edu.monash.merc.system.remote.HttpBarcodeFileGetter.java Source code

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Here is the source code for edu.monash.merc.system.remote.HttpBarcodeFileGetter.java

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/*
 * Copyright (c) 2011-2013, Monash e-Research Centre
 * (Monash University, Australia)
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the Monash University nor the names of its
 *      contributors may be used to endorse or promote products derived from
 *      this software without specific prior written permission.
 *
 * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
 * without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 * See the GNU Affero General Public License for more details.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * You should have received a copy of the GNU Affero General Public License along with
 * this program. If not, see <http://www.gnu.org/licenses/>.
 */

package edu.monash.merc.system.remote;

import edu.monash.merc.exception.DMRemoteException;
import org.apache.http.*;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.DefaultHttpClient;

import java.io.File;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.GregorianCalendar;

/**
 * HttpHpaFileGetter class which downloads the file from the HPA site
 *
 * @author Simon Yu
 *         <p/>
 *         Email: xiaoming.yu@monash.edu
 * @version 1.0
 * @since 1.0
 *        <p/>
 *        Date: 9/10/12 3:49 PM
 */
public class HttpBarcodeFileGetter {

    private static SimpleDateFormat webFileDateFormat = new SimpleDateFormat("EEE, dd MMM yyyy HH:mm:ss 'GMT'");
    private static SimpleDateFormat simpleDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");

    private static int BUFFER_SIZE = 10 * 1024;

    /**
     * download the barcode file
     *
     * @param remoteFile a remote barcode file
     * @param localFile  a local barcode file to be saved
     * @return a timestamp string for this barcode file
     */
    public String downloadBarcodeFile(String remoteFile, String localFile) {

        Date lastModifiedDate = GregorianCalendar.getInstance().getTime();
        //use httpclient to get the remote file
        HttpClient httpClient = new DefaultHttpClient();
        HttpGet httpGet = new HttpGet(remoteFile);
        InputStream in = null;
        FileOutputStream fos = null;
        try {
            HttpResponse response = httpClient.execute(httpGet);
            StatusLine status = response.getStatusLine();
            //get the last modified date for this file
            Header[] headers = response.getHeaders("Last-Modified");
            for (Header header : headers) {
                String name = header.getName();
                String value = header.getValue();
                Date date = webFileDateFormat.parse(value);
                if (date != null) {
                    lastModifiedDate = date;
                }
            }

            if (status.getStatusCode() == HttpStatus.SC_OK) {
                HttpEntity entity = response.getEntity();
                if (entity != null) {
                    in = entity.getContent();

                    File barcodeFile = new File(localFile);
                    fos = new FileOutputStream(barcodeFile);
                    byte[] buffer = new byte[BUFFER_SIZE];
                    int len;
                    while ((len = in.read(buffer)) > 0) {
                        fos.write(buffer, 0, len);
                    }
                }
            } else {
                throw new DMRemoteException("can't get the file from " + remoteFile);
            }
            String lastModified = simpleDateFormat.format(lastModifiedDate);
            // System.out.println("====== last modifed : " + lastModified);
            return lastModified;
        } catch (Exception ex) {
            throw new DMRemoteException(ex);
        } finally {
            try {
                if (fos != null) {
                    fos.close();
                }
                if (in != null) {
                    in.close();
                }
                httpClient.getConnectionManager().shutdown();
            } catch (Exception e) {
                //ignore whatever caught
            }
        }

    }

    public static void main(String[] args) {
        String fileLocation = "http://barcode.luhs.org/transcriptomes/abc.ntc.GPL96.csv";
        HttpBarcodeFileGetter fileGetter = new HttpBarcodeFileGetter();
        long startTime = System.currentTimeMillis();
        fileGetter.downloadBarcodeFile(fileLocation, "abc.ntc.GPL96.csv");
        long endTime = System.currentTimeMillis();
        System.out.println("===== total processing time : " + (endTime - startTime) / 1000 + " seconds.");
    }
}