Fix/read bad icephys table #919
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## dev #919 +/- ##
==========================================
- Coverage 88.33% 88.12% -0.21%
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Files 45 45
Lines 9283 9309 +26
Branches 2651 2661 +10
==========================================
+ Hits 8200 8204 +4
- Misses 765 782 +17
- Partials 318 323 +5
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3 tasks
oruebel
commented
Jul 26, 2023
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+608
| try: | ||
| from pynwb import NWBHDF5IO | ||
| except ImportError: | ||
| self.skipTest("PyNWB not installed for testing") | ||
| test_filename = os.path.join(os.path.dirname(os.path.abspath(__file__)), | ||
| "bad_nwb_icephys_aligned_dynamic_table_file.nwb") | ||
|
|
||
| with NWBHDF5IO(test_filename, 'r', load_namespaces=True) as nwbio: | ||
| with warnings.catch_warnings(record=True) as w: | ||
| _ = nwbio.read() | ||
| self.assertEqual(len(w), 7) |
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@rly the easiest way to test this is to just try an read the broken NWB file which has all the different errors. However, PyNWB is not installed for our CI, so this test gets skipped. Is there a way that we can read the file without just HDF5IO?
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Motivation
Fix #918
Relax the error checking in the
__init__methods ofDynamicTableandAlignedDynamicTableto raise warnings when reading from file and raise errors when creating new data. This is to try and allow users to access bad data files while ensuring that we don't construct bad files ourselves.How to test the behavior?
See #918 for details
Checklist
rufffrom the source directory.