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

Example 86 with StudyEventDAO

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

the class ListEventsForSubjectServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    // checks which module the requests are from
    String module = fp.getString(MODULE);
    request.setAttribute(MODULE, module);
    String pageNumber = fp.getString(ListStudySubjectServlet.SUBJECT_PAGE_NUMBER);
    String filterKeyword = fp.getString(ListStudySubjectServlet.FILTER_KEYWORD);
    String tmpSearch = fp.getString(ListStudySubjectServlet.SEARCH_SUBMITTED);
    boolean searchSubmitted = !(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword);
    SubjectMatrixUtil matrixUtil = new SubjectMatrixUtil();
    String query = matrixUtil.createPaginatingQuery(pageNumber);
    StringBuilder extendedQuery = new StringBuilder(query);
    // URL encode the search keyword, since it will be a parameter in the
    // URL
    String filterKeywordURLEncode = java.net.URLEncoder.encode(filterKeyword, "UTF-8");
    if (searchSubmitted) {
        extendedQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
        extendedQuery.append("&").append(ListStudySubjectServlet.FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
    }
    request.setAttribute(ListStudySubjectServlet.PAGINATING_QUERY, extendedQuery.toString());
    int definitionId = fp.getInt("defId");
    int tabId = fp.getInt("tab");
    if (definitionId <= 0) {
        addPageMessage(respage.getString("please_choose_an_ED_ta_to_vies_details"));
        forwardPage(Page.LIST_STUDY_SUBJECTS);
        return;
    }
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(definitionId);
    StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
    StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
    SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
    EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
    EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    // find all the groups in the current study
    ArrayList studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
    // information for the event tabs
    ArrayList allDefs = seddao.findAllActiveByStudy(currentStudy);
    boolean isASite = false;
    if (currentStudy.getParentStudyId() > 0) {
        StudyDAO stdao = new StudyDAO(sm.getDataSource());
        StudyBean parent = (StudyBean) stdao.findByPK(currentStudy.getParentStudyId());
        allDefs = seddao.findAllActiveByStudy(parent);
    }
    ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(this.currentStudy, definitionId);
    for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
        CRFBean crf = (CRFBean) crfdao.findByPK(edc.getCrfId());
        edc.setCrf(crf);
    }
    request.setAttribute("studyGroupClasses", studyGroupClasses);
    request.setAttribute("allDefsArray", allDefs);
    request.setAttribute("allDefsNumber", new Integer(allDefs.size()));
    request.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
    request.setAttribute("eventDefCRFSize", new Integer(eventDefinitionCRFs.size()));
    request.setAttribute("tabId", new Integer(tabId));
    request.setAttribute("studyEventDef", sed);
    request.setAttribute("eventDefCRFs", eventDefinitionCRFs);
    // find all the subjects in current study
    ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
    ArrayList displayStudySubs = new ArrayList();
    for (int i = 0; i < subjects.size(); i++) {
        StudySubjectBean studySub = (StudySubjectBean) subjects.get(i);
        ArrayList groups = (ArrayList) sgmdao.findAllByStudySubject(studySub.getId());
        ArrayList subGClasses = new ArrayList();
        for (int j = 0; j < studyGroupClasses.size(); j++) {
            StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(j);
            boolean hasClass = false;
            for (int k = 0; k < groups.size(); k++) {
                SubjectGroupMapBean sgmb = (SubjectGroupMapBean) groups.get(k);
                if (sgmb.getGroupClassName().equalsIgnoreCase(sgc.getName())) {
                    subGClasses.add(sgmb);
                    hasClass = true;
                    break;
                }
            }
            if (!hasClass) {
                subGClasses.add(new SubjectGroupMapBean());
            }
        }
        // find all eventcrfs for each event, for each event tab
        ArrayList displaySubjectEvents = new ArrayList();
        ArrayList<DisplayStudyEventBean> displayEvents = new ArrayList<DisplayStudyEventBean>();
        ArrayList events = sedao.findAllByStudySubjectAndDefinition(studySub, sed);
        for (int k = 0; k < events.size(); k++) {
            StudyEventBean seb = (StudyEventBean) events.get(k);
            DisplayStudyEventBean dseb = ListStudySubjectServlet.getDisplayStudyEventsForStudySubject(studySub, seb, sm.getDataSource(), ub, currentRole, this.currentStudy);
            // ArrayList eventCRFs = ecdao.findAllByStudyEvent(seb);
            // ArrayList al =
            // ViewStudySubjectServlet.getUncompletedCRFs(sm.getDataSource(),
            // eventDefinitionCRFs, eventCRFs);
            // dseb.getUncompletedCRFs().add(al);
            displayEvents.add(dseb);
        }
        ArrayList al = new ArrayList();
        for (int k = 0; k < displayEvents.size(); k++) {
            DisplayStudyEventBean dseb = displayEvents.get(k);
            ArrayList eventCRFs = dseb.getDisplayEventCRFs();
            for (int a = 0; a < eventDefinitionCRFs.size(); a++) {
                EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(a);
                int crfId = edc.getCrfId();
                boolean hasCRF = false;
                for (int b = 0; b < eventCRFs.size(); b++) {
                    DisplayEventCRFBean decb = (DisplayEventCRFBean) eventCRFs.get(b);
                    // decb.getStage().getName() );
                    if (decb.getEventCRF().getCrf().getId() == crfId) {
                        dseb.getAllEventCRFs().add(decb);
                        // logger.info("hasCRf" + crfId +
                        // decb.getEventCRF().getCrf().getName());
                        hasCRF = true;
                        break;
                    }
                }
                if (hasCRF == false) {
                    DisplayEventCRFBean db = new DisplayEventCRFBean();
                    db.setEventDefinitionCRF(edc);
                    db.getEventDefinitionCRF().setCrf(edc.getCrf());
                    dseb.getAllEventCRFs().add(db);
                // logger.info("noCRf" + crfId);
                }
            }
            // Issue 3212 BWP <<
            if (currentStudy.getParentStudyId() > 0) {
                // check each eventDefCRFBean and set its isHidden property
                // to true, if its
                // persistent/database-derived hideCrf is true (domain rule:
                // hide the CRF from users logged into a site)
                HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
                hideCRFManager.optionallyCheckHideCRFProperty(dseb);
                // remove a DisplayEventCRFBean from a DisplayStudyEventBean
                // in the list
                // if it contains a hidden CRF in its event definition
                hideCRFManager.removeHiddenEventCRF(dseb);
                // generate a boolean request attribute indicating whether
                // any of the CRFs
                // should be hidden
                boolean hideCRFs = hideCRFManager.studyEventHasAHideCRFProperty(dseb);
                request.setAttribute("hideCRFs", hideCRFs);
            }
        // >>
        }
        DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
        dssb.setStudySubject(studySub);
        dssb.setStudyGroups(subGClasses);
        dssb.setStudyEvents(displayEvents);
        if (definitionId > 0) {
            dssb.setSedId(definitionId);
        } else {
            dssb.setSedId(-1);
        }
        displayStudySubs.add(dssb);
    }
    EntityBeanTable table = fp.getEntityBeanTable();
    ArrayList allStudyRows = DisplayStudySubjectEventsRow.generateRowsFromBeans(displayStudySubs);
    ArrayList columnArray = new ArrayList();
    columnArray.add(resword.getString("ID"));
    columnArray.add(resword.getString("subject_status"));
    columnArray.add(resword.getString("gender"));
    for (int i = 0; i < studyGroupClasses.size(); i++) {
        StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
        columnArray.add(sgc.getName());
    }
    // columnArray.add("Event Sequence");
    columnArray.add(resword.getString("event_status"));
    columnArray.add(resword.getString("event_date"));
    // Issue 3212 BWP <<
    HideCRFManager hideCRFMgr = HideCRFManager.createHideCRFManager();
    hideCRFMgr.hideSpecifiedEventCRFDefBeans(eventDefinitionCRFs);
    for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
        // Issue 3212 BWP <<
        if (!(currentStudy.getParentStudyId() > 0)) {
            columnArray.add(edc.getCrf().getName());
        } else {
            if (!edc.isHideCrf()) {
                columnArray.add(edc.getCrf().getName());
            }
        }
    // >>
    }
    columnArray.add(resword.getString("actions"));
    String[] columns = new String[columnArray.size()];
    columnArray.toArray(columns);
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.setQuery("ListEventsForSubject?module=" + module + "&defId=" + definitionId + "&tab=" + tabId, new HashMap());
    table.hideColumnLink(columnArray.size() - 1);
    // if(currentStudy.getStatus().isAvailable()){
    // table.addLink(resword.getString("add_new_subject"), "AddNewSubject");
    // }
    table.setRows(allStudyRows);
    if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
        table.setKeywordFilter(filterKeyword);
    }
    table.computeDisplay();
    request.setAttribute("table", table);
    forwardPage(Page.LIST_EVENTS_FOR_SUBJECT);
}

Example 87 with StudyEventDAO

use of org.akaza.openclinica.dao.managestudy.StudyEventDAO 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 88 with StudyEventDAO

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

the class InitUpdateEventDefinitionServlet method mayProceed.

/**
     * Checks whether the user has the correct privilege
     */
@Override
public void mayProceed() throws InsufficientPermissionException {
    checkStudyLocked(Page.LIST_DEFINITION_SERVLET, respage.getString("current_study_locked"));
    if (ub.isSysAdmin()) {
        return;
    }
    StudyEventDAO sdao = new StudyEventDAO(sm.getDataSource());
    // get current studyid
    int studyId = currentStudy.getId();
    if (ub.hasRoleInStudy(studyId)) {
        Role r = ub.getRoleByStudy(studyId).getRole();
        if (r.equals(Role.STUDYDIRECTOR) || r.equals(Role.COORDINATOR)) {
            return;
        } else {
            addPageMessage(respage.getString("no_have_permission_to_update_study_event_definition") + respage.getString("please_contact_sysadmin_questions"));
            throw new InsufficientPermissionException(Page.LIST_DEFINITION_SERVLET, resexception.getString("not_study_director"), "1");
        }
    }
    // To Do: the following code doesn't apply to admin for now
    String idString = request.getParameter("id");
    int defId = Integer.valueOf(idString.trim()).intValue();
    logger.info("defId" + defId);
    ArrayList events = (ArrayList) sdao.findAllByDefinition(defId);
    if (events != null && events.size() > 0) {
        logger.info("has events");
        for (int i = 0; i < events.size(); i++) {
            StudyEventBean sb = (StudyEventBean) events.get(i);
            if (!sb.getStatus().equals(Status.DELETED) && !sb.getStatus().equals(Status.AUTO_DELETED)) {
                logger.info("found one event");
                addPageMessage(respage.getString("sorry_but_at_this_time_may_not_modufy_SED"));
                throw new InsufficientPermissionException(Page.LIST_DEFINITION_SERVLET, resexception.getString("not_unpopulated"), "1");
            }
        }
    }
}

Example 89 with StudyEventDAO

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

the class DeleteStudyEventServlet 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_remove"));
        request.setAttribute("id", new Integer(studySubId).toString());
        forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
    } else {
        StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
        StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
        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)) {
            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());
            // construct info needed on view study event page
            DisplayStudyEventBean de = new DisplayStudyEventBean();
            de.setStudyEvent(event);
            request.setAttribute("displayEvent", de);
            //                request.setAttribute("crfs", eventDefinitionCRFs);
            forwardPage(Page.DELETE_STUDY_EVENT);
        } else {
            logger.info("submit to delete the event from study");
            // delete event from study
            event.setSubjectEventStatus(SubjectEventStatus.NOT_SCHEDULED);
            event.setUpdater(ub);
            event.setUpdatedDate(new Date());
            sedao.update(event);
            String emailBody = respage.getString("the_event") + " " + event.getStudyEventDefinition().getName() + " " + respage.getString("has_been_removed_from_the_subject_record_for") + " " + studySub.getLabel() + " " + respage.getString("in_the_study") + " " + study.getName() + ".";
            addPageMessage(emailBody);
            //                sendEmail(emailBody);
            request.setAttribute("id", new Integer(studySubId).toString());
            forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
        }
    }
}

Example 90 with StudyEventDAO

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

the class EnterDataForStudyEventServlet method getStudyEvent.

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("study_event_to_enter_data_not_belong_study"));
        throw new InsufficientPermissionException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("study_event_not_belong_study"), "1");
    }
    StudyEventBean seb = (StudyEventBean) aeb;
    StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
    StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(seb.getStudyEventDefinitionId());
    seb.setStudyEventDefinition(sedb);
    // A. Hamid mantis issue 5048
    if (!(currentRole.isDirector() || currentRole.isCoordinator()) && seb.getSubjectEventStatus().isLocked()) {
        seb.setEditable(false);
    }
    return seb;
}