edu.dfci.cccb.mev.dataset.domain.gzip.GzipTsvInput.java Source code

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Here is the source code for edu.dfci.cccb.mev.dataset.domain.gzip.GzipTsvInput.java

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/**
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package edu.dfci.cccb.mev.dataset.domain.gzip;

import static org.apache.commons.io.FilenameUtils.getBaseName;

import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.net.URLConnection;
import java.util.zip.GZIPInputStream;

import lombok.extern.log4j.Log4j;
import edu.dfci.cccb.mev.dataset.domain.prototype.AbstractRawInput;
import edu.dfci.cccb.mev.io.implementation.TemporaryFile;

/**
 * @author levk
 * 
 */
@Log4j
public class GzipTsvInput extends AbstractRawInput {

    private URL url;
    final int BUFFER = 2048;

    public GzipTsvInput(URL url) {
        if (url == null)
            throw new NullPointerException("URL cannot be null");
        this.url = url;
    }

    /* (non-Javadoc)
     * @see edu.dfci.cccb.mev.dataset.domain.contract.RawInput#contentType() */
    @Override
    public String contentType() {
        return TAB_SEPARATED_VALUES;
    }

    /* (non-Javadoc)
     * @see edu.dfci.cccb.mev.dataset.domain.contract.RawInput#name() */
    @Override
    public String name() {
        return super.name() != null ? super.name() : getBaseName(url.toString());
    }

    /* (non-Javadoc)
     * @see edu.dfci.cccb.mev.dataset.domain.contract.RawInput#input() */
    @Override
    public InputStream input() throws IOException {
        if (log.isDebugEnabled())
            log.debug(url);

        GZIPInputStream zis = null;
        BufferedOutputStream dest = null;
        BufferedInputStream bis = null;
        File unzipped = new TemporaryFile();
        try {
            URLConnection urlc = url.openConnection();
            zis = new GZIPInputStream(urlc.getInputStream());

            int count;
            byte data[] = new byte[BUFFER];
            // write the files to the disk

            FileOutputStream fos = new FileOutputStream(unzipped);
            if (log.isDebugEnabled())
                log.debug("Unzipping SOFT file to " + unzipped.getAbsolutePath());

            dest = new BufferedOutputStream(fos, BUFFER);
            while ((count = zis.read(data, 0, BUFFER)) != -1) {
                dest.write(data, 0, count);
            }
            dest.flush();
            dest.close();
            return new FileInputStream(unzipped);

        } finally {
            if (bis != null) {
                try {
                    bis.close();
                } catch (IOException ioe) {
                }
            }
            if (dest != null) {
                try {
                    dest.close();
                } catch (IOException ioe) {
                }
            }
            if (zis != null) {
                try {
                    zis.close();
                } catch (IOException ioe) {
                }
            }
        }

    }

    /* (non-Javadoc)
     * @see edu.dfci.cccb.mev.dataset.domain.contract.RawInput#size() */
    @Override
    public long size() {
        return -1;
    }
}