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refactor!: multiple subject names - #109

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dbirman merged 41 commits into
devfrom
49-support-multi-subject-data
Oct 16, 2026
Merged

dbirman merged 41 commits into
devfrom
49-support-multi-subject-data

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@dbirman

@dbirman dbirman commented Oct 7, 2026 •

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BREAKING CHANGE: allow multiple subjects for acquisitions

  1. Added support for multiple subjects and specimens, with separate procedures and acquisition details for each subject.
  2. Added validators to keep subject groups consistent in each of the different core files
  3. Updated asset inheritance rules to retain subject records when source subject sets match and remove them when the sets differ.
  4. Changed subject and procedure files to JSON arrays and updated the core file writer API to support arrays.
  5. Removed fixed asset-name formats and automatic name generation, so callers must supply asset names.

BREAKING CHANGE: allow multiple subjects for acquisitions
@dbirman dbirman linked an issue Oct 7, 2026 that may be closed by this pull request
@dbirman
dbirman requested review from dyf and saskiad October 8, 2026 04:31
Comment thread src/biodata_schema/core/acquisition.py Resolved
Comment thread schemas/procedures_schema.json Resolved
Comment thread src/biodata_schema/core/acquisition.py Resolved
Comment thread src/biodata_schema/core/metadata.py Resolved
@dbirman
dbirman requested a review from saskiad October 12, 2026 17:56
Comment thread docs/base/core/procedures.md Resolved
Comment thread docs/source/data_description.md Resolved
Comment thread docs/source/data_description.md Resolved
Comment thread docs/source/inheritance.md Resolved
Comment thread src/biodata_schema/core/procedures.py Resolved
@dbirman
dbirman requested a review from saskiad October 15, 2026 02:37

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I had a minor comment on naming convention (which is largely optional now so I'll approve as is, but check that out)

Comment thread docs/source/inheritance.md Resolved
Comment thread docs/source/inheritance.md Resolved
Comment thread schemas/data_description_schema.json Resolved
Comment thread src/biodata_schema/core/procedures.py Resolved
Comment thread docs/base/core/data_description.md Resolved
Comment thread docs/source/data_description.md Resolved
@dbirman
dbirman merged commit e883a18 into dev Oct 16, 2026
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Support multi-subject data

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