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.
62 lines
2.2 KiB
Python
62 lines
2.2 KiB
Python
import uuid
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from datetime import UTC, datetime
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from fastapi import APIRouter, HTTPException, status
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from sqlalchemy import select
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from sqlalchemy.exc import IntegrityError
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from app.db import SessionDep
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from app.models import Job, JobStatus, Sample
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from app.schemas import JobOut, SampleCreate, SampleOut
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from app.services import events
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router = APIRouter()
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@router.get("", response_model=list[SampleOut])
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async def list_samples(session: SessionDep):
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result = await session.scalars(select(Sample).order_by(Sample.created_at.desc()))
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return result.all()
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@router.post("", response_model=SampleOut, status_code=status.HTTP_201_CREATED)
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async def create_sample(payload: SampleCreate, session: SessionDep):
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sample = Sample(**payload.model_dump())
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session.add(sample)
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try:
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await session.commit()
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except IntegrityError: # samples.name is unique
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await session.rollback()
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raise HTTPException(409, f"a sample named {payload.name!r} already exists") from None
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await session.refresh(sample)
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return sample
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@router.get("/{sample_id}/jobs", response_model=list[JobOut])
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async def list_jobs(sample_id: uuid.UUID, session: SessionDep):
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result = await session.scalars(
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select(Job).where(Job.sample_id == sample_id).order_by(Job.created_at.desc())
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)
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return result.all()
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@router.post("/{sample_id}/annotate", response_model=JobOut, status_code=status.HTTP_202_ACCEPTED)
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async def annotate(sample_id: uuid.UUID, session: SessionDep):
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sample = await session.get(Sample, sample_id)
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if sample is None:
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raise HTTPException(404, "sample not found")
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# Commit `running` before launching: a local run that dies instantly is marked failed by its
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# watcher, and a later status write here would overwrite that.
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job = Job(sample_id=sample.id, status=JobStatus.running)
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session.add(job)
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await session.commit()
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try:
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job.workflow_ref = await events.launch(job.id, sample.vcf_uri, sample.assembly)
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except events.LaunchError as e:
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job.status = JobStatus.failed
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job.log = str(e)
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job.finished_at = datetime.now(UTC)
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await session.commit()
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await session.refresh(job)
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return job
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