Benchling Pipeline Step API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Pipeline 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 (see `PipelineStepType`),

    with configuration options stored in the config field. Steps receive data through

    inputStepDatas and produce results via outputStepDatas (see `PipelineStepData`). The

    incomingEdges and outgoingEdges (see `PipelineStepEdge`) define the data flow connections

    to other steps. Execution state is tracked through statusCode and statusMessage. Steps

    support provenance tracking through the provenanceUri field for tracing data lineage.'
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 (see `PipelineStepType`),

    with configuration options stored in the config field. Steps receive data through

    inputStepDatas and produce results via outputStepDatas (see `PipelineStepData`). The

    incomingEdges and outgoingEdges (see `PipelineStepEdge`) define the data flow connections

    to other steps. Execution state is tracked through statusCode and statusMessage. Steps

    support provenance tracking through the provenanceUri field for tracing data lineage.'
  name: PipelineStep
  x-bnch-organization: Benchling
paths:
  /pipeline-step/items:
    get:
      description: List PipelineStep items.
      operationId: PipelineStep.List
      parameters:
      - $ref: '#/components/parameters/createdAt.gt'
      - $ref: '#/components/parameters/createdAt.gte'
      - $ref: '#/components/parameters/createdAt.lt'
      - $ref: '#/components/parameters/createdAt.lte'
      - $ref: '#/components/parameters/id.anyOf'
      - $ref: '#/components/parameters/modifiedAt.gt'
      - $ref: '#/components/parameters/modifiedAt.gte'
      - $ref: '#/components/parameters/modifiedAt.lt'
      - $ref: '#/components/parameters/modifiedAt.lte'
      - $ref: '#/components/parameters/nextToken'
      - $ref: '#/components/parameters/omit'
      - $ref: '#/components/parameters/pageSize'
      - $ref: '#/components/parameters/returning'
      - description: 'Method by which to order results. Valid sorts are: createdAt (created time, oldest first) and modifiedAt (modified time, oldest first). Use :asc or :desc to specify ascending or descending order. Default is modifiedAt:desc.'
        in: query
        name: sort
        schema:
          default: modifiedAt:desc
          enum:
          - createdAt:asc
          - createdAt:desc
          - modifiedAt:asc
          - modifiedAt:desc
          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/PipelineStepPaginatedList'
          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 PipelineStep items
      tags:
      - PipelineStep
      x-bnch-rate-limit-tier: 4
  /pipeline-step/{pipeline_step_id}:
    get:
      description: Get a single PipelineStep by ID.
      operationId: PipelineStep.Get
      parameters:
      - description: ID of the PipelineStep.
        in: path
        name: pipeline_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/PipelineStep'
          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 PipelineStep by ID
      tags:
      - PipelineStep
      x-bnch-rate-limit-tier: 5
  /pipeline-step/{pipeline_step_id}/input-step-datas/items:
    get:
      description: List PipelineStepData items.
      operationId: PipelineStep.inputStepDatas.List
      parameters:
      - description: ID of the PipelineStep.
        in: path
        name: pipeline_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/PipelineStepDataUnpaginatedList'
          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 PipelineStepData items
      tags:
      - PipelineStep
      x-bnch-rate-limit-tier: 4
  /pipeline-step/{pipeline_step_id}/output-step-datas/items:
    get:
      description: List PipelineStepData items.
      operationId: PipelineStep.outputStepDatas.List
      parameters:
      - description: ID of the PipelineStep.
        in: path
        name: pipeline_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/PipelineStepDataUnpaginatedList'
          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 PipelineStepData items
      tags:
      - PipelineStep
      x-bnch-rate-limit-tier: 4
components:
  schemas:
    PipelineStep:
      description: 'Represents a single operation node within a Pipeline''s directed acyclic graph (DAG). Each

        step performs a specific transformation determined by its stepType (see `PipelineStepType`),

        with configuration options stored in the config field. Steps receive data through

        inputStepDatas and produce results via outputStepDatas (see `PipelineStepData`). The

        incomingEdges and outgoingEdges (see `PipelineStepEdge`) define the data flow connections

        to other steps. Execution state is tracked through statusCode and statusMessage. Steps

        support provenance tracking through the provenanceUri field for tracing data lineage.'
      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
          - DATASET_VIEW
          - DATA_CATALOG_DATASET
          - DATA_CATALOG_FILE
          - DATA_CATALOG_FILES
          - 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_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
          - REGISTER_PLATES_IN_INVENTORY
          - REGRESSION
          - REGRESSION_INTERPOLATION
          - RENAME_COLUMNS
          - REORDER_COLUMNS
          - RETYPE_COLUMNS
          - RUN_HAMILTON_METHOD
          - RUN_HIGHRES_PROTOCOL
          - RUN_OPENTRONS_PROTOCOL
          - 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
          - 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
    PipelineStepPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/PipelineStep'
          type: array
        nextToken:
          type: string
      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
    PipelineStepData:
      description: 'Represents actual data attached to an input or output slot of a PipelineStep during execution.

        Each PipelineStepData 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). PipelineStepData 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/PipelineStepRef'
        rawDatas:
          items:
            $ref: '#/components/schemas/ObjectRef'
            description: Union of Chart, DataFrame, ScratchFile, ScratchPlate
          type: array
      type: object
    PipelineRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    PipelineStepRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    PipelineStepDataUnpaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/PipelineStepData'
          type: array
      type: object
    ObjectRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    GeneralError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
  parameters:
    pageSize:
      description: Number of results to return. Defaults to 50, maximum of 100.
      in: query
      name: pageSize
      schema:
        type: integer
    createdAt.gte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or after the specified time. e.g. >= 2017-04-30.
      in: query
      name: createdAt.gte
      schema:
        format: datetime
        type: string
    modifiedAt.gt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified after the specified time. e.g. > 2017-04-30.
      in: query
      name: modifiedAt.gt
      schema:
        format: datetime
        type: string
    modifiedAt.lte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or before the specified time. e.g. <= 2017-04-30.
      in: query
      name: modifiedAt.lte
      schema:
        format: datetime
        type: string
    id.anyOf:
      description: Restricts results to those matching any of the specified IDs. Comma-separated list.
      explode: false
      in: query
      name: id.anyOf
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    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
    modifiedAt.lt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified before the specified time. e.g. < 2017-04-30.
      in: query
      name: modifiedAt.lt
      schema:
        format: datetime
        type: string
    createdAt.gt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created after the specified time. e.g. > 2017-04-30.
      in: query
      name: createdAt.gt
      schema:
        format: datetime
        type: string
    createdAt.lt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created before the specified time. e.g. < 2017-04-30.
      in: query
      name: createdAt.lt
      schema:
        format: datetime
        type: string
    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
    nextToken:
      description: Token for pagination
      in: query
      name: nextToken
      schema:
        type: string
    modifiedAt.gte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or after the specified time. e.g. >= 2017-04-30.
      in: query
      name: modifiedAt.gte
      schema:
        format: datetime
        type: string
    createdAt.lte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or before the specified time. e.g. <= 2017-04-30.
      in: query
      name: createdAt.lte
      schema:
        format: datetime
        type: string
  responses:
    NotFound:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Not Found
    TooManyRequests:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Too Many Requests
    BadRequest:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Bad Request
    Forbidden:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Forbidden
    InternalServerError:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/InternalServerError'
      description: Internal Server Error
  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: /oauth/token
      type: oauth2