np_codeocean 0.1.7__tar.gz → 0.1.8__tar.gz

{np_codeocean-0.1.7 → np_codeocean-0.1.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: np_codeocean
-Version: 0.1.7
+Version: 0.1.8
 Summary: Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean
 Author-Email: Ben Hardcastle <ben.hardcastle@alleninstitute.org>
 License: MIT

{np_codeocean-0.1.7 → np_codeocean-0.1.8}/pyproject.toml

@@ -40,7 +40,7 @@ composite = [
 
 [project]
 name = "np_codeocean"
-version = "0.1.7"
+version = "0.1.8"
 description = "Tools for uploading and interacting with Mindscope Neuropixels experiments on Code Ocean"
 authors = [
     { name = "Ben Hardcastle", email = "ben.hardcastle@alleninstitute.org" },

{np_codeocean-0.1.7 → np_codeocean-0.1.8}/src/np_codeocean/upload.py

@@ -87,25 +87,33 @@ def create_ephys_symlinks(session: np_session.Session, dest: Path,
 
 def correct_structure(dest: Path) -> None:
     """
-    In case some probes are missing, remove device entries from structure.oebin files with folders that don't actually exist.
+    In case some probes are missing, remove device entries from structure.oebin
+    files for devices with folders that have not been preserved.
     """
-    logger.debug('Creating modified structure.oebin')
-    oebin_paths = dest.rglob('recording[0-9]*/structure.oebin')
-    for oebin_path in oebin_paths:
+    logger.debug('Checking structure.oebin for missing folders...')
+    recording_dirs = dest.rglob('recording[0-9]')
+    for recording_dir in recording_dirs:
+        if not recording_dir.is_dir():
+            continue
+        oebin_path = recording_dir / 'structure.oebin'
+        if not (oebin_path.is_symlink() or oebin_path.exists()):
+            logger.warning(f'No structure.oebin found in {recording_dir}')
+            continue
         logger.debug(f'Examining oebin: {oebin_path} for correction')
         oebin_obj = np_tools.read_oebin(np_config.normalize_path(oebin_path.readlink()))
-
-        for subdir_name in ('events', 'continuous'):
+        any_removed = False
+        for subdir_name in ('events', 'continuous'):    
             subdir = oebin_path.parent / subdir_name
             # iterate over copy of list so as to not disrupt iteration when elements are removed
             for device in [device for device in oebin_obj[subdir_name]]:
                 if not (subdir / device['folder_name']).exists():
                     logger.info(f'{device["folder_name"]} not found in {subdir}, removing from structure.oebin')
                     oebin_obj[subdir_name].remove(device)
-        
-        oebin_path.unlink()
-        oebin_path.write_text(json.dumps(oebin_obj, indent=4))
-        logger.debug('Overwrote symlink to structure.oebin with corrected strcuture.oebin')
+                    any_removed = True
+        if any_removed:
+            oebin_path.unlink()
+            oebin_path.write_text(json.dumps(oebin_obj, indent=4))
+            logger.debug('Overwrote symlink to structure.oebin with corrected strcuture.oebin')
 
 def is_behavior_video_file(path: Path) -> bool:
     if path.is_dir() or path.suffix not in ('.mp4', '.avi', '.json'):
@@ -115,13 +123,10 @@ def is_behavior_video_file(path: Path) -> bool:
         return True
     return False
 
-def create_behavior_symlinks(session: np_session.Session, dest: Path | None) -> None:
+def create_behavior_symlinks(session: np_session.Session, dest: Path) -> None:
     """Create symlinks in `dest` pointing to files in top-level of session
     folder on np-exp, plus all files in `exp` subfolder, if present.
     """
-    if dest is None: 
-        logger.debug(f"No behavior folder supplied for {session}")
-        return
     subfolder_names = ('exp', 'qc')
     logger.info(f'Creating symlinks in {dest} to files in {session.npexp_path}...')
     for src in session.npexp_path.glob('*'):
@@ -138,13 +143,10 @@ def create_behavior_symlinks(session: np_session.Session, dest: Path | None) ->
                 np_tools.symlink(as_posix(src), dest / src.relative_to(session.npexp_path))
         logger.debug(f'Finished creating symlinks to {name!r} files')
 
-def create_behavior_videos_symlinks(session: np_session.Session, dest: Path | None) -> None:
+def create_behavior_videos_symlinks(session: np_session.Session, dest: Path) -> None:
     """Create symlinks in `dest` pointing to MVR video files and info jsons in top-level of session
     folder on np-exp.
     """
-    if dest is None: 
-        logger.debug(f"No behavior_videos folder supplied for {session}")
-        return
     logger.info(f'Creating symlinks in {dest} to files in {session.npexp_path}...')
     for src in session.npexp_path.glob('*'):
         if is_behavior_video_file(src):
@@ -340,10 +342,12 @@ def create_codeocean_upload(session: str | int | np_session.Session,
         job = np_config.normalize_path(root / 'upload.csv'),
         force_cloud_sync=force_cloud_sync,
         )
-
-    create_ephys_symlinks(upload.session, upload.ephys, recording_dirs=recording_dirs)
-    create_behavior_symlinks(upload.session, upload.behavior)
-    create_behavior_videos_symlinks(upload.session, upload.behavior_videos)
+    if upload.ephys:
+        create_ephys_symlinks(upload.session, upload.ephys, recording_dirs=recording_dirs)
+    if upload.behavior:
+        create_behavior_symlinks(upload.session, upload.behavior)
+    if upload.behavior_videos:
+        create_behavior_videos_symlinks(upload.session, upload.behavior_videos)
     create_upload_job(upload)    
     return upload