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✨ Add new Sample table and API #646

Merged
merged 12 commits into from
Feb 12, 2024
Merged

✨ Add new Sample table and API #646

merged 12 commits into from
Feb 12, 2024

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znatty22
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@znatty22 znatty22 commented Feb 1, 2024

Motivation

Dataservice model does not track specimen lineage - which specimens were derived from another (specimen hierarchy tree). See Sample design presentation for design details

Approach

This is an MVP design to satisfy current KF needs and KF Portal Beta requirements. We recognize that this design will not allow one to capture a specimen tree with more than 1 level (e.g. sp1 -> sp2 -sp3).

Sample Table + API

  • Sample represents a parental specimen
  • Biospecimen represents an aliquot/child specimen
  • Population of the Sample table will be done in a Sample ETL script which calls the API. PR is here
image

Sample ETL

The Dataservice to Dewrangle CLI will have a command added to it which will pull all biospecimens, derive the parent samples from them, and create the samples in Dataservice

Todo

  • Push migrations after review is complete

@znatty22 znatty22 added the feature New functionality label Feb 1, 2024
@znatty22 znatty22 changed the base branch from master to preservation-method February 1, 2024 20:19
@znatty22 znatty22 force-pushed the new-sample-table branch 2 times, most recently from bb6dd59 to 23bda81 Compare February 2, 2024 15:57
@znatty22 znatty22 marked this pull request as ready for review February 6, 2024 14:15
@znatty22 znatty22 requested a review from a team as a code owner February 6, 2024 14:15
@znatty22 znatty22 self-assigned this Feb 6, 2024
@znatty22 znatty22 requested a review from awarkow February 6, 2024 14:16
@znatty22 znatty22 requested a review from calkinsh February 6, 2024 15:51
Base automatically changed from preservation-method to master February 12, 2024 15:33
@znatty22 znatty22 merged commit 76cbf79 into master Feb 12, 2024
5 checks passed
@znatty22 znatty22 deleted the new-sample-table branch February 12, 2024 15:51
znatty22 added a commit that referenced this pull request Feb 12, 2024
## Release 1.25.0

### Summary

- Emojis: ✨ x2
- Categories: Additions x2

### New features and changes

- [#646](#646) - ✨ Add new Sample table and API - [76cbf79](76cbf79) by [znatty22](https://github.com/znatty22)
- [#642](#642) - ✨ Add preservation method to biospecimen - [f68ba49](f68ba49) by [znatty22](https://github.com/znatty22)
@znatty22 znatty22 mentioned this pull request Feb 12, 2024
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4 participants