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

Example 46 with SubjectBean

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

the class ListEventsForSubjectTableFactory method setDataAndLimitVariables.

@SuppressWarnings("unchecked")
@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    Limit limit = tableFacade.getLimit();
    ListEventsForSubjectFilter eventsForSubjectFilter = getListEventsForSubjectFilter(limit);
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDAO().getCountWithFilter(eventsForSubjectFilter, getStudyBean());
        tableFacade.setTotalRows(totalRows);
    }
    ListEventsForSubjectSort eventsForSubjectSort = getListEventsForSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDAO().getWithFilterAndSort(getStudyBean(), eventsForSubjectFilter, eventsForSubjectSort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    for (StudySubjectBean studySubjectBean : items) {
        HashMap<Object, Object> theItem = new HashMap<Object, Object>();
        theItem.put("studySubject", studySubjectBean);
        theItem.put("studySubject.label", studySubjectBean.getLabel());
        theItem.put("studySubject.status", studySubjectBean.getStatus());
        theItem.put("enrolledAt", ((StudyBean) getStudyDAO().findByPK(studySubjectBean.getStudyId())).getIdentifier());
        SubjectBean subjectBean = (SubjectBean) getSubjectDAO().findByPK(studySubjectBean.getSubjectId());
        theItem.put("subject", subjectBean);
        theItem.put("subject.charGender", subjectBean.getGender());
        // study group classes
        SubjectGroupMapBean subjectGroupMapBean = new SubjectGroupMapBean();
        for (StudyGroupClassBean studyGroupClass : getStudyGroupClasses()) {
            subjectGroupMapBean = getSubjectGroupMapDAO().findAllByStudySubjectAndStudyGroupClass(studySubjectBean.getId(), studyGroupClass.getId());
            if (null != subjectGroupMapBean) {
                theItem.put("sgc_" + studyGroupClass.getId(), subjectGroupMapBean.getStudyGroupId());
                theItem.put("grpName_sgc_" + studyGroupClass.getId(), subjectGroupMapBean.getStudyGroupName());
            }
        }
        subjectGroupMapBean = null;
        // Get EventCrfs for study Subject
        List<EventCRFBean> eventCrfs = getEventCRFDAO().findAllByStudySubject(studySubjectBean.getId());
        HashMap<String, EventCRFBean> crfAsKeyEventCrfAsValue = new HashMap<String, EventCRFBean>();
        for (EventCRFBean eventCRFBean : eventCrfs) {
            CRFBean crf = getCrfDAO().findByVersionId(eventCRFBean.getCRFVersionId());
            crfAsKeyEventCrfAsValue.put(crf.getId() + "_" + eventCRFBean.getStudyEventId(), eventCRFBean);
        }
        // Get the event Status
        List<StudyEventBean> eventsForStudySubjectAndEventDefinitions = getStudyEventDAO().findAllByDefinitionAndSubject(selectedStudyEventDefinition, studySubjectBean);
        List<DisplayBean> events = new ArrayList<DisplayBean>();
        // study event size < 1
        if (eventsForStudySubjectAndEventDefinitions.size() < 1) {
            DisplayBean d = new DisplayBean();
            d.getProps().put("event", null);
            d.getProps().put("event.status", SubjectEventStatus.NOT_SCHEDULED);
            d.getProps().put("studySubject.createdDate", null);
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                d.getProps().put("crf_" + crf.getId(), DataEntryStage.UNCOMPLETED);
                d.getProps().put("crf_" + crf.getId() + "_eventCrf", null);
                d.getProps().put("crf_" + crf.getId() + "_crf", crf);
                // d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", eventDefinitionCrfs.get(i));
                d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", getEventDefinitionCRFBean(selectedStudyEventDefinition.getId(), crf, studySubjectBean));
                theItem.put("crf_" + crf.getId(), "");
            }
            events.add(d);
        }
        // study event size >0
        for (StudyEventBean studyEventBean : eventsForStudySubjectAndEventDefinitions) {
            DisplayBean d = new DisplayBean();
            d.getProps().put("event", studyEventBean);
            d.getProps().put("event.status", studyEventBean.getSubjectEventStatus());
            d.getProps().put("studySubject.createdDate", studyEventBean.getDateStarted());
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                EventCRFBean eventCRFBean = crfAsKeyEventCrfAsValue.get(crf.getId() + "_" + studyEventBean.getId());
                if (eventCRFBean != null) {
                    d.getProps().put("crf_" + crf.getId(), eventCRFBean.getStage());
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", eventCRFBean);
                } else {
                    d.getProps().put("crf_" + crf.getId(), DataEntryStage.UNCOMPLETED);
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", null);
                }
                d.getProps().put("crf_" + crf.getId() + "_crf", crf);
                // d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", eventDefinitionCrfs.get(i));
                d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", getEventDefinitionCRFBean(selectedStudyEventDefinition.getId(), crf, studySubjectBean));
                theItem.put("crf_" + crf.getId(), "");
            }
            events.add(d);
        }
        theItem.put("events", events);
        theItem.put("event.status", "");
        theItem.put("studySubject.createdDate", "");
        theItem.put("webappContext", tableFacade.getWebContext().getContextPath());
        theItems.add(theItem);
    }
    // Do not forget to set the items back on the tableFacade.
    tableFacade.setItems(theItems);
}

Example 47 with SubjectBean

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

the class StudyAuditLogTableFactory method setDataAndLimitVariables.

@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    // initialize i18n
    resword = ResourceBundleProvider.getWordsBundle(getLocale());
    resformat = ResourceBundleProvider.getFormatBundle(getLocale());
    Limit limit = tableFacade.getLimit();
    StudyAuditLogFilter auditLogStudyFilter = getAuditLogStudyFilter(limit);
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDao().getCountWithFilter(auditLogStudyFilter, getCurrentStudy());
        tableFacade.setTotalRows(totalRows);
    }
    StudyAuditLogSort auditLogStudySort = getAuditLogStudySort(limit);
    /*
         * if (auditLogStudySort.getSorts().size() == 0) {
         * auditLogStudySort.addSort("loginAttemptDate", "desc"); }
         */
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDao().getWithFilterAndSort(getCurrentStudy(), auditLogStudyFilter, auditLogStudySort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    for (StudySubjectBean studySubjectBean : items) {
        SubjectBean subject = (SubjectBean) getSubjectDao().findByPK(studySubjectBean.getSubjectId());
        UserAccountBean owner = (UserAccountBean) getUserAccountDao().findByPK(studySubjectBean.getOwnerId());
        HashMap<Object, Object> h = new HashMap<Object, Object>();
        h.put("studySubject", studySubjectBean);
        h.put("studySubject.label", studySubjectBean.getLabel());
        h.put("studySubject.secondaryLabel", studySubjectBean.getSecondaryLabel());
        h.put("studySubject.oid", studySubjectBean.getOid());
        h.put("studySubject.owner", owner);
        h.put("studySubject.status", studySubjectBean.getStatus());
        h.put("subject", subject);
        h.put("subject.dateOfBirth", resolveBirthDay(subject.getDateOfBirth(), subject.isDobCollected(), getLocale()));
        h.put("subject.uniqueIdentifier", subject.getUniqueIdentifier());
        theItems.add(h);
    }
    tableFacade.setItems(theItems);
}

Example 48 with SubjectBean

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

the class StudySubjectEndpoint method createSubject.

private String createSubject(SubjectTransferBean subjectTransfer) {
    SubjectBean subject = new SubjectBean();
    subject.setUniqueIdentifier(subjectTransfer.getPersonId());
    subject.setLabel(subjectTransfer.getStudySubjectId());
    subject.setDateOfBirth(subjectTransfer.getDateOfBirth());
    // below added tbh 04/2011
    if (subject.getDateOfBirth() != null) {
        subject.setDobCollected(true);
    } else {
        subject.setDobCollected(false);
    }
    // >> above added tbh 04/2011, mantis issue having to 
    // deal with not being able to change DOB after a submit
    subject.setGender(subjectTransfer.getGender());
    if (subjectTransfer.getOwner() != null) {
        subject.setOwner(subjectTransfer.getOwner());
    }
    subject.setCreatedDate(new Date());
    return this.subjectService.createSubject(subject, subjectTransfer.getStudy(), subjectTransfer.getEnrollmentDate(), subjectTransfer.getSecondaryId());
}

Example 49 with SubjectBean

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

the class StudySubjectEndpoint method mapListStudySubjectsInStudyResponse.

/**
     * Build the response for listStudySubjectsInStudy method
     * 
     * @param study
     * @param message
     * @param studyRef
     * @return ListAllByStudyResponse
     * @throws Exception
     */
private ListAllByStudyResponse mapListStudySubjectsInStudyResponse(StudyBean study, String message, StudyRefType studyRef) throws Exception {
    ListAllByStudyResponse response = new ListAllByStudyResponse();
    response.setResult(message);
    StudySubjectsType studySubjectsType = new StudySubjectsType();
    response.setStudySubjects(studySubjectsType);
    List<StudySubjectBean> studySubjects = this.subjectService.getStudySubject(study);
    for (StudySubjectBean studySubjectBean : studySubjects) {
        StudySubjectWithEventsType studySubjectType = new StudySubjectWithEventsType();
        SubjectType subjectType = new SubjectType();
        studySubjectType.setLabel(studySubjectBean.getLabel());
        studySubjectType.setSecondaryLabel(studySubjectBean.getSecondaryLabel());
        if (studySubjectBean.getEnrollmentDate() != null) {
            studySubjectType.setEnrollmentDate(getXMLGregorianCalendarDate(studySubjectBean.getEnrollmentDate()));
        }
        SubjectBean subjectBean = (SubjectBean) getSubjectDao().findByPK(studySubjectBean.getSubjectId());
        subjectType.setUniqueIdentifier(subjectBean.getUniqueIdentifier());
        String genderStr = String.valueOf(subjectBean.getGender());
        if (!"".equals(genderStr.trim())) {
            subjectType.setGender(GenderType.fromValue(genderStr));
        }
        if (subjectBean.getDateOfBirth() != null) {
            subjectType.setDateOfBirth(getXMLGregorianCalendarDate(subjectBean.getDateOfBirth()));
        }
        studySubjectType.setSubject(subjectType);
        // studySubjectType.setStudyRef(studyRef);
        logger.debug(studySubjectBean.getLabel());
        studySubjectType.setEvents(getEvents(studySubjectBean));
        studySubjectsType.getStudySubject().add(studySubjectType);
    }
    return response;
}

Example 50 with SubjectBean

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

the class SubjectTransferValidator method validate.

@Override
public void validate(Object obj, Errors e) {
    SubjectTransferBean subjectTransferBean = (SubjectTransferBean) obj;
    if (subjectTransferBean.getStudyOid() == null) {
        e.reject("studyEventTransferValidator.study_does_not_exist");
        return;
    }
    Status[] included_status = new Status[] { Status.AVAILABLE };
    StudyBean study = helper.verifyStudy(getStudyDAO(), subjectTransferBean.getStudyOid(), included_status, e);
    if (study == null)
        return;
    StudyBean site = null;
    int site_id = -1;
    subjectTransferBean.setStudy(study);
    if (subjectTransferBean.getSiteIdentifier() != null) {
        site = helper.verifySite(getStudyDAO(), subjectTransferBean.getStudyOid(), subjectTransferBean.getSiteIdentifier(), included_status, e);
        if (site == null) {
            return;
        }
        site_id = site.getId();
        subjectTransferBean.setStudy(site);
    }
    boolean isRoleVerified = helper.verifyRole(subjectTransferBean.getOwner(), study.getId(), site_id, Role.MONITOR, e);
    if (!isRoleVerified) {
        return;
    }
    //        StudyBean study = null;
    //        if ( subjectTransferBean.getStudyOid() != null)
    //        {
    //	        study = getStudyDAO().findByUniqueIdentifier(subjectTransferBean.getStudyOid());
    //	        if (study == null) {
    //	            e.reject("subjectTransferValidator.study_does_not_exist", new Object[] { subjectTransferBean.getStudyOid() }, "Study identifier you specified "
    //	                + subjectTransferBean.getStudyOid() + " does not correspond to a valid study.");
    //	            return;
    //	        }
    //	        //validate study status
    //	        if (study != null && !study.getStatus().isAvailable()) {
    //	            e.reject("subjectTransferValidator.study_status_wrong", new Object[] { subjectTransferBean.getStudyOid() }, "Study "
    //	            		+ subjectTransferBean.getStudyOid() +" has wrong status. Subject can be added to an 'AVAILABLE' study only.");
    //	            return;
    //	        }
    //	        subjectTransferBean.setStudy(study);
    //        }
    //        UserAccountBean ua = subjectTransferBean.getOwner();
    //        StudyUserRoleBean role = ua.getRoleByStudy(subjectTransferBean.getStudy());
    //        if (role.getId() == 0 || role.getRole().equals(Role.MONITOR)) {
    //            e.reject("subjectTransferValidator.insufficient_permissions", "You do not have sufficient privileges to proceed with this operation.");
    //            return;
    //        }
    //        StudyBean site = null;
    //        if (subjectTransferBean.getSiteIdentifier() != null) {
    //            site = getStudyDAO().findSiteByUniqueIdentifier(subjectTransferBean.getStudyOid(), subjectTransferBean.getSiteIdentifier());
    // 	        if (site == null) {
    //	            e.reject("subjectTransferValidator.site_does_not_exist", new Object[] { subjectTransferBean.getSiteIdentifier() },
    //	                    "Site identifier you specified does not correspond to a valid site.");
    //	            return;
    //	        }
    //	        //validate site status
    //	        if ( ! site.getStatus().isAvailable()) {
    //	        
    //	            e.reject("subjectTransferValidator.site_status_wrong", new Object[] { subjectTransferBean.getSiteIdentifier() }, "Site "
    //	            		+ site.getName() +" has wrong status. Subject can be added to an 'AVAILABLE' site only.");
    //	            return;
    //	        }
    //	        subjectTransferBean.setStudy(site);//???????????
    //        }
    //        role = ua.getRoleByStudy(site);
    //        if (role.getId() == 0 || role.getRole().equals(Role.MONITOR)) {
    //            e.reject("subjectTransferValidator.insufficient_permissions", "You do not have sufficient privileges to proceed with this operation.");
    //            return;
    //        }
    //      
    int handleStudyId = study.getParentStudyId() > 0 ? study.getParentStudyId() : study.getId();
    StudyParameterValueBean studyParameter = getStudyParameterValueDAO().findByHandleAndStudy(handleStudyId, "subjectPersonIdRequired");
    String personId = subjectTransferBean.getPersonId();
    if (personId.contains("<") || personId.contains(">")) {
        e.reject("subjectTransferValidator.person_id_can_not_contain_html_lessthan_or_greaterthan_elements");
        return;
    }
    if ("required".equals(studyParameter.getValue()) && (personId == null || personId.length() < 1)) {
        e.reject("subjectTransferValidator.personId_required", new Object[] { study.getName() }, "personId is required for the study: " + study.getName());
        return;
    }
    if ("not used".equals(studyParameter.getValue()) && !(personId == null || personId.length() < 1)) {
        e.reject("subjectTransferValidator.personId_not_used", new Object[] { study.getName() }, "personId is not used for the study: " + study.getName());
        return;
    }
    if (personId != null && personId.length() > 255) {
        e.reject("subjectTransferValidator.personId_invalid_length", new Object[] { personId }, "personId: " + personId + " cannot be longer than 255 characters.");
        return;
    }
    // verify that personId is unique 
    if (subjectTransferBean.getPersonId() != null && subjectTransferBean.getPersonId().length() > 0) {
        //	         SubjectBean subjectWithSamePersonId = getSubjectDao().findByUniqueIdentifierAndStudy( subjectTransferBean.getPersonId(), study.getId());
        SubjectBean subjectWithSamePersonId = getSubjectDao().findByUniqueIdentifierAndAnyStudy(subjectTransferBean.getPersonId(), study.getId());
        if (subjectWithSamePersonId.getId() != 0) {
            e.reject("subjectTransferValidator.personId_duplicated", new Object[] { personId }, "A subject with the Person ID: " + personId + " is already enrolled in this study. ");
            return;
        }
    }
    StudyParameterValueBean subjectIdGenerationParameter = getStudyParameterValueDAO().findByHandleAndStudy(handleStudyId, "subjectIdGeneration");
    String idSetting = subjectIdGenerationParameter.getValue();
    if (!(idSetting.equals("auto editable") || idSetting.equals("auto non-editable"))) {
        String studySubjectId = subjectTransferBean.getStudySubjectId();
        if (studySubjectId == null || studySubjectId.length() < 1) {
            e.reject("subjectTransferValidator.studySubjectId_required");
            return;
        } else if (studySubjectId.length() > 30) {
            e.reject("subjectTransferValidator.studySubjectId_invalid_length", new Object[] { studySubjectId }, "studySubjectId: " + studySubjectId + " cannot be longer than 30 characters.");
            return;
        } else {
            // checks whether there is a subject with same id inside current study
            StudySubjectBean subjectWithSame = getStudySubjectDAO().findByLabelAndStudy(studySubjectId, study);
            if (subjectWithSame.getLabel().equals(studySubjectId)) {
                e.reject("subjectTransferValidator.subject_duplicated_label", new Object[] { studySubjectId, study.getIdentifier() }, "studySubjectId: " + studySubjectId + " already exists for " + study.getIdentifier() + " study .");
                return;
            }
        }
        if (studySubjectId.contains("<") || studySubjectId.contains(">")) {
            e.reject("subjectTransferValidator.study_subject_id_can_not_contain_html_lessthan_or_greaterthan_elements");
            return;
        }
    }
    String secondaryId = subjectTransferBean.getSecondaryId();
    if (secondaryId != null && secondaryId.length() > 30) {
        e.reject("subjectTransferValidator.secondaryId_invalid_length", new Object[] { secondaryId }, "secondaryId: " + secondaryId + " cannot be longer than 30 characters.");
        return;
    }
    if (secondaryId.contains("<") || secondaryId.contains(">")) {
        e.reject("subjectTransferValidator.secondary_id_can_not_contain_html_lessthan_or_greaterthan_elements");
        return;
    }
    String gender = String.valueOf(subjectTransferBean.getGender());
    studyParameter = getStudyParameterValueDAO().findByHandleAndStudy(handleStudyId, "genderRequired");
    if ("true".equals(studyParameter.getValue())) {
        if (gender == null || gender.length() < 1) {
            e.reject("subjectTransferValidator.gender_required", new Object[] { study.getName() }, "Gender is required for the study: " + study.getName());
            return;
        }
        if (!"m".equals(gender) && !"f".equals(gender)) {
            e.reject("subjectTransferValidator.gender_is_m_or_f");
            return;
        }
    } else {
        if (gender.trim().length() > 0 && !("m".equals(gender) || "f".equals(gender))) {
            e.reject("subjectTransferValidator.gender_is_m_or_f");
            return;
        }
    }
    Date dateOfBirth = subjectTransferBean.getDateOfBirth();
    String yearOfBirth = subjectTransferBean.getYearOfBirth();
    studyParameter = getStudyParameterValueDAO().findByHandleAndStudy(handleStudyId, "collectDob");
    if ("1".equals(studyParameter.getValue()) && (dateOfBirth == null)) {
        e.reject("subjectTransferValidator.dateOfBirth_required", new Object[] { study.getName() }, "Date of birth is required for the study " + study.getName());
        return;
    } else if ("2".equals(studyParameter.getValue()) && (yearOfBirth == null)) {
        e.reject("subjectTransferValidator.yearOfBirth_required", new Object[] { study.getName() }, "Year of birth is required for the study " + study.getName());
        return;
    } else if ("2".equals(studyParameter.getValue()) && (yearOfBirth != null)) {
        try {
            SimpleDateFormat sdf = new SimpleDateFormat("yyyy");
            subjectTransferBean.setDateOfBirth(sdf.parse(subjectTransferBean.getYearOfBirth()));
        } catch (ParseException xe) {
            e.reject("subjectTransferValidator.yearOfBirth_invalid", new Object[] { yearOfBirth }, "Year of birth: " + yearOfBirth + " is not valid");
            return;
        }
    //not used
    } else if ("3".equals(studyParameter.getValue())) {
        if (dateOfBirth != null || !(yearOfBirth == null || yearOfBirth.length() < 1)) {
            e.reject("subjectTransferValidator.date_of_birth_notused", new Object[] { study.getName() }, "Date of Birth is not used for the study " + study.getName());
            return;
        }
    }
    Date enrollmentDate = subjectTransferBean.getEnrollmentDate();
    if (enrollmentDate == null) {
        e.reject("subjectTransferValidator.enrollmentDate_required");
        return;
    } else {
        if ((new Date()).compareTo(enrollmentDate) < 0) {
            e.reject("subjectTransferValidator.enrollmentDate_should_be_in_past");
            return;
        }
    }
}