Examples with StudyParameterValueDAO org.akaza.openclinica.dao.service.StudyParameterValueDAO used on opensource projects

Example 6 with StudyParameterValueDAO

use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.

the class SecureController method process.

private void process(HttpServletRequest request, HttpServletResponse response) throws OpenClinicaException, UnsupportedEncodingException {
    request.setCharacterEncoding("UTF-8");
    session = request.getSession();
    // BWP >> 1/8/2008
    try {
        // YW 10-03-2007 <<
        session.setMaxInactiveInterval(Integer.parseInt(SQLInitServlet.getField("max_inactive_interval")));
    // YW >>
    } catch (NumberFormatException nfe) {
        // BWP>>3600 is the datainfo.properties maxInactiveInterval on
        // 1/8/2008
        session.setMaxInactiveInterval(3600);
    }
    // If the session already has a value with key SUPPORT_URL don't reset
    if (session.getAttribute(SUPPORT_URL) == null) {
        session.setAttribute(SUPPORT_URL, SQLInitServlet.getSupportURL());
    }
    ub = (UserAccountBean) session.getAttribute(USER_BEAN_NAME);
    currentStudy = (StudyBean) session.getAttribute("study");
    currentRole = (StudyUserRoleBean) session.getAttribute("userRole");
    // Set current language preferences
    Locale locale = LocaleResolver.getLocale(request);
    ResourceBundleProvider.updateLocale(locale);
    resadmin = ResourceBundleProvider.getAdminBundle(locale);
    resaudit = ResourceBundleProvider.getAuditEventsBundle(locale);
    resexception = ResourceBundleProvider.getExceptionsBundle(locale);
    resformat = ResourceBundleProvider.getFormatBundle(locale);
    restext = ResourceBundleProvider.getTextsBundle(locale);
    resterm = ResourceBundleProvider.getTermsBundle(locale);
    resword = ResourceBundleProvider.getWordsBundle(locale);
    respage = ResourceBundleProvider.getPageMessagesBundle(locale);
    resworkflow = ResourceBundleProvider.getWorkflowBundle(locale);
    local_df = I18nFormatUtil.getDateFormat(locale);
    try {
        String userName = request.getRemoteUser();
        // BWP 1/8/08<< the sm variable may already be set with a mock
        // object,
        // from the perspective of
        // JUnit servlets tests
        /*
             * if(sm==null && (!StringUtil.isBlank(userName))) {//check if user logged in, then create a new sessionmanger to
             * get ub //create a new sm in order to get a new ub object sm = new SessionManager(ub, userName); }
             */
        // BWP 01/08 >>
        // sm = new SessionManager(ub, userName);
        sm = new SessionManager(ub, userName, SpringServletAccess.getApplicationContext(context));
        ub = sm.getUserBean();
        session.setAttribute("userBean", ub);
        StudyDAO sdao = new StudyDAO(sm.getDataSource());
        if (currentStudy == null || currentStudy.getId() <= 0) {
            if (ub.getId() > 0 && ub.getActiveStudyId() > 0) {
                StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
                currentStudy = (StudyBean) sdao.findByPK(ub.getActiveStudyId());
                ArrayList studyParameters = spvdao.findParamConfigByStudy(currentStudy);
                currentStudy.setStudyParameters(studyParameters);
                StudyConfigService scs = new StudyConfigService(sm.getDataSource());
                if (currentStudy.getParentStudyId() <= 0) {
                    // top study
                    scs.setParametersForStudy(currentStudy);
                } else {
                    // YW <<
                    currentStudy.setParentStudyName(((StudyBean) sdao.findByPK(currentStudy.getParentStudyId())).getName());
                    // YW >>
                    scs.setParametersForSite(currentStudy);
                }
                // set up the panel here, tbh
                panel.reset();
                /*
                     * panel.setData("Study", currentStudy.getName()); panel.setData("Summary", currentStudy.getSummary());
                     * panel.setData("Start Date", sdf.format(currentStudy.getDatePlannedStart())); panel.setData("End Date",
                     * sdf.format(currentStudy.getDatePlannedEnd())); panel.setData("Principal Investigator",
                     * currentStudy.getPrincipalInvestigator());
                     */
                session.setAttribute(STUDY_INFO_PANEL, panel);
            } else {
                currentStudy = new StudyBean();
            }
            session.setAttribute("study", currentStudy);
        } else if (currentStudy.getId() > 0) {
            // restored
            if (currentStudy.getParentStudyId() > 0) {
                currentStudy.setParentStudyName(((StudyBean) sdao.findByPK(currentStudy.getParentStudyId())).getName());
            }
        // YW >>
        }
        if (currentStudy.getParentStudyId() > 0) {
            /*
                 * The Role decription will be set depending on whether the user logged in at study lever or site level.
                 * issue-2422
                 */
            List roles = Role.toArrayList();
            for (Iterator it = roles.iterator(); it.hasNext(); ) {
                Role role = (Role) it.next();
                switch(role.getId()) {
                    case 2:
                        role.setDescription("site_Study_Coordinator");
                        break;
                    case 3:
                        role.setDescription("site_Study_Director");
                        break;
                    case 4:
                        role.setDescription("site_investigator");
                        break;
                    case 5:
                        role.setDescription("site_Data_Entry_Person");
                        break;
                    case 6:
                        role.setDescription("site_monitor");
                        break;
                    case 7:
                        role.setDescription("site_Data_Entry_Person2");
                        break;
                    default:
                }
            }
        } else {
            /*
                 * If the current study is a site, we will change the role description. issue-2422
                 */
            List roles = Role.toArrayList();
            for (Iterator it = roles.iterator(); it.hasNext(); ) {
                Role role = (Role) it.next();
                switch(role.getId()) {
                    case 2:
                        role.setDescription("Study_Coordinator");
                        break;
                    case 3:
                        role.setDescription("Study_Director");
                        break;
                    case 4:
                        role.setDescription("Investigator");
                        break;
                    case 5:
                        role.setDescription("Data_Entry_Person");
                        break;
                    case 6:
                        role.setDescription("Monitor");
                        break;
                    default:
                }
            }
        }
        if (currentRole == null || currentRole.getId() <= 0) {
            // kept as "invalid" -- YW 06-21-2007
            if (ub.getId() > 0 && currentStudy.getId() > 0 && !currentStudy.getStatus().getName().equals("removed")) {
                currentRole = ub.getRoleByStudy(currentStudy.getId());
                if (currentStudy.getParentStudyId() > 0) {
                    // Checking if currentStudy has been removed or not will
                    // ge good enough -- YW 10-17-2007
                    StudyUserRoleBean roleInParent = ub.getRoleByStudy(currentStudy.getParentStudyId());
                    // inherited role from parent study, pick the higher
                    // role
                    currentRole.setRole(Role.max(currentRole.getRole(), roleInParent.getRole()));
                }
            // logger.info("currentRole:" + currentRole.getRoleName());
            } else {
                currentRole = new StudyUserRoleBean();
            }
            session.setAttribute("userRole", currentRole);
        } else // active study has been removed.
        if (currentRole.getId() > 0 && (currentStudy.getStatus().equals(Status.DELETED) || currentStudy.getStatus().equals(Status.AUTO_DELETED))) {
            currentRole.setRole(Role.INVALID);
            currentRole.setStatus(Status.DELETED);
            session.setAttribute("userRole", currentRole);
        }
        // YW 06-19-2007 >>
        request.setAttribute("isAdminServlet", getAdminServlet());
        this.request = request;
        this.response = response;
        // logger.info(rq_names);
        if (!request.getRequestURI().endsWith("ResetPassword")) {
            passwdTimeOut();
        }
        mayProceed();
        pingJobServer(request);
        processRequest();
    } catch (InconsistentStateException ise) {
        ise.printStackTrace();
        logger.warn("InconsistentStateException: org.akaza.openclinica.control.SecureController: " + ise.getMessage());
        addPageMessage(ise.getOpenClinicaMessage());
        forwardPage(ise.getGoTo());
    } catch (InsufficientPermissionException ipe) {
        ipe.printStackTrace();
        logger.warn("InsufficientPermissionException: org.akaza.openclinica.control.SecureController: " + ipe.getMessage());
        // addPageMessage(ipe.getOpenClinicaMessage());
        forwardPage(ipe.getGoTo());
    } catch (OutOfMemoryError ome) {
        ome.printStackTrace();
        long heapSize = Runtime.getRuntime().totalMemory();
        session.setAttribute("ome", "yes");
    } catch (Exception e) {
        e.printStackTrace();
        logger.error(SecureController.getStackTrace(e));
        forwardPage(Page.ERROR);
    }
}

Example 7 with StudyParameterValueDAO

use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.

the class AddCRFToDefinitionServlet method addCRF.

private void addCRF() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
    ArrayList crfArray = new ArrayList();
    Map tmpCRFIdMap = (HashMap) session.getAttribute("tmpCRFIdMap");
    if (tmpCRFIdMap == null) {
        tmpCRFIdMap = new HashMap();
    }
    ArrayList crfsWithVersion = (ArrayList) session.getAttribute("crfsWithVersion");
    for (int i = 0; i < crfsWithVersion.size(); i++) {
        int id = fp.getInt("id" + i);
        String name = fp.getString("name" + i);
        String selected = fp.getString("selected" + i);
        if (!StringUtil.isBlank(selected) && "yes".equalsIgnoreCase(selected.trim())) {
            logger.info("one crf selected");
            CRFBean cb = new CRFBean();
            cb.setId(id);
            cb.setName(name);
            // only find active verions
            ArrayList versions = (ArrayList) fldao.findAllActiveByCRF(cb.getId());
            cb.setVersions(versions);
            crfArray.add(cb);
        } else {
            if (tmpCRFIdMap.containsKey(id)) {
                tmpCRFIdMap.remove(id);
            }
        }
    }
    for (Iterator tmpCRFIterator = tmpCRFIdMap.keySet().iterator(); tmpCRFIterator.hasNext(); ) {
        int id = (Integer) tmpCRFIterator.next();
        String name = (String) tmpCRFIdMap.get(id);
        boolean isExists = false;
        for (Iterator it = crfArray.iterator(); it.hasNext(); ) {
            CRFBean cb = (CRFBean) it.next();
            if (id == cb.getId()) {
                isExists = true;
            }
        }
        if (!isExists) {
            CRFBean cb = new CRFBean();
            cb.setId(id);
            cb.setName(name);
            // only find active verions
            ArrayList versions = (ArrayList) fldao.findAllActiveByCRF(cb.getId());
            cb.setVersions(versions);
            crfArray.add(cb);
        }
    }
    session.removeAttribute("tmpCRFIdMap");
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    if (crfArray.size() == 0) {
        // no crf seleted
        addPageMessage(respage.getString("no_new_CRF_added"));
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) session.getAttribute("definition");
        String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
        request.setAttribute("participateFormStatus", participateFormStatus);
        sed.setCrfs(new ArrayList());
        session.setAttribute("definition", sed);
        forwardPage(Page.UPDATE_EVENT_DEFINITION1);
    } else {
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) session.getAttribute("definition");
        String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
        if (participateFormStatus.equals("enabled"))
            baseUrl();
        request.setAttribute("participateFormStatus", participateFormStatus);
        ArrayList edcs = (ArrayList) session.getAttribute("eventDefinitionCRFs");
        int ordinalForNewCRF = edcs.size();
        for (int i = 0; i < crfArray.size(); i++) {
            CRFBean crf = (CRFBean) crfArray.get(i);
            EventDefinitionCRFBean edcBean = new EventDefinitionCRFBean();
            edcBean.setCrfId(crf.getId());
            edcBean.setCrfName(crf.getName());
            edcBean.setStudyId(ub.getActiveStudyId());
            edcBean.setStatus(Status.AVAILABLE);
            edcBean.setStudyEventDefinitionId(sed.getId());
            edcBean.setStudyId(ub.getActiveStudyId());
            edcBean.setSourceDataVerification(SourceDataVerification.NOTREQUIRED);
            ordinalForNewCRF = ordinalForNewCRF + 1;
            edcBean.setOrdinal(ordinalForNewCRF);
            edcBean.setVersions(crf.getVersions());
            FormLayoutBean defaultVersion1 = (FormLayoutBean) fldao.findByPK(edcBean.getDefaultVersionId());
            edcBean.setDefaultVersionName(defaultVersion1.getName());
            ordinalForNewCRF++;
            edcs.add(edcBean);
        }
        session.setAttribute("eventDefinitionCRFs", edcs);
        ArrayList<String> sdvOptions = new ArrayList<String>();
        sdvOptions.add(SourceDataVerification.AllREQUIRED.toString());
        sdvOptions.add(SourceDataVerification.PARTIALREQUIRED.toString());
        sdvOptions.add(SourceDataVerification.NOTREQUIRED.toString());
        sdvOptions.add(SourceDataVerification.NOTAPPLICABLE.toString());
        request.setAttribute("sdvOptions", sdvOptions);
        addPageMessage(respage.getString("has_have_been_added_need_confirmation"));
        forwardPage(Page.UPDATE_EVENT_DEFINITION1);
    }
}

Example 8 with StudyParameterValueDAO

use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.

the class CreateStudyServlet method submitStudy.

/**
     * Inserts the new study into database
     *
     */
private void submitStudy() {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    StudyBean newStudy = (StudyBean) session.getAttribute("newStudy");
    logger.info("study bean to be created:" + newStudy.getName() + newStudy.getProtocolDateVerification());
    // newStudy.setType(StudyType.NONGENETIC);//need to refine in the future
    newStudy.setOwner(ub);
    newStudy.setCreatedDate(new Date());
    // newStudy.setStatus(Status.AVAILABLE);
    StudyBean finalStudy = (StudyBean) sdao.create(newStudy);
    logger.info("new study created");
    StudyParameterValueBean spv = new StudyParameterValueBean();
    spv.setStudyId(finalStudy.getId());
    spv.setParameter("collectDob");
    spv.setValue(newStudy.getStudyParameterConfig().getCollectDob());
    spvdao.create(spv);
    spv.setParameter("discrepancyManagement");
    spv.setValue(newStudy.getStudyParameterConfig().getDiscrepancyManagement());
    spvdao.create(spv);
    spv.setParameter("genderRequired");
    spv.setValue(newStudy.getStudyParameterConfig().getGenderRequired());
    spvdao.create(spv);
    spv.setParameter("subjectPersonIdRequired");
    spv.setValue(newStudy.getStudyParameterConfig().getSubjectPersonIdRequired());
    spvdao.create(spv);
    spv.setParameter("interviewerNameRequired");
    spv.setValue(newStudy.getStudyParameterConfig().getInterviewerNameRequired());
    spvdao.create(spv);
    spv.setParameter("interviewerNameDefault");
    spv.setValue(newStudy.getStudyParameterConfig().getInterviewerNameDefault());
    spvdao.create(spv);
    spv.setParameter("interviewerNameEditable");
    spv.setValue(newStudy.getStudyParameterConfig().getInterviewerNameEditable());
    spvdao.create(spv);
    spv.setParameter("interviewDateRequired");
    spv.setValue(newStudy.getStudyParameterConfig().getInterviewDateRequired());
    spvdao.create(spv);
    spv.setParameter("interviewDateDefault");
    spv.setValue(newStudy.getStudyParameterConfig().getInterviewDateDefault());
    spvdao.create(spv);
    spv.setParameter("interviewDateEditable");
    spv.setValue(newStudy.getStudyParameterConfig().getInterviewDateEditable());
    spvdao.create(spv);
    spv.setParameter("subjectIdGeneration");
    spv.setValue(newStudy.getStudyParameterConfig().getSubjectIdGeneration());
    spvdao.create(spv);
    spv.setParameter("subjectIdPrefixSuffix");
    spv.setValue(newStudy.getStudyParameterConfig().getSubjectIdPrefixSuffix());
    spvdao.create(spv);
    spv.setParameter("personIdShownOnCRF");
    spv.setValue(newStudy.getStudyParameterConfig().getPersonIdShownOnCRF());
    spvdao.create(spv);
    spv.setParameter("secondaryLabelViewable");
    spv.setValue(newStudy.getStudyParameterConfig().getSecondaryLabelViewable());
    spvdao.create(spv);
    spv.setParameter("adminForcedReasonForChange");
    spv.setValue(newStudy.getStudyParameterConfig().getAdminForcedReasonForChange());
    spvdao.create(spv);
    logger.info("study parameters created done");
}

Example 9 with StudyParameterValueDAO

use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.

the class InitUpdateEventDefinitionServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyEventDefinitionDAO sdao = new StudyEventDefinitionDAO(sm.getDataSource());
    String idString = request.getParameter("id");
    logger.info("definition id: " + idString);
    if (StringUtil.isBlank(idString)) {
        addPageMessage(respage.getString("please_choose_a_definition_to_edit"));
        forwardPage(Page.LIST_DEFINITION_SERVLET);
    } else {
        // definition id
        int defId = Integer.valueOf(idString.trim()).intValue();
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) sdao.findByPK(defId);
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
        if (participateFormStatus.equals("enabled"))
            baseUrl();
        request.setAttribute("participateFormStatus", participateFormStatus);
        if (currentStudy.getId() != sed.getStudyId()) {
            addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
            forwardPage(Page.MENU_SERVLET);
            return;
        }
        EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
        ArrayList eventDefinitionCRFs = (ArrayList) edao.findAllParentsByDefinition(defId);
        FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
        CRFDAO cdao = new CRFDAO(sm.getDataSource());
        ArrayList newEventDefinitionCRFs = new ArrayList();
        for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
            EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
            ArrayList versions = (ArrayList) fldao.findAllActiveByCRF(edc.getCrfId());
            edc.setVersions(versions);
            CRFBean crf = (CRFBean) cdao.findByPK(edc.getCrfId());
            edc.setCrfName(crf.getName());
            edc.setCrf(crf);
            edc.setParticipantForm(edc.isParticipantForm());
            // TO DO: use a better way on JSP page,eg.function tag
            edc.setNullFlags(processNullValues(edc));
            FormLayoutBean formLayout = (FormLayoutBean) fldao.findByPK(edc.getDefaultVersionId());
            edc.setDefaultVersionName(formLayout.getName());
            String crfPath = sed.getOid() + "." + edc.getCrf().getOid();
            edc.setOffline(getEventDefinitionCrfTagService().getEventDefnCrfOfflineStatus(2, crfPath, true));
            newEventDefinitionCRFs.add(edc);
        }
        session.setAttribute("definition", sed);
        session.setAttribute("eventDefinitionCRFs", newEventDefinitionCRFs);
        // changed above to new list because static, in-place updating is
        // updating all EDCs, tbh 102007
        ArrayList<String> sdvOptions = new ArrayList<String>();
        sdvOptions.add(SourceDataVerification.AllREQUIRED.toString());
        sdvOptions.add(SourceDataVerification.PARTIALREQUIRED.toString());
        sdvOptions.add(SourceDataVerification.NOTREQUIRED.toString());
        sdvOptions.add(SourceDataVerification.NOTAPPLICABLE.toString());
        request.setAttribute("sdvOptions", sdvOptions);
        forwardPage(Page.UPDATE_EVENT_DEFINITION1);
    }
}

Example 10 with StudyParameterValueDAO

use of org.akaza.openclinica.dao.service.StudyParameterValueDAO in project OpenClinica by OpenClinica.

the class ListStudySubjectServlet method processRequest.

// >>
// < ResourceBundleresword;
@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    locale = LocaleResolver.getLocale(request);
    // < resword =
    // ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
    // BWP 3098 << close the info side panel and show icons
    request.setAttribute("closeInfoShowIcons", true);
    // >>
    // BWP 3195, 3330 : designed to address pagination issues
    String pageNumber = fp.getString(SUBJECT_PAGE_NUMBER);
    StringBuilder paginatingQuery = new StringBuilder("");
    String filterKeyword = fp.getString(FILTER_KEYWORD);
    String tmpSearch = fp.getString(SEARCH_SUBMITTED);
    boolean searchSubmitted = !(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword) && !"+".equalsIgnoreCase(filterKeyword);
    if (pageNumber != null && !"".equalsIgnoreCase(pageNumber)) {
        int tempNum = 0;
        try {
            tempNum = Integer.parseInt(pageNumber);
        } catch (NumberFormatException nfe) {
        // tempNum is already initialized to 0
        }
        if (tempNum > 0) {
            paginatingQuery = new StringBuilder(SUBJECT_PAGE_NUMBER).append("=").append(pageNumber);
            paginatingQuery.append("&ebl_paginated=1");
        }
    }
    // URL encode the search keyword, since it will be a parameter in the
    // URL
    String filterKeywordURLEncode = java.net.URLEncoder.encode(filterKeyword, "UTF-8");
    if (searchSubmitted) {
        paginatingQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
        paginatingQuery.append("&").append(FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
    }
    request.setAttribute(PAGINATING_QUERY, paginatingQuery.toString());
    StudyDAO stdao = new StudyDAO(sm.getDataSource());
    StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
    StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    // YW << update study parameters of current study.
    // "collectDob" and "genderRequired" are set as the same as the parent
    // study
    // tbh, also add the params "subjectPersonIdRequired",
    // "subjectIdGeneration", "subjectIdPrefixSuffix"
    int parentStudyId = currentStudy.getParentStudyId();
    ArrayList studyGroupClasses = new ArrayList();
    ArrayList allDefs = new ArrayList();
    // tbh
    if (parentStudyId > 0) {
        StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
        studyGroupClasses = sgcdao.findAllActiveByStudy(parentStudy);
        allDefs = seddao.findAllActiveByStudy(parentStudy);
    } else {
        parentStudyId = currentStudy.getId();
        studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
        allDefs = seddao.findAllActiveByStudy(currentStudy);
    }
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "collectDob");
    currentStudy.getStudyParameterConfig().setCollectDob(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "genderRequired");
    currentStudy.getStudyParameterConfig().setGenderRequired(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectPersonIdRequired");
    currentStudy.getStudyParameterConfig().setSubjectPersonIdRequired(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdGeneration");
    currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue());
    parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdPrefixSuffix");
    currentStudy.getStudyParameterConfig().setSubjectIdPrefixSuffix(parentSPV.getValue());
    // for all the study groups for each group class
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        ArrayList groups = sgdao.findAllByGroupClass(sgc);
        sgc.setStudyGroups(groups);
    }
    request.setAttribute("studyGroupClasses", studyGroupClasses);
    // information for the event tabs
    session.setAttribute("allDefsArray", allDefs);
    session.setAttribute("allDefsNumber", new Integer(allDefs.size()));
    session.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
    // find all the subjects in current study
    ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
    ArrayList<DisplayStudySubjectBean> displayStudySubs = new ArrayList<DisplayStudySubjectBean>();
    // BEGIN LOOPING THROUGH SUBJECTS
    for (int i = 0; i < subjects.size(); i++) {
        StudySubjectBean studySub = (StudySubjectBean) subjects.get(i);
        ArrayList groups = (ArrayList) sgmdao.findAllByStudySubject(studySub.getId());
        ArrayList subGClasses = new ArrayList();
        for (int j = 0; j < studyGroupClasses.size(); j++) {
            StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(j);
            boolean hasClass = false;
            for (int k = 0; k < groups.size(); k++) {
                SubjectGroupMapBean sgmb = (SubjectGroupMapBean) groups.get(k);
                if (sgmb.getGroupClassName().equalsIgnoreCase(sgc.getName())) {
                    subGClasses.add(sgmb);
                    hasClass = true;
                    break;
                }
            }
            if (!hasClass) {
                subGClasses.add(new SubjectGroupMapBean());
            }
        }
        ArrayList subEvents = new ArrayList();
        // find all events order by definition ordinal
        ArrayList events = sedao.findAllByStudySubject(studySub);
        for (int j = 0; j < allDefs.size(); j++) {
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(j);
            boolean hasDef = false;
            // logger.info("...set blank to "+blankid);
            for (int k = 0; k < events.size(); k++) {
                StudyEventBean se = (StudyEventBean) events.get(k);
                if (se.getStudyEventDefinitionId() == sed.getId()) {
                    se.setStudyEventDefinition(sed);
                    // logger.info(">>>found assigned id "+sed.getId()+" sed
                    // name: "+sed.getName()+" "+se.getId());
                    subEvents.add(se);
                    hasDef = true;
                }
            }
            if (!hasDef) {
                StudyEventBean blank = new StudyEventBean();
                blank.setSubjectEventStatus(SubjectEventStatus.NOT_SCHEDULED);
                blank.setStudyEventDefinitionId(sed.getId());
                // how can we set the following:
                // logger.info("...resetting blank id: "+blank.getId()+" to
                // "+blankid);
                // blank.setId(blankid);
                blank.setStudyEventDefinition(sed);
                // logger.info(">>>blank id: "+blank.getId());
                // logger.info(">>>found unassigned id "+sed.getId()+" sed
                // name: "+sed.getName()+" ");
                subEvents.add(blank);
            }
        }
        // logger.info("subevents size after all adds: "+subEvents.size());
        // reorganize the events and find the repeating ones
        // subEvents:[aa bbb cc d ee]
        // finalEvents:[a(2) b(3) c(2) d e(2)]
        int prevDefId = 0;
        int currDefId = 0;
        ArrayList finalEvents = new ArrayList();
        int repeatingNum = 1;
        int count = 0;
        StudyEventBean event = new StudyEventBean();
        // begin looping through subject events
        for (int j = 0; j < subEvents.size(); j++) {
            StudyEventBean se = (StudyEventBean) subEvents.get(j);
            currDefId = se.getStudyEventDefinitionId();
            if (currDefId != prevDefId) {
                // find a new event
                if (repeatingNum > 1) {
                    event.setRepeatingNum(repeatingNum);
                    repeatingNum = 1;
                }
                // add current event to final
                finalEvents.add(se);
                event = se;
                count++;
            // logger.info("event id? "+event.getId());
            } else {
                // repeating event
                repeatingNum++;
                event.getRepeatEvents().add(se);
                // event.getRepeatEvents().size());
                if (j == subEvents.size() - 1) {
                    event.setRepeatingNum(repeatingNum);
                    repeatingNum = 1;
                }
            }
            prevDefId = currDefId;
        }
        // end looping through subject events
        DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
        // logger.info("final events size: "+finalEvents.size());
        dssb.setStudyEvents(finalEvents);
        dssb.setStudySubject(studySub);
        dssb.setStudyGroups(subGClasses);
        displayStudySubs.add(dssb);
    }
    // END LOOPING THROUGH SUBJECTS
    // Set a subject property to determine whether to show a signed-type
    // icon (electronic signature)
    // in the JSP view or not
    // Get all event crfs by studyevent id; then use
    // EventDefinitionCRFDAO.isRequired to
    // determine whether any uncompleted CRFs are required.
    boolean isRequiredUncomplete = false;
    for (DisplayStudySubjectBean subject : displayStudySubs) {
        for (Iterator it = subject.getStudyEvents().iterator(); it.hasNext(); ) {
            StudyEventBean event = (StudyEventBean) it.next();
            if (event.getSubjectEventStatus() != null && event.getSubjectEventStatus().getId() == 3) {
                // disallow the subject from signing any studies
                subject.setStudySignable(false);
                break;
            } else {
                // determine whether the subject has any required,
                // uncompleted event CRFs
                isRequiredUncomplete = eventHasRequiredUncompleteCRFs(event);
                if (isRequiredUncomplete) {
                    subject.setStudySignable(false);
                    break;
                }
            }
        }
    }
    fp = new FormProcessor(request);
    EntityBeanTable table = fp.getEntityBeanTable();
    ArrayList allStudyRows = DisplayStudySubjectRow.generateRowsFromBeans(displayStudySubs);
    ArrayList columnArray = new ArrayList();
    columnArray.add(resword.getString("study_subject_ID"));
    columnArray.add(resword.getString("subject_status"));
    columnArray.add(resword.getString("OID"));
    columnArray.add(resword.getString("gender"));
    // new
    columnArray.add(resword.getString("secondary_ID"));
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        columnArray.add(sgc.getName());
    }
    for (int i = 0; i < allDefs.size(); i++) {
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(i);
        columnArray.add(sed.getName());
    }
    columnArray.add(resword.getString("actions"));
    String[] columns = new String[columnArray.size()];
    columnArray.toArray(columns);
    // String[] columns = {"ID", "Subject Status", "Gender", "Enrollment
    // Date",
    // "Study Events", "Actions" };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.setQuery(getBaseURL(), new HashMap());
    table.hideColumnLink(columnArray.size() - 1);
    // table.addLink("Enroll a new subject",
    // "javascript:leftnavExpand('addSubjectRowExpress');");
    table.setRows(allStudyRows);
    if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
        table.setKeywordFilter(filterKeyword);
    }
    table.computeDisplay();
    request.setAttribute("table", table);
    // request.setAttribute("subjects", subjects);
    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 = ssdao.findTheGreatestLabel() + 1;
        //request.setAttribute("label", new Integer(nextLabel).toString());
        request.setAttribute("label", resword.getString("id_generated_Save_Add"));
    }
    FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
    session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
    forwardPage(getJSP());
}