1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5f3a470e7501/ changeset: 5f3a470e7501 user: greg date: 2012-12-20 20:26:27 summary: Fixes for handling tool dependency installation into a Galaxy instance. affected #: 2 files diff -r 276c47b70c285fe9bee6aef86e65ca9463b661ae -r 5f3a470e75017b36e3fe37e5343043c551b7a2cd lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -79,7 +79,14 @@ invalid_tools, missing_tool_dependencies, readme_files_dict, repository_dependencies, tool_dependencies, valid_tools, workflows ): """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy.""" - containers_dict = dict( readme_files=None, repository_dependencies=None, tool_dependencies=None ) + containers_dict = dict( datatypes=None, + invalid_tools=None, + missing_tool_dependencies=None, + readme_files=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) lock = threading.Lock() lock.acquire( True ) if tool_dependencies: diff -r 276c47b70c285fe9bee6aef86e65ca9463b661ae -r 5f3a470e75017b36e3fe37e5343043c551b7a2cd lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1258,17 +1258,6 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) - log.debug("PPPPP In prepare_for_install, containers_dict: %s" % str( containers_dict )) - """ - PPPPP In prepare_for_install, - containers_dict: - {'repository_dependencies': None, - 'missing_tool_dependencies': <galaxy.webapps.community.util.container_util.Folder object at 0x108a56f0>, - 'readme_files': None, - 'tool_dependencies': None} - FAIL - - """ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, @@ -1538,9 +1527,10 @@ valid_tools = metadata.get( 'tools', None ) workflows = metadata.get( 'workflows', None ) # All tool dependencies will be considered missing since we are reinstalling the repository. - for td in tool_dependencies: - missing_tool_dependencies.append( td ) - tool_dependencies = None + if tool_dependencies: + for td in tool_dependencies: + missing_tool_dependencies.append( td ) + tool_dependencies = None containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=tool_shed_repository.name, 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.