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.
54 lines
1.6 KiB
Python
54 lines
1.6 KiB
Python
import asyncio
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from logging.config import fileConfig
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from alembic import context
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from sqlalchemy import pool
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from sqlalchemy.ext.asyncio import async_engine_from_config
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from app.config import settings
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from app.models import Base
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config = context.config
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config.set_main_option("sqlalchemy.url", settings.database_url)
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if config.config_file_name:
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fileConfig(config.config_file_name)
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target_metadata = Base.metadata
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# Arbitrary constant shared by every `alembic upgrade` (one per API replica's init container).
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MIGRATION_LOCK_ID = 72150001
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def run_migrations(connection):
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context.configure(connection=connection, target_metadata=target_metadata)
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with context.begin_transaction():
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# Held until this transaction commits; a concurrent run waits, then finds nothing to do.
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connection.exec_driver_sql(f"SELECT pg_advisory_xact_lock({MIGRATION_LOCK_ID})")
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context.run_migrations()
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async def run_async():
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engine = async_engine_from_config(
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config.get_section(config.config_ini_section, {}), poolclass=pool.NullPool
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)
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async with engine.connect() as conn:
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await conn.run_sync(run_migrations)
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await engine.dispose()
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def run_offline():
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"""`alembic upgrade head --sql`: emit the SQL instead of running it."""
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context.configure(
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url=settings.database_url,
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target_metadata=target_metadata,
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literal_binds=True,
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dialect_opts={"paramstyle": "named"},
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)
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with context.begin_transaction():
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context.run_migrations()
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if context.is_offline_mode():
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run_offline()
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else:
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asyncio.run(run_async())
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