Sources api

.gitignore

@@ -81,6 +81,7 @@ celerybeat-schedule
 
 # dotenv
 .env
+prod.env
 
 # virtualenv
 .venv

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "libs/stringdb-tools"]
 	path = libs/stringdb-tools
 	url = https://github.com/bielr/stringdb-tools.git
+[submodule "libs/ppi-sources"]
+	path = libs/ppi-sources
+	url = https://github.com/biocom-uib/ppi-sources

dev.env

@@ -0,0 +1,11 @@
+CELERY_BROKER_URL=amqp://util-aligner:util-aligner@rabbitmq:5672//
+CELERY_TASK_TIME_LIMIT=
+SERVER_ALIGNER_CONCURRENCY=1
+
+FINISHED_ALIGNMENT_URL=http://util-aligner-api/v2/finished-alignment
+FINISHED_COMPARISON_URL=http://util-aligner-api/v2/finished-comparison
+
+RABBITMQ_DEFAULT_USER=util-aligner
+RABBITMQ_DEFAULT_PASS=util-aligner
+
+SOURCES_API_URL=http://ltimbigd2.uib.es:11080/

docker-compose.dev.yml

@@ -0,0 +1,24 @@
+version: '3'
+
+services:
+  server-aligner:
+    env_file:
+      - dev.env
+    networks:
+      - util-aligner-net
+
+  server-comparer:
+    env_file:
+      - dev.env
+    networks:
+      - util-aligner-net
+
+  rabbitmq:
+    env_file:
+      - dev.env
+    networks:
+      - util-aligner-net
+
+networks:
+  util-aligner-net:
+    external: true

docker-compose.prod.yml

@@ -0,0 +1,30 @@
+version: '3'
+
+services:
+  server-aligner:
+    env_file:
+      - prod.env
+    networks:
+      - sources-net
+
+
+  server-comparer:
+    env_file:
+      - prod.env
+    networks:
+      - sources-net
+
+  rabbitmq:
+    env_file:
+      - prod.env
+    ports:
+      - 15672:15672
+      - 5672:5672
+
+  mongo:
+    ports:
+      - 27017:27017
+
+networks:
+  sources-net:
+    external: true

docker-compose.yml

@@ -1,137 +1,95 @@
 version: '3'
 
 services:
-    server-aligner:
-      build:
-        context: .
-        dockerfile: ./docker/Dockerfile
-      depends_on:
-        - rabbitmq
-        - mysql
-        - mongo
-      command:
-        - celery
-        - -A
-        - server_queue
-        - worker
-        - -Q
-        - server_aligner
-        - -l
-        - info
-        - -c
-        - "8"
-      volumes:
-        - .:/opt/:rw
-      environment:
-        - CELERY_BROKER_URL=${CELERY_BROKER_URL}
-        - CELERY_TASK_DEFAULT_QUEUE=server_aligner
-        - CELERY_TASK_TIME_LIMIT=
-        - FINISHED_ALIGNMENT_URL=${FINISHED_ALIGNMENT_URL}
-        - FINISHED_COMPARISON_URL=${FINISHED_COMPARISON_URL}
-      networks:
-        server-net:
-          ipv4_address: 172.20.0.2
-          aliases: [server]
-        stringdb-net:
-        geneontology-net:
+  server-aligner:
+    image: bielr/util-aligner-server:0.2
+    restart: unless-stopped
+    build:
+      context: ./docker
+      dockerfile: ./Dockerfile
+    depends_on:
+      - rabbitmq
+      - mongo
+    command:
+      - celery
+      - -A
+      - server_queue
+      - worker
+      - -Q
+      - server_aligner
+      - -l
+      - info
+      - -c
+      - "${SERVER_ALIGNER_CONCURRENCY:?SERVER_ALIGNER_CONCURRENCY not set in .env}"
+    volumes:
+      - .:/opt/:rw
+    environment:
+      - CELERY_TASK_DEFAULT_QUEUE=server_aligner
+    networks:
+      server-net:
+        ipv4_address: 172.20.0.2
+        aliases: [server-aligner]
 
-    server-comparer:
-      build:
-        context: .
-        dockerfile: ./docker/Dockerfile
-      depends_on:
-        - rabbitmq
-        - mysql
-        - mongo
-      command:
-        - celery
-        - -A
-        - server_queue
-        - worker
-        - -Q
-        - server_comparer
-        - -l
-        - info
-        - -c
-        - "1"
-      volumes:
-        - .:/opt/:rw
-      environment:
-        - CELERY_BROKER_URL=${CELERY_BROKER_URL}
-        - CELERY_TASK_DEFAULT_QUEUE=server_comparer
-        - CELERY_TASK_TIME_LIMIT=
-        - FINISHED_ALIGNMENT_URL=${FINISHED_ALIGNMENT_URL}
-        - FINISHED_COMPARISON_URL=${FINISHED_COMPARISON_URL}
-      networks:
-        server-net:
-          ipv4_address: 172.20.0.3
-          aliases: [server]
-        stringdb-net:
-        geneontology-net:
+  server-comparer:
+    image: bielr/util-aligner-server:0.2
+    restart: unless-stopped
+    # build:
+    #   context: ./docker
+    #   dockerfile: ./Dockerfile
+    depends_on:
+      - rabbitmq
+      - mongo
+    command:
+      - celery
+      - -A
+      - server_queue
+      - worker
+      - -Q
+      - server_comparer
+      - -l
+      - info
+    volumes:
+      - .:/opt/:rw
+    environment:
+      - CELERY_TASK_DEFAULT_QUEUE=server_comparer
+    networks:
+      server-net:
+        ipv4_address: 172.20.0.3
+        aliases: [server-comparer]
 
-    mysql:
-      image: mysql:5.7.17
-      ports:
-        - 3306:3306
-      command:
-        - --character-set-server=utf8
-        - --collation-server=utf8_unicode_ci
-        - --skip-character-set-client-handshake
-        - --bind-address=0.0.0.0
-      volumes:
-        - mysql-data:/var/lib/mysql
-        - ./dumps:/opt/dumps
-        - ./mysql-initdb.d:/docker-entrypoint-initdb.d:ro
-      environment:
-        - MYSQL_ROOT_PASSWORD=root
-        - MYSQL_DATABASE=protein_db
-      networks:
-        server-net:
-          ipv4_address: 172.20.0.4
-          aliases: [mysql]
+  rabbitmq:
+    image: rabbitmq:3-management-alpine
+    restart: unless-stopped
+    networks:
+      server-net:
+        ipv4_address: 172.20.0.5
+        aliases: [rabbitmq]
 
-    rabbitmq:
-      image: rabbitmq:3-management-alpine
-      ports:
-        - 15672:15672
-        - 5672:5672
-      environment:
-        - RABBITMQ_DEFAULT_USER
-        - RABBITMQ_DEFAULT_PASS
-      networks:
-        server-net:
-          ipv4_address: 172.20.0.5
-          aliases: [rabbitmq]
-
-    mongo:
-      image: mongo:latest
-      command:
-        - mongod
-        - --storageEngine=mmapv1
-        - --auth
-        - --bind_ip_all
-      security_opt:
-        - seccomp:seccomp_numa.json
-      ports:
-        - 27017:27017
-      volumes:
-        - mongo-data:/data/db
-        - ./mongo-initdb.d:/docker-entrypoint-initdb.d:ro
-      networks:
-        server-net:
-          ipv4_address: 172.20.0.6
-          aliases: [mongo]
+  mongo:
+    image: mongo:latest
+    restart: unless-stopped
+    command:
+      - mongod
+      - --storageEngine=wiredTiger
+      - --auth
+      - --bind_ip_all
+      - --logpath
+      - /var/log/mongodb/mongod.log
+    security_opt:
+      - seccomp:seccomp_numa.json
+    volumes:
+      - mongo-data:/data/db
+      - ./mongo-initdb.d:/docker-entrypoint-initdb.d:ro
+    networks:
+      server-net:
+        ipv4_address: 172.20.0.6
+        aliases: [mongo]
 
 volumes:
-  mysql-data:
   mongo-data:
 
 networks:
   server-net:
     ipam:
       config:
         - subnet: 172.20.0.0/24
-  stringdb-net:
-    external: true
-  geneontology-net:
-    external: true

docker/Dockerfile

@@ -1,19 +1,32 @@
-FROM bielr/util-aligner-server
+FROM python:3.9
 
 ARG APP_ENV=base
 
 ENV APP_ENV=$APP_ENV
 ENV PYTHONUNBUFFERED=1
+ENV DEBIAN_FRONTEND=noninteractive
 
 COPY ./requirements /requirements
 COPY ./r-requirements /r-requirements
 
+RUN apt-get update && apt-get -y install tzdata
+RUN ln -fs /usr/share/zoneinfo/Europe/Madrid /etc/localtime
+RUN dpkg-reconfigure --frontend noninteractive tzdata
+
+RUN apt-get update \
+    && apt-get -y install build-essential libxml2-dev zlib1g-dev pkg-config libffi6 libffi-dev libssl-dev libcurl4-openssl-dev \
+                          r-base gfortran \
+                          libc6-i386 lib32stdc++6
+
+RUN python3.9 -m pip install pip --upgrade
+RUN python3.9 -m pip install wheel
 RUN pip install -r /requirements/${APP_ENV}.txt
 
 RUN Rscript --vanilla /r-requirements/${APP_ENV}.R
 
 CMD ["bash"]
 
-ENV PYTHONPATH /opt/server:/opt/libs/stringdb-tools/scripts:/opt/libs/geneontology-tools/scripts:/opt/libs/semantic-similarity
+
+ENV PYTHONPATH /opt/server:/opt/libs/stringdb-tools/scripts:/opt/libs/geneontology-tools/scripts:/opt/libs/semantic-similarity:/opt/libs/ppi-sources
 WORKDIR /opt
 

docker/Dockerfile_cached

@@ -0,0 +1,19 @@
+FROM bielr/util-aligner-server
+
+ARG APP_ENV=base
+
+ENV APP_ENV=$APP_ENV
+ENV PYTHONUNBUFFERED=1
+
+COPY ./requirements /requirements
+COPY ./r-requirements /r-requirements
+
+RUN pip install -r /requirements/${APP_ENV}.txt
+
+RUN Rscript --vanilla /r-requirements/${APP_ENV}.R
+
+CMD ["bash"]
+
+ENV PYTHONPATH /opt/server:/opt/libs/stringdb-tools/scripts:/opt/libs/geneontology-tools/scripts:/opt/libs/semantic-similarity:/opt/libs/ppi-sources
+WORKDIR /opt
+

r-requirements/base.R → docker/r-requirements/base.R

@@ -9,4 +9,4 @@ install.packages('clue', verbose=TRUE)
 install.packages('plyr', verbose=TRUE)
 install.packages('lpSolveAPI', verbose=TRUE)
 library(devtools)
-install_github("adriaalcala/AligNet", build_vignettes=TRUE)
+install_github("adriaalcala/AligNet", build_vignettes=FALSE)