From e7e30586dd28a35ab2b4d6bc87b7d453bdded8ed Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 1 Apr 2025 11:08:51 +0200
Subject: [PATCH] Update the "get_code" fnction for operations -> when the
option 'get_OG' is true -> it remove the added "e:" or "t:" + updated the
detection of the duplicates to only consider operations (since calls are
renamed anyway)
---
src/main.py | 8 +++++---
src/operation.py | 5 +++++
2 files changed, 10 insertions(+), 3 deletions(-)
diff --git a/src/main.py b/src/main.py
index 7f1f38b..ac73acc 100644
--- a/src/main.py
+++ b/src/main.py
@@ -20,8 +20,9 @@ class Main(Nextflow_Building_Blocks):
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')
+ #We don't have to check the calls -> since there are renamed with their ids when we rewrite the code -> so it solve the issue
+ if(code in seen and e.get_type()=="Operation"):
+ raise BioFlowInsightError(f'Operation "{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
@@ -54,12 +55,13 @@ class Main(Nextflow_Building_Blocks):
for exe in sorted_executor_2_length:
if(exe.get_type()=="Call" or exe.get_type()=="Operation"):
- old = exe.get_code(remove_emit_and_take = True, replace_calls = False)
+ old = exe.get_code(get_OG = True, remove_emit_and_take = True, replace_calls = False)
new = exe.simplify_code(return_tab = False)
if(new!=old):
temp = code
code = code.replace(old, new, 1)
if(temp==code):
+ print(exe)
print(code)
print("- old", f'"{old}"')
print("- new", f'"{new}"')
diff --git a/src/operation.py b/src/operation.py
index ea2188b..42ddcf3 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -698,10 +698,15 @@ class Operation(Executor):
def get_code(self, replace_calls = True, clean_pipe = False, get_OG=False, remove_emit_and_take = False):
+ #exe.get_code(remove_emit_and_take = True, replace_calls = False)
code = self.code.get_code()
if(get_OG):
if(self.OG_code!=""):
code = self.OG_code
+ if(code[:3] in ["e: ", "t: "] and self.get_artificial_status()):
+ #print("-", code)
+ code = code[3:]
+ code = code.strip()
return code
if(clean_pipe):
--
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