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.
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1.8 KiB
Test data
make data fetches the demo slice automatically. Provenance, licences, citations and the
evaluation plan live in ../docs/data.md.
No patient data. Use public sources only:
- ClinVar VCF (GRCh38): https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/
- gnomAD exomes subset for allele frequencies
- A small HG002 (GIAB) chr22 slice for a realistic germline sample
# Example: 2,000 ClinVar variants on chr22 as a smoke-test VCF
wget -O clinvar.vcf.gz https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
tabix -p vcf clinvar.vcf.gz
bcftools view -r 22 clinvar.vcf.gz | bcftools view -H | head -2000 > body.vcf
(bcftools view -h clinvar.vcf.gz; cat body.vcf) | bgzip > example.vcf.gz
tabix -p vcf example.vcf.gz
Samples added in the UI must point at a gs://bucket/object or at a file under /data
(LOCAL_DATA_ROOT), ending in .vcf, .vcf.gz, .vcf.bgz or .bcf.
VEP cache and plugins
The pipeline runs VEP offline. Install the cache once (about 25 GB for GRCh38):
docker run --rm -v $PWD/pipeline/cache/vep:/cache ensemblorg/ensembl-vep:release_113.0 \
INSTALL.pl -a cf -s homo_sapiens -y GRCh38 -c /cache
CADD and AlphaMissense are optional; the model treats their scores as missing without them. To
enable them, put the plugin modules and data files in one directory and pass --vep_plugin_data:
docker run --rm -v $PWD/pipeline/cache/plugins:/plugins ensemblorg/ensembl-vep:release_113.0 \
INSTALL.pl -a p -g CADD,AlphaMissense -r /plugins
# then add whole_genome_SNVs.tsv.gz, gnomad.genomes.r4.0.indel.tsv.gz (CADD) and
# AlphaMissense_hg38.tsv.gz, each with its .tbi index, to pipeline/cache/plugins
pipeline/tests/data/tiny.vcf is a synthetic three-record fixture used by CI's stub run.