uwcirg / patient-summary

Patient summary is a SMART on FHIR application that displays summary overview of patient data, including scoring summary of questionnaire responses

Patient Summary - a SoF App in React

This application was bootstrapped with Create React App. You can learn more in the Create React App documentation. To learn React, check out the React documentation. The app can be launched via the SMART^® app launch framework.

Other Underlying Technologies

Clinical Quality Language (CQL)

CQL is a domain-specific programming language focused on clinical quality applications, including CDS as well as electronic clinical quality measures (eCQMs). Logical expressions written in CQL are human-readable but can also be compiled to a machine-friendly format to facilitate implementation. This application executes CQL logic to provide patient customized behavior. Machine-friendly versions of the CQL are embedded in this app; For more information about CQL see here; For more information about how to compile CQL code into machine-readable format, see here.

CQL Execution Engine

All CQL calculations are executed using the CQL Execution Engine, an open source library that implements the CQL standard.

Web Workers

All CQL calculations are executed within the context of a Web Worker, thereby offloading them to a separate thread. This greatly improves the responsiveness of the application.

React Material UI

Material UI is a library of React UI components that implements Google's Material Design.

Usage

A number of options are available for local usage to support testing with synthetic data.

Setup

This project manages dependencies using the NPM package manager in the Node environment (Node version <= 16 is recommended for this application). Make sure to have both NPM and Node installed before proceeding. The dependencies for the application can be installed locally by typing npm install at the command line. A local version of the app can be launched by typing npm start at the command line and the page will reload when you make changes. A copy suitable for distribution can be built using the npm run build command (see the build folder).

Docker

To start services via docker, first copy the default configuration files and modify as necessary:

# docker-compose service/project configuration
cp .env.default .env

# React App configuration
cp frontend.env.default frontend.env

To start all services, run the below command:

docker-compose up

Download Value Sets from VSAC

The value set content used by the CQL is cached in a file named valueset-db.json, which has been checked into this project in an empty state. In order for the CDS to operate as intended, implementers must populate valueset-db.json with the value sets which have been published on the Value Set Authority Center (VSAC). In order to access VSAC, you must sign up for a UMLS Terminology Services account.

Once a UMLS Terminology Services account has been obtained, the valueset-db.json file can be updated by running the following:

1. Run node src/util/updateValueSetDB.js UMLS_API_KEY (replacing UMLS_API_KEY with your actual UMLS API key)

To get you UMLS API Key:

1. Sign into your UMLS account at https://uts.nlm.nih.gov/uts.html
2. Click 'My Profile' in the orange banner at the top of the screen
3. Your API key should be listed below your username in the table
4. If no API key is listed:
   1. Click ‘Edit Profile’
   2. Select the ‘Generate new API Key’ checkbox
   3. Click ‘Save Profile’
   4. Your new API key should now be listed.

Configuration

Parameters for the app are stored in environmental variables that are stored in an .env file (run cp frontend.env.default .env at command line to create the .env file) and it allows the environment variables thus specified to be read by the application at build time. The dotenv package is used to store the default variable values, which can be overwritten by defining a more specific env (e.g., .env.local) file or by setting the variables in the deployment system. For more information, see the React documentation. Note: for setting up environment file for a docker instance, please read under Docker

Parameters

Parameter	Description	Allowed Values
REACT_APP_FHIR_RESOURCES	Define the FHIR resource(s) to load for the patient	Condition,Procedure,Observation
REACT_APP_FHIR_OBSERVATION_CATEGORIES	Define what categor(ies) of FHIR observations to load for the patient	social-history,vital-signs,imaging,laboratory,procedure,survey,exam,therapy,activity
REACT_APP_AUTH_SCOPES	For allowing the app to specify the delegation of a specific set of access rights via launch context. see App Launch: Scopes and Launch Context	profile roles email patient/*.read openid fhirUser patient/QuestionnaireResponse.write
REACT_APP_QUESTIONNAIRES	Define the questionnaire(s) for which responses and graph should be rendered	example: minicog or minicog,phq9
REACT_APP_DASHBOARD_URL	Define the (f)EMR URL to which the app can return to	example: https://dashboard.acc.dev.cosri.cirg.washington.edu
REACT_APP_PROJECT_ID	Definition of which will allow project-specific theme, logo, etc.	example: DCW
REACT_APP_CLIENT_ID	Define unique client id for when launching as a confidential client	example: summary_openid_client
REACT_APP_SECTIONS	Definition of which sections in app.	ScoreSummary,MedicalHistory,Responses, ScoreSummary, MedicalHistory, Responses
REACT_APP_CONF_API_URL	Define the backend auth URL for launching as a confidential client
REACT_APP_SYSTEM_TYPE	Define the system type of the app	example: development
REACT_APP_DISABLE_HEADER	Define whether the header element should appear, default is false	true, false
REACT_APP_DISABLE_NAV	Define whether the navigation menu element should appear, default is false	true, false
REACT_APP_MATOMO_SITE_ID	Define the site id used to for tracking via MATOMO	Example: 24

Using with Public SMART Sandbox

A public SMART^® App Launcher is available for sandbox tesing of SMART on FHIR apps with synthetic data.

Launch for SMART App Launcher

Launching from a local instance

1. Make sure Node and NPM package manager have been installed
2. Make sure environment file is set up (see under Configuration)
3. Run npm install to install all dependencies (this step can be skipped subsequently unless dependencies have changed)
4. Run npm start to install dependencies
5. Navigate to the public SMART^® App Launcher and choose the "Provider EHR Launch" Launch Type. Uncheck "Simulate launch within the EHR user interface". Leave all other options unselected. Paste the launch URL, e.g. http://localhost:3000/launch.html into the "App Launch URL" box at the bottom of the SMART^® App Launcher page. Select "Launch App!" which will bring up a patient selector widget before the app is launched.

Testing

to test UI components run npm run test to test CQL libraries run npm run cql-test to run all tests run npm run test && npm run cql-test