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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.!

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 git mysql-server mysql-client libmysqlclient-dev git-core curl zlib1g-dev build-essential libssl-dev libreadline-dev libyaml-dev libsqlite3-dev sqlite3 libxml2-dev libxslt1-dev libcurl4-openssl-dev python-software-properties libffi-dev libgdbm-dev libncurses5-dev automake libtool bison libffi-dev gnupg2 libgmp-dev

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 required "gems";

gem install bundler

Install the "rails" framework;

gem install rails --version=3.2.22

Check version;

rails -v

Rails 3.2.22

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/DigitalCurationCentre/DMPonline_v4.git

Step 4 - Configure access to the Rails 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 ~/DMPonline_v4
RAILS_ENV=production rake secret
RAILS_ENV=test rake secret
RAILS_ENV=development rake secret

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

cd ~/DMPonline_v4
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 for the three environments by copying the text in the example below and pasting it into the secrets file. Remember to include the rake secret above.

Sample File

development:
  admin_name: Dev Admin
  admin_email: XXXXXXX
  admin_password: XXXXXX
  secret_key_base: XXXXX


test:
  admin_name: Test User
  admin_email: XXXXXX
  admin_password: XXXXXXX
  secret_key_base: XXXXXX


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

Step 5 - Configure database connections

Configure database access by typing the following;

cd ~/DMPonline_v4
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
development:
  adapter: mysql2
  encoding: utf8
  reconnect: false
  database: dmponline_development
  pool: 5
  username: root
  password: %PASSWORD%
  socket: /var/run/mysqld/mysqld.sock

# Warning: The database defined as "test" will be erased and
# re-generated from your development database when you run "rake".
# Do not set this db to the same as development or production.
test:
  adapter: mysql2
  encoding: utf8
  reconnect: false
  database: dmponline_test
  pool: 5
  username: root
  password: %PASSWORD%
  socket: /var/run/mysqld/mysqld.sock

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 6 - GEM dependency configuration

Type the following;

cd ~/DMPonline_v4
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'

Step 7 - Prepare the MySQL databases

Type the following;

cd ~/DMPonline_v4
rails dbconsole

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

Type the following to create the databases;

For "production";

RAILS_ENV="production" rake db:setup
RAILS_ENV="production" rake db:migrate

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

---

PLEASE NOTE:

There is an error with creating an admin user. Type the following to bypass this error;

nano ~/DMPonline_v4/db/migrate/20130708092900_devise_create_admin_users.rb

Comment out the following line;

AdminUser.create!(:email => 'admin@example.com', :password => 'password', :password_confirmation => 'password') if direction == :up

In addition there are CSS errors.

Type the following to fix them;

/home/dmponline/DMPonline_v4/app/assets/stylesheets/admin.css.less

Comment out the second line.

Another CSS error.

Type the following;

nano /home/dmponline/DMPonline_v4/app/assets/stylesheets/bootstrap_and_overrides.css.less

Comment out the second line.

Step 8 - Deploy the web app using "passenger"

Install the dependencies

Type the following;

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

Compile assets

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

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

• https://github.com/DigitalCurationCentre/DMPonline_v4

Installation

• http://railsapps.github.io/installrubyonrails-ubuntu.html
• https://www.phusionpassenger.com/library/walkthroughs/deploy/ruby/ownserver/apache/oss/rubygems_rvm/install_passenger.html
• https://gorails.com/setup/ubuntu/14.04
• https://en.wikipedia.org/wiki/Capistrano_(software)

Help

• http://guides.rubyonrails.org/getting_started.html