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app

FastAPI application factory for the patient-data API.

Module​

Functions​

build_openapi​

def build_openapi(app: FastAPI) ‑> dict[str, typing.Any]:

Build the OpenAPI document, adding what the route signatures cannot express.

Two additions on top of FastAPI's generation:

  • the EligibilityCriterion family schemas. They are real Pydantic models (CRITERION_VARIANTS) but no route returns one, so nothing would otherwise pull them into components. They are advertised on the base schema as x-variants rather than as a oneOf: several overlap, and a family added later must still validate against the base.
  • ScanImageManifest and ScanSegmentationIndex, which describe files inside the scan-image archive rather than any response body.

Neither is reachable from a path by ordinary means, so both are pointed at by $ref objects — the variants from x-variants/x-family-variants here, the two archive members from the scan-image route's x-archive-members. A bare reference string in an extension is invisible to a tool that walks $refs, which is how a bundler or client generator decides a schema is dead and prunes it.

Existing schemas are never overwritten, so FastAPI stays authoritative for everything it already generated.

Arguments

  • app: The application whose routes the document is built from.

Returns The OpenAPI document.

create_app​

def create_app(    repository: PatientDataRepository,    *,    verifier: JWTVerifier,    allowed_origins: list[str] | None = None,    activity_repository: ActivityRepository | None = None,) ‑> fastapi.applications.FastAPI:

Build the patient-data API app bound to a repository and verifier.

Arguments

  • repository: The data-access implementation handlers depend on.
  • verifier: The JWT verifier the auth dependency uses to authenticate requests.
  • allowed_origins: Browser origins permitted to read the API cross-origin via CORS (the Trials Web App's origin). When empty or None no CORS headers are sent, so cross-origin browser reads are disallowed.
  • activity_repository: The activity domain's data-access implementation. Defaults to PrefectActivityRepository() when omitted.

Returns A configured FastAPI application.

dump_openapi_yaml​

def dump_openapi_yaml(document: dict[str, Any]) ‑> str:

Render an OpenAPI document as YAML.

Shared by the /openapi.yaml route and by dev-scripts/dump_patient_api_openapi.py, so the served document and the committed copy cannot differ in rendering — only a content difference should ever show up in a diff of the two.

Arguments

  • document: The document to render (app.openapi()).

Returns The YAML text, with every multi-line description as a literal block.