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

Example 36 with StudyDAO

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

the class AdminSystemServlet method processRequest.

// < ResourceBundleresword,resexception;
/*
     * (non-Javadoc)
     *
     * @see org.akaza.openclinica.control.core.SecureController#processRequest()
     */
@Override
protected void processRequest() throws Exception {
    // find last 5 modifed studies
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    ArrayList studies = (ArrayList) sdao.findAllByLimit(true);
    request.setAttribute("studies", studies);
    ArrayList allStudies = (ArrayList) sdao.findAll();
    request.setAttribute("allStudyNumber", new Integer(allStudies.size()));
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList users = (ArrayList) udao.findAllByLimit(true);
    request.setAttribute("users", users);
    ArrayList allUsers = (ArrayList) udao.findAll();
    request.setAttribute("allUserNumber", new Integer(allUsers.size()));
    SubjectDAO subdao = new SubjectDAO(sm.getDataSource());
    ArrayList subjects = (ArrayList) subdao.findAllByLimit(true);
    request.setAttribute("subjects", subjects);
    ArrayList allSubjects = (ArrayList) subdao.findAll();
    request.setAttribute("allSubjectNumber", new Integer(allSubjects.size()));
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    ArrayList crfs = (ArrayList) cdao.findAllByLimit(true);
    request.setAttribute("crfs", crfs);
    ArrayList allCrfs = (ArrayList) cdao.findAll();
    request.setAttribute("allCrfNumber", new Integer(allCrfs.size()));
    resetPanel();
    panel.setOrderedData(true);
    setToPanel(resword.getString("in_the_application"), "");
    if (allSubjects.size() > 0) {
        setToPanel(resword.getString("subjects"), new Integer(allSubjects.size()).toString());
    }
    if (allUsers.size() > 0) {
        setToPanel(resword.getString("users"), new Integer(allUsers.size()).toString());
    }
    if (allStudies.size() > 0) {
        setToPanel(resword.getString("studies"), new Integer(allStudies.size()).toString());
    }
    if (allCrfs.size() > 0) {
        setToPanel(resword.getString("CRFs"), new Integer(allCrfs.size()).toString());
    }
    panel.setStudyInfoShown(false);
    forwardPage(Page.ADMIN_SYSTEM);
}

Example 37 with StudyDAO

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

the class AuditLogStudyServlet method processRequest.

/*
     * (non-Javadoc) Assume that we get the user id automatically. We will jump
     * from the edit user page if the user is an admin, they can get to see the
     * users' log
     * 
     * @see org.akaza.openclinica.control.core.SecureController#processRequest()
     */
/*
     * (non-Javadoc) redo this servlet to run the audits per study subject for
     * the study; need to add a studyId param and then use the
     * StudySubjectDAO.findAllByStudyOrderByLabel() method to grab a lot of
     * study subject beans and then return them much like in
     * ViewStudySubjectAuditLogServet.process()
     * 
     * currentStudy instead of studyId?
     */
@Override
protected void processRequest() throws Exception {
    int studyId = currentStudy.getId();
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    AuditDAO adao = new AuditDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    StudyDAO studydao = new StudyDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    HashMap eventCRFAuditsHashMap = new HashMap();
    HashMap eventsHashMap = new HashMap();
    HashMap studySubjectAuditsHashMap = new HashMap();
    HashMap subjectHashMap = new HashMap();
    ArrayList studySubjects = subdao.findAllByStudyOrderByLabel(currentStudy);
    logger.info("found " + studySubjects.size() + " study subjects");
    request.setAttribute("studySubjects", studySubjects);
    for (int ss = 0; ss < studySubjects.size(); ss++) {
        ArrayList studySubjectAudits = new ArrayList();
        ArrayList eventCRFAudits = new ArrayList();
        StudySubjectBean studySubject = (StudySubjectBean) studySubjects.get(ss);
        // request.setAttribute("studySub"+ss, studySubject);
        SubjectBean subject = (SubjectBean) sdao.findByPK(studySubject.getSubjectId());
        subjectHashMap.put(new Integer(studySubject.getId()), subject);
        // logger.info("just set a subject with a status of
        // "+subject.getStatus().getName());
        // request.setAttribute("subject"+ss, subject);
        StudyBean study = (StudyBean) studydao.findByPK(studySubject.getStudyId());
        request.setAttribute("study", study);
        // hmm, repetitive work?
        // Show both study subject and subject audit events together
        // Study
        studySubjectAudits.addAll(adao.findStudySubjectAuditEvents(studySubject.getId()));
        // subject
        // value
        // changed
        // Global
        studySubjectAudits.addAll(adao.findSubjectAuditEvents(subject.getId()));
        // subject
        // value
        // changed
        studySubjectAuditsHashMap.put(new Integer(studySubject.getId()), studySubjectAudits);
        // request.setAttribute("studySubjectAudits"+ss,
        // studySubjectAudits);
        // Get the list of events
        ArrayList events = sedao.findAllByStudySubject(studySubject);
        for (int i = 0; i < events.size(); i++) {
            // Link study event definitions
            StudyEventBean studyEvent = (StudyEventBean) events.get(i);
            studyEvent.setStudyEventDefinition((StudyEventDefinitionBean) seddao.findByPK(studyEvent.getStudyEventDefinitionId()));
            // Link event CRFs
            studyEvent.setEventCRFs(ecdao.findAllByStudyEvent(studyEvent));
        }
        // for (int i = 0; i < events.size(); i++) {
        // StudyEventBean studyEvent = (StudyEventBean) events.get(i);
        // ArrayList eventCRFs = studyEvent.getEventCRFs();
        // for (int j = 0; j < eventCRFs.size(); j++) {
        // //Link CRF and CRF Versions
        // EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(j);
        // eventCRF.setCrfVersion((CRFVersionBean)
        // cvdao.findByPK(eventCRF.getCRFVersionId()));
        // eventCRF.setCrf((CRFBean)
        // cdao.findByVersionId(eventCRF.getCRFVersionId()));
        // //Get the event crf audits
        // eventCRFAudits.addAll(adao.findEventCRFAuditEvents(eventCRF.getId()));
        // }
        // }
        eventsHashMap.put(new Integer(studySubject.getId()), events);
    // request.setAttribute("events"+ss, events);
    // eventCRFAuditsHashMap.put(new Integer(studySubject.getId()),
    // eventCRFAudits);
    // request.setAttribute("eventCRFAudits"+ss, eventCRFAudits);
    }
    // request.setAttribute("eventCRFAudits", eventCRFAuditsHashMap);
    request.setAttribute("events", eventsHashMap);
    request.setAttribute("studySubjectAudits", studySubjectAuditsHashMap);
    request.setAttribute("study", currentStudy);
    request.setAttribute("subjects", subjectHashMap);
    // FormProcessor fp = new FormProcessor(request);
    // 
    // AuditEventDAO aeDAO = new AuditEventDAO(sm.getDataSource());
    // ArrayList al = aeDAO.findAllByStudyId(currentStudy.getId());
    // 
    // EntityBeanTable table = fp.getEntityBeanTable();
    // ArrayList allRows = AuditEventStudyRow.generateRowsFromBeans(al);
    // String[] columns = { "Date and Time", "Action", "Entity/Operation",
    // "Record ID", "Changes and Additions","Other Info" };
    // table.setColumns(new ArrayList(Arrays.asList(columns)));
    // table.hideColumnLink(4);
    // table.hideColumnLink(1);
    // table.hideColumnLink(5);
    // table.setQuery("AuditLogUser?userLogId="+userId, new HashMap());
    // String[] columns =
    // {resword.getString("date_and_time"),resword.getString("action_message"),
    // resword.getString("entity_operation"),
    // resword.getString("updated_by"),resword.getString("subject_unique_ID"),resword.getString("changes_and_additions"),
    // //"Other Info",
    // resword.getString("actions")};
    // table.setColumns(new ArrayList(Arrays.asList(columns)));
    // table.setAscendingSort(false);
    // table.hideColumnLink(1);
    // table.hideColumnLink(5);
    // table.hideColumnLink(6);
    // //table.hideColumnLink(7);
    // table.setQuery("AuditLogStudy", new HashMap());
    // table.setRows(allRows);
    // table.computeDisplay();
    // 
    // 
    // request.setAttribute("table", table);
    logger.warn("*** found servlet, sending to page ***");
    String pattn = "";
    String pattern2 = "";
    pattn = ResourceBundleProvider.getFormatBundle().getString("date_format_string");
    pattern2 = ResourceBundleProvider.getFormatBundle().getString("date_time_format_string");
    request.setAttribute("dateFormatPattern", pattn);
    request.setAttribute("dateTimeFormatPattern", pattern2);
    forwardPage(Page.AUDIT_LOG_STUDY);
}

Example 38 with StudyDAO

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

the class CreateJobImportServlet method setUpServlet.

/*
     * Find all the form items and re-populate as necessary
     */
private void setUpServlet() throws Exception {
    String directory = SQLInitServlet.getField("filePath") + DIR_PATH + File.separator;
    logger.debug("found directory: " + directory);
    // find all the form items and re-populate them if necessary
    FormProcessor fp2 = new FormProcessor(request);
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    // ArrayList studies = udao.findStudyByUser(ub.getName(), (ArrayList)
    // sdao.findAll());
    // request.setAttribute("studies", studies);
    // tbh, replacing the above with another version, 06/2009
    ArrayList<StudyBean> all = (ArrayList<StudyBean>) sdao.findAll();
    ArrayList<StudyBean> finalList = new ArrayList<StudyBean>();
    for (StudyBean sb : all) {
        if (!(sb.getParentStudyId() > 0)) {
            finalList.add(sb);
            // System.out.println("found study name: " + sb.getName());
            finalList.addAll(sdao.findAllByParent(sb.getId()));
        }
    }
    // System.out.println("found list of studies: " + finalList.toString());
    addEntityList("studies", finalList, respage.getString("a_user_cannot_be_created_no_study_as_active"), Page.ADMIN_SYSTEM);
    // YW >>
    // << tbh
    request.setAttribute("filePath", directory);
    // request.setAttribute("activeStudy", activeStudy);
    request.setAttribute(JOB_NAME, fp2.getString(JOB_NAME));
    request.setAttribute(JOB_DESC, fp2.getString(JOB_DESC));
    request.setAttribute(EMAIL, fp2.getString(EMAIL));
    request.setAttribute(HOURS, new Integer(fp2.getInt(HOURS)).toString());
    request.setAttribute(MINUTES, new Integer(fp2.getInt(MINUTES)).toString());
}

Example 39 with StudyDAO

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

the class SecureController method entityIncluded.

/**
 * <p>Check if an entity with passed entity id is included in studies of current user.</p>
 *
 * <p>Note: This method called AuditableEntityDAO.findByPKAndStudy which required
 * "The subclass must define findByPKAndStudyName before calling this
 * method. Otherwise an inactive AuditableEntityBean will be returned."</p>
 * @author ywang 10-18-2007
 * @param entityId int
 * @param userName String
 * @param adao AuditableEntityDAO
 * @param ds javax.sql.DataSource
 */
protected boolean entityIncluded(int entityId, String userName, AuditableEntityDAO adao, DataSource ds) {
    StudyDAO sdao = new StudyDAO(ds);
    ArrayList<StudyBean> studies = (ArrayList<StudyBean>) sdao.findAllByUserNotRemoved(userName);
    for (int i = 0; i < studies.size(); ++i) {
        if (adao.findByPKAndStudy(entityId, studies.get(i)).getId() > 0) {
            return true;
        }
        // visible to parent studies.
        if (studies.get(i).getParentStudyId() <= 0) {
            ArrayList<StudyBean> sites = (ArrayList<StudyBean>) sdao.findAllByParent(studies.get(i).getId());
            if (sites.size() > 0) {
                for (int j = 0; j < sites.size(); ++j) {
                    if (adao.findByPKAndStudy(entityId, sites.get(j)).getId() > 0) {
                        return true;
                    }
                }
            }
        }
    }
    return false;
}

Example 40 with StudyDAO

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

the class SecureController method getStudyGroupClassesByCurrentStudy.

public ArrayList getStudyGroupClassesByCurrentStudy() {
    StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
    StudyGroupClassDAO studyGroupClassDAO = new StudyGroupClassDAO(sm.getDataSource());
    StudyGroupDAO studyGroupDAO = new StudyGroupDAO(sm.getDataSource());
    int parentStudyId = currentStudy.getParentStudyId();
    ArrayList studyGroupClasses = new ArrayList();
    if (parentStudyId > 0) {
        StudyBean parentStudy = (StudyBean) studyDAO.findByPK(parentStudyId);
        studyGroupClasses = studyGroupClassDAO.findAllActiveByStudy(parentStudy);
    } else {
        parentStudyId = currentStudy.getId();
        studyGroupClasses = studyGroupClassDAO.findAllActiveByStudy(currentStudy);
    }
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        ArrayList groups = studyGroupDAO.findAllByGroupClass(sgc);
        sgc.setStudyGroups(groups);
    }
    return studyGroupClasses;
}