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.
98 lines
3.5 KiB
Python
98 lines
3.5 KiB
Python
"""The serverless track: the API starts a Cloud Run job instead of publishing to Pub/Sub."""
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import uuid
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from typing import Any
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import pytest
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from httpx import AsyncClient
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from app.config import settings
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from app.services import events
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class FakeOperation:
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def __init__(self, execution: str) -> None:
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self.metadata = type("Meta", (), {"name": execution})()
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class FakeJobsClient:
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def __init__(self, result: Any = None) -> None:
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self.result = result
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self.requests: list[dict] = []
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def run_job(self, request: dict) -> FakeOperation:
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self.requests.append(request)
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if isinstance(self.result, Exception):
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raise self.result
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return self.result
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async def new_sample(client: AsyncClient) -> str:
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r = await client.post(
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"/api/samples",
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json={"name": f"s-{uuid.uuid4()}", "vcf_uri": "gs://bucket/x.vcf.gz", "assembly": "GRCh37"},
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)
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assert r.status_code == 201, r.text
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return r.json()["id"]
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@pytest.fixture
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def cloudrun(monkeypatch: pytest.MonkeyPatch) -> None:
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monkeypatch.setattr(settings, "pubsub_topic", None)
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monkeypatch.setattr(settings, "cloudrun_job", "rarelens-nextflow")
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monkeypatch.setattr(settings, "gcp_project", "my-proj")
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monkeypatch.setattr(settings, "gcp_region", "europe-west2")
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@pytest.mark.usefixtures("db", "cloudrun")
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async def test_annotate_executes_the_job_with_pipeline_arguments(
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client: AsyncClient, monkeypatch: pytest.MonkeyPatch
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) -> None:
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jobs = FakeJobsClient(FakeOperation("projects/p/locations/l/executions/rarelens-nextflow-abc12"))
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monkeypatch.setattr(events, "_jobs_client", lambda: jobs)
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sample_id = await new_sample(client)
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r = await client.post(f"/api/samples/{sample_id}/annotate")
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assert r.status_code == 202
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job = r.json()
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assert job["status"] == "running"
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assert job["workflow_ref"] == "cloudrun:rarelens-nextflow-abc12"
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[request] = jobs.requests
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assert request["name"] == "projects/my-proj/locations/europe-west2/jobs/rarelens-nextflow"
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[override] = request["overrides"]["container_overrides"]
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args = override["args"]
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assert args[:4] == ["run", "/pipeline/main.nf", "-profile", "gcp"]
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assert args[args.index("--job_id") + 1] == job["id"]
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assert args[args.index("--assembly") + 1] == "GRCh37"
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assert args[args.index("--vcf") + 1] == "gs://bucket/x.vcf.gz"
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@pytest.mark.usefixtures("db", "cloudrun")
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async def test_a_failed_execution_call_marks_the_job_failed(
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client: AsyncClient, monkeypatch: pytest.MonkeyPatch
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) -> None:
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monkeypatch.setattr(
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events, "_jobs_client", lambda: FakeJobsClient(RuntimeError("403 permission denied"))
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)
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sample_id = await new_sample(client)
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job = (await client.post(f"/api/samples/{sample_id}/annotate")).json()
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assert job["status"] == "failed"
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assert "403 permission denied" in job["log"]
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@pytest.mark.usefixtures("db", "cloudrun")
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async def test_cloud_run_job_takes_precedence_over_pubsub(
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client: AsyncClient, monkeypatch: pytest.MonkeyPatch
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) -> None:
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monkeypatch.setattr(settings, "pubsub_topic", "vcf-uploaded")
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jobs = FakeJobsClient(FakeOperation("projects/p/locations/l/executions/x-1"))
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monkeypatch.setattr(events, "_jobs_client", lambda: jobs)
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monkeypatch.setattr(
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events, "_publisher", lambda: pytest.fail("Pub/Sub must not be used in the serverless track")
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)
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sample_id = await new_sample(client)
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assert (await client.post(f"/api/samples/{sample_id}/annotate")).json()["status"] == "running"
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assert len(jobs.requests) == 1
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