diff --git a/update_sc_name/update_scientific_name.py b/update_sc_name/update_scientific_name.py index 70f4083e..4139bf44 100644 --- a/update_sc_name/update_scientific_name.py +++ b/update_sc_name/update_scientific_name.py @@ -9,8 +9,8 @@ from ebi_eva_common_pyutils.pg_utils import execute_query, get_all_results_for_query from ebi_eva_common_pyutils.taxonomy.taxonomy import normalise_taxon_scientific_name, get_scientific_name_from_ensembl -logger = logging_config.get_logger(__name__, logging.DEBUG) - +logging_config.add_stdout_handler() +logger = logging_config.get_logger(__name__) def get_scientific_name_from_eva(taxonomy_id, private_config_xml_file, profile): with get_metadata_connection_handle(profile, private_config_xml_file) as pg_conn: @@ -26,7 +26,7 @@ def update_path_reference_sequence(taxonomy, old_sc_name, new_sc_name, ref_seq_d nmz_new_sc_name = normalise_taxon_scientific_name(new_sc_name) new_species_ref_dir = os.path.join(ref_seq_dir, nmz_new_sc_name) - logger.warning(f"normalize old scientific name : {nmz_old_sc_name}, old species ref dir: {old_species_ref_dir}, " + logger.info(f"normalize old scientific name : {nmz_old_sc_name}, old species ref dir: {old_species_ref_dir}, " f"normalize new scientific name: {nmz_new_sc_name}, new species ref dir: {new_species_ref_dir}") if old_species_ref_dir == new_species_ref_dir: @@ -93,7 +93,7 @@ def main(): # update directory name in reference sequence directory old_sc_name = get_scientific_name_from_eva(args.taxonomy, args.private_config_xml_file, args.profile) new_sc_name = args.scientific_name or get_scientific_name_from_ensembl(args.taxonomy) - logger.warning(f"old scientific name: {old_sc_name}, new scientific name: {new_sc_name}") + logger.info(f"old scientific name: {old_sc_name}, new scientific name: {new_sc_name}") update_path_reference_sequence(args.taxonomy, old_sc_name, new_sc_name, args.ref_seq_dir, args.ref_seq_dir_name, args.retain_old_dir)