Updated the position of subworkflow calls + changed topological order to order...

Updated the position of subworkflow calls + changed topological order to order of definition in the code

src/executor.py

@@ -81,6 +81,13 @@ class Executor(Nextflow_Building_Blocks):
     def get_channels_from_name_all_channels(self, name):
         return self.origin.get_channels_from_name_all_channels(name)
     
+    def get_position_in_main(self, executor):
+        return self.origin.get_position_in_main(executor)
+    
+    def get_subworkflow_calls_to_get_here(self, executor):
+        return self.origin.get_subworkflow_calls_to_get_here(executor)
+
+    
     
     def get_channels_from_name_other_blocks_on_same_level(self, name):
         return self.origin.get_channels_from_name_other_blocks_on_same_level(name)

src/main.py

@@ -15,6 +15,29 @@ class Main(Nextflow_Building_Blocks):
         self.initialised = False
         self.root = None 
 
+    def get_order_execution_executors(self, dico):
+        executors = self.get_all_executors_in_subworkflow()
+        pos = {}
+        for e in executors:
+            pos[e] = e.get_position_in_main(e)
+        #TODO add sort here
+        pos =  {k: v for k, v in sorted(pos.items(), key=lambda item: item[1])}
+        for e in pos:
+            if(e.get_type()=="Call"):
+                if(e.get_first_element_called().get_type()=="Subworkflow"):
+                    dico[e] = {}
+                    e.get_first_element_called().get_order_execution_executors(dico[e])
+                else:
+                    dico[e.get_first_element_called()] = pos[e]
+            else:
+                dico[e] = pos[e]
+        return dico
+
+
+    def get_position_in_main(self, executor):
+        code = self.get_code()
+        return code.find(executor.get_code(get_OG = True))
+
     def get_string_line(self, bit_of_code):
         return self.nextflow_file.get_string_line(bit_of_code)
     

src/root.py

@@ -27,6 +27,19 @@ class Root(Nextflow_Building_Blocks):
     def get_type(self):
         return "Root"
     
+    def get_position_in_main(self, executor):
+        return self.origin.get_position_in_main(executor)
+    
+    def get_subworkflow_calls_to_get_here(self, executor):
+        if(self.origin.get_type()=="Main"):
+            return []
+        elif(self.origin.get_type() in ["Block", "Root"]):
+            return self.origin.get_subworkflow_calls_to_get_here(executor)
+        #Case subworkflow
+        else:
+            call = self.origin.get_call()
+            return [call]+call.get_subworkflow_calls_to_get_here(executor)
+
     def get_blocks(self):
         return self.blocks
     

src/workflow.py

@@ -398,6 +398,22 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
         else:
             raise BioFlowInsightError("Trying to generate random relevant processes however option 'duplicate' is not activated.")
     
+    #Method that returns the order of execution for each executor
+    def get_order_execution_executors(self):
+        dico = {}
+        dico = self.get_workflow_main().get_order_execution_executors(dico)
+        tab = []
+        def explore_dico(dico):
+            if(type(dico)!=dict):
+                None
+            else:
+                for val in dico:
+                    tab.append(val)
+                    explore_dico(dico[val])
+        explore_dico(dico)
+
+        return tab
+
     #This method rewrites the entire workflow into one single file
     def write_workflow_into_one_file(self):
         #This tag is used as an identification to safely manipulate the string 
@@ -723,7 +739,16 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             #    if(len(c)>1):
             #        clusters[i] = self.nextflow_file.graph.get_induced_subgraph(c)
             #Get the topological order
-            clusters = self.graph.get_topogical_order(clusters)
+            executors_in_order = self.get_order_execution_executors()
+            new_clusters = []
+            for cluster in clusters:
+                tab = []
+                for e in executors_in_order:
+                    if(e in cluster):
+                        tab.append(e)
+                new_clusters.append(tab)
+            clusters = new_clusters
+            #clusters = self.graph.get_topogical_order(clusters)
     
 
 
@@ -746,6 +771,21 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                 if(len(elements)>1 and at_least_one_process):
                     name, body, take, emit = "", "", "", ""
                     first_element = True
+
+                    def get_last_operation_or_call(elements):
+                        index = -1
+                        while(True):
+                            if(elements[index].get_type()=="Process"):
+                                return elements[index].get_call()
+                            else:
+                                if(not elements[index].get_artificial_status()):
+                                    return elements[index]
+                                else:
+                                    index = index-1
+                    anker_thing = get_last_operation_or_call(elements).get_code(get_OG = True)
+                    code = code.replace(anker_thing, f"//Anker_cluster{index_cluster}\n\n{anker_thing}")
+
+
                     for ele in elements:
             
                         if(ele.get_type()=="Process"):
@@ -757,11 +797,11 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                             call = ele.get_call()
             
                             #If first element -> add marker for the subworkflow call
-                            if(first_element):
-                                code = code.replace(call.get_code(get_OG = True), f"//Anker_cluster{index_cluster}")
-                                first_element = False
-                            else:
-                                code = code.replace(call.get_code(get_OG = True), "")
+                            #if(first_element):
+                            #    code = code.replace(call.get_code(get_OG = True), f"//Anker_cluster{index_cluster}")
+                            #    first_element = False
+                            #else:
+                            code = code.replace(call.get_code(get_OG = True), "")
             
             
                             processes_added.append(call.get_first_element_called())
@@ -779,12 +819,12 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                             #TODO -> check this verification there might be some "effet de bord"
                             if(not ele.get_artificial_status()):
             
-                                #If first element -> add marker for the subworkflow call
-                                if(first_element):
-                                    code = code.replace(ele.get_code(get_OG = True), f"//Anker_cluster{index_cluster}", 1)
-                                    first_element = False
-                                else:
-                                    code = code.replace(ele.get_code(get_OG = True), "", 1)
+                                ##If first element -> add marker for the subworkflow call
+                                #if(first_element):
+                                #    code = code.replace(ele.get_code(get_OG = True), f"//Anker_cluster{index_cluster}", 1)
+                                #    first_element = False
+                                #else:
+                                code = code.replace(ele.get_code(get_OG = True), "", 1)
                 
                                 #Ignore these cases
                                 #TODO -> you should be able to remove this