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.
35 lines
954 B
Python
35 lines
954 B
Python
"""widen VEP text columns
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VEP joins multiple consequences with "&" and co-located ClinVar significances with ",", which
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overflowed VARCHAR(120) and aborted the whole load transaction.
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Revision ID: 5f2c8e1b9d04
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Revises: a3e9ead256a5
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Create Date: 2026-09-11 18:00:00.000000
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"""
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from collections.abc import Sequence
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import sqlalchemy as sa
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from alembic import op
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revision: str = '5f2c8e1b9d04'
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down_revision: str | None = 'a3e9ead256a5'
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branch_labels: str | Sequence[str] | None = None
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depends_on: str | Sequence[str] | None = None
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COLUMNS = ('consequence', 'clinvar_sig')
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def upgrade() -> None:
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for column in COLUMNS:
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op.alter_column('variants', column, type_=sa.Text(), existing_type=sa.String(length=120))
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def downgrade() -> None:
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for column in COLUMNS:
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op.alter_column(
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'variants', column, type_=sa.String(length=120), existing_type=sa.Text(),
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postgresql_using=f'left({column}, 120)',
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)
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