Dropped Galaxy deployment.

HBPMedical · Jul 20, 2023 · 4191b80 · 4191b80
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commit 4191b80
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diff --git a/.versions_env b/.versions_env
@@ -3,5 +3,4 @@ EXAREME=24.5.1
 PORTALBACKEND=testing
 GATEWAY=1.5.0
 FRONTEND=9.3.1
-GALAXY=1.3.4
 MIP=7.1.0
diff --git a/Federation/doc/MonitoringMIPFederation.md b/Federation/doc/MonitoringMIPFederation.md
@@ -43,7 +43,6 @@ In order for you to have a better understanding of the different available compo
 ||*gateway*|
 ||*portalbackend*|
 ||*portalbackend_db*|
-||*galaxy*|
 ||*create_dbs*|
 
 You can see here that *exareme-master* and *exareme-keystore* contains a dash ( **-** ) character, and not an underscore ( **_** ), as it was indicated in the [components](../../README.md#Components) guide.  

diff --git a/Federation/docker-compose.yml b/Federation/docker-compose.yml
@@ -1,19 +1,6 @@
 version: '3.7'
 
 services:
-  galaxy:
-    image: hbpmip/galaxy:${GALAXY}
-    environment:
-      - EXAREME_IP=${EXAREME_IP}
-      - EXAREME_PORT=9090
-      - PASSWORD=password
-    command: bash -c "htpasswd -bc /etc/apache2/htpasswd admin $$PASSWORD && ./createExaremeVariables.sh && /etc/init.d/apache2 restart && ./run.sh"
-    expose:
-      - '80'
-    ports:
-      - '8090:80'
-    restart: unless-stopped
-
   portalbackend_db:
     image: postgres:11.3-alpine
     volumes:
@@ -59,11 +46,6 @@ services:
       EXAREME2_URL: ${EXAREME2_URL}
       ### Exareme ###
       EXAREME_URL: http://${EXAREME_IP}: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}
@@ -104,10 +86,8 @@ services:
       PORTAL_BACKEND_CONTEXT: services
       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}'
       TRACKER_ID: UA-80660232-5
-      GALAXY_HOST: http://galaxy
-      GALAXY_PATH: /nativeGalaxy
       DATACATALOGUE_SERVER: ${DATACATALOGUE_PROTOCOL}://${DATACATALOGUE_HOST}
       PUBLIC_MIP_HOST: ${PUBLIC_MIP_HOST}
       PUBLIC_MIP_PROTOCOL: ${PUBLIC_MIP_PROTOCOL}

diff --git a/README.md b/README.md
@@ -21,7 +21,6 @@ The "short names" listed here represent the different MIP components, as well as
 * [gateway](https://github.com/HBPMedical/gateway): "Middleware" layer between the MIP Frontend and a federated analytic engine
 * [portalbackend](https://github.com/HBPMedical/portal-backend): The "Backend API" supports the Web App
 * [portalbackend_db](https://github.com/docker-library/postgres): The portal backend's database
-* [galaxy](https://github.com/madgik/galaxy): The "Workflow Engine" provides the ability to unite separate algorithms into one larger one
 * [keycloak](https://github.com/keycloak/keycloak-containers): The "AuthN/AuthZ" system, based on KeyCloak (this component usually doesn't run in a *federated* MIP, as an "external" KeyCloak service does the job). In case this *local* "embedded" component is used, you may need to know some <a id="UsersConfiguration">details</a>, which you can find [here](documentation/UsersConfiguration.md)
 * [keycloak_db](https://github.com/docker-library/postgres): The KeyCloak's database, required only if the *keycloak* component needs to be used
 * [create_dbs](https://github.com/HBPMedical/docker-create-databases): The *one shot* container which creates and populates the DBs when required

diff --git a/config/caddy/Caddyfile b/config/caddy/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/config/keycloak/keycloak_roles_sync.py b/config/keycloak/keycloak_roles_sync.py
@@ -234,7 +234,6 @@ def synchronize_client(self, client_id, pathologies):
             {'name': 'RESEARCH_DATASET_ALL', 'composite': False, 'description': 'All datasets, without distinction'},
             {'name': 'RESEARCH_EXPERIMENT_ALL', 'composite': False},
             {'name': 'RESEARCH_PATHOLOGY_ALL', 'composite': False, 'description': 'All pathologies, without distinction'},
-            {'name': 'WORKFLOW_ADMIN', 'composite': False, 'description': 'Galaxy administrator'}
         ]
 
         full_role_list = []

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -29,21 +29,6 @@ services:
       - ./data:/root/exareme/data/
     restart: unless-stopped
 
-  galaxy:
-    image: hbpmip/galaxy:${GALAXY}
-    environment:
-      - EXAREME_IP=exareme_master
-      - EXAREME_PORT=9090
-      - PASSWORD=password
-    command: bash -c "htpasswd -bc /etc/apache2/htpasswd admin $$PASSWORD && ./createExaremeVariables.sh && /etc/init.d/apache2 restart && ./run.sh"
-    depends_on:
-      - exareme_master
-    expose:
-      - '80'
-    ports:
-      - '8090:80'
-    restart: unless-stopped
-
   portalbackend_db:
     image: postgres:11.3-alpine
     volumes:
@@ -89,11 +74,6 @@ 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}
@@ -133,10 +113,8 @@ services:
       PORTAL_BACKEND_CONTEXT: services
       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}'
       TRACKER_ID: UA-80660232-5
-      GALAXY_HOST: http://galaxy
-      GALAXY_PATH: /nativeGalaxy
       KEYCLOAK_HOST: http://keycloak:8095
       KEYCLOAK_AUTH_PATH: /auth
       PUBLIC_MIP_HOST: ${PUBLIC_MIP_HOST}

diff --git a/documentation/UserAuthorizations.md b/documentation/UserAuthorizations.md
@@ -32,7 +32,6 @@ The following ROLES should exist:
   - One role (RESEARCH_DATASET_ALL) with which the user gets access to all datasets.
   - One role (RESEARCH_PATHOLOGY_ALL) with which the user gets access to all pathologies.
   - One role (RESEARCH_EXPERIMENT_ALL) with which the user gets access to all experiments.
-  - One role (WORKFLOW_ADMIN) with which the user is given the authorization to edit existing and create new workflows through the galaxy workflow engine editor.
 
 ### Adding a new dataset
 

diff --git a/kubernetes/README.md b/kubernetes/README.md
@@ -47,7 +47,6 @@ Now, with the Kubernetes (K8s) deployment, we have 3 main, big components, which
 * [gateway_db](https://github.com/docker-library/postgres): The gateway's database
 * [portalbackend](https://github.com/HBPMedical/portal-backend): The "Backend API" which supports the Web App
 * [portalbackend_db](https://github.com/docker-library/postgres): The portal backend's database
-* [galaxy](https://github.com/madgik/galaxy): The "Workflow Engine" provides the ability to unite separate algorithms into one larger one
 * [keycloak](https://github.com/keycloak/keycloak-containers): The "AuthN/AuthZ" system, based on KeyCloak (this component usually doesn't run in a *federated* MIP, as an "external" KeyCloak service does the job). In case this *local* "embedded" component is used, you may need to know some <a id="UsersConfiguration">details</a>, which you can find [here](documentation/UsersConfiguration.md)
 * [keycloak_db](https://github.com/docker-library/postgres): The KeyCloak's database, required only if the *keycloak* component needs to be used
 * [create_dbs](https://github.com/HBPMedical/docker-create-databases): The *one shot* container which creates and populates the DBs when required

diff --git a/kubernetes/templates/frontend.yaml b/kubernetes/templates/frontend.yaml
@@ -179,10 +179,6 @@ spec:
             configMapKeyRef:
               name: mip-config
               key: mip.LINK
-        - name: GALAXY_HOST
-          value: http://galaxy-service
-        - name: GALAXY_PATH
-          value: /nativeGalaxy
         - name: DATACATALOGUE_SERVER                    # Only used in federated installation
           valueFrom:
             configMapKeyRef:

diff --git a/kubernetes/templates/galaxy.yaml b/kubernetes/templates/galaxy.yaml
diff --git a/kubernetes/templates/mip-secret.yaml b/kubernetes/templates/mip-secret.yaml
@@ -5,10 +5,6 @@ metadata:
   namespace: {{ .Values.namespace }}
 type: Opaque
 data:
-  galaxy.API_KEY: ZDE0YTRjYzVlZWJmODA1ZWIyZmYyNjEzNzRlZDA4YTI=
-  galaxy.USER: YWRtaW4=
-  galaxy.PASSWORD: cGFzc3dvcmQ=
-
   gateway-db.DB_ADMIN_USER: cG9zdGdyZXM=
   gateway-db.DB_ADMIN_PASSWORD: cGFzczEyMw==
 

diff --git a/kubernetes/templates/portalbackend.yaml b/kubernetes/templates/portalbackend.yaml
@@ -187,23 +187,6 @@ spec:
             configMapKeyRef:
               name: mip-config
               key: engines.exareme2.URL
-        - name: GALAXY_URL
-          value: http://galaxy-service
-        - name: GALAXY_API_KEY
-          valueFrom:
-            secretKeyRef:
-              name: mip-secret
-              key: galaxy.API_KEY
-        - name: GALAXY_USERNAME
-          valueFrom:
-            secretKeyRef:
-              name: mip-secret
-              key: galaxy.USER
-        - name: GALAXY_PASSWORD
-          valueFrom:
-            secretKeyRef:
-              name: mip-secret
-              key: galaxy.PASSWORD
         - name: KEYCLOAK_AUTH_URL
           valueFrom:
             configMapKeyRef: