Merge pull request #576 from matthiaskoenig/develop

Minor release: 0.8.0b14

backend/pkdb_app/_version.py

@@ -1,4 +1,4 @@
 """
 Definition of version string.
 """
-__version__ = "0.8.0b13"
+__version__ = "0.8.0b14"

backend/pkdb_app/info_nodes/models.py

@@ -58,6 +58,7 @@ class DTypes(models.TextChoices):
     ntype = models.CharField(null=False, blank=False, choices=NTypes.choices, max_length=20)
     dtype = models.CharField(null=False, blank=False, choices=DTypes.choices, max_length=20)
 
+
     def annotations_strings(self):
         return [f"relation <{annotation.relation}>:, {annotation.term}" for annotation in self.annotations.all()]
 

backend/pkdb_app/info_nodes/serializers.py

@@ -157,6 +157,7 @@ def NTypes():
             "choice": Choice,
         }
 
+
     def update_or_create(self, validated_data, instance=None, update_document=True):
         synonyms_data = validated_data.pop("synonyms", [])
         parents_data = validated_data.pop("parents", [])

backend/requirements.txt

@@ -1,31 +1,31 @@
-pip>=20.0.2
+pip>=20.1.1
 Markdown>=3.1.1
 gunicorn>=20.0.4
 json-logging>=1.0.5
-psycopg2-binary>=2.8.4
+psycopg2-binary>=2.8.5
 
 # django
 Django == 3.0.7
 django-model-utils>=4.0.0
-django-extra-fields>=2.0.2
-django-storages>=1.8
+django-extra-fields>=2.0.3
+django-storages>=1.9.1
 django-filter>=2.2.0
-django-cors-headers>=2.4.0
-django-rest-email-auth
+django-cors-headers>=3.2.1
+django-rest-email-auth>=2.1.0
 
 # REST API
 djangorestframework>=3.11.0
-elasticsearch-dsl==7.1.0
+elasticsearch-dsl==7.2.0
 django-elasticsearch-dsl==7.1.1
 django-elasticsearch-dsl-drf>=0.20.5
 
 # analysis
 ipykernel>=5.1.3
-pandas>=0.25.3
+pandas>=1.0.2
 numpy>=1.18.1
 scipy>=1.4.1
-matplotlib>=3.1.2
-pint>=0.10-1
+matplotlib>=3.2.0
+pint>=0.11
 
--e git://github.com/matthiaskoenig/pkdb_analysis.git@bf6077a4702838886f148c4e70de0b7ec2a3f3b9#egg=pkdb_analysis
+pkdb-analysis>=0.1.5
 

deploy.sh

@@ -39,7 +39,11 @@ echo "-------------------------"
 echo "UPLOAD DATA"
 echo "-------------------------"
 $HOME/envs/pkdb_data/bin/upload_nodes
-$HOME/envs/pkdb_data/bin/upload_studies
+
+# run upload and allow disconnect of connection
+# FIXME: add logging
+nohup $HOME/envs/pkdb_data/bin/upload_studies &
+
 
 
 

docker-compose-develop.yml

@@ -28,11 +28,15 @@ services:
 
   postgres:
     restart: always
-    image: postgres:12.1
+    image: postgres:12.3
     ports:
       - "5433:5432"
     volumes:
       - postgres_data:/var/lib/postgresql/data
+    environment:
+      - POSTGRES_DB=${PKDB_DB_NAME}
+      - POSTGRES_USER=${PKDB_DB_USER}
+      - POSTGRES_PASSWORD=${PKDB_DB_PASSWORD}
 
   elasticsearch:
     restart: always
@@ -47,9 +51,7 @@ services:
       memlock:
         soft: -1
         hard: -1
-
-    image: elasticsearch:7.5.1
-
+    image: elasticsearch:7.7.1
     ports:
       - "9123:9200"
     volumes:

docker-compose-production.yml

@@ -27,15 +27,19 @@ volumes:
 services:
   postgres:
     restart: always
-    image: postgres:12.1
+    image: postgres:12.3
     ports:
       - "5433:5432"
     volumes:
       - postgres_data:/var/lib/postgresql/data
+    environment:
+      - POSTGRES_DB=${PKDB_DB_NAME}
+      - POSTGRES_USER=${PKDB_DB_USER}
+      - POSTGRES_PASSWORD=${PKDB_DB_PASSWORD}
 
   elasticsearch:
     restart: always
-    image: elasticsearch:7.5.1
+    image: elasticsearch:7.7.1
     environment:
       - "ES_JAVA_OPTS=-Xms6g -Xmx6g"
       - bootstrap.memory_lock=true
@@ -86,7 +90,7 @@ services:
 
   nginx:
     restart: always
-    image: nginx:1.17.7
+    image: nginx:1.18.0
     ports:
       - 8888:80
     volumes:

nginx/pk-db.com

@@ -37,11 +37,11 @@ server {
 
         location / {
                 # return 200 "ssl on proxy";
-                proxy_pass http://172.107.0.10:8888;
-                proxy_set_header HOST $host;
-                proxy_set_header X-Real-IP $remote_addr;
-                proxy_set_header X-Forwarded-for $remote_addr;
-                proxy_set_header X-Forwarded-Proto https;
-                port_in_redirect off;
+                proxy_pass http://127.0.0.1:8888;
+                # proxy_set_header HOST $host;
+                # proxy_set_header X-Real-IP $remote_addr;
+                # proxy_set_header X-Forwarded-for $remote_addr;
+                # proxy_set_header X-Forwarded-Proto https;
+                # port_in_redirect off;
         }
 }

nginx/pk-db.com_proxy

@@ -0,0 +1,47 @@
+# ------------------
+# PK-DB
+# ------------------
+access_log /var/www/logs/pk-db.com_access.log;
+error_log /var/www/logs/pk-db.com_error.log;
+
+server {
+    listen 80;
+    listen [::]:80;
+
+    server_name pk-db.com pk-db.de www.pk-db.com www.pk-db.de;
+    return 301 https://pk-db.com$request_uri;
+}
+
+server {
+    listen 443 ssl http2;
+    listen [::]:443 ssl http2;
+
+    server_name www.pk-db.com pk-db.de www.pk-db.de;
+    ssl_certificate     /etc/letsencrypt/live/pk-db.com/fullchain.pem;
+    ssl_certificate_key /etc/letsencrypt/live/pk-db.com/privkey.pem;
+
+    return 301 https://pk-db.com$request_uri;
+}
+
+server {
+        listen 443 ssl http2;
+        listen [::]:443 ssl http2;
+
+        server_name pk-db.com;
+
+        ssl_certificate     /etc/letsencrypt/live/pk-db.com/fullchain.pem;
+        ssl_certificate_key /etc/letsencrypt/live/pk-db.com/privkey.pem;
+        include /etc/nginx/snippets/ssl.conf;
+
+        client_max_body_size 100m;
+
+        location / {
+                # return 200 "ssl on proxy";
+                proxy_pass http://172.107.0.10:8888;
+                proxy_set_header HOST $host;
+                proxy_set_header X-Real-IP $remote_addr;
+                proxy_set_header X-Forwarded-for $remote_addr;
+                proxy_set_header X-Forwarded-Proto https;
+                port_in_redirect off;
+        }
+}

nginx/ssl.conf

@@ -0,0 +1,22 @@
+ssl_session_cache shared:le_nginx_SSL:1m;
+ssl_session_timeout 1440m;
+
+ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
+ssl_prefer_server_ciphers on;
+
+# ssl_ciphers "ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:DHE-RSA-AES128-GCM-SHA256:DHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES128-SHA256:ECDHE-RSA-AES128-SHA256:ECDHE-ECDSA-AES128-SHA:ECDHE-RSA-AES256-SHA384:ECDHE-RSA-AES128-SHA:ECDHE-ECDSA-AES256-SHA384:ECDHE-ECDSA-AES256-SHA:ECDHE-RSA-AES256-SHA:DHE-RSA-AES128-SHA256:DHE-RSA-AES128-SHA:DHE-RSA-AES256-SHA256:DHE-RSA-AES256-SHA:ECDHE-ECDSA-DES-CBC3-SHA:ECDHE-RSA-DES-CBC3-SHA:EDH-RSA-DES-CBC3-SHA:AES128-GCM-SHA256:AES256-GCM-SHA384:AES128-SHA256:AES256-SHA256:AES128-SHA:AES256-SHA:DES-CBC3-SHA:!DSS";
+
+ssl_ciphers EECDH+ECDSA+AESGCM:EECDH+aRSA+AESGCM:EECDH+ECDSA+SHA512:EECDH+ECDSA+SHA384:EECDH+ECDSA+SHA256:ECDH+AESGCM:ECDH+AES256:DH+AESGCM:DH+AES256:RSA+AESGCM:!aNULL:!eNULL:!LOW:!RC4:!3DES:!MD5:!EXP:!PSK:!SRP:!DSS;
+
+ssl_dhparam /etc/ssl/certs/dhparam.pem;
+ssl_ecdh_curve secp384r1; # Requires nginx >= 1.1.0
+
+ssl_session_cache shared:TLS:2m;
+
+# OCSP stapling
+ssl_stapling on;
+ssl_stapling_verify on;
+resolver 8.8.8.8;
+
+# Set HSTS to 365 days
+add_header Strict-Transport-Security 'max-age=31536000; includeSubDomains';