From 972d264eee5105086e30df2a478e48a21f073832 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 16 Apr 2025 14:10:15 +0200
Subject: [PATCH] Started adding upper bound for the whiles
---
src/call.py | 6 +++++-
src/code_.py | 14 +++++++++++---
src/outils.py | 6 +++---
3 files changed, 19 insertions(+), 7 deletions(-)
diff --git a/src/call.py b/src/call.py
index be9135c..1f8bd77 100644
--- a/src/call.py
+++ b/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:
diff --git a/src/code_.py b/src/code_.py
index 6a44399..5c315b9 100644
--- a/src/code_.py
+++ b/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
diff --git a/src/outils.py b/src/outils.py
index c941f71..83b420f 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1,7 +1,7 @@
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]
--
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