de.l3s.dlg.ncbikraken.ftp.NcbiFTPClient.java Source code

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Here is the source code for de.l3s.dlg.ncbikraken.ftp.NcbiFTPClient.java

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/*******************************************************************************
 * Copyright (c) 2013 Sascha Tnnies (toennies@l3s.de). All rights reserved.
 * This program and the accompanying materials are made available under the
 * terms of the GNU Public License v3.0 which accompanies this distribution, and
 * is available at http://www.gnu.org/licenses/gpl.html
 * 
 * Contributors: Sascha Tnnies (toennies@l3s.de) - initial API and
 * implementation
 ******************************************************************************/
package de.l3s.dlg.ncbikraken.ftp;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;

import org.apache.commons.io.IOUtils;
import org.apache.commons.net.ftp.FTPClient;
import org.apache.commons.net.ftp.FTPFile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import de.l3s.dlg.ncbikraken.Configuration;

/**
 * A static helper class for retrieving the open access archives from the NCBI
 * ftp server.
 * 
 * @author toennies
 * 
 */
public final class NcbiFTPClient {

    private static final int BUFFER = 32 * 1024;

    /**
     * The class logger
     */
    private static final Logger LOGGER = LoggerFactory.getLogger(NcbiFTPClient.class);

    /**
     * http://www.nlm.nih.gov/bsd/licensee/access/medline_pubmed.html
     */
    private static final String SERVER_NAME = "ftp.nlm.nih.gov";
    private static final String NCBI_SERVER_NAME = "ftp.ncbi.nlm.nih.gov/";

    private static final String BASELINE_PATH = "/nlmdata/.medleasebaseline";
    private static final String UPDATE_PATH = "/nlmdata/.medlease/";

    private static final String PMC_SERVER_NAME = "nlmpubs.nlm.nih.gov";
    private static final String PMC_SERVER_PATH = "/online/mesh/.xmlmesh";

    /**
     * Hidden constructor for this utility class.
     */
    private NcbiFTPClient() {
        super();
    }

    public static void getMedline(MedlineFileType type) {
        FileOutputStream out = null;
        FTPClient ftp = new FTPClient();
        try {
            // Connection String
            LOGGER.info("Connecting to FTP server " + SERVER_NAME);
            ftp.connect(SERVER_NAME);
            ftp.login("anonymous", "");
            ftp.cwd(BASELINE_PATH);
            ftp.cwd(type.getServerPath());

            try {
                ftp.pasv();
            } catch (IOException e) {
                LOGGER.error(
                        "Can not access the passive mode. Maybe a problem with your (Windows) firewall. Just try to run as administrator: \nnetsh advfirewall set global StatefulFTP disable");
                return;
            }

            for (FTPFile file : ftp.listFiles()) {
                if (file.isFile()) {
                    File meshF = new File(file.getName());
                    LOGGER.debug("Downloading file: " + SERVER_NAME + ":" + BASELINE_PATH + "/"
                            + type.getServerPath() + "/" + meshF.getName());
                    out = new FileOutputStream(Configuration.INSTANCE.getMedlineDir() + File.separator + meshF);
                    ftp.retrieveFile(meshF.getName(), out);
                    out.flush();
                    out.close();
                }
            }

        } catch (IOException ioe) {
            LOGGER.error(ioe.getMessage());

        } finally {
            IOUtils.closeQuietly(out);
            try {
                ftp.disconnect();
            } catch (IOException e) {
                LOGGER.error(e.getMessage());
            }
        }

    }

}