[galaxy-commits] commit/galaxy-central: greg: Minor fixes to the questionable install_repository_revisions method in Galaxy's tool_shed_repositories API controller.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4f4f7bd74074/ Changeset: 4f4f7bd74074 User: greg Date: 2013-03-29 16:22:10 Summary: Minor fixes to the questionable install_repository_revisions method in Galaxy's tool_shed_repositories API controller. Affected #: 1 file diff -r 93f069f8325ca3bd7aff1cfd8673efdb3b61b4d5 -r 4f4f7bd74074090bd0192e76e361d42d9db70060 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -271,11 +271,13 @@ It's questionable whether this method is needed as the above method for installing a single repository can probably cover all desired scenarios. We'll keep this one around just in case... + :param key: the current Galaxy admin user's API key + + The following parameters are included in the payload. :param tool_shed_urls: the base URLs of the Tool Sheds from which to install a specified Repository :param names: the names of the Repositories to be installed :param owners: the owners of the Repositories to be installed :param changset_revisions: the changset_revisions of each RepositoryMetadata object associated with each Repository to be installed - :param key: the current Galaxy admin user's API key :param new_tool_panel_section_label: optional label of a new section to be added to the Galaxy tool panel in which to load tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string, as both cannot be used. @@ -283,6 +285,16 @@ If not set, tools will be loaded outside of any sections in the tool panel. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string, as both cannot be used. + :param install_repository_dependencies (optional): Set to True if you want to install repository dependencies defined for the specified + repository being installed. The default setting is False. + :param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being + installed. The default setting is False. + :param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file + (e.g., universe_wsgi.ini). At least one shed-related tool panel config file is required to be configured. Setting + this parameter to a specific file enables you to choose where the specified repository will be installed because + the tool_path attribute of the <toolbox> from the specified file is used as the installation location + (e.g., <toolbox tool_path="../shed_tools">). If this parameter is not set, a shed-related tool panel configuration + file will be selected automatically. """ if not suc.have_shed_tool_conf_for_install( trans ): # This Galaxy instance is not configured with a shed-related tool panel configuration file. @@ -312,7 +324,7 @@ # forcing all repositories to use the same settings. install_repository_dependencies = payload.get( 'install_repository_dependencies', False ) install_tool_dependencies = payload.get( 'install_tool_dependencies', False ) - new_tool_panel_section = payload.get( 'new_tool_panel_section_label', '' ) + new_tool_panel_section_label = payload.get( 'new_tool_panel_section_label', '' ) shed_tool_conf = payload.get( 'shed_tool_conf', None ) tool_path = payload.get( 'tool_path', None ) tool_panel_section_id = payload.get( 'tool_panel_section_id', '' ) @@ -323,12 +335,11 @@ current_payload[ 'name' ] = names[ index ] current_payload[ 'owner' ] = owners[ index ] current_payload[ 'changeset_revision' ] = changeset_revisions[ index ] + current_payload[ 'new_tool_panel_section_label' ] = new_tool_panel_section_label + current_payload[ 'tool_panel_section_id' ] = tool_panel_section_id current_payload[ 'install_repository_dependencies' ] = install_repository_dependencies current_payload[ 'install_tool_dependencies' ] = install_tool_dependencies - current_payload[ 'new_tool_panel_section' ] = new_tool_panel_section current_payload[ 'shed_tool_conf' ] = shed_tool_conf - current_payload[ 'tool_path' ] = tool_path - current_payload[ 'tool_panel_section_id' ] = tool_panel_section_id installed_tool_shed_repositories = self.install_repository_revision( trans, **current_payload ) if isinstance( installed_tool_shed_repositories, dict ): # We encountered an error. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.