From 040ae50f9a4ce6561ee6300ff84f1f4d29f106a5 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 5 May 2023 13:28:49 +0200
Subject: [PATCH] added drug-target action information
Former-commit-id: b20c62b41036bbf7aa7fcc8c7622c5f83c1fc5d3 [formerly 8c7f0c56bac0e15f052652a2281d739209fb0d7f]
Former-commit-id: 1d3b5790373ca6913a8e0f3346d1562bb925ddcc
---
Dockerfile | 5 ++--
drugstone/celery.py | 1 -
.../management/commands/import_from_nedrex.py | 4 ++-
drugstone/models.py | 5 ++--
drugstone/serializers.py | 8 +++++-
drugstone/views.py | 27 +++++++++++++++++--
requirements.txt | 6 ++---
7 files changed, 44 insertions(+), 12 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index f338d1b..350a5f0 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,10 +8,11 @@ ENV LC_ALL=C.UTF-8
ENV LANG=C.UTF-8
RUN apt update && apt upgrade -y
-RUN apt install -y supervisor nginx libgtk-3-dev wget
+RUN apt install -y supervisor nginx libgtk-3-dev
RUN conda install -y conda python=3.8
-RUN conda install -c conda-forge -y graph-tool=2.46
+#RUN conda install -c conda-forge -y graph-tool=2.46
+RUN conda install -c conda-forge -y graph-tool=2.55
RUN pip install gunicorn
diff --git a/drugstone/celery.py b/drugstone/celery.py
index 05cf2c7..93dcd26 100644
--- a/drugstone/celery.py
+++ b/drugstone/celery.py
@@ -2,7 +2,6 @@ import os
from celery import Celery
-
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'drugstone.settings')
app = Celery('drugstone')
diff --git a/drugstone/management/commands/import_from_nedrex.py b/drugstone/management/commands/import_from_nedrex.py
index 472bca8..a307523 100644
--- a/drugstone/management/commands/import_from_nedrex.py
+++ b/drugstone/management/commands/import_from_nedrex.py
@@ -1,3 +1,4 @@
+import json
from collections import defaultdict
import nedrex
@@ -245,7 +246,8 @@ class NedrexImporter:
try:
drug = self.cache.get_drug_by_drugbank(to_id(edge['sourceDomainId']))
protein = self.cache.get_protein_by_uniprot(to_id(edge['targetDomainId']))
- e = models.ProteinDrugInteraction(pdi_dataset=dataset, drug=drug, protein=protein)
+ actions = json.dumps(edge['actions'])
+ e = models.ProteinDrugInteraction(pdi_dataset=dataset, drug=drug, protein=protein, actions=actions)
if not update or e.__hash__() not in existing:
bulk.add(e)
for source in edge['dataSources']:
diff --git a/drugstone/models.py b/drugstone/models.py
index 3c66432..fdbc10f 100755
--- a/drugstone/models.py
+++ b/drugstone/models.py
@@ -272,6 +272,7 @@ class ProteinDrugInteraction(models.Model):
PDIDataset, null=True, on_delete=models.CASCADE, related_name='pdi_dataset_relation')
protein = models.ForeignKey('Protein', on_delete=models.CASCADE)
drug = models.ForeignKey('Drug', on_delete=models.CASCADE)
+ actions = models.CharField(max_length=255, default='[]')
class Meta:
unique_together = ('pdi_dataset', 'protein', 'drug')
@@ -280,13 +281,13 @@ class ProteinDrugInteraction(models.Model):
return f'{self.pdi_dataset}-{self.protein}-{self.drug}'
def __eq__(self, other):
- return self.pdi_dataset_id == other.pdi_dataset_id and self.protein_id == other.protein_id and self.drug_id == other.drug_id
+ return self.pdi_dataset_id == other.pdi_dataset_id and self.protein_id == other.protein_id and self.drug_id == other.drug_id and self.actions == other.actions
def __ne__(self, other):
return not self.__eq__(other)
def __hash__(self):
- return hash((self.pdi_dataset_id, self.protein_id, self.drug_id))
+ return hash((self.pdi_dataset_id, self.protein_id, self.drug_id, self.actions))
class Task(models.Model):
diff --git a/drugstone/serializers.py b/drugstone/serializers.py
index 3805f42..9398c81 100755
--- a/drugstone/serializers.py
+++ b/drugstone/serializers.py
@@ -157,6 +157,7 @@ class ProteinDrugInteractionSerializer(serializers.ModelSerializer):
dataset = serializers.SerializerMethodField()
protein = serializers.SerializerMethodField()
drug = serializers.SerializerMethodField()
+ actions = serializers.SerializerMethodField()
def get_dataset(self, obj):
return obj.pdi_dataset.name
@@ -167,9 +168,14 @@ class ProteinDrugInteractionSerializer(serializers.ModelSerializer):
def get_drug(self, obj):
return f'dr{obj.drug.id}'
+ def get_actions(self, obj):
+ if obj.actions:
+ return json.loads(obj.actions)
+ return []
+
class Meta:
model = ProteinDrugInteraction
- fields = ['dataset', 'protein', 'drug']
+ fields = ['dataset', 'protein', 'drug', 'actions']
class ProteinDisorderAssociationSerializer(serializers.ModelSerializer):
diff --git a/drugstone/views.py b/drugstone/views.py
index 89081ab..16e515f 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -423,6 +423,27 @@ def result_view(request) -> Response:
nodes_mapped, id_key = query_proteins_by_identifier(edge_endpoint_ids, identifier)
+ pdi_config = result.get("parameters").get('pdi_dataset')
+
+ if pdi_config:
+ pdi_dataset = get_pdi_ds(pdi_config.get('name', DEFAULTS['pdi']), pdi_config.get('licenced', False))
+ for edge in result['network']['edges']:
+ if (edge['from'][:2] == 'dr'):
+ drug = edge['from']
+ edge['from'] = edge['to']
+ edge['to'] = drug
+ if (edge['to'][:2] == 'dr'):
+ drug_id = int(edge['to'][2:])
+ pdi_object = ProteinDrugInteraction.objects.filter(
+ protein_id__in={int(p[1:]) for p in node_attributes['details'][edge['from']]['drugstone_id']},
+ drug_id=drug_id, pdi_dataset_id=pdi_dataset.id)
+ actions = set()
+ for pdi in pdi_object:
+ if pdi.actions:
+ for action in json.loads(pdi.actions):
+ actions.add(action)
+ edge['actions'] = list(actions)
+
if 'autofill_edges' in parameters['config'] and parameters['config']['autofill_edges']:
prots = list(filter(lambda n: n['drugstone_type'] == 'protein',
filter(lambda n: 'drugstone_type' in n and node_name_attribute in n,
@@ -704,11 +725,13 @@ def save_selection(request) -> Response:
config = request.data.get("config")
network = request.data.get("network")
- Network.objects.create(id=token_str, config=json.dumps(config), nodes=json.dumps(network["nodes"]), edges=json.dumps(network["edges"]))
+ Network.objects.create(id=token_str, config=json.dumps(config), nodes=json.dumps(network["nodes"]),
+ edges=json.dumps(network["edges"]))
return Response({
'token': token_str,
})
+
@api_view(['GET'])
def get_view(request) -> Response:
token = request.query_params.get('token')
@@ -726,7 +749,7 @@ def get_view(request) -> Response:
@api_view(['POST'])
def get_view_infos(request) -> Response:
tokens = request.data.get('tokens')
- networks = Network.objects.filter(id__in = tokens)
+ networks = Network.objects.filter(id__in=tokens)
return Response([{
'token': n.id,
'created_at': n.created_at,
diff --git a/requirements.txt b/requirements.txt
index 9763ecd..fd90bc8 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,7 +5,7 @@ chardet==3.0.4
click==8.1.3
cryptography==39.0.1
decorator==4.4.2
-Django==3.2.18
+Django==3.2.19
django-cors-headers==3.4.0
django-redis==4.11.0
django-rq-dashboard==0.3.3
@@ -19,7 +19,7 @@ mccabe==0.6.1
networkx==3.1
numpy==1.23.5
pandas==1.3.5
-pillow==9.3.0
+pillow==9.4.0
psycopg2-binary==2.8.6
pycodestyle==2.5.0
pyflakes==2.1.1
@@ -30,5 +30,5 @@ requests==2.28.1
rq==1.11.1
six==1.15.0
sqlalchemy==1.3.23
-sqlparse==0.4.2
+sqlparse==0.4.4
urllib3==1.26.12
--
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