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.
55 lines
1.9 KiB
YAML
55 lines
1.9 KiB
YAML
# Submitted by the Argo Events sensor in events.yaml for each "vcf-uploaded" Pub/Sub message.
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# The Nextflow driver runs here; its tasks run on Google Batch (see the gcp profile in
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# pipeline/nextflow.config). Image names are rewritten by the gcp overlay and bumped by CI.
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apiVersion: argoproj.io/v1alpha1
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kind: WorkflowTemplate
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metadata: { name: annotate-vcf }
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spec:
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serviceAccountName: rarelens-pipeline
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entrypoint: nextflow
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onExit: exit-handler
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arguments:
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parameters:
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- { name: job_id }
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- { name: vcf_uri }
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- { name: assembly, value: GRCh38 }
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templates:
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- name: nextflow
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container:
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image: rarelens/pipeline
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args:
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- run
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- /pipeline/main.nf
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- -profile
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- gcp
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- --vcf
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- "{{workflow.parameters.vcf_uri}}"
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- --job_id
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- "{{workflow.parameters.job_id}}"
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- --assembly
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- "{{workflow.parameters.assembly}}"
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# GCP_PROJECT / GCS_BUCKET / GCP_REGION feed params in nextflow.config.
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envFrom: [{ configMapRef: { name: pipeline-config } }]
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resources: { requests: { cpu: "1", memory: 2Gi } }
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# The loader marks success; anything else (Nextflow error, OOM, eviction) is marked here
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# so the UI never polls a dead job forever.
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- name: exit-handler
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steps:
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- - name: mark-failed
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template: mark-failed
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when: "{{workflow.status}} != Succeeded"
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- name: mark-failed
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container:
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image: rarelens/loader
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command: [set_job_status.py]
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args:
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- --job-id
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- "{{workflow.parameters.job_id}}"
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- --status
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- failed
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- --log
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- "Argo workflow {{workflow.name}} ended {{workflow.status}}"
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envFrom: [{ secretRef: { name: pipeline-secrets } }]
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resources: { requests: { cpu: 100m, memory: 256Mi } }
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