Tool Visibility feature

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Tool Visibility feature

SAPET, Frederic
Hello

I'm trying to set up this feature :
https://wiki.galaxyproject.org/Admin/Config/Access%20Control

it seems that some files have been moved from : lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/

by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work.

When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error :

Internal Server Error
Galaxy was unable to successfully complete your request

URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user
sys.path: [
    '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg',
    '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg',
    '/softs/bioinfo/galaxy-prod/lib',
    '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg',
    '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg',
    '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg',
    '/usr/lib64/python26.zip',
    '/usr/lib64/python2.6',
    '/usr/lib64/python2.6/plat-linux2',
    '/usr/lib64/python2.6/lib-tk',
    '/usr/lib64/python2.6/lib-old',
    '/usr/lib64/python2.6/lib-dynload',
    '/usr/lib64/python2.6/site-packages/gtk-2.0',
    '/usr/lib64/python2.6/site-packages',
    '/usr/lib/python2.6/site-packages']
Module galaxy.web.framework.middleware.error:151 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:143 in __call__
>>  return self.app( environ, start_response )
Module paste.httpexceptions:633 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:133 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:191 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.web.framework.decorators:68 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters
>>  tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters )
Module galaxy.webapps.galaxy.controllers.user:1284 in get_filter_mapping
>>  module = __import__( module_name, globals(), fromlist=['temp_module'] )
ImportError: No module named examples


Could you please provide me some help ?
I have launched a git pull origin master before testing...

Thank you.

Fred







___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: Tool Visibility feature

John Chilton-4
I have fixed the path to the filter directory on the wiki, have you
copied lib/galaxy/tools/toolbox/filters/examples.py.sample to
lib/galaxy/tools/toolbox/filters/examples.py?

-John

On Fri, Feb 19, 2016 at 4:22 PM, SAPET, Frederic
<[hidden email]> wrote:

> Hello
>
> I'm trying to set up this feature :
> https://wiki.galaxyproject.org/Admin/Config/Access%20Control
>
> it seems that some files have been moved from : lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/
>
> by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work.
>
> When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error :
>
> Internal Server Error
> Galaxy was unable to successfully complete your request
>
> URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user
> sys.path: [
>     '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/lib',
>     '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg',
>     '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg',
>     '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg',
>     '/usr/lib64/python26.zip',
>     '/usr/lib64/python2.6',
>     '/usr/lib64/python2.6/plat-linux2',
>     '/usr/lib64/python2.6/lib-tk',
>     '/usr/lib64/python2.6/lib-old',
>     '/usr/lib64/python2.6/lib-dynload',
>     '/usr/lib64/python2.6/site-packages/gtk-2.0',
>     '/usr/lib64/python2.6/site-packages',
>     '/usr/lib/python2.6/site-packages']
> Module galaxy.web.framework.middleware.error:151 in __call__
>>>  app_iter = self.application(environ, sr_checker)
> Module paste.recursive:84 in __call__
>>>  return self.application(environ, start_response)
> Module galaxy.web.framework.middleware.remoteuser:143 in __call__
>>>  return self.app( environ, start_response )
> Module paste.httpexceptions:633 in __call__
>>>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:133 in __call__
>>>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:191 in handle_request
>>>  body = method( trans, **kwargs )
> Module galaxy.web.framework.decorators:68 in decorator
>>>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters
>>>  tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters )
> Module galaxy.webapps.galaxy.controllers.user:1284 in get_filter_mapping
>>>  module = __import__( module_name, globals(), fromlist=['temp_module'] )
> ImportError: No module named examples
>
>
> Could you please provide me some help ?
> I have launched a git pull origin master before testing...
>
> Thank you.
>
> Fred
>
>
>
>
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Tool Visibility feature

SAPET, Frederic
Hi John

Yes, I have do that :

>ls lib/galaxy/tools/toolbox/filters/examples.py*
lib/galaxy/tools/toolbox/filters/examples.py  lib/galaxy/tools/toolbox/filters/examples.py.sample

I'm currently trying to set up another galaxy server, I will try Galaxy 16.01 with this functionality.

Thank you for the wiki.

Fred


-----Message d'origine-----
De : John Chilton [mailto:[hidden email]]
Envoyé : mercredi 2 mars 2016 21:20
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [galaxy-dev] Tool Visibility feature

I have fixed the path to the filter directory on the wiki, have you copied lib/galaxy/tools/toolbox/filters/examples.py.sample to lib/galaxy/tools/toolbox/filters/examples.py?

-John

On Fri, Feb 19, 2016 at 4:22 PM, SAPET, Frederic <[hidden email]> wrote:

> Hello
>
> I'm trying to set up this feature :
> https://wiki.galaxyproject.org/Admin/Config/Access%20Control
>
> it seems that some files have been moved from :
> lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/
>
> by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work.
>
> When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error :
>
> Internal Server Error
> Galaxy was unable to successfully complete your request
>
> URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user
> sys.path: [
>     '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/lib',
>     '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg',
>     '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg',
>     '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg',
>     '/usr/lib64/python26.zip',
>     '/usr/lib64/python2.6',
>     '/usr/lib64/python2.6/plat-linux2',
>     '/usr/lib64/python2.6/lib-tk',
>     '/usr/lib64/python2.6/lib-old',
>     '/usr/lib64/python2.6/lib-dynload',
>     '/usr/lib64/python2.6/site-packages/gtk-2.0',
>     '/usr/lib64/python2.6/site-packages',
>     '/usr/lib/python2.6/site-packages']
> Module galaxy.web.framework.middleware.error:151 in __call__
>>>  app_iter = self.application(environ, sr_checker)
> Module paste.recursive:84 in __call__
>>>  return self.application(environ, start_response)
> Module galaxy.web.framework.middleware.remoteuser:143 in __call__
>>>  return self.app( environ, start_response )
> Module paste.httpexceptions:633 in __call__
>>>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:133 in __call__
>>>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:191 in handle_request
>>>  body = method( trans, **kwargs )
> Module galaxy.web.framework.decorators:68 in decorator
>>>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters
>>>  tool_filters = get_filter_mapping( saved_user_tool_filters,
>>> trans.app.config.user_tool_filters )
> Module galaxy.webapps.galaxy.controllers.user:1284 in
> get_filter_mapping
>>>  module = __import__( module_name, globals(),
>>> fromlist=['temp_module'] )
> ImportError: No module named examples
>
>
> Could you please provide me some help ?
> I have launched a git pull origin master before testing...
>
> Thank you.
>
> Fred
>
>
>
>
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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Re: Tool Visibility feature

SAPET, Frederic
In reply to this post by John Chilton-4
Hi John

The problem is the same with galaxy 16.01.

>ls lib/galaxy/tools/toolbox/filters/examples.py*
lib/galaxy/tools/toolbox/filters/examples.py  lib/galaxy/tools/toolbox/filters/examples.py.sample

but when I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm still facing this error :


URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user
sys.path: [
    '/softs/bioinfo/galaxy-prod/scripts',
    '/softs/bioinfo/galaxy-prod/lib',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python27.zip',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python2.7',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/plat-linux2',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/lib-tk',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/lib-old',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/lib-dynload',
    '/softs/add-ons/anaconda-2.3.0/lib/python2.7',
    '/softs/add-ons/anaconda-2.3.0/lib/python2.7/plat-linux2',
    '/softs/add-ons/anaconda-2.3.0/lib/python2.7/lib-tk',
    '/softs/bioinfo/galaxy-prod/.venv/lib/python2.7/site-packages']
Module galaxy.web.framework.middleware.error:151 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.recursive:85 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:163 in __call__
>>  return self.app( environ, start_response )
Module paste.httpexceptions:640 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:131 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:189 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.web.framework.decorators:65 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters
>>  tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters )
Module galaxy.webapps.galaxy.controllers.user:1284 in get_filter_mapping
>>  module = __import__( module_name, globals(), fromlist=['temp_module'] )
ImportError: No module named examples


The paster.log shows :
Error - <type 'exceptions.ImportError'>: No module named examples


Do you have any idea ?

Thank you.

Fred


-----Message d'origine-----
De : SAPET, Frederic
Envoyé : jeudi 3 mars 2016 09:10
À : 'John Chilton' <[hidden email]>
Cc : [hidden email]
Objet : RE: [galaxy-dev] Tool Visibility feature

Hi John

Yes, I have do that :

>ls lib/galaxy/tools/toolbox/filters/examples.py*
lib/galaxy/tools/toolbox/filters/examples.py  lib/galaxy/tools/toolbox/filters/examples.py.sample

I'm currently trying to set up another galaxy server, I will try Galaxy 16.01 with this functionality.

Thank you for the wiki.

Fred


-----Message d'origine-----
De : John Chilton [mailto:[hidden email]] Envoyé : mercredi 2 mars 2016 21:20 À : SAPET, Frederic <[hidden email]> Cc : [hidden email]
Objet : Re: [galaxy-dev] Tool Visibility feature

I have fixed the path to the filter directory on the wiki, have you copied lib/galaxy/tools/toolbox/filters/examples.py.sample to lib/galaxy/tools/toolbox/filters/examples.py?

-John

On Fri, Feb 19, 2016 at 4:22 PM, SAPET, Frederic <[hidden email]> wrote:

> Hello
>
> I'm trying to set up this feature :
> https://wiki.galaxyproject.org/Admin/Config/Access%20Control
>
> it seems that some files have been moved from :
> lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/
>
> by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work.
>
> When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error :
>
> Internal Server Error
> Galaxy was unable to successfully complete your request
>
> URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user
> sys.path: [
>     '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg',
>     '/softs/bioinfo/galaxy-prod/lib',
>     '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg',
>     '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg',
>     '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg',
>     '/usr/lib64/python26.zip',
>     '/usr/lib64/python2.6',
>     '/usr/lib64/python2.6/plat-linux2',
>     '/usr/lib64/python2.6/lib-tk',
>     '/usr/lib64/python2.6/lib-old',
>     '/usr/lib64/python2.6/lib-dynload',
>     '/usr/lib64/python2.6/site-packages/gtk-2.0',
>     '/usr/lib64/python2.6/site-packages',
>     '/usr/lib/python2.6/site-packages']
> Module galaxy.web.framework.middleware.error:151 in __call__
>>>  app_iter = self.application(environ, sr_checker)
> Module paste.recursive:84 in __call__
>>>  return self.application(environ, start_response)
> Module galaxy.web.framework.middleware.remoteuser:143 in __call__
>>>  return self.app( environ, start_response )
> Module paste.httpexceptions:633 in __call__
>>>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:133 in __call__
>>>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:191 in handle_request
>>>  body = method( trans, **kwargs )
> Module galaxy.web.framework.decorators:68 in decorator
>>>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters
>>>  tool_filters = get_filter_mapping( saved_user_tool_filters,
>>> trans.app.config.user_tool_filters )
> Module galaxy.webapps.galaxy.controllers.user:1284 in
> get_filter_mapping
>>>  module = __import__( module_name, globals(),
>>> fromlist=['temp_module'] )
> ImportError: No module named examples
>
>
> Could you please provide me some help ?
> I have launched a git pull origin master before testing...
>
> Thank you.
>
> Fred
>
>
>
>
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/