openapi: 3.0.3
info:
  title: Gencove Back array sample API
  version: v2
  contact:
    email: support@gencove.com
  license:
    name: Proprietary
  description: API for Gencove REST service. Visit <a href='https://enterprise.gencove.com/'>enterprise.gencove.com</a> and <a href='https://docs.gencove.com/'>docs.gencove.com</a> for more information. <br><hr><p>To work with Insomnia, you can generate a Gencove API key by <a target='_blank' href='https://web.gencove.com/account?filter=api-keys'>clicking here</a>. Once you have the API key and have imported the project in Insomnia as a <i>Request Collection</i>, enter the key in Insomnia under <i>Manage Environment</i>.</p><a href='https://insomnia.rest/run/?label=back_api2&uri=https%3A%2F%2Fv2-api-files-prod.s3.amazonaws.com%2Fpublic%2Finsomnia%2Finsomnia_gencove_prod.json' target='_blank'>Run in Insomnia</a><hr>
servers:
- url: https://api.gencove.com
tags:
- name: sample
paths:
  /api/v2/sample-ancestry/{sample_id}:
    get:
      operationId: sample_ancestry_retrieve
      parameters:
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleAncestry'
          description: ''
  /api/v2/sample-consumer-report/{sample_id}:
    post:
      operationId: sample_consumer_report_create
      description: "Generate presigned URL for consumer report.\n\nArgs:\n    request: HTTP request\n\nReturns:\n    Response with presigned URL and expiration time"
      parameters:
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SampleConsumerReportCreate'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/SampleConsumerReportCreate'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/SampleConsumerReportCreate'
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleConsumerReportResponse'
          description: ''
  /api/v2/sample-genomic-variants/{sample_id}:
    get:
      operationId: sample_genomic_variants_list
      description: 'Return variant-level results from a sample''s imputed VCF.


        Provide exactly one of the three query modes:


        - point: `?chromosome=chr11&position=<pos>`

        - range: `?chromosome=chr11&start_position=<start>&end_position=<end>`

        - rsid:  `?rsid=rs1,rs2,...`


        `chromosome` must be an h38 contig name with the `chr` prefix

        (chr1..chr22, chrX, chrY, chrM).'
      parameters:
      - in: query
        name: chromosome
        schema:
          type: string
        description: h38 contig name with the `chr` prefix, e.g. `chr1`, `chr11`, `chrX`, `chrY`, `chrM` (point and range queries)
      - in: query
        name: end_position
        schema:
          type: integer
        description: Range end (1-based); use with `start_position`. The span may not exceed 100000 bp.
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: query
        name: position
        schema:
          type: integer
        description: 1-based position for a point query
      - in: query
        name: rsid
        schema:
          type: string
        description: Comma-separated rsIDs, e.g. `rs429358,rs7412` (at most 50 per request).
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      - in: query
        name: start_position
        schema:
          type: integer
        description: Range start (1-based); use with `end_position`
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedGenomicVariantList'
          description: ''
  /api/v2/sample-kit/:
    post:
      operationId: sample_kit_create
      description: Order a new kit for a sample
      tags:
      - sample
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SampleKit'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/SampleKit'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/SampleKit'
        required: true
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleKitResponse'
          description: ''
  /api/v2/sample-kit-form/:
    post:
      operationId: sample_kit_form_create
      description: 'Create a temporary, payment-free kit-order session.


        Auth-gated to ``consumer_provider`` orgs and the ``sample_kit_create`` role

        (project-scoped). Creates a placeholder ``samples.Sample`` (status

        ``consumer_awaiting_kit_order``), pins the JWT ``jti`` on it for replay

        protection, and returns a tokenized URL the partner hands to an end user.

        The ``Kit`` is only created once the end user submits the form.'
      tags:
      - sample
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SampleKitFormCreate'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/SampleKitFormCreate'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/SampleKitFormCreate'
        required: true
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleKitFormResponse'
          description: ''
  /api/v2/sample-manifests-csv-template/:
    get:
      operationId: sample_manifests_csv_template_retrieve
      description: Download a sample manifest CSV template file based on the template_type parameter.
      parameters:
      - in: query
        name: template_type
        schema:
          type: string
          enum:
          - 384_well
          - 96_well
          - tube
        description: Type of the sample manifest CSV template. Options are 96_well, 384_well, tube.
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      - {}
      responses:
        '200':
          description: No response body
  /api/v2/sample-manifests-xlsx-template/:
    get:
      operationId: sample_manifests_xlsx_template_retrieve
      description: Download a sample manifest XLSX template file.
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      - {}
      responses:
        '200':
          description: No response body
  /api/v2/sample-manifests/{sample_manifest_id}:
    get:
      operationId: sample_manifests_retrieve
      parameters:
      - in: path
        name: sample_manifest_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleManifest'
          description: ''
  /api/v2/sample-metadata/{sample_id}:
    get:
      operationId: sample_metadata_retrieve
      description: Return sample metadata.
      parameters:
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleMetadata'
          description: ''
    post:
      operationId: sample_metadata_create
      description: Create sample metadata.
      parameters:
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SampleMetadata'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/SampleMetadata'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/SampleMetadata'
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleMetadata'
          description: ''
  /api/v2/sample-parentage/{sample_id}:
    get:
      operationId: sample_parentage_retrieve
      parameters:
      - in: query
        name: display_results
        schema:
          type: string
          enum:
          - all
          - checks
          - matches
        description: 'Display mode for parentage records. Options are:

          - ''matches'': Only display records where a parent has been identified (default)

          - ''checks'': Only display records where no parent has been identified

          - ''all'': Display all parentage records'
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleParentage'
          description: ''
  /api/v2/sample-quality-controls/{sample_id}:
    get:
      operationId: sample_quality_controls_list
      parameters:
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedQualityControlList'
          description: ''
  /api/v2/sample-restore-group/{restore_group_id}:
    get:
      operationId: sample_restore_group_list
      parameters:
      - in: query
        name: archive_status
        schema:
          type: string
          enum:
          - all
          - archived
          - available
          - restore_requested
        description: Filter samples by their archive status
      - in: query
        name: created_after
        schema:
          type: string
        description: Filter samples by created timestamp; use ISO8601 format
      - in: query
        name: created_before
        schema:
          type: string
        description: Filter samples by created timestamp; use ISO8601 format
      - in: query
        name: hidden_status
        schema:
          type: string
          enum:
          - all
          - hidden
          - visible
        description: Filter samples by their hidden status
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - in: query
        name: modified_after
        schema:
          type: string
        description: Filter samples by modified timestamp; use ISO8601 format
      - in: query
        name: modified_before
        schema:
          type: string
        description: Filter samples by modified timestamp; use ISO8601 format
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: path
        name: restore_group_id
        schema:
          type: string
          format: uuid
        required: true
      - in: query
        name: search
        schema:
          type: string
        description: Search samples by id or client id or metadata content
      - in: query
        name: status
        schema:
          type: string
          enum:
          - all
          - completed
          - failed
          - running
          - succeeded
        description: Filter samples by their status
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedSampleListList'
          description: ''
  /api/v2/sample-sheet/:
    get:
      operationId: sample_sheet_list
      description: Return generated sample sheet.
      parameters:
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: query
        name: search
        schema:
          type: string
        description: gncv:// notated sample path to search for
      - in: query
        name: sort_by
        schema:
          type: string
          enum:
          - created
          - modified
        description: Sort results
      - in: query
        name: sort_order
        schema:
          type: string
          enum:
          - asc
          - desc
        description: Sort direction
      - in: query
        name: status
        schema:
          type: string
          enum:
          - all
          - assigned
          - unassigned
        description: 'One of: assigned, unassigned, all; default is ''all'''
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedSampleSheetList'
          description: ''
  /api/v2/sample-stats/{sample_id}:
    get:
      operationId: sample_stats_retrieve
      parameters:
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleStats'
          description: ''
  /api/v2/sample-statuses/{sample_id}:
    get:
      operationId: sample_statuses_list
      parameters:
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedSampleStatusListList'
          description: ''
  /api/v2/sample-trait-scores/{sample_id}:
    get:
      operationId: sample_trait_scores_list
      parameters:
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedTraitScoreList'
          description: ''
  /api/v2/samples/{sample_id}:
    get:
      operationId: samples_retrieve
      description: Retrieve sample model. Overridden to store audit action.
      parameters:
      - in: path
        name: sample_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - sample
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SampleDetails'
          description: ''
components:
  schemas:
    SampleStatusList:
      type: object
      properties:
        status:
          type: string
        note:
          type: string
        created:
          type: string
          format: date-time
      required:
      - status
    SampleManifest:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        file_name:
          type: string
          maxLength: 256
        file:
          type: string
          readOnly: true
        project:
          type: string
          format: uuid
          readOnly: true
        created:
          type: string
          format: date-time
      required:
      - file
      - file_name
      - id
      - project
    PaginatedGenomicVariantList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/GenomicVariant'
    TraitScore:
      type: object
      description: 'Serializer trait score and associated trait metadata models.


        This is not really optimal, since it pulls data from multiple parent tables

        for objects.'
      properties:
        trait_score:
          $ref: '#/components/schemas/TraitScoreSelfNested'
        trait_distribution:
          $ref: '#/components/schemas/TraitDistribution'
        trait:
          $ref: '#/components/schemas/Trait'
        trait_unit:
          $ref: '#/components/schemas/TraitUnit'
        risk:
          type: string
          nullable: true
          description: "Return risk level for the trait score.\n\nReturns:\n    Optional[str]: \"high_risk\" if the value is greater than or equal to the risk threshold,\n    \"not_high_risk\" otherwise. If the risk threshold or percentile is None, return None."
          readOnly: true
      required:
      - risk
      - trait
      - trait_distribution
      - trait_score
      - trait_unit
    SampleStats:
      type: object
      properties:
        total_size:
          type: integer
      required:
      - total_size
    PaginatedTraitScoreList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/TraitScore'
    TraitUnit:
      type: object
      properties:
        key:
          type: string
          maxLength: 254
      required:
      - key
    SampleKitFormResponse:
      type: object
      description: Response body for ``POST /api/v2/sample-kit-form/``.
      properties:
        sample_id:
          type: string
          format: uuid
          description: UUID of the placeholder ``samples.Sample`` created for the order.
        url:
          type: string
          format: uri
          description: Tokenized kit-order form URL for the end-user.
        expires_at:
          type: string
          format: date-time
          description: When the embedded JWT expires (ISO-8601).
      required:
      - expires_at
      - sample_id
      - url
    ArchiveSampleStatus:
      type: object
      properties:
        id:
          type: string
        status:
          type: string
        created:
          type: string
        transition_cutoff:
          type: string
          format: date-time
          nullable: true
          description: Denotes the transition time for calculated states
      required:
      - created
      - id
      - status
    PaginatedSampleListList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/SampleList'
    SampleStatusNested:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        status:
          type: string
        note:
          type: string
        created:
          type: string
          format: date-time
      required:
      - id
      - status
    PaginatedQualityControlList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/QualityControl'
    AncestrySelfNested:
      type: object
      description: Serializer used to nest ancestry data within other ancestry serializer.
      properties:
        value: {}
    SampleFileNested:
      type: object
      description: 'Sets sample.id as filename in file download_url and skips displaying

        download url if file is not available.'
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        s3_path:
          type: string
          description: S3 object key
          maxLength: 1024
        size:
          type: integer
          maximum: 9223372036854775807
          minimum: -9223372036854775808
          format: int64
          nullable: true
          description: Size as reported by AWS in bytes
        download_url:
          type: string
          format: uri
          readOnly: true
          description: Download url
        file_type:
          type: string
          description: File extension
          readOnly: true
        checksum_sha256:
          type: string
          description: Object's sha256 Checksum
          maxLength: 64
        shadow_mode:
          type: boolean
          nullable: true
          description: If true, file is only accessible by organizations with shadow mode access enabled.
      required:
      - download_url
      - file_type
      - id
    SampleAncestry:
      type: object
      properties:
        ancestry:
          $ref: '#/components/schemas/AncestrySelfNested'
        metadata:
          $ref: '#/components/schemas/AncestryMetadata'
      required:
      - ancestry
      - metadata
    QualityControlSelfNested:
      type: object
      description: Serializer used to nest QC data within other QC serializer.
      properties:
        value_expected:
          type: number
          format: double
          nullable: true
        value_measured:
          type: number
          format: double
          nullable: true
        value_string:
          type: string
          maxLength: 128
        status:
          $ref: '#/components/schemas/QualityControlSelfNestedStatusEnum'
      required:
      - status
    TraitDistribution:
      type: object
      properties:
        value: {}
        version:
          type: string
          maxLength: 100
      required:
      - version
    SampleList:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        run:
          type: string
          format: uuid
          nullable: true
        created:
          type: string
          format: date-time
        hidden:
          type: boolean
          description: Flag to hide the sample.
        modified:
          type: string
          format: date-time
        client_id:
          type: string
          description: 'Legacy: external_id'
          maxLength: 250
        physical_id:
          type: string
          description: 'Legacy: external_id, external_barcode and sample_barcode'
          maxLength: 250
        legacy_id:
          type: string
          description: 'Legacy: sample_id/member_id. Matching sample_ids from back_api app.'
          maxLength: 250
        last_status:
          allOf:
          - $ref: '#/components/schemas/SampleStatusNested'
          readOnly: true
        archive_last_status:
          allOf:
          - $ref: '#/components/schemas/ArchiveSampleStatus'
          readOnly: true
        failed_qc:
          type: string
          readOnly: true
          description: Description of failed_qc status if present
      required:
      - archive_last_status
      - client_id
      - failed_qc
      - id
      - last_status
      - legacy_id
      - modified
      - physical_id
    SampleKit:
      type: object
      description: Serializer for creating kit orders in consumer mode.
      properties:
        project_id:
          type: string
          format: uuid
          writeOnly: true
        metadata:
          writeOnly: true
          nullable: true
        sample_id:
          type: string
          format: uuid
          readOnly: true
        recipient_address_name:
          type: string
          maxLength: 255
        recipient_address_line1:
          type: string
          maxLength: 50
        recipient_address_line2:
          type: string
          maxLength: 50
        recipient_address_line3:
          type: string
          maxLength: 50
        recipient_address_city:
          type: string
          maxLength: 50
        recipient_address_postal_code:
          type: string
          maxLength: 20
        recipient_address_state_region:
          type: string
          maxLength: 50
        recipient_address_country_code:
          $ref: '#/components/schemas/RecipientAddressCountryCodeEnum'
        recipient_phone:
          type: string
          maxLength: 128
        recipient_email:
          type: string
          format: email
          maxLength: 254
        recipient_instructions:
          type: string
          maxLength: 255
        test_mode:
          type: boolean
          default: false
          description: Set to true to create a test order that will not be shipped. Defaults to false.
      required:
      - project_id
      - recipient_address_city
      - recipient_address_country_code
      - recipient_address_line1
      - recipient_address_name
      - recipient_address_postal_code
      - recipient_address_state_region
      - recipient_email
      - recipient_phone
      - sample_id
    PaginatedSampleSheetList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/SampleSheet'
    SampleKitResponse:
      type: object
      properties:
        sample_id:
          type: string
          format: uuid
          readOnly: true
      required:
      - sample_id
    Trait:
      type: object
      properties:
        key:
          type: string
          maxLength: 254
      required:
      - key
    QualityControlSelfNestedStatusEnum:
      enum:
      - succeeded
      - failed
      - skipped
      type: string
      description: '* `succeeded` - succeeded

        * `failed` - failed

        * `skipped` - skipped'
    UploadStatusNested:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        status:
          type: string
        note:
          type: string
        created:
          type: string
          format: date-time
      required:
      - id
      - status
    AncestryMetadata:
      type: object
      properties:
        value: {}
    SampleConsumerReportResponse:
      type: object
      properties:
        url:
          type: string
          format: uri
          description: Presigned URL for accessing the consumer report
        expires_at:
          type: string
          format: date-time
          description: When the presigned URL will expire
      required:
      - expires_at
      - url
    QualityControlType:
      type: object
      properties:
        key:
          type: string
          maxLength: 254
        type:
          type: string
        name:
          type: string
          readOnly: true
        description_markdown:
          type: string
          readOnly: true
        display_type:
          type: string
          readOnly: true
        display_only_if_failed:
          type: string
          readOnly: true
      required:
      - description_markdown
      - display_only_if_failed
      - display_type
      - key
      - name
      - type
    RecipientAddressCountryCodeEnum:
      enum:
      - AF
      - AX
      - AL
      - DZ
      - AS
      - AD
      - AO
      - AI
      - AQ
      - AG
      - AR
      - AM
      - AW
      - AU
      - AT
      - AZ
      - BS
      - BH
      - BD
      - BB
      - BY
      - BE
      - BZ
      - BJ
      - BM
      - BT
      - BO
      - BQ
      - BA
      - BW
      - BV
      - BR
      - IO
      - BN
      - BG
      - BF
      - BI
      - CV
      - KH
      - CM
      - CA
      - KY
      - CF
      - TD
      - CL
      - CN
      - CX
      - CC
      - CO
      - KM
      - CG
      - CD
      - CK
      - CR
      - CI
      - HR
      - CU
      - CW
      - CY
      - CZ
      - DK
      - DJ
      - DM
      - DO
      - EC
      - EG
      - SV
      - GQ
      - ER
      - EE
      - SZ
      - ET
      - FK
      - FO
      - FJ
      - FI
      - FR
      - GF
      - PF
      - TF
      - GA
      - GM
      - GE
      - DE
      - GH
      - GI
      - GR
      - GL
      - GD
      - GP
      - GU
      - GT
      - GG
      - GN
      - GW
      - GY
      - HT
      - HM
      - VA
      - HN
      - HK
      - HU
      - IS
      - IN
      - ID
      - IR
      - IQ
      - IE
      - IM
      - IL
      - IT
      - JM
      - JP
      - JE
      - JO
      - KZ
      - KE
      - KI
      - KW
      - KG
      - LA
      - LV
      - LB
      - LS
      - LR
      - LY
      - LI
      - LT
      - LU
      - MO
      - MG
      - MW
      - MY
      - MV
      - ML
      - MT
      - MH
      - MQ
      - MR
      - MU
      - YT
      - MX
      - FM
      - MD
      - MC
      - MN
      - ME
      - MS
      - MA
      - MZ
      - MM
      - NA
      - NR
      - NP
      - NL
      - NC
      - NZ
      - NI
      - NE
      - NG
      - NU
      - NF
      - KP
      - MK
      - MP
      - 'NO'
      - OM
      - PK
      - PW
      - PS
      - PA
      - PG
      - PY
      - PE
      - PH
      - PN
      - PL
      - PT
      - PR
      - QA
      - RE
      - RO
      - RU
      - RW
      - BL
      - SH
      - KN
      - LC
      - MF
      - PM
      - VC
      - WS
      - SM
      - ST
      - SA
      - SN
      - RS
      - SC
      - SL
      - SG
      - SX
      - SK
      - SI
      - SB
      - SO
      - ZA
      - GS
      - KR
      - SS
      - ES
      - LK
      - SD
      - SR
      - SJ
      - SE
      - CH
      - SY
      - TW
      - TJ
      - TZ
      - TH
      - TL
      - TG
      - TK
      - TO
      - TT
      - TN
      - TR
      - TM
      - TC
      - TV
      - UG
      - UA
      - AE
      - GB
      - UM
      - US
      - UY
      - UZ
      - VU
      - VE
      - VN
      - VG
      - VI
      - WF
      - EH
      - YE
      - ZM
      - ZW
      type: string
      description: '* `AF` - Afghanistan

        * `AX` - Åland Islands

        * `AL` - Albania

        * `DZ` - Algeria

        * `AS` - American Samoa

        * `AD` - Andorra

        * `AO` - Angola

        * `AI` - Anguilla

        * `AQ` - Antarctica

        * `AG` - Antigua and Barbuda

        * `AR` - Argentina

        * `AM` - Armenia

        * `AW` - Aruba

        * `AU` - Australia

        * `AT` - Austria

        * `AZ` - Azerbaijan

        * `BS` - Bahamas

        * `BH` - Bahrain

        * `BD` - Bangladesh

        * `BB` - Barbados

        * `BY` - Belarus

        * `BE` - Belgium

        * `BZ` - Belize

        * `BJ` - Benin

        * `BM` - Bermuda

        * `BT` - Bhutan

        * `BO` - Bolivia

        * `BQ` - Bonaire, Sint Eustatius and Saba

        * `BA` - Bosnia and Herzegovina

        * `BW` - Botswana

        * `BV` - Bouvet Island

        * `BR` - Brazil

        * `IO` - British Indian Ocean Territory

        * `BN` - Brunei

        * `BG` - Bulgaria

        * `BF` - Burkina Faso

        * `BI` - Burundi

        * `CV` - Cabo Verde

        * `KH` - Cambodia

        * `CM` - Cameroon

        * `CA` - Canada

        * `KY` - Cayman Islands

        * `CF` - Central African Republic

        * `TD` - Chad

        * `CL` - Chile

        * `CN` - China

        * `CX` - Christmas Island

        * `CC` - Cocos (Keeling) Islands

        * `CO` - Colombia

        * `KM` - Comoros

        * `CG` - Congo

        * `CD` - Congo (the Democratic Republic of the)

        * `CK` - Cook Islands

        * `CR` - Costa Rica

        * `CI` - Côte d''Ivoire

        * `HR` - Croatia

        * `CU` - Cuba

        * `CW` - Curaçao

        * `CY` - Cyprus

        * `CZ` - Czechia

        * `DK` - Denmark

        * `DJ` - Djibouti

        * `DM` - Dominica

        * `DO` - Dominican Republic

        * `EC` - Ecuador

        * `EG` - Egypt

        * `SV` - El Salvador

        * `GQ` - Equatorial Guinea

        * `ER` - Eritrea

        * `EE` - Estonia

        * `SZ` - Eswatini

        * `ET` - Ethiopia

        * `FK` - Falkland Islands (Malvinas)

        * `FO` - Faroe Islands

        * `FJ` - Fiji

        * `FI` - Finland

        * `FR` - France

        * `GF` - French Guiana

        * `PF` - French Polynesia

        * `TF` - French Southern Territories

        * `GA` - Gabon

        * `GM` - Gambia

        * `GE` - Georgia

        * `DE` - Germany

        * `GH` - Ghana

        * `GI` - Gibraltar

        * `GR` - Greece

        * `GL` - Greenland

        * `GD` - Grenada

        * `GP` - Guadeloupe

        * `GU` - Guam

        * `GT` - Guatemala

        * `GG` - Guernsey

        * `GN` - Guinea

        * `GW` - Guinea-Bissau

        * `GY` - Guyana

        * `HT` - Haiti

        * `HM` - Heard Island and McDonald Islands

        * `VA` - Holy See

        * `HN` - Honduras

        * `HK` - Hong Kong

        * `HU` - Hungary

        * `IS` - Iceland

        * `IN` - India

        * `ID` - Indonesia

        * `IR` - Iran

        * `IQ` - Iraq

        * `IE` - Ireland

        * `IM` - Isle of Man

        * `IL` - Israel

        * `IT` - Italy

        * `JM` - Jamaica

        * `JP` - Japan

        * `JE` - Jersey

        * `JO` - Jordan

        * `KZ` - Kazakhstan

        * `KE` - Kenya

        * `KI` - Kiribati

        * `KW` - Kuwait

        * `KG` - Kyrgyzstan

        * `LA` - Laos

        * `LV` - Latvia

        * `LB` - Lebanon

        * `LS` - Lesotho

        * `LR` - Liberia

        * `LY` - Libya

        * `LI` - Liechtenstein

        * `LT` - Lithuania

        * `LU` - Luxembourg

        * `MO` - Macao

        * `MG` - Madagascar

        * `MW` - Malawi

        * `MY` - Malaysia

        * `MV` - Maldives

        * `ML` - Mali

        * `MT` - Malta

        * `MH` - Marshall Islands

        * `MQ` - Martinique

        * `MR` - Mauritania

        * `MU` - Mauritius

        * `YT` - Mayotte

        * `MX` - Mexico

        * `FM` - Micronesia

        * `MD` - Moldova

        * `MC` - Monaco

        * `MN` - Mongolia

        * `ME` - Montenegro

        * `MS` - Montserrat

        * `MA` - Morocco

        * `MZ` - Mozambique

        * `MM` - Myanmar

        * `NA` - Namibia

        * `NR` - Nauru

        * `NP` - Nepal

        * `NL` - Netherlands

        * `NC` - New Caledonia

        * `NZ` - New Zealand

        * `NI` - Nicaragua

        * `NE` - Niger

        * `NG` - Nigeria

        * `NU` - Niue

        * `NF` - Norfolk Island

        * `KP` - North Korea

        * `MK` - North Macedonia

        * `MP` - Northern Mariana Islands

        * `NO` - Norway

        * `OM` - Oman

        * `PK` - Pakistan

        * `PW` - Palau

        * `PS` - Palestine, State of

        * `PA` - Panama

        * `PG` - Papua New Guinea

        * `PY` - Paraguay

        * `PE` - Peru

        * `PH` - Philippines

        * `PN` - Pitcairn

        * `PL` - Poland

        * `PT` - Portugal

        * `PR` - Puerto Rico

        * `QA` - Qatar

        * `RE` - Réunion

        * `RO` - Romania

        * `RU` - Russia

        * `RW` - Rwanda

        * `BL` - Saint Barthélemy

        * `SH` - Saint Helena, Ascension and Tristan da Cunha

        * `KN` - Saint Kitts and Nevis

        * `LC` - Saint Lucia

        * `MF` - Saint Martin (French part)

        * `PM` - Saint Pierre and Miquelon

        * `VC` - Saint Vincent and the Grenadines

        * `WS` - Samoa

        * `SM` - San Marino

        * `ST` - Sao Tome and Principe

        * `SA` - Saudi Arabia

        * `SN` - Senegal

        * `RS` - Serbia

        * `SC` - Seychelles

        * `SL` - Sierra Leone

        * `SG` - Singapore

        * `SX` - Sint Maarten (Dutch part)

        * `SK` - Slovakia

        * `SI` - Slovenia

        * `SB` - Solomon Islands

        * `SO` - Somalia

        * `ZA` - South Africa

        * `GS` - South Georgia and the South Sandwich Islands

        * `KR` - South Korea

        * `SS` - South Sudan

        * `ES` - Spain

        * `LK` - Sri Lanka

        * `SD` - Sudan

        * `SR` - Suriname

        * `SJ` - Svalbard and Jan Mayen

        * `SE` - Sweden

        * `CH` - Switzerland

        * `SY` - Syria

        * `TW` - Taiwan

        * `TJ` - Tajikistan

        * `TZ` - Tanzania

        * `TH` - Thailand

        * `TL` - Timor-Leste

        * `TG` - Togo

        * `TK` - Tokelau

        * `TO` - Tonga

        * `TT` - Trinidad and Tobago

        * `TN` - Tunisia

        * `TR` - Türkiye

        * `TM` - Turkmenistan

        * `TC` - Turks and Caicos Islands

        * `TV` - Tuvalu

        * `UG` - Uganda

        * `UA` - Ukraine

        * `AE` - United Arab Emirates

        * `GB` - United Kingdom

        * `UM` - United States Minor Outlying Islands

        * `US` - United States of America

        * `UY` - Uruguay

        * `UZ` - Uzbekistan

        * `VU` - Vanuatu

        * `VE` - Venezuela

        * `VN` - Vietnam

        * `VG` - Virgin Islands (British)

        * `VI` - Virgin Islands (U.S.)

        * `WF` - Wallis and Futuna

        * `EH` - Western Sahara

        * `YE` - Yemen

        * `ZM` - Zambia

        * `ZW` - Zimbabwe'
    ReportTypeEnum:
      enum:
      - prs
      type: string
      description: '* `prs` - prs'
    UploadNestedList:
      type: object
      description: Used in sample sheet creation.
      properties:
        upload:
          type: string
          format: uuid
        destination_path:
          type: string
          description: Destination path given by the user as an optional argument
          maxLength: 1024
        last_status:
          allOf:
          - $ref: '#/components/schemas/UploadStatusNested'
          readOnly: true
        source_url:
          type: string
          readOnly: true
      required:
      - last_status
      - source_url
      - upload
    PaginatedSampleStatusListList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/SampleStatusList'
    QualityControl:
      type: object
      properties:
        quality_control_type:
          $ref: '#/components/schemas/QualityControlType'
        quality_control:
          $ref: '#/components/schemas/QualityControlSelfNested'
      required:
      - quality_control
      - quality_control_type
    SampleSheet:
      type: object
      properties:
        client_id:
          type: string
          maxLength: 250
        fastq:
          allOf:
          - $ref: '#/components/schemas/UploadNestedList'
          readOnly: true
          description: Uploaded fastq
      required:
      - client_id
      - fastq
    SampleMetadata:
      type: object
      properties:
        metadata:
          nullable: true
    SampleKitFormCreate:
      type: object
      description: 'Request body for ``POST /api/v2/sample-kit-form/``.


        Mirrors ``ArrayDataUploadFormCreateSerializer`` but is project-scoped: the

        partner names the consumer project the kit''s sample lands in. The end user

        supplies the shipping address later, in the form itself.'
      properties:
        project_id:
          type: string
          format: uuid
          description: UUID of the consumer project to create the kit order in.
        metadata:
          nullable: true
          description: Free-form JSON object stored on the created sample.
        test_mode:
          type: boolean
          default: false
          description: Set to true to create a test order that will not be shipped. Defaults to false.
        redirect_on_success:
          type: string
          format: uri
          default: ''
          description: URL the end-user is redirected to after a successful order.
        redirect_on_failure:
          type: string
          format: uri
          default: ''
          description: URL the end-user is redirected to after a failed order.
        expires_in:
          type: integer
          maximum: 3600
          minimum: 60
          default: 600
          description: JWT lifetime in seconds (default 600, max 3600). Once the URL is opened, a 15-minute session is created that may outlive this token.
      required:
      - project_id
    SampleDetails:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        project:
          type: string
          format: uuid
        run:
          type: string
          format: uuid
          nullable: true
        created:
          type: string
          format: date-time
        modified:
          type: string
          format: date-time
        hidden:
          type: boolean
          description: Flag to hide the sample.
        client_id:
          type: string
          description: 'Legacy: external_id'
          maxLength: 250
        physical_id:
          type: string
          description: 'Legacy: external_id, external_barcode and sample_barcode'
          maxLength: 250
        legacy_id:
          type: string
          description: 'Legacy: sample_id/member_id. Matching sample_ids from back_api app.'
          maxLength: 250
        last_status:
          allOf:
          - $ref: '#/components/schemas/SampleStatusNested'
          readOnly: true
        archive_last_status:
          allOf:
          - $ref: '#/components/schemas/ArchiveSampleStatus'
          readOnly: true
        files:
          type: array
          items:
            $ref: '#/components/schemas/SampleFileNested'
          readOnly: true
          description: Sample files
      required:
      - archive_last_status
      - client_id
      - files
      - id
      - last_status
      - legacy_id
      - modified
      - physical_id
      - project
    TraitScoreSelfNested:
      type: object
      description: Serializer used to nest trait score data within other trait score serializer.
      properties:
        value:
          type: number
          format: double
        percentile:
          type: number
          format: double
          nullable: true
      required:
      - value
    SampleConsumerReportCreate:
      type: object
      properties:
        report_type:
          allOf:
          - $ref: '#/components/schemas/ReportTypeEnum'
          default: prs
          description: 'Type of report to generate


            * `prs` - prs'
        expires_in:
          type: integer
          maximum: 3600
          minimum: 60
          default: 600
          description: Token expiration time in seconds. Note that this value is for the JWT delivered in the URL. Once the URL is accessed, a fixed duration session (15 minutes) is created that may outlive this token
    SampleParentage:
      type: object
      properties:
        parentage_tested:
          type: string
          readOnly: true
        parentage:
          type: string
          readOnly: true
      required:
      - parentage
      - parentage_tested
    GenomicVariant:
      type: object
      description: 'Serializes a `genomic_variants.services.Variant` record.


        `genotype` is an object keyed by the VCF FORMAT field names, e.g.

        `{"GT": "0|0", "DS": "0", "GP": "1,0,0", "RC": "1", "AC": "0", "DP": "1"}`.

        All values are kept as raw strings so the payload mirrors the VCF exactly;

        callers interpret `GT` allele indexes against `alt`.


        `genotype_confidence` is the confidence of the called genotype: the max of

        the `GP` posteriors (the same quantity the VCF''s LOWCONF filter thresholds

        at 0.9), a probability in [0, 1] or null when the record has no `GP` field.'
      properties:
        chromosome:
          type: string
        position:
          type: integer
        rsid:
          type: string
          nullable: true
        ref:
          type: string
        alt:
          type: array
          items:
            type: string
        genotype:
          type: object
          additionalProperties:
            type: string
          nullable: true
        genotype_confidence:
          type: number
          format: double
          nullable: true
        quality:
          type: number
          format: double
          nullable: true
        info:
          type: object
          additionalProperties: {}
      required:
      - alt
      - chromosome
      - genotype
      - genotype_confidence
      - info
      - position
      - quality
      - ref
      - rsid
  securitySchemes:
    API key:
      type: apiKey
      description: 'Authorization header content formated as: `Api-Key <API-key>`

        You can obtain new API key through Gencove''s web UI or `user-api-key` endpoint'
      in: header
      name: Authorization
    JWT:
      type: apiKey
      description: 'Authorization header content formated as: `Bearer <json-web-token>`

        You can obtain access token using `jwt-create` endpoint.'
      in: header
      name: Authorization