Examples with StudySubjectDAO org.akaza.openclinica.dao.managestudy.StudySubjectDAO used on opensource projects

Example 81 with StudySubjectDAO

use of org.akaza.openclinica.dao.managestudy.StudySubjectDAO in project OpenClinica by OpenClinica.

the class PrintDataEntryServlet method processRequest.

@Override
public void processRequest(HttpServletRequest request, HttpServletResponse response) throws Exception {
    FormProcessor fp = new FormProcessor(request);
    boolean isSubmitted = false;
    int eventCRFId = fp.getInt("ecId");
    //JN:The following were the the global variables, moved as local.
    EventCRFBean ecb;
    SectionDAO sdao = new SectionDAO(getDataSource());
    ArrayList<SectionBean> allSectionBeans = new ArrayList<SectionBean>();
    ArrayList sectionBeans = new ArrayList();
    String age = "";
    StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
    SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN);
    // Whether IE6 or IE7 is involved
    String isIE = fp.getString("ie");
    if ("y".equalsIgnoreCase(isIE)) {
        request.setAttribute("isInternetExplorer", "true");
    }
    if (eventCRFId == 0) {
        ecb = new EventCRFBean();
    // super.ecb.setCRFVersionId(sb.getCRFVersionId());
    } else {
        EventCRFDAO ecdao = new EventCRFDAO(getDataSource());
        ecb = (EventCRFBean) ecdao.findByPK(eventCRFId);
        // Get all the SectionBeans attached to this ECB
        ArrayList sects = sdao.findAllByCRFVersionId(ecb.getCRFVersionId());
        for (int i = 0; i < sects.size(); i++) {
            sb = (SectionBean) sects.get(i);
            //                super.sb = sb;
            int sectId = sb.getId();
            if (sectId > 0) {
                allSectionBeans.add((SectionBean) sdao.findByPK(sectId));
            }
        }
        // This is the StudySubjectBean
        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);
        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);
        // Let us process the age
        if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
            // YW 11-16-2007 enrollment-date is used for computing 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("studyEvent", se);
        request.setAttribute("age", age);
        request.setAttribute(INPUT_EVENT_CRF, ecb);
        request.setAttribute(SECTION_BEAN, sb);
        request.setAttribute(ALL_SECTION_BEANS, allSectionBeans);
        // Get the section beans from super
        sectionBeans = super.getAllDisplayBeans(request);
    }
    // Find out whether the sections involve groups
    ItemGroupDAO itemGroupDao = new ItemGroupDAO(getDataSource());
    // Find truely grouped tables, not groups with a name of 'Ungrouped'
    // CRF VERSION ID WILL BE 0 IF "ecId" IS NOT IN THE QUERYSTRING
    int crfVersionId = ecb.getCRFVersionId();
    List<ItemGroupBean> itemGroupBeans = itemGroupDao.findOnlyGroupsByCRFVersionID(crfVersionId);
    boolean sectionsHaveGroups = false;
    if (itemGroupBeans.size() > 0) {
        sectionsHaveGroups = true;
        // get a DisplaySectionBean for each section of the CRF, sort them,
        // then
        // dispatch the request to a print JSP. the constructor for this
        // handler takes
        // a boolean value depending on whether an event or data is involved
        // or not
        DisplaySectionBeanHandler handler = new DisplaySectionBeanHandler(true, getDataSource(), getServletContext());
        handler.setCrfVersionId(crfVersionId);
        handler.setEventCRFId(eventCRFId);
        List<DisplaySectionBean> displaySectionBeans = handler.getDisplaySectionBeans();
        CRFVersionDAO crfVersionDAO = new CRFVersionDAO(getDataSource());
        CRFDAO crfDao = new CRFDAO(getDataSource());
        request.setAttribute("listOfDisplaySectionBeans", displaySectionBeans);
        // Make available the CRF names and versions for
        // the web page's header
        CRFVersionBean crfverBean = (CRFVersionBean) crfVersionDAO.findByPK(crfVersionId);
        request.setAttribute("crfVersionBean", crfverBean);
        CRFBean crfBean = crfDao.findByVersionId(crfVersionId);
        request.setAttribute("crfBean", crfBean);
        // Set an attribute signaling that an event and/or data is involved
        request.setAttribute("dataInvolved", "true");
    }
    request.setAttribute(BEAN_ANNOTATIONS, ecb.getAnnotations());
    request.setAttribute("EventCRFBean", ecb);
    // We do not need most of these attributes if groups are involved
    if (!sectionsHaveGroups) {
        request.setAttribute(INPUT_EVENT_CRF, ecb);
        request.setAttribute(SECTION_BEAN, sb);
        DisplaySectionBean dsb = super.getDisplayBean(false, false, request, isSubmitted);
        request.setAttribute("allSections", sectionBeans);
        request.setAttribute("displayAll", "1");
        request.setAttribute(BEAN_DISPLAY, dsb);
        request.setAttribute("sec", sb);
        forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PRINT, request, response);
    } else {
        // end if(! sectionsHaveGroups)
        forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PRINT_GROUPS, request, response);
    }
}

Example 82 with StudySubjectDAO

use of org.akaza.openclinica.dao.managestudy.StudySubjectDAO in project OpenClinica by OpenClinica.

the class RestoreStudyEventServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    // studyEventId
    int studyEventId = fp.getInt("id");
    // studySubjectId
    int studySubId = fp.getInt("studySubId");
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    if (studyEventId == 0) {
        addPageMessage(respage.getString("please_choose_a_SE_to_restore"));
        request.setAttribute("id", new Integer(studySubId).toString());
        forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
    } else {
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        // YW 11-07-2007, a study event could not be restored if its study
        // subject has been removed
        Status s = studySub.getStatus();
        if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
            addPageMessage(resword.getString("study_event") + resterm.getString("could_not_be") + resterm.getString("restored") + "." + respage.getString("study_subject_has_been_deleted"));
            request.setAttribute("id", new Integer(studySubId).toString());
            forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
        }
        // YW
        StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
        request.setAttribute("studySub", studySub);
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(event.getStudyEventDefinitionId());
        event.setStudyEventDefinition(sed);
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studySub.getStudyId());
        request.setAttribute("study", study);
        String action = request.getParameter("action");
        if ("confirm".equalsIgnoreCase(action)) {
            if (event.getStatus().equals(Status.AVAILABLE)) {
                addPageMessage(respage.getString("this_event_is_already_available_for_study") + " " + respage.getString("please_contact_sysadmin_for_more_information"));
                request.setAttribute("id", new Integer(studySubId).toString());
                forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
                return;
            }
            EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
            // find all crfs in the definition
            ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllByEventDefinitionId(study, sed.getId());
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
            // construct info needed on view study event page
            DisplayStudyEventBean de = new DisplayStudyEventBean();
            de.setStudyEvent(event);
            de.setDisplayEventCRFs(getDisplayEventCRFs(eventCRFs, eventDefinitionCRFs));
            request.setAttribute("displayEvent", de);
            forwardPage(Page.RESTORE_STUDY_EVENT);
        } else {
            logger.info("submit to restore the event to study");
            // restore event to study
            event.setStatus(Status.AVAILABLE);
            event.setUpdater(ub);
            event.setUpdatedDate(new Date());
            sedao.update(event);
            // restore event crfs
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            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.AUTO_DELETED)) {
                    eventCRF.setStatus(Status.AVAILABLE);
                    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.AUTO_DELETED)) {
                            item.setStatus(Status.AVAILABLE);
                            item.setUpdater(ub);
                            item.setUpdatedDate(new Date());
                            iddao.update(item);
                        }
                    }
                }
            }
            String emailBody = respage.getString("the_event") + event.getStudyEventDefinition().getName() + " " + respage.getString("has_been_restored_to_the_study") + " " + study.getName() + ".";
            addPageMessage(emailBody);
            //                sendEmail(emailBody);
            request.setAttribute("id", new Integer(studySubId).toString());
            forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
        }
    }
}

Example 83 with StudySubjectDAO

use of org.akaza.openclinica.dao.managestudy.StudySubjectDAO in project OpenClinica by OpenClinica.

the class RestoreStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    // studySubjectId
    String studySubIdString = request.getParameter("id");
    String subIdString = request.getParameter("subjectId");
    String studyIdString = request.getParameter("studyId");
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    if (StringUtil.isBlank(studySubIdString) || StringUtil.isBlank(subIdString) || StringUtil.isBlank(studyIdString)) {
        addPageMessage(respage.getString("please_choose_study_subject_to_restore"));
        forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
    } else {
        int studyId = Integer.valueOf(studyIdString.trim()).intValue();
        int studySubId = Integer.valueOf(studySubIdString.trim()).intValue();
        int subjectId = Integer.valueOf(subIdString.trim()).intValue();
        SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studyId);
        // find study events
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        //            ArrayList events = sedao.findAllByStudyAndStudySubjectId(study, studySubId);
        ArrayList<DisplayStudyEventBean> displayEvents = ViewStudySubjectServlet.getDisplayStudyEventsForStudySubject(studySub, sm.getDataSource(), ub, currentRole);
        String action = request.getParameter("action");
        if ("confirm".equalsIgnoreCase(action)) {
            if (studySub.getStatus().equals(Status.AVAILABLE)) {
                addPageMessage(respage.getString("this_subject_is_already_available_for_study") + " " + respage.getString("please_contact_sysadmin_for_more_information"));
                forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
                return;
            }
            request.setAttribute("subject", subject);
            request.setAttribute("study", study);
            request.setAttribute("studySub", studySub);
            request.setAttribute("events", displayEvents);
            forwardPage(Page.RESTORE_STUDY_SUBJECT);
        } else {
            logger.info("submit to restore the subject from study");
            // restore subject from study
            studySub.setStatus(Status.AVAILABLE);
            studySub.setUpdater(ub);
            studySub.setUpdatedDate(new Date());
            subdao.update(studySub);
            // restore all study events
            // restore all event crfs
            EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
            for (int j = 0; j < displayEvents.size(); j++) {
                DisplayStudyEventBean dispEvent = displayEvents.get(j);
                StudyEventBean event = dispEvent.getStudyEvent();
                if (event.getStatus().equals(Status.AUTO_DELETED)) {
                    event.setStatus(Status.AVAILABLE);
                    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.AUTO_DELETED)) {
                        eventCRF.setStatus(Status.AVAILABLE);
                        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.AUTO_DELETED)) {
                                item.setStatus(Status.AVAILABLE);
                                item.setUpdater(ub);
                                item.setUpdatedDate(new Date());
                                iddao.update(item);
                            }
                        }
                    }
                }
            }
            String emailBody = respage.getString("the_subject") + " " + subject.getName() + " " + respage.getString("has_been_restored_to_the_study") + " " + study.getName() + ".";
            addPageMessage(emailBody);
            //                try{
            //                    sendEmail(emailBody);
            //                }catch (Exception ex){
            //                    addPageMessage(respage.getString("mail_cannot_be_sent_to_admin"));
            //                }
            forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
        }
    }
}

Example 84 with StudySubjectDAO

use of org.akaza.openclinica.dao.managestudy.StudySubjectDAO in project OpenClinica by OpenClinica.

the class SDVController method renderSubjectsTable.

/*
    Create a JMesa-based table for showing the event CRFs.
    */
private String renderSubjectsTable(List<EventCRFBean> eventCRFBeans, int studySubjectId, HttpServletRequest request) {
    StudySubjectDAO studySubjectDAO = new StudySubjectDAO(dataSource);
    StudySubjectBean subjectBean = (StudySubjectBean) studySubjectDAO.findByPK(studySubjectId);
    Collection<SubjectSDVContainer> items = sdvUtil.getSubjectRows(eventCRFBeans, request);
    //The number of items represents the total number of returned rows
    int totalRowCount = 0;
    if (items != null && items.size() > 0) {
        totalRowCount = items.size();
    }
    TableFacade tableFacade = createTableFacade("sdv", request);
    //set to the total row count
    if (totalRowCount > 1) {
        tableFacade.setMaxRowsIncrements(15, 50, totalRowCount);
    }
    tableFacade.setColumnProperties("studySubjectId", "personId", "secondaryId", "eventName", "eventDate", "enrollmentDate", "subjectStatus", "crfNameVersion", "crfStatus", "lastUpdatedDate", "lastUpdatedBy", "sdvStatusActions");
    tableFacade.setItems(items);
    //Fix column titles
    HtmlTable table = (HtmlTable) tableFacade.getTable();
    //i18n caption; TODO: convert to Spring messages
    ResourceBundle resourceBundle = ResourceBundle.getBundle("org.akaza.openclinica.i18n.words", LocaleResolver.getLocale(request));
    String[] allTitles = { resourceBundle.getString("study_subject_ID"), resourceBundle.getString("person_ID"), resourceBundle.getString("secondary_ID"), resourceBundle.getString("event_name"), resourceBundle.getString("event_date"), resourceBundle.getString("enrollment_date"), resourceBundle.getString("subject_status"), resourceBundle.getString("CRF_name") + " / " + resourceBundle.getString("version"), resourceBundle.getString("CRF_status"), resourceBundle.getString("last_updated_date"), resourceBundle.getString("last_updated_by"), resourceBundle.getString("SDV_status") + " / " + resourceBundle.getString("actions") };
    setTitles(allTitles, table);
    table.getTableRenderer().setWidth("800");
    return tableFacade.render();
}

Example 85 with StudySubjectDAO

use of org.akaza.openclinica.dao.managestudy.StudySubjectDAO in project OpenClinica by OpenClinica.

the class ImportSpringJob method createDiscrepancyNote.

public static DiscrepancyNoteBean createDiscrepancyNote(ItemBean itemBean, String message, EventCRFBean eventCrfBean, DisplayItemBean displayItemBean, Integer parentId, UserAccountBean uab, DataSource ds, StudyBean study) {
    // DisplayItemBean displayItemBean) {
    DiscrepancyNoteBean note = new DiscrepancyNoteBean();
    StudySubjectDAO ssdao = new StudySubjectDAO(ds);
    note.setDescription(message);
    note.setDetailedNotes("Failed Validation Check");
    note.setOwner(uab);
    note.setCreatedDate(new Date());
    note.setResolutionStatusId(ResolutionStatus.OPEN.getId());
    note.setDiscrepancyNoteTypeId(DiscrepancyNoteType.FAILEDVAL.getId());
    if (parentId != null) {
        note.setParentDnId(parentId);
    }
    note.setField(itemBean.getName());
    note.setStudyId(study.getId());
    note.setEntityName(itemBean.getName());
    note.setEntityType(DiscrepancyNoteBean.ITEM_DATA);
    note.setEntityValue(displayItemBean.getData().getValue());
    note.setEventName(eventCrfBean.getName());
    note.setEventStart(eventCrfBean.getCreatedDate());
    note.setCrfName(displayItemBean.getEventDefinitionCRF().getCrfName());
    StudySubjectBean ss = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
    note.setSubjectName(ss.getName());
    note.setEntityId(displayItemBean.getData().getId());
    note.setColumn("value");
    DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(ds);
    note = (DiscrepancyNoteBean) dndao.create(note);
    // so that the below method works, need to set the entity above
    // System.out.println("trying to create mapping with " + note.getId() +
    // " " + note.getEntityId() + " " + note.getColumn() + " " +
    // note.getEntityType());
    dndao.createMapping(note);
    return note;
}