From 54f86c738e57485b79da35dc5ef6e9557a0ad748 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 10 Mar 2025 14:49:53 +0100
Subject: [PATCH] Adding a few updates
---
src/call.py | 85 ++++++++++++++++++++++++----------------------
src/operation.py | 6 ++--
src/subworkflow.py | 4 ++-
src/workflow.py | 45 ++++++++++++++----------
4 files changed, 79 insertions(+), 61 deletions(-)
diff --git a/src/call.py b/src/call.py
index 9e22063..b50e93b 100644
--- a/src/call.py
+++ b/src/call.py
@@ -64,49 +64,54 @@ class Call(Executor):
def simplify_code(self, new_name = ""):
- new_call_name = self.get_first_element_called().get_alias_and_id()
- code = self.get_code()
- code = re.sub(fr'{re.escape(self.get_first_element_called().get_alias())} *\(', f'{new_call_name}(', 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:
- param_new_name = f"{self.get_first_element_called().get_alias_and_id()}_param_{index}"
-
- #Case the param is a call
- if(param.get_type()=="Call"):
- code = code.replace(param.get_code(get_OG=True), 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
- elif(param.get_type()=="Operation"):
- #If it's an artificial operation -> we don't need to do anything
- if(not param.get_artificial_status()):
+ if(self.get_first_element_called().get_type()=="Function"):
+ return self.get_code()
+ else:
+ new_call_name = self.get_first_element_called().get_alias_and_id()
+ code = self.get_code(clean_pipe = True)
+ code = re.sub(fr'{re.escape(self.get_first_element_called().get_alias())} *\(', f'{new_call_name}(', 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:
+ param_new_name = f"{self.get_first_element_called().get_alias_and_id()}_param_{index}"
+ #Case the param is a call
+ if(param.get_type()=="Call"):
+ #If it's not a function -> then we rewrite it
+ if(param.get_first_element_called().get_type()!="Function"):
+ code = code.replace(param.get_code(get_OG=True), 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
+ elif(param.get_type()=="Operation"):
+ #If it's an artificial operation -> we don't need to do anything
+ if(not param.get_artificial_status()):
+
+ code = code.replace(param.get_code(get_OG=True), param_new_name)
+ lines = param.simplify_code().split('\n')
+ if(len(lines)==1):
+ new_bit = f"{param_new_name} = {lines[0]}"
+ else:
+ head = '\n'.join(lines[:-1])
+ new_bit = f"{head}\n{param_new_name} = {lines[-1]}"
+ code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
+
+ #Case Channel
+ elif(param.get_type()=="Channel"):
+ raise Exception("This shouldn't happen")
+ None
+ elif(param.get_type()=="Emitted"):
code = code.replace(param.get_code(get_OG=True), param_new_name)
- lines = param.simplify_code().split('\n')
- if(len(lines)==1):
- new_bit = f"{param_new_name} = {lines[0]}"
- else:
- head = '\n'.join(lines[:-1])
- new_bit = f"{head}\n{param_new_name} = {lines[-1]}"
+ new_bit = f"{param_new_name} = {param.simplify_code()}"
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
-
- #Case Channel
- elif(param.get_type()=="Channel"):
- raise Exception("This shouldn't happen")
- None
- elif(param.get_type()=="Emitted"):
- code = code.replace(param.get_code(get_OG=True), param_new_name)
- new_bit = f"{param_new_name} = {param.simplify_code()}"
- code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
- else:
- raise Exception("This shouldn't happen")
- index+=1
- return code.replace(tag_to_add, "").strip()
+ else:
+ raise Exception("This shouldn't happen")
+ index+=1
+ return code.replace(tag_to_add, "").strip()
diff --git a/src/operation.py b/src/operation.py
index 6e1bf5a..1a88d6e 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -902,8 +902,10 @@ class Operation(Executor):
to_add = []
for o in self.origins:
if(o.get_type()=="Call"):
- to_add.append(add_origin_equals(o, index))
- code = code.replace(o.get_code(get_OG=True), f"operation_{operation_id}_{index}")
+ #If it's not a function -> then we rewrite it
+ if(o.get_first_element_called().get_type()!="Function"):
+ to_add.append(add_origin_equals(o, index))
+ code = code.replace(o.get_code(get_OG=True), f"operation_{operation_id}_{index}")
elif(o.get_type()=="Emitted"):
code = code.replace(o.get_code(get_OG=True), o.simplify_code())
index += 1
diff --git a/src/subworkflow.py b/src/subworkflow.py
index 774a7d2..0e0d1ad 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -169,7 +169,9 @@ class Subworkflow(Main):
#Case nothing is there
if(take_pos==(0, 0) and main_pos==(0, 0) and emit_pos==(0, 0)):
#raise Exception(f"Subworkflow {code} doesn't have anything defined")
- self.work = Code(code, origin = self)
+ firt_curly = code.find("{")
+ last_curly = code.rfind('}')
+ self.work = Code(code[firt_curly+1:last_curly], origin = self)
#Case there is an input but no output
if(take_pos!=(0, 0) and main_pos!=(0, 0) and emit_pos==(0, 0)):
if(take_pos[0]<main_pos[0]):
diff --git a/src/workflow.py b/src/workflow.py
index ace12fe..be488f2 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -359,7 +359,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Putting || back
code = code.replace("$OR$", "||")
- self.rewrite_and_initialise(code, self.processes_2_remove)
+ self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=False)
return code
#This methods generates a random set of processes to consider as relavant
@@ -515,7 +515,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
return subs
- def rewrite_and_initialise(self, code, processes_2_remove):
+ def rewrite_and_initialise(self, code, processes_2_remove, render_graphs):
temp_process_dependency_graph = self.graph.get_process_dependency_graph()
temp_spec_graph = self.graph.full_dico
#Write new code in temporary file
@@ -532,10 +532,12 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
self.initialise()
self.graph.initialise(processes_2_remove = self.processes_2_remove)
if(not self.graph.check_if_process_dependendy_is_equivalent_to_other_without_subworkflows(temp_process_dependency_graph)):
- generate_graph(self.get_output_dir()/ "debug" /"spec_graph_OG", temp_spec_graph, render_graphs = True)
- generate_graph(self.get_output_dir()/ "debug" /"spec_graph", self.graph.full_dico, render_graphs = True)
- generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph_OG", temp_process_dependency_graph, render_graphs = True)
- generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph", self.graph.get_process_dependency_graph() , render_graphs = True)
+ print(render_graphs)
+ if(render_graphs==True):
+ generate_graph(self.get_output_dir()/ "debug" /"spec_graph_OG", temp_spec_graph, render_graphs = True)
+ generate_graph(self.get_output_dir()/ "debug" /"spec_graph", self.graph.full_dico, render_graphs = True)
+ generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph_OG", temp_process_dependency_graph, render_graphs = True)
+ generate_graph(self.get_output_dir()/ "debug" /"process_dependency_graph", self.graph.get_process_dependency_graph() , render_graphs = True)
raise Exception("Something went wrong: The flat dependency graph is not the same!")
@@ -574,7 +576,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
code = code.replace(subworklfow.get_code(), "")
OG_call = subworklfow.get_call()
OG_body = subworklfow.get_work()
-
+
#REPLACE HEADER TAKES
subworkflow_takes = subworklfow.get_takes()
parameters = OG_call.get_parameters()
@@ -614,8 +616,9 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
old, new = r
temp_code = code
#Case of channel = channel
- if(new.split("=")[0].strip()==new.split("=")[1].strip()):
- new = ''
+ if(new.find("=")!=-1):
+ if(new.split("=")[0].strip()==new.split("=")[1].strip()):
+ new = ''
code = code.replace(old, new)
if(temp_code==code):
raise Exception("Something went wrong: The code hasn't changed")
@@ -659,7 +662,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#This Function returns the channels the subworkflow (things_added_in_cluster) emits (other things depend on)
def get_emits(self, things_added_in_cluster):
channel_2_sink = {}
- #Basiccaly this is a deco of channels to opeartions -> when the value is an empty list
+ #Basiccaly this is a deco of channels to opea -> this doesn't really work yetrtions -> when the value is an empty list
#This means that the channel is totally definied in the subworkflow -> so we are searching for
#Channels which aren't totatly defined in the subworkflow
#This means that things outside the subworkflow depend on this channel
@@ -689,13 +692,16 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Method which rewrites the workflow follwong the user view
#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 = []):
+ def convert_workflow_2_user_view(self, relevant_processes = [], render_graphs = True):
+ self.iniatilise_tab_processes_2_remove()
+ self.graph.initialise(processes_2_remove = self.processes_2_remove)
+
if(self.get_DSL()=="DSL1"):
code = self.convert_to_DSL2()
if(self.duplicate):
code = self.simplify_workflow_code()
- self.rewrite_and_initialise(code, self.processes_2_remove)
+ self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
@@ -757,7 +763,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Get the clusters and the code
relevant_processes = self.check_relevant_processes_in_workflow(relevant_processes)
- self.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [])
+ self.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [], render_graphs=render_graphs)
clusters = self.graph.get_clusters_from_user_view()
broken_subworkflows = get_workflows_broken(get_subworkflow_2_executors(), get_clusters_with_calls(clusters))
#While there still are broken workflows -> need to redo the analysis
@@ -765,11 +771,12 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Rewrite broken subworkflows
sub = broken_subworkflows[0]
code = self.rewrite_subworkflow_call(code, sub)
- self.rewrite_and_initialise(code, self.processes_2_remove)
+ self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
#Get the clusters and the code
#TODO -> remove the generate all_graphs -> it is not necessary
- self.generate_all_graphs()
- self.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [])
+ if(render_graphs):
+ self.generate_all_graphs()
+ self.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [], render_graphs=render_graphs)
clusters = self.graph.get_clusters_from_user_view()
broken_subworkflows = get_workflows_broken(get_subworkflow_2_executors(), get_clusters_with_calls(clusters))
@@ -795,7 +802,9 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
new_clusters.append(tab)
clusters = new_clusters
#clusters = self.graph.get_topogical_order(clusters)
-
+ #for e in executors_in_order:
+ # print(e.get_code()[:20])
+ #print(executors_in_order)
#Creating the subworkflows from clusters
@@ -1085,7 +1094,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
f = open(self.get_output_dir()/ "debug" / "rewritten.nf", "w")
f.write(code)
f.close()
- self.rewrite_and_initialise(code, self.processes_2_remove)
+ self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
return code
#return code
#
--
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