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Old 03-22-2012, 05:26 PM   #1
chipseq
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Location: sydney

Join Date: Oct 2011
Posts: 1
Default Galaxy Tool Development: Reading user id before the execution of the tool

I have posted this twice on Galaxy Dev list, however, I did not receive any response, therefore, I am posting this here in a hope that here might be the guy who could stop me pulling my few left hairs.

My tool meant to load up (in a dropdown) some custom data from a non-galaxy database for the user to select and submit a job. I am using dynamic_options for loading such dynamic values, however to restrict data for a logged-in user I need to know the user id.

So far I have tried many things including setting dynamic_options="load_dynamic_values($__user_id__) in the xml wrapper but it did not work. I know $__user_id__ can be passed to the tool as a command line arguments, however, my issue is to read user id even before the execution of main tool.


I have also tried following code in a hope to grab the webapp session.

ini_file = '/galaxy-dist/universe_wsgi.ini'

conf_parser = ConfigParser.ConfigParser( {'here's.getcwd()} )

conf_parser.read( ini_file )

configuration = {}

for key, value in conf_parser.items( "app:main" ):

configuration[key] = value

global_conf = { '__file__' : ini_file }

app = galaxy.app.UniverseApplication(**configuration )



But this generates following error.

UnboundExecutionError: Parent instance <History at 0x581cdd0> is not bound to a Session; lazy load operation of attribute 'active_datasets' cannot proceed.

Thanks for your help guys.
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Old 03-23-2012, 12:24 AM   #2
maubp
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Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Quote:
Originally Posted by chipseq View Post
I have posted this twice on Galaxy Dev list, however, I did not receive any response, therefore, I am posting this here in a hope that here might be the guy who could stop me pulling my few left hairs.
I think the Galaxy dev list is the best place to ask, even if some folk do read both that and SEQanswers.
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