFDAO cdao = new CRFDAO(sm.getDataSource()); StudyBean parentStudy = (StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId()); seds = sedDao.findAllByStudy(parentStudy); int start = 0; for (StudyEventDefinitionBean sed : seds) { int defId = sed.getId(); ArrayList<EventDefinitionCRFBean> edcs = (ArrayList<EventDefinitionCRFBean>) edcdao.findAllByDefinitionAndSiteIdAndParentStudyId( defId, site.getId(), parentStudy.getId()); ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>(); // sed.setCrfNum(edcs.size()); for (EventDefinitionCRFBean edcBean : edcs) { int edcStatusId = edcBean.getStatus().getId(); CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId()); int crfStatusId = crf.getStatusId(); if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) { } else { ArrayList<CRFVersionBean> versions = (ArrayList<CRFVersionBean>) cvdao.findAllActiveByCRF(edcBean.getCrfId()); edcBean.setVersions(versions); edcBean.setCrfName(crf.getName()); CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(edcBean.getDefaultVersionId()); edcBean.setDefaultVersionName(defaultVersion.getName()); String sversionIds = edcBean.getSelectedVersionIds(); ArrayList<Integer> idList = new ArrayList<Integer>(); if (sversionIds.length() > 0) { String[] ids = sversionIds.split("\\,"); for (String id : ids) { idList.add(Integer.valueOf(id)); } } edcBean.setSelectedVersionIdList(idList); defCrfs.add(edcBean); ++start; } } logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size()); sed.setCrfs(defCrfs); sed.setCrfNum(defCrfs.size()); } return seds; }
/** * Increases the ordinal for current object and decrease the ordinal of the previous one * * @param idCurrent * @param idPrevious * @param dao */ private void increase( int idCurrent, int idPrevious, int currOrdinal, int prevOrdinal, int defId, EventDefinitionCRFDAO dao) { EventDefinitionCRFBean current = (EventDefinitionCRFBean) dao.findByPK(idCurrent); EventDefinitionCRFBean previous = (EventDefinitionCRFBean) dao.findByPK(idPrevious); if (current.getOrdinal() == currOrdinal && previous.getOrdinal() == prevOrdinal) { if (idCurrent > 0) { int currentOrdinal = current.getOrdinal(); current.setOrdinal(currentOrdinal - 1); current.setUpdater((UserAccountBean) session.getAttribute("userBean")); dao.update(current); } if (idPrevious > 0) { int previousOrdinal = previous.getOrdinal(); previous.setOrdinal(previousOrdinal + 1); previous.setUpdater((UserAccountBean) session.getAttribute("userBean")); dao.update(previous); } ArrayList currOrdlist = dao.findAllByEventDefinitionIdAndOrdinal(defId, current.getOrdinal()); ArrayList prevOrdlist = dao.findAllByEventDefinitionIdAndOrdinal(defId, previous.getOrdinal()); if (currOrdlist.size() > 1 || prevOrdlist.size() > 1) { fixDuplicates(defId, dao); } } }
public void processRequest() throws Exception { StudyDAO sdao = new StudyDAO(sm.getDataSource()); FormProcessor fp = new FormProcessor(request); int studyId = fp.getInt("id"); StudyBean study = (StudyBean) sdao.findByPK(studyId); // find all sites ArrayList sites = (ArrayList) sdao.findAllByParent(studyId); // find all user and roles in the study, include ones in sites UserAccountDAO udao = new UserAccountDAO(sm.getDataSource()); ArrayList userRoles = udao.findAllByStudyId(studyId); // find all subjects in the study, include ones in sites StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource()); ArrayList subjects = ssdao.findAllByStudy(study); // find all events in the study, include ones in sites StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource()); ArrayList definitions = sefdao.findAllByStudy(study); String action = request.getParameter("action"); if (studyId == 0) { addPageMessage("Please choose a study to restore."); forwardPage(Page.STUDY_LIST_SERVLET); } else { if ("confirm".equalsIgnoreCase(action)) { request.setAttribute("studyToRestore", study); request.setAttribute("sitesToRestore", sites); request.setAttribute("userRolesToRestore", userRoles); request.setAttribute("subjectsToRestore", subjects); request.setAttribute("definitionsToRRestore", definitions); forwardPage(Page.RESTORE_STUDY); } else { logger.info("submit to restore the study"); // change all statuses to unavailable StudyDAO studao = new StudyDAO(sm.getDataSource()); study.setStatus(Status.AVAILABLE); study.setUpdater(ub); study.setUpdatedDate(new Date()); studao.update(study); // remove all sites for (int i = 0; i < sites.size(); i++) { StudyBean site = (StudyBean) sites.get(i); site.setStatus(Status.AVAILABLE); site.setUpdater(ub); site.setUpdatedDate(new Date()); sdao.update(site); } // remove all users and roles for (int i = 0; i < userRoles.size(); i++) { StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i); role.setStatus(Status.AVAILABLE); role.setUpdater(ub); role.setUpdatedDate(new Date()); udao.updateStudyUserRole(role, role.getUserName()); } // remove all subjects for (int i = 0; i < subjects.size(); i++) { StudySubjectBean subject = (StudySubjectBean) subjects.get(i); subject.setStatus(Status.AVAILABLE); subject.setUpdater(ub); subject.setUpdatedDate(new Date()); ssdao.update(subject); } // remove all study_group StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource()); SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource()); ArrayList groups = sgdao.findAllByStudy(study); for (int i = 0; i < groups.size(); i++) { StudyGroupBean group = (StudyGroupBean) groups.get(i); group.setStatus(Status.AVAILABLE); group.setUpdater(ub); group.setUpdatedDate(new Date()); sgdao.update(group); // all subject_group_map ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId()); for (int j = 0; j < subjectGroupMaps.size(); j++) { SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j); sgMap.setStatus(Status.AVAILABLE); sgMap.setUpdater(ub); sgMap.setUpdatedDate(new Date()); sgmdao.update(sgMap); } } // remove all event definitions and event EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource()); StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource()); for (int i = 0; i < definitions.size(); i++) { StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i); definition.setStatus(Status.AVAILABLE); definition.setUpdater(ub); definition.setUpdatedDate(new Date()); sefdao.update(definition); ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId()); for (int j = 0; j < edcs.size(); j++) { EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j); edc.setStatus(Status.AVAILABLE); edc.setUpdater(ub); edc.setUpdatedDate(new Date()); edcdao.update(edc); } ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId()); EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource()); for (int j = 0; j < events.size(); j++) { StudyEventBean event = (StudyEventBean) events.get(j); event.setStatus(Status.AVAILABLE); event.setUpdater(ub); event.setUpdatedDate(new Date()); sedao.update(event); ArrayList eventCRFs = ecdao.findAllByStudyEvent(event); ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource()); for (int k = 0; k < eventCRFs.size(); k++) { EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k); eventCRF.setStatus(Status.AVAILABLE); eventCRF.setUpdater(ub); eventCRF.setUpdatedDate(new Date()); ecdao.update(eventCRF); ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId()); for (int a = 0; a < itemDatas.size(); a++) { ItemDataBean item = (ItemDataBean) itemDatas.get(a); item.setStatus(Status.AVAILABLE); item.setUpdater(ub); item.setUpdatedDate(new Date()); iddao.update(item); } } } } // for definitions DatasetDAO datadao = new DatasetDAO(sm.getDataSource()); ArrayList dataset = datadao.findAllByStudyId(study.getId()); for (int i = 0; i < dataset.size(); i++) { DatasetBean data = (DatasetBean) dataset.get(i); data.setStatus(Status.AVAILABLE); data.setUpdater(ub); data.setUpdatedDate(new Date()); datadao.update(data); } addPageMessage("This study has been restored successfully."); forwardPage(Page.STUDY_LIST_SERVLET); } } }
@Override public void processRequest() throws Exception { FormProcessor fp = new FormProcessor(request); int studySubId = fp.getInt(STUDY_SUB_ID, true); int eventCRFId = fp.getInt(EVENT_CRF_ID); String action = request.getParameter("action"); StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource()); StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource()); EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource()); StudyDAO sdao = new StudyDAO(sm.getDataSource()); if (eventCRFId == 0) { addPageMessage(respage.getString("please_choose_an_event_CRF_to_delete")); request.setAttribute("id", new Integer(studySubId).toString()); forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET); } else { EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId); StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId); request.setAttribute("studySub", studySub); // construct info needed on view event crf page CRFDAO cdao = new CRFDAO(sm.getDataSource()); CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource()); int crfVersionId = eventCRF.getCRFVersionId(); CRFBean cb = cdao.findByVersionId(crfVersionId); eventCRF.setCrf(cb); CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId); eventCRF.setCrfVersion(cvb); // then get the definition so we can call // DisplayEventCRFBean.setFlags int studyEventId = eventCRF.getStudyEventId(); StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId); int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId); StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource()); StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId); event.setStudyEventDefinition(sed); request.setAttribute("event", event); EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource()); StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId()); EventDefinitionCRFBean edc = edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId()); DisplayEventCRFBean dec = new DisplayEventCRFBean(); dec.setEventCRF(eventCRF); dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry()); // find all item data ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource()); dnDao = new DiscrepancyNoteDAO(sm.getDataSource()); ArrayList<ItemDataBean> itemData = iddao.findAllByEventCRFId(eventCRF.getId()); request.setAttribute("items", itemData); if ("confirm".equalsIgnoreCase(action)) { request.setAttribute("displayEventCRF", dec); forwardPage(Page.DELETE_EVENT_CRF); } else { logger.info("submit to delete the event CRF from event"); // OC-6303 Deleting Event CRF resets Show / Hide logic // delete records from DynamicItemForm and DynamicItemGroup getDynamicsItemFormMetadataDao().delete(eventCRFId); getDynamicsItemGroupMetadataDao().delete(eventCRFId); eventCRF.setOldStatus(eventCRF.getStatus()); eventCRF.setStatus(Status.RESET); eventCRF.setUpdater(ub); ecdao.update(eventCRF); for (ItemDataBean itemdata : itemData) { // OC-6343 Rule behaviour must be reset if an Event CRF is deleted // delete the records from ruleActionRunLogDao getRuleActionRunLogDao().delete(itemdata.getId()); // OC-6344 Notes & Discrepancies must be set to "closed" when event CRF is deleted // parentDiscrepancyNoteList is the list of the parent DNs records only ArrayList<DiscrepancyNoteBean> parentDiscrepancyNoteList = getDnDao().findParentNotesOnlyByItemData(itemdata.getId()); for (DiscrepancyNoteBean parentDiscrepancyNote : parentDiscrepancyNoteList) { if (parentDiscrepancyNote.getResolutionStatusId() != 4) { // if the DN's resolution status is not set to Closed String description = resword.getString("dn_auto-closed_description"); String detailedNotes = resword.getString("dn_auto_closed_detailed_notes"); // create new DN record , new DN Map record , also update the parent record createDiscrepancyNoteBean( description, detailedNotes, itemdata.getId(), study, ub, parentDiscrepancyNote); } } iddao = new ItemDataDAO(sm.getDataSource()); ifmdao = new ItemFormMetadataDAO(sm.getDataSource()); ItemDataBean idBean = (ItemDataBean) iddao.findByPK(itemdata.getId()); ItemFormMetadataBean ifmBean = ifmdao.findByItemIdAndCRFVersionId(idBean.getItemId(), crfVersionId); // Updating Dn_item_data_map actovated column into false for the existing DNs ArrayList<DiscrepancyNoteBean> dnBeans = getDnDao().findExistingNotesForItemData(itemdata.getId()); if (dnBeans.size() != 0) { DiscrepancyNoteBean dnBean = new DiscrepancyNoteBean(); dnBean.setEntityId(itemdata.getId()); dnBean.setActivated(false); getDnDao().updateDnMapActivation(dnBean); } // Default Values are not addressed itemdata.setValue(""); itemdata.setOldStatus(itemdata.getStatus()); itemdata.setOwner(ub); itemdata.setStatus(Status.AVAILABLE); itemdata.setUpdater(ub); iddao.updateUser(itemdata); iddao.update(itemdata); } // OC-6291 event_crf status change eventCRF.setOldStatus(eventCRF.getStatus()); eventCRF.setStatus(Status.AVAILABLE); eventCRF.setUpdater(ub); ecdao.update(eventCRF); if (event.getSubjectEventStatus().isCompleted() || event.getSubjectEventStatus().isSigned()) { event.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED); event.setUpdater(ub); sedao = new StudyEventDAO(sm.getDataSource()); sedao.update(event); } String emailBody = respage.getString("the_event_CRF") + cb.getName() + respage.getString("has_been_deleted_from_the_event") + event.getStudyEventDefinition().getName() + ". " + respage.getString("has_been_deleted_from_the_event_cont"); addPageMessage(emailBody); // sendEmail(emailBody); request.setAttribute("id", new Integer(studySubId).toString()); forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET); } } }