Seven Bridges Upload API

openapi: 3.2.0
info:
  title: Seven Bridges Upload API
  version: unknown
  description: 'Operations tagged Upload across 2 of this provider''s published API definitions: seven-bridges-cgc-openapi.json, seven-bridges-platform-openapi.json. Each path carries the servers of the definition it was published in.'
servers:
- url: https://cgc-api.sbgenomics.com/v2
- url: https://api.sbgenomics.com/v2
security:
- {}
tags:
- name: Upload
paths:
  /v2/upload/multipart/{upload_id}/part:
    post:
      summary: Report an uploaded part
      description: /upload/multipart/{upload_id}/part
      operationId: report-an-uploaded-part
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: '{}'
              schema:
                type: object
                properties: {}
        '400':
          description: '400'
          content:
            application/json:
              examples:
                Result:
                  value: '{}'
              schema:
                type: object
                properties: {}
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://cgc-api.sbgenomics.com/v2
  /v2/upload/multipart/{upload_id}/part/{part_number}:
    get:
      summary: Get upload URL for a file part
      description: /upload/multipart/{upload_id}/part/{part_number}
      operationId: get-upload-url-for-a-file-part
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: '{}'
              schema:
                type: object
                properties: {}
        '400':
          description: '400'
          content:
            application/json:
              examples:
                Result:
                  value: '{}'
              schema:
                type: object
                properties: {}
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://cgc-api.sbgenomics.com/v2
  /v2/upload/multipart/{upload_id}:
    post:
      summary: Report uploaded parts
      description: /upload/multipart/{upload_id}
      operationId: report-uploaded-parts
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: '{}'
              schema:
                type: object
                properties: {}
        '400':
          description: '400'
          content:
            application/json:
              examples:
                Result:
                  value: '{}'
              schema:
                type: object
                properties: {}
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://cgc-api.sbgenomics.com/v2
  /upload/multipart/{upload_id}/part/{part_number}:
    get:
      summary: Get upload URL for a file part
      description: This call returns the signed URL required to upload a part of a multipart upload. Once you have obtained this URL for your file part, you can make a `PUT` request to it with the file part as the request body.
      operationId: get-the-upload-url-for-a-file-part
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: upload_id
        in: path
        description: The ID for the upload, returned by the call to [initialize a multipart upload](ref:initialize-a-multipart-upload).
        schema:
          type: string
        required: true
      - name: part_number
        in: path
        description: The number of the file part you are uploading. Part numbers start from 1.
        schema:
          type: integer
          format: int32
        required: true
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: "{\n  \"method\": \"PUT\",\n  \"url\": \"https://bucket-name.s3.amazonaws.com/bd5e95d9-12b3-789c-45b6-34d8696571a9%2BCanFam3.1.dna_rm.toplevel.fa.gz?uploadId=Yrand0mVyTZj2Vc2WwKAQtXUhBFZDzax20oaBf12mSixrrcm78sBzB8YGxUgQi1K&partNumber=1&AWSAccessKeyId=REDACTED_AWS_ACCESS_KEY_ID&Expires=1459113561&Signature=3myyeand0mjkmjX24WApZwNo%3D\",\n  \"expires\": \"2016-02-27T15:55:38Z\",\n  \"headers\": {},\n  \"report\": {\n    \"success_codes\": [\n      200\n    ],\n    \"headers\": [\n      \"ETag\"\n    ]\n  }\n}"
              schema:
                type: object
                properties:
                  method:
                    type: string
                    example: PUT
                  url:
                    type: string
                    example: https://bucket-name.s3.amazonaws.com/bd5e95d9-12b3-789c-45b6-34d8696571a9%2BCanFam3.1.dna_rm.toplevel.fa.gz?uploadId=Yrand0mVyTZj2Vc2WwKAQtXUhBFZDzax20oaBf12mSixrrcm78sBzB8YGxUgQi1K&partNumber=1&AWSAccessKeyId=REDACTED_AWS_ACCESS_KEY_ID&Expires=1459113561&Signature=3myyeand0mjkmjX24WApZwNo%3D
                  expires:
                    type: string
                    example: '2016-02-27T15:55:38Z'
                  headers:
                    type: object
                    properties: {}
                  report:
                    type: object
                    properties:
                      success_codes:
                        type: array
                        items:
                          type: integer
                          example: 200
                          default: 0
                      headers:
                        type: array
                        items:
                          type: string
                          example: ETag
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://api.sbgenomics.com/v2
  /upload/multipart/{upload_id}:
    get:
      summary: Get details of a multipart upload
      description: 'This call will return the details of an active multipart upload.


        The upload is referenced by its ID as returned by a call to initialize a multipart upload or list current multipart uploads.'
      operationId: get-details-of-a-multipart-upload
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: upload_id
        in: path
        description: The ID of the upload. It can be obtained by [initializing a new upload](ref:initialize-a-multipart-upload) or by [listing the ongoing multipart uploads](ref:list-current-multipart-uploads).
        schema:
          type: string
        required: true
      - name: list_parts
        in: query
        description: If `true`, also return a list of parts that have been reported as completed for this multipart upload.
        schema:
          type: boolean
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: "{\n  \"upload_id\": \"Zrand0mrFtYj3rooeFcnawiVhoZp1sF0OK3RVvpWucTKGtNpvDvXFrj4JKOU1qyV\",\n  \"project\": \"RFranklin/my-project\",\n  \"name\": \"1000G_omni2.5.b37.vcf\",\n  \"initiated\": \"2016-01-01T00:00:00Z\",\n  \"parallel_uploads\": true,\n  \"part_size\": 1073741824,\n  \"uploaded_parts_count\": 1,\n  \"parts\": [\n    {\n      \"part_number\": 1,\n      \"response\": {\n        \"headers\": {\n          \"ETag\": \"1234e128411f2bace2sadfdabe610f30\"\n        }\n      }\n    }\n  ]\n}"
              schema:
                type: object
                properties:
                  upload_id:
                    type: string
                    example: Zrand0mrFtYj3rooeFcnawiVhoZp1sF0OK3RVvpWucTKGtNpvDvXFrj4JKOU1qyV
                  project:
                    type: string
                    example: RFranklin/my-project
                  name:
                    type: string
                    example: 1000G_omni2.5.b37.vcf
                  initiated:
                    type: string
                    example: '2016-01-01T00:00:00Z'
                  parallel_uploads:
                    type: boolean
                    example: true
                    default: true
                  part_size:
                    type: integer
                    example: 1073741824
                    default: 0
                  uploaded_parts_count:
                    type: integer
                    example: 1
                    default: 0
                  parts:
                    type: array
                    items:
                      type: object
                      properties:
                        part_number:
                          type: integer
                          example: 1
                          default: 0
                        response:
                          type: object
                          properties:
                            headers:
                              type: object
                              properties:
                                ETag:
                                  type: string
                                  example: 1234e128411f2bace2sadfdabe610f30
      deprecated: false
      tags:
      - Upload
    delete:
      summary: Abort a multipart upload
      description: This call aborts an ongoing upload.
      operationId: abort-a-multipart-upload
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: upload_id
        in: path
        description: The ID for the upload, returned by a call to [initialize a multipart upload](ref:initialize-a-multipart-upload) or to [list current multipart uploads](ref:list-current-multipart-uploads).
        schema:
          type: string
        required: true
      deprecated: false
      x-readme:
        code-samples:
        - language: python
          code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n          token='1e43fEXampLEa5523dfd14exAMPle3e5')\n\n# create and start upload without blocking by using wait=False\nupload = api.files.upload(\n    path='CanFam3.1.dna_rm.toplevel.fa.gz',\n    project='RFranklin/my-project',\n    wait=False\n)\nupload.start()\n\n# send DELETE request to SB API\nupload.stop()"
        samples-languages:
        - python
      tags:
      - Upload
    post:
      summary: Report uploaded parts
      description: This call allows you to report the upload multiple file parts at once.
      operationId: report-that-all-file-parts-have-uploaded
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: upload_id
        in: path
        description: The ID for the upload, returned by the call to [initialize a multipart upload](ref:initialize-a-multipart-upload).
        schema:
          type: string
        required: true
      requestBody:
        content:
          application/json:
            schema:
              type: object
              properties:
                parts:
                  type: array
                  description: This key should contain an array of objects describing the individual part upload reports. Each of these objects should be formatted exactly as the whole body of the [report an uploaded part](ref:report-an-uploaded-file-part) call.
                  items:
                    properties:
                      part_number:
                        type: integer
                        description: The number of the file part you are reporting. Part numbers start from 1.
                        format: int32
                      response:
                        type: object
                        properties:
                          headers:
                            type: object
                            properties:
                              '{key}':
                                type: string
                                description: You should format the response object in this call as a set of key-value mappings. The keys in these mappings are the headers and other response elements described in [getting upload URL for a file part](ref:get-the-upload-url-for-a-file-part), and their values are the strings that you have collected from the HTTP part upload request.
                                default: '{value}'
                    type: object
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://api.sbgenomics.com/v2
  /upload/multipart:
    post:
      summary: Initialize a multipart upload
      description: This call initializes a multipart file upload.
      operationId: initialize-a-multipart-upload
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: overwrite
        in: query
        description: If `overwrite` is set to `true` and a file already exists under the name specified in the request, the existing file will be deleted and a new one created in its place.
        schema:
          type: boolean
      requestBody:
        content:
          application/json:
            schema:
              type: object
              required:
              - name
              properties:
                project:
                  type: string
                  description: The name of the project you want to upload a file to, in the (`<username>/<project-name>`) format.
                parent:
                  type: string
                  description: The ID of the folder to which the item is being uploaded.  Should not be used together with `project`. If `parent` is used, the upload will take place into the specified folder, within the project to which the folder belongs. If `project` is used, the items will be imported to the root of the project's files.
                name:
                  type: string
                  description: The name of the file you are about to upload. This must be unique in the project, unless you are also enabling the `overwrite` query parameter.  Allowed characters in **file names** are all alphanumerics and special characters except slash (`/`). File names can’t be longer than 255 characters.
                size:
                  type: integer
                  description: The size of the file that will be uploaded. This can be used to track progress of an ongoing upload, but is otherwise optional.
                  format: int32
                part_size:
                  type: integer
                  description: The preferred size for upload parts. If omitted or set to a value that is incompatible with the cloud storage provider, a default value will be used.
                  format: int32
                md5:
                  type: string
                  description: 32-byte hexadecimal MD5 checksum of the file. This value is currently only stored but is not used by the Platform.
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: "{\n  \"project\": \"RFranklin/my-project\",\n  \"name\": \"CanFam3.1.dna_rm.toplevel.fa.gz\",\n  \"size\": 433759572,\n  \"upload_id\": \"Yrand0mVyTZj2Vc2WwKAQtXUhBFZDzax20oaBf12mSixrrcm78sBzB8YGxUgQi1K\",\n  \"part_size\": 5242880,\n  \"parallel_uploads\": true\n}"
              schema:
                type: object
                properties:
                  project:
                    type: string
                    example: RFranklin/my-project
                  name:
                    type: string
                    example: CanFam3.1.dna_rm.toplevel.fa.gz
                  size:
                    type: integer
                    example: 433759572
                    default: 0
                  upload_id:
                    type: string
                    example: Yrand0mVyTZj2Vc2WwKAQtXUhBFZDzax20oaBf12mSixrrcm78sBzB8YGxUgQi1K
                  part_size:
                    type: integer
                    example: 5242880
                    default: 0
                  parallel_uploads:
                    type: boolean
                    example: true
                    default: true
      deprecated: false
      x-readme:
        code-samples:
        - language: python
          code: "from sevenbridges import Api\n\napi = Api(url='https://api.sbgenomics.com/v2',\n          token='3210a98c1db9318fa9d9273156740f74')\n\n# send POST request to SB API to initialize a multipart upload\n# start upload to cloud\n# send POST requests to SB API to mark finishing parts\n# send POST request to SB API to mark finishing multipart upload\nupload = api.files.upload(\n    path='CanFam3.1.dna_rm.toplevel.fa.gz',\n    project='RFranklin/my-project'\n)\n\nprint(upload.status, upload.result())"
        samples-languages:
        - python
      tags:
      - Upload
    get:
      summary: List current multipart uploads
      description: This call returns the list of ongoing uploads.
      operationId: list-current-multipart-uploads
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: "{\n  \"items\": [\n    {\n      \"href\": \"http://api.sbgenomics.com/v2/upload/multipart/srand0mB1h7n3UcjUEqcHKahAl1cizencbI1OQvIkGv8qQRDiP2VAtUpO8NnLKFN\",\n      \"project\": \"RFranklin/my-project\",\n      \"name\": \"1000G_phase1.indels.b37.vc\",\n      \"initiated\": \"2016-03-11T15:15:21Z\",\n      \"upload_id\": \"srand0mB1h7n3UcjUEqcHKahAl1cizencbI1OQvIkGv8qQRDiP2VAtUpO8NnLKFN\"\n    },\n    {\n      \"href\": \"http://api.sbgenomics.com/v2/upload/multipart/Zrand0mrFtYj3rooeFcnawiVhoZp1sF0OK3RVvpWucTKGtNpvDvXFrj4JKOU1qyV\",\n      \"project\": \"RFranklin/my-project\",\n      \"name\": \"1000G_omni2.5.b37.vcf\",\n      \"initiated\": \"2016-03-11T16:05:28Z\",\n      \"upload_id\": \"Zrand0mrFtYj3rooeFcnawiVhoZp1sF0OK3RVvpWucTKGtNpvDvXFrj4JKOU1qyV\"\n    }\n  ]\n}"
              schema:
                type: object
                properties:
                  items:
                    type: array
                    items:
                      type: object
                      properties:
                        href:
                          type: string
                          example: http://api.sbgenomics.com/v2/upload/multipart/srand0mB1h7n3UcjUEqcHKahAl1cizencbI1OQvIkGv8qQRDiP2VAtUpO8NnLKFN
                        project:
                          type: string
                          example: RFranklin/my-project
                        name:
                          type: string
                          example: 1000G_phase1.indels.b37.vc
                        initiated:
                          type: string
                          example: '2016-03-11T15:15:21Z'
                        upload_id:
                          type: string
                          example: srand0mB1h7n3UcjUEqcHKahAl1cizencbI1OQvIkGv8qQRDiP2VAtUpO8NnLKFN
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://api.sbgenomics.com/v2
  /upload/multipart/{upload_id}/part:
    post:
      summary: Report an uploaded part
      description: This call allows you to report the upload of a file part.
      operationId: report-an-uploaded-file-part
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: upload_id
        in: path
        description: The ID for the upload, returned by the call to [initialize a multipart upload](ref:initialize-a-multipart-upload).
        schema:
          type: string
        required: true
      requestBody:
        content:
          application/json:
            schema:
              type: object
              properties:
                part_number:
                  type: integer
                  description: The number of the file part you are reporting. Part numbers start from 1.
                  format: int32
                response:
                  type: object
                  description: This object should contain the information collected from a successful HTTP part upload request. See the [formatting the response object](#formatting-the-response-object) section below for an explanation of its structure.
                  properties:
                    headers:
                      type: object
                      properties:
                        '{key}':
                          type: string
                          description: You should format the response object in this call as a set of key-value mappings. The keys in these mappings are the headers and other response elements described in [getting upload URL for a file part](ref:get-the-upload-url-for-a-file-part), and their values are the strings that you have collected from the HTTP part upload request.
                          default: '{value}'
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: "{\n  \"part_number\": 1,\n  \"response\": {\n    \"headers\": {\n      \"ETag\": \"1234e128411f2bace2sadfdabe610f30\"\n    }\n  }\n}"
              schema:
                type: object
                properties:
                  part_number:
                    type: integer
                    example: 1
                    default: 0
                  response:
                    type: object
                    properties:
                      headers:
                        type: object
                        properties:
                          ETag:
                            type: string
                            example: 1234e128411f2bace2sadfdabe610f30
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://api.sbgenomics.com/v2
  /upload/multipart/{upload_id}/complete:
    post:
      summary: Complete a multipart upload
      description: 'This call must be issued to report the completion of a file upload.


        An optional list of remaining parts may be given in the body of this request. The format of this list is the same as described in report uploaded parts.'
      operationId: finalize-a-multipart-upload
      parameters:
      - name: X-SBG-Auth_Token
        in: header
        description: Your Seven Bridges Platform [authentication token](doc:get-your-authentication-token). For security reasons, token will not be automatically populated in the generated code sample. Please replace `<your-token-here>` with your token before executing this call.
        required: true
        schema:
          type: string
      - name: upload_id
        in: path
        description: The ID for the upload, returned by the call to [initialize a multipart upload](ref:initialize-a-multipart-upload).
        schema:
          type: string
        required: true
      responses:
        '200':
          description: '200'
          content:
            application/json:
              examples:
                Result:
                  value: "{\n  \"href\": \"http://api.sbgenomics.com/v2/files/567890abc9b0307bc0414164\",\n  \"path\": \"/Projects/1fd125fa-789c-45b6-12b3-2a3ab3bedcba/CanFam3.1.dna_rm.toplevel.fa.gz\",\n  \"id\": \"36fddf29f5c4568b3c86e09d\",\n  \"project\": \"RFranklin/my-project\",\n  \"name\": \"CanFam3.1.dna_rm.toplevel.fa.gz\",\n  \"type\": \"file\",\n  \"size\": 433759572,\n  \"created_on\": \"2016-02-27T16:36:41Z\",\n  \"modified_on\": \"2016-02-27T16:36:41Z\"\n}"
              schema:
                type: object
                properties:
                  href:
                    type: string
                    example: http://api.sbgenomics.com/v2/files/567890abc9b0307bc0414164
                  path:
                    type: string
                    example: /Projects/1fd125fa-789c-45b6-12b3-2a3ab3bedcba/CanFam3.1.dna_rm.toplevel.fa.gz
                  id:
                    type: string
                    example: 36fddf29f5c4568b3c86e09d
                  project:
                    type: string
                    example: RFranklin/my-project
                  name:
                    type: string
                    example: CanFam3.1.dna_rm.toplevel.fa.gz
                  type:
                    type: string
                    example: file
                  size:
                    type: integer
                    example: 433759572
                    default: 0
                  created_on:
                    type: string
                    example: '2016-02-27T16:36:41Z'
                  modified_on:
                    type: string
                    example: '2016-02-27T16:36:41Z'
      deprecated: false
      tags:
      - Upload
    servers:
    - url: https://api.sbgenomics.com/v2
x-refined-from:
- seven-bridges-cgc-openapi.json
- seven-bridges-platform-openapi.json
x-readme:
  headers: []
x-readme-fauxas: true