One Codex Documents API

openapi: 3.1.0
info:
  description: The One Codex API (v1) -- programmatic access to One Codex's suite of microbial genomics data storage, analysis, and query tools.
  title: One Codex API (v1) Account Documents API
  version: v1
servers:
- url: https://app.onecodex.com
security:
- apiKeyAuth: []
tags:
- name: Documents
paths:
  /api/v1/documents:
    get:
      operationId: get_documents_instances
      parameters:
      - description: Page number. Defaults to 1. See Pagination for more details.
        in: query
        name: page
        required: false
        schema:
          default: 1
          format: int32
          type: integer
      - description: Number of requested paginated records. Defaults to 50. See Pagination for more details.
        in: query
        name: per_page
        required: false
        schema:
          default: 50
          format: int32
          type: integer
      - description: 'Optional Mongo-style JSON sort clause, e.g., `sort={"created_at": true}` to sort by created_at (descending)'
        in: query
        name: sort
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          default: null
      - description: 'Optional Mongo-style JSON filter clause, e.g., `where={"$uri": {"$eq": "/api/v1/samples/0ee172af60e84f61"}}`'
        in: query
        name: where
        required: false
        schema:
          anyOf:
          - type: string
          - type: 'null'
          default: null
      responses:
        '200':
          content:
            application/json:
              schema:
                items:
                  $ref: '#/components/schemas/documents'
                type: array
          description: OK
      summary: GET documents instances
      tags:
      - Documents
  /api/v1/documents/confirm_upload:
    post:
      operationId: post_documents_instances_confirm_upload
      requestBody:
        content:
          application/json:
            schema:
              properties:
                document_id:
                  description: The `document_id` returned by `/documents/init_upload`. Note that the document will not be accessible via `/documents/<id>` until the upload is confirmed.
                  title: Document Id
                  type: string
              required:
              - document_id
              title: DocumentConfirmUploadSchema
              type: object
        required: true
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  document:
                    description: A reference to the uploaded document.
                    properties:
                      $ref:
                        example: /api/v1/documents/a1b2c3d4e5f67890
                        format: uri
                        pattern: ^/api/v1/documents/[a-f0-9]{16}$
                        type: string
                    type: object
                  message:
                    description: A success or error message.
                    title: Message
                    type: string
                  success:
                    description: Whether the upload was successful.
                    title: Success
                    type: boolean
                required:
                - document
                - message
                - success
                title: DocumentConfirmUploadResponse
                type: object
          description: OK
      summary: POST documents instances_confirm_upload
      tags:
      - Documents
  /api/v1/documents/init_multipart_upload:
    post:
      operationId: post_documents_instances_init_multipart_upload
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  callback_url:
                    title: Callback Url
                    type: string
                  file_id:
                    title: File Id
                    type: string
                  import_as_document:
                    title: Import As Document
                    type: boolean
                  s3_bucket:
                    title: S3 Bucket
                    type: string
                  upload_aws_access_key_id:
                    title: Upload Aws Access Key Id
                    type: string
                  upload_aws_secret_access_key:
                    title: Upload Aws Secret Access Key
                    type: string
                required:
                - callback_url
                - file_id
                - import_as_document
                - s3_bucket
                - upload_aws_access_key_id
                - upload_aws_secret_access_key
                title: DocumentInitMultipartUploadResponse
                type: object
          description: OK
      summary: Start a multipart upload directly to S3.
      tags:
      - Documents
  /api/v1/documents/init_upload:
    post:
      operationId: post_documents_instances_init_upload
      requestBody:
        content:
          application/json:
            schema:
              properties:
                filename:
                  description: The filename of the document to be uploaded, optionally gzipped (and ending in `.gz` or `.gzip`). Filenames should only contain alphanumeric characters, dashes, underscores, and periods.
                  title: Filename
                  type: string
                size:
                  description: The size of the file in bytes.
                  minimum: 1
                  title: Size
                  type: integer
              required:
              - filename
              - size
              title: DocumentInitUploadSchema
              type: object
        required: true
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  additional_fields:
                    additionalProperties: true
                    description: Additional fields to include in the upload.
                    title: Additional Fields
                    type: object
                  document_id:
                    description: The `document_id` of the uploaded document.
                    title: Document Id
                    type: string
                  upload_url:
                    description: The URL to POST the document to.
                    title: Upload Url
                    type: string
                required:
                - additional_fields
                - document_id
                - upload_url
                title: DocumentInitUploadResponse
                type: object
          description: OK
      summary: Deprecated in favour of init_multipart_upload
      tags:
      - Documents
  /api/v1/documents/{id}:
    delete:
      operationId: delete_documents_self
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '204':
          description: No Content
      summary: DELETE documents
      tags:
      - Documents
    get:
      operationId: get_documents_self
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/documents'
          description: OK
      summary: GET documents
      tags:
      - Documents
  /api/v1/documents/{id}/add_user:
    post:
      operationId: post_documents_add_user
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              properties:
                user:
                  properties:
                    $ref:
                      example: /api/v1/users/a1b2c3d4e5f67890
                      format: uri
                      pattern: ^/api/v1/users/[a-f0-9]{16}$
                      type: string
                  type: object
              required:
              - user
              title: DocumentAddUserSchema
              type: object
        required: true
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/documents'
          description: OK
      summary: POST documents add_user
      tags:
      - Documents
  /api/v1/documents/{id}/download_uri:
    post:
      operationId: post_documents_download_uri
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                properties:
                  download_uri:
                    description: The presigned download URL.
                    title: Download Uri
                    type: string
                  expires_in_hours:
                    description: The number of hours the download URL will be valid.
                    title: Expires In Hours
                    type: integer
                required:
                - download_uri
                - expires_in_hours
                title: DocumentDownloadSchema
                type: object
          description: OK
      summary: POST documents download_uri
      tags:
      - Documents
  /api/v1/documents/{id}/remove_user:
    post:
      operationId: post_documents_remove_user
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              properties:
                user:
                  properties:
                    $ref:
                      example: /api/v1/users/a1b2c3d4e5f67890
                      format: uri
                      pattern: ^/api/v1/users/[a-f0-9]{16}$
                      type: string
                  type: object
              required:
              - user
              title: DocumentAddUserSchema
              type: object
        required: true
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/documents'
          description: OK
      summary: POST documents remove_user
      tags:
      - Documents
  /api/v1/documents/{id}/rename:
    patch:
      operationId: patch_documents_rename
      parameters:
      - in: path
        name: id
        required: true
        schema:
          type: string
      requestBody:
        content:
          application/json:
            schema:
              properties:
                filename:
                  title: Filename
                  type: string
              required:
              - filename
              title: DocumentRenameSchema
              type: object
        required: true
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/documents'
          description: OK
      summary: PATCH documents rename
      tags:
      - Documents
components:
  schemas:
    documents:
      properties:
        $uri:
          example: /api/v1/documents/0d77065796f8d173
          pattern: ^/api/v1/documents/[a-f0-9]{16}$
          readOnly: true
          title: $Uri
          type: string
        created_at:
          description: Timestamp for when the object was created on the One Codex platform, encoded as a [RFC 3339](https://www.ietf.org/rfc/rfc3339.txt) timestamp.
          format: date-time
          title: Created At
          type: string
        downloaders:
          description: An (optionally empty) array of references to users that the document has been shared with. These users are able to download (but not modify) the document.
          items:
            properties:
              $ref:
                example: /api/v1/users/a1b2c3d4e5f67890
                format: uri
                pattern: ^/api/v1/users/[a-f0-9]{16}$
                type: string
            title: users
            type: object
          title: Downloaders
          type: array
        filename:
          description: The document filename (e.g., "report.pdf")
          title: Filename
          type: string
        size:
          anyOf:
          - minimum: 1
            type: integer
          - type: 'null'
          description: The size of the document in bytes.
          title: Size
        uploader:
          description: 'A reference to the user that uploaded and owns the document, e.g., `{"$ref": "/api/v1/users/5891ee65711c4d5e"}`. Only owners can modify a document (with some exceptions in the case of organization accounts configured for multiple users - please [contact us](mailto:support@onecodex.com) if you''d like to discuss this use case).'
          properties:
            $ref:
              example: /api/v1/users/a1b2c3d4e5f67890
              format: uri
              pattern: ^/api/v1/users/[a-f0-9]{16}$
              type: string
          title: users
          type: object
      required:
      - $uri
      - created_at
      - downloaders
      - filename
      - size
      - uploader
      title: documents
      type: object
  securitySchemes:
    apiKeyAuth:
      in: header
      name: X-API-Key
      type: apiKey