From f607cf9107ce8f67930b402759258ef8b8e87f7e Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 16 Apr 2025 11:50:45 +0200
Subject: [PATCH] Added while upper bound for the while for the extarction of
conditions -> gonna do the same for the rest of the whiles
---
src/constant.py | 2 ++
src/outils.py | 9 ++++++++-
2 files changed, 10 insertions(+), 1 deletion(-)
diff --git a/src/constant.py b/src/constant.py
index 400e439..8f32dbe 100644
--- a/src/constant.py
+++ b/src/constant.py
@@ -2,6 +2,8 @@
# CONSTANT VARIABLES
#==========================
+WHILE_UPPER_BOUND = 1000000
+
ERROR_WORDS = ['null', "params", "log", "workflow", "it", "config"]
ERROR_WORDS_ORIGINS = ['channel', 'Channel', 'null', "params", "logs", "workflow", "log",
diff --git a/src/outils.py b/src/outils.py
index fdc5535..c941f71 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1,6 +1,9 @@
import re
import subprocess
import os
+from .constant import WHILE_UPPER_BOUND
+from .bioflowinsighterror import BioFlowInsightError
+
#=============================================================
# THESE A JUST UTILITY FUNCTIONS TO BE ABLE TO MANIPULATE CODE
@@ -932,7 +935,8 @@ def extract_conditions(code, only_get_inside = True):
triple_single, triple_double = False, False
- while(start<len(code)):
+ timeout = 0
+ while(start<len(code) and timeout < 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):
@@ -1056,6 +1060,9 @@ def extract_conditions(code, only_get_inside = True):
start = end-1
start+=1
+ timeout+=1
+ if(timeout>=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]
return conditions_dico
--
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