1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/8c3ad449b21d/ changeset: 8c3ad449b21d user: greg date: 2012-12-20 01:39:50 summary: Fix for resintalling a single tool shed repository and fix for displaying the contents of an installed tool shed repository in Galaxy. affected #: 2 files

diff -r ddff35a4a9ab3cf22dad10c3b413f919d8d68022 -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -80,69 +80,68 @@ 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 ) - if readme_files_dict or repository_dependencies or tool_dependencies: - lock = threading.Lock() - lock.acquire( True ) + lock = threading.Lock() + lock.acquire( True ) + if tool_dependencies: + # Add the install_dir attribute to the tool_dependencies. + tool_dependencies = add_installation_directories_to_tool_dependencies( trans, + repository_name, + repository_owner, + changeset_revision, + tool_dependencies ) + try: + folder_id = 0 + # Datatypes container. + if datatypes: + folder_id, datatypes_root_folder = container_util.build_datatypes_folder( folder_id, datatypes ) + containers_dict[ 'datatypes' ] = datatypes_root_folder + # Invalid tools container. + if invalid_tools: + folder_id, invalid_tools_root_folder = container_util.build_invalid_tools_folder( folder_id, + invalid_tools, + changeset_revision, + repository=repository, + label='Invalid tools' ) + containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder + # Readme files container. + if readme_files_dict: + folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) + containers_dict[ 'readme_files' ] = readme_files_root_folder + # Repository dependencies container. + if repository_dependencies: + folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, + repository_name=repository_name, + repository_owner=repository_owner, + changeset_revision=changeset_revision, + folder_id=folder_id, + repository_dependencies=repository_dependencies ) + containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + # Tool dependencies container. if tool_dependencies: - # Add the install_dir attribute to the tool_dependencies. - tool_dependencies = add_installation_directories_to_tool_dependencies( trans, - repository_name, - repository_owner, - changeset_revision, - tool_dependencies ) - try: - folder_id = 0 - # Datatypes container. - if datatypes: - folder_id, datatypes_root_folder = container_util.build_datatypes_folder( folder_id, datatypes ) - containers_dict[ 'datatypes' ] = datatypes_root_folder - # Invalid tools container. - if invalid_tools: - folder_id, invalid_tools_root_folder = container_util.build_invalid_tools_folder( folder_id, - invalid_tools, - changeset_revision, - repository=repository, - label='Invalid tools' ) - containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder - # Readme files container. - if readme_files_dict: - folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) - containers_dict[ 'readme_files' ] = readme_files_root_folder - # Repository dependencies container. - if repository_dependencies: - folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, - repository_name=repository_name, - repository_owner=repository_owner, - changeset_revision=changeset_revision, - folder_id=folder_id, - repository_dependencies=repository_dependencies ) - containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder - # Tool dependencies container. - if tool_dependencies: - folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) - containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder - # Missing tool dependencies container. - if missing_tool_dependencies: - folder_id, missing_tool_dependencies_root_folder = \ - container_util.build_tool_dependencies_folder( folder_id, missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True ) - containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder - # Valid tools container. - if valid_tools: - folder_id, valid_tools_root_folder = container_util.build_tools_folder( folder_id, - valid_tools, - repository, - changeset_revision, - label='Valid tools', - description='click the name to inspect the tool metadata' ) - containers_dict[ 'valid_tools' ] = valid_tools_root_folder - # Workflows container. - if workflows: - folder_id, workflows_root_folder = container_util.build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) - containers_dict[ 'workflows' ] = workflows_root_folder - except Exception, e: - log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) - finally: - lock.release() + folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) + containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + # Missing tool dependencies container. + if missing_tool_dependencies: + folder_id, missing_tool_dependencies_root_folder = \ + container_util.build_tool_dependencies_folder( folder_id, missing_tool_dependencies, label='Missing tool dependencies', for_galaxy=True ) + containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder + # Valid tools container. + if valid_tools: + folder_id, valid_tools_root_folder = container_util.build_tools_folder( folder_id, + valid_tools, + repository, + changeset_revision, + label='Valid tools', + description='click the name to inspect the tool metadata' ) + containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Workflows container. + if workflows: + folder_id, workflows_root_folder = container_util.build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) + containers_dict[ 'workflows' ] = workflows_root_folder + except Exception, e: + log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) + finally: + lock.release() return containers_dict def build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata ): """Return a dictionary of containers for the received repository's dependencies and contents for display in the tool shed."""

diff -r ddff35a4a9ab3cf22dad10c3b413f919d8d68022 -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d 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 @@ -1365,10 +1365,7 @@ ctx_rev = suc.get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) repo_info_dicts = [] repo_info_dict = kwd.get( 'repo_info_dict', None ) - if repo_info_dict: - # The repo_info_dict should be encoded. - repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) - else: + if not repo_info_dict: # Entering this if block used to happen only if the tool_shed_repository does not include any valid tools. After repository dependencies # were introduced, it may never happen, but we'll keep the block just in case. if install_repository_dependencies:

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

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