From 2e36c4739f166efaa985600ed9577ab7f09cbe0c Mon Sep 17 00:00:00 2001 From: ThanKarab Date: Thu, 20 Jul 2023 07:27:47 -0700 Subject: [PATCH] Removed Galaxy remnants. --- kubernetes/values.yaml | 7 +--- mip | 14 +++---- tests/backend_components/docker-compose.yml | 5 --- tests/frontend_components/config/Caddyfile | 5 --- tests/frontend_components/docker-compose.yml | 40 ++++++++++++++++++-- 5 files changed, 45 insertions(+), 26 deletions(-) diff --git a/kubernetes/values.yaml b/kubernetes/values.yaml index 5c3a9d16..67520ab8 100644 --- a/kubernetes/values.yaml +++ b/kubernetes/values.yaml @@ -18,7 +18,7 @@ mip: PUBLIC_PROTOCOL: "" PUBLIC_HOST: "" NAME: "MIP {{ .Values.mip.version }}" - VERSION_STRING: "Frontend: {{ .Values.frontend.image.version }}, Gateway: {{ .Values.gateway.image.version }}, Backend: {{ .Values.portalbackend.image.version }}, Engine1 (Exareme): {{ .Values.engines.exareme.image.version }}, Engine2 (Exareme2): {{ .Values.engines.exareme2.image.version }}, Galaxy: {{ .Values.galaxy.image.version }}" + VERSION_STRING: "Frontend: {{ .Values.frontend.image.version }}, Gateway: {{ .Values.gateway.image.version }}, Backend: {{ .Values.portalbackend.image.version }}, Engine1 (Exareme): {{ .Values.engines.exareme.image.version }}, Engine2 (Exareme2): {{ .Values.engines.exareme2.image.version }}" datacatalogue: PROTOCOL: https @@ -117,8 +117,3 @@ keycloak: storage1: data_path: /opt/mip-deployment/config/keycloak/HBPTheme data_size: 100Mi - -galaxy: - image: - name: hbpmip/galaxy - version: 1.3.4 diff --git a/mip b/mip index fc6364e5..48c1b419 100755 --- a/mip +++ b/mip @@ -35,13 +35,13 @@ DOCKERHUB_APP_TOKEN="p5BLk2iEmpkJoJINBl2lIL2DmpnKmChGBlLkk22CAHLNKJ2Kpl2lK3ApmHn DOCKER_PROJECT_NAME="mip" DOCKER_FEDERATION_PROJECT_NAME="mipfederation" -MIP_COMPONENTS="frontend gateway portalbackend portalbackend_db galaxy keycloak keycloak_db create_dbs exareme_master exareme_keystore" -MIP_COMPONENT_LABELS="Portal Frontend,Gateway,Portal Backend,Portal Backend PostgreSQL DB,Galaxy,KeyCloak,KeyCloak DB,Create DBs,Exareme Master,Exareme Keystore" -MIP_COMPONENT_IMAGES=("portainer/portainer" "bitnami/consul" "hbpmip/exareme" "hbpmip/galaxy" "postgres" "hbpmip/create-databases" "hbpmip/portal-backend" "hbpmip/gateway" "hbpmip/portal-frontend" "jboss/keycloak") +MIP_COMPONENTS="frontend gateway portalbackend portalbackend_db keycloak keycloak_db create_dbs exareme_master exareme_keystore" +MIP_COMPONENT_LABELS="Portal Frontend,Gateway,Portal Backend,Portal Backend PostgreSQL DB,KeyCloak,KeyCloak DB,Create DBs,Exareme Master,Exareme Keystore" +MIP_COMPONENT_IMAGES=("portainer/portainer" "bitnami/consul" "hbpmip/exareme" "postgres" "hbpmip/create-databases" "hbpmip/portal-backend" "hbpmip/gateway" "hbpmip/portal-frontend" "jboss/keycloak") MIP_FEDERATION_MS_COMPONENTS="exareme-master exareme-keystore" MIP_FEDERATION_MS_COMPONENT_LABELS="Exareme Master,Exareme Keystore" -MIP_FEDERATION_UI_COMPONENTS="frontend gateway portalbackend portalbackend_db galaxy create_dbs" -MIP_FEDERATION_UI_COMPONENT_LABELS="Portal Frontend,Gateway,Portal Backend,Portal Backend PostgreSQL DB,Galaxy,Create DBs" +MIP_FEDERATION_UI_COMPONENTS="frontend gateway portalbackend portalbackend_db create_dbs" +MIP_FEDERATION_UI_COMPONENT_LABELS="Portal Frontend,Gateway,Portal Backend,Portal Backend PostgreSQL DB,Create DBs" MIP_FEDERATION_WK_COMPONENTS="exareme" MIP_FEDERATION_WK_COMPONENT_LABELS="Exareme" CONFIGURE_PARTS="docker-mtu user ssh pusher pathologies link protocol host exareme-ip logs data keycloak dataset-compilation all" @@ -1081,9 +1081,9 @@ Operate the Human Brain Project MIP, whether it's a local setup or a federation --host [PUBLIC_MIP_HOST] Set the hostname/IP on which the MIP will listen. For "local" installation and "ui" federation node. --component [MIP_COMPONENT] Specific MIP component which can be targetted (in logs, install, version, pull, start, stop, restart action). Typical MIP_COMPONENT for "local" MIP: - [frontend|gateway|portalbackend|portalbackend_db|galaxy|keycloak|keycloak_db|create_dbs|exareme_master|exareme_keystore] + [frontend|gateway|portalbackend|portalbackend_db|keycloak|keycloak_db|create_dbs|exareme_master|exareme_keystore] Typical MIP_COMPONENT for "ui" federation node: - [frontend|gateway|portalbackend|portalbackend_db|galaxy|create_dbs] + [frontend|gateway|portalbackend|portalbackend_db|create_dbs] --pathology [DATASET_PATHOLOGY(IES)] In case of data compile, specify the pathology or pathologies (comma-separated) to compile. --with-keycloak-authentication Use Keycloak authentication. Complementary keycloak parameters may be set, or they may be asked at diff --git a/tests/backend_components/docker-compose.yml b/tests/backend_components/docker-compose.yml index 56f7a485..9668dfa4 100644 --- a/tests/backend_components/docker-compose.yml +++ b/tests/backend_components/docker-compose.yml @@ -228,11 +228,6 @@ services: EXAREME2_URL: ${EXAREME2_URL} ### Exareme ### EXAREME_URL: http://exareme_master:9090 - ### Galaxy ### - #GALAXY_URL: http://galaxy - #GALAXY_API_KEY: d14a4cc5eebf805eb2ff261374ed08a2 - #GALAXY_USERNAME: admin - #GALAXY_PASSWORD: password ### Keycloak ### KEYCLOAK_AUTH_URL: ${KEYCLOAK_PROTOCOL}://${KEYCLOAK_URL}/auth/ KEYCLOAK_REALM: ${KEYCLOAK_REALM} diff --git a/tests/frontend_components/config/Caddyfile b/tests/frontend_components/config/Caddyfile index 2b1ade9a..05030209 100644 --- a/tests/frontend_components/config/Caddyfile +++ b/tests/frontend_components/config/Caddyfile @@ -38,11 +38,6 @@ file_server } - redir {$GALAXY_PATH} {$GALAXY_PATH}/ - handle {$GALAXY_PATH}/* { - import rp-{$MIP_LINK:direct} {$GALAXY_HOST} - } - redir {$KEYCLOAK_AUTH_PATH:/dummyauth} {$KEYCLOAK_AUTH_PATH:/dummyauth}/ handle {$KEYCLOAK_AUTH_PATH:/dummyauth}/* { redir /dummyauth/* / diff --git a/tests/frontend_components/docker-compose.yml b/tests/frontend_components/docker-compose.yml index 76bc0810..b847af07 100644 --- a/tests/frontend_components/docker-compose.yml +++ b/tests/frontend_components/docker-compose.yml @@ -41,11 +41,9 @@ services: - ./.stored_data/caddy/caddy_data:/data environment: ERROR_LOG_LEVEL: info - GALAXY_HOST: http://galaxy - GALAXY_PATH: /nativeGalaxy GATEWAY_SERVER: gateway:8081 INSTANCE_NAME: 'MIP ${MIP}' - VERSION: 'Frontend: ${FRONTEND}, Gateway: ${GATEWAY}, Backend: ${PORTALBACKEND}, Exareme: ${EXAREME}, Galaxy: ${GALAXY}' + VERSION: 'Frontend: ${FRONTEND}, Gateway: ${GATEWAY}, Backend: ${PORTALBACKEND}, Exareme: ${EXAREME}' KEYCLOAK_HOST: http://keycloak:8095 KEYCLOAK_AUTH_PATH: /auth PUBLIC_MIP_HOST: ${PUBLIC_MIP_HOST} @@ -53,3 +51,39 @@ services: EXTERNAL_MIP_PROTOCOL: ${EXTERNAL_MIP_PROTOCOL} MIP_LINK: ${MIP_LINK} restart: unless-stopped + +# keycloak_db: +# image: postgres:12.2 +# volumes: +# - ./.stored_data/keycloak:/var/lib/postgresql/data +# environment: +# POSTGRES_DB: keycloak +# POSTGRES_USER: keycloak +# POSTGRES_PASSWORD: password +# restart: unless-stopped +# +# keycloak: +# image: jboss/keycloak:15.0.2 +# command: -Djboss.http.port=8095 +# volumes: +# - ../../config/keycloak/keycloak.json:/tmp/mip.json +# - ../../config/keycloak/HBPTheme:/opt/jboss/keycloak/themes/HBPTheme +# environment: +# DB_VENDOR: POSTGRES +# DB_ADDR: keycloak_db +# DB_PORT: 5432 +# DB_DATABASE: keycloak +# DB_USER: keycloak +# DB_SCHEMA: public +# DB_PASSWORD: password +# KEYCLOAK_USER: admin +# KEYCLOAK_PASSWORD: Pa55w0rd +# KEYCLOAK_IMPORT: /tmp/mip.json +# KEYCLOAK_HOSTNAME: ${KEYCLOAK_URL} +# PROXY_ADDRESS_FORWARDING: 'true' #important for reverse proxy +# ports: +# - '8095:8095' +# - '8443:8443' +# depends_on: +# - keycloak_db +# restart: unless-stopped