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Make bids-validator conform to BIDS-App (or execution-spec right away) specification #16

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yarikoptic opened this issue Jun 12, 2024 · 2 comments
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help wanted Extra attention is needed

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@yarikoptic
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ATM it is

Usage: bids-validator <dataset_directory> [options]

whenever BIDS-app interface, as described in new exec spec (bep027) https://bids-standard.github.io/execution-spec/inputs.html#backwards-compatibility

bids-app InputDataset OutputLocation AnalysisLevel [options]
...
CLI flag: --subject-label

. Or may be just following new options as described at https://bids-standard.github.io/execution-spec/inputs.html#list-of-custom-object-properties-and-roles-within-the-bids-application-specification

It would have been quite convenient to be able to limit bids-validation to a specific subject or session, and only at "dataset" level provide overall report.

@effigies effigies added the help wanted Extra attention is needed label Jun 12, 2024
@effigies
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If we do want to adopt it, we are required to specify OutputLocation, which we could default to stdout with -o/--output -. I'm not sure what AnalysisLevel would correspond to, but that's also required. Maybe --analyze dataset that's set by default and any other value is an error.

Otherwise, seems fine. --subject-label X Y would simply filter contexts on entities.subject == 'X' || entities.subject == 'Y'. Similarly with any entity you care to define.

@yarikoptic
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NB For BIDS exec spec itself might be worth defaulting OutputLocation to . to encourage YODA style composition ;-)

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