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refactor: only allow wrapped NonSurgeryInjections in Procedures.subject_procedures#1802

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1801-injections-have-no-date-we-need-a-wrapper-class-in-procedures
Apr 23, 2026
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refactor: only allow wrapped NonSurgeryInjections in Procedures.subject_procedures#1802
dbirman merged 6 commits intodevfrom
1801-injections-have-no-date-we-need-a-wrapper-class-in-procedures

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@dbirman dbirman commented Apr 16, 2026 •
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This PR fixes an oversight we had in the Procedures.subject_procedures where we were allowing raw Injection objects. These don't have a start_date field since typically they show up inside a Surgery object. This PR creates a new wrapper NonSurgeryInjection that adds a required start_date, ethics_review_id, and notes.

Alternative
We could also remove Injection from the top-level and only allow Surgery objects, that would avoid adding a new wrapper class to the schema.

@dbirman dbirman linked an issue Apr 16, 2026 that may be closed by this pull request
Injections have no date, we need a wrapper class in Procedures #1801
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@dbirman dbirman requested a review from saskiad April 16, 2026 18:15
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Comment thread src/aind_data_schema/components/subject_procedures.py
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let's discuss this one

@dbirman dbirman mentioned this pull request Apr 22, 2026
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@dbirman dbirman requested a review from saskiad April 22, 2026 22:09
@dbirman dbirman changed the title refactor: only allow InjectionProcedures in Procedures.subject_procedures refactor: only allow wrapped NonSurgeryInjections in Procedures.subject_procedures Apr 23, 2026
@dbirman dbirman added this pull request to the merge queue Apr 23, 2026
Merged via the queue into dev with commit ecf4b9e Apr 23, 2026
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@dbirman dbirman deleted the 1801-injections-have-no-date-we-need-a-wrapper-class-in-procedures branch April 23, 2026 00:53
dbirman added a commit that referenced this pull request May 6, 2026
@dbirman @github-actions
@dougollerenshaw @gouwens @bruno-f-cruz
Release v2.7.0 (#1820)
c9ceea1 
* Allow specimen_id to be a list (#1770)

* Allow specimen_id to be a list

* Removed nonetype test

* Fixed specimen names in test

* Updated specimen_id description to clarify expectation during in-vivo sessions

* Spread args over multi lines to avoid lint fail

* docs: rebuild docs (#1771)

* docs: minor fixes to acquisition.md

* docs: remove bad directives and links

* docs: improve description for AcquisitionSubjectDetails (#1772)

* docs: improve description for AcquisitionSubjectDetails

* docs: rebuild docs

* fix: throw warnings when users include multiple identically named devices in the Instrument (#1773)

* fix: allow both planar and regular sectioning in sectioning procedures (#1777)

* fix: allow NHPSubject as subject_details option (#1778)

* docs: auto-build docs on opening PR (#1760)

* docs: auto-build docs on opening PR

* update docs [skip actions]

* docs: update contribution.md

* update docs [skip actions]

* chore: remove all unnecessary graphviz dependencies

* update docs [skip actions]

* update docs [skip actions]

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Handle lists of specimen IDs in procedures validator (#1783)

* Handle lists of specimen IDs in procedures validator

* Fix to properly handle individual str as well as lists of str

* refactor: simplifying code a tiny bit

---------

Co-authored-by: Dan Birman <danbirman@gmail.com>

* Add ticket linking workflow (#1785)

* Barseq blackbox acquisition (#1781)

* First pass at minimal blackbox acquisition. Has file that generates acquisition for two subjects, plus json outputs

* Added reference to output files

* Added specimen IDs to barseq acquisitions

* Removed readme file

* Updating examples/barseq_acquisition.py docstring

* Cleaned up comments in examples/barseq_acquisition.py

* Set timestamps to pacific with offset

* Changed experimenters to 'Barseq team'

* Removed references to local paths, removed duplicate jsons

* Added ExternalDataStream, made instrument optional, added test, updated example barseq

* Updated example json outputs for barseq subjects

* update docs [skip actions]

* Linting fixes

* Used DiscriminatedList

* Clean up stream adding logic

* Simplify barseq acquisition example

* Removed jsons

* clean up test and import properly

* Add ExternalDataStream support to Metadata validators and test that no instrument warning is raised for external acquisitions.

* Wording updates as suggested by Dan

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* 1792 quality control validator has a bug at line 307 where it fails to check metrics before doing metrics0 (#1793)

* fix: validator would trigger on empty metrics

* fix: do this upfront by bypassing the validator, adds a test

* chore: delete CHANGELOG.md (#1799)

* chore: delete CHANGELOG.md

* update docs [skip actions]

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* refactor: replace root calls to logging with module-level loggers (#1800)

* fix: issue with actions being skipped unnecessarily

* refactor: replace root logger with local loggers

* test: fixes to logger patches

* docs: improve docstring (#1748)

* docs: improve docstring

* docs: update specimen ID

* docs: clarify suffix

* docs: better writing

* update docs

* fix: bad merge

* update docs

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* refactor: only allow wrapped NonSurgeryInjections in Procedures.subject_procedures (#1802)

* refactor: only allow Injections in Procedures.subject_procedures when wrapped with an InjectionProcedure

* chore: add ethics_review_id/protocol_id

* fix: only allow Injection, BrainInjection requires a full CS from Surgery

* update docs [skip actions]

* refactor: NonSurgicalInjection

* update docs

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Add missing `tzdata` dependency (#1811)

* Add git hash to Code model (#1813)

* Add git hash to Code model

* update docs

* Increase hash length upper bound

* Change property name and emit warning if hash and version are not defined

* Refactor type alias

* update docs

* Break lines

* Update tests to reflect longer hashes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* feat: add barseq instrument (#1685)

* feat: add barseq instrument

* refactor: SlapPlane -> Slap2Plane

* Revert "refactor: SlapPlane -> Slap2Plane"

This reverts commit 6f193b8.

* chore: lint

* refactor: fix serialization code in example

* fix: fix issues blocking build

* chore: fix write function for instrument example

* fix: specimen_ids validator correctly flattens lists (#1763)

* feat: working on procedures_sectioning example

* feat: continuing to develop chunk sections

* chore: embed slide regions in python code

* chore: lint

* chore: docstrings

* chore: lint

* chore: remove full sectioning file

---------

Co-authored-by: Doug Ollerenshaw <doug.ollerenshaw@alleninstitute.org>

* chore: bump version

* bump schema version [skip actions]

* chore: bump metadata

* bump schema version [skip actions]

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Doug Ollerenshaw <doug.ollerenshaw@alleninstitute.org>
Co-authored-by: gouwens <ngouwens@gmail.com>
Co-authored-by: Bruno Cruz <7049351+bruno-f-cruz@users.noreply.github.com>
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Injections have no date, we need a wrapper class in Procedures

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