Our upload issues seem to have been resolved. Thanks for checking.

I added the attached comment to another list-serve message - we did have the 
referenced error in our startup logs. The attached email mentions I was still 
having trouble uploading files with the Upload File tool. That is now resolved 
as well.

Steve

-----Original Message-----
From: Dannon Baker [mailto:dannonba...@me.com] 
Sent: Sunday, February 03, 2013 7:14 PM
To: Hakeem Almabrazi
Cc: Stephen Groenewold; Galaxy Dev; galaxy-b...@bx.psu.edu Bugs
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

I just wanted to follow up on this and make sure everything was now working as 
expected.  I've tried to reproduce the original issue and have thus far been 
unsuccessful in doing so with a fresh instance.  Is the configuration of your 
Galaxy instance special in any way?  Did you notice any logged errors (either 
in the Javascript console or in Galaxy's log)?

-Dannon


On Feb 1, 2013, at 3:37 PM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:

> Stephen,,,
>  
> Here is your solution:
>  
> In the Tools panel select "Get Data", "Upload File". You can either upload a 
> file, or enter one or more URLs in the "URL/Text" box. Enter 
> "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute"
>  
> I am not sure what happened there but it seems this triggered some database 
> updates that was needed. 
>  
> It worked J....
>  
>  
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen 
> Groenewold
> Sent: Friday, February 01, 2013 10:41 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] File Upload doesn't generate any activity
>  
> We've  installed a local instance of Galaxy and are having trouble with the 
> first step of uploading files. The only thing that will currently upload is 
> text pasted into the URL/Text box.
>  
> Any attempt to upload a file using the Browse File box not only fails, it 
> never even starts. It's as if the Execute button is disabled.
>  
> I've tried changing the ajax-upload parameter to "false" in 
> tools/data_source/upload.xml (as mentioned in a workaround posted to the list 
> by Daniel Blankenburg in Aug 2012). I've also tried using different browsers 
> (including Internet Explorer) and going the route of Adding Data Libraries as 
> Admin. None of those attempts have worked.
>  
> Am I missing a configuration setup? Could there be permissions issues on the 
> Galaxy machine?
>  
> Thanks.
>  
> Steve
>  
> ___________________________________________________________
> 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/

--- Begin Message ---
We've also seen that same error in our startup log:

======================

Traceback (most recent call last):
  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py",
line 447, in _load_plugin
    module = __import__( module_name )
  File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py",
line 232
    worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ),
target=self.run_next )
                                     ^
SyntaxError: invalid syntax

=======================

And we are also having trouble uploading files. Originally, even attempts to 
add files via the Admin Data Libraries process wouldn't work. That seems to 
have been resolved (coincidentally? or causally?) after another user completed 
a general upload via a URL.

But even now, uploading a specific file with the Get Data -> Upload File 
process is still non-responsive. Either the Execute button never does anything 
at all, or the upload process appears in History and turns blue but never 
completes.


-----Original Message-----
From: Dan Tenenbaum [mailto:dtene...@fhcrc.org]
Sent: Friday, February 01, 2013 3:14 PM
To: Stephen Groenewold
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity

On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold <sgroenew...@idtdna.com> 
wrote:
> We've  installed a local instance of Galaxy and are having trouble
> with the first step of uploading files. The only thing that will
> currently upload is text pasted into the URL/Text box.
>
>
>
> Any attempt to upload a file using the Browse File box not only fails,
> it never even starts. It's as if the Execute button is disabled.
>
>
>
> I've tried changing the ajax-upload parameter to "false" in
> tools/data_source/upload.xml (as mentioned in a workaround posted to
> the list by Daniel Blankenburg in Aug 2012). I've also tried using
> different browsers (including Internet Explorer) and going the route
> of Adding Data Libraries as Admin. None of those attempts have worked.
>
>
>
> Am I missing a configuration setup? Could there be permissions issues
> on the Galaxy machine?
>
>

This sounds like the same issue I've reported to this list, which Carl and 
others have been kind enough to look at. I think their look is still in 
progress but hopefully there will be some news about it soon.
Here is that thread:

http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installation-this-request-returned-None-from-get-history-td4657958.html#a4657960

Dan


>
> Thanks.
>
>
>
> Steve
>
>
>
>
> ___________________________________________________________
> 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/

--- End Message ---
___________________________________________________________
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/

Reply via email to