WebHosting_DMZ/docker-compose.yaml

services:
  # linux-eng@psi.ch
  nginx:
    image: gitea.psi.ch/images/nginx:1.29.8
    container_name: nginx_proxy
    restart: always
    ports:
      - "80:80"
      - "443:443"
    volumes:
      - /etc/letsencrypt/live:/etc/letsencrypt/live:ro
      - /etc/letsencrypt/archive:/etc/letsencrypt/archive:ro
      - /etc/pki/tls/certs:/etc/nginx/certs:ro
      - /etc/pki/tls/private:/etc/nginx/private:ro
      - /etc/nginx/nginx.conf:/etc/nginx/nginx.conf:ro
      - /etc/nginx/conf.d:/etc/nginx/conf.d:ro
      - /opt/webcontent/sinqstatus:/opt/webcontent/sinqstatus:ro
      - /mount/actris:/opt/webcontent/actris:ro
      - /opt/webcontent/DMZ:/opt/webcontent/DMZ:rw
    networks:
      - public
      - backend

  # rfwtools
  # gfa-status-test
  apache:
    image: gitea.psi.ch/images/php-apache:latest
    container_name: apache_app
    restart: always
    volumes:
      - /opt/webcontent/DMZ/rfmwtools:/var/www/rfmwtools:ro
      - /opt/webcontent/DMZ/fluid-eos:/var/www/fluid-eos:rw
      - /opt/webcontent/DMZ/omny:/var/www/omny:rw
      - /opt/webcontent/DMZ/cas-status:/var/www/cas_status:rw
      - /mount/srem/webhosting:/var/www/srem:rw
      - /mount/webhosting_dmz_write/tcpwiki:/var/www/tcpwiki:rw
      - /mount/webhosting_dmz_write/dokuwiki-core:/var/www/dokuwiki-core:r
      - ./apache/conf:/etc/apache2/sites-enabled:ro
    networks:
      - backend

  # MCDA Calculator Huang He <river.huang@psi.ch>
  mcda-calculator:
    image: gitea.psi.ch/images/mcda-calculator:1.0.3
    container_name: mcda-calculator
    restart: always
    networks: 
      - backend

  # MCDA DSS Huang He <river.huang@psi.ch>
  mcda-dss:
    image: gitea.psi.ch/images/mcda-dss:0.5.0
    container_name: mcda-dss
    restart: always
    networks:
      - backend

  # MCDA SRF Huang He <river.huang@psi.ch>
  mcda-srf:
    image: gitea.psi.ch/images/mcda-srf:0.9.6
    container_name: mcda-srf
    restart: always
    networks:
      - backend

  # River Huang <river.huang@psi.ch>
  # UP-MAVT-Suite
  up-mavt-suite-mongo:
    image: mongo:7.0
    container_name: up-mavt-suite-mongo
    environment:
      MONGO_INITDB_DATABASE: elicitation
    volumes:
      - /opt/webcontent/up-mavt-suite/mongo-data:/data/db
    networks:
      - up_mavt_suite_network
    restart: always

  up-mavt-suite-backend:
    image: gitea.psi.ch/images/up-mavt-suite-backend:0.9.8
    container_name: up-mavt-suite-backend
    environment:
      MONGO_URI: mongodb://up-mavt-suite-mongo:27017/elicitation
      FLASK_ENV: production
      ADMIN_PASSWORD: ${MCDA_UP_ADMIN_PASSWORD}
      OAUTH2_CLIENT_SECRET: ${MCDA_UP_OAUTH2_SECRET}
      SMTP_HOST: smtp.office365.com
      SMTP_PORT: 587
      SMTP_USER: mcda@psi.ch
      EMAIL_AUTH_MODE: oauth2
      OAUTH2_TENANT_ID: 50f89ee2-f910-47c5-9913-a6ea08928f11
      OAUTH2_CLIENT_ID: 201ba262-3c76-41fb-8942-dcefb7729caa
      OAUTH2_SCOPE: https://outlook.office365.com/.default
      OAUTH2_USERNAME: mcda@psi.ch
      SMTP_USE_TLS: true
      EMAIL_FROM: mcda@psi.ch
      APP_BASE_URL: https://mcda-up.psi.ch/
    depends_on:
      - up-mavt-suite-mongo
    networks:
      - up_mavt_suite_network
      - backend
    restart: always

  up-mavt-suite-worker:
    image: gitea.psi.ch/images/up-mavt-suite-worker:0.9.8
    container_name: up-mavt-suite-worker
    environment:
      MONGO_URI: mongodb://up-mavt-suite-mongo:27017/elicitation
    depends_on:
      - up-mavt-suite-mongo
    networks:
      - up_mavt_suite_network
    restart: always

  up-mavt-suite-frontend:
    image: gitea.psi.ch/images/up-mavt-suite-frontend:0.9.8
    container_name: up-mavt-suite-frontend
    environment:
      VITE_DEBUG_CONSOLE: true 
    depends_on:
      - up-mavt-suite-backend
    networks:
      - up_mavt_suite_network
      - backend
    restart: always


  # Romain Sacchi <romain.sacchi@psi.ch>
  swiss-ecargo:
    image: gitea.psi.ch/sacchi_r/swiss-ecargo:0.1.2
    container_name: swiss-ecargo
    restart: always
    environment:
      - HOSTED_API_KEY=${ecargo_api_key}
    networks:
      - backend


  # Lange Clemens <clemens.lange@psi.ch>
  # summer-project-selection.psi.ch
  summer-project-selection:
    image: gitea.psi.ch/lange_c/summer-project-selection:latest
    container_name: summer-project-selection
    restart: always
    volumes:
      - /mount/webhosting_dmz_write/summer-project-selection/data:/app/data
      - /opt/webcontent/DMZ/summer-project-selection/projects:/app/projects
      - /opt/webcontent/DMZ/summer-project-selection/applicants:/app/applicants
    networks:
      - backend

  # PEPISCO <andras.boedi@psi.ch> <patrick.hemberger@psi.ch>
  # PhotoElectron PhotoIon Spectral COmpendium
  pepisco:
    image: gitea.psi.ch/images/pepisco:v2026.03.13
    container_name: pepisco
    restart: always
    networks:
      - backend

  # Only on rhodo_network. The `backend` alias is required because
  # the frontend image's internal nginx uses http://backend:8000/
  rhodo-backend:
    image: gitea.psi.ch/images/grn_opsins-backend:1.2.0
    container_name: rhodo-backend
    restart: always
    networks:
      rhodo_network:
        aliases:
          - backend

  rhodo-frontend:
    image: gitea.psi.ch/images/grn_opsins-frontend:1.2.0
    container_name: rhodo-frontend
    restart: always
    depends_on:
      - rhodo-backend
    networks:
      - rhodo_network
      - backend

  scicat-rocrate-qa:
    image: gitea.psi.ch/data-catalog-services/scicat-rocrate:2.6.0-rc-openbis-import.5
    container_name: scicat-rocrate-qa
    restart: always
    networks:
      - backend
    environment:
      - QUARKUS_REST_CLIENT_SCICAT_URL=https://dacat-qa.psi.ch
      - QUARKUS_REST_CLIENT_S3BROKER_URL=https://s3-broker.qa.psi.ch
      - QUARKUS_HTTP_LIMITS_MAX_BODY_SIZE=10G
      - SCICAT_PID_PREFIX=20.500.11935
    volumes:
      - /mount/rocrate_qa:/rocrate:rw

# LEAPS ultrafast frithjof.nolting@psi.ch
  felira-web:
    image: gitea.psi.ch/leaps/leaps-felira:3.0.3
    container_name: felira-web
    restart: always
    # volumes:
    #   - /mount/webhosting_dmz_write/leaps/web:/var/www/html:rw
    depends_on:
      - felira-db
    networks:
      - backend
      - leaps_db
    environment:
      - DB_DATABASE=felira_leaps_ultrafast
      - DB_USERNAME=felira_leaps_ultrafast
      - DB_PASSWORD=${LEAPS_DB_PW}
  felira-db:
    image: mariadb:latest
    container_name: felira-db
    restart: always
    environment:
      - MARIADB_ROOT_PASSWORD=${LEAPS_DB_PW}
      - MARIADB_DATABASE=felira_leaps_ultrafast
      - MARIADB_USER=felira_leaps_ultrafast
      - MARIADB_PASSWORD=${LEAPS_DB_PW}
    volumes:
      - /mount/webhosting_dmz_write/leaps/db_data:/var/lib/mysql
      - /mount/webhosting_dmz_write/leaps/init-db:/docker-entrypoint-initdb.d:ro
    networks:
      - leaps_db

  # João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
  # tubulin.xyz
  neo4j:
    image: neo4j:5
    environment:
      NEO4J_AUTH: neo4j/${NEO4J_PASSWORD}
      NEO4J_server_memory_heap_initial__size: 1G
      NEO4J_server_memory_heap_max__size: 2G
      NEO4J_server_memory_pagecache_size: 1G
    volumes:
      - /mount/webhosting_dmz_write/tubulin/neo4j/data:/data
      - /mount/webhosting_dmz_write/tubulin/neo4j/logs:/logs
    healthcheck:
      test: ["CMD", "cypher-shell", "-u", "neo4j", "-p", "${NEO4J_PASSWORD}", "RETURN 1"]
      interval: 10s
      timeout: 5s
      retries: 10
      start_period: 30s
    restart: always
    networks:
      - tubulinxyz_backend
    stop_grace_period: 60s
    logging:
      driver: json-file
      options:
        max-size: "50m"
        max-file: "5"
    deploy:
      resources:
        limits:
          memory: 4G

  bootstrap:
    image: ghcr.io/rtviii/tubulinxyz:latest
    pull_policy: always
    environment:
      NEO4J_URI: bolt://neo4j:7687
      NEO4J_USER: neo4j
      NEO4J_PASSWORD: ${NEO4J_PASSWORD}
      NEO4J_CURRENTDB: neo4j
      TUBXZ_ROOT: /app
      TUBETL_DATA: /mnt/tubetl_data
      NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
    volumes:
      - /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
      - /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz
    depends_on:
      neo4j:
        condition: service_healthy
    entrypoint: ["/bin/sh", "/app/scripts/init_and_seed.sh"]
    restart: always
    networks:
      - tubulinxyz_backend
    logging:
      driver: json-file
      options:
        max-size: "50m"
        max-file: "3"
    deploy:
      resources:
        limits:
          memory: 4G

  backend:
    image: ghcr.io/rtviii/tubulinxyz:latest
    pull_policy: always
    environment:
      NEO4J_URI: bolt://neo4j:7687
      NEO4J_USER: neo4j
      NEO4J_PASSWORD: ${NEO4J_PASSWORD}
      NEO4J_CURRENTDB: neo4j
      SECRET_KEY: ${SECRET_KEY}
      TUBXZ_ROOT: /app
      TUBETL_DATA: /mnt/tubetl_data
      NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
    volumes:
      - /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
      - /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz:ro
    depends_on:
      neo4j:
        condition: service_healthy
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8000/health"]
      interval: 30s
      timeout: 5s
      retries: 3
      start_period: 15s
    restart: always
    networks:
      - backend
      - tubulinxyz_backend
    stop_grace_period: 30s
    logging:
      driver: json-file
      options:
        max-size: "50m"
        max-file: "5"
    deploy:
      resources:
        limits:
          memory: 2G

  scheduler:
    image: ghcr.io/rtviii/tubulinxyz:latest
    pull_policy: always
    environment:
      NEO4J_URI: bolt://neo4j:7687
      NEO4J_USER: neo4j
      NEO4J_PASSWORD: ${NEO4J_PASSWORD}
      NEO4J_CURRENTDB: neo4j
      TUBXZ_ROOT: /app
      TUBETL_DATA: /mnt/tubetl_data
      NCBI_TAXA_SQLITE: /app/.etetoolkit/taxa.sqlite
    volumes:
      - /mount/webhosting_dmz_write/tubulin/data:/mnt/tubetl_data
      - /mount/webhosting_dmz_write/tubulin/log:/var/log/tubxz
    depends_on:
      neo4j:
        condition: service_healthy
    entrypoint: ["/bin/sh", "/app/scripts/start_scheduler.sh"]
    restart: always
    networks:
      - tubulinxyz_backend
    logging:
      driver: json-file
      options:
        max-size: "50m"
        max-file: "5"
    deploy:
      resources:
        limits:
          memory: 4G

  frontend:
    image: ghcr.io/rtviii/tubulinxyz-frontend:latest
    pull_policy: always
    depends_on:
      backend:
        condition: service_healthy
    restart: always
    networks:
      - backend
      - tubulinxyz_backend
    logging:
      driver: json-file
      options:
        max-size: "50m"
        max-file: "3"
    deploy:
      resources:
        limits:
          memory: 512M

networks:
  public:
  backend:
  up_mavt_suite_network:
  rhodo_network:
  leaps_db:
  tubulinxyz_backend: