[Bug]: errors with patchseq data #582
Description
What happened?
I ran
nwbinspector ~/Downloads/sub-1265174261_ses-1265661925_icephys.nwb
on this file:
sub-1265174261_ses-1265661925_icephys.nwb.zip
Here was the output:
**************************************************
NWBInspector Report Summary
Timestamp: 2025-04-14 09:02:35.307666-07:00
Platform: macOS-15.4-arm64-arm-64bit
NWBInspector version: 0.6.3
Found 121 issues over 1 files:
7 - ERROR
1 - BEST_PRACTICE_VIOLATION
113 - BEST_PRACTICE_SUGGESTION
**************************************************
0 ERROR
========
0.0 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb and 6 other files: During evaluation of 'check_timestamp_of_the_first_sample_is_not_negative' - <class 'IndexError'>: Index (0) out of range for empty dimension - 'None' object with name 'None'
Message: Traceback (most recent call last):
File "/Users/bdichter/miniconda3/lib/python3.12/site-packages/nwbinspector/_nwb_inspection.py", line 445, in run_checks
output = check_function(nwbfile_object)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/bdichter/miniconda3/lib/python3.12/site-packages/nwbinspector/_registration.py", line 62, in auto_parse_some_output
output = check_function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/bdichter/miniconda3/lib/python3.12/site-packages/nwbinspector/checks/_time_series.py", line 131, in check_timestamp_of_the_first_sample_is_not_negative
first_timestamp = time_series.starting_time if time_series.starting_time is not None else time_series.timestamps[0]
~~~~~~~~~~~~~~~~~~~~~~^^^
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/Users/bdichter/miniconda3/lib/python3.12/site-packages/h5py/_hl/dataset.py", line 802, in __getitem__
return self._fast_reader.read(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "h5py/_selector.pyx", line 361, in h5py._selector.Reader.read
File "h5py/_selector.pyx", line 151, in h5py._selector.Selector.apply_args
IndexError: Index (0) out of range for empty dimension
1 BEST_PRACTICE_VIOLATION
==========================
1.1 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_intracellular_electrode_cell_id_exists - 'IntracellularElectrode' object with name 'electrode_0'
Message: Please include a unique cell_id associated with this IntracellularElectrode.
2 BEST_PRACTICE_SUGGESTION
===========================
2.2 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'Subject' object at location '/general/subject'
Message: Description is missing.
2.3 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_9'
Message: Description ('no description') is a placeholder.
2.4 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_8'
Message: Description ('no description') is a placeholder.
2.5 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_7'
Message: Description ('no description') is a placeholder.
2.6 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_6'
Message: Description ('no description') is a placeholder.
2.7 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_5'
Message: Description ('no description') is a placeholder.
2.8 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_42'
Message: Description ('no description') is a placeholder.
2.9 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_41'
Message: Description ('no description') is a placeholder.
2.10 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_40'
Message: Description ('no description') is a placeholder.
2.11 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_39'
Message: Description ('no description') is a placeholder.
2.12 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_38'
Message: Description ('no description') is a placeholder.
2.13 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_26'
Message: Description ('no description') is a placeholder.
2.14 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_25'
Message: Description ('no description') is a placeholder.
2.15 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_24'
Message: Description ('no description') is a placeholder.
2.16 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_23'
Message: Description ('no description') is a placeholder.
2.17 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_22'
Message: Description ('no description') is a placeholder.
2.18 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_21'
Message: Description ('no description') is a placeholder.
2.19 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_20'
Message: Description ('no description') is a placeholder.
2.20 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'TimeSeries' object at location '/processing/spikes/Sweep_19'
Message: Description ('no description') is a placeholder.
2.21 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampStimulusSeries' object at location '/stimulus/presentation/data_00044_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.22 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00043_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.23 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00042_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.24 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00041_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.25 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00040_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.26 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00039_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.27 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00038_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.28 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00037_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.29 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00036_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.30 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00035_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.31 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00034_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.32 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00033_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.33 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00032_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.34 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00031_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.35 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00030_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.36 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00029_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.37 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00028_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.38 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00027_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.39 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00026_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.40 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00025_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.41 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00024_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.42 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00023_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.43 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00022_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.44 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00021_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.45 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00020_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.46 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00019_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.47 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00018_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.48 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00017_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.49 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00016_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.50 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00015_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.51 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00014_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.52 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00013_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.53 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00012_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.54 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00011_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.55 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00010_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.56 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00009_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.57 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00008_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.58 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00007_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.59 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00006_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.60 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00005_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.61 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampStimulusSeries' object at location '/stimulus/presentation/data_00004_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.62 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampStimulusSeries' object at location '/stimulus/presentation/data_00003_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.63 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampStimulusSeries' object at location '/stimulus/presentation/data_00002_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.64 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampStimulusSeries' object at location '/stimulus/presentation/data_00001_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.65 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampStimulusSeries' object at location '/stimulus/presentation/data_00000_DA0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.66 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampSeries' object at location '/acquisition/data_00044_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.67 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00043_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.68 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00042_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.69 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00041_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.70 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00040_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.71 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00039_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.72 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00038_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.73 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00037_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.74 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00036_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.75 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00035_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.76 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00034_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.77 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00033_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.78 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00032_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.79 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00031_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.80 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00030_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.81 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00029_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.82 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00028_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.83 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00027_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.84 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00026_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.85 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00025_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.86 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00024_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.87 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00023_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.88 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00022_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.89 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00021_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.90 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00020_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.91 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00019_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.92 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00018_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.93 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00017_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.94 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00016_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.95 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00015_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.96 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00014_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.97 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00013_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.98 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00012_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.99 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00011_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.100 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00010_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.101 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00009_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.102 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00008_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.103 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00007_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.104 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00006_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.105 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00005_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.106 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'CurrentClampSeries' object at location '/acquisition/data_00004_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.107 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampSeries' object at location '/acquisition/data_00003_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.108 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampSeries' object at location '/acquisition/data_00002_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.109 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampSeries' object at location '/acquisition/data_00001_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.110 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_description - 'VoltageClampSeries' object at location '/acquisition/data_00000_AD0'
Message: Description ('PLACEHOLDER') is a placeholder.
2.111 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_experimenter_exists - 'NWBFile' object at location '/'
Message: Experimenter is missing.
2.112 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_experiment_description - 'NWBFile' object at location '/'
Message: Experiment description is missing.
2.113 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_keywords - 'NWBFile' object at location '/'
Message: Metadata /general/keywords is missing.
2.114 /Users/bdichter/Downloads/sub-1265174261_ses-1265661925_icephys.nwb: check_processing_module_name - 'ProcessingModule' object with name 'spikes'
Message: Processing module is named spikes. It is recommended to use the schema module names: ophys, ecephys, icephys, behavior, misc, ogen, retinotopy
Problems:
- Why are these errors being thrown? The NWB file passed validation.
- Why does the error message say " and 6 other files", when I only tested one file?
- Why doesn't the error message include the location of the neurodata object?
Operating System
M1 macOS
Python Version
3.12
Were you streaming with ROS3?
No
Package Versions
Package Version Editable project location
---------------------------------------- -------------- --------------------------------
aiohappyeyeballs 2.6.1
aiohttp 3.11.14
aiosignal 1.3.2
anaconda-anon-usage 0.5.0
annotated-types 0.6.0
anyio 4.9.0
appnope 0.1.3
archspec 0.2.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.3.0
asciitree 0.3.3
asgiref 3.8.1
asttokens 2.0.5
async-lru 2.0.4
attrs 25.3.0
auto_subtitle 1.0
autosub 0.3.12
babel 2.16.0
backoff 2.2.1
bcrypt 4.3.0
beautifulsoup4 4.12.3
bidsschematools 0.7.2
bleach 6.2.0
blessed 1.20.0
boltons 24.1.0
Brotli 1.0.9
build 1.2.2.post1
cachetools 5.5.2
certifi 2025.1.31
cffi 1.17.1
cfgv 3.4.0
chardet 5.2.0
charset-normalizer 3.3.2
chroma-hnswlib 0.7.6
chromadb 0.6.3
ci-info 0.3.0
click 8.1.8
click-didyoumean 0.3.1
coloredlogs 15.0.1
comm 0.2.1
conda 25.3.0
conda-anaconda-telemetry 0.1.2
conda-anaconda-tos 0.1.2
conda-content-trust 0.2.0
conda-libmamba-solver 25.1.1
conda-package-handling 2.4.0
conda_package_streaming 0.11.0
contourpy 1.3.1
cryptography 43.0.3
cycler 0.12.1
dandi 0.67.2
dandischema 0.11.0
debugpy 1.8.11
decorator 5.1.1
defusedxml 0.7.1
Deprecated 1.2.18
distlib 0.3.9
distro 1.9.0
dnspython 2.7.0
durationpy 0.9
email_validator 2.2.0
etelemetry 0.3.1
executing 0.8.3
fastapi 0.115.12
fasteners 0.19
fastjsonschema 2.21.1
ffmpeg 1.4
filelock 3.18.0
flatbuffers 25.2.10
fonttools 4.56.0
fqdn 1.5.1
frozendict 2.4.2
frozenlist 1.5.0
fscacher 0.4.4
fsspec 2025.3.0
google-api-core 2.24.2
google-api-python-client 2.166.0
google-auth 2.38.0
google-auth-httplib2 0.2.0
googleapis-common-protos 1.69.2
grpcio 1.71.0
h11 0.14.0
h5py 3.13.0
hdmf 4.0.0
hdmf_zarr 0.11.0
httpcore 1.0.2
httplib2 0.22.0
httptools 0.6.4
httpx 0.27.0
httpx-sse 0.4.0
huggingface-hub 0.29.3
humanfriendly 10.0
humanize 4.12.2
identify 2.6.9
idna 3.7
importlib_metadata 8.6.1
importlib_resources 6.5.2
interleave 0.3.0
ipykernel 6.29.5
ipython 8.30.0
ipywidgets 8.1.5
isodate 0.7.2
isoduration 20.11.0
jaraco.classes 3.4.0
jaraco.context 6.0.1
jaraco.functools 4.1.0
jedi 0.19.2
Jinja2 3.1.6
jiter 0.9.0
joblib 1.4.2
json5 0.9.25
jsonpatch 1.33
jsonpointer 2.1
jsonschema 4.23.0
jsonschema-specifications 2024.10.1
jupyter 1.1.1
jupyter_client 8.6.3
jupyter-console 6.6.3
jupyter_core 5.7.2
jupyter-events 0.12.0
jupyter-lsp 2.2.0
jupyter_server 2.15.0
jupyter_server_terminals 0.4.4
jupyterlab 4.3.4
jupyterlab_pygments 0.3.0
jupyterlab_server 2.27.3
jupyterlab_widgets 3.0.13
jupytext 1.16.7
keyring 25.6.0
keyrings.alt 5.0.2
kiwisolver 1.4.8
kubernetes 32.0.1
langchain 0.3.21
langchain-core 0.3.48
langchain-text-splitters 0.3.7
langsmith 0.3.19
libmambapy 2.0.5
lindi 0.4.4
llvmlite 0.44.0
markdown-it-py 2.2.0
MarkupSafe 3.0.2
matplotlib 3.10.1
matplotlib-inline 0.1.6
mcp 1.5.0
mdit-py-plugins 0.4.2
mdurl 0.1.0
menuinst 2.2.0
mistune 3.1.2
mmh3 5.1.0
monotonic 1.6
more-itertools 10.6.0
mpmath 1.3.0
multidict 6.2.0
natsort 8.4.0
nbclient 0.10.2
nbconvert 7.16.6
nbformat 5.10.4
nest-asyncio 1.6.0
networkx 3.4.2
nodeenv 1.9.1
notebook 7.3.2
notebook_shim 0.2.4
numba 0.61.0
numcodecs 0.15.1
numpy 1.26.4
nwb_code_generator 0.1.0 /Users/bdichter/dev/nwb-info/src
nwbinspector 0.6.3
oauthlib 3.2.2
onnxruntime 1.21.0
openai 1.68.2
openai-whisper 20240930
opentelemetry-api 1.31.1
opentelemetry-exporter-otlp-proto-common 1.31.1
opentelemetry-exporter-otlp-proto-grpc 1.31.1
opentelemetry-instrumentation 0.52b1
opentelemetry-instrumentation-asgi 0.52b1
opentelemetry-instrumentation-fastapi 0.52b1
opentelemetry-proto 1.31.1
opentelemetry-sdk 1.31.1
opentelemetry-semantic-conventions 0.52b1
opentelemetry-util-http 0.52b1
orjson 3.10.16
overrides 7.4.0
packaging 24.2
pandas 2.2.3
pandocfilters 1.5.0
parso 0.8.4
pexpect 4.8.0
pillow 11.1.0
pip 25.0
platformdirs 3.10.0
pluggy 1.5.0
posthog 3.23.0
pre_commit 4.2.0
progressbar 2.5
prometheus_client 0.21.0
prompt-toolkit 3.0.43
propcache 0.3.0
proto-plus 1.26.1
protobuf 5.29.4
psutil 5.9.0
ptyprocess 0.7.0
pure-eval 0.2.2
pyasn1 0.6.1
pyasn1_modules 0.4.1
pycosat 0.6.6
pycparser 2.21
pycryptodomex 3.22.0
pydantic 2.10.3
pydantic_core 2.27.1
pydantic-settings 2.8.1
PyGithub 2.6.1
Pygments 2.15.1
PyJWT 2.10.1
PyNaCl 1.5.0
pynapple 0.8.4
pynwb 3.0.0
pyout 0.8.1
pyparsing 3.2.2
PyPika 0.48.9
pyproject_hooks 1.2.0
PyQt6 6.7.1
PyQt6_sip 13.9.1
PySocks 1.7.1
pysrt 1.1.2
python-dateutil 2.9.0.post0
python-dotenv 1.1.0
python-json-logger 3.2.1
pytz 2025.1
PyYAML 6.0.2
pyzmq 26.2.0
qtconsole 5.6.1
QtPy 2.4.1
referencing 0.36.2
regex 2024.11.6
remfile 0.1.13
repo-search 0.1.0 /Users/bdichter/dev/repo-search
requests 2.32.3
requests-oauthlib 2.0.0
requests-toolbelt 1.0.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rfc3987 1.3.8
rich 13.9.4
rpds-py 0.23.1
rsa 4.9
ruamel.yaml 0.18.6
ruamel.yaml.clib 0.2.8
ruff 0.11.3
scipy 1.15.2
seaborn 0.13.2
semantic-version 2.10.0
Send2Trash 1.8.2
setuptools 75.8.0
shellingham 1.5.4
sip 6.10.0
six 1.16.0
sniffio 1.3.0
soupsieve 2.5
SQLAlchemy 2.0.39
sse-starlette 2.2.1
stack-data 0.2.0
starlette 0.46.1
sympy 1.13.1
tabulate 0.9.0
tenacity 9.0.0
terminado 0.17.1
threadpoolctl 3.6.0
tiktoken 0.9.0
tinycss2 1.4.0
tokenizers 0.21.1
torch 2.6.0
tornado 6.4.2
tqdm 4.67.1
traitlets 5.14.3
truststore 0.10.0
typer 0.15.2
types-python-dateutil 2.9.0.20241206
typing_extensions 4.12.2
tzdata 2025.2
uri-template 1.3.0
uritemplate 4.1.1
urllib3 2.3.0
uvicorn 0.34.0
uvloop 0.21.0
virtualenv 20.30.0
watchfiles 1.0.4
wcwidth 0.2.5
webcolors 24.11.1
webencodings 0.5.1
websocket-client 1.8.0
websockets 15.0.1
wheel 0.45.1
widgetsnbextension 4.0.13
wrapt 1.17.2
yarl 1.18.3
zarr 2.18.4
zarr-checksum 0.4.2
zipp 3.21.0
zstandard 0.23.0
Code of Conduct
- I agree to follow this project's Code of Conduct
- Have you ensured this bug was not already reported?
- To the best of your ability, have you ensured this is a bug within the code that checks the NWBFile, rather than a bug in the NWBFile reader (e.g., PyNWB or MatNWB)?