def register_sync(self, root_data_folder, dry=False):
flag_files = Path(root_data_folder).glob('**/register_me.flag')
for flag_file in flag_files:
if dry:
print(flag_file)
continue
file_list = flags.read_flag_file(flag_file)
logger_.info('registering ' + str(flag_file.parent))
status_str = self.register_session(flag_file.parent,
file_list=file_list)
if status_str:
error_message = str(flag_file.parent) + ' failed registration'
error_message += '\n' + ' ' * 8 + status_str
error_message += traceback.format_exc()
logger_.error(error_message)
err_file = flag_file.parent.joinpath('register_me.error')
flag_file.replace(err_file)
with open(err_file, 'w+') as f:
f.write(error_message)
continue
flags.write_flag_file(flag_file.parent.joinpath('flatiron.flag'),
file_list=file_list)
flag_file.unlink()
if flag_file.parent.joinpath('create_me.flag').exists():
flag_file.parent.joinpath('create_me.flag').unlink()
logger_.info('registered' + '\n')
def test_transfer(self):
src_subjects_path = self.root_data_folder / "src"
dst_subjects_path = self.root_data_folder / "dst"
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
gsrc = [x.name for x in list(src_subjects_path.rglob('*.*'))]
gdst = [x.name for x in list(dst_subjects_path.rglob('*.*'))]
self.assertTrue('extract_me.flag' in gdst)
gdst = [x for x in gdst if x != 'extract_me.flag']
self.assertTrue('compress_video.flag' in gdst)
gdst = [x for x in gdst if x != 'compress_video.flag']
self.assertTrue('_iblrig_micData.raw.wav' in gdst)
gdst = [x for x in gdst if x != '_iblrig_micData.raw.wav']
self.assertTrue('_iblrig_leftCamera.raw.avi' in gdst)
gdst = [x for x in gdst if x != '_iblrig_leftCamera.raw.avi']
self.assertEqual(gsrc, gdst)
# Test if folder exists not copy because no flag
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
# Test if flag exists and folder exists in dst
flags.write_flag_file(self.session_path.joinpath("transfer_me.flag"))
(self.session_path / "raw_behavior_data" /
'_iblrig_micData.raw.wav').touch()
(self.session_path / "raw_video_data" /
'_iblrig_leftCamera.raw.avi').touch()
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
# Test transfer w/o video and audio
flags.write_flag_file(self.session_path.joinpath("transfer_me.flag"))
(self.session_path / "raw_behavior_data" / "random.data1.ext").touch()
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
def test_transfer_training(self):
src_subjects_path = self.root_data_folder / "src"
dst_subjects_path = self.root_data_folder / "dst"
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
gsrc = [x.name for x in list(src_subjects_path.rglob('*.*'))]
gdst = [x.name for x in list(dst_subjects_path.rglob('*.*'))]
self.assertTrue(set(gsrc).issubset(set(gdst)))
dst_session_path = dst_subjects_path.joinpath(
self.session_path.relative_to(src_subjects_path))
flag_files = [dst_session_path.joinpath('raw_session.flag')]
for fl in flag_files:
self.assertTrue(fl.exists())
# Test if folder exists not copy because no flag
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
# Test if flag exists and folder exists in dst
flags.write_flag_file(self.session_path.joinpath("transfer_me.flag"))
(self.session_path / "raw_behavior_data" /
'_iblrig_micData.raw.wav').touch()
(self.session_path / "raw_video_data" /
'_iblrig_leftCamera.raw.avi').touch()
transfer_rig_data.main(src_subjects_path,
dst_subjects_path,
force=True)
# Test transfer w/o video and audios
flags.write_flag_file(self.session_path.joinpath("transfer_me.flag"))
(self.session_path / "raw_behavior_data" / "random.data1.ext").touch()
transfer_rig_data.main(src_subjects_path,
dst_subjects_path,
force=True)
def sync_merge_ephys(root_data_folder, dry=False):
"""
Post spike-sorting processing:
- synchronization of probes
- ks2 to ALF conversion for each probes in alf/probeXX folder
- computes spike sorting QC
- creates probes object in alf folder
To start the job for a session, all electrophysiology ap files from session need to be
associated with a `sync_merge_ephys.flag` file
Outputs individual probes
"""
syncflags = list(Path(root_data_folder).rglob('sync_merge_ephys.flag'))
session_paths = list(set([f.parents[2] for f in syncflags]))
for session_path in session_paths:
print(session_path)
if dry:
continue
# first remove the flags
[f.unlink() for f in syncflags if f.parents[2] == session_path]
# first sync the probes
sync_probes.sync(session_path)
# then convert ks2 to ALF and resync spike sorting data
spikes.sync_spike_sortings(session_path)
# outputs the probes object in the ALF folder
spikes.probes_description(session_path)
# wrap up by removing flags and creating register_me flag
flags.write_flag_file(session_path.joinpath('register_me.flag'))
def compress_ephys(root_data_folder, dry=False, max_sessions=5):
"""
Compress ephys files looking for `compress_ephys.flag` whithin the probes folder
Original bin file will be removed
The registration flag created contains targeted file names at the root of the session
"""
qcflags = Path(root_data_folder).rglob('compress_ephys.flag')
c = 0
for qcflag in qcflags:
probe_path = qcflag.parent
c += 1
if c > max_sessions:
return
if dry:
print(qcflag.parent)
continue
# no rglob: only the folder in which the flag is located gets searched
ephys_files = spikeglx.glob_ephys_files(probe_path, recursive=False)
out_files = []
for ef in ephys_files:
for typ in ['ap', 'lf', 'nidq']:
bin_file = ef.get(typ)
if not bin_file:
continue
sr = spikeglx.Reader(bin_file)
if not sr.is_mtscomp:
out_files.append(sr.compress_file(keep_original=False))
qcflag.unlink()
if out_files:
session_path = probe_path.parents[1]
file_list = [str(f.relative_to(session_path)) for f in out_files]
flags.write_flag_file(probe_path.joinpath('register_me.flag'), file_list=file_list)
def bulk(subjects_folder, dry=False):
ses_path = Path(subjects_folder).glob('**/extract_me.flag')
for p in ses_path:
# @alejandro no need for flags until personal project data starts going to server
# the flag file may contains specific file names for a targeted extraction
save = flags.read_flag_file(p)
if dry:
print(p)
continue
try:
from_path(p.parent, force=True, save=save)
except Exception as e:
error_message = str(
p.parent) + ' failed extraction' + '\n ' + str(e)
error_message += traceback.format_exc()
err_file = p.parent.joinpath('extract_me.error')
p.replace(err_file)
with open(err_file, 'w+') as f:
f.write(error_message)
logger_.error(error_message)
continue
p.unlink()
flags.write_flag_file(p.parent.joinpath('register_me.flag'),
file_list=save)
def check_create_raw_session_flag(session_folder: str) -> None:
session_path = Path(session_folder)
ephys = session_path.joinpath('ephys_data_transferred.flag')
video = session_path.joinpath('video_data_transferred.flag')
if ephys.exists() and video.exists():
flags.write_flag_file(session_path.joinpath('raw_session.flag'))
ephys.unlink()
video.unlink()
def main(local_folder: str, remote_folder: str, force: bool = False) -> None:
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
log.info("Nothing to transfer, exiting...")
return
# Create all dst paths
dst_session_paths = []
for s in src_session_paths:
mouse = s.parts[-3]
date = s.parts[-2]
sess = s.parts[-1]
d = remote_folder / mouse / date / sess
dst_session_paths.append(d)
for src, dst in zip(src_session_paths, dst_session_paths):
src_flag_file = src / "transfer_me.flag"
flag = flags.read_flag_file(src_flag_file)
if isinstance(flag, list):
raise NotImplementedError
else:
if force:
shutil.rmtree(dst, ignore_errors=True)
log.info(f"Copying {src}...")
shutil.copytree(src, dst, ignore=ig(str(src_flag_file.name)))
# finally if folder was created delete the src flag_file and create compress_me.flag
if dst.exists():
task_type = ibllib.io.extractors.base.get_session_extractor_type(
Path(src))
if task_type not in ['ephys', 'ephys_sync', 'ephys_mock']:
flags.write_flag_file(dst.joinpath('raw_session.flag'))
settings = raw.load_settings(dst)
if 'ephys' in settings[
'PYBPOD_BOARD']: # Any traing task on an ephys rig
dst.joinpath('raw_session.flag').unlink()
log.info(
f"Copied to {remote_folder}: Session {src_flag_file.parent}")
src_flag_file.unlink()
# Cleanup
src_video_file = src / 'raw_video_data' / '_iblrig_leftCamera.raw.avi'
dst_video_file = dst / 'raw_video_data' / '_iblrig_leftCamera.raw.avi'
src_audio_file = src / 'raw_behavior_data' / '_iblrig_micData.raw.wav'
dst_audio_file = dst / 'raw_behavior_data' / '_iblrig_micData.raw.wav'
if src_audio_file.exists() and \
src_audio_file.stat().st_size == dst_audio_file.stat().st_size:
src_audio_file.unlink()
if src_video_file.exists() and \
src_video_file.stat().st_size == dst_video_file.stat().st_size:
src_video_file.unlink()
def sync_merge(session_path, dry=False, force=False):
"""
Sync probes and merge spike sorting output.
For single probe dataset, output ks2 as ALF dataset
"""
session_path = Path(session_path)
sync(session_path, display=False)
spikes.merge_probes(session_path)
flags.write_flag_file(session_path.joinpath('register_me.flag'))
def setUp(self):
self.tmp_dir = tempfile.TemporaryDirectory()
self.root_data_folder = Path(self.tmp_dir.name)
self.session_path = self.root_data_folder / "src" / 'algernon' / '2019-01-21' / '001'
self.session_path.mkdir(parents=True, exist_ok=True)
flags.write_flag_file(self.session_path.joinpath("transfer_me.flag"))
(self.session_path / "raw_behavior_data").mkdir()
(self.session_path / "raw_video_data").mkdir()
(self.session_path / "raw_behavior_data" / "random.data1.ext").touch()
def bulk(subjects_folder, dry=False, glob_flag='**/extract_me.flag'):
ses_path = Path(subjects_folder).glob(glob_flag)
for p in ses_path:
# the flag file may contains specific file names for a targeted extraction
save = flags.read_flag_file(p)
if dry:
print(p)
continue
from_path(p.parent, force=True, save=save)
p.unlink()
flags.write_flag_file(p.parent.joinpath('register_me.flag'), file_list=save)
def main(local_folder: str, remote_folder: str, force: bool = True) -> None:
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
log.info("Nothing to transfer, exiting...")
return
# Create all dst paths
dst_session_paths = []
for s in src_session_paths:
mouse = s.parts[-3]
date = s.parts[-2]
sess = s.parts[-1]
d = remote_folder / mouse / date / sess
dst_session_paths.append(d)
for src, dst in zip(src_session_paths, dst_session_paths):
src_flag_file = src / "transfer_me.flag"
flag = flags.read_flag_file(src_flag_file)
if isinstance(flag, list):
raise NotImplementedError
else:
if force:
shutil.rmtree(dst, ignore_errors=True)
log.info(f"Copying {src}...")
shutil.copytree(src, dst, ignore=ig(str(src_flag_file.name)))
# finally if folder was created delete the src flag_file and create compress_me.flag
if dst.exists():
dst_flag_file = dst / 'extract_me.flag'
flags.write_flag_file(dst_flag_file)
flags.create_compress_flags(dst)
log.info(
f"Copied to {remote_folder}: Session {src_flag_file.parent}")
src_flag_file.unlink()
# Cleanup
src_audio_file = src / 'raw_behavior_data' / '_iblrig_micData.raw.wav'
src_video_file = src / 'raw_video_data' / '_iblrig_leftCamera.raw.avi'
dst_audio_file = dst / 'raw_behavior_data' / '_iblrig_micData.raw.wav'
dst_video_file = dst / 'raw_video_data' / '_iblrig_leftCamera.raw.avi'
if src_audio_file.exists() and \
src_audio_file.stat().st_size == dst_audio_file.stat().st_size:
src_audio_file.unlink()
if src_video_file.exists() and \
src_video_file.stat().st_size == dst_video_file.stat().st_size:
src_video_file.unlink()
def _compress(root_data_folder,
command,
flag_pattern,
dry=False,
max_sessions=None):
# runs a command of the form command = "ls -1 {file_name}.avi"
c = 0
for flag_file in Path(root_data_folder).rglob(flag_pattern):
ses_path = flag_file.parent
files2compress = flags.read_flag_file(flag_file)
if isinstance(files2compress, bool):
Path(flag_file).unlink()
continue
for f2c in files2compress:
cfile = ses_path.joinpath(PureWindowsPath(f2c))
c += 1
if max_sessions and c > max_sessions:
return
print(cfile)
if dry:
continue
if not cfile.exists():
_logger.error(f'NON-EXISTING RAW FILE: {cfile}. Skipping...')
continue
if flag_file.exists():
flag_file.unlink()
# run the compression command redirecting output
cfile.parent.joinpath(cfile.stem)
# if the output file already exists, overwrite it
outfile = cfile.parent / (cfile.stem + '.mp4')
if outfile.exists():
outfile.unlink()
command2run = command.format(
file_name=cfile.parent.joinpath(cfile.stem))
process = subprocess.Popen(command2run,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
info, error = process.communicate()
if process.returncode != 0:
_logger.error('COMPRESSION FAILED FOR ' + str(cfile))
with open(cfile.parent.joinpath('extract.error'), 'w+') as fid:
fid.write(command2run)
fid.write(error.decode())
else:
# if the command was successful delete the original file
cfile.unlink()
# and add the file to register_me.flag
flags.write_flag_file(ses_path.joinpath('register_me.flag'),
file_list=cfile.stem)
def qc_ephys(root_data_folder, dry=False, max_sessions=10, force=False):
qcflags = Path(root_data_folder).rglob('qc_ephys.flag')
c = 0
for qcflag in qcflags:
session_path = qcflag.parent
c += 1
if c >= max_sessions:
return
if dry:
print(qcflag.parent)
continue
qc_files = ephysqc.qc_session(session_path, dry=dry, force=force)
qcflag.unlink()
flags.write_flag_file(session_path.joinpath('register_me.flag'), file_list=qc_files)
def testFlagFile(self):
# empty file should return True
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
# test with 2 lines and a trailing
with open(self.tempfile.name, 'w+') as fid:
fid.write('file1\nfile2\n')
self.assertEqual(flags.read_flag_file(self.tempfile.name),
['file1', 'file2'])
# test with 2 lines and a trailing, Windows convention
with open(self.tempfile.name, 'w+') as fid:
fid.write('file1\r\nfile2\r\n')
self.assertEqual(flags.read_flag_file(self.tempfile.name),
['file1', 'file2'])
# test read after write
file_list = [
'_ibl_extraRewards.times', '_ibl_lickPiezo.raw',
'_ibl_lickPiezo.timestamps'
]
flags.write_flag_file(self.tempfile.name, file_list)
self.assertEqual(flags.read_flag_file(self.tempfile.name), file_list)
# makes sure that read after write empty list returns True
flags.write_flag_file(self.tempfile.name, [])
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
# makes sure that read after write None also returns True
flags.write_flag_file(self.tempfile.name, None)
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
# make sure that read after write with a string workds
flags.write_flag_file(self.tempfile.name, '_ibl_lickPiezo.raw')
self.assertEqual(flags.read_flag_file(self.tempfile.name),
['_ibl_lickPiezo.raw'])
def create_ephys_flags(session_folder: str):
session_path = Path(session_folder)
flags.write_flag_file(session_path.joinpath('extract_ephys.flag'))
flags.write_flag_file(session_path.joinpath('raw_ephys_qc.flag'))
probe00_path = session_path / 'raw_ephys_data' / 'probe00'
probe01_path = session_path / 'raw_ephys_data' / 'probe01'
flags.write_flag_file(probe00_path.joinpath('spike_sorting.flag'))
flags.write_flag_file(probe01_path.joinpath('spike_sorting.flag'))
def create_ephys_flags(session_folder: str):
session_path = Path(session_folder)
flags.write_flag_file(session_path.joinpath("extract_ephys.flag"))
flags.write_flag_file(session_path.joinpath("raw_ephys_qc.flag"))
probe00_path = session_path / "raw_ephys_data" / "probe00"
probe01_path = session_path / "raw_ephys_data" / "probe01"
flags.write_flag_file(probe00_path.joinpath("spike_sorting.flag"))
flags.write_flag_file(probe01_path.joinpath("spike_sorting.flag"))
def test_transfer(self):
src_subjects_path = self.root_data_folder / "src"
dst_subjects_path = self.root_data_folder / "dst"
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
gsrc = [x.name for x in list(src_subjects_path.rglob('*.*'))]
gdst = [x.name for x in list(dst_subjects_path.rglob('*.*'))]
self.assertTrue('extract_me.flag' in gdst)
gdst = [x for x in gdst if x != 'extract_me.flag']
self.assertEqual(gsrc, gdst)
# Test if folder exists not copy because no flag
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
# Test if flag exists and folder exists in dst
flags.write_flag_file(self.session_path.joinpath("transfer_me.flag"))
transfer_rig_data.main(src_subjects_path, dst_subjects_path)
def check_create_raw_session_flag(session_folder: str) -> None:
session_path = Path(session_folder)
ephys = session_path.joinpath("ephys_data_transferred.flag")
video = session_path.joinpath("video_data_transferred.flag")
sett = raw.load_settings(session_path)
if sett is None:
log.error(f"No flag created for {session_path}")
return
is_biased = True if "biased" in sett["PYBPOD_PROTOCOL"] else False
if video.exists() and is_biased:
flags.write_flag_file(session_path.joinpath("raw_session.flag"))
video.unlink()
if video.exists() and ephys.exists():
flags.write_flag_file(session_path.joinpath("raw_session.flag"))
ephys.unlink()
video.unlink()
def raw_ephys_qc(root_data_folder, dry=False, max_sessions=10, force=False):
"""
Computes raw electrophysiology QC
"""
qcflags = Path(root_data_folder).rglob('raw_ephys_qc.flag')
c = 0
for qcflag in qcflags:
session_path = qcflag.parent
c += 1
if c >= max_sessions:
return
if dry:
print(qcflag.parent)
continue
qc_files = ephysqc.raw_qc_session(session_path, dry=dry, force=force)
qcflag.unlink()
flags.write_flag_file(session_path.joinpath('register_me.flag'), file_list=qc_files)
def extract(subjects_folder, dry=False):
ses_path = Path(subjects_folder).glob('**/extract_me.flag')
for p in ses_path:
# @alejandro no need for flags until personal project data starts going to server
# the flag file may contains specific file names for a targeted extraction
if dry:
print(p)
continue
try:
extract_opto(p.parent, save=True)
except:
pass
#p.unlink() commented we need the flag for the sync merge step
save = flags.read_flag_file(p)
flags.write_flag_file(p.parent.joinpath('opto_extracted.flag'), file_list=save)
def make_session(session_path, type='training'):
flags.write_flag_file(session_path.joinpath("transfer_me.flag"))
session_path.joinpath("raw_behavior_data").mkdir()
session_path.joinpath("raw_video_data").mkdir()
session_path.joinpath("raw_behavior_data",
"_iblrig_micData.raw.wav").touch()
session_path.joinpath("raw_video_data",
'_iblrig_leftCamera.raw.avi').touch()
sf = session_path.joinpath('raw_behavior_data',
'_iblrig_taskSettings.raw.json')
if type == 'training':
pybpod_protcol = 'json_trainingChoiceWorld'
elif type == 'ephys':
pybpod_protcol = 'json_ephysChoiceWorld'
session_path.joinpath("raw_video_data",
'_iblrig_rightCamera.raw.avi').touch()
session_path.joinpath("raw_video_data",
'_iblrig_bodyCamera.raw.avi').touch()
with open(sf, 'w+') as fid:
fid.write(json.dumps({'PYBPOD_PROTOCOL': pybpod_protcol}))
def register_sync(self, root_data_folder, dry=False):
"""
Register sessions looking recursively for flag files
:param root_data_folder: folder to look for register_me.flag
:param dry: bool. Dry run if True
:return:
"""
flag_files = Path(root_data_folder).glob('**/register_me.flag')
for flag_file in flag_files:
if dry:
continue
file_list = flags.read_flag_file(flag_file)
_logger.info('registering ' + str(flag_file.parent))
self.register_session(flag_file.parent, file_list=file_list)
flags.write_flag_file(flag_file.parent.joinpath('flatiron.flag'),
file_list=file_list)
flag_file.unlink()
if flag_file.parent.joinpath('create_me.flag').exists():
flag_file.parent.joinpath('create_me.flag').unlink()
_logger.info('registered' + '\n')
def _create_flags_for_task(dst, task_type):
# create_flags_for_session()
if task_type in ['habituation']:
flags.write_flag_file(dst.joinpath('extract_me.flag'))
if task_type in ['training', 'biased']:
flags.write_flag_file(dst.joinpath('extract_me.flag'))
flags.create_compress_video_flags(dst, flag_name='compress_video.flag')
flags.create_audio_flags(dst, 'audio_training.flag')
elif task_type in ['ephys', 'ephys_sync']:
flags.write_flag_file(dst.joinpath('extract_ephys.flag'))
flags.write_flag_file(dst.joinpath('raw_ephys_qc.flag'))
flags.create_compress_video_flags(
dst, flag_name='compress_video_ephys.flag')
flags.create_audio_flags(dst, 'audio_ephys.flag')
def create_ephys_flags(session_folder: str):
"""
Create flags for processing an ephys session. Should be called after move_ephys_files
:param session_folder: A path to an ephys session
:return:
"""
session_path = Path(session_folder)
flags.write_flag_file(session_path.joinpath("extract_ephys.flag"))
flags.write_flag_file(session_path.joinpath("raw_ephys_qc.flag"))
for probe_path in session_path.joinpath('raw_ephys_data').glob('probe*'):
flags.write_flag_file(probe_path.joinpath("spike_sorting.flag"))
def testAppendFlagFile(self):
# DO NOT CHANGE THE ORDER OF TESTS BELOW
# prepare a file with 3 dataset types
file_list = ['_ibl_extraRewards.times', '_ibl_lickPiezo.raw', '_ibl_lickPiezo.timestamps']
with open(self.tempfile.name, 'w+') as fid:
fid.write('\n'.join(file_list))
self.assertEqual(set(flags.read_flag_file(self.tempfile.name)), set(file_list))
# with an existing file containing files, writing more files append to it
file_list_2 = ['turltu']
# also makes sure that if a string is provided it works
flags.write_flag_file(self.tempfile.name, file_list_2[0])
self.assertEqual(set(flags.read_flag_file(self.tempfile.name)),
set(file_list + file_list_2))
# writing again keeps unique file values
flags.write_flag_file(self.tempfile.name, file_list_2[0])
n = sum([1 for f in flags.read_flag_file(self.tempfile.name) if f == file_list_2[0]])
self.assertEqual(n, 1)
# with an existing file containing files, writing empty filelist returns True for all files
flags.write_flag_file(self.tempfile.name, None)
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
# with an existing empty file, writing filelist returns True for all files
flags.write_flag_file(self.tempfile.name, ['file1', 'file2'])
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
# makes sure that read after write empty list also returns True
flags.write_flag_file(self.tempfile.name, [])
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
# with an existing empty file, writing filelist returns the list if clobber
flags.write_flag_file(self.tempfile.name, ['file1', 'file2', 'file3'], clobber=True)
self.assertEqual(set(flags.read_flag_file(self.tempfile.name)),
set(['file1', 'file2', 'file3']))
# test the removal of a file within the list
flags.excise_flag_file(self.tempfile.name, removed_files='file1')
self.assertEqual(sorted(flags.read_flag_file(self.tempfile.name)), ['file2', 'file3'])
# if file-list is True it means all files and file_list should be empty after read
flags.write_flag_file(self.tempfile.name, file_list=True)
self.assertEqual(flags.read_flag_file(self.tempfile.name), True)
def create_video_transfer_done_flag(session_folder: str) -> None:
session_path = Path(session_folder)
flags.write_flag_file(session_path.joinpath('video_data_transferred.flag'))
def create_ephys_transfer_done_flag(session_folder: str) -> None:
session_path = Path(session_folder)
flags.write_flag_file(session_path.joinpath("ephys_data_transferred.flag"))
