kemal
5463f489a3
ci / api (push) Failing after 10s
ci / terraform (push) Failing after 11s
ci / web (push) Failing after 35s
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ci / images (api) (push) Skipped
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End-to-end variant interpretation platform for rare genetic disease research: SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline, LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure. Public test data only; no clinical claims.
32 lines
1.2 KiB
Python
32 lines
1.2 KiB
Python
"""Event publishing.
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GCP: publish a JSON message to Pub/Sub; an Argo Events sensor turns it into an Argo Workflow.
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Local: run Nextflow directly in a background task so `docker compose up` gives a working demo.
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"""
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import asyncio
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import json
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import uuid
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from app.config import settings
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async def publish_vcf_uploaded(job_id: uuid.UUID, vcf_uri: str) -> None:
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message = {"job_id": str(job_id), "vcf_uri": vcf_uri}
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if settings.pubsub_topic:
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from google.cloud import pubsub_v1 # optional dependency, installed in the GCP image
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publisher = pubsub_v1.PublisherClient()
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publisher.publish(settings.pubsub_topic, json.dumps(message).encode())
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return
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cmd = [
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"nextflow", "run", "/pipeline/main.nf", "-profile", "docker",
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"--vcf", vcf_uri, "--job_id", str(job_id), "--db_url", settings.database_url,
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]
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try:
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await asyncio.create_subprocess_exec(*cmd)
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except FileNotFoundError:
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# Nextflow is not installed in this environment (no Java toolchain yet);
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# leave the job queued instead of crashing the request.
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print(f"[rarelens] nextflow not found; cannot start pipeline for job {job_id}", flush=True)
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