backends/pluggable/VerifyJob.java

	VerifyJob.java revision 8ac57ee1cd50fcc3d02b36bea4ab1335924f1d7a
/*
 * CDDL HEADER START
 *
 * The contents of this file are subject to the terms of the
 * Common Development and Distribution License, Version 1.0 only
 * (the "License").  You may not use this file except in compliance
 * with the License.
 *
 * You can obtain a copy of the license at legal-notices/CDDLv1_0.txt
 * or http://forgerock.org/license/CDDLv1.0.html.
 * See the License for the specific language governing permissions
 * and limitations under the License.
 *
 * When distributing Covered Code, include this CDDL HEADER in each
 * file and include the License file at legal-notices/CDDLv1_0.txt.
 * If applicable, add the following below this CDDL HEADER, with the
 * fields enclosed by brackets "[]" replaced with your own identifying
 * information:
 *      Portions Copyright [yyyy] [name of copyright owner]
 *
 * CDDL HEADER END
 *
 *
 *      Copyright 2006-2010 Sun Microsystems, Inc.
 *      Portions Copyright 2011-2015 ForgeRock AS
 */
package org.opends.server.backends.pluggable;

import static org.opends.messages.BackendMessages.*;
import static org.opends.server.backends.pluggable.DnKeyFormat.*;
import static org.opends.server.backends.pluggable.VLVIndex.*;

import java.util.AbstractSet;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Queue;
import java.util.Set;
import java.util.Timer;
import java.util.TimerTask;
import java.util.concurrent.atomic.AtomicBoolean;

import org.forgerock.i18n.slf4j.LocalizedLogger;
import org.forgerock.opendj.ldap.ByteSequence;
import org.forgerock.opendj.ldap.ByteString;
import org.forgerock.opendj.ldap.ConditionResult;
import org.opends.server.backends.VerifyConfig;
import org.opends.server.backends.pluggable.AttributeIndex.MatchingRuleIndex;
import org.opends.server.backends.pluggable.spi.Cursor;
import org.opends.server.backends.pluggable.spi.ReadOperation;
import org.opends.server.backends.pluggable.spi.ReadableTransaction;
import org.opends.server.backends.pluggable.spi.StorageRuntimeException;
import org.opends.server.core.DirectoryServer;
import org.opends.server.types.AttributeType;
import org.opends.server.types.DN;
import org.opends.server.types.DirectoryException;
import org.opends.server.types.Entry;
import org.opends.server.util.ServerConstants;
import org.opends.server.util.StaticUtils;

/** This class is used to run an index verification process on the backend. */
class VerifyJob
{
  private static final LocalizedLogger logger = LocalizedLogger.getLoggerForThisClass();

  /** The verify configuration. */
  private final VerifyConfig verifyConfig;
  /** The root container used for the verify job. */
  private final RootContainer rootContainer;

  /** The number of milliseconds between job progress reports. */
  private final long progressInterval = 10000;
  /** The number of index keys processed. */
  private long keyCount;
  /** The number of errors found. */
  private long errorCount;
  /** The number of records that have exceeded the entry limit. */
  private long entryLimitExceededCount;
  /** The number of records that reference more than one entry. */
  private long multiReferenceCount;
  /** The total number of entry references. */
  private long entryReferencesCount;
  /** The maximum number of references per record. */
  private long maxEntryPerValue;

  /**
   * This map is used to gather some statistics about values that have
   * exceeded the entry limit.
   */
  private IdentityHashMap<Index, HashMap<ByteString, Long>> entryLimitMap =
       new IdentityHashMap<Index, HashMap<ByteString, Long>>();

  /** Indicates whether dn2id is to be verified. */
  private boolean verifyDN2ID;
  /** Indicates whether the children count tree is to be verified. */
  private boolean verifyID2ChildrenCount;

  /** The entry tree. */
  private ID2Entry id2entry;
  /** The DN tree. */
  private DN2ID dn2id;
  /** The children tree. */
  private ID2Count id2childrenCount;

  /** A list of the attribute indexes to be verified. */
  private final ArrayList<AttributeIndex> attrIndexList = new ArrayList<AttributeIndex>();
  /** A list of the VLV indexes to be verified. */
  private final ArrayList<VLVIndex> vlvIndexList = new ArrayList<VLVIndex>();

  /**
   * Construct a VerifyJob.
   *
   * @param verifyConfig The verify configuration.
   */
  VerifyJob(RootContainer rootContainer, VerifyConfig verifyConfig)
  {
    this.rootContainer = rootContainer;
    this.verifyConfig = verifyConfig;
  }

  /**
   * Verify the backend.
   *
   * @param rootContainer The root container that holds the entries to verify.
   * @return The error count.
   * @throws StorageRuntimeException If an error occurs in the storage.
   * @throws DirectoryException If an error occurs while verifying the backend.
   */
  long verifyBackend() throws StorageRuntimeException,
      DirectoryException
  {
    try
    {
      return rootContainer.getStorage().read(new ReadOperation<Long>()
      {
        @Override
        public Long run(ReadableTransaction txn) throws Exception
        {
          return verifyBackend0(txn);
        }
      });
    }
    catch (StorageRuntimeException e)
    {
      throw e;
    }
    catch (Exception e)
    {
      throw new StorageRuntimeException(e);
    }
  }

  private long verifyBackend0(ReadableTransaction txn) throws StorageRuntimeException, DirectoryException
  {
    EntryContainer entryContainer =
        rootContainer.getEntryContainer(verifyConfig.getBaseDN());

    entryContainer.sharedLock.lock();
    try
    {
      final List<String> completeList = verifyConfig.getCompleteList();
      final List<String> cleanList = verifyConfig.getCleanList();

      boolean cleanMode = false;
      if (completeList.isEmpty() && cleanList.isEmpty())
      {
        verifyDN2ID = true;
        verifyID2ChildrenCount = true;
        attrIndexList.addAll(entryContainer.getAttributeIndexes());
      }
      else
      {
        final List<String> list;
        if (!completeList.isEmpty())
        {
          list = completeList;
        }
        else
        {
          list = cleanList;
          cleanMode = true;
        }

        for (String index : list)
        {
          String lowerName = index.toLowerCase();
          if ("dn2id".equals(lowerName))
          {
            verifyDN2ID = true;
          }
          else if ("id2childrencount".equals(lowerName))
          {
            verifyID2ChildrenCount = true;
          }
          else if(lowerName.startsWith("vlv."))
          {
            if(lowerName.length() < 5)
            {
              throw new StorageRuntimeException(ERR_VLV_INDEX_NOT_CONFIGURED.get(lowerName).toString());
            }

            VLVIndex vlvIndex =
                entryContainer.getVLVIndex(lowerName.substring(4));
            if(vlvIndex == null)
            {
              throw new StorageRuntimeException(ERR_VLV_INDEX_NOT_CONFIGURED.get(lowerName.substring(4)).toString());
            }

            vlvIndexList.add(vlvIndex);
          }
          else
          {
            AttributeType attrType = DirectoryServer.getAttributeType(lowerName);
            if (attrType == null)
            {
              throw new StorageRuntimeException(ERR_ATTRIBUTE_INDEX_NOT_CONFIGURED.get(index).toString());
            }
            AttributeIndex attrIndex = entryContainer.getAttributeIndex(attrType);
            if (attrIndex == null)
            {
              throw new StorageRuntimeException(ERR_ATTRIBUTE_INDEX_NOT_CONFIGURED.get(index).toString());
            }
            attrIndexList.add(attrIndex);
          }
        }
      }

      entryLimitMap = new IdentityHashMap<Index, HashMap<ByteString, Long>>(attrIndexList.size());

      // We will be updating these files independently of the indexes
      // so we need direct access to them rather than going through
      // the entry entryContainer methods.
      id2entry = entryContainer.getID2Entry();
      dn2id = entryContainer.getDN2ID();
      id2childrenCount = entryContainer.getID2ChildrenCount();

      // Make a note of the time we started.
      long startTime = System.currentTimeMillis();

      // Start a timer for the progress report.
      Timer timer = new Timer();
      TimerTask progressTask = new ProgressTask(cleanMode, txn);
      timer.scheduleAtFixedRate(progressTask, progressInterval, progressInterval);

      // Iterate through the index keys.
      try
      {
        if (cleanMode)
        {
          iterateIndex(txn);
        }
        else
        {
          iterateID2Entry(txn);

          // Make sure the vlv indexes are in correct order.
          for(VLVIndex vlvIndex : vlvIndexList)
          {
            iterateVLVIndex(txn, vlvIndex, false);
          }
        }
      }
      finally
      {
        timer.cancel();
      }

      long finishTime = System.currentTimeMillis();
      long totalTime = finishTime - startTime;

      float rate = 0;
      if (totalTime > 0)
      {
        rate = 1000f*keyCount / totalTime;
      }

      if (cleanMode)
      {
        logger.info(NOTE_VERIFY_CLEAN_FINAL_STATUS, keyCount, errorCount, totalTime/1000, rate);

        if (multiReferenceCount > 0)
        {
          float averageEntryReferences = 0;
          if (keyCount > 0)
          {
            averageEntryReferences = entryReferencesCount/keyCount;
          }

          if (logger.isDebugEnabled())
          {
            logger.debug(INFO_VERIFY_MULTIPLE_REFERENCE_COUNT, multiReferenceCount);
            logger.debug(INFO_VERIFY_ENTRY_LIMIT_EXCEEDED_COUNT, entryLimitExceededCount);
            logger.debug(INFO_VERIFY_AVERAGE_REFERENCE_COUNT, averageEntryReferences);
            logger.debug(INFO_VERIFY_MAX_REFERENCE_COUNT, maxEntryPerValue);
          }
        }
      }
      else
      {
        logger.info(NOTE_VERIFY_FINAL_STATUS, keyCount, errorCount, totalTime/1000, rate);
        if (entryLimitMap.size() > 0)
        {
          logger.debug(INFO_VERIFY_ENTRY_LIMIT_STATS_HEADER);

          for (Map.Entry<Index,HashMap<ByteString,Long>> mapEntry :
              entryLimitMap.entrySet())
          {
            Index index = mapEntry.getKey();
            Long[] values = mapEntry.getValue().values().toArray(new Long[0]);

            // Calculate the median value for entry limit exceeded.
            Arrays.sort(values);
            long medianValue;
            int x = values.length / 2;
            if (values.length % 2 == 0)
            {
              medianValue = (values[x] + values[x-1]) / 2;
            }
            else
            {
              medianValue = values[x];
            }

            logger.debug(INFO_VERIFY_ENTRY_LIMIT_STATS_ROW, index, values.length, values[0],
                    values[values.length-1], medianValue);
          }
        }
      }
    }
    finally
    {
      entryContainer.sharedLock.unlock();
    }
    return errorCount;
  }

  /**
   * Iterate through the entries in id2entry to perform a check for
   * index completeness. We check that the ID for the entry is indeed
   * present in the indexes for the appropriate values.
   *
   * @throws StorageRuntimeException If an error occurs in the storage.
   */
  private void iterateID2Entry(ReadableTransaction txn) throws StorageRuntimeException
  {
    try(final Cursor<ByteString, ByteString> cursor = txn.openCursor(id2entry.getName()))
    {
      long storedEntryCount = id2entry.getRecordCount(txn);
      while (cursor.next())
      {
        ByteString key = cursor.getKey();
        ByteString value = cursor.getValue();

        EntryID entryID;
        try
        {
          entryID = new EntryID(key);
        }
        catch (Exception e)
        {
          errorCount++;
          if (logger.isTraceEnabled())
          {
            logger.traceException(e);

            logger.trace("Malformed id2entry ID %s.%n", StaticUtils.bytesToHex(key));
          }
          continue;
        }

        keyCount++;

        Entry entry;
        try
        {
          entry = ID2Entry.entryFromDatabase(value, rootContainer.getCompressedSchema());
        }
        catch (Exception e)
        {
          errorCount++;
          if (logger.isTraceEnabled())
          {
            logger.traceException(e);

            logger.trace("Malformed id2entry record for ID %d:%n%s%n", entryID, StaticUtils.bytesToHex(value));
          }
          continue;
        }

        verifyEntry(txn, entryID, entry);
      }
      if (keyCount != storedEntryCount)
      {
        errorCount++;
        if (logger.isTraceEnabled())
        {
          logger.trace("The stored entry count in id2entry (%d) does " +
              "not agree with the actual number of entry " +
              "records found (%d).%n", storedEntryCount, keyCount);
        }
      }
    }
  }

  /**
   * Iterate through the entries in an index to perform a check for
   * index cleanliness. For each ID in the index we check that the
   * entry it refers to does indeed contain the expected value.
   *
   * @throws StorageRuntimeException If an error occurs in the storage.
   * @throws DirectoryException If an error occurs reading values in the index.
   */
  private void iterateIndex(ReadableTransaction txn) throws StorageRuntimeException, DirectoryException
  {
    if (verifyDN2ID)
    {
      iterateDN2ID(txn);
    }
    else if (verifyID2ChildrenCount)
    {
      iterateID2ChildrenCount(txn);
    }
    else if (attrIndexList.size() > 0)
    {
      AttributeIndex attrIndex = attrIndexList.get(0);
      for (MatchingRuleIndex index : attrIndex.getNameToIndexes().values())
      {
        iterateAttrIndex(txn, index);
      }
    }
    else if (vlvIndexList.size() > 0)
    {
      iterateVLVIndex(txn, vlvIndexList.get(0), true);
    }
  }

  /**
   * Iterate through the entries in DN2ID to perform a check for
   * index cleanliness.
   *
   * @throws StorageRuntimeException If an error occurs in the storage.
   */
  private void iterateDN2ID(ReadableTransaction txn) throws StorageRuntimeException
  {
    final Queue<ChildrenCount> childrenCounters = new LinkedList<>();
    ChildrenCount currentNode = null;

    try(final Cursor<ByteString, ByteString> cursor = txn.openCursor(dn2id.getName()))
    {
      while (cursor.next())
      {
        keyCount++;

        final ByteString key = cursor.getKey();
        final EntryID entryID;
        try
        {
          entryID =  new EntryID(cursor.getValue());
        }
        catch (Exception e)
        {
          errorCount++;
          logger.trace("File dn2id has malformed ID for DN <%s>", key, e);
          continue;
        }

        currentNode = verifyID2ChildrenCount(txn, childrenCounters, key, entryID);

        final Entry entry;
        try
        {
          entry = id2entry.get(txn, entryID);
        }
        catch (Exception e)
        {
          errorCount++;
          logger.traceException(e);
          continue;
        }

        if (entry == null)
        {
          errorCount++;
          logger.trace("File dn2id has DN <%s> referencing unknown ID %d%n", key, entryID);
        }
        else if (!key.equals(dnToDNKey(entry.getName(), verifyConfig.getBaseDN().size())))
        {
          errorCount++;
          logger.trace("File dn2id has DN <%s> referencing entry with wrong DN <%s>%n", key, entry.getName());
        }
      }

      while ((currentNode = childrenCounters.poll()) != null)
      {
        verifyID2ChildrenCount(txn, currentNode);
      }
    }
  }

  private ChildrenCount verifyID2ChildrenCount(ReadableTransaction txn, final Queue<ChildrenCount> childrenCounters,
      final ByteString key, final EntryID entryID)
  {
    while (childrenCounters.peek() != null && !DN2ID.isChild(childrenCounters.peek().baseDN, key))
    {
      // This subtree is fully processed, pop the counter of the parent DN from the stack and verify it's value
      verifyID2ChildrenCount(txn, childrenCounters.remove());
    }
    if (childrenCounters.peek() != null)
    {
      childrenCounters.peek().numberOfChildren++;
    }
    final ChildrenCount node = new ChildrenCount(key, entryID);
    childrenCounters.add(node);
    return node;
  }

  private void verifyID2ChildrenCount(ReadableTransaction txn, ChildrenCount parent) {
    final long expected = parent.numberOfChildren;
    final long currentValue = id2childrenCount.getCount(txn, parent.entryID);
    if (expected != currentValue)
    {
      errorCount++;
      logger.trace("File id2childrenCount has wrong number of children for DN <%s> (got %d, expecting %d)",
          parent.baseDN, currentValue, expected);
    }
  }

  private void iterateID2ChildrenCount(ReadableTransaction txn) throws StorageRuntimeException
  {
    Cursor<EntryID, Long> cursor = id2childrenCount.openCursor(txn);
    if  (!cursor.next()) {
      return;
    }

    EntryID currentEntryID = new EntryID(-1);
    while(cursor.next()) {
      if (cursor.getKey().equals(currentEntryID)) {
        /** Sharded cursor may return the same EntryID multiple times */
        continue;
      }
      currentEntryID = cursor.getKey();
      if (!id2entry.containsEntryID(txn, currentEntryID)) {
        logger.trace("File id2ChildrenCount reference non-existing EntryID <%d>%n", currentEntryID);
        errorCount++;
      }
    }
  }

  /**
   * Increment the counter for a key that has exceeded the
   * entry limit. The counter gives the number of entries that have
   * referenced the key.
   *
   * @param index The index containing the key.
   * @param key A key that has exceeded the entry limit.
   */
  private void incrEntryLimitStats(Index index, ByteString key)
  {
    HashMap<ByteString,Long> hashMap = entryLimitMap.get(index);
    if (hashMap == null)
    {
      hashMap = new HashMap<ByteString, Long>();
      entryLimitMap.put(index, hashMap);
    }
    Long counter = hashMap.get(key);
    if (counter != null)
    {
      counter++;
    }
    else
    {
      counter = 1L;
    }
    hashMap.put(key, counter);
  }

  /**
   * Update the statistical information for an index record.
   *
   * @param entryIDSet The set of entry IDs for the index record.
   */
  private void updateIndexStats(EntryIDSet entryIDSet)
  {
    if (!entryIDSet.isDefined())
    {
      entryLimitExceededCount++;
      multiReferenceCount++;
    }
    else
    {
      if (entryIDSet.size() > 1)
      {
        multiReferenceCount++;
      }
      entryReferencesCount += entryIDSet.size();
      maxEntryPerValue = Math.max(maxEntryPerValue, entryIDSet.size());
    }
  }

  /**
   * Iterate through the entries in a VLV index to perform a check for index
   * cleanliness.
   *
   * @param vlvIndex The VLV index to perform the check against.
   * @param verifyID True to verify the IDs against id2entry.
   * @throws StorageRuntimeException If an error occurs in the storage.
   * @throws DirectoryException If an error occurs reading values in the index.
   */
  private void iterateVLVIndex(ReadableTransaction txn, VLVIndex vlvIndex, boolean verifyID)
      throws StorageRuntimeException, DirectoryException
  {
    if(vlvIndex == null || !verifyID)
    {
      return;
    }

    try(final Cursor<ByteString, ByteString> cursor = txn.openCursor(vlvIndex.getName()))
    {
      while (cursor.next())
      {
        ByteString key = cursor.getKey();
        EntryID id = new EntryID(decodeEntryIDFromVLVKey(key));
        Entry entry;
        try
        {
          entry = id2entry.get(txn, id);
        }
        catch (Exception e)
        {
          logger.traceException(e);
          errorCount++;
          continue;
        }

        if (entry == null)
        {
          errorCount++;
          if (logger.isTraceEnabled())
          {
            logger.trace("Reference to unknown entry ID %s%n%s", id, keyDump(vlvIndex.toString(), key));
          }
          continue;
        }

        ByteString expectedKey = vlvIndex.encodeVLVKey(entry, id.longValue());
        if (expectedKey.compareTo(key) != 0)
        {
          errorCount++;
          if (logger.isTraceEnabled())
          {
            logger.trace("Reference to entry ID %s has a key which does not match the expected key%n%s",
                id, keyDump(vlvIndex.toString(), expectedKey));
          }
        }

      }
    }
  }

  /**
   * Iterate through the entries in an attribute index to perform a check for
   * index cleanliness.
   * @param index The index tree to be checked.
   * @throws StorageRuntimeException If an error occurs in the storage.
   */
  private void iterateAttrIndex(ReadableTransaction txn, MatchingRuleIndex index) throws StorageRuntimeException
  {
    if (index == null)
    {
      return;
    }

    try(final Cursor<ByteString,EntryIDSet> cursor = index.openCursor(txn))
    {
      while (cursor.next())
      {
        keyCount++;

        final ByteString key = cursor.getKey();

        EntryIDSet entryIDSet;
        try
        {
          entryIDSet = cursor.getValue();
        }
        catch (Exception e)
        {
          errorCount++;
          logger.traceException(e);
          logger.trace("Malformed ID list: %n%s", keyDump(index.toString(), key));
          continue;
        }

        updateIndexStats(entryIDSet);

        if (entryIDSet.isDefined())
        {
          EntryID prevID = null;

          for (EntryID id : entryIDSet)
          {
            if (prevID != null && id.equals(prevID) && logger.isTraceEnabled())
            {
              if (logger.isTraceEnabled())
              {
                logger.trace("Duplicate reference to ID %d%n%s", id, keyDump(index.toString(), key));
              }
            }
            prevID = id;

            Entry entry;
            try
            {
              entry = id2entry.get(txn, id);
            }
            catch (Exception e)
            {
              logger.traceException(e);
              errorCount++;
              continue;
            }

            if (entry == null)
            {
              errorCount++;
              if (logger.isTraceEnabled())
              {
                logger.trace("Reference to unknown ID %d%n%s", id, keyDump(index.toString(), key));
              }
              continue;
            }

            // As an optimization avoid passing in a real set and wasting time
            // hashing and comparing a potentially large set of values, as well
            // as using up memory. Instead just intercept the add() method and
            // detect when an equivalent value has been added.

            // We need to use an AtomicBoolean here since anonymous classes
            // require referenced external variables to be final.
            final AtomicBoolean foundMatchingKey = new AtomicBoolean(false);

            Set<ByteString> dummySet = new AbstractSet<ByteString>()
            {
              @Override
              public Iterator<ByteString> iterator()
              {
                // The set is always empty.
                return Collections.<ByteString> emptySet().iterator();
              }

              @Override
              public int size()
              {
                // The set is always empty.
                return 0;
              }

              @Override
              public boolean add(ByteString e)
              {
                if (key.equals(e))
                {
                  // We could terminate processing at this point by throwing an
                  // UnsupportedOperationException, but this optimization is
                  // already ugly enough.
                  foundMatchingKey.set(true);
                }
                return true;
              }

            };

            index.indexEntry(entry, dummySet);

            if (!foundMatchingKey.get())
            {
              errorCount++;
              if (logger.isTraceEnabled())
              {
                logger.trace("Reference to entry <%s> which does not match the value%n%s",
                    entry.getName(), keyDump(index.toString(), key));
              }
            }
          }
        }
      }
    }
  }

  /**
   * Check that an index is complete for a given entry.
   *
   * @param entryID The entry ID.
   * @param entry The entry to be checked.
   */
  private void verifyEntry(ReadableTransaction txn, EntryID entryID, Entry entry)
  {
    if (verifyDN2ID)
    {
      verifyDN2ID(txn, entryID, entry);
    }
    verifyIndex(txn, entryID, entry);
  }

  /**
   * Check that the DN2ID index is complete for a given entry.
   *
   * @param entryID The entry ID.
   * @param entry The entry to be checked.
   */
  private void verifyDN2ID(ReadableTransaction txn, EntryID entryID, Entry entry)
  {
    DN dn = entry.getName();

    // Check the ID is in dn2id with the correct DN.
    try
    {
      EntryID id = dn2id.get(txn, dn);
      if (id == null)
      {
        if (logger.isTraceEnabled())
        {
          logger.trace("File dn2id is missing key %s.%n", dn);
        }
        errorCount++;
      }
      else if (!id.equals(entryID))
      {
        if (logger.isTraceEnabled())
        {
          logger.trace("File dn2id has ID %d instead of %d for key %s.%n", id, entryID, dn);
        }
        errorCount++;
      }
    }
    catch (Exception e)
    {
      if (logger.isTraceEnabled())
      {
        logger.traceException(e);
        logger.trace("File dn2id has error reading key %s: %s.%n", dn, e.getMessage());
      }
      errorCount++;
    }

    // Check the parent DN is in dn2id.
    DN parentDN = getParent(dn);
    if (parentDN != null)
    {
      try
      {
        EntryID id = dn2id.get(txn, parentDN);
        if (id == null)
        {
          if (logger.isTraceEnabled())
          {
            logger.trace("File dn2id is missing key %s.%n", parentDN);
          }
          errorCount++;
        }
      }
      catch (Exception e)
      {
        if (logger.isTraceEnabled())
        {
          logger.traceException(e);
          logger.trace("File dn2id has error reading key %s: %s.%n", parentDN, e.getMessage());
        }
        errorCount++;
      }
    }
  }

  /**
   * Construct a printable string from a raw key value.
   *
   * @param indexName
   *          The name of the index tree containing the key value.
   * @param key
   *          The bytes of the key.
   * @return A string that may be logged or printed.
   */
  private static String keyDump(String indexName, ByteSequence key)
  {
    StringBuilder buffer = new StringBuilder(128);
    buffer.append("Index: ");
    buffer.append(indexName);
    buffer.append(ServerConstants.EOL);
    buffer.append("Key:");
    buffer.append(ServerConstants.EOL);
    StaticUtils.byteArrayToHexPlusAscii(buffer, key.toByteArray(), 6);
    return buffer.toString();
  }

  /**
   * Check that an attribute index is complete for a given entry.
   *
   * @param entryID
   *          The entry ID.
   * @param entry
   *          The entry to be checked.
   */
  private void verifyIndex(ReadableTransaction txn, EntryID entryID, Entry entry)
  {
    for (AttributeIndex attrIndex : attrIndexList)
    {
      verifyAttribute(txn, entryID, entry, attrIndex);
    }

    for (VLVIndex vlvIndex : vlvIndexList)
    {
      try
      {
        if (vlvIndex.verifyEntry(txn, entryID, entry))
        {
          if(logger.isTraceEnabled())
          {
            logger.trace("Missing entry %s in VLV index %s", entry.getName(), vlvIndex.getName());
          }
          errorCount++;
        }
      }
      catch (DirectoryException e)
      {
        if (logger.isTraceEnabled())
        {
          logger.traceException(e);
          logger.trace("Error checking entry %s against filter or base DN for VLV index %s: %s",
                     entry.getName(), vlvIndex.getName(), e.getMessageObject());
        }
        errorCount++;
      }
      catch (StorageRuntimeException e)
      {
        if (logger.isTraceEnabled())
        {
          logger.traceException(e);
          logger.trace("Error reading VLV index %s for entry %s: %s",
              vlvIndex.getName(), entry.getName(), StaticUtils.getBacktrace(e));
        }
        errorCount++;
      }
    }
  }

  /**
   * Check that an attribute index is complete for a given attribute.
   */
  private void verifyAttribute(ReadableTransaction txn, EntryID entryID, Entry entry, AttributeIndex attrIndex)
  {
    for (MatchingRuleIndex index : attrIndex.getNameToIndexes().values())
    {
      Set<ByteString> keys = new HashSet<ByteString>();
      index.indexEntry(entry, keys);
      for (ByteString key : keys)
      {
        verifyAttributeInIndex(index, txn, key, entryID);
      }
    }
  }

  private void verifyAttributeInIndex(Index index, ReadableTransaction txn,
      ByteString key, EntryID entryID)
  {
    try
    {
      ConditionResult cr = indexContainsID(index, txn, key, entryID);
      if (cr == ConditionResult.FALSE)
      {
        if (logger.isTraceEnabled())
        {
          logger.trace("Missing ID %d%n%s", entryID, keyDump(index.toString(), key));
        }
        errorCount++;
      }
      else if (cr == ConditionResult.UNDEFINED)
      {
        incrEntryLimitStats(index, key);
      }
    }
    catch (StorageRuntimeException e)
    {
      if (logger.isTraceEnabled())
      {
        logger.traceException(e);

        logger.trace("Error reading tree: %s%n%s", e.getMessage(), keyDump(index.toString(), key));
      }
      errorCount++;
    }
  }

  private static ConditionResult indexContainsID(Index index, ReadableTransaction txn, ByteString key, EntryID entryID)
  {
    EntryIDSet entryIDSet = index.get(txn, key);
    if (entryIDSet.isDefined())
    {
      return ConditionResult.valueOf(entryIDSet.contains(entryID));
    }
    return ConditionResult.UNDEFINED;
  }

  /**
   * Get the parent DN of a given DN.
   *
   * @param dn The DN.
   * @return The parent DN or null if the given DN is a base DN.
   */
  private DN getParent(DN dn)
  {
    if (dn.equals(verifyConfig.getBaseDN()))
    {
      return null;
    }
    return dn.getParentDNInSuffix();
  }

  /**
   * This class maintain the number of children for a given dn
   */
  private static final class ChildrenCount {
    private final ByteString baseDN;
    private final EntryID entryID;
    private long numberOfChildren;

    private ChildrenCount(ByteString dn, EntryID id) {
      this.baseDN = dn;
      this.entryID = id;
    }
  }

  /** This class reports progress of the verify job at fixed intervals. */
  private final class ProgressTask extends TimerTask
  {
    /** The total number of records to process. */
    private long totalCount;

    /**
     * The number of records that had been processed at the time of the
     * previous progress report.
     */
    private long previousCount;

    /** The time in milliseconds of the previous progress report. */
    private long previousTime;

    /**
     * The number of bytes in a megabyte.
     * Note that 1024*1024 bytes may eventually become known as a mebibyte(MiB).
     */
    private static final int bytesPerMegabyte = 1024*1024;

    /**
     * Create a new verify progress task.
     * @param indexIterator boolean, indicates if the task is iterating
     * through indexes or the entries.
     * @throws StorageRuntimeException An error occurred while accessing the storage.
     */
    private ProgressTask(boolean indexIterator, ReadableTransaction txn) throws StorageRuntimeException
    {
      previousTime = System.currentTimeMillis();

      if (indexIterator)
      {
        if (verifyDN2ID)
        {
          totalCount = dn2id.getRecordCount(txn);
        }
        else if (verifyID2ChildrenCount)
        {
          totalCount = id2childrenCount.getRecordCount(txn);
        }
        else if (!attrIndexList.isEmpty())
        {
          AttributeIndex attrIndex = attrIndexList.get(0);
          totalCount = 0;
          for (MatchingRuleIndex index : attrIndex.getNameToIndexes().values())
          {
            totalCount += getRecordCount(txn, index);
          }
        }
        else if (!vlvIndexList.isEmpty())
        {
          totalCount = vlvIndexList.get(0).getRecordCount(txn);
        }
      }
      else
      {
        totalCount = rootContainer.getEntryContainer(verifyConfig.getBaseDN()).getNumberOfEntriesInBaseDN();
      }
    }

    private long getRecordCount(ReadableTransaction txn, Index index)
    {
      if (index != null)
      {
        return index.getRecordCount(txn);
      }
      return 0;
    }

    /** The action to be performed by this timer task. */
    @Override
    public void run()
    {
      long latestCount = keyCount;
      long deltaCount = latestCount - previousCount;
      long latestTime = System.currentTimeMillis();
      long deltaTime = latestTime - previousTime;

      if (deltaTime == 0)
      {
        return;
      }

      float rate = 1000f*deltaCount / deltaTime;

      logger.info(NOTE_VERIFY_PROGRESS_REPORT, latestCount, totalCount, errorCount, rate);

      try
      {
        Runtime runtime = Runtime.getRuntime();
        long freeMemory = runtime.freeMemory() / bytesPerMegabyte;

        // FIXME JNR compute the cache miss rate
        float cacheMissRate = 0;

        logger.debug(INFO_CACHE_AND_MEMORY_REPORT, freeMemory, cacheMissRate);
      }
      catch (StorageRuntimeException e)
      {
        logger.traceException(e);
      }


      previousCount = latestCount;
      previousTime = latestTime;
    }
  }
}