def Lochness():
args = Args('tmp_lochness')
create_lochness_template(args)
KeyringAndEncryptLochnessTransfer(args.outdir)
lochness = config_load_test('tmp_lochness/config.yml', '')
return lochness
def test_do_init(args):
syncArgs = SyncArgs('tmp_lochness')
create_lochness_template(args)
syncArgs.config = args.outdir / 'config.yml'
_ = KeyringAndEncrypt(args.outdir)
Lochness = config_load_test(syncArgs.config, syncArgs.archive_base)
show_tree_then_delete('tmp_lochness')
def syncArgsForLochnessSync(args):
syncArgs = SyncArgs('tmp_lochness')
create_lochness_template(args)
syncArgs.config = args.outdir / 'config.yml'
syncArgs.update_source(args.sources)
_ = KeyringAndEncryptLochnessTransfer(args.outdir)
return syncArgs
def test_create_lochness_template_for_documentation(args):
args.outdir = 'lochness_root'
args.studies = ['BWH', 'McLean']
args.sources = ['redcap', 'xnat', 'box', 'mindlamp']
args.poll_interval = 43200
args.det_csv = '/data/data_entry_trigger_db.csv'
args.pii_csv = '/data/personally_identifiable_process_mappings.csv'
create_lochness_template(args)
show_tree_then_delete('lochness_root')
def args_and_Lochness():
args = Args('tmp_lochness')
create_lochness_template(args)
keyring = KeyringAndEncrypt(args.outdir)
for study in args.studies:
keyring.update_for_redcap(study)
lochness_obj = config_load_test('tmp_lochness/config.yml', '')
return args, lochness_obj
def test_read_phoenix_data(args):
syncArgs = SyncArgs('tmp_lochness')
create_lochness_template(args)
_ = KeyringAndEncrypt(args.outdir)
args.source = ['xnat', 'box']
args.studies = ['mclean']
args.dry = [False]
Lochness = config.load(syncArgs.config, syncArgs.archive_base)
for subject in lochness.read_phoenix_metadata(Lochness, args.studies):
print(subject)
def test_sync_from_empty(args):
outdir = 'tmp_lochness'
args.outdir = outdir
create_lochness_template(args)
KeyringAndEncryptRPMS(args.outdir)
create_fake_rpms_repo()
dry = False
study_name = 'StudyA'
Lochness = config_load_test(f'{args.outdir}/config.yml', '')
initialize_metadata(Lochness, study_name, 'record_id1', 'Consent')
for subject in lochness.read_phoenix_metadata(Lochness,
studies=['StudyA']):
sync(Lochness, subject, dry)
# print the structure
show_tree_then_delete('tmp_lochness')
def test_do_with_mindlamp(args):
syncArgs = SyncArgs(args.outdir)
sources = ['mindlamp']
syncArgs.update_source(sources)
create_lochness_template(args)
syncArgs.config = args.outdir / 'config.yml'
_ = KeyringAndEncryptMindlamp(args.outdir)
phoenix_root = args.outdir / 'PHOENIX'
information_to_add_to_metadata = {'mindlamp': {'subject_id': '1001',
'source_id': 'U7045332804'}}
initialize_metadata_test(phoenix_root, 'StudyA',
information_to_add_to_metadata)
do(syncArgs)
show_tree_then_delete('tmp_lochness')
def args_and_Lochness():
args = Args('tmp_lochness')
args.sources = ['box']
create_lochness_template(args)
keyring = KeyringAndEncrypt(args.outdir)
information_to_add_to_metadata = {'box': {
'subject_id': '1001',
'source_id': 'O1234'}}
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)
lochness_obj = config_load_test('tmp_lochness/config.yml', '')
return args, lochness_obj
def test_lochness_to_lochness_transfer_receive(Lochness):
print()
protected_dir = Path(Lochness['phoenix_root']) / 'PROTECTED'
for i in range(10):
with tf.NamedTemporaryFile(suffix='tmp.text',
delete=False,
dir=protected_dir) as tmpfilename:
with open(tmpfilename.name, 'w') as f:
f.write('ha')
#pull all
# lochness_to_lochness_transfer(Lochness, general_only=False)
with tf.NamedTemporaryFile(suffix='tmp.tar', delete=False,
dir='.') as tmpfilename:
# compress
compress_new_files(Lochness['lochness_sync_history_csv'],
Lochness['phoenix_root'], tmpfilename.name, False)
show_tree_then_delete('tmp_lochness')
compressed_file = list(Path('.').glob('tmp*tar'))[0]
os.popen(f'tar -xf {compressed_file}').read()
os.remove(str(compressed_file))
show_tree_then_delete('PHOENIX')
out_dir = 'DPACC'
args = DpaccArgs(out_dir)
create_lochness_template(args)
update_keyring_and_encrypt_DPACC(args.outdir)
lochness = config_load_test(f'{out_dir}/config.yml', '')
lochness_to_lochness_transfer_receive(lochness)
show_tree_then_delete('DPACC')
def test_sync_mindlamp(args):
syncArgs = SyncArgs(args.outdir)
syncArgs.studies = ['StudyA']
sources = ['mindlamp']
syncArgs.update_source(sources)
create_lochness_template(args)
syncArgs.config = args.outdir / 'config.yml'
_ = KeyringAndEncryptMindlamp(args.outdir)
phoenix_root = args.outdir / 'PHOENIX'
information_to_add_to_metadata = {'mindlamp': {'subject_id': '1001',
'source_id': 'U7045332804'}}
initialize_metadata_test(phoenix_root, 'StudyA',
information_to_add_to_metadata)
Lochness = config_load_test(syncArgs.config)
for subject in lochness.read_phoenix_metadata(Lochness, syncArgs.studies):
sync(Lochness, subject, False)
show_tree_then_delete('tmp_lochness')
def test_create_lochness_template_multiple_study(args):
args.studies = ['StudyA', 'StudyB']
create_lochness_template(args)
show_tree_then_delete('tmp_lochness')
def test_create_lochness_template(args):
create_lochness_template(args)
show_tree_then_delete('tmp_lochness')