samatpro / ehrbase

EHRbase

EHRbase is an openEHR Clinical Data Repository, providing a standard-based backend for interoperable clinical applications. It implements the latest version of the openEHR Reference Model (RM 1.0.4) and version 1.4 of the Archetype Definition Language (ADL). Applications can use the capabilities of EHRbase through the latest version of the openEHR REST API and model-based queries using the Archetype Query Language.

Release Notes

(click to expand)

Please check the CHANGELOG and/or EHRbase Documentation for more details.

WIP: 2021, XYZ 00

v?.?.? - (...)

Important: Please note that this release introduces Archie's new strict invariant checks. Depending on existing data and clients this might be a breaking change. Please carefully check the EHRbase output and update your input data if EHRbase rejects it. The strict validation can also be deactivated via configuration, but caution in advised!

2021, Sep 9

v0.17.2 - beta release. Bug fixes, enhancements, automatic Docker Hub deployments via Github Actions.

2021, Aug 12

v0.17.1 - beta release. Default handling for audit metadata, bug fixes and SDK version update.

2021, Aug 04

v0.17.0 - fifth beta release. validation using an external terminology server, Attribute-based Access Control, AQL fixes and other enhancements

2021, March 30

v0.16.0 - fourth beta release. New endpoints for versioned Compositions, ATNA Logging, AQL fixes and other enhancements.

2021, February 25

v0.15.0 - third beta release. New admin API endpoints for EHRs, Compositions and Contributions. Fixes and other enhancements.

2020, October 1

v0.14.0 - second beta release.

2020, May 14

This release of EHRbase (v0.13.0) is the first beta release.

Please check the CHANGELOG and/or EHRbase Documentation for more details.

📝 Documentation

EHRbase Documentation is build with Sphinx and hosted on Read the Docs.

Quick Start: Run EHRbase with Docker

See our Run EHRbase + DB with Docker-Compose documentation page for a quick start.

Building and Installing EHRbase

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. Please read these instructions carefully. See deployment for notes on how to deploy the project on a live system.

Prerequisites

You will need Java JDK/JRE 11 (preferably openJDK: e.g. from https://adoptopenjdk.net/)

You will need a Postgres Database (Docker image or local installation). We recommend the Docker image to get started quickly.

When installing locally, the Postgres Database (at least Version 10.4) needs the following extensions:

• temporal tables

   git clone https://github.com/arkhipov/temporal_tables.git
   make
   sudo make install
   make installcheck

• jsquery

  git clone https://github.com/postgrespro/jsquery.git
  cd jsquery
  make USE_PGXS=1
  sudo make USE_PGXS=1 install
  make USE_PGXS=1 installcheck

Installing

1. Setup database

NOTE: Building EHRbase requires a properly set up and running DB for the following steps.

Run ./db-setup/createdb.sql as postgres User.

You can also use this Docker image which is a preconfigured Postgres database:

    docker network create ehrbase-net
    docker run --name ehrdb --network ehrbase-net -e POSTGRES_PASSWORD=postgres -d -p 5432:5432 ehrbase/ehrbase-postgres:latest

(For a preconfigured EHRbase application Docker image and its usage see the documentation)

2. Setup Maven environment

Edit the database properties in ./pom.xml if necessary

3. Build EHRbase

Run mvn package

4. Run EHRbase

Replace the * with the current version, e.g. application/target/application-0.9.0.jar

java -jar application/target/application-*.jar

Authentication Types

1. Basic Auth

EHRbase can use Basic Authentication for all resources. This means you have to send an 'Authorization' header set with keyword Basic followed by the authentication information in Base64 encoded username and password. To generate the Base64 encoded username and password combination create the string after the following schema: username:password.

The Basic Auth mechanism is implemented as "opt-in" and can be activated either by providing an environment variable SECURITY_AUTHTYPE=BASIC with the start command or by adding the value into the target application.yml file.

Currently we have support one user with password which can be set via environment variables SECURITY_AUTHUSER and SECURITY_AUTHPASSWORD. By default these values are set with ehrbase-user and authPassword=SuperSecretPassword and can be overridden by environment values. Alternatively you can set them inside the corresponding application.yml file.

The same applies to the admin user, via SECURITY_AUTHADMINUSER, SECURITY_AUTHADMINPASSWORD and their default values of ehrbase-admin and EvenMoreSecretPassword.

2. OAuth2

Environment variable SECURITY_AUTHTYPE=OAUTH is enabling OAuth2 authentication.

Additionally, setting the following variable to point to the existing OAuth2 server and realm is necessary: SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI=http://localhost:8081/auth/realms/ehrbase

Two roles are available: a user role, and admin role. By default, these roles are expected to be named USER and ADMIN. The names of these roles can be customised through the SECURITY_OAUTH2USERROLE and SECURITY_OAUTH2ADMINROLE environment variables. Users should have their roles assigned accordingly, either in the realm_access.roles or scope claim of the JWT used for authentication.

Running the tests

This command will run all tests from tests/robot folder. DB and server application will be started/stopped by the tests accordingly. You must not start them by hand.

NOTE: Make sure you meet the PREREQUISITES mentioned in tests/README.md prior to test execution.

Please Check the README in tests folder for more details.

cd tests
./run_local_tests.sh

Deployment

1. java -jar application/target/application-*.jar You can override the application properties (like database settings) using the normal spring boot mechanism: Command-Line Arguments in Spring Boot
2. Browse to Swagger UI --> http://localhost:8080/ehrbase/swagger-ui.html

Built With

• Maven - Dependency Management

License

EHRbase uses the Apache License, Version 2.0 (https://www.apache.org/licenses/LICENSE-2.0)

Acknowledgments

EHRbase contains code and derived code from EtherCIS (ethercis.org) which has been developed by Christian Chevalley (ADOC Software Development Co.,Ltd). Dr. Tony Shannon and Phil Berret of the Ripple Foundation CIC Ltd, UK and Dr. Ian McNicoll (FreshEHR Ltd.) greatly contributed to EtherCIS.

EHRbase heavily relies on the openEHR Reference Model implementation (Archie) made by Nedap. Many thanks to Pieter Bos and his team for their work!

EHRbase is jointly developed by Vitasystems GmbH and Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School

Stargazers over time