Repack Nwb Files #1003
Repack Nwb Files #1003
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src/neuroconv/tools/nwb_helpers/_configuration_models/_hdf5_dataset_io.py
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src/neuroconv/tools/nwb_helpers/_configuration_models/_hdf5_dataset_io.py
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@CodyCBakerPhD, the code now reflects my vision for the API: The code then progresses along 2 paths:
lmk what you think! |
...est_backend_and_dataset_configuration/test_helpers/test_get_default_backend_configuration.py
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| print(nwbfile.acquisition["my_video"]) | ||
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| backend_config = get_default_backend_configuration(nwbfile, "hdf5") | ||
| print(backend_config) # TODO: Figure out why this doesn't throw an error like Ben said it did |
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Can we add an integration test where we write a new NWB file with a different backend configuration?
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Hmm... You mean something like 'make a Zarr-backend copy of this existing HDF5-backend NWB file'? Or same type of backend (such as both HDF5) but different configuration?
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good question. Both, I guess. I just want to make sure this works end-to-end and does not require us to do anything funky in practice
| @@ -262,3 +263,22 @@ def test_complex_zarr(zarr_nwbfile_path): | |||
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| assert stdout.getvalue() == expected_print | |||
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| def test_000_ImageSeries(): | |||
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I would like to see many more tests here; starting with more basic types like TimeSeries, DynamicTable, etc. before working our way up to the edge case that is an ImageSeries (external vs. internal mode too on that)
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Keep in mind the intended point of this function; to start with objects that are either uncompressed, unchuncked, or badly chunked; and then we create a new copy of the file that has better compression and chunking on all applicable datasets
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1003 +/- ##
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- Coverage 91.25% 90.37% -0.88%
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Files 127 127
Lines 7555 7645 +90
==========================================
+ Hits 6894 6909 +15
- Misses 661 736 +75
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src/neuroconv/tools/nwb_helpers/_configuration_models/_base_backend.py
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Fixes #892
Depends on hdmf-dev/hdmf#1172
Depends on hdmf-dev/hdmf-zarr#215