overlay: 1.0.0
info:
  title: API Evangelist enhancements for the Genialis Expressions API
  version: 1.0.0
extends: openapi/genialis-base-openapi.yaml
x-generated: '2026-08-21'
x-method: generated
x-source: >-
  Derived from live probes of https://app.genialis.com on 2026-08-21 and from the
  artifacts in this repository. Every value below was observed or read from the
  provider's own material; nothing is invented. The original spec at
  openapi/genialis-base-openapi.yaml is never mutated.
actions:
- target: $.info
  description: >-
    The published spec sets no title beyond "Genialis base", no contact, no licence
    and leaves info.version at the drf-spectacular default 0.0.0. Supply the
    identity a consumer needs, and record what the version field actually is.
  update:
    contact:
      name: Genialis Support
      url: https://genialis.atlassian.net/servicedesk/customer/portal/3
      email: info@genialis.com
    termsOfService: https://www.genialis.com/terms-of-service/
    x-documentation: https://docs.genialis.com/resdk/
    x-spec-source: https://app.genialis.com/api/schema
    x-version-caveat: >-
      info.version is the drf-spectacular default "0.0.0" and does not identify the
      build. Live component versions are served at GET /about/versions.
- target: $
  description: >-
    The published spec declares no servers[]. Its paths are server-root relative and
    span /api, /rest-auth, /saml-auth, /about and /health_check, so a client that
    assumes an /api base silently receives the SPA shell with a 200 on the
    non-/api operations. Name the real server root.
  update:
    servers:
    - url: https://app.genialis.com
      description: >-
        Genialis Expressions production. Verified 2026-08-21: GET /api/data?limit=1
        -> 200 (count 29123); GET /about/versions -> 200.
- target: $
  description: Record the cross-cutting runtime semantics the contract omits.
  update:
    x-conventions:
      pagination:
        style: limit-offset
        params: [limit, offset]
        response_fields: [count, next, previous, results]
      sorting:
        param: ordering
      error_envelope: '{"error": "<message>"} | {"detail": "<message>"}'
      rfc9457: false
      idempotency: none
      dry_run: none
      rate_limit_headers: none
      anonymous_read: true
    x-agent-warning: >-
      app.genialis.com is an SPA catch-all. Unmatched paths return HTTP 200 with a
      1377-byte HTML shell rather than 404. Assert content-type application/json
      before treating any 200 as data.
- target: $
  description: >-
    The contract documents only 2xx responses across all 254 operations — not one
    4xx or 5xx. Attach the error shapes actually observed, as a reusable component,
    without touching any operation.
  update:
    components:
      responses:
        x-ObservedBadRequest:
          description: >-
            Observed 400. Bespoke envelope, not RFC 9457. Example captured live from
            GET /api/data?ordering=zzz.
          content:
            application/json:
              schema:
                type: object
                properties:
                  error:
                    type: string
              example:
                error: "Ordering by field 'zzz' is not supported."
        x-ObservedAuthFailure:
          description: >-
            Django REST Framework default envelope for 401/403. Not documented by
            Genialis and not confirmed on a live response.
          content:
            application/json:
              schema:
                type: object
                properties:
                  detail:
                    type: string
- target: $.paths['/api/data/bulk_delete']
  description: >-
    Flag the highest-consequence operation in the API. It has no idempotency key, no
    dry-run and no documented reversal — see conventions/genialis-conventions.yml.
  update:
    x-consequence: destructive
    x-reversible: false
    x-reversal-window: null
    x-agent-guidance: >-
      Requires explicit human confirmation. There is no restore endpoint for deleted
      data objects anywhere in the contract.
- target: $.paths['/api/collection/bulk_delete']
  update:
    x-consequence: destructive
    x-reversible: false
    x-reversal-window: null
- target: $.paths['/api/sample/bulk_delete']
  update:
    x-consequence: destructive
    x-reversible: false
    x-reversal-window: null
- target: $.paths['/about/versions']
  description: This is the platform's real version signal; mark it as such.
  update:
    x-version-endpoint: true
    x-observed-response: '{"resolwe":"45.1.0","resolwe-bio":"65.0.0","genialis-bio":"63.0.0"}'
    x-observed-on: '2026-08-21'
- target: $.paths['/api/variant']
  description: Record the domain-standard signature carried by the variant model.
  update:
    x-domain-standard: VCF v4.x call model (CHROM/POS/REF/ALT) with dbSNP and ClinVar identifier schemes