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.
41 lines
1.2 KiB
Python
Executable File
41 lines
1.2 KiB
Python
Executable File
#!/usr/bin/env python3
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"""Set a job's status, e.g. from the Argo exit handler when a workflow fails.
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A succeeded job is never overwritten: the loader's success is the source of truth.
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"""
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import argparse
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import os
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import sys
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from load_db import engine_for
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from sqlalchemy import Engine, text
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def set_status(engine: Engine, job_id: str, status: str, log: str | None) -> None:
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with engine.begin() as conn:
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conn.execute(
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text("""
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UPDATE jobs
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SET status = CAST(:status AS jobstatus), log = :log,
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finished_at = CASE WHEN :status IN ('succeeded', 'failed') THEN now() END
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WHERE id = :id AND status <> 'succeeded'
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"""),
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{"id": job_id, "status": status, "log": log},
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)
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def main() -> None:
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p = argparse.ArgumentParser()
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p.add_argument("--job-id", required=True)
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p.add_argument("--status", required=True, choices=["running", "failed"])
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p.add_argument("--log")
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a = p.parse_args()
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url = os.environ.get("DATABASE_URL")
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if not url:
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sys.exit("DATABASE_URL is not set")
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set_status(engine_for(url), a.job_id, a.status, a.log)
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if __name__ == "__main__":
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main()
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