reorganize handling of CLI transfer scripts

iblrig/commands.py

@@ -2,6 +2,7 @@
 import datetime
 import json
 from pathlib import Path
+
 import yaml
 import shutil
 
@@ -17,6 +18,33 @@
 logger = setup_logger('iblrig', level='INFO')
 
 
+def _transfer_parser(description: str) -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=description,
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+                                     argument_default=argparse.SUPPRESS)
+    parser.add_argument("-l", "--local", action="store", type=dir_path, dest='local_path', help="override local data path")
+    parser.add_argument("-r", "--remote", action="store", type=dir_path, dest='remote_path', help="override remote data path")
+    parser.add_argument("-d", "--dry", action="store_true", dest='dry', help="do not remove local data after copying")
+    return parser
+
+
+def dir_path(directory: str) -> Path:
+    directory = Path(directory)
+    if directory.exists():
+        return directory
+    raise argparse.ArgumentError(None, f'Directory `{directory}` not found')
+
+
+def transfer_video_data_cli():
+    args = _transfer_parser("Copy video data to the local server.").parse_args()
+    transfer_video_data(**vars(args))
+
+
+def transfer_data_cli():
+    args = _transfer_parser("Copy behavior data to the local server.").parse_args()
+    transfer_data(**vars(args))
+
+
 def transfer_video_data(local_path=None, remote_path=None, dry=False):
     # If paths not passed, uses those defined in the iblrig_settings.yaml file
     rig_paths = get_local_and_remote_paths(local_path=local_path, remote_path=remote_path)
@@ -34,24 +62,6 @@ def transfer_video_data(local_path=None, remote_path=None, dry=False):
                           remote_path=remote_path, dry=dry, tag='video')
 
 
-def dir_path(directory: str):
-    directory = Path(directory)
-    if directory.exists():
-        return directory
-    raise argparse.ArgumentError(None, f'Directory `{directory}` not found')
-
-
-def transfer_data_cli():
-    parser = argparse.ArgumentParser(description="Copy behavior data to the local server.",
-                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-                                     argument_default=argparse.SUPPRESS)
-    parser.add_argument("-l", "--local", action="store", type=dir_path, dest='local_path', help="override local data path")
-    parser.add_argument("-r", "--remote", action="store", type=dir_path, dest='remote_path', help="override remote data path")
-    parser.add_argument("-d", "--dry", action="store_true", dest='dry', help="do not remove local data after copying")
-    args = parser.parse_args()
-    transfer_data(**vars(args))
-
-
 def transfer_data(local_path: Path = None, remote_path: Path = None, dry: bool = False, lab: str = None) -> None:
     """
     Copies the behavior data from the rig to the local server if the session has more than 42 trials

iblrig/transfer_experiments.py

@@ -14,7 +14,7 @@
 log = setup_logger('iblrig', level='INFO')
 
 
-def _copy_file_md5(src: str, dst: str, *args, **kwargs) -> str:
+def _copy2_md5(src: str, dst: str, *args, **kwargs) -> str:
     """
     Copy a file from source to destination with MD5 hash verification.
 
@@ -43,6 +43,7 @@ def _copy_file_md5(src: str, dst: str, *args, **kwargs) -> str:
     """
     src_md5 = hashfile.md5(src)
     if os.path.exists(dst) and samestat(os.stat(src), os.stat(dst)) and src_md5 == hashfile.md5(dst):
+        log.info(f'Skipping {dst.name} as it already exists at the destination')
         return dst
     return_val = shutil.copy2(src, dst, *args, **kwargs)
     if not src_md5 == hashfile.md5(dst):
@@ -77,7 +78,7 @@ def copy_folders(local_folder: str, remote_folder: str, overwrite: bool = False)
         remote_folder.parent.mkdir(parents=True, exist_ok=True)
         shutil.copytree(local_folder, remote_folder, dirs_exist_ok=overwrite,
                         ignore=shutil.ignore_patterns('transfer_me.flag'),
-                        copy_function=_copy_file_md5)
+                        copy_function=_copy2_md5)
     except OSError:
         log.error(traceback.format_exc())
         log.info(f"Could not copy {local_folder} to {remote_folder}")

pyproject.toml

@@ -50,7 +50,7 @@ DEV = [
 [project.scripts]
 viewsession = "iblrig.commands:viewsession"
 transfer_data = "iblrig.commands:transfer_data_cli"
-transfer_video_data = "iblrig.commands:transfer_video_data"
+transfer_video_data = "iblrig.commands:transfer_video_data_cli"
 flush = "iblrig.commands:flush"
 remove-old-sessions = "iblrig.commands:remove_local_sessions"
 iblrig = "iblrig.gui.wizard:main"