Helena Bioinformatics

Helena Bioinformatics Reclassification API

The reclassification API from Helena Bioinformatics — 7 operation(s) for reclassification.

GitHub OpenAPI

Operations 8

POST /api/v1/reclassification/run Start reclassification #
GET /api/v1/reclassification/status Get currently-running reclassification status #
GET /api/v1/reclassification/runs List past reclassification runs (paginated) #
GET /api/v1/reclassification/runs/{run_id} Get reclassification run detail #
DELETE /api/v1/reclassification/runs/{run_id} Hard-delete a reclassification run + filesystem artifacts #
GET /api/v1/reclassification/runs/{run_id}/log Stream run log (storage-first / compute-fallback) #
GET /api/v1/reclassification/runs/{run_id}/summary.csv Per-session summary CSV (storage-first / compute-fallback) #
GET /api/v1/reclassification/sessions/{session_id}/upgrade-report Per-session classifier upgrade report (clinical review) #

Specifications

⚙
OpenAPI
https://artifacts.apis.io/helena-bio/openapi/helena-bio-reclassification-api-openapi.yml

Schemas & Data

📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-mtdna-curation-fields-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-section-response-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-clin-var-lite-export-request-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-gene-literature-response-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-reclassification-run-detail-schema-schema.json
📊
JSONSchema
https://artifacts.apis.io/helena-bio/json-schema/helena-bio-vep-cache-stats-response-schema.json

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OpenAPI Specification

helena-bio-reclassification-api-openapi.yml Raw ↑ 
openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Reclassification…
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: reclassification
paths:
  /api/v1/reclassification/run:
    post:
      tags:
      - reclassification
      summary: Start reclassification
      description: 'Start a reclassification subprocess (reclassify mode only).


        Requires confirm=true in request body as safety guard -- this operation

        modifies production DuckDB files and sends notification emails.


        HELENA-PLATFORM-RERUN-001 + HELIX-CR-2026-095-A.'
      operationId: run_reclassification_api_v1_reclassification_run_post
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RunReclassificationRequest'
        required: true
      responses:
        '202':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ReclassificationStatusResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
      security:
      - HTTPBearer: []
  /api/v1/reclassification/status:
    get:
      tags:
      - reclassification
      summary: Get currently-running reclassification status
      description: 'Poll the most recent in-memory reclassification status.


        Backwards-compatible with HELENA-PLATFORM-RERUN-001 frontend polling.

        PG-backed history is exposed via GET /runs (see CR-095-A).'
      operationId: get_reclassification_status_api_v1_reclassification_status_get
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ReclassificationStatusResponse'
      security:
      - HTTPBearer: []
  /api/v1/reclassification/runs:
    get:
      tags:
      - reclassification
      summary: List past reclassification runs (paginated)
      operationId: list_runs_api_v1_reclassification_runs_get
      security:
      - HTTPBearer: []
      parameters:
      - name: limit
        in: query
        required: false
        schema:
          type: integer
          maximum: 200
          minimum: 1
          default: 50
          title: Limit
      - name: offset
        in: query
        required: false
        schema:
          type: integer
          minimum: 0
          default: 0
          title: Offset
      - name: status
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            pattern: ^(running|completed|failed)$
          - type: 'null'
          title: Status
      - name: organization_id
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            format: uuid
          - type: 'null'
          title: Organization Id
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ReclassificationRunListResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /api/v1/reclassification/runs/{run_id}:
    get:
      tags:
      - reclassification
      summary: Get reclassification run detail
      operationId: get_run_api_v1_reclassification_runs__run_id__get
      security:
      - HTTPBearer: []
      parameters:
      - name: run_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Run Id
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ReclassificationRunDetailSchema'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
    delete:
      tags:
      - reclassification
      summary: Hard-delete a reclassification run + filesystem artifacts
      operationId: delete_run_api_v1_reclassification_runs__run_id__delete
      security:
      - HTTPBearer: []
      parameters:
      - name: run_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Run Id
      responses:
        '204':
          description: Successful Response
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /api/v1/reclassification/runs/{run_id}/log:
    get:
      tags:
      - reclassification
      summary: Stream run log (storage-first / compute-fallback)
      operationId: get_run_log_api_v1_reclassification_runs__run_id__log_get
      security:
      - HTTPBearer: []
      parameters:
      - name: run_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Run Id
      responses:
        '200':
          description: Successful Response
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /api/v1/reclassification/runs/{run_id}/summary.csv:
    get:
      tags:
      - reclassification
      summary: Per-session summary CSV (storage-first / compute-fallback)
      operationId: get_run_summary_csv_api_v1_reclassification_runs__run_id__summary_csv_get
      security:
      - HTTPBearer: []
      parameters:
      - name: run_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Run Id
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /api/v1/reclassification/sessions/{session_id}/upgrade-report:
    get:
      tags:
      - reclassification
      summary: Per-session classifier upgrade report (clinical review)
      description: 'Return parsed JSON content of classifier_upgrade_report.json for a

        session. Resolved storage-first via path_utils.'
      operationId: get_session_upgrade_report_api_v1_reclassification_sessions__session_id__upgrade_report_get
      security:
      - HTTPBearer: []
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    ReclassificationRunSummarySchema:
      properties:
        id:
          type: string
          format: uuid
          title: Id
        started_at:
          type: string
          format: date-time
          title: Started At
        finished_at:
          anyOf:
          - type: string
            format: date-time
          - type: 'null'
          title: Finished At
        target_version:
          type: string
          title: Target Version
        target_version_label:
          anyOf:
          - type: string
          - type: 'null'
          title: Target Version Label
        scope:
          type: string
          title: Scope
        organization_id:
          anyOf:
          - type: string
            format: uuid
          - type: 'null'
          title: Organization Id
        status:
          type: string
          title: Status
        sessions_total:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Total
        sessions_succeeded:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Succeeded
        sessions_failed:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Failed
        sessions_skipped:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Skipped
        elapsed_seconds:
          anyOf:
          - type: string
            pattern: ^(?!^[-+.]*$)[+-]?0*\d*\.?\d*$
          - type: 'null'
          title: Elapsed Seconds
        triggered_by_user_email:
          anyOf:
          - type: string
          - type: 'null'
          title: Triggered By User Email
      type: object
      required:
      - id
      - started_at
      - target_version
      - scope
      - status
      title: ReclassificationRunSummarySchema
      description: Compact run summary for list endpoint.
    RunReclassificationRequest:
      properties:
        target_version:
          type: string
          title: Target Version
        version_description:
          type: string
          title: Version Description
        scope:
          type: string
          title: Scope
        organization_id:
          anyOf:
          - type: string
          - type: 'null'
          title: Organization Id
        user_ids:
          anyOf:
          - items:
              type: string
            type: array
          - type: 'null'
          title: User Ids
        notify:
          type: boolean
          title: Notify
          default: true
        confirm:
          type: boolean
          title: Confirm
          default: false
      type: object
      required:
      - target_version
      - version_description
      - scope
      title: RunReclassificationRequest
    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
    ReclassificationRunListResponse:
      properties:
        items:
          items:
            $ref: '#/components/schemas/ReclassificationRunSummarySchema'
          type: array
          title: Items
        total:
          type: integer
          title: Total
        limit:
          type: integer
          title: Limit
        offset:
          type: integer
          title: Offset
      type: object
      required:
      - items
      - total
      - limit
      - offset
      title: ReclassificationRunListResponse
      description: Paginated list response.
    ReclassificationStatusResponse:
      properties:
        run_id:
          type: string
          title: Run Id
        status:
          type: string
          title: Status
        target_version:
          anyOf:
          - type: string
          - type: 'null'
          title: Target Version
        progress_current:
          type: integer
          title: Progress Current
          default: 0
        progress_total:
          type: integer
          title: Progress Total
          default: 0
        elapsed_seconds:
          type: number
          title: Elapsed Seconds
          default: 0
        log_lines:
          anyOf:
          - items:
              type: string
            type: array
          - type: 'null'
          title: Log Lines
        error:
          anyOf:
          - type: string
          - type: 'null'
          title: Error
      type: object
      required:
      - run_id
      - status
      title: ReclassificationStatusResponse
    ReclassificationRunDetailSchema:
      properties:
        id:
          type: string
          format: uuid
          title: Id
        started_at:
          type: string
          format: date-time
          title: Started At
        finished_at:
          anyOf:
          - type: string
            format: date-time
          - type: 'null'
          title: Finished At
        target_version:
          type: string
          title: Target Version
        target_version_label:
          anyOf:
          - type: string
          - type: 'null'
          title: Target Version Label
        scope:
          type: string
          title: Scope
        organization_id:
          anyOf:
          - type: string
            format: uuid
          - type: 'null'
          title: Organization Id
        user_ids:
          anyOf:
          - items:
              type: string
            type: array
          - type: 'null'
          title: User Ids
        notify:
          type: boolean
          title: Notify
        status:
          type: string
          title: Status
        sessions_total:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Total
        sessions_succeeded:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Succeeded
        sessions_failed:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Failed
        sessions_skipped:
          anyOf:
          - type: integer
          - type: 'null'
          title: Sessions Skipped
        elapsed_seconds:
          anyOf:
          - type: string
            pattern: ^(?!^[-+.]*$)[+-]?0*\d*\.?\d*$
          - type: 'null'
          title: Elapsed Seconds
        error_message:
          anyOf:
          - type: string
          - type: 'null'
          title: Error Message
        log_storage_path:
          anyOf:
          - type: string
          - type: 'null'
          title: Log Storage Path
        results_storage_path:
          anyOf:
          - type: string
          - type: 'null'
          title: Results Storage Path
        log_compute_path:
          anyOf:
          - type: string
          - type: 'null'
          title: Log Compute Path
        results_compute_path:
          anyOf:
          - type: string
          - type: 'null'
          title: Results Compute Path
        triggered_by_user_id:
          type: string
          format: uuid
          title: Triggered By User Id
        triggered_by_user_name:
          anyOf:
          - type: string
          - type: 'null'
          title: Triggered By User Name
        triggered_by_user_email:
          anyOf:
          - type: string
          - type: 'null'
          title: Triggered By User Email
        created_at:
          type: string
          format: date-time
          title: Created At
        updated_at:
          type: string
          format: date-time
          title: Updated At
      type: object
      required:
      - id
      - started_at
      - target_version
      - scope
      - notify
      - status
      - triggered_by_user_id
      - created_at
      - updated_at
      title: ReclassificationRunDetailSchema
      description: Full run detail for single-run endpoint.
  securitySchemes:
    HTTPBearer:
      type: http
      scheme: bearer