SACGF / SACGF/variantgrid

Patient CSV cannot name the DNA and RNA arms of one specimen

Open
#1,870 0 comments 0 reactions 0 assignees View on GitHub
Has Plan Patients
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

🤖 Written by Claude.

Split out of the TSO 500 plan (SACGF/variantgrid_sapath#431), a leftover from #1704.

The patient CSV import's columns are all `SPECIMEN_*`, so it round-trips one `Extraction` per `Specimen` and cannot name the DNA and RNA arms of one block (TSO 500's `2600000001C` and `2600000001B` are two extractions off one specimen). The API (#1707) can express this; the spreadsheet cannot.

Worth doing when a consumer needs it — nothing currently does. When it is done, note `Extraction.nucleic_acid_source` and `Extraction.extraction_date` are what tell two extractions of one specimen apart, and `Extraction.reference_id` is unique per specimen rather than globally.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with the patient CSV import and compare its specimen-based columns with the representation in API #1707. Use Extraction.nucleic_acid_source and extraction_date to distinguish DNA and RNA extractions while preserving reference_id semantics; done means one specimen's multiple extractions can round-trip through the spreadsheet.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, data
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
35/100

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