openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences 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: '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.

    '
  name: AA Sequences
paths:
  /aa-sequences:
    get:
      description: List AA sequences
      operationId: listAASequences
      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 name, modifiedAt, and createdAt. Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

            '
          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 created 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 created within a certain range using the AND operator.
            value: '> 2022-03-01 AND < 2022-04-01'
          full-rfc-3339-format:
            summary: Filter for created models using the full RFC 3339 format
            value: '> 2020-12-31T21:07:14-05:00'
          greater-than-example:
            summary: Filter for all models created after a certain date
            value: '> 2022-03-01'
        in: query
        name: createdAt
        schema:
          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 an AA Sequence. Restricts results to those with the specified name, alias, or entity registry ID.
        in: query
        name: name
        schema:
          type: string
      - description: Name substring of an AA sequence. Restricts results to those with names, aliases, or entity registry IDs that include the provided substring.
        in: query
        name: nameIncludes
        schema:
          type: string
      - description: String of amino acids. Restricts results to AA sequences exactly matching these amino acids (case-insensitive).
        in: query
        name: aminoAcids
        schema:
          type: string
      - description: ID of a folder. Restricts results to those in the folder.
        in: query
        name: folderId
        schema:
          type: string
      - description: 'Comma-separated list of entry IDs. Restricts results to AA sequences mentioned in those entries.

          '
        in: query
        name: mentionedIn
        schema:
          type: string
      - description: ID of a project. Restricts results to those in the project.
        in: query
        name: projectId
        schema:
          type: string
      - description: 'ID of a registry. Restricts results to those registered in this registry. Specifying "null" returns unregistered items.

          '
        in: query
        name: registryId
        schema:
          nullable: true
          type: string
      - description: 'ID of a schema. Restricts results to those of the specified schema.

          '
        in: query
        name: schemaId
        schema:
          type: string
      - description: 'Filter based on schema field value (not display value). Restricts results to those with a field whose value matches the filter. For Integer, Float, and Date type fields, supports the >= and <= operators (but not < or >). If any schemaField filters are present, the schemaId param must also be present. Note that all operators must be separated from any values by a single space.

          '
        in: query
        name: schemaFields
        schema:
          $ref: '#/components/schemas/SchemaFieldsQueryParam'
      - description: 'Archive reason. Restricts items to those with the specified archive reason. Use "NOT_ARCHIVED" to filter for unarchived AA sequences. Use "ANY_ARCHIVED" to filter for archived AA sequences 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
      - description: 'Comma-separated list of item IDs. Restricts results to those that mention the given items in the description.

          '
        in: query
        name: mentions
        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: prtn_6gxJGfPh,prtn_u7fOvqWg
          type: string
      - description: 'Comma-separated list of entity registry IDs. Maximum of 100. Restricts results to those that match any of the specified registry IDs.

          '
        in: query
        name: entityRegistryIds.anyOf
        schema:
          example: TP001,TP002
          type: string
      - description: 'Comma-separated list of names. Maximum of 100. Restricts results to those that match any of the specified names, aliases, or entity registry IDs, case insensitive.  Warning - this filter can be non-performant due to case insensitivity.

          '
        in: query
        name: names.anyOf
        schema:
          example: MyName1,MyName2
          type: string
      - description: 'Comma-separated list of names. Maximum of 100. Restricts results to those that match any of the specified names, aliases, or entity registry IDs, case sensitive.

          '
        in: query
        name: names.anyOf.caseSensitive
        schema:
          example: MyName1,MyName2
          type: string
      - description: Comma separated list of users IDs
        in: query
        name: creatorIds
        schema:
          example: ent_a0SApq3z
          type: string
      - description: Comma separated list of user or app IDs. Maximum of 100.
        in: query
        name: authorIds.anyOf
        schema:
          example: ent_a0SApq3z,ent_b4AApz9b
          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).


          **Note**: Fields annotations, translations, and primers cannot be introspected with the returning parameter, and any sub fields will be ignored. E.g.: "aaSequences.annotations.id" will return the same as "aaSequences.annotations".

          '
        in: query
        name: returning
        schema:
          example: aaSequences.id,aaSequences.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequencesPaginatedList'
          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 AA sequences
      tags:
      - AA Sequences
    post:
      description: Create an AA sequence
      operationId: createAASequence
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequenceCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequence'
          description: Created
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '503':
          description: Deprecated, a 429 is returned for too many requests
      summary: Create an AA sequence
      tags:
      - AA Sequences
  /aa-sequences/{aa_sequence_id}:
    get:
      description: Get an AA sequence
      operationId: getAASequence
      parameters:
      - in: path
        name: aa_sequence_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).


          **Note**: Fields annotations, translations, and primers cannot be introspected with the returning parameter, and any sub fields will be ignored. E.g.: "annotations.id" will return the same as "annotations".

          '
        in: query
        name: returning
        schema:
          example: id,modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequence'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Get an AA sequence
      tags:
      - AA Sequences
    patch:
      description: Update an AA sequence
      operationId: updateAASequence
      parameters:
      - in: path
        name: aa_sequence_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequenceUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequence'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Update an AA sequence
      tags:
      - AA Sequences
  /aa-sequences/{entity_registry_id}:upsert:
    patch:
      description: 'Create or update a registered AA sequence.


        Schema field links can be populated using entity registry IDs or API IDs. In the `value` field of the [Field](#/components/schemas/FieldWithResolution) resource, the object `{"entityRegistryId": ENTITY_REGISTRY_ID}` may be provided instead of the API ID if desired (see example value).

        '
      operationId: upsertAaSequence
      parameters:
      - in: path
        name: entity_registry_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequenceUpsert'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequence'
          description: OK
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequence'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create or update a registered AA sequence.
      tags:
      - AA Sequences
  /aa-sequences:archive:
    post:
      description: Archive AA sequences
      operationId: archiveAASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequencesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive AA sequences
      tags:
      - AA Sequences
  /aa-sequences:auto-annotate:
    post:
      description: Auto-annotate AA sequences with matching features from specified Feature Libraries
      operationId: autoAnnotateAaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AutoAnnotateAaSequences'
      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.

            When successful, the task has an empty response.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Auto-annotate AA sequences with matching features from specified Feature Libraries
      tags:
      - AA Sequences
  /aa-sequences:back-translate:
    post:
      description: Create back-translated DNA sequences from AA sequences.
      operationId: backTranslate
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/BackTranslate'
      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.

            When successful, the task returns the resources of the DNA Sequence entities that were back-translated.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create back-translated DNA sequences from AA sequences.
      tags:
      - AA Sequences
  /aa-sequences:bulk-create:
    post:
      description: Bulk Create AA sequences. Limit of 1000 AA Sequences per request.
      operationId: bulkCreateAASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesBulkCreateRequest'
      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 AA Sequences that were created.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Create AA sequences
      tags:
      - AA Sequences
  /aa-sequences:bulk-get:
    get:
      description: Bulk get AA sequences by ID
      operationId: bulkGetAASequences
      parameters:
      - description: 'Comma-separated list of IDs of AA sequences to get.

          '
        in: query
        name: aaSequenceIds
        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).


          **Note**: Fields annotations, translations, and primers cannot be introspected with the returning parameter, and any sub fields will be ignored. E.g.: "aaSequences.annotations.id" will return the same as "aaSequences.annotations".

          '
        in: query
        name: returning
        schema:
          example: aaSequences.id, aaSequences.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequencesBulkGet'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk get AA sequences by ID
      tags:
      - AA Sequences
  /aa-sequences:bulk-update:
    post:
      description: Bulk Update AA sequences
      operationId: bulkUpdateAASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesBulkUpdateRequest'
      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.

            When successful, the task returns a full list of [AA Sequence](#/AA%20Sequences/bulkGetAASequences) resources

            that were updated.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Update AA sequences
      tags:
      - AA Sequences
  /aa-sequences:bulk-upsert:
    post:
      description: 'All entities and their schemas must be within the same registry.


        This operation performs the following actions:

        1. Any existing objects are looked up in Benchling by the provided entity registry ID.

        2. Then, all objects are either created or updated accordingly, temporarily skipping any schema field links between objects.

        3. Schema field links can be populated using entity registry IDs or API IDs. In the `value` field of the [Field](#/components/schemas/FieldWithResolution) resource, the object `{"entityRegistryId": ENTITY_REGISTRY_ID}` may be provided instead of the API ID if desired (see example value). You may link to objects being created in the same operation.

        4. Entities are registered, using the provided name and entity registry ID.


        If any action fails, the whole operation is canceled and no objects are created or updated.

        '
      operationId: bulkUpsertAASequences
      parameters:
      - 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: aaSequences.id,aaSequences.creator.handle
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesBulkUpsertRequest'
      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.

            When successful, the task returns the resources of the objects that were upserted.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk upsert AA sequences
      tags:
      - AA Sequences
  /aa-sequences:find-matching-regions:
    post:
      description: Find matching regions for AA sequences
      operationId: findMatchingRegionsAaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesFindMatchingRegion'
      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.

            It is used to search for AA sequences that are either subsequences or exact matches of the provided target sequences.

            Each returned item represents the group of sequences that partially or fully match the target sequence."

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Find matching regions for AA sequences
      tags:
      - AA Sequences
  /aa-sequences:match-amino-acids:
    post:
      description: 'Returns AA Sequences that exactly match the provided amino acids.

        '
      operationId: matchAminoAcidsAaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesMatchBases'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequencesPaginatedList'
          description: A filtered list of AA Sequences
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: List entities with matching amino acids
      tags:
      - AA Sequences
  /aa-sequences:search-amino-acids:
    post:
      description: 'Returns AA Sequences that contain the provided amino acids. Search indexing is asynchronous, so results my be not be available immediately after creation.

        '
      operationId: searchAaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesSearchBases'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequencesPaginatedList'
          description: A filtered list of AA Sequences
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Search AA Sequences
      tags:
      - AA Sequences
  /aa-sequences:unarchive:
    post:
      description: Unarchive AA sequences
      operationId: unarchiveAASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AaSequencesUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AaSequencesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive AA sequences
      tags:
      - AA Sequences
components:
  schemas:
    AaSequenceBaseRequestForCreate:
      allOf:
      - $ref: '#/components/schemas/AaSequenceBaseRequest'
      - required:
        - aminoAcids
        - name
    AaSequenceBaseRequest:
      properties:
        aliases:
          description: Aliases to add to the AA sequence
          items:
            type: string
          type: array
        aminoAcids:
          description: 'Amino acids for the AA sequence.

            '
          type: string
        annotations:
          description: 'Annotations to create on the AA sequence.

            '
          items:
            $ref: '#/components/schemas/AaAnnotation'
          type: array
        authorIds:
          description: IDs of users to set as the AA sequence's authors.
          items:
            type: string
          type: array
        customFields:
          allOf:
          - $ref: '#/components/schemas/CustomFields'
          description: 'Custom fields to add to the AA sequence. Every field should have its name as a key, mapping to an object with information about the value of the field.

            '
        fields:
          allOf:
          - $ref: '#/components/schemas/Fields'
          description: 'Fields to set on the AA sequence. Must correspond with the schema''s field definitions. Every field should have its name as a key, mapping to an object with information about the value of the field.

            '
        folderId:
          description: 'ID of the folder containing the AA sequence.

            '
          type: string
        name:
          description: 'Name of the AA sequence.

            '
          type: string
        schemaId:
          description: 'ID of the AA sequence''s schema.

            '
          type: string
      type: object
    AaSequenceCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/AaSequenceBaseRequestForCreate'
      - $ref: '#/components/schemas/CreateEntityIntoRegistry'
    AaSequencesBulkUpsertRequest:
      additionalProperties: false
      maxItems: 1000
      properties:
        aaSequences:
          items:
            $ref: '#/components/schemas/AaSequenceBulkUpsertRequest'
          type: array
      required:
      - aaSequences
      type: object
    Fields:
      additionalProperties:
        $ref: '#/components/schemas/Field'
      type: object
    FieldWithResolution:
      allOf:
      - $ref: '#/components/schemas/Field'
      - properties:
          value:
            allOf:
            - $ref: '#/components/schemas/FieldValueWithResolution'
            nullable: true
        type: object
    CustomField:
      properties:
        value:
          type: string
      type: object
    AaSequenceBulkUpsertRequest:
      allOf:
      - $ref: '#/components/schemas/EntityBulkUpsertBaseRequest'
      - $ref: '#/components/schemas/AaSequenceBaseRequestForCreate'
      - required:
        - annotations
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    AaSequenceUpsert:
      allOf:
      - $ref: '#/components/schemas/EntityBulkUpsertBaseRequest'
      - $ref: '#/components/schemas/AaSequenceBaseRequestForCreate'
      - required:
        - annotations
    AaSequencesPaginatedList:
      properties:
        aaSequences:
          items:
            $ref: '#/components/schemas/AaSequence'
          type: array
        nextToken:
          type: string
      type: object
    AaAnnotation:
      properties:
        color:
          type: string
        end:
          description: 0-based exclusive end index. The end of the AA sequence is always represented as 0.
          type: integer
        id:
          example: prtnann_o7zMPG0P
          type: string
        name:
          maxLength: 255
          type: string
        notes:
          example: Cong et al Science. 2013 Jan 3.
          maxLength: 10000
          type: string
        start:
          description: 0-based inclusive start index.
          type: integer
        type:
          example: Site
          maxLength: 255
          type: string
      type: object
    SchemaFieldsQueryParam:
      additionalProperties: true
      example:
        schemaField.Cell Count: '>= 10 AND <= 50'
        schemaField.Experiment: MyExperiment
        schemaField.Started On: <= 2023-05-23T00:00:00Z
      type: object
    ArchiveRecordSet:
      additionalProperties: false
      description: Currently, we only support setting a null value for archiveRecord, which unarchives the item
      example: null
      nullable: true
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    ReducedPattern:
      additionalProperties: false
      description: 'DNA patterns to avoid during optimization. Supports two formats: 1) DNA base patterns: strings of ATGC bases (case-insensitive, e.g., "ATGC" or "gat") 2) Repeat patterns: format "nxkmer" specifying n repeats of k-sized sequences (e.g., "3x4mer" matches 3 consecutive 4-base repeats). Maximum total length for repeat patterns is 50 bases (n * k ≤ 50).

        If avoidReverseComplement is true, the pattern''s reverse complement will also be avoided. Note: avoidReverseComplement cannot be true for repeat patterns (nxkmer format).

        '
      properties:
        avoidReverseComplement:
          default: false
          type: boolean
        pattern:
          type: string
      type: object
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    AaSequenceRequestRegistryFields:
      properties:
        entityRegistryId:
          type: string
      type: object
    AaSequencesBulkUpdateRequest:
      additionalProperties: false
      properties:
        aaSequences:
          items:
            $ref: '#/components/schemas/AaSequenceBulkUpdate'
          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
    FieldsWithResolution:
      additionalProperties:
        $ref: '#/components/schemas/FieldWithResolution'
      example:
        Linked Peptide:
          value: prtn_ObbdtGhC
        Linked Sequence:
          value:
            entityRegistryId: DNA001
        Linked Strains:
          value:
          - entityRegistryId: STRAIN001
          - entityRegistryId: STRAIN002
      type: object
    BackTranslate:
      additionalProperties: false
      properties:
        aaSequenceIds:
          description: IDs of AA sequences to back-translate.
          items:
            type: string
          type: array
        avoidedCutsiteEnzymeIds:
          description: 'List of enzyme IDs whose recognition sites will be avoided when creating the back-translated sequence.

            '
          items:
            type: string
          type: array
        codonUsageTableId:
          description: ID of the codon usage table representing the target organism.
          type: string
        folderId:
          description: 'ID of the folder in which the back-translated sequences will be saved.

            '
          type: string
        gcContent:
          default: ANY
          description: 'The amount of GC content in the optimized sequence. LOW is defined as below 0.33, MEDIUM as 0.33-0.66, and HIGH as above 0.66. If neither gcContent nor gcContentRange is specified, the optimization will default to ANY (0-1). Cannot be specified together with gcContentRange.

            '
          enum:
          - ANY
          - LOW
          - MEDIUM
          - HIGH
          type: string
        gcContentRange:
          additionalProperties: false
          description: 'Custom GC content range for the optimized sequence, specified as decimal values between 0 and 1. The maximum must be greater than the minimum. Cannot be specified together with gcContent.

            '
          properties:
            max:
              description: Maximum GC content ratio (e.g., 0.6 for 60%)
              maximum: 1
              minimum: 0
              type: number
            min:
              description: Minimum GC content ratio (e.g., 0.4 for 40%)
              maximum: 1
              minimum: 0
              type: number
          type: object
        hairpinParameters:
          additionalProperties: false
          description: 'These parameters are applied in the AvoidHairpins specification in DNAChisel. If hairpinParameters is not specified, hairpins will not be avoided.

            '
          properties:
            stem:
              default: 20
              type: integer
            window:
              default: 200
              type: integer
          type: object
        method:
          default: MATCH_CODON_USAGE
          description: 'The codon optimization algorithm to use. Requires codonUsageTableId to be specified. MATCH_CODON_USAGE selects codons probabilistically based on the organism''s codon usage frequencies. USE_BEST_CODON always selects the most frequently used codon for each amino acid.

            '
          enum:
          - MATCH_CODON_USAGE
          - USE_BEST_CODON
          type: string
        reducedPatterns:
          description: 'List of patterns to avoid when creating the back-translated sequence, on the coding strand only.

            '
          items:
            $ref: '#/components/schemas/ReducedPattern'
          type: array
        schemaId:
          description: ID of the resulting DNA sequences' schemas
          type: string
        shouldDepleteUridine:
          default: false
          description: 'If not specified, the back-translation will default to false, and mRNA uridine depletion will not be performed.

            '
          type: boolean
      required:
      - aaSequenceIds
      - folderId
      type: object
    FieldValueWithResolution:
      oneOf:
      - type: string
      - type: boolean
      - type: number
      - items:
          type: string
        type: array
      - additionalProperties: false
        description: Look up an entity by its entity registry ID
        properties:
          entityRegistryId:
            type: string
        required:
        - entityRegistryId
        type: object
    NamingStrategy:
      description: 'Specifies the behavior for automatically generated names when registering an entity.

        - NEW_IDS: Generate new registry IDs

        - IDS_FROM_NAMES: Generate registry IDs based on entity names

        - DELETE_NAMES: Generate new registry IDs and replace name with registry ID

        - SET_FROM_NAME_PARTS: Generate new registry IDs, rename according to name template, and keep old name as alias

        - REPLACE_NAMES_FROM_PARTS: Generate new registry IDs, and replace name according to name template

        - KEEP_NAMES: Keep existing entity names as registry IDs

        - REPLACE_ID_AND_NAME_FROM_PARTS: Generate registry IDs and names according to name template

        '
      enum:
      - NEW_IDS
      - IDS_FROM_NAMES
      - DELETE_NAMES
      - SET_FROM_NAME_PARTS
      - REPLACE_NAMES_FROM_PARTS
      - KEEP_NAMES
      - REPLACE_ID_AND_NAME_FROM_PARTS
      type: string
    UserSummary:
      allOf:
      - $ref: '#/components/schemas/PartySummary'
      - example:
          handle: lpasteur
          id: ent_a0SApq3z
          name: Louis Pasteur
    AaSequencesMatchBases:
      additionalProperties: false
      properties:
        aminoAcids:
          type: string
        archiveReason:
          default: NOT_ARCHIVED
          enum:
          - NOT_ARCHIVED
          - Other
          - Archived
          type: string
        nextToken:
          type: string
        pageSize:
          default: 50
          maximum: 100
          minimum: 0
          type: integer
        registryId:
          description: 'ID of a registry. Restricts results to those registered in this registry. Specifying `null` returns unregistered items.

            '
          nullable: true
          type: string
        sort:
          default: modifiedAt:desc
          enum:
          - modifiedAt:asc
          - modifiedAt:desc
          - name:asc
          - name:desc
          type: string
      required:
      - aminoAcids
      type: object
    AaSequenceBulkCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/AaSequenceCreate'
    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
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    AaSequencesBulkGet:
      properties:
        aaSequences:
          items:
            $ref: '#/components/schemas/AaSequence'
          type: array
      type: object
    AaSequencesSearchBases:
      additionalProperties: false
      properties:
        aminoAcids:
          minLength: 3
          type: string
        archiveReason:
          default: NOT_ARCHIVED
          enum:
          - NOT_ARCHIVED
          - Other
          - Archived
          type: string
        nextToken:
          type: string
        pageSize:
          default: 50
          maximum: 100
          minimum: 0
          type: integer
        registryId:
          description: 'ID of a registry. Restricts results to those registered in this registry. Specifying `null` returns unregistered items.

            '
          nullable: true
          type: string
        sort:
          default: modifiedAt:desc
          enum:
          - modifiedAt:asc
          - modifiedAt:desc
          - name:asc
          - name:desc
          type: string
      required:
      - aminoAcids
      type: object
    AaSequencesBulkCreateRequest:
      additionalProperties: false
      properties:
        aaSequences:
          items:
            $ref: '#/components/schemas/AaSequenceBulkCreate'
          maxItems: 1000
          type: array
      type: object
    AaSequencesArchivalChange:
      description: 'IDs of all items that were archived or unarchived, grouped by resource type. This includes the IDs of AA sequences along with any IDs of batches that were archived / unarchived.

        '
      properties:
        aaSequenceIds:
          items:
            type: string
          type: array
        batchIds:
          items:
            type: string
          type: array
      type: object
    AsyncTaskLink:
      properties:
        taskId:
          type: string
      type: object
    AaSequenceBulkUpdate:
      additionalProperties: false
      allOf:
      - properties:
          id:
            type: string
        type: object
      - $ref: '#/components/schemas/AaSequenceBaseRequest'
    CustomFields:
      additionalProperties:
        $ref: '#/components/schemas/CustomField'
      example:
        Legacy ID:
          value: STR100
      type: object
    AaSequenceUpdate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/AaSequenceBaseRequest'
      - $ref: '#/components/schemas/AaSequenceRequestRegistryFields'
    EntityBulkUpsertBaseRequest:
      allOf:
      - $ref: '#/components/schemas/EntityUpsertBaseRequest'
      - properties:
          entityRegistryId:
            description: Registry ID of the entity in Benchling.
            type: string
      - required:
        - entityRegistryId
    AaSequencesArchive:
      additionalProperties: false
      description: 'The request body for archiving AA sequences.

        '
      properties:
        aaSequenceIds:
          items:
            type: string
          type: array
        reason:
          $ref: '#/components/schemas/EntityArchiveReason'
      required:
      - reason
      - aaSequenceIds
      type: object
    AaSequencesFindMatchingRegion:
      additionalProperties: false
      properties:
        registryId:
          description: An optional Registry ID to restrict the region search to
          example: src_ae40j3TZ
          type: string
        schemaId:
          description: Schema ID for the type of AA to match to the source sequence
          example: ts_n4l12nf0
          type: string
        targetAASequenceIds:
          description: API IDs of the AA sequences which matching regions will be found for
          example:
          - prtn_W7KgYydE
          - prtn_g7SI2nih
          items:
            type: string
          type: array
      required:
      - targetAASequenceIds
      - schemaId
      type: object
    RegistrationOrigin:
      properties:
        originEntryId:
          nullable: true
          readOnly: true
          type: string
        registeredAt:
          format: date-time
          readOnly: true
          type: string
      type: object
    CreateEntityIntoRegistry:
      properties:
        entityRegistryId:
          description: 'Entity registry ID to set for the registered entity. Cannot specify both entityRegistryId and namingStrategy at the same time.

            '
          type: string
        folderId:
          description: ID of the folder containing the entity. Can be left empty when registryId is present.
          type: string
        namingStrategy:
          $ref: '#/components/schemas/NamingStrategy'
        registryId:
          description: 'Registry ID into which entity should be registered. this is the ID of the registry which was configured for a particular organization

            To get available registryIds, use the [/registries endpoint](#/Registry/listRegistries)


            Required in order for entities to be created directly in the registry.

            '
          type: string
      type: object
    EntityUpsertBaseRequest:
      properties:
        archiveRecord:
          $ref: '#/components/schemas/ArchiveRecordSet'
        fields:
          $ref: '#/components/schemas/FieldsWithResolution'
        name:
          type: string
        registryId:
          type: string
        schemaId:
          type: string
      required:
      - registryId
      - name
      - schemaId
      type: object
    AaSequencesUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving AA sequences.

        '
      properties:
        aaSequenceIds:
          items:
            type: string
          type: array
      required:
      - aaSequenceIds
      type: object
    AutoAnnotateAaSequences:
      additionalProperties: false
      properties:
        aaSequenceIds:
          description: Array of AA sequence IDs.
          items:
            type: string
          type: array
        featureLibraryIds:
          description: Array of feature library IDs.
          items:
            type: string
          type: array
      required:
      - aaSequenceIds
      - featureLibraryIds
      type: object
    AaSequence:
      properties:
        aliases:
          description: Array of aliases
          items:
            type: string
          type: array
        aminoAcids:
          description: Amino acids of the AA sequence.
          example: IKTATARRELAETSWTGDRLWGFSDNWAPALRRPSPSALGK
          type: string
        annotations:
          description: Array of annotation objects on the AA sequence.
          items:
            $ref: '#/components/schemas/AaAnnotation'
          type: array
        apiURL:
          description: The canonical url of the AA Sequence in the API.
          example: https://benchling.com/api/v2/aa-sequences/prtn_7nMBOMm0
          format: uri
          readOnly: true
          type: string
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          nullable: true
        authors:
          items:
            $ref: '#/components/schemas/UserSummary'
          type: array
        createdAt:
          description: DateTime the AA sequence was created.
          format: date-time
          readOnly: true
          type: string
        creator:
          $ref: '#/components/schemas/UserSummary'
        customFields:
          allOf:
          - $ref: '#/components/schemas/CustomFields'
          description: Custom fields set on the AA sequence.
        entityRegistryId:
          description: Registry ID of the AA sequence if registered.
          nullable: true
          type: string
        fields:
          $ref: '#/components/schemas/Fields'
        folderId:
          description: ID of the folder that contains the AA sequence.
          nullable: true
          type: string
        id:
          description: ID of the AA sequence.
          example: prtn_ObbdtGhC
          type: string
        length:
          description: Number of amino acids in the AA sequence.
          type: integer
        modifiedAt:
          description: DateTime the AA sequence was last modified.
          format: date-time
          readOnly: true
          type: string
        name:
          description: Name of the AA sequence.
          type: string
        registrationOrigin:
          allOf:
          - $ref: '#/components/schemas/RegistrationOrigin'
          nullable: true
          readOnly: true
        registryId:
          description: Registry the AA sequence is registered in.
          nullable: true
          type: string
        schema:
          allOf:
          - $ref: '#/components/schemas/SchemaSummary'
          nullable: true
        url:
          description: The path of the web URL, omitting the tenant domain
          type: string
        webURL:
          description: URL of the AA sequence.
          example: https://benchling.com/benchling/f/lib_55UxcIps-registry/prtn_7nMBOMm0-kedchain11/edit"
          format: uri
          readOnly: true
          type: string
      type: object
    SchemaSummary:
      properties:
        id:
          type: string
        name:
          type: string
      type: object
    EntityArchiveReason:
      description: 'The reason for archiving the provided entities. Accepted reasons may differ based on tenant configuration.

        '
      enum:
      - Made in error
      - Retired
      - Expended
      - Shipped
      - Contaminated
      - Expired
      - Missing
      - Other
      type: string
  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