From 427e67381e2b76283aa178271193406d4f5f5e23 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Mon, 2 Dec 2024 09:14:02 +0100
Subject: [PATCH] Conitnue to clean -> Commented the generation of the pos dot
---
src/nextflow_building_blocks.py | 3 +++
src/nextflow_file.py | 6 +-----
src/outils_graph.py | 4 ++--
src/process.py | 3 ++-
src/workflow.py | 3 +++
5 files changed, 11 insertions(+), 8 deletions(-)
diff --git a/src/nextflow_building_blocks.py b/src/nextflow_building_blocks.py
index ae780ae..0c44921 100644
--- a/src/nextflow_building_blocks.py
+++ b/src/nextflow_building_blocks.py
@@ -80,6 +80,9 @@ class Nextflow_Building_Blocks:
def get_name_file(self):
return self.origin.get_name_file()
+ def get_root_directory(self):
+ return self.origin.get_root_directory()
+
def get_rocrate_key(self, dico):
return f"{self.get_file_address()[len(dico['temp_directory'])+1:]}#{self.get_name()}"
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index bc296df..9299da5 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -208,11 +208,7 @@ class Nextflow_File(Nextflow_Building_Blocks):
def get_file_address(self):
return os.path.normpath(self.file)
- def get_root_directory(self):
- if(self.origin==None):
- return '/'.join(self.get_file_address().split('/')[:-1])
- else:
- return self.origin.get_root_directory()
+
#Returns either a subworkflow or process from the name
def get_element_from_name(self, name):
diff --git a/src/outils_graph.py b/src/outils_graph.py
index f1da30a..b754f91 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -146,8 +146,8 @@ def generate_graph_dot(filename, dico, label_node = True, label_edge = True, ren
fill_dot(dot, dico, label_node, label_edge)
#metro_dot(dot, dico, relevant_nodes = relevant_nodes)
dot.save(filename=f'{filename}.dot')
- dot.format = 'dot'
- dot.render(filename=f'{filename}_pos')
+ #dot.format = 'dot'
+ #dot.render(filename=f'{filename}_pos')
if(render_graphs):
dot.render(filename=f'{filename}.dot', outfile=f'{filename}.png')
diff --git a/src/process.py b/src/process.py
index d593bd5..4648523 100644
--- a/src/process.py
+++ b/src/process.py
@@ -461,7 +461,8 @@ class Process(Nextflow_Building_Blocks):
self.initialise_name()
self.initialise_parts()
self.initialise_inputs_outputs()
- annotations = self.get_processes_annotation()
+ #annotations = self.get_processes_annotation()
+ annotations = None
if(annotations!=None):
self.tools = annotations[self.get_code()]["tools"]
self.commands = annotations[self.get_code()]["commands"]
diff --git a/src/workflow.py b/src/workflow.py
index d2ab751..9252627 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -146,6 +146,9 @@ class Workflow:
"""
return self.address
+ def get_root_directory(self):
+ return '/'.join(self.get_address().split('/')[:-1])
+
def get_workflow_directory(self):
"""Method that returns the workflow directory
--
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