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.

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) → galaxy.tool_util.toolbox.lineages.interface.ToolLineage[source]
get(tool_id) → Optional[galaxy.tool_util.toolbox.lineages.interface.ToolLineage][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, **kwds)[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, galaxy.tool_util.toolbox.lineages.interface.ToolLineage] = {}
lock = <unlocked _thread.lock object>
__init__(tool_id, **kwds)[source]
property tool_ids: List[str]
static from_tool(tool) → galaxy.tool_util.toolbox.lineages.interface.ToolLineage[source]
register_version(tool_version) → None[source]
get_versions()[source]

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

get_version_ids(reverse=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) → galaxy.tool_util.toolbox.lineages.interface.ToolLineage[source]
get(tool_id) → Optional[galaxy.tool_util.toolbox.lineages.interface.ToolLineage][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, version)[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, version)[source]
property id_based

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()[source]
class galaxy.tool_util.toolbox.lineages.interface.ToolLineage(tool_id, **kwds)[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, galaxy.tool_util.toolbox.lineages.interface.ToolLineage] = {}
lock = <unlocked _thread.lock object>
__init__(tool_id, **kwds)[source]
property tool_ids: List[str]
static from_tool(tool) → galaxy.tool_util.toolbox.lineages.interface.ToolLineage[source]
register_version(tool_version) → None[source]
get_versions()[source]

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

get_version_ids(reverse=False) → List[str][source]
to_dict() → Dict[str, Any][source]