From 2932cfbf5fea44ca3f400e7d98d26a3e0b9879f8 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Fri, 4 Nov 2022 21:51:48 +0100
Subject: [PATCH] try to fix tissue expression route
Former-commit-id: 5ab775066d99450d2c685c41f6bb187b11f02033
---
drugstone/urls.py | 6 +--
drugstone/views.py | 93 +++++++++++++++++++++-------------------------
2 files changed, 46 insertions(+), 53 deletions(-)
diff --git a/drugstone/urls.py b/drugstone/urls.py
index 7e0d16a..a24a252 100755
--- a/drugstone/urls.py
+++ b/drugstone/urls.py
@@ -17,9 +17,9 @@ from django.contrib import admin
from django.urls import path
from drugstone.views import map_nodes, tasks_view, result_view, \
- graph_export, TissueView, TissueExpressionView, query_tissue_proteins, TaskView, \
+ graph_export, TissueView, query_tissue_proteins, TaskView, \
adjacent_drugs, adjacent_disorders, fetch_edges, create_network, load_network, get_license, get_datasets, \
- get_max_tissue_expression
+ get_max_tissue_expression, get_tissue_expression
# cache time is 6 hours
urlpatterns = [
@@ -33,7 +33,7 @@ urlpatterns = [
path('query_tissue_proteins/', query_tissue_proteins),
path('adjacent_drugs/', adjacent_drugs),
path('adjacent_disorders/', adjacent_disorders),
- path('tissue_expression/', TissueExpressionView.as_view()),
+ path('tissue_expression/', get_tissue_expression),
path('tissue_max_expression/', get_max_tissue_expression),
path('tissues/', TissueView.as_view()),
path('admin/', admin.site.urls),
diff --git a/drugstone/views.py b/drugstone/views.py
index 7dc744d..8957ffe 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -653,56 +653,49 @@ class TissueView(APIView):
return Response(TissueSerializer(many=True).to_representation(tissues))
-class TissueExpressionView(APIView):
- """
- Expression of host proteins in tissues.
- """
-
- def get(self, request) -> Response:
- return self.post(request)
+@api_view(['POST', 'GET'])
+def get_tissue_expression(request) -> Response:
+ tissue = Tissue.objects.get(id=request.query_params.get('tissue'))
- def post(self, request) -> Response:
- tissue = Tissue.objects.get(id=request.query_params.get('tissue'))
-
- if request.query_params.get('proteins'):
- ids = json.loads(request.query_params.get('proteins'))
- proteins = list(Protein.objects.filter(id__in=ids).all())
- elif request.query_params.get('token'):
- 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 = {}
- parameters = json.loads(task.parameters)
- seeds = parameters['seeds']
- nodes = network['nodes']
- for node in nodes + seeds:
- node_type = node_types.get(node)
- details = None
- if node_type == 'protein':
- if details:
- proteins.append(details)
- else:
- try:
- prot = Protein.objects.get(uniprot_code=node)
- if prot not in proteins:
- proteins.append(Protein.objects.get(uniprot_code=node))
- except Protein.DoesNotExist:
- pass
-
- pt_expressions = {}
-
- for protein in proteins:
- try:
- expression_level = ExpressionLevel.objects.get(protein=protein, tissue=tissue)
- pt_expressions[
- ProteinSerializer().to_representation(protein)['drugstone_id']] = expression_level.expression_level
- except ExpressionLevel.DoesNotExist:
- pt_expressions[ProteinSerializer().to_representation(protein)['drugstone_id']] = None
+ if request.query_params.get('proteins'):
+ ids = json.loads(request.query_params.get('proteins'))
+ proteins = list(Protein.objects.filter(id__in=ids).all())
+ elif request.query_params.get('token'):
+ 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 = {}
+ parameters = json.loads(task.parameters)
+ seeds = parameters['seeds']
+ nodes = network['nodes']
+ for node in nodes + seeds:
+ node_type = node_types.get(node)
+ details = None
+ if node_type == 'protein':
+ if details:
+ proteins.append(details)
+ else:
+ try:
+ prot = Protein.objects.get(uniprot_code=node)
+ if prot not in proteins:
+ proteins.append(Protein.objects.get(uniprot_code=node))
+ except Protein.DoesNotExist:
+ pass
+
+ pt_expressions = {}
+
+ for protein in proteins:
+ try:
+ expression_level = ExpressionLevel.objects.get(protein=protein, tissue=tissue)
+ pt_expressions[
+ ProteinSerializer().to_representation(protein)['drugstone_id']] = expression_level.expression_level
+ except ExpressionLevel.DoesNotExist:
+ pt_expressions[ProteinSerializer().to_representation(protein)['drugstone_id']] = None
return Response(pt_expressions)
--
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