Upload issue in local installation

2 Aug 2012

Hi,

Sorry about that but we get that error too "Failed: Request Entity Too
Large (413)" on Firefox (43.0) but not on chrome (47.0.2526.106 (64-bit)).
The trick to disable "ajax-upload" parameter (set it to false) does not
seem to work (the window is still open and nothing changed).

Any iadea would be greatful

Best,

Remy

2012-10-23 16:23 GMT+02:00 Nate Coraor <nate@bx.psu.edu>:

> On Oct 23, 2012, at 10:06 AM, Peter Briggs wrote:
>
> > 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.
>
> Hi Peter,
>
> Thanks for finding this, I've added this information to our documentation.
>
> --nate
>
> >
> > 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: dan@bx.psu.edu
> >> Date: Fri, 3 Aug 2012 09:24:43 -0400
> >> CC: batsal@gmail.com; galaxy-dev@lists.bx.psu.edu
> >> To: david_roquis@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:batsal@gmail.com <mailto:batsal@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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> >>    >
> >>    >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:
> >>
> >>   http://lists.bx.psu.edu/
> >>
> >
> > --
> > Peter Briggs peter.briggs@manchester.ac.uk
> > Bioinformatics Core Facility University of Manchester
> > B.1083 Michael Smith Bldg Tel: (0161) 2751482
> >
> >
> > ___________________________________________________________
> > 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:
>
>   http://lists.bx.psu.edu/
>

Batsal Devkota

David Roquis

Daniel Blankenberg

David Roquis

Peter Briggs

Nate Coraor

Rémy Dernat

Rémy Dernat

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