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A fork of the Apache Cassandra Project ready to embed Elasticsearch.
/*
* 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.cassandra.db.compaction;
import java.nio.ByteBuffer;
import java.io.*;
import java.util.*;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Throwables;
import org.apache.cassandra.config.CFMetaData;
import org.apache.cassandra.db.*;
import org.apache.cassandra.db.lifecycle.LifecycleTransaction;
import org.apache.cassandra.db.rows.*;
import org.apache.cassandra.db.partitions.*;
import org.apache.cassandra.io.sstable.*;
import org.apache.cassandra.io.sstable.format.SSTableReader;
import org.apache.cassandra.io.sstable.format.SSTableWriter;
import org.apache.cassandra.io.util.FileUtils;
import org.apache.cassandra.io.util.RandomAccessReader;
import org.apache.cassandra.service.ActiveRepairService;
import org.apache.cassandra.utils.*;
public class Scrubber implements Closeable
{
private final ColumnFamilyStore cfs;
private final SSTableReader sstable;
private final LifecycleTransaction transaction;
private final File destination;
private final boolean skipCorrupted;
private final boolean isCommutative;
private final boolean isIndex;
private final boolean checkData;
private final long expectedBloomFilterSize;
private final RandomAccessReader dataFile;
private final RandomAccessReader indexFile;
private final ScrubInfo scrubInfo;
private final RowIndexEntry.IndexSerializer rowIndexEntrySerializer;
private int goodRows;
private int badRows;
private int emptyRows;
private ByteBuffer currentIndexKey;
private ByteBuffer nextIndexKey;
long currentRowPositionFromIndex;
long nextRowPositionFromIndex;
private final OutputHandler outputHandler;
private static final Comparator partitionComparator = new Comparator()
{
public int compare(Partition r1, Partition r2)
{
return r1.partitionKey().compareTo(r2.partitionKey());
}
};
private final SortedSet outOfOrder = new TreeSet<>(partitionComparator);
public Scrubber(ColumnFamilyStore cfs, LifecycleTransaction transaction, boolean skipCorrupted, boolean checkData)
{
this(cfs, transaction, skipCorrupted, new OutputHandler.LogOutput(), checkData);
}
@SuppressWarnings("resource")
public Scrubber(ColumnFamilyStore cfs,
LifecycleTransaction transaction,
boolean skipCorrupted,
OutputHandler outputHandler,
boolean checkData)
{
this.cfs = cfs;
this.transaction = transaction;
this.sstable = transaction.onlyOne();
this.outputHandler = outputHandler;
this.skipCorrupted = skipCorrupted;
this.rowIndexEntrySerializer = sstable.descriptor.version.getSSTableFormat().getIndexSerializer(sstable.metadata,
sstable.descriptor.version,
sstable.header);
List toScrub = Collections.singletonList(sstable);
int locIndex = CompactionStrategyManager.getCompactionStrategyIndex(cfs, cfs.getDirectories(), sstable);
this.destination = cfs.getDirectories().getLocationForDisk(cfs.getDirectories().getWriteableLocations()[locIndex]);
this.isCommutative = cfs.metadata.isCounter();
boolean hasIndexFile = (new File(sstable.descriptor.filenameFor(Component.PRIMARY_INDEX))).exists();
this.isIndex = cfs.isIndex();
if (!hasIndexFile)
{
// if there's any corruption in the -Data.db then rows can't be skipped over. but it's worth a shot.
outputHandler.warn("Missing component: " + sstable.descriptor.filenameFor(Component.PRIMARY_INDEX));
}
this.checkData = checkData && !this.isIndex; //LocalByPartitionerType does not support validation
this.expectedBloomFilterSize = Math.max(
cfs.metadata.params.minIndexInterval,
hasIndexFile ? SSTableReader.getApproximateKeyCount(toScrub) : 0);
// loop through each row, deserializing to check for damage.
// we'll also loop through the index at the same time, using the position from the index to recover if the
// row header (key or data size) is corrupt. (This means our position in the index file will be one row
// "ahead" of the data file.)
this.dataFile = transaction.isOffline()
? sstable.openDataReader()
: sstable.openDataReader(CompactionManager.instance.getRateLimiter());
this.indexFile = hasIndexFile
? RandomAccessReader.open(new File(sstable.descriptor.filenameFor(Component.PRIMARY_INDEX)))
: null;
this.scrubInfo = new ScrubInfo(dataFile, sstable);
this.currentRowPositionFromIndex = 0;
this.nextRowPositionFromIndex = 0;
}
private UnfilteredRowIterator withValidation(UnfilteredRowIterator iter, String filename)
{
return checkData ? UnfilteredRowIterators.withValidation(iter, filename) : iter;
}
public void scrub()
{
List finished = new ArrayList<>();
boolean completed = false;
outputHandler.output(String.format("Scrubbing %s (%s)", sstable, FBUtilities.prettyPrintMemory(dataFile.length())));
try (SSTableRewriter writer = SSTableRewriter.construct(cfs, transaction, false, sstable.maxDataAge))
{
nextIndexKey = indexAvailable() ? ByteBufferUtil.readWithShortLength(indexFile) : null;
if (indexAvailable())
{
// throw away variable so we don't have a side effect in the assert
long firstRowPositionFromIndex = rowIndexEntrySerializer.deserializePositionAndSkip(indexFile);
assert firstRowPositionFromIndex == 0 : firstRowPositionFromIndex;
}
writer.switchWriter(CompactionManager.createWriter(cfs, destination, expectedBloomFilterSize, sstable.getSSTableMetadata().repairedAt, sstable, transaction));
DecoratedKey prevKey = null;
while (!dataFile.isEOF())
{
if (scrubInfo.isStopRequested())
throw new CompactionInterruptedException(scrubInfo.getCompactionInfo());
long rowStart = dataFile.getFilePointer();
outputHandler.debug("Reading row at " + rowStart);
DecoratedKey key = null;
try
{
key = sstable.decorateKey(ByteBufferUtil.readWithShortLength(dataFile));
}
catch (Throwable th)
{
throwIfFatal(th);
// check for null key below
}
updateIndexKey();
long dataStart = dataFile.getFilePointer();
long dataStartFromIndex = -1;
long dataSizeFromIndex = -1;
if (currentIndexKey != null)
{
dataStartFromIndex = currentRowPositionFromIndex + 2 + currentIndexKey.remaining();
dataSizeFromIndex = nextRowPositionFromIndex - dataStartFromIndex;
}
// avoid an NPE if key is null
String keyName = key == null ? "(unreadable key)" : ByteBufferUtil.bytesToHex(key.getKey());
outputHandler.debug(String.format("row %s is %s", keyName, FBUtilities.prettyPrintMemory(dataSizeFromIndex)));
assert currentIndexKey != null || !indexAvailable();
try
{
if (key == null)
throw new IOError(new IOException("Unable to read row key from data file"));
if (currentIndexKey != null && !key.getKey().equals(currentIndexKey))
{
throw new IOError(new IOException(String.format("Key from data file (%s) does not match key from index file (%s)",
//ByteBufferUtil.bytesToHex(key.getKey()), ByteBufferUtil.bytesToHex(currentIndexKey))));
"_too big_", ByteBufferUtil.bytesToHex(currentIndexKey))));
}
if (indexFile != null && dataSizeFromIndex > dataFile.length())
throw new IOError(new IOException("Impossible row size (greater than file length): " + dataSizeFromIndex));
if (indexFile != null && dataStart != dataStartFromIndex)
outputHandler.warn(String.format("Data file row position %d differs from index file row position %d", dataStart, dataStartFromIndex));
if (tryAppend(prevKey, key, writer))
prevKey = key;
}
catch (Throwable th)
{
throwIfFatal(th);
outputHandler.warn("Error reading row (stacktrace follows):", th);
if (currentIndexKey != null
&& (key == null || !key.getKey().equals(currentIndexKey) || dataStart != dataStartFromIndex))
{
outputHandler.output(String.format("Retrying from row index; data is %s bytes starting at %s",
dataSizeFromIndex, dataStartFromIndex));
key = sstable.decorateKey(currentIndexKey);
try
{
dataFile.seek(dataStartFromIndex);
if (tryAppend(prevKey, key, writer))
prevKey = key;
}
catch (Throwable th2)
{
throwIfFatal(th2);
throwIfCannotContinue(key, th2);
outputHandler.warn("Retry failed too. Skipping to next row (retry's stacktrace follows)", th2);
badRows++;
seekToNextRow();
}
}
else
{
throwIfCannotContinue(key, th);
outputHandler.warn("Row starting at position " + dataStart + " is unreadable; skipping to next");
badRows++;
if (currentIndexKey != null)
seekToNextRow();
}
}
}
if (!outOfOrder.isEmpty())
{
// out of order rows, but no bad rows found - we can keep our repairedAt time
long repairedAt = badRows > 0 ? ActiveRepairService.UNREPAIRED_SSTABLE : sstable.getSSTableMetadata().repairedAt;
SSTableReader newInOrderSstable;
try (SSTableWriter inOrderWriter = CompactionManager.createWriter(cfs, destination, expectedBloomFilterSize, repairedAt, sstable, transaction))
{
for (Partition partition : outOfOrder)
inOrderWriter.append(partition.unfilteredIterator());
newInOrderSstable = inOrderWriter.finish(-1, sstable.maxDataAge, true);
}
transaction.update(newInOrderSstable, false);
finished.add(newInOrderSstable);
outputHandler.warn(String.format("%d out of order rows found while scrubbing %s; Those have been written (in order) to a new sstable (%s)", outOfOrder.size(), sstable, newInOrderSstable));
}
// finish obsoletes the old sstable
finished.addAll(writer.setRepairedAt(badRows > 0 ? ActiveRepairService.UNREPAIRED_SSTABLE : sstable.getSSTableMetadata().repairedAt).finish());
completed = true;
}
catch (IOException e)
{
throw Throwables.propagate(e);
}
finally
{
if (transaction.isOffline())
finished.forEach(sstable -> sstable.selfRef().release());
}
if (completed)
{
if (badRows > 0)
outputHandler.warn("No valid rows found while scrubbing " + sstable + "; it is marked for deletion now. If you want to attempt manual recovery, you can find a copy in the pre-scrub snapshot");
else
outputHandler.output("Scrub of " + sstable + " complete; looks like all " + emptyRows + " rows were tombstoned");
}
else
{
outputHandler.output("Scrub of " + sstable + " complete: " + goodRows + " rows in new sstable and " + emptyRows + " empty (tombstoned) rows dropped");
if (badRows > 0)
outputHandler.warn("Unable to recover " + badRows + " rows that were skipped. You can attempt manual recovery from the pre-scrub snapshot. You can also run nodetool repair to transfer the data from a healthy replica, if any");
}
}
@SuppressWarnings("resource")
private boolean tryAppend(DecoratedKey prevKey, DecoratedKey key, SSTableRewriter writer)
{
// OrderCheckerIterator will check, at iteration time, that the rows are in the proper order. If it detects
// that one row is out of order, it will stop returning them. The remaining rows will be sorted and added
// to the outOfOrder set that will be later written to a new SSTable.
OrderCheckerIterator sstableIterator = new OrderCheckerIterator(new RowMergingSSTableIterator(SSTableIdentityIterator.create(sstable, dataFile, key)),
cfs.metadata.comparator);
try (UnfilteredRowIterator iterator = withValidation(sstableIterator, dataFile.getPath()))
{
if (prevKey != null && prevKey.compareTo(key) > 0)
{
saveOutOfOrderRow(prevKey, key, iterator);
return false;
}
if (writer.tryAppend(iterator) == null)
emptyRows++;
else
goodRows++;
}
if (sstableIterator.hasRowsOutOfOrder())
{
outputHandler.warn(String.format("Out of order rows found in partition: %s", key));
outOfOrder.add(sstableIterator.getRowsOutOfOrder());
}
return true;
}
private void updateIndexKey()
{
currentIndexKey = nextIndexKey;
currentRowPositionFromIndex = nextRowPositionFromIndex;
try
{
nextIndexKey = !indexAvailable() ? null : ByteBufferUtil.readWithShortLength(indexFile);
nextRowPositionFromIndex = !indexAvailable()
? dataFile.length()
: rowIndexEntrySerializer.deserializePositionAndSkip(indexFile);
}
catch (Throwable th)
{
JVMStabilityInspector.inspectThrowable(th);
outputHandler.warn("Error reading index file", th);
nextIndexKey = null;
nextRowPositionFromIndex = dataFile.length();
}
}
private boolean indexAvailable()
{
return indexFile != null && !indexFile.isEOF();
}
private void seekToNextRow()
{
while(nextRowPositionFromIndex < dataFile.length())
{
try
{
dataFile.seek(nextRowPositionFromIndex);
return;
}
catch (Throwable th)
{
throwIfFatal(th);
outputHandler.warn(String.format("Failed to seek to next row position %d", nextRowPositionFromIndex), th);
badRows++;
}
updateIndexKey();
}
}
private void saveOutOfOrderRow(DecoratedKey prevKey, DecoratedKey key, UnfilteredRowIterator iterator)
{
// TODO bitch if the row is too large? if it is there's not much we can do ...
outputHandler.warn(String.format("Out of order row detected (%s found after %s)", key, prevKey));
outOfOrder.add(ImmutableBTreePartition.create(iterator));
}
private void throwIfFatal(Throwable th)
{
if (th instanceof Error && !(th instanceof AssertionError || th instanceof IOError))
throw (Error) th;
}
private void throwIfCannotContinue(DecoratedKey key, Throwable th)
{
if (isIndex)
{
outputHandler.warn(String.format("An error occurred while scrubbing the row with key '%s' for an index table. " +
"Scrubbing will abort for this table and the index will be rebuilt.", key));
throw new IOError(th);
}
if (isCommutative && !skipCorrupted)
{
outputHandler.warn(String.format("An error occurred while scrubbing the row with key '%s'. Skipping corrupt " +
"rows in counter tables will result in undercounts for the affected " +
"counters (see CASSANDRA-2759 for more details), so by default the scrub will " +
"stop at this point. If you would like to skip the row anyway and continue " +
"scrubbing, re-run the scrub with the --skip-corrupted option.", key));
throw new IOError(th);
}
}
public void close()
{
FileUtils.closeQuietly(dataFile);
FileUtils.closeQuietly(indexFile);
}
public CompactionInfo.Holder getScrubInfo()
{
return scrubInfo;
}
private static class ScrubInfo extends CompactionInfo.Holder
{
private final RandomAccessReader dataFile;
private final SSTableReader sstable;
private final UUID scrubCompactionId;
public ScrubInfo(RandomAccessReader dataFile, SSTableReader sstable)
{
this.dataFile = dataFile;
this.sstable = sstable;
scrubCompactionId = UUIDGen.getTimeUUID();
}
public CompactionInfo getCompactionInfo()
{
try
{
return new CompactionInfo(sstable.metadata,
OperationType.SCRUB,
dataFile.getFilePointer(),
dataFile.length(),
scrubCompactionId);
}
catch (Exception e)
{
throw new RuntimeException(e);
}
}
}
@VisibleForTesting
public ScrubResult scrubWithResult()
{
scrub();
return new ScrubResult(this);
}
public static final class ScrubResult
{
public final int goodRows;
public final int badRows;
public final int emptyRows;
public ScrubResult(Scrubber scrubber)
{
this.goodRows = scrubber.goodRows;
this.badRows = scrubber.badRows;
this.emptyRows = scrubber.emptyRows;
}
}
/**
* During 2.x migration, under some circumstances rows might have gotten duplicated.
* Merging iterator merges rows with same clustering.
*
* For more details, refer to CASSANDRA-12144.
*/
private static class RowMergingSSTableIterator extends WrappingUnfilteredRowIterator
{
Unfiltered nextToOffer = null;
RowMergingSSTableIterator(UnfilteredRowIterator source)
{
super(source);
}
@Override
public boolean hasNext()
{
return nextToOffer != null || wrapped.hasNext();
}
@Override
public Unfiltered next()
{
Unfiltered next = nextToOffer != null ? nextToOffer : wrapped.next();
if (next.isRow())
{
while (wrapped.hasNext())
{
Unfiltered peek = wrapped.next();
if (!peek.isRow() || !next.clustering().equals(peek.clustering()))
{
nextToOffer = peek; // Offer peek in next call
return next;
}
// Duplicate row, merge it.
next = Rows.merge((Row) next, (Row) peek, FBUtilities.nowInSeconds());
}
}
nextToOffer = null;
return next;
}
}
/**
* In some case like CASSANDRA-12127 the cells might have been stored in the wrong order. This decorator check the
* cells order and collect the out of order cells to correct the problem.
*/
private static final class OrderCheckerIterator extends AbstractIterator implements UnfilteredRowIterator
{
/**
* The decorated iterator.
*/
private final UnfilteredRowIterator iterator;
private final ClusteringComparator comparator;
private Unfiltered previous;
/**
* The partition containing the rows which are out of order.
*/
private Partition rowsOutOfOrder;
public OrderCheckerIterator(UnfilteredRowIterator iterator, ClusteringComparator comparator)
{
this.iterator = iterator;
this.comparator = comparator;
}
public CFMetaData metadata()
{
return iterator.metadata();
}
public boolean isReverseOrder()
{
return iterator.isReverseOrder();
}
public PartitionColumns columns()
{
return iterator.columns();
}
public DecoratedKey partitionKey()
{
return iterator.partitionKey();
}
public Row staticRow()
{
return iterator.staticRow();
}
@Override
public boolean isEmpty()
{
return iterator.isEmpty();
}
public void close()
{
iterator.close();
}
public DeletionTime partitionLevelDeletion()
{
return iterator.partitionLevelDeletion();
}
public EncodingStats stats()
{
return iterator.stats();
}
public boolean hasRowsOutOfOrder()
{
return rowsOutOfOrder != null;
}
public Partition getRowsOutOfOrder()
{
return rowsOutOfOrder;
}
protected Unfiltered computeNext()
{
if (!iterator.hasNext())
return endOfData();
Unfiltered next = iterator.next();
// If we detect that some rows are out of order we will store and sort the remaining ones to insert them
// in a separate SSTable.
if (previous != null && comparator.compare(next, previous) < 0)
{
rowsOutOfOrder = ImmutableBTreePartition.create(UnfilteredRowIterators.concat(next, iterator), false);
return endOfData();
}
previous = next;
return next;
}
}
}
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