Configuration

All command-line arguments described for the scripts below can also be supplied using a YAML format configuration file. You can specify the configuration file using the --config_file or -cfg arguments.

By default, scripts will check for the existence of ~/.cgpclient/config.yaml. If this file exists, it will be read without you needing to provide a filename.

The configuration file should contain parameters with the same names as the command-line options described for each script. Command-line arguments will take priority over values found in the configuration file.

Important: All files and paths used in the configuration file must be absolute, not relative paths.

Example Configuration File (~/.cgpclient/config.yaml):

api_host: sandbox.api.service.nhs.uk
api_name: genomic-data-access
api_key: NHSAPIMAPIKEY # This is the API key from the NHS Developer Hub (not needed for sandbox).
private_key_pem_file: /absolute/path/to/test-1.pem # Path to your private key (see: [https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/application-restricted-restful-apis-signed-jwt-authentication#step-2-generate-a-key-pair](https://digital.nhs.uk/developer/guides-and-documentation/security-and-authorisation/application-restricted-restful-apis-signed-jwt-authentication#step-2-generate-a-key-pair)).
apim_kid: test-1 # The key pair KID.
output_dir: /tmp/output
verbose: true
pretty_print: true

Using the Configuration File:

With this configuration file, you can run the cgpclient/scripts/fetch_genomic_files.py script by supplying only the referral ID:

python cgpclient/scripts/fetch_genomic_files.py -r r30000000001