Warning

This document is for an old release 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)[source]

Bases: object

Failed tool tests object

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

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

Bases: object

Invalid tool dependency definition object

__init__(id=None, name=None, version=None, type=None, error=None)[source]
class tool_shed.utility_containers.MissingTestComponent(id=None, missing_components=None, tool_guid=None, tool_id=None, tool_version=None)[source]

Bases: object

Missing tool test components object

__init__(id=None, missing_components=None, tool_guid=None, tool_id=None, tool_version=None)[source]
class tool_shed.utility_containers.NotTested(id=None, reason=None)[source]

Bases: object

NotTested object

__init__(id=None, reason=None)[source]
class tool_shed.utility_containers.PassedTest(id=None, test_id=None, tool_id=None, tool_version=None)[source]

Bases: object

Passed tool tests object

__init__(id=None, test_id=None, tool_id=None, tool_version=None)[source]
class tool_shed.utility_containers.RepositoryInstallationError(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None, error_message=None)[source]

Bases: object

Repository installation error object

__init__(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None, error_message=None)[source]
class tool_shed.utility_containers.RepositorySuccessfulInstallation(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None)[source]

Bases: object

Repository installation object

__init__(id=None, tool_shed=None, name=None, owner=None, changeset_revision=None)[source]
class tool_shed.utility_containers.ToolDependencyInstallationError(id=None, type=None, name=None, version=None, error_message=None)[source]

Bases: object

Tool dependency installation error object

__init__(id=None, type=None, name=None, version=None, error_message=None)[source]
class tool_shed.utility_containers.ToolDependencySuccessfulInstallation(id=None, type=None, name=None, version=None, installation_directory=None)[source]

Bases: object

Tool dependency installation object

__init__(id=None, type=None, name=None, version=None, installation_directory=None)[source]
class tool_shed.utility_containers.ToolShedUtilityContainerManager(app)[source]

Bases: tool_shed.utility_containers.utility_container_manager.UtilityContainerManager

__init__(app)[source]
build_invalid_repository_dependencies_root_folder(folder_id, invalid_repository_dependencies_dict)[source]

Return a folder hierarchy containing invalid repository dependencies.

build_invalid_tool_dependencies_root_folder(folder_id, invalid_tool_dependencies_dict)[source]

Return a folder hierarchy containing invalid tool dependencies.

build_repository_containers(repository, changeset_revision, repository_dependencies, repository_metadata, exclude=None)[source]

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)[source]

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)[source]

Bases: object

Container object.

__init__(id=None, key=None, label=None, parent=None)[source]
contains_folder(folder)[source]
contains_repository_dependency(repository_dependency)[source]
remove_repository_dependency(repository_dependency)[source]
class tool_shed.utility_containers.utility_container_manager.DataManager(id=None, name=None, version=None, data_tables=None)[source]

Bases: object

Data Manager object

__init__(id=None, name=None, version=None, data_tables=None)[source]
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)[source]

Bases: object

Datatype object

__init__(id=None, extension=None, type=None, mimetype=None, subclass=None, converters=None, display_app_containers=None)[source]
class tool_shed.utility_containers.utility_container_manager.InvalidDataManager(id=None, index=None, error=None)[source]

Bases: object

Invalid data Manager object

__init__(id=None, index=None, error=None)[source]
class tool_shed.utility_containers.utility_container_manager.InvalidTool(id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None)[source]

Bases: object

Invalid tool object

__init__(id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None)[source]
class tool_shed.utility_containers.utility_container_manager.ReadMe(id=None, name=None, text=None)[source]

Bases: object

Readme text object

__init__(id=None, name=None, text=None)[source]
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)[source]

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)[source]
property 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)[source]

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)[source]
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)[source]

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)[source]
property 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)[source]

Bases: object

Workflow object.

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

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)[source]

Bases: object

__init__(app)[source]
build_data_managers_folder(folder_id, data_managers, label=None)[source]

Return a folder hierarchy containing Data Managers.

build_datatypes_folder(folder_id, datatypes, label='Datatypes')[source]

Return a folder hierarchy containing datatypes.

build_invalid_data_managers_folder(folder_id, data_managers, error_messages=None, label=None)[source]

Return a folder hierarchy containing invalid Data Managers.

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

Return a folder hierarchy containing invalid tools.

build_readme_files_folder(folder_id, readme_files_dict, label='Readme files')[source]

Return a folder hierarchy containing readme text files.

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

Return a folder hierarchy containing repository dependencies.

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

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)[source]

Return a folder hierarchy containing tool dependencies.

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

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)[source]

Return a repository dependency label based on the repository dependency key.

get_components_from_repository_dependency_for_installed_repository(repository_dependency)[source]

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

get_folder(folder, key)[source]
handle_repository_dependencies_container_entry(repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys)[source]
is_subfolder_of(folder, repository_dependency)[source]
key_is_current_repositorys_key(repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key)[source]
populate_repository_dependencies_container(repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id)[source]
prune_folder(folder, repository_dependency)[source]
prune_repository_dependencies(folder)[source]

Since the object used to generate a repository dependencies container is a dictionary and not an OrderedDict() (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.