Carl,
Thanks for building a great tool. 

Can you fix the library performance problem?

Steps to reproduce:
1. http://su2c-dev.ucsc.edu/library
2. open library TCGA Pancan. 

It takes more than 20 seconds!
-Robert

On Nov 5, 2013, at 1:29 PM, Carl Eberhard <carlfeberh...@gmail.com> wrote:

> 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 <baert...@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 <carlfeberh...@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
> < database_connection = postgresql://localhost/medbookgalaxycentral3
> 542c541
> < allow_library_path_paste = True
> ---
> > #allow_library_path_paste = False
> 599c598
> < admin_users = baert...@soe.ucsc.edu
> ---
> > #admin_users = None
> 
> 
> <Screen Shot 2013-11-05 at 8.35.09 AM.png>
> <Screen Shot 2013-11-05 at 8.37.04 AM.png>
> 
> On Nov 5, 2013, at 8:21 AM, Carl Eberhard <carlfeberh...@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 <baert...@soe.ucsc.edu> 
>> wrote:
>> 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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>> 
>> 
> 
> 

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