2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ca7110d33157/ Changeset: ca7110d33157 User: Dave Bouvier Date: 2013-11-14 22:31:34 Summary: Rebuild the list of sniffer elem classes after each one is removed from sniffer_elems, in order to keep the mapping current. Affected #: 1 file diff -r 51105146f487822cb1d38ba3396882d610e0282e -r ca7110d331571b4a3bbfdd75037053ea4c40b746 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -358,6 +358,7 @@ for index, s_e_c in enumerate( sniffer_elem_classes ): if sniffer_class == s_e_c: del self.sniffer_elems[ index ] + sniffer_elem_classes = [ e.attrib[ 'type' ] for e in self.sniffer_elems ] self.log.debug( "Removed sniffer element for datatype '%s'" % str( dtype ) ) break for sniffer_class in self.sniff_order: https://bitbucket.org/galaxy/galaxy-central/commits/093626ae621f/ Changeset: 093626ae621f Branch: stable User: greg Date: 2013-11-14 21:51:24 Summary: Display an error message rather than raising an exception when handling invalid complex repository dependencies in the Tool Shed. Affected #: 1 file diff -r e54372d60f111f4be26868ba416649697b551a13 -r 093626ae621f73b9cf904c935eddae98a8823839 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -142,14 +142,13 @@ # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> revised, repository_elem, error_message = handle_repository_dependency_elem( trans, sub_elem, unpopulate=unpopulate ) if error_message: - exception_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message - raise Exception( exception_message ) + error_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message if revised: elem[ sub_elem_index ] = repository_elem sub_elem_altered = True if not altered: altered = True - return altered, sub_elem_altered, elem + return altered, sub_elem_altered, elem, error_message def handle_directory_changes( trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): @@ -359,13 +358,16 @@ for package_index, package_elem in enumerate( root_elem ): if package_elem.tag == 'repository': # We have a complex repository dependency. - altered, package_altered, root_elem = handle_complex_repository_dependency_elem( trans, - root_elem, - package_index, - package_elem, - package_altered, - altered, - unpopulate=unpopulate ) + altered, package_altered, root_elem, message = \ + handle_complex_repository_dependency_elem( trans, + root_elem, + package_index, + package_elem, + package_altered, + altered, + unpopulate=unpopulate ) + if message: + error_message += message elif package_elem.tag == 'install': # <install version="1.0"> for actions_index, actions_elem in enumerate( package_elem ): @@ -392,7 +394,7 @@ for last_actions_elem_package_index, last_actions_elem_package_elem in enumerate( last_actions_elem ): if last_actions_elem_package_elem.tag == 'repository': # We have a complex repository dependency. - altered, last_actions_package_altered, last_actions_elem = \ + altered, last_actions_package_altered, last_actions_elem, message = \ handle_complex_repository_dependency_elem( trans, last_actions_elem, last_actions_elem_package_index, @@ -400,6 +402,8 @@ last_actions_package_altered, altered, unpopulate=unpopulate ) + if message: + error_message += message if last_actions_package_altered: last_actions_elem[ last_actions_elem_package_index ] = last_actions_elem_package_elem actions_group_elem[ last_actions_index ] = last_actions_elem 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.