From c06e5e04270156933bc41e8183dadb7cacc3545e Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 12 Mar 2025 10:33:24 +0100
Subject: [PATCH] Implemented a rewrite which places the clusters based on
topological order -> not the first or last place in the code -> but uses the
order of execution of the clusters
---
src/outils.py | 15 +++++
src/workflow.py | 146 ++++++++++++++++++++++++++++++------------------
2 files changed, 106 insertions(+), 55 deletions(-)
diff --git a/src/outils.py b/src/outils.py
index 88e3e9b..9049cda 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -1343,3 +1343,18 @@ def get_channels_to_add_in_false_conditions(body, emitted_channels):
return body
+#This function removes the empty conditions -> while keeping the anker_clusters -> if it's orignally in a condtion
+def remove_empty_conditions(code):
+ pattern = r"(if *\(.+\)|else)\s*{(\s*|\s*\/\/Anker_clusters\s*)}"
+ def replace(text, pattern):
+ def replacer(match):
+ return match.group(0).replace(match.group(0), match.group(2))
+ return re.sub(pattern, replacer, text)
+ temp = code
+ code = replace(code, pattern)
+ while(code!=temp):
+ temp = code
+ code = replace(code, pattern)
+ return code
+
+
diff --git a/src/workflow.py b/src/workflow.py
index 80585ba..7869116 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -3,7 +3,7 @@
from .nextflow_file import Nextflow_File
from .ro_crate import RO_Crate
from . import constant
-from .outils import is_git_directory, format_with_tabs, replace_thing_by_call, replace_group1, group_together_ifs, extract_curly, remove_extra_jumps, get_channels_to_add_in_false_conditions, extract_conditions
+from .outils import is_git_directory, format_with_tabs, replace_thing_by_call, replace_group1, group_together_ifs, extract_curly, remove_extra_jumps, get_channels_to_add_in_false_conditions, extract_conditions, remove_empty_conditions
from .outils_graph import get_flatten_dico, initia_link_dico_rec, get_number_cycles, generate_graph
from .outils_annotate import get_tools_commands_from_user_for_process
from .bioflowinsighterror import BioFlowInsightError
@@ -766,7 +766,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
relevant_processes = self.check_relevant_processes_in_workflow(relevant_processes)
self.generate_user_view(relevant_processes = relevant_processes, processes_2_remove = [], render_graphs=render_graphs)
clusters = self.graph.get_clusters_from_user_view()
- print(len(clusters))
+
broken_subworkflows = get_workflows_broken(get_subworkflow_2_executors(), get_clusters_with_calls(clusters))
#While there still are broken workflows -> need to redo the analysis
while(len(broken_subworkflows)>0):
@@ -782,7 +782,6 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
clusters = self.graph.get_clusters_from_user_view()
broken_subworkflows = get_workflows_broken(get_subworkflow_2_executors(), get_clusters_with_calls(clusters))
-
#print(code)
@@ -823,41 +822,85 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
# else:
# print(c, c.get_code()[:20], c.artificial)
+
+
+ #This function returns the last executor in the clusters
+ #This is used to place the anker
+ def get_last_executor_in_cluster(executors_in_order, clusters):
+ dico = {}
+ for cluster in clusters:
+ for ele in cluster:
+ dico[ele] = executors_in_order.index(ele)
+ for ele in {k: v for k, v in sorted(dico.items(), key=lambda item: item[1], reverse=True)}:
+ return ele
+
+ #Replace the last executor in the clusters by the cluster anker
+ last_executor_in_cluster = get_last_executor_in_cluster(executors_in_order, clusters)
+ if(last_executor_in_cluster.get_type()=="Process"):
+ call = last_executor_in_cluster.get_call()
+ code = code.replace(call.get_code(get_OG = True), "//Anker_clusters")
+ elif(last_executor_in_cluster.get_type()=="Operation"):
+ if(not last_executor_in_cluster.get_artificial_status()):
+ code = code.replace(last_executor_in_cluster.get_code(get_OG = True), "//Anker_clusters", 1)
+ else:
+ raise Exception("This shoudn't happen")
+ else:
+ raise Exception("This shoudn't happen")
+
+
+ #Removing elements from clusters from the code
+ for cluster in clusters:
+ for ele in cluster:
+ if(ele.get_type()=="Process"):
+ call = ele.get_call()
+ code = code.replace(call.get_code(get_OG = True), "")
+ elif(ele.get_type()=="Operation"):
+ if(not ele.get_artificial_status()):
+ code = code.replace(ele.get_code(get_OG = True), "", 1)
+ else:
+ raise Exception("This shoudn't happen")
+ else:
+ raise Exception("This shoudn't happen")
+
+ #Remove the empty conditions left in the code
+ code = remove_empty_conditions(code)
+
+
+ #Add the subworkflow defintions
+ #-------------------------------------
+ #Adding the anker
+ subworkflow_section = f"//ANKER 4 SUBWORKFLOW DEF"
+ to_replace = ""
+ for match in re.finditer(r"workflow\s*\w*\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}")
#Creating the subworkflows from clusters
calls_in_operations = []
non_relevant_name = 1
- channels_to_replace_outside_of_cluster = []
+
subworkflow_clusters_to_add, subworkflow_cluster_calls_to_add = [], []
- index_cluster = 0
- for elements in clusters:
+ index_cluster = len(clusters)
+ for elements in list(reversed(clusters)):
+
+ channels_to_replace_outside_of_cluster = []
+
#Check that there is at least one process in cluster
at_least_one_process = False
for e in elements:
if(e.get_type()=="Process"):
at_least_one_process = True
- #Only create the subworkflows for clusters with more than one element
+ #Only create the subworkflows for clusters with onr more elements (and that element in a process)
processes_added = []
things_added_in_cluster = []
if(len(elements)>=1 and at_least_one_process):
name, body, take, emit = "", "", "", ""
first_element = True
- def get_last_operation_or_call(elements):
- index = -1
- while(True):
- if(elements[index].get_type()=="Process"):
- return elements[index].get_call()
- else:
- if(not elements[index].get_artificial_status()):
- return elements[index]
- else:
- index = index-1
- anker_thing = get_last_operation_or_call(elements).get_code(get_OG = True)
- code = code.replace(anker_thing, f"//Anker_cluster{index_cluster}\n\n{anker_thing}")
-
-
for ele in elements:
if(ele.get_type()=="Process"):
@@ -867,14 +910,6 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
name = f"cluster_{ele.get_alias()}"
#Get the call of thing (either process or subworkflow)
call = ele.get_call()
-
- #If first element -> add marker for the subworkflow call
- #if(first_element):
- # code = code.replace(call.get_code(get_OG = True), f"//Anker_cluster{index_cluster}")
- # first_element = False
- #else:
- code = code.replace(call.get_code(get_OG = True), "")
-
processes_added.append(call.get_first_element_called())
values = []
@@ -892,13 +927,7 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#TODO -> check this verification there might be some "effet de bord"
if(not ele.get_artificial_status()):
- ##If first element -> add marker for the subworkflow call
- #if(first_element):
- # code = code.replace(ele.get_code(get_OG = True), f"//Anker_cluster{index_cluster}", 1)
- # first_element = False
- #else:
- code = code.replace(ele.get_code(get_OG = True), "", 1)
-
+
#Ignore these cases
#TODO -> you should be able to remove this
if(ele.get_code()[:4] not in ["emit", "take"]):
@@ -1034,11 +1063,32 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
subworkfow_call = subworkfow_call_case_true
- subworkflow_clusters_to_add.append(subworkflow_code)
- subworkflow_cluster_calls_to_add.append(subworkfow_call)
- index_cluster+=1
+ #subworkflow_clusters_to_add.append(subworkflow_code)
+ #subworkflow_cluster_calls_to_add.append(subworkfow_call)
+
+ #Add the subworkflow call
+ new_code = f"//Anker_clusters\n\n//Cluster_{index_cluster}\n{subworkfow_call}\n"
+ code = code.replace("//Anker_clusters", new_code)
+
+ for old, new in channels_to_replace_outside_of_cluster:
+ pattern= fr"[ \(,]({re.escape(old)})[^\w]"
+ code = replace_group1(code, pattern, new)
+ #code = code.replace(old, new)
+
+ #Add the subworkflow defintions
+ #-------------------------------------
+ code = code.replace(f'{subworkflow_section}', f"{subworkflow_code}\n\n{subworkflow_section}")
-
+
+ else:
+ #If there is only one element then we put it back in the code
+ new_code = f"//Anker_clusters\n\n//Cluster_{index_cluster}\n{elements[0].get_code(get_OG = True)}\n"
+ code = code.replace("//Anker_clusters", new_code)
+ index_cluster-=1
+
+
+
+ """
#TODO -> rmoving the conditions which are problematic
#This might not be the probleme -> when rerunnung the analysis isn't totally robust
still_simplifying_conditions = True
@@ -1088,22 +1138,8 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
#code = code.replace(old, new)
- #Add the subworkflow defintions
- #-------------------------------------
- #Add anker
- subworkflow_section = f"//ANKER 4 SUBWORKFLOW DEF"
- to_replace = ""
- for match in re.finditer(r"workflow\s*\w*\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}")
-
- for sub in subworkflow_clusters_to_add:
- code = code.replace(f'{subworkflow_section}', f"{sub}\n\n{subworkflow_section}")
+ """
#Putting || back
code = code.replace("$OR$", "||")
--
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