From 5e182635ba671adacf849b3f31cf47e05200ed58 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 17 Mar 2025 15:58:41 +0100
Subject: [PATCH] Fixed problem with emit outside of condition when calls are
in conditions
---
src/block.py | 3 +++
src/executor.py | 7 +++++++
src/operation.py | 42 ++++++++++++++++++++++++++----------------
src/root.py | 5 +++++
src/workflow.py | 10 ++++++----
5 files changed, 47 insertions(+), 20 deletions(-)
diff --git a/src/block.py b/src/block.py
index 77bb9c9..5cb9d46 100644
--- a/src/block.py
+++ b/src/block.py
@@ -84,6 +84,9 @@ class Block(Root):
tab+=block.get_calls_same_level()
tab+=block.get_calls_inside_level()
return tab
+
+ def get_all_calls_from_root(self):
+ return self.origin.get_all_calls_from_root()
#############
# CHANNELS
diff --git a/src/executor.py b/src/executor.py
index d276bc0..bb09018 100644
--- a/src/executor.py
+++ b/src/executor.py
@@ -287,6 +287,13 @@ class Executor(Nextflow_Building_Blocks):
for c in call.get_all_calls():
if(c.first_element_called.get_alias()==name):
tab.append(c)
+ #If there is no calls found then we search in all root
+ if(len(tab)==0):
+ for call in self.origin.get_all_calls_from_root():
+ #call.initialise()
+ for c in call.get_all_calls():
+ if(c.first_element_called.get_alias()==name):
+ tab.append(c)
return tab
else:
diff --git a/src/operation.py b/src/operation.py
index 28e984b..3cb360b 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -928,6 +928,7 @@ class Operation(Executor):
index += 1
temporary_index = 1
+ new_body = ""
for origin in dico_origin_2_replace:
if(len(dico_origin_2_replace[origin])<=1):
for val in dico_origin_2_replace[origin]:
@@ -937,23 +938,32 @@ class Operation(Executor):
code = code.replace(origin, val.simplify_code())
#Case there are mutiple origins then:
else:
- #TODO -> fix this problem if you have the courage to -> see at what extend it is used
- raise BioFlowInsightError("TODO (update): The output of a emit is ambiguous -> there are multiple instance where it exits")
- #print(dico_origin_2_replace)
- #for e in dico_origin_2_replace[origin]:
- # print(e.get_all_conditions())
- temporary_index+=1
-
- #for o in self.origins:
- # if(o.get_type()=="Call"):
- # #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
+ #For example
+ #if(){
+ # p1(ch1)
+ #} else {
+ # p1(ch2)
+ #}
+ #val = p1.out -> when wanting to rewrite this operation
+ calls = {}
+ temporary_channel = f"temporary_val_{id(self)}_{temporary_index}"
+ for e in dico_origin_2_replace[origin]:
+ try:
+ temp = calls[e.emitted_by]
+ except:
+ calls[e.emitted_by] = []
+ calls[e.emitted_by].append(e.simplify_code())
+ for c in calls:
+ #This is just one value
+ if(len(c.get_all_conditions())>1):
+ raise Exception("This shoudn't happen")
+ for condition in c.get_all_conditions():
+ new_body+=f"if({condition.get_value().strip()}) {{\n{temporary_channel} = {calls[c][0]}\n}}\n"
+ new_body+=temporary_channel
+ code = code.replace(origin, new_body)
+ temporary_index+=1
+
to_add.reverse()
for c in to_add:
code = f"{c}\n{code}"
diff --git a/src/root.py b/src/root.py
index 350055e..60c76ee 100644
--- a/src/root.py
+++ b/src/root.py
@@ -247,6 +247,11 @@ class Root(Nextflow_Building_Blocks):
all_executors = self.get_executors_same_level()+self.get_inside_executors()
for e in all_executors:
calls[e] = ''
+
+ def get_all_calls_from_root(self):
+ dico = {}
+ self.get_all_calls_in_subworkflow(calls=dico)
+ return list(dico.keys())
#############
diff --git a/src/workflow.py b/src/workflow.py
index cd71ce9..9b2873d 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -526,7 +526,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
return subs
- def rewrite_and_initialise(self, code, processes_2_remove, render_graphs):
+ def rewrite_and_initialise(self, code, processes_2_remove, render_graphs, def_check_the_same = True):
temp_process_dependency_graph = self.graph.get_process_dependency_graph()
temp_spec_graph = self.graph.full_dico
@@ -547,7 +547,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
self.initialise()
os.remove(temp_file)
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)):
+ if(def_check_the_same and not self.graph.check_if_process_dependendy_is_equivalent_to_other_without_subworkflows(temp_process_dependency_graph)):
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)
@@ -720,11 +720,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
if(self.get_DSL()=="DSL1"):
code = self.convert_to_DSL2()
+ self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs, def_check_the_same = False)
- if(self.duplicate):
+ if(self.get_DSL()=="DSL2"):
code = self.simplify_workflow_code()
self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
-
+
+ if(self.duplicate):
#DETERMING WHICH SUBWORKFLOWS ARE BROKEN WITH THE CLUSTER
--
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