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araskind / jmzml

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Infinite loop when reading zlib compressed binaryDataArray with no data. #8

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. Create an mzML file with zlib compression, that contains a spectrum whose 
binary data are empty (no peaks)
2. Attempt to read the spectrum peaks
3. You will get an infinte loop in BinaryDataArray.getBinaryArrayAsNumberArray 
-> decompress

What is the expected output? What do you see instead?

I expect to see an array with zero elements.
Instead, the program hangs in an infinite loop.

What version of the product are you using? On what operating system?

jmzml 1.7.1 (from the Maven repository)
CentOS 6.3

Please provide any additional information below.

I attached a snippet showing the spectrum that causes issues.

Original issue reported on code.google.com by Roman.Ze...@gmail.com on 7 Jan 2014 at 2:26

Attachments:

GoogleCodeExporter commented 8 years ago 
Thanks for your comments can you provide the complete mzml file to fix the 
problem. 
Regards

Original comment by ypriverol on 8 Jan 2014 at 1:26

GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
[deleted comment]
GoogleCodeExporter commented 8 years ago 
This file is packed with zlib.

It crashes the GUI viewer, I believe due to the infinite loop issue.

Original comment by Roman.Ze...@gmail.com on 8 Jan 2014 at 3:32

Attachments:

GoogleCodeExporter commented 8 years ago 
Dear Roman:
 You can check out your code and compile. The error was fixed. Let me know if you 
 still have the problem.
Regards

Original comment by ypriverol on 9 Jan 2014 at 7:37

GoogleCodeExporter commented 8 years ago 
I will give it a try and compile a version for my own purposes.

Are you planning to relese e.g. 1.7.2 that contains the fix?

Original comment by Roman.Ze...@gmail.com on 10 Jan 2014 at 3:58

GoogleCodeExporter commented 8 years ago 
Yes Roman we are planning to release in the near future the a new version with 
the fixed issue. Please if you test it the libary give me your feedback or this 
issue.

Original comment by ypriverol on 10 Jan 2014 at 2:48

GoogleCodeExporter commented 8 years ago 
Any news on when version 1.7.2 is going to be available?

Original comment by plu...@gmail.com on 16 Sep 2014 at 1:17