merge

Former-commit-id: 5d58e7f9fcabda96e4c5f13497d96b532b473709 [formerly cc8cc847ae14ce7c696365707b903c7501cac830]
Former-commit-id: 8bb32ba5cfa3abe249c8975b4b7debfc510b7074

deploy_prod.sh

+#!/bin/bash
+
+branch=$(git rev-parse --abbrev-ref HEAD)
+if [ "$branch" == "production" ]; then
 	docker build -t gitlab.rrz.uni-hamburg.de:4567/cosy-bio/drugst.one/backend:prod -f ./Dockerfile .
 	docker push gitlab.rrz.uni-hamburg.de:4567/cosy-bio/drugst.one/backend:prod
+else 
+	echo "DENIED: Your are not in the production branch. Do not push to production from the ${branch} branch."
+fi

docker-compose-prod.yml

+version: '3.3'
+
+services:
+  frontend:
+    container_name: drugstone_frontend
+    image: gitlab.rrz.uni-hamburg.de:4567/cosy-bio/drugst.one/website:prod
+    restart: always
+    ports:
+      - 8031:80
+    networks:
+      - drugstone
+    labels:
+      - "com.centurylinklabs.watchtower.enable=true"
+  backend:
+    image: gitlab.rrz.uni-hamburg.de:4567/cosy-bio/drugst.one/backend:prod
+    container_name: drugstone_backend
+    command: 
+      - "sh"
+      - "scripts/docker-entrypoint.sh"
+    env_file:
+      - 'docker-django.env'
+    restart: always
+    volumes:
+      - drugstone_db_schema_volume:/usr/src/drugstone/drugstone/migrations
+      - drugstone_data_volume:/usr/src/drugstone/data
+    ports:
+      - 8032:8000
+    networks:
+      - drugstone
+    depends_on:
+      - db
+      - redis
+    labels:
+      - "com.centurylinklabs.watchtower.enable=true"
+  db:
+    image: postgres
+    container_name: drugstone_postgres
+    restart: always
+    hostname: drugstone_postgres
+#    ports:
+#      - 5432:5432
+    networks:
+      - drugstone
+    volumes:
+      - drugstone_db_volume:/var/lib/postgresql/data
+    environment:
+      - POSTGRES_DB=drugstone
+      - POSTGRES_USER=drugstone
+      - POSTGRES_PASSWORD=t6278yczAH7rPKVMxaDD
+    command: 
+      - "postgres"
+      - "-c" 
+      - "max_connections=10000"
+      - "-c"
+      - "shared_buffers=2GB"
+  redis:
+    image: redis
+    container_name: drugstone_redis
+    restart: always
+    command: ["redis-server"]
+    networks:
+      - drugstone
+#    ports:
+#      - 6379:6379
+  celery:
+    image: gitlab.rrz.uni-hamburg.de:4567/cosy-bio/drugst.one/backend:prod
+    command:
+      - "sh"
+      - "scripts/start_celery_worker.sh"
+    restart: always
+    container_name: drugstone_celery
+    hostname: drugstone_celery
+    volumes:
+      - drugstone_data_volume:/usr/src/drugstone/data
+    env_file:
+      - './docker-django.env'
+    depends_on:
+      - redis
+      - db
+    networks:
+      - drugstone
+    labels:
+      - "com.centurylinklabs.watchtower.enable=true"
+  celery-beat:
+    image: gitlab.rrz.uni-hamburg.de:4567/cosy-bio/drugst.one/backend:prod
+    command:
+      - "sh"
+      - "scripts/start_celery_beat.sh"
+    container_name: drugstone_celery_beat
+    hostname: drugstone_celery_beat
+    restart: always
+    env_file:
+      - './docker-django.env'
+    depends_on:
+      - redis
+      - db
+    networks:
+      - drugstone
+    labels:
+      - "com.centurylinklabs.watchtower.enable=true"
+  cdn:
+    build: cdn
+    image: drugstone_cdn
+    container_name: drugstone_cdn
+    restart: always
+    volumes:
+      - drugstone_cdn_volume:/app/files
+    ports:
+      - 8033:80
+
+networks:
+  drugstone:
+
+volumes:
+  drugstone_db_volume:
+    external: true
+  drugstone_db_schema_volume:
+    external: true
+  drugstone_data_volume:
+    external: true
+  drugstone_cdn_volume:
+    external: true
\ No newline at end of file

docker-compose.yml

 version: '3.3'
 
 services:
-  app:
+  backend:
     image: drugstone_backend
     container_name: drugstone_backend
     command: 
@@ -72,6 +72,7 @@ services:
     command:
       - "sh"
       - "scripts/start_celery_beat.sh"
+    restart: always
     image: drugstone_backend
     container_name: drugstone_celery_beat
     hostname: drugstone_celery_beat

docker-django.env

@@ -11,3 +11,5 @@ SQL_PORT=5432
 REDIS_HOST=redis
 REDIS_PORT=6379
 GT_THREADS=16
+DJANGO_SETTINGS_MODULE=drugstone.settings
+CELERY_BROKER_URL=redis://redis:6379/0
\ No newline at end of file

drugstone/management/includes/DatasetLoader.py

@@ -146,7 +146,7 @@ def get_drug_target_drugbank():
         name='DrugBank',
         link='https://go.drugbank.com/',
         version='5.1.7',
-        licenced=False
+        licenced=True
     )
     return dataset
 

drugstone/views.py

@@ -375,7 +375,9 @@ def result_view(request) -> Response:
                 detail['ensg'] = list(set(detail['ensg']))
 
     edges = parameters['input_network']['edges']
+
     edge_endpoint_ids = set()
+
     # TODO check for custom edges when working again with ensemble gene ids
     for edge in edges:
         edge_endpoint_ids.add(edge['from'])
@@ -383,11 +385,10 @@ def result_view(request) -> Response:
 
     nodes_mapped, id_key = query_proteins_by_identifier(edge_endpoint_ids, identifier)
 
-
     if 'autofill_edges' in parameters['config'] and parameters['config']['autofill_edges']:
-
         prots = list(filter(lambda n: n['drugstone_type'] == 'protein',
-                filter(lambda n: 'drugstone_type' in n and node_name_attribute in n, parameters['input_network']['nodes'])))
+                            filter(lambda n: 'drugstone_type' in n and node_name_attribute in n,
+                                   parameters['input_network']['nodes'])))
 
         proteins = {node_name[1:] for node in prots for node_name in node[node_name_attribute]}
         dataset = DEFAULTS['ppi'] if 'interaction_protein_protein' not in parameters['config'] else \
@@ -400,7 +401,6 @@ def result_view(request) -> Response:
                               interaction_objects))
         edges.extend(auto_edges)
 
-
     result['network']['edges'].extend(edges)
     uniq_edges = dict()
     for edge in result['network']['edges']:
@@ -530,10 +530,10 @@ def adjacent_disorders(request) -> Response:
     data = request.data
     if 'proteins' in data:
         drugstone_ids = data.get('proteins', [])
-        pdi_dataset = get_pdis_ds(data.get('dataset', DEFAULTS['pdis']), data.get('licenced', False))
+        pdis_dataset = get_pdis_ds(data.get('dataset', DEFAULTS['pdis']), data.get('licenced', False))
         # find adjacent drugs by looking at drug-protein edges
         pdis_objects = ProteinDisorderAssociation.objects.filter(protein__id__in=drugstone_ids,
-                                                                 pdis_dataset_id=pdi_dataset.id)
+                                                                 pdis_dataset_id=pdis_dataset.id)
         disorders = {e.disorder for e in pdis_objects}
         # serialize
         edges = ProteinDisorderAssociationSerializer(many=True).to_representation(pdis_objects)

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 make_graphs
+python3 manage.py populate_db --update -a
+python3 manage.py make_graphs
 
 /usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"

tasks/trust_rank.py

@@ -208,7 +208,6 @@ def trust_rank(task_hook: TaskHook):
     if ppi_dataset['licenced'] or pdi_dataset['licenced']:
         filename += "_licenced"
     filename = os.path.join(task_hook.data_directory, filename+".gt")
-    print(filename)
     g, seed_ids, drug_ids = read_graph_tool_graph(filename, seeds, id_space, max_deg, include_indirect_drugs, include_non_approved_drugs, search_target)
     
     if custom_edges:

tasks/util/read_graph_tool_graph.py

@@ -125,11 +125,6 @@ def read_graph_tool_graph(file_path, seeds, id_space, max_deg, include_indirect_
     for edge in deleted_edges:
         g.remove_edge(edge)
     g.set_fast_edge_removal(fast=False)
-    # vertices = 0
-    # for _ in g.vertices():
-    #     vertices += 1
-    # edges = 0
-    # for _ in g.edges():
-    #     edges += 1
+
     # Return the graph and the indices of the seed_ids and the seeds.
     return g, list(seed_ids.keys()), drug_ids

tasks/util/scores_to_results.py

@@ -45,7 +45,7 @@ def scores_to_results(
 
                 drug_in_path = False
                 for vertex in vertices:
-                    if g.vertex_properties["type"][int(vertex)] == "Drug" and vertex != candidate:
+                    if g.vertex_properties["type"][int(vertex)] == "drug" and vertex != candidate:
                         drug_in_path = True
                         break
                 if drug_in_path:
@@ -67,7 +67,7 @@ def scores_to_results(
 
                 drug_in_path = False
                 for vertex in vertices:
-                    if g.vertex_properties["type"][int(vertex)] == "Drug" and vertex != candidate:
+                    if g.vertex_properties["type"][int(vertex)] == "drug" and vertex != candidate:
                         drug_in_path = True
                         break
                 if drug_in_path: