fix: overhaul the platform skeleton, add a serverless deployment track

An end-to-end audit found the repo could not build, test or run as shipped. This
fixes every finding, then adds a Cloud Run track so the demo costs about £1/month
idle instead of ~£150.

CI (red on its first run)
- api: setuptools could not build the package (flat layout with app/ and alembic/)
- web: missing @types/node; `vitest run` exited 1 with no test files
- pipeline: the stub run needed a gitignored VCF, and no process had a stub block
- ruff pinned, mypy configured, DB tests on real Postgres (pgserver locally, service in CI)

ML serving (scores were meaningless)
- the registered model now carries its own feature engineering and returns predict_proba,
  so serving sends raw columns and cannot drift from training
- resolve by registry alias (stages are deprecated in MLflow 3) and record the real
  version; re-scoring upserts instead of failing on the unique constraint
- ClinVar labels parsed from VEP's lowercase terms

Pipeline
- exact ref/alt recovered from a CHROM_POS_REF_ALT VCF ID; loading is idempotent
- job status reaches running/failed/succeeded, so the UI stops polling dead jobs
- DATABASE_URL travels in the environment or a Nextflow secret, never on a command line
- VEP cache and plugins staged as inputs; the gcp profile runs tasks on Google Batch

Deployment
- the API serves /api (matching the ingress); the web app reads its API URL at runtime
- migrations run in an init container under a Postgres advisory lock
- terraform: custom VPC shared with Batch, private Cloud SQL, API enablement, Workload
  Identity bindings, Secret Manager, deletion protection
- serverless track, now the default: Cloud Run services scaling to zero, a Cloud Run job
  for the Nextflow driver, and Neon or Cloud SQL behind one DATABASE_URL secret. GKE and
  Argo remain, behind -var deploy_kubernetes=true. See docs/cloud.md.

Correctness and security
- 409 on duplicate sample names, 422 on bad paging, natural chromosome ordering, wider
  VEP text columns, enum dropped on downgrade, the sample's assembly actually used
- vcf_uri restricted to gs:// objects or files under the data root, blocking option injection
- CORS restricted to configured origins; `make down` no longer deletes volumes

Data
- docs/data.md records the peer-reviewed, openly licensed sources (GIAB HG002, ClinVar,
  gnomAD) with citations and an honest evaluation plan; `make data` fetches a chr22 slice

Verified: api 50 tests, ml 18, loader 16, web 12; ruff, mypy, svelte-check, terraform
validate and both kustomize overlays clean.

web/src/lib/api.ts

@@ -1,7 +1,13 @@
-import { PUBLIC_API_URL } from '$env/static/public';
+// Dynamic, not static: the same image serves /api behind the ingress and a full URL elsewhere.
+import { env } from '$env/dynamic/public';
+import { variantQuery, type VariantFilters } from './query';
 
-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 Assembly = 'GRCh38' | 'GRCh37';
+export type Sample = { id: string; name: string; vcf_uri: string; assembly: Assembly; created_at: string };
+export type Job = {
+  id: string; sample_id: string; status: 'queued' | 'running' | 'succeeded' | 'failed';
+  log: string | null; 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;
@@ -10,16 +16,30 @@ export type Variant = {
 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 ${path}`);
+  const r = await fetch(`${env.PUBLIC_API_URL ?? '/api'}${path}`, { headers: { 'content-type': 'application/json' }, ...init });
+  if (!r.ok) throw new Error(await errorReason(r));
   return r.json() as Promise<T>;
 }
 
+// FastAPI puts the reason in `detail`: a string, or a list of validation errors.
+async function errorReason(r: Response): Promise<string> {
+  const fallback = `${r.status} ${r.statusText}`;
+  try {
+    const { detail } = await r.json();
+    if (typeof detail === 'string') return detail;
+    if (Array.isArray(detail)) return detail.map((d: { msg?: string }) => d.msg ?? '').join('; ') || fallback;
+  } catch {
+    // not JSON (e.g. a proxy error page)
+  }
+  return fallback;
+}
+
 export const api = {
   samples: () => req<Sample[]>('/samples'),
-  createSample: (body: Pick<Sample, 'name' | 'vcf_uri'>) => req<Sample>('/samples', { method: 'POST', body: JSON.stringify(body) }),
+  createSample: (body: Pick<Sample, 'name' | 'vcf_uri' | 'assembly'>) =>
+    req<Sample>('/samples', { method: 'POST', body: JSON.stringify(body) }),
   jobsForSample: (sampleId: string) => req<Job[]>(`/samples/${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?${new URLSearchParams(q as Record<string, string>)}`)
+  variants: (filters: VariantFilters) => req<VariantPage>(`/variants?${variantQuery(filters)}`)
 };