From 49cf5812de290bf1e987ea5670a92aeb620c8b33 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 5 Feb 2024 15:53:48 +0100
Subject: [PATCH] Add functionnality to remove processes
---
src/call.py | 2 +-
src/function.py | 3 +++
src/graph.py | 43 ++++++++++++++++++++++++++++++++++++++++++-
src/nextflow_file.py | 4 ++--
src/workflow.py | 4 ++--
5 files changed, 50 insertions(+), 6 deletions(-)
diff --git a/src/call.py b/src/call.py
index b79c9b7..7740b65 100644
--- a/src/call.py
+++ b/src/call.py
@@ -52,7 +52,7 @@ class Call(Executor):
tab += [self.first_element_called]
for para in self.parameters:
if(para.get_type()=="Call"):
- tab = para.get_elements_called(tab = tab.copy(), first_call = False)
+ tab = para.get_elements_called(tab_input = tab.copy(), first_call = False)
temp = list(set(tab))
#del tab
return temp
diff --git a/src/function.py b/src/function.py
index 9c55e96..8c9ec00 100644
--- a/src/function.py
+++ b/src/function.py
@@ -23,5 +23,8 @@ class Function(Nextflow_Building_Blocks):
def get_name(self):
return self.name
+ def add_2_rocrate(self, dico, parent_key):
+ None
+
diff --git a/src/graph.py b/src/graph.py
index 73cca9f..99c98cc 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -23,7 +23,48 @@ class Graph():
self.dico_flattened = {}
- def initialise(self):
+
+
+ def initialise(self, processes_2_remove = []):
+
+ def get_node_id(dico, process):
+ for node in dico["nodes"]:
+ if(node['name']==process):
+ return node['id']
+ for sub in dico['subworkflows']:
+ res = get_node_id(dico['subworkflows'][sub], process)
+ if(res!=-1):
+ return res
+ return -1
+
+ #This function removes the process -> by the simpliest way -> it doesn't create new links
+ def remove_node(dico, node_id):
+ #Remove nodes
+ nodes_to_remove = []
+ for node in dico["nodes"]:
+ if(node['id']==node_id):
+ nodes_to_remove.append(node)
+ for node in nodes_to_remove:
+ dico["nodes"].remove(node)
+
+ #Remove edges
+ edges_to_remove = []
+ for edge in dico["edges"]:
+ if(edge['A']==node_id):
+ edges_to_remove.append(edge)
+ if(edge['B']==node_id):
+ edges_to_remove.append(edge)
+ for edge in edges_to_remove:
+ dico["edges"].remove(edge)
+
+ for sub in dico['subworkflows']:
+ remove_node(dico['subworkflows'][sub], node_id)
+
+ for process in processes_2_remove:
+ node_id = get_node_id(self.full_dico, process)
+ remove_node(self.full_dico, node_id)
+
+
self.get_graph_wo_branch_operations()
self.get_graph_wo_operations()
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index e733855..b254a1d 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -637,9 +637,9 @@ class Nextflow_File(Nextflow_Building_Blocks):
if(self.graph==None):
self.graph = Graph(self)
- def generate_all_graphs(self, render_graphs = True):
+ def generate_all_graphs(self, render_graphs = True, processes_2_remove = []):
#Initialisation (obligatory)
- self.graph.initialise()
+ self.graph.initialise(processes_2_remove = processes_2_remove)
#Generate the different graphs
self.graph.get_full_graph(render_graphs = render_graphs)
diff --git a/src/workflow.py b/src/workflow.py
index 6e0fcd3..5342a54 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -123,5 +123,5 @@ class Workflow:
self.nextflow_file.initialise()
self.initialise_rocrate()
- def generate_all_graphs(self, render_graphs = True):
- self.nextflow_file.generate_all_graphs(render_graphs = render_graphs)
+ def generate_all_graphs(self, render_graphs = True, processes_2_remove = []):
+ self.nextflow_file.generate_all_graphs(render_graphs = render_graphs, processes_2_remove = processes_2_remove)
--
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