Update inspector report file counts and output when 0 issues detected

CHANGELOG.md

@@ -5,6 +5,10 @@
 
 ### Improvements
 * Added documentation to API and CLI docs on how to use the dandi config option. [#624](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/624)
+* Updated report summary to include number of files detected and indicate when no issues are found. [#629](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/629)
+
+### Fixes
+* Fixed file count error when checking for non-unique identifiers in a folder [#629](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/629)
 
 # v0.6.5 (July 25, 2025)
 

src/nwbinspector/_dandi_inspection.py

@@ -8,6 +8,7 @@
 from ._configuration import load_config, validate_config
 from ._nwb_inspection import inspect_nwbfile_object
 from ._types import Importance, InspectorMessage
+from .tools import get_nwb_assets_from_dandiset
 
 
 def inspect_dandiset(
@@ -66,14 +67,7 @@ def inspect_dandiset(
     """
     config = config or "dandi"
 
-    if client is None:
-        import dandi.dandiapi
-
-        client = dandi.dandiapi.DandiAPIClient()
-
-    dandiset = client.get_dandiset(dandiset_id=dandiset_id, version_id=dandiset_version)
-
-    nwb_assets = [asset for asset in dandiset.get_assets() if ".nwb" in pathlib.Path(asset.path).suffixes]
+    nwb_assets = get_nwb_assets_from_dandiset(dandiset_id=dandiset_id, dandiset_version=dandiset_version, client=client)
 
     nwb_assets_iterator = nwb_assets
     if show_progress_bar:

src/nwbinspector/_formatting.py

@@ -81,9 +81,11 @@ def __init__(
         reverse: Optional[list[bool]] = None,
         detailed: bool = False,
         formatter_options: Optional[FormatterOptions] = None,
+        nfiles_detected: Optional[int] = None,
     ) -> None:
         self.nmessages = len(messages)
-        self.nfiles = len(set(message.file_path for message in messages))  # type: ignore
+        self.nfiles_with_issues = len(set(message.file_path for message in messages))  # type: ignore
+        self.nfiles_detected = nfiles_detected if nfiles_detected is not None else self.nfiles_with_issues
         self.message_count_by_importance = self._count_messages_by_importance(messages=messages)
         self.initial_organized_messages = organize_messages(messages=messages, levels=levels, reverse=reverse)
         self.detailed = detailed
@@ -206,9 +208,16 @@ def format_messages(self) -> list[str]:
                 f"Platform: {report_header['Platform']}",
                 f"NWBInspector version: {report_header['NWBInspector_version']}",
                 "",
-                f"Found {self.nmessages} issues over {self.nfiles} files:",
             ]
         )
+
+        if self.nmessages == 0:
+            self.formatted_messages.append(f"Scanned {self.nfiles_detected} file(s) - no issues found!")
+        else:
+            self.formatted_messages.append(
+                f"Scanned {self.nfiles_detected} file(s) and found {self.nmessages} issues across {self.nfiles_with_issues} file(s):"
+            )
+
         for importance_level, number_of_results in self.message_count_by_importance.items():
             increment = " " * (8 - len(str(number_of_results)))
             self.formatted_messages.append(f"{increment}{number_of_results} - {importance_level}")
@@ -222,11 +231,14 @@ def format_messages(
     levels: Optional[list[str]] = None,
     reverse: Optional[list[bool]] = None,
     detailed: bool = False,
+    nfiles_detected: Optional[int] = None,
 ) -> list[str]:
     """Print InspectorMessages in order specified by the organization structure."""
     levels = levels or ["file_path", "importance"]
 
-    message_formatter = MessageFormatter(messages=messages, levels=levels, reverse=reverse, detailed=detailed)
+    message_formatter = MessageFormatter(
+        messages=messages, levels=levels, reverse=reverse, detailed=detailed, nfiles_detected=nfiles_detected
+    )
     formatted_messages = message_formatter.format_messages()
 
     return formatted_messages

src/nwbinspector/_nwb_inspection.py

@@ -9,7 +9,6 @@
 from warnings import filterwarnings, warn
 
 import pynwb
-from hdmf_zarr import ZarrIO
 from natsort import natsorted
 from tqdm import tqdm
 
@@ -20,6 +19,7 @@
     OptionalListOfStrings,
     PathType,
     calculate_number_of_cpu,
+    get_nwbfiles_from_path,
 )
 
 
@@ -86,7 +86,6 @@ def inspect_all(
         List of external module names to load; examples would be namespace extensions.
         These modules may also contain their own custom checks for their extensions.
     """
-    in_path = Path(path)
     importance_threshold = (
         Importance[importance_threshold] if isinstance(importance_threshold, str) else importance_threshold
     )
@@ -127,17 +126,8 @@ def inspect_all(
     if progress_bar_options is None:
         progress_bar_options = dict(position=0, leave=False)
 
-    if in_path.is_dir() and (in_path.match("*.nwb*")) and ZarrIO.can_read(in_path):
-        nwbfiles = [in_path]  # if it is a zarr directory
-    elif in_path.is_dir():
-        nwbfiles = list(in_path.rglob("*.nwb*"))
+    nwbfiles = get_nwbfiles_from_path(path=path)
 
-        # Remove any macOS sidecar files
-        nwbfiles = [nwbfile for nwbfile in nwbfiles if not nwbfile.name.startswith("._")]
-    elif in_path.is_file():
-        nwbfiles = [in_path]
-    else:
-        raise ValueError(f"{in_path} should be a directory or an NWB file.")
     # Filtering of checks should apply after external modules are imported, in case those modules have their own checks
     checks = configure_checks(config=config, ignore=ignore, select=select, importance_threshold=importance_threshold)
 
@@ -153,10 +143,11 @@ def inspect_all(
     if len(identifiers) != len(nwbfiles):
         for identifier, nwbfiles_with_identifier in identifiers.items():
             if len(nwbfiles_with_identifier) > 1:
+                non_unique_files = natsorted([x.name for x in nwbfiles_with_identifier])
                 yield InspectorMessage(
                     message=(
                         f"The identifier '{identifier}' is used across the .nwb files: "
-                        f"{natsorted([x.name for x in nwbfiles_with_identifier])}. "
+                        f"{non_unique_files}. "
                         "The identifier of any NWBFile should be a completely unique value - "
                         "we recommend using uuid4 to achieve this."
                     ),
@@ -165,7 +156,7 @@ def inspect_all(
                     object_type="NWBFile",
                     object_name="root",
                     location="/",
-                    file_path=str(path),
+                    file_path=str(non_unique_files[-1]),  # report an example file_path with non-unique identifier
                 )
 
     nwbfiles_iterable = nwbfiles

src/nwbinspector/_nwbinspector_cli.py

@@ -20,7 +20,8 @@
 )
 from ._nwb_inspection import inspect_all
 from ._types import Importance
-from .utils import strtobool
+from .tools import get_nwb_assets_from_dandiset
+from .utils import get_nwbfiles_from_path, strtobool
 
 
 @click.command()
@@ -159,6 +160,8 @@ def _nwbinspector_cli(
             skip_validate=skip_validate,
             show_progress_bar=show_progress_bar,
         )
+        nwb_assets = get_nwb_assets_from_dandiset(dandiset_id=dandiset_id, dandiset_version=dandiset_version)
+        nfiles_detected = len(nwb_assets)
     # Scan a single NWB file in a Dandiset
     elif stream and ":" in path and not path_is_url:
         dandiset_id, dandi_file_path = path.split(":")
@@ -174,6 +177,7 @@ def _nwbinspector_cli(
             importance_threshold=handled_importance_threshold,
             skip_validate=skip_validate,
         )
+        nfiles_detected = 1
     # Scan single NWB file at URL
     elif stream and path_is_url:
         dandi_s3_url = path
@@ -186,6 +190,7 @@ def _nwbinspector_cli(
             importance_threshold=handled_importance_threshold,
             skip_validate=skip_validate,
         )
+        nfiles_detected = 1
     # Scan local file/folder
     else:  # stream is False
         messages_iterator = inspect_all(
@@ -198,6 +203,7 @@ def _nwbinspector_cli(
             skip_validate=skip_validate,
             progress_bar=show_progress_bar,
         )
+        nfiles_detected = len(get_nwbfiles_from_path(path=path))
     messages = list(messages_iterator)
 
     if json_file_path is not None:
@@ -209,7 +215,11 @@ def _nwbinspector_cli(
             print(f"{os.linesep*2}Report saved to {str(Path(json_file_path).absolute())}!{os.linesep}")
 
     formatted_messages = format_messages(
-        messages=messages, levels=handled_levels, reverse=handled_reverse, detailed=detailed
+        messages=messages,
+        levels=handled_levels,
+        reverse=handled_reverse,
+        detailed=detailed,
+        nfiles_detected=nfiles_detected,
     )
     print_to_console(formatted_messages=formatted_messages)
     if report_file_path is not None:

src/nwbinspector/tools/__init__.py

@@ -1,4 +1,4 @@
-from ._dandi import get_s3_urls_and_dandi_paths
+from ._dandi import get_nwb_assets_from_dandiset, get_s3_urls_and_dandi_paths
 from ._nwb import all_of_type, get_nwbfile_path_from_internal_object
 from ._read_nwbfile import BACKEND_IO_CLASSES, read_nwbfile, read_nwbfile_and_io
 
@@ -9,4 +9,5 @@
     "get_nwbfile_path_from_internal_object",
     "read_nwbfile",
     "read_nwbfile_and_io",
+    "get_nwb_assets_from_dandiset",
 ]

src/nwbinspector/tools/_dandi.py

@@ -1,8 +1,9 @@
 """Helper functions related to DANDI for internal use that rely on external dependencies (i.e., dandi)."""
 
+import pathlib
 import re
 from concurrent.futures import ProcessPoolExecutor, as_completed
-from typing import Optional
+from typing import Literal, Optional, Union
 
 from ..utils import calculate_number_of_cpu, is_module_installed
 
@@ -57,3 +58,25 @@ def _get_content_url_and_path(
     Must be globally defined (not as a part of get_s3_urls..) in order to be pickled.
     """
     return {asset.get_content_url(follow_redirects=1, strip_query=True): asset.path}
+
+
+def get_nwb_assets_from_dandiset(
+    dandiset_id: str,
+    dandiset_version: Union[str, Literal["draft"], None] = None,
+    client: Union["dandi.dandiapi.DandiAPIClient", None] = None,  # type: ignore
+) -> list["dandi.dandiapi.BaseRemoteAsset"]:  # type: ignore
+    """
+    Collect NWB assets from a DANDISet ID.
+
+    Returns list of NWB assets.
+    """
+    if client is None:
+        import dandi.dandiapi
+
+        client = dandi.dandiapi.DandiAPIClient()
+
+    dandiset = client.get_dandiset(dandiset_id=dandiset_id, version_id=dandiset_version)
+
+    nwb_assets = [asset for asset in dandiset.get_assets() if ".nwb" in pathlib.Path(asset.path).suffixes]
+
+    return nwb_assets

src/nwbinspector/utils/__init__.py

@@ -11,6 +11,7 @@
     get_package_version,
     calculate_number_of_cpu,
     get_data_shape,
+    get_nwbfiles_from_path,
     PathType,  # TODO: deprecate in favor of explicit typing
     FilePathType,  # TODO: deprecate in favor of explicit typing
     OptionalListOfStrings,  # TODO: deprecate in favor of explicit typing
@@ -29,4 +30,5 @@
     "get_package_version",
     "calculate_number_of_cpu",
     "get_data_shape",
+    "get_nwbfiles_from_path",
 ]

src/nwbinspector/utils/_utils.py

@@ -12,6 +12,7 @@
 import numpy as np
 import zarr
 from hdmf.backends.hdf5.h5_utils import H5Dataset
+from hdmf_zarr import ZarrIO
 from numpy.typing import ArrayLike
 from packaging import version
 
@@ -256,3 +257,26 @@ def strtobool(val: str) -> bool:
         return False
     else:
         raise ValueError(f"Invalid truth value {val!r}")
+
+
+def get_nwbfiles_from_path(path: PathType) -> list[Path]:
+    """
+    Given a path, return a list of NWB files.
+
+    If the path is a directory, check whether it is a zarr directory or search for all NWB files.
+    If the path is a file, return a list containing that file.
+    """
+    in_path = Path(path)
+    if in_path.is_dir() and (in_path.match("*.nwb*")) and ZarrIO.can_read(in_path):
+        nwbfiles = [in_path]  # if it is a zarr directory
+    elif in_path.is_dir():
+        nwbfiles = list(in_path.rglob("*.nwb*"))
+
+        # Remove any macOS sidecar files
+        nwbfiles = [nwbfile for nwbfile in nwbfiles if not nwbfile.name.startswith("._")]
+    elif in_path.is_file():
+        nwbfiles = [in_path]
+    else:
+        raise ValueError(f"{in_path} should be a directory or an NWB file.")
+
+    return nwbfiles

tests/expected_reports/000126_report.txt

@@ -5,7 +5,7 @@ Timestamp: 2024-09-04 14:08:54.703671-04:00
 Platform: macOS-14.6.1-arm64-arm-64bit
 NWBInspector version: 0.4.38
 
-Found 10 issues over 1 files:
+Scanned 1 file(s) and found 10 issues across 1 file(s):
        3 - CRITICAL
        1 - BEST_PRACTICE_VIOLATION
        6 - BEST_PRACTICE_SUGGESTION

tests/expected_reports/true_nwbinspector_default_report_hdf5.txt

@@ -5,7 +5,7 @@ Timestamp: 2022-04-01 13:32:13.756390-04:00
 Platform: Windows-10-10.0.19043-SP0
 NWBInspector version: 0.3.6
 
-Found 5 issues over 2 files:
+Scanned 3 file(s) and found 5 issues across 2 file(s):
        2 - CRITICAL
        2 - BEST_PRACTICE_VIOLATION
        1 - BEST_PRACTICE_SUGGESTION

tests/expected_reports/true_nwbinspector_default_report_zarr.txt

@@ -5,7 +5,7 @@ Timestamp: 2022-04-01 13:32:13.756390-04:00
 Platform: Windows-10-10.0.19043-SP0
 NWBInspector version: 0.3.6
 
-Found 5 issues over 2 files:
+Scanned 3 file(s) and found 5 issues across 2 file(s):
        2 - CRITICAL
        2 - BEST_PRACTICE_VIOLATION
        1 - BEST_PRACTICE_SUGGESTION

tests/expected_reports/true_nwbinspector_report_with_dandi_config_hdf5.txt

@@ -5,7 +5,7 @@ Timestamp: 2022-04-01 13:32:13.756390-04:00
 Platform: Windows-10-10.0.19043-SP0
 NWBInspector version: 0.3.6
 
-Found 10 issues over 2 files:
+Scanned 2 file(s) and found 10 issues across 2 file(s):
        3 - CRITICAL
        7 - BEST_PRACTICE_VIOLATION
 **************************************************

tests/expected_reports/true_nwbinspector_report_with_dandi_config_zarr.txt

@@ -5,7 +5,7 @@ Timestamp: 2022-04-01 13:32:13.756390-04:00
 Platform: Windows-10-10.0.19043-SP0
 NWBInspector version: 0.3.6
 
-Found 10 issues over 2 files:
+Scanned 2 file(s) and found 10 issues across 2 file(s):
        3 - CRITICAL
        7 - BEST_PRACTICE_VIOLATION
 **************************************************