WDK-Strategies TemplateDB

A virtualized server hosting TemplateDB. This is currently an unsupported project used as a test bed for EuPathDB BRC infrastructure reorganization and deployment code rewrites (primarily via Puppet).

Install Dependencies

• Download and install Vagrant
• Download and install VirtualBox
• Download and install Ansible

Clone project

• Clone the project git clone [email protected]:mheiges/vagrant-wdk-templatedb.git

Configure

Copy config/private.yml.sample to config/private.yml and supply desired values. private.yml is excluded from git commits to reduce the changes of publishing sensitive data. The other file in the config directory, config/common.yml, typically does not need to be changed.

For the brave, all the configuration features of Vagrant and VirtualBox are of course available as well, but there is no requirement that you tinker with them.

VPN setup, if needed

The website uses a UGA Postgres database. If off-campus you will need a VPN setup in advance so the WDK can connect. If the WDK can not connect to the database it will not start. There are many options for a VPN. sshuttle is one of them.

sshuttle -r <user>@<ugahost> <uga ip subnet>.0/24

<ugahost> is a server that has clear access to the Postgres database. Tunneling is limited to packets destined to <uga ip subnet> .

Start the virtual machine

In the project dir run vagrant up. Vagrant will download the base box on the first run and cache it for future deployments. The base box represents a server freshly provisioned by Puppet. Here, Vagrant leverages Ansible to deploy and configure a TemplateDB site, simulating how project staff would interact with the server. This provides the opportunity to validate our Puppet deployments.

Accessing the website

Vagrant forwards the tomcat port to 9380 on your host computer, so the website is reachable from your host at

http://localhost:9380/strategies/

Interacting with the server

See Vagrant and Ansible documentation for details.

Log in

vagrant ssh

You will log in as the vagrant user.

Shutdown and preserve state

vagrant halt

Shutdown and remove the instance (losing any changes you've made on the guest)

vagrant destroy

Run the Vagrantfile provisioning steps

vagrant provision

Run ansible

Running vagrant provision will also run ansible but if you can also run ansible manually (useful if you want to use --skip options). The actual ansible command uses several long options so a convenience script is included to simplify it.

bin/runansible

TemplateDB stuff

The source code and build artifacts are under /home/vagrant/TemplateDB, modeling the directory structure of EuPathDB BRC servers.

The instance_manager utility is used to manage Tomcat and deployed webapps.

Doing stuff as root

The vagrant user has full sudo permissions, no password required.

sudo <command>