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From jo...@apache.org
Subject svn commit: r720162 - in /hadoop/core/trunk: CHANGES.txt src/core/org/apache/hadoop/io/compress/LzopCodec.java src/mapred/org/apache/hadoop/mapred/LzoTextInputFormat.java src/test/org/apache/hadoop/mapred/TestLzoTextInputFormat.java
Date Mon, 24 Nov 2008 10:51:29 GMT
Author: johan
Date: Mon Nov 24 02:51:28 2008
New Revision: 720162

URL: http://svn.apache.org/viewvc?rev=720162&view=rev
Log:
HADOOP-4640. Adds an input format that can split lzo compressed text files. (johan)

Added:
    hadoop/core/trunk/src/mapred/org/apache/hadoop/mapred/LzoTextInputFormat.java
    hadoop/core/trunk/src/test/org/apache/hadoop/mapred/TestLzoTextInputFormat.java
Modified:
    hadoop/core/trunk/CHANGES.txt
    hadoop/core/trunk/src/core/org/apache/hadoop/io/compress/LzopCodec.java

Modified: hadoop/core/trunk/CHANGES.txt
URL: http://svn.apache.org/viewvc/hadoop/core/trunk/CHANGES.txt?rev=720162&r1=720161&r2=720162&view=diff
==============================================================================
--- hadoop/core/trunk/CHANGES.txt (original)
+++ hadoop/core/trunk/CHANGES.txt Mon Nov 24 02:51:28 2008
@@ -123,6 +123,9 @@
     it down by monitoring for cumulative memory usage across tasks.
     (Vinod Kumar Vavilapalli via yhemanth)
 
+    HADOOP-4640. Adds an input format that can split lzo compressed
+    text files. (johan)
+
   OPTIMIZATIONS
 
     HADOOP-3293. Fixes FileInputFormat to do provide locations for splits

Modified: hadoop/core/trunk/src/core/org/apache/hadoop/io/compress/LzopCodec.java
URL: http://svn.apache.org/viewvc/hadoop/core/trunk/src/core/org/apache/hadoop/io/compress/LzopCodec.java?rev=720162&r1=720161&r2=720162&view=diff
==============================================================================
--- hadoop/core/trunk/src/core/org/apache/hadoop/io/compress/LzopCodec.java (original)
+++ hadoop/core/trunk/src/core/org/apache/hadoop/io/compress/LzopCodec.java Mon Nov 24 02:51:28
2008
@@ -408,18 +408,21 @@
     }
 
     public void close() throws IOException {
+      byte[] b = new byte[4096];
+      while (!decompressor.finished()) {
+        decompressor.decompress(b, 0, b.length);
+      }
       super.close();
       verifyChecksums();
     }
   }
 
-  protected static class LzopDecompressor extends LzoDecompressor {
+  public static class LzopDecompressor extends LzoDecompressor {
 
     private EnumMap<DChecksum,Checksum> chkDMap =
       new EnumMap<DChecksum,Checksum>(DChecksum.class);
     private EnumMap<CChecksum,Checksum> chkCMap =
       new EnumMap<CChecksum,Checksum>(CChecksum.class);
-    private final int bufferSize;
 
     /**
      * Create an LzoDecompressor with LZO1X strategy (the only lzo algorithm
@@ -427,10 +430,18 @@
      */
     public LzopDecompressor(int bufferSize) {
       super(LzoDecompressor.CompressionStrategy.LZO1X_SAFE, bufferSize);
-      this.bufferSize = bufferSize;
     }
 
     /**
+     * Get the number of checksum implementations
+     * the current lzo file uses.
+     * @return Number of checksum implementations in use.
+     */
+    public int getChecksumsCount() {
+      return this.chkCMap.size() + this.chkDMap.size();
+    }
+    
+    /**
      * Given a set of decompressed and compressed checksums, 
      */
     public void initHeaderFlags(EnumSet<DChecksum> dflags,

Added: hadoop/core/trunk/src/mapred/org/apache/hadoop/mapred/LzoTextInputFormat.java
URL: http://svn.apache.org/viewvc/hadoop/core/trunk/src/mapred/org/apache/hadoop/mapred/LzoTextInputFormat.java?rev=720162&view=auto
==============================================================================
--- hadoop/core/trunk/src/mapred/org/apache/hadoop/mapred/LzoTextInputFormat.java (added)
+++ hadoop/core/trunk/src/mapred/org/apache/hadoop/mapred/LzoTextInputFormat.java Mon Nov
24 02:51:28 2008
@@ -0,0 +1,385 @@
+/**
+ * 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 org.apache.hadoop.mapred;
+
+import java.io.EOFException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+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.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.fs.PathFilter;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.CompressionCodec;
+import org.apache.hadoop.io.compress.CompressionCodecFactory;
+import org.apache.hadoop.io.compress.LzopCodec;
+import org.apache.hadoop.io.compress.LzopCodec.LzopDecompressor;
+import org.apache.hadoop.util.LineReader;
+
+/**
+ * An {@link InputFormat} for lzop compressed text files. Files are broken into
+ * lines. Either linefeed or carriage-return are used to signal end of line.
+ * Keys are the position in the file, and values are the line of text.
+ */
+public class LzoTextInputFormat extends FileInputFormat<LongWritable, Text>
+    implements JobConfigurable {
+
+  private static final Log LOG
+    = LogFactory.getLog(LzoTextInputFormat.class.getName());
+  
+  public static final String LZO_INDEX_SUFFIX = ".index";
+
+  public void configure(JobConf conf) {
+    FileInputFormat.setInputPathFilter(conf, LzopFilter.class);
+  }
+
+  /**
+   * We don't want to process the index files.
+   */
+  static class LzopFilter implements PathFilter {
+    public boolean accept(Path path) {
+      if (path.toString().endsWith(LZO_INDEX_SUFFIX)) {
+        return false;
+      }
+      return true;
+    }
+  }
+
+  protected boolean isSplitable(FileSystem fs, Path file) {
+    Path indexFile = new Path(file.toString()
+        + LzoTextInputFormat.LZO_INDEX_SUFFIX);
+
+    try {
+      // can't split without the index
+      return fs.exists(indexFile);
+    } catch (IOException e) {
+      LOG.warn("Could not check if index file exists", e);
+      return false;
+    }
+  }
+
+  public RecordReader<LongWritable, Text> getRecordReader(
+      InputSplit genericSplit, JobConf job, Reporter reporter)
+    throws IOException {
+
+    reporter.setStatus(genericSplit.toString());
+    return new LzoLineRecordReader(job, (FileSplit) genericSplit);
+  }
+
+  @Override
+  public InputSplit[] getSplits(JobConf job, int numSplits) throws IOException {
+    FileSplit[] splits = (FileSplit[]) super.getSplits(job, numSplits);
+    // find new start/ends of the filesplit that aligns
+    // with the lzo blocks
+
+    List<FileSplit> result = new ArrayList<FileSplit>();
+    FileSystem fs = FileSystem.get(job);
+
+    Map<Path, LzoIndex> indexes = new HashMap<Path, LzoIndex>();
+    for (int i = 0; i < splits.length; i++) {
+      FileSplit fileSplit = splits[i];
+      // load the index
+      Path file = fileSplit.getPath();
+      if (!indexes.containsKey(file)) {
+        LzoIndex index = readIndex(file, fs);
+        if (index.isEmpty()) {
+          // keep it as is since we didn't find an index
+          result.add(fileSplit);
+          continue;
+        }
+
+        indexes.put(file, index);
+      }
+
+      LzoIndex index = indexes.get(file);
+      long start = fileSplit.getStart();
+      long end = start + fileSplit.getLength();
+
+      if (start != 0) {
+        // find the next block position from
+        // the start of the split
+        long newStart = index.findNextPosition(start);
+        if (newStart == -1 || newStart >= end) {
+          // just skip this since it will be handled by another split
+          continue;
+        }
+        start = newStart;
+      }
+
+      long newEnd = index.findNextPosition(end);
+      if (newEnd != -1) {
+        end = newEnd;
+      }
+
+      result.add(new FileSplit(file, start, end - start, fileSplit
+          .getLocations()));
+    }
+
+    return result.toArray(new FileSplit[] {});
+  }
+
+  /**
+   * Read the index of the lzo file.
+   * 
+   * @param split Read the index of this file.
+   * @param fs The index file is on this file system.
+   * @throws IOException
+   */
+  private LzoIndex readIndex(Path file, FileSystem fs) throws IOException {
+    FSDataInputStream indexIn = null;
+    try {
+      Path indexFile = new Path(file.toString() + LZO_INDEX_SUFFIX);
+      if (!fs.exists(indexFile)) {
+        // return empty index, fall back to the unsplittable mode
+        return new LzoIndex();
+      }
+      
+      long indexLen = fs.getFileStatus(indexFile).getLen();
+      int blocks = (int) (indexLen / 8);
+      LzoIndex index = new LzoIndex(blocks);
+      indexIn = fs.open(indexFile);
+      for (int i = 0; i < blocks; i++) {
+        index.set(i, indexIn.readLong());
+      }
+      return index;
+    } finally {
+      if (indexIn != null) {
+        indexIn.close();
+      }
+    }
+  }
+
+  /**
+   * Index an lzo file to allow the input format to split them into separate map
+   * jobs.
+   * 
+   * @param fs File system that contains the file.
+   * @param lzoFile the lzo file to index.
+   * @throws IOException
+   */
+  public static void createIndex(FileSystem fs, Path lzoFile) 
+    throws IOException {
+    
+    Configuration conf = fs.getConf();
+    LzopCodec codec = new LzopCodec();
+    codec.setConf(conf);
+
+    FSDataInputStream is = null;
+    FSDataOutputStream os = null;
+    try {
+      is = fs.open(lzoFile);
+      os = fs.create(new Path(lzoFile.toString()
+          + LzoTextInputFormat.LZO_INDEX_SUFFIX));
+      LzopDecompressor decompressor = (LzopDecompressor) codec
+          .createDecompressor();
+      // for reading the header
+      codec.createInputStream(is, decompressor);
+
+      int numChecksums = decompressor.getChecksumsCount();
+
+      while (true) {
+        //read and ignore, we just want to get to the next int
+        int uncompressedBlockSize = is.readInt();
+        if (uncompressedBlockSize == 0) {
+          break;
+        } else if (uncompressedBlockSize < 0) {
+          throw new EOFException();
+        }
+        
+        int compressedBlockSize = is.readInt();
+        if (compressedBlockSize <= 0) {
+          throw new IOException("Could not read compressed block size");
+        }
+
+        long pos = is.getPos();
+        // write the pos of the block start
+        os.writeLong(pos - 8);
+        // seek to the start of the next block, skip any checksums
+        is.seek(pos + compressedBlockSize + (4 * numChecksums));
+      }
+    } finally {
+      if (is != null) {
+        is.close();
+      }
+
+      if (os != null) {
+        os.close();
+      }
+    }
+  }
+
+  /**
+   * Represents the lzo index.
+   */
+  static class LzoIndex {
+    
+    private long[] blockPositions;
+
+    LzoIndex() {
+    }   
+    
+    LzoIndex(int blocks) {
+      blockPositions = new long[blocks];
+    }
+    
+    /**
+     * Set the position for the block.
+     * @param blockNumber Block to set pos for.
+     * @param pos Position.
+     */
+    public void set(int blockNumber, long pos) {
+      blockPositions[blockNumber] = pos;
+    }
+    
+    /**
+     * Find the next lzo block start from the given position.
+     * @param pos The position to start looking from.
+     * @return Either the start position of the block or -1 if 
+     * it couldn't be found.
+     */
+    public long findNextPosition(long pos) {
+      int block = Arrays.binarySearch(blockPositions, pos);
+
+      if(block >= 0) {
+        //direct hit on a block start position
+        return blockPositions[block];
+      } else {
+        block = Math.abs(block) - 1;
+        if(block > blockPositions.length - 1) {
+          return -1;
+        }
+        return blockPositions[block];
+      }
+    }
+
+    public boolean isEmpty() {
+      return blockPositions == null || blockPositions.length == 0;
+    }    
+    
+  }
+  
+  /**
+   * Reads line from an lzo compressed text file. Treats keys as offset in file
+   * and value as line.
+   */
+  static class LzoLineRecordReader implements RecordReader<LongWritable, Text> {
+
+    private CompressionCodecFactory compressionCodecs = null;
+    private long start;
+    private long pos;
+    private long end;
+    private LineReader in;
+    private FSDataInputStream fileIn;
+
+    public LzoLineRecordReader(Configuration job, FileSplit split)
+      throws IOException {
+
+      start = split.getStart();
+      end = start + split.getLength();
+      final Path file = split.getPath();
+
+      FileSystem fs = file.getFileSystem(job);
+
+      compressionCodecs = new CompressionCodecFactory(job);
+      final CompressionCodec codec = compressionCodecs.getCodec(file);
+      if (codec == null) {
+        throw new IOException("No lzo codec found, cannot run");
+      }
+
+      // open the file and seek to the start of the split
+      fileIn = fs.open(split.getPath());
+
+      // creates input stream and also reads the file header
+      in = new LineReader(codec.createInputStream(fileIn), job);
+
+      if (start != 0) {
+        fileIn.seek(start);
+
+        // read and ignore the first line
+        in.readLine(new Text());
+        start = fileIn.getPos();
+      }
+
+      this.pos = start;
+    }
+
+    public LongWritable createKey() {
+      return new LongWritable();
+    }
+
+    public Text createValue() {
+      return new Text();
+    }
+
+    /** Read a line. */
+    public synchronized boolean next(LongWritable key, Text value)
+      throws IOException {
+
+      //since the lzop codec reads everything in lzo blocks
+      //we can't stop if the pos == end
+      //instead we wait for the next block to be read in when
+      //pos will be > end
+      while (pos <= end) {
+        key.set(pos);
+
+        int newSize = in.readLine(value);
+        if (newSize == 0) {
+          return false;
+        }
+        pos = fileIn.getPos();
+
+        return true;
+      }
+
+      return false;
+    }
+
+    /**
+     * 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 long getPos() throws IOException {
+      return pos;
+    }
+
+    public synchronized void close() throws IOException {
+      if (in != null) {
+        in.close();
+      }
+    }
+  }
+
+}

Added: hadoop/core/trunk/src/test/org/apache/hadoop/mapred/TestLzoTextInputFormat.java
URL: http://svn.apache.org/viewvc/hadoop/core/trunk/src/test/org/apache/hadoop/mapred/TestLzoTextInputFormat.java?rev=720162&view=auto
==============================================================================
--- hadoop/core/trunk/src/test/org/apache/hadoop/mapred/TestLzoTextInputFormat.java (added)
+++ hadoop/core/trunk/src/test/org/apache/hadoop/mapred/TestLzoTextInputFormat.java Mon Nov
24 02:51:28 2008
@@ -0,0 +1,222 @@
+/**
+ * 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 org.apache.hadoop.mapred;
+
+import java.io.IOException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.Arrays;
+import java.util.Random;
+
+import junit.framework.TestCase;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.LzopCodec;
+import org.apache.hadoop.mapred.LzoTextInputFormat.LzoIndex;
+import org.apache.hadoop.util.NativeCodeLoader;
+
+/**
+ * Test the LzoTextInputFormat, make sure it splits the file properly and
+ * returns the right data.
+ */
+public class TestLzoTextInputFormat extends TestCase {
+
+  private static final Log LOG
+    = LogFactory.getLog(TestLzoTextInputFormat.class.getName());
+  
+  private MessageDigest md5;
+  private String lzoFileName = "file";
+  
+  @Override
+  protected void setUp() throws Exception {
+    super.setUp();
+    md5 = MessageDigest.getInstance("MD5");
+  }
+  
+  /**
+   * Make sure the lzo index class works as described.
+   */
+  public void testLzoIndex() {
+    LzoIndex index = new LzoIndex();
+    assertTrue(index.isEmpty());
+    index = new LzoIndex(4);
+    index.set(0, 0);
+    index.set(1, 5);
+    index.set(2, 10);
+    index.set(3, 15);
+    assertFalse(index.isEmpty());
+    
+    assertEquals(0, index.findNextPosition(-1));
+    assertEquals(5, index.findNextPosition(1));
+    assertEquals(5, index.findNextPosition(5));
+    assertEquals(15, index.findNextPosition(11));
+    assertEquals(15, index.findNextPosition(15));
+    assertEquals(-1, index.findNextPosition(16));
+  }
+  
+  /**
+   * Index the file and make sure it splits properly.
+   * @throws NoSuchAlgorithmException
+   * @throws IOException
+   */
+  public void testWithIndex() throws NoSuchAlgorithmException, IOException {
+    runTest(true);
+  }
+  
+  /**
+   * Don't index the file and make sure it can be processed anyway.
+   * @throws NoSuchAlgorithmException
+   * @throws IOException
+   */
+  public void testWithoutIndex() throws NoSuchAlgorithmException, IOException {
+    runTest(false);
+  }
+  
+  private void runTest(boolean testWithIndex) throws IOException, 
+    NoSuchAlgorithmException {
+    
+    if (!NativeCodeLoader.isNativeCodeLoaded()) {
+      LOG.warn("Cannot run this test without the native lzo libraries");
+      return;
+    }
+
+    String attempt = "attempt_200707121733_0001_m_000000_0";
+    Path workDir = new Path(new Path(new Path(System.getProperty(
+        "test.build.data", "."), "data"), FileOutputCommitter.TEMP_DIR_NAME),
+        "_" + attempt);
+    Path outputDir = workDir.getParent().getParent();
+
+    JobConf conf = new JobConf();
+    conf.set("mapred.task.id", attempt);
+    conf.set("io.compression.codecs", LzopCodec.class.getName());
+
+    FileSystem localFs = FileSystem.getLocal(conf);
+    localFs.delete(workDir, true);
+    localFs.mkdirs(workDir);
+    FileInputFormat.setInputPaths(conf, outputDir);
+
+    
+    // create some input data
+    byte[] expectedMd5 = createTestInput(outputDir, workDir, conf, localFs);
+
+    if(testWithIndex) {
+      Path lzoFile = new Path(workDir, lzoFileName);
+      LzoTextInputFormat.createIndex(localFs, new Path(lzoFile
+        + new LzopCodec().getDefaultExtension()));
+    }
+    
+    LzoTextInputFormat inputFormat = new LzoTextInputFormat();
+    inputFormat.configure(conf);
+    
+    //it's left in the work dir
+    FileInputFormat.setInputPaths(conf, workDir);
+
+    int numSplits = 3;
+    InputSplit[] is = inputFormat.getSplits(conf, numSplits);
+    if(testWithIndex) {
+      assertEquals(numSplits, is.length);
+    } else {
+      assertEquals(1, is.length);
+    }
+
+    for (InputSplit inputSplit : is) {
+      RecordReader<LongWritable, Text> rr = inputFormat.getRecordReader(
+          inputSplit, conf, Reporter.NULL);
+      LongWritable key = rr.createKey();
+      Text value = rr.createValue();
+
+      while (rr.next(key, value)) {
+        md5.update(value.getBytes(), 0, value.getLength());
+      }
+
+      rr.close();
+    }
+
+    assertTrue(Arrays.equals(expectedMd5, md5.digest()));
+  }
+
+  /**
+   * Creates an lzo file with random data. 
+   * 
+   * @param outputDir Output directory
+   * @param workDir Work directory, this is where the file is written to
+   * @param fs File system we're using
+   * @throws IOException
+   */
+  private byte[] createTestInput(Path outputDir, Path workDir, JobConf conf,
+      FileSystem fs) throws IOException {
+
+    RecordWriter<Text, Text> rw = null;
+    
+    md5.reset();
+    
+    try {
+      TextOutputFormat<Text, Text> output = new TextOutputFormat<Text, Text>();
+      TextOutputFormat.setCompressOutput(conf, true);
+      TextOutputFormat.setOutputCompressorClass(conf, LzopCodec.class);
+      TextOutputFormat.setOutputPath(conf, outputDir);
+      TextOutputFormat.setWorkOutputPath(conf, workDir);
+
+      rw = output.getRecordWriter(null, conf, lzoFileName, Reporter.NULL);
+
+      //has to be enough data to create a couple of lzo blocks
+      int charsToOutput = 10485760;
+      char[] chars = "abcdefghijklmnopqrstuvwxyz\u00E5\u00E4\u00F6"
+          .toCharArray();
+
+      Random r = new Random(System.currentTimeMillis());
+      Text key = new Text();
+      Text value = new Text();
+      int charsMax = chars.length - 1;
+      for (int i = 0; i < charsToOutput;) {
+        i += fillText(chars, r, charsMax, key);
+        i += fillText(chars, r, charsMax, value);
+        rw.write(key, value);
+        md5.update(key.getBytes(), 0, key.getLength());
+        //text output format writes tab between the key and value
+        md5.update("\t".getBytes("UTF-8")); 
+        md5.update(value.getBytes(), 0, value.getLength());
+      }
+    } finally {
+      if (rw != null) {
+        rw.close(Reporter.NULL);
+      }
+    }
+
+    byte[] result = md5.digest();
+    md5.reset();
+    return result;
+  }
+
+  private int fillText(char[] chars, Random r, int charsMax, Text text) {
+    StringBuilder sb = new StringBuilder();
+    //get a reasonable string length 
+    int stringLength = r.nextInt(charsMax * 2);
+    for (int j = 0; j < stringLength; j++) {
+      sb.append(chars[r.nextInt(charsMax)]);
+    }
+    text.set(sb.toString());
+    return stringLength;
+  }
+
+}



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