Oct '14 and Jan'15 release, trouble installing tools from the toolshed, resetting metadata for installed repositories

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Oct '14 and Jan'15 release, trouble installing tools from the toolshed, resetting metadata for installed repositories

Yves Gagnon
Hello fellow galaxy users :

I noticed that trying to install some tools from the main toolshed, sometimes it works, others it does not.  In a specific case, trying to install clustalw and its dependency, I get this error message :

URL: (redactedURL)/admin_toolshed/prepare_for_install
File '(redacted path)/galaxy_dist_dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File '(redacted path)/galaxy_dist_dev/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '(redacted path)/galaxy_dist_dev/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/base.py', line 132 in __call__
  return self.handle_request( environ, start_response )
File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/base.py', line 190 in handle_request
  body = method( trans, **kwargs )
File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/decorators.py', line 87 in decorator
  return func( self, trans, *args, **kwargs )
File '(redacted path)/galaxy_dist_dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1095 in prepare_for_install
  install_repository_manager.handle_tool_shed_repositories( installation_dict, using_api=False )
File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/install_manager.py', line 636 in handle_tool_shed_repositories
  new_tool_panel_section_label=new_tool_panel_section_label )
File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py', line 200 in create_repository_dependency_objects
  self.app.installed_repository_manager.activate_repository( repository_db_record )
File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/installed_repository_manager.py', line 90 in activate_repository
  repository_tools_tups = irmm.get_repository_tools_tups()
File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 69 in get_repository_tools_tups
  index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) )
TypeError: 'NoneType' object is not iterable



Same goes for resetting all metadata on installed repositories after update, 23 out of ~200 tools work, for the rest I get this error in paster.log :



tool_shed.galaxy_install.metadata.installed_repository_metadata_manager ERROR 2015-01-20 15:18:35,357 Error attempting to reset metadata on repository tabular_to_fasta
Traceback (most recent call last):
  File "(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 114, in reset_metadata_on_selected_repositories
    self.set_repository( repository )
  File "(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 142, in set_repository
    super( InstalledRepositoryMetadataManager, self ).set_repository( repository )
  File "(redacted path)/galaxy_dist_dev/lib/tool_shed/metadata/metadata_generator.py", line 1066, in set_repository
    self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) }
AttributeError: 'NoneType' object has no attribute 'get'


My galaxy contains this line for tool_conf files, and I moved all config files from the distrib root to the config folder:

tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml

Did I do something wrong while updating to the latest releases???

Thanks for your help!

Yves Gagnon


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Re: Oct '14 and Jan'15 release, trouble installing tools from the toolshed, resetting metadata for installed repositories

Yves Gagnon
Just an update on that.  
I found out that if I put back the migrated_tool_conf.xml and shed_tool_conf.xml back in the galaxy_dist root, I can now reset metadata on most of the repositories (but not all)

Same error as before pops up in paster.log for those not working.

Cheers!

Yves Gagnon





From:        Yves Gagnon <[hidden email]>
To:        <[hidden email]>
Date:        20/01/2015 03:26 PM
Subject:        [galaxy-dev] Oct '14 and Jan'15  release, trouble installing tools from the toolshed, resetting metadata for installed repositories
Sent by:        galaxy-dev <[hidden email]>




Hello fellow galaxy users :

I noticed that trying to install some tools from the main toolshed, sometimes it works, others it does not.  In a specific case, trying to install clustalw and its dependency, I get this error message :


URL: (redactedURL)/admin_toolshed/prepare_for_install

File '(redacted path)/galaxy_dist_dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond

 app_iter = self.application(environ, detect_start_response)

File '(redacted path)/galaxy_dist_dev/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__

 return self.application(environ, start_response)

File '(redacted path)/galaxy_dist_dev/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__

 return self.application(environ, start_response)

File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/base.py', line 132 in __call__

 return self.handle_request( environ, start_response )

File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/base.py', line 190 in handle_request

 body = method( trans, **kwargs )

File '(redacted path)/galaxy_dist_dev/lib/galaxy/web/framework/decorators.py', line 87 in decorator

 return func( self, trans, *args, **kwargs )

File '(redacted path)/galaxy_dist_dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1095 in prepare_for_install

 install_repository_manager.handle_tool_shed_repositories( installation_dict, using_api=False )

File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/install_manager.py', line 636 in handle_tool_shed_repositories

 new_tool_panel_section_label=new_tool_panel_section_label )

File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py', line 200 in create_repository_dependency_objects

 self.app.installed_repository_manager.activate_repository( repository_db_record )

File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/installed_repository_manager.py', line 90 in activate_repository

 repository_tools_tups = irmm.get_repository_tools_tups()

File '(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py', line 69 in get_repository_tools_tups

 index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) )

TypeError: 'NoneType' object is not iterable




Same goes for resetting all metadata on installed repositories after update, 23 out of ~200 tools work, for the rest I get this error in paster.log :




tool_shed.galaxy_install.metadata.installed_repository_metadata_manager ERROR 2015-01-20 15:18:35,357 Error attempting to reset metadata on repository tabular_to_fasta

Traceback (most recent call last):

 File "(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 114, in reset_metadata_on_selected_repositories

   self.set_repository( repository )

 File "(redacted path)/galaxy_dist_dev/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 142, in set_repository

   super( InstalledRepositoryMetadataManager, self ).set_repository( repository )

 File "(redacted path)/galaxy_dist_dev/lib/tool_shed/metadata/metadata_generator.py", line 1066, in set_repository

   self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) }

AttributeError: 'NoneType' object has no attribute 'get'



My galaxy contains this line for tool_conf files, and I moved all config files from the distrib root to the config folder:


tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml


Did I do something wrong while updating to the latest releases???


Thanks for your help!


Yves Gagnon
___________________________________________________________
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/