Benchling Feature Libraries 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 Feature Libraries 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: Feature Libraries are collections of shared canonical patterns that can be used to generate annotations on matching regions of DNA Sequences or AA Sequences.
  name: Feature Libraries
paths:
  /feature-libraries:
    get:
      description: List Feature Libraries
      operationId: listFeatureLibraries
      parameters:
      - 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: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      - in: query
        name: sort
        schema:
          default: modifiedAt:desc
          description: 'Method by which to order search results. Valid sorts are modifiedAt (modified time, most recent first) and name (entity name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order.

            '
          enum:
          - createdAt
          - createdAt:asc
          - createdAt:desc
          - modifiedAt
          - modifiedAt:asc
          - modifiedAt:desc
          - name
          - name:asc
          - name:desc
          nullable: false
          type: string
      - description: 'Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30. Date ranges can be specified with the following nomenclature > YYYY-MM-DD AND <YYYY-MM-DD.

          '
        examples:
          and-range:
            summary: Filter for all models modified within a certain range using the AND operator.
            value: '> 2022-03-01 AND < 2022-04-01'
          full-rfc-3339-format:
            summary: Filter for modified models using the full RFC 3339 format
            value: '> 2020-12-31T21:07:14-05:00'
          greater-than-example:
            summary: Filter for all models modified after a certain date
            value: '> 2022-03-01'
        in: query
        name: modifiedAt
        schema:
          type: string
      - description: Name of a Feature Library. Restricts results to those with the specified name.
        in: query
        name: name
        schema:
          type: string
      - description: Name substring of a Feature Library. Restricts results to those with names that include the provided substring.
        in: query
        name: nameIncludes
        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:
          example: featlib_VfVOART1,featlib_RFhDGaaC
          type: string
      - description: 'Comma-separated list of names. Maximum of 100. Restricts results to those that match any of the specified names.

          '
        in: query
        name: names.anyOf
        schema:
          example: MyName1,MyName2
          type: string
      - description: Comma-separated list of fields to return. Modifies the output shape. To return all keys at a given level, enumerate them or use the wildcard, '*'. For more information, [click here](https://docs.benchling.com/docs/getting-started-1#returning-query-parameter).
        in: query
        name: returning
        schema:
          example: featureLibraries.id,featureLibraries.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibrariesPaginatedList'
          description: OK
          headers:
            Result-Count:
              description: The total number of items that match the given query
              schema:
                type: integer
            x-rate-limit-limit:
              description: The number of allowed requests in the current rate-limit period
              schema:
                type: integer
            x-rate-limit-remaining:
              description: The number of requests remaining in the current rate-limit period
              schema:
                type: integer
            x-rate-limit-reset:
              description: The number of seconds remaining in the current rate-limit period
              schema:
                type: integer
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: List Feature Libraries
      tags:
      - Feature Libraries
    post:
      description: Create a Feature Library
      operationId: createFeatureLibrary
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FeatureLibraryCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibrary'
          description: Created
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create a Feature Library
      tags:
      - Feature Libraries
  /feature-libraries/{feature_library_id}:
    get:
      description: Get a feature library by ID
      operationId: getFeatureLibrary
      parameters:
      - description: ID of feature library to get
        in: path
        name: feature_library_id
        required: true
        schema:
          type: string
      - description: Comma-separated list of fields to return. Modifies the output shape. To return all keys at a given level, enumerate them or use the wildcard, '*'. For more information, [click here](https://docs.benchling.com/docs/getting-started-1#returning-query-parameter).
        in: query
        name: returning
        schema:
          example: id,modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibrary'
          description: OK
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Get a feature library by ID
      tags:
      - Feature Libraries
    patch:
      description: 'Update a feature library. Note: Features cannot be updated from this endpoint.

        Use the /features* endpoints to add or modify features.

        '
      operationId: updateFeatureLibrary
      parameters:
      - in: path
        name: feature_library_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FeatureLibraryUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibrary'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Update a feature library
      tags:
      - Feature Libraries
  /features:
    get:
      description: List Features
      operationId: listFeatures
      parameters:
      - 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: Token for pagination
        in: query
        name: nextToken
        schema:
          type: string
      - description: Name of a Feature. Restricts results to those with the specified name.
        in: query
        name: name
        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:
          example: feat_VfVOART1,feat_RFhDGaaC
          type: string
      - description: 'Comma-separated list of names. Maximum of 100. Restricts results to those that match any of the specified names.

          '
        in: query
        name: names.anyOf.caseSensitive
        schema:
          example: MyName1,MyName2
          type: string
      - description: Id of a Feature Library. Restricts results to those associated with the provided feature library
        in: query
        name: featureLibraryId
        schema:
          example: featlib_D0v2x9Q7
          type: string
      - description: 'The type of feature, like gene, promoter, etc. Note: This is an arbitrary string, not an enum

          '
        in: query
        name: featureType
        schema:
          example: terminator
          type: string
      - description: The match type of the feature used to determine how auto-annotate matches are made.
        in: query
        name: matchType
        schema:
          enum:
          - nucleotide
          - protein
          example: nucleotide
          type: string
      - description: Comma-separated list of fields to return. Modifies the output shape. To return all keys at a given level, enumerate them or use the wildcard, '*'. For more information, [click here](https://docs.benchling.com/docs/getting-started-1#returning-query-parameter).
        in: query
        name: returning
        schema:
          example: features.id,features.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeaturesPaginatedList'
          description: OK
          headers:
            Result-Count:
              description: The total number of items that match the given query
              schema:
                type: integer
            x-rate-limit-limit:
              description: The number of allowed requests in the current rate-limit period
              schema:
                type: integer
            x-rate-limit-remaining:
              description: The number of requests remaining in the current rate-limit period
              schema:
                type: integer
            x-rate-limit-reset:
              description: The number of seconds remaining in the current rate-limit period
              schema:
                type: integer
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: List Features
      tags:
      - Feature Libraries
    post:
      description: Create a Feature
      operationId: createFeature
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FeatureCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Feature'
          description: Created
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create a Feature
      tags:
      - Feature Libraries
  /features/{feature_id}:
    get:
      description: Get a feature by ID
      operationId: getFeature
      parameters:
      - description: ID of feature to get
        in: path
        name: feature_id
        required: true
        schema:
          type: string
      - description: Comma-separated list of fields to return. Modifies the output shape. To return all keys at a given level, enumerate them or use the wildcard, '*'. For more information, [click here](https://docs.benchling.com/docs/getting-started-1#returning-query-parameter).
        in: query
        name: returning
        schema:
          example: id,modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Feature'
          description: OK
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Get a feature by ID
      tags:
      - Feature Libraries
    patch:
      description: Update a feature
      operationId: updateFeature
      parameters:
      - in: path
        name: feature_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FeatureUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Feature'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Update a feature
      tags:
      - Feature Libraries
  /features:bulk-create:
    post:
      description: Bulk create Features
      operationId: bulkCreateFeatures
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FeaturesBulkCreateRequest'
      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 features that were created.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk create Features
      tags:
      - Feature Libraries
components:
  schemas:
    FeatureBulkCreate:
      allOf:
      - $ref: '#/components/schemas/FeatureCreate'
    FeatureUpdate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/FeatureBase'
      description: Inputs for updating a feature
      type: object
    FeaturesBulkCreateRequest:
      additionalProperties: false
      description: Inputs for bulk creating a new feature
      properties:
        features:
          items:
            $ref: '#/components/schemas/FeatureBulkCreate'
          maxItems: 1000
          type: array
      type: object
    FeatureLibrariesPaginatedList:
      allOf:
      - $ref: '#/components/schemas/Pagination'
      - properties:
          featureLibraries:
            items:
              $ref: '#/components/schemas/FeatureLibrary'
            type: array
      description: A paginated list of feature libraries
      type: object
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    FeatureLibraryUpdate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/FeatureLibraryBase'
      description: Inputs for updating a feature library
      type: object
    FeatureLibrary:
      allOf:
      - $ref: '#/components/schemas/FeatureLibraryBase'
      - properties:
          createdAt:
            description: DateTime the Feature Library was created
            format: date-time
            type: string
          id:
            description: The id of the feature library
            example: featlib_6ZVdX98t
            type: string
          modifiedAt:
            description: DateTime the Feature Library was last modified
            format: date-time
            type: string
          owner:
            anyOf:
            - $ref: '#/components/schemas/Organization'
            - $ref: '#/components/schemas/UserSummary'
          webURL:
            description: The Benchling web UI url to view the Feature Library
            format: uri
            type: string
      description: A feature library
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    Pagination:
      properties:
        nextToken:
          type: string
    FeatureCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/FeatureBase'
      - properties:
          matchType:
            description: The match type of the feature. Used to determine how auto-annotate matches are made.
            enum:
            - nucleotide
            - protein
            type: string
      - required:
        - name
        - featureType
        - pattern
        - matchType
        - featureLibraryId
      description: Inputs for a new feature
      type: object
    UserSummary:
      allOf:
      - $ref: '#/components/schemas/PartySummary'
      - example:
          handle: lpasteur
          id: ent_a0SApq3z
          name: Louis Pasteur
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    FeatureBase:
      properties:
        color:
          description: The color of the annotations generated by the feature. Must be a valid hex string
          example: '#F58A5E'
          type: string
        featureLibraryId:
          description: The id of the feature library the feature belongs to
          example: featlib_19kd9aDq
          type: string
        featureType:
          description: 'The type of feature, like gene, promoter, etc. Note: This is an arbitrary string, not an enum

            '
          nullable: true
          type: string
        name:
          description: The name of the feature
          type: string
        pattern:
          description: The pattern used for matching during auto-annotation.
          type: string
      type: object
    AsyncTaskLink:
      properties:
        taskId:
          type: string
      type: object
    Feature:
      allOf:
      - $ref: '#/components/schemas/FeatureBase'
      - properties:
          id:
            description: The id of the feature
            example: feat_4YVqX98z
            type: string
          matchType:
            description: The match type of the feature. Used to determine how auto-annotate matches are made.
            enum:
            - nucleotide
            - protein
            type: string
      description: A feature from a feature library
      type: object
    NotFoundError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              invalidId:
                type: string
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    Organization:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    FeaturesPaginatedList:
      allOf:
      - $ref: '#/components/schemas/Pagination'
      - properties:
          features:
            description: List of features for the page
            items:
              $ref: '#/components/schemas/Feature'
            type: array
      description: A paginated list of features
      type: object
    FeatureLibraryBase:
      properties:
        description:
          description: The description for the feature library
          type: string
        name:
          description: The name of the feature library
          type: string
      type: object
    FeatureLibraryCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/FeatureLibraryBase'
      - properties:
          organizationId:
            description: 'The organization that will own the feature library. The requesting user must be an administrator of the organization. If unspecified and the organization allows personal ownables, then the requesting user will own the feature library

              '
            example: ent_a0SApq3z
            type: string
      - required:
        - name
        - description
      description: Inputs for creating a feature library
      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