diff --git a/acmc/phen.py b/acmc/phen.py index 90884db02e627524d5c7736b1bb4e6fe05991721..ad3b9f27b16d1ef51ffc6330bcf9c9a6348a113b 100644 --- a/acmc/phen.py +++ b/acmc/phen.py @@ -233,6 +233,7 @@ def validate(phen_dir): # check codes definition concept_set_mapping_names = [] for item in concept_codes: + required_keys = {"folder", "files"} if required_keys.issubset(item.keys()): # check concept codes path is a directory @@ -393,7 +394,7 @@ def preprocess(df, file, target_code_type=None, codes_file=None, translate=True, # QA for every code type in df run preprocess_code() for code_type_name, code_type in parse.code_types.items(): if code_type_name in file['columns']: - logger.info(f"Processing {k} Codes...") + logger.info(f"Processing {code_type_name} Codes...") out = preprocess_code(out=out, codes=df[file['columns'][code_type_name]].dropna(), codes_file=codes_file,