Merge branch 'master' into enh-lad-errors-api

Author: CodyCBakerPhD

dandi/dandiset.py

@@ -42,7 +42,11 @@ def __init__(
         if not allow_empty and not os.path.lexists(
             self.path_obj / dandiset_metadata_file
         ):
-            raise ValueError(f"No dandiset at {path}")
+            raise ValueError(
+                f"No dandiset at {path}. "
+                f"The directory does not contain a '{dandiset_metadata_file}' file. "
+                "Use 'dandi download' to download a dandiset or check the path."
+            )
         self.metadata: dict | None = None
         self._metadata_file_obj = self.path_obj / dandiset_metadata_file
         self._load_metadata()
@@ -139,11 +143,17 @@ def _get_identifier(metadata: dict) -> str | None:
     @property
     def identifier(self) -> str:
         if self.metadata is None:
-            raise ValueError("No metadata record found in Dandiset")
+            raise ValueError(
+                f"No metadata record found in Dandiset at {self.path}. "
+                f"The '{dandiset_metadata_file}' file may be empty or corrupted. "
+                "Use 'dandi download' to re-download the dandiset metadata."
+            )
         id_ = self._get_identifier(self.metadata)
         if not id_:
             raise ValueError(
-                f"Found no dandiset.identifier in metadata record: {self.metadata}"
+                f"Found no dandiset.identifier in metadata record. "
+                f"The '{dandiset_metadata_file}' file must contain an 'identifier' field. "
+                f"Metadata: {self.metadata}"
             )
         return id_
 

dandi/pynwb_utils.py

@@ -1,3 +1,14 @@
+"""Utilities for working with NWB (Neurodata Without Borders) files.
+
+This module provides helper functions for reading, validating, and extracting
+metadata from NWB files using PyNWB. Features include:
+- NWB file I/O with caching
+- Metadata extraction for DANDI schema
+- Version compatibility checking
+- External link detection
+- Validation against NWB standards
+"""
+
 from __future__ import annotations
 
 from collections import Counter

dandi/upload.py

@@ -4,7 +4,6 @@
 from collections.abc import Iterator, Sequence
 from contextlib import ExitStack
 from enum import Enum
-from functools import reduce
 import io
 import os.path
 from pathlib import Path
@@ -493,7 +492,7 @@ def upload_agg(*ignored: Any) -> str:
             for p in paths:
                 rp = os.path.relpath(p, dandiset.path)
                 relpaths.append("" if rp == "." else rp)
-            path_prefix = reduce(os.path.commonprefix, relpaths)  # type: ignore[arg-type]
+            path_prefix = os.path.commonprefix(relpaths)
             to_delete = []
             for asset in remote_dandiset.get_assets_with_path_prefix(path_prefix):
                 if any(

dandi/validate.py

@@ -1,3 +1,12 @@
+"""Validation of DANDI datasets against schemas and standards.
+
+This module provides validation functionality for dandisets, including:
+- DANDI schema validation
+- BIDS standard validation
+- File layout and organization validation
+- Metadata completeness checking
+"""
+
 from __future__ import annotations
 
 from collections.abc import Iterator