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

Example 26 with StudyParameterValueDAO

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

the class OdmExtractDAO method setStudyParemeterConfig.

protected void setStudyParemeterConfig(StudyBean study) {
    StudyParameterValueBean param = new StudyParameterValueDAO(this.ds).findByHandleAndStudy(study.getId(), "collectDob");
    study.getStudyParameterConfig().setCollectDob(param.getValue());
}

Example 27 with StudyParameterValueDAO

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

the class ViewStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String from = fp.getString("from");
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    // if coming from change crf version -> display message
    String crfVersionChangeMsg = fp.getString("isFromCRFVersionChange");
    if (crfVersionChangeMsg != null && !crfVersionChangeMsg.equals("")) {
        addPageMessage(crfVersionChangeMsg);
    }
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
    } else {
        if (!StringUtil.isBlank(from)) {
            // form ListSubject or
            request.setAttribute("from", from);
        // ListStudySubject
        } else {
            request.setAttribute("from", "");
        }
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        request.setAttribute("studySub", studySub);
        request.setAttribute("originatingPage", URLEncoder.encode("ViewStudySubject?id=" + studySub.getId(), "UTF-8"));
        int studyId = studySub.getStudyId();
        int subjectId = studySub.getSubjectId();
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studyId);
        // Check if this StudySubject would be accessed from the Current Study
        if (studySub.getStudyId() != currentStudy.getId()) {
            if (currentStudy.getParentStudyId() > 0) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            } else {
                // The SubjectStudy is not belong to currentstudy and current study is not a site.
                Collection sites = studydao.findOlnySiteIdsByStudy(currentStudy);
                if (!sites.contains(study.getId())) {
                    addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                    forwardPage(Page.MENU_SERVLET);
                    return;
                }
            }
        }
        // If the study subject derives from a site, and is being viewed
        // from a parent study,
        // then the study IDs will be different. However, since each note is
        // saved with the specific
        // study ID, then its study ID may be different than the study
        // subject's ID.
        boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId();
        boolean isParentStudy = study.getParentStudyId() < 1;
        // Get any disc notes for this subject : studySubId
        DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource());
        List<DiscrepancyNoteBean> allNotesforSubject = new ArrayList<DiscrepancyNoteBean>();
        // These methods return only parent disc notes
        if (subjectStudyIsCurrentStudy && isParentStudy) {
            allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudyAndId(study, subjectId);
            allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudyAndId(study, studySubId));
        } else {
            if (!isParentStudy) {
                StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId());
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(stParent, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(stParent, study, studySubId));
            } else {
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(currentStudy, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(currentStudy, study, studySubId));
            }
        }
        if (!allNotesforSubject.isEmpty()) {
            setRequestAttributesForNotes(allNotesforSubject);
        }
        SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
        if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
            Date dob = subject.getDateOfBirth();
            if (dob != null) {
                Calendar cal = Calendar.getInstance();
                cal.setTime(dob);
                int year = cal.get(Calendar.YEAR);
                request.setAttribute("yearOfBirth", new Integer(year));
            } else {
                request.setAttribute("yearOfBirth", "");
            }
        }
        request.setAttribute("subject", subject);
        /*
             * StudyDAO studydao = new StudyDAO(sm.getDataSource()); StudyBean
             * study = (StudyBean) studydao.findByPK(studyId);
             */
        // YW 11-26-2007 <<
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
        // YW >>
        request.setAttribute("subjectStudy", study);
        if (study.getParentStudyId() > 0) {
            // this is a site,find parent
            StudyBean parentStudy2 = (StudyBean) studydao.findByPK(study.getParentStudyId());
            request.setAttribute("parentStudy", parentStudy2);
        } else {
            request.setAttribute("parentStudy", new StudyBean());
        }
        ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId);
        request.setAttribute("children", children);
        // find study events
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
        StudySubjectService studySubjectService = (StudySubjectService) WebApplicationContextUtils.getWebApplicationContext(getServletContext()).getBean("studySubjectService");
        List<DisplayStudyEventBean> displayEvents = studySubjectService.getDisplayStudyEventsForStudySubject(studySub, ub, currentRole);
        for (int i = 0; i < displayEvents.size(); i++) {
            DisplayStudyEventBean decb = displayEvents.get(i);
            if (!(currentRole.isDirector() || currentRole.isCoordinator()) && decb.getStudyEvent().getSubjectEventStatus().isLocked()) {
                decb.getStudyEvent().setEditable(false);
            }
        }
        if (currentStudy.getParentStudyId() > 0) {
            HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
            for (DisplayStudyEventBean displayStudyEventBean : displayEvents) {
                hideCRFManager.removeHiddenEventCRF(displayStudyEventBean);
            }
        }
        EntityBeanTable table = fp.getEntityBeanTable();
        // sort by start
        table.setSortingIfNotExplicitlySet(1, false);
        // date, desc
        ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents);
        String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("location"), resword.getString("status"), resword.getString("actions"), resword.getString("CRFs_atrib") };
        table.setColumns(new ArrayList(Arrays.asList(columns)));
        table.hideColumnLink(4);
        table.hideColumnLink(5);
        if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) {
            if (currentStudy.getStatus().isAvailable() && !currentRole.getRole().equals(Role.MONITOR)) {
                table.addLink(resword.getString("add_new_event"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId());
            }
        }
        HashMap args = new HashMap();
        args.put("id", new Integer(studySubId).toString());
        table.setQuery("ViewStudySubject", args);
        table.setRows(allEventRows);
        table.computeDisplay();
        request.setAttribute("table", table);
        SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
        ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId);
        request.setAttribute("groups", groupMaps);
        // find audit log for events
        AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
        ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
        // logger.warning("^^^ retrieved logs");
        UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
        ArrayList eventLogs = new ArrayList();
        // logger.warning("^^^ starting to iterate");
        for (int i = 0; i < logs.size(); i++) {
            AuditEventBean avb = (AuditEventBean) logs.get(i);
            StudyEventAuditBean sea = new StudyEventAuditBean();
            sea.setAuditEvent(avb);
            StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId());
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            sea.setDefinition(sed);
            String old = avb.getOldValue().trim();
            try {
                if (!StringUtil.isBlank(old)) {
                    SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue());
                    sea.setOldSubjectEventStatus(oldStatus);
                }
                String newValue = avb.getNewValue().trim();
                if (!StringUtil.isBlank(newValue)) {
                    SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue());
                    sea.setNewSubjectEventStatus(newStatus);
                }
            } catch (NumberFormatException e) {
                e.printStackTrace();
            }
            UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
            sea.setUpdater(updater);
            eventLogs.add(sea);
        }
        request.setAttribute("eventLogs", eventLogs);
        forwardPage(Page.VIEW_STUDY_SUBJECT);
    }
}

Example 28 with StudyParameterValueDAO

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

the class ViewSiteServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    String idString = "";
    if (request.getAttribute("siteId") == null) {
        idString = request.getParameter("id");
    } else {
        idString = request.getAttribute("siteId").toString();
    }
    logger.info("site id:" + idString);
    if (StringUtil.isBlank(idString)) {
        addPageMessage(respage.getString("please_choose_a_site_to_edit"));
        forwardPage(Page.SITE_LIST_SERVLET);
    } else {
        int siteId = Integer.valueOf(idString.trim()).intValue();
        StudyBean study = (StudyBean) sdao.findByPK(siteId);
        checkRoleByUserAndStudy(ub, study.getParentStudyId(), study.getId());
        // if (currentStudy.getId() != study.getId()) {
        ArrayList configs = new ArrayList();
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        configs = spvdao.findParamConfigByStudy(study);
        study.setStudyParameters(configs);
        // }
        String parentStudyName = "";
        if (study.getParentStudyId() > 0) {
            StudyBean parent = (StudyBean) sdao.findByPK(study.getParentStudyId());
            parentStudyName = parent.getName();
        }
        request.setAttribute("parentName", parentStudyName);
        request.setAttribute("siteToView", study);
        request.setAttribute("idToSort", request.getAttribute("idToSort"));
        viewSiteEventDefinitions(study);
        forwardPage(Page.VIEW_SITE);
    }
}

Example 29 with StudyParameterValueDAO

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

the class ViewSiteServlet method viewSiteEventDefinitions.

private void viewSiteEventDefinitions(StudyBean siteToView) throws MalformedURLException {
    int siteId = siteToView.getId();
    ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
    StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    FormLayoutDAO fldao = new FormLayoutDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    seds = sedDao.findAllByStudy(siteToView);
    int start = 0;
    for (StudyEventDefinitionBean sed : seds) {
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
        request.setAttribute("participateFormStatus", participateFormStatus);
        if (participateFormStatus.equals("enabled"))
            baseUrl();
        request.setAttribute("participateFormStatus", participateFormStatus);
        int defId = sed.getId();
        ArrayList<EventDefinitionCRFBean> edcs = (ArrayList<EventDefinitionCRFBean>) edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(defId, siteId, siteToView.getParentStudyId());
        ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
        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();
            ArrayList<FormLayoutBean> versions = (ArrayList<FormLayoutBean>) fldao.findAllActiveByCRF(edcBean.getCrfId());
            edcBean.setVersions(versions);
            edcBean.setCrfName(crf.getName());
            FormLayoutBean defaultVersion = (FormLayoutBean) fldao.findByPK(edcBean.getDefaultVersionId());
            edcBean.setDefaultVersionName(defaultVersion.getName());
            String sversionIds = edcBean.getSelectedVersionIds();
            ArrayList<Integer> idList = new ArrayList<Integer>();
            String idNames = "";
            if (sversionIds.length() > 0) {
                String[] ids = sversionIds.split("\\,");
                for (String id : ids) {
                    idList.add(Integer.valueOf(id));
                    for (FormLayoutBean v : versions) {
                        if (v.getId() == Integer.valueOf(id)) {
                            idNames += v.getName() + ",";
                            break;
                        }
                    }
                }
                idNames = idNames.substring(0, idNames.length() - 1);
            }
            if (edcBean.getParentId() < 1) {
                edcBean.setSubmissionUrl("");
            }
            edcBean.setSelectedVersionIdList(idList);
            edcBean.setSelectedVersionNames(idNames);
            defCrfs.add(edcBean);
            ++start;
        }
        sed.setCrfs(defCrfs);
        sed.setCrfNum(defCrfs.size());
    }
    request.setAttribute("definitions", seds);
    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);
}

Example 30 with StudyParameterValueDAO

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

the class ViewEventDefinitionReadOnlyServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyEventDefinitionDAO sdao = new StudyEventDefinitionDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int defId = fp.getInt(EVENT_ID, true);
    String eventOid = fp.getString(EVENT_OID);
    if (defId == 0 && eventOid == null) {
        addPageMessage(respage.getString("please_choose_a_definition_to_view"));
        forwardPage(Page.LIST_DEFINITION_SERVLET);
        return;
    }
    // definition id
    StudyEventDefinitionBean sed = defId > 0 ? (StudyEventDefinitionBean) sdao.findByPK(defId) : (StudyEventDefinitionBean) sdao.findByOid(eventOid);
    EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
    ArrayList eventDefinitionCRFs = (ArrayList) edao.findAllByDefinition(this.currentStudy, sed.getId());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.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());
        }
        CRFBean cBean = (CRFBean) cdao.findByPK(edc.getCrfId());
        String crfPath = sed.getOid() + "." + cBean.getOid();
        edc.setOffline(getEventDefinitionCrfTagService().getEventDefnCrfOfflineStatus(2, crfPath, true));
        CRFVersionBean defaultVersion = (CRFVersionBean) cvdao.findByPK(edc.getDefaultVersionId());
        edc.setDefaultVersionName(defaultVersion.getName());
    }
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    String participateFormStatus = spvdao.findByHandleAndStudy(sed.getStudyId(), "participantPortal").getValue();
    request.setAttribute("participateFormStatus", participateFormStatus);
    request.setAttribute("definition", sed);
    request.setAttribute("eventDefinitionCRFs", eventDefinitionCRFs);
    request.setAttribute("defSize", new Integer(eventDefinitionCRFs.size()));
    // ArrayList(tm.values()));
    if (defId > 0) {
        forwardPage(Page.VIEW_EVENT_DEFINITION_READONLY);
    } else {
        forwardPage(Page.VIEW_EVENT_DEFINITION_NOSIDEBAR);
    }
}