mkt.databases.config

Environment-variable configuration for cBioPortal, OncoKB, and the requests cache.

Module-level get_*/set_* functions read and write os.environ for the cBioPortal instance and token, OncoKB token, and requests-cache path, re-exporting the output-directory helpers from mkt.schema.config.

Module Attributes

CBIOPORTAL_INSTANCE_VAR	Environment variable for cBioPortal instance; if none provided, default is www.cbioportal.org in CLI scripts
CBIOPORTAL_TOKEN_VAR	Environment variable for cBioPortal token; if none provided, default is None in CLI scripts
REQUESTS_CACHE_VAR	Environment variable for request cache file prefix; if none provided, default is requests_cache in CLI scripts
ONCOKB_TOKEN_VAR	Environment variable for OncoKB token; if none provided, default is None in CLI scripts

Functions

get_cbioportal_instance()	Get the cBioPortal instance from the environment.
maybe_get_cbioportal_token()	Get the cBioPortal token from the environment.
maybe_get_oncokb_token()	Get the OncoKB token from the environment.
maybe_get_request_cache()	Get the request cache path from the environment.
set_cbioportal_instance(val)	Set the cBioPortal instance in the environment variables.
set_cbioportal_token(val)	Set the cBioPortal token in the environment variables.
set_oncokb_token(val)	Set the OncoKB token in the environment variables.
set_request_cache(val)	Set the request cache path in environment variables.

mkt.databases.config.get_output_dir() → str | None

Get the output directory from the environment.

Returns:

str | None

Output directory path if exists, otherwise None

mkt.databases.config.set_output_dir(val: str) → None

Set the output directory in environment variables.

Parameters:

valstr

Output directory path

Returns:

None