KeyError: 'tool_panel_section' when installing a new tool
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 <bjoern@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 - <type 'exceptions.KeyError'>: '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'
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.lindenbaum@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 <bjoern@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 - <type 'exceptions.KeyError'>: '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' ___________________________________________________________ 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/
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 +0000 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 <pierre.lindenbaum@univ-nantes.fr <mailto:pierre.lindenbaum@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 <bjoern@gruenings.eu <mailto:bjoern@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 - <type 'exceptions.KeyError'>: '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'
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.lindenbaum@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 +0000
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 <pierre.lindenbaum@univ-nantes.fr <mailto:pierre.lindenbaum@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 <bjoern@gruenings.eu <mailto:bjoern@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 - <type 'exceptions.KeyError'>: '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'
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
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.lindenbaum@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
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 <pierre.lindenbaum@univ-nantes.fr <mailto:pierre.lindenbaum@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
participants (2)
-
Martin Čech -
Pierre Lindenbaum