openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences RNA 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: Chains of linear, single stranded RNA that support most capabilities and attributes of DNA Sequences.
  name: RNA Sequences
paths:
  /rna-sequences:
    get:
      description: List RNA sequences
      operationId: listRNASequences
      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: '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.

          '
        in: query
        name: sort
        schema:
          default: modifiedAt:desc
          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 RNA 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 RNA 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: Full bases of the RNA sequence. Restricts results to those with the specified bases, case-insensitive, allowing for circular or reverse complement matches. Does not allow partial matching or loose matching via degenerate bases.
        in: query
        name: bases
        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 RNA 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 RNA sequences. Use "ANY_ARCHIVED" to filter for archived RNA 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: seq_VzVOART1,seq_RahDGaaC
          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: ID of the notation to use in populating the customNotation field.
        in: query
        name: customNotationId
        schema:
          example: sntx_lRe007yZ
          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.: "rnaSequences.annotations.id" will return the same as "rnaSequences.annotations".

          '
        in: query
        name: returning
        schema:
          example: rnaSequences.id, rnaSequences.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequencesPaginatedList'
          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 RNA sequences
      tags:
      - RNA Sequences
    post:
      description: Create an RNA sequence
      operationId: createRNASequence
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RnaSequenceCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequence'
          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 RNA sequence
      tags:
      - RNA Sequences
  /rna-sequences/{rna_sequence_id}:
    get:
      description: Get an RNA sequence
      operationId: getRNASequence
      parameters:
      - in: path
        name: rna_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
      - description: ID of the notation to use in populating the customNotation field.
        in: query
        name: customNotationId
        schema:
          example: sntx_lRe007yZ
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequence'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Get an RNA sequence
      tags:
      - RNA Sequences
    patch:
      description: Update an RNA sequence
      operationId: updateRNASequence
      parameters:
      - in: path
        name: rna_sequence_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RnaSequenceUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequence'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Update an RNA sequence
      tags:
      - RNA Sequences
  /rna-sequences:archive:
    post:
      description: Archive RNA Sequences. RNA sequences that are already registered will not be removed from the registry.
      operationId: archiveRNASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RnaSequencesArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequencesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive RNA Sequences
      tags:
      - RNA Sequences
  /rna-sequences:auto-annotate:
    post:
      description: Auto-annotate RNA sequences with matching features from specified Feature Libraries. U/T bases are treated as interchangeable in both features and sequences.
      operationId: autoAnnotateRnaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AutoAnnotateRnaSequences'
      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 RNA sequences with matching features from specified Feature Libraries
      tags:
      - RNA Sequences
  /rna-sequences:autofill-parts:
    post:
      description: Autofill parts from matching RNA Sequences with linked schemas.
      operationId: autofillRNASequenceParts
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AutofillRnaSequences'
      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: Autofill RNA sequence parts
      tags:
      - RNA Sequences
  /rna-sequences:autofill-translations:
    post:
      description: Autofill RNA sequence translations
      operationId: autofillRNASequenceTranslations
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/AutofillRnaSequences'
      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: Autofill RNA sequence translations from Amino Acid sequences with matching schemas
      tags:
      - RNA Sequences
  /rna-sequences:bulk-create:
    post:
      description: Bulk Create RNA sequences. Limit of 1000 RNA Sequences per request.
      operationId: bulkCreateRNASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RnaSequencesBulkCreateRequest'
      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 [RNA Sequence](#/RNA%20Sequences/bulkGetRNASequences) resources that were created.

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

          '
        in: query
        name: rnaSequenceIds
        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.: "rnaSequences.annotations.id" will return the same as "rnaSequences.annotations".

          '
        in: query
        name: returning
        schema:
          example: rnaSequences.id, rnaSequences.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequencesBulkGet'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk get RNA sequences by ID
      tags:
      - RNA Sequences
  /rna-sequences:bulk-update:
    post:
      description: Bulk Update RNA sequences
      operationId: bulkUpdateRNASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RnaSequencesBulkUpdateRequest'
      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 [RNA Sequences](#/RNA%20Sequences/bulkGetRNASequences) resources that were updated.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Update RNA sequences
      tags:
      - RNA Sequences
  /rna-sequences:match-bases:
    post:
      description: Return RNA sequences whose bases exactly match the provided query.
      operationId: matchBasesRnaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/MatchBasesRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequencesPaginatedList'
          description: A filtered list of RNA Sequences
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Match RNA sequences by bases
      tags:
      - RNA Sequences
  /rna-sequences:search-bases:
    post:
      description: 'Returns RNA Sequences that contain the provided bases. Search indexing is asynchronous, so results my be not be available immediately after creation.

        '
      operationId: searchRnaSequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/SearchBasesRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequencesPaginatedList'
          description: A filtered list of DNA Sequences
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Search RNA Sequences
      tags:
      - RNA Sequences
  /rna-sequences:unarchive:
    post:
      description: Unarchive RNA sequences
      operationId: unarchiveRNASequences
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/RnaSequencesUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/RnaSequencesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive RNA sequences
      tags:
      - RNA Sequences
components:
  schemas:
    Primer:
      properties:
        bases:
          readOnly: true
          type: string
        bindPosition:
          readOnly: true
          type: integer
        color:
          readOnly: true
          type: string
        end:
          description: 0-based exclusive end index. The end of the sequence is always represented as 0.
          type: integer
        name:
          readOnly: true
          type: string
        oligoId:
          type: string
        overhangLength:
          readOnly: true
          type: integer
        start:
          description: 0-based inclusive start index.
          type: integer
        strand:
          example: 1
          type: integer
      type: object
    Fields:
      additionalProperties:
        $ref: '#/components/schemas/Field'
      type: object
    RnaSequencePart:
      allOf:
      - $ref: '#/components/schemas/NucleotideSequencePart'
      - properties:
          strand:
            example: 1
            maximum: 1
            minimum: 1
            type: integer
        type: object
    SearchBasesRequest:
      additionalProperties: false
      properties:
        archiveReason:
          default: NOT_ARCHIVED
          enum:
          - NOT_ARCHIVED
          - Other
          - Archived
          type: string
        bases:
          example: GATTACAA
          minLength: 8
          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.

            '
          example: src_pwKo8pHh
          nullable: true
          type: string
        schemaId:
          description: 'ID of the nucleotide sequence''s schema.

            '
          example: ts_Y6t0Zbhg
          type: string
        sort:
          default: modifiedAt:desc
          enum:
          - modifiedAt:asc
          - modifiedAt:desc
          - name:asc
          - name:desc
          type: string
      required:
      - bases
      type: object
    CustomField:
      properties:
        value:
          type: string
      type: object
    RnaSequenceBulkUpdate:
      additionalProperties: false
      allOf:
      - properties:
          id:
            type: string
        type: object
      - $ref: '#/components/schemas/RnaSequenceBaseRequest'
    NucleotideSequencePart:
      properties:
        end:
          description: 0-based exclusive end index. The end of the sequence is always represented as 0.
          type: integer
        sequenceId:
          example: seq_VfVOART1
          type: string
        start:
          description: 0-based inclusive start index.
          type: integer
      type: object
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    SequenceFeatureCustomField:
      description: A name and value pair associated with a sequence feature (annotation or translation). For genbank imports, these are the qualifiers associated with each feature.
      properties:
        name:
          description: Name of the custom field
          type: string
        value:
          description: Value of the custom field
          type: string
      type: object
    SequenceFeatureBase:
      properties:
        color:
          description: Hex color code used when displaying this feature in the UI.
          example: '#F58A5E'
          type: string
        customFields:
          items:
            $ref: '#/components/schemas/SequenceFeatureCustomField'
          maxItems: 100
          type: array
        name:
          maxLength: 2048
          type: string
        notes:
          example: Cong et al Science. 2013 Jan 3.
          maxLength: 10000
          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
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    RnaSequenceUpdate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/RnaSequenceBaseRequest'
      - $ref: '#/components/schemas/RnaSequenceRequestRegistryFields'
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    RnaSequenceCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/RnaSequenceBaseRequestForCreate'
      - $ref: '#/components/schemas/CreateEntityIntoRegistry'
    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
    RnaSequencesArchivalChange:
      description: 'IDs of all RNA Sequences that were archived or unarchived, grouped by resource type.

        '
      properties:
        rnaSequenceIds:
          items:
            type: string
          type: array
      type: object
    RnaSequencesArchive:
      additionalProperties: false
      description: 'The request body for archiving RNA sequences.

        '
      properties:
        reason:
          $ref: '#/components/schemas/EntityArchiveReason'
        rnaSequenceIds:
          items:
            type: string
          type: array
      required:
      - reason
      - rnaSequenceIds
      type: object
    RnaSequenceBaseRequestForCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/RnaSequenceBaseRequest'
      - required:
        - name
    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
    MatchBasesRequest:
      additionalProperties: false
      properties:
        archiveReason:
          default: NOT_ARCHIVED
          enum:
          - NOT_ARCHIVED
          - Other
          - Archived
          type: string
        bases:
          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:
      - bases
      type: object
    RnaSequencesPaginatedList:
      properties:
        nextToken:
          type: string
        rnaSequences:
          items:
            $ref: '#/components/schemas/RnaSequence'
          type: array
      type: object
    Translation:
      allOf:
      - $ref: '#/components/schemas/SequenceFeatureBase'
      - properties:
          aminoAcids:
            readOnly: true
            type: string
          coerceStartCodonToMethionine:
            default: false
            description: Whether to override the translation of the start codon to Methionine. Has no effect when the start codon already translates to Methionine.
            type: boolean
          end:
            description: 0-based exclusive end index. The end of the sequence is always represented as 0.
            type: integer
          geneticCode:
            default: STANDARD
            description: The genetic code to use when translating the nucleotide sequence into amino acids.
            enum:
            - STANDARD
            - VERTEBRATE_MITOCHONDRIAL
            - YEAST_MITOCHONDRIAL
            - MOLD_PROTOZOAN_COELENTERATE_MITOCHONDRIAL_MYCOPLASMA_SPIROPLASMA
            - INVERTEBRATE_MITOCHONDRIAL
            - CILIATE_DASYCLADACEAN_HEXAMITA_NUCLEAR
            - ECHINODERM_FLATWORM_MITOCHONDRIAL
            - EUPLOTID_NUCLEAR
            - BACTERIAL_ARCHAEAL_PLANT_PLASTID
            - ALTERNATIVE_YEAST_NUCLEAR
            - ASCIDIAN_MITOCHONDRIAL
            - ALTERNATIVE_FLATWORM_MITOCHONDRIAL
            - CHLOROPHYCEAN_MITOCHONDRIAL
            - TREMATODE_MITOCHONDRIAL
            - SCENEDESMUS_OBLIQUUS_MITOCHONDRIAL
            - THRAUSTOCHYTRIUM_MITOCHONDRIAL
            - RHABDOPLEURIDAE_MITOCHONDRIAL
            - CANDIDATE_DIVISION_SR1_GRACILIBACTERIA
            - PACHYSOLEN_TANNOPHILUS_NUCLEAR
            - MESODINIUM_NUCLEAR
            - PERITRICH_NUCLEAR
            - CEPHALODISCIDAE_MITOCHONDRIAL_UAA_TYR
            type: string
          regions:
            items:
              properties:
                end:
                  description: 0-based exclusive end index. The end of the sequence is always represented as 0.
                  type: integer
                start:
                  description: 0-based inclusive start index.
                  type: integer
              type: object
            type: array
          start:
            description: 0-based inclusive start index.
            type: integer
          strand:
            example: 1
            type: integer
        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
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    RnaSequencesBulkCreateRequest:
      additionalProperties: false
      properties:
        rnaSequences:
          items:
            $ref: '#/components/schemas/RnaSequenceBulkCreate'
          maxItems: 1000
          type: array
      type: object
    AutoAnnotateRnaSequences:
      additionalProperties: false
      properties:
        featureLibraryIds:
          description: Array of feature library IDs.
          items:
            type: string
          type: array
        rnaSequenceIds:
          description: Array of RNA sequence IDs.
          items:
            type: string
          maxItems: 1000
          type: array
      required:
      - rnaSequenceIds
      - featureLibraryIds
      type: object
    RnaSequencesBulkGet:
      properties:
        rnaSequences:
          items:
            $ref: '#/components/schemas/RnaSequence'
          type: array
      type: object
    AsyncTaskLink:
      properties:
        taskId:
          type: string
      type: object
    CustomFields:
      additionalProperties:
        $ref: '#/components/schemas/CustomField'
      example:
        Legacy ID:
          value: STR100
      type: object
    RnaSequence:
      properties:
        aliases:
          items:
            type: string
          type: array
        alignmentIds:
          description: API IDs of Nucleotide Alignments involving the RNA sequence
          items:
            type: string
          type: array
        annotations:
          items:
            $ref: '#/components/schemas/RnaAnnotation'
          type: array
        apiURL:
          description: The canonical url of the RNA Sequence in the API.
          example: https://benchling.com/api/v2/rna-sequences/seq_asZya4lk
          format: uri
          readOnly: true
          type: string
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          nullable: true
        authors:
          items:
            $ref: '#/components/schemas/UserSummary'
          type: array
        bases:
          type: string
        createdAt:
          format: date-time
          readOnly: true
          type: string
        creator:
          $ref: '#/components/schemas/UserSummary'
        customFields:
          $ref: '#/components/schemas/CustomFields'
        customNotation:
          description: Representation of the RNA Sequence in the custom notation specified in the request. Null if no notation was specified.
          nullable: true
          type: string
        customNotationName:
          description: Name of the custom notation specified in the request. Null if no notation was specified.
          nullable: true
          type: string
        entityRegistryId:
          nullable: true
          type: string
        fields:
          $ref: '#/components/schemas/Fields'
        folderId:
          nullable: true
          type: string
        helm:
          description: Representation of the RNA Sequence in HELM syntax, including any chemical modifications.
          example: RNA1{r(A)p.r(C)[Ssp].r(U)p.r(U)p.r(U)p.r(U)p.r(U)p}$$$$V2.0
          nullable: true
          type: string
        id:
          type: string
        isCircular:
          example: false
          type: boolean
        length:
          type: integer
        modifiedAt:
          format: date-time
          readOnly: true
          type: string
        name:
          type: string
        parts:
          items:
            $ref: '#/components/schemas/RnaSequencePart'
          type: array
        primers:
          items:
            $ref: '#/components/schemas/Primer'
          type: array
        registrationOrigin:
          allOf:
          - $ref: '#/components/schemas/RegistrationOrigin'
          nullable: true
          readOnly: true
        registryId:
          nullable: true
          type: string
        schema:
          allOf:
          - $ref: '#/components/schemas/SchemaSummary'
          nullable: true
        translations:
          items:
            $ref: '#/components/schemas/Translation'
          type: array
        url:
          description: The path of the web URL, omitting the tenant domain
          type: string
        webURL:
          readOnly: true
          type: string
      type: object
    RnaSequenceBaseRequest:
      allOf:
      - properties:
          aliases:
            description: Aliases to add to the RNA sequence
            items:
              type: string
            type: array
          annotations:
            description: 'Annotations to create on the RNA sequence.

              '
            items:
              $ref: '#/components/schemas/RnaAnnotation'
            type: array
          authorIds:
            description: IDs of users to set as the RNA sequence's authors.
            items:
              type: string
            type: array
          bases:
            description: 'Base pairs for the RNA sequence.

              '
            type: string
          customFields:
            allOf:
            - $ref: '#/components/schemas/CustomFields'
            description: 'Custom fields to add to the RNA 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 RNA 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 RNA sequence.

              '
            type: string
          helm:
            description: Representation of the RNA sequence in HELM syntax, including any chemical modifications
            example: RNA1{r(A)p.r([impr2G])p.r(G)[Ssp].r(A)p.r(U)p.r(U)p}$$$$V2.0
            type: string
          isCircular:
            description: 'Whether the RNA sequence is circular or linear. RNA sequences can only be linear

              '
            example: false
            type: boolean
          name:
            description: 'Name of the RNA sequence.

              '
            type: string
          parts:
            items:
              $ref: '#/components/schemas/RnaSequencePart'
            type: array
          primers:
            items:
              $ref: '#/components/schemas/Primer'
            type: array
          schemaId:
            description: 'ID of the RNA sequence''s schema.

              '
            type: string
          translations:
            description: 'Translations to create on the RNA sequence. Translations are specified by either a combination of ''start'' and ''end'' fields, or a list of regions. Both cannot be provided.

              '
            items:
              $ref: '#/components/schemas/Translation'
            type: array
      - $ref: '#/components/schemas/CustomNotationRequest'
      type: object
    AutofillRnaSequences:
      additionalProperties: false
      properties:
        rnaSequenceIds:
          description: Array of RNA sequence IDs.
          items:
            type: string
          maxItems: 1000
          type: array
      required:
      - rnaSequenceIds
      type: object
    CustomNotationRequest:
      properties:
        customNotation:
          description: Representation of the sequence or oligo in the custom notation specified by customNotationId
          type: string
        customNotationId:
          description: ID of the notation used to interpret the string provided in the customNotation field
          type: string
      type: object
    RegistrationOrigin:
      properties:
        originEntryId:
          nullable: true
          readOnly: true
          type: string
        registeredAt:
          format: date-time
          readOnly: true
          type: string
      type: object
    RnaSequencesUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving RNA sequences.

        '
      properties:
        rnaSequenceIds:
          items:
            type: string
          type: array
      required:
      - rnaSequenceIds
      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
    RnaAnnotation:
      allOf:
      - $ref: '#/components/schemas/SequenceFeatureBase'
      - properties:
          end:
            description: 0-based exclusive end index. The end of the sequence is always represented as 0.
            type: integer
          start:
            description: 0-based inclusive start index.
            type: integer
          strand:
            example: 1
            maximum: 1
            minimum: 0
            type: integer
          type:
            type: string
        type: object
    RnaSequencesBulkUpdateRequest:
      additionalProperties: false
      properties:
        rnaSequences:
          items:
            $ref: '#/components/schemas/RnaSequenceBulkUpdate'
          type: array
      type: object
    RnaSequenceBulkCreate:
      allOf:
      - $ref: '#/components/schemas/RnaSequenceCreate'
    RnaSequenceRequestRegistryFields:
      properties:
        entityRegistryId:
          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