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 <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
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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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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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<mailto: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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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/
participants (3)
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Dannon Baker -
John Chilton -
Neil.Burdett＠csiro.au