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Add specimen procedures from SLIMS Histology workflow #280

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dyf opened this issue Oct 16, 2024 · 2 comments · May be fixed by #325
Open
2 tasks

Add specimen procedures from SLIMS Histology workflow #280

dyf opened this issue Oct 16, 2024 · 2 comments · May be fixed by #325
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@dyf
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dyf commented Oct 16, 2024

The procedures endpoint needs to integrate specimen procedures from the SLIMS Histology workflow.

Acceptance criteria

  • an API exists for fetching metadata from the SLIMS Histology workflow called slims_histology.
  • the procedures API integrates this information, mostly as specimen_procedures.
@mekhlakapoor
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mekhlakapoor commented Oct 21, 2024

We should probably break this issue up:
(1) Get SLIMS response in aind-slims-api.
(2) Add endpoint 'specimen_procedures' that maps slims response to specimen procedures in aind-metadata-service
(3) Integrate this information in the procedures endpoint

NOTE: Let's first figure out how this data is stored in SLIMS, and map out whether we'll need an operation class with multiple API calls

@mekhlakapoor
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This ticket took longer than expected:

  • Paused on this for a few days to work on a scientist request
  • In hindsight, merging it into the procedures response could've been handled in another ticket. I spent time trying to refactor the integrate_injection_materials and integrate_protocols steps to handle a response with specimen procedures, but it go overcomplicated and for now it makes sense to just merge specimen procedures after subject procedures are complete

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3 participants