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update bagel bids subcommand to play nice with new derivatives #346

Closed
4 tasks done
Tracked by #342
surchs opened this issue Sep 24, 2024 · 2 comments · Fixed by #349
Closed
4 tasks done
Tracked by #342

update bagel bids subcommand to play nice with new derivatives #346

surchs opened this issue Sep 24, 2024 · 2 comments · Fixed by #349
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@alyssadai
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released This issue/pull request has been released. type:feature Effort to deliver new features, feature changes & improvements

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@surchs
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surchs commented Sep 24, 2024 •
edited by alyssadai
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TODO

update the bagel bids command to

  • accept either a pheno.jsonld (output of bagel pheno) or a pheno-derivatives.jsonld (output of bagel derivatives Add new sub-command for bagel-CLI derivatives: #345) as input
  • update help text
  • find and match existing imaging sessions between a provided pheno-derivatives.jsonld and a raw BIDS dataset so that we do not recreate imaging sessions if the derivatives subcommand has already created them
    • if session is missing, add to potentially existing "ses-nb01"?

Related to #345
@surchs surchs mentioned this issue Sep 24, 2024
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@surchs surchs changed the title update bagel bids with the same logic for checking subject / session IDs update bagel bids subcommand to play nice with new derivatives Sep 24, 2024
@surchs surchs moved this to Specify - Done in Neurobagel Sep 24, 2024
@surchs surchs added feat:add type:feature Effort to deliver new features, feature changes & improvements labels Sep 24, 2024
@alyssadai alyssadai self-assigned this Oct 2, 2024
This was referenced Oct 2, 2024
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@alyssadai alyssadai moved this from Implement - Active to Implement - Done in Neurobagel Oct 4, 2024
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Closed by #349

@github-project-automation github-project-automation bot moved this from Review - Active to Review - Done in Neurobagel Oct 8, 2024
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🚀 Issue was released in v0.3.0 🚀

@neurobagel-bot neurobagel-bot bot added the released This issue/pull request has been released. label Oct 24, 2024
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[ENH] Add derivatives command and pipeline-catalog submodule neurobagel/bagel-cli
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@surchs @alyssadai