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modification of namespace caching to exclude neurodata_types #352

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cechava
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@cechava cechava commented Nov 19, 2021

Fixes #351
Currently, matnwb caches neurodata_types in the namespace of NWB extensions. This differs from the behavior of pynwb, which leads to the file from failing validation.

This PR modifies +schemes/exportJson.m to exclude caching of 'neurodata_types' field from namespace. See issue #351 for further details.

With this modification matnwb-generated files with NWB extension in namespace pass verification:

$ python -m pynwb.validate ndx-ecog_file_test_matnwb.nwb 
Validating ndx-ecog_file_test_matnwb.nwb against cached namespace information using namespace 'ndx-ecog'.
 - no errors found.

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codecov bot commented Nov 19, 2021

Codecov Report

Merging #352 (996028b) into master (8819bba) will increase coverage by 0.00%.
The diff coverage is 87.50%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #352   +/-   ##
=======================================
  Coverage   85.32%   85.32%           
=======================================
  Files         120      120           
  Lines        4335     4342    +7     
=======================================
+ Hits         3699     3705    +6     
- Misses        636      637    +1     
Impacted Files Coverage Δ
+schemes/exportJson.m 98.33% <87.50%> (-1.67%) ⬇️

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@cechava
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cechava commented Nov 22, 2021

this PR is unnecessary because the issue is with pynwb not saving 'data_types'. See issue #351 thread

@cechava cechava closed this Nov 22, 2021
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failing validation of matnwb-generated files with extension in cached namespace
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