kg_microbe.transform_utils.metatraits_gtdb package

Submodules

kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb module

MetaTraits GTDB transform class.

Extends MetaTraitsTransform to process GTDB-based metatraits data. Uses GTDB metadata files to map GTDB species names to NCBITaxon IDs.

class kg_microbe.transform_utils.metatraits_gtdb.metatraits_gtdb.MetaTraitsGTDBTransform(input_dir=None, output_dir=None, use_multiprocessing=True, num_workers=None)

Bases: MetaTraitsTransform

Transform GTDB metatraits summary JSONL files into KGX nodes and edges.

DATA_INPUTS: tuple = ('mappings/kgmicrobe_unified_entity_mappings.sssom.tsv.gz', 'data/raw/taxdump.tar.gz')

Repo-relative curation files this transform reads, beyond its own data/raw/ download.

Declared so freshness tooling can tell that an output is stale against its data rather than only its code. Without it a mapping correction lands, every consumer keeps reporting FRESH, and a re-merge silently ships the old groundings: #778 corrected 16 isolation-source ids and #786 rewrote the unified chemical SSSOM, and the merged KG built afterwards still asserted 75 organisms isolated from a “Cell Line”, because nothing re-ran the transforms that read those files (#812).

Paths are relative to the repo root. Keep them tracked in git — the freshness check uses commit time, not mtime, because git checkout rewrites mtimes without changing content (#797).

List every curation file read, not a representative one. A partial declaration fails silently and looks identical to a complete one: ontologies_stubs declared 1 of the 11 files it read and was reported fresh after changes to the other ten (#839). Where the set comes from a constant, derive this from it rather than restating it.

TRANSFORM_INPUTS: tuple = ('ontologies', 'gtdb')

Reads ontologies/ncbitaxon_nodes.tsv via NCBITAXON_NODES_FILE in _load_ncbitaxon_labels. metatraits_gtdb inherits this. Undeclared until #1035, because the path lives in constants.py rather than here.

run(data_file=None, show_status=True)

Run MetaTraitsGTDBTransform.

Processes GTDB metatraits JSONL files and generates KGX nodes/edges.

Parameters:

  • data_file (Union[Path, None, str]) – Ignored; uses configured GTDB input file list.

  • show_status (bool) – Whether to show progress bar.

Return type:

None

Module contents

MetaTraits GTDB transform module.

class kg_microbe.transform_utils.metatraits_gtdb.MetaTraitsGTDBTransform(input_dir=None, output_dir=None, use_multiprocessing=True, num_workers=None)

Bases: MetaTraitsTransform

Transform GTDB metatraits summary JSONL files into KGX nodes and edges.

DATA_INPUTS: tuple = ('mappings/kgmicrobe_unified_entity_mappings.sssom.tsv.gz', 'data/raw/taxdump.tar.gz')

Repo-relative curation files this transform reads, beyond its own data/raw/ download.

Declared so freshness tooling can tell that an output is stale against its data rather than only its code. Without it a mapping correction lands, every consumer keeps reporting FRESH, and a re-merge silently ships the old groundings: #778 corrected 16 isolation-source ids and #786 rewrote the unified chemical SSSOM, and the merged KG built afterwards still asserted 75 organisms isolated from a “Cell Line”, because nothing re-ran the transforms that read those files (#812).

Paths are relative to the repo root. Keep them tracked in git — the freshness check uses commit time, not mtime, because git checkout rewrites mtimes without changing content (#797).

List every curation file read, not a representative one. A partial declaration fails silently and looks identical to a complete one: ontologies_stubs declared 1 of the 11 files it read and was reported fresh after changes to the other ten (#839). Where the set comes from a constant, derive this from it rather than restating it.

TRANSFORM_INPUTS: tuple = ('ontologies', 'gtdb')

Reads ontologies/ncbitaxon_nodes.tsv via NCBITAXON_NODES_FILE in _load_ncbitaxon_labels. metatraits_gtdb inherits this. Undeclared until #1035, because the path lives in constants.py rather than here.

accession_to_gtdb_species: Dict[str, str]
accession_to_ncbi: Dict[str, str]
gtdb_preferred_ncbi: Dict[str, str]
gtdb_to_ncbi: Dict[str, Counter]
ncbitaxon_name_to_id: Dict[str, str]
run(data_file=None, show_status=True)

Run MetaTraitsGTDBTransform.

Processes GTDB metatraits JSONL files and generates KGX nodes/edges.

Parameters:

  • data_file (Union[Path, None, str]) – Ignored; uses configured GTDB input file list.

  • show_status (bool) – Whether to show progress bar.

Return type:

None

synthetic_nodes_metadata: Dict[str, Dict[str, str]]
trait_mapping: Dict[str, dict]