Examples with DatasetBean org.akaza.openclinica.bean.extract.DatasetBean used on opensource projects

Example 31 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class ShowFileServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int fileId = fp.getInt("fileId");
    int dsId = fp.getInt("datasetId");
    DatasetDAO dsdao = new DatasetDAO(sm.getDataSource());
    DatasetBean db = (DatasetBean) dsdao.findByPK(dsId);
    ArchivedDatasetFileDAO asdfdao = new ArchivedDatasetFileDAO(sm.getDataSource());
    ArchivedDatasetFileBean asdfBean = (ArchivedDatasetFileBean) asdfdao.findByPK(fileId);
    ArrayList newFileList = new ArrayList();
    newFileList.add(asdfBean);
    // request.setAttribute("filelist",newFileList);
    ArrayList filterRows = ArchivedDatasetFileRow.generateRowsFromBeans(newFileList);
    EntityBeanTable table = fp.getEntityBeanTable();
    String[] columns = { resword.getString("file_name"), resword.getString("run_time"), resword.getString("file_size"), resword.getString("created_date"), resword.getString("created_by") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(0);
    table.hideColumnLink(1);
    table.hideColumnLink(2);
    table.hideColumnLink(3);
    table.hideColumnLink(4);
    // table.setQuery("ExportDataset?datasetId=" +db.getId(), new
    // HashMap());
    // trying to continue...
    // session.setAttribute("newDataset",db);
    request.setAttribute("dataset", db);
    request.setAttribute("file", asdfBean);
    table.setRows(filterRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    Page finalTarget = Page.EXPORT_DATA_CUSTOM;
    finalTarget.setFileName("/WEB-INF/jsp/extract/generateMetadataFile.jsp");
    forwardPage(finalTarget);
}

Example 32 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class ViewDatasetsServlet method processRequest.

@Override
public void processRequest() throws Exception {
    DatasetDAO dsdao = new DatasetDAO(sm.getDataSource());
    String action = request.getParameter("action");
    resetPanel();
    request.setAttribute(STUDY_INFO_PANEL, panel);
    // YW, 2-15-2008 <<
    session.removeAttribute("allSelectedItems");
    session.removeAttribute("allSelectedGroups");
    session.removeAttribute("allItems");
    session.removeAttribute("newDataset");
    // YW >>
    if (StringUtil.isBlank(action)) {
        // YW 08-2008 << 2529 fix
        StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
        StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
        EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
        StudyBean studyWithEventDefinitions = currentStudy;
        if (currentStudy.getParentStudyId() > 0) {
            studyWithEventDefinitions = new StudyBean();
            studyWithEventDefinitions.setId(currentStudy.getParentStudyId());
        }
        ArrayList seds = seddao.findAllActiveByStudy(studyWithEventDefinitions);
        CRFDAO crfdao = new CRFDAO(sm.getDataSource());
        HashMap events = new LinkedHashMap();
        for (int i = 0; i < seds.size(); i++) {
            StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seds.get(i);
            ArrayList crfs = (ArrayList) crfdao.findAllActiveByDefinition(sed);
            if (!crfs.isEmpty()) {
                events.put(sed, crfs);
            }
        }
        session.setAttribute("eventsForCreateDataset", events);
        // YW >>
        FormProcessor fp = new FormProcessor(request);
        EntityBeanTable table = fp.getEntityBeanTable();
        ArrayList datasets = new ArrayList();
        //            if (ub.isSysAdmin()) {
        //                datasets = dsdao.findAllByStudyIdAdmin(currentStudy.getId());
        //            } else {
        datasets = dsdao.findAllByStudyId(currentStudy.getId());
        //            }
        ArrayList datasetRows = DatasetRow.generateRowsFromBeans(datasets);
        String[] columns = { resword.getString("dataset_name"), resword.getString("description"), resword.getString("created_by"), resword.getString("created_date"), resword.getString("status"), resword.getString("actions") };
        table.setColumns(new ArrayList(Arrays.asList(columns)));
        table.hideColumnLink(5);
        table.addLink(resword.getString("show_only_my_datasets"), "ViewDatasets?action=owner&ownerId=" + ub.getId());
        table.addLink(resword.getString("create_dataset"), "CreateDataset");
        table.setQuery("ViewDatasets", new HashMap());
        table.setRows(datasetRows);
        table.computeDisplay();
        request.setAttribute("table", table);
        // this is the old code that the tabling code replaced:
        // ArrayList datasets = (ArrayList)dsdao.findAll();
        // request.setAttribute("datasets", datasets);
        forwardPage(Page.VIEW_DATASETS);
    } else {
        if ("owner".equalsIgnoreCase(action)) {
            FormProcessor fp = new FormProcessor(request);
            int ownerId = fp.getInt("ownerId");
            EntityBeanTable table = fp.getEntityBeanTable();
            ArrayList datasets = (ArrayList) dsdao.findByOwnerId(ownerId, currentStudy.getId());
            /*
                 * if (datasets.isEmpty()) {
                 * forwardPage(Page.VIEW_EMPTY_DATASETS); } else {
                 */
            ArrayList datasetRows = DatasetRow.generateRowsFromBeans(datasets);
            String[] columns = { resword.getString("dataset_name"), resword.getString("description"), resword.getString("created_by"), resword.getString("created_date"), resword.getString("status"), resword.getString("actions") };
            table.setColumns(new ArrayList(Arrays.asList(columns)));
            table.hideColumnLink(5);
            table.addLink(resword.getString("show_all_datasets"), "ViewDatasets");
            table.addLink(resword.getString("create_dataset"), "CreateDataset");
            table.setQuery("ViewDatasets?action=owner&ownerId=" + ub.getId(), new HashMap());
            table.setRows(datasetRows);
            table.computeDisplay();
            request.setAttribute("table", table);
            // this is the old code:
            // ArrayList datasets = (ArrayList)dsdao.findByOwnerId(ownerId);
            // request.setAttribute("datasets", datasets);
            forwardPage(Page.VIEW_DATASETS);
        // }
        } else if ("details".equalsIgnoreCase(action)) {
            FormProcessor fp = new FormProcessor(request);
            int datasetId = fp.getInt("datasetId");
            DatasetBean db = initializeAttributes(datasetId);
            StudyDAO sdao = new StudyDAO(sm.getDataSource());
            StudyBean study = (StudyBean) sdao.findByPK(db.getStudyId());
            if (study.getId() != currentStudy.getId() && study.getParentStudyId() != currentStudy.getId()) {
                addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
                forwardPage(Page.MENU_SERVLET);
                return;
            }
            /*
                 * EntityBeanTable table = fp.getEntityBeanTable(); ArrayList
                 * datasetRows = DatasetRow.generateRowFromBean(db); String[]
                 * columns = { "Dataset Name", "Description", "Created By",
                 * "Created Date", "Status", "Actions" }; table.setColumns(new
                 * ArrayList(Arrays.asList(columns))); table.hideColumnLink(5);
                 * table.setQuery("ViewDatasets", new HashMap());
                 * table.setRows(datasetRows); table.computeDisplay();
                 * request.setAttribute("table", table);
                 */
            request.setAttribute("dataset", db);
            forwardPage(Page.VIEW_DATASET_DETAILS);
        }
    }
}

Example 33 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class RestoreStudyServlet method processRequest.

@Override
public void processRequest() throws Exception {
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    int studyId = fp.getInt("id");
    StudyBean study = (StudyBean) sdao.findByPK(studyId);
    // find all sites
    ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
    // find all user and roles in the study, include ones in sites
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList userRoles = udao.findAllByStudyId(studyId);
    // find all subjects in the study, include ones in sites
    StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
    ArrayList subjects = ssdao.findAllByStudy(study);
    // find all events in the study, include ones in sites
    StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
    ArrayList definitions = sefdao.findAllByStudy(study);
    String action = request.getParameter("action");
    if (studyId == 0) {
        addPageMessage(respage.getString("please_choose_a_study_to_restore"));
        forwardPage(Page.STUDY_LIST_SERVLET);
    } else {
        if ("confirm".equalsIgnoreCase(action)) {
            request.setAttribute("studyToRestore", study);
            request.setAttribute("sitesToRestore", sites);
            request.setAttribute("userRolesToRestore", userRoles);
            request.setAttribute("subjectsToRestore", subjects);
            request.setAttribute("definitionsToRRestore", definitions);
            forwardPage(Page.RESTORE_STUDY);
        } else {
            logger.info("submit to restore the study");
            // change all statuses to unavailable
            StudyDAO studao = new StudyDAO(sm.getDataSource());
            study.setStatus(study.getOldStatus());
            study.setUpdater(ub);
            study.setUpdatedDate(new Date());
            studao.update(study);
            // YW 09-27-2007 << restore auto-removed sites
            for (int i = 0; i < sites.size(); i++) {
                StudyBean site = (StudyBean) sites.get(i);
                if (site.getStatus() == Status.AUTO_DELETED) {
                    site.setStatus(site.getOldStatus());
                    site.setUpdater(ub);
                    site.setUpdatedDate(new Date());
                    sdao.update(site);
                }
            }
            // restore all users and roles
            for (int i = 0; i < userRoles.size(); i++) {
                StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
                if (role.getStatus().equals(Status.AUTO_DELETED)) {
                    role.setStatus(Status.AVAILABLE);
                    role.setUpdater(ub);
                    role.setUpdatedDate(new Date());
                    udao.updateStudyUserRole(role, role.getUserName());
                }
            }
            // is current active study
            if (study.getId() == currentStudy.getId()) {
                currentStudy.setStatus(Status.AVAILABLE);
                StudyUserRoleBean r = (new UserAccountDAO(sm.getDataSource())).findRoleByUserNameAndStudyId(ub.getName(), currentStudy.getId());
                currentRole.setRole(r.getRole());
            } else // active site will be restored as well if it was auto-removed
            if (currentStudy.getParentStudyId() == study.getId() && currentStudy.getStatus() == Status.AUTO_DELETED) {
                currentStudy.setStatus(Status.AVAILABLE);
                StudyUserRoleBean r = (new UserAccountDAO(sm.getDataSource())).findRoleByUserNameAndStudyId(ub.getName(), currentStudy.getId());
                StudyUserRoleBean rInParent = (new UserAccountDAO(sm.getDataSource())).findRoleByUserNameAndStudyId(ub.getName(), currentStudy.getParentStudyId());
                // according to logic in SecureController.java: inherited
                // role from parent study, pick the higher role
                currentRole.setRole(Role.get(Role.max(r.getRole(), rInParent.getRole()).getId()));
            }
            // restore all subjects
            for (int i = 0; i < subjects.size(); i++) {
                StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
                if (subject.getStatus().equals(Status.AUTO_DELETED)) {
                    subject.setStatus(Status.AVAILABLE);
                    subject.setUpdater(ub);
                    subject.setUpdatedDate(new Date());
                    ssdao.update(subject);
                }
            }
            // restore all study_group
            StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
            StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
            SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
            ArrayList groups = sgcdao.findAllByStudy(study);
            for (int i = 0; i < groups.size(); i++) {
                StudyGroupClassBean group = (StudyGroupClassBean) groups.get(i);
                if (group.getStatus().equals(Status.AUTO_DELETED)) {
                    group.setStatus(Status.AVAILABLE);
                    group.setUpdater(ub);
                    group.setUpdatedDate(new Date());
                    sgcdao.update(group);
                    // all subject_group_map
                    ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupClassId(group.getId());
                    for (int j = 0; j < subjectGroupMaps.size(); j++) {
                        SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
                        if (sgMap.getStatus().equals(Status.AUTO_DELETED)) {
                            sgMap.setStatus(Status.AVAILABLE);
                            sgMap.setUpdater(ub);
                            sgMap.setUpdatedDate(new Date());
                            sgmdao.update(sgMap);
                        }
                    }
                }
            }
            // restore all event definitions and event
            EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
            StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
            for (int i = 0; i < definitions.size(); i++) {
                StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
                if (definition.getStatus().equals(Status.AUTO_DELETED)) {
                    definition.setStatus(Status.AVAILABLE);
                    definition.setUpdater(ub);
                    definition.setUpdatedDate(new Date());
                    sefdao.update(definition);
                    ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
                    for (int j = 0; j < edcs.size(); j++) {
                        EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
                        if (edc.getStatus().equals(Status.AUTO_DELETED)) {
                            edc.setStatus(Status.AVAILABLE);
                            edc.setUpdater(ub);
                            edc.setUpdatedDate(new Date());
                            edcdao.update(edc);
                        }
                    }
                    ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
                    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.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(eventCRF.getOldStatus());
                                    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.AUTO_DELETED)) {
                                            item.setStatus(item.getOldStatus());
                                            item.setUpdater(ub);
                                            item.setUpdatedDate(new Date());
                                            iddao.update(item);
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
            // for definitions
            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.AUTO_DELETED)) {
                    data.setStatus(Status.AVAILABLE);
                    data.setUpdater(ub);
                    data.setUpdatedDate(new Date());
                    datadao.update(data);
                }
            }
            addPageMessage(respage.getString("this_study_has_been_restored_succesfully"));
            forwardPage(Page.STUDY_LIST_SERVLET);
        }
    }
}

Example 34 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class ViewSelectedServlet method processRequest.

@Override
public void processRequest() throws Exception {
    DatasetBean db = (DatasetBean) session.getAttribute("newDataset");
    HashMap events = (HashMap) session.getAttribute(CreateDatasetServlet.EVENTS_FOR_CREATE_DATASET);
    if (events == null) {
        events = new HashMap();
    }
    request.setAttribute("eventlist", events);
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(sm.getDataSource());
    // new
    ArrayList ids = CreateDatasetServlet.allSedItemIdsInStudy(events, crfdao, idao);
    // ArrayList();
    // ArrayList allItemsInStudy = EditSelectedServlet.selectAll(events,
    // crfdao, idao);
    // for (int j = 0; j < allItemsInStudy.size(); j++) {
    // ItemBean item = (ItemBean) allItemsInStudy.get(j);
    // Integer itemId = new Integer(item.getId());
    // if (!ids.contains(itemId)) {
    // ids.add(itemId);
    // }
    // }
    session.setAttribute("numberOfStudyItems", new Integer(ids.size()).toString());
    ArrayList items = new ArrayList();
    if (db == null || db.getItemIds().size() == 0) {
        session.setAttribute("allSelectedItems", items);
        // FIXME can it be that we have no selected
        setUpStudyGroups();
        // items and
        // some selected groups? tbh
        forwardPage(Page.CREATE_DATASET_VIEW_SELECTED);
        return;
    }
    items = getAllSelected(db, idao, imfdao);
    session.setAttribute("allSelectedItems", items);
    FormProcessor fp = new FormProcessor(request);
    String status = fp.getString("status");
    if (!StringUtil.isBlank(status) && "html".equalsIgnoreCase(status)) {
        forwardPage(Page.CREATE_DATASET_VIEW_SELECTED_HTML);
    } else {
        setUpStudyGroups();
        forwardPage(Page.CREATE_DATASET_VIEW_SELECTED);
    }
}

Example 35 with DatasetBean

use of org.akaza.openclinica.bean.extract.DatasetBean in project OpenClinica by OpenClinica.

the class RestoreDatasetServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int dsId = fp.getInt("dsId");
    DatasetDAO dsDAO = new DatasetDAO(sm.getDataSource());
    DatasetBean dataset = (DatasetBean) dsDAO.findByPK(dsId);
    String action = request.getParameter("action");
    if (resword.getString("restore_this_dataset").equalsIgnoreCase(action)) {
        dataset.setStatus(Status.AVAILABLE);
        dsDAO.update(dataset);
        addPageMessage(respage.getString("dataset_has_been_succesfully_reinstated"));
        request.setAttribute("table", getDatasetTable());
        forwardPage(Page.VIEW_DATASETS);
    } else if (resword.getString("cancel").equalsIgnoreCase(action)) {
        request.setAttribute("table", getDatasetTable());
        forwardPage(Page.VIEW_DATASETS);
    } else {
        request.setAttribute("dataset", dataset);
        forwardPage(Page.RESTORE_DATASET);
    }
}