Merge pull request #222 from bento-platform/releases/v16

Release v16
bento-platform · Jul 23, 2024 · 0b4f527 · 0b4f527
2 parents c161f66 + c1e8dd8
commit 0b4f527
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diff --git a/README.md b/README.md
@@ -22,8 +22,8 @@ that make up the Bento platform.
 
 
 ## Requirements
-- Docker >= 19.03.8
-- Docker Compose >= 2.14.0, <2.24 (plugin form: you should have the `docker compose` command available, without a dash)
+- Docker >= 24.0.4
+- Docker Compose >= 2.20.0 (plugin form: you should have the `docker compose` command available, without a dash)
 - Python >= 3.9 (for `bentoctl`); the services require Python 3.10 but this is included in their Docker images. 
 
 
@@ -44,6 +44,7 @@ that make up the Bento platform.
 
 ### Migration documents
 
+* [v15.2 to v16](./docs/migrating_to_16.md)
 * [v15.1 to v15.2](./docs/migrating_to_15_2.md)
 * [v15 to v15.1](./docs/migrating_to_15_1.md)
 * [v14 to v15](./docs/migrating_to_15.md)

diff --git a/docker-compose.dev.yaml b/docker-compose.dev.yaml
@@ -1,18 +1,12 @@
-# extends main docker-compose.yml and various service-specific compose files;
+# merges with main docker-compose.yml and various service-specific compose files;
 # adds in development/debug environment variables, debugpy ports
 
 services:
   web:
-    extends:
-      file: docker-compose.yaml
-      service: web
     environment:
       - NODE_ENV=development
 
   public:
-    extends:
-      file: $PWD/lib/public/docker-compose.public.yaml
-      service: public
     environment:
       - NODE_ENV=development
     ports:
@@ -76,6 +70,11 @@ services:
           - ${BENTOV2_DOMAIN}
           - ${BENTOV2_PORTAL_DOMAIN}
           - ${BENTOV2_AUTH_DOMAIN}
+      reference-net:
+        aliases:
+          - ${BENTOV2_DOMAIN}
+          - ${BENTOV2_PORTAL_DOMAIN}
+          - ${BENTOV2_AUTH_DOMAIN}
       service-registry-net:
         aliases:
           - ${BENTOV2_DOMAIN}
@@ -91,23 +90,12 @@ services:
           - ${BENTOV2_DOMAIN}
           - ${BENTOV2_PORTAL_DOMAIN}
           - ${BENTOV2_AUTH_DOMAIN}
-    extends:
-      file: docker-compose.yaml
-      service: gateway
 
   authz:
-    extends:
-      file: docker-compose.yaml
-      service: authz
     environment:
       - BENTO_DEBUG=True
 
   katsu:
-    depends_on:
-      - katsu-db
-    extends:
-      file: $PWD/lib/katsu/docker-compose.katsu.yaml
-      service: katsu
     volumes:
       - ${BENTOV2_KATSU_DEV_WES_VOL_TMP_DIR}:/wes/tmp:ro
     environment:
@@ -119,9 +107,6 @@ services:
       - "${BENTOV2_KATSU_DEBUGGER_EXTERNAL_PORT}:${BENTOV2_KATSU_DEBUGGER_INTERNAL_PORT}"
 
   katsu-db:
-    extends:
-      file: $PWD/lib/katsu/docker-compose.katsu.yaml
-      service: katsu-db
     ports:
       - "${BENTOV2_KATSU_DB_EXTERNAL_PORT}:${BENTOV2_KATSU_DB_INTERNAL_PORT}"
     volumes:
@@ -155,9 +140,6 @@ services:
       - LOG_LEVEL=debug
       - PORT=${BENTOV2_AGGREGATION_INTERNAL_PORT}
       - DEBUGGER_PORT=${BENTOV2_AGGREGATION_DEBUGGER_INTERNAL_PORT}
-    extends:
-      file: $PWD/lib/aggregation/docker-compose.aggregation.yaml
-      service: aggregation
     ports:
       - "${BENTOV2_AGGREGATION_EXTERNAL_PORT}:${BENTOV2_AGGREGATION_INTERNAL_PORT}"
       - "${BENTOV2_AGGREGATION_DEBUGGER_EXTERNAL_PORT}:${BENTOV2_AGGREGATION_DEBUGGER_INTERNAL_PORT}"
@@ -169,9 +151,6 @@ services:
       - FLASK_DEBUG=True
       - BENTO_VALIDATE_SSL=False
       - DEBUGGER_PORT=${BENTOV2_WES_DEBUGGER_EXTERNAL_PORT}
-    extends:
-      file: $PWD/lib/wes/docker-compose.wes.yaml
-      service: wes
     volumes:
       - ${BENTOV2_WES_DEV_VOL_DIR}:/wes/data
       - ${BENTOV2_WES_DEV_VOL_TMP_DIR}:/wes/tmp
@@ -184,27 +163,16 @@ services:
     environment:
       - FLASK_DEBUG=True
       - DEBUGGER_PORT=${BENTOV2_DRS_DEBUGGER_EXTERNAL_PORT}
-    extends:
-      file: $PWD/lib/drs/docker-compose.drs.yaml
-      service: drs
     ports:
       - "${BENTOV2_DRS_EXTERNAL_PORT}:5000"
       - "${BENTOV2_DRS_DEBUGGER_EXTERNAL_PORT}:${BENTOV2_DRS_DEBUGGER_INTERNAL_PORT}"
-    volumes:
-      # Override main drs data directory
-      - ${BENTOV2_DRS_DEV_VOL_DIR}:/drs/bento_drs/data
-      - ${BENTOV2_DRS_DEV_WES_VOL_DIR}:/wes/tmp:ro
-      - ${BENTOV2_GOHAN_API_DRS_BRIDGE_HOST_DIR}:${BENTOV2_GOHAN_DRS_API_DRS_BRIDGE_DIR_CONTAINERIZED}
 
   beacon:
     environment:
       - FLASK_DEBUG=True
       - BENTO_DEBUG=True
       - CHORD_DEBUG=True
       - BENTO_BEACON_DEBUG=true
-    extends:
-      file: $PWD/lib/beacon/docker-compose.beacon.yaml
-      service: beacon
     ports:
       - "${BENTO_BEACON_EXTERNAL_PORT}:${BENTO_BEACON_INTERNAL_PORT}"
       - "${BENTO_BEACON_DEBUGGER_EXTERNAL_PORT}:${BENTO_BEACON_DEBUGGER_INTERNAL_PORT}"
@@ -218,19 +186,13 @@ services:
       - LOG_LEVEL=debug
     ports:
       - "${BENTOV2_SERVICE_REGISTRY_EXTERNAL_PORT}:${BENTOV2_SERVICE_REGISTRY_INTERNAL_PORT}"
-    extends:
-      file: docker-compose.yaml
-      service: service-registry
 
   drop-box:
     environment:
       # Runtime
       - BENTO_DEBUG=True
     ports:
       - "${BENTOV2_DROP_BOX_EXTERNAL_PORT}:${BENTOV2_DROP_BOX_INTERNAL_PORT}"
-    extends:
-      file: docker-compose.yaml
-      service: drop-box
 
   notification:
     environment:
@@ -240,17 +202,11 @@ services:
     ports:
       - "${BENTOV2_NOTIFICATION_EXTERNAL_PORT}:${BENTOV2_NOTIFICATION_INTERNAL_PORT}"
       - "${BENTO_NOTIFICATION_DEBUGGER_EXTERNAL_PORT}:${BENTO_NOTIFICATION_DEBUGGER_INTERNAL_PORT}"
-    extends:
-      file: docker-compose.yaml
-      service: notification
 
   event-relay:
     environment:
       - BENTO_DEBUG=true
       - NODE_ENV=development
-    extends:
-      file: docker-compose.yaml
-      service: event-relay
 
   reference:
     environment:
@@ -259,14 +215,8 @@ services:
       - LOG_LEVEL=debug
     ports:
       - "${BENTO_REFERENCE_EXTERNAL_PORT}:${BENTO_REFERENCE_INTERNAL_PORT}"
-    extends:
-      file: $PWD/lib/reference/docker-compose.reference.yaml
-      service: reference
 
   reference-db:
-    extends:
-      file: $PWD/lib/reference/docker-compose.reference.yaml
-      service: reference-db
     ports:
       - "${BENTO_REFERENCE_DB_EXTERNAL_PORT}:5432"
 
@@ -278,11 +228,7 @@ services:
       "http.cors.enabled": "true"
       "http.cors.allow-origin": "http://localhost:8081"
       "http.cors.allow-headers": X-Requested-With,Content-Type,Content-Length,Authorization
-    extends:
-      file: $PWD/lib/gohan/docker-compose.gohan.yaml
-      service: gohan-elasticsearch
 
-  gohan-api:
-    extends:
-      file: $PWD/lib/gohan/docker-compose.gohan.yaml
-      service: gohan-api
+  cbioportal:
+    ports:
+      - "${BENTO_CBIOPORTAL_EXTERNAL_PORT}:${BENTO_CBIOPORTAL_INTERNAL_PORT}"
diff --git a/docker-compose.local.yaml b/docker-compose.local.yaml
@@ -1,4 +1,4 @@
-# extends docker-compose.dev.yaml; adds in repository volumes + git configuration
+# merges with docker-compose.yaml and docker-compose.dev.yaml; adds in repository volumes + git configuration
 
 services:
   web:
@@ -10,22 +10,21 @@ services:
       - BENTO_GIT_NAME
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/web
-    extends:
-      file: docker-compose.dev.yaml
-      service: web
 
   public:
     image: ${BENTO_PUBLIC_IMAGE}:${BENTO_PUBLIC_VERSION_DEV}
     volumes:
       - ./repos/public:/bento-public
       - ./packs:/packs
+      - ${PWD}/lib/public/en_about.html:/bento-public/src/public/en_about.html
+      - ${PWD}/lib/public/fr_about.html:/bento-public/src/public/fr_about.html
+      - ${PWD}/lib/public/branding.png:/bento-public/src/public/assets/branding.png
+      - ${PWD}/lib/public/translations/en.json:/bento-public/src/public/locales/en/translation_en.json
+      - ${PWD}/lib/public/translations/fr.json:/bento-public/src/public/locales/fr/translation_fr.json
     environment:
       - BENTO_GIT_NAME
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/bento-public
-    extends:
-      file: docker-compose.dev.yaml
-      service: public
     profiles:
       - public
 
@@ -38,14 +37,8 @@ services:
       - BENTO_GIT_NAME
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/gateway
-    extends:
-      file: docker-compose.dev.yaml
-      service: gateway
 
   authz:
-    extends:
-      file: docker-compose.dev.yaml
-      service: authz
     image: ${BENTO_AUTHZ_IMAGE}:${BENTO_AUTHZ_VERSION_DEV}
     volumes:
       - ./repos/authz:/authorization
@@ -55,9 +48,6 @@ services:
       - BENTO_GIT_REPOSITORY_DIR=/authorization
 
   katsu:
-    extends:
-      file: docker-compose.dev.yaml
-      service: katsu
     image: ${BENTOV2_KATSU_IMAGE}:${BENTOV2_KATSU_VERSION_DEV}
     depends_on:
       - katsu-db
@@ -69,28 +59,17 @@ services:
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/app
 
-  katsu-db:
-    extends:
-      file: docker-compose.dev.yaml
-      service: katsu-db
-
   adminer:
     # No Docker networks required, bound to host
     ports:
       - 8080:8080
-    extends:
-      file: docker-compose.dev.yaml
-      service: adminer
 
   aggregation:
     image: ${BENTOV2_AGGREGATION_IMAGE}:${BENTOV2_AGGREGATION_VERSION_DEV}
     environment:
       - BENTO_GIT_NAME
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/aggregation
-    extends:
-      file: docker-compose.dev.yaml
-      service: aggregation
     volumes:
       - ./repos/aggregation:/aggregation
 
@@ -101,9 +80,6 @@ services:
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/wes
       - CELERY_DEBUG=true
-    extends:
-      file: docker-compose.dev.yaml
-      service: wes
     volumes:
       - ./repos/wes:/wes
 
@@ -113,9 +89,6 @@ services:
       - BENTO_GIT_NAME
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/drs
-    extends:
-      file: docker-compose.dev.yaml
-      service: drs
     volumes:
       - ./repos/drs:/drs
 
@@ -126,9 +99,6 @@ services:
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/beacon
       - DEBUGGER_PORT=${BENTO_BEACON_DEBUGGER_INTERNAL_PORT}
-    extends:
-      file: docker-compose.dev.yaml
-      service: beacon
     volumes:
       - ./repos/beacon:/beacon
     profiles:
@@ -144,9 +114,6 @@ services:
       - BENTO_GIT_NAME
       - BENTO_GIT_EMAIL
       - BENTO_GIT_REPOSITORY_DIR=/service_registry
-    extends:
-      file: docker-compose.dev.yaml
-      service: service-registry
 
   drop-box:
     image: ${BENTOV2_DROP_BOX_IMAGE}:${BENTOV2_DROP_BOX_VERSION_DEV}
@@ -156,9 +123,6 @@ services:
       - BENTO_GIT_REPOSITORY_DIR=/drop-box
     volumes:
       - ./repos/drop-box:/drop-box
-    extends:
-      file: docker-compose.dev.yaml
-      service: drop-box
 
   notification:
     image: ${BENTOV2_NOTIFICATION_IMAGE}:${BENTOV2_NOTIFICATION_VERSION_DEV}
@@ -168,9 +132,6 @@ services:
       - BENTO_GIT_REPOSITORY_DIR=/notification
     volumes:
       - ./repos/notification:/notification
-    extends:
-      file: docker-compose.dev.yaml
-      service: notification
 
   event-relay:
     image: ${BENTOV2_EVENT_RELAY_IMAGE}:${BENTOV2_EVENT_RELAY_VERSION_DEV}
@@ -180,9 +141,6 @@ services:
       - BENTO_GIT_REPOSITORY_DIR=/app
     volumes:
       - ./repos/event-relay:/app
-    extends:
-      file: docker-compose.dev.yaml
-      service: event-relay
 
   reference:
     image: ${BENTO_REFERENCE_IMAGE}:${BENTO_REFERENCE_VERSION_DEV}
@@ -192,9 +150,6 @@ services:
       - BENTO_GIT_REPOSITORY_DIR=/reference
     volumes:
       - ./repos/reference:/reference
-    extends:
-      file: docker-compose.dev.yaml
-      service: reference
 
   gohan-api:
     image: ${BENTOV2_GOHAN_API_IMAGE}:${BENTOV2_GOHAN_API_VERSION_DEV}
@@ -206,6 +161,3 @@ services:
     volumes:
       - ./repos/gohan-api:/gohan-api
       - ./repos/gohan-api/src/api/workflows:/app/workflows
-    extends:
-      file: docker-compose.dev.yaml
-      service: gohan-api
diff --git a/docker-compose.prod.yaml b/docker-compose.prod.yaml
@@ -1,8 +1,5 @@
 services:
   web:
-    extends:
-      file: docker-compose.yaml
-      service: web
     environment:
       - NODE_ENV=production
     volumes: