setting the right logger level

EBIvariation · Oct 9, 2023 · 86d9ac6 · 86d9ac6
1 parent 45e3c61
commit 86d9ac6
Showing 1 changed file with 4 additions and 4 deletions.
diff --git 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)