Fixed problem with emit outside of condition when calls are in conditions

src/block.py

@@ -84,6 +84,9 @@ class Block(Root):
                 tab+=block.get_calls_same_level()
                 tab+=block.get_calls_inside_level()
         return tab
+    
+    def get_all_calls_from_root(self):
+        return self.origin.get_all_calls_from_root()
 
     #############
     # CHANNELS

src/executor.py

@@ -287,6 +287,13 @@ class Executor(Nextflow_Building_Blocks):
                     for c in call.get_all_calls():
                         if(c.first_element_called.get_alias()==name):
                             tab.append(c)
+            #If there is no calls found then we search in all root
+            if(len(tab)==0):
+                for call in self.origin.get_all_calls_from_root():
+                    #call.initialise()
+                    for c in call.get_all_calls():
+                        if(c.first_element_called.get_alias()==name):
+                            tab.append(c)
             return tab
 
         else:

src/operation.py

@@ -928,6 +928,7 @@ class Operation(Executor):
             index += 1
         
         temporary_index = 1
+        new_body = ""
         for origin in dico_origin_2_replace:
             if(len(dico_origin_2_replace[origin])<=1):
                 for val in dico_origin_2_replace[origin]:
@@ -937,23 +938,32 @@ class Operation(Executor):
                         code = code.replace(origin, val.simplify_code())
             #Case there are mutiple origins then:
             else:
-                #TODO -> fix this problem if you have the courage to -> see at what extend it is used
-                raise BioFlowInsightError("TODO (update): The output of a emit is ambiguous -> there are multiple instance where it exits")
-                #print(dico_origin_2_replace)
-                #for e in dico_origin_2_replace[origin]:
-                #    print(e.get_all_conditions())
-            temporary_index+=1
-
-        #for o in self.origins:
-        #    if(o.get_type()=="Call"):
-        #        #If it's not a function -> then we rewrite it
-        #        if(o.get_first_element_called().get_type()!="Function"):
-        #            to_add.append(add_origin_equals(o, index))
-        #            code = code.replace(o.get_code(get_OG=True), f"operation_{operation_id}_{index}")
-        #    elif(o.get_type()=="Emitted"):
-        #        code = code.replace(o.get_code(get_OG=True), o.simplify_code())
-        #    index += 1
+                #For example 
+                #if(){
+                #   p1(ch1)
+                #} else {
+                #   p1(ch2)
+                #}
+                #val = p1.out -> when wanting to rewrite this operation
+                calls = {}
+                temporary_channel = f"temporary_val_{id(self)}_{temporary_index}"
+                for e in dico_origin_2_replace[origin]:
 
+                    try:
+                        temp = calls[e.emitted_by]
+                    except:
+                        calls[e.emitted_by] = []
+                    calls[e.emitted_by].append(e.simplify_code())
+                for c in calls:
+                    #This is just one value
+                    if(len(c.get_all_conditions())>1):
+                        raise Exception("This shoudn't happen")
+                    for condition in c.get_all_conditions():
+                        new_body+=f"if({condition.get_value().strip()}) {{\n{temporary_channel} = {calls[c][0]}\n}}\n"
+                new_body+=temporary_channel
+                code = code.replace(origin, new_body)
+                temporary_index+=1
+            
         to_add.reverse()
         for c in to_add:
             code = f"{c}\n{code}"

src/root.py

@@ -247,6 +247,11 @@ class Root(Nextflow_Building_Blocks):
         all_executors = self.get_executors_same_level()+self.get_inside_executors()
         for e in all_executors:
             calls[e] = ''
+
+    def get_all_calls_from_root(self):
+        dico = {}
+        self.get_all_calls_in_subworkflow(calls=dico)
+        return list(dico.keys())
     
 
     #############

src/workflow.py

@@ -526,7 +526,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
         return subs
 
 
-    def rewrite_and_initialise(self, code, processes_2_remove, render_graphs):
+    def rewrite_and_initialise(self, code, processes_2_remove, render_graphs, def_check_the_same = True):
         temp_process_dependency_graph = self.graph.get_process_dependency_graph() 
         temp_spec_graph = self.graph.full_dico
 
@@ -547,7 +547,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
         self.initialise()
         os.remove(temp_file)
         self.graph.initialise(processes_2_remove = self.processes_2_remove)
-        if(not self.graph.check_if_process_dependendy_is_equivalent_to_other_without_subworkflows(temp_process_dependency_graph)):
+        if(def_check_the_same and not self.graph.check_if_process_dependendy_is_equivalent_to_other_without_subworkflows(temp_process_dependency_graph)):
             if(render_graphs==True):
                 generate_graph(self.get_output_dir()/ "debug" /"spec_graph_OG", temp_spec_graph, render_graphs = True)
                 generate_graph(self.get_output_dir()/ "debug" /"spec_graph", self.graph.full_dico, render_graphs = True)
@@ -720,11 +720,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
 
         if(self.get_DSL()=="DSL1"):
             code = self.convert_to_DSL2()
+            self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs, def_check_the_same = False)
 
-        if(self.duplicate):
+        if(self.get_DSL()=="DSL2"):
             code = self.simplify_workflow_code()
             self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
-            
+
+        if(self.duplicate):    
             
             
             #DETERMING WHICH SUBWORKFLOWS ARE BROKEN WITH THE CLUSTER