diff --git a/Dockerfile b/Dockerfile
index eb9ebfffb77c09b84161efdf55f95991221d3c07..6abc552ed463399196d426fb23663921f759c811 100755
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,7 +21,7 @@ COPY ./requirements.txt /usr/src/drugstone/requirements.txt
RUN pip install -r /usr/src/drugstone/requirements.txt
COPY ./supervisord.conf /etc/supervisor/conf.d/supervisord.conf
-RUN pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple nedrex==0.1.4
+RUN pip install nedrex
COPY . /usr/src/drugstone/
diff --git a/docker-compose-prod.yml b/docker-compose-prod.yml
index cb01d8975c389a6f3d57b3e3046e6ab395d7b833..8de915488bad2a74c95f9e4f9d61a38c59ae8cbf 100755
--- a/docker-compose-prod.yml
+++ b/docker-compose-prod.yml
@@ -33,7 +33,7 @@ services:
labels:
- "com.centurylinklabs.watchtower.enable=true"
db:
- image: postgres
+ image: postgres:14
container_name: drugstone_postgres
restart: always
hostname: drugstone_postgres
diff --git a/drugstone/management/commands/make_graphs.py b/drugstone/management/commands/make_graphs.py
index 5a1f6ecdb01ccf9277f8ca70ca2322b1dd398dff..1a13741dc17a9d1bab5ef5bb6634580924e86baf 100755
--- a/drugstone/management/commands/make_graphs.py
+++ b/drugstone/management/commands/make_graphs.py
@@ -254,7 +254,7 @@ class Command(BaseCommand):
if hash in uniq_combis:
continue
uniq_combis.add(hash)
- for identifier in ['ensg', 'symbol', 'ensembl', 'uniprot']:
+ for identifier in ['ensg', 'symbol', 'entrez', 'uniprot']:
parameter_combinations.append([ppi_ds, pdi_ds, identifier])
# close all database connections so subprocesses will create their own connections
# this prevents the processes from running into problems because of using the same connection
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 429cf6fc97b2fbc0ba07ec9b1051188b227ae9c0..94f64ce26a18c2afff81b2c5ef2e754a40f8aa25 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/drugstone/management/commands/populate_db.py
@@ -86,8 +86,8 @@ class Command(BaseCommand):
def populate(kwargs):
- nedrex_api_url_unlicenced= "http://82.148.225.92:7123/"
- nedrex_api_url_licenced = "http://82.148.225.92:8123/"
+ nedrex_api_url_unlicenced= "https://nedrex-api-open.zbh.uni-hamburg.de/"
+ nedrex_api_url_licenced = "https://nedrex-api-licenced.zbh.uni-hamburg.de/"
data_dir = kwargs['data_dir']
diff --git a/drugstone/urls.py b/drugstone/urls.py
index a2e5786b93670d486a922e0bd03c6d703c85b12a..886dbdd75f3ba34cc6fe475760096a12eee94879 100755
--- a/drugstone/urls.py
+++ b/drugstone/urls.py
@@ -18,7 +18,8 @@ from django.urls import path
from drugstone.views import map_nodes, tasks_view, result_view, \
graph_export, TissueView, TissueExpressionView, query_tissue_proteins, TaskView, \
- adjacent_drugs, adjacent_disorders, fetch_edges, create_network, load_network, get_license, get_datasets
+ adjacent_drugs, adjacent_disorders, fetch_edges, create_network, load_network, get_license, get_datasets, \
+ get_max_tissue_expression
# cache time is 6 hours
urlpatterns = [
@@ -33,6 +34,7 @@ urlpatterns = [
path('adjacent_drugs/', adjacent_drugs),
path('adjacent_disorders/', adjacent_disorders),
path('tissue_expression/', TissueExpressionView.as_view()),
+ path('tissue_max_expression/', get_max_tissue_expression()),
path('tissues/', TissueView.as_view()),
path('admin/', admin.site.urls),
path('create_network', create_network),
diff --git a/drugstone/views.py b/drugstone/views.py
index b2ef1ea245a923e0cf3d469d3245fe723a539bc4..57597b8f88d88aff18f9ce37951af149431edeac 100755
--- a/drugstone/views.py
+++ b/drugstone/views.py
@@ -4,12 +4,13 @@ import string
import time
import uuid
from collections import defaultdict
+from functools import reduce
import pandas as pd
import networkx as nx
from django.http import HttpResponse
-from django.db.models import Q
+from django.db.models import Q, Max
from django.db import IntegrityError
from rest_framework.decorators import api_view
from rest_framework.response import Response
@@ -415,18 +416,21 @@ def result_view(request) -> Response:
return Response(result)
else:
if view == 'proteins':
+ proteins = list(
+ filter(lambda n: 'drugstone_type' in n and n['drugstone_type'] == 'protein', node_details.values()))
if fmt == 'csv':
items = []
for i in proteins:
new_i = {
- 'uniprot_ac': i['uniprot_ac'],
- 'gene': i['symbol'],
- 'name': i['protein_name'],
- 'ensg': i['ensg'],
- 'entrez': i['entrez'],
- 'seed': is_seed[i[node_name_attribute]],
+ 'id': i['id'],
+ 'uniprot_ac': i['uniprot_ac'] if 'uniprot_ac' in i else [],
+ 'gene': i['symbol'] if 'symbol' in i else [],
+ 'name': i['protein_name'] if 'protein_name' in i else [],
+ 'ensembl': i['ensg'] if 'ensg' in i else [],
+ 'entrez': i['entrez'] if 'entrez' in i else [],
+ 'seed': is_seed[i['id']],
}
- if i.get('score'):
+ if 'score' in i:
new_i['score'] = i['score']
items.append(new_i)
else:
@@ -468,11 +472,6 @@ def graph_export(request) -> Response:
G = nx.Graph()
node_map = dict()
for node in nodes:
- # drugstone_id is not interesting outside of drugstone
- # try:
- # del node['drugstone_id']
- # except KeyError:
- # pass
# networkx does not support datatypes such as lists or dicts
for key in list(node.keys()):
if isinstance(node[key], list) or isinstance(node[key], dict):
@@ -507,7 +506,23 @@ def graph_export(request) -> Response:
data = nx.generate_graphml(G)
response = HttpResponse(data, content_type='application/xml')
elif fmt == 'json':
- data = json.dumps(nx.readwrite.json_graph.node_link_data(G))
+ data = nx.readwrite.json_graph.node_link_data(G)
+ del data['graph']
+ del data['multigraph']
+ remove_node_properties = ['color', 'shape', 'border_width', 'group_name', 'border_width_selected', 'shadow',
+ 'group_id', 'drugstone_type', 'font']
+ remove_edge_properties = ['group_name', 'color', 'dashes', 'shadow', 'id']
+ for node in data['nodes']:
+ for prop in remove_node_properties:
+ if prop in node:
+ del node[prop]
+ for edge in data['links']:
+ for prop in remove_edge_properties:
+ if prop in edge:
+ del edge[prop]
+ data["edges"] = data.pop("links")
+ data = json.dumps(data)
+ data = data.replace('"{', '{').replace('}"', '}').replace('"[', '[').replace(']"', ']').replace('\\"', '"')
response = HttpResponse(data, content_type='application/json')
elif fmt == 'csv':
data = pd.DataFrame(nx.to_numpy_array(G), columns=G.nodes(), index=G.nodes())
@@ -612,6 +627,12 @@ def query_proteins(request) -> Response:
})
+@api_view(['GET'])
+def get_max_tissue_expression(request) -> Response:
+ tissue = Tissue.objects.get(id=request.query_params.get('tissue'))
+ return Response({max: ExpressionLevel.objects.filter(tissue=tissue).aggregate(Max('expression_level'))})
+
+
@api_view(['POST'])
def query_tissue_proteins(request) -> Response:
threshold = request.data['threshold']
@@ -632,6 +653,7 @@ class TissueView(APIView):
return Response(TissueSerializer(many=True).to_representation(tissues))
+
class TissueExpressionView(APIView):
"""
Expression of host proteins in tissues.
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 43bf32df3da5898d25d96f8abd734edf4872ea3c..3c90d86f54ec7daebdfb9694939d1038ed24857c 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"