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.

web/src/lib/api.ts

@@ -0,0 +1,25 @@
+import { PUBLIC_API_URL } from '$env/static/public';
+
+export type Sample = { id: string; name: string; vcf_uri: string; assembly: string; created_at: string };
+export type Job = { id: string; sample_id: string; status: 'queued' | 'running' | 'succeeded' | 'failed'; created_at: string; finished_at: string | null };
+export type Variant = {
+  id: number; chrom: string; pos: number; ref: string; alt: string; gene: string | null;
+  consequence: string | null; impact: string | null; hgvsc: string | null; hgvsp: string | null;
+  gnomad_af: number | null; clinvar_sig: string | null; prediction: { score: number; model_version: string } | null;
+};
+export type VariantPage = { items: Variant[]; total: number; limit: number; offset: number };
+
+async function req<T>(path: string, init?: RequestInit): Promise<T> {
+  const r = await fetch(`${PUBLIC_API_URL}${path}`, { headers: { 'content-type': 'application/json' }, ...init });
+  if (!r.ok) throw new Error(`${r.status} ${r.statusText} on ${path}`);
+  return r.json() as Promise<T>;
+}
+
+export const api = {
+  samples: () => req<Sample[]>('/samples'),
+  createSample: (body: Pick<Sample, 'name' | 'vcf_uri'>) => req<Sample>('/samples', { method: 'POST', body: JSON.stringify(body) }),
+  jobsForSample: (sampleId: string) => req<Job[]>(`/samples/${sampleId}/jobs`),
+  annotate: (sampleId: string) => req<Job>(`/samples/${sampleId}/annotate`, { method: 'POST' }),
+  job: (id: string) => req<Job>(`/jobs/${id}`),
+  variants: (q: Record<string, string | number>) => req<VariantPage>(`/variants?${new URLSearchParams(q as Record<string, string>)}`)
+};