From 4da8821f8f573df67034443d11876f62cb5622b8 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 6 Jan 2025 10:15:04 +0100
Subject: [PATCH] Fixed the problem i had with the subworkflows being broken or
not
---
src/workflow.py | 103 ++++++++++++++++++++----------------------------
1 file changed, 42 insertions(+), 61 deletions(-)
diff --git a/src/workflow.py b/src/workflow.py
index 2b6e538..fd0f4b3 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -812,8 +812,8 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#I do not recommand that the dev uses the same name for the channels inside and outside the channels
#Since the local channels become local at the upper level
- def rewrite_subworkflow_call(seld, code, subworklfow):
- print(subworklfow.get_name())
+ def rewrite_subworkflow_call(self, code, subworklfow):
+
#Remove the defintion from the code
code = code.replace(subworklfow.get_code(), "")
OG_call = subworklfow.get_call()
@@ -838,35 +838,49 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
code = code.replace(OG_call.get_code(get_OG = True), f"{new_header}\n\n{OG_body}")
#REPLACE THE EMITS
+ #TODO admittedly this code below is very moche -> but it's functionnal -> update it
emits = subworklfow.get_emit()
- for o in emits:
- origin = o.get_origins()[0]
- gives = o.get_gives()
- #TODO finish this -> i think that the gives is empty
- print(o.get_type())
- print(o.get_code(), origin.get_code(), gives)
-
-
- #print(code)
+ to_replace = []
+ all_executors = self.get_all_executors()
+ for exe in all_executors:
+ #We don't need to check the case call since the workflow has already been rewriteen -> emits only appear in operations
+ if(exe.get_type()=="Operation"):
+ emited = exe.get_origins()
+ if(len(emited)==1):
+ emited = emited[0]
+ if(emited.get_type()=="Emitted"):
+ if(emited.get_emitted_by()==subworklfow):
+ if(emited.get_emits() not in emits):
+ raise Exception("This shoudn't happen -> since it is the actual subworkflow")
+ to_replace.append((exe.get_code(get_OG = True), f"{exe.get_gives()[0].get_code()} = {emited.get_emits().get_origins()[0].get_code()}"))
+ for r in to_replace:
+ old, new = r
+ #Case of channel == channel
+ if(new.split("=")[0].strip()==new.split("=")[1].strip()):
+ new = ''
+ code = code.replace(old, new)
+
+
return code
+ def rewrite_and_initialise(self, code):
+ #Write new code in temporary file
+ temp_file = self.get_output_dir()/f"temp_{str(self)[-7:-2]}.nf"
+ with open(temp_file, "w") as file:
+ file.write(code)
+
+ #Replace old analysis with new analysis (simplified code)
+ self.__init__(str(temp_file), display_info = False, duplicate=True)
+ self.initialise(create_rocrate=False)
+
#Conert workflow to user_view only makes sense when the option duplicate is activated -> otherwise is doesn't make sense + it makes the analysis way more complicated
def convert_workflow_2_user_view(self, relevant_processes = []):
if(self.duplicate):
- #Write new code in temporary file
code = self.simplify_workflow_code()
- temp_file = self.get_output_dir()/f"temp_{str(self)[-7:-2]}.nf"
- with open(temp_file, "w") as file:
- file.write(code)
-
- #Replace old analysis with new analysis (simplified code)
- self.__init__(str(temp_file), display_info = False, duplicate=True)
- self.initialise(create_rocrate=False)
-
-
+ self.rewrite_and_initialise(code)
#Get the clusters and the code
self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [])
@@ -927,51 +941,18 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
return broken_subworkflows
broken_subworkflows = get_workflows_broken(subworkflow_2_executors, set_clusters_with_calls)
-
+ print(broken_subworkflows)
#Rewrite broken subworkflows
for sub in broken_subworkflows:
code = self.rewrite_subworkflow_call(code, sub)
+
+ #TODO -> this needs to be optimised
+ self.rewrite_and_initialise(code)
+ #Get the clusters and the code
+ self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [])
+ clusters = self.nextflow_file.graph.get_clusters_from_user_view()
- 1/0
-
- #def check_subworkflow_intact(original_sets, new_sets):
- # results = {}
- # for sub in original_sets:
- # original = original_sets[sub]
- # #temp = []
- # #for new in new_sets:
- # # print(original, new, new.issubset(original))
- # # #temp.append(original.issubset(new))
- # #print(temp)
- # intact = all(new.issubset(original) for new in new_sets)
- # results[sub] = intact
- # return results
-
- #print(check_subworkflow_intact(subworkflow_2_executors, set_clusters_with_calls))
- 1/0
-
- #cluster_2_subworkflows = []
- #print(clusters)
- ##Basically here i'm checking if a subworkflow is split
- ##TODO Check this -> i think in the case something is at the root -> it won't work
- #for sub in self.get_subworkflows_called():
- # clusters_in_which_elements_are_taken = []
- # #TODO do this
- # print(sub.get_name(), sub.get_executors())
- # for exe in sub.get_executors():
- # print(exe, exe.get_subworkflow_origin())
- # #If there are multiple clusters and the number of clusters isn't equal to all the clusters -> it means that subworkflow is broken
- # if(len(clusters_in_which_elements_are_taken)>1 and len(clusters_in_which_elements_are_taken)!=len(clusters)):
- # print(sub.get_name())
- #print(clusters)
- #for c in clusters:
- # for ele in c:
- # print(ele.get_type())
-
- #TODO -> need to break clusters here
- #And redo analysis
-
#Get the clsuters with the corresponding operations inside
#for i in range(len(clusters)):
--
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