From ac2bd8b12e5abb3ba1813c3d3208a89f80754225 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 8 Jul 2022 18:07:57 +0200
Subject: [PATCH] fixed network export
---
drugstone/views.py | 30 ++++++++++++++++++++----------
scripts/docker-entrypoint.sh | 2 +-
2 files changed, 21 insertions(+), 11 deletions(-)
diff --git a/drugstone/views.py b/drugstone/views.py
index fa5ea27..b4351d6 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -20,7 +20,8 @@ from drugstone import models
from drugstone import serializers
from drugstone.models import Protein, Task, ProteinDrugInteraction, \
- Drug, Tissue, ExpressionLevel, Network, ProteinDisorderAssociation, DrugDisorderIndication, Disorder, DrDiDataset, PDIDataset, PDisDataset, PPIDataset
+ Drug, Tissue, ExpressionLevel, Network, ProteinDisorderAssociation, DrugDisorderIndication, Disorder, DrDiDataset, \
+ PDIDataset, PDisDataset, PPIDataset
from drugstone.serializers import ProteinSerializer, TaskSerializer, \
ProteinDrugInteractionSerializer, DrugSerializer, TaskStatusSerializer, TissueSerializer, NetworkSerializer, \
ProteinDisorderAssociationSerializer, DisorderSerializer, DrugDisorderIndicationSerializer
@@ -408,12 +409,15 @@ def result_view(request) -> Response:
edge['to'] = nodes_mapped_dict[edge['to']][node_name_attribute] if edge['to'] in nodes_mapped_dict else edge[
'to']
if 'autofill_edges' in parameters['config'] and parameters['config']['autofill_edges']:
- proteins = set(map(lambda n:n[node_name_attribute][1:],filter(lambda n: node_name_attribute in n,parameters['input_network']['nodes'])))
- dataset = 'STRING' if 'interaction_protein_protein' not in parameters['config'] else parameters['config']['interaction_protein_protein']
+ proteins = set(map(lambda n: n[node_name_attribute][1:],
+ filter(lambda n: node_name_attribute in n, parameters['input_network']['nodes'])))
+ dataset = 'STRING' if 'interaction_protein_protein' not in parameters['config'] else parameters['config'][
+ 'interaction_protein_protein']
dataset_object = models.PPIDataset.objects.filter(name__iexact=dataset).last()
interaction_objects = models.ProteinProteinInteraction.objects.filter(
Q(ppi_dataset=dataset_object) & Q(from_protein__in=proteins) & Q(to_protein__in=proteins))
- auto_edges = list(map(lambda n: {"from": f'p{n.from_protein_id}', "to":f'p{n.to_protein_id}'} ,interaction_objects))
+ auto_edges = list(
+ map(lambda n: {"from": f'p{n.from_protein_id}', "to": f'p{n.to_protein_id}'}, interaction_objects))
edges.extend(auto_edges)
result['network']['edges'].extend(edges)
@@ -471,7 +475,7 @@ def graph_export(request) -> Response:
edges = request.data.get('edges', [])
fmt = request.data.get('fmt', 'graphml')
G = nx.Graph()
-
+ node_map = dict()
for node in nodes:
# drugstone_id is not interesting outside of drugstone
# try:
@@ -487,6 +491,10 @@ def graph_export(request) -> Response:
node[key] = ''
try:
node_name = node['label']
+ if 'drugstone_id' in node:
+ node_map[node['drugstone_id']] = node['label']
+ elif 'id' in node:
+ node_map[node['id']] = node['label']
except KeyError:
node_name = node['drugstone_id']
G.add_node(node_name, **node)
@@ -498,9 +506,11 @@ def graph_export(request) -> Response:
e[key] = json.dumps(e[key])
elif e[key] is None:
e[key] = ''
- u_of_edgece = e.pop('from')
+ u_of_edge = e.pop('from')
+ u_of_edge = u_of_edge if u_of_edge not in node_map else node_map[u_of_edge]
v_of_edge = e.pop('to')
- G.add_edge(u_of_edgece, v_of_edge, **e)
+ v_of_edge = node_map[v_of_edge] if v_of_edge in node_map else v_of_edge
+ G.add_edge(u_of_edge, v_of_edge, **e)
if fmt == 'graphml':
data = nx.generate_graphml(G)
@@ -529,7 +539,7 @@ def adjacent_disorders(request) -> Response:
data = request.data
if 'proteins' in data:
drugstone_ids = data.get('proteins', [])
- pdi_dataset = PDisDataset.objects.filter(name__iexact=data.get('dataset','DisGeNET')).last()
+ pdi_dataset = PDisDataset.objects.filter(name__iexact=data.get('dataset', 'DisGeNET')).last()
# find adjacent drugs by looking at drug-protein edges
pdis_objects = ProteinDisorderAssociation.objects.filter(protein__id__in=drugstone_ids,
pdis_dataset=pdi_dataset)
@@ -539,7 +549,7 @@ def adjacent_disorders(request) -> Response:
disorders = DisorderSerializer(many=True).to_representation(disorders)
elif 'drugs' in data:
drugstone_ids = data.get('drugs', [])
- drdi_dataset = DrDiDataset.objects.filter(name__iexact=data.get('dataset','DrugBank')).last()
+ drdi_dataset = DrDiDataset.objects.filter(name__iexact=data.get('dataset', 'DrugBank')).last()
# find adjacent drugs by looking at drug-protein edges
drdi_objects = DrugDisorderIndication.objects.filter(drug__id__in=drugstone_ids,
drdi_dataset=drdi_dataset)
@@ -565,7 +575,7 @@ def adjacent_drugs(request) -> Response:
"""
data = request.data
drugstone_ids = data.get('proteins', [])
- pdi_dataset = PDIDataset.objects.filter(name__iexact=data.get('pdi_dataset','NeDRex')).last()
+ pdi_dataset = PDIDataset.objects.filter(name__iexact=data.get('pdi_dataset', 'NeDRex')).last()
# find adjacent drugs by looking at drug-protein edges
pdi_objects = ProteinDrugInteraction.objects.filter(protein__id__in=drugstone_ids, pdi_dataset=pdi_dataset)
drugs = {e.drug for e in pdi_objects}
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 0245a23..db7a2d3 100755
--- a/scripts/docker-entrypoint.sh
+++ b/scripts/docker-entrypoint.sh
@@ -4,7 +4,7 @@ python3 manage.py makemigrations drugstone
python3 manage.py migrate
python3 manage.py createfixtures
python3 manage.py cleanuptasks
-python3 manage.py populate_db --update -a
+#python3 manage.py populate_db --update -a
#python3 manage.py make_graphs
/usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"
--
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