openapi: 3.0.1
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling AA Sequences Files 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: Files are Benchling objects that represent files and their metadata. Compared to Blobs, which are used by most Benchling products for attachments, Files are primarily used in the Analysis and Connect product.
  name: Files
paths:
  /files:
    get:
      description: List files
      operationId: listFiles
      parameters:
      - $ref: '#/components/parameters/listingPageSize'
      - $ref: '#/components/parameters/listingNextToken'
      - $ref: '#/components/parameters/listingSortNameModifiedCreated'
      - $ref: '#/components/parameters/archiveReasonFilter'
      - $ref: '#/components/parameters/createdAtFilter'
      - $ref: '#/components/parameters/creatorIdsFilter'
      - $ref: '#/components/parameters/folderIdFilter'
      - $ref: '#/components/parameters/mentionedInFilter'
      - $ref: '#/components/parameters/modifiedAtFilter'
      - $ref: '#/components/parameters/nameFilter'
      - $ref: '#/components/parameters/nameIncludesFilter'
      - $ref: '#/components/parameters/namesAnyOfCaseSensitiveFilter'
      - $ref: '#/components/parameters/namesAnyOfFilter'
      - $ref: '#/components/parameters/originFilter'
      - 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: file_Q6uhNZvw,file_OwmERWGE,file_nzuDFhNvz
          type: string
      - description: 'Comma-separated list of display ids. Matches all of the provided IDs, or returns a 400 error that includes a list of which IDs are invalid.

          '
        in: query
        name: displayIds
        schema:
          example: FILE1,FILE2,FILE3
          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: files.id,files.modifiedAt
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FilesPaginatedList'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ListingError'
          description: Bad Request
      summary: List files
      tags:
      - Files
    post:
      description: "Create a file of a supported type. Currently, we support these file extensions: .csv; .html;\n.jmp, .jrn, .jrp (JMP); .jpeg, .jpg (JPEG); .png; .pdf; .zip; and .txt.\n\nA successful file upload requires 3 calls in serial:\n1. [Create a file](#/Analyses/createFile), this endpoint, which returns an S3 `PUT` URL for the 2nd\n   call and a file ID for the 3rd call\n2. Upload the file contents to S3. Add `x-amz-server-side-encryption: AES256` to the request headers,\n   because we use server-side encryption. Here is a `curl` example:\n   ```bash\n   curl -H \"x-amz-server-side-encryption: AES256\" -X PUT -T <LOCAL_FILE> -L <S3_PUT_URL>\n   ```\n3. [Update the file](#/Analyses/patchFile), which marks the upload as `SUCCEEDED`\n\nNote: URL is valid for 1 hour after being returned from this endpoint. It should not be stored\npersistently for later use.\n\nFiles up to 30MB are supported.\n"
      operationId: createFile
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FileCreate'
      responses:
        '200':
          content:
            application/json:
              example:
                errorMessage: null
                folderId: lib_bf0636
                id: file_Of5GuBSq
                name: IC50Chart.png
                uploadStatus: NOT_UPLOADED
              schema:
                $ref: '#/components/schemas/File'
          description: OK
          headers:
            Content-Location:
              description: The S3 URL to which the file contents can be uploaded
              schema:
                example: 'https://benchling-location.s3.amazonaws.com/deploys/location/pipeline_files/.../IC50Chart.png?...

                  '
                type: string
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '403':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ForbiddenError'
          description: Forbidden
      summary: Create a file
      tags:
      - Files
  /files/{file_id}:
    get:
      description: 'Get a file. This endpoint returns an S3 URL, from which you can download the file contents.


        Note: URL is valid for 1 hour after being returned from this endpoint. It should not be stored

        persistently for later use.

        '
      operationId: getFile
      parameters:
      - description: The ID of the file
        in: path
        name: file_id
        required: true
        schema:
          example: file_Of5GuBSq
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/File'
          description: OK
          headers:
            Content-Location:
              description: The S3 URL from which the file contents can be downloaded
              schema:
                example: 'https://benchling-location.s3.amazonaws.com/deploys/location/pipeline_files/.../IC50Chart.png?...

                  '
                type: string
        '403':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ForbiddenError'
          description: Forbidden
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Get a file
      tags:
      - Files
    patch:
      description: 'Update a file. After you upload the file contents to S3, call this endpoint to mark the upload as `SUCCEEDED`. See [Create a file](#/Analyses/createFile) for documentation of the full upload flow.

        '
      operationId: patchFile
      parameters:
      - description: The ID of the file
        example: file_Of5GuBSq
        in: path
        name: file_id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FileUpdate'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/File'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
        '403':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ForbiddenError'
          description: Forbidden
        '404':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/NotFoundError'
          description: Not Found
      summary: Update a file
      tags:
      - Files
  /files:archive:
    post:
      description: Archive files
      operationId: archiveFiles
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FilesArchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FilesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Archive files
      tags:
      - Files
  /files:unarchive:
    post:
      description: Unarchive files.
      operationId: unarchiveFiles
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/FilesUnarchive'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FilesArchivalChange'
          description: OK
        '400':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/BadRequestError'
          description: Bad Request
      summary: Unarchive files.
      tags:
      - Files
components:
  parameters:
    listingPageSize:
      description: Number of results to return.
      in: query
      name: pageSize
      schema:
        default: 50
        maximum: 100
        minimum: 0
        nullable: false
        type: integer
    folderIdFilter:
      description: ID of a folder. Restricts results to those in the folder.
      in: query
      name: folderId
      schema:
        example: lib_a0SApq3z
        type: string
    originFilter:
      description: Comma-separated list of item IDs. Restricts results to those whose origin parent is any of the specified items.
      in: query
      name: originIds
      schema:
        example: cxn_a0SApq3z,ana_jdf8BV24
        type: string
    modifiedAtFilter:
      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
    listingNextToken:
      example: Im5ldyB0ZXN0Ig==
      in: query
      name: nextToken
      schema:
        type: string
    mentionedInFilter:
      description: 'Comma-separated list of entry IDs. Restricts results to items mentioned in those entries.

        '
      in: query
      name: mentionedIn
      schema:
        example: etr_1X1AlQPD, etr_tv7m7B78
        type: string
    nameFilter:
      description: Restricts results to those with the specified name.
      in: query
      name: name
      schema:
        type: string
    createdAtFilter:
      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
    creatorIdsFilter:
      description: Comma separated list of user IDs.
      in: query
      name: creatorIds
      schema:
        example: ent_a0SApq3z
        type: string
    namesAnyOfFilter:
      description: 'Comma-separated list of names. Maximum of 100. Restricts results to those that match any of the specified names, case insensitive.  Warning - this filter can be non-performant due to case insensitivity.

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

        '
      in: query
      name: names.anyOf.caseSensitive
      schema:
        example: MyName1,MyName2
        type: string
    archiveReasonFilter:
      description: 'Archive reason. Restricts items to those with the specified archive reason. Use "NOT_ARCHIVED" to filter for unarchived items. Use "ANY_ARCHIVED" to filter for archived items 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
    nameIncludesFilter:
      description: 'Name substring. Restricts results to those with names that include the provided substring.

        '
      in: query
      name: nameIncludes
      schema:
        type: string
    listingSortNameModifiedCreated:
      description: 'Method by which to order search results. Valid sorts are modifiedAt (modified time, most recent first) createdAt (creation time, most recent first) and name (item name, alphabetical). Optionally add :asc or :desc to specify ascending or descending order. Default is modifiedAt.

        '
      in: query
      name: sort
      schema:
        default: modifiedAt
        enum:
        - modifiedAt
        - name
        - createdAt
        - modifiedAt:asc
        - name:asc
        - createdAt:asc
        - modifiedAt:desc
        - name:desc
        - createdAt:desc
        nullable: false
        type: string
  schemas:
    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
    FilesPaginatedList:
      properties:
        files:
          items:
            $ref: '#/components/schemas/File'
          type: array
        nextToken:
          type: string
      type: object
    ListingError:
      allOf:
      - $ref: '#/components/schemas/BadRequestError'
      properties:
        invalidIds:
          items:
            type: string
          type: array
      type: object
    BaseError:
      properties:
        message:
          type: string
        type:
          type: string
        userMessage:
          type: string
      type: object
    FilesArchive:
      additionalProperties: false
      description: 'The request body for archiving Files.

        '
      properties:
        fileIds:
          items:
            type: string
          maxItems: 100
          type: array
        reason:
          description: 'The reason for archiving the provided Files. Accepted reasons may differ based on tenant configuration.

            '
          enum:
          - Made in error
          - Archived
          - Other
          type: string
      required:
      - reason
      - fileIds
      type: object
    ArchiveRecord:
      properties:
        reason:
          example: Made in error
          type: string
      type: object
    FileCreate:
      properties:
        customFields:
          allOf:
          - $ref: '#/components/schemas/CustomFields'
          description: Custom field values to set on the file
        filename:
          description: Filename for the file
          example: IC50Chart.png
          nullable: false
          type: string
        folderId:
          description: ID of the folder that contains the file
          example: lib_bf0636
          nullable: false
          type: string
        name:
          description: Display name for the file
          example: IC50 Chart
          nullable: false
          type: string
      type: object
    File:
      allOf:
      - $ref: '#/components/schemas/FileStatus'
      - properties:
          archiveRecord:
            allOf:
            - $ref: '#/components/schemas/ArchiveRecord'
            description: 'ArchiveRecord Resource if the file is archived. This is null if the file is not archived.

              '
            nullable: true
          createdAt:
            description: Date and time the file was created
            example: 2023-04-23 01:30:50.970926+00:00
            format: date-time
            readOnly: true
            type: string
          creator:
            allOf:
            - $ref: '#/components/schemas/UserSummary'
            - description: UserSummary of the user who created the file
            - readOnly: true
          customFields:
            allOf:
            - $ref: '#/components/schemas/CustomFields'
            description: Custom field values of the file
          displayId:
            description: User-friendly ID of the file
            readOnly: true
            type: string
          filename:
            example: IC50Chart.png
            type: string
          folderId:
            description: ID of the folder that contains the file
            example: lib_bf0636
            nullable: false
            type: string
          id:
            example: file_Of5GuBSq
            type: string
          modifiedAt:
            description: Date and time the file was last modified
            example: 2023-04-23 01:30:50.970926+00:00
            format: date-time
            readOnly: true
            type: string
          name:
            example: IC50 Chart
            type: string
        type: object
    UserSummary:
      allOf:
      - $ref: '#/components/schemas/PartySummary'
      - example:
          handle: lpasteur
          id: ent_a0SApq3z
          name: Louis Pasteur
    FilesUnarchive:
      additionalProperties: false
      description: 'The request body for unarchiving Files.

        '
      properties:
        fileIds:
          items:
            type: string
          maxItems: 100
          type: array
      required:
      - fileIds
      type: object
    ForbiddenError:
      properties:
        error:
          properties:
            invalidId:
              type: string
            message:
              type: string
            type:
              type: string
            userMessage:
              type: string
          type: object
      type: object
    PartySummary:
      properties:
        handle:
          type: string
        id:
          type: string
        name:
          type: string
      type: object
    FileUpdate:
      properties:
        customFields:
          allOf:
          - $ref: '#/components/schemas/CustomFields'
          description: Custom field values to add to the file
        errorMessage:
          description: Error message for the file upload
          type: string
        folderId:
          description: ID of the folder that the file is moved into
          example: lib_bf0636
          type: string
        uploadStatus:
          enum:
          - SUCCEEDED
          - FAILED_VALIDATION
          type: string
      type: object
    CustomFields:
      additionalProperties:
        $ref: '#/components/schemas/CustomField'
      example:
        Legacy ID:
          value: STR100
      type: object
    NotFoundError:
      properties:
        error:
          allOf:
          - $ref: '#/components/schemas/BaseError'
          - properties:
              invalidId:
                type: string
              type:
                enum:
                - invalid_request_error
                type: string
      type: object
    FilesArchivalChange:
      additionalProperties: false
      description: 'IDs of all items that were archived or unarchived, grouped by resource type.

        '
      properties:
        fileIds:
          items:
            type: string
          type: array
      type: object
    FileStatus:
      properties:
        errorMessage:
          example: null
          nullable: true
          type: string
        uploadStatus:
          enum:
          - IN_PROGRESS
          - SUCCEEDED
          - FAILED_VALIDATION
          - NOT_UPLOADED
          example: SUCCEEDED
          type: string
      type: object
  securitySchemes:
    basicApiKeyAuth:
      description: Use issued API key for standard access to the API
      scheme: basic
      type: http
    basicClientIdSecretAuth:
      description: Auth used as part of client credentials OAuth flow prior to receiving a bearer token.
      scheme: basic
      type: http
    oAuth:
      description: OAuth2 Client Credentials flow intended for service access
      flows:
        clientCredentials:
          scopes: {}
          tokenUrl: /api/v2/token
      type: oauth2
externalDocs:
  description: Additional API Documentation
  url: https://docs.benchling.com