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HED column in tsv file should not give a warning #1875

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VisLab opened this issue Jan 3, 2024 · 3 comments · Fixed by #1896
Closed

HED column in tsv file should not give a warning #1875

VisLab opened this issue Jan 3, 2024 · 3 comments · Fixed by #1896

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@VisLab
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VisLab commented Jan 3, 2024

bids-validator 1.14.0 gives a warning if a HED column appears in a .tsv file other than an events.tsv file:

Example: 3: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
./participants.tsv
Evidence: Columns: HED not defined, please define in: /participants.json

HED can be usefully included in any .tsv file, but particularly participants.tsv and scans.tsv, and it is our understanding that the BIDS specification allows this. However, HED cannot syntactically appear as a top-level key in the JSON file without triggering an error.

Would it be possible to exclude HED from the listing of missing custom column definitions?

P.S. HED currently in the bids-validator appears to validate the participants.tsv and scans.tsv files okay. We are still working on motion, phenotype and samples related .tsv files.

Our demo example is available at: eeg_ds003645s_hed_demo. Once everything is working, we'll be able to replace a number of HED examples on bids-examples with a single demo that shows a lot of different uses.

@sappelhoff @effigies @rwblair @happy5214

@sappelhoff
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However, HED cannot syntactically appear as a top-level key in the JSON file without triggering an error.

I don't understand this point. If you would include an HED column in a participants.tsv file, why would you not be able to place a HED key inside a participants.json file?

I opened https://github.com/bids-standard/bids-validator/pull/1876 anyhow, to show how the request here could be fulfilled.

@VisLab
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VisLab commented Jan 4, 2024 via email

@sappelhoff
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Thanks for the explanation @VisLab! may you please review #1876 then?

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