/*
 * 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 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;
  }

  @Override
  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);
    final FSDataInputStream 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 */
  @Override
  public float getProgress() throws IOException {
    if (start == end) {
      return 0.0f;
    } else {
      return Math.min(1.0f, (getFilePosition() - start) / (float) (end - start));
    }
  }

  @Override
  public synchronized void close() throws IOException {
    try {
      if (in != null) {
        in.close();
      }
    } finally {
      if (decompressor != null) {
        CodecPool.returnDecompressor(decompressor);
      }
    }
  }
}
