From f9d947fdf6cfac09360f1e4b992609432a7f77c4 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 15 Apr 2025 10:57:17 +0200
Subject: [PATCH] Added functionnality that the dot positions for the nodes are
added in the json
---
src/outils_graph.py | 38 ++++++++++++++++++++++++++++++++++++++
src/workflow.py | 14 +++++++++++++-
2 files changed, 51 insertions(+), 1 deletion(-)
diff --git a/src/outils_graph.py b/src/outils_graph.py
index 878a10d..4091730 100644
--- a/src/outils_graph.py
+++ b/src/outils_graph.py
@@ -1254,3 +1254,41 @@ def remove_artificial_nodes(param_dico):
edge = {"A" : source['source'], "B" : sink['sink'], "label" : source['label']}
dico["edges"].append(edge)
return dico
+
+def enrich_json_with_positions(file):
+ import json
+ with open(file, 'r') as JSON:
+ dico = json.load(JSON)
+
+ pos_file = file[:-len(".json")]+"_pos.dot"
+ try:
+ f=open(pos_file)
+ contents_pos =f.read()
+ f.close()
+ except:
+ return
+
+ def search_for_pos(id, text):
+ import re
+ pattern = re.escape(id)+r'.+\n.+\s+pos="([^,]+),([^"]+)",'
+ for match in re.finditer(pattern, text):
+ return match.group(1), match.group(2)
+ return -1, -1
+
+ def enrich_nodes(wf_dico):
+ for node in wf_dico["nodes"]:
+ id = node['id']
+ x_pos, y_pos = search_for_pos(id, contents_pos)
+ if(x_pos==-1 and y_pos==-1):
+ return
+ else:
+ node['position'] = {}
+ node['position']['x'] = x_pos
+ node['position']['y'] = y_pos
+ for sub in wf_dico['subworkflows']:
+ enrich_nodes(wf_dico['subworkflows'][sub])
+ enrich_nodes(dico)
+ with open(file, 'w') as output_file :
+ json.dump(dico, output_file, indent=4)
+
+
diff --git a/src/workflow.py b/src/workflow.py
index 02d0650..16231fe 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -4,7 +4,7 @@ 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, remove_empty_conditions_place_anker
-from .outils_graph import get_flatten_dico, initia_link_dico_rec, get_number_cycles, generate_graph
+from .outils_graph import get_flatten_dico, initia_link_dico_rec, get_number_cycles, generate_graph, enrich_json_with_positions
from .outils_annotate import get_tools_commands_from_user_for_process
from .bioflowinsighterror import BioFlowInsightError
from .graph import Graph
@@ -197,17 +197,29 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
self.iniatilise_tab_processes_2_remove()
self.graph.initialise(processes_2_remove = self.processes_2_remove)
self.graph.get_specification_graph(render_graphs = render_graphs)
+ self.enrich_json_files_with_positions()
def generate_process_dependency_graph(self, render_graphs = True):
self.iniatilise_tab_processes_2_remove()
self.graph.initialise(processes_2_remove = self.processes_2_remove)
self.graph.render_process_dependency_graph(render_graphs = render_graphs)
+ self.enrich_json_files_with_positions()
+
#TODO -> update this
def generate_all_graphs(self, render_graphs = True):
self.generate_specification_graph(render_graphs = render_graphs)
self.generate_process_dependency_graph(render_graphs = render_graphs)
+ self.enrich_json_files_with_positions()
+
+ #This function takes the json files and searches for the corrresponding dot pos files
+ #And adds the information regarding the position of the nodes
+ def enrich_json_files_with_positions(self):
+ jsons = glob.glob(f'{self.get_output_dir()/"graphs"}/*.json', recursive=False)
+ for file in jsons:
+ enrich_json_with_positions(file)
+
#Method that checks if a given graph sepcification is an isomorphism with the workflows
def check_if_json_equal_to_full_structure(self, file):
self.iniatilise_tab_processes_2_remove()
--
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