Thanks for the thorough report, Robert.

I've added some sanity checking to the panel in default:11240:c271cdb443c6

My only guess as to why the panel javascript is trying to load at all in the library section is a link to the controller/datasets methods (unhide, delete, etc.) that still assume histories are in their own frames. Still investigating.


On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote:
Carl,
Just to make sure I just deleted my tree and did a fresh checkout and tried a third time. It happened all three times. I'm using a postgres database and this time I started with a fresh config files and just changed the setting below.

I didn't see the javascript error in Chrome, perhaps it is some strangeness in Firebug. I've seen strange errors before in Firebug.

Attached are two screen grab of the lastest try before and after browser refresh.

changeset:   11227:151b7d3b2f1b
branch:      stable
tag:         tip
parent:      11219:5c789ab4144a
user:        Carl Eberhard <carlfeberhard@gmail.com>
date:        Tue Nov 05 11:33:06 2013 -0500
summary:     History panel: fix naming bug in purge async error handling

-Robert

29c29
< port = 8585
---
> #port = 8080
34c34
< host = 0.0.0.0
---
> #host = 127.0.0.1
96d95
542c541
< allow_library_path_paste = True
---
> #allow_library_path_paste = False
599c598
< admin_users = baertsch@soe.ucsc.edu
---
> #admin_users = None



On Nov 5, 2013, at 8:21 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:

Hello, Robert

I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0.

Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above?

I'll investigate further.


On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote:
I updated to the stable release and reproduced the issue.

Step to reproduce
1. go to admin
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 <marten@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 <baertsch@soe.ucsc.edu> wrote:
It keeps doing posts, and I'm not seeing any new errors. 

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 <james@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 <baertsch@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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