def confirm_remote_folder(local_folder, remote_folder):
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
local_folder = folders.subjects_data_folder(local_folder)
remote_folder = folders.subjects_data_folder(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
for session_path in src_session_paths:
print(f"\nFound session: {session_path}")
resp = input(
f"Transfer to {remote_folder} with the same name ([y]/n/skip/exit)? "
) or 'y'
print(resp)
if resp not in ['y', 'n', 'skip', 'exit']:
return confirm_remote_folder(local_folder, remote_folder)
elif resp == 'y':
transfer_session(session_path, remote_folder, force=False)
elif resp == 'n':
new_session_path = rename_session(session_path)
transfer_session(new_session_path, remote_folder)
elif resp == 'skip':
continue
elif resp == 'exit':
return
def confirm_video_remote_folder(local_folder=False,
remote_folder=False,
force=False):
pars = load_videopc_params()
if not local_folder:
local_folder = pars['DATA_FOLDER_PATH']
if not remote_folder:
remote_folder = pars['REMOTE_DATA_FOLDER_PATH']
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
# Check for Subjects folder
local_folder = folders.subjects_data_folder(local_folder, rglob=True)
remote_folder = folders.subjects_data_folder(remote_folder, rglob=True)
print('LOCAL:', local_folder)
print('REMOTE:', remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
print("Nothing to transfer, exiting...")
return
for session_path in src_session_paths:
print(f"\nFound session: {session_path}")
flag_file = session_path / 'transfer_me.flag'
msg = f"Transfer to {remote_folder} with the same name?"
resp = input(msg + "\n[y]es/[r]ename/[s]kip/[e]xit\n ^\n> ") or 'y'
resp = resp.lower()
print(resp)
if resp not in ['y', 'r', 's', 'e', 'yes', 'rename', 'skip', 'exit']:
return confirm_video_remote_folder(local_folder=local_folder,
remote_folder=remote_folder,
force=force)
elif resp == 'y' or resp == 'yes':
pass
elif resp == 'r' or resp == 'rename':
session_path = rename_session(session_path)
elif resp == 's' or resp == 'skip':
continue
elif resp == 'e' or resp == 'exit':
return
remote_session_path = remote_folder / Path(*session_path.parts[-3:])
if not behavior_exists(remote_session_path):
print(
f"No behavior folder found in {remote_session_path}: skipping session..."
)
return
transfer_folder(session_path / 'raw_video_data',
remote_session_path / 'raw_video_data',
force=force)
flag_file.unlink()
create_video_transfer_done_flag(remote_session_path)
check_create_raw_session_flag(remote_session_path)
def confirm_video_remote_folder(local_folder=False,
remote_folder=False,
force=False):
pars = load_videopc_params()
if not local_folder:
local_folder = pars["DATA_FOLDER_PATH"]
if not remote_folder:
remote_folder = pars["REMOTE_DATA_FOLDER_PATH"]
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
# Check for Subjects folder
local_folder = folders.subjects_data_folder(local_folder, rglob=True)
remote_folder = folders.subjects_data_folder(remote_folder, rglob=True)
print("LOCAL:", local_folder)
print("REMOTE:", remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
print("Nothing to transfer, exiting...")
return
for session_path in src_session_paths:
print(f"\nFound session: {session_path}")
flag_file = session_path / "transfer_me.flag"
msg = f"Transfer to {remote_folder} with the same name?"
resp = input(msg + "\n[y]es/[r]ename/[s]kip/[e]xit\n ^\n> ") or "y"
resp = resp.lower()
print(resp)
if resp not in ["y", "r", "s", "e", "yes", "rename", "skip", "exit"]:
return confirm_video_remote_folder(local_folder=local_folder,
remote_folder=remote_folder,
force=force)
elif resp == "y" or resp == "yes":
pass
elif resp == "r" or resp == "rename":
session_path = rename_session(session_path)
elif resp == "s" or resp == "skip":
continue
elif resp == "e" or resp == "exit":
return
remote_session_path = remote_folder / Path(*session_path.parts[-3:])
if not behavior_exists(remote_session_path):
print(
f"No behavior folder found in {remote_session_path}: skipping session..."
)
return
transfer_folder(session_path / "raw_video_data",
remote_session_path / "raw_video_data",
force=force)
flag_file.unlink()
create_video_transfer_done_flag(remote_session_path)
check_create_raw_session_flag(remote_session_path)
def confirm_ephys_remote_folder(local_folder=False,
remote_folder=False,
force=False,
iblscripts_folder=False):
pars = load_ephyspc_params()
if not local_folder:
local_folder = pars['DATA_FOLDER_PATH']
if not remote_folder:
remote_folder = pars['REMOTE_DATA_FOLDER_PATH']
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
# Check for Subjects folder
local_folder = folders.subjects_data_folder(local_folder, rglob=True)
remote_folder = folders.subjects_data_folder(remote_folder, rglob=True)
print('LOCAL:', local_folder)
print('REMOTE:', remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
print("Nothing to transfer, exiting...")
return
for session_path in src_session_paths:
print(f"\nFound session: {session_path}")
# Rename ephys files
rename_ephys_files(str(session_path))
# Move ephys files
move_ephys_files(str(session_path))
# Copy wiring files
copy_wiring_files(str(session_path), iblscripts_folder)
flag_file = session_path / 'transfer_me.flag'
msg = f"Transfer to {remote_folder} with the same name?"
resp = input(msg + "\n[y]es/[r]ename/[s]kip/[e]xit\n ^\n> ") or 'y'
resp = resp.lower()
print(resp)
if resp not in ['y', 'r', 's', 'e', 'yes', 'rename', 'skip', 'exit']:
return confirm_ephys_remote_folder(local_folder=local_folder,
remote_folder=remote_folder)
elif resp == 'y' or resp == 'yes':
remote_session_path = remote_folder / Path(
*session_path.parts[-3:])
if not behavior_exists(remote_session_path):
print(
f"No behavior folder found in {remote_session_path}: skipping session..."
)
continue
transfer_folder(session_path / 'raw_ephys_data',
remote_session_path / 'raw_ephys_data',
force=force)
flag_file.unlink()
if (remote_session_path / 'extract_me.flag').exists():
(remote_session_path / 'extract_me.flag').unlink()
elif resp == 'r' or resp == 'rename':
new_session_path = rename_session(session_path)
remote_session_path = remote_folder / Path(
*new_session_path.parts[-3:])
if not behavior_exists(remote_session_path):
print(
f"No behavior folder found in {remote_session_path}: skipping session..."
)
continue
transfer_folder(new_session_path / 'raw_ephys_data',
remote_session_path / 'raw_ephys_data')
flag_file.unlink()
# if behavior extract_me.flag exists remove it, no need because of ephys flag
if (remote_session_path / 'extract_me.flag').exists():
(remote_session_path / 'extract_me.flag').unlink()
elif resp == 's' or resp == 'skip':
continue
elif resp == 'e' or resp == 'exit':
return
def confirm_ephys_remote_folder(local_folder=False,
remote_folder=False,
force=False,
iblscripts_folder=False):
pars = load_ephyspc_params()
if not local_folder:
local_folder = pars['DATA_FOLDER_PATH']
if not remote_folder:
remote_folder = pars['REMOTE_DATA_FOLDER_PATH']
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
# Check for Subjects folder
local_folder = folders.subjects_data_folder(local_folder, rglob=True)
remote_folder = folders.subjects_data_folder(remote_folder, rglob=True)
print('LOCAL:', local_folder)
print('REMOTE:', remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
print("Nothing to transfer, exiting...")
return
for session_path in src_session_paths:
print(f"\nFound session: {session_path}")
# Rename ephys files
# FIXME: if transfer has failed and wiring file is there renaming will fail!
rename_ephys_files(str(session_path))
# Move ephys files
move_ephys_files(str(session_path))
# Copy wiring files
copy_wiring_files(str(session_path), iblscripts_folder)
try:
create_alyx_probe_insertions(str(session_path))
except BaseException as e:
print(
e,
"\nCreation failed, please create the probe insertions manually.",
"Continuing transfer...")
msg = f"Transfer to {remote_folder} with the same name?"
resp = input(msg + "\n[y]es/[r]ename/[s]kip/[e]xit\n ^\n> ") or 'y'
resp = resp.lower()
print(resp)
if resp not in ['y', 'r', 's', 'e', 'yes', 'rename', 'skip', 'exit']:
return confirm_ephys_remote_folder(
local_folder=local_folder,
remote_folder=remote_folder,
force=force,
iblscripts_folder=iblscripts_folder)
elif resp == 'y' or resp == 'yes':
pass
elif resp == 'r' or resp == 'rename':
session_path = rename_session(session_path)
elif resp == 's' or resp == 'skip':
continue
elif resp == 'e' or resp == 'exit':
return
remote_session_path = remote_folder / Path(*session_path.parts[-3:])
if not behavior_exists(remote_session_path):
print(
f"No behavior folder found in {remote_session_path}: skipping session..."
)
return
transfer_folder(session_path / 'raw_ephys_data',
remote_session_path / 'raw_ephys_data',
force=force)
# if behavior extract_me.flag exists remove it, because of ephys flag
flag_file = session_path / 'transfer_me.flag'
flag_file.unlink()
if (remote_session_path / 'extract_me.flag').exists():
(remote_session_path / 'extract_me.flag').unlink()
# Create remote flags
create_ephys_transfer_done_flag(remote_session_path)
check_create_raw_session_flag(remote_session_path)
def confirm_ephys_remote_folder(local_folder=False,
remote_folder=False,
force=False,
iblscripts_folder=False):
pars = load_ephyspc_params()
if not local_folder:
local_folder = pars["DATA_FOLDER_PATH"]
if not remote_folder:
remote_folder = pars["REMOTE_DATA_FOLDER_PATH"]
local_folder = Path(local_folder)
remote_folder = Path(remote_folder)
# Check for Subjects folder
local_folder = folders.subjects_data_folder(local_folder, rglob=True)
remote_folder = folders.subjects_data_folder(remote_folder, rglob=True)
print("LOCAL:", local_folder)
print("REMOTE:", remote_folder)
src_session_paths = [
x.parent for x in local_folder.rglob("transfer_me.flag")
]
if not src_session_paths:
print("Nothing to transfer, exiting...")
return
for session_path in src_session_paths:
print(f"\nFound session: {session_path}")
# Rename ephys files
# FIXME: if transfer has failed and wiring file is there renaming will fail!
rename_ephys_files(str(session_path))
# Move ephys files
move_ephys_files(str(session_path))
# Copy wiring files
copy_wiring_files(str(session_path), iblscripts_folder)
try:
create_alyx_probe_insertions(str(session_path))
except BaseException as e:
print(
e,
"\nCreation failed, please create the probe insertions manually.",
"Continuing transfer...",
)
msg = f"Transfer to {remote_folder} with the same name?"
resp = input(msg + "\n[y]es/[r]ename/[s]kip/[e]xit\n ^\n> ") or "y"
resp = resp.lower()
print(resp)
if resp not in ["y", "r", "s", "e", "yes", "rename", "skip", "exit"]:
return confirm_ephys_remote_folder(
local_folder=local_folder,
remote_folder=remote_folder,
force=force,
iblscripts_folder=iblscripts_folder,
)
elif resp == "y" or resp == "yes":
pass
elif resp == "r" or resp == "rename":
session_path = rename_session(session_path)
elif resp == "s" or resp == "skip":
continue
elif resp == "e" or resp == "exit":
return
remote_session_path = remote_folder / Path(*session_path.parts[-3:])
if not behavior_exists(remote_session_path):
print(
f"No behavior folder found in {remote_session_path}: skipping session..."
)
return
# TODO: Check flagfiles on src.and dst + alf dir in session folder then remove
# Try catch? wher catch condition is force transfer maybe
transfer_folder(session_path / "raw_ephys_data",
remote_session_path / "raw_ephys_data",
force=force)
# if behavior extract_me.flag exists remove it, because of ephys flag
flag_file = session_path / "transfer_me.flag"
flag_file.unlink()
if (remote_session_path / "extract_me.flag").exists():
(remote_session_path / "extract_me.flag").unlink()
# Create remote flags
create_ephys_transfer_done_flag(remote_session_path)
check_create_raw_session_flag(remote_session_path)
