Update inspector report summary for PyNWB read errors #603

stephprince · 2025-07-24T00:02:40Z

Motivation

When running NWBInspector on a file that is unable to be opened by PyNWB, io.read() error message outputs are long and sections are repeated multiple times as part of the inspector report.

These updates attempt to improve the readability of the report by removing the duplicated read error outputs when searching for non-unique file identifiers and condensing the inspector message returned by inspect_nwbfile.

Code to reproduce

Create the file in python and remove a required argument

from h5py import File
from pynwb import NWBHDF5IO
from pynwb.testing.mock.file import mock_NWBFile
from pynwb.validation import validate
from nwbinspector import inspect_nwbfile


# create mock NWBFile
path = "test_construct_error.nwb"
nwbfile = mock_NWBFile()
with NWBHDF5IO(path=path, mode="w") as io:
    io.write(nwbfile)

# remove required argument
with File(name=path, mode="r+") as file:
    del file["session_description"]

Run the inspector CLI:

nwbinspector "test_construct_error.nwb"

New inspector report:

**************************************************
NWBInspector Report Summary

Timestamp: 2025-07-23 16:52:08.679265-07:00
Platform: macOS-14.2.1-arm64-arm-64bit
NWBInspector version: 0.6.3

Found 1 issues over 1 files:
       1 - ERROR
**************************************************


0  ERROR
========

0.0  test_construct_error.nwb: During io.read(), an error occurred: hdmf.build.errors.ConstructError. This indicates that PyNWB was unable to read the file. See the traceback message for more details. - 'None' object with name 'None'
       Message: Traceback (most recent call last):
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/build/objectmapper.py", line 1368, in construct
    obj = self.__new_container__(cls, builder.source, parent, builder.attributes.get(self.__spec.id_key()),
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/build/objectmapper.py", line 1381, in __new_container__
    obj.__init__(**kwargs)
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 577, in func_call
    pargs = _check_args(args, kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 570, in _check_args
    raise ExceptionType(msg)
TypeError: NWBFile.__init__: missing argument 'session_description'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/smprince/Documents/code/nwbinspector/src/nwbinspector/_nwb_inspection.py", line 272, in inspect_nwbfile
    in_memory_nwbfile = read_nwbfile(nwbfile_path=nwbfile_path)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/src/nwbinspector/tools/_read_nwbfile.py", line 95, in read_nwbfile
    nwbfile, _ = _read_nwbfile_helper(nwbfile_path=nwbfile_path, method=method, backend=backend)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/src/nwbinspector/tools/_read_nwbfile.py", line 180, in _read_nwbfile_helper
    nwbfile = io.read()
              ^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/pynwb/__init__.py", line 479, in read
    file = super().read(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/backends/hdf5/h5tools.py", line 458, in read
    return super().read(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/backends/io.py", line 60, in read
    container = self.__manager.construct(f_builder)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/build/manager.py", line 286, in construct
    result = self.__type_map.construct(builder, self, None)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/build/manager.py", line 813, in construct
    return obj_mapper.construct(builder, build_manager, parent)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/pynwb/io/file.py", line 161, in construct
    return super().construct(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/Documents/code/nwbinspector/.venv/lib/python3.11/site-packages/hdmf/build/objectmapper.py", line 1372, in construct
    raise ConstructError(builder, msg) from ex
hdmf.build.errors.ConstructError: (root GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'NWBFile', 'nwb_version': '2.8.0', 'object_id': 'a49b2093-a78f-4954-899b-74f7eaf5d2b9'}, 'groups': {'acquisition': root/acquisition GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'analysis': root/analysis GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'general': root/general GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'processing': root/processing GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'stimulus': root/stimulus GroupBuilder {'attributes': {}, 'groups': {'presentation': root/stimulus/presentation GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'templates': root/stimulus/templates GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}}, 'datasets': {}, 'links': {}}}, 'datasets': {'file_create_date': root/file_create_date DatasetBuilder {'attributes': {}, 'data': <HDF5 dataset "file_create_date": shape (1,), type "|O">}, 'identifier': root/identifier DatasetBuilder {'attributes': {}, 'data': '766a7f4e-08a6-44d7-83df-b54753758d47'}, 'session_start_time': root/session_start_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}, 'timestamps_reference_time': root/timestamps_reference_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}}, 'links': {}}, "Could not construct NWBFile object due to: NWBFile.__init__: missing argument 'session_description'")

Old inspector report:

**************************************************
NWBInspector Report Summary

Timestamp: 2025-07-23 16:47:08.514507-07:00
Platform: macOS-14.2.1-arm64-arm-64bit
NWBInspector version: 0.6.3

Found 2 issues over 1 files:
       2 - ERROR
**************************************************


0  ERROR
========

0.0  /Users/smprince/Documents/code/nwbinspector/test_construct_error.nwb: During io.read() - <class 'hdmf.build.errors.ConstructError'>: (root GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'NWBFile', 'nwb_version': '2.8.0', 'object_id': '9ca053ce-bd47-443e-90cd-776cfe8b0d90'}, 'groups': {'acquisition': root/acquisition GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'analysis': root/analysis GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'general': root/general GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'processing': root/processing GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'stimulus': root/stimulus GroupBuilder {'attributes': {}, 'groups': {'presentation': root/stimulus/presentation GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'templates': root/stimulus/templates GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}}, 'datasets': {}, 'links': {}}}, 'datasets': {'file_create_date': root/file_create_date DatasetBuilder {'attributes': {}, 'data': <HDF5 dataset "file_create_date": shape (1,), type "|O">}, 'identifier': root/identifier DatasetBuilder {'attributes': {}, 'data': '1d2dcabe-3a30-48ad-bd43-ffedc3c0ed5b'}, 'session_start_time': root/session_start_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}, 'timestamps_reference_time': root/timestamps_reference_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}}, 'links': {}}, "Could not construct NWBFile object due to: NWBFile.__init__: missing argument 'session_description'") - 'None' object with name 'None'
       Message: Traceback (most recent call last):
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/objectmapper.py", line 1368, in construct
    obj = self.__new_container__(cls, builder.source, parent, builder.attributes.get(self.__spec.id_key()),
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/objectmapper.py", line 1381, in __new_container__
    obj.__init__(**kwargs)
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 577, in func_call
    pargs = _check_args(args, kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 570, in _check_args
    raise ExceptionType(msg)
TypeError: NWBFile.__init__: missing argument 'session_description'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/nwbinspector/_nwb_inspection.py", line 148, in inspect_all
    nwbfile = read_nwbfile(nwbfile_path=nwbfile_path)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/nwbinspector/tools/_read_nwbfile.py", line 95, in read_nwbfile
    nwbfile, _ = _read_nwbfile_helper(nwbfile_path=nwbfile_path, method=method, backend=backend)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/nwbinspector/tools/_read_nwbfile.py", line 180, in _read_nwbfile_helper
    nwbfile = io.read()
              ^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/pynwb/__init__.py", line 479, in read
    file = super().read(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/backends/hdf5/h5tools.py", line 458, in read
    return super().read(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/backends/io.py", line 60, in read
    container = self.__manager.construct(f_builder)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/manager.py", line 286, in construct
    result = self.__type_map.construct(builder, self, None)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/manager.py", line 813, in construct
    return obj_mapper.construct(builder, build_manager, parent)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/pynwb/io/file.py", line 161, in construct
    return super().construct(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/objectmapper.py", line 1372, in construct
    raise ConstructError(builder, msg) from ex
hdmf.build.errors.ConstructError: (root GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'NWBFile', 'nwb_version': '2.8.0', 'object_id': '9ca053ce-bd47-443e-90cd-776cfe8b0d90'}, 'groups': {'acquisition': root/acquisition GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'analysis': root/analysis GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'general': root/general GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'processing': root/processing GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'stimulus': root/stimulus GroupBuilder {'attributes': {}, 'groups': {'presentation': root/stimulus/presentation GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'templates': root/stimulus/templates GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}}, 'datasets': {}, 'links': {}}}, 'datasets': {'file_create_date': root/file_create_date DatasetBuilder {'attributes': {}, 'data': <HDF5 dataset "file_create_date": shape (1,), type "|O">}, 'identifier': root/identifier DatasetBuilder {'attributes': {}, 'data': '1d2dcabe-3a30-48ad-bd43-ffedc3c0ed5b'}, 'session_start_time': root/session_start_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}, 'timestamps_reference_time': root/timestamps_reference_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}}, 'links': {}}, "Could not construct NWBFile object due to: NWBFile.__init__: missing argument 'session_description'")


0.1  /Users/smprince/Documents/code/nwbinspector/test_construct_error.nwb: During io.read() - <class 'hdmf.build.errors.ConstructError'>: (root GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'NWBFile', 'nwb_version': '2.8.0', 'object_id': '9ca053ce-bd47-443e-90cd-776cfe8b0d90'}, 'groups': {'acquisition': root/acquisition GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'analysis': root/analysis GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'general': root/general GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'processing': root/processing GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'stimulus': root/stimulus GroupBuilder {'attributes': {}, 'groups': {'presentation': root/stimulus/presentation GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'templates': root/stimulus/templates GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}}, 'datasets': {}, 'links': {}}}, 'datasets': {'file_create_date': root/file_create_date DatasetBuilder {'attributes': {}, 'data': <HDF5 dataset "file_create_date": shape (1,), type "|O">}, 'identifier': root/identifier DatasetBuilder {'attributes': {}, 'data': '1d2dcabe-3a30-48ad-bd43-ffedc3c0ed5b'}, 'session_start_time': root/session_start_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}, 'timestamps_reference_time': root/timestamps_reference_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}}, 'links': {}}, "Could not construct NWBFile object due to: NWBFile.__init__: missing argument 'session_description'") - 'None' object with name 'None'
       Message: Traceback (most recent call last):
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/objectmapper.py", line 1368, in construct
    obj = self.__new_container__(cls, builder.source, parent, builder.attributes.get(self.__spec.id_key()),
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/objectmapper.py", line 1381, in __new_container__
    obj.__init__(**kwargs)
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 577, in func_call
    pargs = _check_args(args, kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 570, in _check_args
    raise ExceptionType(msg)
TypeError: NWBFile.__init__: missing argument 'session_description'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/nwbinspector/_nwb_inspection.py", line 277, in inspect_nwbfile
    in_memory_nwbfile = read_nwbfile(nwbfile_path=nwbfile_path)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/nwbinspector/tools/_read_nwbfile.py", line 95, in read_nwbfile
    nwbfile, _ = _read_nwbfile_helper(nwbfile_path=nwbfile_path, method=method, backend=backend)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/nwbinspector/tools/_read_nwbfile.py", line 180, in _read_nwbfile_helper
    nwbfile = io.read()
              ^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/pynwb/__init__.py", line 479, in read
    file = super().read(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/backends/hdf5/h5tools.py", line 458, in read
    return super().read(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/backends/io.py", line 60, in read
    container = self.__manager.construct(f_builder)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/manager.py", line 286, in construct
    result = self.__type_map.construct(builder, self, None)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/manager.py", line 813, in construct
    return obj_mapper.construct(builder, build_manager, parent)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/pynwb/io/file.py", line 161, in construct
    return super().construct(**kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/utils.py", line 578, in func_call
    return func(args[0], **pargs)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/smprince/anaconda3/envs/test/lib/python3.12/site-packages/hdmf/build/objectmapper.py", line 1372, in construct
    raise ConstructError(builder, msg) from ex
hdmf.build.errors.ConstructError: (root GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'NWBFile', 'nwb_version': '2.8.0', 'object_id': '9ca053ce-bd47-443e-90cd-776cfe8b0d90'}, 'groups': {'acquisition': root/acquisition GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'analysis': root/analysis GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'general': root/general GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'processing': root/processing GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'stimulus': root/stimulus GroupBuilder {'attributes': {}, 'groups': {'presentation': root/stimulus/presentation GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}, 'templates': root/stimulus/templates GroupBuilder {'attributes': {}, 'groups': {}, 'datasets': {}, 'links': {}}}, 'datasets': {}, 'links': {}}}, 'datasets': {'file_create_date': root/file_create_date DatasetBuilder {'attributes': {}, 'data': <HDF5 dataset "file_create_date": shape (1,), type "|O">}, 'identifier': root/identifier DatasetBuilder {'attributes': {}, 'data': '1d2dcabe-3a30-48ad-bd43-ffedc3c0ed5b'}, 'session_start_time': root/session_start_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}, 'timestamps_reference_time': root/timestamps_reference_time DatasetBuilder {'attributes': {}, 'data': '1970-01-01T00:00:00+00:00'}}, 'links': {}}, "Could not construct NWBFile object due to: NWBFile.__init__: missing argument 'session_description'")

codecov-commenter · 2025-08-29T18:09:20Z

Codecov Report

❌ Patch coverage is 0% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.19%. Comparing base (0ba63f2) to head (3b04946).
⚠️ Report is 11 commits behind head on dev.

Files with missing lines	Patch %	Lines
src/nwbinspector/_nwb_inspection.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #603      +/-   ##
==========================================
+ Coverage   83.04%   87.19%   +4.15%     
==========================================
  Files          47       47              
  Lines        1557     1562       +5     
==========================================
+ Hits         1293     1362      +69     
+ Misses        264      200      -64

Files with missing lines	Coverage Δ
src/nwbinspector/_nwb_inspection.py	`86.61% <0.00%> (+4.01%)`	⬆️

... and 4 files with indirect coverage changes

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update read error message

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stephprince mentioned this pull request Jul 24, 2025

Difficult to read errors for datetime objects that are not timezone aware #594

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update CHANGELOG

e5746ab

stephprince marked this pull request as ready for review July 24, 2025 17:12

stephprince requested a review from rly July 24, 2025 17:12

Merge branch 'dev' into improve-read-error-msg

22c9e4e

rly approved these changes Jul 24, 2025

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Merge branch 'dev' into improve-read-error-msg

3b04946

stephprince enabled auto-merge (squash) July 24, 2025 22:14

stephprince merged commit 2bc824e into dev Jul 24, 2025
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stephprince deleted the improve-read-error-msg branch July 24, 2025 22:17

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Update inspector report summary for PyNWB read errors #603

Update inspector report summary for PyNWB read errors #603

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stephprince commented Jul 24, 2025

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codecov-commenter commented Aug 29, 2025

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Update inspector report summary for PyNWB read errors #603

Update inspector report summary for PyNWB read errors #603

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stephprince commented Jul 24, 2025

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codecov-commenter commented Aug 29, 2025

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