galaxy.model.tool_shed_install package
- galaxy.model.tool_shed_install.now()
Return a new datetime representing UTC day and time.
- class galaxy.model.tool_shed_install.HasToolBox(*args, **kwargs)[source]
Bases:
HasToolShedRegistry
,Protocol
- property toolbox: AbstractToolBox
- tool_shed_registry: ToolShedRegistry
- class galaxy.model.tool_shed_install.Base(**kwargs: Any)[source]
Bases:
object
- registry: RegistryType = <sqlalchemy.orm.decl_api.registry object>
- metadata: MetaData = MetaData()
- __init__(**kwargs: Any) None
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.tool_shed_install.ToolShedRepository(id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None, changeset_revision=None, ctx_rev=None, metadata_=None, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)[source]
Bases:
Base
- tool_versions
- tool_dependencies
- required_repositories
- dict_collection_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes', 'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
- dict_element_visible_keys = ['id', 'tool_shed', 'name', 'owner', 'installed_changeset_revision', 'changeset_revision', 'ctx_rev', 'includes_datatypes', 'tool_shed_status', 'deleted', 'uninstalled', 'dist_to_shed', 'status', 'error_message', 'description']
- class installation_status(value)[source]
-
An enumeration.
- NEW = 'New'
- CLONING = 'Cloning'
- SETTING_TOOL_VERSIONS = 'Setting tool versions'
- INSTALLING_REPOSITORY_DEPENDENCIES = 'Installing repository dependencies'
- INSTALLING_TOOL_DEPENDENCIES = 'Installing tool dependencies'
- LOADING_PROPRIETARY_DATATYPES = 'Loading proprietary datatypes'
- INSTALLED = 'Installed'
- DEACTIVATED = 'Deactivated'
- ERROR = 'Error'
- UNINSTALLED = 'Uninstalled'
- class states(value)[source]
-
An enumeration.
- INSTALLING = 'running'
- OK = 'ok'
- WARNING = 'queued'
- ERROR = 'error'
- UNINSTALLED = 'deleted_new'
- __init__(id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, installed_changeset_revision=None, changeset_revision=None, ctx_rev=None, metadata_=None, tool_shed_status=None, deleted=False, uninstalled=False, dist_to_shed=False, status=None, error_message=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- metadata_
- tool_shed_status
- property can_install
- property can_reset_metadata
- property can_uninstall
- property can_deactivate
- property can_reinstall_or_activate
- get_sharable_url(app: HasToolBox)[source]
- property shed_config_filename
- get_shed_config_dict(app: HasToolBox) Dict[str, Any] [source]
Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict.
- get_tool_relative_path(app: HasToolBox)[source]
- guess_shed_config(app: HasToolBox)[source]
- property has_readme_files
- property has_repository_dependencies
- property has_repository_dependencies_only_if_compiling_contained_td
- property in_error_state
- property includes_data_managers
- property includes_tools
- property includes_tools_for_display_in_tool_panel
- property includes_tool_dependencies
- property installed_repository_dependencies
Return the repository’s repository dependencies that are currently installed.
- property installed_tool_dependencies
Return the repository’s tool dependencies that are currently installed, but possibly in an error state.
- property is_deprecated_in_tool_shed
- property is_deactivated_or_installed
- property is_installed
- property is_latest_installable_revision
- property is_new
- property missing_repository_dependencies
Return the repository’s repository dependencies that are not currently installed, and may not ever have been installed.
- property missing_tool_dependencies
Return the repository’s tool dependencies that are not currently installed, and may not ever have been installed.
- repo_files_directory(app: HasToolBox)[source]
- repo_path(app: HasToolBox)[source]
- property repository_dependencies
Return all of this repository’s repository dependencies, ignoring their attributes like prior_installation_required and only_if_compiling_contained_td.
- property repository_dependencies_being_installed
Return the repository’s repository dependencies that are currently being installed.
- property repository_dependencies_missing_or_being_installed
Return the repository’s repository dependencies that are either missing or currently being installed.
- property repository_dependencies_with_installation_errors
Return the repository’s repository dependencies that have installation errors.
- property requires_prior_installation_of
Return a list of repository dependency tuples like (tool_shed, name, owner, changeset_revision, prior_installation_required) for this repository’s repository dependencies where prior_installation_required is True. By definition, repository dependencies are required to be installed in order for this repository to function correctly. However, those repository dependencies that are defined for this repository with prior_installation_required set to True place them in a special category in that the required repositories must be installed before this repository is installed. Among other things, this enables these “special” repository dependencies to include information that enables the successful installation of this repository. This method is not used during the initial installation of this repository, but only after it has been installed (metadata must be set for this repository in order for this method to be useful).
- property revision_update_available
- to_dict(view='collection', value_mapper: Dict[str, Callable] | None = None) Dict[str, Any] [source]
- property tool_dependencies_being_installed
- property tool_dependencies_installed_or_in_error
Return the repository’s tool dependencies that are currently installed, but possibly in an error state.
- property tool_dependencies_missing_or_being_installed
- property tool_dependencies_with_installation_errors
- property tool_shed_path_name
- property tuples_of_repository_dependencies_needed_for_compiling_td
Return tuples defining this repository’s repository dependencies that are necessary only for compiling this repository’s tool dependencies.
- property uninstalled_repository_dependencies
Return the repository’s repository dependencies that have been uninstalled.
- property uninstalled_tool_dependencies
Return the repository’s tool dependencies that have been uninstalled.
- property upgrade_available
- class galaxy.model.tool_shed_install.RepositoryRepositoryDependencyAssociation(tool_shed_repository_id=None, repository_dependency_id=None)[source]
Bases:
Base
- repository
- repository_dependency
- __init__(tool_shed_repository_id=None, repository_dependency_id=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.tool_shed_install.RepositoryDependency(tool_shed_repository_id=None)[source]
Bases:
Base
- repository
- __init__(tool_shed_repository_id=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.tool_shed_install.ToolDependency(tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None)[source]
Bases:
Base
- tool_shed_repository
- installation_status = <galaxy.util.bunch.Bunch object>
- class states(value)[source]
-
An enumeration.
- INSTALLING = 'running'
- OK = 'ok'
- WARNING = 'queued'
- ERROR = 'error'
- UNINSTALLED = 'deleted_new'
- __init__(tool_shed_repository_id=None, name=None, version=None, type=None, status=None, error_message=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property can_install
- property can_uninstall
- property can_update
- property in_error_state
- installation_directory(app: HasToolBox) str | None [source]
- property is_installed
- class galaxy.model.tool_shed_install.ToolVersion(**kwargs)[source]
Bases:
Base
,Dictifiable
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- parent_tool_association
- child_tool_association
- tool_shed_repository
- dict_element_visible_keys = ['id', 'tool_shed_repository']
- class galaxy.model.tool_shed_install.ToolVersionAssociation(**kwargs)[source]
Bases:
Base
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.