move summary excel into json config

main.py

@@ -255,23 +255,14 @@ def run_all(mapping_file, target_code_type,
 	out = out.drop_duplicates(subset=["CONCEPT_SET", "CONCEPT"])
 	out = out.sort_values(by=["CONCEPT_SET", "CONCEPT"])
 	
-	#Merge with Concept Types in Summary Excel File
-	if "excel_sheet" in summary_config:
-		summary_df = read_table_file(summary_config["file"], excel_sheet=summary_config["excel_sheet"])
-	else:
-		summary_df = read_table_file(summary_config["file"])
-	summary_cols_all = [] #get all column names
-	for v in summary_config["columns"].values(): #TODO: put in seperate function - get all columns in JSON file object
-		if type(v) == str:
-			summary_cols_all.append(v)
-		else:
-			summary_cols_all += v
-
-	output_version = summary_config["version"]
-	summary_df = summary_df[summary_cols_all] #select all relevant columns 
-	summary_df = summary_df.rename(columns={summary_config["columns"]["concept_set_name"]: "CONCEPT_SET"})
+	#Add Concept Set Defintions metadata
+	summary_df = pd.DataFrame(summary_config["concept_set"]) #transform to dataframe
+	if "metadata" in summary_df.columns:
+		summary_df = summary_df.join(pd.json_normalize(summary_df["metadata"])) #metadata to columns
+		summary_df = summary_df.drop(columns=["metadata"])
+	summary_df = summary_df.rename(columns={"concept_set_name":"CONCEPT_SET"})
 	summary_df = summary_df.drop_duplicates() #remove duplicates
-	out = out.merge(summary_df, how="left", on='CONCEPT_SET')
+	out = out.merge(summary_df, how="left", on='CONCEPT_SET') #merge with output
 	
 	# Save Output File
 	print(bcolors.HEADER, "---"*5, "OUTPUT", "---"*5, bcolors.ENDC)