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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

2020, May 14

This release of EHRbase (v0.13.0) is the first beta release. Please see EHRbase Documentation for further details.

Getting Started

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 ehrbaseorg/ehrbase-postgres:latest

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

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

In the given OAuth2 server configuration the roles user and admin are expected to be configured. Users should have their roles assigned accordingly.

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

Docker

Locally Build Docker Image

First build the application as described in Installing

To create a Docker image run the following command and provide the correct build output file name created in the previous step, e.g. application-0.10.0.jar for version 0.10.0.

docker build -f application/Dockerfile --build-arg JAR_FILE=application-*.jar -t ehrbaseorg/ehrbase:latest .

To run the built container image use the following command:

docker run --name ehrbase --network ehrbase-net -d -p 8080:8080 -e DB_URL=jdbc:postgresql://ehrdb:5432/ehrbase -e DB_USER=ehrbase -e DB_PASS=ehrbase -e SYSTEM_NAME=local.ehrbase.org ehrbaseorg/ehrbase.

Adopt the parameters by your needs. The following parameters for -e must be set to start the EHRbase container:

Parameter Usage Example
DB_URL Database URL. Must point to the running database server. jdbc:postgresql://ehrdb:5432/ehrbase
DB_USER Database user configured for the ehr schema. ehrbase
DB_PASS Password for the database user ehrbase
AUTH_TYPE Set HTTP security method BASIC
AUTH_USER Username for Basic Auth myuser
AUTH_PASSWORD Password for Basic Auth myPassword432
SYSTEM_NAME Name for the local system local.ehrbase.org

Pre-build Docker Image

See: https://hub.docker.com/r/ehrbaseorg/ehrbase

There is also a preconfigured docker-compose.yml file, which sets up and starts the necessary database and EHRbase application with, for instance:

cd application
docker-compose up

Notes: It is not necessary to have the whole repository on your machine, just copy the docker-compose.yml file to a local working directory and run it. Using the -d argument starts both containers detached, without blocking the terminal. And the DB data is saved in application/.pgdata for easier access.

Built With

  • Maven - Dependency Management

Continuous Integration (CI/CD with CircleCI)

EHRbase uses CircleCI for continuous integration and deployment. The CI pipeline consists of the following workflows:

workflow 1/3 - build-and-test

  • trigger: commit to any branch (except - release/v*, master, sync/*, feature/sync/*)
  • jobs:
    • build artifacts
    • run unit tests
    • run sdk integraiton tests
    • run robot integration tests
    • perform sonarcloud analysis and OWASP dependency check

workflow 2/3 - release

  • trigger: commit to release/v or master branch
  • jobs:
    • build artifacts
    • run unit tests
    • run sdk integraiton tests
    • run robot integration tests
    • perform sonarcloud analysis and OWASP dependency check
    • TODO: deploy to Maven Central
    • TODO: deploy to Docker Hub

workflow 3/3 - synced-feature-check

⚠️ This is a special workflow to catch errors that can occur when code changes introduced to EHRbase AND openEHR_SDK repository are related in a way that they have to be tested together and otherwise can't be catched in workflow 1 or 2.

  • trigger: commit to sync/* branch
  • jobs:
    • pull, build, and test SDK from sync/* branch of openEHR_SDK repo
    • build and test ehrbase (w/ SDK installed in previous step)
    • start ehrbase server (from .jar packaged in previous step)
    • run SDK's (java) integration tests
    • run EHRbase's (robot) integration tests
HOW TO USE WORKFLOW 3/3
=======================

1. create TWO branches following the naming convention `sync/[issue-id]_some-desciption`
   in both repositories (EHRbase and openEHR_SDK) with exact the same name:

  - ehrbase repo       --> i.e.    sync/123_example-issue
  - openehr_sdk repo   --> i.e.    sync/123_example-issue

2. apply your code changes
3. push to openehr_sdk repo (NO CI will be triggered)
4. push to ehrbase repo (CI will trigger this workflow)
5. create TWO PRs (one in EHRbase, one in openEHR_SDK)
6. merge BOTH PRs considering below notes:
  - make sure both PRs are reviewed and ready to be merged
    at the same time!
  - make sure to sync both PRs w/ develop before merging!
  - MERGE BOTH PRs AT THE SAME TIME!

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

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