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.
60 lines
1.9 KiB
Terraform
60 lines
1.9 KiB
Terraform
variable "project" {
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description = "GCP project id"
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type = string
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}
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variable "region" {
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description = "GCP region for every regional resource"
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type = string
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default = "europe-west2" # London: keeps public genomic test data and the Cambridge team in one jurisdiction
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}
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variable "github_repo" {
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description = "owner/name of the GitHub repo allowed to push images via Workload Identity Federation"
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type = string
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default = "lynchaos/rarelens"
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}
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variable "deletion_protection" {
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description = "Protect the GKE cluster and Cloud SQL instance from `terraform destroy`; set false to tear the lab down"
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type = bool
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default = true
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}
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variable "deploy_kubernetes" {
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description = "Create the GKE cluster (Argo/ArgoCD track). Off by default: it costs ~$150/month idle, while the serverless track costs ~£1 (docs/cloud.md)"
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type = bool
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default = false
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}
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variable "deploy_cloud_sql" {
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description = "Create a Cloud SQL instance (~$10/month). Off by default: set database_url to a free scale-to-zero Postgres such as Neon"
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type = bool
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default = false
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}
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variable "database_url" {
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description = "Postgres URL used when deploy_cloud_sql is false, e.g. postgresql+asyncpg://user:pass@host/db?sslmode=require"
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type = string
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default = ""
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sensitive = true
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}
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variable "image_tag" {
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description = "Image tag deployed to Cloud Run; CI pushes the commit SHA"
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type = string
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default = "latest"
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}
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variable "model_uri" {
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description = "Optional model artifact to score with, e.g. gs://<project>-rarelens-data/models/pathogenicity/1. Empty means use the MLflow registry"
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type = string
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default = ""
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}
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variable "max_instances" {
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description = "Cloud Run instance ceiling per service: scale-to-zero bounds the floor, this bounds the bill"
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type = number
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default = 2
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}
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