From 14e6ee30e2e476966158e60d7ee9a2199790bf50 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Thu, 20 Mar 2025 11:52:03 +0100
Subject: [PATCH] Updated the identification of the scripts within a process +
added a merge operator
---
src/constant.py | 4 ++--
src/process.py | 10 ++++++++++
2 files changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/constant.py b/src/constant.py
index b672359..e1e55a5 100644
--- a/src/constant.py
+++ b/src/constant.py
@@ -109,7 +109,7 @@ DOUBLE_DOT_TUPLE = r"\(\s*\w+\s*(,\s*\w+\s*)+\)\s*=\s*([^\?\n]+)\s*\?([^\n]+)"
END_OPERATOR = r' *(\(|{)'
ILLEGAL_CHARCTER_BEFORE_POTENTIAL_CHANNELS = r"\w|\'|\"|\."
ILLEGAL_CHARCTER_AFTER_POTENTIAL_CHANNELS = r"\w"
-MERGE_OPERATIONS = r'\.\s*((merge|mix|concat|spread|join|phase|cross|combine|fromList|collect|fromPath|value|from|map)\s*(\(|\{))'#I've added map to this list cause channels can appear in map can concatenating channels -> it's a strange way of doing it
+MERGE_OPERATIONS = r'\.\s*((merge|mix|concat|spread|join|phase|cross|combine|fromList|collect|fromPath|value|from|map|fromFilePairs)\s*(\(|\{))'#I've added map to this list cause channels can appear in map can concatenating channels -> it's a strange way of doing it
OPERATOR_IN_PIPE = r"\w+ *{[^}]*}|\w+ *\([^\)]*\)|\w+"
SET_OPERATORS = ["choice", "separate", "tap", "into", "set"]
TUPLE_EQUALS = r'\( *\w+( *, *\w+)+ *\) *=\s*(\w+)\s*\.'
@@ -131,7 +131,7 @@ INTO = r'into +([\w, ]+)'
INTO_2 = r'into +\(?( *\w+ *(, *\w+)*) *\)?'
OUTPUT = r"\n\s*output *:"
PROCESS_HEADER = r'process\s+(\w+|\'[\w ]+\'|\"[\w ]+\")\s*{'
-SCRIPT = r"\n\s*script *:|shell *:|exec *:|\"\"\"|\'\'\'"
+SCRIPT = r"\n\s*script *:|shell *:|exec *:|\"\"\"\s|\'\'\'\s"
WHEN = r"\n\s*when *:"
diff --git a/src/process.py b/src/process.py
index c791e70..07ff0b1 100644
--- a/src/process.py
+++ b/src/process.py
@@ -419,6 +419,8 @@ class Process(Nextflow_Building_Blocks):
self.name = match.group(1)
self.name = self.name.replace("'", "")
self.name = self.name.replace('"', '')
+ if(self.name=="process"):
+ raise Exception("Process is names 'process'")
if(self.alias==""):
self.alias = self.name
self.printed_name = self.alias
@@ -512,9 +514,17 @@ class Process(Nextflow_Building_Blocks):
code = self.get_code()
call = [f"{self.get_name()}({self.get_parameters_call()})"]
if(self.input_code!=""):
+ temp = code
code = code.replace(self.input_code, self.convert_input_code_to_DSL2())
+ if(temp==code):
+ raise Exception("This souldn't happen")
if(self.output_code!=""):
+ temp = code
code = code.replace(self.output_code, self.convert_output_code_to_DSL2())
+ if(temp==code):
+ print(f'"{self.output_code}"')
+ print(f'"{self.convert_output_code_to_DSL2()}"')
+ raise Exception("This souldn't happen")
channels_to_flatten = self.get_channels_to_flatten()
--
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