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

Example 51 with StudyDAO

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

the class ViewUserAccountServlet method getBean.

// public void processRequest(HttpServletRequest request,
// HttpServletResponse response)
// throws OpenClinicaException {
// session = request.getSession();
// session.setMaxInactiveInterval(60 * 60 * 3);
// logger.setLevel(Level.ALL);
// UserAccountBean ub = (UserAccountBean) session.getAttribute("userBean");
// try {
// String userName = request.getRemoteUser();
// 
// sm = new SessionManager(ub, userName);
// ub = sm.getUserBean();
// if (logger.isLoggable(Level.INFO)) {
// logger.info("user bean from DB" + ub.getName());
// }
// 
// FormProcessor fp = new FormProcessor(request);
// int userId = fp.getInt(ARG_USER_ID);
// 
// SQLFactory factory = SQLFactory.getInstance();
// UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
// 
// UserAccountBean user = getBean(udao, userId);
// 
// if ((user.getFirstName() != null) && (!user.getFirstName().equals(""))) {
// request.setAttribute("user", user);
// request.setAttribute("message", "");
// }
// else {
// request.setAttribute("user", new UserAccountBean());
// request.setAttribute("message", "The specified user does not exist!");
// }
// 
// forwardPage(Page.VIEW_USER_ACCOUNT, request, response);
// } catch (Exception e) {
// e.printStackTrace();
// logger.warn("OpenClinicaException::
// OpenClinica.control.viewUserAccount: " + e.getMessage());
// 
// forwardPage(Page.ERROR, request, response);
// }
// }
private UserAccountBean getBean(UserAccountDAO udao, int id) {
    UserAccountBean answer = (UserAccountBean) udao.findByPK(id);
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    ArrayList roles = answer.getRoles();
    for (int i = 0; i < roles.size(); i++) {
        StudyUserRoleBean sur = (StudyUserRoleBean) roles.get(i);
        StudyBean sb = (StudyBean) sdao.findByPK(sur.getStudyId());
        sur.setStudyName(sb.getName());
        roles.set(i, sur);
    }
    answer.setRoles(roles);
    return answer;
}

Example 52 with StudyDAO

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

the class ExportDatasetServlet method processRequest.

@Override
public void processRequest() throws Exception {
    DatasetDAO dsdao = new DatasetDAO(sm.getDataSource());
    ArchivedDatasetFileDAO asdfdao = new ArchivedDatasetFileDAO(sm.getDataSource());
    FormProcessor fp = new FormProcessor(request);
    GenerateExtractFileService generateFileService = new GenerateExtractFileService(sm.getDataSource(), (CoreResources) SpringServletAccess.getApplicationContext(context).getBean("coreResources"), (RuleSetRuleDao) SpringServletAccess.getApplicationContext(context).getBean("ruleSetRuleDao"));
    String action = fp.getString("action");
    int datasetId = fp.getInt("datasetId");
    int adfId = fp.getInt("adfId");
    if (datasetId == 0) {
        try {
            DatasetBean dsb = (DatasetBean) session.getAttribute("newDataset");
            datasetId = dsb.getId();
            logger.info("dataset id was zero, trying session: " + datasetId);
        } catch (NullPointerException e) {
            e.printStackTrace();
            logger.info("tripped over null pointer exception");
        }
    }
    DatasetBean db = (DatasetBean) dsdao.findByPK(datasetId);
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) sdao.findByPK(db.getStudyId());
    checkRoleByUserAndStudy(ub, study.getParentStudyId(), study.getId());
    // Checks if the study is current study or child of current study
    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;
    }
    /**
     * @vbc 08/06/2008 NEW EXTRACT DATA IMPLEMENTATION get study_id and
     *      parentstudy_id int currentstudyid = currentStudy.getId(); int
     *      parentstudy = currentStudy.getParentStudyId(); if (parentstudy >
     *      0) { // is OK } else { // same parentstudy = currentstudyid; } //
     */
    int currentstudyid = currentStudy.getId();
    // YW 11-09-2008 << modified logic here.
    int parentstudy = currentstudyid;
    // YW 11-09-2008 >>
    StudyBean parentStudy = new StudyBean();
    if (currentStudy.getParentStudyId() > 0) {
        // StudyDAO sdao = new StudyDAO(sm.getDataSource());
        parentStudy = (StudyBean) sdao.findByPK(currentStudy.getParentStudyId());
    }
    ExtractBean eb = generateFileService.generateExtractBean(db, currentStudy, parentStudy);
    if (StringUtil.isBlank(action)) {
        loadList(db, asdfdao, datasetId, fp, eb);
        forwardPage(Page.EXPORT_DATASETS);
    } else if ("delete".equalsIgnoreCase(action) && adfId > 0) {
        boolean success = false;
        ArchivedDatasetFileBean adfBean = (ArchivedDatasetFileBean) asdfdao.findByPK(adfId);
        File file = new File(adfBean.getFileReference());
        if (!file.canWrite()) {
            addPageMessage(respage.getString("write_protected"));
        } else {
            success = file.delete();
            if (success) {
                asdfdao.deleteArchiveDataset(adfBean);
                addPageMessage(respage.getString("file_removed"));
            } else {
                addPageMessage(respage.getString("error_removing_file"));
            }
        }
        loadList(db, asdfdao, datasetId, fp, eb);
        forwardPage(Page.EXPORT_DATASETS);
    } else {
        logger.info("**** found action ****: " + action);
        String generateReport = "";
        // generate file, and show screen export
        // String generalFileDir = DATASET_DIR + db.getId() +
        // File.separator;
        // change this up, so that we don't overwrite anything
        String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator;
        SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
        String generalFileDir = DATASET_DIR + db.getId() + File.separator + sdfDir.format(new java.util.Date());
        String fileName = "";
        db.setName(db.getName().replaceAll(" ", "_"));
        Page finalTarget = Page.GENERATE_DATASET;
        finalTarget = Page.EXPORT_DATA_CUSTOM;
        // now display report according to format specified
        // TODO revise final target to set to fileReference????
        long sysTimeBegin = System.currentTimeMillis();
        int fId = 0;
        if ("sas".equalsIgnoreCase(action)) {
            // generateReport =
            // dsdao.generateDataset(db,
            // ExtractBean.SAS_FORMAT,
            // currentStudy,
            // parentStudy);
            long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
            String SASFileName = db.getName() + "_sas.sas";
            // logger.info("found data set: "+generateReport);
            generateFileService.createFile(SASFileName, generalFileDir, generateReport, db, sysTimeEnd, ExportFormatBean.TXTFILE, true, ub);
            logger.info("created sas file");
            request.setAttribute("generate", generalFileDir + SASFileName);
            finalTarget.setFileName(generalFileDir + SASFileName);
            fileName = SASFileName;
        // won't work since page creator is private
        } else if ("odm".equalsIgnoreCase(action)) {
            String odmVersion = fp.getString("odmVersion");
            String ODMXMLFileName = "";
            // DRY
            // HashMap answerMap = generateFileService.createODMFile(odmVersion, sysTimeBegin, generalFileDir, db, this.currentStudy, "");
            HashMap answerMap = generateFileService.createODMFile(odmVersion, sysTimeBegin, generalFileDir, db, this.currentStudy, "", eb, currentStudy.getId(), currentStudy.getParentStudyId(), "99", true, true, true, null, ub);
            for (Iterator it = answerMap.entrySet().iterator(); it.hasNext(); ) {
                java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
                Object key = entry.getKey();
                Object value = entry.getValue();
                ODMXMLFileName = (String) key;
                Integer fileID = (Integer) value;
                fId = fileID.intValue();
            }
            fileName = ODMXMLFileName;
            request.setAttribute("generate", generalFileDir + ODMXMLFileName);
            logger.debug("+++ set the following: " + generalFileDir + ODMXMLFileName);
            // send a link with the SQL file? put the generated SQL file with the dataset?
            if (fp.getString("xalan") != null) {
                XalanTriggerService xts = new XalanTriggerService();
                String propertiesPath = SQLInitServlet.getField("filePath");
                // the trick there, we need to open up the zipped file and get at the XML
                openZipFile(generalFileDir + ODMXMLFileName + ".zip");
                // need to find out how to copy this xml file from /bin to the generalFileDir
                SimpleTrigger simpleTrigger = xts.generateXalanTrigger(propertiesPath + File.separator + "ODMReportStylesheet.xsl", ODMXMLFileName, generalFileDir + "output.sql", db.getId());
                scheduler = getScheduler();
                JobDetailBean jobDetailBean = new JobDetailBean();
                jobDetailBean.setGroup(xts.TRIGGER_GROUP_NAME);
                jobDetailBean.setName(simpleTrigger.getName());
                jobDetailBean.setJobClass(org.akaza.openclinica.web.job.XalanStatefulJob.class);
                jobDetailBean.setJobDataMap(simpleTrigger.getJobDataMap());
                // need durability?
                jobDetailBean.setDurability(true);
                jobDetailBean.setVolatility(false);
                try {
                    Date dateStart = scheduler.scheduleJob(jobDetailBean, simpleTrigger);
                    logger.info("== found job date: " + dateStart.toString());
                } catch (SchedulerException se) {
                    se.printStackTrace();
                }
            }
        } else if ("txt".equalsIgnoreCase(action)) {
            // generateReport =
            // dsdao.generateDataset(db,
            // ExtractBean.TXT_FORMAT,
            // currentStudy,
            // parentStudy);
            // eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            String TXTFileName = "";
            HashMap answerMap = generateFileService.createTabFile(eb, sysTimeBegin, generalFileDir, db, currentstudyid, parentstudy, "", ub);
            // and of course DRY
            for (Iterator it = answerMap.entrySet().iterator(); it.hasNext(); ) {
                java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
                Object key = entry.getKey();
                Object value = entry.getValue();
                TXTFileName = (String) key;
                Integer fileID = (Integer) value;
                fId = fileID.intValue();
            }
            fileName = TXTFileName;
            request.setAttribute("generate", generalFileDir + TXTFileName);
            // finalTarget.setFileName(generalFileDir+TXTFileName);
            logger.debug("+++ set the following: " + generalFileDir + TXTFileName);
        } else if ("html".equalsIgnoreCase(action)) {
            // html based dataset browser
            TabReportBean answer = new TabReportBean();
            eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            eb.getMetadata();
            eb.computeReport(answer);
            request.setAttribute("dataset", db);
            request.setAttribute("extractBean", eb);
            finalTarget = Page.GENERATE_DATASET_HTML;
        } else if ("spss".equalsIgnoreCase(action)) {
            SPSSReportBean answer = new SPSSReportBean();
            // removed three lines here and put them in generate file
            // service, createSPSSFile method. tbh 01/2009
            eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            eb.getMetadata();
            eb.computeReport(answer);
            // System.out.println("*** isShowCRFversion:
            // "+db.isShowCRFversion());
            // TODO in the spirit of DRY, if this works we need to remove
            // lines 443-776 in this servlet, tbh 01/2009
            String DDLFileName = "";
            HashMap answerMap = generateFileService.createSPSSFile(db, eb, currentStudy, parentStudy, sysTimeBegin, generalFileDir, answer, "", ub);
            // hmm, DRY?
            for (Iterator it = answerMap.entrySet().iterator(); it.hasNext(); ) {
                java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
                Object key = entry.getKey();
                Object value = entry.getValue();
                DDLFileName = (String) key;
                Integer fileID = (Integer) value;
                fId = fileID.intValue();
            }
            request.setAttribute("generate", generalFileDir + DDLFileName);
            logger.debug("+++ set the following: " + generalFileDir + DDLFileName);
        } else if ("csv".equalsIgnoreCase(action)) {
            CommaReportBean answer = new CommaReportBean();
            eb = dsdao.getDatasetData(eb, currentstudyid, parentstudy);
            eb.getMetadata();
            eb.computeReport(answer);
            long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
            // logger.info("found data set: "+generateReport);
            String CSVFileName = db.getName() + "_comma.txt";
            fId = generateFileService.createFile(CSVFileName, generalFileDir, answer.toString(), db, sysTimeEnd, ExportFormatBean.CSVFILE, true, ub);
            fileName = CSVFileName;
            logger.info("just created csv file");
            request.setAttribute("generate", generalFileDir + CSVFileName);
        // finalTarget.setFileName(generalFileDir+CSVFileName);
        } else if ("excel".equalsIgnoreCase(action)) {
            // HSSFWorkbook excelReport = dsdao.generateExcelDataset(db,
            // ExtractBean.XLS_FORMAT,
            // currentStudy,
            // parentStudy);
            long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
            // TODO this will change and point to a created excel
            // spreadsheet, tbh
            String excelFileName = db.getName() + "_excel.xls";
            // fId = this.createFile(excelFileName,
            // generalFileDir,
            // excelReport,
            // db, sysTimeEnd,
            // ExportFormatBean.EXCELFILE);
            // logger.info("just created csv file, for excel output");
            // response.setHeader("Content-disposition","attachment;
            // filename="+CSVFileName);
            // logger.info("csv file name: "+CSVFileName);
            finalTarget = Page.GENERATE_EXCEL_DATASET;
            // response.setContentType("application/vnd.ms-excel");
            response.setHeader("Content-Disposition", "attachment; filename=" + db.getName() + "_excel.xls");
            request.setAttribute("generate", generalFileDir + excelFileName);
            logger.info("set 'generate' to :" + generalFileDir + excelFileName);
            fileName = excelFileName;
        // excelReport.write(stream);
        // stream.flush();
        // stream.close();
        // finalTarget.setFileName(WEB_DIR+db.getId()+"/"+excelFileName);
        }
        // <%@page contentType="application/vnd.ms-excel"%>
        if (!finalTarget.equals(Page.GENERATE_EXCEL_DATASET) && !finalTarget.equals(Page.GENERATE_DATASET_HTML)) {
            // to catch all the others and try to set a new path for file
            // capture
            // tbh, 4-18-05
            // request.setAttribute("generate",finalTarget.getFileName());
            // TODO changing path to show refresh page, then window with
            // link to download file, tbh 06-08-05
            // finalTarget.setFileName(
            // "/WEB-INF/jsp/extract/generatedFileDataset.jsp");
            finalTarget.setFileName("" + "/WEB-INF/jsp/extract/generateMetadataCore.jsp");
            // also set up table here???
            asdfdao = new ArchivedDatasetFileDAO(sm.getDataSource());
            ArchivedDatasetFileBean asdfBean = (ArchivedDatasetFileBean) asdfdao.findByPK(fId);
            // *** do we need this below? tbh
            ArrayList newFileList = new ArrayList();
            newFileList.add(asdfBean);
            // request.setAttribute("filelist",newFileList);
            ArrayList filterRows = ArchivedDatasetFileRow.generateRowsFromBeans(newFileList);
            EntityBeanTable table = fp.getEntityBeanTable();
            // sort by date
            table.setSortingIfNotExplicitlySet(3, false);
            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);
        // *** do we need this above? tbh
        }
        logger.info("set first part of 'generate' to :" + generalFileDir);
        logger.info("found file name: " + finalTarget.getFileName());
        // String del = CoreResources.getField("dataset_file_delete");
        // if (del.equalsIgnoreCase("true") || del.equals("")) {
        // File deleteFile = new File(generalFileDir + fileName);
        // deleteFile.delete();
        // }
        forwardPage(finalTarget);
    }
}

Example 53 with StudyDAO

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

the class RemoveDatasetServlet 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);
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    StudyBean study = (StudyBean) sdao.findByPK(dataset.getStudyId());
    checkRoleByUserAndStudy(ub, study.getParentStudyId(), study.getId());
    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;
    }
    if (!ub.isSysAdmin() && dataset.getOwnerId() != ub.getId()) {
        addPageMessage(respage.getString("no_have_correct_privilege_current_study") + " " + respage.getString("change_active_study_or_contact"));
        forwardPage(Page.MENU_SERVLET);
        return;
    }
    String action = request.getParameter("action");
    if (resword.getString("remove_this_dataset").equalsIgnoreCase(action)) {
        dataset.setStatus(Status.DELETED);
        dsDAO.update(dataset);
        // +
        addPageMessage(respage.getString("dataset_removed"));
        // "System Administrators can "+
        // "restore it if necessary.");
        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.REMOVE_DATASET);
    }
}

Example 54 with StudyDAO

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

the class UpdateProfileServlet method processRequest.

@Override
public void processRequest() throws Exception {
    // action sent by user
    String action = request.getParameter("action");
    StudyDAO sdao = new StudyDAO(sm.getDataSource());
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    UserAccountBean userBean1 = (UserAccountBean) udao.findByUserName(ub.getName());
    Collection studies = sdao.findAllByUser(ub.getName());
    if (StringUtils.isBlank(action)) {
        request.setAttribute("studies", studies);
        session.setAttribute("userBean1", userBean1);
        forwardPage(Page.UPDATE_PROFILE);
    } else {
        if ("confirm".equalsIgnoreCase(action)) {
            logger.info("confirm");
            request.setAttribute("studies", studies);
            confirmProfile(userBean1, udao);
        } else if ("submit".equalsIgnoreCase(action)) {
            logger.info("submit");
            submitProfile(udao);
            addPageMessage(respage.getString("profile_updated_succesfully"));
            ub.incNumVisitsToMainMenu();
            forwardPage(Page.MENU_SERVLET);
        }
    }
}

Example 55 with StudyDAO

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

the class AssignUserToStudyServlet method findUsers.

/**
 * Find all users in the system
 *
 * @return
 */
private ArrayList findUsers() {
    UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
    ArrayList userList = (ArrayList) udao.findAll();
    ArrayList userAvailable = new ArrayList();
    for (int i = 0; i < userList.size(); i++) {
        UserAccountBean u = (UserAccountBean) userList.get(i);
        int activeStudyId = currentStudy.getId();
        StudyUserRoleBean sub = udao.findRoleByUserNameAndStudyId(u.getName(), activeStudyId);
        if (!sub.isActive()) {
            // doesn't have a role in the current study
            sub.setRole(Role.RESEARCHASSISTANT);
            sub.setStudyId(activeStudyId);
            u.setActiveStudyId(activeStudyId);
            u.addRole(sub);
            u.setStatus(Status.AVAILABLE);
            // try to find whether this user has role in site or parent
            if (currentStudy.getParentStudyId() > 0) {
                // this is a site
                StudyUserRoleBean subParent = udao.findRoleByUserNameAndStudyId(u.getName(), currentStudy.getParentStudyId());
                if (subParent.isActive()) {
                    u.setNotes(subParent.getRole().getDescription() + " " + respage.getString("in_parent_study"));
                }
            } else {
                // find all the sites for this top study
                StudyDAO sdao = new StudyDAO(sm.getDataSource());
                ArrayList sites = (ArrayList) sdao.findAllByParent(currentStudy.getId());
                String notes = "";
                for (int j = 0; j < sites.size(); j++) {
                    StudyBean site = (StudyBean) sites.get(j);
                    StudyUserRoleBean subSite = udao.findRoleByUserNameAndStudyId(u.getName(), site.getId());
                    if (subSite.isActive()) {
                        notes = notes + subSite.getRole().getDescription() + respage.getString("in_site") + ":" + site.getName() + "; ";
                    }
                }
                u.setNotes(notes);
            }
        } else {
            // already have a role in the current study
            sub.setStudyId(activeStudyId);
            u.setActiveStudyId(activeStudyId);
            u.addRole(sub);
            u.setStatus(Status.UNAVAILABLE);
        }
        userAvailable.add(u);
    }
    return userAvailable;
}