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.gag...@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-boun...@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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