A Virtual Machine for Tinkering with ConceptQL

Introduction

Inspired by rails-dev-box, this project automates the setup of a development environment for working with ConceptQL.

Requirements

VirtualBox
Vagrant 1.6+
Ansible 1.6+
Download the OMOP Vocabulary Files then unzip them and rename them to conceptql-dev-box/omop_vocab
- I can't ship them myself because they contain "restricted" vocabularies like CPT codes
- Sorry for the inconvenience!
Download the following Oracle Instant Client Files then move them into oracle_instant_client_zip_files:
- instantclient-basic-linux.x64-11.2.0.4.0.zip
- instantclient-sdk-linux.x64-11.2.0.4.0.zip
- instantclient-sqlplus-linux.x64-11.2.0.4.0.zip

How To Build The Virtual Machine

Building the virtual machine is this easy:

host $ git clone https://github.com/outcomesinsights/conceptql-dev-box.git
host $ cd conceptql-dev-box
host $ vagrant up

Wait a while (there's a lot of data to load and programs to install).

That's it.

If there are any errors, retry the provisioning step:

host $ vagrant provision

If it keeps failing at the same spot, open up an issue

After the installation has finished, you can access the virtual machine with

host $ vagrant ssh
Welcome to Ubuntu 14.04 LTS (GNU/Linux 3.13.0-30-generic x86_64)
...
vagrant@conceptql-dev-box:~$

What's In The Box

Git
RVM
Ruby 2.1.2 (binary RVM install)
Bundler
PostgreSQL 9.3
Databases and users needed to run the Active Record test suite
Sequelizer
loadmop
ConceptQL
Test ConceptQL

What to Play With

You may play with ConceptQL directly, or with its testing framework

Playing with ConceptQL

ConceptQL comes with a command-line utility: conceptql. This Thor-based script can be run by typing vagrant@conceptql-dev-box:/vagrant/conceptql$ bundle exec concepql

With no arguments, you'll get a list of the commands provided by the conceptql script.

The commands you run will execute against a sample of 250 patients' worth of synthetic data.

Playing with ConceptQL's Tests

The other option is to run the tests in /vagrant/test_conceptql. See Test ConceptQL for instructions on how to run the tests.

Recommended Workflow

The recommended workflow is

edit in the host computer and
test within the virtual machine.

Just clone your ConceptQL fork into the conceptql-dev-box directory on the host computer:

host $ ls
README.md   Vagrantfile puppet
host $ git clone git@github.com:<your username>/conceptql.git

Vagrant mounts that directory as /vagrant within the virtual machine:

vagrant@conceptql-dev-box:~$ ls /vagrant
ansible  conceptql test_conceptql omop_vocab README.md  Vagrantfile LICENSE.txt

Install gem dependencies in there:

vagrant@conceptql-dev-box:~$ cd /vagrant/conceptql
vagrant@conceptql-dev-box:/vagrant/conceptql$ bundle

We are ready to go to edit in the host, and test in the virtual machine.

This workflow is convenient because in the host computer you normally have your editor of choice fine-tuned, Git configured, and SSH keys in place.

Virtual Machine Management

When done just log out with ^D and suspend the virtual machine

host $ vagrant suspend

then, resume to hack again

host $ vagrant resume

Run

host $ vagrant halt

to shutdown the virtual machine, and

host $ vagrant up

to boot it again.

You can find out the state of a virtual machine anytime by invoking

host $ vagrant status

Finally, to completely wipe the virtual machine from the disk destroying all its contents:

host $ vagrant destroy # DANGER: all is gone

Please check the Vagrant documentation for more information on Vagrant.

Thanks

Xavier Noria's rails-dev-box
- For the inspiration (and for being a great way to hack on Rails)!
Outcomes Insights, Inc.
- Many thanks for allowing me to release a portion of my work as Open Source Software!