feat: CSV/TSV download of a gene's eQTL table (#7)#33
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Junbin provisioned a dedicated read-only account (`locuscompare`). Promote it to THE serving account in the connect how-to + .env.example; demote the public `locusview_test` demo login to exploration-only. - how-to §0: new `locuscompare` section (password via secret store / gitignored .env, never committed); verified read-only + PII-safe (990 SELECT/USAGE grants, `user` denied). Old §0 demo → §0b, marked superseded. - Access-model table + §2 note + §4 env block/URL updated to `locuscompare`. - .env.example: user=locuscompare, port=31987, host filled; password stays blank. No secret committed (verified: password only in gitignored .env). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
GET /gene/{key}/download?format=csv|tsv streams the current gene-page view as a
downloadable file (Content-Disposition attachment). Backend only — the in-page
download button waits for the gene-page redesign (#23, Liu Fei).
- web.py: `download` route using the csv stdlib (proper escaping); plain-text
errors (404 unknown gene, 400 bad format) to keep the diff minimal vs #25.
- Advances #7 (CSV/TSV + a documented endpoint); the Parquet/tabix part of #7 is
obsolete under ADR-0008 (we serve from the shared DB).
- 100% coverage in CI; verified live: TP53 -> 1250 data rows.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
boxiangliu
requested review from
GhostAnderson,
MickYang2333,
liufei-f and
wenjing-gakkilove
as code owners
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What
GET /gene/{key}/download?format=csv|tsv— streams the current gene-page eQTL view as a downloadable CSV/TSV (properContent-Dispositionattachment, header row,csvstdlib escaping).Advances #7. Uses the data layer we already have (
eqtls_for_gene).Why now
It's the one download deliverable that needs no design decision — pure backend on top of the existing repository. (The Parquet/tabix part of #7 is obsolete under ADR-0008; we serve from the shared DB.)
Scope / what's deferred
gene.html, which is under Liu Fei's redesign (design: gene-page visualizations (regional plot + body map) #23) — so it lands with the frontend, not here.Testing
ruff/mypy --strictgreen; 100% coverage in CI (locally shows 1 line because a dev.envsets the DB host → default app picks the real repo; CI has no.env). Verified live (read-only):TP53→ HTTP 200,text/csv, 1,250 data rows.Reviewer note
Touches
web.pynear where #25 adds its/apiroutes → a trivial insertion-point conflict is possible if #25 merges first; one-line resolve.