galaxy.tool_util.toolbox.lineages package

class galaxy.tool_util.toolbox.lineages.LineageMap(app)[source]

Bases: object

Map each unique tool id to a lineage object.

__init__(app)[source]

register(tool: Tool) → ToolLineage[source]

get(tool_id: str) → ToolLineage | None[source]

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)[source]

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[source]

property tool_ids: List[str]

classmethod from_tool(tool: Tool) → ToolLineage[source]

register_version(tool_version: str) → None[source]

get_versions() → List[ToolLineageVersion][source]: Return an ordered list of lineages (ToolLineageVersion) in this chain, from oldest to newest.

get_version_ids(reverse: bool = False) → List[str][source]

to_dict() → Dict[str, Any][source]

Submodules

galaxy.tool_util.toolbox.lineages.factory module

class galaxy.tool_util.toolbox.lineages.factory.LineageMap(app)[source]

Bases: object

Map each unique tool id to a lineage object.

__init__(app)[source]

register(tool: Tool) → ToolLineage[source]

get(tool_id: str) → ToolLineage | None[source]

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)[source]

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[source]

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][source]

class galaxy.tool_util.toolbox.lineages.interface.ToolLineage(tool_id: str)[source]

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[source]

property tool_ids: List[str]

classmethod from_tool(tool: Tool) → ToolLineage[source]

register_version(tool_version: str) → None[source]

get_versions() → List[ToolLineageVersion][source]: Return an ordered list of lineages (ToolLineageVersion) in this chain, from oldest to newest.

get_version_ids(reverse: bool = False) → List[str][source]

to_dict() → Dict[str, Any][source]