Removed Galaxy remnants.

HBPMedical · Jul 20, 2023 · 2e36c47 · 2e36c47
1 parent 3a3910e
commit 2e36c47
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Showing 5 changed files with 45 additions and 26 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -41,15 +41,49 @@ 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}
       PUBLIC_MIP_PROTOCOL: ${PUBLIC_MIP_PROTOCOL}
       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