Examples with GeoUtil ubic.gemma.core.loader.expression.geo.util.GeoUtil used on opensource projects

Example 1 with GeoUtil

use of ubic.gemma.core.loader.expression.geo.util.GeoUtil in project Gemma by PavlidisLab.

the class RawDataFetcher method fetch.

/**
 * @param identifier The url for the supplementary file.
 * @return local files
 */
@Override
public Collection<LocalFile> fetch(String identifier) {
    try {
        if (this.ftpClient == null || !this.ftpClient.isConnected())
            this.ftpClient = (new GeoUtil()).connect(FTP.BINARY_FILE_TYPE);
        assert this.ftpClient != null;
        File newDir = this.mkdir(identifier);
        newDir = new File(newDir, "rawDataFiles");
        if (!newDir.canRead() && !newDir.mkdir())
            throw new IOException("Could not create the raw data subdirectory");
        final String outputFileName = this.formLocalFilePath(identifier, newDir);
        final String seekFile = this.formRemoteFilePath(identifier);
        try {
            NetUtils.checkForFile(this.ftpClient, seekFile);
        } catch (FileNotFoundException e) {
            // that's okay, just return.
            AbstractFetcher.log.info("There is apparently no raw data archive for " + identifier + "(sought: " + seekFile + ")");
            EntityUtils.deleteFile(newDir);
            // important to do this!
            this.ftpClient.disconnect();
            return null;
        }
        if (this.ftpClient == null || !this.ftpClient.isConnected()) {
            throw new IOException("Lost FTP connection");
        }
        long expectedSize = this.getExpectedSize(seekFile);
        FutureTask<Boolean> future = this.defineTask(outputFileName, seekFile);
        Collection<LocalFile> result = this.doTask(future, expectedSize, seekFile, outputFileName);
        if (result == null || result.isEmpty()) {
            throw new IOException("Files were not obtained, or download was cancelled.");
        }
        return result;
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}