From 96d9a7176ea026e88060f32b3befc3ae0e73c4ad Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 19 Mar 2025 15:58:41 +0100
Subject: [PATCH] Fixed problem with the remove spaces between \. and the jump
lines -> it only worked in the case of a single line
---
src/call.py | 2 +-
src/code_.py | 2 +-
src/main.py | 7 +++++--
src/operation.py | 20 ++++++++------------
4 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/src/call.py b/src/call.py
index 6361913..604564b 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):
+ def get_code(self, clean_pipe = False, get_OG=False, remove_emit_and_take = False):
if(get_OG):
if(self.OG_code==''):
return self.code.get_code()
diff --git a/src/code_.py b/src/code_.py
index 7d734dc..f9ea145 100644
--- a/src/code_.py
+++ b/src/code_.py
@@ -152,7 +152,7 @@ class Code:
return code
def rewrite_jump_dot(self, code):
- pattern = r"\n *\."
+ pattern = r"(\n *)+\."
code = re.sub(pattern, '.', code)
return code
diff --git a/src/main.py b/src/main.py
index 0239858..0cec5f5 100644
--- a/src/main.py
+++ b/src/main.py
@@ -50,13 +50,16 @@ 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)
+ old = exe.get_code(get_OG = True, remove_emit_and_take = True)
new = exe.simplify_code()
if(new!=old):
temp = code
code = code.replace(exe.get_code(get_OG = True), exe.simplify_code(), 1)
if(temp==code):
- raise Exception("This shouldn't happen the Exeutor was not replaced")
+ print(code)
+ print("- old", f'"{old}"')
+ print("- new", f'"{new}"')
+ raise Exception("This shouldn't happen the Executor was not replaced")
else:
raise Exception("This shouldn't happen")
return code
diff --git a/src/operation.py b/src/operation.py
index 62a1a97..46fa2c1 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -689,22 +689,22 @@ class Operation(Executor):
file.close()
- def get_code(self, replace_calls = True, clean_pipe = False, get_OG=False):
+ def get_code(self, replace_calls = True, clean_pipe = False, get_OG=False, remove_emit_and_take = False):
code = self.code.get_code()
if(get_OG):
if(self.OG_code!=""):
- return self.OG_code
- else:
- return code
-
-
-
+ code = self.OG_code
if(clean_pipe):
code, self.dico_OG_call_2_new_call = self.clean_pipe_operator(code)
if(replace_calls):
for call in self.calls:
code = code.replace(self.calls[call].get_code(), str(call))
+
+ #Remove "emit:" and "takes:" for the subworkklfow inputs and outputs
+ if(remove_emit_and_take and code[:6] in ["emit: ", "take: "]):
+ code = code[6:]
+ code = code.strip()
return code
@@ -923,11 +923,7 @@ class Operation(Executor):
#Method that rewrites operations to simplify it -> decompose it into multiple line -> to be able to manipulate the calls in a easier way
def simplify_code(self):
- code = self.get_code(replace_calls =False, clean_pipe=True)
- #Remove "emit:" and "takes:" for the subworkklfow inputs and outputs
- if(code[:6] in ["emit: ", "take: "]):
- code = code[6:]
- code = code.strip()
+ code = self.get_code(replace_calls =False, clean_pipe=True, remove_emit_and_take=True)
#code = self.get_code(get_OG=True)
index = 1
operation_id = str(self)[-7:-2]
--
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