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

Example 11 with SubjectBean

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

the class ListDiscNotesForCRFTableFactory method setDataAndLimitVariables.

@SuppressWarnings("unchecked")
@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    Limit limit = tableFacade.getLimit();
    ListDiscNotesForCRFFilter listDiscNotesForCRF = getListEventsForSubjectFilter(limit);
    listDiscNotesForCRF.addFilter("dn.discrepancy_note_type_id", this.discNoteType);
    StringBuffer constraints = new StringBuffer();
    if (this.discNoteType > 0 && this.discNoteType < 10) {
        constraints.append(" and dn.discrepancy_note_type_id=" + this.discNoteType);
    }
    if (this.resolutionStatusIds != null && this.resolutionStatusIds.size() > 0) {
        String s = " and (";
        for (Integer resolutionStatusId : this.resolutionStatusIds) {
            s += "dn.resolution_status_id = " + resolutionStatusId + " or ";
        }
        s = s.substring(0, s.length() - 3) + " )";
        listDiscNotesForCRF.addFilter("dn.resolution_status_id", s);
        constraints.append(s);
    }
    if (!limit.isComplete()) {
        int totalRows = getStudySubjectDAO().getCountWithFilter(listDiscNotesForCRF, getStudyBean());
        tableFacade.setTotalRows(totalRows);
    }
    ListDiscNotesForCRFSort eventsForSubjectSort = getListEventsForSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<StudySubjectBean> items = getStudySubjectDAO().getWithFilterAndSort(getStudyBean(), listDiscNotesForCRF, eventsForSubjectSort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    boolean hasDN = false;
    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());
        SubjectBean subjectBean = (SubjectBean) getSubjectDAO().findByPK(studySubjectBean.getSubjectId());
        theItem.put("subject", subjectBean);
        theItem.put("subject.charGender", subjectBean.getGender());
        // 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("event.startDate", null);
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                HashMap<ResolutionStatus, Integer> discCounts = new HashMap<ResolutionStatus, Integer>();
                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() + "_discCounts", discCounts);
                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("event.startDate", studyEventBean.getCreatedDate());
            for (int i = 0; i < getCrfs(selectedStudyEventDefinition).size(); i++) {
                CRFBean crf = getCrfs(selectedStudyEventDefinition).get(i);
                EventCRFBean eventCRFBean = crfAsKeyEventCrfAsValue.get(crf.getId() + "_" + studyEventBean.getId());
                HashMap<ResolutionStatus, Integer> discCounts = new HashMap<ResolutionStatus, Integer>();
                if (eventCRFBean != null) {
                    d.getProps().put("crf_" + crf.getId(), eventCRFBean.getStage());
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", eventCRFBean);
                    // List<DiscrepancyNoteBean> discs =
                    // getDiscrepancyNoteDAO().findAllByStudyEvent(studyEventBean);
                    List<DiscrepancyNoteBean> discs = getDiscrepancyNoteDAO().findAllParentItemNotesByEventCRFWithConstraints(eventCRFBean.getId(), constraints);
                    hasDN = hasDN == false ? discs != null && discs.size() > 0 : hasDN;
                    for (DiscrepancyNoteBean discrepancyNoteBean : discs) {
                        Integer value = discCounts.get(discrepancyNoteBean.getResStatus());
                        if (value != null) {
                            discCounts.put(discrepancyNoteBean.getResStatus(), ++value);
                        } else {
                            discCounts.put(discrepancyNoteBean.getResStatus(), 1);
                        }
                    }
                    d.getProps().put("crf_" + crf.getId() + "_discCounts", discCounts);
                } else {
                    d.getProps().put("crf_" + crf.getId(), DataEntryStage.UNCOMPLETED);
                    d.getProps().put("crf_" + crf.getId() + "_eventCrf", null);
                    d.getProps().put("crf_" + crf.getId() + "_discCounts", discCounts);
                }
                d.getProps().put("crf_" + crf.getId() + "_crf", crf);
                d.getProps().put("crf_" + crf.getId() + "_eventDefinitionCrf", eventDefinitionCrfs.get(i));
                theItem.put("crf_" + crf.getId(), "");
            }
            events.add(d);
        }
        theItem.put("events", events);
        theItem.put("event.status", "");
        theItem.put("event.startDate", "");
        theItems.add(theItem);
    }
    // Do not forget to set the items back on the tableFacade.
    tableFacade.setItems(theItems);
    this.setStudyHasDiscNotes(hasDN);
}

Example 12 with SubjectBean

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

the class SubjectRow 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(SubjectRow.class)) {
        return 0;
    }
    SubjectBean thisSubject = (SubjectBean) bean;
    SubjectBean argSubject = (SubjectBean) ((SubjectRow) row).bean;
    int answer = 0;
    switch(sortingColumn) {
        case COL_NAME:
            answer = thisSubject.getName().toLowerCase().compareTo(argSubject.getName().toLowerCase());
            break;
        case COL_GENDER:
            answer = (thisSubject.getGender() + "").compareTo(argSubject.getGender() + "");
            break;
        case COL_DATE_CREATED:
            answer = compareDate(thisSubject.getCreatedDate(), argSubject.getCreatedDate());
            break;
        case COL_OWNER:
            answer = thisSubject.getOwner().getName().toLowerCase().compareTo(argSubject.getOwner().getName().toLowerCase());
            break;
        case COL_DATE_UPDATED:
            answer = compareDate(thisSubject.getUpdatedDate(), argSubject.getUpdatedDate());
            break;
        case COL_UPDATER:
            answer = thisSubject.getUpdater().getName().toLowerCase().compareTo(argSubject.getUpdater().getName().toLowerCase());
            break;
        case COL_STATUS:
            answer = thisSubject.getStatus().compareTo(argSubject.getStatus());
            break;
    }
    return answer;
}

Example 13 with SubjectBean

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

the class UpdateSubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
    String fromResolvingNotes = fp.getString("fromResolvingNotes", true);
    if (StringUtils.isBlank(fromResolvingNotes)) {
        session.removeAttribute(ViewNotesServlet.WIN_LOCATION);
        session.removeAttribute(ViewNotesServlet.NOTES_TABLE);
        checkStudyLocked(Page.LIST_SUBJECT_SERVLET, respage.getString("current_study_locked"));
        checkStudyFrozen(Page.LIST_SUBJECT_SERVLET, respage.getString("current_study_frozen"));
    }
    int subjectId = fp.getInt("id", true);
    int studySubId = fp.getInt("studySubId", true);
    if (subjectId == 0) {
        addPageMessage(respage.getString("please_choose_subject_to_edit"));
        forwardPage(Page.LIST_SUBJECT_SERVLET);
    } else {
        String action = fp.getString("action", true);
        if (StringUtils.isBlank("action")) {
            addPageMessage(respage.getString("no_action_specified"));
            forwardPage(Page.LIST_SUBJECT_SERVLET);
            return;
        }
        SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
        if (action.equals("show") || action.equals("confirm")) {
            request.setAttribute("studySubId", new Integer(studySubId));
            request.setAttribute("id", new Integer(subjectId));
            request.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
        }
        if ("show".equalsIgnoreCase(action)) {
            // no DOB collected
            request.setAttribute("localBirthDate", "");
            if (!currentStudy.getStudyParameterConfig().getCollectDob().equals("3") && subject.getDateOfBirth() != null) {
                setLocalDOB(subject);
            }
            discNotes = new FormDiscrepancyNotes();
            request.setAttribute("genderDNFlag", "icon_noNote");
            request.setAttribute("birthDNFlag", "icon_noNote");
            request.setAttribute("subjectToUpdate", subject);
            setDNFlag(subjectId);
            forwardPage(Page.UPDATE_SUBJECT);
        } else if ("confirm".equalsIgnoreCase(action)) {
            confirm(subject, subjectId);
        } else {
            String gender = fp.getString("gender");
            subject.setGender(gender.charAt(0));
            if (currentStudy.getStudyParameterConfig().getSubjectPersonIdRequired().equals("required") || currentStudy.getStudyParameterConfig().getSubjectPersonIdRequired().equals("optional")) {
                subject.setUniqueIdentifier(fp.getString("uniqueIdentifier"));
            }
            subject.setUpdater(ub);
            if (!currentStudy.getStudyParameterConfig().getCollectDob().equals("3")) {
                if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
                    String d_date = fp.getString(DATE_DOB_TO_SAVE);
                    if (!(d_date == null || d_date.trim().length() == 0)) {
                        Date date_new = yformat.parse(fp.getString(DATE_DOB_TO_SAVE));
                        subject.setDateOfBirth(date_new);
                    }
                }
                if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
                    Date date_new = local_df.parse(fp.getString(DATE_DOB_TO_SAVE));
                    subject.setDateOfBirth(date_new);
                }
            }
            sdao.update(subject);
            // save discrepancy notes into DB
            DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
            FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
            AddNewSubjectServlet.saveFieldNotes("gender", fdn, dndao, subject.getId(), "subject", currentStudy);
            AddNewSubjectServlet.saveFieldNotes(DATE_DOB, fdn, dndao, subject.getId(), "subject", currentStudy);
            addPageMessage(respage.getString("subject_updated_succcesfully"));
            if (studySubId > 0) {
                request.setAttribute("id", new Integer(studySubId).toString());
                forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
            } else {
                forwardPage(Page.LIST_SUBJECT_SERVLET);
            }
        }
    }
}

Example 14 with SubjectBean

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

the class ListSubjectTableFactory method setDataAndLimitVariables.

@SuppressWarnings("unchecked")
@Override
public void setDataAndLimitVariables(TableFacade tableFacade) {
    // initialize i18n
    resword = ResourceBundleProvider.getWordsBundle(getLocale());
    resformat = ResourceBundleProvider.getFormatBundle(getLocale());
    Limit limit = tableFacade.getLimit();
    ListSubjectFilter listSubjectFilter = getListSubjectFilter(limit);
    if (!limit.isComplete()) {
        Integer totalRows = getSubjectDao().getCountWithFilter(listSubjectFilter, getCurrentStudy());
        if (totalRows == null) {
            totalRows = 0;
        }
        tableFacade.setTotalRows(totalRows.intValue());
    }
    ListSubjectSort listSubjectSort = getListSubjectSort(limit);
    int rowStart = limit.getRowSelect().getRowStart();
    int rowEnd = limit.getRowSelect().getRowEnd();
    Collection<SubjectBean> items = getSubjectDao().getWithFilterAndSort(getCurrentStudy(), listSubjectFilter, listSubjectSort, rowStart, rowEnd);
    Collection<HashMap<Object, Object>> theItems = new ArrayList<HashMap<Object, Object>>();
    for (SubjectBean subject : items) {
        UserAccountBean owner = (UserAccountBean) getUserAccountDao().findByPK(subject.getOwnerId());
        UserAccountBean updater = subject.getUpdaterId() == 0 ? null : (UserAccountBean) getUserAccountDao().findByPK(subject.getUpdaterId());
        HashMap<Object, Object> h = new HashMap<Object, Object>();
        String studySubjectIdAndStudy = "";
        List<StudySubjectBean> studySubjects = getStudySubjectDao().findAllBySubjectId(subject.getId());
        for (StudySubjectBean studySubjectBean : studySubjects) {
            StudyBean study = (StudyBean) getStudyDao().findByPK(studySubjectBean.getStudyId());
            studySubjectIdAndStudy += studySubjectIdAndStudy.length() == 0 ? "" : ",";
            studySubjectIdAndStudy += study.getIdentifier() + "-" + studySubjectBean.getLabel();
        }
        h.put("studySubjectIdAndStudy", studySubjectIdAndStudy);
        h.put("subject", subject);
        h.put("subject.uniqueIdentifier", subject.getUniqueIdentifier());
        h.put("subject.gender", subject.getGender());
        Date tempDate = subject.getCreatedDate();
        String tempDateStr = tempDate == null ? "" : I18nFormatUtil.getDateFormat(getLocale()).format(tempDate);
        h.put("subject.createdDate", tempDateStr);
        h.put("subject.owner", owner);
        tempDate = subject.getUpdatedDate();
        tempDateStr = tempDate == null ? "" : I18nFormatUtil.getDateFormat(getLocale()).format(tempDate);
        h.put("subject.updatedDate", tempDateStr);
        h.put("subject.updater", updater);
        h.put("subject.status", subject.getStatus());
        theItems.add(h);
    }
    tableFacade.setItems(theItems);
}

Example 15 with SubjectBean

use of org.akaza.openclinica.bean.submit.SubjectBean 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);
        }
    }
}