def test_run_override(mock_datetime, with_concept_maps):
mock_datetime.now.return_value = mockdatetime()
run.run(
mapping="test/fixtures/small_mimic_mapping.json",
resource_ids=None,
override=False,
chunksize=None,
bypass_validation=False,
skip_ref_binding=True,
multiprocessing=False,
)
run.run(
mapping="test/fixtures/small_mimic_mapping.json",
resource_ids=None,
override=True,
chunksize=None,
bypass_validation=False,
skip_ref_binding=True,
multiprocessing=False,
)
mongo_client = get_mongo_client()[fhirpipe.global_config["fhirstore"]
["database"]]
assert mongo_client["Patient"].count_documents(
{}) == expected_patients_count
assert mongo_client["Practitioner"].count_documents(
{}) == expected_admissions_count
def test_run_multiprocessing(mock_datetime, with_concept_maps):
mock_datetime.now.return_value = mockdatetime()
run.run(
mapping="test/fixtures/mimic_mapping.json",
resource_ids=None,
override=False,
chunksize=None,
bypass_validation=False,
skip_ref_binding=True,
multiprocessing=True,
)
assert_result_as_expected()
def cli_run():
print(WELCOME_MSG)
# Parse arguments
args = parse_args()
# Define global config
set_global_config(config_path=args.config)
# Setup logging configuration
setup_logging()
run(
mapping=args.mapping,
resource_ids=args.resource_ids,
override=args.override,
chunksize=args.chunksize,
bypass_validation=args.bypass_validation,
skip_ref_binding=args.skip_ref_binding,
multiprocessing=args.multiprocessing,
)
def test_run_ref_binding(mock_datetime, with_concept_maps):
mock_datetime.now.return_value = mockdatetime()
run.run(
mapping="test/fixtures/small_mimic_mapping.json",
resource_ids=None,
override=False,
chunksize=None,
bypass_validation=False,
skip_ref_binding=False,
multiprocessing=False,
)
mongo_client = get_mongo_client()[fhirpipe.global_config["fhirstore"]
["database"]]
db_collections = mongo_client.list_collection_names()
assert "Patient" in db_collections
assert "Practitioner" in db_collections
assert mongo_client["Patient"].count_documents(
{}) == expected_patients_count
compare_sample_patient_referencing(mongo_client)