Merge branch 'production' into 'development'

Production

See merge request !2

Former-commit-id: d17d283f

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/
 

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

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

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']
 

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),

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.

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"