From 5b787ffe30d365febaf230cb0a4f2646ebdc0189 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 19 Mar 2025 16:50:33 +0100
Subject: [PATCH] fixed a small bug + i've started to test if the replaces
actaully work -> it's a good way to catch errors -> perhaps add them to the
rest of the code
---
src/call.py | 31 ++++++++++++++++++++++++++++---
src/main.py | 4 ++--
src/nextflow_file.py | 19 +++++++++++++++++++
src/operation.py | 20 ++++++++++++++++++++
4 files changed, 69 insertions(+), 5 deletions(-)
diff --git a/src/call.py b/src/call.py
index 604564b..60b2052 100644
--- a/src/call.py
+++ b/src/call.py
@@ -52,7 +52,7 @@ class Call(Executor):
def get_parameters(self):
return self.parameters
- def get_code(self, clean_pipe = False, get_OG=False, remove_emit_and_take = False):
+ def get_code(self, clean_pipe = False, get_OG=False, remove_emit_and_take = False, replace_calls = False):
if(get_OG):
if(self.OG_code==''):
return self.code.get_code()
@@ -83,16 +83,25 @@ class Call(Executor):
if(param.get_type()=="Call"):
#If it's not a function -> then we rewrite it
if(param.get_first_element_called().get_type()!="Function"):
+ temp = code
code = replace_group1(code, fr"[^\w]({re.escape(param.get_code(get_OG=True))})", param_new_name)
+ if(temp==code):
+ raise Exception("This souldn't happen")
#code = code.replace(param.get_code(get_OG=True), param_new_name)
new_bit = param.simplify_code(new_name = param_new_name)
+ temp = code
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
+ if(temp==code):
+ raise Exception("This souldn't happen")
#Case the param is an operation
elif(param.get_type()=="Operation"):
#If it's an artificial operation -> we don't need to do anything
if(not param.get_artificial_status()):
- code = replace_group1(code, fr"[^\w]({re.escape(param.get_code(get_OG=True))})", param_new_name)
+ temp = code
+ code = replace_group1(code, fr"[^\w]({re.escape(param.get_code(get_OG=True, replace_calls = False))})", param_new_name)
+ if(temp==code):
+ raise Exception("This souldn't happen")
#code = code.replace(param.get_code(get_OG=True), param_new_name)
lines = param.simplify_code().split('\n')
if(len(lines)==1):
@@ -100,21 +109,34 @@ class Call(Executor):
else:
head = '\n'.join(lines[:-1])
new_bit = f"{head}\n{param_new_name} = {lines[-1]}"
+ temp = code
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
+ if(temp==code):
+ raise Exception("This souldn't happen")
#Case Channel
elif(param.get_type()=="Channel"):
raise Exception("This shouldn't happen")
None
elif(param.get_type()=="Emitted"):
+ temp = code
code = replace_group1(code, fr"[^\w]({re.escape(param.get_code(get_OG=True))})", param_new_name)
+ if(temp==code):
+ raise Exception("This souldn't happen")
#code = code.replace(param.get_code(get_OG=True), param_new_name)
new_bit = f"{param_new_name} = {param.simplify_code()}"
+ temp = code
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
+ if(temp==code):
+ raise Exception("This souldn't happen")
else:
raise Exception("This shouldn't happen")
index+=1
- return code.replace(tag_to_add, "").strip()
+ temp = code
+ code = code.replace(tag_to_add, "").strip()
+ if(temp==code):
+ raise Exception("This souldn't happen")
+ return code
@@ -148,7 +170,10 @@ class Call(Executor):
def get_code_split_space(self, code):
to_add_spaces = ['(', ')', '}', '{']
for character in to_add_spaces:
+ temp = code
code = code.replace(f'{character}', f' {character} ')
+ if(temp==code):
+ raise Exception("This shouldn't happen")
return code.split()
def analye_parameters(self, param):
diff --git a/src/main.py b/src/main.py
index 0cec5f5..63a052a 100644
--- a/src/main.py
+++ b/src/main.py
@@ -50,11 +50,11 @@ class Main(Nextflow_Building_Blocks):
for exe in sorted_executor_2_length:
if(exe.get_type()=="Call" or exe.get_type()=="Operation"):
- old = exe.get_code(get_OG = True, remove_emit_and_take = True)
+ old = exe.get_code(get_OG = True, remove_emit_and_take = True, replace_calls = False)
new = exe.simplify_code()
if(new!=old):
temp = code
- code = code.replace(exe.get_code(get_OG = True), exe.simplify_code(), 1)
+ code = code.replace(old, new, 1)
if(temp==code):
print(code)
print("- old", f'"{old}"')
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 9329ac8..829999c 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -277,15 +277,30 @@ class Nextflow_File(Nextflow_Building_Blocks):
#Code without processes
code = self.get_code()
for proecess in self.processes:
+ temp = code
code = code.replace(proecess.get_code(), "")
+ if(temp==code):
+ raise Exception("This souldn't happen")
for sub in self.subworkflows:
+ temp = code
code = code.replace(sub.get_code(), "")
+ if(temp==code):
+ raise Exception("This souldn't happen")
for fun in self.functions:
+ temp = code
code = code.replace(fun.get_code(), "")
+ if(temp==code):
+ raise Exception("This souldn't happen")
if(self.first_file and self.main!=None):
+ temp = code
code = code.replace(self.main.get_code(), "")
+ if(temp==code):
+ raise Exception("This souldn't happen")
for include in self.includes:
+ temp = code
code = code.replace(include.get_code(), "")
+ if(temp==code):
+ raise Exception("This souldn't happen")
from .root import Root
self.root = Root(code=code, origin= self, modules_defined=self.get_modules_defined(), subworkflow_inputs = [])
@@ -317,7 +332,11 @@ class Nextflow_File(Nextflow_Building_Blocks):
#Code without processes
code = self.get_code()
for proecess in self.processes:
+ temp = code
code = code.replace(proecess.get_code(), "")
+ if(temp==code):
+ raise Exception("This souldn't happen")
+
#Extract includes
self.extract_includes()
diff --git a/src/operation.py b/src/operation.py
index 46fa2c1..1c83604 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -352,7 +352,10 @@ class Operation(Executor):
self.add_origin_emits(full_code, name_called, "")
else:
self.add_origin_emits(full_code, name_called, name_emitted)
+ temp = operation
operation = operation.replace(full_code, "")
+ if(temp==operation):
+ raise Exception("This souldn't happen")
searching_for_emits = True
stop_pattern_search = True
break
@@ -381,9 +384,11 @@ class Operation(Executor):
def replacer(match):
return match.group(0).replace(match.group(0), match.group(1))
return re.sub(f"[^\w\s] *\(\s*({pattern})\s*\)", replacer, text)
+
operation = replace(operation)
+
first_call = True
for pattern in patterns:
@@ -458,7 +463,10 @@ class Operation(Executor):
if(operation_until_out==full_code[:full_code.find("out")]):
self.add_origin_emits(full_code, name_called, "")
case_operation_starts_with_emit = True
+ temp = operation
operation = operation.replace(full_code, "")
+ if(temp==operation):
+ raise Exception("This souldn't happen")
@@ -699,7 +707,10 @@ class Operation(Executor):
if(replace_calls):
for call in self.calls:
+ temp = code
code = code.replace(self.calls[call].get_code(), str(call))
+ if(temp==code):
+ raise Exception("This souldn't happen")
#Remove "emit:" and "takes:" for the subworkklfow inputs and outputs
if(remove_emit_and_take and code[:6] in ["emit: ", "take: "]):
@@ -744,7 +755,10 @@ class Operation(Executor):
while(searching):
searching= False
for c in self.calls:
+ temp = text
text = text.replace(self.calls[c].get_code(), "")
+ if(temp==text):
+ raise Exception("This souldn't happen")
for match in re.finditer(pattern_call, text):
if(match.group(1) in to_call):
start, end = match.span(0)
@@ -960,10 +974,13 @@ class Operation(Executor):
for origin in dico_origin_2_replace:
if(len(dico_origin_2_replace[origin])<=1):
for val in dico_origin_2_replace[origin]:
+ temp = code
if(type(val)==str):
code = code.replace(origin, val)
else:
code = code.replace(origin, val.simplify_code())
+ if(temp==code):
+ raise Exception("This souldn't happen")
#Case there are mutiple origins then:
else:
#For example
@@ -997,7 +1014,10 @@ class Operation(Executor):
for val in values:
new_body+=f"\n{temporary_channel} = {val}"
#new_body+=temporary_channel
+ temp = code
code = code.replace(origin, temporary_channel)
+ if(temp==code):
+ raise Exception("This souldn't happen")
temporary_index+=1
to_add.append(new_body)
--
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