Examples with SubjectBean org.akaza.openclinica.bean.submit.SubjectBean used on opensource projects

Example 21 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class SubjectDAO method getWithFilterAndSort.

public ArrayList<SubjectBean> getWithFilterAndSort(StudyBean currentStudy, ListSubjectFilter filter, ListSubjectSort sort, int rowStart, int rowEnd) {
    ArrayList<SubjectBean> subjects = new ArrayList<SubjectBean>();
    setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), currentStudy.getId());
    variables.put(new Integer(2), currentStudy.getId());
    String sql = digester.getQuery("getWithFilterAndSort");
    sql = sql + filter.execute("");
    if (CoreResources.getDBName().equals("oracle")) {
        sql += " )x)where r between " + (rowStart + 1) + " and " + rowEnd;
        sql = sql + sort.execute("");
    } else {
        sql = sql + sort.execute("");
        sql = sql + " LIMIT " + (rowEnd - rowStart) + " OFFSET " + rowStart;
    }
    // System.out.println("SQL: "+sql);
    ArrayList rows = this.select(sql);
    Iterator it = rows.iterator();
    while (it.hasNext()) {
        SubjectBean subjectBean = (SubjectBean) this.getEntityFromHashMap((HashMap) it.next());
        subjects.add(subjectBean);
    }
    return subjects;
}

Example 22 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class SubjectDAO method findByUniqueIdentifierAndParentStudy.

/**
 * Finds the subject which has the given identifier and is inside given
 * study
 *
 * @param uniqueIdentifier
 * @param studyId
 * @return
 */
public SubjectBean findByUniqueIdentifierAndParentStudy(String uniqueIdentifier, int studyId) {
    SubjectBean answer = new SubjectBean();
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), uniqueIdentifier);
    variables.put(new Integer(2), new Integer(studyId));
    String sql = digester.getQuery("findByUniqueIdentifierAndParentStudy");
    ArrayList alist = this.select(sql, variables);
    Iterator it = alist.iterator();
    if (it.hasNext()) {
        answer = (SubjectBean) this.getEntityFromHashMap((HashMap) it.next());
    }
    return answer;
}

Example 23 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class RandomizeService method getStudySubjectAttrValue.

private String getStudySubjectAttrValue(String expr, EventCRFBean eventCrfBean, RuleSetBean ruleSet) {
    String value = "";
    StudySubjectDAO<String, ArrayList> ssdao = new StudySubjectDAO<>(ds);
    SubjectDAO subdao = new SubjectDAO(ds);
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(ds);
    StudyGroupDAO sgdao = new StudyGroupDAO(ds);
    StudyDAO<String, ArrayList> sdao = new StudyDAO<>(ds);
    StudySubjectBean ssBean = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
    SubjectBean subjectBean = (SubjectBean) subdao.findByPK(ssBean.getSubjectId());
    String prefix = "STUDYGROUPCLASSLIST";
    String param = expr.split("\\.", -1)[1].trim();
    if (param.equalsIgnoreCase("BIRTHDATE")) {
        value = subjectBean.getDateOfBirth().toString();
    } else if (param.equalsIgnoreCase("SEX")) {
        if (String.valueOf(subjectBean.getGender()).equals("m"))
            value = "Male";
        else
            value = "Female";
    // value =String.valueOf(ssBean.getGender());
    } else if (param.startsWith(prefix)) {
        String gcName = param.substring(21, param.indexOf("\"]"));
        StudyGroupBean sgBean = sgdao.findSubjectStudyGroup(ssBean.getId(), gcName);
        if (sgBean != null)
            value = sgBean.getName();
    }
    return value;
}

Example 24 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean 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 25 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean in project OpenClinica by OpenClinica.

the class MaskSubjectDOBRule method doAction.

public EntityBean doAction(EntityBean sb) {
    // cast to a subject bean
    SubjectBean ssb = (SubjectBean) sb;
    // effectively xx-xx-xxxx
    ssb.setDateOfBirth(null);
    return sb;
}