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Formalize columns (MeasurementToolMetadata, Derivative) presence in phenotype/{tool}.json files #2047

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yarikoptic opened this issue Feb 6, 2025 · 1 comment
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schema Issues related to the YAML schema representation of the specification. Patch version release.

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@yarikoptic
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ATM we have

❯ git grep MeasurementToolMetadata
src/modality-agnostic-files.md:      "MeasurementToolMetadata": "OPTIONAL",
src/modality-agnostic-files.md:  "MeasurementToolMetadata": {
src/modality-agnostic-files.md:Please note that in this example `MeasurementToolMetadata` includes information
src/schema/objects/metadata.yaml:MeasurementToolMetadata:
src/schema/objects/metadata.yaml:  name: MeasurementToolMetadata

so there is only description (on https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#phenotypic-and-assessment-data) and definition of those fields within metadata files, but nowhere listing or rules to validate those attribute values within those

phenotype/
    <measurement_tool_name>.tsv
    <measurement_tool_name>.json

files.

Attn @bids-standard/bep036

@effigies
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effigies commented Feb 6, 2025

This would be a straightforward sidecar rule. We probably just failed to look at modality agnostic files when doing our mass conversion.

I would add a phenotype.yaml file to https://github.com/bids-standard/bids-specification/tree/master/src/schema/rules/sidecars. You could use events.yaml as a model.

You could then use

<!-- This block generates a metadata table.
These tables are defined in
src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
src/schema/objects/metadata.yaml
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("events.StimulusPresentation") }}

as a model for constructing the sidecar table in modality-agnostic-files.md.

@effigies effigies added the schema Issues related to the YAML schema representation of the specification. Patch version release. label Feb 7, 2025
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