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

Example 96 with StudyEventBean

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

the class DataEntryServlet method getInputBeans.

/**
 * Get the input beans - the EventCRFBean and the SectionBean. For both beans, look first in the request attributes to see if the bean has been stored
 * there. If not, look in the parameters for the bean id, and then retrieve the bean from the database. The beans are stored as protected class members.
 * @param request TODO
 */
protected void getInputBeans(HttpServletRequest request) throws InsufficientPermissionException {
    HttpSession session = request.getSession();
    StudyBean currentStudy = (StudyBean) session.getAttribute("study");
    // BWP >>we should have the correct crfVersionId, in order to acquire
    // the correct
    // section IDs
    FormProcessor fp = new FormProcessor(request);
    EventCRFDAO ecdao = new EventCRFDAO(getDataSource());
    SectionDAO sdao = new SectionDAO(getDataSource());
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    // JN:Happening when drilling down?
    if (ecb == null) {
        int eventCRFId = fp.getInt(INPUT_EVENT_CRF_ID, true);
        LOGGER.debug("found event crf id: " + eventCRFId);
        if (eventCRFId > 0) {
            LOGGER.debug("***NOTE*** that we didnt have to create an event crf because we already have one: " + eventCRFId);
            // there is an event CRF already, only need to update
            ecb = (EventCRFBean) ecdao.findByPK(eventCRFId);
            // ecb.setUpdatedDate(new Date());
            // ecb.setUpdater(ub);
            // ecb = (EventCRFBean) ecdao.update(ecb);
            // logger.trace("found an event crf id "+eventCRFId);
            // YW 11-12-2007 << if interviewer or/and interview date
            // has/have been updated for study/site from "blank" to
            // "pre-populated"
            // But at this point, this update only shows on web page and
            // will not be updated to database.
            int studyEventId = fp.getInt(INPUT_STUDY_EVENT_ID);
            request.setAttribute(INPUT_EVENT_CRF, ecb);
            if (studyEventId > 0) {
                StudyEventDAO sedao = new StudyEventDAO(getDataSource());
                StudyEventBean sEvent = (StudyEventBean) sedao.findByPK(studyEventId);
                ecb = updateECB(sEvent, request);
            }
            request.setAttribute(INPUT_EVENT_CRF, ecb);
        // YW >>
        } else {
            // CRF id <=0, so we need to create a new CRF
            // use toCreateCRF as a flag to prevent user to submit event CRF
            // more than once
            // for example, user reloads the page
            String toCreateCRF = (String) session.getAttribute("to_create_crf");
            if (StringUtil.isBlank(toCreateCRF) || "0".equals(toCreateCRF)) {
                session.setAttribute("to_create_crf", "1");
            }
            try {
                // if (ecb.getInterviewerName() != null) {
                LOGGER.debug("Initial: to create an event CRF.");
                String toCreateCRF1 = (String) session.getAttribute("to_create_crf");
                if (!StringUtil.isBlank(toCreateCRF1) && "1".equals(toCreateCRF1)) {
                    ecb = createEventCRF(request, fp);
                    session.setAttribute("ecb", ecb);
                    request.setAttribute(INPUT_EVENT_CRF, ecb);
                    session.setAttribute("to_create_crf", "0");
                } else {
                    ecb = (EventCRFBean) session.getAttribute("ecb");
                }
            // }
            } catch (InconsistentStateException ie) {
                ie.printStackTrace();
                addPageMessage(ie.getOpenClinicaMessage(), request);
                throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET, ie.getOpenClinicaMessage(), "1");
            } catch (NullPointerException ne) {
                ne.printStackTrace();
                addPageMessage(ne.getMessage(), request);
                throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET, ne.getMessage(), "1");
            }
        }
    }
    // added to allow sections shown on this page
    DisplayTableOfContentsBean displayBean = new DisplayTableOfContentsBean();
    displayBean = TableOfContentsServlet.getDisplayBean(ecb, getDataSource(), currentStudy);
    // escape apostrophe in event name
    displayBean.getStudyEventDefinition().setName(StringEscapeUtils.escapeJavaScript(displayBean.getStudyEventDefinition().getName()));
    request.setAttribute(TOC_DISPLAY, displayBean);
    int sectionId = fp.getInt(INPUT_SECTION_ID, true);
    ArrayList sections;
    if (sectionId <= 0) {
        StudyEventDAO studyEventDao = new StudyEventDAO(getDataSource());
        int maximumSampleOrdinal = studyEventDao.getMaxSampleOrdinal(displayBean.getStudyEventDefinition(), displayBean.getStudySubject());
        request.setAttribute("maximumSampleOrdinal", maximumSampleOrdinal);
        sections = sdao.findAllByCRFVersionId(ecb.getCRFVersionId());
        for (int i = 0; i < sections.size(); i++) {
            SectionBean sb = (SectionBean) sections.get(i);
            // find the first section of this CRF
            sectionId = sb.getId();
            break;
        }
    }
    SectionBean sb = new SectionBean();
    if (sectionId > 0) {
        // int sectionId = fp.getInt(INPUT_SECTION_ID, true);
        // synchronized(this)
        {
            sb = (SectionBean) sdao.findByPK(sectionId);
        }
    }
    int tabId = fp.getInt("tab", true);
    if (tabId <= 0) {
        tabId = 1;
    }
    request.setAttribute(INPUT_TAB, new Integer(tabId));
    request.setAttribute(SECTION_BEAN, sb);
}

Example 97 with StudyEventBean

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

the class ViewSectionDataEntryPreview method setupStudyBean.

private void setupStudyBean(HttpServletRequest request) {
    String age = "";
    EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
    StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource());
    StudySubjectBean sub = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
    // This is the SubjectBean
    SubjectDAO subjectDao = new SubjectDAO(getDataSource());
    int subjectId = sub.getSubjectId();
    int studyId = sub.getStudyId();
    SubjectBean subject = (SubjectBean) subjectDao.findByPK(subjectId);
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    // Let us process the age
    if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
        StudyEventDAO sedao = new StudyEventDAO(getDataSource());
        StudyEventBean se = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(getDataSource());
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
        se.setStudyEventDefinition(sed);
        request.setAttribute("studyEvent", se);
        // YW 11-16-2007 enrollment-date is used for calculating age
        age = Utils.getInstacne().processAge(sub.getEnrollmentDate(), subject.getDateOfBirth());
    }
    // Get the study then the parent study
    StudyDAO studydao = new StudyDAO(getDataSource());
    StudyBean study = (StudyBean) studydao.findByPK(studyId);
    if (study.getParentStudyId() > 0) {
        // this is a site,find parent
        StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
        request.setAttribute("studyTitle", parentStudy.getName() + " - " + study.getName());
    } else {
        request.setAttribute("studyTitle", study.getName());
    }
    request.setAttribute("studySubject", sub);
    request.setAttribute("subject", subject);
    request.setAttribute("age", age);
}

Example 98 with StudyEventBean

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

the class ViewEventCRFContentServlet method getStudyEvent.

/*
     * Get the Study Event to display on screen as well as print some of its
     * information. Krikor 10/19/2006
     */
private StudyEventBean getStudyEvent(int eventId) throws Exception {
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyBean studyWithSED = currentStudy;
    if (currentStudy.getParentStudyId() > 0) {
        studyWithSED = new StudyBean();
        studyWithSED.setId(currentStudy.getParentStudyId());
    }
    AuditableEntityBean aeb = sedao.findByPKAndStudy(eventId, studyWithSED);
    if (!aeb.isActive()) {
        addPageMessage(respage.getString("the_SE_you_attempting_enter_data_not_belong"));
        throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("SE_does_not_belong_current_study"), "1");
    // >> changed tbh, 06/2009
    }
    StudyEventBean seb = (StudyEventBean) aeb;
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(seb.getStudyEventDefinitionId());
    seb.setStudyEventDefinition(sedb);
    return seb;
}

Example 99 with StudyEventBean

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

the class ViewNoteServlet method processRequest.

@Override
protected void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    Locale locale = LocaleResolver.getLocale(request);
    DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
    dndao.setFetchMapping(true);
    int noteId = fp.getInt(NOTE_ID, true);
    DiscrepancyNoteBean note = (DiscrepancyNoteBean) dndao.findByPK(noteId);
    String entityType = note.getEntityType();
    if (note.getEntityId() > 0 && !entityType.equals("")) {
        if (!StringUtil.isBlank(entityType)) {
            if ("itemData".equalsIgnoreCase(entityType)) {
                ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
                ItemDataBean itemData = (ItemDataBean) iddao.findByPK(note.getEntityId());
                ItemDAO idao = new ItemDAO(sm.getDataSource());
                ItemBean item = (ItemBean) idao.findByPK(itemData.getItemId());
                note.setEntityValue(itemData.getValue());
                note.setEntityName(item.getName());
                // Mantis Issue 5165. It should be itemData.getId() instead of item.getId()
                note.setEntityId(itemData.getId());
                EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
                EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
                StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
                StudyEventBean se = (StudyEventBean) sed.findByPK(ec.getStudyEventId());
                StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
                StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(se.getStudySubjectId());
                note.setStudySub(ssub);
                StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                se.setName(sedb.getName());
                note.setEvent(se);
                CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
                CRFVersionBean cv = (CRFVersionBean) cvdao.findByPK(ec.getCRFVersionId());
                CRFDAO cdao = new CRFDAO(sm.getDataSource());
                CRFBean crf = (CRFBean) cdao.findByPK(cv.getCrfId());
                note.setCrfName(crf.getName());
            } else if ("studySub".equalsIgnoreCase(entityType)) {
                StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
                StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(note.getEntityId());
                note.setStudySub(ssub);
                // System.out.println("column" + note.getColumn());
                SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
                SubjectBean sub = (SubjectBean) sdao.findByPK(ssub.getSubjectId());
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("enrollment_date".equalsIgnoreCase(note.getColumn())) {
                        if (ssub.getEnrollmentDate() != null) {
                            note.setEntityValue(dateFormatter.format(ssub.getEnrollmentDate()));
                        }
                        note.setEntityName(resword.getString("enrollment_date"));
                    } else if ("gender".equalsIgnoreCase(note.getColumn())) {
                        note.setEntityValue(sub.getGender() + "");
                        note.setEntityName(resword.getString("gender"));
                    } else if ("date_of_birth".equalsIgnoreCase(note.getColumn())) {
                        if (sub.getDateOfBirth() != null) {
                            note.setEntityValue(dateFormatter.format(sub.getDateOfBirth()));
                        }
                        note.setEntityName(resword.getString("date_of_birth"));
                    }
                }
            } else if ("subject".equalsIgnoreCase(entityType)) {
                SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
                SubjectBean sub = (SubjectBean) sdao.findByPK(note.getEntityId());
                StudySubjectBean ssub = new StudySubjectBean();
                ssub.setLabel(sub.getUniqueIdentifier());
                note.setStudySub(ssub);
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("gender".equalsIgnoreCase(note.getColumn())) {
                        note.setEntityValue(sub.getGender() + "");
                        note.setEntityName(resword.getString("gender"));
                    } else if ("date_of_birth".equalsIgnoreCase(note.getColumn())) {
                        if (sub.getDateOfBirth() != null) {
                            note.setEntityValue(dateFormatter.format(sub.getDateOfBirth()));
                        }
                        note.setEntityName(resword.getString("date_of_birth"));
                    } else if ("unique_identifier".equalsIgnoreCase(note.getColumn())) {
                        note.setEntityName(resword.getString("unique_identifier"));
                        note.setEntityValue(sub.getUniqueIdentifier());
                    }
                }
            } else if ("studyEvent".equalsIgnoreCase(entityType)) {
                StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
                StudyEventBean se = (StudyEventBean) sed.findByPK(note.getEntityId());
                StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
                StudySubjectBean ssub = (StudySubjectBean) ssdao.findByPK(se.getStudySubjectId());
                note.setStudySub(ssub);
                StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
                StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
                se.setName(sedb.getName());
                note.setEvent(se);
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("location".equalsIgnoreCase(note.getColumn())) {
                        request.setAttribute("entityValue", se.getLocation());
                        request.setAttribute("entityName", resword.getString("location"));
                        note.setEntityName(resword.getString("location"));
                        note.setEntityValue(se.getLocation());
                    } else if ("date_start".equalsIgnoreCase(note.getColumn())) {
                        if (se.getDateStarted() != null) {
                            note.setEntityValue(dateFormatter.format(se.getDateStarted()));
                        }
                        note.setEntityName(resword.getString("start_date"));
                    } else if ("date_end".equalsIgnoreCase(note.getColumn())) {
                        if (se.getDateEnded() != null) {
                            note.setEntityValue(dateFormatter.format(se.getDateEnded()));
                        }
                        note.setEntityName(resword.getString("end_date"));
                    }
                }
            } else if ("eventCrf".equalsIgnoreCase(entityType)) {
                EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
                EventCRFBean ec = (EventCRFBean) ecdao.findByPK(note.getEntityId());
                StudySubjectBean ssub = (StudySubjectBean) new StudySubjectDAO(sm.getDataSource()).findByPK(ec.getStudySubjectId());
                note.setStudySub(ssub);
                StudyEventBean event = (StudyEventBean) new StudyEventDAO(sm.getDataSource()).findByPK(ec.getStudyEventId());
                note.setEvent(event);
                if (!StringUtil.isBlank(note.getColumn())) {
                    if ("date_interviewed".equals(note.getColumn())) {
                        if (ec.getDateInterviewed() != null) {
                            note.setEntityValue(dateFormatter.format(ec.getDateInterviewed()));
                        }
                        note.setEntityName(resword.getString("date_interviewed"));
                    } else if ("interviewer_name".equals(note.getColumn())) {
                        note.setEntityValue(ec.getInterviewerName());
                        note.setEntityName(resword.getString("interviewer_name"));
                    }
                }
            }
        }
    }
    // Mantis Issue 8495.
    if (note.getStudyId() != currentStudy.getId()) {
        if (currentStudy.getParentStudyId() > 0) {
            if (currentStudy.getId() != note.getStudySub().getStudyId()) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            }
        } else {
            // The SubjectStudy is not belong to currentstudy and current study is not a site.
            StudyDAO studydao = new StudyDAO(sm.getDataSource());
            Collection sites;
            sites = studydao.findOlnySiteIdsByStudy(currentStudy);
            if (!sites.contains(note.getStudySub().getStudyId())) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            }
        }
    }
    // Check end
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList<DiscrepancyNoteBean> notes = dndao.findAllEntityByPK(note.getEntityType(), noteId);
    Date lastUpdatedDate = note.getCreatedDate();
    UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
    /*
         * for (int i = 0; i < notes.size(); i++) { DiscrepancyNoteBean n =
         * (DiscrepancyNoteBean) notes.get(i); int pId = n.getParentDnId(); if
         * (pId == 0) { note = n; note.setLastUpdator((UserAccountBean)
         * udao.findByPK(n.getOwnerId()));
         * note.setLastDateUpdated(n.getCreatedDate()); lastUpdatedDate =
         * note.getLastDateUpdated(); lastUpdator = note.getLastUpdator(); } }
         */
    // BWP 3029 >> This algorithm needs to be changed to properly set
    // the parent note's status and updated date
    // First sort the notes on their ID; this will put the parent note
    // first; and
    // the note with the latest status and updated date last
    java.util.Collections.sort(notes);
    DiscrepancyNoteBean lastChild = notes.get(notes.size() - 1);
    lastUpdatedDate = lastChild.getCreatedDate();
    lastUpdator = (UserAccountBean) udao.findByPK(lastChild.getOwnerId());
    note.setLastUpdator(lastUpdator);
    note.setLastDateUpdated(lastUpdatedDate);
    note.setUpdatedDate(lastUpdatedDate);
    for (DiscrepancyNoteBean dnBean : notes) {
        if (dnBean.getParentDnId() > 0) {
            note.getChildren().add(dnBean);
        }
    }
    /*
         * for (int i = 0; i < notes.size(); i++) { DiscrepancyNoteBean n =
         * (DiscrepancyNoteBean) notes.get(i); int pId = n.getParentDnId(); if
         * (pId > 0) { note.getChildren().add(n);
         *
         * if (!n.getCreatedDate().before(lastUpdatedDate)) { lastUpdatedDate =
         * n.getCreatedDate(); lastUpdator = (UserAccountBean)
         * udao.findByPK(n.getOwnerId()); note.setLastUpdator(lastUpdator);
         * note.setLastDateUpdated(lastUpdatedDate);
         * note.setResolutionStatusId(n.getResolutionStatusId());
         * note.setResStatus(ResolutionStatus.get(n.getResolutionStatusId())); } } }
         */
    note.setNumChildren(note.getChildren().size());
    note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
    request.setAttribute(DIS_NOTE, note);
    forwardPage(Page.VIEW_SINGLE_NOTE);
}

Example 100 with StudyEventBean

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

the class CreateOneDiscrepancyNoteServlet method updateStudySubjectStatus.

private void updateStudySubjectStatus(String entityType, int entityId) {
    if ("itemData".equalsIgnoreCase(entityType)) {
        int itemDataId = entityId;
        ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
        ItemDataBean itemData = (ItemDataBean) iddao.findByPK(itemDataId);
        EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
        StudyEventDAO svdao = new StudyEventDAO(sm.getDataSource());
        StudySubjectDAO studySubjectDAO = new StudySubjectDAO(sm.getDataSource());
        EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
        StudyEventBean event = (StudyEventBean) svdao.findByPK(ec.getStudyEventId());
        StudySubjectBean studySubject = (StudySubjectBean) studySubjectDAO.findByPK(event.getStudySubjectId());
        if (studySubject.getStatus() != null && studySubject.getStatus().equals(Status.SIGNED)) {
            studySubject.setStatus(Status.AVAILABLE);
            studySubject.setUpdater(ub);
            studySubject.setUpdatedDate(new Date());
            studySubjectDAO.update(studySubject);
        }
        if (ec.isSdvStatus()) {
            studySubject.setStatus(Status.AVAILABLE);
            studySubject.setUpdater(ub);
            studySubject.setUpdatedDate(new Date());
            studySubjectDAO.update(studySubject);
            ec.setSdvStatus(false);
            ecdao.update(ec);
        }
    }
}