Helena Bioinformatics Flagging API

openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Flagging API
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: flagging
paths:
  /sessions/{session_id}/variants/{variant_idx}/flag:
    post:
      tags:
      - flagging
      summary: Flag a variant with a comment
      description: 'Flag a variant for review by the platform operator.


        Persists flag in PostgreSQL variant_annotations table (upsert).

        Emits variant.flagged audit event. Sends detailed email to operator.'
      operationId: flag_variant_sessions__session_id__variants__variant_idx__flag_post
      security:
      - HTTPBearer: []
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: variant_idx
        in: path
        required: true
        schema:
          type: integer
          title: Variant Idx
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FlagVariantRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FlagVariantResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    delete:
      tags:
      - flagging
      summary: Unflag a variant
      description: 'Remove flag from a variant.


        Clears flag fields in PostgreSQL. If no other annotation remains

        (override), the row is deleted. Emits variant.unflagged audit event.'
      operationId: unflag_variant_sessions__session_id__variants__variant_idx__flag_delete
      security:
      - HTTPBearer: []
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: variant_idx
        in: path
        required: true
        schema:
          type: integer
          title: Variant Idx
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FlagVariantResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    FlagVariantResponse:
      properties:
        variant_idx:
          type: integer
          title: Variant Idx
        gene_symbol:
          anyOf:
          - type: string
          - type: 'null'
          title: Gene Symbol
        is_user_flagged:
          type: boolean
          title: Is User Flagged
        email_sent:
          type: boolean
          title: Email Sent
        message:
          type: string
          title: Message
        flagged_by:
          anyOf:
          - $ref: '#/components/schemas/UserAttribution'
          - type: 'null'
          description: User who set the flag. None on unflag responses.
      type: object
      required:
      - variant_idx
      - is_user_flagged
      - email_sent
      - message
      title: FlagVariantResponse
      description: Response after flagging or unflagging a variant.
    FlagVariantRequest:
      properties:
        comment:
          type: string
          maxLength: 5000
          minLength: 10
          title: Comment
          description: Description of the issue with this variant
      type: object
      required:
      - comment
      title: FlagVariantRequest
      description: Request to flag a variant with a comment.
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    UserAttribution:
      properties:
        user_id:
          anyOf:
          - type: string
            format: uuid
          - type: 'null'
          title: User Id
          description: User UUID. May be None for historical records migrated from DuckDB where original user was not tracked.
        user_name:
          type: string
          title: User Name
          description: Display name of the user. For historical records, may be 'system:historical-migration' or 'unknown-historical'.
        timestamp:
          anyOf:
          - type: string
            format: date-time
          - type: 'null'
          title: Timestamp
          description: When the action occurred. None for historical records without precise timestamp.
      type: object
      required:
      - user_name
      title: UserAttribution
      description: 'Identifies a user who performed an action, with optional timestamp.


        Used in flag/override responses and annotation records. Both user_id

        and user_name are required — user_id for system references, user_name

        for display. timestamp optional because some historical records

        (migrated from DuckDB) lack precise timestamps.'
    ValidationError:
      properties:
        loc:
          items:
            anyOf:
            - type: string
            - type: integer
          type: array
          title: Location
        msg:
          type: string
          title: Message
        type:
          type: string
          title: Error Type
        input:
          title: Input
        ctx:
          type: object
          title: Context
      type: object
      required:
      - loc
      - msg
      - type
      title: ValidationError
  securitySchemes:
    HTTPBearer:
      type: http
      scheme: bearer