Benchling Connect 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 Connect 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: Connect endpoints support Benchling Connect actions, like instrument data conversion.
  name: Connect
paths:
  /connect/convert-to-asm:
    post:
      description: 'Converts an input blob or file containing instrument data to ASM (Allotrope Simple Model) JSON.


        May provide the name of the instrument vendor (see /connect/list-allotropy-vendors) or the ID of a

        connection associated with an instrument vendor.

        '
      operationId: convertToASM
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/ConvertToASM'
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  blobId:
                    type: string
                type: object
          description: Blob ID of a blob containing the converted ASM
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Convert a blob or file containing instrument data to ASM (Allotrope Simple Model) JSON
      tags:
      - Connect
  /connect/convert-to-csv:
    post:
      description: 'Convert a blob or file containing ASM, JSON, or instrument data to CSV.


        If the file is ASM JSON, specify either no transform type (in which case all transform types will be returned),

        a matching transform type for the ASM schema, or a custom JSON mapper config.


        If the file non-ASM JSON, must provide a JSON mapper config argument, which specifies how to map the JSON to CSV.

        Reach out to Benchling Support for more information about how to create a JSON mapper config.


        If the file is an instrument file, must also specify an instrument vendor. The file will be converted first to

        ASM JSON and then to CSV. Only the CSV output will be returned.


        May provide an AutomationOutputFile with CSV transform arguments configured to read the transform type

        or mapper config from.


        May provide a connection ID associated with an instrument to read the vendor from.

        '
      operationId: convertToCSV
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/ConvertToCSV'
      responses:
        '200':
          content:
            application/json:
              schema:
                items:
                  properties:
                    blobId:
                      type: string
                    transformDataType:
                      type: string
                  type: object
                type: array
          description: List of pairs of (transformDataType, blobId) where the blob ID is the ID of a blob containing the converted CSV.
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Convert a blob or file containing ASM, JSON, or instrument data to CSV
      tags:
      - Connect
  /connect/list-allotropy-vendors:
    get:
      description: Returns the list of available allotropy instrument vendor types.
      operationId: listAllotropyVendors
      responses:
        '200':
          content:
            application/json:
              schema:
                items:
                  properties:
                    displayName:
                      type: string
                    id:
                      type: string
                type: array
          description: A list of the available allotropy instrument vendor types.
      summary: Returns the list of available allotropy instrument vendor types
      tags:
      - Connect
components:
  schemas:
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    ConvertToCSV:
      additionalProperties: false
      properties:
        automationOutputFileId:
          description: The ID of an AutomationOutputFile configured to with CSV transform argument. Transform parameters will be read from file settings.
          type: string
        blobOrFileId:
          description: The ID of a blob link or the API ID of a file to process.
          type: string
        connectionId:
          description: The ID of a connection to read the instrument vendor from.
          type: string
        mapperConfig:
          description: A JSON configuration specifying how to convert a JSON file to CSV. Reach out to Benchling Support for more information about how to create a mapperConfig.
          type: string
        transformType:
          description: The transform type to use to convert an ASM file to CSV.
          type: string
        vendor:
          description: The instrument vendor to use for conversion. See /connect/list-allotropy-vendors.
          type: string
      required:
      - blobOrFileId
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    ConvertToASM:
      additionalProperties: false
      properties:
        blobOrFileId:
          description: The ID of a blob link or the API ID of a file to process.
          type: string
        connectionId:
          description: The ID of a connection to read the instrument vendor from.
          type: string
        vendor:
          description: The instrument vendor to use for conversion. See /connect/list-allotropy-vendors.
          type: string
      required:
      - blobOrFileId
      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