merge upstream

2026-09-24 14:58:12 +02:00
commit 5beaca1eaa
@@ -0,0 +1,23 @@
+server {
+    listen 80;
+    server_name pocket.psi.ch;
+    return 301 https://$host$request_uri;
+}
+
+server {
+    listen 443 ssl;
+    server_name pocket.psi.ch;
+
+    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 / {
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection "upgrade";
+        proxy_pass http://pocketapp:4200;
+        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 $scheme;
+    }
+}
@@ -0,0 +1,23 @@
+server {
+    listen 80;
+    server_name psitrail.psi.ch;
+    return 301 https://$host$request_uri;
+}
+
+server {
+    listen 443 ssl;
+    server_name psitrail.psi.ch;
+
+    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 / {
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection "upgrade";
+        proxy_pass http://psitrail:4200;
+        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 $scheme;
+    }
+}
@@ -0,0 +1,29 @@
+server {
+    listen 80;
+    server_name tubulin.xyz;
+    return 301 https://$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;
+    }
+}
@@ -57,7 +57,7 @@ services:

  # MCDA SRF Huang He <river.huang@psi.ch>
  mcda-srf:
-    image: gitea.psi.ch/images/mcda-srf:1.0.0
+    image: gitea.psi.ch/images/mcda-srf:1.0.3
    container_name: mcda-srf
    restart: always
    networks:
@@ -147,7 +147,7 @@ services:
  # Romain Sacchi <romain.sacchi@psi.ch>
  # CLIC Django platform
  clic-web:
-    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:754f9f8}
+    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:a3b90f8@sha256:84c0da77b8aab3a31391e3f713ef3ae701e08824ae4036ffe634105968f581e0}
    container_name: clic-web
    restart: always
    env_file:
@@ -159,6 +159,15 @@ services:
      - CLIC_CACHE_BACKEND=redis
      - CLIC_REDIS_URL=redis://clic-redis:6379/0
      - CLIC_REQUIRE_SHARED_CACHE=1
+      - INVENTORY_ARCHIVE_ENVIRONMENT=production
+      - INVENTORY_ARCHIVE_AUTO_RESTORE=1
+      - INVENTORY_ARCHIVE_PUBLISH_MODE=off
+      - INVENTORY_ARCHIVE_TERMS_REVIEWED=0
+      - INVENTORY_ARCHIVE_TOKEN=
+      - INVENTORY_ARCHIVE_OWNER_ID=86122
+      - INVENTORY_ARCHIVE_SERIES_ID=22850223
+      - INVENTORY_ARCHIVE_BOOTSTRAP_RECORD_ID=
+      - INVENTORY_ARCHIVE_BOOTSTRAP_SHA256=
    volumes:
      - /mount/webhosting_dmz_write/clic/media:/app/media
      - /mount/webhosting_dmz_write/clic/impact_factors:/app/data/impact_factors:ro
@@ -173,17 +182,17 @@ services:
        - CMD
        - python
        - -c
-        - "import urllib.request; r = urllib.request.Request('http://127.0.0.1:8000/health/live/', headers={'Host': 'clic.psi.ch', 'X-Forwarded-Proto': 'https'}); urllib.request.urlopen(r, timeout=5)"
+        - "import urllib.request; r = urllib.request.Request('http://127.0.0.1:8000/health/ready/', headers={'Host': 'clic.psi.ch', 'X-Forwarded-Proto': 'https'}); urllib.request.urlopen(r, timeout=5)"
      interval: 30s
      timeout: 5s
      retries: 5
-      start_period: 30s
+      start_period: 10m
    networks:
      - backend
      - clic_backend

  clic-package-exports:
-    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:754f9f8}
+    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:a3b90f8@sha256:84c0da77b8aab3a31391e3f713ef3ae701e08824ae4036ffe634105968f581e0}
    container_name: clic-package-exports
    restart: always
    env_file:
@@ -195,12 +204,17 @@ services:
      - CLIC_CACHE_BACKEND=redis
      - CLIC_REDIS_URL=redis://clic-redis:6379/0
      - CLIC_REQUIRE_SHARED_CACHE=1
+      - INVENTORY_ARCHIVE_AUTO_RESTORE=0
+      - INVENTORY_ARCHIVE_PUBLISH_MODE=off
+      - INVENTORY_ARCHIVE_TOKEN=
    volumes:
      - /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_package_exports", "--skip-checks"]
+    command: ["manage.py", "process_package_exports"]
    depends_on:
+      clic-web:
+        condition: service_healthy
      clic-db:
        condition: service_healthy
      clic-redis:
@@ -209,7 +223,7 @@ services:
      - clic_backend

  clic-brightway-json-exports:
-    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:754f9f8}
+    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:a3b90f8@sha256:84c0da77b8aab3a31391e3f713ef3ae701e08824ae4036ffe634105968f581e0}
    container_name: clic-brightway-json-exports
    restart: always
    env_file:
@@ -221,12 +235,24 @@ services:
      - CLIC_CACHE_BACKEND=redis
      - CLIC_REDIS_URL=redis://clic-redis:6379/0
      - CLIC_REQUIRE_SHARED_CACHE=1
+      - INVENTORY_ARCHIVE_AUTO_RESTORE=0
+      - INVENTORY_ARCHIVE_PUBLISH_MODE=off
+      - INVENTORY_ARCHIVE_TOKEN=
    volumes:
      - /mount/webhosting_dmz_write/clic/media:/app/media
      - /mount/webhosting_dmz_write/clic/impact_factors:/app/data/impact_factors:ro
    entrypoint: ["python"]
-    command: ["manage.py", "process_brightway_json_exports", "--skip-checks", "--sleep", "${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-web:
+        condition: service_healthy
      clic-db:
        condition: service_healthy
      clic-redis:
@@ -234,12 +260,54 @@ services:
    networks:
      - clic_backend

+  clic-inventory-archive:
+    image: ${CLIC_IMAGE:-gitea.psi.ch/images/clic:a3b90f8@sha256:84c0da77b8aab3a31391e3f713ef3ae701e08824ae4036ffe634105968f581e0}
+    container_name: clic-inventory-archive
+    restart: always
+    env_file:
+      - /mount/webhosting_dmz_write/clic/clic.env
+    environment:
+      - DJANGO_SETTINGS_MODULE=config.settings.production
+      - POSTGRES_HOST=clic-db
+      - POSTGRES_PORT=5432
+      - CLIC_CACHE_BACKEND=redis
+      - CLIC_REDIS_URL=redis://clic-redis:6379/0
+      - CLIC_REQUIRE_SHARED_CACHE=1
+      - IMPACT_SCORES_ENABLED=0
+      - INVENTORY_ARCHIVE_ENVIRONMENT=production
+      - INVENTORY_ARCHIVE_AUTO_RESTORE=0
+      - INVENTORY_ARCHIVE_PUBLISH_MODE=scheduled
+      - INVENTORY_ARCHIVE_TERMS_REVIEWED=1
+      - INVENTORY_ARCHIVE_OWNER_ID=86122
+      - INVENTORY_ARCHIVE_SERIES_ID=22850223
+      - INVENTORY_ARCHIVE_BOOTSTRAP_RECORD_ID=
+      - INVENTORY_ARCHIVE_BOOTSTRAP_SHA256=
+      - INVENTORY_ARCHIVE_METADATA_FILE=/app/config/inventory-archive-metadata.json
+      - INVENTORY_ARCHIVE_REDISTRIBUTION_FILE=
+      - INVENTORY_ARCHIVE_ALERT_EMAIL=romain.sacchi@psi.ch
+    entrypoint: ["python"]
+    command: ["manage.py", "run_inventory_archive_worker"]
+    depends_on:
+      clic-web:
+        condition: service_healthy
+    healthcheck:
+      test: ["CMD", "python", "manage.py", "inventory_archive_status", "--alert"]
+      interval: 5m
+      timeout: 60s
+      retries: 1
+      start_period: 10m
+    stop_grace_period: 3m
+    networks:
+      - clic_backend
+
  clic-db:
    image: postgres:16
    container_name: clic-db
    restart: always
    env_file:
      - /mount/webhosting_dmz_write/clic/clic.env
+    environment:
+      - INVENTORY_ARCHIVE_TOKEN=
    volumes:
      - /mount/webhosting_dmz_write/clic/postgres:/var/lib/postgresql/data
    healthcheck:
@@ -262,7 +330,7 @@ services:

  # Enea Zeolla <enea.zeolla@psi.ch>
  drsa-tiermaker:
-    image: gitea.psi.ch/images/drsa-tiermaker:0.2.3
+    image: gitea.psi.ch/images/drsa-tiermaker:0.2.4
    container_name: drsa-tiermaker
    restart: always
    depends_on:
@@ -362,7 +430,7 @@ services:
      - backend

  scicat-rocrate-qa:
-    image: gitea.psi.ch/data-catalog-services/scicat-rocrate:2.6.5-rc-ra-ingest.1
+    image: gitea.psi.ch/data-catalog-services/scicat-rocrate:2.6.10-rc-openbis-doi.1
    container_name: scicat-rocrate-qa
    restart: always
    networks:
@@ -396,13 +464,13 @@ services:

  # LEAPS ultrafast frithjof.nolting@psi.ch
  felira-web:
-    image: gitea.psi.ch/leaps/leaps-felira:3.1.18
+    image: gitea.psi.ch/leaps/leaps-felira:3.1.45
    container_name: felira-web
    restart: always
    # volumes:
    #   - /mount/webhosting_dmz_write/leaps/web:/var/www/html:rw
    depends_on:
-      - felira-db
+      - felira-database
    networks:
      - backend
      - leaps_db
@@ -410,9 +478,9 @@ services:
      - DB_DATABASE=felira_leaps_ultrafast
      - DB_USERNAME=felira_leaps_ultrafast
      - DB_PASSWORD=${LEAPS_DB_PW}
-  felira-db:
+  felira-database:
    image: mariadb:latest
-    container_name: felira-db
+    container_name: felira-database
    restart: always
    environment:
      - MARIADB_ROOT_PASSWORD=${LEAPS_DB_PW}
@@ -425,6 +493,188 @@ services:
    networks:
      - leaps_db

+  # Noah Pombas Teixeira De Freitas /  <noah.pombas@psi.ch>
+  # PSI Trail - psitrail.psi.ch
+  # Image: gitea.psi.ch/bb_if_produktiv/psitrail:181
+  psitrail:
+    image: gitea.psi.ch/bb_if_produktiv/psitrail:181
+    container_name: psitrail
+    restart: always
+    networks:
+      - backend
+
+  # Noah Pombas Teixeira De Freitas /  <noah.pombas@psi.ch>
+  # Pocket App - pocket.psi.ch
+  # Image: gitea.psi.ch/bb_if_produktiv/pocketapp:17
+  pocketapp:
+    image: gitea.psi.ch/bb_if_produktiv/pocketapp:21
+    container_name: pocketapp
+    restart: always
+    networks:
+      - backend
+
+#   # João Pedro Agostinho de Sousa <joao.agostinho-de-sousa@psi.ch>
+#   # tubulin.xyz
+#   neo4j:
+#     image: neo4j:5
+#     environment:
+#       NEO4J_AUTH: neo4j/${NEO4J_PASSWORD}
+#       NEO4J_server_memory_heap_initial__size: 1G
+#       NEO4J_server_memory_heap_max__size: 2G
+#       NEO4J_server_memory_pagecache_size: 1G
+#     volumes:
+#       - /mount/webhosting_dmz_write/tubulin/neo4j/data:/data
+#       - /mount/webhosting_dmz_write/tubulin/neo4j/logs:/logs
+#     healthcheck:
+#       test:
+#         [
+#           "CMD",
+#           "cypher-shell",
+#           "-u",
+#           "neo4j",
+#           "-p",
+#           "${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:
@@ -433,3 +683,4 @@ networks:
  rhodo_network:
  leaps_db:
  drsa_tiermaker_backend:
+  tubulinxyz_backend: