Omics Files

Omics Files controller allows to manage file processing to use data in AWS Omics.

Copy Files to Omics Bucket

The following code retrieves the metadata of a file with the given its biomed file id.

from genomcore.client import GenomcoreApiClient
api = GenomcoreApiClient(token="A_VALID_TOKEN", refresh_token="A_VALID_REFRESH_TOKEN")

response = api.omics_files.copy_to_omics_bucket(1969539)
s3_path = response["s3Path"]
print(s3_path)

Get Copy Status

Get omics status when copying files to the omics bucket. Available status are:

• Pending.

• Processing

• Completed

• Failed

from genomcore.client import GenomcoreApiClient
api = GenomcoreApiClient(token="A_VALID_TOKEN", refresh_token="A_VALID_REFRESH_TOKEN")

response = api.omics_files.copy_to_omics_bucket(1969539)
tracking_url = response["trackingUrl"]
status = api.omics_files.get_copy_omics_status(tracking_url)
print(status)