Helena Bioinformatics Overrides API

openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Overrides API
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: overrides
paths:
  /sessions/{session_id}/overrides:
    get:
      tags:
      - overrides
      summary: List overridden variants
      description: List all overridden variants for a session.
      operationId: list_overrides_sessions__session_id__overrides_get
      security:
      - HTTPBearer: []
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: variant_idx
        in: query
        required: false
        schema:
          anyOf:
          - type: integer
          - type: 'null'
          description: Filter by variant index
          title: Variant Idx
        description: Filter by variant index
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/OverridesListResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    post:
      tags:
      - overrides
      summary: Reclassify variant
      description: 'Reclassify a variant with clinical justification.


        First override: acmg_class_original is set to pipeline_class from request.

        Subsequent override: original is preserved (pipeline_class ignored).'
      operationId: create_override_sessions__session_id__overrides_post
      security:
      - HTTPBearer: []
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/CreateOverrideRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/OverrideResultResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/overrides/{variant_idx}:
    delete:
      tags:
      - overrides
      summary: Revert to original classification
      description: Revert a variant to its pipeline-assigned ACMG classification.
      operationId: revert_override_sessions__session_id__overrides__variant_idx__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/OverrideResultResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    CreateOverrideRequest:
      properties:
        variant_idx:
          type: integer
          title: Variant Idx
          description: Variant index to reclassify
        new_class:
          type: string
          pattern: ^(P|LP|VUS|LB|B)$
          title: New Class
          description: New ACMG classification
        pipeline_class:
          type: string
          pattern: ^(P|LP|VUS|LB|B)$
          title: Pipeline Class
          description: ACMG class currently assigned by the pipeline (read from variants list). Stored as acmg_class_original on first override; ignored on subsequent overrides (original is preserved per first-override invariant).
        reason:
          type: string
          maxLength: 5000
          minLength: 1
          title: Reason
          description: Clinical justification
      type: object
      required:
      - variant_idx
      - new_class
      - pipeline_class
      - reason
      title: CreateOverrideRequest
      description: Request to reclassify a variant.
    OverrideResultResponse:
      properties:
        variant_idx:
          type: integer
          title: Variant Idx
        acmg_class:
          type: string
          title: Acmg Class
          description: 'Active classification after the operation. On create: new_class. On revert: the original pipeline class (what the frontend should now display).'
        acmg_class_original:
          anyOf:
          - type: string
          - type: 'null'
          title: Acmg Class Original
          description: Pipeline class before override. None after revert.
        override_reason:
          anyOf:
          - type: string
          - type: 'null'
          title: Override Reason
        overridden_by:
          anyOf:
          - $ref: '#/components/schemas/UserAttribution'
          - type: 'null'
      type: object
      required:
      - variant_idx
      - acmg_class
      title: OverrideResultResponse
      description: Result of a create or revert operation.
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    OverrideEntry:
      properties:
        variant_idx:
          type: integer
          title: Variant Idx
        acmg_class:
          type: string
          title: Acmg Class
          description: Current override classification
        acmg_class_original:
          type: string
          title: Acmg Class Original
          description: Pipeline class at override time
        override_reason:
          type: string
          title: Override Reason
          description: Clinical justification
        overridden_by:
          $ref: '#/components/schemas/UserAttribution'
          description: Who reclassified
      type: object
      required:
      - variant_idx
      - acmg_class
      - acmg_class_original
      - override_reason
      - overridden_by
      title: OverrideEntry
      description: Single overridden variant.
    OverridesListResponse:
      properties:
        overrides:
          items:
            $ref: '#/components/schemas/OverrideEntry'
          type: array
          title: Overrides
        total_count:
          type: integer
          title: Total Count
      type: object
      required:
      - overrides
      - total_count
      title: OverridesListResponse
      description: List of overridden variants.
    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