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