Ponos Quick Start Guide: An Automated Build for a Standardized Atlas Development Environment

Introduction

This page provides the process for installing a complete Atlas/WebAPI/CDM instance on a newly provisioned (or existing) Windows machine. A description of what each step does is provided here.

Quick Start Guide

Perform each of the steps below to create your instance of the Ponos development environment.

• Step 1: Provision a machine for your installation
  We will be using an AWS EC2 instance for our installation. This process should work on any modern Windows machine. By creating a new AWS EC2 instance we ensure that our process has not benefited from existing resources that were installed elsewhere.
  Detailed Instructions: Detailed Instructions for Creating a New AWS EC2 Instance
• Step 2: Download and Install the basic tools needed for Java development
  Download the _YES installer
  Download and run this installer to get your basic development tools including things like Java, MVN, Git, Eclipse, etc.
  Detailed Instructions: Detailed Instructions for Downloading and installing the _YES development environment
• Step 3: Run Installers that have not been automated
  • Install NPM
    The NPM installer is included with the _YES install. Run the installer and accept all of the defaults. It is loacated at:
    C:\_YES\tools\npm
    Detailed Instructions: Detailed Instructions for Installing NPM
  • Install PostgreSQL
    The PostgreSQL installer is included with the _YES install. Run the installer and accept all of the defaults. EXCEPT: Unclick the option for "Stack Builder". The installer is located at:
    C:\_YES\databases\postgres
    Detailed Instructions: Detailed Instructions for Installing PostgreSQL
  • Install RTools
    Download the R Installers
    Download the zip file that contains the R installers using the link above. Unzip the zip file and run each of the installers in the order of R for Windows, RTools, RStudio.
    Detailed Instructions: Detailed Instructions for Installing the R components
• Step 4: Run the installer for Atlas/WebAPI/fhir-to-omop
  Download the install-atlas-project.bat file by clicking this download link. Move this file to C:\_YES\workspace.and run it from a cmd prompt. This step will install, build, and deploy the WebAPI, Atlas, and fhir-to-omop projects. NOTE: This process takes a little bit of time because it needs to install Every. Single. Solitary. Dependency. for these projects.
  Detailed Instructions: Detailed Instructions for Installing the Github Projects
• Step 5: Run the fhir-to-omop atlas tool
  From a cmd prompt, navigate to C:\_YES\workspaces\fhir-to-omop\target\fhir-to-omop.
  Run the following:
  fhir-to-omop.bat atlas
  Detailed Instructions: Detailed Instructions for Installing the Atlas Dependencies