Helena Bioinformatics Internal API

openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Internal API
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: Internal
paths:
  /internal/sessions/{session_id}/annotations:
    get:
      tags:
      - Internal
      summary: List all annotations for a session (internal)
      description: 'Return all user annotations for a session.


        No JWT auth — protected by shared secret via X-Internal-Service-Token

        header. Consumed by ai-service (reports), family-analysis, and

        other internal services that need merged views over DuckDB pipeline

        data + PostgreSQL user annotations.'
      operationId: get_session_annotations_internal_sessions__session_id__annotations_get
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: X-Internal-Service-Token
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Internal-Service-Token
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SessionAnnotationsResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /internal/transcript-representations:
    post:
      tags:
      - Internal
      summary: Map Transcript Representations
      operationId: map_transcript_representations_internal_transcript_representations_post
      parameters:
      - name: X-Internal-Service-Token
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Internal-Service-Token
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/TranscriptMappingRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /internal/disease-contexts:
    post:
      tags:
      - Internal
      summary: Disease Contexts
      operationId: disease_contexts_internal_disease_contexts_post
      parameters:
      - name: X-Internal-Service-Token
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Internal-Service-Token
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DiseaseContextRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /internal/reclassification/runs/{run_id}/storage-paths:
    patch:
      tags:
      - Internal
      summary: Update storage paths post-migration (internal)
      description: 'Set log_storage_path + results_storage_path on a reclassification run.


        Called by SO migration worker after successful rsync compute -> storage.

        Idempotent: repeated calls with same paths produce same DB state.


        Returns:

        204 No Content on success.

        404 if run_id not found.'
      operationId: update_storage_paths_internal_reclassification_runs__run_id__storage_paths_patch
      parameters:
      - name: run_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Run Id
      - name: X-Internal-Service-Token
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Internal-Service-Token
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/InternalUpdateStoragePathsRequest'
      responses:
        '204':
          description: Successful Response
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /internal/reclassification/runs/stuck-migrations:
    get:
      tags:
      - Internal
      summary: List runs with stale completed status awaiting migration (internal)
      description: 'Return run IDs that need re-migration.


        Used by SO recovery beat task (storage.recovery_orphan_reclassification_migrations).'
      operationId: list_stuck_migrations_internal_reclassification_runs_stuck_migrations_get
      parameters:
      - name: older_than_minutes
        in: query
        required: false
        schema:
          type: integer
          maximum: 1440
          minimum: 1
          description: Threshold for finished_at age. Runs in completed state with NULL log_storage_path AND finished_at older than this many minutes are returned.
          default: 30
          title: Older Than Minutes
        description: Threshold for finished_at age. Runs in completed state with NULL log_storage_path AND finished_at older than this many minutes are returned.
      - name: X-Internal-Service-Token
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Internal-Service-Token
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/StuckMigrationsResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    DiseaseContextRow:
      properties:
        gene_symbol:
          anyOf:
          - type: string
            maxLength: 64
            pattern: ^[A-Za-z0-9][A-Za-z0-9_.-]*$
          - type: 'null'
          title: Gene Symbol
        genotype:
          anyOf:
          - type: string
            maxLength: 32
          - type: 'null'
          title: Genotype
        chromosome:
          anyOf:
          - type: string
            maxLength: 16
          - type: 'null'
          title: Chromosome
        phenotype_terms:
          items:
            type: string
            maxLength: 10
            pattern: ^HP:[0-9]{7}$
          type: array
          maxItems: 100
          title: Phenotype Terms
      additionalProperties: false
      type: object
      title: DiseaseContextRow
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    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
    DiseaseContextRequest:
      properties:
        rows:
          items:
            $ref: '#/components/schemas/DiseaseContextRow'
          type: array
          maxItems: 100
          title: Rows
      additionalProperties: false
      type: object
      required:
      - rows
      title: DiseaseContextRequest
    StuckMigrationsResponse:
      properties:
        run_ids:
          items:
            type: string
            format: uuid
          type: array
          title: Run Ids
        older_than_minutes:
          type: integer
          title: Older Than Minutes
      type: object
      required:
      - run_ids
      - older_than_minutes
      title: StuckMigrationsResponse
      description: 'Response for GET /internal/reclassification/runs/stuck-migrations.


        Used by SO recovery beat task to find runs that need re-migration

        (status=''completed'' but log_storage_path IS NULL after threshold).'
    AnnotationRecord:
      properties:
        variant_idx:
          type: integer
          title: Variant Idx
        is_user_flagged:
          type: boolean
          title: Is User Flagged
          default: false
        user_flag_comment:
          anyOf:
          - type: string
          - type: 'null'
          title: User Flag Comment
        flagged_by:
          anyOf:
          - $ref: '#/components/schemas/UserAttribution'
          - type: 'null'
        acmg_override_class:
          anyOf:
          - type: string
          - type: 'null'
          title: Acmg Override Class
        acmg_class_original:
          anyOf:
          - type: string
          - type: 'null'
          title: Acmg Class Original
        override_reason:
          anyOf:
          - type: string
          - type: 'null'
          title: Override Reason
        overridden_by:
          anyOf:
          - $ref: '#/components/schemas/UserAttribution'
          - type: 'null'
      type: object
      required:
      - variant_idx
      title: AnnotationRecord
      description: A single variant annotation (flag, override, or both).
    InternalUpdateStoragePathsRequest:
      properties:
        log_storage_path:
          type: string
          title: Log Storage Path
          description: Absolute path to run.log on storage tier (e.g. /mnt/helena-storage/reclassification_runs/{id}/run.log)
        results_storage_path:
          type: string
          title: Results Storage Path
          description: Absolute path to results.json on storage tier
      type: object
      required:
      - log_storage_path
      - results_storage_path
      title: InternalUpdateStoragePathsRequest
      description: 'Request body for PATCH /internal/reclassification/runs/{run_id}/storage-paths.


        Called by SO migration worker after successful rsync compute -> storage.

        Both paths are required (storage migration is atomic for the run).'
    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.'
    SessionAnnotationsResponse:
      properties:
        session_id:
          type: string
          format: uuid
          title: Session Id
        annotations:
          items:
            $ref: '#/components/schemas/AnnotationRecord'
          type: array
          title: Annotations
        total_count:
          type: integer
          title: Total Count
          description: Number of annotated variants in this session.
      type: object
      required:
      - session_id
      - annotations
      - total_count
      title: SessionAnnotationsResponse
      description: All annotations for a session, for internal consumer merging.
    TranscriptMappingRequest:
      properties:
        rows:
          items:
            $ref: '#/components/schemas/TranscriptMappingRow'
          type: array
          maxItems: 100
          title: Rows
      additionalProperties: false
      type: object
      required:
      - rows
      title: TranscriptMappingRequest
    TranscriptMappingRow:
      properties:
        assembly:
          anyOf:
          - type: string
            maxLength: 16
          - type: 'null'
          title: Assembly
        chromosome:
          anyOf:
          - type: string
            maxLength: 16
          - type: 'null'
          title: Chromosome
        position:
          anyOf:
          - type: integer
            exclusiveMinimum: 0.0
          - type: 'null'
          title: Position
        reference_allele:
          anyOf:
          - type: string
            maxLength: 1001
          - type: 'null'
          title: Reference Allele
        alternate_allele:
          anyOf:
          - type: string
            maxLength: 1001
          - type: 'null'
          title: Alternate Allele
        transcript_id:
          anyOf:
          - type: string
            maxLength: 128
          - type: 'null'
          title: Transcript Id
        hgvs_cdna:
          anyOf:
          - type: string
            maxLength: 512
          - type: 'null'
          title: Hgvs Cdna
        hgvs_protein:
          anyOf:
          - type: string
            maxLength: 512
          - type: 'null'
          title: Hgvs Protein
        processing_notes:
          anyOf:
          - type: string
            maxLength: 4096
          - type: 'null'
          title: Processing Notes
      additionalProperties: false
      type: object
      title: TranscriptMappingRow
  securitySchemes:
    HTTPBearer:
      type: http
      scheme: bearer