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 <yves.gagnon@dnalandmarks.ca>
To:        <galaxy-dev@lists.galaxyproject.org>
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 <galaxy-dev-bounces@lists.galaxyproject.org>

---

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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