fixed bug

src/block.py

@@ -88,7 +88,7 @@ class Block(Root):
     #############
     # CHANNELS
     #############
-    def get_channels_above_level_rec(self, dico = {}):
+    def get_channels_above_level_rec(self, dico):
         for c in self.channels:
             dico[c] = ''
         self.origin.get_channels_above_level_rec(dico)
@@ -107,6 +107,9 @@ class Block(Root):
                 tab+=block.get_channels_same_level()
                 tab+=block.get_channels_inside_level()
         return tab
+    
+    def get_channels_from_name_all_channels(self, name):
+        return self.origin.get_channels_from_name_all_channels(name)
 
     #def check_in_channels(self, channel):
     #    for c in self.get_channels():

src/call.py

@@ -157,7 +157,7 @@ class Call(Executor):
                 #Case it's a channel
                 if(re.fullmatch(constant.WORD, param) and not analysed_param):
                 #if(re.fullmatch(constant.WORD, param) and not analysed_param or param in ['[]'] or param[:7]=="params."):
-                    
+                    #TODO this needs to be updated to proper formalise how you search for channels
                     channels = self.origin.get_channels_from_name_same_level(param)
                     if(channels==[]):
                         channels = self.origin.get_channels_from_name_inside_level(param)
@@ -165,6 +165,8 @@ class Call(Executor):
                         channels = self.origin.get_channels_from_name_above_level(param)
                     if(channels==[]):
                         channels = self.origin.get_channels_from_name_other_blocks_on_same_level(param)
+                    if(channels==[]):
+                        channels = self.origin.get_channels_from_name_all_channels(param)
                     if(channels==[]):
                         from .channel import Channel
                         channel = Channel(name=param, origin=self.origin)

src/executor.py

@@ -78,6 +78,10 @@ class Executor(Nextflow_Building_Blocks):
     def get_channels_from_name_above_level(self, name):
         return self.origin.get_channels_from_name_above_level(name)
     
+    def get_channels_from_name_all_channels(self, name):
+        return self.origin.get_channels_from_name_all_channels(name)
+    
+    
     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/root.py

@@ -107,6 +107,14 @@ class Root(Nextflow_Building_Blocks):
             if(c.get_name()==name):
                 tab.append(c)
         return tab
+    
+    def get_channels_from_name_all_channels(self, name):
+        channels = self.get_channels_same_level()+self.get_channels_inside_level()
+        tab = []
+        for c in channels:
+            if(c.get_name()==name):
+                tab.append(c)
+        return tab
 
 
 

src/workflow.py

@@ -382,10 +382,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
                     raise BioFlowInsightError("alpha is not in the interval [0; 1]")
             
             processes_called = []
-            for c in self.get_workflow_main().get_all_calls_in_workflow():
-                p = c.get_first_element_called()
-                if(p.get_type()=="Process"):
-                    processes_called.append(p)
+            if(self.get_DSL()=="DSL2"):
+                for c in self.get_workflow_main().get_all_calls_in_workflow():
+                    p = c.get_first_element_called()
+                    if(p.get_type()=="Process"):
+                        processes_called.append(p)
+            else:
+                processes_called = self.get_first_file().get_processes()
             nb_2_select = int(alpha*len(processes_called))
             sampled = random.sample(set(processes_called), nb_2_select)
             name_select = []
@@ -636,6 +639,10 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
     #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 = []):
+        if(self.get_DSL()=="DSL1"):
+            code = self.convert_to_DSL2()
+            self.rewrite_and_initialise(code)
+
         if(self.duplicate):
             code = self.simplify_workflow_code()
             self.rewrite_and_initialise(code)
@@ -709,8 +716,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             #Get the clusters and the code
             self.generate_user_view(relevant_processes = relevant_processes, processes_2_remove =  [])
             clusters = self.graph.get_clusters_from_user_view()
-            
-            
+
             #Get the clsuters with the corresponding operations inside
             #for i in range(len(clusters)):
             #    c = clusters[i]
@@ -935,7 +941,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
             #Add anker
             subworkflow_section = f"//ANKER 4 SUBWORKFLOW DEF"
             to_replace = ""
-            for match in re.finditer(r"workflow\s+\w*\s*\{", code):
+            for match in re.finditer(r"workflow\s*\w*\s*\{", code):
                 to_replace = match.group(0)
                 break
             if(to_replace==""):