kg_microbe.transform_utils.mim_ingredients package

Submodules

kg_microbe.transform_utils.mim_ingredients.mim_ingredients module

Project reviewed ingredient context without general CultureMech ingestion.

class kg_microbe.transform_utils.mim_ingredients.mim_ingredients.MIMIngredientsTransform(input_dir=None, output_dir=None)

Bases: Transform

Keep source claims on assertions and catalog specifications as distinct records.

REQUIRED_CONSUMED_INPUTS: tuple = ('ingredient_selection', 'ingredient_lookup/lookup_manifest.json', 'ingredient_lookup/legacy.sssom.tsv.gz', 'ingredient_bundle/manifest.json')

Named generated inputs that must actually be read before fresh finalization. Unlike DATA_INPUTS, these are checked after upstream producers have run.

SSSOM_CONSUMED_INPUT = 'ingredient_lookup/legacy.sssom.tsv.gz'

TSV_QUOTING = 3

run(data_file=None, show_status=True)

Consume a pinned candidate lookup and retain every reviewed claim disposition.

kg_microbe.transform_utils.mim_ingredients.mim_ingredients.project_ingredient_context(bundle, loader)

Build a reviewed cohort graph; nested original payloads remain scalar JSON.

Module contents

Explicit candidate ingestion of reviewed MIM ingredient context.