org.apache.hadoop.hbase.util.HBaseFsck.java Source code

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/**
 * 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.FileNotFoundException;
import java.io.IOException;
import java.io.InterruptedIOException;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.URI;
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.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.concurrent.Callable;
import java.util.concurrent.ConcurrentSkipListMap;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Future;
import java.util.concurrent.ScheduledThreadPoolExecutor;
import java.util.concurrent.atomic.AtomicInteger;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.classification.InterfaceAudience;
import org.apache.hadoop.classification.InterfaceStability;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.permission.FsAction;
import org.apache.hadoop.hbase.Abortable;
import org.apache.hadoop.hbase.Cell;
import org.apache.hadoop.hbase.ClusterStatus;
import org.apache.hadoop.hbase.HBaseConfiguration;
import org.apache.hadoop.hbase.HColumnDescriptor;
import org.apache.hadoop.hbase.HConstants;
import org.apache.hadoop.hbase.HRegionInfo;
import org.apache.hadoop.hbase.HRegionLocation;
import org.apache.hadoop.hbase.HTableDescriptor;
import org.apache.hadoop.hbase.KeyValue;
import org.apache.hadoop.hbase.MasterNotRunningException;
import org.apache.hadoop.hbase.ServerName;
import org.apache.hadoop.hbase.TableName;
import org.apache.hadoop.hbase.ZooKeeperConnectionException;
import org.apache.hadoop.hbase.catalog.MetaEditor;
import org.apache.hadoop.hbase.client.Delete;
import org.apache.hadoop.hbase.client.Get;
import org.apache.hadoop.hbase.client.HBaseAdmin;
import org.apache.hadoop.hbase.client.HConnectable;
import org.apache.hadoop.hbase.client.HConnection;
import org.apache.hadoop.hbase.client.HConnectionManager;
import org.apache.hadoop.hbase.client.HTable;
import org.apache.hadoop.hbase.client.MetaScanner;
import org.apache.hadoop.hbase.client.MetaScanner.MetaScannerVisitor;
import org.apache.hadoop.hbase.client.MetaScanner.MetaScannerVisitorBase;
import org.apache.hadoop.hbase.client.Put;
import org.apache.hadoop.hbase.client.Result;
import org.apache.hadoop.hbase.client.RowMutations;
import org.apache.hadoop.hbase.io.hfile.CacheConfig;
import org.apache.hadoop.hbase.io.hfile.HFile;
import org.apache.hadoop.hbase.master.MasterFileSystem;
import org.apache.hadoop.hbase.master.RegionState;
import org.apache.hadoop.hbase.protobuf.ProtobufUtil;
import org.apache.hadoop.hbase.protobuf.generated.AdminProtos.AdminService.BlockingInterface;
import org.apache.hadoop.hbase.regionserver.HRegion;
import org.apache.hadoop.hbase.regionserver.HRegionFileSystem;
import org.apache.hadoop.hbase.regionserver.StoreFileInfo;
import org.apache.hadoop.hbase.regionserver.wal.HLogUtil;
import org.apache.hadoop.hbase.security.UserProvider;
import org.apache.hadoop.hbase.util.Bytes.ByteArrayComparator;
import org.apache.hadoop.hbase.util.HBaseFsck.ErrorReporter.ERROR_CODE;
import org.apache.hadoop.hbase.util.hbck.HFileCorruptionChecker;
import org.apache.hadoop.hbase.util.hbck.TableIntegrityErrorHandler;
import org.apache.hadoop.hbase.util.hbck.TableIntegrityErrorHandlerImpl;
import org.apache.hadoop.hbase.util.hbck.TableLockChecker;
import org.apache.hadoop.hbase.zookeeper.MetaRegionTracker;
import org.apache.hadoop.hbase.zookeeper.ZKTableStateClientSideReader;
import org.apache.hadoop.hbase.zookeeper.ZooKeeperWatcher;
import org.apache.hadoop.io.IOUtils;
import org.apache.hadoop.security.AccessControlException;
import org.apache.hadoop.security.UserGroupInformation;
import org.apache.hadoop.util.ReflectionUtils;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.apache.zookeeper.KeeperException;

import com.google.common.base.Joiner;
import com.google.common.base.Preconditions;
import com.google.common.collect.Lists;
import com.google.common.collect.Multimap;
import com.google.common.collect.TreeMultimap;
import com.google.protobuf.ServiceException;

/**
 * HBaseFsck (hbck) is a tool for checking and repairing region consistency and
 * table integrity problems in a corrupted HBase.
 * <p>
 * Region consistency checks verify that hbase:meta, region deployment on region
 * servers and the state of data in HDFS (.regioninfo files) all are in
 * accordance.
 * <p>
 * Table integrity checks verify that all possible row keys resolve to exactly
 * one region of a table.  This means there are no individual degenerate
 * or backwards regions; no holes between regions; and that there are no
 * overlapping regions.
 * <p>
 * The general repair strategy works in two phases:
 * <ol>
 * <li> Repair Table Integrity on HDFS. (merge or fabricate regions)
 * <li> Repair Region Consistency with hbase:meta and assignments
 * </ol>
 * <p>
 * For table integrity repairs, the tables' region directories are scanned
 * for .regioninfo files.  Each table's integrity is then verified.  If there
 * are any orphan regions (regions with no .regioninfo files) or holes, new
 * regions are fabricated.  Backwards regions are sidelined as well as empty
 * degenerate (endkey==startkey) regions.  If there are any overlapping regions,
 * a new region is created and all data is merged into the new region.
 * <p>
 * Table integrity repairs deal solely with HDFS and could potentially be done
 * offline -- the hbase region servers or master do not need to be running.
 * This phase can eventually be used to completely reconstruct the hbase:meta table in
 * an offline fashion.
 * <p>
 * Region consistency requires three conditions -- 1) valid .regioninfo file
 * present in an HDFS region dir,  2) valid row with .regioninfo data in META,
 * and 3) a region is deployed only at the regionserver that was assigned to
 * with proper state in the master.
 * <p>
 * Region consistency repairs require hbase to be online so that hbck can
 * contact the HBase master and region servers.  The hbck#connect() method must
 * first be called successfully.  Much of the region consistency information
 * is transient and less risky to repair.
 * <p>
 * If hbck is run from the command line, there are a handful of arguments that
 * can be used to limit the kinds of repairs hbck will do.  See the code in
 * {@link #printUsageAndExit()} for more details.
 */
@InterfaceAudience.Public
@InterfaceStability.Evolving
public class HBaseFsck extends Configured {
    public static final long DEFAULT_TIME_LAG = 60000; // default value of 1 minute
    public static final long DEFAULT_SLEEP_BEFORE_RERUN = 10000;
    private static final int MAX_NUM_THREADS = 50; // #threads to contact regions
    private static boolean rsSupportsOffline = true;
    private static final int DEFAULT_OVERLAPS_TO_SIDELINE = 2;
    private static final int DEFAULT_MAX_MERGE = 5;
    private static final String TO_BE_LOADED = "to_be_loaded";

    /**********************
     * Internal resources
     **********************/
    private static final Log LOG = LogFactory.getLog(HBaseFsck.class.getName());
    private ClusterStatus status;
    private HConnection connection;
    private HBaseAdmin admin;
    private HTable meta;
    // threads to do ||izable tasks: retrieve data from regionservers, handle overlapping regions
    protected ExecutorService executor;
    private long startMillis = System.currentTimeMillis();
    private HFileCorruptionChecker hfcc;
    private int retcode = 0;

    /***********
     * Options
     ***********/
    private static boolean details = false; // do we display the full report
    private long timelag = DEFAULT_TIME_LAG; // tables whose modtime is older
    private boolean fixAssignments = false; // fix assignment errors?
    private boolean fixMeta = false; // fix meta errors?
    private boolean checkHdfs = true; // load and check fs consistency?
    private boolean fixHdfsHoles = false; // fix fs holes?
    private boolean fixHdfsOverlaps = false; // fix fs overlaps (risky)
    private boolean fixHdfsOrphans = false; // fix fs holes (missing .regioninfo)
    private boolean fixTableOrphans = false; // fix fs holes (missing .tableinfo)
    private boolean fixVersionFile = false; // fix missing hbase.version file in hdfs
    private boolean fixSplitParents = false; // fix lingering split parents
    private boolean fixReferenceFiles = false; // fix lingering reference store file
    private boolean fixEmptyMetaCells = false; // fix (remove) empty REGIONINFO_QUALIFIER rows
    private boolean fixTableLocks = false; // fix table locks which are expired

    // limit checking/fixes to listed tables, if empty attempt to check/fix all
    // hbase:meta are always checked
    private Set<TableName> tablesIncluded = new HashSet<TableName>();
    private int maxMerge = DEFAULT_MAX_MERGE; // maximum number of overlapping regions to merge
    private int maxOverlapsToSideline = DEFAULT_OVERLAPS_TO_SIDELINE; // maximum number of overlapping regions to sideline
    private boolean sidelineBigOverlaps = false; // sideline overlaps with >maxMerge regions
    private Path sidelineDir = null;

    private boolean rerun = false; // if we tried to fix something, rerun hbck
    private static boolean summary = false; // if we want to print less output
    private boolean checkMetaOnly = false;
    private boolean checkRegionBoundaries = false;
    private boolean ignorePreCheckPermission = false; // if pre-check permission

    /*********
     * State
     *********/
    final private ErrorReporter errors;
    int fixes = 0;

    /**
     * This map contains the state of all hbck items.  It maps from encoded region
     * name to HbckInfo structure.  The information contained in HbckInfo is used
     * to detect and correct consistency (hdfs/meta/deployment) problems.
     */
    private TreeMap<String, HbckInfo> regionInfoMap = new TreeMap<String, HbckInfo>();
    private TreeSet<TableName> disabledTables = new TreeSet<TableName>();
    // Empty regioninfo qualifiers in hbase:meta
    private Set<Result> emptyRegionInfoQualifiers = new HashSet<Result>();

    /**
     * This map from Tablename -> TableInfo contains the structures necessary to
     * detect table consistency problems (holes, dupes, overlaps).  It is sorted
     * to prevent dupes.
     *
     * If tablesIncluded is empty, this map contains all tables.
     * Otherwise, it contains only meta tables and tables in tablesIncluded,
     * unless checkMetaOnly is specified, in which case, it contains only
     * the meta table
     */
    private SortedMap<TableName, TableInfo> tablesInfo = new ConcurrentSkipListMap<TableName, TableInfo>();

    /**
     * When initially looking at HDFS, we attempt to find any orphaned data.
     */
    private List<HbckInfo> orphanHdfsDirs = Collections.synchronizedList(new ArrayList<HbckInfo>());

    private Map<TableName, Set<String>> orphanTableDirs = new HashMap<TableName, Set<String>>();

    /**
     * Constructor
     *
     * @param conf Configuration object
     * @throws MasterNotRunningException if the master is not running
     * @throws ZooKeeperConnectionException if unable to connect to ZooKeeper
     */
    public HBaseFsck(Configuration conf)
            throws MasterNotRunningException, ZooKeeperConnectionException, IOException, ClassNotFoundException {
        super(conf);
        // make a copy, just to be sure we're not overriding someone else's config
        setConf(HBaseConfiguration.create(getConf()));
        // disable blockcache for tool invocation, see HBASE-10500
        getConf().setFloat(HConstants.HFILE_BLOCK_CACHE_SIZE_KEY, 0);
        errors = getErrorReporter(conf);

        int numThreads = conf.getInt("hbasefsck.numthreads", MAX_NUM_THREADS);
        executor = new ScheduledThreadPoolExecutor(numThreads, Threads.newDaemonThreadFactory("hbasefsck"));
    }

    /**
     * Constructor
     *
     * @param conf
     *          Configuration object
     * @throws MasterNotRunningException
     *           if the master is not running
     * @throws ZooKeeperConnectionException
     *           if unable to connect to ZooKeeper
     */
    public HBaseFsck(Configuration conf, ExecutorService exec)
            throws MasterNotRunningException, ZooKeeperConnectionException, IOException, ClassNotFoundException {
        super(conf);
        errors = getErrorReporter(getConf());
        this.executor = exec;
    }

    /**
     * To repair region consistency, one must call connect() in order to repair
     * online state.
     */
    public void connect() throws IOException {
        connection = HConnectionManager.createConnection(getConf());
        admin = new HBaseAdmin(connection);
        meta = new HTable(TableName.META_TABLE_NAME, connection);
        status = admin.getClusterStatus();
    }

    /**
     * Get deployed regions according to the region servers.
     */
    private void loadDeployedRegions() throws IOException, InterruptedException {
        // From the master, get a list of all known live region servers
        Collection<ServerName> regionServers = status.getServers();
        errors.print("Number of live region servers: " + regionServers.size());
        if (details) {
            for (ServerName rsinfo : regionServers) {
                errors.print("  " + rsinfo.getServerName());
            }
        }

        // From the master, get a list of all dead region servers
        Collection<ServerName> deadRegionServers = status.getDeadServerNames();
        errors.print("Number of dead region servers: " + deadRegionServers.size());
        if (details) {
            for (ServerName name : deadRegionServers) {
                errors.print("  " + name);
            }
        }

        // Print the current master name and state
        errors.print("Master: " + status.getMaster());

        // Print the list of all backup masters
        Collection<ServerName> backupMasters = status.getBackupMasters();
        errors.print("Number of backup masters: " + backupMasters.size());
        if (details) {
            for (ServerName name : backupMasters) {
                errors.print("  " + name);
            }
        }

        errors.print("Average load: " + status.getAverageLoad());
        errors.print("Number of requests: " + status.getRequestsCount());
        errors.print("Number of regions: " + status.getRegionsCount());

        Map<String, RegionState> rits = status.getRegionsInTransition();
        errors.print("Number of regions in transition: " + rits.size());
        if (details) {
            for (RegionState state : rits.values()) {
                errors.print("  " + state.toDescriptiveString());
            }
        }

        // Determine what's deployed
        processRegionServers(regionServers);
    }

    /**
     * Clear the current state of hbck.
     */
    private void clearState() {
        // Make sure regionInfo is empty before starting
        fixes = 0;
        regionInfoMap.clear();
        emptyRegionInfoQualifiers.clear();
        disabledTables.clear();
        errors.clear();
        tablesInfo.clear();
        orphanHdfsDirs.clear();
    }

    /**
     * This repair method analyzes hbase data in hdfs and repairs it to satisfy
     * the table integrity rules.  HBase doesn't need to be online for this
     * operation to work.
     */
    public void offlineHdfsIntegrityRepair() throws IOException, InterruptedException {
        // Initial pass to fix orphans.
        if (shouldCheckHdfs() && (shouldFixHdfsOrphans() || shouldFixHdfsHoles() || shouldFixHdfsOverlaps()
                || shouldFixTableOrphans())) {
            LOG.info("Loading regioninfos HDFS");
            // if nothing is happening this should always complete in two iterations.
            int maxIterations = getConf().getInt("hbase.hbck.integrityrepair.iterations.max", 3);
            int curIter = 0;
            do {
                clearState(); // clears hbck state and reset fixes to 0 and.
                // repair what's on HDFS
                restoreHdfsIntegrity();
                curIter++;// limit the number of iterations.
            } while (fixes > 0 && curIter <= maxIterations);

            // Repairs should be done in the first iteration and verification in the second.
            // If there are more than 2 passes, something funny has happened.
            if (curIter > 2) {
                if (curIter == maxIterations) {
                    LOG.warn("Exiting integrity repairs after max " + curIter + " iterations. "
                            + "Tables integrity may not be fully repaired!");
                } else {
                    LOG.info("Successfully exiting integrity repairs after " + curIter + " iterations");
                }
            }
        }
    }

    /**
     * This repair method requires the cluster to be online since it contacts
     * region servers and the masters.  It makes each region's state in HDFS, in
     * hbase:meta, and deployments consistent.
     *
     * @return If > 0 , number of errors detected, if < 0 there was an unrecoverable
     * error.  If 0, we have a clean hbase.
     */
    public int onlineConsistencyRepair() throws IOException, KeeperException, InterruptedException {
        clearState();

        // get regions according to what is online on each RegionServer
        loadDeployedRegions();
        // check whether hbase:meta is deployed and online
        recordMetaRegion();
        // Check if hbase:meta is found only once and in the right place
        if (!checkMetaRegion()) {
            String errorMsg = "hbase:meta table is not consistent. ";
            if (shouldFixAssignments()) {
                errorMsg += "HBCK will try fixing it. Rerun once hbase:meta is back to consistent state.";
            } else {
                errorMsg += "Run HBCK with proper fix options to fix hbase:meta inconsistency.";
            }
            errors.reportError(errorMsg + " Exiting...");
            return -2;
        }
        // Not going with further consistency check for tables when hbase:meta itself is not consistent.
        LOG.info("Loading regionsinfo from the hbase:meta table");
        boolean success = loadMetaEntries();
        if (!success)
            return -1;

        // Empty cells in hbase:meta?
        reportEmptyMetaCells();

        // Check if we have to cleanup empty REGIONINFO_QUALIFIER rows from hbase:meta
        if (shouldFixEmptyMetaCells()) {
            fixEmptyMetaCells();
        }

        // get a list of all tables that have not changed recently.
        if (!checkMetaOnly) {
            reportTablesInFlux();
        }

        // load regiondirs and regioninfos from HDFS
        if (shouldCheckHdfs()) {
            loadHdfsRegionDirs();
            loadHdfsRegionInfos();
        }

        // Get disabled tables from ZooKeeper
        loadDisabledTables();

        // fix the orphan tables
        fixOrphanTables();

        // Check and fix consistency
        checkAndFixConsistency();

        // Check integrity (does not fix)
        checkIntegrity();
        return errors.getErrorList().size();
    }

    /**
     * Contacts the master and prints out cluster-wide information
     * @return 0 on success, non-zero on failure
     */
    public int onlineHbck() throws IOException, KeeperException, InterruptedException, ServiceException {
        // print hbase server version
        errors.print("Version: " + status.getHBaseVersion());
        offlineHdfsIntegrityRepair();

        // turn the balancer off
        boolean oldBalancer = admin.setBalancerRunning(false, true);
        try {
            onlineConsistencyRepair();
        } finally {
            admin.setBalancerRunning(oldBalancer, false);
        }

        if (checkRegionBoundaries) {
            checkRegionBoundaries();
        }

        offlineReferenceFileRepair();

        checkAndFixTableLocks();

        // Print table summary
        printTableSummary(tablesInfo);
        return errors.summarize();
    }

    public static byte[] keyOnly(byte[] b) {
        if (b == null)
            return b;
        int rowlength = Bytes.toShort(b, 0);
        byte[] result = new byte[rowlength];
        System.arraycopy(b, Bytes.SIZEOF_SHORT, result, 0, rowlength);
        return result;
    }

    private static class RegionBoundariesInformation {
        public byte[] regionName;
        public byte[] metaFirstKey;
        public byte[] metaLastKey;
        public byte[] storesFirstKey;
        public byte[] storesLastKey;

        @Override
        public String toString() {
            return "regionName=" + Bytes.toStringBinary(regionName) + "\nmetaFirstKey="
                    + Bytes.toStringBinary(metaFirstKey) + "\nmetaLastKey=" + Bytes.toStringBinary(metaLastKey)
                    + "\nstoresFirstKey=" + Bytes.toStringBinary(storesFirstKey) + "\nstoresLastKey="
                    + Bytes.toStringBinary(storesLastKey);
        }
    }

    public void checkRegionBoundaries() {
        try {
            ByteArrayComparator comparator = new ByteArrayComparator();
            List<HRegionInfo> regions = MetaScanner.listAllRegions(getConf(), false);
            final RegionBoundariesInformation currentRegionBoundariesInformation = new RegionBoundariesInformation();
            Path hbaseRoot = FSUtils.getRootDir(getConf());
            for (HRegionInfo regionInfo : regions) {
                Path tableDir = FSUtils.getTableDir(hbaseRoot, regionInfo.getTable());
                currentRegionBoundariesInformation.regionName = regionInfo.getRegionName();
                // For each region, get the start and stop key from the META and compare them to the
                // same information from the Stores.
                Path path = new Path(tableDir, regionInfo.getEncodedName());
                FileSystem fs = path.getFileSystem(getConf());
                FileStatus[] files = fs.listStatus(path);
                // For all the column families in this region...
                byte[] storeFirstKey = null;
                byte[] storeLastKey = null;
                for (FileStatus file : files) {
                    String fileName = file.getPath().toString();
                    fileName = fileName.substring(fileName.lastIndexOf("/") + 1);
                    if (!fileName.startsWith(".") && !fileName.endsWith("recovered.edits")) {
                        FileStatus[] storeFiles = fs.listStatus(file.getPath());
                        // For all the stores in this column family.
                        for (FileStatus storeFile : storeFiles) {
                            HFile.Reader reader = HFile.createReader(fs, storeFile.getPath(),
                                    new CacheConfig(getConf()), getConf());
                            if ((reader.getFirstKey() != null) && ((storeFirstKey == null)
                                    || (comparator.compare(storeFirstKey, reader.getFirstKey()) > 0))) {
                                storeFirstKey = reader.getFirstKey();
                            }
                            if ((reader.getLastKey() != null) && ((storeLastKey == null)
                                    || (comparator.compare(storeLastKey, reader.getLastKey())) < 0)) {
                                storeLastKey = reader.getLastKey();
                            }
                            reader.close();
                        }
                    }
                }
                currentRegionBoundariesInformation.metaFirstKey = regionInfo.getStartKey();
                currentRegionBoundariesInformation.metaLastKey = regionInfo.getEndKey();
                currentRegionBoundariesInformation.storesFirstKey = keyOnly(storeFirstKey);
                currentRegionBoundariesInformation.storesLastKey = keyOnly(storeLastKey);
                if (currentRegionBoundariesInformation.metaFirstKey.length == 0)
                    currentRegionBoundariesInformation.metaFirstKey = null;
                if (currentRegionBoundariesInformation.metaLastKey.length == 0)
                    currentRegionBoundariesInformation.metaLastKey = null;

                // For a region to be correct, we need the META start key to be smaller or equal to the
                // smallest start key from all the stores, and the start key from the next META entry to
                // be bigger than the last key from all the current stores. First region start key is null;
                // Last region end key is null; some regions can be empty and not have any store.

                boolean valid = true;
                // Checking start key.
                if ((currentRegionBoundariesInformation.storesFirstKey != null)
                        && (currentRegionBoundariesInformation.metaFirstKey != null)) {
                    valid = valid && comparator.compare(currentRegionBoundariesInformation.storesFirstKey,
                            currentRegionBoundariesInformation.metaFirstKey) >= 0;
                }
                // Checking stop key.
                if ((currentRegionBoundariesInformation.storesLastKey != null)
                        && (currentRegionBoundariesInformation.metaLastKey != null)) {
                    valid = valid && comparator.compare(currentRegionBoundariesInformation.storesLastKey,
                            currentRegionBoundariesInformation.metaLastKey) < 0;
                }
                if (!valid) {
                    errors.reportError(ERROR_CODE.BOUNDARIES_ERROR, "Found issues with regions boundaries",
                            tablesInfo.get(regionInfo.getTable()));
                    LOG.warn("Region's boundaries not alligned between stores and META for:");
                    LOG.warn(currentRegionBoundariesInformation);
                }
            }
        } catch (IOException e) {
            LOG.error(e);
        }
    }

    /**
     * Iterates through the list of all orphan/invalid regiondirs.
     */
    private void adoptHdfsOrphans(Collection<HbckInfo> orphanHdfsDirs) throws IOException {
        for (HbckInfo hi : orphanHdfsDirs) {
            LOG.info("Attempting to handle orphan hdfs dir: " + hi.getHdfsRegionDir());
            adoptHdfsOrphan(hi);
        }
    }

    /**
     * Orphaned regions are regions without a .regioninfo file in them.  We "adopt"
     * these orphans by creating a new region, and moving the column families,
     * recovered edits, HLogs, into the new region dir.  We determine the region
     * startkey and endkeys by looking at all of the hfiles inside the column
     * families to identify the min and max keys. The resulting region will
     * likely violate table integrity but will be dealt with by merging
     * overlapping regions.
     */
    @SuppressWarnings("deprecation")
    private void adoptHdfsOrphan(HbckInfo hi) throws IOException {
        Path p = hi.getHdfsRegionDir();
        FileSystem fs = p.getFileSystem(getConf());
        FileStatus[] dirs = fs.listStatus(p);
        if (dirs == null) {
            LOG.warn("Attempt to adopt ophan hdfs region skipped becuase no files present in " + p
                    + ". This dir could probably be deleted.");
            return;
        }

        TableName tableName = hi.getTableName();
        TableInfo tableInfo = tablesInfo.get(tableName);
        Preconditions.checkNotNull(tableInfo, "Table '" + tableName + "' not present!");
        HTableDescriptor template = tableInfo.getHTD();

        // find min and max key values
        Pair<byte[], byte[]> orphanRegionRange = null;
        for (FileStatus cf : dirs) {
            String cfName = cf.getPath().getName();
            // TODO Figure out what the special dirs are
            if (cfName.startsWith(".") || cfName.equals(HConstants.SPLIT_LOGDIR_NAME))
                continue;

            FileStatus[] hfiles = fs.listStatus(cf.getPath());
            for (FileStatus hfile : hfiles) {
                byte[] start, end;
                HFile.Reader hf = null;
                try {
                    CacheConfig cacheConf = new CacheConfig(getConf());
                    hf = HFile.createReader(fs, hfile.getPath(), cacheConf, getConf());
                    hf.loadFileInfo();
                    KeyValue startKv = KeyValue.createKeyValueFromKey(hf.getFirstKey());
                    start = startKv.getRow();
                    KeyValue endKv = KeyValue.createKeyValueFromKey(hf.getLastKey());
                    end = endKv.getRow();
                } catch (IOException ioe) {
                    LOG.warn("Problem reading orphan file " + hfile + ", skipping");
                    continue;
                } catch (NullPointerException ioe) {
                    LOG.warn("Orphan file " + hfile + " is possibly corrupted HFile, skipping");
                    continue;
                } finally {
                    if (hf != null) {
                        hf.close();
                    }
                }

                // expand the range to include the range of all hfiles
                if (orphanRegionRange == null) {
                    // first range
                    orphanRegionRange = new Pair<byte[], byte[]>(start, end);
                } else {
                    // TODO add test

                    // expand range only if the hfile is wider.
                    if (Bytes.compareTo(orphanRegionRange.getFirst(), start) > 0) {
                        orphanRegionRange.setFirst(start);
                    }
                    if (Bytes.compareTo(orphanRegionRange.getSecond(), end) < 0) {
                        orphanRegionRange.setSecond(end);
                    }
                }
            }
        }
        if (orphanRegionRange == null) {
            LOG.warn("No data in dir " + p + ", sidelining data");
            fixes++;
            sidelineRegionDir(fs, hi);
            return;
        }
        LOG.info("Min max keys are : [" + Bytes.toString(orphanRegionRange.getFirst()) + ", "
                + Bytes.toString(orphanRegionRange.getSecond()) + ")");

        // create new region on hdfs.  move data into place.
        HRegionInfo hri = new HRegionInfo(template.getTableName(), orphanRegionRange.getFirst(),
                orphanRegionRange.getSecond());
        LOG.info("Creating new region : " + hri);
        HRegion region = HBaseFsckRepair.createHDFSRegionDir(getConf(), hri, template);
        Path target = region.getRegionFileSystem().getRegionDir();

        // rename all the data to new region
        mergeRegionDirs(target, hi);
        fixes++;
    }

    /**
     * This method determines if there are table integrity errors in HDFS.  If
     * there are errors and the appropriate "fix" options are enabled, the method
     * will first correct orphan regions making them into legit regiondirs, and
     * then reload to merge potentially overlapping regions.
     *
     * @return number of table integrity errors found
     */
    private int restoreHdfsIntegrity() throws IOException, InterruptedException {
        // Determine what's on HDFS
        LOG.info("Loading HBase regioninfo from HDFS...");
        loadHdfsRegionDirs(); // populating regioninfo table.

        int errs = errors.getErrorList().size();
        // First time just get suggestions.
        tablesInfo = loadHdfsRegionInfos(); // update tableInfos based on region info in fs.
        checkHdfsIntegrity(false, false);

        if (errors.getErrorList().size() == errs) {
            LOG.info("No integrity errors.  We are done with this phase. Glorious.");
            return 0;
        }

        if (shouldFixHdfsOrphans() && orphanHdfsDirs.size() > 0) {
            adoptHdfsOrphans(orphanHdfsDirs);
            // TODO optimize by incrementally adding instead of reloading.
        }

        // Make sure there are no holes now.
        if (shouldFixHdfsHoles()) {
            clearState(); // this also resets # fixes.
            loadHdfsRegionDirs();
            tablesInfo = loadHdfsRegionInfos(); // update tableInfos based on region info in fs.
            tablesInfo = checkHdfsIntegrity(shouldFixHdfsHoles(), false);
        }

        // Now we fix overlaps
        if (shouldFixHdfsOverlaps()) {
            // second pass we fix overlaps.
            clearState(); // this also resets # fixes.
            loadHdfsRegionDirs();
            tablesInfo = loadHdfsRegionInfos(); // update tableInfos based on region info in fs.
            tablesInfo = checkHdfsIntegrity(false, shouldFixHdfsOverlaps());
        }

        return errors.getErrorList().size();
    }

    /**
     * Scan all the store file names to find any lingering reference files,
     * which refer to some none-exiting files. If "fix" option is enabled,
     * any lingering reference file will be sidelined if found.
     * <p>
     * Lingering reference file prevents a region from opening. It has to
     * be fixed before a cluster can start properly.
     */
    private void offlineReferenceFileRepair() throws IOException {
        Configuration conf = getConf();
        Path hbaseRoot = FSUtils.getRootDir(conf);
        FileSystem fs = hbaseRoot.getFileSystem(conf);
        Map<String, Path> allFiles = FSUtils.getTableStoreFilePathMap(fs, hbaseRoot);
        for (Path path : allFiles.values()) {
            boolean isReference = false;
            try {
                isReference = StoreFileInfo.isReference(path);
            } catch (Throwable t) {
                // Ignore. Some files may not be store files at all.
                // For example, files under .oldlogs folder in hbase:meta
                // Warning message is already logged by
                // StoreFile#isReference.
            }
            if (!isReference)
                continue;

            Path referredToFile = StoreFileInfo.getReferredToFile(path);
            if (fs.exists(referredToFile))
                continue; // good, expected

            // Found a lingering reference file
            errors.reportError(ERROR_CODE.LINGERING_REFERENCE_HFILE, "Found lingering reference file " + path);
            if (!shouldFixReferenceFiles())
                continue;

            // Now, trying to fix it since requested
            boolean success = false;
            String pathStr = path.toString();

            // A reference file path should be like
            // ${hbase.rootdir}/data/namespace/table_name/region_id/family_name/referred_file.region_name
            // Up 5 directories to get the root folder.
            // So the file will be sidelined to a similar folder structure.
            int index = pathStr.lastIndexOf(Path.SEPARATOR_CHAR);
            for (int i = 0; index > 0 && i < 5; i++) {
                index = pathStr.lastIndexOf(Path.SEPARATOR_CHAR, index - 1);
            }
            if (index > 0) {
                Path rootDir = getSidelineDir();
                Path dst = new Path(rootDir, pathStr.substring(index + 1));
                fs.mkdirs(dst.getParent());
                LOG.info("Trying to sildeline reference file " + path + " to " + dst);
                setShouldRerun();

                success = fs.rename(path, dst);
            }
            if (!success) {
                LOG.error("Failed to sideline reference file " + path);
            }
        }
    }

    /**
     * TODO -- need to add tests for this.
     */
    private void reportEmptyMetaCells() {
        errors.print(
                "Number of empty REGIONINFO_QUALIFIER rows in hbase:meta: " + emptyRegionInfoQualifiers.size());
        if (details) {
            for (Result r : emptyRegionInfoQualifiers) {
                errors.print("  " + r);
            }
        }
    }

    /**
     * TODO -- need to add tests for this.
     */
    private void reportTablesInFlux() {
        AtomicInteger numSkipped = new AtomicInteger(0);
        HTableDescriptor[] allTables = getTables(numSkipped);
        errors.print("Number of Tables: " + allTables.length);
        if (details) {
            if (numSkipped.get() > 0) {
                errors.detail("Number of Tables in flux: " + numSkipped.get());
            }
            for (HTableDescriptor td : allTables) {
                errors.detail("  Table: " + td.getTableName() + "\t" + (td.isReadOnly() ? "ro" : "rw") + "\t"
                        + (td.isMetaRegion() ? "META" : "    ") + "\t" + " families: " + td.getFamilies().size());
            }
        }
    }

    public ErrorReporter getErrors() {
        return errors;
    }

    /**
     * Read the .regioninfo file from the file system.  If there is no
     * .regioninfo, add it to the orphan hdfs region list.
     */
    private void loadHdfsRegioninfo(HbckInfo hbi) throws IOException {
        Path regionDir = hbi.getHdfsRegionDir();
        if (regionDir == null) {
            LOG.warn("No HDFS region dir found: " + hbi + " meta=" + hbi.metaEntry);
            return;
        }

        if (hbi.hdfsEntry.hri != null) {
            // already loaded data
            return;
        }

        FileSystem fs = FileSystem.get(getConf());
        HRegionInfo hri = HRegionFileSystem.loadRegionInfoFileContent(fs, regionDir);
        LOG.debug("HRegionInfo read: " + hri.toString());
        hbi.hdfsEntry.hri = hri;
    }

    /**
     * Exception thrown when a integrity repair operation fails in an
     * unresolvable way.
     */
    public static class RegionRepairException extends IOException {
        private static final long serialVersionUID = 1L;
        final IOException ioe;

        public RegionRepairException(String s, IOException ioe) {
            super(s);
            this.ioe = ioe;
        }
    }

    /**
     * Populate hbi's from regionInfos loaded from file system.
     */
    private SortedMap<TableName, TableInfo> loadHdfsRegionInfos() throws IOException, InterruptedException {
        tablesInfo.clear(); // regenerating the data
        // generate region split structure
        Collection<HbckInfo> hbckInfos = regionInfoMap.values();

        // Parallelized read of .regioninfo files.
        List<WorkItemHdfsRegionInfo> hbis = new ArrayList<WorkItemHdfsRegionInfo>(hbckInfos.size());
        List<Future<Void>> hbiFutures;

        for (HbckInfo hbi : hbckInfos) {
            WorkItemHdfsRegionInfo work = new WorkItemHdfsRegionInfo(hbi, this, errors);
            hbis.add(work);
        }

        // Submit and wait for completion
        hbiFutures = executor.invokeAll(hbis);

        for (int i = 0; i < hbiFutures.size(); i++) {
            WorkItemHdfsRegionInfo work = hbis.get(i);
            Future<Void> f = hbiFutures.get(i);
            try {
                f.get();
            } catch (ExecutionException e) {
                LOG.warn("Failed to read .regioninfo file for region " + work.hbi.getRegionNameAsString(),
                        e.getCause());
            }
        }

        Path hbaseRoot = FSUtils.getRootDir(getConf());
        FileSystem fs = hbaseRoot.getFileSystem(getConf());
        // serialized table info gathering.
        for (HbckInfo hbi : hbckInfos) {

            if (hbi.getHdfsHRI() == null) {
                // was an orphan
                continue;
            }

            // get table name from hdfs, populate various HBaseFsck tables.
            TableName tableName = hbi.getTableName();
            if (tableName == null) {
                // There was an entry in hbase:meta not in the HDFS?
                LOG.warn("tableName was null for: " + hbi);
                continue;
            }

            TableInfo modTInfo = tablesInfo.get(tableName);
            if (modTInfo == null) {
                // only executed once per table.
                modTInfo = new TableInfo(tableName);
                tablesInfo.put(tableName, modTInfo);
                try {
                    HTableDescriptor htd = FSTableDescriptors.getTableDescriptorFromFs(fs, hbaseRoot, tableName);
                    modTInfo.htds.add(htd);
                } catch (IOException ioe) {
                    if (!orphanTableDirs.containsKey(tableName)) {
                        LOG.warn("Unable to read .tableinfo from " + hbaseRoot, ioe);
                        //should only report once for each table
                        errors.reportError(ERROR_CODE.NO_TABLEINFO_FILE,
                                "Unable to read .tableinfo from " + hbaseRoot + "/" + tableName);
                        Set<String> columns = new HashSet<String>();
                        orphanTableDirs.put(tableName, getColumnFamilyList(columns, hbi));
                    }
                }
            }
            if (!hbi.isSkipChecks()) {
                modTInfo.addRegionInfo(hbi);
            }
        }

        loadTableInfosForTablesWithNoRegion();

        return tablesInfo;
    }

    /**
     * To get the column family list according to the column family dirs
     * @param columns
     * @param hbi
     * @return a set of column families
     * @throws IOException
     */
    private Set<String> getColumnFamilyList(Set<String> columns, HbckInfo hbi) throws IOException {
        Path regionDir = hbi.getHdfsRegionDir();
        FileSystem fs = regionDir.getFileSystem(getConf());
        FileStatus[] subDirs = fs.listStatus(regionDir, new FSUtils.FamilyDirFilter(fs));
        for (FileStatus subdir : subDirs) {
            String columnfamily = subdir.getPath().getName();
            columns.add(columnfamily);
        }
        return columns;
    }

    /**
     * To fabricate a .tableinfo file with following contents<br>
     * 1. the correct tablename <br>
     * 2. the correct colfamily list<br>
     * 3. the default properties for both {@link HTableDescriptor} and {@link HColumnDescriptor}<br>
     * @throws IOException
     */
    private boolean fabricateTableInfo(FSTableDescriptors fstd, TableName tableName, Set<String> columns)
            throws IOException {
        if (columns == null || columns.isEmpty())
            return false;
        HTableDescriptor htd = new HTableDescriptor(tableName);
        for (String columnfamimly : columns) {
            htd.addFamily(new HColumnDescriptor(columnfamimly));
        }
        fstd.createTableDescriptor(htd, true);
        return true;
    }

    /**
     * To fix the empty REGIONINFO_QUALIFIER rows from hbase:meta <br>
     * @throws IOException
     */
    public void fixEmptyMetaCells() throws IOException {
        if (shouldFixEmptyMetaCells() && !emptyRegionInfoQualifiers.isEmpty()) {
            LOG.info("Trying to fix empty REGIONINFO_QUALIFIER hbase:meta rows.");
            for (Result region : emptyRegionInfoQualifiers) {
                deleteMetaRegion(region.getRow());
                errors.getErrorList().remove(ERROR_CODE.EMPTY_META_CELL);
            }
            emptyRegionInfoQualifiers.clear();
        }
    }

    /**
     * To fix orphan table by creating a .tableinfo file under tableDir <br>
     * 1. if TableInfo is cached, to recover the .tableinfo accordingly <br>
     * 2. else create a default .tableinfo file with following items<br>
     * &nbsp;2.1 the correct tablename <br>
     * &nbsp;2.2 the correct colfamily list<br>
     * &nbsp;2.3 the default properties for both {@link HTableDescriptor} and {@link HColumnDescriptor}<br>
     * @throws IOException
     */
    public void fixOrphanTables() throws IOException {
        if (shouldFixTableOrphans() && !orphanTableDirs.isEmpty()) {

            List<TableName> tmpList = new ArrayList<TableName>();
            tmpList.addAll(orphanTableDirs.keySet());
            HTableDescriptor[] htds = getHTableDescriptors(tmpList);
            Iterator<Entry<TableName, Set<String>>> iter = orphanTableDirs.entrySet().iterator();
            int j = 0;
            int numFailedCase = 0;
            FSTableDescriptors fstd = new FSTableDescriptors(getConf());
            while (iter.hasNext()) {
                Entry<TableName, Set<String>> entry = (Entry<TableName, Set<String>>) iter.next();
                TableName tableName = entry.getKey();
                LOG.info("Trying to fix orphan table error: " + tableName);
                if (j < htds.length) {
                    if (tableName.equals(htds[j].getTableName())) {
                        HTableDescriptor htd = htds[j];
                        LOG.info("fixing orphan table: " + tableName + " from cache");
                        fstd.createTableDescriptor(htd, true);
                        j++;
                        iter.remove();
                    }
                } else {
                    if (fabricateTableInfo(fstd, tableName, entry.getValue())) {
                        LOG.warn("fixing orphan table: " + tableName + " with a default .tableinfo file");
                        LOG.warn(
                                "Strongly recommend to modify the HTableDescriptor if necessary for: " + tableName);
                        iter.remove();
                    } else {
                        LOG.error("Unable to create default .tableinfo for " + tableName
                                + " while missing column family information");
                        numFailedCase++;
                    }
                }
                fixes++;
            }

            if (orphanTableDirs.isEmpty()) {
                // all orphanTableDirs are luckily recovered
                // re-run doFsck after recovering the .tableinfo file
                setShouldRerun();
                LOG.warn("Strongly recommend to re-run manually hfsck after all orphanTableDirs being fixed");
            } else if (numFailedCase > 0) {
                LOG.error("Failed to fix " + numFailedCase + " OrphanTables with default .tableinfo files");
            }

        }
        //cleanup the list
        orphanTableDirs.clear();

    }

    /**
     * This borrows code from MasterFileSystem.bootstrap()
     *
     * @return an open hbase:meta HRegion
     */
    private HRegion createNewMeta() throws IOException {
        Path rootdir = FSUtils.getRootDir(getConf());
        Configuration c = getConf();
        HRegionInfo metaHRI = new HRegionInfo(HRegionInfo.FIRST_META_REGIONINFO);
        MasterFileSystem.setInfoFamilyCachingForMeta(false);
        HRegion meta = HRegion.createHRegion(metaHRI, rootdir, c, HTableDescriptor.META_TABLEDESC);
        MasterFileSystem.setInfoFamilyCachingForMeta(true);
        return meta;
    }

    /**
     * Generate set of puts to add to new meta.  This expects the tables to be
     * clean with no overlaps or holes.  If there are any problems it returns null.
     *
     * @return An array list of puts to do in bulk, null if tables have problems
     */
    private ArrayList<Put> generatePuts(SortedMap<TableName, TableInfo> tablesInfo) throws IOException {
        ArrayList<Put> puts = new ArrayList<Put>();
        boolean hasProblems = false;
        for (Entry<TableName, TableInfo> e : tablesInfo.entrySet()) {
            TableName name = e.getKey();

            // skip "hbase:meta"
            if (name.compareTo(TableName.META_TABLE_NAME) == 0) {
                continue;
            }

            TableInfo ti = e.getValue();
            for (Entry<byte[], Collection<HbckInfo>> spl : ti.sc.getStarts().asMap().entrySet()) {
                Collection<HbckInfo> his = spl.getValue();
                int sz = his.size();
                if (sz != 1) {
                    // problem
                    LOG.error("Split starting at " + Bytes.toStringBinary(spl.getKey()) + " had " + sz
                            + " regions instead of exactly 1.");
                    hasProblems = true;
                    continue;
                }

                // add the row directly to meta.
                HbckInfo hi = his.iterator().next();
                HRegionInfo hri = hi.getHdfsHRI(); // hi.metaEntry;
                Put p = MetaEditor.makePutFromRegionInfo(hri);
                puts.add(p);
            }
        }
        return hasProblems ? null : puts;
    }

    /**
     * Suggest fixes for each table
     */
    private void suggestFixes(SortedMap<TableName, TableInfo> tablesInfo) throws IOException {
        for (TableInfo tInfo : tablesInfo.values()) {
            TableIntegrityErrorHandler handler = tInfo.new IntegrityFixSuggester(tInfo, errors);
            tInfo.checkRegionChain(handler);
        }
    }

    /**
     * Rebuilds meta from information in hdfs/fs.  Depends on configuration
     * settings passed into hbck constructor to point to a particular fs/dir.
     *
     * @param fix flag that determines if method should attempt to fix holes
     * @return true if successful, false if attempt failed.
     */
    public boolean rebuildMeta(boolean fix) throws IOException, InterruptedException {

        // TODO check to make sure hbase is offline. (or at least the table
        // currently being worked on is off line)

        // Determine what's on HDFS
        LOG.info("Loading HBase regioninfo from HDFS...");
        loadHdfsRegionDirs(); // populating regioninfo table.

        int errs = errors.getErrorList().size();
        tablesInfo = loadHdfsRegionInfos(); // update tableInfos based on region info in fs.
        checkHdfsIntegrity(false, false);

        // make sure ok.
        if (errors.getErrorList().size() != errs) {
            // While in error state, iterate until no more fixes possible
            while (true) {
                fixes = 0;
                suggestFixes(tablesInfo);
                errors.clear();
                loadHdfsRegionInfos(); // update tableInfos based on region info in fs.
                checkHdfsIntegrity(shouldFixHdfsHoles(), shouldFixHdfsOverlaps());

                int errCount = errors.getErrorList().size();

                if (fixes == 0) {
                    if (errCount > 0) {
                        return false; // failed to fix problems.
                    } else {
                        break; // no fixes and no problems? drop out and fix stuff!
                    }
                }
            }
        }

        // we can rebuild, move old meta out of the way and start
        LOG.info("HDFS regioninfo's seems good.  Sidelining old hbase:meta");
        Path backupDir = sidelineOldMeta();

        LOG.info("Creating new hbase:meta");
        HRegion meta = createNewMeta();

        // populate meta
        List<Put> puts = generatePuts(tablesInfo);
        if (puts == null) {
            LOG.fatal("Problem encountered when creating new hbase:meta entries.  "
                    + "You may need to restore the previously sidelined hbase:meta");
            return false;
        }
        meta.batchMutate(puts.toArray(new Put[0]));
        HRegion.closeHRegion(meta);
        LOG.info("Success! hbase:meta table rebuilt.");
        LOG.info("Old hbase:meta is moved into " + backupDir);
        return true;
    }

    private SortedMap<TableName, TableInfo> checkHdfsIntegrity(boolean fixHoles, boolean fixOverlaps)
            throws IOException {
        LOG.info("Checking HBase region split map from HDFS data...");
        for (TableInfo tInfo : tablesInfo.values()) {
            TableIntegrityErrorHandler handler;
            if (fixHoles || fixOverlaps) {
                handler = tInfo.new HDFSIntegrityFixer(tInfo, errors, getConf(), fixHoles, fixOverlaps);
            } else {
                handler = tInfo.new IntegrityFixSuggester(tInfo, errors);
            }
            if (!tInfo.checkRegionChain(handler)) {
                // should dump info as well.
                errors.report("Found inconsistency in table " + tInfo.getName());
            }
        }
        return tablesInfo;
    }

    private Path getSidelineDir() throws IOException {
        if (sidelineDir == null) {
            Path hbaseDir = FSUtils.getRootDir(getConf());
            Path hbckDir = new Path(hbaseDir, HConstants.HBCK_SIDELINEDIR_NAME);
            sidelineDir = new Path(hbckDir, hbaseDir.getName() + "-" + startMillis);
        }
        return sidelineDir;
    }

    /**
     * Sideline a region dir (instead of deleting it)
     */
    Path sidelineRegionDir(FileSystem fs, HbckInfo hi) throws IOException {
        return sidelineRegionDir(fs, null, hi);
    }

    /**
     * Sideline a region dir (instead of deleting it)
     *
     * @param parentDir if specified, the region will be sidelined to
     * folder like .../parentDir/<table name>/<region name>. The purpose
     * is to group together similar regions sidelined, for example, those
     * regions should be bulk loaded back later on. If null, it is ignored.
     */
    Path sidelineRegionDir(FileSystem fs, String parentDir, HbckInfo hi) throws IOException {
        TableName tableName = hi.getTableName();
        Path regionDir = hi.getHdfsRegionDir();

        if (!fs.exists(regionDir)) {
            LOG.warn("No previous " + regionDir + " exists.  Continuing.");
            return null;
        }

        Path rootDir = getSidelineDir();
        if (parentDir != null) {
            rootDir = new Path(rootDir, parentDir);
        }
        Path sidelineTableDir = FSUtils.getTableDir(rootDir, tableName);
        Path sidelineRegionDir = new Path(sidelineTableDir, regionDir.getName());
        fs.mkdirs(sidelineRegionDir);
        boolean success = false;
        FileStatus[] cfs = fs.listStatus(regionDir);
        if (cfs == null) {
            LOG.info("Region dir is empty: " + regionDir);
        } else {
            for (FileStatus cf : cfs) {
                Path src = cf.getPath();
                Path dst = new Path(sidelineRegionDir, src.getName());
                if (fs.isFile(src)) {
                    // simple file
                    success = fs.rename(src, dst);
                    if (!success) {
                        String msg = "Unable to rename file " + src + " to " + dst;
                        LOG.error(msg);
                        throw new IOException(msg);
                    }
                    continue;
                }

                // is a directory.
                fs.mkdirs(dst);

                LOG.info("Sidelining files from " + src + " into containing region " + dst);
                // FileSystem.rename is inconsistent with directories -- if the
                // dst (foo/a) exists and is a dir, and the src (foo/b) is a dir,
                // it moves the src into the dst dir resulting in (foo/a/b).  If
                // the dst does not exist, and the src a dir, src becomes dst. (foo/b)
                FileStatus[] hfiles = fs.listStatus(src);
                if (hfiles != null && hfiles.length > 0) {
                    for (FileStatus hfile : hfiles) {
                        success = fs.rename(hfile.getPath(), dst);
                        if (!success) {
                            String msg = "Unable to rename file " + src + " to " + dst;
                            LOG.error(msg);
                            throw new IOException(msg);
                        }
                    }
                }
                LOG.debug("Sideline directory contents:");
                debugLsr(sidelineRegionDir);
            }
        }

        LOG.info("Removing old region dir: " + regionDir);
        success = fs.delete(regionDir, true);
        if (!success) {
            String msg = "Unable to delete dir " + regionDir;
            LOG.error(msg);
            throw new IOException(msg);
        }
        return sidelineRegionDir;
    }

    /**
     * Side line an entire table.
     */
    void sidelineTable(FileSystem fs, TableName tableName, Path hbaseDir, Path backupHbaseDir) throws IOException {
        Path tableDir = FSUtils.getTableDir(hbaseDir, tableName);
        if (fs.exists(tableDir)) {
            Path backupTableDir = FSUtils.getTableDir(backupHbaseDir, tableName);
            fs.mkdirs(backupTableDir.getParent());
            boolean success = fs.rename(tableDir, backupTableDir);
            if (!success) {
                throw new IOException(
                        "Failed to move  " + tableName + " from " + tableDir + " to " + backupTableDir);
            }
        } else {
            LOG.info("No previous " + tableName + " exists.  Continuing.");
        }
    }

    /**
     * @return Path to backup of original directory
     */
    Path sidelineOldMeta() throws IOException {
        // put current hbase:meta aside.
        Path hbaseDir = FSUtils.getRootDir(getConf());
        FileSystem fs = hbaseDir.getFileSystem(getConf());
        Path backupDir = getSidelineDir();
        fs.mkdirs(backupDir);

        try {
            sidelineTable(fs, TableName.META_TABLE_NAME, hbaseDir, backupDir);
        } catch (IOException e) {
            LOG.fatal("... failed to sideline meta. Currently in inconsistent state.  To restore "
                    + "try to rename hbase:meta in " + backupDir.getName() + " to " + hbaseDir.getName() + ".", e);
            throw e; // throw original exception
        }
        return backupDir;
    }

    /**
     * Load the list of disabled tables in ZK into local set.
     * @throws ZooKeeperConnectionException
     * @throws IOException
     */
    private void loadDisabledTables() throws ZooKeeperConnectionException, IOException {
        HConnectionManager.execute(new HConnectable<Void>(getConf()) {
            @Override
            public Void connect(HConnection connection) throws IOException {
                ZooKeeperWatcher zkw = createZooKeeperWatcher();
                try {
                    for (TableName tableName : ZKTableStateClientSideReader.getDisabledOrDisablingTables(zkw)) {
                        disabledTables.add(tableName);
                    }
                } catch (KeeperException ke) {
                    throw new IOException(ke);
                } catch (InterruptedException e) {
                    throw new InterruptedIOException();
                } finally {
                    zkw.close();
                }
                return null;
            }
        });
    }

    /**
     * Check if the specified region's table is disabled.
     */
    private boolean isTableDisabled(HRegionInfo regionInfo) {
        return disabledTables.contains(regionInfo.getTable());
    }

    /**
     * Scan HDFS for all regions, recording their information into
     * regionInfoMap
     */
    public void loadHdfsRegionDirs() throws IOException, InterruptedException {
        Path rootDir = FSUtils.getRootDir(getConf());
        FileSystem fs = rootDir.getFileSystem(getConf());

        // list all tables from HDFS
        List<FileStatus> tableDirs = Lists.newArrayList();

        boolean foundVersionFile = fs.exists(new Path(rootDir, HConstants.VERSION_FILE_NAME));

        List<Path> paths = FSUtils.getTableDirs(fs, rootDir);
        for (Path path : paths) {
            TableName tableName = FSUtils.getTableName(path);
            if ((!checkMetaOnly && isTableIncluded(tableName)) || tableName.equals(TableName.META_TABLE_NAME)) {
                tableDirs.add(fs.getFileStatus(path));
            }
        }

        // verify that version file exists
        if (!foundVersionFile) {
            errors.reportError(ERROR_CODE.NO_VERSION_FILE, "Version file does not exist in root dir " + rootDir);
            if (shouldFixVersionFile()) {
                LOG.info("Trying to create a new " + HConstants.VERSION_FILE_NAME + " file.");
                setShouldRerun();
                FSUtils.setVersion(fs, rootDir, getConf().getInt(HConstants.THREAD_WAKE_FREQUENCY, 10 * 1000),
                        getConf().getInt(HConstants.VERSION_FILE_WRITE_ATTEMPTS,
                                HConstants.DEFAULT_VERSION_FILE_WRITE_ATTEMPTS));
            }
        }

        // level 1:  <HBASE_DIR>/*
        List<WorkItemHdfsDir> dirs = new ArrayList<WorkItemHdfsDir>(tableDirs.size());
        List<Future<Void>> dirsFutures;

        for (FileStatus tableDir : tableDirs) {
            LOG.debug("Loading region dirs from " + tableDir.getPath());
            dirs.add(new WorkItemHdfsDir(this, fs, errors, tableDir));
        }

        // Invoke and wait for Callables to complete
        dirsFutures = executor.invokeAll(dirs);

        for (Future<Void> f : dirsFutures) {
            try {
                f.get();
            } catch (ExecutionException e) {
                LOG.warn("Could not load region dir ", e.getCause());
            }
        }
    }

    /**
     * Record the location of the hbase:meta region as found in ZooKeeper.
     */
    private boolean recordMetaRegion() throws IOException {
        HRegionLocation metaLocation = connection.locateRegion(TableName.META_TABLE_NAME,
                HConstants.EMPTY_START_ROW);

        // Check if Meta region is valid and existing
        if (metaLocation == null || metaLocation.getRegionInfo() == null || metaLocation.getHostname() == null) {
            errors.reportError(ERROR_CODE.NULL_META_REGION, "META region or some of its attributes are null.");
            return false;
        }
        ServerName sn;
        try {
            sn = getMetaRegionServerName();
        } catch (KeeperException e) {
            throw new IOException(e);
        }
        MetaEntry m = new MetaEntry(metaLocation.getRegionInfo(), sn, System.currentTimeMillis());
        HbckInfo hbckInfo = regionInfoMap.get(metaLocation.getRegionInfo().getEncodedName());
        if (hbckInfo == null) {
            regionInfoMap.put(metaLocation.getRegionInfo().getEncodedName(), new HbckInfo(m));
        } else {
            hbckInfo.metaEntry = m;
        }
        return true;
    }

    private ZooKeeperWatcher createZooKeeperWatcher() throws IOException {
        return new ZooKeeperWatcher(getConf(), "hbase Fsck", new Abortable() {
            @Override
            public void abort(String why, Throwable e) {
                LOG.error(why, e);
                System.exit(1);
            }

            @Override
            public boolean isAborted() {
                return false;
            }

        });
    }

    private ServerName getMetaRegionServerName() throws IOException, KeeperException {
        ZooKeeperWatcher zkw = createZooKeeperWatcher();
        ServerName sn = null;
        try {
            sn = MetaRegionTracker.getMetaRegionLocation(zkw);
        } finally {
            zkw.close();
        }
        return sn;
    }

    /**
     * Contacts each regionserver and fetches metadata about regions.
     * @param regionServerList - the list of region servers to connect to
     * @throws IOException if a remote or network exception occurs
     */
    void processRegionServers(Collection<ServerName> regionServerList) throws IOException, InterruptedException {

        List<WorkItemRegion> workItems = new ArrayList<WorkItemRegion>(regionServerList.size());
        List<Future<Void>> workFutures;

        // loop to contact each region server in parallel
        for (ServerName rsinfo : regionServerList) {
            workItems.add(new WorkItemRegion(this, rsinfo, errors, connection));
        }

        workFutures = executor.invokeAll(workItems);

        for (int i = 0; i < workFutures.size(); i++) {
            WorkItemRegion item = workItems.get(i);
            Future<Void> f = workFutures.get(i);
            try {
                f.get();
            } catch (ExecutionException e) {
                LOG.warn("Could not process regionserver " + item.rsinfo.getHostAndPort(), e.getCause());
            }
        }
    }

    /**
     * Check consistency of all regions that have been found in previous phases.
     */
    private void checkAndFixConsistency() throws IOException, KeeperException, InterruptedException {
        for (java.util.Map.Entry<String, HbckInfo> e : regionInfoMap.entrySet()) {
            checkRegionConsistency(e.getKey(), e.getValue());
        }
    }

    private void preCheckPermission() throws IOException, AccessControlException {
        if (shouldIgnorePreCheckPermission()) {
            return;
        }

        Path hbaseDir = FSUtils.getRootDir(getConf());
        FileSystem fs = hbaseDir.getFileSystem(getConf());
        UserProvider userProvider = UserProvider.instantiate(getConf());
        UserGroupInformation ugi = userProvider.getCurrent().getUGI();
        FileStatus[] files = fs.listStatus(hbaseDir);
        for (FileStatus file : files) {
            try {
                FSUtils.checkAccess(ugi, file, FsAction.WRITE);
            } catch (AccessControlException ace) {
                LOG.warn("Got AccessControlException when preCheckPermission ", ace);
                errors.reportError(ERROR_CODE.WRONG_USAGE,
                        "Current user " + ugi.getUserName() + " does not have write perms to " + file.getPath()
                                + ". Please rerun hbck as hdfs user " + file.getOwner());
                throw new AccessControlException(ace);
            }
        }
    }

    /**
     * Deletes region from meta table
     */
    private void deleteMetaRegion(HbckInfo hi) throws IOException {
        deleteMetaRegion(hi.metaEntry.getRegionName());
    }

    /**
     * Deletes region from meta table
     */
    private void deleteMetaRegion(byte[] metaKey) throws IOException {
        Delete d = new Delete(metaKey);
        meta.delete(d);
        meta.flushCommits();
        LOG.info("Deleted " + Bytes.toString(metaKey) + " from META");
    }

    /**
     * Reset the split parent region info in meta table
     */
    private void resetSplitParent(HbckInfo hi) throws IOException {
        RowMutations mutations = new RowMutations(hi.metaEntry.getRegionName());
        Delete d = new Delete(hi.metaEntry.getRegionName());
        d.deleteColumn(HConstants.CATALOG_FAMILY, HConstants.SPLITA_QUALIFIER);
        d.deleteColumn(HConstants.CATALOG_FAMILY, HConstants.SPLITB_QUALIFIER);
        mutations.add(d);

        HRegionInfo hri = new HRegionInfo(hi.metaEntry);
        hri.setOffline(false);
        hri.setSplit(false);
        Put p = MetaEditor.makePutFromRegionInfo(hri);
        mutations.add(p);

        meta.mutateRow(mutations);
        meta.flushCommits();
        LOG.info("Reset split parent " + hi.metaEntry.getRegionNameAsString() + " in META");
    }

    /**
     * This backwards-compatibility wrapper for permanently offlining a region
     * that should not be alive.  If the region server does not support the
     * "offline" method, it will use the closest unassign method instead.  This
     * will basically work until one attempts to disable or delete the affected
     * table.  The problem has to do with in-memory only master state, so
     * restarting the HMaster or failing over to another should fix this.
     */
    private void offline(byte[] regionName) throws IOException {
        String regionString = Bytes.toStringBinary(regionName);
        if (!rsSupportsOffline) {
            LOG.warn("Using unassign region " + regionString + " instead of using offline method, you should"
                    + " restart HMaster after these repairs");
            admin.unassign(regionName, true);
            return;
        }

        // first time we assume the rs's supports #offline.
        try {
            LOG.info("Offlining region " + regionString);
            admin.offline(regionName);
        } catch (IOException ioe) {
            String notFoundMsg = "java.lang.NoSuchMethodException: "
                    + "org.apache.hadoop.hbase.master.HMaster.offline([B)";
            if (ioe.getMessage().contains(notFoundMsg)) {
                LOG.warn("Using unassign region " + regionString + " instead of using offline method, you should"
                        + " restart HMaster after these repairs");
                rsSupportsOffline = false; // in the future just use unassign
                admin.unassign(regionName, true);
                return;
            }
            throw ioe;
        }
    }

    private void undeployRegions(HbckInfo hi) throws IOException, InterruptedException {
        for (OnlineEntry rse : hi.deployedEntries) {
            LOG.debug("Undeploy region " + rse.hri + " from " + rse.hsa);
            try {
                HBaseFsckRepair.closeRegionSilentlyAndWait(admin, rse.hsa, rse.hri);
                offline(rse.hri.getRegionName());
            } catch (IOException ioe) {
                LOG.warn("Got exception when attempting to offline region "
                        + Bytes.toString(rse.hri.getRegionName()), ioe);
            }
        }
    }

    /**
     * Attempts to undeploy a region from a region server based in information in
     * META.  Any operations that modify the file system should make sure that
     * its corresponding region is not deployed to prevent data races.
     *
     * A separate call is required to update the master in-memory region state
     * kept in the AssignementManager.  Because disable uses this state instead of
     * that found in META, we can't seem to cleanly disable/delete tables that
     * have been hbck fixed.  When used on a version of HBase that does not have
     * the offline ipc call exposed on the master (<0.90.5, <0.92.0) a master
     * restart or failover may be required.
     */
    private void closeRegion(HbckInfo hi) throws IOException, InterruptedException {
        if (hi.metaEntry == null && hi.hdfsEntry == null) {
            undeployRegions(hi);
            return;
        }

        // get assignment info and hregioninfo from meta.
        Get get = new Get(hi.getRegionName());
        get.addColumn(HConstants.CATALOG_FAMILY, HConstants.REGIONINFO_QUALIFIER);
        get.addColumn(HConstants.CATALOG_FAMILY, HConstants.SERVER_QUALIFIER);
        get.addColumn(HConstants.CATALOG_FAMILY, HConstants.STARTCODE_QUALIFIER);
        Result r = meta.get(get);
        ServerName serverName = HRegionInfo.getServerName(r);
        if (serverName == null) {
            errors.reportError("Unable to close region " + hi.getRegionNameAsString() + " because meta does not "
                    + "have handle to reach it.");
            return;
        }

        HRegionInfo hri = HRegionInfo.getHRegionInfo(r);
        if (hri == null) {
            LOG.warn("Unable to close region " + hi.getRegionNameAsString()
                    + " because hbase:meta had invalid or missing " + HConstants.CATALOG_FAMILY_STR + ":"
                    + Bytes.toString(HConstants.REGIONINFO_QUALIFIER) + " qualifier value.");
            return;
        }

        // close the region -- close files and remove assignment
        HBaseFsckRepair.closeRegionSilentlyAndWait(admin, serverName, hri);
    }

    private void tryAssignmentRepair(HbckInfo hbi, String msg)
            throws IOException, KeeperException, InterruptedException {
        // If we are trying to fix the errors
        if (shouldFixAssignments()) {
            errors.print(msg);
            undeployRegions(hbi);
            setShouldRerun();
            HRegionInfo hri = hbi.getHdfsHRI();
            if (hri == null) {
                hri = hbi.metaEntry;
            }
            HBaseFsckRepair.fixUnassigned(admin, hri);
            HBaseFsckRepair.waitUntilAssigned(admin, hri);
        }
    }

    /**
     * Check a single region for consistency and correct deployment.
     */
    private void checkRegionConsistency(final String key, final HbckInfo hbi)
            throws IOException, KeeperException, InterruptedException {
        String descriptiveName = hbi.toString();

        boolean inMeta = hbi.metaEntry != null;
        // In case not checking HDFS, assume the region is on HDFS
        boolean inHdfs = !shouldCheckHdfs() || hbi.getHdfsRegionDir() != null;
        boolean hasMetaAssignment = inMeta && hbi.metaEntry.regionServer != null;
        boolean isDeployed = !hbi.deployedOn.isEmpty();
        boolean isMultiplyDeployed = hbi.deployedOn.size() > 1;
        boolean deploymentMatchesMeta = hasMetaAssignment && isDeployed && !isMultiplyDeployed
                && hbi.metaEntry.regionServer.equals(hbi.deployedOn.get(0));
        boolean splitParent = (hbi.metaEntry == null) ? false
                : hbi.metaEntry.isSplit() && hbi.metaEntry.isOffline();
        boolean shouldBeDeployed = inMeta && !isTableDisabled(hbi.metaEntry);
        boolean recentlyModified = inHdfs && hbi.getModTime() + timelag > System.currentTimeMillis();

        // ========== First the healthy cases =============
        if (hbi.containsOnlyHdfsEdits()) {
            return;
        }
        if (inMeta && inHdfs && isDeployed && deploymentMatchesMeta && shouldBeDeployed) {
            return;
        } else if (inMeta && inHdfs && !shouldBeDeployed && !isDeployed) {
            LOG.info("Region " + descriptiveName + " is in META, and in a disabled "
                    + "tabled that is not deployed");
            return;
        } else if (recentlyModified) {
            LOG.warn("Region " + descriptiveName + " was recently modified -- skipping");
            return;
        }
        // ========== Cases where the region is not in hbase:meta =============
        else if (!inMeta && !inHdfs && !isDeployed) {
            // We shouldn't have record of this region at all then!
            assert false : "Entry for region with no data";
        } else if (!inMeta && !inHdfs && isDeployed) {
            errors.reportError(ERROR_CODE.NOT_IN_META_HDFS,
                    "Region " + descriptiveName + ", key=" + key + ", not on HDFS or in hbase:meta but "
                            + "deployed on " + Joiner.on(", ").join(hbi.deployedOn));
            if (shouldFixAssignments()) {
                undeployRegions(hbi);
            }

        } else if (!inMeta && inHdfs && !isDeployed) {
            if (hbi.isMerged()) {
                // This region has already been merged, the remaining hdfs file will be
                // cleaned by CatalogJanitor later
                hbi.setSkipChecks(true);
                LOG.info("Region " + descriptiveName
                        + " got merge recently, its file(s) will be cleaned by CatalogJanitor later");
                return;
            }
            errors.reportError(ERROR_CODE.NOT_IN_META_OR_DEPLOYED, "Region " + descriptiveName
                    + " on HDFS, but not listed in hbase:meta " + "or deployed on any region server");
            // restore region consistency of an adopted orphan
            if (shouldFixMeta()) {
                if (!hbi.isHdfsRegioninfoPresent()) {
                    LOG.error("Region " + hbi.getHdfsHRI() + " could have been repaired"
                            + " in table integrity repair phase if -fixHdfsOrphans was" + " used.");
                    return;
                }

                LOG.info("Patching hbase:meta with .regioninfo: " + hbi.getHdfsHRI());
                HBaseFsckRepair.fixMetaHoleOnline(getConf(), hbi.getHdfsHRI());

                tryAssignmentRepair(hbi, "Trying to reassign region...");
            }

        } else if (!inMeta && inHdfs && isDeployed) {
            errors.reportError(ERROR_CODE.NOT_IN_META, "Region " + descriptiveName
                    + " not in META, but deployed on " + Joiner.on(", ").join(hbi.deployedOn));
            debugLsr(hbi.getHdfsRegionDir());
            if (shouldFixMeta()) {
                if (!hbi.isHdfsRegioninfoPresent()) {
                    LOG.error("This should have been repaired in table integrity repair phase");
                    return;
                }

                LOG.info("Patching hbase:meta with with .regioninfo: " + hbi.getHdfsHRI());
                HBaseFsckRepair.fixMetaHoleOnline(getConf(), hbi.getHdfsHRI());

                tryAssignmentRepair(hbi, "Trying to fix unassigned region...");
            }

            // ========== Cases where the region is in hbase:meta =============
        } else if (inMeta && inHdfs && !isDeployed && splitParent) {
            // check whether this is an actual error, or just transient state where parent
            // is not cleaned
            if (hbi.metaEntry.splitA != null && hbi.metaEntry.splitB != null) {
                // check that split daughters are there
                HbckInfo infoA = this.regionInfoMap.get(hbi.metaEntry.splitA.getEncodedName());
                HbckInfo infoB = this.regionInfoMap.get(hbi.metaEntry.splitB.getEncodedName());
                if (infoA != null && infoB != null) {
                    // we already processed or will process daughters. Move on, nothing to see here.
                    hbi.setSkipChecks(true);
                    return;
                }
            }
            errors.reportError(ERROR_CODE.LINGERING_SPLIT_PARENT,
                    "Region " + descriptiveName + " is a split parent in META, in HDFS, "
                            + "and not deployed on any region server. This could be transient.");
            if (shouldFixSplitParents()) {
                setShouldRerun();
                resetSplitParent(hbi);
            }
        } else if (inMeta && !inHdfs && !isDeployed) {
            errors.reportError(ERROR_CODE.NOT_IN_HDFS_OR_DEPLOYED, "Region " + descriptiveName
                    + " found in META, but not in HDFS " + "or deployed on any region server.");
            if (shouldFixMeta()) {
                deleteMetaRegion(hbi);
            }
        } else if (inMeta && !inHdfs && isDeployed) {
            errors.reportError(ERROR_CODE.NOT_IN_HDFS,
                    "Region " + descriptiveName + " found in META, but not in HDFS, " + "and deployed on "
                            + Joiner.on(", ").join(hbi.deployedOn));
            // We treat HDFS as ground truth.  Any information in meta is transient
            // and equivalent data can be regenerated.  So, lets unassign and remove
            // these problems from META.
            if (shouldFixAssignments()) {
                errors.print("Trying to fix unassigned region...");
                undeployRegions(hbi);
            }
            if (shouldFixMeta()) {
                // wait for it to complete
                deleteMetaRegion(hbi);
            }
        } else if (inMeta && inHdfs && !isDeployed && shouldBeDeployed) {
            errors.reportError(ERROR_CODE.NOT_DEPLOYED,
                    "Region " + descriptiveName + " not deployed on any region server.");
            tryAssignmentRepair(hbi, "Trying to fix unassigned region...");
        } else if (inMeta && inHdfs && isDeployed && !shouldBeDeployed) {
            errors.reportError(ERROR_CODE.SHOULD_NOT_BE_DEPLOYED,
                    "Region " + descriptiveName + " should not be deployed according "
                            + "to META, but is deployed on " + Joiner.on(", ").join(hbi.deployedOn));
            if (shouldFixAssignments()) {
                errors.print("Trying to close the region " + descriptiveName);
                setShouldRerun();
                HBaseFsckRepair.fixMultiAssignment(admin, hbi.metaEntry, hbi.deployedOn);
            }
        } else if (inMeta && inHdfs && isMultiplyDeployed) {
            errors.reportError(ERROR_CODE.MULTI_DEPLOYED,
                    "Region " + descriptiveName + " is listed in hbase:meta on region server "
                            + hbi.metaEntry.regionServer + " but is multiply assigned to region servers "
                            + Joiner.on(", ").join(hbi.deployedOn));
            // If we are trying to fix the errors
            if (shouldFixAssignments()) {
                errors.print("Trying to fix assignment error...");
                setShouldRerun();
                HBaseFsckRepair.fixMultiAssignment(admin, hbi.metaEntry, hbi.deployedOn);
            }
        } else if (inMeta && inHdfs && isDeployed && !deploymentMatchesMeta) {
            errors.reportError(ERROR_CODE.SERVER_DOES_NOT_MATCH_META,
                    "Region " + descriptiveName + " listed in hbase:meta on region server "
                            + hbi.metaEntry.regionServer + " but found on region server " + hbi.deployedOn.get(0));
            // If we are trying to fix the errors
            if (shouldFixAssignments()) {
                errors.print("Trying to fix assignment error...");
                setShouldRerun();
                HBaseFsckRepair.fixMultiAssignment(admin, hbi.metaEntry, hbi.deployedOn);
                HBaseFsckRepair.waitUntilAssigned(admin, hbi.getHdfsHRI());
            }
        } else {
            errors.reportError(ERROR_CODE.UNKNOWN,
                    "Region " + descriptiveName + " is in an unforeseen state:" + " inMeta=" + inMeta + " inHdfs="
                            + inHdfs + " isDeployed=" + isDeployed + " isMultiplyDeployed=" + isMultiplyDeployed
                            + " deploymentMatchesMeta=" + deploymentMatchesMeta + " shouldBeDeployed="
                            + shouldBeDeployed);
        }
    }

    /**
     * Checks tables integrity. Goes over all regions and scans the tables.
     * Collects all the pieces for each table and checks if there are missing,
     * repeated or overlapping ones.
     * @throws IOException
     */
    SortedMap<TableName, TableInfo> checkIntegrity() throws IOException {
        tablesInfo = new TreeMap<TableName, TableInfo>();
        List<HbckInfo> noHDFSRegionInfos = new ArrayList<HbckInfo>();
        LOG.debug("There are " + regionInfoMap.size() + " region info entries");
        for (HbckInfo hbi : regionInfoMap.values()) {
            // Check only valid, working regions
            if (hbi.metaEntry == null) {
                // this assumes that consistency check has run loadMetaEntry
                noHDFSRegionInfos.add(hbi);
                Path p = hbi.getHdfsRegionDir();
                if (p == null) {
                    errors.report("No regioninfo in Meta or HDFS. " + hbi);
                }

                // TODO test.
                continue;
            }
            if (hbi.metaEntry.regionServer == null) {
                errors.detail("Skipping region because no region server: " + hbi);
                continue;
            }
            if (hbi.metaEntry.isOffline()) {
                errors.detail("Skipping region because it is offline: " + hbi);
                continue;
            }
            if (hbi.containsOnlyHdfsEdits()) {
                errors.detail("Skipping region because it only contains edits" + hbi);
                continue;
            }

            // Missing regionDir or over-deployment is checked elsewhere. Include
            // these cases in modTInfo, so we can evaluate those regions as part of
            // the region chain in META
            //if (hbi.foundRegionDir == null) continue;
            //if (hbi.deployedOn.size() != 1) continue;
            if (hbi.deployedOn.size() == 0)
                continue;

            // We should be safe here
            TableName tableName = hbi.metaEntry.getTable();
            TableInfo modTInfo = tablesInfo.get(tableName);
            if (modTInfo == null) {
                modTInfo = new TableInfo(tableName);
            }
            for (ServerName server : hbi.deployedOn) {
                modTInfo.addServer(server);
            }

            if (!hbi.isSkipChecks()) {
                modTInfo.addRegionInfo(hbi);
            }

            tablesInfo.put(tableName, modTInfo);
        }

        loadTableInfosForTablesWithNoRegion();

        for (TableInfo tInfo : tablesInfo.values()) {
            TableIntegrityErrorHandler handler = tInfo.new IntegrityFixSuggester(tInfo, errors);
            if (!tInfo.checkRegionChain(handler)) {
                errors.report("Found inconsistency in table " + tInfo.getName());
            }
        }
        return tablesInfo;
    }

    /** Loads table info's for tables that may not have been included, since there are no
     * regions reported for the table, but table dir is there in hdfs
     */
    private void loadTableInfosForTablesWithNoRegion() throws IOException {
        Map<String, HTableDescriptor> allTables = new FSTableDescriptors(getConf()).getAll();
        for (HTableDescriptor htd : allTables.values()) {
            if (checkMetaOnly && !htd.isMetaTable()) {
                continue;
            }

            TableName tableName = htd.getTableName();
            if (isTableIncluded(tableName) && !tablesInfo.containsKey(tableName)) {
                TableInfo tableInfo = new TableInfo(tableName);
                tableInfo.htds.add(htd);
                tablesInfo.put(htd.getTableName(), tableInfo);
            }
        }
    }

    /**
     * Merge hdfs data by moving from contained HbckInfo into targetRegionDir.
     * @return number of file move fixes done to merge regions.
     */
    public int mergeRegionDirs(Path targetRegionDir, HbckInfo contained) throws IOException {
        int fileMoves = 0;
        String thread = Thread.currentThread().getName();
        LOG.debug("[" + thread + "] Contained region dir after close and pause");
        debugLsr(contained.getHdfsRegionDir());

        // rename the contained into the container.
        FileSystem fs = targetRegionDir.getFileSystem(getConf());
        FileStatus[] dirs = null;
        try {
            dirs = fs.listStatus(contained.getHdfsRegionDir());
        } catch (FileNotFoundException fnfe) {
            // region we are attempting to merge in is not present!  Since this is a merge, there is
            // no harm skipping this region if it does not exist.
            if (!fs.exists(contained.getHdfsRegionDir())) {
                LOG.warn("[" + thread + "] HDFS region dir " + contained.getHdfsRegionDir()
                        + " is missing. Assuming already sidelined or moved.");
            } else {
                sidelineRegionDir(fs, contained);
            }
            return fileMoves;
        }

        if (dirs == null) {
            if (!fs.exists(contained.getHdfsRegionDir())) {
                LOG.warn(
                        "[" + thread + "] HDFS region dir " + contained.getHdfsRegionDir() + " already sidelined.");
            } else {
                sidelineRegionDir(fs, contained);
            }
            return fileMoves;
        }

        for (FileStatus cf : dirs) {
            Path src = cf.getPath();
            Path dst = new Path(targetRegionDir, src.getName());

            if (src.getName().equals(HRegionFileSystem.REGION_INFO_FILE)) {
                // do not copy the old .regioninfo file.
                continue;
            }

            if (src.getName().equals(HConstants.HREGION_OLDLOGDIR_NAME)) {
                // do not copy the .oldlogs files
                continue;
            }

            LOG.info("[" + thread + "] Moving files from " + src + " into containing region " + dst);
            // FileSystem.rename is inconsistent with directories -- if the
            // dst (foo/a) exists and is a dir, and the src (foo/b) is a dir,
            // it moves the src into the dst dir resulting in (foo/a/b).  If
            // the dst does not exist, and the src a dir, src becomes dst. (foo/b)
            for (FileStatus hfile : fs.listStatus(src)) {
                boolean success = fs.rename(hfile.getPath(), dst);
                if (success) {
                    fileMoves++;
                }
            }
            LOG.debug("[" + thread + "] Sideline directory contents:");
            debugLsr(targetRegionDir);
        }

        // if all success.
        sidelineRegionDir(fs, contained);
        LOG.info("[" + thread + "] Sidelined region dir " + contained.getHdfsRegionDir() + " into "
                + getSidelineDir());
        debugLsr(contained.getHdfsRegionDir());

        return fileMoves;
    }

    static class WorkItemOverlapMerge implements Callable<Void> {
        private TableIntegrityErrorHandler handler;
        Collection<HbckInfo> overlapgroup;

        WorkItemOverlapMerge(Collection<HbckInfo> overlapgroup, TableIntegrityErrorHandler handler) {
            this.handler = handler;
            this.overlapgroup = overlapgroup;
        }

        @Override
        public Void call() throws Exception {
            handler.handleOverlapGroup(overlapgroup);
            return null;
        }
    };

    /**
     * Maintain information about a particular table.
     */
    public class TableInfo {
        TableName tableName;
        TreeSet<ServerName> deployedOn;

        // backwards regions
        final List<HbckInfo> backwards = new ArrayList<HbckInfo>();

        // sidelined big overlapped regions
        final Map<Path, HbckInfo> sidelinedRegions = new HashMap<Path, HbckInfo>();

        // region split calculator
        final RegionSplitCalculator<HbckInfo> sc = new RegionSplitCalculator<HbckInfo>(cmp);

        // Histogram of different HTableDescriptors found.  Ideally there is only one!
        final Set<HTableDescriptor> htds = new HashSet<HTableDescriptor>();

        // key = start split, values = set of splits in problem group
        final Multimap<byte[], HbckInfo> overlapGroups = TreeMultimap.create(RegionSplitCalculator.BYTES_COMPARATOR,
                cmp);

        TableInfo(TableName name) {
            this.tableName = name;
            deployedOn = new TreeSet<ServerName>();
        }

        /**
         * @return descriptor common to all regions.  null if are none or multiple!
         */
        private HTableDescriptor getHTD() {
            if (htds.size() == 1) {
                return (HTableDescriptor) htds.toArray()[0];
            } else {
                LOG.error("None/Multiple table descriptors found for table '" + tableName + "' regions: " + htds);
            }
            return null;
        }

        public void addRegionInfo(HbckInfo hir) {
            if (Bytes.equals(hir.getEndKey(), HConstants.EMPTY_END_ROW)) {
                // end key is absolute end key, just add it.
                sc.add(hir);
                return;
            }

            // if not the absolute end key, check for cycle
            if (Bytes.compareTo(hir.getStartKey(), hir.getEndKey()) > 0) {
                errors.reportError(ERROR_CODE.REGION_CYCLE,
                        String.format(
                                "The endkey for this region comes before the " + "startkey, startkey=%s, endkey=%s",
                                Bytes.toStringBinary(hir.getStartKey()), Bytes.toStringBinary(hir.getEndKey())),
                        this, hir);
                backwards.add(hir);
                return;
            }

            // main case, add to split calculator
            sc.add(hir);
        }

        public void addServer(ServerName server) {
            this.deployedOn.add(server);
        }

        public TableName getName() {
            return tableName;
        }

        public int getNumRegions() {
            return sc.getStarts().size() + backwards.size();
        }

        private class IntegrityFixSuggester extends TableIntegrityErrorHandlerImpl {
            ErrorReporter errors;

            IntegrityFixSuggester(TableInfo ti, ErrorReporter errors) {
                this.errors = errors;
                setTableInfo(ti);
            }

            @Override
            public void handleRegionStartKeyNotEmpty(HbckInfo hi) throws IOException {
                errors.reportError(ERROR_CODE.FIRST_REGION_STARTKEY_NOT_EMPTY,
                        "First region should start with an empty key.  You need to "
                                + " create a new region and regioninfo in HDFS to plug the hole.",
                        getTableInfo(), hi);
            }

            @Override
            public void handleRegionEndKeyNotEmpty(byte[] curEndKey) throws IOException {
                errors.reportError(ERROR_CODE.LAST_REGION_ENDKEY_NOT_EMPTY,
                        "Last region should end with an empty key. You need to "
                                + "create a new region and regioninfo in HDFS to plug the hole.",
                        getTableInfo());
            }

            @Override
            public void handleDegenerateRegion(HbckInfo hi) throws IOException {
                errors.reportError(ERROR_CODE.DEGENERATE_REGION, "Region has the same start and end key.",
                        getTableInfo(), hi);
            }

            @Override
            public void handleDuplicateStartKeys(HbckInfo r1, HbckInfo r2) throws IOException {
                byte[] key = r1.getStartKey();
                // dup start key
                errors.reportError(ERROR_CODE.DUPE_STARTKEYS,
                        "Multiple regions have the same startkey: " + Bytes.toStringBinary(key), getTableInfo(),
                        r1);
                errors.reportError(ERROR_CODE.DUPE_STARTKEYS,
                        "Multiple regions have the same startkey: " + Bytes.toStringBinary(key), getTableInfo(),
                        r2);
            }

            @Override
            public void handleOverlapInRegionChain(HbckInfo hi1, HbckInfo hi2) throws IOException {
                errors.reportError(ERROR_CODE.OVERLAP_IN_REGION_CHAIN, "There is an overlap in the region chain.",
                        getTableInfo(), hi1, hi2);
            }

            @Override
            public void handleHoleInRegionChain(byte[] holeStart, byte[] holeStop) throws IOException {
                errors.reportError(ERROR_CODE.HOLE_IN_REGION_CHAIN, "There is a hole in the region chain between "
                        + Bytes.toStringBinary(holeStart) + " and " + Bytes.toStringBinary(holeStop)
                        + ".  You need to create a new .regioninfo and region " + "dir in hdfs to plug the hole.");
            }
        };

        /**
         * This handler fixes integrity errors from hdfs information.  There are
         * basically three classes of integrity problems 1) holes, 2) overlaps, and
         * 3) invalid regions.
         *
         * This class overrides methods that fix holes and the overlap group case.
         * Individual cases of particular overlaps are handled by the general
         * overlap group merge repair case.
         *
         * If hbase is online, this forces regions offline before doing merge
         * operations.
         */
        private class HDFSIntegrityFixer extends IntegrityFixSuggester {
            Configuration conf;

            boolean fixOverlaps = true;

            HDFSIntegrityFixer(TableInfo ti, ErrorReporter errors, Configuration conf, boolean fixHoles,
                    boolean fixOverlaps) {
                super(ti, errors);
                this.conf = conf;
                this.fixOverlaps = fixOverlaps;
                // TODO properly use fixHoles
            }

            /**
             * This is a special case hole -- when the first region of a table is
             * missing from META, HBase doesn't acknowledge the existance of the
             * table.
             */
            @Override
            public void handleRegionStartKeyNotEmpty(HbckInfo next) throws IOException {
                errors.reportError(ERROR_CODE.FIRST_REGION_STARTKEY_NOT_EMPTY,
                        "First region should start with an empty key.  Creating a new "
                                + "region and regioninfo in HDFS to plug the hole.",
                        getTableInfo(), next);
                HTableDescriptor htd = getTableInfo().getHTD();
                // from special EMPTY_START_ROW to next region's startKey
                HRegionInfo newRegion = new HRegionInfo(htd.getTableName(), HConstants.EMPTY_START_ROW,
                        next.getStartKey());

                // TODO test
                HRegion region = HBaseFsckRepair.createHDFSRegionDir(conf, newRegion, htd);
                LOG.info("Table region start key was not empty.  Created new empty region: " + newRegion + " "
                        + region);
                fixes++;
            }

            @Override
            public void handleRegionEndKeyNotEmpty(byte[] curEndKey) throws IOException {
                errors.reportError(ERROR_CODE.LAST_REGION_ENDKEY_NOT_EMPTY,
                        "Last region should end with an empty key.  Creating a new "
                                + "region and regioninfo in HDFS to plug the hole.",
                        getTableInfo());
                HTableDescriptor htd = getTableInfo().getHTD();
                // from curEndKey to EMPTY_START_ROW
                HRegionInfo newRegion = new HRegionInfo(htd.getTableName(), curEndKey, HConstants.EMPTY_START_ROW);

                HRegion region = HBaseFsckRepair.createHDFSRegionDir(conf, newRegion, htd);
                LOG.info("Table region end key was not empty.  Created new empty region: " + newRegion + " "
                        + region);
                fixes++;
            }

            /**
             * There is a hole in the hdfs regions that violates the table integrity
             * rules.  Create a new empty region that patches the hole.
             */
            @Override
            public void handleHoleInRegionChain(byte[] holeStartKey, byte[] holeStopKey) throws IOException {
                errors.reportError(ERROR_CODE.HOLE_IN_REGION_CHAIN,
                        "There is a hole in the region chain between " + Bytes.toStringBinary(holeStartKey)
                                + " and " + Bytes.toStringBinary(holeStopKey)
                                + ".  Creating a new regioninfo and region " + "dir in hdfs to plug the hole.");
                HTableDescriptor htd = getTableInfo().getHTD();
                HRegionInfo newRegion = new HRegionInfo(htd.getTableName(), holeStartKey, holeStopKey);
                HRegion region = HBaseFsckRepair.createHDFSRegionDir(conf, newRegion, htd);
                LOG.info("Plugged hole by creating new empty region: " + newRegion + " " + region);
                fixes++;
            }

            /**
             * This takes set of overlapping regions and merges them into a single
             * region.  This covers cases like degenerate regions, shared start key,
             * general overlaps, duplicate ranges, and partial overlapping regions.
             *
             * Cases:
             * - Clean regions that overlap
             * - Only .oldlogs regions (can't find start/stop range, or figure out)
             *
             * This is basically threadsafe, except for the fixer increment in mergeOverlaps.
             */
            @Override
            public void handleOverlapGroup(Collection<HbckInfo> overlap) throws IOException {
                Preconditions.checkNotNull(overlap);
                Preconditions.checkArgument(overlap.size() > 0);

                if (!this.fixOverlaps) {
                    LOG.warn("Not attempting to repair overlaps.");
                    return;
                }

                if (overlap.size() > maxMerge) {
                    LOG.warn("Overlap group has " + overlap.size() + " overlapping "
                            + "regions which is greater than " + maxMerge + ", the max number of regions to merge");
                    if (sidelineBigOverlaps) {
                        // we only sideline big overlapped groups that exceeds the max number of regions to merge
                        sidelineBigOverlaps(overlap);
                    }
                    return;
                }

                mergeOverlaps(overlap);
            }

            void mergeOverlaps(Collection<HbckInfo> overlap) throws IOException {
                String thread = Thread.currentThread().getName();
                LOG.info("== [" + thread + "] Merging regions into one region: " + Joiner.on(",").join(overlap));
                // get the min / max range and close all concerned regions
                Pair<byte[], byte[]> range = null;
                for (HbckInfo hi : overlap) {
                    if (range == null) {
                        range = new Pair<byte[], byte[]>(hi.getStartKey(), hi.getEndKey());
                    } else {
                        if (RegionSplitCalculator.BYTES_COMPARATOR.compare(hi.getStartKey(),
                                range.getFirst()) < 0) {
                            range.setFirst(hi.getStartKey());
                        }
                        if (RegionSplitCalculator.BYTES_COMPARATOR.compare(hi.getEndKey(), range.getSecond()) > 0) {
                            range.setSecond(hi.getEndKey());
                        }
                    }
                    // need to close files so delete can happen.
                    LOG.debug("[" + thread + "] Closing region before moving data around: " + hi);
                    LOG.debug("[" + thread + "] Contained region dir before close");
                    debugLsr(hi.getHdfsRegionDir());
                    try {
                        LOG.info("[" + thread + "] Closing region: " + hi);
                        closeRegion(hi);
                    } catch (IOException ioe) {
                        LOG.warn("[" + thread + "] Was unable to close region " + hi + ".  Just continuing... ",
                                ioe);
                    } catch (InterruptedException e) {
                        LOG.warn("[" + thread + "] Was unable to close region " + hi + ".  Just continuing... ", e);
                    }

                    try {
                        LOG.info("[" + thread + "] Offlining region: " + hi);
                        offline(hi.getRegionName());
                    } catch (IOException ioe) {
                        LOG.warn("[" + thread + "] Unable to offline region from master: " + hi
                                + ".  Just continuing... ", ioe);
                    }
                }

                // create new empty container region.
                HTableDescriptor htd = getTableInfo().getHTD();
                // from start key to end Key
                HRegionInfo newRegion = new HRegionInfo(htd.getTableName(), range.getFirst(), range.getSecond());
                HRegion region = HBaseFsckRepair.createHDFSRegionDir(conf, newRegion, htd);
                LOG.info("[" + thread + "] Created new empty container region: " + newRegion
                        + " to contain regions: " + Joiner.on(",").join(overlap));
                debugLsr(region.getRegionFileSystem().getRegionDir());

                // all target regions are closed, should be able to safely cleanup.
                boolean didFix = false;
                Path target = region.getRegionFileSystem().getRegionDir();
                for (HbckInfo contained : overlap) {
                    LOG.info("[" + thread + "] Merging " + contained + " into " + target);
                    int merges = mergeRegionDirs(target, contained);
                    if (merges > 0) {
                        didFix = true;
                    }
                }
                if (didFix) {
                    fixes++;
                }
            }

            /**
             * Sideline some regions in a big overlap group so that it
             * will have fewer regions, and it is easier to merge them later on.
             *
             * @param bigOverlap the overlapped group with regions more than maxMerge
             * @throws IOException
             */
            void sidelineBigOverlaps(Collection<HbckInfo> bigOverlap) throws IOException {
                int overlapsToSideline = bigOverlap.size() - maxMerge;
                if (overlapsToSideline > maxOverlapsToSideline) {
                    overlapsToSideline = maxOverlapsToSideline;
                }
                List<HbckInfo> regionsToSideline = RegionSplitCalculator.findBigRanges(bigOverlap,
                        overlapsToSideline);
                FileSystem fs = FileSystem.get(conf);
                for (HbckInfo regionToSideline : regionsToSideline) {
                    try {
                        LOG.info("Closing region: " + regionToSideline);
                        closeRegion(regionToSideline);
                    } catch (IOException ioe) {
                        LOG.warn("Was unable to close region " + regionToSideline + ".  Just continuing... ", ioe);
                    } catch (InterruptedException e) {
                        LOG.warn("Was unable to close region " + regionToSideline + ".  Just continuing... ", e);
                    }

                    try {
                        LOG.info("Offlining region: " + regionToSideline);
                        offline(regionToSideline.getRegionName());
                    } catch (IOException ioe) {
                        LOG.warn("Unable to offline region from master: " + regionToSideline
                                + ".  Just continuing... ", ioe);
                    }

                    LOG.info("Before sideline big overlapped region: " + regionToSideline.toString());
                    Path sidelineRegionDir = sidelineRegionDir(fs, TO_BE_LOADED, regionToSideline);
                    if (sidelineRegionDir != null) {
                        sidelinedRegions.put(sidelineRegionDir, regionToSideline);
                        LOG.info("After sidelined big overlapped region: "
                                + regionToSideline.getRegionNameAsString() + " to " + sidelineRegionDir.toString());
                        fixes++;
                    }
                }
            }
        }

        /**
         * Check the region chain (from META) of this table.  We are looking for
         * holes, overlaps, and cycles.
         * @return false if there are errors
         * @throws IOException
         */
        public boolean checkRegionChain(TableIntegrityErrorHandler handler) throws IOException {
            // When table is disabled no need to check for the region chain. Some of the regions
            // accidently if deployed, this below code might report some issues like missing start
            // or end regions or region hole in chain and may try to fix which is unwanted.
            if (disabledTables.contains(this.tableName)) {
                return true;
            }
            int originalErrorsCount = errors.getErrorList().size();
            Multimap<byte[], HbckInfo> regions = sc.calcCoverage();
            SortedSet<byte[]> splits = sc.getSplits();

            byte[] prevKey = null;
            byte[] problemKey = null;

            if (splits.size() == 0) {
                // no region for this table
                handler.handleHoleInRegionChain(HConstants.EMPTY_START_ROW, HConstants.EMPTY_END_ROW);
            }

            for (byte[] key : splits) {
                Collection<HbckInfo> ranges = regions.get(key);
                if (prevKey == null && !Bytes.equals(key, HConstants.EMPTY_BYTE_ARRAY)) {
                    for (HbckInfo rng : ranges) {
                        handler.handleRegionStartKeyNotEmpty(rng);
                    }
                }

                // check for degenerate ranges
                for (HbckInfo rng : ranges) {
                    // special endkey case converts '' to null
                    byte[] endKey = rng.getEndKey();
                    endKey = (endKey.length == 0) ? null : endKey;
                    if (Bytes.equals(rng.getStartKey(), endKey)) {
                        handler.handleDegenerateRegion(rng);
                    }
                }

                if (ranges.size() == 1) {
                    // this split key is ok -- no overlap, not a hole.
                    if (problemKey != null) {
                        LOG.warn("reached end of problem group: " + Bytes.toStringBinary(key));
                    }
                    problemKey = null; // fell through, no more problem.
                } else if (ranges.size() > 1) {
                    // set the new problem key group name, if already have problem key, just
                    // keep using it.
                    if (problemKey == null) {
                        // only for overlap regions.
                        LOG.warn("Naming new problem group: " + Bytes.toStringBinary(key));
                        problemKey = key;
                    }
                    overlapGroups.putAll(problemKey, ranges);

                    // record errors
                    ArrayList<HbckInfo> subRange = new ArrayList<HbckInfo>(ranges);
                    //  this dumb and n^2 but this shouldn't happen often
                    for (HbckInfo r1 : ranges) {
                        subRange.remove(r1);
                        for (HbckInfo r2 : subRange) {
                            if (Bytes.compareTo(r1.getStartKey(), r2.getStartKey()) == 0) {
                                handler.handleDuplicateStartKeys(r1, r2);
                            } else {
                                // overlap
                                handler.handleOverlapInRegionChain(r1, r2);
                            }
                        }
                    }

                } else if (ranges.size() == 0) {
                    if (problemKey != null) {
                        LOG.warn("reached end of problem group: " + Bytes.toStringBinary(key));
                    }
                    problemKey = null;

                    byte[] holeStopKey = sc.getSplits().higher(key);
                    // if higher key is null we reached the top.
                    if (holeStopKey != null) {
                        // hole
                        handler.handleHoleInRegionChain(key, holeStopKey);
                    }
                }
                prevKey = key;
            }

            // When the last region of a table is proper and having an empty end key, 'prevKey'
            // will be null.
            if (prevKey != null) {
                handler.handleRegionEndKeyNotEmpty(prevKey);
            }

            // TODO fold this into the TableIntegrityHandler
            if (getConf().getBoolean("hbasefsck.overlap.merge.parallel", true)) {
                LOG.info("Handling overlap merges in parallel. set hbasefsck.overlap.merge.parallel to"
                        + " false to run serially.");
                boolean ok = handleOverlapsParallel(handler, prevKey);
                if (!ok) {
                    return false;
                }
            } else {
                LOG.info("Handling overlap merges serially.  set hbasefsck.overlap.merge.parallel to"
                        + " true to run in parallel.");
                for (Collection<HbckInfo> overlap : overlapGroups.asMap().values()) {
                    handler.handleOverlapGroup(overlap);
                }
            }

            if (details) {
                // do full region split map dump
                errors.print("---- Table '" + this.tableName + "': region split map");
                dump(splits, regions);
                errors.print("---- Table '" + this.tableName + "': overlap groups");
                dumpOverlapProblems(overlapGroups);
                errors.print("There are " + overlapGroups.keySet().size() + " overlap groups with "
                        + overlapGroups.size() + " overlapping regions");
            }
            if (!sidelinedRegions.isEmpty()) {
                LOG.warn("Sidelined big overlapped regions, please bulk load them!");
                errors.print("---- Table '" + this.tableName + "': sidelined big overlapped regions");
                dumpSidelinedRegions(sidelinedRegions);
            }
            return errors.getErrorList().size() == originalErrorsCount;
        }

        private boolean handleOverlapsParallel(TableIntegrityErrorHandler handler, byte[] prevKey)
                throws IOException {
            // we parallelize overlap handler for the case we have lots of groups to fix.  We can
            // safely assume each group is independent.
            List<WorkItemOverlapMerge> merges = new ArrayList<WorkItemOverlapMerge>(overlapGroups.size());
            List<Future<Void>> rets;
            for (Collection<HbckInfo> overlap : overlapGroups.asMap().values()) {
                //
                merges.add(new WorkItemOverlapMerge(overlap, handler));
            }
            try {
                rets = executor.invokeAll(merges);
            } catch (InterruptedException e) {
                LOG.error("Overlap merges were interrupted", e);
                return false;
            }
            for (int i = 0; i < merges.size(); i++) {
                WorkItemOverlapMerge work = merges.get(i);
                Future<Void> f = rets.get(i);
                try {
                    f.get();
                } catch (ExecutionException e) {
                    LOG.warn("Failed to merge overlap group" + work, e.getCause());
                } catch (InterruptedException e) {
                    LOG.error("Waiting for overlap merges was interrupted", e);
                    return false;
                }
            }
            return true;
        }

        /**
         * This dumps data in a visually reasonable way for visual debugging
         *
         * @param splits
         * @param regions
         */
        void dump(SortedSet<byte[]> splits, Multimap<byte[], HbckInfo> regions) {
            // we display this way because the last end key should be displayed as well.
            StringBuilder sb = new StringBuilder();
            for (byte[] k : splits) {
                sb.setLength(0); // clear out existing buffer, if any.
                sb.append(Bytes.toStringBinary(k) + ":\t");
                for (HbckInfo r : regions.get(k)) {
                    sb.append("[ " + r.toString() + ", " + Bytes.toStringBinary(r.getEndKey()) + "]\t");
                }
                errors.print(sb.toString());
            }
        }
    }

    public void dumpOverlapProblems(Multimap<byte[], HbckInfo> regions) {
        // we display this way because the last end key should be displayed as
        // well.
        for (byte[] k : regions.keySet()) {
            errors.print(Bytes.toStringBinary(k) + ":");
            for (HbckInfo r : regions.get(k)) {
                errors.print("[ " + r.toString() + ", " + Bytes.toStringBinary(r.getEndKey()) + "]");
            }
            errors.print("----");
        }
    }

    public void dumpSidelinedRegions(Map<Path, HbckInfo> regions) {
        for (Map.Entry<Path, HbckInfo> entry : regions.entrySet()) {
            TableName tableName = entry.getValue().getTableName();
            Path path = entry.getKey();
            errors.print("This sidelined region dir should be bulk loaded: " + path.toString());
            errors.print("Bulk load command looks like: "
                    + "hbase org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles " + path.toUri().getPath()
                    + " " + tableName);
        }
    }

    public Multimap<byte[], HbckInfo> getOverlapGroups(TableName table) {
        TableInfo ti = tablesInfo.get(table);
        return ti.overlapGroups;
    }

    /**
     * Return a list of user-space table names whose metadata have not been
     * modified in the last few milliseconds specified by timelag
     * if any of the REGIONINFO_QUALIFIER, SERVER_QUALIFIER, STARTCODE_QUALIFIER,
     * SPLITA_QUALIFIER, SPLITB_QUALIFIER have not changed in the last
     * milliseconds specified by timelag, then the table is a candidate to be returned.
     * @return tables that have not been modified recently
     * @throws IOException if an error is encountered
     */
    HTableDescriptor[] getTables(AtomicInteger numSkipped) {
        List<TableName> tableNames = new ArrayList<TableName>();
        long now = System.currentTimeMillis();

        for (HbckInfo hbi : regionInfoMap.values()) {
            MetaEntry info = hbi.metaEntry;

            // if the start key is zero, then we have found the first region of a table.
            // pick only those tables that were not modified in the last few milliseconds.
            if (info != null && info.getStartKey().length == 0 && !info.isMetaRegion()) {
                if (info.modTime + timelag < now) {
                    tableNames.add(info.getTable());
                } else {
                    numSkipped.incrementAndGet(); // one more in-flux table
                }
            }
        }
        return getHTableDescriptors(tableNames);
    }

    HTableDescriptor[] getHTableDescriptors(List<TableName> tableNames) {
        HTableDescriptor[] htd = new HTableDescriptor[0];
        HBaseAdmin admin = null;
        try {
            LOG.info("getHTableDescriptors == tableNames => " + tableNames);
            admin = new HBaseAdmin(getConf());
            htd = admin.getTableDescriptorsByTableName(tableNames);
        } catch (IOException e) {
            LOG.debug("Exception getting table descriptors", e);
        } finally {
            if (admin != null) {
                try {
                    admin.close();
                } catch (IOException e) {
                    LOG.debug("Exception closing HBaseAdmin", e);
                }
            }
        }
        return htd;
    }

    /**
     * Gets the entry in regionInfo corresponding to the the given encoded
     * region name. If the region has not been seen yet, a new entry is added
     * and returned.
     */
    private synchronized HbckInfo getOrCreateInfo(String name) {
        HbckInfo hbi = regionInfoMap.get(name);
        if (hbi == null) {
            hbi = new HbckInfo(null);
            regionInfoMap.put(name, hbi);
        }
        return hbi;
    }

    private void checkAndFixTableLocks() throws IOException {
        TableLockChecker checker = new TableLockChecker(createZooKeeperWatcher(), errors);
        checker.checkTableLocks();

        if (this.fixTableLocks) {
            checker.fixExpiredTableLocks();
        }
    }

    /**
      * Check values in regionInfo for hbase:meta
      * Check if zero or more than one regions with hbase:meta are found.
      * If there are inconsistencies (i.e. zero or more than one regions
      * pretend to be holding the hbase:meta) try to fix that and report an error.
      * @throws IOException from HBaseFsckRepair functions
     * @throws KeeperException
     * @throws InterruptedException
      */
    boolean checkMetaRegion() throws IOException, KeeperException, InterruptedException {
        List<HbckInfo> metaRegions = Lists.newArrayList();
        for (HbckInfo value : regionInfoMap.values()) {
            if (value.metaEntry != null && value.metaEntry.isMetaRegion()) {
                metaRegions.add(value);
            }
        }

        // There will be always one entry in regionInfoMap corresponding to hbase:meta
        // Check the deployed servers. It should be exactly one server.
        List<ServerName> servers = new ArrayList<ServerName>();
        HbckInfo metaHbckInfo = null;
        if (!metaRegions.isEmpty()) {
            metaHbckInfo = metaRegions.get(0);
            servers = metaHbckInfo.deployedOn;
        }
        if (servers.size() != 1) {
            if (servers.size() == 0) {
                errors.reportError(ERROR_CODE.NO_META_REGION, "hbase:meta is not found on any region.");
                if (shouldFixAssignments()) {
                    errors.print("Trying to fix a problem with hbase:meta..");
                    setShouldRerun();
                    // try to fix it (treat it as unassigned region)
                    HBaseFsckRepair.fixUnassigned(admin, HRegionInfo.FIRST_META_REGIONINFO);
                    HBaseFsckRepair.waitUntilAssigned(admin, HRegionInfo.FIRST_META_REGIONINFO);
                }
            } else if (servers.size() > 1) {
                errors.reportError(ERROR_CODE.MULTI_META_REGION, "hbase:meta is found on more than one region.");
                if (shouldFixAssignments()) {
                    if (metaHbckInfo == null) {
                        errors.print("Unable to fix problem with hbase:meta due to hbase:meta region info missing");
                        return false;
                    }
                    errors.print("Trying to fix a problem with hbase:meta..");
                    setShouldRerun();
                    // try fix it (treat is a dupe assignment)
                    HBaseFsckRepair.fixMultiAssignment(admin, metaHbckInfo.metaEntry, servers);
                }
            }
            // rerun hbck with hopefully fixed META
            return false;
        }
        // no errors, so continue normally
        return true;
    }

    /**
     * Scan hbase:meta, adding all regions found to the regionInfo map.
     * @throws IOException if an error is encountered
     */
    boolean loadMetaEntries() throws IOException {
        MetaScannerVisitor visitor = new MetaScannerVisitorBase() {
            int countRecord = 1;

            // comparator to sort KeyValues with latest modtime
            final Comparator<Cell> comp = new Comparator<Cell>() {
                @Override
                public int compare(Cell k1, Cell k2) {
                    return (int) (k1.getTimestamp() - k2.getTimestamp());
                }
            };

            @Override
            public boolean processRow(Result result) throws IOException {
                try {

                    // record the latest modification of this META record
                    long ts = Collections.max(result.listCells(), comp).getTimestamp();
                    Pair<HRegionInfo, ServerName> pair = HRegionInfo.getHRegionInfoAndServerName(result);
                    if (pair == null || pair.getFirst() == null) {
                        emptyRegionInfoQualifiers.add(result);
                        errors.reportError(ERROR_CODE.EMPTY_META_CELL,
                                "Empty REGIONINFO_QUALIFIER found in hbase:meta");
                        return true;
                    }
                    ServerName sn = null;
                    if (pair.getSecond() != null) {
                        sn = pair.getSecond();
                    }
                    HRegionInfo hri = pair.getFirst();
                    if (!(isTableIncluded(hri.getTable()) || hri.isMetaRegion())) {
                        return true;
                    }
                    PairOfSameType<HRegionInfo> daughters = HRegionInfo.getDaughterRegions(result);
                    MetaEntry m = new MetaEntry(hri, sn, ts, daughters.getFirst(), daughters.getSecond());
                    HbckInfo previous = regionInfoMap.get(hri.getEncodedName());
                    if (previous == null) {
                        regionInfoMap.put(hri.getEncodedName(), new HbckInfo(m));
                    } else if (previous.metaEntry == null) {
                        previous.metaEntry = m;
                    } else {
                        throw new IOException("Two entries in hbase:meta are same " + previous);
                    }

                    PairOfSameType<HRegionInfo> mergeRegions = HRegionInfo.getMergeRegions(result);
                    for (HRegionInfo mergeRegion : new HRegionInfo[] { mergeRegions.getFirst(),
                            mergeRegions.getSecond() }) {
                        if (mergeRegion != null) {
                            // This region is already been merged
                            HbckInfo hbInfo = getOrCreateInfo(mergeRegion.getEncodedName());
                            hbInfo.setMerged(true);
                        }
                    }

                    // show proof of progress to the user, once for every 100 records.
                    if (countRecord % 100 == 0) {
                        errors.progress();
                    }
                    countRecord++;
                    return true;
                } catch (RuntimeException e) {
                    LOG.error("Result=" + result);
                    throw e;
                }
            }
        };
        if (!checkMetaOnly) {
            // Scan hbase:meta to pick up user regions
            MetaScanner.metaScan(getConf(), visitor);
        }

        errors.print("");
        return true;
    }

    /**
     * Stores the regioninfo entries scanned from META
     */
    static class MetaEntry extends HRegionInfo {
        ServerName regionServer; // server hosting this region
        long modTime; // timestamp of most recent modification metadata
        HRegionInfo splitA, splitB; //split daughters

        public MetaEntry(HRegionInfo rinfo, ServerName regionServer, long modTime) {
            this(rinfo, regionServer, modTime, null, null);
        }

        public MetaEntry(HRegionInfo rinfo, ServerName regionServer, long modTime, HRegionInfo splitA,
                HRegionInfo splitB) {
            super(rinfo);
            this.regionServer = regionServer;
            this.modTime = modTime;
            this.splitA = splitA;
            this.splitB = splitB;
        }

        @Override
        public boolean equals(Object o) {
            boolean superEq = super.equals(o);
            if (!superEq) {
                return superEq;
            }

            MetaEntry me = (MetaEntry) o;
            if (!regionServer.equals(me.regionServer)) {
                return false;
            }
            return (modTime == me.modTime);
        }

        @Override
        public int hashCode() {
            int hash = Arrays.hashCode(getRegionName());
            hash ^= getRegionId();
            hash ^= Arrays.hashCode(getStartKey());
            hash ^= Arrays.hashCode(getEndKey());
            hash ^= Boolean.valueOf(isOffline()).hashCode();
            hash ^= getTable().hashCode();
            if (regionServer != null) {
                hash ^= regionServer.hashCode();
            }
            hash ^= modTime;
            return hash;
        }
    }

    /**
     * Stores the regioninfo entries from HDFS
     */
    static class HdfsEntry {
        HRegionInfo hri;
        Path hdfsRegionDir = null;
        long hdfsRegionDirModTime = 0;
        boolean hdfsRegioninfoFilePresent = false;
        boolean hdfsOnlyEdits = false;
    }

    /**
     * Stores the regioninfo retrieved from Online region servers.
     */
    static class OnlineEntry {
        HRegionInfo hri;
        ServerName hsa;

        @Override
        public String toString() {
            return hsa.toString() + ";" + hri.getRegionNameAsString();
        }
    }

    /**
     * Maintain information about a particular region.  It gathers information
     * from three places -- HDFS, META, and region servers.
     */
    public static class HbckInfo implements KeyRange {
        private MetaEntry metaEntry = null; // info in META
        private HdfsEntry hdfsEntry = null; // info in HDFS
        private List<OnlineEntry> deployedEntries = Lists.newArrayList(); // on Region Server
        private List<ServerName> deployedOn = Lists.newArrayList(); // info on RS's
        private boolean skipChecks = false; // whether to skip further checks to this region info.
        private boolean isMerged = false;// whether this region has already been merged into another one

        HbckInfo(MetaEntry metaEntry) {
            this.metaEntry = metaEntry;
        }

        public synchronized void addServer(HRegionInfo hri, ServerName server) {
            OnlineEntry rse = new OnlineEntry();
            rse.hri = hri;
            rse.hsa = server;
            this.deployedEntries.add(rse);
            this.deployedOn.add(server);
        }

        @Override
        public synchronized String toString() {
            StringBuilder sb = new StringBuilder();
            sb.append("{ meta => ");
            sb.append((metaEntry != null) ? metaEntry.getRegionNameAsString() : "null");
            sb.append(", hdfs => " + getHdfsRegionDir());
            sb.append(", deployed => " + Joiner.on(", ").join(deployedEntries));
            sb.append(" }");
            return sb.toString();
        }

        @Override
        public byte[] getStartKey() {
            if (this.metaEntry != null) {
                return this.metaEntry.getStartKey();
            } else if (this.hdfsEntry != null) {
                return this.hdfsEntry.hri.getStartKey();
            } else {
                LOG.error("Entry " + this + " has no meta or hdfs region start key.");
                return null;
            }
        }

        @Override
        public byte[] getEndKey() {
            if (this.metaEntry != null) {
                return this.metaEntry.getEndKey();
            } else if (this.hdfsEntry != null) {
                return this.hdfsEntry.hri.getEndKey();
            } else {
                LOG.error("Entry " + this + " has no meta or hdfs region start key.");
                return null;
            }
        }

        public TableName getTableName() {
            if (this.metaEntry != null) {
                return this.metaEntry.getTable();
            } else if (this.hdfsEntry != null) {
                // we are only guaranteed to have a path and not an HRI for hdfsEntry,
                // so we get the name from the Path
                Path tableDir = this.hdfsEntry.hdfsRegionDir.getParent();
                return FSUtils.getTableName(tableDir);
            } else {
                // Currently no code exercises this path, but we could add one for
                // getting table name from OnlineEntry
                return null;
            }
        }

        public String getRegionNameAsString() {
            if (metaEntry != null) {
                return metaEntry.getRegionNameAsString();
            } else if (hdfsEntry != null) {
                if (hdfsEntry.hri != null) {
                    return hdfsEntry.hri.getRegionNameAsString();
                }
            }
            return null;
        }

        public byte[] getRegionName() {
            if (metaEntry != null) {
                return metaEntry.getRegionName();
            } else if (hdfsEntry != null) {
                return hdfsEntry.hri.getRegionName();
            } else {
                return null;
            }
        }

        Path getHdfsRegionDir() {
            if (hdfsEntry == null) {
                return null;
            }
            return hdfsEntry.hdfsRegionDir;
        }

        boolean containsOnlyHdfsEdits() {
            if (hdfsEntry == null) {
                return false;
            }
            return hdfsEntry.hdfsOnlyEdits;
        }

        boolean isHdfsRegioninfoPresent() {
            if (hdfsEntry == null) {
                return false;
            }
            return hdfsEntry.hdfsRegioninfoFilePresent;
        }

        long getModTime() {
            if (hdfsEntry == null) {
                return 0;
            }
            return hdfsEntry.hdfsRegionDirModTime;
        }

        HRegionInfo getHdfsHRI() {
            if (hdfsEntry == null) {
                return null;
            }
            return hdfsEntry.hri;
        }

        public void setSkipChecks(boolean skipChecks) {
            this.skipChecks = skipChecks;
        }

        public boolean isSkipChecks() {
            return skipChecks;
        }

        public void setMerged(boolean isMerged) {
            this.isMerged = isMerged;
        }

        public boolean isMerged() {
            return this.isMerged;
        }
    }

    final static Comparator<HbckInfo> cmp = new Comparator<HbckInfo>() {
        @Override
        public int compare(HbckInfo l, HbckInfo r) {
            if (l == r) {
                // same instance
                return 0;
            }

            int tableCompare = l.getTableName().compareTo(r.getTableName());
            if (tableCompare != 0) {
                return tableCompare;
            }

            int startComparison = RegionSplitCalculator.BYTES_COMPARATOR.compare(l.getStartKey(), r.getStartKey());
            if (startComparison != 0) {
                return startComparison;
            }

            // Special case for absolute endkey
            byte[] endKey = r.getEndKey();
            endKey = (endKey.length == 0) ? null : endKey;
            byte[] endKey2 = l.getEndKey();
            endKey2 = (endKey2.length == 0) ? null : endKey2;
            int endComparison = RegionSplitCalculator.BYTES_COMPARATOR.compare(endKey2, endKey);

            if (endComparison != 0) {
                return endComparison;
            }

            // use regionId as tiebreaker.
            // Null is considered after all possible values so make it bigger.
            if (l.hdfsEntry == null && r.hdfsEntry == null) {
                return 0;
            }
            if (l.hdfsEntry == null && r.hdfsEntry != null) {
                return 1;
            }
            // l.hdfsEntry must not be null
            if (r.hdfsEntry == null) {
                return -1;
            }
            // both l.hdfsEntry and r.hdfsEntry must not be null.
            return (int) (l.hdfsEntry.hri.getRegionId() - r.hdfsEntry.hri.getRegionId());
        }
    };

    /**
     * Prints summary of all tables found on the system.
     */
    private void printTableSummary(SortedMap<TableName, TableInfo> tablesInfo) {
        StringBuilder sb = new StringBuilder();
        errors.print("Summary:");
        for (TableInfo tInfo : tablesInfo.values()) {
            if (errors.tableHasErrors(tInfo)) {
                errors.print("Table " + tInfo.getName() + " is inconsistent.");
            } else {
                errors.print("  " + tInfo.getName() + " is okay.");
            }
            errors.print("    Number of regions: " + tInfo.getNumRegions());
            sb.setLength(0); // clear out existing buffer, if any.
            sb.append("    Deployed on: ");
            for (ServerName server : tInfo.deployedOn) {
                sb.append(" " + server.toString());
            }
            errors.print(sb.toString());
        }
    }

    static ErrorReporter getErrorReporter(final Configuration conf) throws ClassNotFoundException {
        Class<? extends ErrorReporter> reporter = conf.getClass("hbasefsck.errorreporter",
                PrintingErrorReporter.class, ErrorReporter.class);
        return (ErrorReporter) ReflectionUtils.newInstance(reporter, conf);
    }

    public interface ErrorReporter {
        enum ERROR_CODE {
            UNKNOWN, NO_META_REGION, NULL_META_REGION, NO_VERSION_FILE, NOT_IN_META_HDFS, NOT_IN_META, NOT_IN_META_OR_DEPLOYED, NOT_IN_HDFS_OR_DEPLOYED, NOT_IN_HDFS, SERVER_DOES_NOT_MATCH_META, NOT_DEPLOYED, MULTI_DEPLOYED, SHOULD_NOT_BE_DEPLOYED, MULTI_META_REGION, RS_CONNECT_FAILURE, FIRST_REGION_STARTKEY_NOT_EMPTY, LAST_REGION_ENDKEY_NOT_EMPTY, DUPE_STARTKEYS, HOLE_IN_REGION_CHAIN, OVERLAP_IN_REGION_CHAIN, REGION_CYCLE, DEGENERATE_REGION, ORPHAN_HDFS_REGION, LINGERING_SPLIT_PARENT, NO_TABLEINFO_FILE, LINGERING_REFERENCE_HFILE, WRONG_USAGE, EMPTY_META_CELL, EXPIRED_TABLE_LOCK, BOUNDARIES_ERROR
        }

        void clear();

        void report(String message);

        void reportError(String message);

        void reportError(ERROR_CODE errorCode, String message);

        void reportError(ERROR_CODE errorCode, String message, TableInfo table);

        void reportError(ERROR_CODE errorCode, String message, TableInfo table, HbckInfo info);

        void reportError(ERROR_CODE errorCode, String message, TableInfo table, HbckInfo info1, HbckInfo info2);

        int summarize();

        void detail(String details);

        ArrayList<ERROR_CODE> getErrorList();

        void progress();

        void print(String message);

        void resetErrors();

        boolean tableHasErrors(TableInfo table);
    }

    static class PrintingErrorReporter implements ErrorReporter {
        public int errorCount = 0;
        private int showProgress;

        Set<TableInfo> errorTables = new HashSet<TableInfo>();

        // for use by unit tests to verify which errors were discovered
        private ArrayList<ERROR_CODE> errorList = new ArrayList<ERROR_CODE>();

        @Override
        public void clear() {
            errorTables.clear();
            errorList.clear();
            errorCount = 0;
        }

        @Override
        public synchronized void reportError(ERROR_CODE errorCode, String message) {
            if (errorCode == ERROR_CODE.WRONG_USAGE) {
                System.err.println(message);
                return;
            }

            errorList.add(errorCode);
            if (!summary) {
                System.out.println("ERROR: " + message);
            }
            errorCount++;
            showProgress = 0;
        }

        @Override
        public synchronized void reportError(ERROR_CODE errorCode, String message, TableInfo table) {
            errorTables.add(table);
            reportError(errorCode, message);
        }

        @Override
        public synchronized void reportError(ERROR_CODE errorCode, String message, TableInfo table, HbckInfo info) {
            errorTables.add(table);
            String reference = "(region " + info.getRegionNameAsString() + ")";
            reportError(errorCode, reference + " " + message);
        }

        @Override
        public synchronized void reportError(ERROR_CODE errorCode, String message, TableInfo table, HbckInfo info1,
                HbckInfo info2) {
            errorTables.add(table);
            String reference = "(regions " + info1.getRegionNameAsString() + " and " + info2.getRegionNameAsString()
                    + ")";
            reportError(errorCode, reference + " " + message);
        }

        @Override
        public synchronized void reportError(String message) {
            reportError(ERROR_CODE.UNKNOWN, message);
        }

        /**
         * Report error information, but do not increment the error count.  Intended for cases
         * where the actual error would have been reported previously.
         * @param message
         */
        @Override
        public synchronized void report(String message) {
            if (!summary) {
                System.out.println("ERROR: " + message);
            }
            showProgress = 0;
        }

        @Override
        public synchronized int summarize() {
            System.out.println(Integer.toString(errorCount) + " inconsistencies detected.");
            if (errorCount == 0) {
                System.out.println("Status: OK");
                return 0;
            } else {
                System.out.println("Status: INCONSISTENT");
                return -1;
            }
        }

        @Override
        public ArrayList<ERROR_CODE> getErrorList() {
            return errorList;
        }

        @Override
        public synchronized void print(String message) {
            if (!summary) {
                System.out.println(message);
            }
        }

        @Override
        public boolean tableHasErrors(TableInfo table) {
            return errorTables.contains(table);
        }

        @Override
        public void resetErrors() {
            errorCount = 0;
        }

        @Override
        public synchronized void detail(String message) {
            if (details) {
                System.out.println(message);
            }
            showProgress = 0;
        }

        @Override
        public synchronized void progress() {
            if (showProgress++ == 10) {
                if (!summary) {
                    System.out.print(".");
                }
                showProgress = 0;
            }
        }
    }

    /**
     * Contact a region server and get all information from it
     */
    static class WorkItemRegion implements Callable<Void> {
        private HBaseFsck hbck;
        private ServerName rsinfo;
        private ErrorReporter errors;
        private HConnection connection;

        WorkItemRegion(HBaseFsck hbck, ServerName info, ErrorReporter errors, HConnection connection) {
            this.hbck = hbck;
            this.rsinfo = info;
            this.errors = errors;
            this.connection = connection;
        }

        @Override
        public synchronized Void call() throws IOException {
            errors.progress();
            try {
                BlockingInterface server = connection.getAdmin(rsinfo);

                // list all online regions from this region server
                List<HRegionInfo> regions = ProtobufUtil.getOnlineRegions(server);
                regions = filterRegions(regions);

                if (details) {
                    errors.detail(
                            "RegionServer: " + rsinfo.getServerName() + " number of regions: " + regions.size());
                    for (HRegionInfo rinfo : regions) {
                        errors.detail("  " + rinfo.getRegionNameAsString() + " id: " + rinfo.getRegionId()
                                + " encoded_name: " + rinfo.getEncodedName() + " start: "
                                + Bytes.toStringBinary(rinfo.getStartKey()) + " end: "
                                + Bytes.toStringBinary(rinfo.getEndKey()));
                    }
                }

                // check to see if the existence of this region matches the region in META
                for (HRegionInfo r : regions) {
                    HbckInfo hbi = hbck.getOrCreateInfo(r.getEncodedName());
                    hbi.addServer(r, rsinfo);
                }
            } catch (IOException e) { // unable to connect to the region server.
                errors.reportError(ERROR_CODE.RS_CONNECT_FAILURE,
                        "RegionServer: " + rsinfo.getServerName() + " Unable to fetch region information. " + e);
                throw e;
            }
            return null;
        }

        private List<HRegionInfo> filterRegions(List<HRegionInfo> regions) {
            List<HRegionInfo> ret = Lists.newArrayList();
            for (HRegionInfo hri : regions) {
                if (hri.isMetaTable() || (!hbck.checkMetaOnly && hbck.isTableIncluded(hri.getTable()))) {
                    ret.add(hri);
                }
            }
            return ret;
        }
    }

    /**
     * Contact hdfs and get all information about specified table directory into
     * regioninfo list.
     */
    static class WorkItemHdfsDir implements Callable<Void> {
        private HBaseFsck hbck;
        private FileStatus tableDir;
        private ErrorReporter errors;
        private FileSystem fs;

        WorkItemHdfsDir(HBaseFsck hbck, FileSystem fs, ErrorReporter errors, FileStatus status) {
            this.hbck = hbck;
            this.fs = fs;
            this.tableDir = status;
            this.errors = errors;
        }

        @Override
        public synchronized Void call() throws IOException {
            try {
                // level 2: <HBASE_DIR>/<table>/*
                FileStatus[] regionDirs = fs.listStatus(tableDir.getPath());
                for (FileStatus regionDir : regionDirs) {
                    String encodedName = regionDir.getPath().getName();
                    // ignore directories that aren't hexadecimal
                    if (!encodedName.toLowerCase().matches("[0-9a-f]+")) {
                        continue;
                    }

                    LOG.debug("Loading region info from hdfs:" + regionDir.getPath());
                    HbckInfo hbi = hbck.getOrCreateInfo(encodedName);
                    HdfsEntry he = new HdfsEntry();
                    synchronized (hbi) {
                        if (hbi.getHdfsRegionDir() != null) {
                            errors.print("Directory " + encodedName + " duplicate??" + hbi.getHdfsRegionDir());
                        }

                        he.hdfsRegionDir = regionDir.getPath();
                        he.hdfsRegionDirModTime = regionDir.getModificationTime();
                        Path regioninfoFile = new Path(he.hdfsRegionDir, HRegionFileSystem.REGION_INFO_FILE);
                        he.hdfsRegioninfoFilePresent = fs.exists(regioninfoFile);
                        // we add to orphan list when we attempt to read .regioninfo

                        // Set a flag if this region contains only edits
                        // This is special case if a region is left after split
                        he.hdfsOnlyEdits = true;
                        FileStatus[] subDirs = fs.listStatus(regionDir.getPath());
                        Path ePath = HLogUtil.getRegionDirRecoveredEditsDir(regionDir.getPath());
                        for (FileStatus subDir : subDirs) {
                            String sdName = subDir.getPath().getName();
                            if (!sdName.startsWith(".") && !sdName.equals(ePath.getName())) {
                                he.hdfsOnlyEdits = false;
                                break;
                            }
                        }
                        hbi.hdfsEntry = he;
                    }
                }
            } catch (IOException e) {
                // unable to connect to the region server.
                errors.reportError(ERROR_CODE.RS_CONNECT_FAILURE, "Table Directory: " + tableDir.getPath().getName()
                        + " Unable to fetch region information. " + e);
                throw e;
            }
            return null;
        }
    }

    /**
     * Contact hdfs and get all information about specified table directory into
     * regioninfo list.
     */
    static class WorkItemHdfsRegionInfo implements Callable<Void> {
        private HbckInfo hbi;
        private HBaseFsck hbck;
        private ErrorReporter errors;

        WorkItemHdfsRegionInfo(HbckInfo hbi, HBaseFsck hbck, ErrorReporter errors) {
            this.hbi = hbi;
            this.hbck = hbck;
            this.errors = errors;
        }

        @Override
        public synchronized Void call() throws IOException {
            // only load entries that haven't been loaded yet.
            if (hbi.getHdfsHRI() == null) {
                try {
                    hbck.loadHdfsRegioninfo(hbi);
                } catch (IOException ioe) {
                    String msg = "Orphan region in HDFS: Unable to load .regioninfo from table "
                            + hbi.getTableName() + " in hdfs dir " + hbi.getHdfsRegionDir()
                            + "!  It may be an invalid format or version file.  Treating as "
                            + "an orphaned regiondir.";
                    errors.reportError(ERROR_CODE.ORPHAN_HDFS_REGION, msg);
                    try {
                        hbck.debugLsr(hbi.getHdfsRegionDir());
                    } catch (IOException ioe2) {
                        LOG.error("Unable to read directory " + hbi.getHdfsRegionDir(), ioe2);
                        throw ioe2;
                    }
                    hbck.orphanHdfsDirs.add(hbi);
                    throw ioe;
                }
            }
            return null;
        }
    };

    /**
     * Display the full report from fsck. This displays all live and dead region
     * servers, and all known regions.
     */
    public static void setDisplayFullReport() {
        details = true;
    }

    /**
     * Set summary mode.
     * Print only summary of the tables and status (OK or INCONSISTENT)
     */
    void setSummary() {
        summary = true;
    }

    /**
     * Set hbase:meta check mode.
     * Print only info about hbase:meta table deployment/state
     */
    void setCheckMetaOnly() {
        checkMetaOnly = true;
    }

    /**
     * Set region boundaries check mode.
     */
    void setRegionBoundariesCheck() {
        checkRegionBoundaries = true;
    }

    /**
     * Set table locks fix mode.
     * Delete table locks held for a long time
     */
    public void setFixTableLocks(boolean shouldFix) {
        fixTableLocks = shouldFix;
    }

    /**
     * Check if we should rerun fsck again. This checks if we've tried to
     * fix something and we should rerun fsck tool again.
     * Display the full report from fsck. This displays all live and dead
     * region servers, and all known regions.
     */
    void setShouldRerun() {
        rerun = true;
    }

    boolean shouldRerun() {
        return rerun;
    }

    /**
     * Fix inconsistencies found by fsck. This should try to fix errors (if any)
     * found by fsck utility.
     */
    public void setFixAssignments(boolean shouldFix) {
        fixAssignments = shouldFix;
    }

    boolean shouldFixAssignments() {
        return fixAssignments;
    }

    public void setFixMeta(boolean shouldFix) {
        fixMeta = shouldFix;
    }

    boolean shouldFixMeta() {
        return fixMeta;
    }

    public void setFixEmptyMetaCells(boolean shouldFix) {
        fixEmptyMetaCells = shouldFix;
    }

    boolean shouldFixEmptyMetaCells() {
        return fixEmptyMetaCells;
    }

    public void setCheckHdfs(boolean checking) {
        checkHdfs = checking;
    }

    boolean shouldCheckHdfs() {
        return checkHdfs;
    }

    public void setFixHdfsHoles(boolean shouldFix) {
        fixHdfsHoles = shouldFix;
    }

    boolean shouldFixHdfsHoles() {
        return fixHdfsHoles;
    }

    public void setFixTableOrphans(boolean shouldFix) {
        fixTableOrphans = shouldFix;
    }

    boolean shouldFixTableOrphans() {
        return fixTableOrphans;
    }

    public void setFixHdfsOverlaps(boolean shouldFix) {
        fixHdfsOverlaps = shouldFix;
    }

    boolean shouldFixHdfsOverlaps() {
        return fixHdfsOverlaps;
    }

    public void setFixHdfsOrphans(boolean shouldFix) {
        fixHdfsOrphans = shouldFix;
    }

    boolean shouldFixHdfsOrphans() {
        return fixHdfsOrphans;
    }

    public void setFixVersionFile(boolean shouldFix) {
        fixVersionFile = shouldFix;
    }

    public boolean shouldFixVersionFile() {
        return fixVersionFile;
    }

    public void setSidelineBigOverlaps(boolean sbo) {
        this.sidelineBigOverlaps = sbo;
    }

    public boolean shouldSidelineBigOverlaps() {
        return sidelineBigOverlaps;
    }

    public void setFixSplitParents(boolean shouldFix) {
        fixSplitParents = shouldFix;
    }

    boolean shouldFixSplitParents() {
        return fixSplitParents;
    }

    public void setFixReferenceFiles(boolean shouldFix) {
        fixReferenceFiles = shouldFix;
    }

    boolean shouldFixReferenceFiles() {
        return fixReferenceFiles;
    }

    public boolean shouldIgnorePreCheckPermission() {
        return ignorePreCheckPermission;
    }

    public void setIgnorePreCheckPermission(boolean ignorePreCheckPermission) {
        this.ignorePreCheckPermission = ignorePreCheckPermission;
    }

    /**
     * @param mm maximum number of regions to merge into a single region.
     */
    public void setMaxMerge(int mm) {
        this.maxMerge = mm;
    }

    public int getMaxMerge() {
        return maxMerge;
    }

    public void setMaxOverlapsToSideline(int mo) {
        this.maxOverlapsToSideline = mo;
    }

    public int getMaxOverlapsToSideline() {
        return maxOverlapsToSideline;
    }

    /**
     * Only check/fix tables specified by the list,
     * Empty list means all tables are included.
     */
    boolean isTableIncluded(TableName table) {
        return (tablesIncluded.size() == 0) || tablesIncluded.contains(table);
    }

    public void includeTable(TableName table) {
        tablesIncluded.add(table);
    }

    Set<TableName> getIncludedTables() {
        return new HashSet<TableName>(tablesIncluded);
    }

    /**
     * We are interested in only those tables that have not changed their state in
     * hbase:meta during the last few seconds specified by hbase.admin.fsck.timelag
     * @param seconds - the time in seconds
     */
    public void setTimeLag(long seconds) {
        timelag = seconds * 1000; // convert to milliseconds
    }

    /**
     *
     * @param sidelineDir - HDFS path to sideline data
     */
    public void setSidelineDir(String sidelineDir) {
        this.sidelineDir = new Path(sidelineDir);
    }

    protected HFileCorruptionChecker createHFileCorruptionChecker(boolean sidelineCorruptHFiles)
            throws IOException {
        return new HFileCorruptionChecker(getConf(), executor, sidelineCorruptHFiles);
    }

    public HFileCorruptionChecker getHFilecorruptionChecker() {
        return hfcc;
    }

    public void setHFileCorruptionChecker(HFileCorruptionChecker hfcc) {
        this.hfcc = hfcc;
    }

    public void setRetCode(int code) {
        this.retcode = code;
    }

    public int getRetCode() {
        return retcode;
    }

    protected HBaseFsck printUsageAndExit() {
        StringWriter sw = new StringWriter(2048);
        PrintWriter out = new PrintWriter(sw);
        out.println("Usage: fsck [opts] {only tables}");
        out.println(" where [opts] are:");
        out.println("   -help Display help options (this)");
        out.println("   -details Display full report of all regions.");
        out.println("   -timelag <timeInSeconds>  Process only regions that "
                + " have not experienced any metadata updates in the last " + " <timeInSeconds> seconds.");
        out.println("   -sleepBeforeRerun <timeInSeconds> Sleep this many seconds"
                + " before checking if the fix worked if run with -fix");
        out.println("   -summary Print only summary of the tables and status.");
        out.println("   -metaonly Only check the state of the hbase:meta table.");
        out.println("   -sidelineDir <hdfs://> HDFS path to backup existing meta.");
        out.println("   -boundaries Verify that regions boundaries are the same between META and store files.");

        out.println("");
        out.println("  Metadata Repair options: (expert features, use with caution!)");
        out.println("   -fix              Try to fix region assignments.  This is for backwards compatiblity");
        out.println("   -fixAssignments   Try to fix region assignments.  Replaces the old -fix");
        out.println("   -fixMeta          Try to fix meta problems.  This assumes HDFS region info is good.");
        out.println("   -noHdfsChecking   Don't load/check region info from HDFS."
                + " Assumes hbase:meta region info is good. Won't check/fix any HDFS issue, e.g. hole, orphan, or overlap");
        out.println("   -fixHdfsHoles     Try to fix region holes in hdfs.");
        out.println("   -fixHdfsOrphans   Try to fix region dirs with no .regioninfo file in hdfs");
        out.println(
                "   -fixTableOrphans  Try to fix table dirs with no .tableinfo file in hdfs (online mode only)");
        out.println("   -fixHdfsOverlaps  Try to fix region overlaps in hdfs.");
        out.println("   -fixVersionFile   Try to fix missing hbase.version file in hdfs.");
        out.println("   -maxMerge <n>     When fixing region overlaps, allow at most <n> regions to merge. (n="
                + DEFAULT_MAX_MERGE + " by default)");
        out.println("   -sidelineBigOverlaps  When fixing region overlaps, allow to sideline big overlaps");
        out.println(
                "   -maxOverlapsToSideline <n>  When fixing region overlaps, allow at most <n> regions to sideline per group. (n="
                        + DEFAULT_OVERLAPS_TO_SIDELINE + " by default)");
        out.println("   -fixSplitParents  Try to force offline split parents to be online.");
        out.println("   -ignorePreCheckPermission  ignore filesystem permission pre-check");
        out.println("   -fixReferenceFiles  Try to offline lingering reference store files");
        out.println("   -fixEmptyMetaCells  Try to fix hbase:meta entries not referencing any region"
                + " (empty REGIONINFO_QUALIFIER rows)");

        out.println("");
        out.println("  Datafile Repair options: (expert features, use with caution!)");
        out.println("   -checkCorruptHFiles     Check all Hfiles by opening them to make sure they are valid");
        out.println("   -sidelineCorruptHFiles  Quarantine corrupted HFiles.  implies -checkCorruptHFiles");

        out.println("");
        out.println("  Metadata Repair shortcuts");
        out.println("   -repair           Shortcut for -fixAssignments -fixMeta -fixHdfsHoles "
                + "-fixHdfsOrphans -fixHdfsOverlaps -fixVersionFile -sidelineBigOverlaps -fixReferenceFiles -fixTableLocks");
        out.println("   -repairHoles      Shortcut for -fixAssignments -fixMeta -fixHdfsHoles");

        out.println("");
        out.println("  Table lock options");
        out.println(
                "   -fixTableLocks    Deletes table locks held for a long time (hbase.table.lock.expire.ms, 10min by default)");

        out.flush();
        errors.reportError(ERROR_CODE.WRONG_USAGE, sw.toString());

        setRetCode(-2);
        return this;
    }

    /**
     * Main program
     *
     * @param args
     * @throws Exception
     */
    public static void main(String[] args) throws Exception {
        // create a fsck object
        Configuration conf = HBaseConfiguration.create();
        Path hbasedir = FSUtils.getRootDir(conf);
        URI defaultFs = hbasedir.getFileSystem(conf).getUri();
        FSUtils.setFsDefault(conf, new Path(defaultFs));

        int ret = ToolRunner.run(new HBaseFsckTool(conf), args);
        System.exit(ret);
    }

    /**
     * This is a Tool wrapper that gathers -Dxxx=yyy configuration settings from the command line.
     */
    static class HBaseFsckTool extends Configured implements Tool {
        HBaseFsckTool(Configuration conf) {
            super(conf);
        }

        @Override
        public int run(String[] args) throws Exception {
            HBaseFsck hbck = new HBaseFsck(getConf());
            hbck.exec(hbck.executor, args);
            return hbck.getRetCode();
        }
    };

    public HBaseFsck exec(ExecutorService exec, String[] args)
            throws KeeperException, IOException, ServiceException, InterruptedException {
        long sleepBeforeRerun = DEFAULT_SLEEP_BEFORE_RERUN;

        boolean checkCorruptHFiles = false;
        boolean sidelineCorruptHFiles = false;

        // Process command-line args.
        for (int i = 0; i < args.length; i++) {
            String cmd = args[i];
            if (cmd.equals("-help") || cmd.equals("-h")) {
                return printUsageAndExit();
            } else if (cmd.equals("-details")) {
                setDisplayFullReport();
            } else if (cmd.equals("-timelag")) {
                if (i == args.length - 1) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "HBaseFsck: -timelag needs a value.");
                    return printUsageAndExit();
                }
                try {
                    long timelag = Long.parseLong(args[i + 1]);
                    setTimeLag(timelag);
                } catch (NumberFormatException e) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "-timelag needs a numeric value.");
                    return printUsageAndExit();
                }
                i++;
            } else if (cmd.equals("-sleepBeforeRerun")) {
                if (i == args.length - 1) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "HBaseFsck: -sleepBeforeRerun needs a value.");
                    return printUsageAndExit();
                }
                try {
                    sleepBeforeRerun = Long.parseLong(args[i + 1]);
                } catch (NumberFormatException e) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "-sleepBeforeRerun needs a numeric value.");
                    return printUsageAndExit();
                }
                i++;
            } else if (cmd.equals("-sidelineDir")) {
                if (i == args.length - 1) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "HBaseFsck: -sidelineDir needs a value.");
                    return printUsageAndExit();
                }
                i++;
                setSidelineDir(args[i]);
            } else if (cmd.equals("-fix")) {
                errors.reportError(ERROR_CODE.WRONG_USAGE,
                        "This option is deprecated, please use  -fixAssignments instead.");
                setFixAssignments(true);
            } else if (cmd.equals("-fixAssignments")) {
                setFixAssignments(true);
            } else if (cmd.equals("-fixMeta")) {
                setFixMeta(true);
            } else if (cmd.equals("-noHdfsChecking")) {
                setCheckHdfs(false);
            } else if (cmd.equals("-fixHdfsHoles")) {
                setFixHdfsHoles(true);
            } else if (cmd.equals("-fixHdfsOrphans")) {
                setFixHdfsOrphans(true);
            } else if (cmd.equals("-fixTableOrphans")) {
                setFixTableOrphans(true);
            } else if (cmd.equals("-fixHdfsOverlaps")) {
                setFixHdfsOverlaps(true);
            } else if (cmd.equals("-fixVersionFile")) {
                setFixVersionFile(true);
            } else if (cmd.equals("-sidelineBigOverlaps")) {
                setSidelineBigOverlaps(true);
            } else if (cmd.equals("-fixSplitParents")) {
                setFixSplitParents(true);
            } else if (cmd.equals("-ignorePreCheckPermission")) {
                setIgnorePreCheckPermission(true);
            } else if (cmd.equals("-checkCorruptHFiles")) {
                checkCorruptHFiles = true;
            } else if (cmd.equals("-sidelineCorruptHFiles")) {
                sidelineCorruptHFiles = true;
            } else if (cmd.equals("-fixReferenceFiles")) {
                setFixReferenceFiles(true);
            } else if (cmd.equals("-fixEmptyMetaCells")) {
                setFixEmptyMetaCells(true);
            } else if (cmd.equals("-repair")) {
                // this attempts to merge overlapping hdfs regions, needs testing
                // under load
                setFixHdfsHoles(true);
                setFixHdfsOrphans(true);
                setFixMeta(true);
                setFixAssignments(true);
                setFixHdfsOverlaps(true);
                setFixVersionFile(true);
                setSidelineBigOverlaps(true);
                setFixSplitParents(false);
                setCheckHdfs(true);
                setFixReferenceFiles(true);
                setFixTableLocks(true);
            } else if (cmd.equals("-repairHoles")) {
                // this will make all missing hdfs regions available but may lose data
                setFixHdfsHoles(true);
                setFixHdfsOrphans(false);
                setFixMeta(true);
                setFixAssignments(true);
                setFixHdfsOverlaps(false);
                setSidelineBigOverlaps(false);
                setFixSplitParents(false);
                setCheckHdfs(true);
            } else if (cmd.equals("-maxOverlapsToSideline")) {
                if (i == args.length - 1) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE,
                            "-maxOverlapsToSideline needs a numeric value argument.");
                    return printUsageAndExit();
                }
                try {
                    int maxOverlapsToSideline = Integer.parseInt(args[i + 1]);
                    setMaxOverlapsToSideline(maxOverlapsToSideline);
                } catch (NumberFormatException e) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE,
                            "-maxOverlapsToSideline needs a numeric value argument.");
                    return printUsageAndExit();
                }
                i++;
            } else if (cmd.equals("-maxMerge")) {
                if (i == args.length - 1) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "-maxMerge needs a numeric value argument.");
                    return printUsageAndExit();
                }
                try {
                    int maxMerge = Integer.parseInt(args[i + 1]);
                    setMaxMerge(maxMerge);
                } catch (NumberFormatException e) {
                    errors.reportError(ERROR_CODE.WRONG_USAGE, "-maxMerge needs a numeric value argument.");
                    return printUsageAndExit();
                }
                i++;
            } else if (cmd.equals("-summary")) {
                setSummary();
            } else if (cmd.equals("-metaonly")) {
                setCheckMetaOnly();
            } else if (cmd.equals("-boundaries")) {
                setRegionBoundariesCheck();
            } else if (cmd.equals("-fixTableLocks")) {
                setFixTableLocks(true);
            } else if (cmd.startsWith("-")) {
                errors.reportError(ERROR_CODE.WRONG_USAGE, "Unrecognized option:" + cmd);
                return printUsageAndExit();
            } else {
                includeTable(TableName.valueOf(cmd));
                errors.print("Allow checking/fixes for table: " + cmd);
            }
        }

        // pre-check current user has FS write permission or not
        try {
            preCheckPermission();
        } catch (AccessControlException ace) {
            Runtime.getRuntime().exit(-1);
        } catch (IOException ioe) {
            Runtime.getRuntime().exit(-1);
        }

        // do the real work of hbck
        connect();

        try {
            // if corrupt file mode is on, first fix them since they may be opened later
            if (checkCorruptHFiles || sidelineCorruptHFiles) {
                LOG.info("Checking all hfiles for corruption");
                HFileCorruptionChecker hfcc = createHFileCorruptionChecker(sidelineCorruptHFiles);
                setHFileCorruptionChecker(hfcc); // so we can get result
                Collection<TableName> tables = getIncludedTables();
                Collection<Path> tableDirs = new ArrayList<Path>();
                Path rootdir = FSUtils.getRootDir(getConf());
                if (tables.size() > 0) {
                    for (TableName t : tables) {
                        tableDirs.add(FSUtils.getTableDir(rootdir, t));
                    }
                } else {
                    tableDirs = FSUtils.getTableDirs(FSUtils.getCurrentFileSystem(getConf()), rootdir);
                }
                hfcc.checkTables(tableDirs);
                hfcc.report(errors);
            }

            // check and fix table integrity, region consistency.
            int code = onlineHbck();
            setRetCode(code);
            // If we have changed the HBase state it is better to run hbck again
            // to see if we haven't broken something else in the process.
            // We run it only once more because otherwise we can easily fall into
            // an infinite loop.
            if (shouldRerun()) {
                try {
                    LOG.info("Sleeping " + sleepBeforeRerun + "ms before re-checking after fix...");
                    Thread.sleep(sleepBeforeRerun);
                } catch (InterruptedException ie) {
                    LOG.warn("Interrupted while sleeping");
                    return this;
                }
                // Just report
                setFixAssignments(false);
                setFixMeta(false);
                setFixHdfsHoles(false);
                setFixHdfsOverlaps(false);
                setFixVersionFile(false);
                setFixTableOrphans(false);
                errors.resetErrors();
                code = onlineHbck();
                setRetCode(code);
            }
        } finally {
            IOUtils.cleanup(null, connection, meta, admin);
        }
        return this;
    }

    /**
     * ls -r for debugging purposes
     */
    void debugLsr(Path p) throws IOException {
        debugLsr(getConf(), p, errors);
    }

    /**
     * ls -r for debugging purposes
     */
    public static void debugLsr(Configuration conf, Path p) throws IOException {
        debugLsr(conf, p, new PrintingErrorReporter());
    }

    /**
     * ls -r for debugging purposes
     */
    public static void debugLsr(Configuration conf, Path p, ErrorReporter errors) throws IOException {
        if (!LOG.isDebugEnabled() || p == null) {
            return;
        }
        FileSystem fs = p.getFileSystem(conf);

        if (!fs.exists(p)) {
            // nothing
            return;
        }
        errors.print(p.toString());

        if (fs.isFile(p)) {
            return;
        }

        if (fs.getFileStatus(p).isDirectory()) {
            FileStatus[] fss = fs.listStatus(p);
            for (FileStatus status : fss) {
                debugLsr(conf, status.getPath(), errors);
            }
        }
    }
}