1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/a7101734b29e/ Changeset: a7101734b29e User: greg Date: 2014-01-08 21:27:25 Summary: Fix for pruning content from the tool shed's repository dependencies container. Affected #: 1 file

diff -r 8ee5977b21731ee1815995bbcc290b09a46a13cc -r a7101734b29e8ff8aff0a8170bb8d0c5ec1a5455 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -744,7 +744,8 @@ lock.release() return containers_dict

-def build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata, exclude=None ): +def build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata, + exclude=None ): """Return a dictionary of containers for the received repository's dependencies and contents for display in the tool shed.""" if exclude is None: exclude = [] @@ -806,11 +807,12 @@ containers_dict[ 'readme_files' ] = readme_files_root_folder if 'repository_dependencies' not in exclude: # Repository dependencies container. - folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( trans=trans, - folder_id=folder_id, - repository_dependencies=repository_dependencies, - label='Repository dependencies', - installed=False ) + folder_id, repository_dependencies_root_folder = \ + build_repository_dependencies_folder( trans=trans, + folder_id=folder_id, + repository_dependencies=repository_dependencies, + label='Repository dependencies', + installed=False ) if repository_dependencies_root_folder: containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Tool dependencies container. @@ -868,11 +870,13 @@ if metadata: if 'data_manager' not in exclude and 'data_manager' in metadata: data_managers = metadata['data_manager'].get( 'data_managers', None ) - folder_id, data_managers_root_folder = build_data_managers_folder( trans, folder_id, data_managers, label="Data Managers" ) + folder_id, data_managers_root_folder = \ + build_data_managers_folder( trans, folder_id, data_managers, label="Data Managers" ) containers_dict[ 'valid_data_managers' ] = data_managers_root_folder error_messages = metadata['data_manager'].get( 'error_messages', None ) data_managers = metadata['data_manager'].get( 'invalid_data_managers', None ) - folder_id, data_managers_root_folder = build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) + folder_id, data_managers_root_folder = \ + build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder except Exception, e: log.exception( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) @@ -890,15 +894,22 @@ folder_id += 1 # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] - repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) + repository_dependencies_folder = Folder( id=folder_id, + key=repository_dependencies_folder_key, + label=label, + parent=repository_dependencies_root_folder ) del repository_dependencies[ 'root_key' ] - # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more repository_dependency keys. - # We want the description value associated with the repository_dependencies_folder. + # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more + # repository_dependency keys. We want the description value associated with the repository_dependencies_folder. repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) del repository_dependencies[ 'description' ] repository_dependencies_folder, folder_id, repository_dependency_id = \ - populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ) + populate_repository_dependencies_container( trans, + repository_dependencies_folder, + repository_dependencies, + folder_id, + repository_dependency_id ) repository_dependencies_folder = prune_repository_dependencies( repository_dependencies_folder ) else: repository_dependencies_root_folder = None @@ -985,11 +996,13 @@ tools_root_folder = None return folder_id, tools_root_folder

-def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False, reinstalling=False ): +def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, + new_install=False, reinstalling=False ): """Return a folder hierarchy containing tool dependencies.""" - # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, they are considered missing. The tool - # dependency status will be displayed only if a record exists for the tool dependency in the Galaxy database, but the tool dependency is not installed. - # The value for new_install will be True only if the associated repository in being installed for the first time. This value is used in setting the + # When we're in Galaxy (not the tool shed) and the tool dependencies are not installed or are in an error state, + # they are considered missing. The tool dependency status will be displayed only if a record exists for the tool + # dependency in the Galaxy database, but the tool dependency is not installed. The value for new_install will be + # True only if the associated repository in being installed for the first time. This value is used in setting the # container description. if tool_dependencies: tool_dependency_id = 0 @@ -1138,7 +1151,10 @@ else: containing_folder = tool_test_results_root_folder folder_id += 1 - test_environment_folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + test_environment_folder = Folder( id=folder_id, + key='test_environment', + label='Automated test environment', + parent=containing_folder ) containing_folder.folders.append( test_environment_folder ) try: architecture = test_environment_dict.get( 'architecture', '' ) @@ -1184,7 +1200,10 @@ passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if len( passed_tests_dicts ) > 0: folder_id += 1 - passed_tests_folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=containing_folder ) + passed_tests_folder = Folder( id=folder_id, + key='passed_tests', + label='Tests that passed successfully', + parent=containing_folder ) containing_folder.folders.append( passed_tests_folder ) passed_test_id = 0 for passed_tests_dict in passed_tests_dicts: @@ -1395,7 +1414,8 @@ rd_tool_shed = str( repository_dependency_successful_installation_dict.get( 'tool_shed', '' ) ) rd_name = str( repository_dependency_successful_installation_dict.get( 'name', '' ) ) rd_owner = str( repository_dependency_successful_installation_dict.get( 'owner', '' ) ) - rd_changeset_revision = str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) + rd_changeset_revision = \ + str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) except Exception, e: rd_tool_shed = 'unknown' rd_name = 'unknown' @@ -1495,7 +1515,8 @@ # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", # "installation_errors", "missing_test_components" "skipped_tests", "not_tested" or any other # entry that may be added in the future. - display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', 'not_tested', 'passed_tests', 'skipped_tests' ] + display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', + 'not_tested', 'passed_tests', 'skipped_tests' ] for k, v in tool_test_results_dict.items(): if k in display_entries: # We've discovered an entry that can be displayed, so see if it has a value since displaying @@ -1506,8 +1527,9 @@

def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): """ - Change any empty folders contained within the repository dependencies container into a repository dependency since it has no repository dependencies - of it's own. This method is not used (and may not be needed), but here it is just in case. + Change any empty folders contained within the repository dependencies container into a repository dependency + since it has no repository dependencies of it's own. This method is not used (and may not be needed), but here + it is just in case. """ if not folder.folders and not folder.repository_dependencies: repository_dependency_id += 1 @@ -1519,10 +1541,14 @@ return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id ) return folder, repository_dependency_id

-def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, prior_installation_required, - only_if_compiling_contained_td, key ): +def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, + prior_installation_required, only_if_compiling_contained_td, key ): """Return a repository dependency label based on the repository dependency key.""" - if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key ): + if key_is_current_repositorys_key( repository_name, + repository_owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, key ): label = 'Repository dependencies' else: if galaxy.util.asbool( prior_installation_required ): @@ -1533,8 +1559,8 @@ ( repository_name, changeset_revision, repository_owner, prior_installation_required_str ) return label

-def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required, - only_if_compiling_contained_td ): +def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, + prior_installation_required, only_if_compiling_contained_td ): """Assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported.""" return '%s%s%s%s%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ), STRSEP, @@ -1551,13 +1577,6 @@ def generate_tool_dependencies_key( name, version, type ): return '%s%s%s%s%s' % ( str( name ), STRSEP, str( version ), STRSEP, str( type ) )

-def get_folder( folder, key ): - if folder.key == key: - return folder - for sub_folder in folder.folders: - return get_folder( sub_folder, key ) - return None - def get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ): """Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page.""" # Default prior_installation_required and only_if_compiling_contained_td to False. @@ -1610,7 +1629,15 @@ # For backward compatibility to the 12/20/12 Galaxy release we have to return the following, and callers must handle exceptions. return toolshed_base_url, repository_name, repository_owner, changeset_revision

-def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ): +def get_folder( folder, key ): + if folder.key == key: + return folder + for sub_folder in folder.folders: + return get_folder( sub_folder, key ) + return None + +def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, + repository_dependency_id, folder_keys ): repository_components_tuple = get_components_from_key( rd_key ) components_list = suc.extract_components_from_tuple( repository_components_tuple ) toolshed, repository_name, repository_owner, changeset_revision = components_list[ 0:4 ] @@ -1713,11 +1740,21 @@ return True return False

-def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ): - folder_keys = repository_dependencies.keys() +def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, + repository_dependency_id ): + folder_keys = [] + for key in repository_dependencies.keys(): + if key not in folder_keys: + folder_keys.append( key ) for key, value in repository_dependencies.items(): repository_dependencies_folder, folder_id, repository_dependency_id = \ - handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, key, value, folder_id, repository_dependency_id, folder_keys ) + handle_repository_dependencies_container_entry( trans, + repository_dependencies_folder, + key, + value, + folder_id, + repository_dependency_id, + folder_keys ) return repository_dependencies_folder, folder_id, repository_dependency_id

def print_folders( pad, folder ): @@ -1731,19 +1768,22 @@ for sub_folder in folder.folders: print_folders( pad+5, sub_folder )

+def prune_folder( folder, repository_dependency ): + listified_repository_dependency = repository_dependency.listify + if is_subfolder_of( folder, listified_repository_dependency ): + folder.repository_dependencies.remove( repository_dependency ) + def prune_repository_dependencies( folder ): """ - Since the object used to generate a repository dependencies container is a dictionary and not an odict() (it must be json-serialize-able), the - order in which the dictionary is processed to create the container sometimes results in repository dependency entries in a folder that also - includes the repository dependency as a sub-folder (if the repository dependency has it's own repository dependency). This method will remove - all repository dependencies from folder that are also sub-folders of folder. + Since the object used to generate a repository dependencies container is a dictionary and not an odict() (it must be + json-serialize-able), the order in which the dictionary is processed to create the container sometimes results in + repository dependency entries in a folder that also includes the repository dependency as a sub-folder (if the + repository dependency has it's own repository dependency). This method will remove all repository dependencies from + folder that are also sub-folders of folder. """ repository_dependencies = [ rd for rd in folder.repository_dependencies ] for repository_dependency in repository_dependencies: - listified_repository_dependency = repository_dependency.listify - if is_subfolder_of( folder, listified_repository_dependency ): - repository_dependencies.remove( repository_dependency ) - folder.repository_dependencies = repository_dependencies + prune_folder( folder, repository_dependency ) for sub_folder in folder.folders: return prune_repository_dependencies( sub_folder ) return folder

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

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