Fixed the problem i had with the subworkflows being broken or not

src/workflow.py

@@ -812,8 +812,8 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
 
     #I do not recommand that the dev uses the same name for the channels inside and outside the channels
     #Since the local channels become local at the upper level
-    def rewrite_subworkflow_call(seld, code, subworklfow):
-        print(subworklfow.get_name())
+    def rewrite_subworkflow_call(self, code, subworklfow):
+        
         #Remove the defintion from the code
         code = code.replace(subworklfow.get_code(), "")
         OG_call = subworklfow.get_call()
@@ -838,35 +838,49 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
         code = code.replace(OG_call.get_code(get_OG = True), f"{new_header}\n\n{OG_body}")
 
         #REPLACE THE EMITS
+        #TODO admittedly this code below is very moche -> but it's functionnal -> update it 
         emits = subworklfow.get_emit()
-        for o in emits:
-            origin = o.get_origins()[0]
-            gives = o.get_gives()
-            #TODO finish this -> i think that the gives is empty
-            print(o.get_type())
-            print(o.get_code(), origin.get_code(), gives)
-            
-
-        #print(code)
+        to_replace = []
+        all_executors = self.get_all_executors()
+        for exe in all_executors:
+            #We don't need to check the case call since the workflow has already been rewriteen -> emits only appear in operations
+            if(exe.get_type()=="Operation"):
+                emited = exe.get_origins()
+                if(len(emited)==1):
+                    emited = emited[0]
+                    if(emited.get_type()=="Emitted"):
+                        if(emited.get_emitted_by()==subworklfow):
+                            if(emited.get_emits() not in emits):
+                                raise Exception("This shoudn't happen -> since it is the actual subworkflow")
+                            to_replace.append((exe.get_code(get_OG = True), f"{exe.get_gives()[0].get_code()} = {emited.get_emits().get_origins()[0].get_code()}"))
+        for r in to_replace:
+            old, new = r
+            #Case of channel == channel
+            if(new.split("=")[0].strip()==new.split("=")[1].strip()):
+                new = ''
+            code = code.replace(old, new)
+        
+        
         return code
 
+    def rewrite_and_initialise(self, code):
+        #Write new code in temporary file
+        temp_file = self.get_output_dir()/f"temp_{str(self)[-7:-2]}.nf"
+        with open(temp_file, "w") as file:
+            file.write(code)
+        
+        #Replace old analysis with new analysis (simplified code)
+        self.__init__(str(temp_file), display_info = False, duplicate=True)
+        self.initialise(create_rocrate=False)
+
 
 
     #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 = []):
         if(self.duplicate):
 
-            #Write new code in temporary file
             code = self.simplify_workflow_code()
-            temp_file = self.get_output_dir()/f"temp_{str(self)[-7:-2]}.nf"
-            with open(temp_file, "w") as file:
-                file.write(code)
-            
-            #Replace old analysis with new analysis (simplified code)
-            self.__init__(str(temp_file), display_info = False, duplicate=True)
-            self.initialise(create_rocrate=False)
-            
-
+            self.rewrite_and_initialise(code)
 
             #Get the clusters and the code
             self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, processes_2_remove =  [])
@@ -927,51 +941,18 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 return broken_subworkflows
 
             broken_subworkflows = get_workflows_broken(subworkflow_2_executors, set_clusters_with_calls)
-            
+            print(broken_subworkflows)
             #Rewrite broken subworkflows
             for sub in broken_subworkflows:
                 code = self.rewrite_subworkflow_call(code, sub)
+
+            #TODO -> this needs to be optimised
+            self.rewrite_and_initialise(code)
+            #Get the clusters and the code
+            self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, processes_2_remove =  [])
+            clusters = self.nextflow_file.graph.get_clusters_from_user_view()
                 
-            1/0
-
-            #def check_subworkflow_intact(original_sets, new_sets):
-            #    results = {}
-            #    for sub in original_sets:
-            #        original = original_sets[sub]
-            #        #temp = []
-            #        #for new in new_sets:
-            #        #    print(original, new, new.issubset(original))
-            #        #    #temp.append(original.issubset(new))
-            #        #print(temp)
-            #        intact = all(new.issubset(original) for new in new_sets)
-            #        results[sub] = intact
-            #    return results
-
-            #print(check_subworkflow_intact(subworkflow_2_executors, set_clusters_with_calls))
-            1/0
-
-            #cluster_2_subworkflows = []
-            #print(clusters)
-            ##Basically here i'm checking if a subworkflow is split
-            ##TODO Check this -> i think in the case something is at the root -> it won't work
-            #for sub in self.get_subworkflows_called():
-            #    clusters_in_which_elements_are_taken = []
-            #    #TODO do this
-            #    print(sub.get_name(), sub.get_executors())
-            #    for exe in sub.get_executors():
-            #        print(exe, exe.get_subworkflow_origin())
-            #    #If there are multiple clusters and the number of clusters isn't equal to all the clusters -> it means that subworkflow is broken 
-            #    if(len(clusters_in_which_elements_are_taken)>1 and len(clusters_in_which_elements_are_taken)!=len(clusters)):
-            #        print(sub.get_name())
-            #print(clusters)
-            #for c in clusters:
-            #    for ele in c:
-            #        print(ele.get_type())
             
-        
-            #TODO -> need to break clusters here
-            #And redo analysis
-
 
             #Get the clsuters with the corresponding operations inside
             #for i in range(len(clusters)):