Thanks for building a great tool.
Can you fix the library performance problem?
Steps to reproduce:
2. open library TCGA Pancan.
It takes more than 20 seconds!
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
> library section is a link to the controller/datasets methods (unhide, delete,
> etc.) that still assume histories are in their own frames. Still
> On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch <baert...@soe.ucsc.edu>
> 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
> in Firebug. I've seen strange errors before in Firebug.
> Attached are two screen grab of the lastest try before and after browser
> 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
> < port = 8585
> > #port = 8080
> < host = 0.0.0.0
> > #host = 127.0.0.1
> < database_connection = postgresql://localhost/medbookgalaxycentral3
> < allow_library_path_paste = True
> > #allow_library_path_paste = False
> < 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
>> Is this an intermittent error or does it happen reliably each time with the
>> I'll investigate further.
>> On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch <baert...@soe.ucsc.edu>
>> 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
>> If I do a firefox refresh and go back to the library, the formatting is
>> I'm assuming the fix is to just render the page before waiting for the job
>> to complete.
>> On Nov 4, 2013, at 12:45 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>>> 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.
>>> On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch <baert...@soe.ucsc.edu>
>>> 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
>>> 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.
>>> On Nov 4, 2013, at 11:14 AM, James Taylor <ja...@jamestaylor.org> wrote:
>>>> that converts buttons into dropdown menus has not fired.
>>>> 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
>>>> James Taylor, Associate Professor, Biology/CS, Emory University
>>>> On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baert...@soe.ucsc.edu>
>>>> 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
>>>> samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat
>>>> Do you finish rendering the screen after the copy operation is complete?
>>>> <Screen Shot 2013-11-04 at 10.53.02 AM.png>
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