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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 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 7 - Compile assets and test the web app

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: 

bundle exec rake secret

This command will output a secret key. Copy that value to your clipboard. Next, open config/secrets.yml: 

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'
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 4 - Configure database connections

Configure database access by typing the following; 

nano DMPonline_v4/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: mysql
  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: mysql
  encoding: utf8
  reconnect: false
  database: dmponline_test
  pool: 5
  username: root
  password: %PASSWORD%
  socket: /var/run/mysqld/mysqld.sock

production:
  adapter: mysql
  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 - GEM dependency configuration

Type the following; 

nano DMPonline_v4/Gemfile

Delete everything and then copy and paste the following; 

source 'https://rubygems.org'
#
#      RAILS
#
gem 'rails', '3.2.22'
gem 'uglifier'
gem 'less-rails'
gem 'twitter-bootstrap-rails'
gem 'sass-rails',   '~> 3.2.3'
gem 'sass' 
gem 'therubyracer', '0.11.4', platforms: :ruby
gem 'libv8'
# To use debugger
gem 'ledermann-rails-settings'
gem 'jbuilder'
#to notify admin of errors
gem 'exception_notification'

#to allow cloning of objects
gem 'amoeba'
# Gems used only for assets and not required in production environments by default.
group :assets do
  gem 'coffee-rails', '~> 3.2.1'
end

group :development do
  gem "better_errors"
  gem "binding_of_caller"
end

#
#      USERS
#
# devise for user authentication
gem 'devise'
gem 'devise_invitable'
gem 'omniauth'
gem 'omniauth-shibboleth'
#rolify for roles
gem 'rolify'
# Gems for repository integration
gem 'email_validator'
gem 'validate_url'

#
#    DATABASE/SERVER
#
gem 'mysql'
# Use unicorn as the app server
# gem 'unicorn'
#cancan for usergroups
gem 'cancan'

#
#    VIEWS
#
gem 'jquery-rails'
gem 'tinymce-rails'
gem 'friendly_id'
gem 'contact_us' 
gem 'recaptcha'
#implementation of forms
gem 'activeadmin', '1.0.0.pre1'

#
#     EXPORTING PLANS
#
gem 'thin'
gem 'wicked_pdf'
gem 'htmltoword'
gem 'feedjira'
# WORD DOC EXPORTING
gem 'caracal', '~> 1.0'
gem 'caracal-rails', '~> 1.0'

gem 'passenger'

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 "development"; 

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

For "test"; 

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

For "production"; 

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

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

rake db:reset RAILS_ENV="production"
rake db:reset RAILS_ENV="development"
rake db:reset RAILS_ENV="test"

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 8 - 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 9 - 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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