From 69abe4a8e3ecec44f44643fb811e5bf0bc3ae8f0 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 22 Apr 2025 11:00:28 +0200
Subject: [PATCH] Renaming channels inside subworklfows -> to avoid issues when
wanting to write the subworkflow in the main (in the case of multiple
channels)
---
src/code_.py | 8 ++++++--
src/subworkflow.py | 36 ++++++++++++++++++++++++++++++++----
src/workflow.py | 2 +-
3 files changed, 39 insertions(+), 7 deletions(-)
diff --git a/src/code_.py b/src/code_.py
index 0213fc4..adb4c76 100644
--- a/src/code_.py
+++ b/src/code_.py
@@ -175,6 +175,7 @@ class Code:
def rewrite_ternary_operation_to_normal_condition(self, code):
pattern = r"(def)? *(\w+) *\= *([^?\n]+) *\? *([^:\n]+) *\: *([^\n]+)\n"
to_replace = []
+ checked = []
for match in re.finditer(pattern, code):
def_variable = ""
if(match.group(1)!=None):
@@ -191,17 +192,20 @@ class Code:
#Here we check that it's worked correctly -> that we have done a good parsing
if(get_parenthese_count(condition)==0 and get_parenthese_count(exp1)==0 and get_parenthese_count(exp2)==0 and get_curly_count(condition)==0 and get_curly_count(exp1)==0 and get_curly_count(exp2)==0):
to_replace.append((old, new))
+ else:
+ checked.append(match.group(0))
for r in to_replace:
old, new = r
self.add_to_ternary_operation_dico(old, new)
tmp = code
- code = code.replace(old, new)
+ code = code.replace(old, new, 1)
if(old!=new and tmp==code):
raise Exception("This shouldn't happen -> the code wasn't replaced")
#Check if there is still a ternary operation in this case we cannot analyse it
#Cause it is a complexe/multiple ternanry operation
for match in re.finditer(pattern, code):
- raise BioFlowInsightError(f"Detected a multi ternary operation (a ternary operation in a ternary operation) in the file '{self.origin.get_file_address()}'. BioFlow-Insight does not support this, try defining it in a different way.", type="Multi ternary operation")
+ if(match.group(0) not in checked):
+ raise BioFlowInsightError(f"Detected a multi ternary operation (a ternary operation in a ternary operation) in the file '{self.origin.get_file_address()}'. BioFlow-Insight does not support this, try defining it in a different way.", type="Multi ternary operation")
return code
def rewrite_jump_dot(self, code):
diff --git a/src/subworkflow.py b/src/subworkflow.py
index 17a39e3..4749628 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -103,6 +103,22 @@ class Subworkflow(Main):
return self.get_code_with_alias_and_id()
def simplify_code(self):
+ name = self.get_alias()
+
+ code = self.get_code()
+ #Renaming the channels defined inside the subworkflow
+ executors = {}
+ self.root.get_all_executors_in_subworkflow(calls=executors)
+ channels_to_rename = []
+ for exe in executors:
+ if(exe.get_type()=="Operation"):
+ for g in exe.gives:
+ channels_to_rename.append(g.get_code())
+ #channels_to_rename+=exe.gives
+ #for ch in channels_to_rename:
+ # code = replace_group1(code, fr"[^\w]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
+
+
code = super().simplify_code()
#Putting the take, main and emit in that order, if needs be
@@ -129,12 +145,12 @@ class Subworkflow(Main):
start, _ = match.span(0)
code_up_to_emit = code[:start]
code_after_emit = code[start:]
- name = self.get_alias()
+
for t in self.take:
if(len(t.get_gives())!=1):
raise Exception("This shoudn't happen")
ch = t.get_gives()[0]
- code_up_to_emit = replace_group1(code_up_to_emit, fr"[^\w]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
+ code_up_to_emit = replace_group1(code_up_to_emit, fr"[^\w\.]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
@@ -145,7 +161,7 @@ class Subworkflow(Main):
ch = e.gives[0]
if(ch.get_type()=="Channel"):
temp = code_after_emit
- code_after_emit = replace_group1(code_after_emit, fr"[^\w]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
+ code_after_emit = replace_group1(code_after_emit, fr"[^\w\.]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
if(temp==code_after_emit):
raise Exception("This shoudn't happen -> code hasn't been replaced")
elif(ch.get_type()=="Emitted"):
@@ -157,7 +173,7 @@ class Subworkflow(Main):
ch = e.origins[0]
if(ch.get_type()=="Channel"):
temp = code_after_emit
- code_after_emit = replace_group1(code_after_emit, fr"[^\w]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
+ code_after_emit = replace_group1(code_after_emit, fr"[^\w\.]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
code_up_to_emit+=f"\n{ch.get_code()}_{name} = {ch.get_code()}"
if(temp==code_after_emit):
raise Exception("This shoudn't happen -> code hasn't been replaced")
@@ -199,6 +215,18 @@ class Subworkflow(Main):
# raise Exception("This shoudn't happen -> code hasn't been replaced")
code = code_up_to_emit+'\n'+code_after_emit
+
+ #Renaming the channels defined inside the subworkflow
+ for ch in channels_to_rename:
+ code = replace_group1(code, fr"[^\w\.]({re.escape(ch)})[^\w]", f"{ch}_{name}")
+
+ to_replace = []
+ for match in re.finditer(r"(\w+) *= *(\w+) *\n", code):
+ if(match.group(1)==match.group(2)):
+ to_replace.append(match.group(0))
+ for r in to_replace:
+ code = code.replace(r, "", 1)
+
return code
diff --git a/src/workflow.py b/src/workflow.py
index 722b9ec..8bbd39a 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -1047,7 +1047,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#And used as a parameter in a call in the same bloc
#And that the channel is defined somewhere else in the code
def check_that_a_channel_is_not_defined_used_and_redefined_used_in_another_block(self):
- self.channel_that_is_defined_used_and_redefined_used_in_another_block = False
+ self.channel_that_is_defined_used_and_redefined_used_in_another_block = ""
for main in [self.get_workflow_main()]+self.get_subworkflows_called():
problematic_channel = main.check_that_a_channel_is_not_defined_used_and_redefined_used_in_another_block()
if(problematic_channel!=None):
--
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