Hi Sam,

I just want to try and get a working Galaxy on Bio-Linux, and unless
your new code is coming out imminently (ie. next week) I need to make
progress before then.  If I can't debug the problem I think I'm going to
have to revert changes until I get to something that happens to work.
The result will be far removed from anything that could ever become a
proper Debian package, and given the progress I've made I'd prefer not
to quit now.  By the time your next release comes out I'll have other
jobs on my plate.  Is it really that hard to peek into the system and
try to see where the upload is jamming?

Cheers,

TIM

On Fri, 2013-10-04 at 17:05 +0100, sam guerler wrote:
> Hey,
> 
> 
> We are currently refactoring and redesigning the front-end javascript
> code. If the bug you are observing is 1) related to specifics of the
> current front-end implementation and 2) if fixing the bug is time
> consuming it might be reasonable to not invest that time and wait
> until we complete the new client code for the upload process.
> 
> 
> Thanks,
> Sam
> 
> 
> On Fri, Oct 4, 2013 at 11:48 AM, Tim Booth <tbo...@ceh.ac.uk> 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.borr...@gmail.com> wrote:
>         > >> On Fri, Oct 4, 2013 at 8:11 AM, Tim Booth
>         <tbo...@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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>         >
>         >
>         > ___________________________________________________________
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>         
>         
>         --
>         Tim Booth <tbo...@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
>         
>         
>         ___________________________________________________________
>         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/
>         
>         To search Galaxy mailing lists use the unified search at:
>           http://galaxyproject.org/search/mailinglists/
>         
> 
> 

-- 
Tim Booth <tbo...@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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