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.managers package

Submodules

tool_shed.managers.groups module

Manager and Serializer for TS groups.

class tool_shed.managers.groups.GroupManager(*args, **kwargs)[source]

Bases: object

Interface/service object for interacting with TS groups.

__init__(*args, **kwargs)[source]
get(trans, decoded_group_id=None, name=None)[source]

Get the group from the DB based on its ID or name.

Parameters:

decoded_group_id (int) – decoded group id

Returns:

the requested group

Return type:

tool_shed.model.Group

create(trans, name, description='')[source]

Create a new group.

update(trans, group, name=None, description=None)[source]

Update the given group

delete(trans, group, undelete=False)[source]

Mark given group deleted/undeleted based on the flag.

list(trans, deleted=False)[source]

Return a list of groups from the DB.

Returns:

query that will emit all groups

Return type:

sqlalchemy query

tool_shed.managers.groups.get_group_by_name(session, name, group_model)[source]

tool_shed.managers.repositories module

Manager and Serializer for TS repositories.

tool_shed.managers.repositories.search(trans: ProvidesUserContext, q: str, page: int = 1, page_size: int = 10)[source]

Perform the search over TS repositories. Note that search works over the Whoosh index which you have to pre-create with scripts/tool_shed/build_ts_whoosh_index.sh manually. Also TS config option toolshed_search_on has to be True and whoosh_index_dir has to be specified.

class tool_shed.managers.repositories.UpdatesRequest(*, name: str | None = None, owner: str | None = None, changeset_revision: str, hexlify: bool = True)[source]

Bases: BaseModel

name: str | None
owner: str | None
changeset_revision: str
hexlify: bool
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'changeset_revision': FieldInfo(annotation=str, required=True), 'hexlify': FieldInfo(annotation=bool, required=False, default=True), 'name': FieldInfo(annotation=Union[str, NoneType], required=False), 'owner': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

tool_shed.managers.repositories.check_updates(app: ToolShedApp, request: UpdatesRequest) str | Dict[str, Any][source]
tool_shed.managers.repositories.guid_to_repository(app: ToolShedApp, tool_id: str) Repository[source]
tool_shed.managers.repositories.index_tool_ids(app: ToolShedApp, tool_ids: List[str]) Dict[str, Any][source]
tool_shed.managers.repositories.index_repositories(app: ToolShedApp, name: str | None, owner: str | None, deleted: bool)[source]
tool_shed.managers.repositories.can_manage_repo(trans: ProvidesUserContext, repository: Repository) bool[source]
tool_shed.managers.repositories.can_update_repo(trans: ProvidesUserContext, repository: Repository) bool[source]
tool_shed.managers.repositories.get_repository_metadata_for_management(trans: ProvidesUserContext, encoded_repository_id: str, changeset_revision: str) RepositoryMetadata[source]
tool_shed.managers.repositories.get_install_info(trans: ProvidesRepositoriesContext, name, owner, changeset_revision) Tuple[Dict | None, RepositoryMetadataInstallInfoDict | EmptyDict, Dict[str, List] | EmptyDict][source]
tool_shed.managers.repositories.get_value_mapper(app: ToolShedApp) Dict[str, Callable][source]
tool_shed.managers.repositories.get_ordered_installable_revisions(app: ToolShedApp, name: str | None, owner: str | None, tsr_id: str | None) List[str][source]
tool_shed.managers.repositories.get_repository_metadata_dict(app: ToolShedApp, id: str, recursive: bool, downloadable_only: bool) Dict[str, Any][source]
tool_shed.managers.repositories.readmes(app: ToolShedApp, repository: Repository, changeset_revision: str) dict[source]
tool_shed.managers.repositories.reset_metadata_on_repository(trans: ProvidesUserContext, repository_id) ResetMetadataOnRepositoryResponse[source]
tool_shed.managers.repositories.create_repository(trans: ProvidesUserContext, request: CreateRepositoryRequest) Repository[source]
tool_shed.managers.repositories.to_element_dict(app, repository: Repository, include_categories: bool = False) Dict[str, Any][source]
tool_shed.managers.repositories.repositories_by_category(app: ToolShedApp, category_id: str, page: int | None = None, sort_key: str = 'name', sort_order: str = 'asc', installable: bool = True)[source]
tool_shed.managers.repositories.to_model(app, repository: Repository) Repository[source]
tool_shed.managers.repositories.to_detailed_model(app, repository: Repository) DetailedRepository[source]
tool_shed.managers.repositories.upload_tar_and_set_metadata(trans: ProvidesRepositoriesContext, host: str, repository: Repository, uploaded_file, commit_message: str, dry_run: bool = False)[source]