Java tutorial
/* * Copyright (c) 2010, The Regents of the University of California, through Lawrence Berkeley * National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). * All rights reserved. * * Redistribution and use in source and binary forms, with or without modification, are permitted provided * that the following conditions are met: * * (1) Redistributions of source code must retain the above copyright notice, this list of conditions and the * following disclaimer. * * (2) 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. * * (3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. * of Energy, nor the names of its contributors may be used to endorse or promote products derived from * this software without specific prior written permission. * * 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 * OWNER 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 are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the * features, functionality or performance of the source code ("Enhancements") to anyone; however, * if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley * National Laboratory, without imposing a separate written license agreement for such Enhancements, * then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, * use, modify, prepare derivative works, incorporate into other computer software, distribute, and * sublicense such enhancements or derivative works thereof, in binary and source code form. */ package gov.jgi.meta.hadoop.input; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FSDataInputStream; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.apache.hadoop.mapreduce.InputSplit; import org.apache.hadoop.mapreduce.RecordReader; import org.apache.hadoop.mapreduce.TaskAttemptContext; import org.apache.hadoop.mapreduce.lib.input.FileSplit; import java.io.IOException; import java.util.HashMap; import java.util.Map; /** * Treats keys as offset in file and value as line. */ public class FastqBlockRecordReader extends RecordReader<Text, Map<String, String>> { private static final Log LOG = LogFactory.getLog(FastqBlockRecordReader.class); private CompressionCodecFactory compressionCodecs = null; private long start; private long pos; private long end; private FastqBlockLineReader in; private int maxLineLength; private Text key = null; private Map<String, String> value = null; public void initialize(InputSplit genericSplit, TaskAttemptContext context) throws IOException { FileSplit split = (FileSplit) genericSplit; Configuration job = context.getConfiguration(); this.maxLineLength = job.getInt("mapred.linerecordreader.maxlength", Integer.MAX_VALUE); start = split.getStart(); end = start + split.getLength(); final Path file = split.getPath(); compressionCodecs = new CompressionCodecFactory(job); final CompressionCodec codec = compressionCodecs.getCodec(file); // open the file and seek to the start of the split FileSystem fs = file.getFileSystem(job); FSDataInputStream fileIn = fs.open(split.getPath()); boolean skipFirstLine = false; if (codec != null) { in = new FastqBlockLineReader(codec.createInputStream(fileIn), job); end = Long.MAX_VALUE; } else { if (start != 0) { skipFirstLine = false; // don't do this! //--start; or this fileIn.seek(start); } in = new FastqBlockLineReader(fileIn, job); } this.pos = start; } public boolean nextKeyValue() throws IOException { if (key == null) { key = new Text(); } if (value == null) { value = new HashMap<String, String>(); } int newSize = 0; while (pos < end) { newSize = in.readLine(key, value, maxLineLength, Math.min((int) Math.min(Integer.MAX_VALUE, end - pos), maxLineLength)); LOG.info("inside fastqBlockRecordReader: split value is size " + value.size()); if (newSize == 0) { break; } pos += newSize; if (newSize < maxLineLength) { break; } // line too long. try again LOG.info("Skipped line of size " + newSize + " at pos " + (pos - newSize)); } if (newSize == 0) { key = null; value = null; return false; } else { return true; } } @Override public Text getCurrentKey() { return key; } @Override public Map<String, String> getCurrentValue() { return value; } /** * Get the progress within the split */ public float getProgress() { if (start == end) { return 0.0f; } else { return Math.min(1.0f, (pos - start) / (float) (end - start)); } } public synchronized void close() throws IOException { if (in != null) { in.close(); } } }