2 Commits

Include renames

Author	SHA1	Message	Date
Kemal Yaylali	07a01715fd	feat: redesign around phenotype-driven triage, not variant filtering ... A table with filters made the user do the work. Rare disease triage is a different task: which few variants could explain *this* patient's phenotype, and why. The app now answers that, and lets a reviewer act on the answer. Domain - a case is a proband: a VCF plus the HPO terms observed in the patient (samples -> cases) - HPO's gene-to-phenotype annotations are loaded as reference data (scripts/load-hpo.py) - each candidate can be shortlisted or dismissed with a reason and a note Ranking (app/services/triage.py, 21 tests) - weighted sum of phenotype match, rarity, consequence severity and the model's score, with every component shown next to the candidate - rarity and consequence filter; phenotype only ranks, because a real diagnosis can sit in a gene nobody has annotated yet and filtering on it would hide exactly that case - ClinVar is deliberately not an input: it appears beside the result as independent confirmation, so nothing ranks highly merely because ClinVar already said pathogenic UI - the funnel is the headline: variants called -> rare -> coding candidates -> phenotype-matched - ranked candidates with evidence chips, not a grid of everything; filters are demoted - a variant panel showing the score breakdown, the matched HPO terms, the raw VEP record and links out to Ensembl/gnomAD/ClinVar, with the decision controls - a printable case report: phenotype, funnel, shortlisted variants with reasons, provenance API: /cases with phenotypes, /cases/{id}/candidates (funnel + ranked + weights), /variants/{id}, /variants/{id}/decision, /cases/{id}/report, /phenotypes for the picker. Scoring moved under the case and now answers 503 with the reason when no model registry is reachable, instead of a 500. Verified end to end on a simulated proband (scripts/make-demo-case.sh: real GIAB HG002 background + one real ClinVar 2-star pathogenic NF2 variant). 13 variants called -> 1 coding candidate, and the planted variant ranks first at 0.80 on phenotype 1.00, rarity 1.00 and consequence 1.00, with ClinVar agreeing afterwards. Tests: api 75, ml 18, loader 16, web 27; ruff, mypy, svelte-check, terraform validate, both kustomize overlays and the Nextflow stub run all clean.	2026-09-12 08:30:44 +01:00
Kemal Yaylali	11fb6b3d73	fix: overhaul the platform skeleton, add a serverless deployment track ... An end-to-end audit found the repo could not build, test or run as shipped. This fixes every finding, then adds a Cloud Run track so the demo costs about £1/month idle instead of ~£150. CI (red on its first run) - api: setuptools could not build the package (flat layout with app/ and alembic/) - web: missing @types/node; `vitest run` exited 1 with no test files - pipeline: the stub run needed a gitignored VCF, and no process had a stub block - ruff pinned, mypy configured, DB tests on real Postgres (pgserver locally, service in CI) ML serving (scores were meaningless) - the registered model now carries its own feature engineering and returns predict_proba, so serving sends raw columns and cannot drift from training - resolve by registry alias (stages are deprecated in MLflow 3) and record the real version; re-scoring upserts instead of failing on the unique constraint - ClinVar labels parsed from VEP's lowercase terms Pipeline - exact ref/alt recovered from a CHROM_POS_REF_ALT VCF ID; loading is idempotent - job status reaches running/failed/succeeded, so the UI stops polling dead jobs - DATABASE_URL travels in the environment or a Nextflow secret, never on a command line - VEP cache and plugins staged as inputs; the gcp profile runs tasks on Google Batch Deployment - the API serves /api (matching the ingress); the web app reads its API URL at runtime - migrations run in an init container under a Postgres advisory lock - terraform: custom VPC shared with Batch, private Cloud SQL, API enablement, Workload Identity bindings, Secret Manager, deletion protection - serverless track, now the default: Cloud Run services scaling to zero, a Cloud Run job for the Nextflow driver, and Neon or Cloud SQL behind one DATABASE_URL secret. GKE and Argo remain, behind -var deploy_kubernetes=true. See docs/cloud.md. Correctness and security - 409 on duplicate sample names, 422 on bad paging, natural chromosome ordering, wider VEP text columns, enum dropped on downgrade, the sample's assembly actually used - vcf_uri restricted to gs:// objects or files under the data root, blocking option injection - CORS restricted to configured origins; `make down` no longer deletes volumes Data - docs/data.md records the peer-reviewed, openly licensed sources (GIAB HG002, ClinVar, gnomAD) with citations and an honest evaluation plan; `make data` fetches a chr22 slice Verified: api 50 tests, ml 18, loader 16, web 12; ruff, mypy, svelte-check, terraform validate and both kustomize overlays clean.	2026-09-12 07:21:11 +01:00