From 0365b931057d8b5cb8843c8aee5d46b8f58e761b Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Thu, 7 Jul 2022 18:22:22 +0200
Subject: [PATCH] basic adjacency calls checked
Former-commit-id: f339fe90455c5a08947506de7d39d6137eee031f [formerly 0aace5168588fbcc985194394deebd1e92d5f442]
Former-commit-id: 86a31f5b29f95ef9a3a35f54f4ae33b12172504a
---
.../management/includes/DataPopulator.py | 2 +
drugstone/urls.py | 4 +-
drugstone/views.py | 158 +++++++++---------
scripts/docker-entrypoint.sh | 2 +-
4 files changed, 84 insertions(+), 82 deletions(-)
diff --git a/drugstone/management/includes/DataPopulator.py b/drugstone/management/includes/DataPopulator.py
index e01fca1..01715b4 100755
--- a/drugstone/management/includes/DataPopulator.py
+++ b/drugstone/management/includes/DataPopulator.py
@@ -240,12 +240,14 @@ class DataPopulator:
# try fetching protein
drug = self.cache.get_drug_by_drugbank(row['drugbank_id'])
except KeyError:
+ print(f"Did not find drug: {row['drugbank_id']}")
# continue if not found
continue
try:
# try fetching drug
disorder = self.cache.get_disorder_by_mondo(row['mondo_id'])
except KeyError:
+ print(f"Did not find drug: {row['mondo_id']}")
# continue if not found
continue
if not update or (self.cache.is_new_drug(drug) or self.cache.is_new_disease(disorder)):
diff --git a/drugstone/urls.py b/drugstone/urls.py
index 0ef44ab..4de3852 100755
--- a/drugstone/urls.py
+++ b/drugstone/urls.py
@@ -16,7 +16,7 @@ Including another URLconf
from django.contrib import admin
from django.urls import path
-from drugstone.views import ProteinDrugInteractionView, map_nodes, tasks_view, result_view, \
+from drugstone.views import map_nodes, tasks_view, result_view, \
graph_export, query_proteins, TissueView, TissueExpressionView, query_tissue_proteins, TaskView, \
adjacent_drugs, adjacent_disorders, fetch_edges, create_network, load_network
@@ -33,7 +33,7 @@ urlpatterns = [
path('query_tissue_proteins/', query_tissue_proteins),
path('adjacent_drugs/', adjacent_drugs),
path('adjacent_disorders/', adjacent_disorders),
- path('drug_interactions/', ProteinDrugInteractionView.as_view()),
+ # path('drug_interactions/', ProteinDrugInteractionView.as_view()),
path('tissue_expression/', TissueExpressionView.as_view()),
path('tissues/', TissueView.as_view()),
path('admin/', admin.site.urls),
diff --git a/drugstone/views.py b/drugstone/views.py
index 7822f3a..c081718 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -20,7 +20,7 @@ from drugstone import models
from drugstone import serializers
from drugstone.models import Protein, Task, ProteinDrugInteraction, \
- Drug, Tissue, ExpressionLevel, Network, ProteinDisorderAssociation, DrugDisorderIndication, Disorder
+ 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
@@ -71,60 +71,60 @@ from drugstone.backend_tasks import start_task, refresh_from_redis, task_stats,
# return Response(network)
-class ProteinDrugInteractionView(APIView):
- """
- Protein-Drug-Interaction Network
- """
-
- def get(self, request) -> Response:
- if request.query_params.get('proteins'):
- print("getting drugs for proteins")
- protein_ac_list = json.loads(request.query_params.get('proteins'))
- proteins = list(Protein.objects.filter(uniprot_code__in=protein_ac_list).all())
- else:
- proteins = []
- task = Task.objects.get(token=request.query_params['token'])
- result = task_result(task)
- network = result['network']
- node_attributes = result.get('node_attributes')
- if not node_attributes:
- node_attributes = {}
- node_types = node_attributes.get('node_types')
- if not node_types:
- node_types = {}
- nodes = network['nodes']
- for node in nodes:
- node_type = node_types.get(node)
- details = None
- # if not node_type:
- # print('we should not see this 1')
- # node_type, details = infer_node_type_and_details(node)
- if node_type == 'protein':
- if details:
- proteins.append(details)
- else:
- try:
- proteins.append(Protein.objects.get(uniprot_code=node))
- except Protein.DoesNotExist:
- pass
-
- pd_interactions = []
- drugs = []
-
- for protein in proteins:
- pdi_object_list = ProteinDrugInteraction.objects.filter(protein=protein)
- for pdi_object in pdi_object_list:
- pd_interactions.append(pdi_object)
- drug = pdi_object.drug
- if drug not in drugs:
- drugs.append(drug)
-
- protein_drug_edges = {
- 'proteins': ProteinSerializer(many=True).to_representation(proteins),
- 'drugs': DrugSerializer(many=True).to_representation(drugs),
- 'edges': ProteinDrugInteractionSerializer(many=True).to_representation(pd_interactions),
- }
- return Response(protein_drug_edges)
+# class ProteinDrugInteractionView(APIView):
+# """
+# Protein-Drug-Interaction Network
+# """
+#
+# def get(self, request) -> Response:
+# if request.query_params.get('proteins'):
+# print("getting drugs for proteins")
+# protein_ac_list = json.loads(request.query_params.get('proteins'))
+# proteins = list(Protein.objects.filter(uniprot_code__in=protein_ac_list).all())
+# else:
+# proteins = []
+# task = Task.objects.get(token=request.query_params['token'])
+# result = task_result(task)
+# network = result['network']
+# node_attributes = result.get('node_attributes')
+# if not node_attributes:
+# node_attributes = {}
+# node_types = node_attributes.get('node_types')
+# if not node_types:
+# node_types = {}
+# nodes = network['nodes']
+# for node in nodes:
+# node_type = node_types.get(node)
+# details = None
+# # if not node_type:
+# # print('we should not see this 1')
+# # node_type, details = infer_node_type_and_details(node)
+# if node_type == 'protein':
+# if details:
+# proteins.append(details)
+# else:
+# try:
+# proteins.append(Protein.objects.get(uniprot_code=node))
+# except Protein.DoesNotExist:
+# pass
+#
+# pd_interactions = []
+# drugs = []
+#
+# for protein in proteins:
+# pdi_object_list = ProteinDrugInteraction.objects.filter(protein=protein)
+# for pdi_object in pdi_object_list:
+# pd_interactions.append(pdi_object)
+# drug = pdi_object.drug
+# if drug not in drugs:
+# drugs.append(drug)
+#
+# protein_drug_edges = {
+# 'proteins': ProteinSerializer(many=True).to_representation(proteins),
+# 'drugs': DrugSerializer(many=True).to_representation(drugs),
+# 'edges': ProteinDrugInteractionSerializer(many=True).to_representation(pd_interactions),
+# }
+# return Response(protein_drug_edges)
class TaskView(APIView):
@@ -179,7 +179,7 @@ def fetch_edges(request) -> Response:
"""
dataset = request.data.get('dataset', 'STRING')
drugstone_ids = [node['drugstone_id'][1:] for node in request.data.get('nodes', '[]') if 'drugstone_id' in node]
- dataset_object = models.PPIDataset.objects.get(name__iexact=dataset)
+ 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=drugstone_ids) & Q(to_protein__in=drugstone_ids))
@@ -250,23 +250,23 @@ def tasks_view(request) -> Response:
return Response(tasks_info)
-def infer_node_type_and_details(node) -> Tuple[str, Protein or Drug]:
- node_type_indicator = node[0]
- if node_type_indicator == 'p':
- node_id = int(node[1:])
- # protein
- prot = Protein.objects.get(id=node_id)
- return 'protein', prot
- elif node_type_indicator == 'd':
- node_id = int(node[2:])
- # drug
- if node_id[0] == 'r':
- drug = Drug.objects.get(id=node_id[1:])
- return 'drug', drug
- elif node_id[0] == 'i':
- disorder = Disorder.objects.get(id=node_id[1:])
- return 'disorder', disorder
- return None, None
+# def infer_node_type_and_details(node) -> Tuple[str, Protein or Drug]:
+# node_type_indicator = node[0]
+# if node_type_indicator == 'p':
+# node_id = int(node[1:])
+# # protein
+# prot = Protein.objects.get(id=node_id)
+# return 'protein', prot
+# elif node_type_indicator == 'd':
+# node_id = int(node[2:])
+# # drug
+# if node_id[0] == 'r':
+# drug = Drug.objects.get(id=node_id[1:])
+# return 'drug', drug
+# elif node_id[0] == 'i':
+# disorder = Disorder.objects.get(id=node_id[1:])
+# return 'disorder', disorder
+# return None, None
@api_view(['POST'])
@@ -531,20 +531,20 @@ def adjacent_disorders(request) -> Response:
data = request.data
if 'proteins' in data:
drugstone_ids = data.get('proteins', [])
- pdi_dataset = data.get('dataset','DisGeNET')
+ 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__name=pdi_dataset)
+ pdis_dataset=pdi_dataset)
disorders = {e.disorder for e in pdis_objects}
# serialize
edges = ProteinDisorderAssociationSerializer(many=True).to_representation(pdis_objects)
disorders = DisorderSerializer(many=True).to_representation(disorders)
elif 'drugs' in data:
drugstone_ids = data.get('drugs', [])
- drdi_dataset = data.get('dataset','DrugBank')
+ 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__name=drdi_dataset)
+ drdi_dataset=drdi_dataset)
disorders = {e.disorder for e in drdi_objects}
# serialize
edges = DrugDisorderIndicationSerializer(many=True).to_representation(drdi_objects)
@@ -567,9 +567,9 @@ def adjacent_drugs(request) -> Response:
"""
data = request.data
drugstone_ids = data.get('proteins', [])
- pdi_dataset = data.get('pdi_dataset')
+ 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__name=pdi_dataset)
+ pdi_objects = ProteinDrugInteraction.objects.filter(protein__id__in=drugstone_ids, pdi_dataset=pdi_dataset)
drugs = {e.drug for e in pdi_objects}
# serialize
pdis = ProteinDrugInteractionSerializer(many=True).to_representation(pdi_objects)
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 796f1ce..df4a830 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 -a --update
+#python3 manage.py populate_db -u --all
#python3 manage.py make_graphs
/usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"
--
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