kemal
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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.
50 lines
1.8 KiB
Python
50 lines
1.8 KiB
Python
import uuid
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from fastapi import APIRouter, Depends, HTTPException, status
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from sqlalchemy import select
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from sqlalchemy.ext.asyncio import AsyncSession
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from app.db import get_session
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from app.models import Job, Sample
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from app.schemas import JobOut, SampleCreate, SampleOut
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from app.services.events import publish_vcf_uploaded
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router = APIRouter()
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@router.get("", response_model=list[SampleOut])
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async def list_samples(session: AsyncSession = Depends(get_session)):
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result = await session.scalars(select(Sample).order_by(Sample.created_at.desc()))
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return result.all()
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@router.post("", response_model=SampleOut, status_code=status.HTTP_201_CREATED)
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async def create_sample(payload: SampleCreate, session: AsyncSession = Depends(get_session)):
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sample = Sample(**payload.model_dump())
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session.add(sample)
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await session.commit()
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await session.refresh(sample)
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return sample
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@router.get("/{sample_id}/jobs", response_model=list[JobOut])
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async def list_jobs(sample_id: uuid.UUID, session: AsyncSession = Depends(get_session)):
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result = await session.scalars(
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select(Job).where(Job.sample_id == sample_id).order_by(Job.created_at.desc())
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)
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return result.all()
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@router.post("/{sample_id}/annotate", response_model=JobOut, status_code=status.HTTP_202_ACCEPTED)
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async def annotate(sample_id: uuid.UUID, session: AsyncSession = Depends(get_session)):
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sample = await session.get(Sample, sample_id)
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if sample is None:
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raise HTTPException(404, "sample not found")
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job = Job(sample_id=sample.id)
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session.add(job)
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await session.commit()
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await session.refresh(job)
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# Emits to Pub/Sub in GCP; runs the Nextflow pipeline inline for local dev.
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await publish_vcf_uploaded(job_id=job.id, vcf_uri=sample.vcf_uri)
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return job
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