FHIR-CONNECTOR

Table of contents

• FHIR-CONNECTOR
  • Table of contents
  • Introduction
  • Active deployments in FOSPS - Gravitate Health
    • GIT_FSH HL7 EPI resources
    • GIT_FSH HL7 IPS resources
  • Environment variables
    • Environment variables for working mode: GIT_FSH
    • Environment variables for working mode: HAPI_FHIR_SERVER_SYNC
    • Environment variables for working mode: FHIR_SERVER_PROXY
    • Environment variables for working mode: SMM_TOOL
  • Deployment
    • Local deployment
    • Deployment
      • Docker
      • Kubernetes (Kustomize)
  • Usage
  • Known issues and limitations
  • Getting help
  • Contributing
  • License
  • Authors and history
  • Acknowledgments

Introduction

This repository includes an implementation for a tool capable of transforming information from different sources into FHIR format. The connector has different working modes, and the desired one must be specified. The following working modes are currently available:

• fhs-git: pulls a git repository containing .fsh files, converts them to JSON format and uploads them to the specified HAPI FHIR server.
• HAPI FHIR sync: pulls resources from a HAPI FHIR server and writes them to the specified FHIR server.
• HAPI FHIR proxy: the connector acts as a proxy for FHIR resources. When a resource is requested to the connector, it will look for the resource in all the FHIR sources it has available.

The following sections in the README document help to install and deploy the connector and understand how the transformation tool has been developed.

Active deployments in FOSPS - Gravitate Health

GIT_FSH HL7 EPI resources

• Syncs HL7 Gravitate Health ePI repository. Uploads ePI in this folder as bundles to FHIR server.

GIT_FSH HL7 IPS resources

• Syncs HL7 Gravitate Health IPS repository. Uploads IPS in this folder as bundles to FHIR server.

Environment variables

The following environment variables must be set:

Task	Description	Possible values
CONNECTOR_MODE	Working mode of the connector	GIT_FSH, HAPI_FHIR_SERVER_SYNC, FHIR_SERVER_PROXY
WHITELIST	List of resources to get, if not all should be retrieved	["resource1.json", "resource2.json"]
DESTINATION_SERVER	URL of the destination FHIR server
LOG_LEVEL	Log level	CRITICAL, ERROR, WARNING, INFO, DEBUG
EMAIL_ENABLED	Enable sending of emails with the results of the connector	true
EMAIL_SENDER	Email address of the sender
EMAIL_PASSWORD	Must be set as a base64 encoded secret
EMAIL_SMTP_SERVER	SMTP server address
EMAIL_RECIPIENT	Email address or list to send the contents

The environment EMAIL_PASSWORD must be set via k8s secret:

apiVersion: v1
kind: Secret
metadata:
  name: fhir-connector-email-password
data:
  password: BASE64_ENCODED_PASSWORD

Environment variables for working mode: GIT_FSH

Task	Description	Possible values
CONNECTOR_MODE	Working mode of the connector	GIT_FSH
MODE_GIT_FSH_SOURCE_REPO	URL of the git repository
MODE_GIT_FSH_SOURCE_REPO_BRANCH	Branch to pull	"main", "development", etc.

Environment variables for working mode: HAPI_FHIR_SERVER_SYNC

Task	Description	Possible values
CONNECTOR_MODE	Working mode of the connector	HAPI_FHIR_SERVER_SYNC
MODE_HAPI_FHIR_SERVER_SYNC_SOURCE_SERVER	URL of the FHIR server
MODE_HAPI_FHIR_SERVER_SYNC_RESOURCES	["Bundle", "Patient", "Observation", etc.]

Environment variables for working mode: FHIR_SERVER_PROXY

Task	Description	Possible values
CONNECTOR_MODE	Working mode of the connector	GIT_FSH, HAPI_FHIR_SERVER_SYNC, FHIR_SERVER_PROXY
SOURCE_SERVER_LIST	["https://fhir-server1.com", "https://fhir-server2.com"]
DESTINATION_SERVER	https://fosps.gravitatehealth.eu/epi/api/fhir

Environment variables for working mode: SMM_TOOL

Task	Description	Possible values
CONNECTOR_MODE	Working mode of the connector	SMM_TOOL
DESTINATION_SERVER	https://gravitate-health.lst.tfo.upm.es/epi/api/fhir
SMM_SERVER_URL	https://budibase.gravitate-health.lst.tfo.upm.es/api/public/v1
SMM_APP_ID	Budibase app id
SMM_TABLE_ID	Budibase table id
SMM_API_KEY	Read from k8s secret

To create API KEY secret:

kubectl create secret generic budibase-smm-api-key-secret --from-literal=apikey=API_KEY_STRING

kubectl create secret generic budibase-smm-api-key-secret --from-literal=apikey=363d4adf8234c7ac0a9e9a356addd061-c544898c110bd82ee96436d2b95039fc3d84690af962993bf1f196951653f9d0444ad1e8abaff19d

Deployment

Local deployment

First, install requierements:

pip install -r requirements.txt

And run the application:

python3 app.py

To deploy locally, you can create a .env file and change the environment variables.

Deployment

The deployment of the app can be done in Docker or kubernetes.

Docker

git clone https://github.com/Gravitate-Health/fhir-connector
cd fhir-connector
docker build . -t YOUR_IMAGE_NAME
docker run YOUR_IMAGE_NAME

Kubernetes (Kustomize)

Production:

kubectl apply -k kubernetes/base

Development:

kubectl apply -k kubernetes/dev

Usage

Known issues and limitations

Getting help

In case you find a problem or you need extra help, please use the issues tab to report the issue.

Contributing

To contribute, fork this repository and send a pull request with the changes squashed.

License

This project is distributed under the terms of the Apache License, Version 2.0 (AL2). The license applies to this file and other files in the GitHub repository hosting this file.

Copyright 2022 Universidad Politécnica de Madrid

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

Authors and history

• Guillermo Mejías (@gmej)
• Isabel Varona (@isabelvato)

Acknowledgments

• HAPI FHIR
• FHIR SERVER REPOSITORY