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 ___________________________________________________________ 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/
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