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FIX: Validation of BIDS fields fails for non-path arguments #6

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jerdra opened this issue Dec 9, 2021 · 0 comments
Open

FIX: Validation of BIDS fields fails for non-path arguments #6

jerdra opened this issue Dec 9, 2021 · 0 comments
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bug Something isn't working good first issue Good for newcomers

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@jerdra
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jerdra commented Dec 9, 2021

Currently, Niviz attempts to extract BIDS entities for every input into the filespecs: args.

However, this is inappropriate for plot config options and standard paths (i.e MNI templates) where we do not expect BIDS entities at all.

Currently, extract_bids_entities runs on all inputs and checks if any entities are defined, these are of two types:

  1. dynamic entities that are pulled from filepaths
  2. static entities that are to be shared (i.e defining a desc for an output SVG)

If neither dynamic or static entities are defined then extract_bids_entities will raise an error. Which is problematic because if no static entities are defined in the YAML, then nonpath items will always fail.

This should be remediated so that BIDS entities aren't checked for non-path args. Note that this may break things down the line, but we'll discover them as we go :)

Where to look

config.py:FileSpec.gen_args

@jerdra jerdra added bug Something isn't working good first issue Good for newcomers labels Dec 9, 2021
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