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galaxy.tool_util.toolbox.lineages package

class galaxy.tool_util.toolbox.lineages.LineageMap(toolbox: AbstractToolBox)

Bases: object

Map each unique tool id to a lineage object.

__init__(toolbox: AbstractToolBox)

register(tool: Tool) → ToolLineage

get(tool_id: str) → ToolLineage | None

Get lineage for tool_id.

By preference the lineage for a version-agnostic tool_id is returned. Falls back to fetching the lineage only when this fails. This happens when the tool_id does not contain a version.

class galaxy.tool_util.toolbox.lineages.ToolLineage(tool_id: str)

Bases: object

Simple tool’s loaded directly from file system with lineage determined solely by PEP 440 versioning scheme.

lineages_by_id: dict[str, ToolLineage] = {}

lock = <unlocked _thread.lock object>

__init__(tool_id: str) → None

property tool_ids: list[str]

classmethod from_tool(tool: Tool) → ToolLineage

register_version(tool_version: str) → None

classmethod reset() → None

Clear the global lineages_by_id cache.

lineages_by_id is a class attribute, so toolbox shutdown clears it before another boot reconstructs lineages from current metadata.

get_versions() → list[ToolLineageVersion]

Return an ordered list of lineages (ToolLineageVersion) in this chain, from oldest to newest.

get_version_ids(reverse: bool = False) → list[str]

to_dict() → dict[str, Any]

Submodules

galaxy.tool_util.toolbox.lineages.factory module

class galaxy.tool_util.toolbox.lineages.factory.CachedLineageMap(toolbox: AbstractToolBox, versions_for: Callable[[str], Iterable[str]] | None = None)

Bases: LineageMap

Lineage map that derives versions from a callable on first access.

Used by galaxy.tools.cached_toolbox.CachedToolBox so the lineage view over ToolIndex.entries_by_version doesn’t need a boot-time pass to seed every tool’s version set into ToolLineage.tool_versions. Lineage data is already serialised inside the index (ToolIndex.to_dict); this class just exposes it as a LineageMap on demand.

__init__(toolbox: AbstractToolBox, versions_for: Callable[[str], Iterable[str]] | None = None)

get(tool_id: str) → ToolLineage | None

Get lineage for tool_id.

By preference the lineage for a version-agnostic tool_id is returned. Falls back to fetching the lineage only when this fails. This happens when the tool_id does not contain a version.

class galaxy.tool_util.toolbox.lineages.factory.LineageMap(toolbox: AbstractToolBox)

Bases: object

Map each unique tool id to a lineage object.

__init__(toolbox: AbstractToolBox)

register(tool: Tool) → ToolLineage

get(tool_id: str) → ToolLineage | None

Get lineage for tool_id.

By preference the lineage for a version-agnostic tool_id is returned. Falls back to fetching the lineage only when this fails. This happens when the tool_id does not contain a version.

galaxy.tool_util.toolbox.lineages.interface module

class galaxy.tool_util.toolbox.lineages.interface.ToolLineageVersion(id: str, version: str)

Bases: object

Represents a single tool in a lineage. If lineage is based around GUIDs that somehow encode the version (either using GUID or a simple tool id and a version).

__init__(id: str, version: str) → None

property id_based: bool

Return True if the lineage is defined by GUIDs (in this case the indexer of the tools (i.e. the ToolBox) should ignore the tool_version (because it is encoded in the GUID and managed externally).

to_dict() → dict[str, str]

class galaxy.tool_util.toolbox.lineages.interface.ToolLineage(tool_id: str)

Bases: object

Simple tool’s loaded directly from file system with lineage determined solely by PEP 440 versioning scheme.

lineages_by_id: dict[str, ToolLineage] = {}

lock = <unlocked _thread.lock object>

__init__(tool_id: str) → None

property tool_ids: list[str]

classmethod from_tool(tool: Tool) → ToolLineage

register_version(tool_version: str) → None

classmethod reset() → None

Clear the global lineages_by_id cache.

lineages_by_id is a class attribute, so toolbox shutdown clears it before another boot reconstructs lineages from current metadata.

get_versions() → list[ToolLineageVersion]

Return an ordered list of lineages (ToolLineageVersion) in this chain, from oldest to newest.

get_version_ids(reverse: bool = False) → list[str]

to_dict() → dict[str, Any]