From 6b23c6ded45f7bb4f551698939ba42061cd63225 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Fri, 20 Dec 2024 12:15:36 +0100
Subject: [PATCH] update to DSL1 to DSL2: add val around variables in tuple
---
src/outils.py | 27 ++++++++++++++++++++++++++-
src/process.py | 13 +++++++++----
src/workflow.py | 8 ++++----
3 files changed, 39 insertions(+), 9 deletions(-)
diff --git a/src/outils.py b/src/outils.py
index 120fb39..65a91ba 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1053,7 +1053,32 @@ def process_2_DSL2(code):
code = re.sub(r'file( | *\()', replace_file_by_path, code)
code = re.sub(r'set( | *\()', replace_set_by_tuple, code)
- return code
+ return add_vals_when_necessary(code)
+
+#Function that adds vals around variables in a tuple
+def add_vals_when_necessary(line):
+ starts_with_tuple = False
+ code_to_replace = ""
+ for match in re.finditer(r"tuple\s*\((.+)\)", line):
+ starts_with_tuple = True
+ code_to_replace = match.group(1)
+ if(not starts_with_tuple):
+ for match in re.finditer(r"tuple\s*(.+)", line):
+ starts_with_tuple = True
+ code_to_replace = match.group(1)
+
+ if(starts_with_tuple):
+ code_to_replace = re.split(r'\,\s*emit\s*\:', code_to_replace)[0]
+ #Adding val to cases where it's just the variable
+ line_split = code_to_replace.split(',')
+ for y in range(len(line_split)) :
+ param = line_split[y]
+ if(bool(re.fullmatch('\w+', param.strip()))):
+ line_split[y] = f"val({param.strip()})"
+ temp = ", ".join(line_split)
+ line = line.replace(code_to_replace, temp)
+ return line
+
def operation_2_DSL2(code, origin):
diff --git a/src/process.py b/src/process.py
index 4359ea6..f7888f6 100644
--- a/src/process.py
+++ b/src/process.py
@@ -558,15 +558,20 @@ class Process(Nextflow_Building_Blocks):
code = process_2_DSL2(code)
lines = []
for line in code.split("\n"):
- lines.append(line.split(" from ")[0])
+ temp = process_2_DSL2(line.split(" from ")[0])
+ lines.append(temp)
code = "\n".join(lines)
return code
def convert_output_code_to_DSL2(self):
code = self.output_code
- code = process_2_DSL2(code)
- code = code.replace(" into ", ", emit: ")
- code = code.replace(" mode flatten", "")
+ lines = []
+ for line in code.split("\n"):
+ line = line.replace(" into ", ", emit: ")
+ line = line.replace(" mode flatten", "")
+ line = process_2_DSL2(line)
+ lines.append(line)
+ code = "\n".join(lines)
return code
#This method is to detect which are the channels which need to be flattened
diff --git a/src/workflow.py b/src/workflow.py
index 43adf83..1a58051 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -856,7 +856,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
processes_added = []
things_added_in_cluster = []
if(len(elements)>1):
- name, body, take, emit = "", "main:\n", "", ""
+ name, body, take, emit = "", "", "", ""
first_element = True
for ele in elements:
@@ -976,9 +976,9 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Replace names inside subworkflow
- subworkflow_code = f"subworkflow {name} {{\n{take}\n{body}\n{emit}\n}}"
+ subworkflow_code = f"workflow {name} {{\n{take}\nmain:\n{body}\n{emit}\n}}"
for i in range(len(new_param_names)):
- pattern = fr"[\=\,\(] *({re.escape(takes_param[i].get_code())})[\s\,\)]"
+ pattern = fr"[\=\,\(] *({re.escape(takes_param[i].get_code())})[\s\,\)\.]"
subworkflow_code = replace_group1(subworkflow_code, pattern, new_param_names[i])
#subworkflow_code = subworkflow_code.replace(takes_param[i].get_code(), new_param_names[i])
@@ -1011,7 +1011,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
print(format_with_tabs(subworkflow_code))
- print("-----------")
+ print("//-----------")
#TODO -> rmoving the conditions which are problematic
--
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