Benchling Assay Results 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 Assay Results 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: '

    Results represent the output of assays that have been performed. You can customize the schemas of results to fit your needs. Results can link to runs, entities, and other types.


    To learn more about creating results, [click here](https://docs.benchling.com/docs/example-creating-results).

    '
  name: Assay Results
paths:
  /assay-results:
    get:
      description: List results
      operationId: listAssayResults
      parameters:
      - description: ID of the assay result schema to filter by
        in: query
        name: schemaId
        required: false
        schema:
          type: string
      - 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:
          type: string
      - 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:
          type: string
      - description: 'Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created on or before the specified time. e.g. <= 2017-04-30.

          '
        in: query
        name: createdAt.lte
        schema:
          type: string
      - description: 'Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created on or after the specified time. e.g. >= 2017-04-30.

          '
        in: query
        name: createdAt.gte
        schema:
          type: string
      - deprecated: true
        description: Filter by results created after this unix timestamp
        in: query
        name: minCreatedTime
        schema:
          type: integer
      - deprecated: true
        description: Filter by results created before this unix timestamp
        in: query
        name: maxCreatedTime
        schema:
          type: integer
      - description: 'Method by which to order search results. Valid sorts are createdAt (created time, oldest first). Use :asc or :desc to specify ascending or descending order. Default is createdAt:asc.

          '
        in: query
        name: sort
        schema:
          default: createdAt:asc
          enum:
          - createdAt:asc
          - createdAt:desc
          - modifiedAt:asc
          - modifiedAt:desc
          nullable: false
          type: string
      - description: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      - description: Number of results to return. Defaults to 50, maximum of 100.
        in: query
        name: pageSize
        schema:
          default: 50
          maximum: 100
          minimum: 0
          nullable: false
          type: integer
      - description: Filter by comma-separated list of related Entity IDs, maximum of 20.
        in: query
        name: entityIds
        schema:
          type: string
      - description: 'Filter by comma-separated list of related inventory (container, box, plate, or location) IDs, maximum of 20.

          '
        in: query
        name: storageIds
        schema:
          type: string
      - description: Filter by comma-separated list of associated AssayRun IDs. At most one of {assayRunIds, automationOutputProcessorId} may be supplied.
        in: query
        name: assayRunIds
        schema:
          type: string
      - description: Filter by Automation Output Processor ID. Either this or schemaId is required; if both are given, the associated schemas must match. At most one of {assayRunIds, automationOutputProcessorId} may be supplied.
        in: query
        name: automationOutputProcessorId
        schema:
          type: string
      - description: 'Comma-separated list of ids. Matches all of the provided IDs, or returns a 400 error that includes a list of which IDs are invalid.

          '
        in: query
        name: ids
        schema:
          format: uuid
          type: string
      - 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:
          type: string
      - 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:
          type: string
      - description: 'Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified on or before the specified time. e.g. <= 2017-04-30.

          '
        in: query
        name: modifiedAt.lte
        schema:
          type: string
      - description: 'Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified on or after the specified time. e.g. >= 2017-04-30.

          '
        in: query
        name: modifiedAt.gte
        schema:
          type: string
      - description: 'Archive reason. Restricts items to those with the specified archive reason. Use "NOT_ARCHIVED" to filter for unarchived Assay Results. Use "ANY_ARCHIVED" to filter for archived Assay Results regardless of reason. Use "ANY_ARCHIVED_OR_NOT_ARCHIVED" to return items for both archived and unarchived.

          '
        examples:
          1_not_archived:
            summary: Only include unarchived items (default).
            value: NOT_ARCHIVED
          2_archived_reason:
            summary: Includes items archived for a specific reason.
            value: Retired
          3_any_archived:
            summary: Includes items archived for any reason.
            value: ANY_ARCHIVED
          4_any_archived_or_not_archived:
            summary: Includes both archived and unarchived items.
            value: ANY_ARCHIVED_OR_NOT_ARCHIVED
        in: query
        name: archiveReason
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultsPaginatedList'
          description: OK
      summary: List results
      tags:
      - Assay Results
    post:
      description: 'Create 1 or more results.

        If you are looking to add results to a specific table in a notebook entry, please use the  [assay-results bulk-create](#/Assay%20Results/bulkCreateAssayResults) endpoint instead.

        '
      operationId: createAssayResults
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayResultsBulkCreateRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultsCreateResponse'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create 1 or more results.
      tags:
      - Assay Results
  /assay-results/{assay_result_id}:
    get:
      description: Get a result
      operationId: getAssayResult
      parameters:
      - in: path
        name: assay_result_id
        required: true
        schema:
          format: uuid
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResult'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Get a result
      tags:
      - Assay Results
  /assay-results:archive:
    post:
      description: 'Results that have been added to a Legacy Result or Legacy Run table in a Notebook Entry **cannot** be Archived.

        '
      operationId: archiveAssayResults
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayResultsArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultIdsResponse'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive 1 or more results.
      tags:
      - Assay Results
  /assay-results:bulk-create:
    post:
      description: Bulk create results. Limit of 4000 results per request.
      operationId: bulkCreateAssayResults
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayResultsBulkCreateInTableRequest'
      responses:
        '202':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AsyncTaskLink'
          description: 'This endpoint launches a [long-running task](#/Tasks/getTask) and returns the Task ID of the launched task. The task response contains the full list of results that were created.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk create results
      tags:
      - Assay Results
  /assay-results:bulk-get:
    get:
      description: Up to 200 IDs can be specified at once.
      operationId: bulkGetAssayResults
      parameters:
      - description: Comma-separated list of assay result IDs.
        in: query
        name: assayResultIds
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultsBulkGet'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Gets multiple results specified by a list of IDs.
      tags:
      - Assay Results
  /assay-results:unarchive:
    post:
      description: Unarchive 1 or more results.
      operationId: unarchiveAssayResults
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayResultIdsRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultIdsResponse'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive 1 or more results.
      tags:
      - Assay Results
  /result-transactions:
    post:
      description: 'Transactions allow results to be upload in multiple requests. This endpoint lets you create a transaction. You can then upload results to the transaction, abort the transaction, or commit the transaction.

        '
      operationId: createAssayResultsTransaction
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultTransactionCreateResponse'
          description: OK
      summary: Create a transaction
      tags:
      - Assay Results
  /result-transactions/{transaction_id}/results:
    post:
      description: Create results in a transaction
      operationId: createAssayResultsInTransaction
      parameters:
      - in: path
        name: transaction_id
        required: true
        schema:
          format: uuid
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AssayResultsBulkCreateRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultsCreateResponse'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultsCreateErrorResponse'
          description: Bad Request
      summary: Create results in a transaction
      tags:
      - Assay Results
  /result-transactions/{transaction_id}:abort:
    post:
      description: Aborting a transaction will discard all uploaded results.
      operationId: abortAssayResultsTransaction
      parameters:
      - in: path
        name: transaction_id
        required: true
        schema:
          format: uuid
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultTransactionCreateResponse'
          description: OK
      summary: Abort a transaction
      tags:
      - Assay Results
  /result-transactions/{transaction_id}:commit:
    post:
      description: Committing a transaction will cause all results that have been uploaded to be saved and visible to others.
      operationId: commitAssayResultsTransaction
      parameters:
      - in: path
        name: transaction_id
        required: true
        schema:
          format: uuid
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AssayResultTransactionCreateResponse'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Commit a transaction
      tags:
      - Assay Results
components:
  schemas:
    AssayResultIdsRequest:
      additionalProperties: false
      properties:
        assayResultIds:
          items:
            format: uuid
            type: string
          type: array
      required:
      - assayResultIds
      type: object
    UserValidation:
      properties:
        validationComment:
          description: A string explaining the reason for the provided validation status.
          type: string
        validationStatus:
          description: 'Valid values for this enum depend on whether it is used to set a value (e.g., in a POST request), or is a return value for an existing result.

            Acceptable values for setting a status are ''VALID'' or ''INVALID''. Possible return values are ''VALID'', ''INVALID'', or ''PARTIALLY_VALID'' (a result will be partially valid if it has some valid fields and some invalid fields).

            '
          enum:
          - VALID
          - INVALID
          - PARTIALLY_VALID
          type: string
      type: object
    Fields:
      additionalProperties:
        $ref: '#/components/schemas/Field'
      type: object
    AssayResultsBulkCreateInTableRequest:
      allOf:
      - $ref: '#/components/schemas/AssayResultsBulkCreateRequest'
      - properties:
          tableId:
            example: strtbl_IakA58In
            type: string
        required:
        - assayResults
        type: object
    AssayResultsPaginatedList:
      properties:
        assayResults:
          items:
            $ref: '#/components/schemas/AssayResult'
          type: array
        nextToken:
          type: string
      type: object
    AssayResultCreate:
      properties:
        fieldValidation:
          additionalProperties:
            $ref: '#/components/schemas/UserValidation'
          description: 'Dictionary mapping field names to UserValidation Resources.

            '
          type: object
        fields:
          anyOf:
          - $ref: '#/components/schemas/Fields'
          - $ref: '#/components/schemas/AssayFieldsCreate'
          description: 'Dictionary of result fields. Please note the field keys must be the field''s system name, not display name.

            '
          example:
            my_entity_link:
              value: bfi_a0B1cd23
            my_text_field:
              value: some text
        id:
          description: UUID
          type: string
        projectId:
          description: 'The project that the assay result should be uploaded to. Only users with read access to the project will be able to read the assay result. Leaving this empty will result in only the creator having read access.

            '
          nullable: true
          type: string
        schemaId:
          description: ID of result schema under which to upload this result
          type: string
      required:
      - schemaId
      - fields
      type: object
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    AssayResultsBulkGet:
      properties:
        assayResults:
          items:
            $ref: '#/components/schemas/AssayResult'
          type: array
      type: object
    FieldType:
      enum:
      - dna_sequence_link
      - aa_sequence_link
      - custom_entity_link
      - entity_link
      - mixture_link
      - molecule_link
      - dropdown
      - part_link
      - translation_link
      - aa_part_link
      - base_molecule_link
      - blob_link
      - text
      - long_text
      - batch_link
      - storage_link
      - entry_link
      - assay_request_link
      - assay_result_link
      - assay_run_link
      - boolean
      - float
      - integer
      - datetime
      - date
      - json
      type: string
    AssayResultsCreateResponse:
      properties:
        assayResults:
          items:
            format: uuid
            type: string
          type: array
        errors:
          default: null
          nullable: true
          type: object
      type: object
    AssayResultsArchive:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/AssayResultIdsRequest'
      - properties:
          reason:
            description: The reason for archiving the provided results. Accepted reasons may differ based on tenant configuration
            enum:
            - Made in error
            - Archived
            - Other
            type: string
        type: object
    AssayResultIdsResponse:
      properties:
        assayResultIds:
          items:
            format: uuid
            type: string
          type: array
      type: object
    UserSummary:
      allOf:
      - $ref: '#/components/schemas/PartySummary'
      - example:
          handle: lpasteur
          id: ent_a0SApq3z
          name: Louis Pasteur
    AssayFieldsCreate:
      additionalProperties: true
      type: object
    AssayResultTransactionCreateResponse:
      properties:
        id:
          format: uuid
          type: string
      type: object
    Field:
      properties:
        displayValue:
          nullable: true
          readOnly: true
          type: string
        isMulti:
          readOnly: true
          type: boolean
        textValue:
          example: Amp
          nullable: true
          readOnly: true
          type: string
        type:
          allOf:
          - $ref: '#/components/schemas/FieldType'
          readOnly: true
        value:
          description: 'For single link fields, use the id of the item you want to link (eg. "seq_jdf8BV24").

            For multi-link fields, use an array of ids of the items you want to link (eg. ["seq_jdf8BV24"])

            '
          nullable: true
          oneOf:
          - type: string
          - type: boolean
          - type: number
          - type: object
          - items:
              type: string
            type: array
      required:
      - value
      type: object
    AssayResult:
      properties:
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          description: 'ArchiveRecord Resource if the result is archived. This is null if the result is not archived.

            '
          nullable: true
        createdAt:
          description: DateTime at which the the result was created
          format: date-time
          readOnly: true
          type: string
        creator:
          allOf:
          - $ref: '#/components/schemas/UserSummary'
          description: UserSummary Resource of who created the request
          readOnly: true
        entryId:
          description: ID of the entry that this result is attached to
          nullable: true
          type: string
        fieldValidation:
          additionalProperties:
            $ref: '#/components/schemas/UserValidation'
          description: 'Object mapping field names to a UserValidation Resource object for that field. To **set** validation for a result, you *must* use this object.

            '
          type: object
        fields:
          allOf:
          - $ref: '#/components/schemas/Fields'
          description: 'Field values for the returned result. Please note the keys of each field are the field''s system name (additional_prop) instead of the field''s display name (additionalProp).

            '
          example:
          - additional_prop: null
            displayValue: Amp
            isMulti: true
            textValue: Amp
            type: dna_sequence_link
            value:
            - seq_jdf8BV24
        id:
          description: ID of the result
          type: string
        isReviewed:
          description: Whether or not this result is attached to an accepted entry
          type: boolean
        modifiedAt:
          description: DateTime at which the the result was last modified
          format: date-time
          readOnly: true
          type: string
        projectId:
          description: ID of the project to insert the result into
          nullable: true
          type: string
        schema:
          allOf:
          - $ref: '#/components/schemas/SchemaSummary'
          description: Schema that the result belongs to
          title: SchemaProperty
        v3Id:
          description: V3 identifier for the result
          readOnly: true
          type: string
        validationComment:
          readOnly: true
          type: string
        validationStatus:
          readOnly: true
          type: string
      type: object
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    AssayResultsBulkCreateRequest:
      additionalProperties: false
      properties:
        assayResults:
          items:
            $ref: '#/components/schemas/AssayResultCreate'
          type: array
      required:
      - assayResults
      type: object
    AsyncTaskLink:
      properties:
        taskId:
          type: string
      type: object
    AssayResultsCreateErrorResponse:
      properties:
        assayResults:
          default: null
          items:
            type: object
          nullable: true
          type: array
        errors:
          items:
            properties:
              fields:
                type: object
              global:
                items:
                  type: string
                type: array
            type: object
          type: array
      type: object
    SchemaSummary:
      properties:
        id:
          type: string
        name:
          type: string
      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