def test_instantiate_correct_configs(base_config_dict: dict):
# GIVEN a dictionary with the basic configs
# WHEN instantiating a CGConfig object
config_object = CGConfig(**base_config_dict)
# THEN assert that it was successfully created
assert isinstance(config_object, CGConfig)
def test_fetching_the_status_db(base_config_dict: dict, caplog):
caplog.set_level(logging.DEBUG)
# GIVEN a dictionary with the basic configs
# WHEN instantiating a CGConfig object
config_object = CGConfig(**base_config_dict)
# THEN assert that the status db exists
assert isinstance(config_object.status_db, Store)
# THEN assert that it was communicated that it was instantiated
assert "Instantiating status db" in caplog.text
def test_api_instantiated_once(base_config_dict: dict, caplog):
caplog.set_level(logging.DEBUG)
# GIVEN a dictionary with the basic configs
# GIVEN a CGConfig object
config_object = CGConfig(**base_config_dict)
# WHEN fetching (instantiating) the status_db
# THEN assert that it was only instantiated once
config_object.status_db
assert "Instantiating status db" in caplog.text
caplog.clear()
config_object.status_db
assert "Instantiating status db" not in caplog.text
def base(
context: click.Context,
config: click.File,
database: Optional[str],
log_level: str,
verbose: bool,
):
"""cg - interface between tools at Clinical Genomics."""
if verbose:
log_format = "%(asctime)s %(hostname)s %(name)s[%(process)d] %(levelname)s %(message)s"
else:
log_format = "%(message)s" if sys.stdout.isatty() else None
coloredlogs.install(level=log_level, fmt=log_format)
raw_configs: dict = yaml.full_load(config) if config else {"database": database}
context.obj = CGConfig(**raw_configs)
def fixture_cg_config_object(base_config_dict: dict) -> CGConfig:
"""Return a CG config dict"""
return CGConfig(**base_config_dict)
def fixture_cg_context(context_config: dict, base_store: Store,
housekeeper_api: HousekeeperAPI) -> CGConfig:
cg_config = CGConfig(**context_config)
cg_config.status_db_ = base_store
cg_config.housekeeper_api_ = housekeeper_api
return cg_config
