openapi: 3.2.0
info:
  title: Phi — Protein Design Protocols 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: protocols
paths:
  /v1/phi/protocols:
    get:
      tags:
      - protocols
      summary: List Protocols
      description: "List protocols for organization.\n\nArgs:\n    org_id: Organization ID from header\n    visibility: Filter by visibility (private/team/org)\n    tags: Comma-separated tags to filter by\n    starred: Filter by starred status (true/false/null for all)\n    limit: Max results\n    offset: Pagination offset\n    db: Database session\n\nReturns:\n    List of protocols with reputation"
      operationId: list_protocols_v1_phi_protocols_get
      parameters:
      - name: visibility
        in: query
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: Visibility
      - name: tags
        in: query
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: Tags
      - name: starred
        in: query
        required: false
        schema:
          anyOf:
          - type: boolean
          - type: 'null'
          title: Starred
      - name: limit
        in: query
        required: false
        schema:
          type: integer
          default: 100
          title: Limit
      - name: offset
        in: query
        required: false
        schema:
          type: integer
          default: 0
          title: Offset
      - 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:
                type: object
                additionalProperties: true
                title: Response List Protocols V1 Phi Protocols Get
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    post:
      tags:
      - protocols
      summary: Create Protocol
      description: "Create new protocol.\n\nArgs:\n    request: Protocol creation request\n    org_id: Organization ID from header\n    user_id: User ID from header\n    db: Database session\n\nReturns:\n    Created protocol"
      operationId: create_protocol_v1_phi_protocols_post
      parameters:
      - 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/CreateProtocolRequest'
      responses:
        '201':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ProtocolResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /v1/phi/protocols/{protocol_id}:
    get:
      tags:
      - protocols
      summary: Get Protocol
      description: "Get protocol by ID.\n\nArgs:\n    protocol_id: Protocol ID\n    org_id: Organization ID from header\n    db: Database session\n\nReturns:\n    Protocol details"
      operationId: get_protocol_v1_phi_protocols__protocol_id__get
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol 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/ProtocolResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    put:
      tags:
      - protocols
      summary: Update Protocol
      description: "Update protocol metadata.\n\nArgs:\n    protocol_id: Protocol ID\n    request: Update request\n    org_id: Organization ID from header\n    db: Database session\n\nReturns:\n    Updated protocol"
      operationId: update_protocol_v1_phi_protocols__protocol_id__put
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol 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/UpdateProtocolRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ProtocolResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    delete:
      tags:
      - protocols
      summary: Delete Protocol
      description: "Delete a protocol.\n\nDeletes the protocol and cascades to:\n- ProtocolExecution records (CASCADE)\n- ProtocolReputation records (CASCADE)\n\nSets NULL on:\n- Workflow.source_workflow_id (SET NULL)\n- Protocol.parent_protocol_id (SET NULL)\n\nArgs:\n    protocol_id: Protocol ID\n    org_id: Organization ID from header\n    db: Database session\n\nReturns:\n    Success response\n\nRaises:\n    HTTPException: If protocol not found or deletion fails"
      operationId: delete_protocol_v1_phi_protocols__protocol_id__delete
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol 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:
                type: object
                additionalProperties: true
                title: Response Delete Protocol V1 Phi Protocols  Protocol Id  Delete
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /v1/phi/protocols/validate:
    post:
      tags:
      - protocols
      summary: Validate Protocol Template
      description: 'Validate a protocol template without persisting.


        Returns validation errors and warnings. Useful for UI to validate before submit.'
      operationId: validate_protocol_template_v1_phi_protocols_validate_post
      parameters:
      - 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/ValidateProtocolRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                type: object
                additionalProperties: true
                title: Response Validate Protocol Template V1 Phi Protocols Validate Post
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /v1/phi/protocols/{protocol_id}/fork:
    post:
      tags:
      - protocols
      summary: Fork Protocol
      description: "Fork protocol to create variant.\n\nArgs:\n    protocol_id: Protocol to fork\n    request: Fork request\n    org_id: Organization ID from header\n    user_id: User ID from header\n    db: Database session\n\nReturns:\n    Forked protocol"
      operationId: fork_protocol_v1_phi_protocols__protocol_id__fork_post
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol 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/ForkProtocolRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ProtocolResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /v1/phi/protocols/{protocol_id}/executions:
    get:
      tags:
      - protocols
      summary: Get Protocol Executions
      description: "Get execution history for protocol.\n\nArgs:\n    protocol_id: Protocol ID\n    org_id: Organization ID from header\n    limit: Max results\n    offset: Pagination offset\n    db: Database session\n\nReturns:\n    List of protocol executions"
      operationId: get_protocol_executions_v1_phi_protocols__protocol_id__executions_get
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol Id
      - name: limit
        in: query
        required: false
        schema:
          type: integer
          default: 100
          title: Limit
      - name: offset
        in: query
        required: false
        schema:
          type: integer
          default: 0
          title: Offset
      - 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:
                type: object
                additionalProperties: true
                title: Response Get Protocol Executions V1 Phi Protocols  Protocol Id  Executions Get
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /v1/phi/protocols/recommend:
    post:
      tags:
      - protocols
      summary: Recommend Protocols
      description: "Recommend protocols based on user intent.\n\nExtracts intent from prompt, searches for matching protocols,\nand ranks by performance metrics.\n\nArgs:\n    request: Recommendation request with prompt\n    org_id: Organization ID from header\n    db: Database session\n\nReturns:\n    Recommended protocols with match scores and rationale"
      operationId: recommend_protocols_v1_phi_protocols_recommend_post
      parameters:
      - 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/RecommendProtocolRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                type: object
                additionalProperties: true
                title: Response Recommend Protocols V1 Phi Protocols Recommend Post
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /v1/phi/protocols/{protocol_id}/star:
    post:
      tags:
      - protocols
      summary: Star Protocol
      description: "Star a protocol for the organization.\n\nArgs:\n    protocol_id: Protocol ID\n    org_id: Organization ID from header\n    db: Database session\n\nReturns:\n    Success response with updated starred status"
      operationId: star_protocol_v1_phi_protocols__protocol_id__star_post
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol 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:
                type: object
                additionalProperties: true
                title: Response Star Protocol V1 Phi Protocols  Protocol Id  Star Post
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    delete:
      tags:
      - protocols
      summary: Unstar Protocol
      description: "Unstar a protocol for the organization.\n\nArgs:\n    protocol_id: Protocol ID\n    org_id: Organization ID from header\n    db: Database session\n\nReturns:\n    Success response with updated starred status"
      operationId: unstar_protocol_v1_phi_protocols__protocol_id__star_delete
      parameters:
      - name: protocol_id
        in: path
        required: true
        schema:
          type: string
          title: Protocol 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:
                type: object
                additionalProperties: true
                title: Response Unstar Protocol V1 Phi Protocols  Protocol Id  Star Delete
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    CreateProtocolRequest:
      properties:
        name:
          type: string
          title: Name
          description: Protocol name
        description:
          anyOf:
          - type: string
          - type: 'null'
          title: Description
          description: Protocol description
        intent_signature:
          additionalProperties: true
          type: object
          title: Intent Signature
          description: Structured intent
        protocol_template:
          additionalProperties: true
          type: object
          title: Protocol Template
          description: Parameterized workflow template
        source_workflow_id:
          anyOf:
          - type: string
          - type: 'null'
          title: Source Workflow Id
          description: Source workflow ID
        visibility:
          type: string
          title: Visibility
          description: Visibility level
          default: private
        tags:
          anyOf:
          - items:
              type: string
            type: array
          - type: 'null'
          title: Tags
          description: Tags for search
      type: object
      required:
      - name
      - intent_signature
      - protocol_template
      title: CreateProtocolRequest
      description: Request to create protocol.
    UpdateProtocolRequest:
      properties:
        name:
          anyOf:
          - type: string
          - type: 'null'
          title: Name
          description: Protocol name
        description:
          anyOf:
          - type: string
          - type: 'null'
          title: Description
          description: Protocol description
        intent_signature:
          anyOf:
          - additionalProperties: true
            type: object
          - type: 'null'
          title: Intent Signature
          description: Structured intent
        tags:
          anyOf:
          - items:
              type: string
            type: array
          - type: 'null'
          title: Tags
          description: Tags for search
      type: object
      title: UpdateProtocolRequest
      description: Request to update protocol.
    RecommendProtocolRequest:
      properties:
        user_prompt:
          type: string
          title: User Prompt
          description: User's workflow request
        force_refresh:
          type: boolean
          title: Force Refresh
          description: If true, bypass intent cache and re-extract (for 'Regenerate recommendations' button)
          default: false
        filters:
          anyOf:
          - additionalProperties: true
            type: object
          - type: 'null'
          title: Filters
          description: Optional filters (target_type, allowed_tools)
      type: object
      required:
      - user_prompt
      title: RecommendProtocolRequest
      description: Request for protocol recommendations.
    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
    ProtocolResponse:
      properties:
        id:
          type: string
          title: Id
        name:
          type: string
          title: Name
        description:
          anyOf:
          - type: string
          - type: 'null'
          title: Description
        intent_signature:
          additionalProperties: true
          type: object
          title: Intent Signature
        protocol_template:
          additionalProperties: true
          type: object
          title: Protocol Template
        source_workflow_id:
          anyOf:
          - type: string
          - type: 'null'
          title: Source Workflow Id
        parent_protocol_id:
          anyOf:
          - type: string
          - type: 'null'
          title: Parent Protocol Id
        version:
          type: integer
          title: Version
        visibility:
          type: string
          title: Visibility
        tags:
          items:
            type: string
          type: array
          title: Tags
        is_starred:
          type: boolean
          title: Is Starred
        created_at:
          type: string
          title: Created At
        updated_at:
          type: string
          title: Updated At
      type: object
      required:
      - id
      - name
      - description
      - intent_signature
      - protocol_template
      - source_workflow_id
      - parent_protocol_id
      - version
      - visibility
      - tags
      - is_starred
      - created_at
      - updated_at
      title: ProtocolResponse
      description: Protocol response model.
    ValidateProtocolRequest:
      properties:
        protocol_template:
          additionalProperties: true
          type: object
          title: Protocol Template
          description: Parameterized workflow template to validate
        dry_run:
          type: boolean
          title: Dry Run
          description: If true, instantiate with synthetic params and run workflow/preflight validation
          default: true
      type: object
      required:
      - protocol_template
      title: ValidateProtocolRequest
      description: Request to validate a protocol template without persisting.
    ForkProtocolRequest:
      properties:
        new_name:
          anyOf:
          - type: string
          - type: 'null'
          title: New Name
          description: Name for forked protocol
      type: object
      title: ForkProtocolRequest
      description: Request to fork protocol.