Thanks for the help John and Dannon. I'll see if it works tomorrow. No need to raise a trello card

Thanks
Neil
From: Dannon Baker [dannon.baker@gmail.com]
Sent: Tuesday, August 05, 2014 11:14 PM
To: John Chilton
Cc: Burdett, Neil (DP&S, Herston - RBWH); galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy

The method John suggests is definitely a better way to get the user's API key.

That said, the 'get' change is due to sqlalchemy version changes that happened quite a while back.  You can no longer 'get' directly from the model, you must use a query object.  So, for example, this line:

    model.User.get( id )

Became:

    sa_session.query( self.model.User).get( id )

Hope that gives a little context,

-Dannon


On Tue, Aug 5, 2014 at 8:56 AM, John Chilton <jmchilton@gmail.com> wrote:
Hmm...

The following should work for the last at least three releases I
think: ${__user__.api_keys[0].key}. Not sure why get/find are
unavailable on the User model class in the cheetah template now. I
think this version is a little better. Is this okay? If not I can
create a Trello card to investigate and restore the old functionality.

-John


On Tue, Aug 5, 2014 at 2:26 AM,  <Neil.Burdett@csiro.au> wrote:
> Hi,
>     I have recently upgraded Galaxy from a version I had last year. In my
> tool xml file I could state:
>
> ${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
>
> in the <command> section to get the user's API. However, after updating to
> the current version of Galaxy I get the following error when using this
> entry in the xml file:
>
> Traceback (most recent call last):
>   File "/home/bmladmin/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 153, in prepare_job
>     job_wrapper.prepare()
>   File "/home/bmladmin/galaxy-dist/lib/galaxy/jobs/__init__.py", line 712,
> in prepare
>     self.command_line, self.extra_filenames = tool_evaluator.build()
>   File "/home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py", line
> 348, in build
>     self.__build_command_line( )
>   File "/home/bmladmin/galaxy-dist/lib/galaxy/tools/evaluation.py", line
> 364, in __build_command_line
>     command_line = fill_template( command, context=param_dict )
>   File "/home/bmladmin/galaxy-dist/lib/galaxy/util/template.py", line 9, in
> fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File
> "/home/bmladmin/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py",
> line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1407207170_7_53169.py",
> line 92, in respond
> NotFound: cannot find 'get' while searching for 'get'
>
> Any ideas?
>
> Thanks
> Neil
>
>
>
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