/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package fr.ens.biologie.genomique.eoulsan.bio.io.hadoop;
import java.io.IOException;
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.fs.Seekable;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CodecPool;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.hadoop.io.compress.Decompressor;
import org.apache.hadoop.io.compress.SplitCompressionInputStream;
import org.apache.hadoop.io.compress.SplittableCompressionCodec;
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 org.apache.hadoop.mapreduce.lib.input.SplitLineReader;
/**
* Treats keys as offset in file and value as line.
*/
public class FastqLineRecordReader extends RecordReader<LongWritable, Text> {
public static final String MAX_LINE_LENGTH =
"mapreduce.input.linerecordreader.line.maxlength";
private long start;
private long pos;
private long end;
private SplitLineReader in;
private FSDataInputStream fileIn;
private Seekable filePosition;
private int maxLineLength;
private LongWritable key;
private Text value;
private boolean isCompressedInput;
private Decompressor decompressor;
private byte[] recordDelimiterBytes;
public FastqLineRecordReader() {
}
public FastqLineRecordReader(byte[] recordDelimiter) {
this.recordDelimiterBytes = recordDelimiter;
}
public void initialize(InputSplit genericSplit, TaskAttemptContext context)
throws IOException {
FileSplit split = (FileSplit) genericSplit;
Configuration job = context.getConfiguration();
this.maxLineLength = job.getInt(MAX_LINE_LENGTH, Integer.MAX_VALUE);
start = split.getStart();
end = start + split.getLength();
final Path file = split.getPath();
// open the file and seek to the start of the split
final FileSystem fs = file.getFileSystem(job);
fileIn = fs.open(file);
CompressionCodec codec = new CompressionCodecFactory(job).getCodec(file);
if (null != codec) {
isCompressedInput = true;
decompressor = CodecPool.getDecompressor(codec);
if (codec instanceof SplittableCompressionCodec) {
final SplitCompressionInputStream cIn =
((SplittableCompressionCodec) codec).createInputStream(fileIn,
decompressor, start, end,
SplittableCompressionCodec.READ_MODE.BYBLOCK);
in = new CompressedSplitFastqLineReader(cIn, job,
this.recordDelimiterBytes);
start = cIn.getAdjustedStart();
end = cIn.getAdjustedEnd();
filePosition = cIn;
} else {
in = new SplitLineReader(codec.createInputStream(fileIn, decompressor),
job, this.recordDelimiterBytes);
filePosition = fileIn;
}
} else {
fileIn.seek(start);
in = new SplitLineReader(fileIn, job, this.recordDelimiterBytes);
filePosition = fileIn;
}
// If this is not the first split, we always throw away first record
// because we always (except the last split) read one extra line in
// next() method.
if (start != 0) {
start += in.readLine(new Text(), 0, maxBytesToConsume(start));
}
this.pos = start;
}
private int maxBytesToConsume(long pos) {
return isCompressedInput
? Integer.MAX_VALUE
: (int) Math.max(Math.min(Integer.MAX_VALUE, end - pos), maxLineLength);
}
private long getFilePosition() throws IOException {
long retVal;
if (isCompressedInput && null != filePosition) {
retVal = filePosition.getPos();
} else {
retVal = pos;
}
return retVal;
}
private int skipUtfByteOrderMark() throws IOException {
// Strip BOM(Byte Order Mark)
// Text only support UTF-8, we only need to check UTF-8 BOM
// (0xEF,0xBB,0xBF) at the start of the text stream.
int newMaxLineLength =
(int) Math.min(3L + (long) maxLineLength, Integer.MAX_VALUE);
int newSize = in.readLine(value, newMaxLineLength, maxBytesToConsume(pos));
// Even we read 3 extra bytes for the first line,
// we won't alter existing behavior (no backwards incompat issue).
// Because the newSize is less than maxLineLength and
// the number of bytes copied to Text is always no more than newSize.
// If the return size from readLine is not less than maxLineLength,
// we will discard the current line and read the next line.
pos += newSize;
int textLength = value.getLength();
byte[] textBytes = value.getBytes();
if ((textLength >= 3)
&& (textBytes[0] == (byte) 0xEF) && (textBytes[1] == (byte) 0xBB)
&& (textBytes[2] == (byte) 0xBF)) {
// find UTF-8 BOM, strip it.
textLength -= 3;
newSize -= 3;
if (textLength > 0) {
// It may work to use the same buffer and not do the copyBytes
textBytes = value.copyBytes();
value.set(textBytes, 3, textLength);
} else {
value.clear();
}
}
return newSize;
}
@Override
public boolean nextKeyValue() throws IOException {
return nextKeyValue(false);
}
public boolean nextKeyValue(final boolean cont) throws IOException {
if (key == null) {
key = new LongWritable();
}
key.set(pos);
if (value == null) {
value = new Text();
}
int newSize = 0;
long filePosition;
// We always read one extra line, which lies outside the upper
// split limit i.e. (end - 1)
while ((filePosition = getFilePosition()) <= end
|| in.needAdditionalRecordAfterSplit() || cont) {
if (filePosition > end && in instanceof CompressedSplitFastqLineReader) {
((CompressedSplitFastqLineReader) in).setContinue(cont);
}
if (pos == 0) {
newSize = skipUtfByteOrderMark();
} else {
newSize = in.readLine(value, maxLineLength, maxBytesToConsume(pos));
pos += newSize;
}
if ((newSize == 0) || (newSize < maxLineLength)) {
break;
}
}
if (newSize == 0) {
key = null;
value = null;
return false;
} else {
return true;
}
}
@Override
public LongWritable getCurrentKey() {
return key;
}
@Override
public Text getCurrentValue() {
return value;
}
/**
* Get the progress within the split
*/
public float getProgress() throws IOException {
if (start == end) {
return 0.0f;
} else {
return Math.min(1.0f,
(getFilePosition() - start) / (float) (end - start));
}
}
public synchronized void close() throws IOException {
try {
if (in != null) {
in.close();
}
} finally {
if (decompressor != null) {
CodecPool.returnDecompressor(decompressor);
}
}
}
}