GMSA Genomics FHIR web app

Prototype for FHIR genomics reports. Development and project documentation is in the repository wiki

Note If you have cloned the repository and run the docker commands in the Development services section then
the GitHub.io page will connect to your FHIR server that is running on your machine.

Warning This is only for testing, and no clinical data should be entered

Running a development version

Dependencies

The project is built using React and requires an up-to-date version of node and npm to be installed. These can be checked on the command line on unix systems:

node -v

| v18.12.1

npm -v

| 9.1.2

To setup a local version clone the repository and install the npm dependencies

git clone git@github.com:gosh-dre/gmsa_genomic_fhir_webapp.git
cd gmsa_genomic_fhir_webapp
npm install

Configuration

From the root of the project, copy the test env file to the root directory so that the application can use the correct environmental variables. The .env file is ignored by git so won't be accidentally committed.

cp env/dev.env .env 

This file will need to be edited to allow automated testing to determine if the LOINC api is returning different value sets. You may also want to edit other variables

Development services

Start the FHIR server in docker, running in the background

docker compose -f docker-compose.dev.yml up -d

[+] Running 2/2
⠿ Network fhir-report_default      Created                                                                                                                                                                                           0.1s
⠿ Container fhir-report-fhir-1     Started                                                                                                                                                                                           0.8s

The status of the services using ps

docker compose -f docker-compose.dev.yml ps

        Name                       Command               State               Ports             
-----------------------------------------------------------------------------------------------
fhir-report_fhir_1      catalina.sh run                  Up      0.0.0.0:8090->8080/tcp        

Building and running

• From the repository directory, you can build and run development version using npm start
• Tests can be run by: npm test
• A production build can be created using npm run build