rename error log columns, moved omop code definitions to parse.py

base.py

@@ -24,8 +24,8 @@ def log_invalid_code(codes, mask, code_type=None, file_path=None, cause=None):
 	# print("ERROR WITH CODES", file_path, codes[~mask])
 	
 	errors = pd.DataFrame([])
-	errors["CODE"] = codes[~mask].astype(str)
-	errors["CODE_TYPE"] = code_type
+	errors["CONCEPT"] = codes[~mask].astype(str)
+	errors["VOCABULARY"] = code_type
 	errors["SOURCE"] = file_path
 	errors["CAUSE"] = cause
 	

main.py

@@ -17,6 +17,7 @@ from parse import Opcs4_code
 from parse import Atc_code
 from parse import Med_code
 from parse import code_types
+from parse import omop_vocab_types
 
 
 pd.set_option('mode.chained_assignment', None)
@@ -356,20 +357,9 @@ def run_all(mapping_file, target_code_type,
 	if output_path == "atlas":
 		#Export to DB
 		db_path = "codes/omop_54.sqlite"
-		vocab_output = "MELDB"
-
-		vocab_types = {
-			"read2_code": "Read",
-			"read3_code": None,
-			"icd10_code": "ICD10CM",
-			"snomed_code": "SNOMED",
-			"opcs4_code": "OPCS4",
-			"atc_code": "ATC",
-			"med_code": None,
-			"cprd_code": None,
-		}
-
-		omop_publish_concept_sets(out, db_path, vocab_output, vocab_types[target_code_type])
+		vocab_output = "MELDB" #TODO: parameterise output name
+
+		omop_publish_concept_sets(out, db_path, vocab_output, omop_vocab_types[target_code_type])
 	else:
 		# export as CSV to /output
 		out.to_csv(output_path, index=False)
@@ -379,7 +369,7 @@ def run_all(mapping_file, target_code_type,
 	if os.path.exists(log_errors_path):
 		error_df = pd.read_csv(log_errors_path)
 		error_df = error_df.drop_duplicates() #Remove Duplicates from Error file
-		error_df = error_df.sort_values(by=["SOURCE", "VOCABULARY", "CODE"])
+		error_df = error_df.sort_values(by=["SOURCE", "VOCABULARY", "CONCEPT"])
 		error_df.to_csv(log_errors_path, index=False)
 	
 

parse.py

@@ -354,3 +354,14 @@ code_types = {
 	"med_code": Med_code,
 	"cprd_code": Cprd_code,
 }
+
+omop_vocab_types = {
+	"read2_code": "Read",
+	"read3_code": None,
+	"icd10_code": "ICD10CM",
+	"snomed_code": "SNOMED",
+	"opcs4_code": "OPCS4",
+	"atc_code": "ATC",
+	"med_code": None,
+	"cprd_code": None,
+}
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