openapi: 3.0.3
info:
  title: Gencove Back array upload API
  version: v2
  contact:
    email: support@gencove.com
  license:
    name: Proprietary
  description: API for Gencove REST service. Visit <a href='https://enterprise.gencove.com/'>enterprise.gencove.com</a> and <a href='https://docs.gencove.com/'>docs.gencove.com</a> for more information. <br><hr><p>To work with Insomnia, you can generate a Gencove API key by <a target='_blank' href='https://web.gencove.com/account?filter=api-keys'>clicking here</a>. Once you have the API key and have imported the project in Insomnia as a <i>Request Collection</i>, enter the key in Insomnia under <i>Manage Environment</i>.</p><a href='https://insomnia.rest/run/?label=back_api2&uri=https%3A%2F%2Fv2-api-files-prod.s3.amazonaws.com%2Fpublic%2Finsomnia%2Finsomnia_gencove_prod.json' target='_blank'>Run in Insomnia</a><hr>
servers:
- url: https://api.gencove.com
tags:
- name: upload
paths:
  /api/v2/upload-credentials/:
    post:
      operationId: upload_credentials_create
      tags:
      - upload
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GetUploadCredentialsResponse'
          description: ''
  /api/v2/uploads/:
    get:
      operationId: uploads_list
      description: Retrieve list of user uploads.
      parameters:
      - name: limit
        required: false
        in: query
        description: Number of results to return per page.
        schema:
          type: integer
      - name: offset
        required: false
        in: query
        description: The initial index from which to return the results.
        schema:
          type: integer
      - in: query
        name: search
        schema:
          type: string
        description: Search uploads by id
      - in: query
        name: status
        schema:
          type: string
          enum:
          - failed
          - started
          - succeeded
        description: Filter uploads by upload statuses
      tags:
      - upload
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/PaginatedUploadList'
          description: ''
  /api/v2/uploads-delete-unassigned/:
    post:
      operationId: uploads_delete_unassigned_create
      tags:
      - upload
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DeletedUnassignedUploads'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/DeletedUnassignedUploads'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/DeletedUnassignedUploads'
        required: true
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DeletedUnassignedUploads'
          description: ''
  /api/v2/uploads-post-data/:
    post:
      operationId: uploads_post_data_create
      description: 'Returns info about initialized file upload based on posted file

        destination path.'
      tags:
      - upload
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/UploadPostDataCreate'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/UploadPostDataCreate'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/UploadPostDataCreate'
        required: true
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/UploadPostDataResponse'
          description: ''
  /api/v2/uploads-presigned-post-data/:
    post:
      operationId: uploads_presigned_post_data_create
      description: 'Returns S3 presigned parameters needed for file upload as response for

        given file attributes.'
      tags:
      - upload
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/UploadPostDataCreate'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/UploadPostDataCreate'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/UploadPostDataCreate'
        required: true
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/UploadPresignedPostDataResponse'
          description: ''
  /api/v2/uploads-url/:
    post:
      operationId: uploads_url_create
      tags:
      - upload
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/UploadURLCreate'
          application/x-www-form-urlencoded:
            schema:
              $ref: '#/components/schemas/UploadURLCreate'
          multipart/form-data:
            schema:
              $ref: '#/components/schemas/UploadURLCreate'
        required: true
      security:
      - JWT: []
      - API key: []
      responses:
        '201':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/UploadURLResponse'
          description: ''
  /api/v2/uploads/{upload_id}:
    get:
      operationId: uploads_retrieve
      description: Fetch single upload details
      parameters:
      - in: path
        name: upload_id
        schema:
          type: string
          format: uuid
        required: true
      tags:
      - upload
      security:
      - JWT: []
      - API key: []
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Upload'
          description: ''
components:
  schemas:
    DeletedUnassignedUploads:
      type: object
      properties:
        upload_ids:
          type: array
          items:
            type: string
            format: uuid
      required:
      - upload_ids
    UploadPresignedPostDataResponse:
      type: object
      properties:
        url:
          type: string
          format: uri
        fields:
          $ref: '#/components/schemas/AWSPresignedPostData'
      required:
      - fields
      - url
    UploadPostDataResponse:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        destination_path:
          type: string
        s3:
          allOf:
          - $ref: '#/components/schemas/S3ObjectNested'
          readOnly: true
        last_status:
          allOf:
          - $ref: '#/components/schemas/UploadStatusNested'
          readOnly: true
      required:
      - id
      - last_status
      - s3
    SourceEnum:
      enum:
      - cli
      - cli url
      - basespace
      - s3
      - array data
      type: string
      description: '* `cli` - cli

        * `cli url` - cli url

        * `basespace` - basespace

        * `s3` - s3

        * `array data` - array data'
    GetUploadCredentialsResponse:
      type: object
      properties:
        version:
          type: integer
        access_key:
          type: string
        secret_key:
          type: string
        token:
          type: string
        expiry_time:
          type: string
          format: date-time
      required:
      - access_key
      - expiry_time
      - secret_key
      - token
      - version
    UploadPostDataCreate:
      type: object
      description: Used for both normal post data and presigned post data.
      properties:
        destination_path:
          type: string
      required:
      - destination_path
    UploadURLCreate:
      type: object
      properties:
        destination_path:
          type: string
        source_url:
          type: string
          writeOnly: true
      required:
      - destination_path
      - source_url
    AWSPresignedPostData:
      type: object
      properties:
        key:
          type: string
        AWSAccessKeyId:
          type: string
        policy:
          type: string
        signature:
          type: string
      required:
      - AWSAccessKeyId
      - key
      - policy
      - signature
    S3ObjectNested:
      type: object
      properties:
        bucket:
          type: string
        object_name:
          type: string
    UploadURLResponse:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        destination_path:
          type: string
        s3:
          allOf:
          - $ref: '#/components/schemas/S3ObjectNested'
          readOnly: true
        last_status:
          allOf:
          - $ref: '#/components/schemas/UploadStatusNested'
          readOnly: true
        source:
          type: string
        source_url:
          type: string
          readOnly: true
      required:
      - id
      - last_status
      - s3
      - source
      - source_url
    FileNested:
      type: object
      description: Used for all nested files except for files associated with sample.
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        s3_path:
          type: string
          description: S3 object key
          maxLength: 1024
        size:
          type: integer
          maximum: 9223372036854775807
          minimum: -9223372036854775808
          format: int64
          nullable: true
          description: Size as reported by AWS in bytes
        download_url:
          type: string
          readOnly: true
        file_type:
          type: string
          description: File extension
          readOnly: true
        checksum_sha256:
          type: string
          description: Object's sha256 Checksum
          maxLength: 64
        shadow_mode:
          type: boolean
          nullable: true
          description: If true, file is only accessible by organizations with shadow mode access enabled.
      required:
      - download_url
      - file_type
      - id
    PaginatedUploadList:
      type: object
      required:
      - results
      properties:
        meta:
          type: object
          properties:
            count:
              type: integer
            next:
              type: string
              format: uri
              nullable: true
            previous:
              type: string
              format: uri
              nullable: true
          required:
          - count
        results:
          type: array
          items:
            $ref: '#/components/schemas/Upload'
    UploadStatusNested:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        status:
          type: string
        note:
          type: string
        created:
          type: string
          format: date-time
      required:
      - id
      - status
    Upload:
      type: object
      properties:
        id:
          type: string
          format: uuid
          readOnly: true
        last_status:
          allOf:
          - $ref: '#/components/schemas/UploadStatusNested'
          readOnly: true
        file:
          $ref: '#/components/schemas/FileNested'
        created:
          type: string
          format: date-time
        destination_path:
          type: string
          description: Destination path given by the user as an optional argument
          maxLength: 1024
        source:
          $ref: '#/components/schemas/SourceEnum'
        user:
          type: string
          format: uuid
          nullable: true
        organization:
          type: string
          format: uuid
      required:
      - file
      - id
      - last_status
      - organization
      - source
  securitySchemes:
    API key:
      type: apiKey
      description: 'Authorization header content formated as: `Api-Key <API-key>`

        You can obtain new API key through Gencove''s web UI or `user-api-key` endpoint'
      in: header
      name: Authorization
    JWT:
      type: apiKey
      description: 'Authorization header content formated as: `Bearer <json-web-token>`

        You can obtain access token using `jwt-create` endpoint.'
      in: header
      name: Authorization