made a mess ... cleanup

src/ibl_to_nwb/_scripts/_convert_brainwide_map.py

@@ -6,6 +6,8 @@
 
 import spikeglx
 
+from ibl_to_nwb.helpers import create_symlinks
+
 # if running on SDSC, use the OneSdsc, else normal
 if "USE_SDSC_ONE" in os.environ:
     print("using SDSC ONE")
@@ -26,47 +28,6 @@
     WheelInterface,
 )
 
-# def create_symlinks(source_dir, target_dir, remove_uuid=True):
-#     """replicates the tree under source_dir at target dir in the form of symlinks"""
-#     for root, dirs, files in os.walk(source_dir):
-#         for dir in dirs:
-#             folder = target_dir / (Path(root) / dir).relative_to(source_dir)
-#             folder.mkdir(parents=True, exist_ok=True)
-
-#     for root, dirs, files in os.walk(source_dir):
-#         for file in files:
-#             source_file_path = Path(root) / file
-#             target_file_path = target_dir / source_file_path.relative_to(source_dir)
-#             if remove_uuid:
-#                 parent, name = target_file_path.parent, target_file_path.name
-#                 name_parts = name.split(".")
-#                 name_parts.remove(name_parts[-2])
-#                 target_file_path = parent / ".".join(name_parts)
-#             if not target_file_path.exists():
-#                 target_file_path.symlink_to(source_file_path)
-
-
-def create_symlinks(source_dir, target_dir, remove_uuid=True, filter=None):
-    """replicates the tree under source_dir at target dir in the form of symlinks"""
-
-    for root, dirs, files in os.walk(source_dir):
-        for file in files:
-            source_file_path = Path(root) / file
-            if filter is not None:
-                if filter not in str(source_file_path):
-                    continue
-
-            target_file_path = target_dir / source_file_path.relative_to(source_dir)
-            target_file_path.parent.mkdir(parents=True, exist_ok=True)
-
-            if remove_uuid:
-                parent, name = target_file_path.parent, target_file_path.name
-                name_parts = name.split(".")
-                name_parts.remove(name_parts[-2])
-                target_file_path = parent / ".".join(name_parts)
-            if not target_file_path.exists():
-                target_file_path.symlink_to(source_file_path)
-
 
 def get_last_before(eid: str, one: ONE, revision: str):
     revisions = one.list_revisions(eid, revision="*")
@@ -227,6 +188,7 @@ def convert(eid: str, one: ONE, data_interfaces: list, revision: str, mode: str)
     # cleanup
     if cleanup:
         if mode == "raw":
+            # find . -type l -exec unlink {} \;")
             os.system(f"find {session_scratch_folder} -type l -exec unlink {{}} \;")
             shutil.rmtree(session_scratch_folder)
-# find . -type l -exec unlink {} \;")
+

src/ibl_to_nwb/_scripts/post_conversion_check_nwbfile.py

@@ -15,9 +15,8 @@
 from ibl_to_nwb.testing._consistency_checks import check_nwbfile_for_consistency, check_raw_nwbfile_for_consistency
 
 # nwbfile_path = sys.argv[1]
-nwbfile_path = "/mnt/home/graiser/ibl_scratch/nwbfiles/sub-NR_0031/sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-raw_ecephys+image.nwb"
-if "raw" in nwbfile_path:
-    raw = True
+nwbfile_path = "/home/georg/ibl_scratch/nwbfiles/sub-NR_0031/sub-NR_0031_ses-caa5dddc-9290-4e27-9f5e-575ba3598614_desc-processed_behavior+ecephys.nwb"
+mode = "raw" if "raw" in nwbfile_path else "processed"
 
 with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
     nwbfile = io.read()
@@ -47,9 +46,10 @@
 # instantiate one
 one = ONE(**one_kwargs)
 
-if raw:
+if mode == 'raw':
     check_raw_nwbfile_for_consistency(one=one, nwbfile_path=nwbfile_path)
-else:
+if mode == 'processed':
     check_nwbfile_for_consistency(one=one, nwbfile_path=nwbfile_path)
 # %%
-print("all checks passed")
+
+print(f"all checks passed, mode={mode}")