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

Example 6 with SubjectTransferBean

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

the class StudySubjectEndpoint method unMarshallToSubjectTransfer.

/**
 * Process createStudySubject request by creating SubjectTransferBean from received payload.
 *
 * @param subjectElement
 * @return SubjectTransferBean
 * @throws ParseException
 */
private SubjectTransferBean unMarshallToSubjectTransfer(Element subjectElement) throws ParseException, Exception {
    Element studySubjectIdElement = DomUtils.getChildElementByTagName(subjectElement, "label");
    Element secondaryIdElement = DomUtils.getChildElementByTagName(subjectElement, "secondaryLabel");
    Element enrollmentDateElement = DomUtils.getChildElementByTagName(subjectElement, "enrollmentDate");
    Element subject = DomUtils.getChildElementByTagName(subjectElement, "subject");
    Element personIdElement = DomUtils.getChildElementByTagName(subject, "uniqueIdentifier");
    Element genderElement = DomUtils.getChildElementByTagName(subject, "gender");
    Element dateOfBirthElement = DomUtils.getChildElementByTagName(subject, "dateOfBirth");
    Element yearOfBirthElement = DomUtils.getChildElementByTagName(subject, "yearOfBirth");
    Element study = DomUtils.getChildElementByTagName(subjectElement, "studyRef");
    Element studyIdentifierElement = DomUtils.getChildElementByTagName(study, "identifier");
    Element site = DomUtils.getChildElementByTagName(study, "siteRef");
    Element siteIdentifierElement = site == null ? null : DomUtils.getChildElementByTagName(site, "identifier");
    String personIdValue = personIdElement == null ? "" : DomUtils.getTextValue(personIdElement).trim();
    String studySubjectIdValue = studySubjectIdElement == null ? "" : DomUtils.getTextValue(studySubjectIdElement).trim();
    String genderValue = genderElement == null ? null : DomUtils.getTextValue(genderElement).trim();
    String secondaryIdValue = secondaryIdElement == null ? null : DomUtils.getTextValue(secondaryIdElement).trim();
    String enrollmentDateValue = DomUtils.getTextValue(enrollmentDateElement).trim();
    String dateOfBirthValue = dateOfBirthElement == null ? null : DomUtils.getTextValue(dateOfBirthElement).trim();
    String yearOfBirthValue = yearOfBirthElement == null ? null : DomUtils.getTextValue(yearOfBirthElement).trim();
    String studyIdentifier = studyIdentifierElement == null ? null : DomUtils.getTextValue(studyIdentifierElement).trim();
    String siteIdentifier = siteIdentifierElement == null ? null : DomUtils.getTextValue(siteIdentifierElement).trim();
    SubjectTransferBean subjectTransferBean = new SubjectTransferBean();
    subjectTransferBean.setStudyOid(studyIdentifier);
    subjectTransferBean.setSiteIdentifier(siteIdentifier);
    subjectTransferBean.setPersonId(personIdValue);
    subjectTransferBean.setStudySubjectId(studySubjectIdValue);
    if (genderValue == null || genderValue.length() < 1) {
    // Do nothing
    } else {
        subjectTransferBean.setGender(genderValue.toCharArray()[0]);
    }
    subjectTransferBean.setDateOfBirth((dateOfBirthValue == null || dateOfBirthValue.length() == 0) ? null : getDate(dateOfBirthValue));
    subjectTransferBean.setSecondaryId(secondaryIdValue == null ? "" : secondaryIdValue);
    subjectTransferBean.setYearOfBirth(yearOfBirthValue);
    subjectTransferBean.setEnrollmentDate(getDate(enrollmentDateValue));
    return subjectTransferBean;
}

Example 7 with SubjectTransferBean

use of org.akaza.openclinica.bean.managestudy.SubjectTransferBean 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;
        }
    }
}

Example 8 with SubjectTransferBean

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

the class StudySubjectEndpoint method createStudySubject.

/**
 * Use this method to create new study subjects in OpenClinica.
 *
 * @param subject
 * @return Source
 * @throws Exception
 */
@PayloadRoot(localPart = "createRequest", namespace = NAMESPACE_URI_V1)
public Source createStudySubject(@XPathParam("//studySubject:studySubject") NodeList subject) throws Exception {
    Errors errors = null;
    try {
        ResourceBundleProvider.updateLocale(locale);
        Element subjectElement = (Element) subject.item(0);
        SubjectTransferBean subjectTransferBean = unMarshallToSubjectTransfer(subjectElement);
        DataBinder dataBinder = new DataBinder((subjectTransferBean));
        errors = dataBinder.getBindingResult();
        subjectTransferBean.setOwner(getUserAccount());
        SubjectTransferValidator subjectTransferValidator = new SubjectTransferValidator(dataSource);
        subjectTransferValidator.validate((subjectTransferBean), errors);
        if (!errors.hasErrors()) {
            String label = create(subjectTransferBean);
            return new DOMSource(mapConfirmation(messages.getMessage("studySubjectEndpoint.success", null, "Success", locale), label, errors));
        } else {
            return new DOMSource(mapConfirmation(messages.getMessage("studySubjectEndpoint.fail", null, "Fail", locale), null, errors));
        }
    } catch (NullPointerException npe) {
        npe.printStackTrace();
        return new DOMSource(mapConfirmation(messages.getMessage("studySubjectEndpoint.fail", null, "Null Pointer Exception", locale), null, errors));
    } catch (Exception e) {
        List<String> error_messages = new ArrayList<String>();
        error_messages.add(e.getMessage());
        return new DOMSource(mapConfirmation(messages.getMessage("studySubjectEndpoint.fail", null, "Fail", locale), null, errors, "label", error_messages));
    }
}

Example 9 with SubjectTransferBean

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

the class CctsSubjectEndpoint method unMarshallToSubjectTransfer.

/**
 * UnMarshall SubjectTransferBean, aka create SubjectTransferBean from XML
 * @param gridId
 * @param subjectElement
 * @param studyOidValue
 * @return
 * @throws ParseException
 */
private SubjectTransferBean unMarshallToSubjectTransfer(String gridId, Element subjectElement, String studyOidValue) throws ParseException {
    Element personIdElement = DomUtils.getChildElementByTagName(subjectElement, "personId");
    Element studySubjectIdElement = DomUtils.getChildElementByTagName(subjectElement, "studySubjectId");
    Element secondaryIdElement = DomUtils.getChildElementByTagName(subjectElement, "secondaryId");
    Element enrollmentDateElement = DomUtils.getChildElementByTagName(subjectElement, "enrollmentDate");
    Element genderElement = DomUtils.getChildElementByTagName(subjectElement, "gender");
    Element dateOfBirthElement = DomUtils.getChildElementByTagName(subjectElement, "dateOfBirth");
    String personIdValue = DomUtils.getTextValue(personIdElement);
    String studySubjectIdValue = DomUtils.getTextValue(studySubjectIdElement);
    String genderValue = DomUtils.getTextValue(genderElement);
    String secondaryIdValue = DomUtils.getTextValue(secondaryIdElement);
    String enrollmentDateValue = DomUtils.getTextValue(enrollmentDateElement);
    String dateOfBirthValue = DomUtils.getTextValue(dateOfBirthElement);
    SubjectTransferBean subjectTransferBean = new SubjectTransferBean();
    subjectTransferBean.setStudyOid(studyOidValue);
    subjectTransferBean.setPersonId(personIdValue);
    subjectTransferBean.setStudySubjectId(studySubjectIdValue);
    subjectTransferBean.setGender(genderValue.toCharArray()[0]);
    subjectTransferBean.setDateOfBirth(getDate(dateOfBirthValue));
    // subjectTransferBean.setSecondaryId(secondaryIdValue);
    subjectTransferBean.setEnrollmentDate(getDate(enrollmentDateValue));
    return subjectTransferBean;
}

Example 10 with SubjectTransferBean

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

the class CctsService method autoCommit.

public void autoCommit() {
    List<SubjectTransferBean> subjectTransfers = getAllSubjectsInQueue();
    for (SubjectTransferBean subjectTransferBean : subjectTransfers) {
        if (isSubjectInQueueForMoreThanXSeconds(subjectTransferBean)) {
            // TODO: 2. Create Subject , StudySubject then save
            removeSubjectFromQueue(subjectTransferBean);
        }
    }
    logger.debug("The time is : " + new Date());
}