def sync(Lochness, subject, dry):
delete = lochness.dropbox.delete_on_success(Lochness, Basename)
logger.debug('delete_on_success for {0} is {1}'.format(Basename, delete))
for dbx_sid in subject.dropbox[Module]:
logger.debug('exploring {0}/{1}'.format(subject.study, subject.id))
_passphrase = keyring.passphrase(Lochness, subject.study)
enc_key = cryptease.kdf(_passphrase)
api_token = keyring.dropbox_api_token(Lochness, Module)
client = dropbox.Dropbox(api_token)
for datatype, products in iter(CONFIG.items()):
dbx_head = os.path.join(os.sep, datatype, subject.study, dbx_sid)
dbx_head_len = len(dbx_head)
logger.debug('walking %s', dbx_head)
for root, dirs, files in lochness.dropbox.walk(client, dbx_head):
for f in files:
dbx_tail = os.path.join(root,
f)[dbx_head_len:].lstrip(os.sep)
dbx_file = (dbx_head, dbx_tail)
product = _find_product(dbx_tail,
products,
subject=dbx_sid)
if not product:
continue
protect = product.get('protect', False)
compress = product.get('compress', False)
key = enc_key if protect else None
output_base = subject.protected_folder if protect else subject.general_folder
output_base = tree.get(datatype, output_base)
lochness.dropbox.save(client,
dbx_file,
output_base,
key=key,
compress=compress,
delete=delete,
dry=dry)
def sync(Lochness, subject, dry):
delete = lochness.dropbox.delete_on_success(Lochness, Basename)
logger.debug('delete_on_success for {0} is {1}'.format(Basename, delete))
for dbx_sid in subject.dropbox[Module]:
logger.debug('exploring {0}/{1}'.format(subject.study, subject.id))
_passphrase = keyring.passphrase(Lochness, subject.study)
enc_key = cryptease.kdf(_passphrase)
api_token = keyring.dropbox_api_token(Lochness, Module)
client = dropbox.Dropbox(api_token)
patterns = _batch_compile(CONFIG, dbx_sid)
for category,datatype in _iterate(CONFIG):
output_base = subject.protected_folder if category == 'PROTECTED' else subject.general_folder
output_base = tree.get(datatype, output_base)
dbx_head = os.path.join(os.sep, datatype, subject.study)
# shim the dropbox head for certain data types
if datatype == 'onsite_interview':
dbx_head = os.path.join(dbx_head, 'output')
elif datatype == 'behav_qc':
dbx_head = os.path.join(dbx_head, dbx_sid)
dbx_head_len = len(dbx_head)
for root,dirs,files in lochness.dropbox.walk(client, dbx_head):
for f in files:
dbx_tail = os.path.join(root, f)[dbx_head_len:].lstrip(os.sep)
dbx_file = dbx_head,dbx_tail
if patterns[datatype].match(dbx_tail):
key = enc_key if category == 'PROTECTED' else None
lochness.dropbox.save(client, dbx_file, output_base,
key=key, delete=delete, dry=dry)
def write_keyring_and_encrypt(self):
with open(self.keyring_loc, 'w') as f:
json.dump(self.keyring, f)
keyring_content = open(self.keyring_loc, 'rb')
key = crypt.kdf('')
crypt.encrypt(
keyring_content, key,
filename=self.tmp_lochness_dir / '.lochness.enc')
def main():
parser = ap.ArgumentParser('File encryption/decryption utility')
group1 = parser.add_mutually_exclusive_group(required=True)
group1.add_argument('--decrypt', action='store_true', help='Decrypt file')
group1.add_argument('--encrypt', action='store_true', help='Encrypt file')
parser.add_argument('-o', '--output-file', help='Output file')
parser.add_argument('--debug',
action='store_true',
help='Enable debug messages')
parser.add_argument('file', help='File to encrypt or decrypt')
args = parser.parse_args()
# read passphrase (ask twice for --encrypt)
if 'ENCRYPT_PASS' in os.environ:
passphrase = os.environ['ENCRYPT_PASS']
else:
passphrase = gp.getpass('enter passphrase: ')
if args.encrypt:
reentered = gp.getpass('re-enter passphrase: ')
if passphrase != reentered:
logger.critical('passphrases do not match')
sys.exit(1)
# get file handle
raw = get(args.file)
# get key using file header, or build a new one
if args.decrypt:
key = crypt.key_from_file(raw, passphrase)
else:
key = crypt.kdf(passphrase)
# lock or unlock the file
if args.decrypt:
if not args.output_file:
stdout = os.fdopen(sys.stdout.fileno(), 'wb')
for chunk in crypt.decrypt(raw, key):
stdout.write(chunk)
else:
if overwrite(args.output_file):
logger.info('saving {}'.format(args.output_file))
crypt.decrypt(raw, key, filename=args.output_file)
elif args.encrypt:
if not args.output_file:
stdout = os.fdopen(sys.stdout.fileno(), 'wb')
for chunk in crypt.encrypt(raw, key):
stdout.write(chunk)
else:
if overwrite(args.output_file):
logger.info('saving {}'.format(args.output_file))
crypt.encrypt(raw, key, filename=args.output_file)
def update_keyring_and_encrypt_DPACC(tmp_lochness_dir: str):
keyring_loc = Path(tmp_lochness_dir) / 'lochness.json'
with open(keyring_loc, 'r') as f:
keyring = json.load(f)
keyring['lochness_sync']['PATH_IN_HOST'] = '.'
with open(keyring_loc, 'w') as f:
json.dump(keyring, f)
keyring_content = open(keyring_loc, 'rb')
key = crypt.kdf('')
crypt.encrypt(keyring_content,
key,
filename=Path(tmp_lochness_dir) / '.lochness.enc')
def main():
parser = ap.ArgumentParser('File encryption/decryption utility')
parser.add_argument('--keyring',
default='~/.nrg-keyring.enc',
type=os.path.expanduser,
help='Keyring file')
group = parser.add_mutually_exclusive_group()
group.add_argument('--phoenix-study',
help='Return passphrase for PHOENIX study')
group.add_argument('--beiwe-study',
help='Return passphrase for Beiwe study')
parser.add_argument('--debug',
action='store_true',
help='Enable debug messages')
args = parser.parse_args()
# read encrypted keyring file
raw = open(args.keyring)
# get salt from raw file header
salt = None
header, _ = crypt.read_header(raw)
salt = header['kdf'].salt
# read passphrase from an env or command line
if 'NRG_KEYRING_PASS' in os.environ:
passphrase = os.environ['NRG_KEYRING_PASS']
else:
passphrase = gp.getpass('enter passphrase: ')
# construct decryption key
key = crypt.kdf(passphrase, salt=salt)
# decrypt the keyring content
content = ''
for chunk in crypt.decrypt(raw, key):
content += chunk
js = json.loads(content)
# return what the user requested
try:
if args.phoenix_study:
sys.stdout.write(js['kitchen']['SECRETS'][args.phoenix_study])
elif args.beiwe_study:
sys.stdout.write(js['beiwe']['SECRETS'][args.beiwe_study])
except KeyError as e:
logger.critical('key not found {0}'.format(e))
sys.exit(1)
def test_write_file():
original = b'''Lorem ipsum dolor sit amet, consectetur adipiscing elit,
sed do eiusmod tempor incididunt ut labore et dolore
magna aliqua. Ut enim ad minim veniam, quis nostrud
exercitation ullamco laboris nisi ut aliquip ex ea commodo
consequat.'''
passphrase = 'foo bar biz bat'
key = crypt.kdf(passphrase)
with tf.NamedTemporaryFile(dir=DIR, prefix='enc', delete=False) as enc_tmp:
crypt.encrypt_to_file(enc_tmp.name, io.BytesIO(original), key)
key = None
with tf.NamedTemporaryFile(dir=DIR, prefix='dec', delete=False) as dec_tmp:
with open(enc_tmp.name, 'rb') as fo:
key = crypt.key_from_file(fo, passphrase)
crypt.decrypt_to_file(dec_tmp.name, fo, key)
os.remove(enc_tmp.name)
with open(dec_tmp.name, 'rb') as fo:
decrypted = fo.read()
os.remove(dec_tmp.name)
assert decrypted == original
def save(Keyring, archive, user_id, output_dir, lock=None, passphrase=None):
'''
The order of operations here is important to ensure the ability
to reach a state of consistency:
1. Save the file
2. Update the local registry
'''
num_saved = 0
if not archive:
return num_saved
encoding = locale.getpreferredencoding()
if not lock:
lock = list()
else:
if not passphrase:
raise SaveError(
'if you wish to lock a data type, you need a passphrase')
lock_ext = LOCK_EXT.lstrip('.')
# open registry file in downloaded archive
logger.debug('reading registry file from beiwe archive')
with archive.open('registry', 'r') as fo:
registry = json.loads(fo.read().decode('utf-8'))
# if archive registry contains any entries, process them
if registry:
# iterate over archive members
for member in archive.namelist():
# skip over the registry file
if member == 'registry':
continue
# get information about the current archive member
info = archive.getinfo(member)
# parse the data type name from the current archive member
member_datatype = _parse_datatype(member, user_id)
# check if data type should be encrypted
encrypt = True if member_datatype in lock else False
logger.debug('processing archive member: %s (lock=%s)', member,
encrypt)
# create target name
target = member
# add lock extension to target name if necessary
if encrypt:
target = '{0}.{1}'.format(target, lock_ext)
target_abs = os.path.join(output_dir, target)
target_dir = os.path.dirname(target_abs)
# detect if target exists
if os.path.exists(target_abs):
os.remove(target_abs)
# create target directory
if not os.path.exists(target_dir):
_makedirs(target_dir, umask=0o5022)
# read archive member content and encrypt it if necessary
content = archive.open(member)
if encrypt:
key = crypt.kdf(passphrase)
crypt.encrypt(content,
key,
filename=target_abs,
permissions=0o0644)
else:
# write content to persistent storage
_atomic_write(target_abs, content.read())
num_saved += 1
# update local registry file to avoid re-downloading these files
local_registry_file = os.path.join(output_dir, user_id, '.registry')
local_registry = dict()
if os.path.exists(local_registry_file):
with open(local_registry_file, 'r') as fo:
local_registry = json.load(fo)
local_registry.update(registry)
local_registry_str = json.dumps(local_registry, indent=2)
_atomic_write(local_registry_file, local_registry_str.encode(encoding))
# return the number of saved files
return num_saved
def sync_module(Lochness: 'lochness.config', subject: 'subject.metadata',
study_name: 'mediaflux.study_name', dry: bool):
'''sync mediaflux data for the subject'''
if dry:
raise NotImplementedError('--dry option is not implemented')
study_basename = study_name.split('.')[1]
for mf_subid in subject.mediaflux[study_name]:
logger.debug(f'exploring {subject.study}/{subject.id}')
_passphrase = keyring.passphrase(Lochness, subject.study)
enc_key = enc.kdf(_passphrase)
mflux_cfg = keyring.mediaflux_api_token(Lochness, study_name)
mf_base = base(Lochness, study_basename)
print(mf_base)
for datatype, products in \
iter(Lochness['mediaflux'][study_basename]['file_patterns'].items()):
print(datatype, products)
'''
file_patterns:
actigraphy:
- vendor: Philips
product: Actiwatch 2
data_dir: all_BWH_actigraphy
pattern: 'accel/*csv'
protect: True
- vendor: Activinsights
product: GENEActiv
data_dir: all_BWH_actigraphy
pattern: 'GENEActiv/*bin,GENEActiv/*csv'
'''
for prod in products:
for patt in prod['pattern'].split(','):
# consider the case with space
# pattern: 'GENEActiv/*bin, GENEActiv/*csv'
patt = patt.strip()
if '*' not in patt:
raise PatternError(
'Mediaflux pattern must include an asterisk e.g. *csv or GENEActiv/*csv'
)
# construct mediaflux remote dir
mf_remote_pattern = pjoin(mf_base, prod['data_dir'],
mf_subid, patt)
mf_remote_dir = dirname(mf_remote_pattern)
# obtain mediaflux remote paths
with tempfile.TemporaryDirectory() as tmpdir:
diff_path = pjoin(tmpdir, 'diff.csv')
cmd = (' ').join([
'unimelb-mf-check', '--mf.config', mflux_cfg,
'--nb-retries 5', '--direction down', tmpdir,
mf_remote_dir, '-o', diff_path
])
p = Popen(cmd, shell=True)
p.wait()
# ENH
# if dry: exit()
if not isfile(diff_path):
continue
df = pd.read_csv(diff_path)
for remote in df['SRC_PATH'].values:
if remote is nan:
continue
if not re.search(patt.replace('*', '(.+?)'),
remote):
continue
else:
remote = remote.split(':')[1]
# construct local path
protect = prod.get('protect', True)
processed = prod.get('processed', False)
key = enc_key if protect else None
subj_dir = subject.protected_folder \
if protect else subject.general_folder
# mf_local= pjoin(subj_dir, datatype, dirname(patt), basename(remote))
mf_local = str(
tree.get(datatype,
subj_dir,
processed=processed,
BIDS=Lochness['BIDS']))
# ENH set different permissions
# GENERAL: 0o755, PROTECTED: 0700
os.makedirs(mf_local, exist_ok=True)
# subprocess call unimelb-mf-download
cmd = (' ').join([
'unimelb-mf-download', '--mf.config',
mflux_cfg, '-o', mf_local, '--nb-retries 5',
f'\"{remote}\"'
])
p = Popen(cmd, shell=True)
p.wait()
# verify checksum after download completes
# if checksum does not match, data will be downloaded again
# ENH should we verify checksum 5 times?
cmd += ' --csum-check'
p = Popen(cmd, shell=True)
p.wait()
def sync_module(Lochness: 'lochness.config', subject: 'subject.metadata',
module_name: 'box.module_name', dry: bool):
'''Sync box data for the subject'''
# only the module_name string without 'box.'
module_basename = module_name.split('.')[1]
# delete on success
delete = delete_on_success(Lochness, module_basename)
logger.debug(f'delete_on_success for {module_basename} is {delete}')
for bx_sid in subject.box[module_name]:
logger.debug(f'exploring {subject.study}/{subject.id}')
_passphrase = keyring.passphrase(Lochness, subject.study)
enc_key = enc.kdf(_passphrase)
client_id, client_secret, api_token = keyring.box_api_token(
Lochness, module_name)
# box authentication
auth = OAuth2(
client_id=client_id,
client_secret=client_secret,
access_token=api_token,
)
client = Client(auth)
bx_base = base(Lochness, module_basename)
# get the id of the bx_base path in box
bx_base_obj = get_box_object_based_on_name(client, bx_base, '0')
if bx_base_obj == None:
logger.debug('Root of the box is not found')
continue
# loop through the items defined for the BOX data
for datatype, products in iter(
Lochness['box'][module_basename]['file_patterns'].items()):
subject_obj = get_box_object_based_on_name(client, bx_sid,
bx_base_obj.id)
if subject_obj == None:
logger.debug(f'{bx_sid} is not found under {bx_base_obj}')
continue
datatype_obj = get_box_object_based_on_name(
client, datatype, subject_obj.id)
# full path
bx_head = join(bx_base, datatype, bx_sid)
logger.debug('walking %s', bx_head)
# if the directory is empty
if datatype_obj == None:
continue
# walk through the root directory
for root, dirs, files in walk_from_folder_object(
bx_head, datatype_obj):
for box_file_object in files:
bx_tail = join(basename(root), box_file_object.name)
product = _find_product(bx_tail, products, subject=bx_sid)
if not product:
continue
protect = product.get('protect', False)
output_base = subject.protected_folder \
if protect else subject.general_folder
encrypt = product.get('encrypt', False)
key = enc_key if encrypt else None
processed = product.get('processed', False)
# For DPACC, get processed from the config.yml
output_base = tree.get(datatype,
output_base,
processed=processed,
BIDS=Lochness['BIDS'])
compress = product.get('compress', False)
save(box_file_object, (root, box_file_object.name),
output_base,
key=key,
compress=compress,
delete=False,
dry=False)
