I updated to the stable release and reproduced the issue.

Step to reproduce
1. go to admin
2. Manage data libraries
3. add dataset
4. select Upload files from filesystem paths
5. paste full path to any bam file.
6. leave defaults: auto-detect and copy files into galaxy
7. select role to restrict access
8. click upload to start

Screen shows strange formatting and "Job is running" for Bam file.

python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central 
/data/galaxy-central/database/tmp/tmpJoasJl 
/data/galaxy-central/database/tmp/tmpzZO8t1 
8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat

If I do a firefox refresh and go back to the library, the formatting is normal.

I'm assuming the fix is to just render the page before waiting for the job to 
complete.
-Robert

On Nov 4, 2013, at 12:45 PM, Martin Čech <mar...@bx.psu.edu> wrote:

> Hello,
> 
> I have also seen some of these errors while developing libraries. The library 
> code is not in central however it might be related to recent changes to the 
> history panel. Carl Eberhard might now more, adding him to the conversation.
> 
> --Marten
> 
> 
> On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baert...@soe.ucsc.edu> wrote:
> It keeps doing posts, and I'm not seeing any new errors. 
> 
> POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates
> 200 OK                 121ms
> 
> When I did a browser refresh, I got the following javascript error:     (I am 
> logged in)
> 
> Galaxy.currUser is undefined on Line 631 in history-panel.js
> 
> 
> When I opened the data library where the bam file was copying, everything is 
> rendered ok.  It seems the browser refresh fixed things.
> 
> -Robert
> 
> 
> On Nov 4, 2013, at 11:14 AM, James Taylor <ja...@jamestaylor.org> wrote:
> 
>> Robert, I'm not sure what is going on here, other than that the javascript 
>> that converts buttons into dropdown menus has not fired. 
>> 
>> Are there any javascript errors? 
>> 
>> Marten is working on rewriting libraries, and we will be eliminating the 
>> progressive loading popupmenus for something much more efficient, but this 
>> also might indicate a bug so let us know if there is anything odd in the 
>> console. 
>> 
>> 
>> --
>> James Taylor, Associate Professor, Biology/CS, Emory University
>> 
>> 
>> On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baert...@soe.ucsc.edu> 
>> wrote:
>> HI James,
>> I just pulled in the latest code to see how you changed from iframe to divs. 
>> Very exciting update.
>> 
>> 
>> I tried importing a bam file into the library using the admin tool that 
>> reads the file directly from a path on the server.
>> 
>> During the copy operation, the screen gets into a weird state. 
>> ps -ef shows these two processes running:
>>  python /data/galaxy-central/tools/data_source/upload.py 
>> /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE 
>> /data/galaxy-central/database/tmp/tmpXkEvSY 
>> 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat
>>  samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat 
>> /tmp/tmpNbcggh/sorted
>> 
>> Do you finish rendering the screen after the copy operation is complete?
>> 
>> -Robert
>> 
>> <Screen Shot 2013-11-04 at 10.53.02 AM.png>
>> 
> 
> 
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