def test_box_sync_module_protect_processed(args_and_Lochness):
args, Lochness = args_and_Lochness
# change protect to true for all actigraphy
for study in args.studies:
new_list = []
for i in Lochness['box'][study]['file_patterns']['actigraphy']:
i['protect'] = True
i['processed'] = True
new_list.append(i)
Lochness['box'][study]['file_patterns']['actigraphy'] = new_list
for subject in lochness.read_phoenix_metadata(Lochness):
sync(Lochness, subject, dry=False)
for study in args.studies:
subject_dir = protected_root / study / 'processed' / '1001'
assert (subject_dir / 'actigraphy').is_dir()
assert len(list((subject_dir /
'actigraphy').glob('*csv'))) > 1
subject_dir = general_root / study / 'processed' / '1001'
assert not (subject_dir / 'actigraphy').is_dir()
assert len(list((subject_dir /
'actigraphy/processed/').glob('*csv'))) == 0
show_tree_then_delete('tmp_lochness')
def test_box_sync_module_missing_root(args_and_Lochness):
args, Lochness = args_and_Lochness
# change base for StudyA to missing path
Lochness['box']['StudyA']['base'] = 'hahah'
for subject in lochness.read_phoenix_metadata(Lochness):
sync(Lochness, subject, dry=False)
study = 'StudyA'
subject_dir = protected_root / study / 'raw' / '1001'
assert (subject_dir / 'actigraphy').is_dir() == False
show_tree_then_delete('tmp_lochness')
def test_box_sync_module_no_redownload(args_and_Lochness):
args, Lochness = args_and_Lochness
# change subject name
for subject in lochness.read_phoenix_metadata(Lochness):
sync(Lochness, subject, dry=False)
a_file_path = general_root / 'StudyA' / 'raw' / '1001' / 'actigraphy' / \
'BLS-F6VVM-GENEActivQC-day22to51.csv'
init_time = a_file_path.stat().st_mtime
# change subject name
for subject in lochness.read_phoenix_metadata(Lochness):
sync(Lochness, subject, dry=False)
post_time = a_file_path.stat().st_mtime
assert init_time == post_time
show_tree_then_delete('tmp_lochness')
def test_box_sync_module_missing_subject(args_and_Lochness):
args, Lochness = args_and_Lochness
# change subject name
keyring = KeyringAndEncrypt(args.outdir)
information_to_add_to_metadata = {'box': {
'subject_id': '1001',
'source_id': 'O12341234'}}
for study in args.studies:
keyring.update_for_box(study)
# update box metadata
initialize_metadata_test('tmp_lochness/PHOENIX', study,
information_to_add_to_metadata)
for subject in lochness.read_phoenix_metadata(Lochness):
sync(Lochness, subject, dry=False)
show_tree_then_delete('tmp_lochness')