HBASE-12669 - Have compaction scanner save info about delete markers

(Jingcheng Du)

hbase-server/src/main/java/org/apache/hadoop/hbase/mob/DefaultMobCompactor.java

@@ -28,16 +28,21 @@ import org.apache.hadoop.classification.InterfaceAudience;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.hbase.Cell;
+import org.apache.hadoop.hbase.CellUtil;
 import org.apache.hadoop.hbase.KeyValue;
 import org.apache.hadoop.hbase.KeyValueUtil;
 import org.apache.hadoop.hbase.Tag;
 import org.apache.hadoop.hbase.TagType;
+import org.apache.hadoop.hbase.client.Scan;
 import org.apache.hadoop.hbase.regionserver.HMobStore;
 import org.apache.hadoop.hbase.regionserver.HStore;
 import org.apache.hadoop.hbase.regionserver.InternalScanner;
+import org.apache.hadoop.hbase.regionserver.MobCompactionStoreScanner;
+import org.apache.hadoop.hbase.regionserver.ScanType;
 import org.apache.hadoop.hbase.regionserver.Store;
 import org.apache.hadoop.hbase.regionserver.StoreFile;
 import org.apache.hadoop.hbase.regionserver.StoreFile.Writer;
+import org.apache.hadoop.hbase.regionserver.StoreFileScanner;
 import org.apache.hadoop.hbase.regionserver.compactions.DefaultCompactor;
 import org.apache.hadoop.hbase.util.Bytes;
 
@@ -78,6 +83,21 @@ public class DefaultMobCompactor extends DefaultCompactor {
     return writer;
   }
 
+  @Override
+  protected InternalScanner createScanner(Store store, List<StoreFileScanner> scanners,
+      ScanType scanType, long smallestReadPoint, long earliestPutTs) throws IOException {
+    Scan scan = new Scan();
+    scan.setMaxVersions(store.getFamily().getMaxVersions());
+    if (scanType == ScanType.COMPACT_DROP_DELETES) {
+      scanType = ScanType.COMPACT_RETAIN_DELETES;
+      return new MobCompactionStoreScanner(store, store.getScanInfo(), scan, scanners,
+          scanType, smallestReadPoint, earliestPutTs, true);
+    } else {
+      return new MobCompactionStoreScanner(store, store.getScanInfo(), scan, scanners,
+          scanType, smallestReadPoint, earliestPutTs, false);
+    }
+  }
+
   /**
    * Performs compaction on a column family with the mob flag enabled.
    * This is for when the mob threshold size has changed or if the mob
@@ -104,6 +124,14 @@ public class DefaultMobCompactor extends DefaultCompactor {
    * Otherwise, directly write this cell into the store file.
    * </li>
    * </ol>
+   * In the mob compaction, the {@link MobCompactionStoreScanner} is used as a scanner
+   * which could output the normal cells and delete markers together when required.
+   * After the major compaction on the normal hfiles, we have a guarantee that we have purged all
+   * deleted or old version mob refs, and the delete markers are written to a del file with the
+   * suffix _del. Because of this, it is safe to use the del file in the mob compaction.
+   * The mob compaction doesn't take place in the normal hfiles, it occurs directly in the
+   * mob files. When the small mob files are merged into bigger ones, the del file is added into
+   * the scanner to filter the deleted cells.
    * @param fd File details
    * @param scanner Where to read from.
    * @param writer Where to write to.
@@ -115,6 +143,11 @@ public class DefaultMobCompactor extends DefaultCompactor {
   @Override
   protected boolean performCompaction(FileDetails fd, InternalScanner scanner, CellSink writer,
       long smallestReadPoint, boolean cleanSeqId, boolean major) throws IOException {
+    if (!(scanner instanceof MobCompactionStoreScanner)) {
+      throw new IllegalArgumentException(
+          "The scanner should be an instance of MobCompactionStoreScanner");
+    }
+    MobCompactionStoreScanner compactionScanner = (MobCompactionStoreScanner) scanner;
     int bytesWritten = 0;
     // Since scanner.next() can return 'false' but still be delivering data,
     // we have to use a do/while loop.
@@ -125,7 +158,9 @@ public class DefaultMobCompactor extends DefaultCompactor {
     Path path = MobUtils.getMobFamilyPath(conf, store.getTableName(), store.getColumnFamilyName());
     byte[] fileName = null;
     StoreFile.Writer mobFileWriter = null;
+    StoreFile.Writer delFileWriter = null;
     long mobCells = 0;
+    long deleteMarkersCount = 0;
     Tag tableNameTag = new Tag(TagType.MOB_TABLE_NAME_TAG_TYPE, store.getTableName()
             .getName());
     long mobCompactedIntoMobCellsCount = 0;
@@ -144,14 +179,19 @@ public class DefaultMobCompactor extends DefaultCompactor {
                 + "we will continue the compaction by writing MOB cells directly in store files",
             e);
       }
+      delFileWriter = mobStore.createDelFileWriterInTmp(new Date(fd.latestPutTs), fd.maxKeyCount,
+          store.getFamily().getCompression(), store.getRegionInfo().getStartKey());
       do {
-        hasMore = scanner.next(cells, compactionKVMax);
+        hasMore = compactionScanner.next(cells, compactionKVMax);
         // output to writer:
         for (Cell c : cells) {
           // TODO remove the KeyValueUtil.ensureKeyValue before merging back to trunk.
           KeyValue kv = KeyValueUtil.ensureKeyValue(c);
           resetSeqId(smallestReadPoint, cleanSeqId, kv);
-          if (mobFileWriter == null || kv.getTypeByte() != KeyValue.Type.Put.getCode()) {
+          if (compactionScanner.isOutputDeleteMarkers() && CellUtil.isDelete(c)) {
+            delFileWriter.append(kv);
+            deleteMarkersCount++;
+          } else if (mobFileWriter == null || kv.getTypeByte() != KeyValue.Type.Put.getCode()) {
             // If the mob file writer is null or the kv type is not put, directly write the cell
             // to the store file.
             writer.append(kv);
@@ -222,8 +262,12 @@ public class DefaultMobCompactor extends DefaultCompactor {
         mobFileWriter.appendMetadata(fd.maxSeqId, major, mobCells);
         mobFileWriter.close();
       }
+      if (delFileWriter != null) {
+        delFileWriter.appendMetadata(fd.maxSeqId, major, deleteMarkersCount);
+        delFileWriter.close();
+      }
     }
-    if(mobFileWriter!=null) {
+    if (mobFileWriter != null) {
       if (mobCells > 0) {
         // If the mob file is not empty, commit it.
         mobStore.commitFile(mobFileWriter.getPath(), path);
@@ -236,6 +280,20 @@ public class DefaultMobCompactor extends DefaultCompactor {
         }
       }
     }
+    if (delFileWriter != null) {
+      if (deleteMarkersCount > 0) {
+        // If the del file is not empty, commit it.
+        // If the commit fails, the compaction is re-performed again.
+        mobStore.commitFile(delFileWriter.getPath(), path);
+      } else {
+        try {
+          // If the del file is empty, delete it instead of committing.
+          store.getFileSystem().delete(delFileWriter.getPath(), true);
+        } catch (IOException e) {
+          LOG.error("Fail to delete the temp del file", e);
+        }
+      }
+    }
     mobStore.updateMobCompactedFromMobCellsCount(mobCompactedFromMobCellsCount);
     mobStore.updateMobCompactedIntoMobCellsCount(mobCompactedIntoMobCellsCount);
     mobStore.updateMobCompactedFromMobCellsSize(mobCompactedFromMobCellsSize);

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HMobStore.java

@@ -165,8 +165,8 @@ public class HMobStore extends HStore {
   }
 
   /**
-   * Creates the temp directory of mob files for flushing.
-   * @param date The latest date of cells in the flushing.
+   * Creates the writer for the mob file in temp directory.
+   * @param date The latest date of written cells.
    * @param maxKeyCount The key count.
    * @param compression The compression algorithm.
    * @param startKey The start key.
@@ -183,7 +183,30 @@ public class HMobStore extends HStore {
   }
 
   /**
-   * Creates the temp directory of mob files for flushing.
+   * Creates the writer for the del file in temp directory.
+   * The del file keeps tracking the delete markers. Its name has a suffix _del,
+   * the format is [0-9a-f]+(_del)?.
+   * @param date The latest date of written cells.
+   * @param maxKeyCount The key count.
+   * @param compression The compression algorithm.
+   * @param startKey The start key.
+   * @return The writer for the del file.
+   * @throws IOException
+   */
+  public StoreFile.Writer createDelFileWriterInTmp(Date date, long maxKeyCount,
+      Compression.Algorithm compression, byte[] startKey) throws IOException {
+    if (startKey == null) {
+      startKey = HConstants.EMPTY_START_ROW;
+    }
+    Path path = getTempDir();
+    String suffix = UUID
+        .randomUUID().toString().replaceAll("-", "") + "_del";
+    MobFileName mobFileName = MobFileName.create(startKey, MobUtils.formatDate(date), suffix);
+    return createWriterInTmp(mobFileName, path, maxKeyCount, compression);
+  }
+
+  /**
+   * Creates the writer for the mob file in temp directory.
    * @param date The date string, its format is yyyymmmdd.
    * @param basePath The basic path for a temp directory.
    * @param maxKeyCount The key count.
@@ -196,6 +219,20 @@ public class HMobStore extends HStore {
       Compression.Algorithm compression, byte[] startKey) throws IOException {
     MobFileName mobFileName = MobFileName.create(startKey, date, UUID.randomUUID()
         .toString().replaceAll("-", ""));
+    return createWriterInTmp(mobFileName, basePath, maxKeyCount, compression);
+  }
+
+  /**
+   * Creates the writer for the mob file in temp directory.
+   * @param mobFileName The mob file name.
+   * @param basePath The basic path for a temp directory.
+   * @param maxKeyCount The key count.
+   * @param compression The compression algorithm.
+   * @return The writer for the mob file.
+   * @throws IOException
+   */
+  public StoreFile.Writer createWriterInTmp(MobFileName mobFileName, Path basePath, long maxKeyCount,
+      Compression.Algorithm compression) throws IOException {
     final CacheConfig writerCacheConf = mobCacheConfig;
     HFileContext hFileContext = new HFileContextBuilder().withCompression(compression)
         .withIncludesMvcc(false).withIncludesTags(true)

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HStore.java

@@ -363,7 +363,7 @@ public class HStore implements Store {
    * @param family
    * @return TTL in seconds of the specified family
    */
-  private static long determineTTLFromFamily(final HColumnDescriptor family) {
+  static long determineTTLFromFamily(final HColumnDescriptor family) {
     // HCD.getTimeToLive returns ttl in seconds.  Convert to milliseconds.
     long ttl = family.getTimeToLive();
     if (ttl == HConstants.FOREVER) {

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/MobCompactionStoreScanner.java

@@ -0,0 +1,66 @@
+/**
+ *
+ * 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.hbase.regionserver;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.hadoop.classification.InterfaceAudience;
+import org.apache.hadoop.hbase.client.Scan;
+
+/**
+ * Scanner scans the MOB Store. Coalesce KeyValue stream into List<KeyValue>
+ * for a single row. It's only used in the compaction of mob-enabled columns.
+ * It outputs the normal cells and delete markers when outputDeleteMarkers is set as true.
+ */
+@InterfaceAudience.Private
+public class MobCompactionStoreScanner extends StoreScanner {
+
+  /*
+   * The delete markers are probably contained in the output of the scanner, for instance the
+   * minor compaction. If outputDeleteMarkers is set as true, these delete markers could be
+   * written to the del file, otherwise it's not allowed.
+   */
+  protected boolean outputDeleteMarkers;
+
+  /**
+   * Used for compactions.<p>
+   *
+   * Opens a scanner across specified StoreFiles.
+   * @param store who we scan
+   * @param scan the spec
+   * @param scanners ancillary scanners
+   * @param smallestReadPoint the readPoint that we should use for tracking
+   *          versions
+   */
+  public MobCompactionStoreScanner(Store store, ScanInfo scanInfo, Scan scan,
+      List<? extends KeyValueScanner> scanners, ScanType scanType, long smallestReadPoint,
+      long earliestPutTs, boolean outputDeleteMarkers) throws IOException {
+    super(store, scanInfo, scan, scanners, scanType, smallestReadPoint, earliestPutTs);
+    this.outputDeleteMarkers = outputDeleteMarkers;
+  }
+
+  /**
+   * Gets whether the delete markers could be written to the del files.
+   * @return True if the delete markers could be written del files, false if it's not allowed.
+   */
+  public boolean isOutputDeleteMarkers() {
+    return this.outputDeleteMarkers;
+  }
+}

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreFileInfo.java

@@ -49,13 +49,24 @@ public class StoreFileInfo implements Comparable<StoreFileInfo> {
   /**
    * A non-capture group, for hfiles, so that this can be embedded.
    * HFiles are uuid ([0-9a-z]+). Bulk loaded hfiles has (_SeqId_[0-9]+_) has suffix.
+   * The mob del file has (_del) as suffix.
    */
-  public static final String HFILE_NAME_REGEX = "[0-9a-f]+(?:_SeqId_[0-9]+_)?";
+  public static final String HFILE_NAME_REGEX = "[0-9a-f]+(?:(?:_SeqId_[0-9]+_)|(?:_del))?";
 
   /** Regex that will work for hfiles */
   private static final Pattern HFILE_NAME_PATTERN =
     Pattern.compile("^(" + HFILE_NAME_REGEX + ")");
 
+  /**
+   * A non-capture group, for hfiles, so that this can be embedded.
+   * A del file has (_del) as suffix.
+   */
+  public static final String DELFILE_NAME_REGEX = "[0-9a-f]+(?:_del)";
+
+  /** Regex that will work for del files */
+  private static final Pattern DELFILE_NAME_PATTERN =
+    Pattern.compile("^(" + DELFILE_NAME_REGEX + ")");
+
   /**
    * Regex that will work for straight reference names (<hfile>.<parentEncRegion>)
    * and hfilelink reference names (<table>=<region>-<hfile>.<parentEncRegion>)
@@ -361,6 +372,23 @@ public class StoreFileInfo implements Comparable<StoreFileInfo> {
     return m.matches() && m.groupCount() > 0;
   }
 
+  /**
+   * @param path Path to check.
+   * @return True if the path has format of a del file.
+   */
+  public static boolean isDelFile(final Path path) {
+    return isDelFile(path.getName());
+  }
+
+  /**
+   * @param path Path to check.
+   * @return True if the file name has format of a del file.
+   */
+  public static boolean isDelFile(final String fileName) {
+    Matcher m = DELFILE_NAME_PATTERN.matcher(fileName);
+    return m.matches() && m.groupCount() > 0;
+  }
+
   /**
    * @param path Path to check.
    * @return True if the path has format of a HStoreFile reference.

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreScanner.java

@@ -273,7 +273,7 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
       0);
   }
   
-  private StoreScanner(final Scan scan, ScanInfo scanInfo,
+  StoreScanner(final Scan scan, ScanInfo scanInfo,
       ScanType scanType, final NavigableSet<byte[]> columns,
       final List<KeyValueScanner> scanners, long earliestPutTs, long readPt)
           throws IOException {

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestMobCompaction.java

@@ -280,6 +280,60 @@ public class TestMobCompaction {
     scanner.close();
   }
 
+  @Test
+  public void testMajorCompactionAfterDelete() throws Exception {
+    init(UTIL.getConfiguration(), 100);
+    byte[] dummyData = makeDummyData(200); // larger than mob threshold
+    HRegionIncommon loader = new HRegionIncommon(region);
+    // create hfiles and mob hfiles but don't trigger compaction
+    int numHfiles = compactionThreshold - 1;
+    byte[] deleteRow = Bytes.add(STARTROW, Bytes.toBytes(0));
+    for (int i = 0; i < numHfiles; i++) {
+      Put p = createPut(i, dummyData);
+      loader.put(p);
+      loader.flushcache();
+    }
+    assertEquals("Before compaction: store files", numHfiles, countStoreFiles());
+    assertEquals("Before compaction: mob file count", numHfiles, countMobFiles());
+    assertEquals("Before compaction: rows", numHfiles, countRows());
+    assertEquals("Before compaction: mob rows", numHfiles, countMobRows());
+    assertEquals("Before compaction: number of mob cells", numHfiles, countMobCellsInMetadata());
+    // now let's delete some cells that contain mobs
+    Delete delete = new Delete(deleteRow);
+    delete.deleteFamily(COLUMN_FAMILY);
+    region.delete(delete);
+    loader.flushcache();
+
+    assertEquals("Before compaction: store files", numHfiles + 1, countStoreFiles());
+    assertEquals("Before compaction: mob files", numHfiles, countMobFiles());
+    region.compactStores(true);
+    assertEquals("After compaction: store files", 1, countStoreFiles());
+    // still have original mob hfiles and now added a mob del file
+    assertEquals("After compaction: mob files", numHfiles + 1, countMobFiles());
+
+    Scan scan = new Scan();
+    scan.setRaw(true);
+    InternalScanner scanner = region.getScanner(scan);
+    List<Cell> results = new ArrayList<Cell>();
+    scanner.next(results);
+    int deleteCount = 0;
+    while (!results.isEmpty()) {
+      for (Cell c : results) {
+        if (c.getTypeByte() == KeyValue.Type.DeleteFamily.getCode()) {
+          deleteCount++;
+          assertTrue(Bytes.equals(CellUtil.cloneRow(c), deleteRow));
+        }
+      }
+      results.clear();
+      scanner.next(results);
+    }
+    // assert the delete mark is not retained after the major compaction
+    assertEquals(0, deleteCount);
+    scanner.close();
+    // assert the deleted cell is not counted
+    assertEquals("The cells in mob files", numHfiles - 1, countMobCellsInMobFiles(1));
+  }
+
   private int countStoreFiles() throws IOException {
     Store store = region.getStore(COLUMN_FAMILY);
     return store.getStorefilesCount();
@@ -348,14 +402,15 @@ public class TestMobCompaction {
 
     int scannedCount = 0;
     List<Cell> results = new ArrayList<Cell>();
-    boolean hasMore = scanner.next(results);
+    boolean hasMore = true;
     while (hasMore) {
+      hasMore = scanner.next(results);
       for (Cell c : results) {
         if (MobUtils.isMobReferenceCell(c)) {
           scannedCount++;
         }
       }
-      hasMore = scanner.next(results);
+      results.clear();
     }
     scanner.close();
 
@@ -369,10 +424,11 @@ public class TestMobCompaction {
 
     int scannedCount = 0;
     List<Cell> results = new ArrayList<Cell>();
-    boolean hasMore = scanner.next(results);
+    boolean hasMore = true;
     while (hasMore) {
-      scannedCount += results.size();
       hasMore = scanner.next(results);
+      scannedCount += results.size();
+      results.clear();
     }
     scanner.close();
 
@@ -425,4 +481,43 @@ public class TestMobCompaction {
 
     return files.size();
   }
+
+  private int countMobCellsInMobFiles(int expectedNumDelfiles) throws IOException {
+    Configuration copyOfConf = new Configuration(conf);
+    copyOfConf.setFloat(HConstants.HFILE_BLOCK_CACHE_SIZE_KEY, 0f);
+    CacheConfig cacheConfig = new CacheConfig(copyOfConf);
+    Path mobDirPath = new Path(MobUtils.getMobRegionPath(conf, htd.getTableName()),
+        hcd.getNameAsString());
+    List<StoreFile> sfs = new ArrayList<StoreFile>();
+    int numDelfiles = 0;
+    int size = 0;
+    if (fs.exists(mobDirPath)) {
+      for (FileStatus f : fs.listStatus(mobDirPath)) {
+        StoreFile sf = new StoreFile(fs, f.getPath(), conf, cacheConfig, BloomType.NONE);
+        sfs.add(sf);
+        if (StoreFileInfo.isDelFile(sf.getPath())) {
+          numDelfiles++;
+        }
+      }
+      List scanners = StoreFileScanner.getScannersForStoreFiles(sfs, false, true, false, null,
+          HConstants.LATEST_TIMESTAMP);
+      Scan scan = new Scan();
+      scan.setMaxVersions(hcd.getMaxVersions());
+      long timeToPurgeDeletes = Math.max(conf.getLong("hbase.hstore.time.to.purge.deletes", 0), 0);
+      long ttl = HStore.determineTTLFromFamily(hcd);
+      ScanInfo scanInfo = new ScanInfo(hcd, ttl, timeToPurgeDeletes, KeyValue.COMPARATOR);
+      StoreScanner scanner = new StoreScanner(scan, scanInfo, ScanType.COMPACT_DROP_DELETES, null,
+          scanners, 0L, HConstants.LATEST_TIMESTAMP);
+      List<Cell> results = new ArrayList<>();
+      boolean hasMore = true;
+      while (hasMore) {
+        hasMore = scanner.next(results);
+        size += results.size();
+        results.clear();
+      }
+    }
+    // assert the number of the existing del files
+    assertEquals(expectedNumDelfiles, numDelfiles);
+    return size;
+  }
 }