From 2cb08b6b9075ea698341f3b10a6a83bed172db8e Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Thu, 10 Oct 2024 16:36:32 +0200
Subject: [PATCH] added subworkflows to user view
---
src/graph.py | 7 +++++++
src/nextflow_file.py | 8 ++++++++
src/outils_graph.py | 25 +++++++++++++++++++++++++
src/workflow.py | 34 ++++++++++++++++++++++------------
4 files changed, 62 insertions(+), 12 deletions(-)
diff --git a/src/graph.py b/src/graph.py
index 925f15f..e4910e4 100644
--- a/src/graph.py
+++ b/src/graph.py
@@ -300,7 +300,14 @@ class Graph():
with open(self.get_output_dir()/ "graphs/user_view.json", 'w') as output_file :
json.dump(user_view, output_file, indent=4)
+
+ user_view_with_subworkflows = add_subworkflows_2_dico(self.dico_process_dependency_graph, user_view)
+ with open(self.get_output_dir()/ "graphs/user_view_with_subworkflows.json", 'w') as output_file :
+ json.dump(user_view_with_subworkflows, output_file, indent=4)
+
generate_graph(self.get_output_dir()/'graphs'/"user_view", user_view, label_edge=True, label_node=True, render_graphs = render_graphs)
+ generate_graph(self.get_output_dir()/'graphs'/"user_view_with_subworkflows", user_view_with_subworkflows, label_edge=True, label_node=True, render_graphs = render_graphs)
+
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index 87dd9c2..a90e4bb 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -699,6 +699,14 @@ class Nextflow_File(Nextflow_Building_Blocks):
self.graph.get_metadata_dependency_graph()
self.graph.get_metadata_process_dependency_graph()
+ def generate_specification_graph(self, render_graphs = True, processes_2_remove = []):
+ self.graph.initialise(processes_2_remove = processes_2_remove)
+ self.graph.get_specification_graph(render_graphs = render_graphs)
+
+ def generate_process_dependency_graph(self, render_graphs = True, processes_2_remove = []):
+ self.graph.initialise(processes_2_remove = processes_2_remove)
+ self.graph.render_graph_wo_operations(render_graphs = render_graphs)
+
def generate_user_view(self, relevant_processes = [], render_graphs = True, processes_2_remove = []):
self.graph.initialise(processes_2_remove = processes_2_remove)
self.graph.generate_user_view(relevant_processes = relevant_processes, render_graphs = render_graphs)
diff --git a/src/outils_graph.py b/src/outils_graph.py
index 3ba0f6d..3d75e09 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -748,4 +748,29 @@ def relev_user_view_builder(dico, relevant_modules):
new_dico["edges"].append({'A':"input", 'B':input, "label": ""})
return new_dico
+#This function fills the new_dico with the flattened_dico but
+#reintegrates the subworkflows (from the full workflow)
+def add_subworkflows_2_dico(full_dico, flattened_dico, add_root_nodes = True):
+ #Add nodes with subworkflows
+ def add_nodes(full_dico, flattened_dico):
+ new_dico = {}
+ new_dico['nodes'] = []
+ new_dico['edges'] = []
+ new_dico['subworkflows'] = {}
+ for n1 in full_dico["nodes"]:
+ for n2 in flattened_dico["nodes"]:
+ if(n1['id'][1:-1] in n2['id'] and n1['name'] == n2['name']):
+ new_dico["nodes"].append(n2)
+ for sub in full_dico["subworkflows"]:
+ new_dico['subworkflows'][sub] = add_nodes(full_dico["subworkflows"][sub], flattened_dico)
+ return new_dico
+
+ new_dico = add_nodes(full_dico, flattened_dico)
+ new_dico["edges"] = flattened_dico["edges"]
+ if(add_root_nodes):
+ new_dico["nodes"].append({"id": "input","name": "i","shape": "triangle", "fillcolor":"#ffffff"})
+ new_dico["nodes"].append({"id": "output","name": "o","shape": "triangle", "fillcolor":"#ffffff"})
+ return new_dico
+
+
diff --git a/src/workflow.py b/src/workflow.py
index 3fa3c1f..03e0146 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -83,6 +83,7 @@ class Workflow:
self.keywords = keywords
self.producer = producer
self.publisher = publisher
+ self.tab_processes_2_remove = None
self.personnal_acces_token = personnal_acces_token
self.processes_2_tools = processes_2_tools
if(processes_2_remove==""):
@@ -515,26 +516,35 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
print()
print(citation)
+ def iniatilise_tab_processes_2_remove(self):
+ if(self.tab_processes_2_remove==None):
+ tab_processes_2_remove = []
+ if(self.processes_2_remove!=None):
+ temp = self.processes_2_remove.split(",")
+ for t in temp:
+ tab_processes_2_remove.append(t.strip())
+ self.tab_processes_2_remove = tab_processes_2_remove
+
def generate_all_graphs(self, render_graphs = True):
"""Method that generates all graphs representing the workflow
Keyword arguments:
"""
- tab_processes_2_remove = []
- if(self.processes_2_remove!=None):
- temp = self.processes_2_remove.split(",")
- for t in temp:
- tab_processes_2_remove.append(t.strip())
- self.nextflow_file.generate_all_graphs(render_graphs = render_graphs, processes_2_remove = tab_processes_2_remove)
+ self.iniatilise_tab_processes_2_remove()
+ self.nextflow_file.generate_all_graphs(render_graphs = render_graphs, processes_2_remove = self.tab_processes_2_remove)
+
+ def generate_specification_graph(self, render_graphs = True):
+ self.iniatilise_tab_processes_2_remove()
+ self.nextflow_file.generate_specification_graph(render_graphs = render_graphs, processes_2_remove = self.tab_processes_2_remove)
+
+ def generate_process_dependency_graph(self, render_graphs = True):
+ self.iniatilise_tab_processes_2_remove()
+ self.nextflow_file.generate_process_dependency_graph(render_graphs = render_graphs, processes_2_remove = self.tab_processes_2_remove)
def generate_user_view(self, relevant_processes = [], render_graphs = True):
- tab_processes_2_remove = []
- if(self.processes_2_remove!=None):
- temp = self.processes_2_remove.split(",")
- for t in temp:
- tab_processes_2_remove.append(t.strip())
- self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, render_graphs = render_graphs, processes_2_remove = tab_processes_2_remove)
+ self.iniatilise_tab_processes_2_remove()
+ self.nextflow_file.generate_user_view(relevant_processes = relevant_processes, render_graphs = render_graphs, processes_2_remove = self.tab_processes_2_remove)
def build_processes_2_tools(self):
--
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