From 542c5da12b057d8bacbe746c8f8a6dee66924092 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jo=C3=A3o=20Pedro=20Agostinho=20de=20Sousa?=
 <joao.agostinho-de-sousa@psi.ch>
Date: Fri, 31 Jul 2026 17:42:24 +0200
Subject: [PATCH] add tubulin.xyz

---
 conf.d/tubulinxyz.conf |  29 ++++++++
 docker-compose.yaml    | 154 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 183 insertions(+)
 create mode 100644 conf.d/tubulinxyz.conf

diff --git a/conf.d/tubulinxyz.conf b/conf.d/tubulinxyz.conf
new file mode 100644
index 0000000..7f2094b
--- /dev/null
+++ b/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/tubulin.xyz.crt;
+    ssl_certificate_key /etc/nginx/private/tubulin.xyz.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;
+    }
+}
diff --git a/docker-compose.yaml b/docker-compose.yaml
index 303561b..4594eca 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -600,6 +600,159 @@ services:
     networks:
       - backend
 
+  # João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
+  # tubulin.xyz
+  neo4j:
+    image: neo4j:5
+    environment:
+      NEO4J_AUTH: neo4j/${NEO4J_PASSWORD}
+      NEO4J_server_memory_heap_initial__size: 1G
+      NEO4J_server_memory_heap_max__size: 2G
+      NEO4J_server_memory_pagecache_size: 1G
+    volumes:
+      - /opt/webcontent/tubulin/neo4j/data:/data
+      - /opt/webcontent/tubulin/neo4j/logs:/logs
+    healthcheck:
+      test: ["CMD", "cypher-shell", "-u", "neo4j", "-p", "${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:
+      - /opt/webcontent/tubulin/data:/mnt/tubetl_data
+      - /opt/webcontent/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:
+      - /opt/webcontent/tubulin/data:/mnt/tubetl_data
+      - /opt/webcontent/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:
+      - /opt/webcontent/tubulin/data:/mnt/tubetl_data
+      - /opt/webcontent/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:
@@ -607,3 +760,4 @@ networks:
   it_strategy_dashboard_backend:
   panda_maintenance_backend:
   tomcatwiki_backend:
+  tubulinxyz_backend: