Update default values for ACCP

.gitignore

@@ -1,5 +1,6 @@
 .idea/
 .venv/
 .vscode/
+.prettierignore
 k3s/outputs/
 ansible.cfg

README.md

@@ -62,22 +62,42 @@ If running the playbook on the server itself, there is `inventories/locahost` fi
 
 ### Installing Galaxy
 
-Once the inventory file is created, we can run the playbooks to deploy the Kubernetes cluster and the Galaxy instance. The playbook takes the arguments
+Once the inventory file is created, we can run the playbooks to deploy the
+Kubernetes cluster and the Galaxy instance. The playbook takes the arguments:
 
-- `kube_cloud_provider`: must be one of `gcp`, `aws`, or `openstack`
+- `cloud_provider`: must be one of `gcp`, `aws`, or `openstack`
+- `chart_values_file`: Optional. Path relative to `values` subfolder containing
+  values that will be used to configure the Galaxy Helm chart. The default is
+  `accp.yml`.
 
 ```bash
-ansible-playbook -i inventories/my-server.ini playbook.yml --extra-vars "kube_cloud_provider=aws" --extra-vars "application=galaxy" --extra-vars "galaxy_api_key=changeme" --extra-vars "[email protected]"
+ansible-playbook -i inventories/my-server.ini playbook.yml --extra-vars "cloud_provider=aws" --extra-vars "application=galaxy" --extra-vars "galaxy_api_key=changeme" --extra-vars "[email protected]"
 ```
 
 Once the playbook completes, the Galaxy instance will be available at `http://<server-ip>/` after a few minutes.
 
+### Adding users
+
+By default, user registration is disabled on the Galaxy instance. To add users, you can use the `bin/add_user.sh` script. The script takes the following arguments:
+
+- `host`: The IP address of the Galaxy server
+- `galaxy_api_key`: The API key for the Galaxy admin user
+- `email`: The email address of the Galaxy user to be added
+- `password`: The password for the Galaxy user
+- `username`: The username for the Galaxy user
+
+Run the script with:
+
+```bash
+bin/add_user.sh <host> <galaxy_api_key> <email> <password> <username>
+```
+
 ### Installing Pulsar
 
 The playbook can set up a Pulsar node instead of Galaxy. The invocation process is the same with the only difference being the `application` variable.
 
 ```bash
-ansible-playbook -i inventories/my-server.ini playbook.yml --extra-vars "kube_cloud_provider=aws" --extra-vars "application=pulsar" --extra-vars "pulsar_api_key=changeme"
+ansible-playbook -i inventories/my-server.ini playbook.yml --extra-vars "cloud_provider=aws" --extra-vars "application=pulsar" --extra-vars "pulsar_api_key=changeme"
 ```
 
 

bin/add_user.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# Check if all required arguments are provided
+if [ "$#" -ne 5 ]; then
+    echo "Usage: $0 <host> <galaxy_api_key> <email> <password> <username>"
+    echo "Example: $0 localhost:8080 ADMIN_API_KEY [email protected] userpass username"
+    exit 1
+fi
+
+host="$1"
+galaxy_api_key="$2"
+email="$3"
+password="$4"
+username="$5"
+
+json_data=$(cat <<EOF
+{
+    "username": "$username",
+    "email": "$email",
+    "password": "$password"
+}
+EOF
+)
+
+curl -s -X POST \
+    -H "x-api-key: $galaxy_api_key" \
+    -H "Content-Type: application/json" \
+    -d "$json_data" \
+    "http://$host/api/users"
+
+# Add a newline for better formatting
+echo

bin/init_script.sh

@@ -24,4 +24,4 @@ cd galaxy-k8s-boot
 
 sed -i "s|extra_server_args=\"--tls-san localhost --disable traefik --v=4\"|extra_server_args=\"--tls-san $(curl -s http://169.254.169.254/latest/meta-data/public-ipv4) --disable traefik --v=4\"|" inventories/localhost
 
-ansible-playbook -i inventories/localhost playbook.yml --extra-vars "kube_cloud_provider=aws" --extra-vars "job_max_cores=$(($(nproc) - $RESERVED_CORES))" --extra-vars "job_max_mem=$(($(free -m | awk '/^Mem:/{print $2}') - $RESERVED_MEM_MB))" --extra-vars "application=$APPLICATION" --extra-vars "galaxy_api_key=$GALAXY_API_KEY" --extra-vars "pulsar_api_key=$PULSAR_API_KEY"
+ansible-playbook -i inventories/localhost playbook.yml --extra-vars "cloud_provider=aws" --extra-vars "job_max_cores=$(($(nproc) - $RESERVED_CORES))" --extra-vars "job_max_mem=$(($(free -m | awk '/^Mem:/{print $2}') - $RESERVED_MEM_MB))" --extra-vars "application=$APPLICATION" --extra-vars "galaxy_api_key=$GALAXY_API_KEY" --extra-vars "pulsar_api_key=$PULSAR_API_KEY"

galaxy_app.yml

@@ -47,5 +47,8 @@
                   k8s:
                     max_cores: "{{ job_max_cores }}"
                     max_mem: "{{ job_max_mem }}"
+          service:
+            type: "{{ 'LoadBalancer' if cloud_provider == 'gcp' else 'ClusterIP' }}"
+            port: 80
 #        postgresql:
 #          galaxyDatabasePassword: galaxydbpassword

playbook.yml

@@ -12,17 +12,15 @@
 
 - name: Configure Ingress
   import_playbook: ingress.yml
-  when: kube_cloud_provider == "aws" or kube_cloud_provider == "openstack"
+  when: cloud_provider == "aws" or cloud_provider == "openstack"
 
 - name: Configure storage
   import_playbook: storage.yml
-  vars:
-    kube_cloud_provider: "{{ kube_cloud_provider }}"
 
-- name: Install Galaxy on {{ kube_cloud_provider }}
+- name: Install Galaxy
   import_playbook: galaxy_app.yml
   vars:
-    values_file: "values/{{ kube_cloud_provider }}.yml"
+    values_file: "values/{{ chart_values_file | default('accp.yml') }}"
     gxy_admin_users: "{{ galaxy_admin_users | default('') }}"
     gxy_api_key: "{{ galaxy_api_key }}"
   when: application == "galaxy"

setup.yml

@@ -9,7 +9,7 @@
         update_cache: true
       become: true
       vars:
-        install_packages: "{{ base_packages + (gcp_packages if kube_cloud_provider == 'gcp' else []) }}"
+        install_packages: "{{ base_packages + (gcp_packages if cloud_provider == 'gcp' else []) }}"
         base_packages:
           - python3
           - python3-pip

values/accp.yml

@@ -0,0 +1,75 @@
+ingress:
+  enabled: true
+  ingressClassName: ""
+  canary:
+    enabled: false
+  annotations:
+    cert-manager.io/cluster-issuer: letsencrypt-prod
+  hosts:
+  - host: ~
+    paths:
+    - path: /
+  path: /
+
+persistence:
+  storageClass: nfs
+  size: 20Gi
+
+cvmfs:
+  deployPostInstallFix: true
+  cvmfscsi:
+    cache:
+      local:
+        enabled: true
+        pvc:
+          storageClass: nfs
+          name: cvmfs-local-cache
+      alien:
+        enabled: false
+        pvc:
+          name: cvmfs-alien-cache
+    logVerbosityLevel: 5
+
+postgresql:
+  persistence:
+    storageClass: blockstorage
+
+rabbitmq:
+  persistence:
+    storageClassName: blockstorage
+
+configs:
+  galaxy.yml:
+    galaxy:
+      require_login: true
+      show_welcome_with_login: true
+      allow_user_creation: false
+
+extraFileMappings:
+  /galaxy/server/static/welcome.html:
+    applyToWeb: true
+    applyToNginx: true
+    content: |
+      <!DOCTYPE html>
+      <html lang="en">
+          <head>
+              <meta charset="utf-8" />
+              <link rel="stylesheet" href="dist/base.css" type="text/css" />
+          </head>
+          <body class="m-0">
+              <div class="py-4">
+                  <div class="container">
+                      <div class="row mb-4">
+                          <div class="col-md-12">
+                              <h2>Welcome to Galaxy on ACCP</h2>
+                              <p>
+                                  Galaxy is an interactive and workflow analysis
+                                  platform providing a graphical user interface
+                                  for computational tools. This is your own
+                                  Galaxy instance running on the ACCP platform
+                                  that you can customize and use for your own
+                                  research. You can also add others users to
+                                  this Galaxy instance via the ACCP portal.
+                              </p>
+                          </div>
+                      </div>

values/gcp.yml

@@ -1,22 +1,3 @@
-configs:
-  galaxy.yml:
-    galaxy:
-      admin_users: [email protected],[email protected]
-      master_api_key: galaxypassword
-      brand: Google
-
-# Temporary values for the development
-jobs:
-  rules:
-    tpv_rules_local.yml:
-      destinations:
-        k8s:
-          max_cores: 1
-          max_mem: 4
-
-service:
-  type: LoadBalancer
-  port: 80
 ingress:
   enabled: false
   ingressClassName: ""
@@ -27,11 +8,13 @@ ingress:
   hosts:
   - host: ~
     paths:
-    - path: /galaxy
-  path: /galaxy
+    - path: /
+  path: /
+
 persistence:
   storageClass: nfs
   size: 20Gi
+
 cvmfs:
   deployPostInstallFix: true
   cvmfscsi:
@@ -46,9 +29,15 @@ cvmfs:
         pvc:
           name: cvmfs-alien-cache
     logVerbosityLevel: 5
+
 postgresql:
   persistence:
-    storageClass: nfs
+    storageClass: blockstorage
+
 rabbitmq:
   persistence:
-    storageClassName: nfs
+    storageClassName: blockstorage
+
+service:
+  type: LoadBalancer
+  port: 80