Examples with StudySubjectBean org.akaza.openclinica.bean.managestudy.StudySubjectBean used on opensource projects

Example 1 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class SignStudySubjectServlet method getDisplayStudyEventsForStudySubject.

public static ArrayList getDisplayStudyEventsForStudySubject(StudyBean study, StudySubjectBean studySub, DataSource ds, UserAccountBean ub, StudyUserRoleBean currentRole) {
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
    StudyEventDAO sedao = new StudyEventDAO(ds);
    EventCRFDAO ecdao = new EventCRFDAO(ds);
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds);
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    ArrayList events = sedao.findAllByStudySubject(studySub);
    ArrayList displayEvents = new ArrayList();
    for (int i = 0; i < events.size(); i++) {
        StudyEventBean event = (StudyEventBean) events.get(i);
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(event.getStudyEventDefinitionId());
        event.setStudyEventDefinition(sed);
        // find all active crfs in the definition
        ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, sed.getId());
        ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
        // construct info needed on view study event page
        DisplayStudyEventBean de = new DisplayStudyEventBean();
        de.setStudyEvent(event);
        de.setDisplayEventCRFs(getDisplayEventCRFs(study, ds, eventCRFs, ub, currentRole, event.getSubjectEventStatus()));
        ArrayList al = getUncompletedCRFs(ds, eventDefinitionCRFs, eventCRFs, event.getSubjectEventStatus());
        populateUncompletedCRFsWithCRFAndVersions(ds, al);
        de.setUncompletedCRFs(al);
        StudySubjectBean studySubject = (StudySubjectBean) ssdao.findByPK(event.getStudySubjectId());
        de.setMaximumSampleOrdinal(sedao.getMaxSampleOrdinal(sed, studySubject));
        displayEvents.add(de);
    // event.setEventCRFs(createAllEventCRFs(eventCRFs,
    // eventDefinitionCRFs));
    }
    return displayEvents;
}

Example 2 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class SignStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    String action = fp.getString("action");
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
        return;
    }
    StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
    if (!permitSign(studySub, sm.getDataSource())) {
        addPageMessage(respage.getString("subject_event_cannot_signed"));
        // forwardPage(Page.SUBMIT_DATA_SERVLET);
        forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
        // >> changed tbh, 06/2009
        return;
    }
    if (action.equalsIgnoreCase("confirm")) {
        String username = request.getParameter("j_user");
        String password = request.getParameter("j_pass");
        SecurityManager securityManager = ((SecurityManager) SpringServletAccess.getApplicationContext(context).getBean("securityManager"));
        // String encodedUserPass =
        // org.akaza.openclinica.core.SecurityManager
        // .getInstance().encrytPassword(password);
        UserAccountBean ub = (UserAccountBean) session.getAttribute("userBean");
        if (securityManager.verifyPassword(password, getUserDetails()) && ub.getName().equals(username)) {
            if (signSubjectEvents(studySub, sm.getDataSource(), ub)) {
                // Making the StudySubject signed as all the events have
                // become signed.
                studySub.setStatus(Status.SIGNED);
                studySub.setUpdater(ub);
                subdao.update(studySub);
                addPageMessage(respage.getString("subject_event_signed"));
                // forwardPage(Page.SUBMIT_DATA_SERVLET);
                forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
                // >> changed tbh, 06/2009
                return;
            } else {
                addPageMessage(respage.getString("errors_in_submission_see_below"));
                forwardPage(Page.LIST_STUDY_SUBJECTS);
                return;
            }
        } else {
            request.setAttribute("id", new Integer(studySubId).toString());
            addPageMessage(restext.getString("password_match"));
            forwardPage(Page.LIST_STUDY_SUBJECTS);
            return;
        }
    }
    request.setAttribute("studySub", studySub);
    int studyId = studySub.getStudyId();
    int subjectId = studySub.getSubjectId();
    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);
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
    if (study.getParentStudyId() > 0) {
        // this is a site,find parent
        StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
        request.setAttribute("parentStudy", parentStudy);
    } 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());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    // find all eventcrfs for each event
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ArrayList<DisplayStudyEventBean> displayEvents = getDisplayStudyEventsForStudySubject(study, studySub, sm.getDataSource(), ub, currentRole);
    DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil();
    // Don't filter for now; disc note beans are returned with eventCRFId
    // set
    discNoteUtil.injectParentDiscNotesIntoDisplayStudyEvents(displayEvents, new HashSet(), sm.getDataSource(), 0);
    // All the displaystudyevents for one subject
    request.setAttribute("displayStudyEvents", displayEvents);
    // Set up a Map for the JSP view, mapping the eventCRFId to another Map:
    // the
    // inner Map maps the resolution status name to the number of notes for
    // that
    // eventCRF id, as in New --> 2
    Map discNoteByEventCRFid = discNoteUtil.createDiscNoteMapByEventCRF(displayEvents);
    request.setAttribute("discNoteByEventCRFid", discNoteByEventCRFid);
    EntityBeanTable table = fp.getEntityBeanTable();
    // sort by start date,
    table.setSortingIfNotExplicitlySet(1, false);
    // 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())) {
        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);
    AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
    ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList eventLogs = new ArrayList();
    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) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        // logger.warning("^^^ caught NFE");
        }
        UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
        sea.setUpdater(updater);
        eventLogs.add(sea);
    }
    // logger.warning("^^^ finished iteration");
    request.setAttribute("eventLogs", eventLogs);
    forwardPage(Page.SIGN_STUDY_SUBJECT);
}

Example 3 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class ViewEventCRFContentServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int eventCRFId = fp.getInt("ecId", true);
    int studySubId = fp.getInt("id", true);
    int eventId = fp.getInt("eventId", true);
    if (eventCRFId == 0) {
        addPageMessage(respage.getString("please_choose_an_event_CRF_to_view"));
        forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
        return;
    }
    StudyEventBean seb = getStudyEvent(eventId);
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
    request.setAttribute("studySub", studySub);
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);
    DisplayTableOfContentsBean displayBean = TableOfContentsServlet.getDisplayBean(eventCRF, sm.getDataSource(), currentStudy);
    request.setAttribute("toc", displayBean);
    request.getSession().setAttribute(BEAN_STUDY_EVENT, seb);
    forwardPage(Page.VIEW_EVENT_CRF_CONTENT);
}

Example 4 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class EntityDAO method processStudySubjects.

//
/**
     *
     * @param rs
     * @return
     */
public ArrayList processStudySubjects(ResultSet rs) {
    // throws
    // SQLException
    ArrayList al = new ArrayList();
    try {
        while (rs.next()) {
            StudySubjectBean obj = new StudySubjectBean();
            // first column
            obj.setId(rs.getInt("study_subject_id"));
            if (rs.wasNull()) {
                obj.setId(0);
            }
            // second column
            obj.setSubjectId(Integer.valueOf(rs.getInt("subject_id")));
            if (rs.wasNull()) {
                obj.setSubjectId(Integer.valueOf(0));
            }
            // old subject_identifier
            obj.setLabel(rs.getString("label"));
            if (rs.wasNull()) {
                obj.setLabel("");
            }
            obj.setDateOfBirth(rs.getDate("date_of_birth"));
            // what default?
            /*
                 * if (rs.wasNull()) { obj.setDateOfBirth(""); }
                 */
            String gender = rs.getString("gender");
            if (gender != null && gender.length() > 0) {
                obj.setGender(gender.charAt(0));
            } else {
                obj.setGender(' ');
            }
            obj.setUniqueIdentifier(rs.getString("unique_identifier"));
            if (rs.wasNull()) {
                obj.setUniqueIdentifier("");
            }
            // Date of birth
            if (CoreResources.getDBName().equals("oracle")) {
                obj.setDobCollected(new Boolean(rs.getString("dob_collected").equals("1") ? true : false));
            } else {
                obj.setDobCollected(rs.getBoolean("dob_collected"));
            }
            if (rs.wasNull()) {
                obj.setDobCollected(false);
            }
            Integer subjectStatusId = Integer.valueOf(rs.getInt("status_id"));
            if (rs.wasNull()) {
                subjectStatusId = Integer.valueOf(0);
            }
            obj.setStatus(Status.get(subjectStatusId.intValue()));
            obj.setSecondaryLabel(rs.getString("secondary_label"));
            if (rs.wasNull()) {
                obj.setSecondaryLabel("");
            }
            // add
            al.add(obj);
        }
    // while
    } catch (SQLException sqle) {
        if (logger.isWarnEnabled()) {
            logger.warn("Exception while processing result rows, EntityDAO.processStudySubjects: " + ": " + sqle.getMessage() + ": array length: " + al.size());
            logger.error(sqle.getMessage(), sqle);
        }
    }
    return al;
}

Example 5 with StudySubjectBean

use of org.akaza.openclinica.bean.managestudy.StudySubjectBean in project OpenClinica by OpenClinica.

the class StudyEventDAO method getCountofEventsBasedOnEventStatus.

public Integer getCountofEventsBasedOnEventStatus(StudyBean currentStudy, SubjectEventStatus subjectEventStatus) {
    StudySubjectBean studySubjectBean = new StudySubjectBean();
    setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(Integer.valueOf(1), currentStudy.getId());
    variables.put(Integer.valueOf(2), currentStudy.getId());
    variables.put(Integer.valueOf(3), subjectEventStatus.getId());
    String sql = digester.getQuery("getCountofEventsBasedOnEventStatus");
    ArrayList rows = this.select(sql, variables);
    Iterator it = rows.iterator();
    if (it.hasNext()) {
        Integer count = (Integer) ((HashMap) it.next()).get("count");
        return count;
    } else {
        return null;
    }
}