resolve merge

Signed-off-by: Basil Bruhn <basil.bruhn@psi.ch>

conf.d/tubulinxyz.conf

@@ -0,0 +1,29 @@
+server {
+    listen 80;
+    server_name tubulin.xyz;
+    return 301 https://$host$request_uri;
+}
+
+server {
+    listen 443 ssl;
+    server_name tubulin.xyz;
+
+    ssl_certificate /etc/nginx/certs/lx-docker-dmz-01.psi.ch.crt;
+    ssl_certificate_key /etc/nginx/private/lx-docker-dmz-01.psi.ch.key;
+
+    location /api/ {
+        proxy_pass http://backend:8000/;
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Proto $scheme;
+    }
+
+    location / {
+        proxy_pass http://frontend:3000;
+        proxy_set_header Host $host;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection "upgrade";
+        proxy_cache_bypass $http_upgrade;
+    }
+}

docker-compose.yaml

@@ -225,7 +225,14 @@ services:
       - /mount/webhosting_dmz_write/clic/media:/app/media
       - /mount/webhosting_dmz_write/clic/impact_factors:/app/data/impact_factors:ro
     entrypoint: ["python"]
-    command: ["manage.py", "process_brightway_json_exports", "--skip-checks", "--sleep", "${CLIC_API_EXPORT_POLL_SECONDS:-2}"]
+    command:
+      [
+        "manage.py",
+        "process_brightway_json_exports",
+        "--skip-checks",
+        "--sleep",
+        "${CLIC_API_EXPORT_POLL_SECONDS:-2}",
+      ]
     depends_on:
       clic-db:
         condition: service_healthy
@@ -424,6 +431,168 @@ services:
     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:
@@ -432,3 +601,4 @@ networks:
   rhodo_network:
   leaps_db:
   drsa_tiermaker_backend:
+  tubulinxyz_backend: