Merge pull request #140 from bento-platform/releases/v12.1

Release v12.1

docker-compose.dev.yaml

@@ -203,8 +203,9 @@ services:
 
   service-registry:
     environment:
-      - FLASK_DEBUG=True
       - BENTO_DEBUG=True
+      - BENTO_VALIDATE_SSL=False
+      - LOG_LEVEL=debug
     ports:
       - "${BENTOV2_SERVICE_REGISTRY_EXTERNAL_PORT}:${BENTOV2_SERVICE_REGISTRY_INTERNAL_PORT}"
     extends:
@@ -214,7 +215,6 @@ services:
   drop-box:
     environment:
       # Runtime
-      - QUART_DEBUG=True
       - BENTO_DEBUG=True
     ports:
       - "${BENTOV2_DROP_BOX_EXTERNAL_PORT}:${BENTOV2_DROP_BOX_INTERNAL_PORT}"

docker-compose.yaml

@@ -7,19 +7,8 @@ services:
         condition: service_healthy
     environment:
       - BENTO_DEBUG=false
-      - CHORD_DEBUG=false
-      - CHORD_PERMISSIONS=true
-      - CHORD_PRIVATE_MODE=${BENTOV2_PRIVATE_MODE}
-      - CHORD_URL=${BENTOV2_PORTAL_PUBLIC_URL_TRAILING_SLASH}
-      - CBIOPORTAL_URL=${BENTO_CBIOPORTAL_PUBLIC_URL}/
 
       - BENTO_AUTHZ_SERVICE_URL=${BENTO_AUTHZ_SERVICE_URL}
-      - OIDC_DISCOVERY_URI=${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_WELLKNOWN_PATH}
-      - BENTO_OPENID_CONFIG_URL=${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_WELLKNOWN_PATH}
-      - REDIRECT_AFTER_LOGOUT_URI=${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_REDIRECT_AFTER_LOGOUT_PATH}
-      - CLIENT_ID=${BENTOV2_AUTH_CLIENT_ID}
-      - CLIENT_SECRET
-      - TOKEN_ENDPOINT_AUTH_METHOD=client_secret_post
       - BENTOV2_SESSION_SECRET
 
       - BENTOV2_AUTH_DOMAIN
@@ -206,16 +195,12 @@ services:
     container_name: ${BENTOV2_DROP_BOX_CONTAINER_NAME}
     environment:
       - BENTO_UID
-      # Runtime
-      - QUART_DEBUG=False
-      # Storage
-      # - MINIO_URL=${BENTOV2_DROP_BOX_MINIO_URL}
-      # - MINIO_USERNAME=${BENTOV2_DROP_BOX_MINIO_USERNAME}
-      # - MINIO_PASSWORD=${BENTOV2_DROP_BOX_MINIO_PASSWORD}
-      # - MINIO_BUCKET=${BENTOV2_DROP_BOX_MINIO_BUCKET}
+      - BENTO_DEBUG=False
       - SERVICE_DATA=${BENTO_DROP_BOX_FS_BASE_PATH}
-
-      - SERVICE_URL=${BENTOV2_PORTAL_PUBLIC_URL}/api/drop-box
+      - SERVICE_URL=${BENTOV2_PUBLIC_URL}/api/drop-box
+      - CORS_ORIGINS=${BENTO_CORS_ORIGINS}
+      - BENTO_AUTHZ_SERVICE_URL
+      - OPENID_CONFIG_URL=${BENTO_OPENID_CONFIG_URL}
     networks:
       - drop-box-net
     expose:
@@ -251,7 +236,9 @@ services:
       - BENTO_PORTAL_PUBLIC_URL=${BENTOV2_PORTAL_PUBLIC_URL}
 
       - BENTO_DEBUG=False
-      - BENTO_VALIDATE_SSL=False
+      - BENTO_VALIDATE_SSL=True
+      - CORS_ORIGINS=${BENTO_CORS_ORIGINS}
+      - BENTO_AUTHZ_SERVICE_URL
 
       # Timeout, in seconds (integers only), for contacting services from the JSON
       - CONTACT_TIMEOUT=10

etc/bento.env

@@ -14,6 +14,8 @@ BENTOV2_AUTH_PUBLIC_URL=https://${BENTOV2_AUTH_DOMAIN}
 BENTO_CBIOPORTAL_PUBLIC_URL=https://${BENTOV2_CBIOPORTAL_DOMAIN}
 BENTO_AUTHZ_SERVICE_URL=${BENTOV2_PUBLIC_URL}/api/authorization/
 
+BENTO_CORS_ORIGINS="${BENTOV2_PUBLIC_URL};${BENTOV2_PORTAL_PUBLIC_URL}"
+
 BENTOV2_HEALTHCHECK_TIMEOUT=5s
 BENTOV2_HEALTHCHECK_INTERVAL=5m
 
@@ -51,6 +53,8 @@ BENTOV2_AUTH_VOL_DIR=${BENTOV2_ROOT_DATA_DIR}/auth/data
 BENTOV2_AUTH_WELLKNOWN_PATH=/realms/${BENTOV2_AUTH_REALM}/.well-known/openid-configuration
 BENTOV2_AUTH_REDIRECT_AFTER_LOGOUT_PATH=/realms/${BENTOV2_AUTH_REALM}/protocol/openid-connect/logout
 
+BENTO_OPENID_CONFIG_URL="${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_WELLKNOWN_PATH}"
+
 # KEYCLOAK_USER_ID=
 
 BENTOV2_AUTH_LOGIN_REDIRECT_PATH=/*
@@ -71,7 +75,7 @@ BENTO_AUTH_DB_NETWORK="${BENTOV2_PREFIX}-auth-db-net"
 
 # - Authz service
 BENTO_AUTHZ_IMAGE=ghcr.io/bento-platform/bento_authorization_service
-BENTO_AUTHZ_VERSION=0.2.0
+BENTO_AUTHZ_VERSION=0.2.1
 BENTO_AUTHZ_VERSION_DEV=${BENTO_AUTHZ_VERSION}-dev
 BENTO_AUTHZ_CONTAINER_NAME=${BENTOV2_PREFIX}-authz
 BENTO_AUTHZ_NETWORK=${BENTOV2_PREFIX}-authz-net
@@ -91,7 +95,7 @@ BENTO_AUTHZ_DB_MEM_LIM=1G
 # Web
 BENTO_WEB_CUSTOM_HEADER=
 BENTOV2_WEB_IMAGE=ghcr.io/bento-platform/bento_web
-BENTOV2_WEB_VERSION=2.0.0
+BENTOV2_WEB_VERSION=2.1.1
 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev
 BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web
 BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net
@@ -103,7 +107,7 @@ BENTOV2_WEB_CPUS=2
 
 # Drop-Box
 BENTOV2_DROP_BOX_IMAGE=ghcr.io/bento-platform/bento_drop_box_service
-BENTOV2_DROP_BOX_VERSION=0.12.0
+BENTOV2_DROP_BOX_VERSION=1.0.0
 BENTOV2_DROP_BOX_VERSION_DEV=${BENTOV2_DROP_BOX_VERSION}-dev
 BENTOV2_DROP_BOX_CONTAINER_NAME=${BENTOV2_PREFIX}-drop-box
 BENTO_DROP_BOX_NETWORK=${BENTOV2_PREFIX}-drop-box-net
@@ -112,17 +116,12 @@ BENTOV2_DROP_BOX_EXTERNAL_PORT=6000
 BENTOV2_DROP_BOX_VOL_DIR=${BENTOV2_ROOT_DATA_DIR}/drop-box/data-x
 BENTO_DROP_BOX_FS_BASE_PATH='/data'  # Internal base path for drop box mount + absolute paths
 
-BENTOV2_DROP_BOX_MINIO_URL=
-BENTOV2_DROP_BOX_MINIO_USERNAME=
-# BENTOV2_DROP_BOX_MINIO_PASSWORD=  Should be set in local.env if used
-BENTOV2_DROP_BOX_MINIO_BUCKET=
-
 BENTOV2_DROP_BOX_MEM_LIM=2G
 BENTOV2_DROP_BOX_CPUS=3
 
 # Service Registry
 BENTOV2_SERVICE_REGISTRY_IMAGE=ghcr.io/bento-platform/bento_service_registry
-BENTOV2_SERVICE_REGISTRY_VERSION=0.11.2
+BENTOV2_SERVICE_REGISTRY_VERSION=1.0.0
 BENTOV2_SERVICE_REGISTRY_VERSION_DEV=${BENTOV2_SERVICE_REGISTRY_VERSION}-dev
 BENTOV2_SERVICE_REGISTRY_CONTAINER_NAME=${BENTOV2_PREFIX}-service-registry
 BENTO_SERVICE_REGISTRY_NETWORK=${BENTOV2_PREFIX}-service-registry-net
@@ -245,7 +244,7 @@ BENTOV2_KATSU_DB_CPUS=4
 
 # Katsu
 BENTOV2_KATSU_IMAGE=ghcr.io/bento-platform/katsu
-BENTOV2_KATSU_VERSION=3.0.0
+BENTOV2_KATSU_VERSION=3.0.1
 BENTOV2_KATSU_VERSION_DEV=${BENTOV2_KATSU_VERSION}-dev
 BENTOV2_KATSU_CONTAINER_NAME=${BENTOV2_PREFIX}-katsu
 BENTO_KATSU_NETWORK=${BENTOV2_PREFIX}-katsu-net
@@ -268,7 +267,7 @@ CHORD_METADATA_SUB_PATH=/api/metadata
 
 # Redis
 BENTOV2_REDIS_BASE_IMAGE=redis
-BENTOV2_REDIS_BASE_IMAGE_VERSION=7.0.9-alpine
+BENTOV2_REDIS_BASE_IMAGE_VERSION=7.0.11-alpine
 BENTOV2_REDIS_CONTAINER_NAME=${BENTOV2_PREFIX}-redis
 BENTO_REDIS_NETWORK=${BENTOV2_PREFIX}-redis-net
 BENTOV2_REDIS_INTERNAL_PORT=6379
@@ -281,14 +280,14 @@ BENTOV2_REDIS_CPUS=2
 # Gohan
 BENTOV2_GOHAN_DEBUG=false
 BENTOV2_GOHAN_SERVICE_CONTACT=[email protected]
-BENTOV2_GOHAN_SEMVER=3.9.0
+BENTOV2_GOHAN_SEMVER=3.9.1
 
 # -- Host
 BENTOV2_GOHAN_DATA_ROOT=${BENTOV2_ROOT_DATA_DIR}/gohan
 
 # -- API
 BENTOV2_GOHAN_API_IMAGE=ghcr.io/bento-platform/gohan-api
-BENTOV2_GOHAN_API_VERSION=3.9.0
+BENTOV2_GOHAN_API_VERSION=3.9.1
 BENTOV2_GOHAN_API_VERSION_DEV=${BENTOV2_GOHAN_API_VERSION}-dev
 
 BENTOV2_GOHAN_API_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-api
@@ -317,7 +316,7 @@ BENTOV2_GOHAN_ES_USERNAME=elastic
 # BENTOV2_GOHAN_ES_PASSWORD comes from default_config
 
 BENTOV2_GOHAN_ES_IMAGE=ghcr.io/bento-platform/gohan-elasticsearch
-BENTOV2_GOHAN_ES_VERSION=3.9.0
+BENTOV2_GOHAN_ES_VERSION=3.9.1
 
 BENTOV2_GOHAN_ES_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-elasticsearch
 BENTO_GOHAN_ES_NETWORK=${BENTOV2_PREFIX}-gohan-elasticsearch-net
@@ -347,7 +346,7 @@ BENTOV2_GOHAN_PRIVATE_AUTHZ_URL=http://${BENTOV2_GOHAN_AUTHZ_OPA_CONTAINER_NAME}
 # Bento-Public
 
 BENTO_PUBLIC_IMAGE=ghcr.io/bento-platform/bento_public
-BENTO_PUBLIC_VERSION=0.12.1
+BENTO_PUBLIC_VERSION=0.13.2
 BENTO_PUBLIC_VERSION_DEV=${BENTO_PUBLIC_VERSION}-dev
 BENTO_PUBLIC_CONTAINER_NAME=${BENTOV2_PREFIX}-public
 BENTO_PUBLIC_NETWORK=${BENTOV2_PREFIX}-public-net
@@ -364,11 +363,10 @@ BENTO_PUBLIC_MAX_QUERY_PARAMETERS=2
 BENTO_PUBLIC_TRANSLATED=true
 
 # Beacon
-BENTO_BEACON_DEBUG=true
 BENTO_BEACON_CONTAINER_NAME=${BENTOV2_PREFIX}-beacon
 BENTO_BEACON_NETWORK=${BENTOV2_PREFIX}-beacon-net
 BENTO_BEACON_IMAGE=ghcr.io/bento-platform/bento_beacon
-BENTO_BEACON_VERSION=0.6.0
+BENTO_BEACON_VERSION=0.7.1
 BENTO_BEACON_VERSION_DEV=${BENTO_BEACON_VERSION}-dev
 BENTO_BEACON_INTERNAL_PORT=${BENTO_STD_SERVICE_INTERNAL_PORT}
 BENTO_BEACON_EXTERNAL_PORT=5000

etc/bento_dev.env

@@ -3,7 +3,6 @@ MODE=dev
 # Feature switches start ----------------------------------------------
 BENTOV2_USE_EXTERNAL_IDP=0
 BENTOV2_USE_BENTO_PUBLIC=1
-BENTOV2_PRIVATE_MODE=false
 
 BENTO_BEACON_ENABLED='true'
 BENTO_BEACON_UI_ENABLED='true'

etc/bento_services.json

@@ -1,13 +1,13 @@
 {
   "service-registry": {
     "service_kind": "service-registry",
-    "url_template": "{BENTO_PORTAL_PUBLIC_URL}/api/{service_kind}",
+    "url_template": "{BENTO_PUBLIC_URL}/api/{service_kind}",
     "repository": "[email protected]:bento-platform/bento_service_registry",
     "data_service": false
   },
   "drop-box": {
     "service_kind": "drop-box",
-    "url_template": "{BENTO_PORTAL_PUBLIC_URL}/api/{service_kind}",
+    "url_template": "{BENTO_PUBLIC_URL}/api/{service_kind}",
     "repository": "[email protected]:bento-platform/bento_drop_box_service",
     "data_service": false
   },

lib/authz/docker-compose.authz.yaml

@@ -13,7 +13,7 @@ services:
       - DATABASE_URI=postgres://${BENTO_AUTHZ_DB_USER}:${BENTO_AUTHZ_DB_PASSWORD}@${BENTO_AUTHZ_DB_CONTAINER_NAME}:5432/${BENTO_AUTHZ_DB}
       - INTERNAL_PORT=${BENTO_AUTHZ_INTERNAL_PORT}
       - OPENID_CONFIG_URL=${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_WELLKNOWN_PATH}
-      - CORS_ORIGINS=${BENTOV2_PUBLIC_URL};${BENTOV2_PORTAL_PUBLIC_URL}
+      - CORS_ORIGINS=${BENTO_CORS_ORIGINS}
     mem_limit: ${BENTO_AUTHZ_MEM_LIM}
     networks:
       - authz-net

lib/beacon/config/beacon_config.json

@@ -10,9 +10,6 @@
         "cohorts"
     ],
     "serviceInfo": {
-        "id": "c3g.bento.beacon",
-        "name": "Bento Beacon test instance",
-        "environment": "dev",
         "organization": {
             "id": "c3g",
             "name": "Canadian Centre for Computational Genomics",

lib/beacon/docker-compose.beacon.yaml

@@ -5,7 +5,6 @@ services:
     container_name: ${BENTO_BEACON_CONTAINER_NAME}
     environment:
       - BENTO_UID
-      - BENTO_BEACON_DEBUG
       - GOHAN_BASE_URL=${BENTO_BEACON_GOHAN_BASE_URL}
       - KATSU_TIMEOUT=${BENTO_BEACON_KATSU_TIMEOUT}
       - KATSU_BASE_URL=http://${BENTOV2_KATSU_CONTAINER_NAME}:${BENTOV2_KATSU_INTERNAL_PORT}
@@ -23,6 +22,8 @@ services:
       - CLIENT_ID=${BENTOV2_AUTH_CLIENT_ID}
       - BEACON_BASE_URL=${BENTOV2_PUBLIC_URL}/api/beacon
       - BENTO_BEACON_VERSION=${BENTO_BEACON_VERSION}
+      - BENTO_PUBLIC_CLIENT_NAME
+      - BENTOV2_DOMAIN
     volumes:
       - ${BENTO_BEACON_CONFIG_DIR}:/config:ro
     networks: 

lib/gateway/services/drop-box.conf.tpl → lib/gateway/public_services/drop-box.conf.tpl

@@ -1,9 +1,8 @@
-location /api/drop-box { return 302 https://${BENTOV2_PORTAL_DOMAIN}/api/drop-box/; }
+location /api/drop-box { return 302 https://${BENTOV2_DOMAIN}/api/drop-box/; }
 location /api/drop-box/ {
     # Reverse proxy settings
     include /gateway/conf/proxy.conf;
     include /gateway/conf/proxy_extra.conf;
-    include /gateway/conf/proxy_private.conf;
 
     # Forward request to the drop-box
     rewrite ^ $request_uri;

lib/gateway/services/service-registry.conf.tpl → lib/gateway/public_services/service-registry.conf.tpl

@@ -1,9 +1,8 @@
-location /api/service-registry { return 302 https://${BENTOV2_PORTAL_DOMAIN}/api/service-registry/; }
+location /api/service-registry { return 302 https://${BENTOV2_DOMAIN}/api/service-registry/; }
 location /api/service-registry/ {
     # Reverse proxy settings
     include /gateway/conf/proxy.conf;
     include /gateway/conf/proxy_extra.conf;
-    include /gateway/conf/proxy_private.conf;
 
     # Forward request to the service-registry
     rewrite ^ $request_uri;

lib/web/docker-compose.web.yaml

@@ -12,6 +12,7 @@ services:
       - BENTO_CBIOPORTAL_PUBLIC_URL
       - BENTO_DROP_BOX_FS_BASE_PATH
       - BENTO_URL=${BENTOV2_PORTAL_PUBLIC_URL}
+      - BENTO_PUBLIC_URL=${BENTOV2_PUBLIC_URL}
       - CUSTOM_HEADER=${BENTO_WEB_CUSTOM_HEADER}
       - OPENID_CONFIG_URL=${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_WELLKNOWN_PATH}
       - CLIENT_ID=${BENTOV2_AUTH_CLIENT_ID}