Kemal Yaylali
11fb6b3d73
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.
38 lines
1.4 KiB
YAML
38 lines
1.4 KiB
YAML
apiVersion: apps/v1
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kind: Deployment
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metadata: { name: api }
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spec:
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replicas: 2
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selector: { matchLabels: { app: api } }
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template:
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metadata: { labels: { app: api } }
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spec:
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serviceAccountName: rarelens-api
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initContainers:
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# alembic/env.py holds a Postgres advisory lock, so replicas starting together migrate once.
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- name: migrate
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image: rarelens/api
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command: [alembic, upgrade, head]
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envFrom: [{ secretRef: { name: api-secrets } }]
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resources: { requests: { cpu: 100m, memory: 256Mi }, limits: { cpu: 500m, memory: 512Mi } }
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containers:
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- name: api
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image: rarelens/api
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ports: [{ containerPort: 8000 }]
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envFrom:
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- secretRef: { name: api-secrets }
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- configMapRef: { name: api-config }
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readinessProbe: { httpGet: { path: /health, port: 8000 }, periodSeconds: 5 }
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livenessProbe: { httpGet: { path: /health, port: 8000 }, periodSeconds: 10, failureThreshold: 6 }
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resources: { requests: { cpu: 250m, memory: 512Mi }, limits: { cpu: "1", memory: 1Gi } }
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securityContext: { allowPrivilegeEscalation: false }
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---
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apiVersion: v1
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kind: Service
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metadata: { name: api }
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spec: { selector: { app: api }, ports: [{ port: 80, targetPort: 8000 }] }
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---
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apiVersion: v1
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kind: ServiceAccount
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metadata: { name: rarelens-api }
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