CDR Base Installation

Typically, CDR Base will be packed along with HIP CDR and should be installed as part of overall installation process. For the case that CDR Base should be operated as a stand-alone application, you can follow the instructions below.

CDR Base is provided as a Docker container or via HELM chart configuration. please ensure that credentials for the artifact repository (vitagroup Harbor) have been provided as part of the contract agreements.

Setup YugabyteDB

Before EHRbase can be run, a YugabyteDB database needs to be set up and configured. Follow the instructions for YugabyteDB installation. Please note that the YugabyteDB configuration will highly depend on your project and system requirements.

You are provided with a database installation script createdb.sql. This script needs to be run as a role *superuser in order to create the database.

Extentions are installed in a separate schema called ‘ext’.

For production servers these operations should be performed by a configuration management system.

On NIX run this using:

sudo -u postgres psql < createdb.sql

You only have to run this script once. It only contains those operations which require superuser privileges. The actual database schema is managed by flyway which will automatically be executed the first time CDR Base is connected to YugabyteDB.

Docker

EHRbase is delivered as a single Docker container including all plugins (Please note that for the current release of EHRbase running on YugabyteDB, only ATNA Logging and Event Trigger Plugins are packaged).

Prerequisites

• A YugabyteDB is available and is pre-configured in accordance with the steps described above.

• A recent version of a Docker runtime environment (e.g. Docker, Rancher, Colima etc.)

Parameters

To set parameters of EHRbase and the plugins, the default environment variables can be overwritten. Check next example (which assumes you pulled or created an image named ehrbase/ehrbase):

docker run -e DB_URL=jdbc:postgresql://ehrdb:5432/ehrbase \
       -e DB_USER=foouser \
       -e DB_PASS=foopass \
       -e SERVER_NODENAME=what.ever.org \
       ehrbase/ehrbase

Note that while there are parameters for the plugin system, these are rarely of use for the installation as these are set as default values of the docker image provided.

Parameter	Env Variable	Use	Example
plugin-manager.enable	PLUGIN_MANAGER_ENABLE	Enable and disable plugins	“true”
manager.plugin-dir	PLUGIN_MANAGER_PLUGIN_DIR	Directory of the plugins	“/plugin_dir”
plugin-manager.plugin-config-dir	PLUGIN_MANAGER_PLUGIN_CONFIG_DIR	Directory of the plugin configuration file (containing default values)	/plugin_config_dir

Here you can find some example settings for common use cases for the usage of EHRbase Docker containers. You can also use the environent variables with the normal .jar execution by setting the variables according to your operating system.

Use BASIC auth

Run the docker image with this setting:

docker run --network ehrbase-net --name ehrbase -e SECURITY_AUTHTYPE=BASIC \
-e SECURITY_AUTHUSER=myuser -e SECURITY_AUTHPASSWORD=ThePasswordForUser \
-e SECURITY_AUTHADMINUSER=myadmin -e SECURITY_AUTHADMINPASSWORD=SecretAdminPassword \
-d -p 8080:8080 ehrbase/ehrbase:latest

This will set the used authentication method to BASIC auth and all requests against the EHRbase must be provided with the Authorization header set to Basic %username%:%password% whereas the username and password must be encoded with base64.

Note

Ensure you use an encrypted connection over https otherwise the username and password can be descripted easily

Use OAuth2

Run the docker image with this setting.

docker run --network ehrbase-net --name ehrbase -e SECURITY_AUTHTYPE=OAUTH \
-e SPRING_SECURITY_OAUTH2_RESOURCESERVER_JWT_ISSUERURI=https://keycloak.example.com/auth/realms/ehrbase \
-d -p 8080:8080 ehrbase/ehrbase:latest

You have to prepare the authentication server including a valid client at the target server to get this setup run.

HELM Chart

A Helm chart can be used to install CDR Base in a Kubernetes or OpenShift cluster.

Latest Version

• Helm: 0.28.0-early-access-v2

• Docker: 0.28.0-early-access-v2

Prerequisites

• A YugabyteDB is available and is pre-configured in accordance with the steps described above.

• Kubernetes 1.20+

• Helm 3.2.0+

Access

• Docker image: registry.vitasystems.dev/ibm-docker/ehrbase-enterprise-openshift

• Helm chart: registry.vitasystems.dev/ibm-helm/ehrbase-openshift

Installing the chart

Adding the needed chart repository:

$ helm repo add ... <<< TODO: which repo has to be added for an external user?

Install the EHRbase helm chart with a Yugabyte database with a release name ehrbase-openshift in the kubernetes context mykubecontext and the namespace *myinstallnamespace: Update values.yaml and mark *yugabyte.enabled: true

$ helm install --kube-context mykubecontext -n myinstallnamespace -f values.yaml ehrbase-openshift .

Unínstalling the chart

To uninstall the deployment with a release name ehrbase-openshift in the kubernetes context mykubecontext and the namespace myinstallnamespace:

$ helm uninstall --kube-context mykubecontext -n myinstallnamespace ehrbase-openshift

Running against an existing YugabyteDB instance

When disabling Yugabyte from this helm chart and running against an existing YugabyteDB instance, the init DB script that creates the users and DB has to be executed manually against YugabyteDB.

Open config/db_setup.sql and change the GO placeholders with concrete values

• ${EHRBASE_DB_USER} and ${EHRBASE_DB_PASSWORD} - credentials of the ehrbase user that reads/writes data

• ${EHRBASE_DB_USER_ADMIN} and ${EHRBASE_DB_PASSWORD_ADMIN} - credentials of the ehrbase user that manages the schema

Execute the updated script against YugabyteDB.

Parameters

Global Parameters

Table 1: Global parameters

Name	Description	Value
global.baseDomain	Domain value for EHRbase ingress settings	"ehrbase.org"
global.internalImagePullSecrets.ehrbaseImagePullSecret	Secret for pulling the ehrbase image from the docker registry	ehrbase
global.hosts.ehrbase	EHRbase host to be used for ingress	ehrbase.{{ .Values.global.baseDomain }}
global.tlsSecrets.ehrbase	Secret name for the the host certificate	vitasystems-dev
global.initContainer.enabled	Toggle the init container of the DB. To be set to false if the DB init is done manually.	true

CDR Base Application Parameters

This general overview of available CDR Base parameters is complemented by additional parameters within dedicated chapters of this documentation (for example for configuration with an external terminology service)

Table 2: Application parameters

Name	Description	Value
appConfig.database.dbName	Name of the EHRbase database	ehrbase
appConfig.database.adminUsername	Name of the EHRbase admin user	ehrbase
appConfig.database.dbUser	Name of the EHRbase database user	ehrbase_restricted
appConfig.database.dbPort	Port of the EHRbase database server	5433
appConfig.database.dbHostname	Host of the EHRbase database	yb-tservers
appConfig.database.dbDriver	Database driver to use	"jdbc:yugabytedb"
appConfig.database.dbAdditionalParameter	Additional parameter to use for EHRbase database URL (used for Yugabyte)	"?load-balance=true"
appConfig.cacheEnabled	Toggle to activate/deactivate EHRbase caching mechanisms	true
appConfig.adminApiActive	Toggle to activate/deactivate EHRbase admin API	true
appConfig.serviceUrl	External EHRbase URL used for ingress setup	"hip-cdr-core-ehrbase-enterprise-{{ .Release.Namespace }}.{{ .Values.domain }}"
appConfig.commonFullnameOverride	EHRbase service name (also used for naming of EHRbase database service)	hip-cdr-core-ehrbase-enterprise
appConfig.atna.enabled	Enables ATNA logs	false
appConfig.atna.host	Host of the ATNA logs registry	hip-logging
appConfig.atna.port	Port of the ATNA logs registry	514
appConfig.restApiDoc.enabled	Enables the built in REST API documentation like swagger ui and api doc	false
appConfig.restApiDoc.swaggerUi.enabled	Enables the Swagger ui for the EHRbase REST API	false
appConfig.restApiDoc.apiDocs.enabled	Enables the OpenAPI documentation	false
replicaCount	Number of EHRbase replicas to deploy	1

Image Parameters

Table 3: Image parameters

Name	Description	Value
image.repository	EHRbase image repository	ehrbase/ehrbasemvp
image.pullPolicy	EHRbase image pull policy	Always
image.tag	EHRbase image tag	early-access-openshift-2

Service Parameters

Table 4: Service parameters

Name	Description	Value
service.type	EHRbase service type	ClusterIP
service.port	EHRbase service port	8080
service.targetPort	EHRbase service target port	8080
service.protocol	EHRbase service protocol	TCP
service.name	EHRbase service name	http

YugabyteDB Parameters

Table 5: YugabyteDB parameters

Name	Description	Value
yugabyte.enabled	Toggle for choosing database deployment	false
yugabyte.storage.master.size	Storage size of the Yugabyte master database	5Gi
yugabyte.storage.master.storageClass	Storage class of the Yugabyte master database	""
yugabyte.storage.tserver.size	Storage size of the Yugabyte tserver database	5Gi
yugabyte.storage.tserver.storageClass	Storage class of the Yugabyte tserver database	""
yugabyte.enableLoadBalancer	Toggle to activate/deactivate the Yugabyte load balancer	false
yugabyte.gflags.master.minloglevel	Configure log level for Yugabyte master node	2
yugabyte.gflags.tserver.minloglevel	Configure log level for Yugabyte tserver nodes	2
yugabyte.authCredentials.ysql.user	User name of the main Yugabyte YSQL user	yugabyte
yugabyte.authCredentials.ysql.password	Password of the main Yugabyte YSQL user	yugabyte