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/schemas.py

@@ -0,0 +1,63 @@
+from datetime import datetime
+import uuid
+
+from pydantic import BaseModel, ConfigDict, Field
+
+from app.models import JobStatus
+
+
+class ORMModel(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
+
+class SampleCreate(BaseModel):
+    name: str = Field(min_length=1, max_length=120)
+    vcf_uri: str
+    assembly: str = "GRCh38"
+
+
+class SampleOut(ORMModel):
+    id: uuid.UUID
+    name: str
+    vcf_uri: str
+    assembly: str
+    created_at: datetime
+
+
+class JobOut(ORMModel):
+    id: uuid.UUID
+    sample_id: uuid.UUID
+    status: JobStatus
+    workflow_ref: str | None
+    vep_version: str | None
+    created_at: datetime
+    finished_at: datetime | None
+
+
+class PredictionOut(ORMModel):
+    model_name: str
+    model_version: str
+    score: float
+
+
+class VariantOut(ORMModel):
+    id: int
+    chrom: str
+    pos: int
+    ref: str
+    alt: str
+    gene: str | None
+    consequence: str | None
+    impact: str | None
+    hgvsc: str | None
+    hgvsp: str | None
+    gnomad_af: float | None
+    clinvar_sig: str | None
+    prediction: PredictionOut | None = None
+
+
+class VariantPage(BaseModel):
+    items: list[VariantOut]
+    total: int
+    limit: int
+    offset: int