From e3542c323fa99ff4ba55b363cbf0b1856dfdf341 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 1 Apr 2025 10:25:57 +0200
Subject: [PATCH] Add filter "addParams" + upate position subworklfow anker +
update 1 or 2 small bugs
---
src/operation.py | 2 +-
src/workflow.py | 30 +++++++++++++++++++-----------
2 files changed, 20 insertions(+), 12 deletions(-)
diff --git a/src/operation.py b/src/operation.py
index 82b697b..ea2188b 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -1040,7 +1040,7 @@ class Operation(Executor):
# a = ...
#}
#b = a -> when wanting to rewrite this operation
- if(set(types)=={"Channel"}):
+ elif(set(types)=={"Channel"}):
None
#operations = {}
#for c in dico_origin_2_replace[origin]:
diff --git a/src/workflow.py b/src/workflow.py
index 9fc7469..9c0c736 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -506,7 +506,10 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Remove the includes
for match in re.finditer(constant.FULL_INLCUDE_2, code):
- code = re.sub(fr"{re.escape(match.group(0))}.*", "", code)
+ full_include = match.group(0)
+ for temp in re.finditer(fr"{re.escape(full_include)} *addParams\(", code):
+ raise BioFlowInsightError("There is an 'addParams' in an include. BioFlow-Insight doesn not how to rewrite this.")
+ code = re.sub(fr"{re.escape(full_include)}.*", "", code)
processes, subworkflows, functions = [], [], []
for c in self.get_workflow_main().get_all_calls_in_workflow():
@@ -807,20 +810,21 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
ternary_operation_dico = self.ternary_operation_dico
map_element_dico = self.map_element_dico
- 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.get_DSL()=="DSL2"):
- code = self.simplify_workflow_code()
- self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
- if(self.duplicate):
+ if(self.duplicate):
#First check if there are any duplicate operations
#That method is in the "get_order_execution_executors" method -> so we just run that first
self.get_order_execution_executors()
-
+
+ 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.get_DSL()=="DSL2"):
+ code = self.simplify_workflow_code()
+ self.rewrite_and_initialise(code, self.processes_2_remove, render_graphs=render_graphs)
+
#DETERMING WHICH SUBWORKFLOWS ARE BROKEN WITH THE CLUSTER
def get_clusters_with_calls(clusters):
@@ -969,9 +973,13 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#Adding the anker
subworkflow_section = f"//ANKER 4 SUBWORKFLOW DEF"
to_replace = ""
- for match in re.finditer(r"workflow\s*\w*\s*\{", code):
+ for match in re.finditer(r"workflow\s+\w*\s*\{", code):
to_replace = match.group(0)
break
+ if(to_replace==""):
+ for match in re.finditer(r"workflow\s*\{", code):
+ to_replace = match.group(0)
+ break
if(to_replace==""):
raise Exception("No call to a workflow")
code = code.replace(to_replace, f"{subworkflow_section}\n\n{to_replace}")
--
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