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

Example 41 with StudyEventDefinitionBean

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

the class BatchCRFMigrationController method run.

@Override
public void run() {
    dataSource = helperObject.getDataSource();
    cBean = helperObject.getcBean();
    reportLog = helperObject.getReportLog();
    stBean = helperObject.getStBean();
    resterms = helperObject.getResterms();
    userAccountBean = helperObject.getUserAccountBean();
    openClinicaMailSender = helperObject.getOpenClinicaMailSender();
    sessionFactory = helperObject.getSessionFactory();
    Session session = sessionFactory.openSession();
    Transaction tx = session.beginTransaction();
    helperObject.setSession(session);
    int i = 0;
    for (EventCRFBean eventCrfToMigrate : helperObject.getEventCrfListToMigrate()) {
        i++;
        executeMigrationAction(helperObject, eventCrfToMigrate);
        if (i % 50 == 0) {
            session.flush();
            session.clear();
        }
        StudySubjectBean ssBean = (StudySubjectBean) ssdao().findByPK(eventCrfToMigrate.getStudySubjectId());
        StudyBean sBean = (StudyBean) sdao().findByPK(ssBean.getStudyId());
        StudyEventBean seBean = (StudyEventBean) sedao().findByPK(eventCrfToMigrate.getStudyEventId());
        StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) seddao().findByPK(seBean.getStudyEventDefinitionId());
        reportLog.getLogs().add(cBean.getName() + "," + helperObject.getSourceCrfVersionBean().getName() + "," + helperObject.getTargetCrfVersionBean().getName() + "," + ssBean.getLabel() + "," + sBean.getName() + "," + sedBean.getName() + "," + seBean.getSampleOrdinal());
    }
    tx.commit();
    session.close();
    String fileName = new SimpleDateFormat("_yyyy-MM-dd-hhmmssSaa'.txt'").format(new Date());
    fileName = "logFile" + fileName;
    File file = createLogFile(fileName);
    PrintWriter writer = null;
    try {
        writer = openFile(file);
    } catch (FileNotFoundException | UnsupportedEncodingException e) {
        e.printStackTrace();
    } finally {
        writer.print(toStringTextFormat(reportLog, resterms, stBean, cBean));
        closeFile(writer);
    }
    String reportUrl = getReportUrl(fileName, helperObject.getUrlBase());
    String fullName = userAccountBean.getFirstName() + " " + userAccountBean.getLastName();
    StringBuilder body = new StringBuilder();
    body.append(resterms.getString("Dear") + " " + fullName + ",<br><br>" + resterms.getString("Batch_CRF_version_migration_has_finished_running") + "<br>" + resterms.getString("Study") + ": " + stBean.getName() + "<br>" + resterms.getString("CRF") + ": " + cBean.getName() + "<br><br>" + resterms.getString("A_summary_report_of_the_migration_is_available_here") + ":<br>" + reportUrl + "<br><br>" + resterms.getString("Thank_you_Your_OpenClinica_System"));
    logger.info(body.toString());
    openClinicaMailSender.sendEmail(userAccountBean.getEmail(), EmailEngine.getAdminEmail(), resterms.getString("Batch_Migration_Complete_For") + " " + stBean.getName(), body.toString(), true);
}

Example 42 with StudyEventDefinitionBean

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

the class CrfBusinessLogicHelper method markCRFComplete.

/**
 * The following methods are for 'mark CRF complete' Note that we will also wrap Study Event status changes in this
 * code, possibly split out in a later release, tbh 06/2008
 *
 * @return
 */
public boolean markCRFComplete(EventCRFBean ecb, UserAccountBean ub) throws Exception {
    // locale = LocaleResolver.getLocale(request);
    // < respage =
    // ResourceBundle.getBundle("org.akaza.openclinica.i18n.page_messages",
    // locale);
    // < restext =
    // ResourceBundle.getBundle("org.akaza.openclinica.i18n.notes",locale);
    // <
    // resexception=ResourceBundle.getBundle(
    // "org.akaza.openclinica.i18n.exceptions",locale);
    // getEventCRFBean();
    // getEventDefinitionCRFBean();
    DataEntryStage stage = ecb.getStage();
    EventCRFDAO eventCrfDao = new EventCRFDAO(ds);
    ItemDataDAO itemDataDao = new ItemDataDAO(ds);
    StudyDAO sdao = new StudyDAO(ds);
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    StudyBean study = sdao.findByStudySubjectId(ecb.getStudySubjectId());
    EventDefinitionCRFBean edcb = getEventDefinitionCrfByStudyEventAndCrfVersion(ecb, study);
    // StudyEventDAO studyEventDao = new StudyEventDAO(ds);
    // StudyEventBean studyEventBean = (StudyEventBean)
    // studyEventDao.findByPK(ecb.getStudyEventId());
    // Status studyEventStatus = studyEventBean.getStatus();
    StudyEventDefinitionDAO studyEventDefinitionDao = new StudyEventDefinitionDAO(ds);
    StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) studyEventDefinitionDao.findByPK(edcb.getStudyEventDefinitionId());
    CRFDAO crfDao = new CRFDAO(ds);
    ArrayList crfs = (ArrayList) crfDao.findAllActiveByDefinition(sedBean);
    sedBean.setCrfs(crfs);
    // request.setAttribute(TableOfContentsServlet.INPUT_EVENT_CRF_BEAN,
    // ecb);
    // request.setAttribute(INPUT_EVENT_CRF_ID, new
    // Integer(ecb.getId()));
    logger.debug("inout_event_crf_id:" + ecb.getId());
    logger.debug("inout_study_event_def_id:" + sedBean.getId());
    // below bit is from DataEntryServlet, is more appropriate for filling
    // in by hand than by automatic
    // removing this in favor of the more streamlined effect below, tbh
    // 06/2008
    // Page errorPage = getJSPPage();
    // if (stage.equals(DataEntryStage.UNCOMPLETED) ||
    // stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) ||
    // stage.equals(DataEntryStage.LOCKED)) {
    // logger.info(
    // "addPageMessage(respage.getString(\"not_mark_CRF_complete1\"))");
    // return false;
    // }
    // 
    // if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) ||
    // stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
    // 
    // /*
    // * if (!edcb.isDoubleEntry()) {
    // *
    // logger.info(
    // "addPageMessage(respage.getString(\"not_mark_CRF_complete2\"))");
    // * return false; }
    // *
    // */
    // }
    // 
    // /*
    // * if (!isEachSectionReviewedOnce()) { addPageMessage("You may not
    // mark
    // * this Event CRF complete, because there are some sections which have
    // * not been reviewed once."); return false; }
    // */
    // 
    // if (!isEachRequiredFieldFillout(ecb)) {
    // logger.info(
    // "addPageMessage(respage.getString(\"not_mark_CRF_complete4\"))");
    // return false;
    // }
    // 
    // /*
    // * if (ecb.getInterviewerName().trim().equals("")) { throw new
    // * InconsistentStateException(errorPage, "You may not mark this Event
    // * CRF complete, because the interviewer name is blank."); }
    // */
    Status newStatus = ecb.getStatus();
    DataEntryStage newStage = ecb.getStage();
    boolean ide = true;
    // currently we are setting the event crf status to complete, so this
    // block is all to
    // complete, tbh
    // if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) &&
    // edcb.isDoubleEntry()) {
    // newStatus = Status.PENDING;
    // ecb.setUpdaterId(ub.getId());
    // ecb.setUpdater(ub);
    // ecb.setUpdatedDate(new Date());
    // ecb.setDateCompleted(new Date());
    // } else if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) &&
    // !edcb.isDoubleEntry()) {
    // newStatus = Status.UNAVAILABLE;
    // ecb.setUpdaterId(ub.getId());
    // ecb.setUpdater(ub);
    // ecb.setUpdatedDate(new Date());
    // ecb.setDateCompleted(new Date());
    // ecb.setDateValidateCompleted(new Date());
    // } else if
    // (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE)
    // || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
    // newStatus = Status.UNAVAILABLE;
    // ecb.setDateValidateCompleted(new Date());
    // ide = false;
    // }
    newStatus = Status.UNAVAILABLE;
    // ecb.setUpdaterId(ub.getId());
    ecb.setUpdater(ub);
    ecb.setUpdatedDate(new Date());
    ecb.setDateCompleted(new Date());
    ecb.setDateValidateCompleted(new Date());
    /*
         * //for the non-reviewed sections, no item data in DB yet, need to //create them if
         * (!isEachSectionReviewedOnce()) { boolean canSave = saveItemsToMarkComplete(newStatus); if (canSave == false){
         * addPageMessage("You may not mark this Event CRF complete, because there are some required entries which have
         * not been filled out."); return false; } }
         */
    ecb.setStatus(newStatus);
    ecb.setStage(newStage);
    ecb = (EventCRFBean) eventCrfDao.update(ecb);
    logger.debug("just updated event crf id: " + ecb.getId());
    // note the below statement only updates the DATES, not the STATUS
    eventCrfDao.markComplete(ecb, ide);
    // update all the items' status to complete
    itemDataDao.updateStatusByEventCRF(ecb, newStatus);
    // change status for study event
    StudyEventDAO sedao = new StudyEventDAO(ds);
    StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
    seb.setUpdatedDate(new Date());
    seb.setUpdater(ub);
    // updates with Pauls observation from bug:2488:
    // 1. If there is only one CRF in the event (whether the CRF was
    // required or not), and data was imported for it, the status of the
    // event should be Completed.
    // 
    logger.debug("sed bean get crfs get size: " + sedBean.getCrfs().size());
    logger.debug("edcb get crf id: " + edcb.getCrfId() + " version size? " + edcb.getVersions().size());
    logger.debug("ecb get crf id: " + ecb.getCrf().getId());
    logger.debug("ecb get crf version id: " + ecb.getCRFVersionId());
    if (sedBean.getCrfs().size() == 1) {
        seb.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
        logger.info("just set subj event status to -- COMPLETED --");
    } else // removing sedBean.getCrfs().size() > 1 &&
    if (areAllRequired(seb, study) && !areAllCompleted(seb, study)) {
        seb.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
        logger.info("just set subj event status to -- DATAENTRYSTARTED --");
    } else // removing sedBean.getCrfs().size() > 1 &&
    if (!areAllRequired(seb, study)) {
        if (areAllRequiredCompleted(seb, study)) {
            seb.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
            logger.info("just set subj event status to -- 3completed3 --");
        } else {
            seb.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
            logger.info("just set subj event status to -- DATAENTRYSTARTED --");
        }
    } else if (noneAreRequired(seb, study)) {
        seb.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
        logger.info("just set subj event status to -- 5completed5 --");
    }
    logger.debug("just set subj event status, final status is " + seb.getSubjectEventStatus().getName());
    logger.debug("final overall status is " + seb.getStatus().getName());
    seb = (StudyEventBean) sedao.update(seb);
    return true;
}

Example 43 with StudyEventDefinitionBean

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

the class StudyEventDefinitionRow method compareColumn.

/*
     * (non-Javadoc)
     *
     * @see org.akaza.openclinica.core.EntityBeanRow#compareColumn(java.lang.Object,
     *      int)
     */
@Override
protected int compareColumn(Object row, int sortingColumn) {
    if (!row.getClass().equals(StudyEventDefinitionRow.class)) {
        return 0;
    }
    StudyEventDefinitionBean thisDefinition = (StudyEventDefinitionBean) bean;
    StudyEventDefinitionBean argDefinition = (StudyEventDefinitionBean) ((StudyEventDefinitionRow) row).bean;
    int answer = 0;
    switch(sortingColumn) {
        case COL_ORDINAL:
            if (thisDefinition.getOrdinal() > argDefinition.getOrdinal()) {
                answer = 1;
            } else if (thisDefinition.getOrdinal() == argDefinition.getOrdinal()) {
                answer = 0;
            } else {
                answer = -1;
            }
            break;
        case COL_NAME:
            answer = thisDefinition.getName().toLowerCase().compareTo(argDefinition.getName().toLowerCase());
            break;
        case COL_REPEATING:
            if (thisDefinition.isRepeating() && !argDefinition.isRepeating()) {
                answer = 1;
            } else if (!thisDefinition.isRepeating() && argDefinition.isRepeating()) {
                answer = -1;
            } else {
                answer = 0;
            }
            break;
        case COL_TYPE:
            answer = thisDefinition.getType().toLowerCase().compareTo(argDefinition.getType().toLowerCase());
            break;
        case COL_CATEGORY:
            String category = "ZZZZZZZZZ";
            if (!"".equals(thisDefinition.getCategory())) {
                category = thisDefinition.getCategory();
            // System.out.println("switched out ...");
            }
            answer = category.toLowerCase().compareTo(argDefinition.getCategory().toLowerCase());
            // System.out.println("returning " + answer + " for " + category);
            break;
        case COL_POPULATED:
            if (thisDefinition.isPopulated() && !argDefinition.isPopulated()) {
                answer = 1;
            } else if (!thisDefinition.isPopulated() && argDefinition.isPopulated()) {
                answer = -1;
            } else {
                answer = 0;
            }
            break;
        // break;
        case COL_DATE_UPDATED:
            answer = compareDate(thisDefinition.getUpdatedDate(), argDefinition.getUpdatedDate());
            break;
        case COL_UPDATER:
            answer = thisDefinition.getUpdater().getName().toLowerCase().compareTo(argDefinition.getUpdater().getName().toLowerCase());
            break;
        case COL_STATUS:
            answer = thisDefinition.getStatus().compareTo(argDefinition.getStatus());
            break;
    }
    return answer;
}

Example 44 with StudyEventDefinitionBean

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

the class SDVUtil method prepareSDVSelectElements.

public void prepareSDVSelectElements(HttpServletRequest request, StudyBean studyBean) {
    // Study event statuses
    List<String> studyEventStatuses = new ArrayList<String>();
    for (org.akaza.openclinica.domain.Status stat : org.akaza.openclinica.domain.Status.values()) {
        studyEventStatuses.add(stat.getDescription());
    }
    request.setAttribute("studyEventStatuses", studyEventStatuses);
    // SDV requirements
    List<String> sdvRequirements = new ArrayList<String>();
    for (SourceDataVerification sdvRequire : SourceDataVerification.values()) {
        sdvRequirements.add(sdvRequire.getDescription());
    }
    request.setAttribute("sdvRequirements", SourceDataVerification.values());
    // study event definitions
    StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(dataSource);
    List<StudyEventDefinitionBean> studyEventDefinitionBeans = new ArrayList<StudyEventDefinitionBean>();
    studyEventDefinitionBeans = studyEventDefinitionDAO.findAllByStudy(studyBean);
    request.setAttribute("studyEventDefinitions", studyEventDefinitionBeans);
    // study event status
    request.setAttribute("studyEventStatuses", Status.toArrayList());
    // event CRF status
    request.setAttribute("eventCRFDStatuses", SubjectEventStatus.toArrayList());
    StudyEventDAO studyEventDAO = new StudyEventDAO(dataSource);
    List<StudyEventBean> studyEventBeans = studyEventDAO.findAllByStudy(studyBean);
    List<EventCRFBean> eventCRFBeans = getAllEventCRFs(studyEventBeans);
    SortedSet<String> eventCRFNames = new TreeSet<String>();
    for (EventCRFBean bean : eventCRFBeans) {
        eventCRFNames.add(getCRFName(bean.getCRFVersionId()));
    }
    request.setAttribute("eventCRFNames", eventCRFNames);
}

Example 45 with StudyEventDefinitionBean

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

the class ImportCRFDataService method fetchEventCRFStatuses.

/*
     * purpose: Build a map of EventCRFs and the statuses they should have post-import. Assumes EventCRFs have been
     * created for "Not Started" forms.
     */
public void fetchEventCRFStatuses(ODMContainer odmContainer, HashMap<Integer, String> importedCRFStatuses) {
    EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
    StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
    StudyDAO studyDAO = new StudyDAO(ds);
    StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
    String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
    StudyBean studyBean = studyDAO.findByOid(studyOID);
    ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
    for (SubjectDataBean subjectDataBean : subjectDataBeans) {
        ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
        StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
        for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
            ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
            String sampleOrdinal = studyEventDataBean.getStudyEventRepeatKey() == null ? "1" : studyEventDataBean.getStudyEventRepeatKey();
            StudyEventDefinitionBean studyEventDefinitionBean = studyEventDefinitionDAO.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), studyBean.getParentStudyId());
            logger.info("find all by def and subject " + studyEventDefinitionBean.getName() + " study subject " + studySubjectBean.getName());
            StudyEventBean studyEventBean = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(), studyEventDefinitionBean.getId(), Integer.parseInt(sampleOrdinal));
            for (FormDataBean formDataBean : formDataBeans) {
                CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
                ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
                for (CRFVersionBean crfVersionBean : crfVersionBeans) {
                    ArrayList<EventCRFBean> eventCrfBeans = eventCrfDAO.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersionBean);
                    for (EventCRFBean ecb : eventCrfBeans) {
                        Integer ecbId = new Integer(ecb.getId());
                        if (!importedCRFStatuses.keySet().contains(ecbId) && formDataBean.getEventCRFStatus() != null) {
                            importedCRFStatuses.put(ecb.getId(), formDataBean.getEventCRFStatus());
                        }
                    }
                }
            }
        }
    }
}