Initial release: rarelens platform skeleton (AGPL-3.0)

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.

api/app/routers/samples.py

@@ -0,0 +1,49 @@
+import uuid
+
+from fastapi import APIRouter, Depends, HTTPException, status
+from sqlalchemy import select
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from app.db import get_session
+from app.models import Job, Sample
+from app.schemas import JobOut, SampleCreate, SampleOut
+from app.services.events import publish_vcf_uploaded
+
+router = APIRouter()
+
+
+@router.get("", response_model=list[SampleOut])
+async def list_samples(session: AsyncSession = Depends(get_session)):
+    result = await session.scalars(select(Sample).order_by(Sample.created_at.desc()))
+    return result.all()
+
+
+@router.post("", response_model=SampleOut, status_code=status.HTTP_201_CREATED)
+async def create_sample(payload: SampleCreate, session: AsyncSession = Depends(get_session)):
+    sample = Sample(**payload.model_dump())
+    session.add(sample)
+    await session.commit()
+    await session.refresh(sample)
+    return sample
+
+
+@router.get("/{sample_id}/jobs", response_model=list[JobOut])
+async def list_jobs(sample_id: uuid.UUID, session: AsyncSession = Depends(get_session)):
+    result = await session.scalars(
+        select(Job).where(Job.sample_id == sample_id).order_by(Job.created_at.desc())
+    )
+    return result.all()
+
+
+@router.post("/{sample_id}/annotate", response_model=JobOut, status_code=status.HTTP_202_ACCEPTED)
+async def annotate(sample_id: uuid.UUID, session: AsyncSession = Depends(get_session)):
+    sample = await session.get(Sample, sample_id)
+    if sample is None:
+        raise HTTPException(404, "sample not found")
+    job = Job(sample_id=sample.id)
+    session.add(job)
+    await session.commit()
+    await session.refresh(job)
+    # Emits to Pub/Sub in GCP; runs the Nextflow pipeline inline for local dev.
+    await publish_vcf_uploaded(job_id=job.id, vcf_uri=sample.vcf_uri)
+    return job