> ## Documentation Index
> Fetch the complete documentation index at: https://docs.rafflesia.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# List retained homology searches



## OpenAPI

````yaml /api-reference/openapi.json get /v1/homology
openapi: 3.1.0
info:
  description: >-
    Deterministic biological evidence primitives. Every response is the same
    envelope: ok, data, warnings, provenance.
  title: Rafflesia API
  version: 0.1.0
servers:
  - description: Production
    url: https://api.rafflesia.ai
security:
  - bearerAuth: []
paths:
  /v1/homology:
    get:
      tags:
        - Homology
      summary: List retained homology searches
      operationId: homology_list
      parameters:
        - explode: false
          in: query
          name: limit
          schema:
            default: 20
            format: int64
            maximum: 100
            minimum: 1
            type: integer
        - explode: false
          in: query
          name: starting_after
          schema:
            type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/EnvelopeHomologySearchList'
          description: OK
          headers:
            Rafflesia-Contract-Digest:
              schema:
                type: string
            Rafflesia-Version:
              schema:
                type: string
            X-Request-ID:
              schema:
                type: string
        default:
          content:
            application/problem+json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
          description: Error
components:
  schemas:
    EnvelopeHomologySearchList:
      additionalProperties: false
      properties:
        $schema:
          description: A URL to the JSON Schema for this object.
          examples:
            - https://example.com/schemas/EnvelopeHomologySearchList.json
          format: uri
          readOnly: true
          type: string
        data:
          $ref: '#/components/schemas/HomologySearchList'
          description: Operation result data.
        error:
          $ref: '#/components/schemas/APIError'
          description: Structured error information.
        evidence:
          $ref: '#/components/schemas/EvidenceSummary'
          description: Mechanical evidence summary for agent inspection and chaining.
        ok:
          description: Whether the operation succeeded.
          type: boolean
        provenance:
          $ref: '#/components/schemas/Provenance'
          description: Execution provenance.
        warnings:
          description: Non-fatal warnings.
          items:
            $ref: '#/components/schemas/Warning'
          type:
            - array
            - 'null'
      required:
        - ok
        - warnings
        - provenance
      type: object
    ErrorModel:
      additionalProperties: false
      properties:
        $schema:
          description: A URL to the JSON Schema for this object.
          examples:
            - https://example.com/schemas/ErrorModel.json
          format: uri
          readOnly: true
          type: string
        detail:
          description: >-
            A human-readable explanation specific to this occurrence of the
            problem.
          examples:
            - Property foo is required but is missing.
          type: string
        errors:
          description: Optional list of individual error details
          items:
            $ref: '#/components/schemas/ErrorDetail'
          type:
            - array
            - 'null'
        instance:
          description: >-
            A URI reference that identifies the specific occurrence of the
            problem.
          examples:
            - https://example.com/error-log/abc123
          format: uri
          type: string
        status:
          description: HTTP status code
          examples:
            - 400
          format: int64
          type: integer
        title:
          description: >-
            A short, human-readable summary of the problem type. This value
            should not change between occurrences of the error.
          examples:
            - Bad Request
          type: string
        type:
          default: about:blank
          description: A URI reference to human-readable documentation for the error.
          examples:
            - https://example.com/errors/example
          format: uri
          type: string
      type: object
    HomologySearchList:
      additionalProperties: false
      properties:
        data:
          items:
            $ref: '#/components/schemas/HomologySearch'
          type:
            - array
            - 'null'
        has_more:
          type: boolean
        next_cursor:
          type: string
        object:
          type: string
        url:
          type: string
      required:
        - object
        - url
        - data
        - has_more
      type: object
    APIError:
      additionalProperties: false
      properties:
        code:
          description: Stable specific error code.
          type: string
        details:
          additionalProperties: {}
          description: Additional structured error details.
          type: object
        doc_url:
          description: Stable documentation URL for this error code.
          type: string
        message:
          description: Human-readable error message.
          type: string
        param:
          description: Request field responsible for the error when known.
          type: string
        type:
          description: Stable coarse error category.
          enum:
            - invalid_request_error
            - resource_missing
            - conflict_error
            - rate_limit_error
            - authentication_error
            - permission_error
            - billing_error
            - api_error
          type: string
      required:
        - type
        - code
        - message
        - doc_url
      type: object
    EvidenceSummary:
      additionalProperties: false
      properties:
        duration_ms:
          description: >-
            Primary elapsed duration in milliseconds when the response exposes
            one.
          format: int64
          type: integer
        input_refs:
          description: >-
            Input references detected from request fields such as object_id,
            structure_id, target_id, and sequence_id.
          items:
            type: string
          type:
            - array
            - 'null'
        object_refs:
          description: Object ids or object refs visible in the response/provenance.
          items:
            type: string
          type:
            - array
            - 'null'
        output_refs:
          description: Output references detected from response data and generated objects.
          items:
            type: string
          type:
            - array
            - 'null'
        row_count:
          description: >-
            Primary row count or returned row count when the response exposes
            one.
          format: int64
          type: integer
        warnings_count:
          description: Number of non-fatal warnings in the envelope.
          format: int64
          type: integer
      required:
        - warnings_count
      type: object
    Provenance:
      additionalProperties: false
      properties:
        cache_hit:
          description: Whether cached output was reused.
          type: boolean
        created_at:
          description: UTC timestamp.
          type: string
        database_snapshots:
          description: Database snapshots used.
          items:
            $ref: '#/components/schemas/DatabaseSnapshot'
          type:
            - array
            - 'null'
        generated_object_ids:
          description: Object ids created by the operation.
          items:
            type: string
          type:
            - array
            - 'null'
        input_hash:
          description: SHA-256 hash of canonical request input.
          type: string
        operation:
          description: Primitive operation id.
          type: string
        parameters_hash:
          description: SHA-256 hash of parameters.
          type: string
        request_id:
          description: Unique request identifier.
          type: string
        server_version:
          description: Server version.
          type: string
        tool_versions:
          description: Tool versions used.
          items:
            $ref: '#/components/schemas/ToolVersion'
          type:
            - array
            - 'null'
      required:
        - request_id
        - operation
        - created_at
        - server_version
      type: object
    Warning:
      additionalProperties: false
      properties:
        code:
          description: Stable warning code.
          type: string
        details:
          additionalProperties: {}
          description: Additional structured warning details.
          type: object
        message:
          description: Human-readable warning message.
          type: string
      required:
        - code
        - message
      type: object
    ErrorDetail:
      additionalProperties: false
      properties:
        location:
          description: >-
            Where the error occurred, e.g. 'body.items[3].tags' or
            'path.thing-id'
          type: string
        message:
          description: Error message text
          type: string
        value:
          description: The value at the given location
      type: object
    HomologySearch:
      additionalProperties: false
      properties:
        created_at:
          type: string
        failure:
          $ref: '#/components/schemas/HomologySearchFailure'
        id:
          type: string
        object:
          type: string
        policy_id:
          type: string
        query:
          $ref: '#/components/schemas/HomologySearchQuerySummary'
        receipt:
          $ref: '#/components/schemas/HomologySearchReceipt'
        result_set:
          $ref: '#/components/schemas/HomologySearchResultSet'
        results:
          $ref: '#/components/schemas/HomologySearchResultsRequest'
        specification_sha256:
          type: string
        status:
          enum:
            - queued
            - running
            - succeeded
            - failed
          type: string
        target_space:
          $ref: '#/components/schemas/HomologySearchTargetSpace'
          description: >-
            Authoritative searched target population. For filtered async
            searches this is absent until Tomato has compiled immutable
            eligibility.
        warnings:
          items:
            $ref: '#/components/schemas/Warning'
          type:
            - array
            - 'null'
      required:
        - id
        - object
        - created_at
        - status
        - query
        - policy_id
        - results
        - specification_sha256
        - receipt
        - warnings
      type: object
    DatabaseSnapshot:
      additionalProperties: false
      properties:
        digest:
          type: string
        kind:
          type: string
        name:
          type: string
        version:
          type: string
      required:
        - name
        - version
      type: object
    ToolVersion:
      additionalProperties: false
      properties:
        name:
          type: string
        path:
          type: string
        version:
          type: string
      required:
        - name
        - version
      type: object
    HomologySearchFailure:
      additionalProperties: false
      properties:
        code:
          type: string
        detail:
          type: string
        is_retryable:
          type: boolean
      required:
        - code
        - detail
        - is_retryable
      type: object
    HomologySearchQuerySummary:
      additionalProperties: false
      properties:
        kind:
          type: string
        normalization_id:
          type: string
        normalized_length:
          format: int64
          type: integer
        retention:
          type: string
        sha256:
          type: string
      required:
        - kind
        - normalized_length
        - normalization_id
        - sha256
        - retention
      type: object
    HomologySearchReceipt:
      additionalProperties: false
      properties:
        calibration_id:
          type: string
        canonical_filter_sha256:
          type: string
        corpus_snapshot_id:
          type: string
        database_release_id:
          type: string
        engine:
          type: string
        filter_schema_id:
          type: string
        is_deterministic:
          type: boolean
        is_exhaustive:
          type: boolean
        is_policy_complete:
          type: boolean
        job_id:
          type: string
        query_compilation_id:
          type: string
        search_policy_id:
          type: string
        semantic_profile_id:
          type: string
        submission_id:
          type: string
        target_space_id:
          type: string
      required:
        - engine
        - database_release_id
        - corpus_snapshot_id
        - semantic_profile_id
        - search_policy_id
        - is_policy_complete
        - is_exhaustive
        - is_deterministic
      type: object
    HomologySearchResultSet:
      additionalProperties: false
      properties:
        canonical_result_id:
          type: string
        count:
          format: int64
          type: integer
        is_result_limit_reached:
          type: boolean
        object:
          type: string
        sha256:
          type: string
        url:
          type: string
      required:
        - object
        - url
        - count
        - sha256
        - canonical_result_id
        - is_result_limit_reached
      type: object
    HomologySearchResultsRequest:
      additionalProperties: false
      properties:
        evidence:
          enum:
            - candidate_measurement
            - pairwise_sequence_alignment
          type: string
        max_results:
          format: int64
          maximum: 10000
          minimum: 1
          type: integer
        significance_requirement:
          default: not_requested
          enum:
            - not_requested
            - if_available
            - required
          type: string
        unit:
          default: target
          enum:
            - target
          type: string
      required:
        - unit
        - evidence
        - max_results
        - significance_requirement
      type: object
    HomologySearchTargetSpace:
      additionalProperties: false
      properties:
        canonical_filter_sha256:
          type: string
        eligible_record_count:
          format: int64
          type: integer
        eligible_residue_count:
          format: int64
          type: integer
        filter_schema_id:
          type: string
        id:
          description: Opaque immutable identity of the exact target population searched.
          type: string
        is_filtered:
          type: boolean
        total_record_count:
          format: int64
          type: integer
        unknown_record_count:
          format: int64
          type: integer
      required:
        - id
        - is_filtered
        - total_record_count
        - eligible_record_count
        - eligible_residue_count
        - unknown_record_count
      type: object
  securitySchemes:
    bearerAuth:
      description: 'A Rafflesia API key, sent as `Authorization: Bearer <key>`.'
      scheme: bearer
      type: http

````