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DRLS-REMS-Docker-The Ultimate Guide to Running DRLS REMS for Local Development

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 Local Development. Be aware that each component of DRLS has its own README where you will find more detailed documentation. This document is not designed to replace those individual READMEs.

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

Expected Functionality

  1. File Synchronization between local host system and docker container
  2. Automatic Server Reloading whenever source file is changed
    • CRD also reloads on CDS_Library changes
  3. Automatic Dependendency Installation whenever package.json, package-lock.json, or build.gradle are changed
  4. Automatic Data Loader in test-ehr whenever fhirResourcesToLoad directory is changed

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.

    Note: 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 15GB memory and 7 CPU Processors on MITRE issued Mac Devices.

Install Visual Studio Code and Extensions

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 Ruby

Note: The default ruby that comes with Mac may not install the right package version for docker-sync, it is reccomended to install ruby with a package manager, this guide uses rbenv.

Reference: https://github.com/rbenv/rbenv

  1. Install rbenv
      brew install rbenv
  1. Initialize rbenv and follow instructions (setting system path troubleshooting: https://stackoverflow.com/questions/10940736/rbenv-not-changing-ruby-version)
      rbenv init
  1. Close Terminal so changes take affect
  2. Test rbenv is installed correctly
      curl -fsSL https://github.com/rbenv/rbenv-installer/raw/main/bin/rbenv-doctor | bash
  1. Install Ruby
      rbenv install 2.7.2
  1. Verify that the system is using the correct ruby verions
      which ruby   
      /Users/$USER/.rbenv/shims/ruby # Correct

      ....

      which ruby 
      /usr/bin/ruby # Incorrect, using system default ruby. Path not set correctly, reference step 2

Install Docker-sync

  1. Download and Install docker-sync using the following command:

        gem install docker-sync -v 0.7.0

  2. Test that the right version is installed

        docker-sync -v
    0.7.0  # Correct 

    ...

    docker-sync -v
    0.1.1  # Incorrect, make sure you have ruby installed and are not using the default system ruby

    Note: The versioning is important, system default ruby sometimes installs version 0.1.1 if -v tag is not set. The 0.1.1 release will not work for the rest of this guide.

Clone DRLS REMS

  1. Create a root directory for the DRLS development work (we will call this <drlsroot> for the remainder of this setup guide). While this step is not required, having a common root for the DRLS components will make things a lot easier down the line.

    mkdir <drlsroot>

    <drlsroot> will be the base directory into which all the other components will be installed. For example, CRD will be cloned to <drlsroot>/crd.

    Note: If you are using a different project structure from the above description, you will need to change the corresponding repo paths in docker-compose-dev.yml, docker-sync.yml, and docker-compose.yml

  2. Now clone the DRLS component repositories from Github:

    cd <drlsroot>
git clone https://github.com/mcode/CRD.git CRD
git clone https://github.com/mcode/test-ehr.git test-ehr
git clone https://github.com/mcode/crd-request-generator.git crd-request-generator
git clone https://github.com/mcode/dtr.git dtr
git clone https://github.com/mcode/REMS.git REMS

cd CRD/server
git clone https://github.com/mcode/CDS-Library.git CDS-Library

Open DRLS REMS as VsCode workspace

The REMS repository contains the REMS.code-workspace file, which can be used to open the above project structure as a multi-root VS Code workspace. To open this workspace, select File > Open Workspace from File... and navigate to /REMS/REMS.code-workspace. In this workspace configuration, the CDS-Library embedded within CRD is opened as a seperate root for an easier development experience.

The Source Control Tab can be used to easily track changes during the devlopement process and perform git actions, with each root of the workspace having its own source control header. See: https://code.visualstudio.com/docs/editor/versioncontrol

The Docker Extension for VsCode has useful functionality to aid in the development process using this set up guide. This extension lets you easily 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

CRD configs

None

test-ehr configs

None

crd-request-generator configs

None

dtr configs

None

REMS configs

None

Add VSAC credentials to your development environment

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

  2. cd ~/

  3. Open .bash_profile and add the following lines at the very bottom:

    export VSAC_API_KEY=vsac_api_key

  4. 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

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_dev" in the .env file in the REMS Repository

    or

  2. cd ~/

  3. Open .bash_profile and add the following lines at the very bottom:

    export COMPOSE_PROJECT_NAME=rems_dev

  4. Save .bash_profile and complete the update to env:

    source .bash_profile

Run DRLS

Start docker-sync application

Note: Initial set up will take several minutes and spin up fans with high resource use, be patient, future boots will be much quicker, quieter, and less resource intensive

    docker-sync-stack start # This is the equivalent of running docker-sync start followed by docker-compose up

Stop docker-sync application and remove all containers/volumes/images

    docker-sync-stack clean # This is the equivalent of running docker-sync clean followed by docker-compose down
    docker image prune -a #Remove unused images
    docker volume prune # Remove unused volumes

Rebuilding Images and Containers

    docker-compose -f docker-compose-dev.yml up --build --force-recreate  [<service_name1> <service_name2> ...]

or

    docker-compose -f docker-compose-dev.yml build --no-cache --pull [<service_name1> <service_name2> ...] 		
    docker-compose -f docker-compose-dev.yml up --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

After rebuilding imaages and containers, start docker-sync normally

    ctrl + c # Stop running "docker-compose up" command (containers running without sync functionality)		
    docker-sync-stack start # If this command fails to run, running a second time usually fixes the issue

Useful docker-sync commands

Reference: https://docker-sync.readthedocs.io/en/latest/getting-started/commands.html

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