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

Example 36 with DatasetBean

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

the class ExtractController method processSubmit.

/**
     * process the page from whence you came, i.e. extract a dataset
     * @param id, the id of the extract properties bean, gained from Core Resources
     * @param datasetId, the id of the dataset, found through DatasetDAO
     * @param request, http request
     * @return model map, but more importantly, creates a quartz job which runs right away and generates all output there
     */
@RequestMapping(method = RequestMethod.GET)
public ModelMap processSubmit(@RequestParam("id") String id, @RequestParam("datasetId") String datasetId, HttpServletRequest request, HttpServletResponse response) {
    if (!mayProceed(request)) {
        try {
            response.sendRedirect(request.getContextPath() + "/MainMenu?message=authentication_failed");
        } catch (Exception e) {
            e.printStackTrace();
        }
        return null;
    }
    ModelMap map = new ModelMap();
    ResourceBundleProvider.updateLocale(LocaleResolver.getLocale(request));
    // String datasetId = (String)request.getAttribute("datasetId");
    // String id = (String)request.getAttribute("id");
    logger.debug("found both id " + id + " and dataset " + datasetId);
    ExtractUtils extractUtils = new ExtractUtils();
    // get extract id
    // get dataset id
    // if id is a number and dataset id is a number ...
    datasetDao = new DatasetDAO(dataSource);
    UserAccountBean userBean = (UserAccountBean) request.getSession().getAttribute("userBean");
    CoreResources cr = new CoreResources();
    ExtractPropertyBean epBean = cr.findExtractPropertyBeanById(new Integer(id).intValue(), datasetId);
    DatasetBean dsBean = (DatasetBean) datasetDao.findByPK(new Integer(datasetId).intValue());
    // set the job in motion
    String[] files = epBean.getFileName();
    String exportFileName;
    int fileSize = files.length;
    int cnt = 0;
    SimpleTrigger simpleTrigger = null;
    //TODO: if files and export names size is not same... throw an error
    dsBean.setName(dsBean.getName().replaceAll(" ", "_"));
    String[] exportFiles = epBean.getExportFileName();
    String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator;
    SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
    int i = 0;
    String[] temp = new String[exportFiles.length];
    //JN: The following logic is for comma separated variables, to avoid the second file be treated as a old file and deleted.
    while (i < exportFiles.length) {
        temp[i] = resolveVars(exportFiles[i], dsBean, sdfDir, SQLInitServlet.getField("filePath"), extractUtils);
        i++;
    }
    epBean.setDoNotDelFiles(temp);
    epBean.setExportFileName(temp);
    XsltTriggerService xsltService = new XsltTriggerService();
    // TODO get a user bean somehow?
    String generalFileDir = SQLInitServlet.getField("filePath");
    generalFileDir = generalFileDir + "datasets" + File.separator + dsBean.getId() + File.separator + sdfDir.format(new java.util.Date());
    exportFileName = epBean.getExportFileName()[cnt];
    // need to set the dataset path here, tbh
    logger.debug("found odm xml file path " + generalFileDir);
    // next, can already run jobs, translations, and then add a message to be notified later
    //JN all the properties need to have the variables...
    String xsltPath = SQLInitServlet.getField("filePath") + "xslt" + File.separator + files[cnt];
    String endFilePath = epBean.getFileLocation();
    endFilePath = getEndFilePath(endFilePath, dsBean, sdfDir, SQLInitServlet.getField("filePath"), extractUtils);
    //  exportFileName = resolveVars(exportFileName,dsBean,sdfDir);
    if (epBean.getPostProcExportName() != null) {
        //String preProcExportPathName = getEndFilePath(epBean.getPostProcExportName(),dsBean,sdfDir);
        String preProcExportPathName = resolveVars(epBean.getPostProcExportName(), dsBean, sdfDir, SQLInitServlet.getField("filePath"), extractUtils);
        epBean.setPostProcExportName(preProcExportPathName);
    }
    if (epBean.getPostProcLocation() != null) {
        String prePocLoc = getEndFilePath(epBean.getPostProcLocation(), dsBean, sdfDir, SQLInitServlet.getField("filePath"), extractUtils);
        epBean.setPostProcLocation(prePocLoc);
    }
    setAllProps(epBean, dsBean, sdfDir, extractUtils);
    // also need to add the status fields discussed w/ cc:
    // result code, user message, optional URL, archive message, log file message
    // asdf table: sort most recent at top
    logger.debug("found xslt file name " + xsltPath);
    // String xmlFilePath = generalFileDir + ODMXMLFileName;
    simpleTrigger = xsltService.generateXsltTrigger(scheduler, xsltPath, // xml_file_path
    generalFileDir, endFilePath + File.separator, exportFileName, dsBean.getId(), epBean, userBean, LocaleResolver.getLocale(request).getLanguage(), cnt, SQLInitServlet.getField("filePath") + "xslt", this.TRIGGER_GROUP_NAME);
    // System.out.println("just set locale: " + LocaleResolver.getLocale(request).getLanguage());
    cnt++;
    ApplicationContext context = null;
    try {
        context = (ApplicationContext) scheduler.getContext().get("applicationContext");
    } catch (SchedulerException e) {
        e.printStackTrace();
    }
    //WebApplicationContext context = ContextLoader.getCurrentWebApplicationContext();
    JobDetailFactoryBean jobDetailFactoryBean = context.getBean(JobDetailFactoryBean.class, simpleTrigger, this.TRIGGER_GROUP_NAME);
    try {
        Date dateStart = scheduler.scheduleJob(jobDetailFactoryBean.getObject(), simpleTrigger);
        logger.debug("== found job date: " + dateStart.toString());
    } catch (SchedulerException se) {
        se.printStackTrace();
    }
    request.setAttribute("datasetId", datasetId);
    // set the job name here in the user's session, so that we can ping the scheduler to pull it out later
    if (jobDetailFactoryBean != null)
        request.getSession().setAttribute("jobName", jobDetailFactoryBean.getObject().getKey().getName());
    if (simpleTrigger != null)
        request.getSession().setAttribute("groupName", this.TRIGGER_GROUP_NAME);
    request.getSession().setAttribute("datasetId", new Integer(dsBean.getId()));
    return map;
}

Example 37 with DatasetBean

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

the class DatasetRow method compareColumn.

// TODO l10n dates, tbh
@Override
protected int compareColumn(Object row, int sortingColumn) {
    if (!row.getClass().equals(DatasetRow.class)) {
        return 0;
    }
    DatasetBean thisAccount = (DatasetBean) bean;
    DatasetBean argAccount = (DatasetBean) ((DatasetRow) row).bean;
    int answer = 0;
    switch(sortingColumn) {
        case COL_DATASETNAME:
            answer = thisAccount.getName().toLowerCase().compareTo(argAccount.getName().toLowerCase());
            break;
        case COL_DATASETDESC:
            answer = thisAccount.getDescription().toLowerCase().compareTo(argAccount.getDescription().toLowerCase());
            break;
        case COL_DATASETOWNER:
            answer = thisAccount.getOwner().getName().toLowerCase().compareTo(argAccount.getOwner().getName().toLowerCase());
            break;
        case COL_STATUS:
            answer = thisAccount.getStatus().compareTo(argAccount.getStatus());
            break;
        case COL_DATASETCREATEDDATE:
            answer = thisAccount.getCreatedDate().compareTo(argAccount.getCreatedDate());
            break;
    }
    return answer;
}

Example 38 with DatasetBean

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

the class CreateDatasetServlet method finalUpateDatasetBean.

/*
     * Make sure item ids are unique and match SQLStatement for them
     */
protected DatasetBean finalUpateDatasetBean(DatasetBean db) {
    DatasetBean dsb = db;
    ArrayList<Integer> itemIds = new ArrayList<Integer>();
    Set<Integer> ids = new HashSet<Integer>();
    String idList = "item_id in (";
    if (dsb.getItemIds().size() > 0) {
        for (Integer itemId : (ArrayList<Integer>) dsb.getItemIds()) {
            if (!ids.contains(itemId)) {
                ids.add(itemId);
                itemIds.add(itemId);
                idList += itemId + ", ";
            }
        }
    }
    idList = idList.length() > 12 ? idList.substring(0, idList.length() - 2) : idList;
    dsb.getItemIds().clear();
    dsb.setItemIds(itemIds);
    dsb.setSQLStatement(dsb.sqlWithUniqeItemIds(idList));
    return dsb;
}

Example 39 with DatasetBean

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

the class EditSelectedServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    boolean selectAll = fp.getBoolean("all");
    boolean selectAllItemsGroupsAttrs = fp.getBoolean("allAttrsAndItems");
    // BWP 3095: Only show a "select all items" like on a side info panel if
    // it
    // is not part of the EditSelected-related JSP>>
    request.setAttribute("EditSelectedSubmitted", true);
    // <<
    ItemDAO idao = new ItemDAO(sm.getDataSource());
    // CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(sm.getDataSource());
    CRFDAO crfdao = new CRFDAO(sm.getDataSource());
    DatasetBean db = (DatasetBean) session.getAttribute("newDataset");
    if (db == null) {
        db = new DatasetBean();
        session.setAttribute("newDataset", db);
    }
    // << tbh
    // HashMap eventlist = (HashMap) request.getAttribute("eventlist");
    // if (eventlist == null) {
    // System.out.println("TTTTT found the second hashmap!");
    HashMap eventlist = (LinkedHashMap) session.getAttribute("eventsForCreateDataset");
    // }
    ArrayList<String> ids = CreateDatasetServlet.allSedItemIdsInStudy(eventlist, crfdao, idao);
    // >> tbh 11/09, need to fill in a session variable
    if (selectAll) {
        logger.info("select all..........");
        db = selectAll(db);
        MessageFormat msg = new MessageFormat("");
        msg.setLocale(locale);
        msg.applyPattern(respage.getString("choose_include_all_items_dataset"));
        Object[] arguments = { ids.size() };
        addPageMessage(msg.format(arguments));
    // addPageMessage("You choose to include all items in current study
    // for the dataset, " +db.getItemIds().size() + " items total.");
    }
    if (selectAllItemsGroupsAttrs) {
        logger.info("select everything....");
        db = selectAll(db);
        db.setShowCRFcompletionDate(true);
        db.setShowCRFinterviewerDate(true);
        db.setShowCRFinterviewerName(true);
        db.setShowCRFstatus(true);
        db.setShowCRFversion(true);
        db.setShowEventEnd(true);
        db.setShowEventEndTime(true);
        db.setShowEventLocation(true);
        db.setShowEventStart(true);
        db.setShowEventStartTime(true);
        db.setShowEventStatus(true);
        db.setShowSubjectAgeAtEvent(true);
        db.setShowSubjectDob(true);
        db.setShowSubjectGender(true);
        db.setShowSubjectGroupInformation(true);
        db.setShowSubjectStatus(true);
        db.setShowSubjectUniqueIdentifier(true);
        // select all groups
        ArrayList sgclasses = (ArrayList) session.getAttribute("allSelectedGroups");
        //
        ArrayList newsgclasses = new ArrayList();
        StudyDAO studydao = new StudyDAO(sm.getDataSource());
        StudyGroupClassDAO sgclassdao = new StudyGroupClassDAO(sm.getDataSource());
        StudyBean theStudy = (StudyBean) studydao.findByPK(sm.getUserBean().getActiveStudyId());
        sgclasses = sgclassdao.findAllActiveByStudy(theStudy);
        for (int i = 0; i < sgclasses.size(); i++) {
            StudyGroupClassBean sgclass = (StudyGroupClassBean) sgclasses.get(i);
            sgclass.setSelected(true);
            newsgclasses.add(sgclass);
        }
        session.setAttribute("allSelectedGroups", newsgclasses);
        request.setAttribute("allSelectedGroups", newsgclasses);
    }
    session.setAttribute("newDataset", db);
    HashMap events = (HashMap) session.getAttribute(CreateDatasetServlet.EVENTS_FOR_CREATE_DATASET);
    if (events == null) {
        events = new HashMap();
    }
    ArrayList allSelectItems = selectAll ? selectAll(events, crfdao, idao) : ViewSelectedServlet.getAllSelected(db, idao, imfdao);
    // >> tbh
    session.setAttribute("numberOfStudyItems", new Integer(ids.size()).toString());
    // << tbh 11/2009
    session.setAttribute("allSelectedItems", allSelectItems);
    setUpStudyGroups();
    forwardPage(Page.CREATE_DATASET_VIEW_SELECTED);
}

Example 40 with DatasetBean

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

the class AccessFileServlet method processRequest.

@Override
public void processRequest() throws Exception {
    FormProcessor fp = new FormProcessor(request);
    int fileId = fp.getInt("fileId");
    ArchivedDatasetFileDAO asdfdao = new ArchivedDatasetFileDAO(sm.getDataSource());
    DatasetDAO dsDao = new DatasetDAO(sm.getDataSource());
    ArchivedDatasetFileBean asdfBean = (ArchivedDatasetFileBean) asdfdao.findByPK(fileId);
    StudyDAO studyDao = new StudyDAO(sm.getDataSource());
    DatasetBean dsBean = (DatasetBean) dsDao.findByPK(asdfBean.getDatasetId());
    int parentId = currentStudy.getParentStudyId();
    if (//Logged in at study level
    parentId == 0) {
        StudyBean studyBean = (StudyBean) studyDao.findByPK(dsBean.getStudyId());
        //parent id of dataset created
        parentId = studyBean.getParentStudyId();
    }
    //logic: is parentId of the dataset created not equal to currentstudy? or is current study
    if (parentId != currentStudy.getId())
        if (dsBean.getStudyId() != currentStudy.getId()) {
            addPageMessage(respage.getString("no_have_correct_privilege_current_study") + respage.getString("change_study_contact_sysadmin"));
            // TODO
            throw new InsufficientPermissionException(Page.MENU_SERVLET, resexception.getString("not_allowed_access_extract_data_servlet"), "1");
        }
    // asdfBean.setWebPath(WEB_DIR+
    // asdfBean.getDatasetId()+
    // "/"+
    // asdfBean.getName());
    Page finalTarget = Page.EXPORT_DATA_CUSTOM;
    /*
         * if (asdfBean.getExportFormatId() ==
         * ExportFormatBean.EXCELFILE.getId()) { //
         * response.setContentType("application/octet-stream");
         * response.setHeader("Content-Disposition", "attachment; filename=" +
         * asdfBean.getName()); logger.info("found file name: "+
         * finalTarget.getFileName()); //
         * finalTarget.setFileName(asdfBean.getWebPath()); finalTarget =
         * Page.GENERATE_EXCEL_DATASET; } else {
         */
    logger.debug("found file reference: " + asdfBean.getFileReference() + " and file name: " + asdfBean.getName());
    if (asdfBean.getFileReference().endsWith(".zip")) {
        response.setHeader("Content-disposition", "attachment; filename=\"" + asdfBean.getName() + "\";");
        response.setContentType("application/zip");
    // response.setContentType("application/download");
    } else if (asdfBean.getFileReference().endsWith(".pdf")) {
        response.setHeader("Content-disposition", "attachment; filename=\"" + asdfBean.getName() + "\";");
        response.setContentType("application/pdf");
    // response.setContentType("application/download; application/pdf");
    } else if (asdfBean.getFileReference().endsWith(".csv")) {
        response.setHeader("Content-disposition", "attachment; filename=\"" + asdfBean.getName() + "\";");
        response.setContentType("text/csv");
    // response.setContentType("application/download; text/csv");
    } else if (asdfBean.getFileReference().endsWith(".xml")) {
        response.setHeader("Content-disposition", "attachment; filename=\"" + asdfBean.getName() + "\";");
        response.setContentType("text/xml");
    // response.setContentType("application/download; text/xml");
    } else if (asdfBean.getFileReference().endsWith(".html")) {
        response.setHeader("Content-disposition", "filename=\"" + asdfBean.getName() + "\";");
        response.setContentType("text/html; charset=utf-8");
    } else {
    // response.setContentType("text/plain");
    // to ensure backwards compatability to text files shown on server
    // not needed anymore? tbh 10/2010
    }
    finalTarget.setFileName("/WEB-INF/jsp/extract/generatedFileDataset.jsp");
    // }
    // finalTarget.setFileName(asdfBean.getWebPath());
    request.setAttribute("generate", asdfBean.getFileReference());
    response.setHeader("Pragma", "public");
    forwardPage(finalTarget);
}