Install Workbench 2

  1. Update config.yml
  2. Update Nginx configuration
  3. Install arvados-workbench2
  4. Restart the API server and controller
  5. Confirm working installation
  6. Trusted client setting

Workbench2 is the web-based user interface for Arvados.

Note:

Workbench2 is the replacement for Arvados Workbench. Workbench2 is suitable for day-to-day use, but does not yet implement every feature of the traditional Workbench.

Update config.yml

Edit config.yml to set the keys below. The full set of configuration options are in the Workbench section of config.yml

    Services:
      Workbench2:
        ExternalURL: "https://workbench2.ClusterID.example.com"

Update Nginx configuration

Workbench2 does not require its own database. It is a set of html, javascript and css files that are served as static files from Nginx.

Use a text editor to create a new file /etc/nginx/conf.d/arvados-workbench2.conf with the following configuration. Options that need attention are marked in red.

server {
    listen       80;
    server_name  workbench2.ClusterID.example.com;
    return 301   https://workbench2.ClusterID.example.com$request_uri;
}

server {
  listen       *:443 ssl;
  server_name  workbench2.ClusterID.example.com;

  ssl on;
  ssl_certificate     /YOUR/PATH/TO/cert.pem;
  ssl_certificate_key /YOUR/PATH/TO/cert.key;

  index  index.html;

  # Workbench2 uses a call to /config.json to bootstrap itself
  # and find out where to contact the API server.
  location /config.json {
    return 200 '{ "API_HOST": "ClusterID.example.com" }';
  }

  location / {
    root      /var/www/arvados-workbench2/workbench2;
    index     index.html;
    try_files $uri $uri/ /index.html;
    if (-f $document_root/maintenance.html) {
      return 503;
    }
  }
}

Vocabulary configuration (optional)

Workbench2 can load a vocabulary file which lists available metadata properties for groups and collections. To configure the property vocabulary definition, please visit the Workbench2 Vocabulary Format page in the Admin section.

Install arvados-workbench2

Red Hat and Centos

# yum install arvados-workbench2

Debian and Ubuntu

# apt-get install arvados-workbench2

Restart the API server and controller

Make sure the cluster config file is up to date on the API server host then restart the API server and controller processes to ensure the configuration changes are visible to the whole cluster.

# systemctl restart nginx arvados-controller

Confirm working installation

Visit https://workbench2.ClusterID.example.com in a browser. You should be able to log in using the login method you configured in the previous step. If Users.AutoAdminFirstUser is true, you will be an admin user.

Trusted client flag

Log in to Workbench once to ensure that the Arvados API server has a record of the Workbench client. (It’s OK if Workbench says your account hasn’t been activated yet. We’ll deal with that next.)

In the API server project root, start the Rails console.

Change webserver-user to the user that runs your web server process. If you install Phusion Passenger as we recommend, this is www-data on Debian-based systems, and nginx on Red Hat-based systems.
apiserver:~$ cd /var/www/arvados-api/current
apiserver:/var/www/arvados-api/current$ sudo -u webserver-user RAILS_ENV=production bundle exec rails console

At the console, enter the following commands to locate the ApiClient record for your Workbench installation (typically, while you’re setting this up, the last one in the database is the one you want), then set the is_trusted flag for the appropriate client record:

irb(main):001:0> wb = ApiClient.all.last; [wb.url_prefix, wb.created_at]
=> ["https://workbench.example.com/", Sat, 19 Apr 2014 03:35:12 UTC +00:00]
irb(main):002:0> include CurrentApiClient
=> true
irb(main):003:0> act_as_system_user do wb.update_attributes!(is_trusted: true) end
=> true

Previous: Install Workbench Next: Install Composer

The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.