Benchling Assay Runs API

openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences Assay Runs API
  version: 2.0.0
  description: 'AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised of a string of amino acids and collections of other attributes, such as annotations.

    '
servers:
- url: /api/v2
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: Runs capture the details / parameters of a run that was performed. Results are usually nested under a run.
  name: Assay Runs
paths:
  /assay-runs:
    get:
      description: List runs
      operationId: listAssayRuns
      parameters:
      - description: ID of the assay run schema to filter by
        in: query
        name: schemaId
        required: true
        schema:
          type: string
      - description: Filter by runs created after this unix timestamp
        in: query
        name: minCreatedTime
        schema:
          type: integer
      - description: Filter by runs created before this unix timestamp
        in: query
        name: maxCreatedTime
        schema:
          type: integer
      - description: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      - description: Number of results to return. Defaults to 50, maximum of 100.
        in: query
        name: pageSize
        schema:
          default: 50
          maximum: 100
          minimum: 0
          nullable: false
          type: integer
      - description: 'Comma-separated list of ids. Matches all of the provided IDs, or returns a 400 error that includes a list of which IDs are invalid.

          '
        in: query
        name: ids
        schema:
          format: uuid
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRunsPaginatedList'
          description: OK
      summary: List runs
      tags:
      - Assay Runs
    post:
      description: Create 1 or more runs.
      operationId: createAssayRuns
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayRunsBulkCreateRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRunsBulkCreateResponse'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRunsBulkCreateErrorResponse'
          description: Bad Request
      summary: Create 1 or more runs.
      tags:
      - Assay Runs
  /assay-runs/{assay_run_id}:
    get:
      description: Get a run
      operationId: getAssayRun
      parameters:
      - in: path
        name: assay_run_id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRun'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Get a run
      tags:
      - Assay Runs
    patch:
      description: Update a run
      operationId: updateAssayRun
      parameters:
      - description: ID of the Run to be updated
        in: path
        name: assay_run_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayRunUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRun'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Update a run
      tags:
      - Assay Runs
  /assay-runs/{assay_run_id}/automation-input-generators:
    get:
      description: list AutomationInputGenerators by Run
      operationId: listAutomationInputGenerators
      parameters:
      - in: path
        name: assay_run_id
        required: true
        schema:
          type: string
      - description: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      - description: 'Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30. Date ranges can be specified with the following nomenclature > YYYY-MM-DD AND <YYYY-MM-DD.

          '
        examples:
          and-range:
            summary: Filter for all models modified within a certain range using the AND operator.
            value: '> 2022-03-01 AND < 2022-04-01'
          full-rfc-3339-format:
            summary: Filter for modified models using the full RFC 3339 format
            value: '> 2020-12-31T21:07:14-05:00'
          greater-than-example:
            summary: Filter for all models modified after a certain date
            value: '> 2022-03-01'
        in: query
        name: modifiedAt
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AutomationFileInputsPaginatedList'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: list AutomationInputGenerators by Run
      tags:
      - Assay Runs
  /assay-runs/{assay_run_id}/automation-output-processors:
    get:
      deprecated: true
      description: Deprecated in favor of '/automation-output-processors'. For each output config in the run config, will create an empty automationOutputProcessor for the run if one doesn't exist.
      operationId: listAutomationOutputProcessorsDeprecated
      parameters:
      - in: path
        name: assay_run_id
        required: true
        schema:
          type: string
      - description: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DeprecatedAutomationOutputProcessorsPaginatedList'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: list AutomationOutputProcessors by Run
      tags:
      - Assay Runs
  /assay-runs:archive:
    post:
      description: Archive assay runs that are not embedded in a notebook entry
      operationId: archiveAssayRuns
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayRunsArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRunsArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive Assay Runs
      tags:
      - Assay Runs
  /assay-runs:bulk-get:
    get:
      description: Bulk get runs by ID
      operationId: bulkGetAssayRuns
      parameters:
      - description: Comma-separated list of assay run IDs
        in: query
        name: assayRunIds
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRunsBulkGet'
          description: OK
      summary: Bulk get runs by ID
      tags:
      - Assay Runs
  /assay-runs:unarchive:
    post:
      description: Unarchive assay runs
      operationId: unarchiveAssayRuns
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayRunsUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayRunsArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive Assay Runs
      tags:
      - Assay Runs
components:
  schemas:
    SchemaSummary:
      properties:
        id:
          type: string
        name:
          type: string
      type: object
    Fields:
      additionalProperties:
        $ref: '#/components/schemas/Field'
      type: object
    LabAutomationTransform:
      properties:
        apiURL:
          description: The canonical url of the transform in the API.
          format: uri
          readOnly: true
          type: string
        blobId:
          format: uuid
          nullable: true
          type: string
        customTransformId:
          format: uuid
          nullable: true
          type: string
        errors:
          $ref: '#/components/schemas/LabAutomationBenchlingAppErrors'
        id:
          type: string
        inputGeneratorId:
          nullable: true
          type: string
        modifiedAt:
          description: DateTime the transform was last modified.
          format: date-time
          readOnly: true
          type: string
        outputProcessorId:
          nullable: true
          type: string
        status:
          enum:
          - NOT_STARTED
          - RUNNING
          - FAILED
          - SUCCEEDED
          type: string
      type: object
    Blob:
      properties:
        id:
          description: The universally unique identifier (UUID) for the blob.
          example: c33fe52d-fe6a-4c98-adcd-211bdf6778f7
          format: uuid
          type: string
        mimeType:
          description: eg. application/jpeg
          example: text/csv
          maxLength: 100
          type: string
        name:
          description: Name of the blob
          example: MyInstrumentInputFile.csv
          maxLength: 1000
          type: string
        type:
          description: 'One of RAW_FILE or VISUALIZATION. If VISUALIZATION, the blob may be displayed as an image preview.

            '
          enum:
          - RAW_FILE
          - VISUALIZATION
          type: string
        uploadStatus:
          enum:
          - IN_PROGRESS
          - COMPLETE
          - ABORTED
          type: string
      type: object
    AssayRunsBulkCreateRequest:
      additionalProperties: false
      properties:
        assayRuns:
          items:
            $ref: '#/components/schemas/AssayRunCreate'
          type: array
      required:
      - assayRuns
      type: object
    AssayRunsArchive:
      additionalProperties: false
      description: 'The request body for archiving Assay Runs.

        '
      properties:
        assayRunIds:
          items:
            type: string
          type: array
        reason:
          description: 'The reason for archiving the provided Assay Runs. Accepted reasons may differ based on tenant configuration.

            '
          enum:
          - Archived
          - Made in error
          - Other
          type: string
      required:
      - reason
      - assayRunIds
      type: object
    AutomationOutputProcessor:
      allOf:
      - $ref: '#/components/schemas/AutomationFile'
      - properties:
          apiURL:
            description: The canonical url of the Automation Output Processor in the API.
            example: https://benchling.com/api/v2/automation-output-processors/aop_C3wGA9HF
            format: uri
            readOnly: true
            type: string
          archiveRecord:
            allOf:
            - $ref: '#/components/schemas/ArchiveRecord'
            nullable: true
          completeWithErrors:
            description: Specifies whether file processing should complete with errors. False means any error in output file processing will result in no actions being committed. True means that if row-level errors occur, then failing rows and their errors will be saved to errorFile, and actions from successful rows will be committed.
            type: boolean
          createdAt:
            description: DateTime the Automation Output Processor was created
            format: date-time
            type: string
          errorFile:
            allOf:
            - $ref: '#/components/schemas/Blob'
            nullable: true
          id:
            example: aop_C3wGA9HF
            type: string
          modifiedAt:
            description: DateTime the Automation Output Processor was last modified
            format: date-time
            type: string
          progressStats:
            $ref: '#/components/schemas/AutomationProgressStats'
          transforms:
            items:
              allOf:
              - $ref: '#/components/schemas/LabAutomationTransform'
              nullable: true
            type: array
        type: object
    AssayRunsArchivalChange:
      description: 'IDs of all Assay Runs that were archived / unarchived.

        '
      properties:
        assayRunIds:
          items:
            type: string
          type: array
      type: object
    AssayRunValidationStatus:
      description: Must be either VALID or INVALID
      enum:
      - VALID
      - INVALID
      type: string
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    DeprecatedAutomationOutputProcessorsPaginatedList:
      description: Deprecated - A paginated list of automation output processors
      properties:
        automationOutputProcessors:
          items:
            $ref: '#/components/schemas/AutomationOutputProcessor'
          type: array
        nextToken:
          example: Im5ldyB0ZXN0Ig==
          type: string
      type: object
    AssayRunUpdate:
      additionalProperties: false
      properties:
        equipmentId:
          description: The equipment that the assay run should be associated with.  This attribute is only supported if the equipment feature is enabled for the tenant; otherwise, supplying it leads to a 400 request error
          nullable: true
          type: string
        fields:
          $ref: '#/components/schemas/Fields'
      type: object
    FieldType:
      enum:
      - dna_sequence_link
      - aa_sequence_link
      - custom_entity_link
      - entity_link
      - mixture_link
      - molecule_link
      - dropdown
      - part_link
      - translation_link
      - aa_part_link
      - base_molecule_link
      - blob_link
      - text
      - long_text
      - batch_link
      - storage_link
      - entry_link
      - assay_request_link
      - assay_result_link
      - assay_run_link
      - boolean
      - float
      - integer
      - datetime
      - date
      - json
      type: string
    UserSummary:
      allOf:
      - $ref: '#/components/schemas/PartySummary'
      - example:
          handle: lpasteur
          id: ent_a0SApq3z
          name: Louis Pasteur
    AssayFieldsCreate:
      additionalProperties: true
      type: object
    AssayRunCreate:
      properties:
        fields:
          anyOf:
          - $ref: '#/components/schemas/Fields'
          - $ref: '#/components/schemas/AssayFieldsCreate'
          description: Object of assay run fields
        id:
          description: ID of assay run
          type: string
        projectId:
          description: 'The project that the assay run should be uploaded to. Only users with read access to the project will be able to read the assay run. Leaving this empty will result in only the creator having read access.

            '
          type: string
        schemaId:
          description: ID of assay schema that assay run conforms to
          type: string
        validationComment:
          description: Additional information about the validation status
          type: string
        validationStatus:
          $ref: '#/components/schemas/AssayRunValidationStatus'
      required:
      - schemaId
      - fields
      type: object
    AssayRunsPaginatedList:
      properties:
        assayRuns:
          items:
            $ref: '#/components/schemas/AssayRun'
          type: array
        nextToken:
          type: string
      type: object
    Field:
      properties:
        displayValue:
          nullable: true
          readOnly: true
          type: string
        isMulti:
          readOnly: true
          type: boolean
        textValue:
          example: Amp
          nullable: true
          readOnly: true
          type: string
        type:
          allOf:
          - $ref: '#/components/schemas/FieldType'
          readOnly: true
        value:
          description: 'For single link fields, use the id of the item you want to link (eg. "seq_jdf8BV24").

            For multi-link fields, use an array of ids of the items you want to link (eg. ["seq_jdf8BV24"])

            '
          nullable: true
          oneOf:
          - type: string
          - type: boolean
          - type: number
          - type: object
          - items:
              type: string
            type: array
      required:
      - value
      type: object
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    AutomationProgressStats:
      description: Processing progress information.
      properties:
        rowsFailed:
          type: integer
        rowsSucceeded:
          type: integer
        rowsUnprocessed:
          type: integer
      type: object
    AssayRun:
      properties:
        apiURL:
          description: The canonical url of the Run in the API.
          example: https://benchling.com/api/v2/assay-runs/21f50003-0389-4b2a-9293-a17967b85961
          format: uri
          readOnly: true
          type: string
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          nullable: true
        createdAt:
          example: '2021-05-06T13:43:25.752597+00:00'
          type: string
        creator:
          $ref: '#/components/schemas/UserSummary'
        entryId:
          example: etr_Hds1XAaq
          nullable: true
          type: string
        equipmentId:
          example: eqpt_XzU5p4dR
          nullable: true
          type: string
        fields:
          $ref: '#/components/schemas/Fields'
        id:
          example: 77af3205-65af-457f-87f5-75462b85075a
          type: string
        isReviewed:
          type: boolean
        projectId:
          example: src_YzU5p4dR
          nullable: true
          type: string
        schema:
          allOf:
          - $ref: '#/components/schemas/SchemaSummary'
          example:
            id: assaysch_fFLKmdmG
            name: Assay Run
          nullable: true
          title: SchemaProperty
        v3Id:
          description: V3 identifier for the run
          example: run_21f50003
          readOnly: true
          type: string
        validationComment:
          example: Reported valid with no caveats
          nullable: true
          type: string
        validationStatus:
          $ref: '#/components/schemas/AssayRunValidationStatus'
      type: object
    LabAutomationBenchlingAppErrors:
      properties:
        topLevelErrors:
          items:
            properties:
              errorMessage:
                type: string
            type: object
          type: array
      type: object
    AutomationFileInputsPaginatedList:
      properties:
        automationInputGenerators:
          items:
            $ref: '#/components/schemas/AutomationInputGenerator'
          type: array
        nextToken:
          example: Im5ldyB0ZXN0Ig==
          type: string
      type: object
    AssayRunsUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving Assay Runs.

        '
      properties:
        assayRunIds:
          items:
            type: string
          type: array
      required:
      - assayRunIds
      type: object
    AssayRunsBulkCreateResponse:
      properties:
        assayRuns:
          items:
            type: string
          type: array
        errors:
          default: null
          nullable: true
          type: object
      type: object
    AutomationFile:
      properties:
        assayRunId:
          example: 588aca02-1a20-4b94-a40f-b3f3a0081749
          type: string
        automationFileConfig:
          properties:
            name:
              example: MyInstrumentName
              type: string
          type: object
        file:
          allOf:
          - $ref: '#/components/schemas/Blob'
          nullable: true
        id:
          type: string
        status:
          enum:
          - SUCCEEDED
          - FAILED
          - NOT_STARTED
          - RUNNING
          type: string
      type: object
    AutomationInputGenerator:
      allOf:
      - $ref: '#/components/schemas/AutomationFile'
      - properties:
          apiURL:
            description: The canonical url of the Automation Input Generator in the API.
            example: https://benchling.com/api/v2/automation-input-generators/aif_C3wGA9HF
            format: uri
            readOnly: true
            type: string
          createdAt:
            description: DateTime the Automation Input Generator was last modified
            format: date-time
            readOnly: true
            type: string
          id:
            example: aif_C3wGA9HF
            type: string
          modifiedAt:
            description: DateTime the Automation Input Generator was last modified
            format: date-time
            readOnly: true
            type: string
          transforms:
            items:
              allOf:
              - $ref: '#/components/schemas/LabAutomationTransform'
              nullable: true
            type: array
        type: object
    AssayRunsBulkCreateErrorResponse:
      properties:
        assayRuns:
          default: null
          items:
            type: object
          nullable: true
          type: array
        errors:
          items:
            properties:
              fields:
                type: object
              global:
                items:
                  type: string
                type: array
            type: object
          type: array
      type: object
    AssayRunsBulkGet:
      properties:
        assayRuns:
          items:
            $ref: '#/components/schemas/AssayRun'
          type: array
      type: object
  securitySchemes:
    basicApiKeyAuth:
      description: Use issued API key for standard access to the API
      scheme: basic
      type: http
    basicClientIdSecretAuth:
      description: Auth used as part of client credentials OAuth flow prior to receiving a bearer token.
      scheme: basic
      type: http
    oAuth:
      description: OAuth2 Client Credentials flow intended for service access
      flows:
        clientCredentials:
          scopes: {}
          tokenUrl: /api/v2/token
      type: oauth2
externalDocs:
  description: Additional API Documentation
  url: https://docs.benchling.com