From 773221c7ef5811dd4ec30d65c0ef018237b88ba3 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Fri, 21 Mar 2025 15:44:07 +0100
Subject: [PATCH] I've renamed the takes of a subworkflow when simplifying them
-> so that the same name isn't deplicated (it created some problems in
workflows with the same input channels) + i tried to add the id to channels
-> it doesn't work (so it's in a comment)
---
src/channel.py | 4 ++
src/operation.py | 101 +++++++++++++++++++++++++++++++++------------
src/subworkflow.py | 12 +++++-
3 files changed, 89 insertions(+), 28 deletions(-)
diff --git a/src/channel.py b/src/channel.py
index ca7a9e5..f0ffc4b 100644
--- a/src/channel.py
+++ b/src/channel.py
@@ -101,5 +101,9 @@ class Channel(Nextflow_Building_Blocks):
for source in self.get_source():
dico["edges"].append({'A':str(source), 'B':str(B), "label":self.get_name()})
+ def simplify_code(self, return_tab):
+ code = self.get_code(get_OG=True)
+ code = code.replace(code, f"{code}_{id(self)}")
+ return code
diff --git a/src/operation.py b/src/operation.py
index e682a16..d539056 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -969,6 +969,11 @@ class Operation(Executor):
dico_origin_2_replace[OG_code].append(f"operation_{operation_id}_{index}")
elif(o.get_type()=="Emitted"):
dico_origin_2_replace[OG_code].append(o)
+ elif(o.get_type()=="Channel"):
+ #dico_origin_2_replace[OG_code].append(o)
+ None
+ else:
+ raise Exception("This shoudn't happen")
index += 1
temporary_index = 1
@@ -985,36 +990,80 @@ class Operation(Executor):
raise Exception("This souldn't happen")
#Case there are mutiple origins then:
else:
+
+
+ temporary_channel = f"temporary_val_{id(self)}_{temporary_index}"
+ types = []
+ for e in dico_origin_2_replace[origin]:
+ types.append(e.get_type())
+
+
+ if(set(types)=={"Emitted"}):
+ #Case the multiple origins are emits
+ #For example
+ #if(){
+ # p1(ch1)
+ #} else {
+ # p1(ch2)
+ #}
+ #val = p1.out -> when wanting to rewrite this operation
+ calls = {}
+ 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(return_tab = False))
+ for c in calls:
+ #This is just one value
+ if(len(c.get_all_conditions())>1):
+ raise Exception("This shoudn't happen")
+ conditions = c.get_all_conditions()
+ if(conditions!=[]):
+ for condition in conditions:
+ new_body+=f"if({condition.get_value().strip()}) {{\n{temporary_channel} = {calls[c][0]}\n}}\n"
+ else:
+ values = set(calls[c])
+ if(len(values)>1):
+ raise Exception("This souldn't happen")
+ for val in values:
+ new_body+=f"\n{temporary_channel} = {val}"
+
+ #Case the multiple origins are channels
#For example
#if(){
- # p1(ch1)
+ # a = ...
#} else {
- # p1(ch2)
+ # a = ...
#}
- #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(return_tab = False))
- for c in calls:
- #This is just one value
- if(len(c.get_all_conditions())>1):
- raise Exception("This shoudn't happen")
- conditions = c.get_all_conditions()
- if(conditions!=[]):
- for condition in conditions:
- new_body+=f"if({condition.get_value().strip()}) {{\n{temporary_channel} = {calls[c][0]}\n}}\n"
- else:
- values = set(calls[c])
- if(len(values)>1):
- raise Exception("This souldn't happen")
- for val in values:
- new_body+=f"\n{temporary_channel} = {val}"
+ #b = a -> when wanting to rewrite this operation
+ if(set(types)=={"Channel"}):
+ None
+ #operations = {}
+ #for c in dico_origin_2_replace[origin]:
+ # for source in c.get_source():
+ # try:
+ # temp = operations[source]
+ # except:
+ # operations[source] = []
+ # operations[source].append(c.simplify_code(return_tab = False))
+ #for o in operations:
+ # #Turning into one condition
+ # conditions = []
+ # for condition in o.get_all_conditions():
+ # conditions.append(condition.get_value().strip())
+ # if(conditions!=[]):
+ # new_body+=f"if({' && '.join(conditions)}) {{\n{temporary_channel} = {operations[o][0]}\n}}\n"
+ # else:
+ # values = set(operations[o])
+ # if(len(values)>1):
+ # raise Exception("This souldn't happen")
+ # for val in values:
+ # new_body+=f"\n{temporary_channel} = {val}"
+ else:
+ raise Exception("This shoudn't happen")
+
+
#new_body+=temporary_channel
temp = code
code = code.replace(origin, temporary_channel)
diff --git a/src/subworkflow.py b/src/subworkflow.py
index 82883dc..ad6b204 100644
--- a/src/subworkflow.py
+++ b/src/subworkflow.py
@@ -5,7 +5,7 @@ import copy
from .root import Root
from .main import Main
from .bioflowinsighterror import BioFlowInsightError
-from .outils import remove_jumps_inbetween_parentheses, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate
+from .outils import remove_jumps_inbetween_parentheses, replace_group1, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate
@@ -99,10 +99,18 @@ class Subworkflow(Main):
def simplify_code(self):
code = super().simplify_code()
+
for o in self.emit:
code = code.replace(o.get_code(get_OG = True), o.simplify_code(return_tab = False), 1)
- return code
+ #Renaming the takes in the subworkflow
+ name = self.get_alias()
+ for t in self.take:
+ if(len(t.get_gives())!=1):
+ raise Exception("This shoudn't happen")
+ ch = t.get_gives()[0]
+ code = replace_group1(code, fr"[^\w]({re.escape(ch.get_code())})[^\w]", f"{ch.get_code()}_{name}")
+ return code
def set_alias(self, alias):
--
GitLab