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.
30 lines
1.1 KiB
YAML
30 lines
1.1 KiB
YAML
# GitOps: CI only bumps image tags in the gcp overlay; ArgoCD does the deploy.
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name: bump-images
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on:
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workflow_run:
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workflows: [ci]
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types: [completed]
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branches: [main]
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jobs:
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bump:
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if: ${{ github.event.workflow_run.conclusion == 'success' }}
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runs-on: ubuntu-latest
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permissions: { contents: write }
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steps:
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- uses: actions/checkout@v4
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- name: Refuse to deploy an unconfigured overlay
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run: |
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if grep -rl __GCP_PROJECT__ infra/k8s/overlays/gcp infra/argo-workflows; then
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echo "::error::run 'make gcp-configure PROJECT=<id>' and commit before deploying"
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exit 1
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fi
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- uses: imranismail/setup-kustomize@v2
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- run: |
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cd infra/k8s/overlays/gcp
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for c in api web pipeline loader; do
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kustomize edit set image rarelens/$c=europe-west2-docker.pkg.dev/${{ secrets.GCP_PROJECT }}/rarelens/$c:${{ github.event.workflow_run.head_sha }}
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done
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- uses: stefanzweifel/git-auto-commit-action@v5
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with: { commit_message: "chore: bump images to ${{ github.event.workflow_run.head_sha }}" }
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