def test_daris_download():
daris_uid = 'subject01'
latest_pull_mtime = 0
token = Tokens()
token, url, project_cid = token.read_token_or_get_input('daris')
dst_zipfile = 'tmp.zip'
daris_download(daris_uid, latest_pull_mtime, token,
project_cid, url, dst_zipfile)
tmpdir = tf.mkdtemp(dir='.', prefix='.')
with zipfile.ZipFile(dst_zipfile, 'r') as zip_ref:
zip_ref.extractall(tmpdir)
nfiles_in_dirs = []
for root, dirs, files in os.walk(tmpdir):
for directory in dirs:
os.chmod(os.path.join(root, directory), 0o0755)
for f in files:
os.chmod(os.path.join(root, f), 0o0755)
nfiles_in_dirs.append(len(files))
# if there is any new file downloaded save timestamp
if any([x > 1 for x in nfiles_in_dirs]):
print('Downloaded')
else:
print('No file downloaded')
os.remove(dst_zipfile)
shutil.rmtree(tmpdir)
def update_for_xnat(self, study):
token = Tokens()
url, username, password = token.read_token_or_get_input('xnat')
self.keyring[f'xnat.hcpep'] = {}
self.keyring[f'xnat.hcpep']['URL'] = url
self.keyring[f'xnat.hcpep']['USERNAME'] = username
self.keyring[f'xnat.hcpep']['PASSWORD'] = password
self.write_keyring_and_encrypt()
def __init__(self, tmp_dir):
super().__init__(tmp_dir)
token = Tokens()
token, url, project_cid = token.read_token_or_get_input('daris')
self.keyring['daris.StudyA']['TOKEN'] = token
self.keyring['daris.StudyA']['URL'] = url
self.keyring['daris.StudyA']['PROJECT_CID'] = project_cid
self.write_keyring_and_encrypt()
def update_for_box(self, study):
token = Tokens()
client_id, client_secret, api_token = \
token.read_token_or_get_input('box')
self.keyring[f'box.{study}'] = {}
self.keyring[f'box.{study}']['CLIENT_ID'] = client_id
self.keyring[f'box.{study}']['CLIENT_SECRET'] = client_secret
self.keyring[f'box.{study}']['API_TOKEN'] = api_token
self.write_keyring_and_encrypt()
def __init__(self, tmp_dir):
super().__init__(tmp_dir)
token = Tokens()
host, username, password, path_in_host, port = \
token.read_token_or_get_input('transfer')
self.keyring['lochness_sync']['HOST'] = host
self.keyring['lochness_sync']['USERNAME'] = username
self.keyring['lochness_sync']['PASSWORD'] = password
self.keyring['lochness_sync']['PATH_IN_HOST'] = path_in_host
self.keyring['lochness_sync']['PORT'] = port
self.write_keyring_and_encrypt()
def test_lamp_modules():
token = Tokens()
mindlamp_token, access_key, secret_key, api_url = \
token.read_token_or_get_input('mindlamp')
LAMP.connect(access_key, secret_key)
study_id, study_name = get_study_lamp(LAMP)
subject_ids = get_participants_lamp(LAMP, study_id)
for subject_id in subject_ids:
if subject_id == 'U7045332804':
print(subject_id)
# activity_dicts = get_activities_lamp(LAMP, subject_id)
activity_dicts = get_activity_events_lamp(LAMP, subject_id)
sensor_dicts = get_sensor_events_lamp(LAMP, subject_id)
def __init__(self, tmp_dir):
super().__init__(tmp_dir)
token = Tokens()
mindlamp_token, access_key, secret_key, api_url = \
token.read_token_or_get_input('mindlamp')
# mindlamp_token, access_key, secret_key, api_url = \
# token.get_mindlamp_token()
self.keyring['mindlamp.StudyA'] = {}
self.keyring['mindlamp.StudyA']['ACCESS_KEY'] = access_key
self.keyring['mindlamp.StudyA']['SECRET_KEY'] = secret_key
self.keyring['mindlamp.StudyA']['URL'] = api_url
self.write_keyring_and_encrypt()
def test_sftp():
tokens = Tokens(test_dir / 'lochness_test' / 'transfer')
host, username, password, path_in_host, port = \
tokens.read_token_or_get_input()
file_to_send = 'hoho.txt'
with open(file_to_send, 'w') as f:
f.write('hahahah')
transport = paramiko.Transport((host, int(port)))
transport.connect(username=username, password=password)
sftp = paramiko.SFTPClient.from_transport(transport)
sftp.put(file_to_send, str(Path(path_in_host) / Path(file_to_send).name))
sftp.close()
transport.close()
os.remove('hoho.txt')