openapi: 3.2.0
info:
  title: Phi — Protein Design Research Notes API
  description: 'Phi is a biomodal computation platform for protein design. Submit structure-prediction and sequence-design jobs, track their status, and retrieve scored results — all via a single REST API.


    ## Authentication

    All endpoints require an API key supplied as `Authorization: Bearer <key>` or a Clerk session token. Organisation ID is derived automatically from Clerk tokens; static-key callers must include `X-Organization-ID`.


    ## Quick links

    - `POST /v1/phi/jobs` — submit a job

    - `GET  /v1/phi/jobs/{job_id}/status` — poll status

    - `GET  /v1/phi/jobs/{job_id}/scores` — download scored results

    '
  version: 1.0.0
servers:
- url: https://api.dyno-agents.app
  description: Production
- url: http://localhost:8000
  description: Local development
tags:
- name: research-notes
paths:
  /v1/phi/datasets/{dataset_id}/research-notes:
    post:
      tags:
      - research-notes
      summary: Append to dataset research notes
      description: 'Append markdown content to the dataset''s cumulative research notes file in GCS.


        The notes file lives at ``research/{dataset_id}/notes.md``. If it does not exist

        yet it is created. If it does, the new content is appended after a separator.'
      operationId: append_research_notes_v1_phi_datasets__dataset_id__research_notes_post
      parameters:
      - name: dataset_id
        in: path
        required: true
        schema:
          type: string
          title: Dataset Id
      - name: x-api-key
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          description: API key for authentication
          title: X-Api-Key
        description: API key for authentication
      - name: X-User-ID
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-User-Id
      - name: X-Organization-ID
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Organization-Id
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AppendNotesRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResearchNotesResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    get:
      tags:
      - research-notes
      summary: Get dataset research notes
      description: 'Retrieve the accumulated research notes for a dataset.


        Returns the full markdown content inline plus a signed GCS URL for direct

        download. Returns ``exists: false`` (with no content) if no notes have been

        saved for this dataset yet.'
      operationId: get_research_notes_v1_phi_datasets__dataset_id__research_notes_get
      parameters:
      - name: dataset_id
        in: path
        required: true
        schema:
          type: string
          title: Dataset Id
      - name: x-api-key
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          description: API key for authentication
          title: X-Api-Key
        description: API key for authentication
      - name: X-User-ID
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-User-Id
      - name: X-Organization-ID
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Organization-Id
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResearchNotesResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    ValidationError:
      properties:
        loc:
          items:
            anyOf:
            - type: string
            - type: integer
          type: array
          title: Location
        msg:
          type: string
          title: Message
        type:
          type: string
          title: Error Type
      type: object
      required:
      - loc
      - msg
      - type
      title: ValidationError
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    AppendNotesRequest:
      properties:
        content:
          type: string
          title: Content
          description: Markdown content to append to the dataset's research notes
      type: object
      required:
      - content
      title: AppendNotesRequest
    ResearchNotesResponse:
      properties:
        dataset_id:
          type: string
          title: Dataset Id
        exists:
          type: boolean
          title: Exists
        content:
          anyOf:
          - type: string
          - type: 'null'
          title: Content
          description: Full notes content (markdown)
        gcs_url:
          anyOf:
          - type: string
          - type: 'null'
          title: Gcs Url
          description: Signed download URL (24 h TTL)
      type: object
      required:
      - dataset_id
      - exists
      title: ResearchNotesResponse