not dumped all database tables to file on export so they can be versioned

acmc/omop.py

@@ -186,7 +186,7 @@ def concept_set_exist(cursor, concept_set_name):
 	cursor.execute(query, (concept_set_name,))
 	
 	# 1 if exists, 0 otherwise
-	return cursor.fetchone()[0]  1
+	return cursor.fetchone()[0] == 1
 
 def export(map_path, export_path, version, omop_metadata):
 	logger.debug(f"exporting with metadata {omop_metadata} at version {version}")
@@ -271,6 +271,20 @@ def export(map_path, export_path, version, omop_metadata):
 			df_out["concept_set_id"] = concept_set_id
 			df_out.to_sql("CONCEPT_SET_ITEM", conn, if_exists='append', index=False)
 
+	# Output all tables to CSV
+	# Get the list of all tables
+	cur.execute("SELECT name FROM sqlite_master WHERE type='table';")
+	tables = cur.fetchall()  # List of tables
+
+	# Export each table to a separate CSV file
+	for table in tables:
+		table_name = table[0]  # Extract table name
+		df = pd.read_sql_query(f"SELECT * FROM {table_name}", conn)
+		output_file = f"{table_name}.csv"
+		output_path = export_path / output_file
+		df.to_csv(output_path, index=False)  # Save as CSV
+		logger.info(f"Exported {table_name} to {table_name}.csv")
+		
 	conn.close()
 
 	logger.debug(f"Created export db successfully")