From 64ce19e5a966f9af523337ae0816c16c9c550958 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Sat, 14 Dec 2024 11:11:32 +0100
Subject: [PATCH] add rewrite call
---
src/call.py | 29 +++++++++++++++++++++++++----
src/main_DSL2.py | 7 +++++++
src/nextflow_file.py | 3 +++
src/workflow.py | 13 +++++++++++++
4 files changed, 48 insertions(+), 4 deletions(-)
diff --git a/src/call.py b/src/call.py
index 079cb9e..53bb680 100644
--- a/src/call.py
+++ b/src/call.py
@@ -1,6 +1,7 @@
import re
import json
import copy
+import time
from .code_ import Code
@@ -37,6 +38,29 @@ class Call(Executor):
else:
return self.code.get_code()
+
+ def simplify_code(self, new_name = ""):
+ code = self.get_code()
+ if(new_name!=""):
+ code = f"{new_name} = {code}"
+ tag_to_add = "//AREA TO ADD PARAMS"
+ code = f"{tag_to_add}\n{code}"
+ index = 1
+ for param in self.parameters:
+ #Case the param is a call
+ if(param.get_type()=="Call"):
+ param_new_name = f"{self.get_first_element_called().get_name()}_param_{index}"
+ code = code.replace(param.get_code(), param_new_name)
+ new_bit = param.simplify_code(new_name = param_new_name)
+ code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
+
+ #Case the param is an operation
+ #TODO
+ index+=1
+ return code.replace(tag_to_add, "").strip()
+
+
+
def get_type(self):
return "Call"
@@ -377,17 +401,14 @@ class Call(Executor):
subworkflow = self.get_subworkflow_from_name(tab_call[0])
fun = self.get_function_from_name(tab_call[0])
if(process!=None and subworkflow==None and fun==None):
- #If the lements need to duplicated -> then we need to duplicate it
+ #If the elements need to duplicated -> then we need to duplicate it
temp = process
if(self.get_duplicate_status()):
- print(process.get_number_times_called())
if(process.get_number_times_called()>0):
- print("here")
temp = copy.deepcopy(process)
temp.set_alias(f"{process.get_name()}_{process.get_number_times_called()}")
self.first_element_called = temp
temp.incremente_number_times_called()
- print(process.get_name(), process.call)
if(process==None and subworkflow!=None and fun==None):
self.first_element_called = subworkflow
if(process==None and subworkflow==None and fun!=None):
diff --git a/src/main_DSL2.py b/src/main_DSL2.py
index c396134..cc4a188 100644
--- a/src/main_DSL2.py
+++ b/src/main_DSL2.py
@@ -15,6 +15,13 @@ class Main_DSL2(Nextflow_Building_Blocks):
self.initialised = False
self.conditions=None
+ def get_all_executors(self):
+ tab = []
+ tab+=self.get_executors()
+ for sub in self.get_subworkflows_called():
+ tab+=sub.get_executors()
+ return tab
+
def get_channels(self):
return self.channels
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 0b3e1b7..3a3054d 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -133,6 +133,9 @@ class Nextflow_File(Nextflow_Building_Blocks):
self.all_includes = []
self.added_2_rocrate = False
+ def get_all_executors(self):
+ return self.main.get_all_executors()
+
def extract_metadata(self):
#When the start=="" it means it's the first analysis
diff --git a/src/workflow.py b/src/workflow.py
index 5143768..0a0013f 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -97,6 +97,9 @@ class Workflow:
def set_DSL(self, DSL):
self.DSL = DSL
+ def get_all_executors(self):
+ return list(set(self.nextflow_file.get_all_executors()))
+
def get_is_a_git_repo(self):
return is_git_directory(path = self.get_repo_adress())
@@ -734,6 +737,16 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
"subworkflow_section":subworkflow_section}
return code, ankers
+
+ def simplify_workflow_code(self):
+ code, ankers = self.write_workflow_into_one_file()
+ for exe in self.get_all_executors():
+ #print(exe.get_code(), exe.get_type())
+ if(exe.get_type()=="Call"):
+ print(exe.simplify_code())
+ print()
+
+
#Conert workflow to user_view only makes sense when the option duplicate is activated -> otherwise is doesn't make sense + it makes the analysis way more complicated
def convert_workflow_2_user_view(self, relevant_processes = []):
--
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