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Introduction

This wiki page details the installation and use of the DCC RDMP software (RDMP = Research Data Management Plan) on an Ubuntu 14.04 LTS server with the "RubyonRails" web development framework installed.

Installation

Step 1 - Install Ubuntu server

Install an Ubuntu 14.04 LTS server as per: 

http://ubuntu.sun.ac.za/wiki/index.php/Enterprise_Server_Management

Use "tasksel" and install the "LAMP server" and the "OpenSSH server". See screenshot below.

  • When asked for a password for the MySQL server, type in a VERY SECRET password and do not forget it!
  • When asked for the user account details, use "dmponline" as the installed user name.!

Lamp-stack.png

See: http://tecadmin.net/install-lamp-quickly-using-tasksel-on-ubuntu-and-linuxmint/ for reference.

Step 2 - Install web app framework on the server

Install the prerequisites

Login to the server and then type the following; 

sudo apt-get install libmysqlclient-dev curl gnupg2

Install RubyonRails

Install Ruby as a normal user as follows; 

gpg2 --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
\curl -L https://get.rvm.io | bash -s stable --ruby
echo "source ~/.rvm/scripts/rvm" >> ~/.bashrc

Logout and login again, then check the installed Ruby version; 

ruby -v

ruby 2.3.0p0 (2015-12-25 revision 53290) [x86_64-linux]

Install the "rails" framework; 

gem install rails --version=4.2.6

Check version; 

rails -v

Rails 4.2.6

Install Nodejs

Type the following; 

curl -sL https://deb.nodesource.com/setup_4.x | sudo -E bash -
sudo apt-get install -y nodejs

Check version; 

nodejs -v

v4.4.6

Step 3 - Get the DMP code

Type the following; 

git clone https://github.com/CDLUC3/dmptool.git

Step 4 - Configure database connection

Configure database access by typing the following; 

cd ~/dmptool
nano config/database.yml

Copy and paste the following; 

# MySQL.  Versions 4.1 and 5.0 are recommended.
# 
# Install the MYSQL driver
#   gem install mysql2
#
# Ensure the MySQL gem is defined in your Gemfile
#   gem 'mysql2'
#
# And be sure to use new-style password hashing:
#   http://dev.mysql.com/doc/refman/5.0/en/old-client.html
production:
  adapter: mysql2
  encoding: utf8
  reconnect: false
  database: dmponline_production
  pool: 5
  username: root
  password: %PASSWORD%
  socket: /var/run/mysqld/mysqld.sock

Replace %PASSWORD% with the "root" password for your MySQL database.

Step 5 - Prepare the databases

Type the following; 

cd ~/dmptool
RAILS_ENV="production" rails dbconsole

This will connect you to the database. If successful then continue, otherwise check the database config above.

For "production"

Type the following; 

RAILS_ENV="production" rake db:create
RAILS_ENV="production" rake db:migrate
RAILS_ENV="production" rake db:seed

If there is an error and you need to drop the database to try again, then type the following; 

 RAILS_ENV="production" rake db:reset

Step 6 - Configure super-admin access to the application

Install Rails secrets

Rails also needs a unique secret key with which to encrypt its sessions. Starting from Rails 4, this secret key is stored in config/secrets.yml. But first, we need to generate a secret key. Run: 

cd ~/dmptool
RAILS_ENV=production rake secret

The commands will output a secret keys. Copy their values to your clipboard. Next, open config/secrets.yml: 

cd ~/dmptool
nano config/secrets.yml

If the file already exists, look for this: 

 secret_key_base: <%=ENV["SECRET_KEY_BASE"]%>

Then replace it with the following. If the file didn't already exist, simply insert the following. 

 secret_key_base: the value that you copied from 'rake secret'

Now configure admin user access by copying the text in the example below and pasting it into the secrets file. Remember to include the rake secret above.

Sample File
production:
  admin_name: Prod User
  admin_email: XXXXXXX
  admin_password: XXXXXXX
  secret_key_base: XXXXXX

Step 7 - Install the dependencies

Configure the local gem config as follows; 

cd 
nano .gemrc

Copy and paste the following into the open file; 

gem: --no-document

Logout and then login again and then type the following; 

cd ~/dmptool
nano Gemfile

Delete everything and then copy and paste the following; 

source 'https://rubygems.org'

# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '~> 4.2', '>= 4.2.6'
# Use mysql as the database for Active Record
gem 'mysql2', '>= 0.3.18', '< 0.5'
# Use Puma as the app server
gem 'puma', '~> 3.0'
# Use SCSS for stylesheets
#gem 'sass' 
gem 'sass-rails', '~> 5.0'
gem 'less-rails'
gem 'twitter-bootstrap-rails'
# Use Uglifier as compressor for JavaScript assets
gem 'uglifier', '>= 1.3.0'
# Use CoffeeScript for .coffee assets and views
gem 'coffee-rails', '~> 4.2'
# See https://github.com/rails/execjs#readme for more supported runtimes
gem 'therubyracer', platforms: :ruby

# Use jquery as the JavaScript library
gem 'jquery-rails'
# Turbolinks makes navigating your web application faster. Read more: https://github.com/turbolinks/turbolinks
#gem 'turbolinks', '~> 5'
# Build JSON APIs with ease. Read more: https://github.com/rails/jbuilder
gem 'jbuilder', '~> 2.5'
# Use Redis adapter to run Action Cable in production
# gem 'redis', '~> 3.0'
# Use ActiveModel has_secure_password
# gem 'bcrypt', '~> 3.1.7'

# Use Capistrano for deployment
# gem 'capistrano-rails', group: :development

#group :development, :test do
  # Call 'byebug' anywhere in the code to stop execution and get a debugger console
#  gem "better_errors"
#  gem "binding_of_caller"
#  gem 'byebug', platform: :mri
#end

#group :development do
#  # Access an IRB console on exception pages or by using <%= console %> anywhere in the code.
#  gem 'web-console'
#  gem 'listen', '~> 3.0.5'
  # Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
#  gem 'spring'
#  gem 'spring-watcher-listen', '~> 2.0.0'
#end

# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
#gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]

# Custom gems for DMPonline
gem 'activeadmin'
gem 'libv8'
gem 'devise'
gem 'devise_invitable'
gem 'omniauth'
gem 'omniauth-shibboleth'
gem 'recaptcha'
gem 'tinymce-rails'
gem 'ledermann-rails-settings'
gem 'exception_notification'
gem 'amoeba'
gem 'rolify'
gem 'email_validator'
gem 'validate_url'
gem 'cancan'
gem 'friendly_id'
gem 'contact_us' 
gem 'thin'
gem 'wicked_pdf'
gem 'htmltoword'
gem 'feedjira'
gem 'caracal'
gem 'caracal-rails'
gem 'passenger'
gem 'protected_attributes'

Type the following; 

cd ~/DMPonline_v4
gem install bundler
bundle install --deployment --without development test

Step 8 - Deploy the web app using "passenger"

Compile assets

Run the following command to compile assets for the Rails asset pipeline: 

cd ~/DMPonline_v4
bundle exec rake assets:precompile

Test the installation

Type the following; 

rvmsudo rails s -p 80

Follow the on screen instructions.

Install Passenger

Type the following; 

passenger-install-apache2-module

At the end of the installation process, you will be asked to copy and paste a configuration snippet (containing LoadModule, PassengerRoot, etc.) into your Apache configuration file.

Type the following; 

sudo nano /etc/apache2/sites-enabled/000-default.conf

Add the following; 

    LoadModule passenger_module /home/dmponline/.rvm/gems/ruby-2.3.0/gems/passenger-5.0.29/buildout/apache2/mod_passenger.so
   <IfModule mod_passenger.c>
     PassengerRoot /home/dmponline/.rvm/gems/ruby-2.3.0/gems/passenger-5.0.29
     PassengerDefaultRuby /home/dmponline/.rvm/gems/ruby-2.3.0/wrappers/ruby
   </IfModule>

Restart the web server; 

sudo service apache2 restart

Step 9 - Prepare the Apache web server

Update the Apache web server config file as follows; 

 sudo nano /etc/apache2/sites-enabled/000-default.conf

Uncomment the "ServerName" and type the following; 

ServerName rdmp.bib.sun.ac.za

Add the following as the "DocumentRoot"; 

/home/dmponline/DMPonline_v4/public

Add the <Directory> parameters as shown in the example below.

Example Apache web config

<VirtualHost *:80>
        # The ServerName directive sets the request scheme, hostname and port that
        # the server uses to identify itself. This is used when creating
        # redirection URLs. In the context of virtual hosts, the ServerName
        # specifies what hostname must appear in the request's Host: header to
        # match this virtual host. For the default virtual host (this file) this
        # value is not decisive as it is used as a last resort host regardless.
        # However, you must set it for any further virtual host explicitly.
        ServerName rdmp.bib.sun.ac.za

        ServerAdmin webmaster@localhost
        DocumentRoot /home/dmponline/DMPonline_v4/public

        LoadModule passenger_module /home/dmponline/.rvm/gems/ruby-2.3.0/gems/passenger-5.0.29/buildout/apache2/mod_passenger.so
        <IfModule mod_passenger.c>
                PassengerRoot /home/dmponline/.rvm/gems/ruby-2.3.0/gems/passenger-5.0.29
                PassengerDefaultRuby /home/dmponline/.rvm/gems/ruby-2.3.0/wrappers/ruby
        </IfModule>

        <Directory /home/dmponline/DMPonline_v4/public>
                Allow from all
                Options -MultiViews
                # Uncomment this if you're on Apache >= 2.4:
                Require all granted
        </Directory>

        # Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
        # error, crit, alert, emerg.
        # It is also possible to configure the loglevel for particular
        # modules, e.g.
        #LogLevel info ssl:warn

        ErrorLog ${APACHE_LOG_DIR}/error.log
        CustomLog ${APACHE_LOG_DIR}/access.log combined

        # For most configuration files from conf-available/, which are
        # enabled or disabled at a global level, it is possible to
        # include a line for only one particular virtual host. For example the
        # following line enables the CGI configuration for this host only
        # after it has been globally disabled with "a2disconf".
        #Include conf-available/serve-cgi-bin.conf
</VirtualHost>

# vim: syntax=apache ts=4 sw=4 sts=4 sr noet

Step 10 - Start the web app

Restart the Apache web server; 

sudo service apache2 restart

Type the following to check the passenger installation; 

rvmsudo passenger-config validate-install

If everything looks good then go to: 

http://rdmp.bib.sun.ac.za

Type the following to check the memory; 

rvmsudo passenger-memory-stats

References

Source Code

Installation

Help

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