Hi Brent

Glad to help.  The only further thing I'd say is do a lot testing.  Galaxy is a 
large, complex piece of software with some bits hard coded, some bits 
configurable, and there are decentralized policies or behaviors.  So just be 
sure making a change in one place, like commenting out that section, doesn't 
negatively impact some other functionality you or your users may want.

Best of luck,
Eric

________________________________________
From: Brent Pedersen [bpede...@gmail.com]
Sent: Friday, September 30, 2011 1:15 PM
To: Paniagua, Eric
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] upload zip file to custom tool

On Fri, Sep 30, 2011 at 10:41 AM, Paniagua, Eric <epani...@cshl.edu> wrote:
> Hi Brent,
>
> I've encountered this behavior too.  I don't know the ultimate reason or 
> purpose, but compressed files (especially zip) are handled in very specific, 
> restricted ways by the upload framework.  The behavior you describe is hard 
> coded into the upload tool.
>
> For example, check out the use of the 'zipfile' module in 
> tools/data_source/upload.py.  That file (tool) will actually try to sniff 
> your file even if you've set the file type in upload.  See the data flow (or 
> data non-flow) through local variable 'ext' in 
> tools/data_source/upload.py:add_file().  Odd and restrictive policy for 
> treatment of compressed files can be seen elsewhere in the codebase too, 
> including 
> test/base/twilltestcase.py:TwillTestCase.verify_dataset_correctness().
>
> My advice (and this is also basically the advice Nate gave me) is to fork 
> your own copy of the upload tool to make a version that works for your files.
>
> Nate may have more to say on the matter.
>
> Best,
> Eric
>


Eric, thanks for pointing me to that file. I just commented out the
unzip section for now and
also changed one section that was causing it to show "...inappropriate
content" and it seems to
be working now.
-Brent



> ________________________________________
> From: galaxy-user-boun...@lists.bx.psu.edu 
> [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Brent Pedersen 
> [bpede...@gmail.com]
> Sent: Friday, September 30, 2011 11:59 AM
> To: galaxy-user@lists.bx.psu.edu
> Subject: [galaxy-user] upload zip file to custom tool
>
> Hi,
> I have followed the wiki and built a custom tool on a local galaxy 
> installation.
> One of the inputs is a zip file. It seems galaxy automatically unpacks
> it and keeps only
> the first file. Is there any way I can tell galaxy not to unzip the file?
> I tried to register .zip as a datatype, but that didn't seem to change
> the behavior.
>
> thanks for any help.
> $tool.xml is below in case it helps.
> -Brent
>
>  <command interpreter="python">charmqc.py $xyszip $output $organism</command>
>  <inputs>
>   <param format="xys.zip" name="xyszip" type="data" label="Zip of
> .xys files"/>
>   <param type="select" name="organism" label="organism">
>       <option value="Human">Human (hg18)</option>
>       <option value="Mouse">Mouse (mm8)</option>
>    </param>
>  </inputs>
>  <outputs>
>   <data format="data" name="output" />
>  </outputs>
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___________________________________________________________
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