Allow multiple files per concept set - update map function

acmc/phen.py

@@ -593,12 +593,12 @@ def _process_actions(df: pd.DataFrame, concept_set: dict) -> pd.DataFrame:
     # Perform Structural Changes to file before preprocessing
     _logger.debug("Processing file structural actions")
     if (
-        "actions" in concept_set["file"]
-        and "split_col" in concept_set["file"]["actions"]
-        and "codes_col" in concept_set["file"]["actions"]
+        "actions" in concept_set
+        and "split_col" in concept_set["actions"]
+        and "codes_col" in concept_set["actions"]
     ):
-        split_col = concept_set["file"]["actions"]["split_col"]
-        codes_col = concept_set["file"]["actions"]["codes_col"]
+        split_col = concept_set["actions"]["split_col"]
+        codes_col = concept_set["actions"]["codes_col"]
         _logger.debug(
             "Action: Splitting",
             split_col,
@@ -626,12 +626,12 @@ def _preprocess_source_concepts(
 
     # Preprocess codes
     code_types = parse.CodeTypeParser().code_types
-    for code_type in concept_set["file"]["columns"]:
+    for code_type in concept_set["columns"]:
         parser = code_types[code_type]
         _logger.info(f"Processing {code_type} codes for {code_file_path}")
 
         # get codes by column name
-        source_col_name = concept_set["file"]["columns"][code_type]
+        source_col_name = concept_set["columns"][code_type]
         codes = df[source_col_name].dropna()
         codes = codes.astype(str)  # convert to string
         codes = codes.str.strip()  # remove excess spaces