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OpenAPI Specification

openapi: 3.2.0
info:
  title: Helix Insight - Variant Analysis Service Variants API
  description: AI-powered variant analysis and interpretation service
  version: 0.1.0
tags:
- name: Variants
paths:
  /sessions/{session_id}/variants/browse/version:
    get:
      tags:
      - Variants
      summary: Result Version
      operationId: result_version_sessions__session_id__variants_browse_version_get
      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:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/browse:
    get:
      tags:
      - Variants
      summary: Result Page
      operationId: result_page_sessions__session_id__variants_browse_get
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: scope
        in: query
        required: false
        schema:
          enum:
          - variants
          - phenotype
          - screening
          - denovo
          - mtdna
          - carriers
          - dominant
          - review
          type: string
          default: variants
          title: Scope
      - name: gene
        in: query
        required: false
        schema:
          type: string
          maxLength: 200
          default: ''
          title: Gene
      - name: classification
        in: query
        required: false
        schema:
          type: string
          pattern: ^(P|LP|VUS|LB|B)?$
          default: ''
          title: Classification
      - name: tier
        in: query
        required: false
        schema:
          type: string
          maxLength: 20
          default: ''
          title: Tier
      - name: hpo
        in: query
        required: false
        schema:
          type: string
          maxLength: 30
          default: ''
          title: Hpo
      - name: cursor
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            maxLength: 2048
          - type: 'null'
          title: Cursor
      - name: limit
        in: query
        required: false
        schema:
          type: integer
          maximum: 100
          minimum: 1
          default: 50
          title: Limit
      - name: version
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            maxLength: 64
          - type: 'null'
          title: Version
      - name: min_depth
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            minimum: 0
          - type: 'null'
          title: Min Depth
      - name: min_quality
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            minimum: 0
          - type: 'null'
          title: Min Quality
      - name: min_vaf
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 1
            minimum: 0
          - type: 'null'
          title: Min Vaf
      - name: max_vaf
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 1
            minimum: 0
          - type: 'null'
          title: Max Vaf
      - name: max_gnomad_af
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 1
            minimum: 0
          - type: 'null'
          title: Max Gnomad Af
      - name: include_unknown_af
        in: query
        required: false
        schema:
          type: boolean
          default: true
          title: Include Unknown Af
      - name: impact
        in: query
        required: false
        schema:
          anyOf:
          - enum:
            - HIGH
            - MODERATE
            - LOW
            - MODIFIER
            type: string
          - type: 'null'
          title: Impact
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/browse/detail/{variant_idx}:
    get:
      tags:
      - Variants
      summary: Result Detail
      operationId: result_detail_sessions__session_id__variants_browse_detail__variant_idx__get
      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
      - name: scope
        in: query
        required: false
        schema:
          enum:
          - variants
          - phenotype
          - screening
          - denovo
          - mtdna
          - carriers
          - dominant
          - review
          type: string
          default: variants
          title: Scope
      - name: version
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            maxLength: 64
          - type: 'null'
          title: Version
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants:
    get:
      tags:
      - Variants
      summary: Query variants
      description: Query processed variants with filters and pagination
      operationId: query_variants_sessions__session_id__variants_get
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: acmg_class
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: ACMG classifications
          title: Acmg Class
        description: ACMG classifications
      - name: min_confidence
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 100
            minimum: 0
          - type: 'null'
          title: Min Confidence
      - name: min_priority_score
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            minimum: 0
          - type: 'null'
          title: Min Priority Score
      - name: gene_symbol
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: Gene symbols (supports partial match)
          title: Gene Symbol
        description: Gene symbols (supports partial match)
      - name: consequence
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: Consequences
          title: Consequence
        description: Consequences
      - name: impact
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: Impact levels
          title: Impact
        description: Impact levels
      - name: max_gnomad_af
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 1
            minimum: 0
          - type: 'null'
          title: Max Gnomad Af
      - name: include_unknown_af
        in: query
        required: false
        schema:
          type: boolean
          default: true
          title: Include Unknown Af
      - name: min_depth
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            minimum: 0
          - type: 'null'
          title: Min Depth
      - name: min_quality
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            minimum: 0
          - type: 'null'
          title: Min Quality
      - name: min_vaf
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 1
            minimum: 0
          - type: 'null'
          title: Min Vaf
      - name: max_vaf
        in: query
        required: false
        schema:
          anyOf:
          - type: number
            maximum: 1
            minimum: 0
          - type: 'null'
          title: Max Vaf
      - name: sv_only
        in: query
        required: false
        schema:
          type: boolean
          description: Return only rows whose canonical sv_type is non-null
          default: false
          title: Sv Only
        description: Return only rows whose canonical sv_type is non-null
      - name: sv_group
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            pattern: ^(del|dup|other)$
          - type: 'null'
          title: Sv Group
      - name: sv_query
        in: query
        required: false
        schema:
          anyOf:
          - type: string
            maxLength: 200
          - type: 'null'
          title: Sv Query
      - name: page
        in: query
        required: false
        schema:
          type: integer
          minimum: 1
          description: Page number
          default: 1
          title: Page
        description: Page number
      - name: page_size
        in: query
        required: false
        schema:
          type: integer
          maximum: 1000
          minimum: 1
          description: Results per page
          default: 50
          title: Page Size
        description: Results per page
      - name: sort_by
        in: query
        required: false
        schema:
          type: string
          description: Sort column
          default: priority_score
          title: Sort By
        description: Sort column
      - name: sort_order
        in: query
        required: false
        schema:
          type: string
          description: Sort order (ASC/DESC)
          default: DESC
          title: Sort Order
        description: Sort order (ASC/DESC)
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/VariantQueryResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/by-gene:
    get:
      tags:
      - Variants
      summary: Get variants grouped by gene
      description: Returns variants aggregated by gene with summary statistics
      operationId: get_variants_by_gene_sessions__session_id__variants_by_gene_get
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: acmg_class
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: Filter by ACMG classifications
          title: Acmg Class
        description: Filter by ACMG classifications
      - name: impact
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: Filter by impact levels
          title: Impact
        description: Filter by impact levels
      - name: gene_symbol
        in: query
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          description: Filter by gene symbol (partial match)
          title: Gene Symbol
        description: Filter by gene symbol (partial match)
      - name: page
        in: query
        required: false
        schema:
          anyOf:
          - type: integer
            minimum: 1
          - type: 'null'
          description: Page number (optional, returns all if not provided)
          title: Page
        description: Page number (optional, returns all if not provided)
      - name: page_size
        in: query
        required: false
        schema:
          anyOf:
          - type: integer
            maximum: 10000
            minimum: 1
          - type: 'null'
          description: Genes per page (optional)
          title: Page Size
        description: Genes per page (optional)
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GeneAggregatedResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/sv-presence:
    get:
      tags:
      - Variants
      summary: Check for structural variants
      description: Check whether the complete session contains an SV-typed row
      operationId: get_sv_presence_sessions__session_id__variants_sv_presence_get
      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:
                $ref: '#/components/schemas/SvPresenceResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/{variant_idx}:
    get:
      tags:
      - Variants
      summary: Get variant details
      description: Get detailed information for a specific variant
      operationId: get_variant_detail_sessions__session_id__variants__variant_idx__get
      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
      - name: include_review_context
        in: query
        required: false
        schema:
          type: boolean
          default: false
          title: Include Review Context
      - name: X-Review-HPO-Ids
        in: header
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          title: X-Review-Hpo-Ids
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/VariantDetailResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/statistics/summary:
    get:
      tags:
      - Variants
      summary: Get variant statistics
      description: Get aggregated statistics about variants
      operationId: get_variant_statistics_sessions__session_id__variants_statistics_summary_get
      parameters:
      - name: session_id
        in: path
        required: true
        schema:
          type: string
          format: uuid
          title: Session Id
      - name: acmg_class
        in: query
        required: false
        schema:
          anyOf:
          - type: array
            items:
              type: string
          - type: 'null'
          description: Filter by ACMG classifications
          title: Acmg Class
        description: Filter by ACMG classifications
      responses:
        '200':
          description: Successful Response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/VariantStatisticsResponse'
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
  /sessions/{session_id}/variants/{variant_idx}/transcripts:
    get:
      tags:
      - Variants
      summary: Get Transcript Annotations
      operationId: get_transcript_annotations_sessions__session_id__variants__variant_idx__transcripts_get
      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: {}
        '422':
          description: Validation Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/HTTPValidationError'
components:
  schemas:
    VariantStatisticsResponse:
      properties:
        total_variants:
          type: integer
          title: Total Variants
        classification_breakdown:
          additionalProperties:
            type: integer
          type: object
          title: Classification Breakdown
        tier_breakdown:
          additionalProperties:
            type: integer
          type: object
          title: Tier Breakdown
        impact_breakdown:
          additionalProperties:
            type: integer
          type: object
          title: Impact Breakdown
        top_genes:
          items:
            additionalProperties: true
            type: object
          type: array
          title: Top Genes
        curated_count:
          type: integer
          title: Curated Count
          description: mtDNA curated variant count
          default: 0
      type: object
      required:
      - total_variants
      - classification_breakdown
      - impact_breakdown
      - top_genes
      title: VariantStatisticsResponse
      description: Variant statistics response.
      example:
        classification_breakdown:
          benign: 10
          likely_benign: 20
          likely_pathogenic: 25
          pathogenic: 15
          vus: 80
        impact_breakdown:
          high: 30
          low: 40
          moderate: 80
        top_genes:
        - gene_symbol: BRCA1
          variant_count: 15
        - gene_symbol: TP53
          variant_count: 12
        total_variants: 150
    GeneAggregatedResponse:
      properties:
        genes:
          items:
            $ref: '#/components/schemas/GeneAggregated'
          type: array
          title: Genes
          description: Gene-aggregated variant data
        total_genes:
          type: integer
          title: Total Genes
          description: Total number of genes
        total_variants:
          type: integer
          title: Total Variants
          description: Total number of variants across all genes
        page:
          type: integer
          title: Page
          description: Current page number
        page_size:
          type: integer
          title: Page Size
          description: Genes per page
        total_pages:
          type: integer
          title: Total Pages
          description: Total number of pages
        has_next_page:
          type: boolean
          title: Has Next Page
          description: Whether there is a next page
        has_previous_page:
          type: boolean
          title: Has Previous Page
          description: Whether there is a previous page
      type: object
      required:
      - genes
      - total_genes
      - total_variants
      - page
      - page_size
      - total_pages
      - has_next_page
      - has_previous_page
      title: GeneAggregatedResponse
      description: 'Response for gene-aggregated variants endpoint.


        Returns variants grouped by gene, sorted by clinical significance.

        Supports pagination at the gene level.'
      example:
        genes:
        - benign_count: 0
          best_acmg_class: P
          best_acmg_priority: 1
          best_impact: HIGH
          best_priority_score: 92.5
          gene_symbol: BRCA1
          likely_benign_count: 0
          likely_pathogenic_count: 1
          pathogenic_count: 2
          variant_count: 5
          variants: []
          vus_count: 2
        has_next_page: true
        has_previous_page: false
        page: 1
        page_size: 50
        total_genes: 150
        total_pages: 3
        total_variants: 5000
    VariantDetailResponse:
      properties:
        variant:
          additionalProperties: true
          type: object
          title: Variant
          description: Complete variant data
      type: object
      required:
      - variant
      title: VariantDetailResponse
      description: Detailed single variant response.
      example:
        variant:
          acmg_class: P
          alternate_allele: A
          chromosome: chr7
          gene_symbol: CFTR
          position: 117559590
          priority_score: 85.3
          reference_allele: G
          variant_idx: 42
    VariantQueryResponse:
      properties:
        sv_counts:
          anyOf:
          - additionalProperties:
              additionalProperties:
                type: integer
              type: object
            type: object
          - type: 'null'
          title: Sv Counts
        variants:
          items:
            additionalProperties: true
            type: object
          type: array
          title: Variants
          description: List of variants
        total_count:
          type: integer
          title: Total Count
          description: Total number of variants matching filters
        page:
          type: integer
          title: Page
          description: Current page number
        page_size:
          type: integer
          title: Page Size
          description: Number of variants per page
        total_pages:
          type: integer
          title: Total Pages
          description: Total number of pages
        has_next_page:
          type: boolean
          title: Has Next Page
          description: Whether there is a next page
        has_previous_page:
          type: boolean
          title: Has Previous Page
          description: Whether there is a previous page
      type: object
      required:
      - variants
      - total_count
      - page
      - page_size
      - total_pages
      - has_next_page
      - has_previous_page
      title: VariantQueryResponse
      example:
        has_next_page: true
        has_previous_page: false
        page: 1
        page_size: 50
        total_count: 150
        total_pages: 3
        variants:
        - acmg_class: P
          chromosome: chr7
          gene_symbol: CFTR
          position: 117559590
          priority_score: 85.3
          variant_idx: 42
    HTTPValidationError:
      properties:
        detail:
          items:
            $ref: '#/components/schemas/ValidationError'
          type: array
          title: Detail
      type: object
      title: HTTPValidationError
    GeneAggregated:
      properties:
        gene_symbol:
          type: string
          title: Gene Symbol
          description: Gene symbol
        variant_count:
          type: integer
          title: Variant Count
          description: Total variants in gene
        best_acmg_class:
          anyOf:
          - type: string
          - type: 'null'
          title: Best Acmg Class
          description: Most pathogenic ACMG class
        best_acmg_priority:
          type: integer
          title: Best Acmg Priority
          description: ACMG priority (1=P, 2=LP, 3=VUS, 4=LB, 5=B)
          default: 99
        best_impact:
          anyOf:
          - type: string
          - type: 'null'
          title: Best Impact
          description: Highest impact level
        best_priority_score:
          anyOf:
          - type: number
          - type: 'null'
          title: Best Priority Score
          description: Highest priority score
        pathogenic_count:
          type: integer
          title: Pathogenic Count
          description: Pathogenic variants
          default: 0
        likely_pathogenic_count:
          type: integer
          title: Likely Pathogenic Count
          description: Likely Pathogenic variants
          default: 0
        vus_count:
          type: integer
          title: Vus Count
          description: VUS variants
          default: 0
        likely_benign_count:
          type: integer
          title: Likely Benign Count
          description: Likely Benign variants
          default: 0
        benign_count:
          type: integer
          title: Benign Count
          description: Benign variants
          default: 0
        variants:
          items:
            additionalProperties: true
            type: object
          type: array
          title: Variants
          description: Variants in this gene
        mtdna_variant_count:
          type: integer
          title: Mtdna Variant Count
          description: Count of mtDNA variants (classification_framework=mmdwg_2020)
          default: 0
      type: object
      required:
      - gene_symbol
      - variant_count
      title: GeneAggregated
      description: 'Aggregated gene data with variants.


        Contains:

        - Gene-level summary statistics

        - ACMG class counts

        - Best (most pathogenic) ACMG class

        - Best tier and priority score

        - All variants for this gene'
    SvPresenceResponse:
      properties:
        has_sv:
          type: boolean
          title: Has Sv
      type: object
      required:
      - has_sv
      title: SvPresenceResponse
      description: Whether any row in the complete session has a non-null SV type.
    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