--- a/COBRAxy/ras_to_bounds.py	Mon Oct 14 08:51:39 2024 +0000
+++ b/COBRAxy/ras_to_bounds.py	Tue Oct 15 18:31:34 2024 +0000
@@ -180,8 +180,6 @@
         if value is not None:
             model.reactions.get_by_id(reaction).lower_bound = -float(value)
             
-
-    mediumRxns_ids = medium.keys()
             
     # Perform Flux Variability Analysis (FVA) on this medium
     df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
@@ -222,6 +220,11 @@
     if(ARGS.ras_selector == True):
         ras_file_list = ARGS.input_ras.split(",")
         ras_file_names = ARGS.name.split(",")
+        if len(ras_file_names) != len(set(ras_file_names)):
+            error_message = "Duplicated file names in the uploaded RAS matrices."
+            warning(error_message)
+            raise ValueError(error_message)
+            pass
         ras_class_names = []
         for file in ras_file_names:
             ras_class_names.append(file.split(".")[0])
@@ -233,6 +236,8 @@
             ras.set_index("Reactions", drop=True, inplace=True)
             ras = ras.T
             ras = ras.astype(float)
+            #append class name to patient id (dataframe index)
+            ras.index = [f"{idx}_{ras_class_name}" for idx in ras.index]
             ras_list.append(ras)
             for patient_id in ras.index:
                 class_assignments.loc[class_assignments.shape[0]] = [patient_id, ras_class_name]