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

Example 76 with StudyEventBean

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

the class RemoveSiteServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    String idString = request.getParameter("id");
    logger.info("site id:" + idString);
    int siteId = Integer.valueOf(idString.trim()).intValue();
    StudyBean study = (StudyBean) sdao.findByPK(siteId);
    if (currentStudy.getId() != study.getParentStudyId()) {
        addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
        forwardPage(Page.MENU_SERVLET);
        return;
    }
    // find all user and roles
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList userRoles = udao.findAllByStudyId(siteId);
    // find all subjects
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    ArrayList subjects = ssdao.findAllByStudy(study);
    // find all events
    StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
    ArrayList definitions = sefdao.findAllByStudy(study);
    String action = request.getParameter("action");
    if (StringUtil.isBlank(idString)) {
        addPageMessage(respage.getString("please_choose_a_site_to_remove"));
        forwardPage(Page.SITE_LIST_SERVLET);
    } else {
        if ("confirm".equalsIgnoreCase(action)) {
            request.setAttribute("siteToRemove", study);
            request.setAttribute("userRolesToRemove", userRoles);
            request.setAttribute("subjectsToRemove", subjects);
            forwardPage(Page.REMOVE_SITE);
        } else {
            logger.info("submit to remove the site");
            // 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 users and roles
            for (int i = 0; i < userRoles.size(); i++) {
                StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
                if (!role.getStatus().equals(Status.DELETED)) {
                    role.setStatus(Status.AUTO_DELETED);
                    role.setUpdater(ub);
                    role.setUpdatedDate(new Date());
                    // YW << So study_user_role table status_id field can be
                    // updated
                    udao.updateStudyUserRole(role, role.getUserName());
                }
            // YW 06-18-2007 >>
            }
            // YW << bug fix that current active study has been deleted
            if (study.getId() == currentStudy.getId()) {
                currentStudy.setStatus(Status.DELETED);
                // currentRole.setRole(Role.INVALID);
                currentRole.setStatus(Status.DELETED);
            }
            // remove all subjects
            for (int i = 0; i < subjects.size(); i++) {
                StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
            }
            // remove all study_group
            StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
            SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
            ArrayList groups = sgdao.findAllByStudy(study);
            for (int i = 0; i < groups.size(); i++) {
                StudyGroupBean group = (StudyGroupBean) groups.get(i);
                if (!group.getStatus().equals(Status.DELETED)) {
                    group.setStatus(Status.AUTO_DELETED);
                    group.setUpdater(ub);
                    group.setUpdatedDate(new Date());
                    sgdao.update(group);
                    // all subject_group_map
                    ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(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);
                        }
                    }
                }
            }
            // remove all events
            EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
            StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            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);
                    ArrayList events = sedao.findAllByStudySubject(subject);
                    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 subjects
            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(respage.getString("this_site_has_been_removed_succesfully"));
            String fromListSite = (String) session.getAttribute("fromListSite");
            if (fromListSite != null && fromListSite.equals("yes") && currentRole.getRole().equals(Role.STUDYDIRECTOR)) {
                session.removeAttribute("fromListSite");
                forwardPage(Page.SITE_LIST_SERVLET);
            } else {
                session.removeAttribute("fromListSite");
                if (currentRole.getRole().equals(Role.ADMIN)) {
                    forwardPage(Page.STUDY_LIST_SERVLET);
                } else {
                    forwardPage(Page.SITE_LIST_SERVLET);
                }
            }
        }
    }
}

Example 77 with StudyEventBean

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

the class UnlockEventDefinitionServlet method processRequest.

@Override
public void processRequest() throws Exception {
    String idString = request.getParameter("id");
    int defId = Integer.valueOf(idString.trim()).intValue();
    StudyEventDefinitionDAO sdao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sed = (StudyEventDefinitionBean) sdao.findByPK(defId);
    // find all CRFs
    EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
    ArrayList eventDefinitionCRFs = (ArrayList) edao.findAllByDefinition(defId);
    CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
    CRFDAO cdao = new CRFDAO(sm.getDataSource());
    for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
        ArrayList versions = (ArrayList) cvdao.findAllByCRF(edc.getCrfId());
        edc.setVersions(versions);
        CRFBean crf = (CRFBean) cdao.findByPK(edc.getCrfId());
        edc.setCrfName(crf.getName());
    }
    // finds all events
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    ArrayList events = (ArrayList) sedao.findAllByDefinition(sed.getId());
    String action = request.getParameter("action");
    if (StringUtil.isBlank(idString)) {
        addPageMessage(respage.getString("please_choose_a_SED_to_unlock"));
        forwardPage(Page.LIST_DEFINITION_SERVLET);
    } else {
        if ("confirm".equalsIgnoreCase(action)) {
            if (!sed.getStatus().equals(Status.LOCKED)) {
                addPageMessage(respage.getString("this_SED_cannot_be_unlocked") + " " + respage.getString("please_contact_sysadmin_for_more_information"));
                forwardPage(Page.LIST_DEFINITION_SERVLET);
                return;
            }
            request.setAttribute("definitionToUnlock", sed);
            request.setAttribute("eventDefinitionCRFs", eventDefinitionCRFs);
            request.setAttribute("events", events);
            forwardPage(Page.UNLOCK_DEFINITION);
        } else {
            logger.info("submit to lock the definition");
            // unlock definition
            sed.setStatus(Status.AVAILABLE);
            sed.setUpdater(ub);
            sed.setUpdatedDate(new Date());
            sdao.update(sed);
            // lock all crfs
            for (int j = 0; j < eventDefinitionCRFs.size(); j++) {
                EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(j);
                edc.setStatus(Status.AVAILABLE);
                edc.setUpdater(ub);
                edc.setUpdatedDate(new Date());
                edao.update(edc);
            }
            // unlock all events
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            for (int j = 0; j < events.size(); j++) {
                StudyEventBean event = (StudyEventBean) events.get(j);
                event.setStatus(Status.AVAILABLE);
                event.setUpdater(ub);
                event.setUpdatedDate(new Date());
                sedao.update(event);
                ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
                // unlock all the item data
                ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
                for (int k = 0; k < eventCRFs.size(); k++) {
                    EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
                    eventCRF.setStatus(Status.AVAILABLE);
                    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);
                        item.setStatus(Status.AVAILABLE);
                        item.setUpdater(ub);
                        item.setUpdatedDate(new Date());
                        iddao.update(item);
                    }
                }
            }
            String emailBody = respage.getString("the_SED") + " " + sed.getName() + respage.getString("has_been_unlocked_for_the_study") + " " + currentStudy.getName() + ". " + respage.getString("subject_event_data_is_as_it_was_before");
            addPageMessage(emailBody);
            sendEmail(emailBody);
            forwardPage(Page.LIST_DEFINITION_SERVLET);
        }
    }
}

Example 78 with StudyEventBean

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

the class ExtractBean method getCRFCompletionDate.

protected String getCRFCompletionDate(int h, int i, int j) {
    StudyEventBean seb = getEvent(h, i, j);
    EventCRFBean eventCRF = null;
    if (seb.getEventCRFs().size() > 0) {
        eventCRF = (EventCRFBean) seb.getEventCRFs().get(0);
    }
    // need
    return eventCRF.getDateValidateCompleted() == null ? sdf.format(eventCRF.getDateCompleted()) : sdf.format(eventCRF.getDateValidateCompleted());
// to
// be
// fixed?
}

Example 79 with StudyEventBean

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

the class ExtractBean method addStudyEventData.

// addStudySubjectData
/*
     * public void addStudySubjectData(Integer studySubjectId, String
     * studySubjectLabel, Date dateOfBirth, String gender, Integer
     * subjectStatusId, Boolean dobCollected, String uniqueIdentifier, String
     * subjectSecondaryLabel) { if (!subjectsAdded.containsKey(studySubjectId))
     * { StudySubjectBean sub = new StudySubjectBean();
     * sub.setId(studySubjectId.intValue()); sub.setLabel(studySubjectLabel);
     *
     * sub.setDateOfBirth(dateOfBirth); if (gender != null && gender.length() >
     * 0) { sub.setGender(gender.charAt(0)); } else { sub.setGender(' '); }
     * sub.setStatus(Status.get(subjectStatusId.intValue())); //
     * sub.setSecondaryLabel(secondaryID);//????
     * sub.setUniqueIdentifier(uniqueIdentifier);
     * sub.setSecondaryLabel(subjectSecondaryLabel); //
     * sub.setEnrollmentDate(enrollmentDate); // TODO need to find enrollment
     * date, later, tbh subjects.add(sub); subjectsAdded.put(studySubjectId,
     * Boolean.TRUE); } }
     */
/**
 * @vbc 08/06/2008 NEW EXTRACT DATA IMPLEMENTATION Combines the two HashMaps
 *      into eventData entries - the data is already filtered for null
 *      values
 */
public void addStudyEventData() {
    /**
     * The two ArrayList are synchronized because they are extracted with
     * "ORDER BY aitem_data_id"
     */
    boolean isfnd = false;
    // initialize
    eventData = new HashMap();
    for (int ik = 0; ik < aBASE_ITEMDATAID.size(); ik++) {
        // get the item_group side
        extractDataset_ITEMGROUPSIDE objgrp = (extractDataset_ITEMGROUPSIDE) hBASE_ITEMGROUPSIDE.get(ik);
        extractDataset_EVENTSIDE objev = (extractDataset_EVENTSIDE) hBASE_EVENTSIDE.get(ik);
        // sanity check - assume both are not null
        Integer itemdataid = (Integer) aBASE_ITEMDATAID.get(ik);
        Integer itemdataid_objgrp = objgrp.itemDataId;
        Integer itemdataid_objev = objev.itemDataId;
        if (itemdataid_objgrp.intValue() == itemdataid.intValue() && itemdataid_objev.intValue() == itemdataid.intValue()) {
            // OK - add entries to the dataEvent
            // initialize
            StudyEventBean event = new StudyEventBean();
            EventCRFBean eventCRF = new EventCRFBean();
            // 
            // studyEventDefinitionName
            event.setName(objev.studyEventDefinitionName);
            // studyEventStart
            event.setDateStarted(objev.studyEventDateStart);
            // studyEventEnd
            event.setDateEnded(objev.studyEventDateEnd);
            // studyEventLocation
            event.setLocation(objev.studyEventLoacation);
            // sampleOrdinal
            event.setSampleOrdinal(objev.sampleOrdinal.intValue());
            // .
            // intValue
            // ()
            // studyEventDefinitionId
            event.setStudyEventDefinitionId(objev.studyEvenetDefinitionId.intValue());
            // .
            // intValue
            // (
            // )
            // studySubjectId
            event.setStudySubjectId(objev.studySubjectId.intValue());
            // .
            // intValue
            // ()
            // se
            event.setStartTimeFlag(objev.studyEventStartTimeFlag.booleanValue());
            // .
            // getStartTimeFlag
            // (
            // )
            // se
            event.setEndTimeFlag(objev.studyEventEndTimeFlag.booleanValue());
            // .
            // getEndTimeFlag
            // (
            // )
            // below needs to be added, tbh
            // TODO - @vbc - validate this
            // se
            event.setStatus(Status.get(objev.studyEventStatusId.intValue()));
            // .
            // getStatus
            // (
            // )
            // se
            event.setSubjectEventStatus(SubjectEventStatus.get(objev.studyEventSubjectEventStatusId.intValue()));
            // .
            // getSubjectEventStatus
            // (
            // )
            // @vbc 08/06/2008 NEW EXTRACT DATA IMPLEMENTATION
            // the stage is set on setStatus - skip it
            // event.setStage(se.getStage());
            // se.getId()
            event.setId(objev.studyEventId.intValue());
            // end tbh, 03/08
            // completionStatusId
            eventCRF.setCompletionStatusId(objgrp.eventCrfCompletionStatusId);
            // .
            // intValue
            // (
            // )
            // interviewerName
            eventCRF.setInterviewerName(objgrp.interviewerName);
            // dateCompleted
            eventCRF.setDateCompleted(objgrp.eventCrfDateCompleted);
            // dateValidateCompleted
            eventCRF.setDateValidateCompleted(objgrp.eventCrfDateValidateCompleted);
            eventCRF.setStatus(Status.get(objgrp.eventCrfStatusId));
            // eventCRF.setCreatedDate();//same as interviewed date? NO
            // dateInterviewedv
            eventCRF.setDateInterviewed(objgrp.dateInterviewed);
            // eventCRF.setStatus(status); //this is the one that we want,
            // tbh
            CRFVersionBean crfVersion = new CRFVersionBean();
            // crfVersionName
            crfVersion.setName(objgrp.crfVersionName);
            // crfVersionStatusId
            crfVersion.setStatus(Status.get(objgrp.crfVersionStatusId.intValue()));
            // crfVersionStatusId
            crfVersion.setStatusId(objgrp.crfVersionStatusId.intValue());
            // .
            // intValue
            // (
            // )
            eventCRF.setCrfVersion(crfVersion);
            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() */
            objev.studySubjectId.intValue(), /* studyEventDefinitionId.intValue() */
            objev.studyEvenetDefinitionId.intValue(), /* sampleOrdinal.intValue()) */
            objev.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 {
            // OK - already saved
            }
        } else {
            isfnd = true;
        }
    // 
    }
    // for
    // before return quick count
    logger.debug("Number of entries in the eventData is:" + eventData.size());
}

Example 80 with StudyEventBean

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

the class ExtractBean method getCRFStatus.

// below created to support CRF metadata, tbh
protected String getCRFStatus(int h, int i, int j) {
    // return crfbean.getStatus().getName();
    // return currentCRF.getStatus().getName();
    StudyEventBean seb = getEvent(h, i, j);
    ArrayList crfbeans = currentDef.getCrfs();
    EventCRFBean eventCRF = null;
    if (seb.getEventCRFs().size() > 0) {
        eventCRF = (EventCRFBean) seb.getEventCRFs().get(0);
    }
    return eventCRF != null ? eventCRF.getStatus().getName() : "";
}