Examples with SubjectGroupMapDAO org.akaza.openclinica.dao.submit.SubjectGroupMapDAO used on opensource projects

Example 6 with SubjectGroupMapDAO

use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.

the class RestoreSubjectGroupClassServlet method processRequest.

@Override
public void processRequest() throws Exception {
    String action = request.getParameter("action");
    FormProcessor fp = new FormProcessor(request);
    int classId = fp.getInt("id");
    if (classId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_group_class_to_restore"));
        forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
    } else {
        StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
        StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
        SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
        if (action.equalsIgnoreCase("confirm")) {
            StudyGroupClassBean sgcb = (StudyGroupClassBean) sgcdao.findByPK(classId);
            if (sgcb.getStatus().equals(Status.AVAILABLE)) {
                addPageMessage(respage.getString("this_subject_group_class_is_available_cannot_restore"));
                forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
                return;
            }
            ArrayList groups = sgdao.findAllByGroupClass(sgcb);
            for (int i = 0; i < groups.size(); i++) {
                StudyGroupBean sg = (StudyGroupBean) groups.get(i);
                ArrayList subjectMaps = sgmdao.findAllByStudyGroupClassAndGroup(sgcb.getId(), sg.getId());
                sg.setSubjectMaps(subjectMaps);
            }
            session.setAttribute("group", sgcb);
            session.setAttribute("studyGroups", groups);
            forwardPage(Page.RESTORE_SUBJECT_GROUP_CLASS);
        } else if (action.equalsIgnoreCase("submit")) {
            StudyGroupClassBean group = (StudyGroupClassBean) session.getAttribute("group");
            group.setStatus(Status.AVAILABLE);
            group.setUpdater(ub);
            sgcdao.update(group);
            ArrayList subjectMaps = sgmdao.findAllByStudyGroupClassId(group.getId());
            for (int i = 0; i < subjectMaps.size(); i++) {
                SubjectGroupMapBean sgmb = (SubjectGroupMapBean) subjectMaps.get(i);
                if (sgmb.getStatus().equals(Status.AUTO_DELETED)) {
                    sgmb.setStatus(Status.AVAILABLE);
                    sgmb.setUpdater(ub);
                    sgmdao.update(sgmb);
                }
            }
            addPageMessage(respage.getString("this_subject_group_class_was_restored_succesfully"));
            forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
        } else {
            addPageMessage(respage.getString("no_action_specified"));
            forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
        }
    }
}

Example 7 with SubjectGroupMapDAO

use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.

the class SignStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    String action = fp.getString("action");
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
        return;
    }
    StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
    if (!permitSign(studySub, sm.getDataSource())) {
        addPageMessage(respage.getString("subject_event_cannot_signed"));
        // forwardPage(Page.SUBMIT_DATA_SERVLET);
        forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
        // >> changed tbh, 06/2009
        return;
    }
    if (action.equalsIgnoreCase("confirm")) {
        String username = request.getParameter("j_user");
        String password = request.getParameter("j_pass");
        SecurityManager securityManager = ((SecurityManager) SpringServletAccess.getApplicationContext(context).getBean("securityManager"));
        // String encodedUserPass =
        // org.akaza.openclinica.core.SecurityManager
        // .getInstance().encrytPassword(password);
        UserAccountBean ub = (UserAccountBean) session.getAttribute("userBean");
        if (securityManager.verifyPassword(password, getUserDetails()) && ub.getName().equals(username)) {
            if (signSubjectEvents(studySub, sm.getDataSource(), ub)) {
                // Making the StudySubject signed as all the events have
                // become signed.
                studySub.setStatus(Status.SIGNED);
                studySub.setUpdater(ub);
                subdao.update(studySub);
                addPageMessage(respage.getString("subject_event_signed"));
                // forwardPage(Page.SUBMIT_DATA_SERVLET);
                forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
                // >> changed tbh, 06/2009
                return;
            } else {
                addPageMessage(respage.getString("errors_in_submission_see_below"));
                forwardPage(Page.LIST_STUDY_SUBJECTS);
                return;
            }
        } else {
            request.setAttribute("id", new Integer(studySubId).toString());
            addPageMessage(restext.getString("password_match"));
            forwardPage(Page.LIST_STUDY_SUBJECTS);
            return;
        }
    }
    request.setAttribute("studySub", studySub);
    int studyId = studySub.getStudyId();
    int subjectId = studySub.getSubjectId();
    SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
    if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
        Date dob = subject.getDateOfBirth();
        if (dob != null) {
            Calendar cal = Calendar.getInstance();
            cal.setTime(dob);
            int year = cal.get(Calendar.YEAR);
            request.setAttribute("yearOfBirth", new Integer(year));
        } else {
            request.setAttribute("yearOfBirth", "");
        }
    }
    request.setAttribute("subject", subject);
    StudyDAO studydao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) studydao.findByPK(studyId);
    StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
    study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
    if (study.getParentStudyId() > 0) {
        // this is a site,find parent
        StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
        request.setAttribute("parentStudy", parentStudy);
    } else {
        request.setAttribute("parentStudy", new StudyBean());
    }
    ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId);
    request.setAttribute("children", children);
    // find study events
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    // find all eventcrfs for each event
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    ArrayList<DisplayStudyEventBean> displayEvents = getDisplayStudyEventsForStudySubject(study, studySub, sm.getDataSource(), ub, currentRole);
    DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil();
    // Don't filter for now; disc note beans are returned with eventCRFId
    // set
    discNoteUtil.injectParentDiscNotesIntoDisplayStudyEvents(displayEvents, new HashSet(), sm.getDataSource(), 0);
    // All the displaystudyevents for one subject
    request.setAttribute("displayStudyEvents", displayEvents);
    // Set up a Map for the JSP view, mapping the eventCRFId to another Map:
    // the
    // inner Map maps the resolution status name to the number of notes for
    // that
    // eventCRF id, as in New --> 2
    Map discNoteByEventCRFid = discNoteUtil.createDiscNoteMapByEventCRF(displayEvents);
    request.setAttribute("discNoteByEventCRFid", discNoteByEventCRFid);
    EntityBeanTable table = fp.getEntityBeanTable();
    // sort by start date,
    table.setSortingIfNotExplicitlySet(1, false);
    // desc
    ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents);
    String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("location"), resword.getString("status"), resword.getString("actions"), resword.getString("CRFs_atrib") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(4);
    table.hideColumnLink(5);
    if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) {
        table.addLink(resword.getString("add_new_event"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId());
    }
    HashMap args = new HashMap();
    args.put("id", new Integer(studySubId).toString());
    table.setQuery("ViewStudySubject", args);
    table.setRows(allEventRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId);
    request.setAttribute("groups", groupMaps);
    AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
    ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList eventLogs = new ArrayList();
    for (int i = 0; i < logs.size(); i++) {
        AuditEventBean avb = (AuditEventBean) logs.get(i);
        StudyEventAuditBean sea = new StudyEventAuditBean();
        sea.setAuditEvent(avb);
        StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId());
        StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
        sea.setDefinition(sed);
        String old = avb.getOldValue().trim();
        try {
            if (!StringUtil.isBlank(old)) {
                SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue());
                sea.setOldSubjectEventStatus(oldStatus);
            }
            String newValue = avb.getNewValue().trim();
            if (!StringUtil.isBlank(newValue)) {
                SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue());
                sea.setNewSubjectEventStatus(newStatus);
            }
        } catch (NumberFormatException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        // logger.warning("^^^ caught NFE");
        }
        UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
        sea.setUpdater(updater);
        eventLogs.add(sea);
    }
    // logger.warning("^^^ finished iteration");
    request.setAttribute("eventLogs", eventLogs);
    forwardPage(Page.SIGN_STUDY_SUBJECT);
}

Example 8 with SubjectGroupMapDAO

use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO 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 9 with SubjectGroupMapDAO

use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.

the class ListDiscNotesSubjectServlet method processRequest.

// < ResourceBundleresexception,respage;
@Override
protected void processRequest() throws Exception {
    String module = request.getParameter("module");
    String moduleStr = "manage";
    if (module != null && module.trim().length() > 0) {
        if ("submit".equals(module)) {
            request.setAttribute("module", "submit");
            moduleStr = "submit";
        } else if ("admin".equals(module)) {
            request.setAttribute("module", "admin");
            moduleStr = "admin";
        } else {
            request.setAttribute("module", "manage");
        }
    }
    // << tbh 02/2010 filter out the entire module parameter to catch injections
    // BWP 3098>> close the info side panel and show icons
    request.setAttribute("closeInfoShowIcons", true);
    // <<
    // Determine whether to limit the displayed DN's to a certain DN type
    int resolutionStatus = 0;
    try {
        resolutionStatus = Integer.parseInt(request.getParameter("resolutionStatus"));
    } catch (NumberFormatException nfe) {
        // Show all DN's
        resolutionStatus = -1;
    }
    // Determine whether we already have a collection of resolutionStatus
    // Ids, and if not
    // create a new attribute. If there is no resolution status, then the
    // Set object should be cleared,
    // because we do not have to save a set of filter IDs.
    boolean hasAResolutionStatus = resolutionStatus >= 1 && resolutionStatus <= 5;
    Set<Integer> resolutionStatusIds = (HashSet) session.getAttribute(RESOLUTION_STATUS);
    // remove the session if there is no resolution status
    if (!hasAResolutionStatus && resolutionStatusIds != null) {
        session.removeAttribute(RESOLUTION_STATUS);
        resolutionStatusIds = null;
    }
    if (hasAResolutionStatus) {
        if (resolutionStatusIds == null) {
            resolutionStatusIds = new HashSet<Integer>();
        }
        resolutionStatusIds.add(resolutionStatus);
        session.setAttribute(RESOLUTION_STATUS, resolutionStatusIds);
    }
    int discNoteType = 0;
    try {
        discNoteType = Integer.parseInt(request.getParameter("type"));
    } catch (NumberFormatException nfe) {
        // Show all DN's
        discNoteType = -1;
    }
    request.setAttribute(DISCREPANCY_NOTE_TYPE, discNoteType);
    DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil();
    // Generate a summary of how we are filtering;
    Map<String, List<String>> filterSummary = discNoteUtil.generateFilterSummary(discNoteType, resolutionStatusIds);
    if (!filterSummary.isEmpty()) {
        request.setAttribute(FILTER_SUMMARY, filterSummary);
    }
    locale = LocaleResolver.getLocale(request);
    StudyBean sbean = (StudyBean) session.getAttribute("study");
    // List<DiscrepancyNoteBean> allDiscNotes = discNoteUtil.getThreadedDNotesForStudy(sbean, resolutionStatusIds, sm.getDataSource(), discNoteType, true);
    // Map stats = discNoteUtil.generateDiscNoteSummary(allDiscNotes);
    Map stats = discNoteUtil.generateDiscNoteSummaryRefactored(sm.getDataSource(), currentStudy, resolutionStatusIds, discNoteType);
    request.setAttribute("summaryMap", stats);
    Set mapKeys = stats.keySet();
    request.setAttribute("mapKeys", mapKeys);
    // < resword =
    // ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
    StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
    StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
    StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    EventCRFDAO edao = new EventCRFDAO(sm.getDataSource());
    EventDefinitionCRFDAO eddao = new EventDefinitionCRFDAO(sm.getDataSource());
    SubjectDAO subdao = new SubjectDAO(sm.getDataSource());
    DiscrepancyNoteDAO dnDAO = new DiscrepancyNoteDAO(sm.getDataSource());
    ListDiscNotesSubjectTableFactory factory = new ListDiscNotesSubjectTableFactory(ResourceBundleProvider.getTermsBundle(locale));
    factory.setStudyEventDefinitionDao(seddao);
    factory.setSubjectDAO(subdao);
    factory.setStudySubjectDAO(sdao);
    factory.setStudyEventDAO(sedao);
    factory.setStudyBean(currentStudy);
    factory.setStudyGroupClassDAO(sgcdao);
    factory.setSubjectGroupMapDAO(sgmdao);
    factory.setStudyDAO(studyDAO);
    factory.setCurrentRole(currentRole);
    factory.setCurrentUser(ub);
    factory.setEventCRFDAO(edao);
    factory.setEventDefintionCRFDAO(eddao);
    factory.setStudyGroupDAO(sgdao);
    factory.setDiscrepancyNoteDAO(dnDAO);
    factory.setModule(moduleStr);
    factory.setDiscNoteType(discNoteType);
    // factory.setStudyHasDiscNotes(allDiscNotes != null &&
    // !allDiscNotes.isEmpty());
    factory.setResolutionStatus(resolutionStatus);
    factory.setResolutionStatusIds(resolutionStatusIds);
    factory.setResword(ResourceBundleProvider.getWordsBundle(locale));
    String listDiscNotesHtml = factory.createTable(request, response).render();
    request.setAttribute("listDiscNotesHtml", listDiscNotesHtml);
    forwardPage(getJSP());
}

Example 10 with SubjectGroupMapDAO

use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.

the class ViewStudySubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
    StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    // studySubjectId
    int studySubId = fp.getInt("id", true);
    String from = fp.getString("from");
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    // if coming from change crf version -> display message
    String crfVersionChangeMsg = fp.getString("isFromCRFVersionChange");
    if (crfVersionChangeMsg != null && !crfVersionChangeMsg.equals("")) {
        addPageMessage(crfVersionChangeMsg);
    }
    if (studySubId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_to_view"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
    } else {
        if (!StringUtil.isBlank(from)) {
            // form ListSubject or
            request.setAttribute("from", from);
        // ListStudySubject
        } else {
            request.setAttribute("from", "");
        }
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        request.setAttribute("studySub", studySub);
        int studyId = studySub.getStudyId();
        int subjectId = studySub.getSubjectId();
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyBean study = (StudyBean) studydao.findByPK(studyId);
        // Check if this StudySubject would be accessed from the Current Study
        if (studySub.getStudyId() != currentStudy.getId()) {
            if (currentStudy.getParentStudyId() > 0) {
                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.
                Collection sites = studydao.findOlnySiteIdsByStudy(currentStudy);
                if (!sites.contains(study.getId())) {
                    addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                    forwardPage(Page.MENU_SERVLET);
                    return;
                }
            }
        }
        // If the study subject derives from a site, and is being viewed
        // from a parent study,
        // then the study IDs will be different. However, since each note is
        // saved with the specific
        // study ID, then its study ID may be different than the study
        // subject's ID.
        boolean subjectStudyIsCurrentStudy = studyId == currentStudy.getId();
        boolean isParentStudy = study.getParentStudyId() < 1;
        // Get any disc notes for this subject : studySubId
        DiscrepancyNoteDAO discrepancyNoteDAO = new DiscrepancyNoteDAO(sm.getDataSource());
        List<DiscrepancyNoteBean> allNotesforSubject = new ArrayList<DiscrepancyNoteBean>();
        // These methods return only parent disc notes
        if (subjectStudyIsCurrentStudy && isParentStudy) {
            allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudyAndId(study, subjectId);
            allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudyAndId(study, studySubId));
        } else {
            if (!isParentStudy) {
                StudyBean stParent = (StudyBean) studydao.findByPK(study.getParentStudyId());
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(stParent, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(stParent, study, studySubId));
            } else {
                allNotesforSubject = discrepancyNoteDAO.findAllSubjectByStudiesAndSubjectId(currentStudy, study, subjectId);
                allNotesforSubject.addAll(discrepancyNoteDAO.findAllStudySubjectByStudiesAndStudySubjectId(currentStudy, study, studySubId));
            }
        }
        if (!allNotesforSubject.isEmpty()) {
            setRequestAttributesForNotes(allNotesforSubject);
        }
        SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
        if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
            Date dob = subject.getDateOfBirth();
            if (dob != null) {
                Calendar cal = Calendar.getInstance();
                cal.setTime(dob);
                int year = cal.get(Calendar.YEAR);
                request.setAttribute("yearOfBirth", new Integer(year));
            } else {
                request.setAttribute("yearOfBirth", "");
            }
        }
        request.setAttribute("subject", subject);
        /*
             * StudyDAO studydao = new StudyDAO(sm.getDataSource()); StudyBean
             * study = (StudyBean) studydao.findByPK(studyId);
             */
        // YW 11-26-2007 <<
        StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
        study.getStudyParameterConfig().setCollectDob(spvdao.findByHandleAndStudy(studyId, "collectDob").getValue());
        // YW >>
        request.setAttribute("subjectStudy", study);
        if (study.getParentStudyId() > 0) {
            // this is a site,find parent
            StudyBean parentStudy2 = (StudyBean) studydao.findByPK(study.getParentStudyId());
            request.setAttribute("parentStudy", parentStudy2);
        } else {
            request.setAttribute("parentStudy", new StudyBean());
        }
        ArrayList children = (ArrayList) sdao.findAllChildrenByPK(subjectId);
        request.setAttribute("children", children);
        // find study events
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
        StudySubjectService studySubjectService = (StudySubjectService) WebApplicationContextUtils.getWebApplicationContext(getServletContext()).getBean("studySubjectService");
        List<DisplayStudyEventBean> displayEvents = studySubjectService.getDisplayStudyEventsForStudySubject(studySub, ub, currentRole);
        // Mantis Issue 5048: Preventing Investigators from Unlocking Events
        for (int i = 0; i < displayEvents.size(); i++) {
            DisplayStudyEventBean decb = displayEvents.get(i);
            if (!(currentRole.isDirector() || currentRole.isCoordinator()) && decb.getStudyEvent().getSubjectEventStatus().isLocked()) {
                decb.getStudyEvent().setEditable(false);
            }
        }
        // BWP 3212; remove event CRFs that are supposed to be "hidden" >>
        if (currentStudy.getParentStudyId() > 0) {
            HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
            for (DisplayStudyEventBean displayStudyEventBean : displayEvents) {
                hideCRFManager.removeHiddenEventCRF(displayStudyEventBean);
            }
        }
        // >>
        EntityBeanTable table = fp.getEntityBeanTable();
        // sort by start
        table.setSortingIfNotExplicitlySet(1, false);
        // date, desc
        ArrayList allEventRows = DisplayStudyEventRow.generateRowsFromBeans(displayEvents);
        String[] columns = { resword.getString("event") + " (" + resword.getString("occurrence_number") + ")", resword.getString("start_date1"), resword.getString("location"), resword.getString("status"), resword.getString("actions"), resword.getString("CRFs_atrib") };
        table.setColumns(new ArrayList(Arrays.asList(columns)));
        table.hideColumnLink(4);
        table.hideColumnLink(5);
        // YW 11-08-2007 <<
        if (!"removed".equalsIgnoreCase(studySub.getStatus().getName()) && !"auto-removed".equalsIgnoreCase(studySub.getStatus().getName())) {
            if (currentStudy.getStatus().isAvailable() && !currentRole.getRole().equals(Role.MONITOR)) {
                table.addLink(resword.getString("add_new_event"), "CreateNewStudyEvent?" + CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT + "=" + studySub.getId());
            }
        }
        // YW >>
        HashMap args = new HashMap();
        args.put("id", new Integer(studySubId).toString());
        table.setQuery("ViewStudySubject", args);
        table.setRows(allEventRows);
        table.computeDisplay();
        request.setAttribute("table", table);
        // request.setAttribute("displayEvents", displayEvents);
        // find group info
        SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
        ArrayList groupMaps = (ArrayList) sgmdao.findAllByStudySubject(studySubId);
        request.setAttribute("groups", groupMaps);
        // find audit log for events
        AuditEventDAO aedao = new AuditEventDAO(sm.getDataSource());
        ArrayList logs = aedao.findEventStatusLogByStudySubject(studySubId);
        // logger.warning("^^^ retrieved logs");
        UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
        ArrayList eventLogs = new ArrayList();
        // logger.warning("^^^ starting to iterate");
        for (int i = 0; i < logs.size(); i++) {
            AuditEventBean avb = (AuditEventBean) logs.get(i);
            StudyEventAuditBean sea = new StudyEventAuditBean();
            sea.setAuditEvent(avb);
            StudyEventBean se = (StudyEventBean) sedao.findByPK(avb.getEntityId());
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
            sea.setDefinition(sed);
            String old = avb.getOldValue().trim();
            try {
                if (!StringUtil.isBlank(old)) {
                    SubjectEventStatus oldStatus = SubjectEventStatus.get(new Integer(old).intValue());
                    sea.setOldSubjectEventStatus(oldStatus);
                }
                String newValue = avb.getNewValue().trim();
                if (!StringUtil.isBlank(newValue)) {
                    SubjectEventStatus newStatus = SubjectEventStatus.get(new Integer(newValue).intValue());
                    sea.setNewSubjectEventStatus(newStatus);
                }
            } catch (NumberFormatException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            // logger.warning("^^^ caught NFE");
            }
            UserAccountBean updater = (UserAccountBean) udao.findByPK(avb.getUserId());
            sea.setUpdater(updater);
            eventLogs.add(sea);
        }
        // logger.warning("^^^ finished iteration");
        request.setAttribute("eventLogs", eventLogs);
        forwardPage(Page.VIEW_STUDY_SUBJECT);
    }
}