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Add driver argument to new validation functions #1588

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merged 12 commits into from
Jan 18, 2023

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CodyCBakerPhD
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When working on NeurodataWithoutBorders/nwbinspector#265 (the integration of the recent validation changes into the NWB Inspector) I ran into an issue getting the cached namespaces for files when using the streaming mode of the Inspector.

Traced it back to these particular function calls - thankfully, NWBHDF5IO.load_namespaces(...) already supports a driver keyword argument, we just need to add control and propagate it as shown here.

@rly What would your recommendations be for adding tests for this?

@CodyCBakerPhD CodyCBakerPhD self-assigned this Nov 9, 2022
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I'll also add the file argument propagation in a separate PR for fsspec based streaming. That will require just a little bit more since it would need to not conflict with the io vs. path usage and just be an alternate usage of the path

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codecov bot commented Nov 9, 2022

Codecov Report

Merging #1588 (08f33c5) into dev (2930095) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##              dev    #1588   +/-   ##
=======================================
  Coverage   91.31%   91.31%           
=======================================
  Files          25       25           
  Lines        2534     2534           
  Branches      481      481           
=======================================
  Hits         2314     2314           
  Misses        139      139           
  Partials       81       81           
Flag Coverage Δ
integration 70.44% <100.00%> (ø)
unit 84.37% <50.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/pynwb/validate.py 100.00% <100.00%> (ø)

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@CodyCBakerPhD CodyCBakerPhD added category: enhancement improvements of code or code behavior topic: validator issues related to validation of files labels Nov 9, 2022
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rly commented Nov 9, 2022

This looks good. You can add to https://github.com/NeurodataWithoutBorders/pynwb/tree/dev/tests/integration/ros3 which is the only other place in the tests where we test different drivers.

src/pynwb/validate.py Outdated Show resolved Hide resolved
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This looks like a fix specifically for ros3. It's good to support, but let's try to shift our default over to fsspec for all streaming stuff

src/pynwb/validate.py Outdated Show resolved Hide resolved
@CodyCBakerPhD
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This looks like a fix specifically for ros3. It's good to support, but let's try to shift our default over to fsspec for all streaming stuff

#1588 (comment)

I'll also add the file argument propagation in a separate PR for fsspec based streaming. That will require just a little bit more since it would need to not conflict with the io vs. path usage and just be an alternate usage of the path

@CodyCBakerPhD
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This looks good. You can add to https://github.com/NeurodataWithoutBorders/pynwb/tree/dev/tests/integration/ros3 which is the only other place in the tests where we test different drivers.

OK - added tests for the new keyword injections

@CodyCBakerPhD
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Oh wow, forgot about this one. Thanks @rly

@rly rly merged commit 4a38196 into dev Jan 18, 2023
@rly rly deleted the allow_driver_specification_in_validation branch January 18, 2023 19:26
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4 participants