Examples with StudySubjectBean org.akaza.openclinica.bean.managestudy.StudySubjectBean used on opensource projects

Example 61 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class ListDiscNotesForCRFTableFactory method setDataAndLimitVariables.

@SuppressWarnings("unchecked")
@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    Limit limit = tableFacade.getLimit();
    ListDiscNotesForCRFFilter listDiscNotesForCRF = getListEventsForSubjectFilter(limit);
    listDiscNotesForCRF.addFilter("dn.discrepancy_note_type_id", this.discNoteType);
    StringBuffer constraints = new StringBuffer();
    if (this.discNoteType > 0 && this.discNoteType < 10) {
        constraints.append(" and dn.discrepancy_note_type_id=" + this.discNoteType);
    }
    if (this.resolutionStatusIds != null && this.resolutionStatusIds.size() > 0) {
        String s = " and (";
        for (Integer resolutionStatusId : this.resolutionStatusIds) {
            s += "dn.resolution_status_id = " + resolutionStatusId + " or ";
        }
        s = s.substring(0, s.length() - 3) + " )";
        listDiscNotesForCRF.addFilter("dn.resolution_status_id", s);
        constraints.append(s);
    }
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDAO().getCountWithFilter(listDiscNotesForCRF, getStudyBean());
        tableFacade.setTotalRows(totalRows);
    }
    ListDiscNotesForCRFSort eventsForSubjectSort = getListEventsForSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDAO().getWithFilterAndSort(getStudyBean(), listDiscNotesForCRF, eventsForSubjectSort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    boolean hasDN = false;
    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());
        SubjectBean subjectBean = (SubjectBean) getSubjectDAO().findByPK(studySubjectBean.getSubjectId());
        theItem.put("subject", subjectBean);
        theItem.put("subject.charGender", subjectBean.getGender());
        // Get EventCrfs for study Subject
        List<EventCRFBean> eventCrfs = getEventCRFDAO().findAllByStudySubject(studySubjectBean.getId());
        HashMap<String, EventCRFBean> crfAsKeyEventCrfAsValue = new HashMap<String, EventCRFBean>();
        for (EventCRFBean eventCRFBean : eventCrfs) {
            CRFBean crf = getCrfDAO().findByVersionId(eventCRFBean.getCRFVersionId());
            crfAsKeyEventCrfAsValue.put(crf.getId() + "_" + eventCRFBean.getStudyEventId(), eventCRFBean);
        }
        // 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("event.startDate", null);
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                HashMap<ResolutionStatus, Integer> discCounts = new HashMap<ResolutionStatus, Integer>();
                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() + "_discCounts", discCounts);
                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("event.startDate", studyEventBean.getCreatedDate());
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                EventCRFBean eventCRFBean = crfAsKeyEventCrfAsValue.get(crf.getId() + "_" + studyEventBean.getId());
                HashMap<ResolutionStatus, Integer> discCounts = new HashMap<ResolutionStatus, Integer>();
                if (eventCRFBean != null) {
                    d.getProps().put("crf_" + crf.getId(), eventCRFBean.getStage());
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", eventCRFBean);
                    // List<DiscrepancyNoteBean> discs =
                    // getDiscrepancyNoteDAO().findAllByStudyEvent(studyEventBean);
                    List<DiscrepancyNoteBean> discs = getDiscrepancyNoteDAO().findAllParentItemNotesByEventCRFWithConstraints(eventCRFBean.getId(), constraints);
                    hasDN = hasDN == false ? discs != null && discs.size() > 0 : hasDN;
                    for (DiscrepancyNoteBean discrepancyNoteBean : discs) {
                        Integer value = discCounts.get(discrepancyNoteBean.getResStatus());
                        if (value != null) {
                            discCounts.put(discrepancyNoteBean.getResStatus(), ++value);
                        } else {
                            discCounts.put(discrepancyNoteBean.getResStatus(), 1);
                        }
                    }
                    d.getProps().put("crf_" + crf.getId() + "_discCounts", discCounts);
                } else {
                    d.getProps().put("crf_" + crf.getId(), DataEntryStage.UNCOMPLETED);
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", null);
                    d.getProps().put("crf_" + crf.getId() + "_discCounts", discCounts);
                }
                d.getProps().put("crf_" + crf.getId() + "_crf", crf);
                d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", eventDefinitionCrfs.get(i));
                theItem.put("crf_" + crf.getId(), "");
            }
            events.add(d);
        }
        theItem.put("events", events);
        theItem.put("event.status", "");
        theItem.put("event.startDate", "");
        theItems.add(theItem);
    }
    // Do not forget to set the items back on the tableFacade.
    tableFacade.setItems(theItems);
    this.setStudyHasDiscNotes(hasDN);
}

Example 62 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class ListStudySubjectsServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    getCrfLocker().unlockAllForUser(ub.getId());
    FormProcessor fp = new FormProcessor(request);
    if (fp.getString("showMoreLink").equals("")) {
        showMoreLink = true;
    } else {
        showMoreLink = Boolean.parseBoolean(fp.getString("showMoreLink"));
    }
    String idSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
    // set up auto study subject id
    if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
        //Shaoyu Su
        // int nextLabel = getStudySubjectDAO().findTheGreatestLabel() + 1;
        // request.setAttribute("label", new Integer(nextLabel).toString());
        request.setAttribute("label", resword.getString("id_generated_Save_Add"));
        fp.addPresetValue("label", resword.getString("id_generated_Save_Add"));
    }
    if (fp.getRequest().getParameter("subjectOverlay") == null) {
        Date today = new Date(System.currentTimeMillis());
        String todayFormatted = local_df.format(today);
        if (request.getAttribute(PRESET_VALUES) != null) {
            fp.setPresetValues((HashMap) request.getAttribute(PRESET_VALUES));
        }
        fp.addPresetValue(AddNewSubjectServlet.INPUT_ENROLLMENT_DATE, todayFormatted);
        fp.addPresetValue(AddNewSubjectServlet.INPUT_EVENT_START_DATE, todayFormatted);
        setPresetValues(fp.getPresetValues());
    }
    request.setAttribute("closeInfoShowIcons", true);
    if (fp.getString("navBar").equals("yes") && fp.getString("findSubjects_f_studySubject.label").trim().length() > 0) {
        StudySubjectBean studySubject = getStudySubjectDAO().findByLabelAndStudy(fp.getString("findSubjects_f_studySubject.label"), currentStudy);
        if (studySubject.getId() > 0) {
            request.setAttribute("id", new Integer(studySubject.getId()).toString());
            forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
        } else {
            createTable();
        }
    } else {
        createTable();
    }
}

Example 63 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class TableOfContentsServlet method createEventCRF.

/**
     * Creates a new Event CRF or update the exsiting one, that is, an event CRF
     * can be created but not item data yet, in this case, still consider it is
     * not started(called uncompleted before)
     * 
     * @return
     * @throws Exception
     */
private EventCRFBean createEventCRF() throws Exception {
    EventCRFBean ecb;
    ecdao = new EventCRFDAO(sm.getDataSource());
    int crfVersionId = fp.getInt(INPUT_CRF_VERSION_ID);
    int studyEventId = fp.getInt(INPUT_STUDY_EVENT_ID);
    int eventDefinitionCRFId = fp.getInt(INPUT_EVENT_DEFINITION_CRF_ID);
    int subjectId = fp.getInt(INPUT_SUBJECT_ID);
    int eventCRFId = fp.getInt(INPUT_EVENT_CRF_ID);
    logger.info("Creating event CRF within Table of Contents.  Study id: " + currentStudy.getId() + "; CRF Version id: " + crfVersionId + "; Study Event id: " + studyEventId + "; Event Definition CRF id: " + eventDefinitionCRFId + "; Subject: " + subjectId);
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    StudySubjectBean ssb = ssdao.findBySubjectIdAndStudy(subjectId, currentStudy);
    if (!ssb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE1"));
    }
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sedb = seddao.findByEventDefinitionCRFId(eventDefinitionCRFId);
    if (!ssb.isActive() || !sedb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE2"));
    }
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    EntityBean eb = cvdao.findByPK(crfVersionId);
    if (!eb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE3"));
    }
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventBean sEvent = (StudyEventBean) sedao.findByPK(studyEventId);
    StudyBean studyWithSED = currentStudy;
    if (currentStudy.getParentStudyId() > 0) {
        studyWithSED = new StudyBean();
        studyWithSED.setId(currentStudy.getParentStudyId());
    }
    AuditableEntityBean aeb = sedao.findByPKAndStudy(studyEventId, studyWithSED);
    if (!aeb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("trying_to_begin_DE4"));
    }
    ecb = new EventCRFBean();
    if (eventCRFId == 0) {
        // no event CRF created yet
        ecb.setAnnotations("");
        ecb.setCreatedDate(new Date());
        ecb.setCRFVersionId(crfVersionId);
        ecb.setInterviewerName("");
        if (sEvent.getDateStarted() != null) {
            // default date
            ecb.setDateInterviewed(sEvent.getDateStarted());
        } else {
            ecb.setDateInterviewed(null);
        }
        ecb.setOwnerId(ub.getId());
        ecb.setStatus(Status.AVAILABLE);
        ecb.setCompletionStatusId(1);
        ecb.setStudySubjectId(ssb.getId());
        ecb.setStudyEventId(studyEventId);
        ecb.setValidateString("");
        ecb.setValidatorAnnotations("");
        ecb = (EventCRFBean) ecdao.create(ecb);
        logger.info("CREATED EVENT CRF");
    } else {
        // there is an event CRF already, only need to update
        ecb = (EventCRFBean) ecdao.findByPK(eventCRFId);
        ecb.setCRFVersionId(crfVersionId);
        ecb.setUpdatedDate(new Date());
        ecb.setUpdater(ub);
        ecb = (EventCRFBean) ecdao.update(ecb);
    }
    if (!ecb.isActive()) {
        throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("new_event_CRF_not_created_database_error"));
    } else {
        sEvent.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
        sEvent.setUpdater(ub);
        sEvent.setUpdatedDate(new Date());
        sedao.update(sEvent);
    }
    return ecb;
}

Example 64 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class ListStudySubjectTableFactory method setDataAndLimitVariables.

@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    Limit limit = tableFacade.getLimit();
    FindSubjectsFilter subjectFilter = getSubjectFilter(limit);
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDAO().getCountWithFilter(subjectFilter, getStudyBean());
        tableFacade.setTotalRows(totalRows);
    }
    FindSubjectsSort subjectSort = getSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDAO().getWithFilterAndSort(getStudyBean(), subjectFilter, subjectSort, 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());
        theItem.put("studySubject.oid", studySubjectBean.getOid());
        theItem.put("studySubject.secondaryLabel", studySubjectBean.getSecondaryLabel());
        SubjectBean subjectBean = (SubjectBean) getSubjectDAO().findByPK(studySubjectBean.getSubjectId());
        theItem.put("subject", subjectBean);
        theItem.put("subject.charGender", subjectBean.getGender());
        // Get All study events for this study subject and then put list in
        // HashMap with study event definition id as
        // key and a list of study events as the value.
        List<StudyEventBean> allStudyEventsForStudySubject = getStudyEventDAO().findAllByStudySubject(studySubjectBean);
        HashMap<Integer, List<StudyEventBean>> allStudyEventsForStudySubjectBySedId = new HashMap<Integer, List<StudyEventBean>>();
        theItem.put("isSignable", isSignable(allStudyEventsForStudySubject, studySubjectBean));
        for (StudyEventBean studyEventBean : allStudyEventsForStudySubject) {
            if (allStudyEventsForStudySubjectBySedId.get(studyEventBean.getStudyEventDefinitionId()) == null) {
                ArrayList<StudyEventBean> a = new ArrayList<StudyEventBean>();
                a.add(studyEventBean);
                allStudyEventsForStudySubjectBySedId.put(studyEventBean.getStudyEventDefinitionId(), a);
            } else {
                allStudyEventsForStudySubjectBySedId.get(studyEventBean.getStudyEventDefinitionId()).add(studyEventBean);
            }
        }
        SubjectGroupMapBean 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;
        for (StudyEventDefinitionBean studyEventDefinition : getStudyEventDefinitions()) {
            List<StudyEventBean> studyEvents = allStudyEventsForStudySubjectBySedId.get(studyEventDefinition.getId());
            SubjectEventStatus subjectEventStatus = null;
            studyEvents = studyEvents == null ? new ArrayList<StudyEventBean>() : studyEvents;
            if (studyEvents.size() < 1) {
                subjectEventStatus = SubjectEventStatus.NOT_SCHEDULED;
            } else {
                for (StudyEventBean studyEventBean : studyEvents) {
                    if (studyEventBean.getSampleOrdinal() == 1) {
                        subjectEventStatus = studyEventBean.getSubjectEventStatus();
                        break;
                    }
                }
            }
            theItem.put("sed_" + studyEventDefinition.getId(), subjectEventStatus.getId());
            theItem.put("sed_" + studyEventDefinition.getId() + "_studyEvents", studyEvents);
            theItem.put("sed_" + studyEventDefinition.getId() + "_object", studyEventDefinition);
        }
        theItems.add(theItem);
    }
    // Do not forget to set the items back on the tableFacade.
    tableFacade.setItems(theItems);
}

Example 65 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class ViewDiscrepancyNoteServlet method processRequest.

@Override
@SuppressWarnings("unchecked")
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int eventCRFId = fp.getInt(CreateDiscrepancyNoteServlet.EVENT_CRF_ID);
    request.setAttribute(CreateDiscrepancyNoteServlet.EVENT_CRF_ID, new Integer(eventCRFId));
    request.setAttribute(DIS_TYPES, DiscrepancyNoteType.list);
    if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
        ArrayList<ResolutionStatus> resStatuses = new ArrayList();
        resStatuses.add(ResolutionStatus.UPDATED);
        resStatuses.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES, resStatuses);
        // it's for parentDNId is null or 0
        request.setAttribute(WHICH_RES_STATUSES, "22");
        ArrayList<ResolutionStatus> resStatuses2 = new ArrayList<ResolutionStatus>();
        resStatuses2.add(ResolutionStatus.OPEN);
        resStatuses2.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES2, resStatuses2);
        List<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>(DiscrepancyNoteType.list);
        types2.remove(DiscrepancyNoteType.QUERY);
        request.setAttribute(DIS_TYPES2, types2);
    } 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_TYPES2, types2);
    } else {
        // Role.STUDYDIRECTOR Role.COORDINATOR
        List<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>(ResolutionStatus.list);
        resStatuses.remove(ResolutionStatus.NOT_APPLICABLE);
        request.setAttribute(RES_STATUSES, resStatuses);
        ;
        // it's for parentDNId is null or 0 and FVC
        request.setAttribute(WHICH_RES_STATUSES, "2");
        ArrayList<ResolutionStatus> resStatuses2 = new ArrayList<ResolutionStatus>();
        resStatuses2.add(ResolutionStatus.OPEN);
        resStatuses2.add(ResolutionStatus.RESOLVED);
        request.setAttribute(RES_STATUSES2, resStatuses2);
    }
    // logic from CreateDiscrepancyNoteServlet
    request.setAttribute("unlock", "0");
    fp.getBoolean(IS_REASON_FOR_CHANGE);
    fp.getBoolean(ERROR_FLAG);
    String monitor = fp.getString("monitor");
    // } else if ("1".equalsIgnoreCase(monitor)) {// change to allow user to
    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");
    }
    Boolean fromBox = fp.getBoolean(FROM_BOX);
    if (fromBox == null || !fromBox) {
        session.removeAttribute(BOX_TO_SHOW);
        session.removeAttribute(BOX_DN_MAP);
        session.removeAttribute(AUTOVIEWS);
    }
    Boolean refresh = fp.getBoolean("refresh");
    request.setAttribute("refresh", refresh + "");
    String ypos = fp.getString("y");
    if (ypos == null || ypos.length() == 0) {
        ypos = "0";
    }
    request.setAttribute("y", ypos);
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    int entityId = fp.getInt(ENTITY_ID, true);
    String name = fp.getString(ENTITY_TYPE, true);
    String column = fp.getString(ENTITY_COLUMN, true);
    String field = fp.getString(ENTITY_FIELD, true);
    String isLocked = fp.getString(LOCKED_FLAG);
    if (!StringUtil.isBlank(isLocked) && "yes".equalsIgnoreCase(isLocked)) {
        request.setAttribute(LOCKED_FLAG, "yes");
    } else {
        request.setAttribute(LOCKED_FLAG, "no");
    }
    DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
    int subjectId = fp.getInt(CreateDiscrepancyNoteServlet.SUBJECT_ID, true);
    int itemId = fp.getInt(CreateDiscrepancyNoteServlet.ITEM_ID, true);
    StudySubjectBean ssub = new StudySubjectBean();
    if (subjectId > 0) {
        StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
        ssub = (StudySubjectBean) ssdao.findByPK(subjectId);
        request.setAttribute("noteSubject", ssub);
    }
    ItemBean item = new ItemBean();
    if (itemId > 0) {
        ItemDAO idao = new ItemDAO(sm.getDataSource());
        item = (ItemBean) idao.findByPK(itemId);
        request.setAttribute("item", item);
        request.setAttribute("entityName", item.getName());
    }
    ItemDataBean itemData = new ItemDataBean();
    SimpleDateFormat sdf = new SimpleDateFormat("dd-MMM-yyyy");
    int preUserId = 0;
    if (!StringUtil.isBlank(name)) {
        if ("itemData".equalsIgnoreCase(name)) {
            ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
            itemData = (ItemDataBean) iddao.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() > 0 ? ec.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(ec.getCreatedDate()));
            StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
            StudyEventBean se = (StudyEventBean) sed.findByPK(ec.getStudyEventId());
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
            StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            se.setName(sedb.getName());
            request.setAttribute("studyEvent", se);
            CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
            CRFVersionBean cv = (CRFVersionBean) cvdao.findByPK(ec.getCRFVersionId());
            CRFDAO cdao = new CRFDAO(sm.getDataSource());
            CRFBean crf = (CRFBean) cdao.findByPK(cv.getCrfId());
            request.setAttribute("crf", crf);
        } else if ("studySub".equalsIgnoreCase(name)) {
            StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
            ssub = (StudySubjectBean) ssdao.findByPK(entityId);
            SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
            SubjectBean sub = (SubjectBean) sdao.findByPK(ssub.getSubjectId());
            request.setAttribute("noteSubject", ssub);
            if (!StringUtil.isBlank(column)) {
                if ("enrollment_date".equalsIgnoreCase(column)) {
                    if (ssub.getEnrollmentDate() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(ssub.getEnrollmentDate()));
                    }
                    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()));
                    }
                    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"));
                }
            }
            preUserId = ssub.getOwnerId() > 0 ? ssub.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(ssub.getCreatedDate()));
        } else if ("subject".equalsIgnoreCase(name)) {
            SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
            SubjectBean sub = (SubjectBean) sdao.findByPK(entityId);
            // be caution: here for subject, noteSubject is SubjectBean and
            // label is unique_identifier
            sub.setLabel(sub.getUniqueIdentifier());
            request.setAttribute("noteSubject", sub);
            if (!StringUtil.isBlank(column)) {
                if ("gender".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", ssub.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"));
                }
            }
            preUserId = sub.getOwnerId() > 0 ? sub.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(sub.getCreatedDate()));
        } else if ("studyEvent".equalsIgnoreCase(name)) {
            StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
            StudyEventBean se = (StudyEventBean) sed.findByPK(entityId);
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
            StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            se.setName(sedb.getName());
            request.setAttribute("studyEvent", se);
            request.setAttribute("noteSubject", new StudySubjectDAO(sm.getDataSource()).findByPK(se.getStudySubjectId()));
            if (!StringUtil.isBlank(column)) {
                if ("location".equalsIgnoreCase(column)) {
                    request.setAttribute("entityValue", 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()));
                    }
                    request.setAttribute("entityName", resword.getString("start_date"));
                } else if ("end_date".equalsIgnoreCase(column)) {
                    if (se.getDateEnded() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(se.getDateEnded()));
                    }
                    request.setAttribute("entityName", resword.getString("end_date"));
                }
            }
            preUserId = se.getOwnerId() > 0 ? se.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(se.getCreatedDate()));
        } else if ("eventCrf".equalsIgnoreCase(name)) {
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            EventCRFBean ec = (EventCRFBean) ecdao.findByPK(entityId);
            if (!StringUtil.isBlank(column)) {
                if ("date_interviewed".equals(column)) {
                    if (ec.getDateInterviewed() != null) {
                        request.setAttribute("entityValue", dateFormatter.format(ec.getDateInterviewed()));
                    }
                    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"));
                }
            }
            setupStudyEventCRFAttributes(ec);
            preUserId = ec.getOwnerId() > 0 ? ec.getOwnerId() : 0;
            request.setAttribute("entityCreatedDate", sdf.format(ec.getCreatedDate()));
        }
    }
    boolean writeToDB = fp.getBoolean(CreateDiscrepancyNoteServlet.WRITE_TO_DB, true);
    HashMap<Integer, Integer> autoviews = (HashMap<Integer, Integer>) session.getAttribute(AUTOVIEWS);
    autoviews = autoviews == null ? new HashMap<Integer, Integer>() : autoviews;
    HashMap<Integer, DiscrepancyNoteBean> boxDNMap = (HashMap<Integer, DiscrepancyNoteBean>) session.getAttribute(BOX_DN_MAP);
    if (boxDNMap == null || !boxDNMap.containsKey(0)) {
        boxDNMap = new HashMap<Integer, DiscrepancyNoteBean>();
        // initialize dn for a new thread
        DiscrepancyNoteBean dnb = new DiscrepancyNoteBean();
        if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
            dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.ANNOTATION.getId());
            dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
            autoviews.put(0, 0);
        // request.setAttribute("autoView", "0");
        } else {
            dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.QUERY.getId());
            dnb.setAssignedUserId(preUserId);
            autoviews.put(0, 1);
        // request.setAttribute("autoView", "1");
        }
        boxDNMap.put(0, dnb);
    } else if (boxDNMap.containsKey(0)) {
        int dnTypeId = boxDNMap.get(0).getDiscrepancyNoteTypeId();
        autoviews.put(0, dnTypeId == 3 ? 1 : 0);
    }
    if (boxDNMap.containsKey(0)) {
        int dnTypeId0 = boxDNMap.get(0).getDiscrepancyNoteTypeId();
        if (dnTypeId0 == 2 || dnTypeId0 == 4) {
            request.setAttribute("typeID0", dnTypeId0 + "");
        }
    }
    // request.setAttribute("enterData", enterData);
    request.setAttribute("monitor", monitor);
    request.setAttribute(ENTITY_ID, entityId + "");
    request.setAttribute(ENTITY_TYPE, name);
    request.setAttribute(ENTITY_FIELD, field);
    request.setAttribute(ENTITY_COLUMN, column);
    request.setAttribute(CreateDiscrepancyNoteServlet.WRITE_TO_DB, writeToDB ? "1" : "0");
    ArrayList notes = (ArrayList) dndao.findAllByEntityAndColumn(name, entityId, column);
    if (notes.size() > 0) {
        notes.get(0);
        // @pgawade 21-May-2011 Corrected the condition to throw no access
        // error
        StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
        int parentStudyForNoteSub = 0;
        // @pgawade #9801: 07-June-2011 corrected the way to get study
        // subject id associated with discrepancy note
        // int noteSubId = note.getOwnerId();
        StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
        // StudySubjectBean notessub = (StudySubjectBean)
        // ssdao.findByPK(noteSubId);
        StudySubjectBean notessub = (StudySubjectBean) ssdao.findByPK(subjectId);
        StudyBean studyBeanSub = (StudyBean) studyDAO.findByPK(notessub.getStudyId());
        if (null != studyBeanSub) {
            parentStudyForNoteSub = studyBeanSub.getParentStudyId();
        }
        if (notessub.getStudyId() != currentStudy.getId() && currentStudy.getId() != parentStudyForNoteSub) {
            addPageMessage(noAccessMessage);
            throw new InsufficientPermissionException(Page.MENU_SERVLET, exceptionName, "1");
        }
    }
    FormDiscrepancyNotes newNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
    Map<Integer, DiscrepancyNoteBean> noteTree = new LinkedHashMap<Integer, DiscrepancyNoteBean>();
    String session_key = eventCRFId + "_" + field;
    ArrayList newFieldNotes = null;
    if (newNotes != null && (!newNotes.getNotes(field).isEmpty() || !newNotes.getNotes(session_key).isEmpty())) {
        newFieldNotes = newNotes.getNotes(field);
        if (newFieldNotes == null || newFieldNotes.size() == 0) {
            newFieldNotes = newNotes.getNotes(session_key);
        }
        // System.out.println("how many notes:" + newFieldNotes.size());
        for (int i = 0; i < newFieldNotes.size(); i++) {
            DiscrepancyNoteBean note = (DiscrepancyNoteBean) newFieldNotes.get(i);
            note.setLastUpdator(ub);
            note.setLastDateUpdated(new Date());
            note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
            note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
            note.setSaved(false);
            if (itemId > 0) {
                note.setEntityName(item.getName());
                note.setEntityValue(itemData.getValue());
            }
            note.setSubjectName(ssub.getName());
            note.setEntityType(name);
            int pId = note.getParentDnId();
            if (pId == 0) {
                // we can only keep one unsaved note because
                // note.id == 0
                noteTree.put(note.getId(), note);
            }
        }
        for (int i = 0; i < newFieldNotes.size(); i++) {
            DiscrepancyNoteBean note = (DiscrepancyNoteBean) newFieldNotes.get(i);
            int pId = note.getParentDnId();
            if (pId > 0) {
                note.setSaved(false);
                note.setLastUpdator(ub);
                note.setLastDateUpdated(new Date());
                note.setEntityName(item.getName());
                note.setSubjectName(ssub.getName());
                note.setEntityType(name);
                note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
                note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
                DiscrepancyNoteBean parent = noteTree.get(new Integer(pId));
                if (parent != null) {
                    parent.getChildren().add(note);
                }
            }
        }
    }
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    HashMap<Integer, String> fvcInitAssigns = new HashMap<Integer, String>();
    for (int i = 0; i < notes.size(); i++) {
        DiscrepancyNoteBean note = (DiscrepancyNoteBean) notes.get(i);
        note.setColumn(column);
        note.setEntityId(entityId);
        note.setEntityType(name);
        note.setField(field);
        Date lastUpdatedDate = note.getCreatedDate();
        UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
        note.setLastUpdator(lastUpdator);
        note.setLastDateUpdated(lastUpdatedDate);
        int pId = note.getParentDnId();
        note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
        note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
        if (pId == 0) {
            noteTree.put(new Integer(note.getId()), note);
        }
    }
    for (int i = 0; i < notes.size(); i++) {
        DiscrepancyNoteBean note = (DiscrepancyNoteBean) notes.get(i);
        int pId = note.getParentDnId();
        if (itemId > 0) {
            note.setEntityName(item.getName());
            note.setEntityValue(itemData.getValue());
        }
        note.setSubjectName(ssub.getName());
        note.setEntityType(name);
        Date lastUpdatedDate = note.getCreatedDate();
        UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
        note.setLastUpdator(lastUpdator);
        note.setLastDateUpdated(lastUpdatedDate);
        note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
        note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
        if (pId > 0) {
            DiscrepancyNoteBean parent = noteTree.get(new Integer(pId));
            if (parent != null) {
                parent.getChildren().add(note);
                if (!note.getCreatedDate().before(parent.getLastDateUpdated())) {
                    parent.setLastDateUpdated(note.getCreatedDate());
                }
                if (note.getDiscrepancyNoteTypeId() == 1 && note.getAssignedUserId() > 0) {
                    int ownerId = note.getOwnerId();
                    if (fvcInitAssigns.containsKey(pId)) {
                        String f = fvcInitAssigns.get(pId);
                        String fn = note.getId() + "." + ownerId;
                        if (fn.compareTo(f) < 0) {
                            fvcInitAssigns.put(pId, fn);
                        }
                    } else {
                        fvcInitAssigns.put(pId, note.getId() + "." + ownerId);
                    }
                }
            }
        }
    }
    Set parents = noteTree.keySet();
    Iterator it = parents.iterator();
    while (it.hasNext()) {
        Integer key = (Integer) it.next();
        DiscrepancyNoteBean note = noteTree.get(key);
        note.setNumChildren(note.getChildren().size());
        note.setEntityType(name);
        if (!boxDNMap.containsKey(key)) {
            DiscrepancyNoteBean dn = new DiscrepancyNoteBean();
            dn.setId(key);
            int dnTypeId = note.getDiscrepancyNoteTypeId();
            dn.setDiscrepancyNoteTypeId(dnTypeId);
            if (dnTypeId == 3) {
                // JsonQuery
                dn.setAssignedUserId(note.getOwnerId());
            } else if (dnTypeId == 1) {
                // FVC
                if (fvcInitAssigns.containsKey(key)) {
                    String[] s = fvcInitAssigns.get(key).split("\\.");
                    int i = Integer.parseInt(s.length == 2 ? s[1].trim() : "0");
                    dn.setAssignedUserId(i);
                }
            }
            Role r = currentRole.getRole();
            // currentStudy.getId() != currentStudy.getParentStudyId()) {
            if (r.equals(Role.RESEARCHASSISTANT) || r.equals(Role.RESEARCHASSISTANT2) || r.equals(Role.INVESTIGATOR)) {
                if (dn.getDiscrepancyNoteTypeId() == DiscrepancyNoteType.QUERY.getId() && note.getResStatus().getId() == ResolutionStatus.UPDATED.getId()) {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                } else {
                    dn.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
                }
                if (dn.getAssignedUserId() > 0) {
                    autoviews.put(key, 1);
                } else {
                    autoviews.put(key, 0);
                }
            // copied from CreateDiscrepancyNoteServlet
            // request.setAttribute("autoView", "0");
            // hide the panel, tbh
            } else {
                if (note.getResStatus().getId() == ResolutionStatus.RESOLVED.getId()) {
                    dn.setResolutionStatusId(ResolutionStatus.CLOSED.getId());
                } else if (note.getResStatus().getId() == ResolutionStatus.CLOSED.getId()) {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                } else if (r.equals(Role.MONITOR)) {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                } else if (dn.getDiscrepancyNoteTypeId() == 1) {
                    dn.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
                } else {
                    dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
                }
                autoviews.put(key, 1);
                if (dn.getAssignedUserId() > 0) {
                } else {
                    dn.setAssignedUserId(preUserId);
                }
            }
            boxDNMap.put(key, dn);
        }
    }
    session.setAttribute(BOX_DN_MAP, boxDNMap);
    session.setAttribute(AUTOVIEWS, autoviews);
    // noteTree is a Hashmap mapping note id to a parent note, with all the
    // child notes
    // stored in the children List.
    // BWP 3029>>make sure the parent note has an updated resolution status
    // and
    // updated date
    fixStatusUpdatedDate(noteTree);
    request.setAttribute(DIS_NOTES, noteTree);
    // copied from CreatediscrepancyNoteServlet generateUserAccounts
    StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
    StudyBean subjectStudy = studyDAO.findByStudySubjectId(subjectId);
    int studyId = currentStudy.getId();
    ArrayList<UserAccountBean> userAccounts = new ArrayList();
    if (currentStudy.getParentStudyId() > 0) {
        userAccounts = udao.findAllUsersByStudyOrSite(studyId, currentStudy.getParentStudyId(), subjectId);
    } else if (subjectStudy.getParentStudyId() > 0) {
        userAccounts = udao.findAllUsersByStudyOrSite(subjectStudy.getId(), subjectStudy.getParentStudyId(), subjectId);
    } else {
        userAccounts = udao.findAllUsersByStudyOrSite(studyId, 0, subjectId);
    }
    request.setAttribute(USER_ACCOUNTS, userAccounts);
    request.setAttribute(VIEW_DN_LINK, this.getPageServletFileName());
    // audit log items (from ViewItemAuditLogServlet.java)
    AuditDAO adao = new AuditDAO(sm.getDataSource());
    if (name.equalsIgnoreCase("studysub")) {
        name = "study_subject";
    } else if (name.equalsIgnoreCase("eventcrf")) {
        name = "event_crf";
    } else if (name.equalsIgnoreCase("studyevent")) {
        name = "study_event";
    } else if (name.equalsIgnoreCase("itemdata")) {
        name = "item_data";
    }
    ArrayList itemAuditEvents = adao.findItemAuditEvents(entityId, name);
    request.setAttribute("itemAudits", itemAuditEvents);
    forwardPage(Page.VIEW_DISCREPANCY_NOTE);
}