Examples with DiscrepancyNoteThread org.akaza.openclinica.service.DiscrepancyNoteThread used on opensource projects

Example 6 with DiscrepancyNoteThread

use of org.akaza.openclinica.service.DiscrepancyNoteThread in project OpenClinica by OpenClinica.

the class DownloadDiscrepancyNote method downLoadThreadedDiscBeans.

public void downLoadThreadedDiscBeans(List<DiscrepancyNoteThread> listOfThreadedBeans, String format, HttpServletResponse response, String studyIdentifier) throws Exception {
    if (listOfThreadedBeans == null) {
        return;
    }
    StringBuilder allContent = new StringBuilder();
    String singleBeanContent = "";
    int counter = 0;
    int threadCounter = 0;
    if (CSV.equalsIgnoreCase(format)) {
        for (DiscrepancyNoteThread dnThread : listOfThreadedBeans) {
            threadCounter++;
            for (DiscrepancyNoteBean discNoteBean : dnThread.getLinkedNoteList()) {
                //DiscrepancyNoteBean discNoteBean = dnThread.getLinkedNoteList().getFirst();
                ++counter;
                singleBeanContent = counter == 1 ? serializeToString(discNoteBean, true, threadCounter) : serializeToString(discNoteBean, false, threadCounter);
                allContent.append(singleBeanContent);
            }
        }
    }
    //This must be a ServletOutputStream for our purposes
    ServletOutputStream servletStream = null;
    try {
        if (CSV.equalsIgnoreCase(format)) {
            String result = StringEscapeUtils.unescapeJava(allContent.toString());
            response.getWriter().print(result);
        //servletStream.print(allContent.toString());
        } else {
            //Create PDF version
            //this.serializeListToPDF(listOfBeans,servletStream, studyIdentifier);
            servletStream = (ServletOutputStream) response.getOutputStream();
            this.serializeThreadsToPDF(listOfThreadedBeans, servletStream, studyIdentifier);
        }
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        if (servletStream != null) {
            try {
                servletStream.close();
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }
}

Example 7 with DiscrepancyNoteThread

use of org.akaza.openclinica.service.DiscrepancyNoteThread 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);
        }
    }
}