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.
This commit is contained in:
Kemal Yaylali
+12
-1
@@ -8,13 +8,24 @@ spec:
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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: [{ secretRef: { name: api-secrets } }]
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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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@@ -11,8 +11,12 @@ spec:
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- name: web
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image: rarelens/web
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ports: [{ containerPort: 3000 }]
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# Read at runtime ($env/dynamic/public); the ingress routes /api to the API service.
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env: [{ name: PUBLIC_API_URL, value: /api }]
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readinessProbe: { httpGet: { path: /, port: 3000 }, periodSeconds: 5 }
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livenessProbe: { httpGet: { path: /, port: 3000 }, periodSeconds: 10, failureThreshold: 6 }
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resources: { requests: { cpu: 100m, memory: 128Mi }, limits: { cpu: 500m, memory: 256Mi } }
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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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@@ -1,21 +1,53 @@
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apiVersion: kustomize.config.k8s.io/v1beta1
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kind: Kustomization
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resources: [../../base]
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# Project-specific values use the __GCP_PROJECT__ placeholder: run `make gcp-configure PROJECT=<id>`
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# once and commit. Image tags are then bumped by .github/workflows/deploy.yml after each green CI.
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# Generated ConfigMaps must share the Deployments' namespace, or their hashed names are not
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# propagated to envFrom references.
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namespace: rarelens
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resources: [../../base, ../../../argo-workflows]
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configurations: [kustomizeconfig.yaml]
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images:
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- { name: rarelens/api, newName: europe-west2-docker.pkg.dev/PROJECT/rarelens/api, newTag: latest }
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- { name: rarelens/web, newName: europe-west2-docker.pkg.dev/PROJECT/rarelens/web, newTag: latest }
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- { name: rarelens/api, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/api, newTag: latest }
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- { name: rarelens/web, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/web, newTag: latest }
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- { name: rarelens/pipeline, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/pipeline, newTag: latest }
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- { name: rarelens/loader, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/loader, newTag: latest }
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configMapGenerator:
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- name: api-config
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literals: [PUBSUB_TOPIC=vcf-uploaded, GCP_PROJECT=__GCP_PROJECT__]
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- name: pipeline-config
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# Referenced by name from the Argo WorkflowTemplate, which kustomize does not rewrite.
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options: { disableNameSuffixHash: true }
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literals: [GCP_PROJECT=__GCP_PROJECT__, GCP_REGION=europe-west2, GCS_BUCKET=__GCP_PROJECT__-rarelens-data]
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# api-secrets and pipeline-secrets come from Secret Manager: `make gcp-secrets PROJECT=<id>`.
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patches:
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- target: { kind: ServiceAccount, name: rarelens-api }
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patch: |
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- op: add
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path: /metadata/annotations
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value: { iam.gke.io/gcp-service-account: [email protected] }
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value: { iam.gke.io/gcp-service-account: rarelens-api@__GCP_PROJECT__.iam.gserviceaccount.com }
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- target: { kind: ServiceAccount, name: rarelens-pipeline }
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patch: |
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- op: add
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path: /metadata/annotations
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value: { iam.gke.io/gcp-service-account: rarelens-pipeline@__GCP_PROJECT__.iam.gserviceaccount.com }
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- target: { kind: Deployment, name: api }
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patch: |
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- op: add
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path: /spec/template/spec/containers/-
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path: /spec/template/spec/initContainers/0
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value:
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name: cloud-sql-proxy
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image: gcr.io/cloud-sql-connectors/cloud-sql-proxy:2.13.0
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args: ["--structured-logs", "--port=5432", "PROJECT:europe-west2:rarelens-pg"]
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securityContext: { runAsNonRoot: true }
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# Native sidecar: starts (and passes its startup probe) before the migrate init
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# container, then keeps running alongside the API.
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restartPolicy: Always
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args:
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- --structured-logs
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- --private-ip
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- --port=5432
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- --health-check
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- --http-address=0.0.0.0
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- __GCP_PROJECT__:europe-west2:rarelens-pg
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startupProbe: { httpGet: { path: /startup, port: 9090 }, periodSeconds: 1, failureThreshold: 60 }
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securityContext: { runAsNonRoot: true, allowPrivilegeEscalation: false }
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resources: { requests: { cpu: 100m, memory: 128Mi }, limits: { cpu: 500m, memory: 256Mi } }
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@@ -0,0 +1,4 @@
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# Teach the `images:` transformer where Argo WorkflowTemplates keep their images.
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images:
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- path: spec/templates/container/image
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kind: WorkflowTemplate
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@@ -1,5 +1,8 @@
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apiVersion: kustomize.config.k8s.io/v1beta1
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kind: Kustomization
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# `make kind` builds and loads the dev images, then applies this overlay. There is no ingress in
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# kind: port-forward svc/web to 8080 and svc/api to 8000 (the UI calls the API directly).
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namespace: rarelens # generated Secret/ConfigMap names only propagate within one namespace
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resources: [../../base, postgres.yaml]
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images:
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- { name: rarelens/api, newName: rarelens-api, newTag: dev }
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@@ -7,3 +10,17 @@ images:
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secretGenerator:
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- name: api-secrets
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literals: [DATABASE_URL=postgresql+asyncpg://rarelens:rarelens@postgres:5432/rarelens]
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configMapGenerator:
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- name: api-config
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literals: ['CORS_ORIGINS=["http://localhost:8080"]']
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patches:
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- patch: |
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apiVersion: apps/v1
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kind: Deployment
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metadata: { name: web }
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spec:
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template:
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spec:
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containers:
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- name: web
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env: [{ name: PUBLIC_API_URL, value: "http://localhost:8000/api" }]
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@@ -13,6 +13,8 @@ spec:
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- { name: POSTGRES_USER, value: rarelens }
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- { name: POSTGRES_PASSWORD, value: rarelens }
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- { name: POSTGRES_DB, value: rarelens }
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readinessProbe: { exec: { command: [pg_isready, -U, rarelens] }, periodSeconds: 5 }
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resources: { requests: { cpu: 100m, memory: 256Mi }, limits: { cpu: 500m, memory: 512Mi } }
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---
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apiVersion: v1
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kind: Service
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