Benchling Analysis API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Analysis API
  version: 2.0.0
  description: Operations for Analysis
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: Operations for Analysis
  name: Analysis
  x-bnch-organization: Benchling
paths:
  /analysis/items:
    get:
      description: List Analysis items.
      operationId: Analysis.List
      parameters:
      - $ref: '#/components/parameters/archiveReason.anyOf'
      - $ref: '#/components/parameters/archived.anyOf'
      - $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/name.anyOf'
      - $ref: '#/components/parameters/name.anyOf.caseSensitive'
      - $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/AnalysisPaginatedList'
          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 Analysis items
      tags:
      - Analysis
      x-bnch-rate-limit-tier: 4
  /analysis/{analysis_id}:
    get:
      description: Get a single Analysis by ID.
      operationId: Analysis.Get
      parameters:
      - description: ID of the Analysis.
        in: path
        name: analysis_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/Analysis'
          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 Analysis by ID
      tags:
      - Analysis
      x-bnch-rate-limit-tier: 5
  /analysis/{analysis_id}/steps/items:
    get:
      description: List PipelineStep items.
      operationId: Analysis.steps.List
      parameters:
      - description: ID of the Analysis.
        in: path
        name: analysis_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/PipelineStepUnpaginatedList'
          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:
      - Analysis
      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
    AnalysisPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/Analysis'
          type: array
        nextToken:
          type: string
      type: object
    PipelineStepUnpaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/PipelineStep'
          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
    PipelineRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    PrincipalRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    FolderRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    Analysis:
      properties:
        __typename:
          type: string
        archiveReason:
          type:
          - 'null'
          - string
        archived:
          type: boolean
        createdAt:
          format: datetime
          type: string
        creator:
          $ref: '#/components/schemas/PrincipalRef'
        description:
          type:
          - 'null'
          - string
        folder:
          $ref: '#/components/schemas/FolderRef'
        id:
          type: string
        modifiedAt:
          format: datetime
          type: string
        name:
          type: string
        statusCode:
          enum:
          - AI_PROPOSED
          - BLOCKED
          - FAILED
          - HALTED
          - RUNNING
          - SUCCEEDED
          - WAITING
          type: string
        steps:
          format: uri
          type: string
        webUrl:
          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
    archiveReason.anyOf:
      description: Restricts items to those with any of the specified archive reasons. Use "NOT_ARCHIVED" to filter for unarchived items. Use "ANY_ARCHIVED" to filter for archived items regardless of reason. Use "ANY_ARCHIVED_OR_NOT_ARCHIVED" to return items for both archived and unarchived. Comma-separated list.
      explode: false
      in: query
      name: archiveReason.anyOf
      schema:
        items:
          type: string
        maxItems: 10
        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
    archived.anyOf:
      description: If true, returns archived items. If false, returns unarchived items. If both true and false, returns archived and unarchived items. Comma-separated list.
      explode: false
      in: query
      name: archived.anyOf
      schema:
        items:
          type: boolean
        maxItems: 2
        type: array
    nextToken:
      description: Token for pagination
      in: query
      name: nextToken
      schema:
        type: string
    name.anyOf:
      description: Restricts results to those that match any of the specified names. Case insensitive. Warning - this filter can be non-performant due to case insensitivity. Ensure only one name filter is used at a time. Comma-separated list.
      explode: false
      in: query
      name: name.anyOf
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    name.anyOf.caseSensitive:
      description: Restricts results to those that match any of the specified names. Case sensitive. Ensure only one name filter is used at a time. Comma-separated list.
      explode: false
      in: query
      name: name.anyOf.caseSensitive
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    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