Corrupted data

bsp...@proteinms.net

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Jul 12, 2016, 4:33:56 PM7/12/16

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Greetings,

What's the procedure for dealing with corrupted data files? I don't know if the files were damaged during upload, or what, but in the experiment "1962: Erin BSA Response IMS" every file whose name starts with "Yeast_opt1ug..." has a corrupted zipfile on download. Can you advise? I can see where not allowing casual delete and re-upload is good policy, but as it stands these are not useful files. I do have the originals on my local hard drive.

Thanks,

Brian Pratt

Skyline Developer, MacCoss Lab, UW

Alexander Orlov

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Jul 13, 2016, 11:03:05 AM7/13/16

to bsp...@proteinms.net, CHORUS Project

Hello Brian,

We have investigated the issues you have reported. The .zip archives could be un-archived without any errors.

Could you please explain how did you determined that these files are corrupted?

This information would be very helpful in order to investigate and resolve the issue.

Thank you,

Alexander Orlov

QA Engineer | Enterprise Technologies | TeamDev, Ltd.
Phone: +380 57 766-4300

Skype: alexander.smile

Alexand...@teamdev.com | www.teamdev.com

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Brian Pratt

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Jul 13, 2016, 2:07:19 PM7/13/16

to Alexander Orlov, CHORUS Project

Hi Alexander,

Thanks for the quick reply. Your note helped me understand that the actual problem is in how Chorus compresses large (>2GB?) files for upload.

You can demonstrate the problem with these steps:

1) Download Yeast_0pt1ug_a_BSA_0pM_18May15_Fir_15-04-01.d.zip from Chorus to a Windows (10, in my case) filesystem

2) Extract with Windows Explorer - fails during extraction of MSProfile.bin

3) Extract with 7Zip - fails during extraction of MSProfile.bin

4) Extract with WinRAR - success

5) Compress Yeast_0pt1ug_a_BSA_0pM_18May15_Fir_15-04-01.d to Yeast_0pt1ug_a_BSA_0pM_18May15_Fir_15-04-01.d.zip with 7Zip.exe

6) Extract with Windows Explorer - success

I'm hoping it's a pretty simple fix on your end, just an out of date library or something. Also, I'm hoping Chorus will correct any large zip files already uploaded.

Note that there are other issues with Chorus and large files, as already reported - I'm only downloading these files because Chorus can't handle their size for chromatogram extraction. We can expect to see more and more of these large files as IMS-capable mass specs come into wider use.

Thanks,

Brian

Alexander Orlov

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Jul 14, 2016, 5:05:42 AM7/14/16

to Brian Pratt, CHORUS Project

Brian,

Thank you very much for the detailed explanation. I was able to reproduce the issue with the steps you provided.

I've assigned the issue to the dev team. I'll notify you as soon as it is resolved.

Thank you,

Alexander Orlov

QA Engineer | Enterprise Technologies | TeamDev, Ltd.
Phone: +380 57 766-4300

Skype: alexander.smile

Alexand...@teamdev.com | www.teamdev.com

Brian Pratt

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Aug 31, 2016, 1:31:36 PM8/31/16

to Alexander Orlov, CHORUS Project

Hi Alexander,

Any word on this fix? It's holding up a colleague's ability to publish a paper.

Thanks

Brian

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Andrii Loboda

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Sep 1, 2016, 3:50:51 AM9/1/16

to Brian Pratt, CHORUS Project, support, Volodymyr Moiseiev, Alexander Orlov

Hi Brian,

I've started working on this issue.

It seems that js library we use for zipping has to be updated to write zip header correctly so it could be unpacked without errors via standard tools.

I will send you an email as soon as I resolve it.

Sorry for the delay.

Andrii

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Brian Pratt

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Sep 1, 2016, 5:58:20 PM9/1/16

to Andrii Loboda, CHORUS Project, support, Volodymyr Moiseiev, Alexander Orlov

Glad to hear it, thanks. Hopefully you can find a library that implements Zip64.

Thanks!

Brian

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