Re: [galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy
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.ba...@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
mailto:jmchil...@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, 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 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
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
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 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, 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 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
> >
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client. To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> > http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> > http://galaxyproject.org/search/mailinglists/
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy
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, 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 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
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-dev] error using get( $__user_id__ ) in xml file in new Galaxy
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 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
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
