Started adding upper bound for the whiles

src/call.py

@@ -209,10 +209,14 @@ class Call(Executor):
         #Step 1 -> get parameters
         tab_params, start, next_param = [], 0, None
         temp_param = param
-        while(start!=-1):
+        timeout = 0
+        while(start!=-1 and timeout<constant.WHILE_UPPER_BOUND):
             temp_param = temp_param[start:]
             next_param, start = get_next_param(temp_param)
             tab_params.append(next_param.strip())
+            timeout+=1
+        if(timeout>=constant.WHILE_UPPER_BOUND):
+            raise BioFlowInsightError(f"The WHILE_UPPER_BOUND was exceeded. BioFlow-Insight was unable to extract the parameters for the call '{self.get_code(get_OG=True)}'. Make sure the workflow uses correct Nextflow syntaxe (https://www.nextflow.io/docs/latest/index.html).", type="Unable to extract call parameters")
 
         #Step 2 -> analyse paramters
         for param in tab_params:

src/code_.py

@@ -45,8 +45,8 @@ class Code:
         quote_single, quote_double = False, False
         triple_single, triple_double = False, False
 
-
-        while(start<len(code)):         
+        timeout = 0
+        while(start<len(code) and timeout<constant.WHILE_UPPER_BOUND):         
             checked_triple = False
             if(start+3<=len(code)):
                 if(code[start:start+3]=="'''" and not quote_single and not quote_double and not triple_single and not triple_double):
@@ -116,6 +116,9 @@ class Code:
                                     
                             
                 start+=1
+            timeout+=1
+        if(timeout>=constant.WHILE_UPPER_BOUND):
+            raise BioFlowInsightError(f"The WHILE_UPPER_BOUND was exceeded. BioFlow-Insight was unable to turn a single line condition into a multi line condition. Make sure the workflow uses correct Nextflow syntaxe (https://www.nextflow.io/docs/latest/index.html).", type="Unable to turn single line condition into multi line")
 
 
         
@@ -128,7 +131,8 @@ class Code:
     def remove_things_inside_map(self, code):
         index = 0
         searching = True
-        while(searching):
+        timeout = 0
+        while(searching and timeout<constant.WHILE_UPPER_BOUND):
             searching = False
             #TODO -> do the same with flatMap -> 668
             for word in ["map", "flatMap"]:
@@ -153,6 +157,10 @@ class Code:
                         searching = True
                         index+=1
                         break
+            timeout+=1
+        if(timeout>=constant.WHILE_UPPER_BOUND):
+            raise BioFlowInsightError(f"The WHILE_UPPER_BOUND was exceeded. BioFlow-Insight was unable to extract the inside of a 'map' operator. Make sure the workflow uses correct Nextflow syntaxe (https://www.nextflow.io/docs/latest/index.html).", type="Unable to extract the inside of a 'map' operator")
+        
 
         return code
 

src/outils.py

 import re
 import subprocess
 import os
-from .constant import WHILE_UPPER_BOUND
+from . import constant
 from .bioflowinsighterror import BioFlowInsightError
 
 
@@ -936,7 +936,7 @@ def extract_conditions(code, only_get_inside = True):
 
 
     timeout = 0
-    while(start<len(code) and timeout < WHILE_UPPER_BOUND):    
+    while(start<len(code) and timeout < constant.WHILE_UPPER_BOUND):    
         checked_triple = False
         if(start+3<=len(code)):
             if(code[start:start+3]=="'''" and not quote_single and not quote_double and not triple_single and not triple_double):
@@ -1061,7 +1061,7 @@ def extract_conditions(code, only_get_inside = True):
     
             start+=1
         timeout+=1
-    if(timeout>=WHILE_UPPER_BOUND):
+    if(timeout>=constant.WHILE_UPPER_BOUND):
         raise BioFlowInsightError("The WHILE_UPPER_BOUND was exceeded. BioFlow-Insight was unable to extarct the conditions. Make sure the workflow uses correct Nextflow syntaxe (https://www.nextflow.io/docs/latest/index.html).", type="Unable to extract conditions")
     for c in conditions_dico:
         start, end = conditions_dico[c]