the _code suffix makes a difference to a lot of thigns, need to work that out

acmc.py

@@ -97,7 +97,7 @@ def main():
 	map_process_parser = map_subparsers.add_parser("process", help="Process map configuration file")
 	map_process_parser.add_argument("-c", "--config-file", required=True, help="Phenotype configuration file")
 	map_process_parser.add_argument("-s", "--source-codes-dir", required=True, help="Source codes root directory")
-	map_process_parser.add_argument("-t", "--target-coding", required=True, choices=['read2', 'read3', 'icd10', 'snomed', 'opcs4'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
+	map_process_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
 	map_process_parser.add_argument("-o", "--output-file", type=str, default=str(map.OUTPUT_PATH.resolve()), help="Output directory for CSV or OMOP database")	
 	
 	# Flags

example/phenotype_config.json

@@ -22,24 +22,6 @@
                     "CODING LIST": "https://git.soton.ac.uk/meld/meldb-external/phenotype/-/tree/main/codes/ClinicalCodes.org%20from%20the%20University%20of%20Manchester/Symptom%20code%20lists/Abdominal%20pain/res176-abdominal-pain.csv ",
                     "NOTES": "2023-09-08: Clinical SF confirmed that the clinical view would be that this would need to be recurrent or persistent."
                 }
-            },
-		{
-			"concept_set_name": "CVD_EVENTS",
-			"concept_set_status": "AGREED",
-			"metadata": {
-				"#": "9",
-				"CONCEPT DESCRIPTION": "Cardiovascular events",
-				"CONCEPT TYPE": "Outcome event",
-				"CONCEPT ONTOLOGY CLASS": "nan",
-				"DATE ADDED ": "2023-08-25",
-				"REQUEST REASON ": "SF - requested by email - to explore an examplar 'outcome measure'",
-				"SOURCE INFO": "YES",
-				"FUNCTION": "QUERY BY CODING LIST",
-				"FUNCTION.1": "https://clinicalcodes.rss.mhs.man.ac.uk/",
-				"CODING LIST": "https://git.soton.ac.uk/meld/meldb-external/phenotype/-/tree/main/codes/ClinicalCodes.org%20from%20the%20University%20of%20Manchester/Cardiovascular%20events%20(ICD10)/res52-cardiovascular-events-icd10.csv",
-				"NOTES": "2023-11-17 - Code cannot currently be PROCESSED = COMPLETE as no mappings from ICD10 to Read v2 exist, pending confirmation from clinical team on next steps.",
-				"Relation to Ontology": "YES WITH ISSUES"
-			}
             }
         ]
     },
@@ -51,7 +33,7 @@
                 {
                     "file": "Symptom code lists/Abdominal pain/res176-abdominal-pain.csv",
                     "columns": {
-                        "read2": "code",
+                        "read2_code": "code",
                         "metadata": [
                             "description"
                         ]
@@ -59,20 +41,7 @@
                     "concept_set": [
                         "ABDO_PAIN"
                     ]
-                },
-		{
-			"file": "Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv",
-			"columns": {
-				"icd10_code": "code",
-				"metadata": [
-					"description"
-				]
-			},
-			"concept_set": [
-				"CVD_EVENTS"
-			]
                 }
-
             ]
         }
     ]

map.py

@@ -203,6 +203,7 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
 
 				# Perform Structural Changes to file before preprocessing
 				# split column with multiple code types
+				print("Processing actions")
 				if ("actions" in file and "split_col" in file["actions"] and "codes_col" in file["actions"]):
 					split_col = file["actions"]["split_col"]
 					codes_col = file["actions"]["codes_col"]

parse.py

@@ -344,14 +344,14 @@ class Cprd_code(Proto_code):
 		]
 		
 code_types = {
-	"read2": Read2_code,
-	"read3": Read3_code,
-	"icd10": Icd10_code,
-	"snomed": Snomed_code,
-	"opcs4": Opcs4_code,
-	"atc": Atc_code,
-	"med": Med_code,
-	"cprd": Cprd_code,
+	"read2_code": Read2_code,
+	"read3_code": Read3_code,
+	"icd10_code": Icd10_code,
+	"snomed_code": Snomed_code,
+	"opcs4_code": Opcs4_code,
+	"atc_code": Atc_code,
+	"med_code": Med_code,
+	"cprd_code": Cprd_code,
 }
 
 vocab_types = {