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

Example 1 with StudyConfigService

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

the class MetadataUnit method collectMetaDataVersion.

private void collectMetaDataVersion() {
    ArrayList<StudyEventDefinitionBean> sedBeansInStudy = (ArrayList<StudyEventDefinitionBean>) studyBase.getSedBeansInStudy();
    if (sedBeansInStudy == null || sedBeansInStudy.size() < 1) {
        logger.info("null, because there is no study event definition in this study.");
        return;
    }
    StudyBean study = studyBase.getStudy();
    StudyConfigService studyConfig = new StudyConfigService(this.ds);
    study = studyConfig.setParametersForStudy(study);
    MetaDataVersionBean metadata = this.odmStudy.getMetaDataVersion();
    metadata.setStudy(study);
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(this.ds);
    int parentId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
    StudyParameterValueBean spv = spvdao.findByHandleAndStudy(parentId, "discrepancyManagement");
    metadata.setSoftHard(spv.getValue().equalsIgnoreCase("true") ? "Hard" : "Soft");
    OdmExtractDAO oedao = new OdmExtractDAO(this.ds);
    int studyId = study.getId();
    int parentStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : studyId;
    if (this.getCategory() == 1 && study.isSite(study.getParentStudyId())) {
        // populate MetaDataVersion attributes
        if (dataset != null) {
            metadata.setOid(dataset.getODMMetaDataVersionOid() + "-" + study.getOid());
            metadata.setName(dataset.getODMMetaDataVersionName() + "-" + study.getOid());
            this.setParentMetaDataVersionOid(dataset.getODMMetaDataVersionOid());
        }
        if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
            metadata.setOid("v1.0.0" + "-" + study.getOid());
            this.setParentMetaDataVersionOid("v1.0.0");
        }
        if (metadata.getName() == null || metadata.getName().length() <= 0) {
            metadata.setName("MetaDataVersion_v1.0.0" + "-" + study.getOid());
        }
        // populate Include
        this.collectIncludeFromParentInSameFile();
        // populate protocol
        oedao.getUpdatedSiteMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
    } else {
        if (dataset != null) {
            metadata.setOid(dataset.getODMMetaDataVersionOid());
            metadata.setName(dataset.getODMMetaDataVersionName());
        }
        if (metadata.getOid() == null || metadata.getOid().length() <= 0) {
            metadata.setOid("v1.0.0");
        }
        if (metadata.getName() == null || metadata.getName().length() <= 0) {
            metadata.setName("MetaDataVersion_v1.0.0");
        }
        // populate Include
        String psOid = new String();
        String pmOid = new String();
        if (dataset != null) {
            psOid = dataset.getODMPriorStudyOid();
            pmOid = dataset.getODMPriorMetaDataVersionOid();
        }
        if (pmOid != null && pmOid.length() > 0) {
            MetaDataVersionIncludeBean ib = metadata.getInclude();
            ib.setMetaDataVersionOID(pmOid);
            if (psOid != null && psOid.length() > 0) {
                ib.setStudyOID(psOid);
            } else {
                ib.setStudyOID(study.getOid());
            }
        }
        // populate protocol
        // Set<Integer> nullCodeSet = oedao.getMetadata(parentStudyId,
        // studyId,
        // metadata, this.getODMBean().getODMVersion());
        // studyBase.setNullClSet(nullCodeSet);
        oedao.getMetadata(parentStudyId, studyId, metadata, this.odmBean.getODMVersion());
        metadata.setRuleSetRules(getRuleSetRuleDao().findByRuleSetStudyIdAndStatusAvail(parentStudyId));
    }
}

Example 2 with StudyConfigService

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

the class InitUpdateStudyServlet method processRequest.

/**
 * Processes the request
 */
@Override
public void processRequest() throws Exception {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    String idString = request.getParameter("id");
    logger.info("study id:" + idString);
    if (StringUtil.isBlank(idString)) {
        addPageMessage(respage.getString("please_choose_a_study_to_edit"));
        forwardPage(Page.STUDY_LIST_SERVLET);
    } else {
        int studyId = Integer.valueOf(idString.trim()).intValue();
        StudyBean study = (StudyBean) sdao.findByPK(studyId);
        StudyConfigService scs = new StudyConfigService(sm.getDataSource());
        study = scs.setParametersForStudy(study);
        logger.info("date created:" + study.getCreatedDate());
        logger.info("protocol Type:" + study.getProtocolType());
        session.setAttribute("newStudy", study);
        request.setAttribute("facRecruitStatusMap", CreateStudyServlet.facRecruitStatusMap);
        request.setAttribute("statuses", Status.toActiveArrayList());
        resetPanel();
        panel.setStudyInfoShown(false);
        panel.setOrderedData(true);
        panel.setExtractData(false);
        panel.setSubmitDataModule(false);
        panel.setCreateDataset(false);
        panel.setIconInfoShown(true);
        panel.setManageSubject(false);
        forwardPage(Page.UPDATE_STUDY1);
    }
}

Example 3 with StudyConfigService

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

the class MetadataCollectorResource method populateStudyBean.

private StudyBean populateStudyBean(StudyBean studyBean) {
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(this.dataSource);
    @SuppressWarnings("rawtypes") ArrayList studyParameters = spvdao.findParamConfigByStudy(studyBean);
    studyBean.setStudyParameters(studyParameters);
    StudyConfigService scs = new StudyConfigService(this.dataSource);
    if (studyBean.getParentStudyId() <= 0) {
        // top study
        studyBean = scs.setParametersForStudy(studyBean);
    } else {
        // YW <<
        studyBean.setParentStudyName(((StudyBean) getStudyDao().findByPK(studyBean.getParentStudyId())).getName());
        // YW >>
        studyBean = scs.setParametersForSite(studyBean);
    }
    return studyBean;
}

Example 4 with StudyConfigService

use of org.akaza.openclinica.dao.service.StudyConfigService 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());
            // 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 5 with StudyConfigService

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

the class ViewStudyServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int studyId = fp.getInt("id");
    if (studyId == 0) {
        addPageMessage(respage.getString("please_choose_a_study_to_view"));
        forwardPage(Page.STUDY_LIST_SERVLET);
    } else {
        if (currentStudy.getId() != studyId && currentStudy.getParentStudyId() != studyId) {
            checkRoleByUserAndStudy(ub, studyId, 0);
        }
        String viewFullRecords = fp.getString("viewFull");
        StudyBean study = (StudyBean) sdao.findByPK(studyId);
        StudyConfigService scs = new StudyConfigService(sm.getDataSource());
        study = scs.setParametersForStudy(study);
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        String randomizationStatusInOC = spvdao.findByHandleAndStudy(study.getId(), "randomization").getValue();
        String participantStatusInOC = spvdao.findByHandleAndStudy(study.getId(), "participantPortal").getValue();
        if (participantStatusInOC == "")
            participantStatusInOC = "disabled";
        if (randomizationStatusInOC == "")
            randomizationStatusInOC = "disabled";
        RandomizationRegistrar randomizationRegistrar = new RandomizationRegistrar();
        SeRandomizationDTO seRandomizationDTO = randomizationRegistrar.getCachedRandomizationDTOObject(study.getOid(), false);
        if (seRandomizationDTO != null && seRandomizationDTO.getStatus().equalsIgnoreCase("ACTIVE") && randomizationStatusInOC.equalsIgnoreCase("enabled")) {
            study.getStudyParameterConfig().setRandomization("enabled");
        } else {
            study.getStudyParameterConfig().setRandomization("disabled");
        }
        ;
        ParticipantPortalRegistrar participantPortalRegistrar = new ParticipantPortalRegistrar();
        String pStatus = participantPortalRegistrar.getCachedRegistrationStatus(study.getOid(), session);
        if (participantPortalRegistrar != null && pStatus.equalsIgnoreCase("ACTIVE") && participantStatusInOC.equalsIgnoreCase("enabled")) {
            study.getStudyParameterConfig().setParticipantPortal("enabled");
        } else {
            study.getStudyParameterConfig().setParticipantPortal("disabled");
        }
        ;
        request.setAttribute("studyToView", study);
        if ("yes".equalsIgnoreCase(viewFullRecords)) {
            UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
            StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
            ArrayList sites = new ArrayList();
            ArrayList userRoles = new ArrayList();
            ArrayList subjects = new ArrayList();
            if (this.currentStudy.getParentStudyId() > 0 && this.currentRole.getRole().getId() > 3) {
                sites.add(this.currentStudy);
                userRoles = udao.findAllUsersByStudy(currentStudy.getId());
                subjects = ssdao.findAllByStudy(currentStudy);
            } else {
                sites = (ArrayList) sdao.findAllByParent(studyId);
                userRoles = udao.findAllUsersByStudy(studyId);
                subjects = ssdao.findAllByStudy(study);
            }
            // find all subjects in the study, include ones in sites
            StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
            EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
            // StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            // ArrayList displayStudySubs = new ArrayList();
            // for (int i = 0; i < subjects.size(); i++) {
            // StudySubjectBean studySub = (StudySubjectBean) subjects.get(i);
            // // find all events
            // ArrayList events = sedao.findAllByStudySubject(studySub);
            // 
            // // find all eventcrfs for each event
            // EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            // 
            // DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
            // dssb.setStudyEvents(events);
            // dssb.setStudySubject(studySub);
            // displayStudySubs.add(dssb);
            // }
            // find all events in the study, include ones in sites
            ArrayList definitions = seddao.findAllByStudy(study);
            for (int i = 0; i < definitions.size(); i++) {
                StudyEventDefinitionBean def = (StudyEventDefinitionBean) definitions.get(i);
                ArrayList crfs = (ArrayList) edcdao.findAllActiveParentsByEventDefinitionId(def.getId());
                def.setCrfNum(crfs.size());
            }
            String moduleManager = CoreResources.getField("moduleManager");
            request.setAttribute("moduleManager", moduleManager);
            String portalURL = CoreResources.getField("portalURL");
            request.setAttribute("portalURL", portalURL);
            request.setAttribute("config", study);
            request.setAttribute("sitesToView", sites);
            request.setAttribute("siteNum", sites.size() + "");
            request.setAttribute("userRolesToView", userRoles);
            request.setAttribute("userNum", userRoles.size() + "");
            // request.setAttribute("subjectsToView", displayStudySubs);
            // request.setAttribute("subjectNum", subjects.size() + "");
            request.setAttribute("definitionsToView", definitions);
            request.setAttribute("defNum", definitions.size() + "");
            forwardPage(Page.VIEW_FULL_STUDY);
        } else {
            forwardPage(Page.VIEW_STUDY);
        }
    }
}