Added filter to flag when there are duplicate subworkflows -> in that case i cannot rewritte it

src/workflow.py

@@ -419,10 +419,22 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 nb_2_select = int(alpha*len(processes_called))
                 sampled = random.sample(set(processes_called), nb_2_select)
                 
+
+
+                def get_object(address):
+                    address = int(re.findall(r"\dx\w+", address)[0], base=16)
+                    return ctypes.cast(address, ctypes.py_object).value
+
+                edges_create_cycles_names = []
+                for e in edges_create_cycles:
+                    n1, n2 = e
+                    obj1, obj2 = get_object(n1), get_object(n2)
+                    edges_create_cycles_names.append((obj1.get_alias(), obj2.get_alias()))
+
                 sampled_str = []
                 for s in sampled:
-                    sampled_str.append(str(s))
-                for e in edges_create_cycles:
+                    sampled_str.append(s.get_alias())
+                for e in edges_create_cycles_names:
                     if(e[0] in sampled_str and e[1] in sampled_str):
                         #So that means there are the 2 nodes which form the cycle edge in the relevant processes
                         #-> it means we need to regenerated relevant processes
@@ -788,6 +800,15 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             return match.group(1)
         return re.sub(f"(\w+)_GG_\d+", replacer, code)
     
+    def check_multiple_subworkflow(self):
+        seen= []
+        for sub in self.get_subworkflows_called():
+            if(sub.get_code() in seen):
+                raise BioFlowInsightError(f"The subworkflow '{sub.get_name()}' is called multiple times in the workflow, I cannot rewritte it. Try defining the workflow in a different way.", type="Rewrite Error")
+            else:
+                seen.append(sub.get_code())
+  
+
     #Method which rewrites the workflow follwong the user view
     #Conert workflow to user_view only makes sense when the option duplicate is activated -> otherwise is doesn't make sense + it makes the analysis way more complicated
     def convert_workflow_2_user_view(self, relevant_processes = [], render_graphs = True):
@@ -814,6 +835,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
         if(self.duplicate): 
             #First check if there are any duplicate operations
             #That method is in the "get_order_execution_executors" method -> so we just run that first
+            self.check_multiple_subworkflow()
             self.get_order_execution_executors()  
 
             if(self.get_DSL()=="DSL1"):