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DRLS-REMS-Docker-The Ultimate Guide to Running DRLS REMS locally

Purpose of this guide

This document details the installation process for the dockerized version of the Documentation Requirements Lookup Service (DRLS) REMS Workflow system for Production. There are two approaches to doing this:

Option 1 utilizes Docker Compose, which comes with Docker Dektop, and requires the corresponding docker-compose.yml file from the REMS repository. This option has minimal technical set up involved and allows for the customization/modification of the dockerized configuration.

Option 2 utilizes Porter, which requires a seperate installation in addition to Docker Desktop but does not require the use of any local files. This option has the least amount of technical set up involved and is recommended for non-tecnical users of DRLS REMS as it does not allow for the customization/modification of the dockerized configuration.

This document is designed to take you through the entire set up process for DRLS REMS using docker containers. It is a standalone guide that does not depend on any supplementary DRLS REMS documentation.

This guide will take you through the development environment setup for each of the following DRLS components:

  1. Coverage Requirements Discovery (CRD)
  2. (Test) EHR FHIR Service
  3. Documents, Templates, and Rules (DTR) SMART on FHIR app
  4. Clinical Decision Support (CDS) Library
  5. CRD Request Generator
  6. REMS
  7. Keycloak

Table of Contents

Prerequisites

Your computer must have these minimum requirements:

Additionally, you must have credentials (api key) access for the Value Set Authority Center (VSAC). Later on you will add these credentials to your development environment, as they are required for allowing DRLS to pull down updates to value sets that are housed in VSAC. If you don't already have VSAC credentials, you should create them using UMLS.

Install core tools

Installing core tools on MacOS

Install Docker Desktop for Mac

  1. Download the stable version of Docker for Mac and follow the steps in the installer.

  2. Once the installation is complete, you should see a Docker icon on your Mac's menu bar (top of the screen). Click the icon and verify that Docker Desktop is running.

  3. Configure Docker to have access to enough resources. To do this, open Docker Desktop and select Settings > Resources.

    The defaults for memory at 2GB and possibly CPU as well are too low to run the entire DRLS REMS workflow. If not enough resources are provided, you may notice containers unexpectedly crashing and stopping. Exact requirements for these resource values will depend on your machine. That said, as a baseline starting point, the system runs relatively smoothly at 16GB memory and 6 CPU Processors on MITRE issued Mac Devices.

Install Visual Studio Code and Extensions (Option 1 Only)

The recomended IDE for this set up is Visual Studio Code

  1. Install Visual Studio Code - https://code.visualstudio.com
  2. Install Docker extension - https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-docker

Install Porter (Option 2 Only)

  1. Download and install porter as per https://porter.sh/install/ instructions: 
    curl -L https://cdn.porter.sh/latest/install-mac.sh | bash
  2. Open .bash_profile and add the following lines at the very bottom: 
    export PATH=$PATH:~/.porter
  3. Save .bash_profile and complete the update to env: 
    source .bash_profile
  4. Install required Porter plugins 
    porter mixins install docker
porter mixins install docker-compose

Clone REMS repository (Option 1 Only)

  1. clone the REMS repositories from Github:

    git clone https://github.com/mcode/REMS.git REMS

    Alternatively, you can download/copy just the docker-compose.yml file from the REMS reposiotry since that is the only file needed for this set up.

Open REMS in VSCode (Option 1 Only)

The Docker Extension for VsCode has useful functionality to aid in the development process using this set up guide. This extension lets you eaily visualize the containers, images, networks, and volumes created by this set up. Clicking on a running container will open up the file structure of the container. Right clicking on a running container will give the option to view container logs (useful to see output from select services), attach a shell instance within the container, and attach a Visual Studio Code IDE to the container using remote-containers. See: https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-docker

Configure DRLS REMS

Add VSAC credentials to environment (Option 1 only)

At this point, you should have credentials to access VSAC. If not, please refer to Prerequisites for how to create these credentials and return here after you have confirmed you can access VSAC. To download the full ValueSets, your VSAC account will need to be added to the CMS-DRLS author group on https://vsac.nlm.nih.gov/. You will need to request membership access from an admin. If this is not configured, you will get org.hl7.davinci.endpoint.vsac.errors.VSACValueSetNotFoundException: ValueSet 2.16.840.1.113762.1.4.1219.62 Not Found errors.

While this step is optional, we highly recommend that you do it so that DRLS will have the ability to dynamically load value sets from VSAC.

You can see a list of your pre-existing environment variables on your Mac by running env in your Terminal. To add to env:

  1. Set "VSAC_API_KEY" in the .env file in the REMS Repository

or

  1. cd ~/
  2. Open .bash_profile and add the following lines at the very bottom: 
    export VSAC_API_KEY=vsac_api_key
  3. Save .bash_profile and complete the update to env: 
    source .bash_profile

Be aware that if you have chosen to skip this step, you will be required to manually provide your VSAC credentials at http://localhost:8090/data and hit Reload Data every time you want DRLS to use new or updated value sets.

Add Compose Project Name to environment (Option 1 only)

Note: The compose project name is to disambiguate between different set ups on the same machine and can be set to any identifier. If you are following both options mentioned in this guide, it is reccomended to change the compose project name for each so that they differ.

You can see a list of your pre-existing environment variables on your Mac by running env in your Terminal. To add to env:

  1. Set "COMPOSE_PROJECT_NAME" as "rems_prod" in the .env file in the REMS Repository

or

  1. cd ~/
  2. Open .bash_profile and add the following lines at the very bottom: 
    export COMPOSE_PROJECT_NAME=rems_prod
  3. Save .bash_profile and complete the update to env: 
    source .bash_profile

Run DRLS REMS

Option 1 - Docker Compose

Start docker compose application

    cd REMS # Need to execute commands in directory with corresponding docker-compose.yml file located in the REMS repository 
    docker-compose up

Stop docker-compose application

    docker-compose down # Removes application servers

    docker volume prune # Optional - Removes persisted data

Updating docker-compose application images

    docker-compose build --no-cache --pull [<service_name1> <service_name2> ...] 
    docker-compose --force-recreate  [<service_name1> <service_name2> ...]
    # Options:
    #   --force-recreate                        Recreate containers even if their configuration and image haven't changed.
    #   --build                                 Build images before starting containers.
    #   --pull                                  Pull published images before building images.
    #   --no-cache                              Do not use cache when building the image.
    #   [<service_name1> <service_name2> ...]   Services to recreate, not specifying any service will rebuild and recreate all services

Option 2 - Porter Install

Install and Run Porter application

You can set the flag --allow-docker-host-access in the below commands with the PORTER_ALLOW_DOCKER_HOST_ACCESS environment variable so that you don’t have to specify it for every command.

    porter install fullstack_rems --allow-docker-host-access --reference codexrems/fullstack_rems:latest # Initial Installation needs to be from remote repository

    or 

    porter install fullstack_rems --allow-docker-host-access  # Subsequent runs can use the local installation

Note: The project will keep running in the background when you "ctrl + c" out of the above process. To stop running all together, use the stop command below

Stop Running Porter application and Uninstall

    porter invoke fullstack_rems --action stop --allow-docker-host-access

Updating Porter application

    porter upgrade fullstack_rems --allow-docker-host-access # Pull and Update application images and recreate containers

    or 

    porter upgrade fullstack_rems --allow-docker-host-access --reference codexrems/fullstack_rems:latest # Pull and Update Invocation Image in addition to applicaion images from remote repository and recreate containers

Verify DRLS is working

Register the test-ehr

  1. Go to http://localhost:3005/register.
  2. Click Submit

The fun part: Generate a test request

  1. Go to http://localhost:3000/ehr-server/reqgen.
  2. Click Patient Select button in upper left.
  3. Find William Oster in the list of patients and click the dropdown menu next to his name.
  4. Select E0470 in the dropdown menu.
  5. Click anywhere in the row for William Oster.
  6. Click Submit at the bottom of the page.
  7. After several seconds you should receive a response in the form of two CDS cards:
    • Respiratory Assist Device
    • Positive Airway Pressure Device
  8. Select Order Form on one of those CDS cards.
  9. If you are asked for login credentials, use alice for username and alice for password.
  10. A webpage should open in a new tab, and after a few seconds, a questionnaire should appear.
  11. Fill out questionnaire and hit next
  1. Submit PAS request to https://davinci-prior-auth.logicahealth.org/fhir

Congratulations! DRLS is fully installed and ready for you to use!

Troubleshooting docker-sync

Reference: https://docker-sync.readthedocs.io/en/latest/troubleshooting/sync-stopping.html