Capture of real-time data from electronic health records

Author: Nikola Kirilov

In this repository you will find minimal reference implementations for RTD delivery from electronic health records (EHRs).

Warning: The provided code is not intended for production use. The objective of the project is to guide and help developers.

REST Servers - HL7FHIR

Usage

In order to use these featuers they have to be activated by the server. For HAPI FHIR the following lines in the "application.yaml" have to be uncommented and set to true:

subscription:
	resthook_enabled: true
	websocket_enabled: true

Creation of a Subscription resource

To use the script you need to install the requests library:

pip install requests

By default the script does not use any authentication for the connection. If your server needs authentication we provide HTTP Basic Auth support. To use it you need to change line 5-7 of the script:

auth = 1 #Authentication needed (only basic auth supported)
fhir_user = "user"
fhir_password = "password"

The url of the FHIR server and the endpoint for rest hooks is given in the variables line 8-9

fhir_url= "http://localhost:5000/fhir/Subscription/"
endpoint = "http://localhost:5001/" #For rest-hooks, we will use the rtd recipient http endpoint

For endpoint you can use the http endpoint in "rtd_recipient".

The script is executed from terminal with the following two arguments: [PID] - Id of the Patient resource for which we will generate notifications when an Observation resource is created [CHANNEL] - channel type of the subscription (websocket or rest-hook)

py subscriby.py [PID] [CHANNEL]

After executing the script the Subscription resource is printed as a response in the terminal. It is important to note the Subscription resource id if you will use websockets.

RTD Recipient - HTTP-Endpoint - REST hooks

To install flask use the following command:

pip install flask

After starting the script the endpoint is accepting connections:

py http_endpoint.py

When RTD is received it is printed in the terminal.

WebSocket client

pip install websocket-client

The FHIR WebSocket endpoint is set in line 21:

ws = websocket.WebSocketApp("ws://localhost:8080/websocket", ...

To run the script use:

py ws_client.py [SUBID]

Where [SUBID] is the id of the Subscription resource you generated in the previous step.

Create sample Observation resource

In order to test the environment, we set up above, you can generate a sample Observation resource for the patient with the python script "generate_observation.py" in the "fhir_observation" folder. The settings and dependencies are the same as the Subscription generating script:

py generate_observation [PID]

where [PID] is the id of the Patient resource.

Database triggers

Dependencies:

pip install psycopg2

The server host, port, credentials and database are set in line 9-13 in the script:

connection = psycopg2.connect(user="postgres", password="admin", host="127.0.0.1", port="5432", database="fhir")

Once the script is run it is listening for notifications. You can use the "generate_observation.py" script to generate a resource and trigger a notification.

Reverse proxy

For HAPI FHIR this is done in the "application.yaml":

hapi:
  fhir:
    server_address: http://localhost:5000/fhir

and

tester:
      home:
        name: Local Tester
        server_address: 'http://localhost:5000/fhir'

Install Golang (https://go.dev/doc/install).

To set up you FHIR server address you need to change line 59:

rev_proxy, err := NewProxy("http://localhost:8080")

The address of the reverse proxy is set in line 64:

log.Fatal(http.ListenAndServe(":5000", nil))

The address of the RTD recipient http endpoint is defined in line 37:

z, err := http.NewRequest("POST", "http://localhost:5001/", bytes.NewBuffer(jsonData))

You can use the python "http_endpoint.py" in "rtd_recipient".

All these implementations do not include any encryption and are provided only for testing purposes.