From df4699c792923b0482ebbb352f97fec2abb41d25 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Thu, 20 Mar 2025 10:47:04 +0100
Subject: [PATCH] Updated the rewrite of the calls + added filter to catch when
an executor appears twice (throws error)
---
src/call.py | 10 +++++++---
src/main.py | 8 ++++++--
src/operation.py | 2 +-
src/workflow.py | 3 ++-
4 files changed, 16 insertions(+), 7 deletions(-)
diff --git a/src/call.py b/src/call.py
index a07dc6c..0e647eb 100644
--- a/src/call.py
+++ b/src/call.py
@@ -103,12 +103,16 @@ class Call(Executor):
if(temp==code):
raise Exception("This souldn't happen")
#code = code.replace(param.get_code(get_OG=True), param_new_name)
- lines = param.simplify_code().split('\n')
+ simplified_param = param.simplify_code()
+ lines = simplified_param.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]}"
+ if(re.fullmatch(r"\w+", lines[-1].strip())):
+ head = '\n'.join(lines[:-1])
+ new_bit = f"{head}\n{param_new_name} = {lines[-1]}"
+ else:
+ new_bit = f"{param_new_name} = {simplified_param}"
temp = code
code = code.replace(tag_to_add, f"{tag_to_add}\n{new_bit}")
if(temp==code):
diff --git a/src/main.py b/src/main.py
index 63a052a..44f7654 100644
--- a/src/main.py
+++ b/src/main.py
@@ -15,10 +15,14 @@ class Main(Nextflow_Building_Blocks):
self.initialised = False
self.root = None
- def get_order_execution_executors(self, dico):
+ def get_order_execution_executors(self, dico, seen):
executors = self.get_all_executors_in_subworkflow()
pos = {}
for e in executors:
+ code = e.get_code(get_OG = True)
+ if(code in seen):
+ raise BioFlowInsightError(f'Executor "{code}" appears twice in the workflow in the exact same way. BioFlow-Insight cannot rewrite the workflow then, try slighly changing how one of the executors is defined')
+ seen[code] = ''
pos[e] = e.get_position_in_main(e)
#TODO add sort here
pos = {k: v for k, v in sorted(pos.items(), key=lambda item: item[1])}
@@ -26,7 +30,7 @@ class Main(Nextflow_Building_Blocks):
if(e.get_type()=="Call"):
if(e.get_first_element_called().get_type()=="Subworkflow"):
dico[e] = {}
- e.get_first_element_called().get_order_execution_executors(dico[e])
+ e.get_first_element_called().get_order_execution_executors(dico[e], seen)
else:
dico[e.get_first_element_called()] = pos[e]
else:
diff --git a/src/operation.py b/src/operation.py
index f58c833..ebc158a 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -753,9 +753,9 @@ class Operation(Executor):
to_call.append(m.get_alias())
pattern_call = constant.BEGINNING_CALL
searching = True
- text = " "+self.get_code(clean_pipe = clean_pipe)
while(searching):
searching= False
+ text = " "+self.get_code(clean_pipe = clean_pipe, replace_calls = False)
for c in self.calls:
temp = text
text = text.replace(self.calls[c].get_code(), "")
diff --git a/src/workflow.py b/src/workflow.py
index 1826ab7..09be46e 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -420,7 +420,8 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Method that returns the order of execution for each executor
def get_order_execution_executors(self):
dico = {}
- dico = self.get_workflow_main().get_order_execution_executors(dico)
+ seen = {}
+ dico = self.get_workflow_main().get_order_execution_executors(dico, seen)
tab = []
def explore_dico(dico):
if(type(dico)!=dict):
--
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