crunch-hbase/src/main/java/org/apache/crunch/io/hbase/HFileUtils.java

/**
 * 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.crunch.io.hbase;

import static org.apache.crunch.types.writable.Writables.bytes;
import static org.apache.crunch.types.writable.Writables.nulls;
import static org.apache.crunch.types.writable.Writables.tableOf;

import java.io.IOException;
import java.io.Serializable;
import java.nio.ByteBuffer;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.NavigableSet;
import java.util.Set;

import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableSet;
import com.google.common.collect.Lists;
import com.google.common.primitives.Longs;
import org.apache.crunch.DoFn;
import org.apache.crunch.Emitter;
import org.apache.crunch.FilterFn;
import org.apache.crunch.GroupingOptions;
import org.apache.crunch.MapFn;
import org.apache.crunch.PCollection;
import org.apache.crunch.PTable;
import org.apache.crunch.Pair;
import org.apache.crunch.Pipeline;
import org.apache.crunch.impl.dist.DistributedPipeline;
import org.apache.crunch.lib.sort.TotalOrderPartitioner;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.hbase.HColumnDescriptor;
import org.apache.hadoop.hbase.HConstants;
import org.apache.hadoop.hbase.KeyValue;
import org.apache.hadoop.hbase.client.HTable;
import org.apache.hadoop.hbase.client.Put;
import org.apache.hadoop.hbase.client.Result;
import org.apache.hadoop.hbase.client.Scan;
import org.apache.hadoop.hbase.io.TimeRange;
import org.apache.hadoop.hbase.util.Bytes;
import org.apache.hadoop.io.BytesWritable;
import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.io.RawComparator;
import org.apache.hadoop.io.SequenceFile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public final class HFileUtils {

  private static final Logger LOG = LoggerFactory.getLogger(HFileUtils.class);

  /** Compares {@code KeyValue} by its family, qualifier, timestamp (reversely), type (reversely) and memstoreTS. */
  private static final Comparator<KeyValue> KEY_VALUE_COMPARATOR = new Comparator<KeyValue>() {
    @Override
    public int compare(KeyValue l, KeyValue r) {
      int cmp;
      if ((cmp = compareFamily(l, r)) != 0) {
        return cmp;
      }
      if ((cmp = compareQualifier(l, r)) != 0) {
        return cmp;
      }
      if ((cmp = compareTimestamp(l, r)) != 0) {
        return cmp;
      }
      if ((cmp = compareType(l, r)) != 0) {
        return cmp;
      }
      return 0;
    }

    private int compareFamily(KeyValue l, KeyValue r) {
      return Bytes.compareTo(
          l.getBuffer(), l.getFamilyOffset(), l.getFamilyLength(),
          r.getBuffer(), r.getFamilyOffset(), r.getFamilyLength());
    }

    private int compareQualifier(KeyValue l, KeyValue r) {
      return Bytes.compareTo(
          l.getBuffer(), l.getQualifierOffset(), l.getQualifierLength(),
          r.getBuffer(), r.getQualifierOffset(), r.getQualifierLength());
    }

    private int compareTimestamp(KeyValue l, KeyValue r) {
      // These arguments are intentionally reversed, with r then l, to sort
      // the timestamps in descending order as is expected by HBase
      return Longs.compare(r.getTimestamp(), l.getTimestamp());
    }

    private int compareType(KeyValue l, KeyValue r) {
      return (int) r.getType() - (int) l.getType();
    }

  };

  private static class FilterByFamilyFn extends FilterFn<KeyValue> {

    private final byte[] family;

    private FilterByFamilyFn(byte[] family) {
      this.family = family;
    }

    @Override
    public boolean accept(KeyValue input) {
      return Bytes.equals(
          input.getBuffer(), input.getFamilyOffset(), input.getFamilyLength(),
          family, 0, family.length);
    }
  }

  private static class StartRowFilterFn extends FilterFn<KeyValue> {

    private final byte[] startRow;

    private StartRowFilterFn(byte[] startRow) {
      this.startRow = startRow;
    }

    @Override
    public boolean accept(KeyValue input) {
      return Bytes.compareTo(input.getRow(), startRow) >= 0;
    }
  }

  private static class StopRowFilterFn extends FilterFn<KeyValue> {

    private final byte[] stopRow;

    private StopRowFilterFn(byte[] stopRow) {
      this.stopRow = stopRow;
    }

    @Override
    public boolean accept(KeyValue input) {
      return Bytes.compareTo(input.getRow(), stopRow) < 0;
    }
  }

  private static class FamilyMapFilterFn extends FilterFn<KeyValue> {

    private static class Column implements Serializable {

      private final byte[] family;
      private final byte[] qualifier;

      private Column(byte[] family, byte[] qualifier) {
        this.family = family;
        this.qualifier = qualifier;
      }

      private byte[] getFamily() {
        return family;
      }

      private byte[] getQualifier() {
        return qualifier;
      }
    }

    private final List<byte[]> families = Lists.newArrayList();
    private final List<Column> qualifiers = Lists.newArrayList();

    private transient Set<ByteBuffer> familySet;
    private transient Set<Pair<ByteBuffer, ByteBuffer>> qualifierSet;

    private FamilyMapFilterFn(Map<byte[], NavigableSet<byte[]>> familyMap) {
      // Holds good families and qualifiers in Lists, as ByteBuffer is not Serializable.
      for (Map.Entry<byte[], NavigableSet<byte[]>> e : familyMap.entrySet()) {
        byte[] f = e.getKey();
        if (e.getValue() == null) {
          families.add(f);
        } else {
          for (byte[] q : e.getValue()) {
            qualifiers.add(new Column(f, q));
          }
        }
      }
    }

    @Override
    public void initialize() {
      ImmutableSet.Builder<ByteBuffer> familiySetBuilder = ImmutableSet.builder();
      ImmutableSet.Builder<Pair<ByteBuffer, ByteBuffer>> qualifierSetBuilder
          = ImmutableSet.builder();
      for (byte[] f : families) {
        familiySetBuilder.add(ByteBuffer.wrap(f));
      }
      for (Column e : qualifiers) {
        byte[] f = e.getFamily();
        byte[] q = e.getQualifier();
        qualifierSetBuilder.add(Pair.of(ByteBuffer.wrap(f), ByteBuffer.wrap(q)));
      }
      this.familySet = familiySetBuilder.build();
      this.qualifierSet = qualifierSetBuilder.build();
    }

    @Override
    public boolean accept(KeyValue input) {
      byte[] b = input.getBuffer();
      ByteBuffer f = ByteBuffer.wrap(b, input.getFamilyOffset(), input.getFamilyLength());
      ByteBuffer q = ByteBuffer.wrap(b, input.getQualifierOffset(), input.getQualifierLength());
      return familySet.contains(f) || qualifierSet.contains(Pair.of(f, q));
    }
  }

  private static class TimeRangeFilterFn extends FilterFn<KeyValue> {

    private final long minTimestamp;
    private final long maxTimestamp;

    private TimeRangeFilterFn(TimeRange timeRange) {
      // Can't save TimeRange to member directly, as it is not Serializable.
      this.minTimestamp = timeRange.getMin();
      this.maxTimestamp = timeRange.getMax();
    }

    @Override
    public boolean accept(KeyValue input) {
      return (minTimestamp <= input.getTimestamp() && input.getTimestamp() < maxTimestamp);
    }
  }

  public static class KeyValueComparator implements RawComparator<BytesWritable> {

    @Override
    public int compare(byte[] left, int loffset, int llength, byte[] right, int roffset, int rlength) {
      // BytesWritable serialize length in first 4 bytes.
      // We simply ignore it here, because KeyValue has its own size serialized.
      if (llength < 4) {
        throw new AssertionError("Too small llength: " + llength);
      }
      if (rlength < 4) {
        throw new AssertionError("Too small rlength: " + rlength);
      }
      KeyValue leftKey = HBaseTypes.bytesToKeyValue(left, loffset + 4, llength - 4);
      KeyValue rightKey = HBaseTypes.bytesToKeyValue(right, roffset + 4, rlength - 4);

      byte[] lRow = leftKey.getRow();
      byte[] rRow = rightKey.getRow();
      int rowCmp = Bytes.compareTo(lRow, rRow);
      if (rowCmp != 0) {
        return rowCmp;
      } else {
        return KeyValue.COMPARATOR.compare(leftKey, rightKey);
      }
    }

    @Override
    public int compare(BytesWritable left, BytesWritable right) {
      return KeyValue.COMPARATOR.compare(
          HBaseTypes.bytesToKeyValue(left),
          HBaseTypes.bytesToKeyValue(right));
    }
  }

  private static final MapFn<KeyValue, ByteBuffer> EXTRACT_ROW_FN = new MapFn<KeyValue, ByteBuffer>() {
    @Override
    public ByteBuffer map(KeyValue input) {
      // we have to make a copy of row, because the buffer may be changed after this call
      return ByteBuffer.wrap(Arrays.copyOfRange(
          input.getBuffer(), input.getRowOffset(), input.getRowOffset() + input.getRowLength()));
    }
  };

  public static PCollection<Result> scanHFiles(Pipeline pipeline, Path path) {
    return scanHFiles(pipeline, path, new Scan());
  }

  /**
   * Scans HFiles with filter conditions.
   *
   * @param pipeline the pipeline
   * @param path path to HFiles
   * @param scan filtering conditions
   * @return {@code Result}s
   * @see #combineIntoRow(org.apache.crunch.PCollection, org.apache.hadoop.hbase.client.Scan)
   */
  public static PCollection<Result> scanHFiles(Pipeline pipeline, Path path, Scan scan) {
      return scanHFiles(pipeline, ImmutableList.of(path), scan);
  }

  public static PCollection<Result> scanHFiles(Pipeline pipeline, List<Path> paths, Scan scan) {
      PCollection<KeyValue> in = pipeline.read(new HFileSource(paths, scan));
      return combineIntoRow(in, scan);
  }

  public static PCollection<Result> combineIntoRow(PCollection<KeyValue> kvs) {
    return combineIntoRow(kvs, new Scan());
  }

  /**
   * Converts a bunch of {@link KeyValue}s into {@link Result}.
   *
   * All {@code KeyValue}s belong to the same row are combined. Users may provide some filter
   * conditions (specified by {@code scan}). Deletes are dropped and only a specified number
   * of versions are kept.
   *
   * @param kvs the input {@code KeyValue}s
   * @param scan filter conditions, currently we support start row, stop row and family map
   * @return {@code Result}s
   */
  public static PCollection<Result> combineIntoRow(PCollection<KeyValue> kvs, Scan scan) {
    if (!Bytes.equals(scan.getStartRow(), HConstants.EMPTY_START_ROW)) {
      kvs = kvs.filter(new StartRowFilterFn(scan.getStartRow()));
    }
    if (!Bytes.equals(scan.getStopRow(), HConstants.EMPTY_END_ROW)) {
      kvs = kvs.filter(new StopRowFilterFn(scan.getStopRow()));
    }
    if (scan.hasFamilies()) {
      kvs = kvs.filter(new FamilyMapFilterFn(scan.getFamilyMap()));
    }
    TimeRange timeRange = scan.getTimeRange();
    if (timeRange != null && (timeRange.getMin() > 0 || timeRange.getMax() < Long.MAX_VALUE)) {
      kvs = kvs.filter(new TimeRangeFilterFn(timeRange));
    }
    // TODO(chaoshi): support Scan#getFilter

    PTable<ByteBuffer, KeyValue> kvsByRow = kvs.by(EXTRACT_ROW_FN, bytes());
    final int versions = scan.getMaxVersions();
    return kvsByRow.groupByKey().parallelDo("CombineKeyValueIntoRow",
        new DoFn<Pair<ByteBuffer, Iterable<KeyValue>>, Result>() {
          @Override
          public void process(Pair<ByteBuffer, Iterable<KeyValue>> input, Emitter<Result> emitter) {
            List<KeyValue> kvs = Lists.newArrayList();
            for (KeyValue kv : input.second()) {
              try {
                kvs.add(kv.clone()); // assuming the input fits into memory
              } catch (Exception e) {
                throw new RuntimeException(e);
              }
            }
            Result result = doCombineIntoRow(kvs, versions);
            if (result == null) {
              return;
            }
            emitter.emit(result);
          }
        }, HBaseTypes.results());
  }

  public static void writeToHFilesForIncrementalLoad(
      PCollection<KeyValue> kvs,
      HTable table,
      Path outputPath) throws IOException {
    HColumnDescriptor[] families = table.getTableDescriptor().getColumnFamilies();
    if (families.length == 0) {
      LOG.warn("{} has no column families", table);
      return;
    }
    for (HColumnDescriptor f : families) {
      byte[] family = f.getName();
      PCollection<KeyValue> sorted = sortAndPartition(kvs.filter(new FilterByFamilyFn(family)), table);
      sorted.write(new HFileTarget(new Path(outputPath, Bytes.toString(family)), f));
    }
  }

  public static void writePutsToHFilesForIncrementalLoad(
      PCollection<Put> puts,
      HTable table,
      Path outputPath) throws IOException {
    PCollection<KeyValue> kvs = puts.parallelDo("ConvertPutToKeyValue", new DoFn<Put, KeyValue>() {
      @Override
      public void process(Put input, Emitter<KeyValue> emitter) {
        for (List<KeyValue> keyValues : input.getFamilyMap().values()) {
          for (KeyValue keyValue : keyValues) {
            emitter.emit(keyValue);
          }
        }
      }
    }, HBaseTypes.keyValues());
    writeToHFilesForIncrementalLoad(kvs, table, outputPath);
  }

  public static PCollection<KeyValue> sortAndPartition(PCollection<KeyValue> kvs, HTable table) throws IOException {
    Configuration conf = kvs.getPipeline().getConfiguration();
    PTable<KeyValue, Void> t = kvs.parallelDo(new MapFn<KeyValue, Pair<KeyValue, Void>>() {
      @Override
      public Pair<KeyValue, Void> map(KeyValue input) {
        return Pair.of(input, (Void) null);
      }
    }, tableOf(HBaseTypes.keyValues(), nulls()));
    List<KeyValue> splitPoints = getSplitPoints(table);
    Path partitionFile = new Path(((DistributedPipeline) kvs.getPipeline()).createTempPath(), "partition");
    writePartitionInfo(conf, partitionFile, splitPoints);
    GroupingOptions options = GroupingOptions.builder()
        .partitionerClass(TotalOrderPartitioner.class)
        .sortComparatorClass(KeyValueComparator.class)
        .conf(TotalOrderPartitioner.PARTITIONER_PATH, partitionFile.toString())
        .numReducers(splitPoints.size() + 1)
        .build();
    return t.groupByKey(options).ungroup().keys();
  }

  private static List<KeyValue> getSplitPoints(HTable table) throws IOException {
    List<byte[]> startKeys = ImmutableList.copyOf(table.getStartKeys());
    if (startKeys.isEmpty()) {
      throw new AssertionError(table + " has no regions!");
    }
    List<KeyValue> splitPoints = Lists.newArrayList();
    for (byte[] startKey : startKeys.subList(1, startKeys.size())) {
      KeyValue kv = KeyValue.createFirstOnRow(startKey);
      LOG.debug("split row: " + Bytes.toString(kv.getRow()));
      splitPoints.add(kv);
    }
    return splitPoints;
  }

  private static void writePartitionInfo(
      Configuration conf,
      Path path,
      List<KeyValue> splitPoints) throws IOException {
    LOG.info("Writing {} split points to {}", splitPoints.size(), path);
    SequenceFile.Writer writer = SequenceFile.createWriter(
        path.getFileSystem(conf),
        conf,
        path,
        NullWritable.class,
        BytesWritable.class);
    for (KeyValue key : splitPoints) {
      writer.append(NullWritable.get(), HBaseTypes.keyValueToBytes(key));
    }
    writer.close();
  }

  private static Result doCombineIntoRow(List<KeyValue> kvs, int versions) {
    // shortcut for the common case
    if (kvs.isEmpty()) {
      return null;
    }
    if (kvs.size() == 1 && kvs.get(0).getType() == KeyValue.Type.Put.getCode()) {
      return new Result(kvs);
    }

    kvs = maybeDeleteFamily(kvs);

    // In-place sort KeyValues by family, qualifier and then timestamp reversely (whenever ties, deletes appear first).
    Collections.sort(kvs, KEY_VALUE_COMPARATOR);

    List<KeyValue> results = Lists.newArrayListWithCapacity(kvs.size());
    for (int i = 0, j; i < kvs.size(); i = j) {
      j = i + 1;
      while (j < kvs.size() && hasSameFamilyAndQualifier(kvs.get(i), kvs.get(j))) {
        j++;
      }
      results.addAll(getLatestKeyValuesOfColumn(kvs.subList(i, j), versions));
    }
    if (results.isEmpty()) {
      return null;
    }
    return new Result(results);
  }

  /**
   * In-place removes any {@link KeyValue}s whose timestamp is less than or equal to the
   * delete family timestamp. Also removes the delete family {@code KeyValue}s.
   */
  private static List<KeyValue> maybeDeleteFamily(List<KeyValue> kvs) {
    long deleteFamilyCut = -1;
    for (KeyValue kv : kvs) {
      if (kv.getType() == KeyValue.Type.DeleteFamily.getCode()) {
        deleteFamilyCut = Math.max(deleteFamilyCut, kv.getTimestamp());
      }
    }
    if (deleteFamilyCut == 0) {
      return kvs;
    }
    List<KeyValue> results = Lists.newArrayList();
    for (KeyValue kv : kvs) {
      if (kv.getType() == KeyValue.Type.DeleteFamily.getCode()) {
        continue;
      }
      if (kv.getTimestamp() <= deleteFamilyCut) {
        continue;
      }
      results.add(kv);
    }
    return results;
  }

  private static boolean hasSameFamilyAndQualifier(KeyValue l, KeyValue r) {
    return Bytes.equals(
        l.getBuffer(), l.getFamilyOffset(), l.getFamilyLength(),
        r.getBuffer(), r.getFamilyOffset(), r.getFamilyLength())
        && Bytes.equals(
        l.getBuffer(), l.getQualifierOffset(), l.getQualifierLength(),
        r.getBuffer(), r.getQualifierOffset(), r.getQualifierLength());
  }

  /**
   * Goes over the given {@link KeyValue}s and remove {@code Delete}s and {@code DeleteColumn}s.
   *
   * @param kvs {@code KeyValue}s that of same row and column and sorted by timestamps in
   *            descending order
   * @param versions the number of versions to keep
   * @return the resulting {@code KeyValue}s that contains only {@code Put}s
   */
  private static List<KeyValue> getLatestKeyValuesOfColumn(List<KeyValue> kvs, int versions) {
    if (kvs.isEmpty()) {
      return kvs;
    }
    if (kvs.get(0).getType() == KeyValue.Type.Put.getCode()) {
      return kvs; // shortcut for the common case
    }

    List<KeyValue> results = Lists.newArrayListWithCapacity(versions);
    long previousDeleteTimestamp = -1;
    for (KeyValue kv : kvs) {
      if (results.size() >= versions) {
        break;
      }
      if (kv.getType() == KeyValue.Type.DeleteColumn.getCode()) {
        break;
      } else if (kv.getType() == KeyValue.Type.Put.getCode()) {
        if (kv.getTimestamp() != previousDeleteTimestamp) {
          results.add(kv);
        }
      } else if (kv.getType() == KeyValue.Type.Delete.getCode()) {
        previousDeleteTimestamp = kv.getTimestamp();
      } else {
        throw new AssertionError("Unexpected KeyValue type: " + kv.getType());
      }
    }
    return results;
  }
}