fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol.java Source code

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Here is the source code for fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol.java

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/*
 *                  Eoulsan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public License version 2.1 or
 * later and CeCILL-C. This should be distributed with the code.
 * If you do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/lgpl-2.1.txt
 *      http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'cole normale suprieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Eoulsan project and its aims,
 * or to join the Eoulsan Google group, visit the home page
 * at:
 *
 *      http://outils.genomique.biologie.ens.fr/eoulsan
 *
 */

package fr.ens.biologie.genomique.eoulsan.data.protocols;

import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;

import fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata;
import fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry;
import fr.ens.biologie.genomique.eoulsan.io.CompressionType;
import fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils;

/**
 * This class define an abstract class for DataProtocols based on the Hadoop
 * framework Path object.
 * @since 1.0
 * @author Laurent Jourdren
 */
public abstract class PathDataProtocol extends AbstractDataProtocol {

    protected Configuration conf;

    /**
     * Get Convert a DataFile object to a Path object.
     * @param dataFile DataFile to convert
     * @return a Path object
     */
    public Path getPath(final DataFile dataFile) {

        if (dataFile == null) {
            throw new NullPointerException("The source is null.");
        }

        return new Path(dataFile.getSource());
    }

    @Override
    public InputStream getData(final DataFile src) throws IOException {

        return PathUtils.createInputStream(getPath(src), this.conf);
    }

    @Override
    public OutputStream putData(final DataFile src) throws IOException {

        return PathUtils.createOutputStream(getPath(src), this.conf);
    }

    @Override
    public DataFileMetadata getMetadata(final DataFile src) throws IOException {

        if (!exists(src, true)) {
            throw new FileNotFoundException("File not found: " + src);
        }

        final Path path = getPath(src);
        final FileStatus status = path.getFileSystem(this.conf).getFileStatus(path);

        final SimpleDataFileMetadata result = new SimpleDataFileMetadata();
        result.setContentLength(status.getLen());
        result.setLastModified(status.getModificationTime());
        result.setDataFormat(DataFormatRegistry.getInstance().getDataFormatFromFilename(src.getName()));

        final CompressionType ct = CompressionType.getCompressionTypeByFilename(src.getSource());

        if (ct != null) {
            result.setContentEncoding(ct.getContentEncoding());
        }

        if (status.isDirectory()) {
            result.setDirectory(true);
        }

        if (status.isSymlink()) {
            result.setSymbolicLink(new DataFile(status.getSymlink().toUri()));
        }

        return result;
    }

    @Override
    public boolean exists(final DataFile src, final boolean followLink) {

        final Path path = getPath(src);

        try {

            final FileSystem fs = path.getFileSystem(conf);

            final FileStatus status = fs.getFileStatus(path);

            if (status == null) {
                return false;
            }

            if (status.isSymlink()) {

                return fs.getFileStatus(fs.getLinkTarget(path)) != null;
            }

            return true;
        } catch (IOException e) {
            return false;
        }
    }

    @Override
    public boolean canRead() {

        return true;
    }

    @Override
    public boolean canWrite() {

        return true;
    }

    //
    // Constructor
    //

    /**
     * Constructor.
     */
    public PathDataProtocol() {

        final AbstractEoulsanRuntime runtime = EoulsanRuntime.getRuntime();

        if (!runtime.getMode().isHadoopProtocolMode() || !(runtime instanceof HadoopEoulsanRuntime)) {
            throw new IllegalStateException("Can only create PathDataProtocol in hadoop mode.");
        }

        final HadoopEoulsanRuntime hadoopRuntime = (HadoopEoulsanRuntime) runtime;

        this.conf = hadoopRuntime.getConfiguration();

        if (this.conf == null) {
            throw new NullPointerException("The Hadoop configuration object is null");
        }
    }

}