From b6cc4266ef7c84c2b0cadcdaff132779c3437851 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 5 Jun 2023 14:01:03 -0400 Subject: [PATCH 01/29] chore: move drop box out of protected zone --- docker-compose.dev.yaml | 1 - docker-compose.yaml | 10 ++-------- etc/bento.env | 2 ++ etc/bento_services.json | 2 +- lib/authz/docker-compose.authz.yaml | 2 +- .../{services => public_services}/drop-box.conf.tpl | 3 +-- 6 files changed, 7 insertions(+), 13 deletions(-) rename lib/gateway/{services => public_services}/drop-box.conf.tpl (76%) diff --git a/docker-compose.dev.yaml b/docker-compose.dev.yaml index ab501c34..00a109e3 100644 --- a/docker-compose.dev.yaml +++ b/docker-compose.dev.yaml @@ -214,7 +214,6 @@ services: drop-box: environment: # Runtime - - QUART_DEBUG=True - BENTO_DEBUG=True ports: - "${BENTOV2_DROP_BOX_EXTERNAL_PORT}:${BENTOV2_DROP_BOX_INTERNAL_PORT}" diff --git a/docker-compose.yaml b/docker-compose.yaml index 218c690b..166b4a0e 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -206,16 +206,10 @@ 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=${BENTOV2_DROP_BOX_MINIO_BUCKET} + - BENTO_DEBUG=False - SERVICE_DATA=/data - - SERVICE_URL=${BENTOV2_PORTAL_PUBLIC_URL}/api/drop-box + - CORS_ORIGINS=${BENTO_CORS_ORIGINS} networks: - drop-box-net expose: diff --git a/etc/bento.env b/etc/bento.env index 212569ff..200bca70 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -14,6 +14,8 @@ BENTOV2_AUTH_PUBLIC_URL=https://${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 diff --git a/etc/bento_services.json b/etc/bento_services.json index 98eea5b2..98f881ba 100644 --- a/etc/bento_services.json +++ b/etc/bento_services.json @@ -7,7 +7,7 @@ }, "drop-box": { "service_kind": "drop-box", - "url_template": "{BENTO_PORTAL_PUBLIC_URL}/api/{service_kind}", + "url_template": "{BENTO_PUBLIC_URL}/api/{service_kind}", "repository": "git@github.com:bento-platform/bento_drop_box_service", "data_service": false }, diff --git a/lib/authz/docker-compose.authz.yaml b/lib/authz/docker-compose.authz.yaml index eef867be..91e3e3bd 100644 --- a/lib/authz/docker-compose.authz.yaml +++ b/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: ${BENTO_AUTHZ_MEM_LIM} networks: - authz-net diff --git a/lib/gateway/services/drop-box.conf.tpl b/lib/gateway/public_services/drop-box.conf.tpl similarity index 76% rename from lib/gateway/services/drop-box.conf.tpl rename to lib/gateway/public_services/drop-box.conf.tpl index e5acd622..79fde1a8 100644 --- a/lib/gateway/services/drop-box.conf.tpl +++ b/lib/gateway/public_services/drop-box.conf.tpl @@ -1,9 +1,8 @@ -location /api/drop-box { return 302 https://${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 ^ $request_uri; From 5952dca0e84ad2c1f5f38ddbfc5434bfceb3bacd Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 5 Jun 2023 14:07:04 -0400 Subject: [PATCH 02/29] switch web to drop box upload pr --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 200bca70..52d190f0 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -93,7 +93,7 @@ BENTO_AUTHZ_DB_MEM_LIM=1G # Web BENTO_WEB_CUSTOM_HEADER= BENTOV2_WEB_IMAGE=ghcr.io/bento-platform/bento_web -BENTOV2_WEB_VERSION=2.0.0 +BENTOV2_WEB_VERSION=pr-243 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net From 23e3f65b9d417effdbfe25e33764d4e5039708fb Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 5 Jun 2023 14:38:54 -0400 Subject: [PATCH 03/29] switch drop box to pr-28 image --- docker-compose.yaml | 4 +++- etc/bento.env | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 166b4a0e..9f4d7567 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -15,7 +15,7 @@ services: - 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}${BENTOV2_AUTH_WELLKNOWN_PATH} + - BENTO_OPENID_CONFIG_URL - REDIRECT_AFTER_LOGOUT_URI=${BENTOV2_AUTH_PUBLIC_URL}${BENTOV2_AUTH_REDIRECT_AFTER_LOGOUT_PATH} - CLIENT_ID=${BENTOV2_AUTH_CLIENT_ID} - CLIENT_SECRET @@ -210,6 +210,8 @@ services: - SERVICE_DATA=/data - SERVICE_URL=${BENTOV2_PORTAL_PUBLIC_URL}/api/drop-box - CORS_ORIGINS=${BENTO_CORS_ORIGINS} + - BENTO_AUTHZ_SERVICE_URL + - OPENID_CONFIG_URL=${BENTO_OPENID_CONFIG_URL} networks: - drop-box-net expose: diff --git a/etc/bento.env b/etc/bento.env index 52d190f0..d35b681d 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -53,6 +53,8 @@ BENTOV2_AUTH_VOL_DIR=${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=/* @@ -105,7 +107,7 @@ BENTOV2_WEB_CPUS=2 # Drop-Box BENTOV2_DROP_BOX_IMAGE=ghcr.io/bento-platform/bento_drop_box_service -BENTOV2_DROP_BOX_VERSION=0.11.3 +BENTOV2_DROP_BOX_VERSION=pr-28 BENTOV2_DROP_BOX_VERSION_DEV=${BENTOV2_DROP_BOX_VERSION}-dev BENTOV2_DROP_BOX_CONTAINER_NAME=${BENTOV2_PREFIX}-drop-box BENTO_DROP_BOX_NETWORK=${BENTOV2_PREFIX}-drop-box-net From c3236e19e2fd8c4748be4d0941098d34149cb159 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 5 Jun 2023 16:24:28 -0400 Subject: [PATCH 04/29] fix: drop box service url --- docker-compose.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 9f4d7567..6c60920e 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -208,7 +208,7 @@ services: - BENTO_UID - BENTO_DEBUG=False - SERVICE_DATA=/data - - SERVICE_URL=${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=${BENTO_OPENID_CONFIG_URL} From bac2f5edd13fa0d14680bbd3cfd32eef7674858c Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 5 Jun 2023 16:26:15 -0400 Subject: [PATCH 05/29] chore: pass bento public url to web for including token to public requests --- lib/web/docker-compose.web.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/web/docker-compose.web.yaml b/lib/web/docker-compose.web.yaml index 0c760062..63446c8c 100644 --- a/lib/web/docker-compose.web.yaml +++ b/lib/web/docker-compose.web.yaml @@ -11,6 +11,7 @@ services: - BENTO_CBIOPORTAL_ENABLED - BENTO_CBIOPORTAL_PUBLIC_URL - BENTO_URL=${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=${BENTOV2_AUTH_CLIENT_ID} From 4a2ffa53ea3f2e4f49aad18e9b063cfdefdb5221 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 9 Jun 2023 10:11:57 -0400 Subject: [PATCH 06/29] chore: bump authz to 0.2.1 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index a53dd3d4..d51c0c4b 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -75,7 +75,7 @@ BENTO_AUTH_DB_NETWORK="${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=${BENTOV2_PREFIX}-authz-net From 680298989ebed744bd221f9d3fd022b21e4b0ddc Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 9 Jun 2023 15:42:55 -0400 Subject: [PATCH 07/29] chore: remove unused gateway env vars --- docker-compose.yaml | 11 ----------- etc/bento_dev.env | 1 - 2 files changed, 12 deletions(-) diff --git a/docker-compose.yaml b/docker-compose.yaml index 6c60920e..7e548645 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -7,19 +7,8 @@ services: condition: service_healthy environment: - BENTO_DEBUG=false - - CHORD_DEBUG=false - - CHORD_PERMISSIONS=true - - CHORD_PRIVATE_MODE=${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}${BENTOV2_AUTH_WELLKNOWN_PATH} - - BENTO_OPENID_CONFIG_URL - - REDIRECT_AFTER_LOGOUT_URI=${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 diff --git a/etc/bento_dev.env b/etc/bento_dev.env index a75a0440..490ea491 100644 --- a/etc/bento_dev.env +++ b/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' From f1849c22efbd6eb8d472ad46f977d7d8df1c41bb Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 13 Jun 2023 08:46:13 -0400 Subject: [PATCH 08/29] chore: remove unused/deprecated drop box minio variables --- etc/bento.env | 5 ----- 1 file changed, 5 deletions(-) diff --git a/etc/bento.env b/etc/bento.env index 1af0193d..3c2c4076 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -115,11 +115,6 @@ BENTOV2_DROP_BOX_INTERNAL_PORT=${BENTO_STD_SERVICE_INTERNAL_PORT} BENTOV2_DROP_BOX_EXTERNAL_PORT=6000 BENTOV2_DROP_BOX_VOL_DIR=${BENTOV2_ROOT_DATA_DIR}/drop-box/data-x -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 From 88129bd42e6501ad41de0eeeb4d6980425431670 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 13 Jun 2023 15:05:21 -0400 Subject: [PATCH 09/29] pin public to 0.12.0 --- etc/bento.env | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/etc/bento.env b/etc/bento.env index 9a35300b..68e9c228 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -346,8 +346,7 @@ BENTOV2_GOHAN_PRIVATE_AUTHZ_URL=http://${BENTOV2_GOHAN_AUTHZ_OPA_CONTAINER_NAME} # Bento-Public BENTO_PUBLIC_IMAGE=ghcr.io/bento-platform/bento_public -# BENTO_PUBLIC_VERSION=0.12.0 -BENTO_PUBLIC_VERSION=edge +BENTO_PUBLIC_VERSION=0.12.0 BENTO_PUBLIC_VERSION_DEV=${BENTO_PUBLIC_VERSION}-dev BENTO_PUBLIC_CONTAINER_NAME=${BENTOV2_PREFIX}-public BENTO_PUBLIC_NETWORK=${BENTOV2_PREFIX}-public-net From d34653acb7cd504436321a4d233ae130f37f5c48 Mon Sep 17 00:00:00 2001 From: Brennan Brouillette Date: Fri, 9 Jun 2023 18:20:58 -0400 Subject: [PATCH 10/29] patch: gohan envs --- etc/bento.env | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/etc/bento.env b/etc/bento.env index 68e9c228..9196c0cc 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -280,14 +280,14 @@ BENTOV2_REDIS_CPUS=2 # Gohan BENTOV2_GOHAN_DEBUG=false BENTOV2_GOHAN_SERVICE_CONTACT=info@c3g.ca -BENTOV2_GOHAN_SEMVER=3.8.0 +BENTOV2_GOHAN_SEMVER=3.9.0 # -- Host BENTOV2_GOHAN_DATA_ROOT=${BENTOV2_ROOT_DATA_DIR}/gohan # -- API BENTOV2_GOHAN_API_IMAGE=ghcr.io/bento-platform/gohan-api -BENTOV2_GOHAN_API_VERSION=3.8.0 +BENTOV2_GOHAN_API_VERSION=3.9.0 BENTOV2_GOHAN_API_VERSION_DEV=${BENTOV2_GOHAN_API_VERSION}-dev BENTOV2_GOHAN_API_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-api @@ -316,7 +316,7 @@ BENTOV2_GOHAN_ES_USERNAME=elastic # BENTOV2_GOHAN_ES_PASSWORD comes from default_config BENTOV2_GOHAN_ES_IMAGE=ghcr.io/bento-platform/gohan-elasticsearch -BENTOV2_GOHAN_ES_VERSION=3.8.0 +BENTOV2_GOHAN_ES_VERSION=3.9.0 BENTOV2_GOHAN_ES_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-elasticsearch BENTO_GOHAN_ES_NETWORK=${BENTOV2_PREFIX}-gohan-elasticsearch-net From ac7980bfdbc5060c50ad02e969e4b448908e456d Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 14 Jun 2023 11:05:06 -0400 Subject: [PATCH 11/29] start setting up new drop box (permissions + cors) --- docker-compose.dev.yaml | 3 ++- docker-compose.yaml | 3 ++- etc/bento.env | 2 +- .../{services => public_services}/service-registry.conf.tpl | 3 +-- 4 files changed, 6 insertions(+), 5 deletions(-) rename lib/gateway/{services => public_services}/service-registry.conf.tpl (76%) diff --git a/docker-compose.dev.yaml b/docker-compose.dev.yaml index 00a109e3..e64a6873 100644 --- a/docker-compose.dev.yaml +++ b/docker-compose.dev.yaml @@ -203,8 +203,9 @@ services: service-registry: environment: - - FLASK_DEBUG=True - BENTO_DEBUG=True + - BENTO_VALIDATE_SSL=False + - LOG_LEVEL=debug ports: - "${BENTOV2_SERVICE_REGISTRY_EXTERNAL_PORT}:${BENTOV2_SERVICE_REGISTRY_INTERNAL_PORT}" extends: diff --git a/docker-compose.yaml b/docker-compose.yaml index 850cca1b..ea030b00 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -236,7 +236,8 @@ services: - BENTO_PORTAL_PUBLIC_URL=${BENTOV2_PORTAL_PUBLIC_URL} - BENTO_DEBUG=False - - BENTO_VALIDATE_SSL=False + - BENTO_VALIDATE_SSL=True + - CORS_ORIGINS=${BENTO_CORS_ORIGINS} # Timeout, in seconds (integers only), for contacting services from the JSON - CONTACT_TIMEOUT=10 diff --git a/etc/bento.env b/etc/bento.env index 9196c0cc..56d42507 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -121,7 +121,7 @@ BENTOV2_DROP_BOX_CPUS=3 # Service Registry BENTOV2_SERVICE_REGISTRY_IMAGE=ghcr.io/bento-platform/bento_service_registry -BENTOV2_SERVICE_REGISTRY_VERSION=0.11.2 +BENTOV2_SERVICE_REGISTRY_VERSION=pr-14 BENTOV2_SERVICE_REGISTRY_VERSION_DEV=${BENTOV2_SERVICE_REGISTRY_VERSION}-dev BENTOV2_SERVICE_REGISTRY_CONTAINER_NAME=${BENTOV2_PREFIX}-service-registry BENTO_SERVICE_REGISTRY_NETWORK=${BENTOV2_PREFIX}-service-registry-net diff --git a/lib/gateway/services/service-registry.conf.tpl b/lib/gateway/public_services/service-registry.conf.tpl similarity index 76% rename from lib/gateway/services/service-registry.conf.tpl rename to lib/gateway/public_services/service-registry.conf.tpl index 814eb624..7fa10a59 100644 --- a/lib/gateway/services/service-registry.conf.tpl +++ b/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 ^ $request_uri; From c7be31b3a3a0f17e74c08a0e8dafbe22e601c69b Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 14 Jun 2023 11:06:07 -0400 Subject: [PATCH 12/29] chore: pass authz url to service registry --- docker-compose.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/docker-compose.yaml b/docker-compose.yaml index ea030b00..6d9f31fc 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -238,6 +238,7 @@ services: - BENTO_DEBUG=False - BENTO_VALIDATE_SSL=True - CORS_ORIGINS=${BENTO_CORS_ORIGINS} + - BENTO_AUTHZ_SERVICE_URL # Timeout, in seconds (integers only), for contacting services from the JSON - CONTACT_TIMEOUT=10 From d9c8a0882054b112ee77ad136193c0327b1ba57d Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 14 Jun 2023 11:25:27 -0400 Subject: [PATCH 13/29] fix bento services service registry url template --- etc/bento_services.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento_services.json b/etc/bento_services.json index 98f881ba..f1c3c1cc 100644 --- a/etc/bento_services.json +++ b/etc/bento_services.json @@ -1,7 +1,7 @@ { "service-registry": { "service_kind": "service-registry", - "url_template": "{BENTO_PORTAL_PUBLIC_URL}/api/{service_kind}", + "url_template": "{BENTO_PUBLIC_URL}/api/{service_kind}", "repository": "git@github.com:bento-platform/bento_service_registry", "data_service": false }, From fa6de422b760a48649ce31ea4e94a87ef558b229 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 14 Jun 2023 15:37:04 -0400 Subject: [PATCH 14/29] chore: use web pr-249 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 9a35300b..6b0d766c 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -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=pr-243 +BENTOV2_WEB_VERSION=pr-249 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net From 4026b9acd7e8d6a218d8a741669049b7fa410bbb Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Thu, 15 Jun 2023 16:39:04 -0400 Subject: [PATCH 15/29] chore: pin drop box at 1.0.0 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 6d2ab504..c31c25c8 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -107,7 +107,7 @@ BENTOV2_WEB_CPUS=2 # Drop-Box BENTOV2_DROP_BOX_IMAGE=ghcr.io/bento-platform/bento_drop_box_service -BENTOV2_DROP_BOX_VERSION=pr-28 +BENTOV2_DROP_BOX_VERSION=1.0.0 BENTOV2_DROP_BOX_VERSION_DEV=${BENTOV2_DROP_BOX_VERSION}-dev BENTOV2_DROP_BOX_CONTAINER_NAME=${BENTOV2_PREFIX}-drop-box BENTO_DROP_BOX_NETWORK=${BENTOV2_PREFIX}-drop-box-net From d90a84bb25c820aa6f09075cdd872485644214d9 Mon Sep 17 00:00:00 2001 From: Brennan Brouillette Date: Thu, 15 Jun 2023 18:06:10 -0400 Subject: [PATCH 16/29] patch: bump gohan to 3.9.1 --- etc/bento.env | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/etc/bento.env b/etc/bento.env index c31c25c8..d0d3a6f2 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -280,14 +280,14 @@ BENTOV2_REDIS_CPUS=2 # Gohan BENTOV2_GOHAN_DEBUG=false BENTOV2_GOHAN_SERVICE_CONTACT=info@c3g.ca -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=${BENTOV2_PREFIX}-gohan-api @@ -316,7 +316,7 @@ BENTOV2_GOHAN_ES_USERNAME=elastic # BENTOV2_GOHAN_ES_PASSWORD comes from default_config BENTOV2_GOHAN_ES_IMAGE=ghcr.io/bento-platform/gohan-elasticsearch -BENTOV2_GOHAN_ES_VERSION=3.9.0 +BENTOV2_GOHAN_ES_VERSION=3.9.1 BENTOV2_GOHAN_ES_CONTAINER_NAME=${BENTOV2_PREFIX}-gohan-elasticsearch BENTO_GOHAN_ES_NETWORK=${BENTOV2_PREFIX}-gohan-elasticsearch-net From 83f30d45b0718779be810d8f6a5172df53974855 Mon Sep 17 00:00:00 2001 From: Gordon Krieger Date: Fri, 16 Jun 2023 09:04:26 -0400 Subject: [PATCH 17/29] beacon env changes (for beacon pr #43) --- etc/bento.env | 1 - lib/beacon/config/beacon_config.json | 3 --- lib/beacon/docker-compose.beacon.yaml | 3 ++- 3 files changed, 2 insertions(+), 5 deletions(-) diff --git a/etc/bento.env b/etc/bento.env index d0d3a6f2..9ecf60ca 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -363,7 +363,6 @@ BENTO_PUBLIC_MAX_QUERY_PARAMETERS=2 BENTO_PUBLIC_TRANSLATED=true # Beacon -BENTO_BEACON_DEBUG=true BENTO_BEACON_CONTAINER_NAME=${BENTOV2_PREFIX}-beacon BENTO_BEACON_NETWORK=${BENTOV2_PREFIX}-beacon-net BENTO_BEACON_IMAGE=ghcr.io/bento-platform/bento_beacon diff --git a/lib/beacon/config/beacon_config.json b/lib/beacon/config/beacon_config.json index d756b397..32779665 100644 --- a/lib/beacon/config/beacon_config.json +++ b/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", diff --git a/lib/beacon/docker-compose.beacon.yaml b/lib/beacon/docker-compose.beacon.yaml index 818347cc..4b300ce5 100644 --- a/lib/beacon/docker-compose.beacon.yaml +++ b/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: - ${BENTO_BEACON_CONFIG_DIR}:/config:ro networks: From c4919d01fa6c6867c755d2794887665b282d923b Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 19 Jun 2023 13:08:53 -0400 Subject: [PATCH 18/29] chore: set service registry version to 1.0.0 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 56d42507..bca1324d 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -121,7 +121,7 @@ BENTOV2_DROP_BOX_CPUS=3 # Service Registry BENTOV2_SERVICE_REGISTRY_IMAGE=ghcr.io/bento-platform/bento_service_registry -BENTOV2_SERVICE_REGISTRY_VERSION=pr-14 +BENTOV2_SERVICE_REGISTRY_VERSION=1.0.0 BENTOV2_SERVICE_REGISTRY_VERSION_DEV=${BENTOV2_SERVICE_REGISTRY_VERSION}-dev BENTOV2_SERVICE_REGISTRY_CONTAINER_NAME=${BENTOV2_PREFIX}-service-registry BENTO_SERVICE_REGISTRY_NETWORK=${BENTOV2_PREFIX}-service-registry-net From d7fa1a310ac40c77d07b84c719994c39eda54d1a Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 19 Jun 2023 13:11:35 -0400 Subject: [PATCH 19/29] chore: set web to pr-259 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 239efe51..7aebc288 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -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=pr-249 +BENTOV2_WEB_VERSION=pr-259 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net From bbebc0851d2218a71107a8b2ef16b5c0e4e47a33 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 19 Jun 2023 15:04:02 -0400 Subject: [PATCH 20/29] chore: set web to pr-251 (release v2.1 branch) --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 7aebc288..be8558e3 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -95,7 +95,7 @@ BENTO_AUTHZ_DB_MEM_LIM=1G # Web BENTO_WEB_CUSTOM_HEADER= BENTOV2_WEB_IMAGE=ghcr.io/bento-platform/bento_web -BENTOV2_WEB_VERSION=pr-259 +BENTOV2_WEB_VERSION=pr-251 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net From 530a69ab21693b02b9fa0842db535e275b1d81aa Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 21 Jun 2023 14:11:46 -0400 Subject: [PATCH 21/29] chore: bump beacon to 0.7.0 and public to 0.13.0 --- etc/bento.env | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/etc/bento.env b/etc/bento.env index 93282d59..0e2969c8 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -346,7 +346,7 @@ BENTOV2_GOHAN_PRIVATE_AUTHZ_URL=http://${BENTOV2_GOHAN_AUTHZ_OPA_CONTAINER_NAME} # Bento-Public BENTO_PUBLIC_IMAGE=ghcr.io/bento-platform/bento_public -BENTO_PUBLIC_VERSION=0.12.1 +BENTO_PUBLIC_VERSION=0.13.0 BENTO_PUBLIC_VERSION_DEV=${BENTO_PUBLIC_VERSION}-dev BENTO_PUBLIC_CONTAINER_NAME=${BENTOV2_PREFIX}-public BENTO_PUBLIC_NETWORK=${BENTOV2_PREFIX}-public-net @@ -366,7 +366,7 @@ 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=0.6.0 +BENTO_BEACON_VERSION=0.7.0 BENTO_BEACON_VERSION_DEV=${BENTO_BEACON_VERSION}-dev BENTO_BEACON_INTERNAL_PORT=${BENTO_STD_SERVICE_INTERNAL_PORT} BENTO_BEACON_EXTERNAL_PORT=5000 From 7246a59ae9dfe1bbb7019b4f1b8c5e46e5ea2282 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 21 Jun 2023 15:57:47 -0400 Subject: [PATCH 22/29] chore: update redis image to 7.0.11 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 0e2969c8..0bfcf4e7 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -267,7 +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 From 4a58de94b580650cfd7dd21e2c503f364746c304 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 21 Jun 2023 15:58:14 -0400 Subject: [PATCH 23/29] chore: set web version to 2.1.0 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 0bfcf4e7..ff2a4a6b 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -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=pr-251 +BENTOV2_WEB_VERSION=2.1.0 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net From 92172617b8681f1b9a110e44da730e819dd587f9 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 21 Jun 2023 16:06:31 -0400 Subject: [PATCH 24/29] chore: bump katsu to 3.0.1 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index ff2a4a6b..14b0953a 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -244,7 +244,7 @@ BENTOV2_KATSU_DB_CPUS=4 # Katsu BENTOV2_KATSU_IMAGE=ghcr.io/bento-platform/katsu -BENTOV2_KATSU_VERSION=3.0.0 +BENTOV2_KATSU_VERSION=3.0.1 BENTOV2_KATSU_VERSION_DEV=${BENTOV2_KATSU_VERSION}-dev BENTOV2_KATSU_CONTAINER_NAME=${BENTOV2_PREFIX}-katsu BENTO_KATSU_NETWORK=${BENTOV2_PREFIX}-katsu-net From 01e2ab3d402d7cbc129c4e6dbb966933fa2f94af Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 3 Jul 2023 15:29:37 -0400 Subject: [PATCH 25/29] chore: bump public to 0.13.1 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 14b0953a..9ad6a622 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -346,7 +346,7 @@ BENTOV2_GOHAN_PRIVATE_AUTHZ_URL=http://${BENTOV2_GOHAN_AUTHZ_OPA_CONTAINER_NAME} # Bento-Public BENTO_PUBLIC_IMAGE=ghcr.io/bento-platform/bento_public -BENTO_PUBLIC_VERSION=0.13.0 +BENTO_PUBLIC_VERSION=0.13.1 BENTO_PUBLIC_VERSION_DEV=${BENTO_PUBLIC_VERSION}-dev BENTO_PUBLIC_CONTAINER_NAME=${BENTOV2_PREFIX}-public BENTO_PUBLIC_NETWORK=${BENTOV2_PREFIX}-public-net From f1d07147aabead370249eddbdf774e7c2b1973a8 Mon Sep 17 00:00:00 2001 From: Gordon Krieger Date: Tue, 4 Jul 2023 12:33:05 -0400 Subject: [PATCH 26/29] bump beacon to 0.7.1 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 9ad6a622..1f1db26f 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -366,7 +366,7 @@ 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=0.7.0 +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 From 817d8289496afe0485189202c174440ac4954f6e Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Tue, 4 Jul 2023 17:14:04 -0400 Subject: [PATCH 27/29] chore: bump web to 2.1.1 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 1f1db26f..cbf05521 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -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=2.1.0 +BENTOV2_WEB_VERSION=2.1.1 BENTOV2_WEB_VERSION_DEV=${BENTOV2_WEB_VERSION}-dev BENTOV2_WEB_CONTAINER_NAME=${BENTOV2_PREFIX}-web BENTO_WEB_NETWORK=${BENTOV2_PREFIX}-web-net From d63cfeac31687e518f863eb79d2511116b3fce68 Mon Sep 17 00:00:00 2001 From: Victor Rocheleau Date: Wed, 5 Jul 2023 12:00:28 -0400 Subject: [PATCH 28/29] bento_public use edge image --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index cbf05521..372f695d 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -346,7 +346,7 @@ BENTOV2_GOHAN_PRIVATE_AUTHZ_URL=http://${BENTOV2_GOHAN_AUTHZ_OPA_CONTAINER_NAME} # Bento-Public BENTO_PUBLIC_IMAGE=ghcr.io/bento-platform/bento_public -BENTO_PUBLIC_VERSION=0.13.1 +BENTO_PUBLIC_VERSION=edge BENTO_PUBLIC_VERSION_DEV=${BENTO_PUBLIC_VERSION}-dev BENTO_PUBLIC_CONTAINER_NAME=${BENTOV2_PREFIX}-public BENTO_PUBLIC_NETWORK=${BENTOV2_PREFIX}-public-net From a8a945143ce6a8266c5849eb6025f5af346938ba Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Wed, 5 Jul 2023 13:07:37 -0400 Subject: [PATCH 29/29] chore: bump public to 0.13.2 --- etc/bento.env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etc/bento.env b/etc/bento.env index 372f695d..f3386617 100644 --- a/etc/bento.env +++ b/etc/bento.env @@ -346,7 +346,7 @@ BENTOV2_GOHAN_PRIVATE_AUTHZ_URL=http://${BENTOV2_GOHAN_AUTHZ_OPA_CONTAINER_NAME} # Bento-Public BENTO_PUBLIC_IMAGE=ghcr.io/bento-platform/bento_public -BENTO_PUBLIC_VERSION=edge +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