docker-compose.yml

version: '3.7'
services:

  mysql-for-tomcat:
    image: reactome/reactome-mysql:$RELEASE_VERSION
    build:
      context: ./mysql
      dockerfile: mysql.dockerfile
      args:
        RELEASE_VERSION: $RELEASE_VERSION
    hostname: mysql-for-tomcat
    container_name: mysql-for-tomcat
    env_file:
      - tomcat.env
    volumes:
      - ./mysql/init.sh:/init.sh
      - ./logs/mysql/tomcat:/var/log/mysql
      - mysql-for-tomcat-log:/backup
    command: bash -c "/init.sh && exec /entrypoint.sh mysqld"

  neo4j-db:
    image: "reactome/graphdb:${RELEASE_VERSION}"
    build:
      context: ./neo4j
      dockerfile: neo4j_generated_from_mysql.dockerfile
      args:
        RELEASE_VERSION: $RELEASE_VERSION
    container_name: neo4j-db
    hostname: neo4j-db
    env_file:
      - neo4j.env
    volumes:
      - ./logs/neo4j/:/var/lib/neo4j/logs/
    ports:
      - 7474:7474
      - 7687:7687

  solr:
    image: "reactome/solr:${RELEASE_VERSION}"
    container_name: solr-for-reactome
    hostname: solr-for-reactome
    build:
      context: ./solr
      dockerfile: index-builder.dockerfile
      args:
        RELEASE_VERSION: $RELEASE_VERSION
    ports:
      - 8983:8983
    volumes:
      - ./logs/solr/:/opt/solr/server/logs/:rw
      - ./solr/solr-security.json:/opt/solr/server/solr/security.json:rw
    entrypoint: solr start -f

  tomcat:
    image: reactome/tomcat
    container_name: tomcat-server
    hostname: tomcat-server
    build:
      context: ./tomcat
      dockerfile: tomcat.dockerfile
    depends_on:
      - mysql-for-tomcat
      - joomla-sites
      - neo4j-db
      - solr
    links:
      - mysql-for-tomcat
      - joomla-sites
      - neo4j-db
    entrypoint: bash -c "ls -lht /certs && /wait-for.sh neo4j-db:7687 -t 500 && /wait-for.sh neo4j-db:7474 -t 500 && /wait-for.sh solr-for-reactome:8983 -t 500 && /wait-for.sh mysql-for-tomcat:3306 -t 500 && /wait-for.sh joomla-sites:80 -t 500 && { echo yes | keytool -v -import -file /certs/server.crt -alias joomla-sites -keystore cacerts.jks -keypass changeit -storepass changeit || ( keytool -v -delete -alias joomla-sites -keystore  cacerts.jks -storepass changeit && echo yes | keytool -v -import -file /certs/server.crt -alias joomla-sites -keystore cacerts.jks -keypass changeit -storepass changeit ) ; } && catalina.sh run"
    volumes:
      - fireworks-dir:/usr/local/tomcat/webapps/download/current/fireworks
      - diagrams-dir:/usr/local/tomcat/webapps/download/current/diagram
      - ./wait-for.sh:/wait-for.sh
      - ./tomcat/tomcat-users.xml:/usr/local/tomcat/conf/tomcat-users.xml
      - ./tomcat/tomcat-server.xml:/usr/local/tomcat/conf/server.xml
      - ./tomcat/tomcat-manager.xml:/usr/local/tomcat/conf/Catalina/localhost/manager.xml
      - ./tomcat/analysis-service/results:/usr/local/AnalysisService/analysis-results
      - ./tomcat/analysis-service/reports:/usr/local/AnalysisService/analysis-reports
      - ./logs/applications/AnalysisService:/usr/local/AnalysisService/log
      - ./logs/applications/ContentService:/usr/local/search/log/content-service
      - ./logs/applications/DataContent:/usr/local/search/log/data-content
      - ./logs/tomcat/:/usr/local/tomcat/logs/ #to save logs inside host directory of tomcat/logs/
      - ./certificates:/certs
    env_file:
      - tomcat.env
    ports:
      - 8082:8080

  mysql-for-joomla:
    image: mysql:5.7.24
    hostname: mysql-for-joomla
    container_name: mysql-for-joomla
    env_file:
      - joomla.env
    volumes:
      - ./joomla/Website/database/:/docker-entrypoint-initdb.d
      - ./mysql/init.sh:/init.sh
      - ./logs/mysql/joomla:/var/log/mysql
      - mysql-for-joomla-log:/backup
    command: bash -c "/init.sh && exec /entrypoint.sh mysqld"

  joomla-sites:
    hostname: joomla-sites
    image: reactome/joomla
    build:
      context: ./joomla
      dockerfile: joomla.dockerfile
    container_name: joomla-sites
    links:
      - mysql-for-joomla
    depends_on:
      - mysql-for-joomla
    env_file:
      - joomla.env
    ports:
      - 80:80
      - 443:443
    entrypoint: bash -c "/wait-for.sh mysql-for-joomla:3306 -t 360  -- cp /etc/apache2/ssl/* /certs/ && /usr/local/bin/docker-php-entrypoint apache2-foreground"
    volumes:
      - ./wait-for.sh:/wait-for.sh
      - ./joomla/000-default-common.conf:/etc/apache2/sites-common/000-default-common.conf
      - ./joomla/000-default.conf:/etc/apache2/sites-enabled/000-default.conf
      - ./joomla/configuration.php:/var/www/html/configuration.php
      - ./certificates:/certs
      - ./joomla/Secrets.pm:/var/www/html/cgi-modules/GKB/Secrets.pm
      - ./joomla/cgi-modules/GKB/FrontPage3.pm:/var/www/html/cgi-modules/GKB/FrontPage3.pm
      - ./joomla/cgi-modules/GKB/Utils/InstructionLibrary.pm:/var/www/html/cgi-modules/GKB/Utils/InstructionLibrary.pm
      - ./joomla/cgi-modules/GKB/WebUtils.pm:/var/www/html/cgi-modules/GKB/WebUtils.pm
      - ./joomla/cgi-modules/GKB/Config.pm:/var/www/html/cgi-modules/GKB/Config.pm
      - ./joomla/cgi-modules/GKB/URLMaker.pm:/var/www/html/cgi-modules/GKB/URLMaker.pm
      - fireworks-dir:/var/www/html/download/current/fireworks
      - diagrams-dir:/var/www/html/download/current/diagram

volumes:
  mysql-for-joomla-log:
  mysql-for-tomcat-log:
  fireworks-dir:
  diagrams-dir: