Examples with StudyDAO org.akaza.openclinica.dao.managestudy.StudyDAO used on opensource projects

Example 56 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO 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 57 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class CreateSubStudyServlet method initDefinitions.

private ArrayList<StudyEventDefinitionBean> initDefinitions(StudyBean site) throws MalformedURLException {
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
    StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    StudyBean parentStudy = (StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId());
    seds = sedDao.findAllByStudy(parentStudy);
    int start = 0;
    for (StudyEventDefinitionBean sed : seds) {
        String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
        if (participateFormStatus.equals("enabled"))
            baseUrl();
        request.setAttribute("participateFormStatus", participateFormStatus);
        int defId = sed.getId();
        ArrayList<EventDefinitionCRFBean> edcs = (ArrayList<EventDefinitionCRFBean>) edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(defId, site.getId(), parentStudy.getId());
        ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
        // sed.setCrfNum(edcs.size());
        for (EventDefinitionCRFBean edcBean : edcs) {
            CRFBean cBean = (CRFBean) cdao.findByPK(edcBean.getCrfId());
            String crfPath = sed.getOid() + "." + cBean.getOid();
            edcBean.setOffline(getEventDefinitionCrfTagService().getEventDefnCrfOfflineStatus(2, crfPath, true));
            int edcStatusId = edcBean.getStatus().getId();
            CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId());
            int crfStatusId = crf.getStatusId();
            if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) {
            } else {
                ArrayList<CRFVersionBean> versions = (ArrayList<CRFVersionBean>) cvdao.findAllActiveByCRF(edcBean.getCrfId());
                edcBean.setVersions(versions);
                edcBean.setCrfName(crf.getName());
                CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(edcBean.getDefaultVersionId());
                edcBean.setDefaultVersionName(defaultVersion.getName());
                edcBean.setSubmissionUrl("");
                /*                    EventDefinitionCRFBean eBean = (EventDefinitionCRFBean) edcdao.findByPK(edcBean.getId());
                    if (eBean.isActive()){ 
                    	edcBean.setSubmissionUrl(eBean.getSubmissionUrl());
                    }else{
                        edcBean.setSubmissionUrl("");
                    }
*/
                String sversionIds = edcBean.getSelectedVersionIds();
                ArrayList<Integer> idList = new ArrayList<Integer>();
                if (sversionIds.length() > 0) {
                    String[] ids = sversionIds.split("\\,");
                    for (String id : ids) {
                        idList.add(Integer.valueOf(id));
                    }
                }
                edcBean.setSelectedVersionIdList(idList);
                defCrfs.add(edcBean);
                ++start;
            }
        }
        logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size());
        sed.setCrfs(defCrfs);
        sed.setCrfNum(defCrfs.size());
    }
    return seds;
}

Example 58 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class RequestStudyServlet method confirm.

/**
 * @param request
 * @param response
 */
private void confirm() throws Exception {
    Validator v = new Validator(request);
    v.addValidation("studyId", Validator.IS_AN_INTEGER);
    v.addValidation("studyRoleId", Validator.IS_VALID_TERM, TermType.ROLE);
    HashMap errors = v.validate();
    FormProcessor fp = new FormProcessor(request);
    StudyUserRoleBean newRole = new StudyUserRoleBean();
    if (fp.getInt("studyRoleId") > 0) {
        newRole.setRole(Role.get(fp.getInt("studyRoleId")));
    }
    newRole.setStudyId(fp.getInt("studyId"));
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    StudyBean studyRequested = (StudyBean) sdao.findByPK(newRole.getStudyId());
    newRole.setStudyName(studyRequested.getName());
    session.setAttribute("newRole", newRole);
    if (!errors.isEmpty()) {
        logger.info("after processing form,error is not empty");
        request.setAttribute("formMessages", errors);
        forwardPage(Page.REQUEST_STUDY);
    } else {
        logger.info("after processing form,no errors");
        forwardPage(Page.REQUEST_STUDY_CONFIRM);
    }
}

Example 59 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class PrintAllEventCRFServlet method processRequest.

@Override
public void processRequest(HttpServletRequest request, HttpServletResponse response) throws Exception {
    FormProcessor fp = new FormProcessor(request);
    SessionManager sm = (SessionManager) request.getSession().getAttribute("sm");
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN);
    ArrayList<SectionBean> allSectionBeans;
    // The PrintDataEntry servlet handles this parameter
    boolean isSubmitted = false;
    StudyEventDefinitionDAO sedao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    StudyDAO studyDao = new StudyDAO(sm.getDataSource());
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
    seds = sedao.findAllByStudy(currentStudy);
    // ArrayList eventDefinitionCRFs = (ArrayList) edao.findAllByStudy(site);
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    ArrayList<EventDefinitionCRFBean> edcs = new ArrayList();
    for (StudyEventDefinitionBean sed : seds) {
        int defId = sed.getId();
        edcs.addAll(edcdao.findAllByDefinition(currentStudy, defId));
    }
    Map eventDefinitionDefaultVersions = new LinkedHashMap();
    for (int i = 0; i < edcs.size(); i++) {
        EventDefinitionCRFBean edc = edcs.get(i);
        ArrayList versions = (ArrayList) cvdao.findAllByCRF(edc.getCrfId());
        edc.setVersions(versions);
        CRFBean crf = (CRFBean) cdao.findByPK(edc.getCrfId());
        // edc.setCrfLabel(crf.getLabel());
        edc.setCrfName(crf.getName());
        // to show/hide edit action on jsp page
        if (crf.getStatus().equals(Status.AVAILABLE)) {
            edc.setOwner(crf.getOwner());
        }
        CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(edc.getDefaultVersionId());
        StudyEventDefinitionBean studyEventDefinitionBean = (StudyEventDefinitionBean) sedao.findByPK(edc.getStudyEventDefinitionId());
        edc.setDefaultVersionName(defaultVersion.getName());
        if (defaultVersion.getStatus().isAvailable()) {
            List list = (ArrayList) eventDefinitionDefaultVersions.get(studyEventDefinitionBean);
            if (list == null)
                list = new ArrayList();
            list.add(defaultVersion);
            eventDefinitionDefaultVersions.put(studyEventDefinitionBean, list);
        }
    }
    // Whether IE6 or IE7 is involved
    String isIE = fp.getString("ie");
    if ("y".equalsIgnoreCase(isIE)) {
        request.setAttribute("isInternetExplorer", "true");
    }
    SectionDAO sdao = new SectionDAO(sm.getDataSource());
    CRFVersionDAO crfVersionDAO = new CRFVersionDAO(sm.getDataSource());
    CRFDAO crfDao = new CRFDAO(sm.getDataSource());
    Map sedCrfBeans = null;
    for (Iterator it = eventDefinitionDefaultVersions.keySet().iterator(); it.hasNext(); ) {
        if (sedCrfBeans == null)
            sedCrfBeans = new LinkedHashMap();
        StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) it.next();
        List crfVersions = (ArrayList) eventDefinitionDefaultVersions.get(sedBean);
        for (Iterator crfIt = crfVersions.iterator(); crfIt.hasNext(); ) {
            CRFVersionBean crfVersionBean = (CRFVersionBean) crfIt.next();
            allSectionBeans = new ArrayList<SectionBean>();
            ArrayList sectionBeans = new ArrayList();
            ItemGroupDAO itemGroupDao = new ItemGroupDAO(sm.getDataSource());
            // Find truely grouped tables, not groups with a name of 'Ungrouped'
            List<ItemGroupBean> itemGroupBeans = itemGroupDao.findOnlyGroupsByCRFVersionID(crfVersionBean.getId());
            CRFBean crfBean = crfDao.findByVersionId(crfVersionBean.getId());
            if (itemGroupBeans.size() > 0) {
                // get a DisplaySectionBean for each section of the CRF, sort
                // them, then
                // dispatch the request to a print JSP. The constructor for this
                // handler takes
                // a boolean value depending on whether data is involved or not
                // ('false' in terms of this
                // servlet; see PrintDataEntryServlet).
                DisplaySectionBeanHandler handler = new DisplaySectionBeanHandler(false, getDataSource(), getServletContext());
                handler.setCrfVersionId(crfVersionBean.getId());
                // handler.setEventCRFId(eventCRFId);
                List<DisplaySectionBean> displaySectionBeans = handler.getDisplaySectionBeans();
                request.setAttribute("listOfDisplaySectionBeans", displaySectionBeans);
                // Make available the CRF names and versions for
                // the web page's header
                CRFVersionBean crfverBean = (CRFVersionBean) crfVersionDAO.findByPK(crfVersionBean.getId());
                request.setAttribute("crfVersionBean", crfverBean);
                request.setAttribute("crfBean", crfBean);
                // Set an attribute signaling that data is not involved
                request.setAttribute("dataInvolved", "false");
                PrintCRFBean printCrfBean = new PrintCRFBean();
                printCrfBean.setDisplaySectionBeans(displaySectionBeans);
                printCrfBean.setCrfVersionBean(crfVersionBean);
                printCrfBean.setCrfBean(crfBean);
                printCrfBean.setEventCrfBean(ecb);
                printCrfBean.setGrouped(true);
                List list = (ArrayList) sedCrfBeans.get(sedBean);
                if (list == null)
                    list = new ArrayList();
                list.add(printCrfBean);
                sedCrfBeans.put(sedBean, list);
                continue;
            }
            ecb = new EventCRFBean();
            ecb.setCRFVersionId(crfVersionBean.getId());
            CRFVersionBean version = (CRFVersionBean) crfVersionDAO.findByPK(crfVersionBean.getId());
            ArrayList sects = (ArrayList) sdao.findByVersionId(version.getId());
            for (int i = 0; i < sects.size(); i++) {
                sb = (SectionBean) sects.get(i);
                // super.sb = sb;
                int sectId = sb.getId();
                if (sectId > 0) {
                    allSectionBeans.add((SectionBean) sdao.findByPK(sectId));
                }
            }
            request.setAttribute(INPUT_EVENT_CRF, ecb);
            request.setAttribute(SECTION_BEAN, sb);
            request.setAttribute(ALL_SECTION_BEANS, allSectionBeans);
            sectionBeans = super.getAllDisplayBeans(request);
            DisplaySectionBean dsb = super.getDisplayBean(false, false, request, isSubmitted);
            PrintCRFBean printCrfBean = new PrintCRFBean();
            printCrfBean.setAllSections(sectionBeans);
            printCrfBean.setDisplaySectionBean(dsb);
            printCrfBean.setEventCrfBean(ecb);
            printCrfBean.setCrfVersionBean(crfVersionBean);
            printCrfBean.setCrfBean(crfBean);
            printCrfBean.setGrouped(false);
            List list = (ArrayList) sedCrfBeans.get(sedBean);
            if (list == null)
                list = new ArrayList();
            list.add(printCrfBean);
            sedCrfBeans.put(sedBean, list);
        }
    }
    request.setAttribute("sedCrfBeans", sedCrfBeans);
    request.setAttribute("studyName", currentStudy.getName());
    forwardPage(Page.VIEW_ALL_DEFAULT_CRF_VERSIONS_PRINT, request, response);
}

Example 60 with StudyDAO

use of org.akaza.openclinica.dao.managestudy.StudyDAO in project OpenClinica by OpenClinica.

the class PrintCRFByIdServlet method processRequest.

/*
     * (non-Javadoc)
     * @see org.akaza.openclinica.control.managestudy.ViewSectionDataEntryServlet#processRequest()
     */
@Override
public void processRequest(HttpServletRequest request, HttpServletResponse response) throws Exception {
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    StudyDAO studyDao = new StudyDAO(getDataSource());
    currentStudy = (StudyBean) studyDao.findByPK(1);
    CRFVersionDAO crfVersionDao = new CRFVersionDAO(getDataSource());
    if (request.getParameter("id") == null) {
        forwardPage(Page.LOGIN, request, response);
    }
    CRFVersionBean crfVersion = crfVersionDao.findByOid(request.getParameter("id"));
    request.setAttribute("study", currentStudy);
    if (crfVersion != null) {
        request.setAttribute("id", String.valueOf(crfVersion.getId()));
        super.processRequest(request, response);
    } else {
        forwardPage(Page.LOGIN, request, response);
    }
}