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 1.8 and its dependencies. This will take several minutes for the initial install.

Prerequisites

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

This Vagrant box is intended for development and experimentation only. Change default user names and passwords.

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. The source at /usr/local/vivo is based off a 3-tier VIVO build template and under git version control.
• 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 or VMWare Fusion admin user interface.

Upgrading or updating VIVO and Vitro

• If you have a working vivo-vagrant box and don't want to re-provision your system, you can upgrade to a new release of VIVO by checking out the new release branch and rebuilding the application.

$ sudo /etc/init.d/tomcat7 stop
$ cd /usr/local/vivo
$ cd VIVO
$ git fetch
$ git checkout v1.x 
$ cd ../Vitro
$ git fetch
$ git checkout v1.x
$ cd ..
$ sudo ant all
$ sudo /etc/init.d/tomcat7 start

• You might also want to build your VIVO against unreleased code changes. This can be done by identifying the branch that includes the changes you want to include, cd into the VIVO and Vitro updates and use Git to checkout the changes. For example:

$ sudo /etc/init.d/tomcat7 stop
$ cd /usr/local/vivo
$ cd VIVO
$ git fetch
$ git checkout maint-rel-1.8
$ cd ../Vitro
$ git fetch
$ git checkout maint-rel-1.8
$ cd ..
$ sudo ant all
$ sudo /etc/init.d/tomcat7 start

Re-provisioning

You can also, at anytime, re-provision your Vagrant box. By running the following from your host machine. This will reinstall all components of the Vagrant box and reinstall VIVO. This will destroy any changes you've made to your VIVO installation so be sure to backup any data or code changes you have made beforehand.

$ vagrant up --provision

##Running previous releases of VIVO and Vitro If you are interested in running VIVO 1.5, 1.6, or 1.7 there are separate branches for each of those released version.

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

Triplestores

VIVO supports alternate triplestores via SPARQL 1.1. The vivo-vagrant repository contains installation and configuration scripts for two other triple stores in separate branches.

• Stardog - see the stardog branch and README to get started.
• AllegroGraph: see the allegrograph branch and README to get started.

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 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.