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From ctubb...@apache.org
Subject [42/54] [partial] ACCUMULO-658, ACCUMULO-656 Split server into separate modules
Date Fri, 01 Nov 2013 00:56:21 GMT
http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/MetadataTableUtil.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/MetadataTableUtil.java b/server/base/src/main/java/org/apache/accumulo/server/util/MetadataTableUtil.java
new file mode 100644
index 0000000..6979268
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/MetadataTableUtil.java
@@ -0,0 +1,1101 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.accumulo.core.Constants;
+import org.apache.accumulo.core.client.AccumuloException;
+import org.apache.accumulo.core.client.AccumuloSecurityException;
+import org.apache.accumulo.core.client.BatchWriter;
+import org.apache.accumulo.core.client.BatchWriterConfig;
+import org.apache.accumulo.core.client.Connector;
+import org.apache.accumulo.core.client.Instance;
+import org.apache.accumulo.core.client.IsolatedScanner;
+import org.apache.accumulo.core.client.MutationsRejectedException;
+import org.apache.accumulo.core.client.Scanner;
+import org.apache.accumulo.core.client.TableNotFoundException;
+import org.apache.accumulo.core.client.impl.BatchWriterImpl;
+import org.apache.accumulo.core.client.impl.ScannerImpl;
+import org.apache.accumulo.core.client.impl.Writer;
+import org.apache.accumulo.core.data.Key;
+import org.apache.accumulo.core.data.KeyExtent;
+import org.apache.accumulo.core.data.Mutation;
+import org.apache.accumulo.core.data.PartialKey;
+import org.apache.accumulo.core.data.Range;
+import org.apache.accumulo.core.data.Value;
+import org.apache.accumulo.core.master.state.tables.TableState;
+import org.apache.accumulo.core.metadata.MetadataTable;
+import org.apache.accumulo.core.metadata.RootTable;
+import org.apache.accumulo.core.metadata.schema.DataFileValue;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.ChoppedColumnFamily;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.ClonedColumnFamily;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.DataFileColumnFamily;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.LogColumnFamily;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.ScanFileColumnFamily;
+import org.apache.accumulo.core.security.Authorizations;
+import org.apache.accumulo.core.security.Credentials;
+import org.apache.accumulo.core.tabletserver.thrift.ConstraintViolationException;
+import org.apache.accumulo.core.util.ColumnFQ;
+import org.apache.accumulo.core.util.FastFormat;
+import org.apache.accumulo.core.util.Pair;
+import org.apache.accumulo.core.util.StringUtil;
+import org.apache.accumulo.core.util.UtilWaitThread;
+import org.apache.accumulo.core.zookeeper.ZooUtil;
+import org.apache.accumulo.fate.zookeeper.IZooReaderWriter;
+import org.apache.accumulo.fate.zookeeper.ZooUtil.NodeExistsPolicy;
+import org.apache.accumulo.fate.zookeeper.ZooUtil.NodeMissingPolicy;
+import org.apache.accumulo.server.ServerConstants;
+import org.apache.accumulo.server.client.HdfsZooInstance;
+import org.apache.accumulo.server.fs.FileRef;
+import org.apache.accumulo.server.fs.VolumeManager;
+import org.apache.accumulo.server.fs.VolumeManager.FileType;
+import org.apache.accumulo.server.fs.VolumeManagerImpl;
+import org.apache.accumulo.server.security.SystemCredentials;
+import org.apache.accumulo.server.tables.TableManager;
+import org.apache.accumulo.server.zookeeper.ZooLock;
+import org.apache.accumulo.server.zookeeper.ZooReaderWriter;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.DataInputBuffer;
+import org.apache.hadoop.io.DataOutputBuffer;
+import org.apache.hadoop.io.Text;
+import org.apache.log4j.Logger;
+import org.apache.zookeeper.KeeperException;
+
+/**
+ * provides a reference to the metadata table for updates by tablet servers
+ */
+public class MetadataTableUtil {
+
+  private static final Text EMPTY_TEXT = new Text();
+  private static Map<Credentials,Writer> root_tables = new HashMap<Credentials,Writer>();
+  private static Map<Credentials,Writer> metadata_tables = new HashMap<Credentials,Writer>();
+  private static final Logger log = Logger.getLogger(MetadataTableUtil.class);
+
+  private static final int SAVE_ROOT_TABLET_RETRIES = 3;
+
+  private MetadataTableUtil() {}
+
+  public synchronized static Writer getMetadataTable(Credentials credentials) {
+    Writer metadataTable = metadata_tables.get(credentials);
+    if (metadataTable == null) {
+      metadataTable = new Writer(HdfsZooInstance.getInstance(), credentials, MetadataTable.ID);
+      metadata_tables.put(credentials, metadataTable);
+    }
+    return metadataTable;
+  }
+
+  public synchronized static Writer getRootTable(Credentials credentials) {
+    Writer rootTable = root_tables.get(credentials);
+    if (rootTable == null) {
+      rootTable = new Writer(HdfsZooInstance.getInstance(), credentials, RootTable.ID);
+      root_tables.put(credentials, rootTable);
+    }
+    return rootTable;
+  }
+
+  public static void putLockID(ZooLock zooLock, Mutation m) {
+    TabletsSection.ServerColumnFamily.LOCK_COLUMN.put(m, new Value(zooLock.getLockID().serialize(ZooUtil.getRoot(HdfsZooInstance.getInstance()) + "/")
+        .getBytes()));
+  }
+
+  public static void update(Credentials credentials, Mutation m, KeyExtent extent) {
+    update(credentials, null, m, extent);
+  }
+
+  public static void update(Credentials credentials, ZooLock zooLock, Mutation m, KeyExtent extent) {
+    Writer t = extent.isMeta() ? getRootTable(credentials) : getMetadataTable(credentials);
+    if (zooLock != null)
+      putLockID(zooLock, m);
+    while (true) {
+      try {
+        t.update(m);
+        return;
+      } catch (AccumuloException e) {
+        log.error(e, e);
+      } catch (AccumuloSecurityException e) {
+        log.error(e, e);
+      } catch (ConstraintViolationException e) {
+        log.error(e, e);
+      } catch (TableNotFoundException e) {
+        log.error(e, e);
+      }
+      UtilWaitThread.sleep(1000);
+    }
+
+  }
+
+  public static void updateTabletFlushID(KeyExtent extent, long flushID, Credentials credentials, ZooLock zooLock) {
+    if (!extent.isRootTablet()) {
+      Mutation m = new Mutation(extent.getMetadataEntry());
+      TabletsSection.ServerColumnFamily.FLUSH_COLUMN.put(m, new Value((flushID + "").getBytes()));
+      update(credentials, zooLock, m, extent);
+    }
+  }
+
+  public static void updateTabletCompactID(KeyExtent extent, long compactID, Credentials credentials, ZooLock zooLock) {
+    if (!extent.isRootTablet()) {
+      Mutation m = new Mutation(extent.getMetadataEntry());
+      TabletsSection.ServerColumnFamily.COMPACT_COLUMN.put(m, new Value((compactID + "").getBytes()));
+      update(credentials, zooLock, m, extent);
+    }
+  }
+
+  public static void updateTabletDataFile(long tid, KeyExtent extent, Map<FileRef,DataFileValue> estSizes, String time, Credentials credentials, ZooLock zooLock) {
+    Mutation m = new Mutation(extent.getMetadataEntry());
+    byte[] tidBytes = Long.toString(tid).getBytes();
+
+    for (Entry<FileRef,DataFileValue> entry : estSizes.entrySet()) {
+      Text file = entry.getKey().meta();
+      m.put(DataFileColumnFamily.NAME, file, new Value(entry.getValue().encode()));
+      m.put(TabletsSection.BulkFileColumnFamily.NAME, file, new Value(tidBytes));
+    }
+    TabletsSection.ServerColumnFamily.TIME_COLUMN.put(m, new Value(time.getBytes()));
+    update(credentials, zooLock, m, extent);
+  }
+
+  public static void addTablet(KeyExtent extent, String path, Credentials credentials, char timeType, ZooLock lock) {
+    Mutation m = extent.getPrevRowUpdateMutation();
+
+    TabletsSection.ServerColumnFamily.DIRECTORY_COLUMN.put(m, new Value(path.getBytes()));
+    TabletsSection.ServerColumnFamily.TIME_COLUMN.put(m, new Value((timeType + "0").getBytes()));
+
+    update(credentials, lock, m, extent);
+  }
+
+  public static void updateTabletPrevEndRow(KeyExtent extent, Credentials credentials) {
+    Mutation m = extent.getPrevRowUpdateMutation(); //
+    update(credentials, m, extent);
+  }
+
+  /**
+   * convenience method for reading entries from the metadata table
+   */
+  public static SortedMap<KeyExtent,Text> getMetadataDirectoryEntries(SortedMap<Key,Value> entries) {
+    Key key;
+    Value val;
+    Text datafile = null;
+    Value prevRow = null;
+    KeyExtent ke;
+
+    SortedMap<KeyExtent,Text> results = new TreeMap<KeyExtent,Text>();
+
+    Text lastRowFromKey = new Text();
+
+    // text obj below is meant to be reused in loop for efficiency
+    Text colf = new Text();
+    Text colq = new Text();
+
+    for (Entry<Key,Value> entry : entries.entrySet()) {
+      key = entry.getKey();
+      val = entry.getValue();
+
+      if (key.compareRow(lastRowFromKey) != 0) {
+        prevRow = null;
+        datafile = null;
+        key.getRow(lastRowFromKey);
+      }
+
+      colf = key.getColumnFamily(colf);
+      colq = key.getColumnQualifier(colq);
+
+      // interpret the row id as a key extent
+      if (TabletsSection.ServerColumnFamily.DIRECTORY_COLUMN.equals(colf, colq))
+        datafile = new Text(val.toString());
+
+      else if (TabletsSection.TabletColumnFamily.PREV_ROW_COLUMN.equals(colf, colq))
+        prevRow = new Value(val);
+
+      if (datafile != null && prevRow != null) {
+        ke = new KeyExtent(key.getRow(), prevRow);
+        results.put(ke, datafile);
+
+        datafile = null;
+        prevRow = null;
+      }
+    }
+    return results;
+  }
+
+  public static boolean recordRootTabletLocation(String address) {
+    IZooReaderWriter zoo = ZooReaderWriter.getInstance();
+    for (int i = 0; i < SAVE_ROOT_TABLET_RETRIES; i++) {
+      try {
+        log.info("trying to write root tablet location to ZooKeeper as " + address);
+        String zRootLocPath = ZooUtil.getRoot(HdfsZooInstance.getInstance()) + RootTable.ZROOT_TABLET_LOCATION;
+        zoo.putPersistentData(zRootLocPath, address.getBytes(), NodeExistsPolicy.OVERWRITE);
+        return true;
+      } catch (Exception e) {
+        log.error("Master: unable to save root tablet location in zookeeper. exception: " + e, e);
+      }
+    }
+    log.error("Giving up after " + SAVE_ROOT_TABLET_RETRIES + " retries");
+    return false;
+  }
+
+  public static SortedMap<FileRef,DataFileValue> getDataFileSizes(KeyExtent extent, Credentials credentials) throws IOException {
+    TreeMap<FileRef,DataFileValue> sizes = new TreeMap<FileRef,DataFileValue>();
+
+    Scanner mdScanner = new ScannerImpl(HdfsZooInstance.getInstance(), credentials, MetadataTable.ID, Authorizations.EMPTY);
+    mdScanner.fetchColumnFamily(DataFileColumnFamily.NAME);
+    Text row = extent.getMetadataEntry();
+    VolumeManager fs = VolumeManagerImpl.get();
+
+    Key endKey = new Key(row, DataFileColumnFamily.NAME, new Text(""));
+    endKey = endKey.followingKey(PartialKey.ROW_COLFAM);
+
+    mdScanner.setRange(new Range(new Key(row), endKey));
+    for (Entry<Key,Value> entry : mdScanner) {
+
+      if (!entry.getKey().getRow().equals(row))
+        break;
+      DataFileValue dfv = new DataFileValue(entry.getValue().get());
+      sizes.put(new FileRef(fs, entry.getKey()), dfv);
+    }
+
+    return sizes;
+  }
+
+  public static void rollBackSplit(Text metadataEntry, Text oldPrevEndRow, Credentials credentials, ZooLock zooLock) {
+    KeyExtent ke = new KeyExtent(metadataEntry, oldPrevEndRow);
+    Mutation m = ke.getPrevRowUpdateMutation();
+    TabletsSection.TabletColumnFamily.SPLIT_RATIO_COLUMN.putDelete(m);
+    TabletsSection.TabletColumnFamily.OLD_PREV_ROW_COLUMN.putDelete(m);
+    update(credentials, zooLock, m, new KeyExtent(metadataEntry, (Text) null));
+  }
+
+  public static void splitTablet(KeyExtent extent, Text oldPrevEndRow, double splitRatio, Credentials credentials, ZooLock zooLock) {
+    Mutation m = extent.getPrevRowUpdateMutation(); //
+
+    TabletsSection.TabletColumnFamily.SPLIT_RATIO_COLUMN.put(m, new Value(Double.toString(splitRatio).getBytes()));
+
+    TabletsSection.TabletColumnFamily.OLD_PREV_ROW_COLUMN.put(m, KeyExtent.encodePrevEndRow(oldPrevEndRow));
+    ChoppedColumnFamily.CHOPPED_COLUMN.putDelete(m);
+    update(credentials, zooLock, m, extent);
+  }
+
+  public static void finishSplit(Text metadataEntry, Map<FileRef,DataFileValue> datafileSizes, List<FileRef> highDatafilesToRemove, Credentials credentials,
+      ZooLock zooLock) {
+    Mutation m = new Mutation(metadataEntry);
+    TabletsSection.TabletColumnFamily.SPLIT_RATIO_COLUMN.putDelete(m);
+    TabletsSection.TabletColumnFamily.OLD_PREV_ROW_COLUMN.putDelete(m);
+    ChoppedColumnFamily.CHOPPED_COLUMN.putDelete(m);
+
+    for (Entry<FileRef,DataFileValue> entry : datafileSizes.entrySet()) {
+      m.put(DataFileColumnFamily.NAME, entry.getKey().meta(), new Value(entry.getValue().encode()));
+    }
+
+    for (FileRef pathToRemove : highDatafilesToRemove) {
+      m.putDelete(DataFileColumnFamily.NAME, pathToRemove.meta());
+    }
+
+    update(credentials, zooLock, m, new KeyExtent(metadataEntry, (Text) null));
+  }
+
+  public static void finishSplit(KeyExtent extent, Map<FileRef,DataFileValue> datafileSizes, List<FileRef> highDatafilesToRemove, Credentials credentials,
+      ZooLock zooLock) {
+    finishSplit(extent.getMetadataEntry(), datafileSizes, highDatafilesToRemove, credentials, zooLock);
+  }
+
+  public static void addDeleteEntries(KeyExtent extent, Set<FileRef> datafilesToDelete, Credentials credentials) throws IOException {
+
+    String tableId = extent.getTableId().toString();
+
+    // TODO could use batch writer,would need to handle failure and retry like update does - ACCUMULO-1294
+    for (FileRef pathToRemove : datafilesToDelete) {
+      update(credentials, createDeleteMutation(tableId, pathToRemove.path().toString()), extent);
+    }
+  }
+
+  public static void addDeleteEntry(String tableId, String path) throws IOException {
+    update(SystemCredentials.get(), createDeleteMutation(tableId, path), new KeyExtent(new Text(tableId), null, null));
+  }
+
+  public static Mutation createDeleteMutation(String tableId, String pathToRemove) throws IOException {
+    if (!pathToRemove.contains(":")) {
+      if (pathToRemove.startsWith("../"))
+        pathToRemove = pathToRemove.substring(2);
+      else
+        pathToRemove = "/" + tableId + pathToRemove;
+    }
+
+    Path path = VolumeManagerImpl.get().getFullPath(FileType.TABLE, pathToRemove);
+    Mutation delFlag = new Mutation(new Text(MetadataSchema.DeletesSection.getRowPrefix() + path.toString()));
+    delFlag.put(EMPTY_TEXT, EMPTY_TEXT, new Value(new byte[] {}));
+    return delFlag;
+  }
+
+  public static void removeScanFiles(KeyExtent extent, Set<FileRef> scanFiles, Credentials credentials, ZooLock zooLock) {
+    Mutation m = new Mutation(extent.getMetadataEntry());
+
+    for (FileRef pathToRemove : scanFiles)
+      m.putDelete(ScanFileColumnFamily.NAME, pathToRemove.meta());
+
+    update(credentials, zooLock, m, extent);
+  }
+
+  public static void splitDatafiles(Text table, Text midRow, double splitRatio, Map<FileRef,FileUtil.FileInfo> firstAndLastRows,
+      SortedMap<FileRef,DataFileValue> datafiles, SortedMap<FileRef,DataFileValue> lowDatafileSizes, SortedMap<FileRef,DataFileValue> highDatafileSizes,
+      List<FileRef> highDatafilesToRemove) {
+
+    for (Entry<FileRef,DataFileValue> entry : datafiles.entrySet()) {
+
+      Text firstRow = null;
+      Text lastRow = null;
+
+      boolean rowsKnown = false;
+
+      FileUtil.FileInfo mfi = firstAndLastRows.get(entry.getKey());
+
+      if (mfi != null) {
+        firstRow = mfi.getFirstRow();
+        lastRow = mfi.getLastRow();
+        rowsKnown = true;
+      }
+
+      if (rowsKnown && firstRow.compareTo(midRow) > 0) {
+        // only in high
+        long highSize = entry.getValue().getSize();
+        long highEntries = entry.getValue().getNumEntries();
+        highDatafileSizes.put(entry.getKey(), new DataFileValue(highSize, highEntries, entry.getValue().getTime()));
+      } else if (rowsKnown && lastRow.compareTo(midRow) <= 0) {
+        // only in low
+        long lowSize = entry.getValue().getSize();
+        long lowEntries = entry.getValue().getNumEntries();
+        lowDatafileSizes.put(entry.getKey(), new DataFileValue(lowSize, lowEntries, entry.getValue().getTime()));
+
+        highDatafilesToRemove.add(entry.getKey());
+      } else {
+        long lowSize = (long) Math.floor((entry.getValue().getSize() * splitRatio));
+        long lowEntries = (long) Math.floor((entry.getValue().getNumEntries() * splitRatio));
+        lowDatafileSizes.put(entry.getKey(), new DataFileValue(lowSize, lowEntries, entry.getValue().getTime()));
+
+        long highSize = (long) Math.ceil((entry.getValue().getSize() * (1.0 - splitRatio)));
+        long highEntries = (long) Math.ceil((entry.getValue().getNumEntries() * (1.0 - splitRatio)));
+        highDatafileSizes.put(entry.getKey(), new DataFileValue(highSize, highEntries, entry.getValue().getTime()));
+      }
+    }
+  }
+
+  public static void deleteTable(String tableId, boolean insertDeletes, Credentials credentials, ZooLock lock) throws AccumuloException, IOException {
+    Scanner ms = new ScannerImpl(HdfsZooInstance.getInstance(), credentials, MetadataTable.ID, Authorizations.EMPTY);
+    Text tableIdText = new Text(tableId);
+    BatchWriter bw = new BatchWriterImpl(HdfsZooInstance.getInstance(), credentials, MetadataTable.ID, new BatchWriterConfig().setMaxMemory(1000000)
+        .setMaxLatency(120000l, TimeUnit.MILLISECONDS).setMaxWriteThreads(2));
+
+    // scan metadata for our table and delete everything we find
+    Mutation m = null;
+    ms.setRange(new KeyExtent(tableIdText, null, null).toMetadataRange());
+
+    // insert deletes before deleting data from !METADATA... this makes the code fault tolerant
+    if (insertDeletes) {
+
+      ms.fetchColumnFamily(DataFileColumnFamily.NAME);
+      TabletsSection.ServerColumnFamily.DIRECTORY_COLUMN.fetch(ms);
+
+      for (Entry<Key,Value> cell : ms) {
+        Key key = cell.getKey();
+
+        if (key.getColumnFamily().equals(DataFileColumnFamily.NAME)) {
+          FileRef ref = new FileRef(VolumeManagerImpl.get(), key);
+          bw.addMutation(createDeleteMutation(tableId, ref.meta().toString()));
+        }
+
+        if (TabletsSection.ServerColumnFamily.DIRECTORY_COLUMN.hasColumns(key)) {
+          bw.addMutation(createDeleteMutation(tableId, cell.getValue().toString()));
+        }
+      }
+
+      bw.flush();
+
+      ms.clearColumns();
+    }
+
+    for (Entry<Key,Value> cell : ms) {
+      Key key = cell.getKey();
+
+      if (m == null) {
+        m = new Mutation(key.getRow());
+        if (lock != null)
+          putLockID(lock, m);
+      }
+
+      if (key.getRow().compareTo(m.getRow(), 0, m.getRow().length) != 0) {
+        bw.addMutation(m);
+        m = new Mutation(key.getRow());
+        if (lock != null)
+          putLockID(lock, m);
+      }
+      m.putDelete(key.getColumnFamily(), key.getColumnQualifier());
+    }
+
+    if (m != null)
+      bw.addMutation(m);
+
+    bw.close();
+  }
+
+  public static class LogEntry {
+    public KeyExtent extent;
+    public long timestamp;
+    public String server;
+    public String filename;
+    public int tabletId;
+    public Collection<String> logSet;
+
+    @Override
+    public String toString() {
+      return extent.toString() + " " + filename + " (" + tabletId + ")";
+    }
+
+    public String getName() {
+      return server + "/" + filename;
+    }
+
+    public byte[] toBytes() throws IOException {
+      DataOutputBuffer out = new DataOutputBuffer();
+      extent.write(out);
+      out.writeLong(timestamp);
+      out.writeUTF(server);
+      out.writeUTF(filename.toString());
+      out.write(tabletId);
+      out.write(logSet.size());
+      for (String s : logSet) {
+        out.writeUTF(s);
+      }
+      return Arrays.copyOf(out.getData(), out.getLength());
+    }
+
+    public void fromBytes(byte bytes[]) throws IOException {
+      DataInputBuffer inp = new DataInputBuffer();
+      inp.reset(bytes, bytes.length);
+      extent = new KeyExtent();
+      extent.readFields(inp);
+      timestamp = inp.readLong();
+      server = inp.readUTF();
+      filename = inp.readUTF();
+      tabletId = inp.read();
+      int count = inp.read();
+      ArrayList<String> logSet = new ArrayList<String>(count);
+      for (int i = 0; i < count; i++)
+        logSet.add(inp.readUTF());
+      this.logSet = logSet;
+    }
+
+  }
+
+  static String getZookeeperLogLocation() {
+    return ZooUtil.getRoot(HdfsZooInstance.getInstance()) + RootTable.ZROOT_TABLET_WALOGS;
+  }
+
+  public static void addLogEntry(Credentials credentials, LogEntry entry, ZooLock zooLock) {
+    if (entry.extent.isRootTablet()) {
+      String root = getZookeeperLogLocation();
+      while (true) {
+        try {
+          IZooReaderWriter zoo = ZooReaderWriter.getInstance();
+          if (zoo.isLockHeld(zooLock.getLockID())) {
+            String[] parts = entry.filename.split("/");
+            String uniqueId = parts[parts.length - 1];
+            zoo.putPersistentData(root + "/" + uniqueId, entry.toBytes(), NodeExistsPolicy.OVERWRITE);
+          }
+          break;
+        } catch (KeeperException e) {
+          log.error(e, e);
+        } catch (InterruptedException e) {
+          log.error(e, e);
+        } catch (IOException e) {
+          log.error(e, e);
+        }
+        UtilWaitThread.sleep(1000);
+      }
+    } else {
+      String value = StringUtil.join(entry.logSet, ";") + "|" + entry.tabletId;
+      Mutation m = new Mutation(entry.extent.getMetadataEntry());
+      m.put(LogColumnFamily.NAME, new Text(entry.server + "/" + entry.filename), new Value(value.getBytes()));
+      update(credentials, zooLock, m, entry.extent);
+    }
+  }
+
+  public static LogEntry entryFromKeyValue(Key key, Value value) {
+    MetadataTableUtil.LogEntry e = new MetadataTableUtil.LogEntry();
+    e.extent = new KeyExtent(key.getRow(), EMPTY_TEXT);
+    String[] parts = key.getColumnQualifier().toString().split("/", 2);
+    e.server = parts[0];
+    e.filename = parts[1];
+    parts = value.toString().split("\\|");
+    e.tabletId = Integer.parseInt(parts[1]);
+    e.logSet = Arrays.asList(parts[0].split(";"));
+    e.timestamp = key.getTimestamp();
+    return e;
+  }
+
+  public static String getRootTabletDir() throws IOException {
+    IZooReaderWriter zoo = ZooReaderWriter.getInstance();
+    String zpath = ZooUtil.getRoot(HdfsZooInstance.getInstance()) + RootTable.ZROOT_TABLET_PATH;
+    try {
+      return new String(zoo.getData(zpath, null), Constants.UTF8);
+    } catch (KeeperException e) {
+      throw new IOException(e);
+    } catch (InterruptedException e) {
+      throw new IOException(e);
+    }
+  }
+
+  public static Pair<List<LogEntry>,SortedMap<FileRef,DataFileValue>> getFileAndLogEntries(Credentials credentials, KeyExtent extent) throws KeeperException,
+      InterruptedException, IOException {
+    ArrayList<LogEntry> result = new ArrayList<LogEntry>();
+    TreeMap<FileRef,DataFileValue> sizes = new TreeMap<FileRef,DataFileValue>();
+
+    VolumeManager fs = VolumeManagerImpl.get();
+    if (extent.isRootTablet()) {
+      getRootLogEntries(result);
+      Path rootDir = new Path(getRootTabletDir());
+      FileStatus[] files = fs.listStatus(rootDir);
+      for (FileStatus fileStatus : files) {
+        if (fileStatus.getPath().toString().endsWith("_tmp")) {
+          continue;
+        }
+        DataFileValue dfv = new DataFileValue(0, 0);
+        sizes.put(new FileRef(fileStatus.getPath().toString(), fileStatus.getPath()), dfv);
+      }
+
+    } else {
+      String systemTableToCheck = extent.isMeta() ? RootTable.ID : MetadataTable.ID;
+      Scanner scanner = new ScannerImpl(HdfsZooInstance.getInstance(), credentials, systemTableToCheck, Authorizations.EMPTY);
+      scanner.fetchColumnFamily(LogColumnFamily.NAME);
+      scanner.fetchColumnFamily(DataFileColumnFamily.NAME);
+      scanner.setRange(extent.toMetadataRange());
+
+      for (Entry<Key,Value> entry : scanner) {
+        if (!entry.getKey().getRow().equals(extent.getMetadataEntry())) {
+          throw new RuntimeException("Unexpected row " + entry.getKey().getRow() + " expected " + extent.getMetadataEntry());
+        }
+
+        if (entry.getKey().getColumnFamily().equals(LogColumnFamily.NAME)) {
+          result.add(entryFromKeyValue(entry.getKey(), entry.getValue()));
+        } else if (entry.getKey().getColumnFamily().equals(DataFileColumnFamily.NAME)) {
+          DataFileValue dfv = new DataFileValue(entry.getValue().get());
+          sizes.put(new FileRef(fs, entry.getKey()), dfv);
+        } else {
+          throw new RuntimeException("Unexpected col fam " + entry.getKey().getColumnFamily());
+        }
+      }
+    }
+
+    return new Pair<List<LogEntry>,SortedMap<FileRef,DataFileValue>>(result, sizes);
+  }
+
+  public static List<LogEntry> getLogEntries(Credentials credentials, KeyExtent extent) throws IOException, KeeperException, InterruptedException {
+    log.info("Scanning logging entries for " + extent);
+    ArrayList<LogEntry> result = new ArrayList<LogEntry>();
+    if (extent.equals(RootTable.EXTENT)) {
+      log.info("Getting logs for root tablet from zookeeper");
+      getRootLogEntries(result);
+    } else {
+      log.info("Scanning metadata for logs used for tablet " + extent);
+      Scanner scanner = getTabletLogScanner(credentials, extent);
+      Text pattern = extent.getMetadataEntry();
+      for (Entry<Key,Value> entry : scanner) {
+        Text row = entry.getKey().getRow();
+        if (entry.getKey().getColumnFamily().equals(LogColumnFamily.NAME)) {
+          if (row.equals(pattern)) {
+            result.add(entryFromKeyValue(entry.getKey(), entry.getValue()));
+          }
+        }
+      }
+    }
+
+    Collections.sort(result, new Comparator<LogEntry>() {
+      @Override
+      public int compare(LogEntry o1, LogEntry o2) {
+        long diff = o1.timestamp - o2.timestamp;
+        if (diff < 0)
+          return -1;
+        if (diff > 0)
+          return 1;
+        return 0;
+      }
+    });
+    log.info("Returning logs " + result + " for extent " + extent);
+    return result;
+  }
+
+  private static void getRootLogEntries(ArrayList<LogEntry> result) throws KeeperException, InterruptedException, IOException {
+    IZooReaderWriter zoo = ZooReaderWriter.getInstance();
+    String root = getZookeeperLogLocation();
+    // there's a little race between getting the children and fetching
+    // the data. The log can be removed in between.
+    while (true) {
+      result.clear();
+      for (String child : zoo.getChildren(root)) {
+        LogEntry e = new LogEntry();
+        try {
+          e.fromBytes(zoo.getData(root + "/" + child, null));
+          // upgrade from !0;!0<< -> !!R<<
+          e.extent = RootTable.EXTENT;
+          result.add(e);
+        } catch (KeeperException.NoNodeException ex) {
+          continue;
+        }
+      }
+      break;
+    }
+  }
+
+  private static Scanner getTabletLogScanner(Credentials credentials, KeyExtent extent) {
+    String tableId = MetadataTable.ID;
+    if (extent.isMeta())
+      tableId = RootTable.ID;
+    Scanner scanner = new ScannerImpl(HdfsZooInstance.getInstance(), credentials, tableId, Authorizations.EMPTY);
+    scanner.fetchColumnFamily(LogColumnFamily.NAME);
+    Text start = extent.getMetadataEntry();
+    Key endKey = new Key(start, LogColumnFamily.NAME);
+    endKey = endKey.followingKey(PartialKey.ROW_COLFAM);
+    scanner.setRange(new Range(new Key(start), endKey));
+    return scanner;
+  }
+
+  static class LogEntryIterator implements Iterator<LogEntry> {
+
+    Iterator<LogEntry> zookeeperEntries = null;
+    Iterator<LogEntry> rootTableEntries = null;
+    Iterator<Entry<Key,Value>> metadataEntries = null;
+
+    LogEntryIterator(Credentials creds) throws IOException, KeeperException, InterruptedException {
+      zookeeperEntries = getLogEntries(creds, RootTable.EXTENT).iterator();
+      rootTableEntries = getLogEntries(creds, new KeyExtent(new Text(MetadataTable.ID), null, null)).iterator();
+      try {
+        Scanner scanner = HdfsZooInstance.getInstance().getConnector(creds.getPrincipal(), creds.getToken())
+            .createScanner(MetadataTable.NAME, Authorizations.EMPTY);
+        log.info("Setting range to " + MetadataSchema.TabletsSection.getRange());
+        scanner.setRange(MetadataSchema.TabletsSection.getRange());
+        scanner.fetchColumnFamily(LogColumnFamily.NAME);
+        metadataEntries = scanner.iterator();
+      } catch (Exception ex) {
+        throw new IOException(ex);
+      }
+    }
+
+    @Override
+    public boolean hasNext() {
+      return zookeeperEntries.hasNext() || rootTableEntries.hasNext() || metadataEntries.hasNext();
+    }
+
+    @Override
+    public LogEntry next() {
+      if (zookeeperEntries.hasNext()) {
+        return zookeeperEntries.next();
+      }
+      if (rootTableEntries.hasNext()) {
+        return rootTableEntries.next();
+      }
+      Entry<Key,Value> entry = metadataEntries.next();
+      return entryFromKeyValue(entry.getKey(), entry.getValue());
+    }
+
+    @Override
+    public void remove() {
+      throw new UnsupportedOperationException();
+    }
+  }
+
+  public static Iterator<LogEntry> getLogEntries(Credentials creds) throws IOException, KeeperException, InterruptedException {
+    return new LogEntryIterator(creds);
+  }
+
+  public static void removeUnusedWALEntries(KeyExtent extent, List<LogEntry> logEntries, ZooLock zooLock) {
+    for (LogEntry entry : logEntries) {
+      if (entry.extent.isRootTablet()) {
+        String root = getZookeeperLogLocation();
+        while (true) {
+          try {
+            IZooReaderWriter zoo = ZooReaderWriter.getInstance();
+            if (zoo.isLockHeld(zooLock.getLockID()))
+              zoo.recursiveDelete(root + "/" + entry.filename, NodeMissingPolicy.SKIP);
+            break;
+          } catch (Exception e) {
+            log.error(e, e);
+          }
+          UtilWaitThread.sleep(1000);
+        }
+      } else {
+        Mutation m = new Mutation(entry.extent.getMetadataEntry());
+        m.putDelete(LogColumnFamily.NAME, new Text(entry.server + "/" + entry.filename));
+        update(SystemCredentials.get(), zooLock, m, entry.extent);
+      }
+    }
+  }
+
+  private static void getFiles(Set<String> files, Map<Key,Value> tablet, String srcTableId) {
+    for (Entry<Key,Value> entry : tablet.entrySet()) {
+      if (entry.getKey().getColumnFamily().equals(DataFileColumnFamily.NAME)) {
+        String cf = entry.getKey().getColumnQualifier().toString();
+        if (srcTableId != null && !cf.startsWith("../") && !cf.contains(":")) {
+          cf = "../" + srcTableId + entry.getKey().getColumnQualifier();
+        }
+        files.add(cf);
+      }
+    }
+  }
+
+  private static Mutation createCloneMutation(String srcTableId, String tableId, Map<Key,Value> tablet) {
+
+    KeyExtent ke = new KeyExtent(tablet.keySet().iterator().next().getRow(), (Text) null);
+    Mutation m = new Mutation(KeyExtent.getMetadataEntry(new Text(tableId), ke.getEndRow()));
+
+    for (Entry<Key,Value> entry : tablet.entrySet()) {
+      if (entry.getKey().getColumnFamily().equals(DataFileColumnFamily.NAME)) {
+        String cf = entry.getKey().getColumnQualifier().toString();
+        if (!cf.startsWith("../") && !cf.contains(":"))
+          cf = "../" + srcTableId + entry.getKey().getColumnQualifier();
+        m.put(entry.getKey().getColumnFamily(), new Text(cf), entry.getValue());
+      } else if (entry.getKey().getColumnFamily().equals(TabletsSection.CurrentLocationColumnFamily.NAME)) {
+        m.put(TabletsSection.LastLocationColumnFamily.NAME, entry.getKey().getColumnQualifier(), entry.getValue());
+      } else if (entry.getKey().getColumnFamily().equals(TabletsSection.LastLocationColumnFamily.NAME)) {
+        // skip
+      } else {
+        m.put(entry.getKey().getColumnFamily(), entry.getKey().getColumnQualifier(), entry.getValue());
+      }
+    }
+    return m;
+  }
+
+  private static Scanner createCloneScanner(String tableId, Connector conn) throws TableNotFoundException {
+    Scanner mscanner = new IsolatedScanner(conn.createScanner(MetadataTable.NAME, Authorizations.EMPTY));
+    mscanner.setRange(new KeyExtent(new Text(tableId), null, null).toMetadataRange());
+    mscanner.fetchColumnFamily(DataFileColumnFamily.NAME);
+    mscanner.fetchColumnFamily(TabletsSection.CurrentLocationColumnFamily.NAME);
+    mscanner.fetchColumnFamily(TabletsSection.LastLocationColumnFamily.NAME);
+    mscanner.fetchColumnFamily(ClonedColumnFamily.NAME);
+    TabletsSection.TabletColumnFamily.PREV_ROW_COLUMN.fetch(mscanner);
+    TabletsSection.ServerColumnFamily.TIME_COLUMN.fetch(mscanner);
+    return mscanner;
+  }
+
+  static void initializeClone(String srcTableId, String tableId, Connector conn, BatchWriter bw) throws TableNotFoundException, MutationsRejectedException {
+    TabletIterator ti = new TabletIterator(createCloneScanner(srcTableId, conn), new KeyExtent(new Text(srcTableId), null, null).toMetadataRange(), true, true);
+
+    if (!ti.hasNext())
+      throw new RuntimeException(" table deleted during clone?  srcTableId = " + srcTableId);
+
+    while (ti.hasNext())
+      bw.addMutation(createCloneMutation(srcTableId, tableId, ti.next()));
+
+    bw.flush();
+  }
+
+  static int compareEndRows(Text endRow1, Text endRow2) {
+    return new KeyExtent(new Text("0"), endRow1, null).compareTo(new KeyExtent(new Text("0"), endRow2, null));
+  }
+
+  static int checkClone(String srcTableId, String tableId, Connector conn, BatchWriter bw) throws TableNotFoundException, MutationsRejectedException {
+    TabletIterator srcIter = new TabletIterator(createCloneScanner(srcTableId, conn), new KeyExtent(new Text(srcTableId), null, null).toMetadataRange(), true,
+        true);
+    TabletIterator cloneIter = new TabletIterator(createCloneScanner(tableId, conn), new KeyExtent(new Text(tableId), null, null).toMetadataRange(), true, true);
+
+    if (!cloneIter.hasNext() || !srcIter.hasNext())
+      throw new RuntimeException(" table deleted during clone?  srcTableId = " + srcTableId + " tableId=" + tableId);
+
+    int rewrites = 0;
+
+    while (cloneIter.hasNext()) {
+      Map<Key,Value> cloneTablet = cloneIter.next();
+      Text cloneEndRow = new KeyExtent(cloneTablet.keySet().iterator().next().getRow(), (Text) null).getEndRow();
+      HashSet<String> cloneFiles = new HashSet<String>();
+
+      boolean cloneSuccessful = false;
+      for (Entry<Key,Value> entry : cloneTablet.entrySet()) {
+        if (entry.getKey().getColumnFamily().equals(ClonedColumnFamily.NAME)) {
+          cloneSuccessful = true;
+          break;
+        }
+      }
+
+      if (!cloneSuccessful)
+        getFiles(cloneFiles, cloneTablet, null);
+
+      List<Map<Key,Value>> srcTablets = new ArrayList<Map<Key,Value>>();
+      Map<Key,Value> srcTablet = srcIter.next();
+      srcTablets.add(srcTablet);
+
+      Text srcEndRow = new KeyExtent(srcTablet.keySet().iterator().next().getRow(), (Text) null).getEndRow();
+
+      int cmp = compareEndRows(cloneEndRow, srcEndRow);
+      if (cmp < 0)
+        throw new TabletIterator.TabletDeletedException("Tablets deleted from src during clone : " + cloneEndRow + " " + srcEndRow);
+
+      HashSet<String> srcFiles = new HashSet<String>();
+      if (!cloneSuccessful)
+        getFiles(srcFiles, srcTablet, srcTableId);
+
+      while (cmp > 0) {
+        srcTablet = srcIter.next();
+        srcTablets.add(srcTablet);
+        srcEndRow = new KeyExtent(srcTablet.keySet().iterator().next().getRow(), (Text) null).getEndRow();
+        cmp = compareEndRows(cloneEndRow, srcEndRow);
+        if (cmp < 0)
+          throw new TabletIterator.TabletDeletedException("Tablets deleted from src during clone : " + cloneEndRow + " " + srcEndRow);
+
+        if (!cloneSuccessful)
+          getFiles(srcFiles, srcTablet, srcTableId);
+      }
+
+      if (cloneSuccessful)
+        continue;
+
+      if (!srcFiles.containsAll(cloneFiles)) {
+        // delete existing cloned tablet entry
+        Mutation m = new Mutation(cloneTablet.keySet().iterator().next().getRow());
+
+        for (Entry<Key,Value> entry : cloneTablet.entrySet()) {
+          Key k = entry.getKey();
+          m.putDelete(k.getColumnFamily(), k.getColumnQualifier(), k.getTimestamp());
+        }
+
+        bw.addMutation(m);
+
+        for (Map<Key,Value> st : srcTablets)
+          bw.addMutation(createCloneMutation(srcTableId, tableId, st));
+
+        rewrites++;
+      } else {
+        // write out marker that this tablet was successfully cloned
+        Mutation m = new Mutation(cloneTablet.keySet().iterator().next().getRow());
+        m.put(ClonedColumnFamily.NAME, new Text(""), new Value("OK".getBytes()));
+        bw.addMutation(m);
+      }
+    }
+
+    bw.flush();
+    return rewrites;
+  }
+
+  public static void cloneTable(Instance instance, String srcTableId, String tableId, VolumeManager volumeManager) throws Exception {
+
+    Connector conn = instance.getConnector(SystemCredentials.get().getPrincipal(), SystemCredentials.get().getToken());
+    BatchWriter bw = conn.createBatchWriter(MetadataTable.NAME, new BatchWriterConfig());
+
+    while (true) {
+
+      try {
+        initializeClone(srcTableId, tableId, conn, bw);
+
+        // the following loop looks changes in the file that occurred during the copy.. if files were dereferenced then they could have been GCed
+
+        while (true) {
+          int rewrites = checkClone(srcTableId, tableId, conn, bw);
+
+          if (rewrites == 0)
+            break;
+        }
+
+        bw.flush();
+        break;
+
+      } catch (TabletIterator.TabletDeletedException tde) {
+        // tablets were merged in the src table
+        bw.flush();
+
+        // delete what we have cloned and try again
+        deleteTable(tableId, false, SystemCredentials.get(), null);
+
+        log.debug("Tablets merged in table " + srcTableId + " while attempting to clone, trying again");
+
+        UtilWaitThread.sleep(100);
+      }
+    }
+
+    // delete the clone markers and create directory entries
+    Scanner mscanner = conn.createScanner(MetadataTable.NAME, Authorizations.EMPTY);
+    mscanner.setRange(new KeyExtent(new Text(tableId), null, null).toMetadataRange());
+    mscanner.fetchColumnFamily(ClonedColumnFamily.NAME);
+
+    int dirCount = 0;
+
+    for (Entry<Key,Value> entry : mscanner) {
+      Key k = entry.getKey();
+      Mutation m = new Mutation(k.getRow());
+      m.putDelete(k.getColumnFamily(), k.getColumnQualifier());
+      String dir = volumeManager.choose(ServerConstants.getTablesDirs()) + "/" + tableId
+          + new String(FastFormat.toZeroPaddedString(dirCount++, 8, 16, "/c-".getBytes()));
+      TabletsSection.ServerColumnFamily.DIRECTORY_COLUMN.put(m, new Value(dir.getBytes()));
+      bw.addMutation(m);
+    }
+
+    bw.close();
+
+  }
+
+  public static void chopped(KeyExtent extent, ZooLock zooLock) {
+    Mutation m = new Mutation(extent.getMetadataEntry());
+    ChoppedColumnFamily.CHOPPED_COLUMN.put(m, new Value("chopped".getBytes()));
+    update(SystemCredentials.get(), zooLock, m, extent);
+  }
+
+  public static void removeBulkLoadEntries(Connector conn, String tableId, long tid) throws Exception {
+    Scanner mscanner = new IsolatedScanner(conn.createScanner(MetadataTable.NAME, Authorizations.EMPTY));
+    mscanner.setRange(new KeyExtent(new Text(tableId), null, null).toMetadataRange());
+    mscanner.fetchColumnFamily(TabletsSection.BulkFileColumnFamily.NAME);
+    BatchWriter bw = conn.createBatchWriter(MetadataTable.NAME, new BatchWriterConfig());
+    for (Entry<Key,Value> entry : mscanner) {
+      log.debug("Looking at entry " + entry + " with tid " + tid);
+      if (Long.parseLong(entry.getValue().toString()) == tid) {
+        log.debug("deleting entry " + entry);
+        Mutation m = new Mutation(entry.getKey().getRow());
+        m.putDelete(entry.getKey().getColumnFamily(), entry.getKey().getColumnQualifier());
+        bw.addMutation(m);
+      }
+    }
+    bw.close();
+  }
+
+  public static List<FileRef> getBulkFilesLoaded(Connector conn, KeyExtent extent, long tid) throws IOException {
+    List<FileRef> result = new ArrayList<FileRef>();
+    try {
+      VolumeManager fs = VolumeManagerImpl.get();
+      Scanner mscanner = new IsolatedScanner(conn.createScanner(extent.isMeta() ? RootTable.NAME : MetadataTable.NAME, Authorizations.EMPTY));
+      mscanner.setRange(extent.toMetadataRange());
+      mscanner.fetchColumnFamily(TabletsSection.BulkFileColumnFamily.NAME);
+      for (Entry<Key,Value> entry : mscanner) {
+        if (Long.parseLong(entry.getValue().toString()) == tid) {
+          result.add(new FileRef(fs, entry.getKey()));
+        }
+      }
+      return result;
+    } catch (TableNotFoundException ex) {
+      // unlikely
+      throw new RuntimeException("Onos! teh metadata table has vanished!!");
+    }
+  }
+
+  public static Map<FileRef,Long> getBulkFilesLoaded(Credentials credentials, KeyExtent extent) throws IOException {
+    Text metadataRow = extent.getMetadataEntry();
+    Map<FileRef,Long> ret = new HashMap<FileRef,Long>();
+
+    VolumeManager fs = VolumeManagerImpl.get();
+    Scanner scanner = new ScannerImpl(HdfsZooInstance.getInstance(), credentials, extent.isMeta() ? RootTable.ID : MetadataTable.ID, Authorizations.EMPTY);
+    scanner.setRange(new Range(metadataRow));
+    scanner.fetchColumnFamily(TabletsSection.BulkFileColumnFamily.NAME);
+    for (Entry<Key,Value> entry : scanner) {
+      Long tid = Long.parseLong(entry.getValue().toString());
+      ret.put(new FileRef(fs, entry.getKey()), tid);
+    }
+    return ret;
+  }
+
+  public static void addBulkLoadInProgressFlag(String path) {
+
+    Mutation m = new Mutation(MetadataSchema.BlipSection.getRowPrefix() + path);
+    m.put(EMPTY_TEXT, EMPTY_TEXT, new Value(new byte[] {}));
+
+    // new KeyExtent is only added to force update to write to the metadata table, not the root table
+    // because bulk loads aren't supported to the metadata table
+    update(SystemCredentials.get(), m, new KeyExtent(new Text("anythingNotMetadata"), null, null));
+  }
+
+  public static void removeBulkLoadInProgressFlag(String path) {
+
+    Mutation m = new Mutation(MetadataSchema.BlipSection.getRowPrefix() + path);
+    m.putDelete(EMPTY_TEXT, EMPTY_TEXT);
+
+    // new KeyExtent is only added to force update to write to the metadata table, not the root table
+    // because bulk loads aren't supported to the metadata table
+    update(SystemCredentials.get(), m, new KeyExtent(new Text("anythingNotMetadata"), null, null));
+  }
+
+  public static void moveMetaDeleteMarkers(Instance instance, Credentials creds) {
+    // move old delete markers to new location, to standardize table schema between all metadata tables
+    byte[] EMPTY_BYTES = new byte[0];
+    Scanner scanner = new ScannerImpl(instance, creds, RootTable.ID, Authorizations.EMPTY);
+    String oldDeletesPrefix = "!!~del";
+    Range oldDeletesRange = new Range(oldDeletesPrefix, true, "!!~dem", false);
+    scanner.setRange(oldDeletesRange);
+    for (Entry<Key,Value> entry : scanner) {
+      String row = entry.getKey().getRow().toString();
+      if (row.startsWith(oldDeletesPrefix)) {
+        String filename = row.substring(oldDeletesPrefix.length());
+        // add the new entry first
+        log.info("Moving " + filename + " marker in " + RootTable.NAME);
+        Mutation m = new Mutation(MetadataSchema.DeletesSection.getRowPrefix() + filename);
+        m.put(EMPTY_BYTES, EMPTY_BYTES, EMPTY_BYTES);
+        update(creds, m, RootTable.EXTENT);
+        // remove the old entry
+        m = new Mutation(entry.getKey().getRow());
+        m.putDelete(EMPTY_BYTES, EMPTY_BYTES);
+        update(creds, m, RootTable.OLD_EXTENT);
+      } else {
+        break;
+      }
+    }
+
+  }
+
+  public static SortedMap<Text,SortedMap<ColumnFQ,Value>> getTabletEntries(SortedMap<Key,Value> tabletKeyValues, List<ColumnFQ> columns) {
+    TreeMap<Text,SortedMap<ColumnFQ,Value>> tabletEntries = new TreeMap<Text,SortedMap<ColumnFQ,Value>>();
+
+    HashSet<ColumnFQ> colSet = null;
+    if (columns != null) {
+      colSet = new HashSet<ColumnFQ>(columns);
+    }
+
+    for (Entry<Key,Value> entry : tabletKeyValues.entrySet()) {
+
+      if (columns != null && !colSet.contains(new ColumnFQ(entry.getKey()))) {
+        continue;
+      }
+
+      Text row = entry.getKey().getRow();
+
+      SortedMap<ColumnFQ,Value> colVals = tabletEntries.get(row);
+      if (colVals == null) {
+        colVals = new TreeMap<ColumnFQ,Value>();
+        tabletEntries.put(row, colVals);
+      }
+
+      colVals.put(new ColumnFQ(entry.getKey()), entry.getValue());
+    }
+
+    return tabletEntries;
+  }
+
+  public static void convertRootTabletToRootTable(Instance instance, SystemCredentials systemCredentials) throws KeeperException, InterruptedException {
+    ZooReaderWriter zoo = ZooReaderWriter.getInstance();
+    if (zoo.exists(ZooUtil.getRoot(instance) + "/tables/" + RootTable.ID))
+      return;
+    TableManager.prepareNewTableState(instance.getInstanceID(), RootTable.ID, RootTable.NAME, TableState.ONLINE, NodeExistsPolicy.FAIL);
+  }
+
+}

http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/OfflineMetadataScanner.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/OfflineMetadataScanner.java b/server/base/src/main/java/org/apache/accumulo/server/util/OfflineMetadataScanner.java
new file mode 100644
index 0000000..cefec22
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/OfflineMetadataScanner.java
@@ -0,0 +1,281 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NoSuchElementException;
+import java.util.Set;
+
+import org.apache.accumulo.core.client.Scanner;
+import org.apache.accumulo.core.client.impl.ScannerOptions;
+import org.apache.accumulo.core.conf.AccumuloConfiguration;
+import org.apache.accumulo.core.data.Column;
+import org.apache.accumulo.core.data.Key;
+import org.apache.accumulo.core.data.Range;
+import org.apache.accumulo.core.data.Value;
+import org.apache.accumulo.core.file.FileOperations;
+import org.apache.accumulo.core.file.FileSKVIterator;
+import org.apache.accumulo.core.iterators.SortedKeyValueIterator;
+import org.apache.accumulo.core.iterators.system.ColumnFamilySkippingIterator;
+import org.apache.accumulo.core.iterators.system.ColumnQualifierFilter;
+import org.apache.accumulo.core.iterators.system.DeletingIterator;
+import org.apache.accumulo.core.iterators.system.MultiIterator;
+import org.apache.accumulo.core.iterators.system.VisibilityFilter;
+import org.apache.accumulo.core.iterators.user.VersioningIterator;
+import org.apache.accumulo.core.metadata.RootTable;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.DataFileColumnFamily;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.LogColumnFamily;
+import org.apache.accumulo.core.security.Authorizations;
+import org.apache.accumulo.core.util.LocalityGroupUtil;
+import org.apache.accumulo.core.util.TextUtil;
+import org.apache.accumulo.server.client.HdfsZooInstance;
+import org.apache.accumulo.server.conf.ServerConfiguration;
+import org.apache.accumulo.server.fs.VolumeManager;
+import org.apache.accumulo.server.fs.VolumeManagerImpl;
+import org.apache.accumulo.server.util.MetadataTableUtil.LogEntry;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+public class OfflineMetadataScanner extends ScannerOptions implements Scanner {
+  
+  private Set<String> allFiles = new HashSet<String>();
+  private Range range = new Range();
+  private final VolumeManager fs;
+  private final AccumuloConfiguration conf;
+  
+  private List<SortedKeyValueIterator<Key,Value>> openMapFiles(Collection<String> files, VolumeManager fs, AccumuloConfiguration conf) throws IOException {
+    List<SortedKeyValueIterator<Key,Value>> readers = new ArrayList<SortedKeyValueIterator<Key,Value>>();
+    for (String file : files) {
+      FileSystem ns = fs.getFileSystemByPath(new Path(file));
+      FileSKVIterator reader = FileOperations.getInstance().openReader(file, true, ns, ns.getConf(), conf);
+      readers.add(reader);
+    }
+    return readers;
+  }
+  
+  private SortedKeyValueIterator<Key,Value> createSystemIter(Range r, List<SortedKeyValueIterator<Key,Value>> readers, HashSet<Column> columns)
+      throws IOException {
+    MultiIterator multiIterator = new MultiIterator(readers, false);
+    DeletingIterator delIter = new DeletingIterator(multiIterator, false);
+    ColumnFamilySkippingIterator cfsi = new ColumnFamilySkippingIterator(delIter);
+    ColumnQualifierFilter colFilter = new ColumnQualifierFilter(cfsi, columns);
+    VisibilityFilter visFilter = new VisibilityFilter(colFilter, Authorizations.EMPTY, new byte[0]);
+    
+    visFilter.seek(r, LocalityGroupUtil.EMPTY_CF_SET, false);
+    
+    VersioningIterator vi = new VersioningIterator();
+    Map<String,String> opts = new HashMap<String,String>();
+    opts.put("maxVersions", "1");
+    vi.init(visFilter, opts, null);
+    
+    return vi;
+  }
+  
+  private static class MyEntry implements Map.Entry<Key,Value> {
+    
+    private Key k;
+    private Value v;
+    
+    MyEntry(Key k, Value v) {
+      this.k = k;
+      this.v = v;
+    }
+    
+    @Override
+    public Key getKey() {
+      return k;
+    }
+    
+    @Override
+    public Value getValue() {
+      return v;
+    }
+    
+    @Override
+    public Value setValue(Value value) {
+      throw new UnsupportedOperationException();
+    }
+    
+  }
+  
+  public OfflineMetadataScanner(AccumuloConfiguration conf, VolumeManager fs) throws IOException {
+    super();
+    this.fs = fs;
+    this.conf = conf;
+    List<LogEntry> rwal;
+    try {
+      rwal = MetadataTableUtil.getLogEntries(null, RootTable.EXTENT);
+    } catch (Exception e) {
+      throw new RuntimeException("Failed to check if root tablet has write ahead log entries", e);
+    }
+    
+    if (rwal.size() > 0) {
+      throw new RuntimeException("Root tablet has write ahead logs, can not scan offline");
+    }
+    
+    FileStatus[] rootFiles = fs.listStatus(new Path(MetadataTableUtil.getRootTabletDir()));
+    
+    for (FileStatus rootFile : rootFiles) {
+      allFiles.add(rootFile.getPath().toString());
+    }
+    
+    List<SortedKeyValueIterator<Key,Value>> readers = openMapFiles(allFiles, fs, conf);
+    
+    HashSet<Column> columns = new HashSet<Column>();
+    columns.add(new Column(TextUtil.getBytes(DataFileColumnFamily.NAME), null, null));
+    columns.add(new Column(TextUtil.getBytes(LogColumnFamily.NAME), null, null));
+    
+    SortedKeyValueIterator<Key,Value> ssi = createSystemIter(new Range(), readers, columns);
+    
+    int walogs = 0;
+    
+    while (ssi.hasTop()) {
+      if (ssi.getTopKey().compareColumnFamily(DataFileColumnFamily.NAME) == 0) {
+        allFiles.add(fs.getFullPath(ssi.getTopKey()).toString());
+      } else {
+        walogs++;
+      }
+      ssi.next();
+    }
+    
+    closeReaders(readers);
+    
+    if (walogs > 0) {
+      throw new RuntimeException("Metadata tablets have write ahead logs, can not scan offline");
+    }
+  }
+  
+  private void closeReaders(List<SortedKeyValueIterator<Key,Value>> readers) throws IOException {
+    for (SortedKeyValueIterator<Key,Value> reader : readers) {
+      ((FileSKVIterator) reader).close();
+    }
+  }
+  
+  @Override
+  public int getBatchSize() {
+    throw new UnsupportedOperationException();
+  }
+  
+  @Override
+  public Range getRange() {
+    return range;
+  }
+  
+  @Deprecated
+  @Override
+  public int getTimeOut() {
+    throw new UnsupportedOperationException();
+  }
+  
+  @Override
+  public Iterator<Entry<Key,Value>> iterator() {
+    
+    final SortedKeyValueIterator<Key,Value> ssi;
+    final List<SortedKeyValueIterator<Key,Value>> readers;
+    try {
+      readers = openMapFiles(allFiles, fs, conf);
+      ssi = createSystemIter(range, readers, new HashSet<Column>(getFetchedColumns()));
+    } catch (IOException e) {
+      throw new RuntimeException(e);
+    }
+    
+    return new Iterator<Entry<Key,Value>>() {
+      
+      @Override
+      public boolean hasNext() {
+        return ssi.hasTop() && range.contains(ssi.getTopKey());
+      }
+      
+      @Override
+      public Entry<Key,Value> next() {
+        if (!ssi.hasTop()) {
+          throw new NoSuchElementException();
+        }
+        
+        MyEntry e = new MyEntry(new Key(ssi.getTopKey()), new Value(ssi.getTopValue()));
+        try {
+          ssi.next();
+        } catch (IOException e1) {
+          throw new RuntimeException(e1);
+        }
+        return e;
+      }
+      
+      @Override
+      public void remove() {
+        throw new UnsupportedOperationException();
+      }
+      
+    };
+  }
+  
+  @Override
+  public void setBatchSize(int size) {
+    throw new UnsupportedOperationException();
+  }
+  
+  @Override
+  public void setRange(Range range) {
+    this.range = range;
+  }
+  
+  @Deprecated
+  @Override
+  public void setTimeOut(int timeOut) {
+    throw new UnsupportedOperationException();
+  }
+  
+  @Override
+  public void enableIsolation() {
+    // should always give an isolated view since it is scanning immutable files
+  }
+  
+  @Override
+  public void disableIsolation() {
+    
+  }
+  
+  public static void main(String[] args) throws IOException {
+    ServerConfiguration conf = new ServerConfiguration(HdfsZooInstance.getInstance());
+    VolumeManager fs = VolumeManagerImpl.get();
+    OfflineMetadataScanner scanner = new OfflineMetadataScanner(conf.getConfiguration(), fs);
+    scanner.setRange(MetadataSchema.TabletsSection.getRange());
+    for (Entry<Key,Value> entry : scanner)
+      System.out.println(entry.getKey() + " " + entry.getValue());
+  }
+
+  @Override
+  public long getReadaheadThreshold() {
+    throw new UnsupportedOperationException();
+  }
+
+  @Override
+  public void setReadaheadThreshold(long batches) {
+    throw new UnsupportedOperationException();
+  }
+  
+}

http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/PortUtils.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/PortUtils.java b/server/base/src/main/java/org/apache/accumulo/server/util/PortUtils.java
new file mode 100644
index 0000000..f710b0f
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/PortUtils.java
@@ -0,0 +1,51 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.io.IOException;
+import java.net.ServerSocket;
+import java.util.Random;
+
+public class PortUtils {
+
+  public static int getRandomFreePort() {
+    Random r = new Random();
+    int count = 0;
+    
+    while (count < 13) {
+      int port = r.nextInt((1 << 16) - 1024) + 1024;
+      
+      ServerSocket so = null;
+      try {
+        so = new ServerSocket(port);
+        so.setReuseAddress(true);
+        return port;
+      } catch (IOException ioe) {
+        
+      } finally {
+        if (so != null)
+          try {
+            so.close();
+          } catch (IOException e) {}
+      }
+      
+    }
+    
+    throw new RuntimeException("Unable to find port");
+  }
+  
+}

http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/RandomWriter.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/RandomWriter.java b/server/base/src/main/java/org/apache/accumulo/server/util/RandomWriter.java
new file mode 100644
index 0000000..0666297
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/RandomWriter.java
@@ -0,0 +1,108 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.util.Iterator;
+import java.util.Random;
+
+import org.apache.accumulo.core.cli.BatchWriterOpts;
+import org.apache.accumulo.core.client.BatchWriter;
+import org.apache.accumulo.core.client.Connector;
+import org.apache.accumulo.core.data.Mutation;
+import org.apache.accumulo.core.data.Value;
+import org.apache.accumulo.server.cli.ClientOnDefaultTable;
+import org.apache.hadoop.io.Text;
+import org.apache.log4j.Logger;
+
+import com.beust.jcommander.Parameter;
+
+public class RandomWriter {
+  
+  private static String table_name = "test_write_table";
+  private static int num_columns_per_row = 1;
+  private static int num_payload_bytes = 1024;
+  private static final Logger log = Logger.getLogger(RandomWriter.class);
+  
+  public static class RandomMutationGenerator implements Iterable<Mutation>, Iterator<Mutation> {
+    private long max_mutations;
+    private int mutations_so_far = 0;
+    private Random r = new Random();
+    private static final Logger log = Logger.getLogger(RandomMutationGenerator.class);
+    
+    public RandomMutationGenerator(long num_mutations) {
+      max_mutations = num_mutations;
+    }
+    
+    public boolean hasNext() {
+      return mutations_so_far < max_mutations;
+    }
+    
+    public Mutation next() {
+      Text row_value = new Text(Long.toString(((r.nextLong() & 0x7fffffffffffffffl) / 177) % 100000000000l));
+      Mutation m = new Mutation(row_value);
+      for (int column = 0; column < num_columns_per_row; column++) {
+        Text column_fam = new Text("col_fam");
+        byte[] bytes = new byte[num_payload_bytes];
+        r.nextBytes(bytes);
+        m.put(column_fam, new Text("" + column), new Value(bytes));
+      }
+      mutations_so_far++;
+      if (mutations_so_far % 1000000 == 0) {
+        log.info("Created " + mutations_so_far + " mutations so far");
+      }
+      return m;
+    }
+    
+    public void remove() {
+      mutations_so_far++;
+    }
+    
+    @Override
+    public Iterator<Mutation> iterator() {
+      return this;
+    }
+  }
+  static class Opts extends ClientOnDefaultTable {
+    @Parameter(names="--count", description="number of mutations to write", required=true)
+    long count;
+    
+    Opts(String table) { super(table); }
+  }
+  public static void main(String[] args) throws Exception {
+    Opts opts = new Opts(table_name);
+    BatchWriterOpts bwOpts = new BatchWriterOpts();
+    opts.parseArgs(RandomWriter.class.getName(), args, bwOpts);
+    
+    long start = System.currentTimeMillis();
+    log.info("starting at " + start + " for user " + opts.principal);
+    try {
+      Connector connector = opts.getConnector();
+      BatchWriter bw = connector.createBatchWriter(opts.getTableName(), bwOpts.getBatchWriterConfig());
+      log.info("Writing " + opts.count + " mutations...");
+      bw.addMutations(new RandomMutationGenerator(opts.count));
+      bw.close();
+    } catch (Exception e) {
+      log.error(e);
+      throw e;
+    }
+    long stop = System.currentTimeMillis();
+    
+    log.info("stopping at " + stop);
+    log.info("elapsed: " + (((double) stop - (double) start) / 1000.0));
+  }
+  
+}

http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/RemoveEntriesForMissingFiles.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/RemoveEntriesForMissingFiles.java b/server/base/src/main/java/org/apache/accumulo/server/util/RemoveEntriesForMissingFiles.java
new file mode 100644
index 0000000..0b4f896
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/RemoveEntriesForMissingFiles.java
@@ -0,0 +1,214 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicReference;
+
+import org.apache.accumulo.core.cli.BatchWriterOpts;
+import org.apache.accumulo.core.cli.ScannerOpts;
+import org.apache.accumulo.core.client.AccumuloException;
+import org.apache.accumulo.core.client.BatchWriter;
+import org.apache.accumulo.core.client.BatchWriterConfig;
+import org.apache.accumulo.core.client.Connector;
+import org.apache.accumulo.core.client.Instance;
+import org.apache.accumulo.core.client.Scanner;
+import org.apache.accumulo.core.client.impl.Tables;
+import org.apache.accumulo.core.client.security.tokens.AuthenticationToken;
+import org.apache.accumulo.core.data.Key;
+import org.apache.accumulo.core.data.KeyExtent;
+import org.apache.accumulo.core.data.Mutation;
+import org.apache.accumulo.core.data.Range;
+import org.apache.accumulo.core.data.Value;
+import org.apache.accumulo.core.metadata.MetadataTable;
+import org.apache.accumulo.core.metadata.RootTable;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema;
+import org.apache.accumulo.core.metadata.schema.MetadataSchema.TabletsSection.DataFileColumnFamily;
+import org.apache.accumulo.core.security.Authorizations;
+import org.apache.accumulo.server.cli.ClientOpts;
+import org.apache.accumulo.server.fs.VolumeManager;
+import org.apache.accumulo.server.fs.VolumeManagerImpl;
+import org.apache.commons.collections.map.LRUMap;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.Text;
+
+import com.beust.jcommander.Parameter;
+
+/**
+ * Remove file entries for map files that don't exist.
+ * 
+ */
+public class RemoveEntriesForMissingFiles {
+
+  static class Opts extends ClientOpts {
+    @Parameter(names = "--fix")
+    boolean fix = false;
+  }
+
+  private static class CheckFileTask implements Runnable {
+    @SuppressWarnings("rawtypes")
+    private Map cache;
+    private VolumeManager fs;
+    private AtomicInteger missing;
+    private BatchWriter writer;
+    private Key key;
+    private Path path;
+    private Set<Path> processing;
+    private AtomicReference<Exception> exceptionRef;
+
+    @SuppressWarnings({"rawtypes"})
+    CheckFileTask(Map cache, VolumeManager fs, AtomicInteger missing, BatchWriter writer, Key key, Path map, Set<Path> processing,
+        AtomicReference<Exception> exceptionRef) {
+      this.cache = cache;
+      this.fs = fs;
+      this.missing = missing;
+      this.writer = writer;
+      this.key = key;
+      this.path = map;
+      this.processing = processing;
+      this.exceptionRef = exceptionRef;
+    }
+
+    @Override
+    @SuppressWarnings("unchecked")
+    public void run() {
+      try {
+        if (!fs.exists(path)) {
+          missing.incrementAndGet();
+
+          Mutation m = new Mutation(key.getRow());
+          m.putDelete(key.getColumnFamily(), key.getColumnQualifier());
+          if (writer != null) {
+            writer.addMutation(m);
+            System.out.println("Reference " + path + " removed from " + key.getRow());
+          } else {
+            System.out.println("File " + path + " is missing");
+          }
+        } else {
+          synchronized (processing) {
+            cache.put(path, path);
+          }
+        }
+      } catch (Exception e) {
+        exceptionRef.compareAndSet(null, e);
+      } finally {
+        synchronized (processing) {
+          processing.remove(path);
+          processing.notify();
+        }
+      }
+    }
+  }
+
+  private static int checkTable(Instance instance, String principal, AuthenticationToken token, String table, Range range, boolean fix) throws Exception {
+
+    @SuppressWarnings({"rawtypes"})
+    Map cache = new LRUMap(100000);
+    Set<Path> processing = new HashSet<Path>();
+    ExecutorService threadPool = Executors.newFixedThreadPool(16);
+
+    System.out.printf("Scanning : %s %s\n", table, range);
+
+    VolumeManager fs = VolumeManagerImpl.get();
+    Connector connector = instance.getConnector(principal, token);
+    Scanner metadata = connector.createScanner(table, Authorizations.EMPTY);
+    metadata.setRange(range);
+    metadata.fetchColumnFamily(DataFileColumnFamily.NAME);
+    int count = 0;
+    AtomicInteger missing = new AtomicInteger(0);
+    AtomicReference<Exception> exceptionRef = new AtomicReference<Exception>(null);
+    BatchWriter writer = null;
+
+    if (fix)
+      writer = connector.createBatchWriter(MetadataTable.NAME, new BatchWriterConfig());
+
+    for (Entry<Key,Value> entry : metadata) {
+      if (exceptionRef.get() != null)
+        break;
+
+      count++;
+      Key key = entry.getKey();
+      Path map = fs.getFullPath(key);
+
+      synchronized (processing) {
+        while (processing.size() >= 64 || processing.contains(map))
+          processing.wait();
+
+        if (cache.get(map) != null) {
+          continue;
+        }
+
+        processing.add(map);
+      }
+
+      threadPool.submit(new CheckFileTask(cache, fs, missing, writer, key, map, processing, exceptionRef));
+    }
+
+    threadPool.shutdown();
+
+    synchronized (processing) {
+      while (processing.size() > 0)
+        processing.wait();
+    }
+
+    if (exceptionRef.get() != null)
+      throw new AccumuloException(exceptionRef.get());
+
+    if (writer != null && missing.get() > 0)
+      writer.close();
+
+    System.out.printf("Scan finished, %d files of %d missing\n\n", missing.get(), count);
+
+    return missing.get();
+  }
+
+  static int checkAllTables(Instance instance, String principal, AuthenticationToken token, boolean fix) throws Exception {
+    int missing = checkTable(instance, principal, token, RootTable.NAME, MetadataSchema.TabletsSection.getRange(), fix);
+
+    if (missing == 0)
+      return checkTable(instance, principal, token, MetadataTable.NAME, MetadataSchema.TabletsSection.getRange(), fix);
+    else
+      return missing;
+  }
+
+  static int checkTable(Instance instance, String principal, AuthenticationToken token, String tableName, boolean fix) throws Exception {
+    if (tableName.equals(RootTable.NAME)) {
+      throw new IllegalArgumentException("Can not check root table");
+    } else if (tableName.equals(MetadataTable.NAME)) {
+      return checkTable(instance, principal, token, RootTable.NAME, MetadataSchema.TabletsSection.getRange(), fix);
+    } else {
+      String tableId = Tables.getTableId(instance, tableName);
+      Range range = new KeyExtent(new Text(tableId), null, null).toMetadataRange();
+      return checkTable(instance, principal, token, MetadataTable.NAME, range, fix);
+    }
+  }
+
+  public static void main(String[] args) throws Exception {
+    Opts opts = new Opts();
+    ScannerOpts scanOpts = new ScannerOpts();
+    BatchWriterOpts bwOpts = new BatchWriterOpts();
+    opts.parseArgs(RemoveEntriesForMissingFiles.class.getName(), args, scanOpts, bwOpts);
+
+    checkAllTables(opts.getInstance(), opts.principal, opts.getToken(), opts.fix);
+  }
+}

http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/RestoreZookeeper.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/RestoreZookeeper.java b/server/base/src/main/java/org/apache/accumulo/server/util/RestoreZookeeper.java
new file mode 100644
index 0000000..6e5607e
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/RestoreZookeeper.java
@@ -0,0 +1,128 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.util.Stack;
+
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+import org.apache.accumulo.core.Constants;
+import org.apache.accumulo.core.cli.Help;
+import org.apache.accumulo.fate.zookeeper.IZooReaderWriter;
+import org.apache.accumulo.fate.zookeeper.ZooUtil.NodeExistsPolicy;
+import org.apache.accumulo.server.zookeeper.ZooReaderWriter;
+import org.apache.commons.codec.binary.Base64;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.zookeeper.KeeperException;
+import org.xml.sax.Attributes;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.DefaultHandler;
+
+import com.beust.jcommander.Parameter;
+
+public class RestoreZookeeper {
+  
+  private static class Restore extends DefaultHandler {
+    IZooReaderWriter zk = null;
+    Stack<String> cwd = new Stack<String>();
+    boolean overwrite = false;
+    
+    Restore(IZooReaderWriter zk, boolean overwrite) {
+      this.zk = zk;
+      this.overwrite = overwrite;
+    }
+    
+    @Override
+    public void startElement(String uri, String localName, String name, Attributes attributes) throws SAXException {
+      if ("node".equals(name)) {
+        String child = attributes.getValue("name");
+        if (child == null)
+          throw new RuntimeException("name attribute not set");
+        String encoding = attributes.getValue("encoding");
+        String value = attributes.getValue("value");
+        if (value == null)
+          value = "";
+        String path = cwd.lastElement() + "/" + child;
+        create(path, value, encoding);
+        cwd.push(path);
+      } else if ("dump".equals(name)) {
+        String root = attributes.getValue("root");
+        if (root.equals("/"))
+          cwd.push("");
+        else
+          cwd.push(root);
+        create(root, "", Constants.UTF8.name());
+      }
+    }
+    
+    @Override
+    public void endElement(String uri, String localName, String name) throws SAXException {
+      cwd.pop();
+    }
+    
+    // assume UTF-8 if not "base64"
+    private void create(String path, String value, String encoding) {
+      byte[] data = value.getBytes(Constants.UTF8);
+      if ("base64".equals(encoding))
+        data = Base64.decodeBase64(data);
+      try {
+        try {
+          zk.putPersistentData(path, data, overwrite ? NodeExistsPolicy.OVERWRITE : NodeExistsPolicy.FAIL);
+        } catch (KeeperException e) {
+          if (e.code().equals(KeeperException.Code.NODEEXISTS))
+            throw new RuntimeException(path + " exists.  Remove it first.");
+          throw e;
+        }
+      } catch (Exception e) {
+        throw new RuntimeException(e);
+      }
+    }
+  }
+  
+  static class Opts extends Help {
+    @Parameter(names = {"-z", "--keepers"})
+    String keepers = "localhost:2181";
+    @Parameter(names = "--overwrite")
+    boolean overwrite = false;
+    @Parameter(names = "--file")
+    String file;
+  }
+  
+  /**
+   * @param args
+   * @throws Exception
+   */
+  public static void main(String[] args) throws Exception {
+    Logger.getRootLogger().setLevel(Level.WARN);
+    Opts opts = new Opts();
+    opts.parseArgs(RestoreZookeeper.class.getName(), args);
+    
+    InputStream in = System.in;
+    if (opts.file != null) {
+      in = new FileInputStream(opts.file);
+    }
+    
+    SAXParserFactory factory = SAXParserFactory.newInstance();
+    SAXParser parser = factory.newSAXParser();
+    parser.parse(in, new Restore(ZooReaderWriter.getInstance(), opts.overwrite));
+    in.close();
+  }
+}

http://git-wip-us.apache.org/repos/asf/accumulo/blob/598821cd/server/base/src/main/java/org/apache/accumulo/server/util/SendLogToChainsaw.java
----------------------------------------------------------------------
diff --git a/server/base/src/main/java/org/apache/accumulo/server/util/SendLogToChainsaw.java b/server/base/src/main/java/org/apache/accumulo/server/util/SendLogToChainsaw.java
new file mode 100644
index 0000000..d80adc9
--- /dev/null
+++ b/server/base/src/main/java/org/apache/accumulo/server/util/SendLogToChainsaw.java
@@ -0,0 +1,276 @@
+/*
+ * 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.accumulo.server.util;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.Socket;
+import java.net.URLEncoder;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.net.SocketFactory;
+
+import org.apache.accumulo.core.Constants;
+import org.apache.accumulo.core.cli.Help;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
+import org.apache.commons.lang.math.LongRange;
+import org.apache.log4j.Category;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.Filter;
+import org.apache.log4j.spi.LocationInfo;
+import org.apache.log4j.spi.LoggingEvent;
+import org.apache.log4j.spi.ThrowableInformation;
+import org.apache.log4j.varia.LevelRangeFilter;
+import org.apache.log4j.xml.XMLLayout;
+
+import com.beust.jcommander.IStringConverter;
+import com.beust.jcommander.Parameter;
+
+public class SendLogToChainsaw extends XMLLayout {
+  
+  private static Pattern logPattern = Pattern.compile(
+      "^(\\d\\d)\\s(\\d\\d):(\\d\\d):(\\d\\d),(\\d\\d\\d)\\s\\[(.*)\\]\\s(TRACE|DEBUG|INFO|WARN|FATAL|ERROR)\\s*?:(.*)$", Pattern.UNIX_LINES);
+  
+  private File[] logFiles = null;
+  
+  private SocketFactory factory = SocketFactory.getDefault();
+  
+  private WildcardFileFilter fileFilter = null;
+  
+  private Socket socket = null;
+  
+  private Pattern lineFilter = null;
+  
+  private LongRange dateFilter = null;
+  
+  private LevelRangeFilter levelFilter = null;
+  
+  public SendLogToChainsaw(String directory, String fileNameFilter, String host, int port, Date start, Date end, String regex, String level) throws Exception {
+    
+    // Set up the file name filter
+    if (null != fileNameFilter) {
+      fileFilter = new WildcardFileFilter(fileNameFilter);
+    } else {
+      fileFilter = new WildcardFileFilter("*");
+    }
+    
+    // Get the list of files that match
+    File dir = new File(directory);
+    if (dir.isDirectory()) {
+      logFiles = dir.listFiles((FilenameFilter) fileFilter);
+    } else {
+      throw new IllegalArgumentException(directory + " is not a directory or is not readable.");
+    }
+    
+    if (logFiles.length == 0) {
+      throw new IllegalArgumentException("No files match the supplied filter.");
+    }
+    
+    socket = factory.createSocket(host, port);
+    
+    lineFilter = Pattern.compile(regex);
+    
+    // Create Date Filter
+    if (null != start) {
+      if (end == null)
+        end = new Date(System.currentTimeMillis());
+      dateFilter = new LongRange(start.getTime(), end.getTime());
+    }
+    
+    if (null != level) {
+      Level base = Level.toLevel(level.toUpperCase());
+      levelFilter = new LevelRangeFilter();
+      levelFilter.setAcceptOnMatch(true);
+      levelFilter.setLevelMin(base);
+      levelFilter.setLevelMax(Level.FATAL);
+    }
+  }
+  
+  public void processLogFiles() throws IOException {
+    String line = null;
+    String out = null;
+    FileReader fReader = null;
+    BufferedReader reader = null;
+    try {
+      for (File log : logFiles) {
+        // Parse the server type and name from the log file name
+        String threadName = log.getName().substring(0, log.getName().indexOf("."));
+        try {
+          fReader = new FileReader(log);
+        } catch (FileNotFoundException e) {
+          System.out.println("Unable to find file: " + log.getAbsolutePath());
+          throw e;
+        }
+        reader = new BufferedReader(fReader);
+        
+        try {
+          line = reader.readLine();
+          while (null != line) {
+            out = convertLine(line, threadName);
+            if (null != out) {
+              if (socket != null && socket.isConnected())
+                socket.getOutputStream().write(out.getBytes());
+              else
+                System.err.println("Unable to send data to transport");
+            }
+            line = reader.readLine();
+          }
+        } catch (IOException e) {
+          System.out.println("Error processing line: " + line + ". Output was " + out);
+          throw e;
+        } finally {
+          if (reader != null) {
+            reader.close();
+          }
+          if (fReader != null) {
+            fReader.close();
+          }
+        }
+      }
+    } finally {
+      if (socket != null && socket.isConnected()) {
+        socket.close();
+      }
+    }
+  }
+  
+  private String convertLine(String line, String threadName) throws UnsupportedEncodingException {
+    String result = null;
+    Matcher m = logPattern.matcher(line);
+    if (m.matches()) {
+      
+      Calendar cal = Calendar.getInstance();
+      cal.setTime(new Date(System.currentTimeMillis()));
+      Integer date = Integer.parseInt(m.group(1));
+      Integer hour = Integer.parseInt(m.group(2));
+      Integer min = Integer.parseInt(m.group(3));
+      Integer sec = Integer.parseInt(m.group(4));
+      Integer ms = Integer.parseInt(m.group(5));
+      String clazz = m.group(6);
+      String level = m.group(7);
+      String message = m.group(8);
+      // Apply the regex filter if supplied
+      if (null != lineFilter) {
+        Matcher match = lineFilter.matcher(message);
+        if (!match.matches())
+          return null;
+      }
+      // URL encode the message
+      message = URLEncoder.encode(message, Constants.UTF8.name());
+      // Assume that we are processing logs from today.
+      // If the date in the line is greater than today, then it must be
+      // from the previous month.
+      cal.set(Calendar.DATE, date);
+      cal.set(Calendar.HOUR_OF_DAY, hour);
+      cal.set(Calendar.MINUTE, min);
+      cal.set(Calendar.SECOND, sec);
+      cal.set(Calendar.MILLISECOND, ms);
+      if (date > cal.get(Calendar.DAY_OF_MONTH)) {
+        cal.add(Calendar.MONTH, -1);
+      }
+      long ts = cal.getTimeInMillis();
+      // If this event is not between the start and end dates, then skip it.
+      if (null != dateFilter && !dateFilter.containsLong(ts))
+        return null;
+      Category c = Logger.getLogger(clazz);
+      Level l = Level.toLevel(level);
+      LoggingEvent event = new LoggingEvent(clazz, c, ts, l, message, threadName, (ThrowableInformation) null, (String) null, (LocationInfo) null,
+          (Map<?,?>) null);
+      // Check the log level filter
+      if (null != levelFilter && (levelFilter.decide(event) == Filter.DENY)) {
+        return null;
+      }
+      result = format(event);
+    }
+    return result;
+  }
+  
+  private static class DateConverter implements IStringConverter<Date> {
+    @Override
+    public Date convert(String value) {
+      SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMddHHmmss");
+      try {
+        return formatter.parse(value);
+      } catch (ParseException e) {
+        throw new RuntimeException(e);
+      }
+    }
+    
+  }
+  
+  private static class Opts extends Help {
+    
+    @Parameter(names = {"-d", "--logDirectory"}, description = "ACCUMULO log directory path", required = true)
+    String dir;
+    
+    @Parameter(names = {"-f", "--fileFilter"}, description = "filter to apply to names of logs")
+    String filter;
+    
+    @Parameter(names = {"-h", "--host"}, description = "host where chainsaw is running", required = true)
+    String hostname;
+    
+    @Parameter(names = {"-p", "--port"}, description = "port where XMLSocketReceiver is listening", required = true)
+    int portnum;
+    
+    @Parameter(names = {"-s", "--start"}, description = "start date filter (yyyyMMddHHmmss)", required = true, converter = DateConverter.class)
+    Date startDate;
+    
+    @Parameter(names = {"-e", "--end"}, description = "end date filter (yyyyMMddHHmmss)", required = true, converter = DateConverter.class)
+    Date endDate;
+    
+    @Parameter(names = {"-l", "--level"}, description = "filter log level")
+    String level;
+    
+    @Parameter(names = {"-m", "--messageFilter"}, description = "regex filter for log messages")
+    String regex;
+  }
+  
+  /**
+   * 
+   * @param args
+   *          <ol>
+   *          <li>path to log directory</li>
+   *          <li>filter to apply for logs to include (uses wildcards (i.e. logger* and IS case sensitive)</li>
+   *          <li>chainsaw host</li>
+   *          <li>chainsaw port</li>
+   *          <li>start date filter</li>
+   *          <li>end date filter</li>
+   *          <li>optional regex filter to match on each log4j message</li>
+   *          <li>optional level filter</li>
+   *          </ol>
+   */
+  public static void main(String[] args) throws Exception {
+    Opts opts = new Opts();
+    opts.parseArgs(SendLogToChainsaw.class.getName(), args);
+    
+    SendLogToChainsaw c = new SendLogToChainsaw(opts.dir, opts.filter, opts.hostname, opts.portnum, opts.startDate, opts.endDate, opts.regex, opts.level);
+    c.processLogFiles();
+  }
+  
+}


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