/**
    *
    * 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.util;
  
  import java.io.ByteArrayInputStream;
  import java.io.DataInputStream;
  import java.io.EOFException;
  import java.io.FileNotFoundException;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.InterruptedIOException;
  import java.lang.reflect.InvocationTargetException;
  import java.lang.reflect.Method;
  import java.net.InetSocketAddress;
  import java.net.URI;
  import java.net.URISyntaxException;
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.HashMap;
  import java.util.LinkedList;
  import java.util.List;
  import java.util.Map;
  import java.util.concurrent.ArrayBlockingQueue;
  import java.util.concurrent.ConcurrentHashMap;
  import java.util.concurrent.ThreadPoolExecutor;
  import java.util.concurrent.TimeUnit;
  import java.util.regex.Pattern;
  
  import org.apache.commons.logging.Log;
  import org.apache.commons.logging.LogFactory;
  import org.apache.hadoop.hbase.classification.InterfaceAudience;
  import org.apache.hadoop.HadoopIllegalArgumentException;
  import org.apache.hadoop.conf.Configuration;
  import org.apache.hadoop.fs.BlockLocation;
  import org.apache.hadoop.fs.FSDataInputStream;
  import org.apache.hadoop.fs.FSDataOutputStream;
  import org.apache.hadoop.fs.FileStatus;
  import org.apache.hadoop.fs.FileSystem;
  import org.apache.hadoop.fs.Path;
  import org.apache.hadoop.fs.PathFilter;
  import org.apache.hadoop.fs.permission.FsAction;
  import org.apache.hadoop.fs.permission.FsPermission;
  import org.apache.hadoop.hbase.ClusterId;
  import org.apache.hadoop.hbase.HColumnDescriptor;
  import org.apache.hadoop.hbase.HConstants;
  import org.apache.hadoop.hbase.HDFSBlocksDistribution;
  import org.apache.hadoop.hbase.HRegionInfo;
  import org.apache.hadoop.hbase.RemoteExceptionHandler;
  import org.apache.hadoop.hbase.TableName;
  import org.apache.hadoop.hbase.exceptions.DeserializationException;
  import org.apache.hadoop.hbase.fs.HFileSystem;
  import org.apache.hadoop.hbase.master.HMaster;
  import org.apache.hadoop.hbase.regionserver.StoreFileInfo;
  import org.apache.hadoop.hbase.security.AccessDeniedException;
  import org.apache.hadoop.hbase.util.HBaseFsck.ErrorReporter;
  import org.apache.hadoop.hbase.protobuf.ProtobufUtil;
  import org.apache.hadoop.hbase.protobuf.generated.FSProtos;
  import org.apache.hadoop.hbase.regionserver.HRegion;
  import org.apache.hadoop.hdfs.DistributedFileSystem;
  import org.apache.hadoop.io.IOUtils;
  import org.apache.hadoop.io.SequenceFile;
  import org.apache.hadoop.ipc.RemoteException;
  import org.apache.hadoop.security.UserGroupInformation;
  import org.apache.hadoop.util.Progressable;
  import org.apache.hadoop.util.ReflectionUtils;
  import org.apache.hadoop.util.StringUtils;
  
  import com.google.common.primitives.Ints;
  
  /**
   * Utility methods for interacting with the underlying file system.
   */
  @InterfaceAudience.Private
  public abstract class FSUtils {
    private static final Log LOG = LogFactory.getLog(FSUtils.class);
  
    /** Full access permissions (starting point for a umask) */
    public static final String FULL_RWX_PERMISSIONS = "777";
    private static final String THREAD_POOLSIZE = "hbase.client.localityCheck.threadPoolSize";
    private static final int DEFAULT_THREAD_POOLSIZE = 2;
  
    /** Set to true on Windows platforms */
    public static final boolean WINDOWS = System.getProperty("os.name").startsWith("Windows");
 
   protected FSUtils() {
     super();
   }
 
   /**
    * Sets storage policy for given path according to config setting.
    * If the passed path is a directory, we'll set the storage policy for all files
    * created in the future in said directory. Note that this change in storage
    * policy takes place at the HDFS level; it will persist beyond this RS's lifecycle.
    * If we're running on a version of HDFS that doesn't support the given storage policy
    * (or storage policies at all), then we'll issue a log message and continue.
    *
    * See http://hadoop.apache.org/docs/r2.6.0/hadoop-project-dist/hadoop-hdfs/ArchivalStorage.html
    *
    * @param fs We only do anything if an instance of DistributedFileSystem
    * @param conf used to look up storage policy with given key; not modified.
    * @param path the Path whose storage policy is to be set
    * @param policyKey e.g. HConstants.WAL_STORAGE_POLICY
    * @param defaultPolicy usually should be the policy NONE to delegate to HDFS
    */
   public static void setStoragePolicy(final FileSystem fs, final Configuration conf,
       final Path path, final String policyKey, final String defaultPolicy) {
     String storagePolicy = conf.get(policyKey, defaultPolicy).toUpperCase();
     if (storagePolicy.equals(defaultPolicy)) {
       if (LOG.isTraceEnabled()) {
         LOG.trace("default policy of " + defaultPolicy + " requested, exiting early.");
       }
       return;
     }
     if (fs instanceof DistributedFileSystem) {
       DistributedFileSystem dfs = (DistributedFileSystem)fs;
       // Once our minimum supported Hadoop version is 2.6.0 we can remove reflection.
       Class<? extends DistributedFileSystem> dfsClass = dfs.getClass();
       Method m = null;
       try {
         m = dfsClass.getDeclaredMethod("setStoragePolicy",
             new Class<?>[] { Path.class, String.class });
         m.setAccessible(true);
       } catch (NoSuchMethodException e) {
         LOG.info("FileSystem doesn't support"
             + " setStoragePolicy; --HDFS-6584 not available");
       } catch (SecurityException e) {
         LOG.info("Doesn't have access to setStoragePolicy on "
             + "FileSystems --HDFS-6584 not available", e);
         m = null; // could happen on setAccessible()
       }
       if (m != null) {
         try {
           m.invoke(dfs, path, storagePolicy);
           LOG.info("set " + storagePolicy + " for " + path);
         } catch (Exception e) {
           // check for lack of HDFS-7228
           boolean probablyBadPolicy = false;
           if (e instanceof InvocationTargetException) {
             final Throwable exception = e.getCause();
             if (exception instanceof RemoteException &&
                 HadoopIllegalArgumentException.class.getName().equals(
                     ((RemoteException)exception).getClassName())) {
               LOG.warn("Given storage policy, '" + storagePolicy + "', was rejected and probably " +
                   "isn't a valid policy for the version of Hadoop you're running. I.e. if you're " +
                   "trying to use SSD related policies then you're likely missing HDFS-7228. For " +
                   "more information see the 'ArchivalStorage' docs for your Hadoop release.");
               LOG.debug("More information about the invalid storage policy.", exception);
               probablyBadPolicy = true;
             }
           }
           if (!probablyBadPolicy) {
             // This swallows FNFE, should we be throwing it? seems more likely to indicate dev
             // misuse than a runtime problem with HDFS.
             LOG.warn("Unable to set " + storagePolicy + " for " + path, e);
           }
         }
       }
     } else {
       LOG.info("FileSystem isn't an instance of DistributedFileSystem; presuming it doesn't " +
           "support setStoragePolicy.");
     }
   }
 
   /**
    * Compare of path component. Does not consider schema; i.e. if schemas different but <code>path
    * <code> starts with <code>rootPath<code>, then the function returns true
    * @param rootPath
    * @param path
    * @return True if <code>path</code> starts with <code>rootPath</code>
    */
   public static boolean isStartingWithPath(final Path rootPath, final String path) {
     String uriRootPath = rootPath.toUri().getPath();
     String tailUriPath = (new Path(path)).toUri().getPath();
     return tailUriPath.startsWith(uriRootPath);
   }
 
   /**
    * Compare path component of the Path URI; e.g. if hdfs://a/b/c and /a/b/c, it will compare the
    * '/a/b/c' part. Does not consider schema; i.e. if schemas different but path or subpath matches,
    * the two will equate.
    * @param pathToSearch Path we will be trying to match.
    * @param pathTail
    * @return True if <code>pathTail</code> is tail on the path of <code>pathToSearch</code>
    */
   public static boolean isMatchingTail(final Path pathToSearch, String pathTail) {
     return isMatchingTail(pathToSearch, new Path(pathTail));
   }
 
   /**
    * Compare path component of the Path URI; e.g. if hdfs://a/b/c and /a/b/c, it will compare the
    * '/a/b/c' part. If you passed in 'hdfs://a/b/c and b/c, it would return true.  Does not consider
    * schema; i.e. if schemas different but path or subpath matches, the two will equate.
    * @param pathToSearch Path we will be trying to match.
    * @param pathTail
    * @return True if <code>pathTail</code> is tail on the path of <code>pathToSearch</code>
    */
   public static boolean isMatchingTail(final Path pathToSearch, final Path pathTail) {
     if (pathToSearch.depth() != pathTail.depth()) return false;
     Path tailPath = pathTail;
     String tailName;
     Path toSearch = pathToSearch;
     String toSearchName;
     boolean result = false;
     do {
       tailName = tailPath.getName();
       if (tailName == null || tailName.length() <= 0) {
         result = true;
         break;
       }
       toSearchName = toSearch.getName();
       if (toSearchName == null || toSearchName.length() <= 0) break;
       // Move up a parent on each path for next go around.  Path doesn't let us go off the end.
       tailPath = tailPath.getParent();
       toSearch = toSearch.getParent();
     } while(tailName.equals(toSearchName));
     return result;
   }
 
   public static FSUtils getInstance(FileSystem fs, Configuration conf) {
     String scheme = fs.getUri().getScheme();
     if (scheme == null) {
       LOG.warn("Could not find scheme for uri " +
           fs.getUri() + ", default to hdfs");
       scheme = "hdfs";
     }
     Class<?> fsUtilsClass = conf.getClass("hbase.fsutil." +
         scheme + ".impl", FSHDFSUtils.class); // Default to HDFS impl
     FSUtils fsUtils = (FSUtils)ReflectionUtils.newInstance(fsUtilsClass, conf);
     return fsUtils;
   }
 
   /**
    * Delete if exists.
    * @param fs filesystem object
    * @param dir directory to delete
    * @return True if deleted <code>dir</code>
    * @throws IOException e
    */
   public static boolean deleteDirectory(final FileSystem fs, final Path dir)
   throws IOException {
     return fs.exists(dir) && fs.delete(dir, true);
   }
 
   /**
    * Delete the region directory if exists.
    * @param conf
    * @param hri
    * @return True if deleted the region directory.
    * @throws IOException
    */
   public static boolean deleteRegionDir(final Configuration conf, final HRegionInfo hri)
   throws IOException {
     Path rootDir = getRootDir(conf);
     FileSystem fs = rootDir.getFileSystem(conf);
     return deleteDirectory(fs,
       new Path(getTableDir(rootDir, hri.getTable()), hri.getEncodedName()));
   }
 
   /**
    * Return the number of bytes that large input files should be optimally
    * be split into to minimize i/o time.
    *
    * use reflection to search for getDefaultBlockSize(Path f)
    * if the method doesn't exist, fall back to using getDefaultBlockSize()
    *
    * @param fs filesystem object
    * @return the default block size for the path's filesystem
    * @throws IOException e
    */
   public static long getDefaultBlockSize(final FileSystem fs, final Path path) throws IOException {
     Method m = null;
     Class<? extends FileSystem> cls = fs.getClass();
     try {
       m = cls.getMethod("getDefaultBlockSize", new Class<?>[] { Path.class });
     } catch (NoSuchMethodException e) {
       LOG.info("FileSystem doesn't support getDefaultBlockSize");
     } catch (SecurityException e) {
       LOG.info("Doesn't have access to getDefaultBlockSize on FileSystems", e);
       m = null; // could happen on setAccessible()
     }
     if (m == null) {
       return fs.getDefaultBlockSize(path);
     } else {
       try {
         Object ret = m.invoke(fs, path);
         return ((Long)ret).longValue();
       } catch (Exception e) {
         throw new IOException(e);
       }
     }
   }
 
   /*
    * Get the default replication.
    *
    * use reflection to search for getDefaultReplication(Path f)
    * if the method doesn't exist, fall back to using getDefaultReplication()
    *
    * @param fs filesystem object
    * @param f path of file
    * @return default replication for the path's filesystem
    * @throws IOException e
    */
   public static short getDefaultReplication(final FileSystem fs, final Path path) throws IOException {
     Method m = null;
     Class<? extends FileSystem> cls = fs.getClass();
     try {
       m = cls.getMethod("getDefaultReplication", new Class<?>[] { Path.class });
     } catch (NoSuchMethodException e) {
       LOG.info("FileSystem doesn't support getDefaultReplication");
     } catch (SecurityException e) {
       LOG.info("Doesn't have access to getDefaultReplication on FileSystems", e);
       m = null; // could happen on setAccessible()
     }
     if (m == null) {
       return fs.getDefaultReplication(path);
     } else {
       try {
         Object ret = m.invoke(fs, path);
         return ((Number)ret).shortValue();
       } catch (Exception e) {
         throw new IOException(e);
       }
     }
   }
 
   /**
    * Returns the default buffer size to use during writes.
    *
    * The size of the buffer should probably be a multiple of hardware
    * page size (4096 on Intel x86), and it determines how much data is
    * buffered during read and write operations.
    *
    * @param fs filesystem object
    * @return default buffer size to use during writes
    */
   public static int getDefaultBufferSize(final FileSystem fs) {
     return fs.getConf().getInt("io.file.buffer.size", 4096);
   }
 
   /**
    * Create the specified file on the filesystem. By default, this will:
    * <ol>
    * <li>overwrite the file if it exists</li>
    * <li>apply the umask in the configuration (if it is enabled)</li>
    * <li>use the fs configured buffer size (or 4096 if not set)</li>
    * <li>use the default replication</li>
    * <li>use the default block size</li>
    * <li>not track progress</li>
    * </ol>
    *
    * @param fs {@link FileSystem} on which to write the file
    * @param path {@link Path} to the file to write
    * @param perm permissions
    * @param favoredNodes
    * @return output stream to the created file
    * @throws IOException if the file cannot be created
    */
   public static FSDataOutputStream create(FileSystem fs, Path path,
       FsPermission perm, InetSocketAddress[] favoredNodes) throws IOException {
     if (fs instanceof HFileSystem) {
       FileSystem backingFs = ((HFileSystem)fs).getBackingFs();
       if (backingFs instanceof DistributedFileSystem) {
         // Try to use the favoredNodes version via reflection to allow backwards-
         // compatibility.
         try {
           return (FSDataOutputStream) (DistributedFileSystem.class
               .getDeclaredMethod("create", Path.class, FsPermission.class,
                   boolean.class, int.class, short.class, long.class,
                   Progressable.class, InetSocketAddress[].class)
                   .invoke(backingFs, path, perm, true,
                       getDefaultBufferSize(backingFs),
                       getDefaultReplication(backingFs, path),
                       getDefaultBlockSize(backingFs, path),
                       null, favoredNodes));
         } catch (InvocationTargetException ite) {
           // Function was properly called, but threw it's own exception.
           throw new IOException(ite.getCause());
         } catch (NoSuchMethodException e) {
           LOG.debug("DFS Client does not support most favored nodes create; using default create");
           if (LOG.isTraceEnabled()) LOG.trace("Ignoring; use default create", e);
         } catch (IllegalArgumentException e) {
           LOG.debug("Ignoring (most likely Reflection related exception) " + e);
         } catch (SecurityException e) {
           LOG.debug("Ignoring (most likely Reflection related exception) " + e);
         } catch (IllegalAccessException e) {
           LOG.debug("Ignoring (most likely Reflection related exception) " + e);
         }
       }
     }
     return create(fs, path, perm, true);
   }
 
   /**
    * Create the specified file on the filesystem. By default, this will:
    * <ol>
    * <li>apply the umask in the configuration (if it is enabled)</li>
    * <li>use the fs configured buffer size (or 4096 if not set)</li>
    * <li>use the default replication</li>
    * <li>use the default block size</li>
    * <li>not track progress</li>
    * </ol>
    *
    * @param fs {@link FileSystem} on which to write the file
    * @param path {@link Path} to the file to write
    * @param perm
    * @param overwrite Whether or not the created file should be overwritten.
    * @return output stream to the created file
    * @throws IOException if the file cannot be created
    */
   public static FSDataOutputStream create(FileSystem fs, Path path,
       FsPermission perm, boolean overwrite) throws IOException {
     if (LOG.isTraceEnabled()) {
       LOG.trace("Creating file=" + path + " with permission=" + perm + ", overwrite=" + overwrite);
     }
     return fs.create(path, perm, overwrite, getDefaultBufferSize(fs),
         getDefaultReplication(fs, path), getDefaultBlockSize(fs, path), null);
   }
 
   /**
    * Get the file permissions specified in the configuration, if they are
    * enabled.
    *
    * @param fs filesystem that the file will be created on.
    * @param conf configuration to read for determining if permissions are
    *          enabled and which to use
    * @param permssionConfKey property key in the configuration to use when
    *          finding the permission
    * @return the permission to use when creating a new file on the fs. If
    *         special permissions are not specified in the configuration, then
    *         the default permissions on the the fs will be returned.
    */
   public static FsPermission getFilePermissions(final FileSystem fs,
       final Configuration conf, final String permssionConfKey) {
     boolean enablePermissions = conf.getBoolean(
         HConstants.ENABLE_DATA_FILE_UMASK, false);
 
     if (enablePermissions) {
       try {
         FsPermission perm = new FsPermission(FULL_RWX_PERMISSIONS);
         // make sure that we have a mask, if not, go default.
         String mask = conf.get(permssionConfKey);
         if (mask == null)
           return FsPermission.getFileDefault();
         // appy the umask
         FsPermission umask = new FsPermission(mask);
         return perm.applyUMask(umask);
       } catch (IllegalArgumentException e) {
         LOG.warn(
             "Incorrect umask attempted to be created: "
                 + conf.get(permssionConfKey)
                 + ", using default file permissions.", e);
         return FsPermission.getFileDefault();
       }
     }
     return FsPermission.getFileDefault();
   }
 
   /**
    * Checks to see if the specified file system is available
    *
    * @param fs filesystem
    * @throws IOException e
    */
   public static void checkFileSystemAvailable(final FileSystem fs)
   throws IOException {
     if (!(fs instanceof DistributedFileSystem)) {
       return;
     }
     IOException exception = null;
     DistributedFileSystem dfs = (DistributedFileSystem) fs;
     try {
       if (dfs.exists(new Path("/"))) {
         return;
       }
     } catch (IOException e) {
       exception = RemoteExceptionHandler.checkIOException(e);
     }
     try {
       fs.close();
     } catch (Exception e) {
       LOG.error("file system close failed: ", e);
     }
     IOException io = new IOException("File system is not available");
     io.initCause(exception);
     throw io;
   }
 
   /**
    * We use reflection because {@link DistributedFileSystem#setSafeMode(
    * FSConstants.SafeModeAction action, boolean isChecked)} is not in hadoop 1.1
    *
    * @param dfs
    * @return whether we're in safe mode
    * @throws IOException
    */
   private static boolean isInSafeMode(DistributedFileSystem dfs) throws IOException {
     boolean inSafeMode = false;
     try {
       Method m = DistributedFileSystem.class.getMethod("setSafeMode", new Class<?> []{
           org.apache.hadoop.hdfs.protocol.FSConstants.SafeModeAction.class, boolean.class});
       inSafeMode = (Boolean) m.invoke(dfs,
         org.apache.hadoop.hdfs.protocol.FSConstants.SafeModeAction.SAFEMODE_GET, true);
     } catch (Exception e) {
       if (e instanceof IOException) throw (IOException) e;
 
       // Check whether dfs is on safemode.
       inSafeMode = dfs.setSafeMode(
         org.apache.hadoop.hdfs.protocol.FSConstants.SafeModeAction.SAFEMODE_GET);
     }
     return inSafeMode;
   }
 
   /**
    * Check whether dfs is in safemode.
    * @param conf
    * @throws IOException
    */
   public static void checkDfsSafeMode(final Configuration conf)
   throws IOException {
     boolean isInSafeMode = false;
     FileSystem fs = FileSystem.get(conf);
     if (fs instanceof DistributedFileSystem) {
       DistributedFileSystem dfs = (DistributedFileSystem)fs;
       isInSafeMode = isInSafeMode(dfs);
     }
     if (isInSafeMode) {
       throw new IOException("File system is in safemode, it can't be written now");
     }
   }
 
   /**
    * Verifies current version of file system
    *
    * @param fs filesystem object
    * @param rootdir root hbase directory
    * @return null if no version file exists, version string otherwise.
    * @throws IOException e
    * @throws org.apache.hadoop.hbase.exceptions.DeserializationException
    */
   public static String getVersion(FileSystem fs, Path rootdir)
   throws IOException, DeserializationException {
     Path versionFile = new Path(rootdir, HConstants.VERSION_FILE_NAME);
     FileStatus[] status = null;
     try {
       // hadoop 2.0 throws FNFE if directory does not exist.
       // hadoop 1.0 returns null if directory does not exist.
       status = fs.listStatus(versionFile);
     } catch (FileNotFoundException fnfe) {
       return null;
     }
     if (status == null || status.length == 0) return null;
     String version = null;
     byte [] content = new byte [(int)status[0].getLen()];
     FSDataInputStream s = fs.open(versionFile);
     try {
       IOUtils.readFully(s, content, 0, content.length);
       if (ProtobufUtil.isPBMagicPrefix(content)) {
         version = parseVersionFrom(content);
       } else {
         // Presume it pre-pb format.
         InputStream is = new ByteArrayInputStream(content);
         DataInputStream dis = new DataInputStream(is);
         try {
           version = dis.readUTF();
         } finally {
           dis.close();
         }
       }
     } catch (EOFException eof) {
       LOG.warn("Version file was empty, odd, will try to set it.");
     } finally {
       s.close();
     }
     return version;
   }
 
   /**
    * Parse the content of the ${HBASE_ROOTDIR}/hbase.version file.
    * @param bytes The byte content of the hbase.version file.
    * @return The version found in the file as a String.
    * @throws DeserializationException
    */
   static String parseVersionFrom(final byte [] bytes)
   throws DeserializationException {
     ProtobufUtil.expectPBMagicPrefix(bytes);
     int pblen = ProtobufUtil.lengthOfPBMagic();
     FSProtos.HBaseVersionFileContent.Builder builder =
       FSProtos.HBaseVersionFileContent.newBuilder();
     try {
       ProtobufUtil.mergeFrom(builder, bytes, pblen, bytes.length - pblen);
       return builder.getVersion();
     } catch (IOException e) {
       // Convert
       throw new DeserializationException(e);
     }
   }
 
   /**
    * Create the content to write into the ${HBASE_ROOTDIR}/hbase.version file.
    * @param version Version to persist
    * @return Serialized protobuf with <code>version</code> content and a bit of pb magic for a prefix.
    */
   static byte [] toVersionByteArray(final String version) {
     FSProtos.HBaseVersionFileContent.Builder builder =
       FSProtos.HBaseVersionFileContent.newBuilder();
     return ProtobufUtil.prependPBMagic(builder.setVersion(version).build().toByteArray());
   }
 
   /**
    * Verifies current version of file system
    *
    * @param fs file system
    * @param rootdir root directory of HBase installation
    * @param message if true, issues a message on System.out
    *
    * @throws IOException e
    * @throws DeserializationException
    */
   public static void checkVersion(FileSystem fs, Path rootdir, boolean message)
   throws IOException, DeserializationException {
     checkVersion(fs, rootdir, message, 0, HConstants.DEFAULT_VERSION_FILE_WRITE_ATTEMPTS);
   }
 
   /**
    * Verifies current version of file system
    *
    * @param fs file system
    * @param rootdir root directory of HBase installation
    * @param message if true, issues a message on System.out
    * @param wait wait interval
    * @param retries number of times to retry
    *
    * @throws IOException e
    * @throws DeserializationException
    */
   public static void checkVersion(FileSystem fs, Path rootdir,
       boolean message, int wait, int retries)
   throws IOException, DeserializationException {
     String version = getVersion(fs, rootdir);
     if (version == null) {
       if (!metaRegionExists(fs, rootdir)) {
         // rootDir is empty (no version file and no root region)
         // just create new version file (HBASE-1195)
         setVersion(fs, rootdir, wait, retries);
         return;
       }
     } else if (version.compareTo(HConstants.FILE_SYSTEM_VERSION) == 0) return;
 
     // version is deprecated require migration
     // Output on stdout so user sees it in terminal.
     String msg = "HBase file layout needs to be upgraded."
       + " You have version " + version
       + " and I want version " + HConstants.FILE_SYSTEM_VERSION
       + ". Consult http://hbase.apache.org/book.html for further information about upgrading HBase."
       + " Is your hbase.rootdir valid? If so, you may need to run "
       + "'hbase hbck -fixVersionFile'.";
     if (message) {
       System.out.println("WARNING! " + msg);
     }
     throw new FileSystemVersionException(msg);
   }
 
   /**
    * Sets version of file system
    *
    * @param fs filesystem object
    * @param rootdir hbase root
    * @throws IOException e
    */
   public static void setVersion(FileSystem fs, Path rootdir)
   throws IOException {
     setVersion(fs, rootdir, HConstants.FILE_SYSTEM_VERSION, 0,
       HConstants.DEFAULT_VERSION_FILE_WRITE_ATTEMPTS);
   }
 
   /**
    * Sets version of file system
    *
    * @param fs filesystem object
    * @param rootdir hbase root
    * @param wait time to wait for retry
    * @param retries number of times to retry before failing
    * @throws IOException e
    */
   public static void setVersion(FileSystem fs, Path rootdir, int wait, int retries)
   throws IOException {
     setVersion(fs, rootdir, HConstants.FILE_SYSTEM_VERSION, wait, retries);
   }
 
 
   /**
    * Sets version of file system
    *
    * @param fs filesystem object
    * @param rootdir hbase root directory
    * @param version version to set
    * @param wait time to wait for retry
    * @param retries number of times to retry before throwing an IOException
    * @throws IOException e
    */
   public static void setVersion(FileSystem fs, Path rootdir, String version,
       int wait, int retries) throws IOException {
     Path versionFile = new Path(rootdir, HConstants.VERSION_FILE_NAME);
     Path tempVersionFile = new Path(rootdir, HConstants.HBASE_TEMP_DIRECTORY + Path.SEPARATOR +
       HConstants.VERSION_FILE_NAME);
     while (true) {
       try {
         // Write the version to a temporary file
         FSDataOutputStream s = fs.create(tempVersionFile);
         try {
           s.write(toVersionByteArray(version));
           s.close();
           s = null;
           // Move the temp version file to its normal location. Returns false
           // if the rename failed. Throw an IOE in that case.
           if (!fs.rename(tempVersionFile, versionFile)) {
             throw new IOException("Unable to move temp version file to " + versionFile);
           }
         } finally {
           // Cleaning up the temporary if the rename failed would be trying
           // too hard. We'll unconditionally create it again the next time
           // through anyway, files are overwritten by default by create().
 
           // Attempt to close the stream on the way out if it is still open.
           try {
             if (s != null) s.close();
           } catch (IOException ignore) { }
         }
         LOG.info("Created version file at " + rootdir.toString() + " with version=" + version);
         return;
       } catch (IOException e) {
         if (retries > 0) {
           LOG.debug("Unable to create version file at " + rootdir.toString() + ", retrying", e);
           fs.delete(versionFile, false);
           try {
             if (wait > 0) {
               Thread.sleep(wait);
             }
           } catch (InterruptedException ie) {
             throw (InterruptedIOException)new InterruptedIOException().initCause(ie);
           }
           retries--;
         } else {
           throw e;
         }
       }
     }
   }
 
   /**
    * Checks that a cluster ID file exists in the HBase root directory
    * @param fs the root directory FileSystem
    * @param rootdir the HBase root directory in HDFS
    * @param wait how long to wait between retries
    * @return <code>true</code> if the file exists, otherwise <code>false</code>
    * @throws IOException if checking the FileSystem fails
    */
   public static boolean checkClusterIdExists(FileSystem fs, Path rootdir,
       int wait) throws IOException {
     while (true) {
       try {
         Path filePath = new Path(rootdir, HConstants.CLUSTER_ID_FILE_NAME);
         return fs.exists(filePath);
       } catch (IOException ioe) {
         if (wait > 0) {
           LOG.warn("Unable to check cluster ID file in " + rootdir.toString() +
               ", retrying in "+wait+"msec: "+StringUtils.stringifyException(ioe));
           try {
             Thread.sleep(wait);
           } catch (InterruptedException e) {
             throw (InterruptedIOException)new InterruptedIOException().initCause(e);
           }
         } else {
           throw ioe;
         }
       }
     }
   }
 
   /**
    * Returns the value of the unique cluster ID stored for this HBase instance.
    * @param fs the root directory FileSystem
    * @param rootdir the path to the HBase root directory
    * @return the unique cluster identifier
    * @throws IOException if reading the cluster ID file fails
    */
   public static ClusterId getClusterId(FileSystem fs, Path rootdir)
   throws IOException {
     Path idPath = new Path(rootdir, HConstants.CLUSTER_ID_FILE_NAME);
     ClusterId clusterId = null;
     FileStatus status = fs.exists(idPath)? fs.getFileStatus(idPath):  null;
     if (status != null) {
       int len = Ints.checkedCast(status.getLen());
       byte [] content = new byte[len];
       FSDataInputStream in = fs.open(idPath);
       try {
         in.readFully(content);
       } catch (EOFException eof) {
         LOG.warn("Cluster ID file " + idPath.toString() + " was empty");
       } finally{
         in.close();
       }
       try {
         clusterId = ClusterId.parseFrom(content);
       } catch (DeserializationException e) {
         throw new IOException("content=" + Bytes.toString(content), e);
       }
       // If not pb'd, make it so.
       if (!ProtobufUtil.isPBMagicPrefix(content)) {
         String cid = null;
         in = fs.open(idPath);
         try {
           cid = in.readUTF();
           clusterId = new ClusterId(cid);
         } catch (EOFException eof) {
           LOG.warn("Cluster ID file " + idPath.toString() + " was empty");
         } finally {
           in.close();
         }
         rewriteAsPb(fs, rootdir, idPath, clusterId);
       }
       return clusterId;
     } else {
       LOG.warn("Cluster ID file does not exist at " + idPath.toString());
     }
     return clusterId;
   }
 
   /**
    * @param cid
    * @throws IOException
    */
   private static void rewriteAsPb(final FileSystem fs, final Path rootdir, final Path p,
       final ClusterId cid)
   throws IOException {
     // Rewrite the file as pb.  Move aside the old one first, write new
     // then delete the moved-aside file.
     Path movedAsideName = new Path(p + "." + System.currentTimeMillis());
     if (!fs.rename(p, movedAsideName)) throw new IOException("Failed rename of " + p);
     setClusterId(fs, rootdir, cid, 100);
     if (!fs.delete(movedAsideName, false)) {
       throw new IOException("Failed delete of " + movedAsideName);
     }
     LOG.debug("Rewrote the hbase.id file as pb");
   }
 
   /**
    * Writes a new unique identifier for this cluster to the "hbase.id" file
    * in the HBase root directory
    * @param fs the root directory FileSystem
    * @param rootdir the path to the HBase root directory
    * @param clusterId the unique identifier to store
    * @param wait how long (in milliseconds) to wait between retries
    * @throws IOException if writing to the FileSystem fails and no wait value
    */
   public static void setClusterId(FileSystem fs, Path rootdir, ClusterId clusterId,
       int wait) throws IOException {
     while (true) {
       try {
         Path idFile = new Path(rootdir, HConstants.CLUSTER_ID_FILE_NAME);
         Path tempIdFile = new Path(rootdir, HConstants.HBASE_TEMP_DIRECTORY +
           Path.SEPARATOR + HConstants.CLUSTER_ID_FILE_NAME);
         // Write the id file to a temporary location
         FSDataOutputStream s = fs.create(tempIdFile);
         try {
           s.write(clusterId.toByteArray());
           s.close();
           s = null;
           // Move the temporary file to its normal location. Throw an IOE if
           // the rename failed
           if (!fs.rename(tempIdFile, idFile)) {
             throw new IOException("Unable to move temp version file to " + idFile);
           }
         } finally {
           // Attempt to close the stream if still open on the way out
           try {
             if (s != null) s.close();
           } catch (IOException ignore) { }
         }
         if (LOG.isDebugEnabled()) {
           LOG.debug("Created cluster ID file at " + idFile.toString() + " with ID: " + clusterId);
         }
         return;
       } catch (IOException ioe) {
         if (wait > 0) {
           LOG.warn("Unable to create cluster ID file in " + rootdir.toString() +
               ", retrying in " + wait + "msec: " + StringUtils.stringifyException(ioe));
           try {
             Thread.sleep(wait);
           } catch (InterruptedException e) {
             throw (InterruptedIOException)new InterruptedIOException().initCause(e);
           }
         } else {
           throw ioe;
         }
       }
     }
   }
 
   /**
    * Verifies root directory path is a valid URI with a scheme
    *
    * @param root root directory path
    * @return Passed <code>root</code> argument.
    * @throws IOException if not a valid URI with a scheme
    */
   public static Path validateRootPath(Path root) throws IOException {
     try {
       URI rootURI = new URI(root.toString());
       String scheme = rootURI.getScheme();
       if (scheme == null) {
         throw new IOException("Root directory does not have a scheme");
       }
       return root;
     } catch (URISyntaxException e) {
       IOException io = new IOException("Root directory path is not a valid " +
         "URI -- check your " + HConstants.HBASE_DIR + " configuration");
       io.initCause(e);
       throw io;
     }
   }
 
   /**
    * Checks for the presence of the root path (using the provided conf object) in the given path. If
    * it exists, this method removes it and returns the String representation of remaining relative path.
    * @param path
    * @param conf
    * @return String representation of the remaining relative path
    * @throws IOException
    */
   public static String removeRootPath(Path path, final Configuration conf) throws IOException {
     Path root = FSUtils.getRootDir(conf);
     String pathStr = path.toString();
     // check that the path is absolute... it has the root path in it.
     if (!pathStr.startsWith(root.toString())) return pathStr;
     // if not, return as it is.
     return pathStr.substring(root.toString().length() + 1);// remove the "/" too.
   }
 
   /**
    * If DFS, check safe mode and if so, wait until we clear it.
    * @param conf configuration
    * @param wait Sleep between retries
    * @throws IOException e
    */
   public static void waitOnSafeMode(final Configuration conf,
     final long wait)
   throws IOException {
     FileSystem fs = FileSystem.get(conf);
     if (!(fs instanceof DistributedFileSystem)) return;
     DistributedFileSystem dfs = (DistributedFileSystem)fs;
     // Make sure dfs is not in safe mode
     while (isInSafeMode(dfs)) {
       LOG.info("Waiting for dfs to exit safe mode...");
       try {
         Thread.sleep(wait);
       } catch (InterruptedException e) {
         throw (InterruptedIOException)new InterruptedIOException().initCause(e);
       }
     }
   }
 
   /**
    * Return the 'path' component of a Path.  In Hadoop, Path is an URI.  This
    * method returns the 'path' component of a Path's URI: e.g. If a Path is
    * <code>hdfs://example.org:9000/hbase_trunk/TestTable/compaction.dir</code>,
    * this method returns <code>/hbase_trunk/TestTable/compaction.dir</code>.
    * This method is useful if you want to print out a Path without qualifying
    * Filesystem instance.
    * @param p Filesystem Path whose 'path' component we are to return.
    * @return Path portion of the Filesystem
    */
   public static String getPath(Path p) {
     return p.toUri().getPath();
   }
 
   /**
    * @param c configuration
    * @return Path to hbase root directory: i.e. <code>hbase.rootdir</code> from
    * configuration as a qualified Path.
    * @throws IOException e
    */
   public static Path getRootDir(final Configuration c) throws IOException {
     Path p = new Path(c.get(HConstants.HBASE_DIR));
     FileSystem fs = p.getFileSystem(c);
     return p.makeQualified(fs);
   }
 
   public static void setRootDir(final Configuration c, final Path root) throws IOException {
     c.set(HConstants.HBASE_DIR, root.toString());
   }
 
   public static void setFsDefault(final Configuration c, final Path root) throws IOException {
     c.set("fs.defaultFS", root.toString());    // for hadoop 0.21+
   }
 
   /**
    * Checks if meta region exists
    *
    * @param fs file system
    * @param rootdir root directory of HBase installation
    * @return true if exists
    * @throws IOException e
    */
   @SuppressWarnings("deprecation")
   public static boolean metaRegionExists(FileSystem fs, Path rootdir)
   throws IOException {
     Path metaRegionDir =
       HRegion.getRegionDir(rootdir, HRegionInfo.FIRST_META_REGIONINFO);
     return fs.exists(metaRegionDir);
   }
 
   /**
    * Compute HDFS blocks distribution of a given file, or a portion of the file
    * @param fs file system
    * @param status file status of the file
    * @param start start position of the portion
    * @param length length of the portion
    * @return The HDFS blocks distribution
    */
   static public HDFSBlocksDistribution computeHDFSBlocksDistribution(
     final FileSystem fs, FileStatus status, long start, long length)
     throws IOException {
     HDFSBlocksDistribution blocksDistribution = new HDFSBlocksDistribution();
     BlockLocation [] blockLocations =
       fs.getFileBlockLocations(status, start, length);
     for(BlockLocation bl : blockLocations) {
       String [] hosts = bl.getHosts();
       long len = bl.getLength();
       blocksDistribution.addHostsAndBlockWeight(hosts, len);
     }
 
     return blocksDistribution;
   }
 
 
 
   /**
    * Runs through the hbase rootdir and checks all stores have only
    * one file in them -- that is, they've been major compacted.  Looks
    * at root and meta tables too.
    * @param fs filesystem
    * @param hbaseRootDir hbase root directory
    * @return True if this hbase install is major compacted.
    * @throws IOException e
    */
   public static boolean isMajorCompacted(final FileSystem fs,
       final Path hbaseRootDir)
   throws IOException {
     List<Path> tableDirs = getTableDirs(fs, hbaseRootDir);
     PathFilter regionFilter = new RegionDirFilter(fs);
     PathFilter familyFilter = new FamilyDirFilter(fs);
     for (Path d : tableDirs) {
       FileStatus[] regionDirs = fs.listStatus(d, regionFilter);
       for (FileStatus regionDir : regionDirs) {
         Path dd = regionDir.getPath();
         // Else its a region name.  Now look in region for families.
         FileStatus[] familyDirs = fs.listStatus(dd, familyFilter);
         for (FileStatus familyDir : familyDirs) {
           Path family = familyDir.getPath();
           // Now in family make sure only one file.
           FileStatus[] familyStatus = fs.listStatus(family);
           if (familyStatus.length > 1) {
             LOG.debug(family.toString() + " has " + familyStatus.length +
                 " files.");
             return false;
           }
         }
       }
     }
     return true;
   }
 
   // TODO move this method OUT of FSUtils. No dependencies to HMaster
   /**
    * Returns the total overall fragmentation percentage. Includes hbase:meta and
    * -ROOT- as well.
    *
    * @param master  The master defining the HBase root and file system.
    * @return A map for each table and its percentage.
    * @throws IOException When scanning the directory fails.
    */
   public static int getTotalTableFragmentation(final HMaster master)
   throws IOException {
     Map<String, Integer> map = getTableFragmentation(master);
     return map != null && map.size() > 0 ? map.get("-TOTAL-") : -1;
   }
 
   /**
    * Runs through the HBase rootdir and checks how many stores for each table
    * have more than one file in them. Checks -ROOT- and hbase:meta too. The total
    * percentage across all tables is stored under the special key "-TOTAL-".
    *
    * @param master  The master defining the HBase root and file system.
    * @return A map for each table and its percentage.
    *
    * @throws IOException When scanning the directory fails.
    */
   public static Map<String, Integer> getTableFragmentation(
     final HMaster master)
   throws IOException {
     Path path = getRootDir(master.getConfiguration());
     // since HMaster.getFileSystem() is package private
     FileSystem fs = path.getFileSystem(master.getConfiguration());
     return getTableFragmentation(fs, path);
   }
 
   /**
    * Runs through the HBase rootdir and checks how many stores for each table
    * have more than one file in them. Checks -ROOT- and hbase:meta too. The total
    * percentage across all tables is stored under the special key "-TOTAL-".
    *
    * @param fs  The file system to use.
    * @param hbaseRootDir  The root directory to scan.
    * @return A map for each table and its percentage.
    * @throws IOException When scanning the directory fails.
    */
   public static Map<String, Integer> getTableFragmentation(
     final FileSystem fs, final Path hbaseRootDir)
   throws IOException {
     Map<String, Integer> frags = new HashMap<String, Integer>();
     int cfCountTotal = 0;
     int cfFragTotal = 0;
     PathFilter regionFilter = new RegionDirFilter(fs);
     PathFilter familyFilter = new FamilyDirFilter(fs);
     List<Path> tableDirs = getTableDirs(fs, hbaseRootDir);
     for (Path d : tableDirs) {
       int cfCount = 0;
       int cfFrag = 0;
       FileStatus[] regionDirs = fs.listStatus(d, regionFilter);
       for (FileStatus regionDir : regionDirs) {
         Path dd = regionDir.getPath();
         // else its a region name, now look in region for families
         FileStatus[] familyDirs = fs.listStatus(dd, familyFilter);
         for (FileStatus familyDir : familyDirs) {
           cfCount++;
           cfCountTotal++;
           Path family = familyDir.getPath();
           // now in family make sure only one file
           FileStatus[] familyStatus = fs.listStatus(family);
           if (familyStatus.length > 1) {
             cfFrag++;
             cfFragTotal++;
           }
         }
       }
       // compute percentage per table and store in result list
       frags.put(FSUtils.getTableName(d).getNameAsString(),
         cfCount == 0? 0: Math.round((float) cfFrag / cfCount * 100));
     }
     // set overall percentage for all tables
     frags.put("-TOTAL-",
       cfCountTotal == 0? 0: Math.round((float) cfFragTotal / cfCountTotal * 100));
     return frags;
   }
 
   /**
    * Returns the {@link org.apache.hadoop.fs.Path} object representing the table directory under
    * path rootdir
    *
    * @param rootdir qualified path of HBase root directory
    * @param tableName name of table
    * @return {@link org.apache.hadoop.fs.Path} for table
    */
   public static Path getTableDir(Path rootdir, final TableName tableName) {
     return new Path(getNamespaceDir(rootdir, tableName.getNamespaceAsString()),
         tableName.getQualifierAsString());
   }
 
   /**
    * Returns the {@link org.apache.hadoop.hbase.TableName} object representing
    * the table directory under
    * path rootdir
    *
    * @param tablePath path of table
    * @return {@link org.apache.hadoop.fs.Path} for table
    */
   public static TableName getTableName(Path tablePath) {
     return TableName.valueOf(tablePath.getParent().getName(), tablePath.getName());
   }
 
   /**
    * Returns the {@link org.apache.hadoop.fs.Path} object representing
    * the namespace directory under path rootdir
    *
    * @param rootdir qualified path of HBase root directory
    * @param namespace namespace name
    * @return {@link org.apache.hadoop.fs.Path} for table
    */
   public static Path getNamespaceDir(Path rootdir, final String namespace) {
     return new Path(rootdir, new Path(HConstants.BASE_NAMESPACE_DIR,
         new Path(namespace)));
   }
 
   /**
    * A {@link PathFilter} that returns only regular files.
    */
   static class FileFilter implements PathFilter {
     private final FileSystem fs;
 
     public FileFilter(final FileSystem fs) {
       this.fs = fs;
     }
 
     @Override
     public boolean accept(Path p) {
       try {
         return fs.isFile(p);
       } catch (IOException e) {
         LOG.debug("unable to verify if path=" + p + " is a regular file", e);
         return false;
       }
     }
   }
 
   /**
    * Directory filter that doesn't include any of the directories in the specified blacklist
    */
   public static class BlackListDirFilter implements PathFilter {
     private final FileSystem fs;
     private List<String> blacklist;
 
     /**
      * Create a filter on the givem filesystem with the specified blacklist
      * @param fs filesystem to filter
      * @param directoryNameBlackList list of the names of the directories to filter. If
      *          <tt>null</tt>, all directories are returned
      */
     @SuppressWarnings("unchecked")
     public BlackListDirFilter(final FileSystem fs, final List<String> directoryNameBlackList) {
       this.fs = fs;
       blacklist =
         (List<String>) (directoryNameBlackList == null ? Collections.emptyList()
           : directoryNameBlackList);
     }
 
     @Override
     public boolean accept(Path p) {
       boolean isValid = false;
       try {
         if (isValidName(p.getName())) {
           isValid = fs.getFileStatus(p).isDirectory();
         } else {
           isValid = false;
         }
       } catch (IOException e) {
         LOG.warn("An error occurred while verifying if [" + p.toString()
             + "] is a valid directory. Returning 'not valid' and continuing.", e);
       }
       return isValid;
     }
 
     protected boolean isValidName(final String name) {
       return !blacklist.contains(name);
     }
   }
 
   /**
    * A {@link PathFilter} that only allows directories.
    */
   public static class DirFilter extends BlackListDirFilter {
 
     public DirFilter(FileSystem fs) {
       super(fs, null);
     }
   }
 
   /**
    * A {@link PathFilter} that returns usertable directories. To get all directories use the
    * {@link BlackListDirFilter} with a <tt>null</tt> blacklist
    */
   public static class UserTableDirFilter extends BlackListDirFilter {
     public UserTableDirFilter(FileSystem fs) {
       super(fs, HConstants.HBASE_NON_TABLE_DIRS);
     }
 
     protected boolean isValidName(final String name) {
       if (!super.isValidName(name))
         return false;
 
       try {
         TableName.isLegalTableQualifierName(Bytes.toBytes(name));
       } catch (IllegalArgumentException e) {
         LOG.info("INVALID NAME " + name);
         return false;
       }
       return true;
     }
   }
 
   /**
    * Heuristic to determine whether is safe or not to open a file for append
    * Looks both for dfs.support.append and use reflection to search
    * for SequenceFile.Writer.syncFs() or FSDataOutputStream.hflush()
    * @param conf
    * @return True if append support
    */
   public static boolean isAppendSupported(final Configuration conf) {
     boolean append = conf.getBoolean("dfs.support.append", false);
     if (append) {
       try {
         // TODO: The implementation that comes back when we do a createWriter
         // may not be using SequenceFile so the below is not a definitive test.
         // Will do for now (hdfs-200).
         SequenceFile.Writer.class.getMethod("syncFs", new Class<?> []{});
         append = true;
       } catch (SecurityException e) {
       } catch (NoSuchMethodException e) {
         append = false;
       }
     }
     if (!append) {
       // Look for the 0.21, 0.22, new-style append evidence.
       try {
         FSDataOutputStream.class.getMethod("hflush", new Class<?> []{});
         append = true;
       } catch (NoSuchMethodException e) {
         append = false;
       }
     }
     return append;
   }
 
   /**
    * @param conf
    * @return True if this filesystem whose scheme is 'hdfs'.
    * @throws IOException
    */
   public static boolean isHDFS(final Configuration conf) throws IOException {
     FileSystem fs = FileSystem.get(conf);
     String scheme = fs.getUri().getScheme();
     return scheme.equalsIgnoreCase("hdfs");
   }
 
   /**
    * Recover file lease. Used when a file might be suspect
    * to be had been left open by another process.
    * @param fs FileSystem handle
    * @param p Path of file to recover lease
    * @param conf Configuration handle
    * @throws IOException
    */
   public abstract void recoverFileLease(final FileSystem fs, final Path p,
       Configuration conf, CancelableProgressable reporter) throws IOException;
 
   public static List<Path> getTableDirs(final FileSystem fs, final Path rootdir)
       throws IOException {
     List<Path> tableDirs = new LinkedList<Path>();
 
     for(FileStatus status :
         fs.globStatus(new Path(rootdir,
             new Path(HConstants.BASE_NAMESPACE_DIR, "*")))) {
       tableDirs.addAll(FSUtils.getLocalTableDirs(fs, status.getPath()));
     }
     return tableDirs;
   }
 
   /**
    * @param fs
    * @param rootdir
    * @return All the table directories under <code>rootdir</code>. Ignore non table hbase folders such as
    * .logs, .oldlogs, .corrupt folders.
    * @throws IOException
    */
   public static List<Path> getLocalTableDirs(final FileSystem fs, final Path rootdir)
       throws IOException {
     // presumes any directory under hbase.rootdir is a table
     FileStatus[] dirs = fs.listStatus(rootdir, new UserTableDirFilter(fs));
     List<Path> tabledirs = new ArrayList<Path>(dirs.length);
     for (FileStatus dir: dirs) {
       tabledirs.add(dir.getPath());
     }
     return tabledirs;
   }
 
   /**
    * Checks if the given path is the one with 'recovered.edits' dir.
    * @param path
    * @return True if we recovered edits
    */
   public static boolean isRecoveredEdits(Path path) {
     return path.toString().contains(HConstants.RECOVERED_EDITS_DIR);
   }
 
   /**
    * Filter for all dirs that don't start with '.'
    */
   public static class RegionDirFilter implements PathFilter {
     // This pattern will accept 0.90+ style hex region dirs and older numeric region dir names.
     final public static Pattern regionDirPattern = Pattern.compile("^[0-9a-f]*$");
     final FileSystem fs;
 
     public RegionDirFilter(FileSystem fs) {
       this.fs = fs;
     }
 
     @Override
     public boolean accept(Path rd) {
       if (!regionDirPattern.matcher(rd.getName()).matches()) {
         return false;
       }
 
       try {
         return fs.getFileStatus(rd).isDirectory();
       } catch (IOException ioe) {
         // Maybe the file was moved or the fs was disconnected.
         LOG.warn("Skipping file " + rd +" due to IOException", ioe);
         return false;
       }
     }
   }
 
   /**
    * Given a particular table dir, return all the regiondirs inside it, excluding files such as
    * .tableinfo
    * @param fs A file system for the Path
    * @param tableDir Path to a specific table directory <hbase.rootdir>/<tabledir>
    * @return List of paths to valid region directories in table dir.
    * @throws IOException
    */
   public static List<Path> getRegionDirs(final FileSystem fs, final Path tableDir) throws IOException {
     // assumes we are in a table dir.
     FileStatus[] rds = fs.listStatus(tableDir, new RegionDirFilter(fs));
     List<Path> regionDirs = new ArrayList<Path>(rds.length);
     for (FileStatus rdfs: rds) {
       Path rdPath = rdfs.getPath();
       regionDirs.add(rdPath);
     }
     return regionDirs;
   }
 
   /**
    * Filter for all dirs that are legal column family names.  This is generally used for colfam
    * dirs <hbase.rootdir>/<tabledir>/<regiondir>/<colfamdir>.
    */
   public static class FamilyDirFilter implements PathFilter {
     final FileSystem fs;
 
     public FamilyDirFilter(FileSystem fs) {
       this.fs = fs;
     }
 
     @Override
     public boolean accept(Path rd) {
       try {
         // throws IAE if invalid
         HColumnDescriptor.isLegalFamilyName(Bytes.toBytes(rd.getName()));
       } catch (IllegalArgumentException iae) {
         // path name is an invalid family name and thus is excluded.
         return false;
       }
 
       try {
         return fs.getFileStatus(rd).isDirectory();
       } catch (IOException ioe) {
         // Maybe the file was moved or the fs was disconnected.
         LOG.warn("Skipping file " + rd +" due to IOException", ioe);
         return false;
       }
     }
   }
 
   /**
    * Given a particular region dir, return all the familydirs inside it
    *
    * @param fs A file system for the Path
    * @param regionDir Path to a specific region directory
    * @return List of paths to valid family directories in region dir.
    * @throws IOException
    */
   public static List<Path> getFamilyDirs(final FileSystem fs, final Path regionDir) throws IOException {
     // assumes we are in a region dir.
     FileStatus[] fds = fs.listStatus(regionDir, new FamilyDirFilter(fs));
     List<Path> familyDirs = new ArrayList<Path>(fds.length);
     for (FileStatus fdfs: fds) {
       Path fdPath = fdfs.getPath();
       familyDirs.add(fdPath);
     }
     return familyDirs;
   }
 
   public static List<Path> getReferenceFilePaths(final FileSystem fs, final Path familyDir) throws IOException {
     FileStatus[] fds = fs.listStatus(familyDir, new ReferenceFileFilter(fs));
     List<Path> referenceFiles = new ArrayList<Path>(fds.length);
     for (FileStatus fdfs: fds) {
       Path fdPath = fdfs.getPath();
       referenceFiles.add(fdPath);
     }
     return referenceFiles;
   }
 
   /**
    * Filter for HFiles that excludes reference files.
    */
   public static class HFileFilter implements PathFilter {
     final FileSystem fs;
 
     public HFileFilter(FileSystem fs) {
       this.fs = fs;
     }
 
     @Override
     public boolean accept(Path rd) {
       try {
         // only files
         return !fs.getFileStatus(rd).isDirectory() && StoreFileInfo.isHFile(rd);
       } catch (IOException ioe) {
         // Maybe the file was moved or the fs was disconnected.
         LOG.warn("Skipping file " + rd +" due to IOException", ioe);
         return false;
       }
     }
   }
 
   public static class ReferenceFileFilter implements PathFilter {
 
     private final FileSystem fs;
 
     public ReferenceFileFilter(FileSystem fs) {
       this.fs = fs;
     }
 
     @Override
     public boolean accept(Path rd) {
       try {
         // only files can be references.
         return !fs.getFileStatus(rd).isDirectory() && StoreFileInfo.isReference(rd);
       } catch (IOException ioe) {
         // Maybe the file was moved or the fs was disconnected.
         LOG.warn("Skipping file " + rd +" due to IOException", ioe);
         return false;
       }
     }
   }
 
 
   /**
    * @param conf
    * @return Returns the filesystem of the hbase rootdir.
    * @throws IOException
    */
   public static FileSystem getCurrentFileSystem(Configuration conf)
   throws IOException {
     return getRootDir(conf).getFileSystem(conf);
   }
 
 
   /**
    * Runs through the HBase rootdir/tablename and creates a reverse lookup map for
    * table StoreFile names to the full Path.
    * <br>
    * Example...<br>
    * Key = 3944417774205889744  <br>
    * Value = hdfs://localhost:51169/user/userid/-ROOT-/70236052/info/3944417774205889744
    *
    * @param map map to add values.  If null, this method will create and populate one to return
    * @param fs  The file system to use.
    * @param hbaseRootDir  The root directory to scan.
    * @param tableName name of the table to scan.
    * @return Map keyed by StoreFile name with a value of the full Path.
    * @throws IOException When scanning the directory fails.
    */
   public static Map<String, Path> getTableStoreFilePathMap(Map<String, Path> map,
   final FileSystem fs, final Path hbaseRootDir, TableName tableName)
   throws IOException {
     return getTableStoreFilePathMap(map, fs, hbaseRootDir, tableName, null);
   }
 
   /**
    * Runs through the HBase rootdir/tablename and creates a reverse lookup map for
    * table StoreFile names to the full Path.
    * <br>
    * Example...<br>
    * Key = 3944417774205889744  <br>
    * Value = hdfs://localhost:51169/user/userid/-ROOT-/70236052/info/3944417774205889744
    *
    * @param map map to add values.  If null, this method will create and populate one to return
    * @param fs  The file system to use.
    * @param hbaseRootDir  The root directory to scan.
    * @param tableName name of the table to scan.
    * @param errors ErrorReporter instance or null
    * @return Map keyed by StoreFile name with a value of the full Path.
    * @throws IOException When scanning the directory fails.
    */
   public static Map<String, Path> getTableStoreFilePathMap(Map<String, Path> map,
   final FileSystem fs, final Path hbaseRootDir, TableName tableName, ErrorReporter errors)
   throws IOException {
     if (map == null) {
       map = new HashMap<String, Path>();
     }
 
     // only include the directory paths to tables
     Path tableDir = FSUtils.getTableDir(hbaseRootDir, tableName);
     // Inside a table, there are compaction.dir directories to skip.  Otherwise, all else
     // should be regions.
     PathFilter familyFilter = new FamilyDirFilter(fs);
     FileStatus[] regionDirs = fs.listStatus(tableDir, new RegionDirFilter(fs));
     for (FileStatus regionDir : regionDirs) {
       if (null != errors) {
         errors.progress();
       }
       Path dd = regionDir.getPath();
       // else its a region name, now look in region for families
       FileStatus[] familyDirs = fs.listStatus(dd, familyFilter);
       for (FileStatus familyDir : familyDirs) {
         if (null != errors) {
           errors.progress();
         }
         Path family = familyDir.getPath();
         if (family.getName().equals(HConstants.RECOVERED_EDITS_DIR)) {
           continue;
         }
         // now in family, iterate over the StoreFiles and
         // put in map
         FileStatus[] familyStatus = fs.listStatus(family);
         for (FileStatus sfStatus : familyStatus) {
           if (null != errors) {
             errors.progress();
           }
           Path sf = sfStatus.getPath();
           map.put( sf.getName(), sf);
         }
       }
     }
     return map;
   }
 
   public static int getRegionReferenceFileCount(final FileSystem fs, final Path p) {
     int result = 0;
     try {
       for (Path familyDir:getFamilyDirs(fs, p)){
         result += getReferenceFilePaths(fs, familyDir).size();
       }
     } catch (IOException e) {
       LOG.warn("Error Counting reference files.", e);
     }
     return result;
   }
 
   /**
    * Runs through the HBase rootdir and creates a reverse lookup map for
    * table StoreFile names to the full Path.
    * <br>
    * Example...<br>
    * Key = 3944417774205889744  <br>
    * Value = hdfs://localhost:51169/user/userid/-ROOT-/70236052/info/3944417774205889744
    *
    * @param fs  The file system to use.
    * @param hbaseRootDir  The root directory to scan.
    * @return Map keyed by StoreFile name with a value of the full Path.
    * @throws IOException When scanning the directory fails.
    */
   public static Map<String, Path> getTableStoreFilePathMap(
     final FileSystem fs, final Path hbaseRootDir)
   throws IOException {
     return getTableStoreFilePathMap(fs, hbaseRootDir, null);
   }
 
   /**
    * Runs through the HBase rootdir and creates a reverse lookup map for
    * table StoreFile names to the full Path.
    * <br>
    * Example...<br>
    * Key = 3944417774205889744  <br>
    * Value = hdfs://localhost:51169/user/userid/-ROOT-/70236052/info/3944417774205889744
    *
    * @param fs  The file system to use.
    * @param hbaseRootDir  The root directory to scan.
    * @param errors ErrorReporter instance or null
    * @return Map keyed by StoreFile name with a value of the full Path.
    * @throws IOException When scanning the directory fails.
    */
   public static Map<String, Path> getTableStoreFilePathMap(
     final FileSystem fs, final Path hbaseRootDir, ErrorReporter errors)
   throws IOException {
     Map<String, Path> map = new HashMap<String, Path>();
 
     // if this method looks similar to 'getTableFragmentation' that is because
     // it was borrowed from it.
 
     // only include the directory paths to tables
     for (Path tableDir : FSUtils.getTableDirs(fs, hbaseRootDir)) {
       getTableStoreFilePathMap(map, fs, hbaseRootDir,
           FSUtils.getTableName(tableDir), errors);
     }
     return map;
   }
 
   /**
    * Calls fs.listStatus() and treats FileNotFoundException as non-fatal
    * This accommodates differences between hadoop versions, where hadoop 1
    * does not throw a FileNotFoundException, and return an empty FileStatus[]
    * while Hadoop 2 will throw FileNotFoundException.
    *
    * @param fs file system
    * @param dir directory
    * @param filter path filter
    * @return null if dir is empty or doesn't exist, otherwise FileStatus array
    */
   public static FileStatus [] listStatus(final FileSystem fs,
       final Path dir, final PathFilter filter) throws IOException {
     FileStatus [] status = null;
     try {
       status = filter == null ? fs.listStatus(dir) : fs.listStatus(dir, filter);
     } catch (FileNotFoundException fnfe) {
       // if directory doesn't exist, return null
       if (LOG.isTraceEnabled()) {
         LOG.trace(dir + " doesn't exist");
       }
     }
     if (status == null || status.length < 1) return null;
     return status;
   }
 
   /**
    * Calls fs.listStatus() and treats FileNotFoundException as non-fatal
    * This would accommodates differences between hadoop versions
    *
    * @param fs file system
    * @param dir directory
    * @return null if dir is empty or doesn't exist, otherwise FileStatus array
    */
   public static FileStatus[] listStatus(final FileSystem fs, final Path dir) throws IOException {
     return listStatus(fs, dir, null);
   }
 
   /**
    * Calls fs.delete() and returns the value returned by the fs.delete()
    *
    * @param fs
    * @param path
    * @param recursive
    * @return the value returned by the fs.delete()
    * @throws IOException
    */
   public static boolean delete(final FileSystem fs, final Path path, final boolean recursive)
       throws IOException {
     return fs.delete(path, recursive);
   }
 
   /**
    * Calls fs.exists(). Checks if the specified path exists
    *
    * @param fs
    * @param path
    * @return the value returned by fs.exists()
    * @throws IOException
    */
   public static boolean isExists(final FileSystem fs, final Path path) throws IOException {
     return fs.exists(path);
   }
 
   /**
    * Throw an exception if an action is not permitted by a user on a file.
    *
    * @param ugi
    *          the user
    * @param file
    *          the file
    * @param action
    *          the action
    */
   public static void checkAccess(UserGroupInformation ugi, FileStatus file,
       FsAction action) throws AccessDeniedException {
     if (ugi.getShortUserName().equals(file.getOwner())) {
       if (file.getPermission().getUserAction().implies(action)) {
         return;
       }
     } else if (contains(ugi.getGroupNames(), file.getGroup())) {
       if (file.getPermission().getGroupAction().implies(action)) {
         return;
       }
     } else if (file.getPermission().getOtherAction().implies(action)) {
       return;
     }
     throw new AccessDeniedException("Permission denied:" + " action=" + action
         + " path=" + file.getPath() + " user=" + ugi.getShortUserName());
   }
 
   private static boolean contains(String[] groups, String user) {
     for (String group : groups) {
       if (group.equals(user)) {
         return true;
       }
     }
     return false;
   }
 
   /**
    * Log the current state of the filesystem from a certain root directory
    * @param fs filesystem to investigate
    * @param root root file/directory to start logging from
    * @param LOG log to output information
    * @throws IOException if an unexpected exception occurs
    */
   public static void logFileSystemState(final FileSystem fs, final Path root, Log LOG)
       throws IOException {
     LOG.debug("Current file system:");
     logFSTree(LOG, fs, root, "|-");
   }
 
   /**
    * Recursive helper to log the state of the FS
    *
    * @see #logFileSystemState(FileSystem, Path, Log)
    */
   private static void logFSTree(Log LOG, final FileSystem fs, final Path root, String prefix)
       throws IOException {
     FileStatus[] files = FSUtils.listStatus(fs, root, null);
     if (files == null) return;
 
     for (FileStatus file : files) {
       if (file.isDirectory()) {
         LOG.debug(prefix + file.getPath().getName() + "/");
         logFSTree(LOG, fs, file.getPath(), prefix + "---");
       } else {
         LOG.debug(prefix + file.getPath().getName());
       }
     }
   }
 
   public static boolean renameAndSetModifyTime(final FileSystem fs, final Path src, final Path dest)
       throws IOException {
     // set the modify time for TimeToLive Cleaner
     fs.setTimes(src, EnvironmentEdgeManager.currentTime(), -1);
     return fs.rename(src, dest);
   }
 
   /**
    * This function is to scan the root path of the file system to get the
    * degree of locality for each region on each of the servers having at least
    * one block of that region.
    * This is used by the tool {@link org.apache.hadoop.hbase.master.RegionPlacementMaintainer}
    *
    * @param conf
    *          the configuration to use
    * @return the mapping from region encoded name to a map of server names to
    *           locality fraction
    * @throws IOException
    *           in case of file system errors or interrupts
    */
   public static Map<String, Map<String, Float>> getRegionDegreeLocalityMappingFromFS(
       final Configuration conf) throws IOException {
     return getRegionDegreeLocalityMappingFromFS(
         conf, null,
         conf.getInt(THREAD_POOLSIZE, DEFAULT_THREAD_POOLSIZE));
 
   }
 
   /**
    * This function is to scan the root path of the file system to get the
    * degree of locality for each region on each of the servers having at least
    * one block of that region.
    *
    * @param conf
    *          the configuration to use
    * @param desiredTable
    *          the table you wish to scan locality for
    * @param threadPoolSize
    *          the thread pool size to use
    * @return the mapping from region encoded name to a map of server names to
    *           locality fraction
    * @throws IOException
    *           in case of file system errors or interrupts
    */
   public static Map<String, Map<String, Float>> getRegionDegreeLocalityMappingFromFS(
       final Configuration conf, final String desiredTable, int threadPoolSize)
       throws IOException {
     Map<String, Map<String, Float>> regionDegreeLocalityMapping =
         new ConcurrentHashMap<String, Map<String, Float>>();
     getRegionLocalityMappingFromFS(conf, desiredTable, threadPoolSize, null,
         regionDegreeLocalityMapping);
     return regionDegreeLocalityMapping;
   }
 
   /**
    * This function is to scan the root path of the file system to get either the
    * mapping between the region name and its best locality region server or the
    * degree of locality of each region on each of the servers having at least
    * one block of that region. The output map parameters are both optional.
    *
    * @param conf
    *          the configuration to use
    * @param desiredTable
    *          the table you wish to scan locality for
    * @param threadPoolSize
    *          the thread pool size to use
    * @param regionToBestLocalityRSMapping
    *          the map into which to put the best locality mapping or null
    * @param regionDegreeLocalityMapping
    *          the map into which to put the locality degree mapping or null,
    *          must be a thread-safe implementation
    * @throws IOException
    *           in case of file system errors or interrupts
    */
   private static void getRegionLocalityMappingFromFS(
       final Configuration conf, final String desiredTable,
       int threadPoolSize,
       Map<String, String> regionToBestLocalityRSMapping,
       Map<String, Map<String, Float>> regionDegreeLocalityMapping)
       throws IOException {
     FileSystem fs =  FileSystem.get(conf);
     Path rootPath = FSUtils.getRootDir(conf);
     long startTime = EnvironmentEdgeManager.currentTime();
     Path queryPath;
     // The table files are in ${hbase.rootdir}/data/<namespace>/<table>/*
     if (null == desiredTable) {
       queryPath = new Path(new Path(rootPath, HConstants.BASE_NAMESPACE_DIR).toString() + "/*/*/*/");
     } else {
       queryPath = new Path(FSUtils.getTableDir(rootPath, TableName.valueOf(desiredTable)).toString() + "/*/");
     }
 
     // reject all paths that are not appropriate
     PathFilter pathFilter = new PathFilter() {
       @Override
       public boolean accept(Path path) {
         // this is the region name; it may get some noise data
         if (null == path) {
           return false;
         }
 
         // no parent?
         Path parent = path.getParent();
         if (null == parent) {
           return false;
         }
 
         String regionName = path.getName();
         if (null == regionName) {
           return false;
         }
 
         if (!regionName.toLowerCase().matches("[0-9a-f]+")) {
           return false;
         }
         return true;
       }
     };
 
     FileStatus[] statusList = fs.globStatus(queryPath, pathFilter);
 
     if (null == statusList) {
       return;
     } else {
       LOG.debug("Query Path: " + queryPath + " ; # list of files: " +
           statusList.length);
     }
 
     // lower the number of threads in case we have very few expected regions
     threadPoolSize = Math.min(threadPoolSize, statusList.length);
 
     // run in multiple threads
     ThreadPoolExecutor tpe = new ThreadPoolExecutor(threadPoolSize,
         threadPoolSize, 60, TimeUnit.SECONDS,
         new ArrayBlockingQueue<Runnable>(statusList.length));
     try {
       // ignore all file status items that are not of interest
       for (FileStatus regionStatus : statusList) {
         if (null == regionStatus) {
           continue;
         }
 
         if (!regionStatus.isDirectory()) {
           continue;
         }
 
         Path regionPath = regionStatus.getPath();
         if (null == regionPath) {
           continue;
         }
 
         tpe.execute(new FSRegionScanner(fs, regionPath,
             regionToBestLocalityRSMapping, regionDegreeLocalityMapping));
       }
     } finally {
       tpe.shutdown();
       int threadWakeFrequency = conf.getInt(HConstants.THREAD_WAKE_FREQUENCY,
           60 * 1000);
       try {
         // here we wait until TPE terminates, which is either naturally or by
         // exceptions in the execution of the threads
         while (!tpe.awaitTermination(threadWakeFrequency,
             TimeUnit.MILLISECONDS)) {
           // printing out rough estimate, so as to not introduce
           // AtomicInteger
           LOG.info("Locality checking is underway: { Scanned Regions : "
               + tpe.getCompletedTaskCount() + "/"
               + tpe.getTaskCount() + " }");
         }
       } catch (InterruptedException e) {
         throw (InterruptedIOException)new InterruptedIOException().initCause(e);
       }
     }
 
     long overhead = EnvironmentEdgeManager.currentTime() - startTime;
     String overheadMsg = "Scan DFS for locality info takes " + overhead + " ms";
 
     LOG.info(overheadMsg);
   }
 
   /**
    * Do our short circuit read setup.
    * Checks buffer size to use and whether to do checksumming in hbase or hdfs.
    * @param conf
    */
   public static void setupShortCircuitRead(final Configuration conf) {
     // Check that the user has not set the "dfs.client.read.shortcircuit.skip.checksum" property.
     boolean shortCircuitSkipChecksum =
       conf.getBoolean("dfs.client.read.shortcircuit.skip.checksum", false);
     boolean useHBaseChecksum = conf.getBoolean(HConstants.HBASE_CHECKSUM_VERIFICATION, true);
     if (shortCircuitSkipChecksum) {
       LOG.warn("Configuration \"dfs.client.read.shortcircuit.skip.checksum\" should not " +
         "be set to true." + (useHBaseChecksum ? " HBase checksum doesn't require " +
         "it, see https://issues.apache.org/jira/browse/HBASE-6868." : ""));
       assert !shortCircuitSkipChecksum; //this will fail if assertions are on
     }
     checkShortCircuitReadBufferSize(conf);
   }
 
   /**
    * Check if short circuit read buffer size is set and if not, set it to hbase value.
    * @param conf
    */
   public static void checkShortCircuitReadBufferSize(final Configuration conf) {
     final int defaultSize = HConstants.DEFAULT_BLOCKSIZE * 2;
     final int notSet = -1;
     // DFSConfigKeys.DFS_CLIENT_READ_SHORTCIRCUIT_BUFFER_SIZE_KEY is only defined in h2
     final String dfsKey = "dfs.client.read.shortcircuit.buffer.size";
     int size = conf.getInt(dfsKey, notSet);
     // If a size is set, return -- we will use it.
     if (size != notSet) return;
     // But short circuit buffer size is normally not set.  Put in place the hbase wanted size.
     int hbaseSize = conf.getInt("hbase." + dfsKey, defaultSize);
     conf.setIfUnset(dfsKey, Integer.toString(hbaseSize));
   }
 }