Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Pierre Lindenbaum 

That worked !
Many thanks !

At the top of the 'manage installed tools' page there is a filter that 
hides uninstalled and deactivated tools. Click 'advanced search' and 
then 'Deactivated or uninstalled'. Do you see your tool deactivated there?


M.

On Wed, Oct 19, 2016 at 9:49 AM Pierre Lindenbaum 
> wrote:


On 10/19/2016 03:36 PM, Martin Čech wrote:
> Hi Pierre,
>
> It seems that instead of uninstalling you de-activated the
repository.
> I would uninstall the repository again.

  admin > manage installed tools > there is no tool installed.


Search toolshed > select > >> preview and install > "Install to
Galaxy"
 > all unchecked / empty ; submit > ERROR


Pierre



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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Martin Čech 
At the top of the 'manage installed tools' page there is a filter that
hides uninstalled and deactivated tools. Click 'advanced search' and then
'Deactivated or uninstalled'. Do you see your tool deactivated there?

M.

On Wed, Oct 19, 2016 at 9:49 AM Pierre Lindenbaum <
pierre.lindenb...@univ-nantes.fr> wrote:

> On 10/19/2016 03:36 PM, Martin Čech wrote:
> > Hi Pierre,
> >
> > It seems that instead of uninstalling you de-activated the repository.
> > I would uninstall the repository again.
>
>   admin > manage installed tools > there is no tool installed.
>
>
> Search toolshed > select > >> preview and install > "Install to Galaxy"
>  > all unchecked / empty ; submit > ERROR
>
>
> Pierre
>
>
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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Pierre Lindenbaum 

On 10/19/2016 03:36 PM, Martin Čech wrote:

Hi Pierre,

It seems that instead of uninstalling you de-activated the repository. 
I would uninstall the repository again.


 admin > manage installed tools > there is no tool installed.


Search toolshed > select > >> preview and install > "Install to Galaxy" 
> all unchecked / empty ; submit > ERROR



Pierre

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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Martin Čech 
Hi Pierre,

It seems that instead of uninstalling you de-activated the repository. I
would uninstall the repository again. Please mind that there is this UX
hurdle when you want to uninstall - you have to _check_ the checkbox
labeled "Check to uninstall or leave blank to deactivate" that is in the
bottom of the uninstall page.

Hope this helps and please let us know when it does not.

Thanks,

Martin



On Wed, Oct 19, 2016 at 9:29 AM Pierre Lindenbaum <
pierre.lindenb...@univ-nantes.fr> wrote:

> On 10/19/2016 03:23 PM, Martin Čech wrote:
> > Hi Pierre,
> >
> > how old is your Tool Shed? When was the last time a tool installation
> > from it succeeded?
> >
>
> Hi martin,
>
> here is the log from the toolshed :
>
> commit 73f46f4e08141f78927056fa3e4709d0ab323972
> Merge: 05e6682 27dc31a
> Author: Nicola Soranzo
> Date:   Wed Nov 18 10:06:53 2015 +
>
>
> I was able to install my tool from this toolshed a few minutes ago.
> The second attempt failed.
>
> Thanks for the helps,
>
> Pierre
>
>
> > thanks
> >
> > M.
> >
> > On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum
> >  > > wrote:
> >
> > Hi all, I got a "Internal Server Error" ==> "KeyError:
> > 'tool_panel_section' " when I'm trying to install a new tool from our
> > toolshed (see stacktrace below).
> >
> > My galaxy instance was cloned from
> >
> >
> > commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
> > Merge: 056a7e0 ad0d0bc
> > Author: Björn Grüning  > >
> > Date:   Mon Oct 10 10:23:37 2016 +0200
> >
> > with only a few minor(?) (admin...) modifications under config/*
> > This error was raised when I've removed + re-installed a tool from
> the
> > toolshed.
> >
> > How can I fix this ?
> >
> > Thanks
> >
> > Pierre
> >
> >
> > 127.0.0.1 - - [19/Oct/2016:15:15:44 +0200] "POST
> > /admin_toolshed/prepare_for_install HTTP/1.1" 500 -
> > "
> http://127.0.0.1:8080/admin_toolshed/prepare_for_install?changeset_revisions=a38c6719c9c3&repository_ids=9b8af19fb3feae8b&tool_shed_url=http%3A%2F%2Fmasked.host.fr%2Ftoolshed%2F
> "
> > "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101
> > Firefox/49.0"
> > Error - : 'tool_panel_section'
> > URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/middleware/error.py',
> > line 151 in __call__
> >app_iter = self.application(environ, sr_checker)
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/recursive.py',
> > line 85 in __call__
> >return self.application(environ, start_response)
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py',
> > line 640 in __call__
> >return self.application(environ, start_response)
> > File
> >
>  '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
> > line 135 in __call__
> >return self.handle_request( environ, start_response )
> > File
> >
>  '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
> > line 194 in handle_request
> >body = method( trans, **kwargs )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/decorators.py',
> > line 98 in decorator
> >return func( self, trans, *args, **kwargs )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> > line 1080 in prepare_for_install
> >install_repository_manager.handle_tool_shed_repositories(
> > installation_dict )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/install_manager.py',
> > line 633 in handle_tool_shed_repositories
> >new_tool_panel_section_label=new_tool_panel_section_label )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py',
> > line 198 in create_repository_dependency_objects
> >  self.app.installed_repository_manager.activate_repository(
> > repository_db_record )
> > File
> >
>  
> '/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/installed_repository_manager.py',
> > line 94 in activate_repository
> >tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
> > KeyError: 'tool_panel_section'
> >
>
>
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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Pierre Lindenbaum 

On 10/19/2016 03:23 PM, Martin Čech wrote:

Hi Pierre,

how old is your Tool Shed? When was the last time a tool installation 
from it succeeded?




Hi martin,

here is the log from the toolshed :

   commit 73f46f4e08141f78927056fa3e4709d0ab323972
   Merge: 05e6682 27dc31a
   Author: Nicola Soranzo
   Date:   Wed Nov 18 10:06:53 2015 +


I was able to install my tool from this toolshed a few minutes ago.
The second attempt failed.

Thanks for the helps,

Pierre



thanks

M.

On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum 
> wrote:


Hi all, I got a "Internal Server Error" ==> "KeyError:
'tool_panel_section' " when I'm trying to install a new tool from our
toolshed (see stacktrace below).

My galaxy instance was cloned from


commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
Merge: 056a7e0 ad0d0bc
Author: Björn Grüning mailto:bjo...@gruenings.eu>>
Date:   Mon Oct 10 10:23:37 2016 +0200

with only a few minor(?) (admin...) modifications under config/*
This error was raised when I've removed + re-installed a tool from the
toolshed.

How can I fix this ?

Thanks

Pierre


127.0.0.1 - - [19/Oct/2016:15:15:44 +0200] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 500 -

"http://127.0.0.1:8080/admin_toolshed/prepare_for_install?changeset_revisions=a38c6719c9c3&repository_ids=9b8af19fb3feae8b&tool_shed_url=http%3A%2F%2Fmasked.host.fr%2Ftoolshed%2F";
"Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101
Firefox/49.0"
Error - : 'tool_panel_section'
URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/middleware/error.py',
line 151 in __call__
   app_iter = self.application(environ, sr_checker)
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/recursive.py',
line 85 in __call__
   return self.application(environ, start_response)
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__
   return self.application(environ, start_response)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
line 135 in __call__
   return self.handle_request( environ, start_response )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
line 194 in handle_request
   body = method( trans, **kwargs )
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/decorators.py',
line 98 in decorator
   return func( self, trans, *args, **kwargs )
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1080 in prepare_for_install
   install_repository_manager.handle_tool_shed_repositories(
installation_dict )
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/install_manager.py',
line 633 in handle_tool_shed_repositories
   new_tool_panel_section_label=new_tool_panel_section_label )
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py',
line 198 in create_repository_dependency_objects
 self.app.installed_repository_manager.activate_repository(
repository_db_record )
File

'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/installed_repository_manager.py',
line 94 in activate_repository
   tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
KeyError: 'tool_panel_section'



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Re: [galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Martin Čech 
Hi Pierre,

how old is your Tool Shed? When was the last time a tool installation from
it succeeded?

thanks

M.

On Wed, Oct 19, 2016 at 9:20 AM Pierre Lindenbaum <
pierre.lindenb...@univ-nantes.fr> wrote:

Hi all, I got a "Internal Server Error" ==> "KeyError:
'tool_panel_section' " when I'm trying to install a new tool from our
toolshed (see stacktrace below).

My galaxy instance was cloned from


commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
Merge: 056a7e0 ad0d0bc
Author: Björn Grüning 
Date:   Mon Oct 10 10:23:37 2016 +0200

with only a few minor(?) (admin...) modifications under config/*
This error was raised when I've removed + re-installed a tool from the
toolshed.

How can I fix this ?

Thanks

Pierre


127.0.0.1 - - [19/Oct/2016:15:15:44 +0200] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 500 -
"
http://127.0.0.1:8080/admin_toolshed/prepare_for_install?changeset_revisions=a38c6719c9c3&repository_ids=9b8af19fb3feae8b&tool_shed_url=http%3A%2F%2Fmasked.host.fr%2Ftoolshed%2F
"
"Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101 Firefox/49.0"
Error - : 'tool_panel_section'
URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/middleware/error.py',
line 151 in __call__
   app_iter = self.application(environ, sr_checker)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/recursive.py',
line 85 in __call__
   return self.application(environ, start_response)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__
   return self.application(environ, start_response)
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
line 135 in __call__
   return self.handle_request( environ, start_response )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py',
line 194 in handle_request
   body = method( trans, **kwargs )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/decorators.py',
line 98 in decorator
   return func( self, trans, *args, **kwargs )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1080 in prepare_for_install
   install_repository_manager.handle_tool_shed_repositories(
installation_dict )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/install_manager.py',
line 633 in handle_tool_shed_repositories
   new_tool_panel_section_label=new_tool_panel_section_label )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py',
line 198 in create_repository_dependency_objects
   self.app.installed_repository_manager.activate_repository(
repository_db_record )
File
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/installed_repository_manager.py',
line 94 in activate_repository
   tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
KeyError: 'tool_panel_section'

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[galaxy-dev] KeyError: 'tool_panel_section' when installing a new tool

2016-10-19 Thread Pierre Lindenbaum 
Hi all, I got a "Internal Server Error" ==> "KeyError: 
'tool_panel_section' " when I'm trying to install a new tool from our 
toolshed (see stacktrace below).


My galaxy instance was cloned from


   commit 217854827ac7dfc88c5388cd2ecb24fffd86c060
   Merge: 056a7e0 ad0d0bc
   Author: Björn Grüning 
   Date:   Mon Oct 10 10:23:37 2016 +0200

with only a few minor(?) (admin...) modifications under config/*
This error was raised when I've removed + re-installed a tool from the 
toolshed.


How can I fix this ?

Thanks

Pierre


127.0.0.1 - - [19/Oct/2016:15:15:44 +0200] "POST 
/admin_toolshed/prepare_for_install HTTP/1.1" 500 - 
"http://127.0.0.1:8080/admin_toolshed/prepare_for_install?changeset_revisions=a38c6719c9c3&repository_ids=9b8af19fb3feae8b&tool_shed_url=http%3A%2F%2Fmasked.host.fr%2Ftoolshed%2F"; 
"Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:49.0) Gecko/20100101 Firefox/49.0"

Error - : 'tool_panel_section'
URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/middleware/error.py', 
line 151 in __call__

  app_iter = self.application(environ, sr_checker)
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/recursive.py', 
line 85 in __call__

  return self.application(environ, start_response)
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', 
line 640 in __call__

  return self.application(environ, start_response)
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py', 
line 135 in __call__

  return self.handle_request( environ, start_response )
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/base.py', 
line 194 in handle_request

  body = method( trans, **kwargs )
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/web/framework/decorators.py', 
line 98 in decorator

  return func( self, trans, *args, **kwargs )
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', 
line 1080 in prepare_for_install
  install_repository_manager.handle_tool_shed_repositories( 
installation_dict )
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/install_manager.py', 
line 633 in handle_tool_shed_repositories

  new_tool_panel_section_label=new_tool_panel_section_label )
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py', 
line 198 in create_repository_dependency_objects
  self.app.installed_repository_manager.activate_repository( 
repository_db_record )
File 
'/home/lindenb/tmp/GALAXY/galaxy.gitlab/lib/tool_shed/galaxy_install/installed_repository_manager.py', 
line 94 in activate_repository

  tool_panel_dict = repository.metadata[ 'tool_panel_section' ]
KeyError: 'tool_panel_section'

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