Comments (4)
Original comment by Andrew Tritt (Bitbucket: ajtritt, GitHub: ajtritt):
Merged in issue_34 (pull request #67)
fixing issue #34 and issue #35
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Original comment by Andrew Tritt (Bitbucket: ajtritt, GitHub: ajtritt):
From Loren:
Traceback (most recent call last):
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 327, in list_fill
data_dtype = __get_type(data)
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 221, in __get_type
raise ValueError('cannot determine type for empty data')
ValueError: cannot determine type for empty data
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/loren/Src/NWB/franklabnwb/convert_nspike.py", line 492, in
io.write(nwbf)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 231, in func_call
return func(self, **parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/io.py", line 25, in write
self.write_builder(f_builder)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 231, in func_call
return func(self, **parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 120, in write_builder
write_group(self.__file, name, gbldr.groups, gbldr.datasets, gbldr.attributes, gbldr.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 161, in write_group
builder.links)
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 168, in write_group
builder.get('attributes'))
File "/Users/loren/Src/NWB/pynwb/src/form/utils.py", line 238, in func_call
return func(**parsed['args'])
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 261, in write_dataset
dset = list_fill(parent, name, data)
File "/Users/loren/Src/NWB/pynwb/src/form/backends/hdf5/h5tools.py", line 329, in list_fill
raise Exception('cannot add %s to %s - could not determine type' % (name, parent.name)) from exc
Exception: cannot add tags to /epochs/day 3 - could not determine type
Process finished with exit code 1
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Original comment by Loren Frank (Bitbucket: lmfrnk, GitHub: Unknown):
Great; I’ll test it out as soon as I can and get back to you…
Loren
Loren M. Frank
Professor
Howard Hughes Medical Institute
Kavli Institute for Fundamental Neuroscience
Department of Physiology
University of California, San Francisco
Office Phone: 415-502-7357
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Original comment by Andrew Tritt (Bitbucket: ajtritt, GitHub: ajtritt):
Hi Loren,
This looks like a problem when trying to create a file that already exists. I added some logic to deal with this. Please update and let me know if you still get this error.
Andrew
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Related Issues (20)
- [Documentation]: Improve docs around setting "name" for a neurodata_type
- [Feature]: Warn on read rather than error HOT 1
- `electrodes` column in `misc.Units.add_unit()` doesn't adhere to nwb-schema HOT 1
- [Bug]: OSError: [Errno 5] Unable to synchronously open file HOT 2
- [Documentation]: Streaming NWB files - recommend using remfile as the preferred method HOT 10
- [Bug]: `get_data_in_units` fails for ElectricalSeries with `channel_conversion`
- [Feature]: Add new.processing.ImageSementation.PlaneSegmentation remove feature (function) HOT 1
- [Bug]: `TypeError: `dumps_kwargs` keyword arguments are no longer supported.` when running tests on pynwb 2.5.0 HOT 4
- [Bug]: One more test error for `=pynwb-2.5.0` — `AssertionError: UserWarning not triggered` HOT 1
- [Feature]: a way to disable all tests requiring dynamic downloads OR a static archive for test data HOT 4
- [Feature]: Migrate to only use pytest HOT 1
- [Feature]: Test read of dandisets systematically in CI
- [Feature]: Change pynwb.validate(io=...) to match pynwb.validate(paths=[path])
- [Umbrella Feature]: Upgrade validation methods
- [Feature]: load nwb file without initial preload step HOT 3
- [Feature]: Notify user if python package for extension exists and is recommended
- [Bug]: Invalidation of typical session ID HOT 2
- Run streaming benchmarks over time
- [Documentation]: claim of fsspec out-of-the-box faster than ros3 should be backed by some evidence HOT 1
- [Bug]: 2-photon series movie not appearing in file. HOT 15
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