openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences DNA Oligos 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: DNA Oligos are short linear DNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.
  name: DNA Oligos
paths:
  /custom-notations:
    get:
      description: List all available custom notations for specifying modified nucleotide sequences
      operationId: listCustomNotations
      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
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CustomNotationsPaginatedList'
          description: OK
      summary: List custom notations
      tags:
      - DNA Oligos
  /dna-oligos:
    get:
      description: List DNA Oligos
      operationId: listDNAOligos
      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 a DNA Oligo. Restricts results to those with the specified name, alias, or entity registry ID.
        in: query
        name: name
        schema:
          type: string
      - description: Name substring of a DNA Oligo. 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 DNA Oligo. 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 DNA Oligos 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 DNA Oligos. Use "ANY_ARCHIVED" to filter for archived DNA Oligos 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_yWs5X7lv,seq_RhYGVnHF
          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).
        in: query
        name: returning
        schema:
          example: dnaOligos.id,dnaOligos.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/DnaOligosPaginatedList'
          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 DNA Oligos
      tags:
      - DNA Oligos
    post:
      description: Create a DNA Oligo
      operationId: createDNAOligo
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligoCreate'
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DnaOligo'
          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 a DNA Oligo
      tags:
      - DNA Oligos
  /dna-oligos/{entity_registry_id}:upsert:
    patch:
      description: 'Create or update a registered DNA oligo.


        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: upsertDnaOligo
      parameters:
      - example: entity_registry_id_001
        in: path
        name: entity_registry_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/OligoUpsertRequest'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DnaOligo'
          description: Updated
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DnaOligo'
          description: Created
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Create or update a registered DNA oligo
      tags:
      - DNA Oligos
  /dna-oligos/{oligo_id}:
    get:
      description: Get a DNA Oligo
      operationId: getDNAOligo
      parameters:
      - in: path
        name: oligo_id
        required: true
        schema:
          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/DnaOligo'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Get a DNA Oligo
      tags:
      - DNA Oligos
    patch:
      description: Update a DNA Oligo
      operationId: updateDNAOligo
      parameters:
      - in: path
        name: oligo_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligoUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DnaOligo'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Update a DNA Oligo
      tags:
      - DNA Oligos
  /dna-oligos:archive:
    post:
      description: Archive DNA Oligos
      operationId: archiveDNAOligos
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligosArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DnaOligosArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive DNA Oligos
      tags:
      - DNA Oligos
  /dna-oligos:bulk-create:
    post:
      description: Bulk Create DNA Oligos. Limit of 1000 DNA Oligos per request.
      operationId: bulkCreateDNAOligos
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligosBulkCreateRequest'
      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 DNA Oligos that were created.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Create DNA Oligos
      tags:
      - DNA Oligos
  /dna-oligos:bulk-update:
    post:
      description: Bulk Update DNA Oligos
      operationId: bulkUpdateDNAOligos
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligosBulkUpdateRequest'
      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 [DNA Oligo](#/DNA%20Oligos/getDNAOligo) resources that were updated.

            '
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Bulk Update DNA Oligos
      tags:
      - DNA Oligos
  /dna-oligos: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.


        Limit of 1000 entities per request.

        '
      operationId: bulkUpsertDNAOligos
      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: dnaOligos.id,dnaOligos.creator.handle
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligosBulkUpsertRequest'
      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 DNA oligos
      tags:
      - DNA Oligos
  /dna-oligos:unarchive:
    post:
      description: Unarchive DNA Oligos
      operationId: unarchiveDNAOligos
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DnaOligosUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DnaOligosArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive DNA Oligos
      tags:
      - DNA Oligos
components:
  schemas:
    CustomNotationsPaginatedList:
      allOf:
      - $ref: '#/components/schemas/Pagination'
      - properties:
          customNotations:
            items:
              $ref: '#/components/schemas/CustomNotation'
            type: array
      type: object
    DnaOligosBulkUpsertRequest:
      additionalProperties: false
      maxItems: 1000
      properties:
        dnaOligos:
          items:
            $ref: '#/components/schemas/OligoBulkUpsertRequest'
          type: array
      required:
      - dnaOligos
      type: object
    DnaOligoUpdate:
      allOf:
      - $ref: '#/components/schemas/OligoUpdate'
      - properties:
          annotations:
            description: Annotations on the Oligo.
            items:
              $ref: '#/components/schemas/DnaAnnotation'
            type: array
          helm:
            description: Representation of the oligo in HELM syntax, including any chemical modifications
            example: RNA1{d(A)p.d([impd2G])p.d(G)[Ssp].d(A)p.d(T)p.d(T)p}$$$$V2.0
            type: string
      - $ref: '#/components/schemas/CustomNotationRequest'
    Fields:
      additionalProperties:
        $ref: '#/components/schemas/Field'
      type: object
    DnaOligosUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving DNA Oligos.

        '
      properties:
        dnaOligoIds:
          items:
            type: string
          type: array
      required:
      - dnaOligoIds
      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
    BadRequestError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    DnaOligoBulkUpdate:
      additionalProperties: false
      allOf:
      - properties:
          id:
            type: string
        type: object
      - $ref: '#/components/schemas/DnaOligoUpdate'
    OligoBulkUpsertRequest:
      allOf:
      - $ref: '#/components/schemas/EntityBulkUpsertBaseRequest'
      - $ref: '#/components/schemas/OligoBaseRequestForCreate'
    CustomNotationAlias:
      properties:
        baseMonomerId:
          example: mon_a1b2c3
          type: string
        customNotationId:
          example: sntx_a1b2c3
          type: string
        id:
          example: sntxals_a1b2c3
          type: string
        phosphateMonomerId:
          example: mon_a1b2c3
          nullable: true
          type: string
        rank:
          type: number
        sugarMonomerId:
          example: mon_a1b2c3
          type: string
        token:
          type: string
        tokenVariantEnd:
          nullable: true
          type: string
        tokenVariantStart:
          nullable: true
          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
    DnaAnnotation:
      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:
            maximum: 1
            minimum: -1
            type: integer
          type:
            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
    ArchiveRecordSet:
      additionalProperties: false
      description: Currently, we only support setting a null value for archiveRecord, which unarchives the item
      example: null
      nullable: true
      type: object
    DnaOligosArchivalChange:
      description: 'IDs of all items that were archived or unarchived, grouped by resource type. This includes the IDs of DNA Oligos along with any IDs of batches that were archived / unarchived.

        '
      properties:
        batchIds:
          items:
            type: string
          type: array
        dnaOligoIds:
          items:
            type: string
          type: array
      type: object
    DnaOligosArchive:
      additionalProperties: false
      description: 'The request body for archiving DNA Oligos.

        '
      properties:
        dnaOligoIds:
          items:
            type: string
          type: array
        reason:
          $ref: '#/components/schemas/EntityArchiveReason'
      required:
      - reason
      - dnaOligoIds
      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
    Pagination:
      properties:
        nextToken:
          type: string
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    DnaOligosBulkCreateRequest:
      additionalProperties: false
      properties:
        dnaOligos:
          items:
            $ref: '#/components/schemas/DnaOligoCreate'
          maxItems: 1000
          type: array
      type: object
    DnaOligo:
      allOf:
      - $ref: '#/components/schemas/Oligo'
      - properties:
          annotations:
            description: Annotations on the Oligo.
            items:
              $ref: '#/components/schemas/DnaAnnotation'
            type: array
          apiURL:
            example: https://benchling.com/api/v2/dna-oligos/seq_bhuDUw9D
            type: string
          bases:
            example: ACTTTTT
            type: string
          customNotation:
            description: Representation of the oligo 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
          helm:
            description: Representation of the oligo in HELM syntax, including any chemical modifications
            example: RNA1{d(A)p.d(C)[Ssp].d(T)p.d(T)p.d(T)p.d(T)p.d(T)p}$$$$V2.0
            type: string
    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
    OligoBaseRequestForCreate:
      allOf:
      - $ref: '#/components/schemas/OligoBaseRequest'
      - required:
        - name
    OligoBaseRequest:
      properties:
        aliases:
          description: Aliases to add to the Oligo
          items:
            type: string
          type: array
        authorIds:
          description: IDs of users to set as the Oligo's authors.
          items:
            type: string
          type: array
        bases:
          description: 'Base pairs of the oligo.

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

            '
          type: string
        name:
          description: 'Name of the Oligo.

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

            '
          type: string
      type: object
    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
    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
    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
    OligoCreate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/OligoBaseRequestForCreate'
      - $ref: '#/components/schemas/CreateEntityIntoRegistry'
    DnaOligoCreate:
      allOf:
      - $ref: '#/components/schemas/OligoCreate'
      - properties:
          annotations:
            description: Annotations on the Oligo.
            items:
              $ref: '#/components/schemas/DnaAnnotation'
            type: array
          helm:
            description: Representation of the oligo in HELM syntax, including any chemical modifications
            example: RNA1{d(A)p.d([impd2G])p.d(G)[Ssp].d(A)p.d(T)p.d(T)p}$$$$V2.0
            type: string
      - $ref: '#/components/schemas/CustomNotationRequest'
      - required:
        - name
    AsyncTaskLink:
      properties:
        taskId:
          type: string
      type: object
    DnaOligosPaginatedList:
      allOf:
      - $ref: '#/components/schemas/Pagination'
      - properties:
          dnaOligos:
            items:
              $ref: '#/components/schemas/DnaOligo'
            type: array
    CustomFields:
      additionalProperties:
        $ref: '#/components/schemas/CustomField'
      example:
        Legacy ID:
          value: STR100
      type: object
    EntityBulkUpsertBaseRequest:
      allOf:
      - $ref: '#/components/schemas/EntityUpsertBaseRequest'
      - properties:
          entityRegistryId:
            description: Registry ID of the entity in Benchling.
            type: string
      - required:
        - entityRegistryId
    Oligo:
      discriminator:
        mapping:
          DNA: DnaOligo
          RNA: RnaOligo
        propertyName: nucleotideType
      properties:
        aliases:
          description: Array of aliases
          items:
            type: string
          type: array
        apiURL:
          description: The canonical url of the Oligo in the API.
          format: uri
          readOnly: true
          type: string
        archiveRecord:
          allOf:
          - $ref: '#/components/schemas/ArchiveRecord'
          nullable: true
        authors:
          items:
            $ref: '#/components/schemas/UserSummary'
          type: array
        bases:
          description: Base pairs of the Oligo.
          example: ACTTTTT
          type: string
        createdAt:
          description: DateTime the Oligo 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 Oligo.
        entityRegistryId:
          description: Registry ID of the Oligo if registered.
          nullable: true
          type: string
        fields:
          $ref: '#/components/schemas/Fields'
        folderId:
          description: ID of the folder that contains the Oligo.
          nullable: true
          type: string
        id:
          description: ID of the Oligo.
          example: seq_bhuDUw9D
          type: string
        length:
          description: Number of bases in the Oligo.
          type: integer
        modifiedAt:
          description: DateTime the Oligo was last modified.
          format: date-time
          readOnly: true
          type: string
        name:
          description: Name of the Oligo.
          type: string
        nucleotideType:
          description: Nucleotide type of the Oligo.
          enum:
          - DNA
          - RNA
          type: string
        registrationOrigin:
          allOf:
          - $ref: '#/components/schemas/RegistrationOrigin'
          nullable: true
          readOnly: true
        registryId:
          description: Registry the Oligo is registered in.
          nullable: true
          type: string
        schema:
          allOf:
          - $ref: '#/components/schemas/SchemaSummary'
          nullable: true
        webURL:
          description: URL of the Oligo.
          example: https://benchling.com/benchling/f/lib_hBHqKbzE-oligos/seq_bhuDUw9D-test-oligo-abc/edit
          format: uri
          readOnly: true
          type: string
      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
    DnaOligosBulkUpdateRequest:
      additionalProperties: false
      properties:
        dnaOligos:
          items:
            $ref: '#/components/schemas/DnaOligoBulkUpdate'
          type: array
      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
    OligoUpsertRequest:
      allOf:
      - $ref: '#/components/schemas/EntityUpsertBaseRequest'
      - $ref: '#/components/schemas/OligoBaseRequestForCreate'
    CustomNotation:
      properties:
        aliases:
          items:
            $ref: '#/components/schemas/CustomNotationAlias'
          type: array
        id:
          example: sntx_lRe007yZ
          type: string
        name:
          example: Your Custom Notation
          type: string
      type: object
    OligoUpdate:
      additionalProperties: false
      allOf:
      - $ref: '#/components/schemas/OligoBaseRequest'
    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