updated function "remove_empty_conditions_place_anker"

src/outils.py

@@ -1343,9 +1343,9 @@ def get_channels_to_add_in_false_conditions(body, emitted_channels):
     
     return body
 
-#This function removes the empty conditions -> while keeping the anker_clusters -> if it's orignally in a condtion
+#This function removes the empty conditions 
 def remove_empty_conditions(code):
-    pattern = r"(if *\(.+\)|else)\s*{(\s*|\s*\/\/Anker_clusters\s*)}"
+    pattern = r"(if *\(.+\)|else)\s*{(\s*)}"
     def replace(text, pattern):
         def replacer(match):
             return match.group(0).replace(match.group(0), match.group(2))
@@ -1357,4 +1357,21 @@ def remove_empty_conditions(code):
         code = replace(code, pattern)
     return code
 
+#This function removes the empty conditions -> while keeping the anker_clusters -> if it's orignally in a condtion
+def remove_empty_conditions_place_anker(code):
+    conditions = extract_conditions(code)
+    OG_anker= "//Anker_clusters"
+    pos = code.find(OG_anker)
+    conditions_containing_anker = []
+    for condition in conditions:
+        start, end = conditions[condition]
+        if(start<=pos and pos<=end):
+            conditions_containing_anker.append(condition.split('$$__$$')[0])
+    new_anker = OG_anker
+    for condition in conditions_containing_anker:
+        new_anker = f"\n}}\n{new_anker}\nif({condition}) {{\n"
+    code = code.replace(OG_anker, new_anker)
+    code = remove_empty_conditions(code)
+    return code
+    
 

src/workflow.py

@@ -3,7 +3,7 @@
 from .nextflow_file import Nextflow_File
 from .ro_crate import RO_Crate
 from . import constant
-from .outils import is_git_directory, format_with_tabs, replace_thing_by_call, replace_group1, group_together_ifs, extract_curly, remove_extra_jumps, get_channels_to_add_in_false_conditions, extract_conditions, remove_empty_conditions
+from .outils import is_git_directory, format_with_tabs, replace_thing_by_call, replace_group1, group_together_ifs, extract_curly, remove_extra_jumps, get_channels_to_add_in_false_conditions, extract_conditions, remove_empty_conditions_place_anker
 from .outils_graph import get_flatten_dico, initia_link_dico_rec, get_number_cycles, generate_graph
 from .outils_annotate import get_tools_commands_from_user_for_process
 from .bioflowinsighterror import BioFlowInsightError
@@ -838,10 +838,11 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             last_executor_in_cluster = get_last_executor_in_cluster(executors_in_order, clusters)
             if(last_executor_in_cluster.get_type()=="Process"):
                 call = last_executor_in_cluster.get_call()    
-                code = code.replace(call.get_code(get_OG = True), "//Anker_clusters")
+                code = code.replace(call.get_code(get_OG = True), "\n//Anker_clusters\n")
             elif(last_executor_in_cluster.get_type()=="Operation"):
                 if(not last_executor_in_cluster.get_artificial_status()):
-                    code = code.replace(last_executor_in_cluster.get_code(get_OG = True), "//Anker_clusters", 1)
+                    print(last_executor_in_cluster.get_code(get_OG = True))
+                    code = code.replace(last_executor_in_cluster.get_code(get_OG = True), "\n//Anker_clusters\n", 1)
                 else:
                     raise Exception("This shoudn't happen")
             else:
@@ -863,7 +864,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                             raise Exception("This shoudn't happen")
 
             #Remove the empty conditions left in the code
-            code = remove_empty_conditions(code)
+            code = remove_empty_conditions_place_anker(code)
 
 
             #Add the subworkflow defintions
@@ -884,6 +885,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             
             subworkflow_clusters_to_add, subworkflow_cluster_calls_to_add = [], []
             index_cluster = len(clusters)
+            #We replace the last clusters first -> this is cause the outputs of the last clusters aren't used anywhere else in the workflow by definition 
             for elements in list(reversed(clusters)):
 
                 channels_to_replace_outside_of_cluster = []
@@ -1088,58 +1090,6 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
 
 
     
-            """  
-            #TODO -> rmoving the conditions which are problematic
-            #This might not be the probleme -> when rerunnung the analysis isn't totally robust
-            still_simplifying_conditions = True
-            while(still_simplifying_conditions):
-                still_simplifying_conditions = False
-                to_replace, anker1, anker2 = "", "", ""
-                #Replace if/else
-                for match in re.finditer(r"if\s*\([^\{]+\{\s*(\/\/Anker_cluster\d|\s)\s*\}\s*else\s*\{\s*(\/\/Anker_cluster\d|\s)\s*\}", code):
-                    to_replace = match.group(0)
-                    anker1, anker2 = match.group(1), match.group(2)
-                    still_simplifying_conditions = True
-                    break 
-                #Replace empty if on its own
-                if(not still_simplifying_conditions):
-                    for match in re.finditer(r"(if\s*\([^\{]+\{\s*(\/\/Anker_cluster\d|\s)\s*\})\s*[^e]", code):
-                        to_replace = match.group(1)
-                        anker1 = match.group(2)
-                        still_simplifying_conditions = True
-                        break 
-                if(still_simplifying_conditions):
-                    code = code.replace(to_replace, f"{anker1}\n{anker2}")
-        
-            
-            #Replace the ankers by the calls of the subworkflows  
-            for i in range(len(subworkflow_clusters_to_add)):
-                #Extracting the conditions in the code
-                conditions_in_code = extract_conditions(code)
-                anker = f"//Anker_cluster{i}"
-                pos_anker = code.find(anker)
-                #For each anker get the condition in which it is called
-                #Cause we do not want the call of the subworkflows to be done in a condition
-                #So around the call we place ""}} call if(){if(){"" -> so it's executed ouside of a condition
-                conditions_for_anker = []
-                for c in conditions_in_code:
-                    if(conditions_in_code[c][0]<pos_anker and pos_anker <conditions_in_code[c][1]):
-                        conditions_for_anker.append(c.split("$$__$$")[0])
-                #Placing the extract curlies around it
-                subworkflow_call = subworkflow_cluster_calls_to_add[i]
-                for c in conditions_for_anker:
-                    subworkflow_call = f"\n}}\n{subworkflow_call}\nif({c}){{\n"
-                code = code.replace(anker, subworkflow_call)
-            
-            
-            for old, new in channels_to_replace_outside_of_cluster:
-                pattern= fr"[ \(,]({re.escape(old)})[^\w]"
-                code = replace_group1(code, pattern, new)
-                #code = code.replace(old, new)
-            
-          
-            
-            """
             
             #Putting || back
             code = code.replace("$OR$", "||")