def LochnessMetadataInitialized(args_and_Lochness):
args, Lochness = args_and_Lochness
# before initializing metadata
for study in args.studies:
phoenix_path = Path(Lochness['phoenix_root'])
general_path = phoenix_path / 'GENERAL'
metadata = general_path / study / f"{study}_metadata.csv"
initialize_metadata(Lochness, study, 'record_id1', 'cons_date')
return Lochness
def test_initialize_metadata_update_when_initialized_again(
LochnessMetadataInitialized):
args = Args('tmp_lochness')
for study in args.studies:
phoenix_path = Path(LochnessMetadataInitialized['phoenix_root'])
general_path = phoenix_path / 'GENERAL'
metadata = general_path / study / f"{study}_metadata.csv"
prev_st_mtime = metadata.stat().st_mtime
initialize_metadata(LochnessMetadataInitialized, study, 'record_id1',
'cons_date')
post_st_mtime = metadata.stat().st_mtime
assert prev_st_mtime < post_st_mtime
def test_initialize_metadata_then_sync(args_and_Lochness):
args, Lochness = args_and_Lochness
# before initializing metadata
for study in args.studies:
phoenix_path = Path(Lochness['phoenix_root'])
general_path = phoenix_path / 'GENERAL'
metadata = general_path / study / f"{study}_metadata.csv"
initialize_metadata(Lochness, study, 'record_id1', 'cons_date')
for subject in lochness.read_phoenix_metadata(Lochness,
studies=['StudyA']):
sync(Lochness, subject, False)
show_tree_then_delete('tmp_lochness')
def test_initialize_metadata_function_adding_new_data_to_csv(
args_and_Lochness):
args, Lochness = args_and_Lochness
# before initializing metadata
for study in args.studies:
phoenix_path = Path(Lochness['phoenix_root'])
general_path = phoenix_path / 'GENERAL'
metadata = general_path / study / f"{study}_metadata.csv"
assert len(pd.read_csv(metadata)) == 1
initialize_metadata(Lochness, study, 'record_id1', 'cons_date')
assert len(pd.read_csv(metadata)) > 3
rmtree('tmp_lochness')
def initialize_metadata(Lochness, args) -> None:
'''Create (overwrite) metadata.csv using either REDCap or RPMS database'''
for study_name in args.studies:
# if 'redcap' or 'rpms' is in the sources, create (overwrite)
if 'redcap' in args.sources:
id_fieldname = 'record_id1'
consent_fieldname = 'Consent'
REDCap.initialize_metadata(
Lochness, study_name, id_fieldname, consent_fieldname)
elif 'rpms' in args.sources:
# metadata.csv
id_fieldname = 'record_id1'
consent_fieldname = 'Consent'
RPMS.initialize_metadata(
Lochness, study_name, id_fieldname, consent_fieldname)
else:
pass