1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/e7ec387cb3b3/ Changeset: e7ec387cb3b3 User: greg Date: 2014-04-22 17:45:10 Summary: More quickly stop the process of checking for migrated tools when starting Galaxy if there is no internet connection to the tool shed. Affected #: 1 file

diff -r db35188ff312ac07b608bb51eef668fc8691dde8 -r e7ec387cb3b3b8e6aaceade0c8bdd3da0077ac57 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -45,30 +45,37 @@ repository_name, REPOSITORY_OWNER, changeset_revision ) - # Accumulate all tool dependencies defined for repository dependencies for display to the user. - for rd_key, rd_tups in repository_dependencies_dict.items(): - if rd_key in [ 'root_key', 'description' ]: - continue - for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - parse_repository_dependency_tuple( rd_tup ) + if tool_shed_accessible: + # Accumulate all tool dependencies defined for repository dependencies for display to the user. + for rd_key, rd_tups in repository_dependencies_dict.items(): + if rd_key in [ 'root_key', 'description' ]: + continue + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + parse_repository_dependency_tuple( rd_tup ) + tool_shed_accessible, tool_dependencies = get_tool_dependencies( app, + tool_shed_url, + name, + owner, + changeset_revision ) + all_tool_dependencies = accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies ) tool_shed_accessible, tool_dependencies = get_tool_dependencies( app, tool_shed_url, - name, - owner, + repository_name, + REPOSITORY_OWNER, changeset_revision ) all_tool_dependencies = accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies ) - tool_shed_accessible, tool_dependencies = get_tool_dependencies( app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) - all_tool_dependencies = accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies ) - for tool_elem in elem.findall( 'tool' ): - tool_config_file_name = tool_elem.get( 'file' ) - if tool_config_file_name: - # We currently do nothing with repository dependencies except install them (we do not display repositories that will be - # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the - # future. - dependencies_dict = dict( tool_dependencies=all_tool_dependencies, - repository_dependencies=repository_dependencies ) - migrated_tool_configs_dict[ tool_config_file_name ] = dependencies_dict + for tool_elem in elem.findall( 'tool' ): + tool_config_file_name = tool_elem.get( 'file' ) + if tool_config_file_name: + # We currently do nothing with repository dependencies except install them (we do not display repositories that will be + # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the + # future. + dependencies_dict = dict( tool_dependencies=all_tool_dependencies, + repository_dependencies=repository_dependencies ) + migrated_tool_configs_dict[ tool_config_file_name ] = dependencies_dict + else: + break if tool_shed_accessible: # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. for tool_panel_config in tool_panel_configs:

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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