Fixing some bugs (DSL1 -> DSL2)

src/constant.py

@@ -124,7 +124,7 @@ END_PIPE_OPERATOR = r"\s*(\s*\|\s*\w+)+"
 #         PROCESS
 #--------------------------
 FILE = r'file +(\w+) *\n'
-FROM = r'from([^\n]+)\n'
+FROM = r' from ([^\n]+)\n'
 INPUT = r"\n\s*input *:"
 INTO = r'into +([\w, ]+)'
 INTO_2 = r'into +\(?( *\w+ *(, *\w+)*) *\)?'

src/nextflow_building_blocks.py

@@ -348,8 +348,9 @@ class Nextflow_Building_Blocks:
                         parenthese_left, parenthese_right = get_parenthese_count(text[:start]), get_parenthese_count(text[end:])
                         
                         #if(curly_left==0 and curly_right==0 and parenthese_left==0 and parenthese_right==0 and (start, end) not in searched):
-                        if(parenthese_left==0 and parenthese_right==0 and (start, end) not in searched):
-                            searched.append((start, end))
+                        #if(parenthese_left==0 and parenthese_right==0 and (start, end, temp) not in searched):
+                        if(parenthese_left==0 and parenthese_right==0):
+                            
                         
                             try:
                                 pot = extract_executor_from_middle(text, start, end) 
@@ -361,37 +362,39 @@ class Nextflow_Building_Blocks:
                                 raise BioFlowInsightError(f"Failed to extract the operation or call{self.get_string_line(temp)}. Try rewriting it in a simplified version.", num = 11, origin=self)
                             
                             pot = expand_to_pipe_operators(text, pot)
-                            
-                            #If the thing which is extracted is not in the conditon of an if 
-                            if(not checks_in_condition_if(text, pot) and not checks_in_string(text, pot)):
-                                if(self.get_DSL()=="DSL2"):
-                                    to_call = self.get_list_name_processes()+self.get_list_name_subworkflows()+self.get_list_name_includes()
-                                    if(pot.find("|")!=-1):
-                                        if(not checks_in_condition_if(pot, '|') and not checks_in_string(pot, '|')):#TODO checks_in_string is the first occurance
-                                            first_thing_called = pot.split('|')[-1].strip()
-                                            if(first_thing_called in to_call):
-                                                call = Call(code =pot, origin =self)
-                                                self.executors.append(call)
-                                            elif(first_thing_called in constant.LIST_OPERATORS):
-                                                ope = Operation(code =pot, origin =self)
-                                                self.executors.append(ope)
+                            #IF the exact potential hasn't already been searched, then we don't do it
+                            if((start, end, pot) not in searched):
+                                searched.append((start, end, pot))
+                                #If the thing which is extracted is not in the conditon of an if 
+                                if(not checks_in_condition_if(text, pot) and not checks_in_string(text, pot)):
+                                    if(self.get_DSL()=="DSL2"):
+                                        to_call = self.get_list_name_processes()+self.get_list_name_subworkflows()+self.get_list_name_includes()
+                                        if(pot.find("|")!=-1):
+                                            if(not checks_in_condition_if(pot, '|') and not checks_in_string(pot, '|')):#TODO checks_in_string is the first occurance
+                                                first_thing_called = pot.split('|')[-1].strip()
+                                                if(first_thing_called in to_call):
+                                                    call = Call(code =pot, origin =self)
+                                                    self.executors.append(call)
+                                                elif(first_thing_called in constant.LIST_OPERATORS):
+                                                    ope = Operation(code =pot, origin =self)
+                                                    self.executors.append(ope)
+                                                else:
+                                                    raise BioFlowInsightError(f"'{first_thing_called}' is neither a process, subworkflow or an operator. In the executor '{pot}'{self.get_string_line(pot)}.", num=14,origin=self)#TODO -> try rewriting the operation using the standard syntaxe
+                                            
                                             else:
-                                                raise BioFlowInsightError(f"'{first_thing_called}' is neither a process, subworkflow or an operator. In the executor '{pot}'{self.get_string_line(pot)}.", num=14,origin=self)#TODO -> try rewriting the operation using the standard syntaxe
+                                                from .executor import Executor
+                                                executor = Executor(pot, self)
+                                                self.executors.append(executor.return_type())
                                         
                                         else:
                                             from .executor import Executor
                                             executor = Executor(pot, self)
                                             self.executors.append(executor.return_type())
-                                    
                                     else:
-                                        from .executor import Executor
-                                        executor = Executor(pot, self)
-                                        self.executors.append(executor.return_type())
-                                else:
-                                    ope = Operation(pot, self)
-                                    self.executors.append(ope)
-                                searching = True
-                                break
+                                        ope = Operation(pot, self)
+                                        self.executors.append(ope)
+                                    searching = True
+                                    break
                         
 
         #---------------------------------------------------------------

src/process.py

@@ -585,12 +585,12 @@ class Process(Nextflow_Building_Blocks):
             lines.append(line)
         code = "\n".join(lines)
         #Removing the extra emits
-        #For it to only have one
+        #For it to only have one,
         for line in self.outputs_per_line:
             def replacer(match):
-                return ""
+                return match.group(1)
             for o in line[1:]:
-                code = re.sub(fr"\,\s*{re.escape(o.get_code())}", replacer, code)
+                code = re.sub(fr"\,\s*{re.escape(o.get_code())}(\s|\,|\))", replacer, code)
 
         return code