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.

api/app/schemas.py

@@ -1,8 +1,12 @@
-from datetime import datetime
+import re
 import uuid
+from datetime import datetime
+from pathlib import PurePosixPath
+from typing import Literal
 
-from pydantic import BaseModel, ConfigDict, Field
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
+from app.config import settings
 from app.models import JobStatus
 
 
@@ -10,10 +14,34 @@ class ORMModel(BaseModel):
     model_config = ConfigDict(from_attributes=True)
 
 
+Assembly = Literal["GRCh38", "GRCh37"]
+VCF_SUFFIXES = (".vcf", ".vcf.gz", ".vcf.bgz", ".bcf")
+GCS_URI = re.compile(r"gs://[a-z0-9][a-z0-9._-]{1,220}[a-z0-9]/\S+")
+
+
 class SampleCreate(BaseModel):
     name: str = Field(min_length=1, max_length=120)
     vcf_uri: str
-    assembly: str = "GRCh38"
+    # Passed to VEP --assembly; the VEP cache must contain it.
+    assembly: Assembly = "GRCh38"
+
+    @field_validator("vcf_uri")
+    @classmethod
+    def _gcs_object_or_file_under_data_root(cls, v: str) -> str:
+        # The URI becomes a Nextflow argument and a path the pipeline reads: accept a GCS object or
+        # a file under the local data root, never something that parses as an option.
+        if not v or any(ord(c) < 32 for c in v):
+            raise ValueError("vcf_uri must be a non-empty single line")
+        if not v.lower().endswith(VCF_SUFFIXES):
+            raise ValueError(f"vcf_uri must end in one of {', '.join(VCF_SUFFIXES)}")
+        if v.startswith("gs://"):
+            if not GCS_URI.fullmatch(v):
+                raise ValueError("vcf_uri is not a valid gs://bucket/object URI")
+            return v
+        path, root = PurePosixPath(v), PurePosixPath(settings.local_data_root)
+        if not path.is_absolute() or ".." in path.parts or not path.is_relative_to(root):
+            raise ValueError(f"local VCFs must be absolute paths under {root}")
+        return v
 
 
 class SampleOut(ORMModel):
@@ -30,6 +58,7 @@ class JobOut(ORMModel):
     status: JobStatus
     workflow_ref: str | None
     vep_version: str | None
+    log: str | None
     created_at: datetime
     finished_at: datetime | None
 
@@ -56,6 +85,12 @@ class VariantOut(ORMModel):
     prediction: PredictionOut | None = None
 
 
+class ScoreOut(BaseModel):
+    job_id: uuid.UUID
+    scored: int
+    model_version: str
+
+
 class VariantPage(BaseModel):
     items: list[VariantOut]
     total: int