VIVO Vagrant

Vagrant configuration and install scripts for running VIVO on a virtual machine, aka Vagrant box, running an Ubuntu 64 Precise image.

The virtual machine will boot and install VIVO 1.7 and its dependencies. This will take several minutes for the initial install.

Prerequisites

VirtualBox.
Vagrant.
Git - if you are new to git, you might want to use the Github desktop client. Windows and Mac versions are available.

Install the VIVO Vagrant box

$ git clone https://github.com/lawlesst/vivo-vagrant.git vivo-vagrant
$ cd vivo-vagrant
$ vagrant up

When the Vagrant provisioning script is complete, the VIVO web application will be available in a browser on the host machine at http://localhost:8080/vivo. You can log into your new VIVO with the default admin user (vivo_root@school.edu) and password (rootPassword), which are specified in the /provision/vivo/deploy.properties source file in this repository.

The source will be installed on the virtual machine at /usr/local/vivo/. Mac users can log into your Vagrant box securely using this command from a Terminal session. Windows users will want to use an SSH utility, e.g. Putty:

$ vagrant ssh

Once you are logged in, you can view the default VIVO log output with this command:

$ vlog

Commands / system layout

VIVO application: /usr/local/vivo
VIVO data directory: /usr/local/vdata
Tomcat: /var/lib/tomcat7/
To start/stop Tomcat run sudo /etc/init.d/tomcat start|stop|restart.
A Vagrant shared directory is available at /work from the box.
Use the vagrant suspend and vagrant resume commands to manage your Vagrant box when not in use or if you plan to restart or shutdown the host system, as opposed to using the VirtualBox admin user interface.

Background

This Vagrant box is intended for development only. Change default user names and passwords if you intend to use this config for a production deployment.
The source at /usr/local/vivo is based off a 3-tier VIVO build template and under git version control.
On older versions of Vagrant it might be necessary to start Vagrant with the $ vagrant up --no-provision flag to prevent the VIVO installation script from running each time.
Vagrant supports virtualization utilities other than VirtualBox but this package hasn't been tested with those. Please report back if you have adapted this to work with another virtualization tool.

Updates to VIVO and Vitro code

From time to time, updates will be made to the current VIVO or Vitro release. To make sure your VIVO Vagrant box is running the latest code, login to your box, shutdown Tomcat, and checkout the latest VIVO and Vitro code from Github. For example:

$ sudo /etc/init.d/tomcat7 stop
$ cd /usr/local/vivo
$ cd VIVO
$ git pull
$ cd ../Vitro
$ git pull
$ cd ..
$ sudo ant all
$ sudo /etc/init.d/tomcat7 start

You can also, at anytime, re-provision your Vagrant box. By running the following from your host machine. Be sure to backup any data or code changes you have made beforehand.

$ vagrant up --provision

If you are interested in running VIVO 1.5, you can run checkout the v1.5 branch of this repository.

$ git clone https://github.com/lawlesst/vivo-vagrant.git vivo-vagrant
$ cd vivo-vagrant
$ git checkout v1.5
$ vagrant up

Karma

Karma is a tool for mapping raw data in various formats (CSV, XML, etc) to RDF. To assist with using Karma to model data for VIVO, a script is included to install Karma and its dependencies.

To install Karma: run sudo /home/vagrant/provision/karma.sh install. The initial install will take about 10 minutes. Once it's installed Karma can be started with /home/vagrant/provision/karma.sh start. Karma runs in a web browser and will be available on your machine at http://localhost:8000/.

Violeta Ilik from Texas & AM University has presented (starting at about 12:30) on how to model data for VIVO with Karma. More information about Karma can be found in this tutorial and on the project's wiki.