galaxy.tool_util.ontologies package

Submodules

galaxy.tool_util.ontologies.ontology_data module

galaxy.tool_util.ontologies.ontology_data.configure_tool_tag_mapping(file_path: str | None) → None[source]

Replace the in-memory curated tool → tag mapping.

Galaxy calls this once at startup with the value of the tool_tag_mappings_file config option. If file_path is empty or None, the bundled minimal mapping (see tool_tag_mappings.yml) is retained. Missing or unreadable files are logged and the in-memory mapping is left untouched so a typo in galaxy.yml doesn’t take down tool loading.

class galaxy.tool_util.ontologies.ontology_data.OntologyData(xrefs, edam_operations, edam_topics, tool_tags)[source]

Bases: NamedTuple

xrefs: List[XrefDict]: Alias for field number 0

edam_operations: List[str] | None: Alias for field number 1

edam_topics: List[str] | None: Alias for field number 2

tool_tags: List[str]: Alias for field number 3

galaxy.tool_util.ontologies.ontology_data.biotools_reference(xrefs)[source]

galaxy.tool_util.ontologies.ontology_data.legacy_biotools_external_reference(all_ids: List[str]) → List[str][source]

galaxy.tool_util.ontologies.ontology_data.curated_tool_tags(all_ids: List[str]) → List[str][source]

galaxy.tool_util.ontologies.ontology_data.expand_ontology_data(tool_source: ToolSource, all_ids: List[str], biotools_metadata_source: BiotoolsMetadataSource | None) → OntologyData[source]