Examples with SubjectBean org.akaza.openclinica.bean.submit.SubjectBean used on opensource projects

Example 26 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class ListEventsForSubjectTableFactory method setDataAndLimitVariables.

@SuppressWarnings("unchecked")
@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    Limit limit = tableFacade.getLimit();
    ListEventsForSubjectFilter eventsForSubjectFilter = getListEventsForSubjectFilter(limit);
    // Used on Initial sort without filters
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDAO().getCountWithFilter(eventsForSubjectFilter, getStudyBean());
        tableFacade.setTotalRows(totalRows);
    }
    // Preprocess the studysubjectbean list to find subjects with crf status
    ListEventsForSubjectSort eventsForSubjectSort = getListEventsForSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDAO().getWithFilterAndSort(getStudyBean(), eventsForSubjectFilter, eventsForSubjectSort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    for (StudySubjectBean studySubjectBean : items) {
        HashMap<Object, Object> theItem = new HashMap<Object, Object>();
        theItem.put("studySubject", studySubjectBean);
        theItem.put("studySubject.label", studySubjectBean.getLabel());
        theItem.put("studySubject.status", studySubjectBean.getStatus());
        theItem.put("enrolledAt", ((StudyBean) getStudyDAO().findByPK(studySubjectBean.getStudyId())).getIdentifier());
        SubjectBean subjectBean = (SubjectBean) getSubjectDAO().findByPK(studySubjectBean.getSubjectId());
        theItem.put("subject", subjectBean);
        theItem.put("subject.charGender", subjectBean.getGender());
        // study group classes
        SubjectGroupMapBean subjectGroupMapBean = new SubjectGroupMapBean();
        for (StudyGroupClassBean studyGroupClass : getStudyGroupClasses()) {
            subjectGroupMapBean = getSubjectGroupMapDAO().findAllByStudySubjectAndStudyGroupClass(studySubjectBean.getId(), studyGroupClass.getId());
            if (null != subjectGroupMapBean) {
                theItem.put("sgc_" + studyGroupClass.getId(), subjectGroupMapBean.getStudyGroupId());
                theItem.put("grpName_sgc_" + studyGroupClass.getId(), subjectGroupMapBean.getStudyGroupName());
            }
        }
        subjectGroupMapBean = null;
        HashMap<String, EventCRFBean> crfAsKeyEventCrfAsValue = getEventsCrfsForStudySubject(studySubjectBean);
        // Get the event Status
        List<StudyEventBean> eventsForStudySubjectAndEventDefinitions = getStudyEventDAO().findAllByDefinitionAndSubject(selectedStudyEventDefinition, studySubjectBean);
        List<DisplayBean> events = new ArrayList<DisplayBean>();
        // study event size < 1
        if (eventsForStudySubjectAndEventDefinitions.size() < 1) {
            DisplayBean d = new DisplayBean();
            d.getProps().put("event", null);
            d.getProps().put("event.status", SubjectEventStatus.NOT_SCHEDULED);
            d.getProps().put("studySubject.createdDate", null);
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                d.getProps().put("crf_" + crf.getId(), DataEntryStage.UNCOMPLETED);
                d.getProps().put("crf_" + crf.getId() + "_eventCrf", null);
                d.getProps().put("crf_" + crf.getId() + "_crf", crf);
                // d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", eventDefinitionCrfs.get(i));
                d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", getEventDefinitionCRFBean(selectedStudyEventDefinition.getId(), crf, studySubjectBean));
                theItem.put("crf_" + crf.getId(), "");
            }
            events.add(d);
        }
        // study event size >0
        for (StudyEventBean studyEventBean : eventsForStudySubjectAndEventDefinitions) {
            DisplayBean d = new DisplayBean();
            d.getProps().put("event", studyEventBean);
            d.getProps().put("event.status", studyEventBean.getSubjectEventStatus());
            d.getProps().put("studySubject.createdDate", studyEventBean.getDateStarted());
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                EventCRFBean eventCRFBean = crfAsKeyEventCrfAsValue.get(crf.getId() + "_" + studyEventBean.getId());
                if (eventCRFBean != null) {
                    d.getProps().put("crf_" + crf.getId(), eventCRFBean.getStage());
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", eventCRFBean);
                } else {
                    d.getProps().put("crf_" + crf.getId(), DataEntryStage.UNCOMPLETED);
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", null);
                }
                d.getProps().put("crf_" + crf.getId() + "_crf", crf);
                // d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", eventDefinitionCrfs.get(i));
                d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", getEventDefinitionCRFBean(selectedStudyEventDefinition.getId(), crf, studySubjectBean));
                theItem.put("crf_" + crf.getId(), "");
            }
            events.add(d);
        }
        theItem.put("events", events);
        theItem.put("event.status", "");
        theItem.put("studySubject.createdDate", "");
        theItem.put("webappContext", tableFacade.getWebContext().getContextPath());
        theItems.add(theItem);
    }
    // Do not forget to set the items back on the tableFacade.
    tableFacade.setItems(theItems);
}

Example 27 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class ViewStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String from = fp.getString("from");
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    // if coming from change crf version -> display message
    String crfVersionChangeMsg = fp.getString("isFromCRFVersionChange");
    if (crfVersionChangeMsg != null && !crfVersionChangeMsg.equals("")) {
        addPageMessage(crfVersionChangeMsg);
    }
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
    } else {
        if (!StringUtil.isBlank(from)) {
            // form ListSubject or
            request.setAttribute("from", from);
        // ListStudySubject
        } else {
            request.setAttribute("from", "");
        }
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        request.setAttribute("studySub", studySub);
        int studyId = studySub.getStudyId();
        int subjectId = studySub.getSubjectId();
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studyId);
        // Check if this StudySubject would be accessed from the Current Study
        if (studySub.getStudyId() != currentStudy.getId()) {
            if (currentStudy.getParentStudyId() > 0) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            } else {
                // The SubjectStudy is not belong to currentstudy and current study is not a site.
                Collection sites = studydao.findOlnySiteIdsByStudy(currentStudy);
                if (!sites.contains(study.getId())) {
                    addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                    forwardPage(Page.MENU_SERVLET);
                    return;
                }
            }
        }
        // If the study subject derives from a site, and is being viewed
        // from a parent study,
        // then the study IDs will be different. However, since each note is
        // saved with the specific
        // study ID, then its study ID may be different than the study
        // subject's ID.
        boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId();
        boolean isParentStudy = study.getParentStudyId() < 1;
        // Get any disc notes for this subject : studySubId
        DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource());
        List<DiscrepancyNoteBean> allNotesforSubject = new ArrayList<DiscrepancyNoteBean>();
        // These methods return only parent disc notes
        if (subjectStudyIsCurrentStudy && isParentStudy) {
            allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudyAndId(study, subjectId);
            allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudyAndId(study, studySubId));
        } else {
            if (!isParentStudy) {
                StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId());
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(stParent, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(stParent, study, studySubId));
            } else {
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(currentStudy, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(currentStudy, study, studySubId));
            }
        }
        if (!allNotesforSubject.isEmpty()) {
            setRequestAttributesForNotes(allNotesforSubject);
        }
        SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
        if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
            Date dob = subject.getDateOfBirth();
            if (dob != null) {
                Calendar cal = Calendar.getInstance();
                cal.setTime(dob);
                int year = cal.get(Calendar.YEAR);
                request.setAttribute("yearOfBirth", new Integer(year));
            } else {
                request.setAttribute("yearOfBirth", "");
            }
        }
        request.setAttribute("subject", subject);
        /*
             * StudyDAO studydao = new StudyDAO(sm.getDataSource()); StudyBean
             * study = (StudyBean) studydao.findByPK(studyId);
             */
        // YW 11-26-2007 <<
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
        // YW >>
        request.setAttribute("subjectStudy", study);
        if (study.getParentStudyId() > 0) {
            // this is a site,find parent
            StudyBean parentStudy2 = (StudyBean) studydao.findByPK(study.getParentStudyId());
            request.setAttribute("parentStudy", parentStudy2);
        } else {
            request.setAttribute("parentStudy", new StudyBean());
        }
        ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId);
        request.setAttribute("children", children);
        // find study events
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
        StudySubjectService studySubjectService = (StudySubjectService) WebApplicationContextUtils.getWebApplicationContext(getServletContext()).getBean("studySubjectService");
        List<DisplayStudyEventBean> displayEvents = studySubjectService.getDisplayStudyEventsForStudySubject(studySub, ub, currentRole);
        // Mantis Issue 5048: Preventing Investigators from Unlocking Events
        for (int i = 0; i < displayEvents.size(); i++) {
            DisplayStudyEventBean decb = displayEvents.get(i);
            if (!(currentRole.isDirector() || currentRole.isCoordinator()) && decb.getStudyEvent().getSubjectEventStatus().isLocked()) {
                decb.getStudyEvent().setEditable(false);
            }
        }
        // BWP 3212; remove event CRFs that are supposed to be "hidden" >>
        if (currentStudy.getParentStudyId() > 0) {
            HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
            for (DisplayStudyEventBean displayStudyEventBean : displayEvents) {
                hideCRFManager.removeHiddenEventCRF(displayStudyEventBean);
            }
        }
        // >>
        EntityBeanTable table = fp.getEntityBeanTable();
        // sort by start
        table.setSortingIfNotExplicitlySet(1, false);
        // date, desc
        ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents);
        String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("location"), resword.getString("status"), resword.getString("actions"), resword.getString("CRFs_atrib") };
        table.setColumns(new ArrayList(Arrays.asList(columns)));
        table.hideColumnLink(4);
        table.hideColumnLink(5);
        // YW 11-08-2007 <<
        if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) {
            if (currentStudy.getStatus().isAvailable() && !currentRole.getRole().equals(Role.MONITOR)) {
                table.addLink(resword.getString("add_new_event"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId());
            }
        }
        // YW >>
        HashMap args = new HashMap();
        args.put("id", new Integer(studySubId).toString());
        table.setQuery("ViewStudySubject", args);
        table.setRows(allEventRows);
        table.computeDisplay();
        request.setAttribute("table", table);
        // request.setAttribute("displayEvents", displayEvents);
        // find group info
        SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
        ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId);
        request.setAttribute("groups", groupMaps);
        // find audit log for events
        AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
        ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
        // logger.warning("^^^ retrieved logs");
        UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
        ArrayList eventLogs = new ArrayList();
        // logger.warning("^^^ starting to iterate");
        for (int i = 0; i < logs.size(); i++) {
            AuditEventBean avb = (AuditEventBean) logs.get(i);
            StudyEventAuditBean sea = new StudyEventAuditBean();
            sea.setAuditEvent(avb);
            StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId());
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            sea.setDefinition(sed);
            String old = avb.getOldValue().trim();
            try {
                if (!StringUtil.isBlank(old)) {
                    SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue());
                    sea.setOldSubjectEventStatus(oldStatus);
                }
                String newValue = avb.getNewValue().trim();
                if (!StringUtil.isBlank(newValue)) {
                    SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue());
                    sea.setNewSubjectEventStatus(newStatus);
                }
            } catch (NumberFormatException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            // logger.warning("^^^ caught NFE");
            }
            UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
            sea.setUpdater(updater);
            eventLogs.add(sea);
        }
        // logger.warning("^^^ finished iteration");
        request.setAttribute("eventLogs", eventLogs);
        forwardPage(Page.VIEW_STUDY_SUBJECT);
    }
}

Example 28 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class CreateDiscrepancyNoteServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    List<DiscrepancyNoteType> types = DiscrepancyNoteType.list;
    request.setAttribute(DIS_TYPES, types);
    request.setAttribute(RES_STATUSES, ResolutionStatus.list);
    // this should be set based on a new property of DisplayItemBean
    boolean writeToDB = fp.getBoolean(WRITE_TO_DB, true);
    boolean isReasonForChange = fp.getBoolean(IS_REASON_FOR_CHANGE);
    int entityId = fp.getInt(ENTITY_ID);
    // subjectId has to be added to the database when disc notes area saved
    // as entity_type 'subject'
    int subjectId = fp.getInt(SUBJECT_ID);
    int itemId = fp.getInt(ITEM_ID);
    String entityType = fp.getString(ENTITY_TYPE);
    String field = fp.getString(ENTITY_FIELD);
    String column = fp.getString(ENTITY_COLUMN);
    int parentId = fp.getInt(PARENT_ID);
    // patch for repeating groups and RFC on empty fields
    int isGroup = fp.getInt(IS_GROUP_ITEM);
    // request.setAttribute(IS_GROUP_ITEM, new Integer(isGroup));
    int eventCRFId = fp.getInt(EVENT_CRF_ID);
    request.setAttribute(EVENT_CRF_ID, new Integer(eventCRFId));
    int rowCount = fp.getInt(PARENT_ROW_COUNT);
    // run only once: try to recalculate writeToDB
    if (!StringUtils.isBlank(entityType) && "itemData".equalsIgnoreCase(entityType) && isGroup != 0 && eventCRFId != 0) {
        // request.setAttribute(PARENT_ROW_COUNT, new Integer(eventCRFId));
        int ordinal_for_repeating_group_field = calculateOrdinal(isGroup, field, eventCRFId, rowCount);
        int writeToDBStatus = isWriteToDB(isGroup, field, entityId, itemId, ordinal_for_repeating_group_field, eventCRFId);
        writeToDB = (writeToDBStatus == -1) ? false : ((writeToDBStatus == 1) ? true : writeToDB);
    }
    boolean isInError = fp.getBoolean(ERROR_FLAG);
    boolean isNew = fp.getBoolean(NEW_NOTE);
    request.setAttribute(NEW_NOTE, isNew ? "1" : "0");
    String strResStatus = fp.getString(PRESET_RES_STATUS);
    if (!strResStatus.equals("")) {
        request.setAttribute(PRESET_RES_STATUS, strResStatus);
    }
    String monitor = fp.getString("monitor");
    String enterData = fp.getString("enterData");
    request.setAttribute("enterData", enterData);
    boolean enteringData = false;
    if (enterData != null && "1".equalsIgnoreCase(enterData)) {
        // variables are not set in JSP, so not from viewing data and from
        // entering data
        request.setAttribute(CAN_MONITOR, "1");
        request.setAttribute("monitor", monitor);
        enteringData = true;
    } else if ("1".equalsIgnoreCase(monitor)) {
        // change to allow user to
        // enter note for all items,
        // not just blank items
        request.setAttribute(CAN_MONITOR, "1");
        request.setAttribute("monitor", monitor);
    } else {
        request.setAttribute(CAN_MONITOR, "0");
    }
    if ("itemData".equalsIgnoreCase(entityType) && enteringData) {
        request.setAttribute("enterItemData", "yes");
    }
    DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
    int preUserId = 0;
    if (!StringUtils.isBlank(entityType)) {
        if ("itemData".equalsIgnoreCase(entityType) || "itemdata".equalsIgnoreCase(entityType)) {
            ItemBean item = (ItemBean) new ItemDAO(sm.getDataSource()).findByPK(itemId);
            ItemDataBean itemData = (ItemDataBean) new ItemDataDAO(sm.getDataSource()).findByPK(entityId);
            request.setAttribute("entityValue", itemData.getValue());
            request.setAttribute("entityName", item.getName());
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
            preUserId = ec.getOwnerId();
        } else if ("studySub".equalsIgnoreCase(entityType)) {
            StudySubjectBean ssub = (StudySubjectBean) new StudySubjectDAO(sm.getDataSource()).findByPK(entityId);
            SubjectBean sub = (SubjectBean) new SubjectDAO(sm.getDataSource()).findByPK(ssub.getSubjectId());
            preUserId = ssub.getOwnerId();
            if (!StringUtils.isBlank(column)) {
                if ("enrollment_date".equalsIgnoreCase(column)) {
                    if (ssub.getEnrollmentDate() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(ssub.getEnrollmentDate()));
                    } else {
                        request.setAttribute("entityValue", resword.getString("N/A"));
                    }
                    request.setAttribute("entityName", resword.getString("enrollment_date"));
                } else if ("gender".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", sub.getGender() + "");
                    request.setAttribute("entityName", resword.getString("gender"));
                } else if ("date_of_birth".equalsIgnoreCase(column)) {
                    if (sub.getDateOfBirth() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
                    } else {
                        request.setAttribute("entityValue", resword.getString("N/A"));
                    }
                    request.setAttribute("entityName", resword.getString("date_of_birth"));
                } else if ("unique_identifier".equalsIgnoreCase(column)) {
                    if (sub.getUniqueIdentifier() != null) {
                        request.setAttribute("entityValue", sub.getUniqueIdentifier());
                    }
                    request.setAttribute("entityName", resword.getString("unique_identifier"));
                }
            }
        } else if ("subject".equalsIgnoreCase(entityType)) {
            SubjectBean sub = (SubjectBean) new SubjectDAO(sm.getDataSource()).findByPK(entityId);
            preUserId = sub.getOwnerId();
            if (!StringUtils.isBlank(column)) {
                if ("gender".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", sub.getGender() + "");
                    request.setAttribute("entityName", resword.getString("gender"));
                } else if ("date_of_birth".equalsIgnoreCase(column)) {
                    if (sub.getDateOfBirth() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
                    }
                    request.setAttribute("entityName", resword.getString("date_of_birth"));
                } else if ("unique_identifier".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", sub.getUniqueIdentifier());
                    request.setAttribute("entityName", resword.getString("unique_identifier"));
                }
            }
        } else if ("studyEvent".equalsIgnoreCase(entityType)) {
            StudyEventBean se = (StudyEventBean) new StudyEventDAO(sm.getDataSource()).findByPK(entityId);
            preUserId = se.getOwnerId();
            if (!StringUtils.isBlank(column)) {
                if ("location".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", se.getLocation().equals("") || se.getLocation() == null ? resword.getString("N/A") : se.getLocation());
                    request.setAttribute("entityName", resword.getString("location"));
                } else if ("start_date".equalsIgnoreCase(column)) {
                    if (se.getDateStarted() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(se.getDateStarted()));
                    } else {
                        request.setAttribute("entityValue", resword.getString("N/A"));
                    }
                    request.setAttribute("entityName", resword.getString("start_date"));
                } else if ("end_date".equalsIgnoreCase(column)) {
                    if (se.getDateEnded() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(se.getDateEnded()));
                    } else {
                        request.setAttribute("entityValue", resword.getString("N/A"));
                    }
                    request.setAttribute("entityName", resword.getString("end_date"));
                }
            }
        } else if ("eventCrf".equalsIgnoreCase(entityType)) {
            EventCRFBean ec = (EventCRFBean) new EventCRFDAO(sm.getDataSource()).findByPK(entityId);
            preUserId = ec.getOwnerId();
            if (!StringUtils.isBlank(column)) {
                if ("date_interviewed".equals(column)) {
                    if (ec.getDateInterviewed() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(ec.getDateInterviewed()));
                    } else {
                        request.setAttribute("entityValue", resword.getString("N/A"));
                    }
                    request.setAttribute("entityName", resword.getString("date_interviewed"));
                } else if ("interviewer_name".equals(column)) {
                    request.setAttribute("entityValue", ec.getInterviewerName());
                    request.setAttribute("entityName", resword.getString("interviewer_name"));
                }
            }
        }
    }
    // finds all the related notes
    ArrayList notes = (ArrayList) dndao.findAllByEntityAndColumn(entityType, entityId, column);
    DiscrepancyNoteBean parent = new DiscrepancyNoteBean();
    if (parentId > 0) {
        dndao.setFetchMapping(true);
        parent = (DiscrepancyNoteBean) dndao.findByPK(parentId);
        if (parent.isActive()) {
            request.setAttribute("parent", parent);
        }
        dndao.setFetchMapping(false);
    }
    FormDiscrepancyNotes newNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
    if (newNotes == null) {
        newNotes = new FormDiscrepancyNotes();
    }
    boolean isNotesExistInSession = (!newNotes.getNotes(field).isEmpty()) ? true : (!newNotes.getNotes(eventCRFId + "_" + field).isEmpty()) ? true : false;
    if (!notes.isEmpty() || isNotesExistInSession) {
        request.setAttribute("hasNotes", "yes");
    } else {
        request.setAttribute("hasNotes", "no");
        logger.debug("has notes:" + "no");
    }
    // only for adding a new thread
    if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
        ArrayList<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>();
        resStatuses.add(ResolutionStatus.OPEN);
        resStatuses.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES, resStatuses);
        List<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>(DiscrepancyNoteType.list);
        types2.remove(DiscrepancyNoteType.QUERY);
        request.setAttribute(DIS_TYPES, types2);
        request.setAttribute(WHICH_RES_STATUSES, "22");
    } else if (currentRole.getRole().equals(Role.MONITOR)) {
        ArrayList<ResolutionStatus> resStatuses = new ArrayList();
        resStatuses.add(ResolutionStatus.OPEN);
        resStatuses.add(ResolutionStatus.UPDATED);
        resStatuses.add(ResolutionStatus.CLOSED);
        request.setAttribute(RES_STATUSES, resStatuses);
        request.setAttribute(WHICH_RES_STATUSES, "1");
        ArrayList<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>();
        types2.add(DiscrepancyNoteType.QUERY);
        request.setAttribute(DIS_TYPES, types2);
    } else {
        // Role.STUDYDIRECTOR Role.COORDINATOR
        List<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>(ResolutionStatus.list);
        resStatuses.remove(ResolutionStatus.NOT_APPLICABLE);
        request.setAttribute(RES_STATUSES, resStatuses);
        ;
        request.setAttribute(WHICH_RES_STATUSES, "2");
    }
    if (!fp.isSubmitted()) {
        DiscrepancyNoteBean dnb = new DiscrepancyNoteBean();
        if (subjectId > 0) {
            // BWP: this doesn't seem correct, because the SubjectId should
            // be the id for
            // the SubjectBean, different from StudySubjectBean
            StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
            StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(subjectId);
            dnb.setSubjectName(ssub.getName());
            dnb.setSubjectId(ssub.getId());
            dnb.setStudySub(ssub);
            StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
            int parentStudyForSubject = 0;
            StudyBean studyBeanSub = (StudyBean) studyDAO.findByPK(ssub.getStudyId());
            if (null != studyBeanSub) {
                parentStudyForSubject = studyBeanSub.getParentStudyId();
            }
            if (ssub.getStudyId() != currentStudy.getId() && currentStudy.getId() != parentStudyForSubject) {
                addPageMessage(noAccessMessage);
                throw new InsufficientPermissionException(Page.MENU_SERVLET, exceptionName, "1");
            }
        }
        if (itemId > 0) {
            ItemBean item = (ItemBean) new ItemDAO(sm.getDataSource()).findByPK(itemId);
            dnb.setEntityName(item.getName());
            request.setAttribute("item", item);
        }
        dnb.setEntityType(entityType);
        dnb.setColumn(column);
        dnb.setEntityId(entityId);
        dnb.setField(field);
        dnb.setParentDnId(parent.getId());
        dnb.setCreatedDate(new Date());
        if (parent.getId() == 0 || isNew) {
            // no parent, new note thread
            if (enteringData) {
                if (isInError) {
                    dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
                } else {
                    dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.ANNOTATION.getId());
                    dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
                // >> tbh WHO bug: set an assigned user for the parent
                // note
                // dnb.setAssignedUser(ub);
                // dnb.setAssignedUserId(ub.getId());
                // << tbh 08/2009
                }
                if (isReasonForChange) {
                    dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.REASON_FOR_CHANGE.getId());
                    dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
                }
                // << tbh 02/2010, trumps failed evaluation error checks
                // can we put this in admin editing
                request.setAttribute("autoView", "0");
            // above set to automatically open up the user panel
            } else {
                // when the user is a CRC and is adding a note to the thread
                // it should default to Resolution Proposed,
                // and the assigned should be the user who logged the query,
                // NOT the one who is proposing the solution, tbh 02/2009
                // if (currentRole.getRole().equals(Role.COORDINATOR)) {
                // dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.
                // REASON_FOR_CHANGE.getId());
                // request.setAttribute("autoView", "1");
                // // above set to automatically open up the user panel
                // } else {
                dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.QUERY.getId());
                // if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) && currentStudy.getId() != currentStudy.getParentStudyId()
                if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
                    request.setAttribute("autoView", "0");
                } else {
                    request.setAttribute("autoView", "1");
                    dnb.setAssignedUserId(preUserId);
                }
            // above set to automatically open up the user panel
            // }
            }
        } else if (parent.getDiscrepancyNoteTypeId() > 0) {
            dnb.setDiscrepancyNoteTypeId(parent.getDiscrepancyNoteTypeId());
            // adding second rule here, tbh 08/2009
            if ((currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2)) && currentStudy.getId() != currentStudy.getParentStudyId()) {
                dnb.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
                request.setAttribute("autoView", "0");
            // hide the panel, tbh
            } else {
                dnb.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
            }
        }
        dnb.setOwnerId(parent.getOwnerId());
        String detailedDes = fp.getString("strErrMsg");
        if (detailedDes != null) {
            dnb.setDetailedNotes(detailedDes);
            logger.debug("found strErrMsg: " + fp.getString("strErrMsg"));
        }
        // #4346 TBH 10/2009
        // If the data entry form has not been saved yet, collecting info from parent page.
        // populate note infos
        dnb = getNoteInfo(dnb);
        if (dnb.getEventName() == null || dnb.getEventName().equals("")) {
            if (!fp.getString("eventName").equals("")) {
                dnb.setEventName(fp.getString("eventName"));
            } else {
                dnb.setEventName(getStudyEventDefinition(eventCRFId).getName());
            }
        }
        if (dnb.getEventStart() == null) {
            if (fp.getDate("eventDate") != null) {
                dnb.setEventStart(fp.getDate("eventDate"));
            } else {
                dnb.setEventStart(getStudyEvent(eventCRFId).getDateStarted());
            }
        }
        if (dnb.getCrfName() == null || dnb.getCrfName().equals("")) {
            if (!fp.getString("crfName").equals("")) {
                dnb.setCrfName(fp.getString("crfName"));
            } else {
                dnb.setCrfName(getCrf(eventCRFId).getName());
            }
        }
        // // #4346 TBH 10/2009
        request.setAttribute(DIS_NOTE, dnb);
        request.setAttribute("unlock", "0");
        // this should go from UI & here
        request.setAttribute(WRITE_TO_DB, writeToDB ? "1" : "0");
        ArrayList userAccounts = this.generateUserAccounts(ub.getActiveStudyId(), subjectId);
        request.setAttribute(USER_ACCOUNTS, userAccounts);
        // ideally should be only two cases
        if ((currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2)) && currentStudy.getId() != currentStudy.getParentStudyId()) {
            // assigning back to OP, tbh
            request.setAttribute(USER_ACCOUNT_ID, Integer.valueOf(parent.getOwnerId()).toString());
            logger.debug("assigned owner id: " + parent.getOwnerId());
        } else if (dnb.getEventCRFId() > 0) {
            logger.debug("found a event crf id: " + dnb.getEventCRFId());
            EventCRFDAO eventCrfDAO = new EventCRFDAO(sm.getDataSource());
            EventCRFBean eventCrfBean = new EventCRFBean();
            eventCrfBean = (EventCRFBean) eventCrfDAO.findByPK(dnb.getEventCRFId());
            request.setAttribute(USER_ACCOUNT_ID, Integer.valueOf(eventCrfBean.getOwnerId()).toString());
            logger.debug("assigned owner id: " + eventCrfBean.getOwnerId());
        } else {
        // the end case
        }
        // set the user account id for the user who completed data entry
        forwardPage(Page.ADD_DISCREPANCY_NOTE);
    } else {
        // Submit and Close the Discrepancy note
        FormDiscrepancyNotes noteTree = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
        FormDiscrepancyNotes noteTree_RFC_REPEAT = (FormDiscrepancyNotes) session.getAttribute(FLAG_DISCREPANCY_RFC);
        ;
        if (noteTree_RFC_REPEAT == null)
            noteTree_RFC_REPEAT = new FormDiscrepancyNotes();
        if (noteTree == null) {
            noteTree = new FormDiscrepancyNotes();
            logger.debug("No note tree initailized in session");
        }
        Validator v = new Validator(request);
        String description = fp.getString("description");
        int typeId = fp.getInt("typeId");
        int assignedUserAccountId = fp.getInt(SUBMITTED_USER_ACCOUNT_ID);
        int resStatusId = fp.getInt(RES_STATUS_ID);
        String detailedDes = fp.getString("detailedDes");
        int sectionId = fp.getInt("sectionId");
        DiscrepancyNoteBean note = new DiscrepancyNoteBean();
        v.addValidation("description", Validator.NO_BLANKS);
        v.addValidation("description", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255);
        v.addValidation("detailedDes", Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 1000);
        v.addValidation("typeId", Validator.NO_BLANKS);
        HashMap errors = v.validate();
        note.setDescription(description);
        note.setDetailedNotes(detailedDes);
        note.setOwner(ub);
        note.setOwnerId(ub.getId());
        note.setCreatedDate(new Date());
        note.setResolutionStatusId(resStatusId);
        note.setDiscrepancyNoteTypeId(typeId);
        note.setParentDnId(parent.getId());
        if (typeId != DiscrepancyNoteType.ANNOTATION.getId() && typeId != DiscrepancyNoteType.FAILEDVAL.getId() && typeId != DiscrepancyNoteType.REASON_FOR_CHANGE.getId()) {
            if (assignedUserAccountId > 0) {
                note.setAssignedUserId(assignedUserAccountId);
                logger.debug("^^^ found assigned user id: " + assignedUserAccountId);
            } else {
                // a little bit of a workaround, should ideally be always from
                // the form
                note.setAssignedUserId(parent.getOwnerId());
                logger.debug("found user assigned id, in the PARENT OWNER ID: " + parent.getOwnerId() + " note that user assgined id did not work: " + assignedUserAccountId);
            }
        }
        note.setField(field);
        if (DiscrepancyNoteType.ANNOTATION.getId() == note.getDiscrepancyNoteTypeId()) {
            updateStudyEvent(entityType, entityId);
            updateStudySubjectStatus(entityType, entityId);
        }
        if (DiscrepancyNoteType.ANNOTATION.getId() == note.getDiscrepancyNoteTypeId() || DiscrepancyNoteType.REASON_FOR_CHANGE.getId() == note.getDiscrepancyNoteTypeId()) {
            note.setResStatus(ResolutionStatus.NOT_APPLICABLE);
            note.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
        }
        if (DiscrepancyNoteType.FAILEDVAL.getId() == note.getDiscrepancyNoteTypeId() || DiscrepancyNoteType.QUERY.getId() == note.getDiscrepancyNoteTypeId()) {
            if (ResolutionStatus.NOT_APPLICABLE.getId() == note.getResolutionStatusId()) {
                Validator.addError(errors, RES_STATUS_ID, restext.getString("not_valid_res_status"));
            }
        }
        if (!parent.isActive()) {
            note.setEntityId(entityId);
            note.setEntityType(entityType);
            note.setColumn(column);
        } else {
            note.setEntityId(parent.getEntityId());
            note.setEntityType(parent.getEntityType());
            if (!StringUtils.isBlank(parent.getColumn())) {
                note.setColumn(parent.getColumn());
            } else {
                note.setColumn(column);
            }
            note.setParentDnId(parent.getId());
        }
        note.setStudyId(currentStudy.getId());
        // populate note infos
        note = getNoteInfo(note);
        request.setAttribute(DIS_NOTE, note);
        // this should go from UI & here
        request.setAttribute(WRITE_TO_DB, writeToDB ? "1" : "0");
        ArrayList userAccounts = this.generateUserAccounts(ub.getActiveStudyId(), subjectId);
        request.setAttribute(USER_ACCOUNT_ID, Integer.valueOf(note.getAssignedUserId()).toString());
        // formality more than anything else, we should go to say the note
        // is done
        Role r = currentRole.getRole();
        if (r.equals(Role.MONITOR) || r.equals(Role.INVESTIGATOR) || r.equals(Role.RESEARCHASSISTANT) || r.equals(Role.RESEARCHASSISTANT2) || r.equals(Role.COORDINATOR)) {
            // investigator
            request.setAttribute("unlock", "1");
            logger.debug("set UNLOCK to ONE");
        } else {
            request.setAttribute("unlock", "0");
            logger.debug("set UNLOCK to ZERO");
        }
        request.setAttribute(USER_ACCOUNTS, userAccounts);
        if (errors.isEmpty()) {
            if (!writeToDB) {
                noteTree.addNote(field, note);
                noteTree.addIdNote(note.getEntityId(), field);
                noteTree_RFC_REPEAT.addNote(EVENT_CRF_ID + "_" + field, note);
                noteTree_RFC_REPEAT.addIdNote(note.getEntityId(), field);
                // -> catcher                //   FORM_DISCREPANCY_NOTES_NAME
                session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, noteTree);
                session.setAttribute(FLAG_DISCREPANCY_RFC, noteTree_RFC_REPEAT);
                // 
                /*Setting a marker to check later while saving administrative edited data. This is needed to make
                    * sure the system flags error while changing data for items which already has a DiscrepanyNote*/
                manageReasonForChangeState(session, eventCRFId + "_" + field);
                forwardPage(Page.ADD_DISCREPANCY_NOTE_DONE);
            } else {
                // if not creating a new thread(note), update exsiting notes
                // if necessary
                // if ("itemData".equalsIgnoreCase(entityType) && !isNew) {
                int pdnId = note != null ? note.getParentDnId() : 0;
                if (pdnId > 0) {
                    logger.debug("Create:find parent note for item data:" + note.getEntityId());
                    DiscrepancyNoteBean pNote = (DiscrepancyNoteBean) dndao.findByPK(pdnId);
                    logger.debug("setting DN owner id: " + pNote.getOwnerId());
                    note.setOwnerId(pNote.getOwnerId());
                    if (note.getDiscrepancyNoteTypeId() == pNote.getDiscrepancyNoteTypeId()) {
                        if (note.getResolutionStatusId() != pNote.getResolutionStatusId()) {
                            pNote.setResolutionStatusId(note.getResolutionStatusId());
                            dndao.update(pNote);
                        }
                        if (note.getAssignedUserId() != pNote.getAssignedUserId()) {
                            pNote.setAssignedUserId(note.getAssignedUserId());
                            if (pNote.getAssignedUserId() > 0) {
                                dndao.updateAssignedUser(pNote);
                            } else {
                                dndao.updateAssignedUserToNull(pNote);
                            }
                        }
                    }
                }
                note = (DiscrepancyNoteBean) dndao.create(note);
                note.setEntityId(entityId);
                dndao.createMapping(note);
                request.setAttribute(DIS_NOTE, note);
                if (note.getParentDnId() == 0) {
                    // see issue 2659 this is a new thread, we will create
                    // two notes in this case,
                    // This way one can be the parent that updates as the
                    // status changes, but one also stays as New.
                    note.setParentDnId(note.getId());
                    note = (DiscrepancyNoteBean) dndao.create(note);
                    dndao.createMapping(note);
                }
                /*Setting a marker to check later while saving administrative edited data. This is needed to make
                    * sure the system flags error while changing data for items which already has a DiscrepanyNote*/
                // session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, true);
                // session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, true);
                // String field_id_for_RFC_hash = buildDiscrepancyNoteIdForRFCHash(eventCRFId,entityId, isGroup, field, ordinal_for_repeating_group_field);
                String field_id_for_RFC_hash = eventCRFId + "_" + field;
                manageReasonForChangeState(session, field_id_for_RFC_hash);
                logger.debug("found resolution status: " + note.getResolutionStatusId());
                String email = fp.getString(EMAIL_USER_ACCOUNT);
                logger.debug("found email: " + email);
                if (note.getAssignedUserId() > 0 && "1".equals(email.trim()) && DiscrepancyNoteType.QUERY.getId() == note.getDiscrepancyNoteTypeId()) {
                    logger.debug("++++++ found our way here: " + note.getDiscrepancyNoteTypeId() + " id number and " + note.getDisType().getName());
                    // generate email for user here
                    StringBuffer message = new StringBuffer();
                    // generate message here
                    UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
                    ItemDAO itemDAO = new ItemDAO(sm.getDataSource());
                    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
                    ItemBean item = new ItemBean();
                    ItemDataBean itemData = new ItemDataBean();
                    SectionBean section = new SectionBean();
                    StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
                    UserAccountBean assignedUser = (UserAccountBean) userAccountDAO.findByPK(note.getAssignedUserId());
                    String alertEmail = assignedUser.getEmail();
                    message.append(MessageFormat.format(respage.getString("mailDNHeader"), assignedUser.getFirstName(), assignedUser.getLastName()));
                    message.append("<A HREF='" + SQLInitServlet.getField("sysURL.base") + "ViewNotes?module=submit&listNotes_f_discrepancyNoteBean.user=" + assignedUser.getName() + "&listNotes_f_entityName=" + note.getEntityName() + "'>" + SQLInitServlet.getField("sysURL.base") + "</A><BR/>");
                    message.append(respage.getString("you_received_this_from"));
                    StudyBean study = (StudyBean) studyDAO.findByPK(note.getStudyId());
                    SectionDAO sectionDAO = new SectionDAO(sm.getDataSource());
                    if ("itemData".equalsIgnoreCase(entityType)) {
                        itemData = (ItemDataBean) iddao.findByPK(note.getEntityId());
                        item = (ItemBean) itemDAO.findByPK(itemData.getItemId());
                        if (sectionId > 0) {
                            section = (SectionBean) sectionDAO.findByPK(sectionId);
                        } else {
                        // Todo section should be initialized when sectionId = 0
                        }
                    }
                    message.append(respage.getString("email_body_separator"));
                    message.append(respage.getString("disc_note_info"));
                    message.append(respage.getString("email_body_separator"));
                    message.append(MessageFormat.format(respage.getString("mailDNParameters1"), note.getDescription(), note.getDetailedNotes(), ub.getName()));
                    message.append(respage.getString("email_body_separator"));
                    message.append(respage.getString("entity_information"));
                    message.append(respage.getString("email_body_separator"));
                    message.append(MessageFormat.format(respage.getString("mailDNParameters2"), study.getName(), note.getSubjectName()));
                    if (!("studySub".equalsIgnoreCase(entityType) || "subject".equalsIgnoreCase(entityType))) {
                        message.append(MessageFormat.format(respage.getString("mailDNParameters3"), note.getEventName()));
                        if (!"studyEvent".equalsIgnoreCase(note.getEntityType())) {
                            message.append(MessageFormat.format(respage.getString("mailDNParameters4"), note.getCrfName()));
                            if (!"eventCrf".equalsIgnoreCase(note.getEntityType())) {
                                if (sectionId > 0) {
                                    message.append(MessageFormat.format(respage.getString("mailDNParameters5"), section.getName()));
                                }
                                message.append(MessageFormat.format(respage.getString("mailDNParameters6"), item.getName()));
                            }
                        }
                    }
                    message.append(respage.getString("email_body_separator"));
                    message.append(MessageFormat.format(respage.getString("mailDNThanks"), study.getName()));
                    message.append(respage.getString("email_body_separator"));
                    message.append(respage.getString("disclaimer"));
                    message.append(respage.getString("email_body_separator"));
                    message.append(respage.getString("email_footer"));
                    String emailBodyString = message.toString();
                    sendEmail(alertEmail.trim(), EmailEngine.getAdminEmail(), MessageFormat.format(respage.getString("mailDNSubject"), study.getName(), note.getEntityName()), emailBodyString, true, null, null, true);
                } else {
                    logger.debug("did not send email, but did save DN");
                }
                // addPageMessage(
                // "Your discrepancy note has been saved into database.");
                addPageMessage(respage.getString("note_saved_into_db"));
                addPageMessage(respage.getString("page_close_automatically"));
                forwardPage(Page.ADD_DISCREPANCY_NOTE_SAVE_DONE);
            }
        } else {
            if (parentId > 0) {
                if (note.getResolutionStatusId() == ResolutionStatus.NOT_APPLICABLE.getId()) {
                    request.setAttribute("autoView", "0");
                }
            } else {
                if (note.getDiscrepancyNoteTypeId() == DiscrepancyNoteType.QUERY.getId()) {
                    request.setAttribute("autoView", "1");
                } else {
                    request.setAttribute("autoView", "0");
                }
            }
            setInputMessages(errors);
            forwardPage(Page.ADD_DISCREPANCY_NOTE);
        }
    }
}

Example 29 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class ViewSectionDataEntryServlet method processRequest.

// BWP 01/08>>
@Override
public void processRequest(HttpServletRequest request, HttpServletResponse response) throws Exception {
    FormProcessor fp = new FormProcessor(request);
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN);
    boolean isSubmitted = false;
    EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN);
    if (!fp.getString("exitTo").equals("")) {
        request.setAttribute("exitTo", fp.getString("exitTo"));
    }
    int crfVersionId = fp.getInt("crfVersionId", true);
    int sectionId = fp.getInt("sectionId");
    int eventCRFId = fp.getInt(EVENT_CRF_ID, true);
    int studySubjectId = fp.getInt("studySubjectId", true);
    String action = fp.getString("action");
    HttpSession session = request.getSession();
    String fromResolvingNotes = fp.getString("fromResolvingNotes", true);
    if (StringUtil.isBlank(fromResolvingNotes)) {
        session.removeAttribute(ViewNotesServlet.WIN_LOCATION);
        session.removeAttribute(ViewNotesServlet.NOTES_TABLE);
    }
    // Added for
    request.setAttribute("studySubjectId", studySubjectId + "");
    // Mantis
    // Issue
    // 2268
    // Added
    request.setAttribute("crfListPage", fp.getString("crfListPage"));
    // for
    // Mantis
    // Issue
    // 2268
    // Added for
    request.setAttribute("eventId", fp.getString("eventId"));
    // Mantis
    // Issue
    // 2268
    // YW <<
    int sedId = fp.getInt("sedId");
    request.setAttribute("sedId", sedId + "");
    int crfId = fp.getInt("crfId");
    // BWP>> ... try to get crfId from crfVersionId
    if (crfId == 0 && crfVersionId > 0) {
        CRFVersionDAO crfVDao = new CRFVersionDAO(getDataSource());
        CRFVersionBean crvVBean = (CRFVersionBean) crfVDao.findByPK(crfVersionId);
        if (crvVBean != null) {
            crfId = crvVBean.getCrfId();
        }
    }
    // YW >>
    int eventDefinitionCRFId = fp.getInt("eventDefinitionCRFId");
    EventDefinitionCRFDAO eventCrfDao = new EventDefinitionCRFDAO(getDataSource());
    edcb = (EventDefinitionCRFBean) eventCrfDao.findByPK(eventDefinitionCRFId);
    if (eventCRFId == 0 && edcb.getStudyId() != currentStudy.getParentStudyId() && edcb.getStudyId() != currentStudy.getId()) {
        addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_study_contact_sysadmin"), request);
        throw new InsufficientPermissionException(Page.MENU_SERVLET, resexception.getString("not_director"), "1");
    }
    if (crfId == 0 && eventDefinitionCRFId > 0) {
        // eventCrfDao.findByPK(eventDefinitionCRFId);
        if (edcb != null) {
            crfId = edcb.getCrfId();
        }
    }
    request.setAttribute("crfId", crfId + "");
    request.setAttribute("eventDefinitionCRFId", eventDefinitionCRFId + "");
    String printVersion = fp.getString("print");
    // BWP>> this has to be removed for CRFs that do not display an
    // interviewdate
    // for a particular event
    session.removeAttribute("presetValues");
    EventCRFDAO ecdao = new EventCRFDAO(getDataSource());
    SectionDAO sdao = new SectionDAO(getDataSource());
    String age = "";
    if (sectionId == 0 && crfVersionId == 0 && eventCRFId == 0) {
        addPageMessage(respage.getString("please_choose_a_CRF_to_view"), request);
        // forwardPage(Page.SUBMIT_DATA_SERVLET);
        forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response);
        // >> changed tbh, 06/2009
        return;
    }
    if (studySubjectId > 0) {
        StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource());
        StudySubjectBean sub = (StudySubjectBean) ssdao.findByPK(studySubjectId);
        request.setAttribute("studySubject", sub);
    }
    if (eventCRFId > 0) {
        // for event crf, the input crfVersionId from url =0
        ecb = (EventCRFBean) ecdao.findByPK(eventCRFId);
        StudyEventDAO sedao = new StudyEventDAO(getDataSource());
        StudyEventBean event = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
        // event.getSubjectEventStatus().getName());
        if (event.getSubjectEventStatus().equals(SubjectEventStatus.LOCKED)) {
            request.setAttribute("isLocked", "yes");
        // System.out.println("this event crf is locked");
        } else {
            request.setAttribute("isLocked", "no");
        }
        if (studySubjectId <= 0) {
            studySubjectId = event.getStudySubjectId();
            request.setAttribute("studySubjectId", studySubjectId + "");
        }
        // Get the status/number of item discrepancy notes
        DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource());
        ArrayList<DiscrepancyNoteBean> allNotes = new ArrayList<DiscrepancyNoteBean>();
        List<DiscrepancyNoteBean> eventCrfNotes = new ArrayList<DiscrepancyNoteBean>();
        List<DiscrepancyNoteThread> noteThreads = new ArrayList<DiscrepancyNoteThread>();
        // if (eventCRFId > 0) {
        // this method finds only parent notes
        allNotes = dndao.findAllTopNotesByEventCRF(eventCRFId);
        // add interviewer.jsp related notes to this Collection
        eventCrfNotes = dndao.findOnlyParentEventCRFDNotesFromEventCRF(ecb);
        if (!eventCrfNotes.isEmpty()) {
            allNotes.addAll(eventCrfNotes);
            // make sure a necessary request attribute "hasNameNote" is set
            // properly
            this.setAttributeForInterviewerDNotes(eventCrfNotes, request);
        }
        // }
        // Create disc note threads out of the various notes
        DiscrepancyNoteUtil dNoteUtil = new DiscrepancyNoteUtil();
        noteThreads = dNoteUtil.createThreadsOfParents(allNotes, getDataSource(), currentStudy, null, -1, true);
        // variables that provide values for the CRF discrepancy note header
        int updatedNum = 0;
        int openNum = 0;
        int closedNum = 0;
        int resolvedNum = 0;
        int notAppNum = 0;
        DiscrepancyNoteBean tempBean;
        for (DiscrepancyNoteThread dnThread : noteThreads) {
            /*
                 * 3014: do not count parent beans, only the last child disc
                 * note of the thread.
                 */
            tempBean = dnThread.getLinkedNoteList().getLast();
            if (tempBean != null) {
                if (ResolutionStatus.UPDATED.equals(tempBean.getResStatus())) {
                    updatedNum++;
                } else if (ResolutionStatus.OPEN.equals(tempBean.getResStatus())) {
                    openNum++;
                } else if (ResolutionStatus.CLOSED.equals(tempBean.getResStatus())) {
                    // if (dn.getParentDnId() > 0){
                    closedNum++;
                // }
                } else if (ResolutionStatus.RESOLVED.equals(tempBean.getResStatus())) {
                    // if (dn.getParentDnId() > 0){
                    resolvedNum++;
                // }
                } else if (ResolutionStatus.NOT_APPLICABLE.equals(tempBean.getResStatus())) {
                    notAppNum++;
                }
            }
        }
        request.setAttribute("updatedNum", updatedNum + "");
        request.setAttribute("openNum", openNum + "");
        request.setAttribute("closedNum", closedNum + "");
        request.setAttribute("resolvedNum", resolvedNum + "");
        request.setAttribute("notAppNum", notAppNum + "");
        DisplayTableOfContentsBean displayBean = TableOfContentsServlet.getDisplayBean(ecb, getDataSource(), currentStudy);
        // Make sure that the interviewDate in the eventCRF is properly
        // formatted
        // for viewSectionDataEntry.jsp --> interviewer.jsp
        // int studyEventId = (Integer)request.getAttribute("studyEvent");
        // SimpleDateFormat formatter = new SimpleDateFormat("MM/dd/yyyy");
        // 
        Date tmpDate = displayBean.getEventCRF().getDateInterviewed();
        String formattedInterviewerDate;
        try {
            DateFormat local_df = new SimpleDateFormat(resformat.getString("date_format_string"), ResourceBundleProvider.getLocale());
            formattedInterviewerDate = local_df.format(tmpDate);
        } catch (Exception e) {
            formattedInterviewerDate = "";
        }
        HashMap presetVals = (HashMap) session.getAttribute("presetValues");
        if (presetVals == null) {
            presetVals = new HashMap();
            session.setAttribute("presetValues", presetVals);
        }
        presetVals.put("interviewDate", formattedInterviewerDate);
        request.setAttribute("toc", displayBean);
        ArrayList sections = displayBean.getSections();
        request.setAttribute("sectionNum", sections.size() + "");
        if (!sections.isEmpty()) {
            if (sectionId == 0) {
                SectionBean firstSec = (SectionBean) sections.get(0);
                sectionId = firstSec.getId();
            }
        } else {
            addPageMessage(respage.getString("there_are_no_sections_ins_this_CRF"), request);
            // forwardPage(Page.SUBMIT_DATA_SERVLET);
            forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response);
            // >> changed tbh, 06/2009
            return;
        }
    } else if (crfVersionId > 0) {
        // for viewing blank CRF
        DisplayTableOfContentsBean displayBean = ViewTableOfContentServlet.getDisplayBean(getDataSource(), crfVersionId);
        request.setAttribute("toc", displayBean);
        ArrayList sections = displayBean.getSections();
        request.setAttribute("sectionNum", sections.size() + "");
        if (!sections.isEmpty()) {
            if (sectionId == 0) {
                SectionBean firstSec = (SectionBean) sections.get(0);
                sectionId = firstSec.getId();
            }
        } else {
            addPageMessage(respage.getString("there_are_no_sections_ins_this_CRF_version"), request);
            if (eventCRFId == 0) {
                forwardPage(Page.CRF_LIST_SERVLET, request, response);
            } else {
                // forwardPage(Page.SUBMIT_DATA_SERVLET);
                forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response);
            // >> changed tbh, 06/2009
            }
            return;
        }
    }
    sb = (SectionBean) sdao.findByPK(sectionId);
    if (eventCRFId == 0) {
        ecb = new EventCRFBean();
        ecb.setCRFVersionId(sb.getCRFVersionId());
        if (currentStudy.getParentStudyId() > 0) {
            // this is a site,find parent
            StudyDAO studydao = new StudyDAO(getDataSource());
            StudyBean parentStudy = (StudyBean) studydao.findByPK(currentStudy.getParentStudyId());
            request.setAttribute("studyTitle", parentStudy.getName());
            request.setAttribute("siteTitle", currentStudy.getName());
        } else {
            request.setAttribute("studyTitle", currentStudy.getName());
        }
    } else {
        ecb = (EventCRFBean) ecdao.findByPK(eventCRFId);
        request.setAttribute(INPUT_EVENT_CRF, ecb);
        request.setAttribute(SECTION_BEAN, sb);
        // This is the StudySubjectBean
        StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource());
        StudySubjectBean sub = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
        // This is the SubjectBean
        SubjectDAO subjectDao = new SubjectDAO(getDataSource());
        int subjectId = sub.getSubjectId();
        int studyId = sub.getStudyId();
        SubjectBean subject = (SubjectBean) subjectDao.findByPK(subjectId);
        // Let us process the age
        if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
            StudyEventDAO sedao = new StudyEventDAO(getDataSource());
            StudyEventBean se = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(getDataSource());
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            se.setStudyEventDefinition(sed);
            request.setAttribute("studyEvent", se);
            // YW 11-16-2007 enrollment-date is used for computing age
            age = Utils.getInstacne().processAge(sub.getEnrollmentDate(), subject.getDateOfBirth());
        }
        // Get the study then the parent study
        StudyDAO studydao = new StudyDAO(getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studyId);
        if (study.getParentStudyId() > 0) {
            // this is a site,find parent
            StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
            request.setAttribute("studyTitle", parentStudy.getName());
            request.setAttribute("siteTitle", study.getName());
        } else {
            request.setAttribute("studyTitle", study.getName());
        }
        request.setAttribute("studySubject", sub);
        request.setAttribute("subject", subject);
        request.setAttribute("age", age);
    }
    // FormBeanUtil formUtil = new FormBeanUtil();
    // DisplaySectionBean newDisplayBean = new DisplaySectionBean();
    boolean hasItemGroup = false;
    // we will look into db to see if any repeating items for this CRF
    // section
    ItemGroupDAO igdao = new ItemGroupDAO(getDataSource());
    List<ItemGroupBean> itemGroups = igdao.findLegitGroupBySectionId(sectionId);
    if (!itemGroups.isEmpty()) {
        hasItemGroup = true;
    }
    // if the List of DisplayFormGroups is empty, then the servlet defers to
    // the prior method
    // of generating a DisplaySectionBean for the application
    DisplaySectionBean dsb;
    // want to get displayBean with grouped and ungrouped items
    request.setAttribute(EVENT_DEF_CRF_BEAN, edcb);
    request.setAttribute(INPUT_EVENT_CRF, ecb);
    request.setAttribute(SECTION_BEAN, sb);
    dsb = super.getDisplayBean(hasItemGroup, false, request, isSubmitted);
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(getDataSource());
    StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(getDataSource());
    StudyEventDAO studyEventDAO = new StudyEventDAO(getDataSource());
    StudyEventDefinitionBean studyEventDefinition = (StudyEventDefinitionBean) studyEventDefinitionDAO.findByPK(edcb.getStudyEventDefinitionId());
    StudyEventBean studyEvent = (StudyEventBean) studyEventDAO.findByPK(ecb.getStudyEventId());
    VariableSubstitutionHelper.replaceVariables(dsb, currentStudy, (StudySubjectBean) studySubjectDAO.findByPK(studySubjectId), studyEventDefinition, studyEvent, getDataSource());
    FormDiscrepancyNotes discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
    if (discNotes == null) {
        discNotes = new FormDiscrepancyNotes();
        session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
    }
    /*
         * if (hasItemGroup) { //
         * dsb.setDisplayItemGroups(newDisplayBean.getDisplayItemGroups());
         * request.setAttribute("new_table", true); }
         */
    // If the Horizontal type table will be used, then set the
    // DisplaySectionBean's
    // DisplayFormGroups List to the ones we have just generated
    // @pgawade 30-May-2012 Fix for issue 13963 - added an extra parameter
    // 'isSubmitted' to method createItemWithGroups
    List<DisplayItemWithGroupBean> displayItemWithGroups = super.createItemWithGroups(dsb, hasItemGroup, eventDefinitionCRFId, request, isSubmitted);
    dsb.setDisplayItemGroups(displayItemWithGroups);
    super.populateNotesWithDBNoteCounts(discNotes, dsb, request);
    if (fp.getString("fromViewNotes") != null && "1".equals(fp.getString("fromViewNotes"))) {
        request.setAttribute("fromViewNotes", fp.getString("fromViewNotes"));
    } else {
        session.removeAttribute("viewNotesURL");
    }
    if ("saveNotes".equalsIgnoreCase(action)) {
        LOGGER.info("33333how many group rows:" + dsb.getDisplayItemGroups().size());
        // let's save notes for the blank items
        DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource());
        discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
        for (int i = 0; i < dsb.getDisplayItemGroups().size(); i++) {
            DisplayItemWithGroupBean diwb = dsb.getDisplayItemGroups().get(i);
            if (diwb.isInGroup()) {
                List<DisplayItemGroupBean> dgbs = diwb.getItemGroups();
                LOGGER.info("dgbs size: " + dgbs.size());
                for (int j = 0; j < dgbs.size(); j++) {
                    DisplayItemGroupBean displayGroup = dgbs.get(j);
                    List<DisplayItemBean> items = displayGroup.getItems();
                    LOGGER.info("item size: " + items.size());
                    for (DisplayItemBean displayItem : items) {
                        String inputName = getGroupItemInputName(displayGroup, j, displayItem);
                        LOGGER.info("inputName:" + inputName);
                        LOGGER.info("item data id:" + displayItem.getData().getId());
                        AddNewSubjectServlet.saveFieldNotes(inputName, discNotes, dndao, displayItem.getData().getId(), "itemData", currentStudy);
                    }
                }
            } else {
                DisplayItemBean dib = diwb.getSingleItem();
                // TODO work on this line
                String inputName = getInputName(dib);
                AddNewSubjectServlet.saveFieldNotes(inputName, discNotes, dndao, dib.getData().getId(), DiscrepancyNoteBean.ITEM_DATA, currentStudy);
                ArrayList childItems = dib.getChildren();
                for (int j = 0; j < childItems.size(); j++) {
                    DisplayItemBean child = (DisplayItemBean) childItems.get(j);
                    inputName = getInputName(child);
                    AddNewSubjectServlet.saveFieldNotes(inputName, discNotes, dndao, dib.getData().getId(), DiscrepancyNoteBean.ITEM_DATA, currentStudy);
                }
            }
        }
        addPageMessage("Discrepancy notes are saved successfully.", request);
        request.setAttribute("id", studySubjectId + "");
        forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET, request, response);
        // "ViewStudySubject?id=" + studySubjectId));
        return;
    } else {
        request.setAttribute(BEAN_DISPLAY, dsb);
        request.setAttribute(BEAN_ANNOTATIONS, ecb.getAnnotations());
        request.setAttribute("sec", sb);
        request.setAttribute("EventCRFBean", ecb);
        int tabNum = 1;
        if ("".equalsIgnoreCase(fp.getString("tabId"))) {
            tabNum = 1;
        } else {
            tabNum = fp.getInt("tabId");
        }
        request.setAttribute("tabId", new Integer(tabNum).toString());
        // 2808: Signal interviewer.jsp that the containing page is
        // viewSectionData,
        // for the purpose of suppressing discrepancy note icons for the
        // interview date and name fields
        request.setAttribute(ENCLOSING_PAGE, "viewSectionData");
        if ("yes".equalsIgnoreCase(printVersion)) {
            forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PRINT, request, response);
        } else {
            forwardPage(Page.VIEW_SECTION_DATA_ENTRY, request, response);
        }
    }
}

Example 30 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class ViewSectionDataEntryPreview method setupStudyBean.

private void setupStudyBean(HttpServletRequest request) {
    String age = "";
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource());
    StudySubjectBean sub = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
    // This is the SubjectBean
    SubjectDAO subjectDao = new SubjectDAO(getDataSource());
    int subjectId = sub.getSubjectId();
    int studyId = sub.getStudyId();
    SubjectBean subject = (SubjectBean) subjectDao.findByPK(subjectId);
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    // Let us process the age
    if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
        StudyEventDAO sedao = new StudyEventDAO(getDataSource());
        StudyEventBean se = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(getDataSource());
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
        se.setStudyEventDefinition(sed);
        request.setAttribute("studyEvent", se);
        // YW 11-16-2007 enrollment-date is used for calculating age
        age = Utils.getInstacne().processAge(sub.getEnrollmentDate(), subject.getDateOfBirth());
    }
    // Get the study then the parent study
    StudyDAO studydao = new StudyDAO(getDataSource());
    StudyBean study = (StudyBean) studydao.findByPK(studyId);
    if (study.getParentStudyId() > 0) {
        // this is a site,find parent
        StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
        request.setAttribute("studyTitle", parentStudy.getName() + " - " + study.getName());
    } else {
        request.setAttribute("studyTitle", study.getName());
    }
    request.setAttribute("studySubject", sub);
    request.setAttribute("subject", subject);
    request.setAttribute("age", age);
}