Package org.apache.cassandra.io.util

Examples of org.apache.cassandra.io.util.RandomAccessReader


        // 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.)
        final RandomAccessReader dataFile = sstable.openDataReader(true);
        RandomAccessReader indexFile = RandomAccessReader.open(new File(sstable.descriptor.filenameFor(Component.PRIMARY_INDEX)), true);
        ScrubInfo scrubInfo = new ScrubInfo(dataFile, sstable);
        executor.beginCompaction(scrubInfo);

        SSTableWriter writer = null;
        SSTableReader newSstable = null;
        int goodRows = 0, badRows = 0, emptyRows = 0;

        try
        {
            ByteBuffer nextIndexKey = ByteBufferUtil.readWithShortLength(indexFile);
            {
                // throw away variable so we don't have a side effect in the assert
                long firstRowPositionFromIndex = indexFile.readLong();
                assert firstRowPositionFromIndex == 0 : firstRowPositionFromIndex;
            }

            // TODO errors when creating the writer may leave empty temp files.
            writer = maybeCreateWriter(cfs, compactionFileLocation, expectedBloomFilterSize, null, Collections.singletonList(sstable));

            while (!dataFile.isEOF())
            {
                if (scrubInfo.isStopped())
                    throw new CompactionInterruptedException(scrubInfo.getCompactionInfo());
                long rowStart = dataFile.getFilePointer();
                if (logger.isDebugEnabled())
                    logger.debug("Reading row at " + rowStart);

                DecoratedKey key = null;
                long dataSize = -1;
                try
                {
                    key = SSTableReader.decodeKey(sstable.partitioner, sstable.descriptor, ByteBufferUtil.readWithShortLength(dataFile));
                    dataSize = sstable.descriptor.hasIntRowSize ? dataFile.readInt() : dataFile.readLong();
                    if (logger.isDebugEnabled())
                        logger.debug(String.format("row %s is %s bytes", ByteBufferUtil.bytesToHex(key.key), dataSize));
                }
                catch (Throwable th)
                {
                    throwIfFatal(th);
                    // check for null key below
                }

                ByteBuffer currentIndexKey = nextIndexKey;
                long nextRowPositionFromIndex;
                try
                {
                    nextIndexKey = indexFile.isEOF() ? null : ByteBufferUtil.readWithShortLength(indexFile);
                    nextRowPositionFromIndex = indexFile.isEOF() ? dataFile.length() : indexFile.readLong();
                }
                catch (Throwable th)
                {
                    logger.warn("Error reading index file", th);
                    nextIndexKey = null;
                    nextRowPositionFromIndex = dataFile.length();
                }

                long dataStart = dataFile.getFilePointer();
                long dataStartFromIndex = currentIndexKey == null
                                        ? -1
                                        : rowStart + 2 + currentIndexKey.remaining() + (sstable.descriptor.hasIntRowSize ? 4 : 8);
                long dataSizeFromIndex = nextRowPositionFromIndex - dataStartFromIndex;
                assert currentIndexKey != null || indexFile.isEOF();
                if (logger.isDebugEnabled() && currentIndexKey != null)
                    logger.debug(String.format("Index doublecheck: row %s is %s bytes", ByteBufferUtil.bytesToHex(currentIndexKey),  dataSizeFromIndex));

                writer.mark();
                try
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        if (header.file == null)
            return;

        // TODO just use a raw RandomAccessFile since we're managing our own buffer here
        RandomAccessReader file = (header.file.sstable.compression) // try to skip kernel page cache if possible
                                ? CompressedRandomAccessReader.open(header.file.getFilename(), header.file.sstable.getCompressionMetadata(), true)
                                : RandomAccessReader.open(new File(header.file.getFilename()), true);

        // setting up data compression stream
        compressedoutput = new LZFOutputStream(output);

        MessagingService.instance().incrementActiveStreamsOutbound();
        try
        {
            // stream each of the required sections of the file
            for (Pair<Long, Long> section : header.file.sections)
            {
                // seek to the beginning of the section
                file.seek(section.left);

                // length of the section to stream
                long length = section.right - section.left;
                // tracks write progress
                long bytesTransferred = 0;
View Full Code Here

    {
        logger.info("Replaying " + file.getPath());
        CommitLogDescriptor desc = CommitLogDescriptor.fromFileName(file.getName());
        final long segment = desc.id;
        int version = desc.getMessagingVersion();
        RandomAccessReader reader = RandomAccessReader.open(new File(file.getAbsolutePath()), true);
        try
        {
            assert reader.length() <= Integer.MAX_VALUE;
            int replayPosition;
            if (globalPosition.segment < segment)
                replayPosition = 0;
            else if (globalPosition.segment == segment)
                replayPosition = globalPosition.position;
            else
                replayPosition = (int) reader.length();

            if (replayPosition < 0 || replayPosition >= reader.length())
            {
                // replayPosition > reader.length() can happen if some data gets flushed before it is written to the commitlog
                // (see https://issues.apache.org/jira/browse/CASSANDRA-2285)
                logger.debug("skipping replay of fully-flushed {}", file);
                return;
            }

            reader.seek(replayPosition);

            if (logger.isDebugEnabled())
                logger.debug("Replaying " + file + " starting at " + reader.getFilePointer());

            /* read the logs populate RowMutation and apply */
            while (!reader.isEOF())
            {
                if (logger.isDebugEnabled())
                    logger.debug("Reading mutation at " + reader.getFilePointer());

                long claimedCRC32;
                int serializedSize;
                try
                {
                    // any of the reads may hit EOF
                    serializedSize = reader.readInt();
                    if (serializedSize == CommitLog.END_OF_SEGMENT_MARKER)
                    {
                        logger.debug("Encountered end of segment marker at " + reader.getFilePointer());
                        break;
                    }

                    // RowMutation must be at LEAST 10 bytes:
                    // 3 each for a non-empty Table and Key (including the
                    // 2-byte length from writeUTF/writeWithShortLength) and 4 bytes for column count.
                    // This prevents CRC by being fooled by special-case garbage in the file; see CASSANDRA-2128
                    if (serializedSize < 10)
                        break;
                    long claimedSizeChecksum = reader.readLong();
                    checksum.reset();
                    checksum.update(serializedSize);
                    if (checksum.getValue() != claimedSizeChecksum)
                        break; // entry wasn't synced correctly/fully. that's
                               // ok.

                    if (serializedSize > buffer.length)
                        buffer = new byte[(int) (1.2 * serializedSize)];
                    reader.readFully(buffer, 0, serializedSize);
                    claimedCRC32 = reader.readLong();
                }
                catch (EOFException eof)
                {
                    break; // last CL entry didn't get completely written. that's ok.
                }

                checksum.update(buffer, 0, serializedSize);
                if (claimedCRC32 != checksum.getValue())
                {
                    // this entry must not have been fsynced. probably the rest is bad too,
                    // but just in case there is no harm in trying them (since we still read on an entry boundary)
                    continue;
                }

                /* deserialize the commit log entry */
                FastByteArrayInputStream bufIn = new FastByteArrayInputStream(buffer, 0, serializedSize);
                RowMutation rm;
                try
                {
                    // assuming version here. We've gone to lengths to make sure what gets written to the CL is in
                    // the current version. so do make sure the CL is drained prior to upgrading a node.
                    rm = RowMutation.serializer.deserialize(new DataInputStream(bufIn), version, IColumnSerializer.Flag.LOCAL);
                }
                catch (UnknownColumnFamilyException ex)
                {
                    if (ex.cfId == null)
                        continue;
                    AtomicInteger i = invalidMutations.get(ex.cfId);
                    if (i == null)
                    {
                        i = new AtomicInteger(1);
                        invalidMutations.put(ex.cfId, i);
                    }
                    else
                        i.incrementAndGet();
                    continue;
                }

                if (logger.isDebugEnabled())
                    logger.debug(String.format("replaying mutation for %s.%s: %s", rm.getTable(), ByteBufferUtil.bytesToHex(rm.key()), "{" + StringUtils.join(rm.getColumnFamilies().iterator(), ", ")
                            + "}"));

                final long entryLocation = reader.getFilePointer();
                final RowMutation frm = rm;
                Runnable runnable = new WrappedRunnable()
                {
                    public void runMayThrow() throws IOException
                    {
View Full Code Here

        try
        {
            if (input instanceof RandomAccessReader)
            {
                RandomAccessReader file = (RandomAccessReader) input;
                file.seek(this.dataStart);
                if (dataStart + dataSize > file.length())
                    throw new IOException(String.format("dataSize of %s starting at %s would be larger than file %s length %s",
                                          dataSize, dataStart, file.getPath(), file.length()));
                if (checkData && !dataVersion.hasPromotedIndexes)
                {
                    try
                    {
                        IndexHelper.skipBloomFilter(file);
                    }
                    catch (Exception e)
                    {
                        if (e instanceof EOFException)
                            throw (EOFException) e;

                        logger.debug("Invalid bloom filter in {}; will rebuild it", sstable);
                    }
                    try
                    {
                        // skipping the old row-level BF should have left the file position ready to deserialize index
                        IndexHelper.deserializeIndex(file);
                    }
                    catch (Exception e)
                    {
                        logger.debug("Invalid row summary in {}; will rebuild it", sstable);
                    }
                    file.seek(this.dataStart);
                    inputWithTracker.reset(0);
                }
            }

            if (sstable != null && !dataVersion.hasPromotedIndexes)
View Full Code Here

    public String getPath()
    {
        // if input is from file, then return that path, otherwise it's from streaming
        if (input instanceof RandomAccessReader)
        {
            RandomAccessReader file = (RandomAccessReader) input;
            return file.getPath();
        }
        else
        {
            throw new UnsupportedOperationException();
        }
View Full Code Here

    public void reset()
    {
        if (!(input instanceof RandomAccessReader))
            throw new UnsupportedOperationException();

        RandomAccessReader file = (RandomAccessReader) input;
        file.seek(columnPosition);
        inputWithTracker.reset(headerSize());
    }
View Full Code Here

        if (header.file == null)
            return;

        // TODO just use a raw RandomAccessFile since we're managing our own buffer here
        RandomAccessReader file = (header.file.sstable.compression) // try to skip kernel page cache if possible
                                ? CompressedRandomAccessReader.open(header.file.getFilename(), header.file.sstable.getCompressionMetadata(), true)
                                : RandomAccessReader.open(new File(header.file.getFilename()), true);

        // setting up data compression stream
        output = new LZFOutputStream(output);

        try
        {
            // stream each of the required sections of the file
            for (Pair<Long, Long> section : header.file.sections)
            {
                // seek to the beginning of the section
                file.seek(section.left);

                // length of the section to stream
                long length = section.right - section.left;
                // tracks write progress
                long bytesTransferred = 0;
View Full Code Here

        // 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.)
        final RandomAccessReader dataFile = sstable.openDataReader(true);
        RandomAccessReader indexFile = RandomAccessReader.open(new File(sstable.descriptor.filenameFor(Component.PRIMARY_INDEX)), true);
        ScrubInfo scrubInfo = new ScrubInfo(dataFile, sstable);
        executor.beginCompaction(scrubInfo);

        SSTableWriter writer = null;
        SSTableReader newSstable = null;
        int goodRows = 0, badRows = 0, emptyRows = 0;

        try
        {
            ByteBuffer nextIndexKey = ByteBufferUtil.readWithShortLength(indexFile);
            {
                // throw away variable so we don't have a side effect in the assert
                long firstRowPositionFromIndex = indexFile.readLong();
                assert firstRowPositionFromIndex == 0 : firstRowPositionFromIndex;
            }

            // TODO errors when creating the writer may leave empty temp files.
            writer = maybeCreateWriter(cfs, compactionFileLocation, expectedBloomFilterSize, null, Collections.singletonList(sstable));

            while (!dataFile.isEOF())
            {
                long rowStart = dataFile.getFilePointer();
                if (logger.isDebugEnabled())
                    logger.debug("Reading row at " + rowStart);

                DecoratedKey key = null;
                long dataSize = -1;
                try
                {
                    key = SSTableReader.decodeKey(sstable.partitioner, sstable.descriptor, ByteBufferUtil.readWithShortLength(dataFile));
                    dataSize = sstable.descriptor.hasIntRowSize ? dataFile.readInt() : dataFile.readLong();
                    if (logger.isDebugEnabled())
                        logger.debug(String.format("row %s is %s bytes", ByteBufferUtil.bytesToHex(key.key), dataSize));
                }
                catch (Throwable th)
                {
                    throwIfFatal(th);
                    // check for null key below
                }

                ByteBuffer currentIndexKey = nextIndexKey;
                long nextRowPositionFromIndex;
                try
                {
                    nextIndexKey = indexFile.isEOF() ? null : ByteBufferUtil.readWithShortLength(indexFile);
                    nextRowPositionFromIndex = indexFile.isEOF() ? dataFile.length() : indexFile.readLong();
                }
                catch (Throwable th)
                {
                    logger.warn("Error reading index file", th);
                    nextIndexKey = null;
                    nextRowPositionFromIndex = dataFile.length();
                }

                long dataStart = dataFile.getFilePointer();
                long dataStartFromIndex = currentIndexKey == null
                                        ? -1
                                        : rowStart + 2 + currentIndexKey.remaining() + (sstable.descriptor.hasIntRowSize ? 4 : 8);
                long dataSizeFromIndex = nextRowPositionFromIndex - dataStartFromIndex;
                assert currentIndexKey != null || indexFile.isEOF();
                if (logger.isDebugEnabled() && currentIndexKey != null)
                    logger.debug(String.format("Index doublecheck: row %s is %s bytes", ByteBufferUtil.bytesToHex(currentIndexKey),  dataSizeFromIndex));

                writer.mark();
                try
View Full Code Here

    public void recover(File file) throws IOException
    {
        logger.info("Replaying " + file.getPath());
        final long segment = CommitLogSegment.idFromFilename(file.getName());
        RandomAccessReader reader = RandomAccessReader.open(new File(file.getAbsolutePath()), true);
        assert reader.length() <= Integer.MAX_VALUE;
        try
        {
            int replayPosition;
            if (globalPosition.segment < segment)
                replayPosition = 0;
            else if (globalPosition.segment == segment)
                replayPosition = globalPosition.position;
            else
                replayPosition = (int) reader.length();

            if (replayPosition < 0 || replayPosition >= reader.length())
            {
                // replayPosition > reader.length() can happen if some data gets flushed before it is written to the commitlog
                // (see https://issues.apache.org/jira/browse/CASSANDRA-2285)
                logger.debug("skipping replay of fully-flushed {}", file);
                return;
            }

            reader.seek(replayPosition);

            if (logger.isDebugEnabled())
                logger.debug("Replaying " + file + " starting at " + reader.getFilePointer());

            /* read the logs populate RowMutation and apply */
            while (!reader.isEOF())
            {
                if (logger.isDebugEnabled())
                    logger.debug("Reading mutation at " + reader.getFilePointer());

                long claimedCRC32;
                int serializedSize;
                try
                {
                    // any of the reads may hit EOF
                    serializedSize = reader.readInt();
                    if (serializedSize == CommitLog.END_OF_SEGMENT_MARKER)
                    {
                        logger.debug("Encountered end of segment marker at " + reader.getFilePointer());
                        break;
                    }

                    // RowMutation must be at LEAST 10 bytes:
                    // 3 each for a non-empty Table and Key (including the
                    // 2-byte length from writeUTF/writeWithShortLength) and 4 bytes for column count.
                    // This prevents CRC by being fooled by special-case garbage in the file; see CASSANDRA-2128
                    if (serializedSize < 10)
                        break;
                    long claimedSizeChecksum = reader.readLong();
                    checksum.reset();
                    checksum.update(serializedSize);
                    if (checksum.getValue() != claimedSizeChecksum)
                        break; // entry wasn't synced correctly/fully. that's
                               // ok.

                    if (serializedSize > buffer.length)
                        buffer = new byte[(int) (1.2 * serializedSize)];
                    reader.readFully(buffer, 0, serializedSize);
                    claimedCRC32 = reader.readLong();
                }
                catch (EOFException eof)
                {
                    break; // last CL entry didn't get completely written. that's ok.
                }

                checksum.update(buffer, 0, serializedSize);
                if (claimedCRC32 != checksum.getValue())
                {
                    // this entry must not have been fsynced. probably the rest is bad too,
                    // but just in case there is no harm in trying them (since we still read on an entry boundary)
                    continue;
                }

                /* deserialize the commit log entry */
                FastByteArrayInputStream bufIn = new FastByteArrayInputStream(buffer, 0, serializedSize);
                RowMutation rm;
                try
                {
                    // assuming version here. We've gone to lengths to make sure what gets written to the CL is in
                    // the current version. so do make sure the CL is drained prior to upgrading a node.
                    rm = RowMutation.serializer().deserialize(new DataInputStream(bufIn), MessagingService.version_, IColumnSerializer.Flag.LOCAL);
                }
                catch (UnknownColumnFamilyException ex)
                {
                    AtomicInteger i = invalidMutations.get(ex.cfId);
                    if (i == null)
                    {
                        i = new AtomicInteger(1);
                        invalidMutations.put(ex.cfId, i);
                    }
                    else
                        i.incrementAndGet();
                    continue;
                }

                if (logger.isDebugEnabled())
                    logger.debug(String.format("replaying mutation for %s.%s: %s", rm.getTable(), ByteBufferUtil.bytesToHex(rm.key()), "{" + StringUtils.join(rm.getColumnFamilies().iterator(), ", ")
                            + "}"));

                final long entryLocation = reader.getFilePointer();
                final RowMutation frm = rm;
                Runnable runnable = new WrappedRunnable()
                {
                    public void runMayThrow() throws IOException
                    {
View Full Code Here

        // 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.)
        final RandomAccessReader dataFile = sstable.openDataReader(true);
        long rowsRead = 0;
        RandomAccessReader indexFile = RandomAccessReader.open(new File(sstable.descriptor.filenameFor(Component.PRIMARY_INDEX)), true);
        ScrubInfo scrubInfo = new ScrubInfo(dataFile, sstable);
        executor.beginCompaction(scrubInfo);

        SSTableWriter writer = null;
        SSTableReader newSstable = null;
        int goodRows = 0, badRows = 0, emptyRows = 0;

        try
        {
            ByteBuffer nextIndexKey = ByteBufferUtil.readWithShortLength(indexFile);
            {
                // throw away variable so we don't have a side effect in the assert
                long firstRowPositionFromIndex = indexFile.readLong();
                assert firstRowPositionFromIndex == 0 : firstRowPositionFromIndex;
            }

            // TODO errors when creating the writer may leave empty temp files.
            writer = maybeCreateWriter(cfs, compactionFileLocation, expectedBloomFilterSize, null, Collections.singletonList(sstable));

            while (!dataFile.isEOF())
            {
                if (scrubInfo.isStopRequested())
                    throw new CompactionInterruptedException(scrubInfo.getCompactionInfo());
                long rowStart = dataFile.getFilePointer();
                if (logger.isDebugEnabled())
                    logger.debug("Reading row at " + rowStart);

                DecoratedKey key = null;
                long dataSize = -1;
                try
                {
                    key = SSTableReader.decodeKey(sstable.partitioner, sstable.descriptor, ByteBufferUtil.readWithShortLength(dataFile));
                    dataSize = sstable.descriptor.hasIntRowSize ? dataFile.readInt() : dataFile.readLong();
                    if (logger.isDebugEnabled())
                        logger.debug(String.format("row %s is %s bytes", ByteBufferUtil.bytesToHex(key.key), dataSize));
                }
                catch (Throwable th)
                {
                    throwIfFatal(th);
                    // check for null key below
                }

                ByteBuffer currentIndexKey = nextIndexKey;
                long nextRowPositionFromIndex;
                try
                {
                    nextIndexKey = indexFile.isEOF() ? null : ByteBufferUtil.readWithShortLength(indexFile);
                    nextRowPositionFromIndex = indexFile.isEOF() ? dataFile.length() : indexFile.readLong();
                }
                catch (Throwable th)
                {
                    logger.warn("Error reading index file", th);
                    nextIndexKey = null;
                    nextRowPositionFromIndex = dataFile.length();
                }

                long dataStart = dataFile.getFilePointer();
                long dataStartFromIndex = currentIndexKey == null
                                        ? -1
                                        : rowStart + 2 + currentIndexKey.remaining() + (sstable.descriptor.hasIntRowSize ? 4 : 8);
                long dataSizeFromIndex = nextRowPositionFromIndex - dataStartFromIndex;
                assert currentIndexKey != null || indexFile.isEOF();
                if (logger.isDebugEnabled() && currentIndexKey != null)
                    logger.debug(String.format("Index doublecheck: row %s is %s bytes", ByteBufferUtil.bytesToHex(currentIndexKey),  dataSizeFromIndex));

                writer.mark();
                try
View Full Code Here

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