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

Example 61 with StudyEventBean

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

the class RemoveStudyServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int studyId = fp.getInt("id");
    StudyBean study = (StudyBean) sdao.findByPK(studyId);
    // find all sites
    ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
    // find all user and roles in the study, include ones in sites
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList userRoles = udao.findAllByStudyId(studyId);
    // find all subjects in the study, include ones in sites
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    ArrayList subjects = ssdao.findAllByStudy(study);
    // find all events in the study, include ones in sites
    StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
    ArrayList definitions = sefdao.findAllByStudy(study);
    String action = request.getParameter("action");
    if (studyId == 0) {
        addPageMessage(respage.getString("please_choose_a_study_to_remove"));
        forwardPage(Page.STUDY_LIST_SERVLET);
    } else {
        if ("confirm".equalsIgnoreCase(action)) {
            request.setAttribute("studyToRemove", study);
            request.setAttribute("sitesToRemove", sites);
            request.setAttribute("userRolesToRemove", userRoles);
            request.setAttribute("subjectsToRemove", subjects);
            request.setAttribute("definitionsToRemove", definitions);
            forwardPage(Page.REMOVE_STUDY);
        } else {
            logger.info("submit to remove the study");
            // change all statuses to unavailable
            StudyDAO studao = new StudyDAO(sm.getDataSource());
            study.setOldStatus(study.getStatus());
            study.setStatus(Status.DELETED);
            study.setUpdater(ub);
            study.setUpdatedDate(new Date());
            studao.update(study);
            // remove all sites
            for (int i = 0; i < sites.size(); i++) {
                StudyBean site = (StudyBean) sites.get(i);
                if (!site.getStatus().equals(Status.DELETED)) {
                    site.setOldStatus(site.getStatus());
                    site.setStatus(Status.AUTO_DELETED);
                    site.setUpdater(ub);
                    site.setUpdatedDate(new Date());
                    sdao.update(site);
                }
            }
            // remove all users and roles
            for (int i = 0; i < userRoles.size(); i++) {
                StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
                logger.info("remove user role" + role.getName());
                if (!role.getStatus().equals(Status.DELETED)) {
                    role.setStatus(Status.AUTO_DELETED);
                    role.setUpdater(ub);
                    role.setUpdatedDate(new Date());
                    udao.updateStudyUserRole(role, role.getUserName());
                }
            }
            // YW << bug fix for that current active study has been deleted
            if (study.getId() == currentStudy.getId()) {
                currentStudy.setStatus(Status.DELETED);
                currentRole.setStatus(Status.DELETED);
            } else // (auto-removed)
            if (currentStudy.getParentStudyId() == study.getId()) {
                currentStudy.setStatus(Status.AUTO_DELETED);
                // we may need handle this later?
                currentRole.setStatus(Status.DELETED);
            }
            // remove all subjects
            for (int i = 0; i < subjects.size(); i++) {
                StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
                if (!subject.getStatus().equals(Status.DELETED)) {
                    subject.setStatus(Status.AUTO_DELETED);
                    subject.setUpdater(ub);
                    subject.setUpdatedDate(new Date());
                    ssdao.update(subject);
                }
            }
            // remove all study_group_class
            // changed by jxu on 08-31-06, to fix the problem of no study_id
            // in study_group table
            StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
            StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
            SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
            // YW 09-27-2007, enable status updating for StudyGroupClassBean
            ArrayList groups = sgcdao.findAllByStudy(study);
            for (int i = 0; i < groups.size(); i++) {
                StudyGroupClassBean group = (StudyGroupClassBean) groups.get(i);
                if (!group.getStatus().equals(Status.DELETED)) {
                    group.setStatus(Status.AUTO_DELETED);
                    group.setUpdater(ub);
                    group.setUpdatedDate(new Date());
                    sgcdao.update(group);
                    // all subject_group_map
                    ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupClassId(group.getId());
                    for (int j = 0; j < subjectGroupMaps.size(); j++) {
                        SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
                        if (!sgMap.getStatus().equals(Status.DELETED)) {
                            sgMap.setStatus(Status.AUTO_DELETED);
                            sgMap.setUpdater(ub);
                            sgMap.setUpdatedDate(new Date());
                            sgmdao.update(sgMap);
                        }
                    }
                }
            }
            ArrayList groupClasses = sgcdao.findAllActiveByStudy(study);
            for (int i = 0; i < groupClasses.size(); i++) {
                StudyGroupClassBean gc = (StudyGroupClassBean) groupClasses.get(i);
                if (!gc.getStatus().equals(Status.DELETED)) {
                    gc.setStatus(Status.AUTO_DELETED);
                    gc.setUpdater(ub);
                    gc.setUpdatedDate(new Date());
                    sgcdao.update(gc);
                }
            }
            // remove all event definitions and event
            EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
            StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            for (int i = 0; i < definitions.size(); i++) {
                StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
                if (!definition.getStatus().equals(Status.DELETED)) {
                    definition.setStatus(Status.AUTO_DELETED);
                    definition.setUpdater(ub);
                    definition.setUpdatedDate(new Date());
                    sefdao.update(definition);
                    ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
                    for (int j = 0; j < edcs.size(); j++) {
                        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
                        if (!edc.getStatus().equals(Status.DELETED)) {
                            edc.setStatus(Status.AUTO_DELETED);
                            edc.setUpdater(ub);
                            edc.setUpdatedDate(new Date());
                            edcdao.update(edc);
                        }
                    }
                    ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
                    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
                    for (int j = 0; j < events.size(); j++) {
                        StudyEventBean event = (StudyEventBean) events.get(j);
                        if (!event.getStatus().equals(Status.DELETED)) {
                            event.setStatus(Status.AUTO_DELETED);
                            event.setUpdater(ub);
                            event.setUpdatedDate(new Date());
                            sedao.update(event);
                            ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
                            ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
                            for (int k = 0; k < eventCRFs.size(); k++) {
                                EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
                                if (!eventCRF.getStatus().equals(Status.DELETED)) {
                                    eventCRF.setOldStatus(eventCRF.getStatus());
                                    eventCRF.setStatus(Status.AUTO_DELETED);
                                    eventCRF.setUpdater(ub);
                                    eventCRF.setUpdatedDate(new Date());
                                    ecdao.update(eventCRF);
                                    ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
                                    for (int a = 0; a < itemDatas.size(); a++) {
                                        ItemDataBean item = (ItemDataBean) itemDatas.get(a);
                                        if (!item.getStatus().equals(Status.DELETED)) {
                                            item.setOldStatus(item.getStatus());
                                            item.setStatus(Status.AUTO_DELETED);
                                            item.setUpdater(ub);
                                            item.setUpdatedDate(new Date());
                                            iddao.update(item);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
            // for definitions
            DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
            ArrayList dataset = datadao.findAllByStudyId(study.getId());
            for (int i = 0; i < dataset.size(); i++) {
                DatasetBean data = (DatasetBean) dataset.get(i);
                if (!data.getStatus().equals(Status.DELETED)) {
                    data.setStatus(Status.AUTO_DELETED);
                    data.setUpdater(ub);
                    data.setUpdatedDate(new Date());
                    datadao.update(data);
                }
            }
            addPageMessage(resexception.getString("this_study_has_been_removed_succesfully"));
            forwardPage(Page.STUDY_LIST_SERVLET);
        }
    }
}

Example 62 with StudyEventBean

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

the class RemoveSubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int subjectId = fp.getInt("id");
    String action = fp.getString("action");
    if (subjectId == 0 || StringUtil.isBlank(action)) {
        addPageMessage(respage.getString("please_choose_a_subject_to_remove"));
        forwardPage(Page.SUBJECT_LIST_SERVLET);
    } else {
        SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
        // find all study subjects
        StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
        ArrayList studySubs = ssdao.findAllBySubjectId(subjectId);
        // find study events
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        ArrayList events = sedao.findAllBySubjectId(subjectId);
        if ("confirm".equalsIgnoreCase(action)) {
            request.setAttribute("subjectToRemove", subject);
            request.setAttribute("studySubs", studySubs);
            request.setAttribute("events", events);
            forwardPage(Page.REMOVE_SUBJECT);
        } else {
            logger.info("submit to remove the subject");
            // change all statuses to deleted
            subject.setStatus(Status.DELETED);
            subject.setUpdater(ub);
            subject.setUpdatedDate(new Date());
            sdao.update(subject);
            // remove subject references from study
            for (int i = 0; i < studySubs.size(); i++) {
                StudySubjectBean studySub = (StudySubjectBean) studySubs.get(i);
                if (!studySub.getStatus().equals(Status.DELETED)) {
                    studySub.setStatus(Status.AUTO_DELETED);
                    studySub.setUpdater(ub);
                    studySub.setUpdatedDate(new Date());
                    ssdao.update(studySub);
                }
            }
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            for (int j = 0; j < events.size(); j++) {
                StudyEventBean event = (StudyEventBean) events.get(j);
                if (!event.getStatus().equals(Status.DELETED)) {
                    event.setStatus(Status.AUTO_DELETED);
                    event.setUpdater(ub);
                    event.setUpdatedDate(new Date());
                    sedao.update(event);
                    ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
                    ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
                    for (int k = 0; k < eventCRFs.size(); k++) {
                        EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
                        if (!eventCRF.getStatus().equals(Status.DELETED)) {
                            eventCRF.setStatus(Status.AUTO_DELETED);
                            eventCRF.setUpdater(ub);
                            eventCRF.setUpdatedDate(new Date());
                            ecdao.update(eventCRF);
                            // remove all the item data
                            ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
                            for (int a = 0; a < itemDatas.size(); a++) {
                                ItemDataBean item = (ItemDataBean) itemDatas.get(a);
                                if (!item.getStatus().equals(Status.DELETED)) {
                                    item.setStatus(Status.AUTO_DELETED);
                                    item.setUpdater(ub);
                                    item.setUpdatedDate(new Date());
                                    iddao.update(item);
                                }
                            }
                        }
                    }
                }
            }
            String emailBody = respage.getString("the_subject") + " " + subject.getUniqueIdentifier() + " " + respage.getString("has_been_removed_succesfully");
            addPageMessage(emailBody);
            // sendEmail(emailBody);
            forwardPage(Page.SUBJECT_LIST_SERVLET);
        }
    }
}

Example 63 with StudyEventBean

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

the class ExtractBean method getEvent.

/**
 * Get the event correspodning to the provided study subject, SED and sample
 * ordinal.
 *
 * @param h
 *            An index into the array of subjects.
 * @param i
 *            An index into the array of SEDs.
 * @param j
 *            The sample ordinal.
 * @return The event correspodning to the provided study subject, SED and
 *         sample ordinal.
 */
private StudyEventBean getEvent(int h, int i, int j) {
    syncSubjectIndex(h);
    syncSEDIndex(i);
    String key = getStudyEventDataKey(currentSubject.getId(), currentDef.getId(), j);
    StudyEventBean seb = (StudyEventBean) eventData.get(key);
    if (seb == null) {
        // logger.info("dump of event data: "+eventData.toString());
        return new StudyEventBean();
    } else {
        // "+key);
        if (seb.getEventCRFs().size() > 0) {
            EventCRFBean ecbean = (EventCRFBean) seb.getEventCRFs().get(0);
        }
        // logger.info("int.name "+ecbean.getInterviewerName());
        return seb;
    }
}

Example 64 with StudyEventBean

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

the class ExtractBean method addStudyEventDataOld.

// addStudyEventData
/*
     * addStudyEventData, a function which puts information about a
     * study-subject taking an event-crf into the ExtractBean's interface.
     */
public void addStudyEventDataOld(Integer studySubjectId, String studyEventDefinitionName, Integer studyEventDefinitionId, Integer sampleOrdinal, String studyEventLocation, Date studyEventStart, Date studyEventEnd, String crfVersionName, Integer crfVersionStatusId, Date dateInterviewed, String interviewerName, Date dateCompleted, Date dateValidateCompleted, Integer completionStatusId) {
    if (studySubjectId == null || studyEventDefinitionId == null || sampleOrdinal == null || studyEventLocation == null || studyEventStart == null) {
        return;
    }
    if (studyEventDefinitionId.intValue() <= 0 || studySubjectId.intValue() <= 0 || sampleOrdinal.intValue() <= 0) {
        return;
    }
    // YW 08-21-2007 << fetch start_time_flag and end_time_flag
    StudyEventDAO sedao = new StudyEventDAO(ds);
    StudyEventBean se = (StudyEventBean) sedao.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectId, studyEventDefinitionId, sampleOrdinal);
    // YW >>
    if (se == null) {
        se.setStatus(Status.INVALID);
    }
    StudyEventBean event = new StudyEventBean();
    EventCRFBean eventCRF = new EventCRFBean();
    event.setName(studyEventDefinitionName);
    event.setDateStarted(studyEventStart);
    event.setDateEnded(studyEventEnd);
    event.setLocation(studyEventLocation);
    event.setSampleOrdinal(sampleOrdinal.intValue());
    event.setStudyEventDefinitionId(studyEventDefinitionId.intValue());
    event.setStudySubjectId(studySubjectId.intValue());
    event.setStartTimeFlag(se.getStartTimeFlag());
    event.setEndTimeFlag(se.getEndTimeFlag());
    // below needs to be added, tbh
    event.setStatus(se.getStatus());
    event.setSubjectEventStatus(se.getSubjectEventStatus());
    event.setStage(se.getStage());
    logger.info("found stage: " + se.getStage().getName());
    event.setId(se.getId());
    // end tbh, 03/08
    // 
    eventCRF.setCompletionStatusId(completionStatusId.intValue());
    eventCRF.setInterviewerName(interviewerName);
    eventCRF.setDateCompleted(dateCompleted);
    eventCRF.setDateValidateCompleted(dateValidateCompleted);
    // eventCRF.setCreatedDate();//same as interviewed date? NO
    eventCRF.setDateInterviewed(dateInterviewed);
    // eventCRF.setStatus(status); //this is the one that we want, tbh
    // EventCRFDAO ecrfdao = new EventCRFDAO(ds);
    // ArrayList events = ecrfdao.findAllByStudyEvent(se);
    CRFVersionBean crfVersion = new CRFVersionBean();
    crfVersion.setName(crfVersionName);
    crfVersion.setStatus(Status.get(crfVersionStatusId.intValue()));
    crfVersion.setStatusId(crfVersionStatusId.intValue());
    eventCRF.setCrfVersion(crfVersion);
    // logger.info();
    ArrayList events = new ArrayList();
    events.add(eventCRF);
    // logger.info("///adding an event CRF..."
    // + eventCRF.getInterviewerName());
    // hmm, one to one relationship?
    event.setEventCRFs(events);
    // guard clause to see if it's in there already?
    // not rly, the above is only used in auditlogging
    // could fit in crf and crf version ids here, though
    // FIXME def not one to one relationship, tbh, 03.08
    String key = getStudyEventDataKey(studySubjectId.intValue(), studyEventDefinitionId.intValue(), sampleOrdinal.intValue());
    if (eventData == null) {
        eventData = new HashMap();
    }
    StudyEventBean checkEvent = (StudyEventBean) eventData.get(key);
    if (checkEvent == null) {
        eventData.put(key, event);
        logger.info("###just CREATED key: " + key + " event: " + event.getName() + " int.name: " + eventCRF.getInterviewerName());
    } else {
    // ArrayList eventCRFs = checkEvent.getEventCRFs();
    // eventCRFs.add(eventCRF);
    // checkEvent.setEventCRFs(eventCRFs);
    // eventData.put(key, checkEvent);
    // logger.info("count of eventcrfs "+eventCRFs.size());
    // logger.info("other things about the event crf: int.name
    // "+eventCRF.getInterviewerName()+" comp status id
    // "+eventCRF.getCompletionStatusId()+" version name
    // "+eventCRF.getCrfVersion().getName());
    // logger.info("###just UPDATED key: "+key+" event:
    // "+event.getName()+" int.name: "+eventCRF.getInterviewerName());
    }
// the problem: we want to order by start date
// but hashmaps are by their very nature hard to order
// and there is no contigous start date that we can sort on, i.e. we
// only
// look at one at a time.
}

Example 65 with StudyEventBean

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

the class ExtractStudySubjectBean method addStudyEvent.

/**
 * Adds a study event for the subject.
 *
 * @param location
 * @param start
 * @param end
 * @return
 */
public StudyEventBean addStudyEvent(ExtractStudyEventDefinitionBean sedb, Integer idObj, String location, Date start, Date end, Integer dbOrdinalObj) {
    StudyEventBean seb = new StudyEventBean();
    if (idObj == null || location == null || start == null || end == null || dbOrdinalObj == null) {
        return seb;
    }
    int id = idObj.intValue();
    int dbOrdinal = dbOrdinalObj.intValue();
    seb.setLocation(location);
    seb.setDateStarted(start);
    seb.setDateStarted(end);
    seb.setId(id);
    seb.setSampleOrdinal(dbOrdinal);
    int sampleNum = getSampleNum(sedb.getId(), dbOrdinal);
    String key = getStudyEventsKey(sedb.getId(), sampleNum);
    studyEvents.put(key, seb);
    return seb;
}