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openapi: 3.2.0
info:
license:
name: Apache 2.0
url: http://www.apache.org/licenses/LICENSE-2.0.html
title: Benchling Run API
version: 2.0.0
description: 'A Run represents an execution instance of a lab automation workflow in Benchling, capturing
the inputs, outputs, and metadata for a single assay or instrument operation. Runs conform
to a RunSchema that defines their structure including input generators (see AutomationInputGenerator)
for creating worklists and output processors (see AutomationOutputProcessor) for parsing
instrument results. Runs are typically embedded in notebook entries (via the entry field)
and can generate associated Analyses for data processing. Each run tracks validation status
(VALID or INVALID) with optional comments, enabling quality control workflows. Runs belong
to a Project for access control and can be archived when superseded or invalidated. Also
known as "assay runs" in the lab automation context.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: 'A Run represents an execution instance of a lab automation workflow in Benchling, capturing
the inputs, outputs, and metadata for a single assay or instrument operation. Runs conform
to a RunSchema that defines their structure including input generators (see AutomationInputGenerator)
for creating worklists and output processors (see AutomationOutputProcessor) for parsing
instrument results. Runs are typically embedded in notebook entries (via the entry field)
and can generate associated Analyses for data processing. Each run tracks validation status
(VALID or INVALID) with optional comments, enabling quality control workflows. Runs belong
to a Project for access control and can be archived when superseded or invalidated. Also
known as "assay runs" in the lab automation context.'
name: Run
x-bnch-core-type: Run
x-bnch-organization: Benchling
paths:
/run/items:
get:
description: List Run items.
operationId: Run.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/creator.anyOf'
- $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'
- $ref: '#/components/parameters/schema.anyOf'
- $ref: '#/components/parameters/schema.eq'
- 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/RunPaginatedList'
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 Run items
tags:
- Run
x-bnch-rate-limit-tier: 4
/run/{run_id}:
get:
description: Get a single Run by ID.
operationId: Run.Get
parameters:
- description: ID of the Run.
in: path
name: run_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/Run'
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 Run by ID
tags:
- Run
x-bnch-rate-limit-tier: 5
webhooks:
v3.run.created:
post:
description: Sent to Benchling Apps subscribed to `v3.run.created` when a Run they can access is created.
operationId: Run.Created
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/RunCreatedWebhookEnvelopeV3'
description: The `v3.run.created` event.
required: true
responses:
'200':
description: Return a 200 status code to acknowledge receipt of the webhook.
summary: Run created
tags:
- Run
components:
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
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
creator.anyOf:
description: Restricts results to those created by any of the specified user IDs. Comma-separated list.
explode: false
in: query
name: creator.anyOf
schema:
items:
type: string
maxItems: 100
type: array
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
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
schema.anyOf:
description: Restricts results to those that match any of the specified schema IDs. Use only one `schema` filter arg at a time. Comma-separated list.
explode: false
in: query
name: schema.anyOf
schema:
items:
type: string
maxItems: 100
type: array
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
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
schema.eq:
description: Single schema ID. Restricts results to those that match the specified schema exactly. Use only one `schema` filter arg at a time.
in: query
name: schema.eq
schema:
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
schemas:
IRun:
properties:
__typename:
type: string
archiveReason:
description: If the Run is archived, reason for archiving
type:
- 'null'
- string
archived:
description: Whether the Run is archived
type: boolean
createdAt:
description: DateTime at which the run was created
format: datetime
type:
- 'null'
- string
id:
type: string
isReviewed:
description: Whether this run is in a reviewed entry
type:
- 'null'
- boolean
modifiedAt:
description: DateTime at which the run was last modified
format: datetime
type:
- 'null'
- string
project:
description: Project this run is in
oneOf:
- $ref: '#/components/schemas/ProjectRef'
- type: 'null'
schema:
description: Schema that this run belongs to
oneOf:
- $ref: '#/components/schemas/RunSchemaRef'
- type: 'null'
validationComment:
description: Comment for this run's validation status
type:
- 'null'
- string
validationStatus:
description: Validation status of this run - must be either VALID or INVALID
enum:
- VALID
- INVALID
- null
type:
- 'null'
- string
type: object
DateValue:
description: A type that represents date values.
properties:
__typename:
type: string
value:
description: The date value.
format: date
type: string
type: object
BooleanValue:
description: A type that represents boolean values.
properties:
__typename:
type: string
value:
description: The boolean value.
type: boolean
type: object
WebhookApp:
description: The Benchling App the webhook was delivered to.
properties:
id:
description: API ID of the app.
examples:
- app_1jdbvuo2740aslk
type: string
required:
- id
type: object
ProjectRef:
properties:
__typename:
type: string
id:
format: api_id
type: string
type: object
ObjectLinkValue:
description: A type that represents links to other objects.
properties:
__typename:
type: string
value:
$ref: '#/components/schemas/ObjectRef'
description: The object that this value links to, or an Inaccessible object if not found with the current permission set.
type: object
RunSchemaRef:
properties:
__typename:
type: string
id:
format: api_id
type: string
type: object
SchemaFieldValue:
description: 'Represents a field value on a schematized object, pairing a `fieldDefinition` (describing the
field''s type and constraints) with its actual `value` (a `BenchlingValue` such as text, number,
date, or link to another object). The value may be null if no value has been set. Used within
the `schemaFields` collection on objects that implement `HasSchema` to provide access to all
custom field values defined by the object''s schema.'
properties:
__typename:
type: string
fieldDefinition:
$ref: '#/components/schemas/SchemaFieldDefinitionRef'
id:
type: string
linkedEntityId:
type:
- 'null'
- string
value:
description: Union of BooleanValue, DateTimeValue, DateValue, DecimalValue, IntegerValue, JsonValue, ObjectLinkValue, ObjectLinkListValue, TextAndUrlValue, TextValue, ArrayValue
oneOf:
- anyOf:
- $ref: '#/components/schemas/BooleanValue'
- $ref: '#/components/schemas/DateTimeValue'
- $ref: '#/components/schemas/DateValue'
- $ref: '#/components/schemas/DecimalValue'
- $ref: '#/components/schemas/IntegerValue'
- $ref: '#/components/schemas/JsonValue'
- $ref: '#/components/schemas/ObjectLinkValue'
- $ref: '#/components/schemas/ObjectLinkListValue'
- $ref: '#/components/schemas/TextAndUrlValue'
- $ref: '#/components/schemas/TextValue'
- $ref: '#/components/schemas/ArrayValue'
discriminator:
propertyName: __typename
- type: 'null'
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
DecimalValue:
description: A type that represents decimal value as strings.
properties:
__typename:
type: string
numericValue:
deprecated: true
description: Deprecated. The float representation of the decimal value.
type:
- 'null'
- number
value:
description: The decimal value in a string representation
type:
- 'null'
- string
type: object
ArrayValue:
description: A type that represents a list of BenchlingValues, used for multi-value cells (e.g. alias columns).
properties:
__typename:
type: string
value:
items:
anyOf:
- $ref: '#/components/schemas/BooleanValue'
- $ref: '#/components/schemas/DateTimeValue'
- $ref: '#/components/schemas/DateValue'
- $ref: '#/components/schemas/DecimalValue'
- $ref: '#/components/schemas/IntegerValue'
- $ref: '#/components/schemas/JsonValue'
- $ref: '#/components/schemas/ObjectLinkValue'
- $ref: '#/components/schemas/ObjectLinkListValue'
- $ref: '#/components/schemas/TextAndUrlValue'
- $ref: '#/components/schemas/TextValue'
description: Union of BooleanValue, DateTimeValue, DateValue, DecimalValue, IntegerValue, JsonValue, ObjectLinkValue, ObjectLinkListValue, TextAndUrlValue, TextValue
discriminator:
propertyName: __typename
type: array
type: object
RunCreatedWebhookV3:
allOf:
- $ref: '#/components/schemas/V3EventBase'
- properties:
type:
description: The event type.
enum:
- v3.run.created
type: string
required:
- type
type: object
description: Message body of a `v3.run.created` event.
WebhookAppDefinition:
description: The app definition the receiving app was installed from.
properties:
id:
description: API ID of the app definition.
examples:
- appdef_1jdbvuo2740aslk
type:
- 'null'
- string
versionNumber:
description: Version of the app definition the receiving app is installed at.
examples:
- 0.0.1
type: string
required:
- id
- versionNumber
type: object
RunCreatedWebhookEnvelopeV3:
allOf:
- $ref: '#/components/schemas/WebhookEnvelopeBaseV0'
- properties:
message:
$ref: '#/components/schemas/RunCreatedWebhookV3'
required:
- message
type: object
description: Request body Benchling sends for a `v3.run.created` event.
PrincipalRef:
properties:
__typename:
type: string
id:
format: api_id
type: string
type: object
DocumentLikeRef:
properties:
__typename:
type: string
id:
format: api_id
type: string
type: object
DateTimeValue:
description: A type that represents datetime values.
properties:
__typename:
type: string
value:
description: The datetime value with UTC as the timezone.
format: datetime
type: string
type: object
RunPaginatedList:
additionalProperties: false
properties:
items:
items:
$ref: '#/components/schemas/Run'
type: array
nextToken:
type: string
type: object
ObjectRef:
properties:
__typename:
type: string
id:
format: api_id
type: string
type: object
Run:
allOf:
- $ref: '#/components/schemas/IRun'
- description: 'A Run represents an execution instance of a lab automation workflow in Benchling, capturing
the inputs, outputs, and metadata for a single assay or instrument operation. Runs conform
to a RunSchema that defines their structure including input generators (see AutomationInputGenerator)
for creating worklists and output processors (see AutomationOutputProcessor) for parsing
instrument results. Runs are typically embedded in notebook entries (via the entry field)
and can generate associated Analyses for data processing. Each run tracks validation status
(VALID or INVALID) with optional comments, enabling quality control workflows. Runs belong
to a Project for access control and can be archived when superseded or invalidated. Also
known as "assay runs" in the lab automation context.'
properties:
__typename:
type: string
creator:
description: User who created the run
oneOf:
- $ref: '#/components/schemas/PrincipalRef'
- type: 'null'
entry:
description: Entry that this run is attached to
oneOf:
- $ref: '#/components/schemas/DocumentLikeRef'
- type: 'null'
schemaFields:
description: Schema field values that belong to the run
oneOf:
- items:
$ref: '#/components/schemas/SchemaFieldValue'
type: array
- type: 'null'
type: object
TextValue:
description: A type that represents text (string) values.
properties:
__typename:
type: string
value:
description: The text value. It may or may not be an empty string.
type: string
type: object
V3EventBase:
description: Fields common to every v3 event message.
properties:
createdAt:
description: RFC 3339 timestamp of when the event was created.
format: date-time
type: string
deprecated:
description: Whether this event type is deprecated.
type: boolean
id:
description: API ID of the event.
examples:
- evt_1jdbvuo2740aslk
type: string
resourceId:
description: API ID of the resource the event is about.
examples:
- seq_1jdbvuo2740aslk
type: string
stability:
description: Stability of the resource type the event is about.
enum:
- stable
- beta
type: string
type:
description: The event type.
examples:
- v3.dnaSequence.created
type: string
required:
- id
- type
- createdAt
- resourceId
- stability
- deprecated
type: object
JsonValue:
description: A type that represents JSON values.
properties:
__typename:
type: string
value:
description: The JSON value.
type: object
type: object
TextAndUrlValue:
description: A type that represents text (string) values with an associated URL.
properties:
__typename:
type: string
url:
description: The URL associated with the value. Please use `TextValue` if you don't want a URL.
type: string
value:
description: The text value. It may or may not be an empty string.
type: string
type: object
IntegerValue:
description: A type that represents integer values.
properties:
__typename:
type: string
value:
description: The integer value.
type: integer
type: object
SchemaFieldDefinitionRef:
properties:
__typename:
type: string
id:
format: api_id
type: string
type: object
ObjectLinkListValue:
description: A type that represents a list of links to other objects.
properties:
__typename:
type: string
value:
description: The list of objects that this value links to. Inaccessible objects may be returned instead if the object is not found with the current permission set.
items:
$ref: '#/components/schemas/ObjectRef'
description: Union of AaSequence, Box, Container, CustomEntity, DnaSequence, DropdownOption, Entry, Location, Mixture, Molecule, Plate, Result, RnaSequence, Run, DnaOligo, RnaOligo
type: array
type: object
WebhookEnvelopeBaseV0:
description: Fields common to every webhook request body. The event itself is carried in the `message` property of the event-specific payload.
properties:
app:
$ref: '#/components/schemas/WebhookApp'
appDefinition:
$ref: '#/components/schemas/WebhookAppDefinition'
baseURL:
description: Base URL of the tenant the webhook was sent from.
examples:
- https://mytenant.benchling.com
type: string
tenantId:
description: Global ID of the tenant the webhook was sent from.
examples:
- ten_7fbo183
type: string
version:
description: Version of the webhook envelope shape. Always `0`.
enum:
- '0'
type: string
required:
- version
- baseURL
- tenantId
- app
- appDefinition
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
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