Ontohub Build Status Code Climate

A web-based repository for distributed ontologies.

An ontology is a formal, logic-based description of the concepts and relationships that are of interest to an agent (user or service) or to a community of agents. The conceptual model of an ontology reflects a consensus, and the implementation of an ontology is often used to support a variety of applications such as web services, expert systems, or search engines. Therefor, ontologies are typically developed in teams. Ontohub wants to make this step as convenient as possible.

Ontohub aims at satisfying a subset of the requirements for an Open Ontology Repository (OOR) and is being developed in close donnection with the Distributed Ontology Language, which is part of the emerging Ontology Integration and Interoperability standard (OntoIOp, ISO Working Draft 17347). For more information from this perspective, see the Ontohub page in the Ontolog wiki.

This application started at the compact course agile web development given by Carsten Bormann at the University of Bremen in March, 2012. The concept and assignment came from Till Mossakowski and Christoph Lange of the AG Bernd Krieg-Brückner.

Initial developers are Julian Kornberger and Henning Müller.

Installation

These commands should work on Ubuntu 12.04. First of all you need a root shell.

RVM with Ruby 1.9.3

Installation of RVM:

apt-get install -y build-essential openssl libreadline6 libreadline6-dev curl git-core zlib1g zlib1g-dev libssl-dev libyaml-dev libsqlite3-0 libsqlite3-dev sqlite3 libxml2-dev libxslt-dev autoconf libc6-dev ncurses-dev automake libtool bison subversion
curl -L https://get.rvm.io | bash -s stable --ruby

If you have a desktop installation, you should "run command as a login shell" to source rvm automatically as explained in https://rvm.io/integration/gnome-terminal/ .

Apache2 with passenger

A dedicated HTTP server is only required for the production environment. (Skip this section, if you are preparing your development setup.)

Installation

apt-get install apache2 apache2-prefork-dev libapr1-dev
gem install passenger
passenger-install-apache2-module

Passenger Configuration

Depending on the installed ruby and passenger version you need to create a /etc/apache2/mods-available/passenger.load with the LoadModule directive:

LoadModule passenger_module /usr/local/rvm/gems/ruby-1.9.3-p<version>/gems/passenger-<version>/ext/apache2/mod_passenger.so

and a /etc/apache2/mods-available/passenger.conf with the global passenger configuration:

PassengerRoot /usr/local/rvm/gems/ruby-1.9.3-p<version>/gems/passenger-<version>
PassengerRuby /usr/local/rvm/wrappers/ruby-1.9.3-p<version>/ruby

now enable the module an restart apache2:

a2enmod passenger
service apache2 restart

Virtual Host Configuration

<VirtualHost *:80>
  ServerName ontohub.org
  DocumentRoot /srv/http/ontohub.org/current/public

  <Directory /srv/http/ontohub.org/public>
    AllowOverride all 
    Options -MultiViews
  </Directory>
</VirtualHost>

Tomcat with Solr

Tomcat with Solr is only required in the production environment.

apt-get install tomcat6 tomcat6-admin

cd /root/
version=3.6.0
wget http://apache.openmirror.de/lucene/solr/$version/apache-solr-$version.tgz
tar xzf apache-solr-$version.tgz
sudo cp apache-solr-$version/dist/apache-solr-solrj-$version.jar /var/lib/tomcat6/webapps/solr.war
ln -s /srv/http/ontohub.org/current/solr/conf /var/lib/tomcat6/webapps/solr/

The war-Package should be automatically loaded.

SQL Server

The master branch is (and should be) database independent. We are using PostgreSQL in production and development.

PostgreSQL

apt-get -y install postgresql

MySQL

You probably do not need this but we used MySQL in the new-model branch once and these instructions are given for completeness. MariaDB has been tested, too.

The installation will prompt you for a password three times and you are expected to press «enter» with an empty password field.

apt-get -y install mysql-server libmysqlclient-dev

Redis

Redis is a key-value store, in our setup used by resque to provide object persistence between Rails and asynchronous jobs.

apt-get -y install redis-server

hets

apt-add-repository ppa:hets/hets
apt-add-repository "deb http://archive.canonical.com/ubuntu precise partner"
apt-get update
apt-get -y install hets-core subversion

cd /lib/x86_64-linux-gnu/
ln -s libpng12.so.0 libpng14.so.14

If you need the latest nightly build, just update hets (assure you have a working internet connection):

hets -update

Configuration

Change secret token

rake secret

... and save it into config/initializers/secret_token.rb.

Hets environment variables

The Hets installation path and environment variables are to be set in config/hets.yml. For ubuntu, it should be no change required.

Allowed URI schemas

Allowed URI schemas are to be set in config/initializers/ontohub_config.rb.

Clean upload cache

You can run the following command periodically to delete temporary files from uploads.

rails runner CarrierWave.clean_cached_files!

Development

This part should be done with your own user (not as root).

Clone with pushing permission

You need to create an SSH key pair (if you do not already have one) and upload it to your Github account and then be added to the project by a project administrator.

git clone git@github.com:ontohub/ontohub.git

Clone without pushing permission

You do not need to be a project member. Just clone it!

git clone git://github.com/ontohub/ontohub.git

Add yourself to the RVM group

sudo adduser $USER rvm

You have to re-login to apply your group membership.

Installation of gem dependencies

cd ontohub
bundle install

Set up your database

After configuring your config/database.yml you have to create the tables:

rake db:migrate:reset

Solr and Resque

rake sunspot:solr:start
rake resque:work

Seeds

Fill the database with dummy data:

rake db:seed

Start the rails server

Start the rails server. It will be available at http://localhost:3000/ until you stop it by pressing CTRL+C.

rails s

Now you can log in as admin@example.com with password foobar. Alice, Bob, Carol, Dave, Ted @example.com can also be used (with the same password).

Stopping Solr and Resque

Resque has to be stopped with CTRL+C on the terminal you typed rake resque:work. Solr is to be stopped as follows:

rake sunspot:solr:stop

License

Copyright © 2012 Universität Bremen, released under the GNU AGPL 3.0 license.