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

Example 16 with ArchivedDatasetFileBean

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

the class GenerateExtractFileService method createFile.

public int createFile(String name, String dir, String content, DatasetBean datasetBean, long time, ExportFormatBean efb, boolean saveToDB, UserAccountBean userBean) {
    ArchivedDatasetFileBean fbFinal = new ArchivedDatasetFileBean();
    // >> tbh 04/2010 #4915 replace all names' spaces with underscores
    name = name.replaceAll(" ", "_");
    fbFinal.setId(0);
    try {
        File complete = new File(dir);
        if (!complete.isDirectory()) {
            complete.mkdirs();
        }
        File newFile = new File(complete, name);
        newFile.setLastModified(System.currentTimeMillis());
        BufferedWriter w = new BufferedWriter(new FileWriter(newFile));
        w.write(content);
        w.close();
        logger.info("finished writing the text file...");
        // now, we write the file to the zip file
        FileInputStream is = new FileInputStream(newFile);
        ZipOutputStream z = new ZipOutputStream(new FileOutputStream(new File(complete, name + ".zip")));
        logger.info("created zip output stream...");
        // we write over the content no matter what
        // we then check to make sure there are no duplicates
        // TODO need to change the above -- save all content!
        // z.write(content);
        z.putNextEntry(new java.util.zip.ZipEntry(name));
        // int length = (int) newFile.length();
        int bytesRead;
        byte[] buff = new byte[512];
        // while (-1 != (bytesRead = bis.read(buff, 0, buff.length))) {
        while ((bytesRead = is.read(buff)) != -1) {
            z.write(buff, 0, bytesRead);
        }
        logger.info("writing buffer...");
        // }
        z.closeEntry();
        z.finish();
        // w2.close();
        if (is != null) {
            try {
                is.close();
            } catch (java.io.IOException ie) {
                ie.printStackTrace();
            }
        }
        logger.info("finished zipping up file...");
        // set up the zip to go into the database
        if (saveToDB) {
            ArchivedDatasetFileBean fb = new ArchivedDatasetFileBean();
            fb.setName(name + ".zip");
            // logger.info("ODM filename: " + name + ".zip");
            fb.setFileReference(dir + name + ".zip");
            // logger.info("ODM fileReference: " + dir + name + ".zip");
            // current location of the file on the system
            fb.setFileSize((int) newFile.length());
            // logger.info("ODM setFileSize: " + (int)newFile.length() );
            // set the above to compressed size?
            fb.setRunTime((int) time);
            // logger.info("ODM setRunTime: " + (int)time );
            // need to set this in milliseconds, get it passed from above
            // methods?
            fb.setDatasetId(datasetBean.getId());
            // logger.info("ODM setDatasetid: " + ds.getId() );
            fb.setExportFormatBean(efb);
            // logger.info("ODM setExportFormatBean: success" );
            fb.setExportFormatId(efb.getId());
            // logger.info("ODM setExportFormatId: " + efb.getId());
            fb.setOwner(userBean);
            // logger.info("ODM setOwner: " + sm.getUserBean());
            fb.setOwnerId(userBean.getId());
            // logger.info("ODM setOwnerId: " + sm.getUserBean().getId() );
            fb.setDateCreated(new Date(System.currentTimeMillis()));
            boolean write = true;
            ArchivedDatasetFileDAO asdfDAO = new ArchivedDatasetFileDAO(ds);
            // eliminating all checks so that we create multiple files, tbh 6-7
            if (write) {
                fbFinal = (ArchivedDatasetFileBean) asdfDAO.create(fb);
            } else {
                logger.info("duplicate found: " + fb.getName());
            }
        }
    // created in database!
    } catch (Exception e) {
        logger.error("-- exception thrown at createFile: " + e.getMessage());
        e.printStackTrace();
    }
    return fbFinal.getId();
}

Example 17 with ArchivedDatasetFileBean

use of org.akaza.openclinica.bean.extract.ArchivedDatasetFileBean 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 18 with ArchivedDatasetFileBean

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

the class ArchivedDatasetFileRow method compareColumn.

@Override
protected int compareColumn(Object row, int sortingColumn) {
    if (!row.getClass().equals(ArchivedDatasetFileRow.class)) {
        return 0;
    }
    ArchivedDatasetFileBean thisAccount = (ArchivedDatasetFileBean) bean;
    ArchivedDatasetFileBean argAccount = (ArchivedDatasetFileBean) ((ArchivedDatasetFileRow) row).bean;
    int answer = 0;
    switch(sortingColumn) {
        case COL_FILENAME:
            answer = thisAccount.getName().toLowerCase().compareTo(argAccount.getName().toLowerCase());
            break;
        case COL_FILECREATEDDATE:
            answer = thisAccount.getDateCreated().compareTo(argAccount.getDateCreated());
            break;
    }
    return answer;
}

Example 19 with ArchivedDatasetFileBean

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

the class ExportDatasetServlet method generateFileBean.

public ArchivedDatasetFileBean generateFileBean(File datasetFile, String relativePath, int formatId) {
    ArchivedDatasetFileBean adfb = new ArchivedDatasetFileBean();
    adfb.setName(datasetFile.getName());
    if (datasetFile.canRead()) {
        logger.info("File can be read");
    } else {
        logger.info("File CANNOT be read");
    }
    logger.info("Found file length: " + datasetFile.length());
    logger.info("Last Modified: " + datasetFile.lastModified());
    adfb.setFileSize(new Long(datasetFile.length()).intValue());
    adfb.setExportFormatId(formatId);
    adfb.setWebPath(relativePath);
    adfb.setDateCreated(new java.util.Date(datasetFile.lastModified()));
    return adfb;
}

Example 20 with ArchivedDatasetFileBean

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

the class ExportDatasetServlet method loadList.

public void loadList(DatasetBean db, ArchivedDatasetFileDAO asdfdao, int datasetId, FormProcessor fp, ExtractBean eb) {
    logger.info("action is blank");
    request.setAttribute("dataset", db);
    logger.info("just set dataset to request");
    request.setAttribute("extractProperties", CoreResources.getExtractProperties());
    // find out if there are any files here:
    File currentDir = new File(DATASET_DIR + db.getId() + File.separator);
    //JN: Commenting out this, as its creating directories without any reason. TODO: Check why was this added.
    // if (!currentDir.isDirectory()) {
    //      currentDir.mkdirs();
    //  }
    ArrayList fileListRaw = new ArrayList();
    fileListRaw = asdfdao.findByDatasetId(datasetId);
    fileList = new ArrayList();
    Iterator fileIterator = fileListRaw.iterator();
    while (fileIterator.hasNext()) {
        ArchivedDatasetFileBean asdfBean = (ArchivedDatasetFileBean) fileIterator.next();
        // set the correct webPath in each bean here
        // changed here, tbh, 4-18
        // asdfBean.setWebPath(WEB_DIR+db.getId()+"/"+asdfBean.getName());
        // asdfBean.setWebPath(DATASET_DIR+db.getId()+File.separator+
        // asdfBean.getName());
        asdfBean.setWebPath(asdfBean.getFileReference());
        if (new File(asdfBean.getFileReference()).isFile()) {
            // logger.warn(asdfBean.getFileReference()+" is a
            // file!");
            fileList.add(asdfBean);
        } else {
            logger.warn(asdfBean.getFileReference() + " is NOT a file!");
        }
    }
    logger.warn("");
    logger.warn("file list length: " + fileList.size());
    request.setAttribute("filelist", fileList);
    ArrayList filterRows = ArchivedDatasetFileRow.generateRowsFromBeans(fileList);
    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"), resword.getString("action") };
    table.setColumns(new ArrayList(Arrays.asList(columns)));
    table.hideColumnLink(0);
    table.hideColumnLink(1);
    table.hideColumnLink(2);
    table.hideColumnLink(3);
    table.hideColumnLink(4);
    table.hideColumnLink(5);
    table.setQuery("ExportDataset?datasetId=" + db.getId(), new HashMap());
    // trying to continue...
    session.setAttribute("newDataset", db);
    table.setRows(filterRows);
    table.computeDisplay();
    request.setAttribute("table", table);
    // for the side info bar
    TabReportBean answer = new TabReportBean();
    resetPanel();
    panel.setStudyInfoShown(false);
    setToPanel(resword.getString("study_name"), eb.getStudy().getName());
    setToPanel(resword.getString("protocol_ID"), eb.getStudy().getIdentifier());
    setToPanel(resword.getString("dataset_name"), db.getName());
    setToPanel(resword.getString("created_date"), local_df.format(db.getCreatedDate()));
    setToPanel(resword.getString("dataset_owner"), db.getOwner().getName());
    try {
        // do we not set this or is it null b/c we come to the page with no session?
        setToPanel(resword.getString("date_last_run"), local_df.format(db.getDateLastRun()));
    } catch (NullPointerException npe) {
        logger.error("exception: " + npe.getMessage());
    }
    logger.warn("just set file list to request, sending to page");
}