VIVO Vagrant 1.11.0-RC

Vagrant configuration and install scripts for running VIVO on a virtual machine, aka Vagrant box, running an Ubuntu 64 Server 16.04.3 image.

The virtual machine will boot and install VIVO 1.11.0-RC and its dependencies. This will take several minutes for the initial install.

For the most recent version that downloads the full source for VIVO 1.9.3 and is GUI enabled with eclipse please go to branch: https://github.com/vivo-community/vivo-vagrant/tree/gui-developer-v1.9.3

If you have questions or encounter problems, please email the VIVO technical list at vivo-tech@googlegroups.com or open issue here in the Github issue tracker.

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/vivo-community/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/runtime.properties source file in this repository.

The vivo application will be at /home/vagrant/src/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: /home/vagrant/src/vivo.
• VIVO data directory: /opt/vivo
• VIVO TDB triple store: /opt/vivo/tdbContentModels
• Tomcat: /opt/tomcat
• To start/stop Tomcat run sudo systemctl start|stop|restart tomcat.
• A Vagrant shared directory is available at /work from the box.
• A Vagrant shared directory is available at /home/vagrant/src from the box. * This synced directory contains VIVO and Vitro source. Which can be developed from the host machine. *
• 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.

Re-provisioning

You can, 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

Reseting the VIVO database

From time to time, you might also want to rollback to a clean VIVO database. This can be done by stopping tomcat and removing the file-based TDB triple store: rm /opt/vivo/tdbContentModels. Warning - this will delete all of the data you have loaded into VIVO and any ontology changes.

Running previous releases of VIVO and Vitro

If you are interested in running VIVO 1.5, 1.6, 1.7, 1.8, 1.9 there are separate branches for each of those released version.

$ git clone https://github.com/vivo-community/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.