ENCODE Utils package

Installation and configuration instructions are provided on the project’s GitHub wiki.

Examples

• Connection class
  • Imports
  • Connecting to the production and development Portals
  • Log Files
  • GET Request
  • Search
  • PATCH Request
  • File Upload
  • POST Request
  • Removing properties from a record
• Transferring files to GCP
  • The Transfer class
  • The gcp_transfer_from_aws() method of the encode_utils.connection.Connection class
  • Copying files using a URL list
  • Running the script

Scripts

• registration
• eu_add_controlled_by
• eu_check_not_posted
• eu_create_gcp_url_list
• eu_generate_upload_creds.py
• eu_get_aliases
• eu_get_accessions
• eu_get_replicate_fastq_encffs
• eu_get_replicate_numbers
• eu_report_fastq_content_errors
• eu_s3_to_gcp.py

Client API Modules

• encode_utils.aws_storage
• encode_utils.connection
• encode_utils
• encode_utils.profiles
• encode_utils.transfer_to_gcp.py
• encode_utils.utils

Unit Tests

• encode_utils.tests.test_utils
• encode_utils.tests.test_connection

Indices and tables

• Index
• Module Index
• Search Page