agr_ferret

pre-ETL data fetching software for the Alliance of Genome Resources.

Background

The Alliance of Genome Resources "ferret" is designed to parse through a series of YAML files, download datasets listed within those files, and subsequently upload them to the Alliance of Genome Features file management software ("chipmunk").

Use

From the src directory: python app.py

Optional flags:

• -v --verbose: Enable verbose mode. This mode can also be set by declaring the environmental variable DEBUG=True.
• -f --files: Specify the specific filenames to be parsed for datasets. By default, when this flag is not used, every YAML file in the datasets directory is parsed. Individual files can be specified with this flag. Wildcards are also supported:
  • e.g. python app.py -f datasets/MOD_FlyBase.yaml
  • e.g. python app.py -f datasets/MOD*

Additional Information

• YAML files in the datasets folder are grouped by data provider. For example, the MOD_FlyBase.yaml file contains all datasets provided by FlyBase as a list.
• When adding new values for YAML ids (the value at the very top of each YAML dataset file), compression, data types, or data subtypes, be sure to edit the validation file in src/validation/validation.yaml to allow these entries.
• Downloaded files are stored in the files folder. Files from previous runs are overwritten each time if the relevant dataset is processed.

Writing Unit Tests

• Unit tests are required for all appropriate functions within this repository.
• Please see src/unit_tests.py for more information and examples of tests.