From 9babd60c409b495f494c6db3197402a8de93f4a0 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 12 Mar 2024 11:33:42 +0100
Subject: [PATCH] add small error handling
---
src/bioflowinsighterror.py | 2 ++
src/nextflow_building_blocks.py | 15 ++++++++++++---
2 files changed, 14 insertions(+), 3 deletions(-)
diff --git a/src/bioflowinsighterror.py b/src/bioflowinsighterror.py
index dd222bb..0dfc769 100644
--- a/src/bioflowinsighterror.py
+++ b/src/bioflowinsighterror.py
@@ -43,6 +43,8 @@ class BioFlowInsightError(Exception):
#* [5] -> A ternary conditional operator was used with an tuple
#* [7] -> Tuple with emit (ch1, ch2) = emit.out
#* [9] -> Tuple with call (ch1, ch2) = wf()
+#* [11] -> Failed to extract the operation or call at the line x. Try rewriting it in a simplified version.
+
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index c436bf2..ce5144c 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -318,16 +318,24 @@ class Nextflow_Building_Blocks:
if(match.group(1) in constant.LIST_OPERATORS):
#TODO -> the function below might not work perfectly but i don't have any other ideas
- #TODO -> IMPORTANT find another way of doing this -> for example if there isn't the same number of curlies/parentheses
+
#Use if there is an operator called right before opening the curlies/parenthse
- curly_left, curly_right = get_curly_count(text[:start]), get_curly_count(text[end:])
+ #curly_left, curly_right = get_curly_count(text[:start]), get_curly_count(text[end:])
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))
- pot = extract_executor_from_middle(text, start, end)
+ try:
+ pot = extract_executor_from_middle(text, start, end)
+ except:
+ try:
+ temp = text[start-10:end+10]
+ except:
+ temp = text[start:end]
+ 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
@@ -360,6 +368,7 @@ class Nextflow_Building_Blocks:
self.executors.append(ope)
searching = True
break
+
#---------------------------------------------------------------
#STEP4 - Extract the Executors which only use the pipe operators (which start with a channel)
--
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