In case this is of use to someone else: I've been experiencing a similar-sounding issue to that described below - the symptoms were that only very small (e.g. 40kb) files could be uploaded successfully.

The problem seemed to be caused by the SecRequestBodyLimit directive in Apache's mod_security.conf file putting a very low limit on the size of files. The fix (for me) was simply to up the limit to something more appropriate.


Disabling the ajax uploads as described by Dan didn't fix the problem but it did make the source more obvious, as Galaxy immediately reported the error message "413 Request Entity Too Large" (with the clue about mod_security turning up in the Apache log).

I don't think this is the same problem as previously reported but maybe this info will help someone else.

Best wishes

Peter

On 03/08/12 14:58, David Roquis wrote:
Hi Dan,

It works like a charm! Thanks a lot! I have been looking for a
workaround for this issue for almost a month!

Once again, thanks you so much!

David


------------------------------------------------------------------------
Subject: Re: [galaxy-dev] Upload issue in local installation
From: d...@bx.psu.edu
Date: Fri, 3 Aug 2012 09:24:43 -0400
CC: bat...@gmail.com; galaxy-dev@lists.bx.psu.edu
To: david_roq...@hotmail.com

Hi David and Bastal,

We have been able to reproduce this behavior under certain conditions
and are working on a fix. Until this fix is available, you can disable
ajax uploads, which should allow the upload tool to work properly.
In tools/data_source/upload.xml change

<param name="file_data" type="file" size="30" label="File"
ajax-upload="true" help="TIP: Due to browser limitations, uploading
files larger than 2GB is guaranteed to fail.  To upload large files, use
the URL method (below) or FTP (if enabled by the site administrator).">

to

<param name="file_data" type="file" size="30" label="File"
ajax-upload="False" help="TIP: Due to browser limitations, uploading
files larger than 2GB is guaranteed to fail.  To upload large files, use
the URL method (below) or FTP (if enabled by the site administrator).">


Please let us know if this workaround doesn't work for you.


Thanks for using Galaxy,

Dan


On Aug 3, 2012, at 4:20 AM, David Roquis wrote:

    Hi Batsal,

    I have the exact same problem, on 2 different instances of Galaxy,
    on two different servers. I can replicate this problem on a cloned
    instance with no modification, and one using multiple galaxay
    server, nginx proxy and postgresql, both instances being on
    different machines (one on fedora 13, the other one on fedora 17).
     From what I have seen, it seems to be browser related. I can
    sometimes (rarely) upload data with firefox, chrome or safary, but
    for me it has worked ALL the time using internet explorer 8/9. The
    thing is that when you start the upload, the browser shows you that
    it is uploaded, but the upload.py script is never launched, and
    hence, the upload seems to be running forever. Seems we are not the
    only ones with this problem, but no real solution until now.

    Two options for you at the moment
    - try using IE 8/9 to upload the data
    - upload your data using data libraries under the admin menu (this
    works on any browser).

    Keep me in touch if you find a solution

    David



    > From:bat...@gmail.com <mailto:bat...@gmail.com>
    > Date: Thu, 2 Aug 2012 15:48:40 -0400
    > To:galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
    > Subject: [galaxy-dev] Upload issue in local installation
    >
    > I installed galaxy locally in a linux server. However, I cannot upload 
the files (no matter how small, I have tried few kb size fasta files). When I try 
to upload, the link to the file shows up in the History and gets a new number 
(purple box). When I click on the link I get 'Dataset is uploading' forever.
    >
    > In the terminal window where I start galaxy, I get the following error 
report:
    >
    > 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" 
"Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - 
"http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - 
"http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - 
"http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 
200 - "http://redhat:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 5.2;
    rv:13.0) Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create 
HTTP/1.1" 200 - "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message 
HTTP/1.1" 200 - "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - 
"http://redhat:8080/tool_runner/upload_async_message"; "Mozilla/5.0
    (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - 
"http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 
200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    > 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 
200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
    Gecko/20100101 Firefox/13.0.1"
    >
    >
    > The last line keeps going for ever... writes new line every 4 secs.
    >
    > I am stuck and don't know where to look. Please help.
    >
    > Batsal.
    >
    >
    > ___________________________________________________________
    > Please keep all replies on the list by using "reply all"
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    > and other Galaxy lists, please use the interface at:
    >
    >http://lists.bx.psu.edu/
    ___________________________________________________________
    Please keep all replies on the list by using "reply all"
    in your mail client.  To manage your subscriptions to this
    and other Galaxy lists, please use the interface at:

    http://lists.bx.psu.edu/




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


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