Merge pull request #197 from bento-platform/releases/v14

Release v14

README.md

@@ -32,6 +32,7 @@ that make up the Bento platform.
 
 ## Migration documents
 
+* [v13 to v14](./docs/migrating_to_14.md)
 * [v12 to v13](./docs/migrating_to_13.md)
 * [v2.11 to v12](./docs/migrating_to_12.md)
 * [v2.10 to v2.11](./docs/migrating_to_2_11.md)

docker-compose.local.yaml

@@ -44,6 +44,7 @@ services:
     extends:
       file: docker-compose.dev.yaml
       service: authz
+    image: ${BENTO_AUTHZ_IMAGE}:${BENTO_AUTHZ_VERSION_DEV}
     volumes:
       - ./repos/authz:/authorization
     environment:

docs/migrating_to_14.md

@@ -0,0 +1,11 @@
+# Migrating to Bento v14
+
+Version 14 has **removed all MCODE support.** MCODE-specific properties on Individuals in Katsu have been moved to
+`extra_properties`.
+
+Updating to Bento 14 should be as straightforward as:
+
+```bash
+git pull
+./bentoctl.bash start --pull
+```

etc/bento.env

@@ -43,7 +43,7 @@ BENTOV2_GATEWAY_CPUS=2
 
 # - Keycloak IdP - 'auth'
 BENTOV2_AUTH_IMAGE=ghcr.io/bento-platform/bento_keycloak_dist
-BENTOV2_AUTH_VERSION=2023.09.13
+BENTOV2_AUTH_VERSION=2023.10.31
 BENTOV2_AUTH_CONTAINER_NAME=${BENTOV2_PREFIX}-auth
 BENTO_AUTH_NETWORK=${BENTOV2_PREFIX}-auth-net
 BENTOV2_AUTH_SERVICE_HOST=0.0.0.0
@@ -95,7 +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=3.1.2
+BENTOV2_WEB_VERSION=3.2.2
 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev
 BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web
 BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net
@@ -121,7 +121,7 @@ BENTOV2_DROP_BOX_CPUS=3
 
 # Service Registry
 BENTOV2_SERVICE_REGISTRY_IMAGE=ghcr.io/bento-platform/bento_service_registry
-BENTOV2_SERVICE_REGISTRY_VERSION=1.2.1
+BENTOV2_SERVICE_REGISTRY_VERSION=1.2.2
 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
@@ -133,7 +133,7 @@ BENTOV2_SERVICE_REGISTRY_CPUS=1
 
 # Notification
 BENTOV2_NOTIFICATION_IMAGE=ghcr.io/bento-platform/bento_notification_service
-BENTOV2_NOTIFICATION_VERSION=3.0.0
+BENTOV2_NOTIFICATION_VERSION=3.0.1
 BENTOV2_NOTIFICATION_VERSION_DEV=${BENTOV2_NOTIFICATION_VERSION}-dev
 BENTOV2_NOTIFICATION_CONTAINER_NAME=${BENTOV2_PREFIX}-notification
 BENTO_NOTIFICATION_NETWORK=${BENTOV2_PREFIX}-notification-net
@@ -148,7 +148,7 @@ BENTOV2_NOTIFICATION_CPUS=2
 
 # Aggregation
 BENTOV2_AGGREGATION_IMAGE=ghcr.io/bento-platform/bento_aggregation_service
-BENTOV2_AGGREGATION_VERSION=0.19.1
+BENTOV2_AGGREGATION_VERSION=0.19.2
 BENTOV2_AGGREGATION_VERSION_DEV=${BENTOV2_AGGREGATION_VERSION}-dev
 BENTOV2_AGGREGATION_CONTAINER_NAME=${BENTOV2_PREFIX}-aggregation
 BENTO_AGGREGATION_NETWORK=${BENTOV2_PREFIX}-aggregation-net
@@ -176,7 +176,7 @@ BENTOV2_EVENT_RELAY_CPUS=1
 
 # WES
 BENTOV2_WES_IMAGE=ghcr.io/bento-platform/bento_wes
-BENTOV2_WES_VERSION=0.10.1
+BENTOV2_WES_VERSION=0.11.0
 BENTOV2_WES_VERSION_DEV=${BENTOV2_WES_VERSION}-dev
 BENTOV2_WES_CONTAINER_NAME=${BENTOV2_PREFIX}-wes
 BENTO_WES_NETWORK=${BENTOV2_PREFIX}-wes-net
@@ -203,7 +203,7 @@ BENTOV2_WES_WORKFLOW_TIMEOUT=172800
 
 # DRS
 BENTOV2_DRS_IMAGE=ghcr.io/bento-platform/bento_drs
-BENTOV2_DRS_VERSION=0.12.6
+BENTOV2_DRS_VERSION=0.13.0
 BENTOV2_DRS_VERSION_DEV=${BENTOV2_DRS_VERSION}-dev
 BENTOV2_DRS_CONTAINER_NAME=${BENTOV2_PREFIX}-drs
 BENTO_DRS_NETWORK=${BENTOV2_PREFIX}-drs-net
@@ -246,7 +246,7 @@ BENTOV2_KATSU_DB_CPUS=4
 
 # Katsu
 BENTOV2_KATSU_IMAGE=ghcr.io/bento-platform/katsu
-BENTOV2_KATSU_VERSION=4.4.0
+BENTOV2_KATSU_VERSION=5.0.0
 BENTOV2_KATSU_VERSION_DEV=${BENTOV2_KATSU_VERSION}-dev
 BENTOV2_KATSU_CONTAINER_NAME=${BENTOV2_PREFIX}-katsu
 BENTO_KATSU_NETWORK=${BENTOV2_PREFIX}-katsu-net
@@ -269,7 +269,7 @@ CHORD_METADATA_SUB_PATH=/api/metadata
 
 # Redis
 BENTOV2_REDIS_BASE_IMAGE=redis
-BENTOV2_REDIS_BASE_IMAGE_VERSION=7.0.12-alpine
+BENTOV2_REDIS_BASE_IMAGE_VERSION=7.0.14-alpine
 BENTOV2_REDIS_CONTAINER_NAME=${BENTOV2_PREFIX}-redis
 BENTO_REDIS_NETWORK=${BENTOV2_PREFIX}-redis-net
 BENTOV2_REDIS_INTERNAL_PORT=6379
@@ -282,14 +282,14 @@ BENTOV2_REDIS_CPUS=2
 # Gohan
 BENTOV2_GOHAN_DEBUG=false
 BENTOV2_GOHAN_SERVICE_CONTACT=[email protected]
-BENTOV2_GOHAN_SEMVER=4.0.0
+BENTOV2_GOHAN_SEMVER=4.0.1
 
 # -- 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=4.0.0
+BENTOV2_GOHAN_API_VERSION=4.0.1
 BENTOV2_GOHAN_API_VERSION_DEV=${BENTOV2_GOHAN_API_VERSION}-dev
 
 BENTOV2_GOHAN_API_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-api
@@ -318,7 +318,7 @@ 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=4.0.0
+BENTOV2_GOHAN_ES_VERSION=4.0.1
 
 BENTOV2_GOHAN_ES_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-elasticsearch
 BENTO_GOHAN_ES_NETWORK=${BENTOV2_PREFIX}-gohan-elasticsearch-net
@@ -348,7 +348,7 @@ 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=0.15.0
+BENTO_PUBLIC_VERSION=0.16.2
 BENTO_PUBLIC_VERSION_DEV=${BENTO_PUBLIC_VERSION}-dev
 BENTO_PUBLIC_CONTAINER_NAME=${BENTOV2_PREFIX}-public
 BENTO_PUBLIC_NETWORK=${BENTOV2_PREFIX}-public-net
@@ -368,7 +368,7 @@ BENTO_PUBLIC_TRANSLATED=true
 BENTO_BEACON_CONTAINER_NAME=${BENTOV2_PREFIX}-beacon
 BENTO_BEACON_NETWORK=${BENTOV2_PREFIX}-beacon-net
 BENTO_BEACON_IMAGE=ghcr.io/bento-platform/bento_beacon
-BENTO_BEACON_VERSION=0.9.1
+BENTO_BEACON_VERSION=0.11.0
 BENTO_BEACON_VERSION_DEV=${BENTO_BEACON_VERSION}-dev
 BENTO_BEACON_INTERNAL_PORT=${BENTO_STD_SERVICE_INTERNAL_PORT}
 BENTO_BEACON_EXTERNAL_PORT=5000
@@ -379,10 +379,8 @@ BENTO_BEACON_CPUS=2
 BENTO_BEACON_CONFIG_DIR=${PWD}/lib/beacon/config
 
 BENTO_BEACON_GOHAN_BASE_URL=http://${BENTOV2_GOHAN_API_CONTAINER_NAME}:${BENTOV2_GOHAN_API_INTERNAL_PORT}
-BENTO_BEACON_GRANULARITY=count
 BENTO_BEACON_KATSU_TIMEOUT=60
 BENTO_BEACON_GOHAN_TIMEOUT=60
-BENTO_BEACON_ENABLE_AUTHX=True
 BENTO_BEACON_OIDC_ISSUER=${BENTOV2_AUTH_PUBLIC_URL}/auth/realms/${BENTOV2_AUTH_REALM}
 
 # cBioPortal

etc/scripts/renew_certs_and_redeploy.sh

@@ -0,0 +1,45 @@
+#! /usr/bin/env bash
+
+# Set absolute script dir, allows to find absolute project dir & env files
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+# Removing "/etc/scripts" suffix gives project dir
+BENTO_PROJECT_DIR="${SCRIPT_DIR%%/etc/scripts}"
+
+# CD to project dir and source env config
+cd $BENTO_PROJECT_DIR && source etc/default_config.env && source local.env;
+
+# Activate python venv
+source env/bin/activate
+
+# Init services array, gateway is always renewed
+SERVICES=('gateway')
+
+# Auth needs cert renewal when internal only
+if [[ $BENTOV2_USE_EXTERNAL_IDP -eq 0 ]]; then
+    echo "Uses internal IDP, will attemps auth certs renewal."
+    # Append auth to list of services to renew
+    SERVICES+=('auth')
+fi
+
+# Clean and renew service certs
+for SERVICE_NAME in "${SERVICES[@]}"
+do
+
+  ./bentoctl.bash clean "$SERVICE_NAME"
+
+  LOCAL_CERTS=$BENTO_PROJECT_DIR/certs/$SERVICE_NAME
+  LOCAL_LE=$LOCAL_CERTS/letsencrypt
+
+
+  docker run -it --rm --name certbot -v "$LOCAL_LE:/etc/letsencrypt" -v "$LOCAL_LE/lib:/var/lib/letsencrypt" -p 80:80 -p 443:443 certbot/certbot renew --dry-run
+  docker run -it --rm --name certbot -v "$LOCAL_LE:/etc/letsencrypt" -v "$LOCAL_LE/lib:/var/lib/letsencrypt" -p 80:80 -p 443:443 certbot/certbot renew --force-renewal
+
+  sudo chown -R $BENTO_UID:$BENTO_UID $LOCAL_CERTS
+done
+
+# Redeploy services with updated certs
+for SERVICE_NAME in "${SERVICES[@]}"
+do
+  ./bentoctl.bash run "$SERVICE_NAME"
+done

lib/beacon/docker-compose.beacon.yaml

@@ -15,7 +15,6 @@ services:
       - BENTO_BEACON_DEBUGGER_INTERNAL_PORT
       - BENTO_BEACON_DEBUGGER_EXTERNAL_PORT
       - CONFIG_ABSOLUTE_PATH=/config/
-      - ENABLE_AUTHX=${BENTO_BEACON_ENABLE_AUTHX}
       - OIDC_ISSUER=${BENTO_BEACON_OIDC_ISSUER}
       - CLIENT_ID=${BENTOV2_AUTH_CLIENT_ID}
       - BEACON_BASE_URL=${BENTOV2_PUBLIC_URL}/api/beacon
@@ -24,6 +23,8 @@ services:
       - BENTOV2_DOMAIN
       - BENTOV2_PUBLIC_URL
       - BENTO_BEACON_UI_ENABLED
+      - BENTO_AUTHZ_SERVICE_URL
+      - DRS_URL=${BENTOV2_PUBLIC_URL}/api/drs
     volumes:
       - ${BENTO_BEACON_CONFIG_DIR}:/config:ro
     networks: