Benchling Automation Step API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Automation Step API
  version: 2.0.0
  description: Represents a single operation node within a Pipeline's directed acyclic graph (DAG). Each step performs a specific transformation determined by its stepType, with configuration stored in the config field. Steps receive data through inputStepDatas and produce results via outputStepDatas (see `AutomationStepData`). The incomingEdges and outgoingEdges (see `AutomationStepEdge`) define data flow connections to other steps. Execution state is tracked through statusCode and statusMessage.
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: Represents a single operation node within a Pipeline's directed acyclic graph (DAG). Each step performs a specific transformation determined by its stepType, with configuration stored in the config field. Steps receive data through inputStepDatas and produce results via outputStepDatas (see `AutomationStepData`). The incomingEdges and outgoingEdges (see `AutomationStepEdge`) define data flow connections to other steps. Execution state is tracked through statusCode and statusMessage.
  name: AutomationStep
  x-bnch-organization: Benchling
  x-displayName: Automation Step
paths:
  /automation-step/{automation_step_id}:
    get:
      description: Get a single AutomationStep by ID.
      operationId: AutomationStep.Get
      parameters:
      - description: ID of the AutomationStep.
        in: path
        name: automation_step_id
        required: true
        schema:
          type: string
      - $ref: '#/components/parameters/returning'
      - $ref: '#/components/parameters/omit'
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AutomationStep'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Get AutomationStep by ID
      tags:
      - AutomationStep
  /automation-step/{automation_step_id}/input-step-datas/items:
    get:
      description: List AutomationStepData items.
      operationId: AutomationStep.inputStepDatas.List
      parameters:
      - description: ID of the AutomationStep.
        in: path
        name: automation_step_id
        required: true
        schema:
          type: string
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AutomationStepDataUnpaginatedList'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: List AutomationStepData items
      tags:
      - AutomationStep
  /automation-step/{automation_step_id}/output-step-datas/items:
    get:
      description: List AutomationStepData items.
      operationId: AutomationStep.outputStepDatas.List
      parameters:
      - description: ID of the AutomationStep.
        in: path
        name: automation_step_id
        required: true
        schema:
          type: string
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AutomationStepDataUnpaginatedList'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: List AutomationStepData items
      tags:
      - AutomationStep
components:
  schemas:
    GeneralError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        invalidId:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    AutomationStep:
      description: Represents a single operation node within a Pipeline's directed acyclic graph (DAG). Each step performs a specific transformation determined by its stepType, with configuration stored in the config field. Steps receive data through inputStepDatas and produce results via outputStepDatas (see `AutomationStepData`). The incomingEdges and outgoingEdges (see `AutomationStepEdge`) define data flow connections to other steps. Execution state is tracked through statusCode and statusMessage.
      properties:
        __typename:
          type: string
        config:
          type:
          - 'null'
          - object
        createdAt:
          format: datetime
          type: string
        id:
          type: string
        inputStepDatas:
          format: uri
          type: string
        modifiedAt:
          format: datetime
          type: string
        outputStepDatas:
          format: uri
          type: string
        pipeline:
          $ref: '#/components/schemas/PipelineRef'
        statusCode:
          enum:
          - AI_PROPOSED
          - BLOCKED
          - FAILED
          - HALTED
          - RUNNING
          - SUCCEEDED
          - WAITING
          type: string
        statusMessage:
          type:
          - 'null'
          - string
        stepType:
          enum:
          - AGGREGATE_DATASET
          - AUTOFILL_ANTIBODY_ELEMENT_SUBELEMENTS
          - ANNOTATE_ANTIBODY_INPUTS
          - ANOVA
          - APPLY_COLUMN_MAPPING
          - BIN_DATA
          - BOLTZ2
          - BOLTZGEN
          - BOLTZGEN_SUCCESS
          - BULK_IMPORT
          - CHAI1
          - CHART_VIEW
          - COMPUTED_COLUMN
          - CONCATENATE_ANTIBODY_COMPONENT_DOMAINS_TO_CHAINS
          - CONNECTION_DATA_DATASET
          - CONVERT_ASM_TO_CSV
          - CONVERT_FILE_TO_DATASET_WITH_DATA_ENTRY_ASSISTANT
          - CONVERT_JSON_TO_DATASET
          - CONVERT_OPENFOLD2_OUTPUT
          - CONVERT_OPENFOLD3_OUTPUT
          - CONVERT_TO_ASM
          - CREATE_DATASET_FROM_FILE
          - CREATE_ENTITIES
          - CREATE_METERING_USAGE_CHART
          - CREATE_PROCEDURE_DATASET
          - DATA_CATALOG_DATASET
          - DATA_CATALOG_FILE
          - DATA_CATALOG_FILES
          - DATASETS_TO_PLATES
          - DATASET_VIEW
          - DEFINE_TEMPLATE_VARIABLES
          - EXPERIMENT_OPTIMIZATION_BOOTSTRAP
          - EXPERIMENT_OPTIMIZATION_CLEAN_DATA
          - EXPERIMENT_OPTIMIZATION_EXPLANATION
          - EXPERIMENT_OPTIMIZATION_GENERATE_SEARCH_SPACE
          - EXPERIMENT_OPTIMIZATION_POSTERIOR_SUMMARY
          - EXPERIMENT_OPTIMIZATION_RECOMMENDATION
          - EXPERIMENT_OPTIMIZATION_TRAINING
          - EXPLORATORY_DATA_ANALYSIS
          - EXPORT_DATA_CATALOG_DATASET
          - EXPORT_DATA_CATALOG_FILE
          - EXTRACT_DATA_FRAME_VALUE
          - EXTRACT_OR_REMOVE_LINES
          - FILL_PLATE
          - FILTER_DATASET
          - FIND_AND_REPLACE
          - FLAG_ROWS
          - FORMAT_COLUMNS
          - GENERATE_ANALYSIS_VIEW_URL
          - GENERATE_BOLTZGEN_YAML
          - GENERATE_BOLTZ_YAML
          - GENERATE_FASTA
          - GENERATE_MODEL_RUN_INPUT
          - GENERATE_OPENFOLD2_JSON
          - GENERATE_OPENFOLD3_JSON
          - HIDE_COLUMNS
          - IMPORT_PLATES
          - IMPORT_SCRATCH_FILE
          - INITIALIZE_DATASET
          - INSERT_RESULT_URL_IN_DOCUMENT
          - INTERPOLATE_MARKDOWN
          - JOIN
          - LAYOUT
          - LEGACY_DATA_IMPORT_ENTRY_CREATION
          - LEGACY_DATA_IMPORT_INITIATION
          - LEGACY_DATA_IMPORT_TRANSCRIPTION
          - LOOK_UP
          - MAP_COLUMNS
          - MAP_JSON_TO_DATASETS_AND_FILES
          - MODEL_RUN_INFERENCE
          - MOVE_INVENTORY_PLATES
          - COMPUTE_NDC_ENTITY_MERGED_COLUMNS
          - NDC_CREATE_PROTEINS_FROM_DATASET
          - NDC_COMBINE_DOMAINS_TO_VARIABLE_PAIRS
          - NDC_EXPAND_VARIABLE_PAIRS_TO_DOMAINS
          - NDC_REFERENCE_EXISTING_COMPONENTS
          - NOTEBOOK_TABLE_DATASET
          - OPENFOLD2
          - OPENFOLD3
          - PARAMETER_OPTIMIZATION_CONFIGURATION
          - PARAMETER_OPTIMIZATION_DATASET_CONFIGURATION
          - PARAMETER_OPTIMIZATION_MODELING
          - PARAMETER_OPTIMIZATION_PREDICTION
          - PIVOT_DATASET
          - PLATE_SCHEMA_DATASET
          - PLATES_TO_DATASETS
          - POSTPROCESS_MODEL_RUN
          - PROCEDURE_RUN_DATA_FRAMES
          - PROMOTE_DATASET
          - REGISTRY_SCHEMA_DATASET
          - PUT_PLATES_IN_INVENTORY
          - REGRESSION
          - REGRESSION_INTERPOLATION
          - RENAME_COLUMNS
          - REORDER_COLUMNS
          - RETYPE_COLUMNS
          - RUN_BENCHLING_BOLTZGEN
          - RUN_HAMILTON_METHOD
          - RUN_HIGHRES_PROTOCOL
          - RUN_OPENTRONS_PROTOCOL
          - RUN_SCIENTIFIC_MODEL
          - RUN_TECAN_METHOD
          - SAVE_STRUCTURE_PREDICTION
          - SAVE_TO_RESULTS
          - SEND_TO_CONNECTION
          - SEND_TO_DOCUMENT
          - SEND_USER_NOTIFICATION
          - SORT_COLUMNS
          - STATIC_TEMPLATE_INPUT_TABLE
          - TABLE_VIEW
          - TEMPLATE_INPUT
          - TEST_ALL_CONFIGS
          - THIRD_PARTY
          - TRANSFER_PLATES
          - TRANSFORM_PROTEIN_BULK_INGEST_OUTPUT_TO_DATASET
          - TRANSLATE_ANTIBODY_COMPONENT_DNA_TO_AA
          - T_TEST
          - UNION_DATASETS
          - UNPIVOT_DATASET
          - UPDATE_ENTITIES
          - UPDATE_INVENTORY_PLATES
          - UPLOAD_CSV_DATASET
          - USER_DEFINED_FUNCTION
          - GENERATE_NDC_ERROR_CSV
          - VALIDATE_AND_TRANSFORM_ANTIBODY_INPUTS
          - VARIABLE_TEMPLATE_INPUT_TABLE
          - WAREHOUSE_SQL_DATASET
          - WINDOW_FUNCTIONS
          type: string
        stepVersion:
          type: integer
      type: object
    ObjectRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    AutomationStepData:
      description: 'Represents actual data attached to an input or output slot of an AutomationStep during execution.

        Each AutomationStepData corresponds to a defined data shape (input or output) on the step''s

        configuration and holds references to the raw data (see `RawStepData`) that fills that slot.

        The name field identifies which data shape this instance fills. Multiple raw data items can

        be attached when the data shape allows multiple values (isMulti). AutomationStepData enables

        data flow between pipeline steps by tracking data lineage and provenance through the

        provenanceUri field.'
      properties:
        __typename:
          type: string
        createdAt:
          format: datetime
          type: string
        id:
          type: string
        modifiedAt:
          format: datetime
          type: string
        name:
          type: string
        parentStep:
          $ref: '#/components/schemas/AutomationStepRef'
        rawDatas:
          items:
            $ref: '#/components/schemas/ObjectRef'
            description: Union of Chart, DataFrame, ScratchFile, PlateRecord
          type: array
      type: object
    InternalServerError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        errorId:
          type: string
        instance:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    AutomationStepDataUnpaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/AutomationStepData'
          type: array
      type: object
    TooManyRequestsError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        invalidId:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    AutomationStepRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    PipelineRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
  parameters:
    omit:
      description: Comma-separated list of top-level fields to omit from each returned item. Cannot overlap with returning.
      explode: false
      in: query
      name: omit
      schema:
        items:
          type: string
        type: array
    returning:
      description: Comma-separated list of top-level fields to include in each returned item. Cannot overlap with omit.
      explode: false
      in: query
      name: returning
      schema:
        items:
          type: string
        type: array
  responses:
    Forbidden:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Forbidden
    BadRequest:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Bad Request
    TooManyRequests:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/TooManyRequestsError'
      description: Too Many Requests
      headers:
        Retry-After:
          description: Minimum number of seconds to wait before retrying. Only included when the request exceeded a rate limit specific to the caller. Limits shared with other callers, such as tenant-wide limits, omit this header because the wait depends on their traffic.
          required: false
          schema:
            minimum: 1
            type: integer
    NotFound:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Not Found
    InternalServerError:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/InternalServerError'
      description: Internal Server Error
  securitySchemes:
    BearerAuth:
      description: Use a short-lived V3 API Explorer token.
      scheme: bearer
      type: http
      x-fern-playground-description: Copy a short-lived V3 API Explorer token from the user's settings page
    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: /oauth/token
      type: oauth2