diff --git a/acmc/parse.py b/acmc/parse.py index 790cad6ca80b6b2202bc5a3119bf6ace6b5f8feb..2a04067cc3dec59af1c7c2c9f6881a0408464d6a 100644 --- a/acmc/parse.py +++ b/acmc/parse.py @@ -397,14 +397,14 @@ class Cprd(Proto): ] code_types = { - "read2": Read2, - "read3": Read3, - "icd10": Icd10, - "snomed": Snomed, - "opcs4": Opcs4, - "atc": Atc, - "med": Med, - "cprd": Cprd, + "read2": Read2(), + "read3": Read3(), + "icd10": Icd10(), + "snomed": Snomed(), + "opcs4": Opcs4(), + "atc": Atc(), + "med": Med(), + "cprd": Cprd(), } vocab_types = { diff --git a/acmc/phen.py b/acmc/phen.py index bc0d7e52abdd4acdf54611952d29f8f42db1a987..90884db02e627524d5c7736b1bb4e6fe05991721 100644 --- a/acmc/phen.py +++ b/acmc/phen.py @@ -384,21 +384,21 @@ def preprocess(df, file, target_code_type=None, codes_file=None, translate=True, out = preprocess_code(out=out, codes=df[file[columns][target_code_type]].dropna(), codes_file=codes_file, - checker=parse.code_types[target_code_type](), + checker=parse.code_types[target_code_type], output_col=target_code_type, metadata_df=df[meta_columns]) else: logger.warning(f"No {target_code_type} Codes to process") else: # QA for every code type in df run preprocess_code() - for k, v in parse.code_types.items(): - if k in file['columns']: + for code_type_name, code_type in parse.code_types.items(): + if code_type_name in file['columns']: logger.info(f"Processing {k} Codes...") out = preprocess_code(out=out, - codes=df[file['columns'][k]].dropna(), + codes=df[file['columns'][code_type_name]].dropna(), codes_file=codes_file, - checker=v(), - output_col=k, + checker=code_type, + output_col=code_type_name, metadata_df=df[meta_columns]) return out, meta_columns