def fixture_upload_genotypes_hk_api(
real_housekeeper_api: HousekeeperAPI,
upload_genotypes_hk_bundle: dict,
analysis_obj: models.Analysis,
helpers,
) -> HousekeeperAPI:
"""Add and include files from upload genotypes hk bundle"""
helpers.ensure_hk_bundle(real_housekeeper_api, upload_genotypes_hk_bundle)
hk_version = real_housekeeper_api.last_version(
analysis_obj.family.internal_id)
real_housekeeper_api.include(hk_version)
return real_housekeeper_api
def fixture_mip_dna_housekeeper(
real_housekeeper_api: HousekeeperAPI,
mip_delivery_bundle: dict,
fastq_delivery_bundle: dict,
helpers: StoreHelpers,
) -> HousekeeperAPI:
helpers.ensure_hk_bundle(real_housekeeper_api,
bundle_data=mip_delivery_bundle)
helpers.ensure_hk_bundle(real_housekeeper_api,
bundle_data=fastq_delivery_bundle)
# assert that the files exists
version_obj_mip: hk_models.Version = real_housekeeper_api.last_version(
mip_delivery_bundle["name"])
version_obj_fastq: hk_models.Version = real_housekeeper_api.last_version(
fastq_delivery_bundle["name"])
real_housekeeper_api.include(version_obj=version_obj_mip)
real_housekeeper_api.include(version_obj=version_obj_fastq)
return real_housekeeper_api
def ensure_hk_bundle(
store: HousekeeperAPI, bundle_data: dict, include: bool = False
) -> hk_models.Bundle:
"""Utility function to add a bundle of information to a housekeeper api"""
bundle_exists = False
for bundle in store.bundles():
if bundle.name != bundle_data["name"]:
continue
bundle_exists = True
_bundle = bundle
break
if not bundle_exists:
_bundle, _version = store.add_bundle(bundle_data)
store.add_commit(_bundle, _version)
if include:
store.include(_version)
return _bundle