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Commit 2932cfbf authored by AndiMajore's avatar AndiMajore
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try to fix tissue expression route

Former-commit-id: 5ab77506
parent 8a24c048
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......@@ -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),
......
......@@ -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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