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From "Dmitriy Smirnov (JIRA)" <j...@apache.org>
Subject [jira] [Created] (COMPRESS-146) BZip2CompressorInputStream always treats 0x177245385090 as EOF, but should treat this as EOS
Date Sun, 24 Jul 2011 00:01:09 GMT
BZip2CompressorInputStream always treats 0x177245385090 as EOF, but should treat this as EOS
--------------------------------------------------------------------------------------------

                 Key: COMPRESS-146
                 URL: https://issues.apache.org/jira/browse/COMPRESS-146
             Project: Commons Compress
          Issue Type: Bug
          Components: Compressors
         Environment: all
            Reporter: Dmitriy Smirnov
            Priority: Critical


BZip2CompressorInputStream always treats 0x177245385090 as EOF, but should treat this as EOS
This error occurs mostly on large size files as sudden EOF somwere in the middle of the file.

An example of data from archived file:
$ cat fastq.ax.bz2 | od -t x1 | grep -A 1 '17 72 45'
22711660 d0 ff b6 01 20 10 ff ff 17 72 45 38 50 90 2e ff
22711700 b2 d3 42 5a 68 39 31 41 59 26 53 59 84 3c 41 75
--
24637020 c5 49 ff 19 80 49 20 7f ff 17 72 45 38 50 90 a4
24637040 a8 ac bd 42 5a 68 39 31 41 59 26 53 59 0d 9a b4
--
40302720 ff b1 24 80 10 ff ff 17 72 45 38 50 90 24 cb c5
40302740 90 42 5a 68 39 31 41 59 26 53 59 42 05 ae 5e 05
.....


Suggested solution:

    private void initBlock() throws IOException {
        char magic0 = bsGetUByte();
        char magic1 = bsGetUByte();
        char magic2 = bsGetUByte();
        char magic3 = bsGetUByte();
        char magic4 = bsGetUByte();
        char magic5 = bsGetUByte();

        if( magic0 == 0x17 && magic1 == 0x72 && magic2 == 0x45
            && magic3 == 0x38 && magic4 == 0x50 && magic5 == 0x90
) 
          
        {
        	if( complete() ) // end of file);
        	{
        		return;
        	} else
        	{
        		magic0 = bsGetUByte();
                magic1 = bsGetUByte();
                magic2 = bsGetUByte();
                magic3 = bsGetUByte();
                magic4 = bsGetUByte();
                magic5 = bsGetUByte();
        	}
        } 

        if (magic0 != 0x31 || // '1'
                   magic1 != 0x41 || // 'A'
                   magic2 != 0x59 || // 'Y'
                   magic3 != 0x26 || // '&'
                   magic4 != 0x53 || // 'S'
                   magic5 != 0x59 // 'Y'
                   ) {
            this.currentState = EOF;
            throw new IOException("bad block header");
        } else {
            this.storedBlockCRC = bsGetInt();
            this.blockRandomised = bsR(1) == 1;

            /**
             * Allocate data here instead in constructor, so we do not allocate
             * it if the input file is empty.
             */
            if (this.data == null) {
                this.data = new Data(this.blockSize100k);
            }

            // currBlockNo++;
            getAndMoveToFrontDecode();

            this.crc.initialiseCRC();
            this.currentState = START_BLOCK_STATE;
        }
    }


    private boolean 
    complete() throws IOException 
    { 
    	boolean result = false;
        this.storedCombinedCRC = bsGetInt();
        try
        {
            if (in.available() == 0 ) 
            {
                throw new IOException( "EOF" );
            }
            checkMagicChar('B', "first");
            checkMagicChar('Z', "second");
            checkMagicChar('h', "third");

            int blockSize = this.in.read();
            if ((blockSize < '1') || (blockSize > '9')) {
                throw new IOException("Stream is not BZip2 formatted: illegal "
                                      + "blocksize " + (char) blockSize);
            }

            this.blockSize100k = blockSize - '0';
            this.bsLive = 0;
            this.bsBuff = 0;

        } catch( IOException e )
        {
        	this.currentState = EOF;
        	
        	result = true;
        }
        
        this.data = null;
        if (this.storedCombinedCRC != this.computedCombinedCRC) {
            throw new IOException("BZip2 CRC error");
        }
        this.computedCombinedCRC = 0;    
        return result;
    }

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