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tool_shed.galaxy_install.repository_dependencies package

Submodules

tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module

Class encapsulating the management of repository dependencies installed or being installed into Galaxy from the Tool Shed.

class tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager.RepositoryDependencyInstallManager(app)[source]

Bases: object

__init__(app)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

build_repository_dependency_relationships(repo_info_dicts, tool_shed_repositories)[source]

Build relationships between installed tool shed repositories and other installed tool shed repositories upon which they depend. These relationships are defined in the repository_dependencies entry for each dictionary in the received list of repo_info_dicts. Each of these dictionaries is associated with a repository in the received tool_shed_repositories list.

create_repository_dependency_objects(tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False, no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None)[source]

Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as the dependency relationships between installed repositories. This method is called when uninstalled repositories are being reinstalled. If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will be processed. However, if repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed.

get_or_create_tool_shed_repository(tool_shed, name, owner, changeset_revision)[source]

Return a tool shed repository database record defined by the combination of tool shed, repository name, repository owner and changeset_revision or installed_changeset_revision. A new tool shed repository record will be created if one is not located.

get_repository_dependencies_for_installed_tool_shed_repository(app, repository)[source]

Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined for the received repository which is installed into Galaxy. This method is called only from Galaxy.

get_repository_dependency_by_repository_id(install_model, decoded_repository_id)[source]
get_required_repo_info_dicts(tool_shed_url, repo_info_dicts)[source]

Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of them to the list. All repository_dependency entries in each of the received repo_info_dicts includes all required repositories, so only one pass through this method is required to retrieve all repository dependencies.

is_in_repo_info_dicts(repo_info_dict, repo_info_dicts)[source]

Return True if the received repo_info_dict is contained in the list of received repo_info_dicts.

reset_previously_installed_repository(repository)[source]

Reset the attributes of a tool_shed_repository that was previously installed. The repository will be in some state other than INSTALLED, so all attributes will be set to the default NEW state. This will enable the repository to be freshly installed.