Helena Bioinformatics Clinvar Export API

openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Clinvar Export API
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: clinvar-export
paths:
  /sessions/{session_id}/clinvar-lite/suggestions/{variant_idx}:
    get:
      tags:
      - clinvar-export
      summary: Get Export Suggestions
      operationId: get_export_suggestions_sessions__session_id__clinvar_lite_suggestions__variant_idx__get
      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/ClinVarExportSuggestions'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/clinvar-lite/export:
    post:
      tags:
      - clinvar-export
      summary: Export one expert-reviewed variant as a ClinVar Lite package
      description: Create, but never submit, a ClinVar Lite package for manual review.
      operationId: export_reviewed_variant_sessions__session_id__clinvar_lite_export_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/ClinVarLiteExportRequest'
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ClinVarLiteExportResponse'
        '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
    ClinVarLiteExportRequest:
      properties:
        variant_idx:
          type: integer
          minimum: 0.0
          title: Variant Idx
        hgvs_name:
          type: string
          maxLength: 500
          minLength: 1
          title: Hgvs Name
        rationale:
          type: string
          maxLength: 5000
          minLength: 10
          title: Rationale
        evidence_codes:
          items:
            type: string
          type: array
          maxItems: 50
          title: Evidence Codes
        mode_of_inheritance:
          type: string
          maxLength: 80
          title: Mode Of Inheritance
        expert_review_confirmed:
          type: boolean
          title: Expert Review Confirmed
        hgvs_validated:
          type: boolean
          title: Hgvs Validated
        expected_classification:
          type: string
          enum:
          - P
          - LP
          - VUS
          - LB
          - B
          title: Expected Classification
        condition_id_type:
          anyOf:
          - type: string
            maxLength: 40
          - type: 'null'
          title: Condition Id Type
        condition_id_value:
          anyOf:
          - type: string
            maxLength: 200
          - type: 'null'
          title: Condition Id Value
        preferred_condition_name:
          anyOf:
          - type: string
            maxLength: 500
          - type: 'null'
          title: Preferred Condition Name
        collection_method:
          type: string
          title: Collection Method
          default: clinical testing
        allele_origin:
          type: string
          title: Allele Origin
          default: germline
        affected_status:
          type: string
          title: Affected Status
          default: unknown
        number_of_individuals:
          type: integer
          minimum: 1.0
          title: Number Of Individuals
        citations:
          items:
            type: string
          type: array
          maxItems: 100
          title: Citations
        gene_symbol:
          anyOf:
          - type: string
            maxLength: 100
          - type: 'null'
          title: Gene Symbol
        local_id:
          anyOf:
          - type: string
            maxLength: 200
          - type: 'null'
          title: Local Id
        public_url:
          anyOf:
          - type: string
            maxLength: 2000
          - type: 'null'
          title: Public Url
        variation_identifiers:
          items:
            type: string
          type: array
          maxItems: 100
          title: Variation Identifiers
        alternate_designations:
          items:
            type: string
          type: array
          maxItems: 100
          title: Alternate Designations
        clinvar_accession:
          anyOf:
          - type: string
            maxLength: 40
          - type: 'null'
          title: Clinvar Accession
        record_status:
          anyOf:
          - type: string
            enum:
            - novel
            - update
          - type: 'null'
          title: Record Status
      type: object
      required:
      - variant_idx
      - hgvs_name
      - rationale
      - mode_of_inheritance
      - expert_review_confirmed
      - hgvs_validated
      - expected_classification
      - number_of_individuals
      title: ClinVarLiteExportRequest
      description: Reviewed public data for one germline ClinVar Lite assertion.
    ClinVarExportSuggestions:
      properties:
        contract_version:
          type: integer
          const: 2
          title: Contract Version
          default: 2
        hgvs_candidates:
          items:
            type: string
          type: array
          title: Hgvs Candidates
        suggested_hgvs:
          anyOf:
          - type: string
          - type: 'null'
          title: Suggested Hgvs
        requires_hgvs_validation:
          type: boolean
          title: Requires Hgvs Validation
          default: true
      type: object
      required:
      - hgvs_candidates
      title: ClinVarExportSuggestions
    ClinVarLiteExportResponse:
      properties:
        package_name:
          type: string
          title: Package Name
        package_base64:
          type: string
          title: Package Base64
        upload_files:
          items:
            type: string
          type: array
          title: Upload Files
        manifest:
          additionalProperties: true
          type: object
          title: Manifest
      type: object
      required:
      - package_name
      - package_base64
      - upload_files
      - manifest
      title: ClinVarLiteExportResponse
      description: Browser-downloadable ZIP plus the names of the two upload files.
    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