removed the translate flag from teh phen code, not necessary and made the...

removed the translate flag from teh phen code, not necessary and made the logic a little confusing to understand

acmc/main.py

@@ -37,8 +37,7 @@ def phen_validate(args):
 def phen_map(args):
 	"""Handle the `phen map` command."""    
 	phen.map(args.phen_dir,
-			 args.target_coding,
-			 args.translate)
+			 args.target_coding)
 
 def phen_publish(args):
 	"""Handle the `phen publish` command."""  
@@ -114,8 +113,6 @@ def main():
 	phen_map_parser = phen_subparsers.add_parser("map", help="Process phen mapping")
 	phen_map_parser.add_argument("-d", "--phen-dir", type=str, default=str(phen.DEFAULT_PHEN_PATH.resolve()), help="Phenotype directory")
 	phen_map_parser.add_argument("-t", "--target-coding", required=True, choices=['read2', 'read3', 'icd10', 'snomed', 'opcs4'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
-	# phen map flags
-	phen_map_parser.add_argument("-tr", "--translate", action="store_true", default=False, help="Translate code types")
 	phen_map_parser.set_defaults(func=phen_map)    
 
 	# phen publish

acmc/phen.py

@@ -367,7 +367,7 @@ def preprocess_code(out, codes, codes_file, checker, output_col, metadata_df):
 	return out
 
 # Perform QA Checks on columns individually and append to df
-def preprocess(df, file, target_code_type=None, codes_file=None, translate=True,):
+def preprocess(df, file, target_code_type=None, codes_file=None):
 	""" Parses each column individually - Order and length will not be preserved! """
 	out = pd.DataFrame([])  # create output df to append to
 
@@ -406,7 +406,7 @@ def preprocess(df, file, target_code_type=None, codes_file=None, translate=True,
 	return out, meta_columns
 
 # Translate Df with multiple codes into single code type Series
-def convert_codes(df, target_code_type):
+def translate_codes(df, target_code_type):
 	codes = pd.Series([], dtype=str)
 
 	# Convert codes to target type
@@ -440,7 +440,7 @@ def map_file(df, target_code_type, out, concepts, meta_columns=[]):
 	# seperate out meta_columns
 	metadata_df = df[meta_columns]
 	df = df.drop(columns=meta_columns)
-	codes = convert_codes(df, target_code_type)
+	codes = translate_codes(df, target_code_type)
 	codes = codes.dropna()  # delete NaNs
 	
 	# Append to out df
@@ -464,10 +464,9 @@ def sql_row_exist(conn, table, column, value):
 
     return exists
 
-def map(phen_dir, target_code_type, translate=True):
+def map(phen_dir, target_code_type):
 	logger.info(f"Processing phenotype: {phen_dir}")
 	logger.debug(f"Target coding format: {target_code_type}")	
-	logger.debug(f"Translating: {translate}")
 
 	# Validate configuration
 	validate(phen_dir)
@@ -505,8 +504,7 @@ def map(phen_dir, target_code_type, translate=True):
 			df, meta_columns = preprocess(df,
 							file,
 							codes_file=str(codes_file_path.resolve()),
-							target_code_type=target_code_type,
-							translate=translate)
+							target_code_type=target_code_type)
 
 			# partition table by categorical column				
 			if ("actions" in file and "divide_col" in file["actions"] and len(df) > 0):
@@ -533,7 +531,7 @@ def map(phen_dir, target_code_type, translate=True):
 										   concepts=file["concept_set_categories"][cat],
 										   meta_columns=meta_columns,)
 
-	# test if there's any output from processing
+	# Check there is output from processing
 	if len(out.index) == 0:
 		raise Exception(f"No output after map processing, check configuration {str(config_path.resolve())}")
 
@@ -552,10 +550,7 @@ def map(phen_dir, target_code_type, translate=True):
 	out = out.merge(concept_sets_df, how="left", on="CONCEPT_SET")  # merge with output
 
 	# Save output to map directory
-	if translate:
-		output_filename = target_code_type + '.csv'
-	else:
-		output_filename = target_code_type + '_no_translate.csv'
+	output_filename = target_code_type + '.csv'
 	
 	map_path = phen_path / MAP_DIR / output_filename
 		

tests/test_acmc.py

@@ -68,7 +68,7 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog):
 
 	# map phenotype
 	with caplog.at_level(logging.DEBUG):		
-		monkeypatch.setattr(sys, "argv", ["main.py", "phen", "map", "-d", str(phen_path.resolve()), "-t", "read3", "-tr"])
+		monkeypatch.setattr(sys, "argv", ["main.py", "phen", "map", "-d", str(phen_path.resolve()), "-t", "read3"])
 		main.main()
 	assert "Phenotype processed successfully" in caplog.text