Tim,

Just to be certain, if you have AJAX upload enabled, you'll see this message after you click Execute on the upload tool:

  http://www.bx.psu.edu/~nate/galaxy/ajax.png

Whereas with it disabled, you'll see:

  http://www.bx.psu.edu/~nate/galaxy/noajax.png

--nate

On Oct 4, 2013, at 11:48 AM, Tim Booth wrote:

> Hi Guys,
>
> Thanks for the replies.  In that case it looks like the problem with my
> DEB package is not the same as the transient upload issue with Chrome.
> I was indeed using Chrome for most of the testing, but if I try to use
> the DEB package I've made then uploads still don't work at all in either
> Chrome or FF.
>
> The file appears in database/file/000/ but I don't see any job in the
> history.  Setting ajax-upload to false doesn't seem to change anything
> whatsoever - (to reassure myself the XML was actually being reloaded I
> changed the version number and saw that changed).
>
> I've rolled back all the changes in my package that I think would
> reasonably impact the issue, in particular my patch that enables Galaxy
> to use certain system libraries rather than it's own eggs, but the
> problem still persists so I feel I have to try and understand it rather
> than blindly switching things around.
>
> In terms of debugging, I can use tcpflow and FireBug to dig into the
> network communication but how do I get Galaxy to give me more info about
> what it is up to?  I can't see any obvious errors in the server log, and
> when if comes to the internals of the thing I don't know what is
> actually supposed to happening.  What is the expected sequence of events
> when a file is uploaded?  How is the status of the job signalled to the
> right-hand pane?  Where do I start adding debugging statements and
> assertions to help me see what is happening?  Can the in-browser
> debugging mentioned in the config file help me out at all, and where can
> I find out more?
>
> I'm happy to RTFM here but I've not yet found the right bit of the FM to
> read!
>
> Cheers,
>
> TIM
>
> On Fri, 2013-10-04 at 15:12 +0100, Nate Coraor wrote:
>> On Oct 4, 2013, at 10:00 AM, John Chilton wrote:
>>
>>> I have seen this behavior too and I too have switched to Firefox, but
>>> I have only ever seen this with chrome on localhost, never with chrome
>>> on a remote server behind a proxy.
>>
>> I've seen this issue before as well, a few of us have worked on it in the past, but it seems to be transient and not easy to reproduce.  In my testing a couple years ago, I found that the call to ajaxSubmit() to actually POST the data never occurs, and I couldn't get Firebug to tell me why.
>>
>> You can disable the AJAX upload method in tools/data_source/upload.xml, but that makes the UI a lot less usable, especially for large files.
>>
>> --nate
>>
>>>
>>> -John
>>>
>>> On Fri, Oct 4, 2013 at 8:55 AM, Carlos Borroto <carlos.borroto@gmail.com> wrote:
>>>> On Fri, Oct 4, 2013 at 8:11 AM, Tim Booth <tbooth@ceh.ac.uk> wrote:
>>>>> When uploading a file, no job appears in the right-hand panel.  If I
>>>>> click refresh I might see a job but it stays in the blue "Dataset is
>>>>> uploading" state forever.
>>>>
>>>> Hi Tim,
>>>>
>>>> It is great news to hear Galaxy deb packages could be a possibility in
>>>> the near future. Regarding this issue, I can confirm I see it a lot on
>>>> Chrome but never on Firefox. It has been so bad for me that I almost
>>>> completely moved to using only Firefox when working on Galaxy. I
>>>> thought it could be a cookies issue, but clearing out galaxy cookies
>>>> from Chrome doesn't help in my case.
>>>>
>>>> I'll be happy to do further testing as this is something I would love
>>>> to see fixed.
>>>>
>>>> Best,
>>>> Carlos
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>>
>> ___________________________________________________________
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>
> --
> Tim Booth <tbooth@ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>


___________________________________________________________
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