Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

tool_shed.utility_containers package

class tool_shed.utility_containers.FailedTest(id=None, stderr=None, test_id=None, tool_id=None, tool_version=None, traceback=None)

Bases: object

Failed tool tests object

__init__(id=None, stderr=None, test_id=None, tool_id=None, tool_version=None, traceback=None)

class tool_shed.utility_containers.InvalidRepositoryDependency(id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, only_if_compiling_contained_td=False, error=None)

Bases: object

Invalid repository dependency definition object

__init__(id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, only_if_compiling_contained_td=False, error=None)

class tool_shed.utility_containers.InvalidToolDependency(id=None, name=None, version=None, type=None, error=None)

Bases: object

Invalid tool dependency definition object

__init__(id=None, name=None, version=None, type=None, error=None)

class tool_shed.utility_containers.MissingTestComponent(id=None, missing_components=None, tool_guid=None, tool_id=None, tool_version=None)

Bases: object

Missing tool test components object

__init__(id=None, missing_components=None, tool_guid=None, tool_id=None, tool_version=None)

class tool_shed.utility_containers.NotTested(id=None, reason=None)

Bases: object

NotTested object

__init__(id=None, reason=None)

class tool_shed.utility_containers.PassedTest(id=None, test_id=None, tool_id=None, tool_version=None)

Bases: object

Passed tool tests object

__init__(id=None, test_id=None, tool_id=None, tool_version=None)

class tool_shed.utility_containers.RepositoryInstallationError(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None, error_message=None)

Bases: object

Repository installation error object

__init__(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None, error_message=None)

class tool_shed.utility_containers.RepositorySuccessfulInstallation(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None)

Bases: object

Repository installation object

__init__(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None)

class tool_shed.utility_containers.ToolDependencyInstallationError(id=None, type=None, name=None, version=None, error_message=None)

Bases: object

Tool dependency installation error object

__init__(id=None, type=None, name=None, version=None, error_message=None)

class tool_shed.utility_containers.ToolDependencySuccessfulInstallation(id=None, type=None, name=None, version=None, installation_directory=None)

Bases: object

Tool dependency installation object

__init__(id=None, type=None, name=None, version=None, installation_directory=None)

class tool_shed.utility_containers.ToolShedUtilityContainerManager(app)

Bases: tool_shed.utility_containers.utility_container_manager.UtilityContainerManager

__init__(app)

build_invalid_repository_dependencies_root_folder(folder_id, invalid_repository_dependencies_dict)

Return a folder hierarchy containing invalid repository dependencies.

build_invalid_tool_dependencies_root_folder(folder_id, invalid_tool_dependencies_dict)

Return a folder hierarchy containing invalid tool dependencies.

build_repository_containers(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.

generate_tool_dependencies_key(name, version, type)

Submodules

tool_shed.utility_containers.utility_container_manager module

class tool_shed.utility_containers.utility_container_manager.Folder(id=None, key=None, label=None, parent=None)

Bases: object

Container object.

__init__(id=None, key=None, label=None, parent=None)

contains_folder(folder)

contains_repository_dependency(repository_dependency)

remove_repository_dependency(repository_dependency)

class tool_shed.utility_containers.utility_container_manager.DataManager(id=None, name=None, version=None, data_tables=None)

Bases: object

Data Manager object

__init__(id=None, name=None, version=None, data_tables=None)

class tool_shed.utility_containers.utility_container_manager.Datatype(id=None, extension=None, type=None, mimetype=None, subclass=None, converters=None, display_app_containers=None)

Bases: object

Datatype object

__init__(id=None, extension=None, type=None, mimetype=None, subclass=None, converters=None, display_app_containers=None)

class tool_shed.utility_containers.utility_container_manager.InvalidDataManager(id=None, index=None, error=None)

Bases: object

Invalid data Manager object

__init__(id=None, index=None, error=None)

class tool_shed.utility_containers.utility_container_manager.InvalidTool(id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None)

Bases: object

Invalid tool object

__init__(id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None)

class tool_shed.utility_containers.utility_container_manager.ReadMe(id=None, name=None, text=None)

Bases: object

Readme text object

__init__(id=None, name=None, text=None)

class tool_shed.utility_containers.utility_container_manager.RepositoryDependency(id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, only_if_compiling_contained_td=False, installation_status=None, tool_shed_repository_id=None)

Bases: object

Repository dependency object

__init__(id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, only_if_compiling_contained_td=False, installation_status=None, tool_shed_repository_id=None)

listify

class tool_shed.utility_containers.utility_container_manager.Tool(id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, profile=None, requirements=None, repository_id=None, changeset_revision=None, repository_installation_status=None)

Bases: object

Tool object

__init__(id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, profile=None, requirements=None, repository_id=None, changeset_revision=None, repository_installation_status=None)

class tool_shed.utility_containers.utility_container_manager.ToolDependency(id=None, name=None, version=None, type=None, readme=None, installation_status=None, repository_id=None, tool_dependency_id=None)

Bases: object

Tool dependency object

__init__(id=None, name=None, version=None, type=None, readme=None, installation_status=None, repository_id=None, tool_dependency_id=None)

listify

class tool_shed.utility_containers.utility_container_manager.Workflow(id=None, workflow_name=None, steps=None, format_version=None, annotation=None, repository_metadata_id=None, repository_id=None)

Bases: object

Workflow object.

__init__(id=None, workflow_name=None, steps=None, format_version=None, annotation=None, repository_metadata_id=None, repository_id=None)

When rendered in the tool shed, repository_metadata_id will have a value and repository_id will be None. When rendered in Galaxy, repository_id will have a value and repository_metadata_id will be None.

class tool_shed.utility_containers.utility_container_manager.UtilityContainerManager(app)

Bases: object

__init__(app)

build_data_managers_folder(folder_id, data_managers, label=None)

Return a folder hierarchy containing Data Managers.

build_datatypes_folder(folder_id, datatypes, label='Datatypes')

Return a folder hierarchy containing datatypes.

build_invalid_data_managers_folder(folder_id, data_managers, error_messages=None, label=None)

Return a folder hierarchy containing invalid Data Managers.

build_invalid_tools_folder(folder_id, invalid_tool_configs, changeset_revision, repository=None, label='Invalid tools')

Return a folder hierarchy containing invalid tools.

build_readme_files_folder(folder_id, readme_files_dict, label='Readme files')

Return a folder hierarchy containing readme text files.

build_repository_dependencies_folder(folder_id, repository_dependencies, label='Repository dependencies', installed=False)

Return a folder hierarchy containing repository dependencies.

build_tools_folder(folder_id, tool_dicts, repository, changeset_revision, valid=True, label='Valid tools')

Return a folder hierarchy containing valid tools.

build_tool_dependencies_folder(folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False, reinstalling=False)

Return a folder hierarchy containing tool dependencies.

build_workflows_folder(folder_id, workflows, repository_metadata_id=None, repository_id=None, label='Workflows')

Return a folder hierarchy containing workflow objects for each workflow dictionary in the received workflows list. When this method is called from the tool shed, repository_metadata_id will have a value and repository_id will be None. When this method is called from Galaxy, repository_id will have a value only if the repository is not currenlty being installed and repository_metadata_id will be None.

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.

get_components_from_repository_dependency_for_installed_repository(repository_dependency)

Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page.

get_folder(folder, key)

handle_repository_dependencies_container_entry(repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys)

is_subfolder_of(folder, repository_dependency)

key_is_current_repositorys_key(repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key)

populate_repository_dependencies_container(repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id)

prune_folder(folder, repository_dependency)

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 its own repository dependency). This method will remove all repository dependencies from folder that are also sub-folders of folder.