From 2b24ab1e3e59d6872f82f4cb965ebf465960130a Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 4 Feb 2025 21:25:03 +0100 Subject: [PATCH] chore(deposition): small refactors (#3610) --- ena-submission/src/ena_deposition/config.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/ena-submission/src/ena_deposition/config.py b/ena-submission/src/ena_deposition/config.py index 34f2388586..cc7896778a 100644 --- a/ena-submission/src/ena_deposition/config.py +++ b/ena-submission/src/ena_deposition/config.py @@ -40,9 +40,10 @@ class Config: def secure_ena_connection(config: Config): + """Modify passed-in config object""" submit_to_ena_prod = config.submit_to_ena_prod if submit_to_ena_prod and (config.backend_url not in config.allowed_submission_hosts): - logging.warn("WARNING: backend_url not in allowed_hosts") + logging.warning("WARNING: backend_url not in allowed_hosts") submit_to_ena_prod = False submit_to_ena_dev = not submit_to_ena_prod @@ -55,19 +56,19 @@ def secure_ena_connection(config: Config): if submit_to_ena_prod: config.test = False - logging.warn("WARNING: Submitting to ENA production") + logging.warning("WARNING: Submitting to ENA production") config.ena_submission_url = "https://www.ebi.ac.uk/ena/submit/drop-box/submit" config.github_url = "https://pathoplexus.github.io/ena-submission/approved/approved_ena_submission_list.json" config.ena_reports_service_url = "https://www.ebi.ac.uk/ena/submit/report" -def get_config(config_file: str): - with open("config/defaults.yaml") as f: +def get_config(config_file: str) -> Config: + with open("config/defaults.yaml", encoding="utf-8") as f: defaults = yaml.safe_load(f) with open(config_file, encoding="utf-8") as file: full_config = yaml.safe_load(file) for key, value in defaults.items(): - if not key in full_config: + if key not in full_config: full_config[key] = value relevant_config = {key: full_config.get(key, []) for key in Config.__annotations__} config = Config(**relevant_config)