Start an import job

This call lets you queue a job to import a file or folder from a volume into a project on the CGC. Essentially, you are importing an item from your cloud storage provider (Amazon Web Services or Google Cloud Storage) via the volume onto the CGC.

If successful, an alias will be created on the CGC. Aliases appear on the CGC and can be copied, executed, and modified as such. They refer back to the respective file on the given volume.

Learn more about using the Volumes API for Amazon S3 and for Google Cloud Storage.

https://cgc-api.sbgenomics.com/v2/storage/imports

Request

Example request

POST /v2/storage/imports HTTP/1.1
Host: cgc-api.sbgenomics.com
X-SBG-Auth-Token: 3210a98c1db9318fa9d9273156740f74
Content-Type: application/json

curl --data '@import.json' -X POST -H "X-SBG-Auth-Token: 3210a98c1db9318fa9d9273156740f74" -H "Content-Type: application/json" 'https://cgc-api.sbgenomics.com/v2/storage/imports'

Header Fields

Key	Description of value
`X-SBG-Auth-Token` required	Your CGC authentication token.
`Content-type` required	`application/json`

Request body

In the body, you should enter a list of key-value pairs. The keys and the values they take are described in the following table.

Key	Data type of value	Description of value
`source` required	Object	This object should describe the source from which the file should be imported.
`volume_id` required	String	Volume ID from which to import the file.
`location` required	String	Volume-specific location pointing to the file or folder to import. This location should be recognizable to the underlying cloud service as a valid key or path to the item. If the item being imported is a folder, its path should end with a `/`. Please note that if this volume was configured with a `prefix` parameter when it was created, the `prefix` will be prepended to `location` before attempting to locate the file on the volume.
`destination` required	Object	This object should describe the Platform destination for the imported file.
`project` required	String	The project in which to create the alias.
`parent`	String	The ID of the target folder to which the item should be imported. Should not be used together with `project`. If `parent` is used, the import 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`	String	The name of the alias to create. This name should be unique to the project. If the name is already in use in the project, you should use the `overwrite` query parameter in this call to force any file with that name to be deleted before the alias is created. If `name` is omitted, the alias name will default to the last segment of the complete location (including the `prefix`) on the volume. Segments are considered to be separated with forward slashes `/`. Allowed characters in file names are all alphanumerics and special characters except forward slash `/`, while folder names can contain alphanumerics and special characters `_`, `-` and `.`.
`overwrite`	Boolean	Whether to overwrite the file if the file with the same name already exists in the destination.
`autorename`	Boolean	Whether to automatically rename the item (by prefixing it's name with an underscore and number) if another one with the same name already exists at the destination.
`preserve_folder_structure`	Boolean	Whether to keep the exact source folder structure. The default value is `true` if the item being imported is a folder. Should not be used if you are importing a file.

Example request body

{  
   "source":{  
      "volume":"rfranklin/input",
      "location":"example_human_Illumina.pe_1.fastq"
   },
   "destination":{  
      "project":"rfranklin/my_project",
      "name":"my_uploaded_example_human_Illumina.pe_1.fastq"
   },
   "overwrite": true
}

{
     “source”: {
       “volume”: “rfranklin/my_volume”,
       “location”: “samples/november/”
     },
     “destination”: {
         “parent”: “5bcdc234a4b0cbdd7a16e7cc”
     }
}

Response

See a list of CGC-specific response codes that may be contained in the body of the response.

Response body

The response object contains information about the specified volume. The information is structured using the following key-value pairs:

Key	Data type of value	Description of value
`id`	String	ID of this import job
`state`	String	The state of this import job. Possible values are: `PENDING`: the import is queued; `RUNNING`: the import is running; `COMPLETED`: the import has completed successfully; `FAILED`: the import has failed.
`overwrite`	Boolean
`autorename`	Boolean
`source`	Object	Import source, as passed when this job was started by the call to start an import job .
`destination`	Object	Import destination, as passed when this job was started by the call to start an import job
`result`	Object	File object that was imported.
`error`	Object	In case of error in the import job, standard API error is returned here.
`started_on`	Boolean	Time when the import job started.
`finished_on`	Boolean	Time when the import job ended.

Example response body

{
   “href”: “https://cgc-api.sbgenomics.com/v2/storage/imports/EcltWX3Vi4Ey533shgDSv8IXuqeSRCMo“,
   “id”: “EcltWX3Vc5dy533shgAEr8IXuqeSRCMo”,
   “state”: “COMPLETED”,
   “overwrite”: false,
   “autorename”: false,
   “source”: {
       “volume”: “rfranklin/my_volume”,
       “location”: “my-samples/november/sample1.bam”
   },
   “destination”: {
       “project”: “rfranklin/my-project”,
       “name”: “sample1.bam”,
       “parent”: “5ce9dc7be1e0cbdc5f8768a3"
   },
   “result”: {
       “href”: “https://cgc-api.sbgenomics.com/v2/files/5bcdc1d1e4b0cbdd7a82e7b9”,
       “id”: “5bcdc1d2d9b0cbd08a82e7b9”,
       “name”: “sample1.bam”,
       “size”: 1804,
       “project”: “rfranklin/my-project”,
       “created_on”: “2018-10-22T12:25:53Z”,
       “modified_on”: “2018-10-22T12:25:53Z”,
       “storage”: {
           “type”: “VOLUME”,
           “volume”: “rfranklin/my_volume”,
           “location”: “my-samples/november/sample1.bam”
       },
       “origin”: {},
       “tags”: [],
       “metadata”: {}
   },
   “started_on”: “2018-10-22T12:25:53Z”,
   “finished_on”: “2018-10-22T12:25:54Z”
}

{
   “href”: “https://cgc-api.sbgenomics.com/v2/storage/imports/aNiKZPr4u1n7hOOE07lQQ2ql9cRDIcVB“,
   “id”: “aNiKZPr4u1n7hOOE07lQQlele8RDIcVB”,
   “state”: “COMPLETED”,
   “overwrite”: false,
   “autorename”: false,
   “preserve_folder_structure”: true,
   “source”: {
       “volume”: “rfranklin/my_volume”,
       “location”: “my-samples/november"
   },
   “destination”: {
       “project”: “rfranklin/my-project”,
       “name”: “samples”,
       “parent”: “5bcdc211e4b0cb3d7a82e7cc”
   },
   “result”: {
       “href”: “https://cgc-api.sbgenomics.com/v2/files/5bcdc25ae4b0cbdd7a82e7cf”,
       “id”: “5bcdc25ae4b0cbde4e82e7cf”,
       “name”: “samples",
       “project”: “rfranklin/my-project”,
       “created_on”: “2018-10-22T12:28:10Z”,
       “modified_on”: “2018-10-22T12:28:10Z”
   },
   “started_on”: “2018-10-22T12:28:10Z”,
   “finished_on”: “2018-10-22T12:28:10Z”
}